Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008029.1 Hibiscus syriacus cultivar Beakdansim tig00110505_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: 3983240
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 18
Found at i:461443 original size:125 final size:126
Alignment explanation
Indices: 461281--461519 Score: 381
Period size: 125 Copynumber: 1.9 Consensus size: 126
461271 GTAAGCTTAT
* *
461281 TTTACCAATATACTTACCATTAAATCCCTAAGCTCGTAAGTTTATTTTACCAATATACTTACCAT
1 TTTACCAATATACTTACCATTAAATCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCAT
* *
461346 TATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTTCATAAGCTCGTA
66 AATTCCATAAGATCGTAAGCTTATTTTACCAATATACTTACTATAATTTCATAAGCTCGTA
* * * * *
461407 TTTACCAATATGCTTACTA-TAATTTCATAAGCTCGTAAGCTTATTTTACCAATATACTTACTAT
1 TTTACCAATATACTTACCATTAAATCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCAT
*
461471 AATTTCATAAGATCGTAAGCTTATTTTACCAATATACTTACTATAATTT
66 AATTCCATAAGATCGTAAGCTTATTTTACCAATATACTTACTATAATTT
461520 GCATTACTGA
Statistics
Matches: 103, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
125 86 0.83
126 17 0.17
ACGTcount: A:0.34, C:0.19, G:0.06, T:0.41
Consensus pattern (126 bp):
TTTACCAATATACTTACCATTAAATCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCAT
AATTCCATAAGATCGTAAGCTTATTTTACCAATATACTTACTATAATTTCATAAGCTCGTA
Found at i:461789 original size:60 final size:60
Alignment explanation
Indices: 461672--461906 Score: 357
Period size: 60 Copynumber: 3.9 Consensus size: 60
461662 TTCCTTCTCA
* *
461672 TTTTAGCATACGAAGTGCCTTATTCGAGAATCCATACCATTAGTAATGATTCCTTTACCAT
1 TTTTAGCACATGAAGTGCCTTATTCGAGAATCCATACCATTAGT-ATGATTCCTTTACCAT
461733 TTTTAGCACATGAAGTGCCTTATTCGAGAATCCATACCATTAGTATGATTCCTTTACCAT
1 TTTTAGCACATGAAGTGCCTTATTCGAGAATCCATACCATTAGTATGATTCCTTTACCAT
* *
461793 TTTTAGCACATGAAGTGCCCTATTCGAGAATCCATACCATTAGTATGATCCCTTTACCAT
1 TTTTAGCACATGAAGTGCCTTATTCGAGAATCCATACCATTAGTATGATTCCTTTACCAT
* * **
461853 TTTTAGCACATGAAGTG-CTTATAT-AAAAATCCATACTGTTAGTATGATTTCCTT
1 TTTTAGCACATGAAGTGCCTTAT-TCGAGAATCCATACCATTAGTATGA-TTCCTT
461907 ATCCTTGTAG
Statistics
Matches: 162, Mismatches: 10, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
59 23 0.14
60 97 0.60
61 42 0.26
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (60 bp):
TTTTAGCACATGAAGTGCCTTATTCGAGAATCCATACCATTAGTATGATTCCTTTACCAT
Found at i:461969 original size:118 final size:117
Alignment explanation
Indices: 461656--462224 Score: 429
Period size: 118 Copynumber: 4.8 Consensus size: 117
461646 ATATACTTAA
* * * * *
461656 TATGATTTCCTTCTCATTTTAGCATACGA-AGTGCCTT-AT-TCGAGAATCCATAC-CATTAGTA
1 TATGATTTCCTTATCATTTTAGCACA-TATAGTG-CTTCATATGGA-AATCCATACAC-TCAGT-
* * *
461717 ATGATTCCTTTACCATTTTTAGCACATGAAGTGCCTTAT-TCGAGAATCCATACCATTAG
61 ATGATTCCCTTACCA-TTTTAGCACAT-AAGTGCCTTATAT-GAAAATCCATACTATTAG
* * * *
461776 TATGA-TTCCTTTACCATTTTTAGCACATGA-AGTGC--CCTATTCGAGAATCCATAC-CATTAG
1 TATGATTTCC-TTATCA-TTTTAGCACAT-ATAGTGCTTCATA-TGGA-AATCCATACAC-TCAG
* *
461836 TATGA-TCCCTTTACCATTTTTAGCACATGAAGTG-CTTATATAAAAATCCATACTGTTAG
60 TATGATTCCC-TTACCA-TTTTAGCACAT-AAGTGCCTTATATGAAAATCCATACTATTAG
* * * ** *
461895 TATGATTTCCTTATCCTTGTAGCACCCT-TAGTGCTTTTTCTGGAAATCCATACACTCAGTATGA
1 TATGATTTCCTTATCATTTTAGCA-CATATAGTGCTTCATATGGAAATCCATACACTCAGTATGA
* * * *
461959 TTCCCTTACCATTTTAGCACACATAA-TGCCCTATCTGGAAATCCATA-TATTCAA
65 TTCCCTTACCATTTTAG--CACATAAGTGCCTTATATGAAAATCCATACTATT-AG
* *
462013 TATGATTTCCTTATCATTTTAGCACACTCA-A-TGCTTCATATGGAAATTCATACACTGAGTATG
1 TATGATTTCCTTATCATTTTAGCACA-T-ATAGTGCTTCATATGGAAATCCATACACTCAGTATG
* * * * *
462076 ATTTCCTTATCATTTTAGCACATATAGTG-CTCCATATGGAAATCCATAC-ACTCAG
64 ATTCCCTTACCATTTTAGCACATA-AGTGCCT-TATATGAAAATCCATACTA-TTAG
* * * *
462131 TATGATTTCCTTATCATTTTAGGACATATAGTGCTCCATATAGAAATCCATACACTCAATATGAT
1 TATGATTTCCTTATCATTTTAGCACATATAGTGCTTCATATGGAAATCCATACACTCAGTATGAT
* *
462196 TTCCTTATCATTTTAGCACATATAGTGCC
66 TCCCTTACCATTTTAGCACATA-AGTGCC
462225 ATTTGGTAAT
Statistics
Matches: 373, Mismatches: 46, Indels: 61
0.78 0.10 0.13
Matches are distributed among these distances:
116 7 0.02
117 16 0.04
118 217 0.58
119 54 0.14
120 44 0.12
121 35 0.09
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (117 bp):
TATGATTTCCTTATCATTTTAGCACATATAGTGCTTCATATGGAAATCCATACACTCAGTATGAT
TCCCTTACCATTTTAGCACATAAGTGCCTTATATGAAAATCCATACTATTAG
Found at i:462076 original size:177 final size:174
Alignment explanation
Indices: 461761--462216 Score: 476
Period size: 177 Copynumber: 2.6 Consensus size: 174
461751 CTTATTCGAG
* * *
461761 AATCCATAC-CATTAGTATGATTCCTTTACCATTTTTAG-CACATGAAGTGCCCTATTCGAGAAT
1 AATCCATACAC-TCAGTATGATTCCCTTACCA-TTTTAGACACAT-AA-TGCCCTATTAGA-AAT
* * * *
461824 CCATACCATT-AGTATGA-TCCCTTTACCATTTTTAGCACATGAAGTGCTTATATAAAAATCCAT
61 CCATA-CATTCAATATGATTTCC-TTATCA-TTTTAGCACATCAAGTGCTTATATAAAAATCCAT
** * * * *** *
461887 ACTGTTAGTATGATTTCCTTATCCTTGTAGCACCCT-TAGTGCTTTTTCTGGA
123 ACACTGAGTATGATTTCCTTATCATTGTAGCA-CATATAGTGCTCCATATGGA
*
461939 AATCCATACACTCAGTATGATTCCCTTACCATTTTAGCACACATAATGCCCTATCTGGAAATCCA
1 AATCCATACACTCAGTATGATTCCCTTACCATTTTAG-ACACATAATGCCCTAT-TAGAAATCCA
* ** *
462004 TATATTCAATATGATTTCCTTATCATTTTAGCACACTCAA-TGCTTCATATGGAAATTCATACAC
64 TACATTCAATATGATTTCCTTATCATTTTAGCACA-TCAAGTGCTT-ATATAAAAATCCATACAC
*
462068 TGAGTATGATTTCCTTATCATTTTAGCACATATAGTGCTCCATATGGA
127 TGAGTATGATTTCCTTATCATTGTAGCACATATAGTGCTCCATATGGA
* * * *
462116 AATCCATACACTCAGTATGATTTCCTTATCATTTTAGGACATATAGTGCTCC-ATATAGAAATCC
1 AATCCATACACTCAGTATGATTCCCTTACCATTTTA-GACACATAATGC-CCTAT-TAGAAATCC
*
462180 ATACACTCAATATGATTTCCTTATCATTTTAGCACAT
63 ATACATTCAATATGATTTCCTTATCATTTTAGCACAT
462217 ATAGTGCCAT
Statistics
Matches: 238, Mismatches: 29, Indels: 24
0.82 0.10 0.08
Matches are distributed among these distances:
176 21 0.09
177 173 0.73
178 38 0.16
179 6 0.03
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (174 bp):
AATCCATACACTCAGTATGATTCCCTTACCATTTTAGACACATAATGCCCTATTAGAAATCCATA
CATTCAATATGATTTCCTTATCATTTTAGCACATCAAGTGCTTATATAAAAATCCATACACTGAG
TATGATTTCCTTATCATTGTAGCACATATAGTGCTCCATATGGA
Found at i:462217 original size:59 final size:59
Alignment explanation
Indices: 461761--462223 Score: 412
Period size: 59 Copynumber: 7.8 Consensus size: 59
461751 CTTATTCGAG
* * *
461761 AATCCATAC-CATTAGTATGA-TTCCTTTACCATTTTTAGCACATGA-AGTGC-CC-TATTCGA
1 AATCCATACAC-TCAGTATGATTTCC-TTATCA-TTTTAGCACAT-ATAGTGCTCCATA-TGGA
* * * * **
461820 GAATCCATAC-CATTAGTATGA-TCCCTTTACCATTTTTAGCACATGA-AGTGCT-TATATAAA
1 -AATCCATACAC-TCAGTATGATTTCC-TTATCA-TTTTAGCACAT-ATAGTGCTCCATATGGA
** * * * * *** *
461880 AATCCATACTGTTAGTATGATTTCCTTATCCTTGTAGCACCCT-TAGTGCTTTTTCTGGA
1 AATCCATACACTCAGTATGATTTCCTTATCATTTTAGCA-CATATAGTGCTCCATATGGA
* * * * *
461939 AATCCATACACTCAGTATGATTCCCTTACCATTTTAGCACACATAATGC-CCTATCTGGA
1 AATCCATACACTCAGTATGATTTCCTTATCATTTTAGCACATATAGTGCTCC-ATATGGA
* * * *
461998 AATCCATATATTCAATATGATTTCCTTATCATTTTAGCACACTCA-A-TGCTTCATATGGA
1 AATCCATACACTCAGTATGATTTCCTTATCATTTTAGCACA-T-ATAGTGCTCCATATGGA
* *
462057 AATTCATACACTGAGTATGATTTCCTTATCATTTTAGCACATATAGTGCTCCATATGGA
1 AATCCATACACTCAGTATGATTTCCTTATCATTTTAGCACATATAGTGCTCCATATGGA
* *
462116 AATCCATACACTCAGTATGATTTCCTTATCATTTTAGGACATATAGTGCTCCATATAGA
1 AATCCATACACTCAGTATGATTTCCTTATCATTTTAGCACATATAGTGCTCCATATGGA
*
462175 AATCCATACACTCAATATGATTTCCTTATCATTTTAGCACATATAGTGC
1 AATCCATACACTCAGTATGATTTCCTTATCATTTTAGCACATATAGTGC
462224 CATTTGGTAA
Statistics
Matches: 342, Mismatches: 47, Indels: 29
0.82 0.11 0.07
Matches are distributed among these distances:
57 1 0.00
58 16 0.05
59 266 0.78
60 56 0.16
61 3 0.01
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (59 bp):
AATCCATACACTCAGTATGATTTCCTTATCATTTTAGCACATATAGTGCTCCATATGGA
Found at i:465521 original size:21 final size:21
Alignment explanation
Indices: 465495--465545 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
465485 CTCATAACAT
465495 GGTGCATCGGTGCACTATCAA
1 GGTGCATCGGTGCACTATCAA
*
465516 GGTGCATCGGTGCACTATCGA
1 GGTGCATCGGTGCACTATCAA
465537 GGTGCATCG
1 GGTGCATCG
465546 ATACCCCTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.20, C:0.24, G:0.33, T:0.24
Consensus pattern (21 bp):
GGTGCATCGGTGCACTATCAA
Found at i:465706 original size:23 final size:20
Alignment explanation
Indices: 465653--465731 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
465643 TCGAAATTGA
465653 GTGCATGGATGCACTACATG
1 GTGCATGGATGCACTACATG
*
465673 GTGCATCGATGCACTAGTGGCA-G
1 GTGCATGGATGCACTA----CATG
* *
465696 GTGCATGGATGCACAACAAGG
1 GTGCATGGATGCACTAC-ATG
465717 GTGCATGGATGCACT
1 GTGCATGGATGCACT
465732 GCAGGGGTAC
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
19 1 0.02
20 16 0.33
21 15 0.31
23 15 0.31
24 2 0.04
ACGTcount: A:0.25, C:0.20, G:0.33, T:0.22
Consensus pattern (20 bp):
GTGCATGGATGCACTACATG
Found at i:465739 original size:21 final size:21
Alignment explanation
Indices: 465653--465747 Score: 93
Period size: 21 Copynumber: 4.5 Consensus size: 21
465643 TCGAAATTGA
*
465653 GTGCATGGATGCACTACA-TG
1 GTGCATGGATGCACTACAGGG
* **
465673 GTGCATCGATGCACTAGTGGCAG
1 GTGCATGGATGCACTACAGG--G
* *
465696 GTGCATGGATGCACAACAAGG
1 GTGCATGGATGCACTACAGGG
*
465717 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTACAGGG
*
465738 GTACATGGAT
1 GTGCATGGAT
465748 ACACGTTGAC
Statistics
Matches: 59, Mismatches: 13, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
20 15 0.25
21 28 0.47
23 16 0.27
ACGTcount: A:0.25, C:0.19, G:0.35, T:0.21
Consensus pattern (21 bp):
GTGCATGGATGCACTACAGGG
Found at i:467671 original size:17 final size:17
Alignment explanation
Indices: 467649--467685 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
467639 TCCTTCTTCT
467649 TCTTCTTGTTTTTCCTC
1 TCTTCTTGTTTTTCCTC
*
467666 TCTTCTTGTTTTTCTTC
1 TCTTCTTGTTTTTCCTC
467683 TCT
1 TCT
467686 CCTCTTTCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.00, C:0.27, G:0.05, T:0.68
Consensus pattern (17 bp):
TCTTCTTGTTTTTCCTC
Found at i:470207 original size:21 final size:21
Alignment explanation
Indices: 470139--470238 Score: 123
Period size: 21 Copynumber: 4.7 Consensus size: 21
470129 TCGAAATGGA
* *
470139 GTGCATGGATGCACTACA-TG
1 GTGCATGGATGCACTGCAGGG
* *
470159 GTGCATCGATGCACTAG-TGGAAG
1 GTGCATGGATGCACT-GCAGG--G
470182 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
470203 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
470224 GTGCATGGATGCACT
1 GTGCATGGATGCACT
470239 TTGACACCCT
Statistics
Matches: 69, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
20 14 0.20
21 37 0.54
22 1 0.01
23 17 0.25
ACGTcount: A:0.22, C:0.19, G:0.37, T:0.22
Consensus pattern (21 bp):
GTGCATGGATGCACTGCAGGG
Found at i:470485 original size:21 final size:21
Alignment explanation
Indices: 470461--470500 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
470451 ATGTTTAATG
470461 AAAAAGATACCAATTGTTAAC
1 AAAAAGATACCAATTGTTAAC
* *
470482 AAAATGATATCAATTGTTA
1 AAAAAGATACCAATTGTTA
470501 CCAATTTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (21 bp):
AAAAAGATACCAATTGTTAAC
Found at i:474735 original size:21 final size:21
Alignment explanation
Indices: 474711--474750 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
474701 ATATTTAATG
474711 AAAAAGATACCAATTGTTAAC
1 AAAAAGATACCAATTGTTAAC
* *
474732 AAAATGATATCAATTGTTA
1 AAAAAGATACCAATTGTTA
474751 CCAATTTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (21 bp):
AAAAAGATACCAATTGTTAAC
Found at i:478807 original size:21 final size:21
Alignment explanation
Indices: 478781--478852 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
478771 CCCATAACAT
*
478781 GGTGCATCGGTGCACTATCAA
1 GGTGCATCGGTGCACTATCGA
478802 GGTGCATCGGTGCACTATCGA
1 GGTGCATCGGTGCACTATCGA
*
478823 GGAGCATCGGTGCACTATCGA
1 GGTGCATCGGTGCACTATCGA
*
478844 GCTGCATCG
1 GGTGCATCG
478853 ATACCCCTTC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.21, C:0.25, G:0.32, T:0.22
Consensus pattern (21 bp):
GGTGCATCGGTGCACTATCGA
Found at i:479274 original size:21 final size:21
Alignment explanation
Indices: 479250--479289 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
479240 ATGTTTAATG
479250 AAAAAGATACCAATTGTTAAC
1 AAAAAGATACCAATTGTTAAC
* *
479271 AAAATGATATCAATTGTTA
1 AAAAAGATACCAATTGTTA
479290 CCAATTTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (21 bp):
AAAAAGATACCAATTGTTAAC
Found at i:483512 original size:23 final size:22
Alignment explanation
Indices: 483459--483538 Score: 78
Period size: 21 Copynumber: 3.7 Consensus size: 22
483449 TCGAAATGGA
* *
483459 GTGCATGGATGCAC-TACA-TG
1 GTGCATGGATGCACTTGCAGGG
* *
483479 GTGCATCGATGCACTTG-TGGAAG
1 GTGCATGGATGCACTTGCAGG--G
483502 GTGCATGGATGCAC-TGCAGGG
1 GTGCATGGATGCACTTGCAGGG
483523 GTGCATGGATGCACTT
1 GTGCATGGATGCACTT
483539 TGACACCCTT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
20 13 0.27
21 16 0.33
22 3 0.06
23 16 0.33
ACGTcount: A:0.21, C:0.19, G:0.35, T:0.25
Consensus pattern (22 bp):
GTGCATGGATGCACTTGCAGGG
Found at i:484001 original size:65 final size:65
Alignment explanation
Indices: 483899--484081 Score: 178
Period size: 64 Copynumber: 2.8 Consensus size: 65
483889 TAAAATGAAT
* * * * *
483899 ATCGAATGCATTTCATGCATCGATGTA-CATACCATGCACCGATGCATTGAGGAT-TTTATGAAA
1 ATCGAATGCATTTGATGCATCGATGCACCATACAATGCACCGATGCACTCAGGATATTT-TG-AA
483962 AC
64 AC
* * * * *
483964 ATCGAATGCATTTGATGCATCGATGCACCA-GCAATGCATCGATGCCCTCTGGCTATTTTGAAAC
1 ATCGAATGCATTTGATGCATCGATGCACCATACAATGCACCGATGCACTCAGGATATTTTGAAAC
* * * *
484028 ATCGAATGCACTTGATGCATCGATGCACTC-T-TAGTGCACCGATGCACTAAGGAT
1 ATCGAATGCATTTGATGCATCGATGCAC-CATACAATGCACCGATGCACTCAGGAT
484082 CAAACGATCA
Statistics
Matches: 96, Mismatches: 18, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
64 47 0.49
65 44 0.46
66 5 0.05
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (65 bp):
ATCGAATGCATTTGATGCATCGATGCACCATACAATGCACCGATGCACTCAGGATATTTTGAAAC
Found at i:484055 original size:17 final size:19
Alignment explanation
Indices: 484027--484075 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
484017 TATTTTGAAA
484027 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
484045 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
484064 CACCGATGCACT
1 CATCGATGCACT
484076 AAGGATCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:490538 original size:21 final size:21
Alignment explanation
Indices: 490496--490539 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
490486 ACTCTGGGAG
* *
490496 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
490517 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
490538 CT
1 CT
490540 CCTCCAGCTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:491102 original size:2 final size:2
Alignment explanation
Indices: 491095--491141 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
491085 CAGCTTAAGC
491095 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
491137 TA TA T
1 TA TA T
491142 CAATTGGCTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:491744 original size:65 final size:64
Alignment explanation
Indices: 491639--491824 Score: 216
Period size: 65 Copynumber: 2.9 Consensus size: 64
491629 AATTAAATTG
* *
491639 AACATCGAATGCATTTCATGCATCGATGCA-CATACCATGCACCGATGCACTAAGGAT-TTTATG
1 AACATCGAATGCATTTGATGCATCGATGCACCA-ACAATGCACCGATGCACTAAGGATATTT-TG
491702 AA
64 -A
* ** *
491704 AACATCGAATGCATTTGATGCATCGATGCACCAACAATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCACCAACAATGCACCGATGCACTAAGGATATTTTGA
* * ** *
491768 AACATCGAATGCACTTGATGCATCGATCCACTC-TTAGTGCACCGATGCACTAAGGAT
1 AACATCGAATGCATTTGATGCATCGATGCAC-CAACAATGCACCGATGCACTAAGGAT
491825 CCAATGGTCA
Statistics
Matches: 103, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
64 47 0.46
65 51 0.50
66 5 0.05
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.26
Consensus pattern (64 bp):
AACATCGAATGCATTTGATGCATCGATGCACCAACAATGCACCGATGCACTAAGGATATTTTGA
Found at i:494981 original size:21 final size:21
Alignment explanation
Indices: 494939--494982 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
494929 ACTCTGGGAG
* *
494939 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
494960 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
494981 CT
1 CT
494983 CCTCCAGCTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:495840 original size:21 final size:23
Alignment explanation
Indices: 495816--495857 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
495806 AATGAAATTT
495816 AAATGAATTT-TAAG-ATTTTAC
1 AAATGAATTTCTAAGTATTTTAC
*
495837 AAATGATTTTCTAAGTATTTT
1 AAATGAATTTCTAAGTATTTT
495858 CGATTTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 4 0.22
23 5 0.28
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.48
Consensus pattern (23 bp):
AAATGAATTTCTAAGTATTTTAC
Found at i:496245 original size:64 final size:64
Alignment explanation
Indices: 496070--496255 Score: 198
Period size: 65 Copynumber: 2.9 Consensus size: 64
496060 AATTAAATTG
* * * *
496070 AACATCGAATGCATTTCATGCATCGATGCACATATCATGCACCGACGCACTGAGGATTTTATGAA
1 AACATCGAATGCATTTGATGCATCGATGCAC-TCTCATGCACCGATGCACTCAGGATTTTATGAA
* * * *
496135 AACATCGAATGCATTTGATGCATCGATGCAC-CAGCAATGCATCGATGCACTCTGGCTATTT-TG
1 AACATCGAATGCATTTGATGCATCGATGCACTC-TC-ATGCACCGATGCACTCAGGAT-TTTATG
496198 -A
63 AA
* * * *
496199 AACATCGAATGCACTTGATGCATCGATACACTCTTAGTGCACCGATGCACTAAGGAT
1 AACATCGAATGCATTTGATGCATCGATGCACTCTCA-TGCACCGATGCACTCAGGAT
496256 CCAACGGTCA
Statistics
Matches: 100, Mismatches: 16, Indels: 11
0.79 0.13 0.09
Matches are distributed among these distances:
63 1 0.01
64 47 0.47
65 49 0.49
66 3 0.03
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (64 bp):
AACATCGAATGCATTTGATGCATCGATGCACTCTCATGCACCGATGCACTCAGGATTTTATGAA
Found at i:507052 original size:65 final size:65
Alignment explanation
Indices: 506956--507106 Score: 191
Period size: 65 Copynumber: 2.3 Consensus size: 65
506946 GAACATTGTC
* * *
506956 TGCATTTCATGCATCGATGCA-CATACCATGCACCGATGCACTGAGGAT-TTTATGAAAACATCG
1 TGCATTTGATGCATCGATGCACCATACAATGCACCGATGCACTCAGGATATTT-TG-AAACATCG
507019 AA
64 AA
* * * *
507021 TGCATTTGATGCATCGATGCACCA-GCAATGCATCGATGCACTCTGGCTATTTTGAAACATCGAA
1 TGCATTTGATGCATCGATGCACCATACAATGCACCGATGCACTCAGGATATTTTGAAACATCGAA
*
507085 TGCACTTGATGCATCGATGCAC
1 TGCATTTGATGCATCGATGCAC
507107 TCTTAGTGCA
Statistics
Matches: 76, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
64 31 0.41
65 40 0.53
66 5 0.07
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (65 bp):
TGCATTTGATGCATCGATGCACCATACAATGCACCGATGCACTCAGGATATTTTGAAACATCGAA
Found at i:508016 original size:21 final size:21
Alignment explanation
Indices: 507992--508031 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
507982 ATGTTTAATG
507992 AAAAAGATACCAATTGTTAAC
1 AAAAAGATACCAATTGTTAAC
*
508013 AAAAAGATATCAATTGTTA
1 AAAAAGATACCAATTGTTA
508032 CCAATTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.53, C:0.10, G:0.10, T:0.28
Consensus pattern (21 bp):
AAAAAGATACCAATTGTTAAC
Found at i:509146 original size:21 final size:21
Alignment explanation
Indices: 509122--509167 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
509112 GGGGTATCAG
509122 TACATCCGAAGAGTGTATCGC
1 TACATCCGAAGAGTGTATCGC
509143 TACATCCGAAGAGTGTATCGC
1 TACATCCGAAGAGTGTATCGC
509164 TACA
1 TACA
509168 CCCATACTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (21 bp):
TACATCCGAAGAGTGTATCGC
Found at i:511007 original size:23 final size:20
Alignment explanation
Indices: 510954--511011 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 20
510944 TCGAAATGGA
510954 GTGCATGGATGCACTACATG
1 GTGCATGGATGCACTACATG
*
510974 GTGCATCGATGCACTAGTGGCA-G
1 GTGCATGGATGCACTA----CATG
510997 GTGCATGGATGCACT
1 GTGCATGGATGCACT
511012 TTGACACCCT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 15 0.47
23 15 0.47
24 2 0.06
ACGTcount: A:0.22, C:0.21, G:0.33, T:0.24
Consensus pattern (20 bp):
GTGCATGGATGCACTACATG
Found at i:511258 original size:21 final size:21
Alignment explanation
Indices: 511234--511273 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
511224 ATGTTTAATG
511234 AAAAAGATACCAATTGTTAAC
1 AAAAAGATACCAATTGTTAAC
* *
511255 AAAATGATATCAATTGTTA
1 AAAAAGATACCAATTGTTA
511274 CCAATTGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (21 bp):
AAAAAGATACCAATTGTTAAC
Found at i:515729 original size:21 final size:21
Alignment explanation
Indices: 515705--515744 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
515695 ATGTTTAATG
515705 AAAAAGATACCAATTGTTAAC
1 AAAAAGATACCAATTGTTAAC
* *
515726 AAAATGATATCAATTGTTA
1 AAAAAGATACCAATTGTTA
515745 CCAATTTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (21 bp):
AAAAAGATACCAATTGTTAAC
Found at i:518115 original size:21 final size:21
Alignment explanation
Indices: 518091--518136 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
518081 GGGGTATCAG
518091 TACATCCGAAAAGTGTATCGC
1 TACATCCGAAAAGTGTATCGC
* *
518112 TACATCCGAAGAGTGTATCTC
1 TACATCCGAAAAGTGTATCGC
518133 TACA
1 TACA
518137 CCCCTACTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (21 bp):
TACATCCGAAAAGTGTATCGC
Found at i:520238 original size:21 final size:21
Alignment explanation
Indices: 520214--520253 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
520204 ATGTTTAATG
520214 AAAAAGATATCAATTGTTAAC
1 AAAAAGATATCAATTGTTAAC
*
520235 AAAATGATATCAATTGTTA
1 AAAAAGATATCAATTGTTA
520254 CCAATTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (21 bp):
AAAAAGATATCAATTGTTAAC
Found at i:523386 original size:21 final size:22
Alignment explanation
Indices: 523353--523393 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
523343 TTCATTCGAA
*
523353 ATGGAGTGTATGGATGCACTAC
1 ATGGAGTGCATGGATGCACTAC
523375 ATGG-GTGCATGGATGCACT
1 ATGGAGTGCATGGATGCACT
523394 TTGACACCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.24, C:0.15, G:0.34, T:0.27
Consensus pattern (22 bp):
ATGGAGTGCATGGATGCACTAC
Found at i:525371 original size:16 final size:15
Alignment explanation
Indices: 525343--525391 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
525333 TTTTGTGATG
*
525343 ATAATAGATATGAAT
1 ATAAGAGATATGAAT
*
525358 ATAAGATTATATGAA-
1 ATAAGA-GATATGAAT
525373 ATAAGAGATATGAAT
1 ATAAGAGATATGAAT
525388 ATAA
1 ATAA
525392 ATGATTAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 7 0.24
15 15 0.52
16 7 0.24
ACGTcount: A:0.55, C:0.00, G:0.14, T:0.31
Consensus pattern (15 bp):
ATAAGAGATATGAAT
Found at i:525693 original size:18 final size:18
Alignment explanation
Indices: 525670--525810 Score: 212
Period size: 18 Copynumber: 7.9 Consensus size: 18
525660 GAGGGTCTAC
525670 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
*
525688 GTGGTCATTCGGGACATA
1 GTGGTCCTTCGGGACATA
* *
525706 ATGGTCCTTCGGGACACA
1 GTGGTCCTTCGGGACATA
525724 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
*
525742 GTGGTCCTTTGGGACATA
1 GTGGTCCTTCGGGACATA
*
525760 GTGGTCCTTCGGGACACA
1 GTGGTCCTTCGGGACATA
*
525778 GTGGT-CTTTGGGACATA
1 GTGGTCCTTCGGGACATA
*
525795 GTGGTCCTACGGGACA
1 GTGGTCCTTCGGGACA
525811 AATTCTATGC
Statistics
Matches: 109, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
17 15 0.14
18 94 0.86
ACGTcount: A:0.18, C:0.21, G:0.33, T:0.27
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:528088 original size:25 final size:25
Alignment explanation
Indices: 528029--528088 Score: 102
Period size: 25 Copynumber: 2.4 Consensus size: 25
528019 AGATAAATGT
*
528029 ATAAAGGAAATCGACAATTGAAGAA
1 ATAAAGGAAGTCGACAATTGAAGAA
528054 ATAAAGGAAGTCGACAATTGAAGAA
1 ATAAAGGAAGTCGACAATTGAAGAA
*
528079 ATAAATGAAG
1 ATAAAGGAAG
528089 GAAAAATTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.55, C:0.07, G:0.22, T:0.17
Consensus pattern (25 bp):
ATAAAGGAAGTCGACAATTGAAGAA
Found at i:528437 original size:7 final size:7
Alignment explanation
Indices: 528422--528461 Score: 71
Period size: 7 Copynumber: 5.7 Consensus size: 7
528412 TCCAGAGTTC
*
528422 TCTTTCT
1 TCTTCCT
528429 TCTTCCT
1 TCTTCCT
528436 TCTTCCT
1 TCTTCCT
528443 TCTTCCT
1 TCTTCCT
528450 TCTTCCT
1 TCTTCCT
528457 TCTTC
1 TCTTC
528462 ATACGTGAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (7 bp):
TCTTCCT
Found at i:529106 original size:20 final size:23
Alignment explanation
Indices: 529059--529116 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 23
529049 GAATGGATAG
529059 TGCATCGATGCACGTGTTAAAGAA
1 TGCATCGATGCAC-TGTTAAAGAA
529083 TGCATCGATGCACTG-T-AA-AA
1 TGCATCGATGCACTGTTAAAGAA
*
529103 TGCATCGATTCACT
1 TGCATCGATGCACT
529117 TCAAGGGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 15 0.45
21 2 0.06
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (23 bp):
TGCATCGATGCACTGTTAAAGAA
Found at i:529964 original size:18 final size:18
Alignment explanation
Indices: 529941--530082 Score: 212
Period size: 18 Copynumber: 7.9 Consensus size: 18
529931 GAGGGTCTAC
529941 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
529959 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
* *
529977 ATGGTCCTTCGGGACACA
1 GTGGTCCTTCGGGACATA
529995 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
* *
530013 GTGGTCCTTTGGGATATA
1 GTGGTCCTTCGGGACATA
*
530031 GTGGTCCTTCGGGACACA
1 GTGGTCCTTCGGGACATA
* *
530049 CTGGTCCTTTGGGACATA
1 GTGGTCCTTCGGGACATA
*
530067 GTGGTCCTACGGGACA
1 GTGGTCCTTCGGGACA
530083 AATTCTATGC
Statistics
Matches: 109, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 109 1.00
ACGTcount: A:0.18, C:0.23, G:0.32, T:0.27
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:530345 original size:2 final size:2
Alignment explanation
Indices: 530340--530379 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
530330 ATATATGTTA
530340 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
530380 GAATGAATAT
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:535781 original size:117 final size:117
Alignment explanation
Indices: 535575--535811 Score: 296
Period size: 117 Copynumber: 2.0 Consensus size: 117
535565 AAGCTTAACT
* * *
535575 TTTAAATCGAAATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGTTCTAAATCCTTCTT
1 TTTAAATCGAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCATTCTT
* * * * *
535640 CAATATTTCATTTTAATACTCAAAATCTATTTTAGTTTTTAGAAGAAGATCA
66 CAACATTTCATTTTAATACTCAAAATCTACTTTAGCTTTCAAAAGAAGATCA
* * * ** * *
535692 TTTAATTCGAAAATTTCTTTTTCAA-AGTTTTTAGTTTTCATTTTTGAAAGCTCTAACTCATTTT
1 TTTAAATCGAAAATTTCTTTTTCAATA-CTTTCAAATTTCATTTTTGAAAGCTCTAAATCATTCT
* **
535756 TCAACATTTCATTTTGATTTTCAAAATCTACTTTAGCTTTCAAAAGAAGATCA
65 TCAACATTTCATTTTAATACTCAAAATCTACTTTAGCTTTCAAAAGAAGATCA
535809 TTT
1 TTT
535812 TTAGCTATAA
Statistics
Matches: 101, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
116 1 0.01
117 100 0.99
ACGTcount: A:0.32, C:0.14, G:0.07, T:0.48
Consensus pattern (117 bp):
TTTAAATCGAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCATTCTT
CAACATTTCATTTTAATACTCAAAATCTACTTTAGCTTTCAAAAGAAGATCA
Found at i:538123 original size:42 final size:42
Alignment explanation
Indices: 538061--538149 Score: 153
Period size: 42 Copynumber: 2.1 Consensus size: 42
538051 TTTGCAGGGG
* *
538061 AGCTGATCAGTTAAACATTAAGAAAGTTCTAATGCAAACTTA
1 AGCTGATCAGTTAAAAATTAAGAAAGTTCGAATGCAAACTTA
538103 AGCTGATCAGTTAAAAATTAAGAAAGTTCGAATGCAAACTTA
1 AGCTGATCAGTTAAAAATTAAGAAAGTTCGAATGCAAACTTA
538145 A-CTGA
1 AGCTGA
538150 CCAAGAAAGC
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
41 4 0.09
42 41 0.91
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (42 bp):
AGCTGATCAGTTAAAAATTAAGAAAGTTCGAATGCAAACTTA
Found at i:550564 original size:32 final size:32
Alignment explanation
Indices: 550528--550592 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
550518 AAGGTGAATA
* *
550528 ACAATCTTGTTATAATATATATGACAGTCATT
1 ACAATCTTGCTATAATATATATGACAATCATT
* *
550560 ACAATCTTGCTATCATATATTTGACAATCATT
1 ACAATCTTGCTATAATATATATGACAATCATT
550592 A
1 A
550593 GTGAAAAACC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.40
Consensus pattern (32 bp):
ACAATCTTGCTATAATATATATGACAATCATT
Found at i:551174 original size:17 final size:17
Alignment explanation
Indices: 551152--551187 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
551142 CTTGTCCTGC
551152 ATGGATAAACATTTGCA
1 ATGGATAAACATTTGCA
*
551169 ATGGATAACCATTTGCA
1 ATGGATAAACATTTGCA
551186 AT
1 AT
551188 CACAAAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.31
Consensus pattern (17 bp):
ATGGATAAACATTTGCA
Found at i:557006 original size:18 final size:18
Alignment explanation
Indices: 556983--557017 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
556973 GACCCGATCC
556983 AAAATAATATATTTATTA
1 AAAATAATATATTTATTA
* *
557001 AAAATATTATTTTTATT
1 AAAATAATATATTTATT
557018 CAATAAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AAAATAATATATTTATTA
Found at i:558757 original size:17 final size:18
Alignment explanation
Indices: 558725--558760 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
558715 ACCGGACCTG
558725 AAATAATATATTTATTAA
1 AAATAATATATTTATTAA
*
558743 AAATATTAT-TTTATTAA
1 AAATAATATATTTATTAA
558760 A
1 A
558761 TAAAAATAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AAATAATATATTTATTAA
Found at i:559723 original size:18 final size:18
Alignment explanation
Indices: 559692--559750 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 18
559682 ATTCGACCTG
*
559692 AAATAATATATTTATTAA
1 AAATAATATTTTTATTAA
*
559710 AAATATTATTTTTATTCAATAA
1 AAATAATATTTTTA-T---TAA
559732 AAATAATATTTTTATTAA
1 AAATAATATTTTTATTAA
559750 A
1 A
559751 TAAAAATAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
18 16 0.47
19 1 0.03
21 1 0.03
22 16 0.47
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
AAATAATATTTTTATTAA
Found at i:559732 original size:22 final size:22
Alignment explanation
Indices: 559707--559759 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
559697 ATATATTTAT
* *
559707 TAAAAATATTATTTTTATTCAA
1 TAAAAATAATATTTTTATTAAA
559729 TAAAAATAATATTTTTATTAAA
1 TAAAAATAATATTTTTATTAAA
559751 TAAAAATAA
1 TAAAAATAA
559760 GGGATATGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TAAAAATAATATTTTTATTAAA
Found at i:563877 original size:79 final size:79
Alignment explanation
Indices: 563742--563901 Score: 302
Period size: 79 Copynumber: 2.0 Consensus size: 79
563732 TTGGTAAACT
*
563742 TTAAACAAGTTTTGTTCTCCCCCTCTTTTGTTTGGTGGATTTCTTCCACTAGTGTTTTCAAGGTA
1 TTAAACAAGTTTTGTTCTCCCCCTCTTTTGTTTGGTGGATTTCTTCCACTACTGTTTTCAAGGTA
563807 AGTAAGACCCTTGG
66 AGTAAGACCCTTGG
*
563821 TTAAACAAGTTTTGTTCTCCCCCTCTTTTGTTTGGTGGATTTTTTCCACTACTGTTTTCAAGGTA
1 TTAAACAAGTTTTGTTCTCCCCCTCTTTTGTTTGGTGGATTTCTTCCACTACTGTTTTCAAGGTA
563886 AGTAAGACCCTTGG
66 AGTAAGACCCTTGG
563900 TT
1 TT
563902 TTCACTTTCA
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.19, C:0.20, G:0.18, T:0.43
Consensus pattern (79 bp):
TTAAACAAGTTTTGTTCTCCCCCTCTTTTGTTTGGTGGATTTCTTCCACTACTGTTTTCAAGGTA
AGTAAGACCCTTGG
Found at i:565449 original size:172 final size:171
Alignment explanation
Indices: 565105--565451 Score: 660
Period size: 171 Copynumber: 2.0 Consensus size: 171
565095 AGCATCTTTG
565105 GCTGGTCATTGAAGGACTGCTATTGTCATTATATATAACTTTAATGTAAAATTATACTTTTTTTT
1 GCTGGTCATTGAAGGACTGCTATTGTCATTATATATAACTTTAATGTAAAATTATACTTTTTTTT
*
565170 AATGCAAATGAGGTTGTAGTTGCGGGATAAGGGAAGGAATTACAAGTGTTGTGATTTGCCGCAGA
66 AATGCAAATGAGGTTGTAGTTGCGGGATAAGGGAAGGAATTACAAGTGTTGTGATTTGACGCAGA
565235 CCTTTTGGATGTCACCTTCTAAAGGTAATCAATCAGACTAA
131 CCTTTTGGATGTCACCTTCTAAAGGTAATCAATCAGACTAA
565276 GCTGGTCATTGAAGGACTGCTATTGTCATTATATATAACTTTAATGTAAAATTATACTTTTTTTT
1 GCTGGTCATTGAAGGACTGCTATTGTCATTATATATAACTTTAATGTAAAATTATACTTTTTTTT
565341 AATGCAAATGAGGTTGTAGTTGCGGGATAAGGGAAGGAATTACAAGTGTTGTGATTTGAAACGCA
66 AATGCAAATGAGGTTGTAGTTGCGGGATAAGGGAAGGAATTACAAGTGTTGTGATTTG--ACGCA
565406 GACC-TTTGGATGTCACCTTCTAAAGGTAATCAATCAGACTAA
129 GACCTTTTGGATGTCACCTTCTAAAGGTAATCAATCAGACTAA
565448 GCTG
1 GCTG
565452 TTTTTCCTAA
Statistics
Matches: 173, Mismatches: 1, Indels: 3
0.98 0.01 0.02
Matches are distributed among these distances:
171 123 0.71
172 42 0.24
173 8 0.05
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.35
Consensus pattern (171 bp):
GCTGGTCATTGAAGGACTGCTATTGTCATTATATATAACTTTAATGTAAAATTATACTTTTTTTT
AATGCAAATGAGGTTGTAGTTGCGGGATAAGGGAAGGAATTACAAGTGTTGTGATTTGACGCAGA
CCTTTTGGATGTCACCTTCTAAAGGTAATCAATCAGACTAA
Found at i:565501 original size:3 final size:3
Alignment explanation
Indices: 565493--565525 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
565483 GGTTGATTTG
565493 TCT TCT TCT TCT TCT TCT TCT TCT TCT T-T TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
565526 GTGAATTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TCT
Found at i:574522 original size:22 final size:24
Alignment explanation
Indices: 574481--574528 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 24
574471 CAAATTTAAA
*
574481 CCCAAACCAGAACCCGACCCGGAG
1 CCCAAACCAGAACCCGACCCAGAG
574505 CCCAAACCA-AA-CCGACCCAGAG
1 CCCAAACCAGAACCCGACCCAGAG
574527 CC
1 CC
574529 TAACCTAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 12 0.52
23 2 0.09
24 9 0.39
ACGTcount: A:0.35, C:0.48, G:0.17, T:0.00
Consensus pattern (24 bp):
CCCAAACCAGAACCCGACCCAGAG
Found at i:575588 original size:109 final size:109
Alignment explanation
Indices: 575451--575663 Score: 275
Period size: 109 Copynumber: 2.0 Consensus size: 109
575441 GACCAAATCT
*
575451 GTTAGTTTCCCTTTTAGTTGCATATTATATAATTTTTGGTTTATTCACTATTTAGTCCCTCTAAC
1 GTTAGTTTCCCTTTTAGTTGCATATTATATAATTTTTGGTATATTCACTATTTAGTCCCTCTAAC
* * *
575516 TTTAGTGTGTTTTTGCATTTTGGTCATATGTGAG-GACTGAAACC
66 TTTAGCGTGTTTTTACACTTTGGTCATATGT-AGTGACTGAAACC
* ** * * * * * * * *
575560 GTTATTTTCCCTTTTCTTTGCATGTTATATAATTTTTTGTATATTTATTGTTTAGTTCCTTTAAG
1 GTTAGTTTCCCTTTTAGTTGCATATTATATAATTTTTGGTATATTCACTATTTAGTCCCTCTAAC
575625 TTTAGCGTGTTTTTACACTTTGGTCATATGTAGTGACTG
66 TTTAGCGTGTTTTTACACTTTGGTCATATGTAGTGACTG
575664 TTTAAATTTT
Statistics
Matches: 88, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
108 2 0.02
109 86 0.98
ACGTcount: A:0.20, C:0.13, G:0.16, T:0.51
Consensus pattern (109 bp):
GTTAGTTTCCCTTTTAGTTGCATATTATATAATTTTTGGTATATTCACTATTTAGTCCCTCTAAC
TTTAGCGTGTTTTTACACTTTGGTCATATGTAGTGACTGAAACC
Found at i:585898 original size:30 final size:30
Alignment explanation
Indices: 585862--585933 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
585852 CCCGAAGGAC
* *
585862 CTATCCAGAGGTCACAAGGAACCTCGGTAA
1 CTATCCAGAGGTCACAAAGAACCTCGGCAA
* *
585892 CTATCCAGAGGTCATAAAGATCCTCGGCAA
1 CTATCCAGAGGTCACAAAGAACCTCGGCAA
* *
585922 CTGTCCATAGGT
1 CTATCCAGAGGT
585934 TCCAAAAAAC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.21
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGAACCTCGGCAA
Found at i:586024 original size:32 final size:31
Alignment explanation
Indices: 585973--586090 Score: 166
Period size: 32 Copynumber: 3.7 Consensus size: 31
585963 ATTCCTTAGA
585973 ACATAGGTATACTGTCCATATGTCTCGAAAG
1 ACATAGGTATACTGTCCATATGTCTCGAAAG
* * *
586004 ACATAGGTAATTCTGTCCATATTTTTCGTAAA-
1 ACATAGGT-ATACTGTCCATATGTCTCG-AAAG
586036 ACATAGGTATACTGTCCATATGTCTCGAAAG
1 ACATAGGTATACTGTCCATATGTCTCGAAAG
*
586067 ACATAGGTAATTCTGTCCATATGT
1 ACATAGGT-ATACTGTCCATATGT
586091 TCCGTAGAAC
Statistics
Matches: 76, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
30 3 0.04
31 32 0.42
32 38 0.50
33 3 0.04
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (31 bp):
ACATAGGTATACTGTCCATATGTCTCGAAAG
Found at i:586041 original size:63 final size:63
Alignment explanation
Indices: 585945--586110 Score: 271
Period size: 63 Copynumber: 2.7 Consensus size: 63
585935 CCAAAAAACC
* *
585945 TAGGTAA-ACTGTCCATATATTCCTTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACA
1 TAGGTAATTCTGTCCATATATTCCGTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACA
* * *
586007 TAGGTAATTCTGTCCATATTTTTCGTAAAACATAGGTATACTGTCCATATGTCTCGAAAGACA
1 TAGGTAATTCTGTCCATATATTCCGTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACA
*
586070 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATAC
1 TAGGTAATTCTGTCCATATATTCCGTAGAACATAGGTATAC
586111 CCTCAACTCT
Statistics
Matches: 95, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
62 7 0.07
63 88 0.93
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (63 bp):
TAGGTAATTCTGTCCATATATTCCGTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACA
Found at i:586103 original size:32 final size:32
Alignment explanation
Indices: 585921--586107 Score: 181
Period size: 31 Copynumber: 5.9 Consensus size: 32
585911 ATCCTCGGCA
* ** *
585921 ACTGTCCATAGGTTCCAAAAAACCTAGGTAA-
1 ACTGTCCATATGTTCCGTAAAACATAGGTAAT
* * *
585952 ACTGTCCATATATTCCTTAGAACATAGGT-AT
1 ACTGTCCATATGTTCCGTAAAACATAGGTAAT
585983 ACTGTCCATATG-TCTCG-AAAGACATAGGTAAT
1 ACTGTCCATATGTTC-CGTAAA-ACATAGGTAAT
* * *
586015 TCTGTCCATATTTTTCGTAAAACATAGGT-AT
1 ACTGTCCATATGTTCCGTAAAACATAGGTAAT
586046 ACTGTCCATATG-TCTCG-AAAGACATAGGTAAT
1 ACTGTCCATATGTTC-CGTAAA-ACATAGGTAAT
* *
586078 TCTGTCCATATGTTCCGTAGAACATAGGTA
1 ACTGTCCATATGTTCCGTAAAACATAGGTA
586108 TACCCTCAAC
Statistics
Matches: 128, Mismatches: 17, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
30 9 0.07
31 65 0.51
32 46 0.36
33 8 0.06
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Consensus pattern (32 bp):
ACTGTCCATATGTTCCGTAAAACATAGGTAAT
Found at i:590826 original size:30 final size:30
Alignment explanation
Indices: 590790--590861 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
590780 CCCGAAGGAC
* *
590790 CTATCCAGAGGTCACAAGGAACCTCGGTAA
1 CTATCCAGAGGTCACAAAGAACCTCGGCAA
* *
590820 CTATCCAGAGGTCATAAAGATCCTCGGCAA
1 CTATCCAGAGGTCACAAAGAACCTCGGCAA
* *
590850 CTGTCCATAGGT
1 CTATCCAGAGGT
590862 TCCGAAGAAC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.21
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGAACCTCGGCAA
Found at i:590886 original size:31 final size:31
Alignment explanation
Indices: 590848--591035 Score: 195
Period size: 31 Copynumber: 6.0 Consensus size: 31
590838 GATCCTCGGC
* *
590848 AACTGTCCATAGGTTCCGAAGAACCTAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
**
590879 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
*
590910 TACTGTCCATATG-TCTCGAA-AGACATAGGTA
1 AACTGTCCATATGTTC-CGAAGA-ACATAGGTA
* *
590941 ATTCTGTCCATATGTTCCGTAGAACATAGGTA
1 A-ACTGTCCATATGTTCCGAAGAACATAGGTA
* *
590973 TACTGTCCATATG-TCTCGAA-AGATATAGGTA
1 AACTGTCCATATGTTC-CGAAGA-ACATAGGTA
* *
591004 ATTCTGTCCATATGTTCCGTAGAACATAGGTA
1 A-ACTGTCCATATGTTCCGAAGAACATAGGTA
591036 TACCCTCAAC
Statistics
Matches: 129, Mismatches: 18, Indels: 19
0.78 0.11 0.11
Matches are distributed among these distances:
30 6 0.05
31 72 0.56
32 45 0.35
33 6 0.05
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGAAGAACATAGGTA
Found at i:590964 original size:63 final size:63
Alignment explanation
Indices: 590873--591038 Score: 298
Period size: 63 Copynumber: 2.7 Consensus size: 63
590863 CCGAAGAACC
* *
590873 TAGGTAA-ACTGTCCATATGTTCCTTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACA
1 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACA
*
590935 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCGAAAGATA
1 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACA
590998 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATAC
1 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATAC
591039 CCTCAACTCT
Statistics
Matches: 100, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
62 7 0.07
63 93 0.93
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Consensus pattern (63 bp):
TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACA
Found at i:592217 original size:18 final size:18
Alignment explanation
Indices: 592194--592228 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
592184 TTCATTTAGG
592194 GGGGAATCGATACCCCCA
1 GGGGAATCGATACCCCCA
*
592212 GGGGAATTGATACCCCC
1 GGGGAATCGATACCCCC
592229 TGAACATACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.31, G:0.29, T:0.14
Consensus pattern (18 bp):
GGGGAATCGATACCCCCA
Found at i:596278 original size:5 final size:5
Alignment explanation
Indices: 596264--596347 Score: 96
Period size: 5 Copynumber: 15.8 Consensus size: 5
596254 TGCCTAAGAT
596264 AAAAG AAAAAG AAAAG AAAAG AAAAAAG AAAAG AAAAG AAAAAAG AAAAG
1 AAAAG -AAAAG AAAAG AAAAG --AAAAG AAAAG AAAAG --AAAAG AAAAG
* * *
596314 AAAAG AAAAG AAAAG AAATG AAATG AAATG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
596348 ATGAAAAATG
Statistics
Matches: 72, Mismatches: 2, Indels: 9
0.87 0.02 0.11
Matches are distributed among these distances:
5 57 0.79
6 5 0.07
7 10 0.14
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAAG
Found at i:596291 original size:17 final size:17
Alignment explanation
Indices: 596264--596336 Score: 116
Period size: 17 Copynumber: 4.5 Consensus size: 17
596254 TGCCTAAGAT
596264 AAAAG-AAAAAGAAAAG
1 AAAAGAAAAAAGAAAAG
596280 AAAAGAAAAAAGAAAAG
1 AAAAGAAAAAAGAAAAG
596297 AAAAGAAAAAAGAAAAG
1 AAAAGAAAAAAGAAAAG
596314 AAAAG--AAAAGAAAAG
1 AAAAGAAAAAAGAAAAG
*
596329 AAATGAAA
1 AAAAGAAA
596337 TGAAATGAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
15 14 0.26
16 5 0.09
17 34 0.64
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (17 bp):
AAAAGAAAAAAGAAAAG
Found at i:596295 original size:22 final size:22
Alignment explanation
Indices: 596259--596331 Score: 112
Period size: 22 Copynumber: 3.3 Consensus size: 22
596249 TATTATGCCT
*
596259 AAGATAAAAGAAAAAGAAAAGAA
1 AAGAAAAAAG-AAAAGAAAAGAA
596282 AAGAAAAAAGAAAAGAAAAGAA
1 AAGAAAAAAGAAAAGAAAAGAA
596304 AA-AAGAAAAGAAAAGAAAAGAA
1 AAGAA-AAAAGAAAAGAAAAGAA
596326 AAGAAA
1 AAGAAA
596332 TGAAATGAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
21 2 0.04
22 34 0.72
23 11 0.23
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (22 bp):
AAGAAAAAAGAAAAGAAAAGAA
Found at i:596351 original size:7 final size:7
Alignment explanation
Indices: 596339--596492 Score: 276
Period size: 7 Copynumber: 22.3 Consensus size: 7
596329 AAATGAAATG
596339 AAATGAA
1 AAATGAA
596346 AAATGAA
1 AAATGAA
596353 AAATGAA
1 AAATGAA
596360 AAATGAA
1 AAATGAA
596367 AAATGAA
1 AAATGAA
596374 AAATGAA
1 AAATGAA
596381 AAATGAA
1 AAATGAA
596388 AAATGAA
1 AAATGAA
596395 AAATGAA
1 AAATGAA
596402 AAATGAA
1 AAATGAA
596409 AAATGAA
1 AAATGAA
596416 AAATGAA
1 AAATGAA
596423 AAATGAA
1 AAATGAA
596430 AAATGAA
1 AAATGAA
596437 AAATGAA
1 AAATGAA
596444 AAATGAA
1 AAATGAA
596451 AAATGAA
1 AAATGAA
*
596458 AAAAGAA
1 AAATGAA
596465 AAATGAA
1 AAATGAA
596472 AAA-GAA
1 AAATGAA
596478 AAA-GAA
1 AAATGAA
*
596484 AAAAGAA
1 AAATGAA
596491 AA
1 AA
596493 GGAGGGTTTA
Statistics
Matches: 144, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
6 12 0.08
7 132 0.92
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.12
Consensus pattern (7 bp):
AAATGAA
Found at i:597755 original size:140 final size:140
Alignment explanation
Indices: 597506--598129 Score: 864
Period size: 140 Copynumber: 4.4 Consensus size: 140
597496 TAAACCAACC
* * * *
597506 AACATTTCCAGTGGAGAGTTCATAATTAAAAGAACTCATCCGATAG-TGGA-AAG-AGTTCATAA
1 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCATAA
* * *
597568 TGAGAATAACTTGTTCAACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAGCGATGCCTCAC
66 TAAGAAGAACTTGTTCAACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAGCGACGCCTCAC
597633 TCGAGGGATT
131 TCGAGGGATT
* *
597643 AACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCTGATAGAGGGAGAAGAAGTTCATAA
1 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCATAA
* * *
597708 TAAGAAGAACTTGTTCAACCTTTGCTCGATTCATTGCATATGGAGTTGATTCAGCAACGCCTCAC
66 TAAGAAGAACTTGTTCAACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAGCGACGCCTCAC
*
597773 TTGAGGGATT
131 TCGAGGGATT
* * *
597783 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGA-CGAGGGAGAATAAATTCATAA
1 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCATAA
* *
597847 TAAGAAGAACTTGTTTAACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAACGACGCCTCAC
66 TAAGAAGAACTTGTTCAACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAGCGACGCCTCAC
*
597912 TCCAGGGATT
131 TCGAGGGATT
* *
597922 AATATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAATAAGTTCATAA
1 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCATAA
*
597987 TGAGAATG-ACTTGTTCAACCTTTGCTCGATTCATTGCTCGATTCATATTGTATGGAGTTGAATC
66 TAAGAA-GAACTTGTTCAACCTTTGCTCGATTCA----TCG---C--A---TATGGAGTTGAATC
* *
598051 AGTGACGCCTCACTTGAGGGATT
118 AGCGACGCCTCACTCGAGGGATT
*
598074 AACATTTCCAATTGAGAGTTCATAATGAGAAGAACTCATCCGAT-GAGGGAGAAGAA
1 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAA
598130 CTTGTTCAAC
Statistics
Matches: 433, Mismatches: 37, Indels: 20
0.88 0.08 0.04
Matches are distributed among these distances:
137 41 0.09
138 3 0.01
139 131 0.30
140 166 0.38
141 1 0.00
144 3 0.01
147 1 0.00
149 1 0.00
151 11 0.03
152 75 0.17
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (140 bp):
AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCATAA
TAAGAAGAACTTGTTCAACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAGCGACGCCTCAC
TCGAGGGATT
Found at i:598004 original size:279 final size:283
Alignment explanation
Indices: 597506--598126 Score: 898
Period size: 279 Copynumber: 2.2 Consensus size: 283
597496 TAAACCAACC
* * * * * * *
597506 AACATTTCCAGTGGAGAGTTCATAATTAAAAGAACTCATCCGATAGTGGA-AAGAGTTCATAATG
1 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAGAG-GGAGAAAAATTCATAATA
* * *
597570 AGAATAACTTGTTCAACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAGCGATGCCTCACTC
65 AGAAGAACTTGTTCAACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAACGACGCCTCACTC
* *
597635 GAGGGATTAACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCTGATAGAGGGAGAAGAA
130 CAGGGATTAACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAA
*
597700 GTTCATAATAAGAAGAACTTGTTCAACCTTTGCTCGATTCA-T-T-G-C-A-TATGGAGTTGATT
195 GTTCATAATAAGAAGAACTTGTTCAACCTTTGCTCGATTCATTCTCGTCAATTATGGAGTTGAAT
597759 CAGCAACGCCTCACTTGAGGGATT
260 CAGCAACGCCTCACTTGAGGGATT
597783 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAATAAATTCATAAT
1 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGA-GAGGGAGAA-AAATTCATAAT
*
597848 AAGAAGAACTTGTTTAACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAACGACGCCTCACT
64 AAGAAGAACTTGTTCAACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAACGACGCCTCACT
* * *
597913 CCAGGGATTAATATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAATA
129 CCAGGGATTAACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGA
*
597978 AGTTCATAATGAGAATG-ACTTGTTCAACCTTTGCTCGATTCATTGCTCGATTCATATTGTATGG
194 AGTTCATAATAAGAA-GAACTTGTTCAACCTTTGCTCGATTCATT-CTCG--TCA-A-T-TATGG
**
598042 AGTTGAATCAGTGACGCCTCACTTGAGGGATT
252 AGTTGAATCAGCAACGCCTCACTTGAGGGATT
*
598074 AACATTTCCAATTGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAA
1 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGA-GAGGGAGAA
598127 GAACTTGTTC
Statistics
Matches: 306, Mismatches: 22, Indels: 18
0.88 0.06 0.05
Matches are distributed among these distances:
277 43 0.14
278 4 0.01
279 168 0.55
280 2 0.01
282 1 0.00
283 1 0.00
286 1 0.00
288 1 0.00
291 85 0.28
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.28
Consensus pattern (283 bp):
AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAGAGGGAGAAAAATTCATAATAA
GAAGAACTTGTTCAACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAACGACGCCTCACTCC
AGGGATTAACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAG
TTCATAATAAGAAGAACTTGTTCAACCTTTGCTCGATTCATTCTCGTCAATTATGGAGTTGAATC
AGCAACGCCTCACTTGAGGGATT
Found at i:598025 original size:12 final size:12
Alignment explanation
Indices: 598008--598032 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
597998 TGTTCAACCT
598008 TTGCTCGATTCA
1 TTGCTCGATTCA
598020 TTGCTCGATTCA
1 TTGCTCGATTCA
598032 T
1 T
598033 ATTGTATGGA
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:0.16, C:0.24, G:0.16, T:0.44
Consensus pattern (12 bp):
TTGCTCGATTCA
Found at i:598502 original size:23 final size:24
Alignment explanation
Indices: 598463--598528 Score: 75
Period size: 23 Copynumber: 2.8 Consensus size: 24
598453 AAAATTTAAA
*
598463 CCCAAACCAAAACCCGACCCGA-AG
1 CCCAAA-CAGAACCCGACCCGAGAG
*
598487 CCCAAACAGAACCCGA-CCTAGAG
1 CCCAAACAGAACCCGACCCGAGAG
598510 CCCAAAC-GAAACCCGACCC
1 CCCAAACAG-AACCCGACCC
598529 ACAACCTAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
22 4 0.11
23 25 0.68
24 8 0.22
ACGTcount: A:0.39, C:0.45, G:0.14, T:0.02
Consensus pattern (24 bp):
CCCAAACAGAACCCGACCCGAGAG
Found at i:599297 original size:14 final size:14
Alignment explanation
Indices: 599278--599305 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
599268 CGGTAAACGA
599278 TCGGGTCGGGTCAG
1 TCGGGTCGGGTCAG
599292 TCGGGTCGGGTCAG
1 TCGGGTCGGGTCAG
599306 ACCGGTCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.21, G:0.50, T:0.21
Consensus pattern (14 bp):
TCGGGTCGGGTCAG
Found at i:599326 original size:19 final size:19
Alignment explanation
Indices: 599302--599397 Score: 122
Period size: 19 Copynumber: 4.9 Consensus size: 19
599292 TCGGGTCGGG
*
599302 TCAGACCGGTCAAACTGGT
1 TCAGACCGGTCAAACCGGT
599321 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
599340 TCAAACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
599359 TC-GAACCGGTCAGAACCGGT
1 TCAG-ACCGGTCA-AACCGGT
* *
599379 TGAAAACCGGTCAAACCGG
1 T-CAGACCGGTCAAACCGG
599398 CTTCCAGCCC
Statistics
Matches: 68, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
19 46 0.68
20 14 0.21
21 8 0.12
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.16
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:599332 original size:28 final size:28
Alignment explanation
Indices: 599301--599397 Score: 106
Period size: 29 Copynumber: 3.4 Consensus size: 28
599291 GTCGGGTCGG
* * *
599301 GTCAGACCGGTCAAACTGGTTCAGACCG
1 GTCAAACCGGTCAAACCGGTTCAAACCG
599329 GTCAAACCGGTTCAAACCGG-TCAAACCG
1 GTCAAACCGG-TCAAACCGGTTCAAACCG
* *
599357 GTTCGAACCGGTCAGAACCGGTTGAAAACCG
1 G-TCAAACCGGTCA-AACCGGTT-CAAACCG
599388 GTCAAACCGG
1 GTCAAACCGG
599398 CTTCCAGCCC
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
28 20 0.34
29 22 0.38
30 9 0.16
31 7 0.12
ACGTcount: A:0.29, C:0.29, G:0.27, T:0.15
Consensus pattern (28 bp):
GTCAAACCGGTCAAACCGGTTCAAACCG
Found at i:599396 original size:9 final size:9
Alignment explanation
Indices: 599300--599397 Score: 97
Period size: 9 Copynumber: 10.2 Consensus size: 9
599290 AGTCGGGTCG
*
599300 GGTCAGACC
1 GGTCAAACC
*
599309 GGTCAAACT
1 GGTCAAACC
*
599318 GGTTCAGACC
1 GG-TCAAACC
599328 GGTCAAACC
1 GGTCAAACC
599337 GGTTCAAACC
1 GG-TCAAACC
599347 GGTCAAACC
1 GGTCAAACC
*
599356 GGTTCGAACC
1 GG-TCAAACC
599366 GGTCAGAACC
1 GGTCA-AACC
*
599376 GGTTGAAAACC
1 GG-T-CAAACC
599387 GGTCAAACC
1 GGTCAAACC
599396 GG
1 GG
599398 CTTCCAGCCC
Statistics
Matches: 74, Mismatches: 9, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
9 35 0.47
10 31 0.42
11 7 0.09
12 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.28, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:600650 original size:5 final size:5
Alignment explanation
Indices: 600636--600737 Score: 100
Period size: 5 Copynumber: 18.8 Consensus size: 5
600626 TGCCTAAGAT
600636 AAAAG AAAAAG AAAAG AAAAG AAAAAAG AAAAG AAAAG AAAAAAG AAAAG
1 AAAAG -AAAAG AAAAG AAAAG --AAAAG AAAAG AAAAG --AAAAG AAAAG
600686 AAAAG AAAAG AAAAG AAAAATG AAAAAG AAAAAG AAAA- AAGAA- AAAAG
1 AAAAG AAAAG AAAAG -AAAA-G -AAAAG -AAAAG AAAAG AA-AAG AAAAG
600734 AAAA
1 AAAA
600738 TGAGGGTTTA
Statistics
Matches: 88, Mismatches: 0, Indels: 17
0.84 0.00 0.16
Matches are distributed among these distances:
4 4 0.05
5 52 0.59
6 16 0.18
7 16 0.18
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.01
Consensus pattern (5 bp):
AAAAG
Found at i:600663 original size:17 final size:17
Alignment explanation
Indices: 600636--600737 Score: 131
Period size: 17 Copynumber: 5.9 Consensus size: 17
600626 TGCCTAAGAT
600636 AAAAG-AAAAAGAAAAG
1 AAAAGAAAAAAGAAAAG
600652 AAAAGAAAAAAGAAAAG
1 AAAAGAAAAAAGAAAAG
600669 AAAAGAAAAAAGAAAAG
1 AAAAGAAAAAAGAAAAG
600686 AAAAG--AAAAGAAAAG
1 AAAAGAAAAAAGAAAAG
600701 AAAA-ATGAAAAAGAAAAAG
1 AAAAGA--AAAAAG-AAAAG
600720 AAAAAAGAAAAAAGAAAA
1 --AAAAGAAAAAAGAAAA
600738 TGAGGGTTTA
Statistics
Matches: 77, Mismatches: 0, Indels: 15
0.84 0.00 0.16
Matches are distributed among these distances:
15 14 0.18
16 5 0.06
17 33 0.43
18 5 0.06
19 9 0.12
20 6 0.08
21 4 0.05
22 1 0.01
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.01
Consensus pattern (17 bp):
AAAAGAAAAAAGAAAAG
Found at i:600685 original size:39 final size:39
Alignment explanation
Indices: 600631--600737 Score: 132
Period size: 39 Copynumber: 2.7 Consensus size: 39
600621 TATTATGCCT
*
600631 AAGATAAAAGAAAAAGAAAAGAAAAGAAAA-AAGAAAAGAA
1 AAGAAAAAAG-AAAAGAAAAGAAAAGAAAAGAA-AAAAGAA
*
600671 AAGAAAAAAGAAAAGAAAAGAAAAGAAAAGAAAAATGAA
1 AAGAAAAAAGAAAAGAAAAGAAAAGAAAAGAAAAAAGAA
600710 AA-AGAAAAAGAAAA-AAGAA-AAAAGAAAA
1 AAGA-AAAAAGAAAAGAA-AAGAAAAGAAAA
600738 TGAGGGTTTA
Statistics
Matches: 62, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
38 12 0.19
39 39 0.63
40 11 0.18
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (39 bp):
AAGAAAAAAGAAAAGAAAAGAAAAGAAAAGAAAAAAGAA
Found at i:601997 original size:140 final size:139
Alignment explanation
Indices: 601748--602368 Score: 810
Period size: 138 Copynumber: 4.4 Consensus size: 139
601738 TAAACCAACC
* * * * *
601748 AACATTTCCAGTGGAGAGTTCATAATTAAAATAACTCATCCGATAG-TGGA-AAG-AGTTCATAA
1 AACATTTCCAAT-GAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCATAA
* * * *
601810 TGAGAATAACTTGTTTAACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAGCGATGCCTCAC
65 TAAGAAGAACTTGTTCAACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAGCGACGCCTCAC
601875 TCGAGGGATT
130 TCGAGGGATT
* *
601885 AACATTTCCAATGAAGAGTTCATAATGAGAAAAACTCATCTGATAGAGGGAGAAGAAGTTCATAA
1 AACATTTCCAATG-AGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCATAA
*
601950 TAAGAAGAACTTGTTCAACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAGCAACGCCTCAC
65 TAAGAAGAACTTGTTCAACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAGCGACGCCTCAC
*
602015 TTGAGGGATT
130 TCGAGGGATT
* *
602025 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGA-CGA-GGAGAA-ATAATTCATA
1 AACATTTCCAAT-GAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGA-AGTTCATA
* *
602087 ATAAGAAGAACTTGTTTAACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAACGACGCCTCA
64 ATAAGAAGAACTTGTTCAACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAGCGACGCCTCA
*
602152 CTCCAGGGATT
129 CTCGAGGGATT
* *
602163 AATATTTCCAATG-GAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAATAAGTTCATAAT
1 AACATTTCCAATGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCATAAT
*
602227 GAGAATG-ACTTGTTCAACCTTTGCTCGATTCATTGCTCGATTCATATTGTATGGAGTTGAATCA
66 AAGAA-GAACTTGTTCAACCTTTGCTCGATTCA----TCG---C--A---TATGGAGTTGAATCA
* *
602291 GTGACGCCTCACTTGAGGGATT
118 GCGACGCCTCACTCGAGGGATT
602313 AACATTTCCAATTGAGAGTTCATAATGAGAAGAACTCATCCGAT-GAGGGAGAAGAA
1 AACATTTCCAA-TGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAA
602369 CTTGTTCAAC
Statistics
Matches: 428, Mismatches: 32, Indels: 34
0.87 0.06 0.07
Matches are distributed among these distances:
136 29 0.07
137 43 0.10
138 141 0.33
139 7 0.02
140 117 0.27
141 1 0.00
142 3 0.01
145 1 0.00
147 1 0.00
150 43 0.10
151 13 0.03
152 29 0.07
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (139 bp):
AACATTTCCAATGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCATAAT
AAGAAGAACTTGTTCAACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAGCGACGCCTCACT
CGAGGGATT
Found at i:602264 original size:12 final size:12
Alignment explanation
Indices: 602247--602271 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
602237 TGTTCAACCT
602247 TTGCTCGATTCA
1 TTGCTCGATTCA
602259 TTGCTCGATTCA
1 TTGCTCGATTCA
602271 T
1 T
602272 ATTGTATGGA
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:0.16, C:0.24, G:0.16, T:0.44
Consensus pattern (12 bp):
TTGCTCGATTCA
Found at i:602347 original size:288 final size:276
Alignment explanation
Indices: 601748--602365 Score: 873
Period size: 278 Copynumber: 2.2 Consensus size: 276
601738 TAAACCAACC
* * * * * * *
601748 AACATTTCCAGTGGAGAGTTCATAATTAAAATAACTCATCCGATAGTG-GAAAGAGTTCATAATG
1 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAGAG-GAGAAAGAATTCATAATA
* * *
601812 AGAATAACTTGTTTAACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAGCGATGCCTCACTC
65 AGAAGAACTTGTTTAACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAACGACGCCTCACTC
* *
601877 GAGGGATTAACATTTCCAATGAAGAGTTCATAATGAGAAAAACTCATCTGATAGAGGGAGAAGAA
130 CAGGGATTAACATTTCCAATG-AGAGTTCATAATGAGAAAAACTCATCCGATAGAGGGAGAAGAA
601942 GTTCATAATAAGAAGAACTTGTTCAACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAGCAA
194 GTTCATAATAAGAAGAACTTGTTCAACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAGCAA
602007 CGCCTCACTTGAGGGATT
259 CGCCTCACTTGAGGGATT
*
602025 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACGAGGAGAAATAATTCATAATA
1 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGA-GAGGAGAAAGAATTCATAATA
602090 AGAAGAACTTGTTTAACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAACGACGCCTCACTC
65 AGAAGAACTTGTTTAACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAACGACGCCTCACTC
* * *
602155 CAGGGATTAATATTTCCAATG-GAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAATAAG
130 CAGGGATTAACATTTCCAATGAGAGTTCATAATGAGAAAAACTCATCCGATAGAGGGAGAAGAAG
*
602219 TTCATAATGAGAATG-ACTTGTTCAACCTTTGCTCGATTCATTGCTCGATTCATATTGTATGGAG
195 TTCATAATAAGAA-GAACTTGTTCAACCTTTGCTCGATTCA----TCG---C--A---TATGGAG
**
602283 TTGAATCAGTGACGCCTCACTTGAGGGATT
247 TTGAATCAGCAACGCCTCACTTGAGGGATT
*
602313 AACATTTCCAATTGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAA
1 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGA-GA-GGAGAA
602366 GAACTTGTTC
Statistics
Matches: 304, Mismatches: 21, Indels: 20
0.88 0.06 0.06
Matches are distributed among these distances:
276 77 0.25
277 41 0.13
278 96 0.32
280 3 0.01
283 1 0.00
285 1 0.00
288 79 0.26
289 6 0.02
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (276 bp):
AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAGAGGAGAAAGAATTCATAATAA
GAAGAACTTGTTTAACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAACGACGCCTCACTCC
AGGGATTAACATTTCCAATGAGAGTTCATAATGAGAAAAACTCATCCGATAGAGGGAGAAGAAGT
TCATAATAAGAAGAACTTGTTCAACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAGCAACG
CCTCACTTGAGGGATT
Found at i:602744 original size:23 final size:23
Alignment explanation
Indices: 602705--602771 Score: 84
Period size: 23 Copynumber: 2.9 Consensus size: 23
602695 AAAATTTAAA
*
602705 CCCAAACCAAAACCCGACCC-GAAG
1 CCCAAA-CAGAACCCGACCCAG-AG
602729 CCCAAACAGAACCCGACCCAGAG
1 CCCAAACAGAACCCGACCCAGAG
602752 CCCAAAC-GAAACCCGACCCA
1 CCCAAACAG-AACCCGACCCA
602772 TAACCTAACC
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
22 1 0.03
23 32 0.80
24 7 0.17
ACGTcount: A:0.40, C:0.46, G:0.13, T:0.00
Consensus pattern (23 bp):
CCCAAACAGAACCCGACCCAGAG
Found at i:603539 original size:9 final size:9
Alignment explanation
Indices: 603525--603559 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
603515 CAACAATCGG
603525 GTCGGGTCA
1 GTCGGGTCA
603534 GTCGGGTCA
1 GTCGGGTCA
*
603543 GTCGGGTCG
1 GTCGGGTCA
603552 GTCGGGTC
1 GTCGGGTC
603560 GGGTCAGACC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.06, C:0.23, G:0.49, T:0.23
Consensus pattern (9 bp):
GTCGGGTCA
Found at i:603548 original size:23 final size:23
Alignment explanation
Indices: 603521--603566 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
603511 CGGTCAACAA
603521 TCGGGTCGGGTC-AGTCGGGTCAG
1 TCGGGTC-GGTCGAGTCGGGTCAG
*
603544 TCGGGTCGGTCGGGTCGGGTCAG
1 TCGGGTCGGTCGAGTCGGGTCAG
603567 ACCGATCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.07, C:0.22, G:0.50, T:0.22
Consensus pattern (23 bp):
TCGGGTCGGTCGAGTCGGGTCAG
Found at i:603602 original size:19 final size:19
Alignment explanation
Indices: 603563--603641 Score: 79
Period size: 19 Copynumber: 4.1 Consensus size: 19
603553 TCGGGTCGGG
* **
603563 TCAGACCGATCAAACTAGT
1 TCAGACCGGTCAAACCGGT
603582 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
603601 TC-GAACCGGTCAGAACCGGT
1 TCAG-ACCGGTCA-AACCGGT
* *
603621 TAAAAACCGGTCAAACCGGT
1 T-CAGACCGGTCAAACCGGT
603641 T
1 T
603642 TCCAGCCCTC
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
18 1 0.02
19 26 0.51
20 16 0.31
21 8 0.16
ACGTcount: A:0.32, C:0.28, G:0.23, T:0.18
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:603609 original size:10 final size:11
Alignment explanation
Indices: 603580--603641 Score: 57
Period size: 10 Copynumber: 6.3 Consensus size: 11
603570 GATCAAACTA
603580 GTTCAG-ACCG
1 GTTCAGAACCG
603590 G-TCA-AACCG
1 GTTCAGAACCG
603599 GTTC-GAACCG
1 GTTCAGAACCG
603609 G-TCAGAACCG
1 GTTCAGAACCG
* *
603619 GTTAAAAACCG
1 GTTCAGAACCG
603630 G-TCA-AACCG
1 GTTCAGAACCG
603639 GTT
1 GTT
603642 TCCAGCCCTC
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
9 16 0.37
10 19 0.44
11 8 0.19
ACGTcount: A:0.29, C:0.27, G:0.26, T:0.18
Consensus pattern (11 bp):
GTTCAGAACCG
Found at i:603619 original size:20 final size:20
Alignment explanation
Indices: 603586--603641 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
603576 ACTAGTTCAG
**
603586 ACCGGTCAAACCGGTT-CGA
1 ACCGGTCAAACCGGTTAAAA
603605 ACCGGTCAGAACCGGTTAAAA
1 ACCGGTCA-AACCGGTTAAAA
603626 ACCGGTCAAACCGGTT
1 ACCGGTCAAACCGGTT
603642 TCCAGCCCTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 8 0.24
20 16 0.48
21 9 0.27
ACGTcount: A:0.30, C:0.29, G:0.25, T:0.16
Consensus pattern (20 bp):
ACCGGTCAAACCGGTTAAAA
Found at i:609057 original size:43 final size:42
Alignment explanation
Indices: 609010--609256 Score: 144
Period size: 43 Copynumber: 5.7 Consensus size: 42
609000 GAAAATGATT
* * *
609010 AAATTAGGAGCCTAAATTATAAAAGTAAAAAATGAGGTTGAAA
1 AAATTAGG-GCCTCAATTATAAAAGTAAAAAGTGAGATTGAAA
* * * *
609053 AAATTAGGGGTCTCAACTATAAAGGT-AAAAGTGA-ATTTAAAAA
1 AAATTA-GGGCCTCAATTATAAAAGTAAAAAGTGAGA-TT-GAAA
* *
609096 AAATTAGGGACCTCAATTATAAAAGTAGAAAGTAAGATTGAAAA
1 AAATTAGGG-CCTCAATTATAAAAGTAAAAAGTGAGATTG-AAA
* * * * * *
609140 AAATTAAAGGCATCAATTATAAAGATTAAAAA-TAAAATTAAAA
1 AAATT-AGGGCCTCAATTATAAA-AGTAAAAAGTGAGATTGAAA
* * * *
609183 AAATTAGGGATCTCAATTGGAT-AGA-TAGAAAGTGAGATTAAAA
1 AAATTAGGG-CCTCAATT--ATAAAAGTAAAAAGTGAGATTGAAA
** * *
609226 AAATTAGACACCACAATTATAAAAATAAAAA
1 AAATTAG-GGCCTCAATTATAAAAGTAAAAA
609257 ATAAAATAAA
Statistics
Matches: 156, Mismatches: 32, Indels: 32
0.71 0.15 0.15
Matches are distributed among these distances:
41 2 0.01
42 22 0.14
43 83 0.53
44 37 0.24
45 12 0.08
ACGTcount: A:0.54, C:0.06, G:0.15, T:0.24
Consensus pattern (42 bp):
AAATTAGGGCCTCAATTATAAAAGTAAAAAGTGAGATTGAAA
Found at i:609190 original size:87 final size:87
Alignment explanation
Indices: 609010--609267 Score: 230
Period size: 86 Copynumber: 3.0 Consensus size: 87
609000 GAAAATGATT
* * * * ** *
609010 AAATTA-GGAGCCTAAATTATAAAAGTAAAAAATGAGGTTG-AAAAAATTAGGGGTC-TCAACTA
1 AAATTAGGGA-CCTCAATTATAAAAGTAGAAAGTGAGATTGAAAAAAATTAAAGG-CATCAATTA
* * * *
609072 TAAAG-GTAAAAGTGAATTTAAAAA
64 TAAAGATTAAAAATAAAATT-AAAA
*
609096 AAATTAGGGACCTCAATTATAAAAGTAGAAAGTAAGATTGAAAAAAATTAAAGGCATCAATTATA
1 AAATTAGGGACCTCAATTATAAAAGTAGAAAGTGAGATTGAAAAAAATTAAAGGCATCAATTATA
609161 AAGATTAAAAATAAAATTAAAA
66 AAGATTAAAAATAAAATTAAAA
* * *
609183 AAATTAGGGATCTCAATTGGAT-AGA-TAGAAAGTGAGATT-AAAAAAATTAGACA-CCA-CAAT
1 AAATTAGGGACCTCAATT--ATAAAAGTAGAAAGTGAGATTGAAAAAAATTA-A-AGGCATCAAT
* *
609243 TATAAAAATAAAAAATAAAA-TAAAA
62 TATAAAGATTAAAAATAAAATTAAAA
609268 TTCTTTTGGA
Statistics
Matches: 146, Mismatches: 18, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
85 5 0.03
86 64 0.44
87 62 0.42
88 13 0.09
89 2 0.01
ACGTcount: A:0.55, C:0.06, G:0.15, T:0.24
Consensus pattern (87 bp):
AAATTAGGGACCTCAATTATAAAAGTAGAAAGTGAGATTGAAAAAAATTAAAGGCATCAATTATA
AAGATTAAAAATAAAATTAAAA
Found at i:609258 original size:86 final size:86
Alignment explanation
Indices: 609092--609267 Score: 218
Period size: 87 Copynumber: 2.0 Consensus size: 86
609082 AGTGAATTTA
*
609092 AAAAAAATTAGGGACCTCAATTATAAAAGTAGAAAGTAAGATTGAAAAAAATTAAAGGCATCAAT
1 AAAAAAATTAGGGACCTCAATTATAAAAGTAGAAAGTAAGATTGAAAAAAATTAAAGCCATCAAT
* *
609157 TATAAAGATTAAAAATAAAATT
66 TATAAAAATAAAAAATAAAA-T
* * *
609179 AAAAAAATTAGGGATCTCAATTGGAT-AGA-TAGAAAGTGAGATT-AAAAAAATTAGACA-CCA-
1 AAAAAAATTAGGGACCTCAATT--ATAAAAGTAGAAAGTAAGATTGAAAAAAATTA-A-AGCCAT
609239 CAATTATAAAAATAAAAAATAAAAT
62 CAATTATAAAAATAAAAAATAAAAT
609264 AAAA
1 AAAA
609268 TTCTTTTGGA
Statistics
Matches: 79, Mismatches: 6, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
85 5 0.06
86 32 0.41
87 37 0.47
88 3 0.04
89 2 0.03
ACGTcount: A:0.59, C:0.06, G:0.12, T:0.23
Consensus pattern (86 bp):
AAAAAAATTAGGGACCTCAATTATAAAAGTAGAAAGTAAGATTGAAAAAAATTAAAGCCATCAAT
TATAAAAATAAAAAATAAAAT
Found at i:611537 original size:262 final size:262
Alignment explanation
Indices: 611072--611596 Score: 1050
Period size: 262 Copynumber: 2.0 Consensus size: 262
611062 CACGGTGTTG
611072 GGAGCAATGGTGATGACTTTGTACAAAGGCCCTATTATCAACTTCATCAAGTCAGGAGGAGGCGC
1 GGAGCAATGGTGATGACTTTGTACAAAGGCCCTATTATCAACTTCATCAAGTCAGGAGGAGGCGC
611137 ACACTATGTAACCGCCGGTGAATCTGCAGATCAACACTGGGTTTCTGGCACCATAGTGCTTCTCG
66 ACACTATGTAACCGCCGGTGAATCTGCAGATCAACACTGGGTTTCTGGCACCATAGTGCTTCTCG
611202 GAAGTATCTTTGGCTGGTCAAGCTTCTTTATTTTGCAAGTCAGTTGAAATATTTCAAGTCTCTTT
131 GAAGTATCTTTGGCTGGTCAAGCTTCTTTATTTTGCAAGTCAGTTGAAATATTTCAAGTCTCTTT
611267 GAATAATAACTTAAAACCACTTAATTGTTTATGAACCTGCTAAACATCGGTTACTGTTTCTGGCT
196 GAATAATAACTTAAAACCACTTAATTGTTTATGAACCTGCTAAACATCGGTTACTGTTTCTGGCT
611332 CA
261 CA
611334 GGAGCAATGGTGATGACTTTGTACAAAGGCCCTATTATCAACTTCATCAAGTCAGGAGGAGGCGC
1 GGAGCAATGGTGATGACTTTGTACAAAGGCCCTATTATCAACTTCATCAAGTCAGGAGGAGGCGC
611399 ACACTATGTAACCGCCGGTGAATCTGCAGATCAACACTGGGTTTCTGGCACCATAGTGCTTCTCG
66 ACACTATGTAACCGCCGGTGAATCTGCAGATCAACACTGGGTTTCTGGCACCATAGTGCTTCTCG
611464 GAAGTATCTTTGGCTGGTCAAGCTTCTTTATTTTGCAAGTCAGTTGAAATATTTCAAGTCTCTTT
131 GAAGTATCTTTGGCTGGTCAAGCTTCTTTATTTTGCAAGTCAGTTGAAATATTTCAAGTCTCTTT
611529 GAATAATAACTTAAAACCACTTAATTGTTTATGAACCTGCTAAACATCGGTTACTGTTTCTGGCT
196 GAATAATAACTTAAAACCACTTAATTGTTTATGAACCTGCTAAACATCGGTTACTGTTTCTGGCT
611594 CA
261 CA
611596 G
1 G
611597 TCCTTCACAT
Statistics
Matches: 263, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
262 263 1.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.32
Consensus pattern (262 bp):
GGAGCAATGGTGATGACTTTGTACAAAGGCCCTATTATCAACTTCATCAAGTCAGGAGGAGGCGC
ACACTATGTAACCGCCGGTGAATCTGCAGATCAACACTGGGTTTCTGGCACCATAGTGCTTCTCG
GAAGTATCTTTGGCTGGTCAAGCTTCTTTATTTTGCAAGTCAGTTGAAATATTTCAAGTCTCTTT
GAATAATAACTTAAAACCACTTAATTGTTTATGAACCTGCTAAACATCGGTTACTGTTTCTGGCT
CA
Found at i:612016 original size:2 final size:2
Alignment explanation
Indices: 612009--612035 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
611999 CACATGAATG
612009 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
612036 CGCACGCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:612823 original size:22 final size:23
Alignment explanation
Indices: 612785--612827 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
612775 TATTTTTTAA
612785 ATTCATTCCTTAAACATGTTTGT
1 ATTCATTCCTTAAACATGTTTGT
612808 ATTCATTCC-TAAACATGTTT
1 ATTCATTCCTTAAACATGTTT
612828 ATATATGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.28, C:0.19, G:0.07, T:0.47
Consensus pattern (23 bp):
ATTCATTCCTTAAACATGTTTGT
Found at i:614002 original size:14 final size:13
Alignment explanation
Indices: 613972--614022 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
613962 TAAAACAAAT
*
613972 TAAATAATAAATAA
1 TAAAT-ATAATTAA
613986 TAAATATAATTATA
1 TAAATATAATTA-A
*
614000 TAACTATAATTAA
1 TAAATATAATTAA
*
614013 AAAATA-AATT
1 TAAATATAATT
614023 TAGGGCGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
12 4 0.12
13 11 0.34
14 17 0.53
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (13 bp):
TAAATATAATTAA
Found at i:614341 original size:16 final size:16
Alignment explanation
Indices: 614317--614347 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
614307 CTTCTAATTT
*
614317 TTTTTGAGTTCAAGTC
1 TTTTCGAGTTCAAGTC
614333 TTTTCGAGTTCAAGT
1 TTTTCGAGTTCAAGT
614348 TTCAATATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.13, G:0.19, T:0.48
Consensus pattern (16 bp):
TTTTCGAGTTCAAGTC
Found at i:616281 original size:2 final size:2
Alignment explanation
Indices: 616274--616317 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
616264 TTAAAAGTAA
616274 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
616315 AT A
1 AT A
616318 GGTTTAGGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:617730 original size:30 final size:31
Alignment explanation
Indices: 617690--617749 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 31
617680 ATATTATTAA
617690 AAAAACTTAATAA-AACTCAATATTATTTTTT
1 AAAAACTTAATAATAA-TCAATATTATTTTTT
617721 AAAAA-TTAATAATTTAATCAATATTATTT
1 AAAAACTTAATAA--TAATCAATATTATTT
617750 ATGATAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 7 0.27
31 5 0.19
32 12 0.46
33 2 0.08
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (31 bp):
AAAAACTTAATAATAATCAATATTATTTTTT
Found at i:618964 original size:12 final size:12
Alignment explanation
Indices: 618947--618975 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
618937 GATGAGTTTG
618947 AGCCAAGTTACA
1 AGCCAAGTTACA
618959 AGCCAAGTTACA
1 AGCCAAGTTACA
618971 AGCCA
1 AGCCA
618976 TTGAAGGACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.41, C:0.28, G:0.17, T:0.14
Consensus pattern (12 bp):
AGCCAAGTTACA
Found at i:620505 original size:18 final size:18
Alignment explanation
Indices: 620459--620501 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
620449 TCTTCTTATT
*
620459 TTTACTTTAATTGCTTTTA
1 TTTA-TTTAATCGCTTTTA
620478 TTTATTTAATCGCTTTTA
1 TTTATTTAATCGCTTTTA
620496 -TTATTT
1 TTTATTT
620502 TAATATCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.26
18 13 0.57
19 4 0.17
ACGTcount: A:0.21, C:0.09, G:0.05, T:0.65
Consensus pattern (18 bp):
TTTATTTAATCGCTTTTA
Found at i:620511 original size:18 final size:18
Alignment explanation
Indices: 620459--620512 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
620449 TCTTCTTATT
*
620459 TTTACTTTAATTGCTTTTA
1 TTTA-TTTAATAGCTTTTA
*
620478 TTTATTTAATCGCTTTTA
1 TTTATTTAATAGCTTTTA
*
620496 -TTATTTTAATATCTTTT
1 TTTA-TTTAATAGCTTTT
620513 TACCAAAATC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 3 0.10
18 24 0.77
19 4 0.13
ACGTcount: A:0.22, C:0.09, G:0.04, T:0.65
Consensus pattern (18 bp):
TTTATTTAATAGCTTTTA
Found at i:621890 original size:42 final size:42
Alignment explanation
Indices: 621831--621918 Score: 167
Period size: 42 Copynumber: 2.1 Consensus size: 42
621821 AGAACTCGAG
*
621831 ACCGAATCAAGGCTATCAAGTGAGACCTCCACCACCACAACA
1 ACCGAATCAAGGCTATCAAGCGAGACCTCCACCACCACAACA
621873 ACCGAATCAAGGCTATCAAGCGAGACCTCCACCACCACAACA
1 ACCGAATCAAGGCTATCAAGCGAGACCTCCACCACCACAACA
621915 ACCG
1 ACCG
621919 CATAAGTCAT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.38, C:0.38, G:0.15, T:0.10
Consensus pattern (42 bp):
ACCGAATCAAGGCTATCAAGCGAGACCTCCACCACCACAACA
Found at i:622920 original size:64 final size:64
Alignment explanation
Indices: 622852--622973 Score: 172
Period size: 64 Copynumber: 1.9 Consensus size: 64
622842 ATTGTTCAAG
* * * * *
622852 GTGTATCAATGCACATGAAGTGTATCGATGCACTCCTTTAAAATAAAAACATCGAATGCCATCA
1 GTGTATCAATGCACAAGAAGTGCATCGATGAACCCCCTTAAAATAAAAACATCGAATGCCATCA
* * *
622916 GTGTATCGATGCACAAGTAGTGCATCGATGAACCCCCTTAAAATACAAACATCGAATG
1 GTGTATCAATGCACAAGAAGTGCATCGATGAACCCCCTTAAAATAAAAACATCGAATG
622974 TGATTTATGT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
64 50 1.00
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (64 bp):
GTGTATCAATGCACAAGAAGTGCATCGATGAACCCCCTTAAAATAAAAACATCGAATGCCATCA
Found at i:622990 original size:64 final size:64
Alignment explanation
Indices: 622860--623009 Score: 160
Period size: 64 Copynumber: 2.3 Consensus size: 64
622850 AGGTGTATCA
* * * * * * *
622860 ATGCACATGAAGTGTATCGATGCACTCCTTTAAAATAAAAACATCGAATGCCATCAGTGTATCG
1 ATGCACAAGTAGTGCATCGATGAACCCCCTTAAAATAAAAACATCGAATGCCATCAGTGTACCG
* ** *
622924 ATGCACAAGTAGTGCATCGATGAACCCCCTTAAAATACAAACATCGAATGTGATTTA-TGTACCG
1 ATGCACAAGTAGTGCATCGATGAACCCCCTTAAAATAAAAACATCGAATGCCA-TCAGTGTACCG
*
622988 ATGCA-TAGATAGTGCATCGATG
1 ATGCACAAG-TAGTGCATCGATG
623010 CACTCAAAGA
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
63 2 0.03
64 68 0.94
65 2 0.03
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (64 bp):
ATGCACAAGTAGTGCATCGATGAACCCCCTTAAAATAAAAACATCGAATGCCATCAGTGTACCG
Found at i:623791 original size:2 final size:2
Alignment explanation
Indices: 623784--623808 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
623774 TGGAATTATG
623784 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
623809 GACTATATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:624586 original size:22 final size:22
Alignment explanation
Indices: 624549--624606 Score: 89
Period size: 22 Copynumber: 2.5 Consensus size: 22
624539 ACATCTTATA
*
624549 TGGCACTACGGTGCAATTCTACG
1 TGGCACT-TGGTGCAATTCTACG
624572 TGGCACTTGGTGCAATTCTACG
1 TGGCACTTGGTGCAATTCTACG
624594 TGGCACTTCGGTG
1 TGGCACTT-GGTG
624607 TATTTATATG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
22 22 0.67
23 11 0.33
ACGTcount: A:0.17, C:0.24, G:0.29, T:0.29
Consensus pattern (22 bp):
TGGCACTTGGTGCAATTCTACG
Found at i:627486 original size:20 final size:20
Alignment explanation
Indices: 627461--627506 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
627451 CAAGGGATGA
627461 ATCGATACATGGTGTAGTGC
1 ATCGATACATGGTGTAGTGC
627481 ATCGATACATGGTGTAGTGC
1 ATCGATACATGGTGTAGTGC
*
627501 TTCGAT
1 ATCGAT
627507 GCATACCTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (20 bp):
ATCGATACATGGTGTAGTGC
Found at i:628250 original size:2 final size:2
Alignment explanation
Indices: 628243--628267 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
628233 TGGAGTTATG
628243 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
628268 GACTATATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:629042 original size:23 final size:23
Alignment explanation
Indices: 629008--629074 Score: 107
Period size: 23 Copynumber: 2.9 Consensus size: 23
628998 ACATCTTATA
* *
629008 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTATACG
629031 TGGCACTTCGGTGCAATTATACG
1 TGGCACTTCGGTGCAATTATACG
*
629054 TGGCACTTCGGTGCATTTATA
1 TGGCACTTCGGTGCAATTATA
629075 TGAGTTGTGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.21, C:0.22, G:0.25, T:0.31
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTATACG
Found at i:634533 original size:18 final size:19
Alignment explanation
Indices: 634505--634558 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
634495 TCTTCTTATT
*
634505 TTTACTTTAATTTCTTTTA
1 TTTACTTTAATATCTTTTA
634524 TTTA-TTTAATCA-CTTTTA
1 TTTACTTTAAT-ATCTTTTA
*
634542 -TTATTTTAATATCTTTT
1 TTTACTTTAATATCTTTT
634559 TACCAAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
17 4 0.13
18 23 0.74
19 4 0.13
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTACTTTAATATCTTTTA
Found at i:642027 original size:25 final size:26
Alignment explanation
Indices: 641999--642065 Score: 127
Period size: 26 Copynumber: 2.6 Consensus size: 26
641989 TTTGCCCCTA
641999 AAATTTT-ATAAATTTATCTCTCCAT
1 AAATTTTAATAAATTTATCTCTCCAT
642024 AAATTTTAATAAATTTATCTCTCCAT
1 AAATTTTAATAAATTTATCTCTCCAT
642050 AAATTTTAATAAATTT
1 AAATTTTAATAAATTT
642066 TAATAAATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
25 7 0.17
26 34 0.83
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (26 bp):
AAATTTTAATAAATTTATCTCTCCAT
Found at i:642063 original size:10 final size:10
Alignment explanation
Indices: 642048--642084 Score: 74
Period size: 10 Copynumber: 3.7 Consensus size: 10
642038 TTATCTCTCC
642048 ATAAATTTTA
1 ATAAATTTTA
642058 ATAAATTTTA
1 ATAAATTTTA
642068 ATAAATTTTA
1 ATAAATTTTA
642078 ATAAATT
1 ATAAATT
642085 AATCATCTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (10 bp):
ATAAATTTTA
Found at i:643735 original size:14 final size:15
Alignment explanation
Indices: 643718--643754 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
643708 CTATAATCCG
643718 ATATTTATAA-AAAA
1 ATATTTATAATAAAA
*
643732 ATA-TTAAAATAAAA
1 ATATTTATAATAAAA
643746 ATATTTATA
1 ATATTTATA
643755 TATGTATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
13 5 0.26
14 10 0.53
15 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATATTTATAATAAAA
Found at i:647909 original size:21 final size:21
Alignment explanation
Indices: 647871--647935 Score: 103
Period size: 21 Copynumber: 3.0 Consensus size: 21
647861 ATTGTCAGAG
*
647871 GGGAACCGATTCCCCTGCTACA
1 GGGAACCGA-TACCCTGCTACA
647893 GGGAACCGATACCCTGCTACA
1 GGGAACCGATACCCTGCTACA
*
647914 GGGAATCGATACCCTGCTACA
1 GGGAACCGATACCCTGCTACA
647935 G
1 G
647936 TACTGCTACA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
21 32 0.78
22 9 0.22
ACGTcount: A:0.26, C:0.32, G:0.25, T:0.17
Consensus pattern (21 bp):
GGGAACCGATACCCTGCTACA
Found at i:648800 original size:30 final size:31
Alignment explanation
Indices: 648765--648831 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
648755 GAATGACCTA
* * *
648765 TCCATAGGTCATAAAGAACCTCGG-CAACTG
1 TCCATAGGTCACAAAGAACCTAGGTAAACTG
* *
648795 TCCATAGGTCCCGAAGAACCTAGGTAAACTG
1 TCCATAGGTCACAAAGAACCTAGGTAAACTG
648826 TCCATA
1 TCCATA
648832 TGTTCCTTCG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
30 20 0.65
31 11 0.35
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (31 bp):
TCCATAGGTCACAAAGAACCTAGGTAAACTG
Found at i:648943 original size:32 final size:32
Alignment explanation
Indices: 648792--648948 Score: 108
Period size: 32 Copynumber: 4.9 Consensus size: 32
648782 ACCTCGGCAA
* * * *
648792 CTGTCCATAGGTCCCGAAGAACCTAGGTAA-A
1 CTGTCCATATGTTCCGAAGAACATAGGTAATT
***
648823 CTGTCCATATGTTCCTTCGAACATAGGT-ATAT
1 CTGTCCATATGTTCCGAAGAACATAGGTAAT-T
648855 CTGTCCATATGTCTCAC-AAG-ACATAGGTAATT
1 CTGTCCATATGT-TC-CGAAGAACATAGGTAATT
* * * * * *
648887 ATATACATAT-ATCCCAAAAGACATAGGTAATT
1 CTGTCCATATGTTCCGAAGA-ACATAGGTAATT
* *
648919 TTGTCCATATGTTCCGTAGAACATAGGTAA
1 CTGTCCATATGTTCCGAAGAACATAGGTAA
648949 ACCCTCGACT
Statistics
Matches: 96, Mismatches: 21, Indels: 17
0.72 0.16 0.13
Matches are distributed among these distances:
29 1 0.01
30 5 0.05
31 22 0.23
32 57 0.59
33 10 0.10
34 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (32 bp):
CTGTCCATATGTTCCGAAGAACATAGGTAATT
Found at i:654318 original size:24 final size:24
Alignment explanation
Indices: 654286--654338 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
654276 GAATTAAATT
654286 AAAAAGTAATAAAATTTTACGATA
1 AAAAAGTAATAAAATTTTACGATA
* *
654310 AAAAAGTAATAAAATTTTATGGTA
1 AAAAAGTAATAAAATTTTACGATA
654334 AAAAA
1 AAAAA
654339 TTAAAATATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.28
Consensus pattern (24 bp):
AAAAAGTAATAAAATTTTACGATA
Found at i:655535 original size:3 final size:3
Alignment explanation
Indices: 655520--655614 Score: 83
Period size: 3 Copynumber: 32.7 Consensus size: 3
655510 TAACATTATT
* * * *
655520 TAA TAA TAT TAA TAA TAA TAA TAA T-G TAA TAA T-T TCA TATA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
* *
655564 TAA TAG TAG T-A TAA TATA TAA TAA T-A TAA TAA T-A TAA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
655607 TAA TAA TA
1 TAA TAA TA
655615 TGACCGGACG
Statistics
Matches: 76, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
2 7 0.09
3 63 0.83
4 6 0.08
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:655564 original size:29 final size:27
Alignment explanation
Indices: 655520--655614 Score: 103
Period size: 26 Copynumber: 3.7 Consensus size: 27
655510 TAACATTATT
655520 TAATAATAT-TAATAATAATAATAATG
1 TAATAATATATAATAATAATAATAATG
* *
655546 TAATAAT-T-TCATATATAATAATAGTAG
1 TAATAATATATAATA-ATAATAATAAT-G
*
655573 T-ATAATATATAATAAT-ATAATAATA
1 TAATAATATATAATAATAATAATAATG
655598 TAATAATA-ATAATAATA
1 TAATAATATATAATAATA
655615 TGACCGGACG
Statistics
Matches: 58, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
25 14 0.24
26 35 0.60
27 5 0.09
28 4 0.07
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (27 bp):
TAATAATATATAATAATAATAATAATG
Found at i:662075 original size:20 final size:20
Alignment explanation
Indices: 662029--662077 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
662019 GTTTCCAGAT
*
662029 TCGCAACGCGATTATGACTA
1 TCGCAATGCGATTATGACTA
662049 TCGCAATGCGA-TACTGACTA
1 TCGCAATGCGATTA-TGACTA
662069 TCGCAATGC
1 TCGCAATGC
662078 AATTTTCTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 2 0.07
20 25 0.93
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (20 bp):
TCGCAATGCGATTATGACTA
Found at i:662103 original size:21 final size:21
Alignment explanation
Indices: 662079--662135 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 21
662069 TCGCAATGCA
*
662079 ATTTTCTTAATTCGCATTACG
1 ATTTTCATAATTCGCATTACG
* * * *
662100 ATTTACGT-ATTCGCGTTGCG
1 ATTTTCATAATTCGCATTACG
662120 ATTTTCATAATTCGCA
1 ATTTTCATAATTCGCA
662136 ATGCGAATAC
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.23, C:0.19, G:0.14, T:0.44
Consensus pattern (21 bp):
ATTTTCATAATTCGCATTACG
Found at i:662140 original size:21 final size:21
Alignment explanation
Indices: 662069--662141 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
662059 ATACTGACTA
* *
662069 TCGCAATGCAATTTTCTTAAT
1 TCGCAATGCGATTTTCATAAT
* * * *
662090 TCGCATTACGATTTACGT-AT
1 TCGCAATGCGATTTTCATAAT
**
662110 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATTTTCATAAT
662131 TCGCAATGCGA
1 TCGCAATGCGA
662142 ATACGTAAAT
Statistics
Matches: 40, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 16 0.40
21 24 0.60
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (21 bp):
TCGCAATGCGATTTTCATAAT
Found at i:662156 original size:20 final size:20
Alignment explanation
Indices: 662131--662181 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
662121 TTTTCATAAT
662131 TCGCAATGCGAATACGTA-AA
1 TCGCAATGCGAAT-CGTACAA
* *
662151 TCGCAATGCGAATCTTACTA
1 TCGCAATGCGAATCGTACAA
662171 TCGCAATGCGA
1 TCGCAATGCGA
662182 TTTACATAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 3 0.11
20 25 0.89
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (20 bp):
TCGCAATGCGAATCGTACAA
Found at i:662161 original size:41 final size:41
Alignment explanation
Indices: 662068--662161 Score: 100
Period size: 41 Copynumber: 2.3 Consensus size: 41
662058 GATACTGACT
* * * *
662068 ATCGCAATGCAATTTTCTTAATTCGCATTACGATTTACGTA
1 ATCGCAATGCGATTTTCATAATTCGCAATACGATATACGTA
* ** *
662109 TTCGCGTTGCGATTTTCATAATTCGCAATGCGA-ATACGTAA
1 ATCGCAATGCGATTTTCATAATTCGCAATACGATATACGT-A
662150 ATCGCAATGCGA
1 ATCGCAATGCGA
662162 ATCTTACTAT
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
40 5 0.12
41 36 0.88
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (41 bp):
ATCGCAATGCGATTTTCATAATTCGCAATACGATATACGTA
Done.