Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008013.1 Hibiscus syriacus cultivar Beakdansim tig00110478_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: 1461402
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 6
Found at i:870862 original size:15 final size:16
Alignment explanation
Indices: 870842--870876 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
870832 TTTTGCCCCT
*
870842 ATAACCATTAAG-ATA
1 ATAACCAATAAGTATA
870857 ATAACCAATAAGTATA
1 ATAACCAATAAGTATA
870873 ATAA
1 ATAA
870877 TATTATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.57, C:0.11, G:0.06, T:0.26
Consensus pattern (16 bp):
ATAACCAATAAGTATA
Found at i:871031 original size:2 final size:2
Alignment explanation
Indices: 871026--871050 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
871016 TTCCATTCGG
871026 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
871051 CAATTCAAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:874677 original size:21 final size:21
Alignment explanation
Indices: 874635--874709 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 21
874625 ATTCTGACTA
874635 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
874656 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
* * * *
874677 TTGCAATGCGAATTCGCAAA-
1 TCGCATTGCGATTTCCCAAAT
*
874697 TCGCAATGCGATT
1 TCGCATTGCGATT
874710 ACGTAAATCA
Statistics
Matches: 42, Mismatches: 12, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
20 11 0.26
21 31 0.74
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:874753 original size:21 final size:21
Alignment explanation
Indices: 874679--874892 Score: 172
Period size: 20 Copynumber: 10.5 Consensus size: 21
874669 TTCCTAATTT
*
874679 GCAATGCGAATT-CGCAAATC
1 GCAATGCGAATTACGTAAATC
874699 GCAATGCG-ATTACGTAAATC
1 GCAATGCGAATTACGTAAATC
*
874719 ACAATGCG-ATTACGTAAATC
1 GCAATGCGAATTACGTAAATC
* *
874739 ACAATGCGAATTACGT-ATTC
1 GCAATGCGAATTACGTAAATC
* * * * *
874759 GCATTGCGATTTTCCTAATTC
1 GCAATGCGAATTACGTAAATC
* * *
874780 GCATTGCGATTTACGT-ATTC
1 GCAATGCGAATTACGTAAATC
** * * * *
874800 GCGTTGCGATTTTCATAATTC
1 GCAATGCGAATTACGTAAATC
*
874821 GCAATGC-AAATACGTAAATC
1 GCAATGCGAATTACGTAAATC
* * *
874841 GTAATGCGAATTAGGAAAATC
1 GCAATGCGAATTACGTAAATC
*
874862 TCAATGCGAA-TACGTAAATC
1 GCAATGCGAATTACGTAAATC
874882 GCAATGCGAAT
1 GCAATGCGAAT
874893 CTGACTATCG
Statistics
Matches: 159, Mismatches: 29, Indels: 11
0.80 0.15 0.06
Matches are distributed among these distances:
19 3 0.02
20 104 0.65
21 52 0.33
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (21 bp):
GCAATGCGAATTACGTAAATC
Found at i:874788 original size:41 final size:41
Alignment explanation
Indices: 874697--874836 Score: 142
Period size: 41 Copynumber: 3.5 Consensus size: 41
874687 AATTCGCAAA
* * * * * *
874697 TCGCAATGCG-ATTACGTAAATCACAATGCGA-TTACGTAAA
1 TCGCAATGCGAATTACGT-ATTCGCATTGCGATTTTCATAAT
* *
874737 TCACAATGCGAATTACGTATTCGCATTGCGATTTTCCTAAT
1 TCGCAATGCGAATTACGTATTCGCATTGCGATTTTCATAAT
* * *
874778 TCGCATTGCGATTTACGTATTCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGAATTACGTATTCGCATTGCGATTTTCATAAT
*
874819 TCGCAATGC-AAATACGTA
1 TCGCAATGCGAATTACGTA
874837 AATCGTAATG
Statistics
Matches: 83, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 26 0.31
41 57 0.69
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (41 bp):
TCGCAATGCGAATTACGTATTCGCATTGCGATTTTCATAAT
Found at i:874849 original size:41 final size:40
Alignment explanation
Indices: 874679--874890 Score: 99
Period size: 41 Copynumber: 5.2 Consensus size: 40
874669 TTCCTAATTT
* * *
874679 GCAATGCGAATTCGC-AAATCGCAATGCGATTACGTAAATC
1 GCAATGCG-ATTAGCAAAATCGCAATGCAAATACGTAAATC
* * * * *
874719 ACAATGCGATTA-CGTAAATCACAATGCGAATTACGT-ATTC
1 GCAATGCGATTAGC-AAAATCGCAATGC-AAATACGTAAATC
* ** * * * ** *
874759 GCATTGCGATTTTCCTAATTCGCATTGCGATTTACGT-ATTC
1 GCAATGCGA-TTAGCAAAATCGCAATGC-AAATACGTAAATC
** ** *
874800 GCGTTGCGATTTTCATAATTCGCAATGCAAATACGTAAATC
1 GCAATGCGATTAGCA-AAATCGCAATGCAAATACGTAAATC
* * * *
874841 GTAATGCGAATTAGGAAAATCTCAATGCGAATACGTAAATC
1 GCAATGCG-ATTAGCAAAATCGCAATGCAAATACGTAAATC
874882 GCAATGCGA
1 GCAATGCGA
874891 ATCTGACTAT
Statistics
Matches: 135, Mismatches: 29, Indels: 16
0.75 0.16 0.09
Matches are distributed among these distances:
38 1 0.01
39 3 0.02
40 39 0.29
41 87 0.64
42 5 0.04
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (40 bp):
GCAATGCGATTAGCAAAATCGCAATGCAAATACGTAAATC
Found at i:875523 original size:19 final size:19
Alignment explanation
Indices: 875459--875557 Score: 83
Period size: 14 Copynumber: 5.7 Consensus size: 19
875449 TAGTTTCGAG
875459 AATGAAAATCGCAACGCGGA
1 AATGAAAATCGCAACGC-GA
**
875479 AATGACTATCGCAA--C--
1 AATGAAAATCGCAACGCGA
*
875494 AA-GAGAATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
875512 AATGAAAATCGCAA--CG-
1 AATGAAAATCGCAACGCGA
*
875528 -A-GATAATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
875545 AATGAAAATCGCA
1 AATGAAAATCGCA
875558 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 21
0.69 0.08 0.23
Matches are distributed among these distances:
14 19 0.31
15 3 0.05
16 3 0.05
17 2 0.03
18 4 0.06
19 19 0.31
20 12 0.19
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.12
Consensus pattern (19 bp):
AATGAAAATCGCAACGCGA
Found at i:875523 original size:33 final size:33
Alignment explanation
Indices: 875465--875557 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
875455 CGAGAATGAA
**
875465 AATCGCAACGCGGAAATGACTATCGCAACAAGAG
1 AATCGCAACGC-GAAATGAAAATCGCAACAAGAG
* *
875499 AATCGCAACGCGAAATGAAAATCGCAACGAGAT
1 AATCGCAACGCGAAATGAAAATCGCAACAAGAG
875532 AATCGCAACGCGAAATGAAAATCGCA
1 AATCGCAACGCGAAATGAAAATCGCA
875558 TTGCGATTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
33 44 0.80
34 11 0.20
ACGTcount: A:0.44, C:0.23, G:0.22, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACAAGAG
Found at i:875600 original size:33 final size:33
Alignment explanation
Indices: 875558--875672 Score: 178
Period size: 33 Copynumber: 3.5 Consensus size: 33
875548 GAAAATCGCA
* *
875558 TTGCGATTTT-AGTTTCGCATTGCGATTCTATCG
1 TTGCGATTTTCA-TTTCGCGTTGCGATTCTCTCG
* *
875591 TTGCGATTTTCATTTCGTGTTGAGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
875624 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
875657 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
875673 AACCAAAAGA
Statistics
Matches: 75, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
33 74 0.99
34 1 0.01
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:875631 original size:14 final size:14
Alignment explanation
Indices: 875577--875664 Score: 50
Period size: 14 Copynumber: 5.6 Consensus size: 14
875567 TAGTTTCGCA
*
875577 TTGCGATTCTATCG
1 TTGCGATTCTCTCG
*
875591 TTGCGATTTTCATTTCGTG
1 TTGCGA--TTC-TCTC--G
*
875610 TTGAGATTCTCTCG
1 TTGCGATTCTCTCG
*
875624 TTGCGATTTTCATTTCGCG
1 TTGCGA--TTC---TCTCG
875643 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
875657 TTGCGATT
1 TTGCGATT
875665 TTCATTTCAA
Statistics
Matches: 58, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 24 0.41
16 9 0.16
17 9 0.16
19 16 0.28
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:875646 original size:19 final size:19
Alignment explanation
Indices: 875589--875650 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 19
875579 GCGATTCTAT
875589 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* * *
875608 TGTTGAGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
875622 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
875641 CGTTGCGATT
1 CGTTGCGATT
875651 CTCTCGTTGC
Statistics
Matches: 32, Mismatches: 6, Indels: 10
0.67 0.12 0.21
Matches are distributed among these distances:
14 8 0.25
16 3 0.09
17 3 0.09
19 18 0.56
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:877545 original size:94 final size:93
Alignment explanation
Indices: 877358--877733 Score: 625
Period size: 94 Copynumber: 4.1 Consensus size: 93
877348 TAGATTGCTT
* *
877358 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAA-T-TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
877419 ATTTGTCTTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGA
877448 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
877513 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
*
877542 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
877607 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * * * *
877636 AGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTAAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
877701 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
877729 AGTAA
1 AGTAA
877734 TGCAATCCAT
Statistics
Matches: 274, Mismatches: 7, Indels: 7
0.95 0.02 0.02
Matches are distributed among these distances:
90 34 0.12
91 1 0.00
92 3 0.01
93 28 0.10
94 208 0.76
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:877872 original size:33 final size:34
Alignment explanation
Indices: 877830--877901 Score: 119
Period size: 34 Copynumber: 2.1 Consensus size: 34
877820 GGTTGAAATG
*
877830 AAAATCGCAATGAGAAA-CAAAAATCGCAACGAC
1 AAAATCGCAACGAGAAACCAAAAATCGCAACGAC
*
877863 AAAATCGCAACGCGAAACCAAAAATCGCAACGAC
1 AAAATCGCAACGAGAAACCAAAAATCGCAACGAC
877897 AAAAT
1 AAAAT
877902 ATAATCGCGT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
33 15 0.42
34 21 0.58
ACGTcount: A:0.54, C:0.24, G:0.14, T:0.08
Consensus pattern (34 bp):
AAAATCGCAACGAGAAACCAAAAATCGCAACGAC
Found at i:877928 original size:19 final size:19
Alignment explanation
Indices: 877906--878051 Score: 122
Period size: 19 Copynumber: 7.8 Consensus size: 19
877896 CAAAATATAA
*
877906 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
*
877925 TCGCATTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
877939 TCTCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
* *
877958 TCACGTTGCGATTTTCGTT
1 TCGCGTTGCGATTTTCATT
*
877977 TCGCGTTGTGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
877996 CTCTCTTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
**
878016 TCGCGTTGCGATAGTCATTTT
1 TCGCGTTGCGATTTTCA--TT
*
878037 TCACGTTGCGATTTT
1 TCGCGTTGCGATTTT
878052 AAGTTCCAGA
Statistics
Matches: 98, Mismatches: 21, Indels: 14
0.74 0.16 0.11
Matches are distributed among these distances:
14 9 0.09
16 2 0.02
17 2 0.02
19 55 0.56
20 16 0.16
21 14 0.14
ACGTcount: A:0.12, C:0.20, G:0.19, T:0.49
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:878528 original size:42 final size:42
Alignment explanation
Indices: 878452--878540 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
878442 GACTCGCCTG
* * *
878452 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * * * *
878494 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTT
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
878536 TCATC
1 TCATC
878541 GTTGAAGAGG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.21, C:0.38, G:0.16, T:0.25
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
Found at i:879936 original size:14 final size:14
Alignment explanation
Indices: 879917--879952 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
879907 ATTGTTTAAT
879917 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
879931 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
879945 TGATTTGT
1 TGATTTGT
879953 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:880075 original size:19 final size:19
Alignment explanation
Indices: 880059--880105 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
880049 AAAAATGACT
*
880059 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
880078 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
880097 ATCGCAACG
1 ATCGCAACG
880106 ACAAAATCGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:880176 original size:33 final size:33
Alignment explanation
Indices: 880134--880227 Score: 136
Period size: 33 Copynumber: 2.8 Consensus size: 33
880124 ACTAAATTCG
*
880134 CGTTGCGATTTTTATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
* *
880167 CGTTGCGATTTTCATTTCGCATTT-TGATTCTCT
1 CGTTGCGATTTTCATTTCGC-TTTGCGATTCCCT
*
880200 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCTTTGCGAT
880228 AGTCATTTCC
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
32 2 0.04
33 49 0.91
34 3 0.06
ACGTcount: A:0.12, C:0.22, G:0.18, T:0.48
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
Found at i:880226 original size:19 final size:19
Alignment explanation
Indices: 880169--880247 Score: 60
Period size: 19 Copynumber: 4.4 Consensus size: 19
880159 GATTCCCTCG
880169 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
** *
880188 TTTTGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
880202 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
** *
880221 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCA
880241 TTGCGAT
1 TTGCGAT
880248 AGACATTAAG
Statistics
Matches: 45, Mismatches: 9, Indels: 11
0.69 0.14 0.17
Matches are distributed among these distances:
14 4 0.09
16 7 0.16
17 7 0.16
19 17 0.38
20 10 0.22
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:880246 original size:20 final size:20
Alignment explanation
Indices: 880200--880293 Score: 68
Period size: 20 Copynumber: 4.7 Consensus size: 20
880190 TTGATTCTCT
**
880200 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
*
880219 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* **
880239 CGTTGCGATAGACA-TTAAG
1 CGTTGCGATAGTCATTTCCG
*
880258 ATGATTGCGA-ACGTCATTTCCG
1 -CG-TTGCGATA-GTCATTTCCG
*
880280 TGTTGCGATAGTCA
1 CGTTGCGATAGTCA
880294 AATGAATGCC
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
19 17 0.29
20 26 0.45
21 12 0.21
22 3 0.05
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:882796 original size:24 final size:24
Alignment explanation
Indices: 882762--882815 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
882752 CTGAAAAATC
882762 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
882786 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
882810 ATCAAA
1 ATCAAA
882816 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:882829 original size:24 final size:24
Alignment explanation
Indices: 882762--882829 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
882752 CTGAAAAATC
* * *
882762 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
882786 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
882810 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
882830 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:883700 original size:20 final size:20
Alignment explanation
Indices: 883677--883783 Score: 101
Period size: 20 Copynumber: 5.3 Consensus size: 20
883667 AGAATCTCGT
*
883677 TGCGATTAAGTAAATTGCAA
1 TGCGATTAAGTAAATCGCAA
* *
883697 TGCGAATTAGGAAAATCGCAA
1 TGCG-ATTAAGTAAATCGCAA
*
883718 TGCGATTACGTAAATCGCAA
1 TGCGATTAAGTAAATCGCAA
* * *
883738 TGCGATTACGT-ATTCGCAT
1 TGCGATTAAGTAAATCGCAA
* *
883757 TGCGATTTACGT-AATCGCAT
1 TGCGA-TTAAGTAAATCGCAA
883777 TGCGATT
1 TGCGATT
883784 TACGTAATCC
Statistics
Matches: 77, Mismatches: 8, Indels: 5
0.86 0.09 0.06
Matches are distributed among these distances:
19 13 0.17
20 47 0.61
21 17 0.22
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (20 bp):
TGCGATTAAGTAAATCGCAA
Found at i:883712 original size:21 final size:21
Alignment explanation
Indices: 883688--883864 Score: 89
Period size: 21 Copynumber: 8.7 Consensus size: 21
883678 GCGATTAAGT
* *
883688 AAATTGCAATGCGAATTAGGA
1 AAATCGCAATGCGAATTACGA
*
883709 AAATCGCAATGCG-ATTACGT
1 AAATCGCAATGCGAATTACGA
883729 AAATCGCAATGCG-ATTACG-
1 AAATCGCAATGCGAATTACGA
* * * *
883748 TATTCGCATTGCGATTTACG-
1 AAATCGCAATGCGAATTACGA
* * *
883768 TAATCGCATTGCGATTTACG-
1 AAATCGCAATGCGAATTACGA
* * *
883788 TAATCCGCATTGCGATTTACG-
1 AAAT-CGCAATGCGAATTACGA
* * *
883809 TAATCCGCATTGCGATTTACG-
1 AAAT-CGCAATGCGAATTACGA
* * * ** *
883830 TAATCACAACGCGAATTTGGG
1 AAATCGCAATGCGAATTACGA
883851 AAATCGCAATGCGA
1 AAATCGCAATGCGA
883865 TAGTCAGAAT
Statistics
Matches: 136, Mismatches: 17, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
19 10 0.07
20 62 0.46
21 64 0.47
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (21 bp):
AAATCGCAATGCGAATTACGA
Found at i:883784 original size:20 final size:20
Alignment explanation
Indices: 883710--883834 Score: 182
Period size: 20 Copynumber: 6.2 Consensus size: 20
883700 GAATTAGGAA
*
883710 AATCGCAATGCGA-TTACGT
1 AATCGCATTGCGATTTACGT
*
883729 AAATCGCAATGCGA-TTACGT
1 -AATCGCATTGCGATTTACGT
*
883749 ATTCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTACGT
883769 AATCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTACGT
883789 AATCCGCATTGCGATTTACGT
1 AAT-CGCATTGCGATTTACGT
883810 AATCCGCATTGCGATTTACGT
1 AAT-CGCATTGCGATTTACGT
883831 AATC
1 AATC
883835 ACAACGCGAA
Statistics
Matches: 100, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
19 11 0.11
20 48 0.48
21 41 0.41
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (20 bp):
AATCGCATTGCGATTTACGT
Found at i:883828 original size:62 final size:59
Alignment explanation
Indices: 883710--883865 Score: 188
Period size: 62 Copynumber: 2.6 Consensus size: 59
883700 GAATTAGGAA
*
883710 AATCGCAATGCGATTACGTAAATCGCAATGCGATTACGTATTCGCATTGCGATTTACGT
1 AATCGCAATGCGATTACGTAAATCGCAATGCGATTACGTATCCGCATTGCGATTTACGT
* *
883769 AATCGCATTGCGATTTACGT-AATCCGCATTGCGATTTACGTAATCCGCATTGCGATTTACGT
1 AATCGCAATGCGA-TTACGTAAAT-CGCAATGCGA-TTACGT-ATCCGCATTGCGATTTACGT
* * ** *
883831 AATCACAACGCGAATTTGGGAAATCGCAATGCGAT
1 AATCGCAATGCG-ATTACGTAAATCGCAATGCGAT
883866 AGTCAGAATC
Statistics
Matches: 81, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
59 15 0.19
60 15 0.19
61 7 0.09
62 40 0.49
63 4 0.05
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (59 bp):
AATCGCAATGCGATTACGTAAATCGCAATGCGATTACGTATCCGCATTGCGATTTACGT
Found at i:885731 original size:42 final size:42
Alignment explanation
Indices: 885595--885730 Score: 220
Period size: 42 Copynumber: 3.2 Consensus size: 42
885585 TACCTCGAAA
885595 TTCCGTGTTTATTTCACGTAATTCGTTTTTCGGAAAATATTT
1 TTCCGTGTTTATTTCACGTAATTCGTTTTTCGGAAAATATTT
* *
885637 TTTCGTGTTTATTTCACGTAATTCGTTTTTCAGAAAATATTT
1 TTCCGTGTTTATTTCACGTAATTCGTTTTTCGGAAAATATTT
* *
885679 TTCCGTGTTTGTTTCACGTAATTCGTTTTTCGGAAAAT-GTT
1 TTCCGTGTTTATTTCACGTAATTCGTTTTTCGGAAAATATTT
885720 TTCCAGTGTTT
1 TTCC-GTGTTT
885731 GGTTAGAGGA
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
41 6 0.07
42 81 0.93
ACGTcount: A:0.20, C:0.14, G:0.15, T:0.51
Consensus pattern (42 bp):
TTCCGTGTTTATTTCACGTAATTCGTTTTTCGGAAAATATTT
Found at i:886168 original size:27 final size:27
Alignment explanation
Indices: 886088--886179 Score: 66
Period size: 27 Copynumber: 3.3 Consensus size: 27
886078 AATAAAATTT
* *
886088 ATATTATTTAT-TAATTTCATAGAAATA
1 ATATTATTTATAT-ATTTAATATAAATA
*
886115 ATATTA-TTA-A-ATTAGTAATAATGAATA
1 ATATTATTTATATATT--TAAT-ATAAATA
886142 ATATTATTTATATATTTAATATTAATATA
1 ATATTATTTATATATTTAATA-TAA-ATA
*
886171 ATAATATTT
1 ATATTATTT
886180 TAATAAAGAT
Statistics
Matches: 51, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
24 3 0.06
26 6 0.12
27 18 0.35
28 9 0.18
29 12 0.24
30 3 0.06
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTATTTATATATTTAATATAAATA
Found at i:886199 original size:23 final size:23
Alignment explanation
Indices: 886180--886224 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
886170 AATAATATTT
886180 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
886203 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
886225 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:886347 original size:20 final size:17
Alignment explanation
Indices: 886311--886350 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
886301 TAATAAAATT
886311 ATAAAAATAAATATTTA
1 ATAAAAATAAATATTTA
886328 ATAATAAATAAATTATTTTA
1 ATAA-AAATAAA-TA-TTTA
886348 ATA
1 ATA
886351 TTTTAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 4 0.20
18 7 0.35
19 2 0.10
20 7 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATAAAAATAAATATTTA
Found at i:895391 original size:63 final size:63
Alignment explanation
Indices: 895323--895441 Score: 170
Period size: 63 Copynumber: 1.9 Consensus size: 63
895313 AATGATATCT
*
895323 TTTTAATTTGAAATATTCAAAAGG-TATAAACTCAT-TTTACTATTCAAACTTAAATAGATATTA
1 TTTTAATTTGAAATATTCAAAAGGATAT-AA-TCATCTTTAATATTCAAACTTAAATAGATATTA
* * *
895386 TTTTAATTTGAAATATTCAAAATGATATAATTATCTTTAATATTCAAATTTAAATA
1 TTTTAATTTGAAATATTCAAAAGGATATAATCATCTTTAATATTCAAACTTAAATA
895442 TGTGACAAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
62 3 0.06
63 44 0.88
64 3 0.06
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.44
Consensus pattern (63 bp):
TTTTAATTTGAAATATTCAAAAGGATATAATCATCTTTAATATTCAAACTTAAATAGATATTA
Found at i:903377 original size:29 final size:29
Alignment explanation
Indices: 903343--903414 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
903333 TTGATGTTAT
*
903343 TGCTTACATCAATTAGATGAAGATGTCAG
1 TGCTTACATCAATTAGATGAAGATATCAG
* *
903372 TGCTTATATCAATTAGATGAAGATATCAT
1 TGCTTACATCAATTAGATGAAGATATCAG
903401 TGCTTACATCAATT
1 TGCTTACATCAATT
903415 TAGTTAGGTG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (29 bp):
TGCTTACATCAATTAGATGAAGATATCAG
Found at i:911237 original size:17 final size:18
Alignment explanation
Indices: 911204--911238 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
911194 TATAATTAAT
*
911204 TTTATTTTTATAAATTTA
1 TTTATTTATATAAATTTA
911222 TTTATTTATA-AAATTTA
1 TTTATTTATATAAATTTA
911239 AAATTATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTATTTATATAAATTTA
Found at i:911248 original size:25 final size:25
Alignment explanation
Indices: 911210--911259 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
911200 TAATTTTATT
911210 TTTATAAATTTATTTATTTATAAAA
1 TTTATAAATTTATTTATTTATAAAA
* *
911235 TTTA-AAATTATATTTTTTTTTAAAA
1 TTTATAAATT-TATTTATTTATAAAA
911260 ATTCGACAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
TTTATAAATTTATTTATTTATAAAA
Found at i:912010 original size:29 final size:29
Alignment explanation
Indices: 911967--912049 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
911957 CTCACCTAAC
911967 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
911997 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
912026 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
912050 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:916774 original size:29 final size:29
Alignment explanation
Indices: 916731--916813 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
916721 CTCACCTAAC
916731 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
916761 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
916790 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
916814 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:918874 original size:15 final size:15
Alignment explanation
Indices: 918850--918892 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
918840 GTACCGTTAA
*
918850 ATTAATTTATAAAAT
1 ATTAAATTATAAAAT
*
918865 ATTAAATTATAAAGT
1 ATTAAATTATAAAAT
918880 ATTAAATGTATAA
1 ATTAAAT-TATAA
918893 TTATGAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 20 0.80
16 5 0.20
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (15 bp):
ATTAAATTATAAAAT
Found at i:919859 original size:22 final size:22
Alignment explanation
Indices: 919809--919859 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
919799 TCATTACTTA
** *
919809 AACATTTTATTAATTTGGTCCT
1 AACATTTTATTAATTAAGCCCT
919831 AACATTTTATTAATTAAGCCACT
1 AACATTTTATTAATTAAGCC-CT
919854 AA-ATTT
1 AACATTT
919860 GTCTAGTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.35, C:0.14, G:0.06, T:0.45
Consensus pattern (22 bp):
AACATTTTATTAATTAAGCCCT
Found at i:920496 original size:18 final size:17
Alignment explanation
Indices: 920466--920501 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
920456 ATTAATCAGT
*
920466 TATAATATTTGTGTGTG
1 TATAATATGTGTGTGTG
920483 TATATATATGTGTGTGTG
1 TATA-ATATGTGTGTGTG
920501 T
1 T
920502 GTGATATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.22, C:0.00, G:0.25, T:0.53
Consensus pattern (17 bp):
TATAATATGTGTGTGTG
Found at i:920884 original size:15 final size:15
Alignment explanation
Indices: 920864--920899 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
920854 TAATTATACG
920864 TTTAATACTTTATAA
1 TTTAATACTTTATAA
*
920879 TTTAATATTTTATAA
1 TTTAATACTTTATAA
*
920894 ATTAAT
1 TTTAAT
920900 TTAATGGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTAATACTTTATAA
Found at i:937803 original size:47 final size:47
Alignment explanation
Indices: 937707--937805 Score: 110
Period size: 47 Copynumber: 2.1 Consensus size: 47
937697 TTGAATAAAT
* * * **
937707 GCATGCGAACTAGAAATCATGTGGTTAGGTTTATTTTTTTAGAACAA
1 GCATGCGAACTAGAAATCATGCGGTTAGGATTATTTATGAAGAACAA
* * *
937754 GCATGCGAATTAGATATCATGCGGTTAGGATT-TTTATGAATAACAAA
1 GCATGCGAACTAGAAATCATGCGGTTAGGATTATTTATGAAGAAC-AA
937801 GCATG
1 GCATG
937806 GGGTAGATAT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
46 8 0.19
47 35 0.81
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.33
Consensus pattern (47 bp):
GCATGCGAACTAGAAATCATGCGGTTAGGATTATTTATGAAGAACAA
Found at i:944608 original size:42 final size:41
Alignment explanation
Indices: 944542--944643 Score: 123
Period size: 42 Copynumber: 2.5 Consensus size: 41
944532 TAAGCAATTT
* * * *
944542 ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATG
1 ATAAATCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATG
* * *
944583 CTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG
1 -ATAAATCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATG
*
944625 ATAAGTCCTTCGGGCCATC
1 ATAAATCCTTCGGGCCATC
944644 CATAAAACCT
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
41 16 0.32
42 34 0.68
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.29
Consensus pattern (41 bp):
ATAAATCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATG
Found at i:944834 original size:42 final size:41
Alignment explanation
Indices: 944757--944858 Score: 114
Period size: 42 Copynumber: 2.5 Consensus size: 41
944747 TTCACAATTT
* * * *
944757 ATAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATG
1 ATAAATCCTTCGGGCCATCAATAAGCCTTTAGAGCAAGATG
* * **
944798 CTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG
1 -ATAAATCCTTCGGGCCATCAATAAGCCTTTAGAGCAAGATG
*
944840 ATAAGTCCTTCGGGCCATC
1 ATAAATCCTTCGGGCCATC
944859 CTTAAAACCT
Statistics
Matches: 49, Mismatches: 11, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
41 16 0.33
42 33 0.67
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (41 bp):
ATAAATCCTTCGGGCCATCAATAAGCCTTTAGAGCAAGATG
Found at i:945001 original size:20 final size:19
Alignment explanation
Indices: 944972--945048 Score: 55
Period size: 20 Copynumber: 3.8 Consensus size: 19
944962 CACAATTTAC
944972 AAGTCCTTCGGGCCATCAGT
1 AAGTCCTTCGGG-CATCAGT
* * *
944992 AAGTCTTTCGAGCATGATGAT
1 AAGTCCTTCGGGCATCA-G-T
*
945013 GAAATCCTTCGGGTCATCAGT
1 -AAGTCCTTCGGG-CATCAGT
* *
945034 AAGTCTTTCGAGCAT
1 AAGTCCTTCGGGCAT
945049 GATGATTAAA
Statistics
Matches: 43, Mismatches: 10, Indels: 9
0.69 0.16 0.15
Matches are distributed among these distances:
19 7 0.16
20 20 0.47
21 2 0.05
22 10 0.23
23 4 0.09
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (19 bp):
AAGTCCTTCGGGCATCAGT
Found at i:945034 original size:42 final size:42
Alignment explanation
Indices: 944975--945063 Score: 160
Period size: 42 Copynumber: 2.1 Consensus size: 42
944965 AATTTACAAG
944975 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATGAAA
1 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATGAAA
* *
945017 TCCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGATTAAA
1 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATGAAA
945059 TCCTT
1 TCCTT
945064 AAGGTAATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (42 bp):
TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATGAAA
Found at i:945461 original size:53 final size:53
Alignment explanation
Indices: 945178--945437 Score: 348
Period size: 53 Copynumber: 4.9 Consensus size: 53
945168 AGAATCACAC
* * *
945178 CAGAAGATTATTCGAGTTCTACTCCCTGAAGCAATAGGGAGCGAACCCGTATG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
*
945231 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAAGGAG-GAAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCG-AACCCGTAGG
* *
945284 CAGAAGATTGTTCAAGTTTTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* * * *
945337 CAGAAGACTGTTCGAGTTGTACTCCTTGAAGCAAAAGGGAGCGAACCCGCT-GG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCG-TAGG
* *
945390 TC-GAAGATTGTTCGAGTTCTAC-CACTTGAAGCAATAGGGAGCGAACCC
1 -CAGAAGATTGTTCGAGTTCTACTC-CCTGAAGCAAGAGGGAGCGAACCC
945438 ATTTTTAGAA
Statistics
Matches: 187, Mismatches: 15, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
52 2 0.01
53 182 0.97
54 3 0.02
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.21
Consensus pattern (53 bp):
CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
Found at i:949040 original size:17 final size:16
Alignment explanation
Indices: 949005--949042 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
948995 TTAAAATATT
949005 TATTTATTACATTTTA
1 TATTTATTACATTTTA
949021 TATTATATTA-ATTTTAA
1 TATT-TATTACATTTT-A
949038 TATTT
1 TATTT
949043 TCCGAATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (16 bp):
TATTTATTACATTTTA
Found at i:959091 original size:12 final size:12
Alignment explanation
Indices: 959074--959098 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
959064 ACGCTCTCCA
959074 CATCGAGCTACG
1 CATCGAGCTACG
959086 CATCGAGCTACG
1 CATCGAGCTACG
959098 C
1 C
959099 TCCATGTGGC
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:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CATCGAGCTACG
Found at i:959330 original size:36 final size:36
Alignment explanation
Indices: 959289--959364 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
959279 ATTTTCGGGA
*
959289 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
959325 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
959361 TTTT
1 TTTT
959365 TTTGCTATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:960099 original size:12 final size:12
Alignment explanation
Indices: 960082--960106 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
960072 ACGCTCTCCA
960082 CATCGAGCTACG
1 CATCGAGCTACG
960094 CATCGAGCTACG
1 CATCGAGCTACG
960106 C
1 C
960107 TCCATGTGGC
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:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CATCGAGCTACG
Found at i:960338 original size:36 final size:36
Alignment explanation
Indices: 960297--960372 Score: 134
Period size: 36 Copynumber: 2.1 Consensus size: 36
960287 ATTTTCGGGA
* *
960297 TTTTGCTATTTTTGGCAAAATTTGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
960333 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
960369 TTTT
1 TTTT
960373 TTTGCTATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.45
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:960813 original size:15 final size:15
Alignment explanation
Indices: 960793--960822 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
960783 TATCACAATC
960793 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
960808 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
960823 AGCACCGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.47, T:0.13
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Found at i:965338 original size:36 final size:36
Alignment explanation
Indices: 965297--965372 Score: 134
Period size: 36 Copynumber: 2.1 Consensus size: 36
965287 ATTTTCGGGA
* *
965297 TTTTGCTATTTTTGGCAAAATTCGAATAAATATGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
965333 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
965369 TTTT
1 TTTT
965373 TTTTGCTATA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.45
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:966187 original size:75 final size:74
Alignment explanation
Indices: 966045--966206 Score: 288
Period size: 75 Copynumber: 2.2 Consensus size: 74
966035 TTGTTATTTA
* *
966045 AAAGATCAAGCTCTGTGAGATTCTTCAGCTTGGTAGCTCATCTAACTTGATGACACCACTGAAAT
1 AAAGATCAAGCTCTGTGAGATTCTTCAGCTTGGTAGCTCATCTAACTTGATAACACCACTAAAAT
966110 TATTTGATG
66 TATTTGATG
966119 AAAGATCAAGCTCTGTGAGATTCTTCAGCTTGGATAGCTCATCTAACTTGATAACACCACTAAAA
1 AAAGATCAAGCTCTGTGAGATTCTTCAGCTTGG-TAGCTCATCTAACTTGATAACACCACTAAAA
966184 TTATTTGATG
65 TTATTTGATG
*
966194 ACAGATCAAGCTC
1 AAAGATCAAGCTC
966207 CACAAGATTT
Statistics
Matches: 84, Mismatches: 3, Indels: 1
0.95 0.03 0.01
Matches are distributed among these distances:
74 33 0.39
75 51 0.61
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (74 bp):
AAAGATCAAGCTCTGTGAGATTCTTCAGCTTGGTAGCTCATCTAACTTGATAACACCACTAAAAT
TATTTGATG
Found at i:969156 original size:239 final size:239
Alignment explanation
Indices: 968737--969215 Score: 958
Period size: 239 Copynumber: 2.0 Consensus size: 239
968727 AACCTTCAGC
968737 AAGCAACAAGAGAACATTATCACTATTGGTCAGATCGGCCCCGTCCACCAAGGAATCGTGACTAT
1 AAGCAACAAGAGAACATTATCACTATTGGTCAGATCGGCCCCGTCCACCAAGGAATCGTGACTAT
968802 CTTCACTCAATACAGCACCTACAAGTGAAGTGTCACTAGTGGATACATGTTGTGGCAGTACTTCT
66 CTTCACTCAATACAGCACCTACAAGTGAAGTGTCACTAGTGGATACATGTTGTGGCAGTACTTCT
968867 TGAAGACACGGCTTGTGACGCTTAGCAACAACCTCAAGAGCTGCTGATTTCGACGAAGGTTGAGC
131 TGAAGACACGGCTTGTGACGCTTAGCAACAACCTCAAGAGCTGCTGATTTCGACGAAGGTTGAGC
968932 ATGACAACATGCAGTAGTCTTTGTTTCTGCAAAAGGGAAAACAA
196 ATGACAACATGCAGTAGTCTTTGTTTCTGCAAAAGGGAAAACAA
968976 AAGCAACAAGAGAACATTATCACTATTGGTCAGATCGGCCCCGTCCACCAAGGAATCGTGACTAT
1 AAGCAACAAGAGAACATTATCACTATTGGTCAGATCGGCCCCGTCCACCAAGGAATCGTGACTAT
969041 CTTCACTCAATACAGCACCTACAAGTGAAGTGTCACTAGTGGATACATGTTGTGGCAGTACTTCT
66 CTTCACTCAATACAGCACCTACAAGTGAAGTGTCACTAGTGGATACATGTTGTGGCAGTACTTCT
969106 TGAAGACACGGCTTGTGACGCTTAGCAACAACCTCAAGAGCTGCTGATTTCGACGAAGGTTGAGC
131 TGAAGACACGGCTTGTGACGCTTAGCAACAACCTCAAGAGCTGCTGATTTCGACGAAGGTTGAGC
969171 ATGACAACATGCAGTAGTCTTTGTTTCTGCAAAAGGGAAAACAA
196 ATGACAACATGCAGTAGTCTTTGTTTCTGCAAAAGGGAAAACAA
969215 A
1 A
969216 CTCATCAAAT
Statistics
Matches: 240, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
239 240 1.00
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.24
Consensus pattern (239 bp):
AAGCAACAAGAGAACATTATCACTATTGGTCAGATCGGCCCCGTCCACCAAGGAATCGTGACTAT
CTTCACTCAATACAGCACCTACAAGTGAAGTGTCACTAGTGGATACATGTTGTGGCAGTACTTCT
TGAAGACACGGCTTGTGACGCTTAGCAACAACCTCAAGAGCTGCTGATTTCGACGAAGGTTGAGC
ATGACAACATGCAGTAGTCTTTGTTTCTGCAAAAGGGAAAACAA
Found at i:987545 original size:10 final size:10
Alignment explanation
Indices: 987530--987559 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
987520 CTTATATATA
987530 TTAGCAGAAG
1 TTAGCAGAAG
987540 TTAGCAGAAG
1 TTAGCAGAAG
987550 TTAGCAGAAG
1 TTAGCAGAAG
987560 AAACTATATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.30, T:0.20
Consensus pattern (10 bp):
TTAGCAGAAG
Found at i:989243 original size:32 final size:32
Alignment explanation
Indices: 989200--989260 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
989190 AATAATACGG
*
989200 TGTGCATTATACAGAAA-TTGATCTCTGTATGT
1 TGTGCACTATACA-AAATTTGATCTCTGTATGT
989232 TGTGCACTATACAAAATTTGATCTCTGTA
1 TGTGCACTATACAAAATTTGATCTCTGTA
989261 ACAGATAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 3 0.11
32 24 0.89
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.39
Consensus pattern (32 bp):
TGTGCACTATACAAAATTTGATCTCTGTATGT
Found at i:990500 original size:2 final size:2
Alignment explanation
Indices: 990487--990517 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
990477 CAGTTAAGAC
*
990487 AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
990518 ACTAGAATGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1003210 original size:23 final size:23
Alignment explanation
Indices: 1003141--1003228 Score: 113
Period size: 23 Copynumber: 3.8 Consensus size: 23
1003131 TAAATAAGAA
*
1003141 TATTTGTTCTTGTGACACACTTT
1 TATTTGCTCTTGTGACACACTTT
* *
1003164 TATCTGTTCTTGTGACACACTTT
1 TATTTGCTCTTGTGACACACTTT
**
1003187 TATTTGCTCTTGTGACACTTTTT
1 TATTTGCTCTTGTGACACACTTT
* *
1003210 TTTTTGCTCTTGTGGCACA
1 TATTTGCTCTTGTGACACA
1003229 TGTCTTATTG
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.15, C:0.19, G:0.15, T:0.51
Consensus pattern (23 bp):
TATTTGCTCTTGTGACACACTTT
Found at i:1007138 original size:18 final size:18
Alignment explanation
Indices: 1007111--1007164 Score: 99
Period size: 18 Copynumber: 3.0 Consensus size: 18
1007101 CCGATTCCCC
*
1007111 TGCTACAGGGAACCGATA
1 TGCTATAGGGAACCGATA
1007129 TGCTATAGGGAACCGATA
1 TGCTATAGGGAACCGATA
1007147 TGCTATAGGGAACCGATA
1 TGCTATAGGGAACCGATA
1007165 CCTCGCTATA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.33, C:0.19, G:0.28, T:0.20
Consensus pattern (18 bp):
TGCTATAGGGAACCGATA
Found at i:1008464 original size:149 final size:149
Alignment explanation
Indices: 1008194--1008497 Score: 608
Period size: 149 Copynumber: 2.0 Consensus size: 149
1008184 CCGAAGTGCA
1008194 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
1008259 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
1008324 TATATATCCCGAAGGACCG
131 TATATATCCCGAAGGACCG
1008343 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
1008408 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
1008473 TATATATCCCGAAGGACCG
131 TATATATCCCGAAGGACCG
1008492 CGTAGA
1 CGTAGA
1008498 CCCTCGACTC
Statistics
Matches: 155, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
149 155 1.00
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
TATATATCCCGAAGGACCG
Found at i:1013513 original size:149 final size:149
Alignment explanation
Indices: 1013243--1013546 Score: 590
Period size: 149 Copynumber: 2.0 Consensus size: 149
1013233 CCGAAGTGCA
1013243 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
*
1013308 CATATACATATACTAGGAATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACATAATATA
66 CATATACATATACTAGGAATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
1013373 TATATATCCCGAAGGACCG
131 TATATATCCCGAAGGACCG
1013392 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
*
1013457 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
66 CATATACATATACTAGGAATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
1013522 TATATATCCCGAAGGACCG
131 TATATATCCCGAAGGACCG
1013541 CGTAGA
1 CGTAGA
1013547 CCCTCGACTC
Statistics
Matches: 153, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 153 1.00
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
CATATACATATACTAGGAATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
TATATATCCCGAAGGACCG
Found at i:1015477 original size:21 final size:21
Alignment explanation
Indices: 1015451--1015506 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
1015441 TCTTGATGTT
1015451 TAAAGCTTATATAAGCTTTCC
1 TAAAGCTTATATAAGCTTTCC
1015472 TAAAGCTTATATAAGCTTTCC
1 TAAAGCTTATATAAGCTTTCC
*
1015493 TTAAGCTTATATAA
1 TAAAGCTTATATAA
1015507 TACTCCAAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (21 bp):
TAAAGCTTATATAAGCTTTCC
Found at i:1016208 original size:21 final size:21
Alignment explanation
Indices: 1016182--1016241 Score: 120
Period size: 21 Copynumber: 2.9 Consensus size: 21
1016172 CATATGAAAT
1016182 TTGTCCCGAAGGACCACTGTA
1 TTGTCCCGAAGGACCACTGTA
1016203 TTGTCCCGAAGGACCACTGTA
1 TTGTCCCGAAGGACCACTGTA
1016224 TTGTCCCGAAGGACCACT
1 TTGTCCCGAAGGACCACT
1016242 ATAACCCTCG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.23, C:0.30, G:0.23, T:0.23
Consensus pattern (21 bp):
TTGTCCCGAAGGACCACTGTA
Found at i:1016520 original size:2 final size:2
Alignment explanation
Indices: 1016513--1016540 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1016503 TTATATCATC
1016513 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
1016541 CATCTATGTT
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:1017202 original size:14 final size:14
Alignment explanation
Indices: 1017183--1017212 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1017173 GCTTTGATTC
1017183 GAACCTAATTCTTT
1 GAACCTAATTCTTT
1017197 GAACCTAATTCTTT
1 GAACCTAATTCTTT
1017211 GA
1 GA
1017213 TTGTTTCGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (14 bp):
GAACCTAATTCTTT
Found at i:1037318 original size:36 final size:36
Alignment explanation
Indices: 1037274--1037359 Score: 154
Period size: 36 Copynumber: 2.4 Consensus size: 36
1037264 ATTATGTATG
1037274 TAGTTATTTTAATTTAAATGAGATAATATCTAAGCA
1 TAGTTATTTTAATTTAAATGAGATAATATCTAAGCA
*
1037310 TATTTATTTTAATTTAAATGAGATAATATCTAAGCA
1 TAGTTATTTTAATTTAAATGAGATAATATCTAAGCA
*
1037346 TGGTTATTTTAATT
1 TAGTTATTTTAATT
1037360 ATATTTGAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.47
Consensus pattern (36 bp):
TAGTTATTTTAATTTAAATGAGATAATATCTAAGCA
Found at i:1037619 original size:8 final size:7
Alignment explanation
Indices: 1037595--1037637 Score: 52
Period size: 7 Copynumber: 6.3 Consensus size: 7
1037585 CATTAATCAG
1037595 AAAAA-T
1 AAAAATT
1037601 AAAAATT
1 AAAAATT
1037608 AAAAATT
1 AAAAATT
*
1037615 AAAAACT
1 AAAAATT
*
1037622 AAAAGTT
1 AAAAATT
*
1037629 AAAATTT
1 AAAAATT
1037636 AA
1 AA
1037638 TTTTTATTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
6 5 0.16
7 27 0.84
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (7 bp):
AAAAATT
Found at i:1037619 original size:21 final size:21
Alignment explanation
Indices: 1037595--1037637 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1037585 CATTAATCAG
1037595 AAAAATAAAAATTAAAAATTA
1 AAAAATAAAAATTAAAAATTA
* * *
1037616 AAAACTAAAAGTTAAAATTTA
1 AAAAATAAAAATTAAAAATTA
1037637 A
1 A
1037638 TTTTTATTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (21 bp):
AAAAATAAAAATTAAAAATTA
Found at i:1038782 original size:28 final size:28
Alignment explanation
Indices: 1038742--1038800 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
1038732 CCACATAATC
1038742 TAGTTCGTATTAGTGTTAGCACGTGTGA
1 TAGTTCGTATTAGTGTTAGCACGTGTGA
1038770 TAGTTCGTATTAGTGTTAGCACGTGTGA
1 TAGTTCGTATTAGTGTTAGCACGTGTGA
1038798 TAG
1 TAG
1038801 ACACGCAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.22, C:0.10, G:0.29, T:0.39
Consensus pattern (28 bp):
TAGTTCGTATTAGTGTTAGCACGTGTGA
Found at i:1041954 original size:22 final size:22
Alignment explanation
Indices: 1041908--1041955 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
1041898 TTATAATATT
*
1041908 TAAATCATAATTAATCGATTAA
1 TAAATCATAATTAATAGATTAA
1041930 TAAATCA-AATATAATAG-TTATA
1 TAAATCATAAT-TAATAGATTA-A
1041952 TAAA
1 TAAA
1041956 AAAATAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.35
Consensus pattern (22 bp):
TAAATCATAATTAATAGATTAA
Found at i:1049270 original size:37 final size:37
Alignment explanation
Indices: 1049229--1049318 Score: 171
Period size: 37 Copynumber: 2.4 Consensus size: 37
1049219 AATACCCGCA
1049229 GTTTAAGGAACAGCACATAATAATATTACCGGCATCG
1 GTTTAAGGAACAGCACATAATAATATTACCGGCATCG
*
1049266 GTTTAAGGAACAGCACATAATTATATTACCGGCATCG
1 GTTTAAGGAACAGCACATAATAATATTACCGGCATCG
1049303 GTTTAAGGAACAGCAC
1 GTTTAAGGAACAGCAC
1049319 GTAAGCATTG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 52 1.00
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (37 bp):
GTTTAAGGAACAGCACATAATAATATTACCGGCATCG
Found at i:1054478 original size:19 final size:19
Alignment explanation
Indices: 1054456--1054496 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1054446 TTTTATAATT
1054456 TTATAATT-TTATCTTCAAA
1 TTATAATTCTTAT-TTCAAA
*
1054475 TTATAATTCTTATTTTAAA
1 TTATAATTCTTATTTCAAA
1054494 TTA
1 TTA
1054497 ATATTTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (19 bp):
TTATAATTCTTATTTCAAA
Found at i:1054874 original size:23 final size:23
Alignment explanation
Indices: 1054844--1054890 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
1054834 AAACACGAAA
*
1054844 ATGAGAATAATTTAGAAGATTTG
1 ATGAGAATAATTTAAAAGATTTG
1054867 ATGAGAATAATTTAAAAGATTTG
1 ATGAGAATAATTTAAAAGATTTG
1054890 A
1 A
1054891 GAGTGAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.34
Consensus pattern (23 bp):
ATGAGAATAATTTAAAAGATTTG
Found at i:1056406 original size:12 final size:11
Alignment explanation
Indices: 1056384--1056411 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1056374 GAAATCAGAG
1056384 AAAAAAGAAAA
1 AAAAAAGAAAA
1056395 AAAAAAGAAAA
1 AAAAAAGAAAA
1056406 AAAAAA
1 AAAAAA
1056412 TACAAAGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:1058121 original size:45 final size:44
Alignment explanation
Indices: 1057997--1058121 Score: 178
Period size: 45 Copynumber: 2.8 Consensus size: 44
1057987 GCTTCCTCTG
* * *
1057997 TGATGCTTGCCATCAGCAGATCTTGACATTGATCGCTTTCTATCA
1 TGATGCTTGCCATCAGCAGATCTTGAC-TTGACCTCTTTATATCA
*
1058042 CGATGCTTGCCATCAGCAGATCTTGACCTTGACCTCTTTATATCA
1 TGATGCTTGCCATCAGCAGATCTTGA-CTTGACCTCTTTATATCA
*
1058087 TGATGCTTGCCATCCGCAGATCTTGATCTTGACCT
1 TGATGCTTGCCATCAGCAGATCTTGA-CTTGACCT
1058122 TGACCTCTGT
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
45 71 0.99
46 1 0.01
ACGTcount: A:0.21, C:0.27, G:0.18, T:0.34
Consensus pattern (44 bp):
TGATGCTTGCCATCAGCAGATCTTGACTTGACCTCTTTATATCA
Found at i:1058965 original size:42 final size:42
Alignment explanation
Indices: 1058915--1059043 Score: 159
Period size: 42 Copynumber: 3.1 Consensus size: 42
1058905 AGACCTCCTT
* *
1058915 CTTCGCCTATAACTGATTGGTGATCTTGACTTGGACCTTGAC
1 CTTCGCCTATAACTAATTGGTGATCTTGACTTGGATCTTGAC
* *
1058957 CTTCGCCTATAAATAATTGGTGATCTTGACTTGGATCTTGAT
1 CTTCGCCTATAACTAATTGGTGATCTTGACTTGGATCTTGAC
* ** ** * *
1058999 CTTCTCCGGTAACTAAGGGGTGATTTTGATTTGGATCTTGAC
1 CTTCGCCTATAACTAATTGGTGATCTTGACTTGGATCTTGAC
1059041 CTT
1 CTT
1059044 GCACGGGAAG
Statistics
Matches: 74, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 74 1.00
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (42 bp):
CTTCGCCTATAACTAATTGGTGATCTTGACTTGGATCTTGAC
Found at i:1062059 original size:21 final size:21
Alignment explanation
Indices: 1062026--1062070 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1062016 TAATTGTTAC
* **
1062026 AAAATCTGGTAATCGAGACTT
1 AAAATCTCGTAATAAAGACTT
*
1062047 AAAATCTCTTAATAAAGACTT
1 AAAATCTCGTAATAAAGACTT
1062068 AAA
1 AAA
1062071 TTAGAATAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.29
Consensus pattern (21 bp):
AAAATCTCGTAATAAAGACTT
Found at i:1072249 original size:16 final size:16
Alignment explanation
Indices: 1072222--1072256 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
1072212 GGGGTCGAAC
1072222 AAAAATATTTTGACTTT
1 AAAAATATTTTGA-TTT
1072239 AAAAATA-TTTGATTT
1 AAAAATATTTTGATTT
1072254 AAA
1 AAA
1072257 TTAATTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 5 0.28
17 7 0.39
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.43
Consensus pattern (16 bp):
AAAAATATTTTGATTT
Found at i:1080582 original size:2 final size:2
Alignment explanation
Indices: 1080575--1080623 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
1080565 CCTAGTTTAC
* *
1080575 AT AT AT AT AT AT AT GT AT AT AT AT AT AT CT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1080617 AT -T AT AT
1 AT AT AT AT
1080624 GGTTTTAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1080651 original size:38 final size:36
Alignment explanation
Indices: 1080609--1080982 Score: 265
Period size: 38 Copynumber: 10.5 Consensus size: 36
1080599 ATATCTATAT
*
1080609 ATATATATATTATATGGTTTTAAAAACATTTTTTAAA
1 ATATATATATTATATAGTTTTAAAAACA-TTTTTAAA
* * *
1080646 CATATATATAATATATAGTTTTGAAAACATGTTTGAAA
1 -ATATATATATTATATAGTTTTAAAAACAT-TTTTAAA
* * * *
1080684 ATATTTATATATTATATAATTTTTAAAATATTTTGAAA
1 ATA--TATATATTATATAGTTTTAAAAACATTTTTAAA
* * * *
1080722 ATAAATATAATATATAGTTTTTAAAACATTTTTGAAT
1 ATATATATATTATATAGTTTTAAAAACATTTTT-AAA
* * *
1080759 ATATATATATTATATAGTTTT-TAACCATTTTGAAA
1 ATATATATATTATATAGTTTTAAAAACATTTTTAAA
* ** *
1080794 ATATATATAGT-T-T--TTAAAAAAACATTTTGAAAAA
1 ATATATATATTATATAGTTTTAAAAACATTTT--TAAA
* * *
1080828 CATATATATATTATATAGTTTTGAAATCATTTTGAAA
1 -ATATATATATTATATAGTTTTAAAAACATTTTTAAA
*
1080865 ACT-TATA-A-TATATAGTTTTAAAAATATTTTT-AA
1 A-TATATATATTATATAGTTTTAAAAACATTTTTAAA
**
1080898 A-A-A-A-ATTATATAACTTTAAAAACATTTTTAAGAA
1 ATATATATATTATATAGTTTTAAAAACATTTTT-A-AA
* * * **
1080932 ATATATATAATATATAATTTT-AAAATATTTTTTTA
1 ATATATATATTATATAGTTTTAAAAACATTTTTAAA
1080967 A-ATATATATTATATAG
1 ATATATATATTATATAG
1080983 ATTTCTGGAA
Statistics
Matches: 268, Mismatches: 46, Indels: 48
0.74 0.13 0.13
Matches are distributed among these distances:
30 2 0.01
31 23 0.09
32 8 0.03
33 4 0.01
34 39 0.15
35 26 0.10
36 40 0.15
37 41 0.15
38 52 0.19
39 33 0.12
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (36 bp):
ATATATATATTATATAGTTTTAAAAACATTTTTAAA
Found at i:1080916 original size:31 final size:31
Alignment explanation
Indices: 1080872--1080941 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
1080862 AAAACTTATA
** *
1080872 ATATATAGTTTTAAAAATATTTTTAAAAAA-
1 ATATATAACTTTAAAAACATTTTTAAAAAAT
*
1080902 ATTATATAACTTTAAAAACATTTTTAAGAAAT
1 A-TATATAACTTTAAAAACATTTTTAAAAAAT
1080934 ATATATAA
1 ATATATAA
1080942 TATATAATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 1 0.03
31 32 0.94
32 1 0.03
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (31 bp):
ATATATAACTTTAAAAACATTTTTAAAAAAT
Found at i:1080980 original size:34 final size:34
Alignment explanation
Indices: 1080831--1080986 Score: 106
Period size: 34 Copynumber: 4.5 Consensus size: 34
1080821 TGAAAAACAT
* * **
1080831 ATATATATTATATAGTTTTGAAATCA-TTTTGAAA
1 ATATATATTATATAATTTTAAAAT-ATTTTTTTAA
* * *
1080865 ACT-TATAATATATAGTTTTAAAA-ATATTTTTAA
1 A-TATATATTATATAATTTTAAAATATTTTTTTAA
* * * **
1080898 A-A-AAATTATATAACTTTAAAAACATTTTTAAGAA
1 ATATATATTATATAA-TTTTAAAATATTTTT-TTAA
1080932 ATATATATAATATATAATTTTAAAATATTTTTTTAA
1 ATATATAT--TATATAATTTTAAAATATTTTTTTAA
1080968 ATATATATTATATAGATTT
1 ATATATATTATATA-ATTT
1080987 CTGGAATTTT
Statistics
Matches: 94, Mismatches: 17, Indels: 21
0.71 0.13 0.16
Matches are distributed among these distances:
31 8 0.09
32 8 0.09
33 11 0.12
34 28 0.30
35 6 0.06
36 13 0.14
37 13 0.14
38 7 0.07
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.47
Consensus pattern (34 bp):
ATATATATTATATAATTTTAAAATATTTTTTTAA
Found at i:1081025 original size:15 final size:15
Alignment explanation
Indices: 1081005--1081055 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
1080995 TTTTTATTAC
1081005 ATTA-TTATTATTATT
1 ATTATTTATTATT-TT
1081020 ATTATTTACTTATTTT
1 ATTATTTA-TTATTTT
*
1081036 -TTATTTATTTTTTT
1 ATTATTTATTATTTT
1081050 ATTATT
1 ATTATT
1081056 AATTTTATCT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 6 0.19
15 16 0.50
16 5 0.16
17 5 0.16
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (15 bp):
ATTATTTATTATTTT
Found at i:1081032 original size:11 final size:10
Alignment explanation
Indices: 1081006--1081055 Score: 52
Period size: 11 Copynumber: 5.1 Consensus size: 10
1080996 TTTTATTACA
1081006 TTATTATTA-
1 TTATTATTAT
1081015 TTATTATTAT
1 TTATTATTAT
*
1081025 TTACTTATTTT
1 TTA-TTATTAT
1081036 TTATTTATT-T
1 TTA-TTATTAT
1081046 TT-TTATTAT
1 TTATTATTAT
1081055 T
1 T
1081056 AATTTTATCT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
8 5 0.14
9 11 0.31
10 6 0.17
11 14 0.39
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (10 bp):
TTATTATTAT
Found at i:1081073 original size:12 final size:12
Alignment explanation
Indices: 1080995--1081073 Score: 58
Period size: 12 Copynumber: 6.4 Consensus size: 12
1080985 TTCTGGAATT
1080995 TTTTTATTACATTA
1 TTTTTATT--ATTA
*
1081009 TTATTATTATTA
1 TTTTTATTATTA
1081021 TTATTTACTTA-T-
1 TT-TTTA-TTATTA
1081033 TTTTTATTTATT-
1 TTTTTA-TTATTA
1081045 TTTTTATTATTA
1 TTTTTATTATTA
*
1081057 ATTTTATCT-TTA
1 TTTTTAT-TATTA
1081069 TTTTT
1 TTTTT
1081074 GTTTTTTTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
11 12 0.22
12 28 0.51
13 5 0.09
14 10 0.18
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTTTATTATTA
Found at i:1081073 original size:36 final size:35
Alignment explanation
Indices: 1081012--1081084 Score: 87
Period size: 36 Copynumber: 2.1 Consensus size: 35
1081002 TACATTATTA
*
1081012 TTATTATTATTATTTACTTATTTTTTATTTATTTTT
1 TTATTATTAATATTTACTTATTTTTTATTT-TTTTT
*
1081048 TTATTATTAAT-TTTATCTT-TATTTTTGTTTTTTTT
1 TTATTATTAATATTTA-CTTAT-TTTTTATTTTTTTT
1081083 TT
1 TT
1081085 CAGAGTCCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
35 12 0.36
36 21 0.64
ACGTcount: A:0.19, C:0.03, G:0.01, T:0.77
Consensus pattern (35 bp):
TTATTATTAATATTTACTTATTTTTTATTTTTTTT
Found at i:1082769 original size:15 final size:15
Alignment explanation
Indices: 1082743--1082781 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
1082733 GAATAATAAG
1082743 CATGTAGGGTAGATAT
1 CATGT-GGGTAGATAT
1082759 CATGTGGGTAGATAT
1 CATGTGGGTAGATAT
*
1082774 CATATGGG
1 CATGTGGG
1082782 GTAGGACTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.28, C:0.08, G:0.33, T:0.31
Consensus pattern (15 bp):
CATGTGGGTAGATAT
Found at i:1087189 original size:84 final size:82
Alignment explanation
Indices: 1086924--1088181 Score: 1321
Period size: 84 Copynumber: 15.2 Consensus size: 82
1086914 TCTTTGAGAC
*
1086924 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATC-TGCCAACCAAAGACCTTCAAGTTCGAC
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTG---ACCAAAGACCTTCGAGTTCGAC
*
1086988 TACGCTCAGCTCCAAGGCAC
63 TACGCTCAGCTCCAAGGCAT
* * * *
1087008 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATC-TG-CCAAAGAACC-CCGAGTTCGATTA
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTGACCAAAG-ACCTTCGAGTTCGACTA
* * *
1087070 CACTCAGCTTCGAGGGCAT
65 CGCTCAGC-TCCAAGGCAT
* * * *
1087089 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTATGACCAAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-TGACC-AAAGACCTTCGAGTTCGACT
* *
1087154 CCGCTCAGCTCCGAGGCAT
64 ACGCTCAGCTCCAAGGCAT
1087173 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATC-TGCCAACCAAAGACCTTCGAGTTCGAC
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTG---ACCAAAGACCTTCGAGTTCGAC
* * *
1087237 TACGCTTAGCTCCAAGACAC
63 TACGCTCAGCTCCAAGGCAT
* * * * ** *
1087257 ATCATTTGCAGCATAGCTTAAGTCAAGAATGGCTATC-TG-CCAAAGACCCCCGAGTTCGATTAC
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTGACCAAAGACCTTCGAGTTCGACTAC
* * *
1087320 ACTCAGCTTCGAGGGCAT
66 GCTCAGC-TCCAAGGCAT
* * * * *
1087338 ATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTATGACCAAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-TGACC-AAAGACCTTCGAGTTCGACT
1087403 -CTGCTCAGCTCCAAGGCAT
64 AC-GCTCAGCTCCAAGGCAT
1087422 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATC-TGCCAACCAAAGACCTTCGAGTTCGAC
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTG---ACCAAAGACCTTCGAGTTCGAC
* *
1087486 TACGCTCAGCTCCAAGCCAC
63 TACGCTCAGCTCCAAGGCAT
* * ** *
1087506 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATC-TG-CCAAAGACCCCCGAGTTCGATTAC
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTGACCAAAGACCTTCGAGTTCGACTAC
* * *
1087569 ACTCAGCTTCGAGGGCAT
66 GCTCAGC-TCCAAGGCAT
* * * *
1087587 ATCATTTACAGCATAACTCAAAG-CTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCAAC
1 ATCATTTGCAGCATAACT-TAAGTCGAGAAGGGTTATCT-TGACC-AAAGACCTTCGAGTTCGAC
*
1087651 TCCGCTCAGCTCCAAGGCAT
63 TACGCTCAGCTCCAAGGCAT
1087671 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATC-TGCCAACCAAAGACCTTCGAGTTCGAC
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTG---ACCAAAGACCTTCGAGTTCGAC
*
1087735 TACGCTCAGCTCCAAGGCAC
63 TACGCTCAGCTCCAAGGCAT
* * * * *
1087755 ATCATTTGCGGCATAACTTAAGTCGAGAAGGGCTATC-TG-CCAAAGACC-CCTGAGTTGGATTA
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTGACCAAAGACCTTC-GAGTTCGACTA
* * * *
1087817 CACTCATCTTCGATGGCAT
65 CGCTCAGC-TCCAAGGCAT
* * * * * * *
1087836 ATAATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCAAGTTCGACTA
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-TGACCAAAGACCTTCGAGTTCGACTA
*
1087901 CGCTCAGCTCCAAGGTAT
65 CGCTCAGCTCCAAGGCAT
* * * *
1087919 ATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTC-TGCCAACCAAAGACCTTCAAGTTCGAC
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTG---ACCAAAGACCTTCGAGTTCGAC
* * *
1087983 TACGTTCAACTCCAAGGCAC
63 TACGCTCAGCTCCAAGGCAT
* *
1088003 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATC-TG-CCAAAGACCTTCGAGTTCGATTAC
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTGACCAAAGACCTTCGAGTTCGACTAC
* * *
1088066 ACTCAGCTTCGAGGGCAT
66 GCTCAGC-TCCAAGGCAT
* * * * * *
1088084 ATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTA
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-TGACCAAAGACCTTCGAGTTCGACTA
*
1088149 CGCTCAGCTCCAAGGCAC
65 CGCTCAGCTCCAAGGCAT
*
1088167 ATCATTTACAGCATA
1 ATCATTTGCAGCATA
1088182 GCTCAAGGCA
Statistics
Matches: 974, Mismatches: 157, Indels: 87
0.80 0.13 0.07
Matches are distributed among these distances:
79 1 0.00
80 126 0.13
81 186 0.19
82 9 0.01
83 70 0.07
84 504 0.52
85 78 0.08
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (82 bp):
ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTGACCAAAGACCTTCGAGTTCGACTAC
GCTCAGCTCCAAGGCAT
Found at i:1087362 original size:249 final size:249
Alignment explanation
Indices: 1086924--1088181 Score: 2151
Period size: 249 Copynumber: 5.1 Consensus size: 249
1086914 TCTTTGAGAC
*
1086924 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCAAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
1086989 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA
66 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA
*
1087054 ACCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGCTAGAAG
131 CCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGCTAGAAG
* *
1087119 GGTTATCTATGACCAAAAGACCTTCGAGTTCGACTCCGCTCAGCTCCGAGGCAT
196 GGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTCCGCTCAGCTCCAAGGCAT
1087173 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
* * * *
1087238 ACGCTTAGCTCCAAGACACATCATTTGCAGCATAGCTTAAGTCAAGAATGGCTATCTGCCAAAGA
66 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA
*
1087303 CCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACAACATAACTCAAGGCTAGAAG
131 CCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGCTAGAAG
* *
1087368 GGTTATCTATGACCAAAAGACCTTCGAGTTCGACTCTGCTCAGCTCCAAGGCAT
196 GGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTCCGCTCAGCTCCAAGGCAT
1087422 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
*
1087487 ACGCTCAGCTCCAAGCCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA
66 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA
*
1087552 CCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAAGCTAGAAG
131 CCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGCTAGAAG
*
1087617 GGTTATCTGTGACCAAAAGACCTTCGAGTTCAACTCCGCTCAGCTCCAAGGCAT
196 GGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTCCGCTCAGCTCCAAGGCAT
1087671 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
* *
1087736 ACGCTCAGCTCCAAGGCACATCATTTGCGGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGA
66 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA
* * * * *
1087801 CCCCTGAGTTGGATTACACTCATCTTCGATGGCATATAATTTACAGCATAACTCAAGGCTAGAAG
131 CCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGCTAGAAG
* * * *
1087866 GGTTATCTGTCACC-AAAGACCTTCAAGTTCGACTACGCTCAGCTCCAAGGTAT
196 GGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTCCGCTCAGCTCCAAGGCAT
* * * *
1087919 ATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACCAAAGACCTTCAAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
* * *
1087984 ACGTTCAACTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGA
66 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA
** *
1088049 CCTTCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACAACATAACTCAAGGCTAGAAG
131 CCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGCTAGAAG
* * *
1088114 GGTTATCTGTCACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAC
196 GGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTCCGCTCAGCTCCAAGGCAT
*
1088167 ATCATTTACAGCATA
1 ATCATTTGCAGCATA
1088182 GCTCAAGGCA
Statistics
Matches: 957, Mismatches: 52, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
248 278 0.29
249 679 0.71
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (249 bp):
ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA
CCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGCTAGAAG
GGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTCCGCTCAGCTCCAAGGCAT
Found at i:1088740 original size:12 final size:12
Alignment explanation
Indices: 1088723--1088756 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1088713 TCGTCCCATT
1088723 TATATATATACA
1 TATATATATACA
*
1088735 TATATATATAGA
1 TATATATATACA
*
1088747 TAGATATATA
1 TATATATATA
1088757 TGTATATGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (12 bp):
TATATATATACA
Found at i:1088791 original size:37 final size:37
Alignment explanation
Indices: 1088750--1089125 Score: 257
Period size: 38 Copynumber: 10.4 Consensus size: 37
1088740 ATATAGATAG
* * *
1088750 ATATATAT-GTATATGGTTTTAAAAACATTTTTTAAA
1 ATATATATAATATATAGTTTTAAAAACATTTTTGAAA
* *
1088786 CATATATATAATATATAGTTTTGAAAACATGTTTGAAA
1 -ATATATATAATATATAGTTTTAAAAACATTTTTGAAA
* *
1088824 ATATTTATATATTATATAATTTTAAAAACA-TTTTGAAA
1 ATA--TATATAATATATAGTTTTAAAAACATTTTTGAAA
* *
1088862 ATAAATATAATATATAGTTTTTAAAACATTTTTGAATA
1 ATATATATAATATATAGTTTTAAAAACATTTTTGAA-A
* * *
1088900 TATATATATATTATATAGTTTT-TAACCA-TTTTGAAA
1 -ATATATATAATATATAGTTTTAAAAACATTTTTGAAA
* **
1088936 ATATATATAGT-T-T--TTAAAAAAACA-TTTTGAAAAA
1 ATATATATAATATATAGTTTTAAAAACATTTTTG--AAA
* * *
1088970 CATATATATATTATATAGTTTTGAAATCA-TTTT-AAA
1 -ATATATATAATATATAGTTTTAAAAACATTTTTGAAA
* * * **
1089006 A-CT-TATAATATATAGTTTTAAACATATTTTTTTAA
1 ATATATATAATATATAGTTTTAAAAACATTTTTGAAA
* * *
1089041 A-A-A-A-ACTATATAGCTTTAAAAACATTTTTAAGAA
1 ATATATATAATATATAGTTTTAAAAACATTTTTGA-AA
* * **
1089075 ATATATATAATATATAATTTTAAAATA-TTTTTTTTAA
1 ATATATATAATATATAGTTTTAAAA-ACATTTTTGAAA
*
1089112 ATATATATTATATA
1 ATATATATAATATA
1089126 GATTTCTGGA
Statistics
Matches: 268, Mismatches: 48, Indels: 46
0.74 0.13 0.13
Matches are distributed among these distances:
31 2 0.01
32 9 0.03
33 40 0.15
34 13 0.05
35 25 0.09
36 27 0.10
37 42 0.16
38 57 0.21
39 53 0.20
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.45
Consensus pattern (37 bp):
ATATATATAATATATAGTTTTAAAAACATTTTTGAAA
Found at i:1088897 original size:75 final size:75
Alignment explanation
Indices: 1088750--1089024 Score: 289
Period size: 75 Copynumber: 3.7 Consensus size: 75
1088740 ATATAGATAG
* *
1088750 ATATATATGTATATGGTTTTAAAAACATTTTTTAAACATATATATAATATATAGTTTTGAAAACA
1 ATATATAT-TATATAGTTTTAAAAACA-TTTTGAAA-ATATATATAATATATAGTTTTGAAAACA
1088815 TGTTTGAAAATAT
63 TGTTTGAAAATAT
* * * * *
1088828 TTATATATTATATAATTTTAAAAACATTTTGAAAATAAATATAATATATAGTTTTTAAAACATTT
1 ATATATATTATATAGTTTTAAAAACATTTTGAAAATATATATAATATATAGTTTTGAAAACATGT
*
1088893 TTGAATATAT
66 TTGAAAATAT
* * * ***
1088903 ATATATATTATATAGTTTT-TAACCATTTTGAAAATATATATAGT-T-T--TTAAAAAAACAT-T
1 ATATATATTATATAGTTTTAAAAACATTTTGAAAATATATATAATATATAGTTTTGAAAACATGT
*
1088962 TTGAAAAACAT
66 TTG-AAAATAT
* * *
1088973 ATATATATTATATAGTTTTGAAATCATTTT-AAAA-CT-TATAATATATAGTTTT
1 ATATATATTATATAGTTTTAAAAACATTTTGAAAATATATATAATATATAGTTTT
1089025 AAACATATTT
Statistics
Matches: 166, Mismatches: 25, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
68 5 0.03
69 6 0.04
70 38 0.23
71 8 0.05
72 3 0.02
73 1 0.01
74 21 0.13
75 54 0.33
76 7 0.04
77 16 0.10
78 7 0.04
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.45
Consensus pattern (75 bp):
ATATATATTATATAGTTTTAAAAACATTTTGAAAATATATATAATATATAGTTTTGAAAACATGT
TTGAAAATAT
Found at i:1089116 original size:35 final size:36
Alignment explanation
Indices: 1089009--1089130 Score: 103
Period size: 35 Copynumber: 3.4 Consensus size: 36
1088999 TTTTAAAACT
1089009 TATAATATATAG-TTTTAAACATA-TTTTTTTAAA-A
1 TATAATATATAGATTTTAAA-ATATTTTTTTTAAATA
* * * ***
1089043 -A-AACTATATAGCTTTAAAAACATTTTTAAGAAATATA
1 TATAA-TATATAGATTTTAAAATATTTTT-TTTAA-ATA
1089080 TATAATATATA-ATTTTAAAATATTTTTTTTAAATA
1 TATAATATATAGATTTTAAAATATTTTTTTTAAATA
*
1089115 TATATTATATAGATTT
1 TATAATATATAGATTT
1089131 CTGGAATTTT
Statistics
Matches: 67, Mismatches: 12, Indels: 16
0.71 0.13 0.17
Matches are distributed among these distances:
32 2 0.03
33 10 0.15
34 10 0.15
35 15 0.22
36 7 0.10
37 14 0.21
38 7 0.10
39 2 0.03
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (36 bp):
TATAATATATAGATTTTAAAATATTTTTTTTAAATA
Found at i:1094801 original size:20 final size:21
Alignment explanation
Indices: 1094762--1094806 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
1094752 ACTCATTCCC
1094762 TATACAAAAATAAAAAAAATA
1 TATACAAAAATAAAAAAAATA
* * *
1094783 TATACACAAA-AAAATAAATC
1 TATACAAAAATAAAAAAAATA
1094803 TATA
1 TATA
1094807 AGAAATGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.69, C:0.09, G:0.00, T:0.22
Consensus pattern (21 bp):
TATACAAAAATAAAAAAAATA
Found at i:1109670 original size:13 final size:13
Alignment explanation
Indices: 1109644--1109686 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
1109634 GTCATAACCC
* *
1109644 GACCCAACCTGTT
1 GACCCGACCCGTT
1109657 GACCCGACCCGTT
1 GACCCGACCCGTT
1109670 GACCCGACCCGTT
1 GACCCGACCCGTT
1109683 GACC
1 GACC
1109687 GGCGTTGACC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.19, C:0.44, G:0.21, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1111131 original size:26 final size:26
Alignment explanation
Indices: 1111093--1111145 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
1111083 TGACCCAAGA
* *
1111093 ATATCGTCAAGCTCAT-AAATGATTGG
1 ATATCCTCAAGCTC-TGAAATGAATGG
*
1111119 ATATCCTCGAGCTCTGAAATGAATGG
1 ATATCCTCAAGCTCTGAAATGAATGG
1111145 A
1 A
1111146 ATAAAACTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 1 0.04
26 22 0.96
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (26 bp):
ATATCCTCAAGCTCTGAAATGAATGG
Found at i:1112236 original size:24 final size:24
Alignment explanation
Indices: 1112118--1112233 Score: 146
Period size: 24 Copynumber: 4.8 Consensus size: 24
1112108 TTCGATTTGA
1112118 ATTCTGATATGATACTTGACATGG
1 ATTCTGATATGATACTTGACATGG
*
1112142 ATTCTGATATGATA-TCTGACATAG
1 ATTCTGATATGATACT-TGACATGG
* * *
1112166 ATTCTGATCTTATACTTGACTTGG
1 ATTCTGATATGATACTTGACATGG
* *
1112190 ATTCTGATCTGATACTTGACCTGG
1 ATTCTGATATGATACTTGACATGG
1112214 AGTT-TGATATGATACTTGAC
1 A-TTCTGATATGATACTTGAC
1112234 CTGATTTATG
Statistics
Matches: 81, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
23 1 0.01
24 77 0.95
25 3 0.04
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.40
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:1132834 original size:24 final size:25
Alignment explanation
Indices: 1132795--1132842 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
1132785 ATATAATTTA
*
1132795 ATATATTATTGATAAATTAAATATTG
1 ATATATTATT-ATAAAATAAATATTG
1132821 ATATATTATT-TAAAATAAATAT
1 ATATATTATTATAAAATAAATAT
1132843 ATTGTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.52
26 10 0.48
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (25 bp):
ATATATTATTATAAAATAAATATTG
Found at i:1132844 original size:26 final size:26
Alignment explanation
Indices: 1132795--1132846 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1132785 ATATAATTTA
*
1132795 ATATATTATTGATAAATTAAATATTG
1 ATATATTATTGATAAATAAAATATTG
*
1132821 ATATATTATTTA-AAATAAATATATTG
1 ATATATTATTGATAAATAAA-ATATTG
1132847 TTTTTATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 6 0.26
26 17 0.74
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (26 bp):
ATATATTATTGATAAATAAAATATTG
Found at i:1133857 original size:29 final size:31
Alignment explanation
Indices: 1133825--1133889 Score: 100
Period size: 28 Copynumber: 2.2 Consensus size: 31
1133815 TATGAGAATA
1133825 ATATTTAAAATAATATT-TTTATT-AAAATG
1 ATATTTAAAATAATATTATTTATTAAAAATG
*
1133854 ATA-TTAAAATAATGTTATTTATTAAAAATG
1 ATATTTAAAATAATATTATTTATTAAAAATG
1133884 ATATTT
1 ATATTT
1133890 TTCATAAAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 12 0.38
29 9 0.28
30 9 0.28
31 2 0.06
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (31 bp):
ATATTTAAAATAATATTATTTATTAAAAATG
Found at i:1134785 original size:24 final size:24
Alignment explanation
Indices: 1134730--1134789 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
1134720 TTCGTTTATT
* * *
1134730 GTGTTCGCTTACGTTCGTTCGTTC
1 GTGTTCGTTTATGTTCGTTCGCTC
1134754 GTGTTCGTTTATGTTCGTTCGCTC
1 GTGTTCGTTTATGTTCGTTCGCTC
1134778 GTGTTCGTTTAT
1 GTGTTCGTTTAT
1134790 TTATTAAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.05, C:0.20, G:0.25, T:0.50
Consensus pattern (24 bp):
GTGTTCGTTTATGTTCGTTCGCTC
Found at i:1134831 original size:31 final size:31
Alignment explanation
Indices: 1134796--1134907 Score: 215
Period size: 31 Copynumber: 3.6 Consensus size: 31
1134786 TTATTTATTA
1134796 AATGAACGAACATGAACAAGCTATATTCCTT
1 AATGAACGAACATGAACAAGCTATATTCCTT
*
1134827 AATGAACGAACATGAACAAACTATATTCCTT
1 AATGAACGAACATGAACAAGCTATATTCCTT
1134858 AATGAACGAACATGAACAAGCTATATTCCTT
1 AATGAACGAACATGAACAAGCTATATTCCTT
1134889 AATGAACGAACATGAACAA
1 AATGAACGAACATGAACAA
1134908 AAAAAAATTT
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 79 1.00
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.23
Consensus pattern (31 bp):
AATGAACGAACATGAACAAGCTATATTCCTT
Found at i:1134938 original size:16 final size:16
Alignment explanation
Indices: 1134917--1134949 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1134907 AAAAAAAATT
1134917 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1134933 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1134949 T
1 T
1134950 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1135157 original size:16 final size:16
Alignment explanation
Indices: 1135119--1135160 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
1135109 TAGCTATTAA
*
1135119 TATTTATAGTTTTTAC
1 TATTTTTAGTTTTTAC
* *
1135135 TA-ATTTAGTTTTTAT
1 TATTTTTAGTTTTTAC
1135150 TATTTTTAGTT
1 TATTTTTAGTT
1135161 ACATTTAATC
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.67
Consensus pattern (16 bp):
TATTTTTAGTTTTTAC
Found at i:1136024 original size:31 final size:31
Alignment explanation
Indices: 1135986--1136141 Score: 217
Period size: 31 Copynumber: 5.0 Consensus size: 31
1135976 CCCGAATGAC
* *
1135986 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
1136017 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
* *
1136048 CAGTCCGTATGTTCCGAAGAACATAGGTAAT
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
1136079 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1136110 CAGTCCATATG-TCCAGAAGAACATAGGTAAA
1 CAGTCCATATGTTCC-GAAGAACATAGGTAAA
1136141 C
1 C
1136142 CCTCGACCCT
Statistics
Matches: 111, Mismatches: 12, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
30 2 0.02
31 108 0.97
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:1136083 original size:62 final size:62
Alignment explanation
Indices: 1135986--1136139 Score: 249
Period size: 62 Copynumber: 2.5 Consensus size: 62
1135976 CCCGAATGAC
* *
1135986 CAGTCCATA-GATTCCGAAGAACCTAGGTAATCAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATG-TTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
*
1136048 CAGTCCGTATGTTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
1136110 CAGTCCATATG-TCCAGAAGAACATAGGTAA
1 CAGTCCATATGTTCC-GAAGAACATAGGTAA
1136140 ACCCTCGACC
Statistics
Matches: 86, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
61 3 0.03
62 82 0.95
63 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (62 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1136345 original size:23 final size:24
Alignment explanation
Indices: 1136319--1136365 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
1136309 ATATACTTGT
*
1136319 TTTCACATATATA-TTTCATATCA
1 TTTCACATATACACTTTCATATCA
1136342 TTTCACATATACACTTTCATATCA
1 TTTCACATATACACTTTCATATCA
1136366 CATGCCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTCACATATACACTTTCATATCA
Found at i:1136995 original size:21 final size:21
Alignment explanation
Indices: 1136965--1137009 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1136955 ATTCTGTCGT
* *
1136965 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1136986 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1137007 TTG
1 TTG
1137010 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1143654 original size:2 final size:2
Alignment explanation
Indices: 1143647--1143679 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1143637 CTTAATTCGT
1143647 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1143680 TAAGAGGTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1151731 original size:20 final size:20
Alignment explanation
Indices: 1151706--1151744 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1151696 AATGAATCAG
*
1151706 CTGAAAACCAGTAGAACCGA
1 CTGAAAACCAGTAAAACCGA
*
1151726 CTGAAAACCGGTAAAACCG
1 CTGAAAACCAGTAAAACCG
1151745 GGGTGAACCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.26, G:0.21, T:0.10
Consensus pattern (20 bp):
CTGAAAACCAGTAAAACCGA
Found at i:1151782 original size:30 final size:30
Alignment explanation
Indices: 1151719--1151775 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
1151709 AAAACCAGTA
*
1151719 GAACCGACTGAAAACCGGTAAAACCGGGGT
1 GAACCGACTGAAAACCGGCAAAACCGGGGT
*
1151749 GAACCGGCTGAAAACCGGCAAAACCGG
1 GAACCGACTGAAAACCGGCAAAACCGG
1151776 TTTGAACTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.37, C:0.26, G:0.30, T:0.07
Consensus pattern (30 bp):
GAACCGACTGAAAACCGGCAAAACCGGGGT
Found at i:1156318 original size:24 final size:26
Alignment explanation
Indices: 1156272--1156319 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
1156262 TTTAATGTTG
1156272 TATTAACAATAATAATAAATAAATAA
1 TATTAACAATAATAATAAATAAATAA
*
1156298 TATTAA-AATAA-AATACATAAAT
1 TATTAACAATAATAATAAATAAAT
1156320 TTAATAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.48
25 5 0.24
26 6 0.29
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (26 bp):
TATTAACAATAATAATAAATAAATAA
Found at i:1156330 original size:20 final size:20
Alignment explanation
Indices: 1156281--1156334 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 20
1156271 GTATTAACAA
*
1156281 TAATAATAAATAAATAATAT
1 TAATAAAAAATAAATAATAT
*
1156301 TAA-AATAAAATACATAA-ATT
1 TAATAA-AAAATAAATAATA-T
1156321 TAATAAAAAA-AAAT
1 TAATAAAAAATAAAT
1156335 TCAAAGGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 6 0.21
20 20 0.71
21 2 0.07
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (20 bp):
TAATAAAAAATAAATAATAT
Found at i:1162617 original size:15 final size:15
Alignment explanation
Indices: 1162597--1162629 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1162587 AAGATCACTA
1162597 GGAACAAATTGGTTT
1 GGAACAAATTGGTTT
1162612 GGAACAAATTGGTTT
1 GGAACAAATTGGTTT
1162627 GGA
1 GGA
1162630 GCACATGGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.30, T:0.30
Consensus pattern (15 bp):
GGAACAAATTGGTTT
Found at i:1163641 original size:3 final size:3
Alignment explanation
Indices: 1163635--1163745 Score: 159
Period size: 3 Copynumber: 36.0 Consensus size: 3
1163625 TTCATTTAAA
* * *
1163635 ATT ATT ATT ATT ATT ATT AGT ATT ATT ATT ATT ATT ATA ATT ATA ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
1163683 ATTT ATT ATT ATT ATT ATT ATT ATT AAT ATT ATAT ATT ATT ATT ATT
1 A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT
1163730 ATAT ATT ATT ATT ATT
1 AT-T ATT ATT ATT ATT
1163746 TAATAAATAA
Statistics
Matches: 97, Mismatches: 8, Indels: 6
0.87 0.07 0.05
Matches are distributed among these distances:
3 88 0.91
4 9 0.09
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:1164204 original size:17 final size:15
Alignment explanation
Indices: 1164163--1164195 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1164153 CAGACGGCAG
1164163 AGAACGAAAAAAAAC
1 AGAACGAAAAAAAAC
1164178 AGAACGAAAAAAAAC
1 AGAACGAAAAAAAAC
1164193 AGA
1 AGA
1164196 GGAGGAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.73, C:0.12, G:0.15, T:0.00
Consensus pattern (15 bp):
AGAACGAAAAAAAAC
Found at i:1164475 original size:13 final size:13
Alignment explanation
Indices: 1164457--1164485 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1164447 ACCACCGTTA
1164457 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
1164470 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
1164483 CGG
1 CGG
1164486 AATACGGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.31, G:0.62, T:0.07
Consensus pattern (13 bp):
CGGTGGCCGGCGG
Found at i:1172557 original size:83 final size:83
Alignment explanation
Indices: 1172415--1173011 Score: 1043
Period size: 83 Copynumber: 7.2 Consensus size: 83
1172405 AATGGAACAA
*
1172415 ATGAATTTGATCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
1 ATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
1172480 AATCATTGAATTTGGAAG
66 AATCATTGAATTTGGAAG
*
1172498 ATTAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
1 ATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
*
1172563 AATCATTGAATTTAGAAG
66 AATCATTGAATTTGGAAG
*
1172581 ATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACA
1 ATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
1172646 AATCATTGAATTTGGAAG
66 AATCATTGAATTTGGAAG
*
1172664 ATTAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
1 ATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
*
1172729 AATCATTGAATTTAGAAG
66 AATCATTGAATTTGGAAG
*
1172747 ATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACA
1 ATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
1172812 AATCATTGAATTTGGAAG
66 AATCATTGAATTTGGAAG
* * *
1172830 ATTAATGTGATCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
1 ATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
*
1172895 AATCATTGAATTTAGAAG
66 AATCATTGAATTTGGAAG
* *
1172913 ATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGG-TTGGACAGAAC
1 ATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAAAAC
*
1172977 CAGTCATTGAATTTGGAAG
65 CAATCATTGAATTTGGAAG
*
1172996 ATGAATTTGCTCATAG
1 ATGAATTTGTTCATAG
1173012 TAGAAATAAG
Statistics
Matches: 488, Mismatches: 25, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
82 4 0.01
83 484 0.99
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (83 bp):
ATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
AATCATTGAATTTGGAAG
Found at i:1175248 original size:22 final size:22
Alignment explanation
Indices: 1175222--1175273 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
1175212 TACACTCTTC
*
1175222 AAAGATGATAGATTCTCTTTTT
1 AAAGATGACAGATTCTCTTTTT
1175244 AAAGATGACAGATTCTCTTTTT
1 AAAGATGACAGATTCTCTTTTT
1175266 AAAGATGA
1 AAAGATGA
1175274 AAGCTTTATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (22 bp):
AAAGATGACAGATTCTCTTTTT
Done.