Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000114.1 Hibiscus syriacus cultivar Beakdansim tig00000205_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: 799156
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:459386 original size:19 final size:19
Alignment explanation
Indices: 459359--459415 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 19
459349 GGTCGGGTCG
459359 GGTC-AGACCGGTCAAACC
1 GGTCGAGACCGGTCAAACC
459377 GGTTCG-GACCGGTCAAACCC
1 GG-TCGAGACCGGTCAAA-CC
*
459397 GGTCGAAACCGGTCAAACC
1 GGTCGAGACCGGTCAAACC
459416 AGTCAAAACC
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
18 2 0.06
19 18 0.53
20 14 0.41
ACGTcount: A:0.26, C:0.33, G:0.28, T:0.12
Consensus pattern (19 bp):
GGTCGAGACCGGTCAAACC
Found at i:459398 original size:10 final size:9
Alignment explanation
Indices: 459359--459475 Score: 78
Period size: 9 Copynumber: 12.3 Consensus size: 9
459349 GGTCGGGTCG
*
459359 GGTCAGACC
1 GGTCAAACC
459368 GGTCAAACC
1 GGTCAAACC
**
459377 GGTTCGGACC
1 GG-TCAAACC
459387 GGTCAAACCC
1 GGTCAAA-CC
459397 GGTCGAAACC
1 GGTC-AAACC
459407 GGTCAAACC
1 GGTCAAACC
*
459416 AGTCAAAACC
1 GGTC-AAACC
*
459426 GGTTGAAAACC
1 GG-T-CAAACC
459437 GGTCAAA-C
1 GGTCAAACC
459445 --TCAAAACC
1 GGTC-AAACC
*
459453 GGTTGAAAACC
1 GG-T-CAAACC
459464 GGTCAAACC
1 GGTCAAACC
459473 GGT
1 GGT
459476 TTCCAGCAGC
Statistics
Matches: 85, Mismatches: 11, Indels: 24
0.71 0.09 0.20
Matches are distributed among these distances:
6 2 0.02
7 3 0.04
8 2 0.02
9 32 0.38
10 27 0.32
11 19 0.22
ACGTcount: A:0.32, C:0.29, G:0.25, T:0.14
Consensus pattern (9 bp):
GGTCAAACC
Found at i:459456 original size:27 final size:28
Alignment explanation
Indices: 459389--459471 Score: 116
Period size: 27 Copynumber: 3.0 Consensus size: 28
459379 TTCGGACCGG
* *
459389 TCAAACCCGGTCG-AAACCGGTCAAACCA
1 TCAAAACCGGTTGAAAACCGGTCAAA-CA
459417 GTCAAAACCGGTTGAAAACCGGTCAAAC-
1 -TCAAAACCGGTTGAAAACCGGTCAAACA
459445 TCAAAACCGGTTGAAAACCGGTCAAAC
1 TCAAAACCGGTTGAAAACCGGTCAAAC
459472 CGGTTTCCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
27 27 0.53
29 12 0.24
30 12 0.24
ACGTcount: A:0.39, C:0.29, G:0.19, T:0.13
Consensus pattern (28 bp):
TCAAAACCGGTTGAAAACCGGTCAAACA
Found at i:459473 original size:20 final size:19
Alignment explanation
Indices: 459365--459476 Score: 72
Period size: 20 Copynumber: 5.8 Consensus size: 19
459355 GTCGGGTCAG
*
459365 ACCGGTCAAACCGGTTCG-G
1 ACCGGTCAAACCGGTT-GAA
*
459384 ACCGGTCAAACCCGGTCGAA
1 ACCGGTCAAA-CCGGTTGAA
* **
459404 ACCGGTCAAACCAGTCAAA
1 ACCGGTCAAACCGGTTGAA
* *
459423 ACCGGTTGAAAACCGG-TCAA
1 ACCGG-T-CAAACCGGTTGAA
459443 A-C--TCAAAACCGGTTGAAA
1 ACCGGTC-AAACCGGTTG-AA
459461 ACCGGTCAAACCGGTT
1 ACCGGTCAAACCGGTT
459477 TCCAGCAGCG
Statistics
Matches: 73, Mismatches: 10, Indels: 19
0.72 0.10 0.19
Matches are distributed among these distances:
16 8 0.11
17 1 0.01
18 3 0.04
19 25 0.34
20 28 0.38
21 8 0.11
ACGTcount: A:0.33, C:0.29, G:0.23, T:0.14
Consensus pattern (19 bp):
ACCGGTCAAACCGGTTGAA
Found at i:465942 original size:5 final size:5
Alignment explanation
Indices: 465929--465986 Score: 91
Period size: 5 Copynumber: 11.8 Consensus size: 5
465919 AACGGTCAAC
* *
465929 GGTCG GGTCA GGTCG GGTCG GGTCG GGTC- GGTAG GGTCG GGTCG GGTCG
1 GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG
465978 GGTCG GGTC
1 GGTCG GGTC
465987 AGACCGGTCA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
4 3 0.06
5 45 0.94
ACGTcount: A:0.03, C:0.19, G:0.57, T:0.21
Consensus pattern (5 bp):
GGTCG
Found at i:465960 original size:29 final size:29
Alignment explanation
Indices: 465928--465986 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
465918 CAACGGTCAA
*
465928 CGGTCGGGTCAGGTCGGGTCGGGTCGGGT
1 CGGTAGGGTCAGGTCGGGTCGGGTCGGGT
*
465957 CGGTAGGGTCGGGTCGGGTCGGGTCGGGT
1 CGGTAGGGTCAGGTCGGGTCGGGTCGGGT
465986 C
1 C
465987 AGACCGGTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.03, C:0.20, G:0.56, T:0.20
Consensus pattern (29 bp):
CGGTAGGGTCAGGTCGGGTCGGGTCGGGT
Found at i:465967 original size:19 final size:19
Alignment explanation
Indices: 465929--465978 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
465919 AACGGTCAAC
*
465929 GGTCGGGTCAGGTCGGGTCG
1 GGTCGGGTC-GGTAGGGTCG
465949 GGTCGGGTCGGTAGGGTCG
1 GGTCGGGTCGGTAGGGTCG
465968 GGTCGGGTCGG
1 GGTCGGGTCGG
465979 GTCGGGTCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 20 0.69
20 9 0.31
ACGTcount: A:0.04, C:0.18, G:0.58, T:0.20
Consensus pattern (19 bp):
GGTCGGGTCGGTAGGGTCG
Found at i:466001 original size:9 final size:9
Alignment explanation
Indices: 465983--466052 Score: 68
Period size: 10 Copynumber: 7.3 Consensus size: 9
465973 GGTCGGGTCG
*
465983 GGTCAGACC
1 GGTCAAACC
465992 GGTCAAACC
1 GGTCAAACC
**
466001 GGTTCGGACC
1 GG-TCAAACC
466011 GGTCAAACCC
1 GGTCAAA-CC
*
466021 GGTCGAAACT
1 GGTC-AAACC
466031 GGTCAAAACC
1 GGTC-AAACC
466041 GGTCAAACC
1 GGTCAAACC
466050 GGT
1 GGT
466053 TTCCAGCAGC
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
9 21 0.42
10 26 0.52
11 3 0.06
ACGTcount: A:0.27, C:0.30, G:0.29, T:0.14
Consensus pattern (9 bp):
GGTCAAACC
Found at i:467625 original size:31 final size:31
Alignment explanation
Indices: 467568--467654 Score: 79
Period size: 31 Copynumber: 2.8 Consensus size: 31
467558 TAAGGTGACC
*
467568 CTTGGGTAGGCTCCGAGGCCCCGAGATCTTT
1 CTTGGGTAGGCTCCGAGGCCCCGAGATATTT
* **
467599 CTTGGGTAGG-TCCTGCGGCCTTGAGATATTT
1 CTTGGGTAGGCTCC-GAGGCCCCGAGATATTT
* * *
467630 CCTAGGTAGGC-CTCGTGGCCCCGAG
1 CTTGGGTAGGCTC-CGAGGCCCCGAG
467655 TAACTATCTT
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
30 3 0.07
31 40 0.91
32 1 0.02
ACGTcount: A:0.13, C:0.28, G:0.33, T:0.26
Consensus pattern (31 bp):
CTTGGGTAGGCTCCGAGGCCCCGAGATATTT
Found at i:469059 original size:33 final size:33
Alignment explanation
Indices: 469021--469086 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
469011 ATGAATGAAG
*
469021 GATGAT-TTAATGGTGATGAAATGGTAATGGAAT
1 GATGATGTTAATGGCG-TGAAATGGTAATGGAAT
* * *
469054 GATGATGTTATTGGCGTGATATGGTGATGGAAT
1 GATGATGTTAATGGCGTGAAATGGTAATGGAAT
469087 ATGGTGATGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 21 0.75
34 7 0.25
ACGTcount: A:0.30, C:0.02, G:0.33, T:0.35
Consensus pattern (33 bp):
GATGATGTTAATGGCGTGAAATGGTAATGGAAT
Found at i:469090 original size:13 final size:12
Alignment explanation
Indices: 469071--469167 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
469061 TTATTGGCGT
469071 GATATGGTGATG
1 GATATGGTGATG
469083 GAATATGGTGAT-
1 G-ATATGGTGATG
*
469095 GATATAGGCG-T-
1 GATAT-GGTGATG
469106 GATAATGGTGATG
1 GAT-ATGGTGATG
469119 GACTATGGTGAT-
1 GA-TATGGTGATG
*
469131 GATATAGGCG-T-
1 GATAT-GGTGATG
*
469142 GATAATGGAGATG
1 GAT-ATGGTGATG
469155 GATTATGGTGATG
1 GA-TATGGTGATG
469168 AAAATAGTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
11 21 0.30
12 16 0.23
13 30 0.43
14 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:469126 original size:36 final size:35
Alignment explanation
Indices: 469040--469168 Score: 172
Period size: 36 Copynumber: 3.7 Consensus size: 35
469030 ATGGTGATGA
* * * *
469040 AATGGTAATGGA-ATGATGATGTTATTGGCGTGAT
1 AATGGTGATGGATATGGTGATGATATAGGCGTGAT
469074 -ATGGTGATGGAATATGGTGATGATATAGGCGTGAT
1 AATGGTGATGG-ATATGGTGATGATATAGGCGTGAT
469109 AATGGTGATGGACTATGGTGATGATATAGGCGTGAT
1 AATGGTGATGGA-TATGGTGATGATATAGGCGTGAT
*
469145 AATGGAGATGGATTATGGTGATGA
1 AATGGTGATGGA-TATGGTGATGA
469169 AAATAGTATC
Statistics
Matches: 85, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
33 9 0.11
34 1 0.01
35 20 0.24
36 55 0.65
ACGTcount: A:0.29, C:0.03, G:0.36, T:0.32
Consensus pattern (35 bp):
AATGGTGATGGATATGGTGATGATATAGGCGTGAT
Found at i:473490 original size:3 final size:3
Alignment explanation
Indices: 473476--473624 Score: 58
Period size: 3 Copynumber: 48.0 Consensus size: 3
473466 TATATATTAG
* * *
473476 TAA TATA TAA TAA TAAA TAC TAA TAA GAG TAA TAA TAA TAA TATA TAA
1 TAA TA-A TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
** *
473524 -AGA TAA TTC TAA T-G TAA -AA TAAA TAGA TAA TAA TAAA TAA TAA TAA
1 TA-A TAA TAA TAA TAA TAA TAA T-AA TA-A TAA TAA T-AA TAA TAA TAA
* * ** *
473570 -CA TAA -AA AAGA TAA TTT TAA T-G TAA TAAA TAGA TAA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA T-AA TA-A TAA TAA TAA TAA
473615 TAA GTAA TAA
1 TAA -TAA TAA
473625 AAGTAATTTG
Statistics
Matches: 108, Mismatches: 21, Indels: 34
0.66 0.13 0.21
Matches are distributed among these distances:
2 8 0.07
3 70 0.65
4 30 0.28
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:473499 original size:10 final size:10
Alignment explanation
Indices: 473476--473624 Score: 60
Period size: 10 Copynumber: 14.3 Consensus size: 10
473466 TATATATTAG
*
473476 TAATATATAA
1 TAATAAATAA
*
473486 TAATAAATAC
1 TAATAAATAA
473496 TAATAAGAGTAA
1 TAATAA-A-TAA
473508 TAAT-AATAA
1 TAATAAATAA
473517 TATATAAAGATAA
1 TA-AT-AA-ATAA
*
473530 TTCTAATGTAA-AA
1 ---TAAT-AAATAA
*
473543 TAAATAGATAA
1 T-AATAAATAA
473554 TAATAAATAA
1 TAATAAATAA
473564 TAATAACATAA
1 TAATAA-ATAA
473575 -AA-AAGATAA
1 TAATAA-ATAA
* * *
473584 T-TTTAAT-G
1 TAATAAATAA
473592 TAATAAATAGA
1 TAATAAATA-A
473603 TAAT-AATAA
1 TAATAAATAA
*
473612 TAATAAGTAA
1 TAATAAATAA
473622 TAA
1 TAA
473625 AAGTAATTTG
Statistics
Matches: 105, Mismatches: 16, Indels: 36
0.67 0.10 0.23
Matches are distributed among these distances:
8 1 0.01
9 22 0.21
10 47 0.45
11 16 0.15
12 7 0.07
13 6 0.06
14 1 0.01
15 3 0.03
16 2 0.02
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (10 bp):
TAATAAATAA
Found at i:475600 original size:39 final size:40
Alignment explanation
Indices: 475557--475650 Score: 113
Period size: 39 Copynumber: 2.4 Consensus size: 40
475547 GGTGTTTCAC
* * * * *
475557 GCGTCTTCAAGTCAAAT-ATGAAGACTCCATGACTGCATA
1 GCGTCTTCAAGACAAATAAAGAAGACCCCACGACTACATA
*
475596 GCGTCTTC-AGACAAATAAAGAATACCCCACGACTACATA
1 GCGTCTTCAAGACAAATAAAGAAGACCCCACGACTACATA
475635 GCGTCTTC-AGACAAAT
1 GCGTCTTCAAGACAAAT
475651 GGAGAAAACC
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
38 7 0.15
39 41 0.85
ACGTcount: A:0.36, C:0.26, G:0.16, T:0.22
Consensus pattern (40 bp):
GCGTCTTCAAGACAAATAAAGAAGACCCCACGACTACATA
Found at i:476505 original size:79 final size:79
Alignment explanation
Indices: 476414--476575 Score: 299
Period size: 79 Copynumber: 2.1 Consensus size: 79
476404 AGTTATATTT
476414 ATATATTTATTAAAGCTTTTC-TTTGATGATTTAATCTATCTTAATAATGATTTATAAAAGTAAC
1 ATATATTTATTAAAGCTTTTCATTT-ATGATTTAATCTATCTTAATAATGATTTATAAAAGTAAC
476478 TTGCTCGCACGAACA
65 TTGCTCGCACGAACA
*
476493 ATATATTTATTAAATCTTTTCATTTATGATTTAATCTATCTTAATAATGATTTATAAAAGTAACT
1 ATATATTTATTAAAGCTTTTCATTTATGATTTAATCTATCTTAATAATGATTTATAAAAGTAACT
476558 TGCTCGCACGAACA
66 TGCTCGCACGAACA
476572 ATAT
1 ATAT
476576 TTATTTAATA
Statistics
Matches: 81, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
79 78 0.96
80 3 0.04
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.43
Consensus pattern (79 bp):
ATATATTTATTAAAGCTTTTCATTTATGATTTAATCTATCTTAATAATGATTTATAAAAGTAACT
TGCTCGCACGAACA
Found at i:480119 original size:24 final size:24
Alignment explanation
Indices: 480106--480224 Score: 150
Period size: 24 Copynumber: 5.0 Consensus size: 24
480096 ATTTTCGATT
480106 TGAATTCTGATCTGATACTTGACA
1 TGAATTCTGATCTGATACTTGACA
480130 TGAATTCTGATCTGATA-TCTGACA
1 TGAATTCTGATCTGATACT-TGACA
* * *
480154 TGGATTATGATCTGATACTTGACT
1 TGAATTCTGATCTGATACTTGACA
* * *
480178 TGGATTCTGATCTGTTACTTGACC
1 TGAATTCTGATCTGATACTTGACA
* *
480202 TGATTTCTGATATGATACTTGAC
1 TGAATTCTGATCTGATACTTGAC
480225 TTGATTTATG
Statistics
Matches: 83, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
23 1 0.01
24 81 0.98
25 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.40
Consensus pattern (24 bp):
TGAATTCTGATCTGATACTTGACA
Found at i:486046 original size:49 final size:50
Alignment explanation
Indices: 485991--486095 Score: 131
Period size: 50 Copynumber: 2.1 Consensus size: 50
485981 ATCTAAGCCC
* * * *
485991 AAGTAAATTAGAACAC-AAAATTTAGGATGAATAGATAAAACCTAATAAT
1 AAGTAAATTAAAACACTAAAATTTAGGATAAACAAATAAAACCTAATAAT
* * **
486040 AAGTAAATTAAAACACTAGAATTTAGGATAAACAAATGAAACCTAATCCT
1 AAGTAAATTAAAACACTAAAATTTAGGATAAACAAATAAAACCTAATAAT
486090 AAGTAA
1 AAGTAA
486096 TTTTTTTTGG
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
49 15 0.32
50 32 0.68
ACGTcount: A:0.54, C:0.10, G:0.11, T:0.24
Consensus pattern (50 bp):
AAGTAAATTAAAACACTAAAATTTAGGATAAACAAATAAAACCTAATAAT
Found at i:486118 original size:74 final size:70
Alignment explanation
Indices: 486033--486177 Score: 245
Period size: 74 Copynumber: 2.0 Consensus size: 70
486023 AGATAAAACC
486033 TAATAATAAGTAAATTAAAACACTAGAATTTAGGATAAACAAATGAAACCTAATCCTAAGTAATT
1 TAATAATAAGTAAATTAAAACACTAGAATTTAGGAT----AAATGAAACCTAATCCTAAGTAATT
*
486098 TTTTTTGGA
62 CTTTTTGGA
486107 TAATAATAAGTAAATTAAAACACTAGAATTTAGGATAAATGAAACCTAATCCTAAGTAATTCTTT
1 TAATAATAAGTAAATTAAAACACTAGAATTTAGGATAAATGAAACCTAATCCTAAGTAATTCTTT
486172 TTGGA
66 TTGGA
486177 T
1 T
486178 TAAGCTAATG
Statistics
Matches: 70, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
70 34 0.49
74 36 0.51
ACGTcount: A:0.46, C:0.10, G:0.11, T:0.33
Consensus pattern (70 bp):
TAATAATAAGTAAATTAAAACACTAGAATTTAGGATAAATGAAACCTAATCCTAAGTAATTCTTT
TTGGA
Found at i:488515 original size:128 final size:127
Alignment explanation
Indices: 488368--488668 Score: 442
Period size: 128 Copynumber: 2.3 Consensus size: 127
488358 AGATATTCAT
* * * *
488368 TTATTTAGAAATATCAGAAAATGG-CTTCTAGGTGCTTTAAGACAGCTCTTTTCTCAATATTAAA
1 TTATTTA-AAATATCAGAAAATGGACATCCAGTTGCTTTAAGACAGC-CCTTTCTCAATATTAAA
* * *
488432 AAATATATAAATATTAATAAAACATTTATCTAAAAATAATTAAAATATATATAATGTAAAATAC
64 AAATAAATAAATATGAATAAAACATTTATCTAAAAATAATTAAAATATATATAATGGAAAATAC
* * * *
488496 TTATTTAAAATTATAAGAAAATGGACATCCAGTTGCTTTAAGACTGCCCTTTCTTAATATTGAAA
1 TTATTTAAAA-TATCAGAAAATGGACATCCAGTTGCTTTAAGACAGCCCTTTCTCAATATTAAAA
*
488561 AATAAATAAATATGAATAAAACATTTATCTAAAATTAATTAAAATATATATAATGGAAAATAC
65 AATAAATAAATATGAATAAAACATTTATCTAAAAATAATTAAAATATATATAATGGAAAATAC
*
488624 TTATTTAAAAATATCATAAAATGGACATCCAGTTGCTTTAAGACA
1 TTATTT-AAAATATCAGAAAATGGACATCCAGTTGCTTTAAGACA
488669 ATGATTTCTG
Statistics
Matches: 155, Mismatches: 15, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
127 3 0.02
128 130 0.84
129 22 0.14
ACGTcount: A:0.47, C:0.10, G:0.09, T:0.35
Consensus pattern (127 bp):
TTATTTAAAATATCAGAAAATGGACATCCAGTTGCTTTAAGACAGCCCTTTCTCAATATTAAAAA
ATAAATAAATATGAATAAAACATTTATCTAAAAATAATTAAAATATATATAATGGAAAATAC
Found at i:488915 original size:3 final size:3
Alignment explanation
Indices: 488907--488990 Score: 98
Period size: 3 Copynumber: 28.0 Consensus size: 3
488897 GCATGTTTTG
* * * *
488907 TAA TAA TAA TATT TAT TAT TAA TAA TAA TAA AAA T-A TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
488952 TAA TAA TAA TAA TAA CAA TTA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
488991 ACGGGTAAAA
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
2 2 0.03
3 67 0.94
4 2 0.03
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:489664 original size:116 final size:112
Alignment explanation
Indices: 489327--489766 Score: 449
Period size: 116 Copynumber: 3.8 Consensus size: 112
489317 GAATTAAGGC
* * * * *
489327 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTT-TTCCTTCTTTATATGAGTTTTTCTCATT
1 AAGGTTGAACAAGTTCTTCTCATTATGAATTTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * **
489391 ATGAACACTTCTGGAAAATTTGATGTTGATCTATCTCCTTCTGTGATAGAATCAAGCAA
66 ATGAACTCTTCTGG--AA----ATGTTGATCCA--T-C--AAGTGAT-GAATCAAGCAA
* * * * * *
489450 AAGGTTAAACAAGCTCTTCTCATTATGAA-CTTCTTCTTCC-TCTTTAGATAAGTTCTTCTCATT
1 AAGGTTGAACAAGTTCTTCTCATTATGAATTTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
489513 ATGAACTTTTTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAGCAA
66 ATGAAC-TCTTCTGGAAATGTTGATCCATCAAGTGATGAA-TCAAGCAA
* *
489562 AAGGTTGAACAAATTCTTTTCATTATGAATTTTTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 AAGGTTGAACAAGTTCTTCTCATTATGAA--TTTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * *
489627 TTATGAACTCTACCTGGCAATGTTGATCCATCAAGTGATGAACTCGAGCAA
64 TTATGAACTCT-TCTGGAAATGTTGATCCATCAAGTGATGAA-TCAAGCAA
* *
489678 AAGGTTGAACAAGTTCTTCTCATTATGAA-CTTCTTC-TCTCTTCTTCAGATGAGTTCTTCTCAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAATTTTTTTCTTC-CTTCTTCAGATGAGTTCTTCTCAT
489741 TATGAACTCTTCTGGAAATGTTGATC
65 TATGAACTCTTCTGGAAATGTTGATC
489767 AATTGAGTGA
Statistics
Matches: 273, Mismatches: 35, Indels: 29
0.81 0.10 0.09
Matches are distributed among these distances:
111 3 0.01
112 54 0.20
113 39 0.14
114 1 0.00
115 12 0.04
116 87 0.32
117 9 0.03
121 2 0.01
122 29 0.11
123 37 0.14
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (112 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAATTTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTCTTCTGGAAATGTTGATCCATCAAGTGATGAATCAAGCAA
Found at i:491291 original size:20 final size:20
Alignment explanation
Indices: 491266--491317 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
491256 ATATCATCAT
491266 TTTTTTCTTT-TTATTATTTC
1 TTTTTTCTTTCTT-TTATTTC
*
491286 TTTTTTCTTTCTTTTCTTTC
1 TTTTTTCTTTCTTTTATTTC
491306 TTTTTT-TTTCTT
1 TTTTTTCTTTCTT
491318 CTTCAAGCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 6 0.20
20 22 0.73
21 2 0.07
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (20 bp):
TTTTTTCTTTCTTTTATTTC
Found at i:491305 original size:13 final size:12
Alignment explanation
Indices: 491265--491320 Score: 53
Period size: 13 Copynumber: 4.6 Consensus size: 12
491255 TATATCATCA
491265 TTTT-TTTCTTT
1 TTTTCTTTCTTT
*
491276 TTATTATTTC-TT
1 TT-TTCTTTCTTT
491288 TTTTCTTTCTTT
1 TTTTCTTTCTTT
*
491300 TCTTTCTTTTTTT
1 T-TTTCTTTCTTT
491313 TTCTTCTT
1 TT-TTCTT
491321 CAAGCAAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
11 8 0.21
12 10 0.26
13 20 0.53
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTCTTTCTTT
Found at i:499821 original size:24 final size:24
Alignment explanation
Indices: 499794--499865 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 24
499784 GTAAACGGAG
*
499794 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* *
499818 ATATCAGACATCAGAACAGAATCC
1 ATATCAGAAATCAGAACAGAATTC
* *
499842 AGATCATAAATCAGAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
499866 GGGTAATGTA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.50, C:0.19, G:0.11, T:0.19
Consensus pattern (24 bp):
ATATCAGAAATCAGAACAGAATTC
Found at i:499902 original size:24 final size:24
Alignment explanation
Indices: 499797--499904 Score: 87
Period size: 24 Copynumber: 4.5 Consensus size: 24
499787 AACGGAGATA
*
499797 TCAGAAATCAAAACAGAATTCATA-
1 TCAGAAATCAGAACAGAATTCA-AG
* *
499821 TCAGACATCAGAACAGAA-TCCAG
1 TCAGAAATCAGAACAGAATTCAAG
* **
499844 ATCATAAATCAGAACAGAATTCGGG
1 -TCAGAAATCAGAACAGAATTCAAG
* * *
499869 TAATG-TATCATAACAGAATTCAAG
1 TCA-GAAATCAGAACAGAATTCAAG
499893 TCAGAAATCAGA
1 TCAGAAATCAGA
499905 TAAAATATTT
Statistics
Matches: 63, Mismatches: 16, Indels: 10
0.71 0.18 0.11
Matches are distributed among these distances:
22 1 0.02
23 3 0.05
24 56 0.89
25 3 0.05
ACGTcount: A:0.47, C:0.18, G:0.15, T:0.20
Consensus pattern (24 bp):
TCAGAAATCAGAACAGAATTCAAG
Found at i:502409 original size:18 final size:18
Alignment explanation
Indices: 502387--502428 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
502377 GGGGATAACT
502387 GGTCGGGTAGGGTCAACG
1 GGTCGGGTAGGGTCAACG
* *
502405 TGTCGGGTCGGGTCAACG
1 GGTCGGGTAGGGTCAACG
502423 GGTCGG
1 GGTCGG
502429 ATCGGGTTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.12, C:0.19, G:0.50, T:0.19
Consensus pattern (18 bp):
GGTCGGGTAGGGTCAACG
Found at i:502433 original size:18 final size:18
Alignment explanation
Indices: 502396--502435 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
502386 TGGTCGGGTA
* *
502396 GGGTCAACGTGTCGGGTC
1 GGGTCAACGGGTCGGATC
502414 GGGTCAACGGGTCGGATC
1 GGGTCAACGGGTCGGATC
502432 GGGT
1 GGGT
502436 TGTGACCGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.12, C:0.20, G:0.47, T:0.20
Consensus pattern (18 bp):
GGGTCAACGGGTCGGATC
Found at i:503628 original size:77 final size:75
Alignment explanation
Indices: 503467--503628 Score: 279
Period size: 77 Copynumber: 2.1 Consensus size: 75
503457 TTATATTTAT
503467 ATATTTATTAAAGCTTTTCATTGATGATTAATCTATCTTAATAATGATTTATAAAAGTAACTTGC
1 ATATTTATTAAAGCTTTTCATTGATGATTAATCTATCTTAATAATGATTTATAAAAGTAACTTGC
503532 TCGCACGAAC
66 TCGCACGAAC
* *
503542 ATATATTATTAAATCTTTTCATTTATGATTTAATCTATCTTAATAATGATTTATAAAAGTAACTT
1 ATAT-TTATTAAAGCTTTTCATTGATGA-TTAATCTATCTTAATAATGATTTATAAAAGTAACTT
503607 GCTCGCACGAAC
64 GCTCGCACGAAC
503619 AATATTTATT
1 -ATATTTATT
503629 TAATATTAAA
Statistics
Matches: 82, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
75 4 0.05
76 21 0.26
77 53 0.65
78 4 0.05
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.43
Consensus pattern (75 bp):
ATATTTATTAAAGCTTTTCATTGATGATTAATCTATCTTAATAATGATTTATAAAAGTAACTTGC
TCGCACGAAC
Found at i:505425 original size:18 final size:18
Alignment explanation
Indices: 505398--505440 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
505388 CAACGGTCAA
*
505398 CGGGTCAACGGGTCGGGT
1 CGGGTTAACGGGTCGGGT
505416 CGGGTTAACGGGTCGGGT
1 CGGGTTAACGGGTCGGGT
505434 CGGGTTA
1 CGGGTTA
505441 TGACCGGTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.12, C:0.19, G:0.49, T:0.21
Consensus pattern (18 bp):
CGGGTTAACGGGTCGGGT
Found at i:511433 original size:73 final size:74
Alignment explanation
Indices: 511304--511523 Score: 392
Period size: 73 Copynumber: 3.0 Consensus size: 74
511294 AGATAAAACC
*
511304 TAATAATAAGTAAATTAAAACACTAGATTTTAGGATAAAC-AACGAAACCTAATCCTAAGTAATT
1 TAATAATAAGTAAATTAAAACACTAGAATTTAGGATAAACAAACGAAACCTAATCCTAAGTAATT
511368 TTTTTTGGA
66 TTTTTTGGA
511377 TAATAAT-AGTAAATTAAAACACTAGAATTTAGGATAAACAAACGAAACCTAATCCTAAGTAA-T
1 TAATAATAAGTAAATTAAAACACTAGAATTTAGGATAAACAAACGAAACCTAATCCTAAGTAATT
511440 TTTTTTGGA
66 TTTTTTGGA
*
511449 TAATAATAAGTAAATTAAAACACTAGAATTTAGGATAAACAAATGAAACCTAATCCTAAGTAATT
1 TAATAATAAGTAAATTAAAACACTAGAATTTAGGATAAACAAACGAAACCTAATCCTAAGTAATT
*
511514 CTTTTTGGA
66 TTTTTTGGA
511523 T
1 T
511524 TAAACTAATG
Statistics
Matches: 141, Mismatches: 3, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
72 48 0.34
73 83 0.59
74 10 0.07
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (74 bp):
TAATAATAAGTAAATTAAAACACTAGAATTTAGGATAAACAAACGAAACCTAATCCTAAGTAATT
TTTTTTGGA
Found at i:511450 original size:38 final size:38
Alignment explanation
Indices: 511331--511451 Score: 89
Period size: 38 Copynumber: 3.3 Consensus size: 38
511321 AAACACTAGA
511331 TTTTAGGATAAAC-AACGAAACCTAATCCTAAGTAATTT
1 TTTTAGGATAAACAAACGAAACCTAATCCTAAGTAA-TT
* * * *
511369 TTTTTGGATAATA-ATA-GTAAA-TTAAAACACT-AG-AA--
1 TTTTAGGATAA-ACAAACG-AAACCT-AATC-CTAAGTAATT
511404 -TTTAGGATAAACAAACGAAACCTAATCCTAAGTAATT
1 TTTTAGGATAAACAAACGAAACCTAATCCTAAGTAATT
*
511441 TTTTTGGATAA
1 TTTTAGGATAA
511452 TAATAAGTAA
Statistics
Matches: 61, Mismatches: 9, Indels: 26
0.64 0.09 0.27
Matches are distributed among these distances:
33 3 0.05
34 19 0.31
35 4 0.07
38 23 0.38
39 10 0.16
40 2 0.03
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.33
Consensus pattern (38 bp):
TTTTAGGATAAACAAACGAAACCTAATCCTAAGTAATT
Found at i:515159 original size:79 final size:79
Alignment explanation
Indices: 515028--515189 Score: 306
Period size: 79 Copynumber: 2.1 Consensus size: 79
515018 AGTTATATTT
515028 ATATATTTATTAAAGCTTTTCATTGATGATTTAATCTATCTTAATAATGATTTATAAAAGTAACT
1 ATATATTTATTAAAGCTTTTCATTGATGATTTAATCTATCTTAATAATGATTTATAAAAGTAACT
515093 TGCTCGCACGAACA
66 TGCTCGCACGAACA
* *
515107 ATATATTTATTAAATCTTTTCATTTATGATTTAATCTATCTTAATAATGATTTATAAAAGTAACT
1 ATATATTTATTAAAGCTTTTCATTGATGATTTAATCTATCTTAATAATGATTTATAAAAGTAACT
515172 TGCTCGCACGAACA
66 TGCTCGCACGAACA
515186 ATAT
1 ATAT
515190 TTATTTAATA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
79 81 1.00
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.42
Consensus pattern (79 bp):
ATATATTTATTAAAGCTTTTCATTGATGATTTAATCTATCTTAATAATGATTTATAAAAGTAACT
TGCTCGCACGAACA
Found at i:517075 original size:18 final size:18
Alignment explanation
Indices: 517048--517090 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
517038 CAACGGTCAA
*
517048 CGGGTCAACGGGTCGGGT
1 CGGGTTAACGGGTCGGGT
517066 CGGGTTAACGGGTCGGGT
1 CGGGTTAACGGGTCGGGT
517084 CGGGTTA
1 CGGGTTA
517091 TGACCGGTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.12, C:0.19, G:0.49, T:0.21
Consensus pattern (18 bp):
CGGGTTAACGGGTCGGGT
Found at i:523051 original size:39 final size:39
Alignment explanation
Indices: 523002--523125 Score: 104
Period size: 39 Copynumber: 3.3 Consensus size: 39
522992 AAACACTAGA
523002 TTTTAGGATAAACAAACGAAACCTAATCCTAAGTAATTT
1 TTTTAGGATAAACAAACGAAACCTAATCCTAAGTAATTT
* * *
523041 TTTTTGGATAATA-ATAA-GTAAA-TTAAAACACT-AG-AA---
1 TTTTAGGATAA-ACA-AACG-AAACCT-AATC-CTAAGTAATTT
523077 -TTTAGGATAAACAAACGAAACCTAATCCTAAGTAATTT
1 TTTTAGGATAAACAAACGAAACCTAATCCTAAGTAATTT
*
523115 TTTTTGGATAA
1 TTTTAGGATAA
523126 TAATAAGTAA
Statistics
Matches: 64, Mismatches: 7, Indels: 28
0.65 0.07 0.28
Matches are distributed among these distances:
33 2 0.03
34 11 0.17
35 14 0.22
39 24 0.38
40 11 0.17
41 2 0.03
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (39 bp):
TTTTAGGATAAACAAACGAAACCTAATCCTAAGTAATTT
Found at i:523060 original size:74 final size:74
Alignment explanation
Indices: 522975--523197 Score: 419
Period size: 74 Copynumber: 3.0 Consensus size: 74
522965 AGATAAAACC
*
522975 TAATAATAAGTAAATTAAAACACTAGATTTTAGGATAAACAAACGAAACCTAATCCTAAGTAATT
1 TAATAATAAGTAAATTAAAACACTAGAATTTAGGATAAACAAACGAAACCTAATCCTAAGTAATT
523040 TTTTTTGGA
66 TTTTTTGGA
523049 TAATAATAAGTAAATTAAAACACTAGAATTTAGGATAAACAAACGAAACCTAATCCTAAGTAATT
1 TAATAATAAGTAAATTAAAACACTAGAATTTAGGATAAACAAACGAAACCTAATCCTAAGTAATT
523114 TTTTTTGGA
66 TTTTTTGGA
*
523123 TAATAATAAGTAAATTAAAACACTAGAATTTAGGATAAACAAATGAAACCTAATCCTAAGTAATT
1 TAATAATAAGTAAATTAAAACACTAGAATTTAGGATAAACAAACGAAACCTAATCCTAAGTAATT
*
523188 CTTTTTGGA
66 TTTTTTGGA
523197 T
1 T
523198 TAAACTAATG
Statistics
Matches: 146, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
74 146 1.00
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.32
Consensus pattern (74 bp):
TAATAATAAGTAAATTAAAACACTAGAATTTAGGATAAACAAACGAAACCTAATCCTAAGTAATT
TTTTTTGGA
Found at i:523114 original size:35 final size:35
Alignment explanation
Indices: 523003--523114 Score: 81
Period size: 35 Copynumber: 3.1 Consensus size: 35
522993 AACACTAGAT
523003 TTTAGGATAAACAAACGAAACCTAATCCTAAGTAA
1 TTTAGGATAAACAAACGAAACCTAATCCTAAGTAA
* * *
523038 TTTTTTTTGGATAATA-ATAA-GTAAA-TTAAAACACT-AG-AA
1 ----TTTAGGATAA-ACA-AACG-AAACCT-AATC-CTAAGTAA
523077 TTTAGGATAAACAAACGAAACCTAATCCTAAGTAA
1 TTTAGGATAAACAAACGAAACCTAATCCTAAGTAA
523112 TTT
1 TTT
523115 TTTTTGGATA
Statistics
Matches: 57, Mismatches: 6, Indels: 24
0.66 0.07 0.28
Matches are distributed among these distances:
33 2 0.04
34 11 0.19
35 17 0.30
39 14 0.25
40 11 0.19
41 2 0.04
ACGTcount: A:0.46, C:0.12, G:0.11, T:0.30
Consensus pattern (35 bp):
TTTAGGATAAACAAACGAAACCTAATCCTAAGTAA
Found at i:523153 original size:39 final size:39
Alignment explanation
Indices: 523036--523153 Score: 101
Period size: 39 Copynumber: 3.1 Consensus size: 39
523026 AATCCTAAGT
523036 AATTTTTTTTGGATAATAATAAGTAAATTAAAACACTAG
1 AATTTTTTTTGGATAATAATAAGTAAATTAAAACACTAG
* * *
523075 AA----TTTAGGATAA-ACA-AACG-AAACCT-AATC-CTAAG
1 AATTTTTTTTGGATAATA-ATAA-GTAAA-TTAAAACACT-AG
523109 TAATTTTTTTTGGATAATAATAAGTAAATTAAAACACTAG
1 -AATTTTTTTTGGATAATAATAAGTAAATTAAAACACTAG
523149 AATTT
1 AATTT
523154 AGGATAAACA
Statistics
Matches: 59, Mismatches: 6, Indels: 28
0.63 0.06 0.30
Matches are distributed among these distances:
33 2 0.03
34 11 0.19
35 14 0.24
39 19 0.32
40 11 0.19
41 2 0.03
ACGTcount: A:0.47, C:0.08, G:0.10, T:0.35
Consensus pattern (39 bp):
AATTTTTTTTGGATAATAATAAGTAAATTAAAACACTAG
Found at i:526838 original size:79 final size:79
Alignment explanation
Indices: 526707--526868 Score: 306
Period size: 79 Copynumber: 2.1 Consensus size: 79
526697 AGTTATATTT
526707 ATATATTTATTAAAGCTTTTCATTGATGATTTAATCTATCTTAATAATGATTTATAAAAGTAACT
1 ATATATTTATTAAAGCTTTTCATTGATGATTTAATCTATCTTAATAATGATTTATAAAAGTAACT
526772 TGCTCGCACGAACA
66 TGCTCGCACGAACA
* *
526786 ATATATTTATTAAATCTTTTCATTTATGATTTAATCTATCTTAATAATGATTTATAAAAGTAACT
1 ATATATTTATTAAAGCTTTTCATTGATGATTTAATCTATCTTAATAATGATTTATAAAAGTAACT
526851 TGCTCGCACGAACA
66 TGCTCGCACGAACA
526865 ATAT
1 ATAT
526869 TTATTTAATA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
79 81 1.00
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.42
Consensus pattern (79 bp):
ATATATTTATTAAAGCTTTTCATTGATGATTTAATCTATCTTAATAATGATTTATAAAAGTAACT
TGCTCGCACGAACA
Found at i:529877 original size:10 final size:11
Alignment explanation
Indices: 529848--529878 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
529838 ACAAAAATGT
529848 ATAAAAGATAA
1 ATAAAAGATAA
529859 ATAAAAGATAA
1 ATAAAAGATAA
529870 AT-AAAGATA
1 ATAAAAGATA
529879 TAAAGAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.35
11 13 0.65
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (11 bp):
ATAAAAGATAA
Found at i:532140 original size:50 final size:49
Alignment explanation
Indices: 532046--532150 Score: 122
Period size: 50 Copynumber: 2.1 Consensus size: 49
532036 ATCTAATCCC
* * * *
532046 AAGTAAATTAGAACACAAAATTTAGGATGAATAGATAAAGCCTAATAAT
1 AAGTAAATTAAAACACAAAATTTAGGATAAACAAATAAAGCCTAATAAT
* **
532095 AAGTAAATTAAAACACTAGAATTTAGGATAAACAAATGAAA-CCTAATCCT
1 AAGTAAATTAAAACAC-AAAATTTAGGATAAACAAAT-AAAGCCTAATAAT
532145 AAGTAA
1 AAGTAA
532151 TTCTTTTTGG
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
49 15 0.32
50 29 0.62
51 3 0.06
ACGTcount: A:0.53, C:0.10, G:0.12, T:0.24
Consensus pattern (49 bp):
AAGTAAATTAAAACACAAAATTTAGGATAAACAAATAAAGCCTAATAAT
Found at i:549502 original size:18 final size:18
Alignment explanation
Indices: 549475--549517 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
549465 CAACGGTCAA
*
549475 CGGGTCAACGGGTCGGGT
1 CGGGTTAACGGGTCGGGT
549493 CGGGTTAACGGGTCGGGT
1 CGGGTTAACGGGTCGGGT
549511 CGGGTTA
1 CGGGTTA
549518 TGACCGGTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.12, C:0.19, G:0.49, T:0.21
Consensus pattern (18 bp):
CGGGTTAACGGGTCGGGT
Found at i:555475 original size:39 final size:39
Alignment explanation
Indices: 555426--555549 Score: 104
Period size: 39 Copynumber: 3.3 Consensus size: 39
555416 AAACACTAGA
555426 TTTTAGGATAAACAAACGAAACCTAATCCTAAGTAATTT
1 TTTTAGGATAAACAAACGAAACCTAATCCTAAGTAATTT
* * *
555465 TTTTTGGATAATA-ATAA-GTAAA-TTAAAACACT-AG-AA---
1 TTTTAGGATAA-ACA-AACG-AAACCT-AATC-CTAAGTAATTT
555501 -TTTAGGATAAACAAACGAAACCTAATCCTAAGTAATTT
1 TTTTAGGATAAACAAACGAAACCTAATCCTAAGTAATTT
*
555539 TTTTTGGATAA
1 TTTTAGGATAA
555550 TAATAAGTAA
Statistics
Matches: 64, Mismatches: 7, Indels: 28
0.65 0.07 0.28
Matches are distributed among these distances:
33 2 0.03
34 11 0.17
35 14 0.22
39 24 0.38
40 11 0.17
41 2 0.03
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (39 bp):
TTTTAGGATAAACAAACGAAACCTAATCCTAAGTAATTT
Found at i:555484 original size:74 final size:74
Alignment explanation
Indices: 555399--555620 Score: 410
Period size: 74 Copynumber: 3.0 Consensus size: 74
555389 AGATAAAACC
*
555399 TAATAATAAGTAAATTAAAACACTAGATTTTAGGATAAACAAACGAAACCTAATCCTAAGTAATT
1 TAATAATAAGTAAATTAAAACACTAGAATTTAGGATAAACAAACGAAACCTAATCCTAAGTAATT
555464 TTTTTTGGA
66 TTTTTTGGA
555473 TAATAATAAGTAAATTAAAACACTAGAATTTAGGATAAACAAACGAAACCTAATCCTAAGTAATT
1 TAATAATAAGTAAATTAAAACACTAGAATTTAGGATAAACAAACGAAACCTAATCCTAAGTAATT
555538 TTTTTTGGA
66 TTTTTTGGA
*
555547 TAATAATAAGTAAATTAAAACACTAGAATTTAGGATAAACAAATGAAACCTAATCCTAAGTAA-T
1 TAATAATAAGTAAATTAAAACACTAGAATTTAGGATAAACAAACGAAACCTAATCCTAAGTAATT
*
555611 TCTTTTGGA
66 TTTTTTGGA
555620 T
1 T
555621 TAAACTAATG
Statistics
Matches: 145, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
73 10 0.07
74 135 0.93
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.32
Consensus pattern (74 bp):
TAATAATAAGTAAATTAAAACACTAGAATTTAGGATAAACAAACGAAACCTAATCCTAAGTAATT
TTTTTTGGA
Found at i:555538 original size:35 final size:35
Alignment explanation
Indices: 555427--555538 Score: 81
Period size: 35 Copynumber: 3.1 Consensus size: 35
555417 AACACTAGAT
555427 TTTAGGATAAACAAACGAAACCTAATCCTAAGTAA
1 TTTAGGATAAACAAACGAAACCTAATCCTAAGTAA
* * *
555462 TTTTTTTTGGATAATA-ATAA-GTAAA-TTAAAACACT-AG-AA
1 ----TTTAGGATAA-ACA-AACG-AAACCT-AATC-CTAAGTAA
555501 TTTAGGATAAACAAACGAAACCTAATCCTAAGTAA
1 TTTAGGATAAACAAACGAAACCTAATCCTAAGTAA
555536 TTT
1 TTT
555539 TTTTTGGATA
Statistics
Matches: 57, Mismatches: 6, Indels: 24
0.66 0.07 0.28
Matches are distributed among these distances:
33 2 0.04
34 11 0.19
35 17 0.30
39 14 0.25
40 11 0.19
41 2 0.04
ACGTcount: A:0.46, C:0.12, G:0.11, T:0.30
Consensus pattern (35 bp):
TTTAGGATAAACAAACGAAACCTAATCCTAAGTAA
Found at i:555577 original size:39 final size:39
Alignment explanation
Indices: 555460--555577 Score: 101
Period size: 39 Copynumber: 3.1 Consensus size: 39
555450 AATCCTAAGT
555460 AATTTTTTTTGGATAATAATAAGTAAATTAAAACACTAG
1 AATTTTTTTTGGATAATAATAAGTAAATTAAAACACTAG
* * *
555499 AA----TTTAGGATAA-ACA-AACG-AAACCT-AATC-CTAAG
1 AATTTTTTTTGGATAATA-ATAA-GTAAA-TTAAAACACT-AG
555533 TAATTTTTTTTGGATAATAATAAGTAAATTAAAACACTAG
1 -AATTTTTTTTGGATAATAATAAGTAAATTAAAACACTAG
555573 AATTT
1 AATTT
555578 AGGATAAACA
Statistics
Matches: 59, Mismatches: 6, Indels: 28
0.63 0.06 0.30
Matches are distributed among these distances:
33 2 0.03
34 11 0.19
35 14 0.24
39 19 0.32
40 11 0.19
41 2 0.03
ACGTcount: A:0.47, C:0.08, G:0.10, T:0.35
Consensus pattern (39 bp):
AATTTTTTTTGGATAATAATAAGTAAATTAAAACACTAG
Found at i:559236 original size:79 final size:79
Alignment explanation
Indices: 559125--559285 Score: 304
Period size: 79 Copynumber: 2.0 Consensus size: 79
559115 GAGTTATATT
559125 TATATTTATTAAAGCTTTTCATTGATGATTTAATCTATCTTAATAATGATTTATAAAAGTAACTT
1 TATATTTATTAAAGCTTTTCATTGATGATTTAATCTATCTTAATAATGATTTATAAAAGTAACTT
559190 GCTCGCACGAACAA
66 GCTCGCACGAACAA
* *
559204 TATATTTATTAAATCTTTTCATTTATGATTTAATCTATCTTAATAATGATTTATAAAAGTAACTT
1 TATATTTATTAAAGCTTTTCATTGATGATTTAATCTATCTTAATAATGATTTATAAAAGTAACTT
559269 GCTCGCACGAACAA
66 GCTCGCACGAACAA
559283 TAT
1 TAT
559286 TTATTTAATA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
79 80 1.00
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.42
Consensus pattern (79 bp):
TATATTTATTAAAGCTTTTCATTGATGATTTAATCTATCTTAATAATGATTTATAAAAGTAACTT
GCTCGCACGAACAA
Found at i:563964 original size:15 final size:15
Alignment explanation
Indices: 563944--563972 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
563934 TCCGTTGATA
563944 AACGGAGATATCAGC
1 AACGGAGATATCAGC
563959 AACGGAGATATCAG
1 AACGGAGATATCAG
563973 AAATCAAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.17, G:0.28, T:0.14
Consensus pattern (15 bp):
AACGGAGATATCAGC
Found at i:563993 original size:24 final size:24
Alignment explanation
Indices: 563968--564074 Score: 97
Period size: 24 Copynumber: 4.5 Consensus size: 24
563958 CAACGGAGAT
* *
563968 ATCAGAAATCAAAACATAATTCAT
1 ATCAGAAATCAAAACAGAATTCAG
* * *
563992 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
564016 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** *
564040 ATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
564064 ATCAGAAATCA
1 ATCAGAAATCA
564075 GATAAAATAT
Statistics
Matches: 62, Mismatches: 21, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
24 62 1.00
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:564074 original size:48 final size:48
Alignment explanation
Indices: 563968--564076 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
563958 CAACGGAGAT
* * * * *
563968 ATCAGAAATCAAAACATAATTCATATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
564016 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
564064 ATCAGAAATCAGA
1 ATCAGAAATCAGA
564077 TAAAATATTC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:566049 original size:13 final size:13
Alignment explanation
Indices: 566029--566071 Score: 70
Period size: 13 Copynumber: 3.3 Consensus size: 13
566019 GCCGGTCAAC
566029 GGTCAACGGGTC-
1 GGTCAACGGGTCA
566041 GGTTCAACGGGTCA
1 GG-TCAACGGGTCA
566055 GGTCAACGGGTCA
1 GGTCAACGGGTCA
566068 GGTC
1 GGTC
566072 GGGTTGTGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 2 0.07
13 25 0.86
14 2 0.07
ACGTcount: A:0.19, C:0.23, G:0.40, T:0.19
Consensus pattern (13 bp):
GGTCAACGGGTCA
Found at i:573704 original size:22 final size:21
Alignment explanation
Indices: 573659--573704 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
573649 CTGATTGTTA
*
573659 ACTTTGACCAATCAACTGTTG
1 ACTTTGACCAATCAACCGTTG
**
573680 ACTTTGACCGGTCATACCGTTG
1 ACTTTGACCAATCA-ACCGTTG
573702 ACT
1 ACT
573705 GACAGTTAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (21 bp):
ACTTTGACCAATCAACCGTTG
Found at i:575985 original size:6 final size:6
Alignment explanation
Indices: 575974--575999 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
575964 TTGTGTCTTC
575974 TTTATT TTTATT TTTATT TTTATT TT
1 TTTATT TTTATT TTTATT TTTATT TT
576000 CTCAAATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:576688 original size:21 final size:22
Alignment explanation
Indices: 576654--576694 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
576644 TTGAAAATAT
* *
576654 TAAAAAATATTAATATTTTAGA
1 TAAAAAATAATAATACTTTAGA
576676 TAAAAAA-AATAATACTTTA
1 TAAAAAATAATAATACTTTA
576695 AGAAATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (22 bp):
TAAAAAATAATAATACTTTAGA
Found at i:578011 original size:20 final size:20
Alignment explanation
Indices: 577967--578004 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
577957 ATGCTACAAA
*
577967 GTCAATGGTTAACGGTGGCG
1 GTCAATGGTTAACGGCGGCG
*
577987 GTCAATGGTTAATGGCGG
1 GTCAATGGTTAACGGCGG
578005 TGTTCAACAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.13, G:0.39, T:0.26
Consensus pattern (20 bp):
GTCAATGGTTAACGGCGGCG
Found at i:585611 original size:2 final size:2
Alignment explanation
Indices: 585604--585638 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
585594 AGTGAACTAG
585604 TA 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 TA T
585639 TACACACATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:586215 original size:22 final size:22
Alignment explanation
Indices: 586174--586216 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
586164 AATTTACTTT
*
586174 TTAAATATAAAACATTTAAAAA
1 TTAAATATAAAACATATAAAAA
586196 TTAAATATAAAA-ATAATAAAA
1 TTAAATATAAAACAT-ATAAAA
586217 TAAAAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (22 bp):
TTAAATATAAAACATATAAAAA
Found at i:586253 original size:16 final size:14
Alignment explanation
Indices: 586190--586254 Score: 53
Period size: 16 Copynumber: 4.4 Consensus size: 14
586180 ATAAAACATT
586190 TAAAAATT-AAATA
1 TAAAAATTAAAATA
*
586203 TAAAAA-TAATAAAA
1 TAAAAATTAA-AATA
*
586217 TAAAAATTAAATTA
1 TAAAAATTAAAATA
586231 TTAAAAAATTAAAAATA
1 -T-AAAAATT-AAAATA
586248 CTAAAAA
1 -TAAAAA
586255 CACTATTCAT
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
12 1 0.02
13 7 0.17
14 11 0.27
15 4 0.10
16 12 0.29
17 6 0.15
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.28
Consensus pattern (14 bp):
TAAAAATTAAAATA
Found at i:586298 original size:13 final size:14
Alignment explanation
Indices: 586273--586301 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
586263 ATATAACTTA
586273 ATTTTATATATGAT
1 ATTTTATATATGAT
586287 ATTTTATA-ATGAT
1 ATTTTATATATGAT
586300 AT
1 AT
586302 ATGAGTTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (14 bp):
ATTTTATATATGAT
Found at i:587057 original size:2 final size:2
Alignment explanation
Indices: 586991--587049 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
586981 GTTATTTTGT
586991 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
587033 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
587050 TGTATATAGT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:587228 original size:36 final size:36
Alignment explanation
Indices: 587183--587436 Score: 233
Period size: 36 Copynumber: 7.1 Consensus size: 36
587173 ATTTATTTAT
* * *
587183 TATATTTTTTAAAACA-TTTTGAAAACTTATATAGTA
1 TATAGTTTTAAAAACATTTTTGAAAAC-TATATAATA
** *
587219 TATAGTTTTTTAAAAA-AAATTTGAAAAATTATATAATA
1 TATAG--TTTTAAAAACATTTTTG-AAAACTATATAATA
* *
587257 TATAG-TTTAAAAATATTTTTGAAAAATTATATAATA
1 TATAGTTTTAAAAACATTTTTG-AAAACTATATAATA
587293 TATAGTTTTAAAAACATTTTTGAAAACT-TAT-ATA
1 TATAGTTTTAAAAACATTTTTGAAAACTATATAATA
*
587327 -ATA-TTTTTAAAACATTTTTTGAAAACTATATAATA
1 TATAGTTTTAAAAACA-TTTTTGAAAACTATATAATA
*
587362 TATAGTTTTAAAAAC-TTTTTTAAAA--ATATAATA
1 TATAGTTTTAAAAACATTTTTGAAAACTATATAATA
* * *
587395 TATAGTTTAAACAAAATATTTTTGAAATA-TATATATTA
1 TATAGTTT-TA-AAAACATTTTTGAAA-ACTATATAATA
587433 TATA
1 TATA
587437 ATTTATATTA
Statistics
Matches: 186, Mismatches: 16, Indels: 30
0.80 0.07 0.13
Matches are distributed among these distances:
32 10 0.05
33 31 0.17
34 7 0.04
35 27 0.15
36 45 0.24
37 26 0.14
38 36 0.19
39 4 0.02
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (36 bp):
TATAGTTTTAAAAACATTTTTGAAAACTATATAATA
Found at i:587242 original size:38 final size:37
Alignment explanation
Indices: 587183--587436 Score: 205
Period size: 38 Copynumber: 7.1 Consensus size: 37
587173 ATTTATTTAT
* * * *
587183 TATATTTTTTAAAAC-ATTTTGAAAACTTATATAGTA
1 TATAGTTTTAAAAACAATTTTGAAAAATTATATAATA
*
587219 TATAGTTTTTTAAAAA-AAATTTGAAAAATTATATAATA
1 TATAG--TTTTAAAAACAATTTTGAAAAATTATATAATA
* *
587257 TATAG-TTTAAAAATATTTTTGAAAAATTATATAATA
1 TATAGTTTTAAAAACAATTTTGAAAAATTATATAATA
* *
587293 TATAGTTTTAAAAACATTTTTGAAAACTTATAT-A-A
1 TATAGTTTTAAAAACAATTTTGAAAAATTATATAATA
* *
587328 TAT--TTTT-AAAACATTTTTTG-AAAACTATATAATA
1 TATAGTTTTAAAAACA-ATTTTGAAAAATTATATAATA
**
587362 TATAGTTTTAAAAAC--TTTTTTAAAA--ATATAATA
1 TATAGTTTTAAAAACAATTTTGAAAAATTATATAATA
* * *
587395 TATAG-TTTAAACAAAATATTTTTGAAATA-TATATATTA
1 TATAGTTTTAAA-AACA-A-TTTTGAAAAATTATATAATA
587433 TATA
1 TATA
587437 ATTTATATTA
Statistics
Matches: 183, Mismatches: 17, Indels: 34
0.78 0.07 0.15
Matches are distributed among these distances:
32 20 0.11
33 26 0.14
34 8 0.04
35 16 0.09
36 34 0.19
37 37 0.20
38 42 0.23
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (37 bp):
TATAGTTTTAAAAACAATTTTGAAAAATTATATAATA
Found at i:587426 original size:69 final size:70
Alignment explanation
Indices: 587199--587436 Score: 240
Period size: 69 Copynumber: 3.3 Consensus size: 70
587189 TTTTAAAACA
* **
587199 TTTTGAAAACTTATATAGTATATAGTTTTTTAAAAA-AAATTTGAAAAATTATATAATATATAGT
1 TTTTGAAAAC-TATATAATATATAG--TTTTAAAAACATTTTTG-AAAA--ATATAATATATAGT
587263 TT-AAAAATAT
60 TTAAAAAATAT
*
587273 TTTTGAAAAATTATATAATATATAGTTTTAAAAACATTTTTGAAAACTTATATAATAT-T--TTT
1 TTTTG-AAAACTATATAATATATAGTTTTAAAAACATTTTTGAAAA---ATATAATATATAGTTT
*
587335 AAAACAT-T
62 AAAAAATAT
*
587343 TTTTGAAAACTATATAATATATAGTTTTAAAAAC-TTTTTTAAAAATATAATATATAGTTTAAAC
1 TTTTGAAAACTATATAATATATAGTTTTAAAAACATTTTTGAAAAATATAATATATAGTTT-AA-
587407 AAAATAT
64 AAAATAT
*
587414 TTTTGAAATA-TATATATTATATA
1 TTTTGAAA-ACTATATAATATATA
587437 ATTTATATTA
Statistics
Matches: 144, Mismatches: 9, Indels: 25
0.81 0.05 0.14
Matches are distributed among these distances:
65 9 0.06
66 1 0.01
68 12 0.08
69 30 0.21
70 13 0.09
71 26 0.18
72 15 0.10
73 16 0.11
74 18 0.12
75 4 0.03
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (70 bp):
TTTTGAAAACTATATAATATATAGTTTTAAAAACATTTTTGAAAAATATAATATATAGTTTAAAA
AATAT
Found at i:587457 original size:15 final size:15
Alignment explanation
Indices: 587437--587478 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
587427 ATATTATATA
587437 ATTTATATTATTTT-T
1 ATTTAT-TTATTTTCT
587452 ATTTATTTATTTTCT
1 ATTTATTTATTTTCT
*
587467 ATTTATTAATTT
1 ATTTATTTATTT
587479 CTTGTTATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 7 0.28
15 18 0.72
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (15 bp):
ATTTATTTATTTTCT
Found at i:588888 original size:30 final size:30
Alignment explanation
Indices: 588819--588876 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
588809 AATTTAAGGA
588819 AAAATGTTTTTGGACTTGAATTGAATTTGC
1 AAAATGTTTTTGGACTTGAATTGAATTTGC
*
588849 AAAATGTTTTTGGATTTGAATTGAATTT
1 AAAATGTTTTTGGACTTGAATTGAATTT
588877 ATTCAAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.19, T:0.47
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTGC
Found at i:588973 original size:8 final size:8
Alignment explanation
Indices: 588960--589067 Score: 71
Period size: 8 Copynumber: 15.0 Consensus size: 8
588950 GGTGTCAAAG
588960 TGCATCCA
1 TGCATCCA
588968 TGCATCCA
1 TGCATCCA
*
588976 TGCATCCC
1 TGCATCCA
*
588984 TGCA---G
1 TGCATCCA
588989 TGCATCCA
1 TGCATCCA
*
588997 TGCATCCC
1 TGCATCCA
589005 TGCA---A
1 TGCATCCA
589010 TGCATCCA
1 TGCATCCA
589018 TGCAT-C-
1 TGCATCCA
*
589024 TGCA-CTAA
1 TGCATC-CA
*
589032 TGCATCGA
1 TGCATCCA
589040 TGCAT-CA
1 TGCATCCA
589047 TGCA---A
1 TGCATCCA
589052 TGCATCCA
1 TGCATCCA
589060 TGCATCCA
1 TGCATCCA
589068 AACATCGAAT
Statistics
Matches: 79, Mismatches: 8, Indels: 26
0.70 0.07 0.23
Matches are distributed among these distances:
5 13 0.16
6 4 0.05
7 6 0.08
8 55 0.70
9 1 0.01
ACGTcount: A:0.25, C:0.34, G:0.16, T:0.25
Consensus pattern (8 bp):
TGCATCCA
Found at i:588992 original size:21 final size:21
Alignment explanation
Indices: 588967--589066 Score: 125
Period size: 21 Copynumber: 4.8 Consensus size: 21
588957 AAGTGCATCC
588967 ATGCATCCATGCATCCCTGCA
1 ATGCATCCATGCATCCCTGCA
*
588988 GTGCATCCATGCATCCCTGCA
1 ATGCATCCATGCATCCCTGCA
589009 ATGCATCCATGCAT--CTGCACTA
1 ATGCATCCATGCATCCCTG--C-A
* *
589031 ATGCATCGATGCAT-CATGCA
1 ATGCATCCATGCATCCCTGCA
589051 ATGCATCCATGCATCC
1 ATGCATCCATGCATCC
589067 AAACATCGAA
Statistics
Matches: 69, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
19 3 0.04
20 14 0.20
21 36 0.52
22 14 0.20
23 2 0.03
ACGTcount: A:0.25, C:0.34, G:0.16, T:0.25
Consensus pattern (21 bp):
ATGCATCCATGCATCCCTGCA
Found at i:589012 original size:13 final size:13
Alignment explanation
Indices: 588960--589063 Score: 51
Period size: 13 Copynumber: 7.9 Consensus size: 13
588950 GGTGTCAAAG
588960 TGCATCCATGCATCCA
1 TGCATCCATGCA---A
* *
588976 TGCATCCCTGCAG
1 TGCATCCATGCAA
588989 TGCATCCATGC-A
1 TGCATCCATGCAA
589001 T-C--CC-TGCAA
1 TGCATCCATGCAA
*
589010 TGCATCCATGCATC
1 TGCATCCATGCA-A
*
589024 TGCA-CTAATGCATCGA
1 TGCATC-CATGCA---A
589040 TGCAT-CATGCAA
1 TGCATCCATGCAA
589052 TGCATCCATGCA
1 TGCATCCATGCA
589064 TCCAAACATC
Statistics
Matches: 68, Mismatches: 9, Indels: 25
0.67 0.09 0.25
Matches are distributed among these distances:
8 3 0.04
9 4 0.06
10 1 0.01
11 1 0.01
12 9 0.13
13 21 0.31
14 9 0.13
15 5 0.07
16 15 0.22
ACGTcount: A:0.25, C:0.34, G:0.16, T:0.25
Consensus pattern (13 bp):
TGCATCCATGCAA
Found at i:589143 original size:20 final size:21
Alignment explanation
Indices: 589105--589152 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
589095 GCATCTTTCT
*
589105 ATGCATCCTTGCCATGCATCG
1 ATGCATCCTTGCCATGCATCC
*
589126 ATGCATCC-TGCGATGCATCC
1 ATGCATCCTTGCCATGCATCC
589146 ATGCATC
1 ATGCATC
589153 AAGGCTGCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.21, C:0.33, G:0.19, T:0.27
Consensus pattern (21 bp):
ATGCATCCTTGCCATGCATCC
Found at i:592450 original size:30 final size:30
Alignment explanation
Indices: 592379--592438 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
592369 ACAATTTAAG
592379 GCAAAATGTTTTTGGACTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
*
592409 GCAAAATGTTTTTGGATTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
592439 ATTCAAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (30 bp):
GCAAAATGTTTTTGGACTTGAATTGAATTT
Found at i:592535 original size:8 final size:8
Alignment explanation
Indices: 592522--592629 Score: 71
Period size: 8 Copynumber: 15.0 Consensus size: 8
592512 GGTGTCAAAG
592522 TGCATCCA
1 TGCATCCA
592530 TGCATCCA
1 TGCATCCA
*
592538 TGCATCCC
1 TGCATCCA
*
592546 TGCA---G
1 TGCATCCA
592551 TGCATCCA
1 TGCATCCA
*
592559 TGCATCCC
1 TGCATCCA
592567 TGCA---A
1 TGCATCCA
592572 TGCATCCA
1 TGCATCCA
592580 TGCAT-C-
1 TGCATCCA
*
592586 TGCA-CTAA
1 TGCATC-CA
*
592594 TGCATCGA
1 TGCATCCA
592602 TGCAT-CA
1 TGCATCCA
592609 TGCA---A
1 TGCATCCA
592614 TGCATCCA
1 TGCATCCA
592622 TGCATCCA
1 TGCATCCA
592630 AACATCGAAT
Statistics
Matches: 79, Mismatches: 8, Indels: 26
0.70 0.07 0.23
Matches are distributed among these distances:
5 13 0.16
6 4 0.05
7 6 0.08
8 55 0.70
9 1 0.01
ACGTcount: A:0.25, C:0.34, G:0.16, T:0.25
Consensus pattern (8 bp):
TGCATCCA
Found at i:592574 original size:13 final size:13
Alignment explanation
Indices: 592522--592625 Score: 51
Period size: 13 Copynumber: 7.9 Consensus size: 13
592512 GGTGTCAAAG
592522 TGCATCCATGCATCCA
1 TGCATCCATGCA---A
* *
592538 TGCATCCCTGCAG
1 TGCATCCATGCAA
592551 TGCATCCATGC-A
1 TGCATCCATGCAA
592563 T-C--CC-TGCAA
1 TGCATCCATGCAA
*
592572 TGCATCCATGCATC
1 TGCATCCATGCA-A
*
592586 TGCA-CTAATGCATCGA
1 TGCATC-CATGCA---A
592602 TGCAT-CATGCAA
1 TGCATCCATGCAA
592614 TGCATCCATGCA
1 TGCATCCATGCA
592626 TCCAAACATC
Statistics
Matches: 68, Mismatches: 9, Indels: 25
0.67 0.09 0.25
Matches are distributed among these distances:
8 3 0.04
9 4 0.06
10 1 0.01
11 1 0.01
12 9 0.13
13 21 0.31
14 9 0.13
15 5 0.07
16 15 0.22
ACGTcount: A:0.25, C:0.34, G:0.16, T:0.25
Consensus pattern (13 bp):
TGCATCCATGCAA
Found at i:592598 original size:22 final size:20
Alignment explanation
Indices: 592529--592723 Score: 127
Period size: 21 Copynumber: 9.8 Consensus size: 20
592519 AAGTGCATCC
*
592529 ATGCATCCATGCATCCCTGCA
1 ATGCATCCATGCAT-CATGCA
* *
592550 GTGCATCCATGCATCCCTGCA
1 ATGCATCCATGCAT-CATGCA
592571 ATGCATCCATGCATC-TGCACTA
1 ATGCATCCATGCATCATG--C-A
*
592593 ATGCATCGATGCATCATGCA
1 ATGCATCCATGCATCATGCA
592613 ATGCATCCATGCATC---CA
1 ATGCATCCATGCATCATGCA
* * *
592630 A-ACATCGAATGCA--AT-TA
1 ATGCATC-CATGCATCATGCA
* * *
592647 ATGCATCGATGCATCTTGCT
1 ATGCATCCATGCATCATGCA
* * *
592667 ATGCATCGATGCATCCTTGCC
1 ATGCATCCATGCAT-CATGCA
* * *
592688 ATGCATCGATGCATCCTGCG
1 ATGCATCCATGCATCATGCA
592708 ATGCATCCATGCATCA
1 ATGCATCCATGCATCA
592724 AGGCTGCAAC
Statistics
Matches: 145, Mismatches: 17, Indels: 25
0.78 0.09 0.13
Matches are distributed among these distances:
16 4 0.03
17 15 0.10
18 4 0.03
19 3 0.02
20 48 0.33
21 54 0.37
22 15 0.10
23 2 0.01
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (20 bp):
ATGCATCCATGCATCATGCA
Found at i:598728 original size:23 final size:23
Alignment explanation
Indices: 598686--598747 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
598676 ATAGGGTAGA
* *
598686 GGGAATCGATACCCCC-TTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
598708 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
598731 GGGAACCGATTCCCCCT
1 GGGAACCGATTCCCCCT
598748 AGAGGAATCG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
22 14 0.38
23 23 0.62
ACGTcount: A:0.23, C:0.32, G:0.26, T:0.19
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAG
Found at i:602985 original size:12 final size:11
Alignment explanation
Indices: 602970--603062 Score: 50
Period size: 11 Copynumber: 8.1 Consensus size: 11
602960 TTTATTTCGT
602970 TTTTTATTATTA
1 TTTTT-TTATTA
602982 TTTTTTGTA-TA
1 TTTTTT-TATTA
*
602993 TTTTTTTAAATA
1 TTTTTTT-ATTA
*
603005 TTTTTTTCTTTCA
1 TTTTTTT-ATT-A
603018 TTTTTATTATCT-
1 TTTTT-TTAT-TA
*
603030 TTTTTTAATCTA
1 TTTTTTTAT-TA
603042 -TTTTTT-TTA
1 TTTTTTTATTA
*
603051 GTTTTTTATTA
1 TTTTTTTATTA
603062 T
1 T
603063 CATATTAACA
Statistics
Matches: 65, Mismatches: 7, Indels: 19
0.71 0.08 0.21
Matches are distributed among these distances:
9 2 0.03
10 8 0.12
11 23 0.35
12 22 0.34
13 7 0.11
14 3 0.05
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.74
Consensus pattern (11 bp):
TTTTTTTATTA
Found at i:607996 original size:13 final size:13
Alignment explanation
Indices: 607964--607996 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
607954 TAAAATAAAA
607964 ATAATATTTATTC
1 ATAATATTTATTC
607977 ACT-ATATTTATTC
1 A-TAATATTTATTC
607990 ATAATAT
1 ATAATAT
607997 GGTTTAATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.06
13 16 0.89
14 1 0.06
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (13 bp):
ATAATATTTATTC
Found at i:608823 original size:31 final size:31
Alignment explanation
Indices: 608788--608857 Score: 113
Period size: 31 Copynumber: 2.3 Consensus size: 31
608778 AGAATACTAA
608788 TTTGACCCTTAAAATTCAATCGACATATTAT
1 TTTGACCCTTAAAATTCAATCGACATATTAT
* * *
608819 TTTGAACCTTGAAATTCAGTCGACATATTAT
1 TTTGACCCTTAAAATTCAATCGACATATTAT
608850 TTTGACCC
1 TTTGACCC
608858 CAAACTTTAG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (31 bp):
TTTGACCCTTAAAATTCAATCGACATATTAT
Found at i:609508 original size:16 final size:16
Alignment explanation
Indices: 609462--609510 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
609452 TGTTATTCAT
*
609462 GTCATTTTGAATTTGTA
1 GTCATTTTGAATTT-AA
**
609479 -TCATTTTGTGTTTAA
1 GTCATTTTGAATTTAA
609494 GTCATTTTGAATTTAA
1 GTCATTTTGAATTTAA
609510 G
1 G
609511 AGTTAGGATT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
15 1 0.04
16 25 0.96
ACGTcount: A:0.24, C:0.06, G:0.16, T:0.53
Consensus pattern (16 bp):
GTCATTTTGAATTTAA
Found at i:612246 original size:5 final size:5
Alignment explanation
Indices: 612236--612260 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
612226 ATATGAAAAG
612236 ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT
612261 TATTTTTCGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTAT
Found at i:612481 original size:43 final size:43
Alignment explanation
Indices: 612433--612519 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 43
612423 AATCCATCGG
* *
612433 TTTCGAATTAAATTATCATATCCAATTTTGTCATGCAATTTTA
1 TTTCGAATTAAATTATCATACCCAATTGTGTCATGCAATTTTA
*
612476 TTTCGAATTAAATTATCATCCCCAATTGTGTCATGCAATTTTA
1 TTTCGAATTAAATTATCATACCCAATTGTGTCATGCAATTTTA
612519 T
1 T
612520 CTACGCTTGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.31, C:0.16, G:0.08, T:0.45
Consensus pattern (43 bp):
TTTCGAATTAAATTATCATACCCAATTGTGTCATGCAATTTTA
Found at i:613527 original size:30 final size:30
Alignment explanation
Indices: 613472--613529 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
613462 AAGAAACAGT
* *
613472 TGAAAATCGGGAAAATCGGGGTGAACCGGC
1 TGAAAATCGGCAAAACCGGGGTGAACCGGC
**
613502 TGAAAATCGGCAAAACCGGTTTGAACCG
1 TGAAAATCGGCAAAACCGGGGTGAACCG
613530 TCGGTTCACT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.34, C:0.19, G:0.31, T:0.16
Consensus pattern (30 bp):
TGAAAATCGGCAAAACCGGGGTGAACCGGC
Found at i:613782 original size:24 final size:24
Alignment explanation
Indices: 613751--613806 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
613741 TAGAAGTTCG
613751 ATTGAAGCCTAAAATTTAAGCTCA
1 ATTGAAGCCTAAAATTTAAGCTCA
* *
613775 ATTGAAGCCTAAAATTTGAGCTTA
1 ATTGAAGCCTAAAATTTAAGCTCA
613799 ATTGAAGC
1 ATTGAAGC
613807 AAAAGAATAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (24 bp):
ATTGAAGCCTAAAATTTAAGCTCA
Found at i:615147 original size:7 final size:7
Alignment explanation
Indices: 615137--615169 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
615127 TGAATTCTGC
*
615137 ATTTAAA
1 ATTTCAA
615144 ATTTCAA
1 ATTTCAA
615151 ATTTCAA
1 ATTTCAA
615158 ATTTCAA
1 ATTTCAA
615165 ATTTC
1 ATTTC
615170 TAAGTTTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (7 bp):
ATTTCAA
Found at i:618260 original size:48 final size:48
Alignment explanation
Indices: 618167--618513 Score: 262
Period size: 48 Copynumber: 7.3 Consensus size: 48
618157 CTTAGTATTA
* * * *
618167 TGCTCCACTCC-ACA-A-CAAAGGATGTTGGG-TCCTCTCATAAAAATT
1 TGCTCCACTCCTCCATAGCAAAGGATGTTGGGCT-CGCTCGTAATAATT
* * *
618212 TGCTCCACTCCTCCATAGCAAAAGATTTTGGGCTCACTCGTAATAATT
1 TGCTCCACTCCTCCATAGCAAAGGATGTTGGGCTCGCTCGTAATAATT
* * * *
618260 TGCTCCACTACTCCATAACAAAAGATGTTGGGCTTC-TTCGT--TAATTT
1 TGCTCCACTCCTCCATAGCAAAGGATGTTGGGC-TCGCTCGTAATAA-TT
* * *
618307 TTCTCCACTCTTCCATAGCAAAGGATGTTGGGCTCACTC-TCAATAATTT
1 TGCTCCACTCCTCCATAGCAAAGGATGTTGGGCTCGCTCGT-AATAA-TT
* * * * * ** * *
618356 TACTTCACTCCTTCATAGTAGAGGATGTTACGCTCGCTCTTAATAATA
1 TGCTCCACTCCTCCATAGCAAAGGATGTTGGGCTCGCTCGTAATAATT
* * * * * *
618404 TGCTCCACTCTTCGATAGCAAATGATGATGGACTCGCTTGTAATAATT
1 TGCTCCACTCCTCCATAGCAAAGGATGTTGGGCTCGCTCGTAATAATT
* * * * * *
618452 TACTTCACTCCTCCA-AACAAAGGATGTTGGGCTTGCTCTTAATAATA
1 TGCTCCACTCCTCCATAGCAAAGGATGTTGGGCTCGCTCGTAATAATT
*
618499 TGCTCCATTCCTCCA
1 TGCTCCACTCCTCCA
618514 CACAGATGGA
Statistics
Matches: 235, Mismatches: 56, Indels: 20
0.76 0.18 0.06
Matches are distributed among these distances:
45 11 0.05
46 8 0.03
47 69 0.29
48 102 0.43
49 44 0.19
50 1 0.00
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (48 bp):
TGCTCCACTCCTCCATAGCAAAGGATGTTGGGCTCGCTCGTAATAATT
Found at i:618504 original size:95 final size:95
Alignment explanation
Indices: 618174--618505 Score: 321
Period size: 95 Copynumber: 3.5 Consensus size: 95
618164 TTATGCTCCA
* * * * * * *
618174 CTCCACAACAAAGGATGTTGGGTCCTCTCATAAAAATTTGCTCCACTCCTCCATAGCAAAAGATT
1 CTCCATAACAAAGGATGTTGGG-CTTCTCTTAATAATATGCTCCACTCTTCCATAGCAAAAGATG
* * * *
618239 TTGGGCTCACTCGTAATAATTTGCTCCACTA
65 TTGGGCTCACTTGTAATAATTTACTTCACTC
* * * *
618270 CTCCATAACAAAAGATGTTGGGCTTCTTCGTTAAT--TTTTCTCCACTCTTCCATAGCAAAGGAT
1 CTCCATAACAAAGGATGTTGGGCTTC-TC-TTAATAATATGCTCCACTCTTCCATAGCAAAAGAT
*
618333 GTTGGGCTCACTCT-CAATAATTTTACTTCACTC
64 GTTGGGCTCACT-TGTAATAA-TTTACTTCACTC
* ** * ** * * *
618366 CTTCATAGTAGAGGATGTTACGCTCGCTCTTAATAATATGCTCCACTCTTCGATAGCAAATGATG
1 CTCCATAACAAAGGATGTTGGGCT-TCTCTTAATAATATGCTCCACTCTTCCATAGCAAAAGATG
* * *
618431 ATGGACTCGCTTGTAATAATTTACTTCACTC
65 TTGGGCTCACTTGTAATAATTTACTTCACTC
618462 CTCCA-AACAAAGGATGTTGGGCTTGCTCTTAATAATATGCTCCA
1 CTCCATAACAAAGGATGTTGGGCTT-CTCTTAATAATATGCTCCA
618506 TTCCTCCACA
Statistics
Matches: 190, Mismatches: 37, Indels: 19
0.77 0.15 0.08
Matches are distributed among these distances:
95 81 0.43
96 67 0.35
97 42 0.22
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.33
Consensus pattern (95 bp):
CTCCATAACAAAGGATGTTGGGCTTCTCTTAATAATATGCTCCACTCTTCCATAGCAAAAGATGT
TGGGCTCACTTGTAATAATTTACTTCACTC
Found at i:619119 original size:36 final size:37
Alignment explanation
Indices: 618945--619140 Score: 129
Period size: 37 Copynumber: 5.3 Consensus size: 37
618935 GGTTTCAAGG
* * * *
618945 GAGACAAAATTATGCTTCAAGGGAAACTGGTCTCAAT
1 GAGACAAAATTTTGTTTCAAGGAAAACTGATCTCAAT
* * * *
618982 GAAACCAAATTTTGTGTCATATG-AAAC--ATTCTCAAGT
1 GAGACAAAATTTTGTTTCA-AGGAAAACTGA-TCTCAA-T
* *
619019 GAGACAAAA--TTGTTTCTAGGGAAACTGATCTCAAT
1 GAGACAAAATTTTGTTTCAAGGAAAACTGATCTCAAT
* * * *
619054 GAAGACGAATTTTATGTTTCAA-AAGAAACTGATTTCAA-
1 G-AGACAAAATTT-TGTTTCAAGGA-AAACTGATCTCAAT
*
619092 GAGACAAAATTTTGTTTCAAGGAAAACTAGTATC-AAAT
1 GAGACAAAATTTTGTTTCAAGGAAAACT-G-ATCTCAAT
619130 GAGACAAAATT
1 GAGACAAAATT
619141 CCTTGAGACA
Statistics
Matches: 121, Mismatches: 23, Indels: 29
0.70 0.13 0.17
Matches are distributed among these distances:
34 2 0.02
35 12 0.10
36 31 0.26
37 40 0.33
38 17 0.14
39 19 0.16
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (37 bp):
GAGACAAAATTTTGTTTCAAGGAAAACTGATCTCAAT
Found at i:619213 original size:23 final size:23
Alignment explanation
Indices: 619145--619213 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
619135 AAAATTCCTT
* * **
619145 GAGACAAAATTTGTGTTTCAATA
1 GAGACAAAATCTATGTTTCAAGG
*
619168 GAGATAAAATCTATGTTTCAAGG
1 GAGACAAAATCTATGTTTCAAGG
619191 GAGACAAAATCTATGTTTCAAGG
1 GAGACAAAATCTATGTTTCAAGG
619214 TCAATTGGTC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.30
Consensus pattern (23 bp):
GAGACAAAATCTATGTTTCAAGG
Found at i:619267 original size:39 final size:39
Alignment explanation
Indices: 619185--619279 Score: 120
Period size: 39 Copynumber: 2.4 Consensus size: 39
619175 AATCTATGTT
* * * * *
619185 TCAAGGGAGACAAAATCTATGTTTCAAGGTCAATTGGTC
1 TCAAGGGAGACGAAATCTATGTTTCAAGGTAAACTGATA
619224 TCAAGGGAGACGAAATCTATGTTTCAAGAG-AAACTGATA
1 TCAAGGGAGACGAAATCTATGTTTCAAG-GTAAACTGATA
*
619263 TCAAGGGAGATGAAATC
1 TCAAGGGAGACGAAATC
619280 AGAGTTTCAG
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
39 48 0.98
40 1 0.02
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.24
Consensus pattern (39 bp):
TCAAGGGAGACGAAATCTATGTTTCAAGGTAAACTGATA
Found at i:619310 original size:14 final size:14
Alignment explanation
Indices: 619291--619318 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
619281 GAGTTTCAGG
619291 GGAGACTAGTCTTA
1 GGAGACTAGTCTTA
619305 GGAGACTAGTCTTA
1 GGAGACTAGTCTTA
619319 AGGGAGAAAA
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:0.29, C:0.14, G:0.29, T:0.29
Consensus pattern (14 bp):
GGAGACTAGTCTTA
Found at i:619370 original size:39 final size:38
Alignment explanation
Indices: 619309--619433 Score: 105
Period size: 37 Copynumber: 3.3 Consensus size: 38
619299 GTCTTAGGAG
* * *
619309 ACTAGTCTTAAGGGAGAAAAAATCTACGTTTCAAG-GAAA
1 ACTAGTCTCAAGGAAGATAAAAT-TACGTTTCAAGAG-AA
**
619348 ACTAGTCTCAAGGAAGATAAAATTGTGTTTCAAGAGAA
1 ACTAGTCTCAAGGAAGATAAAATTACGTTTCAAGAGAA
* * * *
619386 ACAAGTTTCAA-GAAGATAAAATTGTC-TTTCAAGGGAA
1 ACTAGTCTCAAGGAAGATAAAATT-ACGTTTCAAGAGAA
619423 A-TATGTCTCAA
1 ACTA-GTCTCAA
619434 TGGAGACAAA
Statistics
Matches: 71, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
36 1 0.01
37 29 0.41
38 20 0.28
39 21 0.30
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.26
Consensus pattern (38 bp):
ACTAGTCTCAAGGAAGATAAAATTACGTTTCAAGAGAA
Found at i:619397 original size:38 final size:39
Alignment explanation
Indices: 619336--619538 Score: 193
Period size: 39 Copynumber: 5.3 Consensus size: 39
619326 AAAAATCTAC
* * *
619336 GTTTCAAGGAAAACTAGTCTCAAGGAAGATAAAAT-TGT
1 GTTTCAAGGGAAACAAGTCTCAAGGAAGACAAAATATGT
* * *
619374 GTTTCAAGAGAAACAAGTTTCAA-GAAGATAAAAT-TGT
1 GTTTCAAGGGAAACAAGTCTCAAGGAAGACAAAATATGT
* * *
619411 CTTTCAAGGGAAATATGTCTCAATGG-AGACAAAATATGT
1 GTTTCAAGGGAAACAAGTCTCAA-GGAAGACAAAATATGT
* * * *
619450 GTTTCAAGGGAAACAAGTATCGAGGGAGACAACATATGT
1 GTTTCAAGGGAAACAAGTCTCAAGGAAGACAAAATATGT
** *
619489 GTTTCAAGGGAAACTGGTCTCAA-GATAAACAAAAT-TGT
1 GTTTCAAGGGAAACAAGTCTCAAGGA-AGACAAAATATGT
*
619527 GTTTTAAGGGAA
1 GTTTCAAGGGAA
619539 TAAAAAATAC
Statistics
Matches: 136, Mismatches: 24, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
37 32 0.24
38 44 0.32
39 60 0.44
ACGTcount: A:0.40, C:0.11, G:0.23, T:0.26
Consensus pattern (39 bp):
GTTTCAAGGGAAACAAGTCTCAAGGAAGACAAAATATGT
Found at i:619415 original size:21 final size:20
Alignment explanation
Indices: 619355--619418 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 20
619345 AAAACTAGTC
619355 TCAAGGAAGATAAAATTGTGTT
1 TCAA-GAAGATAAAATTGT-TT
619377 TCAAG-AGA-AACAA--G-TT
1 TCAAGAAGATAA-AATTGTTT
619393 TCAAGAAGATAAAATTGTCTT
1 TCAAGAAGATAAAATTGT-TT
619414 TCAAG
1 TCAAG
619419 GGAAATATGT
Statistics
Matches: 35, Mismatches: 0, Indels: 15
0.70 0.00 0.30
Matches are distributed among these distances:
16 7 0.20
17 5 0.14
18 3 0.09
19 3 0.09
20 5 0.14
21 8 0.23
22 4 0.11
ACGTcount: A:0.44, C:0.09, G:0.19, T:0.28
Consensus pattern (20 bp):
TCAAGAAGATAAAATTGTTT
Found at i:621594 original size:16 final size:16
Alignment explanation
Indices: 621573--621608 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
621563 ATAAGGAAAA
*
621573 TAAAAGTGCATAAATT
1 TAAAAGTGCATAAAGT
621589 TAAAAGTGCATAAAGT
1 TAAAAGTGCATAAAGT
621605 TAAA
1 TAAA
621609 TAGAAGAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.53, C:0.06, G:0.14, T:0.28
Consensus pattern (16 bp):
TAAAAGTGCATAAAGT
Found at i:621942 original size:126 final size:128
Alignment explanation
Indices: 621781--622057 Score: 353
Period size: 127 Copynumber: 2.2 Consensus size: 128
621771 AATTAAAATA
* * *
621781 AAAATAAAAAGTTAGTGGTTAGTAGAGTTCGAACCATAATAATGCGGATCATA-CCCGGATCGAG
1 AAAAT-AAAAGTTAGTGGTTAGCAGAGTTCGAACCATAATAATACGGATCATACCCCAGATCGAG
* * * * *
621845 TCACCACAAGGTTGAATTGATTATTGGAAACAATAAATAAATAAAT-AATTGTTAGAGTGCAAT
65 TCACCACAAGGTCGAATTGAATATTAGAAACAATAAATAAATAAATAAATGGTTAAAGTGCAAT
* * * * *
621908 AAAATAAAAGTCAGTAGTTAGCAGAG-TCTGAACCATAATAATATGGATCTTACCCCAGATCGGG
1 AAAATAAAAGTTAGTGGTTAGCAGAGTTC-GAACCATAATAATACGGATCATACCCCAGATCGAG
* *
621972 TCACCATAAGGTCGAATTGAATATTAGAAATAATAAATAAATAAATAACAATGGTTAAAGTGCAA
65 TCACCACAAGGTCGAATTGAATATTAGAAACAATAAATAAATAAAT-A-AATGGTTAAAGTGCAA
622037 T
128 T
*
622038 GAAATAAAAGTTAGTGGTTA
1 AAAATAAAAGTTAGTGGTTA
622058 ATATGCAATA
Statistics
Matches: 127, Mismatches: 18, Indels: 7
0.84 0.12 0.05
Matches are distributed among these distances:
125 2 0.02
126 38 0.30
127 55 0.43
130 32 0.25
ACGTcount: A:0.43, C:0.12, G:0.19, T:0.26
Consensus pattern (128 bp):
AAAATAAAAGTTAGTGGTTAGCAGAGTTCGAACCATAATAATACGGATCATACCCCAGATCGAGT
CACCACAAGGTCGAATTGAATATTAGAAACAATAAATAAATAAATAAATGGTTAAAGTGCAAT
Found at i:622055 original size:29 final size:29
Alignment explanation
Indices: 622023--622081 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
622013 TAAATAACAA
* *
622023 TGGTTAA-AGTGCAATGAAATAAAAGTTAG
1 TGGTTAATA-TGCAATAAAATAAAAATTAG
622052 TGGTTAATATGCAATAAAATAAAAATTAG
1 TGGTTAATATGCAATAAAATAAAAATTAG
622081 T
1 T
622082 ATAAATCAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 26 0.96
30 1 0.04
ACGTcount: A:0.47, C:0.03, G:0.19, T:0.31
Consensus pattern (29 bp):
TGGTTAATATGCAATAAAATAAAAATTAG
Found at i:623344 original size:91 final size:91
Alignment explanation
Indices: 623189--623387 Score: 299
Period size: 91 Copynumber: 2.2 Consensus size: 91
623179 GAGCCTAGGA
* * *
623189 TGAACAAGTTCTTCTCATTATAAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACT
1 TGAACAAGTTCTTCTCATTATAAACTTCTTCTCCCTCATTGGATAAGTTCTTATCATTATGAACT
*
623254 CTCCACTGTAAATGTTAATCCAAGGT
66 CTCCACTGGAAATGTTAATCCAAGGT
* * *
623280 TGAACAGGTTCTTCTCATTATGAATTTCTTCTCCCTCATTGGATAAGTTCTTATCATTATGAACT
1 TGAACAAGTTCTTCTCATTATAAACTTCTTCTCCCTCATTGGATAAGTTCTTATCATTATGAACT
* *
623345 CTCTACTGGAAATGTTGATCCAAGGT
66 CTCCACTGGAAATGTTAATCCAAGGT
*
623371 TGAACGAACTTCTTCTC
1 TGAAC-AAGTTCTTCTC
623388 CCTCGTTGGA
Statistics
Matches: 96, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
91 87 0.91
92 9 0.09
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (91 bp):
TGAACAAGTTCTTCTCATTATAAACTTCTTCTCCCTCATTGGATAAGTTCTTATCATTATGAACT
CTCCACTGGAAATGTTAATCCAAGGT
Found at i:623428 original size:75 final size:74
Alignment explanation
Indices: 623305--623458 Score: 236
Period size: 75 Copynumber: 2.1 Consensus size: 74
623295 CATTATGAAT
* **
623305 TTCTTCTCCCTCATTGGATAAGTTCTTATCATTATGAACTCTCTACTGGAAATGTTGATCCAAGG
1 TTCTTCTCCCTCATTGGATAAGTTCTTATCATTATGAACTCTCCACTGGAAACATTGATCCAAGG
623370 TTGAACGAAC
66 TTGAAC-AAC
* * *
623380 TTCTTCTCCCTCGTTGGATTAGTTCTTCTCATTATGAACTCTCCACTGGAAACATTGATCCAAGG
1 TTCTTCTCCCTCATTGGATAAGTTCTTATCATTATGAACTCTCCACTGGAAACATTGATCCAAGG
*
623445 TTGAACAAG
66 TTGAACAAC
623454 TTCTT
1 TTCTT
623459 ATCATTATGA
Statistics
Matches: 72, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
74 7 0.10
75 65 0.90
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.37
Consensus pattern (74 bp):
TTCTTCTCCCTCATTGGATAAGTTCTTATCATTATGAACTCTCCACTGGAAACATTGATCCAAGG
TTGAACAAC
Found at i:623505 original size:166 final size:166
Alignment explanation
Indices: 623211--623541 Score: 502
Period size: 166 Copynumber: 2.0 Consensus size: 166
623201 TCTCATTATA
* **
623211 AACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCACTGTAAATGTTAATCCA
1 AACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAACATTAATCCA
* * * * *
623276 AGGTTGAACAGGTTCTTCTCATTATGAATTTCTTCTCCCTCATTGGATAAGTTCTTATCATTATG
66 AGGTTGAACAAGTTCTTATCATTATGAAATTATTCTCCCTCATTAGATAAGTTCTTATCATTATG
* *
623341 AACTCTCTACTGGAAATGTTGATCCAAGGTTGAACG
131 AACTCTCCACTGGAAATGTTGAACCAAGGTTGAACG
* *
623377 AACTTCTTCTCCCTCGTTGGATTAGTTCTTCTCATTATGAACTCTCCACTGGAAACATTGATCCA
1 AACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAACATTAATCCA
* * *
623442 AGGTTGAACAAGTTCTTATCATTATGAAATTATTCTCCCTCGTTAGATGAGGTT-TTCTCATTAT
66 AGGTTGAACAAGTTCTTATCATTATGAAATTATTCTCCCTCATTAGAT-AAGTTCTTATCATTAT
*
623506 GAACTCTCCACTGGAAATGTTGAACCGAGGTTGAAC
130 GAACTCTCCACTGGAAATGTTGAACCAAGGTTGAAC
623542 AAGTTATTCT
Statistics
Matches: 148, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
166 144 0.97
167 4 0.03
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (166 bp):
AACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAACATTAATCCA
AGGTTGAACAAGTTCTTATCATTATGAAATTATTCTCCCTCATTAGATAAGTTCTTATCATTATG
AACTCTCCACTGGAAATGTTGAACCAAGGTTGAACG
Found at i:623614 original size:91 final size:91
Alignment explanation
Indices: 623376--623619 Score: 346
Period size: 91 Copynumber: 2.7 Consensus size: 91
623366 AAGGTTGAAC
* ** *
623376 GAACTTCTTCTCCCTCGTTGGATTAGTTCTTCTCATTATGAACTCTCCACTGGAAACATTGATCC
1 GAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGAACC
*
623441 AAGGTTGAACAAGTTCTTATCATTAT
66 AAGGTTGAACAAGTTATTATCATTAT
* * *
623467 GAAATTATTCTCCCTCGTTAGATGAGGTT-TTCTCATTATGAACTCTCCACTGGAAATGTTGAAC
1 GAACTTCTTCTCCCTCGTTGGATGA-GTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGAAC
* *
623531 CGAGGTTGAACAAGTTATTCTCATTAT
65 CAAGGTTGAACAAGTTATTATCATTAT
* * * *
623558 GAACTTCTTGTCCCTTGTTGGATGAGTTCTTCTCATTATGAACTCTTCATTGGAAATGTTGA
1 GAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGA
623620 TCGATTTATC
Statistics
Matches: 134, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
90 3 0.02
91 128 0.96
92 3 0.02
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (91 bp):
GAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGAACC
AAGGTTGAACAAGTTATTATCATTAT
Found at i:624195 original size:21 final size:21
Alignment explanation
Indices: 624171--624214 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
624161 TTTCTTGATC
624171 ATGTATGTATG-AAATGATG-AA
1 ATGTATG-ATGCAAA-GATGCAA
624192 ATGTATGATGCAAAGATGCAA
1 ATGTATGATGCAAAGATGCAA
624213 AT
1 AT
624215 TCATGTAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.43, C:0.05, G:0.23, T:0.30
Consensus pattern (21 bp):
ATGTATGATGCAAAGATGCAA
Found at i:624537 original size:58 final size:56
Alignment explanation
Indices: 624455--624606 Score: 162
Period size: 58 Copynumber: 2.6 Consensus size: 56
624445 TAAAAACATG
* * * * **
624455 AAGAAACCCCTGAAAATAAAGCTTAGTTTCTAAAAAACTTACTTTTTCAG-TTTTCATC
1 AAGAAACCCCTAAAAATTAGGCTTAGTTTCTAAAAAA-TT-C-TTTGCAGATAATCATC
* * * *
624513 AAGGAACCCCTAAAAATTAGGCTTAGCTTCCTTTAAAAATTCTTTGGAGATAATCATC
1 AAGAAACCCCTAAAAATTAGGCTTAG-TTTC-TAAAAAATTCTTTGCAGATAATCATC
624571 AAGAAACCCCTAAAAATTAGGCTTAGTTTCTAAAAA
1 AAGAAACCCCTAAAAATTAGGCTTAGTTTCTAAAAA
624607 CTCATTTGAA
Statistics
Matches: 78, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
56 5 0.06
57 8 0.10
58 54 0.69
59 5 0.06
60 6 0.08
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.31
Consensus pattern (56 bp):
AAGAAACCCCTAAAAATTAGGCTTAGTTTCTAAAAAATTCTTTGCAGATAATCATC
Found at i:627656 original size:12 final size:11
Alignment explanation
Indices: 627641--627743 Score: 67
Period size: 11 Copynumber: 9.4 Consensus size: 11
627631 GATATGCCTA
627641 TTTTCTTCTTT
1 TTTTCTTCTTT
627652 ATTTT-TTC-TT
1 -TTTTCTTCTTT
*
627662 CTTT-TTCTTT
1 TTTTCTTCTTT
627672 TTTTCTTTCTTT
1 TTTTC-TTCTTT
627684 TTTTCTT-TCTT
1 TTTTCTTCT-TT
627695 TTTTCTT-TTT
1 TTTTCTTCTTT
* *
627705 TCTTTTTTCTGT
1 T-TTTCTTCTTT
627717 TTTTCTGT-TTT
1 TTTTCT-TCTTT
627728 TTATGTC-TCTTT
1 TT-T-TCTTCTTT
627740 TTTT
1 TTTT
627744 GCTATATATT
Statistics
Matches: 75, Mismatches: 6, Indels: 22
0.73 0.06 0.21
Matches are distributed among these distances:
9 6 0.08
10 12 0.16
11 30 0.40
12 25 0.33
13 2 0.03
ACGTcount: A:0.02, C:0.15, G:0.03, T:0.81
Consensus pattern (11 bp):
TTTTCTTCTTT
Found at i:627660 original size:14 final size:13
Alignment explanation
Indices: 627641--627714 Score: 78
Period size: 14 Copynumber: 5.5 Consensus size: 13
627631 GATATGCCTA
627641 TTTTCTTCTTTATT
1 TTTTCTTCTTT-TT
627655 TTTTCTTCTTTTT
1 TTTTCTTCTTTTT
* *
627668 CTTTTTTTCTTTCT
1 -TTTTCTTCTTTTT
627682 TTTT-TTCTTTCTT
1 TTTTCTTCTTT-TT
*
627695 TTTTCTTTTTTCTT
1 TTTTCTTCTTT-TT
627709 TTTTCT
1 TTTTCT
627715 GTTTTTCTGT
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
12 6 0.11
13 11 0.21
14 36 0.68
ACGTcount: A:0.01, C:0.16, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTCTTCTTTTT
Found at i:627674 original size:8 final size:8
Alignment explanation
Indices: 627653--627729 Score: 81
Period size: 7 Copynumber: 9.8 Consensus size: 8
627643 TTCTTCTTTA
627653 TTTTTTCT
1 TTTTTTCT
627661 TCTTTTTCT
1 T-TTTTTCT
627670 TTTTTTCT
1 TTTTTTCT
627678 TTCTTTT-T
1 TT-TTTTCT
*
627686 TTCTTTC-
1 TTTTTTCT
627693 TTTTTTC-
1 TTTTTTCT
627700 TTTTTTC-
1 TTTTTTCT
627707 TTTTTTCT
1 TTTTTTCT
*
627715 GTTTTTCT
1 TTTTTTCT
627723 GTTTTTT
1 -TTTTTT
627730 ATGTCTCTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
7 23 0.38
8 20 0.33
9 17 0.28
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.83
Consensus pattern (8 bp):
TTTTTTCT
Found at i:627694 original size:30 final size:29
Alignment explanation
Indices: 627653--627709 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 29
627643 TTCTTCTTTA
627653 TTTTTTCTTC-TTTTTCTTTTTTTCTTTCT
1 TTTTTTCTTCTTTTTTC-TTTTTTCTTTCT
627682 TTTTTTCTTTCTTTTTTCTTTTTTCTTT
1 TTTTTTC-TTCTTTTTTCTTTTTTCTTT
627710 TTTCTGTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 7 0.27
30 13 0.50
31 6 0.23
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (29 bp):
TTTTTTCTTCTTTTTTCTTTTTTCTTTCT
Found at i:627701 original size:7 final size:7
Alignment explanation
Indices: 627641--627728 Score: 86
Period size: 8 Copynumber: 11.6 Consensus size: 7
627631 GATATGCCTA
627641 TTTTCTT
1 TTTTCTT
* *
627648 CTTTATT
1 TTTTCTT
627655 TTTTCTTCT
1 TTTTC-T-T
627664 TTTTCTTT
1 TTTTC-TT
627672 TTTTCTT
1 TTTTCTT
*
627679 TCTTTTTT
1 T-TTTCTT
627687 TCTTTCTT
1 T-TTTCTT
627695 TTTTCTT
1 TTTTCTT
627702 TTTTCTT
1 TTTTCTT
627709 TTTTCTGT
1 TTTTCT-T
627717 TTTTCTGT
1 TTTTCT-T
627725 TTTT
1 TTTT
627729 TATGTCTCTT
Statistics
Matches: 71, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
7 30 0.42
8 33 0.46
9 8 0.11
ACGTcount: A:0.01, C:0.15, G:0.02, T:0.82
Consensus pattern (7 bp):
TTTTCTT
Found at i:627711 original size:54 final size:59
Alignment explanation
Indices: 627641--627761 Score: 146
Period size: 54 Copynumber: 2.1 Consensus size: 59
627631 GATATGCCTA
* * *
627641 TTTTCTTCTTTATTTTTTCTTCTTTTTCT-TTTTTTCT-T-TCTTTTTTT-CT-T-TCTT
1 TTTTCTTTTTTATTTTTTC-TCTTTTTCTGTTTTTTATGTCTCTTTTTTTGCTATATATT
* *
627695 TTTTCTTTTTTCTTTTTTCTGTTTTTCTGTTTTTTATGTCTCTTTTTTTGCTATATATT
1 TTTTCTTTTTTATTTTTTCTCTTTTTCTGTTTTTTATGTCTCTTTTTTTGCTATATATT
627754 TTTTCTTT
1 TTTTCTTT
627762 CTATCTGTGT
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
53 8 0.14
54 24 0.43
55 1 0.02
56 9 0.16
57 2 0.04
58 1 0.02
59 11 0.20
ACGTcount: A:0.04, C:0.14, G:0.03, T:0.79
Consensus pattern (59 bp):
TTTTCTTTTTTATTTTTTCTCTTTTTCTGTTTTTTATGTCTCTTTTTTTGCTATATATT
Found at i:627739 original size:44 final size:47
Alignment explanation
Indices: 627644--627742 Score: 114
Period size: 44 Copynumber: 2.2 Consensus size: 47
627634 ATGCCTATTT
* * * * *
627644 TCTTCTTTATTTTTTCTTCTTTTTCTTTTTTTCTTTCTTTTTTTCTT
1 TCTTTTTTATTTTTTCTTCTTTTTCTGTTTTTCTGTCTTTTTATCTC
* *
627691 TCTTTTTTCTTTTTTC-T-TTTTTCTGTTTTTCTGT-TTTTTATGTC
1 TCTTTTTTATTTTTTCTTCTTTTTCTGTTTTTCTGTCTTTTTATCTC
627735 TCTTTTTT
1 TCTTTTTT
627743 TGCTATATAT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
44 15 0.33
45 15 0.33
46 1 0.02
47 14 0.31
ACGTcount: A:0.02, C:0.15, G:0.03, T:0.80
Consensus pattern (47 bp):
TCTTTTTTATTTTTTCTTCTTTTTCTGTTTTTCTGTCTTTTTATCTC
Found at i:629088 original size:13 final size:13
Alignment explanation
Indices: 629058--629091 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
629048 TTGGAGTGCA
*
629058 AAATACAAGATGC
1 AAATGCAAGATGC
629071 AAATGCAAGATGC
1 AAATGCAAGATGC
629084 AAATGCAA
1 AAATGCAA
629092 CAAGGAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.53, C:0.15, G:0.18, T:0.15
Consensus pattern (13 bp):
AAATGCAAGATGC
Found at i:631512 original size:17 final size:17
Alignment explanation
Indices: 631482--631536 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
631472 TAATTAAAAT
631482 AAAATAAAAA-AGTACA
1 AAAATAAAAACAGTACA
*
631498 ATAATAAAAACAGTA-A
1 AAAATAAAAACAGTACA
*
631514 AAAAGTAAAAACAATACA
1 AAAA-TAAAAACAGTACA
631532 TAAAA
1 -AAAA
631537 AACTTGAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
16 13 0.41
17 14 0.44
18 1 0.03
19 4 0.12
ACGTcount: A:0.73, C:0.07, G:0.05, T:0.15
Consensus pattern (17 bp):
AAAATAAAAACAGTACA
Found at i:632171 original size:117 final size:112
Alignment explanation
Indices: 631958--632254 Score: 375
Period size: 112 Copynumber: 2.6 Consensus size: 112
631948 TAAGTTAGCG
* * * * * *
631958 ATTAGGGGTTAGTAGGGTCCGAACCATAATAGTGTGGGTCTTACCCCGG--CGGTTCACCACAAG
1 ATTAGCGGTTAGCAGAGTCCGAACCATAATAATGTGGATCTTACCCCGGATCGGGTCACCACAAG
* *
632021 GTCAAATCGAATAATGCAAACAAATATAAAAAAA-CAAATAAAAATTTAAATA
66 GTCGAATCGAATAATGCAAACAAATATAAAAAAATAAAAT-AAAA--T--A-A
* *
632073 ATTAGTGGTTAGCAGAGTCTGAACCATAATAATGTGGATCTTACCCCGGATCGGGTCACCACAAG
1 ATTAGCGGTTAGCAGAGTCCGAACCATAATAATGTGGATCTTACCCCGGATCGGGTCACCACAAG
* *
632138 GTCGAATCGAATAATGTAAACAAATATATAAAAATAAAATAAAATAA
66 GTCGAATCGAATAATGCAAACAAATATAAAAAAATAAAATAAAATAA
* * * *
632185 ATTAGCGGTTAGCATACTCCAAACCATAATAATGTGGATCTTACCCCGGATCGGGTCACCACAAA
1 ATTAGCGGTTAGCAGAGTCCGAACCATAATAATGTGGATCTTACCCCGGATCGGGTCACCACAAG
632250 GTCGA
66 GTCGA
632255 GTAATAAGAG
Statistics
Matches: 162, Mismatches: 17, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
112 65 0.40
113 1 0.01
115 44 0.27
117 48 0.30
118 4 0.02
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (112 bp):
ATTAGCGGTTAGCAGAGTCCGAACCATAATAATGTGGATCTTACCCCGGATCGGGTCACCACAAG
GTCGAATCGAATAATGCAAACAAATATAAAAAAATAAAATAAAATAA
Found at i:632283 original size:112 final size:113
Alignment explanation
Indices: 631979--632288 Score: 339
Period size: 112 Copynumber: 2.7 Consensus size: 113
631969 GTAGGGTCCG
* * * *
631979 AACCATAATAGTGTGGGTCTTACCCCGG--CGGTTCACCACAAGGTCAAATCGAATAATGCAAAC
1 AACCATAATAATGTGGATCTTACCCCGGATCGGGTCACCACAAGGTCGAATC-AATAATGCAAAC
* * * **
632042 AAATATAA-AAAAACAAATAAAAATTTAAATAATTAGTGGTTAGCAGAGTCTG
65 -AATA-AATAAAAA-AAAT-AAAATTAAAATAATTAGCGGTTAGCAGACTCCA
*
632094 AACCATAATAATGTGGATCTTACCCCGGATCGGGTCACCACAAGGTCGAATCGAATAATGTAAAC
1 AACCATAATAATGTGGATCTTACCCCGGATCGGGTCACCACAAGGTCGAATC-AATAATGCAAAC
* * *
632159 AA-ATAT-ATAAAAATAAAA-TAAAATAAATTAGCGGTTAGCATACTCCA
65 AATAAATAAAAAAAATAAAATTAAAAT-AATTAGCGGTTAGCAGACTCCA
* * *
632206 AACCATAATAATGTGGATCTTACCCCGGATCGGGTCACCACAAAGTCGAGT-AATAA-GAGAAAC
1 AACCATAATAATGTGGATCTTACCCCGGATCGGGTCACCACAAGGTCGAATCAATAATG-CAAAC
*
632269 AATAAATAAAAAAAACAAAA
65 AATAAATAAAAAAAATAAAA
632289 GTTAGAATGC
Statistics
Matches: 169, Mismatches: 19, Indels: 17
0.82 0.09 0.08
Matches are distributed among these distances:
109 1 0.01
110 11 0.07
111 8 0.05
112 80 0.47
113 4 0.02
114 4 0.02
115 27 0.16
116 2 0.01
117 32 0.19
ACGTcount: A:0.45, C:0.17, G:0.16, T:0.22
Consensus pattern (113 bp):
AACCATAATAATGTGGATCTTACCCCGGATCGGGTCACCACAAGGTCGAATCAATAATGCAAACA
ATAAATAAAAAAAATAAAATTAAAATAATTAGCGGTTAGCAGACTCCA
Found at i:633801 original size:29 final size:29
Alignment explanation
Indices: 633779--633842 Score: 119
Period size: 29 Copynumber: 2.2 Consensus size: 29
633769 TATTTATTTA
633779 TAACTACTAACTTTTATTTTATTGCATAT
1 TAACTACTAACTTTTATTTTATTGCATAT
*
633808 TAACTACTAACTTTTATTTTATTGCATTT
1 TAACTACTAACTTTTATTTTATTGCATAT
633837 TAACTA
1 TAACTA
633843 TTGTTTATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.31, C:0.14, G:0.03, T:0.52
Consensus pattern (29 bp):
TAACTACTAACTTTTATTTTATTGCATAT
Found at i:633855 original size:4 final size:4
Alignment explanation
Indices: 633846--633875 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
633836 TTAACTATTG
*
633846 TTTA TTTA TTTA TTTA TATA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
633876 GTTTTCTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:634014 original size:112 final size:106
Alignment explanation
Indices: 633891--634176 Score: 364
Period size: 104 Copynumber: 2.7 Consensus size: 106
633881 CTCTTATTAC
* *
633891 TCGACCTTGTGGTGACCCGATTCGAGGTAAGATCCACATTATTATAGTTCGAACTCTACTAACCA
1 TCGACCTTGTGGTGACCCGATTCGAGGTAAGATCCACATTATTATGGTTCGAACTCTGCTAACCA
633956 CTAACTTATTTTATTTTATTTTTATATATTTGT-TTACATTATTCGAT
66 CTAACTT-TTTTA--TT-TTTTTAT-T-TTT-TATTACATTATTCGAT
* * *
634003 TCGACCTTGTGGTGACCCGATCCGGGGTAAGATCCACATTATTATGGTTCGGACTCTGCTAACCA
1 TCGACCTTGTGGTGACCCGATTCGAGGTAAGATCCACATTATTATGGTTCGAACTCTGCTAACCA
*
634068 CT-A-TTTTTTATTTTTTTATTTTTTATTGCATTATTCGAT
66 CTAACTTTTTTATTTTTTTATTTTTTATTACATTATTCGAT
* * * * *
634107 TCGACCTTGTGGTTACCCGA-TCTAGGGTAAGACCCACATTATTATGGTCCGAACCCTGCTAACC
1 TCGACCTTGTGGTGACCCGATTCGA-GGTAAGATCCACATTATTATGGTTCGAACTCTGCTAACC
*
634171 CCTAAC
65 ACTAAC
634177 CGCTAACTTA
Statistics
Matches: 155, Mismatches: 15, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
103 2 0.01
104 72 0.46
105 2 0.01
106 7 0.05
107 2 0.01
109 5 0.03
110 2 0.01
111 1 0.01
112 62 0.40
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.39
Consensus pattern (106 bp):
TCGACCTTGTGGTGACCCGATTCGAGGTAAGATCCACATTATTATGGTTCGAACTCTGCTAACCA
CTAACTTTTTTATTTTTTTATTTTTTATTACATTATTCGAT
Found at i:634341 original size:16 final size:17
Alignment explanation
Indices: 634322--634361 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
634312 TTGCTATATT
*
634322 TTATTTC-AGCTTTTTA
1 TTATTTCGAGCATTTTA
634338 TTATTTCGAGCATTTTA
1 TTATTTCGAGCATTTTA
634355 TGTATTT
1 T-TATTT
634362 GCATTTAAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.33
17 9 0.43
18 5 0.24
ACGTcount: A:0.20, C:0.10, G:0.10, T:0.60
Consensus pattern (17 bp):
TTATTTCGAGCATTTTA
Found at i:634627 original size:16 final size:17
Alignment explanation
Indices: 634602--634641 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
634592 TTTATTTCAA
*
634602 GTTTTT-TTA-TGTATT
1 GTTTTTATTATTGTACT
634617 GTTTTTATTATTGTACT
1 GTTTTTATTATTGTACT
634634 -TTTTTATT
1 GTTTTTATT
634642 TTTATTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 6 0.27
16 11 0.50
17 5 0.23
ACGTcount: A:0.15, C:0.03, G:0.10, T:0.72
Consensus pattern (17 bp):
GTTTTTATTATTGTACT
Found at i:638061 original size:30 final size:31
Alignment explanation
Indices: 638010--638085 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 31
638000 AAAATCAATG
* * * **
638010 GTTAAATTAGTATTTTATCTAA-ATTTTAAA
1 GTTAAATTAGAAATTTATCTAATAATCAAAA
*
638040 GTTAAATTAGAAATTTGTCTAATAATCAAAA
1 GTTAAATTAGAAATTTATCTAATAATCAAAA
*
638071 GTTAAATTAAAAATT
1 GTTAAATTAGAAATT
638086 ATTTTTTTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 19 0.50
31 19 0.50
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (31 bp):
GTTAAATTAGAAATTTATCTAATAATCAAAA
Found at i:642236 original size:2 final size:2
Alignment explanation
Indices: 642229--642327 Score: 191
Period size: 2 Copynumber: 50.0 Consensus size: 2
642219 ATTCCAATAC
642229 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
642271 TA TA TA TA TA TA TA TA TA TA TA TA -A 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
642312 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
642328 CTAAATAAAG
Statistics
Matches: 96, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 95 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:645011 original size:119 final size:120
Alignment explanation
Indices: 644786--645025 Score: 428
Period size: 119 Copynumber: 2.0 Consensus size: 120
644776 TGTTTGGTCA
* *
644786 AAATCATGTGGGGTTGTGAGGCCATTTTCTGACCTCAAATATAGCAATAGAACTGTCATTTCTCT
1 AAATCATATGGGGCTGTGAGGCCATTTTCTGACCTCAAATATAGCAATAGAACTGTCATTTCTCT
* *
644851 ATTGATCGTGAACCAGTTTCGTATTTCAAATGCATTTTTCATTTGACTTTCTTTC
66 ATTGATAGTGAACCAGTTTCGTATTTCAAATGCATTTTTCATTTGACTTCCTTTC
644906 AAATCATAT-GGGCTGTGAGGCCATTTTCTGACCTCAAATATAGCAATAGAACTGTCATTTCTCT
1 AAATCATATGGGGCTGTGAGGCCATTTTCTGACCTCAAATATAGCAATAGAACTGTCATTTCTCT
*
644970 ATTGGTAGTGAACCAGTTTCGTATTTCAAATGCATTTTTCATTTGACTTCCTTTC
66 ATTGATAGTGAACCAGTTTCGTATTTCAAATGCATTTTTCATTTGACTTCCTTTC
645025 A
1 A
645026 TTAATTGATC
Statistics
Matches: 115, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
119 107 0.93
120 8 0.07
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (120 bp):
AAATCATATGGGGCTGTGAGGCCATTTTCTGACCTCAAATATAGCAATAGAACTGTCATTTCTCT
ATTGATAGTGAACCAGTTTCGTATTTCAAATGCATTTTTCATTTGACTTCCTTTC
Done.