Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008463.1 Hibiscus syriacus cultivar Beakdansim tig00111276_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: 1833679
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 11
Found at i:481631 original size:33 final size:33
Alignment explanation
Indices: 481589--481681 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
481579 CAAAATCGCA
*
481589 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
481622 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
481655 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
481682 TTGGTTTCGC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:483574 original size:38 final size:38
Alignment explanation
Indices: 483531--483603 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
483521 AATTGATTGT
*
483531 TTTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
483569 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
483604 TGTAAAAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.53
Consensus pattern (38 bp):
TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
Found at i:483590 original size:19 final size:19
Alignment explanation
Indices: 483526--483590 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
483516 AGTTTAATTG
*
483526 ATTGTTTTTTGATTGTTTA
1 ATTGATTTTTGATTGTTTA
* * ** *
483545 ATTGATTTGTAAAAG-TTG
1 ATTGATTTTTGATTGTTTA
*
483563 ATTCAATTTTTGATTGTTTA
1 ATT-GATTTTTGATTGTTTA
483583 ATTGATTT
1 ATTGATTT
483591 GTAAAAGATG
Statistics
Matches: 31, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
18 5 0.16
19 21 0.68
20 5 0.16
ACGTcount: A:0.25, C:0.02, G:0.15, T:0.58
Consensus pattern (19 bp):
ATTGATTTTTGATTGTTTA
Found at i:483604 original size:14 final size:14
Alignment explanation
Indices: 483585--483620 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
483575 ATTGTTTAAT
483585 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
483599 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
483613 TGATTTGT
1 TGATTTGT
483621 GTAATTGATG
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:483743 original size:19 final size:19
Alignment explanation
Indices: 483727--483827 Score: 158
Period size: 19 Copynumber: 5.6 Consensus size: 19
483717 AAAAATGACT
483727 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
483746 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
483765 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
483779 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
483798 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
483817 ATCGCAATGCG
1 ATCGCAATGCG
483828 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 10
0.86 0.02 0.11
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 59 0.79
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:483874 original size:52 final size:52
Alignment explanation
Indices: 483834--484152 Score: 541
Period size: 52 Copynumber: 6.0 Consensus size: 52
483824 TGCGTTTATA
*
483834 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
483886 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
483938 ATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
483995 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
484047 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGA-TTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
484098 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
484151 AT
1 AT
484153 GTTGGGATTT
Statistics
Matches: 255, Mismatches: 5, Indels: 13
0.93 0.02 0.05
Matches are distributed among these distances:
51 41 0.16
52 150 0.59
53 6 0.02
54 7 0.03
55 8 0.03
57 43 0.17
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:483880 original size:19 final size:19
Alignment explanation
Indices: 483856--484180 Score: 396
Period size: 19 Copynumber: 18.4 Consensus size: 19
483846 GATTATCTCG
483856 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
483875 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
483894 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
483908 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
483927 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
483946 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
483965 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
483984 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
484003 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
484017 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
484036 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
484055 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
484069 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
484088 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
484106 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
484120 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
484140 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
484154 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
484173 TTGCGATT
1 TTGCGATT
484181 GTATTTTCCG
Statistics
Matches: 268, Mismatches: 12, Indels: 52
0.81 0.04 0.16
Matches are distributed among these distances:
14 35 0.13
16 31 0.12
17 28 0.10
18 21 0.08
19 141 0.53
20 12 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:483981 original size:109 final size:102
Alignment explanation
Indices: 483856--484180 Score: 199
Period size: 109 Copynumber: 3.1 Consensus size: 102
483846 GATTATCTCG
*
483856 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTC-TTTCG-TTGCGATTTT
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTCATTTCGATTGCGATTTT
* *
483918 CATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTA
61 CATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* * *
483965 TTGCGATTTTAATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTC-TCTCG-TTGCGATTTT
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTCATTTCGATTGCGATTTT
* * * * *
484027 CATTTCGCATTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
61 CATTTCGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
* *
484069 TTGCGATTTTCATTTCGCATTGCGATTTCATTTCGCATTGCGA-TTC-TCTCG-TTGCGATTTTC
1 TTGCGATTTTCATTTCGCATTGCGA-TTC-TCTCG--TTGCGATTTCATTTCGATTGCGATTTTC
* * *
484131 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTCATTTCGCG
62 ATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTCATTTCGCA
484173 TTGCGATT
1 TTGCGATT
484181 GTATTTTCCG
Statistics
Matches: 194, Mismatches: 14, Indels: 21
0.85 0.06 0.09
Matches are distributed among these distances:
102 7 0.04
103 45 0.23
104 52 0.27
105 6 0.03
106 6 0.03
107 3 0.02
109 75 0.39
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (102 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTCATTTCGATTGCGATTTTCATTT
CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:484135 original size:33 final size:33
Alignment explanation
Indices: 483875--484180 Score: 271
Period size: 33 Copynumber: 8.8 Consensus size: 33
483865 TCATTTCGCA
*
483875 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
483908 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * *
483944 CATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCG
1 --TTGCGATTTTCATTTCGCATTGCGA--TT-CTCTCG
483982 CATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
484017 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
484053 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
484088 TTGCGA-TTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
484120 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
* *
484154 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
484181 GTATTTTCCG
Statistics
Matches: 233, Mismatches: 20, Indels: 40
0.80 0.07 0.14
Matches are distributed among these distances:
30 9 0.04
31 5 0.02
32 10 0.04
33 75 0.32
34 29 0.12
35 13 0.06
36 11 0.05
37 2 0.01
38 67 0.29
39 3 0.01
40 9 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:484150 original size:71 final size:71
Alignment explanation
Indices: 483856--484180 Score: 376
Period size: 71 Copynumber: 4.6 Consensus size: 71
483846 GATTATCTCG
483856 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
483921 TTCGCA
66 TTCGCA
* *
483927 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TT-CTTTCG--TTGCGATT
483992 TTCATTTCGCA
61 TTCATTTCGCA
*
484003 TTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--TTGCGATT
*
484061 TTC-TCTCG--
61 TTCATTTCGCA
*
484069 TTGCGATTTTCATTTCGCATTGCGA-TTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
484133 TTCCGCA
66 TT-CGCA
* *
484140 TTGCGATTTTCA--T-G--TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT
484181 GTATTTTCCG
Statistics
Matches: 225, Mismatches: 11, Indels: 40
0.82 0.04 0.14
Matches are distributed among these distances:
65 6 0.03
66 11 0.05
67 26 0.12
68 13 0.06
69 10 0.04
70 18 0.08
71 102 0.45
73 6 0.03
74 8 0.04
76 25 0.11
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (71 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
TTCGCA
Found at i:486501 original size:12 final size:12
Alignment explanation
Indices: 486484--486508 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
486474 TCTTCGGGGA
486484 CTTTTTCTTCTT
1 CTTTTTCTTCTT
486496 CTTTTTCTTCTT
1 CTTTTTCTTCTT
486508 C
1 C
486509 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:486717 original size:24 final size:24
Alignment explanation
Indices: 486683--486729 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
486673 CTGAAACATC
486683 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
486707 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
486730 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:487430 original size:20 final size:20
Alignment explanation
Indices: 487402--487770 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
487392 AAATTTCAGT
* * * *
487402 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
487422 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
487442 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
487462 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
487482 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
487502 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
487522 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
487542 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
487562 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
487582 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
487602 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
487622 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
487642 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
487662 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
487682 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
487702 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
487722 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
487742 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
487762 GTTGCGATT
1 GTTGCGATT
487771 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:488895 original size:15 final size:16
Alignment explanation
Indices: 488865--488907 Score: 61
Period size: 15 Copynumber: 2.7 Consensus size: 16
488855 ATAAATCACT
488865 TACCCGGATGTTTCGGA
1 TACCCGGAT-TTTCGGA
*
488882 TACCC-GATTTTCGGG
1 TACCCGGATTTTCGGA
488897 TACCCGGATTT
1 TACCCGGATTT
488908 GCACACCCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 11 0.46
16 8 0.33
17 5 0.21
ACGTcount: A:0.16, C:0.26, G:0.26, T:0.33
Consensus pattern (16 bp):
TACCCGGATTTTCGGA
Found at i:493601 original size:20 final size:20
Alignment explanation
Indices: 493566--493626 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
493556 CCGAGTGATG
493566 ATTAT-TATATATATATGT-T
1 ATTATATATATATATAT-TAT
493585 ATTATATATA-ATAATATTAT
1 ATTATATATATAT-ATATTAT
493605 ATTATA-A-ATAT-TATTAT
1 ATTATATATATATATATTAT
493622 -TTATA
1 ATTATA
493627 AATCCTGAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
16 5 0.13
17 6 0.16
18 1 0.03
19 11 0.29
20 15 0.39
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
ATTATATATATATATATTAT
Found at i:493628 original size:16 final size:16
Alignment explanation
Indices: 493566--493629 Score: 76
Period size: 16 Copynumber: 4.0 Consensus size: 16
493556 CCGAGTGATG
*
493566 ATTATTATATATATAT
1 ATTATTATATATAAAT
*
493582 GTTATTATATAT-AAT
1 ATTATTATATATAAAT
*
493597 AATATTATATTATAAAT
1 ATTATTATA-TATAAAT
*
493614 ATTATTATTTATAAAT
1 ATTATTATATATAAAT
493630 CCTGAAGGCC
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
15 9 0.22
16 21 0.52
17 10 0.25
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (16 bp):
ATTATTATATATAAAT
Found at i:500302 original size:22 final size:22
Alignment explanation
Indices: 500274--500355 Score: 110
Period size: 22 Copynumber: 3.7 Consensus size: 22
500264 AATTCGGTAT
*
500274 TGTTCACGGTACTGTTAATTAC
1 TGTTCACGGTACTGTTCATTAC
*
500296 TGTTCACGGTAATGTTCATTAC
1 TGTTCACGGTACTGTTCATTAC
* * *
500318 TATTCACGGCACTGTTCATTAT
1 TGTTCACGGTACTGTTCATTAC
*
500340 TGTTCACGGTTCTGTT
1 TGTTCACGGTACTGTT
500356 TATATCATAT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.43
Consensus pattern (22 bp):
TGTTCACGGTACTGTTCATTAC
Found at i:501294 original size:21 final size:21
Alignment explanation
Indices: 501270--501329 Score: 93
Period size: 21 Copynumber: 2.9 Consensus size: 21
501260 AGTCGAGGAT
* *
501270 TACAGTGTTTTTTCGGGATAA
1 TACAGTGGTCTTTCGGGATAA
*
501291 TACAGTGGTCTTTCAGGATAA
1 TACAGTGGTCTTTCGGGATAA
501312 TACAGTGGTCTTTCGGGA
1 TACAGTGGTCTTTCGGGA
501330 CATAGTGGTC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.23, C:0.13, G:0.27, T:0.37
Consensus pattern (21 bp):
TACAGTGGTCTTTCGGGATAA
Found at i:501617 original size:18 final size:18
Alignment explanation
Indices: 501594--501637 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
501584 AATGTTAATA
*
501594 CATGATAGTGATAGAGAT
1 CATGATAATGATAGAGAT
501612 CATGATAATGATAGAGAT
1 CATGATAATGATAGAGAT
501630 CATGATAA
1 CATGATAA
501638 AGATGTTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.43, C:0.07, G:0.23, T:0.27
Consensus pattern (18 bp):
CATGATAATGATAGAGAT
Found at i:504329 original size:22 final size:22
Alignment explanation
Indices: 504301--504342 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
504291 ATGTTGTAAA
504301 GATGATAGATTCTCTTTTCAAG
1 GATGATAGATTCTCTTTTCAAG
*
504323 GATGATAGATTTTCTTTTCA
1 GATGATAGATTCTCTTTTCA
504343 TAGACAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.12, G:0.17, T:0.45
Consensus pattern (22 bp):
GATGATAGATTCTCTTTTCAAG
Found at i:520624 original size:14 final size:14
Alignment explanation
Indices: 520605--520641 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
520595 CTAAGACCCT
*
520605 CTCTCTCTCTCCCA
1 CTCTCTCTCTCACA
*
520619 CTCTCTCTCTGACA
1 CTCTCTCTCTCACA
520633 CTCTCTCTC
1 CTCTCTCTC
520642 ATGATTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.08, C:0.51, G:0.03, T:0.38
Consensus pattern (14 bp):
CTCTCTCTCTCACA
Found at i:524822 original size:59 final size:59
Alignment explanation
Indices: 524746--524859 Score: 176
Period size: 59 Copynumber: 1.9 Consensus size: 59
524736 TGGGCCCCCC
*
524746 GACTATAGGGTGATGCTTTGTTGAGTCCC-CAACTATTAAAAATTACAAAATGGTCCTCT
1 GACTATAGAGTGATGCTTTGTTGAGTCCCTCAACTATTAAAAATTAC-AAATGGTCCTCT
* * *
524805 GACTATAGAGTGTTGCTTTGTTGAGTCCCTCGACTATTAAAAGTTACAAATGGTC
1 GACTATAGAGTGATGCTTTGTTGAGTCCCTCAACTATTAAAAATTACAAATGGTC
524860 ACCCGACTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
59 35 0.70
60 15 0.30
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (59 bp):
GACTATAGAGTGATGCTTTGTTGAGTCCCTCAACTATTAAAAATTACAAATGGTCCTCT
Found at i:524868 original size:59 final size:57
Alignment explanation
Indices: 524724--524869 Score: 175
Period size: 59 Copynumber: 2.4 Consensus size: 57
524714 AAAATAGGGT
* *
524724 AAAGTATACAAATGGGCCCCCCGACTATAGGGTGATGCTTTGTTGAGTCCCCAACTATTA
1 AAAGT-TACAAAT-GG-TCCCCGACTATAGAGTGATGCTTTGTTGAGTCCCCAACTATTA
* * * *
524784 AAAATTACAAAATGGTCCTCTGACTATAGAGTGTTGCTTTGTTGAGTCCCTCGACTATTA
1 AAAGTTAC-AAATGGTCC-CCGACTATAGAGTGATGCTTTGTTGAGTCCC-CAACTATTA
524844 AAAGTTACAAATGGTCACCCGACTAT
1 AAAGTTACAAATGGTC-CCCGACTAT
524870 TCATTATGTT
Statistics
Matches: 74, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
58 2 0.03
59 48 0.65
60 24 0.32
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.29
Consensus pattern (57 bp):
AAAGTTACAAATGGTCCCCGACTATAGAGTGATGCTTTGTTGAGTCCCCAACTATTA
Found at i:528646 original size:12 final size:12
Alignment explanation
Indices: 528631--528676 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
528621 CGGTTTTTTT
*
528631 ACCGGATAAAAA
1 ACCGGTTAAAAA
528643 ACCGGTTTGAAAAAA
1 ACCGG-TT--AAAAA
528658 ACCGGTTAAAAA
1 ACCGGTTAAAAA
528670 ACCGGTT
1 ACCGGTT
528677 TTTATCCGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 17 0.57
13 1 0.03
14 2 0.07
15 10 0.33
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:528658 original size:15 final size:13
Alignment explanation
Indices: 528637--528677 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
528627 TTTTACCGGA
528637 TAAAAAACCGGTT
1 TAAAAAACCGGTT
528650 TGAAAAAAACCGG-T
1 T--AAAAAACCGGTT
528664 TAAAAAACCGGTT
1 TAAAAAACCGGTT
528677 T
1 T
528678 TTATCCGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 3 0.12
14 2 0.08
15 10 0.40
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:530975 original size:21 final size:21
Alignment explanation
Indices: 530951--530990 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
530941 TTTATTTTAT
530951 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
530972 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
530991 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:531038 original size:33 final size:33
Alignment explanation
Indices: 530985--531083 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
530975 TTTGTTTCAA
530985 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
531017 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
531050 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
531083 T
1 T
531084 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:531112 original size:13 final size:13
Alignment explanation
Indices: 531069--531123 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
531059 TTGGAAGTAT
531069 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
531082 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
531096 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
531109 TTAAGTATTTGAA
1 TTAAGTATTTCAA
531122 TT
1 TT
531124 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:531345 original size:21 final size:21
Alignment explanation
Indices: 531319--531375 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
531309 TGGAGCATGG
*
531319 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
531340 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
531361 GGTAATCGGTTCCCT
1 GGGAATCGGTTCCCT
531376 AAGTGTAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.19, C:0.26, G:0.25, T:0.30
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:531593 original size:18 final size:17
Alignment explanation
Indices: 531564--531610 Score: 85
Period size: 17 Copynumber: 2.8 Consensus size: 17
531554 TTTTATAACT
531564 GGTTTTTTAAAAAAACC
1 GGTTTTTTAAAAAAACC
531581 GGTTTTTTAAAAAAACC
1 GGTTTTTTAAAAAAACC
*
531598 GGTTTTTTTAAAA
1 GGTTTTTTAAAAA
531611 CCGAAACCGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (17 bp):
GGTTTTTTAAAAAAACC
Found at i:531610 original size:15 final size:15
Alignment explanation
Indices: 531541--531613 Score: 65
Period size: 17 Copynumber: 4.6 Consensus size: 15
531531 ATCTGGAATA
*
531541 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
* *
531556 TTATAACTGGTTTTT
1 TTAAAACCGGTTTTT
*
531571 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
*
531588 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
531605 TTAAAACCG
1 TTAAAACCG
531614 AAACCGGTTA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
15 20 0.41
17 29 0.59
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.42
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:531776 original size:21 final size:21
Alignment explanation
Indices: 531750--531789 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
531740 TCCAAGTATT
531750 TGAGAGGAAACCGATTCCCTA
1 TGAGAGGAAACCGATTCCCTA
**
531771 TGAGAGGGTACCGATTCCC
1 TGAGAGGAAACCGATTCCC
531790 CCATGCTCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.25, G:0.28, T:0.20
Consensus pattern (21 bp):
TGAGAGGAAACCGATTCCCTA
Found at i:532006 original size:13 final size:13
Alignment explanation
Indices: 531985--532039 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
531975 AAGTTCGATA
*
531985 AATTCAAATACTT
1 AATTGAAATACTT
531998 AATTGAAATACTT
1 AATTGAAATACTT
* *
532011 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
532025 AATTGAAATACTT
1 AATTGAAATACTT
532038 AA
1 AA
532040 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:532085 original size:34 final size:33
Alignment explanation
Indices: 532025--532124 Score: 157
Period size: 34 Copynumber: 3.0 Consensus size: 33
532015 AACTCAACAT
* * *
532025 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
532058 AATTCAAATACTTAAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTT-AAAAACTTCCAAGTTCGATA
532092 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
532124 A
1 A
532125 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
32 12 0.19
33 20 0.32
34 31 0.49
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:532143 original size:21 final size:21
Alignment explanation
Indices: 532119--532158 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
532109 ACTTCAAGTT
532119 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
532140 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
532159 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:539414 original size:2 final size:2
Alignment explanation
Indices: 539407--539431 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
539397 TCAAAATTAG
539407 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
539432 AATCAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:540398 original size:14 final size:15
Alignment explanation
Indices: 540378--540415 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
540368 AAATATACCT
540378 TAATAATATTAAAAA
1 TAATAATATTAAAAA
540393 -AATAATA-TAAAAA
1 TAATAATATTAAAAA
540406 TAATATATAT
1 TAATA-ATAT
540416 ATATATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
13 6 0.30
14 11 0.55
15 3 0.15
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
TAATAATATTAAAAA
Found at i:540413 original size:2 final size:2
Alignment explanation
Indices: 540408--540438 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
540398 TATAAAAATA
*
540408 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
540439 AAATATTTGT
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:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:543500 original size:2 final size:2
Alignment explanation
Indices: 543484--543528 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
543474 TACAATAGTA
*
543484 AT AT -T AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
543525 AT AT
1 AT AT
543529 TAGACTTAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:547066 original size:12 final size:12
Alignment explanation
Indices: 547049--547075 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
547039 TTAATCGCGA
547049 AAATTGAAATTT
1 AAATTGAAATTT
547061 AAATTGAAATTT
1 AAATTGAAATTT
547073 AAA
1 AAA
547076 ACGTTCGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (12 bp):
AAATTGAAATTT
Found at i:547645 original size:35 final size:35
Alignment explanation
Indices: 547599--547670 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
547589 TGGCAGTGCA
547599 CATGTCATAATCATGCAACATTGGTGAGCTAGGGC
1 CATGTCATAATCATGCAACATTGGTGAGCTAGGGC
547634 CATGTCATAATCATGCAACATTGGTGAGCTAGGGC
1 CATGTCATAATCATGCAACATTGGTGAGCTAGGGC
547669 CA
1 CA
547671 ACTGCATATC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (35 bp):
CATGTCATAATCATGCAACATTGGTGAGCTAGGGC
Found at i:548366 original size:3 final size:3
Alignment explanation
Indices: 548346--548422 Score: 93
Period size: 3 Copynumber: 24.7 Consensus size: 3
548336 GCCTACAAAA
* *
548346 AAT AAA AAT AAA AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
548394 AAT AAAT AAAT AAAT AAAT AAT -AT AAT AA
1 AAT -AAT -AAT -AAT -AAT AAT AAT AAT AA
548423 AATGTTTTTT
Statistics
Matches: 68, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.03
3 51 0.75
4 15 0.22
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:548852 original size:84 final size:84
Alignment explanation
Indices: 548669--549053 Score: 376
Period size: 84 Copynumber: 4.6 Consensus size: 84
548659 ACTCGTCAGT
* * * * * *
548669 TTTTGTTGACATATAGCCCTTCT-GACCTTGAGCTATGATGTAAATTTGATTTGCCTTTGAGTTG
1 TTTTGTTGGCAAATAGCCCTTCTAGA-CTTGAGCTATGCTGCAAA--TGATATGCCTTTGAGCTG
* * *
548733 AATGTAATCGAAGTCAAAGGTC
63 AGTGTAATCGAACTCGAAGGTC
* * * * * * *
548755 TTTGGTTGCCAGATAGCCCTTCTCGACTTAAGCTATGCTGTAAATGATATGGCTTTGAGCTGAGT
1 TTTTGTTGGCAAATAGCCCTTCTAGACTTGAGCTATGCTGCAAATGATATGCCTTTGAGCTGAGT
*
548820 GTAATCGAACTCGAAGGTA
66 GTAATCGAACTCGAAGGTC
* *** * * * * *
548839 TTTTGTTGGCAGATAAATCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
1 TTTTGTTGGCAAATAGCCCTTCTAGACTTGAGCTATGCTGCAAATGATATGCCTTTGAGCTGAGT
* *
548904 ATAGTCGAACTCGAAGGTC
66 GTAATCGAACTCGAAGGTC
* * * * * *
548923 TTTGGTTGGCAAATAACGCTTCTAGCCTTGAGTTATGCTACAAATGATATGCCTTTGAGCTGAGT
1 TTTTGTTGGCAAATAGCCCTTCTAGACTTGAGCTATGCTGCAAATGATATGCCTTTGAGCTGAGT
*
548988 GTAGTCGAACTCGAAGGTC
66 GTAATCGAACTCGAAGGTC
*** * *
549007 TTTTGTTGGCAAATAGCCCTTCTTTCCTTGAGCTATGTTACAAATGA
1 TTTTGTTGGCAAATAGCCCTTCTAGACTTGAGCTATGCTGCAAATGA
549054 ACACGATATC
Statistics
Matches: 253, Mismatches: 45, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
84 215 0.85
86 36 0.14
87 2 0.01
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (84 bp):
TTTTGTTGGCAAATAGCCCTTCTAGACTTGAGCTATGCTGCAAATGATATGCCTTTGAGCTGAGT
GTAATCGAACTCGAAGGTC
Found at i:549257 original size:124 final size:124
Alignment explanation
Indices: 549125--549474 Score: 504
Period size: 124 Copynumber: 2.8 Consensus size: 124
549115 ATCCTTCATT
* * * * * * ** *
549125 GTGAAGTTGAAATCGTAGAGGGCCCTTTCGTTGTGAAAATGAGCCTTGAATTGGATATCCTTCAT
1 GTGAAGTTGAAACCGTGGATGACCCATTCATTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGT
* * * * *
549190 CATGAAGTTGAAATCCAATCTGAAGATGAATGTTGCTGGTGGGCACGA-TTCCTTTCGTC
66 CGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTAGTGAGCACGATTTAC-TTCGTC
* *
549249 GTGAAGTTGAAACCATGGATGACCCCTTCATTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGT
1 GTGAAGTTGAAACCGTGGATGACCCATTCATTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGT
* * *
549314 CGTGAAGTTGAAATTCGATCTAAAGATGAATGTTACTAGTGAGCACGATTTACTTCGTC
66 CGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTAGTGAGCACGATTTACTTCGTC
*
549373 GTGAAGTTGAAACCGTGGATGACCCATTCTTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGT
1 GTGAAGTTGAAACCGTGGATGACCCATTCATTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGT
549438 CGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCT
66 CGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCT
549475 TCGAGTCCAA
Statistics
Matches: 201, Mismatches: 24, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
124 198 0.99
125 3 0.01
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.32
Consensus pattern (124 bp):
GTGAAGTTGAAACCGTGGATGACCCATTCATTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGT
CGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTAGTGAGCACGATTTACTTCGTC
Found at i:549687 original size:110 final size:110
Alignment explanation
Indices: 549543--549942 Score: 316
Period size: 110 Copynumber: 3.5 Consensus size: 110
549533 CCATTCACCA
* *
549543 TGAAGTTGAGCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGTTCGCACG
1 TGAAGTTGAGCTTTGAATTGAATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGTTCGCACA
549608 ATATCCTTCGTCGTGAAGTTGAAATCGTAGACGACCCCTTCGTTG
66 ATATCCTTCGTCGTGAAGTTGAAATCGTAGACGACCCCTTCGTTG
* * * * * * * *
549653 TGAAGCTGAGCCTTGACTTGAATATCTTTCGTCGTAAAGTTGATATCCAAGCTTGTATTGTTTCG
1 TGAAGTTGAGCTTTGAATTGAATATCCTTCGTCGTGAAGTTGAAATCCAATCTAG-A--G-TTCG
* * * ***
549718 -AGTCCAATATCCTTCGCCGTGAAGTTAAAATTGGCTCTGAATGAAACTGGGAAGCCCCTTCACC
62 CA---CAATATCCTTCGTCGTGAAGTTGAAA-----TC-G--T-AGAC---G-A-CCCCTTCGTT
549782 G
110 G
* * * * ** **
549783 TGAAGTTGAGCTTTGAATTGGATATCCTTCATCATGAATTTGAAATCCAATCTAGAGTTTACATT
1 TGAAGTTGAGCTTTGAATTGAATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGTTCGCACA
* * * * *
549848 ATATCCTTTGTCGTGAAGTTGAAATCGTGGATGGCCCATTCGTTG
66 ATATCCTTCGTCGTGAAGTTGAAATCGTAGACGACCCCTTCGTTG
* * *
549893 TGAAGTTGAGCATTGACTTGAATATCCTTCGCCGTGAAGTTGAAATCCAA
1 TGAAGTTGAGCTTTGAATTGAATATCCTTCGTCGTGAAGTTGAAATCCAA
549943 GTATTGTATG
Statistics
Matches: 218, Mismatches: 50, Indels: 44
0.70 0.16 0.14
Matches are distributed among these distances:
110 96 0.44
111 1 0.00
112 1 0.00
113 2 0.01
114 4 0.02
115 1 0.00
116 24 0.11
118 1 0.00
119 2 0.01
121 2 0.01
122 1 0.00
124 22 0.10
125 3 0.01
126 2 0.01
127 2 0.01
128 1 0.00
129 2 0.01
130 51 0.23
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (110 bp):
TGAAGTTGAGCTTTGAATTGAATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGTTCGCACA
ATATCCTTCGTCGTGAAGTTGAAATCGTAGACGACCCCTTCGTTG
Found at i:549789 original size:240 final size:242
Alignment explanation
Indices: 549356--549943 Score: 838
Period size: 240 Copynumber: 2.4 Consensus size: 242
549346 TTACTAGTGA
* * * *
549356 GCACGATTTACTTCGTCGTGAAGTTGAAACCGTGGATGACCCATTCTTTGTGAAGTTGAGCCTTG
1 GCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTTG
* * * *
549421 AATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTTCGAGTCCAAA
66 ACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCT----ATG-ATATTGCTTCGAGTCCAAA
*
549486 ATCCTTCGCCGTGAAGTTGAAATTGGCTCTGAATGAAACTGGGAAGCCCATTCACCATGAAGTTG
126 ATCCTTCGCCGTGAAGTTAAAATTGGCTCTGAATGAAACTGGGAAGCCCATTCACCATGAAGTTG
* *
549551 AGCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGTTC
191 AGCTTTGAATTGGATATCCTTCATCATGAAGTTGAAATCCAATCTAGAGTTC
* * * *
549603 GCACGATATCCTTCGTCGTGAAGTTGAAATCGTAGACGACCCCTTCGTTGTGAAGCTGAGCCTTG
1 GCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTTG
* * * * *
549668 ACTTGAATATCTTTCGTCGTAAAGTTGATATCCAAGCT-TG-TATTGTTTCGAGTCCAATATCCT
66 ACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCTATGATATTGCTTCGAGTCCAAAATCCT
* *
549731 TCGCCGTGAAGTTAAAATTGGCTCTGAATGAAACTGGGAAGCCCCTTCACCGTGAAGTTGAGCTT
131 TCGCCGTGAAGTTAAAATTGGCTCTGAATGAAACTGGGAAGCCCATTCACCATGAAGTTGAGCTT
* *
549796 TGAATTGGATATCCTTCATCATGAATTTGAAATCCAATCTAGAGTTT
196 TGAATTGGATATCCTTCATCATGAAGTTGAAATCCAATCTAGAGTTC
* ** * * *
549843 ACATTATATCCTTTGTCGTGAAGTTGAAATCGTGGATGGCCCATTCGTTGTGAAGTTGAGCATTG
1 GCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTTG
*
549908 ACTTGAATATCCTTCGCCGTGAAGTTGAAATCCAAG
66 ACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAG
549944 TATTGTATGT
Statistics
Matches: 303, Mismatches: 38, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
240 212 0.70
242 2 0.01
247 89 0.29
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.32
Consensus pattern (242 bp):
GCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTTG
ACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCTATGATATTGCTTCGAGTCCAAAATCCT
TCGCCGTGAAGTTAAAATTGGCTCTGAATGAAACTGGGAAGCCCATTCACCATGAAGTTGAGCTT
TGAATTGGATATCCTTCATCATGAAGTTGAAATCCAATCTAGAGTTC
Found at i:551222 original size:95 final size:95
Alignment explanation
Indices: 551035--551283 Score: 331
Period size: 95 Copynumber: 2.6 Consensus size: 95
551025 ATAGATCTGG
* *
551035 GGCGTTTAACCAATTTCTCTAGAGGGATAACTCAA--TATCATTGTATAGGTATTATAATCACCT
1 GGCGTTTAACCAATTTCTCTAGAGGGACAACTCAAGCT-TTATTG--TA--TATTATAATCACCT
*
551098 TTATCAGGCTAACTGAATATTATCTATAAAGTAGA
61 TTATCAGGCTAACTGAATATTATCTATAAAGCAGA
**
551133 GGCGTTTAACCAATTGGTCTAGAGGGACAACTCAAGCTTTATTGTATATTATAATCACCTTTATC
1 GGCGTTTAACCAATTTCTCTAGAGGGACAACTCAAGCTTTATTGTATATTATAATCACCTTTATC
* * * * * *
551198 ATGCTAGCTGAATCTTATTTATAAAGCCGG
66 AGGCTAACTGAATATTATCTATAAAGCAGA
551228 GGCGTTTAACCAATTTCTCTAGAGGGACAACTCAAGCTTTATTGTATATATATAAT
1 GGCGTTTAACCAATTTCTCTAGAGGGACAACTCAAGCTTTATTGTATAT-TATAAT
551284 ATTATAATCT
Statistics
Matches: 135, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
95 89 0.66
96 6 0.04
97 2 0.01
98 32 0.24
99 5 0.04
100 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (95 bp):
GGCGTTTAACCAATTTCTCTAGAGGGACAACTCAAGCTTTATTGTATATTATAATCACCTTTATC
AGGCTAACTGAATATTATCTATAAAGCAGA
Found at i:554452 original size:3 final size:3
Alignment explanation
Indices: 554444--554482 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
554434 GCTTACAAAA
554444 AAT AAT AAT AAT AAT AAT AAT AAAT AAT -AT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT A
554483 TTTTTTTTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 4 0.12
3 26 0.79
4 3 0.09
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:555610 original size:27 final size:26
Alignment explanation
Indices: 555555--555614 Score: 93
Period size: 27 Copynumber: 2.3 Consensus size: 26
555545 ATATTAAATA
*
555555 AATTAAAATTATATAAAAAGCTCTCC
1 AATTATAATTATATAAAAAGCTCTCC
*
555581 AATTATAATTATATAAAAAAGCTCTTC
1 AATTATAATTATAT-AAAAAGCTCTCC
555608 AATTATA
1 AATTATA
555615 TGATGACACA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 13 0.42
27 18 0.58
ACGTcount: A:0.50, C:0.12, G:0.03, T:0.35
Consensus pattern (26 bp):
AATTATAATTATATAAAAAGCTCTCC
Found at i:558615 original size:18 final size:18
Alignment explanation
Indices: 558592--558647 Score: 103
Period size: 18 Copynumber: 3.1 Consensus size: 18
558582 ATGATAATGT
*
558592 CCTAATTCTACAACCATG
1 CCTAATTCTACAGCCATG
558610 CCTAATTCTACAGCCATG
1 CCTAATTCTACAGCCATG
558628 CCTAATTCTACAGCCATG
1 CCTAATTCTACAGCCATG
558646 CC
1 CC
558648 GGTGAACAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.29, C:0.36, G:0.09, T:0.27
Consensus pattern (18 bp):
CCTAATTCTACAGCCATG
Found at i:561314 original size:284 final size:284
Alignment explanation
Indices: 560797--561356 Score: 1066
Period size: 284 Copynumber: 2.0 Consensus size: 284
560787 ATAAAATATA
*
560797 CTTACAGAACTATATACCTTGCTTTTATAGAACTATCCTTGTAAATCAGAGCTCAGCAGGCAATC
1 CTTACAGAACTATATAACTTGCTTTTATAGAACTATCCTTGTAAATCAGAGCTCAGCAGGCAATC
560862 TCGCCATATTACTCGCCATCATCTTTCTAAACAAATAAAGGGATAAACGAAACAGTTCTTTGGCC
66 TCGCCATATTACTCGCCATCATCTTTCTAAACAAATAAAGGGATAAACGAAACAGTTCTTTGGCC
560927 TGGAATTTTCCAATTCAATTAAAATGTCAAATAAGTCTAGAAATACTCGGTTATTTGTTGAGGAT
131 TGGAATTTTCCAATTCAATTAAAATGTCAAATAAGTCTAGAAATACTCGGTTATTTGTTGAGGAT
560992 TTAGGGTTTAAAATGTTAAATTTTTATATAAAACTATAAAACATGTGAAGTCATCAAAGTGAGGA
196 TTAGGGTTTAAAATGTTAAATTTTTATATAAAACTATAAAACATGTGAAGTCATCAAAGTGAGGA
561057 TCTAAAGGAAAATTCAGAGCTATC
261 TCTAAAGGAAAATTCAGAGCTATC
*
561081 CTTATAGAACTATATAACTTGCTTTTATAGAACTATCCTTGTAAATCAGAGCTCAGCAGGCAATC
1 CTTACAGAACTATATAACTTGCTTTTATAGAACTATCCTTGTAAATCAGAGCTCAGCAGGCAATC
* *
561146 TCGCCATATTACTCGCCATCATCTTTGTAAACAAATAAAGGGTTAAACGAAACAGTTCTTTGGCC
66 TCGCCATATTACTCGCCATCATCTTTCTAAACAAATAAAGGGATAAACGAAACAGTTCTTTGGCC
*
561211 TGGAATTTTCTAATTCAATTAAAATGTCAAATAAGTCTAGAAATACTCGGTTATTTGTTGAGGAT
131 TGGAATTTTCCAATTCAATTAAAATGTCAAATAAGTCTAGAAATACTCGGTTATTTGTTGAGGAT
*
561276 TTAGGGTTTAAAATGTTAAATTTTTATATAATACTATAAAACATGTGAAGTCATCAAAGTGAGGA
196 TTAGGGTTTAAAATGTTAAATTTTTATATAAAACTATAAAACATGTGAAGTCATCAAAGTGAGGA
561341 TCTAAAGGAAAATTCA
261 TCTAAAGGAAAATTCA
561357 ACACTTCAAA
Statistics
Matches: 270, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
284 270 1.00
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.33
Consensus pattern (284 bp):
CTTACAGAACTATATAACTTGCTTTTATAGAACTATCCTTGTAAATCAGAGCTCAGCAGGCAATC
TCGCCATATTACTCGCCATCATCTTTCTAAACAAATAAAGGGATAAACGAAACAGTTCTTTGGCC
TGGAATTTTCCAATTCAATTAAAATGTCAAATAAGTCTAGAAATACTCGGTTATTTGTTGAGGAT
TTAGGGTTTAAAATGTTAAATTTTTATATAAAACTATAAAACATGTGAAGTCATCAAAGTGAGGA
TCTAAAGGAAAATTCAGAGCTATC
Found at i:567170 original size:14 final size:15
Alignment explanation
Indices: 567141--567176 Score: 65
Period size: 14 Copynumber: 2.5 Consensus size: 15
567131 TAATAAGGTT
567141 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
567156 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
567170 ATTTATT
1 ATTTATT
567177 AGTATGGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:567243 original size:32 final size:32
Alignment explanation
Indices: 567207--567342 Score: 184
Period size: 32 Copynumber: 4.6 Consensus size: 32
567197 TAAAATATAG
*
567207 ATTGATTTATTTTAAATCATTTATTAGTATGA
1 ATTGATTTATTTTAAATAATTTATTAGTATGA
567239 ATTGATTTATTTT-AA-AA--TA-T-G---G-
1 ATTGATTTATTTTAAATAATTTATTAGTATGA
567261 ATTGATTTATTTTAAATAATTTATTAGTATGA
1 ATTGATTTATTTTAAATAATTTATTAGTATGA
*
567293 ATTGATTTATTTTAAATAATTTATTAGTATGG
1 ATTGATTTATTTTAAATAATTTATTAGTATGA
567325 ATTGATTTATTTTAAATA
1 ATTGATTTATTTTAAATA
567343 TGGATTGATT
Statistics
Matches: 92, Mismatches: 2, Indels: 20
0.81 0.02 0.18
Matches are distributed among these distances:
22 13 0.14
23 3 0.03
24 2 0.02
26 3 0.03
27 2 0.02
28 3 0.03
30 1 0.01
31 3 0.03
32 62 0.67
ACGTcount: A:0.36, C:0.01, G:0.10, T:0.53
Consensus pattern (32 bp):
ATTGATTTATTTTAAATAATTTATTAGTATGA
Found at i:567259 original size:22 final size:22
Alignment explanation
Indices: 567234--567276 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
567224 CATTTATTAG
567234 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
567256 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
567277 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:567276 original size:54 final size:54
Alignment explanation
Indices: 567156--567490 Score: 410
Period size: 54 Copynumber: 6.1 Consensus size: 54
567146 TTTTAAAATA
* *
567156 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTTAAAATATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTA-TTTTAAAATATGGATTG
*
567211 ATTTATTTTAAATCATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTG
*
567265 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT-AAATA---ATTT
1 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTG
* * * * * * * ***
567315 ATTAGTATGGATTGATTTATTT-TAAATATGGATTGATTTATTATTGTAGTTGTATGGATTG
1 ATT--TAT--TTTAAATAATTTATTAGTATGAATTGATTTA-T-TT-TA-AAATATGGATTG
567376 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTG
* *
567430 ATTTATTTTAGATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTG
567484 ATTTATT
1 ATTTATT
567491 ATTGTAGTTG
Statistics
Matches: 239, Mismatches: 28, Indels: 27
0.81 0.10 0.09
Matches are distributed among these distances:
50 6 0.03
52 3 0.01
53 20 0.08
54 133 0.56
55 39 0.16
56 3 0.01
57 9 0.04
58 17 0.07
59 3 0.01
61 6 0.03
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTG
Found at i:567284 original size:14 final size:14
Alignment explanation
Indices: 567265--567317 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
567255 ATATGGATTG
567265 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
567279 ATTTATTAGTATGAATTG
1 ATTTATT--T-T-AAATA
567297 ATTTATTTTAAATA
1 ATTTATTTTAAATA
567311 ATTTATT
1 ATTTATT
567318 AGTATGGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 17 0.55
15 1 0.03
16 2 0.06
17 1 0.03
18 10 0.32
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.57
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:567346 original size:21 final size:21
Alignment explanation
Indices: 567320--567389 Score: 77
Period size: 21 Copynumber: 3.1 Consensus size: 21
567310 AATTTATTAG
567320 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
**
567341 TATGGATTGATTTATTATTGTAGTTG
1 TATGGATTGATTTA-T-TT-TA--AA
567367 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
567388 TA
1 TA
567390 ATTTATTAGT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
21 16 0.40
22 1 0.03
23 4 0.10
24 4 0.10
25 1 0.03
26 14 0.35
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (21 bp):
TATGGATTGATTTATTTTAAA
Found at i:567408 original size:32 final size:32
Alignment explanation
Indices: 567366--567473 Score: 128
Period size: 32 Copynumber: 3.7 Consensus size: 32
567356 TATTGTAGTT
*
567366 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGAATTGATTTATTTTAAATAATTTATTA
567398 GTATGAATTGATTTATTTT-AA-AA--TA-T-
1 GTATGAATTGATTTATTTTAAATAATTTATTA
*
567424 G---G-ATTGATTTATTTTAGATAATTTATTA
1 GTATGAATTGATTTATTTTAAATAATTTATTA
567452 GTATGAATTGATTTATTTTAAA
1 GTATGAATTGATTTATTTTAAA
567474 ATATAGATTG
Statistics
Matches: 63, Mismatches: 3, Indels: 20
0.73 0.03 0.23
Matches are distributed among these distances:
22 13 0.21
23 2 0.03
24 2 0.03
26 3 0.05
27 2 0.03
28 3 0.05
30 2 0.03
31 3 0.05
32 33 0.52
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (32 bp):
GTATGAATTGATTTATTTTAAATAATTTATTA
Found at i:567505 original size:80 final size:80
Alignment explanation
Indices: 567421--567570 Score: 282
Period size: 80 Copynumber: 1.9 Consensus size: 80
567411 TATTTTAAAA
*
567421 TATGGATTGATTTATTTTAGATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTGAT
567486 TTATTATTGTAGTTG
66 TTATTATTGTAGTTG
*
567501 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTGAT
567566 TTATT
66 TTATT
567571 TTAAATAATT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
80 68 1.00
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (80 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTGAT
TTATTATTGTAGTTG
Found at i:568376 original size:30 final size:31
Alignment explanation
Indices: 568322--568405 Score: 98
Period size: 30 Copynumber: 2.7 Consensus size: 31
568312 AGTATGCCCC
*
568322 TAATAACAAATATTGAAAAAAAAATTGGACCCT
1 TAATAACAAATATT--AGAAAAAATTGGACCCT
* * * *
568355 TGATAATAAATATT-GAAAAAATTGGGCCTT
1 TAATAACAAATATTAGAAAAAATTGGACCCT
568385 TAATAACAAATATTAGAAAAA
1 TAATAACAAATATTAGAAAAA
568406 GCAAAAAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
30 25 0.58
31 6 0.14
33 12 0.28
ACGTcount: A:0.54, C:0.08, G:0.11, T:0.27
Consensus pattern (31 bp):
TAATAACAAATATTAGAAAAAATTGGACCCT
Found at i:578355 original size:65 final size:64
Alignment explanation
Indices: 578157--578366 Score: 196
Period size: 65 Copynumber: 3.2 Consensus size: 64
578147 TGCACTAAGA
* * ** * * *
578157 GTGCATCGATGCATCAATTGCATTCGATGTTTCAAAAT-AGCCAGAGTGTATCAATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAG-GTGCATCGATGCATGGTTG
* * * *
578221 GTGCATCAATGCATTAAATGCATTCGATGTTTTC-ATAAAATCCTCA-GTGCATCGGTGCATGGT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCAATATAAT--TCAGGTGCATCGATGCATGGT
578284 AT-
63 -TG
* *
578286 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATGGTGCATCGATGCATGGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCA-GGTGCATCGATGCATGG-TT
578350 G
64 G
*
578351 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
578367 CTCTAAAAAA
Statistics
Matches: 118, Mismatches: 18, Indels: 19
0.76 0.12 0.12
Matches are distributed among these distances:
62 3 0.03
63 3 0.03
64 49 0.42
65 60 0.51
66 1 0.01
67 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAGGTGCATCGATGCATGGTTG
Found at i:581024 original size:23 final size:23
Alignment explanation
Indices: 580994--581075 Score: 73
Period size: 23 Copynumber: 3.6 Consensus size: 23
580984 GCATGACCCT
580994 GTGCATCGATGCACATTCAAGGA
1 GTGCATCGATGCACATTCAAGGA
* *
581017 GTGCATCGGTGCATCA-GCAA-GA
1 GTGCATCGATGCA-CATTCAAGGA
*
581039 -TGAATCGATGCACATTCAAAGG-
1 GTGCATCGATGCACATTC-AAGGA
*
581061 GATGCATCGGTGCAC
1 G-TGCATCGATGCAC
581076 TGTTAAGTGT
Statistics
Matches: 46, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
20 2 0.04
21 11 0.24
22 4 0.09
23 16 0.35
24 13 0.28
ACGTcount: A:0.29, C:0.22, G:0.28, T:0.21
Consensus pattern (23 bp):
GTGCATCGATGCACATTCAAGGA
Found at i:586862 original size:18 final size:17
Alignment explanation
Indices: 586808--586856 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
586798 TTGGACCCTT
* *
586808 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
586826 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
586844 AGTGCATTCGATG
1 AGTGCA-TCGATG
586857 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:587026 original size:65 final size:64
Alignment explanation
Indices: 586828--587037 Score: 232
Period size: 65 Copynumber: 3.2 Consensus size: 64
586818 TGCACTAAGA
* * ** *
586828 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCT-AGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAG-GTGCATCGATGCATGGTTG
* *
586892 GTGCATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAATCCTCA-GTGCATCGGTGCATGGT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCAATATAAT--TCAGGTGCATCGATGCATGGT
586955 AT-
63 -TG
* *
586957 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATGGTGCATCGATGCATGGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCA-GGTGCATCGATGCATGG-TT
587021 G
64 G
*
587022 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
587038 CTCTAAAAAA
Statistics
Matches: 123, Mismatches: 13, Indels: 19
0.79 0.08 0.12
Matches are distributed among these distances:
62 3 0.02
63 3 0.02
64 52 0.42
65 62 0.50
66 2 0.02
67 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAGGTGCATCGATGCATGGTTG
Found at i:588382 original size:30 final size:31
Alignment explanation
Indices: 588332--588394 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 31
588322 GACCGAAATA
* *
588332 TAATAAAACGATAACGTAAGTGACTAAAACT
1 TAATAAAACAATAACGTAAGTGACAAAAACT
*
588363 TAAT-AAACAATAACTTAAGTGACAAAAACT
1 TAATAAAACAATAACGTAAGTGACAAAAACT
588393 TA
1 TA
588395 TGTTGTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 25 0.86
31 4 0.14
ACGTcount: A:0.54, C:0.13, G:0.10, T:0.24
Consensus pattern (31 bp):
TAATAAAACAATAACGTAAGTGACAAAAACT
Found at i:588800 original size:25 final size:24
Alignment explanation
Indices: 588771--588869 Score: 107
Period size: 25 Copynumber: 4.1 Consensus size: 24
588761 TAACAATTAC
588771 AATTAAATTAATATTTTTTACTATT
1 AATTAAATTAATA-TTTTTACTATT
*
588796 AATT-AATATAATATTTTTA-TA-A
1 AATTAAAT-TAATATTTTTACTATT
588818 AATTAAATTAATATTTTTACTATT
1 AATTAAATTAATATTTTTACTATT
*
588842 AATTAACA-AAATAATTTTTACTAGTT
1 AATTAA-ATTAAT-ATTTTTACTA-TT
588868 AA
1 AA
588870 ATATTCAAAT
Statistics
Matches: 64, Mismatches: 3, Indels: 13
0.80 0.04 0.16
Matches are distributed among these distances:
22 15 0.23
23 7 0.11
24 18 0.28
25 20 0.31
26 4 0.06
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.49
Consensus pattern (24 bp):
AATTAAATTAATATTTTTACTATT
Found at i:588838 original size:46 final size:48
Alignment explanation
Indices: 588771--588861 Score: 150
Period size: 46 Copynumber: 1.9 Consensus size: 48
588761 TAACAATTAC
* *
588771 AATTAAATTAATATTTTTTACTATTAATTAATATAAT-ATTTTTATAA
1 AATTAAATTAATATTTTTTACTATTAATTAACAAAATAATTTTTATAA
588818 AATTAAATTAATA-TTTTTACTATTAATTAACAAAATAATTTTTA
1 AATTAAATTAATATTTTTTACTATTAATTAACAAAATAATTTTTA
588862 CTAGTTAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
46 21 0.51
47 20 0.49
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (48 bp):
AATTAAATTAATATTTTTTACTATTAATTAACAAAATAATTTTTATAA
Found at i:589204 original size:20 final size:20
Alignment explanation
Indices: 589179--589216 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
589169 TTTGTGAAGG
589179 GATGCACCGATGCACTCATT
1 GATGCACCGATGCACTCATT
*
589199 GATGCATCGATGCACTCA
1 GATGCACCGATGCACTCA
589217 CCATATCGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (20 bp):
GATGCACCGATGCACTCATT
Found at i:589333 original size:64 final size:63
Alignment explanation
Indices: 589221--589375 Score: 206
Period size: 64 Copynumber: 2.4 Consensus size: 63
589211 CACTCACCAT
* * * *
589221 ATCGAATGTATTTTATACATCGATGCACTACCATGCATCGATACACTCAGG-TT-TTATGAAAAC
1 ATCGAATGCATTTTATGCATCGATGCACGACCATACATCGATACACTCAGGCTTGTT-TG-AAAC
* * *
589284 ATTGAATGCATTTTATGCATCAATGCACAGACCATACATCGATGCACTCAGGCTTGTTTGAAAC
1 ATCGAATGCATTTTATGCATCGATGCAC-GACCATACATCGATACACTCAGGCTTGTTTGAAAC
589348 ATCGAATGCATTTTATGCATCGATGCAC
1 ATCGAATGCATTTTATGCATCGATGCAC
589376 TCTTAGTGCA
Statistics
Matches: 80, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
63 24 0.30
64 50 0.62
65 4 0.05
66 2 0.03
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (63 bp):
ATCGAATGCATTTTATGCATCGATGCACGACCATACATCGATACACTCAGGCTTGTTTGAAAC
Found at i:589388 original size:64 final size:62
Alignment explanation
Indices: 589221--589395 Score: 201
Period size: 64 Copynumber: 2.7 Consensus size: 62
589211 CACTCACCAT
* * *
589221 ATCGAATGTATTTTATACATCGATGCACTACCATGCATCGATACACTCAGGTTTTATGAAAAC
1 ATCGAATGCATTTTATGCATCGATGCACT-CCATGCATCGATGCACTCAGGTTTTATGAAAAC
* * * *
589284 ATTGAATGCATTTTATGCATCAATGCACAGACCATACATCGATGCACTCAGGCTTGTT-TG-AAA
1 ATCGAATGCATTTTATGCATCGATGCAC--TCCATGCATCGATGCACTCAGG-TT-TTATGAAAA
589347 C
62 C
*
589348 ATCGAATGCATTTTATGCATCGATGCACTCTTAGTGCATCGATGCACT
1 ATCGAATGCATTTTATGCATCGATGCACTC-CA-TGCATCGATGCACT
589396 AAGTGTTCCA
Statistics
Matches: 94, Mismatches: 12, Indels: 11
0.80 0.10 0.09
Matches are distributed among these distances:
62 1 0.01
63 25 0.27
64 62 0.66
65 4 0.04
66 2 0.02
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (62 bp):
ATCGAATGCATTTTATGCATCGATGCACTCCATGCATCGATGCACTCAGGTTTTATGAAAAC
Found at i:598071 original size:64 final size:63
Alignment explanation
Indices: 597942--598096 Score: 251
Period size: 64 Copynumber: 2.4 Consensus size: 63
597932 CACTCACCAT
*
597942 ATCGAATGCATTTTATGCATCGATGCACTACCATGCATCGATACACTCAGGTTTTATGAAAAC
1 ATCGAATGCATTTTATGCATCGATGCACGACCATGCATCGATACACTCAGGTTTTATGAAAAC
*
598005 ATCGAATGCATTTTATGCATCGATGCACAGACCATGCATCGATGCACTCAGGCTTGTT-TG-AAA
1 ATCGAATGCATTTTATGCATCGATGCAC-GACCATGCATCGATACACTCAGG-TT-TTATGAAAA
598068 C
63 C
598069 ATCGAATGCATTTTATGCATCGATGCAC
1 ATCGAATGCATTTTATGCATCGATGCAC
598097 TCTTAGTGCA
Statistics
Matches: 87, Mismatches: 2, Indels: 5
0.93 0.02 0.05
Matches are distributed among these distances:
63 28 0.32
64 53 0.61
65 4 0.05
66 2 0.02
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (63 bp):
ATCGAATGCATTTTATGCATCGATGCACGACCATGCATCGATACACTCAGGTTTTATGAAAAC
Found at i:598112 original size:64 final size:62
Alignment explanation
Indices: 597942--598116 Score: 237
Period size: 64 Copynumber: 2.7 Consensus size: 62
597932 CACTCACCAT
*
597942 ATCGAATGCATTTTATGCATCGATGCACTACCATGCATCGATACACTCAGGTTTTATGAAAAC
1 ATCGAATGCATTTTATGCATCGATGCACT-CCATGCATCGATGCACTCAGGTTTTATGAAAAC
*
598005 ATCGAATGCATTTTATGCATCGATGCACAGACCATGCATCGATGCACTCAGGCTTGTT-TG-AAA
1 ATCGAATGCATTTTATGCATCGATGCAC--TCCATGCATCGATGCACTCAGG-TT-TTATGAAAA
598068 C
62 C
* *
598069 ATCGAATGCATTTTATGCATCGATGCACTCTTAGTGCACCGATGCACT
1 ATCGAATGCATTTTATGCATCGATGCACTC-CA-TGCATCGATGCACT
598117 AAGTGTTTCA
Statistics
Matches: 101, Mismatches: 5, Indels: 11
0.86 0.04 0.09
Matches are distributed among these distances:
62 1 0.01
63 29 0.29
64 65 0.64
65 4 0.04
66 2 0.02
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (62 bp):
ATCGAATGCATTTTATGCATCGATGCACTCCATGCATCGATGCACTCAGGTTTTATGAAAAC
Found at i:598993 original size:13 final size:13
Alignment explanation
Indices: 598975--599001 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
598965 AGGAAGTAGG
598975 GGTCACGGTGGCT
1 GGTCACGGTGGCT
598988 GGTCACGGTGGCT
1 GGTCACGGTGGCT
599001 G
1 G
599002 TTGAATCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.22, G:0.48, T:0.22
Consensus pattern (13 bp):
GGTCACGGTGGCT
Found at i:599321 original size:100 final size:100
Alignment explanation
Indices: 599197--599392 Score: 340
Period size: 100 Copynumber: 2.0 Consensus size: 100
599187 CAATATCAAT
*
599197 CGGTTTGAACCTCCACTTAGTTTCACCCAAACTTAAT-TCTGGTCATGGATAGATCACCCACATA
1 CGGTTTAAACCTCCACTTAGTTTCACCCAAACTTAATCT-TGGTCATGGATAGATCACCCACATA
*
599261 GAGGGTGAATCAAACCCATGTTTGAATTAAAACTGA
65 GAGGGTGAATCAAACCCATGTTTAAATTAAAACTGA
* *
599297 CGGTTTAAACCTCCACTTAGTTTCACCCAAGCTTCATCTTGGTCATGGATAGATCACCCACATAG
1 CGGTTTAAACCTCCACTTAGTTTCACCCAAACTTAATCTTGGTCATGGATAGATCACCCACATAG
599362 AGGGTGAATCAAACCCATGTTTAAATTAAAA
66 AGGGTGAATCAAACCCATGTTTAAATTAAAA
599393 TTGAGATACT
Statistics
Matches: 91, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
100 90 0.99
101 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.28
Consensus pattern (100 bp):
CGGTTTAAACCTCCACTTAGTTTCACCCAAACTTAATCTTGGTCATGGATAGATCACCCACATAG
AGGGTGAATCAAACCCATGTTTAAATTAAAACTGA
Found at i:599813 original size:12 final size:12
Alignment explanation
Indices: 599796--599820 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
599786 GATTGAGGTG
599796 AAAAATGACAAC
1 AAAAATGACAAC
599808 AAAAATGACAAC
1 AAAAATGACAAC
599820 A
1 A
599821 TTGGATTGAG
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:0.68, C:0.16, G:0.08, T:0.08
Consensus pattern (12 bp):
AAAAATGACAAC
Found at i:607583 original size:57 final size:57
Alignment explanation
Indices: 607492--607608 Score: 155
Period size: 57 Copynumber: 2.1 Consensus size: 57
607482 TACCAAATCT
*
607492 TCGGGTAGTTCATTGGACGGTCCGTATCCCGACTT-GAATATTATAAGTACTCGAAAA
1 TCGGGTAGTTCATTGGACAGTCCGTATCCCGACTTAG-ATATTATAAGTACTCGAAAA
* ** * * *
607549 TCGGGTAGTTCATTGGACAGTCCGTGTCTTGACTTAGATGTTGTAAGTACTTGAAAA
1 TCGGGTAGTTCATTGGACAGTCCGTATCCCGACTTAGATATTATAAGTACTCGAAAA
607606 TCG
1 TCG
607609 AGTACTCAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
57 51 0.98
58 1 0.02
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (57 bp):
TCGGGTAGTTCATTGGACAGTCCGTATCCCGACTTAGATATTATAAGTACTCGAAAA
Found at i:607737 original size:20 final size:21
Alignment explanation
Indices: 607701--607742 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
607691 AATATACTGC
607701 TTATATTATTCAATAAA-ATA
1 TTATATTATTCAATAAACATA
*
607721 TTATATTAATT-ATTAAACATA
1 TTATATT-ATTCAATAAACATA
607742 T
1 T
607743 AATTGTTGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (21 bp):
TTATATTATTCAATAAACATA
Found at i:612643 original size:4 final size:4
Alignment explanation
Indices: 612634--613056 Score: 792
Period size: 4 Copynumber: 105.8 Consensus size: 4
612624 CTGAGATTAG
612634 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
612682 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
612730 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
612778 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
612826 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
612874 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
612922 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
* * * * *
612970 AGAT AGAT AGAT AGAT AGAT AGAT AGAC AGAC AGAC AGAT AGAC AGAC
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
*
613018 AGAC AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGA
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGA
613057 GAGAATGAAG
Statistics
Matches: 415, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
4 415 1.00
ACGTcount: A:0.50, C:0.01, G:0.25, T:0.23
Consensus pattern (4 bp):
AGAT
Found at i:614700 original size:224 final size:222
Alignment explanation
Indices: 614409--614860 Score: 700
Period size: 224 Copynumber: 2.0 Consensus size: 222
614399 TATTCGGGTT
* * *
614409 GGGTTGAGTTCGGGTTTAGGGTGAAAAATTCCAGACCTGAAAATATATATAATTTTACCGTATAT
1 GGGTTGAGTTCGGGTTTAGGGTGAAAAATTCCAGACCTCAAAAAATATATAATTTTACAGTATAT
614474 ATTTAGGAATAATTACAATAATACCCCTCTATATATA-ATTTTTTTCAATTAAGTCACTATTTTT
66 ATTTAGGAATAATTACAATAATACCCCTCTATATATATA-TTTTTT-AATTAAGTCACTATTTTT
*
614538 ATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGGTC-G-GA-TTTCTAATTCATATATTCG
129 ATTGAATAAAAATAA-ATTTTTATTATTTCGGGTCGGGTCGGCGAGTTTCTAATTCATATATTCG
614600 GGTCGGGTC-GGTGAAACTTTATTTTGGTC
193 GGTCGGGTCGGGTGAAACTTTATTTTGGTC
* * *
614629 GGGTTGGGTTCGGGTTTAGGGTGAAAAATATTCTACCCGACC-CAAAAAATATATAATTTTACAT
1 GGGTTGAGTTCGGGTTTAGGGTG-AAAA-A-T-T-CCAGACCTCAAAAAATATATAATTTTACAG
614693 TATATATTTAGGAATAATTACAATAATACCCCTCTATATATATATTTTTTAATTAAGTCACTATT
61 TATATATTTAGGAATAATTACAATAATACCCCTCTATATATATATTTTTTAATTAAGTCACTATT
614758 TTTATTGAATAAAAATAAATTTTTATTATTTCGGGTCGGGTCGGGTCGAGTTTCTAATTCATATA
126 TTTATTGAATAAAAATAAATTTTTATTATTTCGGGTCGGGTC-GG-CGAGTTTCTAATTCATATA
*
614823 TTCGGGTTGGGTCGGGTGAAACTTTATTTTGGTC
189 TTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTC
614857 GGGT
1 GGGT
614861 CAGGTCTCGG
Statistics
Matches: 212, Mismatches: 8, Indels: 16
0.90 0.03 0.07
Matches are distributed among these distances:
220 22 0.10
221 4 0.02
222 24 0.11
223 34 0.16
224 68 0.32
225 7 0.03
226 2 0.01
227 27 0.13
228 24 0.11
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.40
Consensus pattern (222 bp):
GGGTTGAGTTCGGGTTTAGGGTGAAAAATTCCAGACCTCAAAAAATATATAATTTTACAGTATAT
ATTTAGGAATAATTACAATAATACCCCTCTATATATATATTTTTTAATTAAGTCACTATTTTTAT
TGAATAAAAATAAATTTTTATTATTTCGGGTCGGGTCGGCGAGTTTCTAATTCATATATTCGGGT
CGGGTCGGGTGAAACTTTATTTTGGTC
Found at i:615248 original size:17 final size:18
Alignment explanation
Indices: 615226--615271 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
615216 TATAGAATTT
*
615226 GATTCCAATTCC-TGACA
1 GATTCCAATTCCTTCACA
615243 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
*
615261 GATTTCAATTC
1 GATTCCAATTC
615272 TCTCGTAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.35
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:617494 original size:15 final size:16
Alignment explanation
Indices: 617474--617511 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
617464 AGGTTTGATT
617474 TTATTTTTAAA-TAAA
1 TTATTTTTAAATTAAA
617489 TTATTTTTTAAATTAAA
1 TTA-TTTTTAAATTAAA
*
617506 ATATTT
1 TTATTT
617512 ATGAGTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 3 0.15
16 11 0.55
17 6 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTATTTTTAAATTAAA
Found at i:617498 original size:16 final size:17
Alignment explanation
Indices: 617477--617511 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
617467 TTTGATTTTA
*
617477 TTTTTAAA-TAAATTAT
1 TTTTTAAATTAAAATAT
617493 TTTTTAAATTAAAATAT
1 TTTTTAAATTAAAATAT
617510 TT
1 TT
617512 ATGAGTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTTTAAATTAAAATAT
Found at i:620682 original size:31 final size:31
Alignment explanation
Indices: 620633--620755 Score: 106
Period size: 31 Copynumber: 4.0 Consensus size: 31
620623 CTCGAGAACA
*
620633 GTCCATAGGTCCCGTAGAACCTAGGTAAACT
1 GTCCATATGTCCCGTAGAACCTAGGTAAACT
* * * * *
620664 GTCCATATGTTCCTTAGAACTTAGGTATATT
1 GTCCATATGTCCCGTAGAACCTAGGTAAACT
* * * *
620695 GTCCATATGTCCCG-A-AAGACAAAGTAATTCT
1 GTCCATATGTCCCGTAGAA-CCTAGGTAA-ACT
* *
620726 GTCCATATGTTCCGTAGAACATAGGTAAAC
1 GTCCATATGTCCCGTAGAACCTAGGTAAAC
620756 CCTCGACTCT
Statistics
Matches: 67, Mismatches: 21, Indels: 8
0.70 0.22 0.08
Matches are distributed among these distances:
29 2 0.03
30 5 0.07
31 52 0.78
32 6 0.09
33 2 0.03
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (31 bp):
GTCCATATGTCCCGTAGAACCTAGGTAAACT
Found at i:625181 original size:20 final size:21
Alignment explanation
Indices: 625156--625248 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
625146 TTTTCCCAAT
*
625156 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
625176 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
625197 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
625217 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
625238 TCGCAATGCGA
1 TCGCAATGCGA
625249 TACTTACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:625201 original size:41 final size:41
Alignment explanation
Indices: 625156--625248 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
625146 TTTTCCCAAT
625156 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
625197 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
625238 TCGCAATGCGA
1 TCGCAATGCGA
625249 TACTTACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:625261 original size:41 final size:41
Alignment explanation
Indices: 625175--625309 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
625165 GAATAAGTAA
** *
625175 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTTACT
625216 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
* * ** * * *
625257 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTGACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTTACT
*
625298 TTCGCAACGCGA
1 ATCGCAACGCGA
625310 TTTACATAGC
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
40 5 0.06
41 73 0.91
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
Found at i:625866 original size:19 final size:19
Alignment explanation
Indices: 625828--625894 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
625818 TTCGAGAATG
625828 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
625848 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
625867 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
625886 AAAATCGCA
1 AAAATCGCA
625895 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 30 0.73
20 11 0.27
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:625936 original size:20 final size:19
Alignment explanation
Indices: 625890--626055 Score: 136
Period size: 20 Copynumber: 9.1 Consensus size: 19
625880 GAAACCAAAA
*
625890 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
625909 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
625928 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
625948 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
625964 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
625981 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
625995 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
626014 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
626034 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
626054 TC
1 TC
626056 AACCAAAAGA
Statistics
Matches: 119, Mismatches: 15, Indels: 26
0.74 0.09 0.16
Matches are distributed among these distances:
14 20 0.17
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 41 0.34
20 49 0.41
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:625971 original size:39 final size:39
Alignment explanation
Indices: 625895--625971 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
625885 CAAAATCGCA
* **
625895 TTGCGATTTTCATTTCGCGTTGCGATTTTTATTTCGCGG
1 TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
625934 TTGCGATTTTCATTTCGCGTTGCGATTGTCT-GGTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATT-TCTAGGTCGCG
625972 ATAGTCATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 32 0.94
40 2 0.06
ACGTcount: A:0.09, C:0.19, G:0.26, T:0.45
Consensus pattern (39 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
Found at i:625980 original size:33 final size:33
Alignment explanation
Indices: 625943--626030 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
625933 GTTGCGATTT
* *
625943 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
625976 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
626009 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
626031 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:628117 original size:42 final size:42
Alignment explanation
Indices: 628058--628178 Score: 118
Period size: 42 Copynumber: 2.9 Consensus size: 42
628048 CCGACTCGCT
* * *
628058 TATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCC
1 TATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCC
* * * *
628100 TATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCAC
1 TATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCC
* ** * *
628142 TGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 TATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
628179 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 14, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
42 60 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCC
Found at i:628136 original size:21 final size:21
Alignment explanation
Indices: 628112--628178 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
628102 TCATTCCTCG
628112 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
628133 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
628154 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
628175 AGAG
1 AGAG
628179 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:629555 original size:14 final size:14
Alignment explanation
Indices: 629536--629571 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
629526 ATTGTTTAAT
629536 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
629550 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
629564 TGATTTGT
1 TGATTTGT
629572 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:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:629776 original size:33 final size:32
Alignment explanation
Indices: 629734--629860 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
629724 ATTAAATTCA
629734 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
* **
629767 CGTTGCGATTTTCATTTCGCATTGTGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
629800 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
629833 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
629861 AGTAATTTCC
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
31 3 0.04
33 78 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:632169 original size:12 final size:12
Alignment explanation
Indices: 632152--632176 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
632142 TCTTCGGGGA
632152 CTTTTTCTTCTT
1 CTTTTTCTTCTT
632164 CTTTTTCTTCTT
1 CTTTTTCTTCTT
632176 C
1 C
632177 AAGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:632385 original size:24 final size:24
Alignment explanation
Indices: 632351--632404 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
632341 CTGAAACATC
* *
632351 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
632375 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
632399 ATCAAA
1 ATCAAA
632405 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:633488 original size:20 final size:20
Alignment explanation
Indices: 633463--633520 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
633453 ATTCATTTGA
633463 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
633483 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
633503 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
633521 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:633605 original size:33 final size:33
Alignment explanation
Indices: 633539--633616 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 33
633529 GAAATGAAAA
***
633539 TCGCATTGCGATTTTCTCGTTGCAATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCAATAACCATT
*
633572 TCGCATTGCGATTTTCTCGTTGCGATAACCATT
1 TCGCATTGCGATTTTCTCGTTGCAATAACCATT
*
633605 TCGCGTTGCGAT
1 TCGCATTGCGAT
633617 AGTCTGTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.42
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCAATAACCATT
Found at i:635641 original size:20 final size:19
Alignment explanation
Indices: 635606--635661 Score: 85
Period size: 20 Copynumber: 2.9 Consensus size: 19
635596 GAAACTTAAA
635606 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
635625 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
*
635645 ATCGCAATGCGAAATGA
1 ATCGCAACGCGAAATGA
635662 AAATCACAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.36, C:0.23, G:0.25, T:0.16
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:635739 original size:14 final size:14
Alignment explanation
Indices: 635720--635777 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
635710 TTTCATTTCG
635720 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
635734 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
635750 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
635766 CGTTGCGATTTT
1 CGTTGCGATTTT
635778 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:635784 original size:33 final size:33
Alignment explanation
Indices: 635703--635793 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
635693 ACAAATCGCA
*
635703 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
635736 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
635768 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
635794 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:635812 original size:20 final size:19
Alignment explanation
Indices: 635778--635832 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
635768 TTGCGATTTT
*
635778 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
635797 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
635817 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
635833 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:636340 original size:18 final size:18
Alignment explanation
Indices: 636314--636358 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
636304 GTCGATCAGA
*
636314 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
636332 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
636350 TGATGGCTC
1 TGATGGCTC
636359 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:637702 original size:20 final size:20
Alignment explanation
Indices: 637677--637714 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
637667 AATAGTTTCT
637677 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
637697 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
637715 GAGAGAATCG
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:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:638003 original size:22 final size:22
Alignment explanation
Indices: 637978--638021 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
637968 GATTTAGATA
637978 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
638000 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
638022 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:638234 original size:20 final size:20
Alignment explanation
Indices: 638209--638302 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
638199 GATTATGTAT
638209 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
638229 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
638249 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
638270 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
638290 TATCGCATTGCGA
1 TATCGCGTTGCGA
638303 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:638274 original size:41 final size:41
Alignment explanation
Indices: 638229--638306 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
638219 CGAAAGTCAG
* * *
638229 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
* *
638270 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
638307 CCCAATTCGC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
Found at i:638303 original size:20 final size:20
Alignment explanation
Indices: 638189--638303 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
638179 CGCTTTGAAA
*
638189 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
638210 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
638230 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
638250 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
638271 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
638291 ATCGCATTGCGAT
1 ATCGCATTGCGAT
638304 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:638343 original size:22 final size:21
Alignment explanation
Indices: 638292--638406 Score: 108
Period size: 21 Copynumber: 5.5 Consensus size: 21
638282 ATAGTCAGTA
* ** *
638292 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTACTTATT
638313 TCGCATTGCGATTTACTTATTT
1 TCGCATTGCGATTTACTTA-TT
* *
638335 TCGCGTTGCAATTTACTTA-T
1 TCGCATTGCGATTTACTTATT
* ** *
638355 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTACTTATT
*
638376 TCGCGTTGCGATTTACTTA-T
1 TCGCATTGCGATTTACTTATT
638396 TCGCATTGCGA
1 TCGCATTGCGA
638407 ATTGGGAAAA
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
20 26 0.34
21 32 0.42
22 18 0.24
ACGTcount: A:0.18, C:0.23, G:0.17, T:0.42
Consensus pattern (21 bp):
TCGCATTGCGATTTACTTATT
Found at i:638363 original size:20 final size:20
Alignment explanation
Indices: 638311--638409 Score: 90
Period size: 20 Copynumber: 4.8 Consensus size: 20
638301 GATTTTCCCA
*
638311 ATTCGCATTGCGATTTACTT
1 ATTCGCATTGCAATTTACTT
*
638331 ATTTTCGCGTTGCAATTTACTT
1 A--TTCGCATTGCAATTTACTT
* * **
638353 ATTCGCATTGCGATTTTCCCA
1 ATTCGCATTGC-AATTTACTT
* *
638374 ATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCAATTTACTT
638394 ATTCGCATTGCGAATT
1 ATTCGCATTGC-AATT
638410 GGGAAAATCG
Statistics
Matches: 60, Mismatches: 15, Indels: 7
0.73 0.18 0.09
Matches are distributed among these distances:
20 24 0.40
21 18 0.30
22 18 0.30
ACGTcount: A:0.19, C:0.21, G:0.16, T:0.43
Consensus pattern (20 bp):
ATTCGCATTGCAATTTACTT
Found at i:638391 original size:41 final size:42
Alignment explanation
Indices: 638311--638406 Score: 140
Period size: 41 Copynumber: 2.3 Consensus size: 42
638301 GATTTTCCCA
** *
638311 ATTCGCATTGCGATTTACTTATTTTCGCGTTGCAATTTACTT
1 ATTCGCATTGCGATTTACCCATATTCGCGTTGCAATTTACTT
* *
638353 ATTCGCATTGCGATTTTCCCA-ATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTACCCATATTCGCGTTGCAATTTACTT
638394 ATTCGCATTGCGA
1 ATTCGCATTGCGA
638407 ATTGGGAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 31 0.63
42 18 0.37
ACGTcount: A:0.19, C:0.22, G:0.17, T:0.43
Consensus pattern (42 bp):
ATTCGCATTGCGATTTACCCATATTCGCGTTGCAATTTACTT
Found at i:638440 original size:21 final size:21
Alignment explanation
Indices: 638416--638466 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
638406 AATTGGGAAA
638416 ATCGCAACGATACTGTAGACC
1 ATCGCAACGATACTGTAGACC
638437 ATCGCAACGATACTGTAGACC
1 ATCGCAACGATACTGTAGACC
638458 ATCGCAACG
1 ATCGCAACG
638467 CGATTTTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.33, C:0.29, G:0.20, T:0.18
Consensus pattern (21 bp):
ATCGCAACGATACTGTAGACC
Found at i:648192 original size:20 final size:21
Alignment explanation
Indices: 648152--648194 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
648142 TGAAGATTTG
*
648152 TTTTATTTTGAATACTGATAAA
1 TTTTATTTT-AATACTCATAAA
648174 TTTTATTTT-ATACTCATAAA
1 TTTTATTTTAATACTCATAAA
648194 T
1 T
648195 GATTCTATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
22 9 0.45
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (21 bp):
TTTTATTTTAATACTCATAAA
Found at i:656086 original size:25 final size:23
Alignment explanation
Indices: 656058--656111 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 23
656048 TCGTGTATAT
656058 TCTATGCGACACTTTCGAGTGCAAC
1 TCTATG-G-CACTTTCGAGTGCAAC
656083 TCTACATGGCACTTTCGAGTGCAAC
1 TCT--ATGGCACTTTCGAGTGCAAC
656108 TCTA
1 TCTA
656112 CATGGTACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
23 1 0.04
25 22 0.81
26 1 0.04
27 3 0.11
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.30
Consensus pattern (23 bp):
TCTATGGCACTTTCGAGTGCAAC
Found at i:656112 original size:25 final size:25
Alignment explanation
Indices: 656067--656122 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
656057 TTCTATGCGA
656067 CACTTTCGAGTGCAACTCTACATGG
1 CACTTTCGAGTGCAACTCTACATGG
656092 CACTTTCGAGTGCAACTCTACATGG
1 CACTTTCGAGTGCAACTCTACATGG
*
656117 TACTTT
1 CACTTT
656123 ATGTGCAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32
Consensus pattern (25 bp):
CACTTTCGAGTGCAACTCTACATGG
Found at i:659010 original size:66 final size:68
Alignment explanation
Indices: 658901--659036 Score: 163
Period size: 66 Copynumber: 2.0 Consensus size: 68
658891 ATATATTAAT
* *
658901 ATTTTATTATATTTATATACGATACGTATTCAAATATTGAAATAGATTAT-G-TT-AAAAAAAGT
1 ATTTTATTATATTTATATACGATACATATTCAAATATTAAAATAGATT-TCGATTGAAAAAAAGT
658963 AAGA
65 AAGA
* *** *
658967 ATTTTATTATA-TTAGTATACTATACATATTTGGATATTAAAATAGATTTCGATTGTAAAAAAGT
1 ATTTTATTATATTTA-TATACGATACATATTCAAATATTAAAATAGATTTCGATTGAAAAAAAGT
659031 AAGA
65 AAGA
659035 AT
1 AT
659037 GTAAGGGGTG
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
65 4 0.07
66 39 0.66
67 2 0.03
68 14 0.24
ACGTcount: A:0.44, C:0.04, G:0.11, T:0.40
Consensus pattern (68 bp):
ATTTTATTATATTTATATACGATACATATTCAAATATTAAAATAGATTTCGATTGAAAAAAAGTA
AGA
Found at i:665772 original size:64 final size:64
Alignment explanation
Indices: 665641--665796 Score: 176
Period size: 64 Copynumber: 2.4 Consensus size: 64
665631 AAGGTGTATT
* * * * *
665641 GATGCACAGGTAGTGCATCGATGCA-ATCTTTTAAAATATAAACATCGAATGTAATTAGTGCATC
1 GATGCACAAGCAGTGCATCGATGCATA-CTATTAAAATATAAACATCGAATGCAATTAGTGCACC
* *
665705 GATGCATAAGGCA-TGCATCGATGCATACTATTAATAATA-AAACATCGAATGCATTTTA-TGCA
1 GATGCACAA-GCAGTGCATCGATGCATACTATTAA-AATATAAACATCGAATGCA-ATTAGTGCA
665767 CC
63 CC
*
665769 GATGCACAAGTAGTGCATCGATGCATAC
1 GATGCACAAGCAGTGCATCGATGCATAC
665797 CTTCATTAAA
Statistics
Matches: 78, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
63 2 0.03
64 66 0.85
65 10 0.13
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.28
Consensus pattern (64 bp):
GATGCACAAGCAGTGCATCGATGCATACTATTAAAATATAAACATCGAATGCAATTAGTGCACC
Found at i:666341 original size:15 final size:15
Alignment explanation
Indices: 666307--666341 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
666297 CGAGGGTATA
666307 ATAGTCCTTCGGGAC
1 ATAGTCCTTCGGGAC
* *
666322 GTAGTCCTTCGGGAT
1 ATAGTCCTTCGGGAC
666337 ATAGT
1 ATAGT
666342 GGTCCTACGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.31
Consensus pattern (15 bp):
ATAGTCCTTCGGGAC
Found at i:667931 original size:63 final size:64
Alignment explanation
Indices: 667789--667948 Score: 178
Period size: 63 Copynumber: 2.5 Consensus size: 64
667779 ATTGTTTAAG
* * * * * *
667789 GTGTATCGATGCACATGGAGTGTATTGATGCACTCCTTTAAAATAAAAACATCGAATGCCATTA
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACTCCCTTAAAATAAAAACATCGAAGGCCATTA
* * * * ** *
667853 GTGTATCGATACACAAGTAGTGCATCGATGCAC-CCCTTAAGATTAAAACATCGAGGGTGATTT
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACTCCCTTAAAATAAAAACATCGAAGGCCATTA
* *
667916 GTGTACCGATGCACAAGTAGTGCATCGTTGCAC
1 GTGTATCGATGCACAAGTAGTGCATCGATGCAC
667949 ACGTTATGGA
Statistics
Matches: 80, Mismatches: 16, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
63 52 0.65
64 28 0.35
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (64 bp):
GTGTATCGATGCACAAGTAGTGCATCGATGCACTCCCTTAAAATAAAAACATCGAAGGCCATTA
Found at i:668549 original size:22 final size:22
Alignment explanation
Indices: 668497--668549 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
668487 TCGAGGGTTA
* *
668497 CAGTGGTCATTTGAGACATATC
1 CAGTGGTCCTTCGAGACATATC
*
668519 CAGTGGTCCTTCGGGACATATC
1 CAGTGGTCCTTCGAGACATATC
668541 CAGTGGTCC
1 CAGTGGTCC
668550 GGGACGCAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.26, T:0.28
Consensus pattern (22 bp):
CAGTGGTCCTTCGAGACATATC
Done.