Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007931.1 Hibiscus syriacus cultivar Beakdansim tig00110339_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: 2341804
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 12
Found at i:601736 original size:18 final size:18
Alignment explanation
Indices: 601712--601749 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
601702 GGTTGGACAA
*
601712 AAAAAAAGAATAAAAAAAT
1 AAAAAAA-ATTAAAAAAAT
601731 AAAAAAAATTAAAAAAAT
1 AAAAAAAATTAAAAAAAT
601749 A
1 A
601750 GGAAAACGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.13
Consensus pattern (18 bp):
AAAAAAAATTAAAAAAAT
Found at i:602008 original size:22 final size:23
Alignment explanation
Indices: 601980--602023 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
601970 TAAAAAACTA
*
601980 TATATTATATGT-TTTCAAAAAC
1 TATATTATATATATTTCAAAAAC
602002 TATATTATATATATTTCAAAAA
1 TATATTATATATATTTCAAAAA
602024 ACCATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.45
Consensus pattern (23 bp):
TATATTATATATATTTCAAAAAC
Found at i:602024 original size:24 final size:26
Alignment explanation
Indices: 601971--602031 Score: 76
Period size: 24 Copynumber: 2.5 Consensus size: 26
601961 ATTTTTTTTT
*
601971 AAAAAACTATA-TATTATATGTTTTC
1 AAAAAACTATATTATTATATGATTTC
601996 -AAAAACTATATTA-TATAT-ATTTC
1 AAAAAACTATATTATTATATGATTTC
*
602019 AAAAAACCATATT
1 AAAAAACTATATT
602032 TTGAAAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 4 0.12
24 26 0.81
25 2 0.06
ACGTcount: A:0.49, C:0.10, G:0.02, T:0.39
Consensus pattern (26 bp):
AAAAAACTATATTATTATATGATTTC
Found at i:602102 original size:21 final size:20
Alignment explanation
Indices: 602073--602133 Score: 72
Period size: 19 Copynumber: 3.0 Consensus size: 20
602063 CAAAAATAAG
602073 TTTTCAAAAACTATATTATATA
1 TTTT-AAAAACT-TATTATATA
602095 TTTTAAAAAC-TATTATATA
1 TTTTAAAAACTTATTATATA
**
602114 TTTTTGAAA-TTATTATATA
1 TTTTAAAAACTTATTATATA
602133 T
1 T
602134 CATCATATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
19 26 0.72
21 6 0.17
22 4 0.11
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.51
Consensus pattern (20 bp):
TTTTAAAAACTTATTATATA
Found at i:616042 original size:12 final size:13
Alignment explanation
Indices: 616019--616047 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
616009 TTAAATGCGA
616019 AAATTAAAAATTT
1 AAATTAAAAATTT
616032 AAATT-AAAATTT
1 AAATTAAAAATTT
616044 AAAT
1 AAAT
616048 ATTCGATCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AAATTAAAAATTT
Found at i:617552 original size:45 final size:45
Alignment explanation
Indices: 617503--617598 Score: 117
Period size: 45 Copynumber: 2.2 Consensus size: 45
617493 TCAAATAAAC
*
617503 TATATATTATAAATATTTTCAAA-AAT-CGTTTTAAAAAACTATA-
1 TATATATTATAAATA-TTTAAAATAATACGTTTTAAAAAACTATAT
* * *
617546 TATATATATATATATATTTAAAATAATATGTTTTCAAAAACTATAT
1 TATATAT-TATAAATATTTAAAATAATACGTTTTAAAAAACTATAT
617592 TATATAT
1 TATATAT
617599 GTTTTCAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
43 13 0.29
44 10 0.22
45 15 0.33
46 7 0.16
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (45 bp):
TATATATTATAAATATTTAAAATAATACGTTTTAAAAAACTATAT
Found at i:617597 original size:44 final size:43
Alignment explanation
Indices: 617482--617675 Score: 137
Period size: 39 Copynumber: 4.7 Consensus size: 43
617472 CAAAAACAAT
*
617482 ATAATATGTTTTCAAATAAACTATA-TAT-TATAAATATTTTCAA
1 ATAATATGTTTTC-AA-AAACTATATTATATATAAATATTTTAAA
* * *
617525 A-AAT-CGTTTTAAAAAACTATATATATATATATATATATTTAAA
1 ATAATATGTTTTCAAAAACTATAT-TATATATAAATAT-TTTAAA
* *
617568 ATAATATGTTTTCAAAAACTATATTATATAT--GT-TTTCAAA
1 ATAATATGTTTTCAAAAACTATATTATATATAAATATTTTAAA
* * * * *
617608 A-AACCATTTTTTAAAAAACTATA-TAT-TAT--ATGTTTTCAA
1 ATAA-TATGTTTTCAAAAACTATATTATATATAAATATTTTAAA
*
617647 A-AATATGTTTT-AAAAATTATATTATATAT
1 ATAATATGTTTTCAAAAACTATATTATATAT
617676 TTTCAAAAAC
Statistics
Matches: 124, Mismatches: 17, Indels: 24
0.75 0.10 0.15
Matches are distributed among these distances:
37 9 0.07
38 13 0.10
39 24 0.19
40 24 0.19
41 9 0.07
42 12 0.10
43 7 0.06
44 10 0.08
45 16 0.13
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.44
Consensus pattern (43 bp):
ATAATATGTTTTCAAAAACTATATTATATATAAATATTTTAAA
Found at i:617633 original size:42 final size:41
Alignment explanation
Indices: 617487--617684 Score: 168
Period size: 40 Copynumber: 5.0 Consensus size: 41
617477 ACAATATAAT
* *
617487 ATGTTTTCAAATAAACTATATATTATAAATATTTTCAAAAATC
1 ATGTTTT-AAA-AAACTATATATTATATATATTTTCAAAAAAC
* *
617530 --GTTTTAAAAAACTATATATATATATATATATATTTAAAATAAT
1 ATGTTTTAAAAAACTATATAT-TATATATAT-T-TTCAAAA-AAC
* *
617573 ATGTTTTCAAAAAC--TATATTATATATGTTTTCAAAAAACC
1 ATGTTTTAAAAAACTATATATTATATATATTTTCAAAAAA-C
* * *
617613 ATTTTTTAAAAAACTATATA-T-TATATGTTTTC-AAAAAT
1 ATGTTTTAAAAAACTATATATTATATATATTTTCAAAAAAC
617651 ATGTTTT-AAAAA-T-TATA-T-TATATATTTTCAAAAA
1 ATGTTTTAAAAAACTATATATTATATATATTTTCAAAAA
617685 CTATTATATT
Statistics
Matches: 132, Mismatches: 13, Indels: 27
0.77 0.08 0.16
Matches are distributed among these distances:
35 15 0.11
36 5 0.04
37 5 0.04
38 6 0.05
39 18 0.14
40 40 0.30
41 8 0.06
42 18 0.14
43 6 0.05
45 11 0.08
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (41 bp):
ATGTTTTAAAAAACTATATATTATATATATTTTCAAAAAAC
Found at i:617663 original size:13 final size:14
Alignment explanation
Indices: 617635--617663 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
617625 ACTATATATT
617635 ATATGTTTTCAAAA
1 ATATGTTTTCAAAA
617649 ATATGTTTT-AAAA
1 ATATGTTTTCAAAA
617662 AT
1 AT
617664 TATATTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (14 bp):
ATATGTTTTCAAAA
Found at i:617691 original size:20 final size:18
Alignment explanation
Indices: 617666--617712 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
617656 TTAAAAATTA
617666 TATTATATATTTTCAAAAAC
1 TATTATATATTTT--AAAAC
*
617686 TATTATAT-TTTTAAAAT
1 TATTATATATTTTAAAAC
617703 TATTATATAT
1 TATTATATAT
617713 ATTATCATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 12 0.48
18 1 0.04
19 4 0.16
20 8 0.32
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (18 bp):
TATTATATATTTTAAAAC
Found at i:617698 original size:40 final size:37
Alignment explanation
Indices: 617548--617715 Score: 116
Period size: 39 Copynumber: 4.4 Consensus size: 37
617538 AAACTATATA
* *
617548 TATATATATATATATTT-AAAATA-ATATGTTTTCAAAAAC
1 TATAT-TATATAT-TTTCAAAA-ACATAT-TTTTTAAAAAT
*
617587 TATATTATATATGTTTTCAAAAAACCAT-TTTTTAAAAAACT
1 TATATTATATA--TTTTC-AAAAA-CATATTTTTTAAAAA-T
* *
617628 ATATATTATATGTTTTC-AAAA-ATATGTTTTAAAAAT
1 -TATATTATATATTTTCAAAAACATATTTTTTAAAAAT
617664 TATATTATATATTTTCAAAAACTATTATATTTTT-AAAAT
1 TATATTATATATTTTCAAAAAC-A-TAT-TTTTTAAAAAT
617703 TAT-TATATATATT
1 TATAT-TATATATT
617716 ATCATATATA
Statistics
Matches: 107, Mismatches: 7, Indels: 30
0.74 0.05 0.21
Matches are distributed among these distances:
35 15 0.14
36 7 0.07
37 9 0.08
38 12 0.11
39 27 0.25
40 20 0.19
41 5 0.05
42 12 0.11
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (37 bp):
TATATTATATATTTTCAAAAACATATTTTTTAAAAAT
Found at i:620686 original size:39 final size:39
Alignment explanation
Indices: 620590--620688 Score: 180
Period size: 39 Copynumber: 2.5 Consensus size: 39
620580 GCTTACCCTA
* *
620590 TGCACAAAGCAGAGGAGCATGCGGTAAGGTCTTATCTTG
1 TGCACAAAGCAGAGGAGCCTGCGATAAGGTCTTATCTTG
620629 TGCACAAAGCAGAGGAGCCTGCGATAAGGTCTTATCTTG
1 TGCACAAAGCAGAGGAGCCTGCGATAAGGTCTTATCTTG
620668 TGCACAAAGCAGAGGAGCCTG
1 TGCACAAAGCAGAGGAGCCTG
620689 TGGAAAGCGG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 58 1.00
ACGTcount: A:0.29, C:0.20, G:0.30, T:0.20
Consensus pattern (39 bp):
TGCACAAAGCAGAGGAGCCTGCGATAAGGTCTTATCTTG
Found at i:621530 original size:19 final size:19
Alignment explanation
Indices: 621495--621550 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 19
621485 CATATTGGAT
*
621495 CGGGTCG-GATCGGGCAGG
1 CGGGTCGAGTTCGGGCAGG
* * *
621513 TGGGTCGAGTTTGGGCAGA
1 CGGGTCGAGTTCGGGCAGG
*
621532 CGGGTCGGGTTCGGGCAGG
1 CGGGTCGAGTTCGGGCAGG
621551 ATCTAGAAAT
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
18 6 0.21
19 23 0.79
ACGTcount: A:0.11, C:0.18, G:0.54, T:0.18
Consensus pattern (19 bp):
CGGGTCGAGTTCGGGCAGG
Found at i:625084 original size:21 final size:21
Alignment explanation
Indices: 625055--625107 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
625045 ATTCTGACTA
625055 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
625076 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
625097 TCGCAATGCGA
1 TCGCATTGCGA
625108 ATACGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:625353 original size:22 final size:22
Alignment explanation
Indices: 625328--625372 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
625318 GCGACATCCA
625328 TCCCCATCCCCGACGAAATCAG
1 TCCCCATCCCCGACGAAATCAG
* *
625350 TCCCCATCTCCGACGATATCAG
1 TCCCCATCCCCGACGAAATCAG
625372 T
1 T
625373 TTTCATCTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.24, C:0.42, G:0.13, T:0.20
Consensus pattern (22 bp):
TCCCCATCCCCGACGAAATCAG
Found at i:625786 original size:20 final size:20
Alignment explanation
Indices: 625742--625816 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
625732 GCGATTTTTA
* *
625742 TTTCGCGTTACGATAGTCAA
1 TTTCGCGTTGCGATAGTCAT
*
625762 ATTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
625782 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
* *
625802 TTTCGTGTTGTGATA
1 TTTCGCGTTGCGATA
625817 TAAAGTTTTA
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.17, C:0.16, G:0.23, T:0.44
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:627734 original size:20 final size:20
Alignment explanation
Indices: 627709--627776 Score: 127
Period size: 20 Copynumber: 3.4 Consensus size: 20
627699 AATAATTTAT
627709 TATCGCAATGCGAAAATGAC
1 TATCGCAATGCGAAAATGAC
627729 TATCGCAATGCGAAAATGAC
1 TATCGCAATGCGAAAATGAC
*
627749 TATCGCAACGCGAAAATGAC
1 TATCGCAATGCGAAAATGAC
627769 TATCGCAA
1 TATCGCAA
627777 CGAGAGAATC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.19
Consensus pattern (20 bp):
TATCGCAATGCGAAAATGAC
Found at i:627820 original size:33 final size:34
Alignment explanation
Indices: 627750--627834 Score: 100
Period size: 33 Copynumber: 2.5 Consensus size: 34
627740 GAAAATGACT
** * * *
627750 ATCGCAACGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAACGCGAAAATGAAAATCGCAACAACAAA
*
627784 ATCGCAATGCG-AAATGAAAATCGCAACAACAAA
1 ATCGCAACGCGAAAATGAAAATCGCAACAACAAA
*
627817 ATCGCAACGTGAAAATGA
1 ATCGCAACGCGAAAATGA
627835 CTATCTCAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
33 26 0.62
34 16 0.38
ACGTcount: A:0.46, C:0.21, G:0.20, T:0.13
Consensus pattern (34 bp):
ATCGCAACGCGAAAATGAAAATCGCAACAACAAA
Found at i:627862 original size:87 final size:87
Alignment explanation
Indices: 627730--627895 Score: 251
Period size: 87 Copynumber: 1.9 Consensus size: 87
627720 GAAAATGACT
* * * *
627730 ATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAGAGAATCGCAATGCG
1 ATCGCAACGCGAAAATGACTATCGCAACACGAAAATGAATATCGCAACGAAAGAATCGCAATGCG
627795 AAATGAAAATCGCAACAACAAA
66 AAATGAAAATCGCAACAACAAA
* * * **
627817 ATCGCAACGTGAAAATGACTATCTCAATACGAATTTGAATATCGCAACGAAAGAATCGCAATGCG
1 ATCGCAACGCGAAAATGACTATCGCAACACGAAAATGAATATCGCAACGAAAGAATCGCAATGCG
627882 AAATGAAAATCGCA
66 AAATGAAAATCGCA
627896 TTGCGATTCT
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
87 70 1.00
ACGTcount: A:0.44, C:0.20, G:0.19, T:0.17
Consensus pattern (87 bp):
ATCGCAACGCGAAAATGACTATCGCAACACGAAAATGAATATCGCAACGAAAGAATCGCAATGCG
AAATGAAAATCGCAACAACAAA
Found at i:627935 original size:20 final size:20
Alignment explanation
Indices: 627910--627956 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
627900 GATTCTCTCG
627910 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
627930 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
627950 TTGCGAT
1 TTGCGAT
627957 TTTAAGTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:628531 original size:21 final size:21
Alignment explanation
Indices: 628463--628543 Score: 72
Period size: 21 Copynumber: 3.9 Consensus size: 21
628453 GGCCTCCCCT
628463 ATCGTTCAAGAGGCCCCTATC
1 ATCGTTCAAGAGGCCCCTATC
** * **
628484 ATCCCTCAAGAGTCCCCTCCC
1 ATCGTTCAAGAGGCCCCTATC
* * *
628505 ACCGTTCAAGAGGCCACTGTC
1 ATCGTTCAAGAGGCCCCTATC
* *
628526 ATCGTTGAAGAGGTCCCT
1 ATCGTTCAAGAGGCCCCT
628544 CCCAATATTC
Statistics
Matches: 44, Mismatches: 16, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.22, C:0.36, G:0.20, T:0.22
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCCCTATC
Found at i:628537 original size:42 final size:42
Alignment explanation
Indices: 628465--628547 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
628455 CCTCCCCTAT
*
628465 CGTTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCAC
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGT-CCCTCCCAC
* ** *
628507 CGTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCA
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCA
628548 ATATTCTAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 33 0.94
43 2 0.06
ACGTcount: A:0.22, C:0.39, G:0.19, T:0.20
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCAC
Found at i:629952 original size:14 final size:14
Alignment explanation
Indices: 629933--629968 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
629923 ATTGTTTAAT
629933 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
629947 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
629961 TGATTTGT
1 TGATTTGT
629969 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:630167 original size:34 final size:33
Alignment explanation
Indices: 630097--630169 Score: 119
Period size: 33 Copynumber: 2.2 Consensus size: 33
630087 AATGACTATT
* *
630097 GCAATGAGAGAATCGCAATGCGAAATGAAAATC
1 GCAACGAGAGAATCGCAATGCGAAATAAAAATC
630130 GCAACGAGAGAATCGCAATGCGAAAATAAAAATC
1 GCAACGAGAGAATCGCAATGCG-AAATAAAAATC
630164 GCAACG
1 GCAACG
630170 CAAAACTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
33 21 0.57
34 16 0.43
ACGTcount: A:0.47, C:0.18, G:0.23, T:0.12
Consensus pattern (33 bp):
GCAACGAGAGAATCGCAATGCGAAATAAAAATC
Found at i:630179 original size:20 final size:20
Alignment explanation
Indices: 630140--630179 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
630130 GCAACGAGAG
*
630140 AATCGCAATGCGAAAATAAA
1 AATCGCAACGCGAAAATAAA
630160 AATCGCAACGC-AAAACTAAA
1 AATCGCAACGCGAAAA-TAAA
630180 TTCACGTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.55, C:0.20, G:0.12, T:0.12
Consensus pattern (20 bp):
AATCGCAACGCGAAAATAAA
Found at i:630227 original size:34 final size:34
Alignment explanation
Indices: 630184--630279 Score: 131
Period size: 33 Copynumber: 2.9 Consensus size: 34
630174 ACTAAATTCA
630184 CGTTGCGATTTTCATTTTCGCATTGCGATGATCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATGATCT
**
630218 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATGATCT
** * *
630251 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
630280 AGTCAATTCC
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 29 0.53
34 26 0.47
ACGTcount: A:0.14, C:0.23, G:0.22, T:0.42
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATGATCT
Found at i:630276 original size:20 final size:20
Alignment explanation
Indices: 630251--630339 Score: 126
Period size: 20 Copynumber: 4.5 Consensus size: 20
630241 GCGATTCTCT
630251 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
630271 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
*
630291 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
630311 TGTTGCGAAAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
630331 CGTTGCGAT
1 CGTTGCGAT
630340 TTCCGCGTTG
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
20 58 0.97
21 2 0.03
ACGTcount: A:0.19, C:0.22, G:0.25, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:632804 original size:24 final size:24
Alignment explanation
Indices: 632770--632823 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
632760 CTGAAAAATC
632770 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
632794 ATCAAAGTCCGGGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
632818 ATCAAA
1 ATCAAA
632824 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:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:633692 original size:20 final size:20
Alignment explanation
Indices: 633667--633720 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
633657 AAATTCAGTA
633667 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
633687 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
633707 TTGCGATAGTCAGA
1 TTGCGATAGTCAGA
633721 TTCGCATTGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.30
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCTCG
Found at i:633730 original size:20 final size:20
Alignment explanation
Indices: 633666--633733 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
633656 AAAATTCAGT
*
633666 ATTGCGATAGTCAGAATCTC
1 ATTGCGATAGTCAGAATCGC
* *
633686 GTTGCGATAGTCAGAATCTC
1 ATTGCGATAGTCAGAATCGC
* *
633706 GTTGCGATAGTCAGATTCGC
1 ATTGCGATAGTCAGAATCGC
633726 ATTGCGAT
1 ATTGCGAT
633734 TTACATATTC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (20 bp):
ATTGCGATAGTCAGAATCGC
Found at i:633743 original size:20 final size:20
Alignment explanation
Indices: 633720--633792 Score: 137
Period size: 20 Copynumber: 3.6 Consensus size: 20
633710 CGATAGTCAG
*
633720 ATTCGCATTGCGATTTACAT
1 ATTCGCATTGCGATTTACGT
633740 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
633760 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
633780 ATTCGCATTGCGA
1 ATTCGCATTGCGA
633793 ATTAGGAAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:633815 original size:21 final size:21
Alignment explanation
Indices: 633789--633834 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
633779 TATTCGCATT
633789 GCGAATTAGGAAAATCACAAC
1 GCGAATTAGGAAAATCACAAC
* * *
633810 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCACAAC
633831 GCGA
1 GCGA
633835 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCACAAC
Found at i:634863 original size:27 final size:27
Alignment explanation
Indices: 634825--634879 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
634815 AATACTATTG
*
634825 TGGACATGTGTATTTGTATGACTCTTA
1 TGGACATATGTATTTGTATGACTCTTA
*
634852 TGGACATATGTATTTTTATGACTCTTA
1 TGGACATATGTATTTGTATGACTCTTA
634879 T
1 T
634880 TTTGTATTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.24, C:0.11, G:0.18, T:0.47
Consensus pattern (27 bp):
TGGACATATGTATTTGTATGACTCTTA
Found at i:638105 original size:42 final size:41
Alignment explanation
Indices: 638055--638144 Score: 110
Period size: 41 Copynumber: 2.2 Consensus size: 41
638045 TGGGAAAATG
* * *
638055 AAATAAAATCAAAGACAAATAAAA-AAATACATAAATAAAACA
1 AAATAAAATC-AAGACAAAGAAAATAAAGAAATAAAT-AAACA
* *
638097 AAATAAAATCAGGATAAAGAAAATAAAGAAATAAATAAACA
1 AAATAAAATCAAGACAAAGAAAATAAAGAAATAAATAAACA
638138 AAATAAA
1 AAATAAA
638145 TAAAAGGAGA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
41 22 0.52
42 20 0.48
ACGTcount: A:0.73, C:0.07, G:0.06, T:0.14
Consensus pattern (41 bp):
AAATAAAATCAAGACAAAGAAAATAAAGAAATAAATAAACA
Found at i:638274 original size:13 final size:13
Alignment explanation
Indices: 638256--638280 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
638246 AGAAAGAAAG
638256 AATAAGAAATAAT
1 AATAAGAAATAAT
638269 AATAAGAAATAA
1 AATAAGAAATAA
638281 AGCAAATATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.20
Consensus pattern (13 bp):
AATAAGAAATAAT
Found at i:638339 original size:18 final size:17
Alignment explanation
Indices: 638302--638337 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 17
638292 ATACGTACAT
638302 ATAAATATAAAAAATAA
1 ATAAATATAAAAAATAA
638319 ATAAATGATAAAATAATAA
1 ATAAAT-ATAAAA-AATAA
638338 TATTACTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 6 0.35
19 5 0.29
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (17 bp):
ATAAATATAAAAAATAA
Found at i:640299 original size:110 final size:109
Alignment explanation
Indices: 640092--640352 Score: 377
Period size: 110 Copynumber: 2.4 Consensus size: 109
640082 TGCGTTGCTC
* *
640092 CGAGTCTAATATCCTCCGCTGTGAAGTTGAAATTGGCTCT--A-GAACTGGGAAATTGTTTGTTG
1 CGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAATGAACTGGAAAATTGTTTGTTG
* *
640154 ACAGTCAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTATCT
66 ACAATCAGCCGCCCCTTCATTGTGAAGTTGAGCTTGTGTTATCT
* *
640198 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTAAATGAAACT-GAAAAGTTGTTTGT
1 CGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAATG-AACTGGAAAA-TTGTTTGT
* * *
640262 TGACAATCAGTCGCCCCTTCATTGTGAATTTGAGCTTGTGTTGTCT
64 TGACAATCAGCCGCCCCTTCATTGTGAAGTTGAGCTTGTGTTATCT
*
640308 TGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAAT
1 CGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-AAAT
640353 TAGGAAGCCC
Statistics
Matches: 137, Mismatches: 12, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
106 37 0.27
108 1 0.01
109 5 0.04
110 90 0.66
111 4 0.03
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (109 bp):
CGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAATGAACTGGAAAATTGTTTGTTG
ACAATCAGCCGCCCCTTCATTGTGAAGTTGAGCTTGTGTTATCT
Found at i:641625 original size:25 final size:24
Alignment explanation
Indices: 641581--641636 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 24
641571 CACCTTATTT
641581 TTCTTTTCTCTTTTTATTTTGTTC
1 TTCTTTTCTCTTTTTATTTTGTTC
*
641605 TT-TTTTCTCTTTTTTAATTTTTTTC
1 TTCTTTTCTC-TTTTT-ATTTTGTTC
641630 TTCTTTT
1 TTCTTTT
641637 TTTTTTGACT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 7 0.25
24 7 0.25
25 10 0.36
26 4 0.14
ACGTcount: A:0.05, C:0.14, G:0.02, T:0.79
Consensus pattern (24 bp):
TTCTTTTCTCTTTTTATTTTGTTC
Found at i:648769 original size:21 final size:21
Alignment explanation
Indices: 648731--648773 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
648721 GTTAATATGA
* *
648731 ATATAAAAACATGGAAAATAT
1 ATATAAAAAAATAGAAAATAT
*
648752 ATATAAAAAAATATAAAATAT
1 ATATAAAAAAATAGAAAATAT
648773 A
1 A
648774 AAATGCAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (21 bp):
ATATAAAAAAATAGAAAATAT
Found at i:649778 original size:164 final size:166
Alignment explanation
Indices: 649501--649809 Score: 419
Period size: 164 Copynumber: 1.9 Consensus size: 166
649491 CAAATGAATG
* *
649501 AAATAAAAAAAATAAAGAAACAATACTAGATTAGGTTTGTATTTGATATATTTATAGTACCGAAC
1 AAATAAAAAAAATAAAGAAACAATACTAGATTAGGTTTGTATTTAACATATTTATAGTA-CGAAC
*
649566 TTACCATTTTTTAGTGGAAGAATATATTTTATAAAAAAATTAAAAATTTAATCAATAAAGGAAAT
65 TTACCATTTTTTAGTGGAAGAAGATATTTTATAAAAAAATTAAAAATTTAATCAATAAAGGAAAT
*
649631 GGTAAAGTTAAAAAAATCAAATGAATGAAATCACAAA
130 AGTAAAGTTAAAAAAATCAAATGAATGAAATCACAAA
* * * * * * *
649668 AAATGAAAAAATTAATGAAATAGTACTAGATTAGGTTTGTATTTAACATATTTATA-T-TGAATT
1 AAATAAAAAAAATAAAGAAACAATACTAGATTAGGTTTGTATTTAACATATTTATAGTACGAACT
* * * *
649731 TATCA-TTTTTATGTGGAAGAAGATTTTTTATAAAAAAAATT-AAAATTTAATCAATAAATGATA
66 TACCATTTTTTA-GTGGAAGAAGATATTTTAT-AAAAAAATTAAAAATTTAATCAATAAAGGAAA
*
649794 TAGTAAAGTTGAAAAA
129 TAGTAAAGTTAAAAAA
649810 CTGAAATAAA
Statistics
Matches: 124, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
163 6 0.05
164 59 0.48
165 9 0.07
166 1 0.01
167 49 0.40
ACGTcount: A:0.50, C:0.05, G:0.12, T:0.34
Consensus pattern (166 bp):
AAATAAAAAAAATAAAGAAACAATACTAGATTAGGTTTGTATTTAACATATTTATAGTACGAACT
TACCATTTTTTAGTGGAAGAAGATATTTTATAAAAAAATTAAAAATTTAATCAATAAAGGAAATA
GTAAAGTTAAAAAAATCAAATGAATGAAATCACAAA
Found at i:650451 original size:27 final size:27
Alignment explanation
Indices: 650413--650469 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
650403 TAATGACTAT
650413 GGAAGGGAGAA-GGGGAAGGGGGAAGGG
1 GGAAGGGAGAACGGGGAAGGGGG-AGGG
*
650440 GGAAGGGAGAAGCGGGGGAGGGGGAGGG
1 GGAAGGGAGAA-CGGGGAAGGGGGAGGG
650468 GG
1 GG
650470 CACACATGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 11 0.41
28 6 0.22
29 10 0.37
ACGTcount: A:0.28, C:0.02, G:0.70, T:0.00
Consensus pattern (27 bp):
GGAAGGGAGAACGGGGAAGGGGGAGGG
Found at i:650463 original size:7 final size:7
Alignment explanation
Indices: 650413--650469 Score: 64
Period size: 7 Copynumber: 8.3 Consensus size: 7
650403 TAATGACTAT
650413 GGAAGGG
1 GGAAGGG
*
650420 AGAA-GG
1 GGAAGGG
650426 GGAAGGG
1 GGAAGGG
650433 GGAAGGG
1 GGAAGGG
650440 GGAAGGG
1 GGAAGGG
*
650447 AGAAGCGG
1 GGAAG-GG
*
650455 GGGAGGG
1 GGAAGGG
650462 GG-AGGG
1 GGAAGGG
650468 GG
1 GG
650470 CACACATGGG
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
6 11 0.26
7 27 0.63
8 5 0.12
ACGTcount: A:0.28, C:0.02, G:0.70, T:0.00
Consensus pattern (7 bp):
GGAAGGG
Found at i:654443 original size:37 final size:37
Alignment explanation
Indices: 654367--654443 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
654357 TTTTTATATT
*
654367 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
654404 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
654441 TTT
1 TTT
654444 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:654625 original size:20 final size:20
Alignment explanation
Indices: 654589--654626 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
654579 ATCATATTCC
**
654589 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
654609 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
654627 GTGAACCAAA
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:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:660387 original size:40 final size:40
Alignment explanation
Indices: 660334--660511 Score: 177
Period size: 40 Copynumber: 4.5 Consensus size: 40
660324 ATAAATCATC
*
660334 TGTTTCGAGTGAAACTATCTCAAGCGAGACAAAAATTTGT
1 TGTTTCGAGTGAAACTATCTCAAGCGAGACAAAAATCTGT
* * * *
660374 TGTTTCGATTGAAACTGTCTTAAGAGAGACAAAAATCTGT
1 TGTTTCGAGTGAAACTATCTCAAGCGAGACAAAAATCTGT
** *
660414 TGTTTCGAGTGAAACTATCTCAAGCGA-A-ATGTAATAT-T
1 TGTTTCGAGTGAAACTATCTCAAGCGAGACA-AAAATCTGT
* * ***
660452 CTGTTTCGAGTGAAACTATCTCAAGTGATA-TGTAATCT-T
1 -TGTTTCGAGTGAAACTATCTCAAGCGAGACAAAAATCTGT
660491 GTGTTTCGAGTGAAACTATCT
1 -TGTTTCGAGTGAAACTATCT
660512 TCAGTGAGAT
Statistics
Matches: 119, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
38 2 0.02
39 58 0.49
40 59 0.50
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (40 bp):
TGTTTCGAGTGAAACTATCTCAAGCGAGACAAAAATCTGT
Found at i:660518 original size:39 final size:39
Alignment explanation
Indices: 660414--660511 Score: 160
Period size: 39 Copynumber: 2.5 Consensus size: 39
660404 AAAAATCTGT
*
660414 TGTTTCGAGTGAAACTATCTCAAGCGAAATGTAATATTC
1 TGTTTCGAGTGAAACTATCTCAAGTGAAATGTAATATTC
* * *
660453 TGTTTCGAGTGAAACTATCTCAAGTGATATGTAATCTTG
1 TGTTTCGAGTGAAACTATCTCAAGTGAAATGTAATATTC
660492 TGTTTCGAGTGAAACTATCT
1 TGTTTCGAGTGAAACTATCT
660512 TCAGTGAGAT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 55 1.00
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (39 bp):
TGTTTCGAGTGAAACTATCTCAAGTGAAATGTAATATTC
Found at i:660810 original size:39 final size:39
Alignment explanation
Indices: 660631--660868 Score: 234
Period size: 39 Copynumber: 6.2 Consensus size: 39
660621 AATATGAAGT
* * *
660631 GAGATA-AATCATCTGTTTTGAGTGAAACTATCTCAACC
1 GAGATATAATCTTCTGTTTCGAGTGAAACTATCTCAAGC
* ** * *
660669 AAGATA-AA-AATC-GTTTCGAGTGAAACTGTCTCAAGA
1 GAGATATAATCTTCTGTTTCGAGTGAAACTATCTCAAGC
* * * * * *
660705 AAGACA-AATATTTGTTGTTTCGAGTGAAAATATCTCAAGA
1 GAGATATAAT-CTT-CTGTTTCGAGTGAAACTATCTCAAGC
* * * * *
660745 GGGACAAAAAGCTTCTGTTTCGAGTGAAACTATCTCAAAC
1 GAGA-TATAATCTTCTGTTTCGAGTGAAACTATCTCAAGC
*
660785 GAGATGTAATCTTCTGTTTCGAGTGAAACTATCTCAAGC
1 GAGATATAATCTTCTGTTTCGAGTGAAACTATCTCAAGC
660824 GAGATATAATCTTCTGTTTCGAGTGAAACTATCTCAAGC
1 GAGATATAATCTTCTGTTTCGAGTGAAACTATCTCAAGC
660863 GAGATA
1 GAGATA
660869 ATTAAATCTT
Statistics
Matches: 166, Mismatches: 28, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
36 27 0.16
37 3 0.02
38 8 0.05
39 74 0.45
40 49 0.30
41 3 0.02
42 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (39 bp):
GAGATATAATCTTCTGTTTCGAGTGAAACTATCTCAAGC
Found at i:664866 original size:20 final size:20
Alignment explanation
Indices: 664782--664868 Score: 59
Period size: 22 Copynumber: 4.0 Consensus size: 20
664772 TATTTTACTA
*
664782 AAATATATATCTAGAGTTAATT
1 AAATATATATTTA-A-TTAATT
*
664804 AAATATATGTTTTTAA-TAATCCT
1 AAATATA--TATTTAATTAAT--T
* *
664827 GAATATTTAATTTCAATTAATT
1 AAATATAT-ATTT-AATTAATT
664849 AAATATATATTTAATTAATT
1 AAATATATATTTAATTAATT
664869 TGAAATAATA
Statistics
Matches: 51, Mismatches: 7, Indels: 16
0.69 0.09 0.22
Matches are distributed among these distances:
20 8 0.16
21 9 0.18
22 17 0.33
23 9 0.18
24 8 0.16
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.47
Consensus pattern (20 bp):
AAATATATATTTAATTAATT
Found at i:664945 original size:90 final size:89
Alignment explanation
Indices: 664830--665006 Score: 291
Period size: 90 Copynumber: 2.0 Consensus size: 89
664820 TAATCCTGAA
* * * * *
664830 TATTTAATTTCAATTAATTAAATATATATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATCTGAAATAATAAAA-CCATAATATGAT
664895 TAGGGTAACTTGGATATAAAAGGAT
65 TAGGGTAACTTGGATATAAAAGGAT
664920 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATCTGAAATAATAAAACCATAATATGATT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATCTGAAATAATAAAACCATAATATGATT
*
664985 AGGGTAACTTGGCTATAAAAGG
66 AGGGTAACTTGGATATAAAAGG
665007 GTGTGTTAGG
Statistics
Matches: 81, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
89 33 0.41
90 48 0.59
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.37
Consensus pattern (89 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATCTGAAATAATAAAACCATAATATGATT
AGGGTAACTTGGATATAAAAGGAT
Found at i:671633 original size:13 final size:12
Alignment explanation
Indices: 671617--671667 Score: 68
Period size: 12 Copynumber: 4.2 Consensus size: 12
671607 TAAACATAAT
671617 TAAAATAATAAAA
1 TAAAA-AATAAAA
671630 T-AAAAATAAAA
1 TAAAAAATAAAA
671641 TAAAAAAATAAAA
1 T-AAAAAATAAAA
*
671654 TAAAAAACAAAA
1 TAAAAAATAAAA
671666 TA
1 TA
671668 GAATAAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
11 8 0.23
12 15 0.43
13 12 0.34
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.18
Consensus pattern (12 bp):
TAAAAAATAAAA
Found at i:671641 original size:19 final size:19
Alignment explanation
Indices: 671617--671679 Score: 71
Period size: 17 Copynumber: 3.5 Consensus size: 19
671607 TAAACATAAT
*
671617 TAAAATAATAAAATAAAAA
1 TAAAATAAAAAAATAAAAA
671636 TAAAATAAAAAAAT-AAAA
1 TAAAATAAAAAAATAAAAA
* *
671654 TAAAA-AACAAAAT-AGAA
1 TAAAATAAAAAAATAAAAA
671671 TAAAA-AAAA
1 TAAAATAAAA
671680 CACAAGTACA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
17 18 0.45
18 9 0.22
19 13 0.32
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.16
Consensus pattern (19 bp):
TAAAATAAAAAAATAAAAA
Found at i:671676 original size:11 final size:11
Alignment explanation
Indices: 671623--671659 Score: 56
Period size: 11 Copynumber: 3.2 Consensus size: 11
671613 TAATTAAAAT
671623 AATAAAATAAA
1 AATAAAATAAA
671634 AATAAAATAAAAA
1 AATAAAAT--AAA
671647 AATAAAATAAA
1 AATAAAATAAA
671658 AA
1 AA
671660 ACAAAATAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 13 0.54
13 11 0.46
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AATAAAATAAA
Found at i:671677 original size:17 final size:17
Alignment explanation
Indices: 671626--671679 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 17
671616 TTAAAATAAT
671626 AAAATAAAAATAAAATAAA
1 AAAAT-AAAATAAAA-AAA
*
671645 AAAATAAAATAAAAAAC
1 AAAATAAAATAAAAAAA
*
671662 AAAATAGAATAAAAAAA
1 AAAATAAAATAAAAAAA
671679 A
1 A
671680 CACAAGTACA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
17 18 0.56
18 9 0.28
19 5 0.16
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.13
Consensus pattern (17 bp):
AAAATAAAATAAAAAAA
Found at i:671678 original size:13 final size:13
Alignment explanation
Indices: 671617--671660 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
671607 TAAACATAAT
*
671617 TAAAATAATAAAA
1 TAAAAAAATAAAA
671630 T--AAAAATAAAA
1 TAAAAAAATAAAA
671641 TAAAAAAATAAAA
1 TAAAAAAATAAAA
671654 TAAAAAA
1 TAAAAAA
671661 CAAAATAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 10 0.36
13 18 0.64
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (13 bp):
TAAAAAAATAAAA
Found at i:673988 original size:23 final size:21
Alignment explanation
Indices: 673948--673993 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
673938 ATTATTAAGG
*
673948 ATATATTAAATTTAAATATTA
1 ATATATTAAATTTAAATAATA
*
673969 ATATATTTATATTTATAATAATA
1 ATATA-TTAAATTTA-AATAATA
673992 AT
1 AT
673994 TAAAATTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 5 0.24
22 8 0.38
23 8 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATATATTAAATTTAAATAATA
Found at i:675193 original size:32 final size:33
Alignment explanation
Indices: 675153--675219 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
675143 AAAATAAATC
675153 TCAATTTTCCCATTTT-AAAAAAATATATAACT
1 TCAATTTTCCCATTTTAAAAAAAATATATAACT
*
675185 TCAATTTTCCCATTTTAAAAAAAATATATTACT
1 TCAATTTTCCCATTTTAAAAAAAATATATAACT
675218 TC
1 TC
675220 TTAATTTGCG
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 16 0.48
33 17 0.52
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (33 bp):
TCAATTTTCCCATTTTAAAAAAAATATATAACT
Found at i:675212 original size:31 final size:31
Alignment explanation
Indices: 675141--675212 Score: 112
Period size: 32 Copynumber: 2.3 Consensus size: 31
675131 AAAAATATTT
675141 AAAAAATA-AATCTCAATTTTCCCATTTTAA
1 AAAAAATATAATCTCAATTTTCCCATTTTAA
675171 AAAAATATATAA-CTTCAATTTTCCCATTTTAA
1 AAAAA-ATATAATC-TCAATTTTCCCATTTTAA
675203 AAAAAATATA
1 AAAAAATATA
675213 TTACTTCTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
30 5 0.13
31 9 0.23
32 25 0.64
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (31 bp):
AAAAAATATAATCTCAATTTTCCCATTTTAA
Found at i:677785 original size:19 final size:19
Alignment explanation
Indices: 677761--677799 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
677751 AATTCCATTT
677761 AAATTTTTTCCAAAAAAAA
1 AAATTTTTTCCAAAAAAAA
**
677780 AAATTTTTTTTAAAAAAAA
1 AAATTTTTTCCAAAAAAAA
677799 A
1 A
677800 TTATCATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (19 bp):
AAATTTTTTCCAAAAAAAA
Found at i:678400 original size:30 final size:31
Alignment explanation
Indices: 678366--678425 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
678356 CTCTAAATTT
* * *
678366 TGTGA-GGAACATGTGGACCTGTCACAAATA
1 TGTGATGGAACAAGTAGACCCGTCACAAATA
*
678396 TGTGATGGAATAAGTAGACCCGTCACAAAT
1 TGTGATGGAACAAGTAGACCCGTCACAAAT
678426 TTTATGTTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 5 0.20
31 20 0.80
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (31 bp):
TGTGATGGAACAAGTAGACCCGTCACAAATA
Found at i:678489 original size:216 final size:215
Alignment explanation
Indices: 678206--678615 Score: 637
Period size: 216 Copynumber: 1.9 Consensus size: 215
678196 GGTATGTTTG
*
678206 AAATTTTATGTTTCAATGGAGGAAAATTGGAGGGAATAAGCGGGTAAGTAAAAAACCTCTAAATT
1 AAATTTTATGTTTCAATGGAGGAAAATTGGAGGAAATAAGCGGGTAAGTAAAAAACCTCTAAATT
*
678271 TTGTGACGGAACATGTGAACCCGTCACAAATTTTATGTTTCAATGGAGGGAAATTGGAGGAAATG
66 TTGTGACGGAACATGTGAACCCGTCACAAATTTTATGTTTCAATGGAGGAAAATTGGAGGAAATG
* * **
678336 AGTGGGCAATTAAAAAAAACCTCTAAATTTTGTGA-GGAACATGTGGACCTGTCACAAATATGTG
131 AGCGGGCAATT-AAAAAAA-CTCAAAATTTTGTGATGGAACATGTGGACCCATCACAAATATGTG
678400 ATGGAATAAGTAGACCCGTCAC
194 ATGGAATAAGTAGACCCGTCAC
* *
678422 AAATTTTATGTTTCAATGGATGG-AAATTGGAGGAAATAAGTGGGTAATTTAAAAAA-CTCTAAA
1 AAATTTTATGTTTCAATGGA-GGAAAATTGGAGGAAATAAGCGGGTAA-GTAAAAAACCTCTAAA
* * * *
678485 TTTTGTGACGGAATATGTGAATCTGTCACAAATTTTATGTTTCAATGGAGGAAAATTGGAGGTAA
64 TTTTGTGACGGAACATGTGAACCCGTCACAAATTTTATGTTTCAATGGAGGAAAATTGGAGGAAA
* *
678550 TGAGCGGGTAATTAAAAAAACTCAAAATTTTGTGATGGAACATGTGGACCCATCACAAATTTGTG
129 TGAGCGGGCAATTAAAAAAACTCAAAATTTTGTGATGGAACATGTGGACCCATCACAAATATGTG
678615 A
194 A
678616 GGGTCCACAT
Statistics
Matches: 177, Mismatches: 14, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
214 14 0.08
215 34 0.19
216 120 0.68
217 9 0.05
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (215 bp):
AAATTTTATGTTTCAATGGAGGAAAATTGGAGGAAATAAGCGGGTAAGTAAAAAACCTCTAAATT
TTGTGACGGAACATGTGAACCCGTCACAAATTTTATGTTTCAATGGAGGAAAATTGGAGGAAATG
AGCGGGCAATTAAAAAAACTCAAAATTTTGTGATGGAACATGTGGACCCATCACAAATATGTGAT
GGAATAAGTAGACCCGTCAC
Found at i:678606 original size:92 final size:92
Alignment explanation
Indices: 678396--678611 Score: 299
Period size: 92 Copynumber: 2.3 Consensus size: 92
678386 GTCACAAATA
* *
678396 TGTGATGGAATAAGTAGACCCGTCACAAATTTTATGTTTCAATGGATGGAAATTGGAGGAAATAA
1 TGTGATGGAATATGTGGACCCGTCACAAATTTTATGTTTCAATGGATGGAAATTGGAGGAAATAA
* * *
678461 GTGGGTAATTTAAAAAACTCTAAATTT
66 GCGGGTAATTAAAAAAACTCAAAATTT
* * * * * *
678488 TGTGACGGAATATGTGAATCTGTCACAAATTTTATGTTTCAATGGA-GGAAAATTGGAGGTAATG
1 TGTGATGGAATATGTGGACCCGTCACAAATTTTATGTTTCAATGGATGG-AAATTGGAGGAAATA
678552 AGCGGGTAATTAAAAAAACTCAAAATTT
65 AGCGGGTAATTAAAAAAACTCAAAATTT
* *
678580 TGTGATGGAACATGTGGACCCATCACAAATTT
1 TGTGATGGAATATGTGGACCCGTCACAAATTT
678612 GTGAGGGTCC
Statistics
Matches: 106, Mismatches: 17, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
91 2 0.02
92 104 0.98
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.31
Consensus pattern (92 bp):
TGTGATGGAATATGTGGACCCGTCACAAATTTTATGTTTCAATGGATGGAAATTGGAGGAAATAA
GCGGGTAATTAAAAAAACTCAAAATTT
Found at i:683325 original size:54 final size:54
Alignment explanation
Indices: 683235--683344 Score: 175
Period size: 54 Copynumber: 2.0 Consensus size: 54
683225 AAACCATAAT
* ** *
683235 ATAATCCAAAACCTACAAGTATTCTTGGAAGGAAGATCCCGTTGGACATAGTGG
1 ATAATCCAAAACCTACAAGTACTCTTAAAAGAAAGATCCCGTTGGACATAGTGG
*
683289 ATAATCCCAAACCTACAAGTACTCTTAAAAGAAAGATCCCGTTGGACATAGTGG
1 ATAATCCAAAACCTACAAGTACTCTTAAAAGAAAGATCCCGTTGGACATAGTGG
683343 AT
1 AT
683345 GTTAGGTTGC
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (54 bp):
ATAATCCAAAACCTACAAGTACTCTTAAAAGAAAGATCCCGTTGGACATAGTGG
Found at i:683865 original size:2 final size:2
Alignment explanation
Indices: 683860--683937 Score: 106
Period size: 2 Copynumber: 39.5 Consensus size: 2
683850 GCACATCATA
** *
683860 AT AT AT AT A- AT GC AT AT AGT AT AC AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
683902 AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
683938 AAGTACTAAT
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
1 2 0.03
2 63 0.94
3 2 0.03
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:686079 original size:51 final size:51
Alignment explanation
Indices: 686021--686135 Score: 144
Period size: 51 Copynumber: 2.3 Consensus size: 51
686011 AGAAGTAGAC
* * *
686021 TTATTATTTTATTAGGAACTAAGATCA-AGTTAAAATACTAT-TCTTAGTTTA
1 TTATTATTTTATTAGGAACTAAGAT-AGAATCAAAACACTATCT-TTAGTTTA
* * *
686072 TTATTATTTTATTAGGAATTATGATAGAATCAAAACATTATCTTTAGTTTA
1 TTATTATTTTATTAGGAACTAAGATAGAATCAAAACACTATCTTTAGTTTA
686123 TTATTATTTTATT
1 TTATTATTTTATT
686136 CATTAGTCAT
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
50 1 0.02
51 54 0.96
52 1 0.02
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.50
Consensus pattern (51 bp):
TTATTATTTTATTAGGAACTAAGATAGAATCAAAACACTATCTTTAGTTTA
Found at i:688071 original size:23 final size:25
Alignment explanation
Indices: 688026--688071 Score: 60
Period size: 23 Copynumber: 1.9 Consensus size: 25
688016 TGATAACTTT
* *
688026 TTTAATATATAATATATATATTAAC
1 TTTAATATATAATAAATAAATTAAC
688051 TTTAAT-T-TAATAAATAAATTA
1 TTTAATATATAATAAATAAATTA
688072 TATTAATTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 12 0.63
24 1 0.05
25 6 0.32
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (25 bp):
TTTAATATATAATAAATAAATTAAC
Found at i:688084 original size:30 final size:30
Alignment explanation
Indices: 688019--688077 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 30
688009 TTACAAGTGA
*
688019 TAACTTT--TTTAATATATAATATATATAT
1 TAACTTTAATTTAATAAATAATATATATAT
688047 TAACTTTAATTTAATAAATAA-AT-TATAT
1 TAACTTTAATTTAATAAATAATATATATAT
688075 TAA
1 TAA
688078 TTCTTTATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 15 0.54
29 2 0.07
30 11 0.39
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.49
Consensus pattern (30 bp):
TAACTTTAATTTAATAAATAATATATATAT
Found at i:688640 original size:92 final size:91
Alignment explanation
Indices: 688488--688676 Score: 263
Period size: 92 Copynumber: 2.1 Consensus size: 91
688478 GGTATGTTTG
* ** *
688488 AAATTTTATGTTTCAATGGAGGGAAATTGGAGGGAATGAGCGGGTAAGTAAAAAACCTCTAAATT
1 AAATTTTATGTTTCAATGGAGGAAAATTGGAGAAAATGAGCGGGTAAGTAAAAAAACTCTAAATT
* *
688553 TTGTGACGGAACATTTGAACCCG-CTAC
66 TTGT-AAGGAACATGTGAACCCGTC-AC
* * *
688580 AAATTTTATGTTTCAATGGAGGAAAATTTGAGAAAATGAGTGGGTAATTAAAAAAACTCTAAATT
1 AAATTTTATGTTTCAATGGAGGAAAATTGGAGAAAATGAGCGGGTAAGTAAAAAAACTCTAAATT
*
688645 TTGTAAGGAACATGTGGACCCGTCAC
66 TTGTAAGGAACATGTGAACCCGTCAC
688671 AAATTT
1 AAATTT
688677 GTGACGTAAC
Statistics
Matches: 86, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
91 23 0.27
92 63 0.73
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (91 bp):
AAATTTTATGTTTCAATGGAGGAAAATTGGAGAAAATGAGCGGGTAAGTAAAAAAACTCTAAATT
TTGTAAGGAACATGTGAACCCGTCAC
Found at i:688712 original size:122 final size:123
Alignment explanation
Indices: 688552--688799 Score: 383
Period size: 122 Copynumber: 2.0 Consensus size: 123
688542 ACCTCTAAAT
** * *
688552 TTTGTGACGGAACATTTGAACCCGCTACAAATTTTATGTTTCAATGGAGGAAAATTTGAGAAAAT
1 TTTGTGACGGAACAAGTAAACCCGCTACAAATTTTATGTTTCAATGGAGGAAAATTGGAGAAAAT
* *
688617 GAGTGGGTAATTAAAAAAACTCTAAATTTTGTAA-GGAACATGTGGACCCGTCACAAA
66 GAGTGGGTAATTAAAAAAACTCTAAATTTTGCAACAGAACATGTGGACCCGTCACAAA
* * *
688674 TTTGTGACGTAACAAGTAAACCCG-TCACAAATTTTATGTTTCAATGGATGAAAATTGGAGGAAA
1 TTTGTGACGGAACAAGTAAACCCGCT-ACAAATTTTATGTTTCAATGGAGGAAAATTGGAGAAAA
*
688738 TGAGTGGGTAATTAAAAAATCTCTAAATTTTGCAACAGAACATGTGGACCCGTCACAAA
65 TGAGTGGGTAATTAAAAAAACTCTAAATTTTGCAACAGAACATGTGGACCCGTCACAAA
688797 TTT
1 TTT
688800 TATGTTTCAA
Statistics
Matches: 114, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
121 1 0.01
122 88 0.77
123 25 0.22
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (123 bp):
TTTGTGACGGAACAAGTAAACCCGCTACAAATTTTATGTTTCAATGGAGGAAAATTGGAGAAAAT
GAGTGGGTAATTAAAAAAACTCTAAATTTTGCAACAGAACATGTGGACCCGTCACAAA
Found at i:691247 original size:16 final size:16
Alignment explanation
Indices: 691201--691255 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
691191 GGTATTACCC
691201 GACCTGTTTTCAACCT
1 GACCTGTTTTCAACCT
* ** *
691217 GACTTGTAATGAACCT
1 GACCTGTTTTCAACCT
*
691233 GACCTGTTTTTAACCT
1 GACCTGTTTTCAACCT
*
691249 AACCTGT
1 GACCTGT
691256 AAATGATCCG
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.36
Consensus pattern (16 bp):
GACCTGTTTTCAACCT
Found at i:691815 original size:14 final size:14
Alignment explanation
Indices: 691796--691839 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
691786 TCCATTTACA
* *
691796 TTAGAGTTTAGGGT
1 TTAGAGTTTAAGAT
691810 TTAGAGTTTAAGAT
1 TTAGAGTTTAAGAT
*
691824 TTAGGGTTTAAGAT
1 TTAGAGTTTAAGAT
691838 TT
1 TT
691840 CTATAAACTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.45
Consensus pattern (14 bp):
TTAGAGTTTAAGAT
Found at i:691928 original size:27 final size:28
Alignment explanation
Indices: 691896--691948 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
691886 TTCTATAAAC
*
691896 TATATAAGTAATTTATATATA-TATATA
1 TATATAAATAATTTATATATACTATATA
*
691923 TATATAAATAGTTTATATATACTATA
1 TATATAAATAATTTATATATACTATA
691949 CATAGTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (28 bp):
TATATAAATAATTTATATATACTATATA
Found at i:691953 original size:20 final size:20
Alignment explanation
Indices: 691917--691964 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
691907 TTTATATATA
691917 TATATATA-TATAAATAGTT
1 TATATATACTATAAATAGTT
*
691936 TATATATACTATACATAGTT
1 TATATATACTATAAATAGTT
*
691956 TATACATAC
1 TATATATAC
691965 ATGTATTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (20 bp):
TATATATACTATAAATAGTT
Found at i:692205 original size:6 final size:6
Alignment explanation
Indices: 692194--693151 Score: 1633
Period size: 6 Copynumber: 158.8 Consensus size: 6
692184 TATATAGTTT
692194 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
1 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
692242 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
1 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
692290 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
1 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
* * *
692338 ATACAC ATACAC ATACAC ATACAC ATGCAC ATGCAC ATGCAC ATACAC
1 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
* * * * * *
692386 ATGCAC ATGCAC ATGCAC ATGCAC ATGCAC ATGCAC ATGTACAC ATACAC
1 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC A--TACAC ATACAC
692436 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
1 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
692484 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
1 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
692532 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
1 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
692580 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
1 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
692628 ATACAC ATACAC ATACAC AT--AC ATACAC ATACAC ATACAC ATACAC
1 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
692674 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
1 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
*
692722 ATACAC ATACAC ATACAC ACACATAC ATACAC ATACAC ATACAC ATACAC
1 ATACAC ATACAC ATACAC ATAC--AC ATACAC ATACAC ATACAC ATACAC
692772 ATACAC ATACAC ATACAC ATACACAC ATACAC ATACAC ATACAC ATACAC
1 ATACAC ATACAC ATACAC AT--ACAC ATACAC ATACAC ATACAC ATACAC
692822 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC --ACAC ATACAC
1 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
692868 -TACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
1 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
692915 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
1 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
* * *
692963 ATACAC ACACATAC ATGCAC ATGCAC ATGCACAC ATACAC ATACAC ATACAC
1 ATACAC ATAC--AC ATACAC ATACAC AT--ACAC ATACAC ATACAC ATACAC
693015 AT--AC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
1 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
693061 ATACAC ATACAC ATACAC ATACAC ATACAC ATACACAC ATACAC ATACAC
1 ATACAC ATACAC ATACAC ATACAC ATACAC AT--ACAC ATACAC ATACAC
*
693111 ATATAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACA
1 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACA
693152 AGTGAAAAAA
Statistics
Matches: 921, Mismatches: 12, Indels: 38
0.95 0.01 0.04
Matches are distributed among these distances:
4 12 0.01
5 5 0.01
6 873 0.95
8 31 0.03
ACGTcount: A:0.49, C:0.33, G:0.01, T:0.17
Consensus pattern (6 bp):
ATACAC
Found at i:693285 original size:19 final size:18
Alignment explanation
Indices: 693251--693301 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 18
693241 TTTTCTATTC
693251 CCTCTAAATATCTCAATTT
1 CCTCTAAAT-TCTCAATTT
693270 CTCTCTAAATTCTCAATTT
1 C-CTCTAAATTCTCAATTT
*
693289 CC-CTATATTCTCA
1 CCTCTAAATTCTCA
693302 GAATTTCCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 10 0.33
18 1 0.03
19 11 0.37
20 8 0.27
ACGTcount: A:0.27, C:0.29, G:0.00, T:0.43
Consensus pattern (18 bp):
CCTCTAAATTCTCAATTT
Found at i:693300 original size:17 final size:19
Alignment explanation
Indices: 693252--693301 Score: 68
Period size: 17 Copynumber: 2.7 Consensus size: 19
693242 TTTCTATTCC
693252 CTCTAAATATCTCAATTTCT
1 CTCTAAAT-TCTCAATTTCT
693272 CTCTAAATTCTCAATTTC-
1 CTCTAAATTCTCAATTTCT
*
693290 C-CTATATTCTCA
1 CTCTAAATTCTCA
693302 GAATTTCCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 10 0.34
18 1 0.03
19 10 0.34
20 8 0.28
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.44
Consensus pattern (19 bp):
CTCTAAATTCTCAATTTCT
Found at i:693403 original size:2 final size:2
Alignment explanation
Indices: 693396--693427 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
693386 ACTTTGAATA
693396 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
693428 TAATATGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:693491 original size:13 final size:13
Alignment explanation
Indices: 693463--693552 Score: 56
Period size: 15 Copynumber: 6.3 Consensus size: 13
693453 ATATACTTTT
693463 TATAGTTTATACATA
1 TATAGTTTAT--ATA
693478 TATAGTTTATATA
1 TATAGTTTATATA
*
693491 TATAGTTCATATAAA
1 TATAGTT--TATATA
* *
693506 CATAATTTATATA
1 TATAGTTTATATA
*
693519 GATAGCTTATAATAATTA
1 TATAG-TT-T-AT-A-TA
693537 TATAGTTTATA-A
1 TATAGTTTATATA
693549 TATA
1 TATA
693553 ATTATAGTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
12 5 0.08
13 18 0.30
14 3 0.05
15 23 0.38
16 3 0.05
17 3 0.05
18 6 0.10
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (13 bp):
TATAGTTTATATA
Found at i:693577 original size:19 final size:18
Alignment explanation
Indices: 693537--693570 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
693527 ATAATAATTA
693537 TATAGTTTATAATATAAT
1 TATAGTTTATAATATAAT
693555 TATAGTTTATAA-ATAA
1 TATAGTTTATAATATAA
693571 ACTTATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (18 bp):
TATAGTTTATAATATAAT
Found at i:712215 original size:13 final size:13
Alignment explanation
Indices: 712197--712222 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
712187 TGGCCAAAAA
712197 TGAAAAGGTATGT
1 TGAAAAGGTATGT
712210 TGAAAAGGTATGT
1 TGAAAAGGTATGT
712223 GACAGGTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:716628 original size:28 final size:30
Alignment explanation
Indices: 716581--716657 Score: 104
Period size: 28 Copynumber: 2.6 Consensus size: 30
716571 ATTTATATCC
* *
716581 TATAATATATATATATATACCTGAACATCA
1 TATAATATATATATATATACATGAACATAA
* *
716611 TATAATATATATA-A-ATACATGCATATAA
1 TATAATATATATATATATACATGAACATAA
716639 TATAATATATATATATATA
1 TATAATATATATATATATA
716658 TATATATATA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
28 23 0.56
29 2 0.05
30 16 0.39
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.39
Consensus pattern (30 bp):
TATAATATATATATATATACATGAACATAA
Found at i:716664 original size:28 final size:28
Alignment explanation
Indices: 716541--716665 Score: 84
Period size: 28 Copynumber: 4.6 Consensus size: 28
716531 ATTTTAGTCA
716541 ATATATATATATATATAAT-TAATAT-T
1 ATATATATATATATATAATATAATATAT
** **
716567 A-A-CCAT-T-TATATCCTATAATATAT
1 ATATATATATATATATAATATAATATAT
* *
716591 ATATATATACCTGA-ACATCATATAATATAT
1 ATATATATA--T-ATATATAATATAATATAT
* * **
716621 ATAAATACATGCATATAATATAATATAT
1 ATATATATATATATATAATATAATATAT
716649 ATATATATATATATATA
1 ATATATATATATATATA
716666 TATGCATATA
Statistics
Matches: 72, Mismatches: 17, Indels: 18
0.67 0.16 0.17
Matches are distributed among these distances:
22 6 0.08
23 7 0.10
24 4 0.06
25 2 0.03
26 3 0.04
28 28 0.39
29 1 0.01
30 21 0.29
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.42
Consensus pattern (28 bp):
ATATATATATATATATAATATAATATAT
Found at i:716676 original size:2 final size:2
Alignment explanation
Indices: 716610--716668 Score: 61
Period size: 2 Copynumber: 31.0 Consensus size: 2
716600 CCTGAACATC
* * **
716610 AT AT A- AT AT AT AT AA AT AC AT GC AT AT A- AT AT A- 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
716649 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
716669 GCATATATTT
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
1 3 0.07
2 43 0.93
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (2 bp):
AT
Found at i:716737 original size:14 final size:15
Alignment explanation
Indices: 716718--716746 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
716708 CGTTCGAATT
716718 AAATA-TAAAAAATA
1 AAATATTAAAAAATA
716732 AAATATTAAAAAATA
1 AAATATTAAAAAATA
716747 TTCGAGTAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAATATTAAAAAATA
Found at i:717084 original size:29 final size:29
Alignment explanation
Indices: 717010--717075 Score: 107
Period size: 29 Copynumber: 2.3 Consensus size: 29
717000 TTTAAGTTTC
717010 TCGACTATTAAAAGTTATAAAATAGTCCA
1 TCGACTATTAAAAGTTATAAAATAGTCCA
*
717039 TCGACTATTAAAAGTTATAAATTAGT-CA
1 TCGACTATTAAAAGTTATAAAATAGTCCA
*
717067 TTGACTATT
1 TCGACTATT
717076 CATATGTTAC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
28 10 0.29
29 25 0.71
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (29 bp):
TCGACTATTAAAAGTTATAAAATAGTCCA
Found at i:717604 original size:134 final size:131
Alignment explanation
Indices: 717463--717740 Score: 407
Period size: 134 Copynumber: 2.1 Consensus size: 131
717453 CAAATGAATG
* *
717463 AAAAAAATGAAATAATACTAGATTAGGTTTGTATTTAATATATTTCTATTACTGAATTTA-C-TA
1 AAAAAAATGAAATAATACTAGAATAGGTTTGTATTTAATATATTTATATTACTGAATTTATCATA
717526 TTTTTGAGTGGAAGAAGATATTTTATAAAAAAAATTAAAAATCTAATCAAGAAATGATACGGTAA
66 -TTTT-AGTGGAAGAAGATATTTTAT-AAAAAAA-TAAAAATCTAATCAA-AAATGATACGGTAA
717591 AGTTAA
126 AGTTAA
*
717597 AAAAAAATGAAATAGTACTAGAATAGGTTTGTATTTAATATATTTATATTACTGAATTTATCATA
1 AAAAAAATGAAATAATACTAGAATAGGTTTGTATTTAATATATTTATATTACTGAATTTATCATA
* * * * * *
717662 TTTTAGTGGAAGAAGATATTTTATAGAAACATAAAAATTTAATCAATAATGATATGGTAAAGTTG
66 TTTTAGTGGAAGAAGATATTTTATAAAAAAATAAAAATCTAATCAAAAATGATACGGTAAAGTTA
717727 A
131 A
*
717728 AAAAAAATCAAAT
1 AAAAAAATGAAAT
717741 GAATGAAATC
Statistics
Matches: 132, Mismatches: 10, Indels: 7
0.89 0.07 0.05
Matches are distributed among these distances:
131 29 0.22
132 14 0.11
133 5 0.04
134 77 0.58
135 5 0.04
136 2 0.02
ACGTcount: A:0.47, C:0.05, G:0.13, T:0.36
Consensus pattern (131 bp):
AAAAAAATGAAATAATACTAGAATAGGTTTGTATTTAATATATTTATATTACTGAATTTATCATA
TTTTAGTGGAAGAAGATATTTTATAAAAAAATAAAAATCTAATCAAAAATGATACGGTAAAGTTA
A
Found at i:718865 original size:51 final size:51
Alignment explanation
Indices: 718807--718921 Score: 146
Period size: 51 Copynumber: 2.3 Consensus size: 51
718797 AGAATTAGAC
* *
718807 TTATTATTTTATTAGGAACTGA-GATCA-AGTTAAAACATTAT-TCTCAGTTTA
1 TTATTATTTTATTAGGAACT-ATGAT-AGAATCAAAACATTATCT-TCAGTTTA
* *
718858 TTATTATTTTATTAGGAACTATGATAGAATCGAAACATTATCTTTAGTTTA
1 TTATTATTTTATTAGGAACTATGATAGAATCAAAACATTATCTTCAGTTTA
718909 TTATTATTTTATT
1 TTATTATTTTATT
718922 CGTTAACATG
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
50 2 0.04
51 54 0.95
52 1 0.02
ACGTcount: A:0.34, C:0.08, G:0.10, T:0.48
Consensus pattern (51 bp):
TTATTATTTTATTAGGAACTATGATAGAATCAAAACATTATCTTCAGTTTA
Found at i:719838 original size:20 final size:20
Alignment explanation
Indices: 719813--719868 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
719803 CTCTGTATAG
*
719813 TAGTATCGATACCATAGGTA
1 TAGTATCGATACCATAGGCA
719833 TAGTATCGATACCATAGGCA
1 TAGTATCGATACCATAGGCA
719853 TAGTATCGATACCATA
1 TAGTATCGATACCATA
719869 AGGCCCCAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (20 bp):
TAGTATCGATACCATAGGCA
Found at i:722743 original size:21 final size:21
Alignment explanation
Indices: 722717--722759 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
722707 TTTTCCTCTG
722717 AGAGAAATAGAATTCAGTAGC
1 AGAGAAATAGAATTCAGTAGC
722738 AGAGAAATAGAATTCAGTAGC
1 AGAGAAATAGAATTCAGTAGC
722759 A
1 A
722760 CGTTTGTTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.49, C:0.09, G:0.23, T:0.19
Consensus pattern (21 bp):
AGAGAAATAGAATTCAGTAGC
Found at i:723675 original size:13 final size:13
Alignment explanation
Indices: 723626--723676 Score: 66
Period size: 13 Copynumber: 3.9 Consensus size: 13
723616 AATGACGTGC
*
723626 AATGAGCGTCATA
1 AATGCGCGTCATA
*
723639 AATGCACGTCATA
1 AATGCGCGTCATA
*
723652 AATGCGTGTCATA
1 AATGCGCGTCATA
*
723665 AATGTGCGTCAT
1 AATGCGCGTCAT
723677 CATAAATTCG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:724996 original size:15 final size:15
Alignment explanation
Indices: 724978--725021 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
724968 GAAGAGGATG
724978 ATGATGAAGAA-AAGA
1 ATGAT-AAGAAGAAGA
724993 ATGATAAGAAGAAGA
1 ATGATAAGAAGAAGA
* *
725008 AAGAAAAGAAGAAG
1 ATGATAAGAAGAAG
725022 GAGGTAGGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 5 0.19
15 21 0.81
ACGTcount: A:0.64, C:0.00, G:0.27, T:0.09
Consensus pattern (15 bp):
ATGATAAGAAGAAGA
Found at i:729834 original size:2 final size:2
Alignment explanation
Indices: 729827--729852 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
729817 AATACATTCT
729827 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
729853 CACACTCCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:742040 original size:20 final size:20
Alignment explanation
Indices: 742015--742078 Score: 92
Period size: 20 Copynumber: 3.2 Consensus size: 20
742005 TTATGTTTTG
* *
742015 AGTATCGGTATTGTTCACAC
1 AGTATCGGTATTATTCATAC
* *
742035 AGTATCGATACTATTCATAC
1 AGTATCGGTATTATTCATAC
742055 AGTATCGGTATTATTCATAC
1 AGTATCGGTATTATTCATAC
742075 AGTA
1 AGTA
742079 CAATACTATT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (20 bp):
AGTATCGGTATTATTCATAC
Found at i:742077 original size:40 final size:39
Alignment explanation
Indices: 742015--742092 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
742005 TTATGTTTTG
* *
742015 AGTATCGGTATTGTTCACACAGTATCGATACTATTCATAC
1 AGTATCGGTATTATTCACACAGTA-CAATACTATTCATAC
*
742055 AGTATCGGTATTATTCATACAGTACAATACTATTCATA
1 AGTATCGGTATTATTCACACAGTACAATACTATTCATA
742093 AAAATATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 13 0.37
40 22 0.63
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (39 bp):
AGTATCGGTATTATTCACACAGTACAATACTATTCATAC
Found at i:744561 original size:11 final size:11
Alignment explanation
Indices: 744545--744569 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
744535 TAAAATGCAG
744545 AAAAATAAAAT
1 AAAAATAAAAT
744556 AAAAATAAAAT
1 AAAAATAAAAT
744567 AAA
1 AAA
744570 CAAACAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:745320 original size:16 final size:16
Alignment explanation
Indices: 745299--745331 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
745289 TAATAAATAA
745299 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
745315 ACGAACATGAACGAAC
1 ACGAACATAAACGAAC
745331 A
1 A
745332 AAAAAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.24, G:0.15, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:745380 original size:10 final size:10
Alignment explanation
Indices: 745365--745442 Score: 77
Period size: 10 Copynumber: 7.6 Consensus size: 10
745355 CATTTAAATG
745365 ATAAACGAAC
1 ATAAACGAAC
*
745375 ATAAACAAAC
1 ATAAACGAAC
*
745385 ACAAACGAAC
1 ATAAACGAAC
*
745395 ATAAACAAAC
1 ATAAACGAAC
*
745405 ATAATAAATGAAC
1 ---ATAAACGAAC
745418 ATAAACGAAC
1 ATAAACGAAC
745428 ATAAAC-AAC
1 ATAAACGAAC
*
745437 ACAAAC
1 ATAAAC
745443 ACAAAAAACA
Statistics
Matches: 56, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
9 8 0.14
10 40 0.71
13 8 0.14
ACGTcount: A:0.64, C:0.21, G:0.05, T:0.10
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:745718 original size:14 final size:14
Alignment explanation
Indices: 745699--745726 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
745689 CCTCTGTTCG
745699 AACATAAATGAACA
1 AACATAAATGAACA
745713 AACATAAATGAACA
1 AACATAAATGAACA
745727 TATAATCGAA
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:0.64, C:0.14, G:0.07, T:0.14
Consensus pattern (14 bp):
AACATAAATGAACA
Found at i:748403 original size:15 final size:14
Alignment explanation
Indices: 748383--748459 Score: 51
Period size: 14 Copynumber: 5.8 Consensus size: 14
748373 ATCTTTTAGA
748383 TATTTTTAGTTTGAT
1 TATTTTTA-TTTGAT
*
748398 TA-TTTTATTATTAT
1 TATTTTTATT-TGAT
*
748412 TA-TTTTATTT-AG
1 TATTTTTATTTGAT
*
748424 GATTTTTAGTTTGAT
1 TATTTTTA-TTTGAT
748439 TA-TTTTA-TT-AT
1 TATTTTTATTTGAT
748450 TA-TTTTATTT
1 TATTTTTATTT
748460 AGGAATTAGT
Statistics
Matches: 52, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
11 9 0.17
12 6 0.12
13 8 0.15
14 25 0.48
15 4 0.08
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (14 bp):
TATTTTTATTTGAT
Found at i:748447 original size:38 final size:40
Alignment explanation
Indices: 748384--748463 Score: 137
Period size: 38 Copynumber: 2.0 Consensus size: 40
748374 TCTTTTAGAT
748384 ATTTTTAGTTTGATTATTTTATTATTATTATTTTATTTAGG
1 ATTTTTAGTTTGATTA-TTTATTATTATTATTTTATTTAGG
748425 ATTTTTAGTTTGATTA-TT-TTATTATTATTTTATTTAGG
1 ATTTTTAGTTTGATTATTTATTATTATTATTTTATTTAGG
748463 A
1 A
748464 ATTAGTTATT
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
38 21 0.54
39 2 0.05
41 16 0.41
ACGTcount: A:0.25, C:0.00, G:0.10, T:0.65
Consensus pattern (40 bp):
ATTTTTAGTTTGATTATTTATTATTATTATTTTATTTAGG
Found at i:749893 original size:19 final size:20
Alignment explanation
Indices: 749871--749909 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
749861 TTTTTAATGT
*
749871 ATTTTTTAT-TAAAATTTTA
1 ATTTTATATCTAAAATTTTA
749890 ATTTTATATCTAAAATTTTA
1 ATTTTATATCTAAAATTTTA
749910 TAATTTGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTTTATATCTAAAATTTTA
Found at i:759793 original size:31 final size:31
Alignment explanation
Indices: 759721--759797 Score: 111
Period size: 30 Copynumber: 2.5 Consensus size: 31
759711 TCAAATGGTC
*
759721 AGGGACCATGTTGCAAACAGACTAAATGTTG
1 AGGGACCATATTGCAAACAGACTAAATGTTG
**
759752 -GGGACCATATTGCAAATGGACTAAATGTTG
1 AGGGACCATATTGCAAACAGACTAAATGTTG
*
759782 AGGGACTATATTGCAA
1 AGGGACCATATTGCAA
759798 GTTTAAAAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 27 0.66
31 14 0.34
ACGTcount: A:0.35, C:0.14, G:0.26, T:0.25
Consensus pattern (31 bp):
AGGGACCATATTGCAAACAGACTAAATGTTG
Found at i:762339 original size:21 final size:22
Alignment explanation
Indices: 762314--762364 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
762304 AGTTGTGGGG
762314 ATGTTTTTAGT-TTTATATTAA
1 ATGTTTTTAGTATTTATATTAA
* * *
762335 ATGTTTTTGGTATTTTTATTTA
1 ATGTTTTTAGTATTTATATTAA
762357 AT-TTTTTA
1 ATGTTTTTA
762365 AATAATTATG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.24, C:0.00, G:0.10, T:0.67
Consensus pattern (22 bp):
ATGTTTTTAGTATTTATATTAA
Found at i:762697 original size:2 final size:2
Alignment explanation
Indices: 762690--762719 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
762680 TTAATCGTGA
762690 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
762720 TGGAATACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:763012 original size:8 final size:8
Alignment explanation
Indices: 763001--763025 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
762991 CGATGAAGGT
763001 ACTGGTTC
1 ACTGGTTC
763009 ACTGGTTC
1 ACTGGTTC
763017 ACTGGTTC
1 ACTGGTTC
763025 A
1 A
763026 ATCGGGTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (8 bp):
ACTGGTTC
Found at i:763840 original size:30 final size:30
Alignment explanation
Indices: 763806--763870 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
763796 GTGAACCGGT
*
763806 GGTTCAAACTGGTTTTGCC-GGTTTTCAGCC
1 GGTTCAAACCGGTTTT-CCTGGTTTTCAGCC
** *
763836 GGTTCACCCCGGTTTTCCTGGTTTTCAGTC
1 GGTTCAAACCGGTTTTCCTGGTTTTCAGCC
763866 GGTTC
1 GGTTC
763871 TTCCGGTTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 2 0.07
30 28 0.93
ACGTcount: A:0.09, C:0.26, G:0.26, T:0.38
Consensus pattern (30 bp):
GGTTCAAACCGGTTTTCCTGGTTTTCAGCC
Found at i:780307 original size:27 final size:27
Alignment explanation
Indices: 780276--780330 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
780266 GCTTTGCTGA
780276 AGGATTTGGGTATTCAACGGTGTAAGG
1 AGGATTTGGGTATTCAACGGTGTAAGG
780303 AGGATTTGGGTATTCAACGGTGTAAGG
1 AGGATTTGGGTATTCAACGGTGTAAGG
780330 A
1 A
780331 ACCGGTTGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.27, C:0.07, G:0.36, T:0.29
Consensus pattern (27 bp):
AGGATTTGGGTATTCAACGGTGTAAGG
Found at i:794231 original size:14 final size:14
Alignment explanation
Indices: 794191--794247 Score: 62
Period size: 14 Copynumber: 4.0 Consensus size: 14
794181 CAGGTCTTTT
*
794191 TTATATTATT-TAA
1 TTATATTATTATTA
*
794204 TTTTATTAATTATTA
1 TTATATT-ATTATTA
794219 TTATATTATTATTA
1 TTATATTATTATTA
*
794233 TTAAATTATATATTA
1 TTATATTAT-TATTA
794248 CAAATTTTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
13 6 0.16
14 18 0.49
15 13 0.35
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TTATATTATTATTA
Found at i:794393 original size:25 final size:25
Alignment explanation
Indices: 794364--794462 Score: 166
Period size: 25 Copynumber: 4.0 Consensus size: 25
794354 GAACCAACCC
794364 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
794389 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
794414 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
*
794439 AACA-ATTTAGGGTTTC-AACCCTAA
1 ATCAGA-TTAGGGTTTCAAACCCTAA
794463 TCCCCTAACT
Statistics
Matches: 72, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
24 9 0.12
25 63 0.88
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.28
Consensus pattern (25 bp):
ATCAGATTAGGGTTTCAAACCCTAA
Found at i:801078 original size:11 final size:11
Alignment explanation
Indices: 801062--801086 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
801052 GTTATAAGGT
801062 ATTTTTTTATA
1 ATTTTTTTATA
801073 ATTTTTTTATA
1 ATTTTTTTATA
801084 ATT
1 ATT
801087 ATATATGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
ATTTTTTTATA
Found at i:801241 original size:21 final size:21
Alignment explanation
Indices: 801217--801268 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
801207 GTTATTTTTT
801217 TAAATTATTTACGTTTATATG
1 TAAATTATTTACGTTTATATG
*
801238 TAAATTATTTACGTTTATGTG
1 TAAATTATTTACGTTTATATG
801259 TAAATT-TTTA
1 TAAATTATTTA
801269 TTGTGTTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 4 0.13
21 26 0.87
ACGTcount: A:0.33, C:0.04, G:0.10, T:0.54
Consensus pattern (21 bp):
TAAATTATTTACGTTTATATG
Found at i:804508 original size:13 final size:13
Alignment explanation
Indices: 804490--804538 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
804480 GTAATAATCA
804490 AATTAACAAAATT
1 AATTAACAAAATT
804503 AATTAACAAAA--
1 AATTAACAAAATT
* *
804514 AGTCCAACAAAATT
1 AAT-TAACAAAATT
804528 AATTAACAAAA
1 AATTAACAAAA
804539 AGTCCAACAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
11 2 0.07
12 7 0.24
13 18 0.62
14 2 0.07
ACGTcount: A:0.63, C:0.12, G:0.02, T:0.22
Consensus pattern (13 bp):
AATTAACAAAATT
Found at i:804523 original size:25 final size:25
Alignment explanation
Indices: 804494--804554 Score: 122
Period size: 25 Copynumber: 2.4 Consensus size: 25
804484 TAATCAAATT
804494 AACAAAATTAATTAACAAAAAGTCC
1 AACAAAATTAATTAACAAAAAGTCC
804519 AACAAAATTAATTAACAAAAAGTCC
1 AACAAAATTAATTAACAAAAAGTCC
804544 AACAAAATTAA
1 AACAAAATTAA
804555 CAAATATATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.62, C:0.15, G:0.03, T:0.20
Consensus pattern (25 bp):
AACAAAATTAATTAACAAAAAGTCC
Found at i:806878 original size:12 final size:12
Alignment explanation
Indices: 806813--806882 Score: 56
Period size: 12 Copynumber: 5.6 Consensus size: 12
806803 ACTGCAAAAA
806813 AAAATAATTAAAT
1 AAAAT-ATTAAAT
806826 -AAATATTAAAAT
1 AAAATATT-AAAT
806838 AATTAAATAATTAAAT
1 -A--AAAT-ATTAAAT
*
806854 AAAAT-CT-AAT
1 AAAATATTAAAT
806864 AAAATATTAAAT
1 AAAATATTAAAT
806876 AAAATAT
1 AAAATAT
806883 ACCTTAATTT
Statistics
Matches: 47, Mismatches: 2, Indels: 17
0.71 0.03 0.26
Matches are distributed among these distances:
10 8 0.17
11 5 0.11
12 18 0.38
13 4 0.09
15 1 0.02
16 8 0.17
17 3 0.06
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATATTAAAT
Found at i:806904 original size:10 final size:10
Alignment explanation
Indices: 806889--806933 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
806879 ATATACCTTA
806889 ATTTGAGAGG
1 ATTTGAGAGG
*
806899 ATTTGAGAGA
1 ATTTGAGAGG
* *
806909 AGTTAAGAGG
1 ATTTGAGAGG
*
806919 ATTTAAGAGG
1 ATTTGAGAGG
806929 ATTTG
1 ATTTG
806934 GTGTGATGAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.36, C:0.00, G:0.33, T:0.31
Consensus pattern (10 bp):
ATTTGAGAGG
Found at i:807616 original size:2 final size:2
Alignment explanation
Indices: 807529--807606 Score: 156
Period size: 2 Copynumber: 39.0 Consensus size: 2
807519 GATTATTGCA
807529 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
807571 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
807607 GACGTATATA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 76 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:808191 original size:14 final size:15
Alignment explanation
Indices: 808169--808206 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
808159 TATAAGGTAA
*
808169 TTTTGTTATA-ATAT
1 TTTTATTATACATAT
*
808183 TTTTATTATACTTAT
1 TTTTATTATACATAT
808198 TTTTATTAT
1 TTTTATTAT
808207 GATTATTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (15 bp):
TTTTATTATACATAT
Found at i:812223 original size:22 final size:24
Alignment explanation
Indices: 812198--812244 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
812188 ATAAAAAATT
*
812198 ATATTA-AAAAT-TTAGGGGTGCG
1 ATATTATAAAATCTTAGAGGTGCG
812220 ATATTATAAAATCTTAGAGGTGCG
1 ATATTATAAAATCTTAGAGGTGCG
812244 A
1 A
812245 AGTCAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 6 0.27
23 5 0.23
24 11 0.50
ACGTcount: A:0.38, C:0.06, G:0.23, T:0.32
Consensus pattern (24 bp):
ATATTATAAAATCTTAGAGGTGCG
Found at i:818389 original size:33 final size:33
Alignment explanation
Indices: 818352--818420 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
818342 GGCCTTGGGT
* *
818352 TGCTCCAATTCTTTCTTG-ACCAGGTGCACGGGC
1 TGCTCCAATTC-TTCCTGAACCAGGTACACGGGC
* *
818385 TGCTCTAATTCTTCCTGAACCGGGTACACGGGC
1 TGCTCCAATTCTTCCTGAACCAGGTACACGGGC
818418 TGC
1 TGC
818421 AAAATAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 5 0.16
33 26 0.84
ACGTcount: A:0.16, C:0.30, G:0.25, T:0.29
Consensus pattern (33 bp):
TGCTCCAATTCTTCCTGAACCAGGTACACGGGC
Found at i:818782 original size:33 final size:33
Alignment explanation
Indices: 818740--818813 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
818730 GGGACTTGGA
* * *
818740 CTGCTCCAATTCTTTCTGGACCAGGTGCACGGG
1 CTGCTCCAATTCTTCCTGAACCAGGTACACGGG
* *
818773 CTGCTCCAATTGTTCCTGAACCGGGTACACGGG
1 CTGCTCCAATTCTTCCTGAACCAGGTACACGGG
*
818806 TTGCTCCA
1 CTGCTCCA
818814 CTTCAGATGG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.16, C:0.31, G:0.26, T:0.27
Consensus pattern (33 bp):
CTGCTCCAATTCTTCCTGAACCAGGTACACGGG
Found at i:822193 original size:22 final size:22
Alignment explanation
Indices: 822141--822219 Score: 110
Period size: 22 Copynumber: 3.7 Consensus size: 22
822131 CGGTGTTTGA
822141 GTGCATGGATGCAC---TGCATG
1 GTGCATGGATGCACTAGTGCA-G
* *
822161 GTGTATCGATGCACTAGTGCAG
1 GTGCATGGATGCACTAGTGCAG
822183 GTGCATGGATGCACTAGTGCAG
1 GTGCATGGATGCACTAGTGCAG
822205 GTGCATGGATGCACT
1 GTGCATGGATGCACT
822220 GCAGGGATAC
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
20 12 0.23
22 36 0.69
23 4 0.08
ACGTcount: A:0.22, C:0.19, G:0.34, T:0.25
Consensus pattern (22 bp):
GTGCATGGATGCACTAGTGCAG
Done.