Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007909.1 Hibiscus syriacus cultivar Beakdansim tig00110303_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: 3382237
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 17
Found at i:2486242 original size:18 final size:18
Alignment explanation
Indices: 2486216--2486305 Score: 90
Period size: 18 Copynumber: 4.6 Consensus size: 18
2486206 ACCGGTCACA
*
2486216 ACCCAACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
2486234 ACCCGACCCGACCCATTTACCCG
1 ACCCGACCCGACCC-GTT----G
2486257 ACCCGTTGACCCGACCCGTTG
1 ACCC---GACCCGACCCGTTG
2486278 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
2486296 ACCCGACCCG
1 ACCCGACCCG
2486306 TTGACCGTTG
Statistics
Matches: 61, Mismatches: 3, Indels: 16
0.76 0.04 0.20
Matches are distributed among these distances:
18 37 0.61
19 2 0.03
21 5 0.08
23 5 0.08
25 2 0.03
26 10 0.16
ACGTcount: A:0.19, C:0.50, G:0.19, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:2486284 original size:44 final size:44
Alignment explanation
Indices: 2486221--2486311 Score: 164
Period size: 44 Copynumber: 2.1 Consensus size: 44
2486211 TCACAACCCA
*
2486221 ACCCGACCCGTTGACCCGACCCGACCCATTTACCCGACCCGTTG
1 ACCCGACCCGTTGACCCGACCCGACCCATTGACCCGACCCGTTG
*
2486265 ACCCGACCCGTTGACCCGACCCGACCCGTTGACCCGACCCGTTG
1 ACCCGACCCGTTGACCCGACCCGACCCATTGACCCGACCCGTTG
2486309 ACC
1 ACC
2486312 GTTGACCGGA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.18, C:0.48, G:0.20, T:0.14
Consensus pattern (44 bp):
ACCCGACCCGTTGACCCGACCCGACCCATTGACCCGACCCGTTG
Found at i:2486306 original size:31 final size:31
Alignment explanation
Indices: 2486216--2486311 Score: 135
Period size: 31 Copynumber: 3.1 Consensus size: 31
2486206 ACCGGTCACA
2486216 ACCCAACCCGACCCGTTGACCCGACCC---G
1 ACCCAACCCGACCCGTTGACCCGACCCGTTG
2486244 ACCCATTTACCCGACCCGTTGACCCGACCCGTTG
1 ACCCA---ACCCGACCCGTTGACCCGACCCGTTG
*
2486278 ACCCGACCCGACCCGTTGACCCGACCCGTTG
1 ACCCAACCCGACCCGTTGACCCGACCCGTTG
2486309 ACC
1 ACC
2486312 GTTGACCGGA
Statistics
Matches: 61, Mismatches: 1, Indels: 9
0.86 0.01 0.13
Matches are distributed among these distances:
28 5 0.08
31 51 0.84
34 5 0.08
ACGTcount: A:0.19, C:0.49, G:0.19, T:0.14
Consensus pattern (31 bp):
ACCCAACCCGACCCGTTGACCCGACCCGTTG
Found at i:2487639 original size:18 final size:18
Alignment explanation
Indices: 2487613--2487648 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2487603 TCGAAAGGAC
*
2487613 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
2487631 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
2487649 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:2488882 original size:24 final size:24
Alignment explanation
Indices: 2488787--2488888 Score: 111
Period size: 24 Copynumber: 4.2 Consensus size: 24
2488777 ATTTTCGATT
* *
2488787 TGATTTCTGATTTGATACTTGACA
1 TGATTTCTGATCTGATACTTGACC
*
2488811 TGGA-TTCTGATCTGATA-TATGACT
1 T-GATTTCTGATCTGATACT-TGACC
*
2488835 TGGA-TTCTGATCTGTTACTTGACC
1 T-GATTTCTGATCTGATACTTGACC
*
2488859 TGATTTCTGATATGATACTTGACC
1 TGATTTCTGATCTGATACTTGACC
2488883 TGATTT
1 TGATTT
2488889 ATGTTTTGAT
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
23 3 0.04
24 62 0.91
25 3 0.04
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.44
Consensus pattern (24 bp):
TGATTTCTGATCTGATACTTGACC
Found at i:2491086 original size:13 final size:13
Alignment explanation
Indices: 2491085--2491158 Score: 85
Period size: 13 Copynumber: 5.3 Consensus size: 13
2491075 CCGTTGACCC
*
2491085 GACCCGACCCATT
1 GACCCGACCCGTT
*
2491098 TACCCGACCCGTT
1 GACCCGACCCGTT
2491111 GACCCGACCCGTT
1 GACCCGACCCGTT
2491124 GACCCGACCCGACCCGTT
1 -----GACCCGACCCGTT
2491142 GACCCGACCCGTT
1 GACCCGACCCGTT
2491155 GACC
1 GACC
2491159 GTTGACCGGA
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
13 40 0.75
18 13 0.25
ACGTcount: A:0.18, C:0.47, G:0.20, T:0.15
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:2491089 original size:18 final size:18
Alignment explanation
Indices: 2491063--2491152 Score: 90
Period size: 18 Copynumber: 4.6 Consensus size: 18
2491053 ACCGGTCACA
*
2491063 ACCCAACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
2491081 ACCCGACCCGACCCATTTACCCG
1 ACCCGACCCGACCC-GTT----G
2491104 ACCCGTTGACCCGACCCGTTG
1 ACCC---GACCCGACCCGTTG
2491125 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
2491143 ACCCGACCCG
1 ACCCGACCCG
2491153 TTGACCGTTG
Statistics
Matches: 61, Mismatches: 3, Indels: 16
0.76 0.04 0.20
Matches are distributed among these distances:
18 37 0.61
19 2 0.03
21 5 0.08
23 5 0.08
25 2 0.03
26 10 0.16
ACGTcount: A:0.19, C:0.50, G:0.19, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:2491131 original size:44 final size:44
Alignment explanation
Indices: 2491068--2491158 Score: 164
Period size: 44 Copynumber: 2.1 Consensus size: 44
2491058 TCACAACCCA
*
2491068 ACCCGACCCGTTGACCCGACCCGACCCATTTACCCGACCCGTTG
1 ACCCGACCCGTTGACCCGACCCGACCCATTGACCCGACCCGTTG
*
2491112 ACCCGACCCGTTGACCCGACCCGACCCGTTGACCCGACCCGTTG
1 ACCCGACCCGTTGACCCGACCCGACCCATTGACCCGACCCGTTG
2491156 ACC
1 ACC
2491159 GTTGACCGGA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.18, C:0.48, G:0.20, T:0.14
Consensus pattern (44 bp):
ACCCGACCCGTTGACCCGACCCGACCCATTGACCCGACCCGTTG
Found at i:2491153 original size:31 final size:31
Alignment explanation
Indices: 2491063--2491158 Score: 135
Period size: 31 Copynumber: 3.1 Consensus size: 31
2491053 ACCGGTCACA
2491063 ACCCAACCCGACCCGTTGACCCGACCC---G
1 ACCCAACCCGACCCGTTGACCCGACCCGTTG
2491091 ACCCATTTACCCGACCCGTTGACCCGACCCGTTG
1 ACCCA---ACCCGACCCGTTGACCCGACCCGTTG
*
2491125 ACCCGACCCGACCCGTTGACCCGACCCGTTG
1 ACCCAACCCGACCCGTTGACCCGACCCGTTG
2491156 ACC
1 ACC
2491159 GTTGACCGGA
Statistics
Matches: 61, Mismatches: 1, Indels: 9
0.86 0.01 0.13
Matches are distributed among these distances:
28 5 0.08
31 51 0.84
34 5 0.08
ACGTcount: A:0.19, C:0.49, G:0.19, T:0.14
Consensus pattern (31 bp):
ACCCAACCCGACCCGTTGACCCGACCCGTTG
Found at i:2492487 original size:18 final size:18
Alignment explanation
Indices: 2492461--2492496 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2492451 TCGAAAGGAC
*
2492461 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
2492479 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
2492497 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:2493729 original size:24 final size:24
Alignment explanation
Indices: 2493634--2493735 Score: 111
Period size: 24 Copynumber: 4.2 Consensus size: 24
2493624 ATTTTCGATT
* *
2493634 TGATTTCTGATTTGATACTTGACA
1 TGATTTCTGATCTGATACTTGACC
*
2493658 TGGA-TTCTGATCTGATA-TATGACT
1 T-GATTTCTGATCTGATACT-TGACC
*
2493682 TGGA-TTCTGATCTGTTACTTGACC
1 T-GATTTCTGATCTGATACTTGACC
*
2493706 TGATTTCTGATATGATACTTGACC
1 TGATTTCTGATCTGATACTTGACC
2493730 TGATTT
1 TGATTT
2493736 ATGTTTTGAT
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
23 3 0.04
24 62 0.91
25 3 0.04
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.44
Consensus pattern (24 bp):
TGATTTCTGATCTGATACTTGACC
Found at i:2497675 original size:14 final size:15
Alignment explanation
Indices: 2497658--2497686 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2497648 TACATGATAT
2497658 GCAT-AAACATAAGA
1 GCATAAAACATAAGA
2497672 GCATAAAACATAAGA
1 GCATAAAACATAAGA
2497687 TATATGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.59, C:0.14, G:0.14, T:0.14
Consensus pattern (15 bp):
GCATAAAACATAAGA
Found at i:2497980 original size:15 final size:15
Alignment explanation
Indices: 2497962--2497996 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
2497952 CGAGGGTATT
2497962 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
2497977 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
2497992 GTAGT
1 GTAGT
2497997 GGTCCTACGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.14, C:0.23, G:0.34, T:0.29
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:2506588 original size:24 final size:24
Alignment explanation
Indices: 2506556--2506639 Score: 100
Period size: 24 Copynumber: 3.5 Consensus size: 24
2506546 CCTATATATA
2506556 TAATTTTTATTTTAAAATTTTAAT
1 TAATTTTTATTTTAAAATTTTAAT
** *
2506580 TAATTTTTA--TTAACCTTATACAT
1 TAATTTTTATTTTAAAATTTTA-AT
2506603 ATAATTTTTATTTTAAAATTTTTAAT
1 -TAATTTTTATTTTAAAA-TTTTAAT
2506629 TAATTTTTATT
1 TAATTTTTATT
2506640 AAGGTTATAA
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
22 8 0.16
23 2 0.04
24 18 0.37
25 11 0.22
26 6 0.12
27 4 0.08
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.61
Consensus pattern (24 bp):
TAATTTTTATTTTAAAATTTTAAT
Found at i:2506594 original size:48 final size:49
Alignment explanation
Indices: 2506542--2506641 Score: 175
Period size: 48 Copynumber: 2.1 Consensus size: 49
2506532 AAATGGATAC
*
2506542 TAACCCTATATATATAATTTTTATTTTAAAA-TTTTAATTAATTTTTAT
1 TAACCCTATACATATAATTTTTATTTTAAAATTTTTAATTAATTTTTAT
*
2506590 TAACCTTATACATATAATTTTTATTTTAAAATTTTTAATTAATTTTTAT
1 TAACCCTATACATATAATTTTTATTTTAAAATTTTTAATTAATTTTTAT
2506639 TAA
1 TAA
2506642 GGTTATAAGA
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
48 29 0.59
49 20 0.41
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (49 bp):
TAACCCTATACATATAATTTTTATTTTAAAATTTTTAATTAATTTTTAT
Found at i:2506797 original size:29 final size:28
Alignment explanation
Indices: 2506755--2506839 Score: 134
Period size: 29 Copynumber: 3.0 Consensus size: 28
2506745 CAGTGACAGC
2506755 ATAGGTCGCCATGCACGCCCGGCGTCCTT
1 ATAGGTCGCCATGCACGCCCGGCGTCC-T
2506784 ATAGGTCGCCATGCACGCCCGGCGTCCT
1 ATAGGTCGCCATGCACGCCCGGCGTCCT
* *
2506812 ATAAGGTTGCCATGTACGCCCGGCGTCC
1 AT-AGGTCGCCATGCACGCCCGGCGTCC
2506840 ATCATTCTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
28 3 0.06
29 50 0.94
ACGTcount: A:0.15, C:0.36, G:0.28, T:0.20
Consensus pattern (28 bp):
ATAGGTCGCCATGCACGCCCGGCGTCCT
Found at i:2507078 original size:23 final size:23
Alignment explanation
Indices: 2507048--2507094 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
2507038 AGGATCGGTT
2507048 CTATCGTAGGTTGCCATGGCCGG
1 CTATCGTAGGTTGCCATGGCCGG
2507071 CTATCGTAGGTTGCCATGGCCGG
1 CTATCGTAGGTTGCCATGGCCGG
2507094 C
1 C
2507095 GACATGGTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.13, C:0.28, G:0.34, T:0.26
Consensus pattern (23 bp):
CTATCGTAGGTTGCCATGGCCGG
Found at i:2507160 original size:29 final size:29
Alignment explanation
Indices: 2507090--2507191 Score: 174
Period size: 29 Copynumber: 3.6 Consensus size: 29
2507080 GTTGCCATGG
*
2507090 CCGGCGACATGGTAGGTCGTCATGGAGT-
1 CCGGCGACATGGTAGGTCGCCATGGAGTC
2507118 CC--CGACATGGTAGGTCGCCATGGAGTC
1 CCGGCGACATGGTAGGTCGCCATGGAGTC
2507145 CCGGCGACATGGTAGGTCGCCATGGAGTC
1 CCGGCGACATGGTAGGTCGCCATGGAGTC
2507174 CCGGCGACATGGTAGGTC
1 CCGGCGACATGGTAGGTC
2507192 TGCATCATCA
Statistics
Matches: 70, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
26 23 0.33
27 2 0.03
28 2 0.03
29 43 0.61
ACGTcount: A:0.18, C:0.26, G:0.37, T:0.19
Consensus pattern (29 bp):
CCGGCGACATGGTAGGTCGCCATGGAGTC
Found at i:2507725 original size:21 final size:21
Alignment explanation
Indices: 2507700--2507743 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
2507690 AATCTAGTTA
2507700 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
2507721 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
2507742 AT
1 AT
2507744 ATATTATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:2508565 original size:26 final size:25
Alignment explanation
Indices: 2508536--2508600 Score: 62
Period size: 26 Copynumber: 2.6 Consensus size: 25
2508526 AAATCATATT
*
2508536 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AATAAATATCAAATC
* *
2508562 ATTAGATT-AATAATAATTATTAAATC
1 ATT--ATTAAATAATAAATATCAAATC
2508588 ATTATT-AATAATA
1 ATTATTAAATAATA
2508601 TTAGTAATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
24 10 0.29
26 18 0.53
27 3 0.09
28 3 0.09
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.42
Consensus pattern (25 bp):
ATTATTAAATAATAAATATCAAATC
Found at i:2511508 original size:49 final size:49
Alignment explanation
Indices: 2511451--2511916 Score: 405
Period size: 60 Copynumber: 8.4 Consensus size: 49
2511441 TTATAAGATT
* *
2511451 TAGTAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
*
2511500 TAGTAATGATTTAGTAATAATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTA
1 TAGT-A--A--T-G-----ATTAGTAATAATGAAATTATTATTAAT-TTT--T-AAT-G--ATT-
2511565 ATGA
47 -TGA
2511569 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1 --TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
2511620 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTT-A--A--TGAT--T--TGA
2511678 TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1 -TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
2511728 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTG--A
2511779 GTAATGATTTAGCAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
1 -T-A-G---T---AATGATTAGTAATAATGAAATTATTATTAATTTTT-A--A--TGAT--T--T
2511844 GA
48 GA
2511846 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1 --TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
2511897 TAGTAATGATT--TAATAATGA
1 TAGTAATGATTAGTAATAATGA
2511917 TTAGTAATAA
Statistics
Matches: 359, Mismatches: 5, Indels: 108
0.76 0.01 0.23
Matches are distributed among these distances:
47 9 0.03
49 102 0.28
50 5 0.01
51 7 0.02
52 4 0.01
53 5 0.01
54 10 0.03
55 6 0.02
56 4 0.01
57 3 0.01
58 4 0.01
59 43 0.12
60 123 0.34
61 3 0.01
63 3 0.01
64 2 0.01
65 6 0.02
66 2 0.01
67 6 0.02
68 2 0.01
69 5 0.01
70 1 0.00
71 4 0.01
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (49 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
Found at i:2511624 original size:39 final size:45
Alignment explanation
Indices: 2511602--2511787 Score: 138
Period size: 49 Copynumber: 3.6 Consensus size: 45
2511592 AAATTATTAT
2511602 TAATTTTTAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTAT
1 TAATTTTTAA-GA-TTGATA-T-ATGATTAGTAATAATGAAATTATTAT
2511651 TAATTTTTAATGATTTGATAGTAATGATTAGTAATGATTAGTAATAATGAAATTATTAT
1 TAATTTTT-A--A---G--A-T--TGA-TA-T-ATGATTAGTAATAATGAAATTATTAT
2511710 TAATTTTTAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTAT
1 TAATTTTTAA-GA-TTGATA-T-ATGATTAGTAATAATGAAATTATTAT
2511759 TAATTTTTAATGATTTGATAGTAATGATT
1 TAATTTTTAA-GA-TTGATA-T-ATGATT
2511788 TAGCAATGAT
Statistics
Matches: 125, Mismatches: 2, Indels: 20
0.85 0.01 0.14
Matches are distributed among these distances:
49 68 0.54
50 4 0.03
52 3 0.02
54 4 0.03
56 3 0.02
58 4 0.03
59 39 0.31
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (45 bp):
TAATTTTTAAGATTGATATATGATTAGTAATAATGAAATTATTAT
Found at i:2511636 original size:24 final size:24
Alignment explanation
Indices: 2511609--2511689 Score: 72
Period size: 24 Copynumber: 3.3 Consensus size: 24
2511599 TATTAATTTT
2511609 TAATGATTTGATAGTAATGATTAG
1 TAATGATTTGATAGTAATGATTAG
* *** * * * **
2511633 TAATAATGAAATTATTATTAATTTT
1 TAATGATTTGA-TAGTAATGATTAG
2511658 TAATGATTTGATAGTAATGATTAG
1 TAATGATTTGATAGTAATGATTAG
2511682 TAATGATT
1 TAATGATT
2511690 AGTAATAATG
Statistics
Matches: 38, Mismatches: 18, Indels: 2
0.66 0.31 0.03
Matches are distributed among these distances:
24 23 0.61
25 15 0.39
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.46
Consensus pattern (24 bp):
TAATGATTTGATAGTAATGATTAG
Found at i:2511682 original size:10 final size:10
Alignment explanation
Indices: 2511669--2511695 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
2511659 AATGATTTGA
2511669 TAGTAATGAT
1 TAGTAATGAT
2511679 TAGTAATGAT
1 TAGTAATGAT
2511689 TAGTAAT
1 TAGTAAT
2511696 AATGAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (10 bp):
TAGTAATGAT
Found at i:2511683 original size:59 final size:59
Alignment explanation
Indices: 2511620--2511744 Score: 250
Period size: 59 Copynumber: 2.1 Consensus size: 59
2511610 AATGATTTGA
2511620 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGAT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGAT
2511679 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGAT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGAT
2511738 TAGTAAT
1 TAGTAAT
2511745 AATGAAATTA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 66 1.00
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.46
Consensus pattern (59 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGAT
Found at i:2511916 original size:25 final size:25
Alignment explanation
Indices: 2511886--2512038 Score: 69
Period size: 25 Copynumber: 6.3 Consensus size: 25
2511876 TATTAATTTT
2511886 TAATGATTTGATAGTAATGATTTAA
1 TAATGATTTGATAGTAATGATTTAA
* *
2511911 TAATGATTAG-TAATAATGA---AA
1 TAATGATTTGATAGTAATGATTTAA
* * * *
2511932 TTATTA-TTAATATTTAATGATTTGATA
1 TAATGATTTGATA-GTAATGATTT-A-A
2511959 GTAATGATTT-AT--TAATGATTAGTAA
1 -TAATGATTTGATAGTAATGATT--TAA
* * *
2511984 TAATGAAATTGTTATTAAT-A-TT--
1 TAATG-ATTTGATAGTAATGATTTAA
*
2512006 TAATGATTTGATAGTAATGATTTAG
1 TAATGATTTGATAGTAATGATTTAA
2512031 TAATGATT
1 TAATGATT
2512039 AGTAATAATT
Statistics
Matches: 95, Mismatches: 14, Indels: 38
0.65 0.10 0.26
Matches are distributed among these distances:
20 1 0.01
21 18 0.19
22 12 0.13
23 2 0.02
24 14 0.15
25 29 0.31
26 4 0.04
27 3 0.03
28 10 0.11
29 2 0.02
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.46
Consensus pattern (25 bp):
TAATGATTTGATAGTAATGATTTAA
Found at i:2512085 original size:14 final size:14
Alignment explanation
Indices: 2512066--2512113 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
2512056 TATTAATTTT
2512066 TAATGATTTGATAG
1 TAATGATTTGATAG
2512080 TAATGA-TT--TAG
1 TAATGATTTGATAG
2512091 TAATGATTTGATAG
1 TAATGATTTGATAG
2512105 TAATGATTT
1 TAATGATTT
2512114 ATTATAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
11 9 0.29
12 2 0.06
13 2 0.06
14 18 0.58
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (14 bp):
TAATGATTTGATAG
Found at i:2512094 original size:25 final size:25
Alignment explanation
Indices: 2512066--2512114 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
2512056 TATTAATTTT
2512066 TAATGATTTGATAGTAATGATTTAG
1 TAATGATTTGATAGTAATGATTTAG
2512091 TAATGATTTGATAGTAATGATTTA
1 TAATGATTTGATAGTAATGATTTA
2512115 TTATAAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.00, G:0.18, T:0.45
Consensus pattern (25 bp):
TAATGATTTGATAGTAATGATTTAG
Found at i:2512118 original size:60 final size:60
Alignment explanation
Indices: 2511728--2512098 Score: 679
Period size: 60 Copynumber: 6.2 Consensus size: 60
2511718 AATGATTTGA
2511728 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATT
*
2511788 TAGCAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATT
2511848 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATT
* *
2511908 TAATAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATT
* * *
2511968 TATTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATT
*
2512028 TAGTAATGATTAGTAATAATTAAATTATTATTAATTTTTAATGATTTGATAGTAATGATT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATT
2512088 TAGTAATGATT
1 TAGTAATGATT
2512099 TGATAGTAAT
Statistics
Matches: 301, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 301 1.00
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.46
Consensus pattern (60 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATT
Found at i:2514271 original size:15 final size:16
Alignment explanation
Indices: 2514251--2514284 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
2514241 CAAAAAAATT
2514251 TAATATAAT-AACTTA
1 TAATATAATAAACTTA
2514266 TAATATAATAAACTTA
1 TAATATAATAAACTTA
2514282 TAA
1 TAA
2514285 AGTAACAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
TAATATAATAAACTTA
Found at i:2514371 original size:30 final size:30
Alignment explanation
Indices: 2514337--2514442 Score: 142
Period size: 30 Copynumber: 3.5 Consensus size: 30
2514327 TTTCTTTAAA
2514337 CAACTAATAAACTATTCTTTAATATAACTT
1 CAACTAATAAACTATTCTTTAATATAACTT
2514367 CAACTAATAAACTATTCTTTAATATAACTT
1 CAACTAATAAACTATTCTTTAATATAACTT
* * *
2514397 AAACTAATAAAATATTTTTTAATTATAA-TT
1 CAACTAATAAACTATTCTTTAA-TATAACTT
*
2514427 CACTACTAAAAAACTA
1 CA--ACTAATAAACTA
2514443 ATTAACTAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
30 52 0.78
31 5 0.07
32 10 0.15
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (30 bp):
CAACTAATAAACTATTCTTTAATATAACTT
Found at i:2514389 original size:15 final size:16
Alignment explanation
Indices: 2514341--2514395 Score: 55
Period size: 15 Copynumber: 3.6 Consensus size: 16
2514331 TTTAAACAAC
2514341 TAATA-AACTATTCTT
1 TAATATAACTATTCTT
**
2514356 TAATATAAC--TTCAAC
1 TAATATAACTATTC-TT
2514371 TAATA-AACTATTCTT
1 TAATATAACTATTCTT
2514386 TAATATAACT
1 TAATATAACT
2514396 TAAACTAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
14 6 0.19
15 15 0.48
16 10 0.32
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.42
Consensus pattern (16 bp):
TAATATAACTATTCTT
Found at i:2514808 original size:27 final size:27
Alignment explanation
Indices: 2514770--2514824 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
2514760 AGGGTCGGCT
2514770 GCCATGCACCAATAATTGAAGAATCAC
1 GCCATGCACCAATAATTGAAGAATCAC
2514797 GCCATGCACCAATAATTGAAGAATCAC
1 GCCATGCACCAATAATTGAAGAATCAC
2514824 G
1 G
2514825 AGCCGTTGAT
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:0.40, C:0.25, G:0.16, T:0.18
Consensus pattern (27 bp):
GCCATGCACCAATAATTGAAGAATCAC
Found at i:2515144 original size:12 final size:12
Alignment explanation
Indices: 2515127--2515154 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
2515117 CACGACCCTT
2515127 GTCGGAAGCCAC
1 GTCGGAAGCCAC
2515139 GTCGGAAGCCAC
1 GTCGGAAGCCAC
2515151 GTCG
1 GTCG
2515155 TAGGTCGCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.21, C:0.32, G:0.36, T:0.11
Consensus pattern (12 bp):
GTCGGAAGCCAC
Found at i:2515728 original size:2 final size:2
Alignment explanation
Indices: 2515721--2515745 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2515711 TTGTTTTTGT
2515721 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2515746 TTGTTTCCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2520759 original size:4 final size:4
Alignment explanation
Indices: 2520750--2520776 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2520740 AAAATTTCAA
2520750 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
2520777 AGGAAGAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:2524200 original size:19 final size:20
Alignment explanation
Indices: 2524159--2524200 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2524149 TGGGTTCCTT
*
2524159 TTTTATTTTAACTGATTTCA
1 TTTTATTTTAACTGATTTAA
*
2524179 TTTTATTTTATCT-ATTTAA
1 TTTTATTTTAACTGATTTAA
2524198 TTT
1 TTT
2524201 GCCCTTGAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTTATTTTAACTGATTTAA
Found at i:2542855 original size:17 final size:17
Alignment explanation
Indices: 2542833--2542871 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
2542823 CCGGTCTGAC
2542833 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
2542850 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
2542867 TGACC
1 TGACC
2542872 GTTGACCGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.18, C:0.46, G:0.23, T:0.13
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:2542871 original size:7 final size:7
Alignment explanation
Indices: 2542861--2542891 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
2542851 GACCCGACCC
2542861 GACCGTT
1 GACCGTT
2542868 GACCGTT
1 GACCGTT
2542875 GACCG-T
1 GACCGTT
2542881 GACCGTT
1 GACCGTT
2542888 GACC
1 GACC
2542892 TCCTTTGACC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.16, C:0.32, G:0.29, T:0.23
Consensus pattern (7 bp):
GACCGTT
Found at i:2542885 original size:13 final size:14
Alignment explanation
Indices: 2542861--2542891 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
2542851 GACCCGACCC
2542861 GACCGTTGACCGTT
1 GACCGTTGACCGTT
2542875 GACCG-TGACCGTT
1 GACCGTTGACCGTT
2542888 GACC
1 GACC
2542892 TCCTTTGACC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.16, C:0.32, G:0.29, T:0.23
Consensus pattern (14 bp):
GACCGTTGACCGTT
Found at i:2549576 original size:20 final size:19
Alignment explanation
Indices: 2549534--2549600 Score: 64
Period size: 19 Copynumber: 3.4 Consensus size: 19
2549524 GCAGCTGGAA
* *
2549534 AACCGGTTTGACAGGTTTTG
1 AACCGGTTTGACCGG-TTCG
2549554 AACCGGTTTTGACCGGTTCG
1 AACCGG-TTTGACCGGTTCG
* *
2549574 AACAGGTCTGACCGG-TCTG
1 AACCGGTTTGACCGGTTC-G
2549593 AACCGGTT
1 AACCGGTT
2549601 CGAACCGATC
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
18 2 0.05
19 15 0.38
20 14 0.36
21 8 0.21
ACGTcount: A:0.19, C:0.22, G:0.30, T:0.28
Consensus pattern (19 bp):
AACCGGTTTGACCGGTTCG
Found at i:2549637 original size:17 final size:17
Alignment explanation
Indices: 2549611--2549670 Score: 75
Period size: 17 Copynumber: 3.4 Consensus size: 17
2549601 CGAACCGATC
*
2549611 TGACCCGACCCGACCGT
1 TGACCTGACCCGACCGT
2549628 TGACCTGACCCGACCGT
1 TGACCTGACCCGACCGT
*
2549645 TGACCGTTGACCGTGACCGT
1 TGACC--TGACC-CGACCGT
2549665 TGACCT
1 TGACCT
2549671 CATTTGACCA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
17 21 0.55
18 1 0.03
19 5 0.13
20 11 0.29
ACGTcount: A:0.17, C:0.38, G:0.25, T:0.20
Consensus pattern (17 bp):
TGACCTGACCCGACCGT
Found at i:2549649 original size:7 final size:7
Alignment explanation
Indices: 2549639--2549669 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
2549629 GACCTGACCC
2549639 GACCGTT
1 GACCGTT
2549646 GACCGTT
1 GACCGTT
2549653 GACCG-T
1 GACCGTT
2549659 GACCGTT
1 GACCGTT
2549666 GACC
1 GACC
2549670 TCATTTGACC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.16, C:0.32, G:0.29, T:0.23
Consensus pattern (7 bp):
GACCGTT
Found at i:2549663 original size:13 final size:13
Alignment explanation
Indices: 2549622--2549669 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
2549612 GACCCGACCC
2549622 GACCGTTGACC-T
1 GACCGTTGACCGT
*
2549634 GACC--CGACCGTT
1 GACCGTTGACCG-T
2549646 GACCGTTGACCGT
1 GACCGTTGACCGT
2549659 GACCGTTGACC
1 GACCGTTGACC
2549670 TCATTTGACC
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
10 4 0.13
12 9 0.30
13 12 0.40
14 5 0.17
ACGTcount: A:0.17, C:0.35, G:0.27, T:0.21
Consensus pattern (13 bp):
GACCGTTGACCGT
Found at i:2556308 original size:32 final size:33
Alignment explanation
Indices: 2556266--2556358 Score: 116
Period size: 32 Copynumber: 2.8 Consensus size: 33
2556256 TAAATAAAGT
* * *
2556266 TTTTTTTTTAATAGTTAGTGAATTTTTAGTGG-
1 TTTTTATTTAATAGGTAGTGAGTTTTTAGTGGA
* *
2556298 TTTTTATTTAATGGGTAGTGGGTTTTTAGTGGA
1 TTTTTATTTAATAGGTAGTGAGTTTTTAGTGGA
**
2556331 TGATTATTTAATAGGTAGTGAGTTTTTA
1 TTTTTATTTAATAGGTAGTGAGTTTTTA
2556359 AGTTAGATAA
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
32 27 0.53
33 24 0.47
ACGTcount: A:0.23, C:0.00, G:0.24, T:0.54
Consensus pattern (33 bp):
TTTTTATTTAATAGGTAGTGAGTTTTTAGTGGA
Found at i:2556387 original size:3 final size:3
Alignment explanation
Indices: 2556373--2556409 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
2556363 AGATAAAAAT
*
2556373 TAA TAA -AA TAA TAA TAA TAA TAA TAC TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2556410 TTTAAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:2556610 original size:85 final size:85
Alignment explanation
Indices: 2556467--2556633 Score: 253
Period size: 85 Copynumber: 2.0 Consensus size: 85
2556457 CACTCTTTGC
* * *
2556467 ACATTCTTGTGTTAACAAGGATAAGACATAGAAGAAAAAGACAATCAATTTTTGTCCGATAAATG
1 ACATTCTTATGTTAACAAGGATAAGACAAAGAAGAAAAAGACAACCAATTTTTGTCCGATAAATG
*
2556532 AAACATGTGATATAAAACAA
66 AAACATGTGACATAAAACAA
* * * * *
2556552 ACATTTTTATGTTATCAAGGATAGGACAAAGACGAAAAAGACAACCAGTTTTTGTCCGATAAATG
1 ACATTCTTATGTTAACAAGGATAAGACAAAGAAGAAAAAGACAACCAATTTTTGTCCGATAAATG
2556617 AAACATGTGACATAAAA
66 AAACATGTGACATAAAA
2556634 AATATATCTA
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
85 73 1.00
ACGTcount: A:0.46, C:0.13, G:0.16, T:0.26
Consensus pattern (85 bp):
ACATTCTTATGTTAACAAGGATAAGACAAAGAAGAAAAAGACAACCAATTTTTGTCCGATAAATG
AAACATGTGACATAAAACAA
Found at i:2559942 original size:31 final size:30
Alignment explanation
Indices: 2559906--2559994 Score: 99
Period size: 31 Copynumber: 2.9 Consensus size: 30
2559896 CTAAGGGAAC
2559906 ATCTTGGGGCCTGAGAGCCTACCCAAGAAAG
1 ATCTTGGGGCC-GAGAGCCTACCCAAGAAAG
* *
2559937 TTCTTGGGGCC-ACGGGACCTACCCAAGAAAG
1 ATCTTGGGGCCGA-GAG-CCTACCCAAGAAAG
* *
2559968 ATCTCGGGGCCGTATAGCCTACCCAAG
1 ATCTTGGGGCCG-AGAGCCTACCCAAG
2559995 GTTTCCTTAG
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
29 1 0.02
30 2 0.04
31 43 0.90
32 1 0.02
33 1 0.02
ACGTcount: A:0.26, C:0.29, G:0.28, T:0.17
Consensus pattern (30 bp):
ATCTTGGGGCCGAGAGCCTACCCAAGAAAG
Found at i:2560724 original size:22 final size:22
Alignment explanation
Indices: 2560696--2560750 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
2560686 GATATTTCAA
*
2560696 TCAAAGTCAACAGTCAGACTAG
1 TCAAAGTCAACAGTCAGACCAG
* * * *
2560718 TCAAAGTCCACGGTCCGACCGG
1 TCAAAGTCAACAGTCAGACCAG
2560740 TCAAAGTCAAC
1 TCAAAGTCAAC
2560751 GATTTGACCG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.35, C:0.29, G:0.20, T:0.16
Consensus pattern (22 bp):
TCAAAGTCAACAGTCAGACCAG
Found at i:2560781 original size:21 final size:21
Alignment explanation
Indices: 2560739--2560797 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
2560729 GGTCCGACCG
* * * *
2560739 GTCAAAGTCAACGATTTGACC
1 GTCAAAGTCAATGGTCTAACC
2560760 GTCAAAGTCAATGGTCTAACC
1 GTCAAAGTCAATGGTCTAACC
*
2560781 GAT-AAGGTCAATGGTCT
1 G-TCAAAGTCAATGGTCT
2560798 GCAGGTCAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 31 0.97
22 1 0.03
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.25
Consensus pattern (21 bp):
GTCAAAGTCAATGGTCTAACC
Found at i:2564837 original size:54 final size:54
Alignment explanation
Indices: 2564680--2564837 Score: 280
Period size: 54 Copynumber: 2.9 Consensus size: 54
2564670 ACACTATTGT
* * *
2564680 AGTCTTACGAAACAAGTAATCCAACCTTCGTCGAAGAGACTAAATCCCACGATA
1 AGTCTTACGAAACAAGTAATCCAACCTTAGTCAAAGAGACTAAATCCCATGATA
*
2564734 AGTCTTACGAAACAAGTAATCCAACCCTAGTCAAAGAGACTAAATCCCATGATA
1 AGTCTTACGAAACAAGTAATCCAACCTTAGTCAAAGAGACTAAATCCCATGATA
2564788 AGTCTTACGAAACAAGTAATCCAACCTTAGTCAAAGAGACTAAATCCCAT
1 AGTCTTACGAAACAAGTAATCCAACCTTAGTCAAAGAGACTAAATCCCAT
2564838 ATCGTCATCC
Statistics
Matches: 99, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 99 1.00
ACGTcount: A:0.41, C:0.25, G:0.13, T:0.21
Consensus pattern (54 bp):
AGTCTTACGAAACAAGTAATCCAACCTTAGTCAAAGAGACTAAATCCCATGATA
Found at i:2569257 original size:20 final size:20
Alignment explanation
Indices: 2569234--2569272 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2569224 AAATATAAAC
*
2569234 AAATAAAATTAAAACAATAA
1 AAATAAAACTAAAACAATAA
**
2569254 AAATACCACTAAAACAATA
1 AAATAAAACTAAAACAATA
2569273 TATTTTAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.69, C:0.13, G:0.00, T:0.18
Consensus pattern (20 bp):
AAATAAAACTAAAACAATAA
Found at i:2570682 original size:3 final size:3
Alignment explanation
Indices: 2570674--2570777 Score: 190
Period size: 3 Copynumber: 34.7 Consensus size: 3
2570664 AATATATATT
* *
2570674 TAA TAA TAA TAA TAA TGA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2570722 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2570770 TAA TAA TA
1 TAA TAA TA
2570778 TGGGTAAAAA
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 99 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2571578 original size:228 final size:227
Alignment explanation
Indices: 2570913--2571673 Score: 1080
Period size: 228 Copynumber: 3.3 Consensus size: 227
2570903 ATTGAATAAA
* * ** * *
2570913 TTCTTC-TCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTGCTGGGGATGATGATCCATC
1 TTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTTTCT-CTGGAAAAGCTGATCCATC
*
2570977 AAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTTCTTC
65 AAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
* * * * *
2571042 AGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTGATCCATTAAATGATGAATTCA
130 AGAT-A-GAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCATCAATTGATGAATTCA
* * * *
2571107 AGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
193 GGAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
* * *
2571142 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAAAGTTGATCC
1 TTCTTCTTCCTTCTTCAGAT-A--AGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGCTGATCC
2571206 ATCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTC
62 ATCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTC
2571271 TTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCATCAACTTGATGAA
127 TTCAGAT-A-GAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCATCAA-TTGATGAA
*
2571336 TTCAGAAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
189 TTCAGGAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
2571375 TTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGACTGATCCATC
1 TTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAG-CTGATCCATC
* ** * * *
2571440 AAATGATGGATTCGGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
65 AAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
* *
2571505 AGAT-GAGTTCTTCTCATTATGAAC-CTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCA
130 AGATAGAGTTCTTCTCATTATGAACTCTAC-CTGGCAAAGATAATCCATCAA-TTGATGAATTCA
*
2571568 GGTAAAAGGTTGAACAAATTCTTCTCATTATGAAC
193 GGAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
* * **
2571603 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTAATCTTTCA
1 TTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCA
2571668 AATGAT
66 AATGAT
2571674 AGATTTGAAT
Statistics
Matches: 487, Mismatches: 36, Indels: 20
0.90 0.07 0.04
Matches are distributed among these distances:
227 17 0.03
228 138 0.28
229 8 0.02
230 40 0.08
231 72 0.15
232 129 0.26
233 81 0.17
234 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (227 bp):
TTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCA
AATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
GATAGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCATCAATTGATGAATTCAGGA
AAAAGGTTGAACAAATTCTTCTCATTATGAAC
Found at i:2571662 original size:114 final size:113
Alignment explanation
Indices: 2570913--2571656 Score: 994
Period size: 116 Copynumber: 6.5 Consensus size: 113
2570903 ATTGAATAAA
* ** *
2570913 TTCTTC-TCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTGCTGGGGATGATGATCCATC
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT-CTGGAAAAGATGATCCATC
*
2570977 AAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
65 AAATGATGAATTCAAGCAAAAGATTGAACAAATTCTTCTCATTATGAAC
* * * * *
2571026 TTATTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAATGTTGATCC
1 TTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGATGATCC
* *
2571090 ATTAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
62 ATCAAATGATGAATTCAAGCAAAAGATTGAACAAATTCTTCTCATTATGAAC
* * *
2571142 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAAAGTTGATCC
1 TTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGATGATCC
*
2571206 ATCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
62 ATCAAATGATGAATTCAAGCAAAAGATTGAACAAATTCTTCTCATTATGAAC
* * *
2571258 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAAAGATAATCC
1 TTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGATGATCC
* * *
2571322 ATCAACTTGATGAATTC-AGAAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
62 ATCAA-ATGATGAATTCAAG-CAAAAGATTGAACAAATTCTTCTCATTATGAAC
*
2571375 TTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGACTGATCCATC
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGA-TGATCCATC
* ** * *
2571440 AAATGATGGATTCGGGTAAAAGGTTGAACAAATTCTTCTCATTATGAAC
65 AAATGATGAATTCAAGCAAAAGATTGAACAAATTCTTCTCATTATGAAC
* *
2571489 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCA
* * * *
2571554 ATTTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAAC
66 A-ATGATGAATTCAAGCAAAAGATTGAACAAATTCTTCTCATTATGAAC
2571603 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAG
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAG
2571657 CTAATCTTTC
Statistics
Matches: 589, Mismatches: 31, Indels: 21
0.92 0.05 0.03
Matches are distributed among these distances:
113 17 0.03
114 232 0.39
115 11 0.02
116 246 0.42
117 81 0.14
118 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (113 bp):
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCA
AATGATGAATTCAAGCAAAAGATTGAACAAATTCTTCTCATTATGAAC
Found at i:2572544 original size:83 final size:83
Alignment explanation
Indices: 2572405--2572717 Score: 538
Period size: 83 Copynumber: 3.8 Consensus size: 83
2572395 GTAGTTCTTA
*
2572405 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAA
2572470 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* *
2572488 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCCCA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAA
2572553 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* * * *
2572571 CTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAA
2572636 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
*
2572654 TCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCA
1 -CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCA
2572718 TTTAATGTTT
Statistics
Matches: 215, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
83 214 1.00
84 1 0.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (83 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAA
ATTCAATGATTGGTTCTG
Found at i:2573715 original size:1 final size:1
Alignment explanation
Indices: 2573705--2573777 Score: 56
Period size: 1 Copynumber: 73.0 Consensus size: 1
2573695 CCTTGACCCC
* ** * * ** * *
2573705 TTTTTCTTTTTTCCTTTTTTTTTCTTTTTTTTTTCTTTTTTTCCTTTTTTTTTCTTTTTTTTTCT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
2573770 TTCTTTTT
1 TTTTTTTT
2573778 CTTCAAGCAT
Statistics
Matches: 56, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 56 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (1 bp):
T
Found at i:2573733 original size:19 final size:19
Alignment explanation
Indices: 2573721--2573780 Score: 84
Period size: 19 Copynumber: 3.1 Consensus size: 19
2573711 TTTTTTCCTT
*
2573721 TTTTTTTCTTTTTTTTTTC
1 TTTTTTTCCTTTTTTTTTC
2573740 TTTTTTTCCTTTTTTTTTC
1 TTTTTTTCCTTTTTTTTTC
* *
2573759 TTTTTTTTTCTTTCTTTTTC
1 -TTTTTTTCCTTTTTTTTTC
2573779 TT
1 TT
2573781 CAAGCATAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
19 20 0.54
20 17 0.46
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (19 bp):
TTTTTTTCCTTTTTTTTTC
Found at i:2573747 original size:30 final size:29
Alignment explanation
Indices: 2573705--2573776 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 29
2573695 CCTTGACCCC
2573705 TTTTTC-TTTTTTCCTTTTTTTTTCTTTTT
1 TTTTTCTTTTTTTCCTTTTTTTTTC-TTTT
2573734 TTTTTCTTTTTTTCCTTTTTTTTTCTTTT
1 TTTTTCTTTTTTTCCTTTTTTTTTCTTTT
2573763 TTTTTCTTTCTTTT
1 TTTTTCTTT-TTTT
2573777 TCTTCAAGCA
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
29 19 0.46
30 22 0.54
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (29 bp):
TTTTTCTTTTTTTCCTTTTTTTTTCTTTT
Found at i:2573779 original size:10 final size:10
Alignment explanation
Indices: 2573711--2573780 Score: 97
Period size: 10 Copynumber: 7.0 Consensus size: 10
2573701 CCCCTTTTTC
*
2573711 TTTTTTCCTT
1 TTTTTTTCTT
2573721 TTTTTTTCTT
1 TTTTTTTCTT
2573731 TTTTTTT-TCT
1 TTTTTTTCT-T
*
2573741 TTTTTTCCTT
1 TTTTTTTCTT
2573751 TTTTTTTCTT
1 TTTTTTTCTT
2573761 TTTTTTTCTT
1 TTTTTTTCTT
*
2573771 TCTTTTTCTT
1 TTTTTTTCTT
2573781 CAAGCATAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
9 1 0.02
10 52 0.96
11 1 0.02
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:2587641 original size:45 final size:45
Alignment explanation
Indices: 2587562--2587731 Score: 241
Period size: 45 Copynumber: 3.8 Consensus size: 45
2587552 CCTATATGCA
* * * * * * *
2587562 TTTCAATTATGTCATCCTTACATGTCTTTTATACACTATTATACG
1 TTTCATTTATGGCATCATTTCATGCCTTTGATACACTATTATACC
* *
2587607 TTTAATTTATGGCATCATTTCATGCTTTTGATACACTATTATACC
1 TTTCATTTATGGCATCATTTCATGCCTTTGATACACTATTATACC
* *
2587652 TTTCATTTATGTCATCCTTTCATGCCTTTGATACACTATTATACC
1 TTTCATTTATGGCATCATTTCATGCCTTTGATACACTATTATACC
2587697 TTTCATTTATGGCATCATTTCATGCCTTTGATACA
1 TTTCATTTATGGCATCATTTCATGCCTTTGATACA
2587732 ATTATGCATT
Statistics
Matches: 110, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 110 1.00
ACGTcount: A:0.25, C:0.21, G:0.08, T:0.46
Consensus pattern (45 bp):
TTTCATTTATGGCATCATTTCATGCCTTTGATACACTATTATACC
Found at i:2587662 original size:90 final size:90
Alignment explanation
Indices: 2587562--2587731 Score: 277
Period size: 90 Copynumber: 1.9 Consensus size: 90
2587552 CCTATATGCA
* * *
2587562 TTTCAATTATGTCATCCTTACATGTCTTTTATACACTATTATACGTTTAATTTATGGCATCATTT
1 TTTCAATTATGTCATCCTTACATGCCTTTGATACACTATTATACCTTTAATTTATGGCATCATTT
*
2587627 CATGCTTTTGATACACTATTATACC
66 CATGCCTTTGATACACTATTATACC
* * *
2587652 TTTCATTTATGTCATCCTTTCATGCCTTTGATACACTATTATACCTTTCATTTATGGCATCATTT
1 TTTCAATTATGTCATCCTTACATGCCTTTGATACACTATTATACCTTTAATTTATGGCATCATTT
2587717 CATGCCTTTGATACA
66 CATGCCTTTGATACA
2587732 ATTATGCATT
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 73 1.00
ACGTcount: A:0.25, C:0.21, G:0.08, T:0.46
Consensus pattern (90 bp):
TTTCAATTATGTCATCCTTACATGCCTTTGATACACTATTATACCTTTAATTTATGGCATCATTT
CATGCCTTTGATACACTATTATACC
Found at i:2588486 original size:57 final size:57
Alignment explanation
Indices: 2588334--2589433 Score: 1781
Period size: 57 Copynumber: 19.3 Consensus size: 57
2588324 CGTAGTATAA
* * ** ** *
2588334 ATTTCTTATCATGTTAGCACACGAAGTGCCCTATTTGGAAATTCATACACTTAGTATG
1 ATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT-GAAATTCATACACTTAGTATG
*
2588392 ATTTCCTTATCATTTTAGCGTACGAAACGCCCTATCTGAAATTCATACACTTAGTATG
1 ATTT-CTTAACATTTTAGCGTACGAAACGCCCTATCTGAAATTCATACACTTAGTATG
* *
2588450 ATTTCTTAACATTTTAACGTACGAAATGCCCTATCTGAAATTCATACACTTAGTATG
1 ATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAAATTCATACACTTAGTATG
*
2588507 ATTTCTTAACATTTTAGCATACGAAACGCCCTATCTGAAATTCATACACTTAGTATG
1 ATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAAATTCATACACTTAGTATG
* *
2588564 ATTTCTTAACATTTTAGCGTACGAAATGCCCTATCTGAAATTCATACAGTTAGTATG
1 ATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAAATTCATACACTTAGTATG
* * * *
2588621 ATTTCTTAACATTTTAGAGTACGAAACTCCCTATTTGAAATTCATACACTTAATATG
1 ATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAAATTCATACACTTAGTATG
*
2588678 ATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAAATTCATACACTCAGTATG
1 ATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAAATTCATACACTTAGTATG
2588735 ATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAAATTCATACACTTAGTATG
1 ATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAAATTCATACACTTAGTATG
* *
2588792 ATTTCTTAGCATTTTAGCGTACGAAA-GCCCTATATGAAATTCATACACTTAGTATG
1 ATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAAATTCATACACTTAGTATG
** *
2588848 ATTTCTTAACATTTTAGAATAAGAAACGCCCTATCTGAAATTCATACACTTAGTATG
1 ATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAAATTCATACACTTAGTATG
2588905 ATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAAATTCATACACTTAGTATG
1 ATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAAATTCATACACTTAGTATG
*
2588962 ATTTCTTAACATTTTAGCGTACGAAACGCCTTATCTGAAATTCATACACTTAGTATG
1 ATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAAATTCATACACTTAGTATG
* * * *
2589019 CTTTCTTAACATTTTAGAGCACGAAACGCCTTATCTGAAATTCATACACTTAGTATG
1 ATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAAATTCATACACTTAGTATG
* * * *
2589076 ATTTCTCAACATTTTAGAGTAC-AAATCGCCCTATTTTAAATTCATACACTTAGTATG
1 ATTTCTTAACATTTTAGCGTACGAAA-CGCCCTATCTGAAATTCATACACTTAGTATG
2589133 ATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAAATTCATACACTTAGTATG
1 ATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAAATTCATACACTTAGTATG
*
2589190 ATTTCTTAACATTTTAGCGTACGAAACGTCCTATCTGAAATTCATACACTTAGTATG
1 ATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAAATTCATACACTTAGTATG
* *
2589247 ATTTCTTAACATTTTAGCGTACGAAAAGCCCTATCTGAAATTCATACTCTTAGTATG
1 ATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAAATTCATACACTTAGTATG
*
2589304 ATTTCTTAACATTTTAGCGTACGAAACACCCTATCTGAAATTCATACACTTAGTATG
1 ATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAAATTCATACACTTAGTATG
* * * *
2589361 ATTTCGTAAGATTTTAGCGTACGAAACACCCTATATGAAATTCATACACTTAGTATG
1 ATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAAATTCATACACTTAGTATG
* *
2589418 ATTTCGTAAGATTTTA
1 ATTTCTTAACATTTTA
2589434 ACGCACGATT
Statistics
Matches: 977, Mismatches: 61, Indels: 9
0.93 0.06 0.01
Matches are distributed among these distances:
56 54 0.06
57 865 0.89
58 32 0.03
59 26 0.03
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (57 bp):
ATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAAATTCATACACTTAGTATG
Found at i:2603105 original size:34 final size:33
Alignment explanation
Indices: 2603044--2603107 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
2603034 AGAGGAAAAT
* * *
2603044 AATTTGATATTTAATTATATTTGTATAATAATA
1 AATTTAATATTTAATTATATATATATAATAATA
*
2603077 AATTTAATGTTTAATATATATATATATAATA
1 AATTTAATATTTAAT-TATATATATATAATA
2603108 TTTTTATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 13 0.50
34 13 0.50
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (33 bp):
AATTTAATATTTAATTATATATATATAATAATA
Found at i:2603475 original size:30 final size:29
Alignment explanation
Indices: 2603436--2603544 Score: 96
Period size: 30 Copynumber: 3.7 Consensus size: 29
2603426 AAAAGTTATA
2603436 TTCGTGTTCGTTTATTTATTTTTGAAGATG
1 TTCGTGTTCGTTTATTTATTTTT-AAGATG
* * **
2603466 TTTGTGTTCGTTTA--AATTTTCAATATCATG
1 TTCGTGTTCGTTTATTTATTTT---TAAGATG
* * *
2603496 TTCATGTTCATTTATTTATTTTTAAGGTG
1 TTCGTGTTCGTTTATTTATTTTTAAGATG
*
2603525 TTCGTGTTCGCTTATTTATT
1 TTCGTGTTCGTTTATTTATT
2603545 GTTCAAAAAT
Statistics
Matches: 60, Mismatches: 14, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
28 5 0.08
29 21 0.35
30 28 0.47
31 1 0.02
32 5 0.08
ACGTcount: A:0.18, C:0.09, G:0.16, T:0.57
Consensus pattern (29 bp):
TTCGTGTTCGTTTATTTATTTTTAAGATG
Found at i:2603687 original size:22 final size:22
Alignment explanation
Indices: 2603635--2603699 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
2603625 TTAGTAAACA
*
2603635 TGTTCGTTTAGCGTTCGTTTAG
1 TGTTAGTTTAGCGTTCGTTTAG
* *
2603657 TATTAGTTTAGCGTT-GTTTTGG
1 TGTTAGTTTAGCGTTCG-TTTAG
* * *
2603679 TGTTTGTTTATCGTTCATTTA
1 TGTTAGTTTAGCGTTCGTTTA
2603700 TATATTCGAT
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
21 1 0.03
22 32 0.97
ACGTcount: A:0.12, C:0.09, G:0.23, T:0.55
Consensus pattern (22 bp):
TGTTAGTTTAGCGTTCGTTTAG
Found at i:2623657 original size:20 final size:20
Alignment explanation
Indices: 2623632--2623692 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 20
2623622 TTTTGGTGCA
*
2623632 GAGGGAATCGATCCCCCCAT
1 GAGGGAACCGATCCCCCCAT
**
2623652 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGA-TCCCCCCAT
2623673 GAAGGGGAACCGATCCCCCC
1 G-A-GGGAACCGATCCCCCC
2623693 CACAGGGGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
20 10 0.29
21 8 0.24
22 7 0.21
23 9 0.26
ACGTcount: A:0.23, C:0.36, G:0.26, T:0.15
Consensus pattern (20 bp):
GAGGGAACCGATCCCCCCAT
Found at i:2626388 original size:21 final size:21
Alignment explanation
Indices: 2626363--2626416 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
2626353 CTCGAAGGGA
2626363 ACCGATTCCCCCATAAGGGGT
1 ACCGATTCCCCCATAAGGGGT
*
2626384 ACCGATTCCCCCATAGGGGGT
1 ACCGATTCCCCCATAAGGGGT
2626405 ACCGATTCCCCC
1 ACCGATTCCCCC
2626417 TGTTCAACGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.20, C:0.39, G:0.22, T:0.19
Consensus pattern (21 bp):
ACCGATTCCCCCATAAGGGGT
Found at i:2627584 original size:22 final size:21
Alignment explanation
Indices: 2627559--2627601 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
2627549 TAGGTTGGTT
2627559 TTAAAATATAAACATATAAATA
1 TTAAAATATAAACATA-AAATA
* * *
2627581 TTAAGATTTAAACCTAAAATA
1 TTAAAATATAAACATAAAATA
2627602 ATACAAGTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (21 bp):
TTAAAATATAAACATAAAATA
Found at i:2627718 original size:22 final size:21
Alignment explanation
Indices: 2627693--2627735 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
2627683 TAGGTTGGTT
2627693 TTAAAATATAAACATATAAATA
1 TTAAAATATAAACATA-AAATA
* * *
2627715 TTAAGATTTAAACTTAAAATA
1 TTAAAATATAAACATAAAATA
2627736 ATACAAGTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (21 bp):
TTAAAATATAAACATAAAATA
Found at i:2627838 original size:134 final size:130
Alignment explanation
Indices: 2627560--2627817 Score: 381
Period size: 134 Copynumber: 1.9 Consensus size: 130
2627550 AGGTTGGTTT
2627560 TAAAATATAAACATATAAATATTAAGATTTAAACCTAAAATAATACAAGTGTCCTTGTGGTGGAA
1 TAAAATATAAACATATAAATATTAAGATTTAAACCTAAAATAATACAAGTGTCCTTGTGGTGGAA
2627625 GTCCTAAATTTAAAAAGTACAATAATTAATTGATGTTAGAAAAATTCACATAAATAATTAGGTTG
66 GTCCTAAATTTAAAAAGTACAATAATTAATTGATGTTAGAAAAATTCACAT-AATAATT--GTT-
***
2627690 GTTT
127 GCAA
*
2627694 TAAAATATAAACATATAAATATTAAGATTTAAACTTAAAATAATACAAGTGTCCTTGTGGTGGAA
1 TAAAATATAAACATATAAATATTAAGATTTAAACCTAAAATAATACAAGTGTCCTTGTGGTGGAA
2627759 GTCCTAAATTTTAAAAAAACAAAGTACAATAATTAATTGATGTTAGAAAAATTCACATA
66 GTCCTAAA-TTT-----AA-AAAGTACAATAATTAATTGATGTTAGAAAAATTCACATA
2627818 TATTTCAATA
Statistics
Matches: 116, Mismatches: 1, Indels: 8
0.93 0.01 0.06
Matches are distributed among these distances:
134 72 0.62
135 3 0.03
140 3 0.03
141 38 0.33
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.33
Consensus pattern (130 bp):
TAAAATATAAACATATAAATATTAAGATTTAAACCTAAAATAATACAAGTGTCCTTGTGGTGGAA
GTCCTAAATTTAAAAAGTACAATAATTAATTGATGTTAGAAAAATTCACATAATAATTGTTGCAA
Found at i:2627880 original size:18 final size:19
Alignment explanation
Indices: 2627831--2627881 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 19
2627821 TTCAATAAAG
2627831 ATCATAAATTAATAAAAATTA
1 ATCAT-AATTAA-AAAAATTA
*
2627852 ATCA-ATTTTAAAAAAA-TA
1 ATCATA-ATTAAAAAAATTA
2627870 ATCATAATTAAA
1 ATCATAATTAAA
2627882 GATTAAATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
18 11 0.42
19 7 0.27
20 4 0.15
21 4 0.15
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (19 bp):
ATCATAATTAAAAAAATTA
Found at i:2628810 original size:11 final size:11
Alignment explanation
Indices: 2628794--2628839 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
2628784 GATATTACTA
*
2628794 ATAATATTGTT
1 ATAATATTATT
2628805 ATAATATTATT
1 ATAATATTATT
* *
2628816 ATATTATTAAT
1 ATAATATTATT
*
2628827 ATATTATTATT
1 ATAATATTATT
2628838 AT
1 AT
2628840 TAACAATAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (11 bp):
ATAATATTATT
Found at i:2628828 original size:17 final size:17
Alignment explanation
Indices: 2628786--2628842 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
2628776 TGTTTTTCGA
*
2628786 TATTACTAATA-A-TAT
1 TATTATTAATATATTAT
*
2628801 TGTTA-TAATATTATTA-
1 TATTATTAATA-TATTAT
2628817 TATTATTAATATATTAT
1 TATTATTAATATATTAT
2628834 TATTATTAA
1 TATTATTAA
2628843 CAATAAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
14 5 0.14
15 4 0.11
16 10 0.29
17 16 0.46
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (17 bp):
TATTATTAATATATTAT
Found at i:2630162 original size:3 final size:3
Alignment explanation
Indices: 2630133--2630188 Score: 80
Period size: 3 Copynumber: 18.7 Consensus size: 3
2630123 TAATGTTTCA
2630133 AAT AA- AAT AA- AAT AATT AAT AATT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AA-T AAT AA-T AAT AAT AAT AAT AAT AAT AAT
2630178 AAT AAT AAT AA
1 AAT AAT AAT AA
2630189 GGACACAAAG
Statistics
Matches: 49, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
2 4 0.08
3 39 0.80
4 6 0.12
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2633130 original size:11 final size:11
Alignment explanation
Indices: 2633114--2633144 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
2633104 CAACACCTTG
2633114 CATTGCATTCA
1 CATTGCATTCA
*
2633125 CATTGCATCCA
1 CATTGCATTCA
2633136 CATTGCATT
1 CATTGCATT
2633145 TACTTTTTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.26, C:0.29, G:0.10, T:0.35
Consensus pattern (11 bp):
CATTGCATTCA
Found at i:2637533 original size:114 final size:115
Alignment explanation
Indices: 2637325--2637585 Score: 326
Period size: 114 Copynumber: 2.3 Consensus size: 115
2637315 GTCCTAAAAA
** **
2637325 ATATGATATTTTCTTCAAAGTAAGCGGAACAGGTATCTCTTTCCCAAGATTTGATATTCCCTTCA
1 ATATGATATTCCCTTCAAAGTAAGCGGAACAAATATCTCTTTCCCAAGATTTGATATTCCCTTCA
* * * * *
2637390 GAGTAAATGGAACAAATCTACCTCAATTCAAAGTATCAAATTTCTTC-AG
66 GAATAAATGGAACAAATCTACCCCAATTCAAAGGATCAAATTCCTCCAAG
* * **
2637439 ATATGATATTCCCTTCAAAGTAAACGGAACAAATCTCTCTTTTTCAAGATTTGATATTCCCTTCA
1 ATATGATATTCCCTTCAAAGTAAGCGGAACAAATATCTCTTTCCCAAGATTTGATATTCCCTTCA
* * * * *
2637504 GAATAAGTGGAACAAGTCTGCCCCGATTCAATGGATCAAATTCCTCCAAG
66 GAATAAATGGAACAAATCTACCCCAATTCAAAGGATCAAATTCCTCCAAG
* * *
2637554 ATTTGATATTCCCTTCAGAGTAAGTGGAACAA
1 ATATGATATTCCCTTCAAAGTAAGCGGAACAA
2637586 GTCTGCCTTG
Statistics
Matches: 124, Mismatches: 22, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
114 94 0.76
115 30 0.24
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (115 bp):
ATATGATATTCCCTTCAAAGTAAGCGGAACAAATATCTCTTTCCCAAGATTTGATATTCCCTTCA
GAATAAATGGAACAAATCTACCCCAATTCAAAGGATCAAATTCCTCCAAG
Found at i:2637565 original size:67 final size:67
Alignment explanation
Indices: 2637483--2638179 Score: 1074
Period size: 67 Copynumber: 10.4 Consensus size: 67
2637473 CTCTCTTTTT
* *
2637483 CAAGATTTGATATTCCCTTCAGAATAAGTGGAACAAGTCTGCCCCGATTCAATGGATCAAATTCC
1 CAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCCCGATTCAATGGATCAAACTCC
2637548 TC
66 TC
**
2637550 CAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCTTGATTCAATGGATCAAACTCC
1 CAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCCCGATTCAATGGATCAAACTCC
2637615 TC
66 TC
* *
2637617 TAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCCTGATTCAATGGATCAAACTCC
1 CAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCCCGATTCAATGGATCAAACTCC
2637682 TC
66 TC
* * *
2637684 CAAGATTTGATATTCCCTTCAGAGTAAGTGGAACTAGTCTACCCTGATTCAATGGATCAAACTCC
1 CAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCCCGATTCAATGGATCAAACTCC
2637749 TC
66 TC
*
2637751 CAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCCCGATTCAATGGATCAAACTCT
1 CAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCCCGATTCAATGGATCAAACTCC
2637816 TC
66 TC
* * * * *
2637818 CAAGATTTGATATTCTCTTCAGTGTAAGTGGAACAAATCTGCCCCGATTCAATAGATCAAATTCC
1 CAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCCCGATTCAATGGATCAAACTCC
2637883 TC
66 TC
* * * * *
2637885 CAAGATTTGATATTCCCTTCAGAGTAGGTGGAACAAATATGCACTGATTCAATGGATCAAACTCC
1 CAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCCCGATTCAATGGATCAAACTCC
2637950 TC
66 TC
* * *
2637952 AAATATTTGATATTCCCTAT-AGAGTAAGTGGAACAAGTCTGCCCCGATTCAATGGATCAACCTC
1 CAAGATTTGATATTCCCT-TCAGAGTAAGTGGAACAAGTCTGCCCCGATTCAATGGATCAAACTC
2638016 CTC
65 CTC
* *
2638019 CAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCCTGATTCATTGGATCAAACTCC
1 CAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCCCGATTCAATGGATCAAACTCC
2638084 TC
66 TC
* * * * *
2638086 CAAGATTTGATATTCCCTTCAGAGTAAGTGGAATAACTCTACTCCGATTCAATGGATCAACCTCC
1 CAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCCCGATTCAATGGATCAAACTCC
2638151 T-
66 TC
** *
2638152 TTAGATCTGATATTCCCTTCAGAGTAAG
1 CAAGATTTGATATTCCCTTCAGAGTAAG
2638180 CGTAACAGAT
Statistics
Matches: 578, Mismatches: 50, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
66 26 0.04
67 551 0.95
68 1 0.00
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (67 bp):
CAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCCCGATTCAATGGATCAAACTCC
TC
Found at i:2638531 original size:3 final size:3
Alignment explanation
Indices: 2638516--2638571 Score: 55
Period size: 3 Copynumber: 19.7 Consensus size: 3
2638506 CGTTTTTCAA
* * * *
2638516 TAT TAT TAA TAT TAT TGT TA- TAA TAT TAT TA- TAT TAT TAA T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2638561 TAT TAT TAT TA
1 TAT TAT TAT TA
2638572 ACAATAAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
2 5 0.12
3 38 0.88
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:2638547 original size:11 final size:11
Alignment explanation
Indices: 2638516--2638569 Score: 65
Period size: 11 Copynumber: 4.8 Consensus size: 11
2638506 CGTTTTTCAA
2638516 TATTATTAATAT
1 TATTATT-ATAT
* *
2638528 TATTGTTATAA
1 TATTATTATAT
2638539 TATTATTATAT
1 TATTATTATAT
2638550 TATTAATT-TAT
1 TATT-ATTATAT
2638561 TATTATTAT
1 TATTATTAT
2638570 TAACAATAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
10 3 0.08
11 24 0.67
12 9 0.25
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (11 bp):
TATTATTATAT
Found at i:2638564 original size:14 final size:15
Alignment explanation
Indices: 2638516--2638568 Score: 65
Period size: 14 Copynumber: 3.5 Consensus size: 15
2638506 CGTTTTTCAA
2638516 TATTATTAATATTAT
1 TATTATTAATATTAT
*
2638531 TGTTA-TAATATTATT
1 TATTATTAATATTA-T
2638546 ATATTATTAAT-TTAT
1 -TATTATTAATATTAT
2638561 TATTATTA
1 TATTATTA
2638569 TTAACAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
14 16 0.48
15 6 0.18
16 7 0.21
17 4 0.12
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (15 bp):
TATTATTAATATTAT
Found at i:2638570 original size:17 final size:17
Alignment explanation
Indices: 2638516--2638572 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
2638506 CGTTTTTCAA
2638516 TATTATTAA--TATTAT
1 TATTATTAATTTATTAT
*
2638531 TGTTA-TAATATTATTA-
1 TATTATTAAT-TTATTAT
2638547 TATTATTAATTTATTAT
1 TATTATTAATTTATTAT
2638564 TATTATTAA
1 TATTATTAA
2638573 CAATAAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
14 3 0.09
15 4 0.11
16 10 0.29
17 18 0.51
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
TATTATTAATTTATTAT
Found at i:2644079 original size:6 final size:6
Alignment explanation
Indices: 2644068--2644187 Score: 186
Period size: 6 Copynumber: 20.0 Consensus size: 6
2644058 TATTCTCTCT
2644068 TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC
1 TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC
* * * *
2644116 TTCTTC TTGTTC TTCTTG TTCTTG TTCTTC TTGTTC TTCTTC TTCTTC
1 TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC
* *
2644164 TTCTTC TTTTTC TTCGTC TTCTTC
1 TTCTTC TTCTTC TTCTTC TTCTTC
2644188 CTCTCCAAGG
Statistics
Matches: 104, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 104 1.00
ACGTcount: A:0.00, C:0.29, G:0.04, T:0.67
Consensus pattern (6 bp):
TTCTTC
Found at i:2644080 original size:9 final size:9
Alignment explanation
Indices: 2644068--2644187 Score: 186
Period size: 9 Copynumber: 13.3 Consensus size: 9
2644058 TATTCTCTCT
2644068 TTCTTCTTC
1 TTCTTCTTC
2644077 TTCTTCTTC
1 TTCTTCTTC
2644086 TTCTTCTTC
1 TTCTTCTTC
2644095 TTCTTCTTC
1 TTCTTCTTC
2644104 TTCTTCTTC
1 TTCTTCTTC
2644113 TTCTTCTTC
1 TTCTTCTTC
*
2644122 TTGTTCTTC
1 TTCTTCTTC
* *
2644131 TTGTTCTTG
1 TTCTTCTTC
*
2644140 TTCTTCTTG
1 TTCTTCTTC
2644149 TTCTTCTTC
1 TTCTTCTTC
2644158 TTCTTCTTC
1 TTCTTCTTC
*
2644167 TTCTTTTTC
1 TTCTTCTTC
*
2644176 TTCGTCTTC
1 TTCTTCTTC
2644185 TTC
1 TTC
2644188 CTCTCCAAGG
Statistics
Matches: 104, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 104 1.00
ACGTcount: A:0.00, C:0.29, G:0.04, T:0.67
Consensus pattern (9 bp):
TTCTTCTTC
Found at i:2644088 original size:15 final size:15
Alignment explanation
Indices: 2644068--2644187 Score: 186
Period size: 15 Copynumber: 8.0 Consensus size: 15
2644058 TATTCTCTCT
2644068 TTCTTCTTCTTCTTC
1 TTCTTCTTCTTCTTC
2644083 TTCTTCTTCTTCTTC
1 TTCTTCTTCTTCTTC
2644098 TTCTTCTTCTTCTTC
1 TTCTTCTTCTTCTTC
*
2644113 TTCTTCTTCTTGTTC
1 TTCTTCTTCTTCTTC
* *
2644128 TTCTTGTTCTTGTTC
1 TTCTTCTTCTTCTTC
*
2644143 TTCTTGTTCTTCTTC
1 TTCTTCTTCTTCTTC
*
2644158 TTCTTCTTCTTCTTT
1 TTCTTCTTCTTCTTC
*
2644173 TTCTTCGTCTTCTTC
1 TTCTTCTTCTTCTTC
2644188 CTCTCCAAGG
Statistics
Matches: 98, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 98 1.00
ACGTcount: A:0.00, C:0.29, G:0.04, T:0.67
Consensus pattern (15 bp):
TTCTTCTTCTTCTTC
Found at i:2648815 original size:11 final size:11
Alignment explanation
Indices: 2648799--2648826 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
2648789 GAGTTGGACA
2648799 GTGCTCAACTC
1 GTGCTCAACTC
2648810 GTGCTCAACTC
1 GTGCTCAACTC
2648821 GTGCTC
1 GTGCTC
2648827 GTTAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.14, C:0.36, G:0.21, T:0.29
Consensus pattern (11 bp):
GTGCTCAACTC
Found at i:2650898 original size:26 final size:26
Alignment explanation
Indices: 2650868--2650923 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
2650858 TTAGGGTTTG
*
2650868 AATTTATAAAATTTTAAGAG-AAAATA
1 AATTT-TAAAATTTTAAAAGAAAAATA
2650894 AA-TTTAAAATTTTAAAAGTAAAAATA
1 AATTTTAAAATTTTAAAAG-AAAAATA
2650920 AATT
1 AATT
2650924 ATCAATGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
24 13 0.50
25 2 0.08
26 10 0.38
27 1 0.04
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (26 bp):
AATTTTAAAATTTTAAAAGAAAAATA
Found at i:2650903 original size:24 final size:25
Alignment explanation
Indices: 2650874--2650923 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
2650864 TTTGAATTTA
*
2650874 TAAAATTTTAAGAG-AAAATAAATT
1 TAAAATTTTAAAAGAAAAATAAATT
2650898 TAAAATTTTAAAAGTAAAAATAAATT
1 TAAAATTTTAAAAG-AAAAATAAATT
2650924 ATCAATGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 13 0.57
26 10 0.43
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (25 bp):
TAAAATTTTAAAAGAAAAATAAATT
Found at i:2655783 original size:15 final size:15
Alignment explanation
Indices: 2655765--2655796 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2655755 TTGATACTCC
2655765 TAGTAAAAGTATCGA
1 TAGTAAAAGTATCGA
2655780 TAGTAAAAGTATCGA
1 TAGTAAAAGTATCGA
2655795 TA
1 TA
2655797 CTGGGGATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (15 bp):
TAGTAAAAGTATCGA
Found at i:2662744 original size:18 final size:20
Alignment explanation
Indices: 2662721--2662789 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
2662711 GCCAATTTTG
2662721 GTATCGATACTCAT-G-AGA
1 GTATCGATACTCATAGTAGA
2662739 GTATCGATACT-ATAAGTAGA
1 GTATCGATACTCAT-AGTAGA
**
2662759 GTATCGATACTCCCAGTAAGA
1 GTATCGATACTCATAGT-AGA
*
2662780 GTATTGATAC
1 GTATCGATAC
2662790 CAGGGATATT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
17 2 0.05
18 11 0.26
19 1 0.02
20 17 0.40
21 12 0.28
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (20 bp):
GTATCGATACTCATAGTAGA
Found at i:2665668 original size:15 final size:15
Alignment explanation
Indices: 2665648--2665684 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
2665638 GTTGTAAGAT
2665648 GTTAGTTAGTTACAA
1 GTTAGTTAGTTACAA
2665663 GTTAGTTAGTTACAA
1 GTTAGTTAGTTACAA
2665678 GTTAGTT
1 GTTAGTT
2665685 TTACATTGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.30, C:0.05, G:0.22, T:0.43
Consensus pattern (15 bp):
GTTAGTTAGTTACAA
Found at i:2666810 original size:29 final size:29
Alignment explanation
Indices: 2666788--2666843 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
2666778 TTATTTCAAG
*
2666788 TTAACTACTAACTTTCATTTTATTGCATA
1 TTAACCACTAACTTTCATTTTATTGCATA
*
2666817 TTAACCACTAACTTTTATTTTATTGCA
1 TTAACCACTAACTTTCATTTTATTGCA
2666844 CTCTAACCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.30, C:0.18, G:0.04, T:0.48
Consensus pattern (29 bp):
TTAACCACTAACTTTCATTTTATTGCATA
Found at i:2666850 original size:29 final size:29
Alignment explanation
Indices: 2666789--2666854 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
2666779 TATTTCAAGT
* *
2666789 TAACTACTAACTTTCATTTTATTGCATAT
1 TAACCACTAACTTTCATTTTATTGCATAC
*
2666818 TAACCACTAACTTTTATTTTATTGCACT-C
1 TAACCACTAACTTTCATTTTATTGCA-TAC
2666847 TAACCACT
1 TAACCACT
2666855 GTTATTTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 32 0.97
30 1 0.03
ACGTcount: A:0.30, C:0.23, G:0.03, T:0.44
Consensus pattern (29 bp):
TAACCACTAACTTTCATTTTATTGCATAC
Found at i:2666976 original size:12 final size:12
Alignment explanation
Indices: 2666959--2666986 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
2666949 AACTCCTAAC
2666959 TTTTTTTATTTA
1 TTTTTTTATTTA
2666971 TTTTTTTATTTA
1 TTTTTTTATTTA
2666983 TTTT
1 TTTT
2666987 ATTAATTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTTTTATTTA
Found at i:2667490 original size:2 final size:2
Alignment explanation
Indices: 2667438--2667478 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2667428 TTTTAGTCCC
2667438 AT AT AT AT AT AT 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 AT AT A
2667479 CGTTTCATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2670101 original size:14 final size:14
Alignment explanation
Indices: 2670082--2670135 Score: 60
Period size: 14 Copynumber: 4.0 Consensus size: 14
2670072 CTATACATCG
2670082 TACATTGCATGATA
1 TACATTGCATGATA
* *
2670096 TACATTGTAT-CTCA
1 TACATTGCATGAT-A
2670110 -AC-TTGCATGATA
1 TACATTGCATGATA
2670122 TACATTGCATGATA
1 TACATTGCATGATA
2670136 CTTTTACCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
12 6 0.19
13 6 0.19
14 20 0.62
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (14 bp):
TACATTGCATGATA
Found at i:2670757 original size:39 final size:37
Alignment explanation
Indices: 2670643--2670771 Score: 118
Period size: 38 Copynumber: 3.4 Consensus size: 37
2670633 TAATTTTTTC
* *
2670643 TAACATTTTCGGTTCAATAAAAAATGTTATGAAAAA-A
1 TAACATTTTCGGTTCAATAGAAAATG-TAAGAAAAATA
* ** *
2670680 GTAAAATTTTCGGTCGTCAACCGAAAATGTAAGGAAAATA
1 -TAACATTTTCGGT--TCAATAGAAAATGTAAGAAAAATA
*
2670720 TAACATTTTCGGTTCAATTGAAAATGCTAAGATAAAAT-
1 TAACATTTTCGGTTCAATAGAAAATG-TAAGA-AAAATA
*
2670758 TAACATTTTAGGTT
1 TAACATTTTCGGTT
2670772 ACACCCAACA
Statistics
Matches: 75, Mismatches: 11, Indels: 10
0.78 0.11 0.10
Matches are distributed among these distances:
37 11 0.15
38 29 0.39
39 24 0.32
40 11 0.15
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.33
Consensus pattern (37 bp):
TAACATTTTCGGTTCAATAGAAAATGTAAGAAAAATA
Found at i:2675663 original size:2 final size:2
Alignment explanation
Indices: 2675624--2675651 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2675614 ACTTAATAAA
2675624 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
2675652 GAATAGTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2679228 original size:21 final size:22
Alignment explanation
Indices: 2679191--2679231 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
2679181 TTAAAAATTA
2679191 TAAAGGAAGTACTGATACTCAT
1 TAAAGGAAGTACTGATACTCAT
2679213 TAAAGG-AGTA-TCGATACTC
1 TAAAGGAAGTACT-GATACTC
2679232 CCTGTCTTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 1 0.06
21 11 0.61
22 6 0.33
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.27
Consensus pattern (22 bp):
TAAAGGAAGTACTGATACTCAT
Found at i:2683301 original size:32 final size:32
Alignment explanation
Indices: 2683249--2683344 Score: 97
Period size: 32 Copynumber: 3.0 Consensus size: 32
2683239 CCCGAAGGAC
**
2683249 CATTATCCATATGTTTCGAAGAACATAGGTAA
1 CATTATCCATATGTCCCGAAGAACATAGGTAA
* *
2683281 CATTGTCCATATGTCCCGAAGGACATAGGTAA
1 CATTATCCATATGTCCCGAAGAACATAGGTAA
* * * *
2683313 -ACTATCTATATGTCTCGAA-AGTCATAGGTAA
1 CATTATCCATATGTCCCGAAGA-ACATAGGTAA
2683344 C
1 C
2683345 CCTCGACTCT
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
31 24 0.46
32 28 0.54
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (32 bp):
CATTATCCATATGTCCCGAAGAACATAGGTAA
Found at i:2685085 original size:272 final size:272
Alignment explanation
Indices: 2684596--2685139 Score: 1034
Period size: 272 Copynumber: 2.0 Consensus size: 272
2684586 ATTTAACCAT
2684596 TGACAAGTCAAATTTAACATCCAATTCTACTTATCAACCTTATTCCAAGTTTTCATTCAAAAACT
1 TGACAAGTCAAATTTAACATCCAATTCTACTTATCAACCTTATTCCAAGTTTTCATTCAAAAACT
*
2684661 CCAAATATTTAATCTCTCATAACTCTTTCATTCTTTGTTTTAAACCTAACTTAAGCCTTCCTTAA
66 CCAAATATGTAATCTCTCATAACTCTTTCATTCTTTGTTTTAAACCTAACTTAAGCCTTCCTTAA
2684726 GCTTTTCTATCACTCCAAGAATCAAAACCAACTTTTAAACGAGAGAATTAACCAACTTGAAACCA
131 GCTTTTCTATCACTCCAAGAATCAAAACCAACTTTTAAACGAGAGAATTAACCAACTTGAAACCA
*
2684791 ACTTACCTTATCAATTGAGCCACGAGAAGAGGAGAAGAAAAATGGAAGAAGACTCTGGAGAAATT
196 ACTTACCTTATCAATGGAGCCACGAGAAGAGGAGAAGAAAAATGGAAGAAGACTCTGGAGAAATT
2684856 TCTCCATTCCCA
261 TCTCCATTCCCA
* * *
2684868 TGACAAGTCAAATTTAACTTCTAATTCTACTTATCATCCTTATTCCAAGTTTTCATTCAAAAACT
1 TGACAAGTCAAATTTAACATCCAATTCTACTTATCAACCTTATTCCAAGTTTTCATTCAAAAACT
2684933 CCAAATATGTAATCTCTCATAACTCTTTCATTCTTTGTTTTAAACCTAACTTAAGCCTTCCTTAA
66 CCAAATATGTAATCTCTCATAACTCTTTCATTCTTTGTTTTAAACCTAACTTAAGCCTTCCTTAA
2684998 GCTTTTCTATCACTCCAAGAATCAAAACCAACTTTTAAACGAGAGAATTAACCAACTTGAAACCA
131 GCTTTTCTATCACTCCAAGAATCAAAACCAACTTTTAAACGAGAGAATTAACCAACTTGAAACCA
*
2685063 ACTTACCTTATCAATGGAGCCACGGGAAGAGGAGAAGAAAAATGGAAGAAGACTCTGGAGAAATT
196 ACTTACCTTATCAATGGAGCCACGAGAAGAGGAGAAGAAAAATGGAAGAAGACTCTGGAGAAATT
2685128 TCTCCATTCCCA
261 TCTCCATTCCCA
2685140 CGTACTTAAT
Statistics
Matches: 266, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
272 266 1.00
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.31
Consensus pattern (272 bp):
TGACAAGTCAAATTTAACATCCAATTCTACTTATCAACCTTATTCCAAGTTTTCATTCAAAAACT
CCAAATATGTAATCTCTCATAACTCTTTCATTCTTTGTTTTAAACCTAACTTAAGCCTTCCTTAA
GCTTTTCTATCACTCCAAGAATCAAAACCAACTTTTAAACGAGAGAATTAACCAACTTGAAACCA
ACTTACCTTATCAATGGAGCCACGAGAAGAGGAGAAGAAAAATGGAAGAAGACTCTGGAGAAATT
TCTCCATTCCCA
Found at i:2686023 original size:18 final size:18
Alignment explanation
Indices: 2686000--2686092 Score: 105
Period size: 18 Copynumber: 4.8 Consensus size: 18
2685990 TGAATATTTG
2686000 TCCCGAAGGACCACTATA
1 TCCCGAAGGACCACTATA
*
2686018 TCCCGAAGGACCACTGATTG
1 TCCCGAAGGACCACT-A-TA
* *
2686038 TTCCGAAGAACCACTATA
1 TCCCGAAGGACCACTATA
2686056 TCCCGAAGGACCACTGTATA
1 TCCCGAAGGACCAC--TATA
2686076 TGTCCCGAAGGACCACT
1 --TCCCGAAGGACCACT
2686093 CCTTAAGAAC
Statistics
Matches: 63, Mismatches: 6, Indels: 10
0.80 0.08 0.13
Matches are distributed among these distances:
18 28 0.44
19 2 0.03
20 19 0.30
22 14 0.22
ACGTcount: A:0.30, C:0.31, G:0.19, T:0.19
Consensus pattern (18 bp):
TCCCGAAGGACCACTATA
Found at i:2686053 original size:38 final size:39
Alignment explanation
Indices: 2685997--2686092 Score: 158
Period size: 38 Copynumber: 2.5 Consensus size: 39
2685987 CATTGAATAT
2685997 TTGTCCCGAAGGACCACTATATCCCGAAGGACCACTG-A
1 TTGTCCCGAAGGACCACTATATCCCGAAGGACCACTGTA
* *
2686035 TTGTTCCGAAGAACCACTATATCCCGAAGGACCACTGTA
1 TTGTCCCGAAGGACCACTATATCCCGAAGGACCACTGTA
2686074 TATGTCCCGAAGGACCACT
1 T-TGTCCCGAAGGACCACT
2686093 CCTTAAGAAC
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
38 35 0.67
39 2 0.04
40 15 0.29
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (39 bp):
TTGTCCCGAAGGACCACTATATCCCGAAGGACCACTGTA
Found at i:2690456 original size:32 final size:31
Alignment explanation
Indices: 2690410--2690505 Score: 113
Period size: 31 Copynumber: 3.0 Consensus size: 31
2690400 CCCGAATGAC
2690410 CACTATCCATATGTTCCAAAGAACATAGGTAA
1 CACTATCCATATGTTCCAAAG-ACATAGGTAA
* * *
2690442 CACTTTCCATATGTTTCGAAGGACATAGGTAA
1 CACTATCCATATG-TTCCAAAGACATAGGTAA
* *
2690474 -ACTATCCATATGTCTCGAAAGTCATAGGTAA
1 CACTATCCATATGT-TCCAAAGACATAGGTAA
2690505 C
1 C
2690506 CCTCGACTCT
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
30 1 0.02
31 26 0.47
32 22 0.40
33 6 0.11
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (31 bp):
CACTATCCATATGTTCCAAAGACATAGGTAA
Found at i:2690485 original size:31 final size:32
Alignment explanation
Indices: 2690410--2690505 Score: 122
Period size: 32 Copynumber: 3.0 Consensus size: 32
2690400 CCCGAATGAC
* * *
2690410 CACTATCCATATGTTCCAAAGAACATAGGTAA
1 CACTATCCATATGTTTCGAAGGACATAGGTAA
*
2690442 CACTTTCCATATGTTTCGAAGGACATAGGTAA
1 CACTATCCATATGTTTCGAAGGACATAGGTAA
* * *
2690474 -ACTATCCATATGTCTCGAAAGTCATAGGTAA
1 CACTATCCATATGTTTCGAAGGACATAGGTAA
2690505 C
1 C
2690506 CCTCGACTCT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
31 27 0.49
32 28 0.51
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (32 bp):
CACTATCCATATGTTTCGAAGGACATAGGTAA
Found at i:2692926 original size:26 final size:26
Alignment explanation
Indices: 2692874--2692927 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
2692864 ACAAGTCATT
*
2692874 TATGTTCATTCATACATATATTAATA
1 TATGTTCATTCATACATATAATAATA
2692900 TATGTTCATGT-ATATCATATAAT-ATA
1 TATGTTCAT-TCATA-CATATAATAATA
2692926 TA
1 TA
2692928 CACTAACCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 17 0.68
27 8 0.32
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.46
Consensus pattern (26 bp):
TATGTTCATTCATACATATAATAATA
Found at i:2693213 original size:32 final size:32
Alignment explanation
Indices: 2693162--2693236 Score: 109
Period size: 32 Copynumber: 2.4 Consensus size: 32
2693152 CTCGAAGGAC
*
2693162 CACTATCCATATGTTCCGAAGAACA-AAGGTAA
1 CACTATCCATATGTCCCGAAGAACATAA-GTAA
*
2693194 CACTGTCCATATGTCCCGAAGAACATAAGTAA
1 CACTATCCATATGTCCCGAAGAACATAAGTAA
2693226 -ACTATCCATAT
1 CACTATCCATAT
2693237 ATCTTGAAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
31 10 0.26
32 27 0.69
33 2 0.05
ACGTcount: A:0.39, C:0.24, G:0.13, T:0.24
Consensus pattern (32 bp):
CACTATCCATATGTCCCGAAGAACATAAGTAA
Found at i:2698611 original size:24 final size:24
Alignment explanation
Indices: 2698574--2698644 Score: 79
Period size: 24 Copynumber: 3.0 Consensus size: 24
2698564 AAACAGAGAT
* *
2698574 ATCAAAAATCAAAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATCCAA
* * * *
2698598 ATCGGATATCAAAATAGAATCCAG
1 ATCAGAAATCAAAACAGAATCCAA
*
2698622 ATCAGAAATCAGAACAGAATCCA
1 ATCAGAAATCAAAACAGAATCCA
2698645 GGTCATGTAT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.54, C:0.18, G:0.11, T:0.17
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATCCAA
Found at i:2698645 original size:24 final size:24
Alignment explanation
Indices: 2698574--2698682 Score: 78
Period size: 24 Copynumber: 4.5 Consensus size: 24
2698564 AAACAGAGAT
* * * *
2698574 ATCAAAAATCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATCCAG
* * * *
2698598 ATCGGATATCAAAATAGAATCCAG
1 ATCAGAAATCAGAACAGAATCCAG
2698622 ATCAGAAATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATCCAG
* * * *
2698646 GTCATG-TATCAGAATAGAATTCA-
1 ATCA-GAAATCAGAACAGAATCCAG
2698669 AGTCAGAAATCAGA
1 A-TCAGAAATCAGA
2698683 TAAAATATTT
Statistics
Matches: 66, Mismatches: 16, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
23 1 0.02
24 64 0.97
25 1 0.02
ACGTcount: A:0.50, C:0.17, G:0.15, T:0.19
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATCCAG
Found at i:2703191 original size:18 final size:18
Alignment explanation
Indices: 2703168--2703203 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2703158 AATCTAATTG
2703168 TATTCAATCTTGAAGTCA
1 TATTCAATCTTGAAGTCA
2703186 TATTCAATCTTGAAGTCA
1 TATTCAATCTTGAAGTCA
2703204 GGCATACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (18 bp):
TATTCAATCTTGAAGTCA
Found at i:2703728 original size:23 final size:23
Alignment explanation
Indices: 2703702--2703762 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
2703692 TACTAACTTA
* *
2703702 TCATACGAAATCATATAACAATT
1 TCATACAAAATCACATAACAATT
2703725 TCATACAAAATCACATAACAATT
1 TCATACAAAATCACATAACAATT
2703748 TCATACAAAATCACA
1 TCATACAAAATCACA
2703763 CCTTTTTATA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.51, C:0.21, G:0.02, T:0.26
Consensus pattern (23 bp):
TCATACAAAATCACATAACAATT
Found at i:2703972 original size:2 final size:2
Alignment explanation
Indices: 2703965--2704022 Score: 100
Period size: 2 Copynumber: 29.5 Consensus size: 2
2703955 GCGCATACAT
2703965 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
2704006 TA TA TA TA AA TA TA TA T
1 TA TA TA TA TA TA TA TA T
2704023 TGTATTCATG
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2705678 original size:18 final size:19
Alignment explanation
Indices: 2705632--2705668 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
2705622 TTTAAGGGGG
2705632 TGCATCGATGCACTACTTA
1 TGCATCGATGCACTACTTA
2705651 TGCATCGATGCACTACTT
1 TGCATCGATGCACTACTT
2705669 GTATTCGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.32
Consensus pattern (19 bp):
TGCATCGATGCACTACTTA
Found at i:2711113 original size:19 final size:21
Alignment explanation
Indices: 2711079--2711123 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
2711069 ATTAAATCTC
2711079 TATTTTATTAAATAAAAATAA
1 TATTTTATTAAATAAAAATAA
* *
2711100 TATTTT-TT-AATAAATATAT
1 TATTTTATTAAATAAAAATAA
2711119 TATTT
1 TATTT
2711124 CGATTCGGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 14 0.64
20 2 0.09
21 6 0.27
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TATTTTATTAAATAAAAATAA
Found at i:2712908 original size:2 final size:2
Alignment explanation
Indices: 2712860--2712892 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2712850 AGGGGGTCAC
2712860 AT AT 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 A
2712893 CACACATCTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2714698 original size:23 final size:23
Alignment explanation
Indices: 2714645--2714699 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 23
2714635 CCGAAAATAT
2714645 TGGTG-TTAATTATCATAATTTC
1 TGGTGATTAATTATCATAATTTC
2714667 T--TGATTAATTATCATAATTT-
1 TGGTGATTAATTATCATAATTTC
2714687 TGGGTGATTAATT
1 T-GGTGATTAATT
2714700 CGACTATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
20 3 0.10
21 16 0.55
22 1 0.03
23 9 0.31
ACGTcount: A:0.29, C:0.05, G:0.15, T:0.51
Consensus pattern (23 bp):
TGGTGATTAATTATCATAATTTC
Found at i:2717411 original size:20 final size:20
Alignment explanation
Indices: 2717384--2717447 Score: 110
Period size: 20 Copynumber: 3.2 Consensus size: 20
2717374 AACGCGATAA
2717384 TCGCGTTGCGAATTTGACTT
1 TCGCGTTGCGAATTTGACTT
* *
2717404 TTGCGTTGCGAATTTAACTT
1 TCGCGTTGCGAATTTGACTT
2717424 TCGCGTTGCGAATTTGACTT
1 TCGCGTTGCGAATTTGACTT
2717444 TCGC
1 TCGC
2717448 ATCAATCACA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.16, C:0.20, G:0.23, T:0.41
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGACTT
Found at i:2717724 original size:18 final size:18
Alignment explanation
Indices: 2717701--2717736 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2717691 AAGTTGGTTG
*
2717701 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
2717719 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
2717737 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:2720032 original size:24 final size:24
Alignment explanation
Indices: 2719998--2720051 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2719988 CTGAAACATC
2719998 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
2720022 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
2720046 ATCAAA
1 ATCAAA
2720052 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:2720065 original size:24 final size:24
Alignment explanation
Indices: 2719998--2720065 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
2719988 CTGAAACATC
* * *
2719998 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
2720022 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
2720046 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
2720066 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Done.