Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007923.1 Hibiscus syriacus cultivar Beakdansim tig00110328_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: 8415618
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 40
Found at i:2791293 original size:16 final size:16
Alignment explanation
Indices: 2791261--2791307 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
2791251 TTTAAAAAGT
*
2791261 TTAGTTTGTTAGT-TTA
1 TTAGTTTATTA-TATTA
2791277 TTAGTTTATTATATTA
1 TTAGTTTATTATATTA
*
2791293 TAAG-TTATTATATTA
1 TTAGTTTATTATATTA
2791308 AAGTTTAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.60
Consensus pattern (16 bp):
TTAGTTTATTATATTA
Found at i:2791302 original size:15 final size:14
Alignment explanation
Indices: 2791282--2791312 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
2791272 GTTTATTAGT
2791282 TTATTATATTATAAG
1 TTATTATATTA-AAG
2791297 TTATTATATTAAAG
1 TTATTATATTAAAG
2791311 TT
1 TT
2791313 TAGTGTTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
TTATTATATTAAAG
Found at i:2793628 original size:26 final size:26
Alignment explanation
Indices: 2793593--2794060 Score: 215
Period size: 26 Copynumber: 17.4 Consensus size: 26
2793583 TTGTTAGTAT
2793593 TAAATCATTATTATAAATCATTATTA
1 TAAATCATTATTATAAATCATTATTA
*
2793619 TAAAT-A--ATTACTAAAT-A--ATAA
1 TAAATCATTATTA-TAAATCATTATTA
* *
2793640 CAAATAATTATTATAAAATCATTATTA
1 TAAATCATTATTAT-AAATCATTATTA
*
2793667 T-AATGATTATTATCAAATCATTACTAAATCA
1 TAAATCATTATTAT-AAATCATTA-T---T-A
*
2793698 TCAAATCATTAAATATTTAAATCATTA-T-
1 T-AAATCATT--AT-TATAAATCATTATTA
* *
2793726 TAAATCATTTTTAT-AATGATTATTA
1 TAAATCATTATTATAAATCATTATTA
* *
2793751 CTAAATTATTATTAT-AATGATTATTA
1 -TAAATCATTATTATAAATCATTATTA
* *
2793777 TCAAATCATTACTAT-AATGATTATTA
1 T-AAATCATTATTATAAATCATTATTA
*
2793803 TCAAATCATTACTAAATCATCAAATCATTAAATATT
1 T-AAATCATTA-T---T-AT-AAATCATT--AT-TA
*
2793839 TAAATCATTA-T-TAAATCATTTTTA
1 TAAATCATTATTATAAATCATTATTA
*
2793863 T-AATGATTATTACTAAATCATTATTA
1 TAAATCATTATTA-TAAATCATTATTA
* *
2793889 T-AATGATTATTATCAAATCATTACTA
1 TAAATCATTATTAT-AAATCATTATTA
*
2793915 T-AATGATTATTATCAAATCATTACTAAATCAA
1 TAAATCATTATTAT-AAATCATTA-T---T--A
* *
2793947 CAAATCATTAAATATTTAAATCATTA-T-
1 TAAATCATT--AT-TATAAATCATTATTA
* *
2793974 TAAATCATTTTTAT-AATGATTATTA
1 TAAATCATTATTATAAATCATTATTA
*
2793999 CTAAATCATTATTAT-AATGATTATTA
1 -TAAATCATTATTATAAATCATTATTA
* *
2794025 TCAAATCATTACTAT-AATGATTATTA
1 T-AAATCATTATTATAAATCATTATTA
*
2794051 TCAATCATTA
1 TAAATCATTA
2794061 CTAAATCATC
Statistics
Matches: 358, Mismatches: 34, Indels: 101
0.73 0.07 0.20
Matches are distributed among these distances:
21 7 0.02
22 1 0.00
23 27 0.08
24 22 0.06
25 16 0.04
26 187 0.52
27 28 0.08
28 2 0.01
30 6 0.02
31 4 0.01
32 1 0.00
33 18 0.05
35 33 0.09
36 6 0.02
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (26 bp):
TAAATCATTATTATAAATCATTATTA
Found at i:2793677 original size:12 final size:13
Alignment explanation
Indices: 2793593--2794060 Score: 215
Period size: 12 Copynumber: 34.8 Consensus size: 13
2793583 TTGTTAGTAT
2793593 TAAATCATTATTA
1 TAAATCATTATTA
2793606 TAAATCATTATTA
1 TAAATCATTATTA
2793619 TAAAT-A--ATTA
1 TAAATCATTATTA
*
2793629 CTAAAT-A--ATAA
1 -TAAATCATTATTA
* *
2793640 CAAATAATTATTA
1 TAAATCATTATTA
2793653 TAAAATCATTATTA
1 T-AAATCATTATTA
*
2793667 T-AATGATTATTA
1 TAAATCATTATTA
2793679 TCAAATCATTACTAAATCA
1 T-AAATCATTA-T---T-A
*
2793698 TCAAATCATTAAATATT
1 T-AAATCATT--AT-TA
2793715 TAAATCATTA-T-
1 TAAATCATTATTA
*
2793726 TAAATCATTTTTA
1 TAAATCATTATTA
*
2793739 T-AATGATTATTA
1 TAAATCATTATTA
*
2793751 CTAAATTATTATTA
1 -TAAATCATTATTA
*
2793765 T-AATGATTATTA
1 TAAATCATTATTA
*
2793777 TCAAATCATTACTA
1 T-AAATCATTATTA
*
2793791 T-AATGATTATTA
1 TAAATCATTATTA
2793803 TCAAATCATTACTAAATCA
1 T-AAATCATTA-T---T-A
*
2793822 TCAAATCATTAAATATT
1 T-AAATCATT--AT-TA
2793839 TAAATCATTA-T-
1 TAAATCATTATTA
*
2793850 TAAATCATTTTTA
1 TAAATCATTATTA
*
2793863 T-AATGATTATTA
1 TAAATCATTATTA
2793875 CTAAATCATTATTA
1 -TAAATCATTATTA
*
2793889 T-AATGATTATTA
1 TAAATCATTATTA
*
2793901 TCAAATCATTACTA
1 T-AAATCATTATTA
*
2793915 T-AATGATTATTA
1 TAAATCATTATTA
2793927 TCAAATCATTACTAAATCAA
1 T-AAATCATTA-T---T--A
* *
2793947 CAAATCATTAAATATT
1 TAAATCATT--AT-TA
2793963 TAAATCATTA-T-
1 TAAATCATTATTA
*
2793974 TAAATCATTTTTA
1 TAAATCATTATTA
*
2793987 T-AATGATTATTA
1 TAAATCATTATTA
2793999 CTAAATCATTATTA
1 -TAAATCATTATTA
*
2794013 T-AATGATTATTA
1 TAAATCATTATTA
*
2794025 TCAAATCATTACTA
1 T-AAATCATTATTA
*
2794039 T-AATGATTATTA
1 TAAATCATTATTA
*
2794051 TCAATCATTA
1 TAAATCATTA
2794061 CTAAATCATC
Statistics
Matches: 361, Mismatches: 42, Indels: 104
0.71 0.08 0.21
Matches are distributed among these distances:
10 8 0.02
11 37 0.10
12 108 0.30
13 37 0.10
14 96 0.27
15 3 0.01
16 24 0.07
17 2 0.01
18 9 0.02
19 30 0.08
20 4 0.01
21 3 0.01
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (13 bp):
TAAATCATTATTA
Found at i:2793799 original size:124 final size:124
Alignment explanation
Indices: 2793592--2794118 Score: 911
Period size: 124 Copynumber: 4.3 Consensus size: 124
2793582 TTTGTTAGTA
* * * ** *
2793592 TTAAATCATTATTATAAATCATTATTATAA--ATAATTACTAAAT-AATAACA-AATAATTATTA
1 TTAAATCATTA-T-TAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTA
* *
2793653 TAAAATCATTATTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATAT
64 TCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATAT
*
2793714 TTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATTATTATTATAATGATTATTATC
1 TTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATC
2793779 AAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATAT
66 AAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATAT
2793838 TTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATC
1 TTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATC
*
2793903 AAATCATTACTATAATGATTATTATCAAATCATTACTAAATCAACAAATCATTAAATAT
66 AAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATAT
2793962 TTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATC
1 TTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATC
2794027 AAATCATTACTATAATGATTATTATC-AATCATTACTAAATCATCAAATCATTAAATAT
66 AAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATAT
2794085 TTAAATCATTATTAAATCATTTTTATAATGATTA
1 TTAAATCATTATTAAATCATTTTTATAATGATTA
2794119 ATAAATACAT
Statistics
Matches: 390, Mismatches: 11, Indels: 7
0.96 0.03 0.02
Matches are distributed among these distances:
120 15 0.04
121 1 0.00
122 23 0.06
123 69 0.18
124 282 0.72
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (124 bp):
TTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATC
AAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATAT
Found at i:2796992 original size:26 final size:24
Alignment explanation
Indices: 2796934--2796992 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
2796924 CTAATAAACC
*
2796934 TAATAATGATTTGATAATTACTAT
1 TAATAATGATTTGATAATTAATAT
*
2796958 TAATCTAATGATTTGATATTTAATGATT
1 TAA--TAATGATTTGATAATTAAT-A-T
2796986 TAATAAT
1 TAATAAT
2796993 AATATGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 3 0.10
26 21 0.72
27 1 0.03
28 4 0.14
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (24 bp):
TAATAATGATTTGATAATTAATAT
Found at i:2797850 original size:28 final size:30
Alignment explanation
Indices: 2797802--2797864 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
2797792 AATTTTTATA
*
2797802 TAATATAATATATAACTTAAACTAATAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
2797832 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
2797860 TAATA
1 TAATA
2797865 ATTTATACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 25 0.78
29 1 0.03
30 6 0.19
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:2797871 original size:28 final size:28
Alignment explanation
Indices: 2797806--2797871 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
2797796 TTTATATAAT
*
2797806 ATAATATATAACTTAAACTAATAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
2797834 AT-ATAATATAACTTAAACTAACAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
2797862 ATAATTTATA
1 ATAATATATA
2797872 CTAACAAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 30 0.88
29 2 0.06
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:2797874 original size:21 final size:21
Alignment explanation
Indices: 2797841--2797889 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
2797831 CTAATATAAT
2797841 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
2797862 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
2797883 ATTAACT
1 A-TAACT
2797890 AGATTTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:2798445 original size:25 final size:25
Alignment explanation
Indices: 2798391--2798448 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
2798381 GTTCCCACGT
* *
2798391 CCCATGCACAACATGCATCTGCATG
1 CCCATGCACAACATGCATCTCCATC
* *
2798416 GCCATGCACAACATGCATC-CCCTCC
1 CCCATGCACAACATGCATCTCCAT-C
2798441 CCCATGCA
1 CCCATGCA
2798449 TTCCCACGGC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 2 0.07
25 25 0.93
ACGTcount: A:0.26, C:0.43, G:0.14, T:0.17
Consensus pattern (25 bp):
CCCATGCACAACATGCATCTCCATC
Found at i:2798539 original size:29 final size:29
Alignment explanation
Indices: 2798507--2798586 Score: 142
Period size: 29 Copynumber: 2.8 Consensus size: 29
2798497 TCCACCTTGG
*
2798507 AGGTCGCCCGGATTGCATGGCGACCTCCA
1 AGGTCGCCTGGATTGCATGGCGACCTCCA
*
2798536 AGGTCGCCTGGATTGCATGGCGACCTCTA
1 AGGTCGCCTGGATTGCATGGCGACCTCCA
2798565 AGGTCGCCTGGATTGCATGGCG
1 AGGTCGCCTGGATTGCATGGCG
2798587 TCCTATGGCG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.16, C:0.29, G:0.34, T:0.21
Consensus pattern (29 bp):
AGGTCGCCTGGATTGCATGGCGACCTCCA
Found at i:2799475 original size:2 final size:2
Alignment explanation
Indices: 2799470--2799496 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2799460 GGGGGGGGGG
2799470 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
2799497 GAGTTTTGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2799791 original size:43 final size:43
Alignment explanation
Indices: 2799726--2799809 Score: 141
Period size: 43 Copynumber: 2.0 Consensus size: 43
2799716 CTTATGGGTG
* *
2799726 TCTTTTGGTTCAAATAGTATTACTTGACTGATAGATTACAATT
1 TCTTTTGGTTCAAATAGGATTACTTGAATGATAGATTACAATT
*
2799769 TCTTTTGGTTCCAATAGGATTACTTGAATGATAGATTACAA
1 TCTTTTGGTTCAAATAGGATTACTTGAATGATAGATTACAA
2799810 GAAGGTTTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (43 bp):
TCTTTTGGTTCAAATAGGATTACTTGAATGATAGATTACAATT
Found at i:2818200 original size:16 final size:16
Alignment explanation
Indices: 2818179--2818252 Score: 89
Period size: 16 Copynumber: 4.6 Consensus size: 16
2818169 TAAAAAAAAA
2818179 AAAAAAAGAGGAAATG
1 AAAAAAAGAGGAAATG
2818195 AAAAAAAG-GGAAATG
1 AAAAAAAGAGGAAATG
*
2818210 AAAAAAAAAGGGAAATG
1 AAAAAAAGA-GGAAATG
*
2818227 AAAAAAATGA-AAAATG
1 AAAAAAA-GAGGAAATG
2818243 AAAAAGAAGA
1 AAAAA-AAGA
2818253 AAAATAAATA
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
15 14 0.27
16 20 0.39
17 16 0.31
18 1 0.02
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.07
Consensus pattern (16 bp):
AAAAAAAGAGGAAATG
Found at i:2818217 original size:32 final size:34
Alignment explanation
Indices: 2818178--2818252 Score: 102
Period size: 32 Copynumber: 2.3 Consensus size: 34
2818168 TTAAAAAAAA
**
2818178 AAAAAAAAGA-GGAAATGAAAAAAA-GGGAAATG
1 AAAAAAAAGAGGGAAATGAAAAAAATGAAAAATG
2818210 AAAAAAAA-AGGGAAATGAAAAAAATGAAAAATG
1 AAAAAAAAGAGGGAAATGAAAAAAATGAAAAATG
*
2818243 AAAAAGAAGA
1 AAAAAAAAGA
2818253 AAAATAAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 1 0.03
32 22 0.59
33 13 0.35
34 1 0.03
ACGTcount: A:0.72, C:0.00, G:0.21, T:0.07
Consensus pattern (34 bp):
AAAAAAAAGAGGGAAATGAAAAAAATGAAAAATG
Found at i:2819516 original size:130 final size:130
Alignment explanation
Indices: 2819201--2819509 Score: 415
Period size: 130 Copynumber: 2.3 Consensus size: 130
2819191 TCAACATCAA
*
2819201 CTGACCAGA-CTTCCTCATCACGTAGGAGCCGTGTCAACATTAGGATAACCAGCCGTCCTCATCA
1 CTGACCAGATC-TCCTCATCACGTAGGAGCCGTGTCAACCTTA-GATAACCAGCCGTCCTCATCA
* * * * *
2819265 CGTAGGAACCGAGTTATCACCCTTCCTAAAGGTGGCCAGAGTTTTTCATCATGAATGAACCGTGT
64 CGTAGGAACCGAGTTATCA--C--CCTAAAGATGGCCAGAATTCTTCATCATGAAGGAACAGTGT
2819330 CATCCC
125 CATCCC
* * * *
2819336 CAGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACG
1 CTGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCTTAGATAACCAGCCGTCCTCATCACG
* * *
2819401 TAGGAACCGTGTTATCA-CCTAAAGATGGCCAAGAATTCTTCATCATGTAGGAGCAGTGTCATCC
66 TAGGAACCGAGTTATCACCCTAAAGATGGCC-AGAATTCTTCATCATGAAGGAACAGTGTCATCC
2819465 C
130 C
*
2819466 CTGACCAGATCTCCTCATCACGTAGGAGCCGTGTCACCCTTAGA
1 CTGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCTTAGA
2819510 CGACCAGACC
Statistics
Matches: 154, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
129 12 0.08
130 67 0.44
134 39 0.25
135 35 0.23
136 1 0.01
ACGTcount: A:0.27, C:0.30, G:0.20, T:0.24
Consensus pattern (130 bp):
CTGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCTTAGATAACCAGCCGTCCTCATCACG
TAGGAACCGAGTTATCACCCTAAAGATGGCCAGAATTCTTCATCATGAAGGAACAGTGTCATCCC
Found at i:2821778 original size:25 final size:25
Alignment explanation
Indices: 2821740--2821838 Score: 166
Period size: 25 Copynumber: 4.0 Consensus size: 25
2821730 AGTTAGGGGA
*
2821740 TTAGGG-TTGAAACCCTAAAT-TGTT
1 TTAGGGTTTGAAACCCT-AATCTGAT
2821764 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
2821789 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
2821814 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
2821839 GGGTTGGTTC
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:0.28, C:0.15, G:0.20, T:0.36
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGAT
Found at i:2821975 original size:3 final size:3
Alignment explanation
Indices: 2821967--2822018 Score: 63
Period size: 3 Copynumber: 17.7 Consensus size: 3
2821957 ATATATAATT
* *
2821967 TAA TAA TAA CAA TAA TAA TAA TAA TAA TAA TAA TTAA TAA -AA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA
2822012 -AA TAA TA
1 TAA TAA TA
2822019 TAAAAAAGAC
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
2 3 0.07
3 36 0.86
4 3 0.07
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2832627 original size:45 final size:47
Alignment explanation
Indices: 2832577--2832676 Score: 132
Period size: 47 Copynumber: 2.2 Consensus size: 47
2832567 TATTTTTTAT
*
2832577 AAATAATATTTT-A-TTTTAAGAATAAATTATAAATAAAATTTATAG
1 AAATAATATTTTAATTTTTAAGAACAAATTATAAATAAAATTTATAG
* * * * *
2832622 AAATAATATTTTAATTTTTAAGAACAAGTTATAGATAATATTTTTAT
1 AAATAATATTTTAATTTTTAAGAACAAATTATAAATAAAATTTATAG
2832669 AAATAATA
1 AAATAATA
2832677 CATATATATA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
45 12 0.26
46 1 0.02
47 34 0.72
ACGTcount: A:0.51, C:0.01, G:0.05, T:0.43
Consensus pattern (47 bp):
AAATAATATTTTAATTTTTAAGAACAAATTATAAATAAAATTTATAG
Found at i:2833774 original size:10 final size:10
Alignment explanation
Indices: 2833755--2833841 Score: 57
Period size: 10 Copynumber: 8.0 Consensus size: 10
2833745 TCGTTTATTG
*
2833755 TGTTCCTTTA
1 TGTTCGTTTA
2833765 TGTTCGTTTA
1 TGTTCGTTTA
*
2833775 TGTTCATTTATTA
1 TGTTC--GT-TTA
*
2833788 TGTTCGTTTGTGT
1 TGTTCG-TT-T-A
*
2833801 TCGTTCGTTTG
1 T-GTTCGTTTA
2833812 TGTTCGTTTA
1 TGTTCGTTTA
*
2833822 CGTTCGTTTA
1 TGTTCGTTTA
*
2833832 TGTTCATTTA
1 TGTTCGTTTA
2833842 AATGAACGAA
Statistics
Matches: 61, Mismatches: 9, Indels: 14
0.73 0.11 0.17
Matches are distributed among these distances:
10 39 0.64
11 2 0.03
12 4 0.07
13 11 0.18
14 5 0.08
ACGTcount: A:0.10, C:0.13, G:0.18, T:0.59
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:2833779 original size:33 final size:33
Alignment explanation
Indices: 2833742--2833805 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
2833732 GTGTTTGTGT
* *
2833742 TGTTCGTTTATTGTGTTCCTTTATGTTCGTTTA
1 TGTTCATTTATTATGTTCCTTTATGTTCGTTTA
* *
2833775 TGTTCATTTATTATGTTCGTTTGTGTTCGTT
1 TGTTCATTTATTATGTTCCTTTATGTTCGTT
2833806 CGTTTGTGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.09, C:0.11, G:0.19, T:0.61
Consensus pattern (33 bp):
TGTTCATTTATTATGTTCCTTTATGTTCGTTTA
Found at i:2833808 original size:14 final size:14
Alignment explanation
Indices: 2833789--2833819 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
2833779 CATTTATTAT
2833789 GTTCGTTTGTGTTC
1 GTTCGTTTGTGTTC
2833803 GTTCGTTTGTGTTC
1 GTTCGTTTGTGTTC
2833817 GTT
1 GTT
2833820 TACGTTCGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.00, C:0.13, G:0.29, T:0.58
Consensus pattern (14 bp):
GTTCGTTTGTGTTC
Found at i:2841252 original size:19 final size:19
Alignment explanation
Indices: 2841228--2841274 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
2841218 ATGCAATTAA
2841228 TGCATCGATGCATAAGGAG
1 TGCATCGATGCATAAGGAG
2841247 TGCATCGATGCATAAGGAG
1 TGCATCGATGCATAAGGAG
2841266 TGCATCGAT
1 TGCATCGAT
2841275 ACACACGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (19 bp):
TGCATCGATGCATAAGGAG
Found at i:2845458 original size:19 final size:19
Alignment explanation
Indices: 2845428--2845480 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
2845418 AATTGTTCAG
*
2845428 AGTGTATCGATGCACAGGA
1 AGTGCATCGATGCACAGGA
*
2845447 AGTGCATTGATGCACAGGA
1 AGTGCATCGATGCACAGGA
2845466 AGTGCATCGATGCAC
1 AGTGCATCGATGCAC
2845481 CTCTTAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.30, C:0.19, G:0.30, T:0.21
Consensus pattern (19 bp):
AGTGCATCGATGCACAGGA
Found at i:2845553 original size:24 final size:24
Alignment explanation
Indices: 2845525--2845588 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
2845515 CATCGATGCA
*
2845525 TAAGGAGTGCATCGATGCACACGT
1 TAAGGAGTGCATCGATGCACACGG
2845549 TAAGG-GATGCATCGAT--ACACGG
1 TAAGGAG-TGCATCGATGCACACGG
*
2845571 T-AGGA-TGCATTGATGCAC
1 TAAGGAGTGCATCGATGCAC
2845589 TTGAAGGGGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
20 8 0.24
21 3 0.09
22 8 0.24
23 1 0.03
24 14 0.41
ACGTcount: A:0.30, C:0.19, G:0.30, T:0.22
Consensus pattern (24 bp):
TAAGGAGTGCATCGATGCACACGG
Found at i:2847826 original size:24 final size:24
Alignment explanation
Indices: 2847799--2847846 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
2847789 AAGGAAGTAA
2847799 GGATTTGCATATTTGAGTAAAGTT
1 GGATTTGCATATTTGAGTAAAGTT
2847823 GGATTTGCATATTTGAGTAAAGTT
1 GGATTTGCATATTTGAGTAAAGTT
2847847 AATGATTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.04, G:0.25, T:0.42
Consensus pattern (24 bp):
GGATTTGCATATTTGAGTAAAGTT
Found at i:2849833 original size:24 final size:21
Alignment explanation
Indices: 2849801--2849859 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 21
2849791 TCGATGCATA
*
2849801 AGGAGTGCATCGATGAACACGTT
1 AGGA-TGCATCGATG-ACACGGT
2849824 AAGGGATGCATCGAT-ACACGGT
1 -A-GGATGCATCGATGACACGGT
2849846 AGGATGCATCGATG
1 AGGATGCATCGATG
2849860 CACTTCAAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
20 12 0.38
21 1 0.03
22 6 0.19
24 10 0.31
25 3 0.09
ACGTcount: A:0.31, C:0.17, G:0.32, T:0.20
Consensus pattern (21 bp):
AGGATGCATCGATGACACGGT
Found at i:2852498 original size:18 final size:16
Alignment explanation
Indices: 2852477--2852516 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 16
2852467 TGATTATACA
2852477 TATATGGATGACATGAAT
1 TATATGGATG-CATG-AT
*
2852495 TATATGTATGCATGAT
1 TATATGGATGCATGAT
2852511 TATATG
1 TATATG
2852517 TGTTAATATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.38
17 4 0.19
18 9 0.43
ACGTcount: A:0.35, C:0.05, G:0.20, T:0.40
Consensus pattern (16 bp):
TATATGGATGCATGAT
Found at i:2852514 original size:16 final size:18
Alignment explanation
Indices: 2852477--2852517 Score: 59
Period size: 16 Copynumber: 2.4 Consensus size: 18
2852467 TGATTATACA
*
2852477 TATATGGATGACATGAAT
1 TATATGTATGACATGAAT
2852495 TATATGTATG-CATG-AT
1 TATATGTATGACATGAAT
2852511 TATATGT
1 TATATGT
2852518 GTTAATATGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.41
17 4 0.18
18 9 0.41
ACGTcount: A:0.34, C:0.05, G:0.20, T:0.41
Consensus pattern (18 bp):
TATATGTATGACATGAAT
Found at i:2856627 original size:14 final size:14
Alignment explanation
Indices: 2856602--2856674 Score: 58
Period size: 14 Copynumber: 5.0 Consensus size: 14
2856592 TACATACATT
*
2856602 ATACATAGATATCA
1 ATACATATATATCA
*
2856616 ATTCATATATATCA
1 ATACATATATATCA
*
2856630 TTATACATTATATAT-T
1 --ATACA-TATATATCA
*
2856646 ATACATACATATCA
1 ATACATATATATCA
*
2856660 ATTCATAATATATCA
1 ATACAT-ATATATCA
2856675 TTCGTACATT
Statistics
Matches: 46, Mismatches: 8, Indels: 9
0.73 0.13 0.14
Matches are distributed among these distances:
13 6 0.13
14 22 0.48
15 7 0.15
16 4 0.09
17 7 0.15
ACGTcount: A:0.45, C:0.14, G:0.01, T:0.40
Consensus pattern (14 bp):
ATACATATATATCA
Found at i:2856649 original size:44 final size:46
Alignment explanation
Indices: 2856599--2856692 Score: 147
Period size: 44 Copynumber: 2.1 Consensus size: 46
2856589 ATATACATAC
* *
2856599 ATTATACATAGATATCAATTCAT-ATATATCATT-ATACATTATAT
1 ATTATACATACATATCAATTCATAATATATCATTCATACATTACAT
*
2856643 ATTATACATACATATCAATTCATAATATATCATTCGTACATTACAT
1 ATTATACATACATATCAATTCATAATATATCATTCATACATTACAT
2856689 ATTA
1 ATTA
2856693 ATTAATTATA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 22 0.49
45 10 0.22
46 13 0.29
ACGTcount: A:0.43, C:0.14, G:0.02, T:0.41
Consensus pattern (46 bp):
ATTATACATACATATCAATTCATAATATATCATTCATACATTACAT
Found at i:2856658 original size:30 final size:30
Alignment explanation
Indices: 2856591--2856659 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
2856581 TGCATTTTAT
*
2856591 ATACATA-CATTATACATAGATATCAATTC
1 ATACATATCATTATACATAGATATCAATAC
* * *
2856620 ATATATATCATTATACATTATATAT-TATAC
1 ATACATATCATTATACA-TAGATATCAATAC
2856650 ATACATATCA
1 ATACATATCA
2856660 ATTCATAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
29 6 0.18
30 21 0.64
31 6 0.18
ACGTcount: A:0.45, C:0.14, G:0.01, T:0.39
Consensus pattern (30 bp):
ATACATATCATTATACATAGATATCAATAC
Found at i:2856677 original size:14 final size:15
Alignment explanation
Indices: 2856610--2856683 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
2856600 TTATACATAG
2856610 ATATCAATTCAT--AT
1 ATATC-ATTCATACAT
2856624 ATATCATT-ATACATT
1 ATATCATTCATACA-T
2856639 ATAT-ATT-ATACAT
1 ATATCATTCATACAT
2856652 ACATATCAATTCATA-AT
1 --ATATC-ATTCATACAT
*
2856669 ATATCATTCGTACAT
1 ATATCATTCATACAT
2856684 TACATATTAA
Statistics
Matches: 50, Mismatches: 1, Indels: 17
0.74 0.01 0.25
Matches are distributed among these distances:
12 2 0.04
13 4 0.08
14 20 0.40
15 16 0.32
17 5 0.10
18 3 0.06
ACGTcount: A:0.42, C:0.15, G:0.01, T:0.42
Consensus pattern (15 bp):
ATATCATTCATACAT
Found at i:2856884 original size:2 final size:2
Alignment explanation
Indices: 2856877--2856908 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2856867 TGTTTATGTT
2856877 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2856909 AAATTTTAAG
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):
TA
Found at i:2857127 original size:49 final size:49
Alignment explanation
Indices: 2857050--2857173 Score: 178
Period size: 49 Copynumber: 2.5 Consensus size: 49
2857040 AGCAGTAAAG
* * *
2857050 CGCGCCCCCTGACCCGCGCTATACGCTGATTTGGTGCCACGTGGGGTATA
1 CGCGCCCCCTGA-CCGCGCTATATGCTGATTTGGCGCCACGTAGGGTATA
2857100 -GCGCCCCCTGTACCGCGCTATATGCTGATTTGGCGCCACGTAGGGTATA
1 CGCGCCCCCTG-ACCGCGCTATATGCTGATTTGGCGCCACGTAGGGTATA
2857149 GCGCGCCCCCTGAACCGCGCTATAT
1 -CGCGCCCCCTG-ACCGCGCTATAT
2857174 CTGTGTATTT
Statistics
Matches: 67, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
49 44 0.66
50 1 0.01
51 22 0.33
ACGTcount: A:0.15, C:0.35, G:0.28, T:0.22
Consensus pattern (49 bp):
CGCGCCCCCTGACCGCGCTATATGCTGATTTGGCGCCACGTAGGGTATA
Found at i:2861612 original size:17 final size:18
Alignment explanation
Indices: 2861569--2861609 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
2861559 AATTTATATT
2861569 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
2861586 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
2861604 ATTAAA
1 AGTAAA
2861610 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:2861669 original size:10 final size:10
Alignment explanation
Indices: 2861650--2861680 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2861640 CCTTAAACGA
*
2861650 GAGAGTATTT
1 GAGAGAATTT
2861660 GAGAGAATTT
1 GAGAGAATTT
2861670 GAGAGAATTT
1 GAGAGAATTT
2861680 G
1 G
2861681 GTGTGATGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:2866865 original size:26 final size:26
Alignment explanation
Indices: 2866824--2866879 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
2866814 TAAAACTGAT
* * *
2866824 GCCCCTATATGTTGCCCTGGGCTGTC
1 GCCCCTACATGCTGCCCTGGGCCGTC
2866850 GCCCCTACATGCTGCCCTGGGCCGTC
1 GCCCCTACATGCTGCCCTGGGCCGTC
2866876 GCCC
1 GCCC
2866880 ATCTGGCACA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.07, C:0.43, G:0.27, T:0.23
Consensus pattern (26 bp):
GCCCCTACATGCTGCCCTGGGCCGTC
Found at i:2868752 original size:2 final size:2
Alignment explanation
Indices: 2868745--2868781 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2868735 ATTTTCATAG
2868745 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2868782 TTTATTACAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2872055 original size:6 final size:6
Alignment explanation
Indices: 2872044--2872075 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
2872034 ATTTGATTCT
2872044 TCCCTG TCCCTG TCCCTG TCCCTG TCCCTG TC
1 TCCCTG TCCCTG TCCCTG TCCCTG TCCCTG TC
2872076 TCAACAATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.16, T:0.34
Consensus pattern (6 bp):
TCCCTG
Found at i:2872267 original size:27 final size:27
Alignment explanation
Indices: 2872217--2872269 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
2872207 TATTTATGGA
* *
2872217 TTTAATATTTATATTAAATTTATATTT
1 TTTAATATTTAAATTAAATATATATTT
2872244 TTTAATATTATAAATTAAA-ATATATT
1 TTTAATATT-TAAATTAAATATATATT
2872270 AAATTTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 15 0.65
28 8 0.35
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
TTTAATATTTAAATTAAATATATATTT
Found at i:2872378 original size:68 final size:68
Alignment explanation
Indices: 2872282--2872417 Score: 172
Period size: 72 Copynumber: 2.0 Consensus size: 68
2872272 ATTTATATTC
*
2872282 TTTAATTTGAATATTAGTAAGAT-A-AT-TATTTTTTAAATATGTCAAATTAAAAATATATATAT
1 TTTAATTTGAATATTAGAAAGATAATATATATTTTTTAAATATGTCAAATT-AAAATA-ATAT-T
2872344 TATCTA
63 TATCTA
* *
2872350 TTTAACTTTGAATATTA-AAAGATAATTATATATTTTTTAAATATTTTAAATTAAAATAATATTT
1 TTTAA-TTTGAATATTAGAAAGATAA-TATATATTTTTTAAATATGTCAAATTAAAATAATATTT
2872414 ATCT
64 ATCT
2872418 CAATTTGAAT
Statistics
Matches: 60, Mismatches: 3, Indels: 9
0.83 0.04 0.12
Matches are distributed among these distances:
68 10 0.17
69 18 0.30
70 4 0.07
71 8 0.13
72 20 0.33
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (68 bp):
TTTAATTTGAATATTAGAAAGATAATATATATTTTTTAAATATGTCAAATTAAAATAATATTTAT
CTA
Found at i:2872401 original size:72 final size:68
Alignment explanation
Indices: 2872232--2872564 Score: 252
Period size: 63 Copynumber: 5.0 Consensus size: 68
2872222 TATTTATATT
* * * *
2872232 AAATTTATATTTTTT-AATATTATAAATTAAAATATATTAAATTTATATTCTTTAATTTGAATAT
1 AAATTTATATTTTTTAAATATTTTAAATTAAAATATA-TATA-TTAT-CTATTTAATTTGAATAT
*
2872296 TAGTAAG
63 TA-AAAG
* *
2872303 ATAA--T-TATTTTTTAAATATGTCAAATTAAAAATATATATATTATCTATTTAACTTTGAATAT
1 A-AATTTATATTTTTTAAATATTTTAAATT-AAAATATATATATTATCTATTTAA-TTTGAATAT
2872365 TAAAAG
63 TAAAAG
* *
2872371 ATAATTATATATTTTTTAAATATTTTAAATTAAAATA-ATAT-TTATC---TCAATTTGAATAGT
1 A-AATT-TATATTTTTTAAATATTTTAAATTAAAATATATATATTATCTATTTAATTTGAATATT
2872431 AAAA-
64 AAAAG
* * * * *
2872435 AAGGTTTATATCTTTTGAATATTTTAAATT-AAA-ATA-ATA-TA--TATTTAACTTTAAATAGT
1 AA-ATTTATATTTTTTAAATATTTTAAATTAAAATATATATATTATCTATTTAA-TTTGAATATT
2872494 AAAAG
64 AAAAG
* * * * * *
2872499 AAGTTTATA-TCTTTGAATATTTTAAATTAAAATATAT-TGTTATCTGTTTAAATTTGGATATTA
1 AAATTTATATTTTTTAAATATTTTAAATTAAAATATATATATTATCTATTT-AATTTGAATATTA
2872562 AAA
65 AAA
2872565 TATATATGGT
Statistics
Matches: 216, Mismatches: 23, Indels: 50
0.75 0.08 0.17
Matches are distributed among these distances:
61 5 0.02
62 24 0.11
63 46 0.21
64 9 0.04
65 15 0.07
66 3 0.01
67 15 0.07
68 15 0.07
69 28 0.13
70 18 0.08
71 16 0.07
72 22 0.10
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (68 bp):
AAATTTATATTTTTTAAATATTTTAAATTAAAATATATATATTATCTATTTAATTTGAATATTAA
AAG
Found at i:2872403 original size:36 final size:33
Alignment explanation
Indices: 2872308--2872405 Score: 81
Period size: 36 Copynumber: 2.8 Consensus size: 33
2872298 GTAAGATAAT
*
2872308 TATTTTTTAAATATGTCAAATTAAAAATATATA
1 TATTTTTTAAATATTTCAAATTAAAAATATATA
* * *
2872341 TATTATCTATTTAA-CTTTGAATATTAAAAGATAATTATA
1 TATT-T-T-TTAAATATTTCAA-ATTAAAA-AT-A-TATA
*
2872380 TATTTTTTAAATATTTTAAATTAAAA
1 TATTTTTTAAATATTTCAAATTAAAA
2872406 TAATATTTAT
Statistics
Matches: 50, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
33 4 0.08
34 1 0.02
35 5 0.10
36 22 0.44
37 8 0.16
38 2 0.04
39 8 0.16
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (33 bp):
TATTTTTTAAATATTTCAAATTAAAAATATATA
Found at i:2873148 original size:18 final size:21
Alignment explanation
Indices: 2873127--2873173 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 21
2873117 GAAATTAATA
2873127 AATAATATATT-T-T-TTATT
1 AATAATATATTATATATTATT
*
2873145 AATAATTTATTATATATTATT
1 AATAATATATTATATATTATT
2873166 AA-AATATA
1 AATAATATA
2873174 ATATCTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 10 0.42
19 1 0.04
20 6 0.25
21 7 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
AATAATATATTATATATTATT
Found at i:2873256 original size:26 final size:26
Alignment explanation
Indices: 2873227--2873318 Score: 75
Period size: 23 Copynumber: 3.6 Consensus size: 26
2873217 AATATTAAAA
2873227 AATAATATTATATTATTAAAAATATT
1 AATAATATTATATTATTAAAAATATT
* * *
2873253 AATAA-A-TAT-TTTTTAAATATTTT
1 AATAATATTATATTATTAAAAATATT
* * *
2873276 AATAATTAATATTTTGATTAAATGATATT
1 AATAA-TATTATATT-ATTAAA-AATATT
2873305 AA-AATATTATATTA
1 AATAATATTATATTA
2873319 ATATTAAATT
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
23 16 0.31
24 3 0.06
25 2 0.04
26 9 0.17
27 9 0.17
28 7 0.13
29 6 0.12
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (26 bp):
AATAATATTATATTATTAAAAATATT
Found at i:2881371 original size:33 final size:34
Alignment explanation
Indices: 2881334--2881404 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
2881324 CTTTACAAAC
*
2881334 TCCCTAG-TTTTTCACGGGATAAACTAGAACCTT
1 TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
* * * *
2881367 TCCCTAGCTTTTACACGGGTTTAGCTAGAACTTT
1 TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
2881401 TCCC
1 TCCC
2881405 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 7 0.22
34 25 0.78
ACGTcount: A:0.23, C:0.27, G:0.15, T:0.35
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
Found at i:2881828 original size:19 final size:19
Alignment explanation
Indices: 2881804--2881856 Score: 106
Period size: 19 Copynumber: 2.8 Consensus size: 19
2881794 TCGATACACT
2881804 GTGCATCGGTACACTTGGG
1 GTGCATCGGTACACTTGGG
2881823 GTGCATCGGTACACTTGGG
1 GTGCATCGGTACACTTGGG
2881842 GTGCATCGGTACACT
1 GTGCATCGGTACACT
2881857 AATTGCATTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.17, C:0.23, G:0.34, T:0.26
Consensus pattern (19 bp):
GTGCATCGGTACACTTGGG
Found at i:2881913 original size:20 final size:19
Alignment explanation
Indices: 2881883--2881960 Score: 120
Period size: 20 Copynumber: 3.9 Consensus size: 19
2881873 TGAGTAGTCA
2881883 CAGGTGTATGGATACACTG
1 CAGGTGTATGGATACACTG
*
2881902 CATGGTGCATGGATACACTG
1 CA-GGTGTATGGATACACTG
2881922 CAGTGTGTATGGATACACTG
1 CAG-GTGTATGGATACACTG
2881942 CAGGGTGTATGGATACACT
1 CA-GGTGTATGGATACACT
2881961 TTGACACCCT
Statistics
Matches: 54, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
19 3 0.06
20 50 0.93
21 1 0.02
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.27
Consensus pattern (19 bp):
CAGGTGTATGGATACACTG
Found at i:2885473 original size:20 final size:20
Alignment explanation
Indices: 2885448--2885537 Score: 100
Period size: 20 Copynumber: 4.8 Consensus size: 20
2885438 GCAGTCACAT
*
2885448 GTGCATGGATGCACTACAGG
1 GTGCATGGATACACTACAGG
2885468 GTGCATGGATACACT-----
1 GTGCATGGATACACTACAGG
* *
2885483 GTGCATGGATACACTGCAGA
1 GTGCATGGATACACTACAGG
*
2885503 GTGCATGGATACACTGCAGG
1 GTGCATGGATACACTACAGG
*
2885523 GTGTATGGATACACT
1 GTGCATGGATACACT
2885538 TTGACACCCT
Statistics
Matches: 62, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
15 15 0.24
20 47 0.76
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (20 bp):
GTGCATGGATACACTACAGG
Found at i:2885486 original size:15 final size:15
Alignment explanation
Indices: 2885468--2885498 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2885458 GCACTACAGG
2885468 GTGCATGGATACACT
1 GTGCATGGATACACT
2885483 GTGCATGGATACACT
1 GTGCATGGATACACT
2885498 G
1 G
2885499 CAGAGTGCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (15 bp):
GTGCATGGATACACT
Found at i:2885507 original size:35 final size:35
Alignment explanation
Indices: 2885447--2885518 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
2885437 AGCAGTCACA
* *
2885447 TGTGCATGGATGCACTACAGGGTGCATGGATACAC
1 TGTGCATGGATACACTACAGAGTGCATGGATACAC
*
2885482 TGTGCATGGATACACTGCAGAGTGCATGGATACAC
1 TGTGCATGGATACACTACAGAGTGCATGGATACAC
2885517 TG
1 TG
2885519 CAGGGTGTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (35 bp):
TGTGCATGGATACACTACAGAGTGCATGGATACAC
Found at i:2890650 original size:27 final size:28
Alignment explanation
Indices: 2890598--2890660 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 28
2890588 ACACTTCGAG
* * *
2890598 GGTATTTTGGTTATTTTTACCTCATAAT
1 GGTATTTTCGTTAATTTTACCCCATAAT
*
2890626 GGTATTTTCG-TAATTTTACCCCATAGT
1 GGTATTTTCGTTAATTTTACCCCATAAT
*
2890653 GTTATTTT
1 GGTATTTT
2890661 TTGTAGTTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 21 0.70
28 9 0.30
ACGTcount: A:0.21, C:0.13, G:0.14, T:0.52
Consensus pattern (28 bp):
GGTATTTTCGTTAATTTTACCCCATAAT
Found at i:2893612 original size:18 final size:19
Alignment explanation
Indices: 2893579--2893628 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
2893569 ATTTTAAAAA
*
2893579 AAATAAATTGATAAAATATAT
1 AAAT-AATT-ATAAAATAAAT
2893600 AAAT-ATTATAAAATAAAT
1 AAATAATTATAAAATAAAT
*
2893618 ATATAATTATA
1 AAATAATTATA
2893629 CTAATTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 13 0.50
19 9 0.35
21 4 0.15
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (19 bp):
AAATAATTATAAAATAAAT
Found at i:2894792 original size:60 final size:60
Alignment explanation
Indices: 2894699--2894815 Score: 225
Period size: 60 Copynumber: 1.9 Consensus size: 60
2894689 ACATCAAAGG
2894699 TGAGTATATGTATATTGGAGATCCAGACAATGCCAAAGTAGCATTGTTACTTCAATGATT
1 TGAGTATATGTATATTGGAGATCCAGACAATGCCAAAGTAGCATTGTTACTTCAATGATT
*
2894759 TGAGTATATTTATATTGGAGATCCAGACAATGCCAAAGTAGCATTGTTACTTCAATG
1 TGAGTATATGTATATTGGAGATCCAGACAATGCCAAAGTAGCATTGTTACTTCAATG
2894816 CTTATCTGGT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (60 bp):
TGAGTATATGTATATTGGAGATCCAGACAATGCCAAAGTAGCATTGTTACTTCAATGATT
Found at i:2895769 original size:10 final size:9
Alignment explanation
Indices: 2895737--2895761 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2895727 AATTAAAGGG
2895737 AAAAAATAA
1 AAAAAATAA
2895746 AAAAAATAA
1 AAAAAATAA
2895755 AAAAAAT
1 AAAAAAT
2895762 GAATAAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAAAATAA
Found at i:2897037 original size:3 final size:3
Alignment explanation
Indices: 2897029--2897077 Score: 73
Period size: 3 Copynumber: 16.0 Consensus size: 3
2897019 AAAAACCTAC
2897029 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ATAT ATAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT A-AT AAT AAT AAT
2897075 AAT
1 AAT
2897078 TTTTTGTAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.05
3 35 0.80
4 7 0.16
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:2897540 original size:36 final size:36
Alignment explanation
Indices: 2897442--2897732 Score: 298
Period size: 36 Copynumber: 8.2 Consensus size: 36
2897432 AGGGTTTTTT
*
2897442 TTTGTTTCAAGAGAAATTGTCTCTAA-AGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTC-AAGAGAGACAAAA
* *
2897478 CTTTGTTTCAAGGGAAAATG-CATCAAGAGAGACAAAA
1 -TTTGTTTCAAGAGAAACTGTC-TCAAGAGAGACAAAA
2897515 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * *
2897551 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
2897588 TTTGTTTAAATGA-AAACATAT-TC-A-A-AG----AT
1 TTTGTTTCAA-GAGAAAC-TGTCTCAAGAGAGACAAAA
*
2897617 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
2897653 TTTGTTTCGAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
2897689 TTTGTTTCAAGAGAAAATTTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
2897725 CTTTGTTT
1 -TTTGTTT
2897733 TGAGTAAATT
Statistics
Matches: 213, Mismatches: 25, Indels: 32
0.79 0.09 0.12
Matches are distributed among these distances:
28 3 0.01
29 16 0.08
30 1 0.00
31 1 0.00
32 2 0.01
33 2 0.01
35 1 0.00
36 116 0.54
37 71 0.33
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.27
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:2897645 original size:138 final size:138
Alignment explanation
Indices: 2897479--2897732 Score: 386
Period size: 138 Copynumber: 1.8 Consensus size: 138
2897469 GAGACAAAAC
2897479 TTTGTTTCAAGGGAAAATGCATCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGA
1 TTTGTTTCAAGGGAAAATGCATCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGA
* * *
2897544 GACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAA-TTTGTTTAAATGAAAACATA
66 GACAAAA-TTAGTTCCAAAAGAAAATGTCTCAAGAGAGACAAAACTTTGTTTAAATGAAAACATA
2897608 TTCAAAGAT
130 TTCAAAGAT
* * *
2897617 TTTGTTTCAAGGGAAACTGTC-TCAAGAGAGACAAAATTTGTTTCGAGGGAAACTGTCTCAAGAG
1 TTTGTTTCAAGGGAAAATG-CATCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAG
* * * *
2897681 AGACAAAATTTGTTTCAAGAGAAAATTTCTCAAGAGAGACAAAACTTTGTTT
65 AGACAAAATTAGTTCCAAAAGAAAATGTCTCAAGAGAGACAAAACTTTGTTT
2897733 TGAGTAAATT
Statistics
Matches: 104, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
137 29 0.28
138 74 0.71
139 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (138 bp):
TTTGTTTCAAGGGAAAATGCATCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGA
GACAAAATTAGTTCCAAAAGAAAATGTCTCAAGAGAGACAAAACTTTGTTTAAATGAAAACATAT
TCAAAGAT
Found at i:2897749 original size:37 final size:35
Alignment explanation
Indices: 2897634--2897757 Score: 142
Period size: 36 Copynumber: 3.4 Consensus size: 35
2897624 CAAGGGAAAC
* * *
2897634 TGTCTCAAGAGAGACAAAATTTGTTTCGAGGGAAAC
1 TGTCTCAAGAGAGACAAAATTTGTTTAGA-GAAAAT
2897670 TGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAAAT
1 TGTCTCAAGAGAGACAAAATTTGTTT--AGAGAAAAT
* *
2897707 T-TCTCAAGAGAGACAAAACTTTGTTTTGAGTAAAT
1 TGTCTCAAGAGAGACAAAA-TTTGTTTAGAGAAAAT
*
2897742 TAGTCTCAAGCGAGAC
1 T-GTCTCAAGAGAGAC
2897758 GACCCCTTGT
Statistics
Matches: 77, Mismatches: 6, Indels: 9
0.84 0.07 0.10
Matches are distributed among these distances:
35 8 0.10
36 43 0.56
37 24 0.31
38 2 0.03
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (35 bp):
TGTCTCAAGAGAGACAAAATTTGTTTAGAGAAAAT
Found at i:2901102 original size:19 final size:20
Alignment explanation
Indices: 2901070--2901107 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
2901060 TTGCATAGGA
2901070 TTAGTTTAGGTTTA-ATTAT
1 TTAGTTTAGGTTTATATTAT
2901089 TTAG-TTAGGTTTTATATTA
1 TTAGTTTAGG-TTTATATTA
2901108 ATAGTTTCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.29
19 8 0.47
20 4 0.24
ACGTcount: A:0.26, C:0.00, G:0.16, T:0.58
Consensus pattern (20 bp):
TTAGTTTAGGTTTATATTAT
Found at i:2906657 original size:21 final size:20
Alignment explanation
Indices: 2906631--2906669 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
2906621 CTACATGGAC
2906631 AATATCGATAATCACCCTAGA
1 AATATCGATAATC-CCCTAGA
*
2906652 AATATCGATACTCCCCTA
1 AATATCGATAATCCCCTA
2906670 TGGAAATGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.38, C:0.28, G:0.08, T:0.26
Consensus pattern (20 bp):
AATATCGATAATCCCCTAGA
Found at i:2907570 original size:35 final size:35
Alignment explanation
Indices: 2907468--2907575 Score: 128
Period size: 36 Copynumber: 3.0 Consensus size: 35
2907458 CATATCACAT
* * * *
2907468 ATTATAATAAAGAGATAAAAATAACGAACCTTACAC
1 ATTATATTAAGGAGATAAAAACAA-AAACCTTACAC
2907504 ATTATATTAAGGAGATAAAAACAAAAGACCTTACAC
1 ATTATATTAAGGAGATAAAAACAAAA-ACCTTACAC
* *
2907540 ATTATGTTAAGGAGAT-GAAACAATAAACCTTACAC
1 ATTATATTAAGGAGATAAAAACAA-AAACCTTACAC
2907575 A
1 A
2907576 AGCCTTAAAC
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
35 17 0.27
36 47 0.73
ACGTcount: A:0.52, C:0.14, G:0.11, T:0.23
Consensus pattern (35 bp):
ATTATATTAAGGAGATAAAAACAAAAACCTTACAC
Found at i:2923215 original size:23 final size:23
Alignment explanation
Indices: 2923184--2923228 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2923174 ATTAAATTAG
*
2923184 GAAAATTCA-AATTTACCCTTAAT
1 GAAAATTCATAA-TTACCATTAAT
*
2923207 GAAACTTCATAATTACCATTAA
1 GAAAATTCATAATTACCATTAA
2923229 ACCAAGACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.44, C:0.18, G:0.04, T:0.33
Consensus pattern (23 bp):
GAAAATTCATAATTACCATTAAT
Found at i:2923263 original size:30 final size:31
Alignment explanation
Indices: 2923227--2923288 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
2923217 AATTACCATT
* *
2923227 AAACCAAGACACCT-AACCTTATCATCTTCC
1 AAACCAAAACAACTAAACCTTATCATCTTCC
2923257 AAACCAAAACAACTAAACCTTATCATCTTCC
1 AAACCAAAACAACTAAACCTTATCATCTTCC
2923288 A
1 A
2923289 TAAGTCAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 12 0.41
31 17 0.59
ACGTcount: A:0.42, C:0.34, G:0.02, T:0.23
Consensus pattern (31 bp):
AAACCAAAACAACTAAACCTTATCATCTTCC
Found at i:2928665 original size:18 final size:21
Alignment explanation
Indices: 2928642--2928681 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2928632 TTTCAATATC
2928642 TTATTT-T-TAAA-AAAATAA
1 TTATTTATCTAAATAAAATAA
2928660 TTATTTATCTAAATAAAATAA
1 TTATTTATCTAAATAAAATAA
2928681 T
1 T
2928682 CACACATTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
19 1 0.05
20 4 0.21
21 8 0.42
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (21 bp):
TTATTTATCTAAATAAAATAA
Found at i:2930087 original size:24 final size:24
Alignment explanation
Indices: 2930060--2930118 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
2930050 GCATAAACCA
* *
2930060 ATGAGACATTTGTAACTGAAACTC
1 ATGAGACATTTGTAACTAAAACAC
*
2930084 ATGAAAC-TGTTGTAACTAAAACAC
1 ATGAGACAT-TTGTAACTAAAACAC
2930108 ATGAGACATTT
1 ATGAGACATTT
2930119 AGGACTGAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 1 0.03
24 27 0.93
25 1 0.03
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (24 bp):
ATGAGACATTTGTAACTAAAACAC
Found at i:2933133 original size:2 final size:2
Alignment explanation
Indices: 2933126--2933172 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
2933116 GTTTTTCAAG
2933126 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2933168 TA TA T
1 TA TA T
2933173 TGTCAATTTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2933907 original size:30 final size:30
Alignment explanation
Indices: 2933871--2933937 Score: 134
Period size: 30 Copynumber: 2.2 Consensus size: 30
2933861 CTAAGTCGTC
2933871 CATGTCATCACCATTACGGTCCGTCTGTGT
1 CATGTCATCACCATTACGGTCCGTCTGTGT
2933901 CATGTCATCACCATTACGGTCCGTCTGTGT
1 CATGTCATCACCATTACGGTCCGTCTGTGT
2933931 CATGTCA
1 CATGTCA
2933938 GTGATCCGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.18, C:0.30, G:0.19, T:0.33
Consensus pattern (30 bp):
CATGTCATCACCATTACGGTCCGTCTGTGT
Found at i:2938204 original size:22 final size:22
Alignment explanation
Indices: 2938126--2938206 Score: 135
Period size: 22 Copynumber: 3.6 Consensus size: 22
2938116 CTCGTATAAA
2938126 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
*
2938149 TGCACCGAAGTACCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
2938171 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
2938193 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
2938207 ATATAATGAT
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
22 44 0.80
23 11 0.20
ACGTcount: A:0.26, C:0.30, G:0.26, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:2938862 original size:2 final size:2
Alignment explanation
Indices: 2938855--2938900 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
2938845 TCTCTTAAAC
2938855 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
2938897 AT AT
1 AT AT
2938901 TCACATGTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2939943 original size:21 final size:21
Alignment explanation
Indices: 2939919--2939963 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2939909 TCTTGTTCGT
* *
2939919 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2939940 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2939961 TTG
1 TTG
2939964 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2941428 original size:2 final size:2
Alignment explanation
Indices: 2941421--2941489 Score: 111
Period size: 2 Copynumber: 34.5 Consensus size: 2
2941411 TATGGAATAG
2941421 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
* * *
2941463 AT AT AT AT GT AT AT GT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2941490 GGAATCCAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2948350 original size:2 final size:2
Alignment explanation
Indices: 2948337--2948392 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
2948327 TTTAAGAAAA
2948337 AT AT AT -T A- 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
2948377 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
2948393 TTTTATTTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 50 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2948654 original size:18 final size:20
Alignment explanation
Indices: 2948628--2948667 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
2948618 ATATTAAAAA
*
2948628 TAAATAAATAT-TA-ATATT
1 TAAACAAATATATATATATT
2948646 TAAACAAATATATATATATT
1 TAAACAAATATATATATATT
2948666 TA
1 TA
2948668 TATGACTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 2 0.11
20 7 0.37
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
TAAACAAATATATATATATT
Found at i:2951099 original size:124 final size:113
Alignment explanation
Indices: 2950850--2951310 Score: 608
Period size: 113 Copynumber: 4.0 Consensus size: 113
2950840 GATAGAATCA
* *
2950850 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCT
1 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAATTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * * *
2950914 CATTATGAACTTTCTCTGGAAAAGTTGATGCATCGAGTGATGAATTCG
66 CATTATGAACTTTATCTGGAAATGTTGATCCATCTAGTGATGAATTCG
*
2950962 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAATTCTTCTTCCTTCTTCAGATGAGTTCTTCT
*
2951027 CATTATGAACTTTATCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAA-TCG
66 CATTATGAACTTTATCTGGAAATGTTGAT-C----C-A--T-C-T-AGTGAT-GAATTCG
*
2951086 AGCACAAA-TTTGAACAAGTTCTTCTCATTATGAAATTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AGCA-AAAGGTTGAACAAGTTCTTCTCATTATGAAATTCTTCTTCCTTCTTCAGATGAGTTCTTC
* * *
2951150 TTATTATGAAATTTATCTGGGAATGTTGATCCATCTAGTGATGAATTCG
65 TCATTATGAACTTTATCTGGAAATGTTGATCCATCTAGTGATGAATTCG
* *
2951199 AG-ATAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AGCA-AAAGGTTGAACAAGTTCTTCTCATTATGAAATTCTTCTTCCTTCTTCAGATGAGTTCTTC
* *
2951263 TCATTGTGAACTTTATCTGGAAATGTTGATCCAT-TGAGTGATGGATTC
65 TCATTATGAACTTTATCTGGAAATGTTGATCCATCT-AGTGATGAATTC
2951311 AAATCTTTGC
Statistics
Matches: 311, Mismatches: 21, Indels: 33
0.85 0.06 0.09
Matches are distributed among these distances:
112 53 0.17
113 149 0.48
114 1 0.00
115 1 0.00
116 1 0.00
118 2 0.01
119 2 0.01
121 1 0.00
122 1 0.00
123 1 0.00
124 93 0.30
125 6 0.02
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.39
Consensus pattern (113 bp):
AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAATTCTTCTTCCTTCTTCAGATGAGTTCTTCT
CATTATGAACTTTATCTGGAAATGTTGATCCATCTAGTGATGAATTCG
Found at i:2951227 original size:237 final size:236
Alignment explanation
Indices: 2950733--2951292 Score: 894
Period size: 237 Copynumber: 2.4 Consensus size: 236
2950723 GAATTAAGGC
*
2950733 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-TCCTTCTTCAGATGAGTTCTTCTCGTTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
** *
2950797 TGAACACT-TCTGAAAATGTTGATGATGATCTATCTCCTTCTGTGATAGAATCAAGCAAAAGGTT
66 TGAACTTTATCTGGAAATGTTGATGATGATCTATCTCCTTCTGTGATAGAATCAAGCAAAAGGTT
* *
2950861 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTT
131 GAACAAGTTCTTCTCATTATGAAATTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAAATT
* *
2950926 TCTCTGGAAAAGTTGATGCATCGAGTGATGAATTCGAGCAA
196 TATCTGGAAAAGTTGATCCATCGAGTGATGAATTCGAGCAA
2950967 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * *
2951032 TGAACTTTATCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAATCGAGCACAAA-TT
66 TGAACTTTATCTGGAAATGTTGATGATGATCTATCTCCTTCTGTGATAGAATCAAGCA-AAAGGT
* *
2951096 TGAACAAGTTCTTCTCATTATGAAATTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAAA
130 TGAACAAGTTCTTCTCATTATGAAATTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAAA
* * *
2951161 TTTATCTGGGAATGTTGATCCATCTAGTGATGAATTCGAG-ATA
194 TTTATCTGGAAAAGTTGATCCATCGAGTGATGAATTCGAGCA-A
* * *
2951204 AAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTG
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
2951269 TGAACTTTATCTGGAAATGTTGAT
66 TGAACTTTATCTGGAAATGTTGAT
2951293 CCATTGAGTG
Statistics
Matches: 302, Mismatches: 19, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
234 36 0.12
235 33 0.11
236 82 0.27
237 151 0.50
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (236 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
TGAACTTTATCTGGAAATGTTGATGATGATCTATCTCCTTCTGTGATAGAATCAAGCAAAAGGTT
GAACAAGTTCTTCTCATTATGAAATTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAAATT
TATCTGGAAAAGTTGATCCATCGAGTGATGAATTCGAGCAA
Found at i:2951691 original size:22 final size:22
Alignment explanation
Indices: 2951663--2951716 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
2951653 AATAAAGCTT
*
2951663 TCATCTTTGAAAAGAGAATTTA
1 TCATCTTTGAAAAGAGAATCTA
*
2951685 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
2951707 TCATCTTTGA
1 TCATCTTTGA
2951717 GGAATGTAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:2954440 original size:23 final size:23
Alignment explanation
Indices: 2954414--2954462 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
2954404 TAACAAAGTT
2954414 GAACTGTTTACAAACATGTACAG
1 GAACTGTTTACAAACATGTACAG
2954437 GAACTGTTTACAAACATGTACAG
1 GAACTGTTTACAAACATGTACAG
2954460 GAA
1 GAA
2954463 GTGCCAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.24
Consensus pattern (23 bp):
GAACTGTTTACAAACATGTACAG
Found at i:2955233 original size:18 final size:18
Alignment explanation
Indices: 2955207--2955244 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2955197 ATATTAAAAA
*
2955207 TAAATAAATAT-TAATATT
1 TAAACAAATATAT-ATATT
2955225 TAAACAAATATATATATT
1 TAAACAAATATATATATT
2955243 TA
1 TA
2955245 TATGACTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAACAAATATATATATT
Found at i:2960114 original size:17 final size:18
Alignment explanation
Indices: 2960092--2960138 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
2960082 TCTTTTGAAA
2960092 ATTTTATATTATTA-TAT
1 ATTTTATATTATTATTAT
* * *
2960109 ATTTTAGATTTTTATTTGT
1 ATTTTATATTATTA-TTAT
2960128 ATTTTATATTA
1 ATTTTATATTA
2960139 ATAATATGTA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
17 12 0.52
19 11 0.48
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (18 bp):
ATTTTATATTATTATTAT
Found at i:2961714 original size:86 final size:86
Alignment explanation
Indices: 2961569--2961739 Score: 333
Period size: 86 Copynumber: 2.0 Consensus size: 86
2961559 ATGATTACTC
*
2961569 TCTCCATGAGTATGAATGTTTATAGTAGTGCGGCATATGTATGTTTTTTAGTGGTTAGGTTAAGA
1 TCTCCATGAGTATGAATGTCTATAGTAGTGCGGCATATGTATGTTTTTTAGTGGTTAGGTTAAGA
2961634 TAATGAATTAGATCCAGACTT
66 TAATGAATTAGATCCAGACTT
2961655 TCTCCATGAGTATGAATGTCTATAGTAGTGCGGCATATGTATGTTTTTTAGTGGTTAGGTTAAGA
1 TCTCCATGAGTATGAATGTCTATAGTAGTGCGGCATATGTATGTTTTTTAGTGGTTAGGTTAAGA
2961720 TAATGAATTAGATCCAGACT
66 TAATGAATTAGATCCAGACT
2961740 CACACTTTCC
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 84 1.00
ACGTcount: A:0.28, C:0.10, G:0.23, T:0.39
Consensus pattern (86 bp):
TCTCCATGAGTATGAATGTCTATAGTAGTGCGGCATATGTATGTTTTTTAGTGGTTAGGTTAAGA
TAATGAATTAGATCCAGACTT
Found at i:2965812 original size:16 final size:16
Alignment explanation
Indices: 2965788--2965818 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2965778 GGGTTAGGGT
*
2965788 TAGGTATTTAGATTTA
1 TAGGGATTTAGATTTA
2965804 TAGGGATTTAGATTT
1 TAGGGATTTAGATTT
2965819 TTTATAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.48
Consensus pattern (16 bp):
TAGGGATTTAGATTTA
Found at i:2966711 original size:21 final size:21
Alignment explanation
Indices: 2966668--2966720 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
2966658 TTTGACTATT
* *
2966668 GCATTGCGATTTTCCAAATTC
1 GCATTGCGATTTTACAAAATC
* *
2966689 GCGTTGCGATTTTAGAAAATC
1 GCATTGCGATTTTACAAAATC
*
2966710 GCAATGCGATT
1 GCATTGCGATT
2966721 CTGACTATCG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (21 bp):
GCATTGCGATTTTACAAAATC
Found at i:2966732 original size:20 final size:20
Alignment explanation
Indices: 2966707--2966828 Score: 115
Period size: 20 Copynumber: 6.0 Consensus size: 20
2966697 ATTTTAGAAA
*
2966707 ATCGCAATGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* * **
2966727 ATCGCAATGCAATAAT-ACAT
1 ATCGCAACGCGATTCTGAC-T
2966747 AATCGCAACGCGATTCTGACT
1 -ATCGCAACGCGATTCTGACT
*
2966768 ATCGCAACGCGATAATATG--T
1 ATCGCAACGCGAT--TCTGACT
2966788 AATCGCAACGCGATTCTGACT
1 -ATCGCAACGCGATTCTGACT
*
2966809 ATCGCAACGCGAGTCTGACT
1 ATCGCAACGCGATTCTGACT
2966829 TTTGCAACAT
Statistics
Matches: 84, Mismatches: 10, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
19 5 0.06
20 47 0.56
21 27 0.32
22 5 0.06
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:2966819 original size:41 final size:41
Alignment explanation
Indices: 2966706--2966820 Score: 185
Period size: 41 Copynumber: 2.8 Consensus size: 41
2966696 GATTTTAGAA
* * *
2966706 AATCGCAATGCGATTCTGACTATCGCAATGCAATAATACAT
1 AATCGCAACGCGATTCTGACTATCGCAACGCGATAATACAT
**
2966747 AATCGCAACGCGATTCTGACTATCGCAACGCGATAATATGT
1 AATCGCAACGCGATTCTGACTATCGCAACGCGATAATACAT
2966788 AATCGCAACGCGATTCTGACTATCGCAACGCGA
1 AATCGCAACGCGATTCTGACTATCGCAACGCGA
2966821 GTCTGACTTT
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 69 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.23
Consensus pattern (41 bp):
AATCGCAACGCGATTCTGACTATCGCAACGCGATAATACAT
Found at i:2967684 original size:24 final size:24
Alignment explanation
Indices: 2967657--2967710 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2967647 GTATTCAAAA
2967657 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
2967681 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
2967705 TTTGAT
1 TTTGAT
2967711 GATGTTTCAG
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:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:2967926 original size:14 final size:15
Alignment explanation
Indices: 2967900--2967932 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
2967890 AGAAAAAGAA
2967900 GAAGAAGAAATCCCC
1 GAAGAAGAAATCCCC
2967915 GAAGAA-AAATCCCC
1 GAAGAAGAAATCCCC
2967929 GAAG
1 GAAG
2967933 TAAATACCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.48, C:0.24, G:0.21, T:0.06
Consensus pattern (15 bp):
GAAGAAGAAATCCCC
Found at i:2970303 original size:140 final size:140
Alignment explanation
Indices: 2970050--2970472 Score: 792
Period size: 140 Copynumber: 3.0 Consensus size: 140
2970040 GCAAACGTTT
*
2970050 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATTTATTAGTAACTTGATT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGATT
2970115 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTGTTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTGTTACACATTCATTTGAATATCGCAACG
2970180 CGAATTTGAC
131 CGAATTTGAC
2970190 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGATT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGATT
*
2970255 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTGTTACATATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTGTTACACATTCATTTGAATATCGCAACG
2970320 CGAATTTGAC
131 CGAATTTGAC
* *
2970330 TATTATGTGTATTTTATGTATAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGATT
* *
2970395 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAGCG
66 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTGTTACACATTCATTTGAATATCGCAACG
2970460 CGAATTTGAC
131 CGAATTTGAC
2970470 TAT
1 TAT
2970473 CGCAACGCGA
Statistics
Matches: 276, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 276 1.00
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (140 bp):
TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGATT
TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTGTTACACATTCATTTGAATATCGCAACG
CGAATTTGAC
Found at i:2970468 original size:20 final size:20
Alignment explanation
Indices: 2970443--2970517 Score: 107
Period size: 20 Copynumber: 3.8 Consensus size: 20
2970433 TTACACATTC
*
2970443 ATTTGAATATCGCAGCGCGA
1 ATTTGAATATCGCAACGCGA
*
2970463 ATTTGACTATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
*
2970483 ATTTGACTATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
2970503 ATTT-AACTATCGCAA
1 ATTTGAA-TATCGCAA
2970518 TAGCCTTTGT
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
19 1 0.02
20 50 0.98
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.27
Consensus pattern (20 bp):
ATTTGAATATCGCAACGCGA
Found at i:2970941 original size:42 final size:42
Alignment explanation
Indices: 2970836--2970945 Score: 141
Period size: 42 Copynumber: 2.6 Consensus size: 42
2970826 TAAAATGGTG
* * * * *
2970836 GGAGGGACCTCTTCAACGATGACAGGGGCCTCTTGAACGGTG
1 GGAGAGACCTCTTGAACGATGATAGGGGCCTCTTGAACGATA
**
2970878 GGAAGAGA-CTCTTGAGGGATGATAGGGGCCTCTTGAACGATA
1 GG-AGAGACCTCTTGAACGATGATAGGGGCCTCTTGAACGATA
2970920 GGAGAGACCTCTTGAACGATGATAGG
1 GGAGAGACCTCTTGAACGATGATAGG
2970946 TGAGTCGGGC
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
41 5 0.09
42 48 0.84
43 4 0.07
ACGTcount: A:0.26, C:0.18, G:0.35, T:0.20
Consensus pattern (42 bp):
GGAGAGACCTCTTGAACGATGATAGGGGCCTCTTGAACGATA
Found at i:2971360 original size:20 final size:20
Alignment explanation
Indices: 2971335--2971422 Score: 106
Period size: 20 Copynumber: 4.4 Consensus size: 20
2971325 GAAACTTAAA
2971335 ATCGCAACACGGAAATGACT
1 ATCGCAACACGGAAATGACT
** *
2971355 ATCGCAATGCGAAAATGACT
1 ATCGCAACACGGAAATGACT
*
2971375 ATCCCAACACGGAAATGACT
1 ATCGCAACACGGAAATGACT
* *
2971395 ATCGCAACGC-GAATTTGACT
1 ATCGCAACACGGAA-ATGACT
2971415 ATCGCAAC
1 ATCGCAAC
2971423 GGGATAATCA
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
19 3 0.05
20 54 0.95
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (20 bp):
ATCGCAACACGGAAATGACT
Found at i:2971394 original size:40 final size:40
Alignment explanation
Indices: 2971339--2971422 Score: 132
Period size: 40 Copynumber: 2.1 Consensus size: 40
2971329 CTTAAAATCG
*
2971339 CAACACGGAAATGACTATCGCAATGCGAAAATGACTATCC
1 CAACACGGAAATGACTATCGCAACGCGAAAATGACTATCC
** *
2971379 CAACACGGAAATGACTATCGCAACGCGAATTTGACTATCG
1 CAACACGGAAATGACTATCGCAACGCGAAAATGACTATCC
2971419 CAAC
1 CAAC
2971423 GGGATAATCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (40 bp):
CAACACGGAAATGACTATCGCAACGCGAAAATGACTATCC
Found at i:2971451 original size:32 final size:33
Alignment explanation
Indices: 2971415--2971493 Score: 88
Period size: 32 Copynumber: 2.4 Consensus size: 33
2971405 GAATTTGACT
* * * *
2971415 ATCGCAACGGGATAATCACAATGCGAAA-TAAA
1 ATCGCAACGAGAAAATCACAACGCGAAACCAAA
* *
2971447 ATCGCAATGAGAAAATCGCAACGCGAAACCAAA
1 ATCGCAACGAGAAAATCACAACGCGAAACCAAA
*
2971480 ATCGCAACGCGAAA
1 ATCGCAACGAGAAA
2971494 CTAAATTCGC
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
32 23 0.61
33 15 0.39
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGAGAAAATCACAACGCGAAACCAAA
Found at i:2971503 original size:19 final size:19
Alignment explanation
Indices: 2971458--2971494 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
2971448 TCGCAATGAG
2971458 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
2971477 AAAATCGCAACGCGAAAC
1 AAAATCGCAACGCGAAAC
2971495 TAAATTCGCG
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:0.49, C:0.30, G:0.16, T:0.05
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACC
Found at i:2971566 original size:20 final size:21
Alignment explanation
Indices: 2971538--2971605 Score: 79
Period size: 20 Copynumber: 3.4 Consensus size: 21
2971528 CGATTATCCT
2971538 GTTGCGATAGTCAAATT-CGC
1 GTTGCGATAGTCAAATTCCGC
* *
2971558 GTTGTGATAGTC-ATTTCCGC
1 GTTGCGATAGTCAAATTCCGC
*
2971578 GTTGCGATAGTC-ATTTCCGC
1 GTTGCGATAGTCAAATTCCGC
*
2971598 ATTGCGAT
1 GTTGCGAT
2971606 TTTAAGTTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
19 3 0.07
20 40 0.93
ACGTcount: A:0.19, C:0.21, G:0.25, T:0.35
Consensus pattern (21 bp):
GTTGCGATAGTCAAATTCCGC
Found at i:2973536 original size:20 final size:20
Alignment explanation
Indices: 2973499--2973536 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2973489 TCTGAAACTT
*
2973499 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACAAAAATG
*
2973519 AAAATCGTAACACAAAAA
1 AAAATCGCAACACAAAAA
2973537 AGACCATCGC
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:0.61, C:0.18, G:0.11, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACACAAAAATG
Found at i:2973974 original size:22 final size:22
Alignment explanation
Indices: 2973939--2974007 Score: 90
Period size: 22 Copynumber: 3.2 Consensus size: 22
2973929 TCTGAGAGAT
2973939 GGAGATA--GACGGATTTCG-C
1 GGAGATAGGGACGGATTTCGTC
*
2973958 AGGAGATAGGGACGGATTGCGTC
1 -GGAGATAGGGACGGATTTCGTC
*
2973981 GGAGATGGGGACGGATTTCGTC
1 GGAGATAGGGACGGATTTCGTC
2974003 GGAGA
1 GGAGA
2974008 GAGTGAGAGA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
20 7 0.16
22 35 0.81
23 1 0.02
ACGTcount: A:0.25, C:0.13, G:0.43, T:0.19
Consensus pattern (22 bp):
GGAGATAGGGACGGATTTCGTC
Found at i:2974194 original size:20 final size:20
Alignment explanation
Indices: 2974171--2974269 Score: 95
Period size: 20 Copynumber: 5.2 Consensus size: 20
2974161 TTATCGCAAC
*
2974171 GCGATAGTCAGAATCGCATT
1 GCGATAGTCAGAATCGCGTT
2974191 GCGAT--T----ATCGCGTT
1 GCGATAGTCAGAATCGCGTT
2974205 GCGATAGTCAGAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
* * * *
2974225 GCGAT-TTACATATTCGCATT
1 GCGATAGT-CAGAATCGCGTT
2974245 GCGATAGTCAGAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
2974265 GCGAT
1 GCGAT
2974270 TTACATATTC
Statistics
Matches: 62, Mismatches: 9, Indels: 16
0.71 0.10 0.18
Matches are distributed among these distances:
14 12 0.19
16 1 0.02
18 1 0.02
19 1 0.02
20 46 0.74
21 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.29
Consensus pattern (20 bp):
GCGATAGTCAGAATCGCGTT
Found at i:2974258 original size:40 final size:40
Alignment explanation
Indices: 2974171--2974289 Score: 178
Period size: 40 Copynumber: 3.1 Consensus size: 40
2974161 TTATCGCAAC
* *
2974171 GCGATAGTCAGAATCGCATTGCGA--T---TA-TCGCGTT
1 GCGATAGTCAGAATCGCGTTGCGATTTACATATTCGCATT
2974205 GCGATAGTCAGAATCGCGTTGCGATTTACATATTCGCATT
1 GCGATAGTCAGAATCGCGTTGCGATTTACATATTCGCATT
2974245 GCGATAGTCAGAATCGCGTTGCGATTTACATATTCGCATT
1 GCGATAGTCAGAATCGCGTTGCGATTTACATATTCGCATT
2974285 GCGAT
1 GCGAT
2974290 TTTCTAAAAT
Statistics
Matches: 77, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
34 23 0.30
36 1 0.01
39 2 0.03
40 51 0.66
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.31
Consensus pattern (40 bp):
GCGATAGTCAGAATCGCGTTGCGATTTACATATTCGCATT
Found at i:2974281 original size:20 final size:20
Alignment explanation
Indices: 2974218--2974291 Score: 87
Period size: 20 Copynumber: 3.7 Consensus size: 20
2974208 ATAGTCAGAA
*
2974218 TCGCGTTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
* * *
2974238 TCGCATTGCGATAGT-CAGAA
1 TCGCATTGCGAT-TTACATAT
*
2974258 TCGCGTTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
2974278 TCGCATTGCGATTT
1 TCGCATTGCGATTT
2974292 TCTAAAATCG
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
19 1 0.02
20 41 0.95
21 1 0.02
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:2974309 original size:21 final size:21
Alignment explanation
Indices: 2974285--2974331 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2974275 TATTCGCATT
*
2974285 GCGATTTTCTAAAATCGCAAC
1 GCGATTTTCGAAAATCGCAAC
* * *
2974306 GCGAATTTGGAAAATCGCAAT
1 GCGATTTTCGAAAATCGCAAC
2974327 GCGAT
1 GCGAT
2974332 AGTCAAAATC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (21 bp):
GCGATTTTCGAAAATCGCAAC
Found at i:2974400 original size:19 final size:19
Alignment explanation
Indices: 2974376--2974412 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2974366 TGCGATAATG
* *
2974376 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTACGATTTA
2974395 GAGATCGCATTACGATTT
1 GAGATCGCATTACGATTT
2974413 TATTGGTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTACGATTTA
Found at i:2975317 original size:21 final size:23
Alignment explanation
Indices: 2975273--2975320 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
2975263 CGTATAAGTA
*
2975273 TAAATTAGTTAAAAATTTAAAGG
1 TAAATTAGTTAAAAATTAAAAGG
*
2975296 TAAATTA-TTTAAAA-TAAAAGG
1 TAAATTAGTTAAAAATTAAAAGG
2975317 TAAA
1 TAAA
2975321 CTATACCAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 10 0.43
22 6 0.26
23 7 0.30
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.33
Consensus pattern (23 bp):
TAAATTAGTTAAAAATTAAAAGG
Found at i:2975884 original size:30 final size:29
Alignment explanation
Indices: 2975850--2976222 Score: 206
Period size: 30 Copynumber: 12.6 Consensus size: 29
2975840 TTAAATTCAC
* *
2975850 ATATTAACATTAAAAATGTAATTTATTTTT
1 ATATTAAC-TTAAAAATATATTTTATTTTT
*
2975880 ATATTAACTTATTAAATATATTTTATTATTT
1 ATATTAACTTA-AAAATATATTTTATT-TTT
* * *
2975911 -TTTTAA-TCTAAAAATATAGTTTATTCTT
1 ATATTAACT-TAAAAATATATTTTATTTTT
* *
2975939 ATTTTAACTTAAAAATATATTTTAGTCTTT
1 ATATTAACTTAAAAATATATTTTA-TTTTT
* * *
2975969 ATATTAAGTTAAAAATATATTTAATTCTT
1 ATATTAACTTAAAAATATATTTTATTTTT
* * * * * *
2975998 ATCTTAACTTATTACATAAATTATATTCTT
1 ATATTAACTTA-AAAATATATTTTATTTTT
* * *
2976028 A-ACTTAAATTATTAAATATATTTTATTCTT
1 ATA-TTAACTTA-AAAATATATTTTATTTTT
** * * * * *
2976058 ACCTTAAATTATTAAATATAATTAATTCTT
1 ATATTAACTTA-AAAATATATTTTATTTTT
* * * *
2976088 ATTTTAACTTAAAACGTATCTTTTATTCTT
1 ATATTAACTTAAAA-ATATATTTTATTTTT
*
2976118 ATCTTAACTTAAAAATATATTTT-TATTTT
1 ATATTAACTTAAAAATATATTTTAT-TTTT
*
2976147 A-ACT-AC--AAAAATATATTTTATTTTT
1 ATATTAACTTAAAAATATATTTTATTTTT
*
2976172 -TATCTAAACTAAAAATATATATATTATATTTTT
1 ATAT-T-AACTTAAAA-ATATAT-TT-TATTTTT
* * *
2976205 ATCTTAAATTTAAAATAT
1 ATATTAACTTAAAAATAT
2976223 TATCAAAATA
Statistics
Matches: 272, Mismatches: 49, Indels: 43
0.75 0.13 0.12
Matches are distributed among these distances:
25 18 0.07
26 2 0.01
27 2 0.01
28 6 0.02
29 62 0.23
30 151 0.56
31 13 0.05
32 8 0.03
33 8 0.03
34 2 0.01
ACGTcount: A:0.40, C:0.07, G:0.01, T:0.51
Consensus pattern (29 bp):
ATATTAACTTAAAAATATATTTTATTTTT
Found at i:2975925 original size:29 final size:29
Alignment explanation
Indices: 2975893--2975997 Score: 115
Period size: 29 Copynumber: 3.6 Consensus size: 29
2975883 TTAACTTATT
*
2975893 AAATATATTTTATTATTTTTTTAATCTAA
1 AAATATATTTTATTCTTTTTTTAATCTAA
* *
2975922 AAATATAGTTTATTCTTATTTTAA-CTTAA
1 AAATATATTTTATTCTTTTTTTAATC-TAA
* *
2975951 AAATATATTTTAGTCTTTATATTAAGT-TAA
1 AAATATATTTTATTCTTT-TTTTAA-TCTAA
*
2975981 AAATATATTTAATTCTT
1 AAATATATTTTATTCTT
2975998 ATCTTAACTT
Statistics
Matches: 63, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
28 1 0.02
29 39 0.62
30 23 0.37
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (29 bp):
AAATATATTTTATTCTTTTTTTAATCTAA
Found at i:2976057 original size:60 final size:58
Alignment explanation
Indices: 2975853--2976222 Score: 193
Period size: 59 Copynumber: 6.2 Consensus size: 58
2975843 AATTCACATA
* * * * * * * **
2975853 TTAACATTAAAAATGTAATTTATTTTTATATTAACTTATTAAATATATTTTATTATT-TT
1 TTAA-ATT-AAAATATATTTTATTCTTATCTTAACTTATTAAATATAATTAATTCTTAAC
* * * * * * *
2975912 TTTAATCTAAAAATATAGTTTATTCTTATTTTAACTTA-AAAATATATTTTAGTCTTTATA-
1 TTAAAT-T-AAAATATATTTTATTCTTATCTTAACTTATTAAATATAATTAATTC-TTA-AC
* * *
2975972 TTAAGTTAAAAATATATTTAATTCTTATCTTAACTTATTACATA-AATTATATTCTTAAC
1 TTAAATT-AAAATATATTTTATTCTTATCTTAACTTATTAAATATAATTA-ATTCTTAAC
* * **
2976031 TTAAATTATTAAATATATTTTATTCTTACCTTAAATTATTAAATATAATTAATTCTTATT
1 TTAAATTA--AAATATATTTTATTCTTATCTTAACTTATTAAATATAATTAATTCTTAAC
* * * * *
2976091 TTAACTTAAAACGTATCTTTTATTCTTATCTTAACTTA-AAAATATATTTTTATT-TTAAC
1 TTAAATTAAAA--TATATTTTATTCTTATCTTAACTTATTAAATATA-ATTAATTCTTAAC
* * * ** * *
2976150 -TACA--AAAATATATTTTATTTTTTATCTAAAC-TAAAAATATATATATTATATTTTTATC
1 TTAAATTAAAATATATTTTA-TTCTTATCTTAACTTATTAA-ATATA-ATTA-ATTCTTAAC
2976208 TTAAATTTAAAATAT
1 TTAAA-TTAAAATAT
2976223 TATCAAAATA
Statistics
Matches: 245, Mismatches: 44, Indels: 41
0.74 0.13 0.12
Matches are distributed among these distances:
54 10 0.04
55 14 0.06
56 12 0.05
57 3 0.01
58 26 0.11
59 85 0.35
60 83 0.34
61 5 0.02
62 7 0.03
ACGTcount: A:0.40, C:0.07, G:0.01, T:0.51
Consensus pattern (58 bp):
TTAAATTAAAATATATTTTATTCTTATCTTAACTTATTAAATATAATTAATTCTTAAC
Found at i:2976144 original size:90 final size:89
Alignment explanation
Indices: 2975930--2976140 Score: 244
Period size: 90 Copynumber: 2.4 Consensus size: 89
2975920 AAAAATATAG
* * * * *
2975930 TTTATTCTTATTTTAACTTAAAAATATATTTTAGTCTTTATATTAAGTTAAAAATATATTTAATT
1 TTTATTCTTATCTTAACTTAAAAATATATTTTATTCTTTACATTAAATTAAAAATATAATTAATT
**
2975995 CTTATCTTAACTTATTACATAAAT
66 CTTATCTTAACTTAAAACATAAAT
* * * * * *
2976019 TATATTCTTAACTTAAATTATTAAATATATTTTATTC-TTACCTTAAATTATTAAATATAATTAA
1 TTTATTCTTATCTTAACTTA-AAAATATATTTTATTCTTTACATTAAATTA-AAAATATAATTAA
* * **
2976083 TTCTTATTTTAACTTAAAACGTATCT
64 TTCTTATCTTAACTTAAAACATAAAT
2976109 TTTATTCTTATCTTAACTTAAAAATATATTTT
1 TTTATTCTTATCTTAACTTAAAAATATATTTT
2976141 TATTTTAACT
Statistics
Matches: 99, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
89 37 0.37
90 62 0.63
ACGTcount: A:0.38, C:0.09, G:0.01, T:0.52
Consensus pattern (89 bp):
TTTATTCTTATCTTAACTTAAAAATATATTTTATTCTTTACATTAAATTAAAAATATAATTAATT
CTTATCTTAACTTAAAACATAAAT
Found at i:2976149 original size:54 final size:54
Alignment explanation
Indices: 2976086--2976191 Score: 135
Period size: 54 Copynumber: 2.0 Consensus size: 54
2976076 TAATTAATTC
** * *
2976086 TTATTTTAACTTA-AAACGTATCTTTTA-TTCTTATCTTAACTTAAAAATATATTT
1 TTATTTTAAC-TACAAAAATATATTTTATTTCTTATCTAAAC-TAAAAATATATTT
*
2976140 TTATTTTAACTACAAAAATATATTTTATTTTTTATCTAAACTAAAAATATAT
1 TTATTTTAACTACAAAAATATATTTTATTTCTTATCTAAACTAAAAATATAT
2976192 ATATTATATT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
53 2 0.04
54 32 0.71
55 11 0.24
ACGTcount: A:0.40, C:0.09, G:0.01, T:0.50
Consensus pattern (54 bp):
TTATTTTAACTACAAAAATATATTTTATTTCTTATCTAAACTAAAAATATATTT
Found at i:2976162 original size:25 final size:24
Alignment explanation
Indices: 2976111--2976170 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
2976101 ACGTATCTTT
* * *
2976111 TATTCTTATCTTAACTTAAAAATA
1 TATTTTTATTTTAACTCAAAAATA
2976135 TATTTTTATTTTAACTACAAAAATA
1 TATTTTTATTTTAACT-CAAAAATA
2976160 TA-TTTTATTTT
1 TATTTTTATTTT
2976171 TTATCTAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
24 23 0.72
25 9 0.28
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.53
Consensus pattern (24 bp):
TATTTTTATTTTAACTCAAAAATA
Found at i:2976172 original size:31 final size:32
Alignment explanation
Indices: 2976133--2976211 Score: 108
Period size: 31 Copynumber: 2.5 Consensus size: 32
2976123 AACTTAAAAA
* *
2976133 TATATTTTTATTTTAACTACAAAA-ATATATTT
1 TATATTTTTATCTTAACTA-AAAATATATATAT
*
2976165 TAT-TTTTTATCTAAACTAAAAATATATATAT
1 TATATTTTTATCTTAACTAAAAATATATATAT
2976196 TATATTTTTATCTTAA
1 TATATTTTTATCTTAA
2976212 ATTTAAAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
30 4 0.10
31 23 0.56
32 14 0.34
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (32 bp):
TATATTTTTATCTTAACTAAAAATATATATAT
Found at i:2976202 original size:33 final size:32
Alignment explanation
Indices: 2976132--2976222 Score: 89
Period size: 31 Copynumber: 2.8 Consensus size: 32
2976122 TAACTTAAAA
* *
2976132 ATATATTTTTATTTTAACTACAAAA-ATATATTT
1 ATAT-TTTTTATCTAAACTA-AAAATATATATTT
2976165 -TATTTTTTATCTAAACTAAAAATATATATATT
1 ATATTTTTTATCTAAACTAAAAATATATAT-TT
* *
2976197 ATA-TTTTTATCTTAAATTTAAAATAT
1 ATATTTTTTATC-TAAACTAAAAATAT
2976223 TATCAAAATA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
30 4 0.08
31 19 0.38
32 13 0.26
33 14 0.28
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (32 bp):
ATATTTTTTATCTAAACTAAAAATATATATTT
Found at i:2976318 original size:34 final size:29
Alignment explanation
Indices: 2976229--2976319 Score: 110
Period size: 29 Copynumber: 3.1 Consensus size: 29
2976219 ATATTATCAA
* *
2976229 AATAAAATATAAATATTTAAGTTAAGATAAG
1 AATAAAATAT--ATTTTTAATTTAAGATAAG
*
2976260 AATAAATTATATTTTTAATTTAAGATAAG
1 AATAAAATATATTTTTAATTTAAGATAAG
* * *
2976289 ATTAAAATATATTTTTAAATTAAAATAAG
1 AATAAAATATATTTTTAATTTAAGATAAG
2976318 AA
1 AA
2976320 GGTTCCATGT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
29 43 0.83
31 9 0.17
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (29 bp):
AATAAAATATATTTTTAATTTAAGATAAG
Found at i:2979087 original size:25 final size:25
Alignment explanation
Indices: 2979049--2979106 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
2979039 AGCACCTATG
* *
2979049 GTGCAATTCTACGAGACACTTACAA
1 GTGCAATACAACGAGACACTTACAA
* *
2979074 GTGCAATACAACGAGGCACTTTCAA
1 GTGCAATACAACGAGACACTTACAA
2979099 GTGCAATA
1 GTGCAATA
2979107 TCAATTCTAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.22
Consensus pattern (25 bp):
GTGCAATACAACGAGACACTTACAA
Found at i:2979439 original size:18 final size:19
Alignment explanation
Indices: 2979416--2979463 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
2979406 TGAGAGTAAA
*
2979416 AATATAAGAAAA-AGGAAC
1 AATATAAGAAAATAGAAAC
*
2979434 AATAT-AGAAAATAGAAAT
1 AATATAAGAAAATAGAAAC
*
2979452 ATTATAAGAAAA
1 AATATAAGAAAA
2979464 GAAAAAGTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 6 0.24
18 13 0.52
19 6 0.24
ACGTcount: A:0.67, C:0.02, G:0.12, T:0.19
Consensus pattern (19 bp):
AATATAAGAAAATAGAAAC
Found at i:2990365 original size:18 final size:18
Alignment explanation
Indices: 2990342--2990389 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
2990332 CCAACTCTAG
*
2990342 TTGGGTCAACA-CTAGGGC
1 TTGGGTCAAAATC-AGGGC
2990360 TTGGGTCAAAATCAGGGC
1 TTGGGTCAAAATCAGGGC
2990378 TTGGGTCAAAAT
1 TTGGGTCAAAAT
2990390 GACCTTCAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 27 0.96
19 1 0.04
ACGTcount: A:0.27, C:0.17, G:0.31, T:0.25
Consensus pattern (18 bp):
TTGGGTCAAAATCAGGGC
Found at i:2993502 original size:23 final size:23
Alignment explanation
Indices: 2993459--2993503 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2993449 AATACATCCA
*
2993459 AAATAATATAAATACTGAATACC
1 AAATAATATAAATACTAAATACC
*
2993482 AAATAATAT-TATGACTAAATAC
1 AAATAATATAAAT-ACTAAATAC
2993504 ATAAAAAAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.56, C:0.11, G:0.04, T:0.29
Consensus pattern (23 bp):
AAATAATATAAATACTAAATACC
Found at i:2997219 original size:44 final size:45
Alignment explanation
Indices: 2997118--2997224 Score: 119
Period size: 44 Copynumber: 2.4 Consensus size: 45
2997108 AGTAGACCTC
* * * *
2997118 GGTCACACAACATCAACATCTCATAAGTATCTCAGGAGAGGTCCA
1 GGTCACACAACATCGACACCTCATAAATACCTCAGGAGAGGTCCA
* * **
2997163 GGTCACATAACATCGACACCTC-TAAATACCTTAGGCTAGGTCC-
1 GGTCACACAACATCGACACCTCATAAATACCTCAGGAGAGGTCCA
2997206 GAGTCACACAACATCGACA
1 G-GTCACACAACATCGACA
2997225 ACTTGCCTGG
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
43 1 0.02
44 32 0.62
45 19 0.37
ACGTcount: A:0.35, C:0.29, G:0.17, T:0.20
Consensus pattern (45 bp):
GGTCACACAACATCGACACCTCATAAATACCTCAGGAGAGGTCCA
Found at i:2997484 original size:17 final size:17
Alignment explanation
Indices: 2997462--2997496 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2997452 GTTTCTATGG
2997462 TTATCACACAATTATTA
1 TTATCACACAATTATTA
**
2997479 TTATCACATTATTATTA
1 TTATCACACAATTATTA
2997496 T
1 T
2997497 AAGTTTTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49
Consensus pattern (17 bp):
TTATCACACAATTATTA
Found at i:3002943 original size:21 final size:22
Alignment explanation
Indices: 3002917--3002963 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
3002907 GAATCGGTAC
*
3002917 CCCCTT-GTATGGGTACCGATT
1 CCCCTTGGAATGGGTACCGATT
**
3002938 CCCCTTGGAATGGGTATTGATT
1 CCCCTTGGAATGGGTACCGATT
3002960 CCCC
1 CCCC
3002964 CTTGAGGGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.15, C:0.30, G:0.23, T:0.32
Consensus pattern (22 bp):
CCCCTTGGAATGGGTACCGATT
Done.