Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009604.1 Hibiscus syriacus cultivar Beakdansim tig00116984_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: 3548142
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 17
Found at i:2290280 original size:55 final size:55
Alignment explanation
Indices: 2290094--2290251 Score: 246
Period size: 55 Copynumber: 2.9 Consensus size: 55
2290084 AATGGCATTA
*
2290094 TGTGTGCAAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGAGCACTG
1 TGTGTGC-AAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGAGCACTG
* * * *
2290150 TGTGTACAAAACTATGAAATTCATAATAAATTTATGAA-TTTCAGTATGGGCACTG
1 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTC-GTATGAGCACTG
2290205 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTAT
1 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTAT
2290252 TAGTAGTGGG
Statistics
Matches: 92, Mismatches: 8, Indels: 5
0.88 0.08 0.05
Matches are distributed among these distances:
54 3 0.03
55 79 0.86
56 10 0.11
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (55 bp):
TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGAGCACTG
Found at i:2290470 original size:45 final size:45
Alignment explanation
Indices: 2290419--2290632 Score: 297
Period size: 45 Copynumber: 4.8 Consensus size: 45
2290409 GGCCTAGCGG
* *
2290419 TGCATTAAAGGCATGAAAGGATGTCATAAATGAAATGTATAACGA
1 TGCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGA
* * * *
2290464 TGCATTAAAGGCATGAAAAGATGCAATAAATGAAATGCATAATGT
1 TGCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGA
*
2290509 TGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGCATAAC-A
1 TGCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGA
* * *
2290553 GTGCATTAAAGGCATGAAAGGATACCGTAAATGAAATGCATAACGG
1 -TGCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGA
*
2290599 TGCATTAAAGGCATGAAAAGATGTCC-TAAATGAA
1 TGCATTAAAGGCATGAAAGGATG-CCATAAATGAA
2290633 TAATTACTAA
Statistics
Matches: 149, Mismatches: 17, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
45 147 0.99
46 2 0.01
ACGTcount: A:0.45, C:0.11, G:0.21, T:0.22
Consensus pattern (45 bp):
TGCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGA
Found at i:2296071 original size:45 final size:46
Alignment explanation
Indices: 2296022--2296109 Score: 142
Period size: 45 Copynumber: 1.9 Consensus size: 46
2296012 GAACATCGAA
* * *
2296022 TGCATTTTATGCATCGATGCAC-ATACCATGCATCGATGCACTTAG
1 TGCATTTGATGCATCAATGCACAAGACCATGCATCGATGCACTTAG
2296067 TGCATTTGATGCATCAATGCACAAGACCATGCATCGATGCACT
1 TGCATTTGATGCATCAATGCACAAGACCATGCATCGATGCACT
2296110 CAGGCTATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 20 0.51
46 19 0.49
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.28
Consensus pattern (46 bp):
TGCATTTGATGCATCAATGCACAAGACCATGCATCGATGCACTTAG
Found at i:2301979 original size:23 final size:23
Alignment explanation
Indices: 2301911--2301990 Score: 87
Period size: 23 Copynumber: 3.6 Consensus size: 23
2301901 TTTGTGCTTC
2301911 TGCATCGAT--ACATCCTTGAATG
1 TGCATCGATGCACA-CCTTGAATG
* *
2301933 TGCATCGAT--ACACCATGAAGG
1 TGCATCGATGCACACCTTGAATG
* *
2301954 TGCACCGATGCACGCCTTGAATG
1 TGCATCGATGCACACCTTGAATG
2301977 TGCATCGATGCACA
1 TGCATCGATGCACA
2301991 AGGCCATGCA
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
21 15 0.31
22 12 0.25
23 21 0.44
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.24
Consensus pattern (23 bp):
TGCATCGATGCACACCTTGAATG
Found at i:2304663 original size:20 final size:20
Alignment explanation
Indices: 2304638--2304676 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2304628 TTTTCAAGGG
2304638 CATGCACCGATGCACCAATC
1 CATGCACCGATGCACCAATC
* *
2304658 CATGCATCGATGCATCAAT
1 CATGCACCGATGCACCAAT
2304677 TAATTTCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.33, G:0.15, T:0.21
Consensus pattern (20 bp):
CATGCACCGATGCACCAATC
Found at i:2311440 original size:2 final size:2
Alignment explanation
Indices: 2311433--2311458 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2311423 GGTAATCATA
2311433 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
2311459 CAAATACATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2320032 original size:43 final size:42
Alignment explanation
Indices: 2319981--2320083 Score: 127
Period size: 43 Copynumber: 2.4 Consensus size: 42
2319971 CATTCGAAAT
* *
2319981 GGAGTGCATGGATGCACTGCA-TGGTGCATCGATGCACTAGT
1 GGAGTGCATGGATGCACTGCAGGGGTGCATCGATGCACTAGA
* * * *
2320022 GGCAGGTGCATGGATGCACTGTAGGGGTGCATGGATGGACTGGA
1 GG-A-GTGCATGGATGCACTGCAGGGGTGCATCGATGCACTAGA
2320066 GGAGTGCATGGATGCACT
1 GGAGTGCATGGATGCACT
2320084 TTGACACCCT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
41 2 0.04
42 16 0.30
43 18 0.34
44 17 0.32
ACGTcount: A:0.21, C:0.17, G:0.40, T:0.22
Consensus pattern (42 bp):
GGAGTGCATGGATGCACTGCAGGGGTGCATCGATGCACTAGA
Found at i:2320052 original size:21 final size:21
Alignment explanation
Indices: 2319984--2320083 Score: 105
Period size: 21 Copynumber: 4.7 Consensus size: 21
2319974 TCGAAATGGA
* *
2319984 GTGCATGGATGCACTGCA-TG
1 GTGCATGGATGCACTGTAGGG
*
2320004 GTGCATCGATGCACTAGT-GGCAG
1 GTGCATGGATGCACT-GTAGG--G
2320027 GTGCATGGATGCACTGTAGGG
1 GTGCATGGATGCACTGTAGGG
* * *
2320048 GTGCATGGATGGACTGGAGGA
1 GTGCATGGATGCACTGTAGGG
2320069 GTGCATGGATGCACT
1 GTGCATGGATGCACT
2320084 TTGACACCCT
Statistics
Matches: 67, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
20 14 0.21
21 34 0.51
22 2 0.03
23 17 0.25
ACGTcount: A:0.21, C:0.17, G:0.39, T:0.23
Consensus pattern (21 bp):
GTGCATGGATGCACTGTAGGG
Found at i:2321459 original size:19 final size:20
Alignment explanation
Indices: 2321423--2321470 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
2321413 TCTAAATCAT
*
2321423 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATTCCATTTTGG
*
2321443 TTTTCAAAA-TCCATTTTTG
1 TTTTCAAAATTCCATTTTGG
*
2321462 CTTTCAAAA
1 TTTTCAAAA
2321471 GAAAATTGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.29, C:0.15, G:0.06, T:0.50
Consensus pattern (20 bp):
TTTTCAAAATTCCATTTTGG
Found at i:2322853 original size:21 final size:21
Alignment explanation
Indices: 2322827--2322881 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
2322817 CTAGTGACAC
* *
2322827 GTGCATGGATGCATTGCAGGG
1 GTGCATGGATGCATTACAGGA
2322848 GTGCATGGATGCATTACAGGA
1 GTGCATGGATGCATTACAGGA
2322869 GTGCATGGATGCA
1 GTGCATGGATGCA
2322882 CTTTGACACC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.24, C:0.15, G:0.38, T:0.24
Consensus pattern (21 bp):
GTGCATGGATGCATTACAGGA
Found at i:2330266 original size:15 final size:16
Alignment explanation
Indices: 2330246--2330278 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2330236 CGCCGCCTCG
2330246 CCTTG-CCACCATTAA
1 CCTTGACCACCATTAA
2330261 CCTTGCACCACCATTAA
1 CCTTG-ACCACCATTAA
2330278 C
1 C
2330279 GCACCATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
17 11 0.69
ACGTcount: A:0.27, C:0.42, G:0.06, T:0.24
Consensus pattern (16 bp):
CCTTGACCACCATTAA
Found at i:2333745 original size:13 final size:13
Alignment explanation
Indices: 2333729--2333757 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2333719 ATTTTTATTT
2333729 TTTAGGAATTATC
1 TTTAGGAATTATC
2333742 TTTAGGAATTATC
1 TTTAGGAATTATC
2333755 TTT
1 TTT
2333758 GTTTTGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.07, G:0.14, T:0.52
Consensus pattern (13 bp):
TTTAGGAATTATC
Found at i:2336618 original size:16 final size:16
Alignment explanation
Indices: 2336599--2336651 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
2336589 ATATGTATGC
2336599 ATATATTGTTTTGAAA
1 ATATATTGTTTTGAAA
*
2336615 ATATATAGTTTTGAAA
1 ATATATTGTTTTGAAA
2336631 ATATATAT-TTTT-AAA
1 ATATAT-TGTTTTGAAA
2336646 ATATAT
1 ATATAT
2336652 ATATATATAG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
15 9 0.26
16 25 0.74
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (16 bp):
ATATATTGTTTTGAAA
Found at i:2336646 original size:15 final size:15
Alignment explanation
Indices: 2336607--2336653 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
2336597 GCATATATTG
2336607 TTTTGAAAATATATA
1 TTTTGAAAATATATA
2336622 GTTTTGAAAATATATA
1 -TTTTGAAAATATATA
*
2336638 TTTTTAAAATATATA
1 TTTTGAAAATATATA
2336653 T
1 T
2336654 ATATATAGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
15 15 0.50
16 15 0.50
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (15 bp):
TTTTGAAAATATATA
Found at i:2336655 original size:19 final size:19
Alignment explanation
Indices: 2336615--2336797 Score: 117
Period size: 19 Copynumber: 9.2 Consensus size: 19
2336605 TGTTTTGAAA
* *
2336615 ATATATAGTTTTGAAA-AT
1 ATATATATTTTTAAAATAT
*
2336633 ATATAT-TTTTAAAATATAT
1 ATATATATTTTTAAA-ATAT
2336652 ATATATATAGTTTCTAAAAATATAT
1 ATATATAT--TTT-T--AAA-ATAT
2336677 ATTATATATTTTTTAAAATAT
1 A-TATATA-TTTTTAAAATAT
** *
2336698 ATATAGT-TTTGGAAAAAAT
1 ATATA-TATTTTTAAAATAT
2336717 ATATAGTATTTTT-AAATAT
1 ATATA-TATTTTTAAAATAT
* *
2336736 ATATATAATTTTTGAAA-AC
1 ATATAT-ATTTTTAAAATAT
*
2336755 ATATA-ATTTTGAAAATAT
1 ATATATATTTTTAAAATAT
2336773 ATATTATATATTTTAAAATAT
1 ATA-TATAT-TTTTAAAATAT
2336794 ATAT
1 ATAT
2336798 GGCTTTATTC
Statistics
Matches: 132, Mismatches: 15, Indels: 34
0.73 0.08 0.19
Matches are distributed among these distances:
17 13 0.10
18 12 0.09
19 48 0.36
20 14 0.11
21 19 0.14
22 6 0.05
24 1 0.01
25 12 0.09
26 6 0.05
27 1 0.01
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.48
Consensus pattern (19 bp):
ATATATATTTTTAAAATAT
Found at i:2336657 original size:21 final size:21
Alignment explanation
Indices: 2336631--2336797 Score: 131
Period size: 21 Copynumber: 8.1 Consensus size: 21
2336621 AGTTTTGAAA
2336631 ATATATATTTTTAAAATATAT
1 ATATATATTTTTAAAATATAT
2336652 ATATATATAGTTTCTAAAAATATAT
1 ATATATAT--TTT-T-AAAATATAT
2336677 ATTATATATTTTTTAAAATATAT
1 A-TATATA-TTTTTAAAATATAT
* **
2336700 ATA-GT-TTTGGAAAA-A-AT
1 ATATATATTTTTAAAATATAT
2336717 ATATAGTATTTTT-AAATATAT
1 ATATA-TATTTTTAAAATATAT
* *
2336738 ATATA-ATTTTT-GAA-A-AC
1 ATATATATTTTTAAAATATAT
*
2336755 ATATA-ATTTTGAAAATATAT
1 ATATATATTTTTAAAATATAT
2336775 AT-TATATATTTTAAAATATAT
1 ATATATAT-TTTTAAAATATAT
2336796 AT
1 AT
2336798 GGCTTTATTC
Statistics
Matches: 118, Mismatches: 12, Indels: 32
0.73 0.07 0.20
Matches are distributed among these distances:
17 16 0.14
18 4 0.03
19 22 0.19
20 9 0.08
21 30 0.25
22 2 0.02
23 13 0.11
24 2 0.02
25 13 0.11
26 6 0.05
27 1 0.01
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (21 bp):
ATATATATTTTTAAAATATAT
Found at i:2336671 original size:25 final size:23
Alignment explanation
Indices: 2336631--2336702 Score: 101
Period size: 24 Copynumber: 3.0 Consensus size: 23
2336621 AGTTTTGAAA
2336631 ATATATATTTTTAAAATATATAT
1 ATATATATTTTTAAAATATATAT
*
2336654 ATATATAGTTTCTAAAA-ATATAT
1 ATATATA-TTTTTAAAATATATAT
2336677 ATTATATATTTTTTAAAATATATAT
1 A-TATATA-TTTTTAAAATATATAT
2336702 A
1 A
2336703 GTTTTGGAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
23 14 0.33
24 22 0.51
25 7 0.16
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (23 bp):
ATATATATTTTTAAAATATATAT
Found at i:2336698 original size:42 final size:39
Alignment explanation
Indices: 2336650--2336759 Score: 116
Period size: 40 Copynumber: 2.7 Consensus size: 39
2336640 TTTAAAATAT
2336650 ATATATATATAGTTTCT-AAAAATATATATTATATATTTTTTAA
1 ATATATATATAGTTT-TGAAAAA-ATATA-TA-ATA-TTTTTAA
*
2336693 A-ATATATATAGTTTTGGAAAAAATATATAGTATTTTTAA
1 ATATATATATAGTTTT-GAAAAAATATATAATATTTTTAA
* *
2336732 ATATATATATAATTTTTGAAAACATATA
1 ATATATATAT-AGTTTTGAAAAAATATA
2336760 ATTTTGAAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
39 8 0.13
40 20 0.33
41 8 0.13
42 18 0.30
43 6 0.10
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (39 bp):
ATATATATATAGTTTTGAAAAAATATATAATATTTTTAA
Found at i:2344977 original size:24 final size:26
Alignment explanation
Indices: 2344948--2345006 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
2344938 GAAGGTTTTA
*
2344948 ATGTTTTA-ATTACATTA-AATATTT
1 ATGTTTTATAATACATTATAATATTT
* *
2344972 ATGTTTTATAATACTTTATGATATTT
1 ATGTTTTATAATACATTATAATATTT
2344998 ATGTTTTAT
1 ATGTTTTAT
2345007 CTCACCTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
24 8 0.27
25 7 0.23
26 15 0.50
ACGTcount: A:0.32, C:0.03, G:0.07, T:0.58
Consensus pattern (26 bp):
ATGTTTTATAATACATTATAATATTT
Found at i:2348145 original size:20 final size:20
Alignment explanation
Indices: 2348099--2348137 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2348089 TGATCCTGGT
2348099 TATGTGTTACGAGTCATTTA
1 TATGTGTTACGAGTCATTTA
*
2348119 TATGTGTTCCGAGTCATTT
1 TATGTGTTACGAGTCATTT
2348138 TTGTGTGTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.13, G:0.21, T:0.46
Consensus pattern (20 bp):
TATGTGTTACGAGTCATTTA
Found at i:2349753 original size:78 final size:80
Alignment explanation
Indices: 2349654--2350073 Score: 276
Period size: 78 Copynumber: 5.3 Consensus size: 80
2349644 TTGACTTTGG
* * * * *
2349654 CCACTAAAGTACGAGTATTTAGCGATGTTTGTGCTTAAAACACCACTAAATTTC-ATTATTTAGC
1 CCACTAAAGTACGAGTATTTAGCGACGTTTATGCTTAAAACACCACTAAAGTACGAGTATTTAGC
*
2349718 GGCGTTTGTATAAAA
66 AGCGTTTGTATAAAA
* * *
2349733 CCACT-AAGTACGAGTATTTAGTGACGTTTATGCTTAAAACGCCACTAAAGTACGAGTCTTTAGC
1 CCACTAAAGTACGAGTATTTAGCGACGTTTATGCTTAAAACACCACTAAAGTACGAGTATTTAGC
2349797 AGCGTTTGTATAAAAA
66 AGCGTTTGTAT-AAAA
* * * ** *
2349813 TTCCACTAAATTACGGGT-TATT-G-G-CGTTGT-TG--TCAAATGCCA-TGAAAGTA-TAGTAT
1 --CCACTAAAGTACGAGTAT-TTAGCGACGTT-TATGCTTAAAACACCACT-AAAGTACGAGTAT
* *
2349869 TTAGCAGCATTTATATAAAAA
61 TTAGCAGCGTTTGTAT-AAAA
* * * * *
2349890 TGCCACTAAAGTATGAGTATTTAGCGGCGTTTATACTTAAAACGCCACTAAAGTA-TAGTATTTA
1 --CCACTAAAGTACGAGTATTTAGCGACGTTTATGCTTAAAACACCACTAAAGTACGAGTATTTA
* *
2349954 GCGGCGTTTATATAAAACA
64 GCAGCGTTTGTAT-AAA-A
* * * * * * * *
2349973 CCACTAAAGTATGAGTCTTTAGCGGCGTGTGTAC-AAAAACGCCACTAAA-TAC-AGTATTTAGC
1 CCACTAAAGTACGAGTATTTAGCGACGTTTATGCTTAAAACACCACTAAAGTACGAGTATTTAGC
* * *
2350035 TGTGTTTATATAAAAA
66 AGCGTTTGTAT-AAAA
* *
2350051 CTCCACTAAAGTACAAGTTTTTA
1 --CCACTAAAGTACGAGTATTTA
2350074 CCGGTGTTTA
Statistics
Matches: 286, Mismatches: 35, Indels: 39
0.79 0.10 0.11
Matches are distributed among these distances:
77 40 0.14
78 59 0.21
79 50 0.17
80 47 0.16
81 33 0.12
82 45 0.16
83 12 0.04
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Consensus pattern (80 bp):
CCACTAAAGTACGAGTATTTAGCGACGTTTATGCTTAAAACACCACTAAAGTACGAGTATTTAGC
AGCGTTTGTATAAAA
Found at i:2349819 original size:41 final size:41
Alignment explanation
Indices: 2349653--2350091 Score: 300
Period size: 41 Copynumber: 11.0 Consensus size: 41
2349643 GTTGACTTTG
** * * *
2349653 GCCACTAAAGTACGAGTATTTAGCGATGTTTGTGCTTAAAAC
1 GCCACTAAAGTACGAGTATTTAGCGGCGTTTAT-ATAAAAAC
* * * * *
2349695 ACCACTAAATTTC-ATTATTTAGCGGCGTTTGTAT-AAAA-
1 GCCACTAAAGTACGAGTATTTAGCGGCGTTTATATAAAAAC
* * * *
2349733 -CCACT-AAGTACGAGTATTTAGTGACGTTTATGCTTAAAAC
1 GCCACTAAAGTACGAGTATTTAGCGGCGTTTAT-ATAAAAAC
* * * *
2349773 GCCACTAAAGTACGAGTCTTTAGCAGCGTTTGTATAAAAAT
1 GCCACTAAAGTACGAGTATTTAGCGGCGTTTATATAAAAAC
* * * * * *
2349814 TCCACTAAATTACGGGT-TATT---GGCGTTGT-TGT-CAAAT
1 GCCACTAAAGTACGAGTAT-TTAGCGGCGTT-TATATAAAAAC
* * * *
2349851 GCCA-TGAAAGTA-TAGTATTTAGCAGCATTTATATAAAAAT
1 GCCACT-AAAGTACGAGTATTTAGCGGCGTTTATATAAAAAC
* *
2349891 GCCACTAAAGTATGAGTATTTAGCGGCGTTTATACTTAAAAC
1 GCCACTAAAGTACGAGTATTTAGCGGCGTTTATA-TAAAAAC
*
2349933 GCCACTAAAGTA-TAGTATTTAGCGGCGTTTATAT-AAAAC
1 GCCACTAAAGTACGAGTATTTAGCGGCGTTTATATAAAAAC
* * * * * *
2349972 ACCACTAAAGTATGAGTCTTTAGCGGCGTGTGTACAAAAAC
1 GCCACTAAAGTACGAGTATTTAGCGGCGTTTATATAAAAAC
* *
2350013 GCCACTAAA-TAC-AGTATTTAGCTGTGTTTATATAAAAAC
1 GCCACTAAAGTACGAGTATTTAGCGGCGTTTATATAAAAAC
* * * * * *
2350052 TCCACTAAAGTACAAGTTTTTACCGGTGTTTATTTAAAAA
1 GCCACTAAAGTACGAGTATTTAGCGGCGTTTATATAAAAA
2350092 ATGCCGCTAA
Statistics
Matches: 314, Mismatches: 61, Indels: 45
0.75 0.15 0.11
Matches are distributed among these distances:
36 9 0.03
37 33 0.11
38 9 0.03
39 60 0.19
40 39 0.12
41 116 0.37
42 48 0.15
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (41 bp):
GCCACTAAAGTACGAGTATTTAGCGGCGTTTATATAAAAAC
Found at i:2351888 original size:37 final size:37
Alignment explanation
Indices: 2351843--2351915 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
2351833 TTTTGTTCGG
*
2351843 GTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGA
1 GTCGGGTCGAGTTTTTTAAGTGTGATATTCGGGTCGA
*
2351880 GTCGGGTCGATTTTTTTAAGTGTGATATTCGGGTCG
1 GTCGGGTCGAGTTTTTTAAGTGTGATATTCGGGTCG
2351916 GGTTTAGGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.14, C:0.11, G:0.36, T:0.40
Consensus pattern (37 bp):
GTCGGGTCGAGTTTTTTAAGTGTGATATTCGGGTCGA
Found at i:2352128 original size:31 final size:31
Alignment explanation
Indices: 2352053--2352128 Score: 143
Period size: 31 Copynumber: 2.5 Consensus size: 31
2352043 AATTCATATA
*
2352053 TTCGGGTCGGGTCCGATGAAACTTTATTTTG
1 TTCGGGTCGGGTCGGATGAAACTTTATTTTG
2352084 TTCGGGTCGGGTCGGATGAAACTTTATTTTG
1 TTCGGGTCGGGTCGGATGAAACTTTATTTTG
2352115 TTCGGGTCGGGTCG
1 TTCGGGTCGGGTCG
2352129 AGTTTTTTAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.13, C:0.16, G:0.34, T:0.37
Consensus pattern (31 bp):
TTCGGGTCGGGTCGGATGAAACTTTATTTTG
Found at i:2352182 original size:38 final size:38
Alignment explanation
Indices: 2352119--2352207 Score: 137
Period size: 38 Copynumber: 2.4 Consensus size: 38
2352109 ATTTTGTTCG
*
2352119 GGTCGGGTCGAG-TTTTTTAAGTGTGATATTCGGGTC-
1 GGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCA
*
2352155 GAGTCGGGTCGGGTTTTTTTAAGTGTGATATTTGGGTCA
1 G-GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCA
2352194 GGTCGGGTCGGGTT
1 GGTCGGGTCGGGTT
2352208 CGGGTTTAGG
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
36 1 0.02
37 10 0.21
38 36 0.75
39 1 0.02
ACGTcount: A:0.12, C:0.10, G:0.39, T:0.38
Consensus pattern (38 bp):
GGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCA
Found at i:2358109 original size:60 final size:59
Alignment explanation
Indices: 2358045--2358177 Score: 149
Period size: 60 Copynumber: 2.2 Consensus size: 59
2358035 AGAATTAGAT
** * * * *
2358045 TCATAGTTTGGGGTTGAAATTAAAACGTTCAAAAGTTTAAGTACTAATTCAGAACGAGAG
1 TCATAGTTTCAGGATGAAATTAAAACATTCAAAAGTTTAAG-ACTAATTCAAAAAGAGAG
* * * * *
2358105 TCATAGTTTCAGGATGAAATTGAAATATTTAAAAGTTTATGACTAATTTAAAAAGAGAG
1 TCATAGTTTCAGGATGAAATTAAAACATTCAAAAGTTTAAGACTAATTCAAAAAGAGAG
*
2358164 TCATAGTTTAAGGA
1 TCATAGTTTCAGGA
2358178 CATATGATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
59 28 0.46
60 33 0.54
ACGTcount: A:0.41, C:0.08, G:0.20, T:0.32
Consensus pattern (59 bp):
TCATAGTTTCAGGATGAAATTAAAACATTCAAAAGTTTAAGACTAATTCAAAAAGAGAG
Found at i:2358367 original size:24 final size:24
Alignment explanation
Indices: 2358309--2358368 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
2358299 ATTTAAATTT
*
2358309 AATATAAAAATAACTTAATTTTAT
1 AATATAAAAATAACTTAATTTTAC
* * * *
2358333 ACTACACAAATAACTTATTTTTAC
1 AATATAAAAATAACTTAATTTTAC
2358357 AATATAAAAATA
1 AATATAAAAATA
2358369 TATATTTCTA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (24 bp):
AATATAAAAATAACTTAATTTTAC
Found at i:2358563 original size:15 final size:16
Alignment explanation
Indices: 2358527--2358570 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
2358517 AGTATATAAT
*
2358527 TTAAAATTTTAATAGA
1 TTAAAATTTTATTAGA
*
2358543 TAAAAATTTTATTA-A
1 TTAAAATTTTATTAGA
2358558 TTAAAATTTTATT
1 TTAAAATTTTATT
2358571 TTTTTAATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (16 bp):
TTAAAATTTTATTAGA
Found at i:2361142 original size:24 final size:24
Alignment explanation
Indices: 2361112--2361179 Score: 118
Period size: 24 Copynumber: 2.8 Consensus size: 24
2361102 ATTTTGATAA
**
2361112 TATTGTTTGTTCATAAATTTATTC
1 TATTGTTCATTCATAAATTTATTC
2361136 TATTGTTCATTCATAAATTTATTC
1 TATTGTTCATTCATAAATTTATTC
2361160 TATTGTTCATTCATAAATTT
1 TATTGTTCATTCATAAATTT
2361180 GGAGATTTAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.28, C:0.10, G:0.06, T:0.56
Consensus pattern (24 bp):
TATTGTTCATTCATAAATTTATTC
Found at i:2361938 original size:16 final size:16
Alignment explanation
Indices: 2361917--2361948 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2361907 ACTATTCACA
*
2361917 TGAATAGTAAATTTTG
1 TGAATAGTAAAATTTG
2361933 TGAATAGTAAAATTTG
1 TGAATAGTAAAATTTG
2361949 GTCGGCGAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (16 bp):
TGAATAGTAAAATTTG
Found at i:2366003 original size:22 final size:22
Alignment explanation
Indices: 2365972--2366017 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
2365962 TAAGAAAGGA
* *
2365972 GGCAATGGAGGCCACCGAAAGT
1 GGCAAGGGAGGCCACAGAAAGT
2365994 GGCAAGGGAGGCCACAGAAAGT
1 GGCAAGGGAGGCCACAGAAAGT
2366016 GG
1 GG
2366018 TACATTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.33, C:0.20, G:0.41, T:0.07
Consensus pattern (22 bp):
GGCAAGGGAGGCCACAGAAAGT
Found at i:2374608 original size:64 final size:63
Alignment explanation
Indices: 2374478--2374637 Score: 214
Period size: 64 Copynumber: 2.5 Consensus size: 63
2374468 AATATTTAAA
* * * *
2374478 GTGTATCGATACACAGGAAGTGTATTGATGCACCCCTTAAAATGAAAACATCGAACTTAATTT
1 GTGTATCGATACATAGGAAGTGTATCGATACACCCCTTAAAATAAAAACATCGAACTTAATTT
* * * *
2374541 GTGTATCGATACATAGAAAGTGTATCGATATACTCCTTGTAAATAAAAACATCGAA-TGTAATTT
1 GTGTATCGATACATAGGAAGTGTATCGATACACCCCTT-AAAATAAAAACATCGAACT-TAATTT
*
2374605 GTGTATCGATACATAGGTAGTGTATCGATACAC
1 GTGTATCGATACATAGGAAGTGTATCGATACAC
2374638 ATGTTAAGGA
Statistics
Matches: 84, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
63 33 0.39
64 51 0.61
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (63 bp):
GTGTATCGATACATAGGAAGTGTATCGATACACCCCTTAAAATAAAAACATCGAACTTAATTT
Found at i:2380878 original size:64 final size:63
Alignment explanation
Indices: 2380720--2380878 Score: 219
Period size: 64 Copynumber: 2.5 Consensus size: 63
2380710 AATATTCAAA
* * * *
2380720 GTGTACCGATACACAGGAAGTGTATCGATACACCCCTTAAAATGAAAACATCGAATGTAATTT
1 GTGTATCGATACATAGGAAGTGTATCGATACACCCCTTAAAATAAAAACATCGAATGCAATTT
* * *
2380783 GTGTATCGATACATAGAAAGTGTATCGATACACTCCTTGTAAATAAAAACATCGAATGCAATTT
1 GTGTATCGATACATAGGAAGTGTATCGATACACCCCTT-AAAATAAAAACATCGAATGCAATTT
* * *
2380847 GTGTATCGATACATAGGTAGTCTATCAATACA
1 GTGTATCGATACATAGGAAGTGTATCGATACA
2380879 AATGTTAAGG
Statistics
Matches: 84, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
63 34 0.40
64 50 0.60
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (63 bp):
GTGTATCGATACATAGGAAGTGTATCGATACACCCCTTAAAATAAAAACATCGAATGCAATTT
Found at i:2382279 original size:21 final size:21
Alignment explanation
Indices: 2382241--2382280 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2382231 TCCTTTTAAA
* *
2382241 AAAGGGATCGATCCTTTTTGC
1 AAAGGGATCAATCATTTTTGC
*
2382262 AAAGGGATTAATCATTTTT
1 AAAGGGATCAATCATTTTT
2382281 TAGGAATATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (21 bp):
AAAGGGATCAATCATTTTTGC
Found at i:2383517 original size:18 final size:18
Alignment explanation
Indices: 2383478--2383518 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2383468 AAAAGCCTTC
*
2383478 TTCTTGCTTGATTCATTC
1 TTCTTGCTTGATTCATTA
2383496 TTCTTGCTTGATATC-TTA
1 TTCTTGCTTGAT-TCATTA
2383514 TTCTT
1 TTCTT
2383519 TAGAAGAGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 19 0.90
19 2 0.10
ACGTcount: A:0.12, C:0.20, G:0.10, T:0.59
Consensus pattern (18 bp):
TTCTTGCTTGATTCATTA
Found at i:2386316 original size:18 final size:18
Alignment explanation
Indices: 2386293--2386337 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
2386283 AAAATTGTTG
2386293 AAAAAGAGTTTTTGAACC
1 AAAAAGAGTTTTTGAACC
*
2386311 AAAAAGAGTTTTTGATCC
1 AAAAAGAGTTTTTGAACC
2386329 AAAAAGAGT
1 AAAAAGAGT
2386338 GTTTAAGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.47, C:0.09, G:0.18, T:0.27
Consensus pattern (18 bp):
AAAAAGAGTTTTTGAACC
Found at i:2389996 original size:23 final size:23
Alignment explanation
Indices: 2389970--2390017 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
2389960 ATTGGAATAC
2389970 AAGGGATCGATCCTTTG-GTCAAA
1 AAGGGATCGATCCTTTGAG-CAAA
*
2389993 AAGGGATCGATCGTTTGAGCAAA
1 AAGGGATCGATCCTTTGAGCAAA
2390016 AA
1 AA
2390018 ATGATTGGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 22 0.96
24 1 0.04
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (23 bp):
AAGGGATCGATCCTTTGAGCAAA
Found at i:2391045 original size:55 final size:55
Alignment explanation
Indices: 2390961--2391106 Score: 195
Period size: 55 Copynumber: 2.7 Consensus size: 55
2390951 ATCGGATATA
* ** * * * *
2390961 ACAAA-TCATTATAAATTTCGTGGTTTTGCACACCTAGTGTCGATACGGTAATTC
1 ACAAACTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATACGGAAATTC
*
2391015 ACAAACTCATTATGAATTACGTGGGGTTGCACACATAGTGCCAATACGGAAATTC
1 ACAAACTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATACGGAAATTC
* *
2391070 ACAAACTCATTTTGAATTTCTTGGGGTTGCACACATA
1 ACAAACTCATTATGAATTTCGTGGGGTTGCACACATA
2391107 TACATTAAAC
Statistics
Matches: 80, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
54 5 0.06
55 75 0.94
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Consensus pattern (55 bp):
ACAAACTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATACGGAAATTC
Found at i:2391428 original size:20 final size:21
Alignment explanation
Indices: 2391403--2391457 Score: 76
Period size: 22 Copynumber: 2.6 Consensus size: 21
2391393 ATACTGATTA
*
2391403 GTATCGATAC-CCATTCTATG
1 GTATCGATACTCCATACTATG
*
2391423 GTATCGATACTTCTATACTATG
1 GTATCGATAC-TCCATACTATG
2391445 GTATCGATACTCC
1 GTATCGATACTCC
2391458 CTTCAGTACC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 10 0.33
21 2 0.07
22 18 0.60
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.36
Consensus pattern (21 bp):
GTATCGATACTCCATACTATG
Found at i:2394069 original size:22 final size:21
Alignment explanation
Indices: 2394040--2394103 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
2394030 CATATGAGAT
*
2394040 TTGTCCCGAAGGACCTGTGAA
1 TTGTCCCGAAGGACCTATGAA
* * *
2394061 TATGTCCCGAATGACGTATGAG
1 T-TGTCCCGAAGGACCTATGAA
*
2394083 TTGTCTCGAAGGACCTATGAA
1 TTGTCCCGAAGGACCTATGAA
2394104 ACCCTCAACT
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
21 17 0.50
22 17 0.50
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAA
Found at i:2400839 original size:22 final size:22
Alignment explanation
Indices: 2400802--2400852 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
2400792 CTAAGTGGCA
* *
2400802 TATGAGATTTATCCCGAATGACC
1 TATGA-ATATATCCCGAAGGACC
*
2400825 TGTGAATATATCCCGAAGGACC
1 TATGAATATATCCCGAAGGACC
2400847 TATGAA
1 TATGAA
2400853 ACCCTCGACT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (22 bp):
TATGAATATATCCCGAAGGACC
Found at i:2409116 original size:21 final size:20
Alignment explanation
Indices: 2409092--2409131 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
2409082 AAATAAATAT
2409092 TAAATCATAAAAAAGTTAAAA
1 TAAATCA-AAAAAAGTTAAAA
*
2409113 TAAATGAAAAAAAGTTAAA
1 TAAATCAAAAAAAGTTAAA
2409132 TGCAACAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.68, C:0.03, G:0.07, T:0.23
Consensus pattern (20 bp):
TAAATCAAAAAAAGTTAAAA
Found at i:2409182 original size:15 final size:15
Alignment explanation
Indices: 2409162--2409192 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2409152 AAAGAAATAA
*
2409162 AAATAATATGAAATG
1 AAATAAAATGAAATG
2409177 AAATAAAATGAAATG
1 AAATAAAATGAAATG
2409192 A
1 A
2409193 TATTAAGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.13, T:0.23
Consensus pattern (15 bp):
AAATAAAATGAAATG
Found at i:2409346 original size:21 final size:20
Alignment explanation
Indices: 2409294--2409358 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 20
2409284 CGCAAAAAAG
*
2409294 AAAATAAATA-AATAAATGAGT
1 AAAATAAATATAAT-AAT-AAT
*
2409315 AAAATTAATATAATAATAAT
1 AAAATAAATATAATAATAAT
2409335 AATAATAAATATAA-AAT-AT
1 AA-AATAAATATAATAATAAT
2409354 AAAAT
1 AAAAT
2409359 GCTGCAAATC
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
18 3 0.08
19 4 0.10
20 7 0.18
21 22 0.56
22 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (20 bp):
AAAATAAATATAATAATAAT
Found at i:2410519 original size:3 final size:3
Alignment explanation
Indices: 2410511--2410537 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2410501 ATAAAAAGAC
2410511 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
2410538 TACATTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2410577 original size:2 final size:2
Alignment explanation
Indices: 2410572--2410598 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2410562 TTATTAAAAC
2410572 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 T
2410599 CAAAAATATT
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:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2410623 original size:38 final size:36
Alignment explanation
Indices: 2410577--2410978 Score: 240
Period size: 36 Copynumber: 10.8 Consensus size: 36
2410567 AAAACTATAT
* *
2410577 ATATATATATATATATATATATCAAAAATATTTTTAA
1 ATATATATATATATATAT-TTTCAAAAATATTTTAAA
* * *
2410614 AT-TATATATATAAATTTTTTTAAAAAATATTTTCAAA
1 ATATATATATATATA-TATTTTCAAAAATATTTT-AAA
2410651 A-ATATATAT-TATATAGTTTTCAAAAATATTTTCAAA
1 ATATATATATATATATA-TTTTCAAAAATATTTT-AAA
** *
2410687 ACTATATAT-TATATA-AGTTTTCAAATTTGTTTTAAA
1 A-TATATATATATATATA-TTTTCAAAAATATTTTAAA
* *
2410723 AAACTATATAT-TATATAAGTTTTCAAAAATGTTTTCAAA
1 ATA-TATATATATATAT-A-TTTTCAAAAATATTTT-AAA
* ** *
2410762 AAACTATATATTATATATATTTTTTTAAAATGTTTTCAAA
1 ATA-TATATA-TATATATA-TTTTCAAAAATATTTT-AAA
*
2410802 A-ACTATATATTATATATATTTTTC-AAAATGTTTTTAAA
1 ATA-TATATA-TATATATA-TTTTCAAAAAT-ATTTTAAA
*
2410840 A-ATCATATAT-TATATAAGTTTTC-AAAATGTTTTTAAA
1 ATAT-ATATATATATAT-A-TTTTCAAAAAT-ATTTTAAA
* * *
2410877 AAACTATATAATATATACATTTTCAAAAATCGTTTTCAAA
1 ATA-TATAT-ATATATATATTTTCAAAAAT-ATTTT-AAA
*
2410917 ACTATATAT-TATATATATTTTC-AAAATGTTTTCAAA
1 A-TATATATATATATATATTTTCAAAAATATTTT-AAA
*
2410953 ACTATATA-ACATATATA-TTTCAAAAA
1 A-TATATATATATATATATTTTCAAAAA
2410979 CGATTTTTAA
Statistics
Matches: 313, Mismatches: 26, Indels: 53
0.80 0.07 0.14
Matches are distributed among these distances:
35 6 0.02
36 93 0.30
37 59 0.19
38 63 0.20
39 52 0.17
40 34 0.11
41 6 0.02
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (36 bp):
ATATATATATATATATATTTTCAAAAATATTTTAAA
Found at i:2410628 original size:23 final size:24
Alignment explanation
Indices: 2410592--2410655 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 24
2410582 TATATATATA
2410592 TATATATCAAAAATATTTTTAAAT
1 TATATATCAAAAATATTTTTAAAT
* * *
2410616 TATATAT-ATAAATTTTTTTAAAA
1 TATATATCAAAAATATTTTTAAAT
* *
2410639 AATATTTTCAAAAATAT
1 TATA-TATCAAAAATAT
2410656 ATATTATATA
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
23 16 0.52
24 9 0.29
25 6 0.19
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (24 bp):
TATATATCAAAAATATTTTTAAAT
Found at i:2410656 original size:35 final size:35
Alignment explanation
Indices: 2410600--2410960 Score: 127
Period size: 38 Copynumber: 9.7 Consensus size: 35
2410590 TATATATATC
* * **
2410600 AAAAATATTTTTAAATTATATATATAAATTTTTTTA
1 AAAAATATTTTCAAA-AATATATATAAATAGTTTTA
* *
2410636 AAAAATATTTTCAAAAATATATATTATATAGTTTTC
1 AAAAATATTTTCAAAAATATATA-TAAATAGTTTTA
* * *
2410672 AAAAATATTTTCAAAACTATATATTATATAAGTTTTC
1 AAAAATATTTTCAAAAATATATA-TAAAT-AGTTTTA
** * * * *
2410709 AAATTTGTTTTAAAAAACTATATATTATATAAGTTTTC
1 AAAAATATTTTCAAAAA-TATATA-TAAAT-AGTTTTA
* * *
2410747 AAAAATGTTTTCAAAAAACTATATATTATATATATTTTTT
1 AAAAATATTTTC-AAAAA-TATATA-TA-A-ATAGTTTTA
* * *
2410787 TAAAATGTTTTCAAAAACTATATATTATATATA-TTTTT
1 AAAAATATTTTCAAAAA-TATATA-TA-A-ATAGTTTTA
* * * *
2410825 CAAAATGTTTTTAAAAATCATATATTATATAAGTTTT-
1 AAAAATATTTTCAAAAAT-ATATA-TAAAT-AGTTTTA
* * * * * *
2410862 CAAAATGTTTTTAAAAAACTATATAATATATACATTTTC
1 AAAAAT-ATTTTCAAAAA-TATAT-ATAAATA-GTTTTA
* *
2410901 AAAAATCGTTTTCAAAACTATATATTATATATA-TTTT-
1 AAAAAT-ATTTTCAAAA--ATATA-TATAAATAGTTTTA
* * *
2410938 CAAAATGTTTTCAAAACTATATA
1 AAAAATATTTTCAAAAATATATA
2410961 ACATATATAT
Statistics
Matches: 277, Mismatches: 31, Indels: 37
0.80 0.09 0.11
Matches are distributed among these distances:
33 2 0.01
34 4 0.01
35 7 0.03
36 62 0.22
37 33 0.12
38 87 0.31
39 51 0.18
40 27 0.10
41 4 0.01
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (35 bp):
AAAAATATTTTCAAAAATATATATAAATAGTTTTA
Found at i:2410899 original size:76 final size:76
Alignment explanation
Indices: 2410578--2410972 Score: 391
Period size: 76 Copynumber: 5.2 Consensus size: 76
2410568 AAACTATATA
* * * * * * ** *
2410578 TATATATATATATATATATATCAAAAATATTTT-TAAATTATATA-TATAAATTTTTTTAAAAAA
1 TATATA-ATATATATATTTTTCAAAAATGTTTTCAAAAATATATATTATATATAGTTTT-CAAAA
* *
2410641 TATTTTCAAAAA-
64 TGTTTTAAAAAAC
* * * *
2410653 TATAT-AT-TATATAGTTTTCAAAAATATTTTCAAAACTATATATTATATA-AGTTTTCAAATTT
1 TATATAATATATATATTTTTCAAAAATGTTTTCAAAAATATATATTATATATAGTTTTCAAA-AT
2410715 GTTTTAAAAAAC
65 GTTTTAAAAAAC
* * * *
2410727 TATATATTATATA-AGTTTTCAAAAATGTTTTCAAAAAACTATATATTATATATATTTTTTTAAA
1 TATATAATATATATATTTTTCAAAAATGTTTTC-AAAAA-TATATATTATATATA-GTTTTCAAA
*
2410791 ATGTTTTCAAAAAC
63 ATGTTTTAAAAAAC
* *
2410805 TATATATTATATATATTTTTC-AAAATGTTTTTAAAAATCATATATTATATA-AGTTTTCAAAAT
1 TATATAATATATATATTTTTCAAAAATGTTTTCAAAAAT-ATATATTATATATAGTTTTCAAAAT
2410868 GTTTTTAAAAAAC
65 G-TTTTAAAAAAC
* *
2410881 TATATAATATATACA-TTTTCAAAAATCGTTTTCAAAACTATATATTATATATA-TTTTCAAAAT
1 TATATAATATATATATTTTTCAAAAAT-GTTTTCAAAAATATATATTATATATAGTTTTCAAAAT
*
2410944 GTTTT-CAAAAC
65 GTTTTAAAAAAC
*
2410955 TATATAACATATATATTT
1 TATATAATATATATATTT
2410973 CAAAAACGAT
Statistics
Matches: 272, Mismatches: 31, Indels: 34
0.81 0.09 0.10
Matches are distributed among these distances:
72 23 0.08
73 25 0.09
74 28 0.10
75 45 0.17
76 61 0.22
77 41 0.15
78 36 0.13
79 13 0.05
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (76 bp):
TATATAATATATATATTTTTCAAAAATGTTTTCAAAAATATATATTATATATAGTTTTCAAAATG
TTTTAAAAAAC
Found at i:2411888 original size:85 final size:85
Alignment explanation
Indices: 2411741--2412006 Score: 327
Period size: 85 Copynumber: 3.1 Consensus size: 85
2411731 ATATGTCATC
* * * *
2411741 GAGCTGAATAGAATCCAACTCGACA-GTTTCTTGTTGACATATAGCCCTTCTCGTCTTAAGTTAT
1 GAGCTGAATAGAATCGAACTCGA-AGGTAT-TTGTTGACATATAGCCCTTCTCGCCTTGAGTTAT
* * *
2411805 ACTGTAAATTTGACAAGCCCTT
64 GCTGTAAATTTGATATGCCCTT
* * *
2411827 GAGCTGAATGGAATCGAACTCGAAGGTATTTGTTGACATATAACCCTTCTTGCCTTGAGTTATGC
1 GAGCTGAATAGAATCGAACTCGAAGGTATTTGTTGACATATAGCCCTTCTCGCCTTGAGTTATGC
* *
2411892 TGCAAATTTGATATGTCCTT
66 TGTAAATTTGATATGCCCTT
* * * * * * *
2411912 GAGCTAAATATAATCGAACTTGAAGGTCTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGC
1 GAGCTGAATAGAATCGAACTCGAAGGTATTTGTTGACATATAGCCCTTCTCGCCTTGAGTTATGC
2411977 TGTAAATTTGATATGCCCTT
66 TGTAAATTTGATATGCCCTT
*
2411997 GATCTGAATA
1 GAGCTGAATA
2412007 TAAGGTTTGT
Statistics
Matches: 153, Mismatches: 26, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
85 129 0.84
86 24 0.16
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (85 bp):
GAGCTGAATAGAATCGAACTCGAAGGTATTTGTTGACATATAGCCCTTCTCGCCTTGAGTTATGC
TGTAAATTTGATATGCCCTT
Found at i:2413516 original size:99 final size:98
Alignment explanation
Indices: 2413345--2413540 Score: 293
Period size: 99 Copynumber: 2.0 Consensus size: 98
2413335 GGACAACTCA
* * *
2413345 ATATTATAATCACCTTTATCATGCTAGCTGAATATTATCCATAAAAATGGGTCGTTTAACCAATT
1 ATATTATAATCACCTTTATCAGGCTAACTGAATATTATCCATAAAAATGGGGCGTTTAACCAATT
* *
2413410 GCTCTAGAGGGATAGCTTAAGCTTTATTGTATAG
66 GCTCTAGAGGGACAG-TCAAGCTTTATTGTATAG
* * **
2413444 ATATTATAATCACTTTTATCAGGCTAACTGAATCTTATCCATAAAGCTGGGGCGTTTAACCAATT
1 ATATTATAATCACCTTTATCAGGCTAACTGAATATTATCCATAAAAATGGGGCGTTTAACCAATT
*
2413509 GCTCTAGATGGACAGTCAAGCTTTATTGTATA
66 GCTCTAGAGGGACAGTCAAGCTTTATTGTATA
2413541 TATAGTATTA
Statistics
Matches: 87, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
98 16 0.18
99 71 0.82
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (98 bp):
ATATTATAATCACCTTTATCAGGCTAACTGAATATTATCCATAAAAATGGGGCGTTTAACCAATT
GCTCTAGAGGGACAGTCAAGCTTTATTGTATAG
Found at i:2417479 original size:22 final size:24
Alignment explanation
Indices: 2417449--2417496 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
2417439 ATATAATATG
*
2417449 AAATGAAAT-AAA-GAAAATATTA
1 AAATAAAATAAAATGAAAATATTA
*
2417471 AAATAAAATAAAATGAAAATGTTA
1 AAATAAAATAAAATGAAAATATTA
2417495 AA
1 AA
2417497 TTTTAAAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 8 0.36
23 3 0.14
24 11 0.50
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (24 bp):
AAATAAAATAAAATGAAAATATTA
Found at i:2417580 original size:3 final size:3
Alignment explanation
Indices: 2417572--2417611 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
2417562 TAGTTGTAGT
2417572 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2417612 ATATAAAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2418183 original size:36 final size:37
Alignment explanation
Indices: 2418074--2418185 Score: 122
Period size: 36 Copynumber: 3.1 Consensus size: 37
2418064 AGAGCCCCAC
* * *
2418074 TATATAATATATACATTTTCAAAAATCGTTTTTAAAAT
1 TATATAATATATATATTTTCAAAAA-CGATTTTAAAAA
* * *
2418112 TATAGATTATATATATTTTC-AAAA-TATTTTCAAAAA
1 TATATAATATATATATTTTCAAAAACGATTTT-AAAAA
*
2418148 TATATAACATATATA-TTTCAAAAACGATTTTAAAAA
1 TATATAATATATATATTTTCAAAAACGATTTTAAAAA
2418184 TA
1 TA
2418186 AAACAGAAAT
Statistics
Matches: 61, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
35 8 0.13
36 27 0.44
37 9 0.15
38 17 0.28
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.42
Consensus pattern (37 bp):
TATATAATATATATATTTTCAAAAACGATTTTAAAAA
Found at i:2418962 original size:9 final size:9
Alignment explanation
Indices: 2418948--2418973 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
2418938 GAAATCGATT
2418948 AATTAACCG
1 AATTAACCG
2418957 AATTAACCG
1 AATTAACCG
2418966 AATTAACC
1 AATTAACC
2418974 TTTACATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (9 bp):
AATTAACCG
Found at i:2419098 original size:17 final size:17
Alignment explanation
Indices: 2419076--2419114 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
2419066 TGAATCAAAT
2419076 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
2419093 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
2419110 -AATTA
1 TAATTA
2419115 ATTGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:2419949 original size:24 final size:23
Alignment explanation
Indices: 2419922--2419972 Score: 84
Period size: 24 Copynumber: 2.2 Consensus size: 23
2419912 GTTATTTAAA
*
2419922 CGGGTATTGGGTCGGATATTGGGT
1 CGGGTATTGGGTCGG-TATTGGGC
2419946 CGGGTATTGGGTCGGTATTGGGC
1 CGGGTATTGGGTCGGTATTGGGC
2419969 CGGG
1 CGGG
2419973 AATCGGGCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.10, C:0.12, G:0.49, T:0.29
Consensus pattern (23 bp):
CGGGTATTGGGTCGGTATTGGGC
Found at i:2419964 original size:11 final size:11
Alignment explanation
Indices: 2419924--2419967 Score: 70
Period size: 12 Copynumber: 3.8 Consensus size: 11
2419914 TATTTAAACG
2419924 GGTATTGGGTC
1 GGTATTGGGTC
2419935 GGATATTGGGTC
1 GG-TATTGGGTC
2419947 GGGTATTGGGTC
1 -GGTATTGGGTC
2419959 GGTATTGGG
1 GGTATTGGG
2419968 CCGGGAATCG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.35
12 18 0.58
13 2 0.06
ACGTcount: A:0.11, C:0.07, G:0.48, T:0.34
Consensus pattern (11 bp):
GGTATTGGGTC
Found at i:2426463 original size:2 final size:2
Alignment explanation
Indices: 2426458--2426482 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2426448 TATATATATA
2426458 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
2426483 CTAAATGAAA
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2428398 original size:19 final size:21
Alignment explanation
Indices: 2428376--2428420 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
2428366 CTCCTTCATG
2428376 TTTATG-T-TTTTCTTTCTTT
1 TTTATGTTGTTTTCTTTCTTT
2428395 TTTATGTTTGTTTTCTTTCTTT
1 TTTATG-TTGTTTTCTTTCTTT
2428417 TTTA
1 TTTA
2428421 GCATGAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.26
21 1 0.04
22 16 0.70
ACGTcount: A:0.07, C:0.09, G:0.07, T:0.78
Consensus pattern (21 bp):
TTTATGTTGTTTTCTTTCTTT
Found at i:2428411 original size:18 final size:19
Alignment explanation
Indices: 2428376--2428412 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2428366 CTCCTTCATG
*
2428376 TTTATGTTTTTCTTTCTTT
1 TTTATGTTTGTCTTTCTTT
2428395 TTTATGTTTGT-TTTCTTT
1 TTTATGTTTGTCTTTCTTT
2428413 CTTTTTTAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.05, C:0.08, G:0.08, T:0.78
Consensus pattern (19 bp):
TTTATGTTTGTCTTTCTTT
Found at i:2429255 original size:32 final size:32
Alignment explanation
Indices: 2429213--2429322 Score: 123
Period size: 32 Copynumber: 3.3 Consensus size: 32
2429203 TTTTCTAACT
2429213 TACTAACATTCTAACTTTTATTTTATCGTTCGA
1 TACTAACATTCTAACTTTTATTTTATCGTTC-A
*
2429246 -ACTAACATTCTAACTTTTATTTTATTGTTCA
1 TACTAACATTCTAACTTTTATTTTATCGTTCA
* * * *
2429277 TACTAACATACTGACTTTTTTTATTTTTATTGTTCT
1 TACTAACATTCTAAC---TTTTA-TTTTATCGTTCA
2429313 TACTAACATT
1 TACTAACATT
2429323 TTATTTTATT
Statistics
Matches: 67, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
31 1 0.01
32 41 0.61
35 5 0.07
36 20 0.30
ACGTcount: A:0.27, C:0.16, G:0.05, T:0.52
Consensus pattern (32 bp):
TACTAACATTCTAACTTTTATTTTATCGTTCA
Found at i:2430029 original size:11 final size:11
Alignment explanation
Indices: 2429965--2430030 Score: 62
Period size: 11 Copynumber: 5.9 Consensus size: 11
2429955 CGATAGTCTT
*
2429965 TTTTTATTATA
1 TTTTTATTTTA
*
2429976 TTTTTATCTTA
1 TTTTTATTTTA
2429987 TTATTTTATTTTA
1 -T-TTTTATTTTA
* * *
2430000 -TCTCATTCTA
1 TTTTTATTTTA
2430010 TTTTTATTTTA
1 TTTTTATTTTA
2430021 TTTTTATTTT
1 TTTTTATTTT
2430031 TATCTTTGAT
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
10 7 0.16
11 26 0.60
12 1 0.02
13 9 0.21
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:2431900 original size:29 final size:29
Alignment explanation
Indices: 2431858--2431916 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
2431848 ATATAGAGAG
2431858 ATAAAATTTTCAATCAAACAGTCACGTAC
1 ATAAAATTTTCAATCAAACAGTCACGTAC
2431887 ATAAAATTTTCAATCAAACAGTCACGTAC
1 ATAAAATTTTCAATCAAACAGTCACGTAC
2431916 A
1 A
2431917 CAGACATGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.46, C:0.20, G:0.07, T:0.27
Consensus pattern (29 bp):
ATAAAATTTTCAATCAAACAGTCACGTAC
Found at i:2445007 original size:61 final size:61
Alignment explanation
Indices: 2444841--2445030 Score: 159
Period size: 61 Copynumber: 3.1 Consensus size: 61
2444831 TTTATAGAAT
* * ** *
2444841 ATCTTCAACACCAAAATATCTCTAGATTGACTGGATTTCCTCAACAAGAATGAACAATGTC
1 ATCTTCAACACCAAATTATCTCAAGATTGACCAGATTTCCTCAACAAGAATGAACAAAGTC
** * * * * * * *
2444902 ATCTTCAACAAAAAATTTATCT-AAAAGTGACCAAATCTCTTCAACATGAATGAGCAAAGTC
1 ATCTTCAACACCAAA-TTATCTCAAGATTGACCAGATTTCCTCAACAAGAATGAACAAAGTC
* * * * * * *
2444963 GTCTTTAACACCAAATTATCTCCAGATTGACCCGATTTCCTCAACGACAAGGAACAACA-TC
1 ATCTTCAACACCAAATTATCTCAAGATTGACCAGATTTCCTCAACAAGAATGAACAA-AGTC
2445024 ATCTTCA
1 ATCTTCA
2445031 CCAAACGATT
Statistics
Matches: 94, Mismatches: 32, Indels: 6
0.71 0.24 0.05
Matches are distributed among these distances:
60 6 0.06
61 82 0.87
62 6 0.06
ACGTcount: A:0.38, C:0.24, G:0.11, T:0.27
Consensus pattern (61 bp):
ATCTTCAACACCAAATTATCTCAAGATTGACCAGATTTCCTCAACAAGAATGAACAAAGTC
Found at i:2445065 original size:122 final size:121
Alignment explanation
Indices: 2444842--2445129 Score: 328
Period size: 122 Copynumber: 2.4 Consensus size: 121
2444832 TTATAGAATA
* * ** * * **
2444842 TCTTCAACACCAAAATATCTCTAGATTGACTGGATTTCCTCAACAAGAATGAACAATGTCATCTT
1 TCTTTAACACCAAATTATCTCTAGATTGACCCGATTTCCTCAACAACAAGGAACAACATCATCTT
*
2444907 CAACAAAAAATTTATCTAAAAGTGACCAAATCTCTTCAACATGAATGAGCAAAGTCG
66 CAACAAAAAATTTATCTAAAAGTGACCAAATATCTTCAACATG-ATGAGCAAAGTCG
* *
2444964 TCTTTAACACCAAATTATCTCCAGATTGACCCGATTTCCTCAACGACAAGGAACAACATCATCTT
1 TCTTTAACACCAAATTATCTCTAGATTGACCCGATTTCCTCAACAACAAGGAACAACATCATCTT
* ** * * **
2445029 CACCAAACGATTTATCTGAAAA-TGGCCAGATATCTTCAACATGATGAGCAGTGTCG
66 CAACAAAAAATTTATCT-AAAAGTGACCAAATATCTTCAACATGATGAGCAAAGTCG
* ** **
2445085 T-TTTCAACACTAAATTAAATCTAGATTGACCCGAAGTCCTCAACA
1 TCTTT-AACACCAAATTATCTCTAGATTGACCCGATTTCCTCAACA
2445130 TGAAAGAACA
Statistics
Matches: 139, Mismatches: 25, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
120 3 0.02
121 45 0.32
122 87 0.63
123 4 0.03
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (121 bp):
TCTTTAACACCAAATTATCTCTAGATTGACCCGATTTCCTCAACAACAAGGAACAACATCATCTT
CAACAAAAAATTTATCTAAAAGTGACCAAATATCTTCAACATGATGAGCAAAGTCG
Found at i:2445147 original size:121 final size:121
Alignment explanation
Indices: 2444878--2445149 Score: 300
Period size: 121 Copynumber: 2.2 Consensus size: 121
2444868 TGACTGGATT
* *
2444878 TCCTCAACAAGAATGAACAATGTCATCTTCAACAAAAAATTTATCTAAAAGTGACCAAATCTCTT
1 TCCTCAAC-AGAAAGAACAATGTCATCTTCAACAAAAAATTTATCTAAAAGTGACCAAATATCTT
** **
2444943 CAACATGAATGAGCAAAGTCGTCTTTAACACCAAATTATCTCCAGATTGACCCGATT
65 CAACATGAATGAGCAAAGTCGTCTTTAACACCAAATTAAATCCAGATTGACCCGAAG
** * ** * *
2445000 TCCTCAAC-GACAAGGAACAACATCATCTTCACCAAACGATTTATCTGAAAA-TGGCCAGATATC
1 TCCTCAACAGA-AA-GAACAATGTCATCTTCAACAAAAAATTTATCT-AAAAGTGACCAAATATC
** * *
2445063 TTCAACATG-ATGAGCAGTGTCGT-TTTCAACACTAAATTAAATCTAGATTGACCCGAAG
63 TTCAACATGAATGAGCAAAGTCGTCTTT-AACACCAAATTAAATCCAGATTGACCCGAAG
*
2445121 TCCTCAACATGAAAGAACATTGTCATCTT
1 TCCTCAACA-GAAAGAACAATGTCATCTT
2445150 TAAATTCTCT
Statistics
Matches: 124, Mismatches: 20, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
120 5 0.04
121 58 0.47
122 55 0.44
123 6 0.05
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (121 bp):
TCCTCAACAGAAAGAACAATGTCATCTTCAACAAAAAATTTATCTAAAAGTGACCAAATATCTTC
AACATGAATGAGCAAAGTCGTCTTTAACACCAAATTAAATCCAGATTGACCCGAAG
Found at i:2445497 original size:19 final size:19
Alignment explanation
Indices: 2445457--2445496 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
2445447 CTCCTTTATG
*
2445457 TTTATGTTTTTCTTTCTTT
1 TTTATGTTTGTCTTTCTTT
2445476 TTTATGTTTGT-TTTCTTT
1 TTTATGTTTGTCTTTCTTT
2445494 TTT
1 TTT
2445497 TTTTATCATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.05, C:0.07, G:0.07, T:0.80
Consensus pattern (19 bp):
TTTATGTTTGTCTTTCTTT
Found at i:2446312 original size:33 final size:33
Alignment explanation
Indices: 2446238--2446339 Score: 100
Period size: 33 Copynumber: 3.1 Consensus size: 33
2446228 ATAAATTTTA
* * * *
2446238 TTTTATCGTTCAAACTAACATT-CTAACTTT-TA
1 TTTTATTGTTCATACTAAC-TTACCAACTTTATT
*
2446270 TTTTATTGTTCATACTAATTTACCAACTTTATT
1 TTTTATTGTTCATACTAACTTACCAACTTTATT
* *
2446303 TTTTATTGTTCTTACTAACTTACTAACATTTTATT
1 TTTTATTGTTCATACTAACTTACCAAC--TTTATT
2446338 TT
1 TT
2446340 AATGCACAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
31 2 0.03
32 23 0.40
33 25 0.43
35 8 0.14
ACGTcount: A:0.27, C:0.16, G:0.03, T:0.54
Consensus pattern (33 bp):
TTTTATTGTTCATACTAACTTACCAACTTTATT
Found at i:2446340 original size:33 final size:33
Alignment explanation
Indices: 2446221--2446340 Score: 131
Period size: 32 Copynumber: 3.7 Consensus size: 33
2446211 TCTAACTTAT
* * *
2446221 TAACATTA-TAAATTTTATTTTATCGTTCAAAC
1 TAACATTACTAACTTTTATTTTATTGTTCATAC
2446253 TAACATT-CTAACTTTTATTTTATTGTTCATAC
1 TAACATTACTAACTTTTATTTTATTGTTCATAC
* * * *
2446285 TAA-TTTACCAACTTTATTTTTTATTGTTCTTAC
1 TAACATTACTAACTTT-TATTTTATTGTTCATAC
2446318 TAAC-TTACTAACATTTTATTTTA
1 TAACATTACTAAC-TTTTATTTTA
2446341 ATGCACAAAC
Statistics
Matches: 74, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
31 2 0.03
32 38 0.51
33 31 0.42
34 3 0.04
ACGTcount: A:0.31, C:0.14, G:0.03, T:0.53
Consensus pattern (33 bp):
TAACATTACTAACTTTTATTTTATTGTTCATAC
Found at i:2449487 original size:23 final size:23
Alignment explanation
Indices: 2449409--2449490 Score: 60
Period size: 23 Copynumber: 3.3 Consensus size: 23
2449399 AATTGCATAC
*
2449409 TAAAATTCCTAA-T-AATAAATAAT
1 TAAAA-TCCTAATTAAATAAA-AAA
*
2449432 TAAAATCCTAATTGAAATTCTAAGCAAAC
1 TAAAATCCTAATT-AAA---TAA--AAAA
2449461 TAAAATCCTAATTAAATAAAAAA
1 TAAAATCCTAATTAAATAAAAAA
2449484 TAAAATC
1 TAAAATC
2449491 TAAGATGTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
22 6 0.12
23 16 0.33
25 5 0.10
28 6 0.12
29 15 0.31
30 1 0.02
ACGTcount: A:0.56, C:0.12, G:0.02, T:0.29
Consensus pattern (23 bp):
TAAAATCCTAATTAAATAAAAAA
Found at i:2449773 original size:20 final size:20
Alignment explanation
Indices: 2449725--2449765 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
2449715 TTAGTTAGTG
2449725 ACTAAAATATAAGTTTTAAA
1 ACTAAAATATAAGTTTTAAA
2449745 ACTAAAATATAAGTTTTAAA
1 ACTAAAATATAAGTTTTAAA
2449765 A
1 A
2449766 GTTTAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.34
Consensus pattern (20 bp):
ACTAAAATATAAGTTTTAAA
Found at i:2450995 original size:21 final size:20
Alignment explanation
Indices: 2450951--2450996 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
2450941 TGGGGTGTTC
2450951 AATGCTGAATTTTAATTATGG
1 AATGCTGAATTTTAATTA-GG
2450972 AATGCTGAAATTTTAAGTTA-G
1 AATGCTG-AATTTTAA-TTAGG
2450993 AATG
1 AATG
2450997 ATGATTGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 12 0.52
22 8 0.35
23 3 0.13
ACGTcount: A:0.37, C:0.04, G:0.20, T:0.39
Consensus pattern (20 bp):
AATGCTGAATTTTAATTAGG
Found at i:2452279 original size:36 final size:36
Alignment explanation
Indices: 2452232--2452304 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
2452222 GGAAAGAAAT
* *
2452232 ACAAAATGATTATTTTCTATGATAATGTTTATGATG
1 ACAAAATGATTATTTTATATGATAATGTTTATCATG
2452268 ACAAAATGATTATTTTATATGATAATGTTTATCATG
1 ACAAAATGATTATTTTATATGATAATGTTTATCATG
2452304 A
1 A
2452305 TTTTGATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.44
Consensus pattern (36 bp):
ACAAAATGATTATTTTATATGATAATGTTTATCATG
Found at i:2454502 original size:14 final size:14
Alignment explanation
Indices: 2454473--2454530 Score: 64
Period size: 14 Copynumber: 4.1 Consensus size: 14
2454463 TTATGTACCT
* *
2454473 AAATATATAAAGAA
1 AAATAAATAAATAA
2454487 AAATAAA-AAATAA
1 AAATAAATAAATAA
2454500 AAATAAATAAATAA
1 AAATAAATAAATAA
*
2454514 AATAAAAATAAAGTAA
1 AA-ATAAATAAA-TAA
2454530 A
1 A
2454531 CAGTAAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
13 12 0.32
14 14 0.37
15 8 0.21
16 4 0.11
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (14 bp):
AAATAAATAAATAA
Found at i:2454503 original size:13 final size:13
Alignment explanation
Indices: 2454485--2454525 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
2454475 ATATATAAAG
2454485 AAAAATAAAAAAT
1 AAAAATAAAAAAT
2454498 AAAAATAAATAAAT
1 AAAAATAAA-AAAT
2454512 -AAAAT-AAAAAT
1 AAAAATAAAAAAT
2454523 AAA
1 AAA
2454526 GTAAACAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 4 0.15
12 4 0.15
13 14 0.54
14 4 0.15
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:2454517 original size:19 final size:20
Alignment explanation
Indices: 2454493--2454530 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
2454483 AGAAAAATAA
2454493 AAAATAAAAATAAA-TAAAT
1 AAAATAAAAATAAAGTAAAT
2454512 AAAATAAAAATAAAGTAAA
1 AAAATAAAAATAAAGTAAA
2454531 CAGTAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (20 bp):
AAAATAAAAATAAAGTAAAT
Found at i:2454541 original size:24 final size:20
Alignment explanation
Indices: 2454487--2454530 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 20
2454477 ATATAAAGAA
2454487 AAATAAAAAATAAAAATAAAT
1 AAAT-AAAAATAAAAATAAAT
2454508 AAAT-AAAATAAAAATAAAGT
1 AAATAAAAATAAAAATAAA-T
2454528 AAA
1 AAA
2454531 CAGTAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 14 0.64
20 4 0.18
21 4 0.18
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (20 bp):
AAATAAAAATAAAAATAAAT
Found at i:2458102 original size:37 final size:37
Alignment explanation
Indices: 2458049--2458153 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
2458039 CCTTTTCGTC
2458049 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
2458086 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
** * *
2458123 CTACTATTATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
2458154 CCACAAGCAT
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:2458748 original size:2 final size:2
Alignment explanation
Indices: 2458741--2458767 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2458731 TTCCTAACGT
2458741 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 T
2458768 TCTTACTTCA
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:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2458909 original size:13 final size:14
Alignment explanation
Indices: 2458824--2458926 Score: 56
Period size: 13 Copynumber: 7.2 Consensus size: 14
2458814 ATATTATATG
2458824 TATATTATTTTTCATT
1 TATATTA-TTTT-ATT
2458840 TAT-TTATTATTATT
1 TATATTATT-TTATT
*
2458854 GT-TACTATTTAGTATT
1 -TATATTATTT--TATT
**
2458870 T-TATTATATTATACA
1 TATATTAT-TT-TATT
2458885 TATATT-TTTTATT
1 TATATTATTTTATT
2458898 T-TATTATTTTATT
1 TATATTATTTTATT
*
2458911 TATACTA-TTTATT
1 TATATTATTTTATT
2458924 TAT
1 TAT
2458927 TTTTATTATG
Statistics
Matches: 70, Mismatches: 8, Indels: 21
0.71 0.08 0.21
Matches are distributed among these distances:
12 4 0.06
13 20 0.29
14 13 0.19
15 20 0.29
16 13 0.19
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (14 bp):
TATATTATTTTATT
Found at i:2458931 original size:31 final size:30
Alignment explanation
Indices: 2458838--2458935 Score: 96
Period size: 28 Copynumber: 3.3 Consensus size: 30
2458828 TTATTTTTCA
*
2458838 TTTATTTATTATTATTGT-TACTATTTA-GTAT
1 TTTA-TTATT-TTATT-TATACTATTTATTTAT
* **
2458869 TTTATTATATTATACATA-TATTT-TTTAT
1 TTTATTATTTTATTTATACTATTTATTTAT
2458897 TTTATTATTTTATTTATACTATTTATTTATT
1 TTTATTATTTTATTTATACTATTTATTTA-T
2458928 TTTATTAT
1 TTTATTAT
2458936 GTTTTTAGTT
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
28 23 0.42
29 11 0.20
30 8 0.15
31 13 0.24
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (30 bp):
TTTATTATTTTATTTATACTATTTATTTAT
Found at i:2462959 original size:23 final size:23
Alignment explanation
Indices: 2462933--2463008 Score: 84
Period size: 23 Copynumber: 3.3 Consensus size: 23
2462923 TCCAATCAAG
*
2462933 AACAAAAAAGCAAAGAAGCAAAA
1 AACAAAAAAGAAAAGAAGCAAAA
* *
2462956 AACAAATAAA-AAAGAGAATC-AAG
1 AACAAA-AAAGAAA-AGAAGCAAAA
2462979 AACAAAAAAGAAAAGAAGCAAAA
1 AACAAAAAAGAAAAGAAGCAAAA
*
2463002 ATCAAAA
1 AACAAAA
2463009 GAAAAAGGGA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
22 8 0.19
23 27 0.63
24 8 0.19
ACGTcount: A:0.74, C:0.11, G:0.12, T:0.04
Consensus pattern (23 bp):
AACAAAAAAGAAAAGAAGCAAAA
Found at i:2462976 original size:46 final size:46
Alignment explanation
Indices: 2462926--2463015 Score: 146
Period size: 46 Copynumber: 2.0 Consensus size: 46
2462916 TCGAAGATCC
*
2462926 AATCAAGAACAAAAAAGCAAAGAAGCAAAAAACAAATA-AAAAAGAG
1 AATCAAGAACAAAAAAGAAAAGAAGCAAAAAACAAA-AGAAAAAGAG
*
2462972 AATCAAGAACAAAAAAGAAAAGAAGCAAAAATCAAAAGAAAAAG
1 AATCAAGAACAAAAAAGAAAAGAAGCAAAAAACAAAAGAAAAAG
2463016 GGACAAAAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
45 1 0.02
46 40 0.98
ACGTcount: A:0.72, C:0.10, G:0.13, T:0.04
Consensus pattern (46 bp):
AATCAAGAACAAAAAAGAAAAGAAGCAAAAAACAAAAGAAAAAGAG
Found at i:2463008 original size:16 final size:15
Alignment explanation
Indices: 2462930--2463011 Score: 53
Period size: 16 Copynumber: 5.3 Consensus size: 15
2462920 AGATCCAATC
2462930 AAGAACAAAAAAGC-A
1 AAGAACAAAAAA-CAA
2462945 AAGAAGCAAAAAAC-A
1 AAGAA-CAAAAAACAA
* * *
2462960 AATAA-AAAAGAGAA
1 AAGAACAAAAAACAA
*
2462974 TCAAGAACAAAAAAGAA
1 --AAGAACAAAAAACAA
*
2462991 AAGAAGCAAAAATCAA
1 AAGAA-CAAAAAACAA
2463007 AAGAA
1 AAGAA
2463012 AAAGGGACAA
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
13 5 0.09
14 1 0.02
15 16 0.30
16 24 0.44
17 8 0.15
ACGTcount: A:0.73, C:0.10, G:0.13, T:0.04
Consensus pattern (15 bp):
AAGAACAAAAAACAA
Found at i:2463645 original size:22 final size:22
Alignment explanation
Indices: 2463620--2463696 Score: 154
Period size: 22 Copynumber: 3.5 Consensus size: 22
2463610 ATCACCCCAT
2463620 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
2463642 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
2463664 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
2463686 CAAACCTTTGA
1 CAAACCTTTGA
2463697 CCAAACACAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 55 1.00
ACGTcount: A:0.36, C:0.27, G:0.13, T:0.23
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:2464783 original size:106 final size:106
Alignment explanation
Indices: 2464655--2465293 Score: 1008
Period size: 106 Copynumber: 6.0 Consensus size: 106
2464645 ATATCGTGCC
* * *
2464655 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
2464720 AAATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
2464761 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
2464826 AATTTCAGAGCCAATTTCAACTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
2464867 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGTACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
2464932 AATTTCGGAGCCAATTTCAACTTCACAATGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
2464973 ACTCCAGACAACACAATTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
**
2465038 AATTTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
2465079 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
2465144 AATTTCGGAGCCAATTTTAACTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * **
2465185 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCAT
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * *
2465250 GATTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
2465291 ACT
1 ACT
2465294 TGGAACAATG
Statistics
Matches: 494, Mismatches: 39, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
106 494 1.00
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (106 bp):
ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:2466097 original size:37 final size:37
Alignment explanation
Indices: 2466044--2466148 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
2466034 CCTTTTCGTC
2466044 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
2466081 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
** * *
2466118 CTACTATTATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
2466149 CCACAAGCAT
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:2466649 original size:2 final size:2
Alignment explanation
Indices: 2466642--2466681 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
2466632 ATTTTCCTAT
2466642 TA TA TA TA TA TA TA TA TA T- 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 TA TA T
2466682 TTTTTATCTA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2466663 original size:19 final size:19
Alignment explanation
Indices: 2466639--2466679 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
2466629 ATTATTTTCC
2466639 TATTATATATATATATATA
1 TATTATATATATATATATA
2466658 TATTATATATATATATATA
1 TATTATATATATATATATA
2466677 TAT
1 TAT
2466680 ATTTTTTATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TATTATATATATATATATA
Found at i:2466889 original size:18 final size:18
Alignment explanation
Indices: 2466866--2466929 Score: 67
Period size: 18 Copynumber: 3.5 Consensus size: 18
2466856 TATATTATAC
2466866 ATATATTTTTATATTTTT
1 ATATATTTTTATATTTTT
*
2466884 ATATATTTTTTTATTTTT
1 ATATATTTTTATATTTTT
* *
2466902 -TATTTTATTTATACTATTT
1 ATATATT-TTTATA-TTTTT
*
2466921 ATTTATTTT
1 ATATATTTT
2466930 CATTATGTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
17 5 0.14
18 22 0.59
19 6 0.16
20 4 0.11
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (18 bp):
ATATATTTTTATATTTTT
Found at i:2466911 original size:20 final size:20
Alignment explanation
Indices: 2466848--2466904 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 20
2466838 TACTATTTAG
* * *
2466848 TATTTTATTATA-TTATACA
1 TATTTTTTTATATTTTTATA
*
2466867 TATATTTTTATATTTTTATA
1 TATTTTTTTATATTTTTATA
2466887 TATTTTTTTAT-TTTTTAT
1 TATTTTTTTATATTTTTAT
2466905 TTTATTTATA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (20 bp):
TATTTTTTTATATTTTTATA
Found at i:2484997 original size:21 final size:21
Alignment explanation
Indices: 2484973--2485012 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2484963 ATATTCTAGA
*
2484973 ATTTAGGTCTCAATACCAAAC
1 ATTTAGATCTCAATACCAAAC
* *
2484994 ATTTTGATCTCGATACCAA
1 ATTTAGATCTCAATACCAA
2485013 TTCCTCGATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.23, G:0.10, T:0.33
Consensus pattern (21 bp):
ATTTAGATCTCAATACCAAAC
Found at i:2485959 original size:18 final size:17
Alignment explanation
Indices: 2485918--2485959 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
2485908 GATTAAGCGA
*
2485918 TGAATGATTCAATGGTC
1 TGAATGATTCAAAGGTC
2485935 TGAATGATTCAAAGGCTC
1 TGAATGATTCAAAGG-TC
*
2485953 TGTATGA
1 TGAATGA
2485960 ATTGGATTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.33
Consensus pattern (17 bp):
TGAATGATTCAAAGGTC
Found at i:2486175 original size:23 final size:23
Alignment explanation
Indices: 2486148--2486210 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
2486138 TGTATTTTAA
*
2486148 TGCTGAATCATTCAGTAGTGTTT
1 TGCTGAATCATTCAGCAGTGTTT
**
2486171 TGCTGTTTCATTCAGCAGTGTTT
1 TGCTGAATCATTCAGCAGTGTTT
* **
2486194 TGTTGTTTCATTCAGCA
1 TGCTGAATCATTCAGCA
2486211 TAGTCTTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.17, C:0.16, G:0.21, T:0.46
Consensus pattern (23 bp):
TGCTGAATCATTCAGCAGTGTTT
Found at i:2486690 original size:43 final size:42
Alignment explanation
Indices: 2486643--2486749 Score: 99
Period size: 43 Copynumber: 2.5 Consensus size: 42
2486633 AAAGGTCACG
*
2486643 ACATATAACGATGTTTTGGGAACAAAC-GGCGCAATAGGTCGTA
1 ACATATAACGATGTTTTGGGAACAAACAGG-GCAA-AGGTCCTA
* ** ** * * *
2486686 ACATATAGCGACATTTTGGGTGCAAACATGGCAAATGTCCTG
1 ACATATAACGATGTTTTGGGAACAAACAGGGCAAAGGTCCTA
*
2486728 ACATATAACGGTGTTTTGGGAA
1 ACATATAACGATGTTTTGGGAA
2486750 TAAATGTCAT
Statistics
Matches: 48, Mismatches: 15, Indels: 3
0.73 0.23 0.05
Matches are distributed among these distances:
42 21 0.44
43 26 0.54
44 1 0.02
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (42 bp):
ACATATAACGATGTTTTGGGAACAAACAGGGCAAAGGTCCTA
Found at i:2487138 original size:2 final size:2
Alignment explanation
Indices: 2487131--2487164 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2487121 CATAAAAATG
*
2487131 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2487165 CAAGAAACAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2496629 original size:61 final size:61
Alignment explanation
Indices: 2496507--2496632 Score: 146
Period size: 61 Copynumber: 2.1 Consensus size: 61
2496497 GTAGTGCTAA
* * * ** * * *
2496507 ACCTACCCTAAGTTTACGCTCTAGTGCTAATCAGGATATGATATGTAGGGTCGTGCCCACC
1 ACCTACACTAAGTTTACACTCTAGTGCTAATCAGGATATGACACATAAGGTCATACCCACC
* *
2496568 ACCTACACTAGGTTTACACTCTAGTGCTAATCCA-GATATGACACATAAGGTCATACTCACC
1 ACCTACACTAAGTTTACACTCTAGTGCTAAT-CAGGATATGACACATAAGGTCATACCCACC
2496629 ACCT
1 ACCT
2496633 GCAGTTAGTG
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
61 52 0.96
62 2 0.04
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.27
Consensus pattern (61 bp):
ACCTACACTAAGTTTACACTCTAGTGCTAATCAGGATATGACACATAAGGTCATACCCACC
Found at i:2498209 original size:29 final size:30
Alignment explanation
Indices: 2498144--2498210 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 30
2498134 ACAACCTATC
* ***
2498144 ATTTTTCCAAAATTACCAATTTGGTCTTTAA
1 ATTTTT-CAAAATTACCAATATGGTCCCCAA
*
2498175 ACTTTTCAAAATTACCAA-ATGGTCCCCAA
1 ATTTTTCAAAATTACCAATATGGTCCCCAA
2498204 ATTTTTC
1 ATTTTTC
2498211 TAAGGTCGAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
29 13 0.43
30 12 0.40
31 5 0.17
ACGTcount: A:0.33, C:0.21, G:0.06, T:0.40
Consensus pattern (30 bp):
ATTTTTCAAAATTACCAATATGGTCCCCAA
Found at i:2503150 original size:23 final size:23
Alignment explanation
Indices: 2503109--2503152 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2503099 ATAATTAAGA
**
2503109 GAATTATCTTTTTTAATTTTTAG
1 GAATTATCTTTTAGAATTTTTAG
*
2503132 GAATTATCTTTTAGGATTTTT
1 GAATTATCTTTTAGAATTTTT
2503153 GGAGTTTTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.25, C:0.05, G:0.11, T:0.59
Consensus pattern (23 bp):
GAATTATCTTTTAGAATTTTTAG
Found at i:2512889 original size:33 final size:34
Alignment explanation
Indices: 2512836--2512912 Score: 120
Period size: 33 Copynumber: 2.3 Consensus size: 34
2512826 TTAGTCACTT
* *
2512836 ACCAAAGAAGAATTTTCCAATAAGTTGACCACCA
1 ACCAAAGATGAATTTCCCAATAAGTTGACCACCA
*
2512870 ACC-AAGATGAATTTCCCAATAAGTTGATCACCA
1 ACCAAAGATGAATTTCCCAATAAGTTGACCACCA
2512903 ACCAAAGATG
1 ACCAAAGATG
2512913 TCAACTTTGC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
33 30 0.77
34 9 0.23
ACGTcount: A:0.43, C:0.23, G:0.13, T:0.21
Consensus pattern (34 bp):
ACCAAAGATGAATTTCCCAATAAGTTGACCACCA
Found at i:2517969 original size:2 final size:2
Alignment explanation
Indices: 2517962--2517988 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2517952 CGTACAATTA
2517962 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 A
2517989 GCTCGTTTTC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2521938 original size:18 final size:19
Alignment explanation
Indices: 2521915--2521952 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
2521905 ACGAAAAATT
*
2521915 TAAATTATA-AAATTAAAA
1 TAAATTATATAAACTAAAA
*
2521933 TAAATTTTATAAACTAAAA
1 TAAATTATATAAACTAAAA
2521952 T
1 T
2521953 TTGAATAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATTATATAAACTAAAA
Found at i:2523049 original size:3 final size:3
Alignment explanation
Indices: 2523043--2523099 Score: 62
Period size: 3 Copynumber: 19.3 Consensus size: 3
2523033 GAGGCGGAGG
* * * * *
2523043 AGA AGA ATA AGA AGA AGA AGA AGG AGA AAA AGA A-A AGG AGA AGG AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
2523090 AGA AGA AGA A
1 AGA AGA AGA A
2523100 TGGAGAGTTA
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (3 bp):
AGA
Found at i:2526461 original size:45 final size:46
Alignment explanation
Indices: 2526398--2526485 Score: 133
Period size: 45 Copynumber: 1.9 Consensus size: 46
2526388 GGTGCTCAAT
* *
2526398 TAATGCACCATTTTAGCTACTTTTC-AAGGTCATTTATTGCAGTAA
1 TAATGCACCATTTCAGCTACTTTTCAAAGGTCATTTAATGCAGTAA
* *
2526443 TAATGTACCGTTTCAGCTACTTTTCAAAGGTCATTTAATGCAG
1 TAATGCACCATTTCAGCTACTTTTCAAAGGTCATTTAATGCAG
2526486 AATTCAAGCA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
45 22 0.58
46 16 0.42
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (46 bp):
TAATGCACCATTTCAGCTACTTTTCAAAGGTCATTTAATGCAGTAA
Found at i:2529090 original size:14 final size:14
Alignment explanation
Indices: 2529067--2529105 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
2529057 AAGTTATGAT
2529067 AATTTGTGAAAATA
1 AATTTGTGAAAATA
*
2529081 AATTTTTG-AAATA
1 AATTTGTGAAAATA
2529094 AATTTGTGAAAA
1 AATTTGTGAAAA
2529106 CAAAAGATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (14 bp):
AATTTGTGAAAATA
Found at i:2529630 original size:19 final size:20
Alignment explanation
Indices: 2529608--2529647 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2529598 TTGCATAAAA
2529608 TTCCCTTAA-ATTTTTTGTT
1 TTCCCTTAACATTTTTTGTT
*
2529627 TTCCCTTAACTTTTTTTGTT
1 TTCCCTTAACATTTTTTGTT
2529647 T
1 T
2529648 CATTTTTACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.12, C:0.17, G:0.05, T:0.65
Consensus pattern (20 bp):
TTCCCTTAACATTTTTTGTT
Found at i:2530438 original size:34 final size:34
Alignment explanation
Indices: 2530395--2530474 Score: 124
Period size: 34 Copynumber: 2.4 Consensus size: 34
2530385 CGCAATAAGT
*
2530395 ACTCCAGGTGCTATCATCAGAAACAAAAATATGC
1 ACTCCAGGTGCAATCATCAGAAACAAAAATATGC
* *
2530429 ACTCCAGGTGCAATCATCAGATACATAAATATGC
1 ACTCCAGGTGCAATCATCAGAAACAAAAATATGC
*
2530463 ACTCCATGTGCA
1 ACTCCAGGTGCA
2530475 GTAAGATATG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.38, C:0.25, G:0.15, T:0.23
Consensus pattern (34 bp):
ACTCCAGGTGCAATCATCAGAAACAAAAATATGC
Found at i:2532853 original size:128 final size:128
Alignment explanation
Indices: 2532583--2533020 Score: 411
Period size: 128 Copynumber: 3.4 Consensus size: 128
2532573 GGGTGACAAG
* * * * ** *
2532583 ACTCCTACATAATGA-GAAGATCTAGT-TAGGAGATGACACTGCTCATACGTGATGAAGAGTTCT
1 ACTCCTACATAATGAGGAA-ATCTGGTCGA-GTGATGACACAGCTCATACGCAATGAAGAG-TCA
* * * * * *
2532646 TGGCCATCTTTAGGAAAAGTGATAACTCAGTTTCTACGTTATGAGGACTG-CGGGTTATCTAGGT
63 TGGCCATC-TT---AAGA-TGATAACACGGTTCCTACGTGATGAGGA-TGACTGGTTATCTAGGT
*
2532710 TGACATA
122 TGACACA
* * * * * *
2532717 GCTTCTACATAATGAGGAAATCTAGTCGAGTGATGACACAGTTCCTACGCAATGAGGACGTCAT-
1 ACTCCTACATAATGAGGAAATCTGGTCGAGTGATGACACAGCTCATACGCAATGAAGA-GTCATG
* * * *
2532781 GCCAT-TTAAAGGTGATAACACGGTTCCTATGTGATGAGGATGACTGGTTATCTGGGTTGCCACA
65 GCCATCTT-AAGATGATAACACGGTTCCTACGTGATGAGGATGACTGGTTATCTAGGTTGACACA
* * * ** **
2532845 ACTCCTACATAATGAGGAGATCTGGT-TAGTTGATGACACGGCTCATACGTGATGAAGAGTTTTG
1 ACTCCTACATAATGAGGAAATCTGGTCGAG-TGATGACACAGCTCATACGCAATGAAGAGTCATG
* * *
2532909 GCCATCTTAAGATGATAACACGGTTCCTACGTGATGAGGATGGCTAGTTATCTAGGTTGATACA
65 GCCATCTTAAGATGATAACACGGTTCCTACGTGATGAGGATGACTGGTTATCTAGGTTGACACA
*
2532973 ACTCCTACATAATGAGGAAATCTGGTCGAGTGATGACACTGCTCATAC
1 ACTCCTACATAATGAGGAAATCTGGTCGAGTGATGACACAGCTCATAC
2533021 TATGATAAGT
Statistics
Matches: 250, Mismatches: 46, Indels: 22
0.79 0.14 0.07
Matches are distributed among these distances:
127 7 0.03
128 180 0.72
129 6 0.02
131 2 0.01
133 5 0.02
134 45 0.18
135 5 0.02
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.29
Consensus pattern (128 bp):
ACTCCTACATAATGAGGAAATCTGGTCGAGTGATGACACAGCTCATACGCAATGAAGAGTCATGG
CCATCTTAAGATGATAACACGGTTCCTACGTGATGAGGATGACTGGTTATCTAGGTTGACACA
Found at i:2533149 original size:31 final size:32
Alignment explanation
Indices: 2533110--2533170 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
2533100 TCAAAAGAGA
*
2533110 CAAAATTTTTATTTCT-AAA-GAAACAAAACT
1 CAAAATTTTTATGTCTCAAATGAAACAAAACT
*
2533140 CAAAGATTTTTATGTCTCAAATGATACAAAA
1 CAAA-ATTTTTATGTCTCAAATGAAACAAAA
2533171 TTTGTTTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 4 0.15
31 11 0.42
32 3 0.12
33 8 0.31
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.33
Consensus pattern (32 bp):
CAAAATTTTTATGTCTCAAATGAAACAAAACT
Found at i:2534442 original size:11 final size:11
Alignment explanation
Indices: 2534426--2534469 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
2534416 ATTCTCGTCC
*
2534426 CTTTTTCTTTG
1 CTTTTTCTTTT
2534437 CTTTTT-TTTT
1 CTTTTTCTTTT
*
2534447 CTTTTTTTTTTT
1 C-TTTTTCTTTT
2534459 CTTTTTCTTTT
1 CTTTTTCTTTT
2534470 TCTTCTTCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 4 0.14
11 20 0.69
12 5 0.17
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (11 bp):
CTTTTTCTTTT
Found at i:2534447 original size:15 final size:13
Alignment explanation
Indices: 2534427--2534476 Score: 57
Period size: 15 Copynumber: 3.6 Consensus size: 13
2534417 TTCTCGTCCC
2534427 TTTTTCTTTGCTTTT
1 TTTTTCTTT--TTTT
2534442 TTTTTC-TTTTTT
1 TTTTTCTTTTTTT
2534454 TTTTTCTTTTTCTT
1 TTTTTCTTTTT-TT
2534468 TTTCTTCTT
1 TTT-TTCTT
2534477 CTAGTGTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
12 10 0.31
13 4 0.12
14 7 0.22
15 11 0.34
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (13 bp):
TTTTTCTTTTTTT
Found at i:2534451 original size:6 final size:6
Alignment explanation
Indices: 2534426--2534478 Score: 58
Period size: 6 Copynumber: 9.3 Consensus size: 6
2534416 ATTCTCGTCC
* *
2534426 CTTTTT C-TTTG C-TTTT -TTTTT CTTTTT TTTTTT CTTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
2534471 CTTCTT CT
1 CTTTTT CT
2534479 AGTGTAATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
5 11 0.28
6 29 0.73
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (6 bp):
CTTTTT
Found at i:2538879 original size:62 final size:63
Alignment explanation
Indices: 2538729--2538892 Score: 267
Period size: 63 Copynumber: 2.6 Consensus size: 63
2538719 ATTTATGATG
2538729 ATCATGCAGAATGTGAAGATGCAAATGCAGATGCAAAATTAATGATCCTATGAAATACAATGC
1 ATCATGCAGAATGTGAAGATGCAAATGCAGATGCAAAATTAATGATCCTATGAAATACAATGC
* * * *
2538792 ATCATGCAGAATGCGAAGATACAAATGCAGATGCAAAATTGATGATCCTCTG-AATACAATGC
1 ATCATGCAGAATGTGAAGATGCAAATGCAGATGCAAAATTAATGATCCTATGAAATACAATGC
* *
2538854 ATCATGCAGAATGTAAAGATGCAAATGCAGATGAAAAAT
1 ATCATGCAGAATGTGAAGATGCAAATGCAGATGCAAAAT
2538893 GCAAAGATGC
Statistics
Matches: 93, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
62 45 0.48
63 48 0.52
ACGTcount: A:0.43, C:0.15, G:0.20, T:0.23
Consensus pattern (63 bp):
ATCATGCAGAATGTGAAGATGCAAATGCAGATGCAAAATTAATGATCCTATGAAATACAATGC
Found at i:2538896 original size:19 final size:21
Alignment explanation
Indices: 2538857--2538897 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
2538847 ACAATGCATC
*
2538857 ATGCAGAATGTAAAGATGCAA
1 ATGCAGAATGTAAAAATGCAA
2538878 ATGCAG-ATG-AAAAATGCAA
1 ATGCAGAATGTAAAAATGCAA
2538897 A
1 A
2538898 GATGCAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 10 0.53
20 3 0.16
21 6 0.32
ACGTcount: A:0.51, C:0.10, G:0.22, T:0.17
Consensus pattern (21 bp):
ATGCAGAATGTAAAAATGCAA
Found at i:2538898 original size:27 final size:26
Alignment explanation
Indices: 2538863--2538923 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 26
2538853 CATCATGCAG
*
2538863 AATGTAAAGATGCAAATGCAGATGAAA
1 AATGCAAAGATGCAAATGCAGATG-AA
* *
2538890 AATGCAAAGATGCAAATGCATATGCA
1 AATGCAAAGATGCAAATGCAGATGAA
2538916 AATGCAAA
1 AATGCAAA
2538924 AATAAAATGC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
26 9 0.29
27 22 0.71
ACGTcount: A:0.51, C:0.11, G:0.20, T:0.18
Consensus pattern (26 bp):
AATGCAAAGATGCAAATGCAGATGAA
Found at i:2538914 original size:6 final size:6
Alignment explanation
Indices: 2538872--2538923 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
2538862 GAATGTAAAG
* * *
2538872 ATGCAA ATGCAG ATGAAAA ATGCAAA GATGCAA ATGCAT ATGCAA ATGCAA
1 ATGCAA ATGCAA ATG-CAA ATGC-AA -ATGCAA ATGCAA ATGCAA ATGCAA
2538923 A
1 A
2538924 AATAAAATGC
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
6 25 0.68
7 8 0.22
8 4 0.11
ACGTcount: A:0.50, C:0.13, G:0.19, T:0.17
Consensus pattern (6 bp):
ATGCAA
Found at i:2541481 original size:21 final size:21
Alignment explanation
Indices: 2541455--2541500 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 21
2541445 GGAAACCTTA
2541455 TTACTTTCTTTCATTTATGTT
1 TTACTTTCTTTCATTTATGTT
2541476 TTA----CTTTCATTTATGTT
1 TTACTTTCTTTCATTTATGTT
2541493 TTACTTTC
1 TTACTTTC
2541501 CCATTTCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 8
0.72 0.00 0.28
Matches are distributed among these distances:
17 17 0.81
21 4 0.19
ACGTcount: A:0.15, C:0.15, G:0.04, T:0.65
Consensus pattern (21 bp):
TTACTTTCTTTCATTTATGTT
Found at i:2541482 original size:17 final size:17
Alignment explanation
Indices: 2541462--2541500 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
2541452 TTATTACTTT
2541462 CTTTCATTTATGTTTTA
1 CTTTCATTTATGTTTTA
2541479 CTTTCATTTATGTTTTA
1 CTTTCATTTATGTTTTA
2541496 CTTTC
1 CTTTC
2541501 CCATTTCAAA
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:0.15, C:0.15, G:0.05, T:0.64
Consensus pattern (17 bp):
CTTTCATTTATGTTTTA
Done.