Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003187.1 Hibiscus syriacus cultivar Beakdansim tig00006703_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: 178661
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1919 original size:22 final size:22
Alignment explanation
Indices: 1894--1952 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
1884 ACTTTTAAAT
1894 ATAATTAA-GTAAAAAAATCAAA
1 ATAA-TAATGTAAAAAAATCAAA
*
1916 ATAATAATTTTAAAAAAATCAAA
1 ATAATAA-TGTAAAAAAATCAAA
*
1939 ATTAATAATTTAAA
1 A-TAATAATGTAAA
1953 TACTAAATGT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
21 3 0.09
22 4 0.12
23 20 0.61
24 6 0.18
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (22 bp):
ATAATAATGTAAAAAAATCAAA
Found at i:1933 original size:23 final size:24
Alignment explanation
Indices: 1903--1949 Score: 87
Period size: 23 Copynumber: 2.0 Consensus size: 24
1893 TATAATTAAG
1903 TAAAAAAATCAAAA-TAATAATTT
1 TAAAAAAATCAAAATTAATAATTT
1926 TAAAAAAATCAAAATTAATAATTT
1 TAAAAAAATCAAAATTAATAATTT
1950 AAATACTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (24 bp):
TAAAAAAATCAAAATTAATAATTT
Found at i:2706 original size:16 final size:16
Alignment explanation
Indices: 2685--2718 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
2675 TCATATATTT
2685 TTATTTT-TAAATTATA
1 TTATTTTCTAAA-TATA
2701 TTATTTTCTAAATATA
1 TTATTTTCTAAATATA
2717 TT
1 TT
2719 TACATAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
TTATTTTCTAAATATA
Found at i:2871 original size:33 final size:34
Alignment explanation
Indices: 2831--2901 Score: 99
Period size: 33 Copynumber: 2.1 Consensus size: 34
2821 TGAAGTTGAA
* *
2831 AAAATAATTTAGATTATTAGGGTGAAATAA-TTT
1 AAAATAATTTAGAATATAAGGGTGAAATAATTTT
* *
2864 AAAATAATTTAGAATGTAATGGTGAAATAATTTT
1 AAAATAATTTAGAATATAAGGGTGAAATAATTTT
2898 AAAA
1 AAAA
2902 ATTAAAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 26 0.79
34 7 0.21
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (34 bp):
AAAATAATTTAGAATATAAGGGTGAAATAATTTT
Found at i:12999 original size:19 final size:21
Alignment explanation
Indices: 12955--13011 Score: 73
Period size: 19 Copynumber: 2.8 Consensus size: 21
12945 ATAGGGCAGA
12955 GGGAACCGATACCCCCTTGAAG
1 GGGAACCGATACCCCCTT-AAG
*
12977 GGGAACCGATTCCCCC-T-AG
1 GGGAACCGATACCCCCTTAAG
*
12996 GGGAATCGATACCCCC
1 GGGAACCGATACCCCC
13012 CCCTGGGGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 16 0.50
21 1 0.03
22 15 0.47
ACGTcount: A:0.25, C:0.35, G:0.26, T:0.14
Consensus pattern (21 bp):
GGGAACCGATACCCCCTTAAG
Found at i:16514 original size:24 final size:24
Alignment explanation
Indices: 16468--16514 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
16458 CACTAGTTAT
*
16468 TATATATGATGTTTATCATGAATA
1 TATATATGATGTTTATCACGAATA
*
16492 TATATATGATGTTTATTACGAAT
1 TATATATGATGTTTATCACGAAT
16515 GTTATTTCGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
TATATATGATGTTTATCACGAATA
Found at i:16858 original size:60 final size:61
Alignment explanation
Indices: 16717--16880 Score: 294
Period size: 60 Copynumber: 2.7 Consensus size: 61
16707 GGGTACGACC
** *
16717 TTATGTGTCATATCCGGATCAACACTAGAGTGTAAACTTAGTGAAGATTGTGGGCATGACT
1 TTATGTGTCATATCCGGATCTGCCCTAGAGTGTAAACTTAGTGAAGATTGTGGGCATGACT
16778 TTATGTGTCATATCCGGATCTGCCCTAGAGTGTAAACTTAGTGAAGATTGT-GGCATGACT
1 TTATGTGTCATATCCGGATCTGCCCTAGAGTGTAAACTTAGTGAAGATTGTGGGCATGACT
16838 TTATGTGTCATATCCGGATCTGCCCTAGAGTGTAAACTTAGTG
1 TTATGTGTCATATCCGGATCTGCCCTAGAGTGTAAACTTAGTG
16881 CAGGAGATGG
Statistics
Matches: 100, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
60 52 0.52
61 48 0.48
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.33
Consensus pattern (61 bp):
TTATGTGTCATATCCGGATCTGCCCTAGAGTGTAAACTTAGTGAAGATTGTGGGCATGACT
Found at i:19446 original size:31 final size:31
Alignment explanation
Indices: 19384--19446 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
19374 AGTTGGGCAG
* ***
19384 TGCTCAACTCTTGCTCATTAAAAATTTTTGT
1 TGCTCAACTCGTGCTCATTAAAAAAACTTGT
* *
19415 TGCTCGACTCGTGCTCGTTAAAAAAACTTGT
1 TGCTCAACTCGTGCTCATTAAAAAAACTTGT
19446 T
1 T
19447 CATTGCCTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (31 bp):
TGCTCAACTCGTGCTCATTAAAAAAACTTGT
Found at i:22562 original size:2 final size:2
Alignment explanation
Indices: 22555--22601 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
22545 CTGATATTAC
*
22555 AT AT AT AT AA 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
22597 AT AT A
1 AT AT A
22602 ATAATATCAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:22784 original size:14 final size:14
Alignment explanation
Indices: 22767--22806 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
22757 CATCATAACA
22767 CCTCCTTTCCCTCT
1 CCTCCTTTCCCTCT
*
22781 CCTCCTTTCTCTCT
1 CCTCCTTTCCCTCT
*
22795 CTTCCTTTCCCT
1 CCTCCTTTCCCT
22807 TTGCTTTCCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (14 bp):
CCTCCTTTCCCTCT
Found at i:25453 original size:29 final size:29
Alignment explanation
Indices: 25419--25499 Score: 135
Period size: 29 Copynumber: 2.8 Consensus size: 29
25409 AACTAAATTA
*
25419 ATGTCATTACTTACATCATTTAATTAAAG
1 ATGTCATTGCTTACATCATTTAATTAAAG
*
25448 ATGTCATTGCTTACATCATTTAATTAATG
1 ATGTCATTGCTTACATCATTTAATTAAAG
25477 ATGTCATTGCTTACATCAATTTA
1 ATGTCATTGCTTACATC-ATTTA
25500 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43
Consensus pattern (29 bp):
ATGTCATTGCTTACATCATTTAATTAAAG
Found at i:30222 original size:29 final size:29
Alignment explanation
Indices: 30187--30268 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
30177 AAACTAAATT
*
30187 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
30216 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
30245 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
30269 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:33486 original size:60 final size:60
Alignment explanation
Indices: 33406--33532 Score: 182
Period size: 60 Copynumber: 2.1 Consensus size: 60
33396 AATGGTCCAT
* * * * ** *
33406 CGACTATAGGGTGTTGCTTTGTTGAGTCCCTTGACTATCAAAAGTTACAAAATGATCTCC
1 CGACTATAAGATGTTACTTTGTTAAGTCCCTCAACTATCAAAAGTTACAAAATGATCACC
*
33466 CGACTATAAGATGTTACTTTGTTAAGTCCCTCAACTATTAAAAGTTACAAAATGATCACC
1 CGACTATAAGATGTTACTTTGTTAAGTCCCTCAACTATCAAAAGTTACAAAATGATCACC
33526 CGACTAT
1 CGACTAT
33533 TCATTATGTT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.32
Consensus pattern (60 bp):
CGACTATAAGATGTTACTTTGTTAAGTCCCTCAACTATCAAAAGTTACAAAATGATCACC
Found at i:37286 original size:75 final size:76
Alignment explanation
Indices: 37163--37311 Score: 282
Period size: 75 Copynumber: 2.0 Consensus size: 76
37153 AACATCTCGT
37163 CTCTGAATATATGTAAAGTAAAATGTGAATGAAACTTGGACAAATGTTTCAAATATCCATAC-AA
1 CTCTGAATATATGTAAAGTAAAATGTGAATGAAACTTGGACAAATGTTTCAAATATCCATACAAA
37227 AAAACAATAAG
66 AAAACAATAAG
*
37238 CTCTGAATATATGTAAAGTAAAATGTGAATGAAAGTTGGACAAATGTTTCAAATATCCATACAAA
1 CTCTGAATATATGTAAAGTAAAATGTGAATGAAACTTGGACAAATGTTTCAAATATCCATACAAA
37303 AAAACAATA
66 AAAACAATA
37312 CGCGCACCTG
Statistics
Matches: 72, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
75 61 0.85
76 11 0.15
ACGTcount: A:0.48, C:0.11, G:0.13, T:0.27
Consensus pattern (76 bp):
CTCTGAATATATGTAAAGTAAAATGTGAATGAAACTTGGACAAATGTTTCAAATATCCATACAAA
AAAACAATAAG
Found at i:37497 original size:14 final size:14
Alignment explanation
Indices: 37480--37507 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
37470 CAACTTCAAA
37480 AATTATTGACAGGG
1 AATTATTGACAGGG
37494 AATTATTGACAGGG
1 AATTATTGACAGGG
37508 GATATGCCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.29, T:0.29
Consensus pattern (14 bp):
AATTATTGACAGGG
Found at i:44114 original size:31 final size:31
Alignment explanation
Indices: 44070--44131 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
44060 CAGCCATAAA
* *
44070 CAACCCAAGCTCAAATCTAGTTAGGTACTAG
1 CAACCCAAGCTCAAACCTAGTTAGGGACTAG
* * *
44101 CAACCGAATCTCAAACCTAGTTGGGGACTAG
1 CAACCCAAGCTCAAACCTAGTTAGGGACTAG
44132 TTAACTTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (31 bp):
CAACCCAAGCTCAAACCTAGTTAGGGACTAG
Found at i:51021 original size:22 final size:22
Alignment explanation
Indices: 50993--51037 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
50983 GTCTAAAGAG
50993 TAAACTTCCAAAGTAATCCAGT
1 TAAACTTCCAAAGTAATCCAGT
51015 TAAACTTCCAAAGTAATCCAGT
1 TAAACTTCCAAAGTAATCCAGT
51037 T
1 T
51038 CCAGAAGTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.29
Consensus pattern (22 bp):
TAAACTTCCAAAGTAATCCAGT
Found at i:52492 original size:45 final size:45
Alignment explanation
Indices: 52441--52527 Score: 140
Period size: 45 Copynumber: 1.9 Consensus size: 45
52431 CTAAGCTAGT
* *
52441 GCATCATAAAGGTTA-CATTTTCTTTTTAATTTGATTAATAATAGG
1 GCATCATAAAGG-CAGCATTTTCTTTTTAATCTGATTAATAATAGG
52486 GCATCATAAAGGCAGCATTTTCTTTTTAATCTGATTAATAAT
1 GCATCATAAAGGCAGCATTTTCTTTTTAATCTGATTAATAAT
52528 CAGAGATGAC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
44 1 0.03
45 38 0.97
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.43
Consensus pattern (45 bp):
GCATCATAAAGGCAGCATTTTCTTTTTAATCTGATTAATAATAGG
Found at i:54293 original size:22 final size:24
Alignment explanation
Indices: 54248--54301 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 24
54238 TATAATTTTG
*
54248 TATATATATTGTTTTGACTGTAAT
1 TATATATATTGTTTTGACTATAAT
*
54272 TATAT-TA-TGTTTTGATTATAAT
1 TATATATATTGTTTTGACTATAAT
54294 TGATATAT
1 T-ATATAT
54302 TAAACTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 14 0.54
23 6 0.23
24 6 0.23
ACGTcount: A:0.31, C:0.02, G:0.11, T:0.56
Consensus pattern (24 bp):
TATATATATTGTTTTGACTATAAT
Found at i:61133 original size:12 final size:12
Alignment explanation
Indices: 61112--61181 Score: 63
Period size: 12 Copynumber: 5.8 Consensus size: 12
61102 ACGGAGATAT
* *
61112 CAGAAATCAAAA
1 CAGAATTCAGAA
61124 CAGAATTCA-AA
1 CAGAATTCAGAA
61135 TCAG-ATATCAGAA
1 -CAGAAT-TCAGAA
* *
61148 CAGAATCCAGAT
1 CAGAATTCAGAA
*
61160 CAGAAATCAGAA
1 CAGAATTCAGAA
61172 CAGAATTCAG
1 CAGAATTCAG
61182 GTAATGTATC
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
11 4 0.09
12 39 0.83
13 4 0.09
ACGTcount: A:0.51, C:0.19, G:0.14, T:0.16
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:61137 original size:24 final size:24
Alignment explanation
Indices: 61110--61218 Score: 112
Period size: 24 Copynumber: 4.5 Consensus size: 24
61100 AAACGGAGAT
*
61110 ATCAGAAATCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAA
* * *
61134 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAA
*
61158 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAA
* * * *
61182 GTAATG-TATCAGAACAAAATTCAA
1 ATCA-GAAATCAGAACAGAATTCAA
*
61206 GTCAGAAATCAGA
1 ATCAGAAATCAGA
61219 TAAAATATTT
Statistics
Matches: 70, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
23 1 0.01
24 68 0.97
25 1 0.01
ACGTcount: A:0.50, C:0.17, G:0.15, T:0.18
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAA
Found at i:61192 original size:48 final size:47
Alignment explanation
Indices: 61110--61218 Score: 130
Period size: 48 Copynumber: 2.3 Consensus size: 47
61100 AAACGGAGAT
* * *
61110 ATCAGAAATCAAAACAGAATTCAAATCAGATATCAGAACAGAATCCA
1 ATCAGAAATCAGAACAGAATTCAAATAAGATATCAGAACAAAATCCA
** *
61157 GATCAGAAATCAGAACAGAATTCAGGTAATG-TATCAGAACAAAATTCA
1 -ATCAGAAATCAGAACAGAATTCAAATAA-GATATCAGAACAAAATCCA
61205 AGTCAGAAATCAGA
1 A-TCAGAAATCAGA
61219 TAAAATATTT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
47 1 0.02
48 51 0.96
49 1 0.02
ACGTcount: A:0.50, C:0.17, G:0.15, T:0.18
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCAAATAAGATATCAGAACAAAATCCA
Found at i:62420 original size:43 final size:43
Alignment explanation
Indices: 62323--62422 Score: 132
Period size: 43 Copynumber: 2.3 Consensus size: 43
62313 TCCACGGTAT
* *
62323 TTCA-ATCTTTTTCCTCTATCCGGTCTTATTATTTAATTCCAA
1 TTCATATCTTTTTCCTCCATCCGATCTTATTATTTAATTCCAA
*
62365 TTTATATCTTTTTCCTCCATCCGATCTTATTATTTAATT-CAA
1 TTCATATCTTTTTCCTCCATCCGATCTTATTATTTAATTCCAA
*
62407 TCTCATCATTTTTTTC
1 T-TCAT-ATCTTTTTC
62423 AGTCCTTTCG
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
42 7 0.14
43 35 0.70
44 8 0.16
ACGTcount: A:0.21, C:0.23, G:0.03, T:0.53
Consensus pattern (43 bp):
TTCATATCTTTTTCCTCCATCCGATCTTATTATTTAATTCCAA
Found at i:63772 original size:18 final size:18
Alignment explanation
Indices: 63749--63818 Score: 87
Period size: 18 Copynumber: 4.2 Consensus size: 18
63739 AACGGTCAAA
*
63749 GGTCAATGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
63767 GGTCAA-----CGGGTCG
1 GGTCAACGGGTCGGGTCG
*
63780 GGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
63798 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
63816 GGT
1 GGT
63819 TGTGACCGGT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
13 12 0.27
18 33 0.73
ACGTcount: A:0.13, C:0.19, G:0.50, T:0.19
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:63814 original size:13 final size:13
Alignment explanation
Indices: 63760--63796 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
63750 GTCAATGGGT
63760 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
*
63773 CGGGTCGGGTAAA
1 CGGGTCGGGTCAA
63786 CGGGTCGGGTC
1 CGGGTCGGGTC
63797 GGGTCAACGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.14, C:0.22, G:0.49, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:65899 original size:12 final size:12
Alignment explanation
Indices: 65878--65947 Score: 63
Period size: 12 Copynumber: 5.8 Consensus size: 12
65868 ACGGAGATAT
* *
65878 CAGAAATCAAAA
1 CAGAATTCAGAA
65890 CAGAATTCA-AA
1 CAGAATTCAGAA
65901 TCAG-ATATCAGAA
1 -CAGAAT-TCAGAA
* *
65914 CAGAATCCAGAT
1 CAGAATTCAGAA
*
65926 CAGAAATCAGAA
1 CAGAATTCAGAA
65938 CAGAATTCAG
1 CAGAATTCAG
65948 GTAATGTATC
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
11 4 0.09
12 39 0.83
13 4 0.09
ACGTcount: A:0.51, C:0.19, G:0.14, T:0.16
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:65903 original size:24 final size:24
Alignment explanation
Indices: 65876--65984 Score: 112
Period size: 24 Copynumber: 4.5 Consensus size: 24
65866 AAACGGAGAT
*
65876 ATCAGAAATCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAA
* * *
65900 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAA
*
65924 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAA
* * * *
65948 GTAATG-TATCAGAACAAAATTCAA
1 ATCA-GAAATCAGAACAGAATTCAA
*
65972 GTCAGAAATCAGA
1 ATCAGAAATCAGA
65985 TAAAATATTT
Statistics
Matches: 70, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
23 1 0.01
24 68 0.97
25 1 0.01
ACGTcount: A:0.50, C:0.17, G:0.15, T:0.18
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAA
Found at i:65958 original size:48 final size:47
Alignment explanation
Indices: 65876--65984 Score: 130
Period size: 48 Copynumber: 2.3 Consensus size: 47
65866 AAACGGAGAT
* * *
65876 ATCAGAAATCAAAACAGAATTCAAATCAGATATCAGAACAGAATCCA
1 ATCAGAAATCAGAACAGAATTCAAATAAGATATCAGAACAAAATCCA
** *
65923 GATCAGAAATCAGAACAGAATTCAGGTAATG-TATCAGAACAAAATTCA
1 -ATCAGAAATCAGAACAGAATTCAAATAA-GATATCAGAACAAAATCCA
65971 AGTCAGAAATCAGA
1 A-TCAGAAATCAGA
65985 TAAAATATTT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
47 1 0.02
48 51 0.96
49 1 0.02
ACGTcount: A:0.50, C:0.17, G:0.15, T:0.18
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCAAATAAGATATCAGAACAAAATCCA
Found at i:68550 original size:18 final size:18
Alignment explanation
Indices: 68514--68589 Score: 118
Period size: 18 Copynumber: 4.3 Consensus size: 18
68504 TAACGATCAA
*
68514 CGGGTCAAC-GGTTGGGT
1 CGGGTCAACGGGTCGGGT
*
68531 CGGGTAAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
*
68549 CGGGTCAACGGGCCGGGT
1 CGGGTCAACGGGTCGGGT
68567 CGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
68585 CGGGT
1 CGGGT
68590 TGTGACCGGT
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
17 8 0.15
18 45 0.85
ACGTcount: A:0.12, C:0.21, G:0.50, T:0.17
Consensus pattern (18 bp):
CGGGTCAACGGGTCGGGT
Found at i:69471 original size:34 final size:32
Alignment explanation
Indices: 69399--69493 Score: 111
Period size: 34 Copynumber: 2.9 Consensus size: 32
69389 TTTTCTAACT
*
69399 TACTAACATTCTAACTTTTATTTTATTGTTCA
1 TACTAACATACTAACTTTTATTTTATTGTTCA
*
69431 TACTAACATACTAACTTTTTATTTTTATTGATT-T
1 TACTAACATACTAAC-TTTTA-TTTTATTG-TTCA
* *
69465 TTCTAACTTACTAACATTTTATTTTATTG
1 TACTAACATACTAAC-TTTTATTTTATTG
69494 CACAAACTAA
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
32 14 0.25
33 13 0.24
34 26 0.47
35 2 0.04
ACGTcount: A:0.28, C:0.14, G:0.03, T:0.55
Consensus pattern (32 bp):
TACTAACATACTAACTTTTATTTTATTGTTCA
Found at i:70221 original size:6 final size:6
Alignment explanation
Indices: 70207--70275 Score: 52
Period size: 6 Copynumber: 11.2 Consensus size: 6
70197 TTTGTTTTGT
* * *
70207 TTTTATA TTTTTA -TTTTA -TTTTA TTTTATC TCTTTCTA TTTCTA TTTCTA
1 TTTT-TA TTTTTA TTTTTA TTTTTA TTTT-TA T-TTT-TA TTTTTA TTTTTA
*
70257 TTTTTA TGTTTA TTTTTA T
1 TTTTTA TTTTTA TTTTTA T
70276 CTTTGATATA
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
5 10 0.19
6 29 0.56
7 8 0.15
8 5 0.10
ACGTcount: A:0.17, C:0.07, G:0.01, T:0.74
Consensus pattern (6 bp):
TTTTTA
Found at i:71356 original size:16 final size:16
Alignment explanation
Indices: 71335--71374 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
71325 ATTAAAAACT
*
71335 TACATACATACATCTA
1 TACATACATACATATA
*
71351 TACATACATATATATA
1 TACATACATACATATA
*
71367 TATATACA
1 TACATACA
71375 CTTAAATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.35
Consensus pattern (16 bp):
TACATACATACATATA
Found at i:80075 original size:6 final size:6
Alignment explanation
Indices: 80064--80100 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
80054 CCTTCTCCCC
* *
80064 TTGCTA TTGCTA TTGCTA TTGCTA TTGTTG TTGCTA T
1 TTGCTA TTGCTA TTGCTA TTGCTA TTGCTA TTGCTA T
80101 ACCCTTCATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.14, C:0.14, G:0.19, T:0.54
Consensus pattern (6 bp):
TTGCTA
Found at i:82740 original size:17 final size:17
Alignment explanation
Indices: 82714--82746 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
82704 AGAACTTTGA
82714 AAAATATGTAAACAAAT
1 AAAATATGTAAACAAAT
*
82731 AAAATTTGTAAACAAA
1 AAAATATGTAAACAAA
82747 AATGAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.64, C:0.06, G:0.06, T:0.24
Consensus pattern (17 bp):
AAAATATGTAAACAAAT
Found at i:82777 original size:16 final size:16
Alignment explanation
Indices: 82758--82803 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
82748 ATGAAAAATC
*
82758 TTTAATTAAAAAATAT
1 TTTAATTAAAAAATAA
82774 TTTAATTAAAATAA-AA
1 TTTAATTAAAA-AATAA
*
82790 TTTCATTAAAAAAT
1 TTTAATTAAAAAAT
82804 TGCATTCATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 2 0.08
16 22 0.85
17 2 0.08
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (16 bp):
TTTAATTAAAAAATAA
Found at i:83291 original size:14 final size:14
Alignment explanation
Indices: 83268--83299 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
83258 ACATAATACA
83268 AGTT-AAAAAACAT
1 AGTTAAAAAAACAT
83281 AGTTAAAAAAACAT
1 AGTTAAAAAAACAT
83295 AGTTA
1 AGTTA
83300 CAGTACAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.59, C:0.06, G:0.09, T:0.25
Consensus pattern (14 bp):
AGTTAAAAAAACAT
Found at i:83311 original size:21 final size:21
Alignment explanation
Indices: 83285--83327 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
83275 AAACATAGTT
* *
83285 AAAAAAACATAGTTACAGTAC
1 AAAAAAACATAGATACAATAC
*
83306 AAAAAAGCATAGATACAATAC
1 AAAAAAACATAGATACAATAC
83327 A
1 A
83328 TAATATTTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.60, C:0.14, G:0.09, T:0.16
Consensus pattern (21 bp):
AAAAAAACATAGATACAATAC
Found at i:95669 original size:23 final size:23
Alignment explanation
Indices: 95536--95656 Score: 131
Period size: 23 Copynumber: 5.2 Consensus size: 23
95526 TAGAATTGCA
* *
95536 CCGAAGTACCGCGTAGAATATG-C
1 CCGAAGGACCACGTAGAA-ATGTC
95559 ACCGAAGTG-CCACGTAGAAATG-C
1 -CCGAAG-GACCACGTAGAAATGTC
* * *
95582 CCTGAATGACCACATAGATATGTC
1 CC-GAAGGACCACGTAGAAATGTC
95606 CCGAAGGACCACGTAGAAATGTC
1 CCGAAGGACCACGTAGAAATGTC
*
95629 CCGAAGGACCACGTAGAATTGTC
1 CCGAAGGACCACGTAGAAATGTC
95652 CCGAA
1 CCGAA
95657 TGACTGCGAA
Statistics
Matches: 84, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.04
23 63 0.75
24 18 0.21
ACGTcount: A:0.33, C:0.26, G:0.24, T:0.17
Consensus pattern (23 bp):
CCGAAGGACCACGTAGAAATGTC
Found at i:95779 original size:16 final size:15
Alignment explanation
Indices: 95756--95796 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
95746 CACATAACTT
95756 ATATCACATAT-TCA
1 ATATCACATATATCA
95770 TATAATCACATATATCA
1 -AT-ATCACATATATCA
95787 ATATCACATA
1 ATATCACATA
95797 ATATGGAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 10 0.42
16 11 0.46
17 3 0.12
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (15 bp):
ATATCACATATATCA
Found at i:95800 original size:16 final size:16
Alignment explanation
Indices: 95755--95796 Score: 61
Period size: 15 Copynumber: 2.7 Consensus size: 16
95745 TCACATAACT
95755 TATATCACATAT-TCA
1 TATATCACATATATCA
95770 TATAATCACATATATCA
1 TAT-ATCACATATATCA
95787 -ATATCACATA
1 TATATCACATA
95797 ATATGGAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 11 0.44
16 11 0.44
17 3 0.12
ACGTcount: A:0.45, C:0.19, G:0.00, T:0.36
Consensus pattern (16 bp):
TATATCACATATATCA
Found at i:95963 original size:2 final size:2
Alignment explanation
Indices: 95956--95986 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
95946 CCATAAAACA
95956 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
95987 GTAGTAAGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:98894 original size:3 final size:3
Alignment explanation
Indices: 98886--98935 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
98876 TCTTCCTTGT
98886 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
98934 TT
1 TT
98936 TATTGGAAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:99896 original size:15 final size:16
Alignment explanation
Indices: 99878--99924 Score: 62
Period size: 15 Copynumber: 3.0 Consensus size: 16
99868 TTTAAATTTT
99878 TTAATTTA-ATTAATA
1 TTAATTTATATTAATA
99893 TTAATTTAATATTAAT-
1 TTAATTT-ATATTAATA
*
99909 TTAATATATATTAATA
1 TTAATTTATATTAATA
99925 AAATAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 15 0.54
16 7 0.25
17 6 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAATTTATATTAATA
Found at i:99897 original size:6 final size:6
Alignment explanation
Indices: 99886--99924 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
99876 TTTTAATTTA
99886 ATTAAT ATTAAT -TTAAT ATTAAT -TTAAT A-T-AT ATTAAT A
1 ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT A
99925 AAATAAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
4 3 0.10
5 12 0.41
6 14 0.48
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
ATTAAT
Found at i:99903 original size:11 final size:11
Alignment explanation
Indices: 99877--99915 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
99867 TTTTAAATTT
99877 TTTAAT-TTAA
1 TTTAATATTAA
99887 -TTAATATTAA
1 TTTAATATTAA
99897 TTTAATATTAA
1 TTTAATATTAA
99908 TTTAATAT
1 TTTAATAT
99916 ATATTAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 5 0.19
10 4 0.15
11 18 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TTTAATATTAA
Found at i:99929 original size:26 final size:26
Alignment explanation
Indices: 99878--99929 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
99868 TTTAAATTTT
**
99878 TTAATTTAATTAATATTAATTTAATA
1 TTAATTTAATTAATATTAATAAAATA
99904 TTAATTTAA-TATATATTAATAAAATA
1 TTAATTTAATTA-ATATTAATAAAATA
99930 AAAATAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 2 0.09
26 21 0.91
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
TTAATTTAATTAATATTAATAAAATA
Found at i:102302 original size:47 final size:47
Alignment explanation
Indices: 102233--102372 Score: 149
Period size: 47 Copynumber: 3.0 Consensus size: 47
102223 GTGTTACCCC
**
102233 AGATAACCAACCGCCCTCATCACGTAGGAACCATGTTATCACCCTTT
1 AGATAACCAACCATCCTCATCACGTAGGAACCATGTTATCACCCTTT
* * * * * *
102280 AGATAACTAGCCATCCTCATCACATAGAAACCGTGTTATCACCC-TC
1 AGATAACCAACCATCCTCATCACGTAGGAACCATGTTATCACCCTTT
*** *
102326 AGATAACCAATTGTCCTCATCACGTAGGAACTGA-GTTATCACCCTTT
1 AGATAACCAACCATCCTCATCACGTAGGAAC-CATGTTATCACCCTTT
102373 CTAAAGATGG
Statistics
Matches: 73, Mismatches: 18, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
46 35 0.48
47 38 0.52
ACGTcount: A:0.31, C:0.31, G:0.13, T:0.26
Consensus pattern (47 bp):
AGATAACCAACCATCCTCATCACGTAGGAACCATGTTATCACCCTTT
Found at i:102347 original size:46 final size:46
Alignment explanation
Indices: 102228--102370 Score: 162
Period size: 46 Copynumber: 3.1 Consensus size: 46
102218 GAATCGTGTT
* *
102228 ACCC-CAGATAACCAACCGCCCTCATCACGTAGGAACCATGTTATC
1 ACCCTCAGATAACCAACCGTCCTCATCACGTAGGAACCGTGTTATC
* * * * * *
102273 ACCCTTTAGATAACTAGCCATCCTCATCACATAGAAACCGTGTTATC
1 ACCC-TCAGATAACCAACCGTCCTCATCACGTAGGAACCGTGTTATC
** * *
102320 ACCCTCAGATAACCAATTGTCCTCATCACGTAGGAACTGAGTTATC
1 ACCCTCAGATAACCAACCGTCCTCATCACGTAGGAACCGTGTTATC
102366 ACCCT
1 ACCCT
102371 TTCTAAAGAT
Statistics
Matches: 78, Mismatches: 18, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
45 4 0.05
46 37 0.47
47 37 0.47
ACGTcount: A:0.31, C:0.33, G:0.13, T:0.24
Consensus pattern (46 bp):
ACCCTCAGATAACCAACCGTCCTCATCACGTAGGAACCGTGTTATC
Found at i:103762 original size:16 final size:16
Alignment explanation
Indices: 103743--103774 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
103733 TATATATATA
103743 TATATAATGAATTATT
1 TATATAATGAATTATT
*
103759 TATATTATGAATTATT
1 TATATAATGAATTATT
103775 AGATTTTATA
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:0.06, T:0.53
Consensus pattern (16 bp):
TATATAATGAATTATT
Found at i:104877 original size:31 final size:31
Alignment explanation
Indices: 104834--104903 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
104824 GTTAGCCCCG
104834 AGACACCTAAAATAATAACATTTGTAACGCT
1 AGACACCTAAAATAATAACATTTGTAACGCT
* * *
104865 AGACA-CTCAAAATGATAACGTTTGTAACGTT
1 AGACACCT-AAAATAATAACATTTGTAACGCT
104896 AGACACCT
1 AGACACCT
104904 GGATATGCCG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 2 0.06
31 30 0.88
32 2 0.06
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26
Consensus pattern (31 bp):
AGACACCTAAAATAATAACATTTGTAACGCT
Found at i:108681 original size:14 final size:14
Alignment explanation
Indices: 108658--108700 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
108648 CGATTTATAC
108658 TATATTTTATAAAT
1 TATATTTTATAAAT
*
108672 TATTTTTTATAAA-
1 TATATTTTATAAAT
*
108685 TATATCTTATAAAT
1 TATATTTTATAAAT
108699 TA
1 TA
108701 AAGTTTCTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (14 bp):
TATATTTTATAAAT
Found at i:108694 original size:13 final size:13
Alignment explanation
Indices: 108658--108698 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
108648 CGATTTATAC
108658 TATATTTTATAAA
1 TATATTTTATAAA
*
108671 TTATTTTTTATAAA
1 -TATATTTTATAAA
*
108685 TATATCTTATAAA
1 TATATTTTATAAA
108698 T
1 T
108699 TAAAGTTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (13 bp):
TATATTTTATAAA
Found at i:110868 original size:22 final size:22
Alignment explanation
Indices: 110842--110894 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
110832 TGGGTATTAA
110842 ATTTAATTCGATTTAAATAAAT
1 ATTTAATTCGATTTAAATAAAT
110864 ATTTAATTCGATTTAAATAAAT
1 ATTTAATTCGATTTAAATAAAT
110886 ATTTAATTC
1 ATTTAATTC
110895 TTTTGAGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (22 bp):
ATTTAATTCGATTTAAATAAAT
Found at i:111874 original size:10 final size:10
Alignment explanation
Indices: 111846--111913 Score: 61
Period size: 10 Copynumber: 7.0 Consensus size: 10
111836 CTGCTGGAAT
111846 ACCGGTTTG-
1 ACCGGTTTGA
*
111855 ACCAGTTTTGA
1 ACC-GGTTTGA
111866 ACCGGTTTG-
1 ACCGGTTTGA
*
111875 ACCGGTTCGA
1 ACCGGTTTGA
*
111885 ACCGATTTG-
1 ACCGGTTTGA
*
111894 ACCGGTCTGA
1 ACCGGTTTGA
*
111904 ACCGGGTTGA
1 ACCGGTTTGA
111914 CCCGACCCGA
Statistics
Matches: 46, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
9 18 0.39
10 25 0.54
11 3 0.07
ACGTcount: A:0.19, C:0.24, G:0.29, T:0.28
Consensus pattern (10 bp):
ACCGGTTTGA
Found at i:111888 original size:19 final size:19
Alignment explanation
Indices: 111846--111915 Score: 79
Period size: 19 Copynumber: 3.6 Consensus size: 19
111836 CTGCTGGAAT
* *
111846 ACCGGTTTGACCAGTTTTGA
1 ACCGGTTTGACC-GGTTCGA
111866 ACCGGTTTGACCGGTTCGA
1 ACCGGTTTGACCGGTTCGA
*
111885 ACCGATTTGACCGG-TCTGA
1 ACCGGTTTGACCGGTTC-GA
*
111904 ACCGGGTTGACC
1 ACCGGTTTGACC
111916 CGACCCGACT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
18 2 0.05
19 30 0.68
20 12 0.27
ACGTcount: A:0.19, C:0.26, G:0.29, T:0.27
Consensus pattern (19 bp):
ACCGGTTTGACCGGTTCGA
Found at i:111931 original size:17 final size:17
Alignment explanation
Indices: 111909--111949 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
111899 TCTGAACCGG
*
111909 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
111926 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
111943 GTTGACC
1 GTTGACC
111950 GTTGACCGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.17, C:0.41, G:0.24, T:0.17
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:111963 original size:6 final size:7
Alignment explanation
Indices: 111939--111968 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
111929 GACCCGACCC
111939 GACCGTT
1 GACCGTT
111946 GACCGTT
1 GACCGTT
111953 GACCG-T
1 GACCGTT
111959 GACCGTT
1 GACCGTT
111966 GAC
1 GAC
111969 TCTCTTTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (7 bp):
GACCGTT
Found at i:111963 original size:13 final size:14
Alignment explanation
Indices: 111939--111968 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
111929 GACCCGACCC
111939 GACCGTTGACCGTT
1 GACCGTTGACCGTT
111953 GACCG-TGACCGTT
1 GACCGTTGACCGTT
111966 GAC
1 GAC
111969 TCTCTTTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (14 bp):
GACCGTTGACCGTT
Found at i:119194 original size:17 final size:17
Alignment explanation
Indices: 119172--119246 Score: 123
Period size: 17 Copynumber: 4.4 Consensus size: 17
119162 TCTAAACCGG
* *
119172 GTTGACCTGACCCGACT
1 GTTGACCCGACCCGACC
*
119189 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
119206 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
119223 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
119240 GTTGACC
1 GTTGACC
119247 GTGACCGTTG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 56 1.00
ACGTcount: A:0.17, C:0.41, G:0.24, T:0.17
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:121140 original size:11 final size:11
Alignment explanation
Indices: 121126--121150 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
121116 ATGAATATGA
121126 AATAATTAATG
1 AATAATTAATG
121137 AATAATTAATG
1 AATAATTAATG
121148 AAT
1 AAT
121151 TTCGTGTGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (11 bp):
AATAATTAATG
Found at i:123419 original size:21 final size:20
Alignment explanation
Indices: 123393--123443 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
123383 TGGCCTAAAT
123393 GGATCGATCTTTCACAAAAAG
1 GGATCGATCTTT-ACAAAAAG
**
123414 GGATCGATACTTTTGAAAAAG
1 GGATCGAT-CTTTACAAAAAG
123435 GGATCGATC
1 GGATCGATC
123444 CTTTTGGCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 1 0.04
21 22 0.81
22 4 0.15
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (20 bp):
GGATCGATCTTTACAAAAAG
Found at i:123447 original size:21 final size:21
Alignment explanation
Indices: 123408--123469 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
123398 GATCTTTCAC
*
123408 AAAAAGGGATCGATACTTTTG
1 AAAAAGGGATCGATCCTTTTG
123429 AAAAAGGGATCGATCCTTTTG
1 AAAAAGGGATCGATCCTTTTG
** *
123450 GCAAAGGGATTGATCCTTTT
1 AAAAAGGGATCGATCCTTTT
123470 TTTGGAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (21 bp):
AAAAAGGGATCGATCCTTTTG
Found at i:125273 original size:21 final size:20
Alignment explanation
Indices: 125223--125277 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
125213 TTAAGGGAAG
125223 GGATCGATCATTTTCATCGA
1 GGATCGATCATTTTCATCGA
* * *
125243 GGTATTGATCCTTTTCCTCGA
1 GG-ATCGATCATTTTCATCGA
125264 GAGATCGATCATTT
1 G-GATCGATCATTT
125278 GTACAAGGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 2 0.07
21 25 0.89
22 1 0.04
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (20 bp):
GGATCGATCATTTTCATCGA
Found at i:125520 original size:30 final size:30
Alignment explanation
Indices: 125484--125552 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
125474 TTTTGATAAA
* * *
125484 TTTTGATAAATTCGATTATGTCTAAAATCT
1 TTTTGATAAATTCAACTAAGTCTAAAATCT
125514 TTTTGATAAATTCAACTAAGTCTAAAATCT
1 TTTTGATAAATTCAACTAAGTCTAAAATCT
125544 TTTTGATAA
1 TTTTGATAA
125553 TTTTAATTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.36, C:0.10, G:0.09, T:0.45
Consensus pattern (30 bp):
TTTTGATAAATTCAACTAAGTCTAAAATCT
Found at i:125569 original size:30 final size:30
Alignment explanation
Indices: 125484--125572 Score: 97
Period size: 30 Copynumber: 3.0 Consensus size: 30
125474 TTTTGATAAA
* * * *
125484 TTTTGATAAATTCGATTATGTCTAAAATCT
1 TTTTGATAAATTCAACTAAGCCTAAAATCT
*
125514 TTTTGATAAATTCAACTAAGTCTAAAATCT
1 TTTTGATAAATTCAACTAAGCCTAAAATCT
* * * *
125544 TTTTGATAATTTTAATTCAGCCTAAAATC
1 TTTTGATAAATTCAACTAAGCCTAAAATC
125573 AATTTTACAA
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (30 bp):
TTTTGATAAATTCAACTAAGCCTAAAATCT
Found at i:125892 original size:25 final size:25
Alignment explanation
Indices: 125860--125921 Score: 106
Period size: 25 Copynumber: 2.5 Consensus size: 25
125850 TGTTTTCAAA
*
125860 ATATTTTCAAAACTATATATTATAT
1 ATATTTTCAAAACCATATATTATAT
*
125885 ATGTTTTCAAAACCATATATTATAT
1 ATATTTTCAAAACCATATATTATAT
125910 ATATTTTCAAAA
1 ATATTTTCAAAA
125922 TGTTTTCAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.45
Consensus pattern (25 bp):
ATATTTTCAAAACCATATATTATAT
Found at i:126005 original size:82 final size:79
Alignment explanation
Indices: 125885--126115 Score: 332
Period size: 82 Copynumber: 2.9 Consensus size: 79
125875 TATATTATAT
125885 ATGTTTTCAAAACCATATATTATATATATTTTCAAAATGTTTTCAAAAACTATATATTATGTATA
1 ATGTTTTCAAAA-CATATATTATATATATTTTCAAAATGTTTTCAAAAACTATATATTAT-TATA
125950 TATATATATATTCAAA
64 TATATATATATTCAAA
*
125966 ATGTTTTCAAAAACTATATATTATGTATATTTTCAAAATGTTTTCAAAAACTATATATTA-TATA
1 ATGTTTTC-AAAAC-ATATATTATATATATTTTCAAAATGTTTTCAAAAACTATATATTATTATA
*
126030 TAT-T-T-T-TTTAAA
64 TATATATATATTCAAA
*
126042 ATGTTTTCAAAAC-TATATTATATATATTTTTAAAAATGTTTTC-AAAACTATATATTATATATA
1 ATGTTTTCAAAACATATATTATATATA-TTTTCAAAATGTTTTCAAAAACTATATATTAT-TATA
126105 TATATATATAT
64 TATATATATAT
126116 ATATATTTCA
Statistics
Matches: 137, Mismatches: 4, Indels: 20
0.85 0.02 0.12
Matches are distributed among these distances:
73 26 0.19
74 15 0.11
75 12 0.09
76 14 0.10
77 2 0.01
78 2 0.01
79 2 0.01
80 7 0.05
81 9 0.07
82 48 0.35
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.47
Consensus pattern (79 bp):
ATGTTTTCAAAACATATATTATATATATTTTCAAAATGTTTTCAAAAACTATATATTATTATATA
TATATATATTCAAA
Found at i:126021 original size:35 final size:35
Alignment explanation
Indices: 125792--126105 Score: 272
Period size: 37 Copynumber: 8.6 Consensus size: 35
125782 TAATAATTTA
* *
125792 AAAACTATATATTATATACATTTTCAAAAATATTTTC
1 AAAAC-ATATATTATATATATTTTC-AAAATGTTTTC
*
125829 AAAAACTATATATTATATATATGTTTTCAAAATATTTTC
1 -AAAAC-ATATATTATATATA--TTTTCAAAATGTTTTC
125868 AAAAC-TATA-TAT-TATA---T----ATGTTTTC
1 AAAACATATATTATATATATTTTCAAAATGTTTTC
125893 AAAACCATATATTATATATATTTTCAAAATGTTTTC
1 AAAA-CATATATTATATATATTTTCAAAATGTTTTC
125929 AAAAACTATATATTATGTATATATATATATATTCAAAATGTTTTC
1 -AAAAC---ATA-TA--T-TATATATAT-T-TTCAAAATGTTTTC
*
125974 AAAAACTATATATTATGTATATTTTCAAAATGTTTTC
1 -AAAAC-ATATATTATATATATTTTCAAAATGTTTTC
*
126011 AAAAACTATATATTATATATATTTTTTTAAAATGTTTTC
1 -AAAAC-ATATATTATATATA--TTTTCAAAATGTTTTC
*
126050 AAAAC-TATATTATATATATTTTTAAAAATGTTTTC
1 AAAACATATATTATATATA-TTTTCAAAATGTTTTC
126085 AAAACTATATATTATATATAT
1 AAAAC-ATATATTATATATAT
126106 ATATATATAT
Statistics
Matches: 243, Mismatches: 6, Indels: 56
0.80 0.02 0.18
Matches are distributed among these distances:
25 11 0.05
26 1 0.00
27 4 0.02
28 3 0.01
29 5 0.02
32 1 0.00
34 4 0.02
35 24 0.10
36 27 0.11
37 51 0.21
38 30 0.12
39 37 0.15
40 8 0.03
42 3 0.01
43 13 0.05
44 1 0.00
45 20 0.08
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (35 bp):
AAAACATATATTATATATATTTTCAAAATGTTTTC
Found at i:126102 original size:2 final size:2
Alignment explanation
Indices: 126090--126121 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
126080 TTTTCAAAAC
126090 TA TA TA T- 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 T
126122 TTCAAAAACC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:126161 original size:2 final size:2
Alignment explanation
Indices: 126156--126208 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
126146 AAATTATACG
126156 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
126198 AT AT AT AT AT A
1 AT AT AT AT AT A
126209 GGCTCCAGAC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:126643 original size:21 final size:23
Alignment explanation
Indices: 126607--126653 Score: 80
Period size: 21 Copynumber: 2.1 Consensus size: 23
126597 AAAAATAACA
126607 TTTAATGCACAAGGGATCGACCC
1 TTTAATGCACAAGGGATCGACCC
126630 TTTAATG-A-AAGGGATCGACCC
1 TTTAATGCACAAGGGATCGACCC
126651 TTT
1 TTT
126654 TTCAAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 16 0.67
22 1 0.04
23 7 0.29
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (23 bp):
TTTAATGCACAAGGGATCGACCC
Found at i:127019 original size:30 final size:30
Alignment explanation
Indices: 126962--127019 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
126952 TTTTGATAAA
* * *
126962 TTTTGATAAATTCGATTAAGTCTAAAATAT
1 TTTTGATAAATTCAATTAAGCCCAAAATAT
*
126992 TTTTGATAATTTCAATTAAGCCCAAAAT
1 TTTTGATAAATTCAATTAAGCCCAAAAT
127020 CAATTTTACA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.41
Consensus pattern (30 bp):
TTTTGATAAATTCAATTAAGCCCAAAATAT
Found at i:127180 original size:70 final size:70
Alignment explanation
Indices: 127059--127193 Score: 195
Period size: 70 Copynumber: 1.9 Consensus size: 70
127049 TAATTCAACA
* *
127059 ATCTCGCACGAGAGCCCTGAAAGATTAGAGTGACTCGCACGGGAACACCTAATCATAATTATCCC
1 ATCTCGCACGAGAGCCCTGAAAGATTAAAGTGACTAGCACGGGAACACCTAATCATAATTATCCC
127124 GGGGT
66 GGGGT
*
127129 ATCTCGCACGAGAGTCCC-GAATA-ATTAAAGTGACTAGCAC-GGAAGCTCCTAATCATAATTAT
1 ATCTCGCACGAGAG-CCCTGAA-AGATTAAAGTGACTAGCACGGGAA-CACCTAATCATAATTAT
127191 CCC
63 CCC
127194 ATGTTAACTT
Statistics
Matches: 59, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
69 4 0.07
70 51 0.86
71 4 0.07
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (70 bp):
ATCTCGCACGAGAGCCCTGAAAGATTAAAGTGACTAGCACGGGAACACCTAATCATAATTATCCC
GGGGT
Found at i:127217 original size:70 final size:70
Alignment explanation
Indices: 127061--127217 Score: 158
Period size: 70 Copynumber: 2.2 Consensus size: 70
127051 ATTCAACAAT
* * *
127061 CTCGCACGAG-AGCCCTGAA-AGATTAGAGTGACTCGCACGGGAACACCTAATCATAATTATCCC
1 CTCGCACGAGAATCCC-GAATA-ATTAAAGTGACTAGCACGGGAACACCTAATCATAATTATCCC
* *
127124 GGGGTAT
64 AGGGTAA
* *
127131 CTCGCACGAGAGTCCCGAATAATTAAAGTGACTAGCAC-GGAAGCTCCTAATCATAATTATCCCA
1 CTCGCACGAGAATCCCGAATAATTAAAGTGACTAGCACGGGAA-CACCTAATCATAATTATCCCA
* *
127195 TGTTAA
65 GGGTAA
* * *
127201 CTTGGACGGGAATCCCG
1 CTCGCACGAGAATCCCG
127218 CGGAAAGCTT
Statistics
Matches: 71, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
69 4 0.06
70 63 0.89
71 4 0.06
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (70 bp):
CTCGCACGAGAATCCCGAATAATTAAAGTGACTAGCACGGGAACACCTAATCATAATTATCCCAG
GGTAA
Found at i:130127 original size:4 final size:4
Alignment explanation
Indices: 130118--130148 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
130108 GTATGTTCAT
*
130118 GTTC GTTC GTTT GTTC GTTC GTTC GTTC GTT
1 GTTC GTTC GTTC GTTC GTTC GTTC GTTC GTT
130149 TAACTTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.00, C:0.19, G:0.26, T:0.55
Consensus pattern (4 bp):
GTTC
Found at i:130439 original size:57 final size:57
Alignment explanation
Indices: 130367--130475 Score: 164
Period size: 57 Copynumber: 1.9 Consensus size: 57
130357 AATTTGAAAA
* * * * *
130367 TCGCGTTACGATAGTAGTGTTTATCTATGTCGGTAATTCGTGTTGCAATTTTCCTAT
1 TCGCGTTACGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCAATTTTCCTAT
*
130424 TCGCGTTACGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGATTTT
1 TCGCGTTACGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCAATTTT
130476 GGAACTTGTG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 46 1.00
ACGTcount: A:0.20, C:0.17, G:0.21, T:0.42
Consensus pattern (57 bp):
TCGCGTTACGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCAATTTTCCTAT
Found at i:131161 original size:15 final size:16
Alignment explanation
Indices: 131122--131177 Score: 55
Period size: 15 Copynumber: 3.6 Consensus size: 16
131112 TTTTTATTTA
131122 ATATATTTATGTAAAT
1 ATATATTTATGTAAAT
*
131138 ATATTTTTAT-TAAA-
1 ATATATTTATGTAAAT
* *
131152 ATAATATTTATATAATT
1 AT-ATATTTATGTAAAT
131169 AT-TATTTAT
1 ATATATTTAT
131178 TTAGAATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
14 2 0.06
15 18 0.53
16 12 0.35
17 2 0.06
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
ATATATTTATGTAAAT
Found at i:131162 original size:31 final size:27
Alignment explanation
Indices: 131107--131178 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 27
131097 TTAAATAGTT
* *
131107 ATTATTTTTTATTTAATATATTTATGTAA
1 ATTA-TTTTTATTAAATATATTTATAT-A
131136 ATATATTTTTATTAAAATAATATTTATATA
1 AT-TATTTTTATT-AAAT-ATATTTATATA
131166 ATTATTATTTATT
1 ATTATT-TTTATT
131179 TAGAATTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
29 14 0.38
30 14 0.38
31 9 0.24
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (27 bp):
ATTATTTTTATTAAATATATTTATATA
Found at i:131342 original size:17 final size:17
Alignment explanation
Indices: 131320--131373 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
131310 AATGTTAATA
131320 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
131337 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
131354 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
131371 TTT
1 TTT
131374 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:132919 original size:21 final size:21
Alignment explanation
Indices: 132889--132936 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
132879 GCAGGGGTAC
* *
132889 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
132910 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
132931 ATGCCA
1 ATGCCA
132937 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:132966 original size:21 final size:21
Alignment explanation
Indices: 132940--133033 Score: 145
Period size: 21 Copynumber: 4.5 Consensus size: 21
132930 TATGCCATCT
132940 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
132961 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
*
132982 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCGAGC
* *
133003 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCGAGC
133024 CCGCAGGGTT
1 CCGCAGGGTT
133034 TTATACCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 2 0.03
21 65 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.34, G:0.28, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCGAGC
Found at i:133634 original size:33 final size:31
Alignment explanation
Indices: 133541--133637 Score: 113
Period size: 31 Copynumber: 3.0 Consensus size: 31
133531 GATAAATGTT
*
133541 TTTAAAATACAAATTATATTATTCAAAATTTAA
1 TTTAAAATAAAAATTATA-TATTC-AAATTTAA
** *
133574 AATAAAATAAAAATAATATATTCAAATTTAA
1 TTTAAAATAAAAATTATATATTCAAATTTAA
*
133605 TTTAAAATATAAATTATAGTATTCGAAATTTAA
1 TTTAAAATAAAAATTATA-TATTC-AAATTTAA
133638 CATTAATTTC
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
31 22 0.41
32 10 0.19
33 22 0.41
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (31 bp):
TTTAAAATAAAAATTATATATTCAAATTTAA
Found at i:134284 original size:129 final size:129
Alignment explanation
Indices: 133930--134541 Score: 903
Period size: 129 Copynumber: 4.9 Consensus size: 129
133920 ATTAACGATT
133930 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATA-T-TC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* * *
133993 --AT-ACAAAATATGGAAGGCGTG-CCCCGGGAACGCGCCTTCATG-GAATAGTAAAATAATAGG
66 TGATGACAATA-ATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
134053 TACTGATATATC---TGTCCCCGAGGGA-ATGAGTGGACATAATAGGGCAATGATAACATATTCT
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGT-GACATAATAGGGCAATGATAACATATTCT
* * * * **
134114 ATGA-CAAAATAATGGAAGGCGCACCCCCGAAAACGCGCCTTCATGTGAATAGTGAAATAATAGG
65 CTGATGACAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
* *
134178 TACTAATATATCTAGTGTCCCCGAGGGACATGAGTGATATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
134243 TGATGACAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAATGTGAATAGTGAAATAATAGG
66 TGATGACAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTC-ATGTGAATAGTGAAATAATAGG
*
134308 TA-TGATATATCTAGTGTCCCCGAGGGATATGAGTGACATAATAGGGCAATGATAAC--ATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
134370 TGACGA-AATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGATGACAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
134433 ---T-ATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATA-T-TC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
134492 T-ATGACGAATAATGGAA-GCGCGCCCCCGGGAACGCGCCTTCATGTGAATA
66 TGATGAC-AATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATA
134542 ATACTCCGAT
Statistics
Matches: 449, Mismatches: 22, Indels: 37
0.88 0.04 0.07
Matches are distributed among these distances:
119 6 0.01
120 38 0.08
121 4 0.01
122 88 0.20
123 34 0.08
124 25 0.06
125 50 0.11
126 35 0.08
127 11 0.02
128 44 0.10
129 90 0.20
130 24 0.05
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (129 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGATGACAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:134470 original size:122 final size:125
Alignment explanation
Indices: 133935--134541 Score: 873
Period size: 122 Copynumber: 4.9 Consensus size: 125
133925 CGATTTACTG
* *
133935 ATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC-AT-ACA
1 ATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACA-ATTCTCTGACG
* * *
133998 AAAT-ATGGAAGGCGTG-CCCCGGGAACGCGCCTTCATG-GAATAGTAAAATAATAGGTACTG
65 AAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG-A-TA
*
134058 ATATATC---TGTCCCCGAGGGA-ATGAGTGGACATAATAGGGCAATGATAACATATTCTATGAC
1 ATATATCTAGTGTCCCCGAGGGACATGAGT-GACATAATAGGGCAATGATAACA-ATTCTCTGAC
* * **
134119 AAAATAATGGAAGGCGCACCCCCGAAAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTA
64 GAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG-A-TA
* *
134183 ATATATCTAGTGTCCCCGAGGGACATGAGTGATATAATAGGGCAATGATAACATATTCTCTGATG
1 ATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACA-ATTCTCTGACG
*
134248 ACAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAATGTGAATAGTGAAATAATAGGTATG
65 A-AATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTC-ATGTGAATAGTGAAATAATAGG-ATA
*
134312 ATATATCTAGTGTCCCCGAGGGATATGAGTGACATAATAGGGCAATGATAAC-ATTCTCTGACGA
1 ATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACAATTCTCTGACGA
134376 AATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG-T-
66 AATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGATA
*
134434 ATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTATGACG
1 ATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACA-ATTCTCTGACG
134499 -AATAATGGAA-GCGCGCCCCCGGGAACGCGCCTTCATGTGAATA
65 AAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATA
134542 ATACTCCGAT
Statistics
Matches: 451, Mismatches: 19, Indels: 29
0.90 0.04 0.06
Matches are distributed among these distances:
119 6 0.01
120 41 0.09
121 2 0.00
122 91 0.20
123 28 0.06
124 29 0.06
125 50 0.11
126 35 0.08
127 11 0.02
128 45 0.10
129 89 0.20
130 24 0.05
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.23
Consensus pattern (125 bp):
ATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACAATTCTCTGACGA
AATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGATA
Found at i:134625 original size:8 final size:8
Alignment explanation
Indices: 134612--134652 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
134602 TCACAATCTT
134612 TCAAATTC
1 TCAAATTC
134620 TCAAATT-
1 TCAAATTC
*
134627 TCCAAACTC
1 T-CAAATTC
134636 T-AAATTC
1 TCAAATTC
134643 TCAAATTC
1 TCAAATTC
134651 TC
1 TC
134653 TGAAATGAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
7 7 0.25
8 20 0.71
9 1 0.04
ACGTcount: A:0.37, C:0.27, G:0.00, T:0.37
Consensus pattern (8 bp):
TCAAATTC
Found at i:134628 original size:15 final size:15
Alignment explanation
Indices: 134610--134652 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
134600 GTTCACAATC
134610 TTTCAAATTCTCAAA
1 TTTCAAATTCTCAAA
*
134625 TTTCCAAACTCT-AAA
1 TTT-CAAATTCTCAAA
134640 TTCTCAAATTCTC
1 TT-TCAAATTCTC
134653 TGAAATGAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.35, C:0.26, G:0.00, T:0.40
Consensus pattern (15 bp):
TTTCAAATTCTCAAA
Found at i:137588 original size:18 final size:18
Alignment explanation
Indices: 137558--137595 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
137548 TTTTTTAACT
137558 TTTAAATACATAAATATA
1 TTTAAATACATAAATATA
*
137576 TTTAATATA-ATAATTATA
1 TTTAA-ATACATAAATATA
137594 TT
1 TT
137596 ATTAGTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTAAATACATAAATATA
Found at i:139056 original size:3 final size:3
Alignment explanation
Indices: 139048--139075 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
139038 TTGTTTAAAT
139048 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
139076 AATTAACCGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:144112 original size:2 final size:2
Alignment explanation
Indices: 144105--144144 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
144095 CTTCATTTGC
144105 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
144145 AAGTAAAACT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:144342 original size:2 final size:2
Alignment explanation
Indices: 144335--144363 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
144325 AAAAATAAGA
144335 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
144364 ACTATAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:144426 original size:40 final size:40
Alignment explanation
Indices: 144357--144433 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
144347 ATATATATAT
144357 ATATATAACTATAATAAATTATTAAAATTAAAATTAATTG
1 ATATATAACTATAATAAATTATTAAAATTAAAATTAATTG
* * *
144397 ATATCATAA-TATTATAAA-TATTTATAATTAAATTTAA
1 ATAT-ATAACTATAATAAATTA-TTAAAATTAAAATTAA
144434 ATACAAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
39 2 0.06
40 26 0.81
41 4 0.12
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (40 bp):
ATATATAACTATAATAAATTATTAAAATTAAAATTAATTG
Found at i:146069 original size:17 final size:17
Alignment explanation
Indices: 146047--146082 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
146037 ATGTTAATAT
146047 TCACTAATATTTTTGGA
1 TCACTAATATTTTTGGA
146064 TCACTAATATTTTTGGA
1 TCACTAATATTTTTGGA
146081 TC
1 TC
146083 CGTTAGTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.14, G:0.11, T:0.47
Consensus pattern (17 bp):
TCACTAATATTTTTGGA
Found at i:147082 original size:22 final size:22
Alignment explanation
Indices: 147057--147112 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
147047 AAAATATGGT
147057 ATGAACAATACCGTGAATAGTG
1 ATGAACAATACCGTGAATAGTG
147079 ATGAACAATACCGTGAATAGTG
1 ATGAACAATACCGTGAATAGTG
*
147101 ATGAACAGTACC
1 ATGAACAATACC
147113 CTGCTACAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.21
Consensus pattern (22 bp):
ATGAACAATACCGTGAATAGTG
Found at i:147761 original size:18 final size:19
Alignment explanation
Indices: 147738--147793 Score: 78
Period size: 22 Copynumber: 2.8 Consensus size: 19
147728 ACTGAATATT
147738 TGTCCCGAAGGACCAC-TA
1 TGTCCCGAAGGACCACTTA
147756 TGTCCCGAAGGACCACTGTATA
1 TGTCCCGAAGGACCAC--T-TA
147778 TGTCCCGAAGGACCAC
1 TGTCCCGAAGGACCAC
147794 GTAGAACCCT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
18 16 0.47
22 18 0.53
ACGTcount: A:0.27, C:0.32, G:0.23, T:0.18
Consensus pattern (19 bp):
TGTCCCGAAGGACCACTTA
Found at i:150699 original size:74 final size:74
Alignment explanation
Indices: 150573--150727 Score: 186
Period size: 74 Copynumber: 2.1 Consensus size: 74
150563 ACAATGTCAT
* * * * **
150573 AGCTTTGACATTTGCGTCAAGCTTTGCTTTATTGCTTCTCGTCATGTGGAGACTCTGGTTTAAGA
1 AGCTTTGACATTTGCATCAAGCTCTGATATATTGCTTCTCGTCATGCAGAGACTCTGGTTTAAGA
*
150638 -AAATTCTAC
66 CAAA-TCTAA
* * * * *
150647 AGCTTTGGCATTTGTATCAAGCTCTGATATATTTCTTCTTGTCATGCAGAGACTTTGGTTTAAGA
1 AGCTTTGACATTTGCATCAAGCTCTGATATATTGCTTCTCGTCATGCAGAGACTCTGGTTTAAGA
150712 CAAATCTAA
66 CAAATCTAA
150721 AGCTTTG
1 AGCTTTG
150728 CAAGATCTGG
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
74 65 0.96
75 3 0.04
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.39
Consensus pattern (74 bp):
AGCTTTGACATTTGCATCAAGCTCTGATATATTGCTTCTCGTCATGCAGAGACTCTGGTTTAAGA
CAAATCTAA
Found at i:157080 original size:18 final size:18
Alignment explanation
Indices: 157057--157102 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
157047 ATGCACATAT
157057 ATTATCATTATCAAC-ATC
1 ATTATCATTATC-ACTATC
* *
157075 ATTATCATAATCTCTATC
1 ATTATCATTATCACTATC
157093 ATTATCATTA
1 ATTATCATTA
157103 ACCCATTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 1 0.04
18 23 0.96
ACGTcount: A:0.37, C:0.20, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTATCATTATCACTATC
Found at i:157398 original size:23 final size:22
Alignment explanation
Indices: 157372--157463 Score: 85
Period size: 23 Copynumber: 4.0 Consensus size: 22
157362 CACCACAGCT
*
157372 CGTATAAATGCACCGAAGTGTCA
1 CGTA-AAATGCACCGAAGTGCCA
*
157395 CGTAAAATTGCACTGAAGTGCCA
1 CGTAAAA-TGCACCGAAGTGCCA
**
157418 CGTAGAGTTGCACCGAAGTGCCA
1 CGTA-AAATGCACCGAAGTGCCA
** *
157441 CGTAGAGTTGCACCGTAGTGCCA
1 CGTA-AAATGCACCGAAGTGCCA
157464 TATAAAATTG
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
22 3 0.05
23 57 0.93
24 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.26, T:0.21
Consensus pattern (22 bp):
CGTAAAATGCACCGAAGTGCCA
Found at i:160738 original size:17 final size:17
Alignment explanation
Indices: 160716--160787 Score: 74
Period size: 17 Copynumber: 4.2 Consensus size: 17
160706 TGATGATTAA
160716 TTTATTGTA-TAATTTCT
1 TTTATTGTACT-ATTTCT
*
160733 TTTATTATACTATTTCT
1 TTTATTGTACTATTTCT
* * *
160750 CTTATTGTACTGTATCT
1 TTTATTGTACTATTTCT
* *
160767 TTTATTGTTCTATATCT
1 TTTATTGTACTATTTCT
160784 TTTA
1 TTTA
160788 CTTTTGTTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
17 45 0.98
18 1 0.02
ACGTcount: A:0.21, C:0.11, G:0.06, T:0.62
Consensus pattern (17 bp):
TTTATTGTACTATTTCT
Found at i:166948 original size:21 final size:22
Alignment explanation
Indices: 166906--166953 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 22
166896 CAAATAAATT
* *
166906 AATTTATTTTTTCATGCTCTTAA
1 AATTTATTTTTTAAT-CACTTAA
*
166929 AATTTATTTTTTAAT-ACTTAT
1 AATTTATTTTTTAATCACTTAA
166950 AATT
1 AATT
166954 CTAATAGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 8 0.36
23 14 0.64
ACGTcount: A:0.31, C:0.08, G:0.02, T:0.58
Consensus pattern (22 bp):
AATTTATTTTTTAATCACTTAA
Found at i:167168 original size:14 final size:16
Alignment explanation
Indices: 167138--167173 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
167128 TATTTTTGGT
167138 ATATTTTACAGTTTTA
1 ATATTTTACAGTTTTA
167154 ATATTTTA-A-TTTTA
1 ATATTTTACAGTTTTA
167168 AT-TTTT
1 ATATTTT
167174 TTTTTCAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 4 0.20
14 7 0.35
15 1 0.05
16 8 0.40
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (16 bp):
ATATTTTACAGTTTTA
Found at i:168341 original size:20 final size:20
Alignment explanation
Indices: 168316--168357 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
168306 GAGGCTTGAT
*
168316 TCCTGCTGCTAGGGAATGGA
1 TCCTGCTGCTAGGGAATCGA
168336 TCCTGCTGCTAGGGAATCGA
1 TCCTGCTGCTAGGGAATCGA
168356 TC
1 TC
168358 GTTTGAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.19, C:0.24, G:0.31, T:0.26
Consensus pattern (20 bp):
TCCTGCTGCTAGGGAATCGA
Done.