Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008124.1 Hibiscus syriacus cultivar Beakdansim tig00110678_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: 3296903
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 19
Found at i:2941589 original size:20 final size:20
Alignment explanation
Indices: 2941501--2941617 Score: 78
Period size: 20 Copynumber: 5.7 Consensus size: 20
2941491 ATCAGTTTCC
* *
2941501 AAAATCGCAACGCGATTCTT
1 AAAATCGCAACGCGAATATT
* *
2941521 GAAAATCGCAATGCG-ATAGT
1 -AAAATCGCAACGCGAATATT
** *
2941541 ACAAATTCGCATTGCG-ATTTT
1 A-AAA-TCGCAACGCGAATATT
2941562 CCAAAATCGCAACGCGAATATT
1 --AAAATCGCAACGCGAATATT
* *
2941584 AAAATCGCAACGCGAACA-C
1 AAAATCGCAACGCGAATATT
2941603 ATAAATCGCAACGCG
1 A-AAATCGCAACGCG
2941618 TATCCGTAAA
Statistics
Matches: 78, Mismatches: 12, Indels: 13
0.76 0.12 0.13
Matches are distributed among these distances:
19 2 0.03
20 35 0.45
21 33 0.42
22 7 0.09
23 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (20 bp):
AAAATCGCAACGCGAATATT
Found at i:2941627 original size:20 final size:20
Alignment explanation
Indices: 2941585--2941794 Score: 228
Period size: 20 Copynumber: 10.5 Consensus size: 20
2941575 GCGAATATTA
* *
2941585 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
2941605 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
2941625 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
2941645 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
2941665 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
2941685 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
2941705 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
2941725 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
2941745 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
2941765 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
2941785 AAATCACAAC
1 AAATCGCAAC
2941795 ACTGAAATTT
Statistics
Matches: 162, Mismatches: 23, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
19 1 0.01
20 159 0.98
21 2 0.01
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:2942497 original size:24 final size:24
Alignment explanation
Indices: 2942469--2942514 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
2942459 AAATTTGGTC
2942469 TGGTCAATATC-CGGACTTTGATAT
1 TGGTCAATA-CACGGACTTTGATAT
*
2942493 TGGTCAATACACGGATTTTGAT
1 TGGTCAATACACGGACTTTGAT
2942515 GATGTTTCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (24 bp):
TGGTCAATACACGGACTTTGATAT
Found at i:2944875 original size:68 final size:65
Alignment explanation
Indices: 2944769--2944946 Score: 302
Period size: 68 Copynumber: 2.7 Consensus size: 65
2944759 CGGAAATTAC
2944769 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAATGAAAATCGCAATGCGGATATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAATGAAAATCGCAATGCGGATATGAA
2944834 AATCGCAACAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAT
1 AATCG---CAACGAGAGAATCGCAATGCGAAATGAAAATCCC-A-ATGAAAATCGCAATGCGGAT
2944899 ATGAA
61 ATGAA
*
2944904 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATG
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAATG
2944947 CGAAATGAAA
Statistics
Matches: 107, Mismatches: 1, Indels: 10
0.91 0.01 0.08
Matches are distributed among these distances:
65 8 0.07
66 1 0.01
67 33 0.31
68 34 0.32
69 1 0.01
70 30 0.28
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.15
Consensus pattern (65 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAATGAAAATCGCAATGCGGATATGAA
Found at i:2944893 original size:33 final size:34
Alignment explanation
Indices: 2944783--2945068 Score: 221
Period size: 33 Copynumber: 8.2 Consensus size: 34
2944773 GCAACGAGAG
2944783 AATCGCAATGCGAAATGAAAAT-CC--CAATGAA
1 AATCGCAATGCGAAATGAAAATCCCAACAATGAA
* * *
2944814 AATCGCAATGCGGATATGAAAATCGCAACAACGAGA
1 AATCGCAATGC-GAAATGAAAATCCCAACAATGA-A
2944850 GAATCGCAATGCGAAATGAAAATCCCAAC-ATGAA
1 -AATCGCAATGCGAAATGAAAATCCCAACAATGAA
* * * *
2944884 AATCGCAATGCGGATATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCCCAACAATGAA
*
2944918 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCCCAA--C--AATGAA
* * * * *
2944956 AATCGCAACGAGAGAATCG-CAAT-GCGA-AATGAA
1 AATCGCAATGCGA-AAT-GAAAATCCCAACAATGAA
* * *
2944989 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCCCAACAATGAA
*
2945023 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCCCAA--C--AATGAA
2945061 AATCGCAA
1 AATCGCAA
2945069 CGAGAGAATC
Statistics
Matches: 207, Mismatches: 24, Indels: 41
0.76 0.09 0.15
Matches are distributed among these distances:
31 11 0.05
32 11 0.05
33 64 0.31
34 47 0.23
35 12 0.06
36 16 0.08
37 13 0.06
38 26 0.13
39 6 0.03
40 1 0.00
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCCCAACAATGAA
Found at i:2944942 original size:19 final size:19
Alignment explanation
Indices: 2944783--2945172 Score: 367
Period size: 19 Copynumber: 22.4 Consensus size: 19
2944773 GCAACGAGAG
2944783 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2944802 AATC-C----C--AATGAA
1 AATCGCAATGCGAAATGAA
*
2944814 AATCGCAATGCGGATATGAA
1 AATCGCAATGC-GAAATGAA
*
2944834 AATCGCAA--C-AACGA-GAG
1 AATCGCAATGCGAA--ATGAA
2944851 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2944870 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
*
2944884 AATCGCAATGCGGATATGAA
1 AATCGCAATGC-GAAATGAA
*
2944904 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
2944918 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2944937 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2944956 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
2944970 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2944989 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
2945009 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
2945023 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2945042 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2945061 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
2945075 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2945094 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
2945108 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2945127 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2945146 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2945165 AATCGCAA
1 AATCGCAA
2945173 CGAGAGAATC
Statistics
Matches: 309, Mismatches: 16, Indels: 92
0.74 0.04 0.22
Matches are distributed among these distances:
12 10 0.03
13 1 0.00
14 63 0.20
15 5 0.02
16 12 0.04
17 20 0.06
18 11 0.04
19 143 0.46
20 44 0.14
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:2944988 original size:105 final size:104
Alignment explanation
Indices: 2944783--2945194 Score: 522
Period size: 105 Copynumber: 4.0 Consensus size: 104
2944773 GCAACGAGAG
* * * *
2944783 AATCGCAATGCGAAATGAAAATCCCAATGA-A-AATCGCAATGCGGATATGAAAATCGCAA--C-
1 AATCGCAATGCGGAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCG
* * * * * *
2944843 AACGA-GAGAATCGCAATGCGA-AAT-GAAAATCCCAACATGAA
65 AA--ATGAAAATCGCAACGAGAGAATCG-CAATGCGAA-ATGAA
2944884 AATCGCAATGCGGATATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGGA-ATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCG
2944949 AAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
65 AAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
2944989 AATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGG-AATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCG
2945054 AAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
65 AAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
* * * * *
2945094 AATCGCAACGAGAGAATCG-CAATGCGAAATGA-A-AATCGCAATGCGAAATGAAAATCGCAATG
1 AATCGCAATGCG-GAAT-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATG
2945156 CGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAT
63 CGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAT
2945195 TATAAACGCA
Statistics
Matches: 283, Mismatches: 15, Indels: 23
0.88 0.05 0.07
Matches are distributed among these distances:
101 13 0.05
102 14 0.05
103 16 0.06
104 80 0.28
105 139 0.49
106 20 0.07
107 1 0.00
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (104 bp):
AATCGCAATGCGGAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGA
AATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:2945079 original size:33 final size:33
Alignment explanation
Indices: 2944937--2945194 Score: 308
Period size: 33 Copynumber: 7.5 Consensus size: 33
2944927 GCGAAATGAA
2944937 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
2944970 AATCGCAATGCGAAATGAAAATCGCAATGCG-GA-
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAGAG
* * * *
2945003 AAT-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCG-CAATGCGAAATGA-A-AATCGCAA--CG--A-GAG
2945042 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
2945075 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
*
2945108 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAG
2945146 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
2945179 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
2945195 TATAAACGCA
Statistics
Matches: 199, Mismatches: 9, Indels: 34
0.82 0.04 0.14
Matches are distributed among these distances:
32 7 0.04
33 114 0.57
34 16 0.08
35 4 0.02
36 4 0.02
37 1 0.01
38 39 0.20
39 7 0.04
40 7 0.04
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:2945080 original size:14 final size:14
Alignment explanation
Indices: 2945061--2945115 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
2945051 GCGAAATGAA
2945061 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2945075 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
2945094 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2945108 AATCGCAA
1 AATCGCAA
2945116 TGCGAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2945210 original size:52 final size:52
Alignment explanation
Indices: 2944783--2945194 Score: 522
Period size: 52 Copynumber: 7.9 Consensus size: 52
2944773 GCAACGAGAG
* * *
2944783 AATCGCAATGCGAAATGAAAATCCCAATGA-A-AATCGCAATGCGGATATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAA
* * * * * *
2944834 AATCGCAA--C-AACGA-GAGAATCGCAATGCGA-AAT-GAAAATCCCAACATGAA
1 AATCGCAATGCGAA--ATGAAAATCGCAACGAGAGAATCG-CAATGCGAA-ATGAA
*
2944884 AATCGCAATGCGGATATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
2944937 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
2944989 AATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
2945042 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
* * * * *
2945094 AATCGCAACGAGAGAATCG-CAATGCGAAATGA-A-AATCGCAATGCGAAATGAA
1 AATCGCAATGCGA-AAT-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATGAA
2945146 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAT
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAT
2945195 TATAAACGCA
Statistics
Matches: 317, Mismatches: 25, Indels: 37
0.84 0.07 0.10
Matches are distributed among these distances:
48 2 0.01
49 14 0.04
50 29 0.09
51 15 0.05
52 151 0.48
53 88 0.28
54 17 0.05
55 1 0.00
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:2945305 original size:19 final size:19
Alignment explanation
Indices: 2945219--2945297 Score: 105
Period size: 19 Copynumber: 4.4 Consensus size: 19
2945209 GATTCTCTCG
2945219 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
2945239 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2945258 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2945272 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2945291 TTGCGAT
1 TTGCGAT
2945298 AGTCATTTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
14 6 0.12
16 7 0.13
17 7 0.13
19 17 0.33
20 15 0.29
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2945431 original size:13 final size:14
Alignment explanation
Indices: 2945404--2945439 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
2945394 CATCAATTAC
2945404 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2945418 ACAAATCATC-TTT
1 ACAAATCAACTTTT
2945431 ACAAATCAA
1 ACAAATCAA
2945440 TTAAACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2947371 original size:20 final size:20
Alignment explanation
Indices: 2947346--2947411 Score: 82
Period size: 19 Copynumber: 3.4 Consensus size: 20
2947336 TAGTTTACTT
* *
2947346 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAACTCAAAA
*
2947366 TCGCAATGCGAAAC-CAAAA
1 TCGCAACGCGAAACTCAAAA
*
2947385 TCGCAACGCGAAA-TGAAAA
1 TCGCAACGCGAAACTCAAAA
2947404 TCGCAACG
1 TCGCAACG
2947412 ACAGAATCGC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
19 28 0.70
20 12 0.30
ACGTcount: A:0.45, C:0.26, G:0.17, T:0.12
Consensus pattern (20 bp):
TCGCAACGCGAAACTCAAAA
Found at i:2947386 original size:19 final size:19
Alignment explanation
Indices: 2947362--2947480 Score: 123
Period size: 19 Copynumber: 6.8 Consensus size: 19
2947352 CACGAAACTT
**
2947362 AAAATCGCAATGCGAAACC
1 AAAATCGCAATGCGAAATG
*
2947381 AAAATCGCAACGCGAAATG
1 AAAATCGCAATGCGAAATG
*
2947400 AAAATCGCAA--CGACA-G
1 AAAATCGCAATGCGAAATG
2947416 --AATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
2947433 AAAATCGCAA--CGAAA-G
1 AAAATCGCAATGCGAAATG
*
2947449 --AATCGCAACGCGAAATG
1 AAAATCGCAATGCGAAATG
2947466 AAAATCGCAATGCGA
1 AAAATCGCAATGCGA
2947481 TTTTGGTTTC
Statistics
Matches: 84, Mismatches: 6, Indels: 20
0.76 0.05 0.18
Matches are distributed among these distances:
14 16 0.19
16 11 0.13
17 11 0.13
19 46 0.55
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (19 bp):
AAAATCGCAATGCGAAATG
Found at i:2947421 original size:14 final size:14
Alignment explanation
Indices: 2947402--2947458 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2947392 GCGAAATGAA
*
2947402 AATCGCAACGACAG
1 AATCGCAACGAAAG
2947416 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
2947433 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
2947449 AATCGCAACG
1 AATCGCAACG
2947459 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:2947429 original size:33 final size:33
Alignment explanation
Indices: 2947383--2947475 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
2947373 GCGAAACCAA
*
2947383 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
2947416 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
2947449 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
2947476 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:2947472 original size:52 final size:54
Alignment explanation
Indices: 2947346--2947480 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 54
2947336 TAGTTTACTT
*
2947346 TCGCAACACGAAACTTAAAATCGCAATGCGAAACCAAAATCGCAACGCGAAATGAAAA
1 TCGCAAC-CGAAA-TGAAAATCGCAATGCGAAACCAAAATCGCAAC-CGAAATG-AAA
* **
2947404 TCGCAA-CGACA-G--AATCGCAATGCGAAATGAAAATCGCAA-CGAAA-G-AA
1 TCGCAACCGAAATGAAAATCGCAATGCGAAACCAAAATCGCAACCGAAATGAAA
2947451 TCGCAACGCGAAATGAAAATCGCAATGCGA
1 TCGCAAC-CGAAATGAAAATCGCAATGCGA
2947481 TTTTGGTTTC
Statistics
Matches: 67, Mismatches: 5, Indels: 16
0.76 0.06 0.18
Matches are distributed among these distances:
47 8 0.12
49 5 0.07
50 6 0.09
52 38 0.57
56 4 0.06
58 6 0.09
ACGTcount: A:0.46, C:0.23, G:0.19, T:0.12
Consensus pattern (54 bp):
TCGCAACCGAAATGAAAATCGCAATGCGAAACCAAAATCGCAACCGAAATGAAA
Found at i:2947498 original size:19 final size:19
Alignment explanation
Indices: 2947476--2947604 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
2947466 AAAATCGCAA
2947476 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
2947495 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
2947509 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
2947528 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
2947542 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
2947561 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
2947580 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
2947600 TGCGA
1 TGCGA
2947605 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:2947518 original size:33 final size:33
Alignment explanation
Indices: 2947476--2947567 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
2947466 AAAATCGCAA
2947476 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
2947509 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
2947542 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
2947568 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:2948022 original size:92 final size:93
Alignment explanation
Indices: 2947652--2948025 Score: 718
Period size: 92 Copynumber: 4.1 Consensus size: 93
2947642 ATGGATTGCA
2947652 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
2947716 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
2947744 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
2947809 TAGCAGAATTGGCAGCAACCGAACAAA-
66 TAGCAGAATTGGCAGCAACCGAACAAAT
2947836 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
2947901 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
2947929 TTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
2947993 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
2948021 TTACT
1 TTACT
2948026 AAGCAATCTA
Statistics
Matches: 279, Mismatches: 1, Indels: 4
0.98 0.00 0.01
Matches are distributed among these distances:
92 173 0.62
93 106 0.38
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:2949723 original size:14 final size:14
Alignment explanation
Indices: 2949704--2949791 Score: 77
Period size: 14 Copynumber: 5.7 Consensus size: 14
2949694 TTGAAATGAA
2949704 AATCGCAACGAGAG
1 AATCGCAACGAGAG
* *
2949718 AATCGCAACGCGAAAAC
1 AATCGCAA--CG-AGAG
2949735 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2949749 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
2949768 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2949782 AATCGCAACG
1 AATCGCAACG
2949792 CGAAATGAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
14 30 0.50
15 3 0.05
16 4 0.07
17 12 0.20
18 1 0.02
19 10 0.17
ACGTcount: A:0.44, C:0.24, G:0.24, T:0.08
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2949773 original size:19 final size:19
Alignment explanation
Indices: 2949749--2949804 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
2949739 GCAACGAGAG
2949749 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
2949768 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
2949782 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
2949801 AATC
1 AATC
2949805 ACAATGCGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
14 10 0.33
15 1 0.03
16 2 0.07
17 2 0.07
18 1 0.03
19 14 0.47
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:2949777 original size:33 final size:33
Alignment explanation
Indices: 2949696--2949804 Score: 195
Period size: 33 Copynumber: 3.4 Consensus size: 33
2949686 GTCTTTGGTT
2949696 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
2949729 GAAA--ACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
2949760 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
2949793 GAAATGAAAATC
1 GAAATGAAAATC
2949805 ACAATGCGAT
Statistics
Matches: 72, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
31 30 0.42
33 42 0.58
ACGTcount: A:0.47, C:0.21, G:0.23, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:2949844 original size:14 final size:14
Alignment explanation
Indices: 2949825--2949880 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 14
2949815 TTTGGTTTCG
2949825 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2949839 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
*
2949856 CGCGTGCGATTCTCT
1 CG-TTGCGATTCTCT
2949871 CGTTGCGATT
1 CGTTGCGATT
2949881 TTCATTTCTC
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
14 15 0.44
15 4 0.12
16 6 0.18
17 4 0.12
18 5 0.15
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2949869 original size:32 final size:33
Alignment explanation
Indices: 2949809--2949888 Score: 135
Period size: 32 Copynumber: 2.5 Consensus size: 33
2949799 AAAATCACAA
**
2949809 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
2949842 TGCGATTTTCATTTCGCG-TGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
2949874 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
2949889 TCTCGTTGCG
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 29 0.64
33 16 0.36
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:2949921 original size:41 final size:41
Alignment explanation
Indices: 2949864--2949941 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
2949854 TTCGCGTGCG
*
2949864 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
2949905 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
2949942 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:2949926 original size:20 final size:21
Alignment explanation
Indices: 2949865--2949940 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
2949855 TCGCGTGCGA
2949865 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
2949886 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
2949906 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
2949927 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
2949941 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:2950065 original size:33 final size:33
Alignment explanation
Indices: 2950019--2950089 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
2950009 AATACTAACT
* *
2950019 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCACAACGACAGAATAGCAACGCGAAA
* *
2950052 TGAAAATCACAACGACAGAATCGTAACGCGAAA
1 TGAAAATCACAACGACAGAATAGCAACGCGAAA
2950085 TGAAA
1 TGAAA
2950090 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.49, C:0.18, G:0.21, T:0.11
Consensus pattern (33 bp):
TGAAAATCACAACGACAGAATAGCAACGCGAAA
Found at i:2950319 original size:22 final size:22
Alignment explanation
Indices: 2950267--2950321 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
2950257 TGGTTGTGAG
**
2950267 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
2950289 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
2950311 GGATTTCTTCG
1 GGATTTCTTCG
2950322 CTGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:2950493 original size:20 final size:20
Alignment explanation
Indices: 2950468--2950662 Score: 214
Period size: 20 Copynumber: 9.7 Consensus size: 20
2950458 CTTTAAATAT
2950468 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
2950488 CGCGTTGCGATTTTTATGTATTA
1 CGCGTTGCGA--TTTACGGA-TA
*
2950511 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2950530 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
2950550 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
2950570 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2950590 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
2950610 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
2950630 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
2950650 CGCGTTGCGATTT
1 CGCGTTGCGATTT
2950663 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 1 0.01
22 14 0.10
23 2 0.01
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:2950656 original size:60 final size:60
Alignment explanation
Indices: 2950468--2950662 Score: 246
Period size: 60 Copynumber: 3.2 Consensus size: 60
2950458 CTTTAAATAT
**
2950468 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA--TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
2950530 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
2950590 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
2950650 CGCGTTGCGATTT
1 CGCGTTGCGATTT
2950663 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
62 28 0.25
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:2950679 original size:21 final size:21
Alignment explanation
Indices: 2950649--2950731 Score: 69
Period size: 21 Copynumber: 4.0 Consensus size: 21
2950639 ATTTTCATAT
*
2950649 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
2950670 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
2950691 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
**
2950712 TCGTGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
2950732 CTGATTTGCG
Statistics
Matches: 46, Mismatches: 14, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
20 1 0.02
21 43 0.93
22 2 0.04
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:2958926 original size:13 final size:15
Alignment explanation
Indices: 2958911--2958960 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
2958901 AAGACAACGG
2958911 GTTGACTCGGA-CG-
1 GTTGACTCGGATCGA
**
2958924 GTTGACTTAGATCGA
1 GTTGACTCGGATCGA
2958939 GTTGACTCGGATCGA
1 GTTGACTCGGATCGA
2958954 GTTGACT
1 GTTGACT
2958961 TGGTAACTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
13 9 0.29
14 2 0.06
15 20 0.65
ACGTcount: A:0.20, C:0.18, G:0.32, T:0.30
Consensus pattern (15 bp):
GTTGACTCGGATCGA
Found at i:2962087 original size:23 final size:22
Alignment explanation
Indices: 2962061--2962108 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
2962051 TTTTAAAAGC
*
2962061 TATAATTAAAAAACTATATTATA
1 TATAATT-AAAAACTATACTATA
**
2962084 TAT-ATTTTAAACTATACTATA
1 TATAATTAAAAACTATACTATA
2962105 TATA
1 TATA
2962109 TATATTATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
21 15 0.71
22 3 0.14
23 3 0.14
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (22 bp):
TATAATTAAAAACTATACTATA
Found at i:2962105 original size:70 final size:68
Alignment explanation
Indices: 2962029--2962199 Score: 187
Period size: 68 Copynumber: 2.6 Consensus size: 68
2962019 TACTACATAT
** *
2962029 TATATATATACGTATACTTATATT-T-TAAAAGCTATA-ATTAAAAAACTATAT-TATATATATT
1 TATATATATATATATA-TTAT-TTCTCTAAAACCTATATATT-AAAAACTATATATATATATATT
2962090 TTAAAC
63 TTAAAC
**
2962096 TATACTATATATATATATTATTTCTCTAAAACCTATATATTTTAAACTATATACTATATATATTT
1 TATA-TATATATATATATTATTTCTCTAAAACCTATATATTAAAAACTATATA-TATATATATTT
2962161 TAAAC
64 TAAAC
*
2962166 TATATAT-TATATATA-T-TTTC-CTAAAAACTATATA
1 TATATATATATATATATTATTTCTCTAAAACCTATATA
2962200 CTATATATAT
Statistics
Matches: 92, Mismatches: 6, Indels: 14
0.82 0.05 0.12
Matches are distributed among these distances:
65 13 0.14
66 6 0.07
67 10 0.11
68 37 0.40
69 6 0.07
70 20 0.22
ACGTcount: A:0.44, C:0.09, G:0.01, T:0.46
Consensus pattern (68 bp):
TATATATATATATATATTATTTCTCTAAAACCTATATATTAAAAACTATATATATATATATTTTA
AAC
Found at i:2962109 original size:23 final size:23
Alignment explanation
Indices: 2962071--2962232 Score: 143
Period size: 23 Copynumber: 6.9 Consensus size: 23
2962061 TATAATTAAA
2962071 AAACTATAT--TATATATATTTT
1 AAACTATATACTATATATATTTT
*
2962092 AAACTATACTA-TATATATATATT
1 AAACTATA-TACTATATATATTTT
** * * *
2962115 ATTTCTCTAAAAC-CTATATATTTT
1 A-AACTAT-ATACTATATATATTTT
2962139 AAACTATATACTATATATATTTT
1 AAACTATATACTATATATATTTT
*
2962162 AAACTATATATTATATATATTTTCCT
1 AAACTATATACTATATATA-TTT--T
2962188 AAAAACTATATACTATATATATTTT
1 --AAACTATATACTATATATATTTT
* *
2962213 AGACTATATAGTATATATAT
1 AAACTATATACTATATATAT
2962233 ATTTTTCTAA
Statistics
Matches: 114, Mismatches: 16, Indels: 20
0.76 0.11 0.13
Matches are distributed among these distances:
21 8 0.07
22 4 0.04
23 61 0.54
24 17 0.15
25 2 0.02
26 1 0.01
27 3 0.03
28 18 0.16
ACGTcount: A:0.43, C:0.09, G:0.01, T:0.47
Consensus pattern (23 bp):
AAACTATATACTATATATATTTT
Found at i:2962196 original size:51 final size:53
Alignment explanation
Indices: 2962139--2962262 Score: 216
Period size: 53 Copynumber: 2.4 Consensus size: 53
2962129 TATATATTTT
2962139 AAACTATATACTATATATATTTTAAACTATATA-T-TATATATATTTTCCTAA
1 AAACTATATACTATATATATTTTAAACTATATAGTATATATATATTTTCCTAA
* *
2962190 AAACTATATACTATATATATTTTAGACTATATAGTATATATATATTTTTCTAA
1 AAACTATATACTATATATATTTTAAACTATATAGTATATATATATTTTCCTAA
2962243 AAACTATATACTATATATAT
1 AAACTATATACTATATATAT
2962263 ATATATATTA
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
51 32 0.46
52 1 0.01
53 36 0.52
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.46
Consensus pattern (53 bp):
AAACTATATACTATATATATTTTAAACTATATAGTATATATATATTTTCCTAA
Found at i:2962275 original size:41 final size:39
Alignment explanation
Indices: 2962217--2962324 Score: 109
Period size: 41 Copynumber: 2.8 Consensus size: 39
2962207 TATTTTAGAC
2962217 TATATAGTATATA-TATATTT-TTCTAAAAACTATATACTATA
1 TATATA-TATATATTATATTTATT-TAAAAA-T-TATACTATA
**
2962258 TATATATATATATTATATTTATTTTTAAATTATACTATA
1 TATATATATATATTATATTTATTTAAAAATTATACTATA
*
2962297 TAT-TAT-TATA-TATAATTATTATAAAAAT
1 TATATATATATATTATATTTATT-TAAAAAT
2962325 AAAGTAAAAT
Statistics
Matches: 59, Mismatches: 5, Indels: 10
0.80 0.07 0.14
Matches are distributed among these distances:
36 9 0.15
37 9 0.15
38 3 0.05
39 12 0.20
40 7 0.12
41 17 0.29
42 2 0.03
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.51
Consensus pattern (39 bp):
TATATATATATATTATATTTATTTAAAAATTATACTATA
Found at i:2962280 original size:9 final size:9
Alignment explanation
Indices: 2962247--2962319 Score: 50
Period size: 8 Copynumber: 8.7 Consensus size: 9
2962237 TTCTAAAAAC
*
2962247 TATATACTA
1 TATATATTA
2962256 TATATA-TA
1 TATATATTA
2962264 TATATATTA
1 TATATATTA
*
2962273 TATTTATT-
1 TATATATTA
* *
2962281 TTTAAATTA
1 TATATATTA
*
2962290 TA-CTA-TA
1 TATATATTA
2962297 TAT-TATTA
1 TATATATTA
2962305 TATATAATTA
1 TATAT-ATTA
2962315 T-TATA
1 TATATA
2962320 AAAATAAAGT
Statistics
Matches: 51, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
7 6 0.12
8 20 0.39
9 20 0.39
10 5 0.10
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (9 bp):
TATATATTA
Found at i:2962316 original size:13 final size:15
Alignment explanation
Indices: 2962286--2962319 Score: 54
Period size: 13 Copynumber: 2.4 Consensus size: 15
2962276 TTATTTTTAA
2962286 ATTATACTATATATT
1 ATTATACTATATATT
2962301 ATTATA-TATA-ATT
1 ATTATACTATATATT
2962314 ATTATA
1 ATTATA
2962320 AAAATAAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.47
14 4 0.21
15 6 0.32
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTATACTATATATT
Found at i:2962919 original size:16 final size:16
Alignment explanation
Indices: 2962900--2962932 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2962890 CGACAAGCAT
2962900 TGATGAGCACAATTAA
1 TGATGAGCACAATTAA
*
2962916 TGATGAGCACCATTAA
1 TGATGAGCACAATTAA
2962932 T
1 T
2962933 TTAATTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.27
Consensus pattern (16 bp):
TGATGAGCACAATTAA
Found at i:2964136 original size:21 final size:23
Alignment explanation
Indices: 2964110--2964161 Score: 72
Period size: 21 Copynumber: 2.3 Consensus size: 23
2964100 GATCACTGAT
*
2964110 ATAATTTACCTTT-TATTTT-AA
1 ATAATTTACCTTTAAATTTTCAA
2964131 ATAATTTACCTTTAAATTTTCAA
1 ATAATTTACCTTTAAATTTTCAA
*
2964154 ATATTTTA
1 ATAATTTA
2964162 TAATTATATG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 13 0.48
22 5 0.19
23 9 0.33
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.54
Consensus pattern (23 bp):
ATAATTTACCTTTAAATTTTCAA
Found at i:2964786 original size:64 final size:64
Alignment explanation
Indices: 2964708--2964846 Score: 190
Period size: 64 Copynumber: 2.2 Consensus size: 64
2964698 GGATCTTGGC
* *
2964708 AGGTCGGGTAAAATCGGATACAGGTCA-ATTCAGGTTGATTTGACACCAGATCCAGATCGGGTTA
1 AGGTCGGGTCAAATCAG-TACAGGTCATATTCAGGTTGATTTGACACCAGATCCAGATCGGGTTA
* * * * * *
2964772 AGGTCAGGTCAAATCAGTTCGGGTTATTTTCAGGTTGATTTGACACCAGATCCAGATCGGGTTC
1 AGGTCGGGTCAAATCAGTACAGGTCATATTCAGGTTGATTTGACACCAGATCCAGATCGGGTTA
2964836 AGGTCGGGTCA
1 AGGTCGGGTCA
2964847 TTTTCAGTTC
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
63 6 0.09
64 59 0.91
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27
Consensus pattern (64 bp):
AGGTCGGGTCAAATCAGTACAGGTCATATTCAGGTTGATTTGACACCAGATCCAGATCGGGTTA
Found at i:2965926 original size:13 final size:13
Alignment explanation
Indices: 2965894--2965920 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2965884 TAATTTACAT
2965894 TTAAATAATTTTA
1 TTAAATAATTTTA
2965907 TTAAATAATTTTA
1 TTAAATAATTTTA
2965920 T
1 T
2965921 ATAATATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAAATAATTTTA
Found at i:2966505 original size:23 final size:24
Alignment explanation
Indices: 2966470--2966514 Score: 83
Period size: 23 Copynumber: 1.9 Consensus size: 24
2966460 ATAAACCATG
2966470 TATAGTATATATAAACTATATATA
1 TATAGTATATATAAACTATATATA
2966494 TATA-TATATATAAACTATATA
1 TATAGTATATATAAACTATATA
2966515 AAGTAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.42
Consensus pattern (24 bp):
TATAGTATATATAAACTATATATA
Found at i:2966626 original size:21 final size:21
Alignment explanation
Indices: 2966602--2966660 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
2966592 TCTTAAATCA
**
2966602 TAAACCATAAACCCTAAACTT
1 TAAACCATAAACCCTAAACAC
* * **
2966623 TAAACTACAAACATTAAACAC
1 TAAACCATAAACCCTAAACAC
*
2966644 TAAATCATAAACCCTAA
1 TAAACCATAAACCCTAA
2966661 TGTAAATGGA
Statistics
Matches: 27, Mismatches: 11, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.53, C:0.25, G:0.00, T:0.22
Consensus pattern (21 bp):
TAAACCATAAACCCTAAACAC
Found at i:2967052 original size:15 final size:15
Alignment explanation
Indices: 2967027--2967063 Score: 65
Period size: 15 Copynumber: 2.4 Consensus size: 15
2967017 ATAAACCATG
2967027 TATAGTATATATAAAC
1 TATA-TATATATAAAC
2967043 TATATATATATAAAC
1 TATATATATATAAAC
2967058 TATATA
1 TATATA
2967064 AAGTAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (15 bp):
TATATATATATAAAC
Found at i:2967343 original size:548 final size:548
Alignment explanation
Indices: 2965928--2967828 Score: 3062
Period size: 548 Copynumber: 3.5 Consensus size: 548
2965918 TATATAATAT
* * * **
2965928 GTATGTATAAACCATGTATATATATATGTATATAAAGTAAATTACTTATATAGTTTATAGAAACA
1 GTATATATAAACTATATATATATA-AACTATATAAAGTAAATTACTTATATAGTTTATAGAAACA
* *
2965993 CTATACATAAACTATATAAAGTAATAAAATATATAGTTTATAGAAATCCTAAATCCTAAACCATA
65 CTATACATAAACTATATAAAGTAATAAAATATATAGTTTATAAAAACCCTAAATCCTAAACCATA
* * *
2966058 AACCATAAACTTTAAA--TCACAAACACAAACACTAAATCATAAACCCTAATGTAAATGGACTAT
130 AACC-TAAACTTTAAACTTCA-AACCATAAACACTAAATCATAAACCCTAATGTAAATGGACTAG
* *
2966121 CACTAATGCATATATATTTGTAATAAAAGAGTGGGCTTGCATTGGGCCTATCTAAATTAATGTTA
193 CACTAATGCATATATATTTGTAATAAAAGAGTGGGCTTGCATTGGGCCTATGTAAACTAATGTTA
* *
2966186 ATAGACTAGCACTATTGCAAATGAACTTATTTTTGGGTTTTATTATTACTTATTCATAACAACAA
258 ATGGACTAGCACTATTGCAAATGGACTTATTTTTGGGTTTTATTATTACTTATTCATAACAACAA
* * * * *
2966251 AATAAATGGGCTATTAATGTGAATTAACCTAACATGCAACTAAAATACTAATTATGCAAATGAAA
323 AATAAATGAGCCATTAATGTGAATTAACCTAACATGCAACTAAAATACAAATTATGCAATTTAAA
*
2966316 TTAATATGACATGTACTACTATTTATGAACCATATAATATGGAATGTGACATACT-A--ATTTAA
388 TTAATATGACATGTACTACTATTTATGAACCATATAATATGCAATGTGACATACTAATTATTTAA
2966378 CACCTAATTAATCATGTTTTATATAATTTACATTTAAATAATTTTATTAATTTTATTAAATAATT
453 CACCTAATTAATCATGTTTTATATAATTTACATTTAAATAATTTTATTAATTTTATTAAATAATT
2966443 TTATATAATATGTATGTATAAACCATGTATA
518 TTATATAATATGTATGTATAAACCATGTATA
2966474 GTATATATAAACTATATATATATATATATATAAACTATATAAAGTAAATTACTTATATAGTTTAT
1 GTATATATAAAC--------TATATATATATAAACTATATAAAGTAAATTACTTATATAGTTTAT
* * * *
2966539 AGAAACACTATACATAAACTATATAAAGTAGTAAAATATATAGTTTATAAAAATCTTAAATCATA
58 AGAAACACTATACATAAACTATATAAAGTAATAAAATATATAGTTTATAAAAACCCTAAATCCTA
*
2966604 AACCATAAACCCTAAACTTTAAACTACAAA-CATTAAACACTAAATCATAAACCCTAATGTAAAT
123 AACCATAAA-CCTAAACTTTAAACTTCAAACCA-TAAACACTAAATCATAAACCCTAATGTAAAT
*
2966668 GGACTAGCACTAATGCATATATATTTGTAATAAAAGAGTGGGCTTGCACTGGGCCTATGTAAACT
186 GGACTAGCACTAATGCATATATATTTGTAATAAAAGAGTGGGCTTGCATTGGGCCTATGTAAACT
*
2966733 AATATTAATGGACTAGCACTATTGCAAATGGACTTATTTTTGGGTTTTATTATTACTTATTCATA
251 AATGTTAATGGACTAGCACTATTGCAAATGGACTTATTTTTGGGTTTTATTATTACTTATTCATA
2966798 ACAACAAAATAAATGAGCCATTAATGTGAATTAACCTAACATGCAACTAAAATACAAATTATGCA
316 ACAACAAAATAAATGAGCCATTAATGTGAATTAACCTAACATGCAACTAAAATACAAATTATGCA
2966863 ATTTAAATTAATATGACATGTACTACTATTTATGAACCATATAATATGCAATGTGACATACTAAT
381 ATTTAAATTAATATGACATGTACTACTATTTATGAACCATATAATATGCAATGTGACATACTAAT
2966928 TATTTAACACCTAATTAATCATGTTTTATATAATTTACATTTAAATAATTTTATTAATTTTATTA
446 TATTTAACACCTAATTAATCATGTTTTATATAATTTACATTTAAATAATTTTATTAATTTTATTA
2966993 AATAATTTTATATAATATGTATGTATAAACCATGTATA
511 AATAATTTTATATAATATGTATGTATAAACCATGTATA
*
2967031 GTATATATAAACTATATATATATAAACTATATAAAGTAAATTACTTTTATAGTTTATAGAAACAC
1 GTATATATAAACTATATATATATAAACTATATAAAGTAAATTACTTATATAGTTTATAGAAACAC
* * *
2967096 TATGCATAAACTATATAAAGTAATAAAATATATAGTTTATAGAAACCCTAAACCCTAAATCC-TA
66 TATACATAAACTATATAAAGTAATAAAATATATAGTTTATAAAAACCCTAAATCCTAAA-CCATA
* * * * * *
2967160 AACCTTAA-TTCTAAACTTTAAACCATAAATATTAAACCATAAACCCTAATTTAAATGGACTAGC
130 AACCTAAACTT-TAAACTTCAAACCATAAACACTAAATCATAAACCCTAATGTAAATGGACTAGC
2967224 ACTAATGCATATATATTTGTAATAAAAGAGTGGGCTTGCATTGGGCCTATGTAAACTAATGTTAA
194 ACTAATGCATATATATTTGTAATAAAAGAGTGGGCTTGCATTGGGCCTATGTAAACTAATGTTAA
2967289 TGGACTAGCACTATTGCAAATGGACTTATTTTTGGGTTTTATTATTACTTATTCATAACAACAAA
259 TGGACTAGCACTATTGCAAATGGACTTATTTTTGGGTTTTATTATTACTTATTCATAACAACAAA
* *
2967354 ATAAATGAGCCATTAATGTGAATTAACCTAACATGCAACTAAAATACAAATTATGTAGTTTAAAT
324 ATAAATGAGCCATTAATGTGAATTAACCTAACATGCAACTAAAATACAAATTATGCAATTTAAAT
* *
2967419 TAATATGACATGTACTGCTATTTATGAACCATATAATATGCAACGTGACATACTAATTATTTAAC
389 TAATATGACATGTACTACTATTTATGAACCATATAATATGCAATGTGACATACTAATTATTTAAC
2967484 ACCTAATTAATCATGTTTTATATAATTTACATTTAAATAATTTTATTAATTTTATTAAATAATTT
454 ACCTAATTAATCATGTTTTATATAATTTACATTTAAATAATTTTATTAATTTTATTAAATAATTT
2967549 TATAT-A-ATGTATG--TAAACCATGTATA
519 TATATAATATGTATGTATAAACCATGTATA
2967575 GTATATATAAAC--TATATATATAAACTATATAAAGTAAATTACTTATATAGTTTATAGAAACAC
1 GTATATATAAACTATATATATATAAACTATATAAAGTAAATTACTTATATAGTTTATAGAAACAC
* *
2967638 TATGCATAAACTATATAAAGTAATAAAATATATAGTTTATAAAAACCCTAAATCCTAAATCATAA
66 TATACATAAACTATATAAAGTAATAAAATATATAGTTTATAAAAACCCTAAATCCTAAACCATAA
* * *
2967703 ACCCT-AA-TTCTAAACTTTAAACCATAAACACTAAATCATAAACCCTAATTTAAATAGACTAGC
131 A-CCTAAACTT-TAAACTTCAAACCATAAACACTAAATCATAAACCCTAATGTAAATGGACTAGC
* * * *
2967766 ACTGATGCATATATATTTGTAATAAAAGAGTGAGCTTATGTATT-GGCCTTTGTAAACTAATGT
194 ACTAATGCATATATATTTGTAATAAAAGAGTGGGC-T-TGCATTGGGCCTATGTAAACTAATGT
2967829 ATTGCCAAAA
Statistics
Matches: 1276, Mismatches: 57, Indels: 47
0.92 0.04 0.03
Matches are distributed among these distances:
541 1 0.00
542 198 0.16
543 22 0.02
544 30 0.02
546 18 0.01
547 3 0.00
548 373 0.29
549 110 0.09
550 2 0.00
553 114 0.09
554 288 0.23
555 3 0.00
557 114 0.09
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.36
Consensus pattern (548 bp):
GTATATATAAACTATATATATATAAACTATATAAAGTAAATTACTTATATAGTTTATAGAAACAC
TATACATAAACTATATAAAGTAATAAAATATATAGTTTATAAAAACCCTAAATCCTAAACCATAA
ACCTAAACTTTAAACTTCAAACCATAAACACTAAATCATAAACCCTAATGTAAATGGACTAGCAC
TAATGCATATATATTTGTAATAAAAGAGTGGGCTTGCATTGGGCCTATGTAAACTAATGTTAATG
GACTAGCACTATTGCAAATGGACTTATTTTTGGGTTTTATTATTACTTATTCATAACAACAAAAT
AAATGAGCCATTAATGTGAATTAACCTAACATGCAACTAAAATACAAATTATGCAATTTAAATTA
ATATGACATGTACTACTATTTATGAACCATATAATATGCAATGTGACATACTAATTATTTAACAC
CTAATTAATCATGTTTTATATAATTTACATTTAAATAATTTTATTAATTTTATTAAATAATTTTA
TATAATATGTATGTATAAACCATGTATA
Found at i:2967592 original size:13 final size:13
Alignment explanation
Indices: 2967576--2967605 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2967566 CCATGTATAG
2967576 TATATATAAACTA
1 TATATATAAACTA
2967589 TATATATAAACTA
1 TATATATAAACTA
2967602 TATA
1 TATA
2967606 AAGTAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:2967708 original size:14 final size:14
Alignment explanation
Indices: 2967686--2967750 Score: 69
Period size: 14 Copynumber: 4.7 Consensus size: 14
2967676 ATAAAAACCC
*
2967686 TAAATCCTAAATCA
1 TAAACCCTAAATCA
*
2967700 TAAACCCTAATTC-
1 TAAACCCTAAATCA
** *
2967713 TAAACTTTAAACCA
1 TAAACCCTAAATCA
*
2967727 TAAACACTAAATCA
1 TAAACCCTAAATCA
2967741 TAAACCCTAA
1 TAAACCCTAA
2967751 TTTAAATAGA
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
13 9 0.22
14 31 0.77
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.26
Consensus pattern (14 bp):
TAAACCCTAAATCA
Found at i:2967723 original size:27 final size:28
Alignment explanation
Indices: 2967693--2967745 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
2967683 CCCTAAATCC
* * *
2967693 TAAATCATAAACCCTAATTC-TAAACTT
1 TAAACCATAAACACTAAATCATAAACTT
2967720 TAAACCATAAACACTAAATCATAAAC
1 TAAACCATAAACACTAAATCATAAAC
2967746 CCTAATTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 17 0.77
28 5 0.23
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (28 bp):
TAAACCATAAACACTAAATCATAAACTT
Found at i:2968175 original size:16 final size:16
Alignment explanation
Indices: 2968150--2968190 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
2968140 TCAGATCAGG
*
2968150 TCATTAACAAGTTGAA
1 TCATTTACAAGTTGAA
2968166 TCATTTACAAGTTGAA
1 TCATTTACAAGTTGAA
2968182 TCATTTACA
1 TCATTTACA
2968191 GGTCAAGTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.37
Consensus pattern (16 bp):
TCATTTACAAGTTGAA
Found at i:2968213 original size:16 final size:16
Alignment explanation
Indices: 2968192--2968242 Score: 75
Period size: 16 Copynumber: 3.2 Consensus size: 16
2968182 TCATTTACAG
*
2968192 GTCAAGTTGAAAACAT
1 GTCAAGTTGAAAACAA
*
2968208 GTCAAGTTAAAAACAA
1 GTCAAGTTGAAAACAA
*
2968224 GTCAGGTTGAAAACAA
1 GTCAAGTTGAAAACAA
2968240 GTC
1 GTC
2968243 GGGTAATACC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.45, C:0.14, G:0.20, T:0.22
Consensus pattern (16 bp):
GTCAAGTTGAAAACAA
Found at i:2971688 original size:28 final size:28
Alignment explanation
Indices: 2971601--2971680 Score: 110
Period size: 28 Copynumber: 2.9 Consensus size: 28
2971591 TAAAATTTGT
2971601 TAAA-CTTAAACCCTAAATTTTAAATAC
1 TAAACCTTAAACCCTAAATTTTAAATAC
* *
2971628 TAAAACC-TAAACCCTAAATCTTACATAC
1 T-AAACCTTAAACCCTAAATTTTAAATAC
*
2971656 TAAACCTTAAACTCTAAATTTTAAA
1 TAAACCTTAAACCCTAAATTTTAAA
2971681 CCCTAAACTC
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
27 6 0.13
28 38 0.84
29 1 0.02
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.31
Consensus pattern (28 bp):
TAAACCTTAAACCCTAAATTTTAAATAC
Found at i:2972152 original size:135 final size:135
Alignment explanation
Indices: 2971961--2972234 Score: 523
Period size: 135 Copynumber: 2.0 Consensus size: 135
2971951 GGATGATCAT
2971961 TTTCTCTCAAATATGATTTGATGCACTAATTTTGTTAATTAAGATATTAATGTAAGTCTAAATGA
1 TTTCTCTCAAATATGATTTGATGCACTAATTTTGTTAATTAAGATATTAATGTAAGTCTAAATGA
2972026 GTTTTTTCTTTCTTAATTCTTTATAAAATCGGTTACACTCTATTTTG-ATATTTTTTAAAATTAT
66 GTTTTTTCTTTCTTAATTCTTTATAAAATCGGTTACACTCTATTTTGAATATTTTTTAAAATTAT
2972090 TAATA
131 TAATA
2972095 TTTCTCTCAAATATGATTTGATGCCACTAATTTTGTTAATTAAGATATTAATGTAAGTCTAAATG
1 TTTCTCTCAAATATGATTTGATG-CACTAATTTTGTTAATTAAGATATTAATGTAAGTCTAAATG
2972160 AGTTTTTTCTTTCTTAATTCTTTATAAAATCGGTTACACTCTATTTTGATATATTTTTTAAAATT
65 AGTTTTTTCTTTCTTAATTCTTTATAAAATCGGTTACACTCTATTTTGA-ATATTTTTTAAAATT
2972225 ATTAATA
129 ATTAATA
2972232 TTT
1 TTT
2972235 AAATTGAATC
Statistics
Matches: 137, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
134 23 0.17
135 89 0.65
137 25 0.18
ACGTcount: A:0.32, C:0.10, G:0.09, T:0.50
Consensus pattern (135 bp):
TTTCTCTCAAATATGATTTGATGCACTAATTTTGTTAATTAAGATATTAATGTAAGTCTAAATGA
GTTTTTTCTTTCTTAATTCTTTATAAAATCGGTTACACTCTATTTTGAATATTTTTTAAAATTAT
TAATA
Found at i:2978273 original size:29 final size:29
Alignment explanation
Indices: 2978239--2978297 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
2978229 CCTAAATTAA
*
2978239 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGACATTGCTTACATCAATTTAGT
2978268 TTTGATGACATTGCTTACATCAATTTAGT
1 TTTGATGACATTGCTTACATCAATTTAGT
2978297 T
1 T
2978298 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.47
Consensus pattern (29 bp):
TTTGATGACATTGCTTACATCAATTTAGT
Found at i:2982902 original size:29 final size:29
Alignment explanation
Indices: 2982869--2982938 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
2982859 AAATAAGTTC
2982869 ACATCTAAATTA-ATTTGATGTCA-TTCTTT
1 ACATC-AAATTAGATTTGATGTCATTTC-TT
* *
2982898 ACATCAATTTAGTTTTGATGTCATTTCTT
1 ACATCAAATTAGATTTGATGTCATTTCTT
*
2982927 ACATCAATTTAG
1 ACATCAAATTAG
2982939 TTAGGTGAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
28 5 0.14
29 29 0.78
30 3 0.08
ACGTcount: A:0.30, C:0.14, G:0.09, T:0.47
Consensus pattern (29 bp):
ACATCAAATTAGATTTGATGTCATTTCTT
Found at i:2982939 original size:29 final size:29
Alignment explanation
Indices: 2982882--2982940 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 29
2982872 TCTAAATTAA
2982882 TTTGATGTCATTCTTTACATCAATTTAGT
1 TTTGATGTCATTCTTTACATCAATTTAGT
2982911 TTTGATGTCATT-TCTTACATCAATTTAGT
1 TTTGATGTCATTCT-TTACATCAATTTAGT
2982940 T
1 T
2982941 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 1 0.03
29 28 0.97
ACGTcount: A:0.24, C:0.14, G:0.10, T:0.53
Consensus pattern (29 bp):
TTTGATGTCATTCTTTACATCAATTTAGT
Found at i:2986399 original size:3 final size:3
Alignment explanation
Indices: 2986393--2986504 Score: 161
Period size: 3 Copynumber: 36.7 Consensus size: 3
2986383 TCATTTAAAT
** *
2986393 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
2986441 TTA TAA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
2986487 TTA TATA TTA TTA TTA TT
1 TTA T-TA TTA TTA TTA TT
2986505 TAATAAATAA
Statistics
Matches: 97, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
3 91 0.94
4 6 0.06
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:2987956 original size:17 final size:17
Alignment explanation
Indices: 2987887--2987957 Score: 54
Period size: 18 Copynumber: 4.0 Consensus size: 17
2987877 TTTATTTTAA
2987887 TTATTGTTTAA-ATATATT
1 TTATT-TTTAATAT-TATT
* *
2987905 TTAATTTTATATAATATT
1 TTATTTTTA-ATATTATT
** *
2987923 TTAATTAGTATTATTATT
1 TT-ATTTTTAATATTATT
2987941 TTATTTTTAATATTATT
1 TTATTTTTAATATTATT
2987958 ATTTAATTAA
Statistics
Matches: 40, Mismatches: 10, Indels: 7
0.70 0.18 0.12
Matches are distributed among these distances:
17 16 0.40
18 19 0.47
19 5 0.12
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (17 bp):
TTATTTTTAATATTATT
Found at i:2987967 original size:17 final size:18
Alignment explanation
Indices: 2987901--2987973 Score: 60
Period size: 18 Copynumber: 4.0 Consensus size: 18
2987891 TGTTTAAATA
* *
2987901 TATTTTAATT-TTATATAA
1 TATTTTAATTAATAT-TAT
*
2987919 TATTTTAATTAGTATTAT
1 TATTTTAATTAATATTAT
*
2987937 TATTTTATTTTTAATATTAT
1 TATTTTA--ATTAATATTAT
*
2987957 TA-TTTAATTAATTTTAT
1 TATTTTAATTAATATTAT
2987974 AAATTAATAA
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
17 9 0.20
18 19 0.41
19 7 0.15
20 11 0.24
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (18 bp):
TATTTTAATTAATATTAT
Found at i:2994701 original size:86 final size:89
Alignment explanation
Indices: 2994552--2994793 Score: 343
Period size: 86 Copynumber: 2.8 Consensus size: 89
2994542 GACCCAATAG
*
2994552 CTTCTCGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAATCATTGAA
1 CTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAATCATTGAA
*
2994617 TTTGG-A-A-G-ATGCT-CATAGCAT
66 TTTGGAAGAGGAATG-TGC-TAACAT
* * *
2994638 CTTCTGGAAGTGTCCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAGTTATTGAA
1 CTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAATCATTGAA
*
2994703 TTTGGAAGAGGAATGTGCTAATAT
66 TTTGGAAGAGGAATGTGCTAACAT
* *
2994727 CTTCTGGAAGTGTTCTTTGAATTATCTGATC-GGTTTGGTAAGAACCACAGAACCAATCATTGGA
1 CTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAATCATT-GA
2994791 ATT
65 ATT
2994794 AAAAGATGAA
Statistics
Matches: 139, Mismatches: 11, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
86 66 0.47
87 1 0.01
88 28 0.20
89 40 0.29
90 4 0.03
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (89 bp):
CTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAATCATTGAA
TTTGGAAGAGGAATGTGCTAACAT
Found at i:2997859 original size:31 final size:31
Alignment explanation
Indices: 2997824--2997907 Score: 145
Period size: 31 Copynumber: 2.8 Consensus size: 31
2997814 CTTCAGTGCA
2997824 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
2997855 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
*
2997886 TGATGTTTTC--AAAGCCTTCGGG
1 TGATGTTTCCAAAAAGCCTTCGGG
2997908 TCATCTGTAA
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
29 12 0.23
31 40 0.77
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (31 bp):
TGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
Found at i:2997981 original size:76 final size:76
Alignment explanation
Indices: 2997855--2998184 Score: 507
Period size: 76 Copynumber: 4.2 Consensus size: 76
2997845 GGGAGCTTTT
2997855 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
2997920 CCTTCAGTGCA
66 CCTTCAGTGCA
*
2997931 TGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
2997996 CCTTCAGTGCA
66 CCTTCAGTGCA
*
2998007 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTATAAGT
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
2998072 CCTTCAGTGCATGATGTTAAAAA
66 CCTTCAGTGC------------A
* *
2998095 TGATGTTTCCAAAAAGCCTTCGGGAACTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGC
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
2998160 CCTTCAGTGCA
66 CCTTCAGTGCA
*
2998171 TGATGTTTTCAAAA
1 TGATGTTTCCAAAA
2998185 CCTGCGGGTC
Statistics
Matches: 235, Mismatches: 7, Indels: 24
0.88 0.03 0.09
Matches are distributed among these distances:
76 162 0.69
88 73 0.31
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (76 bp):
TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
CCTTCAGTGCA
Found at i:2998164 original size:88 final size:88
Alignment explanation
Indices: 2998006--2998177 Score: 317
Period size: 88 Copynumber: 2.0 Consensus size: 88
2997996 CCTTCAGTGC
*
2998006 ATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTATAAG
1 ATGATGTTTCCAAAAAGCCTTCGGGAACTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTATAAG
*
2998071 TCCTTCAGTGCATGATGTTAAAA
66 CCCTTCAGTGCATGATGTTAAAA
*
2998094 ATGATGTTTCCAAAAAGCCTTCGGGAACTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAG
1 ATGATGTTTCCAAAAAGCCTTCGGGAACTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTATAAG
2998159 CCCTTCAGTGCATGATGTT
66 CCCTTCAGTGCATGATGTT
2998178 TTCAAAACCT
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
88 81 1.00
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.35
Consensus pattern (88 bp):
ATGATGTTTCCAAAAAGCCTTCGGGAACTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTATAAG
CCCTTCAGTGCATGATGTTAAAA
Found at i:2998175 original size:45 final size:45
Alignment explanation
Indices: 2998126--2998239 Score: 174
Period size: 45 Copynumber: 2.5 Consensus size: 45
2998116 GGGAACTTTT
2998126 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * *
2998171 TGATGTTTTCAAAACCTGCGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
2998216 TGATGTTTCCAAAAAGCCTTCGGG
1 TGATGTTTTC--AAAGCCTTCGGG
2998240 AGCTTTTTGA
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
45 51 0.84
47 10 0.16
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.32
Consensus pattern (45 bp):
TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:2998251 original size:76 final size:76
Alignment explanation
Indices: 2998171--2998837 Score: 1201
Period size: 76 Copynumber: 8.8 Consensus size: 76
2998161 CTTCAGTGCA
* *
2998171 TGATGTTTTCAAAACCTGCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
2998236 CGGGAGCTTTT
66 CGGGAGCTTTT
2998247 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
2998312 CGGGAGCTTTT
66 CGGGAGCTTTT
2998323 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATG-TGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
*
2998387 CAGGAGCTTTT
66 CGGGAGCTTTT
2998398 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
2998463 CGGGAGCTTTT
66 CGGGAGCTTTT
2998474 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
*
2998539 CAGGAGCTTTT
66 CGGGAGCTTTT
*
2998550 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCAAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
2998615 CGGGAGCTTTTT
66 CGGGAGC-TTTT
2998627 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
2998692 CGGGAGCTTTT
66 CGGGAGCTTTT
* * * *
2998703 TAATGTTTTCAAATCCTTCAGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
2998768 CGGGAGCTTTT
66 CGGGAGCTTTT
* * *
2998779 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
1 TGATGTTTTC-AAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAA
2998838 CATTTCAATC
Statistics
Matches: 570, Mismatches: 18, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
75 74 0.13
76 378 0.66
77 118 0.21
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (76 bp):
TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
CGGGAGCTTTT
Found at i:2998566 original size:227 final size:229
Alignment explanation
Indices: 2998171--2998837 Score: 1203
Period size: 227 Copynumber: 2.9 Consensus size: 229
2998161 CTTCAGTGCA
* *
2998171 TGATGTTTTCAAAACCTGCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
2998236 CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTC
66 CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTC
2998301 CAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTG
131 CAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTG
2998366 CATG-TGTTTCCAAAAAGCCTTCAGGAGC-TTTT
196 CATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTT
2998398 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
2998463 CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTC
66 CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTC
*
2998528 CAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTG
131 CAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTG
* *
2998593 CATGATGTTTCAAAAAAGCCTTCGGGAGCTTTTT
196 CATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTT
2998627 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
* * * *
2998692 CGGGAGCTTTTTAATGTTTTCAAATCCTTCAGGTCATCTGTAAGTCCTACAGTGCATGATGTTTC
66 CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTC
* *
2998757 CAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
131 CAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-AAAGCCTTCGGGTCATCTGTAAGTCCTTCAGT
*
2998822 GCATGATGTTTTCAAA
195 GCATGATGTTTCCAAA
2998838 CATTTCAATC
Statistics
Matches: 423, Mismatches: 14, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
227 196 0.46
228 22 0.05
229 161 0.38
230 44 0.10
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (229 bp):
TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTC
CAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTG
CATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTT
Found at i:2998730 original size:153 final size:152
Alignment explanation
Indices: 2998171--2998837 Score: 1201
Period size: 153 Copynumber: 4.4 Consensus size: 152
2998161 CTTCAGTGCA
* *
2998171 TGATGTTTTCAAAACCTGCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
*
2998236 CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTC
66 CAGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTC
2998301 CAAAAAGCCTTCGGGAGCTTTT
131 CAAAAAGCCTTCGGGAGCTTTT
2998323 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATG-TGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
2998387 CAGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTC
66 CAGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTC
2998452 CAAAAAGCCTTCGGGAGCTTTT
131 CAAAAAGCCTTCGGGAGCTTTT
2998474 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
2998539 CAGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTC
66 CAGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTC
*
2998604 AAAAAAGCCTTCGGGAGCTTTTT
131 CAAAAAGCCTTCGGGAGC-TTTT
2998627 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
* * * * *
2998692 CGGGAGCTTTTTAATGTTTTCAAATCCTTCAGGTCATCTGTAAGTCCTACAGTGCATGATGTTTC
66 CAGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTC
2998757 CAAAAAGCCTTCGGGAGCTTTT
131 CAAAAAGCCTTCGGGAGCTTTT
* * *
2998779 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
1 TGATGTTTTC-AAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAA
2998838 CATTTCAATC
Statistics
Matches: 499, Mismatches: 13, Indels: 5
0.97 0.03 0.01
Matches are distributed among these distances:
151 150 0.30
152 158 0.32
153 191 0.38
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (152 bp):
TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
CAGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTC
CAAAAAGCCTTCGGGAGCTTTT
Found at i:2998972 original size:3 final size:3
Alignment explanation
Indices: 2998966--2999068 Score: 143
Period size: 3 Copynumber: 33.7 Consensus size: 3
2998956 TCATTTAAAT
**
2998966 TTA TTA TTA TTA TTA AAA 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
* * *
2999014 TAA TTA TAA GTA TTA TTA TTTA TTA TTA TTA TTA TTA TTA TATA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA T-TA TTA
2999061 TTA TTA TT
1 TTA TTA TT
2999069 TAATAAATAA
Statistics
Matches: 88, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
3 82 0.93
4 6 0.07
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:3000487 original size:18 final size:18
Alignment explanation
Indices: 3000464--3000522 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
3000454 TTGTTTAAAT
3000464 ATATTTTAATTTTATATA
1 ATATTTTAATTTTATATA
*
3000482 ATATTTTAATTAGTAT-TA
1 ATATTTTAATT-TTATATA
* *
3000500 TTATTTTATTTTTA-ATA
1 ATATTTTAATTTTATATA
3000517 TATATT
1 -ATATT
3000523 ATTTAATTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
17 4 0.12
18 26 0.79
19 3 0.09
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.63
Consensus pattern (18 bp):
ATATTTTAATTTTATATA
Found at i:3000536 original size:24 final size:24
Alignment explanation
Indices: 3000475--3000537 Score: 58
Period size: 24 Copynumber: 2.6 Consensus size: 24
3000465 TATTTTAATT
*
3000475 TTATATAATATTTTAATTAGTATTA
1 TTATATTA-ATTTTAATTAGTATTA
* *
3000500 TTATTTTATTTTTAATATA-TATTA
1 TTATATTAATTTTAAT-TAGTATTA
3000524 TT-TAATTAATTTTA
1 TTAT-ATTAATTTTA
3000538 TAAATTAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
23 1 0.03
24 22 0.71
25 8 0.26
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
TTATATTAATTTTAATTAGTATTA
Found at i:3000676 original size:15 final size:17
Alignment explanation
Indices: 3000650--3000683 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
3000640 TAATTTTTTC
3000650 TTAAATTATTTTAC-TT
1 TTAAATTATTTTACATT
3000666 TTAAATT-TTTTACATT
1 TTAAATTATTTTACATT
3000682 TT
1 TT
3000684 TAGTTATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (17 bp):
TTAAATTATTTTACATT
Found at i:3005212 original size:17 final size:17
Alignment explanation
Indices: 3005190--3005229 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
3005180 ATTTATAGAA
*
3005190 AAATAAATATAATTATC
1 AAATAAATATAATCATC
*
3005207 AAATAAATTTAATCATC
1 AAATAAATATAATCATC
*
3005224 GAATAA
1 AAATAA
3005230 TTTTAAACAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (17 bp):
AAATAAATATAATCATC
Found at i:3013304 original size:21 final size:21
Alignment explanation
Indices: 3013278--3013317 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3013268 CGGAACCCCA
*
3013278 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
3013299 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
3013318 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:3013352 original size:20 final size:21
Alignment explanation
Indices: 3013298--3013360 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
3013288 GATTCCCCTG
3013298 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
3013322 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
3013342 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
3013361 TGTACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:3017737 original size:18 final size:18
Alignment explanation
Indices: 3017708--3017742 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3017698 TTTAAAATCT
3017708 TTTTATTTTATTGTTTCTG
1 TTTTATTTTATT-TTTCTG
3017727 TTTTA-TTTATTTTTCT
1 TTTTATTTTATTTTTCT
3017743 TCATCTACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 6 0.38
19 5 0.31
ACGTcount: A:0.11, C:0.06, G:0.06, T:0.77
Consensus pattern (18 bp):
TTTTATTTTATTTTTCTG
Found at i:3018121 original size:9 final size:9
Alignment explanation
Indices: 3018107--3018165 Score: 57
Period size: 9 Copynumber: 6.6 Consensus size: 9
3018097 AGATAACCCA
3018107 TTTTTATTT
1 TTTTTATTT
3018116 TTTTTATTT
1 TTTTTATTT
* **
3018125 GTTCAATTT
1 TTTTTATTT
3018134 TTTTTA-TT
1 TTTTTATTT
**
3018142 TTTAAATTT
1 TTTTTATTT
3018151 TTTTTATTT
1 TTTTTATTT
3018160 ATTTTT
1 -TTTTT
3018166 TTCTTTGAAT
Statistics
Matches: 38, Mismatches: 10, Indels: 3
0.75 0.20 0.06
Matches are distributed among these distances:
8 6 0.16
9 27 0.71
10 5 0.13
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.80
Consensus pattern (9 bp):
TTTTTATTT
Found at i:3018136 original size:17 final size:17
Alignment explanation
Indices: 3018112--3018159 Score: 78
Period size: 17 Copynumber: 2.8 Consensus size: 17
3018102 ACCCATTTTT
*
3018112 ATTTTTTTTATTTGTTCA
1 ATTTTTTTTATTT-TTAA
3018130 ATTTTTTTTATTTTTAA
1 ATTTTTTTTATTTTTAA
3018147 ATTTTTTTTATTT
1 ATTTTTTTTATTT
3018160 ATTTTTTTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 16 0.55
18 13 0.45
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (17 bp):
ATTTTTTTTATTTTTAA
Found at i:3024881 original size:29 final size:28
Alignment explanation
Indices: 3024812--3024882 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
3024802 AAATTATAAC
*
3024812 AAATTAGGGACCCTAATTATAAATATAAA
1 AAATTAGGG-CCCTAATTATAAATACAAA
* *
3024841 ACATTGGGGCCCTAATTATAAATACAAA
1 AAATTAGGGCCCTAATTATAAATACAAA
3024869 AAATTAGAGGCCCT
1 AAATTAG-GGCCCT
3024883 GACAGTTGCT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
28 23 0.64
29 13 0.36
ACGTcount: A:0.45, C:0.15, G:0.14, T:0.25
Consensus pattern (28 bp):
AAATTAGGGCCCTAATTATAAATACAAA
Found at i:3025204 original size:24 final size:24
Alignment explanation
Indices: 3025150--3025205 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
3025140 ACTCAAAATT
*
3025150 ATAAATTTAATTTAATAATATACAA
1 ATAAA-TTAATTTAATAAAATACAA
* * **
3025175 AAAAATTAATTTAGTAAAATATTA
1 ATAAATTAATTTAATAAAATACAA
3025199 ATAAATT
1 ATAAATT
3025206 TGATTAGTTA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
24 21 0.84
25 4 0.16
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (24 bp):
ATAAATTAATTTAATAAAATACAA
Found at i:3025360 original size:16 final size:17
Alignment explanation
Indices: 3025339--3025370 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3025329 TGAGACCATA
3025339 ATATTAT-TTTTATATT
1 ATATTATGTTTTATATT
3025355 ATATTATGTTTTATAT
1 ATATTATGTTTTATAT
3025371 AAATAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (17 bp):
ATATTATGTTTTATATT
Found at i:3030282 original size:15 final size:16
Alignment explanation
Indices: 3030264--3030293 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3030254 AAGAAATATA
3030264 AAATTAAAA-GATTTT
1 AAATTAAAAGGATTTT
3030279 AAATTAAAAGGATTT
1 AAATTAAAAGGATTT
3030294 AACTACAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.37
Consensus pattern (16 bp):
AAATTAAAAGGATTTT
Found at i:3031693 original size:35 final size:35
Alignment explanation
Indices: 3031613--3032009 Score: 424
Period size: 35 Copynumber: 11.2 Consensus size: 35
3031603 TTTTCGATAC
** * * *
3031613 GTTTTCAAAA-TCCTTTAAAACCCATATATTATAC
1 GTTTTCAAAACTATTTTAAAAACTATATATTATAT
* * * *
3031647 G-CTTCAAAACCATTTCAAAAAATATAT-TATATAT
1 GTTTTCAAAACTATTTTAAAAACTATATAT-TATAT
* * * *
3031681 GTTTTCAAAACCATTTTTAAAATTATATATTATAC
1 GTTTTCAAAACTATTTTAAAAACTATATATTATAT
* * ** *
3031716 GTTTTCAAAATTATCTTAAAAACTGGATACTATAT
1 GTTTTCAAAACTATTTTAAAAACTATATATTATAT
* *
3031751 GTTTTCAAAA-TCGTTTTAAAAACTATATATTATAC
1 GTTTTCAAAACT-ATTTTAAAAACTATATATTATAT
3031786 GTTTTCAAAACTATTTTTAAAAAACTATATATTATAT
1 GTTTTCAAAACTA-TTTT-AAAAACTATATATTATAT
* *
3031823 GTTTTCAAAATTATTTTAAAAACTATATACTATAT
1 GTTTTCAAAACTATTTTAAAAACTATATATTATAT
3031858 GTTTTCAAAACTATTTTTTAAAAACTATATATTATAT
1 GTTTTCAAAACTA--TTTTAAAAACTATATATTATAT
* * * * *
3031895 GTTTTTAAAATTATTCTAAAAACTATATACTATAC
1 GTTTTCAAAACTATTTTAAAAACTATATATTATAT
* *
3031930 GTTTTCAAAACTATTTTTAAAACTATATATTATAC
1 GTTTTCAAAACTATTTTAAAAACTATATATTATAT
*
3031965 GTTTTCAAAAGTATTTTTAAAAAACTATATATTATAT
1 GTTTTCAAAACTA-TTTT-AAAAACTATATATTATAT
3032002 GTTTTCAA
1 GTTTTCAA
3032010 TTTTTTTTTA
Statistics
Matches: 303, Mismatches: 48, Indels: 21
0.81 0.13 0.06
Matches are distributed among these distances:
33 8 0.03
34 17 0.06
35 179 0.59
36 14 0.05
37 85 0.28
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.44
Consensus pattern (35 bp):
GTTTTCAAAACTATTTTAAAAACTATATATTATAT
Found at i:3031830 original size:72 final size:71
Alignment explanation
Indices: 3031613--3032009 Score: 466
Period size: 72 Copynumber: 5.6 Consensus size: 71
3031603 TTTTCGATAC
* * * * * * *
3031613 GTTTTCAAAATC-CTTTAAAACCCATATATTATACG-CTTCAAAACCA-TTTCAAAAAATATAT-
1 GTTTTCAAAATCATTTTAAAAACTATATATTATACGTTTTCAAAACTATTTTTAAAAACTATATA
3031674 TATATAT
66 T-TATAT
* * * * * **
3031681 GTTTTCAAAACCATTTTTAAAATTATATATTATACGTTTTCAAAATTA-TCTTAAAAACTGGATA
1 GTTTTCAAAATCATTTTAAAAACTATATATTATACGTTTTCAAAACTATTTTTAAAAACTATATA
*
3031745 CTATAT
66 TTATAT
*
3031751 GTTTTCAAAATCGTTTTAAAAACTATATATTATACGTTTTCAAAACTATTTTTAAAAAACTATAT
1 GTTTTCAAAATCATTTTAAAAACTATATATTATACGTTTTCAAAACTATTTTT-AAAAACTATAT
3031816 ATTATAT
65 ATTATAT
* * *
3031823 GTTTTCAAAATTATTTTAAAAACTATATACTATATGTTTTCAAAACTATTTTTTAAAAACTATAT
1 GTTTTCAAAATCATTTTAAAAACTATATATTATACGTTTTCAAAACTA-TTTTTAAAAACTATAT
3031888 ATTATAT
65 ATTATAT
* * * *
3031895 GTTTTTAAAATTATTCTAAAAACTATATACTATACGTTTTCAAAACTATTTTT-AAAACTATATA
1 GTTTTCAAAATCATTTTAAAAACTATATATTATACGTTTTCAAAACTATTTTTAAAAACTATATA
*
3031959 TTATAC
66 TTATAT
*
3031965 GTTTTCAAAAGT-ATTTTTAAAAAACTATATATTATATGTTTTCAA
1 GTTTTCAAAA-TCA-TTTT-AAAAACTATATATTATACGTTTTCAA
3032010 TTTTTTTTTA
Statistics
Matches: 284, Mismatches: 36, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
68 11 0.04
69 18 0.06
70 92 0.32
71 12 0.04
72 146 0.51
73 5 0.02
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.44
Consensus pattern (71 bp):
GTTTTCAAAATCATTTTAAAAACTATATATTATACGTTTTCAAAACTATTTTTAAAAACTATATA
TTATAT
Found at i:3031845 original size:107 final size:107
Alignment explanation
Indices: 3031609--3032009 Score: 456
Period size: 107 Copynumber: 3.8 Consensus size: 107
3031599 AATGTTTTCG
** * * * * * * * *
3031609 ATACGTTTTCAAAA-TCCTTTAAAACCCATATATTATACG-CTTCAAAAC-CATTTCAAAAAATA
1 ATACGTTTTCAAAATTATTTTAAAAACTATATACTATATGTTTTCAAAACTCTTTTTAAAAACTA
* *
3031671 TAT-TATATATGTTTTCAAAACCATTTTT-AAAATTATATATT
66 TATAT-TATATGTTTTCAAAACTATTTTTAAAAACTATATATT
* ** *
3031712 ATACGTTTTCAAAATTATCTTAAAAACTGGATACTATATGTTTTCAAAA-TCGTTTTAAAAACTA
1 ATACGTTTTCAAAATTATTTTAAAAACTATATACTATATGTTTTCAAAACTCTTTTTAAAAACTA
*
3031776 TATATTATACGTTTTCAAAACTATTTTTAAAAAACTATATATT
66 TATATTATATGTTTTCAAAACTATTTTT-AAAAACTATATATT
* *
3031819 ATATGTTTTCAAAATTATTTTAAAAACTATATACTATATGTTTTCAAAACTATTTTTTAAAAACT
1 ATACGTTTTCAAAATTATTTTAAAAACTATATACTATATGTTTTCAAAACT-CTTTTTAAAAACT
* * * *
3031884 ATATATTATATGTTTTTAAAATTA-TTCTAAAAACTATATACT
65 ATATATTATATGTTTTCAAAACTATTTTTAAAAACTATATATT
* * * * * *
3031926 ATACGTTTTCAAAACTATTTTTAAAACTATATATTATACGTTTTCAAAAGTATTTTTAAAAAACT
1 ATACGTTTTCAAAATTATTTTAAAAACTATATACTATATGTTTTCAAAACTCTTTTT-AAAAACT
3031991 ATATATTATATGTTTTCAA
65 ATATATTATATGTTTTCAA
3032010 TTTTTTTTTA
Statistics
Matches: 254, Mismatches: 35, Indels: 14
0.84 0.12 0.05
Matches are distributed among these distances:
103 14 0.06
104 16 0.06
105 42 0.17
106 6 0.02
107 140 0.55
108 4 0.02
109 32 0.13
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.43
Consensus pattern (107 bp):
ATACGTTTTCAAAATTATTTTAAAAACTATATACTATATGTTTTCAAAACTCTTTTTAAAAACTA
TATATTATATGTTTTCAAAACTATTTTTAAAAACTATATATT
Found at i:3032614 original size:13 final size:13
Alignment explanation
Indices: 3032588--3032622 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
3032578 CAATCCTGGC
3032588 GACATACG-GGGT
1 GACATACGAGGGT
3032600 GACATACGAGGGT
1 GACATACGAGGGT
3032613 GACATACGAG
1 GACATACGAG
3032623 CCATATACGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 8 0.36
13 14 0.64
ACGTcount: A:0.31, C:0.17, G:0.37, T:0.14
Consensus pattern (13 bp):
GACATACGAGGGT
Found at i:3032632 original size:11 final size:11
Alignment explanation
Indices: 3032616--3032649 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
3032606 CGAGGGTGAC
3032616 ATACGAGCCAT
1 ATACGAGCCAT
3032627 ATACGAGCCAT
1 ATACGAGCCAT
*
3032638 ATACGAGTCAT
1 ATACGAGCCAT
3032649 A
1 A
3032650 CGAGCCAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.21
Consensus pattern (11 bp):
ATACGAGCCAT
Found at i:3032680 original size:22 final size:22
Alignment explanation
Indices: 3032649--3032728 Score: 79
Period size: 22 Copynumber: 3.4 Consensus size: 22
3032639 TACGAGTCAT
*
3032649 ACGAGCCAATGGGGAGGATGCA
1 ACGAGCCAATGGGGAGCATGCA
*
3032671 ACGAGGCAATGGGGAGCATGCAGGAA
1 ACGAGCCAATGGGGAGCATGC----A
*
3032697 TAGAGAGCCAATGGGGAGCATGCA
1 -A-CGAGCCAATGGGGAGCATGCA
3032721 ACGAGCCA
1 ACGAGCCA
3032729 TATACGAGCC
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
22 25 0.53
23 1 0.02
24 1 0.02
26 1 0.02
27 1 0.02
28 18 0.38
ACGTcount: A:0.34, C:0.19, G:0.39, T:0.09
Consensus pattern (22 bp):
ACGAGCCAATGGGGAGCATGCA
Found at i:3032709 original size:28 final size:28
Alignment explanation
Indices: 3032677--3032842 Score: 188
Period size: 28 Copynumber: 5.6 Consensus size: 28
3032667 TGCAACGAGG
3032677 CAATGGGGAGCATGCAGGAATAGAGAGC
1 CAATGGGGAGCATGCAGGAATAGAGAGC
* *
3032705 CAATGGGGAGCATGCAACGAGCCATATACGAGC
1 CAATGGGGAGCATGC-A-G-G-AATAGA-GAGC
* *
3032738 CCACGGGGAGCATGCAGGAATAGAGAGC
1 CAATGGGGAGCATGCAGGAATAGAGAGC
* *
3032766 CAATGGGGAGCATGCAACGAGCCATATACGAGC
1 CAATGGGGAGCATGC-A-G-G-AATAGA-GAGC
3032799 CAATGGGGAGCATGCAGGAATAGAGAGC
1 CAATGGGGAGCATGCAGGAATAGAGAGC
3032827 CAATGGGGAGCATGCA
1 CAATGGGGAGCATGCA
3032843 ACGAGCCATA
Statistics
Matches: 116, Mismatches: 12, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
28 52 0.45
29 10 0.09
30 4 0.03
31 4 0.03
32 10 0.09
33 36 0.31
ACGTcount: A:0.34, C:0.20, G:0.36, T:0.11
Consensus pattern (28 bp):
CAATGGGGAGCATGCAGGAATAGAGAGC
Found at i:3032710 original size:50 final size:51
Alignment explanation
Indices: 3032651--3032876 Score: 213
Period size: 61 Copynumber: 4.1 Consensus size: 51
3032641 CGAGTCATAC
* *
3032651 GAGCCAATGGGGAGGATGCAACGAGGCA-ATGGGGAGCATGCAGGAATAGA
1 GAGCCAATGGGGAGCATGCAACGAGCCATATGGGGAGCATGCAGGAATAGA
3032701 GAGCCAATGGGGAGCATGCAACGAGCCATATACGAGCCCACGGGGAGCATGCAGGAATAGA
1 GAGCCAATGGGGAGCATGCAACGAGCCATAT----------GGGGAGCATGCAGGAATAGA
3032762 GAGCCAATGGGGAGCATGCAACGAGCCATATACGAGCCAATGGGGAGCATGCAGGAATAGA
1 GAGCCAATGGGGAGCATGCAACGAGCC--AT--------ATGGGGAGCATGCAGGAATAGA
**
3032823 GAGCCAATGGGGAGCATGCAACGAGCCATAT-ACGAGCCATGCAGGAATAGA
1 GAGCCAATGGGGAGCATGCAACGAGCCATATGGGGAG-CATGCAGGAATAGA
3032874 GAG
1 GAG
3032877 GTCGCCATGC
Statistics
Matches: 150, Mismatches: 4, Indels: 43
0.76 0.02 0.22
Matches are distributed among these distances:
50 29 0.19
51 21 0.14
59 2 0.01
61 94 0.63
63 2 0.01
71 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.36, T:0.11
Consensus pattern (51 bp):
GAGCCAATGGGGAGCATGCAACGAGCCATATGGGGAGCATGCAGGAATAGA
Found at i:3032766 original size:61 final size:61
Alignment explanation
Indices: 3032671--3032861 Score: 346
Period size: 61 Copynumber: 3.1 Consensus size: 61
3032661 GGAGGATGCA
* *
3032671 ACGAGGCAATGGGGAGCATGCAGGAATAGAGAGCCAATGGGGAGCATGCAACGAGCCATAT
1 ACGAGCCAACGGGGAGCATGCAGGAATAGAGAGCCAATGGGGAGCATGCAACGAGCCATAT
*
3032732 ACGAGCCCACGGGGAGCATGCAGGAATAGAGAGCCAATGGGGAGCATGCAACGAGCCATAT
1 ACGAGCCAACGGGGAGCATGCAGGAATAGAGAGCCAATGGGGAGCATGCAACGAGCCATAT
*
3032793 ACGAGCCAATGGGGAGCATGCAGGAATAGAGAGCCAATGGGGAGCATGCAACGAGCCATAT
1 ACGAGCCAACGGGGAGCATGCAGGAATAGAGAGCCAATGGGGAGCATGCAACGAGCCATAT
3032854 ACGAGCCA
1 ACGAGCCA
3032862 TGCAGGAATA
Statistics
Matches: 125, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
61 125 1.00
ACGTcount: A:0.34, C:0.21, G:0.35, T:0.10
Consensus pattern (61 bp):
ACGAGCCAACGGGGAGCATGCAGGAATAGAGAGCCAATGGGGAGCATGCAACGAGCCATAT
Found at i:3032925 original size:29 final size:29
Alignment explanation
Indices: 3032875--3032983 Score: 184
Period size: 29 Copynumber: 3.8 Consensus size: 29
3032865 AGGAATAGAG
* *
3032875 AGGTCGCCATGCAG-CCTAGGCGACCTTGT
1 AGGTCGCCATGTAGTCC-CGGCGACCTTGT
3032904 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
3032933 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
3032962 AGGTCGCCATGTAGTCCCGGCG
1 AGGTCGCCATGTAGTCCCGGCG
3032984 CCATTCCATC
Statistics
Matches: 77, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
29 75 0.97
30 2 0.03
ACGTcount: A:0.15, C:0.31, G:0.32, T:0.22
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:3033101 original size:36 final size:37
Alignment explanation
Indices: 3033033--3033106 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
3033023 CATAGATTCC
3033033 TTCACGTGCTCCCCGCTGCATTGCCTACACCTCCCAA
1 TTCACGTGCTCCCCGCTGCATTGCCTACACCTCCCAA
3033070 TTCACGTGCTCCCCGCTGCA-TGCCTACACCTCCCAA
1 TTCACGTGCTCCCCGCTGCATTGCCTACACCTCCCAA
3033106 T
1 T
3033107 GCATGCATGT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 17 0.46
37 20 0.54
ACGTcount: A:0.16, C:0.46, G:0.14, T:0.24
Consensus pattern (37 bp):
TTCACGTGCTCCCCGCTGCATTGCCTACACCTCCCAA
Found at i:3033134 original size:18 final size:18
Alignment explanation
Indices: 3033111--3033145 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
3033101 CCCAATGCAT
3033111 GCATGTGAACCATTTGAG
1 GCATGTGAACCATTTGAG
3033129 GCATGTGAACCATTTGA
1 GCATGTGAACCATTTGA
3033146 TTATTGGTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.29
Consensus pattern (18 bp):
GCATGTGAACCATTTGAG
Found at i:3033265 original size:23 final size:23
Alignment explanation
Indices: 3033235--3033279 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
3033225 AAAAGAAAGA
3033235 AAGAAAGGGAGAAGAGATTGCAT
1 AAGAAAGGGAGAAGAGATTGCAT
3033258 AAGAAAGGGAGAAGAGATTGCA
1 AAGAAAGGGAGAAGAGATTGCA
3033280 GCCGAGAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.49, C:0.04, G:0.36, T:0.11
Consensus pattern (23 bp):
AAGAAAGGGAGAAGAGATTGCAT
Found at i:3033319 original size:21 final size:21
Alignment explanation
Indices: 3033283--3033341 Score: 93
Period size: 21 Copynumber: 2.9 Consensus size: 21
3033273 GATTGCAGCC
3033283 GAGAAA-GAAAGAAAGAAAGG
1 GAGAAAGGAAAGAAAGAAAGG
*
3033303 GAGAAAGGAAAGGAAGAAAGG
1 GAGAAAGGAAAGAAAGAAAGG
*
3033324 GAGAAAGGAAAGTAAGAA
1 GAGAAAGGAAAGAAAGAA
3033342 GAAGAAAGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 6 0.17
21 30 0.83
ACGTcount: A:0.61, C:0.00, G:0.37, T:0.02
Consensus pattern (21 bp):
GAGAAAGGAAAGAAAGAAAGG
Found at i:3033521 original size:41 final size:41
Alignment explanation
Indices: 3033476--3033564 Score: 92
Period size: 41 Copynumber: 2.2 Consensus size: 41
3033466 TATATGATTG
* *
3033476 TTAGTTTAAG-TT-ATAGTATACATAAATTAAAAATTATTTAA
1 TTAGTTTAAGTTTGATAGT-TACAT-AATTAAAAAATAATTAA
* * * *
3033517 TTAGTATATGTTTGATAGTTATATAGTTAAAAAATAATTAA
1 TTAGTTTAAGTTTGATAGTTACATAATTAAAAAATAATTAA
3033558 TTAGTTT
1 TTAGTTT
3033565 GTATTGTTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
41 28 0.72
42 6 0.15
43 5 0.13
ACGTcount: A:0.43, C:0.01, G:0.10, T:0.46
Consensus pattern (41 bp):
TTAGTTTAAGTTTGATAGTTACATAATTAAAAAATAATTAA
Found at i:3033608 original size:46 final size:48
Alignment explanation
Indices: 3033545--3033636 Score: 136
Period size: 46 Copynumber: 2.0 Consensus size: 48
3033535 TTATATAGTT
3033545 AAAAAATAATTAATTAGTTTGTATT-GTT-AATAGTT-AGTTATATAA
1 AAAAAATAATTAATTAGTTTGTATTAGTTAAATAGTTAAGTTATATAA
* *
3033590 AAAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAAA-TAATTAATTAGTTTGTATTAGTTAAATAGTTAAGTTATAT
3033637 TTGTTTGTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
45 6 0.15
46 17 0.41
47 3 0.07
48 7 0.17
49 8 0.20
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (48 bp):
AAAAAATAATTAATTAGTTTGTATTAGTTAAATAGTTAAGTTATATAA
Found at i:3036029 original size:14 final size:13
Alignment explanation
Indices: 3036010--3036052 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
3036000 AAATCATTAC
3036010 TAGTATCAAATAAT
1 TAGTAT-AAATAAT
*
3036024 TAGTATTAAATCAT
1 TAGTA-TAAATAAT
*
3036038 TATTATAAATAAT
1 TAGTATAAATAAT
3036051 TA
1 TA
3036053 CTAAATAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 9 0.36
14 15 0.60
15 1 0.04
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.42
Consensus pattern (13 bp):
TAGTATAAATAAT
Found at i:3036042 original size:17 final size:17
Alignment explanation
Indices: 3035992--3036042 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
3035982 ACAATGATTT
3035992 TTAGTATCAAATCATTA
1 TTAGTATCAAATCATTA
*
3036009 CTAGTATCAAAT-A--A
1 TTAGTATCAAATCATTA
*
3036023 TTAGTATTAAATCATTA
1 TTAGTATCAAATCATTA
3036040 TTA
1 TTA
3036043 TAAATAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 11 0.39
15 1 0.04
16 1 0.04
17 15 0.54
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.41
Consensus pattern (17 bp):
TTAGTATCAAATCATTA
Found at i:3036094 original size:26 final size:25
Alignment explanation
Indices: 3036030--3036336 Score: 198
Period size: 26 Copynumber: 12.4 Consensus size: 25
3036020 TAATTAGTAT
*
3036030 TAAATCATTATTATAA--ATAATTA
1 TAAATCATTATTATAATGATTATTA
* ** *
3036053 CTAAAT-AATAACATAATAATTATTA
1 -TAAATCATTATTATAATGATTATTA
3036078 TAAAATCATTATTATAATGATTATTA
1 T-AAATCATTATTATAATGATTATTA
* * * *
3036104 TCAAATCATTACTA-AATCATCAAATCA
1 T-AAATCATTATTATAATGAT--TATTA
*
3036131 TTAAAT-A-T-TTA-AATCATTA-T-
1 -TAAATCATTATTATAATGATTATTA
*
3036151 TAAATCATTTTTATAATGATTATTA
1 TAAATCATTATTATAATGATTATTA
*
3036176 CTAAATCATTACTATAATGATTATTA
1 -TAAATCATTATTATAATGATTATTA
* * * *
3036202 TCAAATCATTACTA-AATCATCAAATCA
1 T-AAATCATTATTATAATGAT--TATTA
*
3036229 TTAAAT-A-T-TTA-AATCATTA-T-
1 -TAAATCATTATTATAATGATTATTA
*
3036249 TAAATCATTTTTATAATGATTATTA
1 TAAATCATTATTATAATGATTATTA
3036274 CTAAATCATTATTATAATGATTATTA
1 -TAAATCATTATTATAATGATTATTA
*
3036300 TCAAATCATTACTATAATGATTATTA
1 T-AAATCATTATTATAATGATTATTA
3036326 TCAAATCATTA
1 T-AAATCATTA
3036337 CTAAATCATC
Statistics
Matches: 229, Mismatches: 28, Indels: 50
0.75 0.09 0.16
Matches are distributed among these distances:
19 10 0.04
20 2 0.01
21 2 0.01
22 8 0.03
23 21 0.09
24 24 0.10
25 24 0.10
26 122 0.53
27 14 0.06
28 2 0.01
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.43
Consensus pattern (25 bp):
TAAATCATTATTATAATGATTATTA
Found at i:3036102 original size:12 final size:12
Alignment explanation
Indices: 3036027--3036104 Score: 54
Period size: 11 Copynumber: 6.5 Consensus size: 12
3036017 AAATAATTAG
*
3036027 TATTA-AATCAT
1 TATTATAATAAT
3036038 TATTATAAATAAT
1 TATTAT-AATAAT
*
3036051 TACTA-AATAA-
1 TATTATAATAAT
**
3036061 TAACATAATAAT
1 TATTATAATAAT
*
3036073 TATTATAAAATCAT
1 TATTAT--AATAAT
*
3036087 TATTATAATGAT
1 TATTATAATAAT
3036099 TATTAT
1 TATTAT
3036105 CAAATCATTA
Statistics
Matches: 53, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
10 3 0.06
11 15 0.28
12 15 0.28
13 9 0.17
14 11 0.21
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.44
Consensus pattern (12 bp):
TATTATAATAAT
Found at i:3036234 original size:98 final size:98
Alignment explanation
Indices: 3036065--3036313 Score: 464
Period size: 98 Copynumber: 2.5 Consensus size: 98
3036055 AAATAATAAC
*
3036065 ATAATAATTATTA-TAAAATCATTATTATAATGATTATTATCAAATCATTACTAAATCATCAAAT
1 ATAATGATTATTACT-AAATCATTATTATAATGATTATTATCAAATCATTACTAAATCATCAAAT
3036129 CATTAAATATTTAAATCATTATTAAATCATTTTT
65 CATTAAATATTTAAATCATTATTAAATCATTTTT
*
3036163 ATAATGATTATTACTAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATC
1 ATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTAAATCATCAAATC
3036228 ATTAAATATTTAAATCATTATTAAATCATTTTT
66 ATTAAATATTTAAATCATTATTAAATCATTTTT
3036261 ATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTA
1 ATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTA
3036314 TAATGATTAT
Statistics
Matches: 147, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
98 146 0.99
99 1 0.01
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (98 bp):
ATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTAAATCATCAAATC
ATTAAATATTTAAATCATTATTAAATCATTTTT
Found at i:3036280 original size:124 final size:124
Alignment explanation
Indices: 3036146--3036394 Score: 464
Period size: 124 Copynumber: 2.0 Consensus size: 124
3036136 TATTTAAATC
* *
3036146 ATTATTAAATCATTTTTATAATGATTATTA-CTAAATCATTACTATAATGATTATTATCAAATCA
1 ATTACTAAATCATTATTATAATGATTATTATC-AAATCATTACTATAATGATTATTATCAAATCA
3036210 TTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTATAATGATT
65 TTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTATAATGATT
3036270 ATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCAT
1 ATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCAT
3036335 TACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTATAATGATT
66 TACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTATAATGATT
3036394 A
1 A
3036395 ATAAATACAT
Statistics
Matches: 122, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
124 121 0.99
125 1 0.01
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.44
Consensus pattern (124 bp):
ATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCAT
TACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTATAATGATT
Found at i:3039276 original size:26 final size:24
Alignment explanation
Indices: 3039218--3039276 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
3039208 CTAATAAACC
*
3039218 TAATAATGATTTGATAATTACTAT
1 TAATAATGATTTGATAATTAATAT
*
3039242 TAATCTAATGATTTGATATTTAATGATT
1 TAA--TAATGATTTGATAATTAAT-A-T
3039270 TAATAAT
1 TAATAAT
3039277 AATATGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 3 0.10
26 21 0.72
27 1 0.03
28 4 0.14
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (24 bp):
TAATAATGATTTGATAATTAATAT
Found at i:3040119 original size:26 final size:27
Alignment explanation
Indices: 3040083--3040136 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
3040073 ATATAATATA
*
3040083 ATATATAACTT-AACTAATAAACTAAT
1 ATATATAACTTAAACTAACAAACTAAT
3040109 ATATATAACTTAAACTAACAAACTAAT
1 ATATATAACTTAAACTAACAAACTAAT
3040136 A
1 A
3040137 ATTTATACTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 11 0.42
27 15 0.58
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (27 bp):
ATATATAACTTAAACTAACAAACTAAT
Found at i:3040137 original size:21 final size:21
Alignment explanation
Indices: 3040113--3040161 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
3040103 ACTAATATAT
3040113 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
3040134 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
3040155 ATTAACT
1 A-TAACT
3040162 AGATTTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:3040706 original size:25 final size:25
Alignment explanation
Indices: 3040652--3040709 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
3040642 GTTCCCACGT
* *
3040652 CCCATGCACAGCATGCATCTGCATG
1 CCCATGCACAGCATGCATCTCCATC
* *
3040677 ACCATGCACAGCATGCATC-CCCTCC
1 CCCATGCACAGCATGCATCTCCAT-C
3040702 CCCATGCA
1 CCCATGCA
3040710 TTCCCACGGC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 2 0.07
25 25 0.93
ACGTcount: A:0.24, C:0.43, G:0.16, T:0.17
Consensus pattern (25 bp):
CCCATGCACAGCATGCATCTCCATC
Found at i:3040799 original size:29 final size:29
Alignment explanation
Indices: 3040767--3040846 Score: 151
Period size: 29 Copynumber: 2.8 Consensus size: 29
3040757 TATACCTTGG
*
3040767 AGGTCGCCCGGATTGCATGGCGACCTCCA
1 AGGTCGCCTGGATTGCATGGCGACCTCCA
3040796 AGGTCGCCTGGATTGCATGGCGACCTCCA
1 AGGTCGCCTGGATTGCATGGCGACCTCCA
3040825 AGGTCGCCTGGATTGCATGGCG
1 AGGTCGCCTGGATTGCATGGCG
3040847 TCCTATGGCG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.16, C:0.30, G:0.34, T:0.20
Consensus pattern (29 bp):
AGGTCGCCTGGATTGCATGGCGACCTCCA
Found at i:3041521 original size:56 final size:56
Alignment explanation
Indices: 3041447--3041700 Score: 481
Period size: 56 Copynumber: 4.5 Consensus size: 56
3041437 TGTTATTTTG
**
3041447 AGATATGTTGCGAGTCTTCTTGAAATAATGCTCTTCGTCCAATGATGTTAGTTTCA
1 AGATATGTTGTTAGTCTTCTTGAAATAATGCTCTTCGTCCAATGATGTTAGTTTCA
3041503 AGATATGTTGTTAGTCTTCTTGAAATAATGCTCTTCGTCCAATGATGTTAGTTTCA
1 AGATATGTTGTTAGTCTTCTTGAAATAATGCTCTTCGTCCAATGATGTTAGTTTCA
3041559 AGATATGTTGTTAGTCTTCTTGAAATAATGCTCTTCGTCCAATGATGTTAGTTTCA
1 AGATATGTTGTTAGTCTTCTTGAAATAATGCTCTTCGTCCAATGATGTTAGTTTCA
*
3041615 AGATATGTTGTGAGTCTTCTTGAAATAATGCTCTTCGTCCAATGATGTTAGTTTCA
1 AGATATGTTGTTAGTCTTCTTGAAATAATGCTCTTCGTCCAATGATGTTAGTTTCA
3041671 AGATATGTTGTTAGTCTTCTTGAAATAATG
1 AGATATGTTGTTAGTCTTCTTGAAATAATG
3041701 TTTCTTATCG
Statistics
Matches: 194, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 194 1.00
ACGTcount: A:0.26, C:0.14, G:0.19, T:0.42
Consensus pattern (56 bp):
AGATATGTTGTTAGTCTTCTTGAAATAATGCTCTTCGTCCAATGATGTTAGTTTCA
Found at i:3049440 original size:2 final size:2
Alignment explanation
Indices: 3049433--3049533 Score: 202
Period size: 2 Copynumber: 50.5 Consensus size: 2
3049423 TTATTTAAAT
3049433 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3049475 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3049517 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
3049534 CATAATTGAG
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 99 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3053288 original size:15 final size:15
Alignment explanation
Indices: 3053268--3053323 Score: 85
Period size: 15 Copynumber: 3.7 Consensus size: 15
3053258 CTTCATGGGG
*
3053268 TAAGAAGACAACGTC
1 TAAGAAGAAAACGTC
3053283 TAAGAAGAAAACGTC
1 TAAGAAGAAAACGTC
*
3053298 GAAGAAGAAAACGTC
1 TAAGAAGAAAACGTC
*
3053313 AAAGAAGAAAA
1 TAAGAAGAAAA
3053324 AAGAAAGCAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.57, C:0.12, G:0.21, T:0.09
Consensus pattern (15 bp):
TAAGAAGAAAACGTC
Found at i:3059543 original size:85 final size:84
Alignment explanation
Indices: 3059400--3059622 Score: 281
Period size: 85 Copynumber: 2.6 Consensus size: 84
3059390 GTCTTTTTTA
* *
3059400 ATGACGTGTGCTTCAATGACACGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACA
1 ATGACGGGAGCTTCAATGACACGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACA
3059465 AATGTATGTCAAGC-AGATTT
66 AATGTATGTC-AGCTA-ATTT
* * * *
3059485 ATGACGGGGGCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACGCATA
1 ATGACGGGAGCTTCAATGACACGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACA
* *
3059550 AATGTGTGTCATCTTAATTT
66 AATGTATGTCAGC-TAATTT
* **
3059570 ATGACGGGAGCTTCAATGACACTCAATG-AACGTCATTA-ATGCGCATCATAAAT
1 ATGACGGGAGCTTCAATGACACGCAATGTAA-GTCA-TACATGCGTGTCATAAAT
3059623 GTGTGTCATA
Statistics
Matches: 122, Mismatches: 12, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
84 4 0.03
85 115 0.94
86 3 0.02
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (84 bp):
ATGACGGGAGCTTCAATGACACGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACA
AATGTATGTCAGCTAATTT
Found at i:3059558 original size:28 final size:29
Alignment explanation
Indices: 3059518--3059575 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
3059508 CAATGTAAGT
*
3059518 CATACATGCGTGTCA-TAAATTTATGACG
1 CATAAATGCGTGTCACTAAATTTATGACG
* *
3059546 CATAAATGTGTGTCATCTTAATTTATGACG
1 CATAAATGCGTGTCA-CTAAATTTATGACG
3059576 GGAGCTTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 13 0.52
30 12 0.48
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (29 bp):
CATAAATGCGTGTCACTAAATTTATGACG
Found at i:3064906 original size:3 final size:3
Alignment explanation
Indices: 3064898--3064922 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3064888 TTTCTTTCTT
3064898 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
3064923 ACTTTTGGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3069328 original size:20 final size:20
Alignment explanation
Indices: 3069303--3069372 Score: 140
Period size: 20 Copynumber: 3.5 Consensus size: 20
3069293 AAGGAAGTAG
3069303 TATCGATACTAACATATCGA
1 TATCGATACTAACATATCGA
3069323 TATCGATACTAACATATCGA
1 TATCGATACTAACATATCGA
3069343 TATCGATACTAACATATCGA
1 TATCGATACTAACATATCGA
3069363 TATCGATACT
1 TATCGATACT
3069373 GACTCAGGAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.31
Consensus pattern (20 bp):
TATCGATACTAACATATCGA
Found at i:3072593 original size:2 final size:2
Alignment explanation
Indices: 3072588--3072615 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3072578 TTTTTATTAA
3072588 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
3072616 CCTAAAAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3075296 original size:22 final size:22
Alignment explanation
Indices: 3075254--3075296 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3075244 TTTTCCAATC
* * *
3075254 AAATACTATTTTTATTGAATAA
1 AAATAATATTTTTAATAAATAA
3075276 AAATAATATTTTTAATAAATA
1 AAATAATATTTTTAATAAATA
3075297 TATTATTTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (22 bp):
AAATAATATTTTTAATAAATAA
Found at i:3075761 original size:29 final size:29
Alignment explanation
Indices: 3075697--3075761 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
3075687 ATTTTTATGT
* * *
3075697 TAATTTTTATTATATTTATAATATTAATTA
1 TAATTTTTA-TATATTTATAAAATGAATCA
3075727 TAAATTTTTA-ATATTTATAAAATGAATCCA
1 T-AATTTTTATATATTTATAAAATGAAT-CA
3075757 TAATT
1 TAATT
3075762 AAAATATATC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
29 19 0.63
30 3 0.10
31 8 0.27
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (29 bp):
TAATTTTTATATATTTATAAAATGAATCA
Done.