Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006870.1 Hibiscus syriacus cultivar Beakdansim tig00017495_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: 72906
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:10588 original size:5 final size:6
Alignment explanation
Indices: 10572--10654 Score: 58
Period size: 6 Copynumber: 13.0 Consensus size: 6
10562 GAGGAAACCC
* * * *
10572 ATTTTT ATTTTT ATTTTT CGTTTGCTCA ATTTTT ATTTTT ATTTTC AATTTT
1 ATTTTT ATTTTT ATTTTT -ATTT--T-T ATTTTT ATTTTT ATTTTT ATTTTT
* * *
10624 ATTTTT CTGATTT ATTTTT CTTTTT ATTTTT
1 ATTTTT AT-TTTT ATTTTT ATTTTT ATTTTT
10655 CTTTGAATTT
Statistics
Matches: 58, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
6 46 0.79
7 8 0.14
9 4 0.07
ACGTcount: A:0.16, C:0.07, G:0.04, T:0.73
Consensus pattern (6 bp):
ATTTTT
Found at i:10606 original size:22 final size:20
Alignment explanation
Indices: 10578--10630 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 20
10568 ACCCATTTTT
*
10578 ATTTTTATTTTTCGTTTGCTCA
1 ATTTTTATTTTTCATTT--TCA
10600 ATTTTTATTTTT-ATTTTCA
1 ATTTTTATTTTTCATTTTCA
10619 A-TTTTATTTTTC
1 ATTTTTATTTTTC
10631 TGATTTATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 10 0.34
19 4 0.14
21 3 0.10
22 12 0.41
ACGTcount: A:0.17, C:0.09, G:0.04, T:0.70
Consensus pattern (20 bp):
ATTTTTATTTTTCATTTTCA
Found at i:10637 original size:25 final size:25
Alignment explanation
Indices: 10609--10656 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
10599 AATTTTTATT
10609 TTTA-TTTTCAATTTTATTTTTCTGA
1 TTTATTTTTC-ATTTTATTTTTCTGA
*
10634 TTTATTTTTCTTTTTATTTTTCT
1 TTTATTTTTCATTTTATTTTTCT
10657 TTGAATTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.15, C:0.08, G:0.02, T:0.75
Consensus pattern (25 bp):
TTTATTTTTCATTTTATTTTTCTGA
Found at i:10655 original size:12 final size:12
Alignment explanation
Indices: 10572--10658 Score: 68
Period size: 12 Copynumber: 6.8 Consensus size: 12
10562 GAGGAAACCC
*
10572 ATTTTTATTTTT
1 ATTTTTCTTTTT
*
10584 ATTTTTCGTTTGCTCA
1 ATTTTTC-TTT--T-T
*
10600 ATTTTTATTTTT
1 ATTTTTCTTTTT
*
10612 A-TTTTCAATTTT
1 ATTTTTC-TTTTT
*
10624 ATTTTTCTGATTT
1 ATTTTTCT-TTTT
10637 ATTTTTCTTTTT
1 ATTTTTCTTTTT
10649 ATTTTTCTTT
1 ATTTTTCTTT
10659 GAATTTTCAG
Statistics
Matches: 59, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
11 4 0.07
12 25 0.42
13 20 0.34
15 4 0.07
16 6 0.10
ACGTcount: A:0.15, C:0.08, G:0.03, T:0.74
Consensus pattern (12 bp):
ATTTTTCTTTTT
Found at i:18767 original size:43 final size:43
Alignment explanation
Indices: 18705--18993 Score: 325
Period size: 43 Copynumber: 6.7 Consensus size: 43
18695 ACTCCTTTAC
* *
18705 TGTGTGCAAGGGTACGCCTTACAGTTTCCCCATGTTCGTTTGT
1 TGTGTGCAAGGGTAAGCCTTACAGTTTCCCCATGTTCCTTTGT
* *
18748 TGTGTGCACGAGTAAGCCTTACAGTTTCCCCATGTTCCTTTGT
1 TGTGTGCAAGGGTAAGCCTTACAGTTTCCCCATGTTCCTTTGT
* *
18791 TGTGTGAAAGGGTAAGCCTTACAGTTTCCCCATGTTTCTTTGT
1 TGTGTGCAAGGGTAAGCCTTACAGTTTCCCCATGTTCCTTTGT
* * *
18834 TGTGTGCAAGGGTAAGCCTCACAGTTTCCCCAGGTTCCTTTGC
1 TGTGTGCAAGGGTAAGCCTTACAGTTTCCCCATGTTCCTTTGT
* * * * *
18877 TGTATGCAAGGGTAAGCCTTACAGTTTTCCCTAGGTTTCTTTGA
1 TGTGTGCAAGGGTAAGCCTTACAG-TTTCCCCATGTTCCTTTGT
* * * * *
18921 TGTGTGCAATGGTAAGACCTTATAG-CT-CCCAAGCTCCTTTCG-
1 TGTGTGCAAGGGTAAG-CCTTACAGTTTCCCCATGTTCCTTT-GT
*
18963 TATGTGCAAGGGTAAGACCTTATC-GTTTCCC
1 TGTGTGCAAGGGTAAG-CCTTA-CAGTTTCCC
18994 ATGCTCTTTT
Statistics
Matches: 210, Mismatches: 30, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
42 30 0.14
43 141 0.67
44 32 0.15
45 7 0.03
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.35
Consensus pattern (43 bp):
TGTGTGCAAGGGTAAGCCTTACAGTTTCCCCATGTTCCTTTGT
Found at i:19020 original size:43 final size:42
Alignment explanation
Indices: 18931--19020 Score: 101
Period size: 43 Copynumber: 2.1 Consensus size: 42
18921 TGTGTGCAAT
* *
18931 GGTAAGACCTTATAGCTCCCAAGCTCCTTTCGTATGTGCAAG
1 GGTAAGACCTTATAGCTCCCAAGCTCCTTTCGTATGTACAAA
* * * *
18973 GGTAAGACCTTATCGTTTCCCATGCTCTTTTTC-TATGTACAAA
1 GGTAAGACCTTATAG-CTCCCAAGCTC-CTTTCGTATGTACAAA
19016 GGTAA
1 GGTAA
19021 TTCCTTACCA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
42 14 0.35
43 22 0.55
44 4 0.10
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.33
Consensus pattern (42 bp):
GGTAAGACCTTATAGCTCCCAAGCTCCTTTCGTATGTACAAA
Found at i:20973 original size:11 final size:11
Alignment explanation
Indices: 20952--20991 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
20942 TTTTCAATGG
*
20952 CATTTACCGAC
1 CATTGACCGAC
*
20963 CGTTGACCGAC
1 CATTGACCGAC
20974 CATTGACCGAC
1 CATTGACCGAC
*
20985 CTTTGAC
1 CATTGAC
20992 TTTTTCCGGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.23, C:0.35, G:0.17, T:0.25
Consensus pattern (11 bp):
CATTGACCGAC
Found at i:23563 original size:44 final size:43
Alignment explanation
Indices: 23425--23577 Score: 207
Period size: 43 Copynumber: 3.5 Consensus size: 43
23415 TACCGTATGA
* *
23425 TCCTTTGCTGTGTGCAAGGGTAAGCCATACTGTTTCCCCAGGT
1 TCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGT
**
23468 TCCTTTATTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGT
1 TCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGT
** *
23511 TCCTTTGCTGTGACCAAGGGTAAGCCTTACAGTTTTCCTCAGGT
1 TCCTTTGCTGTGTGCAAGGGTAAGCCTTACAG-TTTCCCCAGGT
* * *
23555 TTCTTTGCTATGTGCAAAGGTAA
1 TCCTTTGCTGTGTGCAAGGGTAA
23578 TACCTTACTG
Statistics
Matches: 95, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
43 67 0.71
44 28 0.29
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.35
Consensus pattern (43 bp):
TCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGT
Found at i:25339 original size:23 final size:21
Alignment explanation
Indices: 25309--25350 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
25299 AGGAAGTTAA
25309 AGTTTCTGACGTTTCAAAATCG
1 AGTTTCTGACG-TTCAAAATCG
*
25331 AGTTCTCTGCCGTTCAAAAT
1 AGTT-TCTGACGTTCAAAAT
25351 TGTGAATCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (21 bp):
AGTTTCTGACGTTCAAAATCG
Found at i:25530 original size:11 final size:11
Alignment explanation
Indices: 25514--25553 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
25504 TTTTCAATGG
*
25514 CATTGACCGGC
1 CATTGACCGAC
*
25525 CATTGATCGAC
1 CATTGACCGAC
25536 CATTGACCGAC
1 CATTGACCGAC
*
25547 CGTTGAC
1 CATTGAC
25554 TTTTTCCGGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.23, C:0.33, G:0.23, T:0.23
Consensus pattern (11 bp):
CATTGACCGAC
Found at i:28179 original size:44 final size:43
Alignment explanation
Indices: 27984--28179 Score: 248
Period size: 43 Copynumber: 4.5 Consensus size: 43
27974 TATCGTATGA
* *
27984 TCCTTTGCTGTGTGCAAGGGTAAGCCTTACTGTTTCCCCAGGT
1 TCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGT
28027 TCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGT
1 TCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGT
* * *
28070 TCCTTTGTTGTGTGCAAGGATAAGACTTACAGTTTCCCCTGGT
1 TCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGT
* * ** * *
28113 TTCTTTGCTGTGACCAAGGGTAAGCCTTACAATTTTCCTCAGGT
1 TCCTTTGTTGTGTGCAAGGGTAAGCCTTAC-AGTTTCCCCAGGT
* * * *
28157 TTCTTTGATATGTGCAAAGGTAA
1 TCCTTTGTTGTGTGCAAGGGTAA
28180 TACCTTACCG
Statistics
Matches: 133, Mismatches: 19, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
43 105 0.79
44 28 0.21
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.36
Consensus pattern (43 bp):
TCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGT
Found at i:32705 original size:18 final size:20
Alignment explanation
Indices: 32667--32713 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
32657 TAACCGGGTT
*
32667 TTATATATTTATTTTTATTA
1 TTATATATTTATTTATATTA
32687 TTATA-ATTTATTTAT-TTA
1 TTATATATTTATTTATATTA
32705 TTAATATAT
1 TT-ATATAT
32714 ATATATATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 5 0.21
19 12 0.50
20 7 0.29
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TTATATATTTATTTATATTA
Found at i:35064 original size:18 final size:18
Alignment explanation
Indices: 35043--35081 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
35033 TATTTATTAA
*
35043 TTTTTGACTATTTTTATT
1 TTTTTGACTAATTTTATT
**
35061 TTTTTGTTTAATTTTATT
1 TTTTTGACTAATTTTATT
35079 TTT
1 TTT
35082 CCCTTAATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.15, C:0.03, G:0.05, T:0.77
Consensus pattern (18 bp):
TTTTTGACTAATTTTATT
Found at i:36133 original size:16 final size:17
Alignment explanation
Indices: 36104--36142 Score: 71
Period size: 16 Copynumber: 2.4 Consensus size: 17
36094 AAGCATGTTC
36104 GGGTAGATTATCATGTG
1 GGGTAGATTATCATGTG
36121 GGGTAGA-TATCATGTG
1 GGGTAGATTATCATGTG
36137 GGGTAG
1 GGGTAG
36143 GACTTTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.23, C:0.05, G:0.41, T:0.31
Consensus pattern (17 bp):
GGGTAGATTATCATGTG
Found at i:38836 original size:106 final size:106
Alignment explanation
Indices: 38651--39605 Score: 1739
Period size: 106 Copynumber: 9.0 Consensus size: 106
38641 TACAGCCTTT
* *
38651 AGAGCCAATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
*
38716 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
* * *
38757 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
* *
38822 CGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
* * * *
38863 GGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
* *
38928 CGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
*
38969 GGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
39034 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
39075 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
39140 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
*
39181 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCATGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
39246 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
39287 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
39352 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
39393 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
39458 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
*
39499 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
* *
39564 CGAAGGGACCGCTGGTTGTCAACAAACAACTTTTCAACTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
39605 A
1 A
39606 CAACGAAGGA
Statistics
Matches: 833, Mismatches: 16, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
106 833 1.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.22
Consensus pattern (106 bp):
AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
Found at i:39569 original size:43 final size:43
Alignment explanation
Indices: 39508--39657 Score: 144
Period size: 43 Copynumber: 3.4 Consensus size: 43
39498 CAGAGCCAAT
39508 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAG
* *** ** * *
39551 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAAC-T--T
1 TTCAACTTCACAACGAA-GGA-TATTGG-ACTC--CAGACAACGTAAG
*
39596 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAG
*
39639 TTCAACTTCACGACGAAGG
1 TTCAACTTCACAACGAAGG
39658 GACCGCTGGT
Statistics
Matches: 81, Mismatches: 18, Indels: 16
0.70 0.16 0.14
Matches are distributed among these distances:
40 7 0.09
42 2 0.02
43 37 0.46
44 6 0.07
45 19 0.23
46 2 0.02
47 1 0.01
48 7 0.09
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (43 bp):
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAG
Found at i:39604 original size:45 final size:43
Alignment explanation
Indices: 39548--39680 Score: 128
Period size: 43 Copynumber: 3.0 Consensus size: 43
39538 CAGACAACGT
39548 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
1 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
* * *** * * *
39591 AACTTTTCAACTTCACAACGAA-GGA-TATTGGACT-CCAGACAACGC
1 AA--GTTCAACTTCACGACGAAGGGACCGCTGG-TTGTCA-ACAA-AC
39636 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
1 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
39679 AA
1 AA
39681 TTTCCCAATT
Statistics
Matches: 66, Mismatches: 16, Indels: 16
0.67 0.16 0.16
Matches are distributed among these distances:
43 26 0.39
44 16 0.24
45 24 0.36
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.20
Consensus pattern (43 bp):
AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
Found at i:39656 original size:88 final size:88
Alignment explanation
Indices: 39507--39680 Score: 339
Period size: 88 Copynumber: 2.0 Consensus size: 88
39497 TCAGAGCCAA
*
39507 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGA
1 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGA
39572 CCGCTGGTTGTCAACAAACAACT
66 CCGCTGGTTGTCAACAAACAACT
39595 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGA
1 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGA
39660 CCGCTGGTTGTCAACAAACAA
66 CCGCTGGTTGTCAACAAACAA
39681 TTTCCCAATT
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 85 1.00
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (88 bp):
TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGA
CCGCTGGTTGTCAACAAACAACT
Found at i:39733 original size:88 final size:86
Alignment explanation
Indices: 39503--39734 Score: 267
Period size: 88 Copynumber: 2.6 Consensus size: 86
39493 AATTTCAGAG
*
39503 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC---A-TACAACTTCACGACGAA
39568 GGGACCGCTGGTTGTCAACAAACAA
62 GGGACCGCTGGTTGTCAACAAACAA
* *
39593 -C-TTTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAA--C-A-TACAACTTCACGACGAA
39656 GGGACCGCTGGTTGTCAACAAACAA
62 GGGACCGCTGGTTGTCAACAAACAA
**
39681 TTTCCCAATTTCAACTTCACGGCGAAGGATATTGGACT-C-GA-AACATCACAACTT
1 ----CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACAT-ACAACTT
39735 TCATTGGATT
Statistics
Matches: 128, Mismatches: 5, Indels: 20
0.84 0.03 0.13
Matches are distributed among these distances:
87 1 0.01
88 90 0.70
89 2 0.02
90 1 0.01
91 2 0.02
92 2 0.02
93 2 0.02
94 28 0.22
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (86 bp):
CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACATACAACTTCACGACGAAGGGA
CCGCTGGTTGTCAACAAACAA
Found at i:39950 original size:18 final size:20
Alignment explanation
Indices: 39912--39975 Score: 66
Period size: 18 Copynumber: 3.5 Consensus size: 20
39902 TAACCGGGTT
*
39912 TTATATATTTATTTTTATTA
1 TTATATATTTATTTATATTA
39932 TTATA-ATTTATTTAT-TTA
1 TTATATATTTATTTATATTA
* *
39950 TTA-ATATATATATATA-TA
1 TTATATATTTATTTATATTA
39968 -TATATATT
1 TTATATATT
39976 GTTTATAGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
17 3 0.08
18 20 0.54
19 9 0.24
20 5 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATATATTTATTTATATTA
Found at i:42302 original size:18 final size:18
Alignment explanation
Indices: 42281--42319 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
42271 TATTTATTAA
*
42281 TTTTTGACTATTTTTATT
1 TTTTTGACTAATTTTATT
**
42299 TTTTTGTTTAATTTTATT
1 TTTTTGACTAATTTTATT
42317 TTT
1 TTT
42320 CCCTTAATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.15, C:0.03, G:0.05, T:0.77
Consensus pattern (18 bp):
TTTTTGACTAATTTTATT
Found at i:44744 original size:14 final size:14
Alignment explanation
Indices: 44725--44761 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
44715 TAGAACATCC
44725 AGTCAACAACTACT
1 AGTCAACAACTACT
44739 AGTCAACAACTACT
1 AGTCAACAACTACT
44753 AGTCAACAA
1 AGTCAACAA
44762 TTCTAGAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.46, C:0.27, G:0.08, T:0.19
Consensus pattern (14 bp):
AGTCAACAACTACT
Found at i:45575 original size:22 final size:19
Alignment explanation
Indices: 45550--45593 Score: 52
Period size: 22 Copynumber: 2.2 Consensus size: 19
45540 CTTATTTTAA
*
45550 TTTTTATTTCTTTTTAATCTTC
1 TTTTTAATT-TTTTT-AT-TTC
45572 TTTTTAATTTTTTTATTTC
1 TTTTTAATTTTTTTATTTC
45591 TTT
1 TTT
45594 GATTCTGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 6 0.29
20 2 0.10
21 5 0.24
22 8 0.38
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTTAATTTTTTTATTTC
Found at i:46044 original size:13 final size:12
Alignment explanation
Indices: 46011--46060 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 12
46001 TTCAATTTTT
46011 ATTTTTATTTTCA
1 ATTTTT-TTTTCA
46024 ATTATTTTTTTCTA
1 ATT-TTTTTTTC-A
46038 ATTTTTTTTTC-
1 ATTTTTTTTTCA
46049 ATTTTATTTTTC
1 ATTTT-TTTTTC
46061 TTTGAATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
11 5 0.15
12 6 0.18
13 16 0.47
14 7 0.21
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (12 bp):
ATTTTTTTTTCA
Found at i:51215 original size:45 final size:45
Alignment explanation
Indices: 51167--51387 Score: 342
Period size: 45 Copynumber: 4.9 Consensus size: 45
51157 AATGATATAA
*
51167 AATAT-CTTA-CATTTATCCCATAAGCTTGTAAGCTTATTTTACC
1 AATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACC
* *
51210 AAAATACTTACCATTTAAT-CCATAAACTCGTAAGCTTATTTTACC
1 AATATACTTACCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACC
51255 AATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACC
1 AATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACC
51300 AATATACTTACCATTTATCCCATAAGCTCGTAAGCAGCTTATTTTACC
1 AATATACTTACCATTTATCCCATAAGCTCGT-A--AGCTTATTTTACC
*
51348 AATATACTTACCA-TTATTCCATAAGCTCGTAAGCTTATTT
1 AATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTT
51388 ACATGGTTAT
Statistics
Matches: 165, Mismatches: 6, Indels: 13
0.90 0.03 0.07
Matches are distributed among these distances:
43 4 0.02
44 15 0.09
45 100 0.61
46 4 0.02
47 16 0.10
48 26 0.16
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.38
Consensus pattern (45 bp):
AATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACC
Found at i:51597 original size:59 final size:59
Alignment explanation
Indices: 51503--51624 Score: 190
Period size: 59 Copynumber: 2.1 Consensus size: 59
51493 CTAACCCTAG
* * **
51503 TATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTATAGTCCCGAA
1 TATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTATAGTCCCGAA
* *
51562 TATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTTAGTATATTCCCGAA
1 TATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTATAGTCCCGAA
51621 TATG
1 TATG
51625 CAGCCTGCTG
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.30
Consensus pattern (59 bp):
TATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTATAGTCCCGAA
Found at i:56895 original size:21 final size:22
Alignment explanation
Indices: 56871--57015 Score: 90
Period size: 22 Copynumber: 6.5 Consensus size: 22
56861 GCAAAGAAAC
56871 TAAAAATATAATG-AAAATAAA
1 TAAAAATATAATGTAAAATAAA
* *
56892 TAAATAGTATAA-ATAAAAT-AA
1 TAAA-AATATAATGTAAAATAAA
*
56913 TAAAAATATATATATAAAA-AATA
1 TAAAAATATA-ATGTAAAATAA-A
*
56936 TAAAAATAT-ATGTATAATATAA
1 TAAAAATATAATGTAAAATA-AA
56958 T-AAAATACTAAATAGTAATAAT-AA
1 TAAAAATA-T-AAT-GTAA-AATAAA
*
56982 TAATAAATA-AATGAAAAATAAA
1 TAA-AAATATAATGTAAAATAAA
* *
57004 TATACATATAAT
1 TAAAAATATAAT
57016 ATTAACTAAA
Statistics
Matches: 98, Mismatches: 9, Indels: 33
0.70 0.06 0.24
Matches are distributed among these distances:
20 5 0.05
21 30 0.31
22 32 0.33
23 14 0.14
24 5 0.05
25 4 0.04
26 8 0.08
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (22 bp):
TAAAAATATAATGTAAAATAAA
Found at i:56999 original size:66 final size:65
Alignment explanation
Indices: 56871--57001 Score: 151
Period size: 66 Copynumber: 2.0 Consensus size: 65
56861 GCAAAGAAAC
* *
56871 TAAAAATATAATGAAAATAAATAAATAGTATAAATAAAATAATAAAAATATATATATAAAAAATA
1 TAAAAATATAATGAAAATAAATAAATAGTATAAATAAAATAATAAAAATAAATAAATAAAAAATA
* * * *
56936 TAAAAATAT-ATGTATAATATAATAAA-A-TACTAAATAGTAATAATAATAATAAATAAATGAAA
1 TAAAAATATAATG-AAAATA-AATAAATAGTA-TAAATA-AAATAATAAAAATAAATAAATAAAA
56998 AATA
62 AATA
57002 AATATACATA
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
64 5 0.09
65 21 0.38
66 30 0.54
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (65 bp):
TAAAAATATAATGAAAATAAATAAATAGTATAAATAAAATAATAAAAATAAATAAATAAAAAATA
Found at i:57755 original size:37 final size:37
Alignment explanation
Indices: 57714--57806 Score: 89
Period size: 37 Copynumber: 2.5 Consensus size: 37
57704 ATGCTTGTGG
** *
57714 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATCTTTAGGAGTTTAAATAATAACAAAACTCT
* * ** *
57751 ATCCTA-CTTTTAAGAGTTTGAATCCTAACAAAATTCT
1 ATCCTATC-TTTAGGAGTTTAAATAATAACAAAACTCT
*
57788 ATCCTATTTTTAGGAGTTT
1 ATCCTATCTTTAGGAGTTT
57807 GAATCCTAGT
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
36 1 0.02
37 43 0.98
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (37 bp):
ATCCTATCTTTAGGAGTTTAAATAATAACAAAACTCT
Found at i:58722 original size:106 final size:106
Alignment explanation
Indices: 58537--59707 Score: 1714
Period size: 106 Copynumber: 11.0 Consensus size: 106
58527 AGCATCGTTC
* * * * * * *
58537 CGAGTCCAATATCCTCCGTCGTGAAGTTAAAATTGGCTCTGGAATCGGGAAATTATTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* * * * *
58602 ACCAGCCGTCCCTTCATTGTGAAGTTTAACTTGTGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * * *
58643 CGAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAATTATTTGTTGAAA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
*
58708 ACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * ** *
58749 CGAGTCCAATAACCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATCCGGAAGTTATTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
58814 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
58855 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
*
58920 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * * * *
58961 GGAGTCCAATATCCTTTGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGGTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
59026 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * * * * *
59067 GGAGCCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCCGAAATCGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* * *
59132 ACCAGTGGTCTCTTCGTCGTGAAGTTGAACTTGCATTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
59173 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTTGGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
*
59238 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * * *
59279 GGAGTCCGATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTATTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* * *
59344 ACCAGCAGTCCCTTCGTCATGAAGTTGAACTTGTGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* ** * *
59385 TGAGTCCAATATCCTTCCCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
*
59450 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTTT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
59491 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* *
59556 ACCAGCGGTCCCTTTGTCGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * *
59597 AGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTTTGAATTTGGGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* *
59662 ACCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
59703 CGAGT
1 CGAGT
59708 GGCACGATAT
Statistics
Matches: 971, Mismatches: 93, Indels: 2
0.91 0.09 0.00
Matches are distributed among these distances:
106 970 1.00
107 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
Found at i:60677 original size:22 final size:22
Alignment explanation
Indices: 60651--60705 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
60641 TTGTGTTTGG
*
60651 TCAAAGGTTTGGCATTTGATGT
1 TCAAAGGTTTGGCATTTGATGC
60673 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
60695 ACAAAGGTTTG
1 TCAAAGGTTTG
60706 ATGGGGTAGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.25, C:0.11, G:0.27, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:61353 original size:15 final size:14
Alignment explanation
Indices: 61325--61383 Score: 68
Period size: 15 Copynumber: 4.3 Consensus size: 14
61315 TTCTTTTTGA
*
61325 TTTTTGTTCTTTCT
1 TTTTTGTTTTTTCT
61339 TTTTTGTTTTCTTCT
1 TTTTTGTTTT-TTCT
*
61354 TTTTTGCTTTTT-T
1 TTTTTGTTTTTTCT
*
61367 TTCTT-TTTTTTCT
1 TTTTTGTTTTTTCT
61380 TTTT
1 TTTT
61384 GCCCTTTTTG
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
12 5 0.13
13 9 0.24
14 11 0.29
15 13 0.34
ACGTcount: A:0.00, C:0.12, G:0.05, T:0.83
Consensus pattern (14 bp):
TTTTTGTTTTTTCT
Found at i:61365 original size:9 final size:9
Alignment explanation
Indices: 61340--61383 Score: 61
Period size: 9 Copynumber: 4.6 Consensus size: 9
61330 GTTCTTTCTT
61340 TTTTGTTTTC
1 TTTT-TTTTC
61350 TTCTTTTTTGC
1 TT-TTTTTT-C
61361 TTTTTTTTC
1 TTTTTTTTC
61370 TTTTTTTTC
1 TTTTTTTTC
61379 TTTTT
1 TTTTT
61384 GCCCTTTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
9 15 0.47
10 12 0.38
11 5 0.16
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:61365 original size:17 final size:15
Alignment explanation
Indices: 61325--61375 Score: 59
Period size: 17 Copynumber: 3.3 Consensus size: 15
61315 TTCTTTTTGA
*
61325 TTTTTGTTCT-TTCT
1 TTTTTGTTTTCTTCT
61339 TTTTTGTTTTCTTCT
1 TTTTTGTTTTCTTCT
*
61354 TTTTTGCTTTTTTTTCT
1 TTTTTG--TTTTCTTCT
61371 TTTTT
1 TTTTT
61376 TTCTTTTTGC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
14 9 0.28
15 10 0.31
17 13 0.41
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.82
Consensus pattern (15 bp):
TTTTTGTTTTCTTCT
Found at i:61367 original size:26 final size:27
Alignment explanation
Indices: 61333--61383 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
61323 GATTTTTGTT
61333 CTTTCTTTTT-TGTTTTCTTCTTTTTTG
1 CTTTCTTTTTCT-TTTTCTTCTTTTTTG
*
61360 CTTT-TTTTTCTTTTTTTTCTTTTT
1 CTTTCTTTTTCTTTTTCTTCTTTTT
61384 GCCCTTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.00, C:0.14, G:0.04, T:0.82
Consensus pattern (27 bp):
CTTTCTTTTTCTTTTTCTTCTTTTTTG
Found at i:61391 original size:25 final size:25
Alignment explanation
Indices: 61337--61392 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
61327 TTTGTTCTTT
*
61337 CTTTTTTGTTTTCTTCTTTTTTGCT
1 CTTTTTTGTTTTCTTCTTTTTTGCC
* * *
61362 TTTTTTTCTTTT-TTTTCTTTTTGCC
1 CTTTTTTGTTTTCTTCT-TTTTTGCC
61387 CTTTTT
1 CTTTTT
61393 GTTCTGATTG
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
24 3 0.12
25 22 0.88
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.79
Consensus pattern (25 bp):
CTTTTTTGTTTTCTTCTTTTTTGCC
Found at i:64771 original size:19 final size:19
Alignment explanation
Indices: 64738--64774 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
64728 TGCGGATGAT
64738 GGAAATAAAATAAAAGAGA
1 GGAAATAAAATAAAAGAGA
64757 GGAAA-AAAATGAAAAGAG
1 GGAAATAAAAT-AAAAGAG
64775 TTAGTAAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.08
Consensus pattern (19 bp):
GGAAATAAAATAAAAGAGA
Found at i:66309 original size:2 final size:2
Alignment explanation
Indices: 66302--66336 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
66292 ATATTAATTA
66302 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
66337 CACATATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:66831 original size:37 final size:37
Alignment explanation
Indices: 66790--66879 Score: 108
Period size: 37 Copynumber: 2.4 Consensus size: 37
66780 ATGCTTGTGG
* * *
66790 ATCCTATCTTTAGGAGGTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGGTTAAATAATAGCAAAACTCT
* * ** *
66827 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGGTTAAATAATAGCAAAACTCT
66864 ATCCTATTTTTAGGAG
1 ATCCTATTTTTAGGAG
66880 TTTGAATCCT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGGTTAAATAATAGCAAAACTCT
Done.