Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008631.1 Hibiscus syriacus cultivar Beakdansim tig00111600_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: 181520
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:19958 original size:13 final size:13
Alignment explanation
Indices: 19936--19965 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
19926 ACTAAACACC
19936 TTTC-ACATACCT
1 TTTCAACATACCT
19948 TTTCAACATACCT
1 TTTCAACATACCT
19961 TTTCA
1 TTTCA
19966 TCTTTGGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:36888 original size:14 final size:14
Alignment explanation
Indices: 36869--36901 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
36859 GTGCTTTCAA
36869 CTTTTCTTTCTT-TT
1 CTTTTCTTT-TTCTT
36883 CTTTTCTTTTTCTT
1 CTTTTCTTTTTCTT
36897 CTTTT
1 CTTTT
36902 TGAGTGCTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 16 0.89
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
CTTTTCTTTTTCTT
Found at i:38568 original size:19 final size:21
Alignment explanation
Indices: 38525--38576 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
38515 GAAACCCCTT
38525 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
38546 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
38565 TGAAGATACATG
1 TGAAAATACATG
38577 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:47754 original size:10 final size:11
Alignment explanation
Indices: 47731--47762 Score: 57
Period size: 10 Copynumber: 3.0 Consensus size: 11
47721 CTTTTTTGAA
47731 TTTCTTTTTCT
1 TTTCTTTTTCT
47742 TTTCTTTTT-T
1 TTTCTTTTTCT
47752 TTTCTTTTTCT
1 TTTCTTTTTCT
47763 GAATTTTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTCTTTTTCT
Found at i:47777 original size:21 final size:20
Alignment explanation
Indices: 47718--47781 Score: 61
Period size: 16 Copynumber: 3.5 Consensus size: 20
47708 TTTGGCTTGC
47718 TTTCTTTTT-TGAA-TTTCT
1 TTTCTTTTTCTGAATTTTCT
47736 TTT-TCTTTTCT---TTTT-T
1 TTTCT-TTTTCTGAATTTTCT
47752 TTTCTTTTTCTGAATTTTCT
1 TTTCTTTTTCTGAATTTTCT
47772 TCTTCTTTTT
1 T-TTCTTTTT
47782 GTCTTTTCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 15
0.71 0.00 0.29
Matches are distributed among these distances:
16 10 0.27
17 5 0.14
18 7 0.19
19 5 0.14
20 2 0.05
21 8 0.22
ACGTcount: A:0.06, C:0.14, G:0.03, T:0.77
Consensus pattern (20 bp):
TTTCTTTTTCTGAATTTTCT
Found at i:47797 original size:28 final size:25
Alignment explanation
Indices: 47737--47797 Score: 59
Period size: 28 Copynumber: 2.3 Consensus size: 25
47727 TGAATTTCTT
47737 TTTCTTTTCTTTTTTTTTCTTTTTC
1 TTTCTTTTCTTTTTTTTTCTTTTTC
*** *
47762 TGAATTTTCTTCTTCTTTTTGTCTTTTC
1 TTTCTTTTCTT-TT-TTTTTCT-TTTTC
47790 TTTCTTTT
1 TTTCTTTT
47798 TGTACTCCAA
Statistics
Matches: 26, Mismatches: 7, Indels: 3
0.72 0.19 0.08
Matches are distributed among these distances:
25 8 0.31
26 2 0.08
27 6 0.23
28 10 0.38
ACGTcount: A:0.03, C:0.16, G:0.03, T:0.77
Consensus pattern (25 bp):
TTTCTTTTCTTTTTTTTTCTTTTTC
Found at i:48546 original size:19 final size:21
Alignment explanation
Indices: 48503--48554 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
48493 GAAACCCCTT
48503 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
48524 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
48543 TGAAGATACATG
1 TGAAAATACATG
48555 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:60122 original size:30 final size:29
Alignment explanation
Indices: 60067--60125 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 29
60057 CTTGGCTTGC
60067 TTTTCTCTTTTTGAAATCTTTTTCTTTTT
1 TTTTCTCTTTTTGAAATCTTTTTCTTTTT
60096 TTTTCTTCTTTTCTG-AAT-TTTCTTCTTTTT
1 TTTTC-TCTTTT-TGAAATCTTT-TTCTTTTT
60126 GTCTTTTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
29 8 0.30
30 17 0.63
31 2 0.07
ACGTcount: A:0.08, C:0.15, G:0.03, T:0.73
Consensus pattern (29 bp):
TTTTCTCTTTTTGAAATCTTTTTCTTTTT
Found at i:60135 original size:30 final size:30
Alignment explanation
Indices: 60066--60136 Score: 74
Period size: 30 Copynumber: 2.3 Consensus size: 30
60056 CCTTGGCTTG
*
60066 CTTTTCTCTTTTTGAAATCTTTTTCTTTTTT
1 CTTTTCT-TTTCTGAAATCTTTTTCTTTTTT
*
60097 TTTCTTCTTTTCTG-AAT-TTTCTTCTTTTTGT
1 CTT-TTCTTTTCTGAAATCTTT-TTCTTTTT-T
60128 CTTTTCTTT
1 CTTTTCTTT
60137 CTTTTTGCAC
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
29 3 0.09
30 17 0.50
31 10 0.29
32 4 0.12
ACGTcount: A:0.07, C:0.17, G:0.04, T:0.72
Consensus pattern (30 bp):
CTTTTCTTTTCTGAAATCTTTTTCTTTTTT
Found at i:61758 original size:2 final size:2
Alignment explanation
Indices: 61747--61788 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
61737 TAACTATAGG
61747 TA TA -A 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
61788 T
1 T
61789 GAAAATAACT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:64707 original size:8 final size:8
Alignment explanation
Indices: 64696--64753 Score: 57
Period size: 8 Copynumber: 7.4 Consensus size: 8
64686 TTTTGAAATC
64696 TTTTTCTT
1 TTTTTCTT
64704 TTTTTC--
1 TTTTTCTT
*
64710 TTCTTCTT
1 TTTTTCTT
*
64718 TTCTTCTT
1 TTTTTCTT
*
64726 TTCTTCTT
1 TTTTTCTT
*
64734 TTTGTCTT
1 TTTTTCTT
64742 TTCTTTCTT
1 TT-TTTCTT
64751 TTT
1 TTT
64754 GCACTCCAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
6 5 0.12
8 31 0.72
9 7 0.16
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (8 bp):
TTTTTCTT
Found at i:64713 original size:11 final size:11
Alignment explanation
Indices: 64699--64753 Score: 56
Period size: 11 Copynumber: 4.7 Consensus size: 11
64689 TGAAATCTTT
64699 TTCTTTTTTTC
1 TTCTTTTTTTC
*
64710 TTCTTCTTTTC
1 TTCTTTTTTTC
*
64721 TTCTTTTCTTC
1 TTCTTTTTTTC
*
64732 TTTTTGTCTTTTC
1 TTCTT-T-TTTTC
64745 TTTCTTTTT
1 -TTCTTTTT
64754 GCACTCCAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
11 23 0.66
12 3 0.09
13 5 0.14
14 4 0.11
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (11 bp):
TTCTTTTTTTC
Found at i:64719 original size:19 final size:18
Alignment explanation
Indices: 64696--64750 Score: 74
Period size: 19 Copynumber: 2.9 Consensus size: 18
64686 TTTTGAAATC
64696 TTTTTCTTTTTTTCTTCT
1 TTTTTCTTTTTTTCTTCT
*
64714 TCTTTTCTTCTTTTCTTCT
1 T-TTTTCTTTTTTTCTTCT
64733 TTTTGTCTTTTCTTTCTT
1 TTTT-TCTTTT-TTTCTT
64751 TTTGCACTCC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 4 0.12
19 22 0.69
20 6 0.19
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (18 bp):
TTTTTCTTTTTTTCTTCT
Found at i:64751 original size:17 final size:16
Alignment explanation
Indices: 64710--64754 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
64700 TCTTTTTTTC
64710 TTCTTCTTTTCT-TCTT
1 TTCTTCTTTT-TGTCTT
64726 TTCTTCTTTTTGTCTT
1 TTCTTCTTTTTGTCTT
64742 TTCTTTCTTTTTG
1 TTC-TTCTTTTTG
64755 CACTCCAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 1 0.04
16 17 0.63
17 9 0.33
ACGTcount: A:0.00, C:0.20, G:0.04, T:0.76
Consensus pattern (16 bp):
TTCTTCTTTTTGTCTT
Found at i:65058 original size:19 final size:20
Alignment explanation
Indices: 65021--65060 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
65011 GGGTAATAAT
65021 ATAAGTAATGAAAATAAATA
1 ATAAGTAATGAAAATAAATA
65041 ATAAG-AAT-AAAATGAAATA
1 ATAAGTAATGAAAAT-AAATA
65060 A
1 A
65061 ATAAAAGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.26
19 9 0.47
20 5 0.26
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.23
Consensus pattern (20 bp):
ATAAGTAATGAAAATAAATA
Found at i:66371 original size:2 final size:2
Alignment explanation
Indices: 66360--66397 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
66350 TAACTATAGG
66360 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
66398 GAAAATAACT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:83035 original size:13 final size:13
Alignment explanation
Indices: 83013--83042 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
83003 ACTAAACACC
83013 TTTC-ACATACCT
1 TTTCAACATACCT
83025 TTTCAACATACCT
1 TTTCAACATACCT
83038 TTTCA
1 TTTCA
83043 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:90800 original size:11 final size:13
Alignment explanation
Indices: 90769--90797 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
90759 GGCCAAAGAT
90769 GAAAAGGTATGTA
1 GAAAAGGTATGTA
90782 GAAAAGGTATGT-
1 GAAAAGGTATGTA
90794 GAAA
1 GAAA
90798 GGTGTTTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.25
13 12 0.75
ACGTcount: A:0.48, C:0.00, G:0.31, T:0.21
Consensus pattern (13 bp):
GAAAAGGTATGTA
Found at i:95220 original size:24 final size:24
Alignment explanation
Indices: 95188--95240 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
95178 TGAATCAAAA
95188 ACTTCAAGACACTTAGTTAAGAGC
1 ACTTCAAGACACTTAGTTAAGAGC
95212 ACTTCAAGACACTTAGTTAAGAGC
1 ACTTCAAGACACTTAGTTAAGAGC
95236 ACTTC
1 ACTTC
95241 CATGAATTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (24 bp):
ACTTCAAGACACTTAGTTAAGAGC
Found at i:95977 original size:20 final size:19
Alignment explanation
Indices: 95952--96002 Score: 75
Period size: 19 Copynumber: 2.6 Consensus size: 19
95942 GAAACCCCTT
95952 TGAAAATACATGATTTTTAA
1 TGAAAATACATGA-TTTTAA
*
95972 TGAAAATAAATGATTTTAA
1 TGAAAATACATGATTTTAA
*
95991 TGAAGATACATG
1 TGAAAATACATG
96003 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.47, C:0.04, G:0.14, T:0.35
Consensus pattern (19 bp):
TGAAAATACATGATTTTAA
Found at i:95990 original size:19 final size:20
Alignment explanation
Indices: 95952--95994 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
95942 GAAACCCCTT
*
95952 TGAAAATACATGATTTTTAA
1 TGAAAATAAATGATTTTTAA
95972 TGAAAATAAATGA-TTTTAA
1 TGAAAATAAATGATTTTTAA
95991 TGAA
1 TGAA
95995 GATACATGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.49, C:0.02, G:0.12, T:0.37
Consensus pattern (20 bp):
TGAAAATAAATGATTTTTAA
Found at i:105564 original size:19 final size:20
Alignment explanation
Indices: 105525--105576 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
105515 GAAACCCCTT
105525 TGAAAATACATGATTTTTTAA
1 TGAAAATACATGA-TTTTTAA
105546 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
105565 TGAAGATACATG
1 TGAAAATACATG
105577 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 17 0.57
21 13 0.43
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:108477 original size:13 final size:13
Alignment explanation
Indices: 108455--108484 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
108445 ACTAAACACC
108455 TTTC-ACATACCT
1 TTTCAACATACCT
108467 TTTCAACATACCT
1 TTTCAACATACCT
108480 TTTCA
1 TTTCA
108485 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:110912 original size:6 final size:7
Alignment explanation
Indices: 110901--110962 Score: 54
Period size: 7 Copynumber: 8.0 Consensus size: 7
110891 TTTTTTTTTT
110901 CAAAAAA
1 CAAAAAA
110908 CAAAAAAA
1 C-AAAAAA
110916 CAAAAAA
1 CAAAAAA
110923 CAAAAAAA
1 C-AAAAAA
110931 GGCAAAAAA
1 --CAAAAAA
110940 -AAAAAA
1 CAAAAAA
110946 GGCAAAAAAA
1 --C-AAAAAA
110956 CAAAAAA
1 CAAAAAA
110963 AGAGCCAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 16
0.75 0.00 0.25
Matches are distributed among these distances:
6 6 0.13
7 14 0.30
8 14 0.30
9 6 0.13
10 7 0.15
ACGTcount: A:0.82, C:0.11, G:0.06, T:0.00
Consensus pattern (7 bp):
CAAAAAA
Found at i:110915 original size:8 final size:8
Alignment explanation
Indices: 110902--110963 Score: 74
Period size: 8 Copynumber: 7.8 Consensus size: 8
110892 TTTTTTTTTC
110902 AAAAAACA
1 AAAAAACA
110910 AAAAAAC-
1 AAAAAACA
110917 AAAAAACA
1 AAAAAACA
110925 AAAAAAGGCA
1 AAAAAA--CA
110935 AAAAAA-A
1 AAAAAACA
**
110942 AAAAGGCA
1 AAAAAACA
110950 AAAAAACA
1 AAAAAACA
110958 AAAAAA
1 AAAAAA
110964 GAGCCAAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
7 12 0.26
8 26 0.57
10 8 0.17
ACGTcount: A:0.84, C:0.10, G:0.06, T:0.00
Consensus pattern (8 bp):
AAAAAACA
Found at i:110921 original size:15 final size:15
Alignment explanation
Indices: 110901--110963 Score: 74
Period size: 15 Copynumber: 4.0 Consensus size: 15
110891 TTTTTTTTTT
110901 CAAAAAACAAAAAAA
1 CAAAAAACAAAAAAA
110916 CAAAAAACAAAAAAA
1 CAAAAAACAAAAAAA
*
110931 GGCAAAAAA-AAAAAAGG
1 --CAAAAAACAAAAAA-A
110948 CAAAAAAACAAAAAAA
1 C-AAAAAACAAAAAAA
110964 GAGCCAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
15 16 0.39
16 12 0.29
17 13 0.32
ACGTcount: A:0.83, C:0.11, G:0.06, T:0.00
Consensus pattern (15 bp):
CAAAAAACAAAAAAA
Found at i:110954 original size:33 final size:32
Alignment explanation
Indices: 110901--110974 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 32
110891 TTTTTTTTTT
110901 CAAAAAACAAAAAAACAAAAAACAAAAAAAG-G
1 CAAAAAA-AAAAAAACAAAAAACAAAAAAAGAG
*
110933 CAAAAAAAAAAAAGGCAAAAAAACAAAAAAAGAG
1 CAAAAAAAAAAAA-AC-AAAAAACAAAAAAAGAG
*
110967 CCAAAAAA
1 CAAAAAAA
110975 GCCAAAATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
31 6 0.16
32 8 0.22
33 15 0.41
34 8 0.22
ACGTcount: A:0.80, C:0.12, G:0.08, T:0.00
Consensus pattern (32 bp):
CAAAAAAAAAAAAACAAAAAACAAAAAAAGAG
Found at i:110981 original size:20 final size:20
Alignment explanation
Indices: 110937--110974 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
110927 AAAAGGCAAA
*
110937 AAAAAAAAAGGCAAAAAAAC
1 AAAAAAAAAGCCAAAAAAAC
*
110957 AAAAAAAGAGCCAAAAAA
1 AAAAAAAAAGCCAAAAAA
110975 GCCAAAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.79, C:0.11, G:0.11, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAGCCAAAAAAAC
Found at i:117794 original size:19 final size:20
Alignment explanation
Indices: 117770--117820 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
117760 CGGCCAAGAG
* *
117770 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
117789 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
117809 CATGTATTTTCA
1 CATGTATTTTCA
117821 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:121974 original size:19 final size:20
Alignment explanation
Indices: 121950--121995 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
121940 CGGCCAAGAG
*
121950 CATGTATCGTCAT-TAAAAT
1 CATGTATCGTCATCAAAAAT
**
121969 CATGTATTTTCATCAAAAAT
1 CATGTATCGTCATCAAAAAT
121989 CATGTAT
1 CATGTAT
121996 TTTCAAAGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (20 bp):
CATGTATCGTCATCAAAAAT
Found at i:125851 original size:13 final size:13
Alignment explanation
Indices: 125829--125858 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
125819 ACTAAACACC
125829 TTTC-ACATACCT
1 TTTCAACATACCT
125841 TTTCAACATACCT
1 TTTCAACATACCT
125854 TTTCA
1 TTTCA
125859 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:131080 original size:25 final size:26
Alignment explanation
Indices: 131038--131101 Score: 67
Period size: 25 Copynumber: 2.4 Consensus size: 26
131028 GCACAATATA
* * * *
131038 AAGAAAGAAATAATTAAATGGAA-AT
1 AAGAAATAAAGAAATAAATGAAAGAT
131063 AAGAAATAAAGAAATAAATGAAATGAT
1 AAGAAATAAAGAAATAAATGAAA-GAT
131090 AAGAAATGAAAG
1 AAGAAAT-AAAG
131102 GGATAGAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
25 19 0.59
27 9 0.28
28 4 0.12
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (26 bp):
AAGAAATAAAGAAATAAATGAAAGAT
Found at i:131096 original size:15 final size:14
Alignment explanation
Indices: 131061--131101 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
131051 TTAAATGGAA
131061 ATAAGAAAT-AAAG
1 ATAAGAAATGAAAG
*
131074 A-AATAAATGAAATG
1 ATAAGAAATGAAA-G
131088 ATAAGAAATGAAAG
1 ATAAGAAATGAAAG
131102 GGATAGAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
12 6 0.26
13 4 0.17
14 3 0.13
15 10 0.43
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (14 bp):
ATAAGAAATGAAAG
Found at i:132327 original size:15 final size:16
Alignment explanation
Indices: 132307--132336 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
132297 AAAGTAAATG
132307 GAAATGG-AAAGAATT
1 GAAATGGAAAAGAATT
132322 GAAATGGAAAAGAAT
1 GAAATGGAAAAGAAT
132337 GTTATCAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.57, C:0.00, G:0.27, T:0.17
Consensus pattern (16 bp):
GAAATGGAAAAGAATT
Found at i:140487 original size:15 final size:15
Alignment explanation
Indices: 140455--140494 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
140445 TTAAATGGAA
140455 ATAAGAAAT--AATG
1 ATAAGAAATGAAATG
140468 A-AAGAAATGAAATG
1 ATAAGAAATGAAATG
140482 ATAAGAAATGAAA
1 ATAAGAAATGAAA
140495 GGGATAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 7 0.29
13 1 0.04
14 5 0.21
15 11 0.46
ACGTcount: A:0.65, C:0.00, G:0.17, T:0.17
Consensus pattern (15 bp):
ATAAGAAATGAAATG
Found at i:141062 original size:19 final size:19
Alignment explanation
Indices: 141038--141074 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
141028 TAGATGATTT
141038 TTTTAATGAAA-ATACATGA
1 TTTTAAT-AAAGATACATGA
141057 TTTTAATAAAGATACATG
1 TTTTAATAAAGATACATG
141075 CTCTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.46, C:0.05, G:0.11, T:0.38
Consensus pattern (19 bp):
TTTTAATAAAGATACATGA
Found at i:142697 original size:19 final size:21
Alignment explanation
Indices: 142659--142699 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
142649 AACCCCTCTG
142659 AAATACATGATTTATTAATGA
1 AAATACATGATTTATTAATGA
*
142680 AAATACTTGA-TT-TTAATGA
1 AAATACATGATTTATTAATGA
142699 A
1 A
142700 TATATATTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 2 0.11
21 9 0.47
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.39
Consensus pattern (21 bp):
AAATACATGATTTATTAATGA
Found at i:143775 original size:15 final size:15
Alignment explanation
Indices: 143726--143777 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
143716 TTAAATGGAA
*
143726 ATAAGAAAAGAAA-G
1 ATAAGAAATGAAAGG
*
143740 A-AAGAAATGAAATG
1 ATAAGAAATGAAAGG
143754 ATAAGAAATGAAAGGG
1 ATAAGAAATGAAA-GG
143770 AT-AGAAAT
1 ATAAGAAAT
143778 TTTATCAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
13 10 0.30
14 3 0.09
15 17 0.52
16 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.23, T:0.13
Consensus pattern (15 bp):
ATAAGAAATGAAAGG
Found at i:144334 original size:19 final size:21
Alignment explanation
Indices: 144295--144346 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
144285 GAAACCCCTT
*
144295 TGAACATACATGAATTTTTAA
1 TGAAAATACATGAATTTTTAA
144316 TGAAAATACATG-A-TTTTAA
1 TGAAAATACATGAATTTTTAA
*
144335 TGAAGATACATG
1 TGAAAATACATG
144347 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
20 1 0.03
21 11 0.38
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGAATTTTTAA
Found at i:144956 original size:24 final size:25
Alignment explanation
Indices: 144927--144981 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
144917 AAGGAATGAT
* **
144927 TAATAATAGAATTAAT-AAAGGGGA
1 TAATAATAGAAGTAATGAAAGGAAA
*
144951 TAATAATATAAGTAATGAAAGGAAA
1 TAATAATAGAAGTAATGAAAGGAAA
144976 TAATAA
1 TAATAA
144982 GAATGAAATG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 14 0.54
25 12 0.46
ACGTcount: A:0.58, C:0.00, G:0.16, T:0.25
Consensus pattern (25 bp):
TAATAATAGAAGTAATGAAAGGAAA
Found at i:144986 original size:19 final size:20
Alignment explanation
Indices: 144958--144997 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
144948 GGATAATAAT
144958 ATAAGTAATGAAAGGAAATA
1 ATAAGTAATGAAAGGAAATA
*
144978 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAGGAAATA
144997 A
1 A
144998 AGAAAGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAGGAAATA
Found at i:150744 original size:13 final size:11
Alignment explanation
Indices: 150703--150787 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
150693 ACAATCTGTC
150703 CATCACCATTAT
1 CATCACCA-TAT
*
150715 CA-CGCCTATAT
1 CATCACC-ATAT
150726 CATCACCATAGT
1 CATCACCATA-T
150738 CCATCACCATTAT
1 -CATCACCA-TAT
*
150751 CA-CGCCTATAT
1 CATCACC-ATAT
150762 CATCACCATATT
1 CATCACCATA-T
150774 CCATCACCATAT
1 -CATCACCATAT
150786 CA
1 CA
150788 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:150747 original size:36 final size:36
Alignment explanation
Indices: 150700--150804 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
150690 GATACAATCT
150700 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
150736 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
150772 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
150805 ACATATAAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.31
36 46 0.69
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:152668 original size:17 final size:18
Alignment explanation
Indices: 152648--152707 Score: 68
Period size: 22 Copynumber: 3.2 Consensus size: 18
152638 TTTGAACTTC
152648 TTTTTC-TTTTCTTTCTT
1 TTTTTCTTTTTCTTTCTT
152665 TTTTTCTGATTTTTCTCTTCTT
1 TTTTTC---TTTTTCT-TTCTT
*
152687 TTTGTCTTTTTCTTTCTT
1 TTTTTCTTTTTCTTTCTT
152705 TTT
1 TTT
152708 GCACTCCAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 6 0.16
18 8 0.22
19 7 0.19
21 6 0.16
22 10 0.27
ACGTcount: A:0.02, C:0.17, G:0.03, T:0.78
Consensus pattern (18 bp):
TTTTTCTTTTTCTTTCTT
Found at i:152688 original size:19 final size:19
Alignment explanation
Indices: 152644--152708 Score: 57
Period size: 18 Copynumber: 3.5 Consensus size: 19
152634 TCTTTTTGAA
*
152644 CTTCTTTTTCT-TTTCTT-T
1 CTTCTTTTTGTATTT-TTCT
*
152662 CTT-TTTTTCTGATTTTTCT
1 CTTCTTTTTGT-ATTTTTCT
*
152681 CTTCTTTTTGTCTTTTTCT
1 CTTCTTTTTGTATTTTTCT
152700 -TTCTTTTTG
1 CTTCTTTTTG
152709 CACTCCAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
17 7 0.17
18 14 0.34
19 14 0.34
20 6 0.15
ACGTcount: A:0.02, C:0.18, G:0.05, T:0.75
Consensus pattern (19 bp):
CTTCTTTTTGTATTTTTCT
Found at i:155338 original size:23 final size:23
Alignment explanation
Indices: 155293--155338 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
155283 TTATACCTAT
*
155293 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
155316 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
155339 TATATTATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:156981 original size:8 final size:8
Alignment explanation
Indices: 156953--156997 Score: 65
Period size: 8 Copynumber: 5.5 Consensus size: 8
156943 TTGGAGTGCA
156953 AAAAGAAAG
1 AAAAG-AAG
156962 AAAAGACA-
1 AAAAGA-AG
156970 AAAAGAAG
1 AAAAGAAG
156978 AAAAGAAG
1 AAAAGAAG
156986 AAAAGAAG
1 AAAAGAAG
156994 AAAA
1 AAAA
156998 AAAAGAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
7 1 0.03
8 27 0.79
9 6 0.18
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (8 bp):
AAAAGAAG
Found at i:156981 original size:25 final size:27
Alignment explanation
Indices: 156952--157011 Score: 81
Period size: 25 Copynumber: 2.3 Consensus size: 27
156942 ATTGGAGTGC
*
156952 AAAAAGAAAGAAAAG-ACAAAAAGAAG
1 AAAAAGAAAGAAAAGAACAAAAAAAAG
*
156978 -AAAAG-AAGAAAAGAAGAAAAAAAAG
1 AAAAAGAAAGAAAAGAACAAAAAAAAG
157003 AAAAAGAAA
1 AAAAAGAAA
157012 AAGATTTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
24 8 0.28
25 14 0.48
26 5 0.17
27 2 0.07
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (27 bp):
AAAAAGAAAGAAAAGAACAAAAAAAAG
Found at i:156998 original size:17 final size:17
Alignment explanation
Indices: 156952--157010 Score: 68
Period size: 16 Copynumber: 3.5 Consensus size: 17
156942 ATTGGAGTGC
*
156952 AAAAAGAAAGAAAAG-AC
1 AAAAAG-AAGAAAAGAAG
156969 AAAAAGAAGAAAAGAAG
1 AAAAAGAAGAAAAGAAG
*
156986 -AAAAGAAGAAAAAAAAG
1 AAAAAGAAG-AAAAGAAG
157003 AAAAAGAA
1 AAAAAGAA
157011 AAAGATTTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
16 16 0.43
17 14 0.38
18 7 0.19
ACGTcount: A:0.80, C:0.02, G:0.19, T:0.00
Consensus pattern (17 bp):
AAAAAGAAGAAAAGAAG
Found at i:157006 original size:8 final size:8
Alignment explanation
Indices: 156952--157013 Score: 61
Period size: 8 Copynumber: 7.4 Consensus size: 8
156942 ATTGGAGTGC
156952 AAAAAGAA
1 AAAAAGAA
*
156960 AGAAAAGAC
1 A-AAAAGAA
156969 AAAAAGAA
1 AAAAAGAA
*
156977 GAAAAGAA
1 AAAAAGAA
*
156985 GAAAAGAA
1 AAAAAGAA
*
156993 GAAAAAAAA
1 -AAAAAGAA
157002 GAAAAAGAA
1 -AAAAAGAA
157011 AAA
1 AAA
157014 GATTTCAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
8 25 0.54
9 21 0.46
ACGTcount: A:0.81, C:0.02, G:0.18, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:157013 original size:16 final size:16
Alignment explanation
Indices: 156952--157013 Score: 54
Period size: 17 Copynumber: 3.7 Consensus size: 16
156942 ATTGGAGTGC
* *
156952 AAAAAGAAAGAAAAGAC
1 AAAAAGAAA-AAAAAAG
*
156969 AAAAAGAAGAAAAGAAG
1 AAAAAGAA-AAAAAAAG
156986 -AAAAGAAGAAAAAAAAG
1 AAAAAG-A-AAAAAAAAG
157003 AAAAAGAAAAA
1 AAAAAGAAAAA
157014 GATTTCAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
16 9 0.24
17 21 0.57
18 7 0.19
ACGTcount: A:0.81, C:0.02, G:0.18, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAAAAAAG
Found at i:157013 original size:24 final size:26
Alignment explanation
Indices: 156952--157015 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 26
156942 ATTGGAGTGC
156952 AAAAAGAAAGAA-AAGACAAAAAGAAG
1 AAAAAGAAA-AAGAAGACAAAAAGAAG
156978 -AAAAGAAGAAAAGAAGA-AAAAA-AAG
1 AAAAAG-A-AAAAGAAGACAAAAAGAAG
157003 AAAAAGAAAAAGA
1 AAAAAGAAAAAGA
157016 TTTCAAAAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
24 6 0.18
25 9 0.26
26 13 0.38
27 6 0.18
ACGTcount: A:0.80, C:0.02, G:0.19, T:0.00
Consensus pattern (26 bp):
AAAAAGAAAAAGAAGACAAAAAGAAG
Found at i:164906 original size:23 final size:23
Alignment explanation
Indices: 164861--164906 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
164851 TTATACCTAT
*
164861 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
164884 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
164907 TATTATACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:172072 original size:15 final size:15
Alignment explanation
Indices: 172037--172080 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 15
172027 TTAAATGGAA
*
172037 ATAAGAAACGAAA-G
1 ATAAGAAATGAAATG
172051 A-AAGAAATGAAATG
1 ATAAGAAATGAAATG
172065 ATAAGAAATGAAATG
1 ATAAGAAATGAAATG
172080 A
1 A
172081 AAGGGATAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 10 0.37
14 3 0.11
15 14 0.52
ACGTcount: A:0.64, C:0.02, G:0.20, T:0.14
Consensus pattern (15 bp):
ATAAGAAATGAAATG
Found at i:172091 original size:20 final size:20
Alignment explanation
Indices: 172048--172093 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
172038 TAAGAAACGA
*
172048 AAGAAA-GAAATGAAATGAT
1 AAGAAATGAAATGAAAGGAT
172067 AAGAAATGAAATGAAAGGGAT
1 AAGAAATGAAATGAAA-GGAT
172088 -AGAAAT
1 AAGAAAT
172094 TTTATCAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 6 0.25
20 15 0.62
21 3 0.12
ACGTcount: A:0.61, C:0.00, G:0.24, T:0.15
Consensus pattern (20 bp):
AAGAAATGAAATGAAAGGAT
Found at i:172881 original size:19 final size:20
Alignment explanation
Indices: 172840--172890 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
172830 GAAACCCCTT
*
172840 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
172860 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
172879 TGAAGATACATG
1 TGAAAATACATG
172891 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:174879 original size:15 final size:15
Alignment explanation
Indices: 174868--174896 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
174858 ACTCAAAAAG
174868 AAGAAAAGCAAAGAA
1 AAGAAAAGCAAAGAA
174883 AAGAAAAG-AAAGAA
1 AAGAAAAGCAAAGAA
174897 GTTGAAGCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGAAAAGCAAAGAA
Found at i:180762 original size:19 final size:20
Alignment explanation
Indices: 180738--180780 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
180728 AGCATTTATA
*
180738 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
180757 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
180777 TTCA
1 TTCA
180781 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:181398 original size:16 final size:16
Alignment explanation
Indices: 181351--181400 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
181341 TTCATTTCTT
181351 ATCATTTCCTTTCTTT-
1 ATCATTT-CTTTCTTTA
* *
181367 TTCATATTCTAT-TTTA
1 ATCAT-TTCTTTCTTTA
181383 ATCATTTCTTTCTTTA
1 ATCATTTCTTTCTTTA
181399 AT
1 AT
181401 TTTGCAGATT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
15 8 0.30
16 17 0.63
17 2 0.07
ACGTcount: A:0.20, C:0.18, G:0.00, T:0.62
Consensus pattern (16 bp):
ATCATTTCTTTCTTTA
Done.