Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001301.1 Hibiscus syriacus cultivar Beakdansim tig00002540_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: 163040
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4692 original size:24 final size:21
Alignment explanation
Indices: 4657--4699 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
4647 GTCTCATTCT
*
4657 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
4680 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
4700 ATCTTGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:5926 original size:5 final size:5
Alignment explanation
Indices: 5912--5947 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
5902 GTACTTCAAC
5912 TTTC- TTTCT TTTCT TTTCT TTTCT TTTCT TTT-T TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
5948 AAGTGCTGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 8 0.26
5 23 0.74
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTCT
Found at i:9978 original size:15 final size:14
Alignment explanation
Indices: 9951--9982 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
9941 GTGCTTCAAC
9951 TTTCTTTCTTTTCT
1 TTTCTTTCTTTTCT
9965 TTTCTTTGCTTTTCT
1 TTTCTTT-CTTTTCT
9980 TTT
1 TTT
9983 TTTTAAGTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.78
Consensus pattern (14 bp):
TTTCTTTCTTTTCT
Found at i:14001 original size:15 final size:14
Alignment explanation
Indices: 13974--14005 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
13964 GTGCTTCAAC
13974 TTTCTTTCTTTTCT
1 TTTCTTTCTTTTCT
13988 TTTCTTTGCTTTTCT
1 TTTCTTT-CTTTTCT
14003 TTT
1 TTT
14006 TTTTAAGTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.78
Consensus pattern (14 bp):
TTTCTTTCTTTTCT
Found at i:17772 original size:24 final size:21
Alignment explanation
Indices: 17738--17780 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
17728 TCCACAAGAT
*
17738 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
17760 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
17781 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:27125 original size:20 final size:22
Alignment explanation
Indices: 27074--27126 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
27064 AAAAATTAGA
27074 AAAAAAAGCACTCAAAAAAAAG
1 AAAAAAAGCACTCAAAAAAAAG
*
27096 AAATTGAAAA-CACTC-AAAAGAAG
1 AAA---AAAAGCACTCAAAAAAAAG
27119 AAAAAAAG
1 AAAAAAAG
27127 AAAGAAAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 9
0.72 0.03 0.25
Matches are distributed among these distances:
20 4 0.15
22 3 0.12
23 10 0.38
24 5 0.19
25 4 0.15
ACGTcount: A:0.70, C:0.11, G:0.11, T:0.08
Consensus pattern (22 bp):
AAAAAAAGCACTCAAAAAAAAG
Found at i:39183 original size:10 final size:9
Alignment explanation
Indices: 39157--39189 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
39147 GTGCTTCAAC
39157 TTCTTTTCT
1 TTCTTTTCT
39166 TTCTTTTCT
1 TTCTTTTCT
39175 TTGCTTTTC-
1 TT-CTTTTCT
39184 TTCTTT
1 TTCTTT
39190 GAGTGCTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 4 0.17
9 13 0.57
10 6 0.26
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (9 bp):
TTCTTTTCT
Found at i:39233 original size:24 final size:25
Alignment explanation
Indices: 39173--39234 Score: 65
Period size: 24 Copynumber: 2.4 Consensus size: 25
39163 TCTTTCTTTT
*
39173 CTTTGCTTTTCTTCTTTGAGTGCTTGA
1 CTTTG-TTTTC-TCTTTGAGTGCTTCA
*
39200 -TTTTTCTTTCT-TTTGAGTGCTTCA
1 CTTTGT-TTTCTCTTTGAGTGCTTCA
39224 CTTTGTTTTCT
1 CTTTGTTTTCT
39235 GATTTTTCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
24 17 0.57
25 6 0.20
26 7 0.23
ACGTcount: A:0.06, C:0.18, G:0.15, T:0.61
Consensus pattern (25 bp):
CTTTGTTTTCTCTTTGAGTGCTTCA
Found at i:42185 original size:19 final size:20
Alignment explanation
Indices: 42161--42203 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
42151 AGCATTTATC
*
42161 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
42180 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
42200 TTCA
1 TTCA
42204 AAGGGATTTC
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:42948 original size:19 final size:20
Alignment explanation
Indices: 42920--42959 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
42910 GAATAATAAT
42920 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
42940 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
42959 A
1 A
42960 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:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:43737 original size:24 final size:24
Alignment explanation
Indices: 43710--43797 Score: 86
Period size: 24 Copynumber: 3.4 Consensus size: 24
43700 TCAAGGTAAG
43710 CTAGGTGAGTGTCTTGGTAGCTAA
1 CTAGGTGAGTGTCTTGGTAGCTAA
* * *
43734 CTAGGTGAGTTATAGCTTGATAAACTCAA
1 CTAGGTGAG-TGT--CTTGGT-AGCT-AA
*
43763 GATAGGTGAGTGTCTTGGTAGCTAA
1 -CTAGGTGAGTGTCTTGGTAGCTAA
43788 CTAGGTGAGT
1 CTAGGTGAGT
43798 TATAGCTTGA
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
24 18 0.36
25 4 0.08
26 3 0.06
27 10 0.20
28 3 0.06
29 4 0.08
30 8 0.16
ACGTcount: A:0.26, C:0.11, G:0.31, T:0.32
Consensus pattern (24 bp):
CTAGGTGAGTGTCTTGGTAGCTAA
Found at i:43771 original size:54 final size:54
Alignment explanation
Indices: 43711--43816 Score: 203
Period size: 54 Copynumber: 2.0 Consensus size: 54
43701 CAAGGTAAGC
43711 TAGGTGAGTGTCTTGGTAGCTAACTAGGTGAGTTATAGCTTGATAAACTCAAGA
1 TAGGTGAGTGTCTTGGTAGCTAACTAGGTGAGTTATAGCTTGATAAACTCAAGA
*
43765 TAGGTGAGTGTCTTGGTAGCTAACTAGGTGAGTTATAGCTTGATGAACTCAA
1 TAGGTGAGTGTCTTGGTAGCTAACTAGGTGAGTTATAGCTTGATAAACTCAA
43817 TCTAGTTAGC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.28, C:0.11, G:0.28, T:0.32
Consensus pattern (54 bp):
TAGGTGAGTGTCTTGGTAGCTAACTAGGTGAGTTATAGCTTGATAAACTCAAGA
Found at i:45645 original size:15 final size:14
Alignment explanation
Indices: 45625--45665 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 14
45615 ATTATATCCC
45625 TTTCATTTCTTATTA
1 TTTCA-TTCTTATTA
45640 TTTCA-T-TTATTA
1 TTTCATTCTTATTA
45652 TTTCAGTTCTTATT
1 TTTCA-TTCTTATT
45666 TCCATAATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
12 11 0.48
13 1 0.04
14 1 0.04
15 10 0.43
ACGTcount: A:0.20, C:0.12, G:0.02, T:0.66
Consensus pattern (14 bp):
TTTCATTCTTATTA
Found at i:48787 original size:69 final size:69
Alignment explanation
Indices: 48660--48811 Score: 173
Period size: 69 Copynumber: 2.2 Consensus size: 69
48650 ATGTCCTCAC
* * * * *
48660 AAGTCACGCCCTTTGGATAAAGAATTGCTTACTTTTGGTTTTCATTAGGCACAACTCTTGATTCT
1 AAGTCACGTCCTTTGGATAAAGAATTACTCACTTTTGCTTTTCAATAGGCACAACTCTTGATTCT
48725 TG-A
66 TGAA
* * * * *
48728 AGGATCACGTCCTTTGGATGAAGAATTAC-CACTCTTTGCTTTTCAATAGTCGCACCTCTTGATT
1 AAG-TCACGTCCTTTGGATAAAGAATTACTCACT-TTTGCTTTTCAATAGGCACAACTCTTGATT
*
48792 TTTGAA
64 CTTGAA
48798 AAGTCACGTCCTTT
1 AAGTCACGTCCTTT
48812 ACTTCACCAA
Statistics
Matches: 69, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
68 5 0.07
69 61 0.88
70 3 0.04
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (69 bp):
AAGTCACGTCCTTTGGATAAAGAATTACTCACTTTTGCTTTTCAATAGGCACAACTCTTGATTCT
TGAA
Found at i:54980 original size:16 final size:15
Alignment explanation
Indices: 54954--55005 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
54944 GAGTTGTAAG
54954 TTATC-TTCATTTTT
1 TTATCTTTCATTTTT
*
54968 TTATCATTTCATTTCT
1 TTATC-TTTCATTTTT
54984 TTATTCTTTCATCTTTT
1 TTA-TCTTTCAT-TTTT
55001 CTTAT
1 -TTAT
55006 TTCATTACCA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
14 5 0.16
16 17 0.55
17 6 0.19
18 3 0.10
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATCTTTCATTTTT
Found at i:57945 original size:20 final size:19
Alignment explanation
Indices: 57902--57952 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
57892 CGGCCAAGAG
* *
57902 AATGTATCTTCATTTAAAT
1 AATGTATTTTCATTAAAAT
57921 AATGTATTTTCATTAAAAAT
1 AATGTATTTTCATT-AAAAT
*
57941 CATGTATTTTCA
1 AATGTATTTTCA
57953 AAGGGGTCTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.47
Consensus pattern (19 bp):
AATGTATTTTCATTAAAAT
Found at i:61256 original size:34 final size:34
Alignment explanation
Indices: 61217--61319 Score: 95
Period size: 34 Copynumber: 3.0 Consensus size: 34
61207 TTGATGAATG
*
61217 AAGGATGAT-TTAATGGTGATGAAATGGTAATGGA
1 AAGGATGATGTTAATGGCG-TGAAATGGTAATGGA
* * *
61251 AAGGATGATGTTATTGGCGTGATATGGTGATGGA
1 AAGGATGATGTTAATGGCGTGAAATGGTAATGGA
* *
61285 ATATGG-TGATGAT-ATGGCGTGATAATGGTGATGGA
1 A-A-GGATGATGTTAATGGCGTGA-AATGGTAATGGA
61320 CAGATTGTAT
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
34 31 0.53
35 25 0.43
36 2 0.03
ACGTcount: A:0.31, C:0.02, G:0.36, T:0.31
Consensus pattern (34 bp):
AAGGATGATGTTAATGGCGTGAAATGGTAATGGA
Found at i:61313 original size:35 final size:35
Alignment explanation
Indices: 61239--61319 Score: 105
Period size: 34 Copynumber: 2.3 Consensus size: 35
61229 ATGGTGATGA
* *
61239 AATGGTAATGGAAAGGATGATGTTATTGGCGTGAT
1 AATGGTGATGGAAAGGATGATGATATTGGCGTGAT
61274 -ATGGTGATGGAATATGG-TGATGATA-TGGCGTGAT
1 AATGGTGATGGAA-A-GGATGATGATATTGGCGTGAT
61308 AATGGTGATGGA
1 AATGGTGATGGA
61320 CAGATTGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
34 20 0.49
35 19 0.46
36 2 0.05
ACGTcount: A:0.30, C:0.02, G:0.37, T:0.31
Consensus pattern (35 bp):
AATGGTGATGGAAAGGATGATGATATTGGCGTGAT
Found at i:62589 original size:19 final size:20
Alignment explanation
Indices: 62548--62598 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
62538 GAAACCCCTT
*
62548 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
62568 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
62587 TGAAGATACATG
1 TGAAAATACATG
62599 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:66788 original size:19 final size:20
Alignment explanation
Indices: 66747--66797 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
66737 GAAACCCCTT
*
66747 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
66767 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
66786 TGAAGATACATG
1 TGAAAATACATG
66798 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:71880 original size:35 final size:35
Alignment explanation
Indices: 71802--71886 Score: 104
Period size: 34 Copynumber: 2.5 Consensus size: 35
71792 TTTAATGGTG
* *
71802 ATGA-AATGGTAATGGAAATGATGATGTTATTGGC
1 ATGATAATGGTGATGGAAATGATGATGATATTGGC
* *
71836 GTGAT-ATGGTGATGGAATATGGTGATGATA-TGGC
1 ATGATAATGGTGATGGAA-ATGATGATGATATTGGC
71870 ATGATAATGGTGATGGA
1 ATGATAATGGTGATGGA
71887 CAGATTGTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
34 22 0.51
35 21 0.49
ACGTcount: A:0.32, C:0.02, G:0.34, T:0.32
Consensus pattern (35 bp):
ATGATAATGGTGATGGAAATGATGATGATATTGGC
Found at i:74155 original size:13 final size:13
Alignment explanation
Indices: 74133--74162 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
74123 ACTAAACACC
74133 TTTC-ACATACCT
1 TTTCAACATACCT
74145 TTTCAACATACCT
1 TTTCAACATACCT
74158 TTTCA
1 TTTCA
74163 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:81453 original size:13 final size:13
Alignment explanation
Indices: 81431--81460 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
81421 ACTAAACACC
81431 TTTC-ACATACCT
1 TTTCAACATACCT
81443 TTTCAACATACCT
1 TTTCAACATACCT
81456 TTTCA
1 TTTCA
81461 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:96633 original size:65 final size:64
Alignment explanation
Indices: 96503--96662 Score: 180
Period size: 65 Copynumber: 2.5 Consensus size: 64
96493 AATTAAATTG
* * *
96503 AACATCGAATGCATTTCATGTATCGATGCACATACCATGCACCGATGCACTGAGGATTTTATGAA
1 AACATCGAATGCATTTGATGCATCGATGCACATACCATGCACCGATGCACTCAGGATTTTATG-A
* ** * *
96568 AACATCGAATGCATTTGATGCATCGATGTACCA-ACCATGCATTGATGCACTCTGGCTATTT-TG
1 AACATCGAATGCATTTGATGCATCGATGCA-CATACCATGCACCGATGCACTCAGGAT-TTTATG
96631 A
64 A
* * *
96632 AACATCGAATACACTTGATACATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
96663 TCTTAGTGCA
Statistics
Matches: 81, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
63 1 0.01
64 27 0.33
65 48 0.59
66 5 0.06
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (64 bp):
AACATCGAATGCATTTGATGCATCGATGCACATACCATGCACCGATGCACTCAGGATTTTATGA
Found at i:99271 original size:9 final size:9
Alignment explanation
Indices: 99257--99282 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
99247 ACATCGAAGG
99257 TATAGGTAC
1 TATAGGTAC
99266 TATAGGTAC
1 TATAGGTAC
99275 TATAGGTA
1 TATAGGTA
99283 ATACCTCTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.08, G:0.23, T:0.35
Consensus pattern (9 bp):
TATAGGTAC
Found at i:101709 original size:23 final size:21
Alignment explanation
Indices: 101659--101715 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
101649 ATCAATGCAT
*
101659 CCTTGAATGTGCATCGATACA
1 CCTTGAATGTGCACCGATACA
* *
101680 CCATGAAGGTGCACCGATGCACA
1 CCTTGAATGTGCACCGAT--ACA
101703 CCTTGAATGTGCA
1 CCTTGAATGTGCA
101716 TTGATGTACA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
21 15 0.52
23 14 0.48
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.23
Consensus pattern (21 bp):
CCTTGAATGTGCACCGATACA
Found at i:101721 original size:23 final size:22
Alignment explanation
Indices: 101629--101721 Score: 79
Period size: 23 Copynumber: 4.3 Consensus size: 22
101619 TGCTTCATGT
101629 ATCGAT-ACACC-T-AATAGTGC
1 ATCGATGACACCTTGAAT-GTGC
*
101649 ATCAATG-CATCCTTGAATGTGC
1 ATCGATGACA-CCTTGAATGTGC
* *
101671 ATCGAT-ACACCATGAAGGTGC
1 ATCGATGACACCTTGAATGTGC
*
101692 ACCGATGCACACCTTGAATGTGC
1 ATCGATG-ACACCTTGAATGTGC
*
101715 ATTGATG
1 ATCGATG
101722 TACAGGGTCA
Statistics
Matches: 57, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
20 7 0.12
21 17 0.30
22 12 0.21
23 21 0.37
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (22 bp):
ATCGATGACACCTTGAATGTGC
Found at i:103298 original size:21 final size:21
Alignment explanation
Indices: 103256--103299 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
103246 ACCCCGGGAG
*
103256 CTAGCTCTTCATGAGCTGCTC
1 CTAGCTCTTCATGAGCTCCTC
*
103277 CTAGCTCTTC-TCGTGCTCCTC
1 CTAGCTCTTCAT-GAGCTCCTC
103298 CT
1 CT
103300 CCTCCTCCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.09, C:0.39, G:0.16, T:0.36
Consensus pattern (21 bp):
CTAGCTCTTCATGAGCTCCTC
Found at i:104520 original size:65 final size:65
Alignment explanation
Indices: 104340--104549 Score: 198
Period size: 65 Copynumber: 3.2 Consensus size: 65
104330 TTTATCAAAG
* * * * * **
104340 TGATGCACCGATGCACCA-ATCCATGCATCGATGCACCATGAATTAAATTG-AACATCGAATGCA
1 TGATGCATCGATGCACCATA-CCATGCACCGATGCACTAAGGATTTTA-TGAAACATCGAATGCA
104403 TT
64 TT
*
104405 TCATGCATCGATGCA-CATACCATGCACCGATGCACTAAGGATTTTATGAAAACATCGAATGCAT
1 TGATGCATCGATGCACCATACCATGCACCGATGCACTAAGGATTTTATG-AAACATCGAATGCAT
104469 T
65 T
* * * *
104470 TGATGCATCGATGCACCA-GCCATGCATCGATGCAC-ACTGGCTATTT-TGAAACATCGAATGCA
1 TGATGCATCGATGCACCATACCATGCACCGATGCACTA-AGGAT-TTTATGAAACATCGAATGCA
*
104532 CT
64 TT
* *
104534 TGATACATCGCTGCAC
1 TGATGCATCGATGCAC
104550 TCTTAGTGTA
Statistics
Matches: 123, Mismatches: 16, Indels: 13
0.81 0.11 0.09
Matches are distributed among these distances:
63 2 0.02
64 53 0.43
65 63 0.51
66 5 0.04
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (65 bp):
TGATGCATCGATGCACCATACCATGCACCGATGCACTAAGGATTTTATGAAACATCGAATGCATT
Found at i:128454 original size:20 final size:19
Alignment explanation
Indices: 128417--128455 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
128407 AAGTAAAGAT
**
128417 GTGAAAACATATGTTATGC
1 GTGAAAACATATAATATGC
128436 GTGAAAATCATATAATATGC
1 GTGAAAA-CATATAATATGC
128456 AAGTGAATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (19 bp):
GTGAAAACATATAATATGC
Found at i:137377 original size:20 final size:21
Alignment explanation
Indices: 137352--137400 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
137342 CATTCAATGT
137352 TATTAGTTCATAGGCATT-CA
1 TATTAGTTCATAGGCATTACA
* * * *
137372 TATTAGCTCCTAGGCTTTATA
1 TATTAGTTCATAGGCATTACA
137393 TATTAGTT
1 TATTAGTT
137401 TACAAATAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.45
Consensus pattern (21 bp):
TATTAGTTCATAGGCATTACA
Found at i:146286 original size:22 final size:23
Alignment explanation
Indices: 146261--146303 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
146251 TCCACAAGAT
146261 ATGT-CCT-TTGACATTTCAAAGG
1 ATGTACCTCTTGACA-TTCAAAGG
*
146283 ATGTACCTCTTGATATTCAAA
1 ATGTACCTCTTGACATTCAAA
146304 ATAATGAGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 9 0.50
24 5 0.28
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (23 bp):
ATGTACCTCTTGACATTCAAAGG
Found at i:152375 original size:34 final size:33
Alignment explanation
Indices: 152331--152399 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 33
152321 ATACAATCTG
152331 TCCATCACCATTATCA-CGCCAATAACATCATCCT
1 TCCATCACCATT-TCATCGCCAATAA-ATCATCCT
* * *
152365 TCCATTACCATTTCATCTCCATTAAATCATCCT
1 TCCATCACCATTTCATCGCCAATAAATCATCCT
152398 TC
1 TC
152400 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 13 0.42
34 18 0.58
ACGTcount: A:0.29, C:0.36, G:0.01, T:0.33
Consensus pattern (33 bp):
TCCATCACCATTTCATCGCCAATAAATCATCCT
Found at i:152767 original size:12 final size:11
Alignment explanation
Indices: 152752--152785 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
152742 AAAAGGCAAC
152752 AAGAAAGAAGAA
1 AAGAAA-AAGAA
152764 AAGAAAAGAGAA
1 AAGAAAA-AGAA
152776 AAGAAAAAGA
1 AAGAAAAAGA
152786 CTCCTACAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.19
12 17 0.81
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (11 bp):
AAGAAAAAGAA
Found at i:156722 original size:13 final size:11
Alignment explanation
Indices: 156682--156765 Score: 73
Period size: 11 Copynumber: 7.2 Consensus size: 11
156672 ACAATCTGTC
156682 CATCACCATAT
1 CATCACCATAT
*
156693 CA-CGCCTATAT
1 CATCACC-ATAT
156704 CATCACCATAGT
1 CATCACCATA-T
156716 CCATCACCATTAT
1 -CATCACCA-TAT
*
156729 CA-CGCCTATAT
1 CATCACC-ATAT
156740 CATCACCATATT
1 CATCACCATA-T
156752 CCATCACCATAT
1 -CATCACCATAT
156764 CA
1 CA
156766 CGCCAATAAC
Statistics
Matches: 60, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
10 3 0.05
11 24 0.40
12 12 0.20
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.37, G:0.04, T:0.27
Consensus pattern (11 bp):
CATCACCATAT
Found at i:156737 original size:36 final size:35
Alignment explanation
Indices: 156679--156779 Score: 166
Period size: 36 Copynumber: 2.9 Consensus size: 35
156669 GATACAATCT
156679 GTCCATCACCATATCACGCCTATATCATCACCATA
1 GTCCATCACCATATCACGCCTATATCATCACCATA
156714 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCA-TATCACGCCTATATCATCACCATA
* * *
156750 TTCCATCACCATATCACGCCAATAACATCA
1 GTCCATCACCATATCACGCCTATATCATCA
156780 TCCTTACATT
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
35 28 0.45
36 34 0.55
ACGTcount: A:0.33, C:0.37, G:0.05, T:0.26
Consensus pattern (35 bp):
GTCCATCACCATATCACGCCTATATCATCACCATA
Found at i:157960 original size:18 final size:18
Alignment explanation
Indices: 157930--157965 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
157920 AGTGCTTCAA
157930 CTTTGTTTCTTTTCTTTT
1 CTTTGTTTCTTTTCTTTT
157948 CTTTGCTTT-TTTTCTTTT
1 CTTTG-TTTCTTTTCTTTT
157966 TTTCTTAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.00, C:0.17, G:0.06, T:0.78
Consensus pattern (18 bp):
CTTTGTTTCTTTTCTTTT
Found at i:160296 original size:19 final size:20
Alignment explanation
Indices: 160249--160299 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
160239 GAAACCCCTT
**
160249 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
160269 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
160288 TGAAGATACATG
1 TGAAAATACATG
160300 CTCTTGGCTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Done.