Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005214.1 Hibiscus syriacus cultivar Beakdansim tig00011801_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: 82050
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.32
Found at i:9135 original size:18 final size:18
Alignment explanation
Indices: 9104--9156 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
9094 ACTGAAAATT
*
9104 TGTCCTGAAAGACCACTA
1 TGTCCCGAAAGACCACTA
*
9122 TGTCCCGAAGGACCACTA
1 TGTCCCGAAAGACCACTA
* *
9140 CGTCCCGAATGACCACT
1 TGTCCCGAAAGACCACT
9157 TATAATCCCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.28, C:0.34, G:0.19, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAAGACCACTA
Found at i:16924 original size:20 final size:20
Alignment explanation
Indices: 16901--16943 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
16891 AATCCACCAC
*
16901 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGCTCCTAA
* *
16921 ATGCATCTAAATGGTCCTAA
1 ATGCAACTAAATGCTCCTAA
16941 ATG
1 ATG
16944 GGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGCTCCTAA
Found at i:18543 original size:13 final size:13
Alignment explanation
Indices: 18527--18566 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
18517 AGGAAACTAG
18527 AAAGTGAAAGTAA
1 AAAGTGAAAGTAA
* *
18540 AAAGAGAAAGTGA
1 AAAGTGAAAGTAA
18553 AAAGTGAAAAGTAA
1 AAAGTG-AAAGTAA
18567 GTGGGGTAGG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.62, C:0.00, G:0.25, T:0.12
Consensus pattern (13 bp):
AAAGTGAAAGTAA
Found at i:26269 original size:20 final size:20
Alignment explanation
Indices: 26246--26288 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
26236 AATCCACCAC
*
26246 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGCTCCTAA
* *
26266 ATGCATCTAAATGGTCCTAA
1 ATGCAACTAAATGCTCCTAA
26286 ATG
1 ATG
26289 GGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGCTCCTAA
Found at i:31472 original size:21 final size:19
Alignment explanation
Indices: 31449--31518 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 19
31439 ATAGGCCGTC
31449 AGTATCGATACTGAGCCTGT
1 AGTATCGATACTGAGCCT-T
31469 CAGTATCGATACTGA-CCTT
1 -AGTATCGATACTGAGCCTT
31488 AGGGTATCGATACTG-GCCTT
1 A--GTATCGATACTGAGCCTT
*
31508 AGTAGCGATAC
1 AGTATCGATAC
31519 CAATTTAAGC
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
18 10 0.22
19 1 0.02
20 20 0.44
21 14 0.31
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (19 bp):
AGTATCGATACTGAGCCTT
Found at i:31620 original size:18 final size:20
Alignment explanation
Indices: 31573--31622 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
31563 CCTGATGTAG
31573 AGTATCGATACTCTCCTAAC
1 AGTATCGATACTCTCCTAAC
*
31593 AGTATTGATACTC-CCATAA-
1 AGTATCGATACTCTCC-TAAC
31612 A-TATCGATACT
1 AGTATCGATACT
31623 AATTTGGCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 9 0.33
19 3 0.11
20 15 0.56
ACGTcount: A:0.34, C:0.24, G:0.10, T:0.32
Consensus pattern (20 bp):
AGTATCGATACTCTCCTAAC
Found at i:33420 original size:120 final size:123
Alignment explanation
Indices: 33212--33437 Score: 363
Period size: 120 Copynumber: 1.9 Consensus size: 123
33202 GAATGTTCAA
* *
33212 TATTTATTATATGACATGATAAATAATATTTAATTTATTTATATTCATTTTGTTTTCAATTCAAA
1 TATTCATTATATGACATGATAAATAATATTTAATTTATTTATATCCATTTTGTTTTCAATTCAAA
**
33277 GAAAATAATAAAAATTATTTTAATTAAAATTGACAGTAAAACGGAAAATAATAAAAAT
66 GAAAATAATAAAAATTATTTTAATTAAAATAAACAGTAAAACGGAAAATAATAAAAAT
33335 TATTCATTATATGACACT-A-AAA-AATATTTAATTTATTTATATCCATTTT-TTTTCAATT-AA
1 TATTCATTATATGACA-TGATAAATAATATTTAATTTATTTATATCCATTTTGTTTTCAATTCAA
33395 ATGAAAATAATAAAAATTATTTTAATTAAAATAAACAGTAAAA
65 A-GAAAATAATAAAAATTATTTTAATTAAAATAAACAGTAAAA
33438 TAAAATTATA
Statistics
Matches: 97, Mismatches: 4, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
119 3 0.03
120 48 0.49
121 26 0.27
122 3 0.03
123 16 0.16
124 1 0.01
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.41
Consensus pattern (123 bp):
TATTCATTATATGACATGATAAATAATATTTAATTTATTTATATCCATTTTGTTTTCAATTCAAA
GAAAATAATAAAAATTATTTTAATTAAAATAAACAGTAAAACGGAAAATAATAAAAAT
Found at i:33945 original size:5 final size:5
Alignment explanation
Indices: 33930--33965 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
33920 AGAAAGTCAT
* *
33930 TTATA TCATA TTATA TTATA TTATA TCATA TTATA T
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA T
33966 CACATCACAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.56
Consensus pattern (5 bp):
TTATA
Found at i:33945 original size:10 final size:10
Alignment explanation
Indices: 33926--33967 Score: 68
Period size: 10 Copynumber: 4.3 Consensus size: 10
33916 CGAAAGAAAG
33926 TCAT-TTATA
1 TCATATTATA
33935 TCATATTATA
1 TCATATTATA
*
33945 TTATATTATA
1 TCATATTATA
33955 TCATATTATA
1 TCATATTATA
33965 TCA
1 TCA
33968 CATCACATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
9 4 0.13
10 26 0.87
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (10 bp):
TCATATTATA
Found at i:33972 original size:15 final size:15
Alignment explanation
Indices: 33926--33977 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
33916 CGAAAGAAAG
33926 TCAT-TTATATCATA
1 TCATATTATATCATA
* *
33940 TTATATTATATTATA
1 TCATATTATATCATA
*
33955 TCATATTATATCACA
1 TCATATTATATCATA
*
33970 TCACATTA
1 TCATATTA
33978 CATTATCAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
14 3 0.10
15 28 0.90
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.48
Consensus pattern (15 bp):
TCATATTATATCATA
Found at i:34909 original size:26 final size:27
Alignment explanation
Indices: 34881--34981 Score: 82
Period size: 28 Copynumber: 3.7 Consensus size: 27
34871 AAATTACTAT
34881 TATAATAATTTATAATAATATATTTT-
1 TATAATAATTTATAATAATATATTTTA
** *
34907 TATTTTAATGGTGTAGAATAA-AT-TTTTGA
1 TATAATAAT--T-TATAATAATATATTTT-A
*
34936 TATAATAATTTATAATAGTATATTTTA
1 TATAATAATTTATAATAATATATTTTA
* *
34963 TTTCAATAATATATAATAA
1 TAT-AATAATTTATAATAA
34982 ACTCTTTCTA
Statistics
Matches: 57, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
26 13 0.23
27 10 0.18
28 20 0.35
29 14 0.25
ACGTcount: A:0.44, C:0.01, G:0.06, T:0.50
Consensus pattern (27 bp):
TATAATAATTTATAATAATATATTTTA
Found at i:37113 original size:3 final size:3
Alignment explanation
Indices: 37105--37290 Score: 241
Period size: 3 Copynumber: 61.7 Consensus size: 3
37095 TTATTTATTA
*
37105 AAT AAT AAT AAT ATAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT
* * *
37152 AAAT ACT AAT AAT AAT AAT AAT AAT ATT AAT AAT GAT AAT AAT AAT
1 -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* ** *
37198 ATT AAT AAT AAT AAT AA- AAT GCT AAT AAT AAT AAT AAT ACT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
37245 AAT AAT AAT -AT AAT AAT AAT ATT AAT ATT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
37291 AATGGATAAA
Statistics
Matches: 158, Mismatches: 20, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
2 4 0.03
3 145 0.92
4 9 0.06
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:38005 original size:113 final size:113
Alignment explanation
Indices: 37587--38379 Score: 1176
Period size: 113 Copynumber: 6.9 Consensus size: 113
37577 GATATCAAAC
* *
37587 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* ** * * * *
37652 CATGAACTTTCTTTGGCCATGTTGATCCATCAAATGATGAATTTAAACA
66 -ATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAAGCA
* *
37701 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * * *
37766 CATGAATTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGTA
66 -ATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAAGCA
*
37815 AAAGGTTGAACAAATTC-T-TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
37878 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGCA
66 ATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAAGCA
37926 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
37991 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGCA
66 ATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAAGCA
*
38039 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
38104 ATGAACTCTTCTTCTGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCA
66 ATGAACT-TTC-TCTGGAAAAG-ATGATCCATCAAATGATGAATTCAAGCA
* *
38155 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGATGAGTTCTTCTC
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTC--A-GATGAGTTCTTCTC
* * *
38220 ATTATGAACTCTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTCAAGCA
63 ATTATGAA--CTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAAGCA
*
38273 AAAGGTTGAACAAGTTCTTCTCATTATGAAATTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
38338 ATGAACCTTCTCTGGTAATGATGATCCATCAAATGATGAATT
66 ATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATT
38380 TGAATCTTTG
Statistics
Matches: 632, Mismatches: 37, Indels: 21
0.92 0.05 0.03
Matches are distributed among these distances:
111 62 0.10
112 45 0.07
113 198 0.31
114 118 0.19
115 32 0.05
116 70 0.11
118 72 0.11
119 30 0.05
120 3 0.00
121 2 0.00
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (113 bp):
AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAAGCA
Found at i:38338 original size:347 final size:338
Alignment explanation
Indices: 37587--38379 Score: 1201
Period size: 347 Copynumber: 2.3 Consensus size: 338
37577 GATATCAAAC
* *
37587 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* ** * *
37652 CATGAACTTTCTTTGGCCATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAGTT
66 -ATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAGTT
*
37717 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTCATGAATTTTCTCTGG
130 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTCATGAATCTTCTCTGG
* * * *
37782 AAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCATTATGAACTTC
195 AAAAGATGATCCACCAAATGATGAATTCAAGCAAAAAGTTGAACAAATTCTTCATTATGAACTTC
37847 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCACCAAAT
260 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCACCAAAT
* *
37912 GATGGATTCAGGCA
325 GATGAATTCAAGCA
37926 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * ** *
37991 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGCAAAAGGTTGAACAAGTTC
66 ATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAGTTC
38056 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATT-ATGAACTCTTCTTCTG
131 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTCATGAA-TCTTC-TCTG
* * *
38120 GAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAA
194 GAAAAG-ATGATCCACCAAATGATGAATTCAAGCAAAAAGTTGAACAAATTC-T-TCATTATGAA
* * *
38185 CTTCTTCTTTCTTCTTCAGATGATGAGTTCTTCTCATTATGAACTCTTTCTCTGGAAATGTTGAT
256 CTTCTTCTTCCTTCTTC--A-GATGAGTTCTTCTCATTATGAA--CTTTCTCTGGAAAAGATGAT
* *
38250 CCATCAAGTGATGAATTCAAGCA
316 CCACCAAATGATGAATTCAAGCA
*
38273 AAAGGTTGAACAAGTTCTTCTCATTATGAAATTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
38338 ATGAACCTTCTCTGGTAATGATGATCCATCAAATGATGAATT
66 ATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAATT
38380 TGAATCTTTG
Statistics
Matches: 410, Mismatches: 34, Indels: 12
0.90 0.07 0.03
Matches are distributed among these distances:
337 5 0.01
338 106 0.26
339 73 0.18
340 38 0.09
341 1 0.00
342 26 0.06
344 1 0.00
345 22 0.05
347 138 0.34
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (338 bp):
AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAGTTC
TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTCATGAATCTTCTCTGGA
AAAGATGATCCACCAAATGATGAATTCAAGCAAAAAGTTGAACAAATTCTTCATTATGAACTTCT
TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCACCAAATG
ATGAATTCAAGCA
Found at i:38953 original size:9 final size:9
Alignment explanation
Indices: 38935--39031 Score: 65
Period size: 9 Copynumber: 10.3 Consensus size: 9
38925 ACCTTGACCC
*
38935 CTTTTTTTT
1 CTTTTTCTT
38944 CTTCTTT-TT
1 CTT-TTTCTT
38953 CTTTTTCTT
1 CTTTTTCTT
*
38962 CTTTTCCCTT
1 CTTTT-TCTT
*
38972 TTTTTTCTTTT
1 CTTTTTC--TT
*
38983 CTTTCTCTT
1 CTTTTTCTT
38992 CTTTTTCTTTT
1 CTTTTTC--TT
39003 CTTTTTTCTT
1 C-TTTTTCTT
*
39013 -TTTTTTTT
1 CTTTTTCTT
39021 CTTTTT-TT
1 CTTTTTCTT
39029 CTT
1 CTT
39032 CAAGCATAAT
Statistics
Matches: 72, Mismatches: 7, Indels: 19
0.73 0.07 0.19
Matches are distributed among these distances:
8 15 0.21
9 29 0.40
10 12 0.17
11 10 0.14
12 6 0.08
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (9 bp):
CTTTTTCTT
Found at i:38956 original size:6 final size:6
Alignment explanation
Indices: 38935--39026 Score: 68
Period size: 6 Copynumber: 15.0 Consensus size: 6
38925 ACCTTGACCC
**
38935 CTTTTT -TTTCTT CTTTTT CTTTTT CTTCTTTT CCCTTT -TTTTT C-TTTT
1 CTTTTT CTTT-TT CTTTTT CTTTTT C-T-TTTT CTTTTT CTTTTT CTTTTT
38983 CTTTCTCTT CTTTTT C-TTTT CTTTTTT CTTTTT -TTTTT CTTTTT
1 C-TT-T-TT CTTTTT CTTTTT C-TTTTT CTTTTT CTTTTT CTTTTT
39027 TTCTTCAAGC
Statistics
Matches: 70, Mismatches: 4, Indels: 24
0.71 0.04 0.24
Matches are distributed among these distances:
5 21 0.30
6 27 0.39
7 11 0.16
8 8 0.11
9 3 0.04
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
CTTTTT
Found at i:38971 original size:34 final size:32
Alignment explanation
Indices: 38933--39031 Score: 112
Period size: 34 Copynumber: 2.9 Consensus size: 32
38923 TCACCTTGAC
38933 CCCTTTTTTTTCTTCTTTTTCTTTTTCTTCTTTT
1 CCCTTTTTTTTCTT-TTTTTCTTTTT-TTCTTTT
38967 CCCTTTTTTTTCTTTTCTTTCTCTTCTTTTTCTTTT
1 CCCTTTTTTTTC-TTT-TTT-TCTT-TTTTTCTTTT
*
39003 --CTTTTTTCTTTTTTTTTTCTTTTTTTCTT
1 CCCTTTTTT-TTCTTTTTTTCTTTTTTTCTT
39032 CAAGCATAAT
Statistics
Matches: 59, Mismatches: 1, Indels: 13
0.81 0.01 0.18
Matches are distributed among these distances:
31 8 0.14
32 4 0.07
33 3 0.05
34 23 0.39
35 7 0.12
36 11 0.19
37 3 0.05
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (32 bp):
CCCTTTTTTTTCTTTTTTTCTTTTTTTCTTTT
Found at i:38987 original size:20 final size:20
Alignment explanation
Indices: 38951--39024 Score: 82
Period size: 20 Copynumber: 3.9 Consensus size: 20
38941 TTTCTTCTTT
*
38951 TTCTTTTTCTTCT-TTTCCC
1 TTCTTTTTCTTTTCTTTCCC
* *
38970 TTTTTTTTCTTTTCTTTCTC
1 TTCTTTTTCTTTTCTTTCCC
*
38990 TTCTTTTTCTTTTCTTT--T
1 TTCTTTTTCTTTTCTTTCCC
*
39008 TTCTTTTTTTTTTCTTT
1 TTCTTTTTCTTTTCTTT
39025 TTTTCTTCAA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
18 16 0.33
19 11 0.23
20 21 0.44
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (20 bp):
TTCTTTTTCTTTTCTTTCCC
Found at i:38991 original size:11 final size:11
Alignment explanation
Indices: 38940--39030 Score: 54
Period size: 10 Copynumber: 8.9 Consensus size: 11
38930 GACCCCTTTT
38940 TTTTC-TTCT-
1 TTTTCTTTCTC
*
38949 TTTTCTTTTTC
1 TTTTCTTTCTC
* *
38960 TTCT-TTTCCC
1 TTTTCTTTCTC
38970 TTTT-TTT-TC
1 TTTTCTTTCTC
38979 TTTTCTTTCTC
1 TTTTCTTTCTC
*
38990 --TTCTTTTTC
1 TTTTCTTTCTC
*
38999 TTTTCTTTTTTC
1 TTTTC-TTTCTC
* *
39011 TTTTTTTTTTC
1 TTTTCTTTCTC
39022 TTTT-TTTCT
1 TTTTCTTTCT
39031 TCAAGCATAA
Statistics
Matches: 66, Mismatches: 9, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
9 18 0.27
10 20 0.30
11 18 0.27
12 10 0.15
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTCTTTCTC
Found at i:51709 original size:3 final size:3
Alignment explanation
Indices: 51701--51876 Score: 239
Period size: 3 Copynumber: 58.7 Consensus size: 3
51691 TTATTTATTA
*
51701 AAT AAT AAT ATAT AAT AAT AAT -AT AAT ATT AAT AAT AAT AAT AAAT
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
* * *
51747 ACT AAT AAT AAT AAT AAT AAT ATT AAT AAT GAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
** *
51795 AAT AAT AAT AA- AAT GCT AAT AAT AAT AAT ACT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
51842 AAT AAT AAT ATT AAT ATT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
51877 AATGGATAAA
Statistics
Matches: 151, Mismatches: 18, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
2 4 0.03
3 141 0.93
4 6 0.04
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:52692 original size:14 final size:16
Alignment explanation
Indices: 52659--52694 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
52649 CGAAATACAT
52659 AAATC-ATATATCAGG
1 AAATCAATATATCAGG
52674 AAATCAATAT-TCAGG
1 AAATCAATATATCAGG
52689 -AATCAA
1 AAATCAA
52695 GTATCATGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 6 0.30
15 10 0.50
16 4 0.20
ACGTcount: A:0.50, C:0.14, G:0.11, T:0.25
Consensus pattern (16 bp):
AAATCAATATATCAGG
Found at i:53475 original size:29 final size:29
Alignment explanation
Indices: 53443--53625 Score: 138
Period size: 29 Copynumber: 6.4 Consensus size: 29
53433 TTAAATTACA
* *
53443 AAAATAGCACCATTTTGAAATTAATTTCC
1 AAAATAGCACCATTTTTAAAATAATTTCC
* * * *
53472 AAAATAGCATCATTTTCAAAATAATTACT
1 AAAATAGCACCATTTTTAAAATAATTTCC
* * * **
53501 AAAATATCACTATTTTTAAAAAAAAAT-C
1 AAAATAGCACCATTTTTAAAATAATTTCC
* * * *
53529 AAAATTGTCA-CTTTTTTAAAA-AAATTAC
1 AAAATAG-CACCATTTTTAAAATAATTTCC
*
53557 AAAATAGCACCATTTTTAAAATAATTACC
1 AAAATAGCACCATTTTTAAAATAATTTCC
* *** * *
53586 AGAATAGCACCATTTCCCAAATAATTACT
1 AAAATAGCACCATTTTTAAAATAATTTCC
53615 AAAATAGCACC
1 AAAATAGCACC
53626 TGGTCAACGG
Statistics
Matches: 120, Mismatches: 30, Indels: 8
0.76 0.19 0.05
Matches are distributed among these distances:
27 6 0.05
28 31 0.26
29 83 0.69
ACGTcount: A:0.48, C:0.16, G:0.04, T:0.32
Consensus pattern (29 bp):
AAAATAGCACCATTTTTAAAATAATTTCC
Found at i:53559 original size:28 final size:28
Alignment explanation
Indices: 53484--53584 Score: 82
Period size: 28 Copynumber: 3.6 Consensus size: 28
53474 AATAGCATCA
* * *
53484 TTTTCAAAATAATTACTAAAA-TATCACT
1 TTTTTAAAAAAATTAC-AAAATTGTCACT
*
53512 ATTTTTAAAAAAA-AATCAAAATTGTCACT
1 -TTTTTAAAAAAATTA-CAAAATTGTCACT
* *
53541 TTTTTAAAAAAATTACAAAATAG-CACCA
1 TTTTTAAAAAAATTACAAAATTGTCA-CT
*
53569 TTTTTAAAATAATTAC
1 TTTTTAAAAAAATTAC
53585 CAGAATAGCA
Statistics
Matches: 60, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
27 2 0.03
28 40 0.67
29 18 0.30
ACGTcount: A:0.50, C:0.12, G:0.02, T:0.37
Consensus pattern (28 bp):
TTTTTAAAAAAATTACAAAATTGTCACT
Found at i:53664 original size:18 final size:18
Alignment explanation
Indices: 53641--53690 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
53631 AACGGTAAAT
53641 GGGTCGGGTCGGGTCAAC
1 GGGTCGGGTCGGGTCAAC
* * *
53659 GGGTCGAGCCGGGTCATC
1 GGGTCGGGTCGGGTCAAC
* *
53677 AGGTCAGGTCGGGT
1 GGGTCGGGTCGGGT
53691 TGCAACCGGT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.12, C:0.22, G:0.48, T:0.18
Consensus pattern (18 bp):
GGGTCGGGTCGGGTCAAC
Found at i:58323 original size:20 final size:20
Alignment explanation
Indices: 58298--58342 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
58288 GCTCCATACC
*
58298 CAGTCGCTCTATTTCCTCAG
1 CAGTCGCTCAATTTCCTCAG
58318 CAGTCGCTCAATTTCCTCAG
1 CAGTCGCTCAATTTCCTCAG
58338 CAGTC
1 CAGTC
58343 TTGGCTATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.18, C:0.36, G:0.16, T:0.31
Consensus pattern (20 bp):
CAGTCGCTCAATTTCCTCAG
Found at i:59923 original size:14 final size:14
Alignment explanation
Indices: 59889--59931 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 14
59879 CCAAAATACA
59889 GAAATCAGATATCAG
1 GAAATCA-ATATCAG
59904 GAAATCAATATTCAG
1 GAAATCAATA-TCAG
59919 G-AATCAAGTATCA
1 GAAATCAA-TATCA
59932 TATCATGTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.47, C:0.14, G:0.16, T:0.23
Consensus pattern (14 bp):
GAAATCAATATCAG
Found at i:60688 original size:29 final size:28
Alignment explanation
Indices: 60656--60789 Score: 133
Period size: 29 Copynumber: 4.6 Consensus size: 28
60646 TTTTTTTTTA
* *
60656 AATTACAAAAATAGCACCATTTTGAAATT
1 AATTACCAAAATAGCACCATTTTCAAA-T
* * *
60685 AATTACCTAAATAGCATCATTTTTAACAT
1 AATTACCAAAATAGCACCATTTTCAA-AT
* * *
60714 AATTACTAAAATATCACCCTTTTCAAAAT
1 AATTACCAAAATAGCACCATTTTC-AAAT
* * *
60743 AATTACCAGAATAGCACCATTTCCCAAAC
1 AATTACCAAAATAGCACCATTT-TCAAAT
60772 AATTACCAAAATAGCACC
1 AATTACCAAAATAGCACC
60790 CAGTCAACGG
Statistics
Matches: 85, Mismatches: 17, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
29 81 0.95
30 4 0.05
ACGTcount: A:0.45, C:0.22, G:0.04, T:0.29
Consensus pattern (28 bp):
AATTACCAAAATAGCACCATTTTCAAAT
Found at i:60776 original size:58 final size:58
Alignment explanation
Indices: 60656--60790 Score: 148
Period size: 58 Copynumber: 2.3 Consensus size: 58
60646 TTTTTTTTTA
* * * * ** *
60656 AATTACAAAAATAGCACCATTTTGAAATTAATTACCTAAATAGCATCATTTTTAACAT
1 AATTACAAAAATAGCACCCTTTTCAAAATAATTACCTAAATAGCACCATTTCCAACAC
* *
60714 AATTACTAAAATATCACCCTTTTCAAAATAATTACC-AGAATAGCACCATTTCCCAA-AC
1 AATTACAAAAATAGCACCCTTTTCAAAATAATTACCTA-AATAGCACCATTT-CCAACAC
*
60772 AATTACCAAAATAGCACCC
1 AATTACAAAAATAGCACCC
60791 AGTCAACGGT
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
57 1 0.02
58 61 0.95
59 2 0.03
ACGTcount: A:0.44, C:0.22, G:0.04, T:0.29
Consensus pattern (58 bp):
AATTACAAAAATAGCACCCTTTTCAAAATAATTACCTAAATAGCACCATTTCCAACAC
Found at i:65053 original size:26 final size:27
Alignment explanation
Indices: 65013--65072 Score: 106
Period size: 26 Copynumber: 2.3 Consensus size: 27
65003 TATTGTCGAA
65013 GTCT-GCAGTGTAAACCAATGCAGGCT
1 GTCTGGCAGTGTAAACCAATGCAGGCT
65039 GT-TGGCAGTGTAAACCAATGCAGGCT
1 GTCTGGCAGTGTAAACCAATGCAGGCT
65065 GTCTGGCA
1 GTCTGGCA
65073 TCAGATCTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
25 1 0.03
26 26 0.81
27 5 0.16
ACGTcount: A:0.25, C:0.22, G:0.30, T:0.23
Consensus pattern (27 bp):
GTCTGGCAGTGTAAACCAATGCAGGCT
Found at i:67128 original size:14 final size:13
Alignment explanation
Indices: 67096--67143 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 13
67086 CAAATACATA
67096 AATCAGATATCAGG
1 AATCA-ATATCAGG
67110 AAATCAATATTCAGG
1 -AATCAATA-TCAGG
*
67125 AATCAAGTATCATG
1 AATCAA-TATCAGG
67139 AATCA
1 AATCA
67144 TGTCATAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 18 0.60
15 12 0.40
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.25
Consensus pattern (13 bp):
AATCAATATCAGG
Found at i:67914 original size:29 final size:29
Alignment explanation
Indices: 67863--67924 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
67853 CATTTTTTAA
* * * *
67863 AATTACGAAAATAGCACCATTTTGAAATT
1 AATTACCAAAATAACACCATTTTCAAAAT
* *
67892 AATTACCAAAATAACATCTTTTTCAAAAT
1 AATTACCAAAATAACACCATTTTCAAAAT
67921 AATT
1 AATT
67925 GCTAAAATGT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.47, C:0.15, G:0.05, T:0.34
Consensus pattern (29 bp):
AATTACCAAAATAACACCATTTTCAAAAT
Found at i:68015 original size:28 final size:28
Alignment explanation
Indices: 67911--68042 Score: 76
Period size: 28 Copynumber: 4.7 Consensus size: 28
67901 AATAACATCT
* *
67911 TTTTCAAAATAATTGCTAAA-ATGT-CTC
1 TTTTCAAAATAATTACCAAATA-GTACTC
* * * *
67938 TTTT-AAAAAAATTACGAAATTGTCACTTT
1 TTTTCAAAATAATTACCAAATAGT-AC-TC
* * *
67967 TTTTAAAAAAAATATA-AAAATAGTACTC
1 TTTTCAAAATAAT-TACCAAATAGTACTC
*
67995 TTTTCAAAATAATTACCAAATAGCAC-C
1 TTTTCAAAATAATTACCAAATAGTACTC
* *
68022 ATTTCCCAAATAATTACCAAA
1 -TTTTCAAAATAATTACCAAA
68043 ATCGCACCCG
Statistics
Matches: 83, Mismatches: 14, Indels: 15
0.74 0.12 0.13
Matches are distributed among these distances:
26 14 0.17
27 7 0.08
28 39 0.47
29 7 0.08
30 14 0.17
31 2 0.02
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (28 bp):
TTTTCAAAATAATTACCAAATAGTACTC
Found at i:69573 original size:21 final size:21
Alignment explanation
Indices: 69549--69588 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
69539 GAAAACGTTA
69549 AAATTAACATATTAGGTAATG
1 AAATTAACATATTAGGTAATG
* *
69570 AAATTAACATTTTATGTAA
1 AAATTAACATATTAGGTAA
69589 CGTTCTACCG
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:0.47, C:0.05, G:0.10, T:0.38
Consensus pattern (21 bp):
AAATTAACATATTAGGTAATG
Found at i:69682 original size:18 final size:18
Alignment explanation
Indices: 69659--69694 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
69649 TTAGGATGCC
69659 GTACAGCATACCTACCCT
1 GTACAGCATACCTACCCT
69677 GTACAGCATACCTACCCT
1 GTACAGCATACCTACCCT
69695 TTAATATCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.39, G:0.11, T:0.22
Consensus pattern (18 bp):
GTACAGCATACCTACCCT
Found at i:69851 original size:20 final size:21
Alignment explanation
Indices: 69826--69875 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
69816 GATCTCGAAT
69826 TCGCAACAC-AGGTTCCAAAA
1 TCGCAACACAAGGTTCCAAAA
* ** *
69846 TCGCAACGCAATTTTCCAAAT
1 TCGCAACACAAGGTTCCAAAA
69867 TCGCAACAC
1 TCGCAACAC
69876 GAACAGTGTT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.36, C:0.32, G:0.12, T:0.20
Consensus pattern (21 bp):
TCGCAACACAAGGTTCCAAAA
Found at i:69931 original size:41 final size:41
Alignment explanation
Indices: 69843--69938 Score: 122
Period size: 41 Copynumber: 2.3 Consensus size: 41
69833 ACAGGTTCCA
* *
69843 AAATCGCAACGCAATTTTCCAAATTCGCAACACGAACAGTG
1 AAATCGCAACGCGATTTTCCAAATTCGCAACACAAACAGTG
** * *
69884 TTATCGCAACGCGATTTTCCAAATTCGCAACGCAAATAGAT-
1 AAATCGCAACGCGATTTTCCAAATTCGCAACACAAACAG-TG
69925 AAATCGCAACGCGA
1 AAATCGCAACGCGA
69939 ATATGTAAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 45 0.98
42 1 0.02
ACGTcount: A:0.38, C:0.26, G:0.16, T:0.21
Consensus pattern (41 bp):
AAATCGCAACGCGATTTTCCAAATTCGCAACACAAACAGTG
Found at i:70031 original size:20 final size:20
Alignment explanation
Indices: 70006--70054 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
69996 AACAGTACTA
70006 TCGCAACGCGATTTTCAAAT
1 TCGCAACGCGATTTTCAAAT
* *
70026 TCGCAATGAGATTTTCAAAT
1 TCGCAACGCGATTTTCAAAT
70046 TCGCAACGC
1 TCGCAACGC
70055 TAATTACCGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (20 bp):
TCGCAACGCGATTTTCAAAT
Found at i:70064 original size:77 final size:78
Alignment explanation
Indices: 69957--70108 Score: 270
Period size: 77 Copynumber: 2.0 Consensus size: 78
69947 ATCATAACGC
*
69957 GATTTTCCAAAATCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGCGATTTTC
1 GATTTTCCAAAATCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGCGATTTAC
70022 AAATTCGCAATGA
66 AAATTCGCAATGA
*
70035 GATTTT-CAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGCGATTTAC
1 GATTTTCCAAAATCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGCGATTTAC
*
70099 AAATTTGCAA
66 AAATTCGCAA
70109 CGCTAATTAC
Statistics
Matches: 71, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
77 65 0.92
78 6 0.08
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (78 bp):
GATTTTCCAAAATCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGCGATTTAC
AAATTCGCAATGA
Found at i:70114 original size:57 final size:57
Alignment explanation
Indices: 70026--70169 Score: 198
Period size: 57 Copynumber: 2.5 Consensus size: 57
70016 ATTTTCAAAT
* * * *
70026 TCGCAATGAGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTA
1 TCGCAACGCGATTTACAAATTAGCAACGCTAATTACCGATATAGGTAAACAGTACTA
* * **
70083 TCGCAACGCGATTTACAAATTTGCAACGCTAATTACCGATGTAGGTAAACAGTGTTA
1 TCGCAACGCGATTTACAAATTAGCAACGCTAATTACCGATATAGGTAAACAGTACTA
*
70140 TCGCAACGCGATTTTCCAAATTAGCAACGC
1 TCGCAACGCGA-TTTACAAATTAGCAACGC
70170 GAATAGATAA
Statistics
Matches: 77, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
57 61 0.79
58 16 0.21
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (57 bp):
TCGCAACGCGATTTACAAATTAGCAACGCTAATTACCGATATAGGTAAACAGTACTA
Found at i:70227 original size:20 final size:20
Alignment explanation
Indices: 70204--70249 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
70194 AGTGTTATCA
70204 CAACGCGATTTTCAAATTCG
1 CAACGCGATTTTCAAATTCG
* *
70224 CAACGAGATTTTTAAATTCG
1 CAACGCGATTTTCAAATTCG
70244 CAACGC
1 CAACGC
70250 TAATTACCGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (20 bp):
CAACGCGATTTTCAAATTCG
Found at i:70293 original size:20 final size:20
Alignment explanation
Indices: 70268--70306 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
70258 GATATAGGTA
70268 AACAGTGTTATCGCAACGCG
1 AACAGTGTTATCGCAACGCG
70288 AACAGTGTTATCGCAACGC
1 AACAGTGTTATCGCAACGC
70307 TAATAGATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.26, G:0.23, T:0.21
Consensus pattern (20 bp):
AACAGTGTTATCGCAACGCG
Found at i:70346 original size:138 final size:135
Alignment explanation
Indices: 70083--70366 Score: 311
Period size: 138 Copynumber: 2.1 Consensus size: 135
70073 AACAGTACTA
* * *
70083 TCGCAACGCGATTTACAAATTTGCAACGCTAATTACCGATGTAGGTAAACAGTGTTATCGCAACG
1 TCGCAACGAGATTTACAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTGTTATCGCAACG
* *** *
70148 CGATTTTCCAAATTAGCAACGCGAATAGATAAATCGTAACGCGAACAGTGTTATCACAACGCGAT
66 CGA---TACAAATTAGCAACGCGAATAGATAAATCGTAACGCGAACAGTCAAATCACAACGAGAT
70213 TTTCAAAT
128 TTTCAAAT
**
70221 TCGCAACGAGATTTTTAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTGTTATCGCAACG
1 TCGCAACGAGATTTACAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTGTTATCGCAACG
** * * *** *
70286 CGA-ACAGTGTTATCGCAACGCTAATAGATAAATCGTATCGCG-ATTTTCCAAATTCGCAACGAG
66 CGATACA-AATTA--GCAACGCGAATAGATAAATCGTAACGCGAACAGT-CAAA-TCACAACGAG
70349 ATTTTCAAAT
126 ATTTTCAAAT
*
70359 TCTCAACG
1 TCGCAACG
70367 CTAATTACCG
Statistics
Matches: 122, Mismatches: 19, Indels: 10
0.81 0.13 0.07
Matches are distributed among these distances:
134 2 0.02
135 3 0.02
136 2 0.02
137 27 0.22
138 88 0.72
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (135 bp):
TCGCAACGAGATTTACAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTGTTATCGCAACG
CGATACAAATTAGCAACGCGAATAGATAAATCGTAACGCGAACAGTCAAATCACAACGAGATTTT
CAAAT
Found at i:70357 original size:20 final size:21
Alignment explanation
Indices: 70327--70366 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
70317 ATCGTATCGC
70327 GATTTTCCAAATTCGCAACGA
1 GATTTTCCAAATTCGCAACGA
*
70348 GATTTT-CAAATTCTCAACG
1 GATTTTCCAAATTCGCAACG
70367 CTAATTACCG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.33
Consensus pattern (21 bp):
GATTTTCCAAATTCGCAACGA
Found at i:70370 original size:118 final size:114
Alignment explanation
Indices: 70204--70520 Score: 368
Period size: 118 Copynumber: 2.7 Consensus size: 114
70194 AGTGTTATCA
*
70204 CAACGCGATTTTCAAATTCGCAACGAGATTTTTAAATTCGCAACGCTAATTACCGATATAGGTAA
1 CAACGCGATTTTCAAATTCGCAACGAGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAA
** * * **
70269 ACAGTGTTATCGCAACGCGAAC-AGTGTTATCGCA-ACGCTAATAGATAAATCG
66 ACAGTGTTATCGCAACGCGAACTACCGATATAG-ATAAAC-AAT-G-T-AATCG
* * *
70321 TATCGCGATTTTCCAAATTCGCAACGAGATTTTCAAATTCTCAACGCTAATTACCGATATAGGTA
1 CAACGCGATTTT-CAAATTCGCAACGAGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTA
** * * *
70386 AACAGTACTATCGCAACGCAAACTACCGATATAGATAAACAGTGTTATCG
65 AACAGTGTTATCGCAACGCGAACTACCGATATAGATAAACAATGTAATCG
* * * * * * *
70436 CAACGAGATTTACAAATTCGCAATGCGATTTTCAAATTCGCAACGCTAATTTCCAATATAGATAA
1 CAACGCGATTTTCAAATTCGCAACGAGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAA
70501 ACAGTGTTATCGCAACGCGA
66 ACAGTGTTATCGCAACGCGA
70521 TTTTCAAATT
Statistics
Matches: 169, Mismatches: 28, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
114 64 0.38
115 12 0.07
116 1 0.01
117 11 0.07
118 73 0.43
119 8 0.05
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (114 bp):
CAACGCGATTTTCAAATTCGCAACGAGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAA
ACAGTGTTATCGCAACGCGAACTACCGATATAGATAAACAATGTAATCG
Found at i:70413 original size:37 final size:37
Alignment explanation
Indices: 70362--70440 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
70352 TTCAAATTCT
* * *
70362 CAACGCTAATTACCGATATAGGTAAACAGTACTATCG
1 CAACGCAAACTACCGATATAGATAAACAGTACTATCG
**
70399 CAACGCAAACTACCGATATAGATAAACAGTGTTATCG
1 CAACGCAAACTACCGATATAGATAAACAGTACTATCG
70436 CAACG
1 CAACG
70441 AGATTTACAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.22
Consensus pattern (37 bp):
CAACGCAAACTACCGATATAGATAAACAGTACTATCG
Found at i:70458 original size:20 final size:20
Alignment explanation
Indices: 70433--70480 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
70423 AACAGTGTTA
70433 TCGCAACGAGATTTACAAAT
1 TCGCAACGAGATTTACAAAT
* * *
70453 TCGCAATGCGATTTTCAAAT
1 TCGCAACGAGATTTACAAAT
70473 TCGCAACG
1 TCGCAACG
70481 CTAATTTCCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (20 bp):
TCGCAACGAGATTTACAAAT
Found at i:70488 original size:20 final size:20
Alignment explanation
Indices: 70433--70488 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
70423 AACAGTGTTA
*
70433 TCGCAACGAG-ATTTACAAAT
1 TCGCAACGCGAATTT-CAAAT
* *
70453 TCGCAATGCGATTTTCAAAT
1 TCGCAACGCGAATTTCAAAT
*
70473 TCGCAACGCTAATTTC
1 TCGCAACGCGAATTTC
70489 CAATATAGAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
20 26 0.90
21 3 0.10
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.30
Consensus pattern (20 bp):
TCGCAACGCGAATTTCAAAT
Found at i:70541 original size:57 final size:57
Alignment explanation
Indices: 70453--70581 Score: 179
Period size: 57 Copynumber: 2.3 Consensus size: 57
70443 ATTTACAAAT
* **
70453 TCGCAATGCGATTTTCAAATTCGCAACGCTAATT-TCCAATATAGATAAACAGTGTTA
1 TCGCAACGCGATTTTCAAATTCGCAACGCTAATTAT-CAATATAGATAAACAGTACTA
* * *
70510 TCGCAACGCGATTTTCAAATTCGCAACGCTAATTATCGATGTAGGTAAACAGTACTA
1 TCGCAACGCGATTTTCAAATTCGCAACGCTAATTATCAATATAGATAAACAGTACTA
*
70567 TCGCAACGTGATTTT
1 TCGCAACGCGATTTT
70582 GGAAACTGTG
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
57 63 0.98
58 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (57 bp):
TCGCAACGCGATTTTCAAATTCGCAACGCTAATTATCAATATAGATAAACAGTACTA
Found at i:70634 original size:20 final size:20
Alignment explanation
Indices: 70579--70641 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
70569 GCAACGTGAT
70579 TTTGGAAACTGTGTTGCG-A
1 TTTGGAAACTGTGTTGCGAA
** * *
70598 TTTAAAAATTCGCGTTGCGAA
1 TTTGGAAACT-GTGTTGCGAA
*
70619 TTTGGAAACTGTGTTGCAAA
1 TTTGGAAACTGTGTTGCGAA
70639 TTT
1 TTT
70642 ACAAATCGCG
Statistics
Matches: 33, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
19 7 0.21
20 18 0.55
21 8 0.24
ACGTcount: A:0.27, C:0.11, G:0.24, T:0.38
Consensus pattern (20 bp):
TTTGGAAACTGTGTTGCGAA
Found at i:74945 original size:18 final size:18
Alignment explanation
Indices: 74918--74953 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
74908 GGGACTGACA
* *
74918 TAAATGATAAGTTTGAAT
1 TAAATAATAAGTCTGAAT
74936 TAAATAATAAGTCTGAAT
1 TAAATAATAAGTCTGAAT
74954 GGAAGGAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.14, T:0.36
Consensus pattern (18 bp):
TAAATAATAAGTCTGAAT
Done.