Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007730.1 Hibiscus syriacus cultivar Beakdansim tig00109982_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: 339569
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:149598 original size:3 final size:3
Alignment explanation
Indices: 149592--149668 Score: 74
Period size: 3 Copynumber: 27.0 Consensus size: 3
149582 AAATATTATT
* * * *
149592 TAA TAA TAA TTA TTA TAA TAA T-A TAA AAA TAA AAA TAA T-A TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
149636 TAA -AA TAA -AA TAA TAA TAA TAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
149669 AAAACAAATG
Statistics
Matches: 62, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
2 10 0.16
3 50 0.81
4 2 0.03
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:149623 original size:14 final size:14
Alignment explanation
Indices: 149606--149656 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
149596 AATAATTATT
149606 ATAATAATATAAAA
1 ATAATAATATAAAA
* *
149620 ATAAAAATAATATAA
1 ATAATAAT-ATAAAA
149635 ATAA-AATA-AAATA
1 ATAATAATATAAA-A
149648 ATAATAATA
1 ATAATAATA
149657 ATAATATAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
12 2 0.06
13 6 0.19
14 14 0.45
15 9 0.29
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
ATAATAATATAAAA
Found at i:149629 original size:20 final size:20
Alignment explanation
Indices: 149606--149668 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
149596 AATAATTATT
*
149606 ATAATAATATA-AAAATAAAA
1 ATAATAATAAATAAAAT-AAA
149626 ATAAT-ATAAATAAAATAAA
1 ATAATAATAAATAAAATAAA
*
149645 ATAATAAT-AATAATAATATA
1 ATAATAATAAATAA-AATAAA
149665 ATAA
1 ATAA
149669 AAAACAAATG
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
19 17 0.45
20 21 0.55
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
ATAATAATAAATAAAATAAA
Found at i:149633 original size:25 final size:25
Alignment explanation
Indices: 149605--149671 Score: 75
Period size: 25 Copynumber: 2.6 Consensus size: 25
149595 TAATAATTAT
149605 TATAATAATATAAAAATAAAAATAA
1 TATAATAATATAAAAATAAAAATAA
* *
149630 TATAAATAAAAT-AAAATAATAATAA
1 TAT-AATAATATAAAAATAAAAATAA
149655 TAATAAT-ATAATAAAAA
1 T-ATAATAAT-ATAAAAA
149672 ACAAATGGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
24 1 0.03
25 21 0.60
26 13 0.37
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (25 bp):
TATAATAATATAAAAATAAAAATAA
Found at i:149654 original size:31 final size:30
Alignment explanation
Indices: 149608--149670 Score: 90
Period size: 31 Copynumber: 2.1 Consensus size: 30
149598 TAATTATTAT
*
149608 AATAATATAAAAATAAAAATAATATAAATAA
1 AATAAAATAAAAATAAAAATAATAT-AATAA
* *
149639 AATAAAATAATAATAATAATAATATAATAA
1 AATAAAATAAAAATAAAAATAATATAATAA
149669 AA
1 AA
149671 AACAAATGGA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 7 0.24
31 22 0.76
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (30 bp):
AATAAAATAAAAATAAAAATAATATAATAA
Found at i:149667 original size:17 final size:17
Alignment explanation
Indices: 149592--149668 Score: 79
Period size: 17 Copynumber: 4.6 Consensus size: 17
149582 AAATATTATT
* *
149592 TAATAATAATTATTATAA
1 TAAT-ATAATAATAATAA
* *
149610 TAATATAAAAATAAAAA
1 TAATATAATAATAATAA
149627 TAATAT-A-AATAA-AA
1 TAATATAATAATAATAA
*
149641 TAAAATAATAATAATAA
1 TAATATAATAATAATAA
149658 TAATATAATAA
1 TAATATAATAA
149669 AAAACAAATG
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
14 7 0.14
15 6 0.12
16 6 0.12
17 27 0.54
18 4 0.08
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TAATATAATAATAATAA
Found at i:150035 original size:101 final size:105
Alignment explanation
Indices: 149917--150173 Score: 317
Period size: 101 Copynumber: 2.4 Consensus size: 105
149907 AATTGAACAA
* * * *
149917 ATTCTTCTTTTTCAGATGAATTCTTCTCATTGTGAACTCTTCTGGA-AATGTTGATCCATC-G-A
1 ATTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCT-GACAATGCTGATCCATCGGAA
*
149979 -TCAAGCTAAA-GTTGAACAAGTTCTTCACATTATGAACTT
65 TTCAAGCAAAAGGTTGAACAAGTTCTTCACATTATGAACTT
* *
150018 CTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGACAATGCTGATCCATCGAGT
1 ATTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCT-TCTGACAATGCTGATCCATC----
* *
150083 GATGAATTCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTT
61 G--GAATTCAAGCAAAAGGTTGAACAAGTTCTTCACATTATGAACTT
150130 ATTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCT
1 ATTCTTC-TTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCT
150174 TCCTCTTCAG
Statistics
Matches: 132, Mismatches: 11, Indels: 15
0.84 0.07 0.09
Matches are distributed among these distances:
101 38 0.29
102 15 0.11
109 1 0.01
110 1 0.01
111 8 0.06
112 36 0.27
113 33 0.25
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (105 bp):
ATTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTGACAATGCTGATCCATCGGAAT
TCAAGCAAAAGGTTGAACAAGTTCTTCACATTATGAACTT
Found at i:150190 original size:38 final size:39
Alignment explanation
Indices: 150109--150208 Score: 166
Period size: 38 Copynumber: 2.6 Consensus size: 39
150099 AGGTTGAACA
* *
150109 AGTTCTTCTCATTATGAACTTATTCTTCATTCTTCAGATG
1 AGTTCTTCTCATTATGAAC-TCTTCTTCACTCTTCAGATG
150149 AGTTCTTCTCATTATGAACTCTTCTTC-CTCTTCAGATG
1 AGTTCTTCTCATTATGAACTCTTCTTCACTCTTCAGATG
150187 AGTTCTTCTCATTATGAACTCT
1 AGTTCTTCTCATTATGAACTCT
150209 ACCTGGAAAT
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
38 32 0.55
39 7 0.12
40 19 0.33
ACGTcount: A:0.21, C:0.23, G:0.10, T:0.46
Consensus pattern (39 bp):
AGTTCTTCTCATTATGAACTCTTCTTCACTCTTCAGATG
Found at i:150196 original size:151 final size:159
Alignment explanation
Indices: 149997--150336 Score: 439
Period size: 151 Copynumber: 2.2 Consensus size: 159
149987 AAGTTGAACA
* *
149997 AGTTCTTCACATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCT
1 AGTTCTTCTCATTATGAAC-TCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCT
* * *
150062 -GACAAT-GC-TGAT-C-C-A-TC-GAGT-G-ATGAATTCGAGCAAAAGGTTGAACAAGTTCTTC
65 GGA-AATGGCTTGATGCTCTATTCTGACTGGAATGAAGTCAAGCAAAAGGTTGAACAAGTTCTTC
*
150117 TCATTATGAACTTATTCTTCATTCTTCAGATG
129 TCATTATGAACTTATTCTTC-CTCTTCAGATG
150149 AGTTCTTCTCATTATGAACTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG
1 AGTTCTTCTCATTATGAACTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG
* ** * *
150214 GAAATGGCTTTGTTGCTCTATTTCTTTCTGGAAATGGAGTCAAGCAAAAGGTTGAACGAGTTCTT
66 GAAATGGC-TTGATGCTCTA-TTCTGACTGG-AATGAAGTCAAGCAAAAGGTTGAACAAGTTCTT
* *
150279 CTCATTATGAGCTTCTTCTTCCTCTTCAGATG
128 CTCATTATGAACTTATTCTTCCTCTTCAGATG
150311 AGTTCTTCTCATTATGAACTCTTCTT
1 AGTTCTTCTCATTATGAACTCTTCTT
150337 GGCAATGTTG
Statistics
Matches: 162, Mismatches: 13, Indels: 16
0.85 0.07 0.08
Matches are distributed among these distances:
151 47 0.29
152 22 0.14
154 3 0.02
155 1 0.01
156 1 0.01
157 1 0.01
159 2 0.01
160 1 0.01
161 1 0.01
162 36 0.22
163 47 0.29
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.40
Consensus pattern (159 bp):
AGTTCTTCTCATTATGAACTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG
GAAATGGCTTGATGCTCTATTCTGACTGGAATGAAGTCAAGCAAAAGGTTGAACAAGTTCTTCTC
ATTATGAACTTATTCTTCCTCTTCAGATG
Found at i:150396 original size:112 final size:112
Alignment explanation
Indices: 150256--150580 Score: 499
Period size: 112 Copynumber: 2.9 Consensus size: 112
150246 AATGGAGTCA
* *
150256 AGCAAAAGGTTGAACGAGTTCTTCTCATTATGAGCTTCTTCTTCC-TCTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
150320 CATTATGAACTCTTCTTGGCAATGTTGATCCATCGAGCGATGAATTCG
66 CATTATGAACTCTTC-TGGCAATGTTGATCCATCGAGCGATGAATTCG
* *
150368 AGCAAAAGGTTGAATAATTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * * *
150433 CATTATGAACTCTTCCGGCAATGTTGATCCATCGAGTGGTGAATTTG
66 CATTATGAACTCTTCTGGCAATGTTGATCCATCGAGCGATGAATTCG
* * *
150480 AGAAAAAGGTTGAACAAGTTCTTCTCATTATGAAATTATTCTTCCTTCTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * *
150545 CATTATGAACTCTATATGGGAATATTGATCCATCGA
66 CATTATGAACTCT-TCTGGCAATGTTGATCCATCGA
150581 ATGATGGATC
Statistics
Matches: 194, Mismatches: 17, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
112 142 0.73
113 52 0.27
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (112 bp):
AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
CATTATGAACTCTTCTGGCAATGTTGATCCATCGAGCGATGAATTCG
Found at i:155860 original size:72 final size:72
Alignment explanation
Indices: 155735--155870 Score: 227
Period size: 72 Copynumber: 1.9 Consensus size: 72
155725 GTATAATAGG
*
155735 TTAGCTGAATATTATCCATAAAGCCGGGGCGATTAACCAATTACTTTAAGGGGATAACTCAAGCA
1 TTAGCTGAATATTATCCATAAAGCCGGGGCGATTAACCAATTACTTTAAGGGGATAAATCAAGCA
155800 TAACAGA
66 TAACAGA
* ** *
155807 TTAGCTGAATATTATCCATAAAGCCGGGGCTATTAACCAATTGTTTTAGGGGGATAAATCAAGC
1 TTAGCTGAATATTATCCATAAAGCCGGGGCGATTAACCAATTACTTTAAGGGGATAAATCAAGC
155871 TTTATTGTAT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 59 1.00
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (72 bp):
TTAGCTGAATATTATCCATAAAGCCGGGGCGATTAACCAATTACTTTAAGGGGATAAATCAAGCA
TAACAGA
Found at i:158299 original size:20 final size:20
Alignment explanation
Indices: 158271--158309 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
158261 GCAAAGATGC
*
158271 AAATGCAAAAATAAAAATGT
1 AAATACAAAAATAAAAATGT
**
158291 AAATACAAACGTAAAAATG
1 AAATACAAAAATAAAAATG
158310 CAAAATGCAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.64, C:0.08, G:0.10, T:0.18
Consensus pattern (20 bp):
AAATACAAAAATAAAAATGT
Found at i:158315 original size:21 final size:20
Alignment explanation
Indices: 158282--158320 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
158272 AATGCAAAAA
*
158282 TAAAAATGTAAATACAAACG
1 TAAAAATGAAAATACAAACG
*
158302 TAAAAATGCAAAATGCAAA
1 TAAAAATG-AAAATACAAA
158321 TGCAATGTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.62, C:0.10, G:0.10, T:0.18
Consensus pattern (20 bp):
TAAAAATGAAAATACAAACG
Found at i:158559 original size:43 final size:44
Alignment explanation
Indices: 158487--158573 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 44
158477 ATGTGCATCA
* *
158487 AACAAAACTTTTACATGTAGGGGACAACTTTCAGTCCTAACTTC
1 AACAAAACTTTTACATATAGGGGACAACTTTCACTCCTAACTTC
* * *
158531 AACAAAAC-TTTACATATATGGGATAACTTTCCCTCCTAACTTC
1 AACAAAACTTTTACATATAGGGGACAACTTTCACTCCTAACTTC
158574 TCTAAAGCCA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
43 30 0.79
44 8 0.21
ACGTcount: A:0.34, C:0.24, G:0.10, T:0.31
Consensus pattern (44 bp):
AACAAAACTTTTACATATAGGGGACAACTTTCACTCCTAACTTC
Found at i:160822 original size:3 final size:3
Alignment explanation
Indices: 160816--160853 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
160806 ATTTATATAC
*
160816 TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA AAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
160854 CTAAACAGTG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:162011 original size:3 final size:3
Alignment explanation
Indices: 162005--162090 Score: 67
Period size: 3 Copynumber: 30.0 Consensus size: 3
161995 AAATATTATT
* * * * *
162005 TAA TAA TAA TTA TTA TAA TAA T-A TAA AAA TAA AAA TAA TAG T-A TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
162052 TAA -AA TAA -AA TAA T-A TCAA TAA TAA T-A TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
162091 AAAACAAATG
Statistics
Matches: 67, Mismatches: 8, Indels: 16
0.74 0.09 0.18
Matches are distributed among these distances:
2 11 0.16
3 52 0.78
4 4 0.06
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:162089 original size:17 final size:17
Alignment explanation
Indices: 162005--162090 Score: 70
Period size: 17 Copynumber: 5.0 Consensus size: 17
161995 AAATATTATT
* *
162005 TAATAATAATTATTATAA
1 TAAT-ATAATAATAATAA
* *
162023 TAATATAAAAATAAAAA
1 TAATATAATAATAATAA
162040 TAATAGT-ATAAATAA-AA
1 TAATA-TAAT-AATAATAA
*
162057 TAAAATAAT-ATCAATAA
1 TAATATAATAAT-AATAA
162074 TAATATAATAATAATAA
1 TAATATAATAATAATAA
162091 AAAACAAATG
Statistics
Matches: 55, Mismatches: 7, Indels: 13
0.73 0.09 0.17
Matches are distributed among these distances:
15 2 0.04
16 3 0.05
17 38 0.69
18 12 0.22
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (17 bp):
TAATATAATAATAATAA
Found at i:167335 original size:11 final size:11
Alignment explanation
Indices: 167321--167379 Score: 75
Period size: 11 Copynumber: 5.4 Consensus size: 11
167311 TTTATGTTAA
167321 TTTAGTGTTTG
1 TTTAGTGTTTG
*
167332 TTTATTGTTTG
1 TTTAGTGTTTG
*
167343 TTTAGTATTTG
1 TTTAGTGTTTG
167354 TTTA-TCGTTTG
1 TTTAGT-GTTTG
*
167365 TTTAGTATTTG
1 TTTAGTGTTTG
167376 TTTA
1 TTTA
167380 TCGTTTTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
10 1 0.02
11 39 0.95
12 1 0.02
ACGTcount: A:0.14, C:0.02, G:0.19, T:0.66
Consensus pattern (11 bp):
TTTAGTGTTTG
Found at i:167346 original size:22 final size:22
Alignment explanation
Indices: 167321--167390 Score: 113
Period size: 22 Copynumber: 3.2 Consensus size: 22
167311 TTTATGTTAA
* *
167321 TTTAGTGTTTGTTTATTGTTTG
1 TTTAGTATTTGTTTATCGTTTG
167343 TTTAGTATTTGTTTATCGTTTG
1 TTTAGTATTTGTTTATCGTTTG
*
167365 TTTAGTATTTGTTTATCGTTTT
1 TTTAGTATTTGTTTATCGTTTG
167387 TTTA
1 TTTA
167391 TTGTTCGATT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.13, C:0.03, G:0.17, T:0.67
Consensus pattern (22 bp):
TTTAGTATTTGTTTATCGTTTG
Found at i:171292 original size:32 final size:32
Alignment explanation
Indices: 171230--171292 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
171220 ATATTCAAAC
*
171230 AATTAAGTAATGAAAAATTAACAAACAAAATA
1 AATTAAGTAATGAAAAATTAACAAAAAAAATA
171262 AATTAAGTAAT-AAATAATTAA-ATAAAAAAAT
1 AATTAAGTAATGAAA-AATTAACA-AAAAAAAT
171293 TACAATTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 4 0.14
32 24 0.86
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.25
Consensus pattern (32 bp):
AATTAAGTAATGAAAAATTAACAAAAAAAATA
Found at i:173620 original size:17 final size:17
Alignment explanation
Indices: 173598--173638 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
173588 AGAATATGAG
173598 AGGGTTTGAGTTTTAAA
1 AGGGTTTGAGTTTTAAA
* *
173615 AGGGTTTGAGTTTTGAG
1 AGGGTTTGAGTTTTAAA
173632 AGGGTTT
1 AGGGTTT
173639 AGATGTTTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.22, C:0.00, G:0.37, T:0.41
Consensus pattern (17 bp):
AGGGTTTGAGTTTTAAA
Found at i:183623 original size:15 final size:15
Alignment explanation
Indices: 183605--183636 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
183595 GTTGATGGTG
*
183605 AATGAAGAGAAAGAA
1 AATGAAGAGAAACAA
183620 AATGAAGAGAAACAA
1 AATGAAGAGAAACAA
183635 AA
1 AA
183637 CAAGCAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.03, G:0.22, T:0.06
Consensus pattern (15 bp):
AATGAAGAGAAACAA
Found at i:192797 original size:20 final size:20
Alignment explanation
Indices: 192768--192805 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
192758 CCTATTCAAA
*
192768 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
192788 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
192806 TGCACCAAAA
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:0.13, C:0.26, G:0.37, T:0.24
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:199358 original size:31 final size:30
Alignment explanation
Indices: 199302--199406 Score: 111
Period size: 31 Copynumber: 3.4 Consensus size: 30
199292 GGGCCTGAGA
*
199302 GCCTACCCAAGAAAGTTACTCGGGGCTACGGG
1 GCCTACCCAAGAAAGAT-CTCGGGGCT-CGGG
* *
199334 GCCTACCCAAGAAGGATCTCGGGGCTGCAGG
1 GCCTACCCAAGAAAGATCTCGGGGCT-CGGG
* * *
199365 GCCAACCCAAGAAAGATCTCAGGGCCTCGGA
1 GCCTACCCAAGAAAGATCTC-GGGGCTCGGG
*
199396 GTCTACCCAAG
1 GCCTACCCAAG
199407 GGTCACTTTA
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
31 41 0.67
32 20 0.33
ACGTcount: A:0.27, C:0.30, G:0.30, T:0.13
Consensus pattern (30 bp):
GCCTACCCAAGAAAGATCTCGGGGCTCGGG
Found at i:199850 original size:34 final size:34
Alignment explanation
Indices: 199811--199878 Score: 104
Period size: 34 Copynumber: 2.0 Consensus size: 34
199801 CATGAACAAT
199811 CATATTTTTCAGTGAAAA-C-TAAAATCAGAGAACA
1 CATATTTTTCAGTGAAAATCGT--AATCAGAGAACA
199845 CATATTTTTCAGTGAAAATCGTAATCAGAGAACA
1 CATATTTTTCAGTGAAAATCGTAATCAGAGAACA
199879 TATACCATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
34 30 0.94
35 1 0.03
36 1 0.03
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (34 bp):
CATATTTTTCAGTGAAAATCGTAATCAGAGAACA
Found at i:201876 original size:29 final size:29
Alignment explanation
Indices: 201843--201900 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
201833 ACATAAAATA
*
201843 TAACCTTTTCGAAAAAGTTGACTTTTTGG
1 TAACCTTTTCGAAAAAGTTAACTTTTTGG
201872 TAACCTTTTCGAAAAAGTTAACTTTTTGG
1 TAACCTTTTCGAAAAAGTTAACTTTTTGG
201901 GTCAATGTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (29 bp):
TAACCTTTTCGAAAAAGTTAACTTTTTGG
Found at i:201925 original size:20 final size:21
Alignment explanation
Indices: 201900--201939 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
201890 TAACTTTTTG
*
201900 GGTCAATGTCAAC-GATCAAC
1 GGTCAAAGTCAACGGATCAAC
201920 GGTCAAAGTCAACGGATCAA
1 GGTCAAAGTCAACGGATCAA
201940 AGTCAATAAG
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:0.38, C:0.23, G:0.23, T:0.17
Consensus pattern (21 bp):
GGTCAAAGTCAACGGATCAAC
Found at i:201931 original size:13 final size:14
Alignment explanation
Indices: 201915--201945 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
201905 ATGTCAACGA
201915 TCAACGG-TCAAAG
1 TCAACGGATCAAAG
201928 TCAACGGATCAAAG
1 TCAACGGATCAAAG
201942 TCAA
1 TCAA
201946 TAAGTTGACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.16
Consensus pattern (14 bp):
TCAACGGATCAAAG
Found at i:201944 original size:20 final size:20
Alignment explanation
Indices: 201901--201945 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
201891 AACTTTTTGG
* *
201901 GTCAATGTCAACGATCAACG
1 GTCAAAGTCAACGATCAACA
201921 GTCAAAGTCAACGGATCAA-A
1 GTCAAAGTCAAC-GATCAACA
201941 GTCAA
1 GTCAA
201946 TAAGTTGACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.40, C:0.22, G:0.20, T:0.18
Consensus pattern (20 bp):
GTCAAAGTCAACGATCAACA
Found at i:204870 original size:32 final size:32
Alignment explanation
Indices: 204832--204898 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
204822 CACATAATTA
** * *
204832 ACCTAAGGGAGTGCCTTGGGGCCTGAGAGCCT
1 ACCTAAGAAAGTGCCTCGGGGCCTCAGAGCCT
**
204864 ACCTAAGAAAGTTTCTCGGGGCCTCAGAGCCT
1 ACCTAAGAAAGTGCCTCGGGGCCTCAGAGCCT
204896 ACC
1 ACC
204899 AGATAAAATC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.22, C:0.28, G:0.30, T:0.19
Consensus pattern (32 bp):
ACCTAAGAAAGTGCCTCGGGGCCTCAGAGCCT
Found at i:205050 original size:34 final size:33
Alignment explanation
Indices: 205003--205068 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 33
204993 GGAACAATCA
*
205003 TATTTTTAGTGAAAACCGA-AATTAGAGAACACG
1 TATTTTTAGTGAAAACC-ATAATCAGAGAACACG
*
205036 TATTTTTCAGTGAAAATCATAATCAGAGAACAC
1 TATTTTT-AGTGAAAACCATAATCAGAGAACAC
205069 ATACCATGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 8 0.28
34 21 0.72
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29
Consensus pattern (33 bp):
TATTTTTAGTGAAAACCATAATCAGAGAACACG
Found at i:210422 original size:3 final size:3
Alignment explanation
Indices: 210414--210443 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
210404 AATTTAAACT
210414 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
210444 CGGTTACATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:213782 original size:19 final size:19
Alignment explanation
Indices: 213755--213793 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
213745 ACTAATTTCC
213755 TATTATAATTATAAATATT
1 TATTATAATTATAAATATT
* *
213774 TATTTTAATTGTAAATATT
1 TATTATAATTATAAATATT
213793 T
1 T
213794 TTCTCTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (19 bp):
TATTATAATTATAAATATT
Found at i:215274 original size:18 final size:20
Alignment explanation
Indices: 215237--215276 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
215227 TGGTTCACGT
215237 AAGATTATAAGTGAGAATAA
1 AAGATTATAAGTGAGAATAA
*
215257 AAGATTATCAG-G-GAATAA
1 AAGATTATAAGTGAGAATAA
215275 AA
1 AA
215277 TTACTGGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 1 0.05
20 10 0.53
ACGTcount: A:0.55, C:0.03, G:0.20, T:0.23
Consensus pattern (20 bp):
AAGATTATAAGTGAGAATAA
Found at i:221111 original size:180 final size:180
Alignment explanation
Indices: 220809--221170 Score: 724
Period size: 180 Copynumber: 2.0 Consensus size: 180
220799 ATTAAGAACC
220809 TTTTGCTCTACTAACTGAGATTGATGGTCATTTCAACAATGTTAGACAAATTTAGATAATTTTAT
1 TTTTGCTCTACTAACTGAGATTGATGGTCATTTCAACAATGTTAGACAAATTTAGATAATTTTAT
220874 CCTTAAGTCAACTAATTAGCTTACAAACATAGACGAAGCTATGTTTTGTCCCGAGGGCCATTTTC
66 CCTTAAGTCAACTAATTAGCTTACAAACATAGACGAAGCTATGTTTTGTCCCGAGGGCCATTTTC
220939 CTCCCTATTTTGTTTTATAATTTTAAAAATATTTGTGTAAATACCAAATA
131 CTCCCTATTTTGTTTTATAATTTTAAAAATATTTGTGTAAATACCAAATA
220989 TTTTGCTCTACTAACTGAGATTGATGGTCATTTCAACAATGTTAGACAAATTTAGATAATTTTAT
1 TTTTGCTCTACTAACTGAGATTGATGGTCATTTCAACAATGTTAGACAAATTTAGATAATTTTAT
221054 CCTTAAGTCAACTAATTAGCTTACAAACATAGACGAAGCTATGTTTTGTCCCGAGGGCCATTTTC
66 CCTTAAGTCAACTAATTAGCTTACAAACATAGACGAAGCTATGTTTTGTCCCGAGGGCCATTTTC
221119 CTCCCTATTTTGTTTTATAATTTTAAAAATATTTGTGTAAATACCAAATA
131 CTCCCTATTTTGTTTTATAATTTTAAAAATATTTGTGTAAATACCAAATA
221169 TT
1 TT
221171 ACCTCCTAAT
Statistics
Matches: 182, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
180 182 1.00
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (180 bp):
TTTTGCTCTACTAACTGAGATTGATGGTCATTTCAACAATGTTAGACAAATTTAGATAATTTTAT
CCTTAAGTCAACTAATTAGCTTACAAACATAGACGAAGCTATGTTTTGTCCCGAGGGCCATTTTC
CTCCCTATTTTGTTTTATAATTTTAAAAATATTTGTGTAAATACCAAATA
Found at i:222759 original size:15 final size:15
Alignment explanation
Indices: 222739--222769 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
222729 GAGAAAACAT
222739 ATTTAAATTGAAATC
1 ATTTAAATTGAAATC
222754 ATTTAAATTGAAATC
1 ATTTAAATTGAAATC
222769 A
1 A
222770 AATAATATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (15 bp):
ATTTAAATTGAAATC
Found at i:222819 original size:18 final size:18
Alignment explanation
Indices: 222769--222805 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
222759 AATTGAAATC
222769 AAATAATATCACAATATT
1 AAATAATATCACAATATT
222787 AAATAATATCACAATATT
1 AAATAATATCACAATATT
222805 A
1 A
222806 TAAATATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (18 bp):
AAATAATATCACAATATT
Found at i:226520 original size:21 final size:21
Alignment explanation
Indices: 226494--226536 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
226484 ATCAGCTCAG
226494 TATATTATTAAGGTTAAGGTA
1 TATATTATTAAGGTTAAGGTA
*
226515 TATATTATTAAGTTTAAGGTA
1 TATATTATTAAGGTTAAGGTA
226536 T
1 T
226537 GAATGTGGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (21 bp):
TATATTATTAAGGTTAAGGTA
Found at i:233624 original size:22 final size:23
Alignment explanation
Indices: 233576--233621 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
233566 AATGGCAGTG
* *
233576 AATACTATTAATATGATTCAAAT
1 AATACTATTAATATAATTAAAAT
233599 AATAC-ATTAA-ATAATTAAAAT
1 AATACTATTAATATAATTAAAAT
233620 AA
1 AA
233622 ATAAATAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 11 0.52
22 5 0.24
23 5 0.24
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.35
Consensus pattern (23 bp):
AATACTATTAATATAATTAAAAT
Found at i:235162 original size:60 final size:59
Alignment explanation
Indices: 235090--235266 Score: 182
Period size: 60 Copynumber: 3.0 Consensus size: 59
235080 AAAGTATGAC
* * *
235090 ATTCATTTTAAATTAGTCCTTAAATTTTTTAATATTCTAATTTCATCCCTAAACTATAAT
1 ATTCATTCTAAATTAGTCCTTAAATTTTTTAACATTCTGATTTCATCCC-AAACTATAAT
* * * * *
235150 -TATCATTCTAAATTAGT-CTTCAAACTTTTGAACA-TGTGATTTTATCCCCAAACTATGAT
1 AT-TCATTCTAAATTAGTCCTT-AAATTTTTTAACATTCTGATTTCAT-CCCAAACTATAAT
**
235209 ATTCATTCTAAATT-GATCCCCAAAATTTTTTAACATTCTGATTTCATCCCAAACTATA
1 ATTCATTCTAAATTAG-T-CCTTAAATTTTTTAACATTCTGATTTCATCCCAAACTATA
235267 CGTATATACT
Statistics
Matches: 94, Mismatches: 15, Indels: 16
0.75 0.12 0.13
Matches are distributed among these distances:
58 1 0.01
59 34 0.36
60 49 0.52
61 10 0.11
ACGTcount: A:0.34, C:0.19, G:0.05, T:0.43
Consensus pattern (59 bp):
ATTCATTCTAAATTAGTCCTTAAATTTTTTAACATTCTGATTTCATCCCAAACTATAAT
Found at i:235478 original size:29 final size:29
Alignment explanation
Indices: 235385--235478 Score: 82
Period size: 29 Copynumber: 3.1 Consensus size: 29
235375 ATGGATTTGG
235385 GGATGAAATTGGAATATTCAAAATTTTAA
1 GGATGAAATTGGAATATTCAAAATTTTAA
* * * * * * *
235414 GGA-CAAATTTAGAATGAGAATCATAGTTCTGA
1 GGATGAAA-TTGGAAT---ATTCAAAATTTTAA
235446 GGATGAAATTGGAATATTCAAAATTTTAA
1 GGATGAAATTGGAATATTCAAAATTTTAA
235475 GGAT
1 GGAT
235479 CAATTTAAGA
Statistics
Matches: 46, Mismatches: 14, Indels: 10
0.66 0.20 0.14
Matches are distributed among these distances:
28 3 0.07
29 22 0.48
32 18 0.39
33 3 0.07
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.32
Consensus pattern (29 bp):
GGATGAAATTGGAATATTCAAAATTTTAA
Found at i:243234 original size:27 final size:27
Alignment explanation
Indices: 243203--243259 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
243193 TAATTTCAAT
243203 TGATAGACGATATGATCTTTAATAGTC
1 TGATAGACGATATGATCTTTAATAGTC
243230 TGATAGACGATATGATCTTTAATAGTC
1 TGATAGACGATATGATCTTTAATAGTC
243257 TGA
1 TGA
243260 AATATAAACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (27 bp):
TGATAGACGATATGATCTTTAATAGTC
Found at i:246579 original size:16 final size:17
Alignment explanation
Indices: 246558--246623 Score: 57
Period size: 16 Copynumber: 3.9 Consensus size: 17
246548 GCCTTCGGGC
246558 TTTATAA-ATAATAATA
1 TTTATAATATAATAATA
*
246574 TTTATAATATAATATTA
1 TTTATAATATAATAATA
* *
246591 -TTATTATATATGATAACA
1 TTTA-TA-ATATAATAATA
*
246609 TATAT-ATATAATAAT
1 TTTATAATATAATAAT
246624 CGTCACTCGG
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
16 18 0.46
17 10 0.26
18 9 0.23
19 2 0.05
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (17 bp):
TTTATAATATAATAATA
Found at i:246587 original size:14 final size:16
Alignment explanation
Indices: 246558--246592 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
246548 GCCTTCGGGC
246558 TTTATAAATAATAATA
1 TTTATAAATAATAATA
*
246574 TTTATAATATAATATTA
1 TTTATAA-ATAATAATA
246591 TT
1 TT
246593 ATTATATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TTTATAAATAATAATA
Found at i:247350 original size:20 final size:20
Alignment explanation
Indices: 247322--247416 Score: 163
Period size: 20 Copynumber: 4.8 Consensus size: 20
247312 AGATGACTCA
*
247322 AAGGCTTTACAAATTATCCG
1 AAGGCTTTACAAATTACCCG
*
247342 AAGGTTTTACAAATTACCCG
1 AAGGCTTTACAAATTACCCG
247362 AAGGCTTTACAAATTACCCG
1 AAGGCTTTACAAATTACCCG
247382 AAGGCTTTACAAATTACCCG
1 AAGGCTTTACAAATTACCCG
*
247402 AAGGTTTTACAAATT
1 AAGGCTTTACAAATT
247417 CATGAGAAAT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 71 1.00
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (20 bp):
AAGGCTTTACAAATTACCCG
Found at i:248316 original size:65 final size:64
Alignment explanation
Indices: 248188--248343 Score: 172
Period size: 65 Copynumber: 2.4 Consensus size: 64
248178 CACACCTATT
* * * *
248188 TCGAATGCATTTTGTGAACCAATGCACAGCCATGCATCGATACACTCTTGAATTTATTAAAACA
1 TCGAATGCATTTTATGTACCGATGCACAGCCATGCATCGATACACTCCTGAATTTATTAAAACA
* * ** *
248252 TCGAATGCATTTTATGTACCGATGCACAGATCATGCATCGATGCACTCCTGGCTCTT-TTGAAAC
1 TCGAATGCATTTTATGTACCGATGCACAG-CCATGCATCGATACACTCCTGAAT-TTATTAAAAC
248316 A
64 A
* *
248317 TCGAATGTA-ATTAGTGTACCGATGCAC
1 TCGAATGCATTTTA-TGTACCGATGCAC
248344 TAAGTCTTAT
Statistics
Matches: 78, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
64 29 0.37
65 47 0.60
66 2 0.03
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.30
Consensus pattern (64 bp):
TCGAATGCATTTTATGTACCGATGCACAGCCATGCATCGATACACTCCTGAATTTATTAAAACA
Found at i:248414 original size:21 final size:22
Alignment explanation
Indices: 248390--248441 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 22
248380 CATAGGGTTT
248390 CGATGCACACC-GATGGTGTAC
1 CGATGCACACCTGATGGTGTAC
248411 CGATGCAC-CCTGATGGTGTAC
1 CGATGCACACCTGATGGTGTAC
*
248432 CAATGCACAC
1 CGATGCACAC
248442 ACACTCCCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 2 0.07
21 25 0.89
22 1 0.04
ACGTcount: A:0.25, C:0.31, G:0.25, T:0.19
Consensus pattern (22 bp):
CGATGCACACCTGATGGTGTAC
Found at i:254153 original size:21 final size:21
Alignment explanation
Indices: 254124--254187 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
254114 ATGCATCCCT
254124 TGAATGTGCATCGATACACCA
1 TGAATGTGCATCGATACACCA
* * * *
254145 TGAAGGTGCACCGATGCATTCCT
1 TGAATGTGCATCGATACA--CCA
254168 TGAATGTGCATCGATACACC
1 TGAATGTGCATCGATACACC
254188 CATCGGGTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
21 17 0.50
23 17 0.50
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (21 bp):
TGAATGTGCATCGATACACCA
Found at i:254169 original size:44 final size:43
Alignment explanation
Indices: 254087--254187 Score: 141
Period size: 44 Copynumber: 2.3 Consensus size: 43
254077 TTGTGAAACA
* * *
254087 TGCATCGATACACTAGAGAGTGTATCGATGCATCCCTTGAATG
1 TGCATCGATACACCAGAGAGTGCACCGATGCATCCCTTGAATG
*
254130 TGCATCGATACACCATGA-AGGTGCACCGATGCATTCCTTGAATG
1 TGCATCGATACACCA-GAGA-GTGCACCGATGCATCCCTTGAATG
254174 TGCATCGATACACC
1 TGCATCGATACACC
254188 CATCGGGTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
43 15 0.29
44 37 0.71
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.26
Consensus pattern (43 bp):
TGCATCGATACACCAGAGAGTGCACCGATGCATCCCTTGAATG
Found at i:254176 original size:23 final size:22
Alignment explanation
Indices: 254110--254182 Score: 85
Period size: 23 Copynumber: 3.3 Consensus size: 22
254100 TAGAGAGTGT
254110 ATCGATGCATCCCTTGAATGTGC
1 ATCGATGCAT-CCTTGAATGTGC
* * *
254133 ATCGATACA-CCATGAAGGTGC
1 ATCGATGCATCCTTGAATGTGC
*
254154 ACCGATGCATTCCTTGAATGTGC
1 ATCGATGCA-TCCTTGAATGTGC
254177 ATCGAT
1 ATCGAT
254183 ACACCCATCG
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
21 17 0.43
23 23 0.57
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (22 bp):
ATCGATGCATCCTTGAATGTGC
Found at i:256889 original size:64 final size:65
Alignment explanation
Indices: 256820--256955 Score: 177
Period size: 65 Copynumber: 2.1 Consensus size: 65
256810 ACACCCTATT
* * * *
256820 TCGAATGCATTTTGTGTACAGATGCACA-ACCATGCATCGATGCACT-CTTGAATTTATTGAAAC
1 TCGAATGCATTTTATGTACAGACGCACATACCATGCATCGATACACTCCTGGAATTT-TTGAAAC
256883 A
65 A
* * **
256884 TCGAATGCATTTTATGTACCGACGCACATACCATGCATTGATACACTCCTGGCGTTTTTGAAACA
1 TCGAATGCATTTTATGTACAGACGCACATACCATGCATCGATACACTCCTGGAATTTTTGAAACA
256949 TCGAATG
1 TCGAATG
256956 TAATTAGTGT
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
64 25 0.40
65 31 0.50
66 6 0.10
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (65 bp):
TCGAATGCATTTTATGTACAGACGCACATACCATGCATCGATACACTCCTGGAATTTTTGAAACA
Found at i:259641 original size:22 final size:22
Alignment explanation
Indices: 259613--259659 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
259603 AAAGTTTTCA
259613 ATCTTTGAAAAGAGAATCTATC
1 ATCTTTGAAAAGAGAATCTATC
* *
259635 ATCTTTGGAAAGAGAATTTATC
1 ATCTTTGAAAAGAGAATCTATC
259657 ATC
1 ATC
259660 CTTACAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (22 bp):
ATCTTTGAAAAGAGAATCTATC
Found at i:266685 original size:7 final size:7
Alignment explanation
Indices: 266659--266699 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
266649 CACAATCCCC
266659 TAAATTCA
1 TAAA-TCA
*
266667 TAAA-CT
1 TAAATCA
266673 TAAATCA
1 TAAATCA
266680 TAAATCA
1 TAAATCA
266687 TAAATCA
1 TAAATCA
266694 TAAATC
1 TAAATC
266700 CAAAATACCC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
6 5 0.17
7 21 0.70
8 4 0.13
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.32
Consensus pattern (7 bp):
TAAATCA
Found at i:275934 original size:2 final size:2
Alignment explanation
Indices: 275921--275953 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
275911 GTGAGGCATA
*
275921 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
275954 ACAATGCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:276227 original size:18 final size:18
Alignment explanation
Indices: 276204--276238 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
276194 ACTGATTATT
*
276204 TGTCCCGAATGACCACTA
1 TGTCCCGAAAGACCACTA
276222 TGTCCCGAAAGACCACT
1 TGTCCCGAAAGACCACT
276239 GATTGTTCCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.34, G:0.17, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAAGACCACTA
Found at i:283101 original size:18 final size:18
Alignment explanation
Indices: 283078--283129 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
283068 ACTGAATATT
283078 TATCCCGAAAGACCACTA
1 TATCCCGAAAGACCACTA
283096 TATCCCGAAAGACCACTA
1 TATCCCGAAAGACCACTA
*
283114 TATCCCGAAGGACCAC
1 TATCCCGAAAGACCAC
283130 AAATTGTTCC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.37, C:0.35, G:0.13, T:0.15
Consensus pattern (18 bp):
TATCCCGAAAGACCACTA
Found at i:283168 original size:18 final size:18
Alignment explanation
Indices: 283078--283168 Score: 92
Period size: 18 Copynumber: 4.9 Consensus size: 18
283068 ACTGAATATT
*
283078 TATCCCGAAAGACCACTA
1 TATCCCGAAGGACCACTA
*
283096 TATCCCGAAAGACCACTA
1 TATCCCGAAGGACCACTA
*
283114 TATCCCGAAGGACCACAAA
1 TATCCCGAAGGACCAC-TA
* * *
283133 TTGTTCCGAAGAACCACTA
1 -TATCCCGAAGGACCACTA
* *
283152 TGTCCCGTAGGACCACT
1 TATCCCGAAGGACCACT
283169 GATAATCCCT
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
18 47 0.76
19 2 0.03
20 13 0.21
ACGTcount: A:0.34, C:0.32, G:0.15, T:0.19
Consensus pattern (18 bp):
TATCCCGAAGGACCACTA
Found at i:283812 original size:64 final size:64
Alignment explanation
Indices: 283740--283879 Score: 160
Period size: 64 Copynumber: 2.2 Consensus size: 64
283730 ATCCCTTGAC
* *
283740 GGGTGCATCGATGCACAA-TCTATGCATCGGTACA-TAAATCCCATTCGATGT-TTGTATTTTAA
1 GGGTGCATCGATGCACAACT-TATGCATCGATACACT-AATCACATTCGATGTATT-TATTTTAA
*
283802 GG
63 AG
* * * *
283804 GGGTGCATCGATGCACCACTTGTGCATCGATACACTGATGACATTCGATGTATTTATTTTAAAG
1 GGGTGCATCGATGCACAACTTATGCATCGATACACTAATCACATTCGATGTATTTATTTTAAAG
*
283868 GAGTGCATCGAT
1 GGGTGCATCGAT
283880 ACACTTCATG
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
64 61 0.94
65 4 0.06
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (64 bp):
GGGTGCATCGATGCACAACTTATGCATCGATACACTAATCACATTCGATGTATTTATTTTAAAG
Found at i:285851 original size:59 final size:59
Alignment explanation
Indices: 285756--285871 Score: 169
Period size: 59 Copynumber: 2.0 Consensus size: 59
285746 AATATTTATG
* * * * * *
285756 CAAGATTTTCGTAATTCATCGTTGCCCAAACTTTTTAATCTTTTGGAATCAAATAAAAA
1 CAAGATTTTCATAATTCACCATAGCCCAAACATTTTAATCTTTTGCAATCAAATAAAAA
*
285815 CAAGATTTTCATAATTCACCATAGCTCAAACATTTTAATCTTTTGCAATCAAATAAA
1 CAAGATTTTCATAATTCACCATAGCCCAAACATTTTAATCTTTTGCAATCAAATAAA
285872 CATCCAAAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
59 50 1.00
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (59 bp):
CAAGATTTTCATAATTCACCATAGCCCAAACATTTTAATCTTTTGCAATCAAATAAAAA
Found at i:286764 original size:16 final size:16
Alignment explanation
Indices: 286725--286762 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
286715 ATTAGATTAT
*
286725 TCAATCTAATCTAATC
1 TCAATTTAATCTAATC
*
286741 TTAATTTAATCTAATC
1 TCAATTTAATCTAATC
286757 -CAATTT
1 TCAATTT
286763 TACCTTGTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.37, C:0.18, G:0.00, T:0.45
Consensus pattern (16 bp):
TCAATTTAATCTAATC
Found at i:291363 original size:22 final size:22
Alignment explanation
Indices: 291335--291378 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
291325 CACTCTCTCA
291335 CCCATCTCCAACGAAATCCGTC
1 CCCATCTCCAACGAAATCCGTC
**
291357 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCAACGAAATCCGTC
291379 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.45, G:0.14, T:0.18
Consensus pattern (22 bp):
CCCATCTCCAACGAAATCCGTC
Found at i:291666 original size:20 final size:20
Alignment explanation
Indices: 291641--291679 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
291631 TTTATTCTCT
291641 TGTTGCGATTGTCATTTTCG
1 TGTTGCGATTGTCATTTTCG
*
291661 TGTTGCGATTTTCATTTTC
1 TGTTGCGATTGTCATTTTC
291680 AGAAACTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.10, C:0.15, G:0.21, T:0.54
Consensus pattern (20 bp):
TGTTGCGATTGTCATTTTCG
Found at i:291867 original size:25 final size:24
Alignment explanation
Indices: 291813--291867 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
291803 TGTTTATTAT
* *
291813 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
291837 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
291863 TGTTT
1 TGTTT
291868 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:293013 original size:18 final size:18
Alignment explanation
Indices: 292992--293039 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
292982 TCCACTTCGG
292992 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
293010 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
293028 GAGCCATCACCT
1 GAGCCATCACCT
293040 GATCGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:293599 original size:20 final size:20
Alignment explanation
Indices: 293574--293619 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
293564 TAGTTTACTT
293574 TCGCAACACGAAAATAACTA
1 TCGCAACACGAAAATAACTA
* * **
293594 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATAACTA
293614 TCGCAA
1 TCGCAA
293620 TGCAAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.39, C:0.26, G:0.20, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATAACTA
Found at i:293646 original size:14 final size:14
Alignment explanation
Indices: 293629--293687 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
293619 ATGCAAAATG
293629 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
293643 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
293662 AAAATCGCAACGAC
1 AAAATCGCAACGAC
293676 AAAATCGCAACG
1 AAAATCGCAACG
293688 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.49, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:293655 original size:33 final size:33
Alignment explanation
Indices: 293613--293704 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
293603 GGAAATGGCT
*
293613 ATCGCAATGCAAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
293646 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
293679 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
293705 TGCGATTTGT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.49, C:0.22, G:0.17, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:293709 original size:19 final size:19
Alignment explanation
Indices: 293613--293709 Score: 88
Period size: 19 Copynumber: 5.6 Consensus size: 19
293603 GGAAATGGCT
*
293613 ATCGCAATGCAAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
293632 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
293646 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
293665 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
293679 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
293698 ATCGCAATGCGA
1 ATCGCAATGCGA
293710 TTTGTGTTTC
Statistics
Matches: 62, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 4 0.06
17 3 0.05
18 2 0.03
19 31 0.50
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:293781 original size:20 final size:19
Alignment explanation
Indices: 293747--293799 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
293737 TTGCGATTTT
*
293747 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
293766 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
293786 CATTTTCGCGTTGC
1 CA-TTTCGCGTTGC
293800 AAAAGTAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 5 0.17
20 22 0.73
21 3 0.10
ACGTcount: A:0.15, C:0.26, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:293812 original size:20 final size:20
Alignment explanation
Indices: 293789--293827 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
293779 CGATAGTCAT
293789 TTTCGCGTTGCAAAAGTAAG
1 TTTCGCGTTGCAAAAGTAAG
* *
293809 TTTCGTGTTGCGAAAGTAA
1 TTTCGCGTTGCAAAAGTAA
293828 ACTATTCTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.33
Consensus pattern (20 bp):
TTTCGCGTTGCAAAAGTAAG
Found at i:294259 original size:44 final size:42
Alignment explanation
Indices: 294169--294259 Score: 110
Period size: 44 Copynumber: 2.1 Consensus size: 42
294159 GACTCACCTT
* * * *
294169 TCATTCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCCCCCAACCGTTCAAGAGGCCACTA
* *
294211 TCATCCCTCAAGAGTCCCCCCCCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGT--CCCCCCCAACCGTTCAAGAGGCCACTA
294255 TCATC
1 TCATC
294260 GTTGAAGAGG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
42 14 0.34
44 27 0.66
ACGTcount: A:0.22, C:0.43, G:0.14, T:0.21
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCCCCCCAACCGTTCAAGAGGCCACTA
Found at i:295704 original size:14 final size:14
Alignment explanation
Indices: 295670--295708 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
295660 TTGATTGTTT
295670 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
295684 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
295698 TGTTGATTTGT
1 AATTGATTTGT
295709 TTAATTGGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:295869 original size:19 final size:19
Alignment explanation
Indices: 295845--295931 Score: 121
Period size: 19 Copynumber: 4.8 Consensus size: 19
295835 ATCGCAACTA
295845 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
295864 GAAAATCGCAATGCGAATT
1 GAAAATCGCAATGCGAAAT
*
295883 GAAAATTGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
295902 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
295916 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
295932 TTTTCATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
14 11 0.18
15 1 0.02
16 2 0.03
17 2 0.03
19 45 0.74
ACGTcount: A:0.46, C:0.16, G:0.22, T:0.16
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:295983 original size:34 final size:36
Alignment explanation
Indices: 295938--296027 Score: 103
Period size: 40 Copynumber: 2.4 Consensus size: 36
295928 GCGATTTTCA
* *
295938 TTTCGCATTGCGATTTTC-T-AGTTGCGATAGCCAT
1 TTTCGCGTTGCGATTTTCTTCAATTGCGATAGCCAT
295972 TTTCGCGTTGCGATTTTTCATTTCGAATTGCGATAGCCAT
1 TTTCGCGTTGCGA-TTTTC--TTC-AATTGCGATAGCCAT
*
296012 TTTCGCGTTGTGATTT
1 TTTCGCGTTGCGATTT
296028 CCCCGTTGTG
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
34 12 0.26
35 5 0.11
38 1 0.02
39 3 0.06
40 26 0.55
ACGTcount: A:0.16, C:0.19, G:0.21, T:0.44
Consensus pattern (36 bp):
TTTCGCGTTGCGATTTTCTTCAATTGCGATAGCCAT
Found at i:296015 original size:20 final size:20
Alignment explanation
Indices: 295959--296016 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
295949 GATTTTCTAG
**
295959 TTGCGATAGCCATTTTCGCG
1 TTGCGATAGCCATTTTCGAA
***
295979 TTGCGATTTTTCA-TTTCGAA
1 TTGCGA-TAGCCATTTTCGAA
295999 TTGCGATAGCCATTTTCG
1 TTGCGATAGCCATTTTCG
296017 CGTTGTGATT
Statistics
Matches: 28, Mismatches: 8, Indels: 4
0.70 0.20 0.10
Matches are distributed among these distances:
19 3 0.11
20 22 0.79
21 3 0.11
ACGTcount: A:0.17, C:0.21, G:0.21, T:0.41
Consensus pattern (20 bp):
TTGCGATAGCCATTTTCGAA
Found at i:296264 original size:20 final size:20
Alignment explanation
Indices: 296239--296288 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
296229 TTAAAGATGA
*
296239 TTGCGATTTTCATAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
296259 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
296279 TTGCGATTTT
1 TTGCGATTTT
296289 GTATTACCTC
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:297169 original size:24 final size:24
Alignment explanation
Indices: 297135--297188 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
297125 GTATTCGAAA
*
297135 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
297159 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
297183 TTTGAT
1 TTTGAT
297189 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:297376 original size:9 final size:9
Alignment explanation
Indices: 297364--297393 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
297354 TATAATCTTG
297364 AAGAAGAAA
1 AAGAAGAAA
297373 AAGAAGAAA
1 AAGAAGAAA
297382 AAGAAGAAA
1 AAGAAGAAA
297391 AAG
1 AAG
297394 TCCCCGAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (9 bp):
AAGAAGAAA
Found at i:299707 original size:19 final size:19
Alignment explanation
Indices: 299685--299782 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
299675 GGAAATTACT
299685 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
299704 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
299718 ATCACAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
299737 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
299751 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
299770 ATCGCAACGCGAA
1 ATCGCAATGCGAA
299783 TTTAGTTTCG
Statistics
Matches: 60, Mismatches: 9, Indels: 20
0.67 0.10 0.22
Matches are distributed among these distances:
14 18 0.30
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 30 0.50
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:299731 original size:33 final size:33
Alignment explanation
Indices: 299689--299778 Score: 162
Period size: 33 Copynumber: 2.7 Consensus size: 33
299679 ATTACTATCG
299689 CAATGCGAAATGAAAATCGCAACGAGAGAATCA
1 CAATGCGAAATGAAAATCGCAACGAGAGAATCA
* *
299722 CAATGCGAAATGAAAATCGCAACGAGGGAATCG
1 CAATGCGAAATGAAAATCGCAACGAGAGAATCA
299755 CAATGCGAAATGAAAATCGCAACG
1 CAATGCGAAATGAAAATCGCAACG
299779 CGAATTTAGT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (33 bp):
CAATGCGAAATGAAAATCGCAACGAGAGAATCA
Found at i:299960 original size:14 final size:14
Alignment explanation
Indices: 299941--299979 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
299931 CATCAATTAA
299941 ACAAATCAATTTTT
1 ACAAATCAATTTTT
**
299955 ACAAATCACCTTTT
1 ACAAATCAATTTTT
299969 ACAAATCAATT
1 ACAAATCAATT
299980 AAACAATCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.36
Consensus pattern (14 bp):
ACAAATCAATTTTT
Found at i:301834 original size:91 final size:90
Alignment explanation
Indices: 301658--301842 Score: 291
Period size: 91 Copynumber: 2.0 Consensus size: 90
301648 ATTTCAAACT
*
301658 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTCAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTCAGC
301723 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
*
301751 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTCAGCA
*
301815 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
301842 T
1 T
301843 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 41 0.47
93 19 0.22
95 27 0.31
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.21
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTCAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:303555 original size:20 final size:20
Alignment explanation
Indices: 303525--303584 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
303515 CTTTTGGTTG
303525 AAATGAAAATCGCAACGAGA
1 AAATGAAAATCGCAACGAGA
* * *
303545 TAATGAGAATCGCAACGCGA
1 AAATGAAAATCGCAACGAGA
** *
303565 AAATGACTATCACAACGAGA
1 AAATGAAAATCGCAACGAGA
303585 GAATCGCAAC
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.48, C:0.18, G:0.20, T:0.13
Consensus pattern (20 bp):
AAATGAAAATCGCAACGAGA
Found at i:303625 original size:14 final size:14
Alignment explanation
Indices: 303577--303628 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
303567 ATGACTATCA
303577 CAACGAGAGAATCG
1 CAACGAGAGAATCG
*
303591 CAACGCGAAATGACTATCG
1 CAA--CGAGA-GA--ATCG
303610 CAACGAGAGAATCG
1 CAACGAGAGAATCG
303624 CAACG
1 CAACG
303629 CGAAATGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
14 12 0.39
16 6 0.19
17 6 0.19
19 7 0.23
ACGTcount: A:0.40, C:0.25, G:0.25, T:0.10
Consensus pattern (14 bp):
CAACGAGAGAATCG
Found at i:303643 original size:33 final size:33
Alignment explanation
Indices: 303549--303645 Score: 158
Period size: 33 Copynumber: 2.9 Consensus size: 33
303539 ACGAGATAAT
*
303549 GAGAATCGCAACGCGAAAATGACTATCACAACGA
1 GAGAATCGCAACGCG-AAATGACTATCGCAACGA
303583 GAGAATCGCAACGCGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
**
303616 GAGAATCGCAACGCGAAATGAAAATCGCAA
1 GAGAATCGCAACGCGAAATGACTATCGCAA
303646 TCGTTGCGAT
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
33 45 0.75
34 15 0.25
ACGTcount: A:0.43, C:0.23, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:303688 original size:33 final size:34
Alignment explanation
Indices: 303646--303709 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 34
303636 AAAATCGCAA
**
303646 TCGTTGCGATTTTTATTT-CGCGTTGCGATTCTC
1 TCGTTGCGATAGTTATTTCCGCGTTGCGATTCTC
303679 TCGTTGCGATAGTTATTTCCGCGTTGCGATT
1 TCGTTGCGATAGTTATTTCCGCGTTGCGATT
303710 TTCATTCTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 16 0.57
34 12 0.43
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.45
Consensus pattern (34 bp):
TCGTTGCGATAGTTATTTCCGCGTTGCGATTCTC
Found at i:304274 original size:20 final size:20
Alignment explanation
Indices: 304251--304344 Score: 125
Period size: 20 Copynumber: 4.7 Consensus size: 20
304241 CGATAGTAAG
*
304251 ATTCGCATTGTGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
304271 ATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGT
*
304291 AATTCGCATTGCGATTTACTT
1 -ATTCGCATTGCGATTTACGT
* *
304312 AATCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
304332 ATTCGCATTGCGA
1 ATTCGCATTGCGA
304345 ATTATGAAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
20 45 0.71
21 18 0.29
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:304300 original size:41 final size:40
Alignment explanation
Indices: 304251--304344 Score: 125
Period size: 41 Copynumber: 2.3 Consensus size: 40
304241 CGATAGTAAG
* * *
304251 ATTCGCATTGTGATTTACGTATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
* * *
304291 AATTCGCATTGCGATTTACTTAATCGCGTTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
304332 ATTCGCATTGCGA
1 ATTCGCATTGCGA
304345 ATTATGAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 13 0.28
41 34 0.72
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.40
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
Found at i:304357 original size:41 final size:42
Alignment explanation
Indices: 304273--304407 Score: 125
Period size: 41 Copynumber: 3.3 Consensus size: 42
304263 ATTTACGTAT
* * * *
304273 TCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACT--TAA
1 TCGCATTGCGATTTACGTAATTCGCATTGCGAATTA-TGAAAA
*
304314 TCGCGTTGCGATTTACGT-ATTCGCATTGCGAATTATGAAAA
1 TCGCATTGCGATTTACGTAATTCGCATTGCGAATTATGAAAA
** * * * *
304355 TCGCAACGCGA-ATACGTAAATCGCAATGCGAATTAGGAAAA
1 TCGCATTGCGATTTACGTAATTCGCATTGCGAATTATGAAAA
*
304396 TTGCATTGCGAT
1 TCGCATTGCGAT
304408 AGTCAGTATC
Statistics
Matches: 75, Mismatches: 15, Indels: 7
0.77 0.15 0.07
Matches are distributed among these distances:
39 1 0.01
40 21 0.28
41 53 0.71
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (42 bp):
TCGCATTGCGATTTACGTAATTCGCATTGCGAATTATGAAAA
Found at i:304365 original size:21 final size:21
Alignment explanation
Indices: 304341--304462 Score: 92
Period size: 21 Copynumber: 5.9 Consensus size: 21
304331 TATTCGCATT
*
304341 GCGAATTATGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
304362 GCGAA-TACGTAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
* **
304382 GCGAATTAGGAAAATTGCATT
1 GCGAATTAGGAAAATCGCAAC
* **
304403 GCG-A-TAGTCAGTATCGCAAC
1 GCGAATTAG-GAAAATCGCAAC
304423 GCGAAATT-GGAAAATCGCAAC
1 GCG-AATTAGGAAAATCGCAAC
304444 GCGAAATT-GGAAAATCGCA
1 GCG-AATTAGGAAAATCGCA
304463 TTGCGATAGT
Statistics
Matches: 80, Mismatches: 16, Indels: 10
0.75 0.15 0.09
Matches are distributed among these distances:
19 3 0.04
20 27 0.34
21 47 0.59
22 2 0.03
23 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.20
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:304468 original size:21 final size:21
Alignment explanation
Indices: 304415--304462 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
304405 GATAGTCAGT
304415 ATCGCAACGCGAAATTGGAAA
1 ATCGCAACGCGAAATTGGAAA
304436 ATCGCAACGCGAAATTGGAAA
1 ATCGCAACGCGAAATTGGAAA
304457 ATCGCA
1 ATCGCA
304463 TTGCGATAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.42, C:0.21, G:0.23, T:0.15
Consensus pattern (21 bp):
ATCGCAACGCGAAATTGGAAA
Found at i:304481 original size:62 final size:62
Alignment explanation
Indices: 304353--304481 Score: 174
Period size: 62 Copynumber: 2.1 Consensus size: 62
304343 GAATTATGAA
* * *
304353 AATCGCAACGCGAATACGTAAATCGCAATGCGAATTAGGAAAATTGCATTGCGATAGTCAGT
1 AATCGCAACGCGAATACGAAAATCGCAACGCGAATTAGGAAAATCGCATTGCGATAGTCAGT
**
304415 -ATCGCAACGCGAAATTGGAAAATCGCAACGCGAAATT-GGAAAATCGCATTGCGATAGTCA-T
1 AATCGCAACGCG-AATACGAAAATCGCAACGCG-AATTAGGAAAATCGCATTGCGATAGTCAGT
304476 AATCGC
1 AATCGC
304482 GTTGCGAATC
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
61 12 0.20
62 43 0.73
63 4 0.07
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.21
Consensus pattern (62 bp):
AATCGCAACGCGAATACGAAAATCGCAACGCGAATTAGGAAAATCGCATTGCGATAGTCAGT
Found at i:304489 original size:62 final size:62
Alignment explanation
Indices: 304354--304497 Score: 163
Period size: 62 Copynumber: 2.3 Consensus size: 62
304344 AATTATGAAA
* * *
304354 ATCGCAACGCGAATAC--GTAAATCGCAATGCGAATTAGGAAAATTGCATTGCGATAGTCAGT
1 ATCGCAACGCGAAT-CTGGAAAATCGCAACGCGAATTAGGAAAATCGCATTGCGATAGTCAGT
304415 ATCGCAACGCGAAAT-TGGAAAATCGCAACGCGAAATT-GGAAAATCGCATTGCGATAGTCA-T
1 ATCGCAACGCG-AATCTGGAAAATCGCAACGCG-AATTAGGAAAATCGCATTGCGATAGTCAGT
***
304476 AATCGCGTTGCGAATCTGGAAA
1 -ATCGCAACGCGAATCTGGAAA
304498 CTGATTTGCG
Statistics
Matches: 71, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
61 15 0.21
62 52 0.73
63 4 0.06
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.22
Consensus pattern (62 bp):
ATCGCAACGCGAATCTGGAAAATCGCAACGCGAATTAGGAAAATCGCATTGCGATAGTCAGT
Found at i:308300 original size:32 final size:33
Alignment explanation
Indices: 308216--308300 Score: 77
Period size: 34 Copynumber: 2.6 Consensus size: 33
308206 ACTTAATTCG
*
308216 TGCACACTTTTATATTTGAATATCTATTAGAACA
1 TGCACACTTTTATATTAGAATATCTATTA-AACA
* ** *
308250 TTC-CTTTTGTTGCT-TTAGAATATCTATT-AACA
1 TGCACACTT-TT-ATATTAGAATATCTATTAAACA
308282 TGCACACTTTTATATTAGA
1 TGCACACTTTTATATTAGA
308301 CTCTTAACTT
Statistics
Matches: 38, Mismatches: 9, Indels: 10
0.67 0.16 0.18
Matches are distributed among these distances:
31 1 0.03
32 13 0.34
33 6 0.16
34 17 0.45
35 1 0.03
ACGTcount: A:0.31, C:0.15, G:0.09, T:0.45
Consensus pattern (33 bp):
TGCACACTTTTATATTAGAATATCTATTAAACA
Found at i:317111 original size:16 final size:17
Alignment explanation
Indices: 317090--317125 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
317080 CAAGCCGAGC
317090 CGCTGACCG-CGTTGAT
1 CGCTGACCGACGTTGAT
*
317106 CGCTGACCGATGTTGAT
1 CGCTGACCGACGTTGAT
317123 CGC
1 CGC
317126 CGTTGACCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.14, C:0.31, G:0.31, T:0.25
Consensus pattern (17 bp):
CGCTGACCGACGTTGAT
Found at i:318623 original size:24 final size:24
Alignment explanation
Indices: 318595--318660 Score: 78
Period size: 24 Copynumber: 2.8 Consensus size: 24
318585 GTTTTATCTT
*
318595 ATTTCCTATTTGAATTCTATTCTG
1 ATTTCCTATCTGAATTCTATTCTG
* *
318619 ATTTCTTATCTGAATTCTGTTCTG
1 ATTTCCTATCTGAATTCTATTCTG
** *
318643 ATTTTTTATCTGGATTCT
1 ATTTCCTATCTGAATTCT
318661 GTTATGATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.18, C:0.15, G:0.11, T:0.56
Consensus pattern (24 bp):
ATTTCCTATCTGAATTCTATTCTG
Found at i:318661 original size:24 final size:24
Alignment explanation
Indices: 318605--318694 Score: 108
Period size: 24 Copynumber: 3.8 Consensus size: 24
318595 ATTTCCTATT
* *
318605 TGAATTCTATTCTGATTTCTTATC
1 TGAATTCTGTTCTGATTTTTTATC
318629 TGAATTCTGTTCTGATTTTTTATC
1 TGAATTCTGTTCTGATTTTTTATC
* * * *
318653 TGGATTCTGTTATGATATTTGATC
1 TGAATTCTGTTCTGATTTTTTATC
* *
318677 TAAATTCTGTTTTGATTT
1 TGAATTCTGTTCTGATTT
318695 CAGATATCTT
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 56 1.00
ACGTcount: A:0.20, C:0.11, G:0.13, T:0.56
Consensus pattern (24 bp):
TGAATTCTGTTCTGATTTTTTATC
Found at i:320861 original size:11 final size:10
Alignment explanation
Indices: 320834--320863 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
320824 GATGTTGATT
320834 GCCGTTGACC
1 GCCGTTGACC
320844 GCCGTTGACC
1 GCCGTTGACC
320854 GACCGTTGAC
1 G-CCGTTGAC
320864 TTTTTTTGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.58
11 8 0.42
ACGTcount: A:0.13, C:0.37, G:0.30, T:0.20
Consensus pattern (10 bp):
GCCGTTGACC
Found at i:322403 original size:24 final size:24
Alignment explanation
Indices: 322337--322439 Score: 93
Period size: 24 Copynumber: 4.3 Consensus size: 24
322327 TTTATCTAAT
* * *
322337 TTTC-GATTTGAATTATGTTCTAA
1 TTTCTGATCTGAATTCTGTTCTGA
* *
322360 TTTCTTATCTGAATTTTGTTCTGA
1 TTTCTGATCTGAATTCTGTTCTGA
*
322384 TTTCTGATCT-AGATTCTGTTATGA
1 TTTCTGATCTGA-ATTCTGTTCTGA
* * * *
322408 TATCTAATCTGAATTCTATTTTGA
1 TTTCTGATCTGAATTCTGTTCTGA
322432 TTTCTGAT
1 TTTCTGAT
322440 ATCTCCGTTT
Statistics
Matches: 64, Mismatches: 13, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
23 5 0.08
24 58 0.91
25 1 0.02
ACGTcount: A:0.22, C:0.12, G:0.13, T:0.53
Consensus pattern (24 bp):
TTTCTGATCTGAATTCTGTTCTGA
Found at i:329180 original size:16 final size:16
Alignment explanation
Indices: 329161--329200 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
329151 CGTTATTAAA
*
329161 CTGAATTGATATTTAT
1 CTGAATTGATATTTAC
*
329177 CTGACTTGATATTTAC
1 CTGAATTGATATTTAC
329193 CTGAATTG
1 CTGAATTG
329201 TAAGTTATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (16 bp):
CTGAATTGATATTTAC
Found at i:330269 original size:57 final size:58
Alignment explanation
Indices: 330160--330272 Score: 167
Period size: 57 Copynumber: 2.0 Consensus size: 58
330150 CATTTATATG
* * *
330160 CTTGTTGAAATTTATGAAAATTTAATAAAAAAACAGCAAATGTAAAATCAGTAGCATA
1 CTTGCTGAAATTCATGAAAATTTAATAAAAAAACAGCAAATGTAAAAGCAGTAGCATA
*
330218 CTTGCTGAAATTCATGAAAA-TTAA-AGAAAAAACAGTAAATGTAAAAGCAGTAGCA
1 CTTGCTGAAATTCATGAAAATTTAATA-AAAAAACAGCAAATGTAAAAGCAGTAGCA
330273 CCCTACAATA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
56 1 0.02
57 31 0.62
58 18 0.36
ACGTcount: A:0.50, C:0.10, G:0.14, T:0.26
Consensus pattern (58 bp):
CTTGCTGAAATTCATGAAAATTTAATAAAAAAACAGCAAATGTAAAAGCAGTAGCATA
Found at i:334213 original size:22 final size:21
Alignment explanation
Indices: 334165--334225 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
334155 ATTCCCCTGT
334165 GGGGGGAATCGGTTCCCTTCAA
1 GGGGGGAATCGGTTCCC-TCAA
*
334187 AGGGGGAATCGGTTCCCTC-A
1 GGGGGGAATCGGTTCCCTCAA
* *
334207 GGGGGGGATCGATTCCCTC
1 GGGGGGAATCGGTTCCCTC
334226 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 17 0.49
21 2 0.06
22 16 0.46
ACGTcount: A:0.16, C:0.25, G:0.38, T:0.21
Consensus pattern (21 bp):
GGGGGGAATCGGTTCCCTCAA
Done.