Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007216.1 Hibiscus syriacus cultivar Beakdansim tig00019080_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: 76273
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2197 original size:2 final size:2
Alignment explanation
Indices: 2190--2247 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
2180 ATGTAGGCAA
2190 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2232 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
2248 TTCTAAAGTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6176 original size:24 final size:24
Alignment explanation
Indices: 6144--6205 Score: 83
Period size: 24 Copynumber: 2.6 Consensus size: 24
6134 TATATAGTGG
6144 ATATATATTATAT-TATTTCAAAAT
1 ATATATATTATATATATTT-AAAAT
6168 ATATATATTATATACTATTTAAAAT
1 ATATATATTATATA-TATTTAAAAT
*
6193 AT-TATAGTATATA
1 ATATATATTATATA
6206 GAAATATATA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
24 23 0.66
25 7 0.20
26 5 0.14
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (24 bp):
ATATATATTATATATATTTAAAAT
Found at i:6228 original size:15 final size:14
Alignment explanation
Indices: 6210--6243 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
6200 TATATAGAAA
6210 TATATATTAGTATAT
1 TATATATTAGTA-AT
*
6225 TATATATTATTAAT
1 TATATATTAGTAAT
6239 TATAT
1 TATAT
6244 TTTATATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (14 bp):
TATATATTAGTAAT
Found at i:6232 original size:7 final size:7
Alignment explanation
Indices: 6210--6257 Score: 50
Period size: 7 Copynumber: 7.1 Consensus size: 7
6200 TATATAGAAA
6210 TATATAT
1 TATATAT
6217 TAGTATAT
1 TA-TATAT
6225 TATATAT
1 TATATAT
6232 TAT-TAAT
1 TATAT-AT
6239 TATAT-T
1 TATATAT
6245 T-TATAT
1 TATATAT
6251 TA-ATAT
1 TATATAT
6257 T
1 T
6258 TTTTTTAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
5 3 0.08
6 10 0.28
7 15 0.42
8 8 0.22
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (7 bp):
TATATAT
Found at i:9537 original size:48 final size:48
Alignment explanation
Indices: 9466--9561 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 48
9456 AAGTAAATGT
*
9466 AAGAGATGCAGTGACCCAAGAGTTCCTAGATCAAGTTCACATGACAGC
1 AAGAGATGCAGTCACCCAAGAGTTCCTAGATCAAGTTCACATGACAGC
*
9514 AAGAGATGTAGTCACCCAAGAGTTCCTAGATCAAGTTCACATGACAGC
1 AAGAGATGCAGTCACCCAAGAGTTCCTAGATCAAGTTCACATGACAGC
9562 TCATCACTTG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (48 bp):
AAGAGATGCAGTCACCCAAGAGTTCCTAGATCAAGTTCACATGACAGC
Found at i:11158 original size:20 final size:20
Alignment explanation
Indices: 11129--11166 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
11119 CCTTATATAA
11129 TGGATACCCTAAAACCATAG
1 TGGATACCCTAAAACCATAG
*
11149 TGGATCCCCTAAAACCAT
1 TGGATACCCTAAAACCAT
11167 CATACCCTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.29, G:0.13, T:0.21
Consensus pattern (20 bp):
TGGATACCCTAAAACCATAG
Found at i:13656 original size:21 final size:22
Alignment explanation
Indices: 13632--13684 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
13622 TAGGTTTGGT
13632 ATTGATCTCTTC-ACCAAAAGG
1 ATTGATCTCTTCAACCAAAAGG
* **
13653 ATTGATC-CCTCAATTAAAAGG
1 ATTGATCTCTTCAACCAAAAGG
13674 ATTGATCTCTT
1 ATTGATCTCTT
13685 TCCCTTTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 3 0.12
21 21 0.81
22 2 0.08
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (22 bp):
ATTGATCTCTTCAACCAAAAGG
Found at i:15046 original size:57 final size:57
Alignment explanation
Indices: 14975--15089 Score: 203
Period size: 57 Copynumber: 2.0 Consensus size: 57
14965 AGAAGAACAA
* *
14975 TAAAAAGAATGTGGGAATCACCTTCAAATCTACCAATGAGAGTAATAAAGACTCAAG
1 TAAAAAGAAGGTGGGAATCACCTTCAAATCCACCAATGAGAGTAATAAAGACTCAAG
*
15032 TAAAAAGAAGGTGGGAATCACCTTCAAATCCATCAATGAGAGTAATAAAGACTCAAG
1 TAAAAAGAAGGTGGGAATCACCTTCAAATCCACCAATGAGAGTAATAAAGACTCAAG
15089 T
1 T
15090 GAAGAGGTGG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.45, C:0.16, G:0.18, T:0.21
Consensus pattern (57 bp):
TAAAAAGAAGGTGGGAATCACCTTCAAATCCACCAATGAGAGTAATAAAGACTCAAG
Found at i:15614 original size:15 final size:15
Alignment explanation
Indices: 15592--15626 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
15582 GCTTTCAAAA
15592 TTGAAAAATGAAAATT
1 TTGAAAAA-GAAAATT
*
15608 TTGAAAAAGAAATTT
1 TTGAAAAAGAAAATT
15623 TTGA
1 TTGA
15627 TTTGAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.34
Consensus pattern (15 bp):
TTGAAAAAGAAAATT
Found at i:19117 original size:22 final size:21
Alignment explanation
Indices: 19086--19149 Score: 58
Period size: 20 Copynumber: 3.0 Consensus size: 21
19076 TGATCGATCA
19086 TTTACAAAAAGGATCGATCCCT
1 TTTACAAAAA-GATCGATCCCT
* * *
19108 TTTACCAAAAGATCGTTCCCC
1 TTTACAAAAAGATCGATCCCT
* * *
19129 TTGA-AAAAATATTGATCCCT
1 TTTACAAAAAGATCGATCCCT
19149 T
1 T
19150 GGATTCCAGT
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
20 12 0.36
21 12 0.36
22 9 0.27
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.31
Consensus pattern (21 bp):
TTTACAAAAAGATCGATCCCT
Found at i:19127 original size:21 final size:22
Alignment explanation
Indices: 19086--19127 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
19076 TGATCGATCA
19086 TTTACAAAAAGGATCGATCCCT
1 TTTACAAAAAGGATCGATCCCT
* *
19108 TTTACCAAAA-GATCGTTCCC
1 TTTACAAAAAGGATCGATCCC
19128 CTTGAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (22 bp):
TTTACAAAAAGGATCGATCCCT
Found at i:19229 original size:21 final size:22
Alignment explanation
Indices: 19205--19305 Score: 111
Period size: 21 Copynumber: 4.8 Consensus size: 22
19195 TCTCTCGAGG
19205 AAAAAGATCAATCCCTTC-ATC
1 AAAAAGATCAATCCCTTCGATC
* *
19226 AAAATGATCAATCCC-TCGATG
1 AAAAAGATCAATCCCTTCGATC
*
19247 AAAAAGATCAATCCCTT-TATC
1 AAAAAGATCAATCCCTTCGATC
* *
19268 AAAAGGATCAATCCC-TCGATG
1 AAAAAGATCAATCCCTTCGATC
* *
19289 AAAATGATCGATCCCTT
1 AAAAAGATCAATCCCTT
19306 TCTTGCAATG
Statistics
Matches: 66, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
20 3 0.05
21 61 0.92
22 2 0.03
ACGTcount: A:0.40, C:0.25, G:0.11, T:0.25
Consensus pattern (22 bp):
AAAAAGATCAATCCCTTCGATC
Found at i:19306 original size:42 final size:42
Alignment explanation
Indices: 19198--19306 Score: 173
Period size: 42 Copynumber: 2.6 Consensus size: 42
19188 GGATTGATCT
* * *
19198 CTCGAGGAAAAAGATCAATCCCTTCATCAAAATGATCAATCC
1 CTCGATGAAAAAGATCAATCCCTTTATCAAAAGGATCAATCC
19240 CTCGATGAAAAAGATCAATCCCTTTATCAAAAGGATCAATCC
1 CTCGATGAAAAAGATCAATCCCTTTATCAAAAGGATCAATCC
* *
19282 CTCGATGAAAATGATCGATCCCTTT
1 CTCGATGAAAAAGATCAATCCCTTT
19307 CTTGCAATGG
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 62 1.00
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.25
Consensus pattern (42 bp):
CTCGATGAAAAAGATCAATCCCTTTATCAAAAGGATCAATCC
Found at i:20757 original size:225 final size:224
Alignment explanation
Indices: 20252--20763 Score: 547
Period size: 225 Copynumber: 2.3 Consensus size: 224
20242 CTGCGATTTG
* * * **
20252 GCTTAACTCAACGACAAGGAGCTAGTTTCCAATTAAAGTTTTCAAGCCAAGTTTCAAAAACACAA
1 GCTTAACTCAACGACGATGAGCTAGTTTCCAGTTAAAGTTTTCAAGCCAAGTTTCAAATTCACAA
* * * * * * * ** *
20317 CGAATGATACTTGACCCGGAAGCGTATTCAGAGCTGACTACAATTTGGCTTAACTCAGTGCGATG
66 CGAACGATACTTGACCCAGAAGCATATTCAGAACTGACTACAAATTAGCCTAACTCAACGCGAGG
* * * * * ** *
20382 AGCCATCTTCTAATCAAATCTTTTCAAAGTTAATTTCAACACCATGATGGAGGATATTGGGTTCG
131 AGCAATCTTATAATCAAACCTTTTCAAAGTCAATTTCAACACCACGACAGAGGATATTGAGTTCG
* **
20447 AAAGCCAATTTAAAATCAACAACATTCTA
196 AAAGCCAATTCAAAATCAACAACAGCCTA
** * * * * * *
20476 GCTTAGGTCAGCGTCGATGAGCTAGTTTCCAGTTGAAGTTTTCAGGCCAAGTTTCAATTTCACAT
1 GCTTAACTCAACGACGATGAGCTAGTTTCCAGTTAAAGTTTTCAAGCCAAGTTTCAAATTCACAA
* *
20541 TGAACGATACTTGACCCAGAAGCATATTCAGAACTGACTACAAATTAGCCTAACTCAACGATGAG
66 CGAACGATACTTGACCCAGAAGCATATTCAGAACTGACTACAAATTAGCCTAACTCAACG-CGAG
* * * * *
20606 GAGCAATCTTATAGTCAAACCTTTTCGAAGTCAATTTCAACTCCACGACATATGATATTGAGTTC
130 GAGCAATCTTATAATCAAACCTTTTCAAAGTCAATTTCAACACCACGACAGAGGATATTGAGTTC
* * * *
20671 GAAAGCCAATTCAGAATCGACTACGGCCTA
195 GAAAGCCAATTCAAAATCAACAACAGCCTA
* * * * * * *
20701 GCTTAACTCAACAACGATGAGTTAGTTTCTAGTTTAACTTTTCAAGCCATGTTTCAACTTCAC
1 GCTTAACTCAACGACGATGAGCTAGTTTCCAGTTAAAGTTTTCAAGCCAAGTTTCAAATTCAC
20764 GGCAAAGGAT
Statistics
Matches: 230, Mismatches: 57, Indels: 1
0.80 0.20 0.00
Matches are distributed among these distances:
224 102 0.44
225 128 0.56
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (224 bp):
GCTTAACTCAACGACGATGAGCTAGTTTCCAGTTAAAGTTTTCAAGCCAAGTTTCAAATTCACAA
CGAACGATACTTGACCCAGAAGCATATTCAGAACTGACTACAAATTAGCCTAACTCAACGCGAGG
AGCAATCTTATAATCAAACCTTTTCAAAGTCAATTTCAACACCACGACAGAGGATATTGAGTTCG
AAAGCCAATTCAAAATCAACAACAGCCTA
Found at i:21013 original size:203 final size:203
Alignment explanation
Indices: 20618--21019 Score: 470
Period size: 203 Copynumber: 2.0 Consensus size: 203
20608 GCAATCTTAT
* * *
20618 AGTCAAACCTTTTCGAAGTCAATTTCAACTCCACGACATATGATATTGAGTTCGAAAGCCAATTC
1 AGTCAAACATTTTCGAAGTCAATTTCAACTCCACGACAGAGGATATTGAGTTCGAAAGCCAATTC
** * * * *
20683 AGAATCGACTACGGCCTAGCTTAACTCAACAACGATGAGTTAGTTTCTAGTTTAACTTTTCAAGC
66 AGAATCGACTACAACCTAGCTTAACTCAACAACAATGAGCTAGTTTCCAGTTGAACTTTTCAAGC
* * * * *
20748 CATGTTTCAACTTCACGGCAAAGGATAATTGACCCAGGAGTGCATTTAGAAATGATTACAATTTG
131 CAAGTTTCAACTTCACGGCAAAGGATAATTGACCCAGAAATGCATTCAGAAATGACTACAATTTG
20813 GCTTTTCA
196 GCTTTTCA
* * * *
20821 AGTCAAATATTTTCGAAGTCAATTTCAATTCCACGA-AGGAGGATATTGGGTTCGAAAGCTAATT
1 AGTCAAACATTTTCGAAGTCAATTTCAACTCCACGACA-GAGGATATTGAGTTCGAAAGCCAATT
* * * * * *
20885 CAGAATGGACTTCAATCTAGCTTAACT-AAGCGACAATGAGCTAGTTTCCAGTTGAAGTTTTCAG
65 CAGAATCGACTACAACCTAGCTTAACTCAA-CAACAATGAGCTAGTTTCCAGTTGAACTTTTCAA
* * * * * *
20949 GCCAAGTTTCACCTTCACGG-AGAAGGATACTTGA-TCTGAAAATGCATTCATACATGACTACAA
129 GCCAAGTTTCAACTTCACGGCA-AAGGATAATTGACCCAG-AAATGCATTCAGAAATGACTACAA
21012 TTTGGCTT
192 TTTGGCTT
21020 AACTCAGCAG
Statistics
Matches: 165, Mismatches: 30, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
202 6 0.04
203 159 0.96
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Consensus pattern (203 bp):
AGTCAAACATTTTCGAAGTCAATTTCAACTCCACGACAGAGGATATTGAGTTCGAAAGCCAATTC
AGAATCGACTACAACCTAGCTTAACTCAACAACAATGAGCTAGTTTCCAGTTGAACTTTTCAAGC
CAAGTTTCAACTTCACGGCAAAGGATAATTGACCCAGAAATGCATTCAGAAATGACTACAATTTG
GCTTTTCA
Found at i:27106 original size:11 final size:11
Alignment explanation
Indices: 27092--27147 Score: 51
Period size: 13 Copynumber: 4.7 Consensus size: 11
27082 TCTTTTTGAA
27092 TTCTTTTTCTT
1 TTCTTTTTCTT
27103 TTCTTTTCTTCTT
1 TTC-TTT-TTCTT
*
27116 TTCTTCTTCTTTT
1 TTCTT-TT-TCTT
27129 TGTCTTTTTC-T
1 T-TCTTTTTCTT
27140 TTCTTTTT
1 TTCTTTTT
27148 GCACTCCAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 7 0.18
11 5 0.13
12 7 0.18
13 15 0.39
14 4 0.11
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:27116 original size:19 final size:18
Alignment explanation
Indices: 27092--27147 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
27082 TCTTTTTGAA
27092 TTCTTTTTCTTTTCTTTT
1 TTCTTTTTCTTTTCTTTT
27110 CTTC-TTTTCTTCTTCTTTT
1 -TTCTTTTTCTT-TTCTTTT
27129 TGTCTTTTTC-TTTCTTTT
1 T-TCTTTTTCTTTTCTTTT
27147 T
1 T
27148 GCACTCCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 16 0.47
19 13 0.38
20 5 0.15
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (18 bp):
TTCTTTTTCTTTTCTTTT
Found at i:29008 original size:15 final size:15
Alignment explanation
Indices: 28988--29024 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
28978 CCTTAACAAG
28988 CACATCAATCAGCGA
1 CACATCAATCAGCGA
29003 CACATCAATCAGCGA
1 CACATCAATCAGCGA
*
29018 CGCATCA
1 CACATCA
29025 TTCAAGCCGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.38, C:0.35, G:0.14, T:0.14
Consensus pattern (15 bp):
CACATCAATCAGCGA
Found at i:31153 original size:11 final size:11
Alignment explanation
Indices: 31130--31164 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
31120 TATACACTTA
31130 TAAAAATATATT
1 TAAAAATA-ATT
31142 TAAAAATAATT
1 TAAAAATAATT
*
31153 TAAAATTAATT
1 TAAAAATAATT
31164 T
1 T
31165 TTTGATGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 14 0.64
12 8 0.36
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TAAAAATAATT
Found at i:36241 original size:12 final size:12
Alignment explanation
Indices: 36214--36249 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
36204 TTGTAAATAA
*
36214 AATAAATTAAATT
1 AATAAATT-TATT
36227 AATAAATTTATT
1 AATAAATTTATT
36239 AATAAATTTAT
1 AATAAATTTAT
36250 ATTATACTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 14 0.64
13 8 0.36
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
AATAAATTTATT
Found at i:36947 original size:28 final size:28
Alignment explanation
Indices: 36877--36947 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
36867 TTCATCTAAG
36877 TACATAAAGTTATCTTTTTAATAAAAAAGA
1 TACATAAAG-TAT-TTTTTAATAAAAAAGA
* * *
36907 TACATCAAA-TATTTTTTATTAAAATAGG
1 TACAT-AAAGTATTTTTTAATAAAAAAGA
*
36935 TATATAAAGTATT
1 TACATAAAGTATT
36948 CAATTTTTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
27 3 0.09
28 21 0.60
29 3 0.09
30 5 0.14
31 3 0.09
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.41
Consensus pattern (28 bp):
TACATAAAGTATTTTTTAATAAAAAAGA
Found at i:53255 original size:14 final size:14
Alignment explanation
Indices: 53238--53272 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
53228 TCGTTTATTG
*
53238 TGTTTGTTTATATC
1 TGTTTATTTATATC
*
53252 TGTTCATTTATATC
1 TGTTTATTTATATC
53266 TGTTTAT
1 TGTTTAT
53273 ATTCATTCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.17, C:0.09, G:0.11, T:0.63
Consensus pattern (14 bp):
TGTTTATTTATATC
Found at i:55819 original size:22 final size:20
Alignment explanation
Indices: 55773--55851 Score: 67
Period size: 19 Copynumber: 4.0 Consensus size: 20
55763 GATGTGATTA
55773 ATTTTAAATTAAATTT--TT
1 ATTTTAAATTAAATTTAGTT
*
55791 ATATTAACATTAAATTTAGGTT
1 ATTTTAA-ATTAAATTTA-GTT
55813 ATTTTAAAATTAAA-TTAGTT
1 ATTTT-AAATTAAATTTAGTT
* *
55833 -TATTTATATTAACTTTAGT
1 AT-TTTAAATTAAATTTAGT
55852 GATATTGTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
18 6 0.12
19 16 0.32
20 11 0.22
21 3 0.06
22 12 0.24
23 2 0.04
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (20 bp):
ATTTTAAATTAAATTTAGTT
Found at i:57664 original size:30 final size:30
Alignment explanation
Indices: 57613--57758 Score: 188
Period size: 30 Copynumber: 4.9 Consensus size: 30
57603 ACCTGACCCG
57613 GTGACATTTTGGGAATT-TTTTTAAAAACA
1 GTGACATTTTGGGAATTATTTTTAAAAACA
* * *
57642 GTGACATTTTGGGATTTTTTTTTAAAAATA
1 GTGACATTTTGGGAATTATTTTTAAAAACA
** *
57672 GTGACATTTTGATAATTATTTTTAAAAATA
1 GTGACATTTTGGGAATTATTTTTAAAAACA
* *
57702 GTGACATTTTGAGAATTATTTGT-AAAACA
1 GTGACATTTTGGGAATTATTTTTAAAAACA
* *
57731 GTGACATTTTGGTAATTATTTGTAAAAA
1 GTGACATTTTGGGAATTATTTTTAAAAA
57759 AAGGCGATAT
Statistics
Matches: 104, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
29 42 0.40
30 62 0.60
ACGTcount: A:0.36, C:0.05, G:0.16, T:0.44
Consensus pattern (30 bp):
GTGACATTTTGGGAATTATTTTTAAAAACA
Found at i:57737 original size:59 final size:60
Alignment explanation
Indices: 57613--57758 Score: 197
Period size: 59 Copynumber: 2.5 Consensus size: 60
57603 ACCTGACCCG
* * * * * *
57613 GTGACATTTTGGGAATT-TTTTTAAAAACAGTGACATTTTGGGATTTTTTTTTAAAAATA
1 GTGACATTTTGGTAATTATTTTTAAAAACAGTGACATTTTGAGAATTATTTGTAAAAACA
* *
57672 GTGACATTTTGATAATTATTTTTAAAAATAGTGACATTTTGAGAATTATTTGT-AAAACA
1 GTGACATTTTGGTAATTATTTTTAAAAACAGTGACATTTTGAGAATTATTTGTAAAAACA
*
57731 GTGACATTTTGGTAATTATTTGTAAAAA
1 GTGACATTTTGGTAATTATTTTTAAAAA
57759 AAGGCGATAT
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
59 46 0.61
60 30 0.39
ACGTcount: A:0.36, C:0.05, G:0.16, T:0.44
Consensus pattern (60 bp):
GTGACATTTTGGTAATTATTTTTAAAAACAGTGACATTTTGAGAATTATTTGTAAAAACA
Found at i:57777 original size:31 final size:29
Alignment explanation
Indices: 57615--57778 Score: 125
Period size: 30 Copynumber: 5.5 Consensus size: 29
57605 CTGACCCGGT
* * *
57615 GACATTTTGGGAATT-TTTTTAAAAACAGT
1 GACATTTTGGTAATTATTTGTAAAAA-AGC
* * * * *
57644 GACATTTTGGGATTTTTTTTTAAAAATAGT
1 GACATTTTGGTAATTATTTGTAAAAA-AGC
* * *
57674 GACATTTTGATAATTATTTTTAAAAATAGT
1 GACATTTTGGTAATTATTTGTAAAAA-AGC
* *
57704 GACATTTTGAG-AATTATTTGTAAAACAGT
1 GACATTTTG-GTAATTATTTGTAAAAAAGC
57733 GACATTTTGGTAATTATTTGTAAAAAAAGGC
1 GACATTTTGGTAATTATTTGT-AAAAAA-GC
* *
57764 GATATTTTTGTAATT
1 GACATTTTGGTAATT
57779 TTCAACGGTA
Statistics
Matches: 117, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
28 1 0.01
29 36 0.31
30 66 0.56
31 14 0.12
ACGTcount: A:0.35, C:0.05, G:0.16, T:0.44
Consensus pattern (29 bp):
GACATTTTGGTAATTATTTGTAAAAAAGC
Found at i:58860 original size:25 final size:25
Alignment explanation
Indices: 58808--58860 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
58798 ATGGTAACTC
* * *
58808 TTTTATGAGATTTACTGTAGTTTAA
1 TTTTATGAGATTTACTGGACTATAA
*
58833 TTTTATGAGATTTACTGGACTATGA
1 TTTTATGAGATTTACTGGACTATAA
58858 TTT
1 TTT
58861 GTTTAGTGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.06, G:0.17, T:0.51
Consensus pattern (25 bp):
TTTTATGAGATTTACTGGACTATAA
Found at i:62474 original size:25 final size:25
Alignment explanation
Indices: 62440--62487 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
62430 ATTTTTGCCT
62440 TGAAGATTTGGAGACACTATCTTTA
1 TGAAGATTTGGAGACACTATCTTTA
62465 TGAAGATTTGGAGACACTATCTT
1 TGAAGATTTGGAGACACTATCTT
62488 CTGACCCAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.35
Consensus pattern (25 bp):
TGAAGATTTGGAGACACTATCTTTA
Found at i:63697 original size:18 final size:18
Alignment explanation
Indices: 63674--63744 Score: 88
Period size: 18 Copynumber: 3.8 Consensus size: 18
63664 ACTGAATATT
*
63674 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
*
63692 TGTCCCGAAGGACCACTGTT
1 TGTCCCGAAGGACCAC--TA
* *
63712 TGTTCCGAAGAACCACTA
1 TGTCCCGAAGGACCACTA
63730 TGTCCCGAAGGACCA
1 TGTCCCGAAGGACCA
63745 TTGTTTATCC
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
18 29 0.66
20 15 0.34
ACGTcount: A:0.27, C:0.31, G:0.21, T:0.21
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:63720 original size:38 final size:38
Alignment explanation
Indices: 63672--63755 Score: 125
Period size: 38 Copynumber: 2.2 Consensus size: 38
63662 GCACTGAATA
63672 TTTGTCCCGAATG-ACCACTATGTCCCGAAGGACCACTG
1 TTTGTCCCGAA-GAACCACTATGTCCCGAAGGACCACTG
* *
63710 TTTGTTCCGAAGAACCACTATGTCCCGAAGGACCATTG
1 TTTGTCCCGAAGAACCACTATGTCCCGAAGGACCACTG
*
63748 TTTATCCC
1 TTTGTCCC
63756 TCGACTCTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
37 1 0.02
38 40 0.98
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (38 bp):
TTTGTCCCGAAGAACCACTATGTCCCGAAGGACCACTG
Found at i:63721 original size:20 final size:20
Alignment explanation
Indices: 63672--63755 Score: 77
Period size: 18 Copynumber: 4.4 Consensus size: 20
63662 GCACTGAATA
*
63672 TTTGTCCCGAATGACCAC--
1 TTTGTCCCGAAGGACCACTG
*
63690 TATGTCCCGAAGGACCACTG
1 TTTGTCCCGAAGGACCACTG
* *
63710 TTTGTTCCGAAGAACCAC--
1 TTTGTCCCGAAGGACCACTG
* *
63728 TATGTCCCGAAGGACCATTG
1 TTTGTCCCGAAGGACCACTG
*
63748 TTTATCCC
1 TTTGTCCC
63756 TCGACTCTTG
Statistics
Matches: 51, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
18 30 0.59
20 21 0.41
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (20 bp):
TTTGTCCCGAAGGACCACTG
Found at i:64562 original size:64 final size:64
Alignment explanation
Indices: 64486--64663 Score: 218
Period size: 64 Copynumber: 2.8 Consensus size: 64
64476 CCTTTAACGT
* * * * *
64486 GTGCATTGATGCACTACC-TGTGCATCGATACA-AGAATTACATTCGATGTTT-TCTTCTTAAGG
1 GTGCATCGATGCACT-CCTTATGCATCGATACACAG-ATGACATTCGATGTTTGTATT-TTAAGA
64548 GG
63 GG
* * *
64550 GTGCATCGATGCACTCCTTATGTATCGATGCACTGATGACATTCGATGTTTGTATTTTAAGAGG
1 GTGCATCGATGCACTCCTTATGCATCGATACACAGATGACATTCGATGTTTGTATTTTAAGAGG
* *
64614 GTGCATCGATGCACTCCTTATGCATCGATGCACTGATGACATTCGATGTT
1 GTGCATCGATGCACTCCTTATGCATCGATACACAGATGACATTCGATGTT
64664 CATTATTTGA
Statistics
Matches: 102, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
63 2 0.02
64 96 0.94
65 4 0.04
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (64 bp):
GTGCATCGATGCACTCCTTATGCATCGATACACAGATGACATTCGATGTTTGTATTTTAAGAGG
Found at i:69806 original size:2 final size:2
Alignment explanation
Indices: 69799--69835 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
69789 TTATGTAAGC
69799 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
69836 CACACAACAC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:70267 original size:64 final size:64
Alignment explanation
Indices: 70195--70372 Score: 227
Period size: 64 Copynumber: 2.8 Consensus size: 64
70185 CCTTTAACGT
* * *
70195 GTGCATCGATGCACTACC-TGTGCATCGATACA-AGAATTACATTCGATGTTT-TCTTCTTAAGG
1 GTGCATCGATGCACT-CCTTATGCATCGATACACAG-ATGACATTCGATGTTTGTATT-TTAAGG
70257 GG
63 GG
* * *
70259 GTGCATCGATGCACTCCTTATGCATCGATGCACTGATGGCATTCGATGTTTGTATTTTAAGGGG
1 GTGCATCGATGCACTCCTTATGCATCGATACACAGATGACATTCGATGTTTGTATTTTAAGGGG
* * *
70323 GTGCATCGATGCACTCCTTATGCATCGATGCACTGATAACATTCGATGTT
1 GTGCATCGATGCACTCCTTATGCATCGATACACAGATGACATTCGATGTT
70373 CATTATTTGA
Statistics
Matches: 103, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
63 2 0.02
64 97 0.94
65 4 0.04
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (64 bp):
GTGCATCGATGCACTCCTTATGCATCGATACACAGATGACATTCGATGTTTGTATTTTAAGGGG
Found at i:73032 original size:29 final size:29
Alignment explanation
Indices: 72986--73069 Score: 89
Period size: 29 Copynumber: 2.9 Consensus size: 29
72976 TGTGAACCGG
* * *
72986 TGACTTTTTGGGATTTTTTATAAAAATAA
1 TGACATTTTGGGAATTTTTATAAAAACAA
*
73015 TGACATTTTGGGAATTTTTTTAAAAACAA
1 TGACATTTTGGGAATTTTTATAAAAACAA
* * *
73044 TGATATTCTGGTAATTATTTA-AAAAA
1 TGACATTTTGGGAATT-TTTATAAAAA
73070 GTGATATTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 43 0.93
30 3 0.07
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.44
Consensus pattern (29 bp):
TGACATTTTGGGAATTTTTATAAAAACAA
Found at i:73075 original size:27 final size:27
Alignment explanation
Indices: 73006--73085 Score: 72
Period size: 29 Copynumber: 2.9 Consensus size: 27
72996 GGATTTTTTA
* * * *
73006 TAAAAATAATGACATTTTGGGAATTTTTT
1 TAAAAACAATGATA-TTTGGTAA-TTATT
73035 TAAAAACAATGATATTCTGGTAATTATT
1 TAAAAACAATGATATT-TGGTAATTATT
* *
73063 TAAAAA-AGTGATATTTTGTAATT
1 TAAAAACAATGATATTTGGTAATT
73086 TTCGACGGTG
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
26 7 0.16
27 8 0.18
28 12 0.27
29 17 0.39
ACGTcount: A:0.41, C:0.04, G:0.12, T:0.42
Consensus pattern (27 bp):
TAAAAACAATGATATTTGGTAATTATT
Found at i:74032 original size:31 final size:30
Alignment explanation
Indices: 73961--74035 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 30
73951 CTAATGTGAC
*
73961 TCTTAGGTAGGCTCTGCGGCCCTGAGATCAT
1 TCTTAGGTAGGC-CTGCGGCCCTAAGATCAT
** **
73992 TCTCGGGTAGGCCTGCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCTGCGGCCCTAAGAT-CAT
74023 TCTTAGGTAGGCC
1 TCTTAGGTAGGCC
74036 CCAAGATGTG
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
30 14 0.39
31 22 0.61
ACGTcount: A:0.15, C:0.25, G:0.32, T:0.28
Consensus pattern (30 bp):
TCTTAGGTAGGCCTGCGGCCCTAAGATCAT
Found at i:74035 original size:24 final size:24
Alignment explanation
Indices: 74008--74062 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
73998 GTAGGCCTGC
*
74008 GGCCCTAAGATGTGTTCTTAGGTA
1 GGCCCCAAGATGTGTTCTTAGGTA
74032 GGCCCCAAGATGTGTTCTTAGGTA
1 GGCCCCAAGATGTGTTCTTAGGTA
74056 GGCCCCA
1 GGCCCCA
74063 CGGCCCCAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (24 bp):
GGCCCCAAGATGTGTTCTTAGGTA
Found at i:74175 original size:25 final size:25
Alignment explanation
Indices: 74123--74175 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
74113 AGAGTAACTC
*
74123 TTTTATGAGATTTACTGCAGTATAA
1 TTTTATGAGATTTACTGCACTATAA
* *
74148 TTTTATGAGATTTACTGGACTATGA
1 TTTTATGAGATTTACTGCACTATAA
74173 TTT
1 TTT
74176 GTTTAGTGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.08, G:0.17, T:0.47
Consensus pattern (25 bp):
TTTTATGAGATTTACTGCACTATAA
Done.