Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007197.1 Hibiscus syriacus cultivar Beakdansim tig00018976_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: 58793
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:2101 original size:125 final size:125
Alignment explanation
Indices: 1880--2254 Score: 698
Period size: 125 Copynumber: 3.0 Consensus size: 125
1870 CAACTCCATT
1880 AATTTCAAAATCAAGTCGAGTTGATTGCACAAACAATT-GGGGGGACAAGGGTTACCTCAAAAAC
1 AATTTCAAAATCAAGTCGAGTTGATTGCACAAACAATTGGGGGGGACAAGGGTTACCTCAAAAAC
*
1944 ATATTAATGAACACCAATGGCCACTTGCATGTGTCGTAACCGTCCTTCGGGTGGGCCCAG
66 ATATTAATGAACACCAAGGGCCACTTGCATGTGTCGTAACCGTCCTTCGGGTGGGCCCAG
2004 AATTTCAAAATCAAGTCGAGTTGATTGCACAAACAATTGGGGGGGACAAGGGTTACCTCAAAAAC
1 AATTTCAAAATCAAGTCGAGTTGATTGCACAAACAATTGGGGGGGACAAGGGTTACCTCAAAAAC
2069 ATATTAATGAACACCAAGGGCCACTTGCATGTGTCGTAACCGTCCTTCGGGTGGGCCCAG
66 ATATTAATGAACACCAAGGGCCACTTGCATGTGTCGTAACCGTCCTTCGGGTGGGCCCAG
* *
2129 AATTTTAAAATCAAGTCGAGTTGATTGCACAAACAATTGGGGGGGACAAGGGTTACCTCAAAAGC
1 AATTTCAAAATCAAGTCGAGTTGATTGCACAAACAATTGGGGGGGACAAGGGTTACCTCAAAAAC
* *
2194 ATATTAATGAACACCAAGGGCCACTTGCATGTGTCGTAATCGTCCTTCGGGTGGGTCCAG
66 ATATTAATGAACACCAAGGGCCACTTGCATGTGTCGTAACCGTCCTTCGGGTGGGCCCAG
2254 A
1 A
2255 GTCGAACTTC
Statistics
Matches: 245, Mismatches: 5, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
124 38 0.16
125 207 0.84
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (125 bp):
AATTTCAAAATCAAGTCGAGTTGATTGCACAAACAATTGGGGGGGACAAGGGTTACCTCAAAAAC
ATATTAATGAACACCAAGGGCCACTTGCATGTGTCGTAACCGTCCTTCGGGTGGGCCCAG
Found at i:2775 original size:47 final size:49
Alignment explanation
Indices: 2678--2779 Score: 149
Period size: 47 Copynumber: 2.1 Consensus size: 49
2668 ATTAAAAGAG
*
2678 AAATAAATAAAAATGAAGAAAATGTTAAATTATAAAAGAAATTTAAAAT
1 AAATAATTAAAAATGAAGAAAATGTTAAATTATAAAAGAAATTTAAAAT
*
2727 AAATAATTAAAAATTAAG-AAATG-TAAAGTT-TAAAAGAAATTTAAAAT
1 AAATAATTAAAAATGAAGAAAATGTTAAA-TTATAAAAGAAATTTAAAAT
2774 -AATAAT
1 AAATAAT
2780 AAAGAAAATG
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
46 6 0.12
47 21 0.42
48 7 0.14
49 16 0.32
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (49 bp):
AAATAATTAAAAATGAAGAAAATGTTAAATTATAAAAGAAATTTAAAAT
Found at i:2842 original size:36 final size:36
Alignment explanation
Indices: 2742--2853 Score: 113
Period size: 36 Copynumber: 3.1 Consensus size: 36
2732 ATTAAAAATT
* *
2742 AAGAAATG-TAAAGTTTAAAAGAAATTTAAAATAATAATA
1 AAGAAATGTTAAATTTTAGAAGAAA--TAAAATAA-AA-A
* *
2781 AAGAAAATGTT--ATTTTTGAAAAAATAAAATAAAAA
1 AAG-AAATGTTAAATTTTAGAAGAAATAAAATAAAAA
*
2816 AAGAAATGTTAAATTTTAGAAGAAATAAAATAATAA
1 AAGAAATGTTAAATTTTAGAAGAAATAAAATAAAAA
2852 AA
1 AA
2854 TTTTAAAAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
34 7 0.11
35 4 0.06
36 25 0.40
37 8 0.13
39 12 0.19
40 5 0.08
41 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.28
Consensus pattern (36 bp):
AAGAAATGTTAAATTTTAGAAGAAATAAAATAAAAA
Found at i:4132 original size:10 final size:10
Alignment explanation
Indices: 4107--4229 Score: 60
Period size: 10 Copynumber: 12.2 Consensus size: 10
4097 ACGTAGACCA
*
4107 AATA-AAAAA
1 AATATAAAAT
4116 AAT-TAAAAT
1 AATATAAAAT
4125 AATATAAAAT
1 AATATAAAAT
4135 AATA-AAAAT
1 AATATAAAAT
* *
4144 AATACATAAT
1 AATATAAAAT
4154 AAATATAAAATTAT
1 -AATAT-AAA--AT
4168 AATATAAAA-
1 AATATAAAAT
* *
4177 ATATATGATAT
1 A-ATATAAAAT
*
4188 AATATATAGAT
1 AATATA-AAAT
*
4199 -ATA-AATAAC
1 AATATAA-AAT
*
4208 AATATAATAT
1 AATATAAAAT
*
4218 AATATATAAT
1 AATATAAAAT
4228 AA
1 AA
4230 AACTATATAA
Statistics
Matches: 87, Mismatches: 14, Indels: 25
0.69 0.11 0.20
Matches are distributed among these distances:
8 1 0.01
9 22 0.25
10 42 0.48
11 10 0.11
12 5 0.06
13 5 0.06
14 2 0.02
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (10 bp):
AATATAAAAT
Found at i:4142 original size:19 final size:20
Alignment explanation
Indices: 4107--4164 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 20
4097 ACGTAGACCA
*
4107 AATA-AAAAAAAT-TAAAAT
1 AATACAAAATAATATAAAAT
*
4125 AATATAAAATAATA-AAAAT
1 AATACAAAATAATATAAAAT
*
4144 AATACATAATAAATATAAAAT
1 AATACAAAAT-AATATAAAAT
4165 TATAATATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
18 4 0.12
19 20 0.61
20 4 0.12
21 5 0.15
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (20 bp):
AATACAAAATAATATAAAAT
Found at i:4144 original size:9 final size:9
Alignment explanation
Indices: 4107--4147 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
4097 ACGTAGACCA
*
4107 AATAAAAAA
1 AATAAAAAT
*
4116 AATTAAAAT
1 AATAAAAAT
4125 AATATAAAAT
1 AATA-AAAAT
4135 AATAAAAAT
1 AATAAAAAT
4144 AATA
1 AATA
4148 CATAATAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
9 19 0.68
10 9 0.32
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
AATAAAAAT
Found at i:4193 original size:12 final size:13
Alignment explanation
Indices: 4176--4242 Score: 54
Period size: 12 Copynumber: 5.4 Consensus size: 13
4166 ATAATATAAA
4176 AATAT-ATGATAT
1 AATATAATGATAT
4188 AATAT-ATAGATAT
1 AATATAAT-GATAT
**
4201 AA-ATAACAATAT
1 AATATAATGATAT
4213 AATATAAT-ATAT
1 AATATAATGATAT
*
4225 AATAAAACT-ATAT
1 AATATAA-TGATAT
4238 AATAT
1 AATAT
4243 TATATTTTCG
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
12 25 0.54
13 21 0.46
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (13 bp):
AATATAATGATAT
Found at i:4242 original size:30 final size:29
Alignment explanation
Indices: 4123--4247 Score: 107
Period size: 30 Copynumber: 4.2 Consensus size: 29
4113 AAAAATTAAA
*
4123 ATAATATAA-A-ATAATAAAAATAATACAT
1 ATAATATAATATATAATATAAATAATA-AT
*
4151 AATAAATATAAAATTATAATATAAA-AAT-AT
1 -AT-AATATAATA-TATAATATAAATAATAAT
* *
4181 ATGATATAATATATAGATATAAATAACAAT
1 ATAATATAATATATA-ATATAAATAATAAT
4211 ATAATATAATATATAATA-AAACTATATAAT
1 ATAATATAATATATAATATAAA-TA-ATAAT
*
4241 ATTATAT
1 ATAATAT
4248 TTTCGAAAAT
Statistics
Matches: 80, Mismatches: 7, Indels: 17
0.77 0.07 0.16
Matches are distributed among these distances:
27 4 0.05
28 17 0.21
29 11 0.14
30 35 0.44
31 1 0.01
32 3 0.04
33 9 0.11
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (29 bp):
ATAATATAATATATAATATAAATAATAAT
Found at i:4247 original size:25 final size:24
Alignment explanation
Indices: 4155--4247 Score: 78
Period size: 25 Copynumber: 3.6 Consensus size: 24
4145 ATACATAATA
* *
4155 AATATAAAATTATAATATAAAAATAT
1 AATATAATATTAT-ATATAAAAA-AC
* *
4181 ATGATATAATATATAGATATAAATAAC
1 A--ATATAATAT-TATATATAAAAAAC
*
4208 AATATAATATAATATATAATAAAAC
1 AATATAATATTATATATAA-AAAAC
*
4233 TATATAATATTATAT
1 AATATAATATTATAT
4248 TTTCGAAAAT
Statistics
Matches: 54, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
24 7 0.13
25 26 0.48
26 1 0.02
27 2 0.04
28 16 0.30
29 2 0.04
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (24 bp):
AATATAATATTATATATAAAAAAC
Found at i:4437 original size:37 final size:35
Alignment explanation
Indices: 4318--4554 Score: 203
Period size: 37 Copynumber: 6.5 Consensus size: 35
4308 TAAAAAAACT
* *
4318 ATATATGTTTTCAAAATATGTTTTTAAAATTATATT
1 ATATATGTTTTCAAAA-ATGTTTTTAAAACTATATA
* *
4354 ATATACGTTTTCAAAAATCATTTTTAAAACTATATA
1 ATATATGTTTTCAAAAAT-GTTTTTAAAACTATATA
* *
4390 TTATACGTTTTCAAAAATGTGTTTTCAAAACTATATA
1 ATATATGTTTTCAAAAATGT-TTTT-AAAACTATATA
*
4427 ATATATGTTTTAAAAAATGTATTTTCAAAA-TCATAT-
1 ATATATGTTTTCAAAAATGT-TTTT-AAAACT-ATATA
* *
4463 -TATATATTTTCAAAAACTGATTCTTTTAAAAAGTATAT-
1 ATATATGTTTTCAAAAA-TG--T-TTTT-AAAACTATATA
* *
4501 ATGATATGCTTTCAAAAACGTTTTCTAAAAACTATATA
1 AT-ATATGTTTTCAAAAATGTTTT-T-AAAACTATATA
*
4539 TTATATGTTTTCAAAA
1 ATATATGTTTTCAAAA
4555 CATATTTTCA
Statistics
Matches: 169, Mismatches: 20, Indels: 23
0.80 0.09 0.11
Matches are distributed among these distances:
35 17 0.10
36 56 0.33
37 66 0.39
38 14 0.08
39 3 0.02
40 13 0.08
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.44
Consensus pattern (35 bp):
ATATATGTTTTCAAAAATGTTTTTAAAACTATATA
Found at i:4473 original size:72 final size:71
Alignment explanation
Indices: 4319--4554 Score: 201
Period size: 72 Copynumber: 3.2 Consensus size: 71
4309 AAAAAAACTA
* * * *
4319 TATATGTTTTCAAAATATGTTTTTAAAATTATATTATATACGTTTTCAAAAATCATTTTTAAAAC
1 TATATGTTTTCAAAA-ATGTTTTTAAAACTATATAATATACGTTTTAAAAAATCATTTTCAAAAC
*
4384 TATATAT
65 TACATAT
* * *
4391 TATACGTTTTCAAAAATGTGTTTTCAAAACTATATAATATATGTTTTAAAAAATGTATTTTCAAA
1 TATATGTTTTCAAAAATGT-TTTT-AAAACTATATAATATACGTTTTAAAAAAT-CATTTTCAAA
4456 A-T-CATAT
63 ACTACATAT
* * * * * *
4463 TATATATTTTCAAAAACTGATTCTTTTAAAAAGTATAT-ATGATATGCTTTCAAAAA-CGTTTTC
1 TATATGTTTTCAAAAA-TG--T-TTTT-AAAACTATATAAT-ATACGTTTTAAAAAATCATTTTC
*
4526 TAAAAACTATATAT
60 --AAAACTACATAT
4540 TATATGTTTTCAAAA
1 TATATGTTTTCAAAA
4555 CATATTTTCA
Statistics
Matches: 134, Mismatches: 19, Indels: 17
0.79 0.11 0.10
Matches are distributed among these distances:
71 4 0.03
72 36 0.27
73 33 0.25
74 11 0.08
75 31 0.23
76 1 0.01
77 18 0.13
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.44
Consensus pattern (71 bp):
TATATGTTTTCAAAAATGTTTTTAAAACTATATAATATACGTTTTAAAAAATCATTTTCAAAACT
ACATAT
Found at i:4537 original size:112 final size:110
Alignment explanation
Indices: 4318--4567 Score: 298
Period size: 112 Copynumber: 2.3 Consensus size: 110
4308 TAAAAAAACT
* *
4318 ATATATGTTTTCAAAATATGT-TTTT-AAAATTATATTATATACGTTTTCAAAAATCATTTTTAA
1 ATATATGTTTTCAAAAAATGTATTTTCAAAATCATATTATATAC-TTTTCAAAAATCATTTTTAA
* * * *
4381 AACTATATATTATACGTTTTCAAAAATGTGTTTTCAAAACTATATA
65 AACTATATATGATACGCTTTCAAAAACGTGTTTTAAAAACTATATA
*
4427 ATATATGTTTT-AAAAAATGTATTTTCAAAATCATATTATATA-TTTTCAAAAACTGATTCTTTT
1 ATATATGTTTTCAAAAAATGTATTTTCAAAATCATATTATATACTTTTCAAAAA-TCA-T-TTTT
* *
4490 AAAAAGTATATATGATATGCTTTCAAAAACGT-TTTCTAAAAACTATATA
63 -AAAACTATATATGATACGCTTTCAAAAACGTGTTT-TAAAAACTATATA
* *
4539 TTATATGTTTTCAAAACA--TATTTTCAAAA
1 ATATATGTTTTCAAAAAATGTATTTTCAAAA
4568 ATTGCATTAT
Statistics
Matches: 122, Mismatches: 11, Indels: 14
0.83 0.07 0.10
Matches are distributed among these distances:
108 18 0.15
109 17 0.14
110 16 0.13
111 18 0.15
112 48 0.39
113 5 0.04
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.44
Consensus pattern (110 bp):
ATATATGTTTTCAAAAAATGTATTTTCAAAATCATATTATATACTTTTCAAAAATCATTTTTAAA
ACTATATATGATACGCTTTCAAAAACGTGTTTTAAAAACTATATA
Found at i:4904 original size:6 final size:7
Alignment explanation
Indices: 4888--4913 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
4878 CCACATCATC
4888 TTTTAAT
1 TTTTAAT
4895 TTTTAAT
1 TTTTAAT
4902 TTTTAAT
1 TTTTAAT
4909 TTTTA
1 TTTTA
4914 TCTAAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTAAT
Found at i:7123 original size:12 final size:12
Alignment explanation
Indices: 7106--7172 Score: 53
Period size: 12 Copynumber: 5.5 Consensus size: 12
7096 AATATTAAAA
7106 AATAAATAAATT
1 AATAAATAAATT
**
7118 AATAAATATTTT
1 AATAAATAAATT
** *
7130 TCTAAAAAAATT
1 AATAAATAAATT
*
7142 AAAAAATAAATT
1 AATAAATAAATT
*
7154 AATATATATAATT
1 AATAAATA-AATT
*
7167 TATAAA
1 AATAAA
7173 AGTAGGATAT
Statistics
Matches: 39, Mismatches: 15, Indels: 1
0.71 0.27 0.02
Matches are distributed among these distances:
12 31 0.79
13 8 0.21
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (12 bp):
AATAAATAAATT
Found at i:7268 original size:2 final size:2
Alignment explanation
Indices: 7263--7294 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
7253 AAATAAATAA
*
7263 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7295 TACTAAATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:8551 original size:3 final size:3
Alignment explanation
Indices: 8543--8594 Score: 77
Period size: 3 Copynumber: 17.0 Consensus size: 3
8533 GCCTGAAATG
* *
8543 TAA TAA TAA TAA TAG TAA TAA TAA TAAA TAA TAG TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
8589 TAA TAA
1 TAA TAA
8595 AACCAAATAG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:9227 original size:123 final size:123
Alignment explanation
Indices: 8963--9400 Score: 684
Period size: 123 Copynumber: 3.6 Consensus size: 123
8953 GAATTAAGGC
* *
8963 AAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATGAGTTATTCTCATTAT
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTATTCTCATTAT
* * * * * **
9028 GAACATT-TCTAGAAATGTTTATGTTGATATATCTCCTTCTGTGATAGTTTCATGCAA
66 GAACTTTCTCTGGAAAAGTGTATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAA
* *
9085 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTATTCTTATTAT
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTATTCTCATTAT
*
9150 GAACTTTCTCTGGAAAAGTGTATGTTGATCTATCTCATTCTGTGATAGAGTCATGCAA
66 GAACTTTCTCTGGAAAAGTGTATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAA
9208 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTATTCTCATTAT
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTATTCTCATTAT
*
9273 GAACTTTCTCTGGAAAAGTGTACGTTGATCTATCTCCTTCTGTGATAGAGTC-TAGCAA
66 GAACTTTCTCTGGAAAAGTGTATGTTGATCTATCTCCTTCTGTGATAGAGTCAT-GCAA
* * * *
9331 AAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTC-TCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTATTCTCATTA
9395 TGAACT
65 TGAACT
9401 CTCATGGAAA
Statistics
Matches: 293, Mismatches: 20, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
122 71 0.24
123 222 0.76
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.41
Consensus pattern (123 bp):
AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTATTCTCATTAT
GAACTTTCTCTGGAAAAGTGTATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAA
Found at i:9889 original size:18 final size:18
Alignment explanation
Indices: 9862--9909 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
9852 CTTTGAAGAG
*
9862 AGAATCTATCATCTTTGA
1 AGAATGTATCATCTTTGA
9880 AGAATGTATCTATCATCTTTGA
1 AGAATG----TATCATCTTTGA
9902 AGAATGTA
1 AGAATGTA
9910 GATGTAGATA
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 7 0.28
22 18 0.72
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (18 bp):
AGAATGTATCATCTTTGA
Found at i:9909 original size:22 final size:22
Alignment explanation
Indices: 9798--9904 Score: 162
Period size: 22 Copynumber: 4.9 Consensus size: 22
9788 AAATCCAATA
* * *
9798 AATCTTTCTTCTTTGAAAAGAG
1 AATCTATCATCTTTGAAGAGAG
9820 AATCTATCATCTTTGAAGAGAG
1 AATCTATCATCTTTGAAGAGAG
9842 AATCTATCATCTTTGAAGAGAG
1 AATCTATCATCTTTGAAGAGAG
9864 AATCTATCATCTTTGAAGA-ATG
1 AATCTATCATCTTTGAAGAGA-G
*
9886 TATCTATCATCTTTGAAGA
1 AATCTATCATCTTTGAAGA
9905 ATGTAGATGT
Statistics
Matches: 80, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
21 1 0.01
22 79 0.99
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (22 bp):
AATCTATCATCTTTGAAGAGAG
Found at i:11297 original size:20 final size:21
Alignment explanation
Indices: 11258--11297 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
11248 TCTTCTTTTT
* *
11258 TTCAAGCATTTATTTTTCTTC
1 TTCAAGCATTAATATTTCTTC
11279 TTCAAGCA-TAATATTTCTT
1 TTCAAGCATTAATATTTCTT
11298 GATAGAATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.25, C:0.17, G:0.05, T:0.53
Consensus pattern (21 bp):
TTCAAGCATTAATATTTCTTC
Found at i:18572 original size:14 final size:16
Alignment explanation
Indices: 18555--18586 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
18545 TTAATTTTTT
18555 TGAAT-TTTA-CTTAA
1 TGAATGTTTATCTTAA
18569 TGAATGTTTATCTTAA
1 TGAATGTTTATCTTAA
18585 TG
1 TG
18587 TAAAATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 4 0.25
16 7 0.44
ACGTcount: A:0.31, C:0.06, G:0.12, T:0.50
Consensus pattern (16 bp):
TGAATGTTTATCTTAA
Found at i:18647 original size:15 final size:15
Alignment explanation
Indices: 18627--18658 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
18617 TGCAATGAAT
18627 AATGAATATATGCAA
1 AATGAATATATGCAA
*
18642 AATGAATGTATGCAA
1 AATGAATATATGCAA
18657 AA
1 AA
18659 GGTATTGATC
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:0.53, C:0.06, G:0.16, T:0.25
Consensus pattern (15 bp):
AATGAATATATGCAA
Found at i:22228 original size:17 final size:18
Alignment explanation
Indices: 22195--22230 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
22185 AATTCCAAGA
22195 AAATATATTAATTTTTAT
1 AAATATATTAATTTTTAT
*
22213 AAATATA-TATTTTTTAT
1 AAATATATTAATTTTTAT
22230 A
1 A
22231 TTTTTATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AAATATATTAATTTTTAT
Found at i:23821 original size:3 final size:3
Alignment explanation
Indices: 23813--23883 Score: 119
Period size: 3 Copynumber: 24.0 Consensus size: 3
23803 GCCTAAAATG
23813 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA
23858 TAA TAA TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
23884 AAACAAATGG
Statistics
Matches: 65, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
2 4 0.06
3 58 0.89
4 3 0.05
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:27918 original size:5 final size:5
Alignment explanation
Indices: 27908--27933 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
27898 CCGGTCAAGT
27908 TCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG T
27934 TGAATGATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:28060 original size:33 final size:34
Alignment explanation
Indices: 28018--28101 Score: 152
Period size: 34 Copynumber: 2.5 Consensus size: 34
28008 GCCCCGATTA
28018 TATATATATAATATTTTATA-TTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTTATATTAAT
28051 TATATATATAATATTTTATATTTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTTATATTAAT
*
28085 TATATATAAAATATTTT
1 TATATATATAATATTTT
28102 CAGGTTCGGG
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 20 0.41
34 29 0.59
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (34 bp):
TATATATATAATATTTTATATTTTTTATATTAAT
Found at i:32046 original size:41 final size:41
Alignment explanation
Indices: 31963--32173 Score: 212
Period size: 41 Copynumber: 5.2 Consensus size: 41
31953 TTTAACGGTG
* * * * * * *
31963 TTAGTGGCG-TTGTATACAAGCGCCTCTAAAAACTCTTACT
1 TTAGTGGCGTTTTTATATAAACGCCACTATAGACTCGTACT
* * *
32003 TTAGTGGTGTTTTTATATAAATGCCGCTATAGACTCGTACT
1 TTAGTGGCGTTTTTATATAAACGCCACTATAGACTCGTACT
* *
32044 TTAGTGG-GATTTTTATATAAACACCACTATAGACTCCTACT
1 TTAGTGGCG-TTTTTATATAAACGCCACTATAGACTCGTACT
* * * *
32085 TTAGTGGCGTTTTTAAACAAACGCCACTATAGATTCATACT
1 TTAGTGGCGTTTTTATATAAACGCCACTATAGACTCGTACT
* * *
32126 TTAGTGGCATTTTTATATAAACGACGCTA-ATGACTCGTACT
1 TTAGTGGCGTTTTTATATAAACGCCACTATA-GACTCGTACT
32167 TTAGTGG
1 TTAGTGG
32174 TTTTTGTGTT
Statistics
Matches: 142, Mismatches: 25, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
40 10 0.07
41 131 0.92
42 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.36
Consensus pattern (41 bp):
TTAGTGGCGTTTTTATATAAACGCCACTATAGACTCGTACT
Found at i:35680 original size:38 final size:42
Alignment explanation
Indices: 35635--35742 Score: 127
Period size: 38 Copynumber: 2.7 Consensus size: 42
35625 AAAAACGCCG
35635 CTAAATATCATAACCTTTAGCGGTGTTTGTAAAA-AA-A-C-
1 CTAAATATCATAACCTTTAGCGGTGTTTGTAAAACAACACCA
* * * *
35673 GTAAATATCATTACATTTAGCGGCGTTTGTAAAACAACACCA
1 CTAAATATCATAACCTTTAGCGGTGTTTGTAAAACAACACCA
*
35715 CTAAGA-AGCATAACCTTTAGCGGTGTTT
1 CTAA-ATATCATAACCTTTAGCGGTGTTT
35743 CCAAACAACA
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
38 30 0.54
39 2 0.04
40 1 0.02
41 1 0.02
42 21 0.38
43 1 0.02
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.31
Consensus pattern (42 bp):
CTAAATATCATAACCTTTAGCGGTGTTTGTAAAACAACACCA
Found at i:36206 original size:19 final size:20
Alignment explanation
Indices: 36174--36211 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
36164 TATTTAGAGA
36174 TTTTTGAATCTTT-ATAATC
1 TTTTTGAATCTTTAATAATC
36193 TTTTTGAGAT-TTTAATAAT
1 TTTTTGA-ATCTTTAATAAT
36212 TGTTTATGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.08, T:0.58
Consensus pattern (20 bp):
TTTTTGAATCTTTAATAATC
Found at i:36825 original size:18 final size:19
Alignment explanation
Indices: 36791--36826 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
36781 AATAGTCATC
*
36791 AAAATATTTATACATAAAT
1 AAAATATTTAAACATAAAT
36810 AAAATA-TTAAACATAAA
1 AAAATATTTAAACATAAA
36827 AATGTGAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAATATTTAAACATAAAT
Found at i:38602 original size:28 final size:28
Alignment explanation
Indices: 38540--38613 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 28
38530 AGGCGGTTTT
* * *
38540 ATTAAAAACAAATTCTAAAATTTCATTT
1 ATTAAAAAAAAATTCTAAAATGTCATTA
*
38568 ATTAAAAAAAAATTCTAGAATGT-ATTA
1 ATTAAAAAAAAATTCTAAAATGTCATTA
* * *
38595 ATTGAAAAAATATTTTAAA
1 ATTAAAAAAAAATTCTAAA
38614 CAATTATTAT
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
27 18 0.47
28 20 0.53
ACGTcount: A:0.54, C:0.05, G:0.04, T:0.36
Consensus pattern (28 bp):
ATTAAAAAAAAATTCTAAAATGTCATTA
Found at i:45338 original size:18 final size:18
Alignment explanation
Indices: 45315--45352 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
45305 TTTCCAGATG
45315 CCCATGCTGGACCACTGC
1 CCCATGCTGGACCACTGC
45333 CCCATGCTGGACCACTGC
1 CCCATGCTGGACCACTGC
45351 CC
1 CC
45353 AATCCTCACG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.16, C:0.47, G:0.21, T:0.16
Consensus pattern (18 bp):
CCCATGCTGGACCACTGC
Found at i:48624 original size:23 final size:22
Alignment explanation
Indices: 48591--48653 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 22
48581 TTCTACACGC
* *
48591 TTGGTATCGATACCCCCTTTGCA
1 TTGGTACCGATACCCCC-TTGAA
*
48614 TTGGTACCGATACCATCCTTGAA
1 TTGGTACCGATACC-CCCTTGAA
*
48637 TGGGTACCGATACCCCC
1 TTGGTACCGATACCCCC
48654 CATTATGGTA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
22 2 0.06
23 30 0.88
24 2 0.06
ACGTcount: A:0.21, C:0.32, G:0.19, T:0.29
Consensus pattern (22 bp):
TTGGTACCGATACCCCCTTGAA
Found at i:53617 original size:35 final size:36
Alignment explanation
Indices: 53578--53646 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
53568 AATGTGATAA
53578 GTAAGGTATATT-TTTTTATCTCCTTAATATAATGT
1 GTAAGGTATATTGTTTTTATCTCCTTAATATAATGT
* * *
53613 GTAAGGTTTGTTGTTTTTATCTCCTTAATGTAAT
1 GTAAGGTATATTGTTTTTATCTCCTTAATATAAT
53647 ATGTGATAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 10 0.33
36 20 0.67
ACGTcount: A:0.25, C:0.09, G:0.14, T:0.52
Consensus pattern (36 bp):
GTAAGGTATATTGTTTTTATCTCCTTAATATAATGT
Found at i:54448 original size:20 final size:20
Alignment explanation
Indices: 54419--54457 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
54409 GACTAGAATG
*
54419 AAAATTATAGATAACAAATA
1 AAAATGATAGATAACAAATA
54439 AAAATGATAGATAACAAAT
1 AAAATGATAGATAACAAAT
54458 GAAGAAGTGA
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:0.64, C:0.05, G:0.08, T:0.23
Consensus pattern (20 bp):
AAAATGATAGATAACAAATA
Found at i:56118 original size:22 final size:25
Alignment explanation
Indices: 56073--56119 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
56063 CCCACTTAGA
56073 TACATAGTCTACAACAAGCAAGATG
1 TACATAGTCTACAACAAGCAAGATG
*
56098 TACA-AGTCTCCAA-AAG-AAGATG
1 TACATAGTCTACAACAAGCAAGATG
56120 GAAATGGTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 3 0.14
24 8 0.38
25 4 0.19
ACGTcount: A:0.45, C:0.19, G:0.17, T:0.19
Consensus pattern (25 bp):
TACATAGTCTACAACAAGCAAGATG
Done.