Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001334.1 Hibiscus syriacus cultivar Beakdansim tig00002603_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: 133167
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:4512 original size:15 final size:14
Alignment explanation
Indices: 4472--4515 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
4462 TAACTCAACA
4472 ATTTTTAAATAAAAT
1 ATTTTTAAA-AAAAT
* *
4487 ATCATTTAAAAATAT
1 AT-TTTTAAAAAAAT
4502 ATTTTTAAAAAAAT
1 ATTTTTAAAAAAAT
4516 CTGATTTGAC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
14 10 0.42
15 8 0.33
16 6 0.25
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (14 bp):
ATTTTTAAAAAAAT
Found at i:9199 original size:3 final size:3
Alignment explanation
Indices: 9191--9254 Score: 65
Period size: 3 Copynumber: 21.3 Consensus size: 3
9181 CCATTTTTAA
* * * * * * *
9191 ATT ATT ATT ATT GTT ATA ATT ATT ATA ATT ATT ATA AAT ATG ATG ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
9239 ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT A
9255 AATAAAATAC
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (3 bp):
ATT
Found at i:9254 original size:9 final size:9
Alignment explanation
Indices: 9190--9252 Score: 72
Period size: 9 Copynumber: 7.0 Consensus size: 9
9180 TCCATTTTTA
9190 AATTATTAT
1 AATTATTAT
* *
9199 TATTGTTAT
1 AATTATTAT
9208 AATTATTAT
1 AATTATTAT
9217 AATTATTAT
1 AATTATTAT
* *
9226 AAATATGAT
1 AATTATTAT
*
9235 GATTATTAT
1 AATTATTAT
*
9244 TATTATTAT
1 AATTATTAT
9253 TAAATAAAAT
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 44 1.00
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (9 bp):
AATTATTAT
Found at i:10792 original size:72 final size:73
Alignment explanation
Indices: 10719--10862 Score: 184
Period size: 72 Copynumber: 2.0 Consensus size: 73
10709 ATTTATTTAT
* * * *
10719 TTTTAAATATTAAG-AAAGGGCGGTCTTAAAATAACTAGATGTCATATTCTGATA-TTTTAAATA
1 TTTTAAATATAAAGAAAAGGACGGTCTTAAAACAACTAGATGTCATATTCTAATATTTTTAAATA
10782 AATAAATA
66 AATAAATA
* * * * * *
10790 TTTTGATTATAAAGAAAAGGACTGTCTTAAAGCAACTAGATGTTATTTTCTAATATTTTTAAATA
1 TTTTAAATATAAAGAAAAGGACGGTCTTAAAACAACTAGATGTCATATTCTAATATTTTTAAATA
10855 AATAAATA
66 AATAAATA
10863 CTCTATTTAT
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
71 11 0.18
72 33 0.54
73 17 0.28
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (73 bp):
TTTTAAATATAAAGAAAAGGACGGTCTTAAAACAACTAGATGTCATATTCTAATATTTTTAAATA
AATAAATA
Found at i:12111 original size:19 final size:19
Alignment explanation
Indices: 12075--12113 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
12065 GTACTAACCA
*
12075 TTTTATTTTTTTCTTATTT
1 TTTTATTTTTTTCATATTT
12094 TTTTATTTTTTAT-ATATTT
1 TTTTATTTTTT-TCATATTT
12113 T
1 T
12114 GCTCTAACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 17 0.94
20 1 0.06
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTTATTTTTTTCATATTT
Found at i:12357 original size:36 final size:36
Alignment explanation
Indices: 12310--12412 Score: 197
Period size: 36 Copynumber: 2.9 Consensus size: 36
12300 AGATTTATGC
12310 ACACAAAGATCCTGTTATATTAATACCAAAAGTATT
1 ACACAAAGATCCTGTTATATTAATACCAAAAGTATT
12346 ACACAAAGATCCTGTTATATTAATACCAAAAGTATT
1 ACACAAAGATCCTGTTATATTAATACCAAAAGTATT
*
12382 ACACAAAGATCCTGTTAGATTAATACCAAAA
1 ACACAAAGATCCTGTTATATTAATACCAAAA
12413 ACATTCTACA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
36 66 1.00
ACGTcount: A:0.46, C:0.17, G:0.09, T:0.28
Consensus pattern (36 bp):
ACACAAAGATCCTGTTATATTAATACCAAAAGTATT
Found at i:12943 original size:43 final size:43
Alignment explanation
Indices: 12877--12966 Score: 162
Period size: 43 Copynumber: 2.1 Consensus size: 43
12867 CTAACTTATC
*
12877 TTTGGAGAAGTTAGGAATGAAAGTTATCCCCTATATGTAAAGT
1 TTTGGAGAAGTTAGGAATAAAAGTTATCCCCTATATGTAAAGT
*
12920 TTTGGAGAAGTTAGGAGTAAAAGTTATCCCCTATATGTAAAGT
1 TTTGGAGAAGTTAGGAATAAAAGTTATCCCCTATATGTAAAGT
12963 TTTG
1 TTTG
12967 TTTGATGTAC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.33, C:0.09, G:0.23, T:0.34
Consensus pattern (43 bp):
TTTGGAGAAGTTAGGAATAAAAGTTATCCCCTATATGTAAAGT
Found at i:13102 original size:26 final size:27
Alignment explanation
Indices: 13047--13108 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
13037 CATACATGCA
*
13047 TTTGCATTTCGTATCTTTGCATTTTCAT
1 TTTGCA-TTCGTATCTTTGCATTTTAAT
*
13075 TTTGCATTCGTA-CTTT-TATGTTTAAT
1 TTTGCATTCGTATCTTTGCAT-TTTAAT
13101 TTTGCATT
1 TTTGCATT
13109 GCACAATTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 2 0.06
26 17 0.55
27 6 0.19
28 6 0.19
ACGTcount: A:0.16, C:0.15, G:0.11, T:0.58
Consensus pattern (27 bp):
TTTGCATTCGTATCTTTGCATTTTAAT
Found at i:13458 original size:42 final size:42
Alignment explanation
Indices: 13397--13480 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
13387 AGAGATGATT
* ** * * *
13397 GATCAAGTAAAAAGGTTCCAGGGTGATTCAAATGAACAAATG
1 GATCAAGCAAAAAAATTCCAAGATGATTCAAAAGAACAAATG
*
13439 GATCAAGCAAAAAAATTCCAAGATGATTCAAAAGAGCAAATG
1 GATCAAGCAAAAAAATTCCAAGATGATTCAAAAGAACAAATG
13481 ACAAAACTAA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.48, C:0.13, G:0.20, T:0.19
Consensus pattern (42 bp):
GATCAAGCAAAAAAATTCCAAGATGATTCAAAAGAACAAATG
Found at i:18969 original size:53 final size:54
Alignment explanation
Indices: 18822--18974 Score: 141
Period size: 54 Copynumber: 2.9 Consensus size: 54
18812 AAATCAGGGA
* ** * * * *
18822 AGAAGCCACACGAAAATATTAATGTGTTGTCAAATGTTTTATGAACATTTGGGC
1 AGAAGCCACATGAAAGGATGAATGAGTTGTCAAATGTTTTACGAACATCTGGGC
* * * *
18876 AGAAGTCACATGAAAGGATGAATGTA-TTATCAAATATTTTACGAAACATCTGTGC
1 AGAAGCCACATGAAAGGATGAATG-AGTTGTCAAATGTTTTACG-AACATCTGGGC
* * *
18931 AGAAGCCACA-G-CAGGATGAATGAGTTGTCCAATGTTTTATGAAC
1 AGAAGCCACATGAAAGGATGAATGAGTTGTCAAATGTTTTACGAAC
18975 CAATGATTAT
Statistics
Matches: 79, Mismatches: 17, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
52 4 0.05
53 23 0.29
54 34 0.43
55 18 0.23
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.29
Consensus pattern (54 bp):
AGAAGCCACATGAAAGGATGAATGAGTTGTCAAATGTTTTACGAACATCTGGGC
Found at i:19379 original size:22 final size:20
Alignment explanation
Indices: 19327--19370 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
19317 ACATCTACAT
19327 TCTTCAAAGATGATAGTTTC
1 TCTTCAAAGATGATAGTTTC
*
19347 TCTTCAAAGATGATAGATTC
1 TCTTCAAAGATGATAGTTTC
19367 TCTT
1 TCTT
19371 TTCAAAGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.41
Consensus pattern (20 bp):
TCTTCAAAGATGATAGTTTC
Found at i:20118 original size:20 final size:20
Alignment explanation
Indices: 20093--20163 Score: 54
Period size: 20 Copynumber: 3.3 Consensus size: 20
20083 TGTTTTCAAA
20093 ACCTTCGGGTCATCTGTAAG
1 ACCTTCGGGTCATCTGTAAG
* * *
20113 ACCTTC-AGTGCATGATGTTTTCAAA
1 ACCTTCGGGT-CAT-CTG---T-AAG
20138 ACCTTCGGGTCATCTGTAAG
1 ACCTTCGGGTCATCTGTAAG
20158 ACCTTC
1 ACCTTC
20164 AGTGCATGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 14
0.66 0.10 0.24
Matches are distributed among these distances:
19 2 0.05
20 17 0.45
21 3 0.08
24 3 0.08
25 11 0.29
26 2 0.05
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (20 bp):
ACCTTCGGGTCATCTGTAAG
Found at i:20122 original size:45 final size:45
Alignment explanation
Indices: 20058--20607 Score: 965
Period size: 45 Copynumber: 12.2 Consensus size: 45
20048 CTATTTCCCA
20058 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
20103 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
20148 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
20193 CAACTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
20238 CATCTATAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGAGT
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
20283 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * *
20328 CATCTGTAAGATCTTCAGTGCATGACGTTTTCAAAACCTTTGGGT
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
20373 CATCTGTAAGACCTTCAGTGCATGATGTTTCCAAAACCTTTGGGT
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
20418 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
20463 CATCTATAAGACCTTCAGTGCATGATGTTTTCAAAACCTTTGGGT
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
20508 CATCTATAAGACCTTCAGTGCATGATGTTTCCAAAACCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
20553 CATCTGTAAGACCTTTAGTGCATGATGTTTTCAAAGCCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
20598 CATTTGTAAG
1 CATCTGTAAG
20608 TCTTCCGAGC
Statistics
Matches: 482, Mismatches: 23, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 482 1.00
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (45 bp):
CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
Found at i:20806 original size:3 final size:3
Alignment explanation
Indices: 20798--20822 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
20788 CTATTTTTAA
20798 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
20823 AATAAAGTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:22279 original size:19 final size:20
Alignment explanation
Indices: 22234--22280 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
22224 AAATTTTCAT
* *
22234 TATTATTTCATTATTACTTTA
1 TATTA-TTCATTATTAATATA
*
22255 TTTTATTCA-TATTAATATA
1 TATTATTCATTATTAATATA
22274 TATTATT
1 TATTATT
22281 TGATTAATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 14 0.64
20 4 0.18
21 4 0.18
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTATTCATTATTAATATA
Found at i:22582 original size:158 final size:159
Alignment explanation
Indices: 22301--22587 Score: 334
Period size: 160 Copynumber: 1.8 Consensus size: 159
22291 TATAAATTAA
* *
22301 TAATATTTATTTATTTTTAAATATTAAGAAAGGGCGATCTTAAAATAACTAGATGTCCTATTATG
1 TAATATTTATTTATTTTTAAATATTAAGAAAGGGCGATCTTAAAACAACTAGATGTCCTATTATA
** ** * * *
22366 ATATTTTAAATAAATAAATATTTTGATTATAAAAATTATATATATTTAATTTAGTTTTA-TTTAA
66 ATATTTTAAATAAATAAATACCTTGATTATAAAAACCATAAAAATCTAA-TTAGTTTTACTTTAA
22430 ATTATTTTTTAAGAAAATTTATCATATTTT
130 ATTATTTTTTAAGAAAATTTATCATATTTT
* * * *
22460 TAAT-TTTATTTATTTTTTAATATTAAAGAAAGGGGCTATCTTAAAGCAACTAGATGTCCTTTTT
1 TAATATTTATTTATTTTTAAATATT-AAGAAA-GGGCGATCTTAAAACAACTAGATGTCC-TATT
* * *
22524 CTAATATTTTTACATAAATAAATACCTT-ATT-TATAAAACCATAAAAATCT-A-TATTTTTACT
63 ATAATA-TTTTAAATAAATAAATACCTTGATTATA-AAAACCATAAAAATCTAATTAGTTTTACT
22585 TTA
126 TTA
22588 GTTTTATAAA
Statistics
Matches: 106, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
158 26 0.25
159 14 0.13
160 27 0.25
161 21 0.20
162 18 0.17
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (159 bp):
TAATATTTATTTATTTTTAAATATTAAGAAAGGGCGATCTTAAAACAACTAGATGTCCTATTATA
ATATTTTAAATAAATAAATACCTTGATTATAAAAACCATAAAAATCTAATTAGTTTTACTTTAAA
TTATTTTTTAAGAAAATTTATCATATTTT
Found at i:31993 original size:3 final size:3
Alignment explanation
Indices: 31985--32050 Score: 114
Period size: 3 Copynumber: 21.7 Consensus size: 3
31975 TCCATACAAA
*
31985 AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AGAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT
32031 AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
32051 AAGAAACAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
3 57 0.95
4 3 0.05
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:54537 original size:14 final size:14
Alignment explanation
Indices: 54518--54548 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
54508 ACAATTGGAA
*
54518 TTATCTTTAGGATT
1 TTATCTCTAGGATT
54532 TTATCTCTAGGATT
1 TTATCTCTAGGATT
54546 TTA
1 TTA
54549 GAGGCTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.10, G:0.13, T:0.55
Consensus pattern (14 bp):
TTATCTCTAGGATT
Found at i:54674 original size:23 final size:23
Alignment explanation
Indices: 54610--54677 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 23
54600 ACTCTTCTTA
* * *
54610 TTATTTCTAGTTTTATAAATTTCTT
1 TTATTTCAAGTTTTAT--TTTTATT
* *
54635 TT-TTTTAAGTTTCATTTTTATT
1 TTATTTCAAGTTTTATTTTTATT
54657 TTATTTCAAGTTTTATTTTTA
1 TTATTTCAAGTTTTATTTTTA
54678 AACATGCAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
22 7 0.20
23 16 0.46
24 10 0.29
25 2 0.06
ACGTcount: A:0.22, C:0.06, G:0.04, T:0.68
Consensus pattern (23 bp):
TTATTTCAAGTTTTATTTTTATT
Found at i:62176 original size:61 final size:61
Alignment explanation
Indices: 62100--62259 Score: 239
Period size: 61 Copynumber: 2.6 Consensus size: 61
62090 GTGTAAGGAC
* * * *
62100 ACTTAATGCAGGTGGTGGGCACGACCTTATGTGTCATATTCAGATCAGTACTAGAGTGTAA
1 ACTTAGTGCAGGTGGTGGGCACAACCTTATGTGTCATATCCAGATCAGCACTAGAGTGTAA
* * * *
62161 ACTTAGTGCAAGTGGTGGGCATAACCTTATGTGTCATATCCGGATTAGCACTAGAGTGTAA
1 ACTTAGTGCAGGTGGTGGGCACAACCTTATGTGTCATATCCAGATCAGCACTAGAGTGTAA
*
62222 ACTTAGTGCAGGTGGTGGGCACAAACTTATGTGTCATA
1 ACTTAGTGCAGGTGGTGGGCACAACCTTATGTGTCATA
62260 GCACTACAGT
Statistics
Matches: 88, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 88 1.00
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (61 bp):
ACTTAGTGCAGGTGGTGGGCACAACCTTATGTGTCATATCCAGATCAGCACTAGAGTGTAA
Found at i:71619 original size:31 final size:31
Alignment explanation
Indices: 71584--71681 Score: 178
Period size: 31 Copynumber: 3.1 Consensus size: 31
71574 ATGCAAACTG
71584 ATAAAACAAAACAAAACAAGTATTGGTCTAA
1 ATAAAACAAAACAAAACAAGTATTGGTCTAA
71615 ATAAAACAAAACAAAACAAGTATTGGTCTAAA
1 ATAAAACAAAACAAAACAAGTATTGGTCT-AA
71647 TATAAAACAAAACAAAACAAGTATTGGTCTAA
1 -ATAAAACAAAACAAAACAAGTATTGGTCTAA
71679 ATA
1 ATA
71682 TAATGCAAAC
Statistics
Matches: 65, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
31 32 0.49
32 4 0.06
33 29 0.45
ACGTcount: A:0.58, C:0.12, G:0.09, T:0.20
Consensus pattern (31 bp):
ATAAAACAAAACAAAACAAGTATTGGTCTAA
Found at i:71657 original size:33 final size:33
Alignment explanation
Indices: 71584--71684 Score: 188
Period size: 33 Copynumber: 3.1 Consensus size: 33
71574 ATGCAAACTG
71584 ATAAAACAAAACAAAACAAGTATTGGTCT-AA-
1 ATAAAACAAAACAAAACAAGTATTGGTCTAAAT
71615 ATAAAACAAAACAAAACAAGTATTGGTCTAAAT
1 ATAAAACAAAACAAAACAAGTATTGGTCTAAAT
71648 ATAAAACAAAACAAAACAAGTATTGGTCTAAAT
1 ATAAAACAAAACAAAACAAGTATTGGTCTAAAT
71681 ATAA
1 ATAA
71685 TGCAAACAAC
Statistics
Matches: 68, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
31 29 0.43
32 2 0.03
33 37 0.54
ACGTcount: A:0.58, C:0.12, G:0.09, T:0.21
Consensus pattern (33 bp):
ATAAAACAAAACAAAACAAGTATTGGTCTAAAT
Found at i:87172 original size:25 final size:25
Alignment explanation
Indices: 87136--87185 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
87126 CTCTATTTGC
87136 ACTTAATATGTTAAGAATAGTGTTG
1 ACTTAATATGTTAAGAATAGTGTTG
* *
87161 ACTTAATGTGTTAAGGATAGTGTTG
1 ACTTAATATGTTAAGAATAGTGTTG
87186 TTCATTAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (25 bp):
ACTTAATATGTTAAGAATAGTGTTG
Found at i:87493 original size:9 final size:9
Alignment explanation
Indices: 87459--87506 Score: 55
Period size: 9 Copynumber: 5.3 Consensus size: 9
87449 GTCAGCAAAA
87459 AATATTATT
1 AATATTATT
87468 AATTATT-TT
1 AA-TATTATT
*
87477 ATTATTATT
1 AATATTATT
87486 AATATTATT
1 AATATTATT
87495 AATCATT-TT
1 AAT-ATTATT
87504 AAT
1 AAT
87507 TACATTTTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
8 4 0.12
9 23 0.68
10 7 0.21
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (9 bp):
AATATTATT
Found at i:92499 original size:22 final size:20
Alignment explanation
Indices: 92474--92514 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 20
92464 GATCAAATCA
92474 AAATAAAGAGAAAATAAGAAAC
1 AAATAAA-AGAAAA-AAGAAAC
92496 AAATAAAAGAAAAAAGAAA
1 AAATAAAAGAAAAAAGAAA
92515 AGAAGCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.32
21 6 0.32
22 7 0.37
ACGTcount: A:0.78, C:0.02, G:0.12, T:0.07
Consensus pattern (20 bp):
AAATAAAAGAAAAAAGAAAC
Found at i:93697 original size:36 final size:37
Alignment explanation
Indices: 93618--93713 Score: 115
Period size: 36 Copynumber: 2.6 Consensus size: 37
93608 AAACAAAGGG
* * *
93618 TCGTCTCGCTAAATACAATATTTCTTAAAAACAAATT
1 TCGTCTCGCTTAAGACAATTTTTCTTAAAAACAAATT
* * *
93655 TTGTCTCGCTTGAGACAATTTTTC-TCAAAACAAATT
1 TCGTCTCGCTTAAGACAATTTTTCTTAAAAACAAATT
*
93691 TCGTCTCACTTAAGAC-ATTTTTC
1 TCGTCTCGCTTAAGACAATTTTTC
93714 CTTTGAGATG
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
35 7 0.14
36 24 0.48
37 19 0.38
ACGTcount: A:0.32, C:0.21, G:0.08, T:0.39
Consensus pattern (37 bp):
TCGTCTCGCTTAAGACAATTTTTCTTAAAAACAAATT
Found at i:93871 original size:63 final size:62
Alignment explanation
Indices: 93791--94005 Score: 247
Period size: 63 Copynumber: 3.4 Consensus size: 62
93781 AAAAACAAAC
* *
93791 TTTGTCTCACTTGAGACAGTATTCCTTAAGAAAAACTTTGAAATTGTTTCTCTTGAAATGAAT
1 TTTGTCTCCCTTAAGACAGT-TTCCTTAAGAAAAACTTTGAAATTGTTTCTCTTGAAATGAAT
* * ** *
93854 TTTGTATCCCTTAAGACAGTTTCTCTT--GAAACACCTATCTTTGAGATCATTTCAT-TTGAAAC
1 TTTGTCTCCCTTAAGACAGTTTC-CTTAAGAAA-A---A-CTTTGAAATTGTTTC-TCTTGAAAT
*
93916 AAAT
59 GAAT
*
93920 TTTGTCTCCCTTGAGACAGTCTTCCTTAAGAAAAACTTTGAAATTGTTTCTCTTGAAATGAAT
1 TTTGTCTCCCTTAAGACAGT-TTCCTTAAGAAAAACTTTGAAATTGTTTCTCTTGAAATGAAT
93983 TTTGTCTCCCTTAAGACAGTTTC
1 TTTGTCTCCCTTAAGACAGTTTC
94006 TCTTGAATCA
Statistics
Matches: 125, Mismatches: 16, Indels: 23
0.76 0.10 0.14
Matches are distributed among these distances:
61 4 0.03
62 8 0.06
63 60 0.48
64 1 0.01
65 1 0.01
66 42 0.34
67 5 0.04
68 4 0.03
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (62 bp):
TTTGTCTCCCTTAAGACAGTTTCCTTAAGAAAAACTTTGAAATTGTTTCTCTTGAAATGAAT
Found at i:94018 original size:129 final size:131
Alignment explanation
Indices: 93783--94278 Score: 596
Period size: 129 Copynumber: 3.8 Consensus size: 131
93773 GTTTTTCTAA
* *
93783 AAACAAACTTTGTCTCACTTGAGACAGTATTCCTTAAGAAA-A-A-CTTTGAAATTGTTTCTCTT
1 AAACAAATTTTGTCTCCCTTGAGACAGT-TTCCTTAAGAAACACATCTTTGAAATTGTTTCTCTT
*
93845 GAAATGAATTTTGTATCCCTTAAGACAGTTTCTCTTGAAACACCTATCTTTGAGATCATTTCATT
65 GAAATGAATTTTGTCTCCCTTAAGACAGTTTCTCTTGAAACACCTATCTTTGAGATCATTTCATT
93910 TG
130 TG
93912 AAACAAATTTTGTCTCCCTTGAGACAGTCTTCCTTAAGAAA-A-A-CTTTGAAATTGTTTCTCTT
1 AAACAAATTTTGTCTCCCTTGAGACAGT-TTCCTTAAGAAACACATCTTTGAAATTGTTTCTCTT
*
93974 GAAATGAATTTTGTCTCCCTTAAGACAGTTTCTCTTGAATCACCTATCTTTGAGATCATTTCATT
65 GAAATGAATTTTGTCTCCCTTAAGACAGTTTCTCTTGAAACACCTATCTTTGAGATCATTTCATT
94039 TG
130 TG
* * * **
94041 AAACAAATTTTGTCTCCCTTGAGACAATTT-CTCATGAAACACGTCATCTTTGAGTTTGTTTCTC
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCCTTAAGAAACA---CATCTTTGAAATTGTTTCTC
** * * ** * **
94105 TTGAAACAAATTTTGCCTCCCTTGAGACAGTTTCTCTTGAAACATGTCATCTTTGAGTTTGTTTC
63 TTGAAATGAATTTTGTCTCCCTTAAGACAGTTTCTCTTGAAACACCT-ATCTTTGAGATCATTTC
*
94170 CTTTG
127 ATTTG
* * * * *
94175 AAACAAATTTTATCTCTCTTGAGACAGTTTCTCTT--GAAACACCCATCTTTGAGATCGTTTCAC
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTC-CTTAAGAAACA--CATCTTTGAAATTGTTTCTC
* * **
94238 TTGAAATGAATTTTGTCTCTCTTGAGACAACTTCTCTTGAA
63 TTGAAATGAATTTTGTCTCCCTTAAGACAGTTTCTCTTGAA
94279 GCATCATCTG
Statistics
Matches: 322, Mismatches: 36, Indels: 14
0.87 0.10 0.04
Matches are distributed among these distances:
127 7 0.02
128 3 0.01
129 151 0.47
132 1 0.00
133 107 0.33
134 51 0.16
136 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.40
Consensus pattern (131 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTTCCTTAAGAAACACATCTTTGAAATTGTTTCTCTTG
AAATGAATTTTGTCTCCCTTAAGACAGTTTCTCTTGAAACACCTATCTTTGAGATCATTTCATTT
G
Found at i:94125 original size:67 final size:66
Alignment explanation
Indices: 93826--94309 Score: 481
Period size: 66 Copynumber: 7.4 Consensus size: 66
93816 TTAAGAAAAA
* ** * *
93826 CTTTGAAATTGTTTCTCTTGAAATGAATTTTGTATCCCTTAAGACAGTTTCTCTTGAAACAC-CT
1 CTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACTC-
93890 AT
65 AT
**
93892 CTTTGAGATCATTTCAT-TTGAAACAAATTTTGTCTCCCTTGAGACAGTCTTC-CTTAAGAAA-A
1 CTTTGAGATTGTTTC-TCTTGAAACAAATTTTGTCTCCCTTGAGACAGT-TTCTCTT--GAAACA
93954 ---A-
62 CTCAT
* ** * *
93955 CTTTGAAATTGTTTCTCTTGAAATGAATTTTGTCTCCCTTAAGACAGTTTCTCTTGAATCAC-CT
1 CTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACTC-
94019 AT
65 AT
** * *
94021 CTTTGAGATCATTTCAT-TTGAAACAAATTTTGTCTCCCTTGAGACAATTTCTCATGAAACACGT
1 CTTTGAGATTGTTTC-TCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAC-T
94085 CAT
64 CAT
* * *
94088 CTTTGAGTTTGTTTCTCTTGAAACAAATTTTGCCTCCCTTGAGACAGTTTCTCTTGAAACATGTC
1 CTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA-CTC
94153 AT
65 AT
* * * *
94155 CTTTGAGTTTGTTTC-CTTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCTCTTGAAACACCC
1 CTTTGAGATTGTTTCTC-TTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACTC
94219 AT
65 AT
* * ** * ** *
94221 CTTTGAGATCGTTTCACTTGAAATGAATTTTGTCTCTCTTGAGACAACTTCTCTTGAAGCA-TCA
1 CTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACTCA
94285 T
66 T
* *
94286 CTGTGAG-TCGGTTTCTCTTGAAAC
1 CTTTGAGAT-TGTTTCTCTTGAAAC
94310 CATTATCCCT
Statistics
Matches: 351, Mismatches: 48, Indels: 39
0.80 0.11 0.09
Matches are distributed among these distances:
61 3 0.01
62 5 0.01
63 43 0.12
64 2 0.01
65 22 0.06
66 149 0.42
67 122 0.35
68 5 0.01
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (66 bp):
CTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACTCA
T
Found at i:94138 original size:36 final size:35
Alignment explanation
Indices: 94098--94215 Score: 102
Period size: 36 Copynumber: 3.4 Consensus size: 35
94088 CTTTGAGTTT
94098 GTTTCTCTTGAAACAAATTTTGCCTCCCTTGAGACA
1 GTTTCTCTTGAAACAAATTTT-CCTCCCTTGAGACA
* * * ***
94134 GTTTCTCTTGAAAC--A-TGTCAT-CTTTGAGTTT
1 GTTTCTCTTGAAACAAATTTTCCTCCCTTGAGACA
* *
94165 GTTTC-CTTTGAAACAAATTTTATCTCTCTTGAGACA
1 GTTTCTC-TTGAAACAAATTTT-CCTCCCTTGAGACA
94201 GTTTCTCTTGAAACA
1 GTTTCTCTTGAAACA
94216 CCCATCTTTG
Statistics
Matches: 61, Mismatches: 14, Indels: 14
0.69 0.16 0.16
Matches are distributed among these distances:
30 1 0.02
31 18 0.30
32 2 0.03
33 3 0.05
34 3 0.05
35 1 0.02
36 32 0.52
37 1 0.02
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.42
Consensus pattern (35 bp):
GTTTCTCTTGAAACAAATTTTCCTCCCTTGAGACA
Found at i:94169 original size:31 final size:31
Alignment explanation
Indices: 94068--94179 Score: 91
Period size: 31 Copynumber: 3.5 Consensus size: 31
94058 CTTGAGACAA
* *
94068 TTTCTCATGAAACACGTCATCTTTGAGTTTG
1 TTTCTCTTGAAACATGTCATCTTTGAGTTTG
* * * ***
94099 TTTCTCTTGAAACAAATTTTGCCTCCCTTGAGACAG
1 TTTCTCTTGAAAC--A-TGT-CAT-CTTTGAGTTTG
94135 TTTCTCTTGAAACATGTCATCTTTGAGTTTG
1 TTTCTCTTGAAACATGTCATCTTTGAGTTTG
94166 TTTC-CTTTGAAACA
1 TTTCTC-TTGAAACA
94180 AATTTTATCT
Statistics
Matches: 61, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
30 1 0.02
31 31 0.51
32 2 0.03
33 3 0.05
34 2 0.03
35 2 0.03
36 20 0.33
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.42
Consensus pattern (31 bp):
TTTCTCTTGAAACATGTCATCTTTGAGTTTG
Found at i:97546 original size:16 final size:16
Alignment explanation
Indices: 97525--97564 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
97515 CGAGTTGTTG
97525 AACGAACCGAACGTTC
1 AACGAACCGAACGTTC
97541 AACGAACCGAACGTTC
1 AACGAACCGAACGTTC
97557 AACGAACC
1 AACGAACC
97565 ATTTATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.40, C:0.33, G:0.17, T:0.10
Consensus pattern (16 bp):
AACGAACCGAACGTTC
Found at i:97740 original size:14 final size:14
Alignment explanation
Indices: 97721--97805 Score: 65
Period size: 14 Copynumber: 6.4 Consensus size: 14
97711 AATATGTTCG
97721 TTTATGTTCTTTCA
1 TTTATGTTCTTTCA
*
97735 TTTATG----TTCG
1 TTTATGTTCTTTCA
*
97745 TTTATGTTCATTCA
1 TTTATGTTCTTTCA
97759 TTTATGTT-TGTTCA
1 TTTATGTTCT-TTCA
97773 TTTATGTTCGTTT-A
1 TTTATGTTC-TTTCA
* * *
97787 TTTATATGCGTTCA
1 TTTATGTTCTTTCA
97801 TTTAT
1 TTTAT
97806 ATTTAACCCA
Statistics
Matches: 57, Mismatches: 6, Indels: 16
0.72 0.08 0.20
Matches are distributed among these distances:
10 9 0.16
13 2 0.04
14 43 0.75
15 2 0.04
16 1 0.02
ACGTcount: A:0.16, C:0.11, G:0.12, T:0.61
Consensus pattern (14 bp):
TTTATGTTCTTTCA
Found at i:97742 original size:24 final size:24
Alignment explanation
Indices: 97713--97766 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
97703 CGATCGGTAA
*
97713 TATGTTCGTTTATGTTCTTTCATT
1 TATGTTCGTTTATGTTCATTCATT
97737 TATGTTCGTTTATGTTCATTCATT
1 TATGTTCGTTTATGTTCATTCATT
97761 TATGTT
1 TATGTT
97767 TGTTCATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.15, C:0.11, G:0.13, T:0.61
Consensus pattern (24 bp):
TATGTTCGTTTATGTTCATTCATT
Found at i:97779 original size:28 final size:26
Alignment explanation
Indices: 97715--97805 Score: 78
Period size: 28 Copynumber: 3.4 Consensus size: 26
97705 ATCGGTAATA
* *
97715 TGTTCGTTTATGTTCTTTCATTTA--
1 TGTTCATTTATGTTCATTCATTTATT
*
97739 TGTTCGTTTATGTTCATTCATTTATGTT
1 TGTTCATTTATGTTCATTCATTTA--TT
* *
97767 TGTTCATTTATGTTCGTTTATTTATAT
1 TGTTCATTTATGTTCATTCATTTAT-T
*
97794 GCGTTCATTTAT
1 -TGTTCATTTAT
97806 ATTTAACCCA
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
24 23 0.41
26 1 0.02
27 1 0.02
28 31 0.55
ACGTcount: A:0.15, C:0.11, G:0.13, T:0.60
Consensus pattern (26 bp):
TGTTCATTTATGTTCATTCATTTATT
Found at i:98070 original size:23 final size:23
Alignment explanation
Indices: 97999--98063 Score: 112
Period size: 24 Copynumber: 2.8 Consensus size: 23
97989 TTTATGTTTA
97999 TTTATTGTGTTTGTTTACGTTCG
1 TTTATTGTGTTTGTTTACGTTCG
98022 TTTATTTGTGTTTGTTTACGTTCG
1 TTTA-TTGTGTTTGTTTACGTTCG
*
98046 TTTATTGTGTTTTTTTAC
1 TTTATTGTGTTTGTTTAC
98064 ATCCGTTCGT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
23 17 0.43
24 23 0.57
ACGTcount: A:0.09, C:0.08, G:0.18, T:0.65
Consensus pattern (23 bp):
TTTATTGTGTTTGTTTACGTTCG
Found at i:104058 original size:21 final size:21
Alignment explanation
Indices: 104032--104084 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
104022 TCTCGTCTCG
104032 GGTCGGGTCGGGTCGGGTCGT
1 GGTCGGGTCGGGTCGGGTCGT
104053 GGTCGGGTCGGGTCGGGTCGT
1 GGTCGGGTCGGGTCGGGTCGT
104074 GGTCGTGGTCG
1 GGTCG-GGTCG
104085 TGGTAATACT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 26 0.84
22 5 0.16
ACGTcount: A:0.00, C:0.19, G:0.57, T:0.25
Consensus pattern (21 bp):
GGTCGGGTCGGGTCGGGTCGT
Found at i:104088 original size:6 final size:5
Alignment explanation
Indices: 104029--104084 Score: 85
Period size: 5 Copynumber: 10.6 Consensus size: 5
104019 TCGTCTCGTC
104029 TCGGG TCGGG TCGGG TCGGG TCGTGG TCGGG TCGGG TCGGG TCGTGG TCGTGG
1 TCGGG TCGGG TCGGG TCGGG TCG-GG TCGGG TCGGG TCGGG TCG-GG TCG-GG
104082 TCG
1 TCG
104085 TGGTAATACT
Statistics
Matches: 49, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
5 33 0.67
6 16 0.33
ACGTcount: A:0.00, C:0.20, G:0.55, T:0.25
Consensus pattern (5 bp):
TCGGG
Found at i:104228 original size:41 final size:41
Alignment explanation
Indices: 104183--104367 Score: 217
Period size: 41 Copynumber: 4.7 Consensus size: 41
104173 CAACGAATTT
*
104183 TCGCAACGAATTTGAAAAATCGCAACGACAACTGTAGACTA
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
* * *
104224 TCGCAACGCGAA-CTGGAAAATCGTAACG----C----GACTT
1 TCGCAA--CGAATTTGGAAAATCGCAACGACAACTGTAGACTA
*
104258 TCGCAACGAATTTGGAAAATCGCAACGACAGCTGTAGACTA
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
104299 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
**
104340 TCGCAACGAGAACTGGAAAATCGCAACG
1 TCGCAACGA-ATTTGGAAAATCGCAACG
104368 CGATTTTCAA
Statistics
Matches: 122, Mismatches: 10, Indels: 23
0.79 0.06 0.15
Matches are distributed among these distances:
32 4 0.03
33 14 0.11
34 10 0.08
37 1 0.01
38 1 0.01
41 59 0.48
42 29 0.24
43 4 0.03
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.18
Consensus pattern (41 bp):
TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
Found at i:104282 original size:19 final size:19
Alignment explanation
Indices: 104258--104326 Score: 75
Period size: 19 Copynumber: 3.5 Consensus size: 19
104248 AACGCGACTT
104258 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
* * **
104277 TCGCAACGACAGCTGTAGACTA
1 TCGCAACGA-A--TTTGGAAAA
104299 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
104318 TCGCAACGA
1 TCGCAACGA
104327 CAACTGTAGA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 23 0.59
20 1 0.03
21 1 0.03
22 14 0.36
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.19
Consensus pattern (19 bp):
TCGCAACGAATTTGGAAAA
Found at i:104353 original size:22 final size:22
Alignment explanation
Indices: 104276--104354 Score: 83
Period size: 22 Copynumber: 3.7 Consensus size: 22
104266 AATTTGGAAA
*
104276 ATCGCAACGACAGCTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
104298 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
104317 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
*
104339 ATCGCAACGAGAACTG
1 ATCGCAACGACAACTG
104355 GAAAATCGCA
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
19 13 0.30
20 1 0.02
21 2 0.05
22 28 0.64
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.18
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:104364 original size:20 final size:20
Alignment explanation
Indices: 104270--104428 Score: 104
Period size: 20 Copynumber: 7.8 Consensus size: 20
104260 GCAACGAATT
* *
104270 TGGAAAATCGCAACGACAGC
1 TGGAAAATCGCAACGAGAAC
** **
104290 TGTAGACTATCGCAACGA-ATT
1 TG--GAAAATCGCAACGAGAAC
*
104311 TGGAAAATCGCAACGACAAC
1 TGGAAAATCGCAACGAGAAC
**
104331 TGTAGACTATCGCAACGAGAAC
1 TG--GAAAATCGCAACGAGAAC
* **
104353 TGGAAAATCGCAACGCGATT
1 TGGAAAATCGCAACGAGAAC
** * *
104373 TTCAACTATCGCAACGCGAAC
1 TGGAA-AATCGCAACGAGAAC
* *
104394 TGGAAAATCGCAACGCGAAA
1 TGGAAAATCGCAACGAGAAC
104414 TGGAAAATCGCAACG
1 TGGAAAATCGCAACG
104429 CAATTTTCAA
Statistics
Matches: 108, Mismatches: 25, Indels: 12
0.74 0.17 0.08
Matches are distributed among these distances:
19 12 0.11
20 49 0.45
21 18 0.17
22 29 0.27
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.16
Consensus pattern (20 bp):
TGGAAAATCGCAACGAGAAC
Found at i:104381 original size:41 final size:41
Alignment explanation
Indices: 104253--104411 Score: 173
Period size: 41 Copynumber: 3.9 Consensus size: 41
104243 ATCGTAACGC
* **
104253 GACTTTCGCAACGA-ATTTGGAAAATCGCAACGAC-AGCTGTA
1 GACTATCGCAACGAGAACTGGAAAATCGCAACG-CGA-CTGTA
** *
104294 GACTATCGCAACGA-ATTTGGAAAATCGCAACGACAACTGTA
1 GACTATCGCAACGAGAACTGGAAAATCGCAACG-CGACTGTA
* *
104335 GACTATCGCAACGAGAACTGGAAAATCGCAACGCGATTTTCA
1 GACTATCGCAACGAGAACTGGAAAATCGCAACGCGACTGT-A
*
104377 -ACTATCGCAACGCGAACTGGAAAATCGCAACGCGA
1 GACTATCGCAACGAGAACTGGAAAATCGCAACGCGA
104412 AATGGAAAAT
Statistics
Matches: 108, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
41 90 0.83
42 18 0.17
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.18
Consensus pattern (41 bp):
GACTATCGCAACGAGAACTGGAAAATCGCAACGCGACTGTA
Found at i:104418 original size:61 final size:61
Alignment explanation
Indices: 104339--104453 Score: 194
Period size: 61 Copynumber: 1.9 Consensus size: 61
104329 ACTGTAGACT
* *
104339 ATCGCAACGAGAACTGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAACTGGAAA
1 ATCGCAACGAGAAATGGAAAATCGCAACGCAATTTTCAACTATCGCAACGCGAACTGGAAA
* *
104400 ATCGCAACGCGAAATGGAAAATCGCAACGCAATTTTCAATTATCGCAACGCGAA
1 ATCGCAACGAGAAATGGAAAATCGCAACGCAATTTTCAACTATCGCAACGCGAA
104454 ATGCAACGCG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 50 1.00
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.17
Consensus pattern (61 bp):
ATCGCAACGAGAAATGGAAAATCGCAACGCAATTTTCAACTATCGCAACGCGAACTGGAAA
Found at i:104429 original size:20 final size:20
Alignment explanation
Indices: 104311--104429 Score: 114
Period size: 20 Copynumber: 5.8 Consensus size: 20
104301 GCAACGAATT
104311 TGGAAAATCGCAACGAC-AAC
1 TGGAAAATCGCAACG-CGAAC
** *
104331 TGTAGACTATCGCAACGAGAAC
1 TG--GAAAATCGCAACGCGAAC
**
104353 TGGAAAATCGCAACGCGATT
1 TGGAAAATCGCAACGCGAAC
** *
104373 TTCAACTATCGCAACGCGAAC
1 TGGAA-AATCGCAACGCGAAC
*
104394 TGGAAAATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGAAC
104414 TGGAAAATCGCAACGC
1 TGGAAAATCGCAACGC
104430 AATTTTCAAT
Statistics
Matches: 78, Mismatches: 17, Indels: 8
0.76 0.17 0.08
Matches are distributed among these distances:
20 47 0.60
21 15 0.19
22 16 0.21
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TGGAAAATCGCAACGCGAAC
Found at i:104522 original size:19 final size:19
Alignment explanation
Indices: 104478--104530 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
104468 TGCGATAGTG
*
104478 GAGATCACAATGCGAATTA
1 GAGATCGCAATGCGAATTA
104497 GAGATCGCAATGCGAATTA
1 GAGATCGCAATGCGAATTA
*
104516 GAGATCGCATTGCGA
1 GAGATCGCAATGCGA
104531 TTTTGTTGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (19 bp):
GAGATCGCAATGCGAATTA
Found at i:109032 original size:50 final size:50
Alignment explanation
Indices: 108957--109103 Score: 206
Period size: 50 Copynumber: 2.9 Consensus size: 50
108947 GGGGACTCAA
* *
108957 AAGGTGAAGTATTGAAGAAATTATTACCTAACGAATCTTTAAGACTAGGC
1 AAGGTGAAGCATTGAAGAAATTATTACCTAACCAATCTTTAAGACTAGGC
* *
109007 AAGGTGAAGCATTGAAGAAATTATTACCTAACCAATCTTTAAGAATAGTC
1 AAGGTGAAGCATTGAAGAAATTATTACCTAACCAATCTTTAAGACTAGGC
* * *
109057 AAGGTGAAGTCATT-AAGACATTATTATCTAACCAACCTTTCAAGACT
1 AAGGTGAAG-CATTGAAGAAATTATTACCTAACCAATCTTT-AAGACT
109104 GCGCCTATCT
Statistics
Matches: 87, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
50 78 0.90
51 9 0.10
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29
Consensus pattern (50 bp):
AAGGTGAAGCATTGAAGAAATTATTACCTAACCAATCTTTAAGACTAGGC
Found at i:116947 original size:44 final size:44
Alignment explanation
Indices: 116893--117010 Score: 193
Period size: 44 Copynumber: 2.7 Consensus size: 44
116883 ATTAATAATA
116893 TTTTATTATTTATTAAAAAATTAATAGATTAGTTAATATATCAT
1 TTTTATTATTTATTAAAAAATTAATAGATTAGTTAATATATCAT
* *
116937 TTTTATTATTTATTAAGAAATTAATAGATTAGTTAATTTATCAT
1 TTTTATTATTTATTAAAAAATTAATAGATTAGTTAATATATCAT
* *
116981 TTTTATTATGTATTAATAAATTAATA-ATTA
1 TTTTATTATTTATTAAAAAATTAATAGATTA
117011 TTATTTAGAT
Statistics
Matches: 70, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
43 4 0.06
44 66 0.94
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (44 bp):
TTTTATTATTTATTAAAAAATTAATAGATTAGTTAATATATCAT
Found at i:117030 original size:44 final size:44
Alignment explanation
Indices: 116876--117017 Score: 168
Period size: 44 Copynumber: 3.3 Consensus size: 44
116866 TATTAAAAAT
* *
116876 ATTA-TTAATTAATAATATTTTATTATTTATTAAAAAATTAATAG
1 ATTAGTTATTTAATCAT-TTTTATTATTTATTAAAAAATTAATAG
* *
116920 ATTAGTTA-ATATATCATTTTTATTATTTATTAAGAAATTAATAG
1 ATTAGTTATTTA-ATCATTTTTATTATTTATTAAAAAATTAATAG
* *
116964 ATTAGTTAATTT-ATCATTTTTATTATGTATTAATAAATTAATA-
1 ATTAGTT-ATTTAATCATTTTTATTATTTATTAAAAAATTAATAG
117007 ATTA-TTATTTA
1 ATTAGTTATTTA
117018 GATTTATTTT
Statistics
Matches: 87, Mismatches: 6, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
41 4 0.05
42 2 0.02
43 4 0.05
44 68 0.78
45 8 0.09
46 1 0.01
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.52
Consensus pattern (44 bp):
ATTAGTTATTTAATCATTTTTATTATTTATTAAAAAATTAATAG
Found at i:118343 original size:71 final size:71
Alignment explanation
Indices: 118263--118396 Score: 252
Period size: 71 Copynumber: 1.9 Consensus size: 71
118253 GGCTTTCCTT
118263 TTTTTCACTAATGTTTAATTATATTGTGGTTGAC-TTTTTTGGTTGAGTTTTAGTTTCAAAGTTA
1 TTTTTCACTAATGTTTAATTATATTGT-GTTGACTTTTTTTGGTTGAGTTTTAGTTTCAAAGTTA
118327 GTTTTCC
65 GTTTTCC
118334 TTTTTCACTAATGTTTAATTATATTGTGTTGACTTTTTTTGGTTGAGTTTTAGTTTCAAAGTT
1 TTTTTCACTAATGTTTAATTATATTGTGTTGACTTTTTTTGGTTGAGTTTTAGTTTCAAAGTT
118397 TAGATTGTTA
Statistics
Matches: 62, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
70 6 0.10
71 56 0.90
ACGTcount: A:0.20, C:0.07, G:0.16, T:0.56
Consensus pattern (71 bp):
TTTTTCACTAATGTTTAATTATATTGTGTTGACTTTTTTTGGTTGAGTTTTAGTTTCAAAGTTAG
TTTTCC
Found at i:132344 original size:30 final size:30
Alignment explanation
Indices: 132310--132369 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
132300 TAGTCAGATA
*
132310 CAAAACCAGTTGCCATTGGAGGTCAATATG
1 CAAAACCAGTTGCCACTGGAGGTCAATATG
*
132340 CAAAACCAGTTGCCACTGGAGGTCGATATG
1 CAAAACCAGTTGCCACTGGAGGTCAATATG
132370 AAATGTCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.22
Consensus pattern (30 bp):
CAAAACCAGTTGCCACTGGAGGTCAATATG
Done.