Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000797.1 Hibiscus syriacus cultivar Beakdansim tig00001545_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: 74876
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:8623 original size:20 final size:20
Alignment explanation
Indices: 8561--8628 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
8551 CAGCCGAGCA
*
8561 GTATCGATACTATGAGGAAG
1 GTATCAATACTATGAGGAAG
* *
8581 GTATCAATATCGA-AAGG--G
1 GTATCAATA-CTATGAGGAAG
8599 GTATCAATACTATGAGGAAG
1 GTATCAATACTATGAGGAAG
8619 GTATCAATAC
1 GTATCAATAC
8629 CATTGATAAC
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
17 2 0.05
18 13 0.33
20 22 0.56
21 2 0.05
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (20 bp):
GTATCAATACTATGAGGAAG
Found at i:9191 original size:27 final size:26
Alignment explanation
Indices: 9107--9191 Score: 61
Period size: 27 Copynumber: 3.2 Consensus size: 26
9097 GTATGGGCAC
9107 TATGTGTGCAACTCACGGAATTCATCA
1 TATGTGTGCAACTCAC-GAATTCATCA
* *
9134 TATGTTGATG-AAC-AACCG-TTTCGA-CA
1 TATG-TG-TGCAACTCA-CGAATTC-ATCA
9160 CTATGTGTGCAACTCACGAAATTCATCA
1 -TATGTGTGCAACTCACG-AATTCATCA
9188 TATG
1 TATG
9192 ATGATGAACA
Statistics
Matches: 44, Mismatches: 4, Indels: 20
0.65 0.06 0.29
Matches are distributed among these distances:
25 2 0.05
26 12 0.27
27 17 0.39
28 11 0.25
29 2 0.05
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Consensus pattern (26 bp):
TATGTGTGCAACTCACGAATTCATCA
Found at i:9237 original size:109 final size:108
Alignment explanation
Indices: 9104--9362 Score: 392
Period size: 109 Copynumber: 2.4 Consensus size: 108
9094 TTTGTATGGG
9104 CACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCGTTTCGACACTATGTGTG
1 CACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCGTTTCGACACTATGTGTG
* *
9169 CAACTCACGAAATTCATCATATGATGATGAACAATCATTTTGA
66 CAACTCACGAAATTCATCATATGATGATGAAAAATCATTTCGA
* *
9212 CACTATGTGGTGCAACTCATGGAATTCATCATATGTTGATGAACAACCGTTTCGGCACTATGTGT
1 CACTATGT-GTGCAACTCACGGAATTCATCATATGTTGATGAACAACCGTTTCGACACTATGTGT
* * *
9277 GCAACTCACGAAATTGATCATATGTTGATTAAAAATCATTTCGA
65 GCAACTCACGAAATTCATCATATGATGATGAAAAATCATTTCGA
* * * * * *
9321 AACTATATGTACAACCCACGGAATTCATAATATGTTTATGAA
1 CACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAA
9363 TGATCATATA
Statistics
Matches: 136, Mismatches: 14, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
108 37 0.27
109 99 0.73
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (108 bp):
CACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCGTTTCGACACTATGTGTG
CAACTCACGAAATTCATCATATGATGATGAAAAATCATTTCGA
Found at i:9369 original size:54 final size:54
Alignment explanation
Indices: 9104--9362 Score: 338
Period size: 54 Copynumber: 4.8 Consensus size: 54
9094 TTTGTATGGG
* *
9104 CACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCGTTTCGA
1 CACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAATCATTTCGA
* * *
9158 CACTATGTGTGCAACTCACGAAATTCATCATATGATGATGAACAATCATTTTGA
1 CACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAATCATTTCGA
* * * *
9212 CACTATGTGGTGCAACTCATGGAATTCATCATATGTTGATGAACAACCGTTTCGG
1 CACTATGT-GTGCAACTCACGGAATTCATCATATGTTGATGAACAATCATTTCGA
* * * *
9267 CACTATGTGTGCAACTCACGAAATTGATCATATGTTGATTAAAAATCATTTCGA
1 CACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAATCATTTCGA
* * * * * *
9321 AACTATATGTACAACCCACGGAATTCATAATATGTTTATGAA
1 CACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAA
9363 TGATCATATA
Statistics
Matches: 175, Mismatches: 29, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
54 128 0.73
55 47 0.27
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (54 bp):
CACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAATCATTTCGA
Found at i:16471 original size:28 final size:31
Alignment explanation
Indices: 16412--16471 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
16402 GAACTAATGG
*
16412 AAGGATCTAATTCAAAAAATATTACTACTTT
1 AAGGATCTAATTCAAAAAATATTACTAATTT
* *
16443 AAGGATTTAATT-AAAATAT-TTAC-AATTT
1 AAGGATCTAATTCAAAAAATATTACTAATTT
16471 A
1 A
16472 GTGACCAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 5 0.19
29 4 0.15
30 6 0.23
31 11 0.42
ACGTcount: A:0.47, C:0.08, G:0.07, T:0.38
Consensus pattern (31 bp):
AAGGATCTAATTCAAAAAATATTACTAATTT
Found at i:22756 original size:23 final size:23
Alignment explanation
Indices: 22729--22786 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
22719 TAAGCTACCA
*
22729 AAAGGCAAATAAAAACGTGCTAC
1 AAAGGCAAATAAAAACGTGCCAC
* * *
22752 AAAGGCAGATATAAACGTGCCAT
1 AAAGGCAAATAAAAACGTGCCAC
*
22775 AAAGGTAAATAA
1 AAAGGCAAATAA
22787 CATGTCACAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.52, C:0.14, G:0.19, T:0.16
Consensus pattern (23 bp):
AAAGGCAAATAAAAACGTGCCAC
Found at i:24299 original size:31 final size:31
Alignment explanation
Indices: 24264--24338 Score: 114
Period size: 31 Copynumber: 2.4 Consensus size: 31
24254 TTAAAAAACA
* *
24264 TAAGTTTTGGTCATTTACGTTATCGTTTTAT
1 TAAGTTTTGGTCAATTACGTTATCGGTTTAT
* *
24295 TAAGTTTTAGTCAATTACGTTATTGGTTTAT
1 TAAGTTTTGGTCAATTACGTTATCGGTTTAT
24326 TAAGTTTTGGTCA
1 TAAGTTTTGGTCA
24339 CTTGGACATT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.23, C:0.08, G:0.17, T:0.52
Consensus pattern (31 bp):
TAAGTTTTGGTCAATTACGTTATCGGTTTAT
Found at i:24827 original size:17 final size:17
Alignment explanation
Indices: 24802--24841 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
24792 GTATGTTGTT
*
24802 CATTAAAGCATGCATTG
1 CATTTAAGCATGCATTG
* *
24819 CATTTAAGCATGTATTT
1 CATTTAAGCATGCATTG
24836 CATTTA
1 CATTTA
24842 GGGAAGTAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGCATTG
Found at i:24868 original size:17 final size:17
Alignment explanation
Indices: 24848--24907 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
24838 TTTAGGGAAG
24848 TAGTTCATTTATGCATC
1 TAGTTCATTTATGCATC
** *
24865 TAGTT-ATTTAATAAAAC
1 TAGTTCATTT-ATGCATC
* * *
24882 TACTTCATTCATGCATT
1 TAGTTCATTTATGCATC
24899 TAGTTCATT
1 TAGTTCATT
24908 GAATAAAGTT
Statistics
Matches: 31, Mismatches: 10, Indels: 4
0.69 0.22 0.09
Matches are distributed among these distances:
16 4 0.13
17 24 0.77
18 3 0.10
ACGTcount: A:0.30, C:0.15, G:0.08, T:0.47
Consensus pattern (17 bp):
TAGTTCATTTATGCATC
Found at i:24943 original size:18 final size:18
Alignment explanation
Indices: 24898--24936 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
24888 ATTCATGCAT
24898 TTAGTTCATTGAATAAAG
1 TTAGTTCATTGAATAAAG
*
24916 TTAGTTCATTGAATAATG
1 TTAGTTCATTGAATAAAG
24934 TTA
1 TTA
24937 TATCATTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.36, C:0.05, G:0.15, T:0.44
Consensus pattern (18 bp):
TTAGTTCATTGAATAAAG
Found at i:26494 original size:17 final size:18
Alignment explanation
Indices: 26451--26505 Score: 67
Period size: 17 Copynumber: 3.1 Consensus size: 18
26441 CTCCCGGGTT
* *
26451 AGTAAAAAACAAAAAAAA
1 AGTAAAAAATAGAAAAAA
*
26469 AGTACAAAAATTGAAAAAA
1 AGTA-AAAAATAGAAAAAA
26488 AGT-AAAAATAGAAAAAA
1 AGTAAAAAATAGAAAAAA
26505 A
1 A
26506 ATTAAAGAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
17 14 0.44
18 4 0.12
19 14 0.44
ACGTcount: A:0.76, C:0.04, G:0.09, T:0.11
Consensus pattern (18 bp):
AGTAAAAAATAGAAAAAA
Found at i:26506 original size:19 final size:19
Alignment explanation
Indices: 26451--26506 Score: 55
Period size: 19 Copynumber: 3.0 Consensus size: 19
26441 CTCCCGGGTT
*
26451 AGTAAAAA-ACAAAAAAAA
1 AGTAAAAATAGAAAAAAAA
*
26469 AGTACAAAAATTG--AAAAAA
1 AGT--AAAAATAGAAAAAAAA
26488 AGTAAAAATAGAAAAAAAA
1 AGTAAAAATAGAAAAAAAA
26507 TTAAAGAGGG
Statistics
Matches: 30, Mismatches: 3, Indels: 9
0.71 0.07 0.21
Matches are distributed among these distances:
17 7 0.23
18 3 0.10
19 15 0.50
20 5 0.17
ACGTcount: A:0.77, C:0.04, G:0.09, T:0.11
Consensus pattern (19 bp):
AGTAAAAATAGAAAAAAAA
Found at i:28593 original size:18 final size:18
Alignment explanation
Indices: 28570--28615 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
28560 ATTCATGCAT
28570 TTAGTTCATTGAATAAAG
1 TTAGTTCATTGAATAAAG
*
28588 TTAGTTCATTGAATAATG
1 TTAGTTCATTGAATAAAG
*
28606 TTATTTCATT
1 TTAGTTCATT
28616 AATCAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.48
Consensus pattern (18 bp):
TTAGTTCATTGAATAAAG
Found at i:31232 original size:31 final size:33
Alignment explanation
Indices: 31197--31276 Score: 80
Period size: 32 Copynumber: 2.5 Consensus size: 33
31187 ATTCAACGTT
*
31197 CAAGTGATCAAAACTTAG-T-AAAACAATAACG
1 CAAGTGATCAAAACTTAGATAAAAACAATAACA
*
31228 CAAGT-CTCCAAAACTT-GATAAAAACAATAACA
1 CAAGTGAT-CAAAACTTAGATAAAAACAATAACA
*
31260 TAAGTGA-CAGAAACTTA
1 CAAGTGATCA-AAACTTA
31277 TGATTTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
30 2 0.05
31 16 0.41
32 21 0.54
ACGTcount: A:0.51, C:0.17, G:0.11, T:0.20
Consensus pattern (33 bp):
CAAGTGATCAAAACTTAGATAAAAACAATAACA
Found at i:31616 original size:18 final size:19
Alignment explanation
Indices: 31581--31620 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
31571 TTTTCAATTT
31581 TTTTGGTATTTCGTTCTTA
1 TTTTGGTATTTCGTTCTTA
31600 TTTTGG-ATTT-GTGTCTTA
1 TTTTGGTATTTCGT-TCTTA
31618 TTT
1 TTT
31621 AGATACTTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 2 0.10
18 12 0.60
19 6 0.30
ACGTcount: A:0.10, C:0.07, G:0.17, T:0.65
Consensus pattern (19 bp):
TTTTGGTATTTCGTTCTTA
Found at i:31789 original size:29 final size:29
Alignment explanation
Indices: 31757--31859 Score: 93
Period size: 29 Copynumber: 3.5 Consensus size: 29
31747 TATTATTTTA
* **
31757 TTTTTATATTATTAACAAATAAATATA-T
1 TTTTTATATTATTAATATGTAAATATATT
* *
31785 TTTTTATTATTA-TATTATGTATATTATATT
1 TTTTTA-TATTATTAATATGTA-AATATATT
* *
31815 TATATATATTATTAATATGTAAATATATT
1 TTTTTATATTATTAATATGTAAATATATT
31844 TATTATTATATTATTA
1 T-TT-TTATATTATTA
31860 TTTATATTAT
Statistics
Matches: 58, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
28 11 0.19
29 23 0.40
30 14 0.24
31 10 0.17
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (29 bp):
TTTTTATATTATTAATATGTAAATATATT
Found at i:31840 original size:58 final size:58
Alignment explanation
Indices: 31745--31881 Score: 170
Period size: 58 Copynumber: 2.3 Consensus size: 58
31735 CTGTTACTTA
* * *
31745 TATATTATTTTATTTTTATATTATTAACAAATAAATATATTTTTTATTAT-TATATTATG
1 TATATTA-TATATTTATATATTATTAACAAATAAATATATTTATTATTATAT-TATTATG
* ** *
31804 TATATTATAT-TTATATATATTATTAATATGTAAATATATTTATTATTATATTATTATT
1 TATATTATATATT-TATATATTATTAACAAATAAATATATTTATTATTATATTATTATG
31862 TATATTATATATTTATATAT
1 TATATTATATATTTATATAT
31882 CTTTTTGTTT
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
57 2 0.03
58 56 0.82
59 10 0.15
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (58 bp):
TATATTATATATTTATATATTATTAACAAATAAATATATTTATTATTATATTATTATG
Found at i:31877 original size:17 final size:17
Alignment explanation
Indices: 31779--31877 Score: 71
Period size: 17 Copynumber: 5.6 Consensus size: 17
31769 TAACAAATAA
31779 ATATATTT-TTTATTATT
1 ATATATTTATTTA-TATT
*
31796 ATATTATGTATATTATATTT
1 ATA-TATTTAT-TTATA-TT
*
31816 ATATATATTATTAATATGT
1 ATATAT-TTATTTATAT-T
*
31835 A-A-ATATATTTATTATT
1 ATATATTTATTTA-TATT
31851 ATAT-TATTATTTATATT
1 ATATAT-TTATTTATATT
31868 ATATATTTAT
1 ATATATTTAT
31878 ATATCTTTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 22
0.70 0.06 0.24
Matches are distributed among these distances:
16 7 0.11
17 22 0.34
18 13 0.20
19 12 0.18
20 11 0.17
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (17 bp):
ATATATTTATTTATATT
Found at i:31921 original size:23 final size:25
Alignment explanation
Indices: 31895--31943 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 25
31885 TTTGTTTTAA
31895 TTTAA-TATACATT-CTT-TTATTTT
1 TTTAATTAT-CATTGCTTATTATTTT
*
31918 TTTAGTTATCATTGCTTATTATTTT
1 TTTAATTATCATTGCTTATTATTTT
31943 T
1 T
31944 ATTTCCTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
23 8 0.36
24 6 0.27
25 8 0.36
ACGTcount: A:0.22, C:0.08, G:0.04, T:0.65
Consensus pattern (25 bp):
TTTAATTATCATTGCTTATTATTTT
Found at i:33221 original size:33 final size:33
Alignment explanation
Indices: 33184--33248 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
33174 AAATGTATTG
*
33184 GGTTAGGATATATTATTCTGCCAAAAAGCATGT
1 GGTTAGGATATATTATTCCGCCAAAAAGCATGT
* * * *
33217 GGTTATGATTTATTATTCCGTCAGAAAGCATG
1 GGTTAGGATATATTATTCCGCCAAAAAGCATG
33249 CGGAATAGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.35
Consensus pattern (33 bp):
GGTTAGGATATATTATTCCGCCAAAAAGCATGT
Found at i:33902 original size:21 final size:21
Alignment explanation
Indices: 33877--33927 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
33867 TTACATCTTG
* **
33877 CATTTGTATCTTTGCATTTTA
1 CATTTGCATCTTTAAATTTTA
*
33898 CATTTGCATCTTTAAATTTTG
1 CATTTGCATCTTTAAATTTTA
33919 CATTTGCAT
1 CATTTGCAT
33928 TTCATATATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.22, C:0.16, G:0.10, T:0.53
Consensus pattern (21 bp):
CATTTGCATCTTTAAATTTTA
Found at i:33911 original size:14 final size:13
Alignment explanation
Indices: 33864--33923 Score: 59
Period size: 14 Copynumber: 4.3 Consensus size: 13
33854 TTTTTCATGT
33864 ATTTTACATCTTGC
1 ATTTTACAT-TTGC
33878 ATTTGTATC-TTTGC
1 ATTT-TA-CATTTGC
33892 ATTTTACATTTGC
1 ATTTTACATTTGC
*
33905 ATCTTTAAATTTTGC
1 AT-TTTACA-TTTGC
33920 ATTT
1 ATTT
33924 GCATTTCATA
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
12 1 0.03
13 9 0.22
14 19 0.47
15 10 0.25
16 1 0.03
ACGTcount: A:0.22, C:0.15, G:0.08, T:0.55
Consensus pattern (13 bp):
ATTTTACATTTGC
Found at i:39592 original size:21 final size:19
Alignment explanation
Indices: 39550--39625 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 19
39540 TTTCAGGGTG
* *
39550 CAAAATTTTGAAACTCTTA
1 CAAAAGTTTCAAACTCTTA
39569 CAAAAGTTTCAAAACTCTTTA
1 CAAAAGTTTC-AAACTC-TTA
*
39590 CAAAATTTTTCAAACTCTTA
1 CAAAA-GTTTCAAACTCTTA
39610 CAAAAGTTTCCAAACT
1 CAAAAGTTT-CAAACT
39626 ATGAACAATA
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
19 11 0.22
20 20 0.41
21 14 0.29
22 4 0.08
ACGTcount: A:0.42, C:0.20, G:0.04, T:0.34
Consensus pattern (19 bp):
CAAAAGTTTCAAACTCTTA
Found at i:39716 original size:20 final size:20
Alignment explanation
Indices: 39680--39720 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
39670 AATGTTTTTG
*
39680 ATATTTTAAAAGTTTTAAAC
1 ATATTTTAAAAGCTTTAAAC
39700 ATATTTTAAACA-CTTTAAAC
1 ATATTTTAAA-AGCTTTAAAC
39720 A
1 A
39721 CGTTTTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.41
Consensus pattern (20 bp):
ATATTTTAAAAGCTTTAAAC
Found at i:39840 original size:31 final size:30
Alignment explanation
Indices: 39805--39862 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
39795 TTTGATTTAT
39805 TTTTA-AAATATTTGATTAAATCCAAAATCAA
1 TTTTACAAATATTTG-TTAAAT-CAAAATCAA
*
39836 TTTTACAAATATTTGTTATATCAAAAT
1 TTTTACAAATATTTGTTAAATCAAAAT
39863 ATAAGTTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 6 0.24
31 10 0.40
32 9 0.36
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (30 bp):
TTTTACAAATATTTGTTAAATCAAAATCAA
Found at i:44465 original size:31 final size:31
Alignment explanation
Indices: 44430--44492 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
44420 CTTCTCTACT
*
44430 GTTAGAGGTTAG-CCAAATTTTAGAGGAATTA
1 GTTAGA-GTTAGTCCAAATTTTAAAGGAATTA
*
44461 GTTAGAGTTTGTCCAAATTTTAAAGGAATTA
1 GTTAGAGTTAGTCCAAATTTTAAAGGAATTA
44492 G
1 G
44493 CTAAAGTCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 4 0.14
31 25 0.86
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.35
Consensus pattern (31 bp):
GTTAGAGTTAGTCCAAATTTTAAAGGAATTA
Found at i:50084 original size:47 final size:48
Alignment explanation
Indices: 50018--50110 Score: 161
Period size: 47 Copynumber: 2.0 Consensus size: 48
50008 AATCCATAAT
50018 TAAAATGCATGAAAGGATGCATT-AAGGCATGAAAGGATGTCATAAAC
1 TAAAATGCATGAAAGGATGCATTCAAGGCATGAAAGGATGTCATAAAC
* *
50065 TAAAATGCATGAAATGATGCATTCAGGGCATGAAAGGATGTCATAA
1 TAAAATGCATGAAAGGATGCATTCAAGGCATGAAAGGATGTCATAA
50111 TTTAAATGGA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
47 22 0.51
48 21 0.49
ACGTcount: A:0.43, C:0.11, G:0.24, T:0.23
Consensus pattern (48 bp):
TAAAATGCATGAAAGGATGCATTCAAGGCATGAAAGGATGTCATAAAC
Found at i:50118 original size:47 final size:46
Alignment explanation
Indices: 50012--50126 Score: 160
Period size: 47 Copynumber: 2.5 Consensus size: 46
50002 AAATCGAATC
*
50012 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGT
1 CATAATTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGT
* *
50058 CATAAACTAAAATGCATGAAATGATGCATTCAGGGCATGAAAGGATGT
1 CAT-AATTAAAATGCATGAAATGATGCATT-AAGGCATGAAAGGATGT
* *
50106 CATAATTTAAATGGAT-AAATG
1 CATAATTAAAATGCATGAAATG
50127 GATATGTTAA
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
46 8 0.13
47 34 0.56
48 19 0.31
ACGTcount: A:0.43, C:0.10, G:0.22, T:0.25
Consensus pattern (46 bp):
CATAATTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGT
Found at i:58717 original size:81 final size:79
Alignment explanation
Indices: 58577--58818 Score: 272
Period size: 81 Copynumber: 3.0 Consensus size: 79
58567 TATAATTCCT
* * * *
58577 TTATTCTTTTACCCAAATGTATTTAGCCTTTAATCTAACTTGCATATTTGAC-ACTTTTCTGTCA
1 TTATTCTTTTACTC-AATGTATTTAACCTTT-ATCTAACTGGCATAATTGACAAC-TTTCTGTCA
*
58641 AATGCACAGCTAGTCCA
63 AATGCACAGCTAGGCCA
* * *
58658 TTATTCTTTTACTCAATGGTATTAAACCATTTATCTAAGTGGCATAATTGACAACTTTCTGCCAA
1 TTATTCTTTTACTCAAT-GTATTTAACC-TTTATCTAACTGGCATAATTGACAACTTTCTGTCAA
*
58723 ATGCACAGTTAGGCCA
64 ATGCACAGCTAGGCCA
* * *
58739 TT-TATCTTTTACTCAATAGTCTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGTCA
1 TTAT-TCTTTTACTCAAT-GTATTTAACC-TTTATCTAACTGGCATAATTGACAACTTTCTGTCA
* *
58803 AAAGCACAGTTAGGCC
63 AATGCACAGCTAGGCC
58819 TCAAAGGCAC
Statistics
Matches: 139, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
80 4 0.03
81 130 0.94
82 5 0.04
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.38
Consensus pattern (79 bp):
TTATTCTTTTACTCAATGTATTTAACCTTTATCTAACTGGCATAATTGACAACTTTCTGTCAAAT
GCACAGCTAGGCCA
Found at i:59129 original size:54 final size:54
Alignment explanation
Indices: 59061--59732 Score: 839
Period size: 54 Copynumber: 12.4 Consensus size: 54
59051 TATACGATAG
*
59061 TTCATCAACTCATGATGAATTCTGTGGGTTGCACACATCATGCCTGTACGGTTA
1 TTCATCAACTCATGATGAATTCTGTGGGTTGCACACATCGTGCCTGTACGGTTA
* *
59115 TTCATCAACTCATGATGAATT-TCGTGGGTTGCATACATCGTGCATGTACGGTTA
1 TTCATCAACTCATGATGAATTCT-GTGGGTTGCACACATCGTGCCTGTACGGTTA
* *
59169 TTCATTAACTCATGATGAATTTCAT-T-GGTTGCACACATCGTGCCTGCACGGTTA
1 TTCATCAACTCATGATGAA-TTC-TGTGGGTTGCACACATCGTGCCTGTACGGTTA
* *
59223 TTCATCAACTCATGATGAATTCTGTGGGTTGCACACATCGTGCTTGTACAGTTA
1 TTCATCAACTCATGATGAATTCTGTGGGTTGCACACATCGTGCCTGTACGGTTA
* * * * * * * *
59277 TTCGTCAACTAATGATGAATTTTATGGGTTACACACATCGTGCCTATAAGATTA
1 TTCATCAACTCATGATGAATTCTGTGGGTTGCACACATCGTGCCTGTACGGTTA
* *
59331 TTCATCAACTCATGATGAATTCTGTGGGTTGCACACATCATGCCTCTACGGTTA
1 TTCATCAACTCATGATGAATTCTGTGGGTTGCACACATCGTGCCTGTACGGTTA
* *
59385 TTCATCAACTCATGAAGAATT-TCATGGGTTGCACACATCGTGCCTGTACGGTTA
1 TTCATCAACTCATGATGAATTCT-GTGGGTTGCACACATCGTGCCTGTACGGTTA
* * * * *
59439 TTTATCAACTCATGATTAATTCCGTGGGATGCACACATCGTGCCTGTAAGGTTA
1 TTCATCAACTCATGATGAATTCTGTGGGTTGCACACATCGTGCCTGTACGGTTA
* * * ** *
59493 TTCATCAACTCATGATGAATTCTGTAGGTTGCTCACATTGTGTTTGTATGGTTA
1 TTCATCAACTCATGATGAATTCTGTGGGTTGCACACATCGTGCCTGTACGGTTA
* ** * * * *
59547 TTCATCAACTCATGATGCATTCCCTGGGTTGCGCACATCATTCATGTACGGTTA
1 TTCATCAACTCATGATGAATTCTGTGGGTTGCACACATCGTGCCTGTACGGTTA
** * * *
59601 TTCATCAACTCATGATGAATTCCATGGATTTGCACACATAGTGTCTGTACGGTTA
1 TTCATCAACTCATGATGAATTCTGTGG-GTTGCACACATCGTGCCTGTACGGTTA
* * * * *
59656 TTCATCAACTCATGATGAATTCTGTGGATTTGCACATATAGTGCATGTATGGTTA
1 TTCATCAACTCATGATGAATTCTGTGG-GTTGCACACATCGTGCCTGTACGGTTA
59711 TTCATCAACTCATGATGAATTC
1 TTCATCAACTCATGATGAATTC
59733 CATAGATTTG
Statistics
Matches: 532, Mismatches: 77, Indels: 17
0.85 0.12 0.03
Matches are distributed among these distances:
52 1 0.00
53 6 0.01
54 430 0.81
55 94 0.18
57 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.35
Consensus pattern (54 bp):
TTCATCAACTCATGATGAATTCTGTGGGTTGCACACATCGTGCCTGTACGGTTA
Found at i:60345 original size:21 final size:21
Alignment explanation
Indices: 60303--60371 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
60293 CCCTTTCCAT
* *
60303 GGTATCGATACT-ACTC-ATC
1 GGTATCGAGACTGATTCAATC
*
60322 GGTATCGAGACTGATTGAATC
1 GGTATCGAGACTGATTCAATC
* *
60343 GGTATCAATACTGATTCAATC
1 GGTATCGAGACTGATTCAATC
*
60364 AGTATCGA
1 GGTATCGA
60372 TGCTACTAAG
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 11 0.28
20 2 0.05
21 27 0.68
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.30
Consensus pattern (21 bp):
GGTATCGAGACTGATTCAATC
Found at i:63502 original size:81 final size:82
Alignment explanation
Indices: 63262--63504 Score: 265
Period size: 81 Copynumber: 3.0 Consensus size: 82
63252 TTACAATTCC
* * ** * * * *
63262 TTTATTATTTTACCCAAAGGTATTTAACTTTTAATCTAACTTGCATATTTTACACTTTTATGTCA
1 TTTATTATTTTACTCAACGGTATTTAACCATTAATCTAACTGGCATAATTGACACATTTATGTCA
* *
63327 AATGCACAGCTAGTCCA
66 AATGCACAGTTAGGCCA
* * * * * *
63344 -TTATTATTTTACTCAACGATATTTAACCATTTATCTGACTGGCATAATTGACATATTTCTGCCA
1 TTTATTATTTTACTCAACGGTATTTAACCATTAATCTAACTGGCATAATTGACACATTTATGTCA
*
63408 AATGCACAATTAGGCCA
66 AATGCACAGTTAGGCCA
* * * * *
63425 TTTA-TATTTTACTCAACGGTCTTTAACCGTTCATCTAACTGGCATAATTGACACATTTATATTA
1 TTTATTATTTTACTCAACGGTATTTAACCATTAATCTAACTGGCATAATTGACACATTTATGTCA
*
63489 AATACACAGTTAGGCC
66 AATGCACAGTTAGGCC
63505 TTAAAGGCAC
Statistics
Matches: 131, Mismatches: 29, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
81 128 0.98
82 3 0.02
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.39
Consensus pattern (82 bp):
TTTATTATTTTACTCAACGGTATTTAACCATTAATCTAACTGGCATAATTGACACATTTATGTCA
AATGCACAGTTAGGCCA
Found at i:63794 original size:54 final size:54
Alignment explanation
Indices: 63728--64288 Score: 628
Period size: 54 Copynumber: 10.4 Consensus size: 54
63718 TGCAAACGTA
* * * * *
63728 GTGCCTATACGG-TAGTTCATCAACTCATGATGAATTGTATGGGTTACAAACATC
1 GTGCCTGTACGGTTA-TTCATCAACTCATGATGAATTCTGTGGGTTGCACACATC
* * * * *
63782 GTACATGTACGGTTATTTATCAACTCATGATGAATT-TCGTGGGTTACATACATC
1 GTGCCTGTACGGTTATTCATCAACTCATGATGAATTCT-GTGGGTTGCACACATC
* * *
63836 GTGCTTGTACGGTTATTCATCAACTCGTGTTGAATTCTGTGGGTTGCACACATC
1 GTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGGTTGCACACATC
* * * * * *
63890 ATACATGTACGGTTATTCATCAGCTCATGATGAATTCTATGGGTTGCACATATC
1 GTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGGTTGCACACATC
*
63944 GTGCCTGTACGGTTATTCATCAACTCATGATGAATTTTGTGGGTTGCACACATC
1 GTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGGTTGCACACATC
* * * * * *
63998 GTGCTTGTACGATTATTCATCAACTCGTGAAGAATT-TCGTGGGTTGTACGCATC
1 GTGCCTGTACGGTTATTCATCAACTCATGATGAATTCT-GTGGGTTGCACACATC
* * *
64052 GTGCCTGTACGGTTAGTCATCAACTCATGATGAATTCCGTGGGTTGTACACATC
1 GTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGGTTGCACACATC
* * *
64106 GTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTATGGGTTTCACACATA
1 GTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGGTTGCACACATC
* * ** * *
64160 GTGCCTGTACGGTTATTTATCAA-T-ATGATGAATTCCGTAGATTTGCATACATA
1 GTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGT-GGGTTGCACACATC
* * * ** *
64213 GTGCATGTACGGTTATTCATCAACTCATGATAAATTCTGTGGATTTGCACATGTA
1 GTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGG-GTTGCACACATC
* *
64268 GTGCCTGTACAGATATTCATC
1 GTGCCTGTACGGTTATTCATC
64289 CACGTAGGAT
Statistics
Matches: 433, Mismatches: 65, Indels: 17
0.84 0.13 0.03
Matches are distributed among these distances:
52 12 0.03
53 34 0.08
54 345 0.80
55 42 0.10
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (54 bp):
GTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGGTTGCACACATC
Found at i:70485 original size:28 final size:28
Alignment explanation
Indices: 70445--70511 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
70435 TCGGGTCTAG
* *
70445 TCGGGTCGGGTTTTTTTAAGTGTGATAT
1 TCGGGTCGGGTTTTTTAAAGTGTAATAT
70473 TCGGGTCGGGTTTTTTAAAGTGTAATAT
1 TCGGGTCGGGTTTTTTAAAGTGTAATAT
*
70501 TCAGGTCGGGT
1 TCGGGTCGGGT
70512 CGGGTTGGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.16, C:0.09, G:0.33, T:0.42
Consensus pattern (28 bp):
TCGGGTCGGGTTTTTTAAAGTGTAATAT
Found at i:71120 original size:17 final size:18
Alignment explanation
Indices: 71095--71141 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
71085 TATGGAATTG
*
71095 GATTCCAATTCC-TGACA
1 GATTCCAATTCCTTCACA
*
71112 GATTTCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
71130 GATTCCAATTCC
1 GATTCCAATTCC
71142 CTCAGAAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.34
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:72985 original size:129 final size:129
Alignment explanation
Indices: 72796--73045 Score: 322
Period size: 129 Copynumber: 1.9 Consensus size: 129
72786 CATATTCGGA
* * * * *
72796 TTTGACTGATAATTTGGAGGCTTTCAAGTTCGAAATGGGCAAAACAGACTTCGAATTCGGATTTA
1 TTTGACTGATAATTTCGAGGCTTTCAAGTTCGAAATGGGAAAAACAGACTTCGAAATCGGACTCA
*
72861 GGACGTCGAAAAACATAAAATATGACTTTTCAAAAATTTTAACTTTTTTGTCAAAGCCAATAGG
66 GGACGTCGAAAAACATAAAATATGACTTTTCAAAAATTTTAACTTTTTGGTCAAAGCCAATAGG
** * * *
72925 TTTGACTGATAATTTCGAGGCTTTCGGGATT-GAATTTGGAAAAACGGACTTCGAAATCGGACTC
1 TTTGACTGATAATTTCGAGGCTTTCAAG-TTCGAAATGGGAAAAACAGACTTCGAAATCGGACTC
* * * * * **
72989 AGGATGTTGAAAAATATAAAGTATGATTTTTTGAAAATTTTAACTTTTTGGTCAAAG
65 AGGACGTCGAAAAACATAAAATATGACTTTTCAAAAATTTTAACTTTTTGGTCAAAG
73046 GCAACGGTCA
Statistics
Matches: 102, Mismatches: 18, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
129 100 0.98
130 2 0.02
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.34
Consensus pattern (129 bp):
TTTGACTGATAATTTCGAGGCTTTCAAGTTCGAAATGGGAAAAACAGACTTCGAAATCGGACTCA
GGACGTCGAAAAACATAAAATATGACTTTTCAAAAATTTTAACTTTTTGGTCAAAGCCAATAGG
Done.