Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005871.1 Hibiscus syriacus cultivar Beakdansim tig00013800_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: 111578
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:576 original size:21 final size:21
Alignment explanation
Indices: 537--576 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
527 ATGGTATTTT
*
537 ATATTTATATCATATAATATA
1 ATATTTATATCATACAATATA
558 ATATTTATAT-ATTACAATA
1 ATATTTATATCA-TACAATA
577 CATTTTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (21 bp):
ATATTTATATCATACAATATA
Found at i:3016 original size:7 final size:7
Alignment explanation
Indices: 2994--3137 Score: 55
Period size: 7 Copynumber: 20.1 Consensus size: 7
2984 AATCCCAACG
*
2994 TATAGTA
1 TATATTA
3001 TAGTATTA
1 TA-TATTA
3009 TATATTA
1 TATATTA
*
3016 TATATAA
1 TATATTA
3023 TATATT-
1 TATATTA
**
3029 TATAGCA
1 TATATTA
3036 TAT-TATA
1 TATAT-TA
3043 TATATTA
1 TATATTA
*
3050 CATAGTGTA
1 TATA-T-TA
* *
3059 GTCTAATA
1 -TATATTA
3067 TTATATTA
1 -TATATTA
*
3075 TATAGGTA
1 TATA-TTA
* *
3083 GATATTT
1 TATATTA
*
3090 TTTA-TA
1 TATATTA
*
3096 AATATTA
1 TATATTA
3103 TATA-TA
1 TATATTA
*
3109 TAATATAA
1 T-ATATTA
*
3117 CATATTA
1 TATATTA
3124 TATA-TA
1 TATATTA
3130 TATATTA
1 TATATTA
3137 T
1 T
3138 CATTATTGGG
Statistics
Matches: 97, Mismatches: 28, Indels: 24
0.65 0.19 0.16
Matches are distributed among these distances:
6 16 0.16
7 56 0.58
8 21 0.22
9 2 0.02
10 2 0.02
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (7 bp):
TATATTA
Found at i:3123 original size:21 final size:20
Alignment explanation
Indices: 3092--3131 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
3082 AGATATTTTT
3092 TATAAATATTATATATATAA
1 TATAAATATTATATATATAA
3112 TATAACATATTATATATATA
1 TATAA-ATATTATATATATA
3132 TATTATCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (20 bp):
TATAAATATTATATATATAA
Found at i:3854 original size:32 final size:32
Alignment explanation
Indices: 3761--3858 Score: 124
Period size: 32 Copynumber: 3.1 Consensus size: 32
3751 GACTATGCTA
* ** * * *
3761 TGCATTATCTAAATGTGATACTGGCTCTATCG
1 TGCATTATCTGAATGCAATACTGACTCTGTTG
* *
3793 TGCATTATATGAATGCAATACTGATTCTGTTG
1 TGCATTATCTGAATGCAATACTGACTCTGTTG
3825 TGCATTATCTGAATGCAATACTGACTCTGTTG
1 TGCATTATCTGAATGCAATACTGACTCTGTTG
3857 TG
1 TG
3859 ACTCATACAC
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 56 1.00
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (32 bp):
TGCATTATCTGAATGCAATACTGACTCTGTTG
Found at i:7247 original size:20 final size:21
Alignment explanation
Indices: 7190--7264 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
7180 TAACATAAAC
* *
7190 ATAAAATTTATAAATTCAAATT
1 ATAAAA-TTATAAAATAAAATT
*
7212 ATATAATCTA-AAAATAAAATT
1 ATAAAAT-TATAAAATAAAATT
* *
7233 TTAAAA-TATAAAATAGAATT
1 ATAAAATTATAAAATAAAATT
7253 ATAAAATTATAA
1 ATAAAATTATAA
7265 CTAAATTGAA
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
19 2 0.05
20 15 0.35
21 19 0.44
22 7 0.16
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (21 bp):
ATAAAATTATAAAATAAAATT
Found at i:18142 original size:18 final size:18
Alignment explanation
Indices: 18119--18154 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
18109 AGGCAACAAC
*
18119 TGTAAGTATTTATTTGTT
1 TGTAAGTATTTATCTGTT
18137 TGTAAGTATTTATCTGTT
1 TGTAAGTATTTATCTGTT
18155 ATCTGTTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.03, G:0.17, T:0.58
Consensus pattern (18 bp):
TGTAAGTATTTATCTGTT
Found at i:27699 original size:31 final size:31
Alignment explanation
Indices: 27664--27722 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
27654 ATAATATATG
*
27664 GTCACTTTTGTTTTTATTTAATTAAGATAAA
1 GTCACTTTCGTTTTTATTTAATTAAGATAAA
27695 GTCACTTTCGTTTTTATTTAATTAAGAT
1 GTCACTTTCGTTTTTATTTAATTAAGAT
27723 GTGGTCACCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.29, C:0.08, G:0.10, T:0.53
Consensus pattern (31 bp):
GTCACTTTCGTTTTTATTTAATTAAGATAAA
Found at i:27730 original size:31 final size:31
Alignment explanation
Indices: 27659--27730 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
27649 AAAACATAAT
*
27659 ATATGGTCACTTTTGTTTTTATTTAATTAAG
1 ATATGGTCACTTTCGTTTTTATTTAATTAAG
**
27690 ATAAAGTCACTTTCGTTTTTATTTAATTAAG
1 ATATGGTCACTTTCGTTTTTATTTAATTAAG
*
27721 ATGTGGTCAC
1 ATATGGTCAC
27731 CATGGGTTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.28, C:0.10, G:0.14, T:0.49
Consensus pattern (31 bp):
ATATGGTCACTTTCGTTTTTATTTAATTAAG
Found at i:37784 original size:7 final size:7
Alignment explanation
Indices: 37772--37801 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
37762 TGATGACCAT
37772 GGAAGGG
1 GGAAGGG
37779 GGAAGGG
1 GGAAGGG
*
37786 GGAAGTG
1 GGAAGGG
37793 GGAAGGG
1 GGAAGGG
37800 GG
1 GG
37802 GCAGTTGAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.27, C:0.00, G:0.70, T:0.03
Consensus pattern (7 bp):
GGAAGGG
Found at i:40632 original size:2 final size:2
Alignment explanation
Indices: 40625--40672 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
40615 TTCTTCGGCC
40625 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40667 TA TA TA
1 TA TA TA
40673 AATCCATTCT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:48434 original size:74 final size:74
Alignment explanation
Indices: 48299--48438 Score: 167
Period size: 74 Copynumber: 1.9 Consensus size: 74
48289 ACACGTGCTT
* * * * *
48299 ACCTTAAAATCCGAGTTTTTTTCGATTAGATATTTATTTTACTAATATTGTCCACCGTGAAATTT
1 ACCTTAAAATCCGAGTTTTCTTCGATTAGATACTTATTTTACGAAGATTGTCCACCCTGAAATTT
48364 TTCATGACC
66 TTCATGACC
** * *
48373 ACCTTAAAATTTGAGTTTTCTTCGATTAGTTGCTTATTTTACGAACGA-TG-CTCACCCTGAAAT
1 ACCTTAAAATCCGAGTTTTCTTCGATTAGATACTTATTTTACGAA-GATTGTC-CACCCTGAAAT
48436 TTT
64 TTT
48439 ATTTGTACTC
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
73 1 0.02
74 53 0.96
75 1 0.02
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43
Consensus pattern (74 bp):
ACCTTAAAATCCGAGTTTTCTTCGATTAGATACTTATTTTACGAAGATTGTCCACCCTGAAATTT
TTCATGACC
Found at i:50177 original size:20 final size:20
Alignment explanation
Indices: 50152--50191 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
50142 TCCAACATGA
50152 ACATGATTAAAATATTCTAT
1 ACATGATTAAAATATTCTAT
*
50172 ACATGATTAATATATTCTAT
1 ACATGATTAAAATATTCTAT
50192 CTTTTTATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.42
Consensus pattern (20 bp):
ACATGATTAAAATATTCTAT
Found at i:50606 original size:38 final size:40
Alignment explanation
Indices: 50564--50640 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 40
50554 TCAATCGCAC
*
50564 AATCATGTAAGGAACG-A-AAGAATGGTTGAAGAACCTAT
1 AATCATGCAAGGAACGAAGAAGAATGGTTGAAGAACCTAT
50602 AATCATGCAAGGAACGAAAGAAGAATGGTTGAAGAACCT
1 AATCATGCAAGGAACG-AAGAAGAATGGTTGAAGAACCT
50641 TACTTGTTGA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
38 15 0.43
40 1 0.03
41 19 0.54
ACGTcount: A:0.45, C:0.12, G:0.25, T:0.18
Consensus pattern (40 bp):
AATCATGCAAGGAACGAAGAAGAATGGTTGAAGAACCTAT
Found at i:51155 original size:2 final size:2
Alignment explanation
Indices: 51148--51179 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
51138 ATCAGAAAGG
*
51148 GA GA GA GA GA GA GA GA GA GG GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
51180 AAACAAGATT
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:0.53, T:0.00
Consensus pattern (2 bp):
GA
Found at i:52143 original size:30 final size:29
Alignment explanation
Indices: 52077--52135 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
52067 CTTTAAATGG
**
52077 AATAAATTAACATTTTATATTCAAAAATA
1 AATAAATTAACATTTTATATAAAAAAATA
52106 AATAAATTAACATTTTATATAAAATAAATA
1 AATAAATTAACATTTTATATAAAA-AAATA
52136 TTGAAATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (29 bp):
AATAAATTAACATTTTATATAAAAAAATA
Found at i:53617 original size:28 final size:28
Alignment explanation
Indices: 53585--53639 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
53575 AATTTTTCCT
53585 AAATCCGAT-TTCAAATGTTTTTTACACA
1 AAATCCGATATTCAAAT-TTTTTTACACA
* *
53613 AAATCTGATATTCAGATTTTTTTACAC
1 AAATCCGATATTCAAATTTTTTTACAC
53640 CTCCGGTGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 18 0.75
29 6 0.25
ACGTcount: A:0.35, C:0.16, G:0.07, T:0.42
Consensus pattern (28 bp):
AAATCCGATATTCAAATTTTTTTACACA
Found at i:55139 original size:25 final size:24
Alignment explanation
Indices: 55101--55147 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
55091 TTTTAAATTT
55101 AGTTAATAATAAAATATATTTAATA
1 AGTTAATAATAAAATAT-TTTAATA
55126 AGTTAAT-ATAAAAATATTTTAA
1 AGTTAATAAT-AAAATATTTTAA
55148 GTTAATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.40
Consensus pattern (24 bp):
AGTTAATAATAAAATATTTTAATA
Found at i:55150 original size:21 final size:23
Alignment explanation
Indices: 55101--55156 Score: 80
Period size: 21 Copynumber: 2.4 Consensus size: 23
55091 TTTTAAATTT
55101 AGTTAATAATAAAATATATTTAATA
1 AGTTAAT-ATAAAATATATTT-ATA
55126 AGTTAATATAAAA-ATATTT-TA
1 AGTTAATATAAAATATATTTATA
55147 AGTTAATATA
1 AGTTAATATA
55157 TATAAAATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
21 12 0.39
23 6 0.19
24 6 0.19
25 7 0.23
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (23 bp):
AGTTAATATAAAATATATTTATA
Found at i:55163 original size:24 final size:24
Alignment explanation
Indices: 55101--55173 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 24
55091 TTTTAAATTT
55101 AGTTAATA-ATAAAATATATTTAATA
1 AGTTAATATATAAAA-ATATTT-ATA
55126 AGTT-A-ATATAAAAATATTT-TA
1 AGTTAATATATAAAAATATTTATA
55147 AGTTAATATATATAAAATTATTATATA
1 AGTTAATATATA-AAAA-TATT-TATA
55174 TAATTCAGGT
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
21 6 0.15
22 1 0.02
23 12 0.29
24 11 0.27
25 8 0.20
26 1 0.02
27 2 0.05
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.42
Consensus pattern (24 bp):
AGTTAATATATAAAAATATTTATA
Found at i:55218 original size:18 final size:19
Alignment explanation
Indices: 55191--55234 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
55181 GGTCACCTGG
*
55191 TTCTTAAATT-TTTTATTT
1 TTCTTAAATTATATTATTT
*
55209 TTCTTTAATTATATTATTT
1 TTCTTAAATTATATTATTT
55228 TT-TTAAA
1 TTCTTAAA
55235 AGTTGTATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (19 bp):
TTCTTAAATTATATTATTT
Found at i:55277 original size:26 final size:27
Alignment explanation
Indices: 55229--55279 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
55219 ATATTATTTT
*
55229 TTTAAAAGTTGTATAAAAAATATAAAA
1 TTTAAAACTTGTATAAAAAATATAAAA
* *
55256 TTTAAAACTT-TATAATATATATAA
1 TTTAAAACTTGTATAAAAAATATAA
55280 TCCACATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 12 0.57
27 9 0.43
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (27 bp):
TTTAAAACTTGTATAAAAAATATAAAA
Found at i:55501 original size:39 final size:39
Alignment explanation
Indices: 55412--55501 Score: 103
Period size: 39 Copynumber: 2.3 Consensus size: 39
55402 TAACTTTAAT
55412 GTGAAATAATTTAAGAAATTAAGATTATAAAACGTTACG
1 GTGAAATAATTTAAGAAATTAAGATTATAAAACGTTACG
* * * * *
55451 GTGTCAA-AATTTAAGAAATTATGATTTTAGAATGTTA-G
1 GTG-AAATAATTTAAGAAATTAAGATTATAAAACGTTACG
55489 AGTGAAATAATTT
1 -GTGAAATAATTT
55502 GAGGGGTATG
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
38 3 0.07
39 37 0.88
40 2 0.05
ACGTcount: A:0.44, C:0.03, G:0.17, T:0.36
Consensus pattern (39 bp):
GTGAAATAATTTAAGAAATTAAGATTATAAAACGTTACG
Found at i:58603 original size:16 final size:16
Alignment explanation
Indices: 58582--58612 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
58572 TATATATATA
58582 TATATATGTATGTATT
1 TATATATGTATGTATT
58598 TATATATGTATGTAT
1 TATATATGTATGTAT
58613 GATATTGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (16 bp):
TATATATGTATGTATT
Found at i:58603 original size:20 final size:21
Alignment explanation
Indices: 58573--58626 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
58563 GTCAAATTAT
*
58573 ATATATATATATATATGTATG
1 ATATTTATATATATATGTATG
*
58594 -TATTTATATATGTATGTATG
1 ATATTTATATATATATGTATG
*
58614 ATATTGAT-TATAT
1 ATATTTATATATAT
58627 GAATGTAGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 22 0.79
21 6 0.21
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (21 bp):
ATATTTATATATATATGTATG
Found at i:58828 original size:8 final size:8
Alignment explanation
Indices: 58817--58852 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
58807 ATAATTATTT
58817 AATTTATC
1 AATTTATC
58825 AATTTATC
1 AATTTATC
58833 AATTTATC
1 AATTTATC
* *
58841 AAATTATT
1 AATTTATC
58849 AATT
1 AATT
58853 ATATTAATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (8 bp):
AATTTATC
Found at i:64694 original size:18 final size:19
Alignment explanation
Indices: 64673--64719 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
64663 GCTAAAATTG
*
64673 GTATCGATA-CTAAGGCTA
1 GTATCGATACCTAAGGCAA
64691 GTATCGATACCCTAAGGCAA
1 GTATCGATA-CCTAAGGCAA
*
64711 GTATAGATA
1 GTATCGATA
64720 TTGACAAGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 9 0.36
20 16 0.64
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (19 bp):
GTATCGATACCTAAGGCAA
Found at i:64981 original size:29 final size:29
Alignment explanation
Indices: 64939--65001 Score: 117
Period size: 29 Copynumber: 2.2 Consensus size: 29
64929 CTGGGTTACT
64939 TGAGCGTATGTATATACTATTAAAATACG
1 TGAGCGTATGTATATACTATTAAAATACG
*
64968 TGAGCGTATGTATATACTATTCAAATACG
1 TGAGCGTATGTATATACTATTAAAATACG
64997 TGAGC
1 TGAGC
65002 AGAGATATCC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (29 bp):
TGAGCGTATGTATATACTATTAAAATACG
Found at i:67019 original size:19 final size:20
Alignment explanation
Indices: 66977--67025 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
66967 CCACCGAAAA
*
66977 TAAAAAAAAGGATGCAAACTT
1 TAAAAAAAAGGATACAAAC-T
*
66998 TAAAAAAAAGGATACAGA-T
1 TAAAAAAAAGGATACAAACT
67017 TAAAAAAAA
1 TAAAAAAAA
67026 TAAAGGTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 10 0.38
21 16 0.62
ACGTcount: A:0.65, C:0.06, G:0.12, T:0.16
Consensus pattern (20 bp):
TAAAAAAAAGGATACAAACT
Found at i:69144 original size:105 final size:105
Alignment explanation
Indices: 68934--69707 Score: 1200
Period size: 105 Copynumber: 7.4 Consensus size: 105
68924 GTATTGTTCC
* * * * * **
68934 GGAGCCCAATATCATTCACTGTGAAGTTGAAATTGGCTCCGAAATTGAGAAGTTGTCGGTTGACA
1 GGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTGTTGACA
** ****
68999 GTCAGCGGTCCCTTCGTCGTGAAGTTGAACTTATACTGTCT
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
69040 TGAGTCCAATATCCTTCGCGGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAA
1 GGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAA
69105 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
69145 GGAGTCCAATATCCTTCG-TGGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACA
1 GGAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACA
69209 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
**
69250 GGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGAATCTG-AA-T--GAAAT-TTTGTTGACAA
1 GGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAA
69310 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * *
69350 GGAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTTTGAAATTGAGAAGTTGTTTGTTGACA
1 GGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTGTTGACA
* * *
69415 ACCAGCGGTCCCTTCGTTGTGAAGTTGAACATGCGTTGTTT
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
*
69456 GGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
1 GGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTGTTGACA
69521 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * *
69562 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTATGAATTTGAGAAATGTTTGTTGACAA
1 GGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAA
69627 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
69667 GGAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTG
1 GGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTG
69708 GGTAAAACCT
Statistics
Matches: 620, Mismatches: 40, Indels: 17
0.92 0.06 0.03
Matches are distributed among these distances:
100 87 0.14
101 7 0.01
102 1 0.00
103 1 0.00
104 5 0.01
105 277 0.45
106 242 0.39
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (105 bp):
GGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
Found at i:81255 original size:19 final size:20
Alignment explanation
Indices: 81213--81261 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
81203 CCACCGAAAA
*
81213 TAAAAAAAAGGATGCAAACTT
1 TAAAAAAAAGGATACAAAC-T
*
81234 TAAAAAAAAGGATACAGA-T
1 TAAAAAAAAGGATACAAACT
81253 TAAAAAAAA
1 TAAAAAAAA
81262 TAAAGGTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 10 0.38
21 16 0.62
ACGTcount: A:0.65, C:0.06, G:0.12, T:0.16
Consensus pattern (20 bp):
TAAAAAAAAGGATACAAACT
Found at i:82875 original size:14 final size:14
Alignment explanation
Indices: 82856--82885 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
82846 ATCCTTGATG
82856 ATTTAACGGTTCAT
1 ATTTAACGGTTCAT
*
82870 ATTTAATGGTTCAT
1 ATTTAACGGTTCAT
82884 AT
1 AT
82886 ATAAAGAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.47
Consensus pattern (14 bp):
ATTTAACGGTTCAT
Found at i:86916 original size:150 final size:150
Alignment explanation
Indices: 86645--86944 Score: 564
Period size: 150 Copynumber: 2.0 Consensus size: 150
86635 TCATTTATAC
*
86645 GTTTCTAGTCATGCATAATCCATTTATTAACTTTCATCTATTAAATTCTGAATGCAATATTATAA
1 GTTTCTAGTCATGCATAATCCAGTTATTAACTTTCATCTATTAAATTCTGAATGCAATATTATAA
* *
86710 TTTATAACTTAAAACAACTTTGAAATAGTTAAGGTTGGTCTAATTATGCTTTCCCCTTTTTTCTT
66 TTTATAACTTAAAACAACTTTGAAACAGTTAAGGTTGGTCTAATTATGCCTTCCCCTTTTTTCTT
86775 TGAACAATCATTTCCCTTAT
131 TGAACAATCATTTCCCTTAT
86795 GTTTCTAGTCATGCATAATCCAGTTATTAACTTTCATCTATTAAATTCTGAATGCAATATTATAA
1 GTTTCTAGTCATGCATAATCCAGTTATTAACTTTCATCTATTAAATTCTGAATGCAATATTATAA
*
86860 TTTATAACTTAAAACAACTTTGAAACAGTTAAGGTTGGTCTATTTATGCCTTCCCCTTTTTTCTT
66 TTTATAACTTAAAACAACTTTGAAACAGTTAAGGTTGGTCTAATTATGCCTTCCCCTTTTTTCTT
86925 TGAACAATCATTTCCCTTAT
131 TGAACAATCATTTCCCTTAT
86945 CATCCTCAGT
Statistics
Matches: 146, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
150 146 1.00
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.43
Consensus pattern (150 bp):
GTTTCTAGTCATGCATAATCCAGTTATTAACTTTCATCTATTAAATTCTGAATGCAATATTATAA
TTTATAACTTAAAACAACTTTGAAACAGTTAAGGTTGGTCTAATTATGCCTTCCCCTTTTTTCTT
TGAACAATCATTTCCCTTAT
Found at i:90972 original size:30 final size:30
Alignment explanation
Indices: 90936--90994 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
90926 ATGTAAATCT
*
90936 TAATCGGATCTTAGACATATCCTGATCCTA
1 TAATCGGATCTTAGACATACCCTGATCCTA
*
90966 TAATCGGGTCTTAGACATACCCTGATCCT
1 TAATCGGATCTTAGACATACCCTGATCCT
90995 GGACTGGGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.32
Consensus pattern (30 bp):
TAATCGGATCTTAGACATACCCTGATCCTA
Found at i:97816 original size:39 final size:41
Alignment explanation
Indices: 97766--97854 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 41
97756 AGTTAGAATA
* *
97766 ATTATTGTTATTTATTAAGGTATTTTGTTTGAACATAAAATT
1 ATTATTATTATTTATTAAGGTATTTTGTTCGAACATAAAA-T
*
97808 ATTATTATTATTTATTAAGGTTTTTTGTTCGAACATTAAGAAT
1 ATTATTATTATTTATTAAGGTATTTTGTTCGAACA-TAA-AAT
97851 ATTA
1 ATTA
97855 ATAATGTACA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
42 32 0.76
43 8 0.19
44 2 0.05
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.52
Consensus pattern (41 bp):
ATTATTATTATTTATTAAGGTATTTTGTTCGAACATAAAAT
Found at i:101615 original size:2 final size:2
Alignment explanation
Indices: 101610--101637 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
101600 TATGTGTGTG
101610 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
101638 ACCTTCATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:106471 original size:31 final size:31
Alignment explanation
Indices: 106433--106500 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
106423 GATCTACTCA
*
106433 CGAGCTTCAGTTT-AGGA-TTTAGAGTTCGAGT
1 CGAGCTTCA-TTTCAGAATTTTAGAG-TCGAGT
*
106464 CGAGCTTCATTTCAGAATTTTCGAGTCGAGT
1 CGAGCTTCATTTCAGAATTTTAGAGTCGAGT
106495 CGAGCT
1 CGAGCT
106501 CAGCAATACT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 3 0.09
31 24 0.73
32 6 0.18
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (31 bp):
CGAGCTTCATTTCAGAATTTTAGAGTCGAGT
Found at i:109472 original size:18 final size:18
Alignment explanation
Indices: 109449--109491 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
109439 ATTTCCTTCC
109449 TCATCTTTCTTGGGTTCG
1 TCATCTTTCTTGGGTTCG
109467 TCATCTTTCTTGGGTTCG
1 TCATCTTTCTTGGGTTCG
109485 TCATCTT
1 TCATCTT
109492 CATCGTCGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.07, C:0.23, G:0.19, T:0.51
Consensus pattern (18 bp):
TCATCTTTCTTGGGTTCG
Found at i:110954 original size:11 final size:10
Alignment explanation
Indices: 110913--110989 Score: 50
Period size: 11 Copynumber: 7.5 Consensus size: 10
110903 TAATAAATTT
*
110913 TTAAAAATTA
1 TTAAATATTA
*
110923 TAAAATAATTA
1 TTAAAT-ATTA
110934 TTAAAT-TTA
1 TTAAATATTA
110943 TTAAATCATTA
1 TTAAAT-ATTA
* *
110954 TGAATATATAA
1 TTAA-ATATTA
110965 TTAAAT-TTA
1 TTAAATATTA
* *
110974 TCAAATTATTC
1 TTAAA-TATTA
110985 TTAAA
1 TTAAA
110990 ATTTATTTAT
Statistics
Matches: 51, Mismatches: 10, Indels: 11
0.71 0.14 0.15
Matches are distributed among these distances:
9 15 0.29
10 7 0.14
11 27 0.53
12 2 0.04
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (10 bp):
TTAAATATTA
Done.