Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009646.1 Hibiscus syriacus cultivar Beakdansim tig00117070_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: 122845
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:16494 original size:7 final size:7
Alignment explanation
Indices: 16482--16533 Score: 67
Period size: 7 Copynumber: 7.9 Consensus size: 7
16472 TGCTAAAAAG
16482 AATAATA
1 AATAATA
16489 AATAATA
1 AATAATA
16496 AATAAT-
1 AATAATA
16502 AATAAT-
1 AATAATA
16508 AA-AATA
1 AATAATA
16514 AATAA-A
1 AATAATA
16520 TAATAATA
1 -AATAATA
16528 AATAAT
1 AATAAT
16534 GTATTATCAT
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
5 3 0.07
6 11 0.27
7 26 0.63
8 1 0.02
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
AATAATA
Found at i:16495 original size:3 final size:3
Alignment explanation
Indices: 16482--16533 Score: 52
Period size: 3 Copynumber: 16.0 Consensus size: 3
16472 TGCTAAAAAG
16482 AAT AAT AAAT AAT AAAT AAT AAT AAT AA- AAT AAAT AAAT AAT AAT AAAT
1 AAT AAT -AAT AAT -AAT AAT AAT AAT AAT AAT -AAT -AAT AAT AAT -AAT
16531 AAT
1 AAT
16534 GTATTATCAT
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
2 2 0.05
3 26 0.59
4 16 0.36
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:16520 original size:22 final size:19
Alignment explanation
Indices: 16482--16529 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
16472 TGCTAAAAAG
16482 AATAATAAATAATAAATAAT
1 AATAATAAA-AATAAATAAT
16502 AATAAT-AAAATAAATAAAT
1 AATAATAAAAATAAAT-AAT
16521 AATAATAAA
1 AATAATAAA
16530 TAATGTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.27
19 11 0.42
20 8 0.31
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (19 bp):
AATAATAAAAATAAATAAT
Found at i:34173 original size:17 final size:17
Alignment explanation
Indices: 34151--34184 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
34141 CGATCTTACG
34151 CTATTACCTACACGTGA
1 CTATTACCTACACGTGA
34168 CTATTACCTACACGTGA
1 CTATTACCTACACGTGA
34185 AACAATCACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.29
Consensus pattern (17 bp):
CTATTACCTACACGTGA
Found at i:39717 original size:21 final size:22
Alignment explanation
Indices: 39674--39726 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
39664 TTTAGTATCA
39674 TAATATTTG-TACATACTAAAT
1 TAATATTTGATACATACTAAAT
*
39695 T-ATATTTGATAC-TAACTACAT
1 TAATATTTGATACAT-ACTAAAT
39716 TAATACTTTGA
1 TAATA-TTTGA
39727 AGACATTTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 8 0.30
21 11 0.41
22 3 0.11
23 5 0.19
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (22 bp):
TAATATTTGATACATACTAAAT
Found at i:42291 original size:40 final size:40
Alignment explanation
Indices: 42247--42436 Score: 317
Period size: 40 Copynumber: 4.8 Consensus size: 40
42237 AGGATACTAA
*
42247 GTGTATATGGTGGGAACGACCTTATGTGTAATACACTTCG
1 GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
42287 GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
1 GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
*
42327 GTGAATATGGTGGGCACGACCTTATGTGTAATACACTTCG
1 GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
* *
42367 GTGAATATAGTGGGCACGACCTTATGTGTAATACACTTCG
1 GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
* * *
42407 GTGTATATGATGGGAACGATCTTATGTGTA
1 GTGTATATGGTGGGCACGACCTTATGTGTA
42437 GCACTATGGT
Statistics
Matches: 142, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 142 1.00
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.32
Consensus pattern (40 bp):
GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
Found at i:49796 original size:40 final size:40
Alignment explanation
Indices: 49752--49940 Score: 272
Period size: 40 Copynumber: 4.8 Consensus size: 40
49742 AGGACACTAA
* * *
49752 GTGTACATGGTGGGCATGACTTTATGTGTAATACACTTCG
1 GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
*
49792 GTGTATATGGTGGGCACGGCCTTATGTGTAATACACTTCG
1 GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
* *
49832 GTGAATATGGT-GGTACGACCTTATGTGTAATACACTTCG
1 GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
* * *
49871 GTGAATATTGTGGGCACGACCTTATGTGTAATATACTTCG
1 GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
**
49911 GTGTATATGGTGGGCACGATTTTATGTGTA
1 GTGTATATGGTGGGCACGACCTTATGTGTA
49941 GCACTACGGT
Statistics
Matches: 134, Mismatches: 14, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
39 36 0.27
40 98 0.73
ACGTcount: A:0.23, C:0.14, G:0.28, T:0.35
Consensus pattern (40 bp):
GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
Found at i:49860 original size:79 final size:79
Alignment explanation
Indices: 49773--49923 Score: 257
Period size: 79 Copynumber: 1.9 Consensus size: 79
49763 GGGCATGACT
* *
49773 TTATGTGTAATACACTTCGGTGTATATGGTGGGCACGGCCTTATGTGTAATACACTTCGGTGAAT
1 TTATGTGTAATACACTTCGGTGAATATGGTGGGCACGACCTTATGTGTAATACACTTCGGTGAAT
49838 ATGGTGGTACGACC
66 ATGGTGGTACGACC
* * *
49852 TTATGTGTAATACACTTCGGTGAATATTGTGGGCACGACCTTATGTGTAATATACTTCGGTGTAT
1 TTATGTGTAATACACTTCGGTGAATATGGTGGGCACGACCTTATGTGTAATACACTTCGGTGAAT
49917 ATGGTGG
66 ATGGTGG
49924 GCACGATTTT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
79 67 1.00
ACGTcount: A:0.23, C:0.15, G:0.27, T:0.35
Consensus pattern (79 bp):
TTATGTGTAATACACTTCGGTGAATATGGTGGGCACGACCTTATGTGTAATACACTTCGGTGAAT
ATGGTGGTACGACC
Found at i:56150 original size:8 final size:8
Alignment explanation
Indices: 56139--56167 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
56129 ACATATAATA
56139 TATATAAG
1 TATATAAG
56147 TATATAAG
1 TATATAAG
56155 TATATAA-
1 TATATAAG
56162 TATATA
1 TATATA
56168 TTATGTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 6 0.29
8 15 0.71
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (8 bp):
TATATAAG
Found at i:56288 original size:38 final size:37
Alignment explanation
Indices: 56189--56288 Score: 102
Period size: 36 Copynumber: 2.7 Consensus size: 37
56179 AAAAAAATCA
*
56189 TTTAAAAAACCATATA-TATATGTTTTCAAAATACGT
1 TTTAAAAAACTATATATTATATGTTTTCAAAATACGT
* *
56225 TTT-CAAAA-T-TATATTATATACGTTTTCAAAAT-TGTTT
1 TTTAAAAAACTATATATTATAT--GTTTTCAAAATACG--T
56262 TTTAAAAAACTATATATTATATGTTTT
1 TTTAAAAAACTATATATTATATGTTTT
56289 TTTTAAATAA
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
33 4 0.08
34 5 0.10
35 5 0.10
36 14 0.27
37 4 0.08
38 9 0.17
39 1 0.02
40 10 0.19
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.47
Consensus pattern (37 bp):
TTTAAAAAACTATATATTATATGTTTTCAAAATACGT
Found at i:56919 original size:32 final size:32
Alignment explanation
Indices: 56881--56961 Score: 137
Period size: 32 Copynumber: 2.5 Consensus size: 32
56871 GGGTACGATA
56881 TCCTTCATCGTGAAGTTCAAATCATGGGTGACT
1 TCCTTCATCGTGAAGTTCAAATCATGGGTGA-T
56914 T-CTTCATCGTGAAGTTCAAATCATGGGTGAT
1 TCCTTCATCGTGAAGTTCAAATCATGGGTGAT
*
56945 TCCTTCGTCGTGAAGTT
1 TCCTTCATCGTGAAGTT
56962 AAGTCCAAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
31 2 0.04
32 43 0.93
33 1 0.02
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (32 bp):
TCCTTCATCGTGAAGTTCAAATCATGGGTGAT
Found at i:69060 original size:26 final size:25
Alignment explanation
Indices: 69026--69074 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 25
69016 TTTGGACCTG
69026 AAAAAAATAAAT-AATATATATAATA
1 AAAAAAATAAATAAATA-ATATAATA
69051 AAAAGAAATAAATAAATAATATAA
1 AAAA-AAATAAATAAATAATATAA
69075 ATTATATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 4 0.18
26 14 0.64
27 4 0.18
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (25 bp):
AAAAAAATAAATAAATAATATAATA
Found at i:69126 original size:15 final size:15
Alignment explanation
Indices: 69106--69151 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
69096 AGGTAATGGA
69106 AATATATGAAC-ATAT
1 AATATAT-AACTATAT
69121 AATATATAACTATAT
1 AATATATAACTATAT
69136 AACTATATAA-TATAT
1 AA-TATATAACTATAT
69151 A
1 A
69152 CTATGTTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 3 0.10
15 19 0.66
16 7 0.24
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (15 bp):
AATATATAACTATAT
Found at i:69134 original size:8 final size:8
Alignment explanation
Indices: 69108--69155 Score: 59
Period size: 8 Copynumber: 6.4 Consensus size: 8
69098 GTAATGGAAA
69108 TATATGAAC
1 TATAT-AAC
69117 -ATATAA-
1 TATATAAC
69123 TATATAAC
1 TATATAAC
69131 TATATAAC
1 TATATAAC
69139 TATATAA-
1 TATATAAC
69146 TATAT-AC
1 TATATAAC
69153 TAT
1 TAT
69156 GTTTTCAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
6 1 0.03
7 16 0.44
8 19 0.53
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (8 bp):
TATATAAC
Found at i:69143 original size:23 final size:22
Alignment explanation
Indices: 69108--69155 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 22
69098 GTAATGGAAA
69108 TATATGAACATATAATATATAAC
1 TATATGAACATATAATATAT-AC
69131 TATAT-AACTATATAATATATAC
1 TATATGAAC-ATATAATATATAC
69153 TAT
1 TAT
69156 GTTTTCAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (22 bp):
TATATGAACATATAATATATAC
Found at i:70731 original size:22 final size:20
Alignment explanation
Indices: 70699--70748 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 20
70689 AAAACTTACA
70699 ATAAACATCATATATATTCAGG
1 ATAAACATC--ATATATTCAGG
*
70721 ATAAACGTCATATATTCAGG
1 ATAAACATCATATATTCAGG
70741 ATAAACAT
1 ATAAACAT
70749 TTAGAATATG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 18 0.69
22 8 0.31
ACGTcount: A:0.46, C:0.14, G:0.10, T:0.30
Consensus pattern (20 bp):
ATAAACATCATATATTCAGG
Found at i:71967 original size:19 final size:20
Alignment explanation
Indices: 71941--71986 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
71931 CAAAATGGCC
71941 TAATTTC-ACA-TCCTAACAT
1 TAATTTCAACACT-CTAACAT
*
71960 TGATTTCAACACTCTAACAT
1 TAATTTCAACACTCTAACAT
71980 TAATTTC
1 TAATTTC
71987 CAGCATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 6 0.26
20 16 0.70
21 1 0.04
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.39
Consensus pattern (20 bp):
TAATTTCAACACTCTAACAT
Found at i:73216 original size:29 final size:30
Alignment explanation
Indices: 73156--73218 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
73146 AATACATATA
* * *
73156 TTTTGAAAATTACACTTTTGTTCTCTGAAC
1 TTTTAAAAATTACACTTTTGATCTCTAAAC
*
73186 TTTTAAAAATTACCCTTTTGATC-CTAAAC
1 TTTTAAAAATTACACTTTTGATCTCTAAAC
73215 TTTT
1 TTTT
73219 CCAAACTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 9 0.31
30 20 0.69
ACGTcount: A:0.29, C:0.17, G:0.06, T:0.48
Consensus pattern (30 bp):
TTTTAAAAATTACACTTTTGATCTCTAAAC
Found at i:74704 original size:149 final size:149
Alignment explanation
Indices: 74434--74885 Score: 823
Period size: 149 Copynumber: 3.0 Consensus size: 149
74424 TAACAATATC
*
74434 AAAATCAAGCTGCTTAAGATTAGGTTCATACTTTCTCAAAAATAACAATTTGTTCTGAAAATGCA
1 AAAATCAAGCTGCTTAAGATTAGGTTCCTACTTTCTCAAAAATAACAATTTGTTCTGAAAATGCA
74499 AAGGACCTCCCTCGAGAATCCAATCCCACATAGTGGAATTCACAAATGAAAAAAATACAGACTAG
66 AAGGACCTCCCTCGAGAATCCAATCCCACATAGTGGAATTCACAAATGAAAAAAATACAGACTAG
74564 GACCAGCCAAACTAACCTT
131 GACCAGCCAAACTAACCTT
* *
74583 AAAATCAAGTTACTTAAGATTAGGTTCCTACTTTCTCAAAAATAACAATTTGTTCTGAAAATGCA
1 AAAATCAAGCTGCTTAAGATTAGGTTCCTACTTTCTCAAAAATAACAATTTGTTCTGAAAATGCA
74648 AAGGACCTCCCTCGAGAATCCAATCCCACATAGTGGAATTCACAAATGAAAAAAATACAGACTAG
66 AAGGACCTCCCTCGAGAATCCAATCCCACATAGTGGAATTCACAAATGAAAAAAATACAGACTAG
*
74713 GACCAGTCAAACTAACCTT
131 GACCAGCCAAACTAACCTT
74732 AAAATCAAGCTGCTTAAGATTAGGTTCCTACTTTCTCAAAAATAACAATTTGTTCTGAAAATGCA
1 AAAATCAAGCTGCTTAAGATTAGGTTCCTACTTTCTCAAAAATAACAATTTGTTCTGAAAATGCA
*
74797 AAGGACCTCCCTCGAGAATCCAATCCCACATAGTGGAATTCACAAATGAAAAAAAAATTATAGAC
66 AAGGACCTCCCTCGAGAATCCAATCCCACATAGTGGAATTCACAAATG--AAAAAAA-TACAGAC
*
74862 TAGGACCAACCAAACTAACCTT
128 TAGGACCAGCCAAACTAACCTT
74884 AA
1 AA
74886 CTGGCGAATC
Statistics
Matches: 291, Mismatches: 9, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
149 256 0.88
151 7 0.02
152 28 0.10
ACGTcount: A:0.41, C:0.22, G:0.13, T:0.24
Consensus pattern (149 bp):
AAAATCAAGCTGCTTAAGATTAGGTTCCTACTTTCTCAAAAATAACAATTTGTTCTGAAAATGCA
AAGGACCTCCCTCGAGAATCCAATCCCACATAGTGGAATTCACAAATGAAAAAAATACAGACTAG
GACCAGCCAAACTAACCTT
Found at i:76112 original size:20 final size:21
Alignment explanation
Indices: 76087--76179 Score: 91
Period size: 21 Copynumber: 4.5 Consensus size: 21
76077 TTTTCCCAAT
*
76087 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* * **
76107 TCGCAACGTGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
76128 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
76148 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
76169 TCGCAATGCGA
1 TCGCAATGCGA
76180 TACTGACTAT
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.46
21 30 0.54
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:76132 original size:41 final size:41
Alignment explanation
Indices: 76087--76179 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
76077 TTTTCCCAAT
*
76087 TCGCAATGCGAATAAGTAAATCGCAACGTGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
76128 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
76169 TCGCAATGCGA
1 TCGCAATGCGA
76180 TACTGACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:76192 original size:41 final size:41
Alignment explanation
Indices: 76106--76240 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
76096 GAATAAGTAA
* * *
76106 ATCGCAACGTGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
76147 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
76188 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
76229 TTCGCAACGCGA
1 ATCGCAACGCGA
76241 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:76193 original size:20 final size:20
Alignment explanation
Indices: 76168--76262 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
76158 AATTGGGAAA
*
76168 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
76188 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
76209 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
76229 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
76249 TTCGCAACGCGATA
1 ATCGCAACGCGATA
76263 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:76478 original size:22 final size:22
Alignment explanation
Indices: 76450--76492 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
76440 CACTCTCTCA
76450 CCATCTCCGACGAAATCCGTCC
1 CCATCTCCGACGAAATCCGTCC
*
76472 CCATCTCCGGCGAAATCCGTC
1 CCATCTCCGACGAAATCCGTC
76493 TATCTCAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.21, C:0.44, G:0.16, T:0.19
Consensus pattern (22 bp):
CCATCTCCGACGAAATCCGTCC
Found at i:76781 original size:20 final size:20
Alignment explanation
Indices: 76756--76793 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
76746 CGATTCTCTC
76756 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
76776 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
76794 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:78136 original size:18 final size:18
Alignment explanation
Indices: 78115--78159 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
78105 TCCACTTCGG
78115 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCGCCCA
*
78133 GAGCTATCACCTCGCCCA
1 GAGCCATCACCTCGCCCA
78151 GAGCCATCA
1 GAGCCATCA
78160 TCTGATCGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.24, C:0.44, G:0.18, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCGCCCA
Found at i:78695 original size:19 final size:20
Alignment explanation
Indices: 78641--78707 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
78631 TAGTTTACTT
* *
78641 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
78661 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
78681 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
78700 TCGCAACG
1 TCGCAACG
78708 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:78715 original size:14 final size:14
Alignment explanation
Indices: 78696--78753 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
78686 ATGCGAAATG
78696 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
78710 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
78726 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
78742 AAAATCGCAACG
1 AAAATCGCAACG
78754 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:78738 original size:32 final size:33
Alignment explanation
Indices: 78680--78770 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
78670 GGAAATGGCT
78680 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
78713 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
78745 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
78771 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:78804 original size:14 final size:14
Alignment explanation
Indices: 78782--78844 Score: 74
Period size: 14 Copynumber: 4.3 Consensus size: 14
78772 GCGATTTGTG
78782 TTTTG-CGTTGCGA
1 TTTTGTCGTTGCGA
78795 TTTTGTCGTTGCGA
1 TTTTGTCGTTGCGA
*
78809 TTTCATTTCGCGTTGCGA
1 TTT--TGT--CGTTGCGA
78827 TTTTGTCGTTGCGA
1 TTTTGTCGTTGCGA
78841 TTTT
1 TTTT
78845 CATTTCGCAT
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
13 5 0.12
14 23 0.53
16 4 0.09
18 11 0.26
ACGTcount: A:0.08, C:0.16, G:0.25, T:0.51
Consensus pattern (14 bp):
TTTTGTCGTTGCGA
Found at i:78825 original size:32 final size:33
Alignment explanation
Indices: 78786--78860 Score: 134
Period size: 32 Copynumber: 2.3 Consensus size: 33
78776 TTTGTGTTTT
78786 GCGTTGCGATTTTGTCGTTGCGA-TTTCATTTC
1 GCGTTGCGATTTTGTCGTTGCGATTTTCATTTC
78818 GCGTTGCGATTTTGTCGTTGCGATTTTCATTTC
1 GCGTTGCGATTTTGTCGTTGCGATTTTCATTTC
*
78851 GCATTGCGAT
1 GCGTTGCGAT
78861 AGCCATTTTC
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
32 23 0.56
33 18 0.44
ACGTcount: A:0.11, C:0.19, G:0.25, T:0.45
Consensus pattern (33 bp):
GCGTTGCGATTTTGTCGTTGCGATTTTCATTTC
Found at i:78859 original size:19 final size:19
Alignment explanation
Indices: 78801--78918 Score: 95
Period size: 20 Copynumber: 6.4 Consensus size: 19
78791 GCGATTTTGT
78801 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
78819 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
78833 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
78852 CATTGCGATAGCCATTTTCG
1 CGTTGCGATTTTCA-TTTCG
**
78872 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
78891 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
78911 TGTTGCGA
1 CGTTGCGA
78919 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 11 0.14
19 26 0.32
20 29 0.36
ACGTcount: A:0.14, C:0.19, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:78910 original size:39 final size:37
Alignment explanation
Indices: 78801--78918 Score: 102
Period size: 39 Copynumber: 3.2 Consensus size: 37
78791 GCGATTTTGT
78801 CGTTGCGATTTCATTTCGCGTTGCGATTTT-G--T--
1 CGTTGCGATTTCATTTCGCGTTGCGATTTTAGTTTCG
* *** *
78833 CGTTGCGATTTTCATTTCGCATTGCGATAGCCATTTTCG
1 CGTTGCGA-TTTCATTTCGCGTTGCGAT-TTTAGTTTCG
*
78872 CGTTGCGATAGTCATTTCGCGTTGCGATTTTAAGTTTCG
1 CGTTGCGAT-TTCATTTCGCGTTGCGATTTT-AGTTTCG
*
78911 TGTTGCGA
1 CGTTGCGA
78919 AAGTAAACTA
Statistics
Matches: 65, Mismatches: 12, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
32 8 0.12
33 18 0.28
37 1 0.02
38 1 0.02
39 37 0.57
ACGTcount: A:0.14, C:0.19, G:0.25, T:0.42
Consensus pattern (37 bp):
CGTTGCGATTTCATTTCGCGTTGCGATTTTAGTTTCG
Found at i:80895 original size:20 final size:20
Alignment explanation
Indices: 80870--80907 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
80860 GCAAAACAGA
*
80870 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGAGAAAATGG
80890 CTATCGCAACGAGAAAAT
1 CTATCGCAACGAGAAAAT
80908 CGCAATGCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGAGAAAATGG
Found at i:80926 original size:19 final size:19
Alignment explanation
Indices: 80902--80969 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
80892 ATCGCAACGA
80902 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
80921 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
80940 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
80954 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
80970 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:81018 original size:20 final size:20
Alignment explanation
Indices: 80995--81065 Score: 142
Period size: 20 Copynumber: 3.5 Consensus size: 20
80985 GCGATTTCCT
80995 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
81015 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
81035 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
81055 CGTTGCGATAG
1 CGTTGCGATAG
81066 TCAAATGAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.15, C:0.24, G:0.27, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCG
Found at i:81021 original size:34 final size:34
Alignment explanation
Indices: 80976--81063 Score: 95
Period size: 40 Copynumber: 2.4 Consensus size: 34
80966 GCGATTTTCA
* *
80976 TTTCGCATTGCGATTTCCTCGTTGCGATAGCCAT
1 TTTCGCGTTGCGATTTCCGCGTTGCGATAGCCAT
*
81010 TTTCGCGTTGCGATAGCCATTTTCGCGTTGCGATAGCCAT
1 TTTCGCGTTGC----G--ATTTCCGCGTTGCGATAGCCAT
81050 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
81064 AGTCAAATGA
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
34 12 0.27
36 1 0.02
38 1 0.02
40 31 0.69
ACGTcount: A:0.14, C:0.25, G:0.24, T:0.38
Consensus pattern (34 bp):
TTTCGCGTTGCGATTTCCGCGTTGCGATAGCCAT
Found at i:82111 original size:24 final size:24
Alignment explanation
Indices: 82084--82137 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
82074 GTATTCGAAA
* *
82084 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
82108 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
82132 TTTGAT
1 TTTGAT
82138 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:84653 original size:19 final size:19
Alignment explanation
Indices: 84628--84758 Score: 85
Period size: 19 Copynumber: 7.7 Consensus size: 19
84618 GGAAATTACT
84628 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
84647 ATTGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
84661 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
84680 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
84694 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
84713 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
84727 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
84746 ATCGCAACGCGAA
1 ATCGCAATGCGAA
84759 TTTAATTTCG
Statistics
Matches: 82, Mismatches: 15, Indels: 30
0.65 0.12 0.24
Matches are distributed among these distances:
14 26 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 38 0.46
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:84670 original size:33 final size:33
Alignment explanation
Indices: 84628--84754 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
84618 GGAAATTACT
*
84628 ATCGCAATGCGAAATGAAAATTGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
84661 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
84693 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
84727 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
84755 CGAATTTAAT
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
32 1 0.01
33 82 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:84735 original size:66 final size:66
Alignment explanation
Indices: 84629--84761 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
84619 GAAATTACTA
* *
84629 TCGCAATGCGAAATGAAAATTGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
84694 T
66 T
*
84695 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
84760 T
66 T
84761 T
1 T
84762 AATTTCGCGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:84776 original size:19 final size:20
Alignment explanation
Indices: 84754--84796 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
84744 AAATCGCAAC
*
84754 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCATT
* *
84773 GCGATTTTCATTTTCGCATT
1 GCGAATTTCAATTTCGCATT
84793 GCGA
1 GCGA
84797 TTCTCTCGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCATT
Found at i:84956 original size:14 final size:14
Alignment explanation
Indices: 84937--84973 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
84927 CATCAATTAA
84937 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
84951 ACAAATCACCTTTT
1 ACAAATCAACTTTT
84965 ACAAATCAA
1 ACAAATCAA
84974 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:88538 original size:33 final size:33
Alignment explanation
Indices: 88481--88579 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
88471 ACGAGATAAT
*
88481 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
88515 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
88548 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
88580 GCGAAATAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:88573 original size:19 final size:19
Alignment explanation
Indices: 88456--88621 Score: 136
Period size: 20 Copynumber: 9.1 Consensus size: 19
88446 TCTTTTGGTT
*
88456 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
88475 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
88495 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
88513 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
88529 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
88547 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
88562 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
88582 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
88601 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
88620 GA
1 GA
88622 TTTTGGTTTC
Statistics
Matches: 119, Mismatches: 15, Indels: 26
0.74 0.09 0.16
Matches are distributed among these distances:
14 19 0.16
15 3 0.03
16 2 0.02
17 1 0.01
18 4 0.03
19 43 0.36
20 45 0.38
21 2 0.02
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:88650 original size:19 final size:19
Alignment explanation
Indices: 88617--88697 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
88607 AAAATCGCAA
**
88617 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
88636 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
88655 TGCGA---TTA--TCTCGT
1 TGCGATTTTTATTTCGCGT
**
88669 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
88689 TGCGATTTT
1 TGCGATTTT
88698 CATTCTCGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
14 10 0.20
16 3 0.06
17 3 0.06
19 23 0.46
20 11 0.22
ACGTcount: A:0.11, C:0.17, G:0.25, T:0.47
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:89242 original size:20 final size:20
Alignment explanation
Indices: 89217--89269 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
89207 GCGCTATGTA
89217 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
89237 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
89257 TATCTCGTTGCGA
1 AATCGCGTTGCGA
89270 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:89361 original size:21 final size:21
Alignment explanation
Indices: 89321--89361 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
89311 ATTGTATACC
**
89321 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
89342 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
89362 GCAAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:89524 original size:15 final size:15
Alignment explanation
Indices: 89504--89533 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
89494 TTTTCTCTAT
89504 AATGAAATACATGTA
1 AATGAAATACATGTA
*
89519 AATGAAATACTTGTA
1 AATGAAATACATGTA
89534 TCATACAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.13, T:0.30
Consensus pattern (15 bp):
AATGAAATACATGTA
Found at i:91079 original size:3 final size:3
Alignment explanation
Indices: 91071--91131 Score: 88
Period size: 3 Copynumber: 20.3 Consensus size: 3
91061 ATGTAATTAA
91071 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
* *
91117 -AT AAC GAT AAT AAT A
1 AAT AAT AAT AAT AAT A
91132 TTAAAAAAAG
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 47 0.90
4 3 0.06
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:92834 original size:35 final size:36
Alignment explanation
Indices: 92786--92886 Score: 150
Period size: 35 Copynumber: 2.8 Consensus size: 36
92776 GATAGTGACA
* *
92786 CAAATTAGATTATCTCACTAGTATTGAAAATATG-T
1 CAAATTAGGTTATCCCACTAGTATTGAAAATATGCT
* *
92821 TAAATTAGGTTATCCCACTAGTATTGCAAATATGCT
1 CAAATTAGGTTATCCCACTAGTATTGAAAATATGCT
92857 CAAATTAGGTTATCCCACTAGTATTTGAAA
1 CAAATTAGGTTATCCCACTAGTA-TTGAAA
92887 TGACGATTTT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
35 30 0.52
36 23 0.40
37 5 0.09
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.36
Consensus pattern (36 bp):
CAAATTAGGTTATCCCACTAGTATTGAAAATATGCT
Found at i:98174 original size:16 final size:17
Alignment explanation
Indices: 98153--98187 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
98143 TTAGTGGGGG
98153 AATGTTGATAATG-CTC
1 AATGTTGATAATGACTC
98169 AATGTTGATAATGACTC
1 AATGTTGATAATGACTC
98186 AA
1 AA
98188 ATTAGGTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.34
Consensus pattern (17 bp):
AATGTTGATAATGACTC
Found at i:98268 original size:36 final size:36
Alignment explanation
Indices: 98182--98286 Score: 167
Period size: 35 Copynumber: 2.9 Consensus size: 36
98172 GTTGATAATG
*
98182 ACTCAAATTAGGTTATCCCACTAGTATTGAAAATAT
1 ACTCAAATTAGGTTATCCCACTAGTATTGAAAATAC
* *
98218 GCT-AAATTAGGTTATCCCACTAGTATTGCAAATAC
1 ACTCAAATTAGGTTATCCCACTAGTATTGAAAATAC
*
98253 ACTCAAATTAGGTTATCCCACTAGTATTGTAAAT
1 ACTCAAATTAGGTTATCCCACTAGTATTGAAAAT
98287 GACGATTTTA
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
35 32 0.51
36 31 0.49
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.33
Consensus pattern (36 bp):
ACTCAAATTAGGTTATCCCACTAGTATTGAAAATAC
Found at i:110792 original size:14 final size:15
Alignment explanation
Indices: 110766--110799 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
110756 GGGCATGGCG
*
110766 AATAATAAATTAAGA
1 AATAATAAATTAAAA
110781 AATAAT-AATTAAAA
1 AATAATAAATTAAAA
110795 AATAA
1 AATAA
110800 AGATAATCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (15 bp):
AATAATAAATTAAAA
Done.