Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005489.1 Hibiscus syriacus cultivar Beakdansim tig00012633_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: 105613
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:4173 original size:2 final size:2
Alignment explanation
Indices: 4166--4204 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
4156 TTGTTTTTCA
4166 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4205 AGAATAAGAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:23480 original size:19 final size:21
Alignment explanation
Indices: 23446--23491 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 21
23436 GTTAAATCTC
23446 TATTTTATTGAATAAAAATAA
1 TATTTTATTGAATAAAAATAA
* *
23467 TATTTT-TT-AATAAATATAT
1 TATTTTATTGAATAAAAATAA
23486 TATTTT
1 TATTTT
23492 GAGTTGGGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 15 0.65
20 2 0.09
21 6 0.26
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
TATTTTATTGAATAAAAATAA
Found at i:24497 original size:23 final size:21
Alignment explanation
Indices: 24459--24501 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
24449 ATAATTATTT
24459 AAAAAATTAAATAAAAATATA
1 AAAAAATTAAATAAAAATATA
*
24480 AAAAATATTTAATAAAAA-ATA
1 AAAAA-ATTAAATAAAAATATA
24501 A
1 A
24502 TTTTTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATATA
Found at i:27367 original size:38 final size:38
Alignment explanation
Indices: 27316--27392 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
27306 TTCTCAATTT
*
27316 ATTTCCTTGGCAATAATAGTAGGATAGAGCATCCATTC
1 ATTTCCTTGGCAATAATAGTAGGACAGAGCATCCATTC
27354 ATTTCCTTGGCAATAATAGTAGGACAGAGCATCCATTC
1 ATTTCCTTGGCAATAATAGTAGGACAGAGCATCCATTC
27392 A
1 A
27393 AGTCAAGTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Consensus pattern (38 bp):
ATTTCCTTGGCAATAATAGTAGGACAGAGCATCCATTC
Found at i:31137 original size:2 final size:2
Alignment explanation
Indices: 31130--31160 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
31120 TAAAATCGGG
31130 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
31161 GTCAAGGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:41553 original size:120 final size:120
Alignment explanation
Indices: 41335--41814 Score: 486
Period size: 120 Copynumber: 4.0 Consensus size: 120
41325 ATTCTTGTGA
* * * * * * * *
41335 TCCCTGAAAACTACCTCCTGAACTGGTTCAGTAGCAGTTATGCTGATATCTTCAAATTGCATTAA
1 TCCCAGAAAACTACCTCCTGAGCTGGTTCAGCAGCAGTTATGTTGGTATCTTCTAAGTGCATTGA
* * * * * * *
41400 ATTCTGATCCTCTAGTGC-AGCACTTGTGTCCTCTTTAACTTCAATTTTGTCACTT
66 ACTGTGATCCTCTTGAGCAAG-AATCGTATCCTCTTTAACTTCAATTTTGTCACTT
** * *
41455 TCCCAGAAAACTTGCTCCTGAGCTGGTTCAGCAGCAGTTATGTCGGTATCTTCTAAGTGTATTGA
1 TCCCAGAAAACTACCTCCTGAGCTGGTTCAGCAGCAGTTATGTTGGTATCTTCTAAGTGCATTGA
* * *
41520 ACTGTGGT-CTCCTTGAGCAAGAATCGTAACCTCTTTAACTTC-ATCTTTTTCACTT
66 ACTGTGATCCT-CTTGAGCAAGAATCGTATCCTCTTTAACTTCAAT-TTTGTCACTT
* * * * * * *
41575 TCCCAGTAAACAACCTCCTGAGCTGGTTCAGCTGCAATTGTGTTGGTATCTTCTAATTGCAGTGA
1 TCCCAGAAAACTACCTCCTGAGCTGGTTCAGCAGCAGTTATGTTGGTATCTTCTAAGTGCATTGA
* * * *
41640 AATCG-GATCCTCTTCAACAAG-A-CGTGAGTCCTCCTTAACTTCAATTTTGTCACTT
66 ACT-GTGATCCTCTTGAGCAAGAATCGT-A-TCCTCTTTAACTTCAATTTTGTCACTT
* *
41695 TCCCAGACAACTACCTCCTGAACTGGTTCAGCAGCAGTTATGTTGGTATCTTCTAAGTGCATTGA
1 TCCCAGAAAACTACCTCCTGAGCTGGTTCAGCAGCAGTTATGTTGGTATCTTCTAAGTGCATTGA
* * * ** * *
41760 ACTGTGATCCTCTGGAGCATGATTTTTGTCCTCTTTAACTTCCATTTTGTCACTT
66 ACTGTGATCCTCTTGAGCAAGAATCGTATCCTCTTTAACTTCAATTTTGTCACTT
41815 GTATAGTTAA
Statistics
Matches: 289, Mismatches: 60, Indels: 22
0.78 0.16 0.06
Matches are distributed among these distances:
118 3 0.01
119 7 0.02
120 271 0.94
121 7 0.02
122 1 0.00
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.36
Consensus pattern (120 bp):
TCCCAGAAAACTACCTCCTGAGCTGGTTCAGCAGCAGTTATGTTGGTATCTTCTAAGTGCATTGA
ACTGTGATCCTCTTGAGCAAGAATCGTATCCTCTTTAACTTCAATTTTGTCACTT
Found at i:52320 original size:35 final size:35
Alignment explanation
Indices: 52281--52416 Score: 173
Period size: 35 Copynumber: 3.9 Consensus size: 35
52271 CGAATAAGAA
52281 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAGT
1 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAGT
* * *
52316 GAACGAAAGGAAGCATCGACACTTTCGACTCAAGAA
1 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAG-T
* *
52352 GAACGAAATGAAGCATCGGCACTTTCGATTTAAGT
1 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAGT
** * **
52387 GAACGGGAGGAAGTATAAGCACTTTCGATT
1 GAACGAAAGGAAGCATCGGCACTTTCGATT
52417 TAATTGTTCA
Statistics
Matches: 86, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
35 56 0.65
36 30 0.35
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (35 bp):
GAACGAAAGGAAGCATCGGCACTTTCGATTCAAGT
Found at i:52410 original size:71 final size:71
Alignment explanation
Indices: 52276--52414 Score: 208
Period size: 71 Copynumber: 2.0 Consensus size: 71
52266 GAAGGCGAAT
*
52276 AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAGTGAACGAAAGGAAGCATCGACACTTT
1 AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAGTGAACGAAAGGAAGCATAGACACTTT
52341 CGACTC
66 CGACTC
* * ** *
52347 AAGAAGAACGAAATGAAGCATCGGCACTTTCGATTTAAGTGAACGGGAGGAAGTATA-AGCACTT
1 AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAGTGAACGAAAGGAAGCATAGA-CACTT
52411 TCGA
65 TCGA
52415 TTTAATTGTT
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
70 1 0.02
71 60 0.98
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.19
Consensus pattern (71 bp):
AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAGTGAACGAAAGGAAGCATAGACACTTT
CGACTC
Found at i:53392 original size:23 final size:24
Alignment explanation
Indices: 53342--53389 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
53332 GTTTGCATAG
*
53342 TTTACCCTTTTAAAATAAAGATGAA
1 TTTACCCTTTTAAAATAAAAAT-AA
53367 TTTACCCTTTTAATAA-AAAAATA
1 TTTACCCTTTTAA-AATAAAAATA
53390 TTTTTAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 1 0.05
25 18 0.86
26 2 0.10
ACGTcount: A:0.46, C:0.12, G:0.04, T:0.38
Consensus pattern (24 bp):
TTTACCCTTTTAAAATAAAAATAA
Found at i:55467 original size:2 final size:2
Alignment explanation
Indices: 55460--55504 Score: 58
Period size: 2 Copynumber: 23.0 Consensus size: 2
55450 TTATTTTTAT
*
55460 TA TA TA TA TC T- TA TA TCA T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
55501 TA TA
1 TA TA
55505 GATGTATTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
1 2 0.05
2 35 0.90
3 2 0.05
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:55682 original size:38 final size:37
Alignment explanation
Indices: 55636--55729 Score: 111
Period size: 38 Copynumber: 2.6 Consensus size: 37
55626 TATATTTTTA
* * *
55636 CTTT-TTTTTTATTTTTTTTTCTTAATATCATGTATAT
1 CTTTATTTTTTATTTGTTTTACTTAATATCATATAT-T
* *
55673 CTTTATTTTTTATTTGTTTTACTTAGTATTATATATT
1 CTTTATTTTTTATTTGTTTTACTTAATATCATATATT
*
55710 TTTTA-TTTTTATTTGTTTTA
1 CTTTATTTTTTATTTGTTTTA
55730 GTAAATACTA
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
36 15 0.30
37 9 0.18
38 26 0.52
ACGTcount: A:0.19, C:0.05, G:0.04, T:0.71
Consensus pattern (37 bp):
CTTTATTTTTTATTTGTTTTACTTAATATCATATATT
Found at i:55719 original size:36 final size:35
Alignment explanation
Indices: 55597--55729 Score: 106
Period size: 38 Copynumber: 3.6 Consensus size: 35
55587 TAATATTCTA
* * *
55597 TTTTTGTTTTTATTTATTTATA-TATATATTATATTT
1 TTTTTATTTTTATTTGTTT-TACT-TATATTATATAT
* * * * *
55633 TTACTTTTTTTTTATTTTTTTTTCTTAATATCATGTAT
1 TT--TTTATTTTTATTTGTTTTACTT-ATATTATATAT
*
55671 ATCTTTATTTTTTATTTGTTTTACTTAGTATTATATAT
1 -TTTTTA-TTTTTATTTGTTTTACTTA-TATTATATAT
55709 TTTTTATTTTTATTTGTTTTA
1 TTTTTATTTTTATTTGTTTTA
55730 GTAAATACTA
Statistics
Matches: 77, Mismatches: 13, Indels: 14
0.74 0.12 0.13
Matches are distributed among these distances:
36 17 0.22
37 11 0.14
38 48 0.62
39 1 0.01
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.71
Consensus pattern (35 bp):
TTTTTATTTTTATTTGTTTTACTTATATTATATAT
Found at i:60692 original size:184 final size:184
Alignment explanation
Indices: 60404--60773 Score: 618
Period size: 184 Copynumber: 2.0 Consensus size: 184
60394 AAATTAAATG
* *
60404 TTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAG
1 TTTTTAATTAAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAG
60469 ATAAAATTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAATT
66 ATAAAATTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAATT
* *
60534 GAGTTTTAAATTGTTTGGGCTTAGCCCAAATGTTATATATAATATATATAATAT
131 GAGTTTTAAATGGTTTGGGCTGAGCCCAAATGTTATATATAATATATATAATAT
60588 TTTTTAATTAAAAAAATAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAAATTT-
1 TTTTTAATTAAAAAAA-AGTTTACAATTAATTTAAATAATATATAATTATAAAAT-AAAAATTTC
* * *
60652 ATAT-AATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAA
64 AGATAAAATTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAA
* * *
60716 TTGGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTATATATAATATATTTAATAT
129 TTGAGTTTTAAATGGTTTGGGCTGAGCCCAAATGTTATATATAATATATATAATAT
60772 TT
1 TT
60774 AAAATTTAAT
Statistics
Matches: 174, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
184 126 0.72
185 40 0.23
186 8 0.05
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.45
Consensus pattern (184 bp):
TTTTTAATTAAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAG
ATAAAATTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAATT
GAGTTTTAAATGGTTTGGGCTGAGCCCAAATGTTATATATAATATATATAATAT
Found at i:62859 original size:24 final size:24
Alignment explanation
Indices: 62830--62879 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
62820 ATAAAGAACC
62830 AAAAT-AAGCTTAAACATACCATTA
1 AAAATAAAGCTTAAACAT-CCATTA
*
62854 AAAATAAAGTTTAAACATCCATTA
1 AAAATAAAGCTTAAACATCCATTA
62878 AA
1 AA
62880 CCAACCACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 13 0.54
25 11 0.46
ACGTcount: A:0.56, C:0.14, G:0.04, T:0.26
Consensus pattern (24 bp):
AAAATAAAGCTTAAACATCCATTA
Found at i:65182 original size:13 final size:14
Alignment explanation
Indices: 65159--65188 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
65149 CTAATATTAA
65159 AAATAAAAATAAAG
1 AAATAAAAATAAAG
65173 AAAT-AAAATAAAG
1 AAATAAAAATAAAG
65186 AAA
1 AAA
65189 AACAAACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (14 bp):
AAATAAAAATAAAG
Found at i:68444 original size:24 final size:24
Alignment explanation
Indices: 68415--68464 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
68405 ATAAAGAACC
68415 AAAAT-AAGCTTAAACATACCATTA
1 AAAATAAAGCTTAAACAT-CCATTA
*
68439 AAAATAAAGTTTAAACATCCATTA
1 AAAATAAAGCTTAAACATCCATTA
68463 AA
1 AA
68465 CCAACCACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 13 0.54
25 11 0.46
ACGTcount: A:0.56, C:0.14, G:0.04, T:0.26
Consensus pattern (24 bp):
AAAATAAAGCTTAAACATCCATTA
Found at i:74958 original size:34 final size:34
Alignment explanation
Indices: 74915--74998 Score: 168
Period size: 34 Copynumber: 2.5 Consensus size: 34
74905 TACTTGTATT
74915 TCAACTTCACGACGAAGGATATTCAAGTCAAGGC
1 TCAACTTCACGACGAAGGATATTCAAGTCAAGGC
74949 TCAACTTCACGACGAAGGATATTCAAGTCAAGGC
1 TCAACTTCACGACGAAGGATATTCAAGTCAAGGC
74983 TCAACTTCACGACGAA
1 TCAACTTCACGACGAA
74999 TGAGCCATCC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (34 bp):
TCAACTTCACGACGAAGGATATTCAAGTCAAGGC
Found at i:75052 original size:43 final size:43
Alignment explanation
Indices: 75004--75125 Score: 217
Period size: 43 Copynumber: 2.8 Consensus size: 43
74994 ACGAATGAGC
*
75004 CATCCGCGATTTCAACTCCACGACAGAGGATATCGTACCCGCA
1 CATCCGCGATTTCAACTCCACGACGGAGGATATCGTACCCGCA
*
75047 CATCCGCGATTTCAACTCCACGACGGAGGATATTGTACCCGCA
1 CATCCGCGATTTCAACTCCACGACGGAGGATATCGTACCCGCA
*
75090 CATCCACGATTTCAACTCCACGACGGAGGATATCGT
1 CATCCGCGATTTCAACTCCACGACGGAGGATATCGT
75126 GCCATTTGAG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 75 1.00
ACGTcount: A:0.27, C:0.33, G:0.20, T:0.20
Consensus pattern (43 bp):
CATCCGCGATTTCAACTCCACGACGGAGGATATCGTACCCGCA
Found at i:75365 original size:110 final size:108
Alignment explanation
Indices: 75158--75417 Score: 350
Period size: 110 Copynumber: 2.4 Consensus size: 108
75148 GACGAAGGGG
* * *
75158 TTTCCCAG-T-TTCAGAGCCAATTTCAACTTCACAGCGAGGGATATTGGACTCAAGACAACACAA
1 TTTCCCAGTTCTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATCGAACTCAAGACAACACAA
*
75221 GCTCAACTTCACAACGAAGGGGTGACTGATTGTCAACAAACAA
66 GCTCAACTTCACAACGAAGGGGTGACTGACTGTCAACAAACAA
** * *
75264 TTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATCGAACTCGAGACAACAC
1 TTTCCCAG-TTC-TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATCGAACTCAAGACAACAC
* * * *
75329 AAGCTCAACTTCACAGCGAATGGGTGGCTGGCTGTCAACAAACAA
64 AAGCTCAACTTCACAACGAAGGGGTGACTGACTGTCAACAAACAA
75374 TTTCCCAGTTC--CAGAGCCAATTTCAACTTCAC-GACGAAGGATAT
1 TTTCCCAGTTCTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATAT
75418 TGGACTTGGA
Statistics
Matches: 134, Mismatches: 15, Indels: 10
0.84 0.09 0.06
Matches are distributed among these distances:
105 1 0.01
106 36 0.27
108 1 0.01
109 3 0.02
110 93 0.69
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (108 bp):
TTTCCCAGTTCTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATCGAACTCAAGACAACACAA
GCTCAACTTCACAACGAAGGGGTGACTGACTGTCAACAAACAA
Found at i:76770 original size:23 final size:23
Alignment explanation
Indices: 76744--76811 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 23
76734 TATATATATA
76744 TATTTTAATTATATTTTTTTATT
1 TATTTTAATTATATTTTTTTATT
*
76767 TA-TTT-ACTATATTCATTTTTATT
1 TATTTTAATTATATT--TTTTTATT
* *
76790 TATATTATATTAT-TTTTATTAT
1 TATTTTA-ATTATATTTTTTTAT
76812 ATATCTTATC
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
21 7 0.19
22 3 0.08
23 18 0.50
24 2 0.06
25 2 0.06
26 4 0.11
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (23 bp):
TATTTTAATTATATTTTTTTATT
Found at i:76804 original size:14 final size:15
Alignment explanation
Indices: 76785--76861 Score: 70
Period size: 16 Copynumber: 5.1 Consensus size: 15
76775 ATATTCATTT
76785 TTATTTATAT-TATA
1 TTATTTATATATATA
*
76799 TTATTTTTAT-TATA
1 TTATTTATATATATA
76813 -TATCTTATCATATATA
1 TTAT-TTAT-ATATATA
*
76829 TATATATATATATATA
1 T-TATTTATATATATA
*
76845 TATATATATATATATA
1 T-TATTTATATATATA
76861 T
1 T
76862 ATATAGATGT
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
13 3 0.05
14 16 0.29
15 2 0.04
16 28 0.51
17 3 0.05
18 3 0.05
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (15 bp):
TTATTTATATATATA
Found at i:76811 original size:19 final size:19
Alignment explanation
Indices: 76732--76813 Score: 73
Period size: 21 Copynumber: 4.3 Consensus size: 19
76722 TTGTCCCATA
*
76732 TATATATATATATATTTTAAT
1 TATAT-TATAT-TATTTTTAT
76753 TATATT-T-TT-TTATTTAT
1 TATATTATATTATT-TTTAT
*
76770 T-TACTATATTCATTTTTATT
1 TATATTATATT-ATTTTTA-T
76790 TATATTATATTATTTTTAT
1 TATATTATATTATTTTTAT
76809 TATAT
1 TATAT
76814 ATCTTATCAT
Statistics
Matches: 51, Mismatches: 3, Indels: 16
0.73 0.04 0.23
Matches are distributed among these distances:
16 5 0.10
17 7 0.14
18 3 0.06
19 11 0.22
20 12 0.24
21 13 0.25
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (19 bp):
TATATTATATTATTTTTAT
Found at i:76820 original size:23 final size:22
Alignment explanation
Indices: 76752--76820 Score: 74
Period size: 21 Copynumber: 3.2 Consensus size: 22
76742 TATATTTTAA
*
76752 TTATATT-TTTTTATTTATTTAC
1 TTATATTATTTTTATTTATAT-C
76774 -TATATTCATTTTTATTTATA--
1 TTATATT-ATTTTTATTTATATC
76794 TTATATTATTTTTATTATATATC
1 TTATATTATTTTTATT-TATATC
76817 TTAT
1 TTAT
76821 CATATATATA
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
20 9 0.22
21 16 0.40
23 15 0.38
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (22 bp):
TTATATTATTTTTATTTATATC
Found at i:76827 original size:2 final size:2
Alignment explanation
Indices: 76809--76866 Score: 91
Period size: 2 Copynumber: 29.0 Consensus size: 2
76799 TTATTTTTAT
*
76809 TA TA TA TC T- TA TCA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
76851 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
76867 GATGTATTAA
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
1 1 0.02
2 50 0.94
3 2 0.04
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:76974 original size:39 final size:36
Alignment explanation
Indices: 76896--77029 Score: 121
Period size: 39 Copynumber: 3.6 Consensus size: 36
76886 ATTTACTATG
* **
76896 TATATATATTTTTCTTAATATATATTTTATACGTTTT
1 TATATATATTTTTCTTAATATTTATTTTAT-TTTTTT
76933 TATATATATCTTTTCTTAATATTCTATTTTATTTTTATT
1 TATATATAT-TTTTCTTAATATT-TATTTTATTTTT-TT
* * *
76972 TATTATATATATTATATT-TTACTTTATTTTATTTTTTT
1 TA-TATATAT-TTTTCTTAATA-TTTATTTTATTTTTTT
77010 CTAT-TAT-TTTTTCTTAATAT
1 -TATATATATTTTTCTTAATAT
77030 CATGTATATC
Statistics
Matches: 80, Mismatches: 10, Indels: 16
0.75 0.09 0.15
Matches are distributed among these distances:
35 6 0.08
36 3 0.04
37 12 0.15
38 17 0.21
39 28 0.35
40 14 0.17
ACGTcount: A:0.27, C:0.06, G:0.01, T:0.66
Consensus pattern (36 bp):
TATATATATTTTTCTTAATATTTATTTTATTTTTTT
Found at i:76979 original size:38 final size:36
Alignment explanation
Indices: 76900--77085 Score: 116
Period size: 39 Copynumber: 4.9 Consensus size: 36
76890 ACTATGTATA
**
76900 TATATTTTTCTTAATA-TATATTTTATACGTTTTTAT
1 TATATTTTTCTTAATATTATATTTTAT-TTTTTTTAT
*
76936 ATATATCTTTTCTTAATATTCTATTTTATTTTTATTTAT
1 -TATAT-TTTTCTTAATATTATATTTTATTTTT-TTTAT
* *
76975 TATATATATTATATT-TTACTT-TATTTTATTTTTTTCTAT
1 TATAT-T-TT-TCTTAATA-TTATATTTTATTTTTTT-TAT
77014 TAT-TTTTTCTTAATATCATGTATATCTTTA--TTTTTTAT
1 TATATTTTTCTT-A-AT-AT-TATAT-TTTATTTTTTTTAT
* * *
77052 T-TGTTTTACTTAGTATTATATATTTATTTTTTTT
1 TATATTTTTCTTAATATTATAT-TTTATTTTTTTT
77086 GTTTTAGTAA
Statistics
Matches: 121, Mismatches: 11, Indels: 35
0.72 0.07 0.21
Matches are distributed among these distances:
34 9 0.07
35 5 0.04
36 9 0.07
37 8 0.07
38 35 0.29
39 43 0.36
40 8 0.07
41 4 0.03
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (36 bp):
TATATTTTTCTTAATATTATATTTTATTTTTTTTAT
Found at i:77157 original size:18 final size:17
Alignment explanation
Indices: 77130--77163 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
77120 TTTTTATTCA
77130 TTTTTAATTTCTTTTACC
1 TTTTTAATTT-TTTTACC
*
77148 TTTTTTATTTTTTTAC
1 TTTTTAATTTTTTTAC
77164 TCCATTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTTAATTTTTTTACC
Found at i:77161 original size:17 final size:17
Alignment explanation
Indices: 77117--77163 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
77107 TATGTACACA
77117 TTATTTTTATT-CATTTT
1 TTATTTTT-TTACATTTT
* *
77134 TAATTTCTTTTACCTTTT
1 TTATTT-TTTTACATTTT
77152 TTATTTTTTTAC
1 TTATTTTTTTAC
77164 TCCATTAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.72
Consensus pattern (17 bp):
TTATTTTTTTACATTTT
Found at i:77238 original size:19 final size:19
Alignment explanation
Indices: 77216--77292 Score: 59
Period size: 19 Copynumber: 3.9 Consensus size: 19
77206 ATTTTATTCA
77216 TTTTGTTTATTTTTATTTT
1 TTTTGTTTATTTTTATTTT
* ** *
77235 TTTT-ATTATTTTTTACGTG
1 TTTTGTTTA-TTTTTATTTT
77254 TTTTG-TTATTTTCTATTTT
1 TTTTGTTTATTTT-TATTTT
77273 TTCTTGTTTTATTTATTATT
1 TT-TTG-TTTATTT-TTATT
77293 CTCACGTTTG
Statistics
Matches: 44, Mismatches: 7, Indels: 11
0.71 0.11 0.18
Matches are distributed among these distances:
18 7 0.16
19 23 0.52
20 3 0.07
22 10 0.23
23 1 0.02
ACGTcount: A:0.13, C:0.04, G:0.06, T:0.77
Consensus pattern (19 bp):
TTTTGTTTATTTTTATTTT
Found at i:77292 original size:22 final size:25
Alignment explanation
Indices: 77231--77292 Score: 60
Period size: 26 Copynumber: 2.6 Consensus size: 25
77221 TTTATTTTTA
* *
77231 TTTTTTTTATTATTTTTTACGTGTT
1 TTTTATTTATTATTTTTTACGTGTG
77256 TTGTTATTT-TCTATTTTTT-C-T-TG
1 TT-TTATTTAT-TATTTTTTACGTGTG
77279 TTTTATTTATTATT
1 TTTTATTTATTATT
77293 CTCACGTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
22 10 0.31
23 4 0.12
24 1 0.03
25 4 0.12
26 13 0.41
ACGTcount: A:0.13, C:0.05, G:0.06, T:0.76
Consensus pattern (25 bp):
TTTTATTTATTATTTTTTACGTGTG
Found at i:80548 original size:26 final size:26
Alignment explanation
Indices: 80508--80581 Score: 71
Period size: 26 Copynumber: 2.7 Consensus size: 26
80498 ATTAATTTTT
80508 TTAAAATTAAA-AAAAAATAATAAAAA
1 TTAAAA-TAAATAAAAAATAATAAAAA
*
80534 TTAAAATAAAT-AAAATTCAATAAAAA
1 TTAAAATAAATAAAAAAT-AATAAAAA
*
80560 TATAATATAAAACTAAAAAATA
1 T-TAAAAT-AAA-TAAAAAATA
80582 TCACCTCTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
25 9 0.23
26 15 0.38
27 5 0.13
28 3 0.08
29 2 0.05
30 5 0.13
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (26 bp):
TTAAAATAAATAAAAAATAATAAAAA
Found at i:81724 original size:29 final size:29
Alignment explanation
Indices: 81680--81742 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 29
81670 TAATTATTAT
81680 TTTTTAACAACAATTAATAATGTT-TATTTA
1 TTTTTAACAACAATTAA-AAT-TTATATTTA
*
81710 TTTTTAATAA-AATTAAAATTTAATATTTA
1 TTTTTAACAACAATTAAAATTT-ATATTTA
81739 TTTT
1 TTTT
81743 ATATTTTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 2 0.07
28 3 0.10
29 16 0.53
30 9 0.30
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (29 bp):
TTTTTAACAACAATTAAAATTTATATTTA
Found at i:81857 original size:10 final size:10
Alignment explanation
Indices: 81815--81851 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
81805 TACATTATAT
81815 TTTTATTGAA
1 TTTTATTGAA
81825 TTTTATTGAA
1 TTTTATTGAA
*
81835 TTTTATT-CA
1 TTTTATTGAA
81844 TTTTATTG
1 TTTTATTG
81852 CCTTTTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 8 0.32
10 17 0.68
ACGTcount: A:0.24, C:0.03, G:0.08, T:0.65
Consensus pattern (10 bp):
TTTTATTGAA
Found at i:89237 original size:21 final size:22
Alignment explanation
Indices: 89213--89258 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
89203 CAGTAATAAA
* *
89213 TTATTTAAAATATT-ATTATTT
1 TTATCTAAAATATTAATAATTT
89234 TTATCTAAAATATTAATAATTT
1 TTATCTAAAATATTAATAATTT
89256 TTA
1 TTA
89259 ACATTTTTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
TTATCTAAAATATTAATAATTT
Found at i:90837 original size:13 final size:12
Alignment explanation
Indices: 90815--90844 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
90805 TAATTGTAAA
90815 TATTTATAATTT
1 TATTTATAATTT
90827 TATTATATAATTT
1 TATT-TATAATTT
90840 TATTT
1 TATTT
90845 CAATTTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TATTTATAATTT
Found at i:92068 original size:14 final size:16
Alignment explanation
Indices: 92046--92077 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
92036 TAAATTCAAG
92046 TTTAGGAATT-ATCTT
1 TTTAGGAATTAATCTT
92061 TTTA-GAATTAATCTT
1 TTTAGGAATTAATCTT
92076 TT
1 TT
92078 GTATGTGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.28, C:0.06, G:0.09, T:0.56
Consensus pattern (16 bp):
TTTAGGAATTAATCTT
Found at i:93397 original size:23 final size:24
Alignment explanation
Indices: 93349--93397 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
93339 AACTTTTTCT
* *
93349 TTTTTTTTCATCTTCTTTATTTTC
1 TTTTTTTTCATCTTCTTTACTCTC
93373 TTTTTTTT-AT-TTACTTTACTCTC
1 TTTTTTTTCATCTT-CTTTACTCTC
93396 TT
1 TT
93398 CATAAGTCCC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 2 0.09
23 12 0.55
24 8 0.36
ACGTcount: A:0.10, C:0.16, G:0.00, T:0.73
Consensus pattern (24 bp):
TTTTTTTTCATCTTCTTTACTCTC
Found at i:94314 original size:31 final size:31
Alignment explanation
Indices: 94279--94354 Score: 125
Period size: 31 Copynumber: 2.5 Consensus size: 31
94269 TAAAAAAACA
*
94279 TAAGATATGATCATTTTCTTTTTCATTTAAT
1 TAAGATATGATCACTTTCTTTTTCATTTAAT
*
94310 TAAGATATGATCACTTTCTTTTTTATTTAAT
1 TAAGATATGATCACTTTCTTTTTCATTTAAT
*
94341 TAAGATGTGATCAC
1 TAAGATATGATCAC
94355 CTCGAGTTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.50
Consensus pattern (31 bp):
TAAGATATGATCACTTTCTTTTTCATTTAAT
Found at i:94640 original size:27 final size:26
Alignment explanation
Indices: 94596--94665 Score: 76
Period size: 27 Copynumber: 2.8 Consensus size: 26
94586 TTTATATATA
* *
94596 TTAACTTAAATT-TTTTA-TGTTAAC
1 TTAATTTAAATTATTTTATTATTAAC
94620 TT-A-TTAAATATATTTTATTATTAAC
1 TTAATTTAAAT-TATTTTATTATTAAC
94645 TTAATTTTAAATTATTTTATT
1 TTAA-TTTAAATTATTTTATT
94666 TTTATTTTCA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
22 6 0.15
23 2 0.05
24 7 0.18
25 8 0.21
26 1 0.03
27 9 0.23
28 6 0.15
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (26 bp):
TTAATTTAAATTATTTTATTATTAAC
Found at i:94894 original size:31 final size:31
Alignment explanation
Indices: 94820--94883 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
94810 TAACCTCTGA
* *
94820 TGACCACATCTTAATTAAATAAAAATGAAAG
1 TGACCATATCTTAATTAAATAAAAAAGAAAG
94851 TGACCATATCTTAATTAAATAAAAAAGAAAG
1 TGACCATATCTTAATTAAATAAAAAAGAAAG
94882 TG
1 TG
94884 GACATGTCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.52, C:0.11, G:0.11, T:0.27
Consensus pattern (31 bp):
TGACCATATCTTAATTAAATAAAAAAGAAAG
Found at i:96291 original size:13 final size:15
Alignment explanation
Indices: 96273--96304 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
96263 TATTTAATAC
96273 ATTAAA-TA-TAAAA
1 ATTAAATTACTAAAA
96286 ATTAAATTACTAAAA
1 ATTAAATTACTAAAA
96301 ATTA
1 ATTA
96305 GCCACATTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 6 0.35
14 2 0.12
15 9 0.53
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (15 bp):
ATTAAATTACTAAAA
Done.