Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007372.1 Hibiscus syriacus cultivar Beakdansim tig00019788_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: 51704
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:905 original size:63 final size:64
Alignment explanation
Indices: 786--946 Score: 218
Period size: 63 Copynumber: 2.5 Consensus size: 64
776 CGGTGCACCA
*
786 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTGGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCAGGTGCATCGATGCATGG
** * **
850 CTTGTGCATCGATGCATCAAATGCA-TCGATGTTTG-AAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCAG-GTGCATCGATGCATGG
* * *
913 AGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
947 CAATTAATTC
Statistics
Matches: 83, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
62 8 0.10
63 45 0.54
64 30 0.36
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.29
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCAGGTGCATCGATGCATGG
Found at i:918 original size:19 final size:19
Alignment explanation
Indices: 894--944 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
884 GAAAATATTC
894 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
913 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
932 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
945 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:957 original size:63 final size:64
Alignment explanation
Indices: 789--991 Score: 163
Period size: 63 Copynumber: 3.2 Consensus size: 64
779 TGCACCAAGT
* * * * *
789 GTGCATCGATGCATGAAATGCATTCGATGTTTGAAAA-ATAGC-CTG-GTGCATCGATGCATGGC
1 GTGCATCGGTGCATCAAATGCA-TCGATGTTTCAAAATAT-TCAC-GAGTGCATCGATGCATGGA
**
851 TT
63 GA
* *
853 GTGCATCGATGCATCAAATGCATCGATGTTTGAAAATATTCA-GAGTGCATCGATGCATGGAGA
1 GTGCATCGGTGCATCAAATGCATCGATGTTTCAAAATATTCACGAGTGCATCGATGCATGGAGA
** *
916 GTGCATCGGTGCATGGAATGCATTCGATG-TTC-AATTAATTCATCGA-TGCATCGATGCA-GGA
1 GTGCATCGGTGCATCAAATGCA-TCGATGTTTCAAAAT-ATTCA-CGAGTGCATCGATGCATGGA
977 CTGA
63 --GA
981 -TGCATCGGTGC
1 GTGCATCGGTGC
992 TGCCTTTGAA
Statistics
Matches: 120, Mismatches: 10, Indels: 18
0.81 0.07 0.12
Matches are distributed among these distances:
62 4 0.03
63 60 0.50
64 52 0.43
65 4 0.03
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.29
Consensus pattern (64 bp):
GTGCATCGGTGCATCAAATGCATCGATGTTTCAAAATATTCACGAGTGCATCGATGCATGGAGA
Found at i:1640 original size:54 final size:55
Alignment explanation
Indices: 1527--1786 Score: 379
Period size: 54 Copynumber: 4.8 Consensus size: 55
1517 TGTACGTTAT
* *
1527 TCAACTTATGATGAATTCTGTGGATTTGAACACAGAGTGCCTGTACTG-TTATTCA
1 TCAACTCATGATGAATTCTGTGGATTTGCACACAGAGTGCCTGTAC-GATTATTCA
* * *
1582 TCAACTCATGATGAATTCCGTGGA-TTGCACATAGAGTGCTTGTACGATTATTCA
1 TCAACTCATGATGAATTCTGTGGATTTGCACACAGAGTGCCTGTACGATTATTCA
* *
1636 TCAACT-TTGATGAATTATGTGGATTTG--CACAGAGTGCCTGTACGATTATTCA
1 TCAACTCATGATGAATTCTGTGGATTTGCACACAGAGTGCCTGTACGATTATTCA
* *
1688 TCAACTCATGATGAATTCCGTGGA-TTGCACACAGAGTGCCTGTACGGTTATTCA
1 TCAACTCATGATGAATTCTGTGGATTTGCACACAGAGTGCCTGTACGATTATTCA
*
1742 TCAACTCATGATGAATTCTGTGGATTTGCACACAGAGCGCCTGTA
1 TCAACTCATGATGAATTCTGTGGATTTGCACACAGAGTGCCTGTA
1787 GTACACTTAG
Statistics
Matches: 183, Mismatches: 16, Indels: 12
0.87 0.08 0.06
Matches are distributed among these distances:
52 32 0.17
53 29 0.16
54 81 0.44
55 41 0.22
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (55 bp):
TCAACTCATGATGAATTCTGTGGATTTGCACACAGAGTGCCTGTACGATTATTCA
Found at i:1708 original size:106 final size:106
Alignment explanation
Indices: 1527--1773 Score: 397
Period size: 106 Copynumber: 2.3 Consensus size: 106
1517 TGTACGTTAT
1527 TCAACTTATGATGAATTCTGTGGATTTGAACACAGAGTGCCTGTACTGTTATTCATCAACTCATG
1 TCAACTT-TGATGAATTCTGTGGATTTG--CACAGAGTGCCTGTACTGTTATTCATCAACTCATG
* *
1592 ATGAATTCCGTGGATTGCACATAGAGTGCTTGTACGATTATTCA
63 ATGAATTCCGTGGATTGCACACAGAGTGCCTGTACGATTATTCA
*
1636 TCAACTTTGATGAATTATGTGGATTTGCACAGAGTGCCTGTAC-GATTATTCATCAACTCATGAT
1 TCAACTTTGATGAATTCTGTGGATTTGCACAGAGTGCCTGTACTG-TTATTCATCAACTCATGAT
*
1700 GAATTCCGTGGATTGCACACAGAGTGCCTGTACGGTTATTCA
65 GAATTCCGTGGATTGCACACAGAGTGCCTGTACGATTATTCA
*
1742 TCAACTCATGATGAATTCTGTGGATTTGCACA
1 TCAACT-TTGATGAATTCTGTGGATTTGCACA
1774 CAGAGCGCCT
Statistics
Matches: 130, Mismatches: 6, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
105 1 0.01
106 80 0.62
107 23 0.18
108 19 0.15
109 7 0.05
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (106 bp):
TCAACTTTGATGAATTCTGTGGATTTGCACAGAGTGCCTGTACTGTTATTCATCAACTCATGATG
AATTCCGTGGATTGCACACAGAGTGCCTGTACGATTATTCA
Found at i:5185 original size:23 final size:23
Alignment explanation
Indices: 5133--5186 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
5123 TATCTTATAT
*
5133 TATTTTATTTATATTTTTATTAA
1 TATTTTATTTATATTTTAATTAA
* *
5156 TAATTTATTTTTATTTTAATTAGA
1 TATTTTATTTATATTTTAATTA-A
5180 -ATTTTAT
1 TATTTTAT
5187 AAGTTCACTC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 25 0.96
24 1 0.04
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (23 bp):
TATTTTATTTATATTTTAATTAA
Found at i:6935 original size:4 final size:4
Alignment explanation
Indices: 6918--6958 Score: 66
Period size: 4 Copynumber: 10.5 Consensus size: 4
6908 TGATGGACTG
*
6918 ATGT ATGC ATGT ATGT AT-T ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
6959 ATATTCTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 3 0.09
4 31 0.91
ACGTcount: A:0.27, C:0.02, G:0.22, T:0.49
Consensus pattern (4 bp):
ATGT
Found at i:6942 original size:19 final size:19
Alignment explanation
Indices: 6918--6954 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
6908 TGATGGACTG
6918 ATGTATGCATGTATGTATT
1 ATGTATGCATGTATGTATT
*
6937 ATGTATGTATGTATGTAT
1 ATGTATGCATGTATGTAT
6955 GTATATATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.03, G:0.22, T:0.49
Consensus pattern (19 bp):
ATGTATGCATGTATGTATT
Found at i:11967 original size:17 final size:18
Alignment explanation
Indices: 11932--11970 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
11922 TTTAAATAGA
*
11932 AAATATATACATTTTTTT
1 AAATATATACATATTTTT
11950 AAATATATA-ATATTTTT
1 AAATATATACATATTTTT
11967 AAAT
1 AAAT
11971 TTTGCGTGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (18 bp):
AAATATATACATATTTTT
Found at i:20403 original size:12 final size:12
Alignment explanation
Indices: 20382--20414 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
20372 GATTTTCCTG
20382 TATATATATCTA
1 TATATATATCTA
*
20394 TATCTATATCTA
1 TATATATATCTA
20406 TATATATAT
1 TATATATAT
20415 TCGTGTTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (12 bp):
TATATATATCTA
Found at i:23904 original size:8 final size:8
Alignment explanation
Indices: 23891--23950 Score: 50
Period size: 8 Copynumber: 7.1 Consensus size: 8
23881 TAGACTGAAG
23891 AAAGAAAA
1 AAAGAAAA
23899 AAAGAAAGA
1 AAAGAAA-A
23908 AAATGAAAA
1 AAA-GAAAA
* *
23917 AAATAATA
1 AAAGAAAA
*
23925 AAATAATAA
1 AAAGAA-AA
23934 AAA-AAGAA
1 AAAGAA-AA
23942 AAAGAAAA
1 AAAGAAAA
23950 A
1 A
23951 GAAAATAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
8 26 0.59
9 14 0.32
10 4 0.09
ACGTcount: A:0.82, C:0.00, G:0.10, T:0.08
Consensus pattern (8 bp):
AAAGAAAA
Found at i:23955 original size:12 final size:11
Alignment explanation
Indices: 23891--23955 Score: 51
Period size: 12 Copynumber: 5.7 Consensus size: 11
23881 TAGACTGAAG
23891 AAAGAAAAAAA
1 AAAGAAAAAAA
*
23902 GAAAGAAAATGAA
1 -AAAGAAAA-AAA
* *
23915 AAA-AATAATA
1 AAAGAAAAAAA
* *
23925 AAATAATAAAA
1 AAAGAAAAAAA
23936 AAAGAAAAAGAA
1 AAAGAAAAA-AA
23948 AAAGAAAA
1 AAAGAAAA
23956 TAAATAAAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
10 4 0.09
11 16 0.37
12 21 0.49
13 2 0.05
ACGTcount: A:0.82, C:0.00, G:0.11, T:0.08
Consensus pattern (11 bp):
AAAGAAAAAAA
Found at i:23963 original size:37 final size:36
Alignment explanation
Indices: 23895--23965 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 36
23885 CTGAAGAAAG
23895 AAAAAAAGAAAGAAAATGAAAAAAATAATAAAATAAT
1 AAAAAAAGAAAGAAAA-GAAAAAAATAATAAAATAAT
23932 AAAAAAAGAAA-AAGAA-AAAGAAAATAAATAAAAT
1 AAAAAAAGAAAGAA-AAGAAA-AAAAT-AATAAAAT
23966 GAGTGTTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
35 3 0.10
36 7 0.23
37 21 0.68
ACGTcount: A:0.80, C:0.00, G:0.08, T:0.11
Consensus pattern (36 bp):
AAAAAAAGAAAGAAAAGAAAAAAATAATAAAATAAT
Found at i:25553 original size:41 final size:41
Alignment explanation
Indices: 25502--25680 Score: 189
Period size: 41 Copynumber: 4.2 Consensus size: 41
25492 TGATCTTGAG
25502 GAGCAGTGGAACAAATCTGCCTTAATTCAATCTACCCTGAA
1 GAGCAGTGGAACAAATCTGCCTTAATTCAATCTACCCTGAA
* *
25543 GAGTAGTGGAACAGATCTGCCTTAATTCAATCTACCCTGAA
1 GAGCAGTGGAACAAATCTGCCTTAATTCAATCTACCCTGAA
* * * * ** * *
25584 GAGTAGTGGAATAGATCCCCTTG-TTTCAGATTTGATCTTCCCTGAG
1 GAGCAGTGGAACAAAT---C-TGCCTT-A-ATTCAATCTACCCTGAA
* *
25630 GAGCAGTGGAACAAATCTGCCTTAATTCAATCTATCTTGAA
1 GAGCAGTGGAACAAATCTGCCTTAATTCAATCTACCCTGAA
25671 GAGCAGTGGA
1 GAGCAGTGGA
25681 GTGAATCAAC
Statistics
Matches: 113, Mismatches: 18, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
41 75 0.66
42 3 0.03
43 3 0.03
44 3 0.03
45 3 0.03
46 26 0.23
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (41 bp):
GAGCAGTGGAACAAATCTGCCTTAATTCAATCTACCCTGAA
Found at i:25630 original size:128 final size:130
Alignment explanation
Indices: 25345--25680 Score: 402
Period size: 128 Copynumber: 2.6 Consensus size: 130
25335 ACGGAGTAGA
* * * * *
25345 CCCTTGTTTCAGATTTGATGTTCCCTGATGAGCAGTGGAACAAATCTGCCTTTACTCAATCTTCC
1 CCCTTGTTTCAGATTTGATCTTCCCTGAGGAGCAGTGGAACAAATCTGCCTTAATTCAATCTACC
* * ** * *
25410 ATGAATAGCAGTGGAATGAATCAATGCTTCCAGATTTGATCCACCCGGTAGAGCAGTGGAGTAGA
66 ATGAAGAGCAGTGGAAAGAATC-ATGCTT-CAGATTCAATCCACCCGGAAGAGCAGTGGAATAGA
25475 TC
129 TC
25477 CCCTTGTTTCA-ACTTTGATC-T---TGAGGAGCAGTGGAACAAATCTGCCTTAATTCAATCTAC
1 CCCTTGTTTCAGA-TTTGATCTTCCCTGAGGAGCAGTGGAACAAATCTGCCTTAATTCAATCTAC
* * * * *
25537 CCTGAAGAGTAGTGGAACAG-ATC-TGCCTT-A-ATTCAATCTACCCTGAAGAGTAGTGGAATAG
65 CATGAAGAGCAGTGGAA-AGAATCATG-CTTCAGATTCAATCCACCCGGAAGAGCAGTGGAATAG
25598 ATC
128 ATC
*
25601 CCCTTGTTTCAGATTTGATCTTCCCTGAGGAGCAGTGGAACAAATCTGCCTTAATTCAATCTATC
1 CCCTTGTTTCAGATTTGATCTTCCCTGAGGAGCAGTGGAACAAATCTGCCTTAATTCAATCTACC
*
25666 TTGAAGAGCAGTGGA
66 ATGAAGAGCAGTGGA
25681 GTGAATCAAC
Statistics
Matches: 177, Mismatches: 19, Indels: 20
0.82 0.09 0.09
Matches are distributed among these distances:
124 45 0.25
125 3 0.02
126 2 0.01
127 3 0.02
128 104 0.59
129 1 0.01
131 2 0.01
132 17 0.10
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (130 bp):
CCCTTGTTTCAGATTTGATCTTCCCTGAGGAGCAGTGGAACAAATCTGCCTTAATTCAATCTACC
ATGAAGAGCAGTGGAAAGAATCATGCTTCAGATTCAATCCACCCGGAAGAGCAGTGGAATAGATC
Found at i:25858 original size:130 final size:132
Alignment explanation
Indices: 25256--25860 Score: 337
Period size: 130 Copynumber: 4.7 Consensus size: 132
25246 CAAGAGAATC
* * * * * * * ** *
25256 AAATCTACCTTGATTCAATCTTCTCTGAAA-AACAGTAGAATGAATCAATGTTTCCAGATCTGAT
1 AAATCTACCTTAATTAAATCTACCCT-AAAGAGCAGTGGAGTGAATCAACATTTCCAGATATGAT
* * * * * * *
25320 CTACCGTGAAGAGCTA-CGGAGTAG-A-CCCTTGTTTCAGATTTGATGTTCCCTGATG-AGCAGT
65 CTACCCTGAAGAG-TAGTGGAGCAGAACCCCTTGTTCCAGATTTGATCTACCCT-AAGAAGCAGT
*
25381 GGAAC
128 GGAAA
* * * * * * * * * *** *
25386 AAATCTGCCTTTACTCAATCTTCCATGAATAGCAGTGGAATGAATCAATGCTTCCAGATTTGATC
1 AAATCTACCTTAATTAAATCTACCCTAAAGAGCAGTGGAGTGAATCAACATTTCCAGATATGATC
* * * * * * * * *
25451 CACCCGGTAGAGCAGTGGAGTAGATCCCCTTGTTTCA-ACTTTGATCT----TGAGGAGCAGTGG
66 TACCCTGAAGAGTAGTGGAGCAGAACCCCTTGTTCCAGA-TTTGATCTACCCTAAGAAGCAGTGG
*
25511 AAC
130 AAA
* * * * ** ** * *
25514 AAATCTGCCTTAATTCAATCTACCCTGAAGAGTAGTGGA-ACAGATCTGC-CTT--A-AT-TCAA
1 AAATCTACCTTAATTAAATCTACCCTAAAGAGCAGTGGAGTGA-ATCAACATTTCCAGATAT-GA
** * * * * *
25573 TCTACCCTGAAGAGTAGTGGAATAGATCCCCTTGTTTCAGATTTGATCTTCCCTGAGGAGCAGTG
64 TCTACCCTGAAGAGTAGTGGAGCAGAACCCCTTGTTCCAGATTTGATCTACCCTAAGAAGCAGTG
*
25638 GAAC
129 GAAA
* * * * * ** *
25642 AAATCTGCCTTAATTCAATCTATCTTGAAGAGCAGTGGAGTGAATCAACATTTTTAGATATGATA
1 AAATCTACCTTAATTAAATCTACCCTAAAGAGCAGTGGAGTGAATCAACATTTCCAGATATGATC
* * *
25707 TACCCTGAAGAGCAGTAGAGCAGAACCCC-T-TTCCAGATTTGATCTACCCTAAGAAGTAGTGGA
66 TACCCTGAAGAGTAGTGGAGCAGAACCCCTTGTTCCAGATTTGATCTACCCTAAGAAGCAGTGGA
25770 AA
131 AA
* ** * *
25772 AAATCTACCTTGATTAAATCTACCCTAAAGAGCAGTGGAGTGAATCAATGTTTCCATATCTGATC
1 AAATCTACCTTAATTAAATCTACCCTAAAGAGCAGTGGAGTGAATCAACATTTCCAGATATGATC
* *
25837 TACCATGAAGAGTAGCGGAGCAGA
66 TACCCTGAAGAGTAGTGGAGCAGA
25861 TCCCTTTTTA
Statistics
Matches: 381, Mismatches: 75, Indels: 38
0.77 0.15 0.08
Matches are distributed among these distances:
123 1 0.00
124 45 0.12
125 2 0.01
127 5 0.01
128 104 0.27
129 6 0.02
130 168 0.44
131 3 0.01
132 46 0.12
133 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.28
Consensus pattern (132 bp):
AAATCTACCTTAATTAAATCTACCCTAAAGAGCAGTGGAGTGAATCAACATTTCCAGATATGATC
TACCCTGAAGAGTAGTGGAGCAGAACCCCTTGTTCCAGATTTGATCTACCCTAAGAAGCAGTGGA
AA
Found at i:26111 original size:13 final size:12
Alignment explanation
Indices: 26055--26112 Score: 50
Period size: 13 Copynumber: 4.8 Consensus size: 12
26045 CACTCGGTTC
26055 TTTTATTTATTTA
1 TTTTA-TTATTTA
*
26068 TTTTATT-TCTA
1 TTTTATTATTTA
26079 TTTT-TTATTT-
1 TTTTATTATTTA
*
26089 TTATTCTTATGTTA
1 TT-TTATTAT-TTA
26103 TTTTATTATT
1 TTTTATTATT
26113 GTTCCAGTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 11
0.73 0.06 0.22
Matches are distributed among these distances:
10 4 0.11
11 11 0.30
12 7 0.19
13 13 0.35
14 2 0.05
ACGTcount: A:0.19, C:0.03, G:0.02, T:0.76
Consensus pattern (12 bp):
TTTTATTATTTA
Found at i:30384 original size:3 final size:3
Alignment explanation
Indices: 30378--30432 Score: 76
Period size: 3 Copynumber: 18.0 Consensus size: 3
30368 CCCGGCTTAA
*
30378 ATT ATT A-T ACTT ATTT ATT ATT ATT ATT ATT AAT ATT ATT ATT ATT
1 ATT ATT ATT A-TT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
30424 ATT ATT ATT
1 ATT ATT ATT
30433 CATTTTGTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
2 2 0.04
3 40 0.85
4 5 0.11
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:32577 original size:18 final size:18
Alignment explanation
Indices: 32554--32588 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
32544 ATAATAAGCG
*
32554 ATTCCATAATCATGAAAT
1 ATTCCACAATCATGAAAT
*
32572 ATTCCACAATCTTGAAA
1 ATTCCACAATCATGAAA
32589 GCAAGTAGTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.20, G:0.06, T:0.31
Consensus pattern (18 bp):
ATTCCACAATCATGAAAT
Found at i:33891 original size:20 final size:19
Alignment explanation
Indices: 33866--33903 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
33856 CCCAAATTGG
33866 TAAGTCCTTCGAGCCATCAA
1 TAAGTCCTTCGAG-CATCAA
*
33886 TAAGTCTTTCGAGCATCA
1 TAAGTCCTTCGAGCATCA
33904 TGATTAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (19 bp):
TAAGTCCTTCGAGCATCAA
Found at i:34167 original size:196 final size:196
Alignment explanation
Indices: 33805--34230 Score: 656
Period size: 196 Copynumber: 2.2 Consensus size: 196
33795 AAATAATTTT
* * * * *
33805 TTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTTTTACCCAATAAACTATTTCCCAAATTGGTAAG
1 TTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTTACCAAATAAACTATTTCCCAAATTGGTAAG
* *
33870 TCCTTCGAGCCATCAATAAGTCTTTCGAGCATCATGATTAAATCCTTCAGGTCATTTGTAAGTCT
66 TCATTCGAGCCATCAATAAGTCTTTCGAGCATCATGATTAAATCCTTCAGGTCATCTGTAAGTCT
* * * * * *
33935 TTCGAGCAAGATGATAATTTCTTCGGGCCTTCCGTAAGACCTTCAGGTAGGATGGTTTCGTATGA
131 TTCGAGAAAGATGATAAGTTCTTCAGGCCATCCGTAAGACATTCAGGTAGGATGGTTTCGAATGA
34000 A
196 A
*
34001 TTTGAAAAATGAGAAAACGATTTCCAAAGTTTCTTACCAAATAAACTATTTCCCAAATTGGTAAG
1 TTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTTACCAAATAAACTATTTCCCAAATTGGTAAG
* * * *
34066 TCATTCGTA-CCATTAGTATGTCTTTCGAGCATGATGATTAAATCCTTCAGGTCATCTGTAAGTC
66 TCATTCG-AGCCATCAATAAGTCTTTCGAGCATCATGATTAAATCCTTCAGGTCATCTGTAAGTC
* *
34130 TTTCGAGAAAGGTGATAAGTTCTTCAGGCCATCCGTAAGACATTCAGGTAGGATGTTTTCGAATG
130 TTTCGAGAAAGATGATAAGTTCTTCAGGCCATCCGTAAGACATTCAGGTAGGATGGTTTCGAATG
34195 AA
195 AA
34197 TTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCT
1 TTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCT
34231 CATTTAGTAT
Statistics
Matches: 208, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
196 207 1.00
197 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Consensus pattern (196 bp):
TTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTTACCAAATAAACTATTTCCCAAATTGGTAAG
TCATTCGAGCCATCAATAAGTCTTTCGAGCATCATGATTAAATCCTTCAGGTCATCTGTAAGTCT
TTCGAGAAAGATGATAAGTTCTTCAGGCCATCCGTAAGACATTCAGGTAGGATGGTTTCGAATGA
A
Found at i:34371 original size:257 final size:255
Alignment explanation
Indices: 34001--34897 Score: 1169
Period size: 257 Copynumber: 3.5 Consensus size: 255
33991 TTCGTATGAA
* * * * *
34001 TTTGAAAAATGAGAAAACGATTTCCAAAGTTTCTTA-CCAAATAAACTATTTCCCAAATTGGTAA
1 TTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAAA-AAACTATTTCCAAAATTAGTAA
** *
34065 GTCATTCGTACCATTAGTATGTCTTTCGAGCATGATGATTAAATCCTTCAGGTCATCTGTAAGTC
65 GTCATTCGGGCCATTAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCAGGTCATCTGTAAGTC
* *
34130 TTTCGAGAAAGGTGATAAGTTCTTCAGG-CCATCCGTAAGACATTCAGGTAGGATGTTTTCGA-A
130 TTTCGAGAAAGATGATAAGTTCTTC-GGTCCATCCGTAAGACCTTCAGGTAGGATGTTTTC-ACA
* *
34193 TGAATTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAGTATTTTTAGAAAATTAAATT
193 TGAATTTGAAAAATGAGAAAG-GATTT-CAAAGTTTCTCATTTAGTATTTTCAGAAAATGAAATT
* * * * *
34258 TTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTTTTACCCAAAAAACTATTTCCCAGATTGGTAAT
1 TTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAAAAAACTATTTCCAAAATTAGTAAG
* *
34323 TCATTCGGGCCATCAGTAAGTCTTCCGAGCATGATGATTAAATCCTTCAGGTCATCTGTAAGTCT
66 TCATTCGGGCCATTAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCAGGTCATCTGTAAGTCT
* * *
34388 TTCGAGAAAGATGATAAGCTCTTCGGTCCATCCGTAAGACCTTCGGGTAGGATGTTTTCATATGA
131 TTCGAGAAAGATGATAAGTTCTTCGGTCCATCCGTAAGACCTTCAGGTAGGATGTTTTCACATGA
* ** *
34453 ATTTGAAAAATGAGAAAGAGATTTTCTAAGTTTCTTGTTTCGTATTTTCAGAAAATGAAATT
196 ATTTGAAAAATGAGAAAG-GA-TTTCAAAGTTTCTCATTTAGTATTTTCAGAAAATGAAATT
* ** *
34515 TTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTAGTAAG
1 TTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAAAAAACTATTTCCAAAATTAGTAAG
* * *
34580 TCCTTCGGGCCATGAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGTCT
66 TCATTCGGGCCATTAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCAGGTCATCTGTAAGTCT
* * * * * * * * *
34645 TTCAAGCAAGATGATAACTCCTTCGGTCCATCCATAACACCTTCAAGCAGGATGTTTCCACATGA
131 TTCGAGAAAGATGATAAGTTCTTCGGTCCATCCGTAAGACCTTCAGGTAGGATGTTTTCACATGA
* * * * *
34710 TTTTTGAAAAATGAGAAA-G---TGAATGTTTCTCATTTAATATTTTCATAAAATGAAATT
196 -ATTTGAAAAATGAGAAAGGATTTCAAAGTTTCTCATTTAGTATTTTCAGAAAATGAAATT
* * ** *
34767 TTTGAAAAGTAAGAAAGCGATTTCCAAATTTTTTTACCCAGTAAATTATTTCCAAAATTAGTAAG
1 TTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAAAAAACTATTTCCAAAATTAGTAAG
* * * *
34832 TCCTTCGGGTCATTAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCAGGTTATCTGTCAGTCT
66 TCATTCGGGCCATTAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCAGGTCATCTGTAAGTCT
34897 T
131 T
34898 ACTTGGGACA
Statistics
Matches: 571, Mismatches: 64, Indels: 15
0.88 0.10 0.02
Matches are distributed among these distances:
252 153 0.27
256 4 0.01
257 390 0.68
258 24 0.04
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Consensus pattern (255 bp):
TTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAAAAAACTATTTCCAAAATTAGTAAG
TCATTCGGGCCATTAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCAGGTCATCTGTAAGTCT
TTCGAGAAAGATGATAAGTTCTTCGGTCCATCCGTAAGACCTTCAGGTAGGATGTTTTCACATGA
ATTTGAAAAATGAGAAAGGATTTCAAAGTTTCTCATTTAGTATTTTCAGAAAATGAAATT
Found at i:34454 original size:453 final size:453
Alignment explanation
Indices: 33607--34488 Score: 1304
Period size: 453 Copynumber: 1.9 Consensus size: 453
33597 AAACTATTTC
* *
33607 GGTAAGTCCTTCGGTCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTCATCTGT
1 GGTAAGTCATTCGGTCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCAGGTCATCTGT
* * * * * * *
33672 CAGTCTTTTAAATAAGATGATAAGCCCGTCGGGCCATCTGTAAGACCTTCGGGTAGGGTATTTTC
66 AAGTCTTTGAAATAAGATGATAAGCCCGTCAGGCCATCCGTAAGACATTCAGGTAGGATATTTTC
* * **
33737 GTATAAATTTGAAAAATTAGAAAGCGATTTTGAAAGTTTCTCATTTAGTATTTTTAGAAAATAAT
131 GAATAAATTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAGTATTTTTAGAAAATAAT
* * *
33802 TTTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTTTTACCCAATAAACTATTTCCCAAATTGGT
196 ATTTTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTTTTACCCAAAAAACTATTTCCCAAATTGGT
* * *
33867 AAGTCCTTCGAGCCATCAATAAGTCTTTCGAGCATCATGATTAAATCCTTCAGGTCATTTGTAAG
261 AAGTCATTCGAGCCATCAATAAGTCTTCCGAGCATCATGATTAAATCCTTCAGGTCATCTGTAAG
* ** * *
33932 TCTTTCGAGCAAGATGATAATTTCTTCGGGCCTTCCGTAAGACCTTCAGGTAGGATGGTTTCGTA
326 TCTTTCGAGAAAGATGATAAGCTCTTCGGGCCATCCGTAAGACCTTCAGGTAGGATGGTTTCATA
33997 TGAATTTGAAAAATGAGAAA-ACGATTTCCAAAGTTTCTTACCAAATAAACTATTTCCCAAATT
391 TGAATTTGAAAAATGAGAAAGA-GATTTCCAAAGTTTCTTACCAAATAAACTATTTCCCAAATT
* * *
34060 GGTAAGTCATTC-GTACCATTAGTATGTCTTTCGAGCATGATGATTAAATCCTTCAGGTCATCTG
1 GGTAAGTCATTCGGT-CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCAGGTCATCTG
* * ** * *
34124 TAAGTCTTTCGAGA-AAGGTGATAAGTTCTTCAGGCCATCCGTAAGACATTCAGGTAGGATGTTT
65 TAAGTCTTT-GAAATAAGATGATAAGCCCGTCAGGCCATCCGTAAGACATTCAGGTAGGATATTT
*
34188 TCGAATGAATTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAGTATTTTTAGAAAATT
129 TCGAATAAATTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAGTATTTTTAGAAAA-T
*
34253 AA-ATTTTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTTTTACCCAAAAAACTATTTCCCAGATT
193 AATATTTTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTTTTACCCAAAAAACTATTTCCCAAATT
* * * *
34317 GGTAATTCATTCGGGCCATCAGTAAGTCTTCCGAGCATGATGATTAAATCCTTCAGGTCATCTGT
258 GGTAAGTCATTCGAGCCATCAATAAGTCTTCCGAGCATCATGATTAAATCCTTCAGGTCATCTGT
* * *
34382 AAGTCTTTCGAGAAAGATGATAAGCTCTTCGGTCCATCCGTAAGACCTTCGGGTAGGATGTTTTC
323 AAGTCTTTCGAGAAAGATGATAAGCTCTTCGGGCCATCCGTAAGACCTTCAGGTAGGATGGTTTC
* *
34447 ATATGAATTTGAAAAATGAGAAAGAGATTTTCTAAGTTTCTT
388 ATATGAATTTGAAAAATGAGAAAGAGATTTCCAAAGTTTCTT
34489 GTTTCGTATT
Statistics
Matches: 381, Mismatches: 44, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
452 2 0.01
453 373 0.98
454 6 0.02
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (453 bp):
GGTAAGTCATTCGGTCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCAGGTCATCTGT
AAGTCTTTGAAATAAGATGATAAGCCCGTCAGGCCATCCGTAAGACATTCAGGTAGGATATTTTC
GAATAAATTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAGTATTTTTAGAAAATAAT
ATTTTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTTTTACCCAAAAAACTATTTCCCAAATTGGT
AAGTCATTCGAGCCATCAATAAGTCTTCCGAGCATCATGATTAAATCCTTCAGGTCATCTGTAAG
TCTTTCGAGAAAGATGATAAGCTCTTCGGGCCATCCGTAAGACCTTCAGGTAGGATGGTTTCATA
TGAATTTGAAAAATGAGAAAGAGATTTCCAAAGTTTCTTACCAAATAAACTATTTCCCAAATT
Found at i:34627 original size:42 final size:41
Alignment explanation
Indices: 34580--34676 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 41
34570 AATTAGTAAG
* * *
34580 TCCTTCGGGCCATGAGTAAGTCTTTCGAGCATGATGATTAAA
1 TCCTTCGGGCCATCAGTAAGTCTTTCAAGCAAGATGA-TAAA
* * *
34622 TCCTTCGGGTCATCTGTAAGTCTTTCAAGCAAGATGATAAC
1 TCCTTCGGGCCATCAGTAAGTCTTTCAAGCAAGATGATAAA
*
34663 TCCTTCGGTCCATC
1 TCCTTCGGGCCATC
34677 CATAACACCT
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 15 0.32
42 32 0.68
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (41 bp):
TCCTTCGGGCCATCAGTAAGTCTTTCAAGCAAGATGATAAA
Found at i:34954 original size:3 final size:3
Alignment explanation
Indices: 34948--35013 Score: 71
Period size: 3 Copynumber: 21.3 Consensus size: 3
34938 TTTTTTCGGG
* *
34948 TTA TTA TTA ATA TTTA GTA TTA TTA TTA TTA TTA TT- TATA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
*
34994 TTA TTA TTAA TTT TTA TTA T
1 TTA TTA TT-A TTA TTA TTA T
35014 CATTTTTTAT
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
2 1 0.02
3 46 0.87
4 6 0.11
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:42984 original size:24 final size:24
Alignment explanation
Indices: 42943--43030 Score: 135
Period size: 24 Copynumber: 3.7 Consensus size: 24
42933 AACATAAATG
42943 AACGAACAT-AACGAACATAACCT
1 AACGAACATAAACGAACATAACCT
*
42966 AACGAACATAAACGAACATAACCA
1 AACGAACATAAACGAACATAACCT
*
42990 AACGAACATAAACGAACATAA-TT
1 AACGAACATAAACGAACATAACCT
43013 GAACGAACATAAACGAAC
1 -AACGAACATAAACGAAC
43031 GAACATAACC
Statistics
Matches: 60, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
23 9 0.15
24 51 0.85
ACGTcount: A:0.56, C:0.23, G:0.10, T:0.11
Consensus pattern (24 bp):
AACGAACATAAACGAACATAACCT
Found at i:42997 original size:38 final size:39
Alignment explanation
Indices: 42947--43045 Score: 105
Period size: 38 Copynumber: 2.6 Consensus size: 39
42937 TAAATGAACG
*
42947 AACATAACGAACATAACCTAACGA-ACA-TAAACGAACATA
1 AACA-AACGAACATAACCAAACGATA-ATTAAACGAACATA
* * * *
42986 ACCAAACGAACATAAACGAAC-ATAATTGAACGAACATA
1 AACAAACGAACATAACCAAACGATAATTAAACGAACATA
*
43024 AACGAACGAACATAACCAAACG
1 AACAAACGAACATAACCAAACG
43046 TTCACGAACG
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
37 2 0.04
38 44 0.90
39 3 0.06
ACGTcount: A:0.56, C:0.23, G:0.10, T:0.11
Consensus pattern (39 bp):
AACAAACGAACATAACCAAACGATAATTAAACGAACATA
Found at i:43045 original size:14 final size:14
Alignment explanation
Indices: 42952--43045 Score: 78
Period size: 14 Copynumber: 7.3 Consensus size: 14
42942 GAACGAACAT
*
42952 AACGAACATAACCT
1 AACGAACATAACCA
42966 AACGAACAT----A
1 AACGAACATAACCA
42976 AACGAACATAACCA
1 AACGAACATAACCA
42990 AACGAACAT----A
1 AACGAACATAACCA
***
43000 AACGAACATAATTG
1 AACGAACATAACCA
* *
43014 AACGAACATAAACG
1 AACGAACATAACCA
43028 AACGAACATAACCA
1 AACGAACATAACCA
43042 AACG
1 AACG
43046 TTCACGAACG
Statistics
Matches: 66, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
10 19 0.29
14 47 0.71
ACGTcount: A:0.55, C:0.23, G:0.11, T:0.11
Consensus pattern (14 bp):
AACGAACATAACCA
Done.