Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007087.1 Hibiscus syriacus cultivar Beakdansim tig00018489_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: 105433
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Found at i:5835 original size:17 final size:16
Alignment explanation
Indices: 5804--5837 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
5794 CACGTGAGGA
5804 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
5820 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
5837 T
1 T
5838 ACAGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:14766 original size:17 final size:16
Alignment explanation
Indices: 14744--14777 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
14734 TAAAAATAGT
14744 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
14761 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
14777 A
1 A
14778 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:17281 original size:18 final size:18
Alignment explanation
Indices: 17258--17327 Score: 104
Period size: 18 Copynumber: 3.8 Consensus size: 18
17248 AATATTTGTC
17258 CCCGAAGGACCACTATGT
1 CCCGAAGGACCACTATGT
17276 CCCGAAGGACCACTGATTGT
1 CCCGAAGGACCACT-A-TGT
* *
17296 TCCGAAGAACCACTATGT
1 CCCGAAGGACCACTATGT
17314 CCCGAAGGACCACT
1 CCCGAAGGACCACT
17328 GATAATCCCT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
18 29 0.63
19 2 0.04
20 15 0.33
ACGTcount: A:0.29, C:0.33, G:0.21, T:0.17
Consensus pattern (18 bp):
CCCGAAGGACCACTATGT
Found at i:19346 original size:19 final size:20
Alignment explanation
Indices: 19324--19364 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
19314 AATAAATCAC
19324 ATAAAAATA-ATTATATTTT
1 ATAAAAATATATTATATTTT
19343 ATAAAAATATATTATATTTT
1 ATAAAAATATATTATATTTT
19363 AT
1 AT
19365 TATTTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATAAAAATATATTATATTTT
Found at i:19679 original size:29 final size:29
Alignment explanation
Indices: 19629--19704 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 29
19619 AAACTAAAAA
*
19629 AATTATTAAATTTAAAAGATTA-GAGACCCT
1 AATTA-TAAATATAAAAGATTAGGAG-CCCT
* *
19659 AATTATAAATATACAAA-ATTAGGAGTCTT
1 AATTATAAATATA-AAAGATTAGGAGCCCT
19688 AATTATAAATA-AAAAGA
1 AATTATAAATATAAAAGA
19705 ATTGGGGACC
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
27 3 0.08
28 2 0.05
29 24 0.60
30 11 0.28
ACGTcount: A:0.53, C:0.07, G:0.09, T:0.32
Consensus pattern (29 bp):
AATTATAAATATAAAAGATTAGGAGCCCT
Found at i:21895 original size:13 final size:13
Alignment explanation
Indices: 21877--21901 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21867 TTAAAATCAA
21877 TTGGGCCCAAGCC
1 TTGGGCCCAAGCC
21890 TTGGGCCCAAGC
1 TTGGGCCCAAGC
21902 TTGAACTACC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.36, G:0.32, T:0.16
Consensus pattern (13 bp):
TTGGGCCCAAGCC
Found at i:23984 original size:21 final size:21
Alignment explanation
Indices: 23960--24024 Score: 50
Period size: 21 Copynumber: 3.3 Consensus size: 21
23950 AATTAAAAAA
23960 TATTAAAAAATATATAAACAT
1 TATTAAAAAATATATAAACAT
***
23981 TATTTTTAAATATAT--A-AT
1 TATTAAAAAATATATAAACAT
*
23999 TA-TAAAAAATAAATAAAC-T
1 TATTAAAAAATATATAAACAT
*
24018 AATTAAA
1 TATTAAA
24025 CAACAGAATT
Statistics
Matches: 32, Mismatches: 8, Indels: 9
0.65 0.16 0.18
Matches are distributed among these distances:
17 8 0.25
18 4 0.12
19 4 0.12
20 4 0.12
21 12 0.38
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (21 bp):
TATTAAAAAATATATAAACAT
Found at i:24973 original size:31 final size:31
Alignment explanation
Indices: 24935--25033 Score: 98
Period size: 31 Copynumber: 3.3 Consensus size: 31
24925 CCAAAAATAT
24935 TTTAGTTACTAAAATGAAGAAGAAAGTATGC
1 TTTAGTTACTAAAATGAAGAAGAAAGTATGC
* *** **
24966 TTTAGTTATTTATTTTGACCCAA-AAA-TAT--
1 TTTAGTTA-CTAAAATGA-AGAAGAAAGTATGC
24995 TTTAGTTACTAAAATGAAGAAGAAAGTATGC
1 TTTAGTTACTAAAATGAAGAAGAAAGTATGC
25026 TTTAGTTA
1 TTTAGTTA
25034 TTTATTTTGA
Statistics
Matches: 50, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
27 2 0.04
28 8 0.16
29 11 0.22
31 19 0.38
32 8 0.16
33 2 0.04
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.37
Consensus pattern (31 bp):
TTTAGTTACTAAAATGAAGAAGAAAGTATGC
Found at i:25002 original size:29 final size:29
Alignment explanation
Indices: 24912--25062 Score: 85
Period size: 29 Copynumber: 5.1 Consensus size: 29
24902 TATCTAAAAG
24912 TATTTATTTTGACCCAAAAATATTTTAGT
1 TATTTATTTTGACCCAAAAATATTTTAGT
* *** **
24941 TA-CTAAAATGA-AGAAGAAAGTATGCTTTAGT
1 TATTTATTTTGACCCAA-AAA-TAT--TTTAGT
24972 TATTTATTTTGACCCAAAAATATTTTAGT
1 TATTTATTTTGACCCAAAAATATTTTAGT
* *** **
25001 TA-CTAAAATGA-AGAAGAAAGTATGCTTTAGT
1 TATTTATTTTGACCCAA-AAA-TAT--TTTAGT
*
25032 TATTTATTTTGACCCAAAAATACTTTAGT
1 TATTTATTTTGACCCAAAAATATTTTAGT
25061 TA
1 TA
25063 CTAAAATGAA
Statistics
Matches: 85, Mismatches: 25, Indels: 24
0.63 0.19 0.18
Matches are distributed among these distances:
27 4 0.05
28 16 0.19
29 24 0.28
31 21 0.25
32 16 0.19
33 4 0.05
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.40
Consensus pattern (29 bp):
TATTTATTTTGACCCAAAAATATTTTAGT
Found at i:25092 original size:60 final size:60
Alignment explanation
Indices: 24912--25072 Score: 313
Period size: 60 Copynumber: 2.7 Consensus size: 60
24902 TATCTAAAAG
24912 TATTTATTTTGACCCAAAAATATTTTAGTTACTAAAATGAAGAAGAAAGTATGCTTTAGT
1 TATTTATTTTGACCCAAAAATATTTTAGTTACTAAAATGAAGAAGAAAGTATGCTTTAGT
24972 TATTTATTTTGACCCAAAAATATTTTAGTTACTAAAATGAAGAAGAAAGTATGCTTTAGT
1 TATTTATTTTGACCCAAAAATATTTTAGTTACTAAAATGAAGAAGAAAGTATGCTTTAGT
*
25032 TATTTATTTTGACCCAAAAATACTTTAGTTACTAAAATGAA
1 TATTTATTTTGACCCAAAAATATTTTAGTTACTAAAATGAA
25073 TAGACTAATG
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
60 100 1.00
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.39
Consensus pattern (60 bp):
TATTTATTTTGACCCAAAAATATTTTAGTTACTAAAATGAAGAAGAAAGTATGCTTTAGT
Found at i:26242 original size:12 final size:11
Alignment explanation
Indices: 26225--26262 Score: 58
Period size: 12 Copynumber: 3.3 Consensus size: 11
26215 ACAATTGACA
26225 TAATTTGTCATC
1 TAATTTGTCA-C
26237 TAATTTGTCAC
1 TAATTTGTCAC
26248 TAACTTTGTCAC
1 TAA-TTTGTCAC
26260 TAA
1 TAA
26263 ATTTATAGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 4 0.16
12 21 0.84
ACGTcount: A:0.29, C:0.18, G:0.08, T:0.45
Consensus pattern (11 bp):
TAATTTGTCAC
Found at i:28996 original size:16 final size:17
Alignment explanation
Indices: 28975--29007 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28965 ATCTGTTAAT
*
28975 TCAATT-TTTTAAAAAA
1 TCAATTATTTCAAAAAA
28991 TCAATTATTTCAAAAAA
1 TCAATTATTTCAAAAAA
29008 ATTACTCGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (17 bp):
TCAATTATTTCAAAAAA
Found at i:39919 original size:16 final size:14
Alignment explanation
Indices: 39890--39931 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
39880 ATCAGAACAC
39890 AATTATAATAATTT
1 AATTATAATAATTT
39904 AATTAGTAATTAATTT
1 AATTA-TAA-TAATTT
*
39920 AA-AATAATAATT
1 AATTATAATAATT
39932 AAAATTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 5 0.20
14 8 0.32
15 4 0.16
16 8 0.32
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (14 bp):
AATTATAATAATTT
Found at i:45221 original size:20 final size:20
Alignment explanation
Indices: 45196--45235 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
45186 TATTTAGATG
45196 CTTAACAGCTAACCAACTTT
1 CTTAACAGCTAACCAACTTT
45216 CTTAACAGCTAACCAACTTT
1 CTTAACAGCTAACCAACTTT
45236 ATGAATACTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.30, G:0.05, T:0.30
Consensus pattern (20 bp):
CTTAACAGCTAACCAACTTT
Found at i:47834 original size:24 final size:24
Alignment explanation
Indices: 47800--47853 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
47790 CTGAAAAATC
47800 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
47824 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
47848 ATCAAA
1 ATCAAA
47854 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:47867 original size:24 final size:24
Alignment explanation
Indices: 47800--47867 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
47790 CTGAAAAATC
* * *
47800 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
47824 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
47848 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
47868 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:48762 original size:20 final size:20
Alignment explanation
Indices: 48734--48825 Score: 78
Period size: 21 Copynumber: 4.5 Consensus size: 20
48724 ATTTAAATTT
48734 GCATTGCGATTTACGT-AATC
1 GCATTGCGATTTA-GTAAATC
*
48754 GCGTTGCGATTTAGTAAATC
1 GCATTGCGATTTAGTAAATC
* *
48774 GCATTGCGAATTAAGAAAATC
1 GCATTGCG-ATTTAGTAAATC
** * *
48795 GCAACGCGAATTTGGGAAATC
1 GCATTGCG-ATTTAGTAAATC
*
48816 GCAATGCGAT
1 GCATTGCGAT
48826 AGTCAGAATC
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
19 2 0.03
20 25 0.42
21 33 0.55
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (20 bp):
GCATTGCGATTTAGTAAATC
Found at i:49374 original size:18 final size:18
Alignment explanation
Indices: 49351--49386 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
49341 ATTTATGTGT
49351 TTTTAAATATAATTTTAA
1 TTTTAAATATAATTTTAA
49369 TTTTAAATATAATTTTAA
1 TTTTAAATATAATTTTAA
49387 AATTATCAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTTAAATATAATTTTAA
Found at i:58963 original size:21 final size:20
Alignment explanation
Indices: 58930--58968 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
58920 TTTTATTTTT
58930 TATTTTTTAATTAAAAATAA
1 TATTTTTTAATTAAAAATAA
*
58950 TATTTTTATTATTAAAAAT
1 TATTTTT-TAATTAAAAAT
58969 GAAAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TATTTTTTAATTAAAAATAA
Found at i:59238 original size:17 final size:17
Alignment explanation
Indices: 59190--59243 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 17
59180 ATTTGTTTAC
* *
59190 TATATTTTTTCTTTTCT
1 TATATTTTTTATTTTTT
59207 TATATTGCATCTTTATTTTTT
1 TATATT---T-TTTATTTTTT
59228 TATATTTTTTATTTTT
1 TATATTTTTTATTTTT
59244 AATAAGTCTG
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
17 15 0.48
18 1 0.03
20 1 0.03
21 14 0.45
ACGTcount: A:0.17, C:0.07, G:0.02, T:0.74
Consensus pattern (17 bp):
TATATTTTTTATTTTTT
Found at i:60892 original size:15 final size:14
Alignment explanation
Indices: 60872--60967 Score: 55
Period size: 15 Copynumber: 7.1 Consensus size: 14
60862 TATATTTAAT
60872 ATAATTTATTACTTA
1 ATAATTTATTA-TTA
* *
60887 ATAATTTAATATCA
1 ATAATTTATTATTA
*
60901 A-AA-TTATTTTTTA
1 ATAATTTA-TTATTA
60914 ATAATTTTATT-TTA
1 ATAA-TTTATTATTA
60928 ATAA-TT-TTA--A
1 ATAATTTATTATTA
*
60938 ATTATTTATTACTTA
1 ATAATTTATTA-TTA
*
60953 ATGATTTATT-TTA
1 ATAATTTATTATTA
60966 AT
1 AT
60968 TTATTTTATA
Statistics
Matches: 64, Mismatches: 7, Indels: 22
0.69 0.08 0.24
Matches are distributed among these distances:
10 4 0.06
11 4 0.06
12 8 0.12
13 11 0.17
14 12 0.19
15 22 0.34
16 3 0.05
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (14 bp):
ATAATTTATTATTA
Found at i:60926 original size:14 final size:14
Alignment explanation
Indices: 60909--60936 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
60899 CAAAATTATT
60909 TTTTAATAATTTTA
1 TTTTAATAATTTTA
60923 TTTTAATAATTTTA
1 TTTTAATAATTTTA
60937 AATTATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTAATAATTTTA
Found at i:64150 original size:22 final size:22
Alignment explanation
Indices: 64122--64178 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
64112 TGTCCCCCTG
64122 AAATTTTATCGTACCCATCCTA
1 AAATTTTATCGTACCCATCCTA
*
64144 AAATTTTATCGTGCCCATCCTA
1 AAATTTTATCGTACCCATCCTA
64166 AAATTTTATCGTA
1 AAATTTTATCGTA
64179 TCTATATAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.39
Consensus pattern (22 bp):
AAATTTTATCGTACCCATCCTA
Found at i:71575 original size:16 final size:16
Alignment explanation
Indices: 71551--71584 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
71541 ATTAAGCTAC
*
71551 TTTTTTAGTTTGACAG
1 TTTTGTAGTTTGACAG
*
71567 TTTTGTAGTTTGCCAG
1 TTTTGTAGTTTGACAG
71583 TT
1 TT
71585 ATGAAGAGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.09, G:0.21, T:0.56
Consensus pattern (16 bp):
TTTTGTAGTTTGACAG
Found at i:75784 original size:20 final size:20
Alignment explanation
Indices: 75736--75797 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 20
75726 AACTTAAATC
*
75736 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-TAATAATATAT
75756 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAATATAT
75774 AAAATAATTT-AT-ATGATAT
1 AAAATAATTTAATAAT-ATAT
75793 AAAAT
1 AAAAT
75798 TAAATATCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 5 0.14
18 13 0.35
19 11 0.30
20 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAATAATTTAATAATATAT
Found at i:75890 original size:22 final size:22
Alignment explanation
Indices: 75863--75904 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
75853 ATATTAAAAT
75863 TAAAATCAAA-TATAATATAATA
1 TAAAATCAAATTA-AATATAATA
*
75885 TAAAATTAAATTAAATATAA
1 TAAAATCAAATTAAATATAA
75905 AACCTCTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATCAAATTAAATATAATA
Found at i:76822 original size:18 final size:18
Alignment explanation
Indices: 76799--76836 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
76789 AAGAACTTAT
*
76799 ATTAGAAATTTTTAGAGG
1 ATTAGAAATTTTTAAAGG
76817 ATTAGAAATTTTTAAAGG
1 ATTAGAAATTTTTAAAGG
76835 AT
1 AT
76837 ACGACCACCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.18, T:0.39
Consensus pattern (18 bp):
ATTAGAAATTTTTAAAGG
Found at i:83127 original size:23 final size:23
Alignment explanation
Indices: 83100--83145 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
83090 TTTTTCTTGG
83100 GAAGCTGCACTTTTTACATAGTT
1 GAAGCTGCACTTTTTACATAGTT
83123 GAAGCTGCACTTTTTACATAGTT
1 GAAGCTGCACTTTTTACATAGTT
83146 TAATAAGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.39
Consensus pattern (23 bp):
GAAGCTGCACTTTTTACATAGTT
Found at i:85901 original size:26 final size:26
Alignment explanation
Indices: 85868--85922 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
85858 TAGTTTTTCA
85868 TATGTTGTTTGTGAAAATGGTTCTTT
1 TATGTTGTTTGTGAAAATGGTTCTTT
85894 TATGTTGTTTGTGAAAATGGTTCTTT
1 TATGTTGTTTGTGAAAATGGTTCTTT
85920 TAT
1 TAT
85923 TGACTTTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.20, C:0.04, G:0.22, T:0.55
Consensus pattern (26 bp):
TATGTTGTTTGTGAAAATGGTTCTTT
Found at i:86958 original size:122 final size:123
Alignment explanation
Indices: 86738--86958 Score: 338
Period size: 122 Copynumber: 1.8 Consensus size: 123
86728 TCACCTATTG
* *
86738 CCAATTGGTTTTAGGTTAGATGCTTAACAACTTTTAATCTATAAAGGTGATGCTTAAAGTTAGAG
1 CCAATTGGTTTTAGGTTAAATGCTTAACAACTTTTAATCTATAAAGATGATGCTTAAAGTTAGAG
* * *
86803 CTTGTTTATTGTTCCTGGATTCAATCGGTAAGTCCTTTGATTGTTTTGGTTTTATTTC
66 CTTGTTTATTATTCCTGAATTCAATCGGCAAGTCCTTTGATTGTTTTGGTTTTATTTC
* *
86861 CCAATTGGTTTTAGGTTAAATGCTT-ACAA-TTTTGAATCTATAAATATGATGCTTAAAGTTTGA
1 CCAATTGGTTTTAGGTTAAATGCTTAACAACTTTT-AATCTATAAAGATGATGCTTAAAGTTAGA
* *
86924 GTTTGTTTATTATTCCTGAATTCAATCTGCAAGTC
65 GCTTGTTTATTATTCCTGAATTCAATCGGCAAGTC
86959 TTGTTTGTAA
Statistics
Matches: 88, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
121 4 0.05
122 60 0.68
123 24 0.27
ACGTcount: A:0.26, C:0.12, G:0.18, T:0.44
Consensus pattern (123 bp):
CCAATTGGTTTTAGGTTAAATGCTTAACAACTTTTAATCTATAAAGATGATGCTTAAAGTTAGAG
CTTGTTTATTATTCCTGAATTCAATCGGCAAGTCCTTTGATTGTTTTGGTTTTATTTC
Found at i:90183 original size:37 final size:37
Alignment explanation
Indices: 90133--90207 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
90123 TTCAGAACAT
90133 TAATTCTCTAATTTCTGAGGTAGATTATTTTACATGA
1 TAATTCTCTAATTTCTGAGGTAGATTATTTTACATGA
90170 TAATTCTCTAATTTCTGAGGTAGATTATTTTACATGA
1 TAATTCTCTAATTTCTGAGGTAGATTATTTTACATGA
90207 T
1 T
90208 TCAGATGTGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.29, C:0.11, G:0.13, T:0.47
Consensus pattern (37 bp):
TAATTCTCTAATTTCTGAGGTAGATTATTTTACATGA
Found at i:96686 original size:2 final size:2
Alignment explanation
Indices: 96679--96707 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
96669 CTTACTTTTC
96679 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
96708 TTGCTAAGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.