Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004995.1 Hibiscus syriacus cultivar Beakdansim tig00011209_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: 87566
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:14850 original size:15 final size:15
Alignment explanation
Indices: 14830--14867 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
14820 GAAGAAGCAA
14830 TGACATCACCAGATT
1 TGACATCACCAGATT
14845 TGACATCACCAGATT
1 TGACATCACCAGATT
14860 TGACATCA
1 TGACATCA
14868 AATCACCCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.26
Consensus pattern (15 bp):
TGACATCACCAGATT
Found at i:15072 original size:21 final size:21
Alignment explanation
Indices: 15034--15074 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
15024 TTGGTTTCTT
* *
15034 TAAATAAAATGGTTTTATAAA
1 TAAATAAAATGCTATTATAAA
*
15055 TAAATAAAATTCTATTATAA
1 TAAATAAAATGCTATTATAA
15075 CATGTGTCAA
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:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (21 bp):
TAAATAAAATGCTATTATAAA
Found at i:17710 original size:31 final size:30
Alignment explanation
Indices: 17648--17715 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 30
17638 CAAAATACAT
* *
17648 AAATTTTAAAAATTATACTTTTGGTCCCTA
1 AAATTTTAAAAATTATACTTCTGCTCCCTA
* * *
17678 AAATTTTGGAAAATTATTCTTCTGCTCTCTA
1 AAATTTT-AAAAATTATACTTCTGCTCCCTA
*
17709 AATTTTT
1 AAATTTT
17716 CTAATATTTG
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
30 7 0.23
31 24 0.77
ACGTcount: A:0.32, C:0.13, G:0.07, T:0.47
Consensus pattern (30 bp):
AAATTTTAAAAATTATACTTCTGCTCCCTA
Found at i:21713 original size:29 final size:30
Alignment explanation
Indices: 21650--21761 Score: 97
Period size: 31 Copynumber: 3.7 Consensus size: 30
21640 TATTCTAAAT
21650 TTAAGATAAAAATAAAATATAGTTATTGAAG
1 TTAAGATAAAAATAAAATATAGTTATT-AAG
*
21681 TTAAGATAAAAATAATATATA--TATATATA-
1 TTAAGATAAAAATAAAATATAGTTAT-TA-AG
* * *
21710 TTAAGATAAAAATAAATTGCACA-TTTTTAAG
1 TTAAGATAAAAATAAAAT--ATAGTTATTAAG
* *
21741 TTAAAATAAGAATAAAATATA
1 TTAAGATAAAAATAAAATATA
21762 TATTTTTATG
Statistics
Matches: 66, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
29 22 0.33
30 3 0.05
31 39 0.59
32 2 0.03
ACGTcount: A:0.56, C:0.02, G:0.08, T:0.34
Consensus pattern (30 bp):
TTAAGATAAAAATAAAATATAGTTATTAAG
Found at i:21931 original size:33 final size:33
Alignment explanation
Indices: 21893--22037 Score: 100
Period size: 33 Copynumber: 4.2 Consensus size: 33
21883 AAGTTCAAAT
*
21893 AAAAATATATTTTTAAAAGTTAAGATAAGAGTA
1 AAAAATATATTTTTAAAAGTTAAGATAAGAATA
* ** * *
21926 AAAAATA-CTTTAGATTAAGTTAAAATAAGAATA
1 AAAAATATATTTTTA-AAAGTTAAGATAAGAATA
*
21959 AAATATATATATTTTT-TAAG-TAAGATAAGAATA
1 AAA-A-ATATATTTTTAAAAGTTAAGATAAGAATA
*
21992 AATATATATATATATATATTAAAA-TTAATATAAGAATA
1 AA-A-A-ATATAT-T-T-TTAAAAGTTAAGATAAGAATA
*
22030 AAATATAT
1 AAAAATAT
22038 TTAATAAGTT
Statistics
Matches: 89, Mismatches: 13, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
32 4 0.04
33 39 0.44
34 15 0.17
35 8 0.09
36 4 0.04
37 3 0.03
38 16 0.18
ACGTcount: A:0.56, C:0.01, G:0.08, T:0.36
Consensus pattern (33 bp):
AAAAATATATTTTTAAAAGTTAAGATAAGAATA
Found at i:21999 original size:34 final size:34
Alignment explanation
Indices: 21940--22037 Score: 117
Period size: 34 Copynumber: 2.8 Consensus size: 34
21930 ATACTTTAGA
21940 TTAAGTTAAAATAAGAATAAAATATATATATTTT
1 TTAAGTTAAAATAAGAATAAAATATATATATTTT
*
21974 TTAAG-TAAGATAAGAATAAATATATATATATATATAT
1 TTAAGTTAAAATAAGAATAAA-ATATATATAT-T-T-T
* * *
22011 TAAAATTAATATAAGAATAAAATATAT
1 TTAAGTTAAAATAAGAATAAAATATAT
22038 TTAATAAGTT
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
33 14 0.25
34 15 0.27
35 1 0.02
36 1 0.02
37 10 0.18
38 14 0.25
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (34 bp):
TTAAGTTAAAATAAGAATAAAATATATATATTTT
Found at i:22025 original size:38 final size:33
Alignment explanation
Indices: 21940--22037 Score: 106
Period size: 33 Copynumber: 2.8 Consensus size: 33
21930 ATACTTTAGA
*
21940 TTAAGTTAAAATAAGAATAAAATATATATATTT
1 TTAAATTAAAATAAGAATAAAATATATATATTT
* * *
21973 TTTAAGTAAGATAAGAATAAATATATATATATATAT
1 TTAAATTAAAATAAGAATAAA-ATATATATAT-T-T
*
22009 ATTAAAATTAATATAAGAATAAAATATAT
1 -TT-AAATTAAAATAAGAATAAAATATAT
22038 TTAATAAGTT
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
33 17 0.32
34 10 0.19
35 1 0.02
36 1 0.02
37 8 0.15
38 16 0.30
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (33 bp):
TTAAATTAAAATAAGAATAAAATATATATATTT
Found at i:22793 original size:32 final size:30
Alignment explanation
Indices: 22754--22817 Score: 92
Period size: 32 Copynumber: 2.1 Consensus size: 30
22744 TCGTTAAAAA
*
22754 TAGGTGCTTAATGTTTTCTCCGTTACACTTTT
1 TAGGTGCTTAATATTTT-TCCGTTACA-TTTT
*
22786 TAGGTGCTTAATATTTTTCCGTTATATTTT
1 TAGGTGCTTAATATTTTTCCGTTACATTTT
22816 TA
1 TA
22818 AATGTCTACG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 6 0.20
31 8 0.27
32 16 0.53
ACGTcount: A:0.19, C:0.14, G:0.14, T:0.53
Consensus pattern (30 bp):
TAGGTGCTTAATATTTTTCCGTTACATTTT
Found at i:25706 original size:31 final size:31
Alignment explanation
Indices: 25668--25726 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
25658 TATATATATT
25668 TAATATTTT-TCATGTTACACTTTTAGGTGTA
1 TAATATTTTAT-ATGTTACACTTTTAGGTGTA
* *
25699 TAATATTTTATATGTTATATTTTTAGGT
1 TAATATTTTATATGTTACACTTTTAGGT
25727 TTCTATACCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 24 0.96
32 1 0.04
ACGTcount: A:0.27, C:0.05, G:0.12, T:0.56
Consensus pattern (31 bp):
TAATATTTTATATGTTACACTTTTAGGTGTA
Found at i:26588 original size:17 final size:17
Alignment explanation
Indices: 26566--26598 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
26556 TTTAAATATG
26566 ATTTAAAAAGATATCAT
1 ATTTAAAAAGATATCAT
26583 ATTTAAAAAGATATCA
1 ATTTAAAAAGATATCA
26599 ACTAAACCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.33
Consensus pattern (17 bp):
ATTTAAAAAGATATCAT
Found at i:29581 original size:3 final size:3
Alignment explanation
Indices: 29575--29620 Score: 74
Period size: 3 Copynumber: 15.0 Consensus size: 3
29565 CGTCGTCGTT
*
29575 TTA TTA TTA TTT TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
29621 AAATATTTGT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:30623 original size:60 final size:60
Alignment explanation
Indices: 30550--30695 Score: 161
Period size: 60 Copynumber: 2.4 Consensus size: 60
30540 CCATTAGGGT
* * * *
30550 AAAG-TATAAAAATGGTCCCTCGACTATAGGGTACTACTTTATTAAGTCTCTCGACTATTA
1 AAAGTTAT-AAAATGGTCCCTCGACTATAGAGTACTACTTTATTAAGTCCCTCAACTATCA
* * * * *
30610 AAAGTTATAAAATGGT-CCTCCAACAATAGAGTTCTACTTTGTTGAGTCCCTCAACTATCA
1 AAAGTTATAAAATGGTCCCT-CGACTATAGAGTACTACTTTATTAAGTCCCTCAACTATCA
* *
30670 AAAGTTACAAAATGGTCACTCGACTA
1 AAAGTTATAAAATGGTCCCTCGACTA
30696 GTCATTATGT
Statistics
Matches: 70, Mismatches: 13, Indels: 6
0.79 0.15 0.07
Matches are distributed among these distances:
59 3 0.04
60 62 0.89
61 5 0.07
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (60 bp):
AAAGTTATAAAATGGTCCCTCGACTATAGAGTACTACTTTATTAAGTCCCTCAACTATCA
Found at i:30828 original size:25 final size:25
Alignment explanation
Indices: 30800--30849 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
30790 GATTCTGAAG
30800 TTAGATTTTATCATATCATATTCAA
1 TTAGATTTTATCATATCATATTCAA
30825 TTAGATTTTATCATATCATATTCAA
1 TTAGATTTTATCATATCATATTCAA
30850 CAAGTTAACG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.12, G:0.04, T:0.48
Consensus pattern (25 bp):
TTAGATTTTATCATATCATATTCAA
Found at i:34542 original size:32 final size:32
Alignment explanation
Indices: 34506--34568 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
34496 GTGATATGTG
* *
34506 TCATGTCATCC-AAAGTGATGGCATGACATATA
1 TCATGTCA-CCAAAAATGATGACATGACATATA
34538 TCATGTCACCAAAAATGATGACATGACATAT
1 TCATGTCACCAAAAATGATGACATGACATAT
34569 GCCATATCAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 2 0.07
32 26 0.93
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.27
Consensus pattern (32 bp):
TCATGTCACCAAAAATGATGACATGACATATA
Found at i:36611 original size:24 final size:24
Alignment explanation
Indices: 36584--36631 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
36574 GCATGACATG
36584 GTACATAGATGTTTTATACATCAT
1 GTACATAGATGTTTTATACATCAT
* *
36608 GTACGTAGATGTTTTATATATCAT
1 GTACATAGATGTTTTATACATCAT
36632 CAGGAAGACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (24 bp):
GTACATAGATGTTTTATACATCAT
Found at i:36994 original size:40 final size:40
Alignment explanation
Indices: 36950--37059 Score: 193
Period size: 40 Copynumber: 2.8 Consensus size: 40
36940 AGGACACTAA
*
36950 GTGTATATGGTGGGCACGACCTTATGTGTAATGCACTTCG
1 GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
* *
36990 GTGTATATGGTGGGCACGACCGTATGTGCAATACACTTCG
1 GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
37030 GTGTATATGGTGGGCACGACCTTATGTGTA
1 GTGTATATGGTGGGCACGACCTTATGTGTA
37060 GCACTACGGT
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 65 1.00
ACGTcount: A:0.21, C:0.17, G:0.31, T:0.31
Consensus pattern (40 bp):
GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
Found at i:37214 original size:44 final size:45
Alignment explanation
Indices: 37164--37250 Score: 131
Period size: 44 Copynumber: 2.0 Consensus size: 45
37154 GTAACCATGC
37164 AAATAAGCTTACAAGCTTATGGAAT-AATGGCAAGTACATTGGTA
1 AAATAAGCTTACAAGCTTATGGAATAAATGGCAAGTACATTGGTA
* * * *
37208 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGG
1 AAATAAGCTTACAAGCTTATGGAATAAATGGCAAGTACATTGG
37251 AAAGAAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
44 23 0.61
45 15 0.39
ACGTcount: A:0.39, C:0.09, G:0.23, T:0.29
Consensus pattern (45 bp):
AAATAAGCTTACAAGCTTATGGAATAAATGGCAAGTACATTGGTA
Found at i:39864 original size:9 final size:9
Alignment explanation
Indices: 39852--39913 Score: 51
Period size: 9 Copynumber: 6.9 Consensus size: 9
39842 AAAAAGAAGA
39852 AAGAAAAAG
1 AAGAAAAAG
39861 AAGAAAAAG
1 AAGAAAAAG
39870 --GAAAAAG
1 AAGAAAAAG
39877 AA-AAATAAG
1 AAGAAA-AAG
39886 AA-AAAGAAG
1 AAGAAA-AAG
*
39895 AGGAAAAAAAG
1 A--AGAAAAAG
39906 AAGAAAAA
1 AAGAAAAA
39914 ATATGAGAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
7 7 0.16
8 3 0.07
9 27 0.60
11 5 0.11
12 3 0.07
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (9 bp):
AAGAAAAAG
Found at i:39867 original size:22 final size:22
Alignment explanation
Indices: 39842--39913 Score: 94
Period size: 22 Copynumber: 3.2 Consensus size: 22
39832 TTAAAATATA
39842 AAAAAGAAGAAAGAAAAAGAAG
1 AAAAAGAAGAAAGAAAAAGAAG
*
39864 AAAAAGGAA-AAAGAAAAATAAG
1 AAAAA-GAAGAAAGAAAAAGAAG
39886 AAAAAGAAGAGGAA-AAAAAGAAG
1 AAAAAGAAGA--AAGAAAAAGAAG
39909 AAAAA
1 AAAAA
39914 ATATGAGAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
21 3 0.07
22 23 0.52
23 16 0.36
24 2 0.05
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.01
Consensus pattern (22 bp):
AAAAAGAAGAAAGAAAAAGAAG
Found at i:39906 original size:11 final size:11
Alignment explanation
Indices: 39841--39914 Score: 69
Period size: 12 Copynumber: 6.5 Consensus size: 11
39831 CTTAAAATAT
39841 AAAAAAGAAGAA
1 AAAAAAGAAG-A
39853 AGAAAAAGAAG-
1 A-AAAAAGAAGA
* *
39864 AAAAAGGAAAA
1 AAAAAAGAAGA
*
39875 AGAAAAATAAGA
1 A-AAAAAGAAGA
*
39887 AAAAGAAGAGGA
1 AAAA-AAGAAGA
39899 AAAAAAGAAGA
1 AAAAAAGAAGA
39910 AAAAA
1 AAAAA
39915 TATGAGAAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
10 7 0.14
11 16 0.32
12 18 0.36
13 9 0.18
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.01
Consensus pattern (11 bp):
AAAAAAGAAGA
Found at i:44729 original size:54 final size:54
Alignment explanation
Indices: 44309--44722 Score: 528
Period size: 54 Copynumber: 7.7 Consensus size: 54
44299 CCAAAATTGA
* * * *
44309 AATTCATAAACTTATTATGAATTCCATGGATTGCACACATAGTGCCGATATGGT
1 AATTCACAAACTCATTATGAATTCCGTGGGTTGCACACATAGTGCCGATATGGT
* * *
44363 AATTCACAAACTCATTATGAATTCCGTGGGTTGCACAGATAGTGCCAATAAGGT
1 AATTCACAAACTCATTATGAATTCCGTGGGTTGCACACATAGTGCCGATATGGT
*
44417 AATTCACAAACTCATTATGAATTCCGTAGGTTGCACACATAGTGCCGATATGGT
1 AATTCACAAACTCATTATGAATTCCGTGGGTTGCACACATAGTGCCGATATGGT
* * * *
44471 AATTCACAAATTCATTATGAATACCGTGGGTTGCACACATAATGTCGATA-GGT
1 AATTCACAAACTCATTATGAATTCCGTGGGTTGCACACATAGTGCCGATATGGT
*
44524 AATTCA-ATAACTCATTATGAATGT-CGTGGGTTTCACACATAGTGCCGATATGGT
1 AATTCACA-AACTCATTATGAAT-TCCGTGGGTTGCACACATAGTGCCGATATGGT
** * * * *
44578 AATTCACAAACTCATTATGAATTATGTGGGTTGTACACACAGTACCGATATGAT
1 AATTCACAAACTCATTATGAATTCCGTGGGTTGCACACATAGTGCCGATATGGT
* ** * * *
44632 AATTCACAAACACATTATGAATAACATGAGTTACACACATAGTGCCGATATGGT
1 AATTCACAAACTCATTATGAATTCCGTGGGTTGCACACATAGTGCCGATATGGT
* ** *
44686 AATTTACAAACTCATTATGAATTTTGTGAGTTGCACA
1 AATTCACAAACTCATTATGAATTCCGTGGGTTGCACA
44723 ATTAGTGTTG
Statistics
Matches: 311, Mismatches: 44, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
52 1 0.00
53 46 0.15
54 263 0.85
55 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (54 bp):
AATTCACAAACTCATTATGAATTCCGTGGGTTGCACACATAGTGCCGATATGGT
Found at i:45094 original size:20 final size:23
Alignment explanation
Indices: 45056--45110 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 23
45046 TTCAGACTGA
45056 ATAGTATCGATA-TCCCTC-T-T
1 ATAGTATCGATACTCCCTCTTCT
*
45076 ATAGTATCGATACT-TCTCTTCT
1 ATAGTATCGATACTCCCTCTTCT
*
45098 ATGGTATCGATAC
1 ATAGTATCGATAC
45111 CCACTTCGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 15 0.50
21 2 0.07
22 13 0.43
ACGTcount: A:0.25, C:0.22, G:0.13, T:0.40
Consensus pattern (23 bp):
ATAGTATCGATACTCCCTCTTCT
Found at i:51185 original size:54 final size:54
Alignment explanation
Indices: 51127--51439 Score: 383
Period size: 54 Copynumber: 5.8 Consensus size: 54
51117 GGAAATTAAT
* * * *
51127 AAACTTATTATGAATTCCATGGATTGCACACATAGTGCCGATATGGTAATTCAC
1 AAACTCATTATGAATTCCGTGGGTTGCACACATAGTGCCGATACGGTAATTCAC
* ** ** * *
51181 AAACTCGTTATGAATGACGTGGGTTGCTTACATAGTGCCGATACAGTAATTCAA
1 AAACTCATTATGAATTCCGTGGGTTGCACACATAGTGCCGATACGGTAATTCAC
* * *
51235 AAACTCATTATGAATACCGTGGGTTGAACACATAGTGTCGATACGGTAATTCAC
1 AAACTCATTATGAATTCCGTGGGTTGCACACATAGTGCCGATACGGTAATTCAC
* * *
51289 AAATTCATTATGAATTCTGTGGGTTGCACACATAGTGTCGATACGGTAATTCAC
1 AAACTCATTATGAATTCCGTGGGTTGCACACATAGTGCCGATACGGTAATTCAC
* ** * * *
51343 AAACTCATTATAAATGACGTGGGTTGCACACATAGTGCCAATACGATAATTCAA
1 AAACTCATTATGAATTCCGTGGGTTGCACACATAGTGCCGATACGGTAATTCAC
* * * *
51397 AAACTCATTATGAATTCTGTGAGTTGCACACTTAGTGTCGATA
1 AAACTCATTATGAATTCCGTGGGTTGCACACATAGTGCCGATA
51440 GTACATATAG
Statistics
Matches: 218, Mismatches: 41, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 218 1.00
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (54 bp):
AAACTCATTATGAATTCCGTGGGTTGCACACATAGTGCCGATACGGTAATTCAC
Found at i:51400 original size:162 final size:162
Alignment explanation
Indices: 51133--51439 Score: 463
Period size: 162 Copynumber: 1.9 Consensus size: 162
51123 TAATAAACTT
* * *
51133 ATTATGAATTCCATGGATTGCACACATAGTGCCGATATGGTAATTCACAAACTCGTTATGAATGA
1 ATTATGAATTCCATGGATTGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATAAATGA
** * *
51198 CGTGGGTTGCTTACATAGTGCCGATACAGTAATTCAAAAACTCATTATGAATACCGTGGGTTGAA
66 CGTGGGTTGCACACATAGTGCCAATACAGTAATTCAAAAACTCATTATGAATACCGTGAGTTGAA
51263 CACATAGTGTCGATACGGTAATTCACAAATTC
131 CACATAGTGTCGATACGGTAATTCACAAATTC
** * *
51295 ATTATGAATTCTGTGGGTTGCACACATAGTGTCGATACGGTAATTCACAAACTCATTATAAATGA
1 ATTATGAATTCCATGGATTGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATAAATGA
* * *
51360 CGTGGGTTGCACACATAGTGCCAATAC-GATAATTCAAAAACTCATTATGAATTCTGTGAGTTGC
66 CGTGGGTTGCACACATAGTGCCAATACAG-TAATTCAAAAACTCATTATGAATACCGTGAGTTGA
*
51424 ACACTTAGTGTCGATA
130 ACACATAGTGTCGATA
51440 GTACATATAG
Statistics
Matches: 129, Mismatches: 15, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
161 1 0.01
162 128 0.99
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.30
Consensus pattern (162 bp):
ATTATGAATTCCATGGATTGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATAAATGA
CGTGGGTTGCACACATAGTGCCAATACAGTAATTCAAAAACTCATTATGAATACCGTGAGTTGAA
CACATAGTGTCGATACGGTAATTCACAAATTC
Found at i:52738 original size:28 final size:28
Alignment explanation
Indices: 52697--52753 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
52687 TTTCACTATA
*
52697 ATCACTAACTCGATGTTTGGGGTATTAC
1 ATCACTAACCCGATGTTTGGGGTATTAC
*
52725 ATCACTGACCCGATGTTTGGGGTATTAC
1 ATCACTAACCCGATGTTTGGGGTATTAC
52753 A
1 A
52754 ATTTTCCCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (28 bp):
ATCACTAACCCGATGTTTGGGGTATTAC
Found at i:64861 original size:19 final size:22
Alignment explanation
Indices: 64837--64884 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
64827 GCATTTTTTA
64837 ATTATTT-TA-ATT-TTTAATT
1 ATTATTTATATATTATTTAATT
64856 ATTATTTATATTATTATTTAATT
1 ATTATTTATA-TATTATTTAATT
64879 ATTATT
1 ATTATT
64885 ATTCAACTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.28
20 2 0.08
22 3 0.12
23 13 0.52
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
ATTATTTATATATTATTTAATT
Found at i:64863 original size:11 final size:11
Alignment explanation
Indices: 64849--64884 Score: 63
Period size: 11 Copynumber: 3.2 Consensus size: 11
64839 TATTTTAATT
64849 TTTAATTATTA
1 TTTAATTATTA
64860 TTTATATTATTA
1 TTTA-ATTATTA
64872 TTTAATTATTA
1 TTTAATTATTA
64883 TT
1 TT
64885 ATTCAACTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 13 0.54
12 11 0.46
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTAATTATTA
Found at i:68014 original size:451 final size:451
Alignment explanation
Indices: 67172--68021 Score: 1416
Period size: 451 Copynumber: 1.9 Consensus size: 451
67162 ATATATGACA
** *
67172 ATTGTTGGGTTATGGGGTCCAACGATCACCCTTAGGGATTCTATCGTGTATGGGCGCGATATCGG
1 ATTGTTGGGTTATGGGGTCCAACGATCACCCTTAGAAATTCTATCGTGTATGGGCGCGATATCAG
* * * * * * *
67237 TGCGTGACTGCCCAACCTACCGAGGCCCACATGTGCCTTGCGAAGCTCTTAGGCCTGTCCGCAGC
66 TGCATGACTGCCCAACATACCGAGGCCCACATGTGACTTACGAAGCTCATAGGCCTGCCCGCAAC
* * *
67302 AAGCTATAGATGCGGGGCTCTGCAATGTCGTGGTGAACTGTGGGGGGTGCCCCACAAGAATCCAC
131 AAGCTATAGATGCAGGGCTCTACAATGCCGTGGTGAACTGTGGGGGGTGCCCCACAAGAATCCAC
*
67367 CTTGGCTTGAGGGAACCCAGTGATCACCCACTACAAAGATATGAGGTTAAAATGGCACACCTACT
196 CTTGGCTTGAAGGAACCCAGTGATCACCCACTACAAAGATATGAGGTTAAAATGGCACACCTACT
* *
67432 TATCACCAATTGGTTTTAAGAAGAAATGGTGACCATTCGCTTCAGAACTCTGTGGTTAAGCGTGC
261 TATCACCAATTGATTTTAAGAAGAAATGATGACCATTCGCTTCAGAACTCTGTGGTTAAGCGTGC
*
67497 TTGGACTAGGGAAATCCAAGGATGGGTGACCCACTGGAAAGTTGTTCAGAAATGAATGACTCGAT
326 TTGGACTAGGGAAATCCAAGGATGGGTGACCCACTGGAAAGTTGTTCAAAAATGAATGACTCGAT
67562 CCTAACAACTGGTATCAGAGTAGGTTGCATGTTCGAATCCCCCAAGTGTCGTTGGGGGGTG
391 CCTAACAACTGGTATCAGAGTAGGTTGCATGTTCGAATCCCCCAAGTGTCGTTGGGGGGTG
*
67623 ATTGTTGGGTTATGGGGTCCAGCGATCACCCTTAGAAATTCTATCGTGTATGGGCGCGATATCAG
1 ATTGTTGGGTTATGGGGTCCAACGATCACCCTTAGAAATTCTATCGTGTATGGGCGCGATATCAG
* * *
67688 TGCATGATTGCCCAACATGCCGAGGCCCACGTGTGACTTACGAAGCTCATAGGCCTGCCCGCAAC
66 TGCATGACTGCCCAACATACCGAGGCCCACATGTGACTTACGAAGCTCATAGGCCTGCCCGCAAC
*
67753 ACA-CTATAGATGCAGGGCTCTACAATGCCGTGGTGAATTGTGGGGGGTGCCCCACAAGAATCCA
131 A-AGCTATAGATGCAGGGCTCTACAATGCCGTGGTGAACTGTGGGGGGTGCCCCACAAGAATCCA
*
67817 CCTTGGCTTGAAGGAACCCAGTGATCACCCACTACAAAGGTATGAGGTTAAAATGGTC-CACCTA
195 CCTTGGCTTGAAGGAACCCAGTGATCACCCACTACAAAGATATGAGGTTAAAATGG-CACACCTA
* ** *
67881 CTTATCACCAATTGATTTTAAGAAGGAATGATGATTATTCGCTTCAGAACTTTGTGGTTAAGCGT
259 CTTATCACCAATTGATTTTAAGAAGAAATGATGACCATTCGCTTCAGAACTCTGTGGTTAAGCGT
*
67946 GCTTGGACTAGGGAAATCCAAGGATGGGTGACCCACTGGGAAGTTGTTCAAAAATGAATGACTCG
324 GCTTGGACTAGGGAAATCCAAGGATGGGTGACCCACTGGAAAGTTGTTCAAAAATGAATGACTCG
68011 ATCCTAACAAC
389 ATCCTAACAAC
68022 AATTTTTAAA
Statistics
Matches: 369, Mismatches: 28, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
451 367 0.99
452 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (451 bp):
ATTGTTGGGTTATGGGGTCCAACGATCACCCTTAGAAATTCTATCGTGTATGGGCGCGATATCAG
TGCATGACTGCCCAACATACCGAGGCCCACATGTGACTTACGAAGCTCATAGGCCTGCCCGCAAC
AAGCTATAGATGCAGGGCTCTACAATGCCGTGGTGAACTGTGGGGGGTGCCCCACAAGAATCCAC
CTTGGCTTGAAGGAACCCAGTGATCACCCACTACAAAGATATGAGGTTAAAATGGCACACCTACT
TATCACCAATTGATTTTAAGAAGAAATGATGACCATTCGCTTCAGAACTCTGTGGTTAAGCGTGC
TTGGACTAGGGAAATCCAAGGATGGGTGACCCACTGGAAAGTTGTTCAAAAATGAATGACTCGAT
CCTAACAACTGGTATCAGAGTAGGTTGCATGTTCGAATCCCCCAAGTGTCGTTGGGGGGTG
Found at i:79753 original size:21 final size:19
Alignment explanation
Indices: 79715--79761 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
79705 AATTAATCCT
79715 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
79735 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
79756 A-TAATA
1 ACTAATA
79762 ATTCAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.24
20 10 0.40
21 9 0.36
ACGTcount: A:0.51, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Done.