Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003054.1 Hibiscus syriacus cultivar Beakdansim tig00006366_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: 58722
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1698 original size:31 final size:32
Alignment explanation
Indices: 1663--1731 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 32
1653 GGACTTTTTG
* * *
1663 TTAATATTTTGTTATTTTTGT-TTA-TTACCA
1 TTAATATATAGTTATTTTTATATTATTTACCA
1693 TTTAATATATAGTTATTTTTATATTATTTACCA
1 -TTAATATATAGTTATTTTTATATTATTTACCA
1726 TTAATA
1 TTAATA
1732 CTTATTATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 18 0.55
32 9 0.27
33 6 0.18
ACGTcount: A:0.30, C:0.06, G:0.04, T:0.59
Consensus pattern (32 bp):
TTAATATATAGTTATTTTTATATTATTTACCA
Found at i:4966 original size:24 final size:22
Alignment explanation
Indices: 4939--4987 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
4929 ATTAAAATAT
4939 AACACAATAAAATTTTTACACATA
1 AACACAA-AAAA-TTTTACACATA
* *
4963 AACATAAATAATTTTACACATA
1 AACACAAAAAATTTTACACATA
4985 AAC
1 AAC
4988 GTAAATAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 14 0.61
23 3 0.13
24 6 0.26
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (22 bp):
AACACAAAAAATTTTACACATA
Found at i:4980 original size:22 final size:22
Alignment explanation
Indices: 4952--4998 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
4942 ACAATAAAAT
4952 TTTTACACATAAACATAAATAA
1 TTTTACACATAAACATAAATAA
*
4974 TTTTACACATAAACGTAAATAA
1 TTTTACACATAAACATAAATAA
4996 TTT
1 TTT
4999 AAATAATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (22 bp):
TTTTACACATAAACATAAATAA
Found at i:5268 original size:21 final size:22
Alignment explanation
Indices: 5244--5288 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
5234 TTATTGTAGT
5244 AGTTGAGAGA-AGTTGAGAGGG
1 AGTTGAGAGAGAGTTGAGAGGG
* * *
5265 AGTTGTGAGAGAGTTTAGGGGG
1 AGTTGAGAGAGAGTTGAGAGGG
5287 AG
1 AG
5289 AGGGGTATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.29, C:0.00, G:0.49, T:0.22
Consensus pattern (22 bp):
AGTTGAGAGAGAGTTGAGAGGG
Found at i:6099 original size:28 final size:29
Alignment explanation
Indices: 6050--6110 Score: 106
Period size: 28 Copynumber: 2.1 Consensus size: 29
6040 AAGAAGTAAT
6050 TTTTACTTTTTTAATAAAAAAATGAATAA
1 TTTTACTTTTTTAATAAAAAAATGAATAA
*
6079 TTTTACTTTTTTAAT-ATAAAATGAATAA
1 TTTTACTTTTTTAATAAAAAAATGAATAA
6107 TTTT
1 TTTT
6111 TACTGGAAGC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 16 0.52
29 15 0.48
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (29 bp):
TTTTACTTTTTTAATAAAAAAATGAATAA
Found at i:6111 original size:29 final size:30
Alignment explanation
Indices: 6046--6114 Score: 115
Period size: 29 Copynumber: 2.4 Consensus size: 30
6036 TTTAAAGAAG
6046 TAATTTTTACTTTTTTAATAAAAAAATGAA
1 TAATTTTTACTTTTTTAATAAAAAAATGAA
*
6076 TAA-TTTTACTTTTTTAAT-ATAAAATGAA
1 TAATTTTTACTTTTTTAATAAAAAAATGAA
6104 TAATTTTTACT
1 TAATTTTTACT
6115 GGAAGCGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
28 12 0.32
29 22 0.59
30 3 0.08
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.51
Consensus pattern (30 bp):
TAATTTTTACTTTTTTAATAAAAAAATGAA
Found at i:17374 original size:18 final size:19
Alignment explanation
Indices: 17351--17386 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
17341 CAAATTATTC
17351 AAATATT-TTAAAAAATAT
1 AAATATTATTAAAAAATAT
17369 AAATATTATTAAAAAATA
1 AAATATTATTAAAAAATA
17387 AATTACTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AAATATTATTAAAAAATAT
Found at i:17817 original size:14 final size:13
Alignment explanation
Indices: 17808--17844 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
17798 TATTTATAAT
17808 ATATTTTTTAAAA
1 ATATTTTTTAAAA
*
17821 ATAATTTTTAAAA
1 ATATTTTTTAAAA
17834 ATATTTTTTAA
1 ATATTTTTTAA
17845 TAGTTTATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATATTTTTTAAAA
Found at i:17967 original size:15 final size:15
Alignment explanation
Indices: 17926--18006 Score: 78
Period size: 15 Copynumber: 5.3 Consensus size: 15
17916 TTAATATGTG
17926 TATTTAA-ATTTTTAA
1 TATTTAATATTTTT-A
17941 TAATTT-AT-TTTTTA
1 T-ATTTAATATTTTTA
*
17955 TATTTAGTATTTTTA
1 TATTTAATATTTTTA
*
17970 TATTTAATATTTTGAA
1 TATTTAATATTTT-TA
*
17986 TATTTGAATAATTTTA
1 TATTT-AATATTTTTA
18002 TATTT
1 TATTT
18007 TATAATTCAA
Statistics
Matches: 55, Mismatches: 5, Indels: 11
0.77 0.07 0.15
Matches are distributed among these distances:
13 4 0.07
14 3 0.05
15 25 0.45
16 16 0.29
17 7 0.13
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (15 bp):
TATTTAATATTTTTA
Found at i:18013 original size:15 final size:15
Alignment explanation
Indices: 17950--18013 Score: 67
Period size: 15 Copynumber: 4.1 Consensus size: 15
17940 ATAATTTATT
* *
17950 TTTTATATTTAGTAT
1 TTTTATATTTAATAA
17965 TTTTATATTTAAT-A
1 TTTTATATTTAATAA
17979 TTTTGAATATTTGAATAA
1 TTTT--ATATTT-AATAA
*
17997 TTTTATATTTTATAA
1 TTTTATATTTAATAA
18012 TT
1 TT
18014 CAAAATAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
14 4 0.10
15 18 0.43
16 12 0.29
17 3 0.07
18 5 0.12
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (15 bp):
TTTTATATTTAATAA
Found at i:21023 original size:15 final size:15
Alignment explanation
Indices: 21005--21036 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
20995 CCCTTTTTCA
21005 TTTTGACCACTACTT
1 TTTTGACCACTACTT
*
21020 TTTTTACCACTACTT
1 TTTTGACCACTACTT
21035 TT
1 TT
21037 GAAATTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.25, G:0.03, T:0.53
Consensus pattern (15 bp):
TTTTGACCACTACTT
Found at i:24763 original size:13 final size:13
Alignment explanation
Indices: 24740--24832 Score: 98
Period size: 13 Copynumber: 7.2 Consensus size: 13
24730 TAGGGTAATA
*
24740 TTTTGTTGTCTTC
1 TTTTCTTGTCTTC
* *
24753 TTATCTTGTCTTT
1 TTTTCTTGTCTTC
*
24766 TTTTCTTATCTTC
1 TTTTCTTGTCTTC
*
24779 TTTTGTTGTCTTC
1 TTTTCTTGTCTTC
* *
24792 TTATCTTGT-TTT
1 TTTTCTTGTCTTC
*
24804 TTTTCTTATCTTC
1 TTTTCTTGTCTTC
*
24817 TTTTGTTGTCTTC
1 TTTTCTTGTCTTC
24830 TTT
1 TTT
24833 CTAATAGTGA
Statistics
Matches: 63, Mismatches: 16, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
12 9 0.14
13 54 0.86
ACGTcount: A:0.04, C:0.16, G:0.09, T:0.71
Consensus pattern (13 bp):
TTTTCTTGTCTTC
Found at i:24814 original size:38 final size:39
Alignment explanation
Indices: 24740--24831 Score: 177
Period size: 38 Copynumber: 2.4 Consensus size: 39
24730 TAGGGTAATA
24740 TTTTGTTGTCTTCTTATCTTGTCTTTTTTTCTTATCTTC
1 TTTTGTTGTCTTCTTATCTTGTCTTTTTTTCTTATCTTC
24779 TTTTGTTGTCTTCTTATCTTGT-TTTTTTTCTTATCTTC
1 TTTTGTTGTCTTCTTATCTTGTCTTTTTTTCTTATCTTC
24817 TTTTGTTGTCTTCTT
1 TTTTGTTGTCTTCTT
24832 TCTAATAGTG
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
38 31 0.58
39 22 0.42
ACGTcount: A:0.04, C:0.16, G:0.09, T:0.71
Consensus pattern (39 bp):
TTTTGTTGTCTTCTTATCTTGTCTTTTTTTCTTATCTTC
Found at i:24825 original size:25 final size:25
Alignment explanation
Indices: 24745--24834 Score: 72
Period size: 25 Copynumber: 3.5 Consensus size: 25
24735 TAATATTTTG
* * *
24745 TTGTCTTCTTATCTTGTCTTTTTTTC
1 TTGTCTTCTT-TCTTATCTTCTTATC
* * *
24771 TTATCTTCTTTTGTTGTCTTCTTATC
1 TTGTCTTC-TTTCTTATCTTCTTATC
* * * *
24797 TTGTTTTTTTTCTTATCTTCTTTTG
1 TTGTCTTCTTTCTTATCTTCTTATC
24822 TTGTCTTCTTTCT
1 TTGTCTTCTTTCT
24835 AATAGTGATT
Statistics
Matches: 50, Mismatches: 13, Indels: 3
0.76 0.20 0.05
Matches are distributed among these distances:
25 24 0.48
26 24 0.48
27 2 0.04
ACGTcount: A:0.04, C:0.18, G:0.08, T:0.70
Consensus pattern (25 bp):
TTGTCTTCTTTCTTATCTTCTTATC
Found at i:30540 original size:45 final size:45
Alignment explanation
Indices: 30491--30576 Score: 154
Period size: 45 Copynumber: 1.9 Consensus size: 45
30481 ACATCAAATA
* *
30491 CATTTTATGCATCGATGCACATACCATGCATCGATGCACTCAGTG
1 CATTTGATGCATCGATGCACAAACCATGCATCGATGCACTCAGTG
30536 CATTTGATGCATCGATGCACAAACCATGCATCGATGCACTC
1 CATTTGATGCATCGATGCACAAACCATGCATCGATGCACTC
30577 TGGCTATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (45 bp):
CATTTGATGCATCGATGCACAAACCATGCATCGATGCACTCAGTG
Found at i:36447 original size:21 final size:22
Alignment explanation
Indices: 36400--36452 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 22
36390 ACATCTAACA
* * *
36400 GTGCATCGATGCATCCTTGAAT
1 GTGCATCGATACATCCATGAAG
*
36422 ATGCATCGATACA-CCATGAAG
1 GTGCATCGATACATCCATGAAG
*
36443 GTGCACCGAT
1 GTGCATCGAT
36453 GCACGCCTTG
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.25
Consensus pattern (22 bp):
GTGCATCGATACATCCATGAAG
Found at i:36469 original size:23 final size:23
Alignment explanation
Indices: 36400--36480 Score: 78
Period size: 23 Copynumber: 3.7 Consensus size: 23
36390 ACATCTAACA
*
36400 GTGCATCGATGCA-TCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
* * *
36422 ATGCATCGAT--ACACCATGAAG
1 GTGCATCGATGCACACCTTGAAT
* *
36443 GTGCACCGATGCACGCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
*
36466 GTGCATCTATGCACA
1 GTGCATCGATGCACA
36481 AGGCCATGCA
Statistics
Matches: 44, Mismatches: 12, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
20 1 0.02
21 14 0.32
22 9 0.20
23 20 0.45
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (23 bp):
GTGCATCGATGCACACCTTGAAT
Found at i:39200 original size:26 final size:26
Alignment explanation
Indices: 39167--39232 Score: 132
Period size: 26 Copynumber: 2.5 Consensus size: 26
39157 TGCATATACC
39167 ATGCATCGATGCACTCAGTGCATTTG
1 ATGCATCGATGCACTCAGTGCATTTG
39193 ATGCATCGATGCACTCAGTGCATTTG
1 ATGCATCGATGCACTCAGTGCATTTG
39219 ATGCATCGATGCAC
1 ATGCATCGATGCAC
39233 AAACCATGCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (26 bp):
ATGCATCGATGCACTCAGTGCATTTG
Found at i:42596 original size:29 final size:30
Alignment explanation
Indices: 42556--42685 Score: 124
Period size: 29 Copynumber: 4.2 Consensus size: 30
42546 TAATAAGGTT
42556 ATTTATTTTAAAATAA-TTATTTTAAAATA
1 ATTTATTTTAAAATAATTTATTTTAAAATA
* *
42585 ATTTATTAT-AAATAATTTATTATAAAA-A
1 ATTTATTTTAAAATAATTTATTTTAAAATA
* * *
42613 AATTATTTTAAAATAAATTATTATAAAATATGGA
1 ATTTATTTTAAAATAATTTATT-TTAAA-AT--A
42647 TTGATTTATTTTAAAATAATTTATTTT-AAATA
1 ---ATTTATTTTAAAATAATTTATTTTAAAATA
42679 ATTTATT
1 ATTTATT
42686 AGTATGTATT
Statistics
Matches: 81, Mismatches: 10, Indels: 20
0.73 0.09 0.18
Matches are distributed among these distances:
28 14 0.17
29 36 0.44
30 3 0.04
31 1 0.01
32 1 0.01
34 3 0.04
35 2 0.02
36 1 0.01
37 20 0.25
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (30 bp):
ATTTATTTTAAAATAATTTATTTTAAAATA
Found at i:42611 original size:43 final size:43
Alignment explanation
Indices: 42556--42639 Score: 141
Period size: 43 Copynumber: 2.0 Consensus size: 43
42546 TAATAAGGTT
* * *
42556 ATTTATTTTAAAATAATTATTTTAAAATAATTTATTATAAATA
1 ATTTATTATAAAAAAATTATTTTAAAATAAATTATTATAAATA
42599 ATTTATTATAAAAAAATTATTTTAAAATAAATTATTATAAA
1 ATTTATTATAAAAAAATTATTTTAAAATAAATTATTATAAA
42640 ATATGGATTG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (43 bp):
ATTTATTATAAAAAAATTATTTTAAAATAAATTATTATAAATA
Found at i:42661 original size:22 final size:22
Alignment explanation
Indices: 42630--42730 Score: 76
Period size: 22 Copynumber: 4.5 Consensus size: 22
42620 TTAAAATAAA
*
42630 TTATTATAAAATATGGATTGAT
1 TTATTTTAAAATATGGATTGAT
** * *
42652 TTATTTTAAAATAATTTATTTTAA
1 TTATTTTAAAAT-ATGGA-TTGAT
* * * * *
42676 ATAATTTATTAGTATGTATTGAT
1 TTATTTTA-AAATATGGATTGAT
*
42699 TTATTTTTAAATATGGATTGAT
1 TTATTTTAAAATATGGATTGAT
42721 TTATTTTAAA
1 TTATTTTAAA
42731 TAATTTATTA
Statistics
Matches: 57, Mismatches: 19, Indels: 6
0.70 0.23 0.07
Matches are distributed among these distances:
22 31 0.54
23 11 0.19
24 13 0.23
25 2 0.04
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (22 bp):
TTATTTTAAAATATGGATTGAT
Found at i:42679 original size:14 final size:15
Alignment explanation
Indices: 42556--42685 Score: 124
Period size: 14 Copynumber: 8.5 Consensus size: 15
42546 TAATAAGGTT
42556 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
42571 A-TTATTTTAAAATA
1 ATTTATTTTAAAATA
*
42585 ATTTATTAT-AAATA
1 ATTTATTTTAAAATA
*
42599 ATTTATTATAAAA-A
1 ATTTATTTTAAAATA
*
42613 AATTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
42628 AATTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
42647 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
42665 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
42679 ATTTATT
1 ATTTATT
42686 AGTATGTATT
Statistics
Matches: 99, Mismatches: 6, Indels: 21
0.79 0.05 0.17
Matches are distributed among these distances:
14 52 0.53
15 27 0.27
16 4 0.04
17 2 0.02
18 1 0.01
19 1 0.01
20 2 0.02
21 4 0.04
22 6 0.06
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:42730 original size:54 final size:54
Alignment explanation
Indices: 42665--43289 Score: 353
Period size: 54 Copynumber: 11.4 Consensus size: 54
42655 TTTTAAAATA
* *
42665 ATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTTAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
42719 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
42773 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATCGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* *
42827 ATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTT-AAATA---ATTT
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * * * * **
42871 A-TTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTTT-AAATAATTTATTAG
1 ATTTATTTTA-AATAATTTA--TT--AGTATGGATTGATTTATTTTAAAAT-ATGGATT-G
** * * * **
42930 TATGAATTGCTT---TATTTTA-AAATATGGATTGATTTATTTT-AAATAATTTATTAG
1 -ATTTATT--TTAAATAATTTATTAGTATGGATTGATTTATTTTAAAAT-ATGGATT-G
** * ** * * * ***
42984 TATGGA-TTGATTTATTTTA-AAATATGGATTGATTTATTATTGTAGTTGTATGGATTG
1 -ATTTATTTTAAATAATTTATTAGTATGGATTGATTTA-T-TT-TA-AAATATGGATTG
* **
43041 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT-AAATAATTTATTAG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAAT-ATGGATT-G
** * ** * * * ** * *
43096 TATGGA-TTGATTTATTTTA-AAATATGGATTGATTTATTATTGTAGT-TGTATATG
1 -ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATT-TTAAAATATGGAT-TG
**
43150 ATTTATTTTAAATAATTTATTAGTATATATTGATTTATTTTAAATAATTTATTAGTATGTATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AA-AA--TA-T-G---G-ATTG
*
43214 ATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
43268 ATTTATTTTAAATAATTTATTA
1 ATTTATTTTAAATAATTTATTA
43290 TTATAGTTGT
Statistics
Matches: 452, Mismatches: 69, Indels: 100
0.73 0.11 0.16
Matches are distributed among these distances:
43 3 0.01
44 4 0.01
45 1 0.00
47 5 0.01
48 23 0.05
49 2 0.00
50 5 0.01
51 3 0.01
52 2 0.00
53 5 0.01
54 257 0.57
55 32 0.07
56 13 0.03
57 12 0.03
58 24 0.05
59 7 0.02
60 4 0.01
61 3 0.01
62 2 0.00
63 3 0.01
64 40 0.09
65 2 0.00
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
Found at i:42748 original size:32 final size:32
Alignment explanation
Indices: 42710--42816 Score: 144
Period size: 32 Copynumber: 3.7 Consensus size: 32
42700 TATTTTTAAA
42710 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
42742 TATGGATTGATTTA-TTT---TAA---A--A-
1 TATGGATTGATTTATTTTAAATAATTTATTAG
42764 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
42796 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
42817 ATATCGATTG
Statistics
Matches: 65, Mismatches: 0, Indels: 20
0.76 0.00 0.24
Matches are distributed among these distances:
22 14 0.22
23 4 0.06
25 1 0.02
26 3 0.05
28 3 0.05
29 1 0.02
31 4 0.06
32 35 0.54
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (32 bp):
TATGGATTGATTTATTTTAAATAATTTATTAG
Found at i:42767 original size:22 final size:22
Alignment explanation
Indices: 42742--42784 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
42732 AATTTATTAG
42742 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
42764 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
42785 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:42848 original size:134 final size:137
Alignment explanation
Indices: 42710--43084 Score: 520
Period size: 134 Copynumber: 2.8 Consensus size: 137
42700 TATTTTTAAA
*
42710 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGAT
*
42775 TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATCGATTGATTTA-TT-AT-T
66 TTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATCGATTGATTTATTTAATAT
42837 GTAGTT-G
131 GTA-TTAG
42844 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGAT
* *
42909 TTATTTTAAATAATTTATTAGTATGAATTGCTTTATTTTAAAATATGGATTGATTTATTTTAAAT
66 TTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATCGATTGATTTA-TTT-AAT
*
42974 AATTTATTAG
129 -ATGTATTAG
* * * * ***
42984 TATGGATTGATTTATTTT-AA-AA--TA-T-GGATTGATTTA-TTATTGTAGTTGTATGGATTGA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTA-AAATATGGATTGA
43042 TTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAA
65 TTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAA
43085 TAATTTATTA
Statistics
Matches: 220, Mismatches: 13, Indels: 16
0.88 0.05 0.06
Matches are distributed among these distances:
133 7 0.03
134 178 0.81
135 1 0.00
136 4 0.02
138 4 0.02
139 4 0.02
140 22 0.10
ACGTcount: A:0.34, C:0.01, G:0.13, T:0.52
Consensus pattern (137 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGAT
TTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATCGATTGATTTATTTAATAT
GTATTAG
Found at i:42859 original size:188 final size:186
Alignment explanation
Indices: 42665--43289 Score: 838
Period size: 188 Copynumber: 3.4 Consensus size: 186
42655 TTTTAAAATA
*
42665 ATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTTAAATATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATG-ATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
42730 ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
65 ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
42795 GTATGGATTGATTTATTTTAAAATATCGATTGATTTATTATTGTAGTTGTATGGATTG
130 GTATGGATTGATTTATTTTAAAATAT-GATTGATTTATTATTGTAGTTGTATGGATTG
42853 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTAT-GATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
* *
42918 ATAATTTATTAGTATGAATTGCTTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
65 ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
42983 GTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTG
130 GTATGGATTGATTTATTTTAAAATAT-GATTGATTTATTATTGTAGTTGTATGGATTG
** **
43041 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT-AAATAATTTATTAGTATGGA-TT
1 ATTTATTTTAAATAATTTATTAGTATG-ATTGATTTATTTTAAAAT-ATGGATT-G-ATTTATTT
* ** * * * ** * *
43104 GATTTATTTTA-AAATATGGATTGATTTATTATTGTAGT-TGTATATGATTTATTTTAAATAATT
62 TAAATAATTTATTAGTATGGATTGATTTATT-TTAAAATATGGAT-TGATTTATTTTAAATAATT
**
43167 TATTAGTATATATTGATTTATTTT--AA-AT-A---ATTTATTA--GTA--TG--T--ATTG
125 TATTAGTATGGATTGATTTATTTTAAAATATGATTGATTTATTATTGTAGTTGTATGGATTG
*
43214 ATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTAT-GATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
43279 ATAATTTATTA
65 ATAATTTATTA
43290 TTATAGTTGT
Statistics
Matches: 394, Mismatches: 32, Indels: 37
0.85 0.07 0.08
Matches are distributed among these distances:
171 3 0.01
172 10 0.03
173 48 0.12
174 5 0.01
175 1 0.00
177 2 0.01
179 3 0.01
181 8 0.02
184 1 0.00
186 2 0.01
187 7 0.02
188 245 0.62
189 56 0.14
190 3 0.01
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.53
Consensus pattern (186 bp):
ATTTATTTTAAATAATTTATTAGTATGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAA
TAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
TATGGATTGATTTATTTTAAAATATGATTGATTTATTATTGTAGTTGTATGGATTG
Found at i:42864 original size:80 final size:80
Alignment explanation
Indices: 42764--42913 Score: 282
Period size: 80 Copynumber: 1.9 Consensus size: 80
42754 TATTTTAAAA
*
42764 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATCGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATCGATTGAT
42829 TTATTATTGTAGTTG
66 TTATTATTGTAGTTG
*
42844 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATCGATTGAT
42909 TTATT
66 TTATT
42914 TTAAATAATT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
80 68 1.00
ACGTcount: A:0.33, C:0.01, G:0.14, T:0.53
Consensus pattern (80 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATCGATTGAT
TTATTATTGTAGTTG
Found at i:42889 original size:32 final size:31
Alignment explanation
Indices: 42843--43004 Score: 153
Period size: 32 Copynumber: 5.7 Consensus size: 31
42833 TATTGTAGTT
42843 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTAT-GATTGATTTATTTTAAATAATTTATTA
42875 GTATAGATTGATTTATTTT-AA-AA--TA-T-
1 GTAT-GATTGATTTATTTTAAATAATTTATTA
42901 G---GATTGATTTATTTTAAATAATTTATTA
1 GTATGATTGATTTATTTTAAATAATTTATTA
*
42929 GTATGAATTGCTTTATTTT-AA-AA--TA-T-
1 GTATG-ATTGATTTATTTTAAATAATTTATTA
42955 G---GATTGATTTATTTTAAATAATTTATTA
1 GTATGATTGATTTATTTTAAATAATTTATTA
42983 GTATGGATTGATTTATTTTAAA
1 GTAT-GATTGATTTATTTTAAA
43005 ATATGGATTG
Statistics
Matches: 107, Mismatches: 3, Indels: 40
0.71 0.02 0.27
Matches are distributed among these distances:
22 26 0.24
23 5 0.05
24 4 0.04
26 6 0.06
27 4 0.04
28 6 0.06
30 4 0.04
31 5 0.05
32 47 0.44
ACGTcount: A:0.35, C:0.01, G:0.12, T:0.52
Consensus pattern (31 bp):
GTATGATTGATTTATTTTAAATAATTTATTA
Found at i:42955 original size:22 final size:22
Alignment explanation
Indices: 42930--42972 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
42920 AATTTATTAG
*
42930 TATGAATTGCTTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
42952 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
42973 TAATTTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:42998 original size:18 final size:18
Alignment explanation
Indices: 42975--43022 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
42965 ATTTTAAATA
*
42975 ATTTATTAGTATGGATTG
1 ATTTATTAATATGGATTG
42993 ATTTATTTTAAAATATGGATTG
1 ATTTA--TT--AATATGGATTG
43015 ATTTATTA
1 ATTTATTA
43023 TTGTAGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 6 0.24
20 4 0.16
22 15 0.60
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (18 bp):
ATTTATTAATATGGATTG
Found at i:43060 original size:14 final size:14
Alignment explanation
Indices: 43041--43093 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
43031 GTATGGATTG
43041 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
43055 ATTTATTAGTATGAATTG
1 ATTTATT--T-T-AAATA
43073 ATTTATTTTAAATA
1 ATTTATTTTAAATA
43087 ATTTATT
1 ATTTATT
43094 AGTATGGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 17 0.55
15 1 0.03
16 2 0.06
17 1 0.03
18 10 0.32
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.57
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:43073 original size:32 final size:32
Alignment explanation
Indices: 43031--43257 Score: 240
Period size: 32 Copynumber: 6.7 Consensus size: 32
43021 TATTGTAGTT
*
43031 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGAATTGATTTATTTTAAATAATTTATTA
43063 GTATGAATTGATTTATTTTAAATAATTTATTA
1 GTATGAATTGATTTATTTTAAATAATTTATTA
* *
43095 GTATGGATTGATTTATTTTAAAATATGGATTGATTTA
1 GTATGAATTGATTTATTTT-AAATA---ATTTA-TTA
* * *
43132 TTATTGTAGTTGTATATGATTTATTTTAAATAATTTATTA
1 GTA-TG-AATTG-AT-TTA-TT---TTAAATAATTTATTA
43172 GTAT-ATATTGATTTATTTTAAATAATTTATTA
1 GTATGA-ATTGATTTATTTTAAATAATTTATTA
* *
43204 GTATGTATTGATTTATTTTAAATAATTTATTT
1 GTATGAATTGATTTATTTTAAATAATTTATTA
*
43236 GTATGGATTGATTTATTTTAAA
1 GTATGAATTGATTTATTTTAAA
43258 ATATGGATTG
Statistics
Matches: 166, Mismatches: 14, Indels: 30
0.79 0.07 0.14
Matches are distributed among these distances:
32 114 0.69
33 5 0.03
35 2 0.01
36 6 0.04
37 8 0.05
38 5 0.03
39 4 0.02
40 7 0.04
41 6 0.04
42 2 0.01
44 5 0.03
45 2 0.01
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.54
Consensus pattern (32 bp):
GTATGAATTGATTTATTTTAAATAATTTATTA
Found at i:43078 original size:18 final size:18
Alignment explanation
Indices: 43055--43111 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
43045 ATTTTAAATA
43055 ATTTATTAGTATGAATTG
1 ATTTATTAGTATGAATTG
* *
43073 ATTTATT--T-T-AAATA
1 ATTTATTAGTATGAATTG
*
43087 ATTTATTAGTATGGATTG
1 ATTTATTAGTATGAATTG
43105 ATTTATT
1 ATTTATT
43112 TTAAAATATG
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
14 10 0.33
15 1 0.03
16 2 0.07
17 1 0.03
18 16 0.53
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.54
Consensus pattern (18 bp):
ATTTATTAGTATGAATTG
Found at i:43187 original size:18 final size:18
Alignment explanation
Indices: 43164--43220 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
43154 ATTTTAAATA
43164 ATTTATTAGTATATATTG
1 ATTTATTAGTATATATTG
* *
43182 ATTTATT--T-TA-AATA
1 ATTTATTAGTATATATTG
*
43196 ATTTATTAGTATGTATTG
1 ATTTATTAGTATATATTG
43214 ATTTATT
1 ATTTATT
43221 TTAAATAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
14 9 0.30
15 2 0.07
16 2 0.07
17 1 0.03
18 16 0.53
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (18 bp):
ATTTATTAGTATATATTG
Found at i:43214 original size:109 final size:111
Alignment explanation
Indices: 42843--43225 Score: 534
Period size: 112 Copynumber: 3.5 Consensus size: 111
42833 TATTGTAGTT
* *
42843 GTATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGA
1 GTATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGA
* * * * ** *
42908 TTTATT-TTAAATAATT-TATTAGTATGAATTGCTTT--AT--TTTA-AA
66 TTTATTATT--GTAGTTGTATGA-T-TGATTTATTTTAAATAATTTATTA
* *
42951 ATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGA
1 GTATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGA
43016 TTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTA
66 TTTATTATTGTAGTTGTAT-GATTGATTTATTTTAAATAATTTATTA
43063 GTATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGA
1 GTATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGA
43128 TTTATTATTGTAGTTGTAT-A-TGATTTATTTTAAATAATTTATTA
66 TTTATTATTGTAGTTGTATGATTGATTTATTTTAAATAATTTATTA
*
43172 GTAT-ATATTGATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAA
1 GTATGA-ATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA
43226 TAATTTATTT
Statistics
Matches: 254, Mismatches: 12, Indels: 17
0.90 0.04 0.06
Matches are distributed among these distances:
107 12 0.05
108 74 0.29
109 80 0.31
110 1 0.00
111 4 0.02
112 83 0.33
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (111 bp):
GTATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGA
TTTATTATTGTAGTTGTATGATTGATTTATTTTAAATAATTTATTA
Found at i:43253 original size:22 final size:22
Alignment explanation
Indices: 43237--43279 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
43227 AATTTATTTG
43237 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
43259 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
43280 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:43339 original size:31 final size:31
Alignment explanation
Indices: 43304--43362 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
43294 AGTTGTATGG
*
43304 ATTATTTAAAT-TTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTT-AGTATTGCAAAACTAAA
43335 ATTATTTAAATCTTAGTATTGCAAAACT
1 ATTATTTAAATCTTAGTATTGCAAAACT
43363 CTTTTATGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATCTTAGTATTGCAAAACTAAA
Found at i:43875 original size:13 final size:14
Alignment explanation
Indices: 43857--43889 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
43847 TCTTTTTAAC
43857 AATATT-AACTCAA
1 AATATTAAACTCAA
*
43870 AATATTAAATTCAA
1 AATATTAAACTCAA
43884 AATATT
1 AATATT
43890 TACATAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (14 bp):
AATATTAAACTCAA
Found at i:44992 original size:15 final size:15
Alignment explanation
Indices: 44972--45002 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
44962 TGGTTGTAGT
*
44972 GGGGGATGACGGTGA
1 GGGGGATGACAGTGA
44987 GGGGGATGACAGTGA
1 GGGGGATGACAGTGA
45002 G
1 G
45003 AGAAAACAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.06, G:0.58, T:0.13
Consensus pattern (15 bp):
GGGGGATGACAGTGA
Found at i:45102 original size:21 final size:21
Alignment explanation
Indices: 45078--45120 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
45068 TATCATGCAA
45078 AGACAATCA-AGAGTCGAAGAG
1 AGAC-ATCAGAGAGTCGAAGAG
* *
45099 AGACTTGAGAGAGTCGAAGAG
1 AGACATCAGAGAGTCGAAGAG
45120 A
1 A
45121 CACTTGAGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.44, C:0.12, G:0.33, T:0.12
Consensus pattern (21 bp):
AGACATCAGAGAGTCGAAGAG
Found at i:45125 original size:21 final size:21
Alignment explanation
Indices: 45087--45129 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
45077 AAGACAATCA
*
45087 AGAGTCGAAGAGAGACTTGAG
1 AGAGTCGAAGAGACACTTGAG
45108 AGAGTCGAAGAGACACTTGAG
1 AGAGTCGAAGAGACACTTGAG
45129 A
1 A
45130 TGCATAAGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.12, G:0.35, T:0.14
Consensus pattern (21 bp):
AGAGTCGAAGAGACACTTGAG
Found at i:45203 original size:33 final size:33
Alignment explanation
Indices: 45166--45263 Score: 169
Period size: 33 Copynumber: 3.0 Consensus size: 33
45156 ATAGATGGAA
* *
45166 TGGTGAAAGAAGTTAAGGTGTTGAGGGGTGAAT
1 TGGTGAAAGAAGTTGAGGTGTTGAGGGGTGAAG
*
45199 TGGTGAAAGTAGTTGAGGTGTTGAGGGGTGAAG
1 TGGTGAAAGAAGTTGAGGTGTTGAGGGGTGAAG
45232 TGGTGAAAGAAGTTGAGGTGTTGAGGGGTGAA
1 TGGTGAAAGAAGTTGAGGTGTTGAGGGGTGAA
45264 CTTAAGATGG
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 61 1.00
ACGTcount: A:0.28, C:0.00, G:0.46, T:0.27
Consensus pattern (33 bp):
TGGTGAAAGAAGTTGAGGTGTTGAGGGGTGAAG
Found at i:45467 original size:18 final size:18
Alignment explanation
Indices: 45444--45482 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
45434 GAAAAAATAT
45444 GAAGAAGAAAAGATGGAG
1 GAAGAAGAAAAGATGGAG
45462 GAAGAAGAAAAGATGGAG
1 GAAGAAGAAAAGATGGAG
45480 GAA
1 GAA
45483 ATGAGGAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.38, T:0.05
Consensus pattern (18 bp):
GAAGAAGAAAAGATGGAG
Found at i:48490 original size:196 final size:198
Alignment explanation
Indices: 48022--48545 Score: 691
Period size: 200 Copynumber: 2.6 Consensus size: 198
48012 ATTGTCCAGA
*
48022 ATATAAAGTGTCGATACATTTATTAAAAGTATCGATCCCAATAACATCGAAACCGATAATTATAA
1 ATATAAAGTGTCGATACATTTA-TAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAA
* * * *
48087 TGTAATAAGTAAATTTATAAAGTAACTGGTATAAATATACCGGTTTTATAAGAAAATAGGTCAGC
65 TGTAATAGGTAAATTTACAATGT-ACCGGTATAAATATACCGGTTTTATAAGAAAATAGGTCAGC
* * *
48152 ATAAAGTATCGACACCATTTAAATTTGTGTCGATACTTTTTGTCCATAATGAATGCCAAATGGGG
129 ATAAAGTATCGACACCATTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACGAGG
48217 TGCAC
194 TGCAC
* * * * *
48222 ACATAAAGTGTCAATACATTTATTAAAAGTATCGATCCCAAAAACATTGAAACCAATAATTACAA
1 ATATAAAGTGTCGATACATTTA-TAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAA
* * * *
48287 TGTAATAGGTAAATTTACAATGTACCCGATAGAAATATACCGGTTTTATGAG-AAATATGTCTA-
65 TGTAATAGGTAAATTTACAATGTA-CCGGTATAAATATACCGGTTTTATAAGAAAATAGGTC-AG
* ** * * *
48350 CATAATGTATCGACACTTTTTAAGTTTGTTTCGATAC-TTTT-TCCAGAATGAATGCCCAACGAG
128 CATAAAGTATCGACACCATTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACGAG
*
48413 GTGCAT
193 GTGCAC
* * *
48419 GTATAAAGTGTCGATACATTTA-AAATTGTATCGATCCAAAAAACATCGAAACCGATAATTATAA
1 ATATAAAGTGTCGATACATTTATAAA-AGTATCGATCCCAAAAACATCGAAACCGATAATTATAA
48483 TGTAATAGGTAAATTTACAATGTTACCGGTATAAATATACCGG-TTTACTAAGAAAATAGGTCA
65 TGTAATAGGTAAATTTACAATG-TACCGGTATAAATATACCGGTTTTA-TAAGAAAATAGGTCA
48546 ATATAAGCGC
Statistics
Matches: 282, Mismatches: 36, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
195 7 0.02
196 75 0.27
197 52 0.18
198 4 0.01
199 41 0.15
200 103 0.37
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (198 bp):
ATATAAAGTGTCGATACATTTATAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
GTAATAGGTAAATTTACAATGTACCGGTATAAATATACCGGTTTTATAAGAAAATAGGTCAGCAT
AAAGTATCGACACCATTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACGAGGTG
CAC
Found at i:48575 original size:23 final size:23
Alignment explanation
Indices: 48546--48593 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
48536 AAATAGGTCA
*
48546 ATATAAGCGCTACCTATTATATT
1 ATATAAGCGCTACCTAATATATT
* *
48569 ATATAAGCGTTACCTAATATGTT
1 ATATAAGCGCTACCTAATATATT
48592 AT
1 AT
48594 TGTATTTGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (23 bp):
ATATAAGCGCTACCTAATATATT
Found at i:48634 original size:64 final size:64
Alignment explanation
Indices: 48558--48684 Score: 209
Period size: 64 Copynumber: 2.0 Consensus size: 64
48548 ATAAGCGCTA
* * *
48558 CCTATTATATTATATAAGCGTTACCTAATATGTTATTGTATTTGATAATATTTCCGGTTAAATG
1 CCTATTATATTATATAAGCGCTACATAATATGTTATTGTATTTGATAATATTTCCGATTAAATG
* *
48622 CCTATTTTATTATATAAGCGCTACATAATATGTTATTGTATTTGATAATATTTTCGATTAAAT
1 CCTATTATATTATATAAGCGCTACATAATATGTTATTGTATTTGATAATATTTCCGATTAAAT
48685 AATATAACAT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 58 1.00
ACGTcount: A:0.32, C:0.10, G:0.11, T:0.46
Consensus pattern (64 bp):
CCTATTATATTATATAAGCGCTACATAATATGTTATTGTATTTGATAATATTTCCGATTAAATG
Found at i:48884 original size:23 final size:23
Alignment explanation
Indices: 48858--48912 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 23
48848 AAAATTTTAG
48858 ATAAATATATATTTAAATTAAA-A
1 ATAAA-ATATATTTAAATTAAATA
**
48881 ATAAAAT-TATTTTTATTAAATA
1 ATAAAATATATTTAAATTAAATA
48903 ATAAAATATA
1 ATAAAATATA
48913 AACACACATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 11 0.39
22 10 0.36
23 7 0.25
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
ATAAAATATATTTAAATTAAATA
Found at i:53614 original size:28 final size:28
Alignment explanation
Indices: 53579--53632 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
53569 GATTCAATTA
*
53579 ATTTGATCATT-ATTTTAATTTAATTCTG
1 ATTTGATC-TTAATTTCAATTTAATTCTG
53607 ATTTGATCTTAATTTCAATTTAATTC
1 ATTTGATCTTAATTTCAATTTAATTC
53633 AATAGGATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 2 0.08
28 22 0.92
ACGTcount: A:0.30, C:0.09, G:0.06, T:0.56
Consensus pattern (28 bp):
ATTTGATCTTAATTTCAATTTAATTCTG
Found at i:57207 original size:24 final size:24
Alignment explanation
Indices: 57180--57234 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
57170 GTAGAGTGAT
57180 GGCGCACGTTAACTGTTTTCTATG
1 GGCGCACGTTAACTGTTTTCTATG
57204 GGCGCACGTTAACTGTTTTCTATG
1 GGCGCACGTTAACTGTTTTCTATG
*
57228 GGTGCAC
1 GGCGCAC
57235 ATTAGCCGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.16, C:0.22, G:0.27, T:0.35
Consensus pattern (24 bp):
GGCGCACGTTAACTGTTTTCTATG
Done.