Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003938.1 Hibiscus syriacus cultivar Beakdansim tig00008511_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: 113632
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1014 original size:17 final size:17
Alignment explanation
Indices: 973--1045 Score: 76
Period size: 17 Copynumber: 4.2 Consensus size: 17
963 ATTCATGCTT
973 CTAGTTCATTGAA-TAAA
1 CTAGTTCATT-AATTAAA
*
990 GTTAGTTCATTAATTAAA
1 -CTAGTTCATTAATTAAA
* *
1008 CTAGTTCATTCATCAAA
1 CTAGTTCATTAATTAAA
*
1025 CTAGTTCATTTTATTAAA
1 CTAGTTCA-TTAATTAAA
1043 CTA
1 CTA
1046 ACTCTTAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
17 24 0.51
18 23 0.49
ACGTcount: A:0.37, C:0.14, G:0.08, T:0.41
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:2935 original size:18 final size:18
Alignment explanation
Indices: 2901--2935 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2891 TTGGAGTGTA
* *
2901 TTGGTGAGGTTTTTTTTG
1 TTGGTGAGGTCTATTTTG
2919 TTGGTGAGGTCTATTTT
1 TTGGTGAGGTCTATTTT
2936 CATTTTTTAT
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:0.09, C:0.03, G:0.31, T:0.57
Consensus pattern (18 bp):
TTGGTGAGGTCTATTTTG
Found at i:3182 original size:28 final size:28
Alignment explanation
Indices: 3150--3205 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
3140 TCGAAGATCA
3150 AAACACAACTAAAAATGAGAGATGATAC
1 AAACACAACTAAAAATGAGAGATGATAC
3178 AAACACAACTAAAAATGAGAGATGATAC
1 AAACACAACTAAAAATGAGAGATGATAC
3206 TCGATCCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.57, C:0.14, G:0.14, T:0.14
Consensus pattern (28 bp):
AAACACAACTAAAAATGAGAGATGATAC
Found at i:4613 original size:18 final size:18
Alignment explanation
Indices: 4574--4617 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
4564 TAAGTGTGTT
4574 GTTCATTT-AAGCATGCA
1 GTTCATTTAAAGCATGCA
*
4591 TTTCATTTAAAGCAT-CTA
1 GTTCATTTAAAGCATGC-A
4609 GTTCATTTA
1 GTTCATTTA
4618 GGGAAGTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (18 bp):
GTTCATTTAAAGCATGCA
Found at i:4717 original size:17 final size:17
Alignment explanation
Indices: 4676--4764 Score: 63
Period size: 17 Copynumber: 5.2 Consensus size: 17
4666 ATTCATGCAT
4676 CTAGTTCATTGAA-TAAA
1 CTAGTTCATT-AATTAAA
*
4693 GTTAGTTCATTAATTAAA
1 -CTAGTTCATTAATTAAA
* *
4711 CTAGTTCATTCATCAAA
1 CTAGTTCATTAATTAAA
* * * *
4728 ATAGTCCATTTATCAAA
1 CTAGTTCATTAATTAAA
* * *
4745 ATAGTCCATTTATTAAA
1 CTAGTTCATTAATTAAA
4762 CTA
1 CTA
4765 ACTCTTAATT
Statistics
Matches: 61, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
17 48 0.79
18 13 0.21
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.38
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:5959 original size:18 final size:18
Alignment explanation
Indices: 5926--5985 Score: 86
Period size: 18 Copynumber: 3.4 Consensus size: 18
5916 CTTACAACAC
*
5926 TTACCACAAC-ACACCAT
1 TTACCACGACAACACCAT
5943 TTACCACGACAACACCAT
1 TTACCACGACAACACCAT
*
5961 TTGCCACGACAACACCAT
1 TTACCACGACAACACCAT
*
5979 TTGCCAC
1 TTACCAC
5986 AACACCATTC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
17 9 0.22
18 31 0.77
ACGTcount: A:0.35, C:0.40, G:0.07, T:0.18
Consensus pattern (18 bp):
TTACCACGACAACACCAT
Found at i:5994 original size:15 final size:18
Alignment explanation
Indices: 5936--5985 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
5926 TTACCACAAC
*
5936 ACACCATTTACCACGACA
1 ACACCATTTGCCACGACA
5954 ACACCATTTGCCACGACA
1 ACACCATTTGCCACGACA
5972 ACACCATTTGCCAC
1 ACACCATTTGCCAC
5986 AACACCATTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.34, C:0.40, G:0.08, T:0.18
Consensus pattern (18 bp):
ACACCATTTGCCACGACA
Found at i:8359 original size:24 final size:24
Alignment explanation
Indices: 8315--8364 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
8305 ATAAAGAACC
*
8315 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
8339 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACATACCATTA
8363 AA
1 AA
8365 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:11563 original size:22 final size:22
Alignment explanation
Indices: 11524--11565 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
11514 TGAATTGAAT
***
11524 TAATTCAAAGTTTTTTTAAAAA
1 TAATTCAAAGTCCATTTAAAAA
11546 TAATTCAAAGTCCATTTAAA
1 TAATTCAAAGTCCATTTAAA
11566 GCTTTGGAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (22 bp):
TAATTCAAAGTCCATTTAAAAA
Found at i:11728 original size:18 final size:19
Alignment explanation
Indices: 11687--11739 Score: 74
Period size: 18 Copynumber: 2.8 Consensus size: 19
11677 AGGTAAGGGA
11687 AGTATCGATACT-CACTAGGT
1 AGTATCGATACTAC-CTA-GT
11707 AGTATCGATACTACCT-GT
1 AGTATCGATACTACCTAGT
11725 AGTATCGATACTACC
1 AGTATCGATACTACC
11740 AGCAATGCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
18 17 0.53
20 14 0.44
21 1 0.03
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (19 bp):
AGTATCGATACTACCTAGT
Found at i:17787 original size:25 final size:26
Alignment explanation
Indices: 17753--17801 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
17743 ATCAATGGAT
17753 CATTTATAT-ACTTTACCTTAAATAC
1 CATTTATATAACTTTACCTTAAATAC
*
17778 CATTTATATAATTTTACCTTAAAT
1 CATTTATATAACTTTACCTTAAAT
17802 TCTATTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.37, C:0.16, G:0.00, T:0.47
Consensus pattern (26 bp):
CATTTATATAACTTTACCTTAAATAC
Found at i:18280 original size:25 final size:25
Alignment explanation
Indices: 18227--18280 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
18217 TATAGTCATC
*
18227 AAAATATTCATACAAATATAAAAAT
1 AAAATATTCATACAAATATAAAAAG
*
18252 AAAATATT-ATACCTAAA-ATATAAAG
1 AAAATATTCATA-C-AAATATAAAAAG
18277 AAAA
1 AAAA
18281 ATAAAACATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
24 3 0.12
25 19 0.76
26 3 0.12
ACGTcount: A:0.65, C:0.07, G:0.02, T:0.26
Consensus pattern (25 bp):
AAAATATTCATACAAATATAAAAAG
Found at i:19037 original size:81 final size:80
Alignment explanation
Indices: 18947--19107 Score: 252
Period size: 81 Copynumber: 2.0 Consensus size: 80
18937 AATATAGGTT
* *
18947 ATCATTTTCTGAAATTTAATTTGTTTCTAATTATATTTTAATTTTATAGT-TATTATTTTTGAAA
1 ATCATTTTCTGAAATTTAATTTG--TCTAAATATATTTTAATTTTATAGTATATTATCTTTGAAA
19011 TTTTAAAATATTGAAAA
64 TTTTAAAATATTGAAAA
*
19028 ATCATTTTCTGAAATTTAATTTGTCTAAATATGTTTTAATTTTATAGTCATATTATCTTTGAAAT
1 ATCATTTTCTGAAATTTAATTTGTCTAAATATATTTTAATTTTATAGT-ATATTATCTTTGAAAT
*
19093 TTTAAAATTTTGAAA
65 TTTAAAATATTGAAA
19108 TTTTTTATCT
Statistics
Matches: 74, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
79 23 0.31
81 51 0.69
ACGTcount: A:0.35, C:0.05, G:0.07, T:0.53
Consensus pattern (80 bp):
ATCATTTTCTGAAATTTAATTTGTCTAAATATATTTTAATTTTATAGTATATTATCTTTGAAATT
TTAAAATATTGAAAA
Found at i:21252 original size:20 final size:20
Alignment explanation
Indices: 21227--21270 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
21217 TAAGGAACAG
21227 CTACTAGTCTGGTCCCACAC
1 CTACTAGTCTGGTCCCACAC
21247 CTACTAGTCTGGTCCCACAC
1 CTACTAGTCTGGTCCCACAC
21267 CTAC
1 CTAC
21271 GTTTCAAGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.41, G:0.14, T:0.25
Consensus pattern (20 bp):
CTACTAGTCTGGTCCCACAC
Found at i:24045 original size:32 final size:33
Alignment explanation
Indices: 24009--24070 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 33
23999 TGTTTTTGAA
24009 AAAATTGAAATTTTAAATACTAAA-ACATATCC
1 AAAATTGAAATTTTAAATACTAAACACATATCC
** **
24041 AAAATTGGTATTTTAGGTACTAAACACATA
1 AAAATTGAAATTTTAAATACTAAACACATA
24071 AAATAATGGG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
32 20 0.80
33 5 0.20
ACGTcount: A:0.48, C:0.11, G:0.08, T:0.32
Consensus pattern (33 bp):
AAAATTGAAATTTTAAATACTAAACACATATCC
Found at i:25695 original size:43 final size:43
Alignment explanation
Indices: 25596--25759 Score: 111
Period size: 43 Copynumber: 3.8 Consensus size: 43
25586 TCAGAAAAAA
* * * * * ** *
25596 AAACGTCGCAGTAGGTGTTGAGATTTAGCGACATTTTACTTAA
1 AAACGTCGCAGTAGGTTTTGATATTTTGCGGCATTTTCCCCAC
* * * *
25639 AAATGCCGTAGTAGGTTTTGATATTTTGCGGCATTTTCCCCAT
1 AAACGTCGCAGTAGGTTTTGATATTTTGCGGCATTTTCCCCAC
* *
25682 AAACG-CTGCAGTAGG---TGATATTTTTAGCGGCGTTTTTCCCAC
1 AAACGTC-GCAGTAGGTTTTGATA-TTTT-GCGGCATTTTCCCCAC
* * * *
25724 AAACGTCGTAGTAGGTTTTCAGATTTAGCGGCATTT
1 AAACGTCGCAGTAGGTTTTGATATTTTGCGGCATTT
25760 GTATCGAAAA
Statistics
Matches: 93, Mismatches: 21, Indels: 14
0.73 0.16 0.11
Matches are distributed among these distances:
40 5 0.05
41 4 0.04
42 26 0.28
43 52 0.56
44 3 0.03
45 3 0.03
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.35
Consensus pattern (43 bp):
AAACGTCGCAGTAGGTTTTGATATTTTGCGGCATTTTCCCCAC
Found at i:25868 original size:44 final size:44
Alignment explanation
Indices: 25800--25885 Score: 163
Period size: 44 Copynumber: 2.0 Consensus size: 44
25790 ATTAGCGACG
25800 TTTCTAGTATACAAATGCCACTAAATGTATGGTATATTGTGGCA
1 TTTCTAGTATACAAATGCCACTAAATGTATGGTATATTGTGGCA
*
25844 TTTCTAGTATACAAATGCCGCTAAATGTATGGTATATTGTGG
1 TTTCTAGTATACAAATGCCACTAAATGTATGGTATATTGTGG
25886 TGTGTTTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (44 bp):
TTTCTAGTATACAAATGCCACTAAATGTATGGTATATTGTGGCA
Found at i:26329 original size:21 final size:21
Alignment explanation
Indices: 26227--26331 Score: 102
Period size: 21 Copynumber: 5.0 Consensus size: 21
26217 TTGTTGATAT
* * *
26227 GCTGCTTCTCTTTGTGCTGCC
1 GCTGCTTCTCTCTCTGCTTCC
* *
26248 GCTGCTTCTCTCTATGCTGCC
1 GCTGCTTCTCTCTCTGCTTCC
* * *
26269 GCTGTTTCTTTCTCTACTTCC
1 GCTGCTTCTCTCTCTGCTTCC
* **
26290 GCTGCTGCTCTGGCTGCTTCC
1 GCTGCTTCTCTCTCTGCTTCC
*
26311 GCTGCTGCTCTCTCTGCTTCC
1 GCTGCTTCTCTCTCTGCTTCC
26332 CTTGTTTCAT
Statistics
Matches: 69, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 69 1.00
ACGTcount: A:0.02, C:0.37, G:0.20, T:0.41
Consensus pattern (21 bp):
GCTGCTTCTCTCTCTGCTTCC
Found at i:34544 original size:19 final size:19
Alignment explanation
Indices: 34502--34544 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
34492 TGTCTTTACT
* *
34502 ATTTTGTTCACTACTCTCT
1 ATTTTGTTCACTACTATCA
* *
34521 GTTTTGTTCACTACTATGA
1 ATTTTGTTCACTACTATCA
34540 ATTTT
1 ATTTT
34545 AGCAAATTTT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.19, C:0.19, G:0.09, T:0.53
Consensus pattern (19 bp):
ATTTTGTTCACTACTATCA
Found at i:36974 original size:42 final size:41
Alignment explanation
Indices: 36910--37100 Score: 135
Period size: 42 Copynumber: 4.7 Consensus size: 41
36900 AATTCAAATA
* * * *
36910 TATTGTGGCGTTTGGTA-AAACACGCCACTATATAGTACACC
1 TATTGCGGCGTTTGTTATAAAAACGCCACTA-ATAATACACC
* * * * **
36951 TATTGCGGCGATTGTTAT--AAACACCATTAATATCTA-ATT
1 TATTGCGGCGTTTGTTATAAAAACGCCACTAATA-ATACACC
* **
36990 TTTTGCGGCGTTT-TTATTTAAAAACGCCACTAA-AATACAAA
1 TATTGCGGCGTTTGTTA--TAAAAACGCCACTAATAATACACC
*
37031 TATGTTGCGGCGTTTGTTATAAAAACGCCACTATATATTACACC
1 TA--TTGCGGCGTTTGTTATAAAAACGCCACTA-ATAATACACC
*
37075 TATTGCGGCGTTTG-TAAAAAAACGCC
1 TATTGCGGCGTTTGTTATAAAAACGCC
37101 GCTATTGTAC
Statistics
Matches: 117, Mismatches: 21, Indels: 24
0.72 0.13 0.15
Matches are distributed among these distances:
38 3 0.03
39 15 0.13
40 13 0.11
41 28 0.24
42 36 0.31
43 12 0.10
44 10 0.09
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (41 bp):
TATTGCGGCGTTTGTTATAAAAACGCCACTAATAATACACC
Found at i:42791 original size:6 final size:6
Alignment explanation
Indices: 42780--42808 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
42770 ATAGGGATGC
42780 TATTTT TATTTT TATTTT TATTTT T-TTTT
1 TATTTT TATTTT TATTTT TATTTT TATTTT
42809 ATAGAAATCC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 19 0.83
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TATTTT
Found at i:44792 original size:15 final size:15
Alignment explanation
Indices: 44773--44809 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
44763 ATTTAATCAT
44773 AATTTTAATAATTTA
1 AATTTTAATAATTTA
* *
44788 GATTTTTATAATTTA
1 AATTTTAATAATTTA
44803 AATTTTA
1 AATTTTA
44810 CACTTAGAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (15 bp):
AATTTTAATAATTTA
Found at i:50999 original size:27 final size:27
Alignment explanation
Indices: 50957--51110 Score: 220
Period size: 27 Copynumber: 5.7 Consensus size: 27
50947 TTTTTGCATC
**
50957 TGCA-TTTGCATCTGCATTTGTATCTT
1 TGCATTTTGCATCTGCATTTACATCTT
*
50983 TGCATTTTGCATATGCATTTACATCTT
1 TGCATTTTGCATCTGCATTTACATCTT
** *
51010 TTTATTTTGCATATGCATTTACATCTT
1 TGCATTTTGCATCTGCATTTACATCTT
* *
51037 TGCATTTTACATCTGTATTTACATCTT
1 TGCATTTTGCATCTGCATTTACATCTT
51064 TGCATTTTGCATCTGCATTTACATCTT
1 TGCATTTTGCATCTGCATTTACATCTT
*
51091 TGCATTTTGCATTTGCATTT
1 TGCATTTTGCATCTGCATTT
51111 CATTTTTAAA
Statistics
Matches: 114, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
26 4 0.04
27 110 0.96
ACGTcount: A:0.19, C:0.18, G:0.11, T:0.51
Consensus pattern (27 bp):
TGCATTTTGCATCTGCATTTACATCTT
Found at i:51042 original size:14 final size:14
Alignment explanation
Indices: 51023--51097 Score: 86
Period size: 12 Copynumber: 5.5 Consensus size: 14
51013 ATTTTGCATA
51023 TGCATTTACATCTT
1 TGCATTTACATCTT
51037 TGCATTTTACATC--
1 TGCA-TTTACATCTT
*
51050 TGTATTTACATCTT
1 TGCATTTACATCTT
*
51064 TGCATTTTGCATC--
1 TGCA-TTTACATCTT
51077 TGCATTTACATCTT
1 TGCATTTACATCTT
51091 TGCATTT
1 TGCATTT
51098 TGCATTTGCA
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
12 15 0.29
13 7 0.14
14 14 0.27
15 15 0.29
ACGTcount: A:0.20, C:0.20, G:0.09, T:0.51
Consensus pattern (14 bp):
TGCATTTACATCTT
Found at i:52312 original size:6 final size:6
Alignment explanation
Indices: 52290--52384 Score: 52
Period size: 6 Copynumber: 15.0 Consensus size: 6
52280 AAAAAAGAGC
* *
52290 AAAAGG AAAAGG AAAAAG AAAAAAG AAATTAAAG AAATTAAAG AAAAAAG
1 AAAAAG AAAAAG AAAAAG -AAAAAG -AA--AAAG AAA--A-AG AA-AAAG
* * *
52340 AGAAAC AAAGAG A-AAA- AAAAAG AAAAA- AAAAAG AAAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
52385 GGATGATAAT
Statistics
Matches: 72, Mismatches: 7, Indels: 20
0.73 0.07 0.20
Matches are distributed among these distances:
4 1 0.01
5 10 0.14
6 36 0.50
7 12 0.17
8 4 0.06
9 8 0.11
10 1 0.01
ACGTcount: A:0.78, C:0.01, G:0.17, T:0.04
Consensus pattern (6 bp):
AAAAAG
Found at i:52368 original size:9 final size:9
Alignment explanation
Indices: 52308--52383 Score: 64
Period size: 9 Copynumber: 8.3 Consensus size: 9
52298 AAGGAAAAAG
52308 AAAAAAGAA
1 AAAAAAGAA
**
52317 ATTAAAGAA
1 AAAAAAGAA
**
52326 ATTAAAGAA
1 AAAAAAGAA
*
52335 AAAAGAGAA
1 AAAAAAGAA
*
52344 ACAAAGAGAAA
1 A-AAAAAG-AA
52355 AAAAAAGAA
1 AAAAAAGAA
52364 AAAAAA-AA
1 AAAAAAGAA
*
52372 GAAAAAGAA
1 AAAAAAGAA
52381 AAA
1 AAA
52384 GGGATGATAA
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
8 7 0.12
9 35 0.62
10 11 0.20
11 3 0.05
ACGTcount: A:0.80, C:0.01, G:0.13, T:0.05
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:52368 original size:10 final size:10
Alignment explanation
Indices: 52329--52382 Score: 56
Period size: 10 Copynumber: 5.3 Consensus size: 10
52319 TAAAGAAATT
52329 AAAG-AAAAA
1 AAAGAAAAAA
* *
52338 AGAGAAACAA
1 AAAGAAAAAA
*
52348 AGAGAAAAAA
1 AAAGAAAAAA
52358 AAAGAAAAAAA
1 AAAG-AAAAAA
52369 AAAGAAAAAGA
1 AAAGAAAAA-A
52380 AAA
1 AAA
52383 AGGGATGATA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
9 3 0.08
10 21 0.55
11 14 0.37
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAA
Found at i:52368 original size:11 final size:11
Alignment explanation
Indices: 52333--52384 Score: 61
Period size: 11 Copynumber: 4.6 Consensus size: 11
52323 GAAATTAAAG
*
52333 AAAAAAG-AGA
1 AAAAAAGAAAA
*
52343 AACAAAGAGAAA
1 AAAAAAGA-AAA
52355 AAAAAAGAAAA
1 AAAAAAGAAAA
52366 AAAAAAGAAAA
1 AAAAAAGAAAA
52377 AGAAAAAG
1 A-AAAAAG
52385 GGATGATAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
10 6 0.17
11 15 0.42
12 15 0.42
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:53546 original size:33 final size:32
Alignment explanation
Indices: 53416--53582 Score: 253
Period size: 32 Copynumber: 5.2 Consensus size: 32
53406 AAGCAATAGA
* *
53416 GGGCATCTTTGAAGATTCGACATCAAATGTTG
1 GGGCATCTTTGGAGATTCAACATCAAATGTTG
*
53448 AGGCATCTTTGGAGATTCAACATCAAATGTTG
1 GGGCATCTTTGGAGATTCAACATCAAATGTTG
*
53480 GGGCATCTTTGGAGATTCATCATCAAATGTTG
1 GGGCATCTTTGGAGATTCAACATCAAATGTTG
53512 GGGCATCTTTGGAGATTCAACATCAAAATGTTG
1 GGGCATCTTTGGAGATTCAACATC-AAATGTTG
* * **
53545 GGGCATCTTTGGAGATTCAATATCGAATACTG
1 GGGCATCTTTGGAGATTCAACATCAAATGTTG
53577 GGGCAT
1 GGGCAT
53583 TCAATATCCT
Statistics
Matches: 124, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
32 93 0.75
33 31 0.25
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (32 bp):
GGGCATCTTTGGAGATTCAACATCAAATGTTG
Found at i:53829 original size:39 final size:34
Alignment explanation
Indices: 53689--53808 Score: 177
Period size: 34 Copynumber: 3.5 Consensus size: 34
53679 ATAAAAAAAT
* *
53689 TCTCAATTGAGACAATTTCTCAAAACAAATTTTG
1 TCTCACTTGAGACAATTTCTCAAAACAAATTTCG
* * * *
53723 TCTCACTTGAGAAAATTTATTAAAGCAAATTTCG
1 TCTCACTTGAGACAATTTCTCAAAACAAATTTCG
53757 TCTCACTTGAGACAATTTCTCAAAACAAATTTCG
1 TCTCACTTGAGACAATTTCTCAAAACAAATTTCG
*
53791 TCTCGCTTGAGACAATTT
1 TCTCACTTGAGACAATTT
53809 TTCTCTGAGA
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 75 1.00
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (34 bp):
TCTCACTTGAGACAATTTCTCAAAACAAATTTCG
Found at i:54163 original size:73 final size:75
Alignment explanation
Indices: 54014--54152 Score: 194
Period size: 73 Copynumber: 1.9 Consensus size: 75
54004 CACTTGAAGG
* * * * *
54014 AAGACATTTCATTTGACTCAATATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAGGTT
1 AAGACATTTCATTTCACT-AACATTGTTTTTCTTAAAACAAAATTTGTCTCCCTTGAGACAGATT
54079 TTACTCAAAAC
65 TTACTCAAAAC
54090 AAGACATTTCATTTCACT-ACA-TGTTTTTCTTAAAACAAAATTTTGTCTCCCTTGAGACA-ATT
1 AAGACATTTCATTTCACTAACATTGTTTTTCTTAAAACAAAA-TTTGTCTCCCTTGAGACAGATT
54152 T
65 T
54153 CTTTTGAAAC
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
73 21 0.37
74 19 0.33
76 17 0.30
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.40
Consensus pattern (75 bp):
AAGACATTTCATTTCACTAACATTGTTTTTCTTAAAACAAAATTTGTCTCCCTTGAGACAGATTT
TACTCAAAAC
Found at i:54225 original size:36 final size:36
Alignment explanation
Indices: 54178--54378 Score: 298
Period size: 36 Copynumber: 5.6 Consensus size: 36
54168 CTTTGAAAAC
*
54178 GTTTCCCTTGAAACGAATTTTGTCTCCCTTGAGACA
1 GTTTCCCTTGAAACCAATTTTGTCTCCCTTGAGACA
* *
54214 GTTTCCCTTGAAACGAATTTTGTCTCCCTTGAGATA
1 GTTTCCCTTGAAACCAATTTTGTCTCCCTTGAGACA
* *
54250 TTTTCCCATGAAACCAATTTTGTCTCCCTTGAGACA
1 GTTTCCCTTGAAACCAATTTTGTCTCCCTTGAGACA
54286 GTTTCCCTTGAAACCAATTTTGTCTCCCTTGAGACA
1 GTTTCCCTTGAAACCAATTTTGTCTCCCTTGAGACA
* *
54322 GTTTCCCTTGAAA-CAA-ATTGTCTCCCTTGAGATA
1 GTTTCCCTTGAAACCAATTTTGTCTCCCTTGAGACA
**
54356 GTTTCTTTTGAAACACAATTTTG
1 GTTTCCCTTGAAAC-CAATTTTG
54379 AAAACGTTTC
Statistics
Matches: 150, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
34 27 0.18
35 3 0.02
36 117 0.78
37 3 0.02
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.38
Consensus pattern (36 bp):
GTTTCCCTTGAAACCAATTTTGTCTCCCTTGAGACA
Found at i:54417 original size:170 final size:171
Alignment explanation
Indices: 54214--54550 Score: 464
Period size: 170 Copynumber: 2.0 Consensus size: 171
54204 CCTTGAGACA
* *
54214 GTTTCCCTTGAAACGAATTTTGTCTCCCTTGAGA-TATTTTCCCATGAAACCAATTTTGTCTCCC
1 GTTTCCCTTGAAACGAATTTTGTCTCCCTTGAGACT-GTTTCCCATGAAACAAATTTTGTCTCCC
* * * *
54278 TTGAGACAGTTTCCCTTGAAACCAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAA-TTG
65 TTGAGACAGTTTCCCTTAAAACAAATTTTGTCTCCATTGAGACAGCTTCCCTTGAAACAAATTTG
* **
54342 TCTCCCTTGAGA-TAGTTTCTTTTGAAACACAATTTTGAAAAC
130 TCTCCCTTGAGACAAGTTTCCCTTGAAACA-AATTTTGAAAAC
* * * **
54384 GTTTCCCTTGAAATGATTTTTGTCTCTCTTGAGACTGTTTCCCATGAAACAAATTTTGTCTTTCT
1 GTTTCCCTTGAAACGAATTTTGTCTCCCTTGAGACTGTTTCCCATGAAACAAATTTTGTCTCCCT
* * *
54449 TGAGATAGTTTCCCTTAAAACAAATTTTTTCTCTATTGAGACAGCTTCCCTTGAAACAAATTTTG
66 TGAGACAGTTTCCCTTAAAACAAATTTTGTCTCCATTGAGACAGCTTCCCTTGAAACAAA-TTTG
*
54514 TCTCTCTTGAGACAAGTTTCCCTTGAAACAAATTTTG
130 TCTCCCTTGAGACAAGTTTCCCTTGAAACAAATTTTG
54551 TCTCCCTTGA
Statistics
Matches: 145, Mismatches: 18, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
170 109 0.75
171 1 0.01
172 21 0.14
173 14 0.10
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.39
Consensus pattern (171 bp):
GTTTCCCTTGAAACGAATTTTGTCTCCCTTGAGACTGTTTCCCATGAAACAAATTTTGTCTCCCT
TGAGACAGTTTCCCTTAAAACAAATTTTGTCTCCATTGAGACAGCTTCCCTTGAAACAAATTTGT
CTCCCTTGAGACAAGTTTCCCTTGAAACAAATTTTGAAAAC
Found at i:54417 original size:206 final size:208
Alignment explanation
Indices: 54122--54649 Score: 722
Period size: 206 Copynumber: 2.5 Consensus size: 208
54112 GTTTTTCTTA
* * * *
54122 AAACAAAATTTTGTCTCCCTTGAGACAATTTCTTTTGAAACATAAACTTTGAAAACGTTTCCCTT
1 AAAC-AAA-TTTGTCTCCCTTGAGATAGTTTCTTTTGAAACA-CAATTTTGAAAACGTTTCCCTT
* * * *
54187 GAAACGAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACGAATTTTGTCTCCCTTGAGATATT
63 GAAATGATTTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATAGT
* * * * *
54252 TTCCCATGAAACCAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACCAATTTTGTCTCCCTTG
128 TTCCCATAAAACAAATTTTGTCTCCATTGAGACAGCTTCCCTTGAAACAAATTTTGTCTCCCTTG
54317 AGAC-AGTTTCCCTTG
193 AGACAAGTTTCCCTTG
54332 AAACAAA-TTGTCTCCCTTGAGATAGTTTCTTTTGAAACACAATTTTGAAAACGTTTCCCTTGAA
1 AAACAAATTTGTCTCCCTTGAGATAGTTTCTTTTGAAACACAATTTTGAAAACGTTTCCCTTGAA
* * * **
54396 ATGATTTTTGTCTCTCTTGAGACTGTTTCCCATGAAACAAATTTTGTCTTTCTTGAGATAGTTTC
66 ATGATTTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATAGTTTC
* * * *
54461 CCTTAAAACAAATTTTTTCTCTATTGAGACAGCTTCCCTTGAAACAAATTTTGTCTCTCTTGAGA
131 CCATAAAACAAATTTTGTCTCCATTGAGACAGCTTCCCTTGAAACAAATTTTGTCTCCCTTGAGA
54526 CAAGTTTCCCTTG
196 CAAGTTTCCCTTG
* * *
54539 AAACAAATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACACAAAATGTTGAGAACGTTTCCCTT
1 AAACAAA-TTTGTCTCCCTTGAGATAGTTTCTTTTGAAACAC--AATTTTGAAAACGTTTCCCTT
** *
54604 GAAATGATTTTTGTCTCCCTT--GACAGTTTCTTTTGAAACAAGTTTT
63 GAAATGATTTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTT
54650 TGAGATAGTT
Statistics
Matches: 282, Mismatches: 31, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
206 136 0.48
207 48 0.17
209 55 0.20
210 4 0.01
211 39 0.14
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (208 bp):
AAACAAATTTGTCTCCCTTGAGATAGTTTCTTTTGAAACACAATTTTGAAAACGTTTCCCTTGAA
ATGATTTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATAGTTTC
CCATAAAACAAATTTTGTCTCCATTGAGACAGCTTCCCTTGAAACAAATTTTGTCTCCCTTGAGA
CAAGTTTCCCTTG
Found at i:54424 original size:36 final size:36
Alignment explanation
Indices: 54384--54579 Score: 234
Period size: 36 Copynumber: 5.4 Consensus size: 36
54374 TTTTGAAAAC
** *
54384 GTTTCCCTTGAAATGATTTTTGTCTCTCTTGAGACT
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACT
* *
54420 GTTTCCCATGAAACAAATTTTGTCTTTCTTGAGA-T
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACT
* * * *
54455 AGTTTCCCTTAAAACAAATTTTTTCTCTATTGAGACA
1 -GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACT
* *
54492 GCTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGAC-T
*
54529 GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGA-T
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACT
*
54564 AGTTTCTCTTGAAACA
1 -GTTTCCCTTGAAACA
54580 CAAAATGTTG
Statistics
Matches: 137, Mismatches: 19, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
35 1 0.01
36 103 0.75
37 33 0.24
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACT
Found at i:54482 original size:72 final size:73
Alignment explanation
Indices: 54399--54579 Score: 240
Period size: 73 Copynumber: 2.5 Consensus size: 73
54389 CCTTGAAATG
* * *
54399 ATTTTTGTCTCTCTTGAGACTGTTTCCCATGAAACAAATTTTGTCTTTCTTGAGA-TAGTTTCCC
1 ATTTTT-TCTCTCTTGAGACTGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAAGTTTCCC
54463 TTAAAACAA
65 TTAAAACAA
* * *
54472 ATTTTTTCTCTATTGAGACAGCTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAAGTTTCCCT
1 ATTTTTTCTCTCTTGAGACTGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAAGTTTCCCT
*
54537 TGAAACAA
66 TAAAACAA
* * *
54545 ATTTTGTCTCCCTTGAGA-TAGTTTCTCTTGAAACA
1 ATTTTTTCTCTCTTGAGACT-GTTTCCCTTGAAACA
54580 CAAAATGTTG
Statistics
Matches: 93, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
72 43 0.46
73 50 0.54
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (73 bp):
ATTTTTTCTCTCTTGAGACTGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAAGTTTCCCT
TAAAACAA
Found at i:54528 original size:21 final size:20
Alignment explanation
Indices: 54497--54560 Score: 64
Period size: 21 Copynumber: 3.3 Consensus size: 20
54487 AGACAGCTTC
54497 CCTTGAAACAAATTTTGTCT
1 CCTTGAAACAAATTTTGTCT
* *
54517 CTCTTGAGAC-AA-GTT-TC-
1 C-CTTGAAACAAATTTTGTCT
54534 CCTTGAAACAAATTTTGTCT
1 CCTTGAAACAAATTTTGTCT
54554 CCCTTGA
1 -CCTTGA
54561 GATAGTTTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 11
0.69 0.08 0.22
Matches are distributed among these distances:
16 7 0.21
17 3 0.09
18 4 0.12
19 4 0.12
20 3 0.09
21 13 0.38
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (20 bp):
CCTTGAAACAAATTTTGTCT
Found at i:55254 original size:19 final size:17
Alignment explanation
Indices: 55231--55284 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
55221 TCTAGAAGAG
55231 TTCATAATGAGAAGAAC
1 TTCATAATGAGAAGAAC
* * *
55248 TCGTCATAAAG-GAAAAAG
1 T--TCATAATGAGAAGAAC
55266 TTCATAATGAGAAGAAC
1 TTCATAATGAGAAGAAC
55283 TT
1 TT
55285 TTTCCTTTCA
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
16 7 0.25
17 8 0.29
18 6 0.21
19 7 0.25
ACGTcount: A:0.46, C:0.11, G:0.19, T:0.24
Consensus pattern (17 bp):
TTCATAATGAGAAGAAC
Found at i:55425 original size:90 final size:92
Alignment explanation
Indices: 55317--55489 Score: 271
Period size: 92 Copynumber: 1.9 Consensus size: 92
55307 AAGGAGATAG
* *
55317 ATCAGTGTTTTCAATGGAGAGTTCATAAT-AGAAGAACTCATCC-AACG-AGAGAAAAGAAGTTC
1 ATCAGTGTTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAAG-GAAAAGAAGTTC
55379 ATAATGAGAAGAACTTGTTTGATCTCGC
65 ATAATGAGAAGAACTTGTTTGATCTCGC
* *
55407 ATCAGTGTTTCCAATGGAGAGTTCATAATGATAAGAACTCATCCGAAAGAAGGAGAAGAAGTTCA
1 ATCAGTGTTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAAGGAAAAGAAGTTCA
*
55472 TAATGAGAAGAGCTTGTT
66 TAATGAGAAGAACTTGTT
55490 CGACCTATCA
Statistics
Matches: 75, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
90 28 0.37
91 13 0.17
92 32 0.43
93 2 0.03
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.26
Consensus pattern (92 bp):
ATCAGTGTTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAAGGAAAAGAAGTTCA
TAATGAGAAGAACTTGTTTGATCTCGC
Found at i:55585 original size:19 final size:17
Alignment explanation
Indices: 55562--55615 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
55552 TCAAGAAGAG
55562 TTCATAATGAGAAGAAC
1 TTCATAATGAGAAGAAC
* * *
55579 TCGTCATAAAG-GAAAAAG
1 T--TCATAATGAGAAGAAC
55597 TTCATAATGAGAAGAAC
1 TTCATAATGAGAAGAAC
55614 TT
1 TT
55616 GTTCCTTTCA
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
16 7 0.25
17 8 0.29
18 6 0.21
19 7 0.25
ACGTcount: A:0.46, C:0.11, G:0.19, T:0.24
Consensus pattern (17 bp):
TTCATAATGAGAAGAAC
Found at i:55835 original size:43 final size:44
Alignment explanation
Indices: 55774--55945 Score: 210
Period size: 43 Copynumber: 4.0 Consensus size: 44
55764 GTGACGCCTC
* *
55774 GCTTG-AGAAACCATCGTGATATGTAGGGGTTTCTTGATGAAAA
1 GCTTGAAGAGACCATCGTGATATGTAGGGGTTTCTTGATGACAA
55817 GCTTGAAG-GACCATCGTGATATGTAGGGG-TTCTTTGATGACAA
1 GCTTGAAGAGACCATCGTGATATGTAGGGGTTTC-TTGATGACAA
* * *
55860 G-TTTAAGAAACCATCGTGATATGTAGGGGTTTCTTGATGACAT
1 GCTTGAAGAGACCATCGTGATATGTAGGGGTTTCTTGATGACAA
* * * * *
55903 GCTTG-AGAGACCAACATGATATGTAGAGGTTCCTTGGTGACAA
1 GCTTGAAGAGACCATCGTGATATGTAGGGGTTTCTTGATGACAA
55946 TTAAGAAACT
Statistics
Matches: 111, Mismatches: 13, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
42 8 0.07
43 96 0.86
44 7 0.06
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.30
Consensus pattern (44 bp):
GCTTGAAGAGACCATCGTGATATGTAGGGGTTTCTTGATGACAA
Found at i:55924 original size:86 final size:84
Alignment explanation
Indices: 55779--55954 Score: 255
Period size: 86 Copynumber: 2.1 Consensus size: 84
55769 GCCTCGCTTG
* * *
55779 AGAAACCATCGTGATATGTAGGGGTTTCTTGATGAAAAGCTTGAAGGACCATCGTGATATGTAGG
1 AGAAACCATCGTGATATGTAGGGGTTTCTTGATGAAAAGCTTGAAGGACCAACATGATATGTAGA
*
55844 GGTTCTTTGATGACAAGTTTA
66 GGTTCCTTGATGACAA--TTA
* *
55865 AGAAACCATCGTGATATGTAGGGGTTTCTTGATGACATGCTTG-AGAGACCAACATGATATGTAG
1 AGAAACCATCGTGATATGTAGGGGTTTCTTGATGAAAAGCTTGAAG-GACCAACATGATATGTAG
*
55929 AGGTTCCTTGGTGACAATTA
65 AGGTTCCTTGATGACAATTA
55949 AGAAAC
1 AGAAAC
55955 TAAGCCTTCG
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
84 9 0.11
85 2 0.02
86 71 0.87
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.30
Consensus pattern (84 bp):
AGAAACCATCGTGATATGTAGGGGTTTCTTGATGAAAAGCTTGAAGGACCAACATGATATGTAGA
GGTTCCTTGATGACAATTA
Found at i:56099 original size:90 final size:88
Alignment explanation
Indices: 55946--56116 Score: 216
Period size: 90 Copynumber: 1.9 Consensus size: 88
55936 TTGGTGACAA
* ** *
55946 TTAAGAAACTAAGCCTTCGGGGGTTTCTTAATTTTTAAATCCTTCGGGCCATTCATAAGACCTTC
1 TTAAGAAACTAAGCCTTCGGGCGTTTCTTAATTTTTAAATAATTCGGGCCATCCATAAGACCTTC
*
56011 AGTGCAGGATGTTTTCAAATGATAT
66 -G-GCAGGATGCTTTCAAATGATAT
* * * ** *
56036 TTAAGAAACTGAGCCTTTGGGCGTTTCTTGATTTTTACGTAATTCGGGCCATCCTTAAGACCTTC
1 TTAAGAAACTAAGCCTTCGGGCGTTTCTTAATTTTTAAATAATTCGGGCCATCCATAAGACCTTC
*
56101 GGTAGGATGCTTTCAA
66 GGCAGGATGCTTTCAA
56117 CATTTCCTTT
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
88 13 0.19
89 1 0.01
90 55 0.80
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (88 bp):
TTAAGAAACTAAGCCTTCGGGCGTTTCTTAATTTTTAAATAATTCGGGCCATCCATAAGACCTTC
GGCAGGATGCTTTCAAATGATAT
Found at i:60961 original size:10 final size:11
Alignment explanation
Indices: 60948--61030 Score: 68
Period size: 10 Copynumber: 7.7 Consensus size: 11
60938 AAAAGGGTTT
60948 TAAAA-AATAA
1 TAAAATAATAA
60958 TAAAATAAGTAA
1 TAAAATAA-TAA
* *
60970 AAAAATCAT--
1 TAAAATAATAA
**
60979 TAAAAGGGATAA
1 TAAAA-TAATAA
60991 TAAAATAATAA
1 TAAAATAATAA
61002 TGAAAATAA-AA
1 T-AAAATAATAA
61013 TAAAATAA-AA
1 TAAAATAATAA
61023 TAAAATAA
1 TAAAATAA
61031 AAAGGAAAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
9 4 0.07
10 24 0.40
11 11 0.18
12 21 0.35
ACGTcount: A:0.71, C:0.01, G:0.06, T:0.22
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:61012 original size:5 final size:5
Alignment explanation
Indices: 60989--61032 Score: 70
Period size: 5 Copynumber: 8.4 Consensus size: 5
60979 TAAAAGGGAT
60989 AATAA AATAA TAATGAA AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA -AAT-AA AATAA AATAA AATAA AATAA AATAA AA
61033 AGGAAAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
5 29 0.78
6 6 0.16
7 2 0.05
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:61024 original size:15 final size:16
Alignment explanation
Indices: 60989--61054 Score: 75
Period size: 15 Copynumber: 4.2 Consensus size: 16
60979 TAAAAGGGAT
60989 AATAAAATAATAATGAA
1 AATAAAATAA-AATGAA
61006 AATAAAATAAAAT-AA
1 AATAAAATAAAATGAA
* *
61021 AATAAAATAAAAAG-G
1 AATAAAATAAAATGAA
61036 AA-AAAATATAAATGAA
1 AATAAAATA-AAATGAA
61052 AAT
1 AAT
61055 TCGAATTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
14 6 0.15
15 20 0.49
16 5 0.12
17 10 0.24
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (16 bp):
AATAAAATAAAATGAA
Found at i:62280 original size:18 final size:18
Alignment explanation
Indices: 62208--62280 Score: 56
Period size: 18 Copynumber: 3.9 Consensus size: 18
62198 TGGATCCAAA
*
62208 AAATAAAATTAAATAAAT
1 AAATAAAAATAAATAAAT
* * *
62226 AAGTAATAATATAAAAATAAC
1 AAATAA-AA-ATAAATA-AAT
**
62247 AAATAATCATAAATAAAT
1 AAATAAAAATAAATAAAT
*
62265 AAATAAAAATATATAA
1 AAATAAAAATAAATAA
62281 TATTACATTT
Statistics
Matches: 40, Mismatches: 12, Indels: 6
0.69 0.21 0.10
Matches are distributed among these distances:
18 20 0.50
19 8 0.20
20 5 0.12
21 7 0.17
ACGTcount: A:0.70, C:0.03, G:0.01, T:0.26
Consensus pattern (18 bp):
AAATAAAAATAAATAAAT
Found at i:62396 original size:39 final size:38
Alignment explanation
Indices: 62299--62740 Score: 323
Period size: 36 Copynumber: 11.7 Consensus size: 38
62289 TTCCGAAAAT
* * ***
62299 AAAATATTTTAAAAACTATATATTATATGT-TTTCAAA
1 AAAATATTTTCAAAACTATATATTATATATATTTTTTA
** *
62336 AAAACGTTTCCAAAA--ACTATATTATATATACTTTTTTA
1 AAAATATTTTCAAAACTA-TATATTATATATA-TTTTTTA
* **
62374 AAAATATTTTAAAAACTATATATTATATAT-TTTTCAA
1 AAAATATTTTCAAAACTATATATTATATATATTTTTTA
62411 AAAATATTTTCAAAACTATATATTATATATA-TTTTT-
1 AAAATATTTTCAAAACTATATATTATATATATTTTTTA
* **
62447 AAAATGTTTTCAAAACTATATATTATATAT-TATTTCAA
1 AAAATATTTTCAAAACTATATATTATATATAT-TTTTTA
* *
62485 AATAATATTTTCAAAACTATATATTATATATA--TATTC
1 AA-AATATTTTCAAAACTATATATTATATATATTTTTTA
* *
62522 AAAATGTTTTCAAAATTATATATTATATATATTTTTTCA
1 AAAATATTTTCAAAACTATATATTATATATATTTTTT-A
* **
62561 AAAATCA-TTTGAAAACTATAATATATATATATATATATATACA
1 AAAAT-ATTTTCAAAACTAT-ATAT-TATATATAT-T-T-TTTA
*
62604 AAAATCATTTTCAAAACTATATAATATATATA-TTTTTA
1 AAAAT-ATTTTCAAAACTATATATTATATATATTTTTTA
* *
62642 AAAATCAATTTT-TAAAC---A-ATTAT-TATATGTTTTCA
1 AAAAT--ATTTTCAAAACTATATATTATATATAT-TTTTTA
* * * *
62677 AAAATCGTTTTATAAAAAT-TATA-TAT-TATATTTTTCA
1 AAAAT-ATTTT-CAAAACTATATATTATATATATTTTTTA
*
62714 AAAATATTTTCAAAAAT-TATATTATAT
1 AAAATATTTTCAAAACTATATATTATAT
62741 TAATATATAT
Statistics
Matches: 326, Mismatches: 48, Indels: 62
0.75 0.11 0.14
Matches are distributed among these distances:
33 4 0.01
34 8 0.02
35 22 0.07
36 77 0.24
37 66 0.20
38 40 0.12
39 61 0.19
40 6 0.02
41 9 0.03
42 9 0.03
43 12 0.04
44 12 0.04
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.45
Consensus pattern (38 bp):
AAAATATTTTCAAAACTATATATTATATATATTTTTTA
Found at i:62413 original size:75 final size:72
Alignment explanation
Indices: 62298--62740 Score: 345
Period size: 75 Copynumber: 5.9 Consensus size: 72
62288 TTTCCGAAAA
* *
62298 TAAAATATTTTAAAAACTATATATTATAT-GTTTTCAAAAAA-ACGTTTCCAAAAACTATAT-TA
1 TAAAATATTTTAAAAACTATATATTATATATTTTTCAAAAAATA--TTTTC-AAAACTATATAT-
62360 TATATACTTTTT
62 TATATA-TTTTT
62372 TAAAAATATTTTAAAAACTATATATTATATATTTTTCAAAAAATATTTTCAAAACTATATATTAT
1 T-AAAATATTTTAAAAACTATATATTATATATTTTTCAAAAAATATTTTCAAAACTATATATTAT
62437 ATATATTTT
65 ATAT-TTTT
* *
62446 TAAAATGTTTTCAAAACTATATATTATATATTATTTCAAAATAATATTTTCAAAACTATATATTA
1 TAAAATATTTTAAAAACTATATATTATATATT-TTTCAAAA-AATATTTTCAAAACTATATATTA
*
62511 TATATATATT
64 TATAT-TTTT
* * * * *
62521 CAAAATGTTTTCAAAATTATATATTATATATATTTTTTC-AAAAATCA-TTTGAAAACTATAATA
1 TAAAATATTTTAAAAACTATATA-T-TATATA-TTTTTCAAAAAAT-ATTTTCAAAACTAT-ATA
62584 TATATATATATATATAT
61 T-TATATAT-T-T-T-T
* * * *
62601 ACAAAAATCATTTTCAAAACTATATAATATATATATTTTT--AAAAATCAATTTT-TAAACAAT-
1 --TAAAAT-ATTTTAAAAACTATAT-AT-TATATATTTTTCAAAAAAT--ATTTTCAAAACTATA
* *
62662 TATTATATGTTTTC
59 TATTATATATTTTT
* * * *
62676 AAAAATCGTTTTATAAAAAT-TATA-TATTATATTTTTC-AAAAATATTTTCAAAAAT-TATATT
1 TAAAAT-ATTTTA-AAAACTATATATTA-TATATTTTTCAAAAAATATTTTCAAAACTATATATT
62737 ATAT
63 ATAT
62741 TAATATATAT
Statistics
Matches: 319, Mismatches: 23, Indels: 57
0.80 0.06 0.14
Matches are distributed among these distances:
70 8 0.03
71 20 0.06
72 7 0.02
73 44 0.14
74 35 0.11
75 100 0.31
76 21 0.07
77 21 0.07
78 3 0.01
79 7 0.02
80 4 0.01
81 6 0.02
82 17 0.05
83 25 0.08
84 1 0.00
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.45
Consensus pattern (72 bp):
TAAAATATTTTAAAAACTATATATTATATATTTTTCAAAAAATATTTTCAAAACTATATATTATA
TATTTTT
Found at i:62750 original size:2 final size:2
Alignment explanation
Indices: 62731--62775 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
62721 TTTCAAAAAT
62731 TA TA T- TA TA T- TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
62770 TA TA TA
1 TA TA TA
62776 ACATAAAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 3 0.08
2 37 0.93
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:62759 original size:158 final size:157
Alignment explanation
Indices: 62299--62757 Score: 371
Period size: 148 Copynumber: 3.0 Consensus size: 157
62289 TTCCGAAAAT
* * * ** * *
62299 AAAAT-ATTTTAAAAACTATATATTATATGTT-TTCAAAAA-AACGTTTCCAAAA-ACTATATTA
1 AAAATCATTTTCAAAACTATATATTATATATTATTTAAAAATAATATTT-TAAAACAATATATTA
* * *
62360 TATATACTTTTTTAAAAATATTTT-AAAAACTATATA-T-TATATA-TTTTTCAAAAAAT-ATTT
65 TATATA---TATTCAAAATGTTTTCAAAAA-TATATATTATATATATTTTTTC-AAAAATCA-TT
* *
62420 TCAAAACTAT-ATAT-TATATATAT-T-T-T--T
124 TAAAAACTATAATATATATATATATATATATACA
* * *
62447 AAAAT-GTTTTCAAAACTATATATTATATATTATTTCAAAATAATATTTTCAAAACTATATATTA
1 AAAATCATTTTCAAAACTATATATTATATATTATTTAAAAATAATATTTT-AAAACAATATATTA
* *
62511 TATATATATTCAAAATGTTTTCAAAATTATATATTATATATATTTTTTCAAAAATCATTTGAAAA
65 TATATATATTCAAAATGTTTTCAAAAATATATATTATATATATTTTTTCAAAAATCATTTAAAAA
62576 CTATAATATATATATATATATATATACA
130 CTATAATATATATATATATATATATACA
62604 AAAATCATTTTCAAAACTATATAATATATATATT-TTTAAAAATCAAT-TTTT-AAACAAT-TAT
1 AAAATCATTTTCAAAACTATAT-AT-TATATATTATTTAAAAAT-AATATTTTAAAACAATATAT
* *
62665 TATATGT-T-TTCAAAAATCGTTTTATAAAAAT-TATA-TAT-TATA-TTTTTCAAAAAT-ATTT
63 TATATATATATTC-AAAAT-GTTTT-CAAAAATATATATTATATATATTTTTTCAAAAATCA-TT
* *
62723 TCAAAAATTATATTATATTAATATATATATATATA
124 T-AAAAACTATAATATA-T-ATATATATATATATA
62758 TATATATATA
Statistics
Matches: 259, Mismatches: 25, Indels: 46
0.78 0.08 0.14
Matches are distributed among these distances:
148 46 0.18
149 11 0.04
150 32 0.12
151 24 0.09
152 10 0.04
153 16 0.06
154 20 0.08
155 11 0.04
156 33 0.13
157 16 0.06
158 15 0.06
159 14 0.05
160 11 0.04
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.45
Consensus pattern (157 bp):
AAAATCATTTTCAAAACTATATATTATATATTATTTAAAAATAATATTTTAAAACAATATATTAT
ATATATATTCAAAATGTTTTCAAAAATATATATTATATATATTTTTTCAAAAATCATTTAAAAAC
TATAATATATATATATATATATATACA
Found at i:73883 original size:31 final size:30
Alignment explanation
Indices: 73822--73884 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 30
73812 CCTCAATGAC
*
73822 AAATACAAACATAAAATAGATAAATAACCA
1 AAATACAAACATAAAAGAGATAAATAACCA
* * *
73852 AAATATAAACATAAAAAGAGATAGATGACCA
1 AAATACAAACAT-AAAAGAGATAAATAACCA
73883 AA
1 AA
73885 TAGATAATTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 11 0.39
31 17 0.61
ACGTcount: A:0.65, C:0.11, G:0.08, T:0.16
Consensus pattern (30 bp):
AAATACAAACATAAAAGAGATAAATAACCA
Found at i:73886 original size:30 final size:29
Alignment explanation
Indices: 73816--73886 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 29
73806 GATCTCCCTC
*
73816 AATGA-CAAATACAAACATAAAATAGATA
1 AATGACCAAATACAAACATAAAAGAGATA
* *
73844 AATAACCAAAATATAAACATAAAAAGAGATA
1 AATGACC-AAATACAAACAT-AAAAGAGATA
*
73875 GATGACCAAATA
1 AATGACCAAATA
73887 GATAATTGAC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 4 0.11
29 1 0.03
30 16 0.46
31 14 0.40
ACGTcount: A:0.63, C:0.11, G:0.08, T:0.17
Consensus pattern (29 bp):
AATGACCAAATACAAACATAAAAGAGATA
Found at i:74763 original size:15 final size:16
Alignment explanation
Indices: 74743--74772 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
74733 ATACAGTGAC
74743 AAATTTT-GTAACTAA
1 AAATTTTAGTAACTAA
74758 AAATTTTAGTAACTA
1 AAATTTTAGTAACTA
74773 TGATAGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (16 bp):
AAATTTTAGTAACTAA
Found at i:80481 original size:21 final size:21
Alignment explanation
Indices: 80442--80481 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
80432 GGACTCTTAG
* *
80442 TTAAAATTAAATGTAAATTGT
1 TTAAAATAAAATATAAATTGT
*
80463 TTAAAATAAAATATTAATT
1 TTAAAATAAAATATAAATT
80482 ACATTAATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (21 bp):
TTAAAATAAAATATAAATTGT
Found at i:81504 original size:18 final size:18
Alignment explanation
Indices: 81481--81515 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
81471 GATGAAAATC
81481 GAGGAGGA-AGAGAAGAAT
1 GAGGAGGAGA-AGAAGAAT
81499 GAGGAGGAGAAGAAGAA
1 GAGGAGGAGAAGAAGAA
81516 GTATGAAGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.94
19 1 0.06
ACGTcount: A:0.51, C:0.00, G:0.46, T:0.03
Consensus pattern (18 bp):
GAGGAGGAGAAGAAGAAT
Found at i:81507 original size:21 final size:21
Alignment explanation
Indices: 81481--81521 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
81471 GATGAAAATC
81481 GAGGAGGAAG-AGAAGAATGAG
1 GAGGA-GAAGAAGAAGAATGAG
*
81502 GAGGAGAAGAAGAAGTATGA
1 GAGGAGAAGAAGAAGAATGA
81522 AGAGTTGTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.49, C:0.00, G:0.44, T:0.07
Consensus pattern (21 bp):
GAGGAGAAGAAGAAGAATGAG
Found at i:85229 original size:25 final size:26
Alignment explanation
Indices: 85201--85251 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
85191 ATTTTGATGA
*
85201 ATCATT-ATGCCAACTAATGCACTTT
1 ATCATTGATACCAACTAATGCACTTT
*
85226 ATCATTGCTACCAACTAATGCACTTT
1 ATCATTGATACCAACTAATGCACTTT
85252 CGGTGCTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 6 0.26
26 17 0.74
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.35
Consensus pattern (26 bp):
ATCATTGATACCAACTAATGCACTTT
Found at i:89059 original size:15 final size:15
Alignment explanation
Indices: 89034--89073 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
89024 TCTTTAGGGA
*
89034 GCTTTTTCTCAGCTG
1 GCTTCTTCTCAGCTG
*
89049 GTTTCTTCTCAGCTG
1 GCTTCTTCTCAGCTG
89064 GCTTCTTCTC
1 GCTTCTTCTC
89074 GGCTTTTGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.05, C:0.30, G:0.17, T:0.47
Consensus pattern (15 bp):
GCTTCTTCTCAGCTG
Found at i:89534 original size:206 final size:206
Alignment explanation
Indices: 89180--90622 Score: 2634
Period size: 206 Copynumber: 7.0 Consensus size: 206
89170 ATATATAGGG
89180 GAAAAGTGTGTAATTTGATTGGTTGGTTTTGGTATGGGAGGATAAATGACGTGGAAAGTATGGGC
1 GAAAAGTGTGTAATTTGATTGGTTGGTTTTGGTATGGGAGGATAAATGACGTGGAAAGTATGGGC
*
89245 CGTTTGATTTAAGTTGGTGGGATTGGACGGAGAGGATCGGTTCTCGTTCATGCTAAGAATTAACA
66 CGTTTGATTTAAGTTGGTGGGATTGGACGGAGAGGATCGGTTCTCGTTCATGCTAAGGATTAACA
*
89310 TAAAAGCGGGGATTTAAGTTTTAGTTTTAAAAATATTTGCGCCTTATTCTTATGTGCTGCGGGTA
131 TAAAAGCGGGGATTTAAGTTTCAGTTTTAAAAATATTTGCGCCTTATTCTTATGTGCTGCGGGTA
89375 AAAACTAAAGT
196 AAAACTAAAGT
*
89386 GAAAAGTGTGTAATTTGATTGGTTGGTTTTGGTATGAGAGGATAAATGACGTGGAAAGTATGGGC
1 GAAAAGTGTGTAATTTGATTGGTTGGTTTTGGTATGGGAGGATAAATGACGTGGAAAGTATGGGC
*
89451 TGTTTGATTTAAGTTGGTGGGATTGGACGGAGAGGATCGGTTCTCGTTCATGCTAAGGATTAACA
66 CGTTTGATTTAAGTTGGTGGGATTGGACGGAGAGGATCGGTTCTCGTTCATGCTAAGGATTAACA
*
89516 TAAATGCGGGGATTTAAGTTTCAGTTTTAAAAATATTTGCGCCTTATTCTTATGTGCTGCGGGTA
131 TAAAAGCGGGGATTTAAGTTTCAGTTTTAAAAATATTTGCGCCTTATTCTTATGTGCTGCGGGTA
89581 AAAACTAAAGT
196 AAAACTAAAGT
*
89592 GAAAAGTGTGTAATTTGATTGGTTAGTTTTGGTATGGGAGGATAAATGACGTGGAAAGTATGGGC
1 GAAAAGTGTGTAATTTGATTGGTTGGTTTTGGTATGGGAGGATAAATGACGTGGAAAGTATGGGC
*
89657 CGTTTGATTTAAGTTGGTGGGATTGGACGGAGAGGAACGGTTCTCGTTCATGCTAAGGATTAACA
66 CGTTTGATTTAAGTTGGTGGGATTGGACGGAGAGGATCGGTTCTCGTTCATGCTAAGGATTAACA
* *
89722 TAAAAGCGGGGATTTAAGTTTTAGTTTTAAAAATATTTGCGCCTTATTCTTATGTGTTGCGGGTA
131 TAAAAGCGGGGATTTAAGTTTCAGTTTTAAAAATATTTGCGCCTTATTCTTATGTGCTGCGGGTA
89787 AAAACTAAAGT
196 AAAACTAAAGT
89798 GAAAAGTGTGTAATTTGATTGGTTGGTTTTGGTATGGGAGGATAAATGACGTGGAAAGTATGGGC
1 GAAAAGTGTGTAATTTGATTGGTTGGTTTTGGTATGGGAGGATAAATGACGTGGAAAGTATGGGC
*
89863 CGTTTGATTTAAGTTGGTGGGATTGGACGGAGAGGATCGATTCTCGTTCATGCTAAGGATTAACA
66 CGTTTGATTTAAGTTGGTGGGATTGGACGGAGAGGATCGGTTCTCGTTCATGCTAAGGATTAACA
* * *
89928 TAAATGCGAGGATTTAAGTTTCAGTTTTAAAAATATTTGCGCCTTATTCTTATGTGCCGCGGGTA
131 TAAAAGCGGGGATTTAAGTTTCAGTTTTAAAAATATTTGCGCCTTATTCTTATGTGCTGCGGGTA
89993 AAAACTAAAGT
196 AAAACTAAAGT
90004 GAAAAGTGTGTAATTTGATTGGTTGGTTTTGGTATGGGAGGATAAATGACGTGGAAAGTATGGGC
1 GAAAAGTGTGTAATTTGATTGGTTGGTTTTGGTATGGGAGGATAAATGACGTGGAAAGTATGGGC
* * *
90069 CGTTTGATTTAAGTTGGTGGGATTAGACGGAGATGATCGATTCTCGTTCATGCTAAGGATTAACA
66 CGTTTGATTTAAGTTGGTGGGATTGGACGGAGAGGATCGGTTCTCGTTCATGCTAAGGATTAACA
* *
90134 TAAAAGCGGGGATTTAAGTTTTAGTTTTAAAAATATTTGTGCCTTATTCTTATGTGCTGCGGGTA
131 TAAAAGCGGGGATTTAAGTTTCAGTTTTAAAAATATTTGCGCCTTATTCTTATGTGCTGCGGGTA
*
90199 AAATCTAAAGT
196 AAAACTAAAGT
*
90210 GAAAAGTGTGTAATTTGATTGGTTGGTTTTGGTATGGGAGGATAAATGACGTGGAAAGTATGGGT
1 GAAAAGTGTGTAATTTGATTGGTTGGTTTTGGTATGGGAGGATAAATGACGTGGAAAGTATGGGC
*
90275 CGTTTGATTTAAGTTGGTGGGATTGGACGGAGAGGATCGCTTCTCGTTCATGCTAAGGATTAACA
66 CGTTTGATTTAAGTTGGTGGGATTGGACGGAGAGGATCGGTTCTCGTTCATGCTAAGGATTAACA
*
90340 TAAAAGCGGGGATTTAAGTTTCAGTTTTAAAAATATTTGCGCCTTATTCTTATGTGTTGCGGGTA
131 TAAAAGCGGGGATTTAAGTTTCAGTTTTAAAAATATTTGCGCCTTATTCTTATGTGCTGCGGGTA
90405 AAAACTAAAGT
196 AAAACTAAAGT
*
90416 GGAAAGTGTGTAATTTGATTGGTTGGTTTTGGTATGGGAGGATAAATGACGTGGAAAGTATGGGC
1 GAAAAGTGTGTAATTTGATTGGTTGGTTTTGGTATGGGAGGATAAATGACGTGGAAAGTATGGGC
* *
90481 CTTTTGATTTAAGTTGGTGGGATTGGACGGAGAGGATCGGTTCTCGTTCATGTTAAGGATTAACA
66 CGTTTGATTTAAGTTGGTGGGATTGGACGGAGAGGATCGGTTCTCGTTCATGCTAAGGATTAACA
* * *
90546 TAAAAGCAGGGATTTAAGTTTCAGTTTTAAAAATATTTGCACCTTATTCTTATGTGATGCGGGTA
131 TAAAAGCGGGGATTTAAGTTTCAGTTTTAAAAATATTTGCGCCTTATTCTTATGTGCTGCGGGTA
90611 AAAACTAAAGT
196 AAAACTAAAGT
90622 G
1 G
90623 TTATCATAAT
Statistics
Matches: 1193, Mismatches: 44, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
206 1193 1.00
ACGTcount: A:0.28, C:0.09, G:0.29, T:0.34
Consensus pattern (206 bp):
GAAAAGTGTGTAATTTGATTGGTTGGTTTTGGTATGGGAGGATAAATGACGTGGAAAGTATGGGC
CGTTTGATTTAAGTTGGTGGGATTGGACGGAGAGGATCGGTTCTCGTTCATGCTAAGGATTAACA
TAAAAGCGGGGATTTAAGTTTCAGTTTTAAAAATATTTGCGCCTTATTCTTATGTGCTGCGGGTA
AAAACTAAAGT
Found at i:98755 original size:14 final size:14
Alignment explanation
Indices: 98736--98778 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
98726 GAAAAATTAT
98736 TATTTTTAAGAATA
1 TATTTTTAAGAATA
* *
98750 TATTTTT-ATACTA
1 TATTTTTAAGAATA
*
98763 TATTTGTAAGAATA
1 TATTTTTAAGAATA
98777 TA
1 TA
98779 ACCAAAATCT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (14 bp):
TATTTTTAAGAATA
Found at i:101136 original size:20 final size:20
Alignment explanation
Indices: 101108--101162 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
101098 AATGTTGATT
* *
101108 GTTGGTCGTTGACCGCTAAC
1 GTTGATCGTTGACCACTAAC
101128 GTTGATCGTTGACCACTAAC
1 GTTGATCGTTGACCACTAAC
*
101148 GTTGATCATTGACCA
1 GTTGATCGTTGACCA
101163 GCATTGACTC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.31
Consensus pattern (20 bp):
GTTGATCGTTGACCACTAAC
Done.