Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002898.1 Hibiscus syriacus cultivar Beakdansim tig00005987_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: 53252
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:335 original size:105 final size:105
Alignment explanation
Indices: 1--462 Score: 819
Period size: 105 Copynumber: 4.4 Consensus size: 105
1 TGTCTGGAGTCCAATATCCTTCG-TGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTT
1 TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTT
65 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
66 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
* *
105 TGTCTGGAGTCCAATATCCTTCGTTTGTGAAGTTG-CACTGGCTCTGAAATTGAGAAA--TTTGT
1 TGTCTGGAGTCCAATATCCTTCG-TTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGT
*
167 TGACAACCCGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
65 TGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
*
208 TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAACGTTTGTT
1 TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTT
273 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
66 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
*
313 TGTCTGGAGTCC-ATATCCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGT
1 TGTCTGGAGTCCAATAT-CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGT
377 TGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
65 TGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
418 TGTCTGGAGTCC-ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
463 GGTAAAACCT
Statistics
Matches: 344, Mismatches: 8, Indels: 12
0.95 0.02 0.03
Matches are distributed among these distances:
102 11 0.03
103 88 0.26
104 56 0.16
105 179 0.52
106 10 0.03
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (105 bp):
TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTT
GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
Found at i:358 original size:208 final size:210
Alignment explanation
Indices: 1--462 Score: 828
Period size: 208 Copynumber: 2.2 Consensus size: 210
*
1 TGTCTGGAGTCCAATATCCTTCG-TGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTT
1 TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAACGTTTGTT
65 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTT
66 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTT
* *
130 TGTGAAGTTGCACTGGCTCTGAAATTGAGAAAT-TT-GTTGACAACCCGCGGTCCCTTCGTCGTG
131 TGTGAAGTTGAACTGGCTCTGAAATTGAGAAATGTTCGTTGACAACCAGCGGTCCCTTCGTCGTG
193 AAGTTGAACTTGCGT
196 AAGTTGAACTTGCGT
208 TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAACGTTTGTT
1 TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAACGTTTGTT
273 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC-ATATCCCTTCG-
66 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT-CCTTCGT
*
336 TTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAACCAGCGGTCCCTTCGTCG
130 TTGTGAAGTTG-AACTGGCTCTGAAATTGAGAAATGTTCGTTGACAACCAGCGGTCCCTTCGTCG
401 TGAAGTTGAACTTGCGT
194 TGAAGTTGAACTTGCGT
418 TGTCTGGAGTCC-ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
463 GGTAAAACCT
Statistics
Matches: 246, Mismatches: 4, Indels: 8
0.95 0.02 0.03
Matches are distributed among these distances:
207 38 0.15
208 119 0.48
209 35 0.14
210 54 0.22
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (210 bp):
TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAACGTTTGTT
GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTT
TGTGAAGTTGAACTGGCTCTGAAATTGAGAAATGTTCGTTGACAACCAGCGGTCCCTTCGTCGTG
AAGTTGAACTTGCGT
Found at i:10672 original size:10 final size:10
Alignment explanation
Indices: 10647--10680 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
10637 AACGTTAGTA
*
10647 AAATAGAAAT
1 AAATAAAAAT
*
10657 AGATAAAAAT
1 AAATAAAAAT
10667 AAATAAAAAT
1 AAATAAAAAT
10677 AAAT
1 AAAT
10681 GGTAAATGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:13557 original size:12 final size:12
Alignment explanation
Indices: 13531--13575 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
13521 AAGAAAAATG
13531 TAATA-AATATA
1 TAATATAATATA
*
13542 TAATATAATTTA
1 TAATATAATATA
13554 TAATATAAATATA
1 TAATAT-AATATA
13567 TATATATAA
1 TA-ATATAA
13576 GGACGAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 9 0.31
14 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TAATATAATATA
Found at i:15979 original size:29 final size:29
Alignment explanation
Indices: 15935--16049 Score: 122
Period size: 29 Copynumber: 3.9 Consensus size: 29
15925 TACCGAAGGT
*
15935 AGGTCGCCATGCACGCCCGGCGACCTACC
1 AGGTCGCCATGCACGCCCAGCGACCTACC
* ***
15964 AGGTCGCCATGTACGCCCAGCGACCTGGT
1 AGGTCGCCATGCACGCCCAGCGACCTACC
* *
15993 AGGTCGCCATGCATGCCCTGCGACCTACC
1 AGGTCGCCATGCACGCCCAGCGACCTACC
** *
16022 AGCAACGCCCATGCACGCCCAACGACCT
1 AG-GTCG-CCATGCACGCCCAGCGACCT
16050 CCATGCACGC
Statistics
Matches: 68, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
29 49 0.72
30 2 0.03
31 17 0.25
ACGTcount: A:0.20, C:0.42, G:0.25, T:0.13
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCAGCGACCTACC
Found at i:16048 original size:31 final size:30
Alignment explanation
Indices: 15999--16142 Score: 130
Period size: 30 Copynumber: 5.1 Consensus size: 30
15989 TGGTAGGTCG
* **
15999 CCATGCATGCCCTGCGACCTACCA-GCAACGC
1 CCATGCACGCCCAACGACCT-CCATGC-ACGC
16030 CCATGCACGCCCAACGACCTCCATGCA---
1 CCATGCACGCCCAACGACCTCCATGCACGC
*
16057 -C--G--C-C-CAACGACCTCCATGCATGC
1 CCATGCACGCCCAACGACCTCCATGCACGC
* * *
16080 CCAGGCACGTCCAACGACCTCCATGCACGG
1 CCATGCACGCCCAACGACCTCCATGCACGC
16110 CCATGCACGCCCAACGACCTCCATGCACGC
1 CCATGCACGCCCAACGACCTCCATGCACGC
16140 CCA
1 CCA
16143 AGCTCGCCAA
Statistics
Matches: 93, Mismatches: 9, Indels: 23
0.74 0.07 0.18
Matches are distributed among these distances:
20 16 0.17
21 1 0.01
22 1 0.01
24 2 0.02
26 2 0.02
28 1 0.01
30 51 0.55
31 19 0.20
ACGTcount: A:0.24, C:0.47, G:0.18, T:0.11
Consensus pattern (30 bp):
CCATGCACGCCCAACGACCTCCATGCACGC
Found at i:16055 original size:20 final size:20
Alignment explanation
Indices: 16030--16143 Score: 101
Period size: 20 Copynumber: 5.7 Consensus size: 20
16020 CCAGCAACGC
16030 CCATGCACGCCCAACGACCT
1 CCATGCACGCCCAACGACCT
16050 CCATGCACGCCCAACGACCT
1 CCATGCACGCCCAACGACCT
* * *
16070 CCATGCATGCCC-AGGCACGT
1 CCATGCACGCCCAACG-ACCT
* * **
16090 CCA---ACGACCTCCATGCACGG
1 CCATGCACG-CC-CAACG-ACCT
16110 CCATGCACGCCCAACGACCT
1 CCATGCACGCCCAACGACCT
16130 CCATGCACGCCCAA
1 CCATGCACGCCCAA
16144 GCTCGCCAAA
Statistics
Matches: 77, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
17 2 0.03
18 2 0.03
19 3 0.04
20 62 0.81
21 3 0.04
22 2 0.03
23 3 0.04
ACGTcount: A:0.25, C:0.47, G:0.18, T:0.11
Consensus pattern (20 bp):
CCATGCACGCCCAACGACCT
Found at i:16062 original size:30 final size:30
Alignment explanation
Indices: 16050--16142 Score: 150
Period size: 30 Copynumber: 3.1 Consensus size: 30
16040 CCAACGACCT
*
16050 CCATGCACGCCCAACGACCTCCATGCATGC
1 CCATGCACGCCCAACGACCTCCATGCACGC
* * *
16080 CCAGGCACGTCCAACGACCTCCATGCACGG
1 CCATGCACGCCCAACGACCTCCATGCACGC
16110 CCATGCACGCCCAACGACCTCCATGCACGC
1 CCATGCACGCCCAACGACCTCCATGCACGC
16140 CCA
1 CCA
16143 AGCTCGCCAA
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 56 1.00
ACGTcount: A:0.24, C:0.47, G:0.18, T:0.11
Consensus pattern (30 bp):
CCATGCACGCCCAACGACCTCCATGCACGC
Found at i:16816 original size:21 final size:21
Alignment explanation
Indices: 16791--16834 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
16781 AATTTAGTTA
16791 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
16812 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
16833 AT
1 AT
16835 ATTATATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:16848 original size:28 final size:28
Alignment explanation
Indices: 16811--16864 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
16801 TAGTATAAAT
*
16811 TATTAGTTTGTTAGTTTAAGTTATATTA
1 TATTAATTTGTTAGTTTAAGTTATATTA
16839 TATTAATTTGTTAGTTTAAGTTATAT
1 TATTAATTTGTTAGTTTAAGTTATAT
16865 ATTAGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (28 bp):
TATTAATTTGTTAGTTTAAGTTATATTA
Found at i:19942 original size:10 final size:10
Alignment explanation
Indices: 19924--19961 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
19914 ATTTCTATGT
19924 ATTTA-TAAG
1 ATTTAGTAAG
19933 ATTTAGTAAG
1 ATTTAGTAAG
19943 ATTTAGTAATG
1 ATTTAGTAA-G
19954 A-TTAGTAA
1 ATTTAGTAA
19962 TAATGAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 5 0.19
10 20 0.74
11 2 0.07
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (10 bp):
ATTTAGTAAG
Found at i:20012 original size:60 final size:59
Alignment explanation
Indices: 19936--20124 Score: 233
Period size: 60 Copynumber: 3.4 Consensus size: 59
19926 TTATAAGATT
19936 TAGTAA-GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGA
1 TAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTAT-TATGATTTGA
*
19995 TAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATT-TT-T-A-ATGA
1 TAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATTATGATTTGA
*
20050 T--T--TGA--TAGTAATGATTAGTAATAAT-AATTTATTATTAA-TATTTAATGATTTGA
1 TAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTA-TT-ATGATTTGA
*
20103 TATTAATGATTTAGTAATGATT
1 TAGTAATGATTTAGTAATGATT
20125 TGATAGTAAT
Statistics
Matches: 114, Mismatches: 3, Indels: 26
0.80 0.02 0.18
Matches are distributed among these distances:
47 1 0.01
48 12 0.11
49 22 0.19
51 4 0.04
52 1 0.01
53 5 0.04
55 5 0.04
56 1 0.01
57 4 0.04
58 1 0.01
59 18 0.16
60 40 0.35
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (59 bp):
TAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATTATGATTTGA
Found at i:20095 original size:21 final size:22
Alignment explanation
Indices: 20071--20140 Score: 63
Period size: 25 Copynumber: 3.1 Consensus size: 22
20061 TGATTAGTAA
20071 TAATAATTT-ATTATTAAT-ATT
1 TAATAATTTGA-TATTAATGATT
*
20092 TAATGATTTGATATTAATGATTT
1 TAATAATTTGATATTAATGA-TT
* *
20115 AGTAATGATTTGATAGTAATGATT
1 --TAATAATTTGATATTAATGATT
20139 TA
1 TA
20141 CGACTTGAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
21 15 0.36
22 4 0.10
23 2 0.05
24 2 0.05
25 19 0.45
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (22 bp):
TAATAATTTGATATTAATGATT
Found at i:20098 original size:48 final size:49
Alignment explanation
Indices: 20006--20120 Score: 187
Period size: 48 Copynumber: 2.3 Consensus size: 49
19996 AGTAATGATT
*
20006 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
*
20055 TAGTAATGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
*
20103 TATTAATGATTTAGTAAT
1 TAGTAATGA-TTAGTAAT
20121 GATTTGATAG
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
48 34 0.55
49 28 0.45
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (49 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
Found at i:20108 original size:14 final size:14
Alignment explanation
Indices: 20092--20139 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
20082 TATTAATATT
*
20092 TAATGATTTGATAT
1 TAATGATTTGATAG
20106 TAATGA-TT--TAG
1 TAATGATTTGATAG
20117 TAATGATTTGATAG
1 TAATGATTTGATAG
20131 TAATGATTT
1 TAATGATTT
20140 ACGACTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 8 0.27
12 2 0.07
13 2 0.07
14 18 0.60
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (14 bp):
TAATGATTTGATAG
Found at i:22480 original size:30 final size:31
Alignment explanation
Indices: 22443--22518 Score: 86
Period size: 30 Copynumber: 2.5 Consensus size: 31
22433 TTTCCCTTAA
22443 ACAACTAATAAACTATTCTTTAA-TATAAATT
1 ACAACTAATAAACTATT-TTTAATTATAAATT
*
22474 A-AACTAATAAA-TGATTTTTAATTATAATTT
1 ACAACTAATAAACT-ATTTTTAATTATAAATT
* *
22504 ACTACTAAAAAACTA
1 ACAACTAATAAACTA
22519 ATTAACTCAT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
29 6 0.16
30 21 0.55
31 10 0.26
32 1 0.03
ACGTcount: A:0.50, C:0.11, G:0.01, T:0.38
Consensus pattern (31 bp):
ACAACTAATAAACTATTTTTAATTATAAATT
Found at i:22721 original size:21 final size:21
Alignment explanation
Indices: 22697--22736 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
22687 TTTCTATATG
22697 ATATAACTTAAACTAACAATA
1 ATATAACTTAAACTAACAATA
22718 ATATAACTTAAACTAACAA
1 ATATAACTTAAACTAACAA
22737 ACTAATTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (21 bp):
ATATAACTTAAACTAACAATA
Found at i:22817 original size:18 final size:18
Alignment explanation
Indices: 22764--22818 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
22754 TTGTTTTACC
*
22764 CTAATTTATAATAATAAA
1 CTAATTTATAACAATAAA
22782 CTAA--T-TAAC--T-AA
1 CTAATTTATAACAATAAA
22794 -TAATTTATAACAATAAA
1 CTAATTTATAACAATAAA
22811 CTAATTTA
1 CTAATTTA
22819 AATAATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
11 3 0.10
12 2 0.07
13 2 0.07
14 4 0.14
15 3 0.10
16 2 0.07
17 2 0.07
18 11 0.38
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (18 bp):
CTAATTTATAACAATAAA
Found at i:22877 original size:35 final size:37
Alignment explanation
Indices: 22838--22911 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 37
22828 TCTTTTATAT
22838 AACTT-AA-ACTAATAAACT-ATTTTTTATTATAATAA
1 AACTTAAACACTAATAAACTAATTTTTTA-TATAATAA
22873 AACTTAAACTACTAATAAACTAATTTTTTATATAATAA
1 AACTTAAAC-ACTAATAAACTAATTTTTTATATAATAA
22911 A
1 A
22912 TTCAACAACC
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
35 5 0.14
36 2 0.06
38 20 0.57
39 8 0.23
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (37 bp):
AACTTAAACACTAATAAACTAATTTTTTATATAATAA
Found at i:22967 original size:27 final size:29
Alignment explanation
Indices: 22932--22996 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
22922 AAAATATAAC
*
22932 TTAACTATTTA-ACTAACT-ACAAACTAA
1 TTAAATATTTAGACTAACTAACAAACTAA
*
22959 TTAAATA-TTAGACTAACTAACACACTAA
1 TTAAATATTTAGACTAACTAACAAACTAA
*
22987 TTAATTATTT
1 TTAAATATTT
22997 TTTAATATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 3 0.09
27 13 0.41
28 14 0.44
29 2 0.06
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.37
Consensus pattern (29 bp):
TTAAATATTTAGACTAACTAACAAACTAA
Found at i:23551 original size:33 final size:33
Alignment explanation
Indices: 23509--23574 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
23499 AAGCATGGAC
*
23509 TGCATGGTGACCTTTGGCGAGCTGGACGTGCAT
1 TGCATGGTGACCTTTGGCGAGATGGACGTGCAT
*
23542 TGCATGGTGACCTTTGGCGAGATGGGCGTGCAT
1 TGCATGGTGACCTTTGGCGAGATGGACGTGCAT
23575 GGGCGTGCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.15, C:0.20, G:0.38, T:0.27
Consensus pattern (33 bp):
TGCATGGTGACCTTTGGCGAGATGGACGTGCAT
Found at i:23578 original size:10 final size:10
Alignment explanation
Indices: 23563--23588 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
23553 CTTTGGCGAG
23563 ATGGGCGTGC
1 ATGGGCGTGC
23573 ATGGGCGTGC
1 ATGGGCGTGC
23583 ATGGGC
1 ATGGGC
23589 ATGGAGGTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.12, C:0.19, G:0.50, T:0.19
Consensus pattern (10 bp):
ATGGGCGTGC
Found at i:23643 original size:29 final size:28
Alignment explanation
Indices: 23608--23723 Score: 133
Period size: 29 Copynumber: 4.0 Consensus size: 28
23598 GTTGGCTGGT
*
23608 AGGTCGCAGGGCATGCATGGCGACCTACC
1 AGGTCGC-GGGCGTGCATGGCGACCTACC
***
23637 AGGTCGCTGGGCGTGCATGGCGACCTGGT
1 AGGTCGC-GGGCGTGCATGGCGACCTACC
***
23666 AGGTCGCCGGGCGTGCATGGCGACCTGGT
1 AGGTCG-CGGGCGTGCATGGCGACCTACC
23695 AGGTCGTCGGGCGTGCATGGCGACCTACC
1 AGGTCG-CGGGCGTGCATGGCGACCTACC
23724 TTCGGTACTG
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
29 76 0.99
30 1 0.01
ACGTcount: A:0.14, C:0.28, G:0.41, T:0.17
Consensus pattern (28 bp):
AGGTCGCGGGCGTGCATGGCGACCTACC
Found at i:23683 original size:58 final size:58
Alignment explanation
Indices: 23603--23720 Score: 175
Period size: 58 Copynumber: 2.0 Consensus size: 58
23593 AGGTCGTTGG
23603 CTGGTAGGTCGCAGGGCATGCATGGCGACCTACCAGGTCG-CTGGGCGTGCATGGCGAC
1 CTGGTAGGTCGCAGGGCATGCATGGCGACCTACCAGGTCGTC-GGGCGTGCATGGCGAC
* * ***
23661 CTGGTAGGTCGCCGGGCGTGCATGGCGACCTGGTAGGTCGTCGGGCGTGCATGGCGAC
1 CTGGTAGGTCGCAGGGCATGCATGGCGACCTACCAGGTCGTCGGGCGTGCATGGCGAC
23719 CT
1 CT
23721 ACCTTCGGTA
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
58 53 0.98
59 1 0.02
ACGTcount: A:0.13, C:0.27, G:0.42, T:0.19
Consensus pattern (58 bp):
CTGGTAGGTCGCAGGGCATGCATGGCGACCTACCAGGTCGTCGGGCGTGCATGGCGAC
Found at i:29740 original size:31 final size:31
Alignment explanation
Indices: 29704--29762 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
29694 AACTTAAAAG
* *
29704 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
29735 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
29763 CCATATAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:29813 original size:22 final size:22
Alignment explanation
Indices: 29787--29829 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
29777 TAATAAATTA
29787 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
29809 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
29830 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:29838 original size:22 final size:22
Alignment explanation
Indices: 29789--29837 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
29779 ATAAATTATT
**
29789 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
29811 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
29834 TAAA
1 TAAA
29838 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:29881 original size:58 final size:54
Alignment explanation
Indices: 29777--29887 Score: 132
Period size: 54 Copynumber: 2.0 Consensus size: 54
29767 ATAACTACAA
* * ** *
29777 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
1 TAATAAATTATTTAAAATAAATAAATCCATACTACAAAATAAATCAATCCATAC
*
29831 TAATAAATTATTTAAAATAAATAAATCTATACAACTACAATAATAAATCAATCCATA
1 TAATAAATTATTTAAAATAAATAAATCCAT---ACTACAA-AATAAATCAATCCATA
29888 TTTTAAAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
54 28 0.60
57 4 0.09
58 15 0.32
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATAAATCCATACTACAAAATAAATCAATCCATAC
Found at i:29916 original size:22 final size:23
Alignment explanation
Indices: 29849--29916 Score: 63
Period size: 22 Copynumber: 3.1 Consensus size: 23
29839 TATTTAAAAT
* *
29849 AAATAAATCTATACA-ACTAC-A
1 AAATAAATCAATCCATACTACTA
**
29870 ATAATAAATCAATCCATA-TTTTA
1 A-AATAAATCAATCCATACTACTA
29893 AAATAAATCAA-CCATACTACTA
1 AAATAAATCAATCCATACTACTA
29915 AA
1 AA
29917 TTATTTAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
21 6 0.16
22 28 0.76
23 3 0.08
ACGTcount: A:0.54, C:0.18, G:0.00, T:0.28
Consensus pattern (23 bp):
AAATAAATCAATCCATACTACTA
Found at i:29930 original size:133 final size:129
Alignment explanation
Indices: 29780--30032 Score: 398
Period size: 133 Copynumber: 1.9 Consensus size: 129
29770 ACTACAATAA
*
29780 TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTA
1 TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTA
*
29845 AAATAAATAAATCTATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAACCATAC
66 AAATAAATAAATCCAT---ACTACAA-AATAAATCAATCCATATTTTAAAATAAATCAACCATAC
29910 TAC
127 TAC
29913 TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTA
1 TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTA
* * ** * *
29978 AAATAAATCAATCCATATTTTAAAATAAATTAATTCATATTTTAAAATAAATCAA
66 AAATAAATAAATCCATACTACAAAATAAATCAATCCATATTTTAAAATAAATCAA
30033 TTCATATTTT
Statistics
Matches: 112, Mismatches: 8, Indels: 4
0.90 0.06 0.03
Matches are distributed among these distances:
129 30 0.27
130 4 0.04
133 78 0.70
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.36
Consensus pattern (129 bp):
TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTA
AAATAAATAAATCCATACTACAAAATAAATCAATCCATATTTTAAAATAAATCAACCATACTAC
Found at i:29940 original size:32 final size:31
Alignment explanation
Indices: 29889--29994 Score: 124
Period size: 32 Copynumber: 3.7 Consensus size: 31
29879 CAATCCATAT
29889 TTTAAAATAAATCAA-CCATACTACTAAATTA
1 TTTAAAATAAATCAATCCATACTA-TAAATTA
29920 TTTAAAATAAATCAAT-C---C-AT--A-T-
1 TTTAAAATAAATCAATCCATACTATAAATTA
29942 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACT-ATAAATTA
29974 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
29995 TTTTAAAATA
Statistics
Matches: 64, Mismatches: 0, Indels: 21
0.75 0.00 0.25
Matches are distributed among these distances:
22 16 0.25
23 2 0.03
24 1 0.02
26 2 0.03
27 1 0.02
28 3 0.05
30 1 0.02
31 17 0.27
32 21 0.33
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (31 bp):
TTTAAAATAAATCAATCCATACTATAAATTA
Found at i:29946 original size:22 final size:22
Alignment explanation
Indices: 29920--29962 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
29910 TACTAAATTA
29920 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
29942 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
29963 CTAATAAATT
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:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:29971 original size:22 final size:22
Alignment explanation
Indices: 29922--29970 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
29912 CTAAATTATT
**
29922 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
29944 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
29967 TAAA
1 TAAA
29971 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:29986 original size:54 final size:54
Alignment explanation
Indices: 29872--30016 Score: 256
Period size: 54 Copynumber: 2.7 Consensus size: 54
29862 CAACTACAAT
*
29872 AATAAATCAATCCATATTTTAAAATAAATCAA-CCATACTACTAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
29925 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* *
29979 AATAAATCAATCCATATTTTAAAATAAATTAATTCATA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATA
30017 TTTTAAAATA
Statistics
Matches: 88, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
53 32 0.36
54 56 0.64
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (54 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:30000 original size:22 final size:22
Alignment explanation
Indices: 29974--30049 Score: 125
Period size: 22 Copynumber: 3.5 Consensus size: 22
29964 TAATAAATTA
*
29974 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATTCATAT
*
29996 TTTAAAATAAATTAATTCATAT
1 TTTAAAATAAATCAATTCATAT
30018 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATTCATAT
*
30040 TTTATAATAA
1 TTTAAAATAA
30050 TTTATTTTAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (22 bp):
TTTAAAATAAATCAATTCATAT
Found at i:30057 original size:15 final size:15
Alignment explanation
Indices: 30037--30096 Score: 93
Period size: 15 Copynumber: 4.0 Consensus size: 15
30027 AATCAATTCA
* *
30037 TATTTTATAATAATT
1 TATTTTAAAATAAAT
30052 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
*
30067 TATTTTATAATAAAT
1 TATTTTAAAATAAAT
30082 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
30097 AACCTTATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 41 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTTAAAATAAAT
Found at i:30073 original size:30 final size:30
Alignment explanation
Indices: 30037--30096 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
30027 AATCAATTCA
*
30037 TATTTTATAATAATTTATTTTAAAATAAAT
1 TATTTTATAATAAATTATTTTAAAATAAAT
30067 TATTTTATAATAAATTATTTTAAAATAAAT
1 TATTTTATAATAAATTATTTTAAAATAAAT
30097 AACCTTATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
TATTTTATAATAAATTATTTTAAAATAAAT
Found at i:34250 original size:21 final size:21
Alignment explanation
Indices: 34177--34256 Score: 56
Period size: 21 Copynumber: 3.9 Consensus size: 21
34167 AAAATGACCA
**
34177 ACAAAATCGCAATGCGATAAT
1 ACAAAATCGCAACACGATAAT
* * **
34198 ACAAAATTGCAACGCGATTCT
1 ACAAAATCGCAACACGATAAT
* *
34219 GAC--TATTGCAACACGATAAT
1 -ACAAAATCGCAACACGATAAT
*
34239 ACAAAATCGCAATACGAT
1 ACAAAATCGCAACACGAT
34257 TTTCCAAATT
Statistics
Matches: 45, Mismatches: 11, Indels: 6
0.73 0.18 0.10
Matches are distributed among these distances:
19 2 0.04
20 13 0.29
21 28 0.62
22 2 0.04
ACGTcount: A:0.44, C:0.21, G:0.14, T:0.21
Consensus pattern (21 bp):
ACAAAATCGCAACACGATAAT
Found at i:34348 original size:40 final size:40
Alignment explanation
Indices: 34304--34381 Score: 156
Period size: 40 Copynumber: 1.9 Consensus size: 40
34294 TCCAAGTTCA
34304 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATT
34344 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAA
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAA
34382 ATCGCAACGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (40 bp):
CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATT
Found at i:34380 original size:21 final size:21
Alignment explanation
Indices: 34283--34373 Score: 132
Period size: 21 Copynumber: 4.4 Consensus size: 21
34273 AGTCCAAATT
*
34283 CGTTGCGATAGTCCAAGTTCA
1 CGTTGCGATAGTCCAAGTTCG
34304 CGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
** *
34325 CGTTGCGATTTTCCAAATT--
1 CGTTGCGATAGTCCAAGTTCG
34344 CGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
34365 CGTTGCGAT
1 CGTTGCGAT
34374 TTTCCAAAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
19 16 0.26
21 45 0.74
ACGTcount: A:0.20, C:0.23, G:0.25, T:0.32
Consensus pattern (21 bp):
CGTTGCGATAGTCCAAGTTCG
Found at i:34386 original size:21 final size:21
Alignment explanation
Indices: 34283--34386 Score: 86
Period size: 21 Copynumber: 5.0 Consensus size: 21
34273 AGTCCAAATT
** *
34283 CGTTGCGATAGTCCAAGTTCA
1 CGTTGCGATAGTCCAAAATCG
**
34304 CGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAAATCG
** *
34325 CGTTGCGATTTTCC-AAAT-T
1 CGTTGCGATAGTCCAAAATCG
**
34344 CGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAAATCG
**
34365 CGTTGCGATTTTCCAAAATCG
1 CGTTGCGATAGTCCAAAATCG
34386 C
1 C
34387 AACGACTGGT
Statistics
Matches: 66, Mismatches: 15, Indels: 4
0.78 0.18 0.05
Matches are distributed among these distances:
19 12 0.18
20 4 0.06
21 50 0.76
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.32
Consensus pattern (21 bp):
CGTTGCGATAGTCCAAAATCG
Found at i:34795 original size:19 final size:19
Alignment explanation
Indices: 34768--34809 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
34758 TATTTTGGAT
*
34768 TTTTCACTATCGCAACACA
1 TTTTAACTATCGCAACACA
34787 TTTTAACTATCGCAACACA
1 TTTTAACTATCGCAACACA
34806 TTTT
1 TTTT
34810 TCAAAATCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.31, C:0.26, G:0.05, T:0.38
Consensus pattern (19 bp):
TTTTAACTATCGCAACACA
Found at i:34862 original size:21 final size:20
Alignment explanation
Indices: 34814--34869 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
34804 CATTTTTCAA
* *
34814 AATCACGTTGCGAATCTTAC
1 AATCGCGTTGCGAATCTGAC
34834 AATCGCGTTGCGAATCTGA-
1 AATCGCGTTGCGAATCTGAC
34853 ATATTCGCGTTGCGAAT
1 A-A-TCGCGTTGCGAAT
34870 TTGGAAACTG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 1 0.03
20 18 0.56
21 13 0.41
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.30
Consensus pattern (20 bp):
AATCGCGTTGCGAATCTGAC
Found at i:35175 original size:23 final size:23
Alignment explanation
Indices: 35149--35203 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
35139 TACCAAAATA
35149 ACAAAACTT-ATGTATCTAATAGC
1 ACAAAACTTGA-GTATCTAATAGC
* *
35172 ACAAAAAATTGAGTATCTAATTGC
1 AC-AAAACTTGAGTATCTAATAGC
*
35196 AAAAAACT
1 ACAAAACT
35204 GAATACTACA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
23 7 0.27
24 18 0.69
25 1 0.04
ACGTcount: A:0.49, C:0.15, G:0.09, T:0.27
Consensus pattern (23 bp):
ACAAAACTTGAGTATCTAATAGC
Found at i:48952 original size:18 final size:18
Alignment explanation
Indices: 48914--48952 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
48904 TTTTCCAACG
* *
48914 CCATATCCAATGCCCTTT
1 CCATATCCAATGCCATAT
*
48932 CCATTTCCAATGCCATAT
1 CCATATCCAATGCCATAT
48950 CCA
1 CCA
48953 ATGTTGTTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.26, C:0.38, G:0.05, T:0.31
Consensus pattern (18 bp):
CCATATCCAATGCCATAT
Found at i:49053 original size:87 final size:87
Alignment explanation
Indices: 48959--49381 Score: 327
Period size: 87 Copynumber: 4.8 Consensus size: 87
48949 TCCAATGTTG
**
48959 TTTCCTGATTGGCCTCCCGATTGTCCAATGCCGTACCCAACACCTTCTCCATCTCCATTGCCAAT
1 TTTCCTGATTGGCCTCCCGATTGTCCAACACCGTACCCAACACCTTCTCCATCTCCATTGCCAAT
* * * *
49024 TCTAATTCAATACCCAACGTC-T
66 TCCAATACAATACCCAAC-ACAA
*
49046 TTTCCTGATTAGCCTCCCGATTGTCCAACACCGTACCCAACACCGACACCTTCTCCATCTCCATT
1 TTTCCTGATTGGCCTCCCGATTGTCCAACACCGTA-CC--CA---ACACCTTCTCCATCTCCATT
* *
49111 GCCAATTCCAATACCATATCCAACACAA
60 GCCAATTCCAATACAATACCCAACACAA
* * * * *
49139 TTTCCTGACTGACCTCCCAATTGTCCAACACCGTACCTAACGCCTTCTCCATCTCCATTGCCAAT
1 TTTCCTGATTGGCCTCCCGATTGTCCAACACCGTACCCAACACCTTCTCCATCTCCATTGCCAAT
* * *****
49204 TCCAATACCATATCCAATGTTG
66 TCCAATACAATACCCAACACAA
* * * * * * ** * ***
49226 TTTTCTGATTGACC-CCAGATTGTCCAACACCATACCCAATACTATTTCTTAAT-T-GACCCCCT
1 TTTCCTGATTGGCCTCCCGATTGTCCAACACCGTACCCAACAC--CTTCTCCATCTCCATTGCC-
* * * *
49288 AATTGCCCAACACCATATCCAATACAA
63 AATT--CCAATACAATACCCAACACAA
* * * *
49315 TTTCTTGATTGACCTCCCGATTGTCCGACACCATACCCAACACC-T-TCCATCTCCATTGCCAAT
1 TTTCCTGATTGGCCTCCCGATTGTCCAACACCGTACCCAACACCTTCTCCATCTCCATTGCCAAT
49378 TCCA
66 TCCA
49382 TTACCATATC
Statistics
Matches: 269, Mismatches: 52, Indels: 32
0.76 0.15 0.09
Matches are distributed among these distances:
85 3 0.01
86 28 0.10
87 97 0.36
88 11 0.04
89 28 0.10
90 28 0.10
92 3 0.01
93 71 0.26
ACGTcount: A:0.26, C:0.37, G:0.09, T:0.29
Consensus pattern (87 bp):
TTTCCTGATTGGCCTCCCGATTGTCCAACACCGTACCCAACACCTTCTCCATCTCCATTGCCAAT
TCCAATACAATACCCAACACAA
Found at i:49310 original size:45 final size:45
Alignment explanation
Indices: 49239--49354 Score: 153
Period size: 45 Copynumber: 2.6 Consensus size: 45
49229 TCTGATTGAC
*
49239 CCCAGATTGTCCAACACCATACCCAATACTATTTCTTAATTGACC-
1 CCCA-ATTGTCCAACACCATACCCAATACAATTTCTTAATTGACCT
* * *
49284 CCCTAATTGCCCAACACCATATCCAATACAATTTCTTGATTGACCT
1 CCC-AATTGTCCAACACCATACCCAATACAATTTCTTAATTGACCT
* *
49330 CCCGATTGTCCGACACCATACCCAA
1 CCCAATTGTCCAACACCATACCCAA
49355 CACCTTCCAT
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
45 57 0.93
46 4 0.07
ACGTcount: A:0.30, C:0.35, G:0.08, T:0.27
Consensus pattern (45 bp):
CCCAATTGTCCAACACCATACCCAATACAATTTCTTAATTGACCT
Done.