Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016259.1 Corchorus capsularis cultivar CVL-1 contig16280, 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: 48456
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.35
Found at i:2036 original size:32 final size:32
Alignment explanation
Indices: 1940--2227 Score: 290
Period size: 32 Copynumber: 8.5 Consensus size: 32
1930 CTCTTTTTAG
*
1940 ATTAAGTTCTTTATTGACTCCACTTAATTACCTTGA
1 ATTAAGTTCTTTATT--CT--ACTTAATTACCCTGA
1976 ATTAAGCTAT-TTTATTGACTCAACTTAATTACCCTGA
1 ATTAAG-T-TCTTTATT--CT--ACTTAATTACCCTGA
*
2013 ATTAAGTTCTTTATTCTTCTTAATTACCCTGA
1 ATTAAGTTCTTTATTCTACTTAATTACCCTGA
*
2045 ATTAAATTCTTTATTCTACTTAATTACCCTGA
1 ATTAAGTTCTTTATTCTACTTAATTACCCTGA
* * *
2077 ATTAAGACTTTTATTGACTCTACTTAATTGCCCTGA
1 ATTAAG--TTCT-TT-ATTCTACTTAATTACCCTGA
*
2113 ATTAAGTTCTTTATTCTACTTAATTATCCTGA
1 ATTAAGTTCTTTATTCTACTTAATTACCCTGA
** * *
2145 ATTAAGCCCTTTATTAACTCTACTTAATTGCCATGA
1 ATTAAGTTCTTTA-T---TCTACTTAATTACCCTGA
2181 ATTAAGTTCTTTATTCTACTTAATTACCCTGA
1 ATTAAGTTCTTTATTCTACTTAATTACCCTGA
**
2213 ATTAAGCCCTTTATT
1 ATTAAGTTCTTTATT
2228 AACTCTACTC
Statistics
Matches: 217, Mismatches: 24, Indels: 26
0.81 0.09 0.10
Matches are distributed among these distances:
32 106 0.49
33 3 0.01
34 8 0.04
35 4 0.02
36 63 0.29
37 32 0.15
38 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.07, T:0.45
Consensus pattern (32 bp):
ATTAAGTTCTTTATTCTACTTAATTACCCTGA
Found at i:2116 original size:68 final size:68
Alignment explanation
Indices: 1948--2241 Score: 373
Period size: 68 Copynumber: 4.3 Consensus size: 68
1938 AGATTAAGTT
* * *
1948 CTTTATTGACTCCACTTAATTACCTTGAATTAAGCTAT-TTTATTGACTCAACTTAATTACCCTG
1 CTTTATTAACTCTACTTAATTACCCTGAATTAAG-T-TCTTTATT--CT--ACTTAATTACCCTG
**
2012 AATTAAGTT
60 AATTAAGCC
*
2021 CTTTATT--CT-T-CTTAATTACCCTGAATTAAATTCTTTATTCTACTTAATTACCCTGAATTAA
1 CTTTATTAACTCTACTTAATTACCCTGAATTAAGTTCTTTATTCTACTTAATTACCCTGAATTAA
*
2082 GAC
66 GCC
* * * *
2085 TTTTATTGACTCTACTTAATTGCCCTGAATTAAGTTCTTTATTCTACTTAATTATCCTGAATTAA
1 CTTTATTAACTCTACTTAATTACCCTGAATTAAGTTCTTTATTCTACTTAATTACCCTGAATTAA
2150 GCC
66 GCC
* *
2153 CTTTATTAACTCTACTTAATTGCCATGAATTAAGTTCTTTATTCTACTTAATTACCCTGAATTAA
1 CTTTATTAACTCTACTTAATTACCCTGAATTAAGTTCTTTATTCTACTTAATTACCCTGAATTAA
2218 GCC
66 GCC
*
2221 CTTTATTAACTCTACTCAATT
1 CTTTATTAACTCTACTTAATT
2242 TCCTTCTCTG
Statistics
Matches: 201, Mismatches: 15, Indels: 15
0.87 0.06 0.06
Matches are distributed among these distances:
64 27 0.13
66 4 0.02
67 2 0.01
68 141 0.70
69 18 0.09
71 2 0.01
73 7 0.03
ACGTcount: A:0.29, C:0.20, G:0.07, T:0.44
Consensus pattern (68 bp):
CTTTATTAACTCTACTTAATTACCCTGAATTAAGTTCTTTATTCTACTTAATTACCCTGAATTAA
GCC
Found at i:2118 original size:100 final size:101
Alignment explanation
Indices: 1961--2227 Score: 328
Period size: 100 Copynumber: 2.6 Consensus size: 101
1951 TATTGACTCC
* *
1961 ACTTAATTACCTTGAATTAAGCTATTTTATTGACTCAACTTAATTACCCTGAATTAAGTTCTTTA
1 ACTTAATTACCATGAATTAAGC--TTTTATTGACTCTACTTAATTACCCTGAATTAAGTTCTTTA
* **
2026 TTCTTCTTAATTACCCTGAATTAAATTCTTTA-T-TCT
64 TTCTACTTAATTACCCTGAATTAAACCCTTTATTATCT
* *
2062 ACTTAATTACCCTGAATTAAGACTTTTATTGACTCTACTTAATTGCCCTGAATTAAGTTCTTTAT
1 ACTTAATTACCATGAATTAAG-CTTTTATTGACTCTACTTAATTACCCTGAATTAAGTTCTTTAT
* *
2127 TCTACTTAATTATCCTGAATTAAGCCCTTTATTAACTCT
65 TCTACTTAATTACCCTGAATTAAACCCTTTATT-A-TCT
* * * **
2166 ACTTAATTGCCATGAATTAAG-TTCT-TT-ATTCTACTTAATTACCCTGAATTAAGCCCTTTATT
1 ACTTAATTACCATGAATTAAGCTTTTATTGACTCTACTTAATTACCCTGAATTAAGTTCTTTATT
2228 AACTCTACTC
Statistics
Matches: 146, Mismatches: 15, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
100 97 0.66
101 23 0.16
102 4 0.03
104 22 0.15
ACGTcount: A:0.29, C:0.19, G:0.07, T:0.45
Consensus pattern (101 bp):
ACTTAATTACCATGAATTAAGCTTTTATTGACTCTACTTAATTACCCTGAATTAAGTTCTTTATT
CTACTTAATTACCCTGAATTAAACCCTTTATTATCT
Found at i:2283 original size:41 final size:40
Alignment explanation
Indices: 2238--2775 Score: 688
Period size: 41 Copynumber: 13.2 Consensus size: 40
2228 AACTCTACTC
*
2238 AATTTCCTT-CTCTGAAATTAAGTATGTGCTTGTCTTTACCT
1 AATTTCCTTCCT-TGAAATTAAGTCTGTGCTT-TCTTTACCT
* *
2279 AATTTCCTTTCTTGAAATTAAGTCTGTGCTATTCTTTACCG
1 AATTTCCTTCCTTGAAATTAAGTCTGTGCT-TTCTTTACCT
* * * *
2320 AATTTCCTTCCTTGAAATTAAGTATGTGCTATACTTAACTT
1 AATTTCCTTCCTTGAAATTAAGTCTGTGCT-TTCTTTACCT
* *
2361 AATTTCCTTCCCTGAAATTAAGTCTGTGTTATTCTTTACCT
1 AATTTCCTTCCTTGAAATTAAGTCTGTGCT-TTCTTTACCT
* *
2402 AATTTCCTTCCTTGAAATTAAGTCTGTGCTTACGTTTTCCT
1 AATTTCCTTCCTTGAAATTAAGTCTGTGCTTTC-TTTACCT
*
2443 AATTTCCTTCCTTGAAATTAAGTTTGTGCTTATCTTTACCT
1 AATTTCCTTCCTTGAAATTAAGTCTGTGCTT-TCTTTACCT
* * * *
2484 AAATTCCTTCTTTGAAATTAAGTATGTGTTGTTCTTTACCT
1 AATTTCCTTCCTTGAAATTAAGTCTGTGCT-TTCTTTACCT
*
2525 AATTTCCTTCCTTGAAATTAAG-CATGTGCTTGTCTTTACCG
1 AATTTCCTTCCTTGAAATTAAGTC-TGTGCTT-TCTTTACCT
* *
2566 AATTTCCCTCCTTGAAA-TAAGTCTGTGCTATACTTTACCT
1 AATTTCCTTCCTTGAAATTAAGTCTGTGCT-TTCTTTACCT
2606 AATTTCCTTCCTTGAAATTAAGTCTGTGCTATTCTTTACCT
1 AATTTCCTTCCTTGAAATTAAGTCTGTGCT-TTCTTTACCT
*
2647 AATTTCCTTCCTTGAAATTAAGTTTGTGCTATTCTTTACCT
1 AATTTCCTTCCTTGAAATTAAGTCTGTGCT-TTCTTTACCT
*
2688 AATTTCCTTCCTTGAAATTAAGTCTATG-TTTGCCTTTACCT
1 AATTTCCTTCCTTGAAATTAAGTCTGTGCTTT--CTTTACCT
* * *
2729 AATTTCCTTCCTTAAAATTAAGTCTGTGCTATACTTTACTT
1 AATTTCCTTCCTTGAAATTAAGTCTGTGCT-TTCTTTACCT
2770 AATTTC
1 AATTTC
2776 AAGGAAATTA
Statistics
Matches: 441, Mismatches: 42, Indels: 28
0.86 0.08 0.05
Matches are distributed among these distances:
39 2 0.00
40 37 0.08
41 395 0.90
42 6 0.01
43 1 0.00
ACGTcount: A:0.23, C:0.20, G:0.11, T:0.46
Consensus pattern (40 bp):
AATTTCCTTCCTTGAAATTAAGTCTGTGCTTTCTTTACCT
Found at i:2847 original size:35 final size:36
Alignment explanation
Indices: 2800--2882 Score: 114
Period size: 35 Copynumber: 2.3 Consensus size: 36
2790 TGTGTTTTAC
* * *
2800 TTTACTTGATTACCATGAATTATGTCC-TTGCTGCT
1 TTTACTTAATTACCATGAATTAAGTCCTTTACTGCT
*
2835 TTTACTTAATTACCATGAATTAAGTCCTTTTATTGCT
1 TTTACTTAATTACCATGAATTAAGTCC-TTTACTGCT
2872 TTTACTTAATT
1 TTTACTTAATT
2883 TCTATTTAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
35 25 0.60
37 17 0.40
ACGTcount: A:0.24, C:0.17, G:0.10, T:0.49
Consensus pattern (36 bp):
TTTACTTAATTACCATGAATTAAGTCCTTTACTGCT
Found at i:3027 original size:41 final size:41
Alignment explanation
Indices: 2982--3337 Score: 304
Period size: 41 Copynumber: 9.3 Consensus size: 41
2972 AGACTTTGCT
*
2982 TTTCTTAATTATCCCAAATTAAGACACTGATTGTGCTTAAC
1 TTTCTTAATTATCCCAAATTAAGACACTGACTGTGCTTAAC
*
3023 TTTCTTAATTATCCCAAATTAAGACACTGATTGTGCTTAAC
1 TTTCTTAATTATCCCAAATTAAGACACTGACTGTGCTTAAC
3064 TTTCTTAATTATCCCAAATTAAG--ACT--C--TGC-T---
1 TTTCTTAATTATCCCAAATTAAGACACTGACTGTGCTTAAC
*
3095 TTTCTTAATTA--CCGAATTAAGAC-CTTGACTGTGCTTAAC
1 TTTCTTAATTATCCCAAATTAAGACAC-TGACTGTGCTTAAC
* * * *
3134 TTTCTTAATTGTCCCAAATTAAGACTCTAACTGTG-TTTAC
1 TTTCTTAATTATCCCAAATTAAGACACTGACTGTGCTTAAC
* * *
3174 TTTCCTTAATTTTTCCAAATTAAGAC-CTTGACTGTGCTTACC
1 TTT-CTTAATTATCCCAAATTAAGACAC-TGACTGTGCTTAAC
**
3216 TTTCTTAATTA-CCTTGAATTAA-A-ACT---T-TGC-T---
1 TTTCTTAATTATCC-CAAATTAAGACACTGACTGTGCTTAAC
3247 TTTCTTAATTA--CCAAATTAAGAC-CTTGACTGTGCTTAAC
1 TTTCTTAATTATCCCAAATTAAGACAC-TGACTGTGCTTAAC
* * **
3286 TTTCTTAATTATCCCAAATTAAGACTCTAACTGTG-TTTGC
1 TTTCTTAATTATCCCAAATTAAGACACTGACTGTGCTTAAC
3326 TTTCCTTAATTA
1 TTT-CTTAATTA
3338 CTCTTAATTA
Statistics
Matches: 261, Mismatches: 20, Indels: 68
0.75 0.06 0.19
Matches are distributed among these distances:
29 15 0.06
30 4 0.02
31 24 0.09
33 1 0.00
34 3 0.01
35 12 0.05
36 3 0.01
39 25 0.10
40 17 0.07
41 149 0.57
42 8 0.03
ACGTcount: A:0.29, C:0.20, G:0.09, T:0.42
Consensus pattern (41 bp):
TTTCTTAATTATCCCAAATTAAGACACTGACTGTGCTTAAC
Found at i:3130 original size:70 final size:70
Alignment explanation
Indices: 3023--3313 Score: 334
Period size: 70 Copynumber: 4.0 Consensus size: 70
3013 TGTGCTTAAC
*
3023 TTTCTTAATTATCCCAAATTAAGACAC-TGATTGTGCTTAACTTTCTTAATTATCCCAAATTAAG
1 TTTCTTAATTA--CCAAATTAAGAC-CTTGACTGTGCTTAACTTTCTTAATTATCCCAAATTAAG
3087 ACTCTGCT
63 ACTCTGCT
* *
3095 TTTCTTAATTACCGAATTAAGACCTTGACTGTGCTTAACTTTCTTAATTGTCCCAAATTAAGACT
1 TTTCTTAATTACCAAATTAAGACCTTGACTGTGCTTAACTTTCTTAATTATCCCAAATTAAGA--
3160 CTAACTGTGTTTACT
64 CT--C--TG----CT
* * * ** *
3175 TTCCTTAATTTTTCCAAATTAAGACCTTGACTGTGCTTACCTTTCTTAATTA-CCTTGAATTAAA
1 TTTCTTAA--TTACCAAATTAAGACCTTGACTGTGCTTAACTTTCTTAATTATCC-CAAATTAAG
*
3239 ACTTTGCT
63 ACTCTGCT
3247 TTTCTTAATTACCAAATTAAGACCTTGACTGTGCTTAACTTTCTTAATTATCCCAAATTAAGACT
1 TTTCTTAATTACCAAATTAAGACCTTGACTGTGCTTAACTTTCTTAATTATCCCAAATTAAGACT
3312 CT
66 CT
3314 AACTGTGTTT
Statistics
Matches: 185, Mismatches: 19, Indels: 32
0.78 0.08 0.14
Matches are distributed among these distances:
69 1 0.01
70 97 0.52
71 2 0.01
72 22 0.12
74 1 0.01
76 4 0.02
80 11 0.06
81 2 0.01
82 45 0.24
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.42
Consensus pattern (70 bp):
TTTCTTAATTACCAAATTAAGACCTTGACTGTGCTTAACTTTCTTAATTATCCCAAATTAAGACT
CTGCT
Found at i:3149 original size:111 final size:112
Alignment explanation
Indices: 2968--3199 Score: 326
Period size: 111 Copynumber: 2.1 Consensus size: 112
2958 ATTACTTTGG
* *
2968 ATTAAGACTTTGCTTTTCTTAATTATCCCAAATTAAGACACTGATTGTGCTTAACTTTCTTAATT
1 ATTAAGACTCTGCTTTTCTTAATTA-CCCAAATTAAGACACTGACTGTGCTTAACTTTCTTAATT
* *
3033 ATCCCAAATTAAGACACTGATTGTGCTTAACTTT-CTTAATTATCCCAA
65 ATCCCAAATTAAGACACTAACTGTG-TTAACTTTCCTTAATTATCCCAA
*
3081 ATTAAGACTCTGCTTTTCTTAATTA-CCGAATTAAGAC-CTTGACTGTGCTTAACTTTCTTAATT
1 ATTAAGACTCTGCTTTTCTTAATTACCCAAATTAAGACAC-TGACTGTGCTTAACTTTCTTAATT
* * * * *
3144 GTCCCAAATTAAGACTCTAACTGTGTTTACTTTCCTTAATTTTTCCAA
65 ATCCCAAATTAAGACACTAACTGTGTTAACTTTCCTTAATTATCCCAA
3192 ATTAAGAC
1 ATTAAGAC
3200 CTTGACTGTG
Statistics
Matches: 107, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
110 8 0.07
111 75 0.70
113 24 0.22
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (112 bp):
ATTAAGACTCTGCTTTTCTTAATTACCCAAATTAAGACACTGACTGTGCTTAACTTTCTTAATTA
TCCCAAATTAAGACACTAACTGTGTTAACTTTCCTTAATTATCCCAA
Found at i:3319 original size:111 final size:106
Alignment explanation
Indices: 3017--3347 Score: 269
Period size: 111 Copynumber: 3.0 Consensus size: 106
3007 ACTGATTGTG
*
3017 CTTAACTTTCTTAATTATCCCAAATTAAGACAC-TGATTGTGCTTAACTTTCTTAATTATCCCAA
1 CTTAACTTTCTTAATTA--CCAAATTAAGAC-CTTGACTGTGCTTAACTTTCTTAATTATCCCAA
* * * * * ** * *
3081 ATTAAGACTCTGCTTTTCTTAATTACCGAATTAAGACCTTGACTGT-G
63 ATTAAGACTCTACTGTGCTTACTTTCTTAATT---ACCTTGAAT-TAA
* * * * *
3128 CTTAACTTTCTTAATTGTCCCAAATTAAGA-CTCTAACTGTG-TTTACTTTCCTTAATTTTTCCA
1 CTTAACTTTCTTAA-T-TACCAAATTAAGACCT-TGACTGTGCTTAACTTT-CTTAATTATCCCA
3191 AATTAAGAC-CTTGACTGTGCTTACCTTTCTTAATTACCTTGAATTAAAA
62 AATTAAGACTC-T-ACTGTGCTTA-CTTTCTTAATTACCTTGAATT--AA
**
3240 CTTTGCTTTTCTTAATTACCAAATTAAGACCTTGACTGTGCTTAACTTTCTTAATTATCCCAAAT
1 CTTAAC-TTTCTTAATTACCAAATTAAGACCTTGACTGTGCTTAACTTTCTTAATTATCCCAAAT
* *
3305 TAAGACTCTAACTGTGTTTGCTTTCCTTAATTACTCTT-AATTA
65 TAAGACTCT-ACTGTGCTTACTTT-CTTAATTAC-CTTGAATTA
3348 TATTGAATTA
Statistics
Matches: 178, Mismatches: 25, Indels: 36
0.74 0.10 0.15
Matches are distributed among these distances:
109 3 0.02
110 20 0.11
111 113 0.63
112 26 0.15
113 16 0.09
ACGTcount: A:0.28, C:0.21, G:0.09, T:0.42
Consensus pattern (106 bp):
CTTAACTTTCTTAATTACCAAATTAAGACCTTGACTGTGCTTAACTTTCTTAATTATCCCAAATT
AAGACTCTACTGTGCTTACTTTCTTAATTACCTTGAATTAA
Found at i:3347 original size:152 final size:151
Alignment explanation
Indices: 2982--3337 Score: 520
Period size: 152 Copynumber: 2.3 Consensus size: 151
2972 AGACTTTGCT
* * * *
2982 TTTCTTAATTATCCCAAATTAAGACACTGATTGTGCTTAACTTT-CTTAATTATCCCAAATTAAG
1 TTTCTTAATTATCCCAAATTAAGACTCTAACTGTG-TTTACTTTCCTTAATTAT-CCAAATTAAG
* * *
3046 ACACTGATTGTGCTTAACTTTCTTAATTATCCCAAATTAAGACTCTGCTTTTCTTAATTACCGAA
64 ACACTGACTGTGCTTAACTTTCTTAATTATCCCAAATTAAAACTCTGCTTTTCTTAATTACCAAA
3111 TTAAGACCTTGACTGTGCTTAAC
129 TTAAGACCTTGACTGTGCTTAAC
* *
3134 TTTCTTAATTGTCCCAAATTAAGACTCTAACTGTGTTTACTTTCCTTAATTTTTCCAAATTAAGA
1 TTTCTTAATTATCCCAAATTAAGACTCTAACTGTGTTTACTTTCCTTAA-TTATCCAAATTAAGA
* ** *
3199 C-CTTGACTGTGCTTACCTTTCTTAATTA-CCTTGAATTAAAACTTTGCTTTTCTTAATTACCAA
65 CAC-TGACTGTGCTTAACTTTCTTAATTATCC-CAAATTAAAACTCTGCTTTTCTTAATTACCAA
3262 ATTAAGACCTTGACTGTGCTTAAC
128 ATTAAGACCTTGACTGTGCTTAAC
*
3286 TTTCTTAATTATCCCAAATTAAGACTCTAACTGTGTTTGCTTTCCTTAATTA
1 TTTCTTAATTATCCCAAATTAAGACTCTAACTGTGTTTACTTTCCTTAATTA
3338 CTCTTAATTA
Statistics
Matches: 184, Mismatches: 16, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
151 12 0.07
152 169 0.92
153 3 0.02
ACGTcount: A:0.29, C:0.20, G:0.09, T:0.42
Consensus pattern (151 bp):
TTTCTTAATTATCCCAAATTAAGACTCTAACTGTGTTTACTTTCCTTAATTATCCAAATTAAGAC
ACTGACTGTGCTTAACTTTCTTAATTATCCCAAATTAAAACTCTGCTTTTCTTAATTACCAAATT
AAGACCTTGACTGTGCTTAAC
Found at i:19738 original size:39 final size:40
Alignment explanation
Indices: 19661--19793 Score: 200
Period size: 40 Copynumber: 3.4 Consensus size: 40
19651 CTGATGACTC
* *
19661 CTTTTACTTTTACT--TTTAATTACCAATTTACTGATTACTT
1 CTTTTACTTTTACTCCTTT--TTACCAATTTTCTGCTTACTT
*
19701 CTTTTATTTTTACTCCTTTTT-CCAATTTTCTGCTTACTT
1 CTTTTACTTTTACTCCTTTTTACCAATTTTCTGCTTACTT
19740 CTTTTACTTTTACTCCTTTTTACCAATTTTCTGCTTACTT
1 CTTTTACTTTTACTCCTTTTTACCAATTTTCTGCTTACTT
19780 CTTTTACTTTTACT
1 CTTTTACTTTTACT
19794 GATTACTTCT
Statistics
Matches: 86, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
39 36 0.42
40 47 0.55
42 3 0.03
ACGTcount: A:0.17, C:0.22, G:0.02, T:0.59
Consensus pattern (40 bp):
CTTTTACTTTTACTCCTTTTTACCAATTTTCTGCTTACTT
Found at i:19802 original size:22 final size:22
Alignment explanation
Indices: 19766--19815 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
19756 TTTTTACCAA
*
19766 TTTT-CTGCTTACTTCTTTTAC
1 TTTTACTGATTACTTCTTTTAC
19787 TTTTACTGATTACTTCTTTTAC
1 TTTTACTGATTACTTCTTTTAC
19809 TTTTACT
1 TTTTACT
19816 CTTTATTACC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 4 0.15
22 23 0.85
ACGTcount: A:0.14, C:0.20, G:0.04, T:0.62
Consensus pattern (22 bp):
TTTTACTGATTACTTCTTTTAC
Found at i:19833 original size:40 final size:40
Alignment explanation
Indices: 19789--20015 Score: 300
Period size: 40 Copynumber: 5.7 Consensus size: 40
19779 TCTTTTACTT
* *
19789 TTACTGATTACTTCTTTTACTTTTACTCTTTATTACCAAC
1 TTACTGATTACTCCTTTTACTTTTACTCTTGATTACCAAC
* *
19829 TTACTGATTTC-CTCTTTTACTTTTACTCTTGATTACCAAT
1 TTACTGATTACTC-CTTTTACTTTTACTCTTGATTACCAAC
19869 TTACT-ACTTACTCCTTTTACTTTTACTCTTGATTACCAA-
1 TTACTGA-TTACTCCTTTTACTTTTACTCTTGATTACCAAC
* *
19908 TCTACTGCTTACTCCTTTTACTTTTACTCTTAATTACCAAC
1 T-TACTGATTACTCCTTTTACTTTTACTCTTGATTACCAAC
* *
19949 TTACTGATTACTCCTTTTACTTTTACTCATT-TTTACCAAT
1 TTACTGATTACTCCTTTTACTTTTACTC-TTGATTACCAAC
* *
19989 TTTCTGATTACTTCTTTTACTTTTACT
1 TTACTGATTACTCCTTTTACTTTTACT
20016 TCATTCTGCC
Statistics
Matches: 168, Mismatches: 12, Indels: 14
0.87 0.06 0.07
Matches are distributed among these distances:
39 2 0.01
40 162 0.96
41 4 0.02
ACGTcount: A:0.21, C:0.24, G:0.03, T:0.52
Consensus pattern (40 bp):
TTACTGATTACTCCTTTTACTTTTACTCTTGATTACCAAC
Found at i:19879 original size:102 final size:101
Alignment explanation
Indices: 19687--19895 Score: 287
Period size: 102 Copynumber: 2.1 Consensus size: 101
19677 TAATTACCAA
* * * * *
19687 TTTACTGATTACTTCTTTTATTTTTACTCCTTTTTCCAATTTTCTGCTTACTTCTTTTACTTTTA
1 TTTACTGATTACTTCTTTTACTTTTACTCCTTTTTCCAACTTACTGATTACCTCTTTTACTTTTA
* * * *
19752 CTCCTTTTTACCAATTTTCTGCTTACTTCTTTTACT
66 CTCCTTATTACCAATTTACTACTTACTCCTTTTACT
*
19788 TTTACTGATTACTTCTTTTACTTTTACT-CTTTATTACCAACTTACTGATTTCCTCTTTTACTTT
1 TTTACTGATTACTTCTTTTACTTTTACTCCTTT-TT-CCAACTTACTGATTACCTCTTTTACTTT
19852 TACT-CTTGATTACCAATTTACTACTTACTCCTTTTACT
64 TACTCCTT-ATTACCAATTTACTACTTACTCCTTTTACT
19890 TTTACT
1 TTTACT
19896 CTTGATTACC
Statistics
Matches: 95, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
100 4 0.04
101 32 0.34
102 59 0.62
ACGTcount: A:0.18, C:0.23, G:0.03, T:0.56
Consensus pattern (101 bp):
TTTACTGATTACTTCTTTTACTTTTACTCCTTTTTCCAACTTACTGATTACCTCTTTTACTTTTA
CTCCTTATTACCAATTTACTACTTACTCCTTTTACT
Found at i:19927 original size:120 final size:120
Alignment explanation
Indices: 19790--20015 Score: 341
Period size: 120 Copynumber: 1.9 Consensus size: 120
19780 CTTTTACTTT
* * *
19790 TACTGATTACTTCTTTTACTTTTACTCTTTATTACCAACTTACTGATTTC-CTCTTTTACTTTTA
1 TACTGATTACTCCTTTTACTTTTACTCTTAATTACCAACTTACTGATTACTC-CTTTTACTTTTA
19854 CTC-TTGATTACCAATTTACT-ACTTACTCCTTTTACTTTTACTCTTGATTACCAATC
65 CTCATT-ATTACCAATTTACTGA-TTACTCCTTTTACTTTTACTCTTGATTACCAATC
*
19910 TACTGCTTACTCCTTTTACTTTTACTCTTAATTACCAACTTACTGATTACTCCTTTTACTTTTAC
1 TACTGATTACTCCTTTTACTTTTACTCTTAATTACCAACTTACTGATTACTCCTTTTACTTTTAC
* * *
19975 TCATTTTTACCAATTTTCTGATTACTTCTTTTACTTTTACT
66 TCATTATTACCAATTTACTGATTACTCCTTTTACTTTTACT
20016 TCATTCTGCC
Statistics
Matches: 96, Mismatches: 7, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
120 92 0.96
121 4 0.04
ACGTcount: A:0.21, C:0.24, G:0.03, T:0.52
Consensus pattern (120 bp):
TACTGATTACTCCTTTTACTTTTACTCTTAATTACCAACTTACTGATTACTCCTTTTACTTTTAC
TCATTATTACCAATTTACTGATTACTCCTTTTACTTTTACTCTTGATTACCAATC
Found at i:19930 original size:142 final size:141
Alignment explanation
Indices: 19648--19935 Score: 393
Period size: 142 Copynumber: 2.0 Consensus size: 141
19638 ATTAAACCCA
* * *
19648 TTACTGATGACTCCTTTTACTTTTACTTTTAATTACCAATTTACTGATTACTTCTTTTATTTTTA
1 TTACTGATGACTCCTTTTACTTTTACTTTTAATTACCAACTTACTGATTACCTCTTTTACTTTTA
* * * * * * *
19713 CTCCTTTTTCCAATTTTCTGCTTACTTCTTTTACTTTTACTCCTTTTTACCAATTTTCTGCTTAC
66 CTCCTTTTACCAATTTACTACTTACTCCTTTTACTTTTACTCCTTATTACCAATCTACTGCTTAC
*
19778 TTCTTTTACTT
131 TCCTTTTACTT
* * *
19789 TTACTGATTACTTCTTTTACTTTTACTCTTT-ATTACCAACTTACTGATTTCCTCTTTTACTTTT
1 TTACTGATGACTCCTTTTACTTTTACT-TTTAATTACCAACTTACTGATTACCTCTTTTACTTTT
19853 ACT-CTTGATTACCAATTTACTACTTACTCCTTTTACTTTTACT-CTTGATTACCAATCTACTGC
65 ACTCCTT--TTACCAATTTACTACTTACTCCTTTTACTTTTACTCCTT-ATTACCAATCTACTGC
19916 TTACTCCTTTTACTT
127 TTACTCCTTTTACTT
19931 TTACT
1 TTACT
19936 CTTAATTACC
Statistics
Matches: 129, Mismatches: 14, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
140 3 0.02
141 60 0.47
142 66 0.51
ACGTcount: A:0.19, C:0.23, G:0.03, T:0.54
Consensus pattern (141 bp):
TTACTGATGACTCCTTTTACTTTTACTTTTAATTACCAACTTACTGATTACCTCTTTTACTTTTA
CTCCTTTTACCAATTTACTACTTACTCCTTTTACTTTTACTCCTTATTACCAATCTACTGCTTAC
TCCTTTTACTT
Found at i:20033 original size:17 final size:17
Alignment explanation
Indices: 20011--20066 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
20001 TCTTTTACTT
20011 TTACTTCATTCTGCCGA
1 TTACTTCATTCTGCCGA
** **
20028 TTACTTC-TT-TTACTT
1 TTACTTCATTCTGCCGA
*
20043 TTACGTCATTCTGCCGA
1 TTACTTCATTCTGCCGA
20060 TTACTTC
1 TTACTTC
20067 TTTTACTTTT
Statistics
Matches: 27, Mismatches: 10, Indels: 4
0.66 0.24 0.10
Matches are distributed among these distances:
15 8 0.30
16 4 0.15
17 15 0.56
ACGTcount: A:0.16, C:0.27, G:0.09, T:0.48
Consensus pattern (17 bp):
TTACTTCATTCTGCCGA
Found at i:20033 original size:32 final size:32
Alignment explanation
Indices: 19994--20113 Score: 206
Period size: 32 Copynumber: 3.8 Consensus size: 32
19984 CCAATTTTCT
19994 GATTACTTCTTTTACTTTTACTTCATTCTGCC
1 GATTACTTCTTTTACTTTTACTTCATTCTGCC
*
20026 GATTACTTCTTTTACTTTTACGTCATTCTGCC
1 GATTACTTCTTTTACTTTTACTTCATTCTGCC
*
20058 GATTACTTCTTTTACTTTTACTTCACTT-TGCT
1 GATTACTTCTTTTACTTTTACTTCA-TTCTGCC
20090 GATTACTTCTTTTACTTTTACTTC
1 GATTACTTCTTTTACTTTTACTTC
20114 TTTTTTACCA
Statistics
Matches: 84, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
32 82 0.98
33 2 0.02
ACGTcount: A:0.16, C:0.23, G:0.07, T:0.54
Consensus pattern (32 bp):
GATTACTTCTTTTACTTTTACTTCATTCTGCC
Found at i:20152 original size:30 final size:30
Alignment explanation
Indices: 20116--20176 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
20106 TTTACTTCTT
* *
20116 TTTTACCAATTTACTAATTACTTCTTTTAC
1 TTTTACCAATTTACTAATCACTTCCTTTAC
* * *
20146 TTTTACCATTTTTCTGATCACTTCCTTTAC
1 TTTTACCAATTTACTAATCACTTCCTTTAC
20176 T
1 T
20177 CTTTTTATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.21, C:0.23, G:0.02, T:0.54
Consensus pattern (30 bp):
TTTTACCAATTTACTAATCACTTCCTTTAC
Found at i:20247 original size:58 final size:56
Alignment explanation
Indices: 20165--20327 Score: 227
Period size: 58 Copynumber: 2.9 Consensus size: 56
20155 TTTTCTGATC
* * * **
20165 ACTTCCTTTACTCTTTTTATTTTAATTACTATGAATTAAACTATCTACTGGTTACT
1 ACTTCTTTTACTCTTTTTAGTTTAATTACTCTGAATTAAACTATCTACTAATTACT
20221 ACTTCTTTTACTATCTTTTTAGTTTAATTACTCTGAATTAAACTATCTACTAATTACT
1 ACTTCTTTTAC--TCTTTTTAGTTTAATTACTCTGAATTAAACTATCTACTAATTACT
** * *
20279 TTTTCTTTTACTCTTTTTAGTTTAATTCCTCCGAATTAAACTATCTACT
1 ACTTCTTTTACTCTTTTTAGTTTAATTACTCTGAATTAAACTATCTACT
20328 TAGCCACCTT
Statistics
Matches: 96, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
56 46 0.48
58 50 0.52
ACGTcount: A:0.26, C:0.18, G:0.04, T:0.51
Consensus pattern (56 bp):
ACTTCTTTTACTCTTTTTAGTTTAATTACTCTGAATTAAACTATCTACTAATTACT
Found at i:20637 original size:6 final size:6
Alignment explanation
Indices: 20628--20660 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
20618 AAAGCAAAGC
20628 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
20661 GCAGATTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:20675 original size:13 final size:13
Alignment explanation
Indices: 20657--20697 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
20647 AATCTAAATC
*
20657 TAAAGCAGATTAA
1 TAAAGCAAATTAA
20670 TAAAGCAAATTAA
1 TAAAGCAAATTAA
20683 TAAAGCAAA-TAA
1 TAAAGCAAATTAA
20695 TAA
1 TAA
20698 TTATAAAGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
12 6 0.22
13 21 0.78
ACGTcount: A:0.61, C:0.07, G:0.10, T:0.22
Consensus pattern (13 bp):
TAAAGCAAATTAA
Found at i:25000 original size:26 final size:27
Alignment explanation
Indices: 24969--25049 Score: 94
Period size: 26 Copynumber: 3.0 Consensus size: 27
24959 GTAATTTAGT
24969 TAAAAAGAGTAGAAAATGGTAATCA-A
1 TAAAAAGAGTAGAAAATGGTAATCAGA
*
24995 TAAAAAAAAGAGTAAAAAATGGTAATCAGA
1 T---AAAAAGAGTAGAAAATGGTAATCAGA
* *
25025 -AAAAAAAGTAGAAAAGGGTAATCAG
1 TAAAAAGAGTAGAAAATGGTAATCAG
25050 TATTTAAGTT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
26 23 0.49
29 23 0.49
30 1 0.02
ACGTcount: A:0.60, C:0.04, G:0.20, T:0.16
Consensus pattern (27 bp):
TAAAAAGAGTAGAAAATGGTAATCAGA
Found at i:25011 original size:27 final size:28
Alignment explanation
Indices: 24970--25118 Score: 103
Period size: 27 Copynumber: 5.1 Consensus size: 28
24960 TAATTTAGTT
24970 AAAAAGAGTAGAAAATGGTAATCAATAAA
1 AAAAAGAGTA-AAAATGGTAATCAATAAA
*
24999 AAAAAGAGTAAAAAATGGTAATC-A-GAA
1 AAAAAGAGT-AAAAATGGTAATCAATAAA
*
25026 AAAAA-AGTAGAAAAGGGTAATCAGTATTTAAGTTA
1 AAAAAGAGTA-AAAATGGTAATCA--A--TAA---A
*
25061 AAAAA-AGGTAGAAAATGGTAATCAGT--A
1 AAAAAGA-GTA-AAAATGGTAATCAATAAA
*
25088 AAAAAGAGTATAAAATGGTAATCAGTAAA
1 AAAAAGAGTA-AAAATGGTAATCAATAAA
25117 AA
1 AA
25119 GGGAGTAAGA
Statistics
Matches: 99, Mismatches: 6, Indels: 30
0.73 0.04 0.22
Matches are distributed among these distances:
25 1 0.01
26 14 0.14
27 31 0.31
28 2 0.02
29 25 0.25
30 1 0.01
32 2 0.02
35 7 0.07
36 16 0.16
ACGTcount: A:0.58, C:0.03, G:0.19, T:0.19
Consensus pattern (28 bp):
AAAAAGAGTAAAAATGGTAATCAATAAA
Found at i:25118 original size:90 final size:90
Alignment explanation
Indices: 24942--25178 Score: 304
Period size: 90 Copynumber: 2.6 Consensus size: 90
24932 TTCCCCAGGC
*
24942 TAAGAAAAGGGTAATCAGTAATTT-AGTTAAAAAGAGTAGAAAATGGTAATCAATAAAAAAAAGA
1 TAAGAAAAGGGTAATCAGT-ATTTAAGTTAAAAAGAGTAGAAAATGGTAATCAGT--AAAAAAGA
25006 GTAAAAAATGGTAATCAGAAAAA-AAAG
63 GTAAAAAATGGTAATCAGAAAAAGAAAG
*
25033 T-AGAAAAGGGTAATCAGTATTTAAGTTAAAAAAAGGTAGAAAATGGTAATCAGTAAAAAAGAGT
1 TAAGAAAAGGGTAATCAGTATTTAAGTTAAAAAGA-GTAGAAAATGGTAATCAGTAAAAAAGAGT
* **
25097 ATAAAATGGTAATCAGTAAAAAGGGAG
65 AAAAAATGGTAATCAG-AAAAAGAAAG
* * * *
25124 TAAGAAAATGGGCAATCAGTAATTAAGTTGAAAAGAGT--AAAATGGTAATGAGTAA
1 TAAGAAAA-GGGTAATCAGTATTTAAGTTAAAAAGAGTAGAAAATGGTAATCAGTAA
25179 TTAAATTAAA
Statistics
Matches: 130, Mismatches: 10, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
89 29 0.22
90 48 0.37
91 22 0.17
92 8 0.06
93 23 0.18
ACGTcount: A:0.54, C:0.03, G:0.22, T:0.22
Consensus pattern (90 bp):
TAAGAAAAGGGTAATCAGTATTTAAGTTAAAAAGAGTAGAAAATGGTAATCAGTAAAAAAGAGTA
AAAAATGGTAATCAGAAAAAGAAAG
Found at i:25143 original size:30 final size:27
Alignment explanation
Indices: 25061--25145 Score: 109
Period size: 27 Copynumber: 3.1 Consensus size: 27
25051 ATTTAAGTTA
25061 AAAAAAG-GTAGAAAATGGTAATCAGT
1 AAAAAAGAGTAGAAAATGGTAATCAGT
*
25087 AAAAAAGAGTATAAAATGGTAATCAGT
1 AAAAAAGAGTAGAAAATGGTAATCAGT
* *
25114 AAAAAGGGAGTAAGAAAATGGGCAATCAGT
1 AAAAA-AGAGT-AGAAAAT-GGTAATCAGT
25144 AA
1 AA
25146 TTAAGTTGAA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
26 7 0.14
27 23 0.45
28 4 0.08
29 6 0.12
30 11 0.22
ACGTcount: A:0.54, C:0.05, G:0.24, T:0.18
Consensus pattern (27 bp):
AAAAAAGAGTAGAAAATGGTAATCAGT
Found at i:25196 original size:33 final size:33
Alignment explanation
Indices: 25141--25205 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
25131 ATGGGCAATC
* * * *
25141 AGTAATTAAGTTGAAAAGAGTAAAATGGTAATG
1 AGTAATTAAATTAAAAAAAGTAAAATAGTAATG
25174 AGTAATTAAATTAAAAAAAGTAAAATAGTAAT
1 AGTAATTAAATTAAAAAAAGTAAAATAGTAAT
25206 TTGCTTAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.55, C:0.00, G:0.17, T:0.28
Consensus pattern (33 bp):
AGTAATTAAATTAAAAAAAGTAAAATAGTAATG
Found at i:26696 original size:3 final size:3
Alignment explanation
Indices: 26688--26713 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
26678 CACCTGTTTT
26688 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
26714 CTTTCCCCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:33769 original size:8 final size:8
Alignment explanation
Indices: 33756--33782 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
33746 TTATTGATTC
33756 AGGATTTA
1 AGGATTTA
33764 AGGATTTA
1 AGGATTTA
33772 AGGATTTA
1 AGGATTTA
33780 AGG
1 AGG
33783 TTGAAGTCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.30, T:0.33
Consensus pattern (8 bp):
AGGATTTA
Found at i:34920 original size:27 final size:27
Alignment explanation
Indices: 34882--34935 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
34872 TTGGAATGCA
* *
34882 GAGATTAGGATAAAATTATATGATGTG
1 GAGATTACGATAAAACTATATGATGTG
34909 GAGATTACGATAAAACTATATGATGTG
1 GAGATTACGATAAAACTATATGATGTG
34936 TCTTCTTGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.41, C:0.04, G:0.24, T:0.31
Consensus pattern (27 bp):
GAGATTACGATAAAACTATATGATGTG
Found at i:41256 original size:2 final size:2
Alignment explanation
Indices: 41245--41281 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
41235 GTTTATCTCT
*
41245 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41282 CACTCTTATC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:42607 original size:11 final size:11
Alignment explanation
Indices: 42563--42601 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
42553 TTCCCTATAA
42563 AAATTAAATTAT
1 AAATT-AATTAT
42575 CAAA-TAATTAT
1 -AAATTAATTAT
42586 AAATTAATTAT
1 AAATTAATTAT
42597 AAATT
1 AAATT
42602 TGTTATGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 3 0.12
11 18 0.72
12 1 0.04
13 3 0.12
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:43560 original size:30 final size:30
Alignment explanation
Indices: 43487--43550 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
43477 AACTGAACTA
*
43487 ACTCAAACATCCAAGATCTAAGATATGGAG
1 ACTCAAACATCCAAGATCTAAGATATGAAG
*
43517 ACTCAAACATCCAAGATCTAAAGATCTGAAG
1 ACTCAAACATCCAAGATCT-AAGATATGAAG
43548 ACT
1 ACT
43551 GATAATCCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 19 0.61
31 12 0.39
ACGTcount: A:0.44, C:0.22, G:0.14, T:0.20
Consensus pattern (30 bp):
ACTCAAACATCCAAGATCTAAGATATGAAG
Found at i:44043 original size:46 final size:46
Alignment explanation
Indices: 43990--44083 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
43980 CTTCCTCTGG
43990 ACAATAAAAAGGGGATAATTCCCTCCCTCCTCAATTCATCACACGT
1 ACAATAAAAAGGGGATAATTCCCTCCCTCCTCAATTCATCACACGT
* *
44036 ACAATAAATAGGGGATAATTCCCTCCCTCCTCAATTCATCATACGT
1 ACAATAAAAAGGGGATAATTCCCTCCCTCCTCAATTCATCACACGT
44082 AC
1 AC
44084 GTACCACAGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.34, C:0.30, G:0.11, T:0.26
Consensus pattern (46 bp):
ACAATAAAAAGGGGATAATTCCCTCCCTCCTCAATTCATCACACGT
Found at i:46498 original size:12 final size:12
Alignment explanation
Indices: 46481--46510 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
46471 TTAATACAGG
46481 TATCGACGGATA
1 TATCGACGGATA
*
46493 TATCGATGGATA
1 TATCGACGGATA
46505 TATCGA
1 TATCGA
46511 GGTATCGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.30
Consensus pattern (12 bp):
TATCGACGGATA
Found at i:48202 original size:10 final size:10
Alignment explanation
Indices: 48187--48212 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
48177 AATTTAATAT
48187 GGATATTTAC
1 GGATATTTAC
48197 GGATATTTAC
1 GGATATTTAC
48207 GGATAT
1 GGATAT
48213 ATCGAGATTT
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:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (10 bp):
GGATATTTAC
Done.