Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006603.1 Hibiscus syriacus cultivar Beakdansim tig00016197_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: 111206
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:856 original size:31 final size:30
Alignment explanation
Indices: 787--864 Score: 77
Period size: 31 Copynumber: 2.5 Consensus size: 30
777 ATTCAACACC
* * ** *
787 AAGTGATCAAAACTTAATAAATGATAACGT
1 AAGTGACCAAAACTTAAAAAACAATAACAT
817 AA-TCGACCAAAACTTGAAAAAACAATAACAT
1 AAGT-GACCAAAACTT-AAAAAACAATAACAT
848 AAGTGACCAAAAACTTA
1 AAGTGACC-AAAACTTA
865 TGTTTTTTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
29 1 0.03
30 12 0.31
31 18 0.46
32 8 0.21
ACGTcount: A:0.54, C:0.15, G:0.10, T:0.21
Consensus pattern (30 bp):
AAGTGACCAAAACTTAAAAAACAATAACAT
Found at i:14418 original size:21 final size:21
Alignment explanation
Indices: 14377--14419 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
14367 TACTCTACCT
* *
14377 AACTTAAAACCATGAATTATA
1 AACTTAAAACCATAAACTATA
*
14398 AACTTAAAACCCTAAACTATA
1 AACTTAAAACCATAAACTATA
14419 A
1 A
14420 CTTCATTGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.53, C:0.19, G:0.02, T:0.26
Consensus pattern (21 bp):
AACTTAAAACCATAAACTATA
Found at i:16203 original size:19 final size:19
Alignment explanation
Indices: 16167--16209 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
16157 TTTCAAAACT
*
16167 TTCATCTTTCACTTTCATA
1 TTCATCTTTCACTCTCATA
*
16186 TTCAT-TTTCACATCTCATT
1 TTCATCTTTCAC-TCTCATA
16205 TTCAT
1 TTCAT
16210 AACTAGTACC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.21, C:0.26, G:0.00, T:0.53
Consensus pattern (19 bp):
TTCATCTTTCACTCTCATA
Found at i:17898 original size:20 final size:20
Alignment explanation
Indices: 17873--17916 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
17863 TTCAGCCCAA
17873 TACCTCAAAATTTCCACCAT
1 TACCTCAAAATTTCCACCAT
*
17893 TACCTCAACATTTCCACCAT
1 TACCTCAAAATTTCCACCAT
17913 TACC
1 TACC
17917 GCTTAAGTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.32, C:0.39, G:0.00, T:0.30
Consensus pattern (20 bp):
TACCTCAAAATTTCCACCAT
Found at i:21989 original size:40 final size:40
Alignment explanation
Indices: 21945--22028 Score: 141
Period size: 40 Copynumber: 2.1 Consensus size: 40
21935 AAAAATCATG
* *
21945 ACATTTTAGGTTGAGTACAACCTAAAATATTAATTTTTTA
1 ACATTTTAGGTTGAGCACAACCTAAAATATTAACTTTTTA
*
21985 ACATTTTCGGTTGAGCACAACCTAAAATATTAACTTTTTA
1 ACATTTTAGGTTGAGCACAACCTAAAATATTAACTTTTTA
22025 ACAT
1 ACAT
22029 GTTCGATTGA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (40 bp):
ACATTTTAGGTTGAGCACAACCTAAAATATTAACTTTTTA
Found at i:24131 original size:65 final size:66
Alignment explanation
Indices: 24022--24165 Score: 200
Period size: 65 Copynumber: 2.2 Consensus size: 66
24012 ATTAAATGGA
* * * * * *
24022 TGTACCGATACACTATTGAATGCATCGATACACTCCTAATTTTATTGAAACATCGAATGCATTTT
1 TGTACCGATACACAATTGAATACATCGATACACTCCTAACTTTATTAAAACATCGAATGCAATTA
24087 G
66 G
* **
24088 TGTACCGATACACAATTG-ATACATCGATGCACTCCTGGCTTTATTAAAACATCGAATGCAATTA
1 TGTACCGATACACAATTGAATACATCGATACACTCCTAACTTTATTAAAACATCGAATGCAATTA
24152 G
66 G
24153 TGTACCGATACAC
1 TGTACCGATACAC
24166 TAGGTCTTAT
Statistics
Matches: 69, Mismatches: 9, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
65 52 0.75
66 17 0.25
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.31
Consensus pattern (66 bp):
TGTACCGATACACAATTGAATACATCGATACACTCCTAACTTTATTAAAACATCGAATGCAATTA
G
Found at i:25888 original size:27 final size:27
Alignment explanation
Indices: 25858--25911 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
25848 TACTCGAGGT
* * *
25858 TATTTTAGTCATTTTAGTGTTTAAGGG
1 TATTTTAGCCATTTTAGGGTTCAAGGG
25885 TATTTTAGCCATTTTAGGGTTCAAGGG
1 TATTTTAGCCATTTTAGGGTTCAAGGG
25912 CATCTTGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.22, C:0.07, G:0.24, T:0.46
Consensus pattern (27 bp):
TATTTTAGCCATTTTAGGGTTCAAGGG
Found at i:26770 original size:23 final size:23
Alignment explanation
Indices: 26743--26803 Score: 113
Period size: 23 Copynumber: 2.7 Consensus size: 23
26733 AATGACTTTT
*
26743 TGGTCAAAGTCAACTGTCAATGC
1 TGGTCAAAGTCAACTATCAATGC
26766 TGGTCAAAGTCAACTATCAATGC
1 TGGTCAAAGTCAACTATCAATGC
26789 TGGTCAAAGTCAACT
1 TGGTCAAAGTCAACT
26804 TTAGACAGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (23 bp):
TGGTCAAAGTCAACTATCAATGC
Found at i:27224 original size:22 final size:23
Alignment explanation
Indices: 27176--27226 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
27166 ACTCTCCCTC
27176 CCATT-TTCCTCGTCATTTATCT
1 CCATTCTTCCTCGTCATTTATCT
* *
27198 -TATTCTTCCTC-TCATTTTTCT
1 CCATTCTTCCTCGTCATTTATCT
27219 CCATTCTT
1 CCATTCTT
27227 TTTCTCTTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.12, C:0.31, G:0.02, T:0.55
Consensus pattern (23 bp):
CCATTCTTCCTCGTCATTTATCT
Found at i:28109 original size:21 final size:21
Alignment explanation
Indices: 28068--28110 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
28058 AAGAAGAGGT
**
28068 AGAATATTGATACTCTCAATA
1 AGAATATTGATACTAACAATA
*
28089 AGAATATTGATACTAAGAATA
1 AGAATATTGATACTAACAATA
28110 A
1 A
28111 TTTTGAAACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.49, C:0.09, G:0.12, T:0.30
Consensus pattern (21 bp):
AGAATATTGATACTAACAATA
Found at i:31802 original size:22 final size:22
Alignment explanation
Indices: 31774--31858 Score: 64
Period size: 22 Copynumber: 3.9 Consensus size: 22
31764 GATTTTCTCC
31774 TATCAGTGCCAAGGCACTTTAG
1 TATCAGTGCCAAGGCACTTTAG
* **
31796 TATCAGTG-CAATCGCACTTCCG
1 TATCAGTGCCAA-GGCACTTTAG
* * * * *
31818 TACCAATGCCGAGGAAATTTAG
1 TATCAGTGCCAAGGCACTTTAG
* *
31840 TATTAGTGCTAAGGCACTT
1 TATCAGTGCCAAGGCACTT
31859 CTGTTATACA
Statistics
Matches: 43, Mismatches: 18, Indels: 4
0.66 0.28 0.06
Matches are distributed among these distances:
21 3 0.07
22 38 0.88
23 2 0.05
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.28
Consensus pattern (22 bp):
TATCAGTGCCAAGGCACTTTAG
Found at i:33025 original size:11 final size:11
Alignment explanation
Indices: 33009--33038 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
32999 GAAAAATATT
33009 TTTTTTTGAAA
1 TTTTTTTGAAA
33020 TTTTTTTGAAA
1 TTTTTTTGAAA
33031 TTTTTTTG
1 TTTTTTTG
33039 GGTGAAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.10, T:0.70
Consensus pattern (11 bp):
TTTTTTTGAAA
Found at i:33905 original size:60 final size:60
Alignment explanation
Indices: 33811--33971 Score: 196
Period size: 60 Copynumber: 2.7 Consensus size: 60
33801 ATTATATTTT
* * *
33811 TAAATTGGTCCTTAAACTATTAAATATTCCAATTTAATCCCTAAACTATGACACTCAGTC
1 TAAATTAGTCCTTAAACTTTTGAATATTCCAATTTAATCCCTAAACTATGACACTCAGTC
* * * * **
33871 TAAATTAGTCCTTAAACTTTTGAACATTCTAATTTCATCCCTAAACTATGACCCTCTTTC
1 TAAATTAGTCCTTAAACTTTTGAATATTCCAATTTAATCCCTAAACTATGACACTCAGTC
* * ** *
33931 TATATTAATCCCCAAACTTTTGAATATTCCAATTTTATCCC
1 TAAATTAGTCCTTAAACTTTTGAATATTCCAATTTAATCCC
33972 CAAATTCATC
Statistics
Matches: 85, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 85 1.00
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.39
Consensus pattern (60 bp):
TAAATTAGTCCTTAAACTTTTGAATATTCCAATTTAATCCCTAAACTATGACACTCAGTC
Found at i:34205 original size:60 final size:58
Alignment explanation
Indices: 34091--34263 Score: 170
Period size: 60 Copynumber: 2.9 Consensus size: 58
34081 GAGTATGCAT
* * ** *
34091 ATAGTATGTGATGAAATTGGAATGTTCAAAATGTTTGGGGGCCAATTTATAATGA-ATGTC
1 ATAGTATGGGATGAAATTGGAATGTTCAAAA-GTTT-AGGATCAATTTAAAATGATA-GTC
*
34151 ATAGTATGGGGATGAAATTGGAATGTTCAAAAGTTTAAGGATTAATTTAAAATGATAGTC
1 ATAGTAT-GGGATGAAATTGGAATGTTCAAAAGTTT-AGGATCAATTTAAAATGATAGTC
** * *
34211 ATAGTTTATGGGA-GAAATTAAAATATTTAAAAGTTTAGAGATCAATTTAAAAT
1 ATAG--TATGGGATGAAATTGGAATGTTCAAAAGTTTAG-GATCAATTTAAAAT
34264 AAAAATTATA
Statistics
Matches: 96, Mismatches: 12, Indels: 10
0.81 0.10 0.08
Matches are distributed among these distances:
59 2 0.02
60 63 0.66
61 28 0.29
62 3 0.03
ACGTcount: A:0.40, C:0.04, G:0.21, T:0.35
Consensus pattern (58 bp):
ATAGTATGGGATGAAATTGGAATGTTCAAAAGTTTAGGATCAATTTAAAATGATAGTC
Found at i:38296 original size:32 final size:32
Alignment explanation
Indices: 38251--38330 Score: 119
Period size: 31 Copynumber: 2.5 Consensus size: 32
38241 CCGAACCCGG
*
38251 AAATATTTTATATATAATTAATATAAAAAATA
1 AAATATATTATATATAATTAATATAAAAAATA
38283 TAAA-ATATTATATAT-ATTAATATAAAAAATA
1 -AAATATATTATATATAATTAATATAAAAAATA
38314 AAATATATATATATATA
1 AAATATAT-TATATATA
38331 TATATATATA
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
30 3 0.07
31 20 0.47
32 17 0.40
33 3 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (32 bp):
AAATATATTATATATAATTAATATAAAAAATA
Found at i:38321 original size:2 final size:2
Alignment explanation
Indices: 38316--38348 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
38306 AAAAAATAAA
38316 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
38349 ATCGGGTCGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38333 original size:28 final size:28
Alignment explanation
Indices: 38271--38334 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 28
38261 TATATAATTA
38271 ATATA-AAAAATATAAAATATTATATAT
1 ATATATAAAAATATAAAATATTATATAT
38298 ATTAATATAAAAA-ATAAAATATATATATAT
1 A-T-ATATAAAAATATAAAATAT-TATATAT
38328 ATATATA
1 ATATATA
38335 TATATATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
27 1 0.03
28 6 0.18
29 13 0.39
30 13 0.39
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (28 bp):
ATATATAAAAATATAAAATATTATATAT
Found at i:42610 original size:24 final size:22
Alignment explanation
Indices: 42583--42627 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 22
42573 CGCTGGTGAT
*
42583 TATTATTTTTCTTGTTGTTTTTCA
1 TATTATGTTT-TTGTT-TTTTTCA
42607 TATTATGTTTTTGTTTTTTTC
1 TATTATGTTTTTGTTTTTTTC
42628 TTGACTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
23 5 0.25
24 9 0.45
ACGTcount: A:0.11, C:0.07, G:0.09, T:0.73
Consensus pattern (22 bp):
TATTATGTTTTTGTTTTTTTCA
Found at i:44644 original size:23 final size:24
Alignment explanation
Indices: 44616--44724 Score: 100
Period size: 23 Copynumber: 4.7 Consensus size: 24
44606 CATTTAAATG
*
44616 ATAAACGAACACAAATGAACGAA-
1 ATAAACGAACACAAATAAACGAAC
44639 ATAAACGAACAC-AATAAACGAAC
1 ATAAACGAACACAAATAAACGAAC
* *** *
44662 ACAAGTAAACACAAACAAACGAAC
1 ATAAACGAACACAAATAAACGAAC
* *
44686 ATAAACGAACAAAAACAAAC--AC
1 ATAAACGAACACAAATAAACGAAC
*
44708 AATAAACGAACATAAAT
1 -ATAAACGAACACAAAT
44725 CACAACAACA
Statistics
Matches: 70, Mismatches: 13, Indels: 6
0.79 0.15 0.07
Matches are distributed among these distances:
22 11 0.16
23 34 0.49
24 25 0.36
ACGTcount: A:0.63, C:0.20, G:0.08, T:0.08
Consensus pattern (24 bp):
ATAAACGAACACAAATAAACGAAC
Found at i:44706 original size:34 final size:33
Alignment explanation
Indices: 44652--44723 Score: 99
Period size: 34 Copynumber: 2.2 Consensus size: 33
44642 AACGAACACA
* **
44652 ATAAACGAACACAAGTAAACACAAACAAACGAAC
1 ATAAACGAACAAAAACAAACAC-AACAAACGAAC
*
44686 ATAAACGAACAAAAACAAACACAATAAACGAAC
1 ATAAACGAACAAAAACAAACACAACAAACGAAC
44719 ATAAA
1 ATAAA
44724 TCACAACAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 15 0.44
34 19 0.56
ACGTcount: A:0.65, C:0.21, G:0.07, T:0.07
Consensus pattern (33 bp):
ATAAACGAACAAAAACAAACACAACAAACGAAC
Found at i:44736 original size:26 final size:23
Alignment explanation
Indices: 44669--44738 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 23
44659 AACACAAGTA
*
44669 AACACAAACAAACGA-ACATAAACG
1 AACAAAAACAAAC-ACA-ATAAACG
44693 AACAAAAACAAACACAATAAACG
1 AACAAAAACAAACACAATAAACG
*
44716 AACATAAATCACAACAACAATAA
1 AACA-AAAACA-AAC-ACAATAA
44739 TCACATAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 12 0.30
24 18 0.45
25 3 0.08
26 7 0.17
ACGTcount: A:0.66, C:0.23, G:0.04, T:0.07
Consensus pattern (23 bp):
AACAAAAACAAACACAATAAACG
Found at i:45416 original size:20 final size:20
Alignment explanation
Indices: 45393--45489 Score: 131
Period size: 20 Copynumber: 4.8 Consensus size: 20
45383 ATTCGCGTTG
45393 CATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
* *
45413 CATTTCGCGTTGCGATAGTTG
1 CATTTCGCGTTGCGAT-TTTC
* ** *
45434 AAAATCGCGTTGCGATATTC
1 CATTTCGCGTTGCGATTTTC
45454 CATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
45474 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
45490 AGTCTACAGT
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
20 50 0.77
21 15 0.23
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.39
Consensus pattern (20 bp):
CATTTCGCGTTGCGATTTTC
Found at i:45590 original size:6 final size:6
Alignment explanation
Indices: 45579--45676 Score: 196
Period size: 6 Copynumber: 16.3 Consensus size: 6
45569 AGACACGCAT
45579 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
45627 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
45675 GA
1 GA
45677 GACGGACGAC
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 92 1.00
ACGTcount: A:0.34, C:0.49, G:0.17, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:54698 original size:22 final size:22
Alignment explanation
Indices: 54670--55099 Score: 506
Period size: 22 Copynumber: 19.6 Consensus size: 22
54660 TGGAGAAGGT
* * *
54670 ATTTATTTAAAAATATAGATTC
1 ATTTATTTTAAAATATGGATTG
* ***
54692 ATTTATTTTAAAAAAT-GAAAA
1 ATTTATTTTAAAATATGGATTG
* **
54713 AGTTATTTTAAAATAAAGATTG
1 ATTTATTTTAAAATATGGATTG
* *
54735 ATTTATTTTAAAATGTAGATTG
1 ATTTATTTTAAAATATGGATTG
**
54757 ATTTATTTTAAAATATTAATTG
1 ATTTATTTTAAAATATGGATTG
54779 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* ***
54801 GTTTATTTTAAAATAT-GAAAA
1 ATTTATTTTAAAATATGGATTG
*
54822 ATTTTATTTTAAAATATGAATTG
1 A-TTTATTTTAAAATATGGATTG
***
54845 ATTTATTTTAAAATATGGAAAA
1 ATTTATTTTAAAATATGGATTG
**
54867 ATTTATTTTAAAATATGGA-AA
1 ATTTATTTTAAAATATGGATTG
54888 ATTTTATTTTAAAATATGGATTG
1 A-TTTATTTTAAAATATGGATTG
*
54911 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
54933 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* ***
54955 ATTTATTTTAAAATATGAAAAA
1 ATTTATTTTAAAATATGGATTG
*
54977 AATTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* *
54999 ATTTATATTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
55021 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
55043 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
*
55065 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
*
55087 ATTTATTTAAAAA
1 ATTTATTTTAAAA
55100 AAATTATTAT
Statistics
Matches: 351, Mismatches: 52, Indels: 10
0.85 0.13 0.02
Matches are distributed among these distances:
21 20 0.06
22 328 0.93
23 3 0.01
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:55161 original size:31 final size:31
Alignment explanation
Indices: 55123--55181 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
55113 AGTTGTATGG
55123 ATTATTTAAATTTCAGTATTATAAAACTAAA
1 ATTATTTAAATTTCAGTATTATAAAACTAAA
*
55154 ATTATTTAAATTTCAGTATTGTAAAACT
1 ATTATTTAAATTTCAGTATTATAAAACT
55182 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (31 bp):
ATTATTTAAATTTCAGTATTATAAAACTAAA
Found at i:55771 original size:25 final size:25
Alignment explanation
Indices: 55734--55786 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
55724 ATGATCACCT
55734 TCATTTTTATTTAATTAAGATATGA
1 TCATTTTTATTTAATTAAGATATGA
* * *
55759 TCATTTTTTTTTATTTAAGATGTGA
1 TCATTTTTATTTAATTAAGATATGA
55784 TCA
1 TCA
55787 CCACGGGTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (25 bp):
TCATTTTTATTTAATTAAGATATGA
Found at i:56011 original size:15 final size:14
Alignment explanation
Indices: 55991--56025 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
55981 GTTGAAAGAC
*
55991 TATTTTAATTTATTT
1 TATTTTAATATA-TT
56006 TATTTTAATATATT
1 TATTTTAATATATT
56020 TATTTT
1 TATTTT
56026 CCACCAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TATTTTAATATATT
Found at i:62257 original size:21 final size:21
Alignment explanation
Indices: 62231--62275 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
62221 GATTTCTGGG
* *
62231 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
62252 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
62273 CAA
1 CAA
62276 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:63300 original size:2 final size:2
Alignment explanation
Indices: 63293--63318 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
63283 GAACATGTGA
63293 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
63319 GTTTAAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:63999 original size:22 final size:22
Alignment explanation
Indices: 63967--64047 Score: 135
Period size: 22 Copynumber: 3.6 Consensus size: 22
63957 ATCATTATAT
*
63967 GGCACTACGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
*
63989 GGCACTTCGGTGCAATTCTACA
1 GGCACTTCGGTGCAATTCTACG
64011 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTAC-G
64034 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
64048 TTTATACGAG
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
22 41 0.75
23 14 0.25
ACGTcount: A:0.20, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
GGCACTTCGGTGCAATTCTACG
Found at i:68498 original size:6 final size:6
Alignment explanation
Indices: 68487--68527 Score: 64
Period size: 6 Copynumber: 6.7 Consensus size: 6
68477 GAAAGTCTCG
*
68487 AATACA AATACA AATACG AATACAA AATACA AATACA AATA
1 AATACA AATACA AATACA AATAC-A AATACA AATACA AATA
68528 TCAAGCACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
6 27 0.84
7 5 0.16
ACGTcount: A:0.66, C:0.15, G:0.02, T:0.17
Consensus pattern (6 bp):
AATACA
Found at i:72959 original size:13 final size:13
Alignment explanation
Indices: 72924--72948 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
72914 ACCATGGTCG
72924 CTGTCTACCACCA
1 CTGTCTACCACCA
72937 CTGTCTACCACC
1 CTGTCTACCACC
72949 GCTGATCACC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.48, G:0.08, T:0.24
Consensus pattern (13 bp):
CTGTCTACCACCA
Found at i:77658 original size:42 final size:43
Alignment explanation
Indices: 77606--77713 Score: 166
Period size: 42 Copynumber: 2.6 Consensus size: 43
77596 AACTTGACTC
*
77606 CCTCGTGAAGAGGAGTCAATCTTTCAATGTCATTATTGA-TTT
1 CCTCGTGAAGAGAAGTCAATCTTTCAATGTCATTATTGACTTT
* * *
77648 CCTCGCGAAGAGAAGTCAATCTTTCAATGTTATTCTTGACTTT
1 CCTCGTGAAGAGAAGTCAATCTTTCAATGTCATTATTGACTTT
77691 -CTCGTGAAGAGAAGTCAATCTTT
1 CCTCGTGAAGAGAAGTCAATCTTT
77714 GTAATTCTTG
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
42 57 0.95
43 3 0.05
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (43 bp):
CCTCGTGAAGAGAAGTCAATCTTTCAATGTCATTATTGACTTT
Found at i:77737 original size:38 final size:38
Alignment explanation
Indices: 77598--78101 Score: 506
Period size: 38 Copynumber: 12.8 Consensus size: 38
77588 GAAGCTTCAA
* * *
77598 CTTGACTCCCTCGTGAAGAGGAGTCAATCTTTCAATGTCATT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATC-TT---TGTTATT
* * *
77640 ATTGATTTCCTCGCGAAGAGAAGTCAATCTTTCAATGTTATT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATC-TT---TGTTATT
* *
77682 CTTGACTTTCTCGTGAAGAGAAGTCAATCTTTGTAATT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
* * * * *
77720 CTTGACATCCTCATGAAGAGTAGTCAATCTTTTTTGTT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
* * **
77758 CCTGACTCCCTCGCAAAGAGGAGTCAGTCAATCTTTGTTATT
1 CTTGACTTCCTCGTGAAGA-GA---AGTCAATCTTTGTTATT
*
77800 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTGTT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
* * *
77838 CCTGACTCCCTCGTGAAGAGGAGTCAATCAATCTTTGTTATT
1 CTTGACTTCCTCGTGAAGA-GA---AGTCAATCTTTGTTATT
* * *
77880 GTTGACTTCCTCATGAAGAGAAGTCAATATTTGTTATT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
* * *
77918 ATTGACTTCCTCGTGAAGGGAAATCAATCTTTGTTATT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
* * *
77956 CTTGACTTCCTCGTGAAGAGAAGTTAATCTTTTTTGTT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
* * * * *
77994 TTTGAATCCCTCGCGAAGAGAATTCAATCTTTGTTATT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
* *
78032 CTTGACTTCCTCATGAAGAGAAGTCAATATTTGTT-TT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
*
78069 CCTTGACTTCCTCGTGAAGAGAAGTCTATCTTT
1 -CTTGACTTCCTCGTGAAGAGAAGTCAATCTTT
78102 TTCCTTCTTA
Statistics
Matches: 382, Mismatches: 71, Indels: 22
0.80 0.15 0.05
Matches are distributed among these distances:
37 2 0.01
38 250 0.65
39 3 0.01
41 6 0.02
42 121 0.32
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (38 bp):
CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
Found at i:78110 original size:76 final size:77
Alignment explanation
Indices: 77598--78101 Score: 516
Period size: 80 Copynumber: 6.4 Consensus size: 77
77588 GAAGCTTCAA
* * * * **
77598 CTTGACTCCCTCGTGAAGAGGAGTCAATCTTTCAATGTCATTATTGATTTCCTCGCGAAGAGAAG
1 CTTGACTCCCTCGTGAAGAGAAGTCAATC-TT---TGTTATTCTTGACTTCCTCATGAAGAGAAG
*
77663 TCAATCTTTCAATGTTATT-
62 TCAATC-TT---TGTTGTTC
** * * *
77682 CTTGACTTTCTCGTGAAGAGAAGTCAATCTTTGTAATTCTTGACATCCTCATGAAGAGTAGTCAA
1 CTTGACTCCCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTGACTTCCTCATGAAGAGAAGTCAA
*
77747 TCTTTTTTGTTC
66 TCTTTGTTGTTC
** *
77759 C-TGACTCCCTCGCAAAGAGGAGTCAGTCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAG
1 CTTGACTCCCTCGTGAAGA-GA---AGTCAATCTTTGTTATTCTTGACTTCCTCATGAAGAGAAG
77823 TCAATCTTTGTTGTTC
62 TCAATCTTTGTTGTTC
* *
77839 C-TGACTCCCTCGTGAAGAGGAGTCAATCAATCTTTGTTATTGTTGACTTCCTCATGAAGAGAAG
1 CTTGACTCCCTCGTGAAGA-GA---AGTCAATCTTTGTTATTCTTGACTTCCTCATGAAGAGAAG
* *
77903 TCAATATTTGTTATT-
62 TCAATCTTTGTTGTTC
* * * * * *
77918 ATTGACTTCCTCGTGAAGGGAAATCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTTAA
1 CTTGACTCCCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTGACTTCCTCATGAAGAGAAGTCAA
*
77983 TCTTTTTTGTT-
66 TCTTTGTTGTTC
* * * *
77994 TTTGAATCCCTCGCGAAGAGAATTCAATCTTTGTTATTCTTGACTTCCTCATGAAGAGAAGTCAA
1 CTTGACTCCCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTGACTTCCTCATGAAGAGAAGTCAA
*
78059 TATTTGTT-TTC
66 TCTTTGTTGTTC
* *
78070 CTTGACTTCCTCGTGAAGAGAAGTCTATCTTT
1 CTTGACTCCCTCGTGAAGAGAAGTCAATCTTT
78102 TTCCTTCTTA
Statistics
Matches: 360, Mismatches: 53, Indels: 22
0.83 0.12 0.05
Matches are distributed among these distances:
75 2 0.01
76 156 0.43
77 3 0.01
79 4 0.01
80 167 0.46
83 2 0.01
84 26 0.07
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (77 bp):
CTTGACTCCCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTGACTTCCTCATGAAGAGAAGTCAA
TCTTTGTTGTTC
Found at i:78579 original size:3 final size:3
Alignment explanation
Indices: 78571--78622 Score: 58
Period size: 3 Copynumber: 18.3 Consensus size: 3
78561 GAGACCCGTT
*
78571 TTA TTA TTA TTA TTA TTA TTA TT- TTA -TA TT- TATA TTA TTT TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
78614 TTA TT- TTA T
1 TTA TTA TTA T
78623 GCAGGCCAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
2 7 0.17
3 34 0.81
4 1 0.02
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:78606 original size:19 final size:19
Alignment explanation
Indices: 78571--78622 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
78561 GAGACCCGTT
*
78571 TTATTATTATTAT-TATTA
1 TTATTATTATTTTATATTA
78589 TTATT-TTATATTTATATTA
1 TTATTATTAT-TTTATATTA
*
78608 TTTTTATTATTTTAT
1 TTATTATTATTTTAT
78623 GCAGGCCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
17 4 0.14
18 7 0.24
19 14 0.48
20 4 0.14
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TTATTATTATTTTATATTA
Found at i:80191 original size:70 final size:67
Alignment explanation
Indices: 80047--80199 Score: 211
Period size: 69 Copynumber: 2.2 Consensus size: 67
80037 GTTCGAACAA
*
80047 AATAATATATTTTATATTCGATGAATTTTTGTTTTAATATTTATTATGTATTTTATCTAAAATTT
1 AATAATATATTTTATATTCGATGAATTTTTGTTTAAATATTTATTATGTATTTTATCTAAAATTT
80112 GG
66 GG
80114 ATAATAATATATTTTATATTCGAATGAA-TTTTGTTTAATATATTTATTATATGTATTTTATCTA
1 --AATAATATATTTTATATTCG-ATGAATTTTTGTTTAA-ATATTTA-T-TATGTATTTTATCT-
80178 AAAATTTGG
59 AAAATTTGG
80187 -ATAATATTATTTT
1 AATAATA-TATTTT
80200 GTAGCGGAAT
Statistics
Matches: 77, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
69 29 0.38
70 18 0.23
71 7 0.09
72 14 0.18
73 9 0.12
ACGTcount: A:0.35, C:0.03, G:0.08, T:0.54
Consensus pattern (67 bp):
AATAATATATTTTATATTCGATGAATTTTTGTTTAAATATTTATTATGTATTTTATCTAAAATTT
GG
Found at i:95968 original size:20 final size:20
Alignment explanation
Indices: 95940--95980 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
95930 TCATATTTAT
*
95940 ATTTCTAAAAATAAATATAA
1 ATTTATAAAAATAAATATAA
* *
95960 ATTTATAAAAGTAAGTATAA
1 ATTTATAAAAATAAATATAA
95980 A
1 A
95981 AAATATTGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (20 bp):
ATTTATAAAAATAAATATAA
Found at i:96893 original size:21 final size:24
Alignment explanation
Indices: 96869--96913 Score: 60
Period size: 21 Copynumber: 2.0 Consensus size: 24
96859 TAAATATTTT
96869 TTAATTCAAA-AA-A-AATTATAA
1 TTAATTCAAATAATATAATTATAA
*
96890 TTAATTTAAATAATATAATTATAA
1 TTAATTCAAATAATATAATTATAA
96914 AATAAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 9 0.45
22 2 0.10
23 1 0.05
24 8 0.40
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (24 bp):
TTAATTCAAATAATATAATTATAA
Found at i:97102 original size:182 final size:179
Alignment explanation
Indices: 96863--97222 Score: 589
Period size: 182 Copynumber: 2.0 Consensus size: 179
96853 AAAAATTAAA
* *
96863 TATTTTTTAATTCAAAAAAAATTATAATTAATTTAAATAATATAATTATAAAATAAAAATTTTAG
1 TATTTTTTAATTCAAAAAAAATTACAATTAATTTAAATAATATAATTATAAAATAAAAAATTTAG
96928 ATAATTTTTTAATTAATTAATATTAATTTAAGTTTAAAAGTTATTGGATCTTAAATTATTAATTG
66 ATAATTTTTTAATTAATTAATATTAATTTAAGTTTAAAAGTTATTGGATCTTAAATTATTAATTG
* *
96993 GGTTTTAAATGGTTTGGGCTT-AGCCCATATTTTATATATAATATATTTT
131 GGTTTTAAATGATTTGGG-TTGAGCCCATATGTTATATATAATATATTTT
*
97042 TATTTTTTAATT-AAAAAACAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAAAT
1 TATTTTTTAATTCAAAAAA-A-ATTACAATTAATTTAAAT-A-ATATAATTATAAAATAAAAAAT
* *
97106 TTATATAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTGGATCTTAAATTATTA
62 TTAGATAATTTTTTAATTAATTAATATTAATTTAAGTTTAAAAGTTATTGGATCTTAAATTATTA
*
97171 ATTGGGTTTTAAATGATTTGGGTTGAGCCCATATGTTGTATATAATATATTT
127 ATTGGGTTTTAAATGATTTGGGTTGAGCCCATATGTTATATATAATATATTT
97223 AATATTTAAA
Statistics
Matches: 168, Mismatches: 8, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
178 6 0.04
179 13 0.08
180 16 0.10
181 3 0.02
182 130 0.77
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (179 bp):
TATTTTTTAATTCAAAAAAAATTACAATTAATTTAAATAATATAATTATAAAATAAAAAATTTAG
ATAATTTTTTAATTAATTAATATTAATTTAAGTTTAAAAGTTATTGGATCTTAAATTATTAATTG
GGTTTTAAATGATTTGGGTTGAGCCCATATGTTATATATAATATATTTT
Found at i:97362 original size:31 final size:31
Alignment explanation
Indices: 97324--97399 Score: 152
Period size: 31 Copynumber: 2.5 Consensus size: 31
97314 GTTAACCGAT
97324 CGAACTAATTCGGTATCCGAACCGAATTAAC
1 CGAACTAATTCGGTATCCGAACCGAATTAAC
97355 CGAACTAATTCGGTATCCGAACCGAATTAAC
1 CGAACTAATTCGGTATCCGAACCGAATTAAC
97386 CGAACTAATTCGGT
1 CGAACTAATTCGGT
97400 TCGGTCGGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (31 bp):
CGAACTAATTCGGTATCCGAACCGAATTAAC
Found at i:97376 original size:17 final size:17
Alignment explanation
Indices: 97324--97376 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
97314 GTTAACCGAT
97324 CGAACTAATTCGGTATC
1 CGAACTAATTCGGTATC
* *
97341 CGAACCGAA-T---TAAC
1 CGAA-CTAATTCGGTATC
97355 CGAACTAATTCGGTATC
1 CGAACTAATTCGGTATC
97372 CGAAC
1 CGAAC
97377 CGAATTAACC
Statistics
Matches: 27, Mismatches: 4, Indels: 10
0.66 0.10 0.24
Matches are distributed among these distances:
13 3 0.11
14 8 0.30
17 13 0.48
18 3 0.11
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (17 bp):
CGAACTAATTCGGTATC
Found at i:97744 original size:13 final size:13
Alignment explanation
Indices: 97726--97773 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
97716 TCTAGACCCA
97726 TTGACTTTGACCG
1 TTGACTTTGACCG
* * *
97739 TTGACTGTTAATCA
1 TTGACT-TTGACCG
*
97753 TTGACTTTGACTG
1 TTGACTTTGACCG
97766 TTGACTTT
1 TTGACTTT
97774 TTCTATTGAC
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
13 17 0.63
14 10 0.37
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.46
Consensus pattern (13 bp):
TTGACTTTGACCG
Found at i:105530 original size:21 final size:21
Alignment explanation
Indices: 105506--105579 Score: 87
Period size: 21 Copynumber: 3.5 Consensus size: 21
105496 AGTTGAAACG
* *
105506 AGAGAAGCAGA-ACGAGAAGCG
1 AGAGAAACAGAGA-GAGAAGCA
* * *
105527 AGAGAAGCTGAGATAGAAGCA
1 AGAGAAACAGAGAGAGAAGCA
105548 AGAGAAACAGAGAGAGAAGCA
1 AGAGAAACAGAGAGAGAAGCA
105569 AGAGAAACAGA
1 AGAGAAACAGA
105580 ACGAAAAGCA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
21 45 0.98
22 1 0.02
ACGTcount: A:0.53, C:0.11, G:0.34, T:0.03
Consensus pattern (21 bp):
AGAGAAACAGAGAGAGAAGCA
Found at i:105588 original size:21 final size:21
Alignment explanation
Indices: 105543--105589 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
105533 GCTGAGATAG
*
105543 AAGCAAGAGAAACAGAGAGAG
1 AAGCAAGAGAAACAGAGAGAA
105564 AAGCAAGAGAAACAGA-ACGAA
1 AAGCAAGAGAAACAGAGA-GAA
105585 AAGCA
1 AAGCA
105590 GTACATCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.60, C:0.13, G:0.28, T:0.00
Consensus pattern (21 bp):
AAGCAAGAGAAACAGAGAGAA
Found at i:109536 original size:19 final size:19
Alignment explanation
Indices: 109519--109567 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
109509 TGAAAAGATT
109519 TAATAAAATAAAATAGATAA
1 TAAT-AAATAAAATAGATAA
** *
109539 TAATAAATAAAAGGGAAAA
1 TAATAAATAAAATAGATAA
109558 TAATAAATAA
1 TAATAAATAA
109568 TAGTAGTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 22 0.85
20 4 0.15
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.22
Consensus pattern (19 bp):
TAATAAATAAAATAGATAA
Found at i:109649 original size:17 final size:18
Alignment explanation
Indices: 109609--109649 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
109599 GTTGTTTTTA
109609 AAATAAAAGATAAGAATT
1 AAATAAAAGATAAGAATT
*
109627 AAATAAAAGA-AATAATT
1 AAATAAAAGATAAGAATT
*
109644 ACATAA
1 AAATAA
109650 TAATTTAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.68, C:0.02, G:0.07, T:0.22
Consensus pattern (18 bp):
AAATAAAAGATAAGAATT
Done.