Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000917.1 Hibiscus syriacus cultivar Beakdansim tig00001830_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: 54078
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:671 original size:14 final size:15
Alignment explanation
Indices: 617--683 Score: 66
Period size: 15 Copynumber: 4.5 Consensus size: 15
607 TTCCAGAAAA
* *
617 TGAATTATTGGAATT
1 TGAATTACTGAAATT
*
632 TGAATTACTGGAAA-A
1 TGAATTACT-GAAATT
647 TGAATTACTGAAATT
1 TGAATTACTGAAATT
**
662 TGAATT-CTGAAAAA
1 TGAATTACTGAAATT
676 TGAATTAC
1 TGAATTAC
684 ATTTCTGTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
14 16 0.37
15 24 0.56
16 3 0.07
ACGTcount: A:0.42, C:0.06, G:0.16, T:0.36
Consensus pattern (15 bp):
TGAATTACTGAAATT
Found at i:683 original size:29 final size:30
Alignment explanation
Indices: 613--683 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
603 GGTTTTCCAG
* * *
613 AAAATGAATTATTGGAATTTGAATTACTGG
1 AAAATGAATTACTGAAATTTGAATTACTGA
643 AAAATGAATTACTGAAATTTGAATT-CTGA
1 AAAATGAATTACTGAAATTTGAATTACTGA
672 AAAATGAATTAC
1 AAAATGAATTAC
684 ATTTCTGTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
29 15 0.39
30 23 0.61
ACGTcount: A:0.45, C:0.06, G:0.15, T:0.34
Consensus pattern (30 bp):
AAAATGAATTACTGAAATTTGAATTACTGA
Found at i:689 original size:20 final size:20
Alignment explanation
Indices: 666--735 Score: 113
Period size: 20 Copynumber: 3.5 Consensus size: 20
656 GAAATTTGAA
666 TTCTGAAAAATGAATTACAT
1 TTCTGAAAAATGAATTACAT
*
686 TTCTGTAAAATGAATTACAT
1 TTCTGAAAAATGAATTACAT
*
706 TTCTGGAAAATGAATTACAT
1 TTCTGAAAAATGAATTACAT
726 TTCTGGAAAA
1 TTCT-GAAAA
736 CATCTGGAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
20 42 0.91
21 4 0.09
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (20 bp):
TTCTGAAAAATGAATTACAT
Found at i:939 original size:28 final size:27
Alignment explanation
Indices: 898--993 Score: 85
Period size: 28 Copynumber: 3.5 Consensus size: 27
888 TCTTACTAAA
*
898 TATTATGAAATATATAAATAATATTAT
1 TATTATTAAATATATAAATAATATTAT
*
925 TCATTATTAAATATATAAA-AAAATTTAT
1 T-ATTATTAAATATATAAATAATA-TTAT
953 TATATATT--ATA-ATAAATAATATCT-T
1 TAT-TATTAAATATATAAATAATAT-TAT
978 ATATTATTATAATATA
1 -TATTATTA-AATATA
994 ATTGATTATT
Statistics
Matches: 56, Mismatches: 3, Indels: 18
0.73 0.04 0.23
Matches are distributed among these distances:
25 11 0.20
26 10 0.18
27 6 0.11
28 28 0.50
29 1 0.02
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (27 bp):
TATTATTAAATATATAAATAATATTAT
Found at i:969 original size:71 final size:69
Alignment explanation
Indices: 894--1060 Score: 153
Period size: 71 Copynumber: 2.3 Consensus size: 69
884 AATATCTTAC
*
894 TAAATATTATGAAATATATAAATAATATTATTCATTATTAAATATATAA-AAAAAT-TTAT-TAT
1 TAAATATTAT-AAATATATAAATAATATAATTCATTATT--ATATATAATAAAAATATTATAT-T
956 ATATTATAA
62 ATATTAT-A
* ** * * *
965 TAAATAATAT-CTTATATTATTATAATATAATTGATTATTTTATATAATTAAAAATATTATATTA
1 TAAATATTATAAATATA-TA-AATAATATAATTCATTATTATATATAA-TAAAAATATTATATTA
1029 TATTATA
63 TATTATA
1036 TAAATATTAATAAATATATTAAATA
1 TAAATATT-ATAAATATA-TAAATA
1061 TTTTAATAAT
Statistics
Matches: 77, Mismatches: 11, Indels: 15
0.75 0.11 0.15
Matches are distributed among these distances:
69 11 0.14
70 2 0.03
71 39 0.51
72 17 0.22
73 8 0.10
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (69 bp):
TAAATATTATAAATATATAAATAATATAATTCATTATTATATATAATAAAAATATTATATTATAT
TATA
Found at i:1002 original size:47 final size:44
Alignment explanation
Indices: 936--1038 Score: 102
Period size: 47 Copynumber: 2.3 Consensus size: 44
926 CATTATTAAA
* * *
936 TATATAAAAAAATTTATTA-TATATTATAA-TAAATAATATCTTATAT
1 TATATAATATAATTGATTATTATA-TATAATTAAA-AATA--TTATAT
*
982 TATTATAATATAATTGATTATTTTATATAATTAAAAATATTATAT
1 TA-TATAATATAATTGATTATTATATATAATTAAAAATATTATAT
*
1027 TATATTATATAA
1 TATATAATATAA
1039 ATATTAATAA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
44 9 0.18
45 8 0.16
46 2 0.04
47 23 0.47
48 7 0.14
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.49
Consensus pattern (44 bp):
TATATAATATAATTGATTATTATATATAATTAAAAATATTATAT
Found at i:1003 original size:50 final size:51
Alignment explanation
Indices: 911--1076 Score: 135
Period size: 50 Copynumber: 3.2 Consensus size: 51
901 TATGAAATAT
* *
911 ATAAATAATATTATT-CATTAT-TAAATATATAAAAAAATTTATTATATATTATA
1 ATAAATAATA-TATTATATTATATAAATAT-T-AATAAA-TTATTATATATTATA
* ** * *
964 ATAAATAATATCTTATATTAT-TATAATA-TAATTGATTATTTTATATAATTA
1 ATAAATAATATATTATATTATATA-AATATTAATAAATTATTATATATTA-TA
* * *
1015 A-AAATATTATATTATATTATATAAATATTAATAAATATATTAAATATTTTA
1 ATAAATAATATATTATATTATATAAATATTAATAAAT-TATTATATATTATA
*
1066 ATAATTAATAT
1 ATAAATAATAT
1077 TTTGATGAAA
Statistics
Matches: 89, Mismatches: 17, Indels: 15
0.74 0.14 0.12
Matches are distributed among these distances:
50 32 0.36
51 17 0.19
52 19 0.21
53 17 0.19
54 4 0.04
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.48
Consensus pattern (51 bp):
ATAAATAATATATTATATTATATAAATATTAATAAATTATTATATATTATA
Found at i:1010 original size:22 final size:21
Alignment explanation
Indices: 955--1044 Score: 83
Period size: 22 Copynumber: 4.1 Consensus size: 21
945 AAATTTATTA
*
955 TATATTATAATAA-ATAATATCT
1 TATATTAT-ATAATATAA-ATAT
*
977 TATATTATTATAATATAATTGAT
1 TATATTA-TATAATATAAAT-AT
* *
1000 TATTTTATATAATTAAAAATAT
1 TATATTATATAA-TATAAATAT
*
1022 TATATTATATTATATAAATAT
1 TATATTATATAATATAAATAT
1043 TA
1 TA
1045 ATAAATATAT
Statistics
Matches: 56, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
21 10 0.18
22 29 0.52
23 17 0.30
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (21 bp):
TATATTATATAATATAAATAT
Found at i:1047 original size:27 final size:28
Alignment explanation
Indices: 998--1056 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
988 AATATAATTG
* * *
998 ATTATTTTATATAATTAAAAAT-ATTAT
1 ATTATATTATATAAATAAAAATAAATAT
**
1025 ATTATATTATATAAATATTAATAAATAT
1 ATTATATTATATAAATAAAAATAAATAT
1053 ATTA
1 ATTA
1057 AATATTTTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 18 0.69
28 8 0.31
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (28 bp):
ATTATATTATATAAATAAAAATAAATAT
Found at i:1308 original size:42 final size:42
Alignment explanation
Indices: 1249--1363 Score: 212
Period size: 42 Copynumber: 2.7 Consensus size: 42
1239 ATGAATTACA
*
1249 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1291 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
*
1333 TTCCGTAAAACGAATTACGTGAAACAAACAC
1 TTCCGGAAAACGAATTACGTGAAACAAACAC
1364 TGAATTCGGG
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.44, C:0.20, G:0.18, T:0.17
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:2363 original size:33 final size:33
Alignment explanation
Indices: 2319--2468 Score: 174
Period size: 33 Copynumber: 4.5 Consensus size: 33
2309 TTTTGCTTAC
*
2319 GCAGAAACATTGCGAGAAGAACCGCCTTGATTG
1 GCAGAAACATTGCGAGAAGAACCGCCTTGAATG
* * * * * * *
2352 ACAGAAGCATTGAGAGGAGGACCTCCTTGATTG
1 GCAGAAACATTGCGAGAAGAACCGCCTTGAATG
* * **
2385 GCAGTAACATTGCGAGGAGAACCTACTTGAATG
1 GCAGAAACATTGCGAGAAGAACCGCCTTGAATG
* *
2418 GCAGAAAAATTGCAAGAAGAACCGCCTTGAATG
1 GCAGAAACATTGCGAGAAGAACCGCCTTGAATG
2451 GCAGAAACATTGCGAGAA
1 GCAGAAACATTGCGAGAA
2469 TGGGGAGAAC
Statistics
Matches: 96, Mismatches: 21, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 96 1.00
ACGTcount: A:0.36, C:0.19, G:0.27, T:0.18
Consensus pattern (33 bp):
GCAGAAACATTGCGAGAAGAACCGCCTTGAATG
Found at i:5308 original size:3 final size:3
Alignment explanation
Indices: 5300--5370 Score: 87
Period size: 3 Copynumber: 24.7 Consensus size: 3
5290 CGTCCATTTG
*
5300 TTA TTA TTA TTA -TA TTA TTA TT- TTA TTTA TTA CTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
*
5343 TAA TTA -TA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5371 TACATTACAG
Statistics
Matches: 59, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
2 8 0.14
3 48 0.81
4 3 0.05
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:5923 original size:28 final size:27
Alignment explanation
Indices: 5874--5930 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
5864 AAGGATAGAC
5874 AGCAACCCAAAAAAAAACACAGCAACAAG
1 AGCAACCCAAAAAAAAACACAG-AA-AAG
*
5903 AGCAA-CCAAAACAACAA-ACAGAAAAG
1 AGCAACCCAAAA-AAAAACACAGAAAAG
5929 AG
1 AG
5931 AGAGAAGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
26 5 0.19
27 2 0.08
28 10 0.38
29 9 0.35
ACGTcount: A:0.63, C:0.25, G:0.12, T:0.00
Consensus pattern (27 bp):
AGCAACCCAAAAAAAAACACAGAAAAG
Found at i:6729 original size:23 final size:22
Alignment explanation
Indices: 6703--6753 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
6693 TCATTGTTTA
6703 TTTTATATTTATATT-TTATATGT
1 TTTTATATTTA-ATTATTAT-TGT
6726 TTTTATATTTAATTATTATTGT
1 TTTTATATTTAATTATTATTGT
*
6748 TATTAT
1 TTTTAT
6754 TATGTAGTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 11 0.42
23 15 0.58
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (22 bp):
TTTTATATTTAATTATTATTGT
Found at i:7549 original size:26 final size:27
Alignment explanation
Indices: 7497--7554 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
7487 TAATTCTTTC
*
7497 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCAAAATATTTATATATAC-TATTA
* *
7525 TTTTCATAATATTTATATGTA-TATTA
1 TTTTCAAAATATTTATATATACTATTA
7551 TTTT
1 TTTT
7555 TTTATTTTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 9 0.33
28 18 0.67
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (27 bp):
TTTTCAAAATATTTATATATACTATTA
Found at i:7556 original size:28 final size:28
Alignment explanation
Indices: 7497--7557 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
7487 TAATTCTTTC
*
7497 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCAAAATTTATATATATACTTATTA
* *
7525 TTTTCATAATATTTATATGTATA-TTATTT
1 TTTTCA-AA-ATTTATATATATACTTATTA
7554 TTTT
1 TTTT
7558 ATTTTCAAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 6 0.21
29 11 0.39
30 11 0.39
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (28 bp):
TTTTCAAAATTTATATATATACTTATTA
Found at i:12242 original size:8 final size:9
Alignment explanation
Indices: 12225--12269 Score: 83
Period size: 9 Copynumber: 5.1 Consensus size: 9
12215 CTCATTCATC
12225 AGGAAAAAA
1 AGGAAAAAA
12234 AGGAAAAAA
1 AGGAAAAAA
12243 AGGAAAAAA
1 AGGAAAAAA
12252 AGG-AAAAA
1 AGGAAAAAA
12260 AGGAAAAAA
1 AGGAAAAAA
12269 A
1 A
12270 ATGAGAAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.23
9 27 0.77
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (9 bp):
AGGAAAAAA
Found at i:12270 original size:18 final size:18
Alignment explanation
Indices: 12225--12269 Score: 83
Period size: 17 Copynumber: 2.6 Consensus size: 18
12215 CTCATTCATC
12225 AGGAAAAAAAGGAAAAAA
1 AGGAAAAAAAGGAAAAAA
12243 AGGAAAAAAAGG-AAAAA
1 AGGAAAAAAAGGAAAAAA
12260 AGGAAAAAAA
1 AGGAAAAAAA
12270 ATGAGAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 15 0.56
18 12 0.44
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (18 bp):
AGGAAAAAAAGGAAAAAA
Found at i:17018 original size:22 final size:22
Alignment explanation
Indices: 16992--17065 Score: 121
Period size: 22 Copynumber: 3.4 Consensus size: 22
16982 ATCTACACTC
16992 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
17014 TTCAAAGATGATAGATTCTCTC
1 TTCAAAGATGATAGATTCTCTT
* *
17036 TTCAAAGATGTTACATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
17058 TTCAAAGA
1 TTCAAAGA
17066 GAAGAAAGAT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.39
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:17614 original size:113 final size:113
Alignment explanation
Indices: 17411--17838 Score: 472
Period size: 113 Copynumber: 3.7 Consensus size: 113
17401 TTTCAAAGAT
* * *
17411 TTGCCAGGTAGAGTTCATAATGAGAAGAGCTTATCTGAAGAAGGAAGAA-AAAGTTCATAATGAG
1 TTGCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAA-TTCATAATGAG
* *
17475 AAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCAGCA
65 AAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTCGATGGATCAACA
*
17524 TTGCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTTATAATGAGA
1 TTGCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGA
* * * *
17589 AGAATTTGTTCAACCTTTTGTTTGAATTCATCACTCGATTGATCAACT
66 AGAACTTGTTCAACCTTTTGCTTGAATTCATCACTCGATGGATCAACA
* * * * * *
17637 TTTCCAGAGAAAGTTTATAATGAGAAGAACTCATCTGAAG-AGG-TGAAGAAGTTCATAATGAGA
1 TTGCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGA
* * ** *
17700 AGAACTTGTTCAACCTTTTGCATG-ACTCTATCACAGAAGGAGGTATATCAGAATCAACA
66 AGAACTTGTTCAACCTTTTGCTTGAATTC-ATCAC---------TCGAT--GGATCAACA
* * *
17759 TTTCCAGA-AGTGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATGAGA
1 TTGCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGA
*
17822 TGAACTTGTTCAACCTT
66 AGAACTTGTTCAACCTT
17839 AATTTGATTC
Statistics
Matches: 270, Mismatches: 31, Indels: 19
0.84 0.10 0.06
Matches are distributed among these distances:
110 3 0.01
111 43 0.16
112 3 0.01
113 135 0.50
114 3 0.01
120 3 0.01
121 31 0.11
122 49 0.18
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (113 bp):
TTGCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGA
AGAACTTGTTCAACCTTTTGCTTGAATTCATCACTCGATGGATCAACA
Found at i:18227 original size:3 final size:3
Alignment explanation
Indices: 18202--18273 Score: 96
Period size: 3 Copynumber: 24.7 Consensus size: 3
18192 CCATTTGTTT
* *
18202 TTA TTA TT- TTA TTTA TTA CTA TTA TTA TT- TTA TAA TTA -TA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
18245 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
18274 TACATTACAT
Statistics
Matches: 61, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
2 6 0.10
3 52 0.85
4 3 0.05
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:19612 original size:23 final size:22
Alignment explanation
Indices: 19586--19628 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
19576 TTTTTTATTT
19586 TATATTTATATT-TTATATGTTTG
1 TATATTTA-ATTATTAT-TGTTTG
19609 TATATTTAATTATTATTGTT
1 TATATTTAATTATTATTGTT
19629 ATTATTATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (22 bp):
TATATTTAATTATTATTGTTTG
Found at i:20903 original size:20 final size:20
Alignment explanation
Indices: 20851--20904 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
20841 AAATGACCAA
*
20851 CAAATTCGCAACACAGTTTC
1 CAAATTCGCAACTCAGTTTC
*
20871 CAAATTCGCAACTCAGTTTT
1 CAAATTCGCAACTCAGTTTC
*
20891 GAAATTCGCAACTC
1 CAAATTCGCAACTC
20905 GAATTTCTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.28, G:0.11, T:0.28
Consensus pattern (20 bp):
CAAATTCGCAACTCAGTTTC
Found at i:20980 original size:20 final size:20
Alignment explanation
Indices: 20893--20983 Score: 71
Period size: 20 Copynumber: 4.5 Consensus size: 20
20883 TCAGTTTTGA
*
20893 AATTCGCAACTCGAATTTCTT
1 AATTCGCAACGCGAATTT-TT
*
20914 --TTCCGCAACGCG-ATTTTCCA
1 AATT-CGCAACGCGAATTTT--T
***
20934 AATTCGCAACGCGAATCGGT
1 AATTCGCAACGCGAATTTTT
*
20954 AAATCGCAACGCGAATTTTT
1 AATTCGCAACGCGAATTTTT
20974 AATTCGCAAC
1 AATTCGCAAC
20984 ACAGAAGTCA
Statistics
Matches: 53, Mismatches: 11, Indels: 13
0.69 0.14 0.17
Matches are distributed among these distances:
18 1 0.02
19 6 0.11
20 33 0.62
21 9 0.17
22 4 0.08
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (20 bp):
AATTCGCAACGCGAATTTTT
Found at i:21200 original size:22 final size:22
Alignment explanation
Indices: 21152--21200 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
21142 ACTCTCTACA
* * * *
21152 GCGACATCCGTCTCCATCTCTG
1 GCGACATCCATCCCCATATCCG
*
21174 ACGACATCCATCCCCATATCCG
1 GCGACATCCATCCCCATATCCG
21196 GCGAC
1 GCGAC
21201 CCCCTCATCT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
GCGACATCCATCCCCATATCCG
Found at i:21558 original size:20 final size:20
Alignment explanation
Indices: 21535--21573 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
21525 TTTGAAACTT
*
21535 AAATTCGCAATACGAAAATG
1 AAATTCGCAACACGAAAATG
21555 AAATTCGCAACACGAAAAT
1 AAATTCGCAACACGAAAAT
21574 CGCAATGCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.18, G:0.13, T:0.18
Consensus pattern (20 bp):
AAATTCGCAACACGAAAATG
Found at i:21601 original size:19 final size:20
Alignment explanation
Indices: 21579--21627 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
21569 AAAATCGCAA
*
21579 TGCGGTTTT-AGTTTCGCGT
1 TGCGATTTTCAGTTTCGCGT
*
21598 TGCGATTTTCATTTTCGCGT
1 TGCGATTTTCAGTTTCGCGT
*
21618 TACGATTTTC
1 TGCGATTTTC
21628 GCGTTGCGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.10, C:0.18, G:0.22, T:0.49
Consensus pattern (20 bp):
TGCGATTTTCAGTTTCGCGT
Found at i:21645 original size:20 final size:20
Alignment explanation
Indices: 21590--21660 Score: 73
Period size: 20 Copynumber: 3.9 Consensus size: 20
21580 GCGGTTTTAG
*
21590 TTTCGCGTTGCGATTTTCAT
1 TTTCGCGTTGCGAATTTCAT
*
21610 TTTCGCGTTACG------AT
1 TTTCGCGTTGCGAATTTCAT
21624 TTTCGCGTTGCGAATTTCAT
1 TTTCGCGTTGCGAATTTCAT
*
21644 TTTCGTGTTGCGAATTT
1 TTTCGCGTTGCGAATTT
21661 AAGTTTCAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
14 13 0.31
20 29 0.69
ACGTcount: A:0.13, C:0.18, G:0.21, T:0.48
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTCAT
Found at i:21667 original size:20 final size:20
Alignment explanation
Indices: 21624--21667 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
21614 GCGTTACGAT
* *
21624 TTTCGCGTTGCGAATTTCAT
1 TTTCGCGTTGCGAATTTAAG
*
21644 TTTCGTGTTGCGAATTTAAG
1 TTTCGCGTTGCGAATTTAAG
21664 TTTC
1 TTTC
21668 AAAAACTACT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.16, C:0.16, G:0.20, T:0.48
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTAAG
Found at i:23075 original size:30 final size:30
Alignment explanation
Indices: 23003--23075 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 30
22993 CCCGAAGGAC
* *
23003 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTTATAAAGATCCTCGGCAA
23033 CTATCCAGAGGTTATAAAGATCCTCGGCAA
1 CTATCCAGAGGTTATAAAGATCCTCGGCAA
* *
23063 CTGTCCATAGGTT
1 CTATCCAGAGGTT
23076 CCGAAGAACC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (30 bp):
CTATCCAGAGGTTATAAAGATCCTCGGCAA
Found at i:23096 original size:31 final size:31
Alignment explanation
Indices: 23061--23248 Score: 202
Period size: 31 Copynumber: 6.0 Consensus size: 31
23051 GATCCTCGGC
* *
23061 AACTGTCCATAGGTTCCGAAGAACCTAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
**
23092 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
* **
23123 TACTGTCCATATGTCTCAAAAG-ACATAGGTA
1 AACTGTCCATATGT-TCCGAAGAACATAGGTA
* *
23154 ATTCTGTCCATATGTTCCGTAGAACATAGGTA
1 A-ACTGTCCATATGTTCCGAAGAACATAGGTA
*
23186 TACTGTCCATATG-TCTCGAA-AGACATAGGTA
1 AACTGTCCATATGTTC-CGAAGA-ACATAGGTA
* *
23217 ATTCTGTCCATATGTTCCGTAGAACATAGGTA
1 A-ACTGTCCATATGTTCCGAAGAACATAGGTA
23249 TACCCTCGAC
Statistics
Matches: 130, Mismatches: 19, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
30 3 0.02
31 76 0.58
32 48 0.37
33 3 0.02
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGAAGAACATAGGTA
Found at i:23177 original size:63 final size:63
Alignment explanation
Indices: 23086--23251 Score: 298
Period size: 63 Copynumber: 2.7 Consensus size: 63
23076 CCGAAGAACC
* *
23086 TAGGTAA-ACTGTCCATATGTTCCTTAGAACATAGGTATACTGTCCATATGTCTCAAAAGACA
1 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCAAAAGACA
*
23148 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACA
1 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCAAAAGACA
23211 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATAC
1 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATAC
23252 CCTCGACTCT
Statistics
Matches: 100, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
62 7 0.07
63 93 0.93
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (63 bp):
TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCAAAAGACA
Found at i:27662 original size:30 final size:30
Alignment explanation
Indices: 27626--27682 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
27616 CCCGAATGAC
27626 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
27656 CTATCCAGAGGTCATAAAGATCCTCGG
1 CTATCCAGAGGTCATAAAGATCCTCGG
27683 CAGCTGTCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.23
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:27722 original size:31 final size:31
Alignment explanation
Indices: 27687--27857 Score: 148
Period size: 31 Copynumber: 5.5 Consensus size: 31
27677 CCTCGGCAGC
* *
27687 TGTCCATAGGTTCCAAAGAACCTAGGTAAAT
1 TGTCCATATGTTCCAAAGAACATAGGTAAAT
** * *
27718 TGTCCATATGTTCCTTAGAACATAGGTATAC
1 TGTCCATATGTTCCAAAGAACATAGGTAAAT
* *
27749 TGTCCATATGTCTCGAAAG-ACATAGGTAATT
1 TGTCCATATGT-TCCAAAGAACATAGGTAAAT
** * *
27780 CTGTCCATATGTTCCGTAGAACATAGGTATAC
1 -TGTCCATATGTTCCAAAGAACATAGGTAAAT
* * * *
27812 TGTCTATATATCTCGAAAG-ACATAGGTAATT
1 TGTCCATATGT-TCCAAAGAACATAGGTAAAT
27843 CTGTCCATATGTTCC
1 -TGTCCATATGTTCC
27858 GTAGAATATA
Statistics
Matches: 106, Mismatches: 29, Indels: 10
0.73 0.20 0.07
Matches are distributed among these distances:
31 69 0.65
32 37 0.35
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (31 bp):
TGTCCATATGTTCCAAAGAACATAGGTAAAT
Found at i:27791 original size:63 final size:63
Alignment explanation
Indices: 27686--27874 Score: 274
Period size: 63 Copynumber: 3.0 Consensus size: 63
27676 TCCTCGGCAG
* * * * *
27686 CTGTCCATAGGT-TCCAAAGAACCTAGGTAAAT-TGTCCATATGTTCCTTAGAACATAGGTATA
1 CTGTCCATATGTCTCGAAAG-ACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATA
27748 CTGTCCATATGTCTCGAAAGACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATA
1 CTGTCCATATGTCTCGAAAGACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATA
* * * *
27811 CTGTCTATATATCTCGAAAGACATAGGTAATTCTGTCCATATGTTCCGTAGAATATAAGTATA
1 CTGTCCATATGTCTCGAAAGACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATA
27874 C
1 C
27875 CCTCGACTCT
Statistics
Matches: 116, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
62 21 0.18
63 95 0.82
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (63 bp):
CTGTCCATATGTCTCGAAAGACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATA
Found at i:30877 original size:42 final size:42
Alignment explanation
Indices: 30818--30916 Score: 162
Period size: 42 Copynumber: 2.4 Consensus size: 42
30808 CCCCCCACTT
* * *
30818 CGAGAGCCATCACCTGATCGAGCCGATTCTACAGCTCGACAC
1 CGAGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAC
*
30860 CGAGAACCATCACCTGATCGAGCCGATTATACACCTCCACAC
1 CGAGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAC
30902 CGAGAGCCATCACCT
1 CGAGAGCCATCACCT
30917 ATTCCATCAT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.28, C:0.37, G:0.18, T:0.16
Consensus pattern (42 bp):
CGAGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAC
Found at i:31055 original size:21 final size:21
Alignment explanation
Indices: 31031--31083 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 21
31021 GTTAGGGGAG
*
31031 TTACGTGATGAGGTCAG-TGCT
1 TTACGTGATGAGGTC-GTTACT
31052 TTACGTGATGAGGTCGTTACT
1 TTACGTGATGAGGTCGTTACT
31073 TTACGTGATGA
1 TTACGTGATGA
31084 CAATGGTGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 1 0.03
21 29 0.97
ACGTcount: A:0.21, C:0.13, G:0.30, T:0.36
Consensus pattern (21 bp):
TTACGTGATGAGGTCGTTACT
Found at i:31203 original size:21 final size:21
Alignment explanation
Indices: 31153--31206 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
31143 ATGACAATGG
*
31153 TGCTTTACGTGGTGAGGTATC
1 TGCTTTACGTGATGAGGTATC
*
31174 TACTTTACGTGATGAGGTAGT-
1 TGCTTTACGTGATGAGGTA-TC
*
31195 TGCTCTACGTGA
1 TGCTTTACGTGA
31207 GATTGTTTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.19, C:0.15, G:0.30, T:0.37
Consensus pattern (21 bp):
TGCTTTACGTGATGAGGTATC
Found at i:31514 original size:21 final size:21
Alignment explanation
Indices: 31488--31542 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
31478 ATTCACCTGT
31488 CATCGTTCAAGAGGCCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
31509 CATCGTTCAAGAGGCCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
*
31530 CACCGTTCAAGAG
1 CATCGTTCAAGAG
31543 CACGATTCAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.22, C:0.40, G:0.20, T:0.18
Consensus pattern (21 bp):
CATCGTTCAAGAGGCCCCTCC
Found at i:33128 original size:29 final size:29
Alignment explanation
Indices: 33087--33190 Score: 190
Period size: 29 Copynumber: 3.6 Consensus size: 29
33077 TTTTTGCGTT
* *
33087 GCGAATTTGACTTTCGCAACAATCGCAAT
1 GCGAATTTGACTTTCGCAATAATCGCAAC
33116 GCGAATTTGACTTTCGCAATAATCGCAAC
1 GCGAATTTGACTTTCGCAATAATCGCAAC
33145 GCGAATTTGACTTTCGCAATAATCGCAAC
1 GCGAATTTGACTTTCGCAATAATCGCAAC
33174 GCGAATTTGACTTTCGC
1 GCGAATTTGACTTTCGC
33191 GTTGCGAATT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 73 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (29 bp):
GCGAATTTGACTTTCGCAATAATCGCAAC
Found at i:35648 original size:24 final size:24
Alignment explanation
Indices: 35621--35667 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
35611 CAAAATCCGA
35621 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
35645 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
35668 AATACTGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:35676 original size:24 final size:24
Alignment explanation
Indices: 35625--35676 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
35615 ATCCGAGTAT
** *
35625 TGACCAAGATCAAAGTTCGGGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
35649 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
35673 TGAC
1 TGAC
35677 TAGTACTCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:38688 original size:20 final size:19
Alignment explanation
Indices: 38644--38691 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
38634 CAAAATATTT
38644 GTGTTGCGAAAATAAAAGC
1 GTGTTGCGAAAATAAAAGC
* *
38663 -TGTTGCGAAATTAAAATTC
1 GTGTTGCGAAAATAAAA-GC
38682 GTGTTGCGAA
1 GTGTTGCGAA
38692 TTTGAAAACC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 15 0.60
19 1 0.04
20 9 0.36
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.29
Consensus pattern (19 bp):
GTGTTGCGAAAATAAAAGC
Found at i:38809 original size:20 final size:20
Alignment explanation
Indices: 38786--38915 Score: 83
Period size: 20 Copynumber: 6.4 Consensus size: 20
38776 GAAATTCACA
*
38786 TTGCGAATTCAGAAATCGAG
1 TTGCGAATTTAGAAATCGAG
*
38806 TTGCGAATTTA-AAATTCCGTG
1 TTGCGAATTTAGAAA-T-CGAG
* *
38827 TTGCGAATTTGGAAATCGCG
1 TTGCGAATTTAGAAATCGAG
*
38847 TTGCGAATTTGAAAAATCGCA-
1 TTGCGAATTT-AGAAATCG-AG
* *
38868 TTGCGAGA--AAGAAATTCGCG
1 TTGCGA-ATTTAGAAA-TCGAG
38888 TTGCG-ATTATAGAAA-CTGAG
1 TTGCGAATT-TAGAAATC-GAG
38908 TTGCGAAT
1 TTGCGAAT
38916 ATGGGAAATT
Statistics
Matches: 85, Mismatches: 12, Indels: 25
0.70 0.10 0.20
Matches are distributed among these distances:
18 1 0.01
19 8 0.09
20 39 0.46
21 33 0.39
22 4 0.05
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (20 bp):
TTGCGAATTTAGAAATCGAG
Found at i:38831 original size:21 final size:20
Alignment explanation
Indices: 38798--38873 Score: 82
Period size: 21 Copynumber: 3.7 Consensus size: 20
38788 GCGAATTCAG
*
38798 AAATCGAGTTGCGAATTT-A
1 AAATCGCGTTGCGAATTTGA
* *
38817 AAATTCCGTGTTGCGAATTTGG
1 AAA-T-CGCGTTGCGAATTTGA
38839 AAATCGCGTTGCGAATTTGAA
1 AAATCGCGTTGCGAATTTG-A
*
38860 AAATCGCATTGCGA
1 AAATCGCGTTGCGA
38874 GAAAGAAATT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
19 3 0.06
20 15 0.31
21 27 0.56
22 3 0.06
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (20 bp):
AAATCGCGTTGCGAATTTGA
Found at i:38872 original size:41 final size:41
Alignment explanation
Indices: 38784--38873 Score: 110
Period size: 41 Copynumber: 2.2 Consensus size: 41
38774 AAGAAATTCA
*
38784 CATTGCGAATTCAGAAATCGAGTTGCGAATTTAAAATTCCG
1 CATTGCGAATTCAGAAATCGAGTTGCGAATTTAAAAATCCG
** ** *
38825 TGTTGCGAATTTGGAAATCGCGTTGCGAATTTGAAAAAT-CG
1 CATTGCGAATTCAGAAATCGAGTTGCGAATTT-AAAAATCCG
38866 CATTGCGA
1 CATTGCGA
38874 GAAAGAAATT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 35 0.88
42 5 0.12
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (41 bp):
CATTGCGAATTCAGAAATCGAGTTGCGAATTTAAAAATCCG
Found at i:38901 original size:21 final size:22
Alignment explanation
Indices: 38775--38928 Score: 80
Period size: 20 Copynumber: 7.5 Consensus size: 22
38765 GTTGCGAAAA
* * *
38775 AGAAATTCACATTGCGAAT-TC
1 AGAAATTCGCGTTGCGAATATG
* *
38796 AGAAA-TCGAGTTGCGAAT-TT
1 AGAAATTCGCGTTGCGAATATG
* *
38816 A-AAATTCCGTGTTGCGAATTTG
1 AGAAATT-CGCGTTGCGAATATG
*
38838 -GAAA-TCGCGTTGCGAATTTG
1 AGAAATTCGCGTTGCGAATATG
* *
38858 A-AAAATCGCATTGCGAGA-A--
1 AGAAATTCGCGTTGCGA-ATATG
*
38877 AGAAATTCGCGTTGCGATTAT-
1 AGAAATTCGCGTTGCGAATATG
* *
38898 AGAAACT-GAGTTGCGAATATG
1 AGAAATTCGCGTTGCGAATATG
*
38919 GGAAATTCGC
1 AGAAATTCGC
38929 ATTACGTGGA
Statistics
Matches: 103, Mismatches: 18, Indels: 23
0.72 0.12 0.16
Matches are distributed among these distances:
19 4 0.04
20 55 0.53
21 38 0.37
22 6 0.06
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (22 bp):
AGAAATTCGCGTTGCGAATATG
Found at i:43338 original size:20 final size:21
Alignment explanation
Indices: 43288--43342 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
43278 CTAATTGTAG
*
43288 TTCCTAATTTTTAGGGATTCT
1 TTCCTAATTTTTAGGAATTCT
*
43309 TTCTTAATTTTTAGGAATTCT
1 TTCCTAATTTTTAGGAATTCT
*
43330 TTCCTATTTTTTA
1 TTCCTAATTTTTA
43343 CACTAATTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.20, C:0.13, G:0.09, T:0.58
Consensus pattern (21 bp):
TTCCTAATTTTTAGGAATTCT
Done.