Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000302.1 Hibiscus syriacus cultivar Beakdansim tig00000559_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: 59292
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:4529 original size:23 final size:23
Alignment explanation
Indices: 4503--4547 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
4493 CACCACAGCT
*
4503 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
4526 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
4548 ATATAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:5229 original size:19 final size:20
Alignment explanation
Indices: 5192--5229 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5182 TTTTTTTATA
*
5192 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
5212 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
5230 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:5280 original size:21 final size:21
Alignment explanation
Indices: 5256--5297 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5246 TTCATATTCG
* *
5256 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
5277 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
5298 CAGCCCAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.26, G:0.29, T:0.29
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:9569 original size:64 final size:64
Alignment explanation
Indices: 9480--9703 Score: 254
Period size: 64 Copynumber: 3.5 Consensus size: 64
9470 TGTTTGAATG
* ** *
9480 TGCACCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAGACATCGAATGCAATTC
1 TGCATCGATGCATAAGTAGTGCATCGATGCATC-CTATTAATAATAAA-ACATCGAATGCAATTC
9543 A
64 A
* **
9544 TGCATCGATGCATAAGTAGTGCATCGATGCATCCTATTAATAATGAAACATCGAATGCAATTGG
1 TGCATCGATGCATAAGTAGTGCATCGATGCATCCTATTAATAATAAAACATCGAATGCAATTCA
* * ** ** * ** *
9608 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCAGCAATAATACTACATCGAATACCTTTTA
1 TGCATCGATGCATAAGTAGTGCATCGATGCATCCTATTAATAATAAAACATCGAATGCAATTCA
*
9672 TGCATCGATGCATCAGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAGTAGTGCATCGATGCAT
9704 ACCTTCATTA
Statistics
Matches: 137, Mismatches: 21, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
64 131 0.96
65 6 0.04
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.28
Consensus pattern (64 bp):
TGCATCGATGCATAAGTAGTGCATCGATGCATCCTATTAATAATAAAACATCGAATGCAATTCA
Found at i:10029 original size:12 final size:12
Alignment explanation
Indices: 10012--10046 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
10002 ATATATGTTC
10012 ATGTGATATGAT
1 ATGTGATATGAT
10024 ATGTGATATGAT
1 ATGTGATATGAT
10036 ATGTGATATGA
1 ATGTGATATGA
10047 GAACATGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.26, T:0.40
Consensus pattern (12 bp):
ATGTGATATGAT
Found at i:10104 original size:29 final size:29
Alignment explanation
Indices: 10062--10133 Score: 128
Period size: 29 Copynumber: 2.5 Consensus size: 29
10052 TGATATGAAG
10062 TGACATGAGCTACATAATCACAAGAGAAA
1 TGACATGAGCTACATAATCACAAGAGAAA
*
10091 TGACATGAGCTACATGATCACAAGAGAAA
1 TGACATGAGCTACATAATCACAAGAGAAA
10120 TGACATGAG-TACAT
1 TGACATGAGCTACAT
10134 GAACATATGA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
28 5 0.12
29 37 0.88
ACGTcount: A:0.44, C:0.17, G:0.19, T:0.19
Consensus pattern (29 bp):
TGACATGAGCTACATAATCACAAGAGAAA
Found at i:18083 original size:26 final size:26
Alignment explanation
Indices: 18052--18102 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
18042 CATTCAAATT
*
18052 TATAATTATCATTGTTTGATTCAGAC
1 TATAATTATCATTGATTGATTCAGAC
**
18078 TATAATTATTGTTGATTGATTCAGA
1 TATAATTATCATTGATTGATTCAGA
18103 TTATGTTATG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.31, C:0.08, G:0.14, T:0.47
Consensus pattern (26 bp):
TATAATTATCATTGATTGATTCAGAC
Found at i:18278 original size:3 final size:3
Alignment explanation
Indices: 18270--18297 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
18260 TTTATAGAAC
18270 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
18298 TGTAATTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:27226 original size:22 final size:22
Alignment explanation
Indices: 27200--27245 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
27190 TTCAGTATTT
27200 GTCCCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
27222 GTCCCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
27244 GT
1 GT
27246 GTTAATTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.30, G:0.28, T:0.15
Consensus pattern (22 bp):
GTCCCGAAGGACCACTGGATAC
Found at i:27618 original size:18 final size:20
Alignment explanation
Indices: 27581--27618 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
27571 ATTATGTTAG
*
27581 AAACAAAATTTAATCAGGAA
1 AAACAAAATTGAATCAGGAA
27601 AAAC-AAATTGAATC-GGAA
1 AAACAAAATTGAATCAGGAA
27619 GATAAAATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 9 0.53
20 4 0.24
ACGTcount: A:0.58, C:0.11, G:0.13, T:0.18
Consensus pattern (20 bp):
AAACAAAATTGAATCAGGAA
Found at i:30183 original size:32 final size:30
Alignment explanation
Indices: 30074--30184 Score: 105
Period size: 32 Copynumber: 3.5 Consensus size: 30
30064 TAAGGCCTTG
* *
30074 AGCCTACCCAATGGATAACCTTGGGGACTTAA
1 AGCCTACCCAA-GGGTTACCTTGGGGAC-TAA
* * *
30106 AGCCTACGCAAGGGATTACTTTGGGGCCTAAA
1 AGCCTACCCAAGGG-TTACCTTGGGGACT-AA
* *
30138 AGCCTACCTAAGGGTGTGCCTTGGGGACTAA
1 AGCCTACCCAAGGGT-TACCTTGGGGACTAA
30169 GAGCCTACCCAAGGGT
1 -AGCCTACCCAAGGGT
30185 CACTTTAGGT
Statistics
Matches: 64, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
31 6 0.09
32 58 0.91
ACGTcount: A:0.27, C:0.24, G:0.28, T:0.21
Consensus pattern (30 bp):
AGCCTACCCAAGGGTTACCTTGGGGACTAA
Found at i:32118 original size:17 final size:17
Alignment explanation
Indices: 32093--32126 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
32083 TTATTTAATC
*
32093 TAGGTCATTTGAGTATT
1 TAGGCCATTTGAGTATT
*
32110 TAGGCCATTTTAGTATT
1 TAGGCCATTTGAGTATT
32127 AAAGGTTATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.09, G:0.21, T:0.47
Consensus pattern (17 bp):
TAGGCCATTTGAGTATT
Found at i:32146 original size:27 final size:27
Alignment explanation
Indices: 32116--32176 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
32106 TATTTAGGCC
*
32116 ATTTTAGTATTAAAGGTTATTTTGGTT
1 ATTTCAGTATTAAAGGTTATTTTGGTT
*
32143 ATTTCAGTATTAGAGGTTATTTTGGTT
1 ATTTCAGTATTAAAGGTTATTTTGGTT
32170 ATTTCAG
1 ATTTCAG
32177 AGCTAATGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.25, C:0.03, G:0.20, T:0.52
Consensus pattern (27 bp):
ATTTCAGTATTAAAGGTTATTTTGGTT
Found at i:32190 original size:27 final size:27
Alignment explanation
Indices: 32133--32200 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
32123 TATTAAAGGT
* *
32133 TATTTTGGTTATTTCAGTATTAGAGGT
1 TATTTTGGTTATTTCAGTACTAGAGGG
32160 TATTTTGGTTATTTCAG-AGCTA-ATGGG
1 TATTTTGGTTATTTCAGTA-CTAGA-GGG
*
32187 TATTTTGGTCATTT
1 TATTTTGGTTATTT
32201 TATTTGATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
26 2 0.06
27 34 0.94
ACGTcount: A:0.21, C:0.06, G:0.22, T:0.51
Consensus pattern (27 bp):
TATTTTGGTTATTTCAGTACTAGAGGG
Found at i:35825 original size:3 final size:3
Alignment explanation
Indices: 35817--35851 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
35807 ATTTATTTAT
*
35817 TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
35852 TGTAATTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:39238 original size:3 final size:3
Alignment explanation
Indices: 39230--39309 Score: 52
Period size: 3 Copynumber: 26.3 Consensus size: 3
39220 TTATTTTATT
* * * * * *
39230 TAA TAA TAA TAA CAA TAA TAA TTA TTA TAA TAA TAC TAC TAA TATT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
* * ** *
39276 TAA TAT TAA TAA TAG TAA TCT TAA AAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
39310 TTAAGTAAAA
Statistics
Matches: 58, Mismatches: 18, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
3 56 0.97
4 2 0.03
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:39568 original size:75 final size:74
Alignment explanation
Indices: 39471--39612 Score: 230
Period size: 75 Copynumber: 1.9 Consensus size: 74
39461 TTATGAATGA
* *
39471 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAAATGACCCGAAGGCTTTGAAAATAT
1 CCCGAAGGTTTTGAAAACATCATGCACTAAAGGGCTTACAAATGACCCGAAGGCTTTGAAAACAT
39536 CAAAAAGCT
66 CAAAAAGCT
* * *
39545 CCCGAAGGCTTTTGAAAATATCATGCACTAAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACA
1 CCCGAAGG-TTTTGAAAACATCATGCACTAAAGGGCTTACAAATGACCCGAAGGCTTTGAAAACA
39610 TCA
65 TCA
39613 TGCACTGAAG
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
74 8 0.13
75 54 0.87
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (74 bp):
CCCGAAGGTTTTGAAAACATCATGCACTAAAGGGCTTACAAATGACCCGAAGGCTTTGAAAACAT
CAAAAAGCT
Found at i:39613 original size:45 final size:45
Alignment explanation
Indices: 39545--39790 Score: 388
Period size: 45 Copynumber: 5.5 Consensus size: 45
39535 TCAAAAAGCT
* *
39545 CCCGAAGGCTTTTGAAAATATCATGCACTAAAGGGCTTACAGATGA
1 CCCGAAGG-TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
*
39591 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTATAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
39636 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
*
39681 CCCGAAGGTTTTGAAAACATCATGCACTGAATGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
* *
39726 CTCGAAGGTTTTG--AACATCATGCACTGAAGGGCTTAAAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
* * *
39769 CCTGAAGGCTTTGAAAATATCA
1 CCCGAAGGTTTTGAAAACATCA
39791 AAAAACTCCC
Statistics
Matches: 186, Mismatches: 12, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
43 38 0.20
45 140 0.75
46 8 0.04
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (45 bp):
CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
Found at i:39926 original size:44 final size:45
Alignment explanation
Indices: 39798--39953 Score: 226
Period size: 45 Copynumber: 3.5 Consensus size: 45
39788 TCAAAAAACT
39798 CCCGAAGGCTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGG-TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
* *
39844 CTCGAAGGTTTTGAAAACATCCTGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
* *
39889 CCCGAAGGTTTTG-AAACATCATGTACTGAAGGTCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
** *
39933 CCTAAAGGCTTTG-AAACATCA
1 CCCGAAGGTTTTGAAAACATCA
39954 AAAAGCTCCC
Statistics
Matches: 101, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
44 46 0.46
45 48 0.48
46 7 0.07
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (45 bp):
CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
Found at i:40021 original size:164 final size:163
Alignment explanation
Indices: 39636--40047 Score: 630
Period size: 163 Copynumber: 2.5 Consensus size: 163
39626 TTATAGATGA
39636 CCCGAAGG-TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACA
1 CCCGAAGGCTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACA
* *
39700 TCATGCACTGAATGGCTTACAGATGACTCGAAGGTTTTGAACATCATGCACTGAAGGGCTTAAAG
66 TCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAACATCATGCACTGAAGGGCTTAAAG
* *
39765 ATGACCTGAAGGCTTTGAAAATATCAAAAAACT
131 ATGACCTAAAGGCTTTGAAAACATCAAAAAACT
*
39798 CCCGAAGGCTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACTCGAAGGTTTTGAAAACA
1 CCCGAAGGCTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACA
* * * *
39863 TCCTGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAACATCATGTACTGAAGGTCTTACA
66 TCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG-AACATCATGCACTGAAGGGCTTAAA
*
39928 GATGACCTAAAGGCTTTG-AAACATCAAAAAGCT
130 GATGACCTAAAGGCTTTGAAAACATCAAAAAACT
* * * * ** *
39961 CCCGAAGGCTTCTTGAAAACATCTTGTACTGCAGGTCTTATGGATGACCCGAATGTTTTGAAAAC
1 CCCGAAGGCTT-TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAAC
*
40026 ATCATGCACTGAAGGTCTTACA
65 ATCATGCACTGAAGGGCTTACA
40048 AATGTGGGAA
Statistics
Matches: 227, Mismatches: 20, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
162 8 0.04
163 115 0.51
164 104 0.46
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (163 bp):
CCCGAAGGCTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACA
TCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAACATCATGCACTGAAGGGCTTAAAG
ATGACCTAAAGGCTTTGAAAACATCAAAAAACT
Found at i:41206 original size:54 final size:54
Alignment explanation
Indices: 41115--41314 Score: 283
Period size: 54 Copynumber: 3.7 Consensus size: 54
41105 TAACTGGTTT
* * *
41115 GTAAAACATTTTGACAACACATTCATCCTTTTATGTGGTTTCTGCTCAGATGTTC
1 GTAAAGCA-TTTGACAACACATTCATCCTTTCATGTGGTTTCTGCTCAAATGTTC
* * * * *
41170 GCAAAGCATTTGACAACATATTCATCCTTTCCTGTGGTTTCTGCCCATATGTTC
1 GTAAAGCATTTGACAACACATTCATCCTTTCATGTGGTTTCTGCTCAAATGTTC
* * *
41224 GTAAAGCATTTGACAACACATTCATCATTTCCTGTGGTTTCTGCTCAAATGTTA
1 GTAAAGCATTTGACAACACATTCATCCTTTCATGTGGTTTCTGCTCAAATGTTC
*
41278 GTAAAACATTTGACAACACATTCATCCTTTCATGTGG
1 GTAAAGCATTTGACAACACATTCATCCTTTCATGTGG
41315 CTTATGTCCA
Statistics
Matches: 129, Mismatches: 16, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
54 123 0.95
55 6 0.05
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (54 bp):
GTAAAGCATTTGACAACACATTCATCCTTTCATGTGGTTTCTGCTCAAATGTTC
Found at i:49669 original size:6 final size:7
Alignment explanation
Indices: 49652--49692 Score: 50
Period size: 6 Copynumber: 6.0 Consensus size: 7
49642 ATAAAAGTAT
49652 AAATGCA
1 AAATGCA
49659 AAATG-A
1 AAATGCA
49665 AAATGCA
1 AAATGCA
*
49672 AAGATACA
1 AA-ATGCA
49680 AAATGC-
1 AAATGCA
49686 AAATGCA
1 AAATGCA
49693 TGTATGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
6 12 0.41
7 11 0.38
8 6 0.21
ACGTcount: A:0.59, C:0.12, G:0.15, T:0.15
Consensus pattern (7 bp):
AAATGCA
Found at i:49852 original size:43 final size:44
Alignment explanation
Indices: 49770--49852 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 44
49760 TGCATCAAAT
* ** *
49770 AAAACTTTTACATGTAGGGGATAGCTTTCAGTCCCAACTTTAAC
1 AAAACTTTTACATATAGGGGATAAATTTCACTCCCAACTTTAAC
* *
49814 AAAAC-TTTACATATAGGGGATAAATTTCTCTCCTAACTT
1 AAAACTTTTACATATAGGGGATAAATTTCACTCCCAACTT
49853 CTCTAAAGCC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
43 28 0.85
44 5 0.15
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (44 bp):
AAAACTTTTACATATAGGGGATAAATTTCACTCCCAACTTTAAC
Found at i:54414 original size:3 final size:3
Alignment explanation
Indices: 54408--54487 Score: 61
Period size: 3 Copynumber: 26.3 Consensus size: 3
54398 TTTTTTTATT
* * * * *
54408 TAA TAA TAA TTA TAA TTA TAA TAA TTA TAA TAA TAA TAC TAA TATT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
* * ** *
54454 TAA TAT TAA TAA TAG TAA TCT TAA AAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
54488 TTAAGTAAAA
Statistics
Matches: 56, Mismatches: 20, Indels: 2
0.72 0.26 0.03
Matches are distributed among these distances:
3 54 0.96
4 2 0.04
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (3 bp):
TAA
Done.