Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008634.1 Hibiscus syriacus cultivar Beakdansim tig00111606_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: 98388
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:2686 original size:42 final size:43
Alignment explanation
Indices: 2524--2749 Score: 302
Period size: 42 Copynumber: 5.3 Consensus size: 43
2514 TGTTGTATAG
* *
2524 AAAAACGCCGCTATAAAT-TCGACCTTTTGCGGCGTTTGTTCC
1 AAAAATGCCGCTATAAATCTCGACCTTTTGCGGCATTTGTTCC
* * *
2566 AAAAATGCTGCTATAGA--T-GACCTTTTGCGGCATTTGTTTC
1 AAAAATGCCGCTATAAATCTCGACCTTTTGCGGCATTTGTTCC
*
2606 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCATTTGTTCC
1 AAAAATGCCGCTATAAATCTCGACCTTTTGCGGCATTTGTTCC
* *
2649 -AAAATCGCCGCTATAGATCT-GACCTTTTACGGCATTTGTTCC
1 AAAAAT-GCCGCTATAAATCTCGACCTTTTGCGGCATTTGTTCC
* *
2691 AAAAATGCCGCTATAAATCTCGACCTTTAGCGCGCGTTTGTTCC
1 AAAAATGCCGCTATAAATCTCGACCTTTTGCG-GCATTTGTTCC
2735 AAAAATGCCGCTATA
1 AAAAATGCCGCTATA
2750 TCACTACCAA
Statistics
Matches: 161, Mismatches: 16, Indels: 12
0.85 0.08 0.06
Matches are distributed among these distances:
40 34 0.21
41 1 0.01
42 53 0.33
43 48 0.30
44 25 0.16
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (43 bp):
AAAAATGCCGCTATAAATCTCGACCTTTTGCGGCATTTGTTCC
Found at i:2706 original size:85 final size:83
Alignment explanation
Indices: 2524--2749 Score: 348
Period size: 85 Copynumber: 2.7 Consensus size: 83
2514 TGTTGTATAG
*
2524 AAAAACGCCGCTATAAAT-TCGACCTTTTGCGGCGTTTGTTCCAAAAATGCTGCTATAGATGACC
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCGTTTGTTCCAAAAATGCCGCTATAGATGACC
* *
2588 TTTTGCGGCATTTGTTTC
66 TTTTACGGCATTTGTTCC
*
2606 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCATTTGTTCC-AAAATCGCCGCTATAGATCTG
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCGTTTGTTCCAAAAAT-GCCGCTATAGA--TG
2670 ACCTTTTACGGCATTTGTTCC
63 ACCTTTTACGGCATTTGTTCC
* *
2691 AAAAATGCCGCTATAAATCTCGACCTTTAGCGCGCGTTTGTTCCAAAAATGCCGCTATA
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCG-GCGTTTGTTCCAAAAATGCCGCTATA
2750 TCACTACCAA
Statistics
Matches: 131, Mismatches: 7, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
82 23 0.18
83 33 0.25
85 51 0.39
86 19 0.15
87 5 0.04
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (83 bp):
AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCGTTTGTTCCAAAAATGCCGCTATAGATGACC
TTTTACGGCATTTGTTCC
Found at i:3890 original size:25 final size:24
Alignment explanation
Indices: 3862--3914 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 24
3852 CTTTTCTTTG
3862 ATATTGATAAATATTAATTTTAATA
1 ATATTGATAAATATTAATTTTAA-A
* * * *
3887 ATATTGTTTACTTTTAATTTTAAA
1 ATATTGATAAATATTAATTTTAAA
3911 ATAT
1 ATAT
3915 CAGAATAGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (24 bp):
ATATTGATAAATATTAATTTTAAA
Found at i:4102 original size:18 final size:18
Alignment explanation
Indices: 4061--4102 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
4051 AAACAATATT
4061 TAAAAACAATAAAATAAA
1 TAAAAACAATAAAATAAA
* *
4079 TGAAAACATATAAAA-AAC
1 TAAAAACA-ATAAAATAAA
4097 TAAAAA
1 TAAAAA
4103 TAAAATTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.74, C:0.07, G:0.02, T:0.17
Consensus pattern (18 bp):
TAAAAACAATAAAATAAA
Found at i:5447 original size:3 final size:3
Alignment explanation
Indices: 5439--5506 Score: 120
Period size: 3 Copynumber: 22.7 Consensus size: 3
5429 TTAATATATT
5439 TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TAAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
5484 TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
5507 TGGATAAAAA
Statistics
Matches: 63, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.03
3 58 0.92
4 3 0.05
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:7170 original size:113 final size:113
Alignment explanation
Indices: 5823--7139 Score: 2318
Period size: 113 Copynumber: 11.6 Consensus size: 113
5813 TAGAATTATG
*
5823 CAAAAAGTTGAACAAGTTC-T-T-ATTATGAACTTCTTCTTTCTTCTTCAGATGACGAGTTCTTC
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTC
* * * *
5885 TCATTATGAACTCTACT-TGGCAATGTTGATCCATCAAATGATGAATTCAAG
63 TCATTATGAAC-CTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAA
* *
5936 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * * * * **
6001 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGG
66 TTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAA
* * *
6049 TAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* *
6114 TTCATGAACTTTCTCTGGCAATGTTGATCCATCAAATGATGAATTTAAA
66 TT-ATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAA
*
6163 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
6228 TTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAA
66 TTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAA
*
6276 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
6341 TTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAA
66 TTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAA
*
6389 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
6454 TTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAA
66 TTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAA
6502 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
6567 TTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAA
66 TTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAA
*
6615 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
6680 TTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAA
66 TTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAA
*
6728 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
6793 TTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAA
66 TTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAA
6841 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
6906 TTATGAACTTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAA
66 TTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAA
6954 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
7019 TTATGAACTTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAA
66 TTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAA
7067 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
7132 TTATGAAC
66 TTATGAAC
7140 TCTACCTTGC
Statistics
Matches: 1171, Mismatches: 28, Indels: 10
0.97 0.02 0.01
Matches are distributed among these distances:
112 3 0.00
113 1036 0.88
114 103 0.09
115 1 0.00
116 28 0.02
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (113 bp):
CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAA
Found at i:7969 original size:83 final size:84
Alignment explanation
Indices: 7816--8206 Score: 560
Period size: 83 Copynumber: 4.7 Consensus size: 84
7806 GTAATTTCTA
* * *
7816 CCAAACCAGATTAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATATTCATTTTTCC-
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCA-TCTTCCA
*
7880 ACTTCAATGATTGATTATGT
65 AATTCAATGATTGATTATGT
* * *
7900 CC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATTG-GCAAATTCATCTTCCA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTTCCA
* *
7963 AATTCAATGATTGGTTCTG-
65 AATTCAATGATTGATTATGT
* *
7982 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG-ACACATTCTTCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
8046 ATTCAATGATTGATTATGT
66 ATTCAATGATTGATTATGT
* * *
8065 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCCC
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTTCCA
*
8130 ACTTCAATGATTGATTATGT
65 AATTCAATGATTGATTATGT
* *
8150 CC-AACCAGATCAGATAACTCAAATAACACTTCCAGAAGATGCTATGAACATATTCAT
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCAT
8207 TTGTTCTATT
Statistics
Matches: 278, Mismatches: 23, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
82 39 0.14
83 159 0.57
84 46 0.17
85 34 0.12
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (84 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
ATTCAATGATTGATTATGT
Found at i:20841 original size:18 final size:18
Alignment explanation
Indices: 20800--20841 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
20790 AACAATATAT
20800 TAAAAACAATAAAATAAA
1 TAAAAACAATAAAATAAA
* *
20818 TGAAAAC-ATATAAATAAC
1 TAAAAACAATA-AAATAAA
20836 TAAAAA
1 TAAAAA
20842 TAAAATTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.71, C:0.07, G:0.02, T:0.19
Consensus pattern (18 bp):
TAAAAACAATAAAATAAA
Found at i:22195 original size:3 final size:3
Alignment explanation
Indices: 22187--22242 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
22177 AATATATATT
22187 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
22235 TAA TAA TA
1 TAA TAA TA
22243 TGGATAAAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:28700 original size:3 final size:3
Alignment explanation
Indices: 28685--28762 Score: 111
Period size: 3 Copynumber: 26.0 Consensus size: 3
28675 GCAAAAAATG
* * * * *
28685 TAA TAA TAT TAA TAA TGA TAA TAA AAA TAA TAA TGA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
28733 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
28763 AACCCATACA
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:33849 original size:2 final size:2
Alignment explanation
Indices: 33844--33882 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
33834 CCTAAATGAA
33844 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33883 GGTTATAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:45480 original size:7 final size:7
Alignment explanation
Indices: 45468--45500 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
45458 TGTGAAATAT
45468 ATTTCTA
1 ATTTCTA
45475 ATTTCTA
1 ATTTCTA
45482 ATTTCTA
1 ATTTCTA
45489 ATTTCTA
1 ATTTCTA
45496 ATTTC
1 ATTTC
45501 CTTTGATTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.27, C:0.15, G:0.00, T:0.58
Consensus pattern (7 bp):
ATTTCTA
Found at i:51271 original size:2 final size:2
Alignment explanation
Indices: 51264--51304 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
51254 AAACATAATG
51264 AT AT AT AT 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 AT AT AT AT A
51305 GATAATAGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:55216 original size:33 final size:33
Alignment explanation
Indices: 55164--55245 Score: 114
Period size: 33 Copynumber: 2.5 Consensus size: 33
55154 AATTTTATAT
* *
55164 TTATTTATTAATGATTATAATTTGAATCTTAAAA
1 TTATTTTTTAATGATTATAATTTGAATATT-AAA
55198 TT-TTTTCTT-ATGATTATAATTTGAATATTAAA
1 TTATTTT-TTAATGATTATAATTTGAATATTAAA
55230 TTATTTTTTAATGATT
1 TTATTTTTTAATGATT
55246 TCATATATAT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
32 7 0.16
33 32 0.74
34 4 0.09
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.56
Consensus pattern (33 bp):
TTATTTTTTAATGATTATAATTTGAATATTAAA
Found at i:64527 original size:43 final size:43
Alignment explanation
Indices: 64479--64561 Score: 157
Period size: 43 Copynumber: 1.9 Consensus size: 43
64469 GGATCGAAAG
*
64479 TTCGATATGATACCATGTAGAAAATAGGTATTAGGAAAAACTC
1 TTCGATATGATACCATGTAGAAAATAGGTATTAGAAAAAACTC
64522 TTCGATATGATACCATGTAGAAAATAGGTATTAGAAAAAA
1 TTCGATATGATACCATGTAGAAAATAGGTATTAGAAAAAA
64562 TTCTCTCTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.45, C:0.10, G:0.18, T:0.28
Consensus pattern (43 bp):
TTCGATATGATACCATGTAGAAAATAGGTATTAGAAAAAACTC
Found at i:69190 original size:17 final size:17
Alignment explanation
Indices: 69168--69207 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
69158 TTCCGCTTCA
69168 ACTATGTACCAGGTACC
1 ACTATGTACCAGGTACC
69185 ACTATGTACCAGGTACC
1 ACTATGTACCAGGTACC
69202 ACTATG
1 ACTATG
69208 AATGATCACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (17 bp):
ACTATGTACCAGGTACC
Found at i:74224 original size:21 final size:19
Alignment explanation
Indices: 74188--74231 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 19
74178 CAAAAACCTT
74188 AAAAGATACATTTAAAATTA
1 AAAAGATACATTTAAAA-TA
74208 AAAAGATA-ATTTCTAAAATA
1 AAAAGATACA-TT-TAAAATA
74228 AAAA
1 AAAA
74232 TAAAATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 1 0.05
20 16 0.73
21 5 0.23
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.27
Consensus pattern (19 bp):
AAAAGATACATTTAAAATA
Found at i:85584 original size:2 final size:2
Alignment explanation
Indices: 85577--85618 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
85567 ATAAACTTTA
85577 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
85619 CCTTAAAACT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:88608 original size:26 final size:25
Alignment explanation
Indices: 88579--88627 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
88569 ATTAAAGTTT
* *
88579 TTTCTTTTTTACTTTTTAAGTTTTTA
1 TTTCTTCTTTA-TTTTCAAGTTTTTA
88605 TTTCTTCTTTATTTTCAAGTTTT
1 TTTCTTCTTTATTTTCAAGTTTT
88628 GTTTTTATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.14, C:0.10, G:0.04, T:0.71
Consensus pattern (25 bp):
TTTCTTCTTTATTTTCAAGTTTTTA
Done.