Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001476.1 Hibiscus syriacus cultivar Beakdansim tig00002866_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: 310879
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
File 2 of 2
Found at i:247268 original size:29 final size:30
Alignment explanation
Indices: 247226--247298 Score: 121
Period size: 30 Copynumber: 2.5 Consensus size: 30
247216 TTCCAGAAAT
*
247226 GTAATTCATTTTCCAG-AATTCAAATTCTA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
*
247255 GTAATTCATTTTCCAGTCATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
247285 GTAATTCATTTTCC
1 GTAATTCATTTTCC
247299 GGAAAATCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 16 0.39
30 25 0.61
ACGTcount: A:0.30, C:0.21, G:0.07, T:0.42
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:247298 original size:15 final size:15
Alignment explanation
Indices: 247226--247298 Score: 85
Period size: 15 Copynumber: 4.9 Consensus size: 15
247216 TTCCAGAAAT
247226 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
** *
247241 G-AATTCAAATTCTA
1 GTAATTCATTTTCCA
247255 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
* **
247270 GTCATTCAAATTCCA
1 GTAATTCATTTTCCA
247285 GTAATTCATTTTCC
1 GTAATTCATTTTCC
247299 GGAAAATCAA
Statistics
Matches: 45, Mismatches: 12, Indels: 2
0.76 0.20 0.03
Matches are distributed among these distances:
14 11 0.24
15 34 0.76
ACGTcount: A:0.30, C:0.21, G:0.07, T:0.42
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:256022 original size:28 final size:29
Alignment explanation
Indices: 255964--256023 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
255954 TTTCTTGTGG
255964 TTTTTTCCTTTTTTTTCGAACAGCTTCTT
1 TTTTTTCCTTTTTTTTCGAACAGCTTCTT
* * *
255993 TTTTTTCTTTTTTTTTTGAACTGCTT-TT
1 TTTTTTCCTTTTTTTTCGAACAGCTTCTT
256021 TTT
1 TTT
256024 CAACATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 5 0.18
29 23 0.82
ACGTcount: A:0.08, C:0.15, G:0.07, T:0.70
Consensus pattern (29 bp):
TTTTTTCCTTTTTTTTCGAACAGCTTCTT
Found at i:262954 original size:20 final size:20
Alignment explanation
Indices: 262929--262974 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
262919 GAATCCAGGC
262929 AAAGAGCATTGGAATACAGT
1 AAAGAGCATTGGAATACAGT
262949 AAAGAGCATTGGAATACAGT
1 AAAGAGCATTGGAATACAGT
262969 AAAGAG
1 AAAGAG
262975 GATCTTGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.48, C:0.09, G:0.26, T:0.17
Consensus pattern (20 bp):
AAAGAGCATTGGAATACAGT
Found at i:265315 original size:43 final size:43
Alignment explanation
Indices: 265250--265640 Score: 325
Period size: 43 Copynumber: 9.2 Consensus size: 43
265240 TGAGAACCAA
* * * *
265250 AAACGCCGCCATAGGTCAAGATCTATAGCGGCGTATTTGGAAC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAAC
* * **
265293 AAACGCCGCAAAAAGTCGAGATCTATAGCGG-TTTTTTTTAAC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAAC
* *
265335 AAACGCCGCAAAAGGTTGAGATCTATAGCGGCATTTTTGGAAC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAAC
* * * *
265378 AAACGCCTC-AAAGAGTCGATATCTATAGTGGTGTTTTTGGAA-
1 AAACGCCGCAAAAG-GTCGAGATCTATAGCGGCGTTTTTGGAAC
* * * * * * *
265420 AAACGTCGCAAAAGGT-TACATCTATAACGACCTTTTTAGAAC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAAC
* * * * *
265462 AAACGCCGTAAAAGGTTGAGATATATAGCGGCGTTTGTT-CAAA
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTT-TTGGAAC
* * *
265505 AAACGCCGCAAAAGGT-GATATCTATTGCGGCGTTTATT-CAA-
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTT-TTGGAAC
* * * * * * **
265546 AAAAGCTGTAAAAAGT-GAGAGCTATAGCGGTGTTTTTTGTTAC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCG-TTTTTGGAAC
265589 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGA-AC
*
265632 AAACACCGC
1 AAACGCCGC
265641 TAATTACCTA
Statistics
Matches: 274, Mismatches: 63, Indels: 22
0.76 0.18 0.06
Matches are distributed among these distances:
41 43 0.16
42 94 0.34
43 135 0.49
44 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAAC
Found at i:265395 original size:85 final size:86
Alignment explanation
Indices: 265250--265635 Score: 360
Period size: 85 Copynumber: 4.5 Consensus size: 86
265240 TGAGAACCAA
* * ** * *
265250 AAACGCCGCCATAGGTCAAGATCTATAGCGGCGTATTTGGAACAAACGCCGCAAAAAGTCGAGAT
1 AAACGCCGCAAAAGGTTGAGATCTATAGCGGCGTTTTTGGAACAAACGCCTCAAAAAGTCGAGAT
265315 CTATAGCGGT-TTTTTTTAAC
66 CTATAGCGGTGTTTTTTTAAC
* * *
265335 AAACGCCGCAAAAGGTTGAGATCTATAGCGGCATTTTTGGAACAAACGCCTCAAAGAGTCGATAT
1 AAACGCCGCAAAAGGTTGAGATCTATAGCGGCGTTTTTGGAACAAACGCCTCAAAAAGTCGAGAT
* **
265400 CTATAGTGGTGTTTTTGGAA-
66 CTATAGCGGTGTTTTTTTAAC
* * * * * * * *
265420 AAACGTCGCAAAAGGTT-ACATCTATAACGACCTTTTTAGAACAAACGCCGT-AAAAGGTTGAGA
1 AAACGCCGCAAAAGGTTGAGATCTATAGCGGCGTTTTTGGAACAAACGCC-TCAAAAAGTCGAGA
* * * * *
265483 TATATAGCGGCGTTTGTTCAAA
65 TCTATAGCGGTGTTTTTTTAAC
* * * * *
265505 AAACGCCGCAAAAGG-TGATATCTATTGCGGCGTTTATT-CAA-AAAAG-CTGTAAAAAGT-GAG
1 AAACGCCGCAAAAGGTTGAGATCTATAGCGGCGTTT-TTGGAACAAACGCCT-CAAAAAGTCGAG
* *
265565 AGCTATAGCGGTGTTTTTTGTTAC
64 ATCTATAGCGGTGTTTTTT-TAAC
*
265589 AAACGCCGCAAAAGG-TCAGATCTATAGCGGCGTTTTTGGATACAAAC
1 AAACGCCGCAAAAGGTTGAGATCTATAGCGGCGTTTTTGGA-ACAAAC
265636 ACCGCTAATT
Statistics
Matches: 241, Mismatches: 49, Indels: 21
0.77 0.16 0.07
Matches are distributed among these distances:
82 1 0.00
83 21 0.09
84 95 0.39
85 112 0.46
86 12 0.05
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (86 bp):
AAACGCCGCAAAAGGTTGAGATCTATAGCGGCGTTTTTGGAACAAACGCCTCAAAAAGTCGAGAT
CTATAGCGGTGTTTTTTTAAC
Found at i:266948 original size:3 final size:3
Alignment explanation
Indices: 266940--266971 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
266930 CTTGGCATGC
266940 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
266972 AATAATATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:274978 original size:17 final size:17
Alignment explanation
Indices: 274929--274968 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
274919 CTGGGTAATT
* *
274929 GATTGCTGAGGCAACTC
1 GATTGCTAAGACAACTC
274946 GATTGCTAAGACAACTC
1 GATTGCTAAGACAACTC
274963 GATTGC
1 GATTGC
274969 ATTGACAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.25
Consensus pattern (17 bp):
GATTGCTAAGACAACTC
Found at i:275607 original size:21 final size:21
Alignment explanation
Indices: 275581--275644 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 21
275571 AGAGTTTTAC
275581 TAGGATTCAAACTCCTAAAAA
1 TAGGATTCAAACTCCTAAAAA
* * *
275602 TAGGA-T-AAAGTTCT---AC
1 TAGGATTCAAACTCCTAAAAA
*
275618 TATGATTCAAACTCCTAAAAA
1 TAGGATTCAAACTCCTAAAAA
275639 TAGGAT
1 TAGGAT
275645 CCAGAAGCAT
Statistics
Matches: 30, Mismatches: 8, Indels: 10
0.62 0.17 0.21
Matches are distributed among these distances:
16 5 0.17
17 1 0.03
18 6 0.20
19 6 0.20
20 1 0.03
21 11 0.37
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (21 bp):
TAGGATTCAAACTCCTAAAAA
Found at i:275619 original size:37 final size:37
Alignment explanation
Indices: 275573--275644 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
275563 ATATCGTTAG
*
275573 AGTTTTACTAGGATTCAAACTCCTAAAAATAGGATAA
1 AGTTCTACTAGGATTCAAACTCCTAAAAATAGGATAA
*
275610 AGTTCTACTATGATTCAAACTCCTAAAAATAGGAT
1 AGTTCTACTAGGATTCAAACTCCTAAAAATAGGAT
275645 CCAGAAGCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (37 bp):
AGTTCTACTAGGATTCAAACTCCTAAAAATAGGATAA
Found at i:276108 original size:16 final size:16
Alignment explanation
Indices: 276087--276146 Score: 72
Period size: 16 Copynumber: 3.9 Consensus size: 16
276077 AATTCCAACA
276087 ATATATTTATTATTAT
1 ATATATTTATTATTAT
276103 ATATATTTA--ATTAT
1 ATATATTTATTATTAT
*
276117 ATATTTTTATTATCTAT
1 ATATATTTATTAT-TAT
*
276134 -TATTTTTATTATT
1 ATATATTTATTATT
276147 TTTTTACTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
14 13 0.32
15 1 0.03
16 23 0.57
17 3 0.08
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (16 bp):
ATATATTTATTATTAT
Found at i:276126 original size:10 final size:9
Alignment explanation
Indices: 276113--276172 Score: 54
Period size: 9 Copynumber: 6.6 Consensus size: 9
276103 ATATATTTAA
276113 TTATATATTT
1 TTAT-TATTT
276123 TTATTA--T
1 TTATTATTT
*
276130 CTATTATTT
1 TTATTATTT
276139 TTATTATTT
1 TTATTATTT
276148 TT-TTACTTTT
1 TTATTA--TTT
276158 TTATTATTAT
1 TTATTATT-T
276168 TTATT
1 TTATT
276173 CTTTCGTCAT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
7 6 0.14
8 3 0.07
9 15 0.36
10 15 0.36
11 3 0.07
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (9 bp):
TTATTATTT
Found at i:276231 original size:35 final size:36
Alignment explanation
Indices: 276192--276260 Score: 106
Period size: 35 Copynumber: 1.9 Consensus size: 36
276182 TTTTAATCTA
*
276192 TATATATATA-TATATTTTATTACTAT-TATATATTT
1 TATATAT-TACTATATTTTATCACTATGTATATATTT
276227 TATATATTACTATATTTTATCACTATGTATATAT
1 TATATATTACTATATTTTATCACTATGTATATAT
276261 GCTTTTGATA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
34 2 0.06
35 22 0.71
36 7 0.23
ACGTcount: A:0.36, C:0.06, G:0.01, T:0.57
Consensus pattern (36 bp):
TATATATTACTATATTTTATCACTATGTATATATTT
Found at i:276257 original size:17 final size:17
Alignment explanation
Indices: 276200--276260 Score: 79
Period size: 17 Copynumber: 3.4 Consensus size: 17
276190 TATATATATA
276200 TATATATTTTATTACTAT
1 TATATATTTTA-TACTAT
276218 TATATATTTTATA-TAT
1 TATATATTTTATACTAT
276234 TACTATATTTTATCACTAT
1 TA-TATATTTTAT-ACTAT
276253 GTATATAT
1 -TATATAT
276261 GCTTTTGATA
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
16 5 0.13
17 12 0.31
18 12 0.31
19 8 0.21
20 2 0.05
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (17 bp):
TATATATTTTATACTAT
Found at i:280843 original size:2 final size:2
Alignment explanation
Indices: 280836--280882 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
280826 TTTTAGCTGC
280836 AT AT AT AT AT AT AT A- AT AT AT AT AT AT A- 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
280876 AT AT AT A
1 AT AT AT A
280883 ACGAAGTATG
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:280856 original size:13 final size:13
Alignment explanation
Indices: 280838--280882 Score: 83
Period size: 13 Copynumber: 3.5 Consensus size: 13
280828 TTAGCTGCAT
280838 ATATATATATATA
1 ATATATATATATA
280851 ATATATATATATA
1 ATATATATATATA
280864 ATATATATATAT-
1 ATATATATATATA
280876 ATATATA
1 ATATATA
280883 ACGAAGTATG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
12 7 0.22
13 25 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
ATATATATATATA
Found at i:291883 original size:23 final size:24
Alignment explanation
Indices: 291831--291884 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
291821 TTCACACATT
*
291831 CAAGGTTAACTAGTCATTGAAATG
1 CAAGGTTAACTAGTCATTAAAATG
291855 CCAAGGTTAACTAGTCA-TAAATATG
1 -CAAGGTTAACTAGTCATTAAA-ATG
291880 -AAGGT
1 CAAGGT
291885 GAAATGAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 5 0.19
24 3 0.11
25 19 0.70
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (24 bp):
CAAGGTTAACTAGTCATTAAAATG
Found at i:296872 original size:148 final size:148
Alignment explanation
Indices: 296604--296897 Score: 507
Period size: 148 Copynumber: 2.0 Consensus size: 148
296594 ATTACCTATG
* *
296604 AAGTTTTGGAAGACAGTTGAAATGTTAAACCGGAGTTACCCAGTTCCTCTTGCATATGCTTCTCC
1 AAGTTTTGGAAGACAGTTGAAATGTTAAACCAGAGTTACCCAGTTCCTCTTGCATAAGCTTCTCC
*
296669 AAGCGTTCAACCATGGCGGGTGTGAGATAGTTGCTCCAATCTCCCACTTCTCCTTTCCTGAAATA
66 AAGCGTTCAACCATGGCGGGTGTGAGATAGTTGCTCCAATCTCCCACTTCTCCTTTCCTGAAAAA
*
296734 TTCTTTGTATGGAATCTC
131 CTCTTTGTATGGAATCTC
* * * *
296752 AAGTTTTGGAGGACGGTTTAAATTTTAAACCAGAGTTACCCAGTTCCTCTTGCATAAGCTTCTCC
1 AAGTTTTGGAAGACAGTTGAAATGTTAAACCAGAGTTACCCAGTTCCTCTTGCATAAGCTTCTCC
296817 AAGCGTTCAACCATGGCGGGTGTGAGATAGTTGCTCCAATCTCCCACTTCTCCTTTCCTGAAAAA
66 AAGCGTTCAACCATGGCGGGTGTGAGATAGTTGCTCCAATCTCCCACTTCTCCTTTCCTGAAAAA
*
296882 CTCTTTGTGTGGAATC
131 CTCTTTGTATGGAATC
296898 CCAGTAACGA
Statistics
Matches: 137, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
148 137 1.00
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.33
Consensus pattern (148 bp):
AAGTTTTGGAAGACAGTTGAAATGTTAAACCAGAGTTACCCAGTTCCTCTTGCATAAGCTTCTCC
AAGCGTTCAACCATGGCGGGTGTGAGATAGTTGCTCCAATCTCCCACTTCTCCTTTCCTGAAAAA
CTCTTTGTATGGAATCTC
Found at i:297469 original size:6 final size:6
Alignment explanation
Indices: 297458--297483 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
297448 TGAGCAATGG
297458 ATGTTC ATGTTC ATGTTC ATGTTC AT
1 ATGTTC ATGTTC ATGTTC ATGTTC AT
297484 CCTTTGCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.15, G:0.15, T:0.50
Consensus pattern (6 bp):
ATGTTC
Found at i:301389 original size:14 final size:14
Alignment explanation
Indices: 301370--301401 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
301360 GTGAAAATAT
301370 ACATATTTTTTTAA
1 ACATATTTTTTTAA
301384 ACATATTTTTTTAA
1 ACATATTTTTTTAA
301398 ACAT
1 ACAT
301402 TTAGAAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (14 bp):
ACATATTTTTTTAA
Found at i:301686 original size:154 final size:153
Alignment explanation
Indices: 301406--301708 Score: 455
Period size: 154 Copynumber: 2.0 Consensus size: 153
301396 AAACATTTAG
* * * *
301406 AAAACATAGTAATTCCCTCAACCGCACACGTCCATAATGTGTAGATTCCCCAGAACCATACAACC
1 AAAACATAGTAAATCCCCCAACCGAACACATCCATAATGTGTAGATTCCCCAGAACCATACAACC
* * *
301471 CCGGCACAACAATAAGGCCCTAAGCACACAGCCGAGGAGCCTTCATATATTCTTCCCCCAACAAT
66 CCGACACAACAATAAGGCCATAAGCACAAAGCCGAGGAGCCTTCATATATTCTTCCCCCAACAAT
301536 AACCCCCAAATAAAACATTTATCA
131 -ACCCCCAAATAAAACATTTATCA
* *
301560 AAAACCATAGTAAATCCCCCAACTGAACACAT-CATAATGTGTAGGTTCCCCAGAACCATACAAC
1 AAAA-CATAGTAAATCCCCCAACCGAACACATCCATAATGTGTAGATTCCCCAGAACCATACAAC
* * * * *
301624 CCCGACACAACAGTTAGGCCATGAGCACAAAGCCGAGGAGCCTTCATATTTTCTTCCTCCAACAA
65 CCCGACACAACAATAAGGCCATAAGCACAAAGCCGAGGAGCCTTCATATATTCTTCCCCCAACAA
301689 TACCCCCAAATAAAACATTT
130 TACCCCCAAATAAAACATTT
301709 TTTGTCAATA
Statistics
Matches: 134, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
153 19 0.14
154 93 0.69
155 22 0.16
ACGTcount: A:0.37, C:0.32, G:0.12, T:0.19
Consensus pattern (153 bp):
AAAACATAGTAAATCCCCCAACCGAACACATCCATAATGTGTAGATTCCCCAGAACCATACAACC
CCGACACAACAATAAGGCCATAAGCACAAAGCCGAGGAGCCTTCATATATTCTTCCCCCAACAAT
ACCCCCAAATAAAACATTTATCA
Found at i:301793 original size:24 final size:24
Alignment explanation
Indices: 301766--301824 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
301756 GATATCATAT
301766 ATCAGAACA-AAATCAAGATCAGAA
1 ATCAGAACATAAATCAA-ATCAGAA
*
301790 ATCAGAACATAATTCAAATCAGAA
1 ATCAGAACATAAATCAAATCAGAA
301814 ATCAGAACATA
1 ATCAGAACATA
301825 TTCCAAATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
24 27 0.82
25 6 0.18
ACGTcount: A:0.56, C:0.17, G:0.10, T:0.17
Consensus pattern (24 bp):
ATCAGAACATAAATCAAATCAGAA
Found at i:301831 original size:24 final size:23
Alignment explanation
Indices: 301766--301832 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 23
301756 GATATCATAT
* *
301766 ATCAGAACAAAATCAAGATCAGAA
1 ATCAGAACATATTCAA-ATCAGAA
301790 ATCAGAACATAATTCAAATCAGAA
1 ATCAGAACAT-ATTCAAATCAGAA
301814 ATCAGAACATATTCCAAAT
1 ATCAGAACATATT-CAAAT
301833 AAAAAACAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
23 3 0.08
24 31 0.79
25 5 0.13
ACGTcount: A:0.54, C:0.18, G:0.09, T:0.19
Consensus pattern (23 bp):
ATCAGAACATATTCAAATCAGAA
Done.