Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007278.1 Hibiscus syriacus cultivar Beakdansim tig00019301_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: 131984
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:1059 original size:16 final size:18
Alignment explanation
Indices: 1027--1059 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
1017 CAATCATATA
1027 ACTAACAAATAAATTATG
1 ACTAACAAATAAATTATG
1045 ACTAA-AAAT-AATTAT
1 ACTAACAAATAAATTAT
1060 AAAAAACCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 4 0.27
18 5 0.33
ACGTcount: A:0.58, C:0.09, G:0.03, T:0.30
Consensus pattern (18 bp):
ACTAACAAATAAATTATG
Found at i:3486 original size:20 final size:20
Alignment explanation
Indices: 3461--3510 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
3451 CAAATTTATG
3461 CTGACATGGATTGCATTTTA
1 CTGACATGGATTGCATTTTA
3481 CTGACATGGATTGCATTTTA
1 CTGACATGGATTGCATTTTA
3501 CTGACATGGA
1 CTGACATGGA
3511 AGTCACCTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (20 bp):
CTGACATGGATTGCATTTTA
Found at i:4001 original size:29 final size:29
Alignment explanation
Indices: 3964--4060 Score: 167
Period size: 29 Copynumber: 3.3 Consensus size: 29
3954 TATTTAAACT
* *
3964 TTTAATTTTTTTCCAAACCAAACTTAGTA
1 TTTAGTTTTTTTCAAAACCAAACTTAGTA
3993 TTTAGTTTTTTTCAAAACCAAACTTAGTA
1 TTTAGTTTTTTTCAAAACCAAACTTAGTA
*
4022 TTTAGTTTTTTTCAAAACCAAACTTAATA
1 TTTAGTTTTTTTCAAAACCAAACTTAGTA
4051 TTTAGTTTTT
1 TTTAGTTTTT
4061 GTTTCATTTT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 65 1.00
ACGTcount: A:0.33, C:0.13, G:0.05, T:0.48
Consensus pattern (29 bp):
TTTAGTTTTTTTCAAAACCAAACTTAGTA
Found at i:7624 original size:22 final size:23
Alignment explanation
Indices: 7581--7629 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
7571 TTGGAGTTGG
*
7581 ATTTTTTTTAAATTAACCTAAT-
1 ATTTATTTTAAATTAACCTAATC
*
7603 ATTTATTTTAAA-TAATCTTAATC
1 ATTTATTTTAAATTAA-CCTAATC
7626 ATTT
1 ATTT
7630 GATAATGAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 3 0.13
22 16 0.70
23 4 0.17
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (23 bp):
ATTTATTTTAAATTAACCTAATC
Found at i:12151 original size:7 final size:7
Alignment explanation
Indices: 12135--12167 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
12125 TAACTAAAAT
*
12135 TATTAAA
1 TATTATA
12142 TATTATA
1 TATTATA
12149 TATTATA
1 TATTATA
12156 TA-TATA
1 TATTATA
12162 TATTAT
1 TATTAT
12168 TTATATATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
TATTATA
Found at i:12161 original size:11 final size:11
Alignment explanation
Indices: 12141--12177 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
12131 AAATTATTAA
12141 ATATTATATAT
1 ATATTATATAT
12152 -TA-TATATAT
1 ATATTATATAT
*
12161 ATATTATTTAT
1 ATATTATATAT
12172 ATATTA
1 ATATTA
12178 GAGTGTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
9 7 0.30
10 4 0.17
11 12 0.52
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
ATATTATATAT
Found at i:12163 original size:13 final size:13
Alignment explanation
Indices: 12135--12175 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
12125 TAACTAAAAT
*
12135 TATTAAATATTATA
1 TATTATATA-TATA
12149 TATTATATATATA
1 TATTATATATATA
*
12162 TATTATTTATATA
1 TATTATATATATA
12175 T
1 T
12176 TAGAGTGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 17 0.68
14 8 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TATTATATATATA
Found at i:22756 original size:15 final size:15
Alignment explanation
Indices: 22736--22783 Score: 87
Period size: 15 Copynumber: 3.2 Consensus size: 15
22726 ATATTTAGCT
*
22736 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGCG
22751 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
22766 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
22781 GGG
1 GGG
22784 TGGGTAATGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.06, C:0.17, G:0.69, T:0.08
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:28233 original size:16 final size:16
Alignment explanation
Indices: 28212--28243 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28202 ACTATTCACA
*
28212 TGAATAGTGAATTTCG
1 TGAATAGTGAAATTCG
28228 TGAATAGTGAAATTCG
1 TGAATAGTGAAATTCG
28244 GTCGGCGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.34
Consensus pattern (16 bp):
TGAATAGTGAAATTCG
Found at i:52542 original size:127 final size:127
Alignment explanation
Indices: 52313--52556 Score: 348
Period size: 127 Copynumber: 1.9 Consensus size: 127
52303 CATAAATCAA
* *
52313 ACTACCTCAGCAGTTAAATGAATTAATATTATTTTTAGAGGTCATAGGTTCGAAGCTTCGACCAC
1 ACTACCTCAGCAGTTAAATGAATTAATATTATTATTAGAAGTCATAGGTTCGAAGCTTCGACCAC
* * * *
52378 TAAAGACTGTAGGATATTTGAGCGGTCATTGTCAAATGGTTGAGAGTCTTTAAAACATATAT
66 CAAAGACTGCAGAATATTTGAACGGTCATTGTCAAATGGTTGAGAGTCTTTAAAACATATAT
* * * *
52440 ACTACCTCAGCGGTTAAATGAATGT-ATATTATTATTAGAAGTCATAGGTTCGAGGCTTTGAGCA
1 ACTACCTCAGCAGTTAAATGAAT-TAATATTATTATTAGAAGTCATAGGTTCGAAGCTTCGACCA
* *
52504 CCAAAGACTGCA-AATTATTTGAACGGTCATTGTTAAATGGTTGATAGTCTTTA
65 CCAAAGACTGCAGAA-TATTTGAACGGTCATTGTCAAATGGTTGAGAGTCTTTA
52557 TCACTCGTAA
Statistics
Matches: 103, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
126 1 0.01
127 101 0.98
128 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (127 bp):
ACTACCTCAGCAGTTAAATGAATTAATATTATTATTAGAAGTCATAGGTTCGAAGCTTCGACCAC
CAAAGACTGCAGAATATTTGAACGGTCATTGTCAAATGGTTGAGAGTCTTTAAAACATATAT
Found at i:54326 original size:60 final size:60
Alignment explanation
Indices: 54262--54407 Score: 154
Period size: 60 Copynumber: 2.4 Consensus size: 60
54252 AGTATGACCC
* * **
54262 TCATTTTAAATCAGT-ATCTAAACTTTTAAAT-TTCTCAATTTCATCCTTAAACTATGATTA
1 TCATTCTAAATCAGTCCTC-AAACTTTTAAATATT-TCAATTTCATCCCCAAACTATGATTA
* * * *
54322 TCATTCTAAATTAGTCCTCAAACTTTTGAATATTTCAGTTTCATCCCCAAACTATGA-CA
1 TCATTCTAAATCAGTCCTCAAACTTTTAAATATTTCAATTTCATCCCCAAACTATGATTA
* *
54381 TTCATTCTAAATTAGTCCCCAAACTTT
1 -TCATTCTAAATCAGTCCTCAAACTTT
54408 CTGAACATTC
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
59 1 0.01
60 69 0.93
61 4 0.05
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.41
Consensus pattern (60 bp):
TCATTCTAAATCAGTCCTCAAACTTTTAAATATTTCAATTTCATCCCCAAACTATGATTA
Found at i:54431 original size:60 final size:59
Alignment explanation
Indices: 54322--54440 Score: 168
Period size: 60 Copynumber: 2.0 Consensus size: 59
54312 ACTATGATTA
* * *
54322 TCATTCTAAATTAGTCCTCAAACTTTTGAATATTTCAGTTTCATCCCCAAACTATGACAT
1 TCATTCTAAATTAGTCCCCAAACTTTTGAACATTCCAGTTTCATCCCCAAACTAT-ACAT
* *
54382 TCATTCTAAATTAGTCCCCAAACTTTCTGAACATTCCATTTTTAT-CCCAAACTATACAT
1 TCATTCTAAATTAGTCCCCAAACTTT-TGAACATTCCAGTTTCATCCCCAAACTATACAT
54441 ATATACTAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
59 4 0.08
60 35 0.66
61 14 0.26
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (59 bp):
TCATTCTAAATTAGTCCCCAAACTTTTGAACATTCCAGTTTCATCCCCAAACTATACAT
Found at i:56934 original size:21 final size:21
Alignment explanation
Indices: 56909--56949 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
56899 GAAATGTTAA
*
56909 AAATATTAATGTTTTAGGTAT
1 AAATAATAATGTTTTAGGTAT
56930 AAATAATAATGTTTTAGGTA
1 AAATAATAATGTTTTAGGTA
56950 ATTTTTTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (21 bp):
AAATAATAATGTTTTAGGTAT
Found at i:59345 original size:16 final size:18
Alignment explanation
Indices: 59301--59346 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 18
59291 ATATTAAATT
*
59301 ATTTTAAATTATAACTAA
1 ATTTTAAAATATAACTAA
*
59319 ATTAATAAAATAT-A-TAA
1 ATT-TTAAAATATAACTAA
59336 ATTTTAAAATA
1 ATTTTAAAATA
59347 AAATTAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 7 0.29
17 6 0.25
18 4 0.17
19 7 0.29
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTTTAAAATATAACTAA
Found at i:68275 original size:18 final size:19
Alignment explanation
Indices: 68252--68294 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
68242 CAGTAATGCT
68252 ATTCCT-TGGTAATCTTAC
1 ATTCCTATGGTAATCTTAC
*
68270 ATTCCTACTGGTAATCTTAT
1 ATTCCTA-TGGTAATCTTAC
68290 ATTCC
1 ATTCC
68295 GTGAACCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.27
20 16 0.73
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.44
Consensus pattern (19 bp):
ATTCCTATGGTAATCTTAC
Found at i:69163 original size:10 final size:10
Alignment explanation
Indices: 69148--69175 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
69138 ATAAGCTCAT
69148 TATATATATG
1 TATATATATG
69158 TATATATATG
1 TATATATATG
69168 TATATATA
1 TATATATA
69176 ACCTCATTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (10 bp):
TATATATATG
Found at i:71788 original size:45 final size:42
Alignment explanation
Indices: 71715--71803 Score: 99
Period size: 41 Copynumber: 2.0 Consensus size: 42
71705 TTCTGATTTT
* *
71715 TTTTTAAATTTATATTTATCTAACTCAAATATTATTTATTAATATC
1 TTTTAAAATTTATAATTATCTAACTC-AA-A--ATTTATTAATATC
**
71761 TTTTAAAATTTA-AATTATCTAGTTCAAAATTTATTAATATC
1 TTTTAAAATTTATAATTATCTAACTCAAAATTTATTAATATC
71802 TT
1 TT
71804 ATAATTAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
41 15 0.38
43 1 0.03
44 2 0.05
45 10 0.26
46 11 0.28
ACGTcount: A:0.38, C:0.08, G:0.01, T:0.53
Consensus pattern (42 bp):
TTTTAAAATTTATAATTATCTAACTCAAAATTTATTAATATC
Found at i:79008 original size:2 final size:2
Alignment explanation
Indices: 79001--79040 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
78991 CATCATTTGG
79001 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
79041 GTTGATGAGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:85041 original size:21 final size:21
Alignment explanation
Indices: 85002--85041 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
84992 AGAAAAGGCA
*
85002 CTCGAGAAAAATGACGATGCC
1 CTCGAGAAAAAGGACGATGCC
* *
85023 CTCGAGAAAACGGAGGATG
1 CTCGAGAAAAAGGACGATG
85042 TAAAGTCCTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.20, G:0.30, T:0.12
Consensus pattern (21 bp):
CTCGAGAAAAAGGACGATGCC
Found at i:90390 original size:45 final size:45
Alignment explanation
Indices: 90341--90428 Score: 158
Period size: 45 Copynumber: 2.0 Consensus size: 45
90331 TTACGAACAT
90341 TTCAGTATTGAGTAATTATCTTTTCCCAAAAATTATTTGTCTTAC
1 TTCAGTATTGAGTAATTATCTTTTCCCAAAAATTATTTGTCTTAC
* *
90386 TTCAGTATTGAGTTATTATCTTTTTCCAAAAATTATTTGTCTT
1 TTCAGTATTGAGTAATTATCTTTTCCCAAAAATTATTTGTCTT
90429 TGGTATGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.27, C:0.14, G:0.09, T:0.50
Consensus pattern (45 bp):
TTCAGTATTGAGTAATTATCTTTTCCCAAAAATTATTTGTCTTAC
Found at i:94763 original size:13 final size:13
Alignment explanation
Indices: 94745--94771 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
94735 TGGCCTGCGC
94745 GTGAAAATGGCAT
1 GTGAAAATGGCAT
94758 GTGAAAATGGCAT
1 GTGAAAATGGCAT
94771 G
1 G
94772 CCTTAACGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.33, T:0.22
Consensus pattern (13 bp):
GTGAAAATGGCAT
Found at i:96652 original size:3 final size:3
Alignment explanation
Indices: 96644--96671 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
96634 AAAAATGTCT
96644 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
96672 CTACAACACC
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:100631 original size:26 final size:27
Alignment explanation
Indices: 100602--100665 Score: 112
Period size: 27 Copynumber: 2.4 Consensus size: 27
100592 ACCAAAAAAT
*
100602 CGTTAACCTAA-TTTTTTCCTCTTAAC
1 CGTTAACCGAATTTTTTTCCTCTTAAC
100628 CGTTAACCGAATTTTTTTCCTCTTAAC
1 CGTTAACCGAATTTTTTTCCTCTTAAC
100655 CGTTAACCGAA
1 CGTTAACCGAA
100666 CTGAAATTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
26 10 0.28
27 26 0.72
ACGTcount: A:0.25, C:0.27, G:0.08, T:0.41
Consensus pattern (27 bp):
CGTTAACCGAATTTTTTTCCTCTTAAC
Found at i:110190 original size:29 final size:29
Alignment explanation
Indices: 110152--110234 Score: 105
Period size: 29 Copynumber: 2.9 Consensus size: 29
110142 GTGTTGACCG
* *
110152 TAGGTCGCCATGTC-TTCCGGGCGACCTTA
1 TAGGTCGCCATG-CACTCCAGGCGACCTTA
*
110181 TAGGTTGCCATGCACTCCAGGCGACCTTA
1 TAGGTCGCCATGCACTCCAGGCGACCTTA
* *
110210 TAGGTCGTCATGCACTCCGGGCGAC
1 TAGGTCGCCATGCACTCCAGGCGAC
110235 TTACCCTTGC
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
28 1 0.02
29 46 0.98
ACGTcount: A:0.17, C:0.31, G:0.28, T:0.24
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCAGGCGACCTTA
Found at i:110387 original size:23 final size:23
Alignment explanation
Indices: 110361--110418 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
110351 CCCTTGCTCG
*
110361 CTCGCTCGGATGCCCTCGCATAA
1 CTCGCTCGGATGCCCTCACATAA
* * * *
110384 CTCGCTCGGCTACCCTTACATAG
1 CTCGCTCGGATGCCCTCACATAA
110407 CTCGCTCGGATG
1 CTCGCTCGGATG
110419 GCATCAGTCG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.16, C:0.38, G:0.22, T:0.24
Consensus pattern (23 bp):
CTCGCTCGGATGCCCTCACATAA
Found at i:112569 original size:40 final size:40
Alignment explanation
Indices: 112512--112602 Score: 157
Period size: 40 Copynumber: 2.3 Consensus size: 40
112502 TTGATTCTAC
*
112512 AAGAACAATAT-AGTATTGTTCATGTGATATCGATACTGT
1 AAGAACAATATCAGTATTGTTCATGCGATATCGATACTGT
*
112551 AAGAACATTATCAGTATTGTTCATGCGATATCGATACTGT
1 AAGAACAATATCAGTATTGTTCATGCGATATCGATACTGT
112591 AAGAACAATATC
1 AAGAACAATATC
112603 GATACTGCTT
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
39 10 0.21
40 38 0.79
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.33
Consensus pattern (40 bp):
AAGAACAATATCAGTATTGTTCATGCGATATCGATACTGT
Found at i:114048 original size:18 final size:18
Alignment explanation
Indices: 114022--114079 Score: 55
Period size: 22 Copynumber: 3.1 Consensus size: 18
114012 CCTAAATTTG
*
114022 GTATAGATACTCAGGCCA
1 GTATCGATACTCAGGCCA
*
114040 GTATCGATACCTCAGTGCTAGA
1 GTATCGATA-CTCAG-GC--CA
114062 GTATCGATACTCA-GCCA
1 GTATCGATACTCAGGCCA
114079 G
1 G
114080 AAGTATCAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
17 2 0.06
18 8 0.24
19 7 0.21
20 2 0.06
21 4 0.12
22 10 0.30
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.24
Consensus pattern (18 bp):
GTATCGATACTCAGGCCA
Found at i:114086 original size:20 final size:20
Alignment explanation
Indices: 114022--114092 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
114012 CCTAAATTTG
*
114022 GTATAGATACTCAGGCC--A
1 GTATCGATACTCAGGCCAGA
*
114040 GTATCGATACCTCAGTGCTAGA
1 GTATCGATA-CTCAG-GCCAGA
114062 GTATCGATACTCA-GCCAGAA
1 GTATCGATACTCAGGCCAG-A
*
114082 GTATCAATACT
1 GTATCGATACT
114093 ACCTTACCCA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
18 8 0.18
19 9 0.20
20 13 0.30
21 4 0.09
22 10 0.23
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (20 bp):
GTATCGATACTCAGGCCAGA
Found at i:129557 original size:25 final size:25
Alignment explanation
Indices: 129506--129558 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
129496 TAAGTACATC
* **
129506 AATTTCTCGTCAAATGTTAACGGTA
1 AATTTCTCGTCAAATATTAACAATA
*
129531 AATTTCTTGTCAAATATTAACAATA
1 AATTTCTCGTCAAATATTAACAATA
129556 AAT
1 AAT
129559 GACTTGATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (25 bp):
AATTTCTCGTCAAATATTAACAATA
Done.