Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008687.1 Hibiscus syriacus cultivar Beakdansim tig00111711_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: 43790
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:2873 original size:14 final size:14
Alignment explanation
Indices: 2854--2895 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
2844 TTTTAGGATT
*
2854 AGGTTTAAGATTTA
1 AGGTTTATGATTTA
*
2868 AGGTTTATGATATA
1 AGGTTTATGATTTA
*
2882 GGGTTTATGATTTA
1 AGGTTTATGATTTA
2896 TGATTCGGGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.31, C:0.00, G:0.24, T:0.45
Consensus pattern (14 bp):
AGGTTTATGATTTA
Found at i:3239 original size:16 final size:18
Alignment explanation
Indices: 3218--3254 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
3208 TTTATTTATC
*
3218 TAAAATTATTA-A-AATA
1 TAAAATAATTATATAATA
3234 TAAAATAATTATATAATA
1 TAAAATAATTATATAATA
3252 TAA
1 TAA
3255 TTGTATTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 10 0.56
17 1 0.06
18 7 0.39
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAAATAATTATATAATA
Found at i:3670 original size:15 final size:16
Alignment explanation
Indices: 3650--3690 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
3640 GTTTACTTCA
*
3650 GAATGATT-AAGCGCT
1 GAATGATTCAAACGCT
*
3665 GAATGATTCAAATGCT
1 GAATGATTCAAACGCT
3681 GAATGATTCA
1 GAATGATTCA
3691 GAGACTCTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (16 bp):
GAATGATTCAAACGCT
Found at i:7003 original size:35 final size:35
Alignment explanation
Indices: 6964--7033 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
6954 TTTTTTAGCT
* * * *
6964 TCAATTCATGATTTCGAGTTCGAGTCGAGCTTGAA
1 TCAATTCATAATTTCAAGTTCGAGTCAAACTTGAA
*
6999 TCAATTCATAATTTCAATTTCGAGTCAAACTTGAA
1 TCAATTCATAATTTCAAGTTCGAGTCAAACTTGAA
7034 AATTTTAGGC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (35 bp):
TCAATTCATAATTTCAAGTTCGAGTCAAACTTGAA
Found at i:9260 original size:11 final size:12
Alignment explanation
Indices: 9220--9263 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
9210 TATTTAAACG
*
9220 GGTATTGGGCCA
1 GGTATTGGGTCA
*
9232 GGTATTGGGTCG
1 GGTATTGGGTCA
9244 GGTATTGGGTC-
1 GGTATTGGGTCA
9255 GGTATTGGG
1 GGTATTGGG
9264 CTGGGAATCG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 9 0.30
12 21 0.70
ACGTcount: A:0.11, C:0.09, G:0.48, T:0.32
Consensus pattern (12 bp):
GGTATTGGGTCA
Found at i:9262 original size:23 final size:24
Alignment explanation
Indices: 9218--9263 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
9208 ATTATTTAAA
9218 CGGGTATTGGGCCAGGTATTGGGT
1 CGGGTATTGGGCCAGGTATTGGGT
*
9242 CGGGTATTGGGTC-GGTATTGGG
1 CGGGTATTGGGCCAGGTATTGGG
9264 CTGGGAATCG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.11, C:0.11, G:0.48, T:0.30
Consensus pattern (24 bp):
CGGGTATTGGGCCAGGTATTGGGT
Found at i:9341 original size:24 final size:25
Alignment explanation
Indices: 9281--9341 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
9271 TCGGGCCGGG
9281 TATATA-TATA-TATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
*
9304 TATATATT-TTTTATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
9328 T-T-TATTAATATTAT
1 TATATATT-ATATTAT
9342 ATATATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
22 4 0.12
23 8 0.25
24 20 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TATATATTATATTATTTAAATTAAA
Found at i:9730 original size:2 final size:2
Alignment explanation
Indices: 9725--9760 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
9715 CGTGTGTATG
*
9725 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9761 CCATTTAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16045 original size:20 final size:20
Alignment explanation
Indices: 16000--16045 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
15990 GACCAACAAA
* *
16000 ATCGCAATGCGATCTCTAAT
1 ATCGCAACGCGATCTCCAAT
*
16020 -TCGCAACGCGATCTCCATT
1 ATCGCAACGCGATCTCCAAT
16039 ATCGCAA
1 ATCGCAA
16046 ATTCGCGTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATCTCCAAT
Found at i:16156 original size:20 final size:20
Alignment explanation
Indices: 16131--16197 Score: 80
Period size: 20 Copynumber: 3.3 Consensus size: 20
16121 AATTCACAAT
16131 GCGAATAAGTAAATCGCAAC
1 GCGAATAAGTAAATCGCAAC
** * *
16151 GCGAATTGGGAAAATCGCAAT
1 GCGAA-TAAGTAAATCGCAAC
*
16172 GCGAATAAGTAAATTGCAAC
1 GCGAATAAGTAAATCGCAAC
16192 GCGAAT
1 GCGAAT
16198 TGGGAAAATC
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 21 0.57
21 16 0.43
ACGTcount: A:0.42, C:0.16, G:0.24, T:0.18
Consensus pattern (20 bp):
GCGAATAAGTAAATCGCAAC
Found at i:16167 original size:21 final size:21
Alignment explanation
Indices: 16141--16216 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
16131 GCGAATAAGT
16141 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
16162 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
*
16182 AAATTGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
*
16203 AAATCGCAATGCGA
1 AAATCGCAACGCGA
16217 TACTGACTAT
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
20 15 0.35
21 28 0.65
ACGTcount: A:0.41, C:0.17, G:0.25, T:0.17
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:16172 original size:41 final size:41
Alignment explanation
Indices: 16127--16216 Score: 171
Period size: 41 Copynumber: 2.2 Consensus size: 41
16117 TCCCAATTCA
16127 CAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCG
1 CAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCG
*
16168 CAATGCGAATAAGTAAATTGCAACGCGAATTGGGAAAATCG
1 CAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCG
16209 CAATGCGA
1 CAATGCGA
16217 TACTGACTAT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.18
Consensus pattern (41 bp):
CAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCG
Found at i:16230 original size:20 final size:20
Alignment explanation
Indices: 16205--16299 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
16195 AATTGGGAAA
*
16205 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
16225 ATCGCAATGCGATAATAAAAAA
1 ATCGCAACGCGATACT--GACT
* *
16247 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
16267 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
16287 TTCGCAACGCGAT
1 ATCGCAACGCGAT
16300 TTACATAGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
20 46 0.77
22 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:16874 original size:19 final size:19
Alignment explanation
Indices: 16852--16896 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
16842 GCGACCAGAC
*
16852 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
16871 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
16890 AATCGCA
1 AATCGCA
16897 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:16914 original size:19 final size:19
Alignment explanation
Indices: 16892--17037 Score: 105
Period size: 19 Copynumber: 8.1 Consensus size: 19
16882 GAAACCAAAA
*
16892 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
16911 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
16930 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
16946 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
16963 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
16977 TCTCATTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
16996 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
17016 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
17036 TC
1 TC
17038 AACCAAAAGA
Statistics
Matches: 100, Mismatches: 15, Indels: 24
0.72 0.11 0.17
Matches are distributed among these distances:
14 19 0.19
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 42 0.42
20 30 0.30
21 1 0.01
ACGTcount: A:0.13, C:0.23, G:0.21, T:0.42
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:16962 original size:33 final size:33
Alignment explanation
Indices: 16925--17012 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 33
16915 GTTGCGATTT
* **
16925 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
*
16958 TCATTTCGCGTTGCGATTCTCTCATTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
16991 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
17013 ATTATCTCGT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 35 0.70
34 15 0.30
ACGTcount: A:0.12, C:0.25, G:0.24, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
Found at i:17014 original size:20 final size:20
Alignment explanation
Indices: 16991--17037 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
16981 ATTGCGATAG
16991 TCATTTCCGCGTTGCGATTC
1 TCATTTCCGCGTTGCGATTC
* *
17011 TCATTAT-CTCGTTGCGATTT
1 TCATT-TCCGCGTTGCGATTC
17031 TCATTTC
1 TCATTTC
17038 AACCAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 1 0.04
20 21 0.91
21 1 0.04
ACGTcount: A:0.13, C:0.26, G:0.15, T:0.47
Consensus pattern (20 bp):
TCATTTCCGCGTTGCGATTC
Found at i:19100 original size:21 final size:21
Alignment explanation
Indices: 19076--19142 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
19066 TCATTCCTCG
19076 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
19097 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
19118 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
19139 AGAG
1 AGAG
19143 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:19100 original size:42 final size:42
Alignment explanation
Indices: 19020--19142 Score: 106
Period size: 42 Copynumber: 2.9 Consensus size: 42
19010 GCTCGACTCG
* * * * * * *
19020 CCTATCATCCCTCAAGATTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
19062 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
* * * * *
19104 ACTGTCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 CCTATCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
19143 CCCGATTCAC
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 61 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.37, G:0.17, T:0.24
Consensus pattern (42 bp):
CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
Found at i:20518 original size:14 final size:14
Alignment explanation
Indices: 20499--20534 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
20489 ATTGTTTAAT
20499 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
20513 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
20527 TGATTTGT
1 TGATTTGT
20535 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:20735 original size:19 final size:19
Alignment explanation
Indices: 20713--20863 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
20703 CGAAATTAAA
20713 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
20732 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
20747 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
20765 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
20779 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
20798 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
20813 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
20831 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
20850 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
20864 GGACATTAAG
Statistics
Matches: 95, Mismatches: 21, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
14 28 0.29
16 6 0.06
17 6 0.06
19 45 0.47
20 10 0.11
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:20759 original size:33 final size:32
Alignment explanation
Indices: 20717--20843 Score: 193
Period size: 33 Copynumber: 3.9 Consensus size: 32
20707 ATTAAATTCG
20717 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
20750 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
20783 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
20816 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
20844 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.03
33 80 0.93
35 3 0.03
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:20806 original size:66 final size:66
Alignment explanation
Indices: 20710--20842 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
20700 ACGCGAAATT
*
20710 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
20775 G
66 G
*
20776 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
20841 G
66 G
20842 A
1 A
20843 TAGTAATTTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:23149 original size:12 final size:12
Alignment explanation
Indices: 23132--23156 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
23122 TCTTCGGGGA
23132 CTTTTTCTTCTT
1 CTTTTTCTTCTT
23144 CTTTTTCTTCTT
1 CTTTTTCTTCTT
23156 C
1 C
23157 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:23365 original size:24 final size:24
Alignment explanation
Indices: 23331--23384 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
23321 CTGAAACATC
* *
23331 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
23355 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
23379 ATCAAA
1 ATCAAA
23385 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:24470 original size:20 final size:20
Alignment explanation
Indices: 24445--24502 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
24435 ATTCATTTGA
24445 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
24465 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
24485 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
24503 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:24562 original size:19 final size:19
Alignment explanation
Indices: 24521--24588 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
24511 GAAATGAAAA
24521 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
*
24537 TCG--TTGCAATTTTCATT
1 TCGCATTGCGATTTTCATT
24554 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
24573 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
24589 TCGTTGCGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
14 10 0.22
16 3 0.07
17 3 0.07
19 29 0.64
ACGTcount: A:0.15, C:0.22, G:0.16, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:26617 original size:20 final size:19
Alignment explanation
Indices: 26582--26647 Score: 87
Period size: 19 Copynumber: 3.4 Consensus size: 19
26572 GAAACTTAAA
26582 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
26601 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
26621 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
26640 ATCGCAAC
1 ATCGCAAC
26648 AACAAAATCG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
19 23 0.57
20 17 0.43
ACGTcount: A:0.38, C:0.24, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:26679 original size:32 final size:33
Alignment explanation
Indices: 26629--26699 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 33
26619 CTATCGCAAT
26629 GCGAAATGAAAATCGCAACAACAAAATCGAAAC
1 GCGAAATGAAAATCGCAACAACAAAATCGAAAC
* *
26662 GCGAAATG-AAATCGCAACGACAAAATCGCAAC
1 GCGAAATGAAAATCGCAACAACAAAATCGAAAC
26694 GCGAAA
1 GCGAAA
26700 CACAAATCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 28 0.78
33 8 0.22
ACGTcount: A:0.51, C:0.23, G:0.18, T:0.08
Consensus pattern (33 bp):
GCGAAATGAAAATCGCAACAACAAAATCGAAAC
Found at i:26694 original size:14 final size:14
Alignment explanation
Indices: 26637--26694 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
26627 ATGCGAAATG
*
26637 AAAATCGCAACAAC
1 AAAATCGCAACGAC
* *
26651 AAAATCGAAACGCGAA
1 AAAATCGCAA--CGAC
26667 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
26683 AAAATCGCAACG
1 AAAATCGCAACG
26695 CGAAACACAA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
14 20 0.57
16 7 0.20
18 8 0.23
ACGTcount: A:0.52, C:0.24, G:0.16, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:26759 original size:32 final size:33
Alignment explanation
Indices: 26709--26801 Score: 143
Period size: 32 Copynumber: 2.8 Consensus size: 33
26699 ACACAAATCG
*
26709 CATTGCGATTTTCATTTCGCGTTGCGATTTTAT
1 CATTGCGATTTTCATTTCGCATTGCGATTTTAT
*
26742 CATTGCGA-TTTCATTTCGCATTGCGATTTTGT
1 CATTGCGATTTTCATTTCGCATTGCGATTTTAT
* *
26774 CGTTGCGATTTTTATTTCGCATTGCGAT
1 CATTGCGATTTTCATTTCGCATTGCGAT
26802 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 29 0.53
33 26 0.47
ACGTcount: A:0.15, C:0.18, G:0.19, T:0.47
Consensus pattern (33 bp):
CATTGCGATTTTCATTTCGCATTGCGATTTTAT
Found at i:26809 original size:19 final size:20
Alignment explanation
Indices: 26787--26829 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
26777 TGCGATTTTT
26787 ATTT-CGCATTGCGATAGCC
1 ATTTCCGCATTGCGATAGCC
* *
26806 ATTTCCGCGTTGCGATAGTC
1 ATTTCCGCATTGCGATAGCC
26826 ATTT
1 ATTT
26830 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (20 bp):
ATTTCCGCATTGCGATAGCC
Found at i:26820 original size:20 final size:20
Alignment explanation
Indices: 26795--26840 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
26785 TTATTTCGCA
26795 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* * *
26815 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGCG
26835 TTGCGA
1 TTGCGA
26841 AAGTAAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:27338 original size:18 final size:18
Alignment explanation
Indices: 27312--27356 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
27302 GTCGATCAGA
*
27312 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
27330 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
27348 TGATGGCTC
1 TGATGGCTC
27357 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:28695 original size:20 final size:20
Alignment explanation
Indices: 28670--28707 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28660 AATAGTTTCT
28670 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
28690 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
28708 GAGAGAATCG
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:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:28997 original size:22 final size:22
Alignment explanation
Indices: 28972--29015 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
28962 GATTTAGATA
28972 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
28994 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
29016 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:29228 original size:20 final size:20
Alignment explanation
Indices: 29203--29255 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
29193 GATTATATAT
*
29203 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTAAG
29223 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
29243 TATCTCGTTGCGA
1 TATCGCGTTGCGA
29256 TTTTTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:29268 original size:41 final size:41
Alignment explanation
Indices: 29223--29300 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
29213 CGAAAGTCAG
* * *
29223 TATCGCGTTGCGAAAGT-AAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTCAA-TATCGCATTGCGATTTTTTAT
*
29264 TATCGCATTGCGATAGTCAATATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTCAATATCGCATTGCGATTTT
29301 CCCAATTCGC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
41 30 0.94
42 2 0.06
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTCAATATCGCATTGCGATTTTTTAT
Found at i:29315 original size:21 final size:21
Alignment explanation
Indices: 29281--29378 Score: 101
Period size: 20 Copynumber: 4.7 Consensus size: 21
29271 TTGCGATAGT
29281 CAATATCGCATTGCGATTTTCC
1 CAAT-TCGCATTGCGATTTTCC
* *
29303 CAATTCGCGTTGCGA-TTTAC
1 CAATTCGCATTGCGATTTTCC
**
29323 TTATTCGCATTGCGATTTTCC
1 CAATTCGCATTGCGATTTTCC
* *
29344 CAATTCGCGTTGCGA-TTTAC
1 CAATTCGCATTGCGATTTTCC
**
29364 TTATTCGCATTGCGA
1 CAATTCGCATTGCGA
29379 ATTGGAAAAA
Statistics
Matches: 62, Mismatches: 13, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
20 32 0.52
21 26 0.42
22 4 0.06
ACGTcount: A:0.19, C:0.24, G:0.17, T:0.39
Consensus pattern (21 bp):
CAATTCGCATTGCGATTTTCC
Found at i:29316 original size:41 final size:41
Alignment explanation
Indices: 29286--29378 Score: 150
Period size: 41 Copynumber: 2.3 Consensus size: 41
29276 ATAGTCAATA
* *
29286 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACATAT
* *
29327 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACATAT
29368 TCGCATTGCGA
1 TCGCATTGCGA
29379 ATTGGAAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACATAT
Found at i:37683 original size:21 final size:21
Alignment explanation
Indices: 37634--37697 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
37624 CATATGAAAT
*
37634 TTGTCCCGAAGGACCTGTGAA
1 TTGTCCCGAAGGACCTATGAA
*
37655 TATGTCCCGAAGGACCTATGAG
1 T-TGTCCCGAAGGACCTATGAA
37677 TTGTCCCGAAGGACCTATGAA
1 TTGTCCCGAAGGACCTATGAA
37698 ACCCTCGACT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
21 20 0.51
22 19 0.49
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAA
Found at i:39068 original size:64 final size:66
Alignment explanation
Indices: 38976--39097 Score: 196
Period size: 64 Copynumber: 1.9 Consensus size: 66
38966 ATGAAGGTAT
*
38976 CATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTTAATGGGGAT
1 CATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAATGGGGAT
39040 G
66 G
*
39041 CATCGATGCACT-C-CTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAA
1 CATCGATGCACTACAC-CATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAA
39098 ATTCTGCATC
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
63 1 0.02
64 30 0.57
65 22 0.42
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.35
Consensus pattern (66 bp):
CATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAATGGGGAT
G
Done.