Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002745.1 Hibiscus syriacus cultivar Beakdansim tig00005655_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: 51112
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Found at i:148 original size:15 final size:15
Alignment explanation
Indices: 128--160 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
118 CGATATCCTC
128 AGAATAAGATGG-AAT
1 AGAATAAG-TGGAAAT
143 AGAATAAGTGGAAAT
1 AGAATAAGTGGAAAT
158 AGA
1 AGA
161 TGAATTACCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.18
15 14 0.82
ACGTcount: A:0.55, C:0.00, G:0.27, T:0.18
Consensus pattern (15 bp):
AGAATAAGTGGAAAT
Found at i:292 original size:21 final size:21
Alignment explanation
Indices: 268--344 Score: 73
Period size: 21 Copynumber: 3.7 Consensus size: 21
258 TAATAAGTGA
*
268 AAGTAGATGAATTAACTTAGT
1 AAGTAGATGAAGTAACTTAGT
* * *
289 AAGTAGAAGAAGTACCTTGGT
1 AAGTAGATGAAGTAACTTAGT
* ** *
310 AAGTAGATAAAGTTCCTTGGT
1 AAGTAGATGAAGTAACTTAGT
*
331 AACTAGATGAAGTA
1 AAGTAGATGAAGTA
345 CCTCAATATG
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.29
Consensus pattern (21 bp):
AAGTAGATGAAGTAACTTAGT
Found at i:4418 original size:111 final size:110
Alignment explanation
Indices: 4213--4420 Score: 299
Period size: 110 Copynumber: 1.9 Consensus size: 110
4203 ACCAAAGCAC
* * * * * *
4213 CGAAATGGTCATTCACCTTTTATGAACACCATGAGTGACACCTTTTATGCCGAAAATGCATCTTA
1 CGAAACGGTAATTCACCTTTTACGAACACCATGAGAGACACCTTTTATGCCAAAAATGCACCTTA
*
4278 TGCATTAAACAAAATTGATCGATAACTTTCATACACGAAGTATGT
66 TGCATTAAACAAAATCGATCGATAACTTTCATACACGAAGTATGT
* * * * *
4323 CGAAACGGTAATTCACCTTTTACGAATACCTTGAGAGGCACTTTTTATGTCAAAAATGCACCATT
1 CGAAACGGTAATTCACCTTTTACGAACACCATGAGAGACACCTTTTATGCCAAAAATGCACC-TT
4388 ATGCATTAAACAAAATCGATCGATAACTTTCAT
65 ATGCATTAAACAAAATCGATCGATAACTTTCAT
4421 TAGTGGCATA
Statistics
Matches: 85, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
110 51 0.60
111 34 0.40
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (110 bp):
CGAAACGGTAATTCACCTTTTACGAACACCATGAGAGACACCTTTTATGCCAAAAATGCACCTTA
TGCATTAAACAAAATCGATCGATAACTTTCATACACGAAGTATGT
Found at i:8306 original size:79 final size:79
Alignment explanation
Indices: 8194--8416 Score: 347
Period size: 79 Copynumber: 2.8 Consensus size: 79
8184 ATAATGCACC
** * *
8194 CCCATATGTATTTCAACGATGGTATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTT
1 CCCATATACATTTCAACTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTT
8259 ATGCTCACAAAGTA
66 ATGCTCACAAAGTA
* * *
8273 CCCATATACATTTCAGCTATGGCATCCTTTCATGCCAATAATGCACTCATATGAATTATTCTTTT
1 CCCATATACATTTCAACTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTT
* * *
8338 ATGTTGACAATGTA
66 ATGCTCACAAAGTA
*
8352 CCCATATACATTTCAACTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTTTTTT
1 CCCATATACATTTCAACTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTT
8417 CATTTGTTTT
Statistics
Matches: 130, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
79 130 1.00
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (79 bp):
CCCATATACATTTCAACTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTT
ATGCTCACAAAGTA
Found at i:8574 original size:34 final size:34
Alignment explanation
Indices: 8531--8599 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
8521 TGTTACATTT
*
8531 TGAATTATTTGTAATCATTATTATATAGTTTGCA
1 TGAATTATTTCTAATCATTATTATATAGTTTGCA
8565 TGAATTATTTCTAATCATTATTATATAGTTTGCA
1 TGAATTATTTCTAATCATTATTATATAGTTTGCA
8599 T
1 T
8600 ACAATAAATG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.32, C:0.07, G:0.10, T:0.51
Consensus pattern (34 bp):
TGAATTATTTCTAATCATTATTATATAGTTTGCA
Found at i:14135 original size:20 final size:21
Alignment explanation
Indices: 14083--14143 Score: 72
Period size: 20 Copynumber: 2.9 Consensus size: 21
14073 TTCCCTTGTG
14083 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
14106 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
*
14126 GGGAGG-ATCGATTCCCTC
1 GGG-GGAATCGGTTCCCTC
14144 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
20 16 0.44
21 4 0.11
22 3 0.08
23 13 0.36
ACGTcount: A:0.20, C:0.26, G:0.33, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:21409 original size:28 final size:27
Alignment explanation
Indices: 21350--21410 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
21340 CGCAAGAAGC
*
21350 CAACCTGAAACATATTACCTCCCAAAT
1 CAACCTGAAACACATTACCTCCCAAAT
* * *
21377 TAACCTTAAACACATTACCTTCCCAAGT
1 CAACCTGAAACACATTACC-TCCCAAAT
21405 CAACCT
1 CAACCT
21411 AATAATTTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 16 0.57
28 12 0.43
ACGTcount: A:0.38, C:0.34, G:0.03, T:0.25
Consensus pattern (27 bp):
CAACCTGAAACACATTACCTCCCAAAT
Found at i:22928 original size:112 final size:110
Alignment explanation
Indices: 22677--23013 Score: 428
Period size: 109 Copynumber: 3.0 Consensus size: 110
22667 CCAAACAACA
* * * * *
22677 TGATATTTTCAAAAGAATTTTTAAAGAAACTAAGTCTGATTTTCAAGGGTTTCTTGATGATGATT
1 TGATGTTTTCAAATGACTTTTT-ATGAAACTAAGTCTGATTTTCAGGGGTTTCTTGATGATGATT
* *
22742 TTCAATGAATTCTTAAAAGAAGCTAAG-CTAATTTTTAGGGCTTTCT
65 TTCAAAGAATT-TTAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCT
* * *
22788 TAATGTTTTCAAATGAGTTTTTAT-AAACTAAGTCTGATTTTCAGGGGTTTATTGATGATGATTT
1 TGATGTTTTCAAATGACTTTTTATGAAACTAAGTCTGATTTTCAGGGGTTTCTTGATGATGATTT
22852 TCAAAGAATTTATTAAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCT
66 TCAAAGAA-TT-TT-AAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCT
* * * * * *
22900 TGATGTTTTCAAATGACTTTTT-TGAAACTAAGCCTAATTTTCAGGGATTTCTTAATGATTATCT
1 TGATGTTTTCAAATGACTTTTTATGAAACTAAGTCTGATTTTCAGGGGTTTCTTGATGATGATTT
* * * *
22964 CCAAAGAATTTTAAAGGAAACTAAGCCTAATTTTTAGGGGTTCCT
66 TCAAAGAATTTTAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCT
23009 TGATG
1 TGATG
23014 ACAACCAAAA
Statistics
Matches: 199, Mismatches: 23, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
109 80 0.40
110 7 0.04
111 34 0.17
112 78 0.39
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (110 bp):
TGATGTTTTCAAATGACTTTTTATGAAACTAAGTCTGATTTTCAGGGGTTTCTTGATGATGATTT
TCAAAGAATTTTAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCT
Found at i:22934 original size:52 final size:53
Alignment explanation
Indices: 22677--23014 Score: 229
Period size: 57 Copynumber: 6.1 Consensus size: 53
22667 CCAAACAACA
* * * * *
22677 TGAT-ATTTTCAAAAGAATTTTTAAAGAAACTAAGTCTGATTTTCAAGGGTTTCTT
1 TGATGATTTTC-AAAGAATTTTT-ATGAAACTAAGCCTAATTTTTAGGGGTTTC-T
* * * * *
22732 GATGATGATTTTCAATGAATTCTTAAAAGAAGCTAAG-CTAATTTTTAGGGCTTTCT
1 --TGATGATTTTCAAAGAATT-TT-TATGAAACTAAGCCTAATTTTTAGGGGTTTCT
* * * * * *
22788 TAATG-TTTTCAAATGAGTTTTTAT-AAACTAAGTCTGATTTTCAGGGGTTTATT
1 TGATGATTTTCAAA-GAATTTTTATGAAACTAAGCCTAATTTTTAGGGGTTT-CT
* *
22841 GATGATGATTTTCAAAGAATTTATTAAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCT
1 --TGATGATTTTCAAAGAATTT-TT---ATGAAACTAAGCCTAATTTTTAGGGGTTTCT
* * *
22900 TGATG-TTTTCAAATGACTTTTT-TGAAACTAAGCCTAATTTTCAGGGATTTCT
1 TGATGATTTTCAAA-GAATTTTTATGAAACTAAGCCTAATTTTTAGGGGTTTCT
* * * *
22952 TAATGATTATCTCCAAAGAATTTTAAAGGAAACTAAGCCTAATTTTTAGGGGTTCCT
1 TGATGATT-T-T-CAAAGAATTTT-TATGAAACTAAGCCTAATTTTTAGGGGTTTCT
23009 TGATGA
1 TGATGA
23015 CAACCAAAAA
Statistics
Matches: 222, Mismatches: 38, Indels: 42
0.74 0.13 0.14
Matches are distributed among these distances:
51 7 0.03
52 45 0.20
53 12 0.05
54 9 0.04
55 16 0.07
56 25 0.11
57 66 0.30
58 18 0.08
59 2 0.01
60 22 0.10
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (53 bp):
TGATGATTTTCAAAGAATTTTTATGAAACTAAGCCTAATTTTTAGGGGTTTCT
Found at i:23026 original size:112 final size:112
Alignment explanation
Indices: 22686--23072 Score: 331
Period size: 112 Copynumber: 3.4 Consensus size: 112
22676 ATGATATTTT
* * * * * *
22686 CAAAAGAATTTTTAAAGAAACTAAGTCTGATTTTCAAGGGTTTCTTGATGATGATTTTCAATGAA
1 CAAATGAATTTTT-ATGAAACTAAGCCTGATTTTC-AGGGTTTCTTGATGATGATCTCCAAAGAA
* * * * * ****
22751 -TTCTT-AAAAGAAGCTAAG-CTAATTTTTAGGGCTTTCTTAATGTTTT
64 TTTATTAAAAAGAAACTAAGCCTAATTTTTAGGGGTTCCTTGATGCAAC
* * * * *
22797 CAAATGAGTTTTTAT-AAACTAAGTCTGATTTTCAGGGGTTTATTGATGATGATTTTCAAAGAAT
1 CAAATGAATTTTTATGAAACTAAGCCTGATTTTCA-GGGTTTCTTGATGATGATCTCCAAAGAAT
* * ****
22861 TTATTAAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTT
65 TTATTAAAAAGAAACTAAGCCTAATTTTTAGGGGTTCCTTGATGCAAC
* * * *
22909 CAAATGACTTTTT-TGAAACTAAGCCTAATTTTCAGGGATTTCTTAATGATTATCTCCAAAGAA-
1 CAAATGAATTTTTATGAAACTAAGCCTGATTTTCAGGG-TTTCTTGATGATGATCTCCAAAGAAT
*
22972 TT-TT-AAAGGAAACTAAGCCTAATTTTTAGGGGTTCCTTGATGACAAC
65 TTATTAAAAAGAAACTAAGCCTAATTTTTAGGGGTTCCTTGATG-CAAC
* *
23019 CAAAAATGAAATATTTTAAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGA
1 C--AAATG-AAT-TTTTATGAAACTAAGCCTGATTTTC-AGGGTTTCTTGATGA
23073 GTAAGTCCTT
Statistics
Matches: 235, Mismatches: 28, Indels: 22
0.82 0.10 0.08
Matches are distributed among these distances:
108 1 0.00
109 79 0.34
110 8 0.03
111 30 0.13
112 80 0.34
113 2 0.01
114 4 0.02
115 27 0.11
116 4 0.02
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.39
Consensus pattern (112 bp):
CAAATGAATTTTTATGAAACTAAGCCTGATTTTCAGGGTTTCTTGATGATGATCTCCAAAGAATT
TATTAAAAAGAAACTAAGCCTAATTTTTAGGGGTTCCTTGATGCAAC
Found at i:23574 original size:61 final size:60
Alignment explanation
Indices: 23333--23558 Score: 305
Period size: 60 Copynumber: 3.8 Consensus size: 60
23323 TTAAAACAAA
* *
23333 CAACACCCCACCAGAGGGGATTACATTTCCTATTGCTCAATTCACAACACCTCGAATCAG
1 CAACGCCCCACCAGAGGGGATAACATTTCCTATTGCTCAATTCACAACACCTCGAATCAG
* *
23393 CAACGCCCCACTAGAGGGGATTACATTTCCTATTGCTCAATTCACAACACCTCGAATCAG
1 CAACGCCCCACCAGAGGGGATAACATTTCCTATTGCTCAATTCACAACACCTCGAATCAG
* * ** *
23453 CAACGCCCCACTAGAGGGGATAACATTT-CTTTTGCTCAATTCACACAACATTTTGAATCAG
1 CAACGCCCCACCAGAGGGGATAACATTTCCTATTGCTCAATT--CACAACACCTCGAATCAG
* *
23514 CAACGCCCCACCAAAGGGGATAACATTT-CTTTTG-TCTAATTCACA
1 CAACGCCCCACCAGAGGGGATAACATTTCCTATTGCTC-AATTCACA
23559 CAACATTTCG
Statistics
Matches: 154, Mismatches: 9, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
59 16 0.10
60 87 0.56
61 51 0.33
ACGTcount: A:0.31, C:0.30, G:0.14, T:0.25
Consensus pattern (60 bp):
CAACGCCCCACCAGAGGGGATAACATTTCCTATTGCTCAATTCACAACACCTCGAATCAG
Found at i:26031 original size:27 final size:26
Alignment explanation
Indices: 26001--26052 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
25991 TTGTAGGTTT
26001 AAATGAATTAGGATTAATATTGATAGA
1 AAATGAATTAGGATTAATATT-ATAGA
* *
26028 AAATTAATTAGGATTAGTATTATAG
1 AAATGAATTAGGATTAATATTATAG
26053 TCTCCATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.46, C:0.00, G:0.17, T:0.37
Consensus pattern (26 bp):
AAATGAATTAGGATTAATATTATAGA
Found at i:28412 original size:16 final size:16
Alignment explanation
Indices: 28391--28427 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
28381 TCATGTCCAT
28391 AAATATTA-AAAAATCA
1 AAATATTATAAAAAT-A
28407 AAATATTATAAAAATA
1 AAATATTATAAAAATA
28423 AAATA
1 AAATA
28428 GTCATGAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (16 bp):
AAATATTATAAAAATA
Found at i:32577 original size:17 final size:15
Alignment explanation
Indices: 32537--32579 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 15
32527 AAATGGTCGA
32537 CTGTTGACCGTTGAC
1 CTGTTGACCGTTGAC
32552 CTGCTTTGACCGTTGAC
1 CTG--TTGACCGTTGAC
32569 CATAGTTGACC
1 C-T-GTTGACC
32580 AAAACTTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
15 3 0.12
17 19 0.79
18 1 0.04
19 1 0.04
ACGTcount: A:0.16, C:0.28, G:0.23, T:0.33
Consensus pattern (15 bp):
CTGTTGACCGTTGAC
Found at i:35601 original size:164 final size:164
Alignment explanation
Indices: 35225--35621 Score: 679
Period size: 163 Copynumber: 2.4 Consensus size: 164
35215 GTAGGAGTGC
* *
35225 AGGTGGGTGTAAGGTTCTGTGGAACCTACACATTATGGAGTGTTGGTTGGAGGGAATAATATGAT
1 AGGTGGGTGTATGGTTCTGGGGAACCTACACATTATGGAGTGTTGGTTGGAGGGAATAATATGAT
* *
35290 TTTTGATAAATGTTTTTATAGAAAGGTGTTGTTGGAGGAAGTTACCGTTACTGCAGGCTCCTCTG
66 TTTTGATAAATGTTTTTATAGAAAGGTGTTGTTGGAGGAAATTACCGTTACTACAGGCTCCTCTG
35355 CTTTGTGCTCAGGGTAAGTCCTTACTTGGTGTGT
131 CTTTGTGCTCAGGGTAAGTCCTTACTTGGTGTGT
35389 AGGTGGGTGTATGGTTCTGGGGAACCTACACATTATGGAGTGTTGGTTGGAGGGAATAATATGAT
1 AGGTGGGTGTATGGTTCTGGGGAACCTACACATTATGGAGTGTTGGTTGGAGGGAATAATATGAT
* * * *
35454 TTTTGATAAATG-TTTTATGGGAGGGTGTTGTTGGAGGAAATTATCGTTACTACAGGCTCCTCTG
66 TTTTGATAAATGTTTTTATAGAAAGGTGTTGTTGGAGGAAATTACCGTTACTACAGGCTCCTCTG
35518 CTTTGTGCTCAGGGTAAGTCCTTACTTGGTGTGT
131 CTTTGTGCTCAGGGTAAGTCCTTACTTGGTGTGT
* * *
35552 AGGTGGGTGTATGGTTCTGGGGAACCTACACATTATTGAGTGTTTGGTTGGAGGGATTAATATGG
1 AGGTGGGTGTATGGTTCTGGGGAACCTACACATTATGGAGTG-TTGGTTGGAGGGAATAATATGA
35617 TTTTT
65 TTTTT
35622 TAATAAAAAT
Statistics
Matches: 221, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
163 121 0.55
164 100 0.45
ACGTcount: A:0.21, C:0.11, G:0.32, T:0.37
Consensus pattern (164 bp):
AGGTGGGTGTATGGTTCTGGGGAACCTACACATTATGGAGTGTTGGTTGGAGGGAATAATATGAT
TTTTGATAAATGTTTTTATAGAAAGGTGTTGTTGGAGGAAATTACCGTTACTACAGGCTCCTCTG
CTTTGTGCTCAGGGTAAGTCCTTACTTGGTGTGT
Found at i:38069 original size:33 final size:33
Alignment explanation
Indices: 38015--38077 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
38005 CCTTTACAAC
* *
38015 TCCCTAGTTTTTCACATGCTAAACTAGAACTTT
1 TCCCTAGCTTTTCACAGGCTAAACTAGAACTTT
*
38048 TCCCTAGCTTTT-AGCAGGCTAAGCTAGAAC
1 TCCCTAGCTTTTCA-CAGGCTAAACTAGAAC
38078 CAAAACCCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 1 0.04
33 25 0.96
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.33
Consensus pattern (33 bp):
TCCCTAGCTTTTCACAGGCTAAACTAGAACTTT
Found at i:38632 original size:21 final size:20
Alignment explanation
Indices: 38606--38658 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 20
38596 GTACAAGTAG
*
38606 GGTATCAATACAGATTCATGT
1 GGTATCGATAC-GATTCATGT
38627 GGTATCGATATCGATTCATGT
1 GGTATCGATA-CGATTCATGT
38648 GGTATCGATAC
1 GGTATCGATAC
38659 TGCAAAGAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 1 0.03
21 28 0.93
22 1 0.03
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (20 bp):
GGTATCGATACGATTCATGT
Found at i:39286 original size:24 final size:24
Alignment explanation
Indices: 39256--39303 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
39246 AATTAAGTGC
39256 ATATGCATAAAGTTTTCTAAAAAT
1 ATATGCATAAAGTTTTCTAAAAAT
39280 ATATGCATAAAGTTTTCTAAAAAT
1 ATATGCATAAAGTTTTCTAAAAAT
39304 GGTATTCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (24 bp):
ATATGCATAAAGTTTTCTAAAAAT
Found at i:46429 original size:57 final size:58
Alignment explanation
Indices: 46360--46475 Score: 225
Period size: 57 Copynumber: 2.0 Consensus size: 58
46350 TAGTTGTACT
46360 ACCAACACAACAACCTGATGATCTACATGATGCACCAACATCCTTAG-TGAAATGCCA
1 ACCAACACAACAACCTGATGATCTACATGATGCACCAACATCCTTAGCTGAAATGCCA
46417 ACCAACACAACAACCTGATGATCTACATGATGCACCAACATCCTTAGCTGAAATGCCA
1 ACCAACACAACAACCTGATGATCTACATGATGCACCAACATCCTTAGCTGAAATGCCA
46475 A
1 A
46476 AGCATAATGA
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
57 47 0.81
58 11 0.19
ACGTcount: A:0.39, C:0.30, G:0.12, T:0.19
Consensus pattern (58 bp):
ACCAACACAACAACCTGATGATCTACATGATGCACCAACATCCTTAGCTGAAATGCCA
Found at i:49686 original size:17 final size:17
Alignment explanation
Indices: 49654--49687 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
49644 AGTGGTCTAA
* *
49654 AACATAAACAAGTAAAT
1 AACATAAAAAAATAAAT
49671 AACATAAAAAAATAAAT
1 AACATAAAAAAATAAAT
49688 GCCATAATTA
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:0.71, C:0.09, G:0.03, T:0.18
Consensus pattern (17 bp):
AACATAAAAAAATAAAT
Done.