Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002260.1 Hibiscus syriacus cultivar Beakdansim tig00004594_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: 44258
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Found at i:4851 original size:20 final size:21
Alignment explanation
Indices: 4821--4859 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
4811 ATTACATGTA
4821 CAAATATGACAAAACCGGTCC
1 CAAATATGACAAAACCGGTCC
4842 CAAA-ATGACAAAACCGGT
1 CAAATATGACAAAACCGGT
4860 AAAACGCTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.46, C:0.26, G:0.15, T:0.13
Consensus pattern (21 bp):
CAAATATGACAAAACCGGTCC
Found at i:5274 original size:198 final size:199
Alignment explanation
Indices: 4908--6125 Score: 1653
Period size: 198 Copynumber: 6.1 Consensus size: 199
4898 ATAAGTATTG
* *
4908 AAAACATCGAAAAATATAATTATAATGTAATAGGTAAATTATTCATGTAAACGGTCTAAATATAC
1 AAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTCATATAAACGGTCTAAATATAC
* *
4973 C-GTTTTTGAGAAAACATGTATACAAAAAGTATCGACACAAATCTAACAAGTGTCGATACTTTTT
66 CGGTTTTTGAGAAAACATGTGTACAAAAAGTATCGACACAAATATAACAAGTGTCGATACTTTTT
* * * * *
5037 CTCCATATTGTATTTCAAATCCAAGTGCACTAAAAAGTGTCAATACATATATAACAAGTGTTGAT
131 CTCCAGAATGTATTTCAAAACCAAGTGCACTAAAAAGTGTCGATACATATATAACAAGTGTCGAT
5102 CCCA
196 CCCA
* * * * *
5106 AAAACATCGAAAACCATAATTATAATGTAATAAGTAAATTA-GCAAAATAATCGGTCTAAATATA
1 AAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTC-ATATAAACGGTCTAAATATA
* * *
5170 CCGGTTTTTGAGAAACCATGTGTACAAACAGTATCGACACAAATAGAACAAGTGTCGATACTTTT
65 CCGGTTTTTGAGAAAACATGTGTACAAAAAGTATCGACACAAATATAACAAGTGTCGATACTTTT
** * * * *
5235 GGTCCAGAATGTATTTCAGAACCAAGTGCAC-ATAAAGTGTCGATACATTTAAAACAAGTGTCGA
130 TCTCCAGAATGTATTTCAAAACCAAGTGCACTAAAAAGTGTCGATACATATATAACAAGTGTCGA
*
5299 TCCCG
195 TCCCA
*
5304 AAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTCATGTAAACGGTCTAAATATAC
1 AAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTCATATAAACGGTCTAAATATAC
* *
5369 CGGTTTTTGAGAAAATAGGTGTACAAAAAGTATCGACACAAATATAACAAGTGTCGATACTTTTT
66 CGGTTTTTGAGAAAACATGTGTACAAAAAGTATCGACACAAATATAACAAGTGTCGATACTTTTT
* * *
5434 CTCCAGACTGTATTTTAAAACCAAGTGCACTAAAAAGTGTTGATACATATATAACAAGTGTCGAT
131 CTCCAGAATGTATTTCAAAACCAAGTGCACTAAAAAGTGTCGATACATATATAACAAGTGTCGAT
5499 CCCA
196 CCCA
* * * *
5503 AAAACATCGAAAACCATAATTATAATGTAATAGGTAAATTA-ACAATATAACCGGTCTAAATCTA
1 AAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTC-ATATAAACGGTCTAAATATA
* * *
5567 CCGGTTTTTGAGAAAACAAGTGTACAAACAGTATCGACACAAATAGAACAAGTGTCGATACTTTT
65 CCGGTTTTTGAGAAAACATGTGTACAAAAAGTATCGACACAAATATAACAAGTGTCGATACTTTT
** * * * *
5632 GGTCCAGAAAGTATTTCAGAACCAAGTGCAC-ATAAAAGTGTCGATACATTTAAAACAAGTGTCG
130 TCTCCAGAATGTATTTCAAAACCAAGTGCACTA-AAAAGTGTCGATACATATATAACAAGTGTCG
*
5696 ATCCCG
194 ATCCCA
*
5702 AAAA-ATCGAAAAACATAATTATAATGTAATAGGTAAATTATTCATGTAAACGGTCTAAATATAC
1 AAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTCATATAAACGGTCTAAATATAC
* *
5766 CGGTTTTTGAGAAAACAGGTGTATAAAAAGTATCGACACAAATATAACAAGTGTCGATACTTTTT
66 CGGTTTTTGAGAAAACATGTGTACAAAAAGTATCGACACAAATATAACAAGTGTCGATACTTTTT
*
5831 CTCCAGAATGTATTTCAAAACCAAGTGCACTAAAAAGTGTAGATACATATATAACAAGTGTCGAT
131 CTCCAGAATGTATTTCAAAACCAAGTGCACTAAAAAGTGTCGATACATATATAACAAGTGTCGAT
5896 CCCA
196 CCCA
* * * *
5900 AAAACATCGAAAACCATAATTATAATGTAATAGGTAAATTA-GCA-ATATAGCTGGTCTAAATGT
1 AAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTCATATA-AAC-GGTCTAAATAT
* * ** * * * *
5963 ACCGGTTTATGAGAAAACATGTATACATGAAGTATCGACACAAATACATCAAGTTTCGAAACATT
64 ACCGGTTTTTGAGAAAACATGTGTACAAAAAGTATCGACACAAATATAACAAGTGTCGATAC-TT
* * * * * * * * *
6028 TTTGTCCAGACTATATTTTAAAAACCAAGTGTAC-AACAAAATTTCGATACATTTATAACAATTG
128 TTTCTCCAGAATGTA-TTTCAAAACCAAGTGCACTAA-AAAGTGTCGATACATATATAACAAGTG
**
6092 TTAATCCCA
191 TCGATCCCA
*
6101 AAAACATCGAAAAATATAATTATAA
1 AAAACATCGAAAAACATAATTATAA
6126 CCAAATGTCT
Statistics
Matches: 896, Mismatches: 110, Indels: 25
0.87 0.11 0.02
Matches are distributed among these distances:
197 3 0.00
198 414 0.46
199 395 0.44
200 16 0.02
201 68 0.08
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.28
Consensus pattern (199 bp):
AAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTCATATAAACGGTCTAAATATAC
CGGTTTTTGAGAAAACATGTGTACAAAAAGTATCGACACAAATATAACAAGTGTCGATACTTTTT
CTCCAGAATGTATTTCAAAACCAAGTGCACTAAAAAGTGTCGATACATATATAACAAGTGTCGAT
CCCA
Found at i:5639 original size:397 final size:397
Alignment explanation
Indices: 4907--6125 Score: 1942
Period size: 397 Copynumber: 3.1 Consensus size: 397
4897 TATAAGTATT
*
4907 GAAAACATCGAAAAATATAATTATAATGTAATAGGTAAATTATTCATGTAAACGGTCTAAATATA
1 GAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTCATGTAAACGGTCTAAATATA
* * *
4972 CC-GTTTTTGAGAAAACATGTATACAAAAAGTATCGACACAAATCTAACAAGTGTCGATACTTTT
66 CCGGTTTTTGAGAAAACAGGTGTACAAAAAGTATCGACACAAATATAACAAGTGTCGATACTTTT
* * * *
5036 TCTCCATATTGTATTTCAAATCCAAGTGCACTAAAAAGTGTCA-ATACATATATAACAAGTGTTG
131 TCTCCAGAATGTATTTCAAAACCAAGTGCACTAAAAAGTGT-AGATACATATATAACAAGTGTCG
* * *
5100 ATCCCAAAAACATCGAAAACCATAATTATAATGTAATAAGTAAATTAGCAAAATAATCGGTCTAA
195 ATCCCAAAAACATCGAAAACCATAATTATAATGTAATAGGTAAATTAGCAATATAACCGGTCTAA
*
5165 ATATACCGGTTTTTGAGAAACCATGTGTACAAACAGTATCGACACAAATAGAACAAGTGTCGATA
260 ATATACCGGTTTTTGAGAAAACATGTGTACAAACAGTATCGACACAAATAGAACAAGTGTCGATA
5230 CTTTTGGTCCAGAATGTATTTCAGAACCAAGTGCACATAAAGTGTCGATACATTTAAAACAAGTG
325 CTTTTGGTCCAGAATGTATTTCAGAACCAAGTGCACATAAAGTGTCGATACATTTAAAACAAGTG
5295 TCGATCCC
390 TCGATCCC
5303 GAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTCATGTAAACGGTCTAAATATA
1 GAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTCATGTAAACGGTCTAAATATA
*
5368 CCGGTTTTTGAGAAAATAGGTGTACAAAAAGTATCGACACAAATATAACAAGTGTCGATACTTTT
66 CCGGTTTTTGAGAAAACAGGTGTACAAAAAGTATCGACACAAATATAACAAGTGTCGATACTTTT
* * *
5433 TCTCCAGACTGTATTTTAAAACCAAGTGCACTAAAAAGTGTTGATACATATATAACAAGTGTCGA
131 TCTCCAGAATGTATTTCAAAACCAAGTGCACTAAAAAGTGTAGATACATATATAACAAGTGTCGA
*
5498 TCCCAAAAACATCGAAAACCATAATTATAATGTAATAGGTAAATTAACAATATAACCGGTCTAAA
196 TCCCAAAAACATCGAAAACCATAATTATAATGTAATAGGTAAATTAGCAATATAACCGGTCTAAA
* *
5563 TCTACCGGTTTTTGAGAAAACAAGTGTACAAACAGTATCGACACAAATAGAACAAGTGTCGATAC
261 TATACCGGTTTTTGAGAAAACATGTGTACAAACAGTATCGACACAAATAGAACAAGTGTCGATAC
*
5628 TTTTGGTCCAGAAAGTATTTCAGAACCAAGTGCACATAAAAGTGTCGATACATTTAAAACAAGTG
326 TTTTGGTCCAGAATGTATTTCAGAACCAAGTGCACAT-AAAGTGTCGATACATTTAAAACAAGTG
5693 TCGATCCC
390 TCGATCCC
5701 GAAAA-ATCGAAAAACATAATTATAATGTAATAGGTAAATTATTCATGTAAACGGTCTAAATATA
1 GAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTCATGTAAACGGTCTAAATATA
*
5765 CCGGTTTTTGAGAAAACAGGTGTATAAAAAGTATCGACACAAATATAACAAGTGTCGATACTTTT
66 CCGGTTTTTGAGAAAACAGGTGTACAAAAAGTATCGACACAAATATAACAAGTGTCGATACTTTT
5830 TCTCCAGAATGTATTTCAAAACCAAGTGCACTAAAAAGTGTAGATACATATATAACAAGTGTCGA
131 TCTCCAGAATGTATTTCAAAACCAAGTGCACTAAAAAGTGTAGATACATATATAACAAGTGTCGA
* *
5895 TCCCAAAAACATCGAAAACCATAATTATAATGTAATAGGTAAATTAGCAATATAGCTGGTCTAAA
196 TCCCAAAAACATCGAAAACCATAATTATAATGTAATAGGTAAATTAGCAATATAACCGGTCTAAA
* * * * * * * *
5960 TGTACCGGTTTATGAGAAAACATGTATACATGA-AGTATCGACACAAATACATCAAGTTTCGAAA
261 TATACCGGTTTTTGAGAAAACATGTGTACA-AACAGTATCGACACAAATAGAACAAGTGTCGATA
* * * * * * * * * *
6024 CATTTTTGTCCAGACTATATTTTAAAAACCAAGTGTACAACAAAATTTCGATACATTTATAACAA
325 C-TTTTGGTCCAGAATGTA-TTTCAGAACCAAGTGCAC-ATAAAGTGTCGATACATTTAAAACAA
* **
6089 TTGTTAATCCC
387 GTGTCGATCCC
* *
6100 AAAAACATCGAAAAATATAATTATAA
1 GAAAACATCGAAAAACATAATTATAA
6126 CCAAATGTCT
Statistics
Matches: 763, Mismatches: 52, Indels: 12
0.92 0.06 0.01
Matches are distributed among these distances:
396 66 0.09
397 575 0.75
398 54 0.07
399 48 0.06
400 20 0.03
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.28
Consensus pattern (397 bp):
GAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTCATGTAAACGGTCTAAATATA
CCGGTTTTTGAGAAAACAGGTGTACAAAAAGTATCGACACAAATATAACAAGTGTCGATACTTTT
TCTCCAGAATGTATTTCAAAACCAAGTGCACTAAAAAGTGTAGATACATATATAACAAGTGTCGA
TCCCAAAAACATCGAAAACCATAATTATAATGTAATAGGTAAATTAGCAATATAACCGGTCTAAA
TATACCGGTTTTTGAGAAAACATGTGTACAAACAGTATCGACACAAATAGAACAAGTGTCGATAC
TTTTGGTCCAGAATGTATTTCAGAACCAAGTGCACATAAAGTGTCGATACATTTAAAACAAGTGT
CGATCCC
Found at i:8082 original size:197 final size:194
Alignment explanation
Indices: 7836--8507 Score: 696
Period size: 197 Copynumber: 3.4 Consensus size: 194
7826 GTATCGACCC
* * ** * *
7836 CAAAAACATTGAAACAAATAATTATAATGTAATATTTAAATTAACAATGTAACCAGTATATATAT
1 CAAAAACATCGAAACCAATAATTATAATGTAATAGGTAAATTTACAATGT-ACCAGTATAAATAT
7901 ACCAGTTAATTATAAAACATGTCAACATAAAAGTATCGACACTTTTTAAGTTTGTGTCGATACTT
65 ACCAGTTAATTATAAAA-ATGTCAA-AT-AAAGTATCGACACTTTTTAAGTTTGTGTCGATACTT
* * * *
7966 TTTTCCA-AAAGAAAGCACAAAC-AGGTTCACGCATAAAGTGTCGATACATTTAAAATTGTATCG
127 TTTTCCAGAATGAAAGCACCAACGAGGTGCAAGCATAAAGTGTCGATACATTTAAAATTGTATCG
8029 ATT
192 ATT
* * * * *
8032 ACAAAAACATCGAAACCGATAATTATAATGTAATAGGTCAATTTACAATGTAACCGGTTTAAATT
1 -CAAAAACATCGAAACCAATAATTATAATGTAATAGGTAAATTTACAATGT-ACCAGTATAAATA
* **
8097 TACCGGTT--TTATGAGAAAATGGTCAGAATAAAGTAT-GACACTTGCGTAA-TTTGTGTCGATA
64 TACCAGTTAATTAT-A-AAAAT-GTCA-AATAAAGTATCGACACTT-TTTAAGTTTGTGTCGATA
* * * * *
8158 CATTTTGTCCATAATGAATGC-CCAACGAGGTGCAAGAATAACGTGTCGATACATTTAAAATTGT
124 C-TTTTTTCCAGAATGAAAGCACCAACGAGGTGCAAGCATAAAGTGTCGATACATTTAAAATTGT
8222 ATCGATCT
188 ATCGAT-T
* * * *
8230 CAAAAACATCGAAA-CAAAAATTACAATGTTATAGGTAAATTTACAATGTACCCGATATAAATAT
1 CAAAAACATCGAAACCAATAATTATAATGTAATAGGTAAATTTACAATGTACCAG-TATAAATAT
* * * * * * *
8294 ACCGATTTTATGAGAAAATAAGTCTAAATAATGTATCGACAC-CTTTATAGTTTGTGTCGATACT
65 ACC-AGTTAATTATAAAA-ATGTC-AAATAAAGTATCGACACTTTTTA-AGTTTGTGTCGATACT
*
8358 TTTTTCCAGAATGAATTAGGAATGCCCAACGAGGTGCAAGCATAAAGTGTCGATACATTTAAAAT
126 TTTTTCCAGAATGAA--A-GCA---CCAACGAGGTGCAAGCATAAAGTGTCGATACATTTAAAAT
*
8423 TGTATCGATC
185 TGTATCGATT
* * *
8433 CAAAAAACAACGAAACCAATAATTATAATGCAATAGGTAAATTTGCAATGCTACCAGTATAAATA
1 C-AAAAACATCGAAACCAATAATTATAATGTAATAGGTAAATTTACAATG-TACCAGTATAAATA
8498 TACCAGTTAA
64 TACCAGTTAA
8508 ATGCTATTTT
Statistics
Matches: 392, Mismatches: 55, Indels: 49
0.79 0.11 0.10
Matches are distributed among these distances:
195 28 0.07
196 67 0.17
197 161 0.41
198 23 0.06
199 2 0.01
200 1 0.00
203 1 0.00
204 63 0.16
205 41 0.10
206 5 0.01
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (194 bp):
CAAAAACATCGAAACCAATAATTATAATGTAATAGGTAAATTTACAATGTACCAGTATAAATATA
CCAGTTAATTATAAAAATGTCAAATAAAGTATCGACACTTTTTAAGTTTGTGTCGATACTTTTTT
CCAGAATGAAAGCACCAACGAGGTGCAAGCATAAAGTGTCGATACATTTAAAATTGTATCGATT
Found at i:8568 original size:23 final size:23
Alignment explanation
Indices: 8518--8562 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
8508 ATGCTATTTT
*
8518 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
8541 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
8563 TGTTATTGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:11200 original size:32 final size:32
Alignment explanation
Indices: 11140--11232 Score: 93
Period size: 32 Copynumber: 2.9 Consensus size: 32
11130 ATTCACGAGA
* *
11140 GGGA-TTCGTCTGGAATGCATGGCAACACCGTT
1 GGGAGTTCG-CTGGAAAGCATGGCGACACCGTT
*
11172 GGGAG-TCGCTTGGAACAGC-TGGCGACACCTTT
1 GGGAGTTCGC-TGGAA-AGCATGGCGACACCGTT
* *
11204 GGGTGTTGGCTGGAAAGCATGGCGACACC
1 GGGAGTTCGCTGGAAAGCATGGCGACACC
11233 CTTTGGTATC
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
31 4 0.08
32 42 0.82
33 5 0.10
ACGTcount: A:0.20, C:0.23, G:0.35, T:0.22
Consensus pattern (32 bp):
GGGAGTTCGCTGGAAAGCATGGCGACACCGTT
Found at i:11250 original size:32 final size:30
Alignment explanation
Indices: 11149--11264 Score: 90
Period size: 32 Copynumber: 3.7 Consensus size: 30
11139 AGGGATTCGT
* * * *
11149 CTGGAATGCATGGCAACACCGTTGGGAGTCG
1 CTGGAAAGCATGGCGACACCTTTGGTA-TCG
* *
11180 CTTGGAACAGC-TGGCGACACCTTTGGGTGTTGG
1 C-TGGAA-AGCATGGCGACACCTTT-GGT-ATCG
11213 CTGGAAAGCATGGCGACACCCTTTGGTATCG
1 CTGGAAAGCATGGCGACA-CCTTTGGTATCG
* *
11244 CATGGAAGGGATGGCGACACC
1 C-TGGAAAGCATGGCGACACC
11265 AATTGTACTG
Statistics
Matches: 68, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
31 9 0.13
32 47 0.69
33 12 0.18
ACGTcount: A:0.22, C:0.23, G:0.34, T:0.21
Consensus pattern (30 bp):
CTGGAAAGCATGGCGACACCTTTGGTATCG
Found at i:11429 original size:5 final size:5
Alignment explanation
Indices: 11419--11444 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
11409 AATTAATTAC
11419 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
11445 TATAATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:12455 original size:31 final size:32
Alignment explanation
Indices: 12411--12495 Score: 93
Period size: 31 Copynumber: 2.7 Consensus size: 32
12401 GAAAATAATT
* * *
12411 GATCGAATATTGATCCAACCCGAAAGTCAATC
1 GATCCAATATTGATCCAACCCGAAAATCAACC
** *
12443 GATCTGAT-TTGATCCGACCC-AAAATCAACC
1 GATCCAATATTGATCCAACCCGAAAATCAACC
*
12473 GATCCAATATTGACCCAACCCGA
1 GATCCAATATTGATCCAACCCGA
12496 CTTATTATAT
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
30 14 0.33
31 21 0.50
32 7 0.17
ACGTcount: A:0.35, C:0.29, G:0.14, T:0.21
Consensus pattern (32 bp):
GATCCAATATTGATCCAACCCGAAAATCAACC
Found at i:13444 original size:22 final size:22
Alignment explanation
Indices: 13416--13463 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
13406 TATATGTAAC
* *
13416 TATATGAGAACGTTATATGAGT
1 TATATGAGAACGTAATATAAGT
* *
13438 TATATGAGCATGTAATATAAGT
1 TATATGAGAACGTAATATAAGT
13460 TATA
1 TATA
13464 AGATCACGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.38
Consensus pattern (22 bp):
TATATGAGAACGTAATATAAGT
Found at i:14311 original size:22 final size:21
Alignment explanation
Indices: 14283--14346 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 21
14273 AGTCGAGGGT
*
14283 TACATAGGTCTTTCGGGACATA
1 TACATAGGTCCTTCGGGACA-A
* *
14305 TACATAGATCCTTCGAGAC-A
1 TACATAGGTCCTTCGGGACAA
14325 TACATGAGGTCCTTCGGGACAA
1 TACAT-AGGTCCTTCGGGACAA
14347 ATTTCATATG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 6 0.17
21 12 0.34
22 17 0.49
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (21 bp):
TACATAGGTCCTTCGGGACAA
Found at i:14329 original size:20 final size:21
Alignment explanation
Indices: 14304--14345 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
14294 TTCGGGACAT
14304 ATACAT-AGATCCTTCGAGAC
1 ATACATGAGATCCTTCGAGAC
* *
14324 ATACATGAGGTCCTTCGGGAC
1 ATACATGAGATCCTTCGAGAC
14345 A
1 A
14346 AATTTCATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (21 bp):
ATACATGAGATCCTTCGAGAC
Found at i:20983 original size:18 final size:18
Alignment explanation
Indices: 20962--21005 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
20952 GAAGAAACAG
20962 AAAGCAGAAAAGAATTGT
1 AAAGCAGAAAAGAATTGT
20980 AAAGCAGAAAAGAATTGT
1 AAAGCAGAAAAGAATTGT
20998 AAAGCAGA
1 AAAGCAGA
21006 GAGTCTTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.57, C:0.07, G:0.23, T:0.14
Consensus pattern (18 bp):
AAAGCAGAAAAGAATTGT
Found at i:39725 original size:33 final size:33
Alignment explanation
Indices: 39683--39745 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
39673 CCTCATTGAT
39683 ACCCGAGTCTTAAGATTCAATATGTCAATCGAG
1 ACCCGAGTCTTAAGATTCAATATGTCAATCGAG
*
39716 ACCCGAGTCTTAAGATTCAGTATGTCAATC
1 ACCCGAGTCTTAAGATTCAATATGTCAATC
39746 AAGAAGTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (33 bp):
ACCCGAGTCTTAAGATTCAATATGTCAATCGAG
Done.