Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003687.1 Hibiscus syriacus cultivar Beakdansim tig00007875_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: 79902
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:5024 original size:22 final size:22
Alignment explanation
Indices: 4992--5042 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
4982 ACCTTAGCAT
*
4992 GCTTGCTCCTATAGGAGGTATA
1 GCTTGCCCCTATAGGAGGTATA
*
5014 GCTTGCCCCTATAGGAGGTCTA
1 GCTTGCCCCTATAGGAGGTATA
5036 GCTTGCC
1 GCTTGCC
5043 ACTACCTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.18, C:0.25, G:0.27, T:0.29
Consensus pattern (22 bp):
GCTTGCCCCTATAGGAGGTATA
Found at i:9931 original size:54 final size:54
Alignment explanation
Indices: 9865--10284 Score: 491
Period size: 54 Copynumber: 7.8 Consensus size: 54
9855 AACAGTCACT
* * *
9865 AAGTGTTCATTTCTCGGAATTCATCGTATGTGGATGAATAACCGTTTCGGCACA
1 AAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACA
* ** * * * * * *
9919 AAGTGTGTATTTCACATAATTTATCCTATGGGGATGAATAAACGTTTTGGTACT
1 AAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACA
* * * *
9973 AAGTGTGTATTTCACAGAATTCATCCTATGTGGATGGAA-AACCGTTTCGGTACT
1 AAGTGTGCATTTCACGGAATTCATCCTATGTGGAT-GAATAACCGTTTCGGCACA
* * * * * * *
10027 AAGTGTACGTTTCACGGAATTCATCTTAAGTGGATGAATAACCATTTCGGTATA
1 AAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACA
* * * *
10081 AAGTGTGCATTTCACAGAATTCATCCTATGAGGATGAATAATCGTTTCGGCACC
1 AAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACA
* * * * *
10135 AAGTGTGCATTTCATGGAATTTATCCTATGTGGATGAATAACCATTTCGACACT
1 AAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACA
* *
10189 AAGTATGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCATA
1 AAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACA
* * *
10243 AAGTGTACATTTCACGGAATTCATCATATGGGGATGAATAAC
1 AAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAAC
10285 ACTAAGTACG
Statistics
Matches: 308, Mismatches: 56, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
53 3 0.01
54 302 0.98
55 3 0.01
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (54 bp):
AAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACA
Found at i:10141 original size:162 final size:162
Alignment explanation
Indices: 9861--10283 Score: 569
Period size: 162 Copynumber: 2.6 Consensus size: 162
9851 ACCAAACAGT
* * * *
9861 CACTAAGTGTTCATTTCTCGGAATTCATCGTATGTGGATGAATAACCGTTTCGGCACAAAGTGTG
1 CACTAAGTGTACATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCATAAAGTGTG
* * * * * * *
9926 TATTTCACATAATTTATCCTATGGGGATGAATAAACGTTTTGGTACTAAGTGTGTATTTCACAGA
66 CATTTCACAGAATTCATCCTATGGGGATGAATAAACGTTTCGGCACCAAGTGTGCATTTCACAGA
* *
9991 ATTCATCCTATGTGGATGGAA-AACCGTTTCGG
131 ATTCATCCTATGTGGAT-GAATAACCATTTCGA
* * * * * *
10023 TACTAAGTGTACGTTTCACGGAATTCATCTTAAGTGGATGAATAACCATTTCGGTATAAAGTGTG
1 CACTAAGTGTACATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCATAAAGTGTG
* * **
10088 CATTTCACAGAATTCATCCTATGAGGATGAATAATCGTTTCGGCACCAAGTGTGCATTTCATGGA
66 CATTTCACAGAATTCATCCTATGGGGATGAATAAACGTTTCGGCACCAAGTGTGCATTTCACAGA
*
10153 ATTTATCCTATGTGGATGAATAACCATTTCGA
131 ATTCATCCTATGTGGATGAATAACCATTTCGA
* * *
10185 CACTAAGTATGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCATAAAGTGTA
1 CACTAAGTGTACATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCATAAAGTGTG
* *
10250 CATTTCACGGAATTCATCATATGGGGATGAATAA
66 CATTTCACAGAATTCATCCTATGGGGATGAATAA
10284 CACTAAGTAC
Statistics
Matches: 225, Mismatches: 35, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
161 3 0.01
162 222 0.99
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.33
Consensus pattern (162 bp):
CACTAAGTGTACATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCATAAAGTGTG
CATTTCACAGAATTCATCCTATGGGGATGAATAAACGTTTCGGCACCAAGTGTGCATTTCACAGA
ATTCATCCTATGTGGATGAATAACCATTTCGA
Found at i:11133 original size:9 final size:9
Alignment explanation
Indices: 11119--11143 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
11109 TCCTCCATCC
11119 CTCCTCCTG
1 CTCCTCCTG
11128 CTCCTCCTG
1 CTCCTCCTG
11137 CTCCTCC
1 CTCCTCC
11144 AGTACCATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.60, G:0.08, T:0.32
Consensus pattern (9 bp):
CTCCTCCTG
Found at i:16299 original size:19 final size:19
Alignment explanation
Indices: 16256--16331 Score: 71
Period size: 19 Copynumber: 3.8 Consensus size: 19
16246 AAATGCAAAA
*
16256 ATGGTATCGATACCATAGG
1 ATGGTATCGATACCATAGT
*
16275 AAGGTATCGATACCATAGT
1 ATGGTATCGATACCATAGT
* *
16294 ATGGTAGTATCGACACCATAATT
1 AT-G--GTATCGATACCAT-AGT
*
16317 AGGGTATCGATACCA
1 ATGGTATCGATACCA
16332 GATAACATCG
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
19 18 0.39
20 12 0.26
22 13 0.28
23 3 0.07
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.26
Consensus pattern (19 bp):
ATGGTATCGATACCATAGT
Found at i:16420 original size:20 final size:21
Alignment explanation
Indices: 16371--16429 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
16361 TACTGGAAGG
* *
16371 GGGTATCGGTACCATAGTATA
1 GGGTATCGATACCATGGTATA
*
16392 GTAGTATCGATACCATGGTA-A
1 G-GGTATCGATACCATGGTATA
*
16413 GGGTATCGATACTATGG
1 GGGTATCGATACCATGG
16430 AGCCAAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
20 14 0.44
21 3 0.09
22 15 0.47
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.29
Consensus pattern (21 bp):
GGGTATCGATACCATGGTATA
Found at i:16825 original size:54 final size:54
Alignment explanation
Indices: 16732--17339 Score: 680
Period size: 54 Copynumber: 11.1 Consensus size: 54
16722 ACCAAATAGG
* * *
16732 CACTAAGTGTGCATTTCACAGAATTCATCCTATATGGATGAATAATCGTTTCGA
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
* ** * * * *
16786 AAAAAAGTGTGCATTTCACGGAATTCATCATATGGGGATGAATAACCATTTCGT
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
* * * * *
16840 CACTAAGTGTGCAATTCATGGAATTCATCCTATGTGGATGAATAACTGTTTTGG
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
* * *
16894 CACTAAGAGTGCATTTCACGCAATTCATCCTATGTATCTTATGTGGATGAATAATCGTTTCGA
1 CACTAAGTGTGCATTTCACGGAATTCAT-C-------C-TATGTGGATGAATAACCGTTTCGA
* *
16957 CACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCGG
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
* * * * * ** * *
17011 CACAAAGTGTGCATGTCGCGAAATTCATCCTATGGGGATGAATAACTATTTTGG
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
** *
17065 CACTGTGTGTGCATTTCACGGAATTCATCCTATTTGGATGAATAACCGTTTCGA
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
* * * * *
17119 CACTAAGTGTGTATTTCATGGAATTCATCCTATGTGGATGAATAATCGTTTTGG
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
* * *
17173 CA-TAAAGTGTGCATTTCATGGAATTCATCCTATGGGGATGAATAACCGTTTTGA
1 CACT-AAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
* * * *
17227 CACTAAGTGTGCATTTCAAGGAATTTATTCTATGTGGATGAATAACCATTTC-A
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
* * *
17280 GCACTAAGTGTGCATTTCACGGAATTCATCCTAAGTGGATGAATAACCATTTCGG
1 -CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
17335 CACTA
1 CACTA
17340 GGTATGGAAA
Statistics
Matches: 463, Mismatches: 78, Indels: 26
0.82 0.14 0.05
Matches are distributed among these distances:
53 2 0.00
54 411 0.89
55 3 0.01
62 2 0.00
63 45 0.10
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.33
Consensus pattern (54 bp):
CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
Found at i:16961 original size:63 final size:63
Alignment explanation
Indices: 16870--16991 Score: 185
Period size: 63 Copynumber: 1.9 Consensus size: 63
16860 GAATTCATCC
* *
16870 TATGTGGATGAATAACTGTTTTGGCACTAAGAGTGCATTTCAC-GCAATTCATCCTATGTATCT
1 TATGTGGATGAATAACTGTTTCGACACTAAGAGTGCATTTCACAG-AATTCATCCTATGTATCT
*
16933 TATGTGGATGAATAA-TCGTTTCGACACTAAGTGTGCATTTCACAGAATTCATCCTATGT
1 TATGTGGATGAATAACT-GTTTCGACACTAAGAGTGCATTTCACAGAATTCATCCTATGT
16992 GGATGAATAA
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
62 1 0.02
63 52 0.96
64 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (63 bp):
TATGTGGATGAATAACTGTTTCGACACTAAGAGTGCATTTCACAGAATTCATCCTATGTATCT
Found at i:17200 original size:162 final size:162
Alignment explanation
Indices: 16730--17336 Score: 768
Period size: 162 Copynumber: 3.7 Consensus size: 162
16720 TTACCAAATA
* * * * **
16730 GGCACTAAGTGTGCATTTCACAGAATTCATCCTATATGGATGAATAATCGTTTCGAAAAAAAGTG
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATTTGGATGAATAACCGTTTCGACACTAAGTG
* * * * *
16795 TGCATTTCACGGAATTCATCATATGGGGATGAATAACCATTTCGTCACT-AAGTGTGCAATTCAT
66 TGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCA-TAAAGTGTGCATTTCAT
*
16859 GGAATTCATCCTATGTGGATGAATAACTGTTTT
130 GGAATTCATCCTATGGGGATGAATAACTGTTTT
* * *
16892 GGCACTAAGAGTGCATTTCACGCAATTCATCCTATGTATCTTATGTGGATGAATAATCGTTTCGA
1 GGCACTAAGTGTGCATTTCACGGAATTCATCC----TA---T-T-TGGATGAATAACCGTTTCGA
* *
16957 CACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACAAAGTGTG
57 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCATAAAGTGTG
* ** * *
17022 CATGTCGCGAAATTCATCCTATGGGGATGAATAACTATTTT
122 CATTTCATGGAATTCATCCTATGGGGATGAATAACTGTTTT
**
17063 GGCACTGTGTGTGCATTTCACGGAATTCATCCTATTTGGATGAATAACCGTTTCGACACTAAGTG
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATTTGGATGAATAACCGTTTCGACACTAAGTG
* * * *
17128 TGTATTTCATGGAATTCATCCTATGTGGATGAATAATCGTTTTGGCATAAAGTGTGCATTTCATG
66 TGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCATAAAGTGTGCATTTCATG
*
17193 GAATTCATCCTATGGGGATGAATAACCGTTTT
131 GAATTCATCCTATGGGGATGAATAACTGTTTT
* * * * * *
17225 GACACTAAGTGTGCATTTCAAGGAATTTATTCTATGTGGATGAATAACCATTTC-AGCACTAAGT
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATTTGGATGAATAACCGTTTCGA-CACTAAGT
* *
17289 GTGCATTTCACGGAATTCATCCTAAGTGGATGAATAACCATTTCGGCA
65 GTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCA
17337 CTAGGTATGG
Statistics
Matches: 383, Mismatches: 51, Indels: 22
0.84 0.11 0.05
Matches are distributed among these distances:
161 1 0.00
162 238 0.62
163 1 0.00
164 1 0.00
166 2 0.01
167 2 0.01
169 1 0.00
171 137 0.36
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (162 bp):
GGCACTAAGTGTGCATTTCACGGAATTCATCCTATTTGGATGAATAACCGTTTCGACACTAAGTG
TGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCATAAAGTGTGCATTTCATG
GAATTCATCCTATGGGGATGAATAACTGTTTT
Found at i:17470 original size:2 final size:2
Alignment explanation
Indices: 17463--17492 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
17453 AAGAATAATG
17463 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
17493 GATTTCAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17897 original size:15 final size:15
Alignment explanation
Indices: 17877--17912 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
17867 CTCATGTACA
17877 AAGGGTATACGGGAG
1 AAGGGTATACGGGAG
17892 AAGGGTATACGGGAG
1 AAGGGTATACGGGAG
*
17907 ATGGGT
1 AAGGGT
17913 GTTACATATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.31, C:0.06, G:0.47, T:0.17
Consensus pattern (15 bp):
AAGGGTATACGGGAG
Found at i:42225 original size:25 final size:20
Alignment explanation
Indices: 42173--42220 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
42163 TACATCCATT
42173 AACACAAAATAAAATCATCC
1 AACACAAAATAAAATCATCC
42193 AACACAAAATAAAATCATCC
1 AACACAAAATAAAATCATCC
*
42213 AACCCAAA
1 AACACAAA
42221 TCAAACACCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.60, C:0.27, G:0.00, T:0.12
Consensus pattern (20 bp):
AACACAAAATAAAATCATCC
Found at i:54973 original size:64 final size:65
Alignment explanation
Indices: 54855--54983 Score: 183
Period size: 64 Copynumber: 2.0 Consensus size: 65
54845 CATTTTGAAG
* **
54855 GCATTTTGTGTACCGATGCACAAGCCATGCATCGATGTACTCTTGAATATTTTG-AACATCAAAT
1 GCATTTTGGGTACCGATGCACAAGCCATGCATCGATGTACTCCAGAATATTTTGAAACATCAAAT
*
54919 GCATTTTGGGTACCGATGCAC-AGACCATGCATCGATGTACTCCAGACTGA-TTTGAAACATCAA
1 GCATTTTGGGTACCGATGCACAAG-CCATGCATCGATGTACTCCAGAAT-ATTTTGAAACATCAA
54982 AT
64 AT
54984 ATAATTAATG
Statistics
Matches: 58, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
63 2 0.03
64 45 0.78
65 11 0.19
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (65 bp):
GCATTTTGGGTACCGATGCACAAGCCATGCATCGATGTACTCCAGAATATTTTGAAACATCAAAT
Found at i:60833 original size:23 final size:23
Alignment explanation
Indices: 60803--60882 Score: 101
Period size: 23 Copynumber: 3.6 Consensus size: 23
60793 ACACTAGATA
60803 GTGCATCGATGCATCCCTTGAAT
1 GTGCATCGATGCATCCCTTGAAT
* * *
60826 GTGCATCGATACA-CCATT-AAG
1 GTGCATCGATGCATCCCTTGAAT
* *
60847 GTGCATAGATGCATTCCTTGAAT
1 GTGCATCGATGCATCCCTTGAAT
60870 GTGCATCGATGCA
1 GTGCATCGATGCA
60883 CTCTGCTGTC
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
21 13 0.28
22 7 0.15
23 26 0.57
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.29
Consensus pattern (23 bp):
GTGCATCGATGCATCCCTTGAAT
Found at i:62849 original size:2 final size:2
Alignment explanation
Indices: 62842--62868 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
62832 TTGAACTTAC
62842 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
62869 TTTTTGTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:70124 original size:16 final size:16
Alignment explanation
Indices: 70100--70139 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
70090 CTAACCACTT
70100 ACCGCTAA-CTTTTCTA
1 ACCGCTAACCTTTT-TA
*
70116 ACTGCTAACCTTTTTA
1 ACCGCTAACCTTTTTA
70132 ACCGCTAA
1 ACCGCTAA
70140 TTACTAATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.28, C:0.30, G:0.07, T:0.35
Consensus pattern (16 bp):
ACCGCTAACCTTTTTA
Found at i:70327 original size:16 final size:16
Alignment explanation
Indices: 70306--70345 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
70296 ATTCTTGTTA
70306 TTTAATTTTATGCACT
1 TTTAATTTTATGCACT
*
70322 TTTAATTTTATGCATT
1 TTTAATTTTATGCACT
70338 TTTAATTT
1 TTTAATTT
70346 CTTTATTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.25, C:0.07, G:0.05, T:0.62
Consensus pattern (16 bp):
TTTAATTTTATGCACT
Found at i:79065 original size:3 final size:3
Alignment explanation
Indices: 79051--79123 Score: 71
Period size: 3 Copynumber: 24.7 Consensus size: 3
79041 TTTTTATCCA
* * * *
79051 TAT TAA TAT TAT TAT CAT TAT TAA T-T TAT TTT TAT TAT TAT TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
79097 TATT TAT ATAT TAT TAT T-T TAT TAT TA
1 TA-T TAT -TAT TAT TAT TAT TAT TAT TA
79124 AATATATTAA
Statistics
Matches: 57, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
2 5 0.09
3 46 0.81
4 6 0.11
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:79108 original size:19 final size:20
Alignment explanation
Indices: 79067--79119 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
79057 TATTATTATC
* *
79067 ATTATTAATTTATTTTTATT
1 ATTATTATTTTATTTATATT
79087 ATTATTATTTTATTTATA-T
1 ATTATTATTTTATTTATATT
79106 ATTATTATTTTATT
1 ATTATTATTTTATT
79120 ATTAAATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
ATTATTATTTTATTTATATT
Found at i:79129 original size:25 final size:25
Alignment explanation
Indices: 79082--79130 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
79072 TAATTTATTT
**
79082 TTATTATTATTATTTTATTTATATA
1 TTATTATTATTATTTTAAATATATA
79107 TTATTATT-TTATTATTAAATATAT
1 TTATTATTATTATT-TTAAATATAT
79131 TAAACACATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (25 bp):
TTATTATTATTATTTTAAATATATA
Found at i:79606 original size:6 final size:6
Alignment explanation
Indices: 79577--79609 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
79567 CGAAAAGAAA
*
79577 AGAGAA AGAGAC AGAGAC AGAGAC AGAGAC AGA
1 AGAGAC AGAGAC AGAGAC AGAGAC AGAGAC AGA
79610 CCGGAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.55, C:0.12, G:0.33, T:0.00
Consensus pattern (6 bp):
AGAGAC
Done.