Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007207.1 Hibiscus syriacus cultivar Beakdansim tig00019044_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: 94614
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Found at i:7230 original size:45 final size:46
Alignment explanation
Indices: 7179--7276 Score: 135
Period size: 45 Copynumber: 2.1 Consensus size: 46
7169 TATTTTTTGA
*
7179 TCAAAATAAGTATCTAACTTTATACGACGTGTCAACATCTTA-TGG
1 TCAAAATAAGTATCTAACTTTATACGACGTGTCAACATCCTATTGG
* * * *
7224 TCAAAATAAGTATCTCATTTTATATGATGTGTCAACATCCTATTGG
1 TCAAAATAAGTATCTAACTTTATACGACGTGTCAACATCCTATTGG
7270 TCCAAAA
1 T-CAAAA
7277 ATATTTTTCT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
45 37 0.80
46 4 0.09
47 5 0.11
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (46 bp):
TCAAAATAAGTATCTAACTTTATACGACGTGTCAACATCCTATTGG
Found at i:9903 original size:28 final size:27
Alignment explanation
Indices: 9871--9925 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
9861 TCTGTTGTAA
*
9871 TAAAAT-ATTTAATTCACTTTTTTATTTT
1 TAAAATAATTTAA-T-AATTTTTTATTTT
9899 TAAAATAATTTAATAATTTTTTATTTT
1 TAAAATAATTTAATAATTTTTTATTTT
9926 ACAGTATAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 12 0.48
28 7 0.28
29 6 0.24
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (27 bp):
TAAAATAATTTAATAATTTTTTATTTT
Found at i:10393 original size:11 final size:10
Alignment explanation
Indices: 10368--10413 Score: 56
Period size: 10 Copynumber: 4.3 Consensus size: 10
10358 CTTGTTTTTT
*
10368 TTTCTATTTG
1 TTTCTGTTTG
10378 TTTCTGTTTGG
1 TTTCTGTTT-G
10389 TTTCTGGTTCTG
1 TTTCT-GTT-TG
10401 TTTCTGTTTG
1 TTTCTGTTTG
10411 TTT
1 TTT
10414 GTCTGTGATG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
10 13 0.41
11 9 0.28
12 9 0.28
13 1 0.03
ACGTcount: A:0.02, C:0.11, G:0.20, T:0.67
Consensus pattern (10 bp):
TTTCTGTTTG
Found at i:10425 original size:23 final size:23
Alignment explanation
Indices: 10376--10425 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
10366 TTTTTCTATT
**
10376 TGTTTCTGTTTGGTTTCTGGTTC
1 TGTTTCTGTTTGGTTTCTGGTGA
*
10399 TGTTTCTGTTTGTTTGTCT-GTGA
1 TGTTTCTGTTTGGTT-TCTGGTGA
10422 TGTT
1 TGTT
10426 GGAATCCACC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 20 0.87
24 3 0.13
ACGTcount: A:0.02, C:0.10, G:0.26, T:0.62
Consensus pattern (23 bp):
TGTTTCTGTTTGGTTTCTGGTGA
Found at i:14262 original size:642 final size:642
Alignment explanation
Indices: 13035--14316 Score: 2368
Period size: 642 Copynumber: 2.0 Consensus size: 642
13025 GACGATAGCC
*
13035 TTTCACACCAGAGGTGATCCCCATAAAGATCGCCTTCTTTGCTCTTGGATCCAGCTTTGACTCCT
1 TTTCACACCAGAGGTGATCCCCATAAAGATCGCATTCTTTGCTCTTGGATCCAGCTTTGACTCCT
* * *
13100 TAACATGGTAGTATGCAGTGAAACCAAACACATGTAAGGCATCATAATCTGTAGCAGGTACTCCA
66 TAACATGGTAGTATGCAGTGAAACCAAAAACATGTAAGGCATCATAATATATAGCAGGTACTCCA
*
13165 AACCATTTCTCTAATGGTGTTTTACCACCAATAGCAGTCGGTGGTAAGCGGTTGACAAGGTGACA
131 AACCATTTCTCTAATGGTGTTTTACCACCAATAGCAGTCGATGGTAAGCGGTTGACAAGGTGACA
13230 AGCATAGACCAAAGCCTCAACCCAAAATTCTTTGCCTAACCCAGCATTAGACAACATACACCGAA
196 AGCATAGACCAAAGCCTCAACCCAAAATTCTTTGCCTAACCCAGCATTAGACAACATACACCGAA
13295 CCTTCTCCACTAATGTTCGATTCATACGCTCTGCCACCCCATTCTGTTGTGGTGTACTTCTGACA
261 CCTTCTCCACTAATGTTCGATTCATACGCTCTGCCACCCCATTCTGTTGTGGTGTACTTCTGACA
*
13360 GTGAAGTGTCTGACAATACCTTCTTCTTCACAGACTTTCAGAAATAGATCATTTTTGTACTCTCC
326 GTGAAGTGCCTGACAATACCTTCTTCTTCACAGACTTTCAGAAATAGATCATTTTTGTACTCTCC
13425 ACCAATGTATGTACGGAGACGTTTGATTTTCCTGCCTGTTTGAGTCTCCACCATCTTTTTCCATT
391 ACCAATGTATGTACGGAGACGTTTGATTTTCCTGCCTGTTTGAGTCTCCACCATCTTTTTCCATT
*
13490 TAAGGAAAAATCCTAGCACCTCATCCTTTGTCTTCATTGTATACACCAAACTCTCCGGGAAAAAT
456 TAAGGAAAAATCCTAACACCTCATCCTTTGTCTTCATTGTATACACCAAACTCTCCGGGAAAAAT
* *
13555 CATCAACAAAGGTGACATAATAGTGTGTTCCTCCCAATGAAGTTGTCTTTGAAGGCCCTCATACA
521 CATCAACAAAGGTGACATAATAGTGTGTTCCTCCCAATGAAGTTGTCTTGGAAGGCCCCCATACA
13620 TCTAAATGAACATAATCCAAAATACCTTTAGTATCATGGATTGTTGTTCCAAATTCT
586 TCTAAATGAACATAATCCAAAATACCTTTAGTATCATGGATTGTTGTTCCAAATTCT
13677 TTTCACACCAGAGGTGATCCCCATAAAGATCGCATTCTTTGCTCTTGGATCCAGCTTTGACTCCT
1 TTTCACACCAGAGGTGATCCCCATAAAGATCGCATTCTTTGCTCTTGGATCCAGCTTTGACTCCT
*
13742 TAACATGGTAGTATGCAGTGGAACCAAAAACATGTAAGGCATCATAATATATAGCAGGTACTCCA
66 TAACATGGTAGTATGCAGTGAAACCAAAAACATGTAAGGCATCATAATATATAGCAGGTACTCCA
13807 AACCATTTCTCTAATGGTGTTTTACCACCAATAGCAGTCGATGGTAAGCGGTTGACAAGGTGACA
131 AACCATTTCTCTAATGGTGTTTTACCACCAATAGCAGTCGATGGTAAGCGGTTGACAAGGTGACA
*
13872 AGCATAGACCAAAGCCTCAGCCCAAAATTCTTTGCCTAACCCAGCATTAGACAACATACACCGAA
196 AGCATAGACCAAAGCCTCAACCCAAAATTCTTTGCCTAACCCAGCATTAGACAACATACACCGAA
* *
13937 CTTTCTCCACTAATGTTCGATTCATATGCTCTGCCACCCCATTCTGTTGTGGTGTAC-TCTGACA
261 CCTTCTCCACTAATGTTCGATTCATACGCTCTGCCACCCCATTCTGTTGTGGTGTACTTCTGACA
* *
14001 GTGAAGTGCCTGACAATACCTTCTTCTTCACAGACTTTCATAAATGGATCATTTTTGTACTCTCC
326 GTGAAGTGCCTGACAATACCTTCTTCTTCACAGACTTTCAGAAATAGATCATTTTTGTACTCTCC
* * *
14066 ACCATTGTCTGTACGGAGACGTTTGATTTTCCTGCCTGTTTGAGTCTCCACTATCTTTTTCCATT
391 ACCAATGTATGTACGGAGACGTTTGATTTTCCTGCCTGTTTGAGTCTCCACCATCTTTTTCCATT
*
14131 TAAGGAAAAATCCTAACACCTCATCCTTTGTCTTCATTGTATACACCCAGACTCTCCGGGAAAAA
456 TAAGGAAAAATCCTAACACCTCATCCTTTGTCTTCATTGTATACA-CCAAACTCTCCGGGAAAAA
14196 TCATCAACAAAGGTGACATAATAGTGTGTTCCTCCCAATGAAGTTGTCTTGGAAGGCCCCCATAC
520 TCATCAACAAAGGTGACATAATAGTGTGTTCCTCCCAATGAAGTTGTCTTGGAAGGCCCCCATAC
*
14261 ATCTGAATGAACATAATCCAAAATACCTTTAGTATCATGGATTGTTGTTCCAAATT
585 ATCTAAATGAACATAATCCAAAATACCTTTAGTATCATGGATTGTTGTTCCAAATT
14317 TCACCATCGT
Statistics
Matches: 619, Mismatches: 20, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
641 175 0.28
642 444 0.72
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.30
Consensus pattern (642 bp):
TTTCACACCAGAGGTGATCCCCATAAAGATCGCATTCTTTGCTCTTGGATCCAGCTTTGACTCCT
TAACATGGTAGTATGCAGTGAAACCAAAAACATGTAAGGCATCATAATATATAGCAGGTACTCCA
AACCATTTCTCTAATGGTGTTTTACCACCAATAGCAGTCGATGGTAAGCGGTTGACAAGGTGACA
AGCATAGACCAAAGCCTCAACCCAAAATTCTTTGCCTAACCCAGCATTAGACAACATACACCGAA
CCTTCTCCACTAATGTTCGATTCATACGCTCTGCCACCCCATTCTGTTGTGGTGTACTTCTGACA
GTGAAGTGCCTGACAATACCTTCTTCTTCACAGACTTTCAGAAATAGATCATTTTTGTACTCTCC
ACCAATGTATGTACGGAGACGTTTGATTTTCCTGCCTGTTTGAGTCTCCACCATCTTTTTCCATT
TAAGGAAAAATCCTAACACCTCATCCTTTGTCTTCATTGTATACACCAAACTCTCCGGGAAAAAT
CATCAACAAAGGTGACATAATAGTGTGTTCCTCCCAATGAAGTTGTCTTGGAAGGCCCCCATACA
TCTAAATGAACATAATCCAAAATACCTTTAGTATCATGGATTGTTGTTCCAAATTCT
Found at i:31279 original size:21 final size:21
Alignment explanation
Indices: 31255--31315 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
31245 AACTTTGAAA
31255 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
31276 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
31290 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
31311 AAATG
1 AAATG
31316 TTTATTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:31293 original size:35 final size:36
Alignment explanation
Indices: 31248--31355 Score: 164
Period size: 35 Copynumber: 3.0 Consensus size: 36
31238 GGTAACCAAC
*
31248 TTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTTC
1 TTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTTA
31285 TTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTTA
1 TTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTTA
* *
31320 TTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 TTTGAAAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
31356 GTTCAAAAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 4
0.90 0.04 0.05
Matches are distributed among these distances:
35 34 0.52
36 5 0.08
37 27 0.41
ACGTcount: A:0.31, C:0.04, G:0.19, T:0.45
Consensus pattern (36 bp):
TTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTTA
Found at i:31782 original size:18 final size:17
Alignment explanation
Indices: 31750--31784 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
31740 ATGAGTGTAT
*
31750 AATTTTTATTAATAATA
1 AATTTTGATTAATAATA
31767 AATTTTGATATAATAATA
1 AATTTTGAT-TAATAATA
31785 TACAAATATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (17 bp):
AATTTTGATTAATAATA
Found at i:32194 original size:76 final size:74
Alignment explanation
Indices: 32027--32196 Score: 250
Period size: 74 Copynumber: 2.3 Consensus size: 74
32017 TACGAAACCC
* * * * *
32027 ATCAACAAACCCTTGAATTATGTTTCATTATAATATTTCTTATATATTTTAAGAATACAAGTGCA
1 ATCAACAAACCCTTGAATTACGTTTCATTATAATATTTATTAAATATTTTAAGAAAACAAATGCA
32092 TGGTCACCA
66 TGGTCACCA
* *
32101 ATCAACAAACCCTTGAATTACGTTTCCTTATAATATTTTATTAAATATTTTAAGAAAACAAATGT
1 ATCAACAAACCCTTGAATTACGTTTCATTATAATA-TTTATTAAATATTTTAAGAAAACAAATGC
32166 ATGGTCATCCA
65 ATGGTCA-CCA
*
32177 ATTAACAAACCCTTGAATTA
1 ATCAACAAACCCTTGAATTA
32197 GCAGTAAATA
Statistics
Matches: 86, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
74 33 0.38
75 31 0.36
76 22 0.26
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.36
Consensus pattern (74 bp):
ATCAACAAACCCTTGAATTACGTTTCATTATAATATTTATTAAATATTTTAAGAAAACAAATGCA
TGGTCACCA
Found at i:42258 original size:7 final size:7
Alignment explanation
Indices: 42130--42268 Score: 134
Period size: 8 Copynumber: 17.7 Consensus size: 7
42120 CGTGTGTCTG
42130 TATATAT
1 TATATAT
42137 ATATATAT
1 -TATATAT
42145 ATATATAT
1 -TATATAT
42153 ATATATAT
1 -TATATAT
42161 ATATATAT
1 -TATATAT
42169 ATATATAT
1 -TATATAT
42177 ATATATAT
1 -TATATAT
42185 ATATATAT
1 -TATATAT
42193 ATATATAT
1 -TATATAT
42201 ATATATAT
1 -TATATAT
42209 ATATATAT
1 -TATATAT
42217 ATATATAT
1 -TATATAT
42225 ATATATAT
1 -TATATAT
42233 ATATATAT
1 -TATATAT
42241 ATATATAT
1 -TATATAT
*
42249 TATATTT
1 TATATAT
42256 TATATAAT
1 TATAT-AT
42264 TATAT
1 TATAT
42269 GGTTATATTG
Statistics
Matches: 128, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
7 11 0.09
8 117 0.91
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
TATATAT
Found at i:42261 original size:2 final size:2
Alignment explanation
Indices: 42130--42253 Score: 241
Period size: 2 Copynumber: 62.5 Consensus size: 2
42120 CGTGTGTCTG
42130 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42172 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42214 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
42254 TTTATATAAT
Statistics
Matches: 121, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 120 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:42274 original size:16 final size:16
Alignment explanation
Indices: 42132--42276 Score: 103
Period size: 18 Copynumber: 8.3 Consensus size: 16
42122 TGTGTCTGTA
*
42132 TATATATATATATATAT
1 TATATATAT-TATATGT
*
42149 ATATATATATATATATAT
1 -TATATATAT-TATATGT
*
42167 ATATATATATATATATAT
1 -TATATATAT-TATATGT
*
42185 ATATATATATATATATAT
1 -TATATATAT-TATATGT
*
42203 ATATATATATATATATAT
1 -TATATATAT-TATATGT
*
42221 ATATATATATATATATAT
1 -TATATATAT-TATATGT
*
42239 ATATATATATTATATTT
1 -TATATATATTATATGT
42256 TATATA-ATTATATGGT
1 TATATATATTATAT-GT
42272 TATAT
1 TATAT
42277 TGTGATATAT
Statistics
Matches: 124, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
15 7 0.06
16 12 0.10
17 6 0.05
18 99 0.80
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (16 bp):
TATATATATTATATGT
Found at i:47759 original size:64 final size:64
Alignment explanation
Indices: 47691--47811 Score: 172
Period size: 64 Copynumber: 1.9 Consensus size: 64
47681 ATTGTTCAAG
* * * *
47691 GTGTATCGATGCACATG-AGGTGTATCGATGCACTCCTTTAAAATAAAAACATCGAATGTCATTA
1 GTGTATCGATGCACAAGTA-GTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGTCATTA
* *
47755 GTGTATCGATGCACAAGTAGTGCATTGATGCACCCCCTTAAAATACAAACATCGAAT
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAAT
47812 ATGATTTATG
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
64 49 0.98
65 1 0.02
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (64 bp):
GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGTCATTA
Found at i:47829 original size:64 final size:64
Alignment explanation
Indices: 47691--47853 Score: 170
Period size: 64 Copynumber: 2.5 Consensus size: 64
47681 ATTGTTCAAG
* * * * * * *
47691 GTGTATCGATGCACATGAG-GTGTATCGATGCACTCCTTTAAAATAAAAACATCGAATGTCATTA
1 GTGTACCGATGCACA-GAGTATGCATTGATGCACCCCCTTAAAATAAAAACATCGAATATCATTA
* * *
47755 GTGTATCGATGCACA-AGTAGTGCATTGATGCACCCCCTTAAAATACAAACATCGAATATGATTT
1 GTGTACCGATGCACAGAGTA-TGCATTGATGCACCCCCTTAAAATAAAAACATCGAATATCA-TT
47819 A
64 A
* *
47820 -TGTACCGATGCATAGATTATGCATTGATGCACCC
1 GTGTACCGATGCACAGAGTATGCATTGATGCACCC
47854 GTCAAGGGAT
Statistics
Matches: 84, Mismatches: 11, Indels: 8
0.82 0.11 0.08
Matches are distributed among these distances:
62 2 0.02
64 76 0.90
65 6 0.07
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (64 bp):
GTGTACCGATGCACAGAGTATGCATTGATGCACCCCCTTAAAATAAAAACATCGAATATCATTA
Found at i:48448 original size:18 final size:18
Alignment explanation
Indices: 48425--48497 Score: 101
Period size: 18 Copynumber: 3.9 Consensus size: 18
48415 AGGGATTATC
48425 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
48443 AGTGGTTCTTCGGAACAATT
1 AGTGGTCCTTCGGGAC-A-T
*
48463 AGTGGTCCTTCGAGACAT
1 AGTGGTCCTTCGGGACAT
48481 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
48498 AATATTCAGT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
18 31 0.66
19 2 0.04
20 14 0.30
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:48480 original size:38 final size:38
Alignment explanation
Indices: 48425--48498 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
48415 AGGGATTATC
* *
48425 AGTGGTCCTTCGGGACATAGTGGTTCTTCGGAACAATT
1 AGTGGTCCTTCGAGACATAGTGGTCCTTCGGAACAATT
*
48463 AGTGGTCCTTCGAGACATAGTGGTCCTTCGGGACAA
1 AGTGGTCCTTCGAGACATAGTGGTCCTTCGGAACAA
48499 ATATTCAGTG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (38 bp):
AGTGGTCCTTCGAGACATAGTGGTCCTTCGGAACAATT
Found at i:50885 original size:21 final size:21
Alignment explanation
Indices: 50843--50885 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
50833 TTTCTGGGCT
* *
50843 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
50864 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
50885 A
1 A
50886 CGAATATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:50937 original size:20 final size:20
Alignment explanation
Indices: 50912--50949 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
50902 GAATGCTAGA
*
50912 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
50932 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
50950 TATAAAAAAA
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:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:51624 original size:23 final size:23
Alignment explanation
Indices: 51580--51624 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
51570 ATTATTATAT
*
51580 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
51603 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
51625 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:57702 original size:21 final size:21
Alignment explanation
Indices: 57660--57702 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
57650 TTTCTGGGCT
* *
57660 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
57681 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
57702 A
1 A
57703 CGAATATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:58440 original size:23 final size:23
Alignment explanation
Indices: 58396--58440 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
58386 ATTATTATAT
*
58396 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
58419 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
58441 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:59221 original size:6 final size:6
Alignment explanation
Indices: 59206--59246 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
59196 GGCTACCCAG
* *
59206 AGAGGA AGAGGT AGAGCT AGAGGT AGAGGT AGAGGT AGAGG
1 AGAGGT AGAGGT AGAGGT AGAGGT AGAGGT AGAGGT AGAGG
59247 AAGAAGTTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.37, C:0.02, G:0.49, T:0.12
Consensus pattern (6 bp):
AGAGGT
Found at i:59233 original size:18 final size:18
Alignment explanation
Indices: 59206--59250 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
59196 GGCTACCCAG
59206 AGAGGAAGAGGTAGAGCT
1 AGAGGAAGAGGTAGAGCT
* *
59224 AGAGGTAGAGGTAGAGGT
1 AGAGGAAGAGGTAGAGCT
59242 AGAGGAAGA
1 AGAGGAAGA
59251 AGTTAGTCAG
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:0.40, C:0.02, G:0.47, T:0.11
Consensus pattern (18 bp):
AGAGGAAGAGGTAGAGCT
Found at i:60383 original size:13 final size:13
Alignment explanation
Indices: 60354--60394 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
60344 ATTTGGATCG
*
60354 ATTCATT-ATGGT
1 ATTCATTGATGAT
60366 ATTCATTGATGAT
1 ATTCATTGATGAT
60379 ATTCATTGATGAT
1 ATTCATTGATGAT
60392 ATT
1 ATT
60395 TTAGTGTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
12 7 0.26
13 20 0.74
ACGTcount: A:0.29, C:0.07, G:0.15, T:0.49
Consensus pattern (13 bp):
ATTCATTGATGAT
Found at i:63080 original size:64 final size:64
Alignment explanation
Indices: 62945--63084 Score: 149
Period size: 64 Copynumber: 2.2 Consensus size: 64
62935 CATGAGGTAT
* * * * *
62945 ATCGATGCACTCCTTTAAAATAAAAACATCGAATGTCATTAGTGTATCGATACATAAGTAGTGC
1 ATCGATGCACCCCCTTAAAATAAAAACATCGAATGGCATTAGTGTACCAATACATAAGTAGTGC
* * * * * *
63009 ATTGATGCACCCCCTTAAAATACAAACATCGAATGGGATTTA-TGTACCAATGCAT-AGATTGTT
1 ATCGATGCACCCCCTTAAAATAAAAACATCGAATGGCA-TTAGTGTACCAATACATAAG-TAGTG
63072 C
64 C
63073 ATCGATGCACCC
1 ATCGATGCACCC
63085 GTCAAGGGAT
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
63 2 0.03
64 57 0.92
65 3 0.05
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.29
Consensus pattern (64 bp):
ATCGATGCACCCCCTTAAAATAAAAACATCGAATGGCATTAGTGTACCAATACATAAGTAGTGC
Found at i:63679 original size:18 final size:18
Alignment explanation
Indices: 63656--63726 Score: 79
Period size: 18 Copynumber: 3.8 Consensus size: 18
63646 AGGGATTATC
63656 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* * *
63674 AGTGGTTCTTCAGAACAAT
1 AGTGGTCCTTCGGGAC-AT
*
63693 CAGTTGTCCTTCGGGACAT
1 -AGTGGTCCTTCGGGACAT
*
63712 AGTTGTCCTTCGGGA
1 AGTGGTCCTTCGGGA
63727 TAAATATTCA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
18 28 0.64
19 4 0.09
20 12 0.27
ACGTcount: A:0.20, C:0.21, G:0.28, T:0.31
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:70852 original size:2 final size:2
Alignment explanation
Indices: 70845--70869 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
70835 AATCAATGTG
70845 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 T
70870 TCTAATTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:87707 original size:31 final size:31
Alignment explanation
Indices: 87672--87733 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
87662 TTAATCTTAT
87672 TTTGATAATTCATCGTAAAAATATTAATGAC
1 TTTGATAATTCATCGTAAAAATATTAATGAC
87703 TTTGATAATTCATCGTAAAAATATTAATGAC
1 TTTGATAATTCATCGTAAAAATATTAATGAC
87734 GAAGGTTGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.39
Consensus pattern (31 bp):
TTTGATAATTCATCGTAAAAATATTAATGAC
Done.