Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003670.1 Hibiscus syriacus cultivar Beakdansim tig00007843_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: 52201
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:2101 original size:43 final size:43
Alignment explanation
Indices: 2053--2569 Score: 502
Period size: 43 Copynumber: 12.2 Consensus size: 43
2043 GAAAGGTTAA
* *
2053 CGGCGTTTGTATCCAAAAACGCTTCTATAGATATGACTTTTTG
1 CGGCGTTTGTATCCAAAAACGCTGCTATAGATATGACCTTTTG
* * *
2096 CGGCGTTTGT-TCCAAAAACACAGTTATAGATATGACCTTTTG
1 CGGCGTTTGTATCCAAAAACGCTGCTATAGATATGACCTTTTG
* * *
2138 CGGCGTTTGTATCCAAAAGCGCCGCTATAGATATGACTTTTTTG
1 CGGCGTTTGTATCCAAAAACGCTGCTATAGATATGAC-CTTTTG
* * *
2182 TGGCGTTTGTATCCAAAAATGCCGCTATAGATATGACCTTTTG
1 CGGCGTTTGTATCCAAAAACGCTGCTATAGATATGACCTTTTG
* * * ** * *
2225 CGGCGTTTGTTTCAAAAAATGCCACTATAGATCTCGACCTTTTA
1 CGGCGTTTGTATCCAAAAACGCTGCTATAGATAT-GACCTTTTG
* *
2269 CGGCGTTTAT-TACAAAAACG-TCGCTATAGATATGACCTTTTG
1 CGGCGTTTGTATCCAAAAACGCT-GCTATAGATATGACCTTTTG
* * * *
2311 TGGCGTTTGTATCCAAAAACGCTGGTGTAGATATGACTTTTTG
1 CGGCGTTTGTATCCAAAAACGCTGCTATAGATATGACCTTTTG
** * ***
2354 CGGTATTTGT-TCCAAAAACACAATTATAGATATGACCTTTTG
1 CGGCGTTTGTATCCAAAAACGCTGCTATAGATATGACCTTTTG
* *
2396 CGGCGTTTGTATCCAAAAATG-TCGCTATAGATATGACTTTTTG
1 CGGCGTTTGTATCCAAAAACGCT-GCTATAGATATGACCTTTTG
* *
2439 CGGCTTTTGTATCCAAAAACGC--C----GCTATGACCTTTTG
1 CGGCGTTTGTATCCAAAAACGCTGCTATAGATATGACCTTTTG
* * *
2476 CGGCGTTTGT-TCTAAAAACGCTGCTATAGATATCGACATTTAG
1 CGGCGTTTGTATCCAAAAACGCTGCTATAGATAT-GACCTTTTG
* * * * * *
2519 TGGCGTTTGT-TTCAAAAACGCCGCTATAGATCTTGACCTATGG
1 CGGCGTTTGTATCCAAAAACGCTGCTATAGAT-ATGACCTTTTG
2562 CGGCGTTT
1 CGGCGTTT
2570 TTTGTTCTCA
Statistics
Matches: 388, Mismatches: 69, Indels: 34
0.79 0.14 0.07
Matches are distributed among these distances:
36 10 0.03
37 21 0.05
38 1 0.00
41 1 0.00
42 91 0.23
43 206 0.53
44 58 0.15
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (43 bp):
CGGCGTTTGTATCCAAAAACGCTGCTATAGATATGACCTTTTG
Found at i:2401 original size:85 final size:85
Alignment explanation
Indices: 2053--2569 Score: 539
Period size: 85 Copynumber: 6.1 Consensus size: 85
2043 GAAAGGTTAA
*
2053 CGGCGTTTGTATCCAAAAACGCTTCTATAGATATGACTTTTTGCGGCGTTTGTTCCAAAAACACA
1 CGGCGTTTGTATCCAAAAACGCTGCTATAGATATGACTTTTTGCGGCGTTTGTTCCAAAAACACA
*
2118 GTTATAGATATGACCTTTTG
66 GCTATAGATATGACCTTTTG
* * * **
2138 CGGCGTTTGTATCCAAAAGCGCCGCTATAGATATGACTTTTTTGTGGCGTTTGTATCCAAAAATG
1 CGGCGTTTGTATCCAAAAACGCTGCTATAGATATGAC-TTTTTGCGGCGTTTGT-TCCAAAAACA
*
2203 CCGCTATAGATATGACCTTTTG
64 CAGCTATAGATATGACCTTTTG
* * * ** * * * * * *
2225 CGGCGTTTGTTTCAAAAAATGCCACTATAGATCTCGACCTTTTACGGCGTTTATTACAAAAACGT
1 CGGCGTTTGTATCCAAAAACGCTGCTATAGATAT-GACTTTTTGCGGCGTTTGTTCCAAAAAC-A
2290 C-GCTATAGATATGACCTTTTG
64 CAGCTATAGATATGACCTTTTG
* * * **
2311 TGGCGTTTGTATCCAAAAACGCTGGTGTAGATATGACTTTTTGCGGTATTTGTTCCAAAAACACA
1 CGGCGTTTGTATCCAAAAACGCTGCTATAGATATGACTTTTTGCGGCGTTTGTTCCAAAAACACA
**
2376 ATTATAGATATGACCTTTTG
66 GCTATAGATATGACCTTTTG
* *
2396 CGGCGTTTGTATCCAAAAATG-TCGCTATAGATATGACTTTTTGCGGCTTTTGTATCC-AAAA-A
1 CGGCGTTTGTATCCAAAAACGCT-GCTATAGATATGACTTTTTGCGGCGTTTGT-TCCAAAAACA
* *
2458 C-GC---CGCTATGACCTTTTG
64 CAGCTATAGATATGACCTTTTG
* * * * * *
2476 CGGCGTTTGT-TCTAAAAACGCTGCTATAGATATCGACATTTAGTGGCGTTTGTTTCAAAAACGC
1 CGGCGTTTGTATCCAAAAACGCTGCTATAGATAT-GACTTTTTGCGGCGTTTGTTCCAAAAACAC
* * * *
2540 CGCTATAGATCTTGACCTATGG
65 AGCTATAGAT-ATGACCTTTTG
2562 CGGCGTTT
1 CGGCGTTT
2570 TTTGTTCTCA
Statistics
Matches: 354, Mismatches: 62, Indels: 31
0.79 0.14 0.07
Matches are distributed among these distances:
79 21 0.06
80 43 0.12
81 1 0.00
82 2 0.01
84 4 0.01
85 125 0.35
86 86 0.24
87 69 0.19
88 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (85 bp):
CGGCGTTTGTATCCAAAAACGCTGCTATAGATATGACTTTTTGCGGCGTTTGTTCCAAAAACACA
GCTATAGATATGACCTTTTG
Found at i:15811 original size:17 final size:17
Alignment explanation
Indices: 15780--15829 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 17
15770 TATAAATTAT
*
15780 TAAAATAAATA-AAAAA
1 TAAAATATATATAAAAA
15796 TAAAGATATA-AT-AAAA
1 TAAA-ATATATATAAAAA
15812 TAAAATATATATAAAAA
1 TAAAATATATATAAAAA
15829 T
1 T
15830 TAACAACGGC
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 5 0.17
16 15 0.52
17 9 0.31
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (17 bp):
TAAAATATATATAAAAA
Found at i:16623 original size:23 final size:23
Alignment explanation
Indices: 16597--16646 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
16587 TTTGTAAAAT
16597 GTTTATCGT-TATCTTTATGACAC
1 GTTTATC-TCTATCTTTATGACAC
* *
16620 GTTTATCTCTGTCTTTGTGACAC
1 GTTTATCTCTATCTTTATGACAC
16643 GTTT
1 GTTT
16647 TTCTTTGTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 1 0.04
23 23 0.96
ACGTcount: A:0.16, C:0.18, G:0.16, T:0.50
Consensus pattern (23 bp):
GTTTATCTCTATCTTTATGACAC
Found at i:16655 original size:23 final size:23
Alignment explanation
Indices: 16608--16658 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
16598 TTTATCGTTA
16608 TCTTTATGACACGTTTATCTCTG
1 TCTTTATGACACGTTTATCTCTG
* * *
16631 TCTTTGTGACACGTTTTTCTTTG
1 TCTTTATGACACGTTTATCTCTG
16654 TCTTT
1 TCTTT
16659 TAGTAGTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.12, C:0.20, G:0.14, T:0.55
Consensus pattern (23 bp):
TCTTTATGACACGTTTATCTCTG
Found at i:20457 original size:154 final size:154
Alignment explanation
Indices: 20218--20531 Score: 540
Period size: 154 Copynumber: 2.0 Consensus size: 154
20208 ATTACTCAAA
* *
20218 ATGACTATGTTATATGACAAAGATGAACTGAATGGAAGTATTGTACGCATCTGAATCATTGAAAC
1 ATGACTATATTATATGACAAAGATGAACTGAATGGAAGTATTGTACGCATATGAATCATTGAAAC
* *
20283 TACCGAATTACTCAGGAAACT-TCGAAATGACTGGGATAAACTTGAATACTAAATGACCTAAGTG
66 GACCGAATTACTCAGGAAACTCT-GAAATGACCGGGATAAACTTGAATACTAAATGACCTAAGTG
20347 CCCTCTATGACCTAGAATTAAGTGG
130 CCCTCTATGACCTAGAATTAAGTGG
* * *
20372 ATGACTATATTATATGACAAATATGAACTGAATGGAAGTATTGTACGTATATGAATCGTTGAAAC
1 ATGACTATATTATATGACAAAGATGAACTGAATGGAAGTATTGTACGCATATGAATCATTGAAAC
*
20437 GACCGAATTACTTAGGAAACTCTGAAATGACCGGGATAAACTTGAATACTAAATGACCTAAGTGC
66 GACCGAATTACTCAGGAAACTCTGAAATGACCGGGATAAACTTGAATACTAAATGACCTAAGTGC
20502 CCTCTATGACCTAGAATTAAGTGG
131 CCTCTATGACCTAGAATTAAGTGG
20526 ATGACT
1 ATGACT
20532 TGGATAAGTC
Statistics
Matches: 151, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
154 150 0.99
155 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (154 bp):
ATGACTATATTATATGACAAAGATGAACTGAATGGAAGTATTGTACGCATATGAATCATTGAAAC
GACCGAATTACTCAGGAAACTCTGAAATGACCGGGATAAACTTGAATACTAAATGACCTAAGTGC
CCTCTATGACCTAGAATTAAGTGG
Found at i:24688 original size:13 final size:13
Alignment explanation
Indices: 24670--24702 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
24660 TTGATTTGGG
24670 GTTCCTGTAAACT
1 GTTCCTGTAAACT
24683 GTTCCTGTAAACT
1 GTTCCTGTAAACT
*
24696 GTCCCTG
1 GTTCCTG
24703 AATTGATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.36
Consensus pattern (13 bp):
GTTCCTGTAAACT
Found at i:25004 original size:40 final size:40
Alignment explanation
Indices: 24949--25026 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 40
24939 TATGTGGAAT
*
24949 TATGGGACTGAACAATAG-TTGTACTTCATCATCAAATTCA
1 TATGGGACTGAACAATAGCTT-AACTTCATCATCAAATTCA
* *
24989 TATGGGATTGAACAATAGCTTAACTTCATCTTCAAATT
1 TATGGGACTGAACAATAGCTTAACTTCATCATCAAATT
25027 TATACTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 32 0.94
41 2 0.06
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.35
Consensus pattern (40 bp):
TATGGGACTGAACAATAGCTTAACTTCATCATCAAATTCA
Found at i:26319 original size:16 final size:17
Alignment explanation
Indices: 26298--26348 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
26288 AGATCTTTAA
26298 ATTTTAATT-TATTTTT
1 ATTTTAATTATATTTTT
* *
26314 ATTTTATTCTCTATTTTT
1 ATTTTAAT-TATATTTTT
26332 ATTATTAATTATATTTT
1 ATT-TTAATTATATTTT
26349 ATCTTCTTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 7 0.24
17 1 0.03
18 17 0.59
19 4 0.14
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (17 bp):
ATTTTAATTATATTTTT
Found at i:27349 original size:42 final size:42
Alignment explanation
Indices: 27254--27392 Score: 181
Period size: 42 Copynumber: 3.3 Consensus size: 42
27244 ATTTTTATTT
* * * *
27254 ACAAACACCGCTATTTATCTTGTCTTTAGTGGCATTTTTTGTC
1 ACAAACGCCGCTAATTCTCTTGTCTTTAGTGGCA-TTTTTGCC
* * *
27297 ACAAATGCCGCTAATTCTCTTATCTTTAGTGGCATTTTTACC
1 ACAAACGCCGCTAATTCTCTTGTCTTTAGTGGCATTTTTGCC
*
27339 ACAAACGCCGCTAATTCGCTTGTCTTTAGTGGC-TTTTTGCC
1 ACAAACGCCGCTAATTCTCTTGTCTTTAGTGGCATTTTTGCC
*
27380 GCAAACGCCGCTA
1 ACAAACGCCGCTA
27393 TGCTATTGGT
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
41 19 0.23
42 36 0.43
43 29 0.35
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.37
Consensus pattern (42 bp):
ACAAACGCCGCTAATTCTCTTGTCTTTAGTGGCATTTTTGCC
Found at i:29809 original size:14 final size:14
Alignment explanation
Indices: 29792--29824 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
29782 ATTTTTATGT
*
29792 AGGGAATTATTTGC
1 AGGGAATTATTTAC
29806 AGGGAATTATTTAC
1 AGGGAATTATTTAC
29820 AGGGA
1 AGGGA
29825 TTACTCCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.30, T:0.30
Consensus pattern (14 bp):
AGGGAATTATTTAC
Found at i:32917 original size:42 final size:42
Alignment explanation
Indices: 32739--32918 Score: 102
Period size: 42 Copynumber: 4.3 Consensus size: 42
32729 TGTCACTTTG
* ** * *
32739 TTGCGGTGTTTGTTGAAAAAACGCCACTATAGATGA--ACCCTA
1 TTGCGGCGTTTGTTGAAAAAATACCACTA-AAAT-ACTACTCTA
* ** * * * *
32781 TTACGGCGTTTG-T-ATAAAAATACTGCTAAAGTACTATTATG
1 TTGCGGCGTTTGTTGA-AAAAATACCACTAAAATACTACTCTA
* * *
32822 TTGCGGCATTTGTTGAAACAATGCCACTAAAATACTACTCTA
1 TTGCGGCGTTTGTTGAAAAAATACCACTAAAATACTACTCTA
* ** *
32864 TTACGATGTTTGTTGAAAAAATACCACTATAAATGA-T-GTCTA
1 TTGCGGCGTTTGTTGAAAAAATACCACTA-AAAT-ACTACTCTA
32906 TTGCGGCGTTTGT
1 TTGCGGCGTTTGT
32919 ATAAAAACGC
Statistics
Matches: 99, Mismatches: 32, Indels: 14
0.68 0.22 0.10
Matches are distributed among these distances:
39 1 0.01
40 3 0.03
41 22 0.22
42 66 0.67
43 6 0.06
44 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (42 bp):
TTGCGGCGTTTGTTGAAAAAATACCACTAAAATACTACTCTA
Found at i:32935 original size:83 final size:83
Alignment explanation
Indices: 32822--33092 Score: 249
Period size: 83 Copynumber: 3.3 Consensus size: 83
32812 TACTATTATG
* * * *
32822 TTGCGGCATTTGT-TGAAACAATGCCACTAAAATACTACTCTATTACGATGTTTGTTGAAAAAAT
1 TTGCGGCGTTTGTAT-AAA-AACGCCACTAAAGTACTACTCTATTGCGATGTTTGTTGAAAAAAT
* ***
32886 ACCACTATAAATGATGTCTA
64 ACCACTATAGATGAACCCTA
* * * * * * * *
32906 TTGCGGCGTTTGTATAAAAACGCCGCTAAAGTAGTAATATATTGCTG-CGTTTATTGTAAAAATG
1 TTGCGGCGTTTGTATAAAAACGCCACTAAAGTACTACTCTATTGC-GATGTTTGTTGAAAAAATA
*
32970 CCACTATAGATAAACCCTA
65 CCACTATAGATGAACCCTA
* ** * * *
32989 TTACGATGTTTGTATAAAAACGTCATTAAAGTACTACTCTATTGCGATGTTTGTTGAAAAAACAC
1 TTGCGGCGTTTGTATAAAAACGCCACTAAAGTACTACTCTATTGCGATGTTTGTTGAAAAAATAC
*
33054 CATTATAGATGAACCCTA
66 CACTATAGATGAACCCTA
****
33072 TTATATCGTTTGTATAAAAAC
1 TTGCGGCGTTTGTATAAAAAC
33093 ATCGCTAAAT
Statistics
Matches: 147, Mismatches: 37, Indels: 7
0.77 0.19 0.04
Matches are distributed among these distances:
82 1 0.01
83 129 0.88
84 16 0.11
85 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (83 bp):
TTGCGGCGTTTGTATAAAAACGCCACTAAAGTACTACTCTATTGCGATGTTTGTTGAAAAAATAC
CACTATAGATGAACCCTA
Found at i:33008 original size:41 final size:41
Alignment explanation
Indices: 32962--33092 Score: 115
Period size: 41 Copynumber: 3.2 Consensus size: 41
32952 GCGTTTATTG
* *
32962 TAAAAATGCCACTATAGATAAACCCTATTACGATGTTTGTA
1 TAAAAACGCCATTATAGATAAACCCTATTACGATGTTTGTA
* * * * *
33003 TAAAAACGTCATTAAAG-TACTACTCTATTGCGATGTTTGT-
1 TAAAAACGCCATTATAGATA-AACCCTATTACGATGTTTGTA
* * *
33043 TGAAAAAACACCATTATAGATGAACCCTATTA-TATCGTTTGTA
1 T--AAAAACGCCATTATAGATAAACCCTATTACGAT-GTTTGTA
33086 TAAAAAC
1 TAAAAAC
33093 ATCGCTAAAT
Statistics
Matches: 69, Mismatches: 15, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
40 3 0.04
41 38 0.55
42 26 0.38
43 2 0.03
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (41 bp):
TAAAAACGCCATTATAGATAAACCCTATTACGATGTTTGTA
Found at i:33008 original size:125 final size:125
Alignment explanation
Indices: 32745--33001 Score: 311
Period size: 125 Copynumber: 2.1 Consensus size: 125
32735 TTTGTTGCGG
** * *** * *
32745 TGTTTGTTGAAAAAACGCCACTATAGATGAACCCTATTACGGCGTTTGTATAAAAATACTGCTAA
1 TGTTTGTTGAAAAAATACCACTATAAATGATGTCTATTACGGCGTTTGTATAAAAACACCGCTAA
* * * * *
32810 AGTACTATTATGTTGCGGCATTTGTTGAAACAATGCCACTAAAATACTACTCTATTACGA
66 AGTACTAATATATTGCGGCATTTATTGAAACAATGCCACTAAAATACAACCCTATTACGA
* *
32870 TGTTTGTTGAAAAAATACCACTATAAATGATGTCTATTGCGGCGTTTGTATAAAAACGCCGCTAA
1 TGTTTGTTGAAAAAATACCACTATAAATGATGTCTATTACGGCGTTTGTATAAAAACACCGCTAA
* * * *
32935 AGTAGTAATATATTGCTGCGTTTATTGTAAA-AATGCCACTATAGATA-AACCCTATTACGA
66 AGTACTAATATATTGCGGCATTTATTG-AAACAATGCCACTA-AAATACAACCCTATTACGA
32995 TGTTTGT
1 TGTTTGT
33002 ATAAAAACGT
Statistics
Matches: 111, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
125 104 0.94
126 7 0.06
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (125 bp):
TGTTTGTTGAAAAAATACCACTATAAATGATGTCTATTACGGCGTTTGTATAAAAACACCGCTAA
AGTACTAATATATTGCGGCATTTATTGAAACAATGCCACTAAAATACAACCCTATTACGA
Found at i:37698 original size:23 final size:23
Alignment explanation
Indices: 37670--37733 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
37660 CAGCTCATAT
*
37670 AAATGCACCGAAGTGCCGCGTAA
1 AAATGCACCGAAGTGCCACGTAA
* *
37693 AAATGCACCGTAGTGCCACGTAG
1 AAATGCACCGAAGTGCCACGTAA
* *
37716 AATTGCACCAAAGTGCCA
1 AAATGCACCGAAGTGCCA
37734 TATAAAATGT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.34, C:0.27, G:0.23, T:0.16
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACGTAA
Found at i:40598 original size:18 final size:18
Alignment explanation
Indices: 40564--40605 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
40554 TAGAAGCATG
40564 AGAAAAGAAAACAAAAAA
1 AGAAAAGAAAACAAAAAA
*
40582 AGAAGAGAAAA-AGAAAAA
1 AGAAAAGAAAACA-AAAAA
*
40600 GGAAAA
1 AGAAAA
40606 AAAGATAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 1 0.05
18 19 0.95
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (18 bp):
AGAAAAGAAAACAAAAAA
Found at i:44315 original size:128 final size:128
Alignment explanation
Indices: 44152--44390 Score: 354
Period size: 128 Copynumber: 1.9 Consensus size: 128
44142 GAAGCAGATC
* * * *
44152 CTTTTTTAAATTTAACCTTCTTAAAGTTTTAGTGAAATAAATTAACGCAGATTCAACCTTCCCTG
1 CTTTTTTAAATTTAACCTTATTAAAGTTGTAGTGAAATAAATAAACACAGATTCAACCTTCCCTG
* * *
44217 AAGATGCAGTAGAGTGAATCATAGTTTT-TCGATCTAATCTTCTTAAAAAGAAGTGAAGTTGAT
66 AAGATGCAGTAGAGTGAATCA-AATTTTCTCAATCTAACCTTCTTAAAAAGAAGTGAAGTTGAT
* * * *
44280 CTTTTTTAGATTTAACCTTATTGAAGTTGTAGTGAAATAAATAAATACATATTCAACCTTCCCTG
1 CTTTTTTAAATTTAACCTTATTAAAGTTGTAGTGAAATAAATAAACACAGATTCAACCTTCCCTG
*
44345 AAGATGCAGTGGAGTGAATCAAATTTTCTCAATCTAACCTTCTTAA
66 AAGATGCAGTAGAGTGAATCAAATTTTCTCAATCTAACCTTCTTAA
44391 TGTTACAAAG
Statistics
Matches: 98, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
127 5 0.05
128 93 0.95
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (128 bp):
CTTTTTTAAATTTAACCTTATTAAAGTTGTAGTGAAATAAATAAACACAGATTCAACCTTCCCTG
AAGATGCAGTAGAGTGAATCAAATTTTCTCAATCTAACCTTCTTAAAAAGAAGTGAAGTTGAT
Found at i:50385 original size:36 final size:36
Alignment explanation
Indices: 50283--50385 Score: 92
Period size: 36 Copynumber: 2.9 Consensus size: 36
50273 CAAGAACAAT
* *
50283 ATGTTCAAAGTTTGGCCACCTACCAA-GAATTTTCCA
1 ATGTTCAAAGTTTGGCCACCAACCAATGAA-ATTCCA
* *
50319 ATGTGT-ACAAG-TTAGCCACCAA--TATGAAATT-CA
1 ATGT-TCA-AAGTTTGGCCACCAACCAATGAAATTCCA
50352 CATGTTCAAAGTTTGGCCACCAACCAATGAAATT
1 -ATGTTCAAAGTTTGGCCACCAACCAATGAAATT
50386 TCTAATAAGT
Statistics
Matches: 53, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
33 6 0.11
34 18 0.34
35 3 0.06
36 22 0.42
37 4 0.08
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (36 bp):
ATGTTCAAAGTTTGGCCACCAACCAATGAAATTCCA
Found at i:51214 original size:75 final size:75
Alignment explanation
Indices: 51120--51279 Score: 225
Period size: 75 Copynumber: 2.1 Consensus size: 75
51110 AGTTAATAGT
* * * * *
51120 ATTACTATATGTATATGGTTTATATTTTTATTAAGTGCATGTTATATTTT-TTT-TGCATATTAG
1 ATTATTATATGTATATGGTTTATATTTTCACTAAGTACATGTTATATTTTATTTGTACATATTAG
*
51183 ATATTAATTA
66 ACATTAATTA
*
51193 TTTATTTATATAGTATATGGTTTATATTTTCACTAAGTACATGTTATATTTTATTTGTACATATT
1 ATTA-TTATAT-GTATATGGTTTATATTTTCACTAAGTACATGTTATATTTTATTTGTACATATT
51258 AGACATTAATTA
64 AGACATTAATTA
51270 ATTATTATAT
1 ATTATTATAT
51280 TATGTTATAG
Statistics
Matches: 75, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
73 3 0.04
74 5 0.07
75 37 0.49
76 9 0.12
77 21 0.28
ACGTcount: A:0.32, C:0.05, G:0.09, T:0.54
Consensus pattern (75 bp):
ATTATTATATGTATATGGTTTATATTTTCACTAAGTACATGTTATATTTTATTTGTACATATTAG
ACATTAATTA
Done.