Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005841.1 Hibiscus syriacus cultivar Beakdansim tig00013694_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: 74899
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:67 original size:31 final size:31
Alignment explanation
Indices: 1--65 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
* *
1 TTTCATTCGCGTTACGATTCTGTCGTGCGAT
1 TTTCATTCGCGTTACGATTCTCTCGTCCGAT
* *
32 TTTCATTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTCGCGTTACGATTCTCTCG-TCCGAT
64 TT
1 TT
66 CAAGTTAGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 22 0.76
32 7 0.24
ACGTcount: A:0.11, C:0.25, G:0.18, T:0.46
Consensus pattern (31 bp):
TTTCATTCGCGTTACGATTCTCTCGTCCGAT
Found at i:191 original size:20 final size:20
Alignment explanation
Indices: 147--221 Score: 98
Period size: 20 Copynumber: 3.8 Consensus size: 20
137 TGCAGAAGAG
* *
147 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGACAA
**
168 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGACAA
188 TCGCAACGAGAGAA-GACAA
1 TCGCAACGAGAGAATGACAA
207 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
222 CGCAACGCGA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
19 17 0.36
20 19 0.40
21 11 0.23
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGACAA
Found at i:224 original size:14 final size:14
Alignment explanation
Indices: 205--261 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
195 GAGAGAAGAC
205 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
219 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
238 AATCGCAACGAGAG
1 AATCGCAACGAGAG
252 AATCGCAACG
1 AATCGCAACG
262 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:242 original size:33 final size:33
Alignment explanation
Indices: 159--277 Score: 132
Period size: 33 Copynumber: 3.4 Consensus size: 33
149 GCAACGAGAT
*
159 AAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAG
1 AAATGAAAATCGCAACGAGAG-A--A---TCGCAACGCG
*
198 AGAA-GACAATCGCAACGAGAGAATCGCAACGCG
1 A-AATGAAAATCGCAACGAGAGAATCGCAACGCG
231 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
264 AAACCAAAATCGCA
1 AAATGAAAATCGCA
278 TTGCGATTTC
Statistics
Matches: 73, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
32 2 0.03
33 50 0.68
36 1 0.01
38 1 0.01
39 17 0.23
40 2 0.03
ACGTcount: A:0.45, C:0.22, G:0.24, T:0.09
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:326 original size:33 final size:33
Alignment explanation
Indices: 278--391 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
268 CAAAATCGCA
278 TTGCGATT-TCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
310 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
*
343 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
*
376 TTGCGATTTTCATTTC
1 TTGCGATTGTCATTTC
392 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
32 8 0.10
33 70 0.90
ACGTcount: A:0.10, C:0.25, G:0.22, T:0.44
Consensus pattern (33 bp):
TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
Found at i:332 original size:19 final size:17
Alignment explanation
Indices: 273--389 Score: 81
Period size: 14 Copynumber: 7.1 Consensus size: 17
263 GAAACCAAAA
*
273 TCGCATTGCGATTTCATT
1 TCGCGTTGCGATTTCA-T
291 TCGCGTTGCGA-TTC--
1 TCGCGTTGCGATTTCAT
*
305 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATT-TCA-T
324 TCGCGTTGCGA-TTC--
1 TCGCGTTGCGATTTCAT
*
338 TCTCGTTGCGATTGTCAT
1 TCGCGTTGCGATT-TCAT
356 CTCGCGTTGCGA-TTC--
1 -TCGCGTTGCGATTTCAT
*
371 TCTCGTTGCGATTTTCAT
1 TCGCGTTGCGA-TTTCAT
389 T
1 T
390 TCAACCAAAA
Statistics
Matches: 79, Mismatches: 6, Indels: 28
0.70 0.05 0.25
Matches are distributed among these distances:
14 30 0.38
15 2 0.03
16 7 0.09
17 7 0.09
18 13 0.16
19 20 0.25
ACGTcount: A:0.10, C:0.25, G:0.22, T:0.43
Consensus pattern (17 bp):
TCGCGTTGCGATTTCAT
Found at i:2367 original size:91 final size:93
Alignment explanation
Indices: 2049--2421 Score: 656
Period size: 92 Copynumber: 4.1 Consensus size: 93
2039 TAGATTGCTT
*
2049 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2114 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2142 AGTAAATTTGTTCGGTTTGCTGCCAATTCTGCTAAACTGTG--TTCTTTAAC-CTGTGAAATAGT
1 AGTAAATTTGTTCGG-TTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGT
2204 -TTTGTCTTTGTTTTGTCTTTTGGTTGAA
65 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
2232 AGTAAATTTGTTCGG-TGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2296 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2324 AGTAAATTTGTTCGG-TGCTGCC-ATTCTGCTAAACTGTGTATTCTTT-A-ACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2385 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2413 AGTAAATTT
1 AGTAAATTT
2422 ATCCATTCAA
Statistics
Matches: 272, Mismatches: 3, Indels: 14
0.94 0.01 0.05
Matches are distributed among these distances:
88 24 0.09
89 51 0.19
90 52 0.19
91 47 0.17
92 59 0.22
93 14 0.05
94 25 0.09
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:2488 original size:20 final size:19
Alignment explanation
Indices: 2463--2589 Score: 91
Period size: 18 Copynumber: 7.3 Consensus size: 19
2453 TAGTTTACTT
*
2463 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-TAAAA
*
2483 TCGCAACGCGAAAC-CAAA
1 TCGCAACGCGAAACTAAAA
2501 TCGCAACGCGAAA-TGAAAA
1 TCGCAACGCGAAACT-AAAA
*
2520 TCGCAA--CG--AC-AGAA
1 TCGCAACGCGAAACTAAAA
*
2534 TCGCAACGCGAAAC-CAAA
1 TCGCAACGCGAAACTAAAA
*
2552 TCGCAA--CG--AC-AAGA
1 TCGCAACGCGAAACTAAAA
*
2566 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACTAAAA
2585 TCGCA
1 TCGCA
2590 TTGCGATTTC
Statistics
Matches: 86, Mismatches: 9, Indels: 25
0.72 0.08 0.21
Matches are distributed among these distances:
14 19 0.22
15 1 0.01
16 6 0.07
17 2 0.02
18 28 0.33
19 17 0.20
20 13 0.15
ACGTcount: A:0.45, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACTAAAA
Found at i:2503 original size:18 final size:18
Alignment explanation
Indices: 2480--2589 Score: 96
Period size: 18 Copynumber: 6.4 Consensus size: 18
2470 ACGAAACTTA
2480 AAATCGCAACGCGAAACC
1 AAATCGCAACGCGAAACC
**
2498 AAATCGCAACGCGAAATGA
1 AAATCGCAACGCGAAA-CC
2517 AAATCGCAA--CG--A-C
1 AAATCGCAACGCGAAACC
2530 AGAATCGCAACGCGAAACC
1 A-AATCGCAACGCGAAACC
2549 AAATCGCAA--CG--A-C
1 AAATCGCAACGCGAAACC
2562 AAGATCGCAACGCGAAACC
1 AA-ATCGCAACGCGAAACC
2581 AAAATCGCA
1 -AAATCGCA
2590 TTGCGATTTC
Statistics
Matches: 75, Mismatches: 3, Indels: 27
0.71 0.03 0.26
Matches are distributed among these distances:
13 4 0.05
14 16 0.21
15 1 0.01
16 6 0.08
17 2 0.03
18 26 0.35
19 18 0.24
20 2 0.03
ACGTcount: A:0.45, C:0.29, G:0.18, T:0.07
Consensus pattern (18 bp):
AAATCGCAACGCGAAACC
Found at i:2558 original size:32 final size:31
Alignment explanation
Indices: 2497--2589 Score: 132
Period size: 32 Copynumber: 2.9 Consensus size: 31
2487 AACGCGAAAC
**
2497 CAAATCGCAACGCGAAATGAAAATCGCAACGA
1 CAAATCGCAACGCGAAA-CCAAATCGCAACGA
2529 CAGAATCGCAACGCGAAACCAAATCGCAACGA
1 CA-AATCGCAACGCGAAACCAAATCGCAACGA
2561 CAAGATCGCAACGCGAAACCAAAATCGCA
1 CAA-ATCGCAACGCGAAACC-AAATCGCA
2590 TTGCGATTTC
Statistics
Matches: 56, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
31 1 0.02
32 32 0.57
33 23 0.41
ACGTcount: A:0.45, C:0.29, G:0.18, T:0.08
Consensus pattern (31 bp):
CAAATCGCAACGCGAAACCAAATCGCAACGA
Found at i:2587 original size:51 final size:51
Alignment explanation
Indices: 2463--2589 Score: 136
Period size: 51 Copynumber: 2.5 Consensus size: 51
2453 TAGTTTACTT
**
2463 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAATCGCAACGCGAAA
* * *
2514 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAATCGCAACG-CGAA-A
*
2566 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
2590 TTGCGATTTC
Statistics
Matches: 61, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
49 3 0.05
50 6 0.10
51 41 0.67
52 3 0.05
53 6 0.10
54 2 0.03
ACGTcount: A:0.45, C:0.29, G:0.17, T:0.09
Consensus pattern (51 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAATCGCAACGCGAAA
Found at i:2620 original size:19 final size:19
Alignment explanation
Indices: 2585--2703 Score: 126
Period size: 19 Copynumber: 6.6 Consensus size: 19
2575 GAAACCAAAA
*
2585 TCGCATTGCGA-TTTCATT
1 TCGCGTTGCGATTTTCATT
2603 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
2622 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
2638 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
2655 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
2674 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
2694 TCG-GTTGCGA
1 TCGCGTTGCGA
2704 AAGTAAACTA
Statistics
Matches: 85, Mismatches: 9, Indels: 13
0.79 0.08 0.12
Matches are distributed among these distances:
14 7 0.08
16 5 0.06
17 5 0.06
18 10 0.12
19 53 0.62
20 5 0.06
ACGTcount: A:0.12, C:0.19, G:0.24, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:4807 original size:18 final size:18
Alignment explanation
Indices: 4732--4829 Score: 123
Period size: 18 Copynumber: 5.5 Consensus size: 18
4722 CAAATTGACT
4732 ATCGCAATGCGAAATGAAAA
1 ATCGCAATGCGAAATG--AA
4752 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG-AA
*
4771 ATCGCAA--CGAGA-G-A
1 ATCGCAATGCGAAATGAA
4785 ATCGCAATGCGAAATGAA
1 ATCGCAATGCGAAATGAA
*
4803 ATCGCAATGCGGAATGAA
1 ATCGCAATGCGAAATGAA
4821 ATCGCAATG
1 ATCGCAATG
4830 GGAGAATCGC
Statistics
Matches: 71, Mismatches: 3, Indels: 10
0.85 0.04 0.12
Matches are distributed among these distances:
14 8 0.11
16 5 0.07
17 5 0.07
18 27 0.38
19 10 0.14
20 16 0.23
ACGTcount: A:0.44, C:0.17, G:0.23, T:0.15
Consensus pattern (18 bp):
ATCGCAATGCGAAATGAA
Found at i:4839 original size:14 final size:17
Alignment explanation
Indices: 4750--4845 Score: 80
Period size: 18 Copynumber: 5.8 Consensus size: 17
4740 GCGAAATGAA
*
4750 AAATCGCAATGCGAAATG
1 AAATCGCAATGCG-GATG
4768 AAAATCGCAA--C-GA-G
1 -AAATCGCAATGCGGATG
*
4782 AGAATCGCAATGCGAAATG
1 A-AATCGCAATGCG-GATG
4801 AAATCGCAATGCGGAATG
1 AAATCGCAATGCGG-ATG
4819 AAATCGCAATG-GGA-G
1 AAATCGCAATGCGGATG
4834 -AATCGCAATGCG
1 AAATCGCAATGCG
4846 ATTTTAATTC
Statistics
Matches: 66, Mismatches: 3, Indels: 20
0.74 0.03 0.22
Matches are distributed among these distances:
13 1 0.02
14 19 0.29
15 3 0.05
16 2 0.03
17 3 0.05
18 27 0.41
19 11 0.17
ACGTcount: A:0.42, C:0.18, G:0.26, T:0.15
Consensus pattern (17 bp):
AAATCGCAATGCGGATG
Found at i:4841 original size:50 final size:52
Alignment explanation
Indices: 4732--4846 Score: 180
Period size: 50 Copynumber: 2.2 Consensus size: 52
4722 CAAATTGACT
4732 ATCGCAATGCGAAATGAAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATG-AAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
4785 ATCGCAATGCGAAATG-AAATCGCAATGCGGAATG-AAATCGCAATGGGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
4835 ATCGCAATGCGA
1 ATCGCAATGCGA
4847 TTTTAATTCG
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
50 26 0.44
51 17 0.29
53 16 0.27
ACGTcount: A:0.43, C:0.17, G:0.25, T:0.15
Consensus pattern (52 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:4918 original size:52 final size:51
Alignment explanation
Indices: 4836--4951 Score: 196
Period size: 52 Copynumber: 2.3 Consensus size: 51
4826 AATGGGAGAA
*
4836 TCGCAATGCGATTTTAATTCGCATTGCGATTATCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTAATTCGCATTGCGATTATCTCGTTGCGATTTTCATT
* *
4887 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTT-AATTCGCATTGCGATTATCTCGTTGCGATTTTCATT
4939 TCGCATTGCGATT
1 TCGCATTGCGATT
4952 CTCTCGTTGC
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
51 14 0.23
52 47 0.77
ACGTcount: A:0.16, C:0.22, G:0.18, T:0.44
Consensus pattern (51 bp):
TCGCATTGCGATTTTAATTCGCATTGCGATTATCTCGTTGCGATTTTCATT
Found at i:4929 original size:33 final size:33
Alignment explanation
Indices: 4892--4983 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
4882 TCATTTCGCA
4892 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
4925 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
4958 TTGCGATTTTCATTTCCGCATTGCGA
1 TTGCGATTTTCATTT-CGCATTGCGA
4984 AATGTAATGG
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 48 0.83
34 10 0.17
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:4930 original size:14 final size:14
Alignment explanation
Indices: 4911--4965 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
4901 TCATTTCGCA
4911 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
4925 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
4942 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
4958 TTGCGATT
1 TTGCGATT
4966 TTCATTTCCG
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:5063 original size:19 final size:19
Alignment explanation
Indices: 5039--5133 Score: 125
Period size: 19 Copynumber: 5.4 Consensus size: 19
5029 AAAATTGACT
5039 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
5058 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
5077 ATCGCAA--CG--A-G--A
1 ATCGCAATGCGAAATGAAA
5089 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
5107 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
5127 ATCGCAA
1 ATCGCAA
5134 CGAGAGAATC
Statistics
Matches: 68, Mismatches: 0, Indels: 15
0.82 0.00 0.18
Matches are distributed among these distances:
12 8 0.12
14 3 0.04
15 1 0.01
16 1 0.01
17 3 0.04
18 11 0.16
19 32 0.47
20 9 0.13
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:5099 original size:50 final size:51
Alignment explanation
Indices: 5039--5152 Score: 196
Period size: 50 Copynumber: 2.2 Consensus size: 51
5029 AAAATTGACT
5039 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAAC-GAGA
1 ATCGCAATGCGAAATG-AAATCGCAATGCGGAAATGAAAATCGCAACAGAGA
5089 ATCGCAATGCGAAATGAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAATCGCAATGCGGAAATGAAAATCGCAAC-AGAGA
5141 ATCGCAATGCGA
1 ATCGCAATGCGA
5153 TTTTCATTTC
Statistics
Matches: 61, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
49 12 0.20
50 33 0.54
52 16 0.26
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (51 bp):
ATCGCAATGCGAAATGAAATCGCAATGCGGAAATGAAAATCGCAACAGAGA
Found at i:8401 original size:20 final size:20
Alignment explanation
Indices: 8373--8602 Score: 248
Period size: 20 Copynumber: 11.5 Consensus size: 20
8363 AAATTTCAGT
* * *
8373 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
8393 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
8413 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
8433 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
8453 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
*
8473 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
8493 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* **
8513 ATTGCGATTTACCCATAT-GC
1 GTTGCGATTTACGGAT-TCGC
*
8533 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
8553 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
8573 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
8593 GTTGCGATTT
1 GTTGCGATTT
8603 TGGAAAATCG
Statistics
Matches: 183, Mismatches: 24, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
20 182 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:8619 original size:21 final size:21
Alignment explanation
Indices: 8589--8671 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
8579 ATTTATGTGT
*
8589 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
8610 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
8631 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
8652 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
8672 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:9641 original size:181 final size:182
Alignment explanation
Indices: 9257--9729 Score: 671
Period size: 181 Copynumber: 2.6 Consensus size: 182
9247 GATCCAAATT
* * * * * **
9257 AAAAATGTATCGATCCACAACGATATAACAGGTAAAACTATAACAAAACCAGTATTGAAATGATA
1 AAAAATGTATCGATCAACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * *
9322 AAACCGGTAAAGCGGTACCGAATATATTTAAAGTGTCGATACTTTAATATAAGGATCGACAATTC
66 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACAATTC
* * **
9387 GTTAATTTAAAAGAGAAGCATTTTTAGCGCCTATAAAGTGTCGATACTTTCA
131 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTAAA
* * * *
9439 AAAAATATATCGATCAACAACGATATAACATGTAAAAATATGATAAAACTGGTATCAAAATGATG
1 AAAAATGTATCGATCAACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * * *
9504 AAACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGAAACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACAATTC
* * *
9568 GTGAATTTAAAAGAGAAGTAGTTTTAGTGTCTATAAAGTGTCGATA-TTAAA
131 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTAAA
9619 AAAAATGTATCGATCAAACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGAT
1 AAAAATGTATCGATC-AACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGAT
*
9684 AAAACCGGTAAAATGATACCGGATATATTAAAAGTGTCGATACTTT
65 AAAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTT
9730 CGTAAGTACG
Statistics
Matches: 257, Mismatches: 33, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
180 17 0.07
181 146 0.57
182 94 0.37
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (182 bp):
AAAAATGTATCGATCAACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACAATTC
GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTAAA
Found at i:9673 original size:20 final size:19
Alignment explanation
Indices: 9650--9696 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
9640 CGATATAACA
9650 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
9670 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
9690 GGTAAAA
1 GGTAAAA
9697 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:9698 original size:17 final size:19
Alignment explanation
Indices: 9659--9701 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
9649 AGGTAAAAAT
9659 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
9679 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
9696 ATGATA
1 ATGATA
9702 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:11854 original size:15 final size:15
Alignment explanation
Indices: 11834--11866 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
11824 TGGTTGTATT
*
11834 GGGGGATGACGGTGA
1 GGGGGACGACGGTGA
11849 GGGGGACGACGGTGA
1 GGGGGACGACGGTGA
11864 GGG
1 GGG
11867 AAAACAGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.09, G:0.64, T:0.09
Consensus pattern (15 bp):
GGGGGACGACGGTGA
Found at i:12047 original size:33 final size:33
Alignment explanation
Indices: 12005--12070 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
11995 AAATAGATGG
*
12005 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
*
12038 AGTGGTGAAAGAAGTTGAGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
12071 TCTTAAGATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.30, C:0.00, G:0.47, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:12295 original size:15 final size:15
Alignment explanation
Indices: 12275--12329 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 15
12265 AGAGGGAGGA
12275 GGAAGAAGAAGAGAT
1 GGAAGAAGAAGAGAT
*
12290 GGAAGAA-AAGAGGGAGGA
1 GGAAGAAGAAGA--GA--T
12308 GGAAGAAGAAGAGAT
1 GGAAGAAGAAGAGAT
12323 GGAAGAA
1 GGAAGAA
12330 ATGAGGAGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 4 0.12
15 14 0.42
16 2 0.06
17 2 0.06
18 7 0.21
19 4 0.12
ACGTcount: A:0.53, C:0.00, G:0.44, T:0.04
Consensus pattern (15 bp):
GGAAGAAGAAGAGAT
Found at i:12296 original size:33 final size:33
Alignment explanation
Indices: 12258--12345 Score: 151
Period size: 33 Copynumber: 2.7 Consensus size: 33
12248 AAAATATGAA
12258 GAAGAAAAGAGGGAGGAGGAAGAAGAAGAGATG
1 GAAGAAAAGAGGGAGGAGGAAGAAGAAGAGATG
12291 GAAGAAAAGAGGGAGGAGGAAGAAGAAGAGATG
1 GAAGAAAAGAGGGAGGAGGAAGAAGAAGAGATG
*
12324 GAAGAAATGA-GGAGGAAGGAAG
1 GAAGAAAAGAGGGAGG-AGGAAG
12346 TCGATGTCAT
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
32 5 0.09
33 48 0.91
ACGTcount: A:0.51, C:0.00, G:0.45, T:0.03
Consensus pattern (33 bp):
GAAGAAAAGAGGGAGGAGGAAGAAGAAGAGATG
Found at i:13928 original size:19 final size:20
Alignment explanation
Indices: 13904--13952 Score: 84
Period size: 19 Copynumber: 2.5 Consensus size: 20
13894 AATGTAGGGT
13904 TAATTTTGTATTA-GATTTA
1 TAATTTTGTATTACGATTTA
13923 TAATTTTGTA-TACGATTTA
1 TAATTTTGTATTACGATTTA
13942 TAATTTTGTAT
1 TAATTTTGTAT
13953 GTGAATGTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 2 0.07
19 26 0.93
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (20 bp):
TAATTTTGTATTACGATTTA
Found at i:14787 original size:200 final size:200
Alignment explanation
Indices: 14187--15373 Score: 2205
Period size: 200 Copynumber: 5.9 Consensus size: 200
14177 AATTTACAAT
14187 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
*
14252 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCAGATTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGATTT
14317 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
14382 AATGA
196 AATGA
14387 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
*
14452 CGAAACCCA-AAGTATAATGTAATAGGTAATTTTTCAATCTAACAGGTATAAGTATACCGGATTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGATTT
14516 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
14581 AATGA
196 AATGA
** *
14586 ATGAAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTATCGATCCCAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
*
14651 CGAAACCTATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGATTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGATTT
14716 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
14781 AATGA
196 AATGA
* *
14786 ATGGCAAACAGGGTGCAATCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCAAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
*
14851 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATATCGGATTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGATTT
*
14916 ATGAGAGAATAGATGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
14981 AATGA
196 AATGA
* *
14986 ATGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTTGATCCCAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
*
15051 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGCATAAGTATACCGGATTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGATTT
* *
15116 ATGAGAGAATATGTGTAATATATGTATCGACACTTTTTAATTTTGTGTTGATACTATTGGTCCAG
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
15181 AATGA
196 AATGA
*
15186 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCTAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
15251 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGATTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGATTT
* *
15316 ATGAGAGAATATGTGTAATATATGTATCAACACTTTTTAATTTTGTGTCGATACTATT
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATT
15374 TTTAAATATC
Statistics
Matches: 956, Mismatches: 30, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
199 193 0.20
200 763 0.80
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (200 bp):
ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGATTT
ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
AATGA
Found at i:18975 original size:182 final size:182
Alignment explanation
Indices: 18332--19171 Score: 1418
Period size: 182 Copynumber: 4.6 Consensus size: 182
18322 TTTTACCTTT
* * *
18332 TTTAAAAGAGAAGAAGTTATATCGTCAATAAAATGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* * *
18397 AACAATATAATAGGTAAAAATATGACAAGACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
* *
18462 CAGTTATGTTGAAAGTGTCGATAATTTATTATACGTATCGACACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
* **
18514 TTTAAAAGAGAAG-AGTTATAACGCCAATAAAGTGTCGATACTTTATAAAGCTGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
18578 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
18643 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCG--ACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
* *
18693 -TTAATAAGAGAAGAAGTTATAGCGCCAATAACGTGTCGATACTTTTTAAAAATGTATCGATCCA
1 TTTAA-AAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCA
*
18757 TAACAATATAACATGTAAAAATATGACAAAACCGGTCTCAAAATGACAAAACAGGTAAAGCGCTA
65 TAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTA
* *
18822 CCGGTTATGTTAAAAGTGTTGATAATTTATTATAAGTATCGACACTTTTGGAA
130 CCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
* *
18875 TTTAAAAGAGAAGAAGTTATAGAGCCAATAAAGTGTCGATATTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
*
18940 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
* *
19005 CGGATATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTAGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
19057 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* * **
19122 AATAATATAACATGTAAAAATATGATAAAACCGGTCTATAAATGACAAAA
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAA
19172 GATGAACGCA
Statistics
Matches: 618, Mismatches: 35, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
178 4 0.01
179 18 0.03
180 148 0.24
181 146 0.24
182 298 0.48
183 4 0.01
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (182 bp):
TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
Found at i:19411 original size:87 final size:87
Alignment explanation
Indices: 19307--19469 Score: 281
Period size: 87 Copynumber: 1.9 Consensus size: 87
19297 AAATAGGTCA
* *
19307 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCACTACCTATTACATTATATAAGCACTACCTAATATGTTATTGTACTTGATAATATTT
*
19372 CCGGTTAAATACTTATTTTATT
66 CCGATTAAATACTTATTTTATT
* *
19394 ATATAAGCACTATCTATTACATTATATAAGCATTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCACTACCTATTACATTATATAAGCACTACCTAATATGTTATTGTACTTGATAATATTT
19459 CCGATTAAATA
66 CCGATTAAATA
19470 ATATAACATA
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (87 bp):
ATATAAGCACTACCTATTACATTATATAAGCACTACCTAATATGTTATTGTACTTGATAATATTT
CCGATTAAATACTTATTTTATT
Found at i:19441 original size:23 final size:23
Alignment explanation
Indices: 19391--19435 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
19381 TACTTATTTT
* *
19391 ATTATATAAGCACTATCTATTAC
1 ATTATATAAGCACTACCTAATAC
*
19414 ATTATATAAGCATTACCTAATA
1 ATTATATAAGCACTACCTAATA
19436 TGTTATTGTA
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:0.42, C:0.16, G:0.04, T:0.38
Consensus pattern (23 bp):
ATTATATAAGCACTACCTAATAC
Found at i:25670 original size:22 final size:22
Alignment explanation
Indices: 25645--25729 Score: 73
Period size: 22 Copynumber: 3.6 Consensus size: 22
25635 TATATTAAAA
25645 TTATTTTTTATTTTTGAATAAT
1 TTATTTTTTATTTTTGAATAAT
**
25667 TTATTTTTTATTGTTTTTAT-AT
1 TTATTTTTTATT-TTTGAATAAT
* *
25689 TTATTTATTTTAATATTTGAATATT
1 TTA-TT-TTTT-ATTTTTGAATAAT
25714 TTAAATTTTTTATTTT
1 TT--ATTTTTTATTTT
25730 AAAAAAATTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
22 17 0.35
23 7 0.14
24 13 0.27
25 9 0.18
26 2 0.04
27 1 0.02
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.71
Consensus pattern (22 bp):
TTATTTTTTATTTTTGAATAAT
Found at i:25691 original size:15 final size:16
Alignment explanation
Indices: 25680--25731 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
25670 TTTTTTATTG
*
25680 TTTTTATATTTATTTA
1 TTTTAATATTTATTTA
*
25696 TTTTAATATTTGA-ATA
1 TTTTAATATTT-ATTTA
25712 TTTTAA-ATTT-TTTA
1 TTTTAATATTTATTTA
25726 TTTTAA
1 TTTTAA
25732 AAAAATTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 8 0.26
15 4 0.13
16 18 0.58
17 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (16 bp):
TTTTAATATTTATTTA
Found at i:25866 original size:21 final size:21
Alignment explanation
Indices: 25840--25881 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
25830 ATCATTGAGC
*
25840 GTCACATCAACACCGTGAATT
1 GTCACATCAACAACGTGAATT
*
25861 GTCACATCAACAATGTGAATT
1 GTCACATCAACAACGTGAATT
25882 ACCTTTTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (21 bp):
GTCACATCAACAACGTGAATT
Found at i:28634 original size:20 final size:20
Alignment explanation
Indices: 28609--28657 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
28599 ATAAATTTGA
28609 TATCGATACCCAGAAGGTAG
1 TATCGATACCCAGAAGGTAG
28629 TATCGATACCCAGAAGGTAG
1 TATCGATACCCAGAAGGTAG
28649 TATCGATAC
1 TATCGATAC
28658 TCCATATGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.22
Consensus pattern (20 bp):
TATCGATACCCAGAAGGTAG
Found at i:31409 original size:59 final size:57
Alignment explanation
Indices: 31337--31496 Score: 160
Period size: 59 Copynumber: 2.7 Consensus size: 57
31327 TATTTGATCC
* * *
31337 TTAATTAATATTTGGCGTAATTTTTTTAATTTAATTCAATTT-TTCCATAATTTAAAATTAG
1 TTAA-TAA-ATTTGGCTTAA-TTTTTTAA-TTAATTCAATTTATT-AATAATTTAAAACTAG
***
31398 TTAATAAATTTGGCTTAAATTTCCCAATTAATTCAATTTAGTTAATAATTTAAAACTAG
1 TTAATAAATTTGGCTT-AATTTTTTAATTAATTCAATTTA-TTAATAATTTAAAACTAG
* *
31457 TTGATAAATTTGGCTTTAATATTTTAATTAACTTCAATTT
1 TTAATAAATTTGGC-TTAATTTTTTAATTAA-TTCAATTT
31497 GCTCTAGTTT
Statistics
Matches: 83, Mismatches: 11, Indels: 11
0.79 0.10 0.10
Matches are distributed among these distances:
58 12 0.14
59 50 0.60
60 17 0.20
61 4 0.05
ACGTcount: A:0.36, C:0.08, G:0.07, T:0.49
Consensus pattern (57 bp):
TTAATAAATTTGGCTTAATTTTTTAATTAATTCAATTTATTAATAATTTAAAACTAG
Found at i:32814 original size:33 final size:33
Alignment explanation
Indices: 32772--32843 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
32762 AAACGAACAC
* *
32772 GAACATAAATGAACATGTTCACGAATGTTAAA-
1 GAACATAAATAAACATGTTCACGAACGTTAAAT
32804 GAACACTAAATAAACATGTTCACGAACGTTAAAT
1 GAACA-TAAATAAACATGTTCACGAACGTTAAAT
32838 GAACAT
1 GAACAT
32844 GTTCGTGAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
32 5 0.14
33 26 0.72
34 5 0.14
ACGTcount: A:0.47, C:0.15, G:0.14, T:0.24
Consensus pattern (33 bp):
GAACATAAATAAACATGTTCACGAACGTTAAAT
Found at i:32822 original size:23 final size:23
Alignment explanation
Indices: 32796--32846 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
32786 ATGTTCACGA
32796 ATGTTAAAGAACACTAAATAAAC
1 ATGTTAAAGAACACTAAATAAAC
* * ** *
32819 ATGTTCACGAACGTTAAATGAAC
1 ATGTTAAAGAACACTAAATAAAC
32842 ATGTT
1 ATGTT
32847 CGTGAACGTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.27
Consensus pattern (23 bp):
ATGTTAAAGAACACTAAATAAAC
Found at i:32847 original size:23 final size:23
Alignment explanation
Indices: 32810--32864 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
32800 TAAAGAACAC
32810 TAAATAAACATGTTCACGAACGT
1 TAAATAAACATGTTCACGAACGT
* **
32833 TAAATGAACATGTTCGTGAACGT
1 TAAATAAACATGTTCACGAACGT
*
32856 TAAACAAAC
1 TAAATAAAC
32865 GAACACGAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.44, C:0.16, G:0.15, T:0.25
Consensus pattern (23 bp):
TAAATAAACATGTTCACGAACGT
Found at i:34308 original size:2 final size:2
Alignment explanation
Indices: 34301--34342 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
34291 GGTTTTTATG
34301 AT AT AT AT AT AT 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 AT AT AT AT AT AT
34343 GTTTACCCTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36841 original size:25 final size:25
Alignment explanation
Indices: 36812--36860 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
36802 GGCACATAGG
36812 TTTGTCCCGAAGGACCACGTAGAAA
1 TTTGTCCCGAAGGACCACGTAGAAA
* *
36837 TTTGTCCTGAAGGACCGCGTAGAA
1 TTTGTCCCGAAGGACCACGTAGAA
36861 CCCTCGATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (25 bp):
TTTGTCCCGAAGGACCACGTAGAAA
Found at i:37512 original size:20 final size:20
Alignment explanation
Indices: 37487--37538 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
37477 TCAGTTATAA
*
37487 TATCGATACCTCAACTTTGG
1 TATCGATACCTCAACCTTGG
37507 TATCGATACCTCAACCTTGG
1 TATCGATACCTCAACCTTGG
37527 TATCGATACCTC
1 TATCGATACCTC
37539 CACATCAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.13, T:0.33
Consensus pattern (20 bp):
TATCGATACCTCAACCTTGG
Found at i:43941 original size:24 final size:24
Alignment explanation
Indices: 43914--43967 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
43904 CAGTCACCAC
* *
43914 TGCCACGTAAAATTTGCACCGAAG
1 TGCCACGTAAAATATGCAACGAAG
* *
43938 TGCCACGTAGAATATGCAATGAAG
1 TGCCACGTAAAATATGCAACGAAG
43962 TGCCAC
1 TGCCAC
43968 ATAGATTTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.20
Consensus pattern (24 bp):
TGCCACGTAAAATATGCAACGAAG
Found at i:58153 original size:34 final size:34
Alignment explanation
Indices: 58110--58179 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
58100 TTTGAGGATA
*
58110 AACAAGCTAGCTTTGAGAAACTGAAGATTGTTCT
1 AACAAGCTAGCTTTGAGAAACTGAAGATTATTCT
58144 AACAAGCTAGCTTTGAGAAACTGAAGATTATTCT
1 AACAAGCTAGCTTTGAGAAACTGAAGATTATTCT
58178 AA
1 AA
58180 TTCAAGCTCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.29
Consensus pattern (34 bp):
AACAAGCTAGCTTTGAGAAACTGAAGATTATTCT
Found at i:61266 original size:21 final size:21
Alignment explanation
Indices: 61240--61281 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
61230 CCAGAATGGG
*
61240 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
61261 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
61282 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:61435 original size:20 final size:19
Alignment explanation
Indices: 61394--61469 Score: 81
Period size: 20 Copynumber: 4.1 Consensus size: 19
61384 AAACCATGCA
61394 GGGGGAATCTGTA--CCC-
1 GGGGGAATCTGTACCCCCT
61410 -GGGGAATC-GATACCCCCT
1 GGGGGAATCTG-TACCCCCT
*
61428 GAGGGGAATCTGTTCCCCCT
1 G-GGGGAATCTGTACCCCCT
61448 GGGGTGAATCTGTACCCCCT
1 GGGG-GAATCTGTACCCCCT
61468 GG
1 GG
61470 ACAATCTGAT
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
14 1 0.02
15 10 0.20
17 3 0.06
19 3 0.06
20 32 0.64
21 1 0.02
ACGTcount: A:0.17, C:0.29, G:0.33, T:0.21
Consensus pattern (19 bp):
GGGGGAATCTGTACCCCCT
Found at i:63395 original size:3 final size:3
Alignment explanation
Indices: 63387--63424 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
63377 TACGTCCTCA
* *
63387 TTC TTC TTC TTC TTC TTC TTC TTG TTT TTC TTC -TC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
63425 CCTTTCTTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.00, C:0.29, G:0.03, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:64796 original size:21 final size:21
Alignment explanation
Indices: 64770--64811 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
64760 CCAGAATGGG
*
64770 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
64791 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
64812 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:64946 original size:15 final size:15
Alignment explanation
Indices: 64926--64982 Score: 53
Period size: 15 Copynumber: 3.5 Consensus size: 15
64916 ACCATGCAGG
64926 GGGGAATCTGTACCC
1 GGGGAATCTGTACCC
64941 GGGGAATC-GATACCCC
1 GGGGAATCTG-TA-CCC
*
64957 TGGGGGGAATCTGTTCCC
1 ---GGGGAATCTGTACCC
64975 GGGGAATC
1 GGGGAATC
64983 GATACCCCCT
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
14 1 0.03
15 18 0.51
16 3 0.09
18 3 0.09
19 9 0.26
20 1 0.03
ACGTcount: A:0.19, C:0.25, G:0.37, T:0.19
Consensus pattern (15 bp):
GGGGAATCTGTACCC
Found at i:64964 original size:34 final size:36
Alignment explanation
Indices: 64924--65011 Score: 144
Period size: 34 Copynumber: 2.5 Consensus size: 36
64914 AAACCATGCA
64924 GGGGGGAATCTGTACCCGGGGAATCGATA-CCCCT-
1 GGGGGGAATCTGTACCCGGGGAATCGATACCCCCTG
*
64958 GGGGGGAATCTGTTCCCGGGGAATCGATACCCCCTGG
1 GGGGGGAATCTGTACCCGGGGAATCGATACCCCCT-G
64995 GGGGGGAATCTGTACCC
1 GGGGGGAATCTGTACCC
65012 CCTGGACAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
34 28 0.57
35 5 0.10
37 16 0.33
ACGTcount: A:0.18, C:0.26, G:0.38, T:0.18
Consensus pattern (36 bp):
GGGGGGAATCTGTACCCGGGGAATCGATACCCCCTG
Found at i:65000 original size:22 final size:22
Alignment explanation
Indices: 64975--65016 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
64965 ATCTGTTCCC
64975 GGGGAATC-GATACCCCCTGGGG
1 GGGGAATCTG-TACCCCCTGGGG
64997 GGGGAATCTGTACCCCCTGG
1 GGGGAATCTGTACCCCCTGG
65017 ACAATCTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.17, C:0.29, G:0.38, T:0.17
Consensus pattern (22 bp):
GGGGAATCTGTACCCCCTGGGG
Found at i:66922 original size:17 final size:17
Alignment explanation
Indices: 66895--66934 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
66885 GAGCAGTAAC
66895 AAGAT-ATTGTATTTAG
1 AAGATAATTGTATTTAG
*
66911 AAGATAATTGTATTTCG
1 AAGATAATTGTATTTAG
66928 AAGATAA
1 AAGATAA
66935 AAATTTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.42, C:0.03, G:0.17, T:0.38
Consensus pattern (17 bp):
AAGATAATTGTATTTAG
Found at i:67587 original size:68 final size:68
Alignment explanation
Indices: 67508--67644 Score: 238
Period size: 68 Copynumber: 2.0 Consensus size: 68
67498 TCACTAGGTA
* *
67508 GTATCGATACTACCAACATTATTTAAATTCCAGAATGTAAAAATGGTACCGATACCCAAAGGGGT
1 GTATCGATACTACCAACATTACTCAAATTCCAGAATGTAAAAATGGTACCGATACCCAAAGGGGT
67573 ACC
66 ACC
* *
67576 GTATCGATACTACCAACATTGCTCAAATTCCAGAATGTAAAAATGGTATCGATACCCAAAGGGGT
1 GTATCGATACTACCAACATTACTCAAATTCCAGAATGTAAAAATGGTACCGATACCCAAAGGGGT
67641 ACC
66 ACC
67644 G
1 G
67645 ATACTACTTT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 65 1.00
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.24
Consensus pattern (68 bp):
GTATCGATACTACCAACATTACTCAAATTCCAGAATGTAAAAATGGTACCGATACCCAAAGGGGT
ACC
Found at i:73255 original size:4 final size:4
Alignment explanation
Indices: 73248--73277 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
73238 AAATGACACA
73248 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
73278 GAGAACCACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Done.