Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004172.1 Hibiscus syriacus cultivar Beakdansim tig00009127_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: 73988
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:66 original size:23 final size:21
Alignment explanation
Indices: 1--71 Score: 72
Period size: 23 Copynumber: 3.3 Consensus size: 21
*
1 ACGAGATAAATGAAAATCGCA
1 ACGAGAAAAATGAAAATCGCA
* **
22 ACGTG-AAAATGACTATCTGCA
1 ACGAGAAAAATGAAAATC-GCA
43 ACGAGAAAAAATGAAAAATCGCA
1 ACGAG-AAAAATG-AAAATCGCA
66 ACGAGA
1 ACGAGA
72 GAATCGCAAC
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
20 9 0.23
21 11 0.28
22 1 0.03
23 14 0.36
24 4 0.10
ACGTcount: A:0.51, C:0.15, G:0.20, T:0.14
Consensus pattern (21 bp):
ACGAGAAAAATGAAAATCGCA
Found at i:121 original size:19 final size:19
Alignment explanation
Indices: 97--202 Score: 82
Period size: 19 Copynumber: 5.8 Consensus size: 19
87 ACCAAATGCA
*
97 TTGCGATTTTCATTTTGCG
1 TTGCGATTTTCATTTCGCG
116 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
135 TTGCGA---TC---TCTCG
1 TTGCGATTTTCATTTCGCG
*
148 TTGCGA-TTTCATTCTCTCG
1 TTGCGATTTTCATT-TCGCG
*** *
167 TTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCATT-TCGCG
187 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
203 AACCAAAAGA
Statistics
Matches: 73, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
13 10 0.14
15 2 0.03
16 2 0.03
19 37 0.51
20 22 0.30
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:199 original size:20 final size:19
Alignment explanation
Indices: 141--200 Score: 84
Period size: 20 Copynumber: 3.1 Consensus size: 19
131 CGCGTTGCGA
141 TCTCTCGTTGCGATTTCAT
1 TCTCTCGTTGCGATTTCAT
**
160 TCTCTCGTTGCGACAGTCAT
1 TCTCTCGTTGCGA-TTTCAT
180 TCTCTCGTTGCGATTTTCAT
1 TCTCTCGTTGCGA-TTTCAT
200 T
1 T
201 TCAACCAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 13 0.37
20 22 0.63
ACGTcount: A:0.12, C:0.27, G:0.17, T:0.45
Consensus pattern (19 bp):
TCTCTCGTTGCGATTTCAT
Found at i:2173 original size:93 final size:93
Alignment explanation
Indices: 1872--2173 Score: 565
Period size: 92 Copynumber: 3.3 Consensus size: 93
1862 TAGTAAATTA
*
1872 TCGGTTGCTGCCAATTCTGCTAAACTGTGTATTC-TTAACACT-AGAAATAGTATTTGTCTTTGT
1 TCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGT
1935 TTTGTCTTTTGGTTGAAAGTAAATTTGT
66 TTTGTCTTTTGGTTGAAAGTAAATTTGT
*
1963 TCGGTTGCTGCCAATTCTGCTAAACTATGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGT
1 TCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGT
2028 TTTGTC-TTTGGTTGAAAGTAAATTTGT
66 TTTGTCTTTTGGTTGAAAGTAAATTTGT
2055 TCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGT
1 TCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGT
2120 TTTGTCTTTTGGTTGAAAGTAAATTTGT
66 TTTGTCTTTTGGTTGAAAGTAAATTTGT
2148 TCGGTTGCTGCCAATTCTGCTAAACT
1 TCGGTTGCTGCCAATTCTGCTAAACT
2174 ATACCTGAAG
Statistics
Matches: 205, Mismatches: 3, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
91 33 0.16
92 99 0.48
93 73 0.36
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.45
Consensus pattern (93 bp):
TCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGT
TTTGTCTTTTGGTTGAAAGTAAATTTGT
Found at i:2304 original size:14 final size:14
Alignment explanation
Indices: 2285--2341 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
2275 CGAAACTTAA
2285 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2299 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
2318 AATCGCAACGACAG
1 AATCGCAACGAGAG
2332 AATCGCAACG
1 AATCGCAACG
2342 CGAAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2323 original size:19 final size:18
Alignment explanation
Indices: 2299--2360 Score: 60
Period size: 19 Copynumber: 3.6 Consensus size: 18
2289 GCAACGAGAG
2299 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAA-GAA
*
2318 AATCGCAA--CGACAG--
1 AATCGCAACGCGAAAGAA
*
2332 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
2351 AATCGCAACG
1 AATCGCAACG
2361 ACAAAATCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 8 0.23
16 5 0.14
17 4 0.11
19 18 0.51
ACGTcount: A:0.45, C:0.27, G:0.19, T:0.08
Consensus pattern (18 bp):
AATCGCAACGCGAAAGAA
Found at i:2325 original size:33 final size:33
Alignment explanation
Indices: 2267--2390 Score: 176
Period size: 33 Copynumber: 3.7 Consensus size: 33
2257 TAGTTTACTT
* * *
2267 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGACAGAA
**
2301 TCGCAACGCGAAATGAAAATCGCAACGACAGAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
*
2334 TCGCAACGCGAAACCAAAATCGCAACGACAAAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
*
2367 TCGCAACGCAAAACCAAAATCGCA
1 TCGCAACGCGAAACCAAAATCGCA
2391 TTGCGATTTT
Statistics
Matches: 82, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
33 70 0.85
34 12 0.15
ACGTcount: A:0.47, C:0.27, G:0.17, T:0.09
Consensus pattern (33 bp):
TCGCAACGCGAAACCAAAATCGCAACGACAGAA
Found at i:2367 original size:14 final size:14
Alignment explanation
Indices: 2316--2379 Score: 67
Period size: 14 Copynumber: 4.3 Consensus size: 14
2306 ACGCGAAATG
2316 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
2330 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
2349 AAAATCGCAACGAC
1 AAAATCGCAACGAC
2363 AAAATCGCAACG-C
1 AAAATCGCAACGAC
2376 AAAA
1 AAAA
2380 CCAAAATCGC
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
13 5 0.12
14 22 0.51
15 1 0.02
16 2 0.05
17 2 0.05
18 1 0.02
19 10 0.23
ACGTcount: A:0.50, C:0.28, G:0.16, T:0.06
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:2376 original size:19 final size:19
Alignment explanation
Indices: 2332--2390 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
2322 GCAACGACAG
*
2332 AATCGCAACGCGAAACCAA
1 AATCGCAACGCAAAACCAA
2351 AATCGCAACG----A-CAA
1 AATCGCAACGCAAAACCAA
2365 AATCGCAACGCAAAACCAA
1 AATCGCAACGCAAAACCAA
2384 AATCGCA
1 AATCGCA
2391 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 13 0.37
15 1 0.03
18 1 0.03
19 20 0.57
ACGTcount: A:0.49, C:0.31, G:0.14, T:0.07
Consensus pattern (19 bp):
AATCGCAACGCAAAACCAA
Found at i:2408 original size:19 final size:19
Alignment explanation
Indices: 2386--2539 Score: 130
Period size: 19 Copynumber: 8.6 Consensus size: 19
2376 AAAACCAAAA
*
2386 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2405 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
2424 TCGCATTGCGA--TT--TG
1 TCGCGTTGCGATTTTCATT
*
2439 T--CGTTACGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
2456 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* **
2475 TCGCGTTACGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
2494 TCTCGTTGCGA---TCATT
1 TCGCGTTGCGATTTTCATT
2510 TCGCGTTGCGATTTT-AGTT
1 TCGCGTTGCGATTTTCA-TT
*
2529 TCGTGTTGCGA
1 TCGCGTTGCGA
2540 AAGTAAACTA
Statistics
Matches: 109, Mismatches: 16, Indels: 20
0.75 0.11 0.14
Matches are distributed among these distances:
13 6 0.06
15 4 0.04
16 13 0.12
17 4 0.04
18 1 0.01
19 81 0.74
ACGTcount: A:0.12, C:0.19, G:0.23, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2454 original size:32 final size:32
Alignment explanation
Indices: 2408--2469 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
2398 TTTCATTTCG
*
2408 CGTTGCGATTTTCATTTCGCATTGCGATTTGT
1 CGTTACGATTTTCATTTCGCATTGCGATTTGT
*
2440 CGTTACGATTTTCATTTCGCGTTGCGATTT
1 CGTTACGATTTTCATTTCGCATTGCGATTT
2470 TGGTTTCGCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.47
Consensus pattern (32 bp):
CGTTACGATTTTCATTTCGCATTGCGATTTGT
Found at i:2522 original size:35 final size:35
Alignment explanation
Indices: 2473--2539 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
2463 GCGATTTTGG
*
2473 TTTCGCGTTACGATTTTGGTTTC-TCGTTGCGATCA
1 TTTCGCGTTACGATTTTAGTTTCGT-GTTGCGATCA
*
2508 TTTCGCGTTGCGATTTTAGTTTCGTGTTGCGA
1 TTTCGCGTTACGATTTTAGTTTCGTGTTGCGA
2540 AAGTAAACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 28 0.97
36 1 0.03
ACGTcount: A:0.10, C:0.18, G:0.25, T:0.46
Consensus pattern (35 bp):
TTTCGCGTTACGATTTTAGTTTCGTGTTGCGATCA
Found at i:3049 original size:20 final size:20
Alignment explanation
Indices: 2991--3050 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
2981 CTCGAGAGTC
*
2991 CCCTCCCACCGTTCAAGAGG
1 CCCTCCCACCATTCAAGAGG
** * *
3011 CCACTGTCATCATTGAAGAGG
1 CC-CTCCCACCATTCAAGAGG
*
3032 TCCTCCCACCATTCAAGAG
1 CCCTCCCACCATTCAAGAG
3051 CCCGATTCAC
Statistics
Matches: 29, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.25, C:0.37, G:0.18, T:0.20
Consensus pattern (20 bp):
CCCTCCCACCATTCAAGAGG
Found at i:4465 original size:14 final size:14
Alignment explanation
Indices: 4446--4481 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
4436 ACTGTTTAAT
4446 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
4460 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
4474 TGATTTGT
1 TGATTTGT
4482 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:4663 original size:20 final size:19
Alignment explanation
Indices: 4587--4685 Score: 136
Period size: 20 Copynumber: 5.4 Consensus size: 19
4577 AAAAATGACT
4587 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
4606 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
4625 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
4639 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
4659 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
4679 ATCGCAA
1 ATCGCAA
4686 CGAGAATCGC
Statistics
Matches: 72, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 1 0.01
17 3 0.04
19 27 0.38
20 30 0.42
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:4691 original size:52 final size:52
Alignment explanation
Indices: 4587--4701 Score: 198
Period size: 52 Copynumber: 2.2 Consensus size: 52
4577 AAAAATGACT
4587 ATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAC-AGAGA
4639 ATCGCAATGCGGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAAC-GAGA
1 ATCGCAATGCGGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACAGAGA
4691 ATCGCAATGCG
1 ATCGCAATGCG
4702 ATTTTCATTT
Statistics
Matches: 61, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
52 25 0.41
53 19 0.31
54 17 0.28
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.14
Consensus pattern (52 bp):
ATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACAGAGA
Found at i:4841 original size:72 final size:71
Alignment explanation
Indices: 4693--4925 Score: 248
Period size: 72 Copynumber: 3.2 Consensus size: 71
4683 CAACGAGAAT
* * * * * *
4693 CGCAATGCGATTTTCATTTCGCATTGCGATT-TTCATTTCCGCA-TTGCGATTCTCTCGTTGCGA
1 CGCATTGCGATTTTCATTTCGCATTGCGATTCTTC-GTTGCG-ATTTTC-ATT-TCGCATTGCGA
4756 TTTTCATTT-
62 TTTTCATTTC
4765 CGCATTGCGATTTTCATTTCGCATTGCGATTCTATCGTTGCGATTTTCATTTCGCATTGCGATTT
1 CGCATTGCGATTTTCATTTCGCATTGCGATTCT-TCGTTGCGATTTTCATTTCGCATTGCGATTT
4830 TCATTTC
65 TCATTTC
*
4837 CGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
1 CGCATTGCGATTTTCATTTCGCATTGCGA--TTC--TTCG--TTGCGATTTTCATTTCGCATTGC
4897 GATTTTCATTTC
60 GATTTTCATTTC
4909 CGCATTGCGATTTTCAT
1 CGCATTGCGATTTTCAT
4926 GTTGGGATTT
Statistics
Matches: 141, Mismatches: 7, Indels: 23
0.82 0.04 0.13
Matches are distributed among these distances:
67 6 0.04
69 7 0.05
70 6 0.04
71 19 0.13
72 89 0.63
73 8 0.06
74 5 0.04
75 1 0.01
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (71 bp):
CGCATTGCGATTTTCATTTCGCATTGCGATTCTTCGTTGCGATTTTCATTTCGCATTGCGATTTT
CATTTC
Found at i:4880 original size:105 final size:109
Alignment explanation
Indices: 4698--4967 Score: 434
Period size: 105 Copynumber: 2.6 Consensus size: 109
4688 AGAATCGCAA
4698 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
4763 TTCGCATTGCGATTTTCATTTCGCATTGCGA-TTC-TAT-CG-T
66 TTCGCATTGCGATTTTCATTTCGCATTGCGATTTCATATCCGAT
4803 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
*
4868 TTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCAT
66 TTCGCATTGCGATTTTCATTTCGCATTGCGA-TTTCATATCCG-AT
*
4914 TGCGATTTTCA--T-G--TTGGGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATT
4968 GTAATTTCCG
Statistics
Matches: 157, Mismatches: 2, Indels: 12
0.92 0.01 0.07
Matches are distributed among these distances:
105 122 0.78
106 14 0.09
107 3 0.02
108 3 0.02
109 3 0.02
111 12 0.08
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (109 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
TTCGCATTGCGATTTTCATTTCGCATTGCGATTTCATATCCGAT
Found at i:4935 original size:72 final size:72
Alignment explanation
Indices: 4720--4953 Score: 288
Period size: 72 Copynumber: 3.3 Consensus size: 72
4710 TTCGCATTGC
*
4720 GATTTTCATTTCCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTT-CGCATTGCGATTTT
1 GATTTTCATTT-CGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTT
*
4779 CAT-TTCG
65 CATGTTGG
* * ** * *
4786 CA-TTGCGATTCTATCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTC
1 GATTTTC-ATT-TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTT
*
4850 TC-TCGTTGC
64 TCAT-GTTGG
4859 GATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTC
1 GATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTC
4924 ATGTTGG
66 ATGTTGG
4931 GATTTTCATTTCGCATTGCGATT
1 GATTTTCATTTCGCATTGCGATT
4954 CTCTCGTTGC
Statistics
Matches: 140, Mismatches: 16, Indels: 18
0.80 0.09 0.10
Matches are distributed among these distances:
65 3 0.02
66 11 0.08
67 1 0.01
68 3 0.02
69 4 0.03
71 16 0.11
72 92 0.66
73 7 0.05
74 3 0.02
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.46
Consensus pattern (72 bp):
GATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTC
ATGTTGG
Found at i:4982 original size:53 final size:52
Alignment explanation
Indices: 4698--4967 Score: 406
Period size: 53 Copynumber: 5.1 Consensus size: 52
4688 AGAATCGCAA
4698 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
*
4751 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTATCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
4803 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
*
4856 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG--T
*
4914 TGCGATTTTCA--T-G--TTGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
4961 TGCGATT
1 TGCGATT
4968 GTAATTTCCG
Statistics
Matches: 205, Mismatches: 5, Indels: 20
0.89 0.02 0.09
Matches are distributed among these distances:
47 8 0.04
49 2 0.01
50 2 0.01
51 3 0.01
52 61 0.30
53 108 0.53
54 3 0.01
55 3 0.01
56 3 0.01
58 12 0.06
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (52 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:7266 original size:12 final size:12
Alignment explanation
Indices: 7249--7273 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
7239 TCTTCGGGGA
7249 CTTTTTCTTCTT
1 CTTTTTCTTCTT
7261 CTTTTTCTTCTT
1 CTTTTTCTTCTT
7273 C
1 C
7274 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:8215 original size:20 final size:20
Alignment explanation
Indices: 8187--8415 Score: 235
Period size: 20 Copynumber: 11.4 Consensus size: 20
8177 AAATTTCAGT
* * *
8187 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
8207 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
8227 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
8247 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
8267 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
8287 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
8307 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
8327 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
8347 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
8367 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
8387 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
8407 GTTGCGATT
1 GTTGCGATT
8416 CTTGAAAATC
Statistics
Matches: 181, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 180 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:8468 original size:21 final size:20
Alignment explanation
Indices: 8383--8480 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
8373 ATTTATGTGT
* *
8383 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCAAAA
*
8403 TCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGATT-TTCAAAA
** **
8424 TCGCAATGCGAATTTGT-ACTA
1 TCGCGTTGCG-ATTT-TCAAAA
*
8445 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTCAA-AA
8466 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
8481 GGAAACTGAT
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
19 1 0.02
20 18 0.29
21 39 0.63
22 4 0.06
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCAAAA
Found at i:8476 original size:42 final size:43
Alignment explanation
Indices: 8383--8481 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
8373 ATTTATGTGT
* *
8383 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
**
8424 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATT-TTCAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTCTTCAA-AA
*
8466 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
8482 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 12 0.26
42 32 0.68
43 3 0.06
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
Found at i:9882 original size:20 final size:21
Alignment explanation
Indices: 9843--9882 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
9833 AGCGCTACCT
*
9843 AAAATATTATTTTTTCTATCG
1 AAAATATTATATTTTCTATCG
*
9864 AAAATATTA-ATTTTGTATC
1 AAAATATTATATTTTCTATC
9883 TAATTTTAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (21 bp):
AAAATATTATATTTTCTATCG
Found at i:10254 original size:50 final size:50
Alignment explanation
Indices: 10186--10308 Score: 144
Period size: 50 Copynumber: 2.5 Consensus size: 50
10176 TTAGCAGAAA
* *
10186 AGCGCG-CCCCTGCACCGCGCTATATGCTGATTTGACGT-CACGTGGGTAT
1 AGCGCGCCCCCTGCACCGCGCTATACGCTGATCTGAC-TCCACGTGGGTAT
* * * *
10235 AGCGCGCCCCCTGCCCCGCGATATACGGTGATCTGGCTCCACGTGGGTAT
1 AGCGCGCCCCCTGCACCGCGCTATACGCTGATCTGACTCCACGTGGGTAT
*
10285 AGCGCGCCCCTTG-ATCCGCGCTAT
1 AGCGCGCCCCCTGCA-CCGCGCTAT
10309 CCCTGGATAT
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
49 7 0.11
50 55 0.89
ACGTcount: A:0.15, C:0.35, G:0.28, T:0.22
Consensus pattern (50 bp):
AGCGCGCCCCCTGCACCGCGCTATACGCTGATCTGACTCCACGTGGGTAT
Found at i:10728 original size:111 final size:111
Alignment explanation
Indices: 10603--10816 Score: 358
Period size: 111 Copynumber: 1.9 Consensus size: 111
10593 ATATATCTCT
* *
10603 ACACTTTGCTGATACGGTAACATTTTAACATTTTAATTTAATTTTAATTATAAGTAATATTTAGT
1 ACACTTTGCTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATAAGTAATAATTAGT
* *
10668 TGATTTA-TTATGTGCATGATTATTAGATTAAGAATTAAATATATCG
66 TGATTCATTTA-ATGCATGATTATTAGATTAAGAATTAAATATATCG
* *
10714 ACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
1 ACACTTTGCTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATAAGTAATAATTAGT
10779 TGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
66 TGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
10817 TTTTTGTAAT
Statistics
Matches: 96, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
111 93 0.97
112 3 0.03
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.44
Consensus pattern (111 bp):
ACACTTTGCTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATAAGTAATAATTAGT
TGATTCATTTAATGCATGATTATTAGATTAAGAATTAAATATATCG
Found at i:16587 original size:50 final size:50
Alignment explanation
Indices: 16500--16597 Score: 124
Period size: 50 Copynumber: 2.0 Consensus size: 50
16490 GGGGGGGGGG
* * * *
16500 GCTATACCCACGTGGCGCCAGATCACCGTATATCGCGGGGCAGGGGGCGC
1 GCTATACCCACGTGACGCCAAATCACCATATAGCGCGGGGCAGGGGGCGC
* * * *
16550 GCTATACCCACGTGACGCTAAATCAGCATATAGCGCGGTGTAGGGGGC
1 GCTATACCCACGTGACGCCAAATCACCATATAGCGCGGGGCAGGGGGC
16598 ACACTTTTCT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 40 1.00
ACGTcount: A:0.21, C:0.29, G:0.34, T:0.16
Consensus pattern (50 bp):
GCTATACCCACGTGACGCCAAATCACCATATAGCGCGGGGCAGGGGGCGC
Found at i:16800 original size:20 final size:20
Alignment explanation
Indices: 16777--16821 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
16767 ATCATTTTAA
*
16777 ATTTTGATGTGACATTTGTG
1 ATTTTGATGTGACATTTATG
*
16797 ATTTTGATGTGACGTTTATG
1 ATTTTGATGTGACATTTATG
16817 ATTTT
1 ATTTT
16822 CACGATATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.20, C:0.04, G:0.22, T:0.53
Consensus pattern (20 bp):
ATTTTGATGTGACATTTATG
Found at i:17318 original size:20 final size:20
Alignment explanation
Indices: 17295--17523 Score: 170
Period size: 20 Copynumber: 11.3 Consensus size: 20
17285 AATATGTAAA
*
17295 TCGCAACACAGAAGTCAAAT
1 TCGCAACACTGAAGTCAAAT
* *
17315 TCGCAAC-GTGATAGTTAAAT
1 TCGCAACACTGA-AGTCAAAT
17335 TCGCAACACTGAAGTCAAAT
1 TCGCAACACTGAAGTCAAAT
**
17355 TCGCAACACAAAAGTCAAAT
1 TCGCAACACTGAAGTCAAAT
*
17375 TCGCAAC-GTGATAGTCAAAT
1 TCGCAACACTGA-AGTCAAAT
* *
17395 TCGTAAC-GTGAA-TCTGTAAA-
1 TCGCAACACTGAAGTC---AAAT
*
17415 TCGCAACGC-GAATTTGT-AAA-
1 TCGCAACACTGAA---GTCAAAT
*
17435 TCGCAACACAGAAGTCAAAT
1 TCGCAACACTGAAGTCAAAT
* *
17455 TCGCAACA-AGATGGTCAAAT
1 TCGCAACACTGA-AGTCAAAT
*
17475 TCGCAACACTGAATTTCAAAT
1 TCGCAACACTGAA-GTCAAAT
*
17496 TCGCAACACTGAATTTCAAAT
1 TCGCAACACTGAA-GTCAAAT
17517 TCGCAAC
1 TCGCAAC
17524 TCGATTTTCG
Statistics
Matches: 174, Mismatches: 18, Indels: 33
0.77 0.08 0.15
Matches are distributed among these distances:
18 4 0.02
19 10 0.06
20 114 0.66
21 45 0.26
24 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.23
Consensus pattern (20 bp):
TCGCAACACTGAAGTCAAAT
Found at i:17419 original size:60 final size:59
Alignment explanation
Indices: 17270--17421 Score: 191
Period size: 60 Copynumber: 2.5 Consensus size: 59
17260 ACTCAGTTTC
* * *
17270 CAAATTCACAACGCGAATATGTAAATCGCAACACAGAAGTCAAATTCGCAACGTGATAGT
1 CAAATTCGCAACGTGAAT-TGTAAATCGCAACACAAAAGTCAAATTCGCAACGTGATAGT
* *
17330 TAAATTCGCAACACTGAA--GTCAAATTCGCAACACAAAAGTCAAATTCGCAACGTGATAGT
1 CAAATTCGCAAC-GTGAATTGT-AAA-TCGCAACACAAAAGTCAAATTCGCAACGTGATAGT
*
17390 CAAATTCGTAACGTGAATCTGTAAATCGCAAC
1 CAAATTCGCAACGTGAAT-TGTAAATCGCAAC
17422 GCGAATTTGT
Statistics
Matches: 78, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
58 2 0.03
59 7 0.09
60 61 0.78
61 6 0.08
62 2 0.03
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.22
Consensus pattern (59 bp):
CAAATTCGCAACGTGAATTGTAAATCGCAACACAAAAGTCAAATTCGCAACGTGATAGT
Found at i:17738 original size:14 final size:15
Alignment explanation
Indices: 17719--17757 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
17709 TCCCCATCTC
17719 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
17733 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
17749 TAATTTTTT
1 TAATTTTTT
17758 AATGATTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 7 0.32
15 5 0.23
16 10 0.45
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:20798 original size:18 final size:18
Alignment explanation
Indices: 20775--20810 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
20765 AAGAAAAAGG
*
20775 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
20793 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
20811 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:21235 original size:14 final size:14
Alignment explanation
Indices: 21218--21251 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
21208 AAATTAAACT
21218 AATCAACTTTTACA
1 AATCAACTTTTACA
21232 AATCAACTTTTACA
1 AATCAACTTTTACA
21246 AATCAA
1 AATCAA
21252 TTAAACAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (14 bp):
AATCAACTTTTACA
Found at i:22678 original size:21 final size:21
Alignment explanation
Indices: 22630--22748 Score: 98
Period size: 21 Copynumber: 5.7 Consensus size: 21
22620 GTGAATCGGG
* *
22630 CTCTTGAACAGTGAGAGGGAC
1 CTCTTGAACAATGAGAGGGGC
*
22651 C-CATTGAACAATGACAGGGGC
1 CTC-TTGAACAATGAGAGGGGC
** *
22672 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACAATGAGAGGGGC
* *
22693 CTCTTGAACGATGAGAGGAGC
1 CTCTTGAACAATGAGAGGGGC
* * *
22714 CTCTTGAACGAT-AGGAGGCGT
1 CTCTTGAACAATGA-GAGGGGC
*
22735 CTCTTGAACGATGA
1 CTCTTGAACAATGA
22749 CAGGTGGATC
Statistics
Matches: 82, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
20 2 0.02
21 78 0.95
22 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.34, T:0.20
Consensus pattern (21 bp):
CTCTTGAACAATGAGAGGGGC
Found at i:22690 original size:42 final size:42
Alignment explanation
Indices: 22630--22723 Score: 118
Period size: 42 Copynumber: 2.2 Consensus size: 42
22620 GTGAATCGGG
* *
22630 CTCTTGAACAGTGAGAGGGACC-CATTGAACAATGACAGGGGC
1 CTCTTGAACGGTGAGAGGGACCTC-TTGAACAATGACAGGAGC
* * * *
22672 CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGAGAGGAGC
1 CTCTTGAACGGTGAGAGGGACCTCTTGAACAATGACAGGAGC
22714 CTCTTGAACG
1 CTCTTGAACG
22724 ATAGGAGGCG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 44 0.98
43 1 0.02
ACGTcount: A:0.26, C:0.21, G:0.34, T:0.19
Consensus pattern (42 bp):
CTCTTGAACGGTGAGAGGGACCTCTTGAACAATGACAGGAGC
Found at i:22731 original size:42 final size:42
Alignment explanation
Indices: 22654--22752 Score: 135
Period size: 42 Copynumber: 2.4 Consensus size: 42
22644 GAGGGACCCA
* * * * *
22654 TTGAACAATGACAGGGGCCTCTTGAACGGTGGGAGGGGCCTC
1 TTGAACGATGACAGGAGCCTCTTGAACGATAGGAGGCGCCTC
* *
22696 TTGAACGATGAGAGGAGCCTCTTGAACGATAGGAGGCGTCTC
1 TTGAACGATGACAGGAGCCTCTTGAACGATAGGAGGCGCCTC
22738 TTGAACGATGACAGG
1 TTGAACGATGACAGG
22753 TGGATCGAGC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.25, C:0.19, G:0.35, T:0.20
Consensus pattern (42 bp):
TTGAACGATGACAGGAGCCTCTTGAACGATAGGAGGCGCCTC
Found at i:23132 original size:63 final size:63
Alignment explanation
Indices: 23065--23204 Score: 158
Period size: 63 Copynumber: 2.2 Consensus size: 63
23055 TTAAAGTAGA
* *
23065 TACCTCATCACGTAGTGCACCATTGTCATCGCGTAAAACATCCACCTCACCACGTAAAG-ACCG
1 TACCTCATCACGTA-TGCACCATTGTCATCACGTAAAACATCCACCTCACCACGCAAAGCACCG
** * ** * **
23128 TACCTCATCACACCATGCACCATTGTCTTCACGTAAAGTATCGACCTCATGACGCAAAGCACCG
1 TACCTCATCAC-GTATGCACCATTGTCATCACGTAAAACATCCACCTCACCACGCAAAGCACCG
23192 -ACCTCATCACGTA
1 TACCTCATCACGTA
23205 ACTCCCCTAA
Statistics
Matches: 63, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
62 1 0.02
63 57 0.90
64 5 0.08
ACGTcount: A:0.30, C:0.35, G:0.14, T:0.21
Consensus pattern (63 bp):
TACCTCATCACGTATGCACCATTGTCATCACGTAAAACATCCACCTCACCACGCAAAGCACCG
Found at i:24945 original size:20 final size:20
Alignment explanation
Indices: 24920--24957 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
24910 TTCGCAACGA
24920 GAAAATCGCAACGCGAAAAT
1 GAAAATCGCAACGCGAAAAT
*
24940 GAAAATCGCAACTCGAAA
1 GAAAATCGCAACGCGAAA
24958 CTAAAATTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.21, G:0.18, T:0.11
Consensus pattern (20 bp):
GAAAATCGCAACGCGAAAAT
Found at i:25602 original size:20 final size:20
Alignment explanation
Indices: 25537--25712 Score: 151
Period size: 20 Copynumber: 8.8 Consensus size: 20
25527 TAAAATAAAA
* *
25537 TTTGCGTTGAGAATTTGACT
1 TTTGTGTTGCGAATTTGACT
* *
25557 TTCGCGTTGCGAATTTGACT
1 TTTGTGTTGCGAATTTGACT
* *
25577 TCTGTGTTGTGAATTTGACT
1 TTTGTGTTGCGAATTTGACT
* *
25597 TTTGTGTTACG-ATTT-ACAAA
1 TTTGTGTTGCGAATTTGAC--T
* * *
25617 TTCGCGTTGC-AAATTGACT
1 TTTGTGTTGCGAATTTGACT
* *
25636 TTTGTATTGCGAATTTAACT
1 TTTGTGTTGCGAATTTGACT
25656 TTTGTGTTGCGAATTTGACT
1 TTTGTGTTGCGAATTTGACT
* * * *
25676 ATCGCGTTGCGAATTTAACT
1 TTTGTGTTGCGAATTTGACT
*
25696 TCTGTGTTGCGAATTTG
1 TTTGTGTTGCGAATTTG
25713 GAAACTGGGT
Statistics
Matches: 120, Mismatches: 31, Indels: 10
0.75 0.19 0.06
Matches are distributed among these distances:
18 2 0.02
19 11 0.09
20 105 0.88
21 2 0.02
ACGTcount: A:0.20, C:0.14, G:0.22, T:0.44
Consensus pattern (20 bp):
TTTGTGTTGCGAATTTGACT
Found at i:25674 original size:40 final size:40
Alignment explanation
Indices: 25537--25712 Score: 167
Period size: 40 Copynumber: 4.4 Consensus size: 40
25527 TAAAATAAAA
* * *
25537 TTTGCGTTGAGAATTTGACTTTCGCGTTGCGAATTTGACT
1 TTTGTGTTGCGAATTTGACTTTCGCGTTGCGAATTTAACT
* * * * * **
25577 TCTGTGTTGTGAATTTGACTTTTGTGTTACG-ATTTACAAA
1 TTTGTGTTGCGAATTTGACTTTCGCGTTGCGAATTTA-ACT
* * * * **
25617 TTCGCGTTGC-AAATTGACTTTTGTATTGCGAATTTAACT
1 TTTGTGTTGCGAATTTGACTTTCGCGTTGCGAATTTAACT
*
25656 TTTGTGTTGCGAATTTGACTATCGCGTTGCGAATTTAACT
1 TTTGTGTTGCGAATTTGACTTTCGCGTTGCGAATTTAACT
*
25696 TCTGTGTTGCGAATTTG
1 TTTGTGTTGCGAATTTG
25713 GAAACTGGGT
Statistics
Matches: 107, Mismatches: 26, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
39 30 0.28
40 77 0.72
ACGTcount: A:0.20, C:0.14, G:0.22, T:0.44
Consensus pattern (40 bp):
TTTGTGTTGCGAATTTGACTTTCGCGTTGCGAATTTAACT
Found at i:25725 original size:99 final size:100
Alignment explanation
Indices: 25547--25732 Score: 225
Period size: 99 Copynumber: 1.9 Consensus size: 100
25537 TTTGCGTTGA
* * * * *
25547 GAATTTGACTTTCGCGTTGCGAATTTGACTTCTGTGTTGTGAATTTGACTTTTGTGTTACGATTT
1 GAATTTAACTTTCGCGTTGCGAATTTGACTTCTGCGTTGCGAATTTAACTTCTGTGTTACGATTT
*
25612 ACAAATTCGCGTTGC-AAATTGACTTTTGTATTGC
66 ACAAACTCGCGTTGCGAAATTGACTTTTGTATTGC
* * *
25646 GAATTTAACTTTTGTGTTGCGAATTTGACTATC-GCGTTGCGAATTTAACTTCTGTGTTGCGAAT
1 GAATTTAACTTTCGCGTTGCGAATTTGACT-TCTGCGTTGCGAATTTAACTTCTGTGTTACG-AT
** *
25710 TTGGAAACT-GGGTTGCGAAATTG
64 TTACAAACTCGCGTTGCGAAATTG
25733 GAGTTCGCGT
Statistics
Matches: 72, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
99 56 0.78
100 16 0.22
ACGTcount: A:0.22, C:0.13, G:0.23, T:0.42
Consensus pattern (100 bp):
GAATTTAACTTTCGCGTTGCGAATTTGACTTCTGCGTTGCGAATTTAACTTCTGTGTTACGATTT
ACAAACTCGCGTTGCGAAATTGACTTTTGTATTGC
Found at i:25744 original size:20 final size:19
Alignment explanation
Indices: 25721--25769 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
25711 TGGAAACTGG
*
25721 GTTGCGAAATTGGAGTTCGC
1 GTTGCG-AATTGGAGATCGC
*
25741 GTTGCGAATTTGAGATCGC
1 GTTGCGAATTGGAGATCGC
*
25760 GTTGTGAATT
1 GTTGCGAATT
25770 TGTTGGTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 20 0.77
20 6 0.23
ACGTcount: A:0.20, C:0.12, G:0.33, T:0.35
Consensus pattern (19 bp):
GTTGCGAATTGGAGATCGC
Found at i:26292 original size:22 final size:24
Alignment explanation
Indices: 26262--26305 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
26252 GTTTGAAATA
26262 TTAAGATATAATAA-ATTTTAACC
1 TTAAGATATAATAATATTTTAACC
*
26285 TTAA-ATATATTAATATTTTAA
1 TTAAGATATAATAATATTTTAA
26306 AATCTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (24 bp):
TTAAGATATAATAATATTTTAACC
Found at i:26482 original size:34 final size:34
Alignment explanation
Indices: 26418--26482 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
26408 CCCAATTGAT
* *
26418 TTTATATTCGTTTGTTTACGTTCGTTTATGTACG
1 TTTATATTCGTTTGTTTACGTTCATGTATGTACG
* **
26452 TTTATGTTCGTTTGTTTGTGTTCATGTATGT
1 TTTATATTCGTTTGTTTACGTTCATGTATGT
26483 TCATTCATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.12, C:0.09, G:0.20, T:0.58
Consensus pattern (34 bp):
TTTATATTCGTTTGTTTACGTTCATGTATGTACG
Found at i:29123 original size:16 final size:16
Alignment explanation
Indices: 29102--29135 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
29092 AATTAAAATC
*
29102 TAAATATTTAGACATA
1 TAAATATTAAGACATA
*
29118 TAAATATTAATACATA
1 TAAATATTAAGACATA
29134 TA
1 TA
29136 GGATTAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (16 bp):
TAAATATTAAGACATA
Found at i:30910 original size:136 final size:136
Alignment explanation
Indices: 30719--31158 Score: 742
Period size: 136 Copynumber: 3.2 Consensus size: 136
30709 CCTTTAAGAC
* * **
30719 GAGTTCTTCTCATTATGAACTCTT--TTGGAAATGTCAATCCCTCTAA-CGAGGTGTCACTGATT
1 GAGTTCTTCTCATTATGAACTCTTCACTGGAAATTTTGATCCCTC-AAGCGAGGTGTCACTGATT
* *
30781 CGAAATGTCGTGAATCGAGTGATAGGTCGAACAAGCTCTTTTCATTATGATCTTCTTCTCCCTCT
65 CGAAATGTCGTGAATCGAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCT
* *
30846 GTTGGAT
130 ATCGGAT
30853 GAGTTCTTCTCATTATGAACTCTTCACTGGAAATTTTGATCCCTCAAGCGAGGTGTCACTGATTC
1 GAGTTCTTCTCATTATGAACTCTTCACTGGAAATTTTGATCCCTCAAGCGAGGTGTCACTGATTC
*
30918 GAAATGTTGTGAATCGAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTA
66 GAAATGTCGTGAATCGAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTA
30983 TCGGAT
131 TCGGAT
30989 GAGTTCTTCTCATTATGAACTCTTCACTGGAAATTTTGATCCCTCAAGCGAGGTGTCACTGATTC
1 GAGTTCTTCTCATTATGAACTCTTCACTGGAAATTTTGATCCCTCAAGCGAGGTGTCACTGATTC
*
31054 AAAATGTCGTGAATCGAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTA
66 GAAATGTCGTGAATCGAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTA
31119 TCGGAT
131 TCGGAT
* *
31125 GAGTTCTTCTCATTATGAACTCTCCATTGGAAAT
1 GAGTTCTTCTCATTATGAACTCTTCACTGGAAAT
31159 GTTGGTTCCC
Statistics
Matches: 290, Mismatches: 13, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
134 24 0.08
135 2 0.01
136 264 0.91
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (136 bp):
GAGTTCTTCTCATTATGAACTCTTCACTGGAAATTTTGATCCCTCAAGCGAGGTGTCACTGATTC
GAAATGTCGTGAATCGAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTA
TCGGAT
Found at i:32022 original size:20 final size:20
Alignment explanation
Indices: 31993--32075 Score: 75
Period size: 20 Copynumber: 4.2 Consensus size: 20
31983 AACCCTCCTT
*
31993 TTTCTCTTTTT-ATTTTTTCA
1 TTTCTTTTTTTCA-TTTTTCA
32013 TTTCTTTTTTTCATTTTTCA
1 TTTCTTTTTTTCATTTTTCA
32033 -TT-TTTTTTTC-TTTTTCA
1 TTTCTTTTTTTCATTTTTCA
* *
32050 TTTTTTCATTTTTCATCTTTTTA
1 TTTCTT--TTTTTCAT-TTTTCA
32073 TTT
1 TTT
32076 GTTCCTTTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
17 7 0.13
18 10 0.19
19 4 0.07
20 17 0.31
21 7 0.13
22 1 0.02
23 8 0.15
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTCTTTTTTTCATTTTTCA
Found at i:32037 original size:17 final size:17
Alignment explanation
Indices: 32017--32071 Score: 71
Period size: 18 Copynumber: 3.3 Consensus size: 17
32007 TTTTCATTTC
32017 TTTTTTTCATTTTTCATT
1 TTTTTTTCATTTTTCA-T
32035 TTTTTTTC-TTTTTCA-
1 TTTTTTTCATTTTTCAT
32050 -TTTTTTCATTTTTCAT
1 TTTTTTTCATTTTTCAT
32066 CTTTTT
1 -TTTTT
32072 ATTTGTTCCT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
14 7 0.21
15 7 0.21
17 7 0.21
18 12 0.36
ACGTcount: A:0.09, C:0.13, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTTTCATTTTTCAT
Found at i:32051 original size:24 final size:24
Alignment explanation
Indices: 32019--32087 Score: 79
Period size: 24 Copynumber: 2.9 Consensus size: 24
32009 TTCATTTCTT
*
32019 TTTTTCATTTTTCATTTTTTTTTC
1 TTTTTCATTTTTCATTTTTTTATC
*
32043 TTTTTCATTTTTTCA-TTTTTCATC
1 TTTTTCA-TTTTTCATTTTTTTATC
*
32067 TTTTT-ATTTGTTCCTTTTTTT
1 TTTTTCATTT-TTCATTTTTTT
32088 CTTCAAGCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
22 3 0.08
23 4 0.11
24 24 0.63
25 7 0.18
ACGTcount: A:0.09, C:0.13, G:0.01, T:0.77
Consensus pattern (24 bp):
TTTTTCATTTTTCATTTTTTTATC
Found at i:32054 original size:32 final size:31
Alignment explanation
Indices: 32005--32071 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 31
31995 TCTCTTTTTA
* *
32005 TTTTTTCATTTCTTTTTTTCATTTTTCATTT
1 TTTTTTCATTTCATTTTTTCATTTTTCATCT
*
32036 TTTTTTCTTTTTCATTTTTTCATTTTTCATCT
1 TTTTTTC-ATTTCATTTTTTCATTTTTCATCT
32068 TTTT
1 TTTT
32072 ATTTGTTCCT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 7 0.22
32 25 0.78
ACGTcount: A:0.09, C:0.13, G:0.00, T:0.78
Consensus pattern (31 bp):
TTTTTTCATTTCATTTTTTCATTTTTCATCT
Found at i:32086 original size:32 final size:32
Alignment explanation
Indices: 32016--32088 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
32006 TTTTTCATTT
* * *
32016 CTTTTTTTCATTTTTCATTTTTTTTTCTTTTT
1 CTTTTTTTCATTTTTCATTTTTTATTCTGTTC
*
32048 CATTTTTTCATTTTTCATCTTTTTATT-TGTTC
1 CTTTTTTTCATTTTTCAT-TTTTTATTCTGTTC
32080 CTTTTTTTC
1 CTTTTTTTC
32089 TTCAAGCATA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
32 28 0.80
33 7 0.20
ACGTcount: A:0.08, C:0.15, G:0.01, T:0.75
Consensus pattern (32 bp):
CTTTTTTTCATTTTTCATTTTTTATTCTGTTC
Found at i:43994 original size:17 final size:17
Alignment explanation
Indices: 43972--44005 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
43962 ATTAAAATCT
*
43972 AAATATTTAGACATATA
1 AAATATTAAGACATATA
*
43989 AAATATTAATACATATA
1 AAATATTAAGACATATA
44006 GGATTAAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.35
Consensus pattern (17 bp):
AAATATTAAGACATATA
Found at i:50942 original size:11 final size:11
Alignment explanation
Indices: 50922--50954 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
50912 GGAATGGCAA
50922 CGGGGCGGGTT
1 CGGGGCGGGTT
*
50933 CGGGGTGGGTT
1 CGGGGCGGGTT
50944 CGGGGCGGGTT
1 CGGGGCGGGTT
50955 TTGCTCTCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.64, T:0.21
Consensus pattern (11 bp):
CGGGGCGGGTT
Found at i:51130 original size:9 final size:9
Alignment explanation
Indices: 51116--51154 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
51106 ACCCGTATTA
*
51116 AAAAAATAG
1 AAAAAATAT
51125 AAAAAATAT
1 AAAAAATAT
51134 -AAAAATAT
1 AAAAAATAT
51142 AAAAAATAT
1 AAAAAATAT
51151 AAAA
1 AAAA
51155 TATTATATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
8 8 0.29
9 20 0.71
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (9 bp):
AAAAAATAT
Found at i:51137 original size:7 final size:7
Alignment explanation
Indices: 51127--51186 Score: 50
Period size: 7 Copynumber: 8.0 Consensus size: 7
51117 AAAAATAGAA
51127 AAAATAT
1 AAAATAT
51134 AAAAATAT
1 -AAAATAT
51142 AAAAAATAT
1 --AAAATAT
51151 AAAATAT
1 AAAATAT
* *
51158 TATATAT
1 AAAATAT
51165 AATTAATAT
1 AA--AATAT
51174 AAAA-AT
1 AAAATAT
51180 AAAATAT
1 AAAATAT
51187 TATATATATA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
6 6 0.14
7 17 0.39
8 7 0.16
9 14 0.32
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
AAAATAT
Found at i:51139 original size:17 final size:17
Alignment explanation
Indices: 51117--51154 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
51107 CCCGTATTAA
51117 AAAAATAGAAAAAATAT
1 AAAAATAGAAAAAATAT
*
51134 AAAAATATAAAAAATAT
1 AAAAATAGAAAAAATAT
51151 AAAA
1 AAAA
51155 TATTATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (17 bp):
AAAAATAGAAAAAATAT
Found at i:51194 original size:2 final size:2
Alignment explanation
Indices: 51183--51212 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
51173 TAAAAATAAA
51183 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
51213 ATCGGGGCGG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52159 original size:60 final size:60
Alignment explanation
Indices: 52092--52204 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
52082 GAACATATGA
* *
52092 ATAGTCGGATGACTC-TTTTGTAATTTTTAATAGTCGAA-GGACTCAACAAAGCAAAGCTTT
1 ATAGTCGGAGGAC-CATTTTGTAACTTTTAATAGTC-AATGGACTCAACAAAGCAAAGCTTT
* *
52152 ATAGTCGGAGGACCATTTTGTAACTTTTAATAGTCAATGGACTTAATAAAGCA
1 ATAGTCGGAGGACCATTTTGTAACTTTTAATAGTCAATGGACTCAACAAAGCA
52205 TTACCCTATA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
59 3 0.06
60 44 0.94
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (60 bp):
ATAGTCGGAGGACCATTTTGTAACTTTTAATAGTCAATGGACTCAACAAAGCAAAGCTTT
Found at i:54845 original size:29 final size:29
Alignment explanation
Indices: 54799--54860 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
54789 GTAGTAAACT
*
54799 ATAGTCGAGGGACCATTTTATAACTTTTA
1 ATAGGCGAGGGACCATTTTATAACTTTTA
* *
54828 ATAGGCGATGGACTATTTTATAACTTTTA
1 ATAGGCGAGGGACCATTTTATAACTTTTA
54857 ATAG
1 ATAG
54861 CCGGTGACTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (29 bp):
ATAGGCGAGGGACCATTTTATAACTTTTA
Found at i:54905 original size:88 final size:89
Alignment explanation
Indices: 54753--54919 Score: 232
Period size: 88 Copynumber: 1.9 Consensus size: 89
54743 TCGAATGACC
* ** *
54753 ATTTTGTAACTTTTAATAGGTGAATGACTCAACAAAGTAGTAAACTATAGTCGAGGGACCATTTT
1 ATTTTATAACTTTTAATAGCCGAATGACTCAACAAAGCAGTAAACTATAGTCGAGGGACCATTTT
54818 ATAACTTTTAATAGGCGATGGACT
66 ATAACTTTTAATAGGCGATGGACT
* * *
54842 ATTTTATAACTTTTAATAGCCG-GTGACTCAACAAAGCA-TAATCCTATAGTCG-GGAGACTATT
1 ATTTTATAACTTTTAATAGCCGAATGACTCAACAAAGCAGTAA-ACTATAGTCGAGG-GACCATT
54904 TTATAACTTTTAATAG
64 TTATAACTTTTAATAG
54920 TCAAGAGACC
Statistics
Matches: 69, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
87 5 0.07
88 45 0.65
89 19 0.28
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.35
Consensus pattern (89 bp):
ATTTTATAACTTTTAATAGCCGAATGACTCAACAAAGCAGTAAACTATAGTCGAGGGACCATTTT
ATAACTTTTAATAGGCGATGGACT
Found at i:55983 original size:5 final size:6
Alignment explanation
Indices: 55958--55982 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
55948 TGTATTACTT
55958 AATAAA AATAAA AATAAA AATAAA A
1 AATAAA AATAAA AATAAA AATAAA A
55983 TGATATATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AATAAA
Found at i:58164 original size:31 final size:31
Alignment explanation
Indices: 58087--58168 Score: 101
Period size: 31 Copynumber: 2.6 Consensus size: 31
58077 AATATGATTC
* * *
58087 TTAAAATTTAGATAAAATCTTAATTTAACCC
1 TTAAAATTTAGATAAAATATTAATATAACCA
* * * *
58118 TGAAATTTTAAATAAAATATTAATATAATCA
1 TTAAAATTTAGATAAAATATTAATATAACCA
58149 TTAAAATTTAGATAAAATAT
1 TTAAAATTTAGATAAAATAT
58169 CAATTTAAAT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (31 bp):
TTAAAATTTAGATAAAATATTAATATAACCA
Found at i:63275 original size:29 final size:29
Alignment explanation
Indices: 63242--63302 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
63232 AAATATTTAA
* *
63242 AATATA-TTTATTAATATTTCTAATAATAT
1 AATATATTTTATTAATA-TTATAATAAAAT
*
63271 AATATATTTTTTTAATATTATAATAAAAT
1 AATATATTTTATTAATATTATAATAAAAT
63300 AAT
1 AAT
63303 CAATTATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 19 0.68
30 9 0.32
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (29 bp):
AATATATTTTATTAATATTATAATAAAAT
Found at i:63486 original size:23 final size:23
Alignment explanation
Indices: 63460--63504 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
63450 AATATAATAA
63460 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
63483 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
63505 ATATAACACT
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:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:63882 original size:15 final size:15
Alignment explanation
Indices: 63849--63921 Score: 62
Period size: 14 Copynumber: 5.1 Consensus size: 15
63839 TTCCAGAAAT
* *
63849 GTAATTCATTTTCCA
1 GTAATTCAATTTACA
63864 -TAATTCAATTTACA
1 GTAATTCAATTTACA
* *
63878 GTAATTCATTTTTCA
1 GTAATTCAATTTACA
*
63893 G-AATTCAATTTCCA
1 GTAATTCAATTTACA
* *
63907 GAAAATCAA-TTACA
1 GTAATTCAATTTACA
63921 G
1 G
63922 CCAAACAAGC
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
14 29 0.60
15 19 0.40
ACGTcount: A:0.37, C:0.16, G:0.07, T:0.40
Consensus pattern (15 bp):
GTAATTCAATTTACA
Found at i:63908 original size:14 final size:14
Alignment explanation
Indices: 63851--63909 Score: 64
Period size: 14 Copynumber: 4.1 Consensus size: 14
63841 CCAGAAATGT
* *
63851 AATTCATTTTCCAT
1 AATTCAATTTCCAG
*
63865 AATTCAATTTACAG
1 AATTCAATTTCCAG
* *
63879 TAATTCATTTTTCAG
1 -AATTCAATTTCCAG
63894 AATTCAATTTCCAG
1 AATTCAATTTCCAG
63908 AA
1 AA
63910 AATCAATTAC
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
14 25 0.68
15 12 0.32
ACGTcount: A:0.36, C:0.17, G:0.05, T:0.42
Consensus pattern (14 bp):
AATTCAATTTCCAG
Found at i:65000 original size:2 final size:2
Alignment explanation
Indices: 64993--65030 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
64983 GCATACGAAG
64993 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
65031 GGTTAAAGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:67954 original size:21 final size:21
Alignment explanation
Indices: 67912--67954 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
67902 GTGATTTTAG
* *
67912 TTTTTTAATTTAATTAATATT
1 TTTTTTAATTTAATCAACATT
*
67933 TTTTTTATTTTAATCAACATT
1 TTTTTTAATTTAATCAACATT
67954 T
1 T
67955 ATTAATATAA
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:0.05, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTTTAATTTAATCAACATT
Found at i:71297 original size:18 final size:18
Alignment explanation
Indices: 71246--71297 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
71236 TTGTTGAAGG
*
71246 ATAACTTAAACAAA-TTA
1 ATAATTTAAACAAATTTA
* **
71263 ATAATTAAAACTTATTTA
1 ATAATTTAAACAAATTTA
71281 ATAATTTAAACAAATTT
1 ATAATTTAAACAAATTT
71298 TAACATTATA
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
17 10 0.37
18 17 0.63
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAATTTAAACAAATTTA
Done.