Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003482.1 Hibiscus syriacus cultivar Beakdansim tig00007356_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: 89927
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:115 original size:21 final size:22
Alignment explanation
Indices: 85--134 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
75 GAAATAAACT
85 TAAAAA-AATTTTAAT-AAAAA
1 TAAAAATAATTTTAATAAAAAA
105 TAAAAATAATTTTAATAAAAAA
1 TAAAAATAATTTTAATAAAAAA
127 TAAAAATA
1 TAAAAATA
135 CTTAATTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 6 0.21
21 9 0.32
22 13 0.46
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (22 bp):
TAAAAATAATTTTAATAAAAAA
Found at i:4104 original size:15 final size:17
Alignment explanation
Indices: 4084--4116 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
4074 ACGAACATAA
4084 AATTTT-AT-ATTAAAT
1 AATTTTAATGATTAAAT
4099 AATTTTAATGATTAAAT
1 AATTTTAATGATTAAAT
4116 A
1 A
4117 GAGTAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 2 0.12
17 8 0.50
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
AATTTTAATGATTAAAT
Found at i:12637 original size:21 final size:21
Alignment explanation
Indices: 12613--12652 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
12603 AGTTTATTTT
12613 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
12634 TAAACTTTGTTTCAATTAT
1 TAAACTTTATTTCAATTAT
12653 TGAACTTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.12, G:0.05, T:0.50
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:12707 original size:33 final size:32
Alignment explanation
Indices: 12643--12719 Score: 102
Period size: 33 Copynumber: 2.4 Consensus size: 32
12633 GTAAACTTTG
* *
12643 TTTCAATTATTGAACTTGTAAGTTTTCAAGTA
1 TTTCAATTATCGAACTTGGAAGTTTTCAAGTA
*
12675 TTTGAATTTATCGAACTTGGAAGTATTT-AAGTA
1 TTTCAA-TTATCGAACTTGGAAGT-TTTCAAGTA
12708 TTTCAATTATCG
1 TTTCAATTATCG
12720 TAAACTTTGT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
32 11 0.28
33 25 0.64
34 3 0.08
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.45
Consensus pattern (32 bp):
TTTCAATTATCGAACTTGGAAGTTTTCAAGTA
Found at i:12933 original size:15 final size:17
Alignment explanation
Indices: 12907--12938 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
12897 GTCTATGGTA
12907 AAAAACTGGAT-CGGAT
1 AAAAACTGGATCCGGAT
12923 AAAAACT-GATCCGGAT
1 AAAAACTGGATCCGGAT
12939 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.16, G:0.22, T:0.19
Consensus pattern (17 bp):
AAAAACTGGATCCGGAT
Found at i:13300 original size:120 final size:122
Alignment explanation
Indices: 13134--13432 Score: 372
Period size: 120 Copynumber: 2.5 Consensus size: 122
13124 TAAGTTTTGT
* * * * * * *
13134 AAAAAATTGAAAGTTTAGATACTAAAACAGATCAAAAGTGATAGTTTAGATATTAAACGTGCTAA
1 AAAAAATTAAAAGTTTAGATACTAAAATAAATCAAAACTGAAAGTTTAGATAATAAACATGCTAA
* * * * *
13199 GTTTTAAACGGTGGGTACT-AAAATGAAATCAAAACTAAACGTTAGGTATGATTTTA
66 GTTTTAAACGGTGGGTACTAAAAATAAAATAAAAACTAAAAGTTAGGAATGATTTAA
* * * * *
13255 AAAAAATT-AAAGTTTAGGTACTAAAATGAACCAAAACTGAAAGTTTAGGTAATAAACATGTTAA
1 AAAAAATTAAAAGTTTAGATACTAAAATAAATCAAAACTGAAAGTTTAGATAATAAACATGCTAA
* *
13319 GTTTTAAACGGTGTGTACTAAAAATAAAATAAAAACTAAAAGTTATGAATGATTTAA
66 GTTTTAAACGGTGGGTACTAAAAATAAAATAAAAACTAAAAGTTAGGAATGATTTAA
*
13376 AAAAAATTAAAAGTTTA-ATTACTAAAATAAATCAAAACTGATAA-TTTAGATACTAAA
1 AAAAAATTAAAAGTTTAGA-TACTAAAATAAATCAAAACTGA-AAGTTTAGATAATAAA
13433 TATATAATTT
Statistics
Matches: 151, Mismatches: 23, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
120 63 0.42
121 47 0.31
122 39 0.26
123 2 0.01
ACGTcount: A:0.49, C:0.07, G:0.14, T:0.29
Consensus pattern (122 bp):
AAAAAATTAAAAGTTTAGATACTAAAATAAATCAAAACTGAAAGTTTAGATAATAAACATGCTAA
GTTTTAAACGGTGGGTACTAAAAATAAAATAAAAACTAAAAGTTAGGAATGATTTAA
Found at i:16617 original size:31 final size:31
Alignment explanation
Indices: 16576--16634 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
16566 GAACATTAAT
* *
16576 ATTATTGATTTGTGATAAAATGGTCACTAAC
1 ATTATCGATTTGTAATAAAATGGTCACTAAC
*
16607 ATTATCGATTTGTAATAAAGTGGTCACT
1 ATTATCGATTTGTAATAAAATGGTCACT
16635 CTACTATCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (31 bp):
ATTATCGATTTGTAATAAAATGGTCACTAAC
Found at i:18323 original size:2 final size:2
Alignment explanation
Indices: 18316--18405 Score: 60
Period size: 2 Copynumber: 51.0 Consensus size: 2
18306 GAAAATATTT
* *
18316 TA TA TA TA -A T- TA -A TA TA -A AA TA TA TA -A AA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
18352 TA TA TA TA TA TA -A T- TA -A TA TA -A AA TA TA TA -A AA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18388 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
18406 ATCGGGGCGG
Statistics
Matches: 72, Mismatches: 4, Indels: 24
0.72 0.04 0.24
Matches are distributed among these distances:
1 12 0.17
2 60 0.83
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (2 bp):
TA
Found at i:18380 original size:9 final size:9
Alignment explanation
Indices: 18328--18401 Score: 67
Period size: 10 Copynumber: 7.6 Consensus size: 9
18318 TATATAATTA
18328 ATATAAAAT
1 ATATAAAAT
18337 ATATAAAAT
1 ATATAAAAT
*
18346 ATTATATATAT
1 A-TATA-AAAT
*
18357 ATATATAATT
1 ATATA-AAAT
18367 AATATAAAAT
1 -ATATAAAAT
18377 ATATAAAAT
1 ATATAAAAT
*
18386 ATTATATATAT
1 A-TATA-AAAT
18397 ATATA
1 ATATA
18402 TATAATCGGG
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
9 20 0.36
10 22 0.40
11 13 0.24
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
ATATAAAAT
Found at i:18407 original size:42 final size:40
Alignment explanation
Indices: 18316--18403 Score: 176
Period size: 40 Copynumber: 2.2 Consensus size: 40
18306 GAAAATATTT
18316 TATATATAATTAATATAAAATATATAAAATATTATATATA
1 TATATATAATTAATATAAAATATATAAAATATTATATATA
18356 TATATATAATTAATATAAAATATATAAAATATTATATATA
1 TATATATAATTAATATAAAATATATAAAATATTATATATA
18396 TATATATA
1 TATATATA
18404 TAATCGGGGC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (40 bp):
TATATATAATTAATATAAAATATATAAAATATTATATATA
Found at i:19557 original size:24 final size:23
Alignment explanation
Indices: 19513--19558 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 23
19503 GAATTTAATA
19513 TTAATAAAATATTTTAATATTATT
1 TTAATAAAATA-TTTAATATTATT
19537 TTAATCAAAATA-TTAATTATTA
1 TTAAT-AAAATATTTAA-TATTA
19559 AAATATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 4 0.20
24 10 0.50
25 6 0.30
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
TTAATAAAATATTTAATATTATT
Found at i:19586 original size:21 final size:23
Alignment explanation
Indices: 19560--19609 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
19550 TAATTATTAA
19560 AATATTTAAAAT-ATATT-TATT
1 AATATTTAAAATAATATTATATT
*
19581 AATATTTCAAATAATATTATATT
1 AATATTTAAAATAATATTATATT
19604 -ATATTT
1 AATATTT
19610 TTAATATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 11 0.42
22 11 0.42
23 4 0.15
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATTTAAAATAATATTATATT
Found at i:19605 original size:26 final size:24
Alignment explanation
Indices: 19543--19605 Score: 62
Period size: 24 Copynumber: 2.6 Consensus size: 24
19533 TATTTTAATC
19543 AAAATATTA-ATTATTAAAATATTT
1 AAAATATTATATTATT-AAATATTT
19567 AAAATA-TAT-TTATT-AATATTT
1 AAAATATTATATTATTAAATATTT
19588 CAAATAATATTATATTAT
1 --AA-AATATTATATTAT
19606 ATTTTTAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
21 7 0.21
23 9 0.27
24 10 0.30
25 3 0.09
26 4 0.12
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATTATATTATTAAATATTT
Found at i:32839 original size:20 final size:20
Alignment explanation
Indices: 32814--32861 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
32804 ATGGTGGGTG
32814 ACGATGATTGTAAACAATGA
1 ACGATGATTGTAAACAATGA
32834 ACGATGATTGTAAACAATGA
1 ACGATGATTGTAAACAATGA
32854 ACGATGAT
1 ACGATGAT
32862 AAAGAACTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.25
Consensus pattern (20 bp):
ACGATGATTGTAAACAATGA
Found at i:36567 original size:43 final size:43
Alignment explanation
Indices: 36382--36567 Score: 178
Period size: 43 Copynumber: 4.3 Consensus size: 43
36372 AATAACAACT
* ** * * * * *
36382 TTTGGGTGAAAAACCCCACTATATATAATGAATTTTAACGGTG
1 TTTGTGTGAAAAACATCACTATATATCATGACTATTAGCGGCG
* ** *
36425 TTTGGGTGAAAATTATCACTATATATCATGACTATTACCGGCG
1 TTTGTGTGAAAAACATCACTATATATCATGACTATTAGCGGCG
* * * *
36468 TTATG-GTGAAAAGAC-GCAATTATATATCATGACTATTAGCGACA
1 TT-TGTGTGAAAA-ACATC-ACTATATATCATGACTATTAGCGGCG
36512 TTTGTGTGAAAAACATCACTATATATCATGACTATTAGCGGCG
1 TTTGTGTGAAAAACATCACTATATATCATGACTATTAGCGGCG
*
36555 TCTGTGTGAAAAA
1 TTTGTGTGAAAAA
36568 TGCCGCTAAA
Statistics
Matches: 117, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
43 83 0.71
44 34 0.29
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (43 bp):
TTTGTGTGAAAAACATCACTATATATCATGACTATTAGCGGCG
Found at i:42720 original size:24 final size:24
Alignment explanation
Indices: 42687--42743 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
42677 CCCAATTAAT
42687 TTTATATTCATTCAT-TTACGTTCG
1 TTTATATTCATTCATGTT-CGTTCG
* *
42711 TTTATGTTCATTTATGTTCGTTCG
1 TTTATATTCATTCATGTTCGTTCG
*
42735 TTTGTATTC
1 TTTATATTC
42744 GTTTATCATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 26 0.93
25 2 0.07
ACGTcount: A:0.16, C:0.14, G:0.12, T:0.58
Consensus pattern (24 bp):
TTTATATTCATTCATGTTCGTTCG
Found at i:44469 original size:21 final size:21
Alignment explanation
Indices: 44428--44469 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
44418 ATAATAAGTT
44428 AGTTTTTAATTAGTTAAGGATC
1 AGTTTTTAATTAGTT-AGGATC
44450 AGTTTTGTAATTAGTT-GGAT
1 AGTTTT-TAATTAGTTAGGAT
44470 ATCACTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.21
22 6 0.32
23 9 0.47
ACGTcount: A:0.29, C:0.02, G:0.21, T:0.48
Consensus pattern (21 bp):
AGTTTTTAATTAGTTAGGATC
Found at i:45025 original size:33 final size:33
Alignment explanation
Indices: 44988--45050 Score: 78
Period size: 33 Copynumber: 1.9 Consensus size: 33
44978 TTCGATGTTT
44988 ATTAT-ATATATATAATA-ATTAAGTT-TAATTGTA
1 ATTATAAT-TATA-AATATATT-AGTTCTAATTGTA
45021 ATTATAATTATAAATATATTAGTTCTAATT
1 ATTATAATTATAAATATATTAGTTCTAATT
45051 AGATTATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
32 8 0.30
33 17 0.63
34 2 0.07
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (33 bp):
ATTATAATTATAAATATATTAGTTCTAATTGTA
Found at i:45178 original size:22 final size:22
Alignment explanation
Indices: 45153--45195 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
45143 TAAACAAACA
45153 CCATATCCGACGAAATCCGTCC
1 CCATATCCGACGAAATCCGTCC
* *
45175 CCATCTCCGGCGAAATCCGTC
1 CCATATCCGACGAAATCCGTC
45196 TATCTCCATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.42, G:0.16, T:0.19
Consensus pattern (22 bp):
CCATATCCGACGAAATCCGTCC
Found at i:45493 original size:20 final size:20
Alignment explanation
Indices: 45444--45502 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
45434 TTTATTCTCT
* **
45444 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
45464 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
45484 TGTTGCGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
45503 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:45693 original size:25 final size:24
Alignment explanation
Indices: 45639--45693 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
45629 TGTTTATTAT
* *
45639 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
45663 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
45689 TGTTT
1 TGTTT
45694 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:46744 original size:16 final size:16
Alignment explanation
Indices: 46723--46759 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
46713 CATTACAGAG
46723 GCTGACACCCACGGAA
1 GCTGACACCCACGGAA
46739 GCTGACACCCACGGAA
1 GCTGACACCCACGGAA
46755 GCTGA
1 GCTGA
46760 GCTTGCCACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.30, C:0.35, G:0.27, T:0.08
Consensus pattern (16 bp):
GCTGACACCCACGGAA
Found at i:46861 original size:18 final size:18
Alignment explanation
Indices: 46834--46880 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
46824 CCACTTCGGA
46834 AGCCATCACCTCACCCAG
1 AGCCATCACCTCACCCAG
*
46852 AGCTATCACCTCACCCAG
1 AGCCATCACCTCACCCAG
46870 AGCCATCACCT
1 AGCCATCACCT
46881 GATCGACCCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.28, C:0.47, G:0.11, T:0.15
Consensus pattern (18 bp):
AGCCATCACCTCACCCAG
Found at i:47467 original size:19 final size:20
Alignment explanation
Indices: 47413--47478 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 20
47403 TAGTTTACTT
* *
47413 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
47433 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
47453 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
47472 TCGCAAC
1 TCGCAAC
47479 TACAAAATCG
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 13 0.34
20 25 0.66
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:47534 original size:19 final size:19
Alignment explanation
Indices: 47452--47534 Score: 95
Period size: 19 Copynumber: 4.6 Consensus size: 19
47442 GGAAATGGCT
47452 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
47471 ATCGCAA--C--TA-CAAA
1 ATCGCAATGCGAAATGAAA
*
47485 ATCGCAATACGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
47504 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
47523 ATCGCAATGCGA
1 ATCGCAATGCGA
47535 TTTGTGTTTC
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 1 0.02
17 1 0.02
18 1 0.02
19 38 0.73
ACGTcount: A:0.47, C:0.20, G:0.18, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:47565 original size:14 final size:14
Alignment explanation
Indices: 47546--47604 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
47536 TTGTGTTTCG
47546 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
47560 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
47577 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
47593 CGTTGCGATTTT
1 CGTTGCGATTTT
47605 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 18 0.47
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:47578 original size:33 final size:33
Alignment explanation
Indices: 47541--47620 Score: 151
Period size: 33 Copynumber: 2.4 Consensus size: 33
47531 GCGATTTGTG
*
47541 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
47574 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
47607 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
47621 AGCCATTTCC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:47586 original size:19 final size:19
Alignment explanation
Indices: 47562--47640 Score: 78
Period size: 19 Copynumber: 4.4 Consensus size: 19
47552 GATTTTGTCG
47562 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
47581 TTGCGA-TTT--TGTCG--
1 TTGCGATTTTCATTTCGCA
47595 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
***
47614 TTGCGATAGCCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
47634 TTGCGAT
1 TTGCGAT
47641 AGTTATTTCC
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
14 6 0.12
15 3 0.06
16 4 0.08
17 4 0.08
18 3 0.06
19 18 0.37
20 11 0.22
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:47635 original size:20 final size:20
Alignment explanation
Indices: 47604--47679 Score: 100
Period size: 20 Copynumber: 3.9 Consensus size: 20
47594 GTTGCGATTT
47604 TCATTT-CGCATTGCGATAG
1 TCATTTCCGCATTGCGATAG
*
47623 CCATTTCCGCATTGCGATAG
1 TCATTTCCGCATTGCGATAG
* *
47643 TTATTTCCGCGTTGCGATAG
1 TCATTTCCGCATTGCGATAG
* *
47663 TCATTTTCGCGTTGCGA
1 TCATTTCCGCATTGCGA
47680 AAGTAAGTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
19 5 0.10
20 45 0.90
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.37
Consensus pattern (20 bp):
TCATTTCCGCATTGCGATAG
Found at i:47690 original size:20 final size:20
Alignment explanation
Indices: 47650--47705 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
47640 TAGTTATTTC
* * *
47650 CGCGTTGCGATAGTCATTTT
1 CGCGTTGCGAAAGTAAGTTT
47670 CGCGTTGCGAAAGTAAGTTT
1 CGCGTTGCGAAAGTAAGTTT
*
47690 CGTGTTGCGAAAGTAA
1 CGCGTTGCGAAAGTAA
47706 ACTATTCTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.32
Consensus pattern (20 bp):
CGCGTTGCGAAAGTAAGTTT
Found at i:47697 original size:40 final size:40
Alignment explanation
Indices: 47606--47699 Score: 102
Period size: 40 Copynumber: 2.4 Consensus size: 40
47596 TGCGATTTTC
* * *
47606 ATTT-CGCATTGCGATAGCCATTTCCGCATTGCGATAGTT
1 ATTTCCGCGTTGCGATAGCCATTTCCGCATTGCGAAAGTA
* * *
47645 ATTTCCGCGTTGCGATAGTCATTTTCGCGTTGCGAAAGTA
1 ATTTCCGCGTTGCGATAGCCATTTCCGCATTGCGAAAGTA
*
47685 AGTTT-CGTGTTGCGA
1 A-TTTCCGCGTTGCGA
47700 AAGTAAACTA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
39 4 0.09
40 39 0.85
41 3 0.07
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.36
Consensus pattern (40 bp):
ATTTCCGCGTTGCGATAGCCATTTCCGCATTGCGAAAGTA
Found at i:48080 original size:21 final size:20
Alignment explanation
Indices: 48054--48121 Score: 64
Period size: 21 Copynumber: 3.3 Consensus size: 20
48044 CTGTCATCCC
48054 TCAAGAGTCCCCTCCAATCGT
1 TCAAGAGTCCCCTCC-ATCGT
* * **
48075 TCAAGAGGCCCCTATCATCCC
1 TCAAGAGTCCCCT-CCATCGT
* *
48096 TCAAGAGTCCCCCCCACCGT
1 TCAAGAGTCCCCTCCATCGT
48116 TCAAGA
1 TCAAGA
48122 TGCCACTGTC
Statistics
Matches: 36, Mismatches: 10, Indels: 3
0.73 0.20 0.06
Matches are distributed among these distances:
20 9 0.25
21 26 0.72
22 1 0.03
ACGTcount: A:0.25, C:0.41, G:0.15, T:0.19
Consensus pattern (20 bp):
TCAAGAGTCCCCTCCATCGT
Found at i:48134 original size:41 final size:42
Alignment explanation
Indices: 48044--48134 Score: 130
Period size: 41 Copynumber: 2.2 Consensus size: 42
48034 CCCGACTCAC
* *
48044 CTGTCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
* * *
48086 CTATCATCCCTCAAGAGTCCCC-CCCACCGTTCAAGATGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
48127 CTGTCATC
1 CTGTCATC
48135 GTTGAAGAGG
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 22 0.51
42 21 0.49
ACGTcount: A:0.22, C:0.42, G:0.14, T:0.22
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
Found at i:49741 original size:19 final size:19
Alignment explanation
Indices: 49717--49784 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
49707 ATCGCAACGA
*
49717 GAAAATCGCAATGTGAAAT
1 GAAAATCGCAATGCGAAAT
49736 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
49755 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
49769 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
49785 TTTTCATTTC
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 29 0.64
ACGTcount: A:0.47, C:0.16, G:0.22, T:0.15
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:49825 original size:20 final size:20
Alignment explanation
Indices: 49800--49858 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
49790 ATTTCGCATT
49800 GCCATTTTCGCGTTGCGATA
1 GCCATTTTCGCGTTGCGATA
49820 GCCATTTTCGCGTTGCGATA
1 GCCATTTTCGCGTTGCGATA
*
49840 GCCATTTTCACGTTGCGAT
1 GCCATTTTCGCGTTGCGAT
49859 TTCCCCGTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.15, C:0.25, G:0.24, T:0.36
Consensus pattern (20 bp):
GCCATTTTCGCGTTGCGATA
Found at i:50238 original size:20 final size:20
Alignment explanation
Indices: 50081--50237 Score: 233
Period size: 20 Copynumber: 7.8 Consensus size: 20
50071 ATTGCGATTT
*
50081 TCAGAATCTCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
*
50101 TCAGAATCTCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
50121 TCAGAATCGCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
*
50141 TTAGAATCGCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
50161 TCAGAATCGCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
**
50181 TCATTATCGCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
* *
50201 TCAGTATCGCGTTGCGATAG
1 TCAGAATCGCGTTGCGAAAG
* *
50221 TCAGTATCGCATTGCGA
1 TCAGAATCGCGTTGCGA
50238 TTTTCCAAAT
Statistics
Matches: 129, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 129 1.00
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.25
Consensus pattern (20 bp):
TCAGAATCGCGTTGCGAAAG
Found at i:50494 original size:12 final size:12
Alignment explanation
Indices: 50475--50508 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
50465 CTCTCCGGCG
50475 ACATCCGTTCCT
1 ACATCCGTTCCT
*
50487 ATATCCGTTCCT
1 ACATCCGTTCCT
50499 ACATCC-TTCC
1 ACATCCGTTCC
50509 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:53646 original size:19 final size:17
Alignment explanation
Indices: 53633--53748 Score: 79
Period size: 14 Copynumber: 7.0 Consensus size: 17
53623 TATCGCAATG
53633 CGAAATGAAAATCGCAA
1 CGAAATGAAAATCGCAA
*
53650 CG--A-GATAATCGCAATA
1 CGAAATGAAAATCGC-A-A
53666 CGAAATGAAAATCGCAA
1 CGAAATGAAAATCGCAA
*
53683 CG--A-GAGAATCGCAATA
1 CGAAATGAAAATCGC-A-A
53699 CGAAATGAAAATCGCAA
1 CGAAATGAAAATCGCAA
**
53716 CG--A-GGGAATCGCAAA
1 CGAAATGAAAATCGC-AA
53731 GCGAAATGAAAATCGCAA
1 -CGAAATGAAAATCGCAA
53749 AGCGAATTTA
Statistics
Matches: 76, Mismatches: 8, Indels: 29
0.67 0.07 0.26
Matches are distributed among these distances:
14 23 0.30
15 7 0.09
16 8 0.11
17 8 0.11
18 7 0.09
19 23 0.30
ACGTcount: A:0.48, C:0.18, G:0.22, T:0.12
Consensus pattern (17 bp):
CGAAATGAAAATCGCAA
Found at i:53670 original size:33 final size:33
Alignment explanation
Indices: 53624--53748 Score: 207
Period size: 33 Copynumber: 3.8 Consensus size: 33
53614 GGAAATTACT
* *
53624 ATCGCAATGCGAAATGAAAATCGCAACGAGATA
1 ATCGCAATACGAAATGAAAATCGCAACGAGAGA
53657 ATCGCAATACGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATACGAAATGAAAATCGCAACGAGAGA
*
53690 ATCGCAATACGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATACGAAATGAAAATCGCAACGAGAGA
53723 ATCGCAA-AGCGAAATGAAAATCGCAA
1 ATCGCAATA-CGAAATGAAAATCGCAA
53749 AGCGAATTTA
Statistics
Matches: 88, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
32 1 0.01
33 87 0.99
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (33 bp):
ATCGCAATACGAAATGAAAATCGCAACGAGAGA
Found at i:53749 original size:19 final size:18
Alignment explanation
Indices: 53633--53754 Score: 88
Period size: 19 Copynumber: 7.2 Consensus size: 18
53623 TATCGCAATG
53633 CGAAATGAAAATCGC-AA
1 CGAAATGAAAATCGCAAA
*
53650 CG--A-GATAATCGCAATA
1 CGAAATGAAAATCGCAA-A
53666 CGAAATGAAAATCGC-AA
1 CGAAATGAAAATCGCAAA
*
53683 CG--A-GAGAATCGCAATA
1 CGAAATGAAAATCGCAA-A
53699 CGAAATGAAAATCGC-AA
1 CGAAATGAAAATCGCAAA
**
53716 CG--A-GGGAATCGCAAA
1 CGAAATGAAAATCGCAAA
53731 GCGAAATGAAAATCGCAAA
1 -CGAAATGAAAATCGCAAA
53750 GCGAA
1 -CGAA
53755 TTTAGTTTCG
Statistics
Matches: 82, Mismatches: 8, Indels: 28
0.69 0.07 0.24
Matches are distributed among these distances:
14 23 0.28
15 7 0.09
16 8 0.10
17 8 0.10
18 5 0.06
19 31 0.38
ACGTcount: A:0.48, C:0.18, G:0.22, T:0.11
Consensus pattern (18 bp):
CGAAATGAAAATCGCAAA
Found at i:53785 original size:19 final size:19
Alignment explanation
Indices: 53750--53826 Score: 85
Period size: 19 Copynumber: 4.3 Consensus size: 19
53740 AAATCGCAAA
*
53750 GCGAATTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
53769 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
53788 GCGATTTT-G--T--CGTT
1 GCGATTTTAGTTTCGCGTT
*
53802 GCGATTTTCA-TTTCGCATT
1 GCGATTTT-AGTTTCGCGTT
53821 GCGATT
1 GCGATT
53827 CTCTCGTTGC
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
14 12 0.24
16 1 0.02
17 1 0.02
18 1 0.02
19 35 0.70
ACGTcount: A:0.13, C:0.17, G:0.25, T:0.45
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:53807 original size:33 final size:33
Alignment explanation
Indices: 53765--53858 Score: 145
Period size: 33 Copynumber: 2.8 Consensus size: 33
53755 TTTAGTTTCG
* * *
53765 CGTTGCGATTTT-AGTTTCGCGTTGCGATTTTGT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
53798 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
53831 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
53859 AGTAATTTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 56 0.98
34 1 0.02
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:53857 original size:19 final size:18
Alignment explanation
Indices: 53760--53858 Score: 72
Period size: 19 Copynumber: 5.7 Consensus size: 18
53750 GCGAATTTAG
53760 TTTCGCGTTGCGATTTT-A
1 TTTCGC-TTGCGATTTTCA
53778 GTTTCGCGTTGCGA-TTT--
1 -TTTCGC-TTGCGATTTTCA
*
53795 TGTCG-TTGCGATTTTCA
1 TTTCGCTTGCGATTTTCA
53812 TTTCGCATTGCGA--TTC-
1 TTTCGC-TTGCGATTTTCA
*
53828 TCTCG-TTGCGATTTTCA
1 TTTCGCTTGCGATTTTCA
53845 TTTCGCATTGCGAT
1 TTTCGC-TTGCGAT
53859 AGTAATTTTT
Statistics
Matches: 66, Mismatches: 4, Indels: 20
0.73 0.04 0.22
Matches are distributed among these distances:
14 12 0.18
15 3 0.05
16 11 0.17
17 11 0.17
18 3 0.05
19 26 0.39
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.46
Consensus pattern (18 bp):
TTTCGCTTGCGATTTTCA
Found at i:53986 original size:14 final size:14
Alignment explanation
Indices: 53967--54001 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
53957 TCAATTAAAC
53967 AAATCAACTTTTAA
1 AAATCAACTTTTAA
* *
53981 AAATCACCTTTTAC
1 AAATCAACTTTTAA
53995 AAATCAA
1 AAATCAA
54002 TTAAACAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (14 bp):
AAATCAACTTTTAA
Found at i:55372 original size:21 final size:20
Alignment explanation
Indices: 55344--55408 Score: 60
Period size: 21 Copynumber: 3.2 Consensus size: 20
55334 CCATGTGAAT
*
55344 AGGG-CTCTTGAATGGTGGG
1 AGGGCCTCTTGAACGGTGGG
* * **
55363 AGGGACCTCTTCAACGATGAC
1 AGGG-CCTCTTGAACGGTGGG
55384 AGTGGCCTCTTGAACGGTGGG
1 AG-GGCCTCTTGAACGGTGGG
55405 AGGG
1 AGGG
55409 GACTCTCGAG
Statistics
Matches: 34, Mismatches: 9, Indels: 5
0.71 0.19 0.10
Matches are distributed among these distances:
19 4 0.12
20 2 0.06
21 26 0.76
22 2 0.06
ACGTcount: A:0.20, C:0.18, G:0.40, T:0.22
Consensus pattern (20 bp):
AGGGCCTCTTGAACGGTGGG
Found at i:55433 original size:42 final size:41
Alignment explanation
Indices: 55348--55470 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
55338 GTGAATAGGG
* * * *
55348 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
55390 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
55432 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
55471 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:55866 original size:91 final size:93
Alignment explanation
Indices: 55688--55872 Score: 297
Period size: 91 Copynumber: 2.0 Consensus size: 93
55678 ATTTCAAACT
55688 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACATAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACATAGTTTAGC
55753 AGAATTGGCAGCAACCGAATAAATTTAC
66 AGAATTGGCAGCAACCGAATAAATTTAC
* *
55781 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACATTGTT-AATAA-ACA-A-TTTA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAAGAATACATAGTTTA
*
55842 GCAGTATTGGCAGCAACCGAATAAATTTAC
64 GCAGAATTGGCAGCAACCGAATAAATTTAC
55872 T
1 T
55873 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 34 0.39
92 1 0.01
93 22 0.25
94 4 0.05
95 26 0.30
ACGTcount: A:0.48, C:0.18, G:0.11, T:0.23
Consensus pattern (93 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACATAGTTTAGC
AGAATTGGCAGCAACCGAATAAATTTAC
Found at i:57607 original size:40 final size:38
Alignment explanation
Indices: 57563--57703 Score: 140
Period size: 33 Copynumber: 3.9 Consensus size: 38
57553 TCTTTTGGTT
**
57563 GAAATGAAAATCGCAACGAGATAATGAAAATCGCAACGCG
1 GAAATGACTATCGCAACGAGA-AATGAAAATCGCAACG-G
*
57603 GAAATGACTATCGCAACGAG--A-G--AATCGCAACGT
1 GAAATGACTATCGCAACGAGAAATGAAAATCGCAACGG
*
57636 GAAATGACTATCGCAACGCGAAATGAAAATCGCAAC--
1 GAAATGACTATCGCAACGAGAAATGAAAATCGCAACGG
* *
57672 GAGA-GA--ATCGCAACGCGAAATGAAAATCGCAA
1 GAAATGACTATCGCAACGAGAAATGAAAATCGCAA
57704 TGCGATTTTG
Statistics
Matches: 91, Mismatches: 5, Indels: 17
0.81 0.04 0.15
Matches are distributed among these distances:
33 45 0.49
34 10 0.11
35 3 0.03
36 5 0.05
37 1 0.01
38 9 0.10
40 18 0.20
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.13
Consensus pattern (38 bp):
GAAATGACTATCGCAACGAGAAATGAAAATCGCAACGG
Found at i:57672 original size:52 final size:52
Alignment explanation
Indices: 57571--57708 Score: 195
Period size: 52 Copynumber: 2.6 Consensus size: 52
57561 TTGAAATGAA
**
57571 AATCGCAACGAGATAATGAAAATCGCAACGCGGAAATGACTATCGCAACGAGAG
1 AATCGCAACGAGA-AATGAAAATCGCAACGC-GAAATGAAAATCGCAACGAGAG
* **
57625 AATCGCAACGTGAAATGACTATCGCAACGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGAGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAG
* *
57677 AATCGCAACGCGAAATGAAAATCGCAATGCGA
1 AATCGCAACGAGAAATGAAAATCGCAACGCGA
57709 TTTTGGTTTC
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
52 48 0.64
53 15 0.20
54 12 0.16
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.13
Consensus pattern (52 bp):
AATCGCAACGAGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:57708 original size:19 final size:19
Alignment explanation
Indices: 57563--57708 Score: 123
Period size: 19 Copynumber: 8.1 Consensus size: 19
57553 TCTTTTGGTT
*
57563 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
57582 GATAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
57602 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
* *
57620 G--A-GAGAATCGCAACGT
1 GAAATGAAAATCGCAACGC
**
57636 GAAATGACTATCGCAACGC
1 GAAATGAAAATCGCAACGC
57655 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
57672 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
57688 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
57707 GA
1 GA
57709 TTTTGGTTTC
Statistics
Matches: 101, Mismatches: 14, Indels: 24
0.73 0.10 0.17
Matches are distributed among these distances:
14 19 0.19
15 2 0.02
16 3 0.03
17 3 0.03
18 3 0.03
19 41 0.41
20 28 0.28
21 2 0.02
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:57752 original size:33 final size:33
Alignment explanation
Indices: 57704--57775 Score: 117
Period size: 33 Copynumber: 2.2 Consensus size: 33
57694 AAAATCGCAA
**
57704 TGCGATTTTGGTTTCGCGTTGCGATTATCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
*
57737 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
57770 TGCGAT
1 TGCGAT
57776 AGTTATTTCC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.10, C:0.21, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
Found at i:57784 original size:33 final size:33
Alignment explanation
Indices: 57715--57784 Score: 106
Period size: 33 Copynumber: 2.1 Consensus size: 33
57705 GCGATTTTGG
*
57715 TTTCGCGTTGCGATTATCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTATCTCGTTGCGATGTTCA
*
57748 TTTCGCGTTGCGATTCTCTCGTTGCGATAGTT-A
1 TTTCGCGTTGCGATTATCTCGTTGCGAT-GTTCA
57781 TTTC
1 TTTC
57785 CGTATTGCGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 32 0.94
34 2 0.06
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.46
Consensus pattern (33 bp):
TTTCGCGTTGCGATTATCTCGTTGCGATGTTCA
Found at i:58347 original size:20 final size:20
Alignment explanation
Indices: 58322--58433 Score: 73
Period size: 20 Copynumber: 5.5 Consensus size: 20
58312 GCTATGTAAA
58322 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-GTAAGTAT
* *
58342 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATGTAAGTAT
* ***
58362 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATGTAAGT-AT
* * ** *
58383 TCGCATTACGATTTACTTAA
1 TCGCATTGCGATGTAAGTAT
* * *
58403 TCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATGTAAGTAT
58423 TCGCATTGCGA
1 TCGCATTGCGA
58434 ATTATGAAAA
Statistics
Matches: 77, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
19 3 0.04
20 57 0.74
21 17 0.22
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATGTAAGTAT
Found at i:58395 original size:41 final size:40
Alignment explanation
Indices: 58340--58429 Score: 117
Period size: 41 Copynumber: 2.2 Consensus size: 40
58330 CGATAGTAAG
* * *
58340 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCT
1 ATTCGCATTACGATTTACGTAATCGCATTGCGATTTACCT
* * *
58380 AATTCGCATTACGATTTACTTAATCGCGTTGCGATTTACGT
1 -ATTCGCATTACGATTTACGTAATCGCATTGCGATTTACCT
58421 ATTCGCATT
1 ATTCGCATT
58430 GCGAATTATG
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 9 0.21
41 34 0.79
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.41
Consensus pattern (40 bp):
ATTCGCATTACGATTTACGTAATCGCATTGCGATTTACCT
Found at i:58446 original size:41 final size:40
Alignment explanation
Indices: 58401--58571 Score: 146
Period size: 41 Copynumber: 4.2 Consensus size: 40
58391 CGATTTACTT
* *
58401 AATCGCGTTGCGATTTACGTATTCGCATTGCGAATTATGAA
1 AATCGCATTGCGA-TTACGTATTCGCATTGCGAATTAGGAA
** * * *
58442 AATCGCAACGCGAATACGTAAATCGCAATGCGAATTAGGAA
1 AATCGCATTGCGATTACGT-ATTCGCATTGCGAATTAGGAA
* * * ***
58483 AATTGCATTGCGATAATCAGTA-TCGCATTGCGATTTTCCAA
1 AATCGCATTGCGATTA-C-GTATTCGCATTGCGAATTAGGAA
* * *
58524 ATTCGCATTGCGATTTACTTATTCGCATTGCGAATTGGGAA
1 AATCGCATTGCGA-TTACGTATTCGCATTGCGAATTAGGAA
58565 AATCGCA
1 AATCGCA
58572 ACGCGAAATT
Statistics
Matches: 99, Mismatches: 26, Indels: 10
0.73 0.19 0.07
Matches are distributed among these distances:
40 7 0.07
41 86 0.87
42 4 0.04
43 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (40 bp):
AATCGCATTGCGATTACGTATTCGCATTGCGAATTAGGAA
Found at i:58454 original size:21 final size:21
Alignment explanation
Indices: 58430--58485 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
58420 TATTCGCATT
*
58430 GCGAATTATGAAAATCGCAAC
1 GCGAATTACGAAAATCGCAAC
* *
58451 GCGAA-TACGTAAATCGCAAT
1 GCGAATTACGAAAATCGCAAC
*
58471 GCGAATTAGGAAAAT
1 GCGAATTACGAAAAT
58486 TGCATTGCGA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.20
Consensus pattern (21 bp):
GCGAATTACGAAAATCGCAAC
Found at i:58494 original size:21 final size:21
Alignment explanation
Indices: 58423--58495 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
58413 ATTTACGTAT
* *
58423 TCGCATTGCGAATTATGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
58444 TCGCAACGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGAAAA
*
58464 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
58485 TTGCATTGCGA
1 TCGCAATGCGA
58496 TAATCAGTAT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 17 0.40
21 25 0.60
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTACGAAAA
Found at i:58549 original size:20 final size:21
Alignment explanation
Indices: 58505--58556 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
58495 ATAATCAGTA
*
58505 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
58526 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
58546 TCGCATTGCGA
1 TCGCATTGCGA
58557 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:58598 original size:21 final size:22
Alignment explanation
Indices: 58546--58598 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
58536 ATTTACTTAT
58546 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
58567 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
58588 TCGCATTGCGA
1 TCGCATTGCGA
58599 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:59099 original size:33 final size:33
Alignment explanation
Indices: 59062--59124 Score: 78
Period size: 33 Copynumber: 1.9 Consensus size: 33
59052 TTCGATATTT
59062 ATTAT-ATATATATAATA-ATTAAGTT-TAATTGTA
1 ATTATAAT-TATA-AATATATT-AGTTCTAATTGTA
59095 ATTATAATTATAAATATATTAGTTCTAATT
1 ATTATAATTATAAATATATTAGTTCTAATT
59125 AGATTATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
32 8 0.30
33 17 0.63
34 2 0.07
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (33 bp):
ATTATAATTATAAATATATTAGTTCTAATTGTA
Found at i:59197 original size:2 final size:2
Alignment explanation
Indices: 59190--59215 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
59180 TAAATTTTGA
59190 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
59216 TATTAAACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59491 original size:39 final size:39
Alignment explanation
Indices: 59434--59526 Score: 143
Period size: 39 Copynumber: 2.4 Consensus size: 39
59424 GTGTTTCACG
*
59434 CGTCTTCAAGCTAGATATGAAAATTTTATGACTGCATGA
1 CGTCTTCAAGCTAAATATGAAAATTTTATGACTGCATGA
* *
59473 CGTCTTCAAGCTAAATATGAAGATTTTATGACTGCATGT
1 CGTCTTCAAGCTAAATATGAAAATTTTATGACTGCATGA
*
59512 CGTCTTTAAG-TAAAT
1 CGTCTTCAAGCTAAAT
59527 GAAGAATACC
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
38 5 0.10
39 45 0.90
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.35
Consensus pattern (39 bp):
CGTCTTCAAGCTAAATATGAAAATTTTATGACTGCATGA
Found at i:65633 original size:6 final size:6
Alignment explanation
Indices: 65622--65664 Score: 86
Period size: 6 Copynumber: 7.2 Consensus size: 6
65612 TGAAACCAAC
65622 CCAAAA CCAAAA CCAAAA CCAAAA CCAAAA CCAAAA CCAAAA C
1 CCAAAA CCAAAA CCAAAA CCAAAA CCAAAA CCAAAA CCAAAA C
65665 ATATACATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.65, C:0.35, G:0.00, T:0.00
Consensus pattern (6 bp):
CCAAAA
Found at i:85598 original size:23 final size:24
Alignment explanation
Indices: 85534--85609 Score: 136
Period size: 24 Copynumber: 3.2 Consensus size: 24
85524 GCAGTGTATT
*
85534 GATACACCAGTGAAGGGATGTATC
1 GATACACCAGTGAAGGGATGTACC
85558 GATACACCAGTGAAGGGATGTACC
1 GATACACCAGTGAAGGGATGTACC
85582 GATACACCA-TGAAGGGATGTACC
1 GATACACCAGTGAAGGGATGTACC
85605 GATAC
1 GATAC
85610 CCTATAGAGT
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
23 19 0.37
24 32 0.63
ACGTcount: A:0.34, C:0.20, G:0.28, T:0.18
Consensus pattern (24 bp):
GATACACCAGTGAAGGGATGTACC
Found at i:86498 original size:15 final size:16
Alignment explanation
Indices: 86480--86509 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
86470 AGTACAAACC
86480 ATAAGTTA-TATATGA
1 ATAAGTTATTATATGA
86495 ATAAGTTATTATATG
1 ATAAGTTATTATATG
86510 GACATGATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (16 bp):
ATAAGTTATTATATGA
Found at i:86688 original size:52 final size:52
Alignment explanation
Indices: 86627--86744 Score: 218
Period size: 52 Copynumber: 2.3 Consensus size: 52
86617 TGTGATCTTA
*
86627 TGAAAATGTGATAATGAGCTATGTTAAAGAACTATGAGATTATGGGTATATG
1 TGAATATGTGATAATGAGCTATGTTAAAGAACTATGAGATTATGGGTATATG
86679 TGAATATGTGATAATGAGCTATGTTAAAGAACTATGAGATTATGGGTATATG
1 TGAATATGTGATAATGAGCTATGTTAAAGAACTATGAGATTATGGGTATATG
*
86731 TGAATGTGTGATAA
1 TGAATATGTGATAA
86745 CTTAAATATT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 64 1.00
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.34
Consensus pattern (52 bp):
TGAATATGTGATAATGAGCTATGTTAAAGAACTATGAGATTATGGGTATATG
Found at i:86980 original size:23 final size:23
Alignment explanation
Indices: 86954--87013 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
86944 ATGGAATTTT
*
86954 GGTGCATTTTTACGCGGCACTTC
1 GGTGCATTTATACGCGGCACTTC
* ** *
86977 GGTGCAATCCTACGTGGCACTTC
1 GGTGCATTTATACGCGGCACTTC
87000 GGTGCATTTATACG
1 GGTGCATTTATACG
87014 AGCTATGGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.17, C:0.25, G:0.27, T:0.32
Consensus pattern (23 bp):
GGTGCATTTATACGCGGCACTTC
Done.