Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003149.1 Hibiscus syriacus cultivar Beakdansim tig00006624_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: 61772
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:11063 original size:17 final size:17
Alignment explanation
Indices: 11038--11097 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
11028 TTTTATATCC
*
11038 AAATAATAATTTTAACT
1 AAATTATAATTTTAACT
* *
11055 AAATTATAAATTTATC-
1 AAATTATAATTTTAACT
*
11071 AAATTATTAATTATAA-T
1 AAATTA-TAATTTTAACT
11088 AAATATATAA
1 AAAT-TATAA
11098 ATATTCTATA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
16 6 0.18
17 26 0.76
18 2 0.06
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATTATAATTTTAACT
Found at i:11652 original size:21 final size:21
Alignment explanation
Indices: 11613--11652 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
11603 CTACCTCTAA
*
11613 CTTAAACCATAAATTATAAAT
1 CTTAAACCATAAATCATAAAT
* *
11634 CTTAAACCCTATATCATAA
1 CTTAAACCATAAATCATAA
11653 CTCTATATCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (21 bp):
CTTAAACCATAAATCATAAAT
Found at i:16595 original size:62 final size:62
Alignment explanation
Indices: 16512--16708 Score: 277
Period size: 71 Copynumber: 3.0 Consensus size: 62
16502 TGCATTTCGC
*
16512 GTTGAAAATCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCGCGTTGCGATA
1 GTTGAAAATCGCGTTGCGATAGTGTACAGTGTCGTTGCGATTTTCCATTTCGCGTTGCGATA
16574 GTTGAAAATCGCGTTGCGATAGTGTACAGTGTCATTGCGATCGTTGCGATTTTCCATTTCGCGTT
1 GTTGAAAATCGCGTTGCGATAGTGTACA--G----T--G-TCGTTGCGATTTTCCATTTCGCGTT
16639 GCGATA
57 GCGATA
* * *
16645 GTTGAAAATCGCGTTGCGATAGTGTACAGTGTCATTGCGATTTTCCATCTCGCATTGCGATA
1 GTTGAAAATCGCGTTGCGATAGTGTACAGTGTCGTTGCGATTTTCCATTTCGCGTTGCGATA
16707 GT
1 GT
16709 GTACAGATAG
Statistics
Matches: 122, Mismatches: 4, Indels: 18
0.85 0.03 0.12
Matches are distributed among these distances:
62 57 0.47
63 1 0.01
64 1 0.01
65 1 0.01
68 1 0.01
69 1 0.01
70 1 0.01
71 59 0.48
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (62 bp):
GTTGAAAATCGCGTTGCGATAGTGTACAGTGTCGTTGCGATTTTCCATTTCGCGTTGCGATA
Found at i:16623 original size:71 final size:71
Alignment explanation
Indices: 16543--16685 Score: 286
Period size: 71 Copynumber: 2.0 Consensus size: 71
16533 GTCTACAGTG
16543 TCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTGTACAGTGTCA
1 TCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTGTACAGTGTCA
16608 TTGCGA
66 TTGCGA
16614 TCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTGTACAGTGTCA
1 TCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTGTACAGTGTCA
16679 TTGCGA
66 TTGCGA
16685 T
1 T
16686 TTTCCATCTC
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 72 1.00
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.36
Consensus pattern (71 bp):
TCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTGTACAGTGTCA
TTGCGA
Found at i:17326 original size:5 final size:5
Alignment explanation
Indices: 17316--17343 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
17306 CCGCCGCCGC
17316 CGTCT CGTCT CGTCT CGTCT CGTCT CGT
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGT
17344 GGTCGTGGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.39, G:0.21, T:0.39
Consensus pattern (5 bp):
CGTCT
Found at i:17351 original size:6 final size:6
Alignment explanation
Indices: 17340--17365 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
17330 TCGTCTCGTC
17340 TCGTGG TCGTGG TCGTGG TCGTGG TC
1 TCGTGG TCGTGG TCGTGG TCGTGG TC
17366 ATACGTGTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.19, G:0.46, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:20118 original size:60 final size:59
Alignment explanation
Indices: 19992--20123 Score: 147
Period size: 60 Copynumber: 2.2 Consensus size: 59
19982 AACTATAACC
* * * * ** * * * * *
19992 CTCATTTTAAATTAGTCTTTAAACTTTTAATATTTTAATTTTATCCTCAAATTACGACT
1 CTCATTCTAAATTACTCTTTAAACTTTGAACATTCCAATTTCATCCCCAAACTACAAAT
*
20051 CTCATTCTAAATTACTCTTTAAGCATTTGAACATTCCAATTTCATCCCCAAACTACAAAT
1 CTCATTCTAAATTACTCTTTAAAC-TTTGAACATTCCAATTTCATCCCCAAACTACAAAT
20111 CTCATTCTAAATT
1 CTCATTCTAAATT
20124 GGTCCCTAAA
Statistics
Matches: 60, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
59 21 0.35
60 39 0.65
ACGTcount: A:0.33, C:0.21, G:0.03, T:0.42
Consensus pattern (59 bp):
CTCATTCTAAATTACTCTTTAAACTTTGAACATTCCAATTTCATCCCCAAACTACAAAT
Found at i:20425 original size:60 final size:60
Alignment explanation
Indices: 20291--20457 Score: 160
Period size: 60 Copynumber: 2.8 Consensus size: 60
20281 CGTATAATTT
* * * * *
20291 AGGATAAAATTGAAATATTCAAAAAGTTTG-GGACCAATTTAGAATGAAGATCACAATTTG
1 AGGATAAAATTGAAATATT-AAAAAGTTTGAGGACTAATTTAAAATGAAGATAACAAGTTA
* * * * * *
20351 GGGATGAAAA-TGAAATGTTAAAAATTTTGAGGACTAATTTATAATGATA-ATAATAGGTTA
1 AGGAT-AAAATTGAAATATTAAAAAGTTTGAGGACTAATTTAAAATGA-AGATAACAAGTTA
* **
20411 AGGATAAAATTGAAATATTTAAAAGTTCAAGGACTAATTTAAAATGA
1 AGGATAAAATTGAAATATTAAAAAGTTTGAGGACTAATTTAAAATGA
20458 GAATCATAAA
Statistics
Matches: 86, Mismatches: 17, Indels: 8
0.77 0.15 0.07
Matches are distributed among these distances:
59 13 0.15
60 68 0.79
61 5 0.06
ACGTcount: A:0.47, C:0.05, G:0.18, T:0.31
Consensus pattern (60 bp):
AGGATAAAATTGAAATATTAAAAAGTTTGAGGACTAATTTAAAATGAAGATAACAAGTTA
Found at i:20472 original size:60 final size:58
Alignment explanation
Indices: 20286--20474 Score: 155
Period size: 60 Copynumber: 3.2 Consensus size: 58
20276 ATATACGTAT
* ** * * *
20286 AATTTAGGATAAAATTGAAATATTCAAAAAGTTTGGGACCAATTTAGAATGAAGATCACA
1 AATTAAGGATAAAATTGAAATATT-AAAAAGTTAAGGACTAATTTAAAATGAA-ATCATA
* ** * * * * *
20346 ATTTGGGGATGAAAA-TGAAATGTTAAAAATTTTGAGGACTAATTTATAATGATAATAATA
1 AATTAAGGAT-AAAATTGAAATATTAAAAA-GTTAAGGACTAATTTAAAATGA-AATCATA
** *
20406 GGTTAAGGATAAAATTGAAATATTTAAAAGTTCAAGGACTAATTTAAAATGAGAATCATA
1 AATTAAGGATAAAATTGAAATATTAAAAAGTT-AAGGACTAATTTAAAATGA-AATCATA
20466 AATTAAGGA
1 AATTAAGGA
20475 CGTAATATAA
Statistics
Matches: 100, Mismatches: 24, Indels: 10
0.75 0.18 0.07
Matches are distributed among these distances:
59 11 0.11
60 84 0.84
61 5 0.05
ACGTcount: A:0.47, C:0.05, G:0.17, T:0.31
Consensus pattern (58 bp):
AATTAAGGATAAAATTGAAATATTAAAAAGTTAAGGACTAATTTAAAATGAAATCATA
Found at i:20510 original size:14 final size:14
Alignment explanation
Indices: 20493--20520 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
20483 AATTATTCAA
20493 GTAAAATTTTAAAG
1 GTAAAATTTTAAAG
20507 GTAAAATTTTAAAG
1 GTAAAATTTTAAAG
20521 TGCTTAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (14 bp):
GTAAAATTTTAAAG
Found at i:22082 original size:41 final size:41
Alignment explanation
Indices: 22019--22100 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
22009 CTACACTCCC
*
22019 TCCTTTACTATACTATCTGTTTTCAATGACATCTGCTTTAT
1 TCCTTTACTATACTATCCGTTTTCAATGACATCTGCTTTAT
* *
22060 TCCTTTACTATATTATCCGTTTTCGATGACATCTGCTTTAT
1 TCCTTTACTATACTATCCGTTTTCAATGACATCTGCTTTAT
22101 ATGCTTGACT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.21, C:0.22, G:0.09, T:0.49
Consensus pattern (41 bp):
TCCTTTACTATACTATCCGTTTTCAATGACATCTGCTTTAT
Found at i:25868 original size:19 final size:20
Alignment explanation
Indices: 25844--25889 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
25834 TTTTATCGTA
* *
25844 TTAAAAA-CTGGTATGGGGT
1 TTAAAAATCCGGTATGAGGT
*
25863 TTAAAAATCCGGTCTGAGGT
1 TTAAAAATCCGGTATGAGGT
25883 TTAAAAA
1 TTAAAAA
25890 ATTGGATGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.37, C:0.09, G:0.24, T:0.30
Consensus pattern (20 bp):
TTAAAAATCCGGTATGAGGT
Found at i:25950 original size:20 final size:20
Alignment explanation
Indices: 25918--25972 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
25908 TTACCGGATT
*
25918 AAAAACCGGTTTTTTT-AAA
1 AAAAACCAGTTTTTTTAAAA
*
25937 AAAAATCAGTTTTTTTAAAA
1 AAAAACCAGTTTTTTTAAAA
*
25957 AAAAACCGGTTTTTTT
1 AAAAACCAGTTTTTTT
25973 CAAACCGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (20 bp):
AAAAACCAGTTTTTTTAAAA
Found at i:25969 original size:19 final size:19
Alignment explanation
Indices: 25918--25971 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
25908 TTACCGGATT
25918 AAAAACCGGTTTTTTTAAAA
1 AAAAACCGG-TTTTTTAAAA
* * *
25938 AAAATCAGTTTTTTTAAAA
1 AAAAACCGGTTTTTTAAAA
25957 AAAAACCGGTTTTTT
1 AAAAACCGGTTTTTT
25972 TCAAACCGAA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 22 0.79
20 6 0.21
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (19 bp):
AAAAACCGGTTTTTTAAAA
Found at i:28653 original size:32 final size:32
Alignment explanation
Indices: 28591--28698 Score: 130
Period size: 32 Copynumber: 3.4 Consensus size: 32
28581 TTTTATTCAA
* * * *
28591 TAAATTTT-TAAAAAAAATATAAAATCATCAT
1 TAAATTTTATCAAAATATTATAAAATAATCAT
*
28622 TAAATTTTATCAAAATATTATAACATAATCAT
1 TAAATTTTATCAAAATATTATAAAATAATCAT
* * *
28654 TAAATTTTATCAAATTATTACAAAATGATCAT
1 TAAATTTTATCAAAATATTATAAAATAATCAT
28686 TAAA-TTTATCAAA
1 TAAATTTTATCAAA
28699 CTTCTATAAT
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
31 17 0.25
32 50 0.75
ACGTcount: A:0.52, C:0.08, G:0.01, T:0.39
Consensus pattern (32 bp):
TAAATTTTATCAAAATATTATAAAATAATCAT
Found at i:29336 original size:21 final size:20
Alignment explanation
Indices: 29310--29407 Score: 74
Period size: 21 Copynumber: 4.8 Consensus size: 20
29300 ATCAGTTTCC
29310 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
* **
29331 AAAATCGCAATGCGATAGT-
1 AAAATCGCAACGCGATTTTG
**
29350 ACAAATTCGCATTGCGATTTT-
1 A-AAA-TCGCAACGCGATTTTG
* *
29371 ACAGAATCGCAACGCGAATATG
1 A-A-AATCGCAACGCGATTTTG
29393 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
29408 ACACATAAAT
Statistics
Matches: 63, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
19 1 0.02
20 17 0.27
21 42 0.67
22 3 0.05
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.21
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:29469 original size:20 final size:20
Alignment explanation
Indices: 29375--29603 Score: 248
Period size: 20 Copynumber: 11.4 Consensus size: 20
29365 GATTTTACAG
* ** *
29375 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
29395 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
29415 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
29435 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
29455 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
29475 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
29495 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
29515 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
29535 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
29555 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
29575 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
29595 AATCACAAC
1 AATCGCAAC
29604 ACTGAAATTT
Statistics
Matches: 179, Mismatches: 24, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.01
20 175 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:30334 original size:24 final size:24
Alignment explanation
Indices: 30295--30341 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
30285 AAATTTGGTC
30295 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
30319 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
30342 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:32903 original size:53 final size:52
Alignment explanation
Indices: 32835--33057 Score: 349
Period size: 53 Copynumber: 4.2 Consensus size: 52
32825 ACAACGAGAG
* *
32835 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGC-GAAATGAA
* *
32888 AATCGCAATGTGAAATGAAAATCGCAGCGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAA
32941 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
* *
32993 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCACAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
*
33045 AATCGCATTGCGA
1 AATCGCAATGCGA
33058 TTCTCTCGTT
Statistics
Matches: 160, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
52 70 0.44
53 89 0.56
54 1 0.01
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.15
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:32904 original size:19 final size:19
Alignment explanation
Indices: 32835--33057 Score: 216
Period size: 19 Copynumber: 12.7 Consensus size: 19
32825 ACAACGAGAG
32835 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
32854 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
32868 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
32888 AATCGCAATGTGAAATGAA
1 AATCGCAATGCGAAATGAA
*
32907 AATCGC-A-GCG--A-GAG
1 AATCGCAATGCGAAATGAA
32921 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
32941 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
32960 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
32974 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
32993 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
33012 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
* *
33026 AATCACAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
33045 AATCGCATTGCGA
1 AATCGCAATGCGA
33058 TTCTCTCGTT
Statistics
Matches: 168, Mismatches: 14, Indels: 44
0.74 0.06 0.19
Matches are distributed among these distances:
14 39 0.23
15 4 0.02
16 7 0.04
17 8 0.05
18 3 0.02
19 79 0.47
20 28 0.17
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:32978 original size:86 final size:84
Alignment explanation
Indices: 32829--32999 Score: 215
Period size: 86 Copynumber: 2.0 Consensus size: 84
32819 ACAATCACAA
32829 CGAGAGAATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGC
1 CGAGAGAATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAA-GCGG-AATGAAAATCGC
*
32894 AATGTGAAATGAAAATCGCAG
64 AATGCGAAATGAAAATCGCAG
* *
32915 CGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-C-G-A-GAGAA
1 CGAGAGAATCGCAATGC-GAAATGAAAATCCCAA--C---ATGAAAATCGCAAGCGGAATGAAAA
32976 TCGCAATGCGAAATGAAAATCGCA
60 TCGCAATGCGAAATGAAAATCGCA
33000 ATGCGAAATG
Statistics
Matches: 76, Mismatches: 3, Indels: 12
0.84 0.03 0.13
Matches are distributed among these distances:
86 44 0.58
87 16 0.21
89 2 0.03
90 1 0.01
92 13 0.17
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (84 bp):
CGAGAGAATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAAGCGGAATGAAAATCGCAA
TGCGAAATGAAAATCGCAG
Found at i:32997 original size:33 final size:33
Alignment explanation
Indices: 32821--33000 Score: 147
Period size: 33 Copynumber: 5.2 Consensus size: 33
32811 CGGAAATTAC
* *
32821 AATCACAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAAAATCGCAATGCGAAATGAA
*
32854 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACGA-GAAAATCGCAATGC-GAAATGAA
* *
32888 AATCGCAATGTGAAATGAAAATCGC-A-GCG--A-GAG
1 AATCGCAA--CG--A-GAAAATCGCAATGCGAAATGAA
32921 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C-G--A-GAAAATCGCAATGCGAAATGAA
*
32960 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAAAATCGCAATGCGAAATGAA
32993 AATCGCAA
1 AATCGCAA
33001 TGCGAAATGA
Statistics
Matches: 126, Mismatches: 8, Indels: 26
0.79 0.05 0.16
Matches are distributed among these distances:
32 1 0.01
33 62 0.49
34 31 0.25
35 1 0.01
36 5 0.04
37 3 0.02
38 2 0.02
39 21 0.17
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (33 bp):
AATCGCAACGAGAAAATCGCAATGCGAAATGAA
Found at i:33040 original size:33 final size:33
Alignment explanation
Indices: 32888--33051 Score: 136
Period size: 33 Copynumber: 4.8 Consensus size: 33
32878 CGGAAATGAA
* *
32888 AATCGCAATGTGAAATGAAAATCGCAGCGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
* *
32921 AATCGCAATGCGGAAATGAAAATCGCAATGCGA-
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAG
* * * *
32954 AAT-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCG-CAATGCGAAATGA-A-AATCGCAA--CG--A-GAG
32993 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
* *
33026 AATCACAATGCGAAATTAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
33052 TTGCGATTCT
Statistics
Matches: 104, Mismatches: 15, Indels: 24
0.73 0.10 0.17
Matches are distributed among these distances:
31 5 0.05
32 3 0.03
33 50 0.48
34 19 0.18
35 1 0.01
36 2 0.02
38 10 0.10
39 7 0.07
40 7 0.07
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.15
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:33160 original size:52 final size:53
Alignment explanation
Indices: 33047--33163 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
33037 GAAATTAAAA
33047 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
33100 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
33152 TCGCATTGCGAT
1 TCGCATTGCGAT
33164 AGTCATTTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 30 0.47
53 34 0.53
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:33171 original size:19 final size:19
Alignment explanation
Indices: 33066--33163 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
33056 GATTCTCTCG
33066 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
33086 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
33105 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
33119 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
33138 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
33157 TTGCGAT
1 TTGCGAT
33164 AGTCATTTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:33289 original size:14 final size:14
Alignment explanation
Indices: 33270--33306 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
33260 CATCAATTAC
33270 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
33284 ACAAATCATCTTTT
1 ACAAATCAACTTTT
33298 ACAAATCAA
1 ACAAATCAA
33307 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:35270 original size:19 final size:19
Alignment explanation
Indices: 35228--35400 Score: 150
Period size: 19 Copynumber: 9.6 Consensus size: 19
35218 TAGTTTACTT
* *
35228 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
* *
35248 TCGCAACGCGAATTGAGAA
1 TCGCAACGCGAAATGAAAA
* **
35267 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
**
35286 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
35305 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
35324 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
35338 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
35357 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
35371 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
35390 TCGCAATGCGA
1 TCGCAACGCGA
35401 TTTTGGTTTC
Statistics
Matches: 126, Mismatches: 17, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
14 18 0.14
15 1 0.01
16 7 0.06
17 7 0.06
18 1 0.01
19 81 0.64
20 11 0.09
ACGTcount: A:0.45, C:0.24, G:0.20, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:35341 original size:14 final size:14
Alignment explanation
Indices: 35322--35378 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
35312 GCGAAATGAA
*
35322 AATCGCAACGACAG
1 AATCGCAACGAAAG
35336 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
*
35353 AAAATCGCAACGAGAG
1 --AATCGCAACGAAAG
35369 AATCGCAACG
1 AATCGCAACG
35379 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 18 0.50
16 5 0.14
17 5 0.14
19 8 0.22
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:35349 original size:33 final size:33
Alignment explanation
Indices: 35303--35395 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
35293 GCGAAACCAA
35303 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
* *
35336 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
35369 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
35396 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:35392 original size:52 final size:52
Alignment explanation
Indices: 35262--35400 Score: 147
Period size: 52 Copynumber: 2.7 Consensus size: 52
35252 AACGCGAATT
* * * *
35262 GAGAATCGCAACGAGAAACCAAAATCGCAACGCGAAACCAAAATCGCAACGC
1 GAGAATCGCAACGCGAAACGAAAATCGCAATGCGAAACCAAAATCGCAACGA
* ** * **
35314 GA-AAT-GAAAATCGCAACGACAGAATCGCAATGCGAAATGAAAATCGCAACGA
1 GAGAATCGCAACGCGAAACGA-A-AATCGCAATGCGAAACCAAAATCGCAACGA
*
35366 GAGAATCGCAACGCGAAATGAAAATCGCAATGCGA
1 GAGAATCGCAACGCGAAACGAAAATCGCAATGCGA
35401 TTTTGGTTTC
Statistics
Matches: 68, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
50 8 0.12
51 4 0.06
52 43 0.63
53 4 0.06
54 9 0.13
ACGTcount: A:0.46, C:0.23, G:0.22, T:0.09
Consensus pattern (52 bp):
GAGAATCGCAACGCGAAACGAAAATCGCAATGCGAAACCAAAATCGCAACGA
Found at i:35444 original size:33 final size:34
Alignment explanation
Indices: 35396--35486 Score: 114
Period size: 33 Copynumber: 2.7 Consensus size: 34
35386 AAAATCGCAA
* * *
35396 TGCGATTTT-GGTTTCGCGTTGCGATTCTTTTGT
1 TGCGATTTTAAGTTTCGCGTTGCGATTCTCTCGT
* *
35429 TGTGATTTTCA-TTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTAAGTTTCGCGTTGCGATTCTCTCGT
*
35462 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTTAAGTTTCGCGTTGCGA
35487 AAGTAAACTA
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
33 37 0.76
34 12 0.24
ACGTcount: A:0.10, C:0.16, G:0.25, T:0.48
Consensus pattern (34 bp):
TGCGATTTTAAGTTTCGCGTTGCGATTCTCTCGT
Found at i:35717 original size:92 final size:93
Alignment explanation
Indices: 35534--36000 Score: 886
Period size: 92 Copynumber: 5.1 Consensus size: 93
35524 ATGGATTGCA
35534 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
35598 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
35626 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCATAGTGTTAAAGAATACACAG-T
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
35690 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
35718 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
35783 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
35811 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
35876 TAGCAGAATTGGCAGCAACCGAAC-AAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
35903 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
* *
35968 TAGTAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
35996 TTACT
1 TTACT
36001 AAGCAATCTA
Statistics
Matches: 368, Mismatches: 4, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
92 185 0.50
93 183 0.50
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:35850 original size:185 final size:185
Alignment explanation
Indices: 35534--36000 Score: 884
Period size: 185 Copynumber: 2.5 Consensus size: 185
35524 ATGGATTGCA
35534 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
35598 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
*
35663 ATTTCATAGTGTTAAAGAATACACAG-TTAGCAGAATTGGCAGCAACCGAACAAAT
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC-AAT
35718 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
35783 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
35848 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAT
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAT
35903 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
* *
35968 TAGTAGAATTGGCAGCAACCGAATAAATTTACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACT
36001 AAGCAATCTA
Statistics
Matches: 278, Mismatches: 3, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
184 4 0.01
185 249 0.90
186 25 0.09
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (185 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAT
Found at i:37714 original size:20 final size:20
Alignment explanation
Indices: 37683--37779 Score: 100
Period size: 20 Copynumber: 5.2 Consensus size: 20
37673 TTTTGGTTGA
37683 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
37703 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
37723 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
37742 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
37757 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
37777 AAT
1 AAT
37780 CGCAACGCGA
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 9 0.15
16 4 0.06
17 2 0.03
19 15 0.24
20 20 0.32
21 12 0.19
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:37735 original size:21 final size:21
Alignment explanation
Indices: 37681--37745 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
37671 TCTTTTGGTT
37681 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
37702 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
37722 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
37743 GAA
1 GAA
37746 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:37749 original size:14 final size:14
Alignment explanation
Indices: 37730--37786 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
37720 GAGAAATGAA
37730 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
37744 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
37763 AATCGCAACGAGAG
1 AATCGCAACGAGAG
37777 AATCGCAACG
1 AATCGCAACG
37787 CGAAATGAAA
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:37762 original size:33 final size:33
Alignment explanation
Indices: 37681--37803 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
37671 TCTTTTGGTT
*
37681 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAAC--GC
37722 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
37755 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
37788 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
37804 TGCGATTTTG
Statistics
Matches: 81, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
33 50 0.62
35 7 0.09
38 1 0.01
40 1 0.01
41 22 0.27
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:37905 original size:42 final size:39
Alignment explanation
Indices: 37831--37922 Score: 121
Period size: 42 Copynumber: 2.3 Consensus size: 39
37821 GTTGCGATTC
* * *
37831 TCTCGTTGCGATTTCATTTCGCGTTGCAATTTTCATTTT
1 TCTCGTTGCGATGTCATTTCACGTTGCAATTTTCATTTA
*
37870 TCTCGTTGCAGATAGTCATTTTCACGTTGCGATTTTCATTTA
1 TCTCGTTGC-GAT-GTCA-TTTCACGTTGCAATTTTCATTTA
37912 TCTCGTTGCGA
1 TCTCGTTGCGA
37923 CTCTTCTGCA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
39 9 0.20
40 3 0.07
41 5 0.11
42 29 0.63
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (39 bp):
TCTCGTTGCGATGTCATTTCACGTTGCAATTTTCATTTA
Found at i:37921 original size:21 final size:20
Alignment explanation
Indices: 37831--37922 Score: 98
Period size: 21 Copynumber: 4.5 Consensus size: 20
37821 GTTGCGATTC
37831 TCTCGTTGCGA-TTTCA-TT
1 TCTCGTTGCGATTTTCATTT
* *
37849 TCGCGTTGCAATTTTCATTTT
1 TCTCGTTGCGATTTTCA-TTT
**
37870 TCTCGTTGCAGATAGTCATTT
1 TCTCGTTGC-GATTTTCATTT
*
37891 TCACGTTGCGATTTTCATTT
1 TCTCGTTGCGATTTTCATTT
37911 ATCTCGTTGCGA
1 -TCTCGTTGCGA
37923 CTCTTCTGCA
Statistics
Matches: 59, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
18 9 0.15
19 5 0.08
20 9 0.15
21 31 0.53
22 5 0.08
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (20 bp):
TCTCGTTGCGATTTTCATTT
Found at i:38050 original size:33 final size:33
Alignment explanation
Indices: 38008--38078 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
37998 AATACTAACT
*
38008 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACAAGAGAATAGCAACGCGAAA
* *
38041 TGAAAATCGCAACAAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACAAGAGAATAGCAACGCGAAA
38074 TGAAA
1 TGAAA
38079 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.49, C:0.17, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACAAGAGAATAGCAACGCGAAA
Found at i:38483 original size:20 final size:20
Alignment explanation
Indices: 38458--38650 Score: 228
Period size: 20 Copynumber: 9.6 Consensus size: 20
38448 CTTTAAAAAT
38458 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
38478 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
* *
38498 TGTCTTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
38519 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
38539 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
38559 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
38579 CACGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* *
38599 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
38619 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
38639 CGCGTTGCGATT
1 CGCGTTGCGATT
38651 CTGTAAAATC
Statistics
Matches: 148, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
20 131 0.89
21 17 0.11
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:38668 original size:21 final size:20
Alignment explanation
Indices: 38644--38693 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
38634 ATATTCGCGT
38644 TGCGATTCTGTAAAATCGCAA
1 TGCGATT-TGTAAAATCGCAA
** *
38665 TGCGAATTTGTACTATCGCAT
1 TGCG-ATTTGTAAAATCGCAA
38686 TGCGATTT
1 TGCGATTT
38694 TCAAGAATCG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 4 0.16
21 18 0.72
22 3 0.12
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (20 bp):
TGCGATTTGTAAAATCGCAA
Found at i:48408 original size:33 final size:33
Alignment explanation
Indices: 48345--48409 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
48335 TTACAGTTCG
*
48345 AATGAAGGTCGTCGGGTGGTTTGGGAGACCAAC
1 AATGAAGGTCGTCGGGTGGTTTGAGAGACCAAC
*
48378 AATGAAGGTCGTCGGGT-GTTCTGAGCGACCAA
1 AATGAAGGTCGTCGGGTGGTT-TGAGAGACCAA
48410 TGAAGGTCGC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 3 0.10
33 26 0.90
ACGTcount: A:0.25, C:0.17, G:0.37, T:0.22
Consensus pattern (33 bp):
AATGAAGGTCGTCGGGTGGTTTGAGAGACCAAC
Found at i:48621 original size:49 final size:50
Alignment explanation
Indices: 48563--48664 Score: 197
Period size: 50 Copynumber: 2.1 Consensus size: 50
48553 GTTTATCCTA
48563 ATTTAGTATGTATTTA-TTTAAAATTGATTATTGGGATATCTTGTTTTGT
1 ATTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGT
48612 ATTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGT
1 ATTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGT
48662 ATT
1 ATT
48665 CAATAATTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
49 16 0.31
50 36 0.69
ACGTcount: A:0.26, C:0.02, G:0.16, T:0.56
Consensus pattern (50 bp):
ATTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGT
Found at i:49368 original size:2 final size:2
Alignment explanation
Indices: 49361--49385 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
49351 TCTGTTGCAA
49361 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 A
49386 ATTAGTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:50410 original size:28 final size:29
Alignment explanation
Indices: 50379--50436 Score: 68
Period size: 28 Copynumber: 2.0 Consensus size: 29
50369 CTTGTGAGAA
50379 AAAAATA-AATAGAAG-AGAAAACTT-TAAT
1 AAAAATAGAA-AGAAGAAGAAAA-TTGTAAT
*
50407 AAAACTAGAAAGAAGAAGAAAATTGTAAT
1 AAAAATAGAAAGAAGAAGAAAATTGTAAT
50436 A
1 A
50437 TGAGTTGTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
28 13 0.50
29 13 0.50
ACGTcount: A:0.64, C:0.03, G:0.14, T:0.19
Consensus pattern (29 bp):
AAAAATAGAAAGAAGAAGAAAATTGTAAT
Found at i:53240 original size:43 final size:43
Alignment explanation
Indices: 53193--53484 Score: 325
Period size: 43 Copynumber: 6.8 Consensus size: 43
53183 GCAAAAAATA
* *
53193 TTGATATTTAGCGGCGTTTGTCATAAAAACGCCGTAATAGGTG
1 TTGATATTTAGCGGCGTTTGTTATAAAAACGCCGCAATAGGTG
* * *
53236 TTGATATTTAGTGGCGTTTGTTATAAAAACACCGCAATAAGTG
1 TTGATATTTAGCGGCGTTTGTTATAAAAACGCCGCAATAGGTG
* *
53279 TTGATATTTAGTGGCGTTTGTTATAAAAACACCGCAATAGGTG
1 TTGATATTTAGCGGCGTTTGTTATAAAAACGCCGCAATAGGTG
* * * *
53322 TTGATATTTAGTGGCGTTTGTTATATAAACGTCGTAATAGGTG
1 TTGATATTTAGCGGCGTTTGTTATAAAAACGCCGCAATAGGTG
* * * * *
53365 TTGATATTTAGCGGTGTTTGTCATGAAAACGCCACAGTAGGTG
1 TTGATATTTAGCGGCGTTTGTTATAAAAACGCCGCAATAGGTG
* * * * * *
53408 TTGATATTTTGCGGCGTTT-TTTTCACAAACGCCGCAGTATGTA
1 TTGATATTTAGCGGCGTTTGTTAT-AAAAACGCCGCAATAGGTG
* * * * *
53451 TTAATGTTTTGCGGCGTTTCTTCTAAAAACGCCG
1 TTGATATTTAGCGGCGTTTGTTATAAAAACGCCG
53485 GTATAAAGTC
Statistics
Matches: 215, Mismatches: 32, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
42 2 0.01
43 210 0.98
44 3 0.01
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (43 bp):
TTGATATTTAGCGGCGTTTGTTATAAAAACGCCGCAATAGGTG
Found at i:53443 original size:129 final size:129
Alignment explanation
Indices: 53158--53443 Score: 333
Period size: 129 Copynumber: 2.2 Consensus size: 129
53148 GCTAAAGTTC
53158 GCGGCG-TTTTTTCACAAAACACGCCGCAAAAAATATTGATATTTAGCGGCGTTTGTCATAAAAA
1 GCGGCGTTTTTTTCAC--AA-ACGCCGCAAAAAATATTGATATTTAGCGGCGTTTGTCATAAAAA
* * *
53222 CGCCGTAATAGGTGTTGATATTTAGTGGCGTTTGTTATAAAAACACCGCAATAAGTGTTGATATT
63 CGCCGTAATAGGTGTTGATATTTAGCGGCGTTTGTCATAAAAACACCACAATAAGTGTTGATATT
53287 TA
128 TA
* * * * * ** * * * *
53289 GTGGCGTTTGTTAT-AAAAACACCGCAATAGGTGTTGATATTTAGTGGCGTTTGTTATATAAACG
1 GCGGCGTTT-TTTTCACAAACGCCGCAAAAAATATTGATATTTAGCGGCGTTTGTCATAAAAACG
* * * * * * *
53353 TCGTAATAGGTGTTGATATTTAGCGGTGTTTGTCATGAAAACGCCACAGTAGGTGTTGATATTTT
65 CCGTAATAGGTGTTGATATTTAGCGGCGTTTGTCATAAAAACACCACAATAAGTGTTGATATTTA
53418 GCGGCGTTTTTTTCACAAACGCCGCA
1 GCGGCGTTTTTTTCACAAACGCCGCA
53444 GTATGTATTA
Statistics
Matches: 127, Mismatches: 25, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
128 3 0.02
129 111 0.87
130 2 0.02
131 5 0.04
132 3 0.02
133 3 0.02
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (129 bp):
GCGGCGTTTTTTTCACAAACGCCGCAAAAAATATTGATATTTAGCGGCGTTTGTCATAAAAACGC
CGTAATAGGTGTTGATATTTAGCGGCGTTTGTCATAAAAACACCACAATAAGTGTTGATATTTA
Found at i:53965 original size:21 final size:22
Alignment explanation
Indices: 53916--53967 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
53906 GCTGCTTCTT
*
53916 TCTCTGCTT-TCGTTGTTGCTC
1 TCTCTGCTTCTCGTTGCTGCTC
*
53937 TGGT-TGCTTCT-GTTGCTGCTC
1 T-CTCTGCTTCTCGTTGCTGCTC
53958 TCTCTGCTTC
1 TCTCTGCTTC
53968 CCTTGCTTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
20 1 0.04
21 22 0.88
22 2 0.08
ACGTcount: A:0.00, C:0.29, G:0.21, T:0.50
Consensus pattern (22 bp):
TCTCTGCTTCTCGTTGCTGCTC
Found at i:54308 original size:22 final size:22
Alignment explanation
Indices: 54283--54326 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
54273 ATTAATTAAT
54283 TAAA-ATAAA-AAATGTCATGGTA
1 TAAATATAAATAAA-GTCA-GGTA
54305 TAAATATAAATAAAGTCAGGTA
1 TAAATATAAATAAAGTCAGGTA
54327 AATTTAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 8 0.40
23 9 0.45
24 3 0.15
ACGTcount: A:0.55, C:0.05, G:0.14, T:0.27
Consensus pattern (22 bp):
TAAATATAAATAAAGTCAGGTA
Found at i:56382 original size:36 final size:36
Alignment explanation
Indices: 56342--56412 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
56332 AAAATATCGA
56342 CATTGGTGTAGCTAATTATTCTAGGTAAACTATATT
1 CATTGGTGTAGCTAATTATTCTAGGTAAACTATATT
*
56378 CATTGGTGTAGTTAATTATTCTAGGTAAACTATAT
1 CATTGGTGTAGCTAATTATTCTAGGTAAACTATAT
56413 ATAATAATCC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (36 bp):
CATTGGTGTAGCTAATTATTCTAGGTAAACTATATT
Found at i:58420 original size:82 final size:83
Alignment explanation
Indices: 58268--58451 Score: 219
Period size: 82 Copynumber: 2.2 Consensus size: 83
58258 GTTTTCATTC
* * * *
58268 AAAACGCCACTAAAGTACGAGTTTATAGCGGCGTTTAGATTGAAAACACCACTAAAGTATGAATA
1 AAAACGCCACTAAAGTACGAGTATATAGCAGCGTTTAGATTAAAAACACCACTAAAGTACGAATA
58333 TATAGCGACATTTGTATA
66 TATAGCGACATTTGTATA
* * * * * * *
58351 GAAACACCACTAAAGTACTAGTATATAGCAGTGTTT-GCA-TAAAAACGCCACTAACGTACGATT
1 AAAACGCCACTAAAGTACGAGTATATAGCAGCGTTTAG-ATTAAAAACACCACTAAAGTACGAAT
* * *
58414 CTATAGCGGCGTTTGTATA
65 ATATAGCGACATTTGTATA
58433 AAAACGCCACTAAAGTACG
1 AAAACGCCACTAAAGTACG
58452 TACCTATAGC
Statistics
Matches: 83, Mismatches: 17, Indels: 3
0.81 0.17 0.03
Matches are distributed among these distances:
82 52 0.63
83 31 0.37
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (83 bp):
AAAACGCCACTAAAGTACGAGTATATAGCAGCGTTTAGATTAAAAACACCACTAAAGTACGAATA
TATAGCGACATTTGTATA
Found at i:58459 original size:41 final size:40
Alignment explanation
Indices: 58211--58468 Score: 198
Period size: 41 Copynumber: 6.2 Consensus size: 40
58201 ATAAATATTT
** * *
58211 GCGGCGTTTGT-TGAAAAAACGCTGCTAAAGTATGAGTCTTTA
1 GCGGCGTTTGTAT--AAAAACGCCACTAAAGTACGA-TCTATA
* *
58253 GCGGCGTTT-TCATTCAAAACGCCACTAAAGTACGAGTTTATA
1 GCGGCGTTTGT-A-TAAAAACGCCACTAAAGTACGA-TCTATA
* * * *
58295 GCGGCGTTTAG-ATTGAAAACACCACTAAAGTATGAATATATA
1 GCGGCGTTT-GTA-TAAAAACGCCACTAAAGTACG-ATCTATA
* * * * * *
58337 GCGACATTTGTATAGAAACACCACTAAAGTACTAGTATATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGA-TCTATA
* * * *
58378 GCAGTGTTTGCATAAAAACGCCACTAACGTACGATTCTATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGA-TCTATA
*
58419 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGTACCTATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACG-ATCTATA
58460 GCGGCGTTT
1 GCGGCGTTT
58469 ATTGGAAAAA
Statistics
Matches: 175, Mismatches: 32, Indels: 19
0.77 0.14 0.08
Matches are distributed among these distances:
40 1 0.01
41 98 0.56
42 74 0.42
43 1 0.01
44 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.28
Consensus pattern (40 bp):
GCGGCGTTTGTATAAAAACGCCACTAAAGTACGATCTATA
Found at i:59932 original size:41 final size:41
Alignment explanation
Indices: 59865--60015 Score: 162
Period size: 41 Copynumber: 3.7 Consensus size: 41
59855 GTTTATACAA
*
59865 AAAAAACGCCACTATTGATT-ACACTATTATGGCGTTTGTT-
1 AAAAAACGCCACTATTGATTAACACTATTACGGCGTTT-TTC
* * *
59905 AAAAAATGTCACTATTGATTAAGACTATTACGGCGTTTTTC
1 AAAAAACGCCACTATTGATTAACACTATTACGGCGTTTTTC
* * * * * *
59946 TAAAAACGCCACTATTGATTAACACTGTTGCTGCATTTATC
1 AAAAAACGCCACTATTGATTAACACTATTACGGCGTTTTTC
* * *
59987 TAAAAACGCCACTATTTATTATCACTATT
1 AAAAAACGCCACTATTGATTAACACTATT
60016 GCAGCATTTT
Statistics
Matches: 93, Mismatches: 16, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
40 20 0.22
41 73 0.78
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.36
Consensus pattern (41 bp):
AAAAAACGCCACTATTGATTAACACTATTACGGCGTTTTTC
Found at i:60043 original size:42 final size:41
Alignment explanation
Indices: 59866--60043 Score: 128
Period size: 41 Copynumber: 4.3 Consensus size: 41
59856 TTTATACAAA
*** * *
59866 AAAAACGCCACTATTGATT-ACACTATTATGGCGTTTGTTA-
1 AAAAACGCCACTATTGATTAACACTATTGCAGCATTT-ATAG
* * * * * * * **
59906 AAAAATGTCACTATTGATTAAGACTATTACGGCGTTTTTCT
1 AAAAACGCCACTATTGATTAACACTATTGCAGCATTTATAG
* * **
59947 AAAAACGCCACTATTGATTAACACTGTTGCTGCATTTATCT
1 AAAAACGCCACTATTGATTAACACTATTGCAGCATTTATAG
* *
59988 AAAAACGCCACTATTTATTATCACTATTGCAGCATTT-TAAG
1 AAAAACGCCACTATTGATTAACACTATTGCAGCATTTAT-AG
60029 AATAAACGCCACTAT
1 AA-AAACGCCACTAT
60044 ATGTGTAATA
Statistics
Matches: 115, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
40 20 0.17
41 83 0.72
42 12 0.10
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.34
Consensus pattern (41 bp):
AAAAACGCCACTATTGATTAACACTATTGCAGCATTTATAG
Found at i:61448 original size:31 final size:31
Alignment explanation
Indices: 61410--61497 Score: 122
Period size: 31 Copynumber: 2.8 Consensus size: 31
61400 TGAGCCCATT
61410 TTAATTAAATAAAAACGAAAGTGATCATATC
1 TTAATTAAATAAAAACGAAAGTGATCATATC
* * *
61441 TTAATTAAATAAAAATGAAAGTGGTTATATC
1 TTAATTAAATAAAAACGAAAGTGATCATATC
* * *
61472 TTAACTAAATAAAAACAAAAATGATC
1 TTAATTAAATAAAAACGAAAGTGATC
61498 GTATATTATG
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.53, C:0.08, G:0.09, T:0.30
Consensus pattern (31 bp):
TTAATTAAATAAAAACGAAAGTGATCATATC
Done.