Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009454.1 Hibiscus syriacus cultivar Beakdansim tig00113688_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: 170847
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
File 1 of 2
Found at i:899 original size:18 final size:18
Alignment explanation
Indices: 876--912 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
866 CCAATCATTT
876 TTTTTTCGTTCGGTGCTA
1 TTTTTTCGTTCGGTGCTA
894 TTTTTTCGTTCGGTGCTA
1 TTTTTTCGTTCGGTGCTA
912 T
1 T
913 AAGGGGGTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.05, C:0.16, G:0.22, T:0.57
Consensus pattern (18 bp):
TTTTTTCGTTCGGTGCTA
Found at i:6032 original size:17 final size:17
Alignment explanation
Indices: 6010--6044 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
6000 CTTGAGGAGA
6010 TTTGATTCATTCCGAAT
1 TTTGATTCATTCCGAAT
6027 TTTGATTCATTCCGAAT
1 TTTGATTCATTCCGAAT
6044 T
1 T
6045 AAAGAATTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.17, G:0.11, T:0.49
Consensus pattern (17 bp):
TTTGATTCATTCCGAAT
Found at i:7291 original size:32 final size:32
Alignment explanation
Indices: 7255--7316 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
7245 AGCTTTTGGT
7255 TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
1 TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
*
7287 TTTTTCGTGTTGTCAAAGAGTTGAACAATG
1 TTTTTCATGTTGTCAAAGAGTTGAACAATG
7317 AAAATAGATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.39
Consensus pattern (32 bp):
TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
Found at i:15503 original size:14 final size:14
Alignment explanation
Indices: 15484--15511 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
15474 ATCTAATACT
15484 AATAGAATAGAAAA
1 AATAGAATAGAAAA
15498 AATAGAATAGAAAA
1 AATAGAATAGAAAA
15512 GACTAATATA
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:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (14 bp):
AATAGAATAGAAAA
Found at i:15531 original size:17 final size:17
Alignment explanation
Indices: 15481--15547 Score: 86
Period size: 17 Copynumber: 4.1 Consensus size: 17
15471 CTAATCTAAT
15481 ACTAATAGAATAGAAA-
1 ACTAATAGAATAGAAAG
15497 A--AATAGAATAGAAAAG
1 ACTAATAGAATAG-AAAG
*
15513 ACTAATATAATAGAAAG
1 ACTAATAGAATAGAAAG
*
15530 ACTAATATAATAGAAAG
1 ACTAATAGAATAGAAAG
15547 A
1 A
15548 AAAGAACTGT
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.22
15 3 0.07
16 2 0.04
17 22 0.48
18 9 0.20
ACGTcount: A:0.63, C:0.04, G:0.13, T:0.19
Consensus pattern (17 bp):
ACTAATAGAATAGAAAG
Found at i:16103 original size:15 final size:14
Alignment explanation
Indices: 16075--16114 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
16065 AGAGGGAAAA
16075 AAAAATAA-TAAAT
1 AAAAATAAGTAAAT
16088 AATAAATAAGTAAAT
1 AA-AAATAAGTAAAT
16103 AAAAATGAAGTA
1 AAAAAT-AAGTA
16115 GAAGAACCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 2 0.08
14 10 0.42
15 12 0.50
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (14 bp):
AAAAATAAGTAAAT
Found at i:20794 original size:20 final size:22
Alignment explanation
Indices: 20769--20811 Score: 72
Period size: 20 Copynumber: 2.0 Consensus size: 22
20759 TGTCCATCTT
20769 TTTAATATAATC-T-ATATATA
1 TTTAATATAATCTTAATATATA
20789 TTTAATATAATCTTAATATATA
1 TTTAATATAATCTTAATATATA
20811 T
1 T
20812 AAGACATCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 12 0.57
21 1 0.05
22 8 0.38
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTAATATAATCTTAATATATA
Found at i:23459 original size:18 final size:18
Alignment explanation
Indices: 23402--23461 Score: 93
Period size: 18 Copynumber: 3.3 Consensus size: 18
23392 GTCACGATCG
* *
23402 ATATCGTCACTATCGTCA
1 ATATCGTCACTAGCATCA
*
23420 ATAGCGTCACTAGCATCA
1 ATATCGTCACTAGCATCA
23438 ATATCGTCACTAGCATCA
1 ATATCGTCACTAGCATCA
23456 ATATCG
1 ATATCG
23462 ATATCATCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.32, C:0.27, G:0.13, T:0.28
Consensus pattern (18 bp):
ATATCGTCACTAGCATCA
Found at i:25869 original size:21 final size:21
Alignment explanation
Indices: 25839--25907 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
25829 CTCACAAAGA
* * *
25839 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTGGAC
*
25859 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
25880 AAAAAGAGAAGTAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
25901 AAAAAGA
1 AAAAAGA
25908 AACGAAGTGG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 6 0.14
21 37 0.86
ACGTcount: A:0.55, C:0.09, G:0.25, T:0.12
Consensus pattern (21 bp):
AAAAAGAGAAGTAACTTGGAC
Found at i:30075 original size:14 final size:14
Alignment explanation
Indices: 30056--30086 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
30046 TACAATATAT
30056 ATAAGAATTATACG
1 ATAAGAATTATACG
30070 ATAAGAATTATACG
1 ATAAGAATTATACG
30084 ATA
1 ATA
30087 TATATCCATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.52, C:0.06, G:0.13, T:0.29
Consensus pattern (14 bp):
ATAAGAATTATACG
Found at i:30696 original size:16 final size:16
Alignment explanation
Indices: 30675--30707 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
30665 ACAAAAACAA
30675 AAAATAGAAAATATAT
1 AAAATAGAAAATATAT
*
30691 AAAATAGATAATATAT
1 AAAATAGAAAATATAT
30707 A
1 A
30708 TTAAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (16 bp):
AAAATAGAAAATATAT
Found at i:32939 original size:18 final size:18
Alignment explanation
Indices: 32918--32957 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
32908 TCATTTTTAT
32918 TTAATTTATTATTTAATA
1 TTAATTTATTATTTAATA
32936 TTAATTTATTATTTAATA
1 TTAATTTATTATTTAATA
32954 TTAA
1 TTAA
32958 ATAATAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTAATTTATTATTTAATA
Found at i:32952 original size:12 final size:11
Alignment explanation
Indices: 32901--32934 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
32891 CAAGACCCAA
*
32901 TTTTATTTCAT
1 TTTTATTTAAT
32912 TTTTATTTAAT
1 TTTTATTTAAT
32923 TTATTATTTAAT
1 TT-TTATTTAAT
32935 ATTAATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 12 0.57
12 9 0.43
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTTATTTAAT
Found at i:32955 original size:25 final size:25
Alignment explanation
Indices: 32921--32969 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
32911 TTTTTATTTA
* * * *
32921 ATTTATTATTTAATATTAATTTATT
1 ATTTAATATTAAATAATAAATTATT
32946 ATTTAATATTAAATAATAAATTAT
1 ATTTAATATTAAATAATAAATTAT
32970 AATAAATTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
ATTTAATATTAAATAATAAATTATT
Found at i:33391 original size:19 final size:19
Alignment explanation
Indices: 33367--33406 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
33357 TCCAATATAT
33367 ATACAAACAAGATATAAAA
1 ATACAAACAAGATATAAAA
33386 ATACAAACAAGATATAAAA
1 ATACAAACAAGATATAAAA
33405 AT
1 AT
33407 TTCTAATAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.68, C:0.10, G:0.05, T:0.17
Consensus pattern (19 bp):
ATACAAACAAGATATAAAA
Found at i:37320 original size:14 final size:14
Alignment explanation
Indices: 37301--37329 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
37291 TTAATCCATT
37301 TAATCCACATTTAA
1 TAATCCACATTTAA
37315 TAATCCACATTTAA
1 TAATCCACATTTAA
37329 T
1 T
37330 CCATTTTCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (14 bp):
TAATCCACATTTAA
Found at i:38955 original size:20 final size:20
Alignment explanation
Indices: 38926--38966 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
38916 ATATAGCTAT
* *
38926 GGTCTGTATTCTCTCTAAAG
1 GGTCTATATTCTCTATAAAG
38946 GGTCTATATTCTCTATAAAG
1 GGTCTATATTCTCTATAAAG
38966 G
1 G
38967 ACCAGAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (20 bp):
GGTCTATATTCTCTATAAAG
Found at i:39686 original size:20 final size:20
Alignment explanation
Indices: 39661--39698 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
39651 ATTTCATCTC
39661 GTACAGCTCAAACAAAAATG
1 GTACAGCTCAAACAAAAATG
39681 GTACAGCTCAAACAAAAA
1 GTACAGCTCAAACAAAAA
39699 CACCCAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.53, C:0.21, G:0.13, T:0.13
Consensus pattern (20 bp):
GTACAGCTCAAACAAAAATG
Found at i:39918 original size:21 final size:20
Alignment explanation
Indices: 39894--39941 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 20
39884 GCCTCTTGAA
39894 TCTTCTATTTACCTACTTATT
1 TCTTCTATTTA-CTACTTATT
*
39915 TCTTCTTCTTTACTACTTATT
1 TCTTC-TATTTACTACTTATT
39936 TCTTCT
1 TCTTCT
39942 TTCTTCTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 1 0.04
21 19 0.76
22 5 0.20
ACGTcount: A:0.15, C:0.25, G:0.00, T:0.60
Consensus pattern (20 bp):
TCTTCTATTTACTACTTATT
Found at i:39942 original size:21 final size:22
Alignment explanation
Indices: 39901--39942 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
39891 GAATCTTCTA
39901 TTTACCTACTTATTTCTTCTTC
1 TTTACCTACTTATTTCTTCTTC
39923 TTTA-CTACTTATTTCTTCTT
1 TTTACCTACTTATTTCTTCTT
39943 TCTTCTTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.14, C:0.24, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTACCTACTTATTTCTTCTTC
Found at i:43289 original size:27 final size:27
Alignment explanation
Indices: 43258--43312 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
43248 TTATGGCCTT
43258 ATTCTATCTATGTATAAAATATGATAA
1 ATTCTATCTATGTATAAAATATGATAA
43285 ATTCTATCTATGTATAAAATATGATAA
1 ATTCTATCTATGTATAAAATATGATAA
43312 A
1 A
43313 GGCCAATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.40
Consensus pattern (27 bp):
ATTCTATCTATGTATAAAATATGATAA
Found at i:47592 original size:21 final size:20
Alignment explanation
Indices: 47563--47601 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
47553 ACGCCTACGA
47563 AAAGATCGCTTGGATTTAAG
1 AAAGATCGCTTGGATTTAAG
47583 AAAGAGTCGCTTGGATTTA
1 AAAGA-TCGCTTGGATTTA
47602 TCCATGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.33, C:0.10, G:0.26, T:0.31
Consensus pattern (20 bp):
AAAGATCGCTTGGATTTAAG
Found at i:47636 original size:18 final size:18
Alignment explanation
Indices: 47613--47648 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
47603 CCATGATTTC
47613 TTTATTCCTTATTTCTAA
1 TTTATTCCTTATTTCTAA
47631 TTTATTCCTTATTTCTAA
1 TTTATTCCTTATTTCTAA
47649 AAAGAATCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.17, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTATTCCTTATTTCTAA
Found at i:47737 original size:32 final size:32
Alignment explanation
Indices: 47701--47766 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
47691 TCAAATTAAA
47701 TTATAGAATGAATATAATAAACAGGATTTGGT
1 TTATAGAATGAATATAATAAACAGGATTTGGT
47733 TTATAGAATGAATATAATAAACAGGATTTGGT
1 TTATAGAATGAATATAATAAACAGGATTTGGT
47765 TT
1 TT
47767 GTTTATTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.42, C:0.03, G:0.18, T:0.36
Consensus pattern (32 bp):
TTATAGAATGAATATAATAAACAGGATTTGGT
Found at i:49331 original size:12 final size:12
Alignment explanation
Indices: 49316--49341 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
49306 TTTACAGTCT
49316 TATTTATTATGA
1 TATTTATTATGA
49328 TATTTATTATGA
1 TATTTATTATGA
49340 TA
1 TA
49342 AGAAAGCGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.58
Consensus pattern (12 bp):
TATTTATTATGA
Found at i:49522 original size:14 final size:14
Alignment explanation
Indices: 49503--49556 Score: 53
Period size: 14 Copynumber: 4.1 Consensus size: 14
49493 TCTCCTTGGA
*
49503 TTAAATTATTAAAT
1 TTAAATTATAAAAT
49517 TTAAATTATAAAAT
1 TTAAATTATAAAAT
49531 TT---TTATAAAA-
1 TTAAATTATAAAAT
*
49541 TTAAAGATATAAAAT
1 TTAAA-TTATAAAAT
49556 T
1 T
49557 AAAGAATTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
10 2 0.06
11 8 0.24
14 22 0.67
15 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (14 bp):
TTAAATTATAAAAT
Found at i:49567 original size:14 final size:14
Alignment explanation
Indices: 49534--49561 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
49524 ATAAAATTTT
49534 TATAAAATTAAAGA
1 TATAAAATTAAAGA
49548 TATAAAATTAAAGA
1 TATAAAATTAAAGA
49562 ATTAAAGAAA
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:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (14 bp):
TATAAAATTAAAGA
Found at i:52010 original size:14 final size:14
Alignment explanation
Indices: 51991--52019 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
51981 ATATATTTAA
51991 TATTTATATTTCTT
1 TATTTATATTTCTT
52005 TATTTATATTTCTT
1 TATTTATATTTCTT
52019 T
1 T
52020 TTTTTGGTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (14 bp):
TATTTATATTTCTT
Found at i:52152 original size:36 final size:36
Alignment explanation
Indices: 52110--52204 Score: 113
Period size: 25 Copynumber: 2.9 Consensus size: 36
52100 TATTACTTAT
52110 TCTATTATCTATTATAAGTAAATCAAAAAAAAAATA
1 TCTATTATCTATTATAAGTAAATCAAAAAAAAAATA
52146 TCTATTATC-----T-A-T---T-AAAAAAAAAATA
1 TCTATTATCTATTATAAGTAAATCAAAAAAAAAATA
52171 TCTATTATCTATTATAAGTAAATCAAAAAAAAAA
1 TCTATTATCTATTATAAGTAAATCAAAAAAAAAA
52205 AGAAAGGGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 22
0.69 0.00 0.31
Matches are distributed among these distances:
25 21 0.44
26 1 0.02
29 1 0.02
30 2 0.04
31 2 0.04
32 1 0.02
35 1 0.02
36 19 0.40
ACGTcount: A:0.56, C:0.08, G:0.02, T:0.34
Consensus pattern (36 bp):
TCTATTATCTATTATAAGTAAATCAAAAAAAAAATA
Found at i:55252 original size:23 final size:23
Alignment explanation
Indices: 55225--55271 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
55215 TTCTGAAGAA
55225 ACTTCAGTTTAGTTCTGCTATAG
1 ACTTCAGTTTAGTTCTGCTATAG
55248 ACTTCAGTTTAGTTCTGCTATAG
1 ACTTCAGTTTAGTTCTGCTATAG
55271 A
1 A
55272 AAAAAGAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43
Consensus pattern (23 bp):
ACTTCAGTTTAGTTCTGCTATAG
Found at i:56512 original size:17 final size:17
Alignment explanation
Indices: 56490--56523 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
56480 TTCGTATATT
56490 ATACTAAATATATCTAA
1 ATACTAAATATATCTAA
* *
56507 ATACTAAGTATTTCTAA
1 ATACTAAATATATCTAA
56524 GCGAGTCTAG
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:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (17 bp):
ATACTAAATATATCTAA
Found at i:59239 original size:14 final size:14
Alignment explanation
Indices: 59220--59248 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
59210 AGTCTTTTAT
59220 TTTTGTATTTAAGA
1 TTTTGTATTTAAGA
59234 TTTTGTATTTAAGA
1 TTTTGTATTTAAGA
59248 T
1 T
59249 ATATCTAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.59
Consensus pattern (14 bp):
TTTTGTATTTAAGA
Found at i:61184 original size:8 final size:8
Alignment explanation
Indices: 61143--61208 Score: 50
Period size: 8 Copynumber: 8.4 Consensus size: 8
61133 AATGAAATAG
61143 AAATATA-
1 AAATATAT
61150 AAATATAT
1 AAATATAT
61158 AAATA-AGT
1 AAATATA-T
61166 AAATA-A-
1 AAATATAT
*
61172 GAATATAT
1 AAATATAT
61180 AAATAATAT
1 AAAT-ATAT
* *
61189 AAAAAAAT
1 AAATATAT
61197 AAATAATAT
1 AAAT-ATAT
61206 AAA
1 AAA
61209 AAAAGAATAT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
6 4 0.09
7 9 0.19
8 21 0.45
9 13 0.28
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (8 bp):
AAATATAT
Found at i:61189 original size:31 final size:29
Alignment explanation
Indices: 61144--61202 Score: 82
Period size: 31 Copynumber: 2.0 Consensus size: 29
61134 ATGAAATAGA
* *
61144 AATATAAAATATATAAATAAGTAAATAAG
1 AATATAAAATATATAAAAAAATAAATAAG
61173 AATATATAAATAATATAAAAAAATAAATAA
1 AATATA-AAAT-ATATAAAAAAATAAATAA
61203 TATAAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 6 0.23
30 4 0.15
31 16 0.62
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.27
Consensus pattern (29 bp):
AATATAAAATATATAAAAAAATAAATAAG
Found at i:61217 original size:20 final size:17
Alignment explanation
Indices: 61178--61212 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
61168 ATAAGAATAT
61178 ATAAATAATATAAAAAA
1 ATAAATAATATAAAAAA
61195 ATAAATAATATAAAAAA
1 ATAAATAATATAAAAAA
61212 A
1 A
61213 GAATATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (17 bp):
ATAAATAATATAAAAAA
Found at i:61260 original size:18 final size:19
Alignment explanation
Indices: 61239--61282 Score: 63
Period size: 18 Copynumber: 2.3 Consensus size: 19
61229 AATAATTAAT
61239 AATATTAAATT-AATATTA
1 AATATTAAATTAAATATTA
*
61257 AATATTAATTTAAATATTA
1 AATATTAAATTAAATATTA
61276 ATATATT
1 A-ATATT
61283 CTAAATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.43
19 8 0.35
20 5 0.22
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
AATATTAAATTAAATATTA
Found at i:61271 original size:12 final size:13
Alignment explanation
Indices: 61238--61279 Score: 63
Period size: 12 Copynumber: 3.5 Consensus size: 13
61228 TAATAATTAA
61238 TAATATT-AA-AT
1 TAATATTAAATAT
61249 TAATATTAAATAT
1 TAATATTAAATAT
61262 TAAT-TTAAATAT
1 TAATATTAAATAT
61274 TAATAT
1 TAATAT
61280 ATTCTAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 7 0.25
12 14 0.50
13 7 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TAATATTAAATAT
Found at i:61316 original size:19 final size:20
Alignment explanation
Indices: 61279--61317 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
61269 AATATTAATA
61279 TATTCTAAATAAAATTATAT
1 TATTCTAAATAAAATTATAT
61299 TATTCTAAATAAAA-TATAT
1 TATTCTAAATAAAATTATAT
61318 AAATAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (20 bp):
TATTCTAAATAAAATTATAT
Found at i:61324 original size:17 final size:17
Alignment explanation
Indices: 61160--61325 Score: 55
Period size: 17 Copynumber: 9.6 Consensus size: 17
61150 AAATATATAA
*
61160 ATAAGTAAATAAGAATAT
1 ATAAATAAATAA-AATAT
*
61178 ATAAATAATATAAAA-AA
1 ATAAATAA-ATAAAATAT
61195 ATAAATAATATAAAA-A-
1 ATAAATAA-ATAAAATAT
61211 A-AGAATATAA-AAAATA-
1 ATA-AATA-AATAAAATAT
*
61227 AT-AATAATTAATAATAT
1 ATAAATAAATAA-AATAT
*
61244 -TAAATTAATATTAAATAT
1 ATAAA-TAA-ATAAAATAT
* *
61262 -TAATTTAAATATTAATAT
1 ATAA-ATAAATA-AAATAT
**
61280 AT-TCTAAATAAAATTAT
1 ATAAATAAATAAAA-TAT
**
61297 ATTATTCTAAATAAAATAT
1 A-TA-AATAAATAAAATAT
61316 ATAAATAAAT
1 ATAAATAAAT
61326 TAGAAGATAT
Statistics
Matches: 117, Mismatches: 13, Indels: 37
0.70 0.08 0.22
Matches are distributed among these distances:
14 1 0.01
15 11 0.09
16 15 0.13
17 37 0.32
18 31 0.26
19 11 0.09
20 11 0.09
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (17 bp):
ATAAATAAATAAAATAT
Found at i:61339 original size:12 final size:12
Alignment explanation
Indices: 61324--61369 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
61314 ATATAAATAA
*
61324 ATTAGAAGATAT
1 ATTAGAATATAT
61336 ATTAGAATATATAT
1 ATTAG-A-ATATAT
61350 ATTAGAATATAT
1 ATTAGAATATAT
*
61362 AATAGAAT
1 ATTAGAAT
61370 TAATATTCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 18 0.60
13 2 0.07
14 10 0.33
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (12 bp):
ATTAGAATATAT
Found at i:61351 original size:14 final size:14
Alignment explanation
Indices: 61332--61362 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
61322 AAATTAGAAG
61332 ATATATTAGAATAT
1 ATATATTAGAATAT
61346 ATATATTAGAATAT
1 ATATATTAGAATAT
61360 ATA
1 ATA
61363 ATAGAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (14 bp):
ATATATTAGAATAT
Found at i:61354 original size:26 final size:24
Alignment explanation
Indices: 61324--61376 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 24
61314 ATATAAATAA
*
61324 ATTAGAAGATATATTAGAATATATAT
1 ATTAGAAGATATAATAGAAT-TA-AT
*
61350 ATTAGAATATATAATAGAATTAAT
1 ATTAGAAGATATAATAGAATTAAT
61374 ATT
1 ATT
61377 CTAACTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 5 0.20
25 2 0.08
26 18 0.72
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (24 bp):
ATTAGAAGATATAATAGAATTAAT
Found at i:61375 original size:14 final size:13
Alignment explanation
Indices: 61319--61375 Score: 55
Period size: 12 Copynumber: 4.4 Consensus size: 13
61309 AAAATATATA
*
61319 AATAAATTAGAA-
1 AATATATTAGAAT
*
61331 GATATATTAGAAT
1 AATATATTAGAAT
61344 ATATATATTAGAAT
1 A-ATATATTAGAAT
*
61358 -ATATAATAGAATT
1 AATATATTAGAA-T
61371 AATAT
1 AATAT
61376 TCTAACTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
12 20 0.54
13 1 0.03
14 16 0.43
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (13 bp):
AATATATTAGAAT
Found at i:61403 original size:15 final size:13
Alignment explanation
Indices: 61369--61394 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
61359 TATAATAGAA
61369 TTAATATTCTAAC
1 TTAATATTCTAAC
61382 TTAATATTCTAAC
1 TTAATATTCTAAC
61395 ATCTAATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (13 bp):
TTAATATTCTAAC
Found at i:61406 original size:20 final size:20
Alignment explanation
Indices: 61383--61425 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
61373 TATTCTAACT
61383 TAATATTCTAACATCTAATA
1 TAATATTCTAACATCTAATA
61403 TAATATTCTAACATCTAATA
1 TAATATTCTAACATCTAATA
61423 TAA
1 TAA
61426 ATTATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (20 bp):
TAATATTCTAACATCTAATA
Found at i:61641 original size:13 final size:13
Alignment explanation
Indices: 61623--61649 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
61613 GAAATGAGAT
61623 AAATGAGATAGAA
1 AAATGAGATAGAA
61636 AAATGAGATAGAA
1 AAATGAGATAGAA
61649 A
1 A
61650 TAAGGAATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.22, T:0.15
Consensus pattern (13 bp):
AAATGAGATAGAA
Found at i:63956 original size:28 final size:28
Alignment explanation
Indices: 63916--63973 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
63906 TTATACATCC
63916 CATTTTGATTCTGCCGATTAAATAGAAT
1 CATTTTGATTCTGCCGATTAAATAGAAT
63944 CATTTTGATTCTGCCGATTAAATAGAAT
1 CATTTTGATTCTGCCGATTAAATAGAAT
63972 CA
1 CA
63974 AATACAATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.38
Consensus pattern (28 bp):
CATTTTGATTCTGCCGATTAAATAGAAT
Found at i:65141 original size:23 final size:23
Alignment explanation
Indices: 65107--65153 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
65097 ATCTCTTTTA
*
65107 TTAATTTTAAATATTCATTAAAT
1 TTAATTTAAAATATTCATTAAAT
65130 TTAATTTAAAATATTCATTAAAT
1 TTAATTTAAAATATTCATTAAAT
65153 T
1 T
65154 AATAAAAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (23 bp):
TTAATTTAAAATATTCATTAAAT
Found at i:65623 original size:13 final size:13
Alignment explanation
Indices: 65607--65631 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
65597 CGGTAAAGGT
65607 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
65620 AAAAAAAAAAAA
1 AAAAAAAAAAAA
65632 CCAGCCTAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.96, C:0.00, G:0.04, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:65791 original size:11 final size:11
Alignment explanation
Indices: 65772--65806 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
65762 ATACAGAATC
65772 TATTAAATATA
1 TATTAAATATA
*
65783 TATTCAATATA
1 TATTAAATATA
65794 TATATAAATATA
1 TAT-TAAATATA
65806 T
1 T
65807 TATTTAGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 13 0.62
12 8 0.38
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (11 bp):
TATTAAATATA
Found at i:67428 original size:22 final size:22
Alignment explanation
Indices: 67403--67446 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
67393 GAATAACAAA
67403 CAACGAATTAATCTTCATAAAT
1 CAACGAATTAATCTTCATAAAT
67425 CAACGAATTAATCTTCATAAAT
1 CAACGAATTAATCTTCATAAAT
67447 TAGATTTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.32
Consensus pattern (22 bp):
CAACGAATTAATCTTCATAAAT
Found at i:68488 original size:14 final size:15
Alignment explanation
Indices: 68464--68493 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
68454 AAGATGTCCC
68464 TTTTAATAAAATATG
1 TTTTAATAAAATATG
68479 TTTT-ATAAAATATG
1 TTTTAATAAAATATG
68493 T
1 T
68494 ATGAAGTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (15 bp):
TTTTAATAAAATATG
Found at i:69063 original size:8 final size:10
Alignment explanation
Indices: 69030--69070 Score: 64
Period size: 10 Copynumber: 4.0 Consensus size: 10
69020 GATTTGTACG
*
69030 TATATCATATA
1 TATATCACA-A
69041 TATATCACAA
1 TATATCACAA
69051 TATATCACAA
1 TATATCACAA
69061 TATATCACAA
1 TATATCACAA
69071 GACTTGTGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
10 21 0.72
11 8 0.28
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.34
Consensus pattern (10 bp):
TATATCACAA
Found at i:69530 original size:20 final size:20
Alignment explanation
Indices: 69505--69546 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
69495 TCGGGTCGTC
69505 TTTTTTGAGATAGTTTTTCA
1 TTTTTTGAGATAGTTTTTCA
69525 TTTTTTGAGATAGTTTTTCA
1 TTTTTTGAGATAGTTTTTCA
69545 TT
1 TT
69547 AGTATACCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.19, C:0.05, G:0.14, T:0.62
Consensus pattern (20 bp):
TTTTTTGAGATAGTTTTTCA
Found at i:69959 original size:22 final size:22
Alignment explanation
Indices: 69934--69985 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
69924 TTCCTTTCCC
69934 CTTTCTTTCATTTGTTTATTTT
1 CTTTCTTTCATTTGTTTATTTT
69956 CTTT-TTATCATTTGTTTATTTT
1 CTTTCTT-TCATTTGTTTATTTT
69978 CTTTCTTT
1 CTTTCTTT
69986 TTATGCGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 2 0.07
22 24 0.86
23 2 0.07
ACGTcount: A:0.10, C:0.13, G:0.04, T:0.73
Consensus pattern (22 bp):
CTTTCTTTCATTTGTTTATTTT
Found at i:70499 original size:17 final size:17
Alignment explanation
Indices: 70459--70502 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
70449 AAAGATATTT
*
70459 AATATATAGATAAATTG
1 AATATATAGATAAATAG
70476 AATATATAGATAAATAAG
1 AATATATAGATAAAT-AG
70494 AAATATATA
1 -AATATATA
70503 ACTATTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 15 0.62
18 1 0.04
19 8 0.33
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.32
Consensus pattern (17 bp):
AATATATAGATAAATAG
Found at i:70542 original size:19 final size:18
Alignment explanation
Indices: 70514--70553 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
70504 CTATTTTTAT
*
70514 AATTATTTTTATTATTAG
1 AATTATTTTTATAATTAG
70532 AATTCATTTTTATAATTAG
1 AATT-ATTTTTATAATTAG
70551 AAT
1 AAT
70554 ATAATTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.55
Consensus pattern (18 bp):
AATTATTTTTATAATTAG
Found at i:70739 original size:12 final size:12
Alignment explanation
Indices: 70722--70757 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
70712 TTCTATCAAC
70722 ATTAGATTGAAT
1 ATTAGATTGAAT
70734 ATTAGATTGAAT
1 ATTAGATTGAAT
*
70746 ATTAGATCGAAT
1 ATTAGATTGAAT
70758 CTACCATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.42, C:0.03, G:0.17, T:0.39
Consensus pattern (12 bp):
ATTAGATTGAAT
Found at i:70794 original size:18 final size:18
Alignment explanation
Indices: 70771--70807 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
70761 CCATTATTTT
70771 AATTATATTAAATTTATA
1 AATTATATTAAATTTATA
**
70789 AATTATATTCGATTTATA
1 AATTATATTAAATTTATA
70807 A
1 A
70808 TTAATATGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (18 bp):
AATTATATTAAATTTATA
Found at i:71299 original size:16 final size:16
Alignment explanation
Indices: 71278--71325 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
71268 AAAAAGGAAA
71278 CTTTTTGGTTTAATTT
1 CTTTTTGGTTTAATTT
** **
71294 CTTTTTTTTTTTTTTT
1 CTTTTTGGTTTAATTT
*
71310 CTTTTTGGTTAAATTT
1 CTTTTTGGTTTAATTT
71326 ATTTATATAT
Statistics
Matches: 23, Mismatches: 9, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.10, C:0.06, G:0.08, T:0.75
Consensus pattern (16 bp):
CTTTTTGGTTTAATTT
Found at i:71384 original size:11 final size:11
Alignment explanation
Indices: 71357--71412 Score: 55
Period size: 11 Copynumber: 5.3 Consensus size: 11
71347 TTATATTCAA
*
71357 TTTATTTCTAT
1 TTTATATCTAT
*
71368 ATTATATCTAT
1 TTTATATCTAT
71379 TTTATA--TAT
1 TTTATATCTAT
*
71388 TATATAT-TAT
1 TTTATATCTAT
71398 TATTATATCTAT
1 T-TTATATCTAT
71410 TTT
1 TTT
71413 TTATTTTTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
9 8 0.22
10 4 0.11
11 21 0.57
12 4 0.11
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.64
Consensus pattern (11 bp):
TTTATATCTAT
Found at i:71403 original size:20 final size:18
Alignment explanation
Indices: 71365--71412 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
71355 AATTTATTTC
71365 TATATTATATCTATTTTA
1 TATATTATATCTATTTTA
71383 TATATTATA--TA--TTA
1 TATATTATATCTATTTTA
71397 T-TATTATATCTATTTT
1 TATATTATATCTATTTT
71413 TTATTTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
13 7 0.27
14 4 0.15
15 2 0.08
16 2 0.08
17 2 0.08
18 9 0.35
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (18 bp):
TATATTATATCTATTTTA
Found at i:71403 original size:31 final size:30
Alignment explanation
Indices: 71325--71425 Score: 95
Period size: 31 Copynumber: 3.4 Consensus size: 30
71315 TGGTTAAATT
* *
71325 TATTTATATATTGAATATTATAT-TATATTCA
1 TATTTATATATT-ATTATTATATCTAT-TTTA
71356 -ATTTAT-T-TCTA-TATTATATCTATTTTA
1 TATTTATATAT-TATTATTATATCTATTTTA
*
71383 TATATTATATATTATTATTATATCTATTTTT
1 TAT-TTATATATTATTATTATATCTATTTTA
*
71414 TATTTTTATATT
1 TATTTATATATT
71426 TTAATATTGA
Statistics
Matches: 60, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
27 11 0.18
28 7 0.12
29 6 0.10
30 17 0.28
31 19 0.32
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (30 bp):
TATTTATATATTATTATTATATCTATTTTA
Found at i:71416 original size:13 final size:14
Alignment explanation
Indices: 71367--71416 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 14
71357 TTTATTTCTA
71367 TATTATATCTATTT
1 TATTATATCTATTT
*
71381 TATATATTATATATTAT
1 TAT-TA-TATCTATT-T
71398 TATTATATCTATTT
1 TATTATATCTATTT
71412 T-TTAT
1 TATTAT
71417 TTTTATATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
13 4 0.13
14 5 0.16
15 9 0.29
16 9 0.29
17 4 0.13
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (14 bp):
TATTATATCTATTT
Found at i:73049 original size:9 final size:10
Alignment explanation
Indices: 73035--73090 Score: 84
Period size: 9 Copynumber: 6.0 Consensus size: 10
73025 TAATATATAT
73035 TTTACTTTA-
1 TTTACTTTAC
73044 TTTACTTTAC
1 TTTACTTTAC
73054 TTTA-TTTAC
1 TTTACTTTAC
73063 TTTA-TTTAC
1 TTTACTTTAC
73072 TTTACTTTA-
1 TTTACTTTAC
73081 TTTACTTTAC
1 TTTACTTTAC
73091 CGCTCTCAGT
Statistics
Matches: 44, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
9 36 0.82
10 8 0.18
ACGTcount: A:0.21, C:0.14, G:0.00, T:0.64
Consensus pattern (10 bp):
TTTACTTTAC
Found at i:73052 original size:14 final size:14
Alignment explanation
Indices: 73035--73090 Score: 80
Period size: 14 Copynumber: 4.0 Consensus size: 14
73025 TAATATATAT
73035 TTTACTTTATTTAC
1 TTTACTTTATTTAC
73049 TTTACTTTATTTAC
1 TTTACTTTATTTAC
73063 TTTA-TTTACTTTAC
1 TTTACTTTA-TTTAC
73077 TTTA-TTTACTTTAC
1 TTTACTTTA-TTTAC
73091 CGCTCTCAGT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.10
14 37 0.90
ACGTcount: A:0.21, C:0.14, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTACTTTATTTAC
Found at i:73062 original size:23 final size:23
Alignment explanation
Indices: 73035--73089 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
73025 TAATATATAT
73035 TTTACTTTATTTACTTTACTTTA
1 TTTACTTTATTTACTTTACTTTA
73058 TTTACTTTATTTACTTTACTTTA
1 TTTACTTTATTTACTTTACTTTA
73081 TTTACTTTA
1 TTTACTTTA
73090 CCGCTCTCAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.22, C:0.13, G:0.00, T:0.65
Consensus pattern (23 bp):
TTTACTTTATTTACTTTACTTTA
Found at i:75647 original size:14 final size:15
Alignment explanation
Indices: 75621--75650 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
75611 ATAACTAAAG
75621 AAAAAATAGATAGAT
1 AAAAAATAGATAGAT
75636 AAAAAATA-ATAGAT
1 AAAAAATAGATAGAT
75650 A
1 A
75651 GATGAGAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (15 bp):
AAAAAATAGATAGAT
Found at i:81380 original size:22 final size:22
Alignment explanation
Indices: 81355--81397 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
81345 ATTTCGATTT
*
81355 ATAAATCTATATTTGTATATAA
1 ATAAATCTATATTTCTATATAA
81377 ATAAATCTATATTTCTATATA
1 ATAAATCTATATTTCTATATA
81398 GTATTATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (22 bp):
ATAAATCTATATTTCTATATAA
Found at i:81414 original size:19 final size:19
Alignment explanation
Indices: 81390--81444 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
81380 AATCTATATT
81390 TCTATATAGTATTATTAAG
1 TCTATATAGTATTATTAAG
81409 TCTATATAGTATTATTAAG
1 TCTATATAGTATTATTAAG
*
81428 -ATATATAAG-ATTATTAA
1 TCTATAT-AGTATTATTAA
81445 TATATTATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 13 0.38
19 21 0.62
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.45
Consensus pattern (19 bp):
TCTATATAGTATTATTAAG
Found at i:81453 original size:11 final size:11
Alignment explanation
Indices: 81437--81557 Score: 57
Period size: 11 Copynumber: 11.6 Consensus size: 11
81427 GATATATAAG
81437 ATTATTAATAT
1 ATTATTAATAT
*
81448 ATTATTAAGA-
1 ATTATTAATAT
*
81458 ATAATATAAT-T
1 ATTAT-TAATAT
*
81469 ATAATATAATAT
1 ATTAT-TAATAT
*
81481 AATATT-AT-T
1 ATTATTAATAT
*
81490 CTTA-TAATAT
1 ATTATTAATAT
*
81500 A-TATT-ATTT
1 ATTATTAATAT
81509 ATATATTAAT-T
1 AT-TATTAATAT
*
81520 AATATT-ATAT
1 ATTATTAATAT
*
81530 ATTATT-ATTT
1 ATTATTAATAT
81540 AATTATT-ATAT
1 -ATTATTAATAT
81551 ATTATTA
1 ATTATTA
81558 TTTAAATAAT
Statistics
Matches: 85, Mismatches: 13, Indels: 24
0.70 0.11 0.20
Matches are distributed among these distances:
8 1 0.01
9 13 0.15
10 27 0.32
11 38 0.45
12 6 0.07
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (11 bp):
ATTATTAATAT
Found at i:81507 original size:3 final size:3
Alignment explanation
Indices: 81483--81559 Score: 50
Period size: 3 Copynumber: 24.3 Consensus size: 3
81473 TATAATATAA
* * *
81483 TAT TAT TCT TA- TAA TAT ATAT TATT TAT ATAT TAAT TAA TAT TAT ATAT
1 TAT TAT TAT TAT TAT TAT -TAT TA-T TAT -TAT T-AT TAT TAT TAT -TAT
*
81532 TAT TAT T-T AAT TAT TAT ATAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT T
81560 TAAATAATAT
Statistics
Matches: 59, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
2 3 0.05
3 38 0.64
4 18 0.31
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:81518 original size:21 final size:20
Alignment explanation
Indices: 81444--81554 Score: 80
Period size: 18 Copynumber: 5.9 Consensus size: 20
81434 AAGATTATTA
* *
81444 ATATATTATTA-AGAATAAT
1 ATATATTATTATATATTAAT
81463 ATA-ATTA-TA-ATA-TAAT
1 ATATATTATTATATATTAAT
*
81479 ATAATATTATTCT-TA-TAAT
1 AT-ATATTATTATATATTAAT
81498 ATATATTATTTATATATTAAT
1 ATATATTA-TTATATATTAAT
*
81519 -TA-A-TATTATATATTATT
1 ATATATTATTATATATTAAT
*
81536 ATTTAATTATTATATATTA
1 ATAT-ATTATTATATATTA
81555 TTATTTAAAT
Statistics
Matches: 76, Mismatches: 5, Indels: 20
0.75 0.05 0.20
Matches are distributed among these distances:
16 6 0.08
17 16 0.21
18 17 0.22
19 16 0.21
20 5 0.07
21 16 0.21
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (20 bp):
ATATATTATTATATATTAAT
Found at i:81529 original size:28 final size:28
Alignment explanation
Indices: 81492--81559 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
81482 ATATTATTCT
*
81492 TATAATATATATTATT-TATATATTAATTA
1 TATATTATATATTATTATATA-ATT-ATTA
*
81521 -ATATTATATATTATTATTTAATTATTA
1 TATATTATATATTATTATATAATTATTA
81548 TATATTAT-TATT
1 TATATTATATATT
81560 TAAATAATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 8 0.23
28 24 0.69
29 3 0.09
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (28 bp):
TATATTATATATTATTATATAATTATTA
Found at i:81530 original size:49 final size:55
Alignment explanation
Indices: 81469--81589 Score: 137
Period size: 56 Copynumber: 2.3 Consensus size: 55
81459 TAATATAATT
* *
81469 ATAATATAATATAATATTA-TT-CTTATAATATA-TATTATTT-AT-ATA-TTAA
1 ATAATATTATATAATATTATTTAATTATAATATATTATTATTTAATAATATTTAA
* * *
81518 TTAATATTATATATTATTATTTAATTATTATATATTATTATTTAAATAATATTTAA
1 ATAATATTATATAATATTATTTAATTATAATATATTATTATTT-AATAATATTTAA
*
81574 ATAATAATATATAATA
1 ATAATATTATATAATA
81590 ATTTAAGTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
49 16 0.28
50 2 0.04
51 9 0.16
52 8 0.14
54 2 0.04
55 3 0.05
56 17 0.30
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (55 bp):
ATAATATTATATAATATTATTTAATTATAATATATTATTATTTAATAATATTTAA
Found at i:81541 original size:24 final size:23
Alignment explanation
Indices: 81469--81570 Score: 95
Period size: 24 Copynumber: 4.3 Consensus size: 23
81459 TAATATAATT
* * *
81469 ATAATATAATATAATATTATTCTT
1 ATAATATTATATATTATTATT-TA
81493 ATAATA-TATATTATT-TATATATTA
1 ATAATATTATA-TATTAT-TAT-TTA
81517 ATTAATATTATATATTATTATTTA
1 A-TAATATTATATATTATTATTTA
81541 AT--TATTATATATTATTATTTAA
1 ATAATATTATATATTATTATTT-A
81563 ATAATATT
1 ATAATATT
81571 TAAATAATAA
Statistics
Matches: 66, Mismatches: 3, Indels: 18
0.76 0.03 0.21
Matches are distributed among these distances:
21 18 0.27
22 3 0.05
23 5 0.08
24 22 0.33
25 13 0.20
26 5 0.08
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (23 bp):
ATAATATTATATATTATTATTTA
Found at i:81555 original size:21 final size:21
Alignment explanation
Indices: 81502--81562 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
81492 TATAATATAT
*
81502 ATTATT-TATA-TATTAATTA
1 ATTATTATATATTATTATTTA
81521 A-TATTATATATTATTATTTA
1 ATTATTATATATTATTATTTA
81541 ATTATTATATATTATTATTTA
1 ATTATTATATATTATTATTTA
81562 A
1 A
81563 ATAATATTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
18 4 0.11
19 5 0.13
20 9 0.24
21 20 0.53
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATTATTATATATTATTATTTA
Found at i:81592 original size:49 final size:50
Alignment explanation
Indices: 81428--81592 Score: 119
Period size: 52 Copynumber: 3.2 Consensus size: 50
81418 TATTATTAAG
*
81428 ATATATA-AGATTATTA-ATA-TATTATTAAGAATAATATAATTATAAT-ATAAT
1 ATATATATA-ATTATTATATATTATTATTTA-AATAATAT--TTA-AATAATAAT
* * * * * *
81479 ATA-ATATTATTCTTATAATATATATTATTTATATATTAATT-AATATTATAT
1 ATATATATAATTATTAT-ATAT-TATTATTTAAATAATATTTAAATAATA-AT
*
81530 ATTATTATTTAATTATTATATATTATTATTTAAATAATATTTAAATAATAAT
1 A-TA-TATATAATTATTATATATTATTATTTAAATAATATTTAAATAATAAT
81582 ATATA-ATAATT
1 ATATATATAATT
81593 TAAGTTTTAA
Statistics
Matches: 88, Mismatches: 15, Indels: 24
0.69 0.12 0.19
Matches are distributed among these distances:
49 8 0.09
50 13 0.15
51 10 0.11
52 24 0.27
53 15 0.17
54 18 0.20
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (50 bp):
ATATATATAATTATTATATATTATTATTTAAATAATATTTAAATAATAAT
Found at i:81656 original size:14 final size:14
Alignment explanation
Indices: 81637--81664 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
81627 ATAATTAAAA
81637 ATTTATTTAATAAT
1 ATTTATTTAATAAT
81651 ATTTATTTAATAAT
1 ATTTATTTAATAAT
81665 TTAAAATCTC
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:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTTATTTAATAAT
Found at i:85654 original size:13 final size:13
Alignment explanation
Indices: 85636--85666 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
85626 CCATCAACTA
85636 ATCTTATTCTTGG
1 ATCTTATTCTTGG
85649 ATCTTATTCTTGG
1 ATCTTATTCTTGG
85662 ATCTT
1 ATCTT
85667 GTTCGTGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.16, G:0.13, T:0.55
Consensus pattern (13 bp):
ATCTTATTCTTGG
Found at i:86534 original size:27 final size:27
Alignment explanation
Indices: 86504--86558 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
86494 GTTTTGTCGC
86504 TTCAAGAGACGACTTATTATTATTCAT
1 TTCAAGAGACGACTTATTATTATTCAT
86531 TTCAAGAGACGACTTATTATTATTCAT
1 TTCAAGAGACGACTTATTATTATTCAT
86558 T
1 T
86559 ATAATAAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.42
Consensus pattern (27 bp):
TTCAAGAGACGACTTATTATTATTCAT
Found at i:86901 original size:13 final size:13
Alignment explanation
Indices: 86883--86923 Score: 64
Period size: 13 Copynumber: 3.0 Consensus size: 13
86873 CGGATAAGAT
86883 CTATTTATATATA
1 CTATTTATATATA
86896 CTATTTATATATATA
1 CTA-TT-TATATATA
86911 CTATTTATATATA
1 CTATTTATATATA
86924 TAAGTATATG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 11 0.42
14 4 0.15
15 11 0.42
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (13 bp):
CTATTTATATATA
Found at i:86908 original size:15 final size:15
Alignment explanation
Indices: 86888--86925 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
86878 AAGATCTATT
86888 TATATATACTATTTA
1 TATATATACTATTTA
86903 TATATATACTATTTA
1 TATATATACTATTTA
86918 TATATATA
1 TATATATA
86926 AGTATATGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATATACTATTTA
Found at i:87120 original size:21 final size:21
Alignment explanation
Indices: 87096--87137 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
87086 AACAAAATTC
87096 ATTTATTTGATTTGATTAATA
1 ATTTATTTGATTTGATTAATA
87117 ATTTATTTGATTTGATTAATA
1 ATTTATTTGATTTGATTAATA
87138 CATGTACCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (21 bp):
ATTTATTTGATTTGATTAATA
Found at i:89939 original size:16 final size:16
Alignment explanation
Indices: 89918--89949 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
89908 AAAATTTAGG
89918 AAGAATTCTTTTTTCT
1 AAGAATTCTTTTTTCT
89934 AAGAATTCTTTTTTCT
1 AAGAATTCTTTTTTCT
89950 TTTTTAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.12, G:0.06, T:0.56
Consensus pattern (16 bp):
AAGAATTCTTTTTTCT
Found at i:91234 original size:19 final size:19
Alignment explanation
Indices: 91210--91248 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
91200 GAAAAAAAAC
91210 TGGATACATAACTAATCAG
1 TGGATACATAACTAATCAG
91229 TGGATACATAACTAATCAG
1 TGGATACATAACTAATCAG
91248 T
1 T
91249 ATTGATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.28
Consensus pattern (19 bp):
TGGATACATAACTAATCAG
Found at i:91295 original size:14 final size:14
Alignment explanation
Indices: 91276--91305 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
91266 ATAAAAAAAC
*
91276 TTTCTGAATTTGAA
1 TTTCTGAATTTCAA
91290 TTTCTGAATTTCAA
1 TTTCTGAATTTCAA
91304 TT
1 TT
91306 ATATTATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.10, G:0.10, T:0.53
Consensus pattern (14 bp):
TTTCTGAATTTCAA
Found at i:91759 original size:11 final size:12
Alignment explanation
Indices: 91746--91789 Score: 65
Period size: 11 Copynumber: 3.8 Consensus size: 12
91736 CTCTCCCTAT
91746 ATATATTTTAT-
1 ATATATTTTATG
91757 ATATATTTTATG
1 ATATATTTTATG
91769 AATATATTTTATG
1 -ATATATTTTATG
91782 AT-TATTTT
1 ATATATTTT
91790 GTCTTTATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 17 0.55
12 2 0.06
13 12 0.39
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (12 bp):
ATATATTTTATG
Found at i:91781 original size:13 final size:13
Alignment explanation
Indices: 91746--91782 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
91736 CTCTCCCTAT
91746 ATATATTTTAT--
1 ATATATTTTATGA
91757 ATATATTTTATGA
1 ATATATTTTATGA
91770 ATATATTTTATGA
1 ATATATTTTATGA
91783 TTATTTTGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.46
13 13 0.54
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (13 bp):
ATATATTTTATGA
Found at i:96447 original size:11 final size:11
Alignment explanation
Indices: 96431--96455 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
96421 AATCGAAATC
96431 AATAAAAGAAG
1 AATAAAAGAAG
96442 AATAAAAGAAG
1 AATAAAAGAAG
96453 AAT
1 AAT
96456 GAATCAATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.16, T:0.12
Consensus pattern (11 bp):
AATAAAAGAAG
Found at i:96584 original size:21 final size:21
Alignment explanation
Indices: 96558--96601 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
96548 TCTTTATCTT
96558 TATTTGTTTATTTGGTGTAAC
1 TATTTGTTTATTTGGTGTAAC
96579 TATTTGTTTATTTGGTGTAAC
1 TATTTGTTTATTTGGTGTAAC
96600 TA
1 TA
96602 CTTGAGCCGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.05, G:0.18, T:0.57
Consensus pattern (21 bp):
TATTTGTTTATTTGGTGTAAC
Found at i:104979 original size:22 final size:22
Alignment explanation
Indices: 104954--104997 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
104944 GCTGTTCTTT
104954 CTATAGAATGATTCCCATTTCA
1 CTATAGAATGATTCCCATTTCA
104976 CTATAGAATGATTCCCATTTCA
1 CTATAGAATGATTCCCATTTCA
104998 GCCGATTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (22 bp):
CTATAGAATGATTCCCATTTCA
Found at i:106312 original size:24 final size:24
Alignment explanation
Indices: 106267--106356 Score: 152
Period size: 24 Copynumber: 3.9 Consensus size: 24
106257 AAGAGAAACC
106267 TTTTTTATTATTTATG-TT---TA
1 TTTTTTATTATTTATGTTTAAATA
106287 TTTTTTATTATTTATGTTTAAATA
1 TTTTTTATTATTTATGTTTAAATA
106311 TTTTTTATTATTTATGTTTAAATA
1 TTTTTTATTATTTATGTTTAAATA
106335 TTTTTTATTATTTATGTTTAAA
1 TTTTTTATTATTTATGTTTAAA
106357 GGAGTGTTGC
Statistics
Matches: 66, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
20 16 0.24
21 2 0.03
24 48 0.73
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (24 bp):
TTTTTTATTATTTATGTTTAAATA
Found at i:106528 original size:13 final size:13
Alignment explanation
Indices: 106496--106544 Score: 62
Period size: 13 Copynumber: 3.5 Consensus size: 13
106486 TGAAAATTGA
*
106496 TAATAATCAATAATT
1 TAATAATAAAT-A-T
106511 TAATAATAAATAT
1 TAATAATAAATAT
106524 TAATAATAAATAT
1 TAATAATAAATAT
106537 TAAATAAT
1 T-AATAAT
106545 TGATTATTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
13 15 0.47
14 7 0.22
15 10 0.31
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (13 bp):
TAATAATAAATAT
Found at i:109785 original size:13 final size:13
Alignment explanation
Indices: 109769--109815 Score: 59
Period size: 13 Copynumber: 4.0 Consensus size: 13
109759 AATTATCTAA
109769 TTATATAGATAAT
1 TTATATAGATAAT
109782 TTATATAG---A-
1 TTATATAGATAAT
109791 -TATATAGATAAT
1 TTATATAGATAAT
109803 TTATATAGATAAT
1 TTATATAGATAAT
109816 AATTTAGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
8 7 0.24
10 1 0.03
11 1 0.03
13 20 0.69
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.45
Consensus pattern (13 bp):
TTATATAGATAAT
Found at i:109794 original size:21 final size:21
Alignment explanation
Indices: 109770--109813 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
109760 ATTATCTAAT
109770 TATATAGATAATTTATATAGA
1 TATATAGATAATTTATATAGA
109791 TATATAGATAATTTATATAGA
1 TATATAGATAATTTATATAGA
109812 TA
1 TA
109814 ATAATTTAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (21 bp):
TATATAGATAATTTATATAGA
Found at i:109808 original size:34 final size:35
Alignment explanation
Indices: 109769--109837 Score: 97
Period size: 34 Copynumber: 2.0 Consensus size: 35
109759 AATTATCTAA
*
109769 TTATATAGATAATTTATATAG-ATA-TATAGATAAT
1 TTATATAGATAA-TAATATAGAATATTATAGATAAT
*
109803 TTATATAGATAATAATTTAGAATATTATAGATAAT
1 TTATATAGATAATAATATAGAATATTATAGATAAT
109838 AATCTAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
33 6 0.19
34 15 0.48
35 10 0.32
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (35 bp):
TTATATAGATAATAATATAGAATATTATAGATAAT
Found at i:109823 original size:25 final size:24
Alignment explanation
Indices: 109774--109840 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 24
109764 TCTAATTATA
109774 TAGATAATTTATATAGAT-AT-A-
1 TAGATAATTTATATAGATAATAAT
109795 TAGATAATTTATATAGATAATAATT
1 TAGATAATTTATATAGATAATAA-T
*
109820 TAG--AATAT-TATAGATAATAAT
1 TAGATAATTTATATAGATAATAAT
109841 CTAATATATT
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
21 19 0.46
22 14 0.34
23 5 0.12
25 3 0.07
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (24 bp):
TAGATAATTTATATAGATAATAAT
Found at i:109834 original size:22 final size:22
Alignment explanation
Indices: 109806--109853 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
109796 AGATAATTTA
*
109806 TATAGATAATAATTTAGA-ATAT
1 TATAGATAATAATCTA-ATATAT
109828 TATAGATAATAATCTAATATAT
1 TATAGATAATAATCTAATATAT
109850 TATA
1 TATA
109854 ATATATAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 1 0.04
22 23 0.96
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (22 bp):
TATAGATAATAATCTAATATAT
Found at i:111717 original size:21 final size:21
Alignment explanation
Indices: 111691--111731 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
111681 AATTACTGAT
*
111691 AAAAGTTCTATATATCTATAG
1 AAAAGTTCGATATATCTATAG
*
111712 AAAAGTTGGATATATCTATA
1 AAAAGTTCGATATATCTATA
111732 TTCTATATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (21 bp):
AAAAGTTCGATATATCTATAG
Found at i:111788 original size:8 final size:8
Alignment explanation
Indices: 111775--111825 Score: 57
Period size: 8 Copynumber: 6.0 Consensus size: 8
111765 ATTAAGAATC
111775 TATATATT
1 TATATATT
*
111783 TATATATC
1 TATATATT
111791 TATATATT
1 TATATATT
111799 TATATATT
1 TATATATT
*
111807 AATAATATAAT
1 --T-ATATATT
111818 TATATATT
1 TATATATT
111826 AATAATAATC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
8 28 0.78
9 1 0.03
10 1 0.03
11 6 0.17
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (8 bp):
TATATATT
Found at i:111793 original size:16 final size:16
Alignment explanation
Indices: 111772--111841 Score: 69
Period size: 16 Copynumber: 4.6 Consensus size: 16
111762 AAAATTAAGA
111772 ATCTATATATTTATAT
1 ATCTATATATTTATAT
111788 ATCTATATATTTATAT
1 ATCTATATATTTATAT
*
111804 AT-TA-ATA-ATATA-
1 ATCTATATATTTATAT
*
111816 AT-TATATATTAATAAT
1 ATCTATATATTTAT-AT
111832 AATCTATATA
1 -ATCTATATA
111842 AATAAATAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
12 4 0.09
13 7 0.16
14 5 0.11
15 3 0.07
16 18 0.40
17 2 0.04
18 6 0.13
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (16 bp):
ATCTATATATTTATAT
Found at i:111820 original size:19 final size:19
Alignment explanation
Indices: 111792--111832 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
111782 TTATATATCT
*
111792 ATATATTTATATATTAATA
1 ATATAATTATATATTAATA
111811 ATATAATTATATATTAATA
1 ATATAATTATATATTAATA
111830 ATA
1 ATA
111833 ATCTATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATAATTATATATTAATA
Found at i:111821 original size:17 final size:18
Alignment explanation
Indices: 111801--111860 Score: 61
Period size: 20 Copynumber: 3.3 Consensus size: 18
111791 TATATATTTA
111801 TATATTAATAATATAAT-
1 TATATTAATAATATAATC
*
111818 TATA-TATTAATAATAATC
1 TATATTAATAAT-ATAATC
*
111836 TATATAAATAAATAATAATC
1 TATATTAAT-AAT-ATAATC
111856 TATAT
1 TATAT
111861 AACCTATATA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
16 6 0.17
17 9 0.25
18 4 0.11
19 2 0.06
20 15 0.42
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
TATATTAATAATATAATC
Found at i:111862 original size:16 final size:17
Alignment explanation
Indices: 111801--111851 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 17
111791 TATATATTTA
*
111801 TATATTAATAATATAAT-
1 TATATAAATAA-ATAATC
111818 TATATATTAAT-AATAATC
1 TATATA--AATAAATAATC
111836 TATATAAATAAATAAT
1 TATATAAATAAATAAT
111852 AATCTATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
16 3 0.10
17 16 0.55
18 7 0.24
19 3 0.10
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
TATATAAATAAATAATC
Found at i:112586 original size:13 final size:13
Alignment explanation
Indices: 112568--112594 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
112558 TGTAAGACTT
112568 ATCTGATCTTTTC
1 ATCTGATCTTTTC
112581 ATCTGATCTTTTC
1 ATCTGATCTTTTC
112594 A
1 A
112595 ATTGTTAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.19, C:0.22, G:0.07, T:0.52
Consensus pattern (13 bp):
ATCTGATCTTTTC
Found at i:112665 original size:17 final size:17
Alignment explanation
Indices: 112643--112676 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
112633 TTTTCTAGGA
112643 CAGTATTTAAGGATCTC
1 CAGTATTTAAGGATCTC
112660 CAGTATTTAAGGATCTC
1 CAGTATTTAAGGATCTC
112677 ATCGAAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (17 bp):
CAGTATTTAAGGATCTC
Found at i:115161 original size:16 final size:16
Alignment explanation
Indices: 115140--115193 Score: 63
Period size: 16 Copynumber: 3.1 Consensus size: 16
115130 TCTTATTACT
115140 TTGCTACTATAGAATA
1 TTGCTACTATAGAATA
115156 TTGCTACTCCACTATAGAATA
1 TTG---CT--ACTATAGAATA
115177 TTGCTACTATAGAATA
1 TTGCTACTATAGAATA
115193 T
1 T
115194 AGAATACCGT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
16 15 0.45
18 2 0.06
19 2 0.06
21 14 0.42
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (16 bp):
TTGCTACTATAGAATA
Found at i:115169 original size:21 final size:21
Alignment explanation
Indices: 115145--115184 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
115135 TTACTTTGCT
115145 ACTATAGAATATTGCTACTCC
1 ACTATAGAATATTGCTACTCC
115166 ACTATAGAATATTGCTACT
1 ACTATAGAATATTGCTACT
115185 ATAGAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (21 bp):
ACTATAGAATATTGCTACTCC
Found at i:115275 original size:22 final size:22
Alignment explanation
Indices: 115247--115288 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
115237 AAATTTTATT
115247 GCTATAAAATATAGAGAAAATC
1 GCTATAAAATATAGAGAAAATC
115269 GCTATAAAATATAGAGAAAA
1 GCTATAAAATATAGAGAAAA
115289 AAGATCAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.57, C:0.07, G:0.14, T:0.21
Consensus pattern (22 bp):
GCTATAAAATATAGAGAAAATC
Found at i:115347 original size:22 final size:22
Alignment explanation
Indices: 115322--115368 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
115312 AATTGCATTT
*
115322 TAAAAAATA-AGATAAAATAAGA
1 TAAAAAA-ACAGATAAAATAAAA
*
115344 TAAAAAAACAGATAAGATAAAA
1 TAAAAAAACAGATAAAATAAAA
115366 TAA
1 TAA
115369 CATATAACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.72, C:0.02, G:0.09, T:0.17
Consensus pattern (22 bp):
TAAAAAAACAGATAAAATAAAA
Found at i:115360 original size:17 final size:17
Alignment explanation
Indices: 115338--115375 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
115328 ATAAGATAAA
115338 ATAAGATAAAAAAACAG
1 ATAAGATAAAAAAACAG
* *
115355 ATAAGATAAAATAACAT
1 ATAAGATAAAAAAACAG
115372 ATAA
1 ATAA
115376 CATACATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.68, C:0.05, G:0.08, T:0.18
Consensus pattern (17 bp):
ATAAGATAAAAAAACAG
Found at i:115457 original size:41 final size:44
Alignment explanation
Indices: 115400--115486 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 44
115390 ATAAAAATAG
*
115400 AAAATATTATTAATAAATAAAG-AAT-AA-ATTAAATAATTAAT
1 AAAATATTATTAATAAATAAAGAAATAAAGAATAAATAATTAAT
115441 AAAATATTATTAATAAATAAAGTAAATAAAGAATAAATAATTAAT
1 AAAATATTATTAATAAATAAAG-AAATAAAGAATAAATAATTAAT
115486 A
1 A
115487 CAAAAGAATT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
41 22 0.54
43 3 0.07
44 2 0.05
45 14 0.34
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.32
Consensus pattern (44 bp):
AAAATATTATTAATAAATAAAGAAATAAAGAATAAATAATTAAT
Found at i:115767 original size:22 final size:22
Alignment explanation
Indices: 115739--115782 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
115729 CAGGTTTTTT
115739 TTTATTGTATTGAAAAAAAATA
1 TTTATTGTATTGAAAAAAAATA
115761 TTTATTGTATTGAAAAAAAATA
1 TTTATTGTATTGAAAAAAAATA
115783 GATAACAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (22 bp):
TTTATTGTATTGAAAAAAAATA
Found at i:120521 original size:16 final size:16
Alignment explanation
Indices: 120500--120532 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
120490 AATTATTTAA
120500 TATATATTATCTATTT
1 TATATATTATCTATTT
*
120516 TATATATTTTCTATTT
1 TATATATTATCTATTT
120532 T
1 T
120533 TTGTTTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (16 bp):
TATATATTATCTATTT
Found at i:121138 original size:14 final size:14
Alignment explanation
Indices: 121121--121151 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
121111 GATGGATATA
121121 TATCGTATAATTCT
1 TATCGTATAATTCT
121135 TATCGTATAATTCT
1 TATCGTATAATTCT
121149 TAT
1 TAT
121152 ATATATTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.13, G:0.06, T:0.52
Consensus pattern (14 bp):
TATCGTATAATTCT
Found at i:125365 original size:20 final size:21
Alignment explanation
Indices: 125299--125367 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
125289 CCACTTCGTT
125299 TCTTTTTGTCCAAGTTACTTC
1 TCTTTTTGTCCAAGTTACTTC
*
125320 TCTTTTTGTCCAAGTTGCTTC
1 TCTTTTTGTCCAAGTTACTTC
* * *
125341 TCTTTTTGTCTAACTCACTTC
1 TCTTTTTGTCCAAGTTACTTC
125362 -CTTTTT
1 TCTTTTT
125368 TCTTTGTGAG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 6 0.14
21 37 0.86
ACGTcount: A:0.12, C:0.25, G:0.09, T:0.55
Consensus pattern (21 bp):
TCTTTTTGTCCAAGTTACTTC
Found at i:127768 original size:18 final size:18
Alignment explanation
Indices: 127745--127804 Score: 93
Period size: 18 Copynumber: 3.3 Consensus size: 18
127735 TTGATGATAT
127745 CGATATTGATGCTAGTGA
1 CGATATTGATGCTAGTGA
127763 CGATATTGATGCTAGTGA
1 CGATATTGATGCTAGTGA
* * *
127781 CGCTATTGACGATAGTGA
1 CGATATTGATGCTAGTGA
127799 CGATAT
1 CGATAT
127805 CGATCGTGAC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.28, C:0.13, G:0.27, T:0.32
Consensus pattern (18 bp):
CGATATTGATGCTAGTGA
Found at i:130422 original size:20 final size:20
Alignment explanation
Indices: 130395--130437 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 20
130385 AGGATGTCTT
130395 ATATATATTAAGATTATATTAA
1 ATATATA-T-AGATTATATTAA
130417 ATATATATAGATTATATTAA
1 ATATATATAGATTATATTAA
130437 A
1 A
130438 AAGATGGACA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 13 0.62
21 1 0.05
22 7 0.33
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (20 bp):
ATATATATAGATTATATTAA
Found at i:135127 original size:14 final size:14
Alignment explanation
Indices: 135092--135131 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
135082 TGGGTTCTTC
135092 TACTTCATTTTTATT
1 TACTT-ATTTTTATT
135107 TACTTATTTATTATT
1 TACTTATTT-TTATT
135122 TA-TTATTTTT
1 TACTTATTTTT
135132 TTTTCCCTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 2 0.08
14 10 0.42
15 12 0.50
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (14 bp):
TACTTATTTTTATT
Done.