Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004690.1 Hibiscus syriacus cultivar Beakdansim tig00010524_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: 76954
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:3899 original size:22 final size:22
Alignment explanation
Indices: 3874--3915 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3864 CATTTCAACT
*
3874 TCAACATCATCAACATCTTCCA
1 TCAACACCATCAACATCTTCCA
**
3896 TCAAGGCCATCAACATCTTC
1 TCAACACCATCAACATCTTC
3916 ATAATTCCGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.33, C:0.36, G:0.05, T:0.26
Consensus pattern (22 bp):
TCAACACCATCAACATCTTCCA
Found at i:3972 original size:20 final size:21
Alignment explanation
Indices: 3944--4003 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 21
3934 CTATTCATTT
*
3944 CATTACTTATCTTATAT-ATC
1 CATTTCTTATCTTATATAATC
3964 CATTTCTTATTCCATTAT-TAATC
1 CATTTCTTA-T-C-TTATATAATC
3987 CTATTTCTT-TCTTATAT
1 C-ATTTCTTATCTTATAT
4004 TTGTTGCAGC
Statistics
Matches: 33, Mismatches: 1, Indels: 11
0.73 0.02 0.24
Matches are distributed among these distances:
20 12 0.36
21 3 0.09
22 3 0.09
23 8 0.24
24 7 0.21
ACGTcount: A:0.25, C:0.20, G:0.00, T:0.55
Consensus pattern (21 bp):
CATTTCTTATCTTATATAATC
Found at i:7567 original size:10 final size:10
Alignment explanation
Indices: 7536--7560 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
7526 TCGTATTTAT
7536 TTTATTATTA
1 TTTATTATTA
7546 TTTATTATTA
1 TTTATTATTA
7556 TTTAT
1 TTTAT
7561 ATATATTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTATTATTA
Found at i:7652 original size:37 final size:37
Alignment explanation
Indices: 7608--7926 Score: 333
Period size: 37 Copynumber: 8.8 Consensus size: 37
7598 TAGAAAATAA
*
7608 TTTTTGAAAATGTATATATTATATAGTTTTTGAAAAC
1 TTTTTGAAAATATATATATTATATAGTTTTTGAAAAC
* *
7645 TTTTTGAAAATATATATAATATAAAGTTTTTGAAAAC
1 TTTTTGAAAATATATATATTATATAGTTTTTGAAAAC
* * *
7682 ATTTTGAAAATATATATATTATACAATTTTTGAAAAC
1 TTTTTGAAAATATATATATTATATAGTTTTTGAAAAC
* *
7719 TTTTTGAAAATATATATAATAAATAGTTTTTGAAAA-
1 TTTTTGAAAATATATATATTATATAGTTTTTGAAAAC
7755 TGTTTTGAAAATATATATATAATATATAGTTTTTGAAAAC
1 T-TTTTGAAAATATATATAT--TATATAGTTTTTGAAAAC
* * * * *
7795 ATTTTAAAAATATATTTAATATATTGTTTTT--AAAC
1 TTTTTGAAAATATATATATTATATAGTTTTTGAAAAC
*
7830 ATTTTTGAAACTATATGATA-TATA-A--TTTTGAAAAC
1 -TTTTTGAAAATATAT-ATATTATATAGTTTTTGAAAAC
* *
7865 ATTTTTTAAAATGTATA-A-TATATAGTTTTT--AAAC
1 -TTTTTGAAAATATATATATTATATAGTTTTTGAAAAC
7899 TATTTT-AAAA-A-ATATATTATATAGTTTT
1 T-TTTTGAAAATATATATATTATATAGTTTT
7927 ATTTTGGAAA
Statistics
Matches: 240, Mismatches: 28, Indels: 32
0.80 0.09 0.11
Matches are distributed among these distances:
31 3 0.01
32 1 0.00
33 25 0.10
34 10 0.04
35 21 0.09
36 21 0.09
37 128 0.53
39 31 0.13
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (37 bp):
TTTTTGAAAATATATATATTATATAGTTTTTGAAAAC
Found at i:9381 original size:17 final size:17
Alignment explanation
Indices: 9356--9400 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
9346 AAATTTAATA
9356 TTTTT-TTATTTCAT-TT
1 TTTTTCTTATTT-ATATT
*
9372 TTTTTCTTATTTTTATT
1 TTTTTCTTATTTATATT
9389 TTTTTCTTATTT
1 TTTTTCTTATTT
9401 TTTCTTATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 6 0.23
17 20 0.77
ACGTcount: A:0.11, C:0.07, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTCTTATTTATATT
Found at i:9401 original size:17 final size:17
Alignment explanation
Indices: 9370--9402 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
9360 TTTATTTCAT
9370 TTTTTTTCTTATTTTTA
1 TTTTTTTCTTATTTTTA
9387 TTTTTTTCTTATTTTT
1 TTTTTTTCTTATTTTT
9403 TCTTATTCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.09, C:0.06, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTTTTCTTATTTTTA
Found at i:9474 original size:17 final size:17
Alignment explanation
Indices: 9371--9477 Score: 58
Period size: 17 Copynumber: 6.1 Consensus size: 17
9361 TTATTTCATT
*
9371 TTTTTTCTTATTTTTAT-
1 TTTTTTCTT-TTTTTTTC
*
9388 TTTTTTCTTATTTTTTC
1 TTTTTTCTTTTTTTTTC
* * * *
9405 TTATTCCTTTTTTATTA
1 TTTTTTCTTTTTTTTTC
9422 TTTTTTCTCTCTTAATATTTT-
1 TTTTTTCT-T-TT--T-TTTTC
* *
9443 TATTATT-TATTTTTTTC
1 T-TTTTTCTTTTTTTTTC
9460 TTTTTTCTTTTTTTTTC
1 TTTTTTCTTTTTTTTTC
9477 T
1 T
9478 AAAATTTAAC
Statistics
Matches: 67, Mismatches: 14, Indels: 18
0.68 0.14 0.18
Matches are distributed among these distances:
16 13 0.19
17 39 0.58
18 1 0.01
19 4 0.06
21 3 0.04
22 7 0.10
ACGTcount: A:0.11, C:0.10, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTTCTTTTTTTTTC
Found at i:9559 original size:4 final size:4
Alignment explanation
Indices: 9550--9591 Score: 54
Period size: 4 Copynumber: 11.0 Consensus size: 4
9540 CCCTTCTTTG
9550 ATTT ATTT ATTT ATTT ATTT -TTCT -TTT -TTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATT-T ATTT ATTT ATTT ATTT ATTT
9592 TTTGATGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 6 0.17
4 30 0.83
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (4 bp):
ATTT
Found at i:9602 original size:26 final size:26
Alignment explanation
Indices: 9551--9604 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
9541 CCTTCTTTGA
*
9551 TTTATTTATTTATTTATTTTTCTTTT
1 TTTATTTATTTATTTATTTATCTTTT
*
9577 TTTATTTATTTATTT-TTTGATGTTTT
1 TTTATTTATTTATTTATTT-ATCTTTT
9603 TT
1 TT
9605 ATTCTACTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 3 0.12
26 22 0.88
ACGTcount: A:0.15, C:0.02, G:0.04, T:0.80
Consensus pattern (26 bp):
TTTATTTATTTATTTATTTATCTTTT
Found at i:10127 original size:18 final size:19
Alignment explanation
Indices: 10106--10141 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
10096 ATTTTTAAAA
10106 TATTAAAATATT-TTTTAT
1 TATTAAAATATTATTTTAT
10124 TATTAAAATATTATTTTA
1 TATTAAAATATTATTTTA
10142 ATAATTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATTAAAATATTATTTTAT
Found at i:10151 original size:14 final size:14
Alignment explanation
Indices: 10118--10159 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
10108 TTAAAATATT
10118 TTTTATTATTAAAA
1 TTTTATTATTAAAA
*
10132 TATTATT-TTAATAA
1 TTTTATTATTAA-AA
*
10146 TTTTATTAATAAAA
1 TTTTATTATTAAAA
10160 ATAAAAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 4 0.17
14 16 0.70
15 3 0.13
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTTATTATTAAAA
Found at i:10212 original size:33 final size:31
Alignment explanation
Indices: 10118--10217 Score: 84
Period size: 28 Copynumber: 3.3 Consensus size: 31
10108 TTAAAATATT
* *
10118 TTTTATTATTAAAATATT--ATT-TTAATAA
1 TTTTATTAATAAAATATTAAATTATTAATTA
* * **
10146 TTTTATTAATAAAA-ATAAAAATATTTGTATA
1 TTTTATTAATAAAATATTAAATTATTAAT-TA
10177 TTTTATTGAAATAAAATATTAAATTATTAATTA
1 TTTTATT--AATAAAATATTAAATTATTAATTA
10210 -TTTATTAA
1 TTTTATTAA
10218 AGTAATAGTG
Statistics
Matches: 55, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
27 2 0.04
28 13 0.24
29 2 0.04
30 5 0.09
31 8 0.15
32 6 0.11
33 9 0.16
34 10 0.18
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (31 bp):
TTTTATTAATAAAATATTAAATTATTAATTA
Found at i:10900 original size:16 final size:18
Alignment explanation
Indices: 10879--10943 Score: 71
Period size: 19 Copynumber: 3.6 Consensus size: 18
10869 ACATTTGGAA
10879 TAACATTA-TT-GGAATG
1 TAACATTACTTAGGAATG
10895 TAACATTACTTTAGGAATG
1 TAACATTAC-TTAGGAATG
*
10914 TAACATTACTTTGGGAATG
1 TAACATTAC-TTAGGAATG
**
10933 TTGCATTACTT
1 TAACATTACTT
10944 TGTTTGGTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
16 8 0.19
18 4 0.09
19 31 0.72
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (18 bp):
TAACATTACTTAGGAATG
Found at i:10945 original size:19 final size:19
Alignment explanation
Indices: 10889--10945 Score: 87
Period size: 19 Copynumber: 3.0 Consensus size: 19
10879 TAACATTATT
*
10889 GGAATGTAACATTACTTTA
1 GGAATGTAACATTACTTTG
10908 GGAATGTAACATTACTTTG
1 GGAATGTAACATTACTTTG
**
10927 GGAATGTTGCATTACTTTG
1 GGAATGTAACATTACTTTG
10946 TTTGGTTTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.39
Consensus pattern (19 bp):
GGAATGTAACATTACTTTG
Found at i:11186 original size:22 final size:21
Alignment explanation
Indices: 11146--11186 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
11136 TTTTTAAATA
* *
11146 ATTTTTATAAGTATCATATTT
1 ATTTTTATAAATATAATATTT
11167 ATTTTTATAAAATATAATAT
1 ATTTTTAT-AAATATAATAT
11187 AAAATAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (21 bp):
ATTTTTATAAATATAATATTT
Found at i:11770 original size:35 final size:37
Alignment explanation
Indices: 11730--11943 Score: 294
Period size: 37 Copynumber: 5.9 Consensus size: 37
11720 TATAATGATA
** *
11730 ATATAATATA-A-TTTTGAAAACATTTTTTTAAATAT
1 ATATAATATATAGTTTTGAAAACATTTTTGAAAACAT
*
11765 ATATAATATATAGTTTT-AAAACATTTTTGAAAACGT
1 ATATAATATATAGTTTTGAAAACATTTTTGAAAACAT
* * *
11801 ATATAATATATAGTTTTGGAAACATTTTTAAAAACGT
1 ATATAATATATAGTTTTGAAAACATTTTTGAAAACAT
*
11838 ATATAATATATAG-TTTGAAAACA-TTTTGAAAACGT
1 ATATAATATATAGTTTTGAAAACATTTTTGAAAACAT
11873 ATATAATATATAGTTTTGAAAACATTTTTGAAAACAT
1 ATATAATATATAGTTTTGAAAACATTTTTGAAAACAT
* * *
11910 ATATAATATATAATTTCGAAAACATTTTTTAAAA
1 ATATAATATATAGTTTTGAAAACATTTTTGAAAA
11944 TAGTTTTGAA
Statistics
Matches: 162, Mismatches: 12, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
35 34 0.21
36 52 0.32
37 76 0.47
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (37 bp):
ATATAATATATAGTTTTGAAAACATTTTTGAAAACAT
Found at i:11880 original size:72 final size:72
Alignment explanation
Indices: 11730--11937 Score: 312
Period size: 72 Copynumber: 2.9 Consensus size: 72
11720 TATAATGATA
** * *
11730 ATATAATATA-A-TTTTGAAAACATTTTTTTAAATATATATAATATATAGTTTTAAAACATTTTT
1 ATATAATATATAGTTTTGAAAACATTTTTAAAAACATATATAATATATAGTTTGAAAACA-TTTT
11793 GAAAACGT
65 GAAAACGT
* *
11801 ATATAATATATAGTTTTGGAAACATTTTTAAAAACGTATATAATATATAGTTTGAAAACATTTTG
1 ATATAATATATAGTTTTGAAAACATTTTTAAAAACATATATAATATATAGTTTGAAAACATTTTG
11866 AAAACGT
66 AAAACGT
* *
11873 ATATAATATATAGTTTTGAAAACATTTTTGAAAACATATATAATATATAATTTCGAAAACATTTT
1 ATATAATATATAGTTTTGAAAACATTTTTAAAAACATATATAATATATAGTTT-GAAAACATTTT
11938 TTAAAATAGT
Statistics
Matches: 124, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
71 10 0.08
72 62 0.50
73 52 0.42
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (72 bp):
ATATAATATATAGTTTTGAAAACATTTTTAAAAACATATATAATATATAGTTTGAAAACATTTTG
AAAACGT
Found at i:12007 original size:34 final size:35
Alignment explanation
Indices: 11935--12038 Score: 113
Period size: 34 Copynumber: 2.9 Consensus size: 35
11925 TCGAAAACAT
* * *
11935 TTTTTAAAATAGTTTTGAAAACATATAGTATGTGG
1 TTTTTAAAATAGTTTTGAAAACATATAATATATAG
*
11970 TTTTGAAAAT-GTTTTGAAAACATATAATATATAG
1 TTTTTAAAATAGTTTTGAAAACATATAATATATAG
* *
12004 TTTTTAAAACATA-TTTTAAAAAAATATATATATAT
1 TTTTT-AAA-ATAGTTTTGAAAACATATA-ATATAT
12039 GTGTGTGTGT
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
34 25 0.43
35 12 0.21
36 15 0.26
37 6 0.10
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.43
Consensus pattern (35 bp):
TTTTTAAAATAGTTTTGAAAACATATAATATATAG
Found at i:13868 original size:18 final size:18
Alignment explanation
Indices: 13833--13882 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
13823 TTTATTCTTC
13833 TAAATAAA-AAA-TAGAAA
1 TAAATAAATAAATTA-AAA
*
13850 TAATTAAATAAATTAAAA
1 TAAATAAATAAATTAAAA
*
13868 TAAATATATAAATTA
1 TAAATAAATAAATTA
13883 TTACAGATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 7 0.25
18 19 0.68
19 2 0.07
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (18 bp):
TAAATAAATAAATTAAAA
Found at i:14506 original size:14 final size:15
Alignment explanation
Indices: 14479--14508 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
14469 TCATGCAAAT
14479 AATTTAATAATATAA
1 AATTTAATAATATAA
14494 AATTTAA-AATATAA
1 AATTTAATAATATAA
14508 A
1 A
14509 TTAAAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AATTTAATAATATAA
Found at i:18412 original size:27 final size:26
Alignment explanation
Indices: 18374--18424 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
18364 AAATTACAAT
*
18374 TAATATAATTATGTTATTTTAAATTTA
1 TAATATAATTATGATA-TTTAAATTTA
18401 TAATA-AACTTATGATATTTAAATT
1 TAATATAA-TTATGATATTTAAATT
18425 AATACGATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (26 bp):
TAATATAATTATGATATTTAAATTTA
Found at i:18516 original size:18 final size:18
Alignment explanation
Indices: 18453--18515 Score: 74
Period size: 18 Copynumber: 3.4 Consensus size: 18
18443 AATTTAGTTT
18453 TTATATTAATTATAATT-
1 TTATATTAATTATAATTC
**
18470 TGTATATTAATTCCAATTC
1 T-TATATTAATTATAATTC
*
18489 TTTATATTATTTATAATTC
1 -TTATATTAATTATAATTC
18508 TTATATTA
1 TTATATTA
18516 TAAATTTTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
17 1 0.03
18 22 0.58
19 14 0.37
20 1 0.03
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.57
Consensus pattern (18 bp):
TTATATTAATTATAATTC
Found at i:18529 original size:13 final size:14
Alignment explanation
Indices: 18495--18531 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
18485 ATTCTTTATA
18495 TTATTTAT-AATTC
1 TTATTTATAAATTC
18508 TTATATTATAAATT-
1 TTAT-TTATAAATTC
18522 TTATTTATAA
1 TTATTTATAA
18532 TCATTCAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.45
14 8 0.36
15 4 0.18
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATTTATAAATTC
Found at i:19104 original size:23 final size:23
Alignment explanation
Indices: 19078--19131 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 23
19068 CAACAATCGA
*
19078 CAAGCATCA-CTGTATCAATTCAG
1 CAAGCATCATC-GCATCAATTCAG
19101 CAAGCATCATCGCATCAATTCAG
1 CAAGCATCATCGCATCAATTCAG
19124 CAAGCATC
1 CAAGCATC
19132 CTGCATTAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 28 0.97
24 1 0.03
ACGTcount: A:0.35, C:0.30, G:0.13, T:0.22
Consensus pattern (23 bp):
CAAGCATCATCGCATCAATTCAG
Found at i:19249 original size:20 final size:20
Alignment explanation
Indices: 19224--19277 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
19214 AACCCTTACA
** *
19224 AATATCAAGTAGAAGCAAGC
1 AATATCAAACAGAAGCAAAC
19244 AATATCAAACAGAAGCAAAC
1 AATATCAAACAGAAGCAAAC
*
19264 AATATAAAACAGAA
1 AATATCAAACAGAA
19278 TCAAGCACCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.59, C:0.15, G:0.13, T:0.13
Consensus pattern (20 bp):
AATATCAAACAGAAGCAAAC
Found at i:21915 original size:6 final size:6
Alignment explanation
Indices: 21904--22049 Score: 132
Period size: 6 Copynumber: 24.3 Consensus size: 6
21894 TTGGATTGGA
* * * * * *
21904 TTGGGT TTGGGT CTGGAT TCGGGT TAGGGT TTGAGT TTGGGT TTGAGT
1 TTGGGT TTGGGT TTGGGT TTGGGT TTGGGT TTGGGT TTGGGT TTGGGT
* * * * * *
21952 TCGGGT TTGGGT TTGGGT TT-GGT TTCAGGT TCGGGT TTGAGT TCGAGT
1 TTGGGT TTGGGT TTGGGT TTGGGT TT-GGGT TTGGGT TTGGGT TTGGGT
* * * *
22000 TTGGGT TTGGGT TTAGGT TTGAGC TTGGAT TTGGGT TTGGGT TTGGGT
1 TTGGGT TTGGGT TTGGGT TTGGGT TTGGGT TTGGGT TTGGGT TTGGGT
22048 TT
1 TT
22050 TAGTTCGGGT
Statistics
Matches: 110, Mismatches: 28, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
5 5 0.05
6 101 0.92
7 4 0.04
ACGTcount: A:0.07, C:0.05, G:0.42, T:0.46
Consensus pattern (6 bp):
TTGGGT
Found at i:22059 original size:24 final size:24
Alignment explanation
Indices: 21930--22067 Score: 89
Period size: 24 Copynumber: 5.5 Consensus size: 24
21920 ATTCGGGTTA
* *
21930 GGGTTTGAGTTTGGGTTTGAGTTC
1 GGGTTTGGGTTTGGGTTTTAGTTC
*
21954 GGGTTTGGGTTTGGG-TTTGGTTTC
1 GGGTTTGGGTTTGGGTTTTAG-TTC
* * * ** *
21978 AGGTTCGGGTTTGAGTTCGAGTTT
1 GGGTTTGGGTTTGGGTTTTAGTTC
* * *
22002 GGGTTTGGGTTTAGGTTTGAGCTTGGATTT
1 GGGTTTGGGTTT-GGGTT----TTAG-TTC
22032 GGGTTTGGGTTTGGGTTTTAGTTC
1 GGGTTTGGGTTTGGGTTTTAGTTC
22056 GGGTTTAGGGTT
1 GGGTTT-GGGTT
22068 AGAGAATATG
Statistics
Matches: 85, Mismatches: 20, Indels: 17
0.70 0.16 0.14
Matches are distributed among these distances:
23 3 0.04
24 49 0.58
25 13 0.15
29 5 0.06
30 15 0.18
ACGTcount: A:0.07, C:0.04, G:0.42, T:0.46
Consensus pattern (24 bp):
GGGTTTGGGTTTGGGTTTTAGTTC
Found at i:22355 original size:112 final size:112
Alignment explanation
Indices: 22235--22571 Score: 299
Period size: 104 Copynumber: 3.1 Consensus size: 112
22225 TGCTTGTTTG
*
22235 TAAGGGTTTGGGGAAGAACAAG-GATGAACACAGATGAATA-ATAGATGAACTTTTGGGTGTTTG
1 TAAGGGTTTGGGGAAGAA-AAGAGATGAACACAGATGAACACAT-GATGAACTTTTGGGTGTTTG
*
22298 A-TAAAAAAA-ATAGGAATGAGTTTAGGTTTTGGTGTTTGTGAAGATCAAA
64 ACTAAAAAAACAT-GAAATG-GTTTAGGTTTTGGTGTTTGTGAAGATCAAA
* ** * * * *
22347 TAATGGTTTGGGGAAGAATTGAGATGAACACGGATGAACACGTGATGAATTTTTTGGTGTTTGAT
1 TAAGGGTTTGGGGAAGAAAAGAGATGAACACAGATGAACACATGATGAACTTTTGGGTGTTTGA-
* *
22412 CTAAAAAAACATGAAATGGTTTGGGTTTTGGTGTTTTTGAAGATCAAA
65 CTAAAAAAACATGAAATGGTTTAGGTTTTGGTGTTTGTGAAGATCAAA
** * * * * *
22460 TAAGGGTTT----TTG----G-GATGAACACGGATAAACA-ATGGTTGAAATTATGGGTGTTTGA
1 TAAGGGTTTGGGGAAGAAAAGAGATGAACACAGATGAACACAT-GATGAACTTTTGGGTGTTTGA
* ** *
22515 TCGAAAAAAACACAAAATGGTTT-GGTTTTGGTGTTTGTGAAGATTAAA
65 -CTAAAAAAACATGAAATGGTTTAGGTTTTGGTGTTTGTGAAGATCAAA
*
22563 TGAGGGTTT
1 TAAGGGTTT
22572 TTGGGATGAA
Statistics
Matches: 193, Mismatches: 26, Indels: 21
0.80 0.11 0.09
Matches are distributed among these distances:
103 32 0.17
104 54 0.28
105 1 0.01
109 1 0.01
111 1 0.01
112 52 0.27
113 37 0.19
114 13 0.07
115 2 0.01
ACGTcount: A:0.34, C:0.05, G:0.28, T:0.33
Consensus pattern (112 bp):
TAAGGGTTTGGGGAAGAAAAGAGATGAACACAGATGAACACATGATGAACTTTTGGGTGTTTGAC
TAAAAAAACATGAAATGGTTTAGGTTTTGGTGTTTGTGAAGATCAAA
Found at i:22713 original size:18 final size:18
Alignment explanation
Indices: 22690--22956 Score: 171
Period size: 18 Copynumber: 15.7 Consensus size: 18
22680 ACAAAATAAC
*
22690 TATATAATATATAGTTTA
1 TATATACTATATAGTTTA
*
22708 TATATACTA-AT-G--AA
1 TATATACTATATAGTTTA
* *
22722 CTATATAATGTATAGTTTA
1 -TATATACTATATAGTTTA
*
22741 TATATACCATATAGTTTA
1 TATATACTATATAGTTTA
22759 TATATACTATATAGTTTA
1 TATATACTATATAGTTTA
22777 TATATACTATATAGTTTA
1 TATATACTATATAGTTTA
* *
22795 TATATACGA-AT-G--AA
1 TATATACTATATAGTTTA
*
22809 CTATATAATATATAGTTTA
1 -TATATACTATATAGTTTA
**
22828 TATATACTA-ATA-ACTA
1 TATATACTATATAGTTTA
*
22844 TATA-A-TATATAGTTTG
1 TATATACTATATAGTTTA
* *
22860 TATATACCATATA-CTT-
1 TATATACTATATAGTTTA
*
22876 TATATA-TATA-GGTTT-
1 TATATACTATATAGTTTA
22891 T-T-TA-TATATAGTTCATA
1 TATATACTATATAGTT--TA
* * *
22908 TGTAAACTATATAGTATA
1 TATATACTATATAGTTTA
* *
22926 TATAAACTATATAG-GTA
1 TATATACTATATAGTTTA
22943 GTATATACTATATA
1 -TATATACTATATA
22957 AATAGTTTAT
Statistics
Matches: 195, Mismatches: 31, Indels: 46
0.72 0.11 0.17
Matches are distributed among these distances:
13 6 0.03
14 8 0.04
15 24 0.12
16 24 0.12
17 15 0.08
18 107 0.55
19 3 0.02
20 8 0.04
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.45
Consensus pattern (18 bp):
TATATACTATATAGTTTA
Found at i:22761 original size:9 final size:9
Alignment explanation
Indices: 22749--22798 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
22739 TATATATACC
22749 ATATAGTTT
1 ATATAGTTT
*
22758 ATATA-TACT
1 ATATAGT-TT
22767 ATATAGTTT
1 ATATAGTTT
*
22776 ATATA-TACT
1 ATATAGT-TT
22785 ATATAGTTT
1 ATATAGTTT
22794 ATATA
1 ATATA
22799 TACGAATGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
8 2 0.06
9 29 0.88
10 2 0.06
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (9 bp):
ATATAGTTT
Found at i:22885 original size:87 final size:87
Alignment explanation
Indices: 22698--22883 Score: 272
Period size: 87 Copynumber: 2.2 Consensus size: 87
22688 ACTATATAAT
* * **
22698 ATATAGTTTATATATACTAATGAACTATATAATGTATAGTTTATATATACCATATAGTTTATATA
1 ATATAGTTTATATATACGAATGAACTATATAATATATAGTTTATATATACCATATAGACTATATA
*
22763 TACTATATAGTTTATATATACT
66 TACTATATAGTTTATATATACC
*
22785 ATATAGTTTATATATACGAATGAACTATATAATATATAGTTTATATATACTA-ATA-ACTATATA
1 ATATAGTTTATATATACGAATGAACTATATAATATATAGTTTATATATACCATATAGACTATATA
*
22848 -A-TATATAGTTTGTATATACC
66 TACTATATAGTTTATATATACC
*
22868 ATATACTTTATATATA
1 ATATAGTTTATATATA
22884 TAGGTTTTTT
Statistics
Matches: 91, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
83 32 0.35
84 1 0.01
85 6 0.07
86 3 0.03
87 49 0.54
ACGTcount: A:0.42, C:0.07, G:0.06, T:0.45
Consensus pattern (87 bp):
ATATAGTTTATATATACGAATGAACTATATAATATATAGTTTATATATACCATATAGACTATATA
TACTATATAGTTTATATATACC
Found at i:22898 original size:65 final size:64
Alignment explanation
Indices: 22749--22886 Score: 163
Period size: 69 Copynumber: 2.1 Consensus size: 64
22739 TATATATACC
** *
22749 ATATAGTTTATATATACTATATAGTTTATATATACTATATAGTTTATATATACGAATGAACTATA
1 ATATAGTTTATATATACTA-ATA-ACTATATA-A-TATATAGTTTATATATACCAAT-AACTATA
22814 TAAT
61 TAAT
* *
22818 ATATAGTTTATATATACTAATAACTATATAATATATAGTTTGTATATACC-ATATACTTTAT-AT
1 ATATAGTTTATATATACTAATAACTATATAATATATAGTTTATATATACCAATA-ACTATATAAT
22881 ATATAG
1 ATATAG
22887 GTTTTTTATA
Statistics
Matches: 63, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
63 9 0.14
64 8 0.13
65 17 0.27
66 1 0.02
67 6 0.10
68 3 0.05
69 19 0.30
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.45
Consensus pattern (64 bp):
ATATAGTTTATATATACTAATAACTATATAATATATAGTTTATATATACCAATAACTATATAAT
Found at i:22962 original size:18 final size:18
Alignment explanation
Indices: 22910--22962 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
22900 AGTTCATATG
*
22910 TAAACTATATAGTATA-TA
1 TAAACTATATA-AATAGTA
**
22928 TAAACTATATAGGTAGTA
1 TAAACTATATAAATAGTA
*
22946 TATACTATATAAATAGT
1 TAAACTATATAAATAGT
22963 TTATTAATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
17 2 0.07
18 27 0.93
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (18 bp):
TAAACTATATAAATAGTA
Found at i:23039 original size:14 final size:15
Alignment explanation
Indices: 23020--23054 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
23010 TACTTTGAAT
23020 TTATAT-AGTAAAAA
1 TTATATAAGTAAAAA
23034 TTATATAAGTAAAAA
1 TTATATAAGTAAAAA
23049 TTATAT
1 TTATAT
23055 TATATAGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (15 bp):
TTATATAAGTAAAAA
Found at i:23080 original size:27 final size:25
Alignment explanation
Indices: 23050--23141 Score: 76
Period size: 27 Copynumber: 3.5 Consensus size: 25
23040 AAGTAAAAAT
*
23050 TATATTATATAGTATATAAATATCAAC
1 TATATTATATAGT-T-TAAATATAAAC
* *
23077 TATAGTATATAGTTTATATATAAAC
1 TATATTATATAGTTTAAATATAAAC
* * * *
23102 TATAGTTTATATAGTTCATATGTAAAT
1 TATA--TTATATAGTTTAAATATAAAC
*
23129 TATACTATATAGT
1 TATATTATATAGT
23142 ATGTATAGTT
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
25 21 0.38
26 1 0.02
27 33 0.60
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (25 bp):
TATATTATATAGTTTAAATATAAAC
Found at i:24648 original size:29 final size:29
Alignment explanation
Indices: 24616--24686 Score: 106
Period size: 29 Copynumber: 2.4 Consensus size: 29
24606 AAAAAATTTA
***
24616 CCAAAATAGCACCAATTTCGAATTAATTC
1 CCAAAATAGCACCAAAACCGAATTAATTC
24645 CCAAAATAGCACCAAAACCGAATTAATTC
1 CCAAAATAGCACCAAAACCGAATTAATTC
*
24674 CCATAATAGCACC
1 CCAAAATAGCACC
24687 GGTCAACGGT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.44, C:0.28, G:0.07, T:0.21
Consensus pattern (29 bp):
CCAAAATAGCACCAAAACCGAATTAATTC
Found at i:24721 original size:13 final size:13
Alignment explanation
Indices: 24705--24750 Score: 83
Period size: 13 Copynumber: 3.5 Consensus size: 13
24695 GTCAACAGGT
24705 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
24718 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
*
24731 CGGGTCGGGTAAA
1 CGGGTCGGGTCAA
24744 CGGGTCG
1 CGGGTCG
24751 TGACCGGTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.15, C:0.22, G:0.48, T:0.15
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:24740 original size:18 final size:18
Alignment explanation
Indices: 24694--24728 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
24684 ACCGGTCAAC
24694 GGTCAACAGGTCGGGTCG
1 GGTCAACAGGTCGGGTCG
*
24712 GGTCAACGGGTCGGGTC
1 GGTCAACAGGTCGGGTC
24729 AACGGGTCGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.23, G:0.46, T:0.17
Consensus pattern (18 bp):
GGTCAACAGGTCGGGTCG
Found at i:24767 original size:9 final size:9
Alignment explanation
Indices: 24753--24801 Score: 53
Period size: 9 Copynumber: 5.1 Consensus size: 9
24743 ACGGGTCGTG
24753 ACCGGTCAA
1 ACCGGTCAA
24762 ACCGGTCAAA
1 ACCGGTC-AA
24772 ACCGGTTCAAA
1 ACCGG-TC-AA
* *
24783 ACCGATTAA
1 ACCGGTCAA
24792 ACCGGTCAA
1 ACCGGTCAA
24801 A
1 A
24802 ATCGGTTTCC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
9 17 0.50
10 8 0.24
11 9 0.26
ACGTcount: A:0.39, C:0.29, G:0.18, T:0.14
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:24773 original size:10 final size:10
Alignment explanation
Indices: 24753--24807 Score: 60
Period size: 10 Copynumber: 5.6 Consensus size: 10
24743 ACGGGTCGTG
24753 ACCGGTC-AA
1 ACCGGTCAAA
24762 ACCGGTCAAA
1 ACCGGTCAAA
24772 ACCGGTTCAAA
1 ACCGG-TCAAA
* *
24783 ACCGAT-TAA
1 ACCGGTCAAA
24792 ACCGGTCAAA
1 ACCGGTCAAA
*
24802 ATCGGT
1 ACCGGT
24808 TTCCAGCGTT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
9 14 0.37
10 15 0.39
11 9 0.24
ACGTcount: A:0.36, C:0.27, G:0.20, T:0.16
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:31889 original size:29 final size:29
Alignment explanation
Indices: 31857--31927 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 29
31847 AAAAAATTTA
**
31857 CCAAAATAGCACCAATTTC-GAATTAATTC
1 CCAAAATAGCACCAA-AACAGAATTAATTC
31886 CCAAAATAGCACCAAAACAGAATTAATTC
1 CCAAAATAGCACCAAAACAGAATTAATTC
*
31915 CCAGAATAGCACC
1 CCAAAATAGCACC
31928 GGTCAACGGT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 1 0.03
29 37 0.97
ACGTcount: A:0.45, C:0.27, G:0.08, T:0.20
Consensus pattern (29 bp):
CCAAAATAGCACCAAAACAGAATTAATTC
Found at i:31962 original size:13 final size:13
Alignment explanation
Indices: 31946--31991 Score: 83
Period size: 13 Copynumber: 3.5 Consensus size: 13
31936 GTCAACAGGT
31946 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
31959 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
*
31972 CGGGTCGGGTAAA
1 CGGGTCGGGTCAA
31985 CGGGTCG
1 CGGGTCG
31992 TGACCGGTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.15, C:0.22, G:0.48, T:0.15
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:31981 original size:18 final size:18
Alignment explanation
Indices: 31935--31969 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
31925 ACCGGTCAAC
31935 GGTCAACAGGTCGGGTCG
1 GGTCAACAGGTCGGGTCG
*
31953 GGTCAACGGGTCGGGTC
1 GGTCAACAGGTCGGGTC
31970 AACGGGTCGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.23, G:0.46, T:0.17
Consensus pattern (18 bp):
GGTCAACAGGTCGGGTCG
Found at i:32014 original size:10 final size:10
Alignment explanation
Indices: 31994--32069 Score: 111
Period size: 10 Copynumber: 7.6 Consensus size: 10
31984 ACGGGTCGTG
31994 ACCGGTC-AA
1 ACCGGTCAAA
32003 ACCGGTCAAA
1 ACCGGTCAAA
32013 ACCGGTTCAAA
1 ACCGG-TCAAA
*
32024 ACCGGT-TAA
1 ACCGGTCAAA
32033 ACCGGTCAAA
1 ACCGGTCAAA
32043 ACCGGTTCAAA
1 ACCGG-TCAAA
32054 ACCGGTCAAA
1 ACCGGTCAAA
32064 ACCGGT
1 ACCGGT
32070 TTCCAGCGTT
Statistics
Matches: 61, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
9 15 0.25
10 26 0.43
11 20 0.33
ACGTcount: A:0.36, C:0.29, G:0.21, T:0.14
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:32029 original size:30 final size:30
Alignment explanation
Indices: 31994--32069 Score: 134
Period size: 30 Copynumber: 2.5 Consensus size: 30
31984 ACGGGTCGTG
31994 ACCGGTCAAACCGGTCAAAACCGGTTCAAA
1 ACCGGTCAAACCGGTCAAAACCGGTTCAAA
*
32024 ACCGGTTAAACCGGTCAAAACCGGTTCAAA
1 ACCGGTCAAACCGGTCAAAACCGGTTCAAA
32054 ACCGGTCAAAACCGGT
1 ACCGGTC-AAACCGGT
32070 TTCCAGCGTT
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
30 35 0.81
31 8 0.19
ACGTcount: A:0.36, C:0.29, G:0.21, T:0.14
Consensus pattern (30 bp):
ACCGGTCAAACCGGTCAAAACCGGTTCAAA
Found at i:32070 original size:21 final size:21
Alignment explanation
Indices: 31994--32070 Score: 117
Period size: 21 Copynumber: 3.8 Consensus size: 21
31984 ACGGGTCGTG
31994 ACCGGTC-AAACCGG-TCAAA
1 ACCGGTCAAAACCGGTTCAAA
32013 ACCGGTTCAAAACCGGTT--AA
1 ACCGG-TCAAAACCGGTTCAAA
32033 ACCGGTCAAAACCGGTTCAAA
1 ACCGGTCAAAACCGGTTCAAA
32054 ACCGGTCAAAACCGGTT
1 ACCGGTCAAAACCGGTT
32071 TCCAGCGTTC
Statistics
Matches: 53, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
19 17 0.32
20 9 0.17
21 26 0.49
22 1 0.02
ACGTcount: A:0.35, C:0.29, G:0.21, T:0.16
Consensus pattern (21 bp):
ACCGGTCAAAACCGGTTCAAA
Found at i:32921 original size:18 final size:18
Alignment explanation
Indices: 32897--32937 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
32887 TAAACCATAT
*
32897 ATATAGTTCATATGTAAA
1 ATATAGTTCATATATAAA
*
32915 CTATAGTTCATATATAAA
1 ATATAGTTCATATATAAA
32933 ATATA
1 ATATA
32938 TAATTTATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (18 bp):
ATATAGTTCATATATAAA
Found at i:32979 original size:27 final size:28
Alignment explanation
Indices: 32916--32986 Score: 99
Period size: 27 Copynumber: 2.5 Consensus size: 28
32906 ATATGTAAAC
*
32916 TATAGTTCATATATAAAATATATAATTTA
1 TATAGTTTATATAT-AAATATATAATTTA
*
32945 TATAGTTTATATATAAA-CTATAATTTA
1 TATAGTTTATATATAAATATATAATTTA
*
32972 TATAGTTTTTATATA
1 TATAGTTTATATATA
32987 TAGTTCATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
27 23 0.59
28 3 0.08
29 13 0.33
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (28 bp):
TATAGTTTATATATAAATATATAATTTA
Found at i:33022 original size:9 final size:9
Alignment explanation
Indices: 33008--33044 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
32998 TAAATTATAC
33008 TATATAGTA
1 TATATAGTA
33017 TATATAGT-
1 TATATAGTA
33025 T-TATA-TA
1 TATATAGTA
33032 TATATAGTA
1 TATATAGTA
33041 TATA
1 TATA
33045 AATATCAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
6 1 0.04
7 5 0.20
8 5 0.20
9 14 0.56
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (9 bp):
TATATAGTA
Found at i:33129 original size:23 final size:23
Alignment explanation
Indices: 33099--33144 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
33089 ATATATATAG
* *
33099 TATATACTATATATATAGTTTAT
1 TATATACTATATAAATAATTTAT
33122 TATATACTATATAAATAATTTAT
1 TATATACTATATAAATAATTTAT
33145 ACAGTTCACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.50
Consensus pattern (23 bp):
TATATACTATATAAATAATTTAT
Found at i:33169 original size:24 final size:24
Alignment explanation
Indices: 33142--33191 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
33132 ATAAATAATT
33142 TATACAGTTCACTA-ATAAACTATA
1 TATACAGTTCA-TACATAAACTATA
* *
33166 TATATAGTTCATACGTAAACTATA
1 TATACAGTTCATACATAAACTATA
33190 TA
1 TA
33192 GTTTACATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 2 0.09
24 21 0.91
ACGTcount: A:0.44, C:0.14, G:0.06, T:0.36
Consensus pattern (24 bp):
TATACAGTTCATACATAAACTATA
Found at i:33202 original size:29 final size:29
Alignment explanation
Indices: 33164--33312 Score: 150
Period size: 29 Copynumber: 5.4 Consensus size: 29
33154 TAATAAACTA
*
33164 TATATATAGTTCATACGTAAACTATATAG
1 TATATATAGTTCATATGTAAACTATATAG
* * * *
33193 TTTACATAGTT--TA--TATAGT-T-TA-
1 TATATATAGTTCATATGTAAACTATATAG
* * *
33215 TACATATAGTTCACATGTAAACTATATAA
1 TATATATAGTTCATATGTAAACTATATAG
*
33244 TATATATAGTTCATATGTAAACTATAAAG
1 TATATATAGTTCATATGTAAACTATATAG
**
33273 TATCCATAGTTCATATGTAAACTATATAG
1 TATATATAGTTCATATGTAAACTATATAG
33302 TATATATAGTT
1 TATATATAGTT
33313 TACATATAGT
Statistics
Matches: 94, Mismatches: 19, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
22 8 0.09
23 2 0.02
24 2 0.02
25 4 0.04
26 4 0.04
27 3 0.03
28 2 0.02
29 69 0.73
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.41
Consensus pattern (29 bp):
TATATATAGTTCATATGTAAACTATATAG
Found at i:33215 original size:9 final size:9
Alignment explanation
Indices: 33186--33216 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
33176 ATACGTAAAC
33186 TATATAGTT
1 TATATAGTT
*
33195 TACATAGTT
1 TATATAGTT
33204 TATATAGTT
1 TATATAGTT
33213 TATA
1 TATA
33217 CATATAGTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.52
Consensus pattern (9 bp):
TATATAGTT
Found at i:33253 original size:51 final size:51
Alignment explanation
Indices: 33162--33259 Score: 133
Period size: 51 Copynumber: 1.9 Consensus size: 51
33152 ACTAATAAAC
* * * * *
33162 TATATATATAGTTCATACGTAAACTATATAGTTTACATAGTTTATATAGTT
1 TATACATATAGTTCACACGTAAACTATATAATATACATAGTTCATATAGTT
* *
33213 TATACATATAGTTCACATGTAAACTATATAATATATATAGTTCATAT
1 TATACATATAGTTCACACGTAAACTATATAATATACATAGTTCATAT
33260 GTAAACTATA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 40 1.00
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.43
Consensus pattern (51 bp):
TATACATATAGTTCACACGTAAACTATATAATATACATAGTTCATATAGTT
Found at i:33400 original size:28 final size:30
Alignment explanation
Indices: 33345--33401 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
33335 ATATTGTTTA
33345 TATATAGTTTAAATACTAATATCCATAAAC
1 TATATAGTTTAAATACTAATATCCATAAAC
* *
33375 TATATAGTTTATATA-TAAT-TTCATAAA
1 TATATAGTTTAAATACTAATATCCATAAA
33402 TTAACCCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 7 0.28
29 4 0.16
30 14 0.56
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.42
Consensus pattern (30 bp):
TATATAGTTTAAATACTAATATCCATAAAC
Found at i:33471 original size:11 final size:11
Alignment explanation
Indices: 33455--33479 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
33445 TATATATAAT
33455 TATATAGTTTA
1 TATATAGTTTA
33466 TATATAGTTTA
1 TATATAGTTTA
33477 TAT
1 TAT
33480 TAATAAACTA
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:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (11 bp):
TATATAGTTTA
Found at i:33498 original size:22 final size:22
Alignment explanation
Indices: 33466--33523 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
33456 ATATAGTTTA
33466 TATATAGTTTATATTAATAAAC
1 TATATAGTTTATATTAATAAAC
*
33488 TATATAATTTATATTAATAAAC
1 TATATAGTTTATATTAATAAAC
*
33510 TATGTAGTTTATAT
1 TATATAGTTTATAT
33524 ATAGTTCAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.48
Consensus pattern (22 bp):
TATATAGTTTATATTAATAAAC
Found at i:33582 original size:2 final size:2
Alignment explanation
Indices: 33575--33729 Score: 104
Period size: 2 Copynumber: 76.0 Consensus size: 2
33565 TTATACATGG
* * * *
33575 TA TA TA TA GTT TA TA CA TA -A TA TA TA TA TA GTT TA TA TA CA GTA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA
* * *
33619 TA TA -A TA -A TA TA AA TA TA AA CTA TA TA GTT TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA
* * * *
33661 TA TA TA TA TA TA -A TA TA TA TA CTT TA CA TA TA CA CTA TA TA GTT
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA -TA
33705 TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
33730 GTTGTTTTAA
Statistics
Matches: 118, Mismatches: 22, Indels: 26
0.71 0.13 0.16
Matches are distributed among these distances:
1 5 0.04
2 105 0.89
3 8 0.07
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:33587 original size:20 final size:20
Alignment explanation
Indices: 33552--33627 Score: 73
Period size: 20 Copynumber: 3.7 Consensus size: 20
33542 TATAAACTGT
33552 ATAGTAT-TATAATTTATAC
1 ATAGTATATATAATTTATAC
* *
33571 ATGGTATATATAGTTTATAC
1 ATAGTATATATAATTTATAC
* *
33591 ATAATATATATATAGTTTATAT
1 ATAGTATATATA-A-TTTATAC
*
33613 ACAGTATATAATAAT
1 ATAGTATAT-ATAAT
33628 ATAAATATAA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
19 6 0.13
20 21 0.47
21 1 0.02
22 14 0.31
23 3 0.07
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (20 bp):
ATAGTATATATAATTTATAC
Found at i:33589 original size:11 final size:11
Alignment explanation
Indices: 33575--33613 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
33565 TTATACATGG
33575 TATATATAGTT
1 TATATATAGTT
* * *
33586 TATACATAATA
1 TATATATAGTT
33597 TATATATAGTT
1 TATATATAGTT
33608 TATATA
1 TATATA
33614 CAGTATATAA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (11 bp):
TATATATAGTT
Found at i:33725 original size:56 final size:59
Alignment explanation
Indices: 33577--33725 Score: 196
Period size: 56 Copynumber: 2.5 Consensus size: 59
33567 ATACATGGTA
*
33577 TATATAGTTTATACATAATATATATATAGTTTATATACAGTATATAATAATATAAATATAAAC
1 TATATAGTTTAT--AT-ATATATATATA-TATATATACAGTATATAATAATATAAATATAAAC
* * * *
33640 TATATAGTTTATATATATATATATATATATATA-A-TATAT-ATACTTTACATATACAC
1 TATATAGTTTATATATATATATATATATATATACAGTATATAATAATATAAATATAAAC
33696 TATATAGTTTATATATATATATATATATAT
1 TATATAGTTTATATATATATATATATATAT
33726 TATAGTTGTT
Statistics
Matches: 81, Mismatches: 5, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
56 43 0.53
57 5 0.06
58 1 0.01
59 7 0.09
60 11 0.14
61 2 0.02
63 12 0.15
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (59 bp):
TATATAGTTTATATATATATATATATATATATACAGTATATAATAATATAAATATAAAC
Found at i:34026 original size:26 final size:26
Alignment explanation
Indices: 33985--34059 Score: 105
Period size: 26 Copynumber: 2.8 Consensus size: 26
33975 AACGTTCGCA
*
33985 AAAGATGAAAATATGGGATGCAAATGC
1 AAAGATG-AAATATGGGATGCAAATAC
*
34012 AAAGATGCAATATGGGATGCAAATAC
1 AAAGATGAAATATGGGATGCAAATAC
**
34038 AAAGATGAAATGCGGGATGCAA
1 AAAGATGAAATATGGGATGCAA
34060 GTGAAAATGG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
26 36 0.84
27 7 0.16
ACGTcount: A:0.47, C:0.09, G:0.27, T:0.17
Consensus pattern (26 bp):
AAAGATGAAATATGGGATGCAAATAC
Found at i:35861 original size:105 final size:106
Alignment explanation
Indices: 35744--35959 Score: 258
Period size: 106 Copynumber: 2.0 Consensus size: 106
35734 GTCACAATTG
* ** * * * *
35744 TTTTTTTTGTGACCATTTATTTGACA-CAATTATTAATATAAATTGTGAT-GATTCT-TTTTACA
1 TTTTTTTAGTGACCAAATATTTGACATC-ATTATCAATAGAAATTGTGATAAATT-TATTTGACA
*
35806 CTAAAAATATATTTTGTGACCATCAATATTGTCACACTAAGTA
64 CTAAAAATATATTTTGTGACCACCAATATTGTCACACTAAGTA
* *
35849 TTTTTTTAGTGACCAAATGTTTGATATCATTATCAATAGAAATTGTGATAAATTTATTTGACACT
1 TTTTTTTAGTGACCAAATATTTGACATCATTATCAATAGAAATTGTGATAAATTTATTTGACACT
* * * * *
35914 GAAAGTATATTTTGTGACCACCAATGTTGTCACAGTAAGTG
66 AAAAATATATTTTGTGACCACCAATATTGTCACACTAAGTA
35955 TTTTT
1 TTTTT
35960 AGTGACAAAA
Statistics
Matches: 93, Mismatches: 15, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
105 41 0.44
106 52 0.56
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (106 bp):
TTTTTTTAGTGACCAAATATTTGACATCATTATCAATAGAAATTGTGATAAATTTATTTGACACT
AAAAATATATTTTGTGACCACCAATATTGTCACACTAAGTA
Found at i:35947 original size:106 final size:103
Alignment explanation
Indices: 35772--35978 Score: 263
Period size: 106 Copynumber: 2.0 Consensus size: 103
35762 ATTTGACACA
* * * * *
35772 ATTATTAATATAAATTGTGATGATTCTTTTTACACTAAAAATATATTTTGTGACCATCAATATTG
1 ATTATCAATAGAAATTGTGATAATTCTTTTGACACTAAAAATATATTTTGTGACCACCAATATTG
* * *
35837 TCACACTAAGTATTTTTTTAGTGACCAAATGTTTGATATC
66 TCACACTAAG--TGTTTTTAGTGACAAAATGTTCGATATC
* * *
35877 ATTATCAATAGAAATTGTGATAAATT-TATTTGACACTGAAAGTATATTTTGTGACCACCAATGT
1 ATTATCAATAGAAATTGTGAT-AATTCT-TTTGACACTAAAAATATATTTTGTGACCACCAATAT
*
35941 TGTCACAGTAAGTGTTTTTAGTGACAAAATGTTCGATA
64 TGTCACACTAAGTGTTTTTAGTGACAAAATGTTCGATA
35979 CTATTGACAA
Statistics
Matches: 88, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
104 23 0.26
105 20 0.23
106 45 0.51
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.41
Consensus pattern (103 bp):
ATTATCAATAGAAATTGTGATAATTCTTTTGACACTAAAAATATATTTTGTGACCACCAATATTG
TCACACTAAGTGTTTTTAGTGACAAAATGTTCGATATC
Found at i:36458 original size:20 final size:20
Alignment explanation
Indices: 36435--36476 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
36425 ATATACAATA
36435 TTAATT-ATTATTATAATAAT
1 TTAATTAATT-TTATAATAAT
*
36455 TTAATTAATTTTTTAATAAT
1 TTAATTAATTTTATAATAAT
36475 TT
1 TT
36477 CTCATATGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTAATTAATTTTATAATAAT
Found at i:39261 original size:44 final size:44
Alignment explanation
Indices: 39189--39273 Score: 109
Period size: 44 Copynumber: 1.9 Consensus size: 44
39179 TATTTTCCCC
* *
39189 CAAAAACGACGCTAAATGTTCTGACATATAATGACATTTGTTCT
1 CAAAAACGACGCTAAATATTATGACATATAATGACATTTGTTCT
* * *
39233 CAAAAAC-ACCGCTAAATATTATGTCATATAGTGATATTTGT
1 CAAAAACGA-CGCTAAATATTATGACATATAATGACATTTGT
39274 GAATGTAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 1 0.03
44 34 0.97
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (44 bp):
CAAAAACGACGCTAAATATTATGACATATAATGACATTTGTTCT
Found at i:39540 original size:21 final size:21
Alignment explanation
Indices: 39491--39540 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
39481 TAGCATTATC
* *
39491 TAATAAACTTGACATCCATAA
1 TAATAAATTTGAAATCCATAA
* *
39512 CAAGAAATTTGAAATCCATAA
1 TAATAAATTTGAAATCCATAA
39533 TAATAAAT
1 TAATAAAT
39541 CAAAGTTTAC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.52, C:0.14, G:0.06, T:0.28
Consensus pattern (21 bp):
TAATAAATTTGAAATCCATAA
Found at i:42071 original size:40 final size:41
Alignment explanation
Indices: 42017--42707 Score: 443
Period size: 41 Copynumber: 17.0 Consensus size: 41
42007 GTACGAGTCT
* * * *
42017 TATACAAACACCACTAAAGTAC-AATATTTATCGGTGTTTA
1 TATAAAAACACCACTAAAGTACGAGTATTTAGCGGCGTTTA
** *
42057 TATAAAAATGCCACTAAAGTACGAGTATTTAGCGGCGTTTG
1 TATAAAAACACCACTAAAGTACGAGTATTTAGCGGCGTTTA
* * * * ** *
42098 TGCTTAAAACACCATTAAAGTACGAGTATTTGGCACCGTTTG
1 T-ATAAAAACACCACTAAAGTACGAGTATTTAGCGGCGTTTA
* * *
42140 TATACAAACGCCACTAAAGTA-TAGTATTTAGCGGCGTTTA
1 TATAAAAACACCACTAAAGTACGAGTATTTAGCGGCGTTTA
* **
42180 TATAAAAACACCACTAAAGTACGAGTCTTT---GGCGTCGA
1 TATAAAAACACCACTAAAGTACGAGTATTTAGCGGCGTTTA
* ** * * *
42218 TATACAAATGCCACTAAAGTA-TAGTATTTAGCGACGTGTA
1 TATAAAAACACCACTAAAGTACGAGTATTTAGCGGCGTTTA
* * * *
42258 TATAAAAACACCACTAAAGTATGAGTATTCAGCGACGTTTG
1 TATAAAAACACCACTAAAGTACGAGTATTTAGCGGCGTTTA
* *** * * * ** *
42299 TACTTAAAATGTCACTAAAGTACGTGTCTTT-GTCAGTTTTTG
1 TA-TAAAAACACCACTAAAGTACGAGTATTTAG-CGGCGTTTA
* * * * * * *
42341 TATACAAGCGCCACTAAAGTA-TAATATTTAGCTGTGTTTA
1 TATAAAAACACCACTAAAGTACGAGTATTTAGCGGCGTTTA
* * * *
42381 TATAAAAAC-CTCACTAAAGTATGAGTATTTAACGGCGTGTG
1 TATAAAAACAC-CACTAAAGTACGAGTATTTAGCGGCGTTTA
* * * * * * * *
42422 TGCTTAAAACACCACTAAAGTATGAGTCTTCAGCAGTGTTTG
1 T-ATAAAAACACCACTAAAGTACGAGTATTTAGCGGCGTTTA
* * * ** *
42464 TATAAAAACACTACTAAAGTATGAGTCTTTAGCGAAGTTTG
1 TATAAAAACACCACTAAAGTACGAGTATTTAGCGGCGTTTA
* *
42505 TATACAAACACCACTAAAGTAC-AATATTTAGCGGCGTTTA
1 TATAAAAACACCACTAAAGTACGAGTATTTAGCGGCGTTTA
* * * * *
42545 AATAAAAATGA-CACTAAAGAACGTGTATTTAGCGGCGTTTG
1 TATAAAAA-CACCACTAAAGTACGAGTATTTAGCGGCGTTTA
* * * * * * *
42586 TGCTTAAAACACCACTAAAGTACGAGTCTTTAGTGACATTTG
1 T-ATAAAAACACCACTAAAGTACGAGTATTTAGCGGCGTTTA
* * * *
42628 TACAAAAACGCCACTAAAGTA-TAGTATTTAGCAGCGTTTA
1 TATAAAAACACCACTAAAGTACGAGTATTTAGCGGCGTTTA
** * * *
42668 TATAAAAATGCCACTAACGTACGAGTATTTACCGACGTTT
1 TATAAAAACACCACTAAAGTACGAGTATTTAGCGGCGTTT
42708 GTTCAAAAAA
Statistics
Matches: 495, Mismatches: 137, Indels: 37
0.74 0.20 0.06
Matches are distributed among these distances:
37 6 0.01
38 24 0.05
39 1 0.00
40 161 0.33
41 181 0.37
42 121 0.24
43 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (41 bp):
TATAAAAACACCACTAAAGTACGAGTATTTAGCGGCGTTTA
Found at i:42245 original size:78 final size:80
Alignment explanation
Indices: 42056--42697 Score: 304
Period size: 81 Copynumber: 7.9 Consensus size: 80
42046 ATCGGTGTTT
* * * * * *
42056 ATATAAAAATGCCACTAAAGTACGAGTATTTAGCGGCGTTTGTGCTTAAAACACCATTAAAGTAC
1 ATATACAAATGCCACTAAAGTA-TAGTATTTAGCGGCGTTTAT-ATAAAAACACCACTAAAGTAC
*
42121 GAGTATTTGGCACCGTTTG
64 GAGTATTTGG--CCGTTCG
*
42140 -TATACAAACGCCACTAAAGTATAGTATTTAGCGGCGTTTATATAAAAACACCACTAAAGTACGA
1 ATATACAAATGCCACTAAAGTATAGTATTTAGCGGCGTTTATATAAAAACACCACTAAAGTACGA
*
42204 GTCTTTGG-CG-TCG
66 GTATTTGGCCGTTCG
* * *
42217 ATATACAAATGCCACTAAAGTATAGTATTTAGCGACGTGTATATAAAAACACCACTAAAGTATGA
1 ATATACAAATGCCACTAAAGTATAGTATTTAGCGGCGTTTATATAAAAACACCACTAAAGTACGA
* * *
42282 GTATTCAGCGACGTTTG
66 GTATT-TG-GCCGTTCG
* * * ** * * * *
42299 -TACTTA-AAATGTCACTAAAGTACGT-GTCTTT-GTCAGTTTTTGTATACAAGCGCCACTAAAG
1 ATA--TACAAATGCCACTAAAGTA--TAGTATTTAG-CGGCGTTTATATAAAAACACCACTAAAG
* * * * **
42360 TA-TAATATTTAGCTGTGTTT
61 TACGAGTATTTGGCCGT-TCG
** * * * * *
42380 ATATA-AAAACCTCACTAAAGTATGAGTATTTAACGGCGTGTGTGCTTAAAACACCACTAAAGTA
1 ATATACAAATGC-CACTAAAGTAT-AGTATTTAGCGGCGTTTAT-ATAAAAACACCACTAAAGTA
* * ** * *
42444 TGAGTCTTCAGCAGTGTTTG
63 CGAGTATTTGGC--CGTTCG
* ** * * ** * *
42464 -TATAAAAACACTACTAAAGTATGAGTCTTTAGCGAAGTTTGTATACAAACACCACTAAAGTAC-
1 ATATACAAATGCCACTAAAGTAT-AGTATTTAGCGGCGTTTATATAAAAACACCACTAAAGTACG
* * *
42527 AATATTTAGCGGCGTT-T
65 AGTATTT-G-GCCGTTCG
* * * * * * *
42544 AAATAAAAATGACACTAAAGAACGT-GTATTTAGCGGCGTTTGTGCTTAAAACACCACTAAAGTA
1 ATATACAAATGCCACTAAAGTA--TAGTATTTAGCGGCGTTTAT-ATAAAAACACCACTAAAGTA
* * * *
42608 CGAGTCTTTAGTGACATTTG
63 CGAGTATTT-G-GCCGTTCG
* * * * ** *
42628 -TACAAAAACGCCACTAAAGTATAGTATTTAGCAGCGTTTATATAAAAATGCCACTAACGTACGA
1 ATATACAAATGCCACTAAAGTATAGTATTTAGCGGCGTTTATATAAAAACACCACTAAAGTACGA
42692 GTATTT
66 GTATTT
42698 ACCGACGTTT
Statistics
Matches: 425, Mismatches: 103, Indels: 63
0.72 0.17 0.11
Matches are distributed among these distances:
77 2 0.00
78 66 0.16
79 2 0.00
80 9 0.02
81 115 0.27
82 109 0.26
83 112 0.26
84 7 0.02
85 3 0.01
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (80 bp):
ATATACAAATGCCACTAAAGTATAGTATTTAGCGGCGTTTATATAAAAACACCACTAAAGTACGA
GTATTTGGCCGTTCG
Found at i:42586 original size:287 final size:283
Alignment explanation
Indices: 42145--42698 Score: 648
Period size: 287 Copynumber: 1.9 Consensus size: 283
42135 GTTTGTATAC
* * *
42145 AAACGCCACTAAAGTATAGTATTTAGCGGCGTTTATATAAAAACACCACTAAAGTACGAGTCTTT
1 AAACACCACTAAAGTATAGTATTCAGCAGCGTTTATATAAAAACACCACTAAAGTACGAGTCTTT
* ** * * *
42210 GGCGTCGATATACAAATGCCACTAAAGTATAGTATTTAGCGACGTGTATATAAAAACACCACTAA
66 GGAGTCGATATACAAACACCACTAAAGTACAATATTTAGCGACGTGTAAATAAAAACACCACTAA
* * *** * **
42275 AGTATGAGTATTCAGCGACGTTTGTACTTAAAATGTCACTAAAGTACGTGTCTTT-GTCAGTTTT
131 AGAACGAGTATTCAGCGACGTTTGTACTTAAAACACCACTAAAGTACGAGTCTTTAGTCA-CATT
* * * * * *
42339 TGTATACAAGCGCCACTAAAGTATAATATTTAGCTGTGTTTATATAAAAA-CCTCACTAAAGTAT
195 TGTACAAAAACGCCACTAAAGTATAATATTTAGCAGCGTTTATATAAAAATCC-CACTAAAGTAC
42403 GAGTATTTAACGGCGTGTGTGCTTA
259 GAGTATTTAACGGCGTGTGTGCTTA
* * * * *
42428 AAACACCACTAAAGTATGAGTCTTCAGCAGTGTTTGTATAAAAACACTACTAAAGTATGAGTCTT
1 AAACACCACTAAAGTAT-AGTATTCAGCAGCGTTTATATAAAAACACCACTAAAGTACGAGTCTT
* * * *
42493 TAGCGAAGTTTG-TATACAAACACCACTAAAGTACAATATTTAGCGGCGTTTAAATAAAAATGA-
65 T-G-G-AG-TCGATATACAAACACCACTAAAGTACAATATTTAGCGACGTGTAAATAAAAA-CAC
* * * * *
42556 CACTAAAGAACGTGTATTTAGCGGCGTTTGTGCTTAAAACACCACTAAAGTACGAGTCTTTAGTG
125 CACTAAAGAACGAGTATTCAGCGACGTTTGTACTTAAAACACCACTAAAGTACGAGTCTTTAGTC
* * *
42621 ACATTTGTACAAAAACGCCACTAAAGTATAGTATTTAGCAGCGTTTATATAAAAATGCCACTAAC
190 ACATTTGTACAAAAACGCCACTAAAGTATAATATTTAGCAGCGTTTATATAAAAATCCCACTAAA
42686 GTACGAGTATTTA
255 GTACGAGTATTTA
42699 CCGACGTTTG
Statistics
Matches: 223, Mismatches: 40, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
283 16 0.07
284 41 0.18
285 1 0.00
286 1 0.00
287 157 0.70
288 7 0.03
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.30
Consensus pattern (283 bp):
AAACACCACTAAAGTATAGTATTCAGCAGCGTTTATATAAAAACACCACTAAAGTACGAGTCTTT
GGAGTCGATATACAAACACCACTAAAGTACAATATTTAGCGACGTGTAAATAAAAACACCACTAA
AGAACGAGTATTCAGCGACGTTTGTACTTAAAACACCACTAAAGTACGAGTCTTTAGTCACATTT
GTACAAAAACGCCACTAAAGTATAATATTTAGCAGCGTTTATATAAAAATCCCACTAAAGTACGA
GTATTTAACGGCGTGTGTGCTTA
Found at i:42646 original size:164 final size:162
Alignment explanation
Indices: 42017--42659 Score: 626
Period size: 164 Copynumber: 4.0 Consensus size: 162
42007 GTACGAGTCT
* *
42017 TATACAAACACCACTAAAGTACAATATTTATCGGTGTTTATATAAAAATGCCACTAAAGTACGAG
1 TATACAAACACCACTAAAGTACAATATTTAGCGGCGTTTATATAAAAATGCCACTAAAGTACGAG
* * * * *
42082 TATTTAGCGGCGTTTGTGCTTAAAACACCATTAAAGTACGAGTATT-TGGCACCGTTTGTATACA
66 TATTTAGCGGCGTGTGTGCTTAAAACACCACTAAAGTACGAGTATTCAGG-ACCGTTTGTACAAA
* *
42146 AACGCCACTAAAGTATAGTATTTAGCGGCGTTTA
130 AACGCCACTAAAGTATAGTATTTAGC-GAGTTTG
* * * ** * *
42180 TATAAAAACACCACTAAAGTACGAGTCTTT---GGCGTCGATATACAAATGCCACTAAAGTA-TA
1 TATACAAACACCACTAAAGTAC-AATATTTAGCGGCGTTTATATAAAAATGCCACTAAAGTACGA
* * * * * *
42241 GTATTTAGCGACGTGTAT-ATAAAAACACCACTAAAGTATGAGTATTCAGCGA-CGTTTGTACTT
65 GTATTTAGCGGCGTGTGTGCTTAAAACACCACTAAAGTACGAGTATTCAG-GACCGTTTGTAC-A
* * *
42304 AAAATGTCACTAAAGTACGT-GTCTTT-GTC-AGTTTTTG
128 AAAACGCCACTAAAGTA--TAGTATTTAG-CGAG--TTTG
* * * * * * *
42341 TATACAAGCGCCACTAAAGTATAATATTTAGCTGTGTTTATATAAAAA-CCTCACTAAAGTATGA
1 TATACAAACACCACTAAAGTACAATATTTAGCGGCGTTTATATAAAAATGC-CACTAAAGTACGA
* * * * ** *
42405 GTATTTAACGGCGTGTGTGCTTAAAACACCACTAAAGTATGAGTCTTCAGCAGTGTTTGTATAAA
65 GTATTTAGCGGCGTGTGTGCTTAAAACACCACTAAAGTACGAGTATTCAGGACCGTTTGTACAAA
* * *
42470 AACACTACTAAAGTATGAGTCTTTAGCGAAGTTTG
130 AACGCCACTAAAGTAT-AGTATTTAGCG-AGTTTG
* * * *
42505 TATACAAACACCACTAAAGTACAATATTTAGCGGCGTTTAAATAAAAATGACACTAAAGAACGTG
1 TATACAAACACCACTAAAGTACAATATTTAGCGGCGTTTATATAAAAATGCCACTAAAGTACGAG
* * * *
42570 TATTTAGCGGCGTTTGTGCTTAAAACACCACTAAAGTACGAGTCTTTAGTGA-CATTTGTACAAA
66 TATTTAGCGGCGTGTGTGCTTAAAACACCACTAAAGTACGAGTATTCAG-GACCGTTTGTACAAA
42634 AACGCCACTAAAGTATAGTATTTAGC
130 AACGCCACTAAAGTATAGTATTTAGC
42660 AGCGTTTATA
Statistics
Matches: 384, Mismatches: 73, Indels: 46
0.76 0.15 0.09
Matches are distributed among these distances:
159 33 0.09
160 38 0.10
161 53 0.14
162 3 0.01
163 51 0.13
164 167 0.43
165 37 0.10
166 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (162 bp):
TATACAAACACCACTAAAGTACAATATTTAGCGGCGTTTATATAAAAATGCCACTAAAGTACGAG
TATTTAGCGGCGTGTGTGCTTAAAACACCACTAAAGTACGAGTATTCAGGACCGTTTGTACAAAA
ACGCCACTAAAGTATAGTATTTAGCGAGTTTG
Found at i:42707 original size:123 final size:122
Alignment explanation
Indices: 42017--42709 Score: 548
Period size: 123 Copynumber: 5.7 Consensus size: 122
42007 GTACGAGTCT
* * * * *
42017 TATACAAACACCACTAAAGTACAATATTTATCGGTGTTTATATAAAAATGCCACTAAAGTACGAG
1 TATAAAAACACCACTAAAGTATAGTATTTAGCGGCGTTTATATAAAAATGCCACTAAAGTACGAG
* * *
42082 TATTTAGCGGCGTTTGTGCTTAAAACACCATTAAAGTACGAGTATTTGGC-ACCGTTTG
66 TATTTAGCGACGTTTGTGCTTAAAACACCACTAAAGTA-GAGTATTTAGCGA-CGTTTG
* * **
42140 TATACAAACGCCACTAAAGTATAGTATTTAGCGGCGTTTATATAAAAACACCACTAAAGTACGAG
1 TATAAAAACACCACTAAAGTATAGTATTTAGCGGCGTTTATATAAAAATGCCACTAAAGTACGAG
* * * * * * ** * * *
42205 TCTTTGGCGTCG-ATATAC---AAATGCCACTAAAGTATAGTATTTAGCGACGTGTA
66 TATTTAGCGACGTTTGTGCTTAAAACACCACTAAAGTAGAGTATTTAGCGACGTTTG
* * * * *
42258 TATAAAAACACCACTAAAGTATGAGTATTCAGCGACGTTTGTACTTAAAATGTCACTAAAGTACG
1 TATAAAAACACCACTAAAGTAT-AGTATTTAGCGGCGTTTATA-TAAAAATGCCACTAAAGTACG
* * * * * * * * *
42323 TGTCTTT-GTC-A-GTTTTTG-TATACAAGCGCCACTAAAGTATAATATTTAGCTG-TGTTTA
64 AGTATTTAG-CGACGTTTGTGCT-TA-AAACACCACTAAAGTAGAGTATTTAGC-GACGTTTG
* * * * * ** *
42381 TATAAAAAC-CTCACTAAAGTATGAGTATTTAACGGCGTGTGTGCTTAAAACACCACTAAAGTAT
1 TATAAAAACAC-CACTAAAGTAT-AGTATTTAGCGGCGTTTAT-ATAAAAATGCCACTAAAGTAC
* * * * * * * *
42445 GAGTCTTCAGC-AGTGTTTGT-ATAAAAACACTACTAAAGTATGAGTCTTTAGCGAAGTTTG
63 GAGTATTTAGCGA-CGTTTGTGCTTAAAACACCACTAAAGTA-GAGTATTTAGCGACGTTTG
* * * * * * *
42505 TATACAAACACCACTAAAGTACAATATTTAGCGGCGTTTAAATAAAAATGACACTAAAGAACGTG
1 TATAAAAACACCACTAAAGTATAGTATTTAGCGGCGTTTATATAAAAATGCCACTAAAGTACGAG
* * * *
42570 TATTTAGCGGCGTTTGTGCTTAAAACACCACTAAAGTACGAGTCTTTAGTGACATTTG
66 TATTTAGCGACGTTTGTGCTTAAAACACCACTAAAGTA-GAGTATTTAGCGACGTTTG
* * * *
42628 TACAAAAACGCCACTAAAGTATAGTATTTAGCAGCGTTTATATAAAAATGCCACTAACGTACGAG
1 TATAAAAACACCACTAAAGTATAGTATTTAGCGGCGTTTATATAAAAATGCCACTAAAGTACGAG
*
42693 TATTTACCGACGTTTGT
66 TATTTAGCGACGTTTGT
42710 TCAAAAAACG
Statistics
Matches: 449, Mismatches: 99, Indels: 44
0.76 0.17 0.07
Matches are distributed among these distances:
118 34 0.08
119 34 0.08
120 24 0.05
122 32 0.07
123 285 0.63
124 33 0.07
125 7 0.02
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (122 bp):
TATAAAAACACCACTAAAGTATAGTATTTAGCGGCGTTTATATAAAAATGCCACTAAAGTACGAG
TATTTAGCGACGTTTGTGCTTAAAACACCACTAAAGTAGAGTATTTAGCGACGTTTG
Found at i:43677 original size:7 final size:7
Alignment explanation
Indices: 43665--43690 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
43655 TCAAAGAAGG
43665 AAATATT
1 AAATATT
43672 AAATATT
1 AAATATT
43679 AAATATT
1 AAATATT
43686 AAATA
1 AAATA
43691 ATGTTATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
AAATATT
Found at i:43841 original size:17 final size:16
Alignment explanation
Indices: 43821--43856 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
43811 AAGAAGTGAG
43821 AAAATAAAAAAAATTAA
1 AAAATAAAAAAAA-TAA
*
43838 AAAATAAAACAAATAA
1 AAAATAAAAAAAATAA
43854 AAA
1 AAA
43857 TTTGTAGGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (16 bp):
AAAATAAAAAAAATAA
Found at i:43967 original size:5 final size:5
Alignment explanation
Indices: 43957--43983 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
43947 GAAAATGTAT
43957 AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AA
43984 GGGAAATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:44066 original size:18 final size:18
Alignment explanation
Indices: 44045--44087 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
44035 GTTGTTTTTA
*
44045 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAAGAATT
*
44063 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
44081 AAATAAA
1 AAATAAA
44088 TAATCTAACG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:65038 original size:62 final size:61
Alignment explanation
Indices: 64962--65090 Score: 154
Period size: 62 Copynumber: 2.1 Consensus size: 61
64952 AAAATAAAAG
* *
64962 AAATATCAAATAAAAA-TTAAAATTAAAAAAATAAATCAAA-GAAGGAAATATTAAATTTTAAA
1 AAATATCAAATAAAAAGTTAAAA-GAAAAAAATAAAT-AAATGAA-GAAATATTAAATTTCAAA
* * * *
65024 AAATATTATATAAAAATGTTAAAAGAAAAAATTAAATAAATGAAGAAATATTAAATTTCAGA
1 AAATATCAAATAAAAA-GTTAAAAGAAAAAAATAAATAAATGAAGAAATATTAAATTTCAAA
65086 AAATA
1 AAATA
65091 AAAATAATAA
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
62 38 0.66
63 14 0.24
64 6 0.10
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.27
Consensus pattern (61 bp):
AAATATCAAATAAAAAGTTAAAAGAAAAAAATAAATAAATGAAGAAATATTAAATTTCAAA
Found at i:65120 original size:17 final size:14
Alignment explanation
Indices: 65085--65180 Score: 65
Period size: 15 Copynumber: 6.6 Consensus size: 14
65075 TAAATTTCAG
65085 AAAATAAAAATAAT
1 AAAATAAAAATAAT
65099 AAAATATAAAATAATTT
1 AAAATA-AAAATAA--T
65116 AAAATAGAAAAT-A-
1 AAAATA-AAAATAAT
*
65129 AAAATAAAATAAAAT
1 AAAATAAAA-ATAAT
***
65144 AAAA-AAAGAAGTGGG
1 AAAATAAA-AA-TAAT
65159 AAAATAAAAATAA-
1 AAAATAAAAATAAT
65172 AAAATAAAA
1 AAAATAAAA
65181 GAAAAGAAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 19
0.71 0.09 0.21
Matches are distributed among these distances:
12 3 0.05
13 16 0.25
14 12 0.18
15 18 0.28
16 4 0.06
17 12 0.18
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (14 bp):
AAAATAAAAATAAT
Found at i:65185 original size:17 final size:17
Alignment explanation
Indices: 65165--65197 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
65155 TGGGAAAATA
*
65165 AAAATAAAAAATAAAAG
1 AAAAGAAAAAATAAAAG
65182 AAAAGAAAAAATAAAA
1 AAAAGAAAAAATAAAA
65198 ATTTGGGGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.06, T:0.09
Consensus pattern (17 bp):
AAAAGAAAAAATAAAAG
Found at i:65193 original size:30 final size:31
Alignment explanation
Indices: 65091--65199 Score: 89
Period size: 30 Copynumber: 3.4 Consensus size: 31
65081 TCAGAAAATA
65091 AAAATAATAAAATATAAAATAATTTAAAATAGAAAA-
1 AAAA-AATAAAA-ATAAAATAA---AAAA-AGAAAAG
* **
65127 TAAAAAT-AAAATAAAATAAAAAAAGAAGTG
1 AAAAAATAAAAATAAAATAAAAAAAGAAAAG
** *
65157 GGAAAATAAAAATAAAA-AATAAAAGAAAAG
1 AAAAAATAAAAATAAAATAAAAAAAGAAAAG
65187 AAAAAATAAAAAT
1 AAAAAATAAAAAT
65200 TTGGGGGGTA
Statistics
Matches: 61, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
29 4 0.07
30 30 0.49
31 9 0.15
33 9 0.15
34 3 0.05
35 3 0.05
36 3 0.05
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.17
Consensus pattern (31 bp):
AAAAAATAAAAATAAAATAAAAAAAGAAAAG
Found at i:66250 original size:24 final size:21
Alignment explanation
Indices: 66208--66249 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
66198 TTTTATATTT
66208 TTATGATAACACATCATCATC
1 TTATGATAACACATCATCATC
*
66229 TTATGATGACACATCATCATC
1 TTATGATAACACATCATCATC
66250 ACCATTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.33
Consensus pattern (21 bp):
TTATGATAACACATCATCATC
Found at i:67070 original size:16 final size:17
Alignment explanation
Indices: 67049--67084 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
67039 AAATTTTAAA
67049 TAATTAACTAATTT-TT
1 TAATTAACTAATTTATT
*
67065 TAATTAAGTAATTTATT
1 TAATTAACTAATTTATT
67082 TAA
1 TAA
67085 ATAAAATCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (17 bp):
TAATTAACTAATTTATT
Found at i:68142 original size:25 final size:29
Alignment explanation
Indices: 68114--68167 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
68104 CATGACAATT
68114 AATAAAAGAT-A-AT-A-TAATTTTTATA
1 AATAAAAGATGATATCATTAATTTTTATA
68139 AATAAAAGATGATATCATTAATTTTTATA
1 AATAAAAGATGATATCATTAATTTTTATA
68168 GATATGATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 10 0.40
26 1 0.04
27 2 0.08
28 1 0.04
29 11 0.44
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.41
Consensus pattern (29 bp):
AATAAAAGATGATATCATTAATTTTTATA
Done.