Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006988.1 Hibiscus syriacus cultivar Beakdansim tig00018025_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: 119611
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:2219 original size:43 final size:43
Alignment explanation
Indices: 1997--2271 Score: 157
Period size: 43 Copynumber: 6.3 Consensus size: 43
1987 CCATATTTCA
* * * **
1997 CTGATCCAACTTCTTATGTGAAGGATCAATTAAAGATTGTT-A--
1 CTGATCCAACTCCTTCTGTGAAGAATCAAACAAA-A-TGTTGATG
* * *
2039 CTGATCCAACTCCTACTATGAAGAATCAAACAAAATGTCGATG
1 CTGATCCAACTCCTTCTGTGAAGAATCAAACAAAATGTTGATG
* * * * * * *
2082 TTGATCTACCTCATTCTGTGATATAATCGAGCAAAATAAAGTT-ATG
1 CTGATCCAACTCCTTCTGTGA-AGAATCAAACAAAAT---GTTGATG
* * ** **
2128 CTAATTCAACTCCTTCTGTGAAGAATCAAACGGAATG-ACATTG
1 CTGATCCAACTCCTTCTGTGAAGAATCAAACAAAATGTTGA-TG
* * *
2171 TTGATCCAATTCCTTTTGTGAAGAATCAAACAAAATGTTGATG
1 CTGATCCAACTCCTTCTGTGAAGAATCAAACAAAATGTTGATG
* * * ** *
2214 CTGATCTACCTCCTTCTGTGATAGAATC-AGCAAAATAATGTTG
1 CTGATCCAACTCCTTCTGTGA-AGAATCAAACAAAATGTTGATG
*
2257 CTGGTCCAACTCCTT
1 CTGATCCAACTCCTT
2272 TTGCGAATGA
Statistics
Matches: 171, Mismatches: 51, Indels: 21
0.70 0.21 0.09
Matches are distributed among these distances:
40 3 0.02
41 2 0.01
42 29 0.17
43 88 0.51
44 19 0.11
45 10 0.06
46 18 0.11
47 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (43 bp):
CTGATCCAACTCCTTCTGTGAAGAATCAAACAAAATGTTGATG
Found at i:2840 original size:15 final size:15
Alignment explanation
Indices: 2822--2906 Score: 58
Period size: 15 Copynumber: 6.1 Consensus size: 15
2812 TTTGAATTCA
2822 TTTTCTTTTATTTTT
1 TTTTCTTTTATTTTT
*
2837 TTTTC-TTCA--TTT
1 TTTTCTTTTATTTTT
2849 TTTTCTTTT-TCTTTT
1 TTTTCTTTTAT-TTTT
* * *
2864 CTTTC--GT-TTTCT
1 TTTTCTTTTATTTTT
*
2876 TTTTCTTTTATTCTT
1 TTTTCTTTTATTTTT
*
2891 TTTTCTTTTCTTTTT
1 TTTTCTTTTATTTTT
2906 T
1 T
2907 CATTAGCAAC
Statistics
Matches: 52, Mismatches: 11, Indels: 14
0.68 0.14 0.18
Matches are distributed among these distances:
12 15 0.29
13 4 0.08
14 4 0.08
15 29 0.56
ACGTcount: A:0.04, C:0.14, G:0.01, T:0.81
Consensus pattern (15 bp):
TTTTCTTTTATTTTT
Found at i:2852 original size:27 final size:26
Alignment explanation
Indices: 2822--2905 Score: 100
Period size: 27 Copynumber: 3.2 Consensus size: 26
2812 TTTGAATTCA
2822 TTTTCTTTTATTTTTTTTTCTTCATT-T
1 TTTTCTTTTATTTTTTTTTCTT--TTCT
*
2849 TTTTCTTTT-TCTTTTCTTTCGTTTTCT
1 TTTTCTTTTAT-TTTTTTTTC-TTTTCT
*
2876 TTTTCTTTTATTCTTTTTTCTTTTCT
1 TTTTCTTTTATTTTTTTTTCTTTTCT
2902 TTTT
1 TTTT
2906 TCATTAGCAA
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
26 13 0.26
27 34 0.68
28 3 0.06
ACGTcount: A:0.04, C:0.14, G:0.01, T:0.81
Consensus pattern (26 bp):
TTTTCTTTTATTTTTTTTTCTTTTCT
Found at i:2857 original size:21 final size:20
Alignment explanation
Indices: 2822--2910 Score: 71
Period size: 21 Copynumber: 4.4 Consensus size: 20
2812 TTTGAATTCA
2822 TTTTC-TTTTATTT-TTTTT-
1 TTTTCATTTT-TTTCTTTTTC
*
2840 TCTTCATTTTTTTCTTTTTC
1 TTTTCATTTTTTTCTTTTTC
2860 TTTTC-TTTCGTTTTCTTTTTC
1 TTTTCATTT--TTTTCTTTTTC
*
2881 TTTT-ATTCTTTTTTCTTTTCTT
1 TTTTCA-T-TTTTTTCTTTT-TC
2903 TTTTCATT
1 TTTTCATT
2911 AGCAACAATT
Statistics
Matches: 58, Mismatches: 3, Indels: 17
0.74 0.04 0.22
Matches are distributed among these distances:
18 7 0.12
19 12 0.21
20 4 0.07
21 25 0.43
22 7 0.12
23 3 0.05
ACGTcount: A:0.04, C:0.15, G:0.01, T:0.80
Consensus pattern (20 bp):
TTTTCATTTTTTTCTTTTTC
Found at i:2859 original size:6 final size:6
Alignment explanation
Indices: 2848--2905 Score: 52
Period size: 6 Copynumber: 9.8 Consensus size: 6
2838 TTTCTTCATT
*
2848 TTTTTC TTTTTC -TTTTC --TTTC GTTTTC TTTTTC TTTTATTC TTTTT-
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC -TTT-TTC TTTTTC
2894 TCTTTTC TTTTT
1 T-TTTTC TTTTT
2906 TCATTAGCAA
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
4 4 0.09
5 6 0.13
6 25 0.56
7 7 0.16
8 3 0.07
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.81
Consensus pattern (6 bp):
TTTTTC
Found at i:3598 original size:14 final size:13
Alignment explanation
Indices: 3589--3663 Score: 62
Period size: 14 Copynumber: 5.4 Consensus size: 13
3579 TATTTTGTTC
*
3589 TTTTTCTTTTTTT
1 TTTTTCTTTTTCT
3602 TTCTTTC-TTTTCAT
1 TT-TTTCTTTTTC-T
*
3616 TTTTTCCTTTCTTAT
1 TTTTT-CTTT-TTCT
3631 TTTTTCTTTTTCT
1 TTTTTCTTTTTCT
*
3644 CTTTTCTCTTTTTAT
1 -TTTT-TCTTTTTCT
3659 TTTTT
1 TTTTT
3664 TTCAAGCAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
13 13 0.25
14 20 0.39
15 16 0.31
16 2 0.04
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTCTTTTTCT
Found at i:3612 original size:28 final size:26
Alignment explanation
Indices: 3571--3664 Score: 73
Period size: 28 Copynumber: 3.3 Consensus size: 26
3561 CCCCTTATTA
* *
3571 TTTTATTTTATTTTGTTCTTTTTCTTT
1 TTTTTTTTTCTTTT-TTCTTTTTCTTT
*
3598 TTTTTTCTTTCTTTTCATT-TTTTCCTTT
1 TTTTTT-TTTCTTTT--TTCTTTTTCTTT
*
3626 CTTATTTTTTCTTTTTCTCTTTTCTCTTT
1 -TTTTTTTTTCTTTTT-TCTTTT-TCTTT
3655 TTATTTTTTT
1 TT-TTTTTTT
3665 TCAAGCAAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
26 1 0.02
27 6 0.11
28 29 0.55
29 17 0.32
ACGTcount: A:0.05, C:0.14, G:0.01, T:0.80
Consensus pattern (26 bp):
TTTTTTTTTCTTTTTTCTTTTTCTTT
Found at i:3620 original size:22 final size:22
Alignment explanation
Indices: 3595--3663 Score: 65
Period size: 23 Copynumber: 3.2 Consensus size: 22
3585 GTTCTTTTTC
3595 TTTTT-TTTTCTTTCTTTTCAT
1 TTTTTCTTTTCTTTCTTTTCAT
* *
3616 TTTTTCCTTTCTTATTTTTTC-T
1 TTTTTCTTTTCTT-TCTTTTCAT
*
3638 TTTTCTCTTTTC--TCTTTTTAT
1 TTTT-TCTTTTCTTTCTTTTCAT
3659 TTTTT
1 TTTTT
3664 TTCAAGCAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
20 6 0.15
21 10 0.26
22 11 0.28
23 12 0.31
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (22 bp):
TTTTTCTTTTCTTTCTTTTCAT
Found at i:7139 original size:16 final size:16
Alignment explanation
Indices: 7118--7152 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
7108 CAAATGAAAT
7118 AAAATATAA-AAATGTA
1 AAAATA-AAGAAATGTA
7134 AAAATAAAGAAATGTA
1 AAAATAAAGAAATGTA
7150 AAA
1 AAA
7153 TGTAAGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 2 0.11
16 16 0.89
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.20
Consensus pattern (16 bp):
AAAATAAAGAAATGTA
Found at i:11933 original size:16 final size:16
Alignment explanation
Indices: 11912--11947 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
11902 TCTTTCCACG
11912 ACCTGATATTGGTACA
1 ACCTGATATTGGTACA
*
11928 ACCTGATATTGGTACG
1 ACCTGATATTGGTACA
11944 ACCT
1 ACCT
11948 AGTTGTGCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (16 bp):
ACCTGATATTGGTACA
Found at i:12038 original size:19 final size:19
Alignment explanation
Indices: 12014--12060 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
12004 AAGCAATTTC
*
12014 TCATCTTGCAAAAATTTGA
1 TCATCTTGCAAAAATTCGA
12033 TCATCTTGCAAAAATTCGA
1 TCATCTTGCAAAAATTCGA
12052 TCATCTTGC
1 TCATCTTGC
12061 GACAGTACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (19 bp):
TCATCTTGCAAAAATTCGA
Found at i:12725 original size:16 final size:18
Alignment explanation
Indices: 12698--12741 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
12688 GTTTTAATGA
12698 ATGAATATGAATA-TAAAC
1 ATGAA-ATGAATATTAAAC
*
12716 AT-AAATGAATATTAACC
1 ATGAAATGAATATTAAAC
12733 ATGAAATGA
1 ATGAAATGA
12742 TAAAAATGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 7 0.30
17 8 0.35
18 8 0.35
ACGTcount: A:0.55, C:0.07, G:0.11, T:0.27
Consensus pattern (18 bp):
ATGAAATGAATATTAAAC
Found at i:18515 original size:24 final size:24
Alignment explanation
Indices: 18459--18508 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
18449 TTATTTACTT
* * *
18459 TAATTTAATATATAATATTATTAA
1 TAATTAAATATATAATAATATAAA
18483 TAATTAAATATATAATAATAGTAAA
1 TAATTAAATATATAATAATA-TAAA
18508 T
1 T
18509 CATAAATTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
TAATTAAATATATAATAATATAAA
Found at i:20709 original size:45 final size:46
Alignment explanation
Indices: 20641--20743 Score: 115
Period size: 50 Copynumber: 2.2 Consensus size: 46
20631 CTAATGAATA
*
20641 AAAATAATAATAAACTAAAAATG-TT-T-CAATTCTAATTCCTAAT
1 AAAATAATAATAAACAAAAAATGTTTATACAATTCTAATTCCTAAT
*
20684 -AAATAATAATAAACCAAGAATAATGTTTTAATACAATTTTAATTCCTAAT
1 AAAATAATAATAAA-CAA-AA-AATG-TTT-ATACAATTCTAATTCCTAAT
20734 AAAATAATAA
1 AAAATAATAA
20744 ATCTAATTCT
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
42 13 0.27
43 2 0.04
44 2 0.04
45 4 0.08
47 2 0.04
49 1 0.02
50 16 0.33
51 9 0.18
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.34
Consensus pattern (46 bp):
AAAATAATAATAAACAAAAAATGTTTATACAATTCTAATTCCTAAT
Found at i:23237 original size:14 final size:14
Alignment explanation
Indices: 23202--23244 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
23192 AGAAAATATA
23202 TTATTTCAT-TATTT
1 TTATTT-ATATATTT
23216 TATATTTATATATTT
1 T-TATTTATATATTT
*
23231 TTATTTATAAATTT
1 TTATTTATATATTT
23245 AAATTCTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 15 0.58
15 11 0.42
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATTTATATATTT
Found at i:24046 original size:6 final size:6
Alignment explanation
Indices: 24035--24668 Score: 1261
Period size: 6 Copynumber: 105.8 Consensus size: 6
24025 GTTCTTTAAT
24035 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
24083 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
24131 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
24179 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
24227 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
24275 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
24323 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
24371 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
24419 AAATTA AAATTA AAATTA AAATTA AAATTA AAATT- AAATTA AAATTA
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
24466 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
24514 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
24562 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
24610 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
24658 AAATTA AAATT
1 AAATTA AAATT
24669 TTAAGATTTC
Statistics
Matches: 627, Mismatches: 0, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
5 5 0.01
6 622 0.99
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
AAATTA
Found at i:25246 original size:27 final size:26
Alignment explanation
Indices: 25216--25266 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
25206 AAAATTTTAC
25216 ATTAAAAATTAAAAGATATATAAATAA
1 ATTAAAAATTAAAA-ATATATAAATAA
** *
25243 ATTATCAATTAAAAATATCTAAAT
1 ATTAAAAATTAAAAATATATAAAT
25267 TATATAATGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 9 0.43
27 12 0.57
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (26 bp):
ATTAAAAATTAAAAATATATAAATAA
Found at i:29526 original size:2 final size:2
Alignment explanation
Indices: 29519--29548 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
29509 GAACTGACAC
29519 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
29549 TTCAGATGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:30982 original size:43 final size:43
Alignment explanation
Indices: 30931--31022 Score: 184
Period size: 43 Copynumber: 2.1 Consensus size: 43
30921 GAATTAACTT
30931 TCATTATGTGTAACTCGTATCTAAATATACTCTAATTTAAGTC
1 TCATTATGTGTAACTCGTATCTAAATATACTCTAATTTAAGTC
30974 TCATTATGTGTAACTCGTATCTAAATATACTCTAATTTAAGTC
1 TCATTATGTGTAACTCGTATCTAAATATACTCTAATTTAAGTC
31017 TCATTA
1 TCATTA
31023 ATCTGAATGC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (43 bp):
TCATTATGTGTAACTCGTATCTAAATATACTCTAATTTAAGTC
Found at i:36438 original size:21 final size:21
Alignment explanation
Indices: 36414--36454 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
36404 TTAAAAATAG
36414 TAAAAAATTATAAA-ATTATTT
1 TAAAAAATT-TAAATATTATTT
*
36435 TAAAATATTTAAATATTATT
1 TAAAAAATTTAAATATTATT
36455 ATCTGATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TAAAAAATTTAAATATTATTT
Found at i:41725 original size:24 final size:24
Alignment explanation
Indices: 41697--41807 Score: 114
Period size: 24 Copynumber: 4.6 Consensus size: 24
41687 GAATGTTTTA
* *
41697 TCTGATTTCCGATTTGAATTCTGT
1 TCTGATTTCTGATATGAATTCTGT
* * * *
41721 TCTGATTTTTTATCTGAATTATGT
1 TCTGATTTCTGATATGAATTCTGT
*
41745 TCTGATTTCTGATATGGATTCTGT
1 TCTGATTTCTGATATGAATTCTGT
* * * *
41769 TCTAATATATGATATTAATTCTGT
1 TCTGATTTCTGATATGAATTCTGT
*
41793 TTTGATTTCTGATAT
1 TCTGATTTCTGATAT
41808 CTCCGTTTAT
Statistics
Matches: 68, Mismatches: 19, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 68 1.00
ACGTcount: A:0.22, C:0.11, G:0.14, T:0.53
Consensus pattern (24 bp):
TCTGATTTCTGATATGAATTCTGT
Found at i:43110 original size:20 final size:20
Alignment explanation
Indices: 43067--43110 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
43057 TGGATCGAAC
*
43067 TTAAATGTTATATTTTTTAT
1 TTAAATGTTATATTTTTTAA
43087 TTAAAT-TTATATTTTTGTAA
1 TTAAATGTTATATTTTT-TAA
43107 TTAA
1 TTAA
43111 GATAACCAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (20 bp):
TTAAATGTTATATTTTTTAA
Found at i:60772 original size:133 final size:133
Alignment explanation
Indices: 60534--60796 Score: 508
Period size: 133 Copynumber: 2.0 Consensus size: 133
60524 AAACAAAATA
* *
60534 GGAAGAGGAGTGTTTGATTACCGTGAGTCGGAGTCGTTAGTCAAGACTAGGGCCGTCGGGGTCGC
1 GGAAGAGGAGTGTTTGATTACAGTGAGTCGGAGTCGTTAGTCAAGACTAGGGCCATCGGGGTCGC
60599 GTTCTTAGGCCAACCAAGTGCTTGCATGTAGGTTTCAGAGTCGATCTCTGGGTTTTAGGAGGTAA
66 GTTCTTAGGCCAACCAAGTGCTTGCATGTAGGTTTCAGAGTCGATCTCTGGGTTTTAGGAGGTAA
60664 AAC
131 AAC
60667 GGAAGAGGAGTGTTTGATTACAGTGAGTCGGAGTCGTTAGTCAAGACTAGGGCCATCGGGGTCGC
1 GGAAGAGGAGTGTTTGATTACAGTGAGTCGGAGTCGTTAGTCAAGACTAGGGCCATCGGGGTCGC
60732 GTTCTTAGGCCAACCAAGTGCTTGCATGTAGGTTTCAGAGTCGATCTCTGGGTTTTAGGAGGTAA
66 GTTCTTAGGCCAACCAAGTGCTTGCATGTAGGTTTCAGAGTCGATCTCTGGGTTTTAGGAGGTAA
60797 CACAGAGGGA
Statistics
Matches: 128, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
133 128 1.00
ACGTcount: A:0.22, C:0.17, G:0.34, T:0.27
Consensus pattern (133 bp):
GGAAGAGGAGTGTTTGATTACAGTGAGTCGGAGTCGTTAGTCAAGACTAGGGCCATCGGGGTCGC
GTTCTTAGGCCAACCAAGTGCTTGCATGTAGGTTTCAGAGTCGATCTCTGGGTTTTAGGAGGTAA
AAC
Found at i:63520 original size:6 final size:6
Alignment explanation
Indices: 63509--63544 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
63499 TAACACCTCA
* *
63509 TGCATT TGCATT TGCATT TGCATC TACATT TGCATT
1 TGCATT TGCATT TGCATT TGCATT TGCATT TGCATT
63545 CTTATTTTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.14, T:0.47
Consensus pattern (6 bp):
TGCATT
Found at i:63561 original size:32 final size:32
Alignment explanation
Indices: 63519--63593 Score: 123
Period size: 32 Copynumber: 2.3 Consensus size: 32
63509 TGCATTTGCA
*
63519 TTTGCATTTGCATCTACATTTGCATTCTTATT
1 TTTGCATTTGCATCTACATTTGCATTCTTAAT
* *
63551 TTTGTATTTGCATCTATATTTGCATTCTTAAT
1 TTTGCATTTGCATCTACATTTGCATTCTTAAT
63583 TTTGCATTTGC
1 TTTGCATTTGC
63594 TTATTAATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.19, C:0.16, G:0.11, T:0.55
Consensus pattern (32 bp):
TTTGCATTTGCATCTACATTTGCATTCTTAAT
Found at i:64187 original size:13 final size:13
Alignment explanation
Indices: 64169--64195 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
64159 AGATAAGAGA
64169 AAAGAGCAGATGT
1 AAAGAGCAGATGT
64182 AAAGAGCAGATGT
1 AAAGAGCAGATGT
64195 A
1 A
64196 CAGGTGGGAT
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:0.48, C:0.07, G:0.30, T:0.15
Consensus pattern (13 bp):
AAAGAGCAGATGT
Found at i:67856 original size:40 final size:39
Alignment explanation
Indices: 67794--67869 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 39
67784 AGATGAACCC
* *
67794 TTCAGCTAGCCCGATAGAGGCAAATTACAATAAAGTTGAT
1 TTCAGCTAGCCAGAAAGAGGCAAATTA-AATAAAGTTGAT
*
67834 TTCAGCTAGCCAGACAAG-GGCAAATTAAATCAAGTT
1 TTCAGCTAGCCAGA-AAGAGGCAAATTAAATAAAGTT
67870 TATCTAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
39 8 0.25
40 22 0.69
41 2 0.06
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (39 bp):
TTCAGCTAGCCAGAAAGAGGCAAATTAAATAAAGTTGAT
Found at i:69816 original size:34 final size:34
Alignment explanation
Indices: 69668--69873 Score: 238
Period size: 35 Copynumber: 5.9 Consensus size: 34
69658 AGCAAAGTCA
* *
69668 ATCTTAAGCCTTCACCA-AAGAGGAGTGAAGTAAACC
1 ATCTTAAGCCTTCA-CAGAAGAGTAGTGAAG--CACC
* *
69704 ATCTTAAGCCTTCATC-GGAGAGTAGTGAAGCAATC
1 ATCTTAAGCCTTCA-CAGAAGAGTAGTGAAGC-ACC
* *
69739 ATCTTAAGCCTTCACAGAAGAATAGTGAAGCAGTC
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCA-CC
*
69774 ATCTTAAGCCTTCATAGAAGAGTAGTGAAGCACC
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCACC
69808 ATCTTAAGCCTTCACA-AAGGAGTAGTGAAGCACC
1 ATCTTAAGCCTTCACAGAA-GAGTAGTGAAGCACC
* * *
69842 ATCTTAAACATTCACCGAAGAGTAGTGAAGCA
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCA
69874 AATCCATCCA
Statistics
Matches: 150, Mismatches: 14, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
33 2 0.01
34 59 0.39
35 63 0.42
36 26 0.17
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.22
Consensus pattern (34 bp):
ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCACC
Found at i:70300 original size:41 final size:42
Alignment explanation
Indices: 70203--70304 Score: 125
Period size: 42 Copynumber: 2.5 Consensus size: 42
70193 TTCACAATTT
* * * * *
70203 ATAAGTCCTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGC
1 ATAAGTCCTTCGGGTCATCAGTAAGCCTTTAGAGCAAGATGC
* * *
70245 TTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG-
1 ATAAGTCCTTCGGGTCATCAGTAAGCCTTTAGAGCAAGATGC
70286 ATAAGTCCTTCGGGTCATC
1 ATAAGTCCTTCGGGTCATC
70305 CATAAGACCT
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
41 17 0.34
42 33 0.66
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (42 bp):
ATAAGTCCTTCGGGTCATCAGTAAGCCTTTAGAGCAAGATGC
Found at i:70462 original size:215 final size:215
Alignment explanation
Indices: 69877--71123 Score: 1915
Period size: 215 Copynumber: 5.8 Consensus size: 215
69867 TGAAGCAAAT
* * **
69877 CCATCCATAAAACCTTAGGGTAGGATGTTTTCA-TTGAA--T--GAA-AAAATGATGATGTTTTA
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAGAATAAAAAAATGATGTTTTA
*
69936 AGAAGATGAAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTCG
66 AGAAGATGAAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCG
*
70001 GGCCATCAGTATGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
131 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
*
70066 AAGATAATAAGTCCTTCGGG
196 AAGATGATAAGTCCTTCGGG
* * **
70086 CCATCCATAAGACCTTCGGGTAAGATGTTTTCACATGAATTTG-GAA-ATGGAAAATGATGTTTT
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAGAATA-AAAAAATGATGTTTT
*
70149 AAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTC
65 AAGAAGATGAAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTC
*
70214 AGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAG
130 GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAG
70279 CAAGATGATAAGTCCTTCGGG
195 CAAGATGATAAGTCCTTCGGG
* * * *
70300 TCATCCATAAGACCTTTGGGTAGGACGTTTTCACATGAATTTG-GAAATAAAAAAATGATGTTTT
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAG-AATAAAAAAATGATGTTTT
* * *
70364 AAGAATATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTT
65 AAGAAGATGAAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTC
* *
70429 GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATTTGTAAGCCTTTAGAG
130 GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAG
* *
70494 TAAGATGATAAGTCCTTTGGG
195 CAAGATGATAAGTCCTTCGGG
* * * *
70515 CCATTCATAAAACCTTTGGGTAGGATGTTTTCATATGAATTTGAGAAT--AAAAATTATGTTTTA
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAGAATAAAAAAATGATGTTTTA
* *
70578 AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACGATTTATAAGTCCTTCG
66 AGAAGATGAAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCG
* * *
70643 GGTCATCAGTTAGTCTTTCGAGCATGATGCTTAAATCCTTCGAGTCATCTGTAAGCCTTTAGAGC
131 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
* *
70708 AAGATGATAAGTCTTTCAGG
196 AAGATGATAAGTCCTTCGGG
70728 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAGAATGAAAAAAAATGATGTTT
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAGAAT--AAAAAAATGATGTTT
*
70793 TAAGAAGATGAAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACGATTTATAAGTCCTT
64 TAAGAAGATGAAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTT
* * *
70858 CGGGCCATCAGTAAGCCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGACTTCAGA
129 CGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGA
*
70923 GCAAGATGATAAGTCCTTCAGG
194 GCAAGATGATAAGTCCTTCGGG
*
70945 CCATCCATAAAACCTTCGGGTAGGATATTTTCACATGAATTTGAGAATGAAAAAAATGATGTTTT
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAGAAT-AAAAAAATGATGTTTT
*
71010 AAGAAGATGAAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACGATTTATAAGTCCTTC
65 AAGAAGATGAAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTC
** ** * * * *
71075 GGGTTATTTGTGAGTCTCTCGAGCAAGATG-ATAAATCCTTCGGGTCATC
130 GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATC
71124 CATAAGACCT
Statistics
Matches: 959, Mismatches: 67, Indels: 18
0.92 0.06 0.02
Matches are distributed among these distances:
209 30 0.03
210 4 0.00
212 1 0.00
213 201 0.21
214 197 0.21
215 218 0.23
216 105 0.11
217 203 0.21
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (215 bp):
CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAGAATAAAAAAATGATGTTTTA
AGAAGATGAAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCG
GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
AAGATGATAAGTCCTTCGGG
Found at i:71282 original size:56 final size:55
Alignment explanation
Indices: 71194--71312 Score: 145
Period size: 56 Copynumber: 2.1 Consensus size: 55
71184 GACTTCTCAG
* * *
71194 AAGAATAGGGAACAAACCCGTTTTCAGAAGATT-TCTTGAGT-TCTATACTCCCTGA
1 AAGAATAGGGAACAAACACGTTTGCAGAAGATTAT-TCGAGTCT-TATACTCCCTGA
*
71249 AAGGAATAGGGAGA-AAACACGTTTGCGGAAGATTATTCGAGTCTTATACTCCCTGA
1 AA-GAATAGGGA-ACAAACACGTTTGCAGAAGATTATTCGAGTCTTATACTCCCTGA
71305 AAGAATAG
1 AAGAATAG
71313 AGAGCAGCGA
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
55 8 0.14
56 45 0.80
57 3 0.05
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (55 bp):
AAGAATAGGGAACAAACACGTTTGCAGAAGATTATTCGAGTCTTATACTCCCTGA
Found at i:71345 original size:55 final size:56
Alignment explanation
Indices: 71237--71345 Score: 141
Period size: 55 Copynumber: 2.0 Consensus size: 56
71227 TCTTGAGTTC
* *
71237 TATACTCCCTGAAAGGAATAGGGAGAAAACACGTTTGCGGAAGATTATTCGAGTCT
1 TATACTCCCTGAAAGGAATAGAGAGAAAACACGTTTGCGGAAGATTATGCGAGTCT
* * * *
71293 TATACTCCCTGAAA-GAATAGAGAG-CAGCGACGTTTGTGGAAGATTGTGCGAGT
1 TATACTCCCTGAAAGGAATAGAGAGAAAAC-ACGTTTGCGGAAGATTATGCGAGT
71346 TCCATATACC
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
54 2 0.04
55 30 0.65
56 14 0.30
ACGTcount: A:0.32, C:0.16, G:0.28, T:0.25
Consensus pattern (56 bp):
TATACTCCCTGAAAGGAATAGAGAGAAAACACGTTTGCGGAAGATTATGCGAGTCT
Found at i:76562 original size:17 final size:16
Alignment explanation
Indices: 76520--76564 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
76510 TATCCGATCT
*
76520 GAAATTTAGGATATCC
1 GAAATTTCGGATATCC
76536 GAAATTTCGGATATCC
1 GAAATTTCGGATATCC
*
76552 GAATTTTTCGGAT
1 GAA-ATTTCGGAT
76565 CGGATACGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 18 0.69
17 8 0.31
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (16 bp):
GAAATTTCGGATATCC
Found at i:77202 original size:133 final size:133
Alignment explanation
Indices: 76964--77229 Score: 487
Period size: 133 Copynumber: 2.0 Consensus size: 133
76954 AAACAAAATA
* *
76964 GGAAGAGGAGTGTTTGATTACCATGAGTTGGAGTCGTTAGTCAAGACTAGGGCCGTCGGGGTCGC
1 GGAAGAGGAGTGTTTGATTACCATGAGTCGGAGTCGTTAGTCAAGACTAGGGCCGTCAGGGTCGC
*
77029 GTCCTTAGGCCAACCAAGTGCTTGCATGTAGGTTTTAGAGTCGATCTCTGGGTTTTAGGAGGTAA
66 GTCCTTAGGCCAACCAAGTGCTTGCATGTAGGTTTCAGAGTCGATCTCTGGGTTTTAGGAGGTAA
77094 AAC
131 AAC
*
77097 GGAAGAGGAGTGTTTGATTACCGTGAGTCGGAGTCGTTAGTCAAGACTAGGGCCGTCAGGGTCGC
1 GGAAGAGGAGTGTTTGATTACCATGAGTCGGAGTCGTTAGTCAAGACTAGGGCCGTCAGGGTCGC
*
77162 GTCCTTAGGCCAACCAAGTGCTTGCATGTAGGTTTCAGAGTCGATCTTTGGGTTTTAGGAGGTAA
66 GTCCTTAGGCCAACCAAGTGCTTGCATGTAGGTTTCAGAGTCGATCTCTGGGTTTTAGGAGGTAA
77227 AAC
131 AAC
77230 AGAGGGATTC
Statistics
Matches: 128, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
133 128 1.00
ACGTcount: A:0.23, C:0.17, G:0.33, T:0.27
Consensus pattern (133 bp):
GGAAGAGGAGTGTTTGATTACCATGAGTCGGAGTCGTTAGTCAAGACTAGGGCCGTCAGGGTCGC
GTCCTTAGGCCAACCAAGTGCTTGCATGTAGGTTTCAGAGTCGATCTCTGGGTTTTAGGAGGTAA
AAC
Found at i:83228 original size:20 final size:20
Alignment explanation
Indices: 83203--83240 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
83193 TGGGTTTGAG
*
83203 TATCGATAATGGATGAACAT
1 TATCGATAATAGATGAACAT
*
83223 TATCGATACTAGATGAAC
1 TATCGATAATAGATGAAC
83241 TAGGACAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.29
Consensus pattern (20 bp):
TATCGATAATAGATGAACAT
Found at i:86079 original size:36 final size:36
Alignment explanation
Indices: 86026--86100 Score: 105
Period size: 36 Copynumber: 2.1 Consensus size: 36
86016 AGCTTATGAC
* * *
86026 TTATGGAATATATCCATGGGTCAAGTTGCCTCCACT
1 TTATGGAATATACCCATGGGACAAGTTACCTCCACT
* *
86062 TTATGGAATTTACCCATGGGACAAGTTACCTCTACT
1 TTATGGAATATACCCATGGGACAAGTTACCTCCACT
86098 TTA
1 TTA
86101 GTAATAGAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (36 bp):
TTATGGAATATACCCATGGGACAAGTTACCTCCACT
Found at i:88728 original size:39 final size:40
Alignment explanation
Indices: 88684--88779 Score: 115
Period size: 39 Copynumber: 2.4 Consensus size: 40
88674 ATATTTTAAA
*
88684 AATAATTTAGAGTGTTAACGTG-AAATAATTTAAG-AAATT
1 AATAATTTAGAATGTTAACGTGTAAA-AATTTAAGAAAATT
** *
88723 AATAATTTAGAATGTTATGGTGTTAAAATTTAAGAAAATT
1 AATAATTTAGAATGTTAACGTGTAAAAATTTAAGAAAATT
**
88763 AGGAATTTAGAATGTTA
1 AATAATTTAGAATGTTA
88780 GAGCGAAACA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
39 27 0.55
40 22 0.45
ACGTcount: A:0.45, C:0.01, G:0.17, T:0.38
Consensus pattern (40 bp):
AATAATTTAGAATGTTAACGTGTAAAAATTTAAGAAAATT
Found at i:91235 original size:17 final size:17
Alignment explanation
Indices: 91209--91244 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
91199 GGCAATGACC
*
91209 AAATCGGGAAGAGGACA
1 AAATCAGGAAGAGGACA
91226 AAATCAGGAAGAGGACA
1 AAATCAGGAAGAGGACA
91243 AA
1 AA
91245 CTGGGAAGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.53, C:0.11, G:0.31, T:0.06
Consensus pattern (17 bp):
AAATCAGGAAGAGGACA
Found at i:91266 original size:16 final size:16
Alignment explanation
Indices: 91208--91269 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
91198 AGGCAATGAC
*
91208 CAAATCGGGAAGAGGA
1 CAAACCGGGAAGAGGA
* *
91224 CAAAATCAGGAAGAGGA
1 C-AAACCGGGAAGAGGA
* *
91241 CAAACTGGGAAGGGGA
1 CAAACCGGGAAGAGGA
*
91257 CAAGCCGGGAAGA
1 CAAACCGGGAAGA
91270 AGTTGAGCTT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
16 22 0.59
17 15 0.41
ACGTcount: A:0.44, C:0.15, G:0.37, T:0.05
Consensus pattern (16 bp):
CAAACCGGGAAGAGGA
Found at i:93779 original size:40 final size:41
Alignment explanation
Indices: 93684--93792 Score: 166
Period size: 40 Copynumber: 2.7 Consensus size: 41
93674 CAATTAATCA
*
93684 ATTAATAGATTAAATATTAATGATTATATAAAAAATAATTG
1 ATTAATAGATCAAATATTAATGATTATATAAAAAATAATTG
* * *
93725 ATTAATAAATCAAATATTAATGATTATAT-AAGATTAATTG
1 ATTAATAGATCAAATATTAATGATTATATAAAAAATAATTG
*
93765 ATTAATAGACCAAATATTAATGATTATA
1 ATTAATAGATCAAATATTAATGATTATA
93793 AGAGTATGAA
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
40 35 0.56
41 27 0.44
ACGTcount: A:0.51, C:0.03, G:0.07, T:0.39
Consensus pattern (41 bp):
ATTAATAGATCAAATATTAATGATTATATAAAAAATAATTG
Found at i:93811 original size:40 final size:40
Alignment explanation
Indices: 93686--93811 Score: 105
Period size: 40 Copynumber: 3.1 Consensus size: 40
93676 ATTAATCAAT
** * * *
93686 TAATAGATTAAATATTAATGATTATATAAAAAAT-AATTGAT
1 TAATAGACCAAATATTAATGATTATAT--AAGATGAAATGAC
* * * * *
93727 TAATAAATCAAATATTAATGATTATATAAGATTAATTGAT
1 TAATAGACCAAATATTAATGATTATATAAGATGAAATGAC
93767 TAATAGACCAAATATTAATGATTATA-AGAGTATGAAATG-C
1 TAATAGACCAAATATTAATGATTATATA-AG-ATGAAATGAC
93807 TAATA
1 TAATA
93812 CAATAATAAT
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
39 5 0.07
40 38 0.51
41 31 0.42
ACGTcount: A:0.51, C:0.03, G:0.10, T:0.37
Consensus pattern (40 bp):
TAATAGACCAAATATTAATGATTATATAAGATGAAATGAC
Found at i:97081 original size:26 final size:26
Alignment explanation
Indices: 97045--97122 Score: 120
Period size: 26 Copynumber: 3.0 Consensus size: 26
97035 CACTACAGTT
*
97045 TAGAAAAAAATGAGAGGGTAGACATC
1 TAGAGAAAAATGAGAGGGTAGACATC
*
97071 TAGAGAAAAATGAGAGGATAGACATC
1 TAGAGAAAAATGAGAGGGTAGACATC
* *
97097 TAGAGAAAAATGAGATGGTAGGCATC
1 TAGAGAAAAATGAGAGGGTAGACATC
97123 GTAAAATAAG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 47 1.00
ACGTcount: A:0.47, C:0.08, G:0.28, T:0.17
Consensus pattern (26 bp):
TAGAGAAAAATGAGAGGGTAGACATC
Found at i:100904 original size:23 final size:23
Alignment explanation
Indices: 100878--100955 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
100868 CACCATAGCT
100878 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
100901 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* * *
100924 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
100947 TATAATAAT
1 CAT-ATAAT
100956 GTCCATAAGG
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 41 0.91
24 4 0.09
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:101133 original size:103 final size:103
Alignment explanation
Indices: 100962--101282 Score: 615
Period size: 103 Copynumber: 3.1 Consensus size: 103
100952 TAATGTCCAT
*
100962 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACTA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
101027 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
101065 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
101130 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
101168 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
101233 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
101271 AAGGACCACATA
1 AAGGACCACATA
101283 GACCCTCGAC
Statistics
Matches: 215, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 215 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:106470 original size:215 final size:216
Alignment explanation
Indices: 106084--106518 Score: 847
Period size: 216 Copynumber: 2.0 Consensus size: 216
106074 TGACTAATTT
106084 ACATAAAAACATTTTCATTATTACAAAACCAATTAGAGCATGTATATTTCACTTATTTATTTACA
1 ACATAAAAACATTTTCATTATTACAAAACCAATTAGAGCATGTATATTTCACTTATTTATTTACA
106149 TATAACTATTCGAAACATTTATAAAACTGTTCATAGCTTAAACAATAGATTCTTTTGAAAACATG
66 TATAACTATTCGAAACATTTATAAAACTGTTCATAGCTTAAACAATAGATTCTTTTGAAAACATG
106214 CCAACTAGAACTTTATACTAAAATACATATTATTCACATCTTTTCTGATCTGACCTTTAGTAAGG
131 CCAACTAGAACTTTATACTAAAATACATATTATTCACATCTTTTCTGATCTGACCTTTAGTAAGG
106279 AGAACTGACATATCTTT-TCC
196 AGAACTGACATATCTTTCTCC
106299 ACATAAAAAACATTTTCATTATTACAAAACCAATTAGAGCATGTATATTTCACTTATTTATTTAC
1 ACAT-AAAAACATTTTCATTATTACAAAACCAATTAGAGCATGTATATTTCACTTATTTATTTAC
106364 ATATAACTATTCGAAACATTTATAAAACTGTTCATAGCTTAAACAATAGATTC-TTTGAAAACAT
65 ATATAACTATTCGAAACATTTATAAAACTGTTCATAGCTTAAACAATAGATTCTTTTGAAAACAT
106428 GCCAACTAGAACTTTATACTAAAATACATATTATTCACATCTTTTCTGATCTGACCTTTAGTAAG
130 GCCAACTAGAACTTTATACTAAAATACATATTATTCACATCTTTTCTGATCTGACCTTTAGTAAG
106493 GAGAACTGACATATCTTTCTCC
195 GAGAACTGACATATCTTTCTCC
106515 ACAT
1 ACAT
106519 TGCTCTTTAC
Statistics
Matches: 218, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
215 98 0.45
216 120 0.55
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.36
Consensus pattern (216 bp):
ACATAAAAACATTTTCATTATTACAAAACCAATTAGAGCATGTATATTTCACTTATTTATTTACA
TATAACTATTCGAAACATTTATAAAACTGTTCATAGCTTAAACAATAGATTCTTTTGAAAACATG
CCAACTAGAACTTTATACTAAAATACATATTATTCACATCTTTTCTGATCTGACCTTTAGTAAGG
AGAACTGACATATCTTTCTCC
Found at i:107120 original size:23 final size:23
Alignment explanation
Indices: 107079--107155 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
107069 ACCACAGCTA
*
107079 ATATAATTGCATCGAAGTGCCAC
1 ATATAATTGCACCGAAGTGCCAC
*
107102 ATATAATTGCACC-AGAGTGCCGC
1 ATATAATTGCACCGA-AGTGCCAC
* * * *
107125 GTAGAATTGCACCGTAGTGCCAT
1 ATATAATTGCACCGAAGTGCCAC
107148 ATAATAAT
1 AT-ATAAT
107156 GTCCATAAGG
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
22 1 0.02
23 37 0.88
24 4 0.10
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (23 bp):
ATATAATTGCACCGAAGTGCCAC
Found at i:107333 original size:103 final size:103
Alignment explanation
Indices: 107162--107482 Score: 597
Period size: 103 Copynumber: 3.1 Consensus size: 103
107152 TAATGTCCAT
*
107162 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACTA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
107227 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
107265 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
*
107330 GACTTCAAACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* * *
107368 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
107433 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
107471 AAGGACCACATA
1 AAGGACCACATA
107483 GACCCTCGAC
Statistics
Matches: 212, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 212 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:112494 original size:24 final size:22
Alignment explanation
Indices: 112469--112526 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 22
112459 AAATACCCCA
*
112469 AAATATCAAATGAATATAATTTC
1 AAATATCAAATGAAAATAA-TTC
*
112492 AAATATCCAACATGAAAATCATTC
1 AAATAT-CAA-ATGAAAATAATTC
112516 AAATATCAAAT
1 AAATATCAAAT
112527 AAACATAGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 2 0.06
23 9 0.29
24 12 0.39
25 8 0.26
ACGTcount: A:0.53, C:0.14, G:0.03, T:0.29
Consensus pattern (22 bp):
AAATATCAAATGAAAATAATTC
Found at i:117371 original size:42 final size:41
Alignment explanation
Indices: 117320--117416 Score: 108
Period size: 42 Copynumber: 2.4 Consensus size: 41
117310 GTTACAAGAA
* *
117320 AGAGATCGATCCTTTAGGGGAGAGG-ATCGATCATTTACATCG
1 AGAGATCGATCATTTAGGGGA-AGGAATCAATCATTT-CATCG
* * * *
117362 AGGGATCGATCATTTTGGTGAAGGAATCAATCATTTCCTCG
1 AGAGATCGATCATTTAGGGGAAGGAATCAATCATTTCATCG
117403 AGAGATCGAT-ATTT
1 AGAGATCGATCATTT
117417 TTATGAAGGG
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
40 4 0.09
41 16 0.34
42 27 0.57
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (41 bp):
AGAGATCGATCATTTAGGGGAAGGAATCAATCATTTCATCG
Found at i:117477 original size:21 final size:20
Alignment explanation
Indices: 117451--117508 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
117441 TAAAGAATCC
117451 AAGGGATCGATCCTTTGGTCA
1 AAGGGATCGATCCTTT-GTCA
* *
117472 AAGGGAT-TAGTCCATTT-TCT
1 AAGGGATCGA-TCC-TTTGTCA
117492 AAGGGATCGATCCTTTG
1 AAGGGATCGATCCTTTG
117509 AGCCAAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 9
0.71 0.07 0.21
Matches are distributed among these distances:
19 3 0.10
20 13 0.43
21 11 0.37
22 3 0.10
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (20 bp):
AAGGGATCGATCCTTTGTCA
Done.