Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013625.1 Kokia drynarioides strain JFW-HI SEQ_128653, 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: 117745
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 105 characters in sequence are not A, C, G, or T
Found at i:2919 original size:23 final size:22
Alignment explanation
Indices: 2879--2940 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 22
2869 AAAATAGTGA
* *
2879 AAAACAACAAGAAAATAGAAAT
1 AAAACAACAAAAAAATAGAAAG
*
2901 AAAACAACAAAAAATATAGCAAG
1 AAAACAACAAAAAA-ATAGAAAG
**
2924 AAAACAGTAAAAAAATA
1 AAAACAACAAAAAAATA
2941 ACAGTTTCTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
22 16 0.47
23 18 0.53
ACGTcount: A:0.73, C:0.10, G:0.08, T:0.10
Consensus pattern (22 bp):
AAAACAACAAAAAAATAGAAAG
Found at i:3665 original size:3 final size:3
Alignment explanation
Indices: 3657--3686 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
3647 ACACGTGTTT
3657 TTA TTA TTA TTA TTA TTA TTA TTA TATA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TT
3687 TAAAAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3964 original size:12 final size:12
Alignment explanation
Indices: 3948--3987 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
3938 AAAATTGAAG
3948 GAAAAAAA-AAA
1 GAAAAAAAGAAA
3959 GAAAAAAGAGAAA
1 GAAAAAA-AGAAA
*
3972 GAAAGAAAGAAA
1 GAAAAAAAGAAA
3984 GAAA
1 GAAA
3988 GAAGAAGAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 7 0.27
12 10 0.38
13 9 0.35
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (12 bp):
GAAAAAAAGAAA
Found at i:3974 original size:4 final size:4
Alignment explanation
Indices: 3956--3990 Score: 52
Period size: 4 Copynumber: 8.5 Consensus size: 4
3946 AGGAAAAAAA
*
3956 AAAG AAAA AAGAG AAAG AAAG AAAG AAAG AAAG AA
1 AAAG AAAG AA-AG AAAG AAAG AAAG AAAG AAAG AA
3991 GAAGAAGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 25 0.89
5 3 0.11
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:3988 original size:12 final size:13
Alignment explanation
Indices: 3956--3992 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
3946 AGGAAAAAAA
*
3956 AAAGAAAAAAGAG
1 AAAGAAAGAAGAG
3969 AAAGAAAGAA-AG
1 AAAGAAAGAAGAG
3981 AAAGAAAGAAGA
1 AAAGAAAGAAGA
3993 AGAAGGAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAGAG
Found at i:4001 original size:7 final size:7
Alignment explanation
Indices: 3986--4031 Score: 55
Period size: 7 Copynumber: 7.1 Consensus size: 7
3976 GAAAGAAAGA
3986 AAGAA-G
1 AAGAAGG
3992 AAGAAGG
1 AAGAAGG
3999 AAGAAGG
1 AAGAAGG
4006 AAGAAGG
1 AAGAAGG
4013 -AGAA-G
1 AAGAAGG
*
4018 AAG-GGG
1 AAGAAGG
4024 AAGAAGG
1 AAGAAGG
4031 A
1 A
4032 GAAAGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
5 1 0.03
6 15 0.44
7 18 0.53
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (7 bp):
AAGAAGG
Found at i:4002 original size:25 final size:25
Alignment explanation
Indices: 3944--4039 Score: 72
Period size: 25 Copynumber: 3.8 Consensus size: 25
3934 NNNGAAAATT
* * *
3944 GAAGGAAAAAAAAAAGAAAAAAG-A
1 GAAGGAAGAAAGAAAGAAAGAAGAA
*
3968 GAAAGAAAGAAAGAAAGAAAGAAGAA
1 G-AAGGAAGAAAGAAAGAAAGAAGAA
*
3994 GAAGGAAG-AAGGAAGAAGGAGAAGAA
1 GAAGGAAGAAAGAAAGAA--AGAAGAA
*
4020 G-GGGAAGAAGGAGAAAGAAA
1 GAAGGAAGAA--AGAAAGAAA
4040 AAAAGGATAA
Statistics
Matches: 57, Mismatches: 8, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
24 9 0.16
25 29 0.51
26 12 0.21
28 7 0.12
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (25 bp):
GAAGGAAGAAAGAAAGAAAGAAGAA
Found at i:4019 original size:9 final size:9
Alignment explanation
Indices: 3987--4034 Score: 55
Period size: 9 Copynumber: 5.4 Consensus size: 9
3977 AAAGAAAGAA
*
3987 AGAAGAAGA
1 AGAAGAAGG
3996 AGGAAGAA-G
1 A-GAAGAAGG
4005 -GAAGAAGG
1 AGAAGAAGG
4013 AGAAGAAGG
1 AGAAGAAGG
*
4022 GGAAGAAGG
1 AGAAGAAGG
4031 AGAA
1 AGAA
4035 AGAAAAAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
7 6 0.18
8 1 0.03
9 20 0.61
10 6 0.18
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (9 bp):
AGAAGAAGG
Found at i:4657 original size:16 final size:16
Alignment explanation
Indices: 4612--4661 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
4602 TAAACCTAAC
*
4612 TAATTAATTACCAAAA
1 TAATTAATTATCAAAA
*
4628 T-A-TAA-TATAAAAAA
1 TAATTAATTAT-CAAAA
4642 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
4658 TAAT
1 TAAT
4662 ATCTCCATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 2 0.07
16 12 0.44
17 3 0.11
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:6020 original size:43 final size:43
Alignment explanation
Indices: 5939--6022 Score: 116
Period size: 43 Copynumber: 2.0 Consensus size: 43
5929 ATTAACATGT
* *
5939 TAAATTATATTACTTGACTTGTGTTAATATGGTTACATGTTTC
1 TAAATTATATTACTTGACTTGTATTAATATGATTACATGTTTC
* *
5982 TAAATTATATTACTTTACTTTTATTAATAT-ATTGACATGTT
1 TAAATTATATTACTTGACTTGTATTAATATGATT-ACATGTT
6023 ATTAATTGTG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
42 2 0.06
43 34 0.94
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.51
Consensus pattern (43 bp):
TAAATTATATTACTTGACTTGTATTAATATGATTACATGTTTC
Found at i:6903 original size:24 final size:23
Alignment explanation
Indices: 6861--6914 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
6851 ATTGGCTAAA
6861 GTAAAAATTCTGAAATTTTTATG
1 GTAAAAATTCTGAAATTTTTATG
6884 GTAAAAATTCTGAAATTTTTATG
1 GTAAAAATTCTGAAATTTTTATG
6907 GTAAAAAT
1 GTAAAAAT
6915 ATATTTGAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.43, C:0.04, G:0.13, T:0.41
Consensus pattern (23 bp):
GTAAAAATTCTGAAATTTTTATG
Found at i:9856 original size:4 final size:4
Alignment explanation
Indices: 9837--9901 Score: 69
Period size: 4 Copynumber: 16.0 Consensus size: 4
9827 ACGCATTACT
* * * *
9837 TTTC TTTC CTTC -TTC TTTC TTTCC TCTC CTTC TTCC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTT-C TTTC TTTC TTTC TTTC TTTC TTTC
9885 TTTTC TTTC TTTC TTTC
1 -TTTC TTTC TTTC TTTC
9902 CCGTTTATTT
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
3 3 0.06
4 41 0.80
5 7 0.14
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (4 bp):
TTTC
Found at i:9870 original size:17 final size:15
Alignment explanation
Indices: 9837--9897 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 15
9827 ACGCATTACT
9837 TTTCTTTCCTTCTTC
1 TTTCTTTCCTTCTTC
9852 TTTCTTTCC-TC-TC
1 TTTCTTTCCTTCTTC
*
9865 CTTC-TTCC-T-TTC
1 TTTCTTTCCTTCTTC
9877 TTTCTTT-CTT-TTC
1 TTTCTTTCCTTCTTC
9890 TTTCTTTC
1 TTTCTTTC
9898 TTTCCCGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
12 11 0.28
13 18 0.45
14 2 0.05
15 9 0.22
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTCTTTCCTTCTTC
Found at i:9894 original size:25 final size:24
Alignment explanation
Indices: 9835--9901 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 24
9825 AAACGCATTA
9835 CTTTTCTTTCCTTC-TTCTTTCTTT
1 CTTTTCTTT-CTTCTTTCTTTCTTT
* * *
9859 CCTCTCCTTCTTCCTTTCTTTCTTT
1 CTTTTCTTTCTT-CTTTCTTTCTTT
9884 CTTTTCTTTCTTTCTTTC
1 CTTTTCTTTC-TTCTTTC
9902 CCGTTTATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
23 3 0.09
24 7 0.21
25 22 0.65
26 2 0.06
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (24 bp):
CTTTTCTTTCTTCTTTCTTTCTTT
Found at i:9898 original size:17 final size:16
Alignment explanation
Indices: 9837--9901 Score: 69
Period size: 17 Copynumber: 4.0 Consensus size: 16
9827 ACGCATTACT
*
9837 TTTCTTTCCTTC-TTC
1 TTTCTTTCTTTCTTTC
* *
9852 TTTCTTTCCTCTCCTTC
1 TTTCTTT-CTTTCTTTC
*
9869 TTCCTTTCTTTCTTTC
1 TTTCTTTCTTTCTTTC
9885 TTTTCTTTCTTTCTTTC
1 -TTTCTTTCTTTCTTTC
9902 CCGTTTATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
15 7 0.17
16 10 0.24
17 24 0.59
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTCTTTCTTTCTTTC
Found at i:11483 original size:101 final size:101
Alignment explanation
Indices: 11378--11580 Score: 388
Period size: 101 Copynumber: 2.0 Consensus size: 101
11368 TTAGTTTATT
* *
11378 AGTTTATTACTTAGAAACTTATTTGTATGTTAATTATTTGCTTATTATTTTATTTCTTTATATGT
1 AGTTTATTACTTAGAAACTTACTTGTATGTTAATTATTTGCTTATTATTTTATTACTTTATATGT
11443 TAAATATTTGTATATTAATATATTTAATTTAACGAG
66 TAAATATTTGTATATTAATATATTTAATTTAACGAG
11479 AGTTTATTACTTAGAAACTTACTTGTATGTTAATTATTTGCTTATTATTTTATTACTTTATATGT
1 AGTTTATTACTTAGAAACTTACTTGTATGTTAATTATTTGCTTATTATTTTATTACTTTATATGT
11544 TAAATATTTGTATATTAATATATTTAATTTAACGAG
66 TAAATATTTGTATATTAATATATTTAATTTAACGAG
11580 A
1 A
11581 ACCCCGTGAG
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
101 100 1.00
ACGTcount: A:0.33, C:0.05, G:0.09, T:0.53
Consensus pattern (101 bp):
AGTTTATTACTTAGAAACTTACTTGTATGTTAATTATTTGCTTATTATTTTATTACTTTATATGT
TAAATATTTGTATATTAATATATTTAATTTAACGAG
Found at i:18631 original size:19 final size:18
Alignment explanation
Indices: 18607--18661 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 18
18597 GGCCCGCTTT
18607 TAATTTTATACATATTATG
1 TAATTTTATA-ATATTATG
18626 TAATTTTTTATATATATTATG
1 TAA--TTTTATA-ATATTATG
18647 TAA-TTTATAATATTA
1 TAATTTTATAATATTA
18662 AAATAATGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
17 6 0.18
18 6 0.18
19 3 0.09
21 18 0.55
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (18 bp):
TAATTTTATAATATTATG
Found at i:18636 original size:21 final size:21
Alignment explanation
Indices: 18610--18652 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
18600 CCGCTTTTAA
18610 TTTTATACATATTATGTAATT
1 TTTTATACATATTATGTAATT
*
18631 TTTTATATATATTATGTAATT
1 TTTTATACATATTATGTAATT
18652 T
1 T
18653 ATAATATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (21 bp):
TTTTATACATATTATGTAATT
Found at i:18696 original size:16 final size:17
Alignment explanation
Indices: 18655--18693 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
18645 TGTAATTTAT
18655 AATATTAAAATAATGTA
1 AATATTAAAATAATGTA
*
18672 AACATTAAAA-AATGTTA
1 AATATTAAAATAATG-TA
18689 AATAT
1 AATAT
18694 AAATTTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (17 bp):
AATATTAAAATAATGTA
Found at i:20019 original size:44 final size:44
Alignment explanation
Indices: 19969--20056 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
19959 AGCTTGAGTA
19969 AGAATAAAATATGTTAATATCATGCCTAAATCTGACCCAAACCC
1 AGAATAAAATATGTTAATATCATGCCTAAATCTGACCCAAACCC
20013 AGAATAAAATATGTTAATATCATGCCTAAATCTGACCCAAACCC
1 AGAATAAAATATGTTAATATCATGCCTAAATCTGACCCAAACCC
20057 GGCCAAACTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.43, C:0.23, G:0.09, T:0.25
Consensus pattern (44 bp):
AGAATAAAATATGTTAATATCATGCCTAAATCTGACCCAAACCC
Found at i:21195 original size:18 final size:18
Alignment explanation
Indices: 21161--21196 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
21151 TTCGGTTAAC
**
21161 CGATCGATTAATTGAATT
1 CGATCGATTAACCGAATT
21179 CGATCGATTAACCGAATT
1 CGATCGATTAACCGAATT
21197 AATTTAGTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (18 bp):
CGATCGATTAACCGAATT
Found at i:22828 original size:30 final size:28
Alignment explanation
Indices: 22794--22850 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
22784 ATAGAAGTTA
22794 TTAAATTTTAATGAAAAACTATAAAAATAT
1 TTAAATTTT-ATGAAAAACTA-AAAAATAT
* *
22824 TTAAATTTTATTAAAAATTAAAAAATA
1 TTAAATTTTATGAAAAACTAAAAAATA
22851 AAAAAAATCG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 7 0.28
29 9 0.36
30 9 0.36
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (28 bp):
TTAAATTTTATGAAAAACTAAAAAATAT
Found at i:23073 original size:20 final size:20
Alignment explanation
Indices: 23058--23169 Score: 70
Period size: 19 Copynumber: 5.7 Consensus size: 20
23048 TTTTTATGCA
23058 TTTTATAAAATTTTTATAAT
1 TTTTATAAAATTTTTATAAT
* *
23078 TTTTATAAAA-GTTTACAAT
1 TTTTATAAAATTTTTATAAT
* * * *
23097 TTTT-TTATATTTTTATGAC
1 TTTTATAAAATTTTTATAAT
*** *
23116 TTTTATAAAAAAAATTCTAAT
1 TTTTAT-AAAATTTTTATAAT
*
23137 TTTTA-ATAAA-TTTTATATT
1 TTTTATA-AAATTTTTATAAT
23156 TTTTATTAAAATTT
1 TTTTA-TAAAATTT
23170 AATATTTTTT
Statistics
Matches: 65, Mismatches: 20, Indels: 13
0.66 0.20 0.13
Matches are distributed among these distances:
18 3 0.05
19 31 0.48
20 17 0.26
21 14 0.22
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (20 bp):
TTTTATAAAATTTTTATAAT
Found at i:23079 original size:19 final size:19
Alignment explanation
Indices: 23057--23125 Score: 59
Period size: 20 Copynumber: 3.6 Consensus size: 19
23047 TTTTTTATGC
23057 ATTTTATAAAATTTTTATA
1 ATTTTATAAAATTTTTATA
* *
23076 ATTTTTATAAAA-GTTTACA
1 A-TTTTATAAAATTTTTATA
* * *
23095 ATTTTTTTATATTTTTATGA
1 ATTTTATAAAATTTTTAT-A
*
23115 CTTTTATAAAA
1 ATTTTATAAAA
23126 AAAATTCTAA
Statistics
Matches: 36, Mismatches: 11, Indels: 5
0.69 0.21 0.10
Matches are distributed among these distances:
18 7 0.19
19 11 0.31
20 18 0.50
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (19 bp):
ATTTTATAAAATTTTTATA
Found at i:23160 original size:19 final size:20
Alignment explanation
Indices: 23136--23179 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
23126 AAAATTCTAA
*
23136 TTTTTAAT-AAATTTTATAT
1 TTTTTAATAAAATTTAATAT
*
23155 TTTTTATTAAAATTTAATAT
1 TTTTTAATAAAATTTAATAT
23175 TTTTT
1 TTTTT
23180 TATTTATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTTAATAAAATTTAATAT
Found at i:23196 original size:18 final size:18
Alignment explanation
Indices: 23136--23198 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 18
23126 AAAATTCTAA
*
23136 TTTTTAATAAATTTTATAT
1 TTTTTATTAAA-TTTATAT
23155 TTTTTATTAAAATTTAATATT
1 TTTTTATT-AAATTT-ATA-T
*
23176 TTTTTATT-TATTTATAGT
1 TTTTTATTAAATTTATA-T
23194 TTTTT
1 TTTTT
23199 GTCATATGTC
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
18 9 0.24
19 14 0.37
20 6 0.16
21 9 0.24
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (18 bp):
TTTTTATTAAATTTATAT
Found at i:23565 original size:87 final size:87
Alignment explanation
Indices: 23402--23569 Score: 198
Period size: 88 Copynumber: 1.9 Consensus size: 87
23392 TTTGACAGCC
* * ** *
23402 TTTTTATGTATTTTGAAAGTTCAAGCTCCCAATTGAGTGCAAAAAAAATAGGGGTTTAATTGTTT
1 TTTTTATGCATTTTGAAAGTTCAAGCTCCAAATTGAGTGCAAAAAAAATAGGAATTTAATTG-CT
** *
23467 TTTTTCAAAAAAGTTGAGGATCT
65 TTTTAAAAAAAAATTGAGGATCT
* *
23490 TTTTTATGCATTTTGACAGTTTAAG-TACCAAATTGAGTGCAAAAAAACA-A-GAATTTAATTGC
1 TTTTTATGCATTTTGAAAGTTCAAGCT-CCAAATTGAGTGCAAAAAAA-ATAGGAATTTAATTGC
23552 TTTTTAAAAAAAAATTGA
64 TTTTTAAAAAAAAATTGA
23570 AATTTTTTTA
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
86 15 0.22
87 10 0.15
88 42 0.62
89 1 0.01
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (87 bp):
TTTTTATGCATTTTGAAAGTTCAAGCTCCAAATTGAGTGCAAAAAAAATAGGAATTTAATTGCTT
TTTAAAAAAAAATTGAGGATCT
Found at i:24023 original size:37 final size:38
Alignment explanation
Indices: 23982--24061 Score: 92
Period size: 37 Copynumber: 2.1 Consensus size: 38
23972 TGAGTTTAAG
** *
23982 AAAAAGTA-ATTATAATTTAATTTATAATTATTAGTT-A
1 AAAAAGTATATTA-AATTTAAAATATAATTATTACTTGA
* *
24019 AAAAATTATATTAATTTTAAAATATAATTATTACTTGA
1 AAAAAGTATATTAAATTTAAAATATAATTATTACTTGA
24057 AAAAA
1 AAAAA
24062 CTGAATAAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
37 26 0.72
38 10 0.28
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.42
Consensus pattern (38 bp):
AAAAAGTATATTAAATTTAAAATATAATTATTACTTGA
Found at i:25238 original size:95 final size:95
Alignment explanation
Indices: 25063--25251 Score: 333
Period size: 95 Copynumber: 2.0 Consensus size: 95
25053 AACACGACCA
*
25063 TCCAAACAAATGCAAGCAATATGATACTCGAGTCTTCATGTTTTCATTGGGAACGTGGTGTCACT
1 TCCAAACAAATGCAAGCAATATGATACCCGAGTCTTCATGTTTTCATTGGGAACGTGGTGTCACT
25128 AGTTACGAAACATCACGCGGGCTCAACTGG
66 AGTTACGAAACATCACGCGGGCTCAACTGG
25158 TCCAAACAAATGCAAGCAATATGATACCCGAGTCTTCATGTTTTCATTGGGAACGTGGTGTCACT
1 TCCAAACAAATGCAAGCAATATGATACCCGAGTCTTCATGTTTTCATTGGGAACGTGGTGTCACT
* * * *
25223 GGTTATGAAATATCACGTGGGCTCAACTG
66 AGTTACGAAACATCACGCGGGCTCAACTG
25252 CTCTATACCA
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
95 89 1.00
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (95 bp):
TCCAAACAAATGCAAGCAATATGATACCCGAGTCTTCATGTTTTCATTGGGAACGTGGTGTCACT
AGTTACGAAACATCACGCGGGCTCAACTGG
Found at i:43817 original size:30 final size:31
Alignment explanation
Indices: 43762--43819 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
43752 TAGTACAGTG
*
43762 ACTTAAATAAAATTTTTTGGATAATTCAATT
1 ACTTAAATAAAATCTTTTGGATAATTCAATT
43793 ACTTAAATAAAA-CTTTT-GATTAATTCA
1 ACTTAAATAAAATCTTTTGGA-TAATTCA
43820 GTAACCAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 2 0.08
30 11 0.44
31 12 0.48
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.43
Consensus pattern (31 bp):
ACTTAAATAAAATCTTTTGGATAATTCAATT
Found at i:44442 original size:45 final size:47
Alignment explanation
Indices: 44341--44436 Score: 120
Period size: 51 Copynumber: 2.0 Consensus size: 47
44331 AACATGTGTG
*
44341 AACATAACACATGCACAATTTGGATCTAATGTATAAAAAAATAAAGGAATA
1 AACATAACACAAGCACAATTTGGATCTAATGTATAAAAAAAT--A--AATA
* * *
44392 AACATAGCACAAGCACAATTTGGATTTAATGTATTAAAAAATAAA
1 AACATAACACAAGCACAATTTGGATCTAATGTATAAAAAAATAAA
44437 AACATATGGC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
47 2 0.05
49 1 0.02
51 38 0.93
ACGTcount: A:0.52, C:0.11, G:0.11, T:0.25
Consensus pattern (47 bp):
AACATAACACAAGCACAATTTGGATCTAATGTATAAAAAAATAAATA
Found at i:47935 original size:21 final size:21
Alignment explanation
Indices: 47909--47948 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
47899 GCCTAGATAT
*
47909 TTCTACCGATACTTAAATTAG
1 TTCTACCGATACTAAAATTAG
*
47930 TTCTACCGGTACTAAAATT
1 TTCTACCGATACTAAAATT
47949 GATAGTGAGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.38
Consensus pattern (21 bp):
TTCTACCGATACTAAAATTAG
Found at i:48718 original size:37 final size:38
Alignment explanation
Indices: 48668--48782 Score: 164
Period size: 37 Copynumber: 3.1 Consensus size: 38
48658 CAGAGCTTGT
* *
48668 TAGGCACATAGCCTGAATAA-ACCGGCATGAAGTCTAC
1 TAGGCACATAGCCTGAATAACACCGGCACGAAGCCTAC
48705 TAGGCACATAGCCTGAA-AACACCGGCACGAAGCCTAC
1 TAGGCACATAGCCTGAATAACACCGGCACGAAGCCTAC
** *
48742 TAGGCACATAGCCTGAAT-ACATTGGCACAAAGCCTAC
1 TAGGCACATAGCCTGAATAACACCGGCACGAAGCCTAC
48779 TAGG
1 TAGG
48783 TACACAATGT
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
36 2 0.03
37 69 0.97
ACGTcount: A:0.35, C:0.27, G:0.22, T:0.17
Consensus pattern (38 bp):
TAGGCACATAGCCTGAATAACACCGGCACGAAGCCTAC
Found at i:49279 original size:71 final size:70
Alignment explanation
Indices: 49159--49303 Score: 263
Period size: 71 Copynumber: 2.1 Consensus size: 70
49149 ATTGTTATAT
* *
49159 ATTAAAAAATAGTAAAGGGACCAAAATGGTAATTAAACCATGGTCAAAAATTCCAAGTGTTGGTG
1 ATTAAAAAATAGTAAAGGGACCAAAATGGTAATTAAACCATGGTAAAAAATTCCAAGCGTTGGTG
49224 ACATGG
66 ACAT-G
49230 ATTAAAAAATAGTAAAGGGACCAAAATGGTAATTAAACCATGGTAAAAAATTCCAAGCGTTGGTG
1 ATTAAAAAATAGTAAAGGGACCAAAATGGTAATTAAACCATGGTAAAAAATTCCAAGCGTTGGTG
49295 ACATG
66 ACATG
49300 ATTA
1 ATTA
49304 CCATCCACTA
Statistics
Matches: 72, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
70 5 0.07
71 67 0.93
ACGTcount: A:0.45, C:0.11, G:0.20, T:0.24
Consensus pattern (70 bp):
ATTAAAAAATAGTAAAGGGACCAAAATGGTAATTAAACCATGGTAAAAAATTCCAAGCGTTGGTG
ACATG
Found at i:50937 original size:36 final size:36
Alignment explanation
Indices: 50895--51029 Score: 216
Period size: 36 Copynumber: 3.8 Consensus size: 36
50885 TTGTAACAAG
50895 CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
1 CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
*
50931 CATGACCTTTTGGTCAACAGGGAGTAAAATGAGCAT
1 CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
* * *
50967 CATGACCTTTTGGTCAACAAGGAATAAAATGAGCAT
1 CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
* *
51003 CATGACTTTTGGGTCAATAGGGAGTAA
1 CATGACCTTTGGGTCAACAGGGAGTAA
51030 GCATGACCTT
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 91 1.00
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (36 bp):
CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
Found at i:51035 original size:28 final size:28
Alignment explanation
Indices: 51003--51057 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
50993 AAATGAGCAT
* * *
51003 CATGACTTTTGGGTCAATAGGGAGTAAG
1 CATGACCTTTGGGTCAACAAGGAGTAAG
51031 CATGACCTTTGGGTCAACAAGGAGTAA
1 CATGACCTTTGGGTCAACAAGGAGTAA
51058 ATCGGATATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.31, C:0.15, G:0.29, T:0.25
Consensus pattern (28 bp):
CATGACCTTTGGGTCAACAAGGAGTAAG
Found at i:52243 original size:36 final size:37
Alignment explanation
Indices: 52184--52271 Score: 133
Period size: 36 Copynumber: 2.4 Consensus size: 37
52174 TTGGGTGTTA
* *
52184 CACATAGCCTAAATACACCAGCACAAAGCATACTAGG
1 CACATAGCTTGAATACACCAGCACAAAGCATACTAGG
*
52221 CACATAGCTTGAATA-ACCAGCACAAAGCCTACTAGG
1 CACATAGCTTGAATACACCAGCACAAAGCATACTAGG
*
52257 CACATAACTTGAATA
1 CACATAGCTTGAATA
52272 TTTAGATGCA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
36 34 0.72
37 13 0.28
ACGTcount: A:0.42, C:0.27, G:0.14, T:0.17
Consensus pattern (37 bp):
CACATAGCTTGAATACACCAGCACAAAGCATACTAGG
Found at i:57844 original size:30 final size:30
Alignment explanation
Indices: 57808--57868 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
57798 GGAAGAGGGG
57808 AGCAGACTTTGTTTGTTCCTTTGGTGCATC
1 AGCAGACTTTGTTTGTTCCTTTGGTGCATC
57838 AGCAGACTTTGTTTGTTCCTTTGGTGCATC
1 AGCAGACTTTGTTTGTTCCTTTGGTGCATC
57868 A
1 A
57869 TTGTTTTGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.15, C:0.20, G:0.23, T:0.43
Consensus pattern (30 bp):
AGCAGACTTTGTTTGTTCCTTTGGTGCATC
Found at i:58126 original size:13 final size:13
Alignment explanation
Indices: 58108--58133 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
58098 ACCGTTGACC
58108 GACCGTTGACTTT
1 GACCGTTGACTTT
58121 GACCGTTGACTTT
1 GACCGTTGACTTT
58134 TAAAAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.38
Consensus pattern (13 bp):
GACCGTTGACTTT
Found at i:59199 original size:3 final size:3
Alignment explanation
Indices: 59191--59241 Score: 86
Period size: 3 Copynumber: 17.3 Consensus size: 3
59181 ATTTACGTCA
*
59191 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TGT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
59238 TAT T
1 TAT T
59242 TTGGTTTGGG
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:60702 original size:22 final size:24
Alignment explanation
Indices: 60677--60720 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
60667 ATTTTGTTCA
60677 ACTTTAACTT-TTAT-TCAAAAAT
1 ACTTTAACTTGTTATATCAAAAAT
*
60699 ACTTTAATTTGTTATATCAAAA
1 ACTTTAACTTGTTATATCAAAA
60721 TATATTATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.41, C:0.11, G:0.02, T:0.45
Consensus pattern (24 bp):
ACTTTAACTTGTTATATCAAAAAT
Found at i:70215 original size:6 final size:6
Alignment explanation
Indices: 70176--70206 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
70166 TGGTAATGAA
70176 GGAGAT GGAGAT GGAGAT GGAGAT GGAGAT G
1 GGAGAT GGAGAT GGAGAT GGAGAT GGAGAT G
70207 ATGGAGATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.52, T:0.16
Consensus pattern (6 bp):
GGAGAT
Found at i:81556 original size:32 final size:30
Alignment explanation
Indices: 81520--81633 Score: 84
Period size: 32 Copynumber: 3.6 Consensus size: 30
81510 TAAAATGAAG
*
81520 TTTTAGGTTCATTAAAAGTTAAAAAAAAAAAA
1 TTTTAGG-CCATTAAAAGTT-AAAAAAAAAAA
* * **
81552 TTTTAGGTCTTGTAAAAGTTGGTAAAAAAAAA
1 TTTTAGGCCAT-TAAAAGTT-AAAAAAAAAAA
* ** * *
81584 TTATAAACCCTTAAAAGTTAAAAATAAAAA
1 TTTTAGGCCATTAAAAGTTAAAAAAAAAAA
*
81614 TTTTGGGGCCATTAAAAGTT
1 TTTT-AGGCCATTAAAAGTT
81634 GATAATTTTT
Statistics
Matches: 63, Mismatches: 17, Indels: 5
0.74 0.20 0.06
Matches are distributed among these distances:
30 11 0.17
31 22 0.35
32 30 0.48
ACGTcount: A:0.48, C:0.06, G:0.13, T:0.32
Consensus pattern (30 bp):
TTTTAGGCCATTAAAAGTTAAAAAAAAAAA
Found at i:81685 original size:16 final size:17
Alignment explanation
Indices: 81652--81691 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
81642 TTTTCTACCT
81652 TTAAAAATTTTAAAAAA
1 TTAAAAATTTTAAAAAA
*
81669 TTAAACATTTT-AAAAA
1 TTAAAAATTTTAAAAAA
81685 TTAAAAA
1 TTAAAAA
81692 ACAAAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
TTAAAAATTTTAAAAAA
Found at i:84234 original size:20 final size:21
Alignment explanation
Indices: 84198--84269 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 21
84188 GTCTGGAGCA
84198 AATTTGACTTGTTTTAAAAGC
1 AATTTGACTTGTTTTAAAAGC
*
84219 AATTTGA-TTTTTTTAAAATG-
1 AATTTGACTTGTTTTAAAA-GC
* *
84239 ATTTTGACATTG--TTAAAATC
1 AATTTGAC-TTGTTTTAAAAGC
*
84259 ATTTTGACTTG
1 AATTTGACTTG
84270 ATTAAATCAT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
19 3 0.07
20 30 0.70
21 8 0.19
22 2 0.05
ACGTcount: A:0.32, C:0.07, G:0.12, T:0.49
Consensus pattern (21 bp):
AATTTGACTTGTTTTAAAAGC
Found at i:84278 original size:19 final size:20
Alignment explanation
Indices: 84231--84291 Score: 81
Period size: 19 Copynumber: 3.1 Consensus size: 20
84221 TTTGATTTTT
*
84231 TTAAAATGATTTTGACATTG-
1 TTAAAATCATTTTGAC-TTGA
84251 TTAAAATCATTTTGACTTGA
1 TTAAAATCATTTTGACTTGA
*
84271 TT-AAATCATTTTAACTTGA
1 TTAAAATCATTTTGACTTGA
84290 TT
1 TT
84292 TTAAAATTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
19 21 0.55
20 17 0.45
ACGTcount: A:0.34, C:0.08, G:0.10, T:0.48
Consensus pattern (20 bp):
TTAAAATCATTTTGACTTGA
Found at i:86548 original size:20 final size:19
Alignment explanation
Indices: 86525--86562 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
86515 TTTTCACGAG
86525 TATCAATATTTTTATAAAAA
1 TATCAATATTTTT-TAAAAA
86545 TATCAATATTTTTTAAAA
1 TATCAATATTTTTTAAAA
86563 TCGATACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (19 bp):
TATCAATATTTTTTAAAAA
Found at i:92596 original size:101 final size:102
Alignment explanation
Indices: 92396--92621 Score: 262
Period size: 102 Copynumber: 2.2 Consensus size: 102
92386 ATACTTTAAG
* * ** *
92396 AAAAAAGTATCGATACTTTGTATG-GTTTGTAAAAAATAAAATGTCATTTTGGTATCGCTTTTTA
1 AAAAATGTATCGATACTTTTTA-GCGTTT-TTGAAAATAAAATGTCATTTTGGTATCACTTTTTA
** * * *
92460 TGATGTGTATCAATATTTCATAAAATATCAATACTTGGC
64 AAAAGAGTATCAATATTTCAGAAAATATCAATACTTGGC
* *
92499 -AAAATGGTATCGATATTTTTTAGCGTTTTTGAAAATAGAATGTCATTTTGGTATCAC-TTTTAA
1 AAAAAT-GTATCGATACTTTTTAGCGTTTTTGAAAATAAAATGTCATTTTGGTATCACTTTTTAA
*
92562 AAAGAGTATCAATAATTT-AGAAAATATCGATACTTGGC
65 AAAGAGTATCAAT-ATTTCAGAAAATATCAATACTTGGC
92600 GAAAAATGTATCGATACTTTTT
1 -AAAAATGTATCGATACTTTTT
92622 GGTGTGGAGC
Statistics
Matches: 104, Mismatches: 14, Indels: 11
0.81 0.11 0.09
Matches are distributed among these distances:
101 33 0.32
102 48 0.46
103 23 0.22
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.39
Consensus pattern (102 bp):
AAAAATGTATCGATACTTTTTAGCGTTTTTGAAAATAAAATGTCATTTTGGTATCACTTTTTAAA
AAGAGTATCAATATTTCAGAAAATATCAATACTTGGC
Found at i:92678 original size:19 final size:20
Alignment explanation
Indices: 92656--92697 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
92646 TGAAAAGCAC
*
92656 TTTGA-TTTGTTAAAATGAT
1 TTTGACTTTGTTAAAATCAT
92675 TTTGACTTTGTTAAAATCAT
1 TTTGACTTTGTTAAAATCAT
92695 TTT
1 TTT
92698 AAATTGATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.29, C:0.05, G:0.12, T:0.55
Consensus pattern (20 bp):
TTTGACTTTGTTAAAATCAT
Found at i:96307 original size:52 final size:52
Alignment explanation
Indices: 96225--96472 Score: 252
Period size: 52 Copynumber: 4.8 Consensus size: 52
96215 GCCATAAACG
* * * * * * *
96225 AAGAGGTTTGACGATTATGAGTCATTGTGAGTATATGAATCATTTACGAATT
1 AAGAGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATT
* *
96277 AA-ACGGTTCGATGACTAAGTGTCATCGTGAGTATATGGATCCTTTACGGATT
1 AAGA-GGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATT
* * *
96329 AAGAGG-TCTGATGACTTTGTGCCATCGTGAGTATATGGATCCTTTACGGATT
1 AAGAGGTTC-GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATT
* * * * *
96381 AAGAGGTCCGATGACTCTGTGTCATCGTGAGTATATGAATCCCTTGCAGATT
1 AAGAGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATT
* * *
96433 ATA-AGG-TCCAGTGGCTATGTGTCATCATGAGTATATGAAT
1 A-AGAGGTTCGA-TGACTATGTGTCATCGTGAGTATATGAAT
96473 GAAGTGAAAT
Statistics
Matches: 166, Mismatches: 24, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
51 5 0.03
52 158 0.95
53 3 0.02
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.33
Consensus pattern (52 bp):
AAGAGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATT
Found at i:97108 original size:21 final size:24
Alignment explanation
Indices: 97067--97121 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 24
97057 TGAATTGTGA
*
97067 GTATCGGTAGTTATATGTATAGAT
1 GTATCGGTAGTTATATGTATACAT
*
97091 GTATCGGTAG-T-T-TGTATACTT
1 GTATCGGTAGTTATATGTATACAT
97112 GTATCGGTAG
1 GTATCGGTAG
97122 AAGTTGCAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 17 0.59
22 1 0.03
23 1 0.03
24 10 0.34
ACGTcount: A:0.24, C:0.07, G:0.27, T:0.42
Consensus pattern (24 bp):
GTATCGGTAGTTATATGTATACAT
Found at i:99738 original size:34 final size:34
Alignment explanation
Indices: 99674--99739 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
99664 ATATATATGG
* *
99674 AAATGCAATGACAATGTAGATGCAGCGACAATAA
1 AAATGCAATGACAATATAGATACAGCGACAATAA
* *
99708 AAATGCAATGACATTAATA-ATACAGGGACAAT
1 AAATGCAATGACAAT-ATAGATACAGCGACAAT
99740 TATACTATAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 25 0.93
35 2 0.07
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.20
Consensus pattern (34 bp):
AAATGCAATGACAATATAGATACAGCGACAATAA
Found at i:106024 original size:20 final size:21
Alignment explanation
Indices: 105999--106041 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
105989 ATCACCAACT
105999 TATTAATCA-CAACATAAA-AA
1 TATTAATCACCAAC-TAAACAA
106019 TATTAATCACCAACTAAACAA
1 TATTAATCACCAACTAAACAA
106040 TA
1 TA
106042 AAAATTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.56, C:0.19, G:0.00, T:0.26
Consensus pattern (21 bp):
TATTAATCACCAACTAAACAA
Found at i:109074 original size:21 final size:21
Alignment explanation
Indices: 109048--109122 Score: 68
Period size: 20 Copynumber: 3.7 Consensus size: 21
109038 TTAGTATGAT
109048 AATTTTTATAATTTTTTTATG
1 AATTTTTATAATTTTTTTATG
*
109069 AA-TTTTAT-ATTTCTTTAT-
1 AATTTTTATAATTTTTTTATG
*
109087 -ATTTTCTATAATTTTCTTATG
1 AATTTT-TATAATTTTTTTATG
* * *
109108 ACTTTATAAAATTTT
1 AATTTTTATAATTTT
109123 ATAATTTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
17 1 0.02
18 3 0.07
19 12 0.28
20 14 0.33
21 10 0.23
22 3 0.07
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (21 bp):
AATTTTTATAATTTTTTTATG
Found at i:109100 original size:10 final size:9
Alignment explanation
Indices: 109046--109191 Score: 75
Period size: 9 Copynumber: 15.1 Consensus size: 9
109036 TTTTAGTATG
109046 ATAATTTTT
1 ATAATTTTT
109055 ATAATTTTTTT
1 ATAA--TTTTT
109066 ATGAA-TTTT
1 AT-AATTTTT
*
109075 ATATTTCTTT
1 ATAATT-TTT
109085 AT-ATTTTCT
1 ATAATTTT-T
109094 ATAATTTTCTT
1 ATAA-TTT-TT
* *
109105 ATGA-CTTT
1 ATAATTTTT
*
109113 ATAAAATTTT
1 AT-AATTTTT
109123 ATAATTTTTTT
1 ATAA--TTTTT
*
109134 CTATATTTTT
1 ATA-ATTTTT
*
109144 CT-ATATTTT
1 ATAAT-TTTT
109153 ATAATTTTT
1 ATAATTTTT
109162 ATAATTTTTTT
1 ATAA--TTTTT
*
109173 ATGATTTTT
1 ATAATTTTT
109182 ATAATTTTT
1 ATAATTTTT
109191 A
1 A
109192 ATAAAATTTA
Statistics
Matches: 108, Mismatches: 11, Indels: 36
0.70 0.07 0.23
Matches are distributed among these distances:
8 9 0.08
9 47 0.44
10 20 0.19
11 28 0.26
12 4 0.04
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (9 bp):
ATAATTTTT
Found at i:109124 original size:68 final size:66
Alignment explanation
Indices: 109051--109193 Score: 166
Period size: 68 Copynumber: 2.1 Consensus size: 66
109041 GTATGATAAT
*
109051 TTTTATAATTTTTT-TATGAATTTTATATTTCTTTAT-ATTTTCTATAATTTTCTTATGACTTTA
1 TTTTATAATTTTTTCTAT-AATTTTATATAT-TTTATAATTTT-TATAATTTTCTTATGA-TTTA
109114 TAAAA
62 TAAAA
* * * * *
109119 TTTTATAATTTTTTTCTATATTTTTCTATATTTTATAATTTTTATAATTTTTTTATGATTTTTAT
1 TTTTATAA-TTTTTTCTATAATTTTATATATTTTATAATTTTTATAATTTTCTTATGATTTATAA
109184 AA
65 AA
109186 TTTT-TAAT
1 TTTTATAAT
109194 AAAATTTAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 9
0.81 0.07 0.11
Matches are distributed among these distances:
65 1 0.02
66 3 0.05
67 11 0.17
68 28 0.42
69 20 0.30
70 3 0.05
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (66 bp):
TTTTATAATTTTTTCTATAATTTTATATATTTTATAATTTTTATAATTTTCTTATGATTTATAAA
A
Found at i:109130 original size:39 final size:38
Alignment explanation
Indices: 109046--109169 Score: 103
Period size: 39 Copynumber: 3.2 Consensus size: 38
109036 TTTTAGTATG
* *
109046 ATAATTTT-TATAATTTTTTTATGAATTT-TATATTTCT
1 ATAATTTTCTATAATTTTCTTATGAATTTATAAATTT-T
* *
109083 TTATATTTTCTATAATTTTCTTATGACTTTATAAAATTTT
1 ATA-ATTTTCTATAATTTTCTTATGAATTTAT-AAATTTT
* * *
109123 ATAATTTTTTTCTATATTTTTC-TAT-ATTTTATAATTTTT
1 ATAA---TTTTCTATAATTTTCTTATGAATTTATAAATTTT
109162 ATAATTTT
1 ATAATTTT
109170 TTTATGATTT
Statistics
Matches: 72, Mismatches: 8, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
36 4 0.06
37 2 0.03
38 5 0.07
39 29 0.40
40 10 0.14
41 8 0.11
42 14 0.19
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.65
Consensus pattern (38 bp):
ATAATTTTCTATAATTTTCTTATGAATTTATAAATTTT
Found at i:109152 original size:20 final size:19
Alignment explanation
Indices: 109119--109275 Score: 71
Period size: 20 Copynumber: 8.2 Consensus size: 19
109109 CTTTATAAAA
*
109119 TTTTATAATTTTTTTCTATAT
1 TTTTATAA--TTTTTATATAT
*
109140 TTTTCT-ATATTTTATA-AT
1 TTTTATAAT-TTTTATATAT
*
109158 TTTTATAATTTTTTTATGAT
1 TTTTATAATTTTTATAT-AT
*
109178 TTTTATAATTTTTA-ATAAA
1 TTTTATAATTTTTATAT-AT
* * *
109197 ATTTAAATATTTTTTTATAGTT
1 TTTTATA-ATTTTTATATA--T
**
109219 TTTTATTAAAATTTA-ATAT
1 TTTTA-TAATTTTTATATAT
*
109238 TTTT-T-ACTTTTAT-TAT
1 TTTTATAATTTTTATATAT
109254 TTTT-TAATTTTT-TATCAT
1 TTTTATAATTTTTATAT-AT
109272 TTTT
1 TTTT
109276 TGCCATATGT
Statistics
Matches: 104, Mismatches: 19, Indels: 29
0.68 0.12 0.19
Matches are distributed among these distances:
16 14 0.13
17 7 0.07
18 20 0.19
19 21 0.20
20 23 0.22
21 10 0.10
22 8 0.08
23 1 0.01
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.68
Consensus pattern (19 bp):
TTTTATAATTTTTATATAT
Found at i:109160 original size:17 final size:17
Alignment explanation
Indices: 109046--109193 Score: 64
Period size: 20 Copynumber: 7.8 Consensus size: 17
109036 TTTTAGTATG
109046 ATAATTTTTATAATTTTTTT
1 ATAA-TTTTATAA--TTTTT
*
109066 ATGAATTTTATATTTCTTT
1 AT-AATTTTATAATT-TTT
*
109085 ATATTTTCTATAATTTTCTT
1 ATAATTT-TATAA-TTT-TT
* * *
109105 ATGACTTTATAAAATTTT
1 ATAATTTTAT-AATTTTT
*
109123 ATAATTTTTTTCTATATTTTT
1 ATAA---TTTTATA-ATTTTT
*
109144 CTATATTTTATAATTTTT
1 ATA-ATTTTATAATTTTT
*
109162 ATAATTTTTTTATGATTTTT
1 ATAA---TTTTATAATTTTT
109182 ATAATTTT-TAAT
1 ATAATTTTATAAT
109194 AAAATTTAAA
Statistics
Matches: 98, Mismatches: 16, Indels: 32
0.67 0.11 0.22
Matches are distributed among these distances:
16 3 0.03
17 5 0.05
18 19 0.19
19 21 0.21
20 36 0.37
21 13 0.13
22 1 0.01
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (17 bp):
ATAATTTTATAATTTTT
Found at i:109172 original size:39 final size:42
Alignment explanation
Indices: 109088--109172 Score: 122
Period size: 39 Copynumber: 2.1 Consensus size: 42
109078 TTTCTTTATA
109088 TTTTCTATAATTTTCTTATGACTTTATAAAATTTTATAATTT
1 TTTTCTATAATTTTCTTATGACTTTATAAAATTTTATAATTT
* * *
109130 TTTTCTATATTTTTC-TAT-ATTTTAT-AATTTTTATAATTT
1 TTTTCTATAATTTTCTTATGACTTTATAAAATTTTATAATTT
109169 TTTT
1 TTTT
109173 ATGATTTTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
39 17 0.43
40 6 0.15
41 3 0.08
42 14 0.35
ACGTcount: A:0.27, C:0.06, G:0.01, T:0.66
Consensus pattern (42 bp):
TTTTCTATAATTTTCTTATGACTTTATAAAATTTTATAATTT
Found at i:109215 original size:31 final size:31
Alignment explanation
Indices: 109177--109242 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
109167 TTTTTTATGA
109177 TTTTTATA-ATTTTTAATAAAATTTAAATATT
1 TTTTTATAGATTTTTAATAAAATTT-AATATT
* *
109208 TTTTTATAGTTTTTTATTAAAATTTAATATT
1 TTTTTATAGATTTTTAATAAAATTTAATATT
109239 TTTT
1 TTTT
109243 ACTTTTATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 18 0.56
32 14 0.44
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (31 bp):
TTTTTATAGATTTTTAATAAAATTTAATATT
Found at i:109254 original size:16 final size:16
Alignment explanation
Indices: 109230--109268 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
109220 TTTATTAAAA
* *
109230 TTTAATATTTTTTACT
1 TTTATTATTTTTTAAT
109246 TTTATTATTTTTTAAT
1 TTTATTATTTTTTAAT
109262 TTT-TTAT
1 TTTATTAT
109269 CATTTTTTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTATTATTTTTTAAT
Found at i:111137 original size:6 final size:6
Alignment explanation
Indices: 111128--111158 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
111118 ATAGACATAA
111128 CTCCAC CTCCAC CTCCAC CTCCAC CTCCAC C
1 CTCCAC CTCCAC CTCCAC CTCCAC CTCCAC C
111159 CAACCTGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.68, G:0.00, T:0.16
Consensus pattern (6 bp):
CTCCAC
Done.