Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009434.1 Kokia drynarioides strain JFW-HI SEQ_124141, 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: 185263
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3284 original size:12 final size:13
Alignment explanation
Indices: 3258--3285 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3248 TTAAGTTTAA
3258 TTTAAAAATATTT
1 TTTAAAAATATTT
3271 TTTAAAAATATTT
1 TTTAAAAATATTT
3284 TT
1 TT
3286 GTTCGGGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTAAAAATATTT
Found at i:3411 original size:17 final size:17
Alignment explanation
Indices: 3361--3415 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
3351 GAAAAAACCC
3361 TTTTTATCTCGAAAAATA
1 TTTTTATCTC-AAAAATA
* * *
3379 -ATTTAT-TTATAAATA
1 TTTTTATCTCAAAAATA
3394 TTTTTATCTCAAAAATA
1 TTTTTATCTCAAAAATA
3411 TTTTT
1 TTTTT
3416 TAAAAACAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
15 6 0.21
16 6 0.21
17 17 0.59
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (17 bp):
TTTTTATCTCAAAAATA
Found at i:3965 original size:20 final size:19
Alignment explanation
Indices: 3924--3963 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
3914 AAATATCATA
*
3924 TAAATAAATTTAATATATT
1 TAAATAAATTTAAAATATT
3943 TAAATTAAATTTTAAAATATT
1 TAAA-TAAA-TTTAAAATATT
3964 AATTTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 4 0.22
21 10 0.56
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TAAATAAATTTAAAATATT
Found at i:9901 original size:23 final size:23
Alignment explanation
Indices: 9874--9938 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
9864 CCCAATCCAG
** *
9874 ATTGATCGAACCTGGCCCGACCT
1 ATTGATCGAACCTAACCCGACCC
*
9897 ATTGATCGAACCCAACCCGACCC
1 ATTGATCGAACCTAACCCGACCC
*
9920 ATTGATCAAACCTAACCCG
1 ATTGATCGAACCTAACCCG
9939 TTGACCAACC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.29, C:0.37, G:0.15, T:0.18
Consensus pattern (23 bp):
ATTGATCGAACCTAACCCGACCC
Found at i:17166 original size:24 final size:23
Alignment explanation
Indices: 17139--17215 Score: 75
Period size: 24 Copynumber: 3.3 Consensus size: 23
17129 GACCTGTCGA
* *
17139 TTGACCTAACCCAAATCGTTGACT
1 TTGACC-AACCCGAACCGTTGACT
**
17163 TTGAACCAACTTGAACCGTTGACT
1 TTG-ACCAACCCGAACCGTTGACT
*
17187 TTGACCGAA-CCGAACCGTTAACT
1 TTGACC-AACCCGAACCGTTGACT
17210 TTGACC
1 TTGACC
17216 GATCGTTGAC
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
23 20 0.45
24 21 0.48
25 3 0.07
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.27
Consensus pattern (23 bp):
TTGACCAACCCGAACCGTTGACT
Found at i:17205 original size:23 final size:24
Alignment explanation
Indices: 17155--17217 Score: 85
Period size: 23 Copynumber: 2.7 Consensus size: 24
17145 TAACCCAAAT
*
17155 CGTTGACTTTGAACC-AACTTGAAC
1 CGTTGACTTTG-ACCGAACTCGAAC
17179 CGTTGACTTTGACCGAAC-CGAAC
1 CGTTGACTTTGACCGAACTCGAAC
*
17202 CGTTAACTTTGACCGA
1 CGTTGACTTTGACCGA
17218 TCGTTGACTT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
23 22 0.61
24 14 0.39
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (24 bp):
CGTTGACTTTGACCGAACTCGAAC
Found at i:18487 original size:8 final size:8
Alignment explanation
Indices: 18474--18498 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
18464 TCTGGATCCG
18474 ATCATATA
1 ATCATATA
18482 ATCATATA
1 ATCATATA
18490 ATCATATA
1 ATCATATA
18498 A
1 A
18499 CCTTTGATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (8 bp):
ATCATATA
Found at i:21414 original size:29 final size:28
Alignment explanation
Indices: 21355--21424 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
21345 AAAAATTCAA
*
21355 AAAAATATAAAAATTATTTTTAAAAATT
1 AAAAATATAAAAATTATTTTGAAAAATT
* *
21383 AAAAATCATTAAAATTA-TTTGAAAAGTAT
1 AAAAAT-ATAAAAATTATTTTGAAAAAT-T
*
21412 AAAAATAAAAAAA
1 AAAAATATAAAAA
21425 ATGAATATAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 19 0.54
29 16 0.46
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.31
Consensus pattern (28 bp):
AAAAATATAAAAATTATTTTGAAAAATT
Found at i:28169 original size:31 final size:31
Alignment explanation
Indices: 28125--28190 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 31
28115 TATAAATTTT
* *
28125 TTTTATCCAATTTGGTA-TTCAAACTTGACAC
1 TTTTATCCAATTTGGTACCT-AAACATGACAC
28156 TTTT-TCCTAATTTGGTACCTAAACATGACAC
1 TTTTATCC-AATTTGGTACCTAAACATGACAC
28187 TTTT
1 TTTT
28191 CTTAAGTTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 3 0.10
31 27 0.87
32 1 0.03
ACGTcount: A:0.27, C:0.20, G:0.09, T:0.44
Consensus pattern (31 bp):
TTTTATCCAATTTGGTACCTAAACATGACAC
Found at i:28201 original size:30 final size:31
Alignment explanation
Indices: 28145--28208 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 31
28135 TTTGGTATTC
* *
28145 AAACTTGACACTTTTTCCTAATTTGGTACCT
1 AAACATGACACTTTTTCCTAAGTTGGTACCT
* *
28176 AAACATGACAC-TTTTCTTAAGTTGGTACTT
1 AAACATGACACTTTTTCCTAAGTTGGTACCT
28206 AAA
1 AAA
28209 TTTTTTGGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 19 0.66
31 10 0.34
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (31 bp):
AAACATGACACTTTTTCCTAAGTTGGTACCT
Found at i:29211 original size:51 final size:51
Alignment explanation
Indices: 29135--29244 Score: 202
Period size: 51 Copynumber: 2.2 Consensus size: 51
29125 AAATATACTA
*
29135 ACAGTCATAATTAAGAGTCATTAAAAGTGCTAAAGTTGACCGAGTCCCTCG
1 ACAGTCATAATTAAGAGTCATTAAAAGTGCTAAAGGTGACCGAGTCCCTCG
29186 ACAGTCATAATTAAGAGTCATTAAAAGTGCTAAAGGTGACCGAGTCCCTCG
1 ACAGTCATAATTAAGAGTCATTAAAAGTGCTAAAGGTGACCGAGTCCCTCG
*
29237 ACCGTCAT
1 ACAGTCAT
29245 GCTTGAGAAG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 57 1.00
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.25
Consensus pattern (51 bp):
ACAGTCATAATTAAGAGTCATTAAAAGTGCTAAAGGTGACCGAGTCCCTCG
Found at i:39640 original size:18 final size:18
Alignment explanation
Indices: 39617--39654 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
39607 TATTCCATGC
39617 CATTGTGTAGGTATAGAA
1 CATTGTGTAGGTATAGAA
39635 CATTGTGTAGGTATAGAA
1 CATTGTGTAGGTATAGAA
39653 CA
1 CA
39655 GGTTCTGCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.08, G:0.26, T:0.32
Consensus pattern (18 bp):
CATTGTGTAGGTATAGAA
Found at i:52405 original size:43 final size:43
Alignment explanation
Indices: 52342--52428 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 43
52332 TTCGTGACAT
*
52342 TAAGAGCCACTCTTAAACGACAAAAATCTCCAAGAACCTCTGC
1 TAAGAACCACTCTTAAACGACAAAAATCTCCAAGAACCTCTGC
* *
52385 TAAGAACCACTCTTATACGACAAAAATCTCCAAGAACCTTTGC
1 TAAGAACCACTCTTAAACGACAAAAATCTCCAAGAACCTCTGC
52428 T
1 T
52429 CGACGTAAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.39, C:0.29, G:0.10, T:0.22
Consensus pattern (43 bp):
TAAGAACCACTCTTAAACGACAAAAATCTCCAAGAACCTCTGC
Found at i:53934 original size:18 final size:18
Alignment explanation
Indices: 53913--53956 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
53903 AAGAATATAA
*
53913 AAATATTTAACAATTTAT
1 AAATATTTAACAAATTAT
*
53931 AAATATATAACAAATTAT
1 AAATATTTAACAAATTAT
53949 AAA-ATTTA
1 AAATATTTA
53957 TTTTCCTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (18 bp):
AAATATTTAACAAATTAT
Found at i:54076 original size:16 final size:16
Alignment explanation
Indices: 54051--54104 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 16
54041 TATTATTTTG
*
54051 AAATTAAAAATATATA
1 AAATTTAAAATATATA
*
54067 AAATTTAAAATATTTA
1 AAATTTAAAATATATA
54083 AAATTATATAAATATTATA
1 AAATT-TA-AAATA-TATA
54102 AAA
1 AAA
54105 AATATATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
16 19 0.59
17 2 0.06
18 5 0.16
19 6 0.19
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AAATTTAAAATATATA
Found at i:54101 original size:11 final size:10
Alignment explanation
Indices: 54055--54120 Score: 52
Period size: 10 Copynumber: 6.9 Consensus size: 10
54045 ATTTTGAAAT
*
54055 TAAAAATATA
1 TAAAATTATA
54065 TAAAA-T-T-
1 TAAAATTATA
*
54072 TAAAA-TATT
1 TAAAATTATA
54081 TAAAATTATA
1 TAAAATTATA
54091 TAAATATTATA
1 TAAA-ATTATA
*
54102 -AAAAATATA
1 TAAAATTATA
54111 TAAAACTTAT
1 TAAAA-TTAT
54121 TTCACTTTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
7 6 0.13
8 2 0.04
9 11 0.23
10 19 0.40
11 9 0.19
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (10 bp):
TAAAATTATA
Found at i:54120 original size:20 final size:20
Alignment explanation
Indices: 54061--54114 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
54051 AAATTAAAAA
* *
54061 TATATAAAATTTA-AAATAT
1 TATAAAAAATATATAAATAT
*
54080 T-T-AAAATTATATAAATAT
1 TATAAAAAATATATAAATAT
54098 TATAAAAAATATATAAA
1 TATAAAAAATATATAAA
54115 ACTTATTTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
17 6 0.21
18 8 0.29
19 2 0.07
20 12 0.43
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TATAAAAAATATATAAATAT
Found at i:60257 original size:16 final size:16
Alignment explanation
Indices: 60238--60284 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
60228 AATTTTCAAT
60238 AAATAAAAAATATATA
1 AAATAAAAAATATATA
**
60254 AAATTATTAAATAT-TA
1 AAA-TAAAAAATATATA
60270 AAATAAAACAATATA
1 AAATAAAA-AATATA
60285 AATATTTTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
15 3 0.12
16 13 0.54
17 8 0.33
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATAAAAAATATATA
Found at i:61693 original size:21 final size:21
Alignment explanation
Indices: 61659--61708 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
61649 AATGTCAATC
* * *
61659 CCATAAATAGTGGAATCAAGT
1 CCATAAACAATGGAATCAAAT
*
61680 CCATAAACAATGGAGTCAAAT
1 CCATAAACAATGGAATCAAAT
61701 -CATAAACA
1 CCATAAACA
61709 GTAACAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.48, C:0.18, G:0.14, T:0.20
Consensus pattern (21 bp):
CCATAAACAATGGAATCAAAT
Found at i:62876 original size:27 final size:27
Alignment explanation
Indices: 62837--62909 Score: 110
Period size: 27 Copynumber: 2.7 Consensus size: 27
62827 CCATGGCCAT
*
62837 GGGCTTTCAATATAAGAGATTCGTCAC
1 GGGCTTTCCATATAAGAGATTCGTCAC
* *
62864 GGGCTTTCCATATCAGAGATTCGTCAT
1 GGGCTTTCCATATAAGAGATTCGTCAC
*
62891 GGGCTTTCCATATGAGAGA
1 GGGCTTTCCATATAAGAGA
62910 ATAGAATGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (27 bp):
GGGCTTTCCATATAAGAGATTCGTCAC
Found at i:65610 original size:18 final size:18
Alignment explanation
Indices: 65587--65621 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
65577 AAAAAATTGT
*
65587 AAGCATCAAAATGGTTTC
1 AAGCATCAAAATAGTTTC
*
65605 AAGCATGAAAATAGTTT
1 AAGCATCAAAATAGTTT
65622 GACACATCAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.29
Consensus pattern (18 bp):
AAGCATCAAAATAGTTTC
Found at i:66868 original size:21 final size:20
Alignment explanation
Indices: 66840--66881 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
66830 CCTCAAAATC
66840 CATCTCAT-TGTCTCCCTCCT
1 CATCTCATCT-TCTCCCTCCT
*
66860 CATCGTCATCTTCTCCTTCCT
1 CATC-TCATCTTCTCCCTCCT
66881 C
1 C
66882 TTTGCTCTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 14 0.74
22 1 0.05
ACGTcount: A:0.10, C:0.45, G:0.05, T:0.40
Consensus pattern (20 bp):
CATCTCATCTTCTCCCTCCT
Found at i:77073 original size:12 final size:12
Alignment explanation
Indices: 77043--77081 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
77033 GTATTGAGGT
77043 AGAAAAAGAAGA
1 AGAAAAAGAAGA
77055 A-AGAAAAGAAGA
1 AGA-AAAAGAAGA
*
77067 AGAAAAAGGAGA
1 AGAAAAAGAAGA
77079 AGA
1 AGA
77082 CATTGTCCCG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
11 1 0.04
12 22 0.92
13 1 0.04
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
AGAAAAAGAAGA
Found at i:77509 original size:17 final size:18
Alignment explanation
Indices: 77489--77528 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
77479 ATTGTCATTA
77489 CATTTTTA-TTG-TCTCTG
1 CATTTTTACTTGTTCTC-G
77506 CA-TTTTACTTGTTCTCG
1 CATTTTTACTTGTTCTCG
77523 CATTTT
1 CATTTT
77529 CATTATCGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
16 5 0.25
17 8 0.40
18 7 0.35
ACGTcount: A:0.12, C:0.20, G:0.10, T:0.57
Consensus pattern (18 bp):
CATTTTTACTTGTTCTCG
Found at i:86822 original size:17 final size:17
Alignment explanation
Indices: 86800--86833 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
86790 TATCAATCGC
86800 TATACGTCTATTTCCAT
1 TATACGTCTATTTCCAT
86817 TATACGTCTATTTCCAT
1 TATACGTCTATTTCCAT
86834 GCAAAACAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.06, T:0.47
Consensus pattern (17 bp):
TATACGTCTATTTCCAT
Found at i:92974 original size:27 final size:27
Alignment explanation
Indices: 92936--92987 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
92926 CGACATAACC
92936 CATGTATGCCACGACAAAGAAGTCAGT
1 CATGTATGCCACGACAAAGAAGTCAGT
92963 CATGTATGCCACGACAAAGAAGTCA
1 CATGTATGCCACGACAAAGAAGTCA
92988 ATCTTCACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.17
Consensus pattern (27 bp):
CATGTATGCCACGACAAAGAAGTCAGT
Found at i:103832 original size:17 final size:17
Alignment explanation
Indices: 103764--103843 Score: 79
Period size: 17 Copynumber: 4.6 Consensus size: 17
103754 CATTAAATTA
103764 CAATGACAAATGGAAATG
1 CAATGAC-AATGGAAATG
*
103782 CAATGACAATGCAAATG
1 CAATGACAATGGAAATG
* **
103799 CAGTGACAATTAAAATG
1 CAATGACAATGGAAATG
* *
103816 TAATGACAATGGGAATG
1 CAATGACAATGGAAATG
**
103833 TGATGACAATG
1 CAATGACAATG
103844 CTTACTAACA
Statistics
Matches: 52, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
17 45 0.87
18 7 0.13
ACGTcount: A:0.45, C:0.11, G:0.23, T:0.21
Consensus pattern (17 bp):
CAATGACAATGGAAATG
Found at i:104289 original size:12 final size:12
Alignment explanation
Indices: 104272--104311 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
104262 TTCCTCAGCT
*
104272 TCTTTTCCTTCC
1 TCTTTTTCTTCC
104284 TCTTTTTCTTCC
1 TCTTTTTCTTCC
104296 T-TTTCTTCTTCC
1 TCTTT-TTCTTCC
104308 TCTT
1 TCTT
104312 CTTCAACTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 3 0.12
12 20 0.80
13 2 0.08
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (12 bp):
TCTTTTTCTTCC
Found at i:104313 original size:12 final size:12
Alignment explanation
Indices: 104279--104315 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
104269 GCTTCTTTTC
*
104279 CTTCCTCTTTTT
1 CTTCCTCTTCTT
*
104291 CTTCCTTTTCTT
1 CTTCCTCTTCTT
104303 CTTCCTCTTCTT
1 CTTCCTCTTCTT
104315 C
1 C
104316 AACTTGCATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (12 bp):
CTTCCTCTTCTT
Found at i:112345 original size:14 final size:15
Alignment explanation
Indices: 112315--112348 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
112305 ATTCAAGAAG
112315 AAAATCAATTCGAAA
1 AAAATCAATTCGAAA
112330 AAAATCAA-TCTGAAA
1 AAAATCAATTC-GAAA
112345 AAAA
1 AAAA
112349 GACTCCTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 2 0.11
15 16 0.89
ACGTcount: A:0.65, C:0.12, G:0.06, T:0.18
Consensus pattern (15 bp):
AAAATCAATTCGAAA
Found at i:115915 original size:22 final size:23
Alignment explanation
Indices: 115890--115935 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
115880 ATTTTGTTCA
115890 ACTTTAACTT-TTAT-TCAATAAC
1 ACTTTAACTTGTTATATCAA-AAC
*
115912 ACTTTAATTTGTTATATCAAAAC
1 ACTTTAACTTGTTATATCAAAAC
115935 A
1 A
115936 TATTATCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 9 0.43
23 8 0.38
24 4 0.19
ACGTcount: A:0.39, C:0.15, G:0.02, T:0.43
Consensus pattern (23 bp):
ACTTTAACTTGTTATATCAAAAC
Found at i:116311 original size:8 final size:8
Alignment explanation
Indices: 116298--116328 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
116288 AACCTTTTTA
116298 TTTTATTT
1 TTTTATTT
116306 TTTTATTT
1 TTTTATTT
116314 TTTTA-TT
1 TTTTATTT
116321 TTTTATTT
1 TTTTATTT
116329 AGGATAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.32
8 15 0.68
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTATTT
Found at i:116322 original size:15 final size:16
Alignment explanation
Indices: 116298--116328 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
116288 AACCTTTTTA
116298 TTTTATTTTTTTATTT
1 TTTTATTTTTTTATTT
116314 TTTTA-TTTTTTATTT
1 TTTTATTTTTTTATTT
116329 AGGATAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (16 bp):
TTTTATTTTTTTATTT
Found at i:121563 original size:16 final size:15
Alignment explanation
Indices: 121544--121589 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
121534 GTCGTTTGTC
121544 TATTTTATTATGTACA
1 TATTTTATTATGTA-A
*
121560 TATTTTATTTATTTAA
1 TATTTTA-TTATGTAA
121576 T-TTTTATTAT-TAA
1 TATTTTATTATGTAA
121589 T
1 T
121590 CTCTTTTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 4 0.14
14 4 0.14
15 5 0.18
16 9 0.32
17 6 0.21
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (15 bp):
TATTTTATTATGTAA
Found at i:126923 original size:26 final size:25
Alignment explanation
Indices: 126860--126926 Score: 82
Period size: 26 Copynumber: 2.6 Consensus size: 25
126850 TAATTTAAAG
*
126860 AAATATCTTTTAAA-TAATTAATATA
1 AAATAT-TTTAAAATTAATTAATATA
*
126885 AATTATTTGTAAAATTAATTATATATA
1 AAATATTT-TAAAATTAATTA-ATATA
126912 AAATATTTTAAAATT
1 AAATATTTTAAAATT
126927 TTAAATATAG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
24 2 0.06
25 9 0.25
26 13 0.36
27 12 0.33
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (25 bp):
AAATATTTTAAAATTAATTAATATA
Found at i:126935 original size:28 final size:27
Alignment explanation
Indices: 126880--126935 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 27
126870 TAAATAATTA
* *
126880 ATATAAATTATTTGTAAAATTAATTAT
1 ATATAAAATATTTGTAAAATTAAATAT
126907 ATATAAAATATTT-TAAAATTTTAAATAT
1 ATATAAAATATTTGTAAAA--TTAAATAT
126935 A
1 A
126936 GTGGTAAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 5 0.20
27 12 0.48
28 8 0.32
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (27 bp):
ATATAAAATATTTGTAAAATTAAATAT
Found at i:130012 original size:87 final size:87
Alignment explanation
Indices: 129913--130088 Score: 280
Period size: 87 Copynumber: 2.0 Consensus size: 87
129903 GGCTACTCCT
* * * *
129913 GAGGCGCTTGGGCATTGGCAACAAAAGATGTATAAAGACAATAAAGGTCGCATGAACTTTTTTAT
1 GAGGCGCGTGGGCATTGGCAACAAAAGAGGTATAAAGACAACAAAGGTCGCATGAACTTTTTGAT
129978 TAGAGAGATTGATAAACTTGTA
66 TAGAGAGATTGATAAACTTGTA
** * *
130000 GAGGCGCGTGGGCATTGGCAATTAAAGAGGTATAGAGACAACAAAGGTTGCATGAACTTTTTGAT
1 GAGGCGCGTGGGCATTGGCAACAAAAGAGGTATAAAGACAACAAAGGTCGCATGAACTTTTTGAT
130065 TAGAGAGATTGATAAACTTGTA
66 TAGAGAGATTGATAAACTTGTA
130087 GA
1 GA
130089 TAAGTAGAGG
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 81 1.00
ACGTcount: A:0.36, C:0.11, G:0.27, T:0.27
Consensus pattern (87 bp):
GAGGCGCGTGGGCATTGGCAACAAAAGAGGTATAAAGACAACAAAGGTCGCATGAACTTTTTGAT
TAGAGAGATTGATAAACTTGTA
Found at i:150202 original size:12 final size:12
Alignment explanation
Indices: 150182--150216 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
150172 TAAATAAACA
*
150182 ATAGCATTCATT
1 ATAGAATTCATT
150194 ATAGAATTCATT
1 ATAGAATTCATT
*
150206 ATAGTATTCAT
1 ATAGAATTCAT
150217 CATAACAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (12 bp):
ATAGAATTCATT
Found at i:154210 original size:15 final size:15
Alignment explanation
Indices: 154190--154219 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
154180 TCAGTCACAT
154190 GAAAAAAAAGAAAAA
1 GAAAAAAAAGAAAAA
*
154205 GAAAAAGAAGAAAAA
1 GAAAAAAAAGAAAAA
154220 AATTTATGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
GAAAAAAAAGAAAAA
Found at i:158948 original size:31 final size:31
Alignment explanation
Indices: 158912--158990 Score: 95
Period size: 35 Copynumber: 2.4 Consensus size: 31
158902 AAATTAATTT
158912 GTTAGTAAGTAATTTTATTTTGTTAGTAGTA
1 GTTAGTAAGTAATTTTATTTTGTTAGTAGTA
*
158943 GTTAGTAAGTAAGTAATTTTGTTTTGTTAGTAGTA
1 G-T--T-AGTAAGTAATTTTATTTTGTTAGTAGTA
* *
158978 GTAAGTAATTAAT
1 GTTAGTAAGTAAT
158991 ATAAATTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
31 10 0.24
32 1 0.02
34 2 0.05
35 28 0.68
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (31 bp):
GTTAGTAAGTAATTTTATTTTGTTAGTAGTA
Found at i:158954 original size:35 final size:35
Alignment explanation
Indices: 158915--158985 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
158905 TTAATTTGTT
*
158915 AGTAAGTAATTTTATTTTGTTAGTAGTAGTTAGTA
1 AGTAAGTAATTTTATTTTGTTAGTAGTAGTAAGTA
*
158950 AGTAAGTAATTTTGTTTTGTTAGTAGTAGTAAGTA
1 AGTAAGTAATTTTATTTTGTTAGTAGTAGTAAGTA
158985 A
1 A
158986 TTAATATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.46
Consensus pattern (35 bp):
AGTAAGTAATTTTATTTTGTTAGTAGTAGTAAGTA
Found at i:160421 original size:43 final size:44
Alignment explanation
Indices: 160330--160429 Score: 107
Period size: 43 Copynumber: 2.3 Consensus size: 44
160320 TTATTCATTA
* * * *
160330 ACATGTTACTAAATCATATTACTTTATTTGTGTTAAAATGGTTG
1 ACATGTTACTAAATCATATTACTTGATCTGTATTAAAATGCTTG
* *
160374 -CATGTTACTAAATTATATTACTTGACTCT-TATTAATAT-CTTG
1 ACATGTTACTAAATCATATTACTTGA-TCTGTATTAAAATGCTTG
*
160416 ACATGTTATTAAAT
1 ACATGTTACTAAAT
160430 GTGTAGTTCA
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
42 3 0.06
43 42 0.89
44 2 0.04
ACGTcount: A:0.33, C:0.11, G:0.10, T:0.46
Consensus pattern (44 bp):
ACATGTTACTAAATCATATTACTTGATCTGTATTAAAATGCTTG
Found at i:161342 original size:7 final size:7
Alignment explanation
Indices: 161327--161386 Score: 59
Period size: 7 Copynumber: 8.7 Consensus size: 7
161317 GTCTTTGATT
161327 CCCTAAA
1 CCCTAAA
*
161334 CCTTAAA
1 CCCTAAA
161341 CCCTAAA
1 CCCTAAA
*
161348 CCC-CAA
1 CCCTAAA
* *
161354 TCATAAA
1 CCCTAAA
*
161361 CCCAAAA
1 CCCTAAA
*
161368 CCCAAAA
1 CCCTAAA
161375 CCCTAAA
1 CCCTAAA
161382 CCCTA
1 CCCTA
161387 TACACCTTAA
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
6 3 0.07
7 39 0.93
ACGTcount: A:0.45, C:0.42, G:0.00, T:0.13
Consensus pattern (7 bp):
CCCTAAA
Found at i:163793 original size:24 final size:24
Alignment explanation
Indices: 163766--163815 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
163756 CACCATACAC
163766 GGAGTTGGATCTTCATTTTCTACT
1 GGAGTTGGATCTTCATTTTCTACT
*
163790 GGAGTTGGATCTTCATTTTGTACT
1 GGAGTTGGATCTTCATTTTCTACT
163814 GG
1 GG
163816 TTCCAAATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.16, C:0.14, G:0.26, T:0.44
Consensus pattern (24 bp):
GGAGTTGGATCTTCATTTTCTACT
Found at i:167080 original size:564 final size:566
Alignment explanation
Indices: 166001--167123 Score: 1738
Period size: 564 Copynumber: 2.0 Consensus size: 566
165991 ATTCTGTAAA
* *
166001 ATCTTGTTCTGTACTATCCATGAGATCTCTATAGCCAAGTAATAACCATACCTCTTTTGCAATAG
1 ATCTTGTTCTGTACTATCCATGAGATCTCTATAGCCAAGTAATAACCATACCTCTTTTACAATAA
* *
166066 GGAACCTTCTAAAAACATGGTTTGCATCCTCGGGTTCCAAATTACATCTGGGGCACACTGTTGTA
66 GGAACCTTCTAAAAACATGGTTTACATCCTCGGGTTCCAAATTACATCTGGGGCACACTGTTATA
* *
166131 GTCACCAATATTTTGCACAACATATTTTTCAAAGTGGGGAAAAAAATTCAGAAAGAATTGCTAAA
131 GTCACCAATATTTTGCACAACATATTTTTCAAAGTGGGGAAAAAAATTCAGAAAGAATCGCCAAA
* * * *
166196 TCATAATTTTAATTTTTGATGGGATGTTTAAACCTCGAAGTTGTTTGTAGAAGTTCCTATATTTG
196 TCATAATTTTAATTTTTGATAGGATGTTTAAACCTCAAAGTTGTTTGTAAAAGTTCCTATATTCG
* * * * *
166261 AGCTGTAAATTATTAAACATAGGATTAGTGTGCTTTCTTGTAACAATTTGTATGCACTCTTGATT
261 AGCTGTAAATTATTAAACATAAGATTAGTGTGCTTTCTAGTAACAATTTGTAAGCACTCATGACT
* * * ** *
166326 GAGAAATCGCCAACCGGTTCCCCACCCCACACCATCTCATTGACCTTTGGAAACGATGACAACAT
326 AAGAAATCGCCAACCGGTTCCCCACCCCACACAATCTCATCGACCCCTAGAAACGATGACAACAT
**
166391 CATTTGCATAATATGAGCCGTATCATCCGCAACAAAATTCATGGTAACGAGATCTCTATCCCACT
391 CATTTGCATAATATGAGCCACATCATCCGCAACAAAATTCATGGTAACGAGATCTCTATCCCACT
* * *
166456 GTCTAGTATTACTATTTATCAAATTTGCTACTGTTGAGATAGTAGGAGTAGCATTAAGACACCAT
456 GTCTAGTATTACTATTTATCAAATCTGCCACTGTTGAGATAGTAGGAGTAGCACTAAGACACCAT
*
166521 AACTCATAATTTGGTAGACCAAGTAATCAAGATTGATTACCATGAG
521 AACTCATAATTTGGTAGACCAAGTAACCAAGATTGATTACCATGAG
*
166567 ATCTTGTTCTGTACTATCCATGAGATCTCTGTAGCCAAGTAATAACCATACCTCTTTTACAATAA
1 ATCTTGTTCTGTACTATCCATGAGATCTCTATAGCCAAGTAATAACCATACCTCTTTTACAATAA
* * *
166632 GGCACCTTTTAAAAACATGGTTTACATCCTTGGGTTCCAAATTACATCTGGGGCACACTGTTATA
66 GGAACCTTCTAAAAACATGGTTTACATCCTCGGGTTCCAAATTACATCTGGGGCACACTGTTATA
*
166697 GTCACTAATATTTTGCACAACATATTTTTCAAAGTGGGG-AAAAAATTCA-AAGAGAATCGCCAA
131 GTCACCAATATTTTGCACAACATATTTTTCAAAGTGGGGAAAAAAATTCAGAA-AGAATCGCCAA
166760 ATCATAATTTTAATTTTTGATAGGATGTTTAAACC-CTAAAGTTGTTTGTAAAAGTTCCTATATT
195 ATCATAATTTTAATTTTTGATAGGATGTTTAAACCTC-AAAGTTGTTTGTAAAAGTTCCTATATT
166824 CGA-CTTGTAAATTATTAAACATAAGATTAGTGTGCTTTC-AGTAACAATTTGTAAGCACTCATG
259 CGAGC-TGTAAATTATTAAACATAAGATTAGTGTGCTTTCTAGTAACAATTTGTAAGCACTCATG
* * ** ** *
166887 ACTAAGAAATTGCTAGTCGGTTCCTTACCCCACACAATC-CTATCGACCCCTAGAGACGATGACA
323 ACTAAGAAATCGCCAACCGGTTCCCCACCCCACACAATCTC-ATCGACCCCTAGAAACGATGACA
* * * *
166951 ACGA-GATTTGTATAATATGAGCCACATCATCCGCAGCAAAATTCATGGTAATGAGATCTCTATC
387 AC-ATCATTTGCATAATATGAGCCACATCATCCGCAACAAAATTCATGGTAACGAGATCTCTATC
*
167015 CCATTGTCTAGTATTACTATTTATCAAATCTGCCACTGTTGAGATAGTAGGAGTAGCACTAAGAC
451 CCACTGTCTAGTATTACTATTTATCAAATCTGCCACTGTTGAGATAGTAGGAGTAGCACTAAGAC
* *
167080 ACCGTAACTCATAATTTGGTAGACCAGGTAACCAAGATTGATTA
516 ACCATAACTCATAATTTGGTAGACCAAGTAACCAAGATTGATTA
167124 AAAATTGAGA
Statistics
Matches: 506, Mismatches: 46, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
563 1 0.00
564 231 0.46
565 114 0.23
566 160 0.32
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (566 bp):
ATCTTGTTCTGTACTATCCATGAGATCTCTATAGCCAAGTAATAACCATACCTCTTTTACAATAA
GGAACCTTCTAAAAACATGGTTTACATCCTCGGGTTCCAAATTACATCTGGGGCACACTGTTATA
GTCACCAATATTTTGCACAACATATTTTTCAAAGTGGGGAAAAAAATTCAGAAAGAATCGCCAAA
TCATAATTTTAATTTTTGATAGGATGTTTAAACCTCAAAGTTGTTTGTAAAAGTTCCTATATTCG
AGCTGTAAATTATTAAACATAAGATTAGTGTGCTTTCTAGTAACAATTTGTAAGCACTCATGACT
AAGAAATCGCCAACCGGTTCCCCACCCCACACAATCTCATCGACCCCTAGAAACGATGACAACAT
CATTTGCATAATATGAGCCACATCATCCGCAACAAAATTCATGGTAACGAGATCTCTATCCCACT
GTCTAGTATTACTATTTATCAAATCTGCCACTGTTGAGATAGTAGGAGTAGCACTAAGACACCAT
AACTCATAATTTGGTAGACCAAGTAACCAAGATTGATTACCATGAG
Found at i:176788 original size:25 final size:23
Alignment explanation
Indices: 176760--176805 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
176750 GTTGGATCCA
176760 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAA-TCTAAAAA-ATAATTTG
*
176785 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
176806 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTTG
Found at i:177859 original size:29 final size:28
Alignment explanation
Indices: 177802--177859 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
177792 AGACATATTT
*
177802 TTTTCTTTTTCTTCTTTTTTTCTATCAA
1 TTTTCTTTTTCTTCTTTTTTTCTAACAA
*
177830 TTTTCTTTTT-TTTTCTTTTTTCTAAACAA
1 TTTTCTTTTTCTTCT-TTTTTTCT-AACAA
177859 T
1 T
177860 AAAATTCAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 3 0.12
28 18 0.69
29 5 0.19
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.71
Consensus pattern (28 bp):
TTTTCTTTTTCTTCTTTTTTTCTAACAA
Found at i:180324 original size:3 final size:3
Alignment explanation
Indices: 180318--180461 Score: 73
Period size: 3 Copynumber: 50.7 Consensus size: 3
180308 TATAAAGCAA
* * *
180318 AAT AAT AAT ATT AA- AA- AAT AAT AAT AAA AAGT -AT AAT AAT ACT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT
* *
180361 AAT AAT AAT GAT AAT AAT AA- ATCT AA- ACA- AAT AAT AAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT A-AT AAT AAT AAT AAT AAT
* *
180404 GAA- AGA- AAT AAT AA- AAT GAAA AAA AAT AAT AAT AA- AAT AA- AAT
1 -AAT A-AT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT
180447 AAT AA- AAT AA- AAT AA
1 AAT AAT AAT AAT AAT AA
180462 AGAAAAGTGA
Statistics
Matches: 112, Mismatches: 12, Indels: 34
0.71 0.08 0.22
Matches are distributed among these distances:
2 22 0.20
3 85 0.76
4 5 0.04
ACGTcount: A:0.69, C:0.02, G:0.03, T:0.25
Consensus pattern (3 bp):
AAT
Found at i:180337 original size:13 final size:13
Alignment explanation
Indices: 180316--180462 Score: 69
Period size: 13 Copynumber: 11.2 Consensus size: 13
180306 AATATAAAGC
*
180316 AAAATAATAATATT
1 AAAA-AATAATAAT
180330 AAAAAATAATAAT
1 AAAAAATAATAAT
180343 AAAAAGTATAATAAT
1 AAAAA--ATAATAAT
**
180358 -ACTAATAATAAT
1 AAAAAATAATAAT
* *
180370 GATAATAATAA-ATCT
1 -A-AAAAATAATA-AT
180385 AAACAAATAATAAT
1 AAA-AAATAATAAT
* *
180399 --AAAATGA-AAG
1 AAAAAATAATAAT
*
180409 AAATAATAA-AAT
1 AAAAAATAATAAT
180421 GAAAAAA-AATAAT
1 -AAAAAATAATAAT
180434 AATAAAATAA-AAT
1 AA-AAAATAATAAT
180447 AATAAAATAA-AAT
1 AA-AAAATAATAAT
180460 AAA
1 AAA
180463 GAAAAGTGAA
Statistics
Matches: 106, Mismatches: 13, Indels: 30
0.71 0.09 0.20
Matches are distributed among these distances:
10 2 0.02
11 5 0.05
12 21 0.20
13 45 0.42
14 16 0.15
15 17 0.16
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.24
Consensus pattern (13 bp):
AAAAAATAATAAT
Found at i:180396 original size:20 final size:19
Alignment explanation
Indices: 180330--180467 Score: 72
Period size: 20 Copynumber: 7.2 Consensus size: 19
180320 TAATAATATT
180330 AAAA-AATAAT-AATAAAA
1 AAAATAATAATAAATAAAA
** *
180347 AGTATAATAATACTAATAATA
1 AAAATAATAATA--AATAAAA
** *
180368 ATGATAATAATAAATCTAAA
1 AAAATAATAATAAAT-AAAA
* *
180388 CAAATAATAATAAAATGAAA
1 AAAATAATAAT-AAATAAAA
*
180408 GAAATAAT-A-AAATGAAAA
1 AAAATAATAATAAAT-AAAA
180426 AAAATAATAATAAA-ATAAA
1 AAAATAATAATAAATA-AAA
*
180445 ATAATAA-AATAAAATAAAGA
1 AAAATAATAAT-AAATAAA-A
180465 AAA
1 AAA
180468 GTGAAGAGCA
Statistics
Matches: 92, Mismatches: 16, Indels: 23
0.70 0.12 0.18
Matches are distributed among these distances:
17 6 0.07
18 20 0.22
19 19 0.21
20 27 0.29
21 20 0.22
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.22
Consensus pattern (19 bp):
AAAATAATAATAAATAAAA
Found at i:180413 original size:17 final size:16
Alignment explanation
Indices: 180393--180458 Score: 73
Period size: 17 Copynumber: 4.0 Consensus size: 16
180383 CTAAACAAAT
180393 AATAATAAAATGAAAGA
1 AATAATAAAATGAAA-A
180410 AATAATAAAATGAAAA
1 AATAATAAAATGAAAA
*
180426 AA-AATAATAATAAAATAA
1 AATAATAA-AAT-GAA-AA
180444 AATAATAAAAT-AAAA
1 AATAATAAAATGAAAA
180459 TAAAGAAAAG
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
15 7 0.16
16 8 0.18
17 17 0.39
18 7 0.16
19 5 0.11
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (16 bp):
AATAATAAAATGAAAA
Found at i:180431 original size:38 final size:38
Alignment explanation
Indices: 180332--180467 Score: 107
Period size: 38 Copynumber: 3.5 Consensus size: 38
180322 ATAATATTAA
** *
180332 AAAATAATAATAAAAAGTATAATAATACTAATAATAATG-AT
1 AAAATAA-AATAAAAAAAATAATAATA-AAATAA-AA-GAAT
* * *
180373 AATAAT-AAATCTAAACAAATAATAATAAAATGAAAGAA-
1 AA-AATAAAAT-AAAAAAAATAATAATAAAATAAAAGAAT
* *
180411 ATAATAAAATGAAAAAAAATAATAATAAAATAAAATAAT
1 AAAATAAAAT-AAAAAAAATAATAATAAAATAAAAGAAT
*
180450 AAAATAAAATAAAGAAAA
1 AAAATAAAATAAAAAAAA
180468 GTGAAGAGCA
Statistics
Matches: 76, Mismatches: 14, Indels: 13
0.74 0.14 0.13
Matches are distributed among these distances:
37 3 0.04
38 36 0.47
39 12 0.16
40 7 0.09
41 15 0.20
42 3 0.04
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.23
Consensus pattern (38 bp):
AAAATAAAATAAAAAAAATAATAATAAAATAAAAGAAT
Found at i:180447 original size:34 final size:35
Alignment explanation
Indices: 180303--180458 Score: 106
Period size: 34 Copynumber: 4.5 Consensus size: 35
180293 TAATAGAAAT
* * * *
180303 AATAATATAAA-GCAAAATAATAATATTAAAA-AAT
1 AATAATA-AAATGAAAAAAAATAATAATAAAATAAA
* * * * * * *
180337 AATAATAAAAAGTATAATAATACTAATAATAATGAT
1 AATAATAAAATGAAAAAAAATAATAATAA-AATAAA
** *
180373 AATAAT-AAATCTAAACAAATAATAATAAAATGAAAGA
1 AATAATAAAATGAAAAAAAATAATAATAAAAT--AA-A
180410 AATAATAAAATGAAAAAAAATAATAATAAAAT-AA
1 AATAATAAAATGAAAAAAAATAATAATAAAATAAA
180444 AATAATAAAAT-AAAA
1 AATAATAAAATGAAAA
180459 TAAAGAAAAG
Statistics
Matches: 99, Mismatches: 16, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
33 7 0.07
34 36 0.36
35 19 0.19
36 9 0.09
37 6 0.06
38 22 0.22
ACGTcount: A:0.69, C:0.03, G:0.04, T:0.24
Consensus pattern (35 bp):
AATAATAAAATGAAAAAAAATAATAATAAAATAAA
Found at i:180524 original size:20 final size:20
Alignment explanation
Indices: 180496--180539 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
180486 GTGGTCGACG
*
180496 ACGGGTCGAACGGAGTGACC
1 ACGGCTCGAACGGAGTGACC
*
180516 ACGGCTCGAACGGAGTGACG
1 ACGGCTCGAACGGAGTGACC
180536 ACGG
1 ACGG
180540 TGCGTGCAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.25, C:0.25, G:0.41, T:0.09
Consensus pattern (20 bp):
ACGGCTCGAACGGAGTGACC
Found at i:180792 original size:12 final size:14
Alignment explanation
Indices: 180762--180793 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
180752 AAGCGGAGGG
180762 GAAAGGTTAGAGAA
1 GAAAGGTTAGAGAA
180776 GAAAGGTTAG-G-A
1 GAAAGGTTAGAGAA
180788 GAAAGG
1 GAAAGG
180794 GGGAAATGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.39
13 1 0.06
14 10 0.56
ACGTcount: A:0.47, C:0.00, G:0.41, T:0.12
Consensus pattern (14 bp):
GAAAGGTTAGAGAA
Done.