Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003854.1 Hibiscus syriacus cultivar Beakdansim tig00008285_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: 151844
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
File 1 of 2
Found at i:3271 original size:23 final size:23
Alignment explanation
Indices: 3252--3305 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
3242 TCTCGAATGA
*
3252 CCACATAGGTTTGCACCGAAGTG
1 CCACATAAGTTTGCACCGAAGTG
*
3275 TCACATAAGTTTGCACCGAAGTG
1 CCACATAAGTTTGCACCGAAGTG
3298 CCACATAA
1 CCACATAA
3306 TTGTCCCGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.22
Consensus pattern (23 bp):
CCACATAAGTTTGCACCGAAGTG
Found at i:5213 original size:30 final size:30
Alignment explanation
Indices: 5179--5278 Score: 98
Period size: 30 Copynumber: 3.3 Consensus size: 30
5169 CTCATCTTCA
5179 TTTCCCAATATGCTATTTAATACATTATCT
1 TTTCCCAATATGCTATTTAATACATTATCT
* *
5209 TTTCCCAAGCTATAAC-A-TTAATGCCATCT-TCT
1 TTTCCCAA--TAT-GCTATTTAAT-ACAT-TATCT
* *
5241 TTTCCCAATCTGCTATTTATTACATTATCT
1 TTTCCCAATATGCTATTTAATACATTATCT
5271 TTTCCCAA
1 TTTCCCAA
5279 ATTATTTTAA
Statistics
Matches: 56, Mismatches: 6, Indels: 16
0.72 0.08 0.21
Matches are distributed among these distances:
29 2 0.04
30 25 0.45
31 9 0.16
32 18 0.32
33 2 0.04
ACGTcount: A:0.27, C:0.25, G:0.04, T:0.44
Consensus pattern (30 bp):
TTTCCCAATATGCTATTTAATACATTATCT
Found at i:5259 original size:62 final size:62
Alignment explanation
Indices: 5162--5278 Score: 191
Period size: 62 Copynumber: 1.9 Consensus size: 62
5152 TTGTTAATAG
5162 CATTAATCTCATCTTCATTTCCCAATATGCTATTTAATACATTATCTTTTCCCAAGCTATAA
1 CATTAATCTCATCTTCATTTCCCAATATGCTATTTAATACATTATCTTTTCCCAAGCTATAA
* * *
5224 CATTAATGC-CATCTTCTTTTCCCAATCTGCTATTTATTACATTATCTTTTCCCAA
1 CATTAAT-CTCATCTTCATTTCCCAATATGCTATTTAATACATTATCTTTTCCCAA
5279 ATTATTTTAA
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
62 50 0.98
63 1 0.02
ACGTcount: A:0.27, C:0.26, G:0.03, T:0.44
Consensus pattern (62 bp):
CATTAATCTCATCTTCATTTCCCAATATGCTATTTAATACATTATCTTTTCCCAAGCTATAA
Found at i:13221 original size:32 final size:31
Alignment explanation
Indices: 13167--13244 Score: 111
Period size: 32 Copynumber: 2.5 Consensus size: 31
13157 TCGTTAAAAA
*
13167 TAGGTATCTAACGTTTTCGACGTTACACTTT
1 TAGGTATCTAACATTTTCGACGTTACACTTT
* * *
13198 TAGGTGTCTTAACATTTTTGACGTTATACTTT
1 TAGGTATC-TAACATTTTCGACGTTACACTTT
13230 TAGGTATCTAACATT
1 TAGGTATCTAACATT
13245 ACACTTGTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
31 14 0.34
32 27 0.66
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.45
Consensus pattern (31 bp):
TAGGTATCTAACATTTTCGACGTTACACTTT
Found at i:13284 original size:22 final size:21
Alignment explanation
Indices: 13218--13284 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 21
13208 AACATTTTTG
*
13218 ACGTTATACTTTTAGGTATCTA
1 ACGTTACAC-TTTAGGTATCTA
* * *
13240 ACATTACAC-TT--GTTTTTA
1 ACGTTACACTTTAGGTATCTA
13258 ACGTTACACTTTAAGGTATCTA
1 ACGTTACACTTT-AGGTATCTA
13280 ACGTT
1 ACGTT
13285 TTCAACTGGA
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
18 13 0.38
19 2 0.06
20 2 0.06
22 17 0.50
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.43
Consensus pattern (21 bp):
ACGTTACACTTTAGGTATCTA
Found at i:13951 original size:11 final size:11
Alignment explanation
Indices: 13935--14031 Score: 60
Period size: 11 Copynumber: 9.2 Consensus size: 11
13925 AACTCAAATT
13935 TATTTTATTAA
1 TATTTTATTAA
13946 TATTTTATTAA
1 TATTTTATTAA
* *
13957 -ATTCTAATAA
1 TATTTTATTAA
* **
13967 -AATAAATT--
1 TATTTTATTAA
13975 TATTTTATTAA
1 TATTTTATTAA
13986 TATTTTATTAA
1 TATTTTATTAA
* ** *
13997 TAACTCAATT-T
1 T-ATTTTATTAA
14008 TATTTTATTAA
1 TATTTTATTAA
*
14019 TATTTTACTAA
1 TATTTTATTAA
14030 TA
1 TA
14032 GATGCGACGT
Statistics
Matches: 63, Mismatches: 18, Indels: 10
0.69 0.20 0.11
Matches are distributed among these distances:
9 5 0.08
10 17 0.27
11 36 0.57
12 5 0.08
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:14749 original size:21 final size:23
Alignment explanation
Indices: 14717--14758 Score: 54
Period size: 21 Copynumber: 1.9 Consensus size: 23
14707 TGGAAGAGAA
14717 TAATATTTTTAA-ATA-ATATTT
1 TAATATTTTTAATATATATATTT
14738 TAAT-TTTCTTAATATATATAT
1 TAATATTT-TTAATATATATAT
14759 AAACGTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 3 0.17
21 8 0.44
22 3 0.17
23 4 0.22
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (23 bp):
TAATATTTTTAATATATATATTT
Found at i:15444 original size:21 final size:21
Alignment explanation
Indices: 15382--15444 Score: 58
Period size: 22 Copynumber: 3.0 Consensus size: 21
15372 AACGCGAACT
* *
15382 CCAATTTCGCAACACAGTTT-
1 CCAAATTCGCAACTCAGTTTC
* *
15402 CCAAATTCGTAA-TGCGATTTTC
1 CCAAATTCGCAACT-C-AGTTTC
15424 CCAAATTCGCAACTCAGTTTC
1 CCAAATTCGCAACTCAGTTTC
15445 TACAATCGCA
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
20 11 0.33
21 9 0.27
22 12 0.36
23 1 0.03
ACGTcount: A:0.29, C:0.29, G:0.11, T:0.32
Consensus pattern (21 bp):
CCAAATTCGCAACTCAGTTTC
Found at i:15525 original size:41 final size:39
Alignment explanation
Indices: 15470--15658 Score: 112
Period size: 40 Copynumber: 4.7 Consensus size: 39
15460 AATTTCTTTA
* * *
15470 TCGCAACGCAAATTTCTTTCTCGCAACGCAATTTCAAAAT
1 TCGCAACACGAATTTCTTT-TCGCAACACAATTTCAAAAT
** * * **
15510 TCGCAACACGGAATTTCAAATTCGCAACTCGATTTCTGAAT
1 TCGCAACAC-GAATTTC-TTTTCGCAACACAATTTCAAAAT
* ***
15551 TCGCAACGCGAATTTCTTTTTCGCAACACAAGTTTCCTTA-
1 TCGCAACACGAATTTC-TTTTCGCAACACAA-TTTCAAAAT
* * ** ***
15591 TCGCAACACGAATTTTGTTTTCGCAACTCGGTTTTTGAAT
1 TCGCAACACGAA-TTTCTTTTCGCAACACAATTTCAAAAT
15631 TCGCAACACGAATTT-TAATTTCGCAACA
1 TCGCAACACGAATTTCT--TTTCGCAACA
15659 GCTTTTATTT
Statistics
Matches: 115, Mismatches: 27, Indels: 14
0.74 0.17 0.09
Matches are distributed among these distances:
38 1 0.01
39 7 0.06
40 68 0.59
41 38 0.33
42 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (39 bp):
TCGCAACACGAATTTCTTTTCGCAACACAATTTCAAAAT
Found at i:15565 original size:81 final size:80
Alignment explanation
Indices: 15470--15645 Score: 210
Period size: 80 Copynumber: 2.2 Consensus size: 80
15460 AATTTCTTTA
* *
15470 TCGCAACGCAAATTTCTTTCTCGCAACGCAA-TTTCAAAATTCGCAACACGGAATTTCAAATTCG
1 TCGCAACGCGAATTTCTTTCTCGCAACACAAGTTTCAAAA-TCGCAACAC-GAATTTCAAATTCG
15534 CAACTCGATTTCTGAAT
64 CAACTCGATTTCTGAAT
* *** ****
15551 TCGCAACGCGAATTTCTTTTTCGCAACACAAGTTTCCTTATCGCAACACGAATTTTGTTTTCGCA
1 TCGCAACGCGAATTTCTTTCTCGCAACACAAGTTTCAAAATCGCAACACGAATTTCAAATTCGCA
* *
15616 ACTCGGTTTTTGAAT
66 ACTCGATTTCTGAAT
*
15631 TCGCAACACGAATTT
1 TCGCAACGCGAATTT
15646 TAATTTCGCA
Statistics
Matches: 81, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
80 39 0.48
81 37 0.46
82 5 0.06
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (80 bp):
TCGCAACGCGAATTTCTTTCTCGCAACACAAGTTTCAAAATCGCAACACGAATTTCAAATTCGCA
ACTCGATTTCTGAAT
Found at i:15567 original size:21 final size:21
Alignment explanation
Indices: 15364--15567 Score: 104
Period size: 20 Copynumber: 10.0 Consensus size: 21
15354 AATGACCAAC
* *
15364 AAATTCGCAACGCGAA-CTCC
1 AAATTCGCAACGCGAATTTCT
* * * *
15384 AATTTCGCAACAC-AGTTTCC
1 AAATTCGCAACGCGAATTTCT
* * * *
15404 AAATTCGTAATGCGATTTTCCC
1 AAATTCGCAACGCGAATTT-CT
* *
15426 AAATTCGCAACTC-AGTTTCT
1 AAATTCGCAACGCGAATTTCT
* *
15446 ACAA-TCGCAATGCAAATTTCT
1 A-AATTCGCAACGCGAATTTCT
** *
15467 TTA-TCGCAACGCAAATTTCT
1 AAATTCGCAACGCGAATTTCT
* *
15487 --TTCTCGCAACGC-AATTTCA
1 AAAT-TCGCAACGCGAATTTCT
*
15506 AAATTCGCAACACGGAATTTC-
1 AAATTCGCAACGC-GAATTTCT
*
15527 AAATTCGCAACTCG-ATTTCT
1 AAATTCGCAACGCGAATTTCT
*
15547 GAATTCGCAACGCGAATTTCT
1 AAATTCGCAACGCGAATTTCT
15568 TTTTCGCAAC
Statistics
Matches: 144, Mismatches: 27, Indels: 25
0.73 0.14 0.13
Matches are distributed among these distances:
19 12 0.08
20 79 0.55
21 35 0.24
22 18 0.12
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.30
Consensus pattern (21 bp):
AAATTCGCAACGCGAATTTCT
Found at i:15573 original size:20 final size:20
Alignment explanation
Indices: 15450--15617 Score: 92
Period size: 20 Copynumber: 8.3 Consensus size: 20
15440 GTTTCTACAA
* * *
15450 TCGCAATGCAAATTTCTTTA
1 TCGCAACGCGAATTTCTTTT
* *
15470 TCGCAACGCAAATTTCTTTC
1 TCGCAACGCGAATTTCTTTT
***
15490 TCGCAACGC-AATTTCAAAAT
1 TCGCAACGCGAATTTC-TTTT
* ***
15510 TCGCAACACGGAATTTCAAAT
1 TCGCAACGC-GAATTTCTTTT
* **
15531 TCGCAACTCG-ATTTCTGAAT
1 TCGCAACGCGAATTTCT-TTT
15551 TCGCAACGCGAATTTCTTTT
1 TCGCAACGCGAATTTCTTTT
* * *
15571 TCGCAACAC-AAGTTTCCTTA
1 TCGCAACGCGAA-TTTCTTTT
*
15591 TCGCAACACGAATTT-TGTTT
1 TCGCAACGCGAATTTCT-TTT
15611 TCGCAAC
1 TCGCAAC
15618 TCGGTTTTTG
Statistics
Matches: 123, Mismatches: 17, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
19 13 0.11
20 84 0.68
21 20 0.16
22 6 0.05
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (20 bp):
TCGCAACGCGAATTTCTTTT
Found at i:15635 original size:40 final size:40
Alignment explanation
Indices: 15507--15657 Score: 139
Period size: 40 Copynumber: 3.8 Consensus size: 40
15497 GCAATTTCAA
* * * *
15507 AATTCGCAACACGGAATTTCAAATTCGCAACTCGATTTCTG
1 AATTCGCAACAC-GAATTTTAATTTCGCAACTCGGTTTTTG
* * * *
15548 AATTCGCAACGCGAATTTCT-TTTTCGCAACACAAGTTTCCTT-
1 AATTCGCAACACGAATTT-TAATTTCGCAACTC-GGTTT--TTG
**
15590 -A-TCGCAACACGAATTTTGTTTTCGCAACTCGGTTTTTG
1 AATTCGCAACACGAATTTTAATTTCGCAACTCGGTTTTTG
15628 AATTCGCAACACGAATTTTAATTTCGCAAC
1 AATTCGCAACACGAATTTTAATTTCGCAAC
15658 AGCTTTTATT
Statistics
Matches: 89, Mismatches: 13, Indels: 17
0.75 0.11 0.14
Matches are distributed among these distances:
37 2 0.02
39 6 0.07
40 65 0.73
41 15 0.17
43 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (40 bp):
AATTCGCAACACGAATTTTAATTTCGCAACTCGGTTTTTG
Found at i:15646 original size:20 final size:20
Alignment explanation
Indices: 15507--15658 Score: 96
Period size: 20 Copynumber: 7.5 Consensus size: 20
15497 GCAATTTCAA
**
15507 AATTCGCAACACGGAATTTCA
1 AATTCGCAACAC-GAATTTTG
*
15528 AATTCGCAACTCG-ATTTCTG
1 AATTCGCAACACGAATTT-TG
*
15548 AATTCGCAACGCGAATTTCT-
1 AATTCGCAACACGAATTT-TG
** * *
15568 TTTTCGCAACAC-AAGTTTC
1 AATTCGCAACACGAATTTTG
**
15587 CTTATCGCAACACGAATTTTG
1 AAT-TCGCAACACGAATTTTG
** * **
15608 TTTTCGCAACTCGGTTTTTG
1 AATTCGCAACACGAATTTTG
15628 AATTCGCAACACGAATTTT-
1 AATTCGCAACACGAATTTTG
15647 AATTTCGCAACA
1 AA-TTCGCAACA
15659 GCTTTTATTT
Statistics
Matches: 105, Mismatches: 20, Indels: 13
0.76 0.14 0.09
Matches are distributed among these distances:
18 1 0.01
19 12 0.11
20 68 0.65
21 24 0.23
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.34
Consensus pattern (20 bp):
AATTCGCAACACGAATTTTG
Found at i:15687 original size:80 final size:78
Alignment explanation
Indices: 15530--15681 Score: 173
Period size: 80 Copynumber: 1.9 Consensus size: 78
15520 GAATTTCAAA
* * *
15530 TTCGCAACTCGATTTCTGAATTCGCAACGCGAATTTCTTTTTCGCAACACAAGTTTCCTTATCGC
1 TTCGCAACTCGATTTCTGAATTCGCAACACGAATTTCTATTTCGCAACAC-A-TTTCATTATCGC
*
15595 AACACGAATTTTGTT
64 AACACAAATTTTGTT
* * * *
15610 TTCGCAACTCGGTTTTTGAATTCGCAACACGAATTT-TAATTTCGCAACAGC-TTTTATTTTCGC
1 TTCGCAACTCGATTTCTGAATTCGCAACACGAATTTCT-ATTTCGCAACA-CATTTCATTATCGC
*
15673 TACACAAAT
64 AACACAAAT
15682 GTTTTGGGTA
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
78 16 0.26
79 1 0.02
80 43 0.70
81 1 0.02
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (78 bp):
TTCGCAACTCGATTTCTGAATTCGCAACACGAATTTCTATTTCGCAACACATTTCATTATCGCAA
CACAAATTTTGTT
Found at i:15843 original size:16 final size:15
Alignment explanation
Indices: 15815--15853 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
15805 TCCCCATCTC
15815 TAATTTTTTTTTACA
1 TAATTTTTTTTTACA
*
15830 TAATTTTATTTTTATA
1 TAATTTT-TTTTTACA
15846 TAATTTTT
1 TAATTTTT
15854 CAATGATTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (15 bp):
TAATTTTTTTTTACA
Found at i:16468 original size:12 final size:12
Alignment explanation
Indices: 16447--16480 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
16437 ACCACAATTC
*
16447 CAATACCAAACA
1 CAATATCAAACA
16459 CAATATCAAACA
1 CAATATCAAACA
*
16471 CAATCTCAAA
1 CAATATCAAA
16481 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:16657 original size:24 final size:24
Alignment explanation
Indices: 16606--16659 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
16596 GTATTCAAAA
*
16606 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
16630 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
16654 TTTGAT
1 TTTGAT
16660 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:18936 original size:18 final size:18
Alignment explanation
Indices: 18913--18948 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
18903 AAACAAAAGG
* *
18913 AAATCAAATTCGCAATCA
1 AAATCAAAATCCCAATCA
18931 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
18949 CAACCGGCTT
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:0.53, C:0.25, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:19202 original size:29 final size:29
Alignment explanation
Indices: 19160--19220 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
19150 AATTCGCAAC
19160 GCGAAAGTCAAATTCACGTTGCGATTGTT
1 GCGAAAGTCAAATTCACGTTGCGATTGTT
* * *
19189 GCGAAAGTTAAATTCGCGTTGCGATTTTT
1 GCGAAAGTCAAATTCACGTTGCGATTGTT
19218 GCG
1 GCG
19221 TTGCGATTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (29 bp):
GCGAAAGTCAAATTCACGTTGCGATTGTT
Found at i:19223 original size:14 final size:14
Alignment explanation
Indices: 19204--19234 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
19194 AGTTAAATTC
*
19204 GCGTTGCGATTTTT
1 GCGTTGCGATTGTT
19218 GCGTTGCGATTGTT
1 GCGTTGCGATTGTT
19232 GCG
1 GCG
19235 AAAGAGTACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.06, C:0.16, G:0.35, T:0.42
Consensus pattern (14 bp):
GCGTTGCGATTGTT
Found at i:20727 original size:21 final size:21
Alignment explanation
Indices: 20701--20768 Score: 100
Period size: 21 Copynumber: 3.2 Consensus size: 21
20691 GTGAATCAAG
* *
20701 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
*
20722 CTCTTGAACAATGAGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
*
20743 CTCTTGAACGATGAGAGAGGC
1 CTCTTGAACGATGAGAGGGGC
20764 CTCTT
1 CTCTT
20769 AAACAACATG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.22, C:0.21, G:0.35, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGGGGC
Found at i:20765 original size:42 final size:42
Alignment explanation
Indices: 20701--20796 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 42
20691 GTGAATCAAG
* * * * *
20701 CTCTTGAACGGTGGGAGGGGCCTCTTGAACAATGA-GAGGGGC
1 CTCTTGAACGATGAGAGAGGCCTCTTAAACAA-CATGAGGGGC
*
20743 CTCTTGAACGATGAGAGAGGCCTCTTAAACAACATGAGGGTC
1 CTCTTGAACGATGAGAGAGGCCTCTTAAACAACATGAGGGGC
*
20785 CTCTTAAACGAT
1 CTCTTGAACGAT
20797 TGCAGATGAA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
41 1 0.02
42 45 0.98
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (42 bp):
CTCTTGAACGATGAGAGAGGCCTCTTAAACAACATGAGGGGC
Found at i:20779 original size:23 final size:20
Alignment explanation
Indices: 20718--20793 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 20
20708 ACGGTGGGAG
*
20718 GGGCCTCTTGAACAATGAGA
1 GGGCCTCTTAAACAATGAGA
* *
20738 GGGGCCTCTTGAACGATGAGA
1 -GGGCCTCTTAAACAATGAGA
20759 GAGGCCTCTTAAACAACATGAG-
1 G-GGCCTCTTAAAC-A-ATGAGA
*
20781 GGTCCTCTTAAAC
1 GGGCCTCTTAAAC
20794 GATTGCAGAT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.02
21 41 0.85
22 1 0.02
23 5 0.10
ACGTcount: A:0.29, C:0.22, G:0.28, T:0.21
Consensus pattern (20 bp):
GGGCCTCTTAAACAATGAGA
Found at i:20963 original size:4 final size:4
Alignment explanation
Indices: 20942--20980 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
20932 GGGCTGCTAA
* *
20942 AAAT AAAT TAAT ACAT AAAT AAAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AA
20981 TGTCGAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
4 26 0.87
5 4 0.13
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:20967 original size:21 final size:21
Alignment explanation
Indices: 20941--20980 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
20931 CGGGCTGCTA
* *
20941 AAAATAAATTAATACATAAAT
1 AAAATAAATAAATAAATAAAT
20962 AAAATAAATAAATAAATAA
1 AAAATAAATAAATAAATAA
20981 TGTCGAAAAA
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:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (21 bp):
AAAATAAATAAATAAATAAAT
Found at i:20971 original size:17 final size:17
Alignment explanation
Indices: 20942--20980 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
20932 GGGCTGCTAA
* *
20942 AAAT-AAATTAATACAT
1 AAATAAAATAAATAAAT
20958 AAATAAAATAAATAAAT
1 AAATAAAATAAATAAAT
20975 AAATAA
1 AAATAA
20981 TGTCGAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (17 bp):
AAATAAAATAAATAAAT
Found at i:21421 original size:42 final size:42
Alignment explanation
Indices: 21346--21444 Score: 144
Period size: 42 Copynumber: 2.4 Consensus size: 42
21336 GTGATGGAAT
* * * *
21346 AGGTGATGGCTCTCGTTGTGGAGGTGTATAATCGGCTCGATC
1 AGGTGATGGCTCTCGGTGTCGAGCTGTAGAATCGGCTCGATC
*
21388 AGGTGATGGCTCTGGGTGTCGAGCTGTAGAATCGGCTCGATC
1 AGGTGATGGCTCTCGGTGTCGAGCTGTAGAATCGGCTCGATC
*
21430 AGGTGATGACTCTCG
1 AGGTGATGGCTCTCG
21445 AAGTGGGGGT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.17, C:0.18, G:0.36, T:0.28
Consensus pattern (42 bp):
AGGTGATGGCTCTCGGTGTCGAGCTGTAGAATCGGCTCGATC
Found at i:22978 original size:19 final size:19
Alignment explanation
Indices: 22927--22984 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 19
22917 AGTAGTTTTT
*
22927 GAAACTTAAATTCGCAACAC
1 GAAAC-TAAAATCGCAACAC
* *
22947 GAAAATGAAAATCGCAACGC
1 GAAACT-AAAATCGCAACAC
22967 GAAACTAAAATCGCAACA
1 GAAACTAAAATCGCAACA
22985 TTTTCGCGTT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
19 12 0.38
20 20 0.62
ACGTcount: A:0.50, C:0.22, G:0.14, T:0.14
Consensus pattern (19 bp):
GAAACTAAAATCGCAACAC
Found at i:23008 original size:20 final size:20
Alignment explanation
Indices: 22983--23022 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
22973 AAAATCGCAA
22983 CATTTTCGCGTTGCAAATTT
1 CATTTTCGCGTTGCAAATTT
* *
23003 CATTTTCGTGTTGCGAATTT
1 CATTTTCGCGTTGCAAATTT
23023 AAGTTTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.47
Consensus pattern (20 bp):
CATTTTCGCGTTGCAAATTT
Found at i:23029 original size:20 final size:20
Alignment explanation
Indices: 22986--23029 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
22976 ATCGCAACAT
* *
22986 TTTCGCGTTGCAAATTTCAT
1 TTTCGCGTTGCAAATTTAAG
* *
23006 TTTCGTGTTGCGAATTTAAG
1 TTTCGCGTTGCAAATTTAAG
23026 TTTC
1 TTTC
23030 AAAAACTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.18, C:0.16, G:0.18, T:0.48
Consensus pattern (20 bp):
TTTCGCGTTGCAAATTTAAG
Found at i:23579 original size:20 final size:20
Alignment explanation
Indices: 23554--23602 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
23544 TAAACACGCT
*
23554 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTTCTGTG
23574 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTCTGTG
23594 TTGCGAATT
1 TTGCGAATT
23603 ACAAATTAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.16, C:0.12, G:0.24, T:0.47
Consensus pattern (20 bp):
TTGCGAATTTGACTTCTGTG
Found at i:29816 original size:6 final size:6
Alignment explanation
Indices: 29805--29832 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
29795 GGTCGGAGGA
29805 GGGGGT GGGGGT GGGGGT GGGGGT GGGG
1 GGGGGT GGGGGT GGGGGT GGGGGT GGGG
29833 ATGATTAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.86, T:0.14
Consensus pattern (6 bp):
GGGGGT
Found at i:30870 original size:19 final size:19
Alignment explanation
Indices: 30846--30882 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
30836 ATGACTAAAA
*
30846 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
30865 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
30883 CAGTATCGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:30979 original size:21 final size:20
Alignment explanation
Indices: 30955--31002 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
30945 AAATTCGTGT
*
30955 TGCGATTTTGTAAAATCGCAA
1 TGCGATTATGT-AAATCGCAA
*
30976 TGCGAATATGTAAATCGCAA
1 TGCGATTATGTAAATCGCAA
*
30996 CGCGATT
1 TGCGATT
31003 CTGACTGTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (20 bp):
TGCGATTATGTAAATCGCAA
Found at i:31726 original size:23 final size:23
Alignment explanation
Indices: 31690--31762 Score: 87
Period size: 23 Copynumber: 3.3 Consensus size: 23
31680 CACCACAGCT
*
31690 CATATA-AA-TGCACCGAAGTGC
1 CATATAGAATTGCACCGTAGTGC
31711 CATATAGAATTGCACCGTAGTGC
1 CATATAGAATTGCACCGTAGTGC
*** *
31734 CGCGTAGAGTTGCACCGTAGTGC
1 CATATAGAATTGCACCGTAGTGC
31757 CATATA
1 CATATA
31763 ATAATGTCCA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
21 6 0.14
22 2 0.05
23 34 0.81
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.23
Consensus pattern (23 bp):
CATATAGAATTGCACCGTAGTGC
Found at i:31945 original size:103 final size:103
Alignment explanation
Indices: 31774--31991 Score: 427
Period size: 103 Copynumber: 2.1 Consensus size: 103
31764 TAATGTCCAT
*
31774 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTCACCA
31839 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
31877 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTCACCA
31942 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
31980 AAGGACCACATA
1 AAGGACCACATA
31992 GACCCTCGAC
Statistics
Matches: 114, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 114 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:35059 original size:24 final size:24
Alignment explanation
Indices: 35027--35080 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
35017 GTATTCGAAA
35027 TTTGATCTTGGTCAATACTCGGAC
1 TTTGATCTTGGTCAATACTCGGAC
*
35051 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACTCGGAC
35075 TTTGAT
1 TTTGAT
35081 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACTCGGAC
Found at i:35290 original size:14 final size:14
Alignment explanation
Indices: 35265--35300 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
35255 GAAGAAGAAG
35265 AAGAAGAAATCCCCA
1 AAGAA-AAATCCCCA
*
35280 AAGAAAAATCCCCG
1 AAGAAAAATCCCCA
35294 AAGAAAA
1 AAGAAAA
35301 TGCCGCGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.58, C:0.22, G:0.14, T:0.06
Consensus pattern (14 bp):
AAGAAAAATCCCCA
Found at i:37657 original size:133 final size:133
Alignment explanation
Indices: 37419--37686 Score: 482
Period size: 133 Copynumber: 2.0 Consensus size: 133
37409 AAACGTTGTA
* * *
37419 TTATGTGTATTTTATGTGTAAACTTTTAATATTTTTAGTTAGGCATGTATTAGTAACTTGAGTTT
1 TTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAAGCATGTATTAGTAACTTGAGTTT
*
37484 GAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAAAGCA
66 GAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAAAGCA
37549 AAT
131 AAT
37552 TTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAAGCATGTATTAGTAACTTGAGTTT
1 TTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAAGCATGTATTAGTAACTTGAGTTT
* *
37617 GAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCG
66 GAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAAAGCA
37682 AAT
131 AAT
37685 TT
1 TT
37687 GATCATCGCA
Statistics
Matches: 129, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
133 129 1.00
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (133 bp):
TTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAAGCATGTATTAGTAACTTGAGTTT
GAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAAAGCA
AAT
Found at i:37730 original size:20 final size:20
Alignment explanation
Indices: 37705--37847 Score: 154
Period size: 20 Copynumber: 7.5 Consensus size: 20
37695 CAACTCAAAA
*
37705 ATCGCAACGCAAATTTGACT
1 ATCGCAACGCGAATTTGACT
*
37725 ATCGCAACCCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
* *
37745 ATCGCAATGC-AA----A-A
1 ATCGCAACGCGAATTTGACT
* *
37759 ATAGCAATGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
37779 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
* *
37799 ATCGCAACGTGAATTTGATT
1 ATCGCAACGCGAATTTGACT
* *
37819 ATCGCAACGGGTATTTGACT
1 ATCGCAACGCGAATTTGACT
37839 ATCGCAACG
1 ATCGCAACG
37848 AGAAAATATC
Statistics
Matches: 103, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
14 9 0.09
15 3 0.03
19 3 0.03
20 88 0.85
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGAATTTGACT
Found at i:37749 original size:54 final size:55
Alignment explanation
Indices: 37663--37806 Score: 213
Period size: 54 Copynumber: 2.7 Consensus size: 55
37653 TTACACATTC
* *
37663 ATTTGAATATCGCAACGCGAATTTGA-TCATCGCAACT-CAAAAATCGCAACGCAA
1 ATTTGACTATCGCAACGCGAATTTGACT-ATCGCAACTGCAAAAATAGCAACGCAA
* * *
37717 ATTTGACTATCGCAACCCGAATTTGACTATCGCAA-TGCAAAAATAGCAATGCGA
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACTGCAAAAATAGCAACGCAA
37771 ATTTGACTATCGCAACGCGAATTTGACTATCGCAAC
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAAC
37807 GTGAATTTGA
Statistics
Matches: 81, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
53 1 0.01
54 79 0.98
55 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (55 bp):
ATTTGACTATCGCAACGCGAATTTGACTATCGCAACTGCAAAAATAGCAACGCAA
Found at i:37835 original size:94 final size:93
Alignment explanation
Indices: 37705--37891 Score: 250
Period size: 94 Copynumber: 2.0 Consensus size: 93
37695 CAACTCAAAA
* *
37705 ATCGCAACGCAAATTTGACTATCGCAACCCGAATTTGACTATCGCAATGCA-AAAATAGCAATGC
1 ATCGCAACGCAAATTTGACTATCGCAACCCGAATTTGACTATCGCAACG-AGAAAATAGCAAAGC
*
37769 GAATTTGACTATCGCAACGCGAATTTGACT
65 GAATTAGACTATCGCAACGCGAA-TTGACT
** * ** * *
37799 ATCGCAACGTGAATTTGATTATCGCAACGGGTATTTGACTATCGCAACGAGAAAATATCAAAGCG
1 ATCGCAACGCAAATTTGACTATCGCAACCCGAATTTGACTATCGCAACGAGAAAATAGCAAAGCG
*
37864 TATTAGACTATCGCAACGCGAATTGACT
66 AATTAGACTATCGCAACGCGAATTGACT
37892 TTCGTGTTAC
Statistics
Matches: 81, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
93 7 0.09
94 74 0.91
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (93 bp):
ATCGCAACGCAAATTTGACTATCGCAACCCGAATTTGACTATCGCAACGAGAAAATAGCAAAGCG
AATTAGACTATCGCAACGCGAATTGACT
Found at i:38081 original size:29 final size:28
Alignment explanation
Indices: 38047--38101 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
38037 ATAAGAATTA
*
38047 TTTACACATCAATATTAAACAAATCAACT
1 TTTACAAATCAATATTAAA-AAATCAACT
* *
38076 TTTACAAATCAATTTTTAAAAATCAA
1 TTTACAAATCAATATTAAAAAATCAA
38102 TTAAACAAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 7 0.30
29 16 0.70
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (28 bp):
TTTACAAATCAATATTAAAAAATCAACT
Found at i:38102 original size:14 final size:14
Alignment explanation
Indices: 38067--38103 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
38057 AATATTAAAC
* *
38067 AAATCAACTTTTAC
1 AAATCAATTTTTAA
38081 AAATCAATTTTTAA
1 AAATCAATTTTTAA
38095 AAATCAATT
1 AAATCAATT
38104 AAACAAGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.38
Consensus pattern (14 bp):
AAATCAATTTTTAA
Found at i:39532 original size:21 final size:21
Alignment explanation
Indices: 39508--39606 Score: 83
Period size: 21 Copynumber: 4.7 Consensus size: 21
39498 GTGGGAGAGA
*
39508 CCTCTTCAACGATGACAGGGG
1 CCTCTTGAACGATGACAGGGG
* **
39529 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAACGATGACAGGGG
* ** *
39550 ACTCTTGAGGGATGATAGGGG
1 CCTCTTGAACGATGACAGGGG
* *
39571 CCTCTTGAACGAT-AGGAGAGG
1 CCTCTTGAACGATGA-CAGGGG
*
39592 CCTCTTGAATGATGA
1 CCTCTTGAACGATGA
39607 AAGGTGAGTT
Statistics
Matches: 60, Mismatches: 16, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 1 0.02
21 58 0.97
22 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.35, T:0.22
Consensus pattern (21 bp):
CCTCTTGAACGATGACAGGGG
Found at i:39555 original size:42 final size:42
Alignment explanation
Indices: 39488--39606 Score: 123
Period size: 42 Copynumber: 2.8 Consensus size: 42
39478 ATGAATCAGG
*
39488 CTCTTGAATGGTGGGAGAGACCTCTTCAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGAGACCTCTTCAACGATGACAGGGGC
* * ** *
39530 CTCTTGAACGGTGGGAGGGGA-CTCTTGAGGGATGATAGGGGC
1 CTCTTGAACGGTGGGA-GAGACCTCTTCAACGATGACAGGGGC
* * * * *
39572 CTCTTGAACGATAGGAGAGGCCTCTTGAATGATGA
1 CTCTTGAACGGTGGGAGAGACCTCTTCAACGATGA
39607 AAGGTGAGTT
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
41 2 0.03
42 58 0.92
43 3 0.05
ACGTcount: A:0.24, C:0.18, G:0.36, T:0.23
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGAGACCTCTTCAACGATGACAGGGGC
Found at i:40140 original size:20 final size:20
Alignment explanation
Indices: 40115--40163 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
40105 CGAAACTTAA
*
40115 ATCGCAATGCAAAAATGACT
1 ATCGCAACGCAAAAATGACT
**
40135 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCAAAAATGACT
40155 ATCGCAACG
1 ATCGCAACG
40164 TGAATTTGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCAAAAATGACT
Found at i:40213 original size:19 final size:20
Alignment explanation
Indices: 40180--40218 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
40170 TGACTATCAC
* *
40180 AATCGCAATGTGAAA-TAAA
1 AATCGCAACGCGAAACTAAA
40199 AATCGCAACGCGAAACTAAA
1 AATCGCAACGCGAAACTAAA
40219 TTCGCGTTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.51, C:0.18, G:0.15, T:0.15
Consensus pattern (20 bp):
AATCGCAACGCGAAACTAAA
Found at i:40316 original size:20 final size:20
Alignment explanation
Indices: 40291--40354 Score: 94
Period size: 20 Copynumber: 3.2 Consensus size: 20
40281 CGATTATCCT
*
40291 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCAATTTCGC
40311 GTTGCGATAGTC-ATTTCCGC
1 GTTGCGATAGTCAATTT-CGC
*
40331 GTTGCGATAGTCATTTTCGC
1 GTTGCGATAGTCAATTTCGC
40351 GTTG
1 GTTG
40355 AGATTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.08
20 34 0.85
21 3 0.08
ACGTcount: A:0.17, C:0.20, G:0.27, T:0.36
Consensus pattern (20 bp):
GTTGCGATAGTCAATTTCGC
Found at i:42293 original size:20 final size:20
Alignment explanation
Indices: 42268--42404 Score: 108
Period size: 20 Copynumber: 7.2 Consensus size: 20
42258 GAAACTTAAA
*
42268 ATCGCAACACAAAAATGACT
1 ATCGCAACACGAAAATGACT
42288 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
* **
42308 ATCGCAACGCGAATTTGACT
1 ATCGCAACACGAAAATGACT
*
42328 ATCGC-A-ACG-AGAT-A--
1 ATCGCAACACGAAAATGACT
* * **
42342 ATCACAACGCG-AAATGAAA
1 ATCGCAACACGAAAATGACT
42361 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
* * **
42381 ATCGTAACGCGAATTTGACT
1 ATCGCAACACGAAAATGACT
42401 ATCG
1 ATCG
42405 TTGCGATTTT
Statistics
Matches: 93, Mismatches: 18, Indels: 12
0.76 0.15 0.10
Matches are distributed among these distances:
14 4 0.04
15 1 0.01
16 6 0.06
17 3 0.03
18 2 0.02
19 10 0.11
20 67 0.72
ACGTcount: A:0.42, C:0.23, G:0.17, T:0.18
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:43032 original size:20 final size:20
Alignment explanation
Indices: 42948--43023 Score: 82
Period size: 20 Copynumber: 3.8 Consensus size: 20
42938 TGGCGCTTTA
42948 AAAATCGCGTTGCGATAGTC
1 AAAATCGCGTTGCGATAGTC
* * *
42968 AGAATTGTGTTGCGATTATGT-
1 AAAATCGCGTTGCGA-TA-GTC
**
42989 ATTATCGCGTTGCGATAGTC
1 AAAATCGCGTTGCGATAGTC
43009 AAAATCGCGTTGCGA
1 AAAATCGCGTTGCGA
43024 ATCTGAAAAC
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
19 2 0.05
20 27 0.61
21 13 0.30
22 2 0.05
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (20 bp):
AAAATCGCGTTGCGATAGTC
Found at i:43061 original size:20 final size:19
Alignment explanation
Indices: 43038--43083 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
43028 GAAAACTTAT
*
43038 TTGCGATACTAGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
43058 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
43077 TTGCGAT
1 TTGCGAT
43084 TTTGTTGGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:43071 original size:19 final size:19
Alignment explanation
Indices: 43047--43085 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
43037 TTTGCGATAC
*
43047 TAGAGATCGCGTTGCGATT
1 TAGAGATCGCATTGCGATT
43066 TAGAGATCGCATTGCGATT
1 TAGAGATCGCATTGCGATT
43085 T
1 T
43086 TGTTGGTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.33
Consensus pattern (19 bp):
TAGAGATCGCATTGCGATT
Found at i:44355 original size:20 final size:21
Alignment explanation
Indices: 44332--44381 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
44322 TTAATTTTAC
44332 AAATATAAAAAATA-AAAAAA
1 AAATATAAAAAATACAAAAAA
*
44352 AAAT-TACAAAATTACAAAAAA
1 AAATATA-AAAAATACAAAAAA
44373 ATAATATAA
1 A-AATATAA
44382 TTATTTATCT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
19 2 0.08
20 10 0.40
21 7 0.28
22 4 0.16
23 2 0.08
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (21 bp):
AAATATAAAAAATACAAAAAA
Found at i:44411 original size:21 final size:22
Alignment explanation
Indices: 44374--44418 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
44364 TACAAAAAAA
44374 TAATATAATTATTTATCTAATTT
1 TAATATAATTATTTATCT-ATTT
44397 TAATAT-ATT-TTTATCTATTT
1 TAATATAATTATTTATCTATTT
44417 TA
1 TA
44419 TAATTTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.27
21 7 0.32
22 3 0.14
23 6 0.27
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (22 bp):
TAATATAATTATTTATCTATTT
Found at i:45761 original size:21 final size:21
Alignment explanation
Indices: 45735--45779 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
45725 GTGAGACATA
45735 ATAATTAGTAATGAATGAAAG
1 ATAATTAGTAATGAATGAAAG
45756 ATAATTAGTAATGAATGAAAG
1 ATAATTAGTAATGAATGAAAG
45777 ATA
1 ATA
45780 TGTGATATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.18, T:0.29
Consensus pattern (21 bp):
ATAATTAGTAATGAATGAAAG
Found at i:46470 original size:23 final size:22
Alignment explanation
Indices: 46444--46487 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
46434 TTTATAACGC
* *
46444 GTTTATCTCTGTCTTTGTGGTAT
1 GTTTATCGCTATCTTT-TGGTAT
*
46467 GTTTTTCGCTATCTTTTGGTA
1 GTTTATCGCTATCTTTTGGTA
46488 GCTTACGATT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.09, C:0.14, G:0.20, T:0.57
Consensus pattern (22 bp):
GTTTATCGCTATCTTTTGGTAT
Found at i:47819 original size:16 final size:17
Alignment explanation
Indices: 47788--47823 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
47778 GATAATTAAT
47788 TAATCATTCAAAAAAAA
1 TAATCATTCAAAAAAAA
*
47805 TAATC-TTCTAAAAAAA
1 TAATCATTCAAAAAAAA
47821 TAA
1 TAA
47824 ATTTATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (17 bp):
TAATCATTCAAAAAAAA
Found at i:49776 original size:22 final size:23
Alignment explanation
Indices: 49741--49785 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
49731 GTTCAGGACT
49741 AATATTTTATATTT-TGATTATA
1 AATATTTTATATTTATGATTATA
*
49763 AATATTTCTA-ATTTATGTTTATA
1 AATATTT-TATATTTATGATTATA
49786 CTTACTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (23 bp):
AATATTTTATATTTATGATTATA
Found at i:53894 original size:24 final size:24
Alignment explanation
Indices: 53865--53911 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
53855 GATCGATACA
*
53865 CTATGAAAGTACATCGATGCATCC
1 CTATGAAAGTACATCGATACATCC
* *
53889 CTATGAATGTGCATCGATACATC
1 CTATGAAAGTACATCGATACATC
53912 ATGAAGATGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (24 bp):
CTATGAAAGTACATCGATACATCC
Found at i:54720 original size:20 final size:20
Alignment explanation
Indices: 54695--54771 Score: 120
Period size: 20 Copynumber: 3.9 Consensus size: 20
54685 TTTATGAAGG
54695 GATGCACCGATGCA-TACATT
1 GATGCACCGATGCACT-CATT
*
54715 GATGCACCGTTGCACTCATT
1 GATGCACCGATGCACTCATT
54735 GATGCACCGATGCACTCATT
1 GATGCACCGATGCACTCATT
*
54755 GATGCATCGATGCACTC
1 GATGCACCGATGCACTC
54772 TCCAATTCGA
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
20 52 0.98
21 1 0.02
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.26
Consensus pattern (20 bp):
GATGCACCGATGCACTCATT
Found at i:64288 original size:29 final size:28
Alignment explanation
Indices: 64225--64289 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 28
64215 GATTCAATAT
* *
64225 GTAAAGTTCAGTGAGCAAATTAGAAAAA
1 GTAAAGTTCAGTAAGCAAAATAGAAAAA
* * *
64253 TTAAAAGTTCAGTAAGCAAAATATGAGACA
1 GT-AAAGTTCAGTAAGCAAAATA-GAAAAA
64283 GTAAAGT
1 GTAAAGT
64290 AGAGTGAGGA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
28 1 0.03
29 23 0.79
30 5 0.17
ACGTcount: A:0.49, C:0.08, G:0.20, T:0.23
Consensus pattern (28 bp):
GTAAAGTTCAGTAAGCAAAATAGAAAAA
Found at i:65194 original size:32 final size:32
Alignment explanation
Indices: 65132--65284 Score: 238
Period size: 32 Copynumber: 4.8 Consensus size: 32
65122 CCCCGCCTCG
* * *
65132 ATTATATAT-ATATATAATATTTTTTTTATTA
1 ATTATATATAATATTTTATATTTTTTATATTA
*
65163 ATTATATATAATATTCTATATTTTTTATATTA
1 ATTATATATAATATTTTATATTTTTTATATTA
65195 ATTATATATATAATATTTTATA-TTTTTATATTA
1 A-T-TATATATAATATTTTATATTTTTTATATTA
65228 ATTATATATAATATTTTATATTTTTTATATTA
1 ATTATATATAATATTTTATATTTTTTATATTA
65260 ATTATATATAATATTTTATATTTTT
1 ATTATATATAATATTTTATATTTTT
65285 CTATTTTTTT
Statistics
Matches: 113, Mismatches: 5, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
31 27 0.24
32 56 0.50
33 13 0.12
34 17 0.15
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (32 bp):
ATTATATATAATATTTTATATTTTTTATATTA
Found at i:65203 original size:65 final size:65
Alignment explanation
Indices: 65134--65284 Score: 234
Period size: 65 Copynumber: 2.3 Consensus size: 65
65124 CCGCCTCGAT
* *
65134 TATATATATATATAATATTTTTTTTATTAATTATATATAATATTCTATATTTTTTATATTAATTA
1 TATATATATATATTATATTTTTTATATTAATTATATATAATATTCTATATTTTTTATATTAATTA
* *
65199 TATATATA-ATATTTTATATTTTTATATTAATTATATATAATATTTTATATTTTTTATATTAATT
1 TATATATATATATTATAT-TTTTTATATTAATTATATATAATATTCTATATTTTTTATATTAATT
65263 A
65 A
*
65264 TATATA-ATATTTTATATTTTT
1 TATATATATATATTATATTTTT
65285 CTATTTTTTT
Statistics
Matches: 78, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
64 12 0.15
65 66 0.85
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.62
Consensus pattern (65 bp):
TATATATATATATTATATTTTTTATATTAATTATATATAATATTCTATATTTTTTATATTAATTA
Found at i:65255 original size:23 final size:22
Alignment explanation
Indices: 65153--65261 Score: 82
Period size: 23 Copynumber: 5.0 Consensus size: 22
65143 ATATAATATT
*
65153 TTTTTTATTAATTATATATAATA
1 TTTTATATTAATTATAT-TAATA
* **
65176 TTCTATATTTTTTATATT-A-A
1 TTTTATATTAATTATATTAATA
* *
65196 TTATATATATAA-TAT-TTTATA
1 TTTTATAT-TAATTATATTAATA
65217 TTTTTATATTAATTATATATAATA
1 -TTTTATATTAATTATAT-TAATA
**
65241 TTTTATATTTTTTATATTAAT
1 TTTTATATTAATTATATTAAT
65262 TATATATAAT
Statistics
Matches: 68, Mismatches: 11, Indels: 15
0.72 0.12 0.16
Matches are distributed among these distances:
19 2 0.03
20 12 0.18
21 6 0.09
22 15 0.22
23 29 0.43
24 4 0.06
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTTATATTAATTATATTAATA
Found at i:65291 original size:7 final size:7
Alignment explanation
Indices: 65173--65283 Score: 62
Period size: 7 Copynumber: 15.0 Consensus size: 7
65163 ATTATATATA
*
65173 ATATTCT
1 ATATTTT
65180 ATATTTT
1 ATATTTT
* *
65187 TTATATT
1 ATATTTT
*
65194 A-ATTAT
1 ATATTTT
* *
65200 ATATATA
1 ATATTTT
65207 ATATTTT
1 ATATTTT
65214 ATATTTTT
1 ATA-TTTT
65222 ATATTAATT
1 ATATT--TT
* *
65231 ATATATA
1 ATATTTT
65238 ATATTTT
1 ATATTTT
65245 ATATTTTTT
1 ATA--TTTT
65254 ATATTAATT
1 ATATT--TT
* *
65263 ATATATA
1 ATATTTT
65270 ATATTTT
1 ATATTTT
65277 ATATTTT
1 ATATTTT
65284 TCTATTTTTT
Statistics
Matches: 77, Mismatches: 19, Indels: 16
0.69 0.17 0.14
Matches are distributed among these distances:
6 4 0.05
7 47 0.61
8 7 0.09
9 19 0.25
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (7 bp):
ATATTTT
Found at i:66547 original size:26 final size:25
Alignment explanation
Indices: 66501--66555 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 25
66491 TAATTTTAAT
* *
66501 AAATTAAAATAAATTAAATATTTTC
1 AAATGAAAATAAATAAAATATTTTC
*
66526 AAATGAAAATAAAATAAAATATTTTT
1 AAATGAAAAT-AAATAAAATATTTTC
66552 AAAT
1 AAAT
66556 TAAGTTAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 9 0.35
26 17 0.65
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (25 bp):
AAATGAAAATAAATAAAATATTTTC
Found at i:66590 original size:25 final size:24
Alignment explanation
Indices: 66539--66612 Score: 84
Period size: 20 Copynumber: 3.1 Consensus size: 24
66529 TGAAAATAAA
*
66539 ATAAAATATTTTTAAATTAAGTTAAT
1 ATAAAATATATTT-AA-TAAGTTAAT
66565 AGTAAAATATATTTAATAAGTTAAT
1 A-TAAAATATATTTAATAAGTTAAT
66590 ATAAAA-A-ATTT--TAAGTTAAT
1 ATAAAATATATTTAATAAGTTAAT
66610 ATA
1 ATA
66613 TATAAGATTA
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
20 12 0.26
22 4 0.09
23 1 0.02
24 5 0.11
25 10 0.22
26 3 0.07
27 11 0.24
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (24 bp):
ATAAAATATATTTAATAAGTTAAT
Found at i:66613 original size:22 final size:23
Alignment explanation
Indices: 66555--66614 Score: 56
Period size: 22 Copynumber: 2.7 Consensus size: 23
66545 TATTTTTAAA
*
66555 TTAAGTTAATAGTA-AAATATATT
1 TTAAGTTAATA-TATAAATAAATT
66578 TAATAAGTT-A-ATATAAA-AAATT
1 T--TAAGTTAATATATAAATAAATT
66600 TTAAGTTAATATATA
1 TTAAGTTAATATATA
66615 TAAGATTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 11
0.72 0.02 0.26
Matches are distributed among these distances:
20 6 0.19
21 1 0.03
22 12 0.39
23 5 0.16
24 1 0.03
25 6 0.19
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.42
Consensus pattern (23 bp):
TTAAGTTAATATATAAATAAATT
Found at i:66974 original size:39 final size:39
Alignment explanation
Indices: 66869--66974 Score: 108
Period size: 39 Copynumber: 2.7 Consensus size: 39
66859 TTTAAAAAAT
** *
66869 AATTTAGAATGTTAATATGAAATAAATTAAGAAATTAAG
1 AATTTAGAATGTTAAGGTGAAATAATTTAAGAAATTAAG
* * *
66908 AATTTAGAACT-TTATGGTGTCAA-AATTTAAGAAATTAGG
1 AATTTAGAA-TGTTAAGGTG-AAATAATTTAAGAAATTAAG
* *
66947 ATTTTAGAATGTTAGGGTGAAATAATTT
1 AATTTAGAATGTTAAGGTGAAATAATTT
66975 GAGGATTATG
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
38 3 0.06
39 48 0.89
40 3 0.06
ACGTcount: A:0.44, C:0.02, G:0.17, T:0.37
Consensus pattern (39 bp):
AATTTAGAATGTTAAGGTGAAATAATTTAAGAAATTAAG
Found at i:67391 original size:31 final size:32
Alignment explanation
Indices: 67345--67422 Score: 104
Period size: 33 Copynumber: 2.4 Consensus size: 32
67335 TTAACTCGAG
*
67345 GTGACCACATCTTAATGAAAT-AAAAACGAAA
1 GTGACCATATCTTAATGAAATAAAAAACGAAA
* * *
67376 GTGCCCATATCTTAATTAAATAAAAAAACGTAA
1 GTGACCATATCTTAATGAAAT-AAAAAACGAAA
67409 GTGACCATATCTTA
1 GTGACCATATCTTA
67423 TGTATTTTGA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 18 0.45
33 22 0.55
ACGTcount: A:0.46, C:0.17, G:0.12, T:0.26
Consensus pattern (32 bp):
GTGACCATATCTTAATGAAATAAAAAACGAAA
Found at i:67923 original size:31 final size:31
Alignment explanation
Indices: 67885--67946 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
67875 CGACCTATTT
67885 AGGTCACCATGCAAGCGGTGCGCCATTGTTG
1 AGGTCACCATGCAAGCGGTGCGCCATTGTTG
*
67916 AGGTCACCATGCAAGCTGTGCGCCATTGTTG
1 AGGTCACCATGCAAGCGGTGCGCCATTGTTG
67947 GTCGCCATGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.19, C:0.26, G:0.31, T:0.24
Consensus pattern (31 bp):
AGGTCACCATGCAAGCGGTGCGCCATTGTTG
Found at i:68218 original size:20 final size:22
Alignment explanation
Indices: 68190--68229 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
68180 ATTGTTATGG
68190 TAAAGTATA-T-AAATATTTAA
1 TAAAGTATATTAAAATATTTAA
*
68210 TAAATTATATTAAAATATTT
1 TAAAGTATATTAAAATATTT
68230 TTTTATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 1 0.06
22 8 0.47
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (22 bp):
TAAAGTATATTAAAATATTTAA
Found at i:69279 original size:33 final size:32
Alignment explanation
Indices: 69235--69302 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 32
69225 CTTACTAAAA
*
69235 TTTATAACCCTAAGCCCTAAACCCTAAAATAT
1 TTTATAACCCTAAACCCTAAACCCTAAAATAT
69267 TTTATGAACCCTAAACCCTAAACCCTAAAATAT
1 TTTAT-AACCCTAAACCCTAAACCCTAAAATAT
69300 TTT
1 TTT
69303 GGTTGTTGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 5 0.15
33 29 0.85
ACGTcount: A:0.40, C:0.26, G:0.03, T:0.31
Consensus pattern (32 bp):
TTTATAACCCTAAACCCTAAACCCTAAAATAT
Found at i:69326 original size:36 final size:37
Alignment explanation
Indices: 69279--69405 Score: 127
Period size: 36 Copynumber: 3.4 Consensus size: 37
69269 TATGAACCCT
*
69279 AAACCCTAAACCCTAAAATATTTTGGTTGTTGA-TAA
1 AAACCCTAAACCCTAAAATATTTTGGTTATTGATTAA
* ** **
69315 AAACCCTAAACCC--AATTATTTGTTATATATTGATTTTGC
1 AAACCCTAAACCCTAAAATATTT-TGGT-TATTGA--TTAA
*
69354 AAACCCTAAGCCCTAAAATATTTTGGTTATT-ATTAA
1 AAACCCTAAACCCTAAAATATTTTGGTTATTGATTAA
69390 AAACCCTAAACCCTAA
1 AAACCCTAAACCCTAA
69406 CCATTATCCC
Statistics
Matches: 71, Mismatches: 13, Indels: 14
0.72 0.13 0.14
Matches are distributed among these distances:
34 7 0.10
35 2 0.03
36 35 0.49
38 1 0.01
39 17 0.24
40 2 0.03
41 7 0.10
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.34
Consensus pattern (37 bp):
AAACCCTAAACCCTAAAATATTTTGGTTATTGATTAA
Found at i:69856 original size:2 final size:2
Alignment explanation
Indices: 69849--69931 Score: 166
Period size: 2 Copynumber: 41.5 Consensus size: 2
69839 TTGAATTTGG
69849 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
69891 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
69932 CAAAATAATC
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:71301 original size:14 final size:13
Alignment explanation
Indices: 71282--71332 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 13
71272 GTTATATTTT
71282 TAATTTTTTATATA
1 TAATTTTTTAT-TA
71296 TAATTTTTTATTAA
1 TAATTTTTTATT-A
*
71310 TAATTTGTTTTTTTA
1 TAA-TT-TTTTATTA
71325 TAATTTTT
1 TAATTTTT
71333 ATGTTCGTCC
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
13 4 0.12
14 17 0.52
15 6 0.18
16 6 0.18
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (13 bp):
TAATTTTTTATTA
Found at i:75132 original size:13 final size:14
Alignment explanation
Indices: 75100--75133 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
75090 CATTTATATT
75100 TTTTAAATATTTTAA
1 TTTT-AATATTTTAA
75115 TTTTAATATTTT-A
1 TTTTAATATTTTAA
75128 TTTTAA
1 TTTTAA
75134 CATAAAATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.37
14 8 0.42
15 4 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTTAATATTTTAA
Found at i:76492 original size:32 final size:32
Alignment explanation
Indices: 76451--76520 Score: 113
Period size: 32 Copynumber: 2.2 Consensus size: 32
76441 GTTGTGGGCA
* * *
76451 TCATCTTCAATCTCTTACATATCACACTCATT
1 TCATCTTCAATCTCTTACACAACAAACTCATT
76483 TCATCTTCAATCTCTTACACAACAAACTCATT
1 TCATCTTCAATCTCTTACACAACAAACTCATT
76515 TCATCT
1 TCATCT
76521 AACTAAAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.30, C:0.31, G:0.00, T:0.39
Consensus pattern (32 bp):
TCATCTTCAATCTCTTACACAACAAACTCATT
Found at i:79125 original size:78 final size:79
Alignment explanation
Indices: 79043--79208 Score: 228
Period size: 78 Copynumber: 2.1 Consensus size: 79
79033 TGCCAAATCT
* * * *
79043 TTTTTTTTTTTTCAAATTTGTTAAAAA-TTCTAAAAGTTTTATATTATTTTTAACTTTGAAATTT
1 TTTTTTTTTTTTCAAATTTATTAAAAATTTCTAAAAATTTGATATTATTTTTAACTTCGAAATTT
*
79107 TAAAATTTTTAATA
66 TAAAAATTTTAATA
****
79121 -TTTTTAAAATTCAAATTTATTAAAAATTTCTAAAAATTTGATATTATTTTTAACTTCGAAATTT
1 TTTTTTTTTTTTCAAATTTATTAAAAATTTCTAAAAATTTGATATTATTTTTAACTTCGAAATTT
79185 TAAAAATTTTAATA
66 TAAAAATTTTAATA
*
79199 TTTTTATTTT
1 TTTTTTTTTT
79209 ATTAACTACA
Statistics
Matches: 72, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
77 21 0.29
78 47 0.65
79 4 0.06
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.55
Consensus pattern (79 bp):
TTTTTTTTTTTTCAAATTTATTAAAAATTTCTAAAAATTTGATATTATTTTTAACTTCGAAATTT
TAAAAATTTTAATA
Found at i:79137 original size:32 final size:34
Alignment explanation
Indices: 79067--79138 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 34
79057 AATTTGTTAA
* * ** *
79067 AAATTCTAAAAGTTTTATATTATTTTTAACTTTG
1 AAATTTTAAAAGTTTTATAATATTTTTAAAATTC
79101 AAATTTTAAAA-TTTT-TAATATTTTTAAAATTC
1 AAATTTTAAAAGTTTTATAATATTTTTAAAATTC
79133 AAATTT
1 AAATTT
79139 ATTAAAAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
32 19 0.58
33 4 0.12
34 10 0.30
ACGTcount: A:0.40, C:0.04, G:0.03, T:0.53
Consensus pattern (34 bp):
AAATTTTAAAAGTTTTATAATATTTTTAAAATTC
Found at i:86261 original size:14 final size:15
Alignment explanation
Indices: 86223--86263 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 15
86213 GTTTTTTCGG
86223 TTCGGTTCGGGTTTT
1 TTCGGTTCGGGTTTT
86238 TTAACGGTTCGGG-TTT
1 TT--CGGTTCGGGTTTT
86254 TTCGGTTCGG
1 TTCGGTTCGG
86264 TTCAGTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 8 0.33
15 2 0.08
16 5 0.21
17 9 0.38
ACGTcount: A:0.05, C:0.15, G:0.34, T:0.46
Consensus pattern (15 bp):
TTCGGTTCGGGTTTT
Found at i:88827 original size:21 final size:21
Alignment explanation
Indices: 88789--88829 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
88779 GCACCTTAGT
*
88789 TTTATTTTATTTATTTATTTA
1 TTTATTTTATTGATTTATTTA
88810 TTTATTTTACTTGA-TTATTT
1 TTTATTTTA-TTGATTTATTT
88830 TAAAACCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (21 bp):
TTTATTTTATTGATTTATTTA
Found at i:92906 original size:31 final size:31
Alignment explanation
Indices: 92871--92944 Score: 96
Period size: 32 Copynumber: 2.4 Consensus size: 31
92861 TTCAAAATCA
92871 TACCTAACATTT-ACTTTTTATTTCATTTTAG
1 TACCTAA-ATTTAACTTTTTATTTCATTTTAG
** *
92902 TACCTCATTTTTAACTTTTTGTTTCATTTTAG
1 TACCT-AAATTTAACTTTTTATTTCATTTTAG
92934 TACCTAAATTT
1 TACCTAAATTT
92945 TTAATGTCTG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
31 12 0.33
32 24 0.67
ACGTcount: A:0.24, C:0.16, G:0.04, T:0.55
Consensus pattern (31 bp):
TACCTAAATTTAACTTTTTATTTCATTTTAG
Found at i:92927 original size:32 final size:33
Alignment explanation
Indices: 92883--92948 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 33
92873 CCTAACATTT
*
92883 ACTTTTTATTTCATTTTAGTACCT-CATTTTTA
1 ACTTTTTATTTCATTTTAGTACCTAAATTTTTA
*
92915 ACTTTTTGTTTCATTTTAGTACCTAAATTTTTA
1 ACTTTTTATTTCATTTTAGTACCTAAATTTTTA
92948 A
1 A
92949 TGTCTGATAC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 23 0.74
33 8 0.26
ACGTcount: A:0.24, C:0.14, G:0.05, T:0.58
Consensus pattern (33 bp):
ACTTTTTATTTCATTTTAGTACCTAAATTTTTA
Found at i:95746 original size:20 final size:20
Alignment explanation
Indices: 95721--95814 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
95711 ATTCGGGAAA
*
95721 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
95741 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
95762 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
* *
95782 TTCGCAACGCGATACAGACT
1 ATCGCAACGCGATACTGACT
*
95802 TTCGCAACGCGAT
1 ATCGCAACGCGAT
95815 TTACTTAGCG
Statistics
Matches: 59, Mismatches: 14, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
20 45 0.76
21 14 0.24
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:95776 original size:41 final size:41
Alignment explanation
Indices: 95718--95795 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
95708 GAAATTCGGG
* * *
95718 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
* *
95759 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATA
95796 CAGACTTTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
Found at i:96395 original size:19 final size:19
Alignment explanation
Indices: 96371--96415 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
96361 GCAACGAGAT
*
96371 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
96390 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
96409 AATCGCA
1 AATCGCA
96416 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:96509 original size:58 final size:57
Alignment explanation
Indices: 96411--96519 Score: 173
Period size: 58 Copynumber: 1.9 Consensus size: 57
96401 GAAACCAAAA
*
96411 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* * *
96468 TCGCGTTGTGATTTTAATTTCGCGGTTGCGATTTTCATTTCGCGTTGCGATT
1 TCGCATTGCGATTTTAATTTCGC-ATTGCGATTTTCATTTCGCGTTGCGATT
96520 GTCTGGTCGC
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
57 20 0.43
58 27 0.57
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.47
Consensus pattern (57 bp):
TCGCATTGCGATTTTAATTTCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:96530 original size:39 final size:38
Alignment explanation
Indices: 96416--96600 Score: 168
Period size: 39 Copynumber: 4.9 Consensus size: 38
96406 CAAAATCGCA
*
96416 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGC-G
1 TTGCGATTTTCATTTCGCGTTGCGATTTTC-TTTCGCGG
* *
96454 TTGCGATTTTCATTTCGCGTTGTGATTTTAATTTCGCGG
1 TTGCGATTTTCATTTCGCGTTGCGATTTT-CTTTCGCGG
*
96493 TTGCGATTTTCATTTCGCGTTGCGATTGTC--T---GG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTCTTTCGCGG
* ** **
96526 TCGCGATAGTCATTTCGCGTTGCGATAGTCATTTC-CGCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTC-TTTCGCG-G
* *
96565 TTGCGATTCTCATTATCTCGTTGCGATTTTCATTTC
1 TTGCGATTTTCATT-TCGCGTTGCGATTTTC-TTTC
96601 AACCAAAAGA
Statistics
Matches: 122, Mismatches: 16, Indels: 16
0.79 0.10 0.10
Matches are distributed among these distances:
33 28 0.23
36 2 0.02
38 34 0.28
39 40 0.33
40 18 0.15
ACGTcount: A:0.13, C:0.21, G:0.22, T:0.45
Consensus pattern (38 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTCTTTCGCGG
Found at i:96530 original size:58 final size:57
Alignment explanation
Indices: 96411--96600 Score: 165
Period size: 58 Copynumber: 3.4 Consensus size: 57
96401 GAAACCAAAA
* * * *
96411 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATTTCGCATTGCGATTTTCATTTCGCGTTGCGATTGTCATG
* *
96468 TCGCGTTGTGATTTTAATTTCGCGGTTGCGATTTTCATTTCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTAATTTCGC-ATTGCGATTTTCATTTCGCGTTGCGATTGTCATG
* ** * * ** * *
96523 T-G-GTCGCGATAGTCATTTCGCGTTGCGATAGTCATTTCCGCGTTGCGATTCTCATTA
1 TCGCGTTGCGATTTTAATTTCGCATTGCGATTTTCATTT-CGCGTTGCGATTGTCA-TG
* *
96580 TCTCGTTGCGATTTTCATTTC
1 TCGCGTTGCGATTTTAATTTC
96601 AACCAAAAGA
Statistics
Matches: 108, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
52 14 0.13
53 28 0.26
54 1 0.01
55 1 0.01
57 21 0.19
58 29 0.27
59 14 0.13
ACGTcount: A:0.13, C:0.21, G:0.22, T:0.44
Consensus pattern (57 bp):
TCGCGTTGCGATTTTAATTTCGCATTGCGATTTTCATTTCGCGTTGCGATTGTCATG
Found at i:96577 original size:20 final size:19
Alignment explanation
Indices: 96411--96600 Score: 210
Period size: 19 Copynumber: 10.1 Consensus size: 19
96401 GAAACCAAAA
*
96411 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
96430 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
96449 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
96468 TCGCGTTGTGATTTTAATT
1 TCGCGTTGCGATTTTCATT
96487 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
96507 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
96523 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
**
96540 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
96559 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
96579 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
96599 TC
1 TC
96601 AACCAAAAGA
Statistics
Matches: 150, Mismatches: 13, Indels: 16
0.84 0.07 0.09
Matches are distributed among these distances:
14 10 0.07
15 1 0.01
16 1 0.01
17 1 0.01
18 1 0.01
19 86 0.57
20 49 0.33
21 1 0.01
ACGTcount: A:0.13, C:0.21, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:98651 original size:42 final size:42
Alignment explanation
Indices: 98591--98683 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
98581 GCCCGACTCG
* * *
98591 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
98633 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* *
98675 ACTGTCATC
1 CCTATCATC
98684 GTTGAAGAGG
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.22, C:0.39, G:0.16, T:0.24
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:100090 original size:13 final size:14
Alignment explanation
Indices: 100065--100099 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
100055 ATTGTTTAAT
100065 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
100079 TGATTTGT-AAAGT
1 TGATTTGTAAAAGG
100092 TGATTTGT
1 TGATTTGT
100100 TTAATTGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.46
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:100108 original size:13 final size:14
Alignment explanation
Indices: 100052--100100 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 14
100042 TTGCTTATTT
*
100052 TTGA-TTGTTTAA-
1 TTGATTTGTTAAAG
*
100064 TTGATTTGTAAAAG
1 TTGATTTGTTAAAG
*
100078 GTGATTTG-TAAAG
1 TTGATTTGTTAAAG
100091 TTGATTTGTT
1 TTGATTTGTT
100101 TAATTGATGT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
12 4 0.14
13 17 0.59
14 8 0.28
ACGTcount: A:0.27, C:0.00, G:0.22, T:0.51
Consensus pattern (14 bp):
TTGATTTGTTAAAG
Found at i:100330 original size:32 final size:33
Alignment explanation
Indices: 100281--100372 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
100271 ATTAAATTCG
100281 CGTTGCGA-TTTCATTTCGCATTGCGATTC-CT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
100312 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
100345 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
100373 AGTAATTTCC
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
31 8 0.14
32 21 0.36
33 30 0.51
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:102663 original size:12 final size:12
Alignment explanation
Indices: 102646--102670 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
102636 TCTTCGGGGA
102646 CTTTTTCTTCTT
1 CTTTTTCTTCTT
102658 CTTTTTCTTCTT
1 CTTTTTCTTCTT
102670 C
1 C
102671 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:104159 original size:14 final size:14
Alignment explanation
Indices: 104140--104176 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
104130 CATCAATTAA
104140 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
104154 ACAAATCATCTTTT
1 ACAAATCAACATTT
104168 ACAAATCAA
1 ACAAATCAA
104177 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:104748 original size:14 final size:14
Alignment explanation
Indices: 104729--104765 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
104719 CATCAATTAA
104729 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
104743 ACAAATCATCTTTT
1 ACAAATCAACATTT
104757 ACAAATCAA
1 ACAAATCAA
104766 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:104910 original size:588 final size:588
Alignment explanation
Indices: 103766--105600 Score: 3586
Period size: 588 Copynumber: 3.1 Consensus size: 588
103756 TTTAACAATT
*
103766 ATTATTGAATTCTAGGTACTT-ACCAAATATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
103830 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
66 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
103895 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
131 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
103960 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATG-AAATCGCATTGCGATTTTC
196 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
104024 TCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
261 TCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
104089 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
326 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
104154 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCA
391 ACAAATCATCTTTTACAAATCAATTAAACAATC-AAAAATAATAATAATTCTTATTTCTTCATCA
104219 ATTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGG
455 ATTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGG
104284 ATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACA
520 ATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACA
104349 GCAA
585 GCAA
*
104353 ATTATTGAATTCTATGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
*
104418 CATGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
66 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
104483 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
131 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
104548 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
196 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
104613 TCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
261 TCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
*
104678 TCAACAAATCAACTATTACATTTCAACATAAATTATGTACACATCAATTAAACAAATCAACATTT
326 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
104743 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAATAATAATAATTCTTATTTCTTCATCAA
391 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAATAATAATAATTCTTATTTCTTCATCAA
104808 TTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGA
456 TTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGA
104873 TTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAG
521 TTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAG
104938 CAA
586 CAA
104941 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
105006 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
66 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
*
105071 GAGTTTGAACATTGCTATGATATGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
131 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
105136 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
196 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
105201 TCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
261 TCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
*
105266 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATTAATTAAACAAATCAACATTT
326 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
105331 AC-AATCATCTTTTACAAATCAATTAAACAATCAAAAATAATAATAATTCTTATTTCTTCATCAA
391 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAATAATAATAATTCTTATTTCTTCATCAA
105395 TTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGA
456 TTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGA
105460 TTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAG
521 TTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAG
105525 CAA
586 CAA
105528 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
105593 CTTGCATT
66 CTTGCATT
105601 TGACTTACCA
Statistics
Matches: 1237, Mismatches: 9, Indels: 4
0.99 0.01 0.00
Matches are distributed among these distances:
587 288 0.23
588 768 0.62
589 181 0.15
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (588 bp):
ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
TCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAATAATAATAATTCTTATTTCTTCATCAA
TTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGA
TTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAG
CAA
Found at i:107252 original size:20 final size:19
Alignment explanation
Indices: 107217--107283 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
107207 GAAACTTAAA
107217 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
107236 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
107256 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
107275 ATCGCAACG
1 ATCGCAACG
107284 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:107291 original size:14 final size:14
Alignment explanation
Indices: 107272--107361 Score: 90
Period size: 14 Copynumber: 5.9 Consensus size: 14
107262 ATGCGAAATG
107272 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
107286 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
107302 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
107318 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
107334 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
107350 AAAATCGCAACG
1 AAAATCGCAACG
107362 CGAAACACAA
Statistics
Matches: 64, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
14 30 0.47
16 16 0.25
18 18 0.28
ACGTcount: A:0.48, C:0.26, G:0.18, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:107375 original size:18 final size:17
Alignment explanation
Indices: 107287--107376 Score: 75
Period size: 18 Copynumber: 5.5 Consensus size: 17
107277 CGCAACGACA
*
107287 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAA-C
*
107305 AAATCGCAA--CGACA-
1 AAATCGCAACGCGAAAC
*
107319 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAA-C
*
107337 AAATCGCAA--CGACA-
1 AAATCGCAACGCGAAAC
107351 AAATCGCAACGCGAAAC
1 AAATCGCAACGCGAAAC
107368 ACAATCGCA
1 A-AATCGCA
107377 TTGCGATTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
14 18 0.30
16 16 0.27
17 1 0.02
18 25 0.42
ACGTcount: A:0.47, C:0.27, G:0.18, T:0.09
Consensus pattern (17 bp):
AAATCGCAACGCGAAAC
Found at i:107376 original size:32 final size:32
Alignment explanation
Indices: 107256--107366 Score: 204
Period size: 32 Copynumber: 3.4 Consensus size: 32
107246 GGAAATGGCT
*
107256 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
107289 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
107321 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
107353 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
107367 CACAATCGCA
Statistics
Matches: 77, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
32 62 0.81
33 15 0.19
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAATCGCAACGACAAA
Found at i:107399 original size:19 final size:19
Alignment explanation
Indices: 107372--107506 Score: 85
Period size: 19 Copynumber: 7.6 Consensus size: 19
107362 CGAAACACAA
*
107372 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
107391 TCGCGTTGCGA-TTT--TG
1 TCGCGTTGCGATTTTCATT
107407 T--CGTTGCGA-TTTCATT
1 TCGCGTTGCGATTTTCATT
*
107423 TCGCGTTGCGA-TTT--TG
1 TCGCGTTGCGATTTTCATT
107439 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* ***
107456 TCGCATTGCGATAGCCATT
1 TCGCGTTGCGATTTTCATT
**
107475 TCCGCGTTGCGATAGTCATTT
1 T-CGCGTTGCGATTTTCA-TT
*
107496 TCGTGTTGCGA
1 TCGCGTTGCGA
107507 AAGTAAACTA
Statistics
Matches: 93, Mismatches: 12, Indels: 21
0.74 0.10 0.17
Matches are distributed among these distances:
14 19 0.20
15 3 0.03
16 6 0.06
17 2 0.02
18 14 0.15
19 23 0.25
20 23 0.25
21 3 0.03
ACGTcount: A:0.13, C:0.21, G:0.24, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:107413 original size:14 final size:14
Alignment explanation
Indices: 107394--107451 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
107384 TTTCATTTCG
107394 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
107408 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
107424 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
107440 CGTTGCGATTTT
1 CGTTGCGATTTT
107452 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:107458 original size:33 final size:33
Alignment explanation
Indices: 107377--107467 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
107367 CACAATCGCA
107377 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
107410 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
107442 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
107468 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:107486 original size:20 final size:19
Alignment explanation
Indices: 107452--107506 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
107442 TTGCGATTTT
*
107452 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
107471 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
107491 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
107507 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:108005 original size:18 final size:18
Alignment explanation
Indices: 107979--108023 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
107969 GTCGATCAGA
*
107979 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
107997 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
108015 TGATGGCTC
1 TGATGGCTC
108024 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:109366 original size:20 final size:20
Alignment explanation
Indices: 109341--109394 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
109331 AATAGTTTCT
109341 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
** *
109361 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACAC
*
109381 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
109395 GTTGCGATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:109653 original size:22 final size:22
Alignment explanation
Indices: 109628--109671 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
109618 GATTTAGATA
109628 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
109650 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
109672 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:109884 original size:20 final size:20
Alignment explanation
Indices: 109859--109952 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
109849 GATTATGTAT
109859 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
109879 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
109899 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
109920 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
109940 TATCGCATTGCGA
1 TATCGCGTTGCGA
109953 TTTTCTCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:109924 original size:41 final size:42
Alignment explanation
Indices: 109879--110014 Score: 118
Period size: 41 Copynumber: 3.3 Consensus size: 42
109869 CGAAAGTCAG
* * * *
109879 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTAT
1 TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
* * *
109920 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCTCAA
1 TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
** ** * *
109962 T-TCGCGTTGCG-ATTTACTTATTCGCATTGCGAATTTCCCAA
1 TATCGCGTTGCGAAAGTAAGTA-TCGCATTGCGATTTTCTCAA
110003 T-TCGCGTTGCGA
1 TATCGCGTTGCGA
110015 TTTACTTATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
40 3 0.04
41 70 0.92
42 3 0.04
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (42 bp):
TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
Found at i:109953 original size:20 final size:20
Alignment explanation
Indices: 109839--109953 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
109829 CGCTTTGAAA
*
109839 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
109860 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
109880 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
109900 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
109921 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
109941 ATCGCATTGCGAT
1 ATCGCATTGCGAT
109954 TTTCTCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:109986 original size:20 final size:20
Alignment explanation
Indices: 109942--110034 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
109932 ATAGTCAGTA
*
109942 TCGCATTGCGATTTTCTCAAT
1 TCGCATTGCGATTTACT-AAT
* *
109963 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
* *
109983 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTAAT
* *
110004 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
110024 TCGCATTGCGA
1 TCGCATTGCGA
110035 ATTGGGAAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.47
21 31 0.53
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTAAT
Found at i:110015 original size:41 final size:41
Alignment explanation
Indices: 109942--110037 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
109932 ATAGTCAGTA
* *
109942 TCGCATTGCGATTTTCTCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
109983 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
110024 TCGCATTGCGAATT
1 TCGCATTGCGAATT
110038 GGGAAAATCG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:110805 original size:22 final size:22
Alignment explanation
Indices: 110757--110807 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
110747 ATAATTGTTT
* **
110757 ATTTAAATATCTACAATTGTTT
1 ATTTAAATATCTACAATTATAA
110779 ATTTAAATATCTACAA-TATAA
1 ATTTAAATATCTACAATTATAA
110800 AGTTTAAA
1 A-TTTAAA
110808 AACCTTAGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 3 0.12
22 22 0.88
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (22 bp):
ATTTAAATATCTACAATTATAA
Found at i:110805 original size:26 final size:22
Alignment explanation
Indices: 110749--110795 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
110739 GGAAATATAT
110749 AATTGTTTATTTAAATATCTAC
1 AATTGTTTATTTAAATATCTAC
110771 AATTGTTTATTTAAATATCTAC
1 AATTGTTTATTTAAATATCTAC
110793 AAT
1 AAT
110796 ATAAAGTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.38, C:0.09, G:0.04, T:0.49
Consensus pattern (22 bp):
AATTGTTTATTTAAATATCTAC
Found at i:111061 original size:21 final size:21
Alignment explanation
Indices: 111011--111062 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
111001 CTTTTATAAC
111011 ACATTTATATATGTCTTTGTGAT
1 ACATTT-T-TATGTCTTTGTGAT
*
111034 ACGTTTTTATGTCTTTGTGAT
1 ACATTTTTATGTCTTTGTGAT
*
111055 GCATTTTT
1 ACATTTTT
111063 CTTTGTCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 20 0.77
22 1 0.04
23 5 0.19
ACGTcount: A:0.19, C:0.10, G:0.15, T:0.56
Consensus pattern (21 bp):
ACATTTTTATGTCTTTGTGAT
Done.