Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006817.1 Corchorus capsularis cultivar CVL-1 contig06838, 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: 156117
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:2852 original size:20 final size:21
Alignment explanation
Indices: 2829--2868 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
2819 GAAAATATTT
*
2829 TTAT-AATTTTTTTAACCTTC
1 TTATAAATTTTGTTAACCTTC
2849 TTATGAAATTTTGTTAACCT
1 TTAT-AAATTTTGTTAACCT
2869 CCCTAAAGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
22 13 0.76
ACGTcount: A:0.28, C:0.12, G:0.05, T:0.55
Consensus pattern (21 bp):
TTATAAATTTTGTTAACCTTC
Found at i:3054 original size:22 final size:22
Alignment explanation
Indices: 3029--3245 Score: 224
Period size: 22 Copynumber: 9.9 Consensus size: 22
3019 AGTCAAACTC
* * *
3029 TGAAATTTTGATAATCACACTA
1 TGAAATTTTGATAACCTCCCTA
*
3051 TGAAATTTTGATAACCTCGCTA
1 TGAAATTTTGATAACCTCCCTA
* *
3073 TGAAATTTTGATACATCTTCCTA
1 TGAAATTTTGATA-ACCTCCCTA
*
3096 TAAAATTTTGATAAACCTCCCTA
1 TGAAATTTTGAT-AACCTCCCTA
*
3119 TAAAATTTTGATAACCTCCCTA
1 TGAAATTTTGATAACCTCCCTA
** **
3141 TGATTTTTTGATAACCTCATTA
1 TGAAATTTTGATAACCTCCCTA
* *
3163 TGAAATTTTGTTAATCTCCCTA
1 TGAAATTTTGATAACCTCCCTA
*
3185 TGAAATTTTGATAACC-CTCTTA
1 TGAAATTTTGATAACCTC-CCTA
*
3207 TGAAATTTTGATATCCTCCC--
1 TGAAATTTTGATAACCTCCCTA
* *
3227 TGGAATTTTGATATCCTCC
1 TGAAATTTTGATAACCTCC
3246 ATAATAAAAG
Statistics
Matches: 165, Mismatches: 26, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
20 18 0.11
21 1 0.01
22 108 0.65
23 37 0.22
24 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.09, T:0.41
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCCCTA
Found at i:3077 original size:44 final size:43
Alignment explanation
Indices: 3029--3738 Score: 208
Period size: 44 Copynumber: 16.4 Consensus size: 43
3019 AGTCAAACTC
3029 TGAAATTTTGATAATCACACTATGAAATTTTGATAACCTCGCTA
1 TGAAATTTTGATAATCACACTATGAAATTTTGATAACCTC-CTA
* *
3073 TGAAATTTTGATACATCTTC-CTATAAAATTTTGATAAACCTCCCTA
1 TGAAATTTTGATA-ATC-ACACTATGAAATTTTGAT-AACCT-CCTA
* * * * ** *
3119 TAAAATTTTGATAACCTCCCTATGATTTTTTGATAACCTCATTA
1 TGAAATTTTGATAATCACACTATGAAATTTTGATAACCTC-CTA
* * * *
3163 TGAAATTTTGTTAATCTCCCTATGAAATTTTGATAACCCTCTTA
1 TGAAATTTTGATAATCACACTATGAAATTTTGATAA-CCTCCTA
* ** * *
3207 TGAAATTTTGAT-ATC-CTCCCTGGAATTTTGATATCCTCCATAA
1 TGAAATTTTGATAATCACACTATGAAATTTTGATAACCTCC-T-A
** * ** * * *
3250 T-AAAAGTT--TAATAAC-CT-TCCTAA-TTTGGTAACTATACTA
1 TGAAATTTTGATAATCACACTAT-GAAATTTTGATAAC-CTCCTA
* * * *
3289 TGAAATTTTGATAACCTTC-CCA-G-AA-----AT-ACC-ACTA
1 TGAAATTTTGATAATC-ACACTATGAAATTTTGATAACCTCCTA
* * * * *
3323 TGAAATTTTTG-TAATCACATTCTGAAAATTTGATAACCTCTTTC
1 TGAAA-TTTTGATAATCACACTATGAAATTTTGATAACCTC-CTA
* * ** * * *
3367 TGAAATTTTGATAACCTCTTTATAAAATTTT-ATTGACCCCTCTA
1 TGAAATTTTGATAATCACACTATGAAATTTTGA-TAACCTC-CTA
* * * *
3411 TGAAATTCTGATAATCACATTATGTAATTTTGATAACCTCGCTT
1 TGAAATTTTGATAATCACACTATGAAATTTTGATAACCTC-CTA
* * * **
3455 TGGAATTTTGATAA-CAACATTATGAAATTTTGATAATCTTTTTA
1 TGAAATTTTGATAATC-ACACTATGAAATTTTGATAA-CCTCCTA
* *
3499 T-AAATTTTGATAATCTGATCTCTATGAAATTTCGATAATCACT-CTA
1 TGAAATTTTGATAATC--A-CACTATGAAATTTTGATAA-C-CTCCTA
* * * *
3545 TGAGA-TTTGATAA-C-CTTCTATCAAATTTTGGT-A-CTCCTTA
1 TGAAATTTTGATAATCAC-ACTATGAAATTTTGATAACCTCC-TA
** * * *
3585 TGAAATTGAGACTTTTATAAC-CTTTATATGAAATTTTGATAACCACGCTA
1 TGAAATTTTGA---TAATCACAC----TATGAAATTTTGATAACCTC-CTA
* * * * *
3635 TAAAATTTTGATAATCTCCCCATGAAATATT-AGTAACCTCCTAA
1 TGAAATTTTGATAATCACACTATGAAATTTTGA-TAACCTCCT-A
* *
3679 TGAAATTTTGTTAACCACACTATGAAATTCTT-ATAACC-CAGCTA
1 TGAAATTTTGATAATCACACTATGAAATT-TTGATAACCTC--CTA
*
3723 TGACATTTTGATAATC
1 TGAAATTTTGATAATC
3739 TCTTTGATAA
Statistics
Matches: 492, Mismatches: 112, Indels: 124
0.68 0.15 0.17
Matches are distributed among these distances:
33 1 0.00
34 13 0.03
35 6 0.01
36 4 0.01
37 1 0.00
38 2 0.00
39 3 0.01
40 21 0.04
41 20 0.04
42 40 0.08
43 30 0.06
44 220 0.45
45 45 0.09
46 51 0.10
47 8 0.02
48 13 0.03
49 1 0.00
50 12 0.02
51 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (43 bp):
TGAAATTTTGATAATCACACTATGAAATTTTGATAACCTCCTA
Found at i:3397 original size:22 final size:22
Alignment explanation
Indices: 3345--3591 Score: 139
Period size: 22 Copynumber: 11.3 Consensus size: 22
3335 AATCACATTC
* *
3345 TGAAAATTTGATAACCTCTTTC
1 TGAAATTTTGATAACCTCTTTA
3367 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
* * * *
3389 TAAAATTTT-ATTGACCCCTCTA
1 TGAAATTTTGA-TAACCTCTTTA
* * * *
3411 TGAAATTCTGATAATCACATTA
1 TGAAATTTTGATAACCTCTTTA
* *
3433 TGTAATTTTGATAACCTCGCTT-
1 TGAAATTTTGATAACCTC-TTTA
* ** *
3455 TGGAATTTTGATAACAACATTA
1 TGAAATTTTGATAACCTCTTTA
* *
3477 TGAAATTTTGATAATCTTTTTA
1 TGAAATTTTGATAACCTCTTTA
* *
3499 T-AAATTTTGATAATCTGATCTCTA
1 TGAAATTTTGATAA-C--CTCTTTA
* * * *
3523 TGAAATTTCGATAATCACTCTA
1 TGAAATTTTGATAACCTCTTTA
* *
3545 TGAGA-TTTGATAACCT-TCTA
1 TGAAATTTTGATAACCTCTTTA
* * *
3565 TCAAATTTTGGT-A-CTCCTTA
1 TGAAATTTTGATAACCTCTTTA
3585 TGAAATT
1 TGAAATT
3592 GAGACTTTTA
Statistics
Matches: 169, Mismatches: 46, Indels: 22
0.71 0.19 0.09
Matches are distributed among these distances:
19 2 0.01
20 16 0.09
21 28 0.17
22 104 0.62
23 3 0.02
24 5 0.03
25 11 0.07
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTTTA
Found at i:3505 original size:21 final size:22
Alignment explanation
Indices: 3474--3538 Score: 78
Period size: 21 Copynumber: 2.9 Consensus size: 22
3464 GATAACAACA
3474 TTATGAAATTTTGATAATCTTT
1 TTATGAAATTTTGATAATCTTT
3496 TTAT-AAATTTTGATAATCTGATCT
1 TTATGAAATTTTGATAATCT--T-T
* *
3520 CTATGAAATTTCGATAATC
1 TTATGAAATTTTGATAATC
3539 ACTCTATGAG
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
21 15 0.41
22 4 0.11
23 1 0.03
24 4 0.11
25 13 0.35
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.48
Consensus pattern (22 bp):
TTATGAAATTTTGATAATCTTT
Found at i:3626 original size:22 final size:22
Alignment explanation
Indices: 3597--3736 Score: 54
Period size: 22 Copynumber: 6.4 Consensus size: 22
3587 AAATTGAGAC
*
3597 TTTT-ATAACCTTTATATGAAA
1 TTTTGATAACCTTTCTATGAAA
*** *
3618 TTTTGATAACCACGCTATAAAA
1 TTTTGATAACCTTTCTATGAAA
* ** *
3640 TTTTGATAATCTCCCCATGAAA
1 TTTTGATAACCTTTCTATGAAA
* *
3662 TATT-AGTAACC-TCCTAATGAAA
1 TTTTGA-TAACCTTTCT-ATGAAA
* ***
3684 TTTTGTTAACCACACTATGAAA
1 TTTTGATAACCTTTCTATGAAA
*** *
3706 TTCTT-ATAACCCAGCTATGACA
1 TT-TTGATAACCTTTCTATGAAA
3728 TTTTGATAA
1 TTTTGATAA
3737 TCTCTTTGAT
Statistics
Matches: 89, Mismatches: 23, Indels: 13
0.71 0.18 0.10
Matches are distributed among these distances:
21 9 0.10
22 76 0.85
23 4 0.04
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.37
Consensus pattern (22 bp):
TTTTGATAACCTTTCTATGAAA
Found at i:3804 original size:22 final size:22
Alignment explanation
Indices: 3772--3955 Score: 115
Period size: 22 Copynumber: 8.3 Consensus size: 22
3762 TTGTGAAAAT
* *
3772 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTATGAAATTTTAA
*
3794 TAACCAACCTAAGAAATTTTAA
1 TAACCAACCTATGAAATTTTAA
* **
3816 TAACCTGATCCTATGAAATTTTGG
1 TAACC--AACCTATGAAATTTTAA
*
3840 TAACC-ACACTATGAAATTTTGA
1 TAACCAAC-CTATGAAATTTTAA
** **
3862 TAA-CTTCCATATGAAATTTTGG
1 TAACCAACC-TATGAAATTTTAA
* **
3884 TAACC-ACGCTATGGAATTTTGT
1 TAACCAAC-CTATGAAATTTTAA
* *
3906 TAACC-TCCTCATGAAATTATAA
1 TAACCAACCT-ATGAAATTTTAA
* * *
3928 TAACCATCTTATGAAATTTTGA
1 TAACCAACCTATGAAATTTTAA
3950 TAACCA
1 TAACCA
3956 CATAGAGACA
Statistics
Matches: 131, Mismatches: 22, Indels: 18
0.77 0.13 0.11
Matches are distributed among these distances:
21 5 0.04
22 103 0.79
23 5 0.04
24 18 0.14
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.34
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAA
Found at i:3844 original size:46 final size:44
Alignment explanation
Indices: 3779--3889 Score: 127
Period size: 46 Copynumber: 2.5 Consensus size: 44
3769 AATTAACCAC
***
3779 CCTATGAAATTTCAATAACCAAC-CTAAGAAATTTTAATAACCTGAT
1 CCTATGAAATTTTGGTAACCAACACTAAGAAATTTTAATAA-CT--T
* *
3825 CCTATGAAATTTTGGTAACC-ACACTATGAAATTTTGATAACTT
1 CCTATGAAATTTTGGTAACCAACACTAAGAAATTTTAATAACTT
3868 CCATATGAAATTTTGGTAACCA
1 CC-TATGAAATTTTGGTAACCA
3890 CGCTATGGAA
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
43 3 0.05
44 18 0.32
45 4 0.07
46 32 0.56
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.33
Consensus pattern (44 bp):
CCTATGAAATTTTGGTAACCAACACTAAGAAATTTTAATAACTT
Found at i:3889 original size:44 final size:42
Alignment explanation
Indices: 3779--3954 Score: 163
Period size: 44 Copynumber: 4.0 Consensus size: 42
3769 AATTAACCAC
*** * *
3779 CCTATGAAATTTCAATAACCAACCTAAGAAATTTTAATAACCTGAT
1 CCTATGAAATTTTGGTAACC-ACCTATGAAATTTTGATAACC---T
*
3825 CCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACTT
1 CCTATGAAATTTTGGTAACCAC-CTATGAAATTTTGATAACCT
* *
3868 CCATATGAAATTTTGGTAACCACGCTATGGAATTTTGTTAACCT
1 CC-TATGAAATTTTGGTAACCAC-CTATGAAATTTTGATAACCT
* ** *
3912 CCTCATGAAATTATAATAACCATCTTATGAAATTTTGATAACC
1 CCT-ATGAAATTTTGGTAACCA-CCTATGAAATTTTGATAACC
3955 ACATAGAGAC
Statistics
Matches: 110, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
43 4 0.04
44 70 0.64
45 3 0.03
46 33 0.30
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (42 bp):
CCTATGAAATTTTGGTAACCACCTATGAAATTTTGATAACCT
Found at i:3931 original size:66 final size:66
Alignment explanation
Indices: 3772--3956 Score: 171
Period size: 66 Copynumber: 2.8 Consensus size: 66
3762 TTGTGAAAAT
* * * * *
3772 TAACCACCCTATGAAATT-TCAATAACCAACCTAAGAAATTTTAATAACCTGATC-CTATGAAAT
1 TAACCACACTATGAAATTAT-AATAACCATCATATGAAATTTTGATAACC--A-CGCTATGAAAT
3835 TTTGG
62 TTTGG
* * * * *
3840 TAACCACACTATGAAATTTTGATAA-CTTCCATATGAAATTTTGGTAACCACGCTATGGAATTTT
1 TAACCACACTATGAAATTATAATAACCAT-CATATGAAATTTTGATAACCACGCTATGAAATTTT
*
3904 GT
65 GG
* *
3906 TAACCTC-CTCATGAAATTATAATAACCATCTTATGAAATTTTGATAACCAC
1 TAACCACACT-ATGAAATTATAATAACCATCATATGAAATTTTGATAACCAC
3957 ATAGAGACAA
Statistics
Matches: 96, Mismatches: 16, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
65 3 0.03
66 52 0.54
67 3 0.03
68 37 0.39
69 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (66 bp):
TAACCACACTATGAAATTATAATAACCATCATATGAAATTTTGATAACCACGCTATGAAATTTTG
G
Found at i:4157 original size:19 final size:20
Alignment explanation
Indices: 4126--4163 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
4116 TATTGCCATT
4126 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
4145 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
4164 TCTAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:4310 original size:15 final size:15
Alignment explanation
Indices: 4290--4338 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
4280 ACAATCTAAT
4290 ATAATTAATAATGGA
1 ATAATTAATAATGGA
* *
4305 ATAATTTATAAT-TA
1 ATAATTAATAATGGA
4319 A-AA--AATAATGGA
1 ATAATTAATAATGGA
4331 ATAATTAA
1 ATAATTAA
4339 AATATTATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
11 5 0.19
12 2 0.08
13 4 0.15
14 2 0.08
15 13 0.50
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (15 bp):
ATAATTAATAATGGA
Found at i:4409 original size:30 final size:32
Alignment explanation
Indices: 4364--4429 Score: 109
Period size: 31 Copynumber: 2.1 Consensus size: 32
4354 TGGTAATTTA
*
4364 GAAATATGTTTTTAAAAA-AAGGGTACAATTG
1 GAAATATGTTTTTAAAAATAAGGGTACAATCG
4395 GAAATATG-TTTTAAAAATAAGGGTACAATCG
1 GAAATATGTTTTTAAAAATAAGGGTACAATCG
4426 GAAA
1 GAAA
4430 ACATAAAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
30 9 0.27
31 24 0.73
ACGTcount: A:0.47, C:0.05, G:0.20, T:0.29
Consensus pattern (32 bp):
GAAATATGTTTTTAAAAATAAGGGTACAATCG
Found at i:6314 original size:21 final size:19
Alignment explanation
Indices: 6282--6320 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
6272 CAATCAAGCA
6282 AATCAAGATTCAAAGCATC
1 AATCAAGATTCAAAGCATC
*
6301 AATCATAGCATTCATAGCAT
1 AATCA-AG-ATTCAAAGCAT
6321 ATGGGTCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 2 0.12
21 10 0.59
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.26
Consensus pattern (19 bp):
AATCAAGATTCAAAGCATC
Found at i:13832 original size:35 final size:35
Alignment explanation
Indices: 13783--13860 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 35
13773 GAATTGCTGT
* * * *
13783 TTTATTTAATTACACCAAATTAAGTT-AGTTACCAA
1 TTTACTTAACTACACCAAACTAAGTTGA-TTACAAA
*
13818 TTTACTTAACTACACCGAACTAAGTTGATTACAAA
1 TTTACTTAACTACACCAAACTAAGTTGATTACAAA
*
13853 ATTACTTA
1 TTTACTTA
13861 GTCTAATCTC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
35 35 0.97
36 1 0.03
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.37
Consensus pattern (35 bp):
TTTACTTAACTACACCAAACTAAGTTGATTACAAA
Found at i:13882 original size:56 final size:56
Alignment explanation
Indices: 13813--14493 Score: 1018
Period size: 56 Copynumber: 12.3 Consensus size: 56
13803 TAAGTTAGTT
* * * * *
13813 ACCAATTTACTTAACTACACCGAACTAAGTTGATTACAAAATTACTTAGTCTAATC
1 ACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATC
* * * * * * * *
13869 TCTAATTTTCTTAATTACACCGAATTAAGTTGATTACAAAATTATTTAGTCTAGTC
1 ACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATC
13925 ACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATC
1 ACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATC
* * *
13981 ACCAATTTACTTAATTACATCGAATTAAGTTGATTACCAAATTACTTAACTTAATT
1 ACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATC
* *
14037 TCCAA-TTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAGTTTAATC
1 ACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATC
* *
14092 ACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATGACTTAATTTAATT
1 ACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATC
* * *
14148 ACCAATTTACTTAATTACGCTGAATTAAGTTGATTACCAAATTACTTAACTTAATC
1 ACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATC
* *
14204 ACCAATTTACTTAATTACACCGAATTAAGTTAATTACCAAATTACCTAA--T--T-
1 ACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATC
* *
14255 ACCAATTTACTTAATTACATCGAATTAAGTTAATTACCAAATTACTTAA-TTAATC
1 ACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATC
*
14310 ACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATT
1 ACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATC
*
14366 ACCAATTTACTTAATTACACCGAATTAAGTTAATTACCAAATTACTTAATTTAATC
1 ACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATC
* * *
14422 ACCAATTTACTTAATTACACTGAACTAAGTTGATTACCAAATTACTTAATTTAATT
1 ACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATC
14478 ACCAATTTAC-TAATTA
1 ACCAATTTACTTAATTA
14494 ATCCCTTTTA
Statistics
Matches: 572, Mismatches: 47, Indels: 13
0.91 0.07 0.02
Matches are distributed among these distances:
51 47 0.08
52 2 0.00
54 2 0.00
55 103 0.18
56 418 0.73
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.38
Consensus pattern (56 bp):
ACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATC
Found at i:14023 original size:27 final size:27
Alignment explanation
Indices: 13993--14080 Score: 81
Period size: 27 Copynumber: 3.2 Consensus size: 27
13983 CAATTTACTT
13993 AATTACATCGAATTAAGTTGATTACCA
1 AATTACATCGAATTAAGTTGATTACCA
* * * **
14020 AATTAC-T-TAACTTAATTTCCAATTACTT
1 AATTACATCGAA-TTAAGTT--GATTACCA
*
14048 AATTACACCGAATTAAGTTGATTACCA
1 AATTACATCGAATTAAGTTGATTACCA
14075 AATTAC
1 AATTAC
14081 TTAGTTTAAT
Statistics
Matches: 45, Mismatches: 11, Indels: 10
0.68 0.17 0.15
Matches are distributed among these distances:
25 2 0.04
26 7 0.16
27 17 0.38
28 11 0.24
29 6 0.13
30 2 0.04
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.36
Consensus pattern (27 bp):
AATTACATCGAATTAAGTTGATTACCA
Found at i:14127 original size:19 final size:19
Alignment explanation
Indices: 14040--14128 Score: 53
Period size: 19 Copynumber: 4.8 Consensus size: 19
14030 CTTAATTTCC
*
14040 AATT-ACTTAATTACACCG
1 AATTAACTTGATTACACCG
* *
14058 AATTAAGTTGATT--ACCA
1 AATTAACTTGATTACACCG
*
14075 AATT-ACTTAGTTTAATCACC-
1 AATTAACTT-GATT-A-CACCG
* *
14095 AATTTACTTAATTACACCG
1 AATTAACTTGATTACACCG
*
14114 AATTAAGTTGATTAC
1 AATTAACTTGATTAC
14129 CAAATGACTT
Statistics
Matches: 53, Mismatches: 10, Indels: 15
0.68 0.13 0.19
Matches are distributed among these distances:
16 3 0.06
17 10 0.19
18 8 0.15
19 19 0.36
20 6 0.11
21 7 0.13
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.37
Consensus pattern (19 bp):
AATTAACTTGATTACACCG
Found at i:14148 original size:21 final size:21
Alignment explanation
Indices: 14124--14163 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
14114 AATTAAGTTG
14124 ATTACCAAATGACTTAATTTA
1 ATTACCAAATGACTTAATTTA
* *
14145 ATTACCAATTTACTTAATT
1 ATTACCAAATGACTTAATT
14164 ACGCTGAATT
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:0.40, C:0.15, G:0.03, T:0.42
Consensus pattern (21 bp):
ATTACCAAATGACTTAATTTA
Found at i:14366 original size:21 final size:21
Alignment explanation
Indices: 14342--14492 Score: 89
Period size: 21 Copynumber: 7.9 Consensus size: 21
14332 AATTAAGTTG
14342 ATTACCAAATTACTTAATTTA
1 ATTACCAAATTACTTAATTTA
*
14363 ATTACCAATTTACTTAA-TT-
1 ATTACCAAATTACTTAATTTA
* * *
14382 A-CACC-GA--A-TTAAGTTA
1 ATTACCAAATTACTTAATTTA
14398 ATTACCAAATTACTTAATTTA
1 ATTACCAAATTACTTAATTTA
* *
14419 ATCACCAATTTACTTAA-TT-
1 ATTACCAAATTACTTAATTTA
* ** * *
14438 A-CA-CTGA--AC-TAAGTTG
1 ATTACCAAATTACTTAATTTA
14454 ATTACCAAATTACTTAATTTA
1 ATTACCAAATTACTTAATTTA
*
14475 ATTACCAATTTAC-TAATT
1 ATTACCAAATTACTTAATT
14493 AATCCCTTTT
Statistics
Matches: 98, Mismatches: 18, Indels: 29
0.68 0.12 0.20
Matches are distributed among these distances:
14 7 0.07
15 7 0.07
16 2 0.02
17 5 0.05
18 8 0.08
19 2 0.02
20 12 0.12
21 55 0.56
ACGTcount: A:0.40, C:0.17, G:0.03, T:0.40
Consensus pattern (21 bp):
ATTACCAAATTACTTAATTTA
Found at i:14381 original size:274 final size:277
Alignment explanation
Indices: 13802--14493 Score: 1038
Period size: 274 Copynumber: 2.5 Consensus size: 277
13792 TTACACCAAA
* * * * * * *
13802 TTAAGTTAGTTACCAATTTACTTAACTACACCGAACTAAGTTGATTACAAAATTACTTAGTCTAA
1 TTAATTTAATTACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAA
* * * * * * *
13867 TCT-CTAATTTTCTTAATTACACCGAATTAAGTTGATTACAAAATTA-TTTAGTCTAGTCACCAA
66 T-TACCAATTTACTTAATTACACTGAATTAAGTTGATTACCAAATTACTTAACT-TAATCACCAA
* *
13930 TTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATCACCAATTTACTTAA
129 TTTACTTAATTACACCGAATTAAGTTAATTACCAAATTACCTAA-TT-ATCACCAATTTACTTAA
* **
13995 TTACATCGAATTAAGTTGATTACCAAATTACTTAACTTAATTTCCAATTACTTAATTACACCGAA
192 TTACATCGAATTAAGTTAATTACCAAATTACTTAACTTAATCACCAATTACTTAATTACACCGAA
14060 TTAAGTTGATTACCAAATTAC
257 TTAAGTTGATTACCAAATTAC
* * *
14081 TTAGTTTAATCACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATGACTTAATTTAA
1 TTAATTTAATTACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAA
*
14146 TTACCAATTTACTTAATTACGCTGAATTAAGTTGATTACCAAATTACTTAACTTAATCACCAATT
66 TTACCAATTTACTTAATTACACTGAATTAAGTTGATTACCAAATTACTTAACTTAATCACCAATT
14211 TACTTAATTACACCGAATTAAGTTAATTACCAAATTACCTAA-T-T-ACCAATTTACTTAATTAC
131 TACTTAATTACACCGAATTAAGTTAATTACCAAATTACCTAATTATCACCAATTTACTTAATTAC
14273 ATCGAATTAAGTTAATTACCAAATTACTTAA-TTAATCACCAATTTACTTAATTACACCGAATTA
196 ATCGAATTAAGTTAATTACCAAATTACTTAACTTAATCACCAA-TTACTTAATTACACCGAATTA
14337 AGTTGATTACCAAATTAC
260 AGTTGATTACCAAATTAC
*
14355 TTAATTTAATTACCAATTTACTTAATTACACCGAATTAAGTTAATTACCAAATTACTTAATTTAA
1 TTAATTTAATTACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAA
* * * *
14420 TCACCAATTTACTTAATTACACTGAACTAAGTTGATTACCAAATTACTTAATTTAATTACCAATT
66 TTACCAATTTACTTAATTACACTGAATTAAGTTGATTACCAAATTACTTAACTTAATCACCAATT
14485 TAC-TAATTA
131 TACTTAATTA
14494 ATCCCTTTTA
Statistics
Matches: 378, Mismatches: 32, Indels: 12
0.90 0.08 0.03
Matches are distributed among these distances:
273 15 0.04
274 211 0.56
275 1 0.00
277 1 0.00
278 1 0.00
279 145 0.38
280 4 0.01
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.38
Consensus pattern (277 bp):
TTAATTTAATTACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAA
TTACCAATTTACTTAATTACACTGAATTAAGTTGATTACCAAATTACTTAACTTAATCACCAATT
TACTTAATTACACCGAATTAAGTTAATTACCAAATTACCTAATTATCACCAATTTACTTAATTAC
ATCGAATTAAGTTAATTACCAAATTACTTAACTTAATCACCAATTACTTAATTACACCGAATTAA
GTTGATTACCAAATTAC
Found at i:14546 original size:40 final size:36
Alignment explanation
Indices: 14501--14622 Score: 127
Period size: 40 Copynumber: 3.2 Consensus size: 36
14491 TTAATCCCTT
*
14501 TTAATTACCGATTTACTGATTATTACTTTCACCTTGACTC
1 TTAATTATCGATTTACTGATTATTA-TTT---CTTGACTC
*
14541 TTAATTATCGATTTACTGATTATTATTTTTTGACTC
1 TTAATTATCGATTTACTGATTATTATTTCTTGACTC
* * * *
14577 TTAATTATCAATTCTACTAATTATTATTACTTTGATTC
1 TTAATTATCGATT-TACTGATTATTATTTC-TTGACTC
*
14615 TTGATTAT
1 TTAATTAT
14623 TAACTTTATT
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
36 19 0.26
37 13 0.18
38 13 0.18
39 3 0.04
40 24 0.33
ACGTcount: A:0.27, C:0.15, G:0.07, T:0.52
Consensus pattern (36 bp):
TTAATTATCGATTTACTGATTATTATTTCTTGACTC
Found at i:17202 original size:16 final size:16
Alignment explanation
Indices: 17149--17206 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
17139 TCCTCTCTCC
* *
17149 TTTTTATTAACTACCA
1 TTTTTACTAATTACCA
* *
17165 TCTTTACTAATTATCCTC
1 TTTTTACTAATTA-CC-A
*
17183 TTTTTACTGATTACCA
1 TTTTTACTAATTACCA
17199 TTTTTACT
1 TTTTTACT
17207 TTTGCCACCT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
16 18 0.55
17 4 0.12
18 11 0.33
ACGTcount: A:0.24, C:0.21, G:0.02, T:0.53
Consensus pattern (16 bp):
TTTTTACTAATTACCA
Found at i:17276 original size:28 final size:27
Alignment explanation
Indices: 17226--17285 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
17216 TTTATCATTT
*
17226 TTACTCTTTTCTTACTCTTTTTACTAA
1 TTACCCTTTTCTTACTCTTTTTACTAA
* * *
17253 TTACCCTTTTTTTACTCTCTTTTATTGA
1 TTACCCTTTTCTTACTCT-TTTTACTAA
17281 TTACC
1 TTACC
17286 ACTTGTTACT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 16 0.57
28 12 0.43
ACGTcount: A:0.17, C:0.23, G:0.02, T:0.58
Consensus pattern (27 bp):
TTACCCTTTTCTTACTCTTTTTACTAA
Found at i:17512 original size:28 final size:29
Alignment explanation
Indices: 17460--17520 Score: 90
Period size: 28 Copynumber: 2.1 Consensus size: 29
17450 TACTTTTTAC
17460 TACTCTTTGCCATTTTTACTTTTACTGAT
1 TACTCTTTGCCATTTTTACTTTTACTGAT
*
17489 TACTCTTTG-C-TTTTTCCTCTTTACTGAT
1 TACTCTTTGCCATTTTTACT-TTTACTGAT
17517 TACT
1 TACT
17521 ATTTTACCCT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 7 0.23
28 14 0.47
29 9 0.30
ACGTcount: A:0.15, C:0.23, G:0.07, T:0.56
Consensus pattern (29 bp):
TACTCTTTGCCATTTTTACTTTTACTGAT
Found at i:17838 original size:16 final size:16
Alignment explanation
Indices: 17817--17881 Score: 69
Period size: 16 Copynumber: 4.1 Consensus size: 16
17807 TGTTCTTTTA
17817 CTTTTACTGATTACTT
1 CTTTTACTGATTACTT
* * **
17833 CTTTTACT-TTTGCCC
1 CTTTTACTGATTACTT
17848 CTTTTACTGATTACTT
1 CTTTTACTGATTACTT
* *
17864 CCTTTACCGATTACTT
1 CTTTTACTGATTACTT
17880 CT
1 CT
17882 CTTGATTACG
Statistics
Matches: 37, Mismatches: 11, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
15 11 0.30
16 26 0.70
ACGTcount: A:0.15, C:0.26, G:0.06, T:0.52
Consensus pattern (16 bp):
CTTTTACTGATTACTT
Found at i:17881 original size:111 final size:112
Alignment explanation
Indices: 17706--17912 Score: 310
Period size: 111 Copynumber: 1.9 Consensus size: 112
17696 TTAATTACCA
* *
17706 TTTTACTGATTACTTCTTTCACTTTCACTCCATTTTACTGATTACTTCTTCTACGGGTTACTTCT
1 TTTTACTGATTACTTCTTTCACTTTCACTCCATTTTACTGATTACTTCTTCTACCGATTACTTCT
*
17771 CTTGGTTACCATTTTTCTGATTACTTCTTTTAATTTTGTTCTTTTAC
66 CTTGATTACCATTTTTCTGATTACTTCTTTTAATTTTGTTCTTTTAC
* ** *
17818 TTTTACTGATTACTTCTTTTACTTTTGC-CCCTTTTACTGATTACTTCCTT-TACCGATTACTTC
1 TTTTACTGATTACTTCTTTCACTTTCACTCCATTTTACTGATTACTT-CTTCTACCGATTACTTC
* *
17881 TCTTGATTACGATTTTTCTGATTACTTTTTTT
65 TCTTGATTACCATTTTTCTGATTACTTCTTTT
17913 TACTTTGACT
Statistics
Matches: 85, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
111 57 0.67
112 28 0.33
ACGTcount: A:0.16, C:0.21, G:0.08, T:0.55
Consensus pattern (112 bp):
TTTTACTGATTACTTCTTTCACTTTCACTCCATTTTACTGATTACTTCTTCTACCGATTACTTCT
CTTGATTACCATTTTTCTGATTACTTCTTTTAATTTTGTTCTTTTAC
Found at i:17942 original size:111 final size:111
Alignment explanation
Indices: 17708--17935 Score: 284
Period size: 111 Copynumber: 2.1 Consensus size: 111
17698 AATTACCATT
* *
17708 TTACTGATTACTTCTTTCACTTTCACTCCATTTTACTGATTACTTCTTCTACGGGTTACTTCTCT
1 TTACTGATTACTTCTTTCACTTTCACTCCATTTTACTGATTACTTCTTCTACCGATTACTTCTCT
* * * *
17773 TGGTTACCATTTTTCTGATTACTTCTTTTAATTTTGTTCTTTTACTT
66 TGATTACCATTTTTCTGATTACTTCTTTTAACTTTGCTCTTTTAC-A
* ** *
17820 TTACTGATTACTTCTTTTACTTTTGC-CCCTTTTACTGATTACTTCCTT-TACCGATTACTTCTC
1 TTACTGATTACTTCTTTCACTTTCACTCCATTTTACTGATTACTT-CTTCTACCGATTACTTCTC
* * *
17883 TTGATTACGATTTTTCTGATTACTTTTTTTTACTTTGACTC-TTTA-A
65 TTGATTACCATTTTTCTGATTACTTCTTTTAACTTTG-CTCTTTTACA
17929 TTACTGA
1 TTACTGA
17936 CTTTACTGAT
Statistics
Matches: 101, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
109 7 0.07
111 66 0.65
112 28 0.28
ACGTcount: A:0.17, C:0.21, G:0.08, T:0.54
Consensus pattern (111 bp):
TTACTGATTACTTCTTTCACTTTCACTCCATTTTACTGATTACTTCTTCTACCGATTACTTCTCT
TGATTACCATTTTTCTGATTACTTCTTTTAACTTTGCTCTTTTACA
Found at i:18654 original size:26 final size:26
Alignment explanation
Indices: 18625--18674 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
18615 AAACCCAAAA
*
18625 ACATAAGCAAAGTTAACAGCCCAAGT
1 ACATAAGCAAAGTTAAAAGCCCAAGT
18651 ACATAAGCAAAGTTAAAAGCCCAA
1 ACATAAGCAAAGTTAAAAGCCCAA
18675 ATGCAGCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.50, C:0.22, G:0.14, T:0.14
Consensus pattern (26 bp):
ACATAAGCAAAGTTAAAAGCCCAAGT
Found at i:20173 original size:27 final size:27
Alignment explanation
Indices: 20143--20195 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
20133 TTACCTTACT
20143 TTGCTTGTAATTGCCTTATTCTCTGCG
1 TTGCTTGTAATTGCCTTATTCTCTGCG
20170 TTGCTTGTAATTGCCTTATTCTCTGC
1 TTGCTTGTAATTGCCTTATTCTCTGC
20196 CATGGGGTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.11, C:0.23, G:0.17, T:0.49
Consensus pattern (27 bp):
TTGCTTGTAATTGCCTTATTCTCTGCG
Found at i:21455 original size:27 final size:27
Alignment explanation
Indices: 21358--21455 Score: 133
Period size: 27 Copynumber: 3.6 Consensus size: 27
21348 GGCTACTAAT
* * * *
21358 TGACTAAAGTGCTACTGAATGTGCAAT
1 TGACCAAAATGCTCCTGAATGTGCAAA
* *
21385 TGACTAAAATGCTCATGAATGTGCAAA
1 TGACCAAAATGCTCCTGAATGTGCAAA
21412 TGACCAAAATGCTCCTGAATGTGCAAA
1 TGACCAAAATGCTCCTGAATGTGCAAA
*
21439 TGACCAAAATGCCCCTG
1 TGACCAAAATGCTCCTG
21456 GATGACCCTA
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 64 1.00
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.24
Consensus pattern (27 bp):
TGACCAAAATGCTCCTGAATGTGCAAA
Found at i:25246 original size:13 final size:13
Alignment explanation
Indices: 25228--25252 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25218 TTCAATGTTC
25228 TAAATATTATTTA
1 TAAATATTATTTA
25241 TAAATATTATTT
1 TAAATATTATTT
25253 GGAATTCCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAATATTATTTA
Found at i:25476 original size:32 final size:32
Alignment explanation
Indices: 25426--25491 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
25416 AATCTACCAA
*
25426 TGGGGGCGGCTGCGTACGCAAGGTCTCGAACC
1 TGGGGGCGGCTGCATACGCAAGGTCTCGAACC
* *
25458 TGGGGGCGGTTGCATACGCATGGTCTCGAACC
1 TGGGGGCGGCTGCATACGCAAGGTCTCGAACC
25490 TG
1 TG
25492 AGACCTGTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.15, C:0.26, G:0.39, T:0.20
Consensus pattern (32 bp):
TGGGGGCGGCTGCATACGCAAGGTCTCGAACC
Found at i:27063 original size:32 final size:32
Alignment explanation
Indices: 27022--27083 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
27012 TCTGGTCAAA
*
27022 TTAGGGTTTGGATCAATTTAAAGTCAGGTTTT
1 TTAGAGTTTGGATCAATTTAAAGTCAGGTTTT
* * *
27054 TTAGAGTTTGGGTCAATTTCAGGTCAGGTT
1 TTAGAGTTTGGATCAATTTAAAGTCAGGTT
27084 AATTCGGATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.23, C:0.08, G:0.27, T:0.42
Consensus pattern (32 bp):
TTAGAGTTTGGATCAATTTAAAGTCAGGTTTT
Found at i:27772 original size:19 final size:20
Alignment explanation
Indices: 27736--27773 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
27726 AATTTATAAA
*
27736 TTATTTAATTTACCAATTTT
1 TTATTTAATTTACAAATTTT
27756 TTATTTAA-TTACAAATTT
1 TTATTTAATTTACAAATTT
27774 CCTTATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (20 bp):
TTATTTAATTTACAAATTTT
Found at i:27779 original size:20 final size:20
Alignment explanation
Indices: 27736--27782 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
27726 AATTTATAAA
* *
27736 TTATTTAATTTACCAATTTT
1 TTATTTAATTTACAAATTTC
27756 TTATTTAA-TTACAAATTTCC
1 TTATTTAATTTACAAATTT-C
27776 TTATTTA
1 TTATTTA
27783 TAAATATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.57
Consensus pattern (20 bp):
TTATTTAATTTACAAATTTC
Found at i:34963 original size:32 final size:31
Alignment explanation
Indices: 34927--35001 Score: 105
Period size: 33 Copynumber: 2.3 Consensus size: 31
34917 GTTTAGGTCG
34927 GTGCCGCCCCAAGGGGCGGCCTGGCCACGGTA
1 GTGCCGCCCCAA-GGGCGGCCTGGCCACGGTA
* *
34959 GTGCCGCCCCCCTAGGGCGGCCTGGCCATGGTA
1 GTGCCG--CCCCAAGGGCGGCCTGGCCACGGTA
34992 GTGCCGCCCC
1 GTGCCGCCCC
35002 CCTAGGGCGG
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
31 4 0.10
32 6 0.15
33 24 0.62
34 5 0.13
ACGTcount: A:0.09, C:0.41, G:0.37, T:0.12
Consensus pattern (31 bp):
GTGCCGCCCCAAGGGCGGCCTGGCCACGGTA
Found at i:34982 original size:33 final size:33
Alignment explanation
Indices: 34940--35012 Score: 137
Period size: 33 Copynumber: 2.2 Consensus size: 33
34930 CCGCCCCAAG
34940 GGGCGGCCTGGCCACGGTAGTGCCGCCCCCCTA
1 GGGCGGCCTGGCCACGGTAGTGCCGCCCCCCTA
*
34973 GGGCGGCCTGGCCATGGTAGTGCCGCCCCCCTA
1 GGGCGGCCTGGCCACGGTAGTGCCGCCCCCCTA
35006 GGGCGGC
1 GGGCGGC
35013 ATGAGCATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.08, C:0.40, G:0.40, T:0.12
Consensus pattern (33 bp):
GGGCGGCCTGGCCACGGTAGTGCCGCCCCCCTA
Found at i:36672 original size:11 final size:11
Alignment explanation
Indices: 36656--36686 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
36646 TTTAGGGCTT
36656 ATTTCTATGTA
1 ATTTCTATGTA
36667 ATTTCTATGTA
1 ATTTCTATGTA
36678 ATTTC-ATGT
1 ATTTCTATGT
36687 TTTGGGTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.20
11 16 0.80
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.55
Consensus pattern (11 bp):
ATTTCTATGTA
Found at i:44429 original size:21 final size:21
Alignment explanation
Indices: 44405--44454 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
44395 GCTCTATACA
44405 AAGAATCACAA-TCTCCACACC
1 AAGAATCACAATTCT-CACACC
* * *
44426 AAGAACCACAATTCTCATATC
1 AAGAATCACAATTCTCACACC
44447 AAGAATCA
1 AAGAATCA
44455 TCTACATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.46, C:0.30, G:0.06, T:0.18
Consensus pattern (21 bp):
AAGAATCACAATTCTCACACC
Found at i:56170 original size:2 final size:2
Alignment explanation
Indices: 56165--56191 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
56155 TCTCTCTCTC
56165 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
56192 TTTAATTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:61865 original size:16 final size:16
Alignment explanation
Indices: 61844--61874 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
61834 TTGAAAAATA
61844 TTACTAAATATTTATT
1 TTACTAAATATTTATT
*
61860 TTACTAAATCTTTAT
1 TTACTAAATATTTAT
61875 AATATGTGGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (16 bp):
TTACTAAATATTTATT
Found at i:63110 original size:194 final size:194
Alignment explanation
Indices: 62208--63274 Score: 1051
Period size: 194 Copynumber: 5.3 Consensus size: 194
62198 TTTATAATAA
* * *
62208 GATTATTATACAAATACACTGTCAATGTAAATTTTGTACTCCATAAGTGGGTTAAGAAGTTGACA
1 GATTATTATAC-AATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACA
* * *
62273 CACACCCTCATTTCATAATTAACTAAATATATTTGATATTAGTACATA-TTCCTTAAGGGGACAC
65 CATACCCT-ATTTCATAA-T---T-AA-ATATTTAATATTAATACATATTTCC-TAAGGGGACAC
* * * * * *
62337 ATGTGAATCCTTAAA-CCATGCACGTACAGTCTACTAAACTCTACTGACGATGT-TTGTATTATT
122 ATGTCAACCCTTAAATCC-TGCACGTGCAGTCTGCTAAACTCCACTGACG-TGTATTGTATAATT
*
62400 TTTTTTATAG
185 TTTCTTATAG
* * * **
62410 GATTATTATACAATACACTGTCAGTGTAAATTTTGAACTTCATAACCGACTTAAGAAGTTGACAC
1 GATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACAC
* ** *
62475 ATACCCTATATCATAATTAGTTAGATATAAAATATTAATACATTATTCCCTAAGGCCTAAGAGGA
66 ATACCCTATTTCATAATTA---A-ATATTTAATATTAATACA-TATT---T----CCTAAGGGGA
** * * * * *
62540 CACATGTCAACCCTTAAGCCCCGCGCGTGTAGTCTGCTAAACTCCATTGACAATGTATTGTAATA
119 CACATGTCAACCCTTAAATCCTGCACGTGCAGTCTGCTAAACTCCACTGAC-GTGTATTGT-ATA
* *
62605 TTTTTTTGTTTTATATG
182 --ATTTT-TCTTATA-G
*
62622 G-TTATTATACAATACACTGTCAGTGTAAAATTTTGGACTCCATAAGCGGGTTAGGAAGTTGACA
1 GATTATTATACAATACACTGTCAGTGT-AAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACA
* * * * *
62686 CATA-CGTCATTTCATAATTAATTAAATATTTAATATT-ACACATATTCCCTAA-GGGATACATC
65 CATACCCT-ATTTC---A-TAATTAAATATTTAATATTAATACATATTTCCTAAGGGGACACATG
* *
62748 TCAACCCTTAAACTCC-GCACGTGCAGTCTGCTAAACTCCATTGACTGTGTATTGCATAATTTTT
125 TCAACCCTTAAA-TCCTGCACGTGCAGTCTGCTAAACTCCACTGAC-GTGTATTGTATAATTTTT
62812 CTTATAG
188 CTTATAG
* * * * *
62819 G---ATT-TACAATACACTGTCAGTATAAATTATGGACTCCATAAGCGAGTTAAGAAGCTAACAC
1 GATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACAC
*
62880 ATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTTCCTAAGGGGACACATGTC
66 ATACCCTATTTC---A-TAATTAAATATTTAATATTAATACATATTTCCTAAGGGGACACATGTC
* *
62945 AACCCTTAAATCCTGCACGTGCAGTCTGCTAAAATCCACTGACGGGTATTGTATAATTTTTCTTA
127 AACCCTTAAATCCTGCACGTGCAGTCTGCTAAACTCCACTGACGTGTATTGTATAATTTTTCTTA
63010 TAG
192 TAG
* * *
63013 GATTATTATACAATATACTGTCAGTGTAAATTTTGGACTCCATAAACAGGTTAAGAAGTTGACAC
1 GATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACAC
* * * *
63078 ATACCCTATTTCATAATTAAATATTTAATATTAATACATATTCCCTAAGCGTACACATGTCAAAC
66 ATACCCTATTTCATAATTAAATATTTAATATTAATACATATTTCCTAAGGGGACACATGTCAACC
* * * *
63143 CTTAAAATTAAAGCCTGCATGTGCAGTCTGCTAAACTCCACTGATGGTGTATTATATAAATTTTC
131 CTT-AAA-T----CCTGCACGTGCAGTCTGCTAAACTCCACTGA-CGTGTATTGTATAATTTTTC
63208 TTATAG
189 TTATAG
* * * *
63214 GATTATCATACAATACACTGTCAGTGCAAATTTTTGGATTACATAAGCGGGTTAAGAAGTT
1 GATTATTATACAATACACTGTCAGTGTAAA-TTTTGGACTCCATAAGCGGGTTAAGAAGTT
63275 TTTGTGCCAA
Statistics
Matches: 728, Mismatches: 94, Indels: 86
0.80 0.10 0.09
Matches are distributed among these distances:
193 65 0.09
194 110 0.15
195 55 0.08
196 2 0.00
197 5 0.01
198 81 0.11
199 7 0.01
200 38 0.05
201 105 0.14
202 89 0.12
203 8 0.01
206 48 0.07
207 8 0.01
208 2 0.00
210 8 0.01
211 38 0.05
212 51 0.07
213 1 0.00
215 1 0.00
216 6 0.01
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (194 bp):
GATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACAC
ATACCCTATTTCATAATTAAATATTTAATATTAATACATATTTCCTAAGGGGACACATGTCAACC
CTTAAATCCTGCACGTGCAGTCTGCTAAACTCCACTGACGTGTATTGTATAATTTTTCTTATAG
Found at i:64576 original size:199 final size:199
Alignment explanation
Indices: 64045--64587 Score: 770
Period size: 189 Copynumber: 2.8 Consensus size: 199
64035 ATGAAGATTT
*
64045 ATAAGCGGGTTAAGAAGTTGACACAT--CCCATTTCATAATTAATTAAATATTTTATATTAATAC
1 ATAAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATAC
* *** * * * ** * *
64108 ATATTCTCTAAACAGACATATGTCAATCCTTAAATCCCGTGCGTGTAGTCTGCTAAACTCCATTA
66 ATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGAACGTGCAGTCTGCTAAACTCCACTA
* *
64173 ACGGTGTATTGTATAATTTTTCTTATAGGATTGTTATACAATACACTGTCAGTGTAAATTTTAGA
131 ACGGTGTATTGTATAATTTTTCTTATAGGATTATTATACAATACACTATCAGTGTAAATTTTAGA
*
64238 CTCT
196 CTCC
*
64242 ATAAACGGGTTAAGAAGTTGACACATACCCCATTT--T-A-TAATT--A-A-TTAA-A-TAATAC
1 ATAAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATAC
*
64297 ATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGAACGTGCAGTCTGCTAAACTCCACTG
66 ATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGAACGTGCAGTCTGCTAAACTCCACTA
*
64362 ACGGTGTATTGTATAATTTTTCTTAT-GGCATTATTATACAATACACTATCAGTGTAAATTTTGG
131 ACGGTGTATTGTATAATTTTTCTTATAGG-ATTATTATACAATACACTATCAGTGTAAATTTTAG
64426 ACTCC
195 ACTCC
* *
64431 ATAAGCGGGTTAAGAAGTTAACACATACCCCATTTCATAATTAATTAAATATTTAATATTAGTAC
1 ATAAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATAC
* * **
64496 ATATTCCCTAAGGGGATACATGTCAACCCTTAAACCCCAAATATGCAGTCTGCTAAACTCCACTA
66 ATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGAACGTGCAGTCTGCTAAACTCCACTA
64561 ACGGTGTATTGTATAATTTTTCTTATA
131 ACGGTGTATTGTATAATTTTTCTTATA
64588 ATAACTTTCA
Statistics
Matches: 306, Mismatches: 26, Indels: 25
0.86 0.07 0.07
Matches are distributed among these distances:
188 2 0.01
189 154 0.50
190 1 0.00
191 4 0.01
192 2 0.01
193 6 0.02
195 6 0.02
196 2 0.01
197 30 0.10
198 1 0.00
199 98 0.32
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (199 bp):
ATAAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATAC
ATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGAACGTGCAGTCTGCTAAACTCCACTA
ACGGTGTATTGTATAATTTTTCTTATAGGATTATTATACAATACACTATCAGTGTAAATTTTAGA
CTCC
Found at i:65703 original size:13 final size:13
Alignment explanation
Indices: 65685--65709 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
65675 CGGACCCAGC
65685 AAAAATGGACTGG
1 AAAAATGGACTGG
65698 AAAAATGGACTG
1 AAAAATGGACTG
65710 AAGAAGGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.28, T:0.16
Consensus pattern (13 bp):
AAAAATGGACTGG
Found at i:67343 original size:24 final size:22
Alignment explanation
Indices: 67316--67366 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 22
67306 TTGTTTGGCA
67316 TTGTTTCCGTTTTCTTGTTTT-TTT
1 TTGTTT-CG-TTT-TTGTTTTGTTT
67340 TTGTTTCGTTTTTGTTTTGTTT
1 TTGTTTCGTTTTTGTTTTGTTT
67362 TTGTT
1 TTGTT
67367 GCGCTGTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 7 0.27
22 11 0.42
23 2 0.08
24 6 0.23
ACGTcount: A:0.00, C:0.08, G:0.16, T:0.76
Consensus pattern (22 bp):
TTGTTTCGTTTTTGTTTTGTTT
Found at i:67351 original size:11 final size:11
Alignment explanation
Indices: 67337--67366 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
67327 TTCTTGTTTT
67337 TTTTTGTTTCG
1 TTTTTGTTTCG
*
67348 TTTTTGTTTTG
1 TTTTTGTTTCG
67359 TTTTTGTT
1 TTTTTGTT
67367 GCGCTGTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.03, G:0.17, T:0.80
Consensus pattern (11 bp):
TTTTTGTTTCG
Found at i:67357 original size:16 final size:15
Alignment explanation
Indices: 67332--67361 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
67322 CCGTTTTCTT
67332 GTTTTTTTTTGTTTC
1 GTTTTTTTTTGTTTC
67347 GTTTTTGTTTTGTTT
1 GTTTTT-TTTTGTTT
67362 TTGTTGCGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.00, C:0.03, G:0.17, T:0.80
Consensus pattern (15 bp):
GTTTTTTTTTGTTTC
Found at i:73394 original size:15 final size:15
Alignment explanation
Indices: 73374--73403 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
73364 ATCAGGCTGC
*
73374 CACGATACACGATAT
1 CACGATACACAATAT
73389 CACGATACACAATAT
1 CACGATACACAATAT
73404 TTCAACCAAT
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:0.43, C:0.27, G:0.10, T:0.20
Consensus pattern (15 bp):
CACGATACACAATAT
Found at i:75119 original size:15 final size:15
Alignment explanation
Indices: 75101--75136 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
75091 ATAAAAAAGA
75101 ATTTGTCAAAATAAC
1 ATTTGTCAAAATAAC
75116 ATTTGTCAAAATAAC
1 ATTTGTCAAAATAAC
75131 ATTTGT
1 ATTTGT
75137 TAAATGCACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39
Consensus pattern (15 bp):
ATTTGTCAAAATAAC
Found at i:79305 original size:21 final size:21
Alignment explanation
Indices: 79263--79305 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
79253 TTTTTTTCCC
* *
79263 TTGCTTTCTTATTCTTTTTCT
1 TTGCTTTCTTATTCTATCTCT
79284 TTGCTTTCTT-TTCTGATCTCT
1 TTGCTTTCTTATTCT-ATCTCT
79305 T
1 T
79306 CTCCCCCTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.05, C:0.21, G:0.07, T:0.67
Consensus pattern (21 bp):
TTGCTTTCTTATTCTATCTCT
Found at i:83627 original size:13 final size:13
Alignment explanation
Indices: 83609--83639 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
83599 CGGTTCTCTT
83609 AAAATATATTTTA
1 AAAATATATTTTA
*
83622 AAAATATATTTTT
1 AAAATATATTTTA
83635 AAAAT
1 AAAAT
83640 TTTTATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
AAAATATATTTTA
Found at i:83713 original size:11 final size:11
Alignment explanation
Indices: 83699--83730 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
83689 ATATTTTATA
83699 TATAATATATT
1 TATAATATATT
83710 TATAATATA--
1 TATAATATATT
83719 TATAATATATT
1 TATAATATATT
83730 T
1 T
83731 TTATATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
9 9 0.47
11 10 0.53
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
TATAATATATT
Found at i:83720 original size:20 final size:17
Alignment explanation
Indices: 83686--83747 Score: 83
Period size: 16 Copynumber: 3.6 Consensus size: 17
83676 TATATTTTTA
83686 AATATA-TTTTATATAT
1 AATATATTTTTATATAT
83702 AATATATTTATAATATATAT
1 AATATATTT-T--TATATAT
83722 AATATATTTTTATATA-
1 AATATATTTTTATATAT
83738 AATATATTTT
1 AATATATTTT
83748 AAAATTTTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
16 16 0.38
17 8 0.19
18 1 0.02
19 1 0.02
20 16 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
AATATATTTTTATATAT
Found at i:84775 original size:31 final size:30
Alignment explanation
Indices: 84704--84775 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 30
84694 ATCTATCAGC
* **
84704 TTTTAATTTGTTTAATTTAAGGCTTTTATT
1 TTTTAATTTGTTTAACTTAAGGCTTAAATT
*
84734 TTAATT-ATTTGTTTAACTTAATGCTTAAATT
1 TT--TTAATTTGTTTAACTTAAGGCTTAAATT
84765 GTTTTAATTTG
1 -TTTTAATTTG
84776 CAATAATTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
30 4 0.12
31 26 0.76
32 4 0.12
ACGTcount: A:0.26, C:0.04, G:0.10, T:0.60
Consensus pattern (30 bp):
TTTTAATTTGTTTAACTTAAGGCTTAAATT
Found at i:85072 original size:10 final size:9
Alignment explanation
Indices: 85023--85073 Score: 50
Period size: 9 Copynumber: 5.3 Consensus size: 9
85013 TATTCAATCT
85023 TTATATATA
1 TTATATATA
*
85032 TTGATAATCATG
1 TT-AT-AT-ATA
85044 TTATATATA
1 TTATATATA
85053 TTAT-TATA
1 TTATATATA
85061 TTATATATTA
1 TTATATA-TA
85071 TTA
1 TTA
85074 ATAAACTCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
8 8 0.23
9 10 0.29
10 9 0.26
11 4 0.11
12 4 0.11
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (9 bp):
TTATATATA
Found at i:85230 original size:23 final size:23
Alignment explanation
Indices: 85196--85260 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
85186 ATCGAAATCA
*
85196 AACCCGAGCCCGAACCCGACCC-
1 AACCCGAACCCGAACCCGACCCG
*
85218 AACCCTGAACCCGAACCCTACCCG
1 AACCC-GAACCCGAACCCGACCCG
* *
85242 AAACCGAACCCGAGCCCGA
1 AACCCGAACCCGAACCCGA
85261 AAATATCCGA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
22 5 0.14
23 27 0.75
24 4 0.11
ACGTcount: A:0.31, C:0.49, G:0.17, T:0.03
Consensus pattern (23 bp):
AACCCGAACCCGAACCCGACCCG
Found at i:85248 original size:17 final size:17
Alignment explanation
Indices: 85204--85262 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
85194 CAAACCCGAG
*
85204 CCCGAACCCG-ACCCAA
1 CCCGAAACCGAACCCAA
* *
85220 CCCTGAACCCGAACCCTA
1 CCC-GAAACCGAACCCAA
*
85238 CCCGAAACCGAACCCGAG
1 CCCGAAACCGAACCC-AA
85256 CCCGAAA
1 CCCGAAA
85263 ATATCCGAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
16 3 0.08
17 18 0.50
18 15 0.42
ACGTcount: A:0.32, C:0.49, G:0.15, T:0.03
Consensus pattern (17 bp):
CCCGAAACCGAACCCAA
Found at i:85280 original size:6 final size:6
Alignment explanation
Indices: 85196--85261 Score: 66
Period size: 6 Copynumber: 11.3 Consensus size: 6
85186 ATCGAAATCA
* *
85196 AACCCG AGCCCG AACCCG -ACCC- AACCCTG AACCCG AACCC- TACCCG
1 AACCCG AACCCG AACCCG AACCCG AACCC-G AACCCG AACCCG AACCCG
* *
85242 AAACCG AACCCG AGCCCG AA
1 AACCCG AACCCG AACCCG AA
85262 AATATCCGAA
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
5 12 0.25
6 31 0.65
7 5 0.10
ACGTcount: A:0.32, C:0.48, G:0.17, T:0.03
Consensus pattern (6 bp):
AACCCG
Found at i:85658 original size:31 final size:31
Alignment explanation
Indices: 85610--85669 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
85600 TTTATAAAAC
* *
85610 TTTTAAAACACCTATTATGCCCTTATTTAAT
1 TTTTAAAACACCAATTATACCCTTATTTAAT
* *
85641 TTTTGAAACACCAATTATATCCTTATTTA
1 TTTTAAAACACCAATTATACCCTTATTTA
85670 TCTAACATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.33, C:0.18, G:0.03, T:0.45
Consensus pattern (31 bp):
TTTTAAAACACCAATTATACCCTTATTTAAT
Found at i:87577 original size:2 final size:2
Alignment explanation
Indices: 87570--87594 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
87560 GTCCTTGAAA
87570 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 A
87595 ATTTATTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:88196 original size:2 final size:2
Alignment explanation
Indices: 88189--88241 Score: 81
Period size: 2 Copynumber: 27.0 Consensus size: 2
88179 AAATAGAGGA
* *
88189 AT AT AT AT AT AT AT AT AT AT -T AT AC AC 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
88230 AT AT AT AT AT AT
1 AT AT AT AT AT AT
88242 CAAATAATAA
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:94659 original size:15 final size:15
Alignment explanation
Indices: 94635--94708 Score: 103
Period size: 15 Copynumber: 4.9 Consensus size: 15
94625 CACAACATGA
*
94635 TTGTTCGCACCATTG
1 TTGTTTGCACCATTG
*
94650 TTGTTTGCACCATGG
1 TTGTTTGCACCATTG
*
94665 TTGTTCGCACCATTG
1 TTGTTTGCACCATTG
*
94680 TGGTTTGCACCATTG
1 TTGTTTGCACCATTG
*
94695 TTGTTTGCGCCATT
1 TTGTTTGCACCATT
94709 CACCCTAGCA
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 51 1.00
ACGTcount: A:0.12, C:0.23, G:0.23, T:0.42
Consensus pattern (15 bp):
TTGTTTGCACCATTG
Found at i:97420 original size:19 final size:17
Alignment explanation
Indices: 97392--97428 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
97382 TAAATAACTA
97392 ATTAATTATATTACTTAT
1 ATTAATTATATTA-TTAT
97410 ATTATATTATATTATTAT
1 ATTA-ATTATATTATTAT
97428 A
1 A
97429 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTAATTATATTATTAT
Found at i:98140 original size:2 final size:2
Alignment explanation
Indices: 98135--98167 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
98125 ACATATATAG
*
98135 AC AC AC AC AC AC AC AC AC AC AC AC CC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
98168 TAAAGTTCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:98571 original size:97 final size:97
Alignment explanation
Indices: 98405--98599 Score: 345
Period size: 97 Copynumber: 2.0 Consensus size: 97
98395 AGTCCTGAAG
* *
98405 AGCAAAATCAATTTTGCTGCCCAATTAAAATCCCAGAATGAGCTAGACTAAGTTGACTAATGGAT
1 AGCAAAATCAATTGTGCTGCCCAATTAAAATCCCAGAATGAGCAAGACTAAGTTGACTAATGGAT
98470 TTTCATATTCTTCAAGGGAGTTCAAGTTTTCA
66 TTTCATATTCTTCAAGGGAGTTCAAGTTTTCA
* * *
98502 AGCAAGATCAATTGTGTTGCCCAATTAAAATCCCAGAATGAGCAAGTCTAAGTTGACTAATGGAT
1 AGCAAAATCAATTGTGCTGCCCAATTAAAATCCCAGAATGAGCAAGACTAAGTTGACTAATGGAT
98567 TTTCATATTCTTCAAGGGAGTTCAAGTTTTCA
66 TTTCATATTCTTCAAGGGAGTTCAAGTTTTCA
98599 A
1 A
98600 CAACTTTTAA
Statistics
Matches: 93, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
97 93 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (97 bp):
AGCAAAATCAATTGTGCTGCCCAATTAAAATCCCAGAATGAGCAAGACTAAGTTGACTAATGGAT
TTTCATATTCTTCAAGGGAGTTCAAGTTTTCA
Found at i:111966 original size:41 final size:41
Alignment explanation
Indices: 111921--112002 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
111911 CTCTTTGAGT
*
111921 TCAACCCTTGTTCATTTTTTGGAACAATCATGGCATCCACA
1 TCAACCCTTGTTCATTTTTTAGAACAATCATGGCATCCACA
111962 TCAACCCTTGTTCATTTTTTAGAACAATCATGGCATCCACA
1 TCAACCCTTGTTCATTTTTTAGAACAATCATGGCATCCACA
112003 CATTTACTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.28, C:0.27, G:0.11, T:0.34
Consensus pattern (41 bp):
TCAACCCTTGTTCATTTTTTAGAACAATCATGGCATCCACA
Found at i:121361 original size:31 final size:31
Alignment explanation
Indices: 121325--121386 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
121315 GAAATTGTAA
121325 AATCACACAAAGGAATTGCATTTTGAATTAG
1 AATCACACAAAGGAATTGCATTTTGAATTAG
121356 AATCACACAAAGGAATTGCATTTTGAATTAG
1 AATCACACAAAGGAATTGCATTTTGAATTAG
121387 CCCGGTGTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (31 bp):
AATCACACAAAGGAATTGCATTTTGAATTAG
Found at i:124836 original size:40 final size:40
Alignment explanation
Indices: 124792--124898 Score: 178
Period size: 40 Copynumber: 2.7 Consensus size: 40
124782 GTTAAAGAAT
*
124792 TTAATTCATAGAAATTAAGTAAAAACAACAATCAGAAGAC
1 TTAATTCATAGAAATTAAGTAAAAACAACAATCAAAAGAC
* *
124832 TTAATTCATAGAAATTAAGTAAAAACAACAGTTAAAAGAC
1 TTAATTCATAGAAATTAAGTAAAAACAACAATCAAAAGAC
*
124872 TTAATTCATAGTAATTAAGTAAAAACA
1 TTAATTCATAGAAATTAAGTAAAAACA
124899 TCAAAGCACA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 63 1.00
ACGTcount: A:0.54, C:0.10, G:0.09, T:0.26
Consensus pattern (40 bp):
TTAATTCATAGAAATTAAGTAAAAACAACAATCAAAAGAC
Found at i:124988 original size:12 final size:12
Alignment explanation
Indices: 124971--125048 Score: 133
Period size: 12 Copynumber: 6.7 Consensus size: 12
124961 AAAATTAGGC
124971 AAAAGAAGACTG
1 AAAAGAAGACTG
124983 AAAAGAAGACTG
1 AAAAGAAGACTG
*
124995 AAAAGAAGTCTG
1 AAAAGAAGACTG
125007 AAAAGAAGACTG
1 AAAAGAAGACTG
125019 AAAAGAAGACTG
1 AAAAGAAGACTG
125031 -AAAGAAGACTG
1 AAAAGAAGACTG
125042 -AAAGAAG
1 AAAAGAAG
125049 TTAGCAAAGA
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
11 18 0.28
12 46 0.72
ACGTcount: A:0.58, C:0.08, G:0.26, T:0.09
Consensus pattern (12 bp):
AAAAGAAGACTG
Found at i:125099 original size:36 final size:36
Alignment explanation
Indices: 125049--125172 Score: 203
Period size: 36 Copynumber: 3.4 Consensus size: 36
125039 CTGAAAGAAG
*
125049 TTAGCAAAGACTTAATTTCACAAAAATTAAGTAAAA
1 TTAGCAAAGACTTAATTTCACAAGAATTAAGTAAAA
*
125085 TTGGCAAAGACTTAATTTCACAAGAATTAAGTAAAA
1 TTAGCAAAGACTTAATTTCACAAGAATTAAGTAAAA
*
125121 TTAGCAAAGACTTAATTTCACAAGAATTAAGTAAAG
1 TTAGCAAAGACTTAATTTCACAAGAATTAAGTAAAA
* *
125157 TCAGCAAAGATTTAAT
1 TTAGCAAAGACTTAAT
125173 CCAAAGATGA
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 82 1.00
ACGTcount: A:0.48, C:0.11, G:0.12, T:0.28
Consensus pattern (36 bp):
TTAGCAAAGACTTAATTTCACAAGAATTAAGTAAAA
Found at i:125186 original size:36 final size:36
Alignment explanation
Indices: 125051--125190 Score: 167
Period size: 36 Copynumber: 3.9 Consensus size: 36
125041 GAAAGAAGTT
* * *
125051 AGCAAAGACTTAATTTCACAAAAATTAAGTAAAATT
1 AGCAAAGACTTAATTCCACAAGAATTAAGTAAAATC
* * *
125087 GGCAAAGACTTAATTTCACAAGAATTAAGTAAAATT
1 AGCAAAGACTTAATTCCACAAGAATTAAGTAAAATC
* *
125123 AGCAAAGACTTAATTTCACAAGAATTAAGTAAAGTC
1 AGCAAAGACTTAATTCCACAAGAATTAAGTAAAATC
*
125159 AGCAAAGATTTAA-TCCA-AAGATGATTAAGTAA
1 AGCAAAGACTTAATTCCACAAGA--ATTAAGTAA
125191 GATAAGACAA
Statistics
Matches: 95, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
34 4 0.04
35 3 0.03
36 88 0.93
ACGTcount: A:0.49, C:0.11, G:0.13, T:0.26
Consensus pattern (36 bp):
AGCAAAGACTTAATTCCACAAGAATTAAGTAAAATC
Found at i:125186 original size:72 final size:72
Alignment explanation
Indices: 125049--125214 Score: 201
Period size: 72 Copynumber: 2.3 Consensus size: 72
125039 CTGAAAGAAG
** *
125049 TTAGCAAAGACTTAATTTCACAAAAATTAAGTAAAATTGGCAAAGACTTAATTTCACAAGAATTA
1 TTAGCAAAGACTTAATTTCACAAAAATTAAGTAAAATCAGCAAAGACTTAATTCCACAAGAATTA
125114 AGTAAAA
66 AGTAAAA
* * *
125121 TTAGCAAAGACTTAATTTCACAAGAATTAAGTAAAGTCAGCAAAGATTTAA-TCCA-AAGATGAT
1 TTAGCAAAGACTTAATTTCACAAAAATTAAGTAAAATCAGCAAAGACTTAATTCCACAAGA--AT
*
125184 TAAGTAAGA
64 TAAGTAAAA
* *
125193 TAAGACAAAGGGCTTAATTTCA
1 TTAG-CAAA-GACTTAATTTCA
125215 AGGAAATTAG
Statistics
Matches: 81, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
70 4 0.05
71 3 0.04
72 59 0.73
73 4 0.05
74 11 0.14
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.27
Consensus pattern (72 bp):
TTAGCAAAGACTTAATTTCACAAAAATTAAGTAAAATCAGCAAAGACTTAATTCCACAAGAATTA
AGTAAAA
Found at i:125288 original size:12 final size:12
Alignment explanation
Indices: 125228--125295 Score: 61
Period size: 12 Copynumber: 5.7 Consensus size: 12
125218 AAATTAGGCA
125228 AAAGACTGAAAG
1 AAAGACTGAAAG
*
125240 -AAGACT-AAAA
1 AAAGACTGAAAG
*
125250 ACAAGACTGAAAAAA
1 A-AAGACTG--AAAG
*
125265 AAATACTGAAAG
1 AAAGACTGAAAG
125277 AAAGACTGAAAG
1 AAAGACTGAAAG
125289 -AAGACTG
1 AAAGACTG
125296 GCTTAATTTC
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
10 3 0.06
11 13 0.28
12 20 0.43
14 6 0.13
15 5 0.11
ACGTcount: A:0.60, C:0.10, G:0.19, T:0.10
Consensus pattern (12 bp):
AAAGACTGAAAG
Found at i:125331 original size:36 final size:36
Alignment explanation
Indices: 125289--125959 Score: 839
Period size: 36 Copynumber: 18.9 Consensus size: 36
125279 AGACTGAAAG
* * *
125289 AAGACTGGCTTAATTTCAGGGAAATTAAATAAAGAA
1 AAGACTGGCTTAGTTTCAAGGAAATTAAGTAAAGAA
125325 AAGACTGGCTT-GATTTCAAGGAAATTAAGTAAAGAA
1 AAGACTGGCTTAG-TTTCAAGGAAATTAAGTAAAGAA
* *
125361 AAGACTGACTTAGTTTCAAGGAAACTAAGTAAA-AA
1 AAGACTGGCTTAGTTTCAAGGAAATTAAGTAAAGAA
* *
125396 AA-A-GGGCTTAGCTTCAAGGAAATTAAGTAAAGAA
1 AAGACTGGCTTAGTTTCAAGGAAATTAAGTAAAGAA
* *
125430 AAGACTGGCTTAATTTCAAGAAAATTAAGTAAAGAA
1 AAGACTGGCTTAGTTTCAAGGAAATTAAGTAAAGAA
* * *
125466 AAGATTGGCTTAGTTTTAGGGAAATTAAGTAAAGAA
1 AAGACTGGCTTAGTTTCAAGGAAATTAAGTAAAGAA
*
125502 AAGACTGGCTTAGTTTCAAGGAAACTAAGTAAAGAA
1 AAGACTGGCTTAGTTTCAAGGAAATTAAGTAAAGAA
* *
125538 AAG---GGCTTAGCTTCAAGGAAACTAAGTAAAGAA
1 AAGACTGGCTTAGTTTCAAGGAAATTAAGTAAAGAA
* * *
125571 AAG---GGCTTAGCTTCAAGGAAACTAGGTAAAGAA
1 AAGACTGGCTTAGTTTCAAGGAAATTAAGTAAAGAA
* * *
125604 AAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGTA
1 AAGACTGGCTTAGTTTCAAGGAAATTAAGTAAAGAA
*
125640 TAGACTGGCTT-GATTTCAAGGAAATTAAGTAAAGAA
1 AAGACTGGCTTAG-TTTCAAGGAAATTAAGTAAAGAA
* * *
125676 AAGACTGGCTTAGTTTCAAGAAAACTAGGTAAAGAA
1 AAGACTGGCTTAGTTTCAAGGAAATTAAGTAAAGAA
* * *
125712 AGGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAA
1 AAGACTGGCTTAGTTTCAAGGAAATTAAGTAAAGAA
*
125748 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
1 AAGACTGGCTTAGTTTCAAGGAAATTAAGTAAAGAA
* * **
125784 AAGACTGGCTTAGTTTCAAGAAAACTGGGTAAAGAA
1 AAGACTGGCTTAGTTTCAAGGAAATTAAGTAAAGAA
* * *
125820 AAAACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAA
1 AAGACTGGCTTAGTTTCAAGGAAATTAAGTAAAGAA
*
125856 AAGACTGGCTT-GATTTCAAGGAAATTACGTAAAG-A
1 AAGACTGGCTTAG-TTTCAAGGAAATTAAGTAAAGAA
* * *
125891 TAGACTGGCTTAATTTCAAGGAAATT-AGATAAAGGA
1 AAGACTGGCTTAGTTTCAAGGAAATTAAG-TAAAGAA
*
125927 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAA
1 AAGACTGGCTTAGTTTCAAGGAAATTAAGTAAA
125960 AAGACACAGA
Statistics
Matches: 565, Mismatches: 55, Indels: 30
0.87 0.08 0.05
Matches are distributed among these distances:
33 88 0.16
34 6 0.01
35 36 0.06
36 431 0.76
37 4 0.01
ACGTcount: A:0.44, C:0.10, G:0.22, T:0.24
Consensus pattern (36 bp):
AAGACTGGCTTAGTTTCAAGGAAATTAAGTAAAGAA
Found at i:126025 original size:32 final size:32
Alignment explanation
Indices: 125988--126095 Score: 128
Period size: 32 Copynumber: 3.2 Consensus size: 32
125978 CAGGAAAGGA
125988 AATTAAGTAAAATAAAGAACTTAATTCAGGGT
1 AATTAAGTAAAATAAAGAACTTAATTCAGGGT
* *
126020 AATTAAGTGAAGTCGATAAA-AGGCTTAATTCAGGGT
1 AATTAAGT-AA---AATAAAGA-ACTTAATTCAGGGT
* *
126056 AATTAAGTAGAATAAAGAACTTAATTCAAGGT
1 AATTAAGTAAAATAAAGAACTTAATTCAGGGT
126088 AATTAAGT
1 AATTAAGT
126096 GAAGTCAATA
Statistics
Matches: 64, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
32 33 0.52
33 3 0.05
35 2 0.03
36 26 0.41
ACGTcount: A:0.46, C:0.06, G:0.19, T:0.29
Consensus pattern (32 bp):
AATTAAGTAAAATAAAGAACTTAATTCAGGGT
Found at i:126039 original size:36 final size:36
Alignment explanation
Indices: 125998--126116 Score: 149
Period size: 36 Copynumber: 3.4 Consensus size: 36
125988 AATTAAGTAA
125998 AATAAAGAACTTAATTCAGGGTAATTAAGTGAAGTC
1 AATAAAGAACTTAATTCAGGGTAATTAAGTGAAGTC
* *
126034 GATAAA-AGGCTTAATTCAGGGTAATTAAGT--AG--
1 AATAAAGA-ACTTAATTCAGGGTAATTAAGTGAAGTC
*
126066 AATAAAGAACTTAATTCAAGGTAATTAAGTGAAGTC
1 AATAAAGAACTTAATTCAGGGTAATTAAGTGAAGTC
* *
126102 AATAGAGAGCTTAAT
1 AATAAAGAACTTAAT
126117 CTAGAAAAGA
Statistics
Matches: 70, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
32 25 0.36
33 1 0.01
34 4 0.06
35 1 0.01
36 39 0.56
ACGTcount: A:0.45, C:0.08, G:0.20, T:0.28
Consensus pattern (36 bp):
AATAAAGAACTTAATTCAGGGTAATTAAGTGAAGTC
Found at i:129425 original size:198 final size:198
Alignment explanation
Indices: 129087--129484 Score: 778
Period size: 198 Copynumber: 2.0 Consensus size: 198
129077 TGATTTTCCG
*
129087 TAAACGCATCCACCATGAGAGCCACAAAGAGAGCATGATTTGATTACTTAGGAGTTTAGGACCCC
1 TAAACGCATCCACCATGAGAGCCACAAAGAGAGCATGATTTGATTACTTAGCAGTTTAGGACCCC
129152 ACCAAGTGTGTGATGCGGCCATTGCTAAAAGTTAAACTTAAACACTGTTTAAAAGAGAAAGAAGA
66 ACCAAGTGTGTGATGCGGCCATTGCTAAAAGTTAAACTTAAACACTGTTTAAAAGAGAAAGAAGA
129217 AGAAGAAGAGACAGAGAGCCATTCACTTTCACTCAATCATTAATTCATTGGCCTCATTCAATTCA
131 AGAAGAAGAGACAGAGAGCCATTCACTTTCACTCAATCATTAATTCATTGGCCTCATTCAATTCA
129282 ATA
196 ATA
129285 TAAACGCATCCACCATGAGAGCCACAAAGAGAGCATGATTTGATTACTTAGCAGTTTAGGACCCC
1 TAAACGCATCCACCATGAGAGCCACAAAGAGAGCATGATTTGATTACTTAGCAGTTTAGGACCCC
129350 ACCAAGTGTGTGATGCGGCCATTGCTAAAAGTTAAACTTAAACACTGTTTAAAAGAGAAAGAAGA
66 ACCAAGTGTGTGATGCGGCCATTGCTAAAAGTTAAACTTAAACACTGTTTAAAAGAGAAAGAAGA
*
129415 AGAAGAAGAGACGGAGAGCCATTCACTTTCACTCAATCATTAATTCATTGGCCTCATTCAATTCA
131 AGAAGAAGAGACAGAGAGCCATTCACTTTCACTCAATCATTAATTCATTGGCCTCATTCAATTCA
129480 ATA
196 ATA
129483 TA
1 TA
129485 TTAATTCCTT
Statistics
Matches: 198, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
198 198 1.00
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (198 bp):
TAAACGCATCCACCATGAGAGCCACAAAGAGAGCATGATTTGATTACTTAGCAGTTTAGGACCCC
ACCAAGTGTGTGATGCGGCCATTGCTAAAAGTTAAACTTAAACACTGTTTAAAAGAGAAAGAAGA
AGAAGAAGAGACAGAGAGCCATTCACTTTCACTCAATCATTAATTCATTGGCCTCATTCAATTCA
ATA
Found at i:130012 original size:46 final size:47
Alignment explanation
Indices: 129960--130050 Score: 157
Period size: 47 Copynumber: 2.0 Consensus size: 47
129950 ACAAAAATTA
*
129960 TTATATGAATA-TTTTTTTGTTGCTGTAAATTATTTGTAGGAGATTC
1 TTATATGAATAGTTTCTTTGTTGCTGTAAATTATTTGTAGGAGATTC
*
130006 TTATATGAATAGTTTCTTTGTTGCTGTAAGTTATTTGTAGGAGAT
1 TTATATGAATAGTTTCTTTGTTGCTGTAAATTATTTGTAGGAGAT
130051 GAGTTGCAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
46 11 0.26
47 31 0.74
ACGTcount: A:0.25, C:0.04, G:0.20, T:0.51
Consensus pattern (47 bp):
TTATATGAATAGTTTCTTTGTTGCTGTAAATTATTTGTAGGAGATTC
Found at i:135918 original size:13 final size:13
Alignment explanation
Indices: 135902--135940 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
135892 ATTTCAAGTC
135902 ATAAACCAAAATA
1 ATAAACCAAAATA
* *
135915 ATAAACCAGAATC
1 ATAAACCAAAATA
135928 ATAAACCAAAATA
1 ATAAACCAAAATA
135941 GTTAGATAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.64, C:0.18, G:0.03, T:0.15
Consensus pattern (13 bp):
ATAAACCAAAATA
Found at i:141550 original size:13 final size:13
Alignment explanation
Indices: 141541--141566 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
141531 ATAAAAAATC
141541 ATTTATAAAAACA
1 ATTTATAAAAACA
141554 ATTTATAAAAACA
1 ATTTATAAAAACA
141567 GTAATAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (13 bp):
ATTTATAAAAACA
Found at i:141788 original size:13 final size:13
Alignment explanation
Indices: 141750--141787 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
141740 TAATTTCAAG
141750 TCATAAACCAAAA
1 TCATAAACCAAAA
*
141763 TAATAAACCAAAA
1 TCATAAACCAAAA
141776 TCATAAA-CAAAA
1 TCATAAACCAAAA
141788 ACAGTTAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 5 0.22
13 18 0.78
ACGTcount: A:0.66, C:0.18, G:0.00, T:0.16
Consensus pattern (13 bp):
TCATAAACCAAAA
Found at i:144194 original size:21 final size:21
Alignment explanation
Indices: 144170--144209 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
144160 ATGGAAAAAT
144170 GGAAAAT-CCATGAGGAGATTA
1 GGAAAATACC-TGAGGAGATTA
*
144191 GGAACATACCTGAGGAGAT
1 GGAAAATACCTGAGGAGAT
144210 AAATCGGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.40, C:0.12, G:0.30, T:0.17
Consensus pattern (21 bp):
GGAAAATACCTGAGGAGATTA
Found at i:149545 original size:21 final size:21
Alignment explanation
Indices: 149507--149559 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
149497 GCACTGGAGT
* * * *
149507 ACATGGGTCGCGAGGCAAATA
1 ACATGGGGCGCCAAGCAAACA
*
149528 ACATGGGGCGCCAAGCAAACC
1 ACATGGGGCGCCAAGCAAACA
149549 ACAT-GGGCGCC
1 ACATGGGGCGCC
149560 CAGCGCTAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 7 0.26
21 20 0.74
ACGTcount: A:0.30, C:0.28, G:0.32, T:0.09
Consensus pattern (21 bp):
ACATGGGGCGCCAAGCAAACA
Found at i:153534 original size:19 final size:18
Alignment explanation
Indices: 153498--153560 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 18
153488 CAAACTCATG
*
153498 AAAGCAAAGACAAAAAAAAA
1 AAAG-AAAGA-AAGAAAAAA
153518 AAAGAAAGAAAGGAAAAAA
1 AAAGAAAGAAA-GAAAAAA
153537 AAAGAAAGAAAGAAAGAAA
1 AAAGAAAGAAAGAAA-AAA
153556 AAAGA
1 AAAGA
153561 GGCAGATTAG
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
18 6 0.15
19 30 0.75
20 4 0.10
ACGTcount: A:0.79, C:0.03, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAGAAAGAAAGAAAAAA
Found at i:153535 original size:23 final size:22
Alignment explanation
Indices: 153497--153558 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 22
153487 TCAAACTCAT
153497 GAAAGCAAAGACAAAAAAAAAAAA
1 GAAAG-AAAGA-AAAAAAAAAAAA
*
153521 GAAAGAAAGGAAAAAAAAAGAAA
1 GAAAGAAA-GAAAAAAAAAAAAA
153544 GAAAGAAAGAAAAAA
1 GAAAGAAAGAAAAAA
153559 GAGGCAGATT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
22 7 0.19
23 22 0.61
24 7 0.19
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (22 bp):
GAAAGAAAGAAAAAAAAAAAAA
Done.