Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008010.1 Hibiscus syriacus cultivar Beakdansim tig00110472_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: 3152856
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 14
Found at i:127463 original size:22 final size:22
Alignment explanation
Indices: 127435--127478 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
127425 CACTCTCTCA
127435 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
127457 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
127479 TATCTCCATC
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:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:127795 original size:20 final size:20
Alignment explanation
Indices: 127741--127799 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
127731 GCGATTCTCT
**
127741 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
127761 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
127781 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
127800 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:127990 original size:25 final size:24
Alignment explanation
Indices: 127936--127990 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
127926 TGTTTATTAT
* *
127936 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
127960 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
127986 TGTTT
1 TGTTT
127991 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:129140 original size:18 final size:18
Alignment explanation
Indices: 129119--129163 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
129109 TCCACTTCGG
**
129119 GAGCCATCACCTCGTCCA
1 GAGCCATCACCTCACCCA
*
129137 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
129155 GAGCCATCA
1 GAGCCATCA
129164 TCTGATCGAC
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:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:129670 original size:20 final size:20
Alignment explanation
Indices: 129645--129690 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
129635 TAGTTTACTT
*
129645 TCGCAACATGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
129665 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
129685 TCGCAA
1 TCGCAA
129691 TGCGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:129699 original size:19 final size:20
Alignment explanation
Indices: 129656--129711 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
129646 CGCAACATGA
129656 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
* *
129676 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
**
129695 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
129712 ACAAAATCGC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.16
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:129719 original size:14 final size:14
Alignment explanation
Indices: 129700--129756 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
129690 ATGCGAAATG
129700 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
129714 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
129733 AAAATCGCAACGAC
1 AAAATCGCAACGAC
129747 AAAATCGCAA
1 AAAATCGCAA
129757 TGCGAAATGA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.51, C:0.23, G:0.16, T:0.11
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:129726 original size:33 final size:33
Alignment explanation
Indices: 129684--129775 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
129674 GGAAATGGCT
129684 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
129717 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
129750 ATCGCAATGCGAAATGAAAGTCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
129776 TGCGATTTGT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:129738 original size:19 final size:19
Alignment explanation
Indices: 129684--129780 Score: 97
Period size: 19 Copynumber: 5.6 Consensus size: 19
129674 GGAAATGGCT
129684 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
129703 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
129717 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
129736 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
129750 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
129769 GTCGCAATGCGA
1 ATCGCAATGCGA
129781 TTTGTGTTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.49
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:129813 original size:14 final size:14
Alignment explanation
Indices: 129792--129849 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
129782 TTGTGTTTCG
129792 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
* *
129806 CATTGCGATTTCATTT
1 CGTTGCGATTT--TGT
129822 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
129838 CGTTGCGATTTT
1 CGTTGCGATTTT
129850 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.61
16 4 0.11
18 10 0.28
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:129826 original size:32 final size:33
Alignment explanation
Indices: 129787--129865 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
129777 GCGATTTGTG
129787 TTTCGCGTTGCGATTTTGTCATTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCATTGCGATTTTCA
*
129819 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCATTGCGATTTTCA
*
129852 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
129866 AGCCATTTCT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 26 0.59
33 18 0.41
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCATTGCGATTTTCA
Found at i:129884 original size:20 final size:20
Alignment explanation
Indices: 129850--129905 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
129840 TTGCGATTTT
*
129850 CATTTC-GCATTGCGATAGC
1 CATTTCTGCGTTGCGATAGC
*
129869 CATTTCTGCGTTGCGATAGT
1 CATTTCTGCGTTGCGATAGC
129889 CATTT-TCGCGTTGCGAT
1 CATTTCT-GCGTTGCGAT
129906 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 7 0.21
20 26 0.79
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (20 bp):
CATTTCTGCGTTGCGATAGC
Found at i:131721 original size:14 final size:14
Alignment explanation
Indices: 131687--131725 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
131677 TTGATTGTTT
131687 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
131701 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
131715 TGTTGATTTGT
1 AATTGATTTGT
131726 TTAATTGGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:131871 original size:14 final size:14
Alignment explanation
Indices: 131852--131905 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
131842 GAAACTGACT
131852 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
131866 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
131885 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
131899 ATCGCAA
1 ATCGCAA
131906 TGCGGTTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.31
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:131954 original size:20 final size:20
Alignment explanation
Indices: 131929--132004 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
131919 TCGCATTGCG
*
131929 ATTTTCTAGTTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
* ***
131949 ATTTTCGCGTTGCGATTTTTC
1 ATTTTCGAGTTGCGA-TAGCC
*
131970 A-TTTCGAATTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
*
131989 ATTTTCGCGTTGCGAT
1 ATTTTCGAGTTGCGAT
132005 TTCCCCGTTG
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
19 3 0.07
20 36 0.86
21 3 0.07
ACGTcount: A:0.17, C:0.20, G:0.21, T:0.42
Consensus pattern (20 bp):
ATTTTCGAGTTGCGATAGCC
Found at i:132020 original size:34 final size:34
Alignment explanation
Indices: 131917--132020 Score: 100
Period size: 40 Copynumber: 2.9 Consensus size: 34
131907 GCGGTTTTCA
* * *
131917 TTTCGCATTGCGATTTTCTAGTTGCGATAGCCAT
1 TTTCGCGTTGCGATTTCCTCGTTGCGATAGCCAT
*
131951 TTTCGCGTTGCGATTTTTCATTTCGAATTGCGATAGCCAT
1 TTTCGCGTTGCGA--TTTC--CTCG--TTGCGATAGCCAT
* *
131991 TTTCGCGTTGCGATTTCCCCGTTGTGATAG
1 TTTCGCGTTGCGATTTCCTCGTTGCGATAG
132021 TCAAATGAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
34 20 0.35
36 5 0.09
38 6 0.11
40 26 0.46
ACGTcount: A:0.15, C:0.21, G:0.22, T:0.41
Consensus pattern (34 bp):
TTTCGCGTTGCGATTTCCTCGTTGCGATAGCCAT
Found at i:134700 original size:33 final size:33
Alignment explanation
Indices: 134658--134781 Score: 178
Period size: 33 Copynumber: 3.8 Consensus size: 33
134648 AATTACTATC
*
134658 GCAATGCGAAATGAAAATCACAACGAGAGAATT
1 GCAATGCGAAATGAAAATCGCAACGAGAGAATT
** *
134691 GCAATGCGAAATGAAAATCGCAACGCTA-ATTT
1 GCAATGCGAAATGAAAATCGCAACGAGAGAATT
* *
134723 CGCAATGCGAAATGAAAATCGCAACGAGGGAATC
1 -GCAATGCGAAATGAAAATCGCAACGAGAGAATT
134757 GCAATGCGAAATGAAAATCGCAACG
1 GCAATGCGAAATGAAAATCGCAACG
134782 CGAATTTAAT
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
32 3 0.04
33 75 0.94
34 2 0.03
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.15
Consensus pattern (33 bp):
GCAATGCGAAATGAAAATCGCAACGAGAGAATT
Found at i:134738 original size:66 final size:66
Alignment explanation
Indices: 134656--134788 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
134646 GAAATTACTA
* *
134656 TCGCAATGCGAAATGAAAATCACAACGAGAGAATTGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
134721 T
66 T
* *
134722 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
134787 T
66 T
134788 T
1 T
134789 AATTTCTCGT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:134949 original size:14 final size:14
Alignment explanation
Indices: 134930--134966 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
134920 CATCAATTAA
134930 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
134944 ACAAATCACCTTTT
1 ACAAATCAACTTTT
134958 ACAAATCAA
1 ACAAATCAA
134967 TTAAACAATC
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:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:136367 original size:21 final size:21
Alignment explanation
Indices: 136338--136418 Score: 65
Period size: 21 Copynumber: 3.9 Consensus size: 21
136328 GAATGGTGGG
*
136338 AGGGACCTCTTCAACGATGAT
1 AGGGGCCTCTTCAACGATGAT
* * * **
136359 AGTGGCCTCTTGAACGGTGGG
1 AGGGGCCTCTTCAACGATGAT
* * *
136380 AGGGGACTC-TCGAGGAATGAT
1 AGGGGCCTCTTCAACG-ATGAT
136401 AGGGGCCTCTTCAACGAT
1 AGGGGCCTCTTCAACGAT
136419 AGGAGTGGAC
Statistics
Matches: 41, Mismatches: 17, Indels: 4
0.66 0.27 0.06
Matches are distributed among these distances:
20 3 0.07
21 34 0.83
22 4 0.10
ACGTcount: A:0.23, C:0.21, G:0.33, T:0.22
Consensus pattern (21 bp):
AGGGGCCTCTTCAACGATGAT
Found at i:136400 original size:42 final size:41
Alignment explanation
Indices: 136323--136441 Score: 114
Period size: 42 Copynumber: 2.8 Consensus size: 41
136313 GTGAATCGGG
* * * *
136323 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGATAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
136365 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
136407 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGA
136442 CAGGCGAGTC
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
41 4 0.06
42 55 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.36, T:0.24
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:136837 original size:91 final size:90
Alignment explanation
Indices: 136663--136847 Score: 291
Period size: 91 Copynumber: 2.0 Consensus size: 90
136653 ATATCAAACT
*
136663 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAATGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAATGTT--A-AATAAACAGTTTAGC
136728 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
*
136756 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAATGTTAAATAAACAGTTTAGCA
*
136820 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
136847 T
1 T
136848 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 42 0.48
93 19 0.22
95 26 0.30
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAATGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:138601 original size:34 final size:33
Alignment explanation
Indices: 138558--138654 Score: 131
Period size: 33 Copynumber: 2.9 Consensus size: 33
138548 ACGAGATAAT
*
138558 GAGAATCGCAATGCGGAAATGACTATTGCAACGA
1 GAGAATCGCAATGC-GAAATGACTATCGCAACGA
*
138592 GAGAATCGCAATGCTAAATGACTATCGCAACGA
1 GAGAATCGCAATGCGAAATGACTATCGCAACGA
* * **
138625 GAGAATCGAAACGCGAAATGAAAATCGCAA
1 GAGAATCGCAATGCGAAATGACTATCGCAA
138655 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
33 42 0.75
34 14 0.25
ACGTcount: A:0.42, C:0.19, G:0.24, T:0.15
Consensus pattern (33 bp):
GAGAATCGCAATGCGAAATGACTATCGCAACGA
Found at i:138688 original size:19 final size:19
Alignment explanation
Indices: 138655--138721 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
138645 AAAATCGCAA
**
138655 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
138674 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
138693 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
*
138713 TGCAATTTT
1 TGCGATTTT
138722 CATTCTCGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 29 0.73
20 11 0.28
ACGTcount: A:0.12, C:0.16, G:0.24, T:0.48
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:139282 original size:20 final size:20
Alignment explanation
Indices: 139241--139312 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
139231 GCTATGTAAA
* *
139241 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-TTACGTAT
139261 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
* * *
139281 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGT-AT
139302 TCGCATTGCGA
1 TCGCATTGCGA
139313 ATTATGAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
19 3 0.07
20 29 0.66
21 12 0.27
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:139326 original size:21 final size:20
Alignment explanation
Indices: 139302--139374 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 20
139292 TTTTCCTAAT
* *
139302 TCGCATTGCGAATTATGAAAA
1 TCGCAATGCGAA-TACGAAAA
* *
139323 TCGCAACGCGAATACGTAAA
1 TCGCAATGCGAATACGAAAA
*
139343 TCGCAATGCGAAATAGGAAAA
1 TCGCAATGCG-AATACGAAAA
* *
139364 TTGCATTGCGA
1 TCGCAATGCGA
139375 TAGTCAGTAT
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
20 16 0.38
21 26 0.62
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGAAAA
Found at i:139428 original size:20 final size:21
Alignment explanation
Indices: 139384--139431 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
139374 ATAGTCAGTA
*
139384 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
139405 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
139425 TCGCATT
1 TCGCATT
139432 ACGAATTGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.42
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:139477 original size:21 final size:22
Alignment explanation
Indices: 139425--139477 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
139415 ATTTACTTAT
*
139425 TCGCATTACG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
* **
139446 TTGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
139467 TCGCATTGCGA
1 TCGCATTGCGA
139478 TAGTCATAAT
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.23
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:139779 original size:58 final size:58
Alignment explanation
Indices: 139717--139850 Score: 155
Period size: 58 Copynumber: 2.3 Consensus size: 58
139707 GGGCTCTTGT
* *** * *
139717 TTTTTTCAGTTTTATAAAATCTTTCCCACTTTCTACCTTTATAATTGAGGG-TCCCT-AC
1 TTTTTTCAATTTTATAAAA-AGGTCCCACTTTCTACATTTATAAGTGAGGGCT-CCTAAC
* * *
139775 TTTTTTTAATTTTATAAAAAGGTCTCACTTTCTACATTTATAAGTGAGGGCTCCTAAT
1 TTTTTTCAATTTTATAAAAAGGTCCCACTTTCTACATTTATAAGTGAGGGCTCCTAAC
139833 TTTTTTCAATTTTATAAA
1 TTTTTTCAATTTTATAAA
139851 TTTCTCAATT
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
57 28 0.44
58 36 0.56
ACGTcount: A:0.27, C:0.16, G:0.09, T:0.48
Consensus pattern (58 bp):
TTTTTTCAATTTTATAAAAAGGTCCCACTTTCTACATTTATAAGTGAGGGCTCCTAAC
Found at i:139871 original size:58 final size:56
Alignment explanation
Indices: 139746--139863 Score: 141
Period size: 57 Copynumber: 2.1 Consensus size: 56
139736 TCTTTCCCAC
* * * *
139746 TTTCTACCTTTATAATTGAGGGTCCCTACTTTTTTTAATTTTATAAAAAGGTCTCAC
1 TTTCTACATTTATAAGTGAGGGTCCCTAATTTTTTTAATTTTAT-AAAAGGTCTCAA
**
139803 TTTCTACATTTATAAGTGAGGG-CTCCTAATTTTTTTCAATTTTAT-AAATTTCTCAA
1 TTTCTACATTTATAAGTGAGGGTC-CCTAATTTTTTT-AATTTTATAAAAGGTCTCAA
139859 TTTCT
1 TTTCT
139864 CATCATTTTC
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
56 14 0.26
57 31 0.58
58 8 0.15
ACGTcount: A:0.26, C:0.16, G:0.09, T:0.48
Consensus pattern (56 bp):
TTTCTACATTTATAAGTGAGGGTCCCTAATTTTTTTAATTTTATAAAAGGTCTCAA
Found at i:140196 original size:20 final size:21
Alignment explanation
Indices: 140155--140199 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
140145 CTTCAACAAT
*
140155 TATTCTTTTTTTAATAAGAAA
1 TATTCTTTTGTTAATAAGAAA
*
140176 TATTCTTTTGTTAA-AATAAA
1 TATTCTTTTGTTAATAAGAAA
140196 TATT
1 TATT
140200 TTGGCATATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.53
Consensus pattern (21 bp):
TATTCTTTTGTTAATAAGAAA
Found at i:150034 original size:21 final size:21
Alignment explanation
Indices: 149991--150104 Score: 124
Period size: 21 Copynumber: 5.5 Consensus size: 21
149981 TTTTCCCAAT
* * *
149991 TCGCAATGCGAA-TAAGTAAA
1 TCGCAACGCGAATTGAGAAAA
*
150011 TCGCAACGCGAATTGGGAAAA
1 TCGCAACGCGAATTGAGAAAA
* *
150032 TCGCAACGCGAATTGGGAAAT
1 TCGCAACGCGAATTGAGAAAA
* * *
150053 TCGCAATGCGAA-TAAGTAAA
1 TCGCAACGCGAATTGAGAAAA
150073 TCGCAACGCGAATTGAGAAAA
1 TCGCAACGCGAATTGAGAAAA
*
150094 TCGCAATGCGA
1 TCGCAACGCGA
150105 TACTGACTAT
Statistics
Matches: 78, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
20 26 0.33
21 52 0.67
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (21 bp):
TCGCAACGCGAATTGAGAAAA
Found at i:150054 original size:62 final size:62
Alignment explanation
Indices: 149988--150104 Score: 216
Period size: 62 Copynumber: 1.9 Consensus size: 62
149978 CGATTTTCCC
*
149988 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGAAAATCGCAACGCGAATTGGGA
*
150050 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGAAAATCGCAATGCGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGAAAATCGCAACGCGA
150105 TACTGACTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 53 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (62 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGAAAATCGCAACGCGAATTGGGA
Found at i:150117 original size:41 final size:41
Alignment explanation
Indices: 150031--150165 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
150021 AATTGGGAAA
* * * *
150031 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGAGAAAATCGCAATGCG-ATACTG-ACT
150072 ATCGCAACGCGAATTGAGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGAGAAAATCGCAATGCGATACTGACT
* * * * * *
150113 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGAGAAAATCGCAATGCGATACTGACT
*
150154 TTCGCAACGCGA
1 ATCGCAACGCGA
150166 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGAGAAAATCGCAATGCGATACTGACT
Found at i:150118 original size:20 final size:20
Alignment explanation
Indices: 150093--150186 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
150083 AATTGAGAAA
*
150093 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
150113 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
150134 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
150154 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
150174 TTCGCAACGCGAT
1 ATCGCAACGCGAT
150187 TTACTTAGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:150136 original size:62 final size:61
Alignment explanation
Indices: 149988--150142 Score: 199
Period size: 62 Copynumber: 2.5 Consensus size: 61
149978 CGATTTTCCC
* *
149988 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGAAAATCGCAACGCGAACT-GGA
*
150050 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGAAAATCGCAATGCGATACT-G-
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGAAAATCGCAACGCGA-ACTGGA
* *
150110 ACTATCGCAATGCGATAATAA-AAAATCGCAACG
1 AAT-TCGCAATGCG--AATAAGTAAATCGCAACG
150143 AGATACTTAC
Statistics
Matches: 84, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
60 2 0.02
61 11 0.13
62 64 0.76
63 7 0.08
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.19
Consensus pattern (61 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGAAAATCGCAACGCGAACTGGA
Found at i:150747 original size:19 final size:19
Alignment explanation
Indices: 150709--150775 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
150699 TTCGAGAATG
*
150709 AAAATCGCAAAGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
150729 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
150748 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
150767 AAAATCGCA
1 AAAATCGCA
150776 TTGCGATTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 30 0.75
20 10 0.25
ACGTcount: A:0.49, C:0.24, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:150793 original size:19 final size:19
Alignment explanation
Indices: 150771--150935 Score: 134
Period size: 19 Copynumber: 9.1 Consensus size: 19
150761 GAAACCAAAA
*
150771 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
150790 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
150809 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
150828 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
150842 TCTCGTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
150861 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
150875 TCTCATTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* *
150894 TCCGCGTTGCAATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
150914 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
150934 TC
1 TC
150936 AACCAAAAGA
Statistics
Matches: 116, Mismatches: 18, Indels: 24
0.73 0.11 0.15
Matches are distributed among these distances:
14 18 0.16
16 4 0.03
17 5 0.04
19 60 0.52
20 28 0.24
21 1 0.01
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:150827 original size:38 final size:33
Alignment explanation
Indices: 150776--150910 Score: 144
Period size: 33 Copynumber: 3.9 Consensus size: 33
150766 CAAAATCGCA
*
150776 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGA--TTC---TCTCG
150814 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* ** *
150847 TCGCGATAGTCATTTCGCGTTGCGATTCTCTCA
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
** *
150880 TTGCGATAGTCATTTCCGCGTTGCAATTCTC
1 TTGCGATTTTCATTT-CGCGTTGCGATTCTC
150911 ATTATCTCGT
Statistics
Matches: 89, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
33 47 0.53
34 14 0.16
36 3 0.03
38 25 0.28
ACGTcount: A:0.13, C:0.24, G:0.21, T:0.42
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:150912 original size:20 final size:20
Alignment explanation
Indices: 150889--150935 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
150879 ATTGCGATAG
150889 TCATTTCCGCGTTGCAATTC
1 TCATTTCCGCGTTGCAATTC
* * *
150909 TCATTAT-CTCGTTGCGATTT
1 TCATT-TCCGCGTTGCAATTC
150929 TCATTTC
1 TCATTTC
150936 AACCAAAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
19 1 0.05
20 20 0.91
21 1 0.05
ACGTcount: A:0.15, C:0.26, G:0.13, T:0.47
Consensus pattern (20 bp):
TCATTTCCGCGTTGCAATTC
Found at i:152994 original size:42 final size:42
Alignment explanation
Indices: 152934--153056 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
152924 AGCCGACTCG
* * *
152934 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
152976 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
153018 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
153057 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:153014 original size:21 final size:21
Alignment explanation
Indices: 152990--153056 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
152980 TCATTCCTCG
152990 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
153011 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
153032 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
153053 AGAG
1 AGAG
153057 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:154434 original size:14 final size:14
Alignment explanation
Indices: 154415--154450 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
154405 ATTGTTTAAT
154415 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
* *
154429 TGATTTGTACAAGT
1 TGATTTGTAAAAGG
154443 TGATTTGT
1 TGATTTGT
154451 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.28, C:0.03, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:154651 original size:19 final size:19
Alignment explanation
Indices: 154629--154746 Score: 76
Period size: 19 Copynumber: 6.7 Consensus size: 19
154619 CGAAATTAAA
154629 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
154648 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
154663 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
154681 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
154696 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
154714 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
154733 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
154747 GGACATTAAG
Statistics
Matches: 73, Mismatches: 15, Indels: 21
0.67 0.14 0.19
Matches are distributed among these distances:
14 17 0.23
16 6 0.08
17 6 0.08
19 34 0.47
20 10 0.14
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:154675 original size:33 final size:33
Alignment explanation
Indices: 154633--154726 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
154623 ATTAAATTCG
154633 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
154666 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
154699 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
154727 AGTAATTTCC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:157039 original size:12 final size:12
Alignment explanation
Indices: 157022--157046 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
157012 TCTTCGGGGA
157022 CTTTTTCTTCTT
1 CTTTTTCTTCTT
157034 CTTTTTCTTCTT
1 CTTTTTCTTCTT
157046 C
1 C
157047 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:158541 original size:14 final size:14
Alignment explanation
Indices: 158522--158558 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
158512 CATCAATTAA
158522 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
158536 ACAAATCATCTTTT
1 ACAAATCAACATTT
158550 ACAAATCAA
1 ACAAATCAA
158559 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:159126 original size:14 final size:14
Alignment explanation
Indices: 159107--159143 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
159097 CATCAATTAA
159107 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
159121 ACAAATCATCTTTT
1 ACAAATCAACATTT
159135 ACAAATCAA
1 ACAAATCAA
159144 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:159535 original size:20 final size:20
Alignment explanation
Indices: 159510--159566 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
159500 TTCATTTGAC
*
159510 TATCGCAATGCGAAAATGGT
1 TATCGCAACGCGAAAATGGT
159530 TATCGCAACGCGAAAATGGT
1 TATCGCAACGCGAAAATGGT
*
159550 TATCGCAACGAGAAAAT
1 TATCGCAACGCGAAAAT
159567 CGCAATGCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.21
Consensus pattern (20 bp):
TATCGCAACGCGAAAATGGT
Found at i:159626 original size:19 final size:19
Alignment explanation
Indices: 159585--159671 Score: 139
Period size: 19 Copynumber: 4.8 Consensus size: 19
159575 GAAATGAAAA
159585 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
159601 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
159618 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
159637 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
159656 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
159672 TCGTTGCGAT
Statistics
Matches: 66, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.17
16 3 0.05
17 3 0.05
19 49 0.74
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:159655 original size:38 final size:33
Alignment explanation
Indices: 159585--159700 Score: 151
Period size: 33 Copynumber: 3.4 Consensus size: 33
159575 GAAATGAAAA
159585 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
159618 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTC---TCG--TTGCGATTTTCATT
***
159656 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
*
159689 TCGCGTTGCGAT
1 TCGCATTGCGAT
159701 AGTCTGTTCT
Statistics
Matches: 74, Mismatches: 4, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
33 38 0.51
35 3 0.04
36 3 0.04
38 30 0.41
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.44
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
Found at i:159807 original size:14 final size:15
Alignment explanation
Indices: 159788--159825 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
159778 CATCAATTAA
159788 ACAAATCAA-CATTT
1 ACAAATCAATCATTT
*
159802 ACAAAT-AATCTTTT
1 ACAAATCAATCATTT
159816 ACAAATCAAT
1 ACAAATCAAT
159826 TAAACAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 2 0.10
14 16 0.76
15 3 0.14
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (15 bp):
ACAAATCAATCATTT
Found at i:161726 original size:20 final size:19
Alignment explanation
Indices: 161691--161757 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
161681 GAAACTTAAA
161691 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
161710 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
161730 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
161749 ATCGCAACG
1 ATCGCAACG
161758 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:161765 original size:14 final size:14
Alignment explanation
Indices: 161746--161803 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
161736 ATGCGAAATG
161746 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
161760 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
161776 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
161792 AAAATCGCAACG
1 AAAATCGCAACG
161804 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:161788 original size:32 final size:33
Alignment explanation
Indices: 161730--161808 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
161720 GGAAATGGCT
*
161730 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
161763 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
161795 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
161809 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:161837 original size:19 final size:17
Alignment explanation
Indices: 161815--161910 Score: 78
Period size: 19 Copynumber: 5.6 Consensus size: 17
161805 GAAACACAAA
161815 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGA-TTTCATT
*
161834 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
161850 TCG-TTGCGATTTCATT
1 TCGCTTGCGATTTCATT
*
161866 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
161882 TCG-TTGCGATTTTCATT
1 TCGCTTGCGA-TTTCATT
161899 TCGCATTGCGAT
1 TCGC-TTGCGAT
161911 AGCCATTTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
14 15 0.24
15 3 0.05
16 12 0.19
17 4 0.06
18 13 0.21
19 16 0.25
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (17 bp):
TCGCTTGCGATTTCATT
Found at i:161856 original size:14 final size:14
Alignment explanation
Indices: 161837--161894 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
161827 TTTCATTTCG
161837 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
161851 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
161867 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
161883 CGTTGCGATTTT
1 CGTTGCGATTTT
161895 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:161901 original size:33 final size:33
Alignment explanation
Indices: 161820--161910 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
161810 ACAAATCGCA
161820 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
161853 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
161885 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
161911 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:161929 original size:20 final size:19
Alignment explanation
Indices: 161895--161949 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
161885 TTGCGATTTT
*
161895 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
161914 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
161934 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
161950 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:163804 original size:20 final size:20
Alignment explanation
Indices: 163779--163817 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
163769 GAATAGTTTC
163779 TGAAAATGAAAATCGCAACA
1 TGAAAATGAAAATCGCAACA
**
163799 TGAAAATGACTATCGCAAC
1 TGAAAATGAAAATCGCAAC
163818 GAGAGAATCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.18, G:0.15, T:0.18
Consensus pattern (20 bp):
TGAAAATGAAAATCGCAACA
Found at i:164106 original size:22 final size:22
Alignment explanation
Indices: 164081--164124 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
164071 GATTTAGATA
164081 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
164103 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
164125 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:164338 original size:20 final size:20
Alignment explanation
Indices: 164313--164406 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
164303 GATTATGTAT
164313 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
164333 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
164353 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
164374 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
164394 TATCGCATTGCGA
1 TATCGCGTTGCGA
164407 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:164378 original size:41 final size:42
Alignment explanation
Indices: 164333--164468 Score: 118
Period size: 41 Copynumber: 3.3 Consensus size: 42
164323 CGAAAGTCAG
* * * *
164333 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTAT
1 TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
* * *
164374 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCTCAA
1 TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
** ** * *
164416 T-TCGCGTTGCG-ATTTACTTATTCGCATTGCGAATTTCCCAA
1 TATCGCGTTGCGAAAGTAAGTA-TCGCATTGCGATTTTCTCAA
164457 T-TCGCGTTGCGA
1 TATCGCGTTGCGA
164469 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:164407 original size:20 final size:20
Alignment explanation
Indices: 164293--164407 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
164283 GCTTTGAAAA
*
164293 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
164314 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
164334 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
164354 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
164375 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
164395 ATCGCATTGCGAT
1 ATCGCATTGCGAT
164408 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:164440 original size:20 final size:20
Alignment explanation
Indices: 164396--164488 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
164386 ATAGTCAGTA
*
164396 TCGCATTGCGATTTTCTCAAT
1 TCGCATTGCGATTTACT-AAT
* *
164417 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
* *
164437 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTAAT
* *
164458 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
164478 TCGCATTGCGA
1 TCGCATTGCGA
164489 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:164469 original size:41 final size:41
Alignment explanation
Indices: 164396--164491 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
164386 ATAGTCAGTA
* *
164396 TCGCATTGCGATTTTCTCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
164437 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
164478 TCGCATTGCGAATT
1 TCGCATTGCGAATT
164492 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:166225 original size:22 final size:23
Alignment explanation
Indices: 166178--166225 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
166168 TATATTAATG
**
166178 AAATTAATAATGATTTTTAGGGA
1 AAATTAATAATGATTTTTAGCCA
166201 AAATTAATATAT-ATTTTTA-CCA
1 AAATTAATA-ATGATTTTTAGCCA
166223 AAA
1 AAA
166226 CAAAACATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 4 0.18
23 16 0.73
24 2 0.09
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (23 bp):
AAATTAATAATGATTTTTAGCCA
Found at i:176084 original size:28 final size:28
Alignment explanation
Indices: 176053--176108 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
176043 TTTAACTTAA
* *
176053 TAAACGAATATTATACAAATGTTTCACG
1 TAAACAAATATTATACAAATGATTCACG
*
176081 TAAACAAATGTTATACAAATGATTCACG
1 TAAACAAATATTATACAAATGATTCACG
176109 AATATAAACC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.30
Consensus pattern (28 bp):
TAAACAAATATTATACAAATGATTCACG
Found at i:177754 original size:2 final size:2
Alignment explanation
Indices: 177749--177773 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
177739 AAATATGAAG
177749 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
177774 AATCTTCATA
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:181254 original size:19 final size:20
Alignment explanation
Indices: 181227--181264 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
181217 CCAAATTAGT
* *
181227 TCAATTTCA-CATTTTAACA
1 TCAAATTCAGCATTCTAACA
181246 TCAAATTCAGCATTCTAAC
1 TCAAATTCAGCATTCTAAC
181265 TTTTTAGTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.37
Consensus pattern (20 bp):
TCAAATTCAGCATTCTAACA
Found at i:185293 original size:11 final size:11
Alignment explanation
Indices: 185282--185319 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
185272 TTAATAGTTT
185282 TTATTTTATT-
1 TTATTTTATTA
185292 TTATTTTAATTA
1 TTATTTT-ATTA
*
185304 TTATTATATTA
1 TTATTTTATTA
185315 TTATT
1 TTATT
185320 AGTAGTAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
10 7 0.28
11 12 0.48
12 6 0.24
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:185332 original size:18 final size:18
Alignment explanation
Indices: 185309--185346 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
185299 AATTATTATT
*
185309 ATATTATTATTAGTAGTA
1 ATATTATTAGTAGTAGTA
*
185327 ATATTATTAGTAGTATTA
1 ATATTATTAGTAGTAGTA
185345 AT
1 AT
185347 TACTATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (18 bp):
ATATTATTAGTAGTAGTA
Found at i:185333 original size:15 final size:15
Alignment explanation
Indices: 185300--185341 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
185290 TTTTATTTTA
* *
185300 ATTATTATTA-TATT
1 ATTATTAGTAGTAAT
185314 ATTATTAGTAGTAAT
1 ATTATTAGTAGTAAT
185329 ATTATTAGTAGTA
1 ATTATTAGTAGTA
185342 TTAATTACTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 9 0.36
15 16 0.64
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (15 bp):
ATTATTAGTAGTAAT
Found at i:185371 original size:30 final size:30
Alignment explanation
Indices: 185337--185579 Score: 238
Period size: 30 Copynumber: 8.1 Consensus size: 30
185327 ATATTATTAG
*
185337 TAGTATTAATTACTATTTAATTTA-ATTTAT
1 TAGTATTAATTACTATTTAA-TTAGTTTTAT
*
185367 TAGTATTAACTACTATTTAATTAGTTTTAT
1 TAGTATTAATTACTATTTAATTAGTTTTAT
* * ** * *
185397 TATTACTAACAATTATTTCATTAGTTTTAT
1 TAGTATTAATTACTATTTAATTAGTTTTAT
* ** *
185427 TAGTAGTAATTGTTATTTAATTAGCTTTAT
1 TAGTATTAATTACTATTTAATTAGTTTTAT
* *
185457 TAGCATTAACTACTATTTAATTAGTTTTAT
1 TAGTATTAATTACTATTTAATTAGTTTTAT
*
185487 TAGTATTAATT-TTCATTTAATTAGTTTTAT
1 TAGTATTAATTACT-ATTTAATTAGTTTTAT
* * * **
185517 TAGTATTAATTGCCATCTAATTAGCCTTAT
1 TAGTATTAATTACTATTTAATTAGTTTTAT
* * *
185547 TAGTGTTAATTAATATTTAATTAATTATTAT
1 TAGTATTAATTACTATTTAATTAGTT-TTAT
185578 TA
1 TA
185580 TTAGTAATAT
Statistics
Matches: 173, Mismatches: 36, Indels: 7
0.80 0.17 0.03
Matches are distributed among these distances:
29 4 0.02
30 163 0.94
31 6 0.03
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (30 bp):
TAGTATTAATTACTATTTAATTAGTTTTAT
Found at i:185448 original size:90 final size:90
Alignment explanation
Indices: 185337--185582 Score: 289
Period size: 90 Copynumber: 2.7 Consensus size: 90
185327 ATATTATTAG
* * *
185337 TAGTATTAATTACTATTTAATTTA-ATTTATTAGTATTAACTACTATTTAATTAGTTTTATTATT
1 TAGTAGTAATTGCTATTTAA-TTAGCTTTATTAGTATTAACTACTATTTAATTAGTTTTATTATT
*
185401 ACTAACAATT-ATTTCATTAGTTTTAT
65 ACTAA-AATTCATTTAATTAGTTTTAT
* * *
185427 TAGTAGTAATTGTTATTTAATTAGCTTTATTAGCATTAACTACTATTTAATTAGTTTTATTAGTA
1 TAGTAGTAATTGCTATTTAATTAGCTTTATTAGTATTAACTACTATTTAATTAGTTTTATTATTA
* **
185492 TTAATTTTCATTTAATTAGTTTTAT
66 CTAAAATTCATTTAATTAGTTTTAT
* * * * * * * *
185517 TAGTATTAATTGCCATCTAATTAGCCTTATTAGTGTTAATTAATATTTAATTAATTATTATTATT
1 TAGTAGTAATTGCTATTTAATTAGCTTTATTAGTATTAACTACTATTTAATTAGTT-TTATTATT
185582 A
65 A
185583 GTAATATAAT
Statistics
Matches: 132, Mismatches: 21, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
89 5 0.04
90 119 0.90
91 8 0.06
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (90 bp):
TAGTAGTAATTGCTATTTAATTAGCTTTATTAGTATTAACTACTATTTAATTAGTTTTATTATTA
CTAAAATTCATTTAATTAGTTTTAT
Found at i:185494 original size:15 final size:15
Alignment explanation
Indices: 185476--185524 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
185466 CTACTATTTA
185476 ATTAGTTTTATTAGT
1 ATTAGTTTTATTAGT
*
185491 ATTAATTTTCATT--T
1 ATTAGTTTT-ATTAGT
185505 AATTAGTTTTATTAGT
1 -ATTAGTTTTATTAGT
185521 ATTA
1 ATTA
185525 ATTGCCATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 4 0.14
15 20 0.71
16 4 0.14
ACGTcount: A:0.31, C:0.02, G:0.08, T:0.59
Consensus pattern (15 bp):
ATTAGTTTTATTAGT
Found at i:188593 original size:54 final size:54
Alignment explanation
Indices: 188463--188586 Score: 212
Period size: 54 Copynumber: 2.3 Consensus size: 54
188453 CGAATGCAAT
* *
188463 AGCTCAAAATGAATAAGCCGTGCCAACGCCTTAACTAAAGACCTCTTCTGCGAA
1 AGCTCAAAATGAATAAGCCGTGCCCACGCCTTAACTAAAGACCTCTTCTACGAA
* *
188517 AGCTCCAAATGAATAAGCCGTGCCCACGCCTTAACTAAATACCTCTTCTACGAA
1 AGCTCAAAATGAATAAGCCGTGCCCACGCCTTAACTAAAGACCTCTTCTACGAA
188571 AGCTCAAAATGAATAA
1 AGCTCAAAATGAATAA
188587 TTCGTGCTCA
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 65 1.00
ACGTcount: A:0.37, C:0.27, G:0.15, T:0.21
Consensus pattern (54 bp):
AGCTCAAAATGAATAAGCCGTGCCCACGCCTTAACTAAAGACCTCTTCTACGAA
Found at i:188619 original size:54 final size:54
Alignment explanation
Indices: 188463--188603 Score: 192
Period size: 54 Copynumber: 2.6 Consensus size: 54
188453 CGAATGCAAT
* * * *
188463 AGCTCAAAATGAATAAGCCGTGCCAACGCCTTAACTAAAGACCTCTTCTGCGAA
1 AGCTCAAAATGAATAAGCCGTGCCCACACCTTAACTAAAAACCTCTTCTACGAA
* * *
188517 AGCTCCAAATGAATAAGCCGTGCCCACGCCTTAACTAAATACCTCTTCTACGAA
1 AGCTCAAAATGAATAAGCCGTGCCCACACCTTAACTAAAAACCTCTTCTACGAA
** *
188571 AGCTCAAAATGAATAATTCGTGCTCACACCTTA
1 AGCTCAAAATGAATAAGCCGTGCCCACACCTTA
188604 TGAGAAAACT
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 78 1.00
ACGTcount: A:0.35, C:0.28, G:0.14, T:0.23
Consensus pattern (54 bp):
AGCTCAAAATGAATAAGCCGTGCCCACACCTTAACTAAAAACCTCTTCTACGAA
Found at i:188669 original size:19 final size:19
Alignment explanation
Indices: 188645--188696 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
188635 GAATACAATT
188645 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
188664 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
188683 AGTGCATCGATGCA
1 AGTGCATCGATGCA
188697 CCCCCTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.21
Consensus pattern (19 bp):
AGTGCATCGATGCATAAGG
Found at i:189890 original size:24 final size:24
Alignment explanation
Indices: 189804--189897 Score: 88
Period size: 23 Copynumber: 4.0 Consensus size: 24
189794 CAATCTTATA
*
189804 TGGCACTACGGTGCAA-TTCTACG
1 TGGCACTTCGGTGCAATTTCTACG
* *
189827 TGGCACTTCGGTG-TATTTCTATG
1 TGGCACTTCGGTGCAATTTCTACG
*
189850 CGGTC-CTTCGG-GACAATTTCTACG
1 TGG-CACTTCGGTG-CAATTTCTACG
* *
189874 TGGCACTTTGGTGCAATTTATACG
1 TGGCACTTCGGTGCAATTTCTACG
189898 AGCTGTGGTG
Statistics
Matches: 56, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
22 2 0.04
23 27 0.48
24 26 0.46
25 1 0.02
ACGTcount: A:0.18, C:0.22, G:0.26, T:0.34
Consensus pattern (24 bp):
TGGCACTTCGGTGCAATTTCTACG
Found at i:190287 original size:12 final size:12
Alignment explanation
Indices: 190270--190294 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
190260 CTCAAACAGA
190270 GAGAATGAACGT
1 GAGAATGAACGT
190282 GAGAATGAACGT
1 GAGAATGAACGT
190294 G
1 G
190295 TTACATGGCA
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:0.40, C:0.08, G:0.36, T:0.16
Consensus pattern (12 bp):
GAGAATGAACGT
Found at i:190356 original size:29 final size:29
Alignment explanation
Indices: 190323--190378 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
190313 TCCCAACACA
*
190323 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
*
190352 TAGGTCTCCATGCACTCCGGGCGACCT
1 TAGGTCGCCATGCACTCCGGGCGACCT
190379 ACCCTCGCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.12, C:0.38, G:0.29, T:0.21
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCGGGCGACCTTG
Found at i:190431 original size:33 final size:33
Alignment explanation
Indices: 190394--190535 Score: 167
Period size: 33 Copynumber: 4.3 Consensus size: 33
190384 CGCTCGGCTT
* * *
190394 CCCTCGGATTCCCTCGCATAGCTCGCTCAGTTG
1 CCCTCGGATGCCCTCGCATAGCTCGTTCAGATG
*
190427 CCCTCGGATGCCCTCGCATAGCTCGTTCGGATG
1 CCCTCGGATGCCCTCGCATAGCTCGTTCAGATG
*
190460 GCCTCGGATGCCCTCGCATAGCTCGTTCAGATG
1 CCCTCGGATGCCCTCGCATAGCTCGTTCAGATG
* * * * * *
190493 GCCTCGGATGCTCTCGGATGGCGTCGGTCGGATG
1 CCCTCGGATGCCCTCGCATAGC-TCGTTCAGATG
*
190527 GCCTCGGAT
1 CCCTCGGAT
190536 TCCCAGCGTG
Statistics
Matches: 97, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
33 79 0.81
34 18 0.19
ACGTcount: A:0.12, C:0.34, G:0.30, T:0.25
Consensus pattern (33 bp):
CCCTCGGATGCCCTCGCATAGCTCGTTCAGATG
Found at i:190440 original size:10 final size:10
Alignment explanation
Indices: 190425--190512 Score: 50
Period size: 10 Copynumber: 8.2 Consensus size: 10
190415 CTCGCTCAGT
190425 TGCCCTCGGA
1 TGCCCTCGGA
*
190435 TGCCCTCGCA
1 TGCCCTCGGA
*
190445 TAGCTCGTTCGGA
1 T-GC-C-CTCGGA
*
190458 TGGCCTCGGA
1 TGCCCTCGGA
*
190468 TGCCCTCGCA
1 TGCCCTCGGA
* *
190478 TAGCTCGTTCAGA
1 T-GC-C-CTCGGA
*
190491 TGGCCTCGGA
1 TGCCCTCGGA
*
190501 TGCTCTCGGA
1 TGCCCTCGGA
190511 TG
1 TG
190513 GCGTCGGTCG
Statistics
Matches: 57, Mismatches: 15, Indels: 12
0.68 0.18 0.14
Matches are distributed among these distances:
10 38 0.67
11 6 0.11
12 4 0.07
13 9 0.16
ACGTcount: A:0.12, C:0.33, G:0.30, T:0.25
Consensus pattern (10 bp):
TGCCCTCGGA
Found at i:190501 original size:66 final size:67
Alignment explanation
Indices: 190395--190535 Score: 203
Period size: 66 Copynumber: 2.1 Consensus size: 67
190385 GCTCGGCTTC
* * *
190395 CCTCGGATTCCCTCGCATAGCTCGCTCAGTTGCCCTCGGATGCCCTCGCATAGC-TCGTTCGGAT
1 CCTCGGATGCCCTCGCATAGCTCGCTCAGATGCCCTCGGATGCCCTCGCATAGCGTCGGTCGGAT
190459 GG
66 GG
* * * * *
190461 CCTCGGATGCCCTCGCATAGCTCGTTCAGATGGCCTCGGATGCTCTCGGATGGCGTCGGTCGGAT
1 CCTCGGATGCCCTCGCATAGCTCGCTCAGATGCCCTCGGATGCCCTCGCATAGCGTCGGTCGGAT
190526 GG
66 GG
190528 CCTCGGAT
1 CCTCGGAT
190536 TCCCAGCGTG
Statistics
Matches: 66, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
66 47 0.71
67 19 0.29
ACGTcount: A:0.12, C:0.33, G:0.30, T:0.25
Consensus pattern (67 bp):
CCTCGGATGCCCTCGCATAGCTCGCTCAGATGCCCTCGGATGCCCTCGCATAGCGTCGGTCGGAT
GG
Found at i:190533 original size:10 final size:10
Alignment explanation
Indices: 190453--190535 Score: 51
Period size: 10 Copynumber: 7.6 Consensus size: 10
190443 CATAGCTCGT
190453 TCGGATGGCC
1 TCGGATGGCC
*
190463 TCGGATGCCC
1 TCGGATGGCC
* *
190473 TCGCATAGCTC
1 TCGGATGGC-C
*
190484 GTTCAGATGGCC
1 --TCGGATGGCC
190496 TCGGAT-GCTC
1 TCGGATGGC-C
190506 TCGGATGGCGTC
1 TCGGATGGC--C
190518 GGTCGGATGGCC
1 --TCGGATGGCC
190530 TCGGAT
1 TCGGAT
190536 TCCCAGCGTG
Statistics
Matches: 57, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
9 2 0.04
10 33 0.58
11 3 0.05
12 4 0.07
13 6 0.11
14 9 0.16
ACGTcount: A:0.12, C:0.29, G:0.35, T:0.24
Consensus pattern (10 bp):
TCGGATGGCC
Found at i:191273 original size:14 final size:14
Alignment explanation
Indices: 191254--191280 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
191244 AACATTCGGG
191254 TACTGTTCATACGA
1 TACTGTTCATACGA
191268 TACTGTTCATACG
1 TACTGTTCATACG
191281 TATTTCACTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (14 bp):
TACTGTTCATACGA
Found at i:195807 original size:54 final size:54
Alignment explanation
Indices: 195724--195864 Score: 228
Period size: 54 Copynumber: 2.6 Consensus size: 54
195714 CGAATGCAAT
*
195724 AGCTCAAAATGAATAAGCCGTGCCAACGCCTTAACTAAAGACCTCTTCTGCGAA
1 AGCTCAAAATGAATAAGCCGTGCCCACGCCTTAACTAAAGACCTCTTCTGCGAA
* *
195778 AGCTCCAAATGAATAAGCCGTGCCCACGCCTTAACTAAATACCTCTTCTGCGAA
1 AGCTCAAAATGAATAAGCCGTGCCCACGCCTTAACTAAAGACCTCTTCTGCGAA
** *
195832 AGCTCAAAATGAATAATTCGTGCTCACGCCTTA
1 AGCTCAAAATGAATAAGCCGTGCCCACGCCTTA
195865 TGAGAAAACT
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 80 1.00
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.23
Consensus pattern (54 bp):
AGCTCAAAATGAATAAGCCGTGCCCACGCCTTAACTAAAGACCTCTTCTGCGAA
Found at i:197075 original size:24 final size:24
Alignment explanation
Indices: 196997--197090 Score: 115
Period size: 23 Copynumber: 4.0 Consensus size: 24
196987 CAATCTTATA
*
196997 TGGCACTACGGTGCAA-TTCTACG
1 TGGCACTTCGGTGCAATTTCTACG
197020 TGGCACTTCGGTGC-ATTTCTACG
1 TGGCACTTCGGTGCAATTTCTACG
*
197043 CGGTC-CTTCGG-GACAATTTCTACG
1 TGG-CACTTCGGTG-CAATTTCTACG
*
197067 TGGCACTTCGGTGCAATTTATACG
1 TGGCACTTCGGTGCAATTTCTACG
197091 AGCTGTGGTG
Statistics
Matches: 61, Mismatches: 4, Indels: 11
0.80 0.05 0.14
Matches are distributed among these distances:
22 2 0.03
23 30 0.49
24 28 0.46
25 1 0.02
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.31
Consensus pattern (24 bp):
TGGCACTTCGGTGCAATTTCTACG
Found at i:197707 original size:2 final size:2
Alignment explanation
Indices: 197700--197731 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
197690 GTTTTAAATA
197700 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
197732 GTAAATGATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:198299 original size:27 final size:27
Alignment explanation
Indices: 198281--198362 Score: 146
Period size: 27 Copynumber: 3.0 Consensus size: 27
198271 GAATGATAAA
*
198281 TTTAAGAGTTGCATTTAGAATGCTTTG
1 TTTATGAGTTGCATTTAGAATGCTTTG
*
198308 TTTATGAGTTGCACTTAGAATGCTTTG
1 TTTATGAGTTGCATTTAGAATGCTTTG
198335 TTTATGAGTTGCATTTAGAATGCTTTG
1 TTTATGAGTTGCATTTAGAATGCTTTG
198362 T
1 T
198363 CCAGCCTTGG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.23, C:0.09, G:0.22, T:0.46
Consensus pattern (27 bp):
TTTATGAGTTGCATTTAGAATGCTTTG
Found at i:201926 original size:17 final size:17
Alignment explanation
Indices: 201904--201949 Score: 92
Period size: 17 Copynumber: 2.7 Consensus size: 17
201894 GGAAAGAGAG
201904 ACTTATGTTTCGAGGAT
1 ACTTATGTTTCGAGGAT
201921 ACTTATGTTTCGAGGAT
1 ACTTATGTTTCGAGGAT
201938 ACTTATGTTTCG
1 ACTTATGTTTCG
201950 TTTACTTAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.22, C:0.13, G:0.22, T:0.43
Consensus pattern (17 bp):
ACTTATGTTTCGAGGAT
Found at i:210773 original size:19 final size:19
Alignment explanation
Indices: 210762--210808 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 19
210752 GGGGTATCGA
210762 TTCCCCTAGGGGGAATCAG
1 TTCCCCTAGGGGGAATCAG
210781 TTCCCCTTCAAAGGGGGAATCAG
1 TTCCCC-T---AGGGGGAATCAG
210804 TTCCC
1 TTCCC
210809 TCATGGGGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 1 0.04
23 17 0.71
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (19 bp):
TTCCCCTAGGGGGAATCAG
Found at i:216605 original size:21 final size:20
Alignment explanation
Indices: 216578--216632 Score: 92
Period size: 21 Copynumber: 2.7 Consensus size: 20
216568 CGTTGAACAG
216578 TGGGGGGAATCGGTACCCCC
1 TGGGGGGAATCGGTACCCCC
*
216598 TGGGGGGGAATCGATACCCCC
1 T-GGGGGGAATCGGTACCCCC
216619 TGGGGGGAATCGGT
1 TGGGGGGAATCGGT
216633 TCCCTCCGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 13 0.41
21 19 0.59
ACGTcount: A:0.16, C:0.24, G:0.44, T:0.16
Consensus pattern (20 bp):
TGGGGGGAATCGGTACCCCC
Found at i:218430 original size:59 final size:60
Alignment explanation
Indices: 218367--218519 Score: 222
Period size: 60 Copynumber: 2.6 Consensus size: 60
218357 TAGAATATTA
218367 CTTTGTTGAGTCCTCTGACTATTAAAAGTTACAAAATAGTCCC-TGACTAT-AGAGAGTTG
1 CTTTGTTGAGTCCTCTGACTATTAAAAGTTACAAAATAGTCCCTTGACTATAAG-GAGTTG
** * *
218426 CTTTGTTGAGTCCTCCAACTATTAAAAGTTGCAAAATGGTCCCTTGACTATAAGGAGTTG
1 CTTTGTTGAGTCCTCTGACTATTAAAAGTTACAAAATAGTCCCTTGACTATAAGGAGTTG
*
218486 CTTTGTTGAGTCC-CTTGACTATTACAAGTTACAA
1 CTTTGTTGAGTCCTC-TGACTATTAAAAGTTACAA
218520 CAAGATCACT
Statistics
Matches: 83, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
59 40 0.48
60 41 0.49
61 2 0.02
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (60 bp):
CTTTGTTGAGTCCTCTGACTATTAAAAGTTACAAAATAGTCCCTTGACTATAAGGAGTTG
Found at i:219769 original size:3 final size:3
Alignment explanation
Indices: 219763--219830 Score: 91
Period size: 3 Copynumber: 22.0 Consensus size: 3
219753 TTTACCCATT
* * *
219763 TTA TTA TTA TTA TAA TTA TTA TTA TAA TTA TTA TTA TTA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
219811 TATA TATA TTA TTA TTA TTA
1 T-TA T-TA TTA TTA TTA TTA
219831 AAAAATAATA
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
3 51 0.88
4 7 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:221212 original size:23 final size:25
Alignment explanation
Indices: 221159--221212 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 25
221149 AATTGTATTT
* *
221159 TTATTATTTTAATTTTACTTGTTTA
1 TTATTATTTAAATATTACTTGTTTA
221184 -TA-TATTTAAATATTA-TT-TTTA
1 TTATTATTTAAATATTACTTGTTTA
221205 TTATTATT
1 TTATTATT
221213 ATATAGTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 4 0.16
22 4 0.16
23 15 0.60
24 2 0.08
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (25 bp):
TTATTATTTAAATATTACTTGTTTA
Found at i:221516 original size:25 final size:24
Alignment explanation
Indices: 221469--221532 Score: 78
Period size: 25 Copynumber: 2.7 Consensus size: 24
221459 CCTTTTCTGA
*
221469 TATTTCTAAATA-AATAAATATTT
1 TATTTATAAATATAATAAATATTT
221492 TATTTATAAATATATATAAATATTT
1 TATTTATAAATATA-ATAAATATTT
*
221517 T-TTATATAATTATAAT
1 TATT-TATAAATATAAT
221533 TTTGAAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
23 11 0.31
24 5 0.14
25 20 0.56
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (24 bp):
TATTTATAAATATAATAAATATTT
Found at i:228420 original size:24 final size:25
Alignment explanation
Indices: 228393--228440 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
228383 TTATAAAAAA
*
228393 AAATTAAATAAA-TTGATTCGACTC
1 AAATTAAATAAACTTGATTAGACTC
**
228417 AAATTTCATAAACTTGATTAGACT
1 AAATTAAATAAACTTGATTAGACT
228441 TAAAAAAGTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.35
Consensus pattern (25 bp):
AAATTAAATAAACTTGATTAGACTC
Found at i:232448 original size:2 final size:2
Alignment explanation
Indices: 232443--232475 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
232433 TTATCAACAG
232443 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
232476 CAAACACATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:235285 original size:34 final size:35
Alignment explanation
Indices: 235227--235295 Score: 122
Period size: 34 Copynumber: 2.0 Consensus size: 35
235217 TTCATTTAGG
235227 GGGGAATCGATACCCCCCAAGGGGAATCTGTTCCC
1 GGGGAATCGATACCCCCCAAGGGGAATCTGTTCCC
*
235262 GGGGAATCGATA-CCCCCAGGGGGAATCTGTTCCC
1 GGGGAATCGATACCCCCCAAGGGGAATCTGTTCCC
235296 CCTGCACATA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 21 0.64
35 12 0.36
ACGTcount: A:0.22, C:0.30, G:0.30, T:0.17
Consensus pattern (35 bp):
GGGGAATCGATACCCCCCAAGGGGAATCTGTTCCC
Found at i:235296 original size:19 final size:18
Alignment explanation
Indices: 235240--235297 Score: 52
Period size: 19 Copynumber: 3.3 Consensus size: 18
235230 GAATCGATAC
235240 CCCCCAAGGGGAATCTGTT
1 CCCCC-AGGGGAATCTGTT
*
235259 --CCC-GGGGAATC-GATA
1 CCCCCAGGGGAATCTG-TT
235274 CCCCCAGGGGGAATCTGTT
1 CCCCCA-GGGGAATCTGTT
235293 CCCCC
1 CCCCC
235298 TGCACATACT
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
14 1 0.03
15 9 0.29
17 6 0.19
19 14 0.45
20 1 0.03
ACGTcount: A:0.19, C:0.36, G:0.28, T:0.17
Consensus pattern (18 bp):
CCCCCAGGGGAATCTGTT
Found at i:240591 original size:15 final size:15
Alignment explanation
Indices: 240571--240620 Score: 91
Period size: 15 Copynumber: 3.3 Consensus size: 15
240561 CCGTAGGACC
240571 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
240586 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
*
240601 ACTACATCCCGAAGG
1 ACTACGTCCCGAAGG
240616 ACTAC
1 ACTAC
240621 AATACCCTCG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.30, C:0.34, G:0.22, T:0.14
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:241814 original size:11 final size:12
Alignment explanation
Indices: 241796--241835 Score: 55
Period size: 11 Copynumber: 3.2 Consensus size: 12
241786 CCACGGTTGG
241796 GAGAAGAAGAAA
1 GAGAAGAAGAAA
241808 GGAAGAAGAAGAAA
1 -G-AGAAGAAGAAA
241822 G-GAAGAAGAAA
1 GAGAAGAAGAAA
241833 GAG
1 GAG
241836 TTTTCAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 11 0.44
12 1 0.04
13 2 0.08
14 11 0.44
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (12 bp):
GAGAAGAAGAAA
Found at i:241816 original size:14 final size:14
Alignment explanation
Indices: 241797--241831 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
241787 CACGGTTGGG
241797 AGAAGAAGAAAGGA
1 AGAAGAAGAAAGGA
241811 AGAAGAAGAAAGGA
1 AGAAGAAGAAAGGA
241825 AGAAGAA
1 AGAAGAA
241832 AGAGTTTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (14 bp):
AGAAGAAGAAAGGA
Found at i:242430 original size:29 final size:29
Alignment explanation
Indices: 242394--242491 Score: 85
Period size: 29 Copynumber: 3.3 Consensus size: 29
242384 AAATATCAGT
242394 TTTGTTTCATTTTAGTACATAAACTTTTA
1 TTTGTTTCATTTTAGTACATAAACTTTTA
** *
242423 TTTGTTTCAAAATCA-TACAT-AA-TATTTA
1 TTTGTTTC-ATTTTAGTACATAAACT-TTTA
*
242451 CCCTTTGTTTCATTTTAGTACCTAAACTTTTA
1 ---TTTGTTTCATTTTAGTACATAAACTTTTA
*
242483 TTTATTTCA
1 TTTGTTTCA
242492 AAACCATACA
Statistics
Matches: 53, Mismatches: 8, Indels: 16
0.69 0.10 0.21
Matches are distributed among these distances:
27 1 0.02
28 6 0.11
29 21 0.40
30 6 0.11
31 12 0.23
32 6 0.11
33 1 0.02
ACGTcount: A:0.29, C:0.14, G:0.05, T:0.52
Consensus pattern (29 bp):
TTTGTTTCATTTTAGTACATAAACTTTTA
Found at i:242532 original size:60 final size:60
Alignment explanation
Indices: 242394--242532 Score: 233
Period size: 60 Copynumber: 2.3 Consensus size: 60
242384 AAATATCAGT
* * *
242394 TTTGTTTCATTTTAGTACATAAACTTTTATTTGTTTCAAAATCATACATAATATTTACCC
1 TTTGTTTCATTTTAGTACCTAAACTTTTATTTATTTCAAAACCATACATAATATTTACCC
*
242454 TTTGTTTCATTTTAGTACCTAAACTTTTATTTATTTCAAAACCATACATAATGTTTACCC
1 TTTGTTTCATTTTAGTACCTAAACTTTTATTTATTTCAAAACCATACATAATATTTACCC
*
242514 TTTGTTTCATTTTGGTACC
1 TTTGTTTCATTTTAGTACC
242533 CACAGTTAAA
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 74 1.00
ACGTcount: A:0.28, C:0.17, G:0.06, T:0.49
Consensus pattern (60 bp):
TTTGTTTCATTTTAGTACCTAAACTTTTATTTATTTCAAAACCATACATAATATTTACCC
Found at i:249699 original size:18 final size:19
Alignment explanation
Indices: 249676--249711 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
249666 CTTAGACTAA
*
249676 TAAAAAA-TACTATTCATT
1 TAAAAAATTACAATTCATT
249694 TAAAAAATTACAATTCAT
1 TAAAAAATTACAATTCAT
249712 AAATCAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAAAAATTACAATTCATT
Found at i:256241 original size:25 final size:24
Alignment explanation
Indices: 256212--256258 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
256202 GATAAAATTT
256212 TAAAAGCTTAAAAGAGAAAAATACA
1 TAAAAGCTTAAAA-AGAAAAATACA
** *
256237 TAAAATTTTAAAAATAAAAATA
1 TAAAAGCTTAAAAAGAAAAATA
256259 TATTATCAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 8 0.42
25 11 0.58
ACGTcount: A:0.66, C:0.04, G:0.06, T:0.23
Consensus pattern (24 bp):
TAAAAGCTTAAAAAGAAAAATACA
Found at i:269938 original size:15 final size:15
Alignment explanation
Indices: 269918--269959 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
269908 AATGAAATGC
269918 TATTATATTTAAAAA
1 TATTATATTTAAAAA
* *
269933 TATTATATTCAAACA
1 TATTATATTTAAAAA
269948 -ATTATATTTAAA
1 TATTATATTTAAA
269960 GGACGTGTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTATATTTAAAAA
Found at i:276555 original size:32 final size:31
Alignment explanation
Indices: 276519--276594 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
276509 GGGGCCGTGA
*
276519 GGCCTACCTAAGAACACATCTTAGGGCCGCAG
1 GGCCTACCTAAGAA-ACATCTCAGGGCCGCAG
** **
276551 GGCCTACCCGAGAATGATCTCAGGGCCGCAG
1 GGCCTACCTAAGAAACATCTCAGGGCCGCAG
*
276582 AGCCTACCTAAGA
1 GGCCTACCTAAGA
276595 GTCACATTAG
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 24 0.67
32 12 0.33
ACGTcount: A:0.28, C:0.32, G:0.26, T:0.14
Consensus pattern (31 bp):
GGCCTACCTAAGAAACATCTCAGGGCCGCAG
Found at i:276577 original size:63 final size:63
Alignment explanation
Indices: 276471--276594 Score: 155
Period size: 63 Copynumber: 2.0 Consensus size: 63
276461 CCCTAAGGGA
* * *
276471 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCG-TGAGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGA-GCCTACCTAAGAAC
* *
276534 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
276595 GTCACATTAG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
62 2 0.04
63 49 0.92
64 2 0.04
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:277505 original size:22 final size:22
Alignment explanation
Indices: 277477--277519 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
277467 AACGGTCAAC
277477 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
277499 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
277520 AGACCGGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:277534 original size:9 final size:9
Alignment explanation
Indices: 277516--277614 Score: 90
Period size: 9 Copynumber: 10.3 Consensus size: 9
277506 GGTCGGGTCG
*
277516 GGTCAGACC
1 GGTCAAACC
277525 GGTCAAACC
1 GGTCAAACC
* *
277534 GATTCAGACC
1 G-GTCAAACC
277544 GGTCAAACC
1 GGTCAAACC
*
277553 GGTTCGAACC
1 GG-TCAAACC
*
277563 GGTTGAAACC
1 GG-TCAAACC
277573 GGTCAAACC
1 GGTCAAACC
277582 GGTCAGAACC
1 GGTCA-AACC
*
277592 GGTTGAAAACC
1 GG-T-CAAACC
277603 GGTCAAACC
1 GGTCAAACC
277612 GGT
1 GGT
277615 TTCCAGCAGC
Statistics
Matches: 74, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
9 36 0.49
10 30 0.41
11 7 0.09
12 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:277540 original size:19 final size:19
Alignment explanation
Indices: 277518--277615 Score: 101
Period size: 19 Copynumber: 5.1 Consensus size: 19
277508 TCGGGTCGGG
*
277518 TCAGACCGGTCAAACCGAT
1 TCAGACCGGTCAAACCGGT
277537 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
277556 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
*
277575 TCAAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
* *
277595 TGAAAACCGGTCAAACCGGT
1 T-CAGACCGGTCAAACCGGT
277615 T
1 T
277616 TCCAGCAGCC
Statistics
Matches: 68, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
18 3 0.04
19 38 0.56
20 17 0.25
21 10 0.15
ACGTcount: A:0.30, C:0.29, G:0.26, T:0.16
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:277573 original size:29 final size:31
Alignment explanation
Indices: 277541--277615 Score: 129
Period size: 29 Copynumber: 2.5 Consensus size: 31
277531 ACCGATTCAG
277541 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
277570 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
277600 ACCGGTCAAACCGGTT
1 ACCGGTCAAACCGGTT
277616 TCCAGCAGCC
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.56
30 16 0.37
31 1 0.02
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.16
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:283860 original size:32 final size:31
Alignment explanation
Indices: 283824--283899 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
283814 GGGGCCGTGA
*
283824 GGCCTACCTAAGAACACATCTTAGGGCCGCAG
1 GGCCTACCTAAGAA-ACATCTCAGGGCCGCAG
** **
283856 GGCCTACCCGAGAATGATCTCAGGGCCGCAG
1 GGCCTACCTAAGAAACATCTCAGGGCCGCAG
*
283887 AGCCTACCTAAGA
1 GGCCTACCTAAGA
283900 GTCACATTAG
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 24 0.67
32 12 0.33
ACGTcount: A:0.28, C:0.32, G:0.26, T:0.14
Consensus pattern (31 bp):
GGCCTACCTAAGAAACATCTCAGGGCCGCAG
Found at i:283882 original size:63 final size:63
Alignment explanation
Indices: 283776--283899 Score: 155
Period size: 63 Copynumber: 2.0 Consensus size: 63
283766 CCCTAAGGGA
* * *
283776 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCG-TGAGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGA-GCCTACCTAAGAAC
* *
283839 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
283900 GTCACATTAG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
62 2 0.04
63 49 0.92
64 2 0.04
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:284806 original size:5 final size:5
Alignment explanation
Indices: 284796--284848 Score: 52
Period size: 5 Copynumber: 9.8 Consensus size: 5
284786 AACGGTCAAC
* *
284796 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG
284845 GGTC
1 GGTC
284849 AGACCGGTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 32 0.80
7 8 0.20
ACGTcount: A:0.08, C:0.23, G:0.51, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:284811 original size:17 final size:17
Alignment explanation
Indices: 284789--284849 Score: 77
Period size: 17 Copynumber: 3.3 Consensus size: 17
284779 AACGGTCAAC
284789 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
284806 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAA----C-GGTCGGGTCG
284828 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
284845 GGTCA
1 GGTCA
284850 GACCGGTCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
17 21 0.54
18 1 0.03
21 1 0.03
22 16 0.41
ACGTcount: A:0.11, C:0.23, G:0.48, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Done.