Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008488.1 Hibiscus syriacus cultivar Beakdansim tig00111330_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: 12876159
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 23 of 54
Found at i:5769384 original size:38 final size:37
Alignment explanation
Indices: 5769266--5769385 Score: 102
Period size: 38 Copynumber: 3.2 Consensus size: 37
5769256 TTTTCACTTG
* *
5769266 AAACATAAATTTTATCTCACTTAAGATTGTTTTTCTTA
1 AAACAAAAATTTTATCACA-TTAAGATTGTTTTTCTTA
* * *** *
5769304 AAAC-AAACTTTATATCAC-TTGAGA-CAATTTTCACTA
1 AAACAAAAATTT-TATCACATTAAGATTGTTTTTC-TTA
5769340 GAAACAAAAATTTTATCACATTCAAGATTGTTTTTCTTA
1 -AAACAAAAATTTTATCACATT-AAGATTGTTTTTCTTA
5769379 AAACAAA
1 AAACAAA
5769386 CTTCGTCTCG
Statistics
Matches: 61, Mismatches: 14, Indels: 14
0.69 0.16 0.16
Matches are distributed among these distances:
35 5 0.08
36 7 0.11
37 15 0.25
38 24 0.39
39 5 0.08
40 5 0.08
ACGTcount: A:0.41, C:0.15, G:0.06, T:0.38
Consensus pattern (37 bp):
AAACAAAAATTTTATCACATTAAGATTGTTTTTCTTA
Found at i:5769874 original size:103 final size:103
Alignment explanation
Indices: 5769643--5769923 Score: 352
Period size: 103 Copynumber: 2.7 Consensus size: 103
5769633 TTACTCGAAG
* * *
5769643 CAAGAAATTTCATTTCAATCGAGATT-TTGTTTCTTAAAACAAATTTCATCTCGCTTTAGAAAGT
1 CAAGAAATTT-ATTTCACTAGAGATTGTT-TTTCTTAAAACAAATTTCATCTCGCTTGAGAAAGT
* *
5769707 TTCCC-TCAAATATAAAATTTGAAATTGTTTCACTTGTAA
64 TTCCCTTGAAATATAAAATTTGAAATTGTTTCACTTGAAA
* * * *
5769746 C-AGAAATTTTATCTCGCTACAGATTGTTTTTCTTGAAACAAATTTCATCTCGCTTGAGAAAGTT
1 CAAGAAA-TTTATTTCACTAGAGATTGTTTTTCTTAAAACAAATTTCATCTCGCTTGAGAAAGTT
*
5769810 TCCCTTGAAATATTAAATTTGAAATTGTTTCACTTGAAA
65 TCCCTTGAAATATAAAATTTGAAATTGTTTCACTTGAAA
* * * * * *
5769849 CAAGAAGTTTATTTCACTTGAGATTGTTTTTCTTAAAACAAACTTCGTCTCACTTGAGATAGTTT
1 CAAGAAATTTATTTCACTAGAGATTGTTTTTCTTAAAACAAATTTCATCTCGCTTGAGAAAG-TT
*
5769914 TCCCTCGAAA
65 TCCCTTGAAA
5769924 CAAATTTTAT
Statistics
Matches: 152, Mismatches: 21, Indels: 9
0.84 0.12 0.05
Matches are distributed among these distances:
102 53 0.35
103 84 0.55
104 15 0.10
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (103 bp):
CAAGAAATTTATTTCACTAGAGATTGTTTTTCTTAAAACAAATTTCATCTCGCTTGAGAAAGTTT
CCCTTGAAATATAAAATTTGAAATTGTTTCACTTGAAA
Found at i:5769937 original size:37 final size:36
Alignment explanation
Indices: 5769856--5769963 Score: 85
Period size: 37 Copynumber: 3.0 Consensus size: 36
5769846 AAACAAGAAG
* * * *
5769856 TTTATTTCACTTGAGATTGTTTTTCTTAAAACAAAC
1 TTTATCTCACTTGAGATAGTTTTCCTCAAAACAAAC
** * *
5769892 TTCGTCTCACTTGAGATAGTTTTCCCTCGAAACAAAT
1 TTTATCTCACTTGAGATAGTTTT-CCTCAAAACAAAC
* *
5769929 TTTATCTCACCT-ATGATAGTTCTTCTTC-AAACAAA
1 TTTATCTCACTTGA-GATAGTT-TTCCTCAAAACAAA
5769964 TTTCTTTTCA
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
36 27 0.47
37 28 0.49
38 2 0.04
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (36 bp):
TTTATCTCACTTGAGATAGTTTTCCTCAAAACAAAC
Found at i:5775100 original size:58 final size:58
Alignment explanation
Indices: 5775027--5775155 Score: 233
Period size: 58 Copynumber: 2.2 Consensus size: 58
5775017 ATATCACTCT
*
5775027 TGTATGC-TTCTGCTTTTCTTAAGGAATTGAAGATGGAAGATAAGCTTTGGAAACTAC
1 TGTATGCATGCTGCTTTTCTTAAGGAATTGAAGATGGAAGATAAGCTTTGGAAACTAC
*
5775084 TGTATGCATGCTGCTTTTCTTAAGTAATTGAAGATGGAAGATAAGCTTTGGAAACTAC
1 TGTATGCATGCTGCTTTTCTTAAGGAATTGAAGATGGAAGATAAGCTTTGGAAACTAC
5775142 TGTATGCATGCTGC
1 TGTATGCATGCTGC
5775156 CTGCAGATTC
Statistics
Matches: 69, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
57 7 0.10
58 62 0.90
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.35
Consensus pattern (58 bp):
TGTATGCATGCTGCTTTTCTTAAGGAATTGAAGATGGAAGATAAGCTTTGGAAACTAC
Found at i:5776019 original size:15 final size:16
Alignment explanation
Indices: 5775999--5776031 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5775989 GTCAATGCAT
5775999 AATTTTT-TGAATTAA
1 AATTTTTCTGAATTAA
*
5776014 AATTTTTCTTAATTAA
1 AATTTTTCTGAATTAA
5776030 AA
1 AA
5776032 AGTATCCTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (16 bp):
AATTTTTCTGAATTAA
Found at i:5776869 original size:16 final size:16
Alignment explanation
Indices: 5776834--5776873 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
5776824 AACTTGACTT
*
5776834 GAAAGTAATCCAAACG
1 GAAAGTAATCCAAACC
* *
5776850 GAAATTAATCCGAACC
1 GAAAGTAATCCAAACC
5776866 GAAAGTAA
1 GAAAGTAA
5776874 GAATCTTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.50, C:0.17, G:0.17, T:0.15
Consensus pattern (16 bp):
GAAAGTAATCCAAACC
Found at i:5777124 original size:18 final size:18
Alignment explanation
Indices: 5777069--5777129 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 18
5777059 TTTTTTAAAA
**
5777069 TTTAATAAAATATTAAATT
1 TTTAATAAAA-ATTATTTT
* *
5777088 TTTAATTGAAAATAAATTTT
1 TTTAA-TAAAAAT-TATTTT
*
5777108 TTTAATAAAAATTATTTC
1 TTTAATAAAAATTATTTT
5777126 TTTA
1 TTTA
5777130 TCAAATAGAT
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
18 8 0.24
19 13 0.39
20 12 0.36
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (18 bp):
TTTAATAAAAATTATTTT
Found at i:5784555 original size:26 final size:26
Alignment explanation
Indices: 5784519--5784572 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
5784509 ACTGAAGTGC
*
5784519 TAATACACATAAGGTCGTGCCCACCA
1 TAATACACATAAGGTCATGCCCACCA
*
5784545 TAATACACATAAGGTCATGGCCACCA
1 TAATACACATAAGGTCATGCCCACCA
5784571 TA
1 TA
5784573 TGCACTTAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.37, C:0.28, G:0.15, T:0.20
Consensus pattern (26 bp):
TAATACACATAAGGTCATGCCCACCA
Found at i:5789854 original size:21 final size:21
Alignment explanation
Indices: 5789829--5789908 Score: 117
Period size: 21 Copynumber: 3.7 Consensus size: 21
5789819 TTTTCATAAG
5789829 AGTACTTTGTGTACTTGGAGT
1 AGTACTTTGTGTACTTGGAGT
*
5789850 AGTACTTTGTGTAATATGGAAAG-
1 AGTACTTTGTGTACT-TGG--AGT
5789873 AGTACTTTGTGTACTTGGAGT
1 AGTACTTTGTGTACTTGGAGT
5789894 AGTACTTTGTGTACT
1 AGTACTTTGTGTACT
5789909 ATGGCACTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
20 2 0.04
21 29 0.55
22 6 0.11
23 14 0.26
24 2 0.04
ACGTcount: A:0.24, C:0.09, G:0.26, T:0.41
Consensus pattern (21 bp):
AGTACTTTGTGTACTTGGAGT
Found at i:5789889 original size:44 final size:44
Alignment explanation
Indices: 5789826--5789912 Score: 165
Period size: 44 Copynumber: 2.0 Consensus size: 44
5789816 GCATTTTCAT
5789826 AAGAGTACTTTGTGTACTTGGAGTAGTACTTTGTGTAATATGGA
1 AAGAGTACTTTGTGTACTTGGAGTAGTACTTTGTGTAATATGGA
*
5789870 AAGAGTACTTTGTGTACTTGGAGTAGTACTTTGTGTACTATGG
1 AAGAGTACTTTGTGTACTTGGAGTAGTACTTTGTGTAATATGG
5789913 CACTTTGTGT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.25, C:0.08, G:0.28, T:0.39
Consensus pattern (44 bp):
AAGAGTACTTTGTGTACTTGGAGTAGTACTTTGTGTAATATGGA
Found at i:5789919 original size:17 final size:17
Alignment explanation
Indices: 5789897--5789938 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
5789887 TTGGAGTAGT
5789897 ACTTTGTGTACTATGGC
1 ACTTTGTGTACTATGGC
5789914 ACTTTGTGTACTATGGC
1 ACTTTGTGTACTATGGC
5789931 ACTTTGTG
1 ACTTTGTG
5789939 GGCAATGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.17, C:0.17, G:0.24, T:0.43
Consensus pattern (17 bp):
ACTTTGTGTACTATGGC
Found at i:5790486 original size:3 final size:3
Alignment explanation
Indices: 5790478--5790506 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5790468 GAATTTTAAC
5790478 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
5790507 ATATGTATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:5798080 original size:21 final size:21
Alignment explanation
Indices: 5798009--5798082 Score: 73
Period size: 21 Copynumber: 3.5 Consensus size: 21
5797999 TACTAGCATA
*
5798009 GTATCGATACTGCTTCAATGG
1 GTATCGATACTGCTTCAACGG
* *
5798030 GTAACGATACTG-TTCTTAAC-A
1 GTATCGATACTGCTTC--AACGG
5798051 GTA-CTGATACTGCTTCAACGG
1 GTATC-GATACTGCTTCAACGG
5798072 GTATCGATACT
1 GTATCGATACT
5798083 CTAGTATCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
20 7 0.16
21 30 0.70
22 6 0.14
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.32
Consensus pattern (21 bp):
GTATCGATACTGCTTCAACGG
Found at i:5798634 original size:12 final size:13
Alignment explanation
Indices: 5798607--5798639 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
5798597 ATATTATAAT
*
5798607 TTTTCAAACTTAG
1 TTTTCAAACATAG
5798620 TTTTCAAA-ATAG
1 TTTTCAAACATAG
5798632 TTTTCAAA
1 TTTTCAAA
5798640 TTTGCCAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.45
Consensus pattern (13 bp):
TTTTCAAACATAG
Found at i:5810461 original size:20 final size:20
Alignment explanation
Indices: 5810436--5810485 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
5810426 ATTGAACTCG
*
5810436 GTATCGATACCA-CCCTATGA
1 GTATCGATACCATACCTAT-A
*
5810456 GTATCGATACCATACTTATA
1 GTATCGATACCATACCTATA
5810476 GTATCGATAC
1 GTATCGATAC
5810486 TCATTACATG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 23 0.85
21 4 0.15
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (20 bp):
GTATCGATACCATACCTATA
Found at i:5811660 original size:16 final size:15
Alignment explanation
Indices: 5811632--5811682 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 15
5811622 AAGTTATTTT
*
5811632 AAATTTTAAATATAA
1 AAATATTAAATATAA
*
5811647 AATTATTCAAATATTCAA
1 AAATATT-AAATA-T-AA
5811665 AAATATTAAATATAA
1 AAATATTAAATATAA
5811680 AAA
1 AAA
5811683 AATATTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 10 0.33
16 6 0.20
17 6 0.20
18 8 0.27
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (15 bp):
AAATATTAAATATAA
Found at i:5811677 original size:17 final size:16
Alignment explanation
Indices: 5811632--5811691 Score: 59
Period size: 17 Copynumber: 3.6 Consensus size: 16
5811622 AAGTTATTTT
*
5811632 AAATTTTAAATA-TAA
1 AAATATTAAATATTAA
*
5811647 AATTATTCAAATATTCAA
1 AAATATT-AAATATT-AA
*
5811665 AAATATTAAATATAAAA
1 AAATATTAAATAT-TAA
5811682 AAATATTAAA
1 AAATATTAAA
5811692 AAAATAAAGG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
15 5 0.14
16 5 0.14
17 19 0.51
18 8 0.22
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATATTAAATATTAA
Found at i:5812600 original size:25 final size:25
Alignment explanation
Indices: 5812572--5812619 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
5812562 GTAAGTTTCA
5812572 ACTAATACAAAATTTGTAAGTCTAG
1 ACTAATACAAAATTTGTAAGTCTAG
** *
5812597 ACTAATTTAAACTTTGTAAGTCT
1 ACTAATACAAAATTTGTAAGTCT
5812620 CTATTAATCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (25 bp):
ACTAATACAAAATTTGTAAGTCTAG
Found at i:5813808 original size:12 final size:12
Alignment explanation
Indices: 5813791--5813815 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5813781 CTAATTTAAC
5813791 TCATTTGTCATG
1 TCATTTGTCATG
5813803 TCATTTGTCATG
1 TCATTTGTCATG
5813815 T
1 T
5813816 TATCAACCAT
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:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (12 bp):
TCATTTGTCATG
Found at i:5821328 original size:16 final size:16
Alignment explanation
Indices: 5821309--5821343 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
5821299 GAGGCTGGAA
5821309 CAAATGGCCTCATTGG
1 CAAATGGCCTCATTGG
5821325 CAAATGGCCTCATTGG
1 CAAATGGCCTCATTGG
5821341 CAA
1 CAA
5821344 CTGCACTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.23
Consensus pattern (16 bp):
CAAATGGCCTCATTGG
Found at i:5822667 original size:35 final size:36
Alignment explanation
Indices: 5822621--5822755 Score: 211
Period size: 36 Copynumber: 3.8 Consensus size: 36
5822611 AAAGATGAAC
* *
5822621 ACTTGAATCGAAAGT-CCGATGCCTCCTTTCGTTCG
1 ACTTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCG
* *
5822656 ACTTGAATCGAAAGGGCCGATGCTTCATTCCGTTCG
1 ACTTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCG
5822692 ACTTGAATCGAAAGTGCCGATGCTTCCTTCCGTTC-
1 ACTTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCG
*
5822727 ACTTGAATCGAAAGTGCTGATGCTTCCTT
1 ACTTGAATCGAAAGTGCCGATGCTTCCTT
5822756 TCTTTTTTCT
Statistics
Matches: 92, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
35 42 0.46
36 50 0.54
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.31
Consensus pattern (36 bp):
ACTTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCG
Found at i:5822737 original size:71 final size:71
Alignment explanation
Indices: 5822621--5822752 Score: 212
Period size: 71 Copynumber: 1.9 Consensus size: 71
5822611 AAAGATGAAC
*
5822621 ACTTGAATCGAAAGTCCGATGCCTCCTTTCGTTCGACTTGAATCGAAAGGGCCGATGCTTCATTC
1 ACTTGAATCGAAAGTCCGATGCCTCCTTCCGTTCGACTTGAATCGAAAGGGCCGATGCTTCATTC
5822686 CGTTCG
66 CGTTCG
* * *
5822692 ACTTGAATCGAAAGTGCCGATGCTTCCTTCCGTTC-ACTTGAATCGAAAGTGCTGATGCTTC
1 ACTTGAATCGAAAGT-CCGATGCCTCCTTCCGTTCGACTTGAATCGAAAGGGCCGATGCTTC
5822753 CTTTCTTTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
71 39 0.70
72 17 0.30
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (71 bp):
ACTTGAATCGAAAGTCCGATGCCTCCTTCCGTTCGACTTGAATCGAAAGGGCCGATGCTTCATTC
CGTTCG
Found at i:5826017 original size:2 final size:2
Alignment explanation
Indices: 5826010--5826047 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5826000 AAAGGGTTTG
5826010 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5826048 TATTAAACTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5829211 original size:20 final size:21
Alignment explanation
Indices: 5829182--5829231 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
5829172 AAGTCAGTAA
*
5829182 TATCGATACTCAGAGG-TTAG
1 TATCGATACTAAGAGGCTTAG
* *
5829202 TATTGATACTAAGGGGCTTAG
1 TATCGATACTAAGAGGCTTAG
5829223 TATCGATAC
1 TATCGATAC
5829232 CGATAAACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (21 bp):
TATCGATACTAAGAGGCTTAG
Found at i:5831546 original size:16 final size:16
Alignment explanation
Indices: 5831521--5831556 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
5831511 ATAAAGAAAA
*
5831521 TAAAAATGCATAAATT
1 TAAAAATGCATAAAGT
*
5831537 TAAAAGTGCATAAAGT
1 TAAAAATGCATAAAGT
5831553 TAAA
1 TAAA
5831557 TAACTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.56, C:0.06, G:0.11, T:0.28
Consensus pattern (16 bp):
TAAAAATGCATAAAGT
Found at i:5831749 original size:16 final size:16
Alignment explanation
Indices: 5831730--5831782 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
5831720 TTAATTAGTG
5831730 GTTAGAAAGGTTAGCT
1 GTTAGAAAGGTTAGCT
5831746 GTTAGAAAGGTTAGCT
1 GTTAGAAAGGTTAGCT
* * *
5831762 ATTAGAAAAGTTAGCG
1 GTTAGAAAGGTTAGCT
5831778 GTTAG
1 GTTAG
5831783 CGGAGTCTGG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.34, C:0.06, G:0.30, T:0.30
Consensus pattern (16 bp):
GTTAGAAAGGTTAGCT
Found at i:5833520 original size:139 final size:140
Alignment explanation
Indices: 5833263--5833910 Score: 641
Period size: 139 Copynumber: 4.7 Consensus size: 140
5833253 TCAATCTAGA
* ** * * * * *
5833263 GATAATTTGGTGTTAACATGGTTCCTACTTGATGAGAAAGTCTGGTTGTCAT-ATGATGACACTG
1 GATAATTTGGAGACAACACGGTTCCTACGTGATGAGAAAGTCTGGTTATC-TGAGGATGACGCTG
** * * * *
5833327 CTATTTCGCGTTGAGGAGATCTGGTCGGTGAACGATA-A-TGTTCATTCGTAATGAGGATGTCTA
65 CTCCTACGCGTTGAGGAGATCTGGTCGGTGGAC-ATACATTGTTCCTTCGTGATGAGGATGTCTA
5833390 GCCATCTTTAGG
129 GCCATCTTTAGG
*
5833402 GATAATTTGGAGACAACACGGTTCCTACGTGATGAGAAAGTCTGGTTATCT-AGGGATGATGCTG
1 GATAATTTGGAGACAACACGGTTCCTACGTGATGAGAAAGTCTGGTTATCTGA-GGATGACGCTG
* * * *
5833466 CTCTTACGCGTTGAGGAGATCTGTTCGGTGGA-ATACATTGTTCCTTCATGATGAGGATGTTTAG
65 CTCCTACGCGTTGAGGAGATCTGGTCGGTGGACATACATTGTTCCTTCGTGATGAGGATGTCTAG
* *
5833530 CCCTTTTTAGG
130 CCATCTTTAGG
* * * * * * **
5833541 GATAATTTAGAGACAACAC-GATCCTATGTGATGAGAAAGTCTGATTGTCTGAGGATGATGCTAT
1 GATAATTTGGAGACAACACGGTTCCTACGTGATGAGAAAGTCTGGTTATCTGAGGATGACGCTGC
* * * *
5833605 TCCTACACATTGAGGAGATCTGGTCGGTGGACA-ACATTGTTCCTAT-GTGATGAGGATATCTAA
66 TCCTACGCGTTGAGGAGATCTGGTCGGTGGACATACATTGTTCCT-TCGTGATGAGGATGTCTAG
***
5833668 TGGTCTTTAGG
130 CCATCTTTAGG
* * ** * * *
5833679 GATACTTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTAATTACCTGAAGATGACGTTGC
1 GATAATTTGGAGACAACACGGTTCCTACGTGATGAGAAAGTCTGGTTATCTGAGGATGACGCTGC
* * * * * * *
5833744 TCCTATGCATTGAGGAGATATGGTCAGTGGATA-ACATTGTTCCTACGTGATGAGGATGTTTAGC
66 TCCTACGCGTTGAGGAGATCTGGTCGGTGGACATACATTGTTCCTTCGTGATGAGGATGTCTAGC
5833808 CATCTTTAGG
131 CATCTTTAGG
* * ** * * * * *
5833818 GATACTTTGGAGATAACACAATTCTTACATGATGAGAAAAG-CTGGTTATCTGATGATGAAGCTA
1 GATAATTTGGAGACAACACGGTTCCTACGTGATGAG-AAAGTCTGGTTATCTGAGGATGACGCTG
*
5833882 CTCCTACACGTTGAGGAGATCTGGTCGGT
65 CTCCTACGCGTTGAGGAGATCTGGTCGGT
5833911 TTCCAATGAT
Statistics
Matches: 419, Mismatches: 81, Indels: 18
0.81 0.16 0.03
Matches are distributed among these distances:
137 3 0.01
138 115 0.27
139 298 0.71
140 3 0.01
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.32
Consensus pattern (140 bp):
GATAATTTGGAGACAACACGGTTCCTACGTGATGAGAAAGTCTGGTTATCTGAGGATGACGCTGC
TCCTACGCGTTGAGGAGATCTGGTCGGTGGACATACATTGTTCCTTCGTGATGAGGATGTCTAGC
CATCTTTAGG
Found at i:5833759 original size:277 final size:278
Alignment explanation
Indices: 5833394--5833910 Score: 700
Period size: 277 Copynumber: 1.9 Consensus size: 278
5833384 TGTCTAGCCA
** * *
5833394 TCTTTAGGGATAATTTGGAGACAACACGGTTCCTACGTGATGAGAAAGTCTGGTTATCTAGGGAT
1 TCTTTAGGGATAATTTGGAGACAACACGGTTCCTACGTGATGAGAAAGTCTAATTACCTAGAGAT
* * * * * * *
5833459 GATGCTGCTCTTACGCGTTGAGGAGATCTGTTCGGTGGA-ATACATTGTTCCTTCATGATGAGGA
66 GACGCTGCTCCTACGCATTGAGGAGATATGGTCAGTGGATA-ACATTGTTCCTACATGATGAGGA
* * * **
5833523 TGTTTAGCCCTTTTTAGGGATAATTTAGAGACAACACGA-TCCTATGTGATGAG-AAAGTCTGAT
130 TGTTTAGCCATCTTTAGGGATAATTTAGAGACAACACAATTCCTACATGATGAGAAAAG-CTGAT
* * *
5833586 TGTCTGAGGATGATGCTATTCCTACACATTGAGGAGATCTGGTCGGTGGACAACATTGTTCCTAT
194 TATCTGAGGATGAAGCTACTCCTACACATTGAGGAGATCTGGTCGGTGGACAACATTGTTCCTAT
5833651 GTGATGAGGATATCTAATGG
259 GTGATGAGGATATCTAATGG
* *
5833671 TCTTTAGGGATACTTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTAATTACCT-GAAGA
1 TCTTTAGGGATAATTTGGAGACAACACGGTTCCTACGTGATGAGAAAGTCTAATTACCTAG-AGA
* * *
5833735 TGACGTTGCTCCTATGCATTGAGGAGATATGGTCAGTGGATAACATTGTTCCTACGTGATGAGGA
65 TGACGCTGCTCCTACGCATTGAGGAGATATGGTCAGTGGATAACATTGTTCCTACATGATGAGGA
* * * * *
5833800 TGTTTAGCCATCTTTAGGGATACTTTGGAGATAACACAATTCTTACATGATGAGAAAAGCTGGTT
130 TGTTTAGCCATCTTTAGGGATAATTTAGAGACAACACAATTCCTACATGATGAGAAAAGCTGATT
* *
5833865 ATCTGATGATGAAGCTACTCCTACACGTTGAGGAGATCTGGTCGGT
195 ATCTGAGGATGAAGCTACTCCTACACATTGAGGAGATCTGGTCGGT
5833911 TTCCAATGAT
Statistics
Matches: 205, Mismatches: 31, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
276 1 0.00
277 142 0.69
278 58 0.28
279 4 0.02
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.31
Consensus pattern (278 bp):
TCTTTAGGGATAATTTGGAGACAACACGGTTCCTACGTGATGAGAAAGTCTAATTACCTAGAGAT
GACGCTGCTCCTACGCATTGAGGAGATATGGTCAGTGGATAACATTGTTCCTACATGATGAGGAT
GTTTAGCCATCTTTAGGGATAATTTAGAGACAACACAATTCCTACATGATGAGAAAAGCTGATTA
TCTGAGGATGAAGCTACTCCTACACATTGAGGAGATCTGGTCGGTGGACAACATTGTTCCTATGT
GATGAGGATATCTAATGG
Found at i:5834187 original size:67 final size:67
Alignment explanation
Indices: 5834083--5834536 Score: 581
Period size: 67 Copynumber: 6.8 Consensus size: 67
5834073 AAGGAAAATA
* ** * * *
5834083 TGTCTCAACCGAGATGAAACTTCGTTTCGAGAAAAACAATCTCAAAGGTTTATGTTTCAAAAGAA
1 TGTCTCAAGCGAGACAAAACTTTGTTTCGAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAA
5834148 AC
66 AC
* * * *
5834150 TGTTTCAAGCGAGACAAAACTTTGTTTTGAGAGAAACAATCTCAAAGGTTTATATTT-AATGAGG
1 TGTCTCAAGCGAGACAAAACTTTGTTTCGAGAGAAACAATCTCAAAGGTTTATGTTTCAA-GAGA
*
5834214 AAT
65 AAC
* * **
5834217 TGTCTGAAGTGAGACAAAACTTTGTTTTAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAA
1 TGTCTCAAGCGAGACAAAACTTTGTTTCGAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAA
5834282 AC
66 AC
** * * *
5834284 AATCTCAAGAGAGACTAAA-TTTGTTTCGAGAGAAAGAATCTCAAAGGTTTATGTTTCAAGAGAA
1 TGTCTCAAGCGAGACAAAACTTTGTTTCGAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAA
5834348 AC
66 AC
* * *
5834350 TGTCTCAAGCGAGGCAAAACTTTTTTTTGAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAA
1 TGTCTCAAGCGAGACAAAACTTTGTTTCGAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAA
5834415 AC
66 AC
* * * * *
5834417 TGTCGCAAGCGAGACAAAACTTTGTTTCAAGTGAAACAATCTTAATGGTTTATGTTTCAAGAGAA
1 TGTCTCAAGCGAGACAAAACTTTGTTTCGAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAA
*
5834482 AT
66 AC
* * *
5834484 TTTCTCAAGCGAGACAAAACTTTGTTTCGAGATAATA-AATCTCAAAGATTTAT
1 TGTCTCAAGCGAGACAAAACTTTGTTTCGAGAGAA-ACAATCTCAAAGGTTTAT
5834537 TAATTTTGTT
Statistics
Matches: 332, Mismatches: 51, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
66 60 0.18
67 269 0.81
68 3 0.01
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (67 bp):
TGTCTCAAGCGAGACAAAACTTTGTTTCGAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAA
AC
Found at i:5834455 original size:200 final size:200
Alignment explanation
Indices: 5834099--5834536 Score: 621
Period size: 200 Copynumber: 2.2 Consensus size: 200
5834089 AACCGAGATG
* *
5834099 AAACTTCGTTTCGAGAAAAACAATCTCAAAGGTTTATGTTTCAAAAGAAACTGTTTCAAGCGAGA
1 AAACTTTGTTTCGAGAAAAA-AATCTCAAAGGTTTATGTTTCAAAAGAAACTGTCTCAAGCGAGA
* * *
5834164 CAAAACTTTGTTTTGAGAGAAACAATCTCAAAGGTTTATATTTAATGAGGAATTGTCTGAAGTGA
65 CAAAACTTTGTTTTGAGAGAAACAATCTCAAAGGTTTATATTTAATGAGAAACTGTCTGAAGCGA
*
5834229 GACAAAACTTTGTTTTAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACAATCTCAAGA
130 GACAAAACTTTGTTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACAATCTCAAGA
*
5834294 GAGACT
195 GAGACA
* * *
5834300 AAA-TTTGTTTCGAGAGAAAGAATCTCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGCGAGG
1 AAACTTTGTTTCGAGA-AAAAAATCTCAAAGGTTTATGTTTCAAAAGAAACTGTCTCAAGCGAGA
* *
5834364 CAAAACTTTTTTTTGAGAGAAACAATCTCAAAGGTTTATGTTTCAA-GAGAAACTGTC-GCAAGC
65 CAAAACTTTGTTTTGAGAGAAACAATCTCAAAGGTTTATATTT-AATGAGAAACTGTCTG-AAGC
* * * ***
5834427 GAGACAAAACTTTGTTTCAAGTGAAACAATCTTAATGGTTTATGTTTCAAGAGAAATTTTCTCAA
128 GAGACAAAACTTTGTTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACAATCTCAA
*
5834492 GCGAGACA
193 GAGAGACA
* *
5834500 AAACTTTGTTTCGAGATAATAAATCTCAAAGATTTAT
1 AAACTTTGTTTCGAGA-AAAAAATCTCAAAGGTTTAT
5834537 TAATTTTGTT
Statistics
Matches: 210, Mismatches: 23, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
199 1 0.00
200 172 0.82
201 37 0.18
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.30
Consensus pattern (200 bp):
AAACTTTGTTTCGAGAAAAAAATCTCAAAGGTTTATGTTTCAAAAGAAACTGTCTCAAGCGAGAC
AAAACTTTGTTTTGAGAGAAACAATCTCAAAGGTTTATATTTAATGAGAAACTGTCTGAAGCGAG
ACAAAACTTTGTTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACAATCTCAAGAG
AGACA
Found at i:5841676 original size:120 final size:117
Alignment explanation
Indices: 5841444--5841692 Score: 270
Period size: 120 Copynumber: 2.1 Consensus size: 117
5841434 AGCTATTAGG
* * * * * *
5841444 AAAGTTAGTGGTTAGCAGAGTCTAGACCATAATAATGCGTGTCATACCCCGGATCGGGTCACCAC
1 AAAGTTAGTGGTCAACAGAGTCCAAACCATAACAATGCGTGTCATACCCCGAATCGGGTCACCAC
* * *
5841509 GAGGTTGAATCGAATAATCCAAACAAATAATAAAATAAAATAAAATAAAA-A
66 AAGGTCGAATCGAATAATACAAACAAATAATAAAATAAAATAAAATAAAATA
* *
5841560 AAAGTTAGTGGTCAACAGAGTCCAAACCATAACAATGTGGATGGATCATACCCTGAATCGGGTCA
1 AAAGTTAGTGGTCAACAGAGTCCAAACCATAACAATG-CG-T-G-TCATACCCCGAATCGGGTCA
* * * **
5841625 CCACAAGGTCGAATCGAATATTAGAAAC-AATAA-ATAAATAACAGTGCAATAAAATA
62 CCACAAGGTCGAATCGAATAATACAAACAAATAATA-AAATAA-AATAAAATAAAATA
*
5841681 AAAGTGAGTGGT
1 AAAGTTAGTGGT
5841693 TAATATGTAA
Statistics
Matches: 109, Mismatches: 17, Indels: 9
0.81 0.13 0.07
Matches are distributed among these distances:
116 32 0.29
117 1 0.01
118 2 0.02
119 12 0.11
120 50 0.46
121 12 0.11
ACGTcount: A:0.43, C:0.16, G:0.19, T:0.21
Consensus pattern (117 bp):
AAAGTTAGTGGTCAACAGAGTCCAAACCATAACAATGCGTGTCATACCCCGAATCGGGTCACCAC
AAGGTCGAATCGAATAATACAAACAAATAATAAAATAAAATAAAATAAAATA
Found at i:5843053 original size:20 final size:21
Alignment explanation
Indices: 5843011--5843055 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
5843001 GGAGTATCAG
*
5843011 TACCATAGTATAGAAGTATCGA
1 TACCATAG-ATAGAAGTACCGA
*
5843033 TACCATAG-TAGGAGTACCGA
1 TACCATAGATAGAAGTACCGA
5843053 TAC
1 TAC
5843056 TATTGAGCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 13 0.62
22 8 0.38
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (21 bp):
TACCATAGATAGAAGTACCGA
Found at i:5843448 original size:54 final size:54
Alignment explanation
Indices: 5843362--5843473 Score: 170
Period size: 54 Copynumber: 2.1 Consensus size: 54
5843352 GCATTTTTAT
* * *
5843362 GTATCGGCACTAAGTGTGCAACCCACGAAATTCGTAATAAGTTTATGAACAACC
1 GTATCGGCACTAACTGTACAACCCACGAAATTCATAATAAGTTTATGAACAACC
* * *
5843416 GTATCGGCACTAACTGTACAACCCATGGAATTCATAATAAGTTTATGAACGACC
1 GTATCGGCACTAACTGTACAACCCACGAAATTCATAATAAGTTTATGAACAACC
5843470 GTAT
1 GTAT
5843474 AAACATTATG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (54 bp):
GTATCGGCACTAACTGTACAACCCACGAAATTCATAATAAGTTTATGAACAACC
Found at i:5854276 original size:46 final size:46
Alignment explanation
Indices: 5854221--5854443 Score: 308
Period size: 46 Copynumber: 4.8 Consensus size: 46
5854211 GAAAGAATAC
* * *
5854221 CATAATTAAAGTGCATGAAATGATGCATTAAGGTATGAAATGATGT
1 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAATGATGT
* *
5854267 CATAATTAAAATGCATGAAATGATGCAATAAGGCATGAACA-GAT-T
1 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAA-ATGATGT
*
5854312 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAATGATGC
1 -CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAATGATGT
*
5854359 CATAATTAAAATGCATGAAAAGATGCATTAAGGCATG-AATGGATGT
1 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAT-GATGT
* * *
5854405 CATAATTAAAATGTATGAAAGGATGCCTTAAGGTATGAA
1 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAA
5854444 CGGATACCTT
Statistics
Matches: 159, Mismatches: 12, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
45 5 0.03
46 152 0.96
47 2 0.01
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.26
Consensus pattern (46 bp):
CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAATGATGT
Found at i:5854285 original size:26 final size:25
Alignment explanation
Indices: 5854221--5854430 Score: 113
Period size: 20 Copynumber: 9.0 Consensus size: 25
5854211 GAAAGAATAC
*
5854221 CATAATTAAAGTGCATGAAATGATG
1 CATAATTAAAATGCATGAAATGATG
* *
5854246 C---ATT--AAGGTATGAAATGATG
1 CATAATTAAAATGCATGAAATGATG
5854266 TCATAATTAAAATGCATGAAATGATG
1 -CATAATTAAAATGCATGAAATGATG
* *
5854292 C--AA-T--AAGGCATGAACA-GATTC
1 CATAATTAAAATGCATGAA-ATGA-TG
*
5854313 CATAATTAAAATGCATGAAAGGATG
1 CATAATTAAAATGCATGAAATGATG
*
5854338 C---ATT--AAGGCATGAAATGATG
1 CATAATTAAAATGCATGAAATGATG
*
5854358 CCATAATTAAAATGCATGAAAAGATG
1 -CATAATTAAAATGCATGAAATGATG
*
5854384 C---ATT--AAGGCATG-AATGGATG
1 CATAATTAAAATGCATGAAAT-GATG
* *
5854404 TCATAATTAAAATGTATGAAAGGATG
1 -CATAATTAAAATGCATGAAATGATG
5854430 C
1 C
5854431 CTTAAGGTAT
Statistics
Matches: 139, Mismatches: 18, Indels: 56
0.65 0.08 0.26
Matches are distributed among these distances:
19 2 0.01
20 49 0.35
21 6 0.04
22 10 0.07
23 4 0.03
24 10 0.07
25 7 0.05
26 49 0.35
27 2 0.01
ACGTcount: A:0.44, C:0.10, G:0.20, T:0.26
Consensus pattern (25 bp):
CATAATTAAAATGCATGAAATGATG
Found at i:5854329 original size:92 final size:93
Alignment explanation
Indices: 5854220--5854443 Score: 344
Period size: 92 Copynumber: 2.4 Consensus size: 93
5854210 GGAAAGAATA
* * *
5854220 CCATAATTAAAGTGCATGAAATGATGCATTAAGGTATGAAATGATGTCATAATTAAAATGCATGA
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGTATGAAATGATGCCATAATTAAAATGCATGA
*
5854285 AATGATGCAATAAGGCATGAACAGAT-T
66 AAAGATGCAATAAGGCATGAACAGATGT
*
5854312 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAATGATGCCATAATTAAAATGCATGA
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGTATGAAATGATGCCATAATTAAAATGCATGA
* **
5854377 AAAGATGCATTAAGGCATGAATGGATGT
66 AAAGATGCAATAAGGCATGAACAGATGT
* *
5854405 -CATAATTAAAATGTATGAAAGGATGCCTTAAGGTATGAA
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGTATGAA
5854444 CGGATACCTT
Statistics
Matches: 120, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
92 119 0.99
93 1 0.01
ACGTcount: A:0.43, C:0.10, G:0.21, T:0.26
Consensus pattern (93 bp):
CCATAATTAAAATGCATGAAAGGATGCATTAAGGTATGAAATGATGCCATAATTAAAATGCATGA
AAAGATGCAATAAGGCATGAACAGATGT
Found at i:5854395 original size:66 final size:65
Alignment explanation
Indices: 5854325--5854602 Score: 200
Period size: 66 Copynumber: 4.2 Consensus size: 65
5854315 TAATTAAAAT
*
5854325 GCATGAAAGGATGC-ATT-AAGGCATGAAATGATGCCATAATTAAAATGCATGAAAAGATGCATT
1 GCATGAAAGGATGCAATTAAAGGCATGAAATGATGCC---ATTAAAATGCATGAAAGGATGCATT
5854388 AAG
63 AAG
* * * * * * * * *
5854391 GCATGAATGGATGTCATAATTAAAATGTATGAAAGGATGCC-TT--AAGGTATGAACGGATACCT
1 GCATGAAAGGATG-C--AATT-AAAGGCATGAAATGATGCCATTAAAATGCATGAAAGGATGCAT
5854453 TAAG
62 TAAG
* * * **
5854457 GTATGAACGGATGCCATAATTAAAATGCATGAAATGATG-CATTAAGGTG--TGAAAGGATGCAT
1 GCATGAAAGGATG-C--AATT-AAAGGCATGAAATGATGCCATTAAAATGCATGAAAGGATGCAT
5854519 TAAG
62 TAAG
*
5854523 GCATGAAAGGATGC-ATT-AAGGCATGAACA-GATGTCATAATAAATATGCATGAAAGGATGCAT
1 GCATGAAAGGATGCAATTAAAGGCATGAA-ATGATGCCAT--TAAA-ATGCATGAAAGGATGCAT
5854585 TAAG
62 TAAG
5854589 GCATGAAAGGATGC
1 GCATGAAAGGATGC
5854603 CATAAAATGT
Statistics
Matches: 170, Mismatches: 26, Indels: 32
0.75 0.11 0.14
Matches are distributed among these distances:
60 13 0.08
61 4 0.02
62 3 0.02
63 3 0.02
64 2 0.01
65 2 0.01
66 121 0.71
67 1 0.01
68 3 0.02
70 3 0.02
72 15 0.09
ACGTcount: A:0.41, C:0.10, G:0.25, T:0.24
Consensus pattern (65 bp):
GCATGAAAGGATGCAATTAAAGGCATGAAATGATGCCATTAAAATGCATGAAAGGATGCATTAAG
Found at i:5854403 original size:20 final size:20
Alignment explanation
Indices: 5854325--5854602 Score: 162
Period size: 20 Copynumber: 12.7 Consensus size: 20
5854315 TAATTAAAAT
5854325 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
5854345 GCATGAAATGATGCCATAATTAAAAT
1 GCATGAAAGGATG-C---ATT--AAG
*
5854371 GCATGAAAAGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
5854391 GCATGAATGGATGTCATAATTAAAAT
1 GCATGAAAGGATG-C---ATT--AAG
* *
5854417 GTATGAAAGGATGCCTTAAG
1 GCATGAAAGGATGCATTAAG
* * * *
5854437 GTATGAACGGATACCTTAAG
1 GCATGAAAGGATGCATTAAG
* * *
5854457 GTATGAACGGATGCCATAATTAAAAT
1 GCATGAAAGGATG-C---ATT--AAG
*
5854483 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
**
5854503 GTGTGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
5854523 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
5854543 GCATGAACA-GATGTCATAATAAATAT
1 GCATGAA-AGGATG-CAT--T--A-AG
5854569 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
5854589 GCATGAAAGGATGC
1 GCATGAAAGGATGC
5854603 CATAAAATGT
Statistics
Matches: 205, Mismatches: 27, Indels: 52
0.72 0.10 0.18
Matches are distributed among these distances:
20 120 0.59
21 8 0.04
22 8 0.04
23 2 0.01
24 8 0.04
25 8 0.04
26 51 0.25
ACGTcount: A:0.41, C:0.10, G:0.25, T:0.24
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:5854522 original size:86 final size:86
Alignment explanation
Indices: 5854419--5854602 Score: 253
Period size: 86 Copynumber: 2.1 Consensus size: 86
5854409 ATTAAAATGT
* * * * * *
5854419 ATGAAAGGATGCCTTAAGGTATGAACGGATACCTTAAGGTATGAACGGATGCCATAATTAAA-AT
1 ATGAAAGGATGCATTAAGGCATGAAAGGATACATTAAGGCATGAACAGATGCCATAA-TAAATAT
* *
5854483 GCATGAAATGATGCATTAAGGT
65 GCATGAAAGGATGCATTAAGGC
* * *
5854505 GTGAAAGGATGCATTAAGGCATGAAAGGATGCATTAAGGCATGAACAGATGTCATAATAAATATG
1 ATGAAAGGATGCATTAAGGCATGAAAGGATACATTAAGGCATGAACAGATGCCATAATAAATATG
5854570 CATGAAAGGATGCATTAAGGC
66 CATGAAAGGATGCATTAAGGC
5854591 ATGAAAGGATGC
1 ATGAAAGGATGC
5854603 CATAAAATGT
Statistics
Matches: 85, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
85 4 0.05
86 81 0.95
ACGTcount: A:0.40, C:0.11, G:0.26, T:0.23
Consensus pattern (86 bp):
ATGAAAGGATGCATTAAGGCATGAAAGGATACATTAAGGCATGAACAGATGCCATAATAAATATG
CATGAAAGGATGCATTAAGGC
Found at i:5854642 original size:47 final size:46
Alignment explanation
Indices: 5854452--5854648 Score: 187
Period size: 46 Copynumber: 4.4 Consensus size: 46
5854442 AACGGATACC
* * *
5854452 TTAAGGTATGAACGGATGCCATAATTAAA-ATGCATGAAATGATGCA
1 TTAAGGCATGAAAGGATGCCATAA-TAAATATGCATGAAAGGATGCA
** *
5854498 TTAAGGTGTGAAAGGATG-CAT--T--A-AGGCATGAAAGGATGCA
1 TTAAGGCATGAAAGGATGCCATAATAAATATGCATGAAAGGATGCA
*
5854538 TTAAGGCATGAACA-GATGTCATAATAAATATGCATGAAAGGATGCA
1 TTAAGGCATGAA-AGGATGCCATAATAAATATGCATGAAAGGATGCA
* *
5854584 TTAAGGCATGAAAGGATGCCATAA-AATGTAATGCATGAAAAGATGCA
1 TTAAGGCATGAAAGGATGCCATAATAA-AT-ATGCATGAAAGGATGCA
* * *
5854631 TTAAAGTATGAATGGATG
1 TTAAGGCATGAAAGGATG
5854649 TGTTAATACG
Statistics
Matches: 128, Mismatches: 13, Indels: 19
0.80 0.08 0.12
Matches are distributed among these distances:
40 30 0.23
41 4 0.03
42 1 0.01
43 1 0.01
45 7 0.05
46 54 0.42
47 31 0.24
ACGTcount: A:0.42, C:0.09, G:0.25, T:0.24
Consensus pattern (46 bp):
TTAAGGCATGAAAGGATGCCATAATAAATATGCATGAAAGGATGCA
Found at i:5860288 original size:11 final size:11
Alignment explanation
Indices: 5860272--5860299 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
5860262 AACAATTTGT
5860272 TTTTCTGGTAA
1 TTTTCTGGTAA
5860283 TTTTCTGGTAA
1 TTTTCTGGTAA
5860294 TTTTCT
1 TTTTCT
5860300 CTGTCATCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.14, C:0.11, G:0.14, T:0.61
Consensus pattern (11 bp):
TTTTCTGGTAA
Found at i:5862999 original size:35 final size:35
Alignment explanation
Indices: 5862948--5863021 Score: 103
Period size: 35 Copynumber: 2.1 Consensus size: 35
5862938 AATAGCCCTT
* *
5862948 AATTTCATTCTAAACCCCAAATTCCAAAATAATTC
1 AATTACATTATAAACCCCAAATTCCAAAATAATTC
* * *
5862983 AATTACATTATAAACCCCAAATTCTAAAATTATTG
1 AATTACATTATAAACCCCAAATTCCAAAATAATTC
5863018 AATT
1 AATT
5863022 TAAGGTTTAG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.45, C:0.20, G:0.01, T:0.34
Consensus pattern (35 bp):
AATTACATTATAAACCCCAAATTCCAAAATAATTC
Found at i:5864876 original size:18 final size:19
Alignment explanation
Indices: 5864834--5864882 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 19
5864824 ATATTTGAAC
5864834 AAAAAGAAAAAAGAAGTTCCAA
1 AAAAAG-AAAAAG-AGTTCC-A
5864856 AAAAAGAAAAAG-GTT-CA
1 AAAAAGAAAAAGAGTTCCA
5864873 AAAAAGAAAA
1 AAAAAGAAAA
5864883 TAGAAAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 11 0.41
18 1 0.04
19 3 0.11
21 6 0.22
22 6 0.22
ACGTcount: A:0.71, C:0.06, G:0.14, T:0.08
Consensus pattern (19 bp):
AAAAAGAAAAAGAGTTCCA
Found at i:5867136 original size:19 final size:20
Alignment explanation
Indices: 5867047--5867158 Score: 79
Period size: 21 Copynumber: 5.3 Consensus size: 20
5867037 ATAATTAAGA
5867047 ATTATTTTAAATTTTTATATTTT
1 ATTATTTTAAA--TTTATA-TTT
*
5867070 ATTATTTATACATATTAT-TATT
1 ATTATTT-TAAAT-TTATAT-TT
* *
5867092 -TTATTTTAGATGTA-ATTTT
1 ATTATTTTAAATTTATA-TTT
5867111 ATTTATTTTAAAGTTTATATTTT
1 A-TTATTTTAAA-TTTATA-TTT
5867134 ATTATTTTAAATTTATA-TT
1 ATTATTTTAAATTTATATTT
5867153 ATTATT
1 ATTATT
5867159 ATTTAATGAT
Statistics
Matches: 75, Mismatches: 5, Indels: 22
0.74 0.05 0.22
Matches are distributed among these distances:
19 12 0.16
20 5 0.07
21 22 0.29
22 16 0.21
23 17 0.23
24 3 0.04
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.64
Consensus pattern (20 bp):
ATTATTTTAAATTTATATTT
Found at i:5867164 original size:21 final size:21
Alignment explanation
Indices: 5867047--5867162 Score: 112
Period size: 22 Copynumber: 5.3 Consensus size: 21
5867037 ATAATTAAGA
5867047 ATTATTTTAAATTTTTATATTTT
1 ATTATTTTAAA--TTTATATTTT
* *
5867070 ATTATTTATACATATTAT-TATT
1 ATTATTT-TAAAT-TTATATTTT
* *
5867092 -TTATTTTAGATGTA-ATTTT
1 ATTATTTTAAATTTATATTTT
5867111 ATTTATTTTAAAGTTTATATTTT
1 A-TTATTTTAAA-TTTATATTTT
5867134 ATTATTTTAAATTTATATTATT
1 ATTATTTTAAATTTATATT-TT
5867156 ATTATTT
1 ATTATTT
5867163 AATGATATTC
Statistics
Matches: 78, Mismatches: 7, Indels: 17
0.76 0.07 0.17
Matches are distributed among these distances:
19 5 0.06
20 4 0.05
21 23 0.29
22 26 0.33
23 17 0.22
24 3 0.04
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.65
Consensus pattern (21 bp):
ATTATTTTAAATTTATATTTT
Found at i:5867182 original size:64 final size:65
Alignment explanation
Indices: 5867049--5867183 Score: 163
Period size: 64 Copynumber: 2.1 Consensus size: 65
5867039 AATTAAGAAT
* * *
5867049 TATTTTAAATTTTTATATTTTATTATTTATACATATTATTATTTTATTTTAGATGTAATTTTATT
1 TATTTTAAATGTTTATATTTTATTATTTATAAATATTATTATTTTATTTTAGATGTAATTTTATA
*
5867114 TATTTTAAA-GTTTATATTTTATTATTT-TAAATTTATATTATTATTA-TTTA-ATG-ATATTCT
1 TATTTTAAATGTTTATATTTTATTATTTATAAATAT-TATTATT-TTATTTTAGATGTA-ATT-T
5867174 TATA
62 TATA
5867178 TATTTT
1 TATTTT
5867184 GCTTATGTTA
Statistics
Matches: 62, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
62 1 0.02
63 11 0.18
64 38 0.61
65 12 0.19
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.64
Consensus pattern (65 bp):
TATTTTAAATGTTTATATTTTATTATTTATAAATATTATTATTTTATTTTAGATGTAATTTTATA
Found at i:5867506 original size:13 final size:14
Alignment explanation
Indices: 5867481--5867509 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
5867471 TAAATAAATA
5867481 ATTTAATTTATATT
1 ATTTAATTTATATT
5867495 ATTTAA-TTATATT
1 ATTTAATTTATATT
5867508 AT
1 AT
5867510 ACATTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
ATTTAATTTATATT
Found at i:5867997 original size:36 final size:35
Alignment explanation
Indices: 5867950--5868017 Score: 109
Period size: 36 Copynumber: 1.9 Consensus size: 35
5867940 TGGTTTTTCA
*
5867950 GAAAATGAATTACTAGAATTTGAATTACTGGAACTG
1 GAAAATGAATTAATAGAATTTGAATT-CTGGAACTG
*
5867986 GAAAATGAATTAATGGAATTTGAATTCTGGAA
1 GAAAATGAATTAATAGAATTTGAATTCTGGAA
5868018 AATAAATTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 6 0.20
36 24 0.80
ACGTcount: A:0.43, C:0.06, G:0.21, T:0.31
Consensus pattern (35 bp):
GAAAATGAATTAATAGAATTTGAATTCTGGAACTG
Found at i:5868402 original size:12 final size:11
Alignment explanation
Indices: 5868358--5868408 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 11
5868348 TTGTTATATT
5868358 ATATTTTAAAA
1 ATATTTTAAAA
**
5868369 ATATTAATT-AGT
1 ATATT--TTAAAA
5868381 ATATTTTAAAA
1 ATATTTTAAAA
5868392 ATATTTATAAAA
1 ATATTT-TAAAA
5868404 ATATT
1 ATATT
5868409 ATTTAAATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
10 2 0.06
11 12 0.38
12 16 0.50
13 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (11 bp):
ATATTTTAAAA
Found at i:5868407 original size:23 final size:23
Alignment explanation
Indices: 5868358--5868426 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 23
5868348 TTGTTATATT
* **
5868358 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATAAAA
*
5868381 ATATTTTAAAAATATTTATAAAA
1 ATATTTTAAAAATATTAATAAAA
* *
5868404 ATATTATTTAAATATATAAATAA
1 ATA-T-TTTAAAAATATTAATAA
5868427 TATTATTCAT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
23 22 0.59
24 1 0.03
25 14 0.38
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATAAAA
Found at i:5868410 original size:11 final size:11
Alignment explanation
Indices: 5868358--5868432 Score: 53
Period size: 11 Copynumber: 6.6 Consensus size: 11
5868348 TTGTTATATT
*
5868358 ATATTTTAAAA
1 ATATTATAAAA
* **
5868369 ATATTAATTAGT
1 ATATT-ATAAAA
*
5868381 ATATTTTAAAA
1 ATATTATAAAA
5868392 ATATTTATAAAA
1 ATA-TTATAAAA
**
5868404 ATATTATTTAA
1 ATATTATAAAA
5868415 ATA-TATAAATA
1 ATATTATAAA-A
5868426 ATATTAT
1 ATATTAT
5868433 TCATTATTAA
Statistics
Matches: 47, Mismatches: 13, Indels: 7
0.70 0.19 0.10
Matches are distributed among these distances:
10 4 0.09
11 23 0.49
12 20 0.43
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (11 bp):
ATATTATAAAA
Found at i:5868429 original size:34 final size:34
Alignment explanation
Indices: 5868358--5868430 Score: 87
Period size: 34 Copynumber: 2.1 Consensus size: 34
5868348 TTGTTATATT
* *
5868358 ATATTTTAAAAATATTAATTAGTATATTTTAAAA
1 ATATTTTAAAAATATTAATTAGAATATTATAAAA
*
5868392 ATATTTATAAAAATATTATTTA-AATA-TATAAATA
1 ATATTT-TAAAAATATTAATTAGAATATTATAAA-A
5868426 ATATT
1 ATATT
5868431 ATTCATTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
33 5 0.15
34 15 0.44
35 14 0.41
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (34 bp):
ATATTTTAAAAATATTAATTAGAATATTATAAAA
Found at i:5868539 original size:31 final size:32
Alignment explanation
Indices: 5868493--5868569 Score: 88
Period size: 31 Copynumber: 2.4 Consensus size: 32
5868483 ATAATATCTT
* *
5868493 ATATTATTATAATATAATTGATTATTTTA-TAT-A
1 ATATTAATA-AATAT-ATT-ATTATATTATTATAA
5868526 ATATTAA-AAATATATTATTATATTATTATAA
1 ATATTAATAAATATATTATTATATTATTATAA
5868557 ATATTAATAAATA
1 ATATTAATAAATA
5868570 AATAAATATT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
29 8 0.21
30 6 0.15
31 13 0.33
32 6 0.15
33 6 0.15
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (32 bp):
ATATTAATAAATATATTATTATATTATTATAA
Found at i:5868547 original size:22 final size:22
Alignment explanation
Indices: 5868492--5868560 Score: 61
Period size: 22 Copynumber: 3.1 Consensus size: 22
5868482 TATAATATCT
**
5868492 TATATTATTATAATA-TAATTGA
1 TATATTATTATAATATTAA-AAA
*
5868514 T-TATTTTATATAATATTAAAAA
1 TATATTAT-TATAATATTAAAAA
* *
5868536 TATATTATTATATTATTATAAA
1 TATATTATTATAATATTAAAAA
5868558 TAT
1 TAT
5868561 TAATAAATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
21 5 0.13
22 25 0.66
23 8 0.21
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (22 bp):
TATATTATTATAATATTAAAAA
Found at i:5868810 original size:42 final size:42
Alignment explanation
Indices: 5868751--5868864 Score: 192
Period size: 42 Copynumber: 2.7 Consensus size: 42
5868741 ATGAATTATA
*
5868751 TTCCGGAAAACCAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
*
5868793 TTCCGGAAAACGAATTACTTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
* *
5868835 TTTCGAAAAACGAATTACGTGAAACAAACA
1 TTCCGGAAAACGAATTACGTGAAACAAACA
5868865 AGGAAATTCG
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 67 1.00
ACGTcount: A:0.46, C:0.19, G:0.16, T:0.18
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:5869377 original size:6 final size:6
Alignment explanation
Indices: 5869366--5869393 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
5869356 AAAAGTGATT
5869366 TAATTA TAATTA TAATTA TAATTA TAAT
1 TAATTA TAATTA TAATTA TAATTA TAAT
5869394 ATTGTTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TAATTA
Found at i:5869434 original size:151 final size:155
Alignment explanation
Indices: 5869268--5869577 Score: 565
Period size: 151 Copynumber: 2.0 Consensus size: 155
5869258 AATTTATATA
5869268 TAAATTAAAAAATAATTCATAATTGAAAAAAATTGGGTTCATGTATTAGTAAAAGTTTTTAAGAT
1 TAAATTAAAAAATAATTCATAATTGAAAAAAATTGGGTTCATGTATTAGTAAAAGTTTTTAAGAT
5869333 TTAAAAAAACTCTAAAAATCATTAAAAGTGA-TT-TAATTATAATTATAATTATAATTATAA-TA
66 TTAAAAAAACTCTAAAAATCATTAAAAGTGATTTATAATTATAATTATAATTATAATTATAATTA
5869395 TTGTTATTATA-TTTATAATAAGTT
131 TTGTTATTATATTTTATAATAAGTT
5869419 TAAATTAAAAAATAATTCATAATTGAAAAAAATTGGGTTCATGTATTAGTAAAAGTTTTTAAGAT
1 TAAATTAAAAAATAATTCATAATTGAAAAAAATTGGGTTCATGTATTAGTAAAAGTTTTTAAGAT
5869484 TTAAAAAAACTCTAAAAATCATTAAAAGTGATTTTTTATAATTATAATTATAATTATAATTATAA
66 TTAAAAAAACTCTAAAAATCATTAAAAGTGA---TTTATAATTATAATTATAATTATAATTATAA
5869549 TTATTGTTATTATATTTTATAATAAGTT
128 TTATTGTTATTATATTTTATAATAAGTT
5869577 T
1 T
5869578 TGCGAACTTA
Statistics
Matches: 152, Mismatches: 0, Indels: 7
0.96 0.00 0.04
Matches are distributed among these distances:
151 96 0.63
155 2 0.01
156 27 0.18
157 13 0.09
158 14 0.09
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (155 bp):
TAAATTAAAAAATAATTCATAATTGAAAAAAATTGGGTTCATGTATTAGTAAAAGTTTTTAAGAT
TTAAAAAAACTCTAAAAATCATTAAAAGTGATTTATAATTATAATTATAATTATAATTATAATTA
TTGTTATTATATTTTATAATAAGTT
Found at i:5869530 original size:6 final size:6
Alignment explanation
Indices: 5869519--5869552 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
5869509 AAGTGATTTT
5869519 TTATAA TTATAA TTATAA TTATAA TTATAA TTAT
1 TTATAA TTATAA TTATAA TTATAA TTATAA TTAT
5869553 TGTTATTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
TTATAA
Found at i:5872735 original size:35 final size:35
Alignment explanation
Indices: 5872669--5872761 Score: 105
Period size: 35 Copynumber: 2.6 Consensus size: 35
5872659 ACTACCCAAA
* * *
5872669 CATCACCATTTTCACGCCTATAACATCACCATCTTC
1 CATCACCA-TTGCACACCTATATCATCACCATCTTC
* *
5872705 CATTACCATTGCACACCTATATCATTACCATCTTC
1 CATCACCATTGCACACCTATATCATCACCATCTTC
* * *
5872740 TATCACCATTTCACGCCTATAT
1 CATCACCATTGCACACCTATAT
5872762 AACCACCAAT
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
35 41 0.85
36 7 0.15
ACGTcount: A:0.28, C:0.35, G:0.03, T:0.33
Consensus pattern (35 bp):
CATCACCATTGCACACCTATATCATCACCATCTTC
Found at i:5874520 original size:19 final size:20
Alignment explanation
Indices: 5874496--5874534 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
5874486 CAACCCGACT
*
5874496 CGACCCGTTGTCT-TTGACC
1 CGACCCGTTGACTATTGACC
5874515 CGACCCGTTGACTATTGACC
1 CGACCCGTTGACTATTGACC
5874535 GATCTGAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.15, C:0.36, G:0.21, T:0.28
Consensus pattern (20 bp):
CGACCCGTTGACTATTGACC
Found at i:5878728 original size:17 final size:17
Alignment explanation
Indices: 5878670--5878735 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 17
5878660 TCAACCGACC
*
5878670 ATTTTTCTGTTTTTTC-
1 ATTTTTCTTTTTTTTCG
*
5878686 ATTCTTT-TTTTTTTTTG
1 ATT-TTTCTTTTTTTTCG
5878703 AAATGTTTTCTTTTTTTTCG
1 --AT-TTTTCTTTTTTTTCG
5878723 ATTTTTCTGTTTT
1 ATTTTTCT-TTTT
5878736 ATTTTTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
16 10 0.25
17 9 0.22
18 6 0.15
19 5 0.12
20 10 0.25
ACGTcount: A:0.09, C:0.09, G:0.08, T:0.74
Consensus pattern (17 bp):
ATTTTTCTTTTTTTTCG
Found at i:5879545 original size:158 final size:158
Alignment explanation
Indices: 5879380--5879699 Score: 631
Period size: 158 Copynumber: 2.0 Consensus size: 158
5879370 CAAGTAAGGT
5879380 GAAATTATCATGAAATCTTTACCCCTCACTTAAGTTGTATTGCCTCAATAAGGAAATAAAATTAA
1 GAAATTATCATGAAATCTTTACCCCTCACTTAAGTTGTATTGCCTCAATAAGGAAATAAAATTAA
5879445 AAATGCAAGAGAAAAGGTAAAAAAAAATATTCCCCATGTTCATTGGTGACCGCAGCGTAAGGGGT
66 AAATGCAAGAGAAAAGGTAAAAAAAAATATTCCCCATGTTCATTGGTGACCGCAGCGTAAGGGGT
*
5879510 TGTTCAGTTGGGTCTGACCGCTCAAAGA
131 TGTTCAATTGGGTCTGACCGCTCAAAGA
5879538 GAAATTATCATGAAATCTTTACCCCTCACTTAAGTTGTATTGCCTCAATAAGGAAATAAAATTAA
1 GAAATTATCATGAAATCTTTACCCCTCACTTAAGTTGTATTGCCTCAATAAGGAAATAAAATTAA
5879603 AAATGCAAGAGAAAAGGTAAAAAAAAATATTCCCCATGTTCATTGGTGACCGCAGCGTAAGGGGT
66 AAATGCAAGAGAAAAGGTAAAAAAAAATATTCCCCATGTTCATTGGTGACCGCAGCGTAAGGGGT
5879668 TGTTCAATTGGGTCTGACCGCTCAAAGA
131 TGTTCAATTGGGTCTGACCGCTCAAAGA
5879696 GAAA
1 GAAA
5879700 CTGTTGGAGT
Statistics
Matches: 161, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
158 161 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (158 bp):
GAAATTATCATGAAATCTTTACCCCTCACTTAAGTTGTATTGCCTCAATAAGGAAATAAAATTAA
AAATGCAAGAGAAAAGGTAAAAAAAAATATTCCCCATGTTCATTGGTGACCGCAGCGTAAGGGGT
TGTTCAATTGGGTCTGACCGCTCAAAGA
Found at i:5880507 original size:18 final size:18
Alignment explanation
Indices: 5880484--5880531 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
5880474 TTAAAAAATG
5880484 AAATAAATAAAATGATGA
1 AAATAAATAAAATGATGA
5880502 AAATAAATAAAATGATGA
1 AAATAAATAAAATGATGA
5880520 AAATAAA-AAAAT
1 AAATAAATAAAAT
5880532 AAAAAAAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 5 0.17
18 25 0.83
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (18 bp):
AAATAAATAAAATGATGA
Found at i:5880537 original size:24 final size:24
Alignment explanation
Indices: 5880501--5880559 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
5880491 TAAAATGATG
*
5880501 AAAATAAATAAAATGATGAAAATAAA
1 AAAATAAA-AAAA-GATAAAAATAAA
*
5880527 AAAATAAAAAAAGATAAAAATTAA
1 AAAATAAAAAAAGATAAAAATAAA
*
5880551 AAATTAAAA
1 AAAATAAAA
5880560 TCAAAGAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
24 18 0.60
25 4 0.13
26 8 0.27
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (24 bp):
AAAATAAAAAAAGATAAAAATAAA
Found at i:5883789 original size:22 final size:21
Alignment explanation
Indices: 5883762--5883828 Score: 57
Period size: 22 Copynumber: 3.0 Consensus size: 21
5883752 CAAGAATAAG
5883762 CAAATTAAGTTTTGGAAAAGC
1 CAAATTAAGTTTTGGAAAAGC
* *
5883783 CACAATTATTGTCGTTAGGACAAA--
1 CA-AATTA-AGT--TTTGGA-AAAGC
5883807 CAAATTAAGTTTTGGAAAAGC
1 CAAATTAAGTTTTGGAAAAGC
5883828 C
1 C
5883829 CGACTCAGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 14
0.66 0.08 0.26
Matches are distributed among these distances:
19 3 0.09
20 5 0.14
21 3 0.09
22 7 0.20
23 7 0.20
24 2 0.06
25 5 0.14
26 3 0.09
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.28
Consensus pattern (21 bp):
CAAATTAAGTTTTGGAAAAGC
Found at i:5886897 original size:3 final size:3
Alignment explanation
Indices: 5886883--5886931 Score: 80
Period size: 3 Copynumber: 16.0 Consensus size: 3
5886873 TGTGTAACAA
*
5886883 AAT AATT AAT AAT AAT AAT AAT AAT AAT CAT AAT AAT AAT AAT AAT
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5886929 AAT
1 AAT
5886932 TTTGGTAGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 40 0.93
4 3 0.07
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:5887997 original size:16 final size:16
Alignment explanation
Indices: 5887978--5888014 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
5887968 ATTTTTTTAA
*
5887978 ATTTTTATATTTTATT
1 ATTTTTATATATTATT
*
5887994 ATTTATATATATTATT
1 ATTTTTATATATTATT
5888010 ATTTT
1 ATTTT
5888015 ATTATAGATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
ATTTTTATATATTATT
Found at i:5888020 original size:16 final size:16
Alignment explanation
Indices: 5887980--5888020 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
5887970 TTTTTTAAAT
*
5887980 TTTTA-TATTTTATTA
1 TTTTATTATATTATTA
5887995 -TTTATATATATTATTA
1 TTTTAT-TATATTATTA
5888011 TTTTATTATA
1 TTTTATTATA
5888021 GATGAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
14 4 0.18
16 13 0.59
17 5 0.23
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTATTATATTATTA
Found at i:5894335 original size:34 final size:34
Alignment explanation
Indices: 5894259--5894327 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 34
5894249 AAATCTTTTG
* *
5894259 ATAATTTTACTATTTCTAAAGTTGTTAAAAATTT
1 ATAATTTTACTATTTCTAAAATCGTTAAAAATTT
5894293 ATAATTTTACTATTTC-AAAATCGTTAAAAATTT
1 ATAATTTTACTATTTCTAAAATCGTTAAAAATTT
5894326 AT
1 AT
5894328 GACTTTTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
33 17 0.52
34 16 0.48
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (34 bp):
ATAATTTTACTATTTCTAAAATCGTTAAAAATTT
Found at i:5900220 original size:118 final size:116
Alignment explanation
Indices: 5900085--5900311 Score: 305
Period size: 118 Copynumber: 1.9 Consensus size: 116
5900075 AATATAATTG
* * *
5900085 GTTAATTACTGAAAATATTATCAAGCATAATAATATATTAGGTAATACTTGTATAAAGTAATAGG
1 GTTAATTACTGAAAATATTATCAAGCATAATAACATATTAGGTAACACTTATATAAAGTAATAGG
* * *
5900150 TAGCGTCTTTTTAAAGCTAAT-AGGACTTTGAAAATCTGACGATAACTTAACCT
66 TAGC-AC-CTTTAAAGCTAATGAGG-CTTTGAAAATCCGACGATAACTTAACCT
* * *
5900203 GTTAATTACTTG-AAATATTATCAATCATAATAACATATTATGTAACACTTATATAACGTAATAG
1 GTTAATTAC-TGAAAATATTATCAAGCATAATAACATATTAGGTAACACTTATATAAAGTAATAG
* *
5900267 GTAGCACCTTTAAAGCTGATGAGGCTTTGGAAATCCGACGATAAC
65 GTAGCACCTTTAAAGCTAATGAGGCTTTGAAAATCCGACGATAAC
5900312 AAAATAAGTT
Statistics
Matches: 96, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
116 30 0.31
117 4 0.04
118 60 0.62
119 2 0.02
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (116 bp):
GTTAATTACTGAAAATATTATCAAGCATAATAACATATTAGGTAACACTTATATAAAGTAATAGG
TAGCACCTTTAAAGCTAATGAGGCTTTGAAAATCCGACGATAACTTAACCT
Found at i:5900434 original size:108 final size:108
Alignment explanation
Indices: 5900279--5900673 Score: 296
Period size: 108 Copynumber: 3.6 Consensus size: 108
5900269 AGCACCTTTA
* * * * *
5900279 AAGCTGAT-GAGGCTTTGGAAATCCGACGATAACAAAATAAGTTAATTACTTAATTTTTTATTAG
1 AAGCTGATGGAGCCTTAGG-AATCCGACGATAACAAAATAGGTTAATTACTTAATTTGTTATAAG
5900343 TATTATCAATATATTAGGTAACGCCTAAAATGCTAACAAAATTT
65 TATTATCAATATATTAGGTAACGCCTAAAATGCTAACAAAATTT
* * * ***
5900387 AAGCTGATGGAGCCTTAGGAATCTGACGATAACATAACT-GGTTAATTACTGGAA-ACATTATCA
1 AAGCTGATGGAGCCTTAGGAATCCGACGATAACA-AAATAGGTTAATTACT-TAATTTGTTAT-A
* * * * * * * ** *
5900450 AGCATAAT-AATGTATTAGGTAGCGCTTATGTAACGTAATAGGTAGCGCATTATTA
63 AGTATTATCAATATATTAGGTAACGC----CTAA---AAT-GCTA--ACAAAATTT
* * * * ** *
5900505 AAGCTAATTTGA-TCTTAGAAATTTGACGATAACAAAATAGGTTAATTACTTAATTTGTTATCAG
1 AAGCTGA-TGGAGCCTTAGGAATCCGACGATAACAAAATAGGTTAATTACTTAATTTGTTATAAG
* * *
5900569 TATTATCAACATATTAGGTAACGCTTAAAATGTTAACAAAATTT
65 TATTATCAATATATTAGGTAACGCCTAAAATGCTAACAAAATTT
* * * * *
5900613 AAGTTGATGGAACCTTAGGAATCCGACGATAACATAATCGGTTAATTACTTGATTTGTTAT
1 AAGCTGATGGAGCCTTAGGAATCCGACGATAACAAAATAGGTTAATTACTTAATTTGTTAT
5900674 CAAGCTTTAT
Statistics
Matches: 216, Mismatches: 52, Indels: 38
0.71 0.17 0.12
Matches are distributed among these distances:
107 3 0.01
108 103 0.48
109 19 0.09
110 3 0.01
111 3 0.01
112 3 0.01
114 3 0.01
115 3 0.01
116 3 0.01
117 11 0.05
118 59 0.27
119 3 0.01
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (108 bp):
AAGCTGATGGAGCCTTAGGAATCCGACGATAACAAAATAGGTTAATTACTTAATTTGTTATAAGT
ATTATCAATATATTAGGTAACGCCTAAAATGCTAACAAAATTT
Found at i:5900512 original size:24 final size:23
Alignment explanation
Indices: 5900465--5900512 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
5900455 AATAATGTAT
*
5900465 TAGGTAGCGCTTATGTAACGTAA
1 TAGGTAGCGCTTATGTAAAGTAA
5900488 TAGGTAGCGCATTAT-TAAAGCTAA
1 TAGGTAGCGC-TTATGTAAAG-TAA
5900512 T
1 T
5900513 TTGATCTTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.31
Consensus pattern (23 bp):
TAGGTAGCGCTTATGTAAAGTAA
Found at i:5900678 original size:226 final size:223
Alignment explanation
Indices: 5900182--5900665 Score: 648
Period size: 226 Copynumber: 2.1 Consensus size: 223
5900172 GGACTTTGAA
* * * *
5900182 AATCTGACGATAACTTAACCTGTTAATTACTTGAAATATTATCAATCATAATAACATATTATGTA
1 AATCTGACGATAACATAA-CGGTTAATTACTTGAAATATTATCAAGCATAATAACATATTAGGTA
* *
5900247 ACACTTATATAACGTAATAGGTAGCACCTTTAAAGCTGATGAGGCTTTGGAAATCCGACGATAAC
65 ACACTTATATAACGTAATAGGTAGCACCTTTAAAGCTAATGAGGCTTTAGAAATCCGACGATAAC
* * *
5900312 AAAATAAGTTAATTACTTAATTTTTTATTAGTATTATCAATATATTAGGTAACGCCTAAAATGCT
130 AAAATAAGTTAATTACTTAATTTGTTATCAGTATTATCAACATATTAGGTAACGCCTAAAATGCT
*
5900377 AACAAAATTTAAGCTGATGGAGCCTTAGG
195 AACAAAATTTAAGCTGATGGAACCTTAGG
* * **
5900406 AATCTGACGATAACATAACTGGTTAATTACTGGAAACATTATCAAGCATAATAATGTATTAGGTA
1 AATCTGACGATAACATAAC-GGTTAATTACTTGAAATATTATCAAGCATAATAACATATTAGGTA
* * * * * * **
5900471 GCGCTTATGTAACGTAATAGGTAGCGCATTATTAAAGCTAATTTGA-TC-TTAGAAATTTGACGA
65 ACACTTATATAACGTAATAGGTAGCAC-CT-TTAAAGCTAA--TGAGGCTTTAGAAATCCGACGA
* *
5900534 TAACAAAATAGGTTAATTACTTAATTTGTTATCAGTATTATCAACATATTAGGTAACGCTTAAAA
126 TAACAAAATAAGTTAATTACTTAATTTGTTATCAGTATTATCAACATATTAGGTAACGCCTAAAA
* *
5900599 TGTTAACAAAATTTAAGTTGATGGAACCTTAGG
191 TGCTAACAAAATTTAAGCTGATGGAACCTTAGG
*
5900632 AATCCGACGATAACATAATCGGTTAATTACTTGA
1 AATCTGACGATAACATAA-CGGTTAATTACTTGA
5900666 TTTGTTATCA
Statistics
Matches: 226, Mismatches: 28, Indels: 10
0.86 0.11 0.04
Matches are distributed among these distances:
223 1 0.00
224 78 0.35
225 1 0.00
226 141 0.62
227 2 0.01
228 3 0.01
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (223 bp):
AATCTGACGATAACATAACGGTTAATTACTTGAAATATTATCAAGCATAATAACATATTAGGTAA
CACTTATATAACGTAATAGGTAGCACCTTTAAAGCTAATGAGGCTTTAGAAATCCGACGATAACA
AAATAAGTTAATTACTTAATTTGTTATCAGTATTATCAACATATTAGGTAACGCCTAAAATGCTA
ACAAAATTTAAGCTGATGGAACCTTAGG
Found at i:5900808 original size:2 final size:2
Alignment explanation
Indices: 5900801--5900856 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
5900791 TAAGTATGAA
5900801 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5900843 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
5900857 CGATACATTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5911550 original size:45 final size:45
Alignment explanation
Indices: 5911481--5911686 Score: 340
Period size: 45 Copynumber: 4.6 Consensus size: 45
5911471 TTTTTTTAAT
* * *
5911481 TATAGCATATTTTTCTGTTGATAATGCACCCATATGCATTTCAAC
1 TATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCAAC
*
5911526 TATATCATACTTTTCTGTTGATAATGTACCCATATACATTTCAAC
1 TATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCAAC
*
5911571 TATAGCATACTTTTCTGTTGATAGTGTACCCATATACATTTCAAC
1 TATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCAAC
* *
5911616 TATAACATACTTTTTTGTTGATAATGTACCCATATACATTTCAAC
1 TATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCAAC
*
5911661 TATAGCATACTTTTCTATTGATAATG
1 TATAGCATACTTTTCTGTTGATAATG
5911687 CACCTATCCG
Statistics
Matches: 149, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 149 1.00
ACGTcount: A:0.31, C:0.18, G:0.09, T:0.42
Consensus pattern (45 bp):
TATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCAAC
Found at i:5912243 original size:20 final size:20
Alignment explanation
Indices: 5912218--5912274 Score: 71
Period size: 22 Copynumber: 2.8 Consensus size: 20
5912208 CAATGTTTCC
5912218 TGGTATCGATACCCTTACCA
1 TGGTATCGATACCCTTACCA
*
5912238 TGGTATCGGTACTACCC-TACTA
1 TGGTATC-G-A-TACCCTTACCA
5912260 TGGTATCGATACCCT
1 TGGTATCGATACCCT
5912275 CTTACGGTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
19 5 0.16
20 8 0.25
21 2 0.06
22 12 0.38
23 5 0.16
ACGTcount: A:0.23, C:0.28, G:0.18, T:0.32
Consensus pattern (20 bp):
TGGTATCGATACCCTTACCA
Found at i:5912274 original size:19 final size:19
Alignment explanation
Indices: 5912218--5912291 Score: 78
Period size: 19 Copynumber: 3.7 Consensus size: 19
5912208 CAATGTTTCC
*
5912218 TGGTATCGATACCCTTACCA
1 TGGTATCGATACCC-TACTA
5912238 TGGTATCGGTACTACCCTACTA
1 TGGTATC-G-A-TACCCTACTA
5912260 TGGTATCGATACCCT-CTTA
1 TGGTATCGATACCCTAC-TA
*
5912279 CGGTATCGATACC
1 TGGTATCGATACC
5912292 GAAATTAGAT
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
18 1 0.02
19 20 0.42
20 8 0.17
21 2 0.04
22 12 0.25
23 5 0.10
ACGTcount: A:0.23, C:0.28, G:0.18, T:0.31
Consensus pattern (19 bp):
TGGTATCGATACCCTACTA
Found at i:5918470 original size:45 final size:45
Alignment explanation
Indices: 5918406--5918641 Score: 364
Period size: 45 Copynumber: 5.2 Consensus size: 45
5918396 GCATTTTTTT
* * *
5918406 AACTATAGCATAATTTTCTGTTGATAATGCACCCATATGCATTTC
1 AACTATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTC
* *
5918451 AACTATAACATATTTTTCTGTTGATAATGTACCCATATACATTTC
1 AACTATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTC
* *
5918496 AAATATAGCATACTTTTCTGTTGATAATGTACCCATATATATTTC
1 AACTATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTC
* *
5918541 AACTATAGCATACTTTTATGCTGATAATGTACCCATATACATTTC
1 AACTATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTC
* *
5918586 AACTATAGCATACTTTTATGTTGATAATGTACCCATATGCATTTC
1 AACTATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTC
*
5918631 AACTATGGCAT
1 AACTATAGCAT
5918642 CATTTCATAT
Statistics
Matches: 176, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 176 1.00
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.39
Consensus pattern (45 bp):
AACTATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTC
Found at i:5918668 original size:45 final size:45
Alignment explanation
Indices: 5918406--5918674 Score: 226
Period size: 45 Copynumber: 6.0 Consensus size: 45
5918396 GCATTTTTTT
* * *
5918406 AACTATAGCATAATTTTC-TGTTGATAATGCACCCATATGCATTTC
1 AACTATAGCAT-ACTTTCATATCGATAATGCACCCATATGCATTTC
* * * * * *
5918451 AACTATAACATATTTTTC-TGTTGATAATGTACCCATATACATTTC
1 AACTATAGCATA-CTTTCATATCGATAATGCACCCATATGCATTTC
* * * * **
5918496 AAATATAGCATACTTTTC-TGTTGATAATGTACCCATATATATTTC
1 AACTATAGCATAC-TTTCATATCGATAATGCACCCATATGCATTTC
* *
5918541 AACTATAGCATACTTT--TATGCTGATAATGTACCCATATACATTTC
1 AACTATAGCATACTTTCATAT-C-GATAATGCACCCATATGCATTTC
* * * *
5918586 AACTATAGCATACTTTTATGTTGATAATGTACCCATATGCATTTC
1 AACTATAGCATACTTTCATATCGATAATGCACCCATATGCATTTC
* * *
5918631 AACTATGGCAT-CATTTCATATCGATCATGCACTCATATGCATTT
1 AACTATAGCATAC-TTTCATATCGATAATGCACCCATATGCATTT
5918675 TTATTTTCAT
Statistics
Matches: 196, Mismatches: 21, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
43 2 0.01
44 5 0.03
45 187 0.95
47 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.39
Consensus pattern (45 bp):
AACTATAGCATACTTTCATATCGATAATGCACCCATATGCATTTC
Found at i:5918668 original size:90 final size:89
Alignment explanation
Indices: 5918406--5918674 Score: 344
Period size: 90 Copynumber: 3.0 Consensus size: 89
5918396 GCATTTTTTT
* * * *
5918406 AACTATAGCATAATTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAACATATTTTTCTG
1 AACTATAGCATACTTTTCTGTTGATAATGTACCCATATGCATTTCAACTATAGCATA-TTTTCTA
*
5918471 TTGATAATGTACCCATATACATTTC
65 TCGATAATGTACCCATATACATTTC
* ** *
5918496 AAATATAGCATACTTTTCTGTTGATAATGTACCCATATATATTTCAACTATAGCATACTTT-TAT
1 AACTATAGCATACTTTTCTGTTGATAATGTACCCATATGCATTTCAACTATAGCATATTTTCTAT
5918560 GCTGATAATGTACCCATATACATTTC
66 -C-GATAATGTACCCATATACATTTC
* *
5918586 AACTATAGCATACTTTTATGTTGATAATGTACCCATATGCATTTCAACTATGGCATCA-TTTCAT
1 AACTATAGCATACTTTTCTGTTGATAATGTACCCATATGCATTTCAACTATAGCAT-ATTTTC-T
* * * *
5918650 ATCGATCATGCACTCATATGCATTT
64 ATCGATAATGTACCCATATACATTT
5918675 TTATTTTCAT
Statistics
Matches: 156, Mismatches: 18, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
88 2 0.01
89 3 0.02
90 146 0.94
91 2 0.01
92 3 0.02
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.39
Consensus pattern (89 bp):
AACTATAGCATACTTTTCTGTTGATAATGTACCCATATGCATTTCAACTATAGCATATTTTCTAT
CGATAATGTACCCATATACATTTC
Found at i:5918668 original size:135 final size:135
Alignment explanation
Indices: 5918406--5918668 Score: 357
Period size: 135 Copynumber: 1.9 Consensus size: 135
5918396 GCATTTTTTT
* * * * *
5918406 AACTATAGCATAATTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAACATATTTTTCTG
1 AACTATAGCATAATTTTATGCTGATAATGCACCCATATACATTTCAACTATAACATACTTTTATG
* * * *
5918471 TTGATAATGTACCCATATACATTTCAAATATAGCATACTTTTCTGTTGATAATGTACCCATATAT
66 TTGATAATGTACCCATATACATTTCAAATATAGCATACATTTCTATCGATAATGCACCCATATAT
5918536 ATTTC
131 ATTTC
* * *
5918541 AACTATAGCATACTTTTATGCTGATAATGTACCCATATACATTTCAACTATAGCATACTTTTATG
1 AACTATAGCATAATTTTATGCTGATAATGCACCCATATACATTTCAACTATAACATACTTTTATG
* * * * *
5918606 TTGATAATGTACCCATATGCATTTCAACTATGGCAT-CATTTCATATCGATCATGCACTCATAT
66 TTGATAATGTACCCATATACATTTCAAATATAGCATACATTTC-TATCGATAATGCACCCATAT
5918669 GCATTTTTAT
Statistics
Matches: 110, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
134 5 0.05
135 105 0.95
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.39
Consensus pattern (135 bp):
AACTATAGCATAATTTTATGCTGATAATGCACCCATATACATTTCAACTATAACATACTTTTATG
TTGATAATGTACCCATATACATTTCAAATATAGCATACATTTCTATCGATAATGCACCCATATAT
ATTTC
Found at i:5922581 original size:39 final size:39
Alignment explanation
Indices: 5922521--5922651 Score: 181
Period size: 39 Copynumber: 3.4 Consensus size: 39
5922511 TCTATGACTT
* * *
5922521 GTAAGTCCTTACCGTAAGCTCCTCGGCTTTGTGCTCAGG
1 GTAAGTCCTTACCGCAGGCTCCTCGACTTTGTGCTCAGG
5922560 GTAAGTCCTTACCGCAGGCTCCTCGACTTTGTGCTCAGG
1 GTAAGTCCTTACCGCAGGCTCCTCGACTTTGTGCTCAGG
* *** *
5922599 GTAAGTCCTTACCGCAGGTTCCTTTTCTTTGTGCACAGG
1 GTAAGTCCTTACCGCAGGCTCCTCGACTTTGTGCTCAGG
*
5922638 GTAAGTGCTTACCG
1 GTAAGTCCTTACCG
5922652 TAGGTCTTTA
Statistics
Matches: 83, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 83 1.00
ACGTcount: A:0.16, C:0.27, G:0.25, T:0.31
Consensus pattern (39 bp):
GTAAGTCCTTACCGCAGGCTCCTCGACTTTGTGCTCAGG
Found at i:5924044 original size:21 final size:21
Alignment explanation
Indices: 5924010--5924049 Score: 64
Period size: 20 Copynumber: 1.9 Consensus size: 21
5924000 TGTTGTATAT
5924010 AGCCGTTTGGGATG-TTTTGG
1 AGCCGTTTGGGATGATTTTGG
5924030 AGCCGTTTGGGGATGATTTT
1 AGCCGTTT-GGGATGATTTT
5924050 TCTACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 6 0.33
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.38, T:0.40
Consensus pattern (21 bp):
AGCCGTTTGGGATGATTTTGG
Found at i:5924105 original size:21 final size:21
Alignment explanation
Indices: 5924079--5924119 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5924069 CCGTACAGGG
5924079 GGTATCGATACCCATTCATAT
1 GGTATCGATACCCATTCATAT
* *
5924100 GGTATCGGTACCCCTTCATA
1 GGTATCGATACCCATTCATA
5924120 AAATTCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.27, G:0.17, T:0.32
Consensus pattern (21 bp):
GGTATCGATACCCATTCATAT
Found at i:5924188 original size:17 final size:18
Alignment explanation
Indices: 5924149--5924201 Score: 72
Period size: 17 Copynumber: 2.9 Consensus size: 18
5924139 GTTGCAGCCA
* *
5924149 GGGGGTATGGATACCCCTG
1 GGGGGTATCGATA-CCATG
5924168 GGGGGTATCGATACCAT-
1 GGGGGTATCGATACCATG
5924185 GGGGGTATCGATACCAT
1 GGGGGTATCGATACCAT
5924202 CCGAGCAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
17 17 0.53
18 3 0.09
19 12 0.38
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.23
Consensus pattern (18 bp):
GGGGGTATCGATACCATG
Found at i:5927435 original size:17 final size:17
Alignment explanation
Indices: 5927413--5927480 Score: 77
Period size: 17 Copynumber: 4.0 Consensus size: 17
5927403 GATTGCTCGG
5927413 ATGGTATCTATACCCCC
1 ATGGTATCTATACCCCC
5927430 ATGGTATCTATACCCCC
1 ATGGTATCTATACCCCC
*
5927447 --GGTATCGATACTCCCC
1 ATGGTATCTATAC-CCCC
* *
5927463 AGTTGTATCCATACCCCC
1 A-TGGTATCTATACCCCC
5927481 TGGCTGCAAC
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
15 10 0.23
16 4 0.09
17 17 0.39
18 4 0.09
19 9 0.20
ACGTcount: A:0.22, C:0.37, G:0.13, T:0.28
Consensus pattern (17 bp):
ATGGTATCTATACCCCC
Found at i:5927477 original size:34 final size:32
Alignment explanation
Indices: 5927415--5927480 Score: 87
Period size: 34 Copynumber: 2.0 Consensus size: 32
5927405 TTGCTCGGAT
* *
5927415 GGTATCTATACCCCCATGGTATCTATACCCCC
1 GGTATCGATACCCCCATGGTATCCATACCCCC
*
5927447 GGTATCGATACTCCCCAGTTGTATCCATACCCCC
1 GGTATCGATAC-CCCCA-TGGTATCCATACCCCC
5927481 TGGCTGCAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 10 0.34
33 5 0.17
34 14 0.48
ACGTcount: A:0.21, C:0.38, G:0.14, T:0.27
Consensus pattern (32 bp):
GGTATCGATACCCCCATGGTATCCATACCCCC
Found at i:5927536 original size:21 final size:21
Alignment explanation
Indices: 5927510--5927550 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
5927500 ATTTGAATTT
5927510 TATGAAGGGGTACCGATACCA
1 TATGAAGGGGTACCGATACCA
*
5927531 TATGAATGGGTACCGATACC
1 TATGAAGGGGTACCGATACC
5927551 CCCTGTACGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.22
Consensus pattern (21 bp):
TATGAAGGGGTACCGATACCA
Found at i:5927618 original size:20 final size:22
Alignment explanation
Indices: 5927580--5927619 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
5927570 TTAGAGCAGA
5927580 AAAATCATCCCCAAACGGCTCT
1 AAAATCATCCCCAAACGGCTCT
5927602 AAAAT-ATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
5927620 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 6 0.33
22 5 0.28
ACGTcount: A:0.38, C:0.35, G:0.10, T:0.17
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCT
Found at i:5931688 original size:20 final size:20
Alignment explanation
Indices: 5931659--5931697 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5931649 ATTCCACCAC
*
5931659 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
5931679 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
5931698 TATGAGCTCT
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:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:5932048 original size:62 final size:62
Alignment explanation
Indices: 5931971--5932100 Score: 251
Period size: 62 Copynumber: 2.1 Consensus size: 62
5931961 TCTCATTGTT
5931971 GTTTCTTTCGTCAAAGAATTTGGACTTGAGTTCTACGAGCTCTTGCTTTGATCTTCAGGTCAA
1 GTTT-TTTCGTCAAAGAATTTGGACTTGAGTTCTACGAGCTCTTGCTTTGATCTTCAGGTCAA
5932034 GTTTTTTCGTCAAAGAATTTGGACTTGAGTTCTACGAGCTCTTGCTTTGATCTTCAGGTCAA
1 GTTTTTTCGTCAAAGAATTTGGACTTGAGTTCTACGAGCTCTTGCTTTGATCTTCAGGTCAA
5932096 GTTTT
1 GTTTT
5932101 ACTAAATTTC
Statistics
Matches: 67, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
62 63 0.94
63 4 0.06
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.42
Consensus pattern (62 bp):
GTTTTTTCGTCAAAGAATTTGGACTTGAGTTCTACGAGCTCTTGCTTTGATCTTCAGGTCAA
Found at i:5944489 original size:21 final size:21
Alignment explanation
Indices: 5944428--5944479 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
5944418 ATTGAGTAGT
5944428 GGAGTACTCGGCGGTTGCTCG
1 GGAGTACTCGGCGGTTGCTCG
5944449 GGAGTACTCGGCGGTTGCTCG
1 GGAGTACTCGGCGGTTGCTCG
5944470 GGAGTACTCG
1 GGAGTACTCG
5944480 ACGATAGCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.12, C:0.23, G:0.42, T:0.23
Consensus pattern (21 bp):
GGAGTACTCGGCGGTTGCTCG
Found at i:5945226 original size:3 final size:3
Alignment explanation
Indices: 5945220--5945289 Score: 106
Period size: 3 Copynumber: 23.0 Consensus size: 3
5945210 CCATTTTTAT
*
5945220 TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA -TA TTTA TTA TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA -TTA
5945266 TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
5945290 AATAATAATT
Statistics
Matches: 62, Mismatches: 2, Indels: 6
0.89 0.03 0.09
Matches are distributed among these distances:
2 2 0.03
3 55 0.89
4 5 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:5946702 original size:27 final size:27
Alignment explanation
Indices: 5946672--5946723 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
5946662 ATAAATATAT
*
5946672 AATA-TAAATAATTTATTTTTTAATAAA
1 AATATTAAAT-ATTTATTTTTCAATAAA
*
5946699 AATATTTAATATTTATTTTTCAATA
1 AATATTAAATATTTATTTTTCAATA
5946724 TCGAAGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (27 bp):
AATATTAAATATTTATTTTTCAATAAA
Found at i:5947608 original size:323 final size:310
Alignment explanation
Indices: 5946979--5947618 Score: 1129
Period size: 323 Copynumber: 2.0 Consensus size: 310
5946969 ATTAAAAAGT
5946979 ACCAATTTTGGGCGTGTAGGGGTGTAATCCTTCCCTAAAACGTAACCGACCACGAATCCCTTTTT
1 ACCAATTTTGGGCGTGTAGGGGTGTAATCCTTCCCTAAAACGTAACCGACCACGAATCCCTTTTT
5947044 ATTTAAAAGAACGAATTTTGGTTATAAACGCAGATCAGTTCATCTTTTCATTGATGTTTCTTAAA
66 ATTTAAAAGAACGAATTTTGGTTATAAACGCAGATCAGTTCATCTTTTCATTGATGTTTCTTAAA
*
5947109 ACTCTTTTAAATAATTTTTTAGGTATTCGACCTACCTGACCCAAAAGGCGATGGCGACTCCCAAA
131 ACTCTTTTAAAAAATTTTTTAGGTATTCGACCTACCTGACCCAAAAGGCGATGGCGACTCCCAAA
5947174 TTATTTTCAAAACCATTTATCACATCAATTTTCCCGCCAAAAAATATTTCGTGCCGGACGAAAAC
196 TTATTTTCAAAACCATTTATCACATCAATTTTCCCGCCAAAAAATATTTCGTGCCGGACGAAAAC
5947239 GGTTACGACAGCTTGGTGACTCCGCTGGGGATCCTGGTCAAACTTTTAAA
261 GGTTACGACAGCTTGGTGACTCCGCTGGGGATCCTGGTCAAACTTTTAAA
5947289 ACCAATTTTGGGCGTTGTAGGGGTGTTAATCCTTCCCT-AAACGTAACCGACCACGAATCCCTTT
1 ACCAATTTTGGGCG-TGTAGGGGTG-TAATCCTTCCCTAAAACGTAACCGACCACGAATCCCTTT
5947353 TTATTATTAAAAAGAACGAATTTTTGGTTATAAACGCAGATCAGTTCATCTTTTCATTGATGTTT
64 TTA-T-TT-AAAAGAACGAA-TTTTGGTTATAAACGCAGATCAGTTCATCTTTTCATTGATG-TT
5947418 TCTTAAAACTCTTTTAAAAAATAATTTTTAGGTATTCGACCTACCTGACCCAAAAGGCCGATGGC
124 TCTTAAAACTCTTTTAAAAAAT--TTTTTAGGTATTCGACCTACCTGACCCAAAAGG-CGATGGC
5947483 GACTCCCAAATTATTTTCAAAACCATTTATTCACATCAATTTTCCCGCCAAATAAATATTTCGTG
186 GACTCCCAAATTATTTTCAAAACCATTTA-TCACATCAATTTTCCCGCCAAA-AAATATTTCGTG
5947548 CCCGGACGAAAACCGGTTACGACAGCTTGGTGACTCCGCTGGGGATCCTGGTCAAACTTTTAAA
249 -CCGGACGAAAA-CGGTTACGACAGCTTGGTGACTCCGCTGGGGATCCTGGTCAAACTTTTAAA
*
5947612 ATCAATT
1 ACCAATT
5947619 ATAAATTGTC
Statistics
Matches: 314, Mismatches: 2, Indels: 15
0.95 0.01 0.05
Matches are distributed among these distances:
310 14 0.04
311 39 0.12
312 13 0.04
313 2 0.01
314 11 0.04
315 41 0.13
316 23 0.07
318 33 0.11
319 36 0.11
320 22 0.07
321 12 0.04
322 11 0.04
323 57 0.18
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (310 bp):
ACCAATTTTGGGCGTGTAGGGGTGTAATCCTTCCCTAAAACGTAACCGACCACGAATCCCTTTTT
ATTTAAAAGAACGAATTTTGGTTATAAACGCAGATCAGTTCATCTTTTCATTGATGTTTCTTAAA
ACTCTTTTAAAAAATTTTTTAGGTATTCGACCTACCTGACCCAAAAGGCGATGGCGACTCCCAAA
TTATTTTCAAAACCATTTATCACATCAATTTTCCCGCCAAAAAATATTTCGTGCCGGACGAAAAC
GGTTACGACAGCTTGGTGACTCCGCTGGGGATCCTGGTCAAACTTTTAAA
Found at i:5951037 original size:15 final size:15
Alignment explanation
Indices: 5951019--5951050 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5951009 ATCAATACCT
5951019 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
5951034 TTTTGCATACATTCA
1 TTTTGCATACATGCA
5951049 TT
1 TT
5951051 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:5958333 original size:1 final size:1
Alignment explanation
Indices: 5958314--5958377 Score: 65
Period size: 1 Copynumber: 64.0 Consensus size: 1
5958304 GCTTGAAGAG
* * * * * * *
5958314 AAAAATAAAAGAAAGAAAAAAAAAAAGAAAAAAAAAAAGAAAAAAAAAGAAAAAAGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
5958378 GGGGGTCAAG
Statistics
Matches: 49, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.89, C:0.00, G:0.09, T:0.02
Consensus pattern (1 bp):
A
Found at i:5958340 original size:12 final size:12
Alignment explanation
Indices: 5958315--5958378 Score: 83
Period size: 12 Copynumber: 5.0 Consensus size: 12
5958305 CTTGAAGAGA
5958315 AAAATAAAAGAAAG
1 AAAA-AAAA-AAAG
5958329 AAAAAAAAAAAG
1 AAAAAAAAAAAG
5958341 AAAAAAAAAAAG
1 AAAAAAAAAAAG
*
5958353 AAAAAAAAAGAAA
1 AAAAAAAAA-AAG
5958366 AAAGAAAAAAAAG
1 AAA-AAAAAAAAG
5958379 GGGGTCAAGG
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
12 25 0.54
13 11 0.24
14 10 0.22
ACGTcount: A:0.88, C:0.00, G:0.11, T:0.02
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:5958346 original size:29 final size:29
Alignment explanation
Indices: 5958309--5958377 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
5958299 ATTATGCTTG
* *
5958309 AAGAGAAAAATAAAAGAAAGAAAAA-AAAA
1 AAGA-AAAAAAAAAAGAAAAAAAAAGAAAA
5958338 AAGAAAAAAAAAAAGAAAAAAAAAGAAAA
1 AAGAAAAAAAAAAAGAAAAAAAAAGAAAA
5958367 AAGAAAAAAAA
1 AAGAAAAAAAA
5958378 GGGGGTCAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 18 0.49
29 19 0.51
ACGTcount: A:0.87, C:0.00, G:0.12, T:0.01
Consensus pattern (29 bp):
AAGAAAAAAAAAAAGAAAAAAAAAGAAAA
Found at i:5958378 original size:16 final size:16
Alignment explanation
Indices: 5958309--5958378 Score: 77
Period size: 17 Copynumber: 4.2 Consensus size: 16
5958299 ATTATGCTTG
* *
5958309 AAGAGAAAAATAAAAGA
1 AAGA-AAAAAGAAAAAA
*
5958326 AAGAAAAAAAAAAAGAA
1 AAGAAAAAAGAAAA-AA
*
5958343 AAAAAAAAAGAAAAAAA
1 AAGAAAAAAG-AAAAAA
5958360 AAGAAAAAAGAAAAAA
1 AAGAAAAAAGAAAAAA
5958376 AAG
1 AAG
5958379 GGGGTCAAGG
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
16 18 0.39
17 24 0.52
18 4 0.09
ACGTcount: A:0.86, C:0.00, G:0.13, T:0.01
Consensus pattern (16 bp):
AAGAAAAAAGAAAAAA
Found at i:5959570 original size:93 final size:93
Alignment explanation
Indices: 5959357--5959715 Score: 591
Period size: 93 Copynumber: 3.9 Consensus size: 93
5959347 AGTAGAACAA
*
5959357 GTGCTCAAAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAACTC-CAA
1 GTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAAC-CAC-A
5959421 AAAACCAATCATTGAATTTGGAAGATGAAT
64 AAAACCAATCATTGAATTTGGAAGATGAAT
5959451 GTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAACCACAAA
1 GTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAACCACAAA
*
5959516 AACCAATCATTGGATTTGGAAGATGAAT
66 AACCAATCATTGAATTTGGAAGATGAAT
*
5959544 GTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAA--AAAAA
1 GTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAACCACAAA
5959607 AACCAATCATTGAATTTGGAAGATGAAT
66 AACCAATCATTGAATTTGGAAGATGAAT
* * * *
5959635 GTGCTCATGGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAGAACCAC-AG
1 GTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAACCACAAA
*
5959699 AACGAATCATTGGAATT
66 AACCAATCATT-GAATT
5959716 AAAAGATGAA
Statistics
Matches: 251, Mismatches: 10, Indels: 9
0.93 0.04 0.03
Matches are distributed among these distances:
91 86 0.34
92 11 0.04
93 95 0.38
94 59 0.24
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (93 bp):
GTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAACCACAAA
AACCAATCATTGAATTTGGAAGATGAAT
Found at i:5959669 original size:184 final size:184
Alignment explanation
Indices: 5959357--5959712 Score: 615
Period size: 184 Copynumber: 1.9 Consensus size: 184
5959347 AGTAGAACAA
*
5959357 GTGCTCAAAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAACTCCAAA
1 GTGCTCAAAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAA--CAAAA
5959422 AAACCAATCATTGAATTTGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTT
64 AAACCAATCATTGAATTTGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTT
*
5959487 ATCTGATCTGGTTTGATATGAACCACAAAAACCAATCATTGGATTTGGAAGATGAAT
129 ATCTGATCTGGTTTGATAAGAACCAC-AAAACCAATCATTGGATTTGGAAGATGAAT
*
5959544 GTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAA-AAAAAA
1 GTGCTCAAAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAACAAAAAA
*
5959608 ACCAATCATTGAATTTGGAAGATGAATGTGCTCATGGCATCTTCTGGAAGTGTTCTTTGAGTTAT
66 ACCAATCATTGAATTTGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
* * *
5959673 CTGATCTGGTTTGGTAAGAACCACAGAACGAATCATTGGA
131 CTGATCTGGTTTGATAAGAACCACAAAACCAATCATTGGA
5959713 ATTAAAAGAT
Statistics
Matches: 162, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
183 14 0.09
184 91 0.56
187 57 0.35
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (184 bp):
GTGCTCAAAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAACAAAAAA
ACCAATCATTGAATTTGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
CTGATCTGGTTTGATAAGAACCACAAAACCAATCATTGGATTTGGAAGATGAAT
Found at i:5960832 original size:228 final size:226
Alignment explanation
Indices: 5960414--5961171 Score: 890
Period size: 228 Copynumber: 3.3 Consensus size: 226
5960404 GATTCAAATC
* * * * * * *
5960414 CATCAATTGATGGATCATCATTACCAGATAGAGTTCATAATGAGAATAACTCATCATCTGAAGAA
1 CATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAA
* *
5960479 GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATTATTTGATGGA
63 GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTGTTTAAATTCATCATTTGATGGA
* * * * * *
5960544 TTAACATTGCCAGAAAGAGTTCATAATAAGAAGAA--C-TCATTTAAAGAAAAAGAAGAAATTCG
128 TTAACATTTCCAG-GAGAGTTCATAATGAGAAGAACTCATCATTTGAAGAAGAAGAAGAAATTCA
* *
5960606 TAATGAGAAGAATTTGTTCAACATTTTGCTTGAATT
192 AAATGAGAAGAATTTGTTCAACCTTTTGCTT-AATT
5960642 CATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
5960707 AGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTT-TTTGAATTCATCATTTGATGGATTA
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTGTTTAAATTCATCATTTGATGGATTA
*
5960771 AAATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCATTTGAAGAAGGAAGAAGAAATTCAAA
131 ACATTTCCAGG-AGAGTTCATAATGAGAAGAACTCATCATTTGAAGAA-GAAGAAGAAATTCAAA
* * *
5960836 ATGAGAAGAATTTGTTCAACCTTTTACTCAAATC
194 ATGAGAAGAATTTGTTCAACCTTTTGCT-TAATT
**** *
5960870 CATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGAAGAAGGA
1 CATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * * *
5960935 AGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGTTCAAATTCATCACTTGATGGATCA
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTGTTTAAATTCATCATTTGATGGATTA
* *
5961000 ACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATC---TGAAGAAGAAGAAG---TTCACAA
131 ACATTTCCAG-GAGAGTTCATAATGAGAAGAACTCATCATTTGAAGAAGAAGAAGAAATTCAAAA
** *
5961059 TGAGAAGAGCTTGTTCAACCTTTTGCATAATT
195 TGAGAAGAATTTGTTCAACCTTTTGCTTAATT
** * *
5961091 CTATCACAGAAGCAGATAGATTAGCATAAACCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCA
1 C-ATCAC-----TTGATGGATCAGC-T-----TTTCCAGAGAAAGTTCATAATGAGAAGAACTCA
5961156 TCTGAAGAA-GAAGAAG
54 TCTGAAGAAGGAAGAAG
5961172 TTCACAATAA
Statistics
Matches: 460, Mismatches: 50, Indels: 36
0.84 0.09 0.07
Matches are distributed among these distances:
221 4 0.01
222 34 0.07
224 50 0.11
225 60 0.13
226 9 0.02
227 20 0.04
228 183 0.40
229 55 0.12
230 1 0.00
232 7 0.02
233 37 0.08
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.29
Consensus pattern (226 bp):
CATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTGTTTAAATTCATCATTTGATGGATTA
ACATTTCCAGGAGAGTTCATAATGAGAAGAACTCATCATTTGAAGAAGAAGAAGAAATTCAAAAT
GAGAAGAATTTGTTCAACCTTTTGCTTAATT
Found at i:5960955 original size:24 final size:23
Alignment explanation
Indices: 5960912--5960956 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
5960902 GTTCATAATG
*
5960912 AGAAGAATTCATCTGAAGAAGGA
1 AGAAGAATTCATATGAAGAAGGA
5960935 AGAAGAAGTTCATAATG-AGAAG
1 AGAAGAA-TTCAT-ATGAAGAAG
5960957 AACTTGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 7 0.37
24 10 0.53
25 2 0.11
ACGTcount: A:0.49, C:0.07, G:0.27, T:0.18
Consensus pattern (23 bp):
AGAAGAATTCATATGAAGAAGGA
Found at i:5960987 original size:113 final size:113
Alignment explanation
Indices: 5960406--5961083 Score: 821
Period size: 113 Copynumber: 6.0 Consensus size: 113
5960396 TTAGCAAAGA
* * * * *
5960406 TTCAAATCCATCAATTGATGGATCATCATTACCAGATAGAGTTCATAATGAGAATAACTCATCAT
1 TTCAAATTCATCACTTGATGGATCAACATTTCCAGATAGAGTTCATAATGAGAAGAA--C-TCAT
5960471 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
63 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
* * * * * * * * *
5960522 TTTAAATTCATTATTTGATGGATTAACATTGCCAGAAAGAGTTCATAATAAGAAGAACTCATTTA
1 TTCAAATTCATCACTTGATGGATCAACATTTCCAGATAGAGTTCATAATGAGAAGAACTCATCTG
* * * *
5960587 AAGAA-AAAGAAGAAATTCGTAATGAGAAGAATTTGTTCAACATTTTG
66 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
* * * * *
5960634 CTT-GAATTCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT
1 -TTCAAATTCATCACTTGATGGATCAACATTTCCAGATAGAGTTCATAATGAGAAGAACTCATCT
*
5960698 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTT-
65 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
** * * * *
5960746 TTTGAATTCATCATTTGATGGATTAAAATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCAT
1 TTCAAATTCATCACTTGATGGATCAACATTTCCAGATAGAGTTCATAATGAGAAGAACTCATC--
* * *
5960811 TTGAAGAAGGAAGAAGAAATTCAAAATGAGAAGAATTTGTTCAACCTTTTA
64 -TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
* * * * * * *
5960862 CTCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTG
1 TTCAAATTCATCACTTGATGGATCAACATTTCCAGATAGAGTTCATAATGAGAAGAACTCATCTG
* *
5960927 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTG
66 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
* *
5960975 TTCAAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT-
1 TTCAAATTCATCACTTGATGGATCAACATTTCCAGATAGAGTTCATAATGAGAAGAACTCATCTG
* **
5961039 --GAA-GAAGAAGAAGTTCACAATGAGAAGAGCTTGTTCAACCTTTTG
66 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
5961084 CATAATTCTA
Statistics
Matches: 482, Mismatches: 73, Indels: 21
0.84 0.13 0.04
Matches are distributed among these distances:
109 39 0.08
110 3 0.01
111 2 0.00
112 145 0.30
113 148 0.31
114 1 0.00
115 46 0.10
116 98 0.20
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.30
Consensus pattern (113 bp):
TTCAAATTCATCACTTGATGGATCAACATTTCCAGATAGAGTTCATAATGAGAAGAACTCATCTG
AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
Found at i:5961432 original size:3 final size:3
Alignment explanation
Indices: 5961426--5961485 Score: 88
Period size: 3 Copynumber: 20.0 Consensus size: 3
5961416 CCATTTTTAT
5961426 TTA TTA TTA TTA -TA TTTA TTA TTA TTA TTA -TA TTTA TTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
5961471 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
5961486 AATAATAATT
Statistics
Matches: 53, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.08
3 45 0.85
4 4 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5961449 original size:18 final size:18
Alignment explanation
Indices: 5961421--5961485 Score: 105
Period size: 18 Copynumber: 3.6 Consensus size: 18
5961411 TTTACCCATT
5961421 TTTATTTATTATTATTATA
1 TTTA-TTATTATTATTATA
5961440 TTTATTATTATTATTATA
1 TTTATTATTATTATTATA
5961458 TTTATTATTATTATTAT-
1 TTTATTATTATTATTATA
5961475 TATTATTATTA
1 T-TTATTATTA
5961486 AATAATAATT
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
17 1 0.02
18 40 0.89
19 4 0.09
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTATTATTATTATTATA
Found at i:5966266 original size:21 final size:21
Alignment explanation
Indices: 5966240--5966279 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
5966230 AATACTTTAT
5966240 TTTCAAAA-TACAAAAATGATG
1 TTTCAAAATTA-AAAAATGATG
5966261 TTTCAAAATTAAAAAATGA
1 TTTCAAAATTAAAAAATGA
5966280 AAATATTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (21 bp):
TTTCAAAATTAAAAAATGATG
Found at i:5970058 original size:22 final size:22
Alignment explanation
Indices: 5970032--5970114 Score: 80
Period size: 23 Copynumber: 3.8 Consensus size: 22
5970022 TTGGTGCAAA
5970032 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATACCCCCTTGAAG
*
5970054 GGGAA-CTGATTCCCCCTTTGAAG
1 GGGAATC-GATACCCCC-TTGAAG
* * * * *
5970077 GGGAACCAATTCCCCC-CGTAG
1 GGGAATCGATACCCCCTTGAAG
5970098 GGGAATCGATACCCCCT
1 GGGAATCGATACCCCCT
5970115 GGGGGTTCTG
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
21 17 0.34
22 13 0.26
23 19 0.38
24 1 0.02
ACGTcount: A:0.24, C:0.31, G:0.25, T:0.19
Consensus pattern (22 bp):
GGGAATCGATACCCCCTTGAAG
Found at i:5985245 original size:3 final size:3
Alignment explanation
Indices: 5985231--5985298 Score: 118
Period size: 3 Copynumber: 22.0 Consensus size: 3
5985221 TGTGTAACAA
5985231 AAT AATT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ATAT
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
5985278 AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT
5985299 TTTGTAGACC
Statistics
Matches: 63, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
3 57 0.90
4 6 0.10
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:5987903 original size:33 final size:33
Alignment explanation
Indices: 5987865--5987930 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
5987855 AAATGTTTTG
**
5987865 ATAATTTTACTATTTCTAAAGTTGTTAAAAATT
1 ATAATTTTACTATTTCTAAAACTGTTAAAAATT
*
5987898 ATAATTTTACTATTTTTAAAACTGTTAAAAATT
1 ATAATTTTACTATTTCTAAAACTGTTAAAAATT
5987931 GATGACTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.48
Consensus pattern (33 bp):
ATAATTTTACTATTTCTAAAACTGTTAAAAATT
Found at i:6003122 original size:19 final size:18
Alignment explanation
Indices: 6003098--6003145 Score: 73
Period size: 17 Copynumber: 2.7 Consensus size: 18
6003088 GAATATAAGC
6003098 ATGTGTTTGATATAAGTAT
1 ATGTGTTT-ATATAAGTAT
6003117 ATGTG-TTATATAAGTAT
1 ATGTGTTTATATAAGTAT
6003134 ATGTG-TTATATA
1 ATGTGTTTATATA
6003146 TTATGGTATG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
17 22 0.76
18 2 0.07
19 5 0.17
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48
Consensus pattern (18 bp):
ATGTGTTTATATAAGTAT
Found at i:6003143 original size:15 final size:17
Alignment explanation
Indices: 6003107--6003145 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
6003097 CATGTGTTTG
6003107 ATATAAGTATATGTGTT
1 ATATAAGTATATGTGTT
6003124 ATATAAGTATATGTGTT
1 ATATAAGTATATGTGTT
6003141 ATATA
1 ATATA
6003146 TTATGGTATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (17 bp):
ATATAAGTATATGTGTT
Found at i:6011951 original size:38 final size:38
Alignment explanation
Indices: 6011908--6011994 Score: 140
Period size: 38 Copynumber: 2.3 Consensus size: 38
6011898 GTGAGAATTC
6011908 AATTTAAAAAGATAATAAAAAAGTGAAAAAAT-ATCTAA
1 AATTTAAAAAGATAATAAAAAA-TGAAAAAATAATCTAA
*
6011946 AATTTAAAAAGATAATATAAAATGAAAAAATAATCTAA
1 AATTTAAAAAGATAATAAAAAATGAAAAAATAATCTAA
6011984 AATTTTAAAAA
1 AA-TTTAAAAA
6011995 ATTAAAATTA
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
37 9 0.20
38 29 0.63
39 8 0.17
ACGTcount: A:0.66, C:0.02, G:0.06, T:0.26
Consensus pattern (38 bp):
AATTTAAAAAGATAATAAAAAATGAAAAAATAATCTAA
Found at i:6011954 original size:18 final size:18
Alignment explanation
Indices: 6011933--6012020 Score: 74
Period size: 18 Copynumber: 4.8 Consensus size: 18
6011923 TAAAAAAGTG
6011933 AAAAAATATCTAAAATTT
1 AAAAAATATCTAAAATTT
* *
6011951 AAAAAGATAATATAAAA-TG
1 AAAAA-AT-ATCTAAAATTT
6011970 AAAAAATAATCTAAAATTT
1 AAAAAAT-ATCTAAAATTT
*
6011989 TAAAAA-AT-TAAAATTAT
1 AAAAAATATCTAAAATT-T
*
6012006 GAAAAATATCATAAA
1 AAAAAATATC-TAAA
6012021 GTTTTATGTT
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
16 7 0.12
17 8 0.14
18 17 0.30
19 14 0.25
20 11 0.19
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.28
Consensus pattern (18 bp):
AAAAAATATCTAAAATTT
Found at i:6011966 original size:20 final size:19
Alignment explanation
Indices: 6011908--6011996 Score: 83
Period size: 20 Copynumber: 4.6 Consensus size: 19
6011898 GTGAGAATTC
*
6011908 AATTTAAAAAGATAATAAAA
1 AATTTAAAAA-ATAATATAA
* * *
6011928 AAGTGAAAAAAT-ATCTAA
1 AATTTAAAAAATAATATAA
6011946 AATTTAAAAAGATAATATAA
1 AATTTAAAAA-ATAATATAA
* *
6011966 AA-TGAAAAAATAATCTAA
1 AATTTAAAAAATAATATAA
6011984 AATTTTAAAAAAT
1 AA-TTTAAAAAAT
6011997 TAAAATTATG
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
18 22 0.40
19 10 0.18
20 23 0.42
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (19 bp):
AATTTAAAAAATAATATAA
Found at i:6020518 original size:13 final size:13
Alignment explanation
Indices: 6020502--6020527 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6020492 GATGCAACAA
6020502 TTTTTTTGTAGAT
1 TTTTTTTGTAGAT
6020515 TTTTTTTGTAGAT
1 TTTTTTTGTAGAT
6020528 CTGCAACTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.69
Consensus pattern (13 bp):
TTTTTTTGTAGAT
Found at i:6024986 original size:13 final size:13
Alignment explanation
Indices: 6024968--6025024 Score: 87
Period size: 13 Copynumber: 4.4 Consensus size: 13
6024958 GTCATAAATC
6024968 TATGACGCGCATT
1 TATGACGCGCATT
*
6024981 TATGACACGCATT
1 TATGACGCGCATT
*
6024994 TATGACGCTCATT
1 TATGACGCGCATT
*
6025007 TATGACGTGCATT
1 TATGACGCGCATT
6025020 TATGA
1 TATGA
6025025 TGTGCATTGC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 39 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:6025029 original size:13 final size:13
Alignment explanation
Indices: 6024968--6025032 Score: 78
Period size: 13 Copynumber: 5.0 Consensus size: 13
6024958 GTCATAAATC
*
6024968 TATGACGCGCATT
1 TATGACGTGCATT
**
6024981 TATGACACGCATT
1 TATGACGTGCATT
6024994 TATGACGCT-CATT
1 TATGACG-TGCATT
6025007 TATGACGTGCATT
1 TATGACGTGCATT
*
6025020 TATGATGTGCATT
1 TATGACGTGCATT
6025033 GCGCTTCATT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
12 1 0.02
13 45 0.98
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (13 bp):
TATGACGTGCATT
Found at i:6025127 original size:85 final size:85
Alignment explanation
Indices: 6025004--6025161 Score: 221
Period size: 85 Copynumber: 1.9 Consensus size: 85
6024994 TATGACGCTC
* * * *
6025004 ATTTATGACGTGCATTTATGATGTGCATTGCGCTTCATTGAAGCCCCCATCATAAATGAAAATGA
1 ATTTATGACATGCATGTATGATGTACATTGCGCTTCATTAAAGCCCCCATCATAAATGAAAATGA
6025069 CACACATTTGTTTGTCATAA
66 CACACATTTGTTTGTCATAA
* * *
6025089 ATTTATGACATGCATGTATGACT-TACATTGTG-TGTCATTAAAGCCCCCGTCATAAATGAAGAT
1 ATTTATGACATGCATGTATGA-TGTACATTGCGCT-TCATTAAAGCCCCCATCATAAATGAAAAT
6025152 GACACACATT
64 GACACACATT
6025162 CGTGTGTCGT
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
84 1 0.02
85 62 0.97
86 1 0.02
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (85 bp):
ATTTATGACATGCATGTATGATGTACATTGCGCTTCATTAAAGCCCCCATCATAAATGAAAATGA
CACACATTTGTTTGTCATAA
Done.