Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 87 of 198
Found at i:28041840 original size:44 final size:44
Alignment explanation
Indices: 28041792--28042107 Score: 146
Period size: 44 Copynumber: 7.2 Consensus size: 44
28041782 AATATTGTAG
*
28041792 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACTACAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACTACAA
* * *
28041836 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAG-CCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACTA-CAA
** * * * * * * * * ** *
28041880 GCCTTGTCTCCCTGAGCAGCAGCGGGGTAGGTTGAAGATTGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACTACAA
*
28041924 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAC-AGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACTA-CAA
* * * * *
28041968 ATCTTATTTTCC-AAG-A-TAGTGGGAAACAGATTTAAG-CCACCAA
1 ATCTTATCTCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACTA-CAA
** * * * * * * * ** *
28042011 GCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACTACAA
* ** *
28042055 TTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACTACAA
28042099 ATCTTATCT
1 ATCTTATCT
28042108 TGCCAAGATA
Statistics
Matches: 183, Mismatches: 73, Indels: 32
0.64 0.25 0.11
Matches are distributed among these distances:
41 4 0.02
42 8 0.04
43 31 0.17
44 127 0.69
45 9 0.05
46 4 0.02
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.25
Consensus pattern (44 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACTACAA
Found at i:28043977 original size:18 final size:18
Alignment explanation
Indices: 28043952--28044006 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 18
28043942 ATTTTTATTT
28043952 TATTTTTATTTATATGTA
1 TATTTTTATTTATATGTA
* *
28043970 TTTTTTTATCTATATGTA
1 TATTTTTATTTATATGTA
*
28043988 TATATTTATTT-TA-GTA
1 TATTTTTATTTATATGTA
28044004 TAT
1 TAT
28044007 ATATGTATGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
16 6 0.19
17 2 0.06
18 24 0.75
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.65
Consensus pattern (18 bp):
TATTTTTATTTATATGTA
Found at i:28043991 original size:26 final size:26
Alignment explanation
Indices: 28043962--28044014 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
28043952 TATTTTTATT
** *
28043962 TATATGTATTTTTTTATCTATATGTA
1 TATATGTATTTTAGTATATATATGTA
*
28043988 TATATTTATTTTAGTATATATATGTA
1 TATATGTATTTTAGTATATATATGTA
28044014 T
1 T
28044015 GTATACATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.30, C:0.02, G:0.08, T:0.60
Consensus pattern (26 bp):
TATATGTATTTTAGTATATATATGTA
Found at i:28044071 original size:22 final size:23
Alignment explanation
Indices: 28044045--28044105 Score: 70
Period size: 22 Copynumber: 2.6 Consensus size: 23
28044035 AACTAATTTT
28044045 TATTTATTTATATAAATG-AATA
1 TATTTATTTATATAAATGAAATA
* *
28044067 TATTTATTTTTAAAAATGAAAATA
1 TATTTATTTATATAAATG-AAATA
*
28044091 TATGTTTTTTATATA
1 TAT-TTATTTATATA
28044106 CTTTATAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
22 16 0.52
24 7 0.23
25 8 0.26
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (23 bp):
TATTTATTTATATAAATGAAATA
Found at i:28047672 original size:3 final size:3
Alignment explanation
Indices: 28047664--28047694 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
28047654 GCTCATTTAT
28047664 TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
28047695 CATATATATG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:28047684 original size:14 final size:14
Alignment explanation
Indices: 28047660--28047693 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
28047650 TTTTGCTCAT
28047660 TTATT-TATTATTA
1 TTATTATATTATTA
28047673 TTATTATATTATTA
1 TTATTATATTATTA
28047687 TTATTAT
1 TTATTAT
28047694 TCATATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TTATTATATTATTA
Found at i:28052017 original size:8 final size:8
Alignment explanation
Indices: 28052004--28052043 Score: 62
Period size: 8 Copynumber: 4.8 Consensus size: 8
28051994 TAGACTCAAA
28052004 AAAAAATC
1 AAAAAATC
28052012 AAAAAATC
1 AAAAAATC
28052020 AAAAAATC
1 AAAAAATC
28052028 AAAAAAAATC
1 --AAAAAATC
28052038 AAAAAA
1 AAAAAA
28052044 AAAATCAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
8 22 0.73
10 8 0.27
ACGTcount: A:0.80, C:0.10, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAAATC
Found at i:28052025 original size:18 final size:16
Alignment explanation
Indices: 28052004--28052043 Score: 62
Period size: 18 Copynumber: 2.4 Consensus size: 16
28051994 TAGACTCAAA
28052004 AAAAAATCAAAAAATC
1 AAAAAATCAAAAAATC
28052020 AAAAAATCAAAAAAAATC
1 AAAAAATC--AAAAAATC
28052038 AAAAAA
1 AAAAAA
28052044 AAAATCAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 8 0.36
18 14 0.64
ACGTcount: A:0.80, C:0.10, G:0.00, T:0.10
Consensus pattern (16 bp):
AAAAAATCAAAAAATC
Found at i:28052057 original size:18 final size:18
Alignment explanation
Indices: 28052001--28052060 Score: 61
Period size: 18 Copynumber: 3.2 Consensus size: 18
28051991 GTTTAGACTC
28052001 AAAAAAAAATCAAAAAATCA
1 AAAAAAAAATC--AAAATCA
28052021 AAAAATCAAAA--AAAATCA
1 AAAAA--AAAATCAAAATCA
*
28052039 AAAAAAAAATCAAAGTCA
1 AAAAAAAAATCAAAATCA
28052057 AAAA
1 AAAA
28052061 TAGGAGAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
16 4 0.11
18 22 0.63
20 5 0.14
22 4 0.11
ACGTcount: A:0.78, C:0.10, G:0.02, T:0.10
Consensus pattern (18 bp):
AAAAAAAAATCAAAATCA
Found at i:28052074 original size:6 final size:6
Alignment explanation
Indices: 28052065--28052105 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
28052055 CAAAAATAGG
*
28052065 AGAAAA AGAAAA A-AGAA A-AAAA AGAAAA AGAAAA AGAAAA A
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA A
28052106 AGGAGAGGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 8 0.25
6 24 0.75
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:28052076 original size:16 final size:16
Alignment explanation
Indices: 28052056--28052111 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 16
28052046 AATCAAAGTC
28052056 AAAAATAGGAGAAAAAG
1 AAAAA-AGGAGAAAAAG
28052073 AAAAAA-GA-AAAAA-
1 AAAAAAGGAGAAAAAG
28052086 AAGAAAA--AGAAAAAG
1 AA-AAAAGGAGAAAAAG
28052101 AAAAAAGGAGA
1 AAAAAAGGAGA
28052112 GGTCAAGGCG
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
13 3 0.09
14 18 0.53
15 4 0.12
16 4 0.12
17 5 0.15
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.02
Consensus pattern (16 bp):
AAAAAAGGAGAAAAAG
Found at i:28052079 original size:7 final size:7
Alignment explanation
Indices: 28052067--28052107 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
28052057 AAAATAGGAG
28052067 AAAAAGA
1 AAAAAGA
28052074 AAAAAGA
1 AAAAAGA
*
28052081 AAAAAAA
1 AAAAAGA
28052088 GAAAAAG-
1 -AAAAAGA
28052095 AAAAAGA
1 AAAAAGA
28052102 AAAAAG
1 AAAAAG
28052108 GAGAGGTCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 6 0.20
7 19 0.63
8 5 0.17
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:28052092 original size:15 final size:16
Alignment explanation
Indices: 28052067--28052099 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
28052057 AAAATAGGAG
28052067 AAAAAGAAAAAAGAAA
1 AAAAAGAAAAAAGAAA
28052083 AAAAAG-AAAAAGAAA
1 AAAAAGAAAAAAGAAA
28052098 AA
1 AA
28052100 GAAAAAAGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAAAGAAA
Found at i:28052093 original size:22 final size:21
Alignment explanation
Indices: 28052065--28052106 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
28052055 CAAAAATAGG
28052065 AGAAAAAGAAAAAAGAAAAAAA
1 AGAAAAAG-AAAAAGAAAAAAA
28052087 AGAAAAAGAAAAAGAAAAAA
1 AGAAAAAGAAAAAGAAAAAA
28052107 GGAGAGGTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (21 bp):
AGAAAAAGAAAAAGAAAAAAA
Found at i:28052960 original size:8 final size:9
Alignment explanation
Indices: 28052947--28053010 Score: 50
Period size: 9 Copynumber: 7.3 Consensus size: 9
28052937 AAACAAAAAC
28052947 AAAAAT-AA
1 AAAAATGAA
28052955 AAAAATG--
1 AAAAATGAA
28052962 -AAAATGAAA
1 AAAAATG-AA
28052971 AAATGAATGGAA
1 AAA--AAT-GAA
28052983 AAAAATG--
1 AAAAATGAA
28052990 AAAAATGAA
1 AAAAATGAA
28052999 AAAAATGAA
1 AAAAATGAA
28053008 AAA
1 AAA
28053011 TGGAGAGGCT
Statistics
Matches: 46, Mismatches: 0, Indels: 19
0.71 0.00 0.29
Matches are distributed among these distances:
6 6 0.13
7 7 0.15
8 6 0.13
9 13 0.28
10 5 0.11
12 8 0.17
13 1 0.02
ACGTcount: A:0.75, C:0.00, G:0.12, T:0.12
Consensus pattern (9 bp):
AAAAATGAA
Found at i:28052999 original size:16 final size:16
Alignment explanation
Indices: 28052947--28053012 Score: 81
Period size: 14 Copynumber: 4.4 Consensus size: 16
28052937 AAACAAAAAC
28052947 AAAAAT-AAAAAAATG
1 AAAAATGAAAAAAATG
28052962 -AAAATG-AAAAAATG
1 AAAAATGAAAAAAATG
28052976 ---AATGGAAAAAAATG
1 AAAAAT-GAAAAAAATG
28052990 AAAAATGAAAAAAATG
1 AAAAATGAAAAAAATG
28053006 AAAAATG
1 AAAAATG
28053013 GAGAGGCTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
12 3 0.07
13 1 0.02
14 21 0.47
16 17 0.38
17 3 0.07
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.14
Consensus pattern (16 bp):
AAAAATGAAAAAAATG
Found at i:28054592 original size:44 final size:44
Alignment explanation
Indices: 28054543--28055135 Score: 290
Period size: 44 Copynumber: 13.6 Consensus size: 44
28054533 CTTGCCTTCA
* * *
28054543 TGAGATTACAGCGGAGTAGATTGAAATTAGTAATCCTATCTCCC
1 TGAGATTACAGTGGAGCAGATTGAAATTAGTAATCTTATCTCCC
*** * * * * *
28054587 TGAGATTACAGTGGAATGGATTAAAATAAAG-GATCTTTTCTCTC
1 TGAGATTACAGTGGAGCAGATTGAAAT-TAGTAATCTTATCTCCC
* * * ** *
28054631 TGA-ATTTACAGTAGAGTAGATCG-TGTCAG--ATCTTATCTCCC
1 TGAGA-TTACAGTGGAGCAGATTGAAATTAGTAATCTTATCTCCC
* * *
28054672 TGAGATTACAGCGGAGCAGATTGAAGTTAGTAATCCTATCTCCC
1 TGAGATTACAGTGGAGCAGATTGAAATTAGTAATCTTATCTCCC
* ** * * * * *
28054716 TGATATTACAGTGGAGTGGATTAAAATGAATGATCTTATCTCTC
1 TGAGATTACAGTGGAGCAGATTGAAATTAGTAATCTTATCTCCC
* ** * * ** * * *
28054760 T-AAAGTTACAGCAGAGTAGATCG-CGTCAG--GTCTTATTTCCC
1 TGAGA-TTACAGTGGAGCAGATTGAAATTAGTAATCTTATCTCCC
* ** * *
28054801 TGAGATTACAGTGGAACAGACCGAAGAAT-GTCAGTCTTATCTCCC
1 TGAGATTACAGTGGAGCAGATTGAA-ATTAGT-AATCTTATCTCCC
* * ** *
28054846 TGAGATTACAGTAGAGCAGATCGAAGCTAGTAATCCTATCTCCC
1 TGAGATTACAGTGGAGCAGATTGAAATTAGTAATCTTATCTCCC
* * * * *
28054890 TGAGATTACAGTGGAGCGGATTAAAATAAAG-GATCTTATCTCTC
1 TGAGATTACAGTGGAGCAGATTGAAAT-TAGTAATCTTATCTCCC
* * * * * *
28054934 TGA-AGTTACAGTAGAGTAGATCG-CATCAG--GTCTTATCTCCC
1 TGAGA-TTACAGTGGAGCAGATTGAAATTAGTAATCTTATCTCCC
* *
28054975 TGAGATTACAGTGGAGCAGACTGAAGAATT--TCAGATCTTATCTCCT
1 TGAGATTACAGTGGAGCAGATTG-A-AATTAGT-A-ATCTTATCTCCC
* *
28055021 TGAGATTACAGCGGAGCAGATTGAAGA-TAGTAATCCTATCTCCC
1 TGAGATTACAGTGGAGCAGATTGAA-ATTAGTAATCTTATCTCCC
**
28055065 TGAGATTACAGTGGAGCAGACCGAAGAATT--TCAGATCTTATCTCCC
1 TGAGATTACAGTGGAGCAGATTG-A-AATTAGT-A-ATCTTATCTCCC
* * *
28055111 GGAGACTACAGCGGAGCAGATTGAA
1 TGAGATTACAGTGGAGCAGATTGAA
28055136 TCTGATAATC
Statistics
Matches: 409, Mismatches: 108, Indels: 64
0.70 0.19 0.11
Matches are distributed among these distances:
41 77 0.19
42 13 0.03
43 9 0.02
44 201 0.49
45 46 0.11
46 63 0.15
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (44 bp):
TGAGATTACAGTGGAGCAGATTGAAATTAGTAATCTTATCTCCC
Found at i:28054702 original size:129 final size:129
Alignment explanation
Indices: 28054543--28054857 Score: 425
Period size: 129 Copynumber: 2.4 Consensus size: 129
28054533 CTTGCCTTCA
* *
28054543 TGAGATTACAGCGGAGTAGATTGAAATTAGTAATCCTATCTCCCTGAGATTACAGTGGAATGGAT
1 TGAGATTACAGCGGAGCAGATTGAAGTTAGTAATCCTATCTCCCTGAGATTACAGTGGAATGGAT
* * * * *
28054608 TAAAATAAAGGATCTTTTCTCTCTGAATTTACAGTAGAGTAGATCGTGTCAGATCTTATCTCCC
66 TAAAATAAAGGATCTTATCTCTCTAAAGTTACAGCAGAGTAGATCGCGTCAGATCTTATCTCCC
* *
28054672 TGAGATTACAGCGGAGCAGATTGAAGTTAGTAATCCTATCTCCCTGATATTACAGTGGAGTGGAT
1 TGAGATTACAGCGGAGCAGATTGAAGTTAGTAATCCTATCTCCCTGAGATTACAGTGGAATGGAT
* * * *
28054737 TAAAATGAATGATCTTATCTCTCTAAAGTTACAGCAGAGTAGATCGCGTCAGGTCTTATTTCCC
66 TAAAATAAAGGATCTTATCTCTCTAAAGTTACAGCAGAGTAGATCGCGTCAGATCTTATCTCCC
* * ** * * *
28054801 TGAGATTACAGTGGAACAGACCGAAG-AATGTCAGTCTTATCTCCCTGAGATTACAGT
1 TGAGATTACAGCGGAGCAGATTGAAGTTA-GT-AATCCTATCTCCCTGAGATTACAGT
28054858 AGAGCAGATC
Statistics
Matches: 163, Mismatches: 21, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
128 1 0.01
129 140 0.86
130 22 0.13
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.31
Consensus pattern (129 bp):
TGAGATTACAGCGGAGCAGATTGAAGTTAGTAATCCTATCTCCCTGAGATTACAGTGGAATGGAT
TAAAATAAAGGATCTTATCTCTCTAAAGTTACAGCAGAGTAGATCGCGTCAGATCTTATCTCCC
Found at i:28054952 original size:174 final size:175
Alignment explanation
Indices: 28054654--28055081 Score: 696
Period size: 174 Copynumber: 2.5 Consensus size: 175
28054644 GAGTAGATCG
*
28054654 TGTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGTTAGTAATCCTATCTCCCTGA
1 TGTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGA
* * * *
28054719 TATTACAGTGGAGTGGATTAAAATGAATGATCTTATCTCTCTAAAGTTACAGCAGAGTAGATCGC
66 GATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGCAGAGTAGATCGC
* *
28054784 GTCAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAA
131 ATCAGGTCTTATCTCCCTGAGATTACAGTGGAACAGACCGAAGAA
** * *
28054829 TGTCAG-TCTTATCTCCCTGAGATTACAGTAGAGCAGATCGAAGCTAGTAATCCTATCTCCCTGA
1 TGTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGA
* *
28054893 GATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGC
66 GATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGCAGAGTAGATCGC
* *
28054958 ATCAGGTCTTATCTCCCTGAGATTACAGTGGAGCAGACTGAAGAA
131 ATCAGGTCTTATCTCCCTGAGATTACAGTGGAACAGACCGAAGAA
* *
28055003 TTTCAGATCTTATCTCCTTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGA
1 TGTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGA
28055068 GATTACAGTGGAGC
66 GATTACAGTGGAGC
28055082 AGACCGAAGA
Statistics
Matches: 232, Mismatches: 20, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
174 159 0.69
175 73 0.31
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (175 bp):
TGTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGA
GATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGCAGAGTAGATCGC
ATCAGGTCTTATCTCCCTGAGATTACAGTGGAACAGACCGAAGAA
Found at i:28055073 original size:90 final size:90
Alignment explanation
Indices: 28054967--28055165 Score: 305
Period size: 90 Copynumber: 2.2 Consensus size: 90
28054957 CATCAGGTCT
* ** *
28054967 TATCTCCCTGAGATTACAGTGGAGCAGACTGAAGAATTTCAGATCTTATCTCCTTGAGATTACAG
1 TATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTTCAGATCTTATCTCCCGGAGACTACAG
28055032 CGGAGCAGATTGAAGAT-AGTAATCC
66 CGGAGCAGATTGAAGATGA-TAATCC
28055057 TATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTTCAGATCTTATCTCCCGGAGACTACAG
1 TATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTTCAGATCTTATCTCCCGGAGACTACAG
**
28055122 CGGAGCAGATTGAATCTGATAATCC
66 CGGAGCAGATTGAAGATGATAATCC
*
28055147 -A-ATCCCTGAGATTACAGTG
1 TATCTCCCTGAGATTACAGTG
28055166 AAGCGGATTA
Statistics
Matches: 101, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
88 17 0.17
89 1 0.01
90 82 0.81
91 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (90 bp):
TATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTTCAGATCTTATCTCCCGGAGACTACAG
CGGAGCAGATTGAAGATGATAATCC
Found at i:28055074 original size:131 final size:128
Alignment explanation
Indices: 28054834--28055219 Score: 309
Period size: 131 Copynumber: 3.0 Consensus size: 128
28054824 AAGAATGTCA
*
28054834 GTCTTATCTCCCTGAGATTACAGTAGAGCAGATCGAAGCTAGTAATCCTATCTCCCTGAGATTAC
1 GTCTTATCTCCCTGAGATTACAGTAGAGCAGATCGAAGATAGTAATCCTATCTCCCTGAGATTAC
* * * * *
28054899 AGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
66 AGCGGAGCAGATTAAAAT-AAGAATCCTATCTCCCTGAAGTTACAGTAGAGTAGATCGCATCAG
* * * *
28054963 GTCTTATCTCCCTGAGATTACAGTGGAGCAGA-CTGAAGA-ATTTCAGATCTTATCTCCTTGAGA
1 GTCTTATCTCCCTGAGATTACAGTAGAGCAGATC-GAAGATA-GT-A-ATCCTATCTCCCTGAGA
* * * *
28055026 TTACAGCGGAGCAGATTGAAGAT-AGTAATCCTATCTCCCTG-AGATTACAGTGGAGCAGACCGA
62 TTACAGCGGAGCAGATT-AAAATAAG-AATCCTATCTCCCTGAAG-TTACAGTAGAGTAGATC--
*
28055089 AGAATTTCAG
122 -GCA--TCAG
* * * ** * ** *
28055099 ATCTTATCTCCCGGAGACTACAGCGGAGCAGATTGAATCT-GATAATCC-A-ATCCCTGAGATTA
1 GTCTTATCTCCCTGAGATTACAGTAGAGCAGATCGAAGATAG-TAATCCTATCTCCCTGAGATTA
* * * * * * *
28055161 CAGTGAAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTGGATCG
65 CAGCGGAGCAGATTAAAAT-AAGAATCCTATCTCCCTGAAGTTACAGTAGAGTAGATCG
28055220 TATTAGATTC
Statistics
Matches: 202, Mismatches: 37, Indels: 36
0.73 0.13 0.13
Matches are distributed among these distances:
128 2 0.01
129 37 0.18
130 5 0.02
131 60 0.30
132 51 0.25
133 5 0.02
134 5 0.02
135 1 0.00
136 36 0.18
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.27
Consensus pattern (128 bp):
GTCTTATCTCCCTGAGATTACAGTAGAGCAGATCGAAGATAGTAATCCTATCTCCCTGAGATTAC
AGCGGAGCAGATTAAAATAAGAATCCTATCTCCCTGAAGTTACAGTAGAGTAGATCGCATCAG
Found at i:28056822 original size:3 final size:3
Alignment explanation
Indices: 28056814--28056844 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
28056804 GCTCATTTAT
28056814 TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
28056845 CATATATATG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:28056834 original size:14 final size:14
Alignment explanation
Indices: 28056810--28056843 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
28056800 TTTTGCTCAT
28056810 TTATT-TATTATTA
1 TTATTATATTATTA
28056823 TTATTATATTATTA
1 TTATTATATTATTA
28056837 TTATTAT
1 TTATTAT
28056844 TCATATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TTATTATATTATTA
Found at i:28059923 original size:13 final size:13
Alignment explanation
Indices: 28059905--28059960 Score: 91
Period size: 13 Copynumber: 4.5 Consensus size: 13
28059895 TAAATTTTTC
28059905 CTAAATATTATCA
1 CTAAATATTATCA
28059918 CTAAATA--ATC-
1 CTAAATATTATCA
28059928 CTAAATATTATCA
1 CTAAATATTATCA
28059941 CTAAATATTATCA
1 CTAAATATTATCA
28059954 CTAAATA
1 CTAAATA
28059961 ATTCAAAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
10 7 0.17
11 3 0.08
12 3 0.08
13 27 0.68
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:28059931 original size:23 final size:23
Alignment explanation
Indices: 28059903--28059947 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
28059893 GCTAAATTTT
28059903 TCCTAAATATTATCACTAAATAA
1 TCCTAAATATTATCACTAAATAA
28059926 TCCTAAATATTATCACTAAATA
1 TCCTAAATATTATCACTAAATA
28059948 TTATCACTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.36
Consensus pattern (23 bp):
TCCTAAATATTATCACTAAATAA
Found at i:28068290 original size:3 final size:3
Alignment explanation
Indices: 28068277--28068327 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
28068267 TGGCAAGAGC
*
28068277 ATT AGT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
28068325 ATT
1 ATT
28068328 CACTAGTAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:28076430 original size:14 final size:14
Alignment explanation
Indices: 28076411--28076441 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
28076401 CTCAGGTTAC
28076411 TTATTTTAATGGGA
1 TTATTTTAATGGGA
28076425 TTA-TTTAATGGGA
1 TTATTTTAATGGGA
28076438 TTAT
1 TTAT
28076442 AATCATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 13 0.81
14 3 0.19
ACGTcount: A:0.29, C:0.00, G:0.19, T:0.52
Consensus pattern (14 bp):
TTATTTTAATGGGA
Found at i:28079385 original size:15 final size:14
Alignment explanation
Indices: 28079342--28079387 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 14
28079332 AAATATTTTC
28079342 TAAAATTAAATATA
1 TAAAATTAAATATA
*
28079356 -ATAATT-AATA-A
1 TAAAATTAAATATA
28079367 TAAAATTAAATATA
1 TAAAATTAAATATA
*
28079381 TTAAATT
1 TAAAATT
28079388 TTTATATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
11 1 0.04
12 9 0.35
13 9 0.35
14 7 0.27
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TAAAATTAAATATA
Found at i:28089708 original size:35 final size:35
Alignment explanation
Indices: 28089660--28089728 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
28089650 ATTGTTGGTC
*
28089660 ATGCATTTTTAAGTTTGACATGTAAATTACTTGAG
1 ATGCATTTGTAAGTTTGACATGTAAATTACTTGAG
28089695 ATGCATTTGTAAGTTTGACATGTAAATTACTTGA
1 ATGCATTTGTAAGTTTGACATGTAAATTACTTGA
28089729 TTATATAAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.42
Consensus pattern (35 bp):
ATGCATTTGTAAGTTTGACATGTAAATTACTTGAG
Found at i:28102985 original size:24 final size:24
Alignment explanation
Indices: 28102926--28102988 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
28102916 ATTTTTACAA
*
28102926 CTCGTGTGAGCATTTACATTCATAG
1 CTCGTGTGAGCA-TTACATTCACAG
** * *
28102951 CTCAAGAGAGCATTATATTCACAG
1 CTCGTGTGAGCATTACATTCACAG
28102975 CTCGTGTGAGCATT
1 CTCGTGTGAGCATT
28102989 GTTATCCCGC
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
24 21 0.70
25 9 0.30
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.32
Consensus pattern (24 bp):
CTCGTGTGAGCATTACATTCACAG
Found at i:28104505 original size:23 final size:23
Alignment explanation
Indices: 28104463--28104507 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
28104453 GTGTTATTTA
* **
28104463 TCAGTGGTAGCTTCGGCTACATT
1 TCAGTGGTAGCTACAACTACATT
28104486 TCAGTGGTAGCTACAACTACAT
1 TCAGTGGTAGCTACAACTACAT
28104508 ATCGGTAGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (23 bp):
TCAGTGGTAGCTACAACTACATT
Found at i:28107838 original size:27 final size:27
Alignment explanation
Indices: 28107811--28107907 Score: 95
Period size: 27 Copynumber: 3.6 Consensus size: 27
28107801 CAACGGGCTA
*
28107811 CCCAGTGTTTGACGTCCTATCAGACTAC
1 CCCA-TGTTTAACGTCCTATCAGACTAC
* **
28107839 CCCATGTTTAACGTCCTATCAGAGTGT
1 CCCATGTTTAACGTCCTATCAGACTAC
* * * **
28107866 CCCGTCTTTAACGTCCCATTGGACTAC
1 CCCATGTTTAACGTCCTATCAGACTAC
*
28107893 CCCATGTTTAGCGTC
1 CCCATGTTTAACGTC
28107908 TCGTCGGACT
Statistics
Matches: 54, Mismatches: 15, Indels: 1
0.77 0.21 0.01
Matches are distributed among these distances:
27 50 0.93
28 4 0.07
ACGTcount: A:0.20, C:0.32, G:0.18, T:0.31
Consensus pattern (27 bp):
CCCATGTTTAACGTCCTATCAGACTAC
Found at i:28111032 original size:45 final size:45
Alignment explanation
Indices: 28110956--28111073 Score: 139
Period size: 45 Copynumber: 2.6 Consensus size: 45
28110946 GACAATCAAC
* * * *
28110956 GATGCCATAGCATCTTTCAGTTATGGCCCTACCCATTTCAGT-TAT
1 GATGTCATAGCATCTTTTAGCTATGGTCCTACCCATTTCAGTCT-T
* * *
28111001 GATGTCATAACATCTTTTAGCTATGGTCCTACTCATTTTAGTCTT
1 GATGTCATAGCATCTTTTAGCTATGGTCCTACCCATTTCAGTCTT
* *
28111046 GATGTCATAGCATCTTTTAACTACGGTC
1 GATGTCATAGCATCTTTTAGCTATGGTC
28111074 TTAATCATTT
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
45 61 0.98
46 1 0.02
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.39
Consensus pattern (45 bp):
GATGTCATAGCATCTTTTAGCTATGGTCCTACCCATTTCAGTCTT
Found at i:28111082 original size:45 final size:45
Alignment explanation
Indices: 28111000--28111086 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 45
28110990 ATTTCAGTTA
* * *
28111000 TGATGTCATAACATCTTTTAGCTATGGTCCTACTCATTTTAGTCT
1 TGATGTCATAACATCTTTTAACTACGGTCCTAATCATTTTAGTCT
* *
28111045 TGATGTCATAGCATCTTTTAACTACGGTCTTAATCATTTTAG
1 TGATGTCATAACATCTTTTAACTACGGTCCTAATCATTTTAG
28111087 GCATACAACC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.24, C:0.18, G:0.14, T:0.44
Consensus pattern (45 bp):
TGATGTCATAACATCTTTTAACTACGGTCCTAATCATTTTAGTCT
Found at i:28114990 original size:24 final size:24
Alignment explanation
Indices: 28114921--28114990 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
28114911 TATGCCCATT
28114921 TTCACAGCTCGTGTGAGCATTTATA
1 TTCACAGCTCGTGTGAGCA-TTATA
* * ** * *
28114946 ATCATAGCTCAAGGGATCATTATA
1 TTCACAGCTCGTGTGAGCATTATA
28114970 TTCACAGCTCGTGTGAGCATT
1 TTCACAGCTCGTGTGAGCATT
28114991 GTTATCCCAC
Statistics
Matches: 33, Mismatches: 12, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
24 20 0.61
25 13 0.39
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (24 bp):
TTCACAGCTCGTGTGAGCATTATA
Found at i:28120069 original size:21 final size:19
Alignment explanation
Indices: 28120037--28120080 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
28120027 TAAATTGATG
28120037 ATTTATGATAGATTATGAAT
1 ATTTATGATAGATT-TGAAT
* *
28120057 ATTTGATGTTAGATTTTAAT
1 ATTT-ATGATAGATTTGAAT
28120077 ATTT
1 ATTT
28120081 TATAAAGTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (19 bp):
ATTTATGATAGATTTGAAT
Found at i:28120748 original size:43 final size:42
Alignment explanation
Indices: 28120650--28120806 Score: 165
Period size: 43 Copynumber: 3.7 Consensus size: 42
28120640 TTAGGGTTTC
* *
28120650 TGAGATTACGTGTAAGACCATATCTGGGATATGGCATCGATA
1 TGAGATTACGTGTAAGACCATATCTGGGACATTGCATCGATA
* *
28120692 TGAGAATT-TGTGTAAGACCATGTCTGGGACATTCGCATCGATA
1 TGAG-ATTACGTGTAAGACCATATCTGGGACATT-GCATCGATA
* * ** *
28120735 TGTGATTTCGTGTAAGACCATGGCTGGG-CTATTGACATTGATA
1 TGAGATTACGTGTAAGACCATATCTGGGAC-ATTG-CATCGATA
* *
28120778 CGAGATTACATGTAAGACCATATCTGGGA
1 TGAGATTACGTGTAAGACCATATCTGGGA
28120807 TATGGCATTG
Statistics
Matches: 95, Mismatches: 14, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
42 30 0.32
43 65 0.68
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (42 bp):
TGAGATTACGTGTAAGACCATATCTGGGACATTGCATCGATA
Found at i:28134779 original size:57 final size:57
Alignment explanation
Indices: 28134717--28134890 Score: 269
Period size: 57 Copynumber: 3.1 Consensus size: 57
28134707 TTAAACATCT
* * * *
28134717 TATTCTATCATCAATCCATAAGATCATACCAATTTCACAAAGTTCATTTCCATGTCA
1 TATTCTATTATCAATCTATAATATCATACCAATTTCACAAAGTTCATTTCCATGTAA
28134774 TATTCTATTATCAATCTATAATATCATACCAATTTCACAAAGTTCATTTCCATGTAA
1 TATTCTATTATCAATCTATAATATCATACCAATTTCACAAAGTTCATTTCCATGTAA
* * *
28134831 TATTCTATTATCAATCTATAATATCATACCCATTTCACACAA-TTCATTTCAATGTTA
1 TATTCTATTATCAATCTATAATATCATACCAATTTCACA-AAGTTCATTTCCATGTAA
28134888 TAT
1 TAT
28134891 AAAATTAGTT
Statistics
Matches: 109, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
57 107 0.98
58 2 0.02
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.40
Consensus pattern (57 bp):
TATTCTATTATCAATCTATAATATCATACCAATTTCACAAAGTTCATTTCCATGTAA
Found at i:28139624 original size:24 final size:24
Alignment explanation
Indices: 28139585--28139654 Score: 72
Period size: 24 Copynumber: 2.9 Consensus size: 24
28139575 CTCTCTCTCG
*
28139585 AGCCATAT-ACGGGAAGCTCATTC
1 AGCCATGTAACGGGAAGCTCATTC
*
28139608 AGCCATGTAACGGGAAGCTTATTC
1 AGCCATGTAACGGGAAGCTCATTC
* *
28139632 GGGC-TGTATAACGGGAAGCTCAT
1 AGCCATG--TAACGGGAAGCTCAT
28139655 AAGAGCTGTA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
23 9 0.23
24 16 0.41
25 14 0.36
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (24 bp):
AGCCATGTAACGGGAAGCTCATTC
Found at i:28139662 original size:25 final size:25
Alignment explanation
Indices: 28139615--28139665 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
28139605 TTCAGCCATG
* ** *
28139615 TAACGGGAAGCTTATTCGGGCTGTA
1 TAACGGGAAGCTCATAAGAGCTGTA
28139640 TAACGGGAAGCTCATAAGAGCTGTA
1 TAACGGGAAGCTCATAAGAGCTGTA
28139665 T
1 T
28139666 TTAAGAAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (25 bp):
TAACGGGAAGCTCATAAGAGCTGTA
Found at i:28148805 original size:333 final size:333
Alignment explanation
Indices: 28148199--28148867 Score: 1293
Period size: 333 Copynumber: 2.0 Consensus size: 333
28148189 TACACCGTAA
28148199 TTGATTGTTCTATAAAGGCTGATGTTGGATATGCCACGATCTATGTAGAGGGATATGGTTGATCG
1 TTGATTGTTCTATAAAGGCTGATGTTGGATATGCCACGATCTATGTAGAGGGATATGGTTGATCG
28148264 ATATAGGATAAGTCCCTCCTACATAATGGGAGTAATATCTTAGGCCACTTGATTGAGTGAGACTA
66 ATATAGGATAAGTCCCTCCTACATAATGGGAGTAATATCTTAGGCCACTTGATTGAGTGAGACTA
*
28148329 GAAATGCATGGCCATGCTCAAATAAGCTGATATGAGATGTTGTACTTATTTGTATATCATAGTCT
131 GAAATGCATGGCCATGCTCAAATAAGCTGATATGAGATGTTGTACTTATTTGTATACCATAGTCT
28148394 ACTCAAGATATCAAGGAACATGGGATGGACTATGCAAGTGTGACTATTCCATAACTTGTGTCCAT
196 ACTCAAGATATCAAGGAACATGGGATGGACTATGCAAGTGTGACTATTCCATAACTTGTGTCCAT
28148459 CCCAGAGATAAAGGACTTAAGGATTAATGCATAAATGGTTAATCACAAAAAGGTTATGTTGAATC
261 CCCAGAGATAAAGGACTTAAGGATTAATGCATAAATGGTTAATCACAAAAAGGTTATGTTGAATC
28148524 ATGTTATC
326 ATGTTATC
*
28148532 TTGATTGTTCTATAAAGGTTGATGTTGGATATGCCACGATCTATGTAGAGGGATATGGTTGATCG
1 TTGATTGTTCTATAAAGGCTGATGTTGGATATGCCACGATCTATGTAGAGGGATATGGTTGATCG
28148597 ATATAGGATAAGTCCCTCCTACATAATGGGAGTAATATCTTAGGCCACTTGATTGAGTGAGACTA
66 ATATAGGATAAGTCCCTCCTACATAATGGGAGTAATATCTTAGGCCACTTGATTGAGTGAGACTA
*
28148662 GAAATGCATGGGCATGCTCAAATAAGCTGATATGAGATGTTGTACTTATTTGTATACCATAGTCT
131 GAAATGCATGGCCATGCTCAAATAAGCTGATATGAGATGTTGTACTTATTTGTATACCATAGTCT
28148727 ACTCAAGATATCAAGGAACATGGGATGGACTATGCAAGTGTGACTATTCCATAACTTGTGTCCAT
196 ACTCAAGATATCAAGGAACATGGGATGGACTATGCAAGTGTGACTATTCCATAACTTGTGTCCAT
*
28148792 CCCAGAGATAAAGGACTTAAGGATTAATGCATAAATGGTTAATCGCAAAAAGGTTATGTTGAATC
261 CCCAGAGATAAAGGACTTAAGGATTAATGCATAAATGGTTAATCACAAAAAGGTTATGTTGAATC
*
28148857 ATGTTTTC
326 ATGTTATC
28148865 TTG
1 TTG
28148868 TAACTTAGGT
Statistics
Matches: 331, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
333 331 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (333 bp):
TTGATTGTTCTATAAAGGCTGATGTTGGATATGCCACGATCTATGTAGAGGGATATGGTTGATCG
ATATAGGATAAGTCCCTCCTACATAATGGGAGTAATATCTTAGGCCACTTGATTGAGTGAGACTA
GAAATGCATGGCCATGCTCAAATAAGCTGATATGAGATGTTGTACTTATTTGTATACCATAGTCT
ACTCAAGATATCAAGGAACATGGGATGGACTATGCAAGTGTGACTATTCCATAACTTGTGTCCAT
CCCAGAGATAAAGGACTTAAGGATTAATGCATAAATGGTTAATCACAAAAAGGTTATGTTGAATC
ATGTTATC
Found at i:28152138 original size:20 final size:20
Alignment explanation
Indices: 28152025--28152129 Score: 124
Period size: 20 Copynumber: 5.2 Consensus size: 20
28152015 GTAAATTATA
28152025 CCCTGATTGCACTTACGTGC
1 CCCTGATTGCACTTACGTGC
* * *
28152045 CCCTGTTTGTACTT-CGGTAC
1 CCCTGATTGCACTTAC-GTGC
*
28152065 CCCTAATTGCACTTACGTGC
1 CCCTGATTGCACTTACGTGC
* *
28152085 CCCTGTTTGTACTT-CAGTGC
1 CCCTGATTGCACTTAC-GTGC
28152105 CCCTGATTGCACTTACGTGC
1 CCCTGATTGCACTTACGTGC
28152125 CCCTG
1 CCCTG
28152130 TTTGTACTTC
Statistics
Matches: 69, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
19 2 0.03
20 65 0.94
21 2 0.03
ACGTcount: A:0.13, C:0.34, G:0.19, T:0.33
Consensus pattern (20 bp):
CCCTGATTGCACTTACGTGC
Found at i:28152149 original size:20 final size:20
Alignment explanation
Indices: 28152041--28152140 Score: 105
Period size: 20 Copynumber: 5.0 Consensus size: 20
28152031 TTGCACTTAC
*
28152041 GTGCCCCTGTTTGTACTTCG
1 GTGCCCCTGTTTGTACTTCA
* ** *
28152061 GTACCCCTAATTGCACTT-A
1 GTGCCCCTGTTTGTACTTCA
28152080 CGTGCCCCTGTTTGTACTTCA
1 -GTGCCCCTGTTTGTACTTCA
* *
28152101 GTGCCCCTGATTGCACTT-A
1 GTGCCCCTGTTTGTACTTCA
28152120 CGTGCCCCTGTTTGTACTTCA
1 -GTGCCCCTGTTTGTACTTCA
28152141 ATACCCCTGA
Statistics
Matches: 63, Mismatches: 13, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
19 1 0.02
20 60 0.95
21 2 0.03
ACGTcount: A:0.13, C:0.32, G:0.19, T:0.36
Consensus pattern (20 bp):
GTGCCCCTGTTTGTACTTCA
Found at i:28152168 original size:40 final size:40
Alignment explanation
Indices: 28152025--28152156 Score: 203
Period size: 40 Copynumber: 3.3 Consensus size: 40
28152015 GTAAATTATA
* *
28152025 CCCTGATTGCACTTACGTGCCCCTGTTTGTACTTCGGTAC
1 CCCTGAATGCACTTACGTGCCCCTGTTTGTACTTCAGTAC
*
28152065 CCCT-AATTGCACTTACGTGCCCCTGTTTGTACTTCAGTGC
1 CCCTGAA-TGCACTTACGTGCCCCTGTTTGTACTTCAGTAC
* *
28152105 CCCTGATTGCACTTACGTGCCCCTGTTTGTACTTCAATAC
1 CCCTGAATGCACTTACGTGCCCCTGTTTGTACTTCAGTAC
28152145 CCCTGAATGCAC
1 CCCTGAATGCAC
28152157 ATCGGTTCCC
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
39 1 0.01
40 81 0.98
41 1 0.01
ACGTcount: A:0.16, C:0.33, G:0.17, T:0.33
Consensus pattern (40 bp):
CCCTGAATGCACTTACGTGCCCCTGTTTGTACTTCAGTAC
Found at i:28152204 original size:80 final size:80
Alignment explanation
Indices: 28152025--28152178 Score: 222
Period size: 80 Copynumber: 1.9 Consensus size: 80
28152015 GTAAATTATA
** * *
28152025 CCCTGATTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTAATTGCACTTACGTGCCCCTG
1 CCCTGATTGCACTTACGTGCCCCTGTTTGTACTTCAATACCCCTAATTGCACATACGTGCCCCTA
*
28152090 TTTGTACTTCAGTGC
66 TTTGCACTTCAGTGC
*
28152105 CCCTGATTGCACTTACGTGCCCCTGTTTGTACTTCAATACCCCTGAA-TGCACAT-CGGTTCCCC
1 CCCTGATTGCACTTACGTGCCCCTGTTTGTACTTCAATACCCCT-AATTGCACATAC-GTGCCCC
28152168 TATTTGCACTT
64 TATTTGCACTT
28152179 TGATTCCCCT
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
79 1 0.02
80 63 0.95
81 2 0.03
ACGTcount: A:0.16, C:0.33, G:0.17, T:0.34
Consensus pattern (80 bp):
CCCTGATTGCACTTACGTGCCCCTGTTTGTACTTCAATACCCCTAATTGCACATACGTGCCCCTA
TTTGCACTTCAGTGC
Found at i:28154204 original size:15 final size:16
Alignment explanation
Indices: 28154175--28154205 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28154165 GGGACAATAT
28154175 CTATGTTATTGATTGA
1 CTATGTTATTGATTGA
28154191 CTATGTTA-TGATTGA
1 CTATGTTATTGATTGA
28154206 TGTTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.26, C:0.06, G:0.19, T:0.48
Consensus pattern (16 bp):
CTATGTTATTGATTGA
Found at i:28155188 original size:18 final size:18
Alignment explanation
Indices: 28155165--28155200 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
28155155 TCATCATTTT
28155165 GTTTAAACTTT-AACTTTA
1 GTTTAAA-TTTAAACTTTA
28155183 GTTTAAATTTAAACTTTA
1 GTTTAAATTTAAACTTTA
28155201 ATTAAGTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.18
18 14 0.82
ACGTcount: A:0.36, C:0.08, G:0.06, T:0.50
Consensus pattern (18 bp):
GTTTAAATTTAAACTTTA
Found at i:28155214 original size:24 final size:24
Alignment explanation
Indices: 28155166--28155212 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
28155156 CATCATTTTG
* *
28155166 TTTAAACTTTAACTTTAGTTTAAA
1 TTTAAACTTTAACTTAAGTTAAAA
28155190 TTTAAACTTTAA-TTAAGTTAAAA
1 TTTAAACTTTAACTTAAGTTAAAA
28155213 ATCTTATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (24 bp):
TTTAAACTTTAACTTAAGTTAAAA
Found at i:28161374 original size:57 final size:57
Alignment explanation
Indices: 28161306--28161420 Score: 162
Period size: 57 Copynumber: 2.0 Consensus size: 57
28161296 ACTCATCTCA
* *
28161306 AATATCATATTCTATCATCAATCCATAAGA-TAATAC-CAATTTCACATAGTTCATTTC
1 AATATCATATTCTATCATCAATCCATAAGAGT-ATACAC-ATTTCACACAATTCATTTC
* *
28161363 AATATCATATTCTATTATCAATCTATAAGAGTATACACATTTCACACAATTCATTTC
1 AATATCATATTCTATCATCAATCCATAAGAGTATACACATTTCACACAATTCATTTC
28161420 A
1 A
28161421 TTGTTATATC
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
57 50 0.96
58 2 0.04
ACGTcount: A:0.39, C:0.20, G:0.03, T:0.37
Consensus pattern (57 bp):
AATATCATATTCTATCATCAATCCATAAGAGTATACACATTTCACACAATTCATTTC
Found at i:28163486 original size:4 final size:4
Alignment explanation
Indices: 28163477--28163511 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
28163467 TTTTGCTTTC
*
28163477 AATA AATA AATA TATA AATA AA-A AATA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA
28163512 TATTAAGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 3 0.11
4 25 0.89
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:28163711 original size:164 final size:164
Alignment explanation
Indices: 28163528--28163858 Score: 549
Period size: 164 Copynumber: 2.0 Consensus size: 164
28163518 GTTTTAAGTC
28163528 TAAAATTAACAAATTTAATCTTATTTGATTCAAAATAAAAATTAAAACAATTAAATTAAAGGGTA
1 TAAAATTAACAAATTTAATCTTATTTGATTCAAAATAAAAATTAAAACAATTAAATTAAA-GGTA
* *
28163593 ACCCTATACCCATGGTCACTCTAAAATAGGGTTTGTCATATTTTGGTCACTC-AA-TTTTTTTCT
65 A-CCTATACCCATGGTCACTCTAAAATAGAGTTTATCATATTTTGGTCACTCAAATTTTTTTTCT
*
28163656 CAATTTAGTCACCTTAATTAAGATAATTGTTTGAAT
129 CAATTTAGTAACCTTAATTAAGATAATTGTTTGAAT
* *
28163692 TAAACTTAACAAATTTAATCTTATTTGCTTCAAAATAAAAATTAAAACAATTAAATTAAAGGTAA
1 TAAAATTAACAAATTTAATCTTATTTGATTCAAAATAAAAATTAAAACAATTAAATTAAAGGTAA
* *
28163757 CTTATGCCCATGGTCACTCTAAAATAGAGTTTATCATATTTTGGTCACTCTAAATTTTTTTTCTC
66 CCTATACCCATGGTCACTCTAAAATAGAGTTTATCATATTTTGGTCACTC-AAATTTTTTTTCTC
*
28163822 AATTTAGTAACCTTAATTAAGATGATTGTTTGAAT
130 AATTTAGTAACCTTAATTAAGATAATTGTTTGAAT
28163857 TA
1 TA
28163859 GTCACTATCG
Statistics
Matches: 156, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
162 46 0.29
163 5 0.03
164 60 0.38
165 45 0.29
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.39
Consensus pattern (164 bp):
TAAAATTAACAAATTTAATCTTATTTGATTCAAAATAAAAATTAAAACAATTAAATTAAAGGTAA
CCTATACCCATGGTCACTCTAAAATAGAGTTTATCATATTTTGGTCACTCAAATTTTTTTTCTCA
ATTTAGTAACCTTAATTAAGATAATTGTTTGAAT
Found at i:28165930 original size:78 final size:75
Alignment explanation
Indices: 28165796--28165972 Score: 255
Period size: 78 Copynumber: 2.3 Consensus size: 75
28165786 TACGTGAAGT
* * *
28165796 CTTTGTGGTGAATTATCTGATAAGCCTTTGTGGCAAATCATCTGATAAGCCTTTGTGGTGCTGAA
1 CTTTATGGTGAATCATCTGATAAGCCTTTGTGGCAAATCATCTGATAAGCCTTTGT-G-GC-AAA
*
28165861 TCATCTGATAAGC
63 TCATCTGATAAAC
* * *
28165874 CTTTATGGTGAATCATTTGATAAGCCTTTGTGGCGAATCATCTGATAAGCCTTTGTGGCAAATTA
1 CTTTATGGTGAATCATCTGATAAGCCTTTGTGGCAAATCATCTGATAAGCCTTTGTGGCAAATCA
28165939 TCTGATAAAC
66 TCTGATAAAC
*
28165949 CTCTATGGTGAATCATCTGATAAG
1 CTTTATGGTGAATCATCTGATAAG
28165973 TCTCTGCAGT
Statistics
Matches: 90, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
75 35 0.39
76 2 0.02
77 1 0.01
78 52 0.58
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (75 bp):
CTTTATGGTGAATCATCTGATAAGCCTTTGTGGCAAATCATCTGATAAGCCTTTGTGGCAAATCA
TCTGATAAAC
Found at i:28165977 original size:25 final size:25
Alignment explanation
Indices: 28165796--28165972 Score: 219
Period size: 25 Copynumber: 7.0 Consensus size: 25
28165786 TACGTGAAGT
*
28165796 CTTTGTGGTGAATTATCTGATAAGC
1 CTTTGTGGTGAATCATCTGATAAGC
**
28165821 CTTTGTGGCAAATCATCTGATAAGC
1 CTTTGTGGTGAATCATCTGATAAGC
28165846 CTTTGTGGTGCTGAATCATCTGATAAGC
1 CTTTGT-G-G-TGAATCATCTGATAAGC
* *
28165874 CTTTATGGTGAATCATTTGATAAGC
1 CTTTGTGGTGAATCATCTGATAAGC
*
28165899 CTTTGTGGCGAATCATCTGATAAGC
1 CTTTGTGGTGAATCATCTGATAAGC
** * *
28165924 CTTTGTGGCAAATTATCTGATAAAC
1 CTTTGTGGTGAATCATCTGATAAGC
* *
28165949 CTCTATGGTGAATCATCTGATAAG
1 CTTTGTGGTGAATCATCTGATAAG
28165973 TCTCTGCAGT
Statistics
Matches: 130, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
25 106 0.82
26 2 0.02
27 2 0.02
28 20 0.15
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (25 bp):
CTTTGTGGTGAATCATCTGATAAGC
Found at i:28173768 original size:35 final size:35
Alignment explanation
Indices: 28173713--28173782 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
28173703 CACACGAGGA
28173713 AGGATTAGCACCCTCAATACGCCCAAAATTGGTAC
1 AGGATTAGCACCCTCAATACGCCCAAAATTGGTAC
* *
28173748 AGGATTAGCACTCTCGATACGCCCAAAATTGGTAC
1 AGGATTAGCACCCTCAATACGCCCAAAATTGGTAC
28173783 CTAGTTGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (35 bp):
AGGATTAGCACCCTCAATACGCCCAAAATTGGTAC
Found at i:28176885 original size:38 final size:38
Alignment explanation
Indices: 28176842--28176921 Score: 160
Period size: 38 Copynumber: 2.1 Consensus size: 38
28176832 TACCTTACGC
28176842 TGAATGTTTATCTCTCGGGATGTTACCTTTTTTGAGAA
1 TGAATGTTTATCTCTCGGGATGTTACCTTTTTTGAGAA
28176880 TGAATGTTTATCTCTCGGGATGTTACCTTTTTTGAGAA
1 TGAATGTTTATCTCTCGGGATGTTACCTTTTTTGAGAA
28176918 TGAA
1 TGAA
28176922 CAATACTTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.23, C:0.12, G:0.21, T:0.44
Consensus pattern (38 bp):
TGAATGTTTATCTCTCGGGATGTTACCTTTTTTGAGAA
Found at i:28179056 original size:13 final size:13
Alignment explanation
Indices: 28179038--28179063 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28179028 CTTAGGAAGT
28179038 TACTGATTTTTAG
1 TACTGATTTTTAG
28179051 TACTGATTTTTAG
1 TACTGATTTTTAG
28179064 GGATTGTTTC
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:0.23, C:0.08, G:0.15, T:0.54
Consensus pattern (13 bp):
TACTGATTTTTAG
Found at i:28179315 original size:3 final size:3
Alignment explanation
Indices: 28179295--28179352 Score: 53
Period size: 3 Copynumber: 19.3 Consensus size: 3
28179285 ACAATTTAAC
* * * * * *
28179295 AAT AAT ATT AAT ATT AAT AAT AAT GAT GAT GAT GAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
28179343 AAA AAT AAT A
1 AAT AAT AAT A
28179353 GAAATCTAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:28180030 original size:32 final size:33
Alignment explanation
Indices: 28179969--28180034 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
28179959 CTTATTTAAA
28179969 CCAAATTTTTTTCTAAAAACTTCATTTTTTTTC
1 CCAAATTTTTTTCTAAAAACTTCATTTTTTTTC
*
28180002 CCAATTTTTTTTCTAAAAACTTCATTTTTTTTC
1 CCAAATTTTTTTCTAAAAACTTCATTTTTTTTC
28180035 TTCTTTCTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.26, C:0.18, G:0.00, T:0.56
Consensus pattern (33 bp):
CCAAATTTTTTTCTAAAAACTTCATTTTTTTTC
Found at i:28182641 original size:28 final size:28
Alignment explanation
Indices: 28182588--28182641 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
28182578 TACTTTTCCC
**
28182588 CAAAACTTTTACTCCCTCACTTTCCCCT
1 CAAAACTTTTACTCCCTCACCATCCCCT
*
28182616 CAAAACTTTTACTATCCTC-CCATCCC
1 CAAAACTTTTACT-CCCTCACCATCCC
28182642 ACCCCCCTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
28 18 0.82
29 4 0.18
ACGTcount: A:0.24, C:0.43, G:0.00, T:0.33
Consensus pattern (28 bp):
CAAAACTTTTACTCCCTCACCATCCCCT
Found at i:28183584 original size:21 final size:21
Alignment explanation
Indices: 28183531--28183573 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
28183521 ACATGTATGC
28183531 AAAATTAAAATATATTTTTTT
1 AAAATTAAAATATATTTTTTT
28183552 AAAATTAAAATATATTTTTTT
1 AAAATTAAAATATATTTTTTT
28183573 A
1 A
28183574 TATTTTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AAAATTAAAATATATTTTTTT
Found at i:28183613 original size:26 final size:26
Alignment explanation
Indices: 28183562--28183613 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
28183552 AAAATTAAAA
* * * *
28183562 TATATTTTTTTATATTTTTAATAATT
1 TATAATTTTTTAAATTTTAAAAAATT
28183588 TATAATTTTTTAAATTTTAAAAAATT
1 TATAATTTTTTAAATTTTAAAAAATT
28183614 AATTAATTAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (26 bp):
TATAATTTTTTAAATTTTAAAAAATT
Found at i:28190970 original size:3 final size:3
Alignment explanation
Indices: 28190962--28190998 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
28190952 AATTAGGCAA
28190962 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
28190999 AAACAAAGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:28191499 original size:6 final size:6
Alignment explanation
Indices: 28191483--28191518 Score: 54
Period size: 6 Copynumber: 5.7 Consensus size: 6
28191473 TTTTTATATT
28191483 TTTTAAA TTTTAA TTTTAA TTTTAA TTTTTAA TTTT
1 TTTT-AA TTTTAA TTTTAA TTTTAA -TTTTAA TTTT
28191519 TATAATTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 18 0.64
7 10 0.36
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTTAA
Found at i:28191501 original size:13 final size:12
Alignment explanation
Indices: 28191483--28191518 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 12
28191473 TTTTTATATT
28191483 TTTTAAATTTTAA
1 TTTT-AATTTTAA
28191496 TTTTAATTTTAA
1 TTTTAATTTTAA
28191508 TTTTTAATTTT
1 -TTTTAATTTT
28191519 TATAATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 8 0.36
13 14 0.64
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTAATTTTAA
Found at i:28191519 original size:7 final size:7
Alignment explanation
Indices: 28191482--28191520 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
28191472 CTTTTTATAT
28191482 TTTTTAA
1 TTTTTAA
*
28191489 ATTTTAA
1 TTTTTAA
28191496 -TTTTAA
1 TTTTTAA
28191502 -TTTTAA
1 TTTTTAA
28191508 TTTTTAA
1 TTTTTAA
28191515 TTTTTA
1 TTTTTA
28191521 TAATTTTTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
6 12 0.40
7 18 0.60
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
TTTTTAA
Found at i:28196925 original size:30 final size:31
Alignment explanation
Indices: 28196891--28196949 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
28196881 ATTTTTATGC
*
28196891 TTTTAT-ACTTTTTGACTTTTTAAAATAATT
1 TTTTATAACTTTTTGAATTTTTAAAATAATT
*
28196921 TTTTATAATTTTTTGAATTTTTAAAATAA
1 TTTTATAACTTTTTGAATTTTTAAAATAA
28196950 AAAACCAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 6 0.23
31 20 0.77
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (31 bp):
TTTTATAACTTTTTGAATTTTTAAAATAATT
Found at i:28197850 original size:30 final size:31
Alignment explanation
Indices: 28197814--28197879 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
28197804 AATTATATGT
* * *
28197814 AAATTTTAATT-TGATATGATTATATTCATG
1 AAATTTTAATTGTGATATAAATATATACATG
* *
28197844 AAATTTTGATTGTGATCTAAATATATACATG
1 AAATTTTAATTGTGATATAAATATATACATG
28197875 AAATT
1 AAATT
28197880 ATCATTTTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 10 0.33
31 20 0.67
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (31 bp):
AAATTTTAATTGTGATATAAATATATACATG
Found at i:28198226 original size:21 final size:21
Alignment explanation
Indices: 28198185--28198228 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
28198175 AGAAATATAT
**
28198185 AAAAATATATAAATATTTTTA
1 AAAAATATATAAATAAATTTA
28198206 AAAAATATA-ATAATAAATTTA
1 AAAAATATATA-AATAAATTTA
28198227 AA
1 AA
28198229 TTTTATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AAAAATATATAAATAAATTTA
Found at i:28199922 original size:17 final size:18
Alignment explanation
Indices: 28199874--28199922 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
28199864 TAATTAATTA
28199874 ATTTTAAATCATATATTTC
1 ATTTTAAATC-TATATTTC
*
28199893 ATTATT-TAT-TATATTT-
1 ATT-TTAAATCTATATTTC
28199909 ATTTTAAATCTATA
1 ATTTTAAATCTATA
28199923 ATTTGTGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
15 2 0.08
16 5 0.20
17 11 0.44
19 5 0.20
20 2 0.08
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTTAAATCTATATTTC
Found at i:28200458 original size:9 final size:8
Alignment explanation
Indices: 28200430--28200482 Score: 54
Period size: 9 Copynumber: 6.4 Consensus size: 8
28200420 TAATAAAAAA
28200430 TTTATAAT
1 TTTATAAT
*
28200438 TTTAAAATT
1 TTTATAA-T
28200447 TTTATAACT
1 TTTATAA-T
*
28200456 TTTATATT
1 TTTATAAT
28200464 TTTAATAAT
1 TTT-ATAAT
28200473 TTTA-AAT
1 TTTATAAT
28200480 TTT
1 TTT
28200483 TAAAAGAGCT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
7 6 0.16
8 11 0.29
9 21 0.55
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (8 bp):
TTTATAAT
Found at i:28200464 original size:17 final size:16
Alignment explanation
Indices: 28200430--28200484 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 16
28200420 TAATAAAAAA
28200430 TTTATAATTTTAAAATT
1 TTTATAATTTT-AAATT
*
28200447 TTTATAACTTTTATATT
1 TTTATAA-TTTTAAATT
28200464 TTTAATAATTTTAAATT
1 TTT-ATAATTTTAAATT
28200481 TTTA
1 TTTA
28200485 AAAGAGCTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
16 1 0.03
17 25 0.74
18 8 0.24
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTATAATTTTAAATT
Found at i:28202605 original size:5 final size:5
Alignment explanation
Indices: 28202595--28202628 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
28202585 TCAGACACTA
28202595 AATCT AATCT AATCT AATCT AATCT AATCT AATC
1 AATCT AATCT AATCT AATCT AATCT AATCT AATC
28202629 ATTTTCTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (5 bp):
AATCT
Found at i:28211120 original size:19 final size:20
Alignment explanation
Indices: 28211083--28211130 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
28211073 TCCTTTCTCG
* * *
28211083 TTCTCCTTCCTTTTGTTCTT
1 TTCTCTTTCTTTTTCTTCTT
28211103 TTCT-TTTCTTTTTCTTCTT
1 TTCTCTTTCTTTTTCTTCTT
28211122 TTCTCTTTC
1 TTCTCTTTC
28211131 GCTATATAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.00, C:0.27, G:0.02, T:0.71
Consensus pattern (20 bp):
TTCTCTTTCTTTTTCTTCTT
Found at i:28220826 original size:8 final size:8
Alignment explanation
Indices: 28220809--28220838 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
28220799 GTCTTTAAAG
*
28220809 GGTAACAT
1 GGTAAAAT
28220817 GGTAAAAT
1 GGTAAAAT
28220825 GGTAAAAT
1 GGTAAAAT
28220833 GGTAAA
1 GGTAAA
28220839 TAAGGATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.47, C:0.03, G:0.27, T:0.23
Consensus pattern (8 bp):
GGTAAAAT
Found at i:28222047 original size:22 final size:22
Alignment explanation
Indices: 28222019--28222061 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
28222009 CTTATGGCTA
28222019 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTC
28222041 ACGTACTAAGCTCTCATGTTT
1 ACGTACTAAGCTCTCATGTTT
28222062 GAACAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTC
Found at i:28222915 original size:13 final size:13
Alignment explanation
Indices: 28222894--28222938 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
28222884 ACGGCCTGGC
28222894 ACACGGGCGTGTG
1 ACACGGGCGTGTG
* *
28222907 ACCCGGGCGTGAG
1 ACACGGGCGTGTG
**
28222920 ACACGATCGTGTG
1 ACACGGGCGTGTG
28222933 ACACGG
1 ACACGG
28222939 TCTGTGACCC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.20, C:0.27, G:0.40, T:0.13
Consensus pattern (13 bp):
ACACGGGCGTGTG
Found at i:28224135 original size:31 final size:29
Alignment explanation
Indices: 28224097--28224171 Score: 96
Period size: 31 Copynumber: 2.5 Consensus size: 29
28224087 GATCATTGGC
*
28224097 TAATGAAAAGGGATACCTTCGGTTATCAAAA
1 TAATGAAAAGGGATACC-TCGGCTATC-AAA
*
28224128 TAATGAAAAGGGATTGCCTCGGCTATCAAA
1 TAATGAAAAGGGA-TACCTCGGCTATCAAA
*
28224158 TTATGAAAAGGGAT
1 TAATGAAAAGGGAT
28224172 GGTAACGAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
29 1 0.03
30 15 0.38
31 21 0.52
32 3 0.08
ACGTcount: A:0.40, C:0.12, G:0.23, T:0.25
Consensus pattern (29 bp):
TAATGAAAAGGGATACCTCGGCTATCAAA
Found at i:28224166 original size:30 final size:30
Alignment explanation
Indices: 28224099--28224321 Score: 123
Period size: 30 Copynumber: 7.4 Consensus size: 30
28224089 TCATTGGCTA
* *
28224099 ATGAAAAGGGATA-CCTTCGGTTATCAAAATA
1 ATGAAAAGGGATAGCC-TCGGCTATC-AAATT
*
28224130 ATGAAAAGGGATTGCCTCGGCTATCAAATT
1 ATGAAAAGGGATAGCCTCGGCTATCAAATT
* *** * *
28224160 ATGAAAAGGGATGGTAACGAAAC-ATC-AATA
1 ATGAAAAGGGATAGCCTCG--GCTATCAAATT
* ** * * **
28224190 ATGAAAAGGGATGGTGAT-GGCCATCGAACA
1 ATGAAAAGGGATAG-CCTCGGCTATCAAATT
*
28224220 ATGAAAAGGGATAG-CTCTGGCTATCGAATT
1 ATGAAAAGGGATAGCCTC-GGCTATCAAATT
* * * * *
28224250 GTGATAAGGGATAGCTTCGGTTATCGAATT
1 ATGAAAAGGGATAGCCTCGGCTATCAAATT
* * * *
28224280 GTGAAAAGGGATAACTTCAGCTATCAAATT
1 ATGAAAAGGGATAGCCTCGGCTATCAAATT
28224310 ATGAAAAGGGAT
1 ATGAAAAGGGAT
28224322 GGTGAAGGCC
Statistics
Matches: 155, Mismatches: 28, Indels: 19
0.77 0.14 0.09
Matches are distributed among these distances:
28 2 0.01
29 3 0.02
30 121 0.78
31 26 0.17
32 3 0.02
ACGTcount: A:0.38, C:0.12, G:0.26, T:0.24
Consensus pattern (30 bp):
ATGAAAAGGGATAGCCTCGGCTATCAAATT
Found at i:28224259 original size:60 final size:60
Alignment explanation
Indices: 28224190--28224350 Score: 159
Period size: 60 Copynumber: 2.7 Consensus size: 60
28224180 AACATCAATA
* * * *
28224190 ATGAAAAGGGATGGTGATGGCCATCGAACAATGAAAAGGGATAGC-TCTGGCTATCGAATT
1 ATGAAAAGGGATGGTGATGGCCATCGAATAATGAAAAGGGATAACTTC-AGCTATCAAATT
* * * ** **
28224250 GTGATAAGGGATAGCT--TCGGTTATCGAATTGTGAAAAGGGATAACTTCAGCTATCAAATT
1 ATGAAAAGGGAT-GGTGAT-GGCCATCGAATAATGAAAAGGGATAACTTCAGCTATCAAATT
*
28224310 ATGAAAAGGGATGGTGAAGGCCATC-AATAATGAAAAGGGAT
1 ATGAAAAGGGATGGTGATGGCCATCGAATAATGAAAAGGGAT
28224351 GGTGACGACC
Statistics
Matches: 77, Mismatches: 19, Indels: 11
0.72 0.18 0.10
Matches are distributed among these distances:
59 17 0.22
60 56 0.73
61 4 0.05
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (60 bp):
ATGAAAAGGGATGGTGATGGCCATCGAATAATGAAAAGGGATAACTTCAGCTATCAAATT
Found at i:28224351 original size:29 final size:30
Alignment explanation
Indices: 28224302--28224380 Score: 124
Period size: 29 Copynumber: 2.7 Consensus size: 30
28224292 AACTTCAGCT
* *
28224302 ATCAAATTATGAAAAGGGATGGTGAAGGCC
1 ATCAAATAATGAAAAGGGATGGTGAAGACC
*
28224332 ATC-AATAATGAAAAGGGATGGTGACGACC
1 ATCAAATAATGAAAAGGGATGGTGAAGACC
28224361 ATCAAATAATGAAAAGGGAT
1 ATCAAATAATGAAAAGGGAT
28224381 AGCTTCGACT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
29 26 0.58
30 19 0.42
ACGTcount: A:0.44, C:0.10, G:0.27, T:0.19
Consensus pattern (30 bp):
ATCAAATAATGAAAAGGGATGGTGAAGACC
Found at i:28224376 original size:149 final size:150
Alignment explanation
Indices: 28224103--28224425 Score: 420
Period size: 149 Copynumber: 2.2 Consensus size: 150
28224093 TGGCTAATGA
* * ** *
28224103 AAAGGGATACCTTCGGTTATCAAAATAATGAAAAGGGATTGCCTCGGCTATCAAATTATGAAAAG
1 AAAGGGATAGCTTCGGTTATC-GAATAATGAAAAGGGATAACCTCAGCTATCAAATTATGAAAAG
* * *
28224168 GGATGGTAACGAAACATCAATAATGAAAAGGGATGGTGATGGCCATCGAACAATGAAAAGGGATA
65 GGATGGTAACGAAACATCAATAATGAAAAGGGATGGTGACGACCATCAAACAATGAAAAGGGATA
*
28224233 GC-TCTGGCTATCGAATTG-TG
130 GCTTC-GACTATCGAATTGCTG
** *
28224253 ATAAGGGATAGCTTCGGTTATCGAATTGTGAAAAGGGATAACTTCAGCTATCAAATTATGAAAAG
1 A-AAGGGATAGCTTCGGTTATCGAATAATGAAAAGGGATAACCTCAGCTATCAAATTATGAAAAG
** *
28224318 GGATGGTGAA-G-GCCATCAATAATGAAAAGGGATGGTGACGACCATCAAATAATGAAAAGGGAT
65 GGATGGT-AACGAAACATCAATAATGAAAAGGGATGGTGACGACCATCAAACAATGAAAAGGGAT
*
28224381 AGCTTCGACTATCGAGTTGCTG
129 AGCTTCGACTATCGAATTGCTG
* *
28224403 AAAGGGATAGCTTCAGCTATCGA
1 AAAGGGATAGCTTCGGTTATCGA
28224426 GCTATGAAAA
Statistics
Matches: 151, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
149 80 0.53
150 50 0.33
151 21 0.14
ACGTcount: A:0.37, C:0.13, G:0.26, T:0.23
Consensus pattern (150 bp):
AAAGGGATAGCTTCGGTTATCGAATAATGAAAAGGGATAACCTCAGCTATCAAATTATGAAAAGG
GATGGTAACGAAACATCAATAATGAAAAGGGATGGTGACGACCATCAAACAATGAAAAGGGATAG
CTTCGACTATCGAATTGCTG
Found at i:28224432 original size:119 final size:120
Alignment explanation
Indices: 28224190--28224435 Score: 293
Period size: 119 Copynumber: 2.1 Consensus size: 120
28224180 AACATCAATA
* * * * ** *
28224190 ATGAAAAGGGATGGTGATGGCCATCGAACAATGAAAAGGGATAGCTCTGGCTATCGAATTGTGAT
1 ATGAAAAGGGATGGTGAAGGCCATCGAACAATGAAAAGGGATAGCTCTGACCATCAAATAATGAA
** *
28224255 AAGGGATAGCTTCGGTTATCGAATTGTGAAAAGGGATAACTTCAGCTATCAAATT
66 AAGGGATAGCTTCGACTATCGAATTGTGAAAAGGGATAACTTCAGCTATCAAACT
* *
28224310 ATGAAAAGGGATGGTGAAGGCCATC-AATAATGAAAAGGGAT-GGTGAC-GACCATCAAATAATG
1 ATGAAAAGGGATGGTGAAGGCCATCGAACAATGAAAAGGGATAGCT--CTGACCATCAAATAATG
* * * *
28224372 AAAAGGGATAGCTTCGACTATCGAGTTGCTG-AAAGGGATAGCTTCAGCTATCGAGCT
64 AAAAGGGATAGCTTCGACTATCGAATTG-TGAAAAGGGATAACTTCAGCTATCAAACT
28224429 ATGAAAA
1 ATGAAAA
28224436 AGGTTGGGAC
Statistics
Matches: 107, Mismatches: 16, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
118 2 0.02
119 78 0.73
120 27 0.25
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.23
Consensus pattern (120 bp):
ATGAAAAGGGATGGTGAAGGCCATCGAACAATGAAAAGGGATAGCTCTGACCATCAAATAATGAA
AAGGGATAGCTTCGACTATCGAATTGTGAAAAGGGATAACTTCAGCTATCAAACT
Found at i:28229947 original size:12 final size:12
Alignment explanation
Indices: 28229930--28229954 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28229920 GGTGTTCATT
28229930 CGGTTAACCGAC
1 CGGTTAACCGAC
28229942 CGGTTAACCGAC
1 CGGTTAACCGAC
28229954 C
1 C
28229955 CGAAATAACA
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:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:28230130 original size:9 final size:9
Alignment explanation
Indices: 28230116--28230209 Score: 134
Period size: 9 Copynumber: 10.4 Consensus size: 9
28230106 TTTGGTTAAA
28230116 AATTAACCG
1 AATTAACCG
28230125 AATTAACCG
1 AATTAACCG
*
28230134 AATTACCCG
1 AATTAACCG
28230143 AATTAACCG
1 AATTAACCG
*
28230152 AATTACCCG
1 AATTAACCG
*
28230161 AATTACCCG
1 AATTAACCG
28230170 AATTAACCG
1 AATTAACCG
*
28230179 AATTACCCG
1 AATTAACCG
*
28230188 AATTAACCA
1 AATTAACCG
*
28230197 AATTAACCA
1 AATTAACCG
28230206 AATT
1 AATT
28230210 GAATCACTAC
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 78 1.00
ACGTcount: A:0.43, C:0.26, G:0.09, T:0.23
Consensus pattern (9 bp):
AATTAACCG
Found at i:28230154 original size:27 final size:27
Alignment explanation
Indices: 28230116--28230209 Score: 152
Period size: 27 Copynumber: 3.5 Consensus size: 27
28230106 TTTGGTTAAA
*
28230116 AATTAACCGAATTAACCGAATTACCCG
1 AATTAACCGAATTACCCGAATTACCCG
28230143 AATTAACCGAATTACCCGAATTACCCG
1 AATTAACCGAATTACCCGAATTACCCG
* *
28230170 AATTAACCGAATTACCCGAATTAACCA
1 AATTAACCGAATTACCCGAATTACCCG
*
28230197 AATTAACCAAATT
1 AATTAACCGAATT
28230210 GAATCACTAC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 63 1.00
ACGTcount: A:0.43, C:0.26, G:0.09, T:0.23
Consensus pattern (27 bp):
AATTAACCGAATTACCCGAATTACCCG
Found at i:28236668 original size:4 final size:4
Alignment explanation
Indices: 28236649--28236693 Score: 74
Period size: 4 Copynumber: 11.5 Consensus size: 4
28236639 ATTTTCTGGA
*
28236649 AAAT AAAT GAAT -AAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
28236694 GGGGGGCTCG
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
3 3 0.08
4 36 0.92
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:28240018 original size:13 final size:13
Alignment explanation
Indices: 28240000--28240024 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28239990 ACAAACGATA
28240000 AAATTTTCACACG
1 AAATTTTCACACG
28240013 AAATTTTCACAC
1 AAATTTTCACAC
28240025 ATATAAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:28244438 original size:21 final size:22
Alignment explanation
Indices: 28244395--28244439 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
28244385 TTCTGATCTA
* *
28244395 TTCTGCATCTGTATCTGATCTG
1 TTCTGCATCTGTATCTAAACTG
*
28244417 TTCTGCAT-TTTATCTAAACTG
1 TTCTGCATCTGTATCTAAACTG
28244438 TT
1 TT
28244440 ACGATTATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.18, C:0.20, G:0.13, T:0.49
Consensus pattern (22 bp):
TTCTGCATCTGTATCTAAACTG
Found at i:28262098 original size:24 final size:24
Alignment explanation
Indices: 28262059--28262136 Score: 95
Period size: 24 Copynumber: 3.2 Consensus size: 24
28262049 TCCTGAAACC
**
28262059 ATGAAAAGGTTGAAAAGGAT-CCGA
1 ATGAAAAGGTCAAAAAGGATACC-A
*
28262083 ATGAAAAGGTCAAAAAGGTTACCA
1 ATGAAAAGGTCAAAAAGGATACCA
* *
28262107 TTGAAAAGGTCAAAAAGGATATCA
1 ATGAAAAGGTCAAAAAGGATACCA
28262131 ATGAAA
1 ATGAAA
28262137 TGGTTATTAT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
24 44 0.96
25 2 0.04
ACGTcount: A:0.50, C:0.09, G:0.23, T:0.18
Consensus pattern (24 bp):
ATGAAAAGGTCAAAAAGGATACCA
Found at i:28264878 original size:15 final size:15
Alignment explanation
Indices: 28264858--28264889 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
28264848 CGACCCAAAT
28264858 AATCAATAATAATTA
1 AATCAATAATAATTA
28264873 AATCAATAATAATTA
1 AATCAATAATAATTA
28264888 AA
1 AA
28264890 CTAAATTTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (15 bp):
AATCAATAATAATTA
Found at i:28271126 original size:26 final size:27
Alignment explanation
Indices: 28271068--28271127 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 27
28271058 CTACTTACAG
28271068 TAGTTTCAGAATATCATAACATATAAC
1 TAGTTTCAGAATATCATAACATATAAC
* * *
28271095 -AATTTCAGAATATCATAGCATGT-AC
1 TAGTTTCAGAATATCATAACATATAAC
28271120 TAGTTTCA
1 TAGTTTCA
28271128 AAACACTTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
25 2 0.07
26 26 0.93
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (27 bp):
TAGTTTCAGAATATCATAACATATAAC
Found at i:28281057 original size:23 final size:23
Alignment explanation
Indices: 28281030--28281151 Score: 190
Period size: 23 Copynumber: 5.3 Consensus size: 23
28281020 AGTGTTATTG
28281030 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
28281053 TTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
28281076 ATCGGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * *
28281099 TTCAGTGGTAGCTACGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
28281122 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
28281145 ATCAGTG
1 ATCAGTG
28281152 TGGCACTTAT
Statistics
Matches: 87, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 87 1.00
ACGTcount: A:0.20, C:0.21, G:0.28, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:28281101 original size:46 final size:46
Alignment explanation
Indices: 28281030--28281151 Score: 217
Period size: 46 Copynumber: 2.7 Consensus size: 46
28281020 AGTGTTATTG
28281030 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACAT
* *
28281076 ATCGGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACAT
*
28281122 ATCAGTGGTAGCTTCGGCTACATATCAGTG
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTG
28281152 TGGCACTTAT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 72 1.00
ACGTcount: A:0.20, C:0.21, G:0.28, T:0.30
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACAT
Found at i:28282936 original size:27 final size:27
Alignment explanation
Indices: 28282913--28283357 Score: 453
Period size: 27 Copynumber: 16.5 Consensus size: 27
28282903 AGAGGTATAA
**
28282913 CAATCATTTTACCCTAT-TGGGGTATTT
1 CAATCATTTTACCCT-TCAAGGGTATTT
*
28282940 CAGTCATTTTACCCTTCAAGGGTATTT
1 CAATCATTTTACCCTTCAAGGGTATTT
*
28282967 CAATCATTTTACCCTTCGAGGGTATTT
1 CAATCATTTTACCCTTCAAGGGTATTT
** * *
28282994 CGGTCATTTTACCTTTC-GGGGTATTT
1 CAATCATTTTACCCTTCAAGGGTATTT
** **
28283020 TGATCATTTTACCCTTCGGGGGTATTT
1 CAATCATTTTACCCTTCAAGGGTATTT
* **
28283047 CAATTATTTTACCCTTCGGGGGTATTT
1 CAATCATTTTACCCTTCAAGGGTATTT
* *
28283074 CAGTTATTTTACCCTTCAAGGGTATTT
1 CAATCATTTTACCCTTCAAGGGTATTT
* *
28283101 CGATCATTTTACCCTTCGAGGGTATTT
1 CAATCATTTTACCCTTCAAGGGTATTT
* * *
28283128 CAATCATTTTACCTTTCGAGGGTATTG
1 CAATCATTTTACCCTTCAAGGGTATTT
* *
28283155 CAGTCATTTTACCCTTCGAGGGTATTT
1 CAATCATTTTACCCTTCAAGGGTATTT
* *
28283182 CGATCATTTCACCCTTCAAGGGTATTT
1 CAATCATTTTACCCTTCAAGGGTATTT
* * * **
28283209 CGATTATTTTATCCTTCGGGGGTATTT
1 CAATCATTTTACCCTTCAAGGGTATTT
* * *
28283236 CAGTCATTTTACCCTTTAGGGGTATTT
1 CAATCATTTTACCCTTCAAGGGTATTT
*** * *
28283263 TGGTCATTTTACCCCTCGAGGGTATTT
1 CAATCATTTTACCCTTCAAGGGTATTT
* **
28283290 CAGTCATTTTACCCTTCGGGGGTATTT
1 CAATCATTTTACCCTTCAAGGGTATTT
** *
28283317 CGGTCATTTTACCCTTCGAGGGTATTT
1 CAATCATTTTACCCTTCAAGGGTATTT
*
28283344 CAGTCATTTTACCC
1 CAATCATTTTACCC
28283358 ATGAATCATA
Statistics
Matches: 360, Mismatches: 56, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
26 23 0.06
27 337 0.94
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.42
Consensus pattern (27 bp):
CAATCATTTTACCCTTCAAGGGTATTT
Found at i:28282990 original size:54 final size:54
Alignment explanation
Indices: 28282913--28283357 Score: 549
Period size: 54 Copynumber: 8.3 Consensus size: 54
28282903 AGAGGTATAA
* *
28282913 CAATCATTTTACCCTATTG-GGGTATTTCAGTCATTTTACCCTTCAAGGGTATTT
1 CAATCATTTTACCCT-TCGAGGGTATTTCAGTCATTTTACCCTTCGAGGGTATTT
* *
28282967 CAATCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCTTTCG-GGGTATTT
1 CAATCATTTTACCCTTCGAGGGTATTTCAGTCATTTTACCCTTCGAGGGTATTT
** * * * *
28283020 TGATCATTTTACCCTTCGGGGGTATTTCAATTATTTTACCCTTCGGGGGTATTT
1 CAATCATTTTACCCTTCGAGGGTATTTCAGTCATTTTACCCTTCGAGGGTATTT
* * *
28283074 CAGTTATTTTACCCTTCAAGGGTATTTC-GATCATTTTACCCTTCGAGGGTATTT
1 CAATCATTTTACCCTTCGAGGGTATTTCAG-TCATTTTACCCTTCGAGGGTATTT
* *
28283128 CAATCATTTTACCTTTCGAGGGTATTGCAGTCATTTTACCCTTCGAGGGTATTT
1 CAATCATTTTACCCTTCGAGGGTATTTCAGTCATTTTACCCTTCGAGGGTATTT
* * * * * *
28283182 CGATCATTTCACCCTTCAAGGGTATTTC-GATTATTTTATCCTTCGGGGGTATTT
1 CAATCATTTTACCCTTCGAGGGTATTTCAG-TCATTTTACCCTTCGAGGGTATTT
* * ** *
28283236 CAGTCATTTTACCCTT-TAGGGGTATTTTGGTCATTTTACCCCTCGAGGGTATTT
1 CAATCATTTTACCCTTCGA-GGGTATTTCAGTCATTTTACCCTTCGAGGGTATTT
* * *
28283290 CAGTCATTTTACCCTTCGGGGGTATTTCGGTCATTTTACCCTTCGAGGGTATTT
1 CAATCATTTTACCCTTCGAGGGTATTTCAGTCATTTTACCCTTCGAGGGTATTT
*
28283344 CAGTCATTTTACCC
1 CAATCATTTTACCC
28283358 ATGAATCATA
Statistics
Matches: 337, Mismatches: 46, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
53 50 0.15
54 285 0.85
55 2 0.01
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.42
Consensus pattern (54 bp):
CAATCATTTTACCCTTCGAGGGTATTTCAGTCATTTTACCCTTCGAGGGTATTT
Found at i:28283130 original size:81 final size:81
Alignment explanation
Indices: 28282932--28283357 Score: 579
Period size: 81 Copynumber: 5.3 Consensus size: 81
28282922 TACCCTATTG
* * *
28282932 GGGTATTTC-AGTCATTTTACCCTTCAAGGGTATTTCAATCATTTTACCCTTCGAGGGTATTTCG
1 GGGTATTTCGA-TCATTTTACCCTTCGAGGGTATTTCAATCATTTTACCCTTCGGGGGTATTTCA
* *
28282996 GTCATTTTACCTTTC-G
65 GTCATTTTACCCTTCAA
* * *
28283012 GGGTATTTTGATCATTTTACCCTTCGGGGGTATTTCAATTATTTTACCCTTCGGGGGTATTTCAG
1 GGGTATTTCGATCATTTTACCCTTCGAGGGTATTTCAATCATTTTACCCTTCGGGGGTATTTCAG
*
28283077 TTATTTTACCCTTCAA
66 TCATTTTACCCTTCAA
* * *
28283093 GGGTATTTCGATCATTTTACCCTTCGAGGGTATTTCAATCATTTTACCTTTCGAGGGTATTGCAG
1 GGGTATTTCGATCATTTTACCCTTCGAGGGTATTTCAATCATTTTACCCTTCGGGGGTATTTCAG
*
28283158 TCATTTTACCCTTCGA
66 TCATTTTACCCTTCAA
* * * * *
28283174 GGGTATTTCGATCATTTCACCCTTCAAGGGTATTTCGATTATTTTATCCTTCGGGGGTATTTCAG
1 GGGTATTTCGATCATTTTACCCTTCGAGGGTATTTCAATCATTTTACCCTTCGGGGGTATTTCAG
* *
28283239 TCATTTTACCCTTTAG
66 TCATTTTACCCTTCAA
* * * * *
28283255 GGGTATTTTGGTCATTTTACCCCTCGAGGGTATTTCAGTCATTTTACCCTTCGGGGGTATTTCGG
1 GGGTATTTCGATCATTTTACCCTTCGAGGGTATTTCAATCATTTTACCCTTCGGGGGTATTTCAG
*
28283320 TCATTTTACCCTTCGA
66 TCATTTTACCCTTCAA
28283336 GGGTATTTC-AGTCATTTTACCC
1 GGGTATTTCGA-TCATTTTACCC
28283358 ATGAATCATA
Statistics
Matches: 300, Mismatches: 43, Indels: 5
0.86 0.12 0.01
Matches are distributed among these distances:
80 69 0.23
81 231 0.77
ACGTcount: A:0.18, C:0.21, G:0.19, T:0.42
Consensus pattern (81 bp):
GGGTATTTCGATCATTTTACCCTTCGAGGGTATTTCAATCATTTTACCCTTCGGGGGTATTTCAG
TCATTTTACCCTTCAA
Found at i:28285797 original size:19 final size:18
Alignment explanation
Indices: 28285773--28285826 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 18
28285763 CATGTGGCAG
*
28285773 AAAATATAAAAAAATGCTA
1 AAAATATAAAAAAAT-ATA
*
28285792 AAAATATAAAAGAATATA
1 AAAATATAAAAAAATATA
28285810 AAAATATTAGAAAAAAT
1 AAAATA-TA-AAAAAAT
28285827 TATATAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 8 0.27
19 16 0.53
20 6 0.20
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.22
Consensus pattern (18 bp):
AAAATATAAAAAAATATA
Found at i:28287589 original size:6 final size:6
Alignment explanation
Indices: 28287578--28287609 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
28287568 CATACATATC
28287578 GATGAA GATGAA GATGAA GATGAA GATGAA GA
1 GATGAA GATGAA GATGAA GATGAA GATGAA GA
28287610 AAGAAGGTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.34, T:0.16
Consensus pattern (6 bp):
GATGAA
Found at i:28312338 original size:17 final size:17
Alignment explanation
Indices: 28312312--28312345 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28312302 GTTTAGATCA
28312312 TGATACGAGTCACAAAG
1 TGATACGAGTCACAAAG
* *
28312329 TGATATGAGTCATAAAG
1 TGATACGAGTCACAAAG
28312346 GCCCAATCCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.24
Consensus pattern (17 bp):
TGATACGAGTCACAAAG
Found at i:28321771 original size:43 final size:42
Alignment explanation
Indices: 28321697--28321867 Score: 188
Period size: 43 Copynumber: 4.0 Consensus size: 42
28321687 ACATAGGATT
* * *
28321697 TCGATATGTGTTTTCGTGTAAAACCACGTCTGGGACGTTGGCA
1 TCGAT-TGTGTTTACGTGTAAGACCATGTCTGGGACGTTGGCA
*
28321740 TCGACTTGTGTTTACGTGTAAGACCATGTCTGGGACATTGGCA
1 TCGA-TTGTGTTTACGTGTAAGACCATGTCTGGGACGTTGGCA
* *
28321783 TCGTATT-TGATTT--GTGTAAGACCCTGTCTGGGGCAG-TGGCA
1 TCG-ATTGTG-TTTACGTGTAAGACCATGTCTGGGAC-GTTGGCA
* *
28321824 TCGATATGTGATTACATGTAAGACCATGTCTGGGACGTTGGCA
1 TCGAT-TGTGTTTACGTGTAAGACCATGTCTGGGACGTTGGCA
28321867 T
1 T
28321868 TGTACGAGTC
Statistics
Matches: 108, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
40 2 0.02
41 30 0.28
42 5 0.05
43 69 0.64
44 2 0.02
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.33
Consensus pattern (42 bp):
TCGATTGTGTTTACGTGTAAGACCATGTCTGGGACGTTGGCA
Found at i:28322015 original size:16 final size:17
Alignment explanation
Indices: 28321986--28322017 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
28321976 TGAATTGATG
28321986 ATATGAAGTTATGTGAA
1 ATATGAAGTTATGTGAA
28322003 ATATGAA-TTATGTGA
1 ATATGAAGTTATGTGA
28322018 TTGCATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.38
Consensus pattern (17 bp):
ATATGAAGTTATGTGAA
Found at i:28332133 original size:236 final size:237
Alignment explanation
Indices: 28331720--28332202 Score: 817
Period size: 236 Copynumber: 2.0 Consensus size: 237
28331710 AAAGATTGTC
*
28331720 CTTTAAAT-GACCTACAAGTACCGAGAGAAACATAGAAGATAATCCTATACAAATACTATTTGAC
1 CTTTAAATAGACCTACAAGTACCGAGAGAAACATAAAAGATAATCCTATACAAATACTATTTGAC
* * *
28331784 CAGTCAATTCTGTTGGTTCCTAACCAGATCTCATTACCAAAACTTGCTTGACACAGTGTTCAAGC
66 CAGTCAATTCTGTTGGTTCCTAACCAGATCTCATTACCAAAACCTACTTGACACAGCGTTCAAGC
* *
28331849 AAACCAGGCATACTATACCTTTGGCGGTAACCTTTGTAACACCCCTAACCTGTCTTCGTCTCTAG
131 AAACCAGGCATACTATACCTTTGGCGGTAACCTTTGCAACACCCCTAACCCGTCTTCGTCTCTAG
28331914 ATTAGGGTTACAAAGTATTACAGTACAAATCAGAACATTTAA
196 ATTAGGGTTACAAAGTATTACAGTACAAATCAGAACATTTAA
* * *
28331956 CTTTAAATAG-CCTACAAGTATCGAGAGAAACATAAAAGATAATCCTATACATATATTATTTGAC
1 CTTTAAATAGACCTACAAGTACCGAGAGAAACATAAAAGATAATCCTATACAAATACTATTTGAC
28332020 CAGTCAATTCTGTTGGTTCCTAACCAGATCTCATTACCAAAACCTACTTGACACAGCGTTCAAGC
66 CAGTCAATTCTGTTGGTTCCTAACCAGATCTCATTACCAAAACCTACTTGACACAGCGTTCAAGC
* * *
28332085 AAACTAGGCATACTATACCTTTGGCGGTAACCTTTGCAACACCCCTAACCCGTCTTCGTCTTTGG
131 AAACCAGGCATACTATACCTTTGGCGGTAACCTTTGCAACACCCCTAACCCGTCTTCGTCTCTAG
* * *
28332150 ATTAGGGTTACGAAGTATTACAGTACAAATTAGAACATTTAG
196 ATTAGGGTTACAAAGTATTACAGTACAAATCAGAACATTTAA
28332192 CTTTAAATAGA
1 CTTTAAATAGA
28332203 AAGAAATATG
Statistics
Matches: 230, Mismatches: 15, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
236 229 1.00
237 1 0.00
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.29
Consensus pattern (237 bp):
CTTTAAATAGACCTACAAGTACCGAGAGAAACATAAAAGATAATCCTATACAAATACTATTTGAC
CAGTCAATTCTGTTGGTTCCTAACCAGATCTCATTACCAAAACCTACTTGACACAGCGTTCAAGC
AAACCAGGCATACTATACCTTTGGCGGTAACCTTTGCAACACCCCTAACCCGTCTTCGTCTCTAG
ATTAGGGTTACAAAGTATTACAGTACAAATCAGAACATTTAA
Found at i:28344676 original size:15 final size:15
Alignment explanation
Indices: 28344656--28344685 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
28344646 CGAATCACAA
28344656 TAAGGGAGTTGCCTT
1 TAAGGGAGTTGCCTT
28344671 TAAGGGAGTTGCCTT
1 TAAGGGAGTTGCCTT
28344686 CGAAAATCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.33, T:0.33
Consensus pattern (15 bp):
TAAGGGAGTTGCCTT
Found at i:28350372 original size:69 final size:67
Alignment explanation
Indices: 28350279--28350422 Score: 156
Period size: 69 Copynumber: 2.1 Consensus size: 67
28350269 ATGGATTTAA
*
28350279 ATAATATTCAAATTAATTAATATTATGATATTTACTAAGAATATA-AAA-AT-AATTTATTATTT
1 ATAATATT-AAATTAATTAATA-T-T-AT-TTTACTAAGAATATAGAAATATAAATTAATTATTT
28350341 -AAATATC
61 GAAATA-C
28350348 ATAATATT-AATTAATTTGAATATTATTTTACTAAGAATATATGAAATATAAATTAATTATTTGA
1 ATAATATTAAATTAA-TT-AATATTATTTTACTAAGAATATA-GAAATATAAATTAATTATTTGA
28350412 AATAC
63 AATAC
28350417 A-AATAT
1 ATAATAT
28350423 GCATTTAATT
Statistics
Matches: 67, Mismatches: 1, Indels: 15
0.81 0.01 0.18
Matches are distributed among these distances:
65 15 0.22
66 2 0.03
67 10 0.15
68 10 0.15
69 25 0.37
70 5 0.07
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.43
Consensus pattern (67 bp):
ATAATATTAAATTAATTAATATTATTTTACTAAGAATATAGAAATATAAATTAATTATTTGAAAT
AC
Found at i:28354851 original size:18 final size:17
Alignment explanation
Indices: 28354818--28354864 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 17
28354808 ATAATTTGTA
*
28354818 TAATAA-TATATATTAT
1 TAATAATTATATTTTAT
*
28354834 TATTAATTCATATTTTAT
1 TAATAATT-ATATTTTAT
28354852 TAATAATTATATT
1 TAATAATTATATT
28354865 AAAAATGTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 5 0.19
17 6 0.23
18 15 0.58
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (17 bp):
TAATAATTATATTTTAT
Found at i:28354925 original size:58 final size:58
Alignment explanation
Indices: 28354828--28354974 Score: 158
Period size: 58 Copynumber: 2.5 Consensus size: 58
28354818 TAATAATATA
* * *
28354828 TATTATTATT-AATTCATATTTTATTAATAATTATATTAAAA-ATGTTATTAAATTATATGT
1 TATTTTTATTAAATT-ATA-TTTAATAATAATTATATTAAAATATG--ATCAAATTATATGT
* * * *
28354888 TA-TTTTATTAAAATT-TATTTAATAATAATTATGTTAAAATATGATCGAATTATTTTT
1 TATTTTTATT-AAATTATATTTAATAATAATTATATTAAAATATGATCAAATTATATGT
28354945 TATTTTTATTAAATTATATTTAATAATAAT
1 TATTTTTATTAAATTATATTTAATAATAAT
28354975 CTTTTTAAAA
Statistics
Matches: 75, Mismatches: 7, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
57 17 0.23
58 41 0.55
59 11 0.15
60 2 0.03
61 4 0.05
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (58 bp):
TATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATGATCAAATTATATGT
Found at i:28358356 original size:26 final size:28
Alignment explanation
Indices: 28358303--28358356 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 28
28358293 TATTCTTTTC
*
28358303 ATTTAATTAATTTTGGTAATGTAGATATT
1 ATTTAATTAATTTT-GTAATCTAGATATT
*
28358332 ATTTAATT-ATTTT-TAATCTATATAT
1 ATTTAATTAATTTTGTAATCTAGATAT
28358357 ACATATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 10 0.43
28 5 0.22
29 8 0.35
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.56
Consensus pattern (28 bp):
ATTTAATTAATTTTGTAATCTAGATATT
Found at i:28358626 original size:14 final size:14
Alignment explanation
Indices: 28358607--28358636 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
28358597 TTTATATGTA
28358607 TTATATATATTAAT
1 TTATATATATTAAT
28358621 TTATATATATTAAT
1 TTATATATATTAAT
28358635 TT
1 TT
28358637 CGTTTATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTATATATATTAAT
Found at i:28363206 original size:16 final size:16
Alignment explanation
Indices: 28363166--28363197 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
28363156 TCAGATTCTA
28363166 AAAAAAAAATCAAAAT
1 AAAAAAAAATCAAAAT
28363182 AAAAAAAAATCAAAAT
1 AAAAAAAAATCAAAAT
28363198 GATGAAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.12
Consensus pattern (16 bp):
AAAAAAAAATCAAAAT
Found at i:28364584 original size:44 final size:44
Alignment explanation
Indices: 28364513--28365373 Score: 683
Period size: 44 Copynumber: 19.5 Consensus size: 44
28364503 GCAGGCTAAA
* *
28364513 AAGA-AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGCGTGAAGTAGATCG
* * * *
28364556 AAGATAGCAGATCCTGTCTTCCTATATTGGTAG-GAATTGGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGG-CGTGAAGTAGATCG
* * *
28364600 AAGAT-GCAGATCTTGTCTTCCCATATTGGTG-GCAAAGTAGATCA
1 AAGATAGCAGATCTTGTCTTCCTATATTGGCGTG--AAGTAGATCG
* * * * *
28364644 AAGAAAGCAGATCTTATCTTCATGTATTGGCGTAAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGCGTGAAGTAGATCG
* * * * * *
28364688 AAGATAACATATCATGTCTTCCTATATTGGTAGCGAAGTGGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGG-CGTGAAGTAGATCG
* * * * * *
28364733 AAGATA-CAGATCTTGTCTTCCCATACTGGTGGCGAAGAAGATCA
1 AAGATAGCAGATCTTGTCTTCCTATATTGG-CGTGAAGTAGATCG
* * * * *
28364777 AAGAAAGAAGATCTTGCCTTCATGTATTGGCGTGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGCGTGAAGTAGATCG
* * * *
28364821 AAGATAACAGATGC-TGTCTTCCTATATTGGTAGCGAAGTGGATCG
1 AAGATAGCAGAT-CTTGTCTTCCTATATTGG-CGTGAAGTAGATCG
*
28364866 AAGATA-CAGATCTTGTCTTCCCATACTGATGGC--GAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATA-T--TGGCGTGAAGTAGATCG
* * * * *
28364910 AAGAAAGCAGATCGTGTCTTCATGTATTGGCGTGAACTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGCGTGAAGTAGATCG
* * * * *
28364954 AAGATAACAGATCATGTCTTCCTATATTGGTAGCGAAGTGGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGG-CGTGAAGTAGATCG
* * * * *
28364999 AAGATA-CAGATCTTATCTTCCCATACTGGTGGCGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGG-CGTGAAGTAGATCG
* ** * * *
28365043 AAGAAAGCAGATCTCATCTTCATGTATTGGCGTGAAGTAAATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGCGTGAAGTAGATCG
* * * *
28365087 AAGGTAGCAGATCATGTCTTCCTATATTGGTAG-GAAGTGGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGG-CGTGAAGTAGATCG
* * *
28365131 AAGAT-GCAGATCTTGTATTCCCATATTGGTG-GCAAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGCGTG--AAGTAGATCG
* * * * *
28365175 AAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAATAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGCGTGAAGTAGATCG
* * * *
28365219 AAGATAACAGATCCTGTCTTCCTATATTGGTAG-GAAGTGGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGG-CGTGAAGTAGATCG
* * * *
28365263 AAGAT-GCAGATCTTGTCTTCCCACATTGGTGGCGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGG-CGTGAAGTAGATCG
* * * * * *
28365307 AAGAAAGCAGATCTTATCTTCATGTATTGGCATGAAGTGGATCGG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGCGTGAAGTAGATC-G
* *
28365352 AA-ATAGCAGATATTGCCTTCCT
1 AAGATAGCAGATCTTGTCTTCCT
28365374 GTACTAATAG
Statistics
Matches: 644, Mismatches: 146, Indels: 55
0.76 0.17 0.07
Matches are distributed among these distances:
42 8 0.01
43 70 0.11
44 396 0.61
45 166 0.26
46 1 0.00
47 3 0.00
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (44 bp):
AAGATAGCAGATCTTGTCTTCCTATATTGGCGTGAAGTAGATCG
Found at i:28365362 original size:132 final size:133
Alignment explanation
Indices: 28364516--28365350 Score: 1309
Period size: 133 Copynumber: 6.3 Consensus size: 133
28364506 GGCTAAAAAG
* *
28364516 AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTAT
1 AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGATCATGTCTTCCTAT
* * * * *
28364581 ATTGGTAG-GAATTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCAAAGTAGATCAA
66 ATTGGTAGCGAAGTGGATCGAAGATACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGA
28364645 AGA
131 AGA
* * *
28364648 AAGCAGATCTTATCTTCATGTATTGGCGTAAAGTAGATCGAAGATAACATATCATGTCTTCCTAT
1 AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGATCATGTCTTCCTAT
* *
28364713 ATTGGTAGCGAAGTGGATCGAAGATACAGATCTTGTCTTCCCATACTGGTGGCGAAGAAGATCAA
66 ATTGGTAGCGAAGTGGATCGAAGATACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGA
28364778 AGA
131 AGA
* *
28364781 AAGAAGATCTTGCCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGATGC-TGTCTTCCTA
1 AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGAT-CATGTCTTCCTA
*
28364845 TATTGGTAGCGAAGTGGATCGAAGATACAGATCTTGTCTTCCCATACTGATGGCGAAGTAGATCG
65 TATTGGTAGCGAAGTGGATCGAAGATACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCG
28364910 AAGA
130 AAGA
* *
28364914 AAGCAGATCGTGTCTTCATGTATTGGCGTGAACTAGATCGAAGATAACAGATCATGTCTTCCTAT
1 AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGATCATGTCTTCCTAT
*
28364979 ATTGGTAGCGAAGTGGATCGAAGATACAGATCTTATCTTCCCATACTGGTGGCGAAGTAGATCGA
66 ATTGGTAGCGAAGTGGATCGAAGATACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGA
28365044 AGA
131 AGA
** * * *
28365047 AAGCAGATCTCATCTTCATGTATTGGCGTGAAGTAAATCGAAGGTAGCAGATCATGTCTTCCTAT
1 AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGATCATGTCTTCCTAT
* * * *
28365112 ATTGGTAG-GAAGTGGATCGAAGATGCAGATCTTGTATTCCCATATTGGTGGCAAAGTAGATCGA
66 ATTGGTAGCGAAGTGGATCGAAGATACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGA
28365176 AGA
131 AGA
* * *
28365179 AAGCAGATCTTGTCTTCATGTATTGGCATGAAATAGATCGAAGATAACAGATCCTGTCTTCCTAT
1 AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGATCATGTCTTCCTAT
* * *
28365244 ATTGGTAG-GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCACATTGGTGGCGAAGTAGATCGA
66 ATTGGTAGCGAAGTGGATCGAAGATACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGA
28365308 AGA
131 AGA
* * *
28365311 AAGCAGATCTTATCTTCATGTATTGGCATGAAGTGGATCG
1 AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCG
28365351 GAAATAGCAG
Statistics
Matches: 650, Mismatches: 50, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
132 281 0.43
133 368 0.57
134 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (133 bp):
AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGATCATGTCTTCCTAT
ATTGGTAGCGAAGTGGATCGAAGATACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGA
AGA
Found at i:28365434 original size:132 final size:132
Alignment explanation
Indices: 28364516--28365464 Score: 607
Period size: 133 Copynumber: 7.2 Consensus size: 132
28364506 GGCTAAAAAG
* * * * * *
28364516 AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTAT
1 AAGCAGATCTTATCTTCATGTATTGGCATGAAATAGATCGAAGATAACAGATACTGCCTTCCTAT
* ** *** ** * * * * ** * *
28364581 ATTGGTAGGAATTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCAAAGTAGATCAAA
66 ACTAATAGGAAGCAGATCGAAGACACAGACCTTGTCCTCCCACAGTGGCAGCGAAGTAGATCGAA
28364646 GA
131 GA
* * *
28364648 AAGCAGATCTTATCTTCATGTATTGGCGT-AAAGTAGATCGAAGATAACATAT-CATGTCTTCCT
1 AAGCAGATCTTATCTTCATGTATTGGCATGAAA-TAGATCGAAGATAACAGATAC-TGCCTTCCT
* ** ** * * * * * ** *
28364711 ATATTGGTAGCGAAGTGGATCGAAGATACAGATCTTGTCTTCCCATACTGGTGGCGAAGAAGATC
64 ATACTAATAG-GAAGCAGATCGAAGACACAGACCTTGTCCTCCCACAGTGGCAGCGAAGTAGATC
*
28364776 AAAGA
128 GAAGA
* ** * * * *
28364781 AAGAAGATCTTGCCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGATGCTGTCTTCCTAT
1 AAGCAGATCTTATCTTCATGTATTGGCATGAAATAGATCGAAGATAACAGATACTGCCTTCCTAT
* ** ** * * * * * ***
28364846 ATTGGTAGCGAAGTGGATCGAAGATACAGATCTTGTCTTCCCATACTGATGGCGAAGTAGATCGA
66 ACTAATAG-GAAGCAGATCGAAGACACAGACCTTGTCCTCCCACAGTGGCAGCGAAGTAGATCGA
28364911 AGA
130 AGA
* * * * *
28364914 AAGCAGATCGTGTCTTCATGTATTGGCGTGAACTAGATCGAAGATAACAGAT-CATGTCTTCCTA
1 AAGCAGATCTTATCTTCATGTATTGGCATGAAATAGATCGAAGATAACAGATAC-TGCCTTCCTA
* ** ** * * * * * * **
28364978 TATTGGTAGCGAAGTGGATCGAAGATACAGATCTTATCTTCCCATACTGGTGGCGAAGTAGATCG
65 TACTAATAG-GAAGCAGATCGAAGACACAGACCTTGTCCTCCCACAGTGGCAGCGAAGTAGATCG
28365043 AAGA
129 AAGA
* * * * * * *
28365047 AAGCAGATCTCATCTTCATGTATTGGCGTGAAGTAAATCGAAGGTAGCAGAT-CATGTCTTCCTA
1 AAGCAGATCTTATCTTCATGTATTGGCATGAAATAGATCGAAGATAACAGATAC-TGCCTTCCTA
* ** ** ** * ** * * ** *
28365111 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTATTCCCATATTGGTGGCAAAGTAGATCGA
65 TACTAATAGGAAGCAGATCGAAGACACAGACCTTGTCCTCCCACAGTGGCAGCGAAGTAGATCGA
28365176 AGA
130 AGA
* * *
28365179 AAGCAGATCTTGTCTTCATGTATTGGCATGAAATAGATCGAAGATAACAGATCCTGTCTTCCTAT
1 AAGCAGATCTTATCTTCATGTATTGGCATGAAATAGATCGAAGATAACAGATACTGCCTTCCTAT
* ** ** ** * * * **
28365244 ATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCACATTGGTGGCGAAGTAGATCGAA
66 ACTAATAGGAAGCAGATCGAAGACACAGACCTTGTCCTCCCACAGTGGCAGCGAAGTAGATCGAA
28365309 GA
131 GA
* * * * *
28365311 AAGCAGATCTTATCTTCATGTATTGGCATGAAGTGGATCGGAA-ATAGCAGATATTGCCTTCCTG
1 AAGCAGATCTTATCTTCATGTATTGGCATGAAATAGATC-GAAGATAACAGATACTGCCTTCCTA
* * * * *
28365375 TACTAATAGTGAAGCAGATTGAAGACACTAG-CCTTG-CCTCCCTCAGTGGCAGCGGAGTAGGTT
65 TACTAATAG-GAAGCAGATCGAAGACAC-AGACCTTGTCCTCCCACAGTGGCAGCGAAGTAGATC
*
28365438 AAAGA
128 GAAGA
* * *
28365443 TAGCAGATCTTACCTTCCTGTA
1 AAGCAGATCTTATCTTCATGTA
28365465 CTAACAGTGA
Statistics
Matches: 733, Mismatches: 74, Indels: 20
0.89 0.09 0.02
Matches are distributed among these distances:
131 3 0.00
132 339 0.46
133 386 0.53
134 5 0.01
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.29
Consensus pattern (132 bp):
AAGCAGATCTTATCTTCATGTATTGGCATGAAATAGATCGAAGATAACAGATACTGCCTTCCTAT
ACTAATAGGAAGCAGATCGAAGACACAGACCTTGTCCTCCCACAGTGGCAGCGAAGTAGATCGAA
GA
Found at i:28365513 original size:88 final size:88
Alignment explanation
Indices: 28365354--28365666 Score: 448
Period size: 88 Copynumber: 3.6 Consensus size: 88
28365344 TGGATCGGAA
* *
28365354 ATAGCAGATATTGCCTTCCTGTACTAATAGTGAAGCAGATTGAAGACACTAGCCTTGCCTCCCTC
1 ATAGCAGATCTTGCCTTCCTGTACTAACAGTGAAGCAGATTGAAGACACTAGCCTTGCCTCCCTC
*
28365419 -AGTGGCAGCGGAGTAGGTTAAAG
66 GA-TGGCAGCGGAGCAGGTTAAAG
* * *
28365442 ATAGCAGATCTTACCTTCCTGTACTAACAGTGAAGCAGATTGACGACACTAGCCTTGCCTTCCTC
1 ATAGCAGATCTTGCCTTCCTGTACTAACAGTGAAGCAGATTGAAGACACTAGCCTTGCCTCCCTC
*
28365507 GATGGCAGTGGAGCAGGTTAAAG
66 GATGGCAGCGGAGCAGGTTAAAG
* * * * *
28365530 ATAGCAGATCTTGCATTTCTGTACTGACAGTGAAGCAGATTGAAGACACTAGCCCTACCTCCCTC
1 ATAGCAGATCTTGCCTTCCTGTACTAACAGTGAAGCAGATTGAAGACACTAGCCTTGCCTCCCTC
* *
28365595 GGTGGTAGCGGAGCAGGTTAAAG
66 GATGGCAGCGGAGCAGGTTAAAG
* * **
28365618 ATAGCAAATCTTGCCTTCCTGTACTGACAGTGAAGCAGATCAAAGACAC
1 ATAGCAGATCTTGCCTTCCTGTACTAACAGTGAAGCAGATTGAAGACAC
28365667 CAGTCTTATC
Statistics
Matches: 201, Mismatches: 23, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
88 200 1.00
89 1 0.00
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (88 bp):
ATAGCAGATCTTGCCTTCCTGTACTAACAGTGAAGCAGATTGAAGACACTAGCCTTGCCTCCCTC
GATGGCAGCGGAGCAGGTTAAAG
Found at i:28365543 original size:44 final size:45
Alignment explanation
Indices: 28365407--28365655 Score: 113
Period size: 45 Copynumber: 5.6 Consensus size: 45
28365397 AGACACTAGC
* * * *
28365407 CTTGCCTCCCTC-AGTGGCAGCGGAGTAGGTTAAAGATAGCAGAT
1 CTTGCCTTCCTCGACTGGCAGTGGAGCAGGTTAAAGATAGCAGAT
* ** * * * * * *
28365451 CTTACCTTCCT-GTACTAACAGTGAAGCAGATTGACGACA-CTAG-C
1 CTTGCCTTCCTCG-ACTGGCAGTGGAGCAGGTTAAAGATAGC-AGAT
28365495 CTTGCCTTCCTCGA-TGGCAGTGGAGCAGGTTAAAGATAGCAGAT
1 CTTGCCTTCCTCGACTGGCAGTGGAGCAGGTTAAAGATAGCAGAT
* * * * * * * *
28365539 CTTGCATTTCT-GTACTGACAGTGAAGCAGATTGAAGACA-CTAG-C
1 CTTGCCTTCCTCG-ACTGGCAGTGGAGCAGGTTAAAGATAGC-AGAT
* * * * * * *
28365583 CCTACCTCCCTCG-GTGGTAGCGGAGCAGGTTAAAGATAGCAAAT
1 CTTGCCTTCCTCGACTGGCAGTGGAGCAGGTTAAAGATAGCAGAT
* *
28365627 CTTGCCTTCCT-GTACTGACAGTGAAGCAG
1 CTTGCCTTCCTCG-ACTGGCAGTGGAGCAG
28365656 ATCAAAGACA
Statistics
Matches: 138, Mismatches: 53, Indels: 27
0.63 0.24 0.12
Matches are distributed among these distances:
43 39 0.28
44 48 0.35
45 51 0.37
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24
Consensus pattern (45 bp):
CTTGCCTTCCTCGACTGGCAGTGGAGCAGGTTAAAGATAGCAGAT
Found at i:28367599 original size:24 final size:24
Alignment explanation
Indices: 28367562--28367620 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 24
28367552 AATTATTATT
*
28367562 TTTATTTTTATAATTTTCATATGTA-A
1 TTTATTTTT-TAA-TAT-ATATGTATA
28367588 -TTATTTTTTAATATATATGTATA
1 TTTATTTTTTAATATATATGTATA
28367611 TTTATTTTTT
1 TTTATTTTTT
28367621 TATGTACATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 7 0.23
23 3 0.10
24 12 0.40
25 8 0.27
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (24 bp):
TTTATTTTTTAATATATATGTATA
Found at i:28367743 original size:26 final size:28
Alignment explanation
Indices: 28367690--28367743 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 28
28367680 TATTCTTTTC
*
28367690 ATTTAATTAATTTTGGTAATGTAGATATT
1 ATTTAATTAATTTT-GTAATCTAGATATT
*
28367719 ATTTAATT-ATTTT-TAATCTATATAT
1 ATTTAATTAATTTTGTAATCTAGATAT
28367744 ACATATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 10 0.43
28 5 0.22
29 8 0.35
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.56
Consensus pattern (28 bp):
ATTTAATTAATTTTGTAATCTAGATATT
Found at i:28371687 original size:30 final size:29
Alignment explanation
Indices: 28371652--28371739 Score: 115
Period size: 30 Copynumber: 2.9 Consensus size: 29
28371642 GTTTATCTAC
28371652 AAGATAAACATTAAATTAAATTTAATATT
1 AAGATAAACATTAAATTAAATTTAATATT
*
28371681 ATAGATAAACATTAAATTTAATTTAATATT
1 A-AGATAAACATTAAATTAAATTTAATATT
*
28371711 AAGATAATCACTTTAATATTAAA-TTAATA
1 AAGATAA--ACATTAA-ATTAAATTTAATA
28371740 AAATACTATT
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
29 7 0.13
30 28 0.54
31 12 0.23
32 5 0.10
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (29 bp):
AAGATAAACATTAAATTAAATTTAATATT
Found at i:28371725 original size:25 final size:24
Alignment explanation
Indices: 28371697--28371763 Score: 64
Period size: 25 Copynumber: 2.7 Consensus size: 24
28371687 AAACATTAAA
*
28371697 TTTAATTTAATATTAAGATAATCAC
1 TTTAATTTAATATTAAGAAAAT-AC
*
28371722 TTTAATATTAA-ATTAATAAAATAC
1 TTTAAT-TTAATATTAAGAAAATAC
*
28371746 TATTAATATAAGTATTAA
1 T-TTAATTTAA-TATTAA
28371764 ATTAAATTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
24 6 0.17
25 20 0.57
26 9 0.26
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.43
Consensus pattern (24 bp):
TTTAATTTAATATTAAGAAAATAC
Found at i:28374907 original size:21 final size:20
Alignment explanation
Indices: 28374867--28374907 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
28374857 TAACAATTCA
*
28374867 AAATATAATATTATTTTAAT
1 AAATATAATATTAATTTAAT
*
28374887 AAATTTAATATTTAATTTAAT
1 AAATATAATA-TTAATTTAAT
28374908 TTAATATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AAATATAATATTAATTTAAT
Found at i:28377123 original size:21 final size:21
Alignment explanation
Indices: 28377079--28377119 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28377069 TAGAGACTCT
* *
28377079 TTTAAAATGTTTTCAATATGA
1 TTTAAAATGTATTCAAAATGA
28377100 TTTAAAATGTATT-AAAATGA
1 TTTAAAATGTATTCAAAATGA
28377120 ATTTTGATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (21 bp):
TTTAAAATGTATTCAAAATGA
Done.