Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 142 of 163
Found at i:38478916 original size:14 final size:16
Alignment explanation
Indices: 38478890--38478926 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
38478880 AATGCCTATG
38478890 AACTTGATATTTT-TT
1 AACTTGATATTTTATT
*
38478905 AA-TTGATTTTTTATT
1 AACTTGATATTTTATT
38478920 AACTTGA
1 AACTTGA
38478927 GTTAACCATC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 9 0.47
15 6 0.32
16 4 0.21
ACGTcount: A:0.30, C:0.05, G:0.08, T:0.57
Consensus pattern (16 bp):
AACTTGATATTTTATT
Found at i:38479083 original size:15 final size:17
Alignment explanation
Indices: 38479065--38479096 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
38479055 AAAATTTGAG
38479065 GTTGTT-TT-ATTTTTT
1 GTTGTTGTTCATTTTTT
38479080 GTTGTTGTTCATTTTTT
1 GTTGTTGTTCATTTTTT
38479097 TTATTGAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 2 0.13
17 7 0.47
ACGTcount: A:0.06, C:0.03, G:0.16, T:0.75
Consensus pattern (17 bp):
GTTGTTGTTCATTTTTT
Found at i:38479320 original size:8 final size:8
Alignment explanation
Indices: 38479302--38479330 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
38479292 TTTAACGACT
38479302 AATAA-TA
1 AATAATTA
38479309 AATAATTA
1 AATAATTA
38479317 AATAATTA
1 AATAATTA
38479325 AATAAT
1 AATAAT
38479331 CATTTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 5 0.24
8 16 0.76
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
AATAATTA
Found at i:38480615 original size:18 final size:18
Alignment explanation
Indices: 38480588--38480635 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
38480578 ATTTTCAATA
*
38480588 AAAATATAAAAAAT-TGTG
1 AAAATTTAAAAAATCT-TG
* *
38480606 AAAATTTAAAAACTCTTT
1 AAAATTTAAAAAATCTTG
38480624 AAAATTTAAAAA
1 AAAATTTAAAAA
38480636 TATATTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 25 0.96
19 1 0.04
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.31
Consensus pattern (18 bp):
AAAATTTAAAAAATCTTG
Found at i:38480643 original size:18 final size:18
Alignment explanation
Indices: 38480606--38480645 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
38480596 AAAAATTGTG
*
38480606 AAAATTTAAAAACTCTTT
1 AAAATTTAAAAACTATTT
38480624 AAAATTTAAAAA-TATATT
1 AAAATTTAAAAACTAT-TT
38480642 AAAA
1 AAAA
38480646 AATATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (18 bp):
AAAATTTAAAAACTATTT
Found at i:38480657 original size:14 final size:12
Alignment explanation
Indices: 38480631--38480676 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
38480621 TTTAAAATTT
38480631 AAAAATATATTA
1 AAAAATATATTA
38480643 AAAAATATATT-
1 AAAAATATATTA
** *
38480654 TTAAATAT-TCA
1 AAAAATATATTA
38480665 AAAAATATATTA
1 AAAAATATATTA
38480677 TTTACTCCAT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
10 1 0.04
11 12 0.46
12 13 0.50
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (12 bp):
AAAAATATATTA
Found at i:38481134 original size:21 final size:23
Alignment explanation
Indices: 38481094--38481139 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
38481084 TAATTAAATT
*
38481094 TACATAGGAATATTTTTTTAATA
1 TACATAGGAATATATTTTTAATA
38481117 TACATA-GAA-ATATTTTTAATA
1 TACATAGGAATATATTTTTAATA
38481138 TA
1 TA
38481140 TAATCAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 13 0.59
22 3 0.14
23 6 0.27
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (23 bp):
TACATAGGAATATATTTTTAATA
Found at i:38481495 original size:20 final size:20
Alignment explanation
Indices: 38481472--38481522 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
38481462 ACAAAGTACA
38481472 AAAAAATTCAAAATAATTTT
1 AAAAAATTCAAAATAATTTT
*
38481492 AAAAAATTTAAAATAATTTT
1 AAAAAATTCAAAATAATTTT
*
38481512 TAAAAATTCAA
1 AAAAAATTCAA
38481523 CATATTCATG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAAAATTCAAAATAATTTT
Found at i:38484984 original size:3 final size:3
Alignment explanation
Indices: 38484976--38485025 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
38484966 TAGCAAGTTT
* * *
38484976 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCT TCC TCT TCC TCT TCC -CC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC
38485023 TCC
1 TCC
38485026 CTCTTCCTCT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (3 bp):
TCC
Found at i:38485034 original size:6 final size:6
Alignment explanation
Indices: 38484975--38485035 Score: 68
Period size: 6 Copynumber: 10.2 Consensus size: 6
38484965 TTAGCAAGTT
* * * * *
38484975 TTCCTC CTCCTC CTCCTC CTCCTC CTCCTC TTCCTC TTCCTC TTCCCC
1 TTCCTC TTCCTC TTCCTC TTCCTC TTCCTC TTCCTC TTCCTC TTCCTC
*
38485023 TCCCTC TTCCTC T
1 TTCCTC TTCCTC T
38485036 CTCTCTCATA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (6 bp):
TTCCTC
Found at i:38505797 original size:7 final size:7
Alignment explanation
Indices: 38505785--38505822 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
38505775 AGAAAATAAT
38505785 GGAGGAA
1 GGAGGAA
38505792 GGAGGAA
1 GGAGGAA
38505799 GGAGGAA
1 GGAGGAA
38505806 GGAGGAA
1 GGAGGAA
38505813 GGAGGAA
1 GGAGGAA
38505820 GGA
1 GGA
38505823 AGATTCAGCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.42, C:0.00, G:0.58, T:0.00
Consensus pattern (7 bp):
GGAGGAA
Found at i:38514502 original size:6 final size:6
Alignment explanation
Indices: 38514491--38514516 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
38514481 GGAGGGAGAA
38514491 GATGAG GATGAG GATGAG GATGAG GA
1 GATGAG GATGAG GATGAG GATGAG GA
38514517 CGGAGATCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.50, T:0.15
Consensus pattern (6 bp):
GATGAG
Found at i:38523420 original size:24 final size:24
Alignment explanation
Indices: 38523369--38523427 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
38523359 TAGGTAGATA
**
38523369 AAAAAATAAAAATAAAATTTTATC
1 AAAAAATAAAAATAAAAAATTATC
*
38523393 AAAAAATAAAAGTAAAAAAATTAT-
1 AAAAAATAAAAAT-AAAAAATTATC
38523417 -AAAAATAAAAA
1 AAAAAATAAAAA
38523428 AGTATTTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 10 0.33
24 12 0.40
25 8 0.27
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (24 bp):
AAAAAATAAAAATAAAAAATTATC
Found at i:38523682 original size:6 final size:6
Alignment explanation
Indices: 38523671--38523701 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
38523661 TTTCAAAGTT
38523671 TATAAA TATAAA TATAAA TATAAA TAATAAA
1 TATAAA TATAAA TATAAA TATAAA T-ATAAA
38523702 ATTTTATTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.79
7 5 0.21
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
TATAAA
Found at i:38529887 original size:11 final size:13
Alignment explanation
Indices: 38529859--38529885 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
38529849 ACTTATTTAA
38529859 ATAATTATTTTTT
1 ATAATTATTTTTT
38529872 ATAATTATTTTTT
1 ATAATTATTTTTT
38529885 A
1 A
38529886 ATCAGAGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
ATAATTATTTTTT
Found at i:38533029 original size:23 final size:24
Alignment explanation
Indices: 38532989--38533043 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
38532979 TGACCAAATT
*
38532989 AAAAAAAATTGATAGTTGGGTGAC
1 AAAAAAAATTAATAGTTGGGTGAC
* *
38533013 AAAAAAAA-TAATTGTTGTGTGAC
1 AAAAAAAATTAATAGTTGGGTGAC
*
38533036 TAAAAAAA
1 AAAAAAAA
38533044 GAAAAGGGGC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 19 0.70
24 8 0.30
ACGTcount: A:0.53, C:0.04, G:0.18, T:0.25
Consensus pattern (24 bp):
AAAAAAAATTAATAGTTGGGTGAC
Found at i:38534180 original size:58 final size:58
Alignment explanation
Indices: 38534113--38534267 Score: 229
Period size: 58 Copynumber: 2.7 Consensus size: 58
38534103 TGTTATTTAG
* *
38534113 GAATAAAATTATATTTGGGTTTAAAAATATATGGGTTTAATTTATGAGTATTTTTGAA
1 GAATGAAATTATATTTGGGTTTAAAAATATTTGGGTTTAATTTATGAGTATTTTTGAA
* * *
38534171 GAATGAAATTATATTTGAGTTTAAAAATATTTGGGTTTAGTTTATGAGTGTTTTTGAA
1 GAATGAAATTATATTTGGGTTTAAAAATATTTGGGTTTAATTTATGAGTATTTTTGAA
* * * *
38534229 AAATGAAATTATATGTGGATTTAAAATTATTTGGGTTTA
1 GAATGAAATTATATTTGGGTTTAAAAATATTTGGGTTTA
38534268 GTTTGTTGAT
Statistics
Matches: 87, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
58 87 1.00
ACGTcount: A:0.36, C:0.00, G:0.19, T:0.45
Consensus pattern (58 bp):
GAATGAAATTATATTTGGGTTTAAAAATATTTGGGTTTAATTTATGAGTATTTTTGAA
Found at i:38538602 original size:28 final size:25
Alignment explanation
Indices: 38538551--38538602 Score: 59
Period size: 28 Copynumber: 2.0 Consensus size: 25
38538541 AAGCGGATTG
* *
38538551 AATAATTTATATTTATTATTTTTAA
1 AATAATTAATATTTATTATATTTAA
38538576 AATAATTAAATATTTAACTTATATTTA
1 AATAATT-AATATTT-A-TTATATTTA
38538603 TATATTATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 7 0.32
26 6 0.27
27 1 0.05
28 8 0.36
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (25 bp):
AATAATTAATATTTATTATATTTAA
Found at i:38547248 original size:18 final size:18
Alignment explanation
Indices: 38547225--38547272 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
38547215 ACAATTCATA
38547225 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* * *
38547243 TCACTTTCACTTTCACTT
1 TCACTTTCAATTCCAATT
*
38547261 TCATTTTCAATT
1 TCACTTTCAATT
38547273 TTGATCACAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.23, C:0.27, G:0.00, T:0.50
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:38547250 original size:6 final size:6
Alignment explanation
Indices: 38547225--38547269 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
38547215 ACAATTCATA
* * * *
38547225 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCATTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
38547270 ATTTTGATCA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.22, C:0.29, G:0.00, T:0.49
Consensus pattern (6 bp):
TCACTT
Found at i:38547393 original size:18 final size:19
Alignment explanation
Indices: 38547370--38547405 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
38547360 ATTCACTTAT
*
38547370 TAAATA-TAAATATTGAAA
1 TAAATATTAAATAATGAAA
38547388 TAAATATTAAATAATGAA
1 TAAATATTAAATAATGAA
38547406 TAATTCAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (19 bp):
TAAATATTAAATAATGAAA
Found at i:38551910 original size:20 final size:20
Alignment explanation
Indices: 38551887--38551932 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
38551877 TATTAATCAA
38551887 AATTTTTAACTAATAATTAT
1 AATTTTTAACTAATAATTAT
* ** *
38551907 AATTTATATTTTATAATTAT
1 AATTTTTAACTAATAATTAT
38551927 AATTTT
1 AATTTT
38551933 CACAACCTTT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
AATTTTTAACTAATAATTAT
Found at i:38555144 original size:16 final size:16
Alignment explanation
Indices: 38555123--38555186 Score: 65
Period size: 16 Copynumber: 3.8 Consensus size: 16
38555113 TAATTTATTT
*
38555123 TAAAATTAAATTTGATA
1 TAAATTTAAATTT-ATA
* *
38555140 TAAATTTAGATTTATT
1 TAAATTTAAATTTATA
*
38555156 TAAATTTAAATTTAAA
1 TAAATTTAAATTTATA
38555172 TTAAACTTTAAATTT
1 -TAAA-TTTAAATTT
38555187 GAATTTAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
16 15 0.38
17 15 0.38
18 9 0.23
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (16 bp):
TAAATTTAAATTTATA
Found at i:38555162 original size:6 final size:6
Alignment explanation
Indices: 38555121--38555236 Score: 75
Period size: 6 Copynumber: 20.3 Consensus size: 6
38555111 CTTAATTTAT
* * * *
38555121 TTTAAA ATTAAA TTT-GA TATAAA TTTAGA TTT--A TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * * * *
38555166 TTTAAA -TTAAA CTTTAAA TTTGAA TTT-AA TTTGAG TCTGAA TTT-AT
1 TTTAAA TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
38555212 TTTAAA TTTAAA ATT-AA TTTAAA TT
1 TTTAAA TTTAAA TTTAAA TTTAAA TT
38555237 AAAGTCCAAA
Statistics
Matches: 86, Mismatches: 16, Indels: 16
0.73 0.14 0.14
Matches are distributed among these distances:
4 4 0.05
5 21 0.24
6 56 0.65
7 5 0.06
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:38555170 original size:12 final size:12
Alignment explanation
Indices: 38555121--38555236 Score: 75
Period size: 11 Copynumber: 10.2 Consensus size: 12
38555111 CTTAATTTAT
*
38555121 TTTAAAATTAAA
1 TTTAAATTTAAA
* *
38555133 TTT-GATATAAA
1 TTTAAATTTAAA
*
38555144 TTTAGATTT--A
1 TTTAAATTTAAA
38555154 TTTAAATTTAAA
1 TTTAAATTTAAA
38555166 TTTAAA-TTAAA
1 TTTAAATTTAAA
*
38555177 CTTTAAATTTGAA
1 -TTTAAATTTAAA
* *
38555190 TTT-AATTTGAG
1 TTTAAATTTAAA
* * *
38555201 TCTGAATTT-AT
1 TTTAAATTTAAA
38555212 TTTAAATTTAAA
1 TTTAAATTTAAA
*
38555224 ATT-AATTTAAA
1 TTTAAATTTAAA
38555235 TT
1 TT
38555237 AAAGTCCAAA
Statistics
Matches: 83, Mismatches: 14, Indels: 15
0.74 0.12 0.13
Matches are distributed among these distances:
10 9 0.11
11 39 0.47
12 31 0.37
13 4 0.05
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:38555183 original size:18 final size:17
Alignment explanation
Indices: 38555122--38555236 Score: 74
Period size: 17 Copynumber: 6.8 Consensus size: 17
38555112 TTAATTTATT
* *
38555122 TTAAAATTAAATTT-GA
1 TTAAATTTAAATTTAAA
* *
38555138 TATAAATTTAGATTT-AT
1 T-TAAATTTAAATTTAAA
38555155 TTAAATTTAAATTTAAA
1 TTAAATTTAAATTTAAA
*
38555172 TTAAACTTTAAATTTGAA
1 TTAAA-TTTAAATTTAAA
* * * * *
38555190 TTTAATTTGAGTCTGAA
1 TTAAATTTAAATTTAAA
* *
38555207 TTTATTTTAAATTTAAAA
1 TTAAATTTAAATTT-AAA
38555225 TT-AATTTAAATT
1 TTAAATTTAAATT
38555237 AAAGTCCAAA
Statistics
Matches: 78, Mismatches: 17, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
16 13 0.17
17 46 0.59
18 19 0.24
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (17 bp):
TTAAATTTAAATTTAAA
Found at i:38556027 original size:15 final size:16
Alignment explanation
Indices: 38556009--38556050 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
38555999 TAAATATGGC
38556009 ATTAATAATAACAAT-
1 ATTAATAATAACAATA
* *
38556024 ATTAATATTAATAATA
1 ATTAATAATAACAATA
*
38556040 ATAAATAATAA
1 ATTAATAATAA
38556051 TCCTTAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (16 bp):
ATTAATAATAACAATA
Found at i:38563365 original size:14 final size:14
Alignment explanation
Indices: 38563320--38563363 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
38563310 AGCCAGATGT
38563320 GAAAGAAAG-G-AA
1 GAAAGAAAGAGAAA
*
38563332 GAAAGAAATAGAAA
1 GAAAGAAAGAGAAA
38563346 GAAAGAAAGAGACAA
1 GAAAGAAAGAGA-AA
38563361 GAA
1 GAA
38563364 GAGCACGACA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 8 0.30
13 1 0.04
14 13 0.48
15 5 0.19
ACGTcount: A:0.68, C:0.02, G:0.27, T:0.02
Consensus pattern (14 bp):
GAAAGAAAGAGAAA
Found at i:38566894 original size:75 final size:75
Alignment explanation
Indices: 38566771--38567266 Score: 812
Period size: 75 Copynumber: 6.6 Consensus size: 75
38566761 CAGACCGCAC
38566771 CAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATT
1 CAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATT
38566836 GAAGTAAGAG
66 GAAGTAAGAG
* *
38566846 CAAGATCTTTCCCTATCCTCTTGAAGTTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATT
1 CAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATT
38566911 GAAGTAAGAG
66 GAAGTAAGAG
*
38566921 CAAGATCTTTTCCTATCCTCTTAAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATT
1 CAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATT
38566986 GAAGTAAGAG
66 GAAGTAAGAG
*
38566996 CAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCCCTGAAATT
1 CAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATT
38567061 GAAGTAAGAG
66 GAAGTAAGAG
* * * * * * *
38567071 CAAGATCATTTCCTATCCTTTTGAAATTGAAGTAAAACTGGATATCAAGTCTTTATCTTTGAAAT
1 CAAGATCTTTTCCTATCCTCTTGAAATTGAAGT-AGAGTGGATAACACGTCTTTATCTCTGAAAT
38567136 TGAAGTAAGAG
65 TGAAGTAAGAG
* * *
38567147 CAAGATCATTTCCCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAAT
1 CAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAAAT
*
38567212 TGAAGTAAAAG
65 TGAAGTAAGAG
* *
38567223 CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATA
1 CAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAG-TGGATA
38567267 GCAAGCATTT
Statistics
Matches: 395, Mismatches: 24, Indels: 3
0.94 0.06 0.01
Matches are distributed among these distances:
75 251 0.64
76 144 0.36
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (75 bp):
CAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATT
GAAGTAAGAG
Found at i:38568122 original size:16 final size:16
Alignment explanation
Indices: 38568101--38568145 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
38568091 TAATTTATTT
*
38568101 TAAAATTAAATTTGATA
1 TAAATTTAAATTT-ATA
* *
38568118 TAAATTTAGATTTATT
1 TAAATTTAAATTTATA
38568134 TAAATTTAAATT
1 TAAATTTAAATT
38568146 AAACTTTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 13 0.54
17 11 0.46
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (16 bp):
TAAATTTAAATTTATA
Found at i:38568140 original size:6 final size:6
Alignment explanation
Indices: 38568099--38568208 Score: 63
Period size: 6 Copynumber: 19.3 Consensus size: 6
38568089 CTTAATTTAT
* * * *
38568099 TTTAAA ATTAAA TTT-GA TATAAA TTTAGA TTT--A TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * * * *
38568144 -TTAAA CTTTAAA TTTGAA TTT-AA TTTGAG TCTGAA TTT-AT TTTAAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
38568190 TTTAAA ATT-AA TTTAAA TT
1 TTTAAA TTTAAA TTTAAA TT
38568209 AAAGTTCAAA
Statistics
Matches: 80, Mismatches: 16, Indels: 16
0.71 0.14 0.14
Matches are distributed among these distances:
4 4 0.05
5 21 0.26
6 50 0.62
7 5 0.06
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:38568206 original size:17 final size:16
Alignment explanation
Indices: 38568099--38568208 Score: 67
Period size: 17 Copynumber: 6.5 Consensus size: 16
38568089 CTTAATTTAT
* *
38568099 TTTAAAATTAAATTTGA
1 TTTAAATTTAAA-TTAA
* * *
38568116 TATAAATTTAGATTTA
1 TTTAAATTTAAATTAA
38568132 TTTAAATTTAAATTAAA
1 TTTAAATTTAAATT-AA
*
38568149 CTTTAAATTTGAATTTAA
1 -TTTAAATTT-AAATTAA
* * * * *
38568167 TTTGAGTCTGAATTTAT
1 TTTAAAT-TTAAATTAA
38568184 TTTAAATTTAAAATTAA
1 TTTAAATTT-AAATTAA
38568201 TTTAAATT
1 TTTAAATT
38568209 AAAGTTCAAA
Statistics
Matches: 71, Mismatches: 17, Indels: 10
0.72 0.17 0.10
Matches are distributed among these distances:
16 16 0.23
17 39 0.55
18 12 0.17
19 4 0.06
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (16 bp):
TTTAAATTTAAATTAA
Found at i:38568575 original size:11 final size:11
Alignment explanation
Indices: 38568559--38568592 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
38568549 ATCTGTAATG
38568559 AAAAAAAGAAA
1 AAAAAAAGAAA
38568570 AAAAAAAGAAA
1 AAAAAAAGAAA
38568581 AAAGAAAA-AAA
1 AAA-AAAAGAAA
38568592 A
1 A
38568593 CAGATTCTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 18 0.82
12 4 0.18
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:38569004 original size:15 final size:16
Alignment explanation
Indices: 38568986--38569027 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
38568976 TAAATATGGC
38568986 ATTAATAATAACAAT-
1 ATTAATAATAACAATA
* *
38569001 ATTAATATTAATAATA
1 ATTAATAATAACAATA
*
38569017 ATAAATAATAA
1 ATTAATAATAA
38569028 TCCTTAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (16 bp):
ATTAATAATAACAATA
Found at i:38570126 original size:30 final size:28
Alignment explanation
Indices: 38570071--38570259 Score: 114
Period size: 29 Copynumber: 6.5 Consensus size: 28
38570061 CAAACAGTCT
* *
38570071 AAAAATTGCATTTTAACCCTGAAACTTCC
1 AAAAATTCCATTTT-ACCCTCAAACTTCC
38570100 AAAAATTACCTATTTTACCCTCAAACTTCC
1 AAAAATT-CC-ATTTTACCCTCAAACTTCC
* * * * **
38570130 TAAAATTCTATTTTTAACCTCGATTTTACC
1 AAAAATTCCA-TTTTACCCTCAAACTT-CC
* *
38570160 AAAAATTACCATTTTACCCCCGAACTTCC
1 AAAAATT-CCATTTTACCCTCAAACTTCC
* * *
38570189 CAAAATTCCATTTTAACCC-C-GATTTCAC
1 AAAAATTCCATTTT-ACCCTCAAACTTC-C
* * *
38570217 CAAAATTACCATTTTACCC-CTAAATTTTC
1 AAAAATT-CCATTTTACCCTC-AAACTTCC
*
38570246 TAAAATTCCATTTT
1 AAAAATTCCATTTT
38570260 CGACCCCGAT
Statistics
Matches: 130, Mismatches: 20, Indels: 21
0.76 0.12 0.12
Matches are distributed among these distances:
27 4 0.03
28 29 0.22
29 46 0.35
30 44 0.34
31 7 0.05
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.36
Consensus pattern (28 bp):
AAAAATTCCATTTTACCCTCAAACTTCC
Found at i:38570228 original size:29 final size:29
Alignment explanation
Indices: 38570141--38570290 Score: 121
Period size: 28 Copynumber: 5.1 Consensus size: 29
38570131 AAAATTCTAT
* *
38570141 TTTTAACCTCGATTTTACCAAAAATTACCA
1 TTTTAACCCCGATTTCACC-AAAATTACCA
* *
38570171 TTTTACCCCCGAACTTC-CCAAAATT-CCA
1 TTTTAACCCCG-ATTTCACCAAAATTACCA
38570199 TTTTAACCCCGATTTCACCAAAATTACCA
1 TTTTAACCCCGATTTCACCAAAATTACCA
* * *
38570228 TTTT-ACCCCTAAATTT-TCTAAAATT-CCA
1 TTTTAACCCC--GATTTCACCAAAATTACCA
* * *
38570256 TTTTCGACCCCGATTTTACCAAAAATTATCA
1 TTTT-AACCCCGATTTCACC-AAAATTACCA
38570287 TTTT
1 TTTT
38570291 GCCCCACGGG
Statistics
Matches: 97, Mismatches: 13, Indels: 19
0.75 0.10 0.15
Matches are distributed among these distances:
27 4 0.04
28 37 0.38
29 21 0.22
30 26 0.27
31 9 0.09
ACGTcount: A:0.32, C:0.28, G:0.03, T:0.37
Consensus pattern (29 bp):
TTTTAACCCCGATTTCACCAAAATTACCA
Found at i:38570266 original size:58 final size:58
Alignment explanation
Indices: 38570072--38570295 Score: 247
Period size: 59 Copynumber: 3.8 Consensus size: 58
38570062 AAACAGTCTA
* * **
38570072 AAAATTGCATTTTAACCCTGAAACTT-CCAAAAATTACCTATTTTA-CCCTCAAACTTCCT
1 AAAATTCCATTTTAACCCCG-ATTTTACCAAAAATTACC-ATTTTACCCCT-AAACTTCCT
* * ** *
38570131 AAAATTCTATTTTTAACCTCGATTTTACCAAAAATTACCATTTTACCCCCGAACTTCCC
1 AAAATTCCA-TTTTAACCCCGATTTTACCAAAAATTACCATTTTACCCCTAAACTTCCT
* * *
38570190 AAAATTCCATTTTAACCCCGATTTCACC-AAAATTACCATTTTACCCCTAAATTTTCT
1 AAAATTCCATTTTAACCCCGATTTTACCAAAAATTACCATTTTACCCCTAAACTTCCT
* * *
38570247 AAAATTCCATTTTCGACCCCGATTTTACCAAAAATTATCATTTTGCCCC
1 AAAATTCCATTTT-AACCCCGATTTTACCAAAAATTACCATTTTACCCC
38570296 ACGGGTATCC
Statistics
Matches: 139, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
57 37 0.27
58 30 0.22
59 48 0.35
60 24 0.17
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.35
Consensus pattern (58 bp):
AAAATTCCATTTTAACCCCGATTTTACCAAAAATTACCATTTTACCCCTAAACTTCCT
Found at i:38570308 original size:116 final size:119
Alignment explanation
Indices: 38570101--38570332 Score: 278
Period size: 116 Copynumber: 2.0 Consensus size: 119
38570091 GAAACTTCCA
* * *
38570101 AAAATTACCTATTTTACCCTCAAACTTCCTAAAATTCTATTTTTAACCTCGATTTTACCAAAAAT
1 AAAATTACCTATTTTACCCTCAAACTTCCTAAAATTCCATTTTCAACCCCGATTTTACCAAAAAT
*
38570166 TACCATTTTACCCCCGAACTTCCCAAAATTCC-ATTTT-AACCCCGATTTCACC
66 TACCATTTTACCCCCGAACTTCCCAAAAGTCCTATTTTCAACCCCGATTTCACC
* * *
38570218 AAAATTACC-ATTTTACCC-CTAAATTTTCTAAAATTCCATTTTCGACCCCGATTTTACCAAAAA
1 AAAATTACCTATTTTACCCTC-AAACTTCCTAAAATTCCATTTTCAACCCCGATTTTACCAAAAA
* * ** * *
38570281 TTATCATTTTGCCCCACG-GGTAT-CCAAAAGTCCTGTTTTCAACCTCGATTTC
65 TTACCATTTTACCCC-CGAACT-TCCCAAAAGTCCTATTTTCAACCCCGATTTC
38570333 GTCGTTTCTT
Statistics
Matches: 97, Mismatches: 13, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
115 1 0.01
116 69 0.71
117 16 0.16
118 11 0.11
ACGTcount: A:0.31, C:0.28, G:0.05, T:0.35
Consensus pattern (119 bp):
AAAATTACCTATTTTACCCTCAAACTTCCTAAAATTCCATTTTCAACCCCGATTTTACCAAAAAT
TACCATTTTACCCCCGAACTTCCCAAAAGTCCTATTTTCAACCCCGATTTCACC
Found at i:38575656 original size:13 final size:13
Alignment explanation
Indices: 38575627--38575668 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
38575617 CTTTGTAAAC
38575627 AAATACTTTAGAAAA
1 AAAT-CTTTA-AAAA
38575642 AAATCTTTAAAAA
1 AAATCTTTAAAAA
*
38575655 AAAT-TGTAAAAA
1 AAATCTTTAAAAA
38575667 AA
1 AA
38575669 TTATTAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 9 0.35
13 8 0.31
14 5 0.19
15 4 0.15
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.26
Consensus pattern (13 bp):
AAATCTTTAAAAA
Found at i:38575675 original size:24 final size:25
Alignment explanation
Indices: 38575653--38575713 Score: 97
Period size: 24 Copynumber: 2.5 Consensus size: 25
38575643 AATCTTTAAA
38575653 AAAAATTGTAAAAAAATTATTAATT
1 AAAAATTGTAAAAAAATTATTAATT
* *
38575678 AAAAATTAT-AAAATATTATTAATT
1 AAAAATTGTAAAAAAATTATTAATT
38575702 AAAAATTGTAAA
1 AAAAATTGTAAA
38575714 TTTTATAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
24 22 0.69
25 10 0.31
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (25 bp):
AAAAATTGTAAAAAAATTATTAATT
Found at i:38575681 original size:14 final size:14
Alignment explanation
Indices: 38575664--38575708 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
38575654 AAAATTGTAA
38575664 AAAAATTATTAATT
1 AAAAATTATTAATT
38575678 AAAAATTA-T-A--
1 AAAAATTATTAATT
*
38575688 AAATATTATTAATT
1 AAAAATTATTAATT
38575702 AAAAATT
1 AAAAATT
38575709 GTAAATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
10 7 0.28
11 1 0.04
12 2 0.08
13 1 0.04
14 14 0.56
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AAAAATTATTAATT
Found at i:38577250 original size:136 final size:135
Alignment explanation
Indices: 38576986--38577258 Score: 483
Period size: 136 Copynumber: 2.0 Consensus size: 135
38576976 GATTTCCTTG
* *
38576986 TGATTCAAGTCTCTTGTTGAATACTCAAATATAGAGAATCATAGATTTTGATACTATTCTTTTTA
1 TGATTCAAGTCTCTGGTTGAATACTCAAATATAGAGAATCATAGATTTTGATACTATCCTTTTTA
* * *
38577051 CTTGTAAAGGTATATCTGATGAAAAAAGTAAAAGAAATTAGGGAGAACTTCAATTAAGTAGGCAT
66 CTTGTAAAGGTATAACTAATGAAAAAAGTAAAAGAAATTAGGGAGAACTTCAATTAAGCAGGCAT
38577116 TTTCA
131 TTTCA
*
38577121 TGATTCAGGTCTCTGGTTGAATACTCAAATATAGAGAATCATAGATTTTGATACTATCCTTTCTT
1 TGATTCAAGTCTCTGGTTGAATACTCAAATATAGAGAATCATAGATTTTGATACTATCCTTT-TT
38577186 ACTTGTAAAGGTATAACTAATGAAAAAAGTAAAAGAAATTAGGGAGAACTTCAATTAAGCAGGCA
65 ACTTGTAAAGGTATAACTAATGAAAAAAGTAAAAGAAATTAGGGAGAACTTCAATTAAGCAGGCA
38577251 TTTTCA
130 TTTTCA
38577257 TG
1 TG
38577259 CTTATCGCCT
Statistics
Matches: 131, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
135 59 0.45
136 72 0.55
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (135 bp):
TGATTCAAGTCTCTGGTTGAATACTCAAATATAGAGAATCATAGATTTTGATACTATCCTTTTTA
CTTGTAAAGGTATAACTAATGAAAAAAGTAAAAGAAATTAGGGAGAACTTCAATTAAGCAGGCAT
TTTCA
Found at i:38587448 original size:19 final size:19
Alignment explanation
Indices: 38587432--38587476 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
38587422 TTCAAAAACG
38587432 TATAAAAA-TTATTAAAAA
1 TATAAAAATTTATTAAAAA
38587450 -ATTAAAAATTTATTAAAAA
1 TA-TAAAAATTTATTAAAAA
38587469 TATAAAAA
1 TATAAAAA
38587477 AATTTAATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 1 0.04
18 6 0.25
19 16 0.67
20 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TATAAAAATTTATTAAAAA
Found at i:38587467 original size:28 final size:29
Alignment explanation
Indices: 38587405--38587480 Score: 88
Period size: 28 Copynumber: 2.7 Consensus size: 29
38587395 ATTTCTAAAA
38587405 TATAAAAATT-TT-AAAAATTCAAAAACG
1 TATAAAAATTATTAAAAAATTCAAAAACG
**
38587432 TATAAAAATTATTAAAAAATT-AAAAATT
1 TATAAAAATTATTAAAAAATTCAAAAACG
*
38587460 TATTAAAAA-TATAAAAAAATT
1 TA-TAAAAATTATTAAAAAATT
38587481 TAATTGCTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
27 10 0.23
28 20 0.47
29 13 0.30
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (29 bp):
TATAAAAATTATTAAAAAATTCAAAAACG
Found at i:38587469 original size:18 final size:19
Alignment explanation
Indices: 38587432--38587476 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 19
38587422 TTCAAAAACG
38587432 TATAAAAATTATTAAAAAA
1 TATAAAAATTATTAAAAAA
38587451 T-TAAAAATTTATT-AAAAA
1 TATAAAAA-TTATTAAAAAA
38587469 TATAAAAA
1 TATAAAAA
38587477 AATTTAATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TATAAAAATTATTAAAAAA
Found at i:38587830 original size:59 final size:59
Alignment explanation
Indices: 38587694--38587829 Score: 217
Period size: 59 Copynumber: 2.4 Consensus size: 59
38587684 TTTTATGAAC
38587694 ATAAATAAATATAAAATAATATTAATTTTATTTTATTATTTATTATTTTATGAATATAA
1 ATAAATAAATATAAAATAATATTAATTTTATTTTATTATTTATTATTTTATGAATATAA
* *
38587753 ATAAATAAATGTAAAATAATATTAATTTTGTTTTATTATTTATTATTATTAT-AA-ATAA
1 ATAAATAAATATAAAATAATATTAATTTTATTTTATTATTTATTATT-TTATGAATATAA
38587811 ATAAAT-AA-ATAAAATAATA
1 ATAAATAAATATAAAATAATA
38587830 AATCCAAAGT
Statistics
Matches: 73, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
56 10 0.14
57 2 0.03
58 10 0.14
59 47 0.64
60 4 0.05
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (59 bp):
ATAAATAAATATAAAATAATATTAATTTTATTTTATTATTTATTATTTTATGAATATAA
Found at i:38592653 original size:31 final size:31
Alignment explanation
Indices: 38592618--38592686 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
38592608 ACTACAAAAT
* *
38592618 AGTCATTAAATTATTC-AAAAGTTTTCATTTA
1 AGTCATTAAACTAGTCGAAAA-TTTTCATTTA
* * *
38592649 AGTCACTGAACTAGTCGAAAATTTTTATTTA
1 AGTCATTAAACTAGTCGAAAATTTTCATTTA
38592680 AGTCATT
1 AGTCATT
38592687 GGACTATTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
31 27 0.87
32 4 0.13
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (31 bp):
AGTCATTAAACTAGTCGAAAATTTTCATTTA
Found at i:38605053 original size:33 final size:32
Alignment explanation
Indices: 38604987--38605055 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 32
38604977 GATATTTCAT
* *
38604987 ATATCATATTTCATTTGCCATTAAATAAATTC
1 ATATCACATTTCATTTACCATTAAATAAATTC
* * *
38605019 ATATCACATTTCATTATACCGTTGAATAATTTC
1 ATATCACATTTCATT-TACCATTAAATAAATTC
38605052 ATAT
1 ATAT
38605056 TATCAAATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
32 14 0.45
33 17 0.55
ACGTcount: A:0.36, C:0.16, G:0.04, T:0.43
Consensus pattern (32 bp):
ATATCACATTTCATTTACCATTAAATAAATTC
Found at i:38619110 original size:32 final size:32
Alignment explanation
Indices: 38619064--38619134 Score: 108
Period size: 32 Copynumber: 2.2 Consensus size: 32
38619054 TGGCTTTTTA
38619064 ATTTCGTATAACTATTT-AGATTTTAATTTATAG
1 ATTT-GTATAACTATTTGA-ATTTTAATTTATAG
*
38619097 ATTTGTATAACTATTTGAATTTTGATTTATAG
1 ATTTGTATAACTATTTGAATTTTAATTTATAG
38619129 ATTTGT
1 ATTTGT
38619135 GATGTTTAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
32 31 0.86
33 5 0.14
ACGTcount: A:0.31, C:0.04, G:0.11, T:0.54
Consensus pattern (32 bp):
ATTTGTATAACTATTTGAATTTTAATTTATAG
Found at i:38620459 original size:2 final size:2
Alignment explanation
Indices: 38620452--38620478 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
38620442 TAACTTCATC
38620452 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
38620479 CCCTAGTGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38622216 original size:21 final size:21
Alignment explanation
Indices: 38622178--38622217 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
38622168 CTTGAAGATT
* * *
38622178 GGTTTCTTATGGATTAAGTCG
1 GGTTACTTATGAAATAAGTCG
38622199 GGTTACTTATGAAATAAGT
1 GGTTACTTATGAAATAAGT
38622218 AAAGTCACTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.07, G:0.25, T:0.40
Consensus pattern (21 bp):
GGTTACTTATGAAATAAGTCG
Found at i:38626426 original size:17 final size:17
Alignment explanation
Indices: 38626396--38626443 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
38626386 TGGACCCATT
38626396 TTTTTAAAATTTTAATTTA
1 TTTTT-AAA-TTTAATTTA
*
38626415 TTTTTAAATTTAGTTTA
1 TTTTTAAATTTAATTTA
**
38626432 AATTTAAATTTA
1 TTTTTAAATTTA
38626444 GAAAGTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 18 0.69
18 3 0.12
19 5 0.19
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
TTTTTAAATTTAATTTA
Found at i:38627057 original size:11 final size:11
Alignment explanation
Indices: 38627041--38627077 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
38627031 AAAAAAAAGA
38627041 AGAGAGAAGGG
1 AGAGAGAAGGG
38627052 AGAGAGAAGGG
1 AGAGAGAAGGG
*
38627063 AGAGAGAAAGG
1 AGAGAGAAGGG
38627074 AGAG
1 AGAG
38627078 GATTTGTGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (11 bp):
AGAGAGAAGGG
Found at i:38627665 original size:29 final size:30
Alignment explanation
Indices: 38627584--38627955 Score: 432
Period size: 29 Copynumber: 12.7 Consensus size: 30
38627574 GAGGCACCTG
*
38627584 AACTTCTCAAAAATTACATTTTAACCCTCA
1 AACTTCTCAAAAATTACATTTTTACCCTCA
*
38627614 AACTT-TCCAAAAATTACATTTTAACCCTCA
1 AACTTCT-CAAAAATTACATTTTTACCCTCA
*
38627644 AACTTCTCAAAAA-TACATTTTAACCC-CTA
1 AACTTCTCAAAAATTACATTTTTACCCTC-A
*
38627673 AACTT-TCTAAAAATTACATTTTGACCCTCA
1 AACTTCTC-AAAAATTACATTTTTACCCTCA
* *
38627703 AACTTTTCAAAAATTACA-TTTTACCCTCG
1 AACTTCTCAAAAATTACATTTTTACCCTCA
*
38627732 AACTTC-CAAAAATCACATTTTTACCCTCA
1 AACTTCTCAAAAATTACATTTTTACCCTCA
* * *
38627761 TACTTC-CTAAAATTACATTTTTACCCTTA
1 AACTTCTCAAAAATTACATTTTTACCCTCA
* * *
38627790 AATTTCT-AAAAATTACATTTTTATCCTCG
1 AACTTCTCAAAAATTACATTTTTACCCTCA
*
38627819 AACTTCTCAAAAATTACA-TTTTACCCTCG
1 AACTTCTCAAAAATTACATTTTTACCCTCA
*
38627848 AACTTCTCAAAAATTACA-TTTTACCCTCG
1 AACTTCTCAAAAATTACATTTTTACCCTCA
*
38627877 AACTTC-CAAAAATCACATTTTTACTCCT-A
1 AACTTCTCAAAAATTACATTTTTAC-CCTCA
* *
38627906 TACTTC-CTAAAATTACATTTTTACCCTCA
1 AACTTCTCAAAAATTACATTTTTACCCTCA
38627935 AACTTC-C-AAAATTACCATTTT
1 AACTTCTCAAAAATTA-CATTTT
38627956 GCCTCGAGTA
Statistics
Matches: 304, Mismatches: 24, Indels: 29
0.85 0.07 0.08
Matches are distributed among these distances:
28 33 0.11
29 187 0.62
30 80 0.26
31 4 0.01
ACGTcount: A:0.36, C:0.26, G:0.01, T:0.37
Consensus pattern (30 bp):
AACTTCTCAAAAATTACATTTTTACCCTCA
Found at i:38627832 original size:116 final size:113
Alignment explanation
Indices: 38627584--38627991 Score: 479
Period size: 116 Copynumber: 3.5 Consensus size: 113
38627574 GAGGCACCTG
* *
38627584 AACTTCTCAAAAATTACATTTTAACCCTCAAACTTTCCAAAAATTACATTTTAACCCTCAAACTT
1 AACTTCTCAAAAATTACATTTT-ACCCTCGAAC-TTCCAAAAATCACATTTT-ACCCTC-AACTT
* * *
38627649 -CTCAAAAATACATTTTAACCCCTAAACTTTCTAAAAATTACATTTTGACCCTCA
62 CCT-AAAATTACATTTTTA-CCCTAAA-TTTCTAAAAATTACATTTTTACCCTCA
*
38627703 AACTTTTCAAAAATTACATTTTACCCTCGAACTTCCAAAAATCACATTTTTACCCTCATACTTCC
1 AACTTCTCAAAAATTACATTTTACCCTCGAACTTCCAAAAATCACA-TTTTACCCTCA-ACTTCC
* *
38627768 TAAAATTACATTTTTACCCTTAAATTTCTAAAAATTACATTTTTATCCTCG
64 TAAAATTACATTTTTACCC-TAAATTTCTAAAAATTACATTTTTACCCTCA
*
38627819 AACTTCTCAAAAATTACATTTTACCCTCGAACTTCTCAAAAATTACATTTTACCCTCGAACTTCC
1 AACTTCTCAAAAATTACATTTTACCCTCGAACTTC-CAAAAATCACATTTTACCCTC-AACTTCC
* * * *
38627884 AAAAATCACATTTTTACTCCTATACTTCCT-AAAATTACATTTTTACCCTCA
64 TAAAATTACATTTTTAC-CCTA-AATTTCTAAAAATTACATTTTTACCCTCA
*
38627935 AACTTC-C-AAAATTACCATTTT-GCCTCGAGTA-TT-CAAAAATCACCATTTTACCCTCAA
1 AACTTCTCAAAAATTA-CATTTTACCCTCGA--ACTTCCAAAAATCA-CATTTTACCCTCAA
38627992 ATTTTCCAAA
Statistics
Matches: 259, Mismatches: 18, Indels: 30
0.84 0.06 0.10
Matches are distributed among these distances:
113 10 0.04
114 25 0.10
115 9 0.03
116 121 0.47
117 58 0.22
118 15 0.06
119 21 0.08
ACGTcount: A:0.36, C:0.26, G:0.02, T:0.36
Consensus pattern (113 bp):
AACTTCTCAAAAATTACATTTTACCCTCGAACTTCCAAAAATCACATTTTACCCTCAACTTCCTA
AAATTACATTTTTACCCTAAATTTCTAAAAATTACATTTTTACCCTCA
Found at i:38628002 original size:29 final size:27
Alignment explanation
Indices: 38627590--38628004 Score: 307
Period size: 29 Copynumber: 14.3 Consensus size: 27
38627580 CCTGAACTTC
38627590 TCAAAAATTACATTTTAACCCTCAAACTT
1 TCAAAAATTACATTTT-ACCCTCAAA-TT
38627619 TCCAAAAATTACATTTTAACCCTCAAACTT
1 T-CAAAAATTACATTTT-ACCCTCAAA-TT
38627649 CTCAAAAA-TACATTTTAACCC-CTAAACTT
1 -TCAAAAATTACATTTT-ACCCTC-AAA-TT
38627678 TCTAAAAATTACATTTTGACCCTCAAACTTT
1 TC-AAAAATTACATTTT-ACCCTCAAA--TT
*
38627709 TCAAAAATTACATTTTACCCTCGAACTT
1 TCAAAAATTACATTTTACCCTC-AAATT
* * *
38627737 CCAAAAATCACATTTTTACCCTCATACTT
1 TCAAAAATTACA-TTTTACCCTCA-AATT
* * *
38627766 CCTAAAATTACATTTTTACCCTTAAATT
1 TCAAAAATTACA-TTTTACCCTCAAATT
* *
38627794 TCTAAAAATTACATTTTTATCCTCGAACTT
1 TC-AAAAATTACA-TTTTACCCTC-AAATT
*
38627824 CTCAAAAATTACATTTTACCCTCGAACTT
1 -TCAAAAATTACATTTTACCCTC-AAATT
*
38627853 CTCAAAAATTACATTTTACCCTCGAACTT
1 -TCAAAAATTACATTTTACCCTC-AAATT
* * *
38627882 CCAAAAATCACATTTTTACTCCT-ATACTT
1 TCAAAAATTACA-TTTTAC-CCTCA-AATT
* * *
38627911 CCTAAAATTACATTTTTACCCTCAAACT
1 TCAAAAATTACA-TTTTACCCTCAAATT
* * * *
38627939 TCCAAAATTACCATTTT-GCCTCGAGTAT
1 TCAAAAATTA-CATTTTACCCTCAAAT-T
*
38627967 TCAAAAATCACCATTTTACCCTCAAATTT
1 TCAAAAATTA-CATTTTACCCTCAAA-TT
*
38627996 TCCAAAATT
1 TCAAAAATT
38628005 TTGATTTAGT
Statistics
Matches: 331, Mismatches: 34, Indels: 42
0.81 0.08 0.10
Matches are distributed among these distances:
27 5 0.02
28 64 0.19
29 171 0.52
30 83 0.25
31 8 0.02
ACGTcount: A:0.36, C:0.26, G:0.02, T:0.36
Consensus pattern (27 bp):
TCAAAAATTACATTTTACCCTCAAATT
Found at i:38631530 original size:23 final size:23
Alignment explanation
Indices: 38631501--38631552 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
38631491 TCATCATCTG
*
38631501 CCACCACCAGTAACTTGCCTCTA
1 CCACCACCAGCAACTTGCCTCTA
* *
38631524 CCACCACGAGCAACTTGCCTCTG
1 CCACCACCAGCAACTTGCCTCTA
38631547 CCACCA
1 CCACCA
38631553 TTATCACCTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.25, C:0.46, G:0.12, T:0.17
Consensus pattern (23 bp):
CCACCACCAGCAACTTGCCTCTA
Found at i:38631917 original size:14 final size:15
Alignment explanation
Indices: 38631892--38631923 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
38631882 GGGTTATTCC
38631892 TATTATATATATATT
1 TATTATATATATATT
38631907 TATTA-ATATATATT
1 TATTATATATATATT
38631921 TAT
1 TAT
38631924 ATTTTCATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TATTATATATATATT
Found at i:38631942 original size:22 final size:22
Alignment explanation
Indices: 38631894--38631942 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
38631884 GTTATTCCTA
*
38631894 TTATATATATATTTATTAATAT
1 TTATTTATATATTTATTAATAT
* *
38631916 ATATTTATAT-TTTCATTATTAT
1 TTATTTATATATTT-ATTAATAT
38631938 TTATT
1 TTATT
38631943 ATTTCTAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 3 0.14
22 19 0.86
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (22 bp):
TTATTTATATATTTATTAATAT
Found at i:38633071 original size:29 final size:30
Alignment explanation
Indices: 38633012--38633268 Score: 181
Period size: 30 Copynumber: 8.7 Consensus size: 30
38633002 GCCTCTGAAC
* * * *
38633012 TTCTCAAAAATTATATTTTAATCCTTAAACT
1 TTCT-AAAAATTACATTTTTACCCTCAAACT
* *
38633043 TTCTAAAAATTAC-TTTTGACCCTCGAAC-
1 TTCTAAAAATTACATTTTTACCCTCAAACT
* * *
38633071 TTCTCAAAATTATATTTTGACCC-CTAAACT
1 TTCTAAAAATTACATTTTTACCCTC-AAACT
* * * *
38633101 TTCTAACAATTACAATTTGACCCTTAAACT
1 TTCTAAAAATTACATTTTTACCCTCAAACT
38633131 TT-TCAAAAATTACATTTTTACCC-CTAAAC-
1 TTCT-AAAAATTACATTTTTACCCTC-AAACT
* * * * **
38633160 TTCCAAAAATCATATTTTTTCCCTCGTACT
1 TTCTAAAAATTACATTTTTACCCTCAAACT
* * *
38633190 TCCT-AAAATCACATTTTTACCC-CAAAAT
1 TTCTAAAAATTACATTTTTACCCTCAAACT
* *
38633218 TTCCAAAAATTACATTTTTTACCCTCGAAC-
1 TTCTAAAAATTACA-TTTTTACCCTCAAACT
38633248 TTCTTAAAAATTACATTTTTA
1 TTC-TAAAAATTACATTTTTA
38633269 TTCTTAAATT
Statistics
Matches: 177, Mismatches: 36, Indels: 27
0.74 0.15 0.11
Matches are distributed among these distances:
28 17 0.10
29 68 0.38
30 75 0.42
31 17 0.10
ACGTcount: A:0.35, C:0.23, G:0.02, T:0.40
Consensus pattern (30 bp):
TTCTAAAAATTACATTTTTACCCTCAAACT
Found at i:38633267 original size:30 final size:30
Alignment explanation
Indices: 38633009--38633268 Score: 155
Period size: 29 Copynumber: 8.8 Consensus size: 30
38632999 AAGGCCTCTG
* * * * *
38633009 AACTTCTCAAAAATTATATTTTAATCCTTA
1 AACTTCTTAAAAATTACATTTTTACCCTCA
* *
38633039 AACTT-TCTAAAAATTAC-TTTTGACCCTCG
1 AACTTCT-TAAAAATTACATTTTTACCCTCA
* * *
38633068 AACTTC-TCAAAATTATATTTTGACCC-CTA
1 AACTTCTTAAAAATTACATTTTTACCCTC-A
* * * *
38633097 AACTT-TCTAACAATTACAATTTGACCCTTA
1 AACTTCT-TAAAAATTACATTTTTACCCTCA
38633127 AACTT-TTCAAAAATTACATTTTTACCC-CTA
1 AACTTCTT-AAAAATTACATTTTTACCCTC-A
* * * * *
38633157 AACTTC-CAAAAATCATATTTTTTCCCTCG
1 AACTTCTTAAAAATTACATTTTTACCCTCA
* * *
38633186 TACTTCCT-AAAATCACATTTTTACCC-CA
1 AACTTCTTAAAAATTACATTTTTACCCTCA
* * *
38633214 AAATT-TCCAAAAATTACATTTTTTACCCTCG
1 AACTTCT-TAAAAATTACA-TTTTTACCCTCA
38633245 AACTTCTTAAAAATTACATTTTTA
1 AACTTCTTAAAAATTACATTTTTA
38633269 TTCTTAAATT
Statistics
Matches: 177, Mismatches: 36, Indels: 34
0.72 0.15 0.14
Matches are distributed among these distances:
28 13 0.07
29 74 0.42
30 74 0.42
31 15 0.08
32 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.02, T:0.39
Consensus pattern (30 bp):
AACTTCTTAAAAATTACATTTTTACCCTCA
Found at i:38633285 original size:118 final size:117
Alignment explanation
Indices: 38633003--38633289 Score: 287
Period size: 118 Copynumber: 2.4 Consensus size: 117
38632993 GCACAGAAGG
* * *
38633003 CCTCTGAACTTCTCAAAAATTATATTTTAATCCTTAAACTTTCTAAAAATTACTTTTGACCCTCG
1 CCTC-GAACTTCTTAAAAATTACATTTTTATCCTTAAACTTTC-AAAAATTACTTTTGACCCTCG
* * * * *
38633068 AACTTCTCAAAATTATATTTTGACCCCTAAACTTTCTAACAATTACAATTTGAC
64 AACTTCTCAAAATCACATTTTGACCCCTAAAATTTCCAAAAATTACAATTTGAC
** * * * **
38633122 CCTTAAACTT-TTCAAAAATTACATTTTTACCCCTAAACTTCCAAAAATCATA-TTTTTTCCCTC
1 CCTCGAACTTCTT-AAAAATTACATTTTTATCCTTAAACTTTCAAAAAT--TACTTTTGACCCTC
* * * *
38633185 GTACTTC-CTAAAATCACATTTTTACCCC-AAAATTTCCAAAAATTACATTTTTTAC
63 GAACTTCTC-AAAATCACATTTTGACCCCTAAAATTTCCAAAAATTACA-ATTTGAC
* *
38633240 CCTCGAACTTCTTAAAAATTACATTTTTATTCTTAAATTTTC-AAAATTAC
1 CCTCGAACTTCTTAAAAATTACATTTTTATCCTTAAACTTTCAAAAATTAC
38633290 CATTTTACCC
Statistics
Matches: 135, Mismatches: 26, Indels: 17
0.76 0.15 0.10
Matches are distributed among these distances:
115 2 0.01
117 29 0.21
118 97 0.72
119 7 0.05
ACGTcount: A:0.35, C:0.23, G:0.02, T:0.40
Consensus pattern (117 bp):
CCTCGAACTTCTTAAAAATTACATTTTTATCCTTAAACTTTCAAAAATTACTTTTGACCCTCGAA
CTTCTCAAAATCACATTTTGACCCCTAAAATTTCCAAAAATTACAATTTGAC
Found at i:38647007 original size:24 final size:23
Alignment explanation
Indices: 38646980--38647032 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
38646970 AATTTTTTTT
**
38646980 TAAAATTAATAGAAGTTTATAAAA
1 TAAAATTAATA-AAAATTATAAAA
*
38647004 TAAAATTTATAAAAATTATAAAA
1 TAAAATTAATAAAAATTATAAAA
38647027 -AAAATT
1 TAAAATT
38647033 TGTTATTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 6 0.23
23 10 0.38
24 10 0.38
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (23 bp):
TAAAATTAATAAAAATTATAAAA
Found at i:38673114 original size:21 final size:21
Alignment explanation
Indices: 38673075--38673115 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
38673065 CTCATTTATA
* *
38673075 TTTTAATTAATCATGATTTAG
1 TTTTAATCAATCATAATTTAG
*
38673096 TTTTAATCAATCTTAATTTA
1 TTTTAATCAATCATAATTTA
38673116 CTTAATTAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.54
Consensus pattern (21 bp):
TTTTAATCAATCATAATTTAG
Found at i:38673779 original size:37 final size:38
Alignment explanation
Indices: 38673710--38673785 Score: 102
Period size: 37 Copynumber: 2.0 Consensus size: 38
38673700 AAAAAATTAT
* * *
38673710 TTTTGAGGAATTAAATTGTAAAATAGTAAAAATTTGAA
1 TTTTGAGGAATTAAATCGTAAAATAATAAAAATTAGAA
38673748 TTTT-AGGAATTAAATCGTAAAA-AATATAAAATTAGAA
1 TTTTGAGGAATTAAATCGTAAAATAATA-AAAATTAGAA
38673785 T
1 T
38673786 ATAAGGGAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 3 0.09
37 27 0.79
38 4 0.12
ACGTcount: A:0.50, C:0.01, G:0.13, T:0.36
Consensus pattern (38 bp):
TTTTGAGGAATTAAATCGTAAAATAATAAAAATTAGAA
Found at i:38685198 original size:26 final size:29
Alignment explanation
Indices: 38685153--38685228 Score: 81
Period size: 26 Copynumber: 2.7 Consensus size: 29
38685143 TTTAAGTAAT
38685153 TAATATAAAT-TATTTGTAAAA-TTAATAATA
1 TAATATAAATATA-TT-TAAAATTTAA-AATA
38685183 T-AT-TAAATA-ATTTAAAATTTAAAATA
1 TAATATAAATATATTTAAAATTTAAAATA
38685209 TAATAATAAATATATTTAAA
1 TAAT-ATAAATATATTTAAA
38685229 TAATTTAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
26 10 0.25
27 8 0.20
28 6 0.15
29 8 0.20
30 8 0.20
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (29 bp):
TAATATAAATATATTTAAAATTTAAAATA
Found at i:38696239 original size:17 final size:17
Alignment explanation
Indices: 38696217--38696250 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
38696207 TTTTTATAGG
38696217 TTACCA-TAAACACAAAT
1 TTACCATTAAA-ACAAAT
38696234 TTACCATTAAAACAAAT
1 TTACCATTAAAACAAAT
38696251 AATTTGACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.53, C:0.21, G:0.00, T:0.26
Consensus pattern (17 bp):
TTACCATTAAAACAAAT
Found at i:38709443 original size:33 final size:32
Alignment explanation
Indices: 38709397--38709469 Score: 76
Period size: 32 Copynumber: 2.2 Consensus size: 32
38709387 CTATTTACTT
* **
38709397 AAAATAAATAATTTTAGTCAAAATGAAATTAAG
1 AAAATAAATAA-TTTAATCAAAACAAAATTAAG
*
38709430 AAAATAACA-AATTTAATCAAAACAAAATTAAT
1 AAAATAA-ATAATTTAATCAAAACAAAATTAAG
*
38709462 TAAATAAA
1 AAAATAAA
38709470 GAACTTTTAC
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
31 1 0.03
32 23 0.68
33 9 0.26
34 1 0.03
ACGTcount: A:0.63, C:0.05, G:0.04, T:0.27
Consensus pattern (32 bp):
AAAATAAATAATTTAATCAAAACAAAATTAAG
Found at i:38714325 original size:6 final size:6
Alignment explanation
Indices: 38714314--38714355 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
38714304 TAATGACTTG
38714314 CCCCCA CCCCCA CCCCCA CCCCCA CCCCCA CCCCCA CCCCCA
1 CCCCCA CCCCCA CCCCCA CCCCCA CCCCCA CCCCCA CCCCCA
38714356 GGAAAGAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.17, C:0.83, G:0.00, T:0.00
Consensus pattern (6 bp):
CCCCCA
Found at i:38715627 original size:29 final size:28
Alignment explanation
Indices: 38715594--38715666 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 28
38715584 ATTTTTTTTT
* *
38715594 TGGTCATCTAACTATGAAAAATTATAAAA
1 TGGTCA-CCAACTATGAAAAATTACAAAA
**
38715623 TGGTCACACAACTATGAAAGGTTACAAAA
1 TGGTCAC-CAACTATGAAAAATTACAAAA
38715652 TGGTCACCGAACTAT
1 TGGTCACC-AACTAT
38715667 TTGACTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 2 0.05
29 36 0.95
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.26
Consensus pattern (28 bp):
TGGTCACCAACTATGAAAAATTACAAAA
Found at i:38719993 original size:12 final size:13
Alignment explanation
Indices: 38719971--38720004 Score: 52
Period size: 12 Copynumber: 2.6 Consensus size: 13
38719961 AGTTCAATAT
38719971 TGATCGAAGATGA
1 TGATCGAAGATGA
38719984 TGAT-GAAGATGA
1 TGATCGAAGATGA
38719996 TGTATCGAA
1 TG-ATCGAA
38720005 TAAGAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 10 0.53
13 6 0.32
14 3 0.16
ACGTcount: A:0.38, C:0.06, G:0.29, T:0.26
Consensus pattern (13 bp):
TGATCGAAGATGA
Found at i:38726818 original size:22 final size:23
Alignment explanation
Indices: 38726793--38726835 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
38726783 GCCGAACCCA
*
38726793 ACCCGAACCAGA-CCGTTGACCG
1 ACCCGAACCAAACCCGTTGACCG
*
38726815 ACCCGACCCAAACCCGTTGAC
1 ACCCGAACCAAACCCGTTGAC
38726836 TTTAACTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.28, C:0.44, G:0.19, T:0.09
Consensus pattern (23 bp):
ACCCGAACCAAACCCGTTGACCG
Found at i:38726890 original size:20 final size:20
Alignment explanation
Indices: 38726843--38726890 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
38726833 GACTTTAACT
38726843 TTGACTTTGACTGTTGACCA
1 TTGACTTTGACTGTTGACCA
* * *
38726863 TTGGCTTTGATTGTTGACCG
1 TTGACTTTGACTGTTGACCA
38726883 TTGACTTT
1 TTGACTTT
38726891 TTTTCGAGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.15, C:0.17, G:0.23, T:0.46
Consensus pattern (20 bp):
TTGACTTTGACTGTTGACCA
Found at i:38734996 original size:16 final size:16
Alignment explanation
Indices: 38734975--38735018 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
38734965 TTTGGTTCGC
*
38734975 TGTAATGGAATAGAGT
1 TGTAATGGAATAGAGA
38734991 TGTAATGGAATAGAGA
1 TGTAATGGAATAGAGA
38735007 TGTAATGGAATA
1 TGTAATGGAATA
38735019 TGACTGTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.30, T:0.30
Consensus pattern (16 bp):
TGTAATGGAATAGAGA
Found at i:38735026 original size:16 final size:16
Alignment explanation
Indices: 38734973--38735028 Score: 78
Period size: 16 Copynumber: 3.5 Consensus size: 16
38734963 CGTTTGGTTC
38734973 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
38734989 GTTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
38735005 GATGTAATGGAATATGA
1 GCTGTAATGGAATA-GA
38735022 -CTGTAAT
1 GCTGTAAT
38735029 CAGTAATTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
16 34 0.94
17 2 0.06
ACGTcount: A:0.38, C:0.04, G:0.29, T:0.30
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:38735100 original size:44 final size:46
Alignment explanation
Indices: 38735010--38735103 Score: 133
Period size: 44 Copynumber: 2.1 Consensus size: 46
38735000 ATAGAGATGT
38735010 AATGGAATATGACTGTAATCAGTAATTCAGTTGTTTGGTTGAATGG
1 AATGGAATATGACTGTAATCAGTAATTCAGTTGTTTGGTTGAATGG
*
38735056 AATGGAATA-GAGCTGTAAT-AGT-ATTC-TTGTGTTTGGTTGAATGG
1 AATGGAATATGA-CTGTAATCAGTAATTCAGT-TGTTTGGTTGAATGG
38735100 AATG
1 AATG
38735104 ATGCCGCAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
43 1 0.02
44 23 0.51
45 5 0.11
46 16 0.36
ACGTcount: A:0.30, C:0.05, G:0.28, T:0.37
Consensus pattern (46 bp):
AATGGAATATGACTGTAATCAGTAATTCAGTTGTTTGGTTGAATGG
Found at i:38735250 original size:58 final size:59
Alignment explanation
Indices: 38735188--38735349 Score: 188
Period size: 58 Copynumber: 2.8 Consensus size: 59
38735178 TTGTTATGAA
* *
38735188 ATTTTAATA-AGATTATTATTAATTATAATTTAATAAAAATAATAAATAATTTAATTA-T
1 ATTTTAATATA-ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATAACT
* * * *
38735246 ATTTTAACATAATTATTATTAAATATAATTAAAT-AAAGTAATATATAATTTAATAACGT
1 ATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATAAC-T
* * *
38735305 -TTTTAATATAATTATTATTAAAATATAAATTAGTAAAAATTATAA
1 ATTTTAATATAATTATTATT-AAATATAATTTAATAAAAATAATAA
38735350 TATATAATAT
Statistics
Matches: 86, Mismatches: 13, Indels: 8
0.80 0.12 0.07
Matches are distributed among these distances:
57 19 0.22
58 47 0.55
59 13 0.15
60 7 0.08
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.44
Consensus pattern (59 bp):
ATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATAACT
Found at i:38735366 original size:24 final size:24
Alignment explanation
Indices: 38735318--38735376 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
38735308 TAATATAATT
*
38735318 ATTATTAAAATATAAATTAGTAAAA
1 ATTA-TAATATATAAATTAGTAAAA
38735343 ATTATAATATATAATATTAG-AAAA
1 ATTATAATATATAA-ATTAGTAAAA
*
38735367 ATAAT-ATATA
1 ATTATAATATA
38735377 ACTTACTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 5 0.16
24 17 0.55
25 9 0.29
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.37
Consensus pattern (24 bp):
ATTATAATATATAAATTAGTAAAA
Found at i:38740412 original size:18 final size:18
Alignment explanation
Indices: 38740389--38740427 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
38740379 TTTTTGGAGT
38740389 TTATAAGTACAAGTA-AAA
1 TTATAAGTACAA-TATAAA
38740407 TTATAAGTACAATATAAA
1 TTATAAGTACAATATAAA
38740425 TTA
1 TTA
38740428 CAAACAATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.33
Consensus pattern (18 bp):
TTATAAGTACAATATAAA
Found at i:38742895 original size:21 final size:21
Alignment explanation
Indices: 38742871--38742916 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
38742861 GGCTGCAGTG
38742871 CTTCCTCATCTTCA-TCTTCTT
1 CTTCCTCATCTTCATTC-TCTT
*
38742892 CTTCCTCGTCTTCATTCTCTT
1 CTTCCTCATCTTCATTCTCTT
38742913 CTTC
1 CTTC
38742917 TTCAACATCC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.07, C:0.39, G:0.02, T:0.52
Consensus pattern (21 bp):
CTTCCTCATCTTCATTCTCTT
Found at i:38742941 original size:6 final size:6
Alignment explanation
Indices: 38742930--38742995 Score: 53
Period size: 6 Copynumber: 10.5 Consensus size: 6
38742920 AACATCCTCT
* * * *
38742930 TCATCC TCATCC TC-TCC ATCATCGTC GTCGTCG TCATCC TCGTCC TCGTCC
1 TCATCC TCATCC TCATCC -TCATC--C -TCATCC TCATCC TCATCC TCATCC
38742981 TCATCC TCATCC TCA
1 TCATCC TCATCC TCA
38742996 GGGTCTTCAC
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
5 3 0.06
6 39 0.80
7 2 0.04
9 5 0.10
ACGTcount: A:0.12, C:0.45, G:0.09, T:0.33
Consensus pattern (6 bp):
TCATCC
Found at i:38742986 original size:18 final size:18
Alignment explanation
Indices: 38742930--38742994 Score: 64
Period size: 18 Copynumber: 3.8 Consensus size: 18
38742920 AACATCCTCT
38742930 TCATCCTCATCCTC-T-C
1 TCATCCTCATCCTCGTCC
* * * *
38742946 -CATCATCGTCGTCGTCG
1 TCATCCTCATCCTCGTCC
*
38742963 TCATCCTCGTCCTCGTCC
1 TCATCCTCATCCTCGTCC
38742981 TCATCCTCATCCTC
1 TCATCCTCATCCTC
38742995 AGGGTCTTCA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
15 10 0.26
16 1 0.03
18 27 0.71
ACGTcount: A:0.11, C:0.46, G:0.09, T:0.34
Consensus pattern (18 bp):
TCATCCTCATCCTCGTCC
Found at i:38744356 original size:34 final size:35
Alignment explanation
Indices: 38744292--38744362 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
38744282 ATTGAATTAT
* *
38744292 AATTAAATTTTTTTATATATATATATTTAAATCAA
1 AATTAAATTTTTATATATATATATAATTAAATCAA
38744327 AATTAAATTTTTATATATA-AT-TACATTAAATCAA
1 AATTAAATTTTTATATATATATATA-ATTAAATCAA
38744361 AA
1 AA
38744363 CTTAGATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
33 2 0.06
34 13 0.39
35 18 0.55
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.46
Consensus pattern (35 bp):
AATTAAATTTTTATATATATATATAATTAAATCAA
Found at i:38752128 original size:24 final size:25
Alignment explanation
Indices: 38752101--38752147 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
38752091 ATAAATATTT
*
38752101 AAAAAATATATTTCAAT-ATTTACC
1 AAAAAAAATATTTCAATCATTTACC
38752125 AAAAAAAATATTTCAATCATTTA
1 AAAAAAAATATTTCAATCATTTA
38752148 TGCTTAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (25 bp):
AAAAAAAATATTTCAATCATTTACC
Found at i:38753502 original size:30 final size:31
Alignment explanation
Indices: 38753450--38753520 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 31
38753440 GATTAAATTG
* *
38753450 AATTAAAATTATATATATATAAT-CAGATAA
1 AATTAAAATTATACATACATAATACAGATAA
* *
38753480 AATTAAAATTCATACAT-CATAATACATATTA
1 AATTAAAATT-ATACATACATAATACAGATAA
*
38753511 AATCAAAATT
1 AATTAAAATT
38753521 GATATATAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
30 15 0.44
31 19 0.56
ACGTcount: A:0.55, C:0.08, G:0.01, T:0.35
Consensus pattern (31 bp):
AATTAAAATTATACATACATAATACAGATAA
Found at i:38755496 original size:23 final size:23
Alignment explanation
Indices: 38755470--38755530 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
38755460 GTTCGTGCTC
**
38755470 GTTCGTTTGTCGTTCACGAACAT
1 GTTCGTTTAACGTTCACGAACAT
**
38755493 GTTCGTTTAACGTTTGCGAACAT
1 GTTCGTTTAACGTTCACGAACAT
*
38755516 GTTCGTTTAATGTTC
1 GTTCGTTTAACGTTC
38755531 GTTTAACGTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.43
Consensus pattern (23 bp):
GTTCGTTTAACGTTCACGAACAT
Found at i:38755531 original size:34 final size:34
Alignment explanation
Indices: 38755491--38755558 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
38755481 GTTCACGAAC
* *
38755491 ATGTTCGTTTAACGTTTGCGAACATGTTCGTTTA
1 ATGTTCGTTTAACGTTCGCGAACATGTTCATTTA
38755525 ATGTTCGTTTAACGTTCGCGAACATGTTCATTTA
1 ATGTTCGTTTAACGTTCGCGAACATGTTCATTTA
38755559 TGCGTTCGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.43
Consensus pattern (34 bp):
ATGTTCGTTTAACGTTCGCGAACATGTTCATTTA
Found at i:38755541 original size:57 final size:58
Alignment explanation
Indices: 38755470--38755582 Score: 147
Period size: 57 Copynumber: 2.0 Consensus size: 58
38755460 GTTCGTGCTC
** * * * *
38755470 GTTCGTTTGTCGTTCACGAACATGTTCGTTTA-ACGTTTGCGAACATGTTCGTTTAAT
1 GTTCGTTTAACGTTCACGAACATGTTCATTTATACGTTCGCAAACATATTCGTTTAAT
* *
38755527 GTTCGTTTAACGTTCGCGAACATGTTCATTTATGCGTTCGCAAACATATTCGTTTA
1 GTTCGTTTAACGTTCACGAACATGTTCATTTATACGTTCGCAAACATATTCGTTTA
38755583 TAACTAACCA
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
57 28 0.60
58 19 0.40
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (58 bp):
GTTCGTTTAACGTTCACGAACATGTTCATTTATACGTTCGCAAACATATTCGTTTAAT
Found at i:38755552 original size:23 final size:24
Alignment explanation
Indices: 38755525--38755584 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
38755515 TGTTCGTTTA
*
38755525 ATGTTCGTTTA-ACGTTCGCGAAC
1 ATGTTCGTTTATACGTTCGCAAAC
* *
38755548 ATGTTCATTTATGCGTTCGCAAAC
1 ATGTTCGTTTATACGTTCGCAAAC
*
38755572 ATATTCGTTTATA
1 ATGTTCGTTTATA
38755585 ACTAACCAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 10 0.33
24 20 0.67
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.40
Consensus pattern (24 bp):
ATGTTCGTTTATACGTTCGCAAAC
Found at i:38755620 original size:19 final size:19
Alignment explanation
Indices: 38755596--38755636 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
38755586 CTAACCAAAC
38755596 AAACAAAAAAAATTAAATA
1 AAACAAAAAAAATTAAATA
**
38755615 AAACAAAACCAATTAAATA
1 AAACAAAAAAAATTAAATA
38755634 AAA
1 AAA
38755637 AACTTAGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.76, C:0.10, G:0.00, T:0.15
Consensus pattern (19 bp):
AAACAAAAAAAATTAAATA
Found at i:38757076 original size:2 final size:2
Alignment explanation
Indices: 38757065--38757100 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
38757055 TTATGACACA
38757065 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
38757101 AGCCTATGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38767350 original size:13 final size:13
Alignment explanation
Indices: 38767318--38767350 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
38767308 AATTTGGACC
38767318 TTTAA-TTAAATT
1 TTTAATTTAAATT
38767330 TTTAAATTTAAATT
1 TTT-AATTTAAATT
38767344 TTTAATT
1 TTTAATT
38767351 CGAAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.16
13 6 0.32
14 10 0.53
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TTTAATTTAAATT
Found at i:38768355 original size:76 final size:76
Alignment explanation
Indices: 38768226--38769119 Score: 1368
Period size: 76 Copynumber: 11.7 Consensus size: 76
38768216 ATCTCCACTA
* *
38768226 GCTCTTACTTCAATTTCAGAGGGATGAAGGCTTGATATCCAACTTTACTTCAATTTCAAGAGGAT
1 GCTCTTACTTCAATTTCAGA--GATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGAT
38768291 AGAAAATGATCTT
64 AGAAAATGATCTT
* * **
38768304 GCTCTTACTTTAATTTCAGAGATAAAGACCTGATATCCTGCTTTACTTCAATTTCAAGAGGATA-
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAG
38768368 AGAAATGATCTT
66 A-AAATGATCTT
* * **
38768380 ACTCTTACTTCAATTTCAGAGATAGAGACTTGATATCCAGTTTTACTTCAATTTCAAGAGGATAG
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAG
*
38768445 GAAATGATCTT
66 AAAATGATCTT
*
38768456 GCTCTTACTTCAATTTCGGAGATAAAGACTTGATATCCAAC-TTACTTCAATTTCAAGAGGATAG
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATA-
38768520 GAAAA-GATCTT
65 GAAAATGATCTT
* * *
38768531 ACTCTTACTTCAATTTCAGAGAGACGAAGGCTTGATATCCAACTTTACTTCAATTTCAAGAGGAT
1 GCTCTTACTTCAATTTCAGAGATA--AAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGAT
38768596 AGAAAATGATCTT
64 AGAAAATGATCTT
* *
38768609 GCTCTTACTTCAATTTCAGAGATAAAGACCTGATATCCAGCTTTACTTCAATTTCAAGAGGATA-
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAG
38768673 AGAAATGATCTT
66 A-AAATGATCTT
* * *
38768685 ACTCTTACTTCAATTTCAGAGATAGAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAG
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAG
*
38768750 GAAATGATCTT
66 AAAATGATCTT
* * *
38768761 GCTCTTACTTCAATTTCAAAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAG
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAG
* *
38768826 GAAATAATCTT
66 AAAATGATCTT
*
38768837 GCTCTTACTTCAATTTCGGAGATAAAGACTTGATATCCAAC-TTACTTCAATTTCAAGAGGATAG
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATA-
38768901 GAAAA-GATCTT
65 GAAAATGATCTT
**
38768912 GCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGTTTTACTTCAATTTCAAGAGGATAG
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAG
*
38768977 GAAATGATCTT
66 AAAATGATCTT
* * *
38768988 ACTTTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAG
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAG
*
38769053 GAAATGATCTT
66 AAAATGATCTT
38769064 GCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCA
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCA
38769120 GAGATAAAGA
Statistics
Matches: 749, Mismatches: 55, Indels: 26
0.90 0.07 0.03
Matches are distributed among these distances:
75 119 0.16
76 540 0.72
77 21 0.03
78 69 0.09
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (76 bp):
GCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAG
AAAATGATCTT
Found at i:38769110 original size:38 final size:39
Alignment explanation
Indices: 38768230--38769324 Score: 602
Period size: 38 Copynumber: 28.4 Consensus size: 39
38768220 CCACTAGCTC
* *
38768230 TTACTTCAATTTCAGAGGGATGAAGGCTTGATATCCAACT
1 TTACTTCAATTTCAGA-GGATAAAGACTTGATATCCAACT
* ***
38768270 TTACTTCAATTTCAAGAGGATAGAA-A-ATG--ATCTTGCT
1 TTACTTCAATTTC-AGAGGATA-AAGACTTGATATCCAACT
* * **
38768307 CTTACTTTAATTTCAGA-GATAAAGACCTGATATCCTGCT
1 -TTACTTCAATTTCAGAGGATAAAGACTTGATATCCAACT
** **
38768346 TTACTTCAATTTCAAGAGGAT-AAGAAATG--ATCTTACT
1 TTACTTCAATTTC-AGAGGATAAAGACTTGATATCCAACT
* **
38768383 CTTACTTCAATTTCAGA-GATAGAGACTTGATATCCAGTT
1 -TTACTTCAATTTCAGAGGATAAAGACTTGATATCCAACT
* ** ***
38768422 TTACTTCAATTTCAAGAGGAT-AGGAAATG--ATCTTGCT
1 TTACTTCAATTTC-AGAGGATAAAGACTTGATATCCAACT
*
38768459 CTTACTTCAATTTCGGA-GATAAAGACTTGATATCCAAC-
1 -TTACTTCAATTTCAGAGGATAAAGACTTGATATCCAACT
* ** * **
38768497 TTACTTCAATTTCAAGAGGAT-AGGA--AAAGATCTTACT
1 TTACTTCAATTTC-AGAGGATAAAGACTTGATATCCAACT
** *
38768534 CTTACTTCAATTTCAGAGAGACGAAGGCTTGATATCCAACT
1 -TTACTTCAATTTCAGAG-GATAAAGACTTGATATCCAACT
* ***
38768575 TTACTTCAATTTCAAGAGGATAGAA-A-ATG--ATCTTGCT
1 TTACTTCAATTTC-AGAGGATA-AAGACTTGATATCCAACT
* *
38768612 CTTACTTCAATTTCAGA-GATAAAGACCTGATATCCAGCT
1 -TTACTTCAATTTCAGAGGATAAAGACTTGATATCCAACT
** **
38768651 TTACTTCAATTTCAAGAGGAT-AAGAAATG--ATCTTACT
1 TTACTTCAATTTC-AGAGGATAAAGACTTGATATCCAACT
* *
38768688 CTTACTTCAATTTCAGA-GATAGAGACTTGATATCCAGCT
1 -TTACTTCAATTTCAGAGGATAAAGACTTGATATCCAACT
* ** ***
38768727 TTACTTCAATTTCAAGAGGAT-AGGAAATG--ATCTTGCT
1 TTACTTCAATTTC-AGAGGATAAAGACTTGATATCCAACT
* *
38768764 CTTACTTCAATTTCA-AAGATAAAGACTTGTTATCCAACT
1 -TTACTTCAATTTCAGAGGATAAAGACTTGATATCCAACT
* * ** ***
38768803 CTACTTCAATTTCAAGAGGAT-AGGAAAT-A-ATCTTGCT
1 TTACTTCAATTTC-AGAGGATAAAGACTTGATATCCAACT
*
38768840 CTTACTTCAATTTCGGA-GATAAAGACTTGATATCCAAC-
1 -TTACTTCAATTTCAGAGGATAAAGACTTGATATCCAACT
* ** * ***
38768878 TTACTTCAATTTCAAGAGGAT-AGGA--AAAGATCTTGCT
1 TTACTTCAATTTC-AGAGGATAAAGACTTGATATCCAACT
**
38768915 CTTACTTCAATTTCAGA-GATAAAGACTTGATATCCAGTT
1 -TTACTTCAATTTCAGAGGATAAAGACTTGATATCCAACT
* ** **
38768954 TTACTTCAATTTCAAGAGGAT-AGGAAATG--ATCTTACTT
1 TTACTTCAATTTC-AGAGGATAAAGACTTGATATCCAAC-T
*
38768992 TTACTTCAATTTCAGA-GATAAAGACTTGATATCCAGCT
1 TTACTTCAATTTCAGAGGATAAAGACTTGATATCCAACT
* ** ***
38769030 TTACTTCAATTTCAAGAGGAT-AGGAAATG--ATCTTGCT
1 TTACTTCAATTTC-AGAGGATAAAGACTTGATATCCAACT
38769067 CTTACTTCAATTTCAGA-GATAAAGACTTGATATCCAACT
1 -TTACTTCAATTTCAGAGGATAAAGACTTGATATCCAACT
38769106 TTACTTCAATTTCAGA-GATAAAGACTTGATATCCAACT
1 TTACTTCAATTTCAGAGGATAAAGACTTGATATCCAACT
* **
38769144 TTACTTCAATTTCAAGAGGATAGGAAATGATCTTAGTGCTTCATCTTACT
1 TTACTTCAATTTC-AGAGGAT---AAA-GA-C-T--TG-AT-ATCCAACT
* * * *
38769194 CTTACTTCAATTTCAGATAGACAAAGGCTTGATATCCAGCT
1 -TTACTTCAATTTCAGA-GGATAAAGACTTGATATCCAACT
* * ** **
38769235 CTACTTCAATTTCAAGAGGAT-AGGAAATG--ATCTTACT
1 TTACTTCAATTTC-AGAGGATAAAGACTTGATATCCAACT
38769272 CTTACTTCAATTTCAGA-GATAAAGACTTGATATCCAACT
1 -TTACTTCAATTTCAGAGGATAAAGACTTGATATCCAACT
38769311 TTACTTCAATTTCA
1 TTACTTCAATTTCA
38769325 ATAGGATAGG
Statistics
Matches: 799, Mismatches: 166, Indels: 182
0.70 0.14 0.16
Matches are distributed among these distances:
35 4 0.01
36 49 0.06
37 156 0.20
38 322 0.40
39 128 0.16
40 71 0.09
41 26 0.03
42 1 0.00
43 5 0.01
44 2 0.00
45 2 0.00
46 2 0.00
47 1 0.00
48 5 0.01
49 1 0.00
50 9 0.01
51 15 0.02
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (39 bp):
TTACTTCAATTTCAGAGGATAAAGACTTGATATCCAACT
Found at i:38769259 original size:91 final size:89
Alignment explanation
Indices: 38769106--38769269 Score: 274
Period size: 91 Copynumber: 1.8 Consensus size: 89
38769096 ATATCCAACT
* *
38769106 TTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAA
1 TTACTTCAATTTCAGAGACAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAGGATAGGAAA
38769171 TGATCTTAGTGCTTCATCTTACTC
66 TGATCTTAGTGCTTCATCTTACTC
* *
38769195 TTACTTCAATTTCAGATAGACAAAGGCTTGATATCCAGCTCTACTTCAATTTCAAGAGGATAGGA
1 TTACTTCAATTTCAG--AGACAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAGGATAGGA
38769260 AATGATCTTA
64 AATGATCTTA
38769270 CTCTTACTTC
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
89 15 0.22
91 54 0.78
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.34
Consensus pattern (89 bp):
TTACTTCAATTTCAGAGACAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAGGATAGGAAA
TGATCTTAGTGCTTCATCTTACTC
Found at i:38769279 original size:167 final size:167
Alignment explanation
Indices: 38769106--38769426 Score: 633
Period size: 167 Copynumber: 1.9 Consensus size: 167
38769096 ATATCCAACT
38769106 TTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAA
1 TTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAA
38769171 TGATCTTAGTGCTTCATCTTACTCTTACTTCAATTTCAGATAGACAAAGGCTTGATATCCAGCTC
66 TGATCTTAGTGCTTCATCTTACTCTTACTTCAATTTCAGATAGACAAAGGCTTGATATCCAGCTC
38769236 TACTTCAATTTCAAGAGGATAGGAAATGATCTTACTC
131 TACTTCAATTTCAAGAGGATAGGAAATGATCTTACTC
*
38769273 TTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAATAGGATAGGAAA
1 TTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAA
38769338 TGATCTTAGTGCTTCATCTTACTCTTACTTCAATTTCAGATAGACAAAGGCTTGATATCCAGCTC
66 TGATCTTAGTGCTTCATCTTACTCTTACTTCAATTTCAGATAGACAAAGGCTTGATATCCAGCTC
38769403 TACTTCAATTTCAAGAGGATAGGA
131 TACTTCAATTTCAAGAGGATAGGA
38769427 CTTGTCATTT
Statistics
Matches: 153, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
167 153 1.00
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.34
Consensus pattern (167 bp):
TTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAA
TGATCTTAGTGCTTCATCTTACTCTTACTTCAATTTCAGATAGACAAAGGCTTGATATCCAGCTC
TACTTCAATTTCAAGAGGATAGGAAATGATCTTACTC
Found at i:38769325 original size:76 final size:77
Alignment explanation
Indices: 38769186--38769345 Score: 259
Period size: 76 Copynumber: 2.1 Consensus size: 77
38769176 TTAGTGCTTC
* *
38769186 ATCTTACTCTTACTTCAATTTCAGATAGACAAAGGCTTGATATCCAGCTCTACTTCAATTTCAAG
1 ATCTTACTCTTACTTCAATTTCAGA-AGACAAAGACTTGATATCCAACTCTACTTCAATTTCAAG
38769251 AGGATAGGAAATG
65 AGGATAGGAAATG
* * *
38769264 ATCTTACTCTTACTTCAATTTCAG-AGATAAAGACTTGATATCCAACTTTACTTCAATTTCAATA
1 ATCTTACTCTTACTTCAATTTCAGAAGACAAAGACTTGATATCCAACTCTACTTCAATTTCAAGA
38769328 GGATAGGAAATG
66 GGATAGGAAATG
38769340 ATCTTA
1 ATCTTA
38769346 GTGCTTCATC
Statistics
Matches: 77, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
76 53 0.69
78 24 0.31
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.34
Consensus pattern (77 bp):
ATCTTACTCTTACTTCAATTTCAGAAGACAAAGACTTGATATCCAACTCTACTTCAATTTCAAGA
GGATAGGAAATG
Found at i:38769702 original size:51 final size:50
Alignment explanation
Indices: 38769605--38769726 Score: 158
Period size: 51 Copynumber: 2.4 Consensus size: 50
38769595 TTCATGTATC
* *
38769605 GCCGTTACGA-CTTAGATCTTTCTCGTCGTGTTTTCGTGGTACTAGATCT
1 GCCGTTGCGATCTTAGATCTTTCCCGTCGTGTTTTCGTGGTACTAGATCT
* *
38769654 GCCGTTGCGATCTTAGATCTTTCCCTTC-TGTATCTTTGTGGTACTAGATCT
1 GCCGTTGCGATCTTAGATCTTTCCCGTCGTGT-T-TTCGTGGTACTAGATCT
* *
38769705 ACCGTTGCGGTCTTAGATCTTT
1 GCCGTTGCGATCTTAGATCTTT
38769727 TCGGTCCATG
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
49 12 0.19
50 16 0.25
51 36 0.56
ACGTcount: A:0.14, C:0.23, G:0.21, T:0.42
Consensus pattern (50 bp):
GCCGTTGCGATCTTAGATCTTTCCCGTCGTGTTTTCGTGGTACTAGATCT
Found at i:38769792 original size:50 final size:49
Alignment explanation
Indices: 38769738--38769941 Score: 114
Period size: 50 Copynumber: 4.1 Consensus size: 49
38769728 CGGTCCATGC
38769738 TTTTGAGGTACACGG-TCCGCAGTTGCGACTTAGACCTTTCCCTTTTCTAT
1 TTTTGAGGTAC-CGGATCCGCAGTTGCGACTTAGACCTTT-CCTTTTCTAT
* * * * * * *
38769788 TTTTGAAGTACTGGATCTGCCA-TTGTGACTTAGACCTTTTCTTGTTGT-G
1 TTTTGAGGTACCGGATCCG-CAGTTGCGACTTAGACCTTTCCTT-TTCTAT
* * * * * * * ** *
38769837 TTTT-ATGGTGCTGGATCCACCGTTGCGGTCTTAGATCTTTTC-GGTCCAT
1 TTTTGA-GGTACCGGATCCGCAGTTGC-GACTTAGACCTTTCCTTTTCTAT
*
38769886 GCTTTTGAGGTACACGG-TCCGCAGTTGCGACTTAGACCTTTCCCTTTTCTGT
1 --TTTTGAGGTAC-CGGATCCGCAGTTGCGACTTAGACCTTT-CCTTTTCTAT
38769938 TTTT
1 TTTT
38769942 AAAGTACTGG
Statistics
Matches: 110, Mismatches: 31, Indels: 26
0.66 0.19 0.16
Matches are distributed among these distances:
48 3 0.03
49 21 0.19
50 60 0.55
51 20 0.18
52 6 0.05
ACGTcount: A:0.14, C:0.23, G:0.22, T:0.41
Consensus pattern (49 bp):
TTTTGAGGTACCGGATCCGCAGTTGCGACTTAGACCTTTCCTTTTCTAT
Found at i:38769864 original size:150 final size:150
Alignment explanation
Indices: 38769700--38769999 Score: 546
Period size: 150 Copynumber: 2.0 Consensus size: 150
38769690 TGTGGTACTA
*
38769700 GATCTACCGTTGCGGTCTTAGATCTTTTCGGTCCATGCTTTTGAGGTACACGGTCCGCAGTTGCG
1 GATCCACCGTTGCGGTCTTAGATCTTTTCGGTCCATGCTTTTGAGGTACACGGTCCGCAGTTGCG
* *
38769765 ACTTAGACCTTTCCCTTTTCTATTTTTGAAGTACTGGATCTGCCATTGTGACTTAGACCTTTTCT
66 ACTTAGACCTTTCCCTTTTCTATTTTTAAAGTACTGGATCTGCCATTATGACTTAGACCTTTTCT
38769830 TGTTGTGTTTTATGGTGCTG
131 TGTTGTGTTTTATGGTGCTG
38769850 GATCCACCGTTGCGGTCTTAGATCTTTTCGGTCCATGCTTTTGAGGTACACGGTCCGCAGTTGCG
1 GATCCACCGTTGCGGTCTTAGATCTTTTCGGTCCATGCTTTTGAGGTACACGGTCCGCAGTTGCG
* *
38769915 ACTTAGACCTTTCCCTTTTCTGTTTTTAAAGTACTGGATCTGCCATTATGACTTAGACTTTTTCT
66 ACTTAGACCTTTCCCTTTTCTATTTTTAAAGTACTGGATCTGCCATTATGACTTAGACCTTTTCT
*
38769980 TGTTGTGTTTTGTGGTGCTG
131 TGTTGTGTTTTATGGTGCTG
38770000 AGACCTATAA
Statistics
Matches: 144, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
150 144 1.00
ACGTcount: A:0.15, C:0.21, G:0.23, T:0.41
Consensus pattern (150 bp):
GATCCACCGTTGCGGTCTTAGATCTTTTCGGTCCATGCTTTTGAGGTACACGGTCCGCAGTTGCG
ACTTAGACCTTTCCCTTTTCTATTTTTAAAGTACTGGATCTGCCATTATGACTTAGACCTTTTCT
TGTTGTGTTTTATGGTGCTG
Found at i:38774727 original size:29 final size:27
Alignment explanation
Indices: 38774695--38774851 Score: 122
Period size: 29 Copynumber: 5.4 Consensus size: 27
38774685 TACGGATACC
38774695 CGGGGGTAAAATGGTAATTTTGGTGAAAT
1 CGGGGGTAAAATGG-AATTTT-GTGAAAT
* *
38774724 CGGGGTTAAAAATGGAATTTT-AGAAGATT
1 CGGGGGT-AAAATGGAATTTTGTGAA-A-T
*
38774753 CGAGGGGTAAAATGGTAATCTTCAGTGAAAT
1 CG-GGGGTAAAATGG-AAT-TT-TGTGAAAT
* *
38774784 CGGGGTTAAAATGGAATTTT-AGAAGATT
1 CGGGGGTAAAATGGAATTTTGTGAA-A-T
38774812 CGGGGGTAAAATGGCAAATTTTGGTGAAAT
1 CGGGGGTAAAATGG--AATTTT-GTGAAAT
38774842 C-GGGGTAAAA
1 CGGGGGTAAAA
38774852 AAATGGTTTT
Statistics
Matches: 104, Mismatches: 10, Indels: 28
0.73 0.07 0.20
Matches are distributed among these distances:
26 3 0.03
27 4 0.04
28 17 0.16
29 34 0.33
30 33 0.32
31 6 0.06
32 4 0.04
33 3 0.03
ACGTcount: A:0.35, C:0.06, G:0.31, T:0.28
Consensus pattern (27 bp):
CGGGGGTAAAATGGAATTTTGTGAAAT
Found at i:38774738 original size:30 final size:28
Alignment explanation
Indices: 38774695--38774852 Score: 117
Period size: 30 Copynumber: 5.4 Consensus size: 28
38774685 TACGGATACC
*
38774695 CGGGGGTAAAATGGTAATTTTGGTGAAAT
1 CGGGGTTAAAATGGTAATTTT-GTGAAAT
*
38774724 CGGGGTTAAAAATGG-AATTTT-AGAAGATT
1 CGGGGTT-AAAATGGTAATTTTGTGAA-A-T
* *
38774753 CGAGGGGTAAAATGGTAATCTTCAGTGAAAT
1 CG-GGGTTAAAATGGTAAT-TT-TGTGAAAT
*
38774784 CGGGGTTAAAATGG-AATTTT-AGAAGATT
1 CGGGGTTAAAATGGTAATTTTGTGAA-A-T
* *
38774812 CGGGGGTAAAATGGCAAATTTTGGTGAAAT
1 CGGGGTTAAAATGG-TAATTTT-GTGAAAT
*
38774842 CGGGGTAAAAA
1 CGGGGTTAAAA
38774853 AATGGTTTTT
Statistics
Matches: 103, Mismatches: 12, Indels: 27
0.73 0.08 0.19
Matches are distributed among these distances:
26 3 0.03
27 4 0.04
28 17 0.17
29 25 0.24
30 41 0.40
31 6 0.06
32 4 0.04
33 3 0.03
ACGTcount: A:0.35, C:0.06, G:0.31, T:0.28
Consensus pattern (28 bp):
CGGGGTTAAAATGGTAATTTTGTGAAAT
Found at i:38774864 original size:59 final size:57
Alignment explanation
Indices: 38774695--38774852 Score: 244
Period size: 59 Copynumber: 2.7 Consensus size: 57
38774685 TACGGATACC
38774695 CGGGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATT
1 CGGGGGTAAAATGGTAATTTTGGTGAAATCGGGG-TAAAAATGGAATTTTAGAAGATT
** *
38774753 CGAGGGGTAAAATGGTAATCTTCAGTGAAATCGGGGTTAAAATGGAATTTTAGAAGATT
1 CG-GGGGTAAAATGGTAAT-TTTGGTGAAATCGGGGTAAAAATGGAATTTTAGAAGATT
*
38774812 CGGGGGTAAAATGGCAAATTTTGGTGAAATCGGGGTAAAAA
1 CGGGGGTAAAATGG-TAATTTTGGTGAAATCGGGGTAAAAA
38774853 AATGGTTTTT
Statistics
Matches: 90, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
58 33 0.37
59 43 0.48
60 14 0.16
ACGTcount: A:0.35, C:0.06, G:0.31, T:0.28
Consensus pattern (57 bp):
CGGGGGTAAAATGGTAATTTTGGTGAAATCGGGGTAAAAATGGAATTTTAGAAGATT
Found at i:38774906 original size:30 final size:30
Alignment explanation
Indices: 38774867--38774981 Score: 153
Period size: 30 Copynumber: 3.9 Consensus size: 30
38774857 GTTTTTAGGG
* *
38774867 AAGTTTAGGGG-TAAAATGATAATTTTCG-A
1 AAGTTTTGGGGTTAAAATG-TAATTTTGGAA
* * *
38774896 AAGTTTTAGGGTCAAAATGCAATTTTGGAA
1 AAGTTTTGGGGTTAAAATGTAATTTTGGAA
38774926 AAGTTTTGGGGTTAAAATGTAATTTTGGAA
1 AAGTTTTGGGGTTAAAATGTAATTTTGGAA
*
38774956 AAGTTTTGGGGTTAAAATGAAATTTT
1 AAGTTTTGGGGTTAAAATGTAATTTT
38774982 TGGATTGTTT
Statistics
Matches: 75, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
29 16 0.21
30 59 0.79
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.37
Consensus pattern (30 bp):
AAGTTTTGGGGTTAAAATGTAATTTTGGAA
Found at i:38774913 original size:118 final size:115
Alignment explanation
Indices: 38774695--38774921 Score: 255
Period size: 118 Copynumber: 1.9 Consensus size: 115
38774685 TACGGATACC
* *
38774695 CGGGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTCGAGGGG
1 CGGGGGTAAAATGGAAATTTTGGTGAAATCGGGGTAAAAAATGGAATTTTAGAAGATTCGAGGGG
* * * *
38774760 TAAAATGGTAATCTTCAGTGAAATCGGGGTTAAAATGGAATTTTAGAAGATT
66 TAAAATGATAATCTTCA--GAAATCAGGGTCAAAATGCAATTTTAGAAGATT
* *
38774812 CGGGGGTAAAATGGCAAATTTTGGTGAAATCGGGGTAAAAAAATGG-TTTTTAGGGAAG-TT-TA
1 CGGGGGTAAAATGG-AAATTTTGGTGAAATCGGGGT-AAAAAATGGAATTTTA--GAAGATTCGA
* *
38774874 GGGGTAAAATGATAATTTTC-GAAAGTTTTAGGGTCAAAATGCAATTTT
62 GGGGTAAAATGATAATCTTCAGAAA---TCAGGGTCAAAATGCAATTTT
38774922 GGAAAAGTTT
Statistics
Matches: 93, Mismatches: 10, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
115 4 0.04
117 14 0.15
118 61 0.66
119 10 0.11
120 4 0.04
ACGTcount: A:0.35, C:0.05, G:0.29, T:0.31
Consensus pattern (115 bp):
CGGGGGTAAAATGGAAATTTTGGTGAAATCGGGGTAAAAAATGGAATTTTAGAAGATTCGAGGGG
TAAAATGATAATCTTCAGAAATCAGGGTCAAAATGCAATTTTAGAAGATT
Found at i:38776819 original size:17 final size:16
Alignment explanation
Indices: 38776794--38776843 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 16
38776784 CAAATTTACT
* *
38776794 AAATCTAAATTTAACAC
1 AAATTTAAATTTAA-AA
38776811 AAATTTAAATTTAAAA
1 AAATTTAAATTTAAAA
38776827 ATTAATTTAAATTTAAA
1 A--AATTTAAATTTAAA
38776844 TTTTAAGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 2 0.07
17 13 0.45
18 14 0.48
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATTTAAATTTAAAA
Found at i:38776855 original size:18 final size:18
Alignment explanation
Indices: 38776834--38776882 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
38776824 AAAATTAATT
38776834 TAAATTTAAATTT-TAAGA
1 TAAATTTAAATTTGTAA-A
**
38776852 TAAATCCAAATTTGTAAA
1 TAAATTTAAATTTGTAAA
38776870 TAAATTTAGAATT
1 TAAATTTA-AATT
38776883 AACTTAAATC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.41
Consensus pattern (18 bp):
TAAATTTAAATTTGTAAA
Found at i:38776862 original size:24 final size:24
Alignment explanation
Indices: 38776810--38776864 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
38776800 AAATTTAACA
* *
38776810 CAAATTTAAATTTAAAAATTAATT
1 CAAATTTAAATTTAAAAATAAATC
* * *
38776834 TAAATTTAAATTTTAAGATAAATC
1 CAAATTTAAATTTAAAAATAAATC
38776858 CAAATTT
1 CAAATTT
38776865 GTAAATAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (24 bp):
CAAATTTAAATTTAAAAATAAATC
Found at i:38779443 original size:13 final size:13
Alignment explanation
Indices: 38779411--38779443 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
38779401 AATTTGGACC
38779411 TTTAA-TTAAATT
1 TTTAATTTAAATT
38779423 TTTAAATTTAAATT
1 TTT-AATTTAAATT
38779437 TTTAATT
1 TTTAATT
38779444 CGAAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.16
13 6 0.32
14 10 0.53
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TTTAATTTAAATT
Found at i:38784103 original size:12 final size:12
Alignment explanation
Indices: 38784080--38784131 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
38784070 TATGGGTCTA
*
38784080 ATAAACGAGCTT
1 ATAAATGAGCTT
*
38784092 ATAAATGGGCTT
1 ATAAATGAGCTT
* *
38784104 -TAAACGAGCTA
1 ATAAATGAGCTT
*
38784115 ATAAATGAGCTC
1 ATAAATGAGCTT
38784127 ATAAA
1 ATAAA
38784132 CGAACCATAA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
11 8 0.25
12 24 0.75
ACGTcount: A:0.44, C:0.13, G:0.17, T:0.25
Consensus pattern (12 bp):
ATAAATGAGCTT
Found at i:38786967 original size:13 final size:13
Alignment explanation
Indices: 38786941--38786979 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
38786931 TAGCTTCTCT
38786941 ATTTTAACTTTTTA
1 ATTTTAA-TTTTTA
*
38786955 GTTTTAATTTTTA
1 ATTTTAATTTTTA
*
38786968 ATTTTACTTTTT
1 ATTTTAATTTTT
38786980 TATACGAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.69
Consensus pattern (13 bp):
ATTTTAATTTTTA
Found at i:38787779 original size:18 final size:18
Alignment explanation
Indices: 38787756--38787796 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
38787746 TGCCCATGTT
38787756 CCTTTTGCTGTGGTTATA
1 CCTTTTGCTGTGGTTATA
38787774 CCTTTTGCTGTGGTTATA
1 CCTTTTGCTGTGGTTATA
38787792 -CTTTT
1 CCTTTT
38787797 ACTAATTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.10, C:0.17, G:0.20, T:0.54
Consensus pattern (18 bp):
CCTTTTGCTGTGGTTATA
Found at i:38793409 original size:6 final size:6
Alignment explanation
Indices: 38793395--38793447 Score: 88
Period size: 6 Copynumber: 8.8 Consensus size: 6
38793385 ATTTAAATTA
* *
38793395 AATAAG AATAGG AATAGG AATAGG AATAGG AATAGG AGTAGG AATAGG
1 AATAGG AATAGG AATAGG AATAGG AATAGG AATAGG AATAGG AATAGG
38793443 AATAG
1 AATAG
38793448 AGCAGAAGAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.51, C:0.00, G:0.32, T:0.17
Consensus pattern (6 bp):
AATAGG
Found at i:38794879 original size:24 final size:23
Alignment explanation
Indices: 38794862--38794928 Score: 109
Period size: 24 Copynumber: 2.9 Consensus size: 23
38794852 ACAAAATTGA
38794862 AAAGTACAAAAACTACAATTAATC
1 AAAGTACAAAAACTACAA-TAATC
38794886 AAAGTACAAAAACTACAATTAATC
1 AAAGTACAAAAACTACAA-TAATC
38794910 AAAGTACAAAAACTA-AATA
1 AAAGTACAAAAACTACAATA
38794929 CATGACTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
22 2 0.05
23 2 0.05
24 39 0.91
ACGTcount: A:0.61, C:0.15, G:0.04, T:0.19
Consensus pattern (23 bp):
AAAGTACAAAAACTACAATAATC
Found at i:38795083 original size:6 final size:6
Alignment explanation
Indices: 38795024--38795082 Score: 109
Period size: 6 Copynumber: 9.8 Consensus size: 6
38795014 CATGGGCAAA
38795024 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG
1 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG
*
38795072 GAGAGA GAGAG
1 GAGAGG GAGAG
38795083 ACAAGTCTGA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 52 1.00
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (6 bp):
GAGAGG
Found at i:38805047 original size:18 final size:18
Alignment explanation
Indices: 38805024--38805059 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
38805014 ATTTGTAAGG
*
38805024 TTTTATATTATGTTATTT
1 TTTTATATTATGTAATTT
38805042 TTTTATATTATGTAATTT
1 TTTTATATTATGTAATTT
38805060 ATAACACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (18 bp):
TTTTATATTATGTAATTT
Found at i:38806186 original size:49 final size:49
Alignment explanation
Indices: 38806114--38806214 Score: 175
Period size: 49 Copynumber: 2.1 Consensus size: 49
38806104 AAGCAGTGTC
* *
38806114 TGTATTCTTATCGTTTGGAAGAAAATGCGTCTGTGCACGAACACTTGAA
1 TGTATTCTCATCGTTTGGAAGAAAATGCGTCTGTGCACAAACACTTGAA
*
38806163 TGTATTCTCATCGTTTGGAAGAAAGTGCGTCTGTGCACAAACACTTGAA
1 TGTATTCTCATCGTTTGGAAGAAAATGCGTCTGTGCACAAACACTTGAA
38806212 TGT
1 TGT
38806215 GTTTAAAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.33
Consensus pattern (49 bp):
TGTATTCTCATCGTTTGGAAGAAAATGCGTCTGTGCACAAACACTTGAA
Found at i:38809984 original size:5 final size:5
Alignment explanation
Indices: 38809974--38809998 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
38809964 ACTAGACTTC
38809974 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
38809999 ATTAGAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:38810854 original size:26 final size:26
Alignment explanation
Indices: 38810825--38810876 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
38810815 AGAACTTAGT
38810825 TAAGGAACTCATAAGGCAATTAAACC
1 TAAGGAACTCATAAGGCAATTAAACC
*
38810851 TAAGGGACTCATAAGGCAATTAAACC
1 TAAGGAACTCATAAGGCAATTAAACC
38810877 ATGATTCTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.19
Consensus pattern (26 bp):
TAAGGAACTCATAAGGCAATTAAACC
Found at i:38814466 original size:21 final size:21
Alignment explanation
Indices: 38814442--38814483 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
38814432 TAAACTTAAG
38814442 TTAGAACTTAGTCCTAAAAGC
1 TTAGAACTTAGTCCTAAAAGC
38814463 TTAGAACTTAGTCCTAAAAGC
1 TTAGAACTTAGTCCTAAAAGC
38814484 AATTTTGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (21 bp):
TTAGAACTTAGTCCTAAAAGC
Done.