Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001289.1 Hibiscus syriacus cultivar Beakdansim tig00002525_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 109021
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:322 original size:6 final size:6
Alignment explanation
Indices: 311--339 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
301 GTGTTTACCC
311 TAATTA TAATTA TAATTA TAATTA TAATT
1 TAATTA TAATTA TAATTA TAATTA TAATT
340 TTTGAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TAATTA
Found at i:737 original size:16 final size:16
Alignment explanation
Indices: 716--748 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
706 TAAAAAATAA
*
716 ACGAACATAAACGAAC
1 ACGAACATAAACAAAC
732 ACGAACATAAACAAAC
1 ACGAACATAAACAAAC
748 A
1 A
749 AATTTTTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.61, C:0.24, G:0.09, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACAAAC
Found at i:837 original size:16 final size:16
Alignment explanation
Indices: 806--871 Score: 84
Period size: 16 Copynumber: 4.3 Consensus size: 16
796 TCGTTCATTA
806 ATAAAT-AA-ACGAAC
1 ATAAATGAACACGAAC
*
820 ATAAATGAACATGAAC
1 ATAAATGAACACGAAC
*
836 ATAAACG-ACACGAAC
1 ATAAATGAACACGAAC
*
851 ATAAATGAATACGAAC
1 ATAAATGAACACGAAC
867 ATAAA
1 ATAAA
872 CAAACATAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
14 6 0.14
15 15 0.34
16 23 0.52
ACGTcount: A:0.59, C:0.15, G:0.11, T:0.15
Consensus pattern (16 bp):
ATAAATGAACACGAAC
Found at i:849 original size:31 final size:31
Alignment explanation
Indices: 814--872 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
804 TAATAAATAA
*
814 ACGAACATAAATGAACATGAACATAAACGAC
1 ACGAACATAAATGAACACGAACATAAACGAC
*
845 ACGAACATAAATGAATACGAACATAAAC
1 ACGAACATAAATGAACACGAACATAAAC
873 AAACATAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.56, C:0.19, G:0.12, T:0.14
Consensus pattern (31 bp):
ACGAACATAAATGAACACGAACATAAACGAC
Found at i:1990 original size:13 final size:14
Alignment explanation
Indices: 1969--2011 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
1959 GAATGAACAT
*
1969 AAACAAACA-AACG
1 AAACGAACATAACG
1982 AAACGAACATAACG
1 AAACGAACATAACG
1996 -AACGAACATAAACG
1 AAACGAACAT-AACG
2010 AA
1 AA
2012 CATAACTGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
13 17 0.65
14 8 0.31
15 1 0.04
ACGTcount: A:0.63, C:0.21, G:0.12, T:0.05
Consensus pattern (14 bp):
AAACGAACATAACG
Found at i:1991 original size:23 final size:24
Alignment explanation
Indices: 1963--2016 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
1953 ATAAATGAAT
1963 GAACATAAACAAACAAAC-GAAAC
1 GAACATAAACAAACAAACAGAAAC
* * *
1986 GAACAT-AACGAACGAACATAAAC
1 GAACATAAACAAACAAACAGAAAC
2009 GAACATAA
1 GAACATAA
2017 CTGAACGTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 9 0.35
23 16 0.62
24 1 0.04
ACGTcount: A:0.61, C:0.20, G:0.11, T:0.07
Consensus pattern (24 bp):
GAACATAAACAAACAAACAGAAAC
Found at i:2012 original size:14 final size:14
Alignment explanation
Indices: 1977--2012 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1967 ATAAACAAAC
1977 AAACGAAACGAACAT
1 AAACG-AACGAACAT
1992 -AACGAACGAACAT
1 AAACGAACGAACAT
2005 AAACGAAC
1 AAACGAAC
2013 ATAACTGAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.58, C:0.22, G:0.14, T:0.06
Consensus pattern (14 bp):
AAACGAACGAACAT
Found at i:8459 original size:20 final size:20
Alignment explanation
Indices: 8431--8479 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
8421 AACTCCCCTC
* *
8431 CTTCTCCCTCTTCTGTCATT
1 CTTCCCCCTCTTCGGTCATT
8451 CTTCCCCCTCTTCGGTCATT
1 CTTCCCCCTCTTCGGTCATT
8471 CTTCCCCCT
1 CTTCCCCCT
8480 ATCCACTGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.04, C:0.47, G:0.06, T:0.43
Consensus pattern (20 bp):
CTTCCCCCTCTTCGGTCATT
Found at i:9607 original size:22 final size:21
Alignment explanation
Indices: 9582--9670 Score: 69
Period size: 19 Copynumber: 4.3 Consensus size: 21
9572 TATATATATC
*
9582 ATATATTTTCAAAAAGTATAGA
1 ATATATTTTCAAAAACTATA-A
* * *
9604 ATATGTTTTTAAAAACTATAT
1 ATATATTTTCAAAAACTATAA
* *
9625 ATATA-TTT-AAAAACCATAT
1 ATATATTTTCAAAAACTATAA
*
9644 ATAT-TTTTC-AAAACTATATT
1 ATATATTTTCAAAAACTATA-A
9664 ATATATT
1 ATATATT
9671 ATACGTTTTC
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
19 25 0.45
20 8 0.14
21 6 0.11
22 17 0.30
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (21 bp):
ATATATTTTCAAAAACTATAA
Found at i:9633 original size:19 final size:19
Alignment explanation
Indices: 9611--9670 Score: 84
Period size: 19 Copynumber: 3.1 Consensus size: 19
9601 AGAATATGTT
9611 TTTAAAAACTATATATATA
1 TTTAAAAACTATATATATA
* *
9630 TTTAAAAACCATATATATT
1 TTTAAAAACTATATATATA
*
9649 TTTCAAAACTATATTATATA
1 TTTAAAAACTATA-TATATA
9669 TT
1 TT
9671 ATACGTTTTC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 28 0.80
20 7 0.20
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (19 bp):
TTTAAAAACTATATATATA
Found at i:9690 original size:22 final size:21
Alignment explanation
Indices: 9663--9712 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 21
9653 AAAACTATAT
*
9663 TATATATTATACGTTTTCCAAAA
1 TATATATTATA--TTTTCAAAAA
9686 T-TATATTATATTTTCAAAAA
1 TATATATTATATTTTCAAAAA
9706 TATATAT
1 TATATAT
9713 ACTATATATC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 10 0.40
21 5 0.20
22 9 0.36
23 1 0.04
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.48
Consensus pattern (21 bp):
TATATATTATATTTTCAAAAA
Found at i:9709 original size:19 final size:21
Alignment explanation
Indices: 9664--9715 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 21
9654 AAACTATATT
9664 ATATATTATACGTTTTCCAAAA
1 ATATATTATAC-TTTTCCAAAA
*
9686 TTATATTATA-TTTT-CAAAA
1 ATATATTATACTTTTCCAAAA
9705 ATATA-TATACT
1 ATATATTATACT
9716 ATATATCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 4 0.15
19 10 0.37
20 4 0.15
22 9 0.33
ACGTcount: A:0.42, C:0.10, G:0.02, T:0.46
Consensus pattern (21 bp):
ATATATTATACTTTTCCAAAA
Found at i:9741 original size:15 final size:16
Alignment explanation
Indices: 9713--9746 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
9703 AAATATATAT
*
9713 ACTATATATCTTTTAAA
1 ACTATATAT-TTTCAAA
9730 ACTATATATTTTCAAA
1 ACTATATATTTTCAAA
9746 A
1 A
9747 AAATTATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (16 bp):
ACTATATATTTTCAAA
Found at i:9744 original size:42 final size:37
Alignment explanation
Indices: 9692--9776 Score: 107
Period size: 37 Copynumber: 2.2 Consensus size: 37
9682 AAAATTATAT
9692 TATATTTTCAAAAATATATATACTATATATCTTTTAAAACTA
1 TATATTTTCAAAAA-A-AT-TA-TATATAT-TTTTAAAACTA
*
9734 TATATTTTCAAAAAAATTATATATATTTTTTAAACTA
1 TATATTTTCAAAAAAATTATATATATTTTTAAAACTA
*
9771 CATATT
1 TATATT
9777 ATTATAAGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
37 15 0.37
38 7 0.17
39 2 0.05
40 2 0.05
41 1 0.02
42 14 0.34
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (37 bp):
TATATTTTCAAAAAAATTATATATATTTTTAAAACTA
Found at i:12919 original size:9 final size:9
Alignment explanation
Indices: 12868--12980 Score: 51
Period size: 9 Copynumber: 12.9 Consensus size: 9
12858 TGGAAGGAAA
12868 AAATAAAAG
1 AAATAAAAG
*
12877 TGAATAAAAG
1 -AAATAAAAG
*
12887 -AA-AAAAC
1 AAATAAAAG
* *
12894 AAGTAAAAT
1 AAATAAAAG
12903 AAAGTAAAAG
1 AAA-TAAAAG
12913 AAATAAAA-
1 AAATAAAAG
*
12921 AAA-AAGA-
1 AAATAAAAG
*
12928 AAAGAAAAG
1 AAATAAAAG
* *
12937 TGAATAAAAT
1 -AAATAAAAG
*
12947 AAATAAAAT
1 AAATAAAAG
12956 AAATAAATA-
1 AAATAAA-AG
*
12965 AAAT-AAAT
1 AAATAAAAG
12973 AAATAAAA
1 AAATAAAA
12981 TAAAGACAAT
Statistics
Matches: 82, Mismatches: 12, Indels: 19
0.73 0.11 0.17
Matches are distributed among these distances:
7 11 0.13
8 15 0.18
9 33 0.40
10 23 0.28
ACGTcount: A:0.75, C:0.01, G:0.09, T:0.15
Consensus pattern (9 bp):
AAATAAAAG
Found at i:12947 original size:5 final size:5
Alignment explanation
Indices: 12879--12984 Score: 66
Period size: 5 Copynumber: 22.2 Consensus size: 5
12869 AATAAAAGTG
* * * * *
12879 AATAA AAGAA AA-AA CAAGTAA AATAA AGTAA AA-GA AATAA AAAAA AAGAA
1 AATAA AATAA AATAA -AA-TAA AATAA AATAA AATAA AATAA AATAA AATAA
* *
12929 AAGAA AAGT-G AATAA AAT-A AATAA AAT-A AAT-A AATAA AAT-A AAT-A
1 AATAA AA-TAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA
12974 AATAA AATAA A
1 AATAA AATAA A
12985 GACAATAATG
Statistics
Matches: 82, Mismatches: 10, Indels: 18
0.75 0.09 0.16
Matches are distributed among these distances:
4 26 0.32
5 52 0.63
6 2 0.02
7 2 0.02
ACGTcount: A:0.76, C:0.01, G:0.08, T:0.15
Consensus pattern (5 bp):
AATAA
Found at i:12952 original size:4 final size:4
Alignment explanation
Indices: 12943--13070 Score: 61
Period size: 4 Copynumber: 30.8 Consensus size: 4
12933 AAAGTGAATA
*
12943 AAAT AAAT AAAAT AAAT AAAT AAAAT AAAT AAAT AAAAT AAAG ACAAT
1 AAAT AAAT -AAAT AAAT AAAT -AAAT AAAT AAAT -AAAT AAAT A-AAT
* ** *
12991 -AAT GACAAC ATCT AAATGT GAGAT -AAT -AAT AAAT -AAT AAAT -AA-
1 AAAT -A-AAT AAAT AAA--T -AAAT AAAT AAAT AAAT AAAT AAAT AAAT
*
13034 AAAT AAAAT AAGT AAAT AAAT AAAT AAAT AAAAT AAA
1 AAAT -AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAA
13071 GATGCATATA
Statistics
Matches: 96, Mismatches: 12, Indels: 32
0.69 0.09 0.23
Matches are distributed among these distances:
3 15 0.16
4 52 0.54
5 24 0.25
6 3 0.03
7 2 0.02
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:12961 original size:13 final size:13
Alignment explanation
Indices: 12943--12984 Score: 84
Period size: 13 Copynumber: 3.2 Consensus size: 13
12933 AAAGTGAATA
12943 AAATAAATAAAAT
1 AAATAAATAAAAT
12956 AAATAAATAAAAT
1 AAATAAATAAAAT
12969 AAATAAATAAAAT
1 AAATAAATAAAAT
12982 AAA
1 AAA
12985 GACAATAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AAATAAATAAAAT
Found at i:12981 original size:9 final size:9
Alignment explanation
Indices: 12897--13148 Score: 84
Period size: 9 Copynumber: 27.9 Consensus size: 9
12887 AAAAAACAAG
12897 TAAAATAAA
1 TAAAATAAA
*
12906 GTAAAAGAAA
1 -TAAAATAAA
12916 TAAAA-AAA
1 TAAAATAAA
*
12924 -AAGA-AAA
1 TAAAATAAA
* *
12931 GAAAAGTGAA
1 TAAAA-TAAA
12941 TAAAATAAA
1 TAAAATAAA
12950 TAAAATAAA
1 TAAAATAAA
12959 T-AAATAAA
1 TAAAATAAA
12967 -ATAAATAAA
1 TA-AAATAAA
12976 TAAAATAAA
1 TAAAATAAA
* *
12985 GACAAT-AA
1 TAAAATAAA
* * **
12993 TGACAACATC
1 T-AAAATAAA
* *
13003 TAAATGTGAGA
1 TAAA-AT-AAA
13014 TAATAATAAA
1 TAA-AATAAA
13024 T--AATAAA
1 TAAAATAAA
13031 T--AA-AAA
1 TAAAATAAA
*
13037 TAAAATAAG
1 TAAAATAAA
13046 T-AAATAAA
1 TAAAATAAA
13054 T-AAATAAA
1 TAAAATAAA
13062 TAAAATAAAGA
1 TAAAAT-AA-A
* *
13073 TGCATATAAA
1 T-AAAATAAA
13083 TAAAATATTAA
1 TAAAATA--AA
*
13094 GAGAAA-AAA
1 TA-AAATAAA
13103 TAAAATAAAA
1 TAAAAT-AAA
**
13113 TAAAATATG
1 TAAAATAAA
*
13122 TAAAATATA
1 TAAAATAAA
13131 TAATAAT-AA
1 TAA-AATAAA
13140 TAATAATAA
1 TAA-AATAA
13149 TAATGAAATA
Statistics
Matches: 186, Mismatches: 31, Indels: 50
0.70 0.12 0.19
Matches are distributed among these distances:
6 4 0.02
7 15 0.08
8 35 0.19
9 76 0.41
10 36 0.19
11 13 0.07
12 7 0.04
ACGTcount: A:0.69, C:0.02, G:0.07, T:0.22
Consensus pattern (9 bp):
TAAAATAAA
Found at i:13141 original size:6 final size:6
Alignment explanation
Indices: 13101--13183 Score: 50
Period size: 6 Copynumber: 13.8 Consensus size: 6
13091 TAAGAGAAAA
*
13101 AATAA- AATAA- AATAA- AATATGT AA-AAT ATATAAT AATAAT AATAAT
1 AATAAT AATAAT AATAAT AATA-AT AATAAT A-ATAAT AATAAT AATAAT
* * *
13147 AATAAT GA-AAT ATATATAT ATATAAC GATAAT AATAA
1 AATAAT AATAAT A-ATA-AT A-ATAAT AATAAT AATAA
13184 AGACAAAAGA
Statistics
Matches: 63, Mismatches: 8, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
5 19 0.30
6 29 0.46
7 8 0.13
8 7 0.11
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (6 bp):
AATAAT
Found at i:13162 original size:32 final size:31
Alignment explanation
Indices: 13102--13183 Score: 84
Period size: 32 Copynumber: 2.7 Consensus size: 31
13092 AAGAGAAAAA
13102 ATAA-AATAAAATAA-AAT-ATGTAAAATAT
1 ATAATAATAAAATAATAATAATGTAAAATAT
13130 ATAATAATAATAATAATAATAATG--AAATAT
1 ATAATAATAA-AATAATAATAATGTAAAATAT
*
13160 ATATATATATAACGATAATAATAA
1 ATA-ATA-ATAA-AATAATAATAA
13184 AGACAAAAGA
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
28 4 0.09
29 5 0.11
30 14 0.30
31 6 0.13
32 17 0.37
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.32
Consensus pattern (31 bp):
ATAATAATAAAATAATAATAATGTAAAATAT
Found at i:13168 original size:38 final size:38
Alignment explanation
Indices: 13101--13183 Score: 98
Period size: 38 Copynumber: 2.2 Consensus size: 38
13091 TAAGAGAAAA
* *
13101 AATAA-AATAAAATAAAATATGTAAAATATATAATAAT
1 AATAATAATAAAATAAAATATATAAAATATATAACAAT
* * *
13138 AATAATAATAATAATGAAATATAT-ATATATATAACGAT
1 AATAATAATAA-AATAAAATATATAAAATATATAACAAT
13176 AATAATAA
1 AATAATAA
13184 AGACAAAAGA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
37 5 0.13
38 24 0.62
39 10 0.26
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (38 bp):
AATAATAATAAAATAAAATATATAAAATATATAACAAT
Found at i:13256 original size:21 final size:21
Alignment explanation
Indices: 13230--13492 Score: 62
Period size: 21 Copynumber: 12.0 Consensus size: 21
13220 AAAAAATAGA
13230 AATAAAAATAATATATAATAT
1 AATAAAAATAATATATAATAT
* *
13251 AATAAAAAATAAAAAATAA-AT
1 AAT-AAAAATAATATATAATAT
*
13272 AAAAAAAATATAATTATATATATAT
1 -AATAAAA-ATAA-TATATA-ATAT
* * *
13297 AATGATAA-AATATAGTACT-T
1 AATAAAAATAATATA-TAATAT
* *
13317 AAATAAAAAATAATCAAATAAAAAT
1 -AAT-AAAAATAAT-ATAT-AATAT
**
13342 AATTTAAAT-ATATATATATAT
1 AATAAAAATAATATATA-ATAT
** * *
13363 ATATATTAATAATAGGTGTAAATAA
1 A-ATAAAAATAATA--TAT-AATAT
* *
13388 AATATTAACAA-AATATTTGTATAT
1 AATA--AA-AATAATATAT-AATAT
*
13412 ATATATAAAACAA-A-ATAA-AT
1 A-ATA-AAAATAATATATAATAT
*
13432 AATAGAAAATAATA-ATAAAAT
1 AATA-AAAATAATATATAATAT
*
13453 AATAATAATAATA-ATAATAAT
1 AATAAAAATAATATATAAT-AT
*
13474 AATAATAATAATA-ATAATA
1 AATAAAAATAATATATAATA
13493 ATACAAGGAT
Statistics
Matches: 181, Mismatches: 34, Indels: 55
0.67 0.13 0.20
Matches are distributed among these distances:
19 9 0.05
20 23 0.13
21 51 0.28
22 35 0.19
23 19 0.10
24 25 0.14
25 12 0.07
26 5 0.03
27 2 0.01
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.32
Consensus pattern (21 bp):
AATAAAAATAATATATAATAT
Found at i:13259 original size:22 final size:22
Alignment explanation
Indices: 13233--13308 Score: 73
Period size: 22 Copynumber: 3.3 Consensus size: 22
13223 AAATAGAAAT
13233 AAAAATAATATATAATATAATA
1 AAAAATAATATATAATATAATA
* * *
13255 AAAAATAAAAAATAA-ATAAAA
1 AAAAATAATATATAATATAATA
13276 AAAATATAATTATATATATATAATGA
1 AAAA-ATAA-TATATA-ATATAAT-A
*
13302 TAAAATA
1 AAAAATA
13309 TAGTACTTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
21 9 0.21
22 17 0.40
23 4 0.10
24 1 0.02
25 7 0.17
26 4 0.10
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (22 bp):
AAAAATAATATATAATATAATA
Found at i:13279 original size:42 final size:46
Alignment explanation
Indices: 13220--13308 Score: 107
Period size: 41 Copynumber: 2.0 Consensus size: 46
13210 TAATGCAGTA
* *
13220 AAAAAAT-AGAAATAAAA-ATAA-TATATA-ATATAAT-AAAAAAT
1 AAAAAATAAAAAAAAAAATATAATTATATATATATAATGAAAAAAT
*
13261 AAAAAATAAATAAAAAAAATATAATTATATATATATAATGATAAAAT
1 AAAAAATAAA-AAAAAAAATATAATTATATATATATAATGAAAAAAT
13308 A
1 A
13309 TAGTACTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
41 7 0.18
42 1 0.03
43 7 0.18
44 4 0.10
45 6 0.15
46 7 0.18
47 7 0.18
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (46 bp):
AAAAAATAAAAAAAAAAATATAATTATATATATATAATGAAAAAAT
Found at i:13445 original size:3 final size:3
Alignment explanation
Indices: 13429--13495 Score: 109
Period size: 3 Copynumber: 22.3 Consensus size: 3
13419 AAACAAAATA
*
13429 AAT AAT AGAA AAT AAT AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
13474 AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT A
13496 CAAGGATTAC
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
2 2 0.03
3 56 0.93
4 2 0.03
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:15407 original size:10 final size:10
Alignment explanation
Indices: 15392--15417 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
15382 TGGAAGACTA
15392 AATTTATTTT
1 AATTTATTTT
15402 AATTTATTTT
1 AATTTATTTT
15412 AATTTA
1 AATTTA
15418 ATATTATTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
AATTTATTTT
Found at i:15417 original size:15 final size:16
Alignment explanation
Indices: 15394--15426 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
15384 GAAGACTAAA
*
15394 TTTATTTTAAT-TTAT
1 TTTAATTTAATATTAT
15409 TTTAATTTAATATTAT
1 TTTAATTTAATATTAT
15425 TT
1 TT
15427 CTACCATCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTAATTTAATATTAT
Found at i:15699 original size:29 final size:29
Alignment explanation
Indices: 15666--15725 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
15656 AATTATCTCA
*
15666 TTATTTTTG-CTTTAGCTTATTAAATATTT
1 TTATTTTTGTC-TTAACTTATTAAATATTT
*
15695 TTATTTTTGTCTTAATTTATTAAATATTT
1 TTATTTTTGTCTTAACTTATTAAATATTT
15724 TT
1 TT
15726 TTTATTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 27 0.96
30 1 0.04
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.65
Consensus pattern (29 bp):
TTATTTTTGTCTTAACTTATTAAATATTT
Found at i:15796 original size:35 final size:33
Alignment explanation
Indices: 15717--15815 Score: 116
Period size: 35 Copynumber: 3.0 Consensus size: 33
15707 TAATTTATTA
15717 AATATTTT-TT-TTATTTTAATGTAAAAA-ATAT
1 AATATTTTATTCTTATTTTAAT-TAAAAATATAT
*
15748 -ATATTTTACTCTTATTTTAAATTAAAAAATATAT
1 AATATTTTATTCTTATTTT-AATT-AAAAATATAT
*
15782 AATATTTTATTCTTATCTTTACTTAAAAATATAT
1 AATATTTTATTCTTAT-TTTAATTAAAAATATAT
15816 TTTATTATTA
Statistics
Matches: 58, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
30 7 0.12
31 1 0.02
32 8 0.14
33 8 0.14
34 14 0.24
35 17 0.29
36 3 0.05
ACGTcount: A:0.41, C:0.05, G:0.01, T:0.53
Consensus pattern (33 bp):
AATATTTTATTCTTATTTTAATTAAAAATATAT
Found at i:15815 original size:29 final size:30
Alignment explanation
Indices: 15783--15847 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 30
15773 AAAATATATA
* **
15783 ATATTTTATTCTTATCTTTAC-TTAAAAAT
1 ATATTTTATTATTATCTCAACTTTAAAAAT
15812 ATATTTTATTATTATCTCAACTTTTAAAAAT
1 ATATTTTATTATTATCTCAAC-TTTAAAAAT
15843 ATATT
1 ATATT
15848 AAATATTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 18 0.58
31 13 0.42
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (30 bp):
ATATTTTATTATTATCTCAACTTTAAAAAT
Found at i:15824 original size:32 final size:32
Alignment explanation
Indices: 15727--15824 Score: 94
Period size: 32 Copynumber: 3.0 Consensus size: 32
15717 AATATTTTTT
* *
15727 TTATTTT-AATGTAAAAAATATATATTTTACTC
1 TTATTTTAAAT-TAAAAAATATATTTTTTATTC
15759 TTATTTTAAATTAAAAAATATATAATATTTTATTC
1 TTATTTTAAATTAAAAAATATAT--T-TTTTATTC
*
15794 TTATCTTT-ACTT-AAAAATATATTTTATTATT
1 TTAT-TTTAAATTAAAAAATATATTTT-TTATT
15825 ATCTCAACTT
Statistics
Matches: 57, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
31 2 0.04
32 25 0.44
33 3 0.05
34 10 0.18
35 14 0.25
36 3 0.05
ACGTcount: A:0.41, C:0.05, G:0.01, T:0.53
Consensus pattern (32 bp):
TTATTTTAAATTAAAAAATATATTTTTTATTC
Found at i:16070 original size:29 final size:29
Alignment explanation
Indices: 16002--16061 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
15992 TTAAGATAAA
16002 AAAATATATTTAATAAATTAAAACAAAAAT
1 AAAA-ATATTTAATAAATTAAAACAAAAAT
*
16032 AAAAATATTTAATAAGTT-AAAC-AAAAT
1 AAAAATATTTAATAAATTAAAACAAAAAT
16059 AAA
1 AAA
16062 GAGTAATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 8 0.28
28 4 0.14
29 13 0.45
30 4 0.14
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (29 bp):
AAAAATATTTAATAAATTAAAACAAAAAT
Found at i:16247 original size:30 final size:30
Alignment explanation
Indices: 16211--16271 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
16201 TTTTTCAAAG
*
16211 TGTCCTATGTTCGAATCCCCATATTTGCTT
1 TGTCCTATGTTCGAATCCCCATACTTGCTT
*
16241 TGTCCTATGTTTGAATCCCCATACTTGCTT
1 TGTCCTATGTTCGAATCCCCATACTTGCTT
16271 T
1 T
16272 ATTTGTTGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.16, C:0.26, G:0.13, T:0.44
Consensus pattern (30 bp):
TGTCCTATGTTCGAATCCCCATACTTGCTT
Found at i:19390 original size:29 final size:29
Alignment explanation
Indices: 19355--19429 Score: 123
Period size: 29 Copynumber: 2.6 Consensus size: 29
19345 AAGTCTCTCT
* *
19355 ACTATAAAAAGTTATAAAATAATCATTTG
1 ACTATAAAAAGTTACAAAATAATCAATTG
*
19384 ACTATAAAAAGTTACAAAATAGTCAATTG
1 ACTATAAAAAGTTACAAAATAATCAATTG
19413 ACTATAAAAAGTTACAA
1 ACTATAAAAAGTTACAA
19430 GTCACTTAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.53, C:0.09, G:0.08, T:0.29
Consensus pattern (29 bp):
ACTATAAAAAGTTACAAAATAATCAATTG
Found at i:19492 original size:23 final size:22
Alignment explanation
Indices: 19448--19516 Score: 102
Period size: 22 Copynumber: 3.1 Consensus size: 22
19438 ATAATCTATC
*
19448 TAAAATAATTTTTGATTATTTT
1 TAAAATAATTTTTAATTATTTT
*
19470 TAAAATAACTTTTAATTATTTT
1 TAAAATAATTTTTAATTATTTT
*
19492 TAAAATAATTTTTTTATTATTTT
1 TAAAATAA-TTTTTAATTATTTT
19515 TA
1 TA
19517 TTGAAATTAC
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
22 28 0.67
23 14 0.33
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (22 bp):
TAAAATAATTTTTAATTATTTT
Found at i:20731 original size:5 final size:5
Alignment explanation
Indices: 20723--20754 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
20713 CCCGTCTGAT
20723 CCGAC CCGAC CCGAC CCGAC CCGAC CCGAC CC
1 CCGAC CCGAC CCGAC CCGAC CCGAC CCGAC CC
20755 ATCTGCCTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.19, C:0.62, G:0.19, T:0.00
Consensus pattern (5 bp):
CCGAC
Found at i:20847 original size:22 final size:22
Alignment explanation
Indices: 20822--20871 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
20812 AGTCAACCTG
* *
20822 TTGACCGGTCTGACCGTGGACT
1 TTGACAGGTCAGACCGTGGACT
* *
20844 TTGACATGTCAGACCGTTGACT
1 TTGACAGGTCAGACCGTGGACT
20866 TTGACA
1 TTGACA
20872 AAAAAGTCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (22 bp):
TTGACAGGTCAGACCGTGGACT
Found at i:25586 original size:29 final size:29
Alignment explanation
Indices: 25551--25625 Score: 123
Period size: 29 Copynumber: 2.6 Consensus size: 29
25541 AAGTCTCTCT
* *
25551 ACTATAAAAAGTTATAAAATAATCATTTG
1 ACTATAAAAAGTTACAAAATAATCAATTG
*
25580 ACTATAAAAAGTTACAAAATAGTCAATTG
1 ACTATAAAAAGTTACAAAATAATCAATTG
25609 ACTATAAAAAGTTACAA
1 ACTATAAAAAGTTACAA
25626 GTCACTTAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.53, C:0.09, G:0.08, T:0.29
Consensus pattern (29 bp):
ACTATAAAAAGTTACAAAATAATCAATTG
Found at i:25683 original size:22 final size:22
Alignment explanation
Indices: 25646--25735 Score: 119
Period size: 22 Copynumber: 4.0 Consensus size: 22
25636 AATCTATCTT
*
25646 AAATAATTTTTATATTATTTTTA
1 AAATAAATTTT-TATTATTTTTA
25669 AAATAAATTTTTATTATTTTTA
1 AAATAAATTTTTATTATTTTTA
*
25691 AAAT-AATTTGTGATTATTTTTA
1 AAATAAATTT-TTATTATTTTTA
*
25713 AAATAATTTTTTTATTATTTTTA
1 AAATAA-ATTTTTATTATTTTTA
25736 TTGAAATTGC
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
21 5 0.08
22 30 0.50
23 22 0.37
24 3 0.05
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
AAATAAATTTTTATTATTTTTA
Found at i:31941 original size:21 final size:21
Alignment explanation
Indices: 31915--31954 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
31905 CAGAACCCCA
*
31915 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
31936 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
31955 TCAAAGGAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:31986 original size:20 final size:21
Alignment explanation
Indices: 31937--31997 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
31927 TTCCCCTGTG
31937 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
*
31960 GGAGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
*
31980 GGGGGAATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
31998 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 18 0.51
21 2 0.06
22 3 0.09
23 12 0.34
ACGTcount: A:0.21, C:0.26, G:0.31, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:38477 original size:66 final size:66
Alignment explanation
Indices: 38351--38480 Score: 154
Period size: 66 Copynumber: 2.0 Consensus size: 66
38341 GGGATGAAGA
** * ** *
38351 CTCTAACAGGTTCAGTCGCTGATGGTTATTCCTTGTATAGGTTCAGTATCGGCTGATAATTCCTA
1 CTCTAACAGGTTCAGTCGCTGATGGCAATTCCTTGTATAGATTCAACATCGACTGATAATTCCTA
38416 T
66 T
* * * *
38417 CTCTAGCAGGTTTAGTCGCTGCTGGCAATTCCTTGTATAGATTCAACA-CTGACTGGTAATTCCT
1 CTCTAACAGGTTCAGTCGCTGATGGCAATTCCTTGTATAGATTCAACATC-GACTGATAATTCCT
38481 TATGGACCTA
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
65 1 0.02
66 52 0.98
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.36
Consensus pattern (66 bp):
CTCTAACAGGTTCAGTCGCTGATGGCAATTCCTTGTATAGATTCAACATCGACTGATAATTCCTA
T
Found at i:40128 original size:15 final size:16
Alignment explanation
Indices: 40088--40132 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
40078 ACCTGACATA
40088 CGGGTACCCGCAAAATC
1 CGGGTACCCG-AAAATC
* *
40105 TGAGTACCCGAAAA-C
1 CGGGTACCCGAAAATC
40120 CGGGTACCCGAAA
1 CGGGTACCCGAAA
40133 CATTCGAGTC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
15 12 0.50
16 4 0.17
17 8 0.33
ACGTcount: A:0.33, C:0.31, G:0.24, T:0.11
Consensus pattern (16 bp):
CGGGTACCCGAAAATC
Found at i:40972 original size:43 final size:43
Alignment explanation
Indices: 40880--40974 Score: 102
Period size: 43 Copynumber: 2.2 Consensus size: 43
40870 TTTTTGTTAA
* *
40880 AAAAACGCCTCAATAGGTATTGATATTTAGCGGCGTTTGTGTG
1 AAAAATGCCGCAATAGGTATTGATATTTAGCGGCGTTTGTGTG
* * * * * *
40923 ACAAATGCCGCAATAGGTGTTGATGTTTTGCGGTGTTTTTGCT-
1 AAAAATGCCGCAATAGGTATTGATATTTAGCGGCGTTTGTG-TG
40966 AAAAATGCC
1 AAAAATGCC
40975 TGTAAAGGTT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
43 41 0.98
44 1 0.02
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (43 bp):
AAAAATGCCGCAATAGGTATTGATATTTAGCGGCGTTTGTGTG
Found at i:41394 original size:12 final size:12
Alignment explanation
Indices: 41361--41425 Score: 50
Period size: 12 Copynumber: 5.7 Consensus size: 12
41351 TCTCTATGTG
*
41361 CTGCCGCTGCTT
1 CTGCTGCTGCTT
*
41373 CTTTCT-CTGCTT
1 C-TGCTGCTGCTT
41385 CTGCTGCTGC-T
1 CTGCTGCTGCTT
41396 CTG--GCTGCTT
1 CTGCTGCTGCTT
*
41406 CTGCTACTGCTCT
1 CTGCTGCTGCT-T
41419 CT-CTGCT
1 CTGCTGCT
41426 TCCCTTGCTT
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
9 5 0.12
10 4 0.10
11 7 0.17
12 21 0.50
13 5 0.12
ACGTcount: A:0.02, C:0.37, G:0.20, T:0.42
Consensus pattern (12 bp):
CTGCTGCTGCTT
Found at i:41403 original size:21 final size:21
Alignment explanation
Indices: 41379--41427 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
41369 GCTTCTTTCT
* *
41379 CTGCTTCTGCTGCTGCTCTGG
1 CTGCTTCTGCTACTGCTCTCG
*
41400 CTGCTTCTGCTACTGCTCTCT
1 CTGCTTCTGCTACTGCTCTCG
41421 CTGCTTC
1 CTGCTTC
41428 CCTTGCTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.02, C:0.37, G:0.20, T:0.41
Consensus pattern (21 bp):
CTGCTTCTGCTACTGCTCTCG
Found at i:49734 original size:147 final size:146
Alignment explanation
Indices: 49514--49962 Score: 544
Period size: 147 Copynumber: 3.0 Consensus size: 146
49504 TGTATCGTTA
* * * *
49514 ATTTACGACGTTTGTTACTAAAACGCCGCTATATGTGCAAACTATTGCGGCATTTTTGTTAAAAC
1 ATTTGCGACGTTTGTTACCAAAACGCCGCTATATGTG-AACCTATTGCGGCATTTTTGTCAAAAC
** ** * *
49579 GCTACTAAAGTACTAATTTATTGCAGCATTTATTAAAAAACGCCGCTATATGTCTAAAGTAAATG
65 GCCGCTAAAGTACTAATTTATTGTGGCGTTTATTAAAAAACGCCGCTATATGTCTAAAGTTAATG
49644 ACGTTTAAATAAAAAAC
130 ACGTTTAAATAAAAAAC
* * * *
49661 ATTTGCGGCGTTTGTTACCAAAACACCGCTATATGTGAACCCTATTACGACATTTTTGTCAAAAC
1 ATTTGCGACGTTTGTTACCAAAACGCCGCTATATGTGAA-CCTATTGCGGCATTTTTGTCAAAAC
* * *
49726 ACCGCTAAAGTACTAATTTATTATGGCGTTTATTAAAAAATGCCGCTATATGTCTAAAGTTAATG
65 GCCGCTAAAGTACTAATTTATTGTGGCGTTTATTAAAAAACGCCGCTATATGTCTAAAGTTAATG
49791 ACGTTTAAATAAAAAAC
130 ACGTTTAAATAAAAAAC
* ** * * * * * *
49808 ATTTGCGACGTTTTTTTGTCTAAACGCCAC-AAATGTACGAATC-ATTTGCGGCGTTTGTTATCA
1 ATTTGCGACG-TTTGTTACCAAAACGCCGCTATATGT--GAACCTA-TTGCGGCATTT-TTGTCA
* *
49871 AAACGCCGCTAAAGTACTAATCTATTGTGGCGTTTATT-AAAAACGCTGCTATATGTCTAAAGTT
61 AAACGCCGCTAAAGTACTAATTTATTGTGGCGTTTATTAAAAAACGCCGCTATATGTCTAAAGTT
*
49935 AATAACGTTTAAATAAAAAAAC
126 AATGACGTTTAAAT-AAAAAAC
49957 ATTTGC
1 ATTTGC
49963 AGCATTTTCT
Statistics
Matches: 259, Mismatches: 36, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
146 2 0.01
147 142 0.55
148 59 0.23
149 56 0.22
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (146 bp):
ATTTGCGACGTTTGTTACCAAAACGCCGCTATATGTGAACCTATTGCGGCATTTTTGTCAAAACG
CCGCTAAAGTACTAATTTATTGTGGCGTTTATTAAAAAACGCCGCTATATGTCTAAAGTTAATGA
CGTTTAAATAAAAAAC
Found at i:49947 original size:148 final size:148
Alignment explanation
Indices: 49574--50029 Score: 546
Period size: 148 Copynumber: 3.1 Consensus size: 148
49564 CATTTTTGTT
** ** *
49574 AAAACGCTACTAAAGTACTAATTTATTGCAGCATTTATTAAAAAACGCCGCTATATGTCTAAAGT
1 AAAACGCCGCTAAAGTACTAATTTATTGTGGCGTTTATTAAAAAACGCCGCTATATGTCTAAAGT
* * * * * * * * *
49639 AAATGACGTTTAAATAAAAAACATTTGCGGCGTTTGTTACCAAAACACCGCTATATGT-GAACCC
66 TAATGACGTTTAAATAAAAAACATTTGCGACGTTTTTTATCAAAACGCCACTAAATGTCGAATCA
* * * *
49703 TATTACGACATTT-TTGTC
131 T-TTGCGGCGTTTGTTATC
* * *
49721 AAAACACCGCTAAAGTACTAATTTATTATGGCGTTTATTAAAAAATGCCGCTATATGTCTAAAGT
1 AAAACGCCGCTAAAGTACTAATTTATTGTGGCGTTTATTAAAAAACGCCGCTATATGTCTAAAGT
* *
49786 TAATGACGTTTAAATAAAAAACATTTGCGACGTTTTTTTGTCTAAACGCCAC-AAATGTACGAAT
66 TAATGACGTTTAAATAAAAAACATTTGCGACG-TTTTTTATCAAAACGCCACTAAATGT-CGAAT
49850 CATTTGCGGCGTTTGTTATC
129 CATTTGCGGCGTTTGTTATC
* *
49870 AAAACGCCGCTAAAGTACTAATCTATTGTGGCGTTTATT-AAAAACGCTGCTATATGTCTAAAGT
1 AAAACGCCGCTAAAGTACTAATTTATTGTGGCGTTTATTAAAAAACGCCGCTATATGTCTAAAGT
* * *
49934 TAATAACGTTTAAATAAAAAAACATTTGC-AGCATTTTCTATCAAAACGCCACTAAA-GTCCGAA
66 TAATGACGTTTAAAT-AAAAAACATTTGCGA-CGTTTTTTATCAAAACGCCACTAAATGT-CGAA
* *
49997 TCATTTGCGGCGTTTGATACC
128 TCATTTGCGGCGTTTGTTATC
50018 AAAACGCCGCTA
1 AAAACGCCGCTA
50030 TATGTTAACC
Statistics
Matches: 266, Mismatches: 36, Indels: 13
0.84 0.11 0.04
Matches are distributed among these distances:
147 92 0.35
148 112 0.42
149 62 0.23
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (148 bp):
AAAACGCCGCTAAAGTACTAATTTATTGTGGCGTTTATTAAAAAACGCCGCTATATGTCTAAAGT
TAATGACGTTTAAATAAAAAACATTTGCGACGTTTTTTATCAAAACGCCACTAAATGTCGAATCA
TTTGCGGCGTTTGTTATC
Found at i:52116 original size:12 final size:13
Alignment explanation
Indices: 52099--52127 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
52089 TTTACTCTCC
52099 AAACGCCGCTA-A
1 AAACGCCGCTACA
52111 AAACGCCGCTACA
1 AAACGCCGCTACA
52124 AAAC
1 AAAC
52128 ACTTTTGCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.45, C:0.34, G:0.14, T:0.07
Consensus pattern (13 bp):
AAACGCCGCTACA
Found at i:55065 original size:31 final size:32
Alignment explanation
Indices: 55004--55067 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
54994 AATAAGTTTG
* * **
55004 AAAGTTAGAGTAATTAAATTAAGATTAATTTA
1 AAAGTTAGAGTAATTAAACTAAAAACAATTTA
55036 AAAGTTA-AGTAATTAAACTAAAAACAATTTA
1 AAAGTTAGAGTAATTAAACTAAAAACAATTTA
55067 A
1 A
55068 CTTTAGTGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 21 0.75
32 7 0.25
ACGTcount: A:0.55, C:0.03, G:0.09, T:0.33
Consensus pattern (32 bp):
AAAGTTAGAGTAATTAAACTAAAAACAATTTA
Found at i:56343 original size:37 final size:38
Alignment explanation
Indices: 56260--56347 Score: 135
Period size: 38 Copynumber: 2.3 Consensus size: 38
56250 CTTAAACCTG
*
56260 ACCCGACCCGACCTGACTCGAATATCACACTTAAAAAA
1 ACCCGACCCGACCTGACCCGAATATCACACTTAAAAAA
56298 ACCCGACCCGA-CTCGACCCGAATATCACACTT-AAAAA
1 ACCCGACCCGACCT-GACCCGAATATCACACTTAAAAAA
*
56335 ATCCGACCCGACC
1 ACCCGACCCGACC
56348 CGAACAAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
37 17 0.37
38 29 0.63
ACGTcount: A:0.36, C:0.39, G:0.11, T:0.14
Consensus pattern (38 bp):
ACCCGACCCGACCTGACCCGAATATCACACTTAAAAAA
Found at i:59013 original size:40 final size:40
Alignment explanation
Indices: 58953--59030 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
58943 AGTCGAGGGT
* *
58953 TATACAGTGGTCCTTAGGGACATAGTGGTCCTTCGGGACA
1 TATACAATGGTCCTTAGGGACATAGTGGTCATTCGGGACA
*
58993 TATACAATGGTCCTTTGGGACATAGTGGTCATTCGGGA
1 TATACAATGGTCCTTAGGGACATAGTGGTCATTCGGGA
59031 TAAATATTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.29
Consensus pattern (40 bp):
TATACAATGGTCCTTAGGGACATAGTGGTCATTCGGGACA
Found at i:59030 original size:18 final size:18
Alignment explanation
Indices: 58958--59030 Score: 74
Period size: 18 Copynumber: 3.8 Consensus size: 18
58948 AGGGTTATAC
*
58958 AGTGGTCCTTAGGGACAT
1 AGTGGTCCTTCGGGACAT
58976 AGTGGTCCTTCGGGACATAT
1 AGTGGTCCTTCGGGAC--AT
* *
58996 ACAATGGTCCTTTGGGACAT
1 --AGTGGTCCTTCGGGACAT
*
59016 AGTGGTCATTCGGGA
1 AGTGGTCCTTCGGGA
59031 TAAATATTCA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
18 27 0.60
20 4 0.09
22 14 0.31
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:62173 original size:2 final size:2
Alignment explanation
Indices: 62166--62192 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
62156 TTTTTACATT
62166 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
62193 TTTATTTTTT
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:69046 original size:13 final size:13
Alignment explanation
Indices: 69025--69059 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
69015 CCCGCTTACT
69025 TTTCACTTTTCAC
1 TTTCACTTTTCAC
* *
69038 TTTCTCTTTTTAC
1 TTTCACTTTTCAC
69051 TTTCACTTT
1 TTTCACTTT
69060 CTAGTTTCCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTCACTTTTCAC
Found at i:71689 original size:20 final size:20
Alignment explanation
Indices: 71664--71706 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
71654 TCTAAGAGCC
*
71664 CATTTAGGACCATTTAGATG
1 CATTTAGGACCATATAGATG
* *
71684 CATTTAGGAGCATATAGTTG
1 CATTTAGGACCATATAGATG
71704 CAT
1 CAT
71707 GTGGTGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:76124 original size:110 final size:110
Alignment explanation
Indices: 75960--76745 Score: 1287
Period size: 110 Copynumber: 7.2 Consensus size: 110
75950 GATGGTGGTT
*
75960 GCTCAACTTCATAGCGAA-GGG-G-C-GACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* *
76021 AATTTCAATTTCACAGCGAAGGATATTGGACTCGAGACAAAACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
76066 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* ** *
76131 AATTTCAACTTCAC-GACAAAATATATTGGACTTGAGACAACACAA
66 AATTTCAACTTCACAG-CGAAGGATATTGGACTCGAGACAACACAA
*
76176 GCTCAACTTCACAGCGAAGAGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
*
76241 AATTTCAACTTCAAAGCGAAGGATATTGGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* *
76286 GCTCAACTTCACAGCGAAGGGGTGACTGACTGTCAACAAACAACATTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
*
76351 AATTTCAACTTCAC-GACGAAGGATATTGGACTTGAGACAACACAA
66 AATTTCAACTTCACAG-CGAAGGATATTGGACTCGAGACAACACAA
* * *
76396 GCTCAACTTCACAGCGAATGGGCGACTGACTGTCAACAAATAACTTTTTAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
*
76461 AATTTCAACTTCACAGTGAAGGATATTGGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
76506 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
*
76571 AATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* * * *
76616 GCTTAACTTCACAGCGAATGGGCGACTGACTATCAACAAACAACTTTCCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* * *
76681 AATTTTAACTTCACAACGAAGGATATTAGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
*
76726 GCTCAACTTCACAGCAAAGG
1 GCTCAACTTCACAGCGAAGG
76746 ATATTAGACT
Statistics
Matches: 633, Mismatches: 39, Indels: 12
0.93 0.06 0.02
Matches are distributed among these distances:
106 17 0.03
107 3 0.00
108 1 0.00
109 3 0.00
110 607 0.96
111 2 0.00
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (110 bp):
GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
Found at i:76748 original size:43 final size:43
Alignment explanation
Indices: 76687--76788 Score: 186
Period size: 43 Copynumber: 2.4 Consensus size: 43
76677 AGTCAATTTT
* *
76687 AACTTCACAACGAAGGATATTAGACTCGAGACAACACAAGCTC
1 AACTTCACAGCAAAGGATATTAGACTCGAGACAACACAAGCTC
76730 AACTTCACAGCAAAGGATATTAGACTCGAGACAACACAAGCTC
1 AACTTCACAGCAAAGGATATTAGACTCGAGACAACACAAGCTC
76773 AACTTCACAGCAAAGG
1 AACTTCACAGCAAAGG
76789 GGCAACTGAC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.42, C:0.25, G:0.17, T:0.16
Consensus pattern (43 bp):
AACTTCACAGCAAAGGATATTAGACTCGAGACAACACAAGCTC
Found at i:76768 original size:153 final size:153
Alignment explanation
Indices: 76575--76898 Score: 540
Period size: 153 Copynumber: 2.1 Consensus size: 153
76565 AGAGTCAATT
* * * * *
76575 TCAACTTCACAGCGAAGGATATTAGACTCGAGACAACACAAGCTTAACTTCACAGCGAATGGGCG
1 TCAACTTCACAGCAAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCACAGCAAAGGGGCA
* *
76640 ACTGACTATCAACAAACAACTTTCCAGTTTCATTCAGAGTCAATTTTAACTTCACAACGAAGGAT
66 ACTGACTATCAACAAACAACTTTCCAGTTCCATTCAGAGTCAATTTCAACTTCACAACGAAGGAT
76705 ATTAGACTCGAGACAACACAAGC
131 ATTAGACTCGAGACAACACAAGC
76728 TCAACTTCACAGCAAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCACAGCAAAGGGGCA
1 TCAACTTCACAGCAAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCACAGCAAAGGGGCA
* * **
76793 ACTGACTGTCAACAAACAACTTTTCAGTTCCATTCAGAGTCAATTTCAACTTCACAGTGAAGGAT
66 ACTGACTATCAACAAACAACTTTCCAGTTCCATTCAGAGTCAATTTCAACTTCACAACGAAGGAT
*
76858 ATTGGACTCGAGACAACACAAGC
131 ATTAGACTCGAGACAACACAAGC
76881 TCAACTTCACAGCAAAGG
1 TCAACTTCACAGCAAAGG
76899 GGCGATTGGC
Statistics
Matches: 159, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
153 159 1.00
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.21
Consensus pattern (153 bp):
TCAACTTCACAGCAAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCACAGCAAAGGGGCA
ACTGACTATCAACAAACAACTTTCCAGTTCCATTCAGAGTCAATTTCAACTTCACAACGAAGGAT
ATTAGACTCGAGACAACACAAGC
Found at i:76829 original size:263 final size:259
Alignment explanation
Indices: 76465--76984 Score: 842
Period size: 263 Copynumber: 2.0 Consensus size: 259
76455 AGAGTCAATT
** * * *
76465 TCAACTTCACAGTGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGGCG
1 TCAACTTCACAGCAAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCACAGCAAAGGGGCA
*
76530 ACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGAT
66 ACTGACTGTCAACAAACAACTTTTCAGTTCCATTCAGAGTCAATTTCAACTTCACAGCGAAGGAT
* * *
76595 ATTAGACTCGAGACAACACAAGCTTAACTTCACAGCGAATGGGCGACTGACTATCAACAAACAAC
131 ATTAGACTCGAGACAACACAAGCTCAACTTCACAGCAAAGGGGCGACTGACTATCAACAAACAAC
*
76660 TTTCCAGTTTCATTCAGAGTCAATTTTAACTTCACAACGAAGGATATTAGACTCGAGACAACACA
196 TTTCCAG--T--TTCAGAGTCAATTTTAACTTCACAACGAAGGATATTAGACTCGAAACAACACA
76725 AGC
257 AGC
76728 TCAACTTCACAGCAAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCACAGCAAAGGGGCA
1 TCAACTTCACAGCAAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCACAGCAAAGGGGCA
*
76793 ACTGACTGTCAACAAACAACTTTTCAGTTCCATTCAGAGTCAATTTCAACTTCACAGTGAAGGAT
66 ACTGACTGTCAACAAACAACTTTTCAGTTCCATTCAGAGTCAATTTCAACTTCACAGCGAAGGAT
* * * *
76858 ATTGGACTCGAGACAACACAAGCTCAACTTCACAGCAAAGGGGCGATTGGCTATTAACAAACAAC
131 ATTAGACTCGAGACAACACAAGCTCAACTTCACAGCAAAGGGGCGACTGACTATCAACAAACAAC
* * *
76923 TTTCCAGTTTCAGAGTCAATTTTAACTTCACAGCGAAGGATATTGGCCTCGAAACAACACAA
196 TTTCCAGTTTCAGAGTCAATTTTAACTTCACAACGAAGGATATTAGACTCGAAACAACACAA
76985 ATATTTGTCT
Statistics
Matches: 239, Mismatches: 18, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
259 50 0.21
261 1 0.00
263 188 0.79
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (259 bp):
TCAACTTCACAGCAAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCACAGCAAAGGGGCA
ACTGACTGTCAACAAACAACTTTTCAGTTCCATTCAGAGTCAATTTCAACTTCACAGCGAAGGAT
ATTAGACTCGAGACAACACAAGCTCAACTTCACAGCAAAGGGGCGACTGACTATCAACAAACAAC
TTTCCAGTTTCAGAGTCAATTTTAACTTCACAACGAAGGATATTAGACTCGAAACAACACAAGC
Found at i:76921 original size:110 final size:106
Alignment explanation
Indices: 76728--76984 Score: 370
Period size: 110 Copynumber: 2.4 Consensus size: 106
76718 CAACACAAGC
* *
76728 TCAACTTCACAGCAAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCACAGCAAAGGGGCA
1 TCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAGCAAAGGGGCA
* *
76793 ACTGACTGTCAACAAACAACTTTTCAGTTCCATTCAGAGTCAATT
66 ACTGACTATCAACAAACAACTTTCCAG-T---TTCAGAGTCAATT
* *
76838 TCAACTTCACAGTGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAGCAAAGGGGCG
1 TCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAGCAAAGGGGCA
* * *
76903 ATTGGCTATTAACAAACAACTTTCCAGTTTCAGAGTCAATT
66 ACTGACTATCAACAAACAACTTTCCAGTTTCAGAGTCAATT
* * *
76944 TTAACTTCACAGCGAAGGATATTGGCCTCGAAACAACACAA
1 TCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
76985 ATATTTGTCT
Statistics
Matches: 134, Mismatches: 13, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
106 50 0.37
109 1 0.01
110 83 0.62
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (106 bp):
TCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAGCAAAGGGGCA
ACTGACTATCAACAAACAACTTTCCAGTTTCAGAGTCAATT
Found at i:77172 original size:84 final size:83
Alignment explanation
Indices: 77027--77610 Score: 521
Period size: 84 Copynumber: 7.0 Consensus size: 83
77017 GTGCCCACCA
* * * * *
77027 AAAG-CCTTCCAGTTTGACTACGCTCAACTCCAAGGTATATCATTTGCAGCATAACTTAAGTCGA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGA
77091 GAAGGGTTATCTGCCAAC
66 GAAGGGTTATCTGCCAAC
* * * *
77109 TAAAGACCTTCGAGTTCGACTATGCTCAGCTCCAAGACACATCATTTGCAACATAGCTTAAGTCG
1 -AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCG
*
77174 AGAAGGGCTATCTG-C--C
65 AGAAGGGTTATCTGCCAAC
* * * * * * * * * * *
77190 AAAGACCCTCGAGTTCAATTACACTCAGCTTCGAGGGCGCATCATTTACTGCATAACTCAAG-GG
1 AAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTCG
* *
77254 TAGAAGGGTTATCTGTCACC
65 -AGAAGGGTTATCTGCCAAC
* * * * * * * *
77274 AAAATACCTTTGAGTTTGACTACGCTCAGCTCTAAGGCATAGCATTTGTAGCATAACCTAAGTCG
1 -AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCG
77339 AGAAGGGTTATCTGCCAACC
65 AGAAGGGTTATCTGCCAA-C
* * * ** * ** * * * *
77359 AAAGACATTCAAGTTCGATTATACTCATCTCCGGGGGCACAACATTTGCAGCATAACTCAAGGCT
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCC-AAGGCACATCATTTGCAGCATAACTTAAGTCG
77424 AGAAGGGTTATCTGCCAAC
65 AGAAGGGTTATCTGCCAAC
* * *
77443 AAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCAA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGA
*
77508 GAAGGGTTATCTGTCAAACC
66 GAAGGGTTATCTG-CCAA-C
* * * * * * * * * * *
77528 AAAGACCTTCAAGTTCGACTCCACTCAACTCAAAGGAACCATCATTTGCAGTATAGCTCAAGGCA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCA-CATCATTTGCAGCATAACTTAAGTCG
*
77593 AGAAAGGTTATCTGCCAA
65 AGAAGGGTTATCTGCCAA
77611 ATACCTTCGA
Statistics
Matches: 398, Mismatches: 90, Indels: 24
0.78 0.18 0.05
Matches are distributed among these distances:
80 25 0.06
81 37 0.09
82 1 0.00
83 44 0.11
84 153 0.38
85 102 0.26
86 36 0.09
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (83 bp):
AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGA
GAAGGGTTATCTGCCAAC
Found at i:77338 original size:165 final size:164
Alignment explanation
Indices: 77067--77525 Score: 549
Period size: 165 Copynumber: 2.8 Consensus size: 164
77057 CAAGGTATAT
* * * * *
77067 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACTAAAGACCTTCGAGTTCGACTAT
1 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTCGACTAC
* * * * *
77132 GCTCAGCTCCAAGACACATCATTTGCAACATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
65 GCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACA
* * * *
77197 CTCGAGTTCAATTACACTCAGCTTCGAGGGCGCAT
130 CTCAAGTTCAATTACACTCAGCTCCGAGGGCACAA
* * * * * * *
77232 CATTTACTGCATAACTCAAGGGTAGAAGGGTTATCTGTCACCAAAATACCTTTGAGTTTGACTAC
1 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTCGACTAC
* * * * * *
77297 GCTCAGCTCTAAGGCATAGCATTTGTAGCATAACCTAAGTCGAGAAGGGTTATCTGCCAACCAAA
65 GCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTG----CCAAA
* * * * *
77362 GACATTCAAGTTCGATTATACTCATCTCCGGGGGCACAA
126 GACACTCAAGTTCAATTACACTCAGCTCCGAGGGCACAA
*
77401 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACG
1 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACG
* *
77466 CTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAGGGTTATCTGTCAAA
66 CTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAA
77526 CCAAAGACCT
Statistics
Matches: 242, Mismatches: 48, Indels: 9
0.81 0.16 0.03
Matches are distributed among these distances:
164 4 0.02
165 99 0.41
168 68 0.28
169 71 0.29
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (164 bp):
CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACG
CTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACAC
TCAAGTTCAATTACACTCAGCTCCGAGGGCACAA
Found at i:77576 original size:169 final size:167
Alignment explanation
Indices: 77065--77610 Score: 614
Period size: 169 Copynumber: 3.3 Consensus size: 167
77055 TCCAAGGTAT
* * * *
77065 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACTAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACT
* * * * *
77130 ATGCTCAGCTCCAAGACACATCATTTGCAACATAGCTTAAGTCGAGAAGGGCTATCTG---CCAA
66 ACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCAACCAA
* * * * * *
77192 AGACCCTCGAGTTCAATTACACTCAGCTTCGAGGGCGC
131 AGACCTTCAAGTTCGATTACACTCAAC-TCAAGGGCAC
* * * * * * * *
77230 ATCATTTACTGCATAACTCAAGGGTAGAAGGGTTATCTGTCACCAAAATACCTTTGAGTTTGACT
1 ATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACT
* * * * * *
77295 ACGCTCAGCTCTAAGGCATAGCATTTGTAGCATAACCTAAGTCGAGAAGGGTTATCTGCCAACCA
66 ACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTG-CAACCA
* * * **
77360 AAGACATTCAAGTTCGATTATACTCATCTCCGGGGGCAC
130 AAGACCTTCAAGTTCGATTACACTCAACT-CAAGGGCAC
*
77399 AACATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACT
*
77463 ACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAGGGTTATCTGTCAAACC
66 ACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTG-C-AACC
* * * *
77528 AAAGACCTTCAAGTTCGACTCCACTCAACTCAAAGGAACC
129 AAAGACCTTCAAGTTCGATTACACTCAACTCAAGGGCA-C
* * * *
77568 ATCATTTGCAGTATAGCTCAAGGCAAGAAAGGTTATCTGCCAA
1 ATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAA
77611 ATACCTTCGA
Statistics
Matches: 313, Mismatches: 61, Indels: 10
0.82 0.16 0.03
Matches are distributed among these distances:
165 101 0.32
168 74 0.24
169 138 0.44
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.25
Consensus pattern (167 bp):
ATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACT
ACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCAACCAA
AGACCTTCAAGTTCGATTACACTCAACTCAAGGGCAC
Found at i:77968 original size:10 final size:10
Alignment explanation
Indices: 77953--78001 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
77943 AAAAACATTT
77953 TATTATATTA
1 TATTATATTA
77963 TATTATATT-
1 TATTATATTA
77972 TATT-TATT-
1 TATTATATTA
77980 TATTATTATTA
1 TATTA-TATTA
77991 TTATTAT-TTA
1 -TATTATATTA
78001 T
1 T
78002 TTTTGTAGGC
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
8 8 0.23
9 5 0.14
10 16 0.46
11 1 0.03
12 5 0.14
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TATTATATTA
Found at i:78003 original size:27 final size:23
Alignment explanation
Indices: 77951--78002 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
77941 ACAAAAACAT
77951 TTTATTATATTATATTATATTTA
1 TTTATTATATTATATTATATTTA
77974 TTTATT-TATTATTATTAT-TATTA
1 TTTATTATATTA-TATTATAT-TTA
77997 TTTATT
1 TTTATT
78003 TTTGTAGGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
22 6 0.22
23 21 0.78
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (23 bp):
TTTATTATATTATATTATATTTA
Found at i:84413 original size:19 final size:19
Alignment explanation
Indices: 84389--84426 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
84379 TTTTGGTGCA
*
84389 GAGGGAATCGATCCCCCCT
1 GAGGGAACCGATCCCCCCT
*
84408 GAGGGAACCGATTCCCCCT
1 GAGGGAACCGATCCCCCCT
84427 TTGAAGGGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.21, C:0.37, G:0.26, T:0.16
Consensus pattern (19 bp):
GAGGGAACCGATCCCCCCT
Found at i:88227 original size:12 final size:12
Alignment explanation
Indices: 88210--88236 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
88200 GAATTGAATT
88210 TTTAAATTCTAA
1 TTTAAATTCTAA
88222 TTTAAATTCTAA
1 TTTAAATTCTAA
88234 TTT
1 TTT
88237 TCGCAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (12 bp):
TTTAAATTCTAA
Found at i:89230 original size:20 final size:20
Alignment explanation
Indices: 89183--89230 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
89173 TTATTAATTA
89183 ATTATTAAAATATCACATCT
1 ATTATTAAAATATCACATCT
* **
89203 -TTATTTAAAATATTATTTCT
1 ATTA-TTAAAATATCACATCT
89223 ATTATTAA
1 ATTATTAA
89231 TTTTAAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 3 0.13
20 17 0.74
21 3 0.13
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTATTAAAATATCACATCT
Found at i:91803 original size:27 final size:28
Alignment explanation
Indices: 91755--91830 Score: 136
Period size: 28 Copynumber: 2.8 Consensus size: 28
91745 ATCCGTTTTA
91755 ATACTTAAATTTTTAATTTTTTAAAATC
1 ATACTTAAATTTTTAATTTTTTAAAATC
91783 ATACTTAAATTTTTAATTTTTTAAAATC
1 ATACTTAAATTTTTAATTTTTTAAAATC
*
91811 ATACTTAAA-GTTTAATTTTT
1 ATACTTAAATTTTTAATTTTT
91831 GTTTTATTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
27 10 0.21
28 37 0.79
ACGTcount: A:0.38, C:0.07, G:0.01, T:0.54
Consensus pattern (28 bp):
ATACTTAAATTTTTAATTTTTTAAAATC
Found at i:93384 original size:76 final size:75
Alignment explanation
Indices: 93293--93437 Score: 247
Period size: 76 Copynumber: 1.9 Consensus size: 75
93283 GTTCTAGAAC
* *
93293 GATCCAGTATAAAATAAAAATATTTTAATAGTTTTTTTAATAATGAT-AATGTGATATCATAAAA
1 GATCAAGTATAAAATAAAAATATTTTAATAGGTTTTTTAATAATGATCAATGTG--ATCATAAAA
93357 TATTATATGAAT
64 TATTATATGAAT
93369 GATCAAGTATAAAATAAAAATATTTTAATAGGTTTTTTAATAATGATCAATGTGATCATAAAATA
1 GATCAAGTATAAAATAAAAATATTTTAATAGGTTTTTTAATAATGATCAATGTGATCATAAAATA
93434 TTAT
66 TTAT
93438 GTTCATAAAT
Statistics
Matches: 66, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
75 15 0.23
76 45 0.68
77 6 0.09
ACGTcount: A:0.46, C:0.04, G:0.10, T:0.40
Consensus pattern (75 bp):
GATCAAGTATAAAATAAAAATATTTTAATAGGTTTTTTAATAATGATCAATGTGATCATAAAATA
TTATATGAAT
Found at i:94885 original size:30 final size:30
Alignment explanation
Indices: 94849--94907 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
94839 TTGTACCATA
94849 AAGTTCTCCTATTTTAATATATATTATATC
1 AAGTTCTCCTATTTTAATATATATTATATC
94879 AAGTTCTCCTATTTTAATATATATTATAT
1 AAGTTCTCCTATTTTAATATATATTATAT
94908 AATAAAGGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.12, G:0.03, T:0.51
Consensus pattern (30 bp):
AAGTTCTCCTATTTTAATATATATTATATC
Found at i:96129 original size:26 final size:26
Alignment explanation
Indices: 96100--96153 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
96090 ATGATCCTAA
*
96100 AGATAATAAGGACTTTAAGATCTTAT
1 AGATAATAAAGACTTTAAGATCTTAT
96126 AGATAATAAAGACTTTAAGATCTTAT
1 AGATAATAAAGACTTTAAGATCTTAT
96152 AG
1 AG
96154 TTTATTGGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.33
Consensus pattern (26 bp):
AGATAATAAAGACTTTAAGATCTTAT
Found at i:96335 original size:56 final size:56
Alignment explanation
Indices: 96261--96410 Score: 219
Period size: 56 Copynumber: 2.7 Consensus size: 56
96251 TAAAATTTTC
* * * * *
96261 TAGATTTAGAGATCTTTAATGAGACATTTTTCCTTAATGTATTCTTTTCTTTTATA
1 TAGATTTAGAGATATTTAACGAGACATTTTTCTTTAATATATTCTTTTCTTTCATA
* * *
96317 TAGGTTTAGAGATATTTAACGAGACATTCTTCTTTAATATATTTTTTTCTTTCATA
1 TAGATTTAGAGATATTTAACGAGACATTTTTCTTTAATATATTCTTTTCTTTCATA
*
96373 TAGATTTAGAGATTTTTAACGAGACATTTTTCTTTAAT
1 TAGATTTAGAGATATTTAACGAGACATTTTTCTTTAAT
96411 CAATACTTTA
Statistics
Matches: 83, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 83 1.00
ACGTcount: A:0.29, C:0.10, G:0.11, T:0.50
Consensus pattern (56 bp):
TAGATTTAGAGATATTTAACGAGACATTTTTCTTTAATATATTCTTTTCTTTCATA
Found at i:100735 original size:31 final size:31
Alignment explanation
Indices: 100700--100790 Score: 96
Period size: 31 Copynumber: 2.9 Consensus size: 31
100690 TTTGAACGGT
100700 TACAAAATAATCATTAAATTTATCAAACTAG
1 TACAAAATAATCATTAAATTTATCAAACTAG
* * *
100731 TACAAAATAGTCGTTAGAATTTATCAGAA--AT
1 TACAAAATAATCATTA-AATTTATCA-AACTAG
* * *
100762 TACGAAATTATCATTAAGTTTATCAAACT
1 TACAAAATAATCATTAAATTTATCAAACT
100791 TTTAGAATTA
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
29 2 0.04
30 8 0.17
31 27 0.56
32 9 0.19
33 2 0.04
ACGTcount: A:0.46, C:0.12, G:0.08, T:0.34
Consensus pattern (31 bp):
TACAAAATAATCATTAAATTTATCAAACTAG
Found at i:105864 original size:17 final size:17
Alignment explanation
Indices: 105842--105875 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
105832 GATTGCATAA
105842 CTGATATAAAGGCAGGG
1 CTGATATAAAGGCAGGG
105859 CTGATATAAAGGCAGGG
1 CTGATATAAAGGCAGGG
105876 GTTGATTCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.35, T:0.18
Consensus pattern (17 bp):
CTGATATAAAGGCAGGG
Found at i:107907 original size:65 final size:65
Alignment explanation
Indices: 107709--107909 Score: 234
Period size: 65 Copynumber: 3.1 Consensus size: 65
107699 TACACTAAGA
* * * *
107709 GTGCATCGATGCATGAAATACATTCGATGTTTCAAAATAGCCA-GAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATATATCCATGAGTGCATCGATGCATGGTTG
* * * *
107773 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAAT-C-TGAGTGCATCGATGCATAGT
1 GTGCATCGATGCATGAAATGCATTCGATG-TTTCA-ATATATCCATGAGTGCATCGATGCATGGT
107836 AT-
64 -TG
*
107838 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTATTCCATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATATA-TCCATGAGTGCATCGATGCATGG-T
107901 TG
64 TG
107903 GTGCATC
1 GTGCATC
107910 ACTCTGAAAA
Statistics
Matches: 117, Mismatches: 11, Indels: 17
0.81 0.08 0.12
Matches are distributed among these distances:
62 2 0.02
63 5 0.04
64 44 0.38
65 61 0.52
66 5 0.04
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTCAATATATCCATGAGTGCATCGATGCATGGTTG
Done.