Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D01
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: 62811768
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 736185 characters in sequence are not A, C, G, or T
File 150 of 211
Found at i:44484852 original size:14 final size:13
Alignment explanation
Indices: 44484824--44484865 Score: 57
Period size: 14 Copynumber: 3.1 Consensus size: 13
44484814 ATTTAAGAAC
*
44484824 AAATAACAAATAA
1 AAATAATAAATAA
44484837 AAATAATAATATAA
1 AAATAATAA-ATAA
44484851 AAATAAATAAATAA
1 AAAT-AATAAATAA
44484865 A
1 A
44484866 CAATTTAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 8 0.31
14 13 0.50
15 5 0.19
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.21
Consensus pattern (13 bp):
AAATAATAAATAA
Found at i:44486575 original size:26 final size:26
Alignment explanation
Indices: 44486528--44486577 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
44486518 CCCACACACC
* * *
44486528 AATATTGCAGCATAGTTACCAGTAAT
1 AATATCGCAGCAGAGCTACCAGTAAT
*
44486554 AATATCGCAGCAGAGCTGCCAGTA
1 AATATCGCAGCAGAGCTACCAGTA
44486578 CTGTATATGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (26 bp):
AATATCGCAGCAGAGCTACCAGTAAT
Found at i:44486617 original size:27 final size:27
Alignment explanation
Indices: 44486585--44486636 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
44486575 GTACTGTATA
44486585 TGTGGCAAAGCCACCAGTAACAGTAAT
1 TGTGGCAAAGCCACCAGTAACAGTAAT
* *
44486612 TGTGGCAGAGCCACTAGTAACAGTA
1 TGTGGCAAAGCCACCAGTAACAGTA
44486637 CTTCCTCCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.19
Consensus pattern (27 bp):
TGTGGCAAAGCCACCAGTAACAGTAAT
Found at i:44491899 original size:49 final size:49
Alignment explanation
Indices: 44491827--44491927 Score: 157
Period size: 49 Copynumber: 2.1 Consensus size: 49
44491817 TGATTCATGC
** *
44491827 TATACAATGCTAAACTTGGTCTTCAACTGTCTACACTCTTATCACTATT
1 TATACAATGCTAAACTTAATCTTCAACTGTCTACACTATTATCACTATT
* *
44491876 TATACATTGCTAAACTTAATCTTCCACTGTCTACACTATTATCACTATT
1 TATACAATGCTAAACTTAATCTTCAACTGTCTACACTATTATCACTATT
44491925 TAT
1 TAT
44491928 CCCTTCTTGA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.30, C:0.24, G:0.06, T:0.41
Consensus pattern (49 bp):
TATACAATGCTAAACTTAATCTTCAACTGTCTACACTATTATCACTATT
Found at i:44498293 original size:22 final size:22
Alignment explanation
Indices: 44498262--44498303 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
44498252 TGTCATTAAC
44498262 TTAAGTTAATTAAAGATTAAGGT
1 TTAAGTTAATTAAA-ATTAAGGT
*
44498285 TTAA-TTAATTATAATTAAG
1 TTAAGTTAATTAAAATTAAG
44498304 TAAAATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 8 0.44
23 4 0.22
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.43
Consensus pattern (22 bp):
TTAAGTTAATTAAAATTAAGGT
Found at i:44508388 original size:24 final size:23
Alignment explanation
Indices: 44508347--44508477 Score: 81
Period size: 24 Copynumber: 5.5 Consensus size: 23
44508337 CCCTTCTTCC
*
44508347 TTATT-TTATTTTATATTTATTTAT
1 TTATTATTATTTT-CATTTATTT-T
* * *
44508371 TTATTATTATTTCCATTTCTATTA
1 TTATTATTATTTTCATTTAT-TTT
*
44508395 TTA-TATTTATTTTCATTTGTTTT
1 TTATTA-TTATTTTCATTTATTTT
* *
44508418 CTTATTATTCTTTTCATTTACTTTC
1 -TTATTATTATTTTCATTTA-TTTT
*
44508443 TTATTATTATGCTT-A-TTACTTTT
1 TTATTATTAT-TTTCATTTA-TTTT
44508466 ATTATTATTATT
1 -TTATTATTATT
44508478 GCTATGTTAT
Statistics
Matches: 85, Mismatches: 14, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
23 11 0.13
24 59 0.69
25 15 0.18
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.68
Consensus pattern (23 bp):
TTATTATTATTTTCATTTATTTT
Found at i:44536727 original size:50 final size:50
Alignment explanation
Indices: 44536652--44536893 Score: 258
Period size: 50 Copynumber: 4.9 Consensus size: 50
44536642 CATTTGGGTA
*
44536652 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
* * *
44536702 AAGAGGTCCCATGTAAGACCATGTCTAGGACATGACATTGTCACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
* * ** * *
44536752 GAGAGTTCCCCCGTAAGACCATGTCTGGGACATAGCATGGGCACCGATG-T
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA-GAT
* ** * * *
44536802 GAGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA--G-TAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
** *
44536849 AAGAAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AAG--AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
44536894 TGTTATTATC
Statistics
Matches: 160, Mismatches: 28, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
47 3 0.02
48 1 0.01
49 35 0.22
50 120 0.75
51 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (50 bp):
AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
Found at i:44547066 original size:40 final size:40
Alignment explanation
Indices: 44547011--44547091 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
44547001 CAACATTTAG
44547011 TTGAAATTCCTCTTTGTCTTAAGCTACAATAGGCTCATCT
1 TTGAAATTCCTCTTTGTCTTAAGCTACAATAGGCTCATCT
* *
44547051 TTGAAATTCCTCTTTGTCTTGAGCTACAATAGGTTCATCT
1 TTGAAATTCCTCTTTGTCTTAAGCTACAATAGGCTCATCT
44547091 T
1 T
44547092 GAACCTCAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.42
Consensus pattern (40 bp):
TTGAAATTCCTCTTTGTCTTAAGCTACAATAGGCTCATCT
Found at i:44548810 original size:5 final size:5
Alignment explanation
Indices: 44548800--44548824 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
44548790 TTTAACTAAG
44548800 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
44548825 GTTCCAATGC
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:44550258 original size:10 final size:10
Alignment explanation
Indices: 44550235--44550284 Score: 64
Period size: 10 Copynumber: 4.8 Consensus size: 10
44550225 GAATCTGTTG
*
44550235 AAAATAAATT
1 AAAATTAATT
*
44550245 AAAATTAATC
1 AAAATTAATT
44550255 AAAATTAATTAT
1 AAAATTAA-T-T
44550267 AAAATTAATT
1 AAAATTAATT
44550277 AAAATTAA
1 AAAATTAA
44550285 AAATATTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
10 25 0.71
11 2 0.06
12 8 0.23
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (10 bp):
AAAATTAATT
Found at i:44550998 original size:25 final size:25
Alignment explanation
Indices: 44550959--44551058 Score: 94
Period size: 25 Copynumber: 4.0 Consensus size: 25
44550949 AACAAGACAA
* *
44550959 AGCCTTTGGGA-AAATTATCTGAAG
1 AGCCTTTGTGACAAATTATCTAAAG
* *
44550983 ATCGTTTGTGACAAATTATCTAAAG
1 AGCCTTTGTGACAAATTATCTAAAG
* * *
44551008 AGCCTTTGTGGCGAATTATATAAAG
1 AGCCTTTGTGACAAATTATCTAAAG
* * * *
44551033 AGTCTTTTTGGCGAATTATCTAAAG
1 AGCCTTTGTGACAAATTATCTAAAG
44551058 A
1 A
44551059 ATCTTTTTTG
Statistics
Matches: 63, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
24 8 0.13
25 55 0.87
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.34
Consensus pattern (25 bp):
AGCCTTTGTGACAAATTATCTAAAG
Found at i:44551063 original size:25 final size:25
Alignment explanation
Indices: 44550996--44551105 Score: 121
Period size: 25 Copynumber: 4.4 Consensus size: 25
44550986 GTTTGTGACA
*
44550996 AATTATCTAAAGAGCCTTTGTGGCG
1 AATTATCTAAAGAGCCTTTTTGGCG
* *
44551021 AATTATATAAAGAGTCTTTTTGGCG
1 AATTATCTAAAGAGCCTTTTTGGCG
* * *
44551046 AATTATCTAAAGAATCTTTTTTGGTG
1 AATTATCTAAAG-AGCCTTTTTGGCG
* * *
44551072 AATTATCTGAAGACCCTTTATGGCG
1 AATTATCTAAAGAGCCTTTTTGGCG
*
44551097 TATTATCTA
1 AATTATCTA
44551106 GAATGTCTAG
Statistics
Matches: 69, Mismatches: 15, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
25 49 0.71
26 20 0.29
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.39
Consensus pattern (25 bp):
AATTATCTAAAGAGCCTTTTTGGCG
Found at i:44553928 original size:50 final size:50
Alignment explanation
Indices: 44553782--44553947 Score: 181
Period size: 50 Copynumber: 3.3 Consensus size: 50
44553772 TATCCCAAAT
** * * * *
44553782 ATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGACATGTCCTAGAC
1 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGACATGTCCCAGAC
** * * **
44553832 ATGGTCTTACGGGGGACCTCTCATCTCGATGCCAAC-ACAATATCCCAGGT
1 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGAC-ATGTCCCAGAC
* *
44553882 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGTCATGTCCCAAAC
1 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGACATGTCCCAGAC
*
44553932 ATGTTCTTACATGGGA
1 ATGGTCTTACATGGGA
44553948 TCTCATTCCC
Statistics
Matches: 93, Mismatches: 21, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
49 2 0.02
50 90 0.97
51 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.28
Consensus pattern (50 bp):
ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGACATGTCCCAGAC
Found at i:44561060 original size:16 final size:16
Alignment explanation
Indices: 44561018--44561060 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
44561008 ATTAGGATCT
* *
44561018 TTACTTTCTTCTTTAC
1 TTACTTACTTGTTTAC
*
44561034 TTACTCACTTGTTTAC
1 TTACTTACTTGTTTAC
*
44561050 TTACTTGCTTG
1 TTACTTACTTG
44561061 CTTAAATATC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.14, C:0.23, G:0.07, T:0.56
Consensus pattern (16 bp):
TTACTTACTTGTTTAC
Found at i:44572359 original size:33 final size:33
Alignment explanation
Indices: 44572315--44572384 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
44572305 CCTTTCTAGG
* *
44572315 AGAAAGGTTAGAATTATCAAAAACAACATGCAT
1 AGAAAGATTAGAATCATCAAAAACAACATGCAT
*
44572348 AGAAAGATTAGAATCATCGAAAACAACATGCAT
1 AGAAAGATTAGAATCATCAAAAACAACATGCAT
44572381 AGAA
1 AGAA
44572385 TCTTCAACCA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.53, C:0.13, G:0.16, T:0.19
Consensus pattern (33 bp):
AGAAAGATTAGAATCATCAAAAACAACATGCAT
Found at i:44574019 original size:50 final size:50
Alignment explanation
Indices: 44573913--44574154 Score: 209
Period size: 50 Copynumber: 4.7 Consensus size: 50
44573903 GGTAATGAGA
* *
44573913 TCCCATGTAAGACCATGTCTGGGACATGGCATTTGCATCATTGAGGTTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGA-G--ATGAGAGG
*
44573969 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
** * * * **
44574019 TCCCCCGTAAGACCATGTTTGGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * * * * * * * **
44574069 TCCCATGTAAGACCATATTTGGGATATGGTATT-G-ACAGTACAAGAAACA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAGAGG
* *
44574118 TCCCATGTAAGACCATTTCTGGGACATGGCTTTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
44574155 TGTTATTATC
Statistics
Matches: 155, Mismatches: 28, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
48 3 0.02
49 34 0.22
50 78 0.50
51 1 0.01
52 1 0.01
53 2 0.01
55 1 0.01
56 35 0.23
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
Found at i:44576932 original size:21 final size:20
Alignment explanation
Indices: 44576906--44576946 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
44576896 GCAACTCATC
44576906 AAATGAATCAGAAGTTGACCT
1 AAATGAATCAGAAGTT-ACCT
* *
44576927 AAATGAGTTAGAAGTTACCT
1 AAATGAATCAGAAGTTACCT
44576947 TTGATTCATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (20 bp):
AAATGAATCAGAAGTTACCT
Found at i:44580168 original size:23 final size:24
Alignment explanation
Indices: 44580127--44580171 Score: 83
Period size: 23 Copynumber: 1.9 Consensus size: 24
44580117 TCATCTTTAA
44580127 TTATGCTTAGTTTTAGTTGTTTTC
1 TTATGCTTAGTTTTAGTTGTTTTC
44580151 TTATGCTTAG-TTTAGTTGTTT
1 TTATGCTTAGTTTTAGTTGTTT
44580172 CCTATATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.13, C:0.07, G:0.18, T:0.62
Consensus pattern (24 bp):
TTATGCTTAGTTTTAGTTGTTTTC
Found at i:44586175 original size:6 final size:6
Alignment explanation
Indices: 44586164--44586190 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
44586154 GTCGAAACCA
44586164 TTCCTT TTCCTT TTCCTT TTCCTT TTC
1 TTCCTT TTCCTT TTCCTT TTCCTT TTC
44586191 ATCAATGCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (6 bp):
TTCCTT
Found at i:44593391 original size:21 final size:22
Alignment explanation
Indices: 44593365--44593422 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
44593355 TTTTTCCCTT
44593365 CTTTTTATTAATAAAATA-TTA
1 CTTTTTATTAATAAAATACTTA
**
44593386 CTTTTTAAAAACTAAAATACTTA
1 CTTTTTATTAA-TAAAATACTTA
44593409 --TTTTATATAATAAA
1 CTTTTTAT-TAATAAA
44593423 TTTAAATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
21 18 0.60
22 9 0.30
23 3 0.10
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (22 bp):
CTTTTTATTAATAAAATACTTA
Found at i:44599293 original size:24 final size:23
Alignment explanation
Indices: 44599239--44599293 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
44599229 ATACATACTA
*
44599239 AATATATTAATAAAATTTTAATTT
1 AATAT-TTAATAAAACTTTAATTT
** *
44599263 ACCATTTAATTAAAACTTTATTTT
1 AATATTTAA-TAAAACTTTAATTT
44599287 AATATTT
1 AATATTT
44599294 TTATGCATTT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (23 bp):
AATATTTAATAAAACTTTAATTT
Found at i:44605036 original size:11 final size:11
Alignment explanation
Indices: 44605020--44605048 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
44605010 CCACCACATT
44605020 CTCCTCCTTAG
1 CTCCTCCTTAG
44605031 CTCCTCCTTAG
1 CTCCTCCTTAG
44605042 CTCCTCC
1 CTCCTCC
44605049 CTTATTAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.07, C:0.52, G:0.07, T:0.34
Consensus pattern (11 bp):
CTCCTCCTTAG
Found at i:44607576 original size:30 final size:31
Alignment explanation
Indices: 44607517--44607576 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
44607507 TTAACATCCC
44607517 AGTGACTTAAATAAAAACTTTTAAATAGTTT
1 AGTGACTTAAATAAAAACTTTTAAATAGTTT
* *
44607548 AGTGGCTTAAATAAAAA-TTTTGAATAGTT
1 AGTGACTTAAATAAAAACTTTTAAATAGTT
44607577 CAATAACCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.43, C:0.05, G:0.13, T:0.38
Consensus pattern (31 bp):
AGTGACTTAAATAAAAACTTTTAAATAGTTT
Found at i:44608764 original size:22 final size:22
Alignment explanation
Indices: 44608736--44608777 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
44608726 ATCACTAATT
*
44608736 AAACCAAAGCCTCAACAAACAA
1 AAACCAAAACCTCAACAAACAA
*
44608758 AAACCAAAATCTCAACAAAC
1 AAACCAAAACCTCAACAAAC
44608778 CCAATAACTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.31, G:0.02, T:0.07
Consensus pattern (22 bp):
AAACCAAAACCTCAACAAACAA
Found at i:44611659 original size:12 final size:12
Alignment explanation
Indices: 44611642--44611666 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44611632 CAACCATAAT
44611642 CGCAAGCTAGTG
1 CGCAAGCTAGTG
44611654 CGCAAGCTAGTG
1 CGCAAGCTAGTG
44611666 C
1 C
44611667 ATTTAAGCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.28, G:0.32, T:0.16
Consensus pattern (12 bp):
CGCAAGCTAGTG
Found at i:44613199 original size:45 final size:45
Alignment explanation
Indices: 44613015--44613202 Score: 193
Period size: 45 Copynumber: 4.2 Consensus size: 45
44613005 AATAATAACA
* * * * *
44613015 GATACACGGTGG-ATTAACACATAGC-ACCACCCTTATAGTCAAT
1 GATACCCGGTGGAATCAGCACATAGCAACCACCTTTATAATCAAT
** * * *
44613058 GATACTTGGTGGAATCAACACATAGCAACCATCTTCATAATCAAT
1 GATACCCGGTGGAATCAGCACATAGCAACCACCTTTATAATCAAT
*** * *
44613103 AGA-AAATGGTGGAATCAGCACACATCAACCACCTTTATAATCAAT
1 -GATACCCGGTGGAATCAGCACATAGCAACCACCTTTATAATCAAT
*
44613148 GATACCCGGCGGAATCAGCACATAGCAACCACCTTTATAATCAAT
1 GATACCCGGTGGAATCAGCACATAGCAACCACCTTTATAATCAAT
*
44613193 GGTACCCGGT
1 GATACCCGGT
44613203 ACACGTAATA
Statistics
Matches: 119, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
43 10 0.08
44 14 0.12
45 93 0.78
46 2 0.02
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23
Consensus pattern (45 bp):
GATACCCGGTGGAATCAGCACATAGCAACCACCTTTATAATCAAT
Found at i:44617773 original size:16 final size:17
Alignment explanation
Indices: 44617746--44617794 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
44617736 TAGAATTGAG
*
44617746 TTGAGAAAATTATTTAA
1 TTGAGAAAATTAATTAA
44617763 TTGAG-AAATTAATTAA
1 TTGAGAAAATTAATTAA
* *
44617779 TTAATTAAAATTAATT
1 TTGA-GAAAATTAATT
44617795 TATGATTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 13 0.48
17 5 0.19
18 9 0.33
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (17 bp):
TTGAGAAAATTAATTAA
Found at i:44617940 original size:30 final size:30
Alignment explanation
Indices: 44617906--44617968 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
44617896 GAAAGGCACA
44617906 AAAGCCCCTCATGTTAATACATGGGACAAC
1 AAAGCCCCTCATGTTAATACATGGGACAAC
44617936 AAAGCCCCTCATGTTAATACATGGGACAAC
1 AAAGCCCCTCATGTTAATACATGGGACAAC
44617966 AAA
1 AAA
44617969 CCCAAGTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.40, C:0.25, G:0.16, T:0.19
Consensus pattern (30 bp):
AAAGCCCCTCATGTTAATACATGGGACAAC
Found at i:44618616 original size:26 final size:27
Alignment explanation
Indices: 44618568--44618618 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
44618558 AGTGTTCATC
*
44618568 TCTTTTTTCACTTATTATGTATTGTGT
1 TCTTTTTTCACTTATCATGTATTGTGT
44618595 TCTTTTTTCTAC-TATCAT-TATTGT
1 TCTTTTTTC-ACTTATCATGTATTGT
44618619 TAAAACTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 6 0.27
27 14 0.64
28 2 0.09
ACGTcount: A:0.16, C:0.14, G:0.08, T:0.63
Consensus pattern (27 bp):
TCTTTTTTCACTTATCATGTATTGTGT
Found at i:44620379 original size:110 final size:106
Alignment explanation
Indices: 44620159--44620444 Score: 403
Period size: 110 Copynumber: 2.7 Consensus size: 106
44620149 TGAGAAATTA
* * *
44620159 AAACCCAGCACATTAAGGCACG-TTCCTCGAATTTCCAAATGCTAAACATTGCCTTATTTTGAAA
1 AAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCCAAACGCTAAACATTGCCTTATTTTGAAA
* **
44620223 ATTTTGAAAGGATTGGCTATTTGGTTGAACGAGAAAAATCG
66 ATTTTAAAAGGATTAACTATTTGGTTGAACGAGAAAAATCG
* * *
44620264 AAACCCAGCATATTAGGGCACGTTTTCTCAAATTTCCAAACGCAAAACATTGCCTTATTTTGAAA
1 AAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCCAAACGCTAAACATTGCCTTATTTTGAAA
*
44620329 TTTTTTAAAAGGATACTTAACTATTTGGTTGAACGAGAAAAATCG
66 -ATTTTAAAAGG--A-TTAACTATTTGGTTGAACGAGAAAAATCG
* * *
44620374 AAACCCAACACATTAGGGCACGTTTTCTCGAATTTCCAAACGCTAAATATTGCCTTATTTAGAAA
1 AAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCCAAACGCTAAACATTGCCTTATTTTG-AA
44620439 AATTTT
65 AATTTT
44620445 CCTTTTGAAG
Statistics
Matches: 158, Mismatches: 17, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
105 20 0.13
106 38 0.24
107 9 0.06
109 1 0.01
110 87 0.55
111 3 0.02
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (106 bp):
AAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCCAAACGCTAAACATTGCCTTATTTTGAAA
ATTTTAAAAGGATTAACTATTTGGTTGAACGAGAAAAATCG
Found at i:44620567 original size:4 final size:4
Alignment explanation
Indices: 44620558--44620622 Score: 62
Period size: 4 Copynumber: 16.0 Consensus size: 4
44620548 ATACCATAAC
* *
44620558 AAAT AAAT AAAT AAAT AAAT AAAT AAACT AAA- ACAT AAA- AAAG ACATAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA-T AAAT AAAT AAAT AAAT A-A-AT
*
44620607 AAAT AAAT ACAT AAAT
1 AAAT AAAT AAAT AAAT
44620623 GAACATAAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
3 5 0.10
4 38 0.75
5 6 0.12
6 2 0.04
ACGTcount: A:0.71, C:0.06, G:0.02, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:44620615 original size:37 final size:33
Alignment explanation
Indices: 44620567--44620642 Score: 98
Period size: 37 Copynumber: 2.2 Consensus size: 33
44620557 CAAATAAATA
44620567 AATAAATAAATAAATAAACTAAAACATAAAAAAGAC
1 AATAAATAAATAAATAAA-T-AAACATAAAAAA-AC
* *
44620603 ATATAAATAAATACATAAATGAACATAAAAAAAC
1 A-ATAAATAAATAAATAAATAAACATAAAAAAAC
44620637 AATAAA
1 AATAAA
44620643 GGAAAATAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
33 5 0.14
34 3 0.08
35 11 0.30
36 2 0.05
37 16 0.43
ACGTcount: A:0.71, C:0.08, G:0.03, T:0.18
Consensus pattern (33 bp):
AATAAATAAATAAATAAATAAACATAAAAAAAC
Found at i:44620925 original size:3 final size:3
Alignment explanation
Indices: 44620917--44620984 Score: 54
Period size: 3 Copynumber: 23.3 Consensus size: 3
44620907 AAGCTATTAT
* * * *
44620917 ATA ATA AT- ATG ATA AGTA ACA ATA AT- ATAA ACA ATA ATA AAA ATA
1 ATA ATA ATA ATA ATA A-TA ATA ATA ATA AT-A ATA ATA ATA ATA ATA
44620962 ATA ATA A-A A-A ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
44620985 AATTACTGAA
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
2 8 0.15
3 41 0.77
4 4 0.08
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (3 bp):
ATA
Found at i:44620968 original size:22 final size:21
Alignment explanation
Indices: 44620928--44620984 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
44620918 TAATAATATG
* *
44620928 ATAAGTAACAATAATATAAACA
1 ATAA-TAAAAATAATATAAAAA
44620950 ATAATAAAAATAATAATAAAAA
1 ATAATAAAAATAAT-ATAAAAA
*
44620972 ATAATAATAATAA
1 ATAATAAAAATAA
44620985 AATTACTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 9 0.29
22 22 0.71
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.25
Consensus pattern (21 bp):
ATAATAAAAATAATATAAAAA
Found at i:44620973 original size:13 final size:13
Alignment explanation
Indices: 44620949--44620987 Score: 62
Period size: 13 Copynumber: 3.0 Consensus size: 13
44620939 TAATATAAAC
44620949 AATAAT-AAAAAT
1 AATAATAAAAAAT
44620961 AATAATAAAAAAT
1 AATAATAAAAAAT
44620974 AATAATAATAAAAT
1 AATAATAA-AAAAT
44620988 TACTGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 6 0.24
13 14 0.56
14 5 0.20
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
AATAATAAAAAAT
Found at i:44622350 original size:132 final size:132
Alignment explanation
Indices: 44622197--44622926 Score: 1049
Period size: 132 Copynumber: 5.6 Consensus size: 132
44622187 ACTACTGCTT
* *
44622197 AGGGAGACAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATC
1 AGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATC
* * * ***
44622262 TTCGATCTGCTCCACTACTTCTTAGGGAGATTAGATCTGTAATCTTCAATCTATTCCACTGCTGC
66 TTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAA
44622327 CC
131 CC
* * * *
44622329 AGTGAGATAGAATTTCTGGCTTCAAAGTACTCCACTATAACCACAGGGAGGTAAAAT-TCGCCAT
1 AGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCT-GCCAT
* *
44622393 CTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTG-CT
65 CTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCA
*
44622457 GCC
130 ACC
** *
44622460 TAGGGAGATAGAATTTTTGGCTTCAATATACTCCACTGTAACCACAGGGAGGTAAAATCAT-CCA
1 -AGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATC-TGCCA
44622524 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCC
64 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCC
44622589 AACC
129 AACC
* * * * *
44622593 AGGGAGATAGAATTATTGGCTTCAATGTAAATCCACTATAATCACTGGGAGGTAAAATCTGCCAT
1 AGGGAGATAGAATTACTGGCTTCAATGT-ACTCCACTGTAACCACAGGGAGGTAAAATCTGCCAT
44622658 CTTCGATCTGCT-C-C-A---CTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCA
65 CTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCA
*
44622717 ATC
130 ACC
* *
44622720 AGGGAGATAGAATCACTGGCTTCAATGTACTCCACTGTAATCACAGGGAGGTAAAATCTGCCATC
1 AGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATC
* *
44622785 TTCTATCTGCT----T-C-ACTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAA
66 TTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAA
44622844 CC
131 CC
**
44622846 AGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGATATC
1 AGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATC
44622911 TTCGATCTGCTCCACT
66 TTCGATCTGCTCCACT
44622927 GTCGATGCAG
Statistics
Matches: 546, Mismatches: 38, Indels: 30
0.89 0.06 0.05
Matches are distributed among these distances:
126 161 0.29
127 72 0.13
130 2 0.00
131 3 0.01
132 262 0.48
133 45 0.08
134 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.28
Consensus pattern (132 bp):
AGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATC
TTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAA
CC
Found at i:44622439 original size:44 final size:44
Alignment explanation
Indices: 44622391--44622585 Score: 130
Period size: 44 Copynumber: 4.4 Consensus size: 44
44622381 AAAATTCGCC
* *
44622391 ATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTA
1 ATCTTCAATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTA
* * * * *
44622435 ATCTTCAATCTATTCCACTGCTGCCTAGGGAGAT-AGAAT-TTTT
1 ATCTTCAATCTACTCCACTACTGCTTAGGGAGATAAG-ATCTGTA
** * ** * * **
44622478 GGCTTCAATATACTCCACTGTAAC--CACAGGGAGGTAAAATCAT-CC
1 ATCTTCAATCTACTCCAC--T-ACTGCTTAGGGAGATAAGATC-TGTA
* * *
44622523 ATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAA
1 ATCTTCAATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTA
*
44622567 ATCTTCAATCTATTCCACT
1 ATCTTCAATCTACTCCACT
44622586 GCCAACCAGG
Statistics
Matches: 109, Mismatches: 32, Indels: 20
0.68 0.20 0.12
Matches are distributed among these distances:
42 2 0.02
43 20 0.18
44 70 0.64
45 15 0.14
46 2 0.02
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (44 bp):
ATCTTCAATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTA
Found at i:44622725 original size:44 final size:43
Alignment explanation
Indices: 44622549--44622854 Score: 128
Period size: 38 Copynumber: 7.2 Consensus size: 43
44622539 ACTACTGCTT
*
44622549 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACC
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTG-CAATC
* * * **
44622593 AGGGAGAT-AGAAT-T--ATTGGCTTCAATGTAAATCCACTATAATC
1 AGGGAGATAAG-ATCTGAAAT--CTTCAATCT-ATTCCACTGCAATC
* * ** * **
44622636 ACTGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACT----T-
1 A--GGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCAATC
44622676 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAATC
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTG-CAATC
* * * *
44622720 AGGGAGAT-AGAATCACTG---GCTTCAATGTACTCCACTGTAATCAC
1 AGGGAGATAAG-AT--CTGAAATCTTCAATCTATTCCACTGCAAT--C
* * ** * *
44622764 AGGGAGGTAAAATCTGCCATCTTCTATCTGCTT-CACT----T-
1 AGGGAGATAAGATCTGAAATCTTCAATCT-ATTCCACTGCAATC
*
44622802 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACC
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTG-CAATC
44622846 AGGGAGATA
1 AGGGAGATA
44622855 GAATTACTGG
Statistics
Matches: 190, Mismatches: 39, Indels: 66
0.64 0.13 0.22
Matches are distributed among these distances:
37 2 0.01
38 57 0.30
40 1 0.01
41 4 0.02
42 6 0.03
43 34 0.18
44 46 0.24
45 26 0.14
46 13 0.07
48 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (43 bp):
AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCAATC
Found at i:44624368 original size:13 final size:14
Alignment explanation
Indices: 44624350--44624388 Score: 57
Period size: 13 Copynumber: 3.0 Consensus size: 14
44624340 CCTCTCCTTC
44624350 CTTTTTTTCTT-TT
1 CTTTTTTTCTTCTT
44624363 C-TTTTTTCTTCTT
1 CTTTTTTTCTTCTT
44624376 C-TTTTTTCTTCTT
1 CTTTTTTTCTTCTT
44624389 TTTCCTCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 9 0.36
13 16 0.64
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
CTTTTTTTCTTCTT
Found at i:44624369 original size:7 final size:7
Alignment explanation
Indices: 44624350--44624416 Score: 57
Period size: 7 Copynumber: 9.0 Consensus size: 7
44624340 CCTCTCCTTC
44624350 CTTTTTT
1 CTTTTTT
*
44624357 -TCTTTT
1 CTTTTTT
44624363 CTTTTTT
1 CTTTTTT
44624370 CTTCTTCTT
1 CTT-TT-TT
44624379 -TTTTCTT
1 CTTTT-TT
44624386 CTTTTTCCT
1 CTTTTT--T
44624395 CTTTTTTT
1 C-TTTTTT
44624403 CTTTTTT
1 CTTTTTT
44624410 CTTTTTT
1 CTTTTTT
44624417 AAATCTGAAC
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
6 5 0.10
7 27 0.53
8 10 0.20
9 4 0.08
10 5 0.10
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (7 bp):
CTTTTTT
Found at i:44624374 original size:10 final size:10
Alignment explanation
Indices: 44624359--44624416 Score: 63
Period size: 9 Copynumber: 6.2 Consensus size: 10
44624349 CCTTTTTTTC
44624359 TTTTCTT-TT
1 TTTTCTTCTT
44624368 TTCTTCTTCTT
1 TT-TTCTTCTT
44624379 TTTTCTTC-T
1 TTTTCTTCTT
*
44624388 TTTTCCTC-T
1 TTTTCTTCTT
44624397 TTTT-TTCTT
1 TTTTCTTCTT
44624406 TTTTCTT-TT
1 TTTTCTTCTT
44624415 TT
1 TT
44624417 AAATCTGAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
8 2 0.05
9 24 0.56
10 13 0.30
11 4 0.09
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTCTTCTT
Found at i:44628809 original size:109 final size:110
Alignment explanation
Indices: 44628610--44628926 Score: 453
Period size: 110 Copynumber: 2.9 Consensus size: 110
44628600 AGAATTCAAG
* * * *
44628610 AGGATATTTGGCTATTTGGTTAAATGAG--AAATCAAAACCCAGCACATTAGGGCACG-TTCCTC
1 AGGATATTTGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
* *
44628672 GAATTTCCAAACGCAAAACATTGGCTTATTTTGAAA-TTTTTGAA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTTAAA
*
44628716 AGGATATTTGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCATATTAGGGCACGTTTTCTC
1 AGGATATTTGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
*
44628781 GAATTTCCAAATGCAAAACATTGCCTTATTTTGAAATTTTTTAAA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTTAAA
* ** * * *
44628826 AGGATACTTAACTATTTGGTTGAACAAGAAAAATCGAAACCCAACACATTAGGGCACGTTTTCTT
1 AGGATATTTGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
* * *
44628891 GAATTTCCAAACGCTAAATATTGCCTTATTTAGAAA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAA
44628927 AATTTTCCTT
Statistics
Matches: 188, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
106 26 0.14
108 26 0.14
109 39 0.21
110 97 0.52
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Consensus pattern (110 bp):
AGGATATTTGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTTAAA
Found at i:44629049 original size:4 final size:4
Alignment explanation
Indices: 44629040--44629071 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
44629030 ATACCATAAC
44629040 AAAT AAAT AAAT AAAT AAAT AAAT AAACT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA-T AAA
44629072 ACATAAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:44631012 original size:3 final size:3
Alignment explanation
Indices: 44631006--44631042 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
44630996 CTCCTCCCCC
44631006 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
44631043 GAGTTTTAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:44640284 original size:37 final size:37
Alignment explanation
Indices: 44640229--44640308 Score: 142
Period size: 37 Copynumber: 2.2 Consensus size: 37
44640219 ATAATAATTT
*
44640229 AATTAAATTATCCAATTCAATTACTTAAAAATACTTA
1 AATTCAATTATCCAATTCAATTACTTAAAAATACTTA
*
44640266 AATTCAATTATCCAATTCAATTACTTTAAAATACTTA
1 AATTCAATTATCCAATTCAATTACTTAAAAATACTTA
44640303 AATTCA
1 AATTCA
44640309 TGTAATTGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.39
Consensus pattern (37 bp):
AATTCAATTATCCAATTCAATTACTTAAAAATACTTA
Found at i:44641144 original size:15 final size:15
Alignment explanation
Indices: 44641124--44641163 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
44641114 AAAAACAAGG
44641124 TCCCAAAACCTTATT
1 TCCCAAAACCTTATT
*
44641139 TCCCAAAACGTTATT
1 TCCCAAAACCTTATT
44641154 TCCCAAAACC
1 TCCCAAAACC
44641164 ACTTGACTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.35, C:0.35, G:0.03, T:0.28
Consensus pattern (15 bp):
TCCCAAAACCTTATT
Found at i:44644262 original size:39 final size:39
Alignment explanation
Indices: 44644217--44644362 Score: 166
Period size: 39 Copynumber: 3.7 Consensus size: 39
44644207 AACATGTTTT
* * *
44644217 TGAGTATTGTGATATATGATTGAATGTTATGTGATTATT
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* * * ** *
44644256 TAAGTATTGCGATATGTGCTTAAACATTATGTAATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
*
44644295 TGAGTATCGTGATATATGCTTAAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* * * *
44644334 TGTGTAATGTGATATATGTTTAAAAGTTA
1 TGAGTATTGTGATATATGCTTAAATGTTA
44644363 ATATGTTTAC
Statistics
Matches: 86, Mismatches: 21, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
39 86 1.00
ACGTcount: A:0.32, C:0.03, G:0.20, T:0.45
Consensus pattern (39 bp):
TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
Found at i:44650073 original size:99 final size:100
Alignment explanation
Indices: 44649963--44650156 Score: 282
Period size: 99 Copynumber: 1.9 Consensus size: 100
44649953 TTTTCTGTAC
* * *
44649963 TGCCAATGCCATATCCCAGATATGGTCTTACATGAGAGCTCTCATATCGGTGCC-ATGCCATGTC
1 TGCCAACGCCATATCCCAGACATGGTCTTACATGAGAGCTCTCATATCGGTGCCAACGCCATGTC
* *
44650027 CCAAACATGGTCTTACGGGGGACCTCTCATCTCGG
66 CCAAACATGGTCTTACAGGAGACCTCTCATCTCGG
* * * *
44650062 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGATCTCTCATCTCGGTGCCAACGCCATGTC
1 TGCCAACGCCATATCCCAGACATGGTCTTACATGAGAGCTCTCATATCGGTGCCAACGCCATGTC
* *
44650127 CCAGACATGGTCTTACATGAGACCTCTCAT
66 CCAAACATGGTCTTACAGGAGACCTCTCAT
44650157 AATCTCAATG
Statistics
Matches: 83, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
99 48 0.58
100 35 0.42
ACGTcount: A:0.22, C:0.31, G:0.21, T:0.26
Consensus pattern (100 bp):
TGCCAACGCCATATCCCAGACATGGTCTTACATGAGAGCTCTCATATCGGTGCCAACGCCATGTC
CCAAACATGGTCTTACAGGAGACCTCTCATCTCGG
Found at i:44650091 original size:50 final size:50
Alignment explanation
Indices: 44649963--44650301 Score: 326
Period size: 50 Copynumber: 6.6 Consensus size: 50
44649953 TTTTCTGTAC
* * * * *
44649963 TGCCAATGCCATATCCCAGATATGGTCTTACATGAGAGCTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* **
44650013 TGCC-ATGCCATGTCCCAAACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
44650062 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGATCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
44650112 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC---GG
* * *
44650168 TGCCAATGTCATGTCCTAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC---GG
* * * * *
44650224 TGCCAATGCCATGTCCCAGACATGGCCTGACACT-GG--CTCACATATCGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACA-TGGGACCTCTCATCTCGG
* *
44650272 TGTCGATGCCATGTCCCAGACATGGTCTTA
1 TGCCAATGCCATGTCCCAGACATGGTCTTA
44650302 TATGAGATCG
Statistics
Matches: 251, Mismatches: 30, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
48 28 0.11
49 41 0.16
50 85 0.34
51 4 0.02
53 5 0.02
54 4 0.02
56 83 0.33
57 1 0.00
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:44650181 original size:56 final size:56
Alignment explanation
Indices: 44650112--44650248 Score: 238
Period size: 56 Copynumber: 2.4 Consensus size: 56
44650102 CTCATCTCGG
*
44650112 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATAATCTCAATGA
* * *
44650168 TGCCAATGTCATGTCCTAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATAATCTCAATGA
44650224 TGCCAATGCCATGTCCCAGACATGG
1 TGCCAATGCCATGTCCCAGACATGG
44650249 CCTGACACTG
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 75 1.00
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.26
Consensus pattern (56 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATAATCTCAATGA
Found at i:44653124 original size:30 final size:30
Alignment explanation
Indices: 44653088--44653154 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
44653078 ACCCTTAAAA
** * *
44653088 TATTTACACTATTGGTCCTTCAAATTTT-TG
1 TATTTACACT-TTACTCCCTCAAATTTTGAG
44653118 TATTTACACTTTACTCCCTCAAATTTTGAG
1 TATTTACACTTTACTCCCTCAAATTTTGAG
44653148 TATTTAC
1 TATTTAC
44653155 TCTTGGGCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 14 0.44
30 18 0.56
ACGTcount: A:0.25, C:0.19, G:0.07, T:0.48
Consensus pattern (30 bp):
TATTTACACTTTACTCCCTCAAATTTTGAG
Found at i:44657443 original size:25 final size:25
Alignment explanation
Indices: 44657405--44657517 Score: 118
Period size: 25 Copynumber: 4.5 Consensus size: 25
44657395 TTAACTATCC
**
44657405 CCTCTACTACATCGCCGTCAACACT
1 CCTCTACCGCATCGCCGTCAACACT
* * *
44657430 CTTCTGCCGCATCGCCATCAACACT
1 CCTCTACCGCATCGCCGTCAACACT
*
44657455 CCTCTACCGCATCGCCGTCGACACT
1 CCTCTACCGCATCGCCGTCAACACT
** * * *
44657480 CCTCTATTGCGTCACCGTCGACACT
1 CCTCTACCGCATCGCCGTCAACACT
*
44657505 CCTCTACTGCATC
1 CCTCTACCGCATC
44657518 ATCATGTAAG
Statistics
Matches: 73, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 73 1.00
ACGTcount: A:0.19, C:0.44, G:0.12, T:0.25
Consensus pattern (25 bp):
CCTCTACCGCATCGCCGTCAACACT
Found at i:44658992 original size:19 final size:19
Alignment explanation
Indices: 44658968--44659021 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
44658958 AATCTTCAAG
*
44658968 GATATGCAATCTTAGATGT
1 GATATGCAATCTTAGATAT
*
44658987 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
44659006 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
44659022 AGATATGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:44659047 original size:22 final size:21
Alignment explanation
Indices: 44658968--44659047 Score: 78
Period size: 19 Copynumber: 3.9 Consensus size: 21
44658958 AATCTTCAAG
* *
44658968 GATATGCAATCTT--AGATGT
1 GATATGTAATCTTAGAGATAT
44658987 GATATGTAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
44659006 GATATGCAATCTTAGAAGATAT
1 GATATGTAATCTTAG-AGATAT
*
44659028 GATTTTGTAATCTTAGAGAT
1 GA-TATGTAATCTTAGAGAT
44659048 TTAATTTGTA
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
19 29 0.56
22 12 0.23
23 11 0.21
ACGTcount: A:0.35, C:0.07, G:0.19, T:0.39
Consensus pattern (21 bp):
GATATGTAATCTTAGAGATAT
Found at i:44659511 original size:6 final size:6
Alignment explanation
Indices: 44659504--44659538 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
44659494 TGTATCATTA
44659504 TTATTAT TTATTT TTATTT TTATTT TTATTT TTAT
1 TTATT-T TTATTT TTATTT TTATTT TTATTT TTAT
44659539 ATTCATGCGC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 23 0.82
7 5 0.18
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
TTATTT
Found at i:44661255 original size:28 final size:28
Alignment explanation
Indices: 44661223--44661315 Score: 91
Period size: 32 Copynumber: 3.2 Consensus size: 28
44661213 AATTTTTGAT
44661223 TAATTAAATAAATAATCATATTTCATAA
1 TAATTAAATAAATAATCATATTTCATAA
* * *
44661251 TAATTCTATGAATAATTAATTAGT-TTTCA-AT
1 TAA-T-TA--AATAAATAATCA-TATTTCATAA
*
44661282 TAATTAAATAAATAATCATATTTTATAA
1 TAATTAAATAAATAATCATATTTCATAA
44661310 TAATTA
1 TAATTA
44661316 TAGCACGAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
26 1 0.02
27 14 0.27
28 10 0.20
29 3 0.06
30 3 0.06
31 4 0.08
32 15 0.29
33 1 0.02
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.44
Consensus pattern (28 bp):
TAATTAAATAAATAATCATATTTCATAA
Found at i:44661268 original size:59 final size:59
Alignment explanation
Indices: 44661176--44661314 Score: 242
Period size: 59 Copynumber: 2.4 Consensus size: 59
44661166 ATTTAACTAT
**
44661176 TAATCATATTTCATAATAATTCTATGAATAATTAATTAATTTTTGATTAATTAAATAAA
1 TAATCATATTTCATAATAATTCTATGAATAATTAATTAATTTTCAATTAATTAAATAAA
*
44661235 TAATCATATTTCATAATAATTCTATGAATAATTAATTAGTTTTCAATTAATTAAATAAA
1 TAATCATATTTCATAATAATTCTATGAATAATTAATTAATTTTCAATTAATTAAATAAA
*
44661294 TAATCATATTTTATAATAATT
1 TAATCATATTTCATAATAATT
44661315 ATAGCACGAA
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 76 1.00
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (59 bp):
TAATCATATTTCATAATAATTCTATGAATAATTAATTAATTTTCAATTAATTAAATAAA
Found at i:44661279 original size:32 final size:31
Alignment explanation
Indices: 44661174--44661279 Score: 89
Period size: 32 Copynumber: 3.5 Consensus size: 31
44661164 AGATTTAACT
*
44661174 ATTAATCATATTTCATAATAATTCTATGAATA
1 ATTAATTAT-TTTCATAATAATTCTATGAATA
*
44661206 ATTAATTAATTTT--TGATTAA-T-TA--AATA
1 ATTAATT-ATTTTCAT-AATAATTCTATGAATA
* *
44661233 AATAATCATATTTCATAATAATTCTATGAATA
1 ATTAATTAT-TTTCATAATAATTCTATGAATA
44661265 ATTAATTAGTTTTCA
1 ATTAATTA-TTTTCA
44661280 ATTAATTAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 20
0.68 0.08 0.24
Matches are distributed among these distances:
26 2 0.04
27 12 0.21
28 4 0.07
29 4 0.07
30 4 0.07
31 4 0.07
32 24 0.42
33 3 0.05
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (31 bp):
ATTAATTATTTTCATAATAATTCTATGAATA
Found at i:44662580 original size:66 final size:66
Alignment explanation
Indices: 44662466--44662593 Score: 150
Period size: 66 Copynumber: 1.9 Consensus size: 66
44662456 GCAAATTGCT
* * * * * *
44662466 CAACTTAAAGCGGAGGCAGCATCGAGAGAAGCAGAGGCTCAAATAAAATCTGATGAACTCCAACT
1 CAACTTAAAGCGGAGGCAGCAGCGAGAGAAGCAAAGGCACAAAGAAAATATGACGAACTCCAACT
44662531 A
66 A
* * * *
44662532 CAACTTAAAGTGGAGGTAGTAGCGAGGGAAGCAAAGGCA-ACAAGAAAATATGACGAACTCCA
1 CAACTTAAAGCGGAGGCAGCAGCGAGAGAAGCAAAGGCACA-AAGAAAATATGACGAACTCCA
44662594 GTTACAGCTT
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
65 1 0.02
66 50 0.98
ACGTcount: A:0.42, C:0.19, G:0.25, T:0.14
Consensus pattern (66 bp):
CAACTTAAAGCGGAGGCAGCAGCGAGAGAAGCAAAGGCACAAAGAAAATATGACGAACTCCAACT
A
Found at i:44669969 original size:18 final size:18
Alignment explanation
Indices: 44669927--44669970 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
44669917 AGGAAATGAT
**
44669927 ATATGGATATGGATATGG
1 ATATGGATATGGATAAAG
44669945 ATATGGATATGGATAAAG
1 ATATGGATATGGATAAAG
*
44669963 ATGTGGAT
1 ATATGGAT
44669971 GTGAATATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (18 bp):
ATATGGATATGGATAAAG
Found at i:44669973 original size:6 final size:6
Alignment explanation
Indices: 44669927--44669959 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
44669917 AGGAAATGAT
44669927 ATATGG ATATGG ATATGG ATATGG ATATGG ATA
1 ATATGG ATATGG ATATGG ATATGG ATATGG ATA
44669960 AAGATGTGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.36, C:0.00, G:0.30, T:0.33
Consensus pattern (6 bp):
ATATGG
Found at i:44674078 original size:25 final size:24
Alignment explanation
Indices: 44674045--44674094 Score: 57
Period size: 25 Copynumber: 2.0 Consensus size: 24
44674035 TACCATTTTT
44674045 AATTATATAAAAAATTAAAAATTAAA
1 AATTATATAAAAAA-TAAAAA-TAAA
**
44674071 AATT-TATATTAAATAAAAATAAA
1 AATTATATAAAAAATAAAAATAAA
44674094 A
1 A
44674095 TAAATTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 5 0.23
24 6 0.27
25 7 0.32
26 4 0.18
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (24 bp):
AATTATATAAAAAATAAAAATAAA
Found at i:44674106 original size:26 final size:24
Alignment explanation
Indices: 44674060--44674111 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
44674050 TATAAAAAAT
* *
44674060 TAAAAATTAAAAATTTATATTAAA
1 TAAAAATAAAAAAATTATATTAAA
*
44674084 TAAAAATAAAATAAATTATTATTTAA
1 TAAAAATAAAA-AAATTA-TATTAAA
44674110 TA
1 TA
44674112 TTATATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 10 0.43
25 5 0.22
26 8 0.35
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
TAAAAATAAAAAAATTATATTAAA
Found at i:44674151 original size:6 final size:6
Alignment explanation
Indices: 44674140--44674188 Score: 89
Period size: 6 Copynumber: 8.2 Consensus size: 6
44674130 CTCCGTCCCC
*
44674140 CTTCAT CTTCAT CTTCAT CTTCAT CTTCAT CTTCAT CTTCAC CTTCAT
1 CTTCAT CTTCAT CTTCAT CTTCAT CTTCAT CTTCAT CTTCAT CTTCAT
44674188 C
1 C
44674189 CTTCCTAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.16, C:0.37, G:0.00, T:0.47
Consensus pattern (6 bp):
CTTCAT
Found at i:44677253 original size:50 final size:50
Alignment explanation
Indices: 44677140--44677338 Score: 184
Period size: 51 Copynumber: 3.8 Consensus size: 50
44677130 ATTTGGGTAA
* * * *
44677140 AGAGATCCCATTTAAGACCATGTTTGAGACATGGCATTGGCATCATTGAGGTTAA-G
1 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCATTGGCA-C--CGA----AATG
* * *
44677196 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCATTGGCACCGAAATG
** *
44677246 AGAGGTCCCCCCGTAAGACCATGTTTGGGACATGGCATGGGCACCGAAATG
1 AGAGGT-CCCATGTAAGACCATGTTTGGGACATGGCATTGGCACCGAAATG
** * * *
44677297 AGAACTCCCATGTAAGATCATATTTGGGATATGGCATTGGCA
1 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCATTGGCA
44677339 GTACAGAAAA
Statistics
Matches: 120, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
49 1 0.01
50 37 0.31
51 42 0.35
53 2 0.02
55 1 0.01
56 37 0.31
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.24
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCATTGGCACCGAAATG
Found at i:44677592 original size:12 final size:12
Alignment explanation
Indices: 44677575--44677613 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
44677565 ATGAGTTATT
44677575 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
44677587 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
44677599 TAAGTGAGTAAG
1 TAAGTAAGCAAG
44677611 TAA
1 TAA
44677614 AGAAGCGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:44683885 original size:6 final size:6
Alignment explanation
Indices: 44683869--44683910 Score: 66
Period size: 6 Copynumber: 6.8 Consensus size: 6
44683859 TATGTTTCTC
*
44683869 AAAATG GAAATG AAAATG AAAATG AAAATG AAAATG AGAAAT
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG A-AAAT
44683911 ACTTCATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
6 29 0.88
7 4 0.12
ACGTcount: A:0.64, C:0.00, G:0.19, T:0.17
Consensus pattern (6 bp):
AAAATG
Found at i:44685104 original size:21 final size:19
Alignment explanation
Indices: 44685079--44685128 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 19
44685069 TTCAAGGATG
44685079 TGCAATCTTAAATATGATATA
1 TGCAATCTTAAATATG--ATA
*
44685100 TGCAATCTTAGATATGATA
1 TGCAATCTTAAATATGATA
44685119 TGCAATCTTA
1 TGCAATCTTA
44685129 GAAGATGTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 13 0.46
21 15 0.54
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (19 bp):
TGCAATCTTAAATATGATA
Found at i:44685121 original size:19 final size:20
Alignment explanation
Indices: 44685079--44685130 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
44685069 TTCAAGGATG
*
44685079 TGCAATCTTAAATATGATATA
1 TGCAATCTTAGATATGA-ATA
44685100 TGCAATCTTAGATATG-ATA
1 TGCAATCTTAGATATGAATA
44685119 TGCAATCTTAGA
1 TGCAATCTTAGA
44685131 AGATGTGATT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 15 0.50
21 15 0.50
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (20 bp):
TGCAATCTTAGATATGAATA
Found at i:44687581 original size:14 final size:15
Alignment explanation
Indices: 44687555--44687587 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
44687545 TCCCAAGCTG
44687555 GGAAGGACCTTATGT
1 GGAAGGACCTTATGT
*
44687570 GGAAGG-CCTTATTT
1 GGAAGGACCTTATGT
44687584 GGAA
1 GGAA
44687588 AAGCATCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.27, C:0.12, G:0.33, T:0.27
Consensus pattern (15 bp):
GGAAGGACCTTATGT
Found at i:44689078 original size:88 final size:88
Alignment explanation
Indices: 44688921--44689680 Score: 830
Period size: 88 Copynumber: 8.6 Consensus size: 88
44688911 ATCATTCAAG
* * * * ** *
44688921 ATAGTAGATCTTGCCTTCCTGTACCGGCAG-TAGAGCAGATCAAAGACACCAG-CTTTGTCTCCC
1 ATAGCAGATCTTGCCTTCCTGTACTGACAGCGA-AGCAGATTGAAGACACCAGTC-TTGCCTCCC
* * *
44688984 TGGGTTGCAGCGGAGCAGGTTGAAA
64 TAGGTTGCAGTGGAGCAGATTGAAA
* *
44689009 ATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAACAGATTGAAGGCACCAGTCTTGCCTCCCTA
1 ATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATTGAAGACACCAGTCTTGCCTCCCTA
* * *
44689074 GGTTGCAGTGGAGTAGACTGAAG
66 GGTTGCAGTGGAGCAGATTGAAA
* * * * *
44689097 ATAGCAGATCTTGCCTTTCTATACTTACAGTGAAGCAGATCGAAGACACCAGTCTTGCCTCCCTA
1 ATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATTGAAGACACCAGTCTTGCCTCCCTA
* *
44689162 GGTTGCAGTGGAGCAGACTGAAG
66 GGTTGCAGTGGAGCAGATTGAAA
* * * *
44689185 ATAGCAGATCTTGCCTTCCTGTACCGACAGCGAAGCAGA-TCAAGGACACCAGCCTTGCCTCTCT
1 ATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATTGAA-GACACCAGTCTTGCCTCCCT
* * * *
44689249 GGGTTACAGCGGAGCAGGTTGAAA
65 AGGTTGCAGTGGAGCAGATTGAAA
*
44689273 ATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCTCCCTA
1 ATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATTGAAGACACCAGTCTTGCCTCCCTA
* * *
44689338 GGTTGCAGTGGAGTAAATTGAAG
66 GGTTGCAGTGGAGCAGATTGAAA
* * * * * *
44689361 ATGGCAGATCTTGCCTTCCTGTACTGGCATCGAAGCAGATTAAAGATACCAGCCTTGCCTCCCT-
1 ATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATTGAAGACACCAGTCTTGCCTCCCTA
* *
44689425 GGATTGCAGCGGAGCAGGTTGAAA
66 GG-TTGCAGTGGAGCAGATTGAAA
* * * * * *
44689449 ATAGTAGATCTTGCCTTCCTATATTGACAGTGAAGCAGATTGAAGACGCTAGTCTTGCCTCCCTA
1 ATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATTGAAGACACCAGTCTTGCCTCCCTA
* * * *
44689514 GGTTGTAGTGGAACAGACTGAAG
66 GGTTGCAGTGGAGCAGATTGAAA
* * * * * * * *
44689537 ATAGCAGATCTTACCTTTCTGTACCGACAGCGAAGCAGATCGAAAACTCCGGTCTTGTCTCCCT-
1 ATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATTGAAGACACCAGTCTTGCCTCCCTA
** * *
44689601 GAGCAGCAGTGGAGTAGGTTGAAA
66 G-GTTGCAGTGGAGCAGATTGAAA
* *
44689625 ATAGCAGATCTTGCCTTCCTGTACT-AGCAGTGAAGCAGATTGAAGACATCAGTCTT
1 ATAGCAGATCTTGCCTTCCTGTACTGA-CAGCGAAGCAGATTGAAGACACCAGTCTT
44689681 ATTGCCTTGA
Statistics
Matches: 554, Mismatches: 110, Indels: 16
0.81 0.16 0.02
Matches are distributed among these distances:
87 6 0.01
88 542 0.98
89 6 0.01
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24
Consensus pattern (88 bp):
ATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATTGAAGACACCAGTCTTGCCTCCCTA
GGTTGCAGTGGAGCAGATTGAAA
Found at i:44689398 original size:264 final size:262
Alignment explanation
Indices: 44688918--44689680 Score: 958
Period size: 264 Copynumber: 2.9 Consensus size: 262
44688908 CAGATCATTC
* * * *
44688918 AAGATAGTAGATCTTGCCTTCCTGTACCGGCAGTAGAGCAGATCAAAGACACCAGCTTTGTCTCC
1 AAGATAGTAGATCTTGCCTTCCTGTACCGACAGGA-AGCAGATC-AAGACACCAGCCTTGCCTCC
*
44688983 CTGGGTTGCAGCGGAGCAGGTTGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAACAGA
64 CTGGGTTGCAGCGGAGCAGGTTGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGA
* * *
44689048 TTGAAGGCACCAGTCTTGCCTCCCTAGGTTGCAGTGGAGTAGACTGAAGATAGCAGATCTTGCCT
129 TCGAAGACACCAGTCTTGCCTCCCTAGGTTGCAGTGGAGTAGATTGAAGATAGCAGATCTTGCCT
* * * *
44689113 TTCTATACTTA-CAGTGAAGCAGATCGAAGACACCAGTCTTGCCTCCCTAGG-TTGCAGTGGAGC
194 TCCTGTAC-TAGCAGTGAAGCAGATTGAAGACACCAGTCTTGCCTCCCT-GGATTGCAGCGGAGC
44689176 AGACTG
257 AGACTG
* *
44689182 AAGATAGCAGATCTTGCCTTCCTGTACCGACAGCGAAGCAGATCAAGGACACCAGCCTTGCCTCT
1 AAGATAGTAGATCTTGCCTTCCTGTACCGACAG-GAAGCAGATCAA-GACACCAGCCTTGCCTCC
*
44689247 CTGGGTTACAGCGGAGCAGGTTGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGA
64 CTGGGTTGCAGCGGAGCAGGTTGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGA
* *
44689312 TCGAAGACACCAGTCTTGCCTCCCTAGGTTGCAGTGGAGTAAATTGAAGATGGCAGATCTTGCCT
129 TCGAAGACACCAGTCTTGCCTCCCTAGGTTGCAGTGGAGTAGATTGAAGATAGCAGATCTTGCCT
* * * *
44689377 TCCTGTACTGGCA-TCGAAGCAGATTAAAGATACCAGCCTTGCCTCCCTGGATTGCAGCGGAGCA
194 TCCTGTACTAGCAGT-GAAGCAGATTGAAGACACCAGTCTTGCCTCCCTGGATTGCAGCGGAGCA
**
44689441 GGTTG
258 GACTG
* * ** * * * *
44689446 AAAATAGTAGATCTTGCCTTCCTATATTGACAGTGAAGCAGATTGAAGACGCTAGTCTTGCCTCC
1 AAGATAGTAGATCTTGCCTTCCTGTACCGACAG-GAAGCAGA-TCAAGACACCAGCCTTGCCTCC
* * * * ** * * * *
44689511 CTAGGTTGTAGTGGAACAGACTGAAGATAGCAGATCTTACCTTTCTGTACCGACAGCGAAGCAGA
64 CTGGGTTGCAGCGGAGCAGGTTGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGA
* * * * ** * *
44689576 TCGAAAACTCCGGTCTTGTCTCCCT-GAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGCC
129 TCGAAGACACCAGTCTTGCCTCCCTAG-GTTGCAGTGGAGTAGATTGAAGATAGCAGATCTTGCC
*
44689640 TTCCTGTACTAGCAGTGAAGCAGATTGAAGACATCAGTCTT
193 TTCCTGTACTAGCAGTGAAGCAGATTGAAGACACCAGTCTT
44689681 ATTGCCTTGA
Statistics
Matches: 431, Mismatches: 60, Indels: 16
0.85 0.12 0.03
Matches are distributed among these distances:
263 7 0.02
264 419 0.97
265 5 0.01
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24
Consensus pattern (262 bp):
AAGATAGTAGATCTTGCCTTCCTGTACCGACAGGAAGCAGATCAAGACACCAGCCTTGCCTCCCT
GGGTTGCAGCGGAGCAGGTTGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATC
GAAGACACCAGTCTTGCCTCCCTAGGTTGCAGTGGAGTAGATTGAAGATAGCAGATCTTGCCTTC
CTGTACTAGCAGTGAAGCAGATTGAAGACACCAGTCTTGCCTCCCTGGATTGCAGCGGAGCAGAC
TG
Found at i:44689926 original size:115 final size:116
Alignment explanation
Indices: 44689750--44689989 Score: 356
Period size: 115 Copynumber: 2.1 Consensus size: 116
44689740 GCGTTGTAGC
* * **
44689750 GGAGCATATTGAAGCCATGACGGTGAATCTTATCTTCCTGGCGTTAAGGCTTGGATTAGCTGAA-
1 GGAGCAGATTGAAGCCACGACGACGAATCTTATCTTCCTGGCGTTAAGGCTTGGATTAGCTGAAG
**
44689814 GGAGCGGATTAAAGCTGAAGGCAGTGAATCCTATCTCTTTGGCATTCCAGT
66 GGAGCGGATTAAAGCTGAAGGCAACGAATCCTATCTCTTTGGCATTCCAGT
* *
44689865 GGAGCAGATTGAAGCCACGATGACGAATCTTATCTTCTTGGCGTTAAGGCTTGGATTAGCTGAAG
1 GGAGCAGATTGAAGCCACGACGACGAATCTTATCTTCCTGGCGTTAAGGCTTGGATTAGCTGAAG
** * *
44689930 TGGAGTTGATTAAAGCTGAGGGCAACGAATCCTATCTCTTTGGCATTGCAGT
66 -GGAGCGGATTAAAGCTGAAGGCAACGAATCCTATCTCTTTGGCATTCCAGT
44689982 GGAGCAGA
1 GGAGCAGA
44689990 CTGAGTAAGA
Statistics
Matches: 111, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
115 58 0.52
117 53 0.48
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (116 bp):
GGAGCAGATTGAAGCCACGACGACGAATCTTATCTTCCTGGCGTTAAGGCTTGGATTAGCTGAAG
GGAGCGGATTAAAGCTGAAGGCAACGAATCCTATCTCTTTGGCATTCCAGT
Found at i:44690034 original size:44 final size:44
Alignment explanation
Indices: 44689974--44690072 Score: 119
Period size: 44 Copynumber: 2.2 Consensus size: 44
44689964 TCTCTTTGGC
* * * * *
44689974 ATTGCAGTGGAGCAGACTGAGT-AAGAAAGTCTTATCCCCCTAAA
1 ATTGTAGTGGAACAGACTGAATGAACAAA-TCCTATCCCCCTAAA
*
44690018 ATTGTAGTGGAACAGACTGAATGAACAAATCCTATCTCCCTAAA
1 ATTGTAGTGGAACAGACTGAATGAACAAATCCTATCCCCCTAAA
*
44690062 GTTGTAGTGGA
1 ATTGTAGTGGA
44690073 GTGGATTAGA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
44 42 0.89
45 5 0.11
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.25
Consensus pattern (44 bp):
ATTGTAGTGGAACAGACTGAATGAACAAATCCTATCCCCCTAAA
Found at i:44690556 original size:19 final size:20
Alignment explanation
Indices: 44690514--44690565 Score: 88
Period size: 21 Copynumber: 2.6 Consensus size: 20
44690504 TTCAAGGATG
44690514 TGCAATCTTAGATATGATATA
1 TGCAATCTTAGATATGA-ATA
44690535 TGCAATCTTAGATATG-ATA
1 TGCAATCTTAGATATGAATA
44690554 TGCAATCTTAGA
1 TGCAATCTTAGA
44690566 AGATGTGATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 15 0.48
21 16 0.52
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (20 bp):
TGCAATCTTAGATATGAATA
Found at i:44691081 original size:17 final size:17
Alignment explanation
Indices: 44691059--44691093 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
44691049 TTTATATACA
* *
44691059 TATATATATTTACATTT
1 TATATACATATACATTT
44691076 TATATACATATACATTT
1 TATATACATATACATTT
44691093 T
1 T
44691094 TTATTTCCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (17 bp):
TATATACATATACATTT
Found at i:44691688 original size:6 final size:6
Alignment explanation
Indices: 44691672--44691713 Score: 66
Period size: 6 Copynumber: 6.8 Consensus size: 6
44691662 TATGTTTCTC
*
44691672 AAAATG GAAATG AAAATG AAAATG AAAATG AAAATG AGAAAT
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG A-AAAT
44691714 ACTTCATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
6 29 0.88
7 4 0.12
ACGTcount: A:0.64, C:0.00, G:0.19, T:0.17
Consensus pattern (6 bp):
AAAATG
Found at i:44692924 original size:24 final size:23
Alignment explanation
Indices: 44692892--44692938 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
44692882 GTGCAATCTT
44692892 AGATATGATATATGCAATCTTAGA
1 AGATATGAT-TATGCAATCTTAGA
* * *
44692916 AGATGTGATTATGTACTCTTAGA
1 AGATATGATTATGCAATCTTAGA
44692939 GATTTAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (23 bp):
AGATATGATTATGCAATCTTAGA
Found at i:44693424 original size:56 final size:55
Alignment explanation
Indices: 44693364--44693482 Score: 129
Period size: 56 Copynumber: 2.1 Consensus size: 55
44693354 ACATATTATA
44693364 TATATTTTATTATA-A-TTCTATTTGCATAACTTTTATATGCATATATATTTACA-TTT
1 TATATTTTA-TATACATTTCTATTT-CATAACTTTTATATGCATATATA--TACACTTT
** * *
44693420 TATA-TACATATACATTTTTTATTTCCTAACTTTTATATGCATATATATACACTTT
1 TATATTTTATATACA-TTTCTATTTCATAACTTTTATATGCATATATATACACTTT
44693475 TATATTTT
1 TATATTTT
44693483 TGTACTTTAC
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
54 8 0.15
55 10 0.19
56 27 0.52
57 7 0.13
ACGTcount: A:0.32, C:0.11, G:0.03, T:0.55
Consensus pattern (55 bp):
TATATTTTATATACATTTCTATTTCATAACTTTTATATGCATATATATACACTTT
Found at i:44693581 original size:23 final size:26
Alignment explanation
Indices: 44693561--44693627 Score: 68
Period size: 27 Copynumber: 2.6 Consensus size: 26
44693551 TCTAAATTAA
44693561 TTAATTTTA-ATATATGTAATTATTAT
1 TTAATTTTATATATATGTAATTA-TAT
** *
44693587 TTGTTTTTATATATATGTAATTATCT
1 TTAATTTTATATATATGTAATTATAT
44693613 TT--TTTTATAATATAT
1 TTAATTTTAT-ATATAT
44693628 ATATGTAGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
24 6 0.17
25 6 0.17
26 11 0.31
27 13 0.36
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.61
Consensus pattern (26 bp):
TTAATTTTATATATATGTAATTATAT
Found at i:44693625 original size:27 final size:27
Alignment explanation
Indices: 44693570--44693629 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 27
44693560 ATTAATTTTA
*
44693570 ATATATGTAATTATTATTTGTTTTTAT
1 ATATATGTAATTATTATTTGTTTTAAT
44693597 ATATATGTAATTATCT-TTT-TTTATAAT
1 ATATATGTAATTAT-TATTTGTTT-TAAT
44693624 ATATAT
1 ATATAT
44693630 ATGTAGATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 3 0.10
27 26 0.87
28 1 0.03
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (27 bp):
ATATATGTAATTATTATTTGTTTTAAT
Found at i:44693644 original size:29 final size:29
Alignment explanation
Indices: 44693594--44693650 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
44693584 TATTTGTTTT
* *
44693594 TATATATATGTAATTATCTTTTTTTATAA
1 TATATATATGTAATAATCTTTTTATATAA
44693623 TATATATATGTAGATAAT-TTTTTATATA
1 TATATATATGTA-ATAATCTTTTTATATA
44693651 TGTACATGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (29 bp):
TATATATATGTAATAATCTTTTTATATAA
Found at i:44697269 original size:27 final size:27
Alignment explanation
Indices: 44697239--44697343 Score: 99
Period size: 27 Copynumber: 3.9 Consensus size: 27
44697229 CTGTCACGAC
* *
44697239 AGACTACCCCGTGTTTATTGTCCTAGT
1 AGACTACCCCGTGTTTACTGTCCTCGT
* * *
44697266 AGACTACTCCATGTTTACTAT-CTCG-
1 AGACTACCCCGTGTTTACTGTCCTCGT
44697291 ACGGACTACCCCGTGTTTACTGTCC-CGAT
1 A--GACTACCCCGTGTTTACTGTCCTCG-T
* *
44697320 GGACTACCCTGTGTTTACTGTCCT
1 AGACTACCCCGTGTTTACTGTCCT
44697344 TACGAACTAT
Statistics
Matches: 62, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
25 1 0.02
26 3 0.05
27 57 0.92
28 1 0.02
ACGTcount: A:0.18, C:0.30, G:0.18, T:0.34
Consensus pattern (27 bp):
AGACTACCCCGTGTTTACTGTCCTCGT
Found at i:44697352 original size:27 final size:27
Alignment explanation
Indices: 44697224--44697352 Score: 93
Period size: 27 Copynumber: 4.8 Consensus size: 27
44697214 GTAACTTCGA
*
44697224 GTTTACTGTCACGAC-AGACTACCCCGT
1 GTTTACTGTCCCGACGA-ACTACCCCGT
* * * *
44697251 GTTTATTGT-CCTA-GTAGACTACTCCAT
1 GTTTACTGTCCCGACG-A-ACTACCCCGT
* * *
44697278 GTTTACTATCTCGACGGACTACCCCGT
1 GTTTACTGTCCCGACGAACTACCCCGT
* * *
44697305 GTTTACTGTCCCGATGGACTACCCTGT
1 GTTTACTGTCCCGACGAACTACCCCGT
**
44697332 GTTTACTGTCCTTACGAACTA
1 GTTTACTGTCCCGACGAACTA
44697353 TACTGGTTGT
Statistics
Matches: 78, Mismatches: 20, Indels: 8
0.74 0.19 0.08
Matches are distributed among these distances:
26 2 0.03
27 73 0.94
28 2 0.03
29 1 0.01
ACGTcount: A:0.20, C:0.29, G:0.18, T:0.33
Consensus pattern (27 bp):
GTTTACTGTCCCGACGAACTACCCCGT
Found at i:44710083 original size:62 final size:59
Alignment explanation
Indices: 44710014--44710128 Score: 167
Period size: 62 Copynumber: 1.9 Consensus size: 59
44710004 AGTGATTATC
* * *
44710014 TTAATATTAAATTTAATTTAATTTTTATCTTATAGATAAATATTTTATTATTTTAATAAGAT
1 TTAATATTAAATTTAATCTAATTTTTATC-T-T-GATAAATATTATATTAATTTAATAAGAT
*
44710076 TTAATATTAAATTTAATCTAATTTTTCTCTTGATAAATATTATATTAATTTAA
1 TTAATATTAAATTTAATCTAATTTTTATCTTGATAAATATTATATTAATTTAA
44710129 CTTTAAAATG
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 20 0.41
60 1 0.02
61 1 0.02
62 27 0.55
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (59 bp):
TTAATATTAAATTTAATCTAATTTTTATCTTGATAAATATTATATTAATTTAATAAGAT
Found at i:44724074 original size:6 final size:6
Alignment explanation
Indices: 44724063--44724115 Score: 70
Period size: 6 Copynumber: 8.7 Consensus size: 6
44724053 TATCTTTGTC
* * *
44724063 TTTAAT TGTAAT CTTTAAT TTTAAT TTTAAT TTTAAT TTTAAT GTTAGT
1 TTTAAT TTTAAT -TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT
44724112 TTTA
1 TTTA
44724116 TTTATTTTGC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
6 36 0.88
7 5 0.12
ACGTcount: A:0.30, C:0.02, G:0.06, T:0.62
Consensus pattern (6 bp):
TTTAAT
Found at i:44727407 original size:38 final size:38
Alignment explanation
Indices: 44727365--44727439 Score: 150
Period size: 38 Copynumber: 2.0 Consensus size: 38
44727355 TACCTTCACC
44727365 TATTTTTAGTAAACTTAAACCTATTTCCATCATCCCTT
1 TATTTTTAGTAAACTTAAACCTATTTCCATCATCCCTT
44727403 TATTTTTAGTAAACTTAAACCTATTTCCATCATCCCT
1 TATTTTTAGTAAACTTAAACCTATTTCCATCATCCCT
44727440 CATCACTCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.29, C:0.24, G:0.03, T:0.44
Consensus pattern (38 bp):
TATTTTTAGTAAACTTAAACCTATTTCCATCATCCCTT
Found at i:44729659 original size:25 final size:25
Alignment explanation
Indices: 44729628--44729684 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 25
44729618 ACATCGAGCT
44729628 TCTGTGGTGAGTTATCGGTAAAGCC
1 TCTGTGGTGAGTTATCGGTAAAGCC
* *
44729653 TTTGTGGTGAGTTATCTGTAAAGCC
1 TCTGTGGTGAGTTATCGGTAAAGCC
44729678 TCTGTGG
1 TCTGTGG
44729685 CAAGCTATCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.18, C:0.14, G:0.32, T:0.37
Consensus pattern (25 bp):
TCTGTGGTGAGTTATCGGTAAAGCC
Found at i:44729693 original size:25 final size:25
Alignment explanation
Indices: 44729640--44729699 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
44729630 TGTGGTGAGT
* * ** *
44729640 TATCGGTAAAGCCTTTGTGGTGAGT
1 TATCTGTAAAGCCTCTGTGGCAAGC
44729665 TATCTGTAAAGCCTCTGTGGCAAGC
1 TATCTGTAAAGCCTCTGTGGCAAGC
*
44729690 TATCTATAAA
1 TATCTGTAAA
44729700 TCCATATAGC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (25 bp):
TATCTGTAAAGCCTCTGTGGCAAGC
Found at i:44729788 original size:25 final size:25
Alignment explanation
Indices: 44729760--44729866 Score: 117
Period size: 25 Copynumber: 4.3 Consensus size: 25
44729750 ATCAAGCTTC
*
44729760 TGTGGCGGGTTATCTGTAAAGCCTT
1 TGTGGCGAGTTATCTGTAAAGCCTT
* *
44729785 TGTGGCGAGTTATCTATGAAGCCTT
1 TGTGGCGAGTTATCTGTAAAGCCTT
* * *
44729810 TGTGGCGAGTTATTTGTAAGGCCCT
1 TGTGGCGAGTTATCTGTAAAGCCTT
* * *
44729835 TGTGGCGAATTATCT-AACAAGCCTA
1 TGTGGCGAGTTATCTGTA-AAGCCTT
44729860 TGTGGCG
1 TGTGGCG
44729867 TATTATTTGG
Statistics
Matches: 67, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
24 1 0.01
25 66 0.99
ACGTcount: A:0.20, C:0.17, G:0.30, T:0.34
Consensus pattern (25 bp):
TGTGGCGAGTTATCTGTAAAGCCTT
Found at i:44729799 original size:130 final size:130
Alignment explanation
Indices: 44729566--44729815 Score: 376
Period size: 130 Copynumber: 1.9 Consensus size: 130
44729556 TGACTCTAGG
* * * *
44729566 TAAATCCATATCATCAAACACGATAGTTGGTGTGGTGCATTGGTGGCAAACTACATCGAGCTTCT
1 TAAATCCATATCACCAAACACAATAGTTGGTGTGGTGCATTGGTGGCAAACCACATCAAGCTTCT
* * *
44729631 GTGGTGAGTTATCGGTAAAGCCTTTGTGGTGAGTTATCTGTAAAGCCTCTGTGGCAAGCTATCTA
66 GTGGCGAGTTATCGGTAAAGCCTTTGTGGCGAGTTATCTATAAAGCCTCTGTGGCAAGCTATCTA
*
44729696 TAAATCCATAT-AGCCAAACACAATAGTTGGTGTGGTGCCTTGGTGGCAAACCACATCAAGCTTC
1 TAAATCCATATCA-CCAAACACAATAGTTGGTGTGGTGCATTGGTGGCAAACCACATCAAGCTTC
* * * *
44729760 TGTGGCGGGTTATCTGTAAAGCCTTTGTGGCGAGTTATCTATGAAGCCTTTGTGGC
65 TGTGGCGAGTTATCGGTAAAGCCTTTGTGGCGAGTTATCTATAAAGCCTCTGTGGC
44729816 GAGTTATTTG
Statistics
Matches: 107, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
129 1 0.01
130 106 0.99
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.31
Consensus pattern (130 bp):
TAAATCCATATCACCAAACACAATAGTTGGTGTGGTGCATTGGTGGCAAACCACATCAAGCTTCT
GTGGCGAGTTATCGGTAAAGCCTTTGTGGCGAGTTATCTATAAAGCCTCTGTGGCAAGCTATCTA
Found at i:44729822 original size:50 final size:50
Alignment explanation
Indices: 44729760--44729866 Score: 142
Period size: 50 Copynumber: 2.1 Consensus size: 50
44729750 ATCAAGCTTC
* * * ** *
44729760 TGTGGCGGGTTATCTGTAAAGCCTTTGTGGCGAGTTATCTATGAAGCCTT
1 TGTGGCGAGTTATCTGTAAAGCCCTTGTGGCGAATTATCTAACAAGCCTA
* *
44729810 TGTGGCGAGTTATTTGTAAGGCCCTTGTGGCGAATTATCTAACAAGCCTA
1 TGTGGCGAGTTATCTGTAAAGCCCTTGTGGCGAATTATCTAACAAGCCTA
44729860 TGTGGCG
1 TGTGGCG
44729867 TATTATTTGG
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.20, C:0.17, G:0.30, T:0.34
Consensus pattern (50 bp):
TGTGGCGAGTTATCTGTAAAGCCCTTGTGGCGAATTATCTAACAAGCCTA
Found at i:44732113 original size:19 final size:19
Alignment explanation
Indices: 44732089--44732127 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
44732079 ATGAAAAAAA
44732089 ATAGAAAAATTCATACTAC
1 ATAGAAAAATTCATACTAC
44732108 ATAGAAAAATTCATACTAC
1 ATAGAAAAATTCATACTAC
44732127 A
1 A
44732128 GGAGTCATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.54, C:0.15, G:0.05, T:0.26
Consensus pattern (19 bp):
ATAGAAAAATTCATACTAC
Found at i:44734351 original size:26 final size:26
Alignment explanation
Indices: 44734321--44734391 Score: 97
Period size: 26 Copynumber: 2.7 Consensus size: 26
44734311 CCTGTACATA
*
44734321 TATGCTCACACGATCTGTGAAATGAG
1 TATGCTCACACGAGCTGTGAAATGAG
* *
44734347 TATGCTCACATGAGATGTGAAATGAG
1 TATGCTCACACGAGCTGTGAAATGAG
**
44734373 CCTGCTCACACGAGCTGTG
1 TATGCTCACACGAGCTGTG
44734392 GGTCAGAATG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.25
Consensus pattern (26 bp):
TATGCTCACACGAGCTGTGAAATGAG
Found at i:44737827 original size:50 final size:50
Alignment explanation
Indices: 44737716--44737962 Score: 228
Period size: 50 Copynumber: 4.8 Consensus size: 50
44737706 ATTTGGGTAA
* * *
44737716 AGAGATCCCATATAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGGTTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGA-G--ATG
* *
44737772 AGAGGTTCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
44737822 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * * * *
44737872 AGAGCTCCCATGTAAGACCATATATGGGATATGACATTGGCA--GTACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* ** * * *
44737921 AAACATCCCATGTAAGACCATGTTTGGGATATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
44737963 TGTTATTTTC
Statistics
Matches: 163, Mismatches: 27, Indels: 9
0.82 0.14 0.05
Matches are distributed among these distances:
48 1 0.01
49 39 0.24
50 81 0.50
52 1 0.01
53 2 0.01
55 1 0.01
56 38 0.23
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:44745527 original size:16 final size:16
Alignment explanation
Indices: 44745506--44745573 Score: 109
Period size: 16 Copynumber: 4.2 Consensus size: 16
44745496 TTTGGTTCGC
*
44745506 TGTATTAGATTAGAGG
1 TGTATTGGATTAGAGG
44745522 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
44745538 TGTAATGGATTAGAGG
1 TGTATTGGATTAGAGG
*
44745554 TGTATTGGAATAGAGG
1 TGTATTGGATTAGAGG
44745570 TGTA
1 TGTA
44745574 ATAGCAAATC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.29, C:0.00, G:0.35, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:44745620 original size:45 final size:44
Alignment explanation
Indices: 44745554--44745644 Score: 110
Period size: 45 Copynumber: 2.0 Consensus size: 44
44745544 GGATTAGAGG
* *
44745554 TGTATTGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAG-AAATCAACTGTTTGGTTGAA
* * ***
44745599 TGTAATGGATTAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
44745643 TG
1 TG
44745645 GAATAGAGGT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 18 0.46
45 21 0.54
ACGTcount: A:0.30, C:0.05, G:0.29, T:0.36
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
Found at i:44745826 original size:16 final size:16
Alignment explanation
Indices: 44745789--44745830 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
44745779 TTAATCATAT
*
44745789 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
44745805 TT-AAATATATTATAA
1 TTAAAATATATTATAA
44745820 TTAAAATATAT
1 TTAAAATATAT
44745831 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:44745837 original size:14 final size:15
Alignment explanation
Indices: 44745798--44745839 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
44745788 TTTAAACATA
*
44745798 ATTATTATTAAATAT
1 ATTATAATTAAATAT
44745813 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
44745827 A-TATAATTTAATA
1 ATTATAATTAAATA
44745840 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:44745931 original size:120 final size:121
Alignment explanation
Indices: 44745787--44746055 Score: 456
Period size: 120 Copynumber: 2.2 Consensus size: 121
44745777 ATTTAATCAT
44745787 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
*
44745852 ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAA-GATA
66 ATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATG-TA
44745908 ATTT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
* *
44745972 ATTAATATTCTTATATGAATTTATTAAAATCATAATATATGATACTATAAAATGTA
66 ATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATGTA
* *
44746028 ATTTGAA-ATAATTAATATTAAATA-ATTA
1 ATTTAAACATAATTATTATTAAATATATTA
44746056 ATGTTGACAA
Statistics
Matches: 142, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
119 4 0.03
120 131 0.92
121 7 0.05
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.43
Consensus pattern (121 bp):
ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
ATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATGTA
Found at i:44745948 original size:16 final size:16
Alignment explanation
Indices: 44745905--44745950 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
44745895 ACTATAAAAG
*
44745905 ATAATTTAACATA-ATT
1 ATAA-TTAAAATATATT
*
44745921 ATTATT-AAATATATT
1 ATAATTAAAATATATT
44745936 ATAATTAAAATATAT
1 ATAATTAAAATATAT
44745951 AATTTAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 4 0.16
15 10 0.40
16 11 0.44
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
ATAATTAAAATATATT
Found at i:44745957 original size:14 final size:15
Alignment explanation
Indices: 44745905--44745959 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
44745895 ACTATAAAAG
44745905 ATAATTTAACATA-ATT
1 ATAA-TTAA-ATATATT
*
44745921 ATTATTAAATATATT
1 ATAATTAAATATATT
44745936 ATAATTAAA-ATA-T
1 ATAATTAAATATATT
*
44745949 ATAATTTAATA
1 ATAATTAAATA
44745960 AAATTCTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 9 0.26
14 7 0.21
15 15 0.44
16 3 0.09
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAATTAAATATATT
Found at i:44746022 original size:61 final size:61
Alignment explanation
Indices: 44745837--44746024 Score: 181
Period size: 61 Copynumber: 3.1 Consensus size: 61
44745827 ATATAATTTA
* * *
44745837 ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
1 ATAAAATTCTTAATAATTAATATTCTTATATGAATTTATTAAAATCATAATATATGATACT
** * * * * * * * *
44745898 ATAAAA--GATAAT--TTAACATAATTATTAT-TAAATATATTATAATTAAAATATATAAT-TT
1 ATAAAATTCTTAATAATT-A-AT-ATTCTTATATGAATTTATTAAAATCATAATATATGATACT
44745956 AATAAAATTCTTAATAATTAATATTCTTATATGAATTTATTAAAATCATAATATATGATACT
1 -ATAAAATTCTTAATAATTAATATTCTTATATGAATTTATTAAAATCATAATATATGATACT
44746018 ATAAAAT
1 ATAAAAT
44746025 GTAATTTGAA
Statistics
Matches: 94, Mismatches: 23, Indels: 20
0.69 0.17 0.15
Matches are distributed among these distances:
57 1 0.01
58 2 0.02
59 32 0.34
60 14 0.15
61 41 0.44
62 2 0.02
63 2 0.02
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (61 bp):
ATAAAATTCTTAATAATTAATATTCTTATATGAATTTATTAAAATCATAATATATGATACT
Found at i:44754589 original size:599 final size:600
Alignment explanation
Indices: 44753446--44754630 Score: 2077
Period size: 599 Copynumber: 2.0 Consensus size: 600
44753436 TTATTTTATT
*
44753446 ATTATTTTAATGTTTATGGAATTTTAGTAAGTTCATATAAAAATTTTGTTAAGAAATTTTGACGT
1 ATTATTTTAATGTTTATGGAATTTTAGTAAGTTCATATAAAAATTTTGTTAAGAAATTTTGACAT
** * *
44753511 TTGCATGTTTAATTATGTAAAAATGACTAAATCGTACAAGGTACAGAGTTCTATTAGTTAAAAGG
66 TTGCATGTTTAATTACATAAAAATGACTAAATCGTAAAAGGTACAGAGTTCTATTAGTTAAAAAG
44753576 GTTAAATGACTATGAAACTTTAAAGTGAAAGGACTTAGATTGTAATTAGACCATTTGAGTGGTTA
131 GTTAAATGACTATGAAACTTTAAAGTGAAAGGACTTAGATTGTAATTAGACCATTTGAGTGGTTA
*
44753641 GTGGATATTCATGGCAAGGTTTATTTGAAATTTTGAATGTTTTTAAAGGTTAAAAAGGTAAATGA
196 GTGGATATTCATGGCAAGGTTTATTTGAAAATTTGAATGTTTTTAAAGGTTAAAAAGGTAAATGA
*
44753706 GTAAATCAGGGTAAATTAAATAAAACAAAATATTTTCCCATTTTCATTCATCTTCTTCCACCGAA
261 GTAAATAAGGGTAAATTAAATAAAACAAAATATTTTCCCATTTTCATTCATCTTCTTCCACCGAA
* *
44753771 ATTGAAGGTAGAAGAAACCATTTTTAGGGTTCTTGATTTCGACAAGCTTGGGTGGTGCATGTAAG
326 ATTGAAGGGAGAAGAAACCATTTTTAGGGTTCCTGATTTCGACAAGCTTGGGTGGTGCATGTAAG
** *
44753836 TGATTTTTGAGCTTGTTTTTAATGATTTTCATGTTTTTGGGATCGTTGTAGCTTAATCTAGCTAA
391 TGATTTTTGAGCTCATTTTTAATGATTTTCATGTTTTTGGGACCGTTGTAGCTTAATCTAGCTAA
* *
44753901 CCAGGGGATCAATTTGCAAAAAGTTTAAAGATTTAGGGTTTTCCTATGAATGTTCTTGCATGATT
456 CCAGGGGATCAATTTGCAAAAAGTTTAAAAATTTAGGGTTTTCCCATGAATGTTCTTGCATGATT
44753966 CTTGATGTTTTATGAAAGATTATGAGTCCTTACTGATAAATAAACAAGTTTTGAAAAGTAATTTT
521 CTTGATGTTTTATGAAAGATTATGAGTCCTTACTGATAAATAAACAAGTTTTGAAAAGTAATTTT
44754031 TATGAAATTGTAAAG
586 TATGAAATTGTAAAG
*
44754046 ATTATTTTAATGTTTATGGAATTTTAGTAAGTTCGTATAAAAATTTTGTTAAGAAATTTTGACAT
1 ATTATTTTAATGTTTATGGAATTTTAGTAAGTTCATATAAAAATTTTGTTAAGAAATTTTGACAT
* *
44754111 TTGTATGTTTAATTACATAAAAATGACTAAATCGTAAAAGGTGCAGAGTTCTATTAGTTAAAAAG
66 TTGCATGTTTAATTACATAAAAATGACTAAATCGTAAAAGGTACAGAGTTCTATTAGTTAAAAAG
* * *
44754176 GTTAAATGACTATGAAACTTTAAAGTGGAATGACTTAGATTGTAATTAGACCGTTTGAGTGGTTA
131 GTTAAATGACTATGAAACTTTAAAGTGAAAGGACTTAGATTGTAATTAGACCATTTGAGTGGTTA
44754241 GTGGATATTCATGGCAAGGTTTATTTGAAAATTTGAATGTTTTTAAAGGTTAAAAAGGTAAATG-
196 GTGGATATTCATGGCAAGGTTTATTTGAAAATTTGAATGTTTTTAAAGGTTAAAAAGGTAAATGA
44754305 GTAAATAAGGGTAAATTAAATAAAACAAAATATTTTCCCATTTTCATTCATCTTCTTCCACCGAA
261 GTAAATAAGGGTAAATTAAATAAAACAAAATATTTTCCCATTTTCATTCATCTTCTTCCACCGAA
44754370 ATTGAAGGGAGAAGAAACCATTTTTAGGGTTCCTGATTTCGACAAGCTTGGGTGGTGCATGTAAG
326 ATTGAAGGGAGAAGAAACCATTTTTAGGGTTCCTGATTTCGACAAGCTTGGGTGGTGCATGTAAG
*
44754435 TGATTTTTGAGCTCATTTTTAATGATTTTTAT-TTTTCTGGGACCGTTGTAGCTTAATCTAGCTA
391 TGATTTTTGAGCTCATTTTTAATGATTTTCATGTTTT-TGGGACCGTTGTAGCTTAATCTAGCTA
* * * ** *
44754499 GCCTGGTGATCAATTTGCAAAACTTTTAAAAATTTAGGGTTTTCCCATGAATTTTCTTGCATGAT
455 ACCAGGGGATCAATTTGCAAAAAGTTTAAAAATTTAGGGTTTTCCCATGAATGTTCTTGCATGAT
* * *
44754564 TCTTGATGTTTTATGAAAGATTATGAGTCCTTGCTTATAAATAAACAAGTTTTGTAAAGTAATTT
520 TCTTGATGTTTTATGAAAGATTATGAGTCCTTACTGATAAATAAACAAGTTTTGAAAAGTAATTT
44754629 TT
585 TT
44754631 TTTATGAAAT
Statistics
Matches: 554, Mismatches: 30, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
598 4 0.01
599 303 0.55
600 247 0.45
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.39
Consensus pattern (600 bp):
ATTATTTTAATGTTTATGGAATTTTAGTAAGTTCATATAAAAATTTTGTTAAGAAATTTTGACAT
TTGCATGTTTAATTACATAAAAATGACTAAATCGTAAAAGGTACAGAGTTCTATTAGTTAAAAAG
GTTAAATGACTATGAAACTTTAAAGTGAAAGGACTTAGATTGTAATTAGACCATTTGAGTGGTTA
GTGGATATTCATGGCAAGGTTTATTTGAAAATTTGAATGTTTTTAAAGGTTAAAAAGGTAAATGA
GTAAATAAGGGTAAATTAAATAAAACAAAATATTTTCCCATTTTCATTCATCTTCTTCCACCGAA
ATTGAAGGGAGAAGAAACCATTTTTAGGGTTCCTGATTTCGACAAGCTTGGGTGGTGCATGTAAG
TGATTTTTGAGCTCATTTTTAATGATTTTCATGTTTTTGGGACCGTTGTAGCTTAATCTAGCTAA
CCAGGGGATCAATTTGCAAAAAGTTTAAAAATTTAGGGTTTTCCCATGAATGTTCTTGCATGATT
CTTGATGTTTTATGAAAGATTATGAGTCCTTACTGATAAATAAACAAGTTTTGAAAAGTAATTTT
TATGAAATTGTAAAG
Found at i:44758068 original size:22 final size:21
Alignment explanation
Indices: 44758042--44758087 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
44758032 AAATATTATA
44758042 AAAAAGATAAATTTAATATTTTT
1 AAAAA-ATAAATTTAA-ATTTTT
*
44758065 AAAAAATAATTTTAAATTTTT
1 AAAAAATAAATTTAAATTTTT
44758086 AA
1 AA
44758088 TCCAGTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.36
22 9 0.41
23 5 0.23
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
AAAAAATAAATTTAAATTTTT
Found at i:44758083 original size:21 final size:23
Alignment explanation
Indices: 44758028--44758087 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
44758018 AAGTGATAAT
* * *
44758028 AATTAAATATTATAAAAAAGATA
1 AATTTAATATTTTTAAAAAGATA
44758051 AATTTAATATTTTTAAAAA-ATA
1 AATTTAATATTTTTAAAAAGATA
*
44758073 ATTTTAA-ATTTTTAA
1 AATTTAATATTTTTAA
44758088 TCCAGTTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.24
22 9 0.27
23 16 0.48
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
AATTTAATATTTTTAAAAAGATA
Found at i:44760245 original size:12 final size:12
Alignment explanation
Indices: 44760230--44760272 Score: 70
Period size: 12 Copynumber: 3.6 Consensus size: 12
44760220 TAAATATTAG
44760230 ATTAAATTTAAT
1 ATTAAATTTAAT
44760242 ATTAAATATTAA-
1 ATTAAAT-TTAAT
44760254 ATTAAATTTAAT
1 ATTAAATTTAAT
44760266 ATTAAAT
1 ATTAAAT
44760273 CTATTAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.14
12 21 0.72
13 4 0.14
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
ATTAAATTTAAT
Found at i:44760248 original size:24 final size:24
Alignment explanation
Indices: 44760220--44760272 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
44760210 TTTATCAAGA
*
44760220 TAAATATTAGATTAAATTTAATAT
1 TAAATATTAAATTAAATTTAATAT
44760244 TAAATATTAAATTAAATTTAATAT
1 TAAATATTAAATTAAATTTAATAT
44760268 TAAAT
1 TAAAT
44760273 CTATTAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (24 bp):
TAAATATTAAATTAAATTTAATAT
Found at i:44762241 original size:144 final size:144
Alignment explanation
Indices: 44761981--44762265 Score: 525
Period size: 144 Copynumber: 2.0 Consensus size: 144
44761971 AATCCTCTCA
*
44761981 TTGGTATTACATTGTTGATGAAAAGTAAACGTGGCCACGAGTCATTCGTCTTTGAGATGAATGAC
1 TTGGTATTACATTGTTGATGAAAAGTAAACGTGGCCACGAGTCATTCGTCTTTAAGATGAATGAC
* * *
44762046 TTGAATTATTTTTTGATAGAAATTGACTTTTGAAGAATGAAGATGCAATGGTTGTCATGAGATAA
66 TTGAATTATTATTTGATAGAAATTGACTTTTCAAGAATGAAGATGCAATGGTTGTCATGAAATAA
*
44762111 AATATGATTATTAT
131 AATACGATTATTAT
44762125 TTGGTATTACATTGTTGATGAAAAGTAAACGTGGCCACGAGTCATTCGTCTTTAAGATGAATGAC
1 TTGGTATTACATTGTTGATGAAAAGTAAACGTGGCCACGAGTCATTCGTCTTTAAGATGAATGAC
44762190 TTGAATTATTATTTGATAGAAATTGACTTTTCAAGAATGAAGATGCAATGGTTGTCATGAAATAA
66 TTGAATTATTATTTGATAGAAATTGACTTTTCAAGAATGAAGATGCAATGGTTGTCATGAAATAA
44762255 AATACGATTAT
131 AATACGATTAT
44762266 ACTAGGAGAA
Statistics
Matches: 136, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
144 136 1.00
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.36
Consensus pattern (144 bp):
TTGGTATTACATTGTTGATGAAAAGTAAACGTGGCCACGAGTCATTCGTCTTTAAGATGAATGAC
TTGAATTATTATTTGATAGAAATTGACTTTTCAAGAATGAAGATGCAATGGTTGTCATGAAATAA
AATACGATTATTAT
Found at i:44767897 original size:50 final size:50
Alignment explanation
Indices: 44767656--44767897 Score: 251
Period size: 50 Copynumber: 4.9 Consensus size: 50
44767646 GATAATAACA
* * * * * *
44767656 TGCCAAAGCTATGTCGCAGACATAGTCTTACATGGGA--TGTT-TCTTGTAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCG--G
* * * ** * *
44767705 TGGCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
* *
44767755 TGCCCATGCCATGTCCCAGACATGGTCTT--ATGGAGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAT-G-GGACCTCTTATCTCGG
* *
44767805 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGAACTCTTATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
*
44767855 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTT
44767898 TACCCAAATG
Statistics
Matches: 161, Mismatches: 25, Indels: 13
0.81 0.13 0.07
Matches are distributed among these distances:
48 2 0.01
49 31 0.19
50 120 0.75
51 3 0.02
52 5 0.03
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.29
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
Found at i:44775781 original size:23 final size:23
Alignment explanation
Indices: 44775744--44775787 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
44775734 AGAATCCTAC
44775744 CCATCAACCTCTACACACCATCT
1 CCATCAACCTCTACACACCATCT
44775767 CCATCCAACCT-TACACACCAT
1 CCAT-CAACCTCTACACACCAT
44775788 GTGGGGATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.32, C:0.48, G:0.00, T:0.20
Consensus pattern (23 bp):
CCATCAACCTCTACACACCATCT
Found at i:44777764 original size:39 final size:39
Alignment explanation
Indices: 44777710--44777886 Score: 212
Period size: 39 Copynumber: 4.5 Consensus size: 39
44777700 AACATGTTGT
44777710 TGAGTATTGTGATATATGCTTGAATGTTAAGTGATTATA
1 TGAGTATTGTGATATATGCTTGAATGTTAAGTGATTATA
* * * *
44777749 TGAGTATTGTGATATATGCTTGAAAGTTATGTAATTATT
1 TGAGTATTGTGATATATGCTTGAATGTTAAGTGATTATA
** *
44777788 TGAGTATTAAGATATATGCTTGAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTGAATGTTAAGTGATTATA
* * * *
44777827 TGAGTATTGTGCTATATGTTTGATTGTTATA-TGATTACA
1 TGAGTATTGTGATATATGCTTGAATGTTA-AGTGATTATA
* * *
44777866 TGTGTAATGTGCTATATGCTT
1 TGAGTATTGTGATATATGCTT
44777887 AAAAGTGAAT
Statistics
Matches: 118, Mismatches: 19, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
39 118 1.00
ACGTcount: A:0.29, C:0.04, G:0.21, T:0.46
Consensus pattern (39 bp):
TGAGTATTGTGATATATGCTTGAATGTTAAGTGATTATA
Found at i:44778693 original size:20 final size:20
Alignment explanation
Indices: 44778653--44778693 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
44778643 TTAAAGAAAA
*
44778653 TATCGATACACTAGTGTTAG
1 TATCGATACACTAGTGATAG
44778673 TATCGATAC-CTACGTGATAG
1 TATCGATACACTA-GTGATAG
44778693 T
1 T
44778694 TTTGAGATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (20 bp):
TATCGATACACTAGTGATAG
Found at i:44781467 original size:55 final size:55
Alignment explanation
Indices: 44781385--44781496 Score: 145
Period size: 54 Copynumber: 2.0 Consensus size: 55
44781375 AAGAAATGAA
* *
44781385 AATCATTTAGGAAATGATTATGGTTTTCCCCAAAATGAAAATGAAAATGAAAATGG
1 AATCATTTAGGAAATAAATATGGTTTT-CCCAAAATGAAAATGAAAATGAAAATGG
* * * * *
44781441 AATCATTT-GGAAATAAATGTGGTTTTCTCAAAATGGAAATGGAAATGGAAATGG
1 AATCATTTAGGAAATAAATATGGTTTTCCCAAAATGAAAATGAAAATGAAAATGG
44781495 AA
1 AA
44781497 ATAAAAATGA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
54 26 0.53
55 15 0.31
56 8 0.16
ACGTcount: A:0.44, C:0.07, G:0.21, T:0.29
Consensus pattern (55 bp):
AATCATTTAGGAAATAAATATGGTTTTCCCAAAATGAAAATGAAAATGAAAATGG
Found at i:44781482 original size:6 final size:6
Alignment explanation
Indices: 44781471--44781512 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
44781461 GGTTTTCTCA
**
44781471 AAATGG AAATGG AAATGG AAATGG AAATAA AAATGAG AAATG
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAATG-G AAATG
44781513 AATTCATTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
6 26 0.84
7 5 0.16
ACGTcount: A:0.57, C:0.00, G:0.26, T:0.17
Consensus pattern (6 bp):
AAATGG
Found at i:44782687 original size:57 final size:57
Alignment explanation
Indices: 44782626--44782746 Score: 165
Period size: 57 Copynumber: 2.1 Consensus size: 57
44782616 AGAAATGGTA
44782626 AAAATGGAGAAATGAGAAACATTT-AAAATGAATGAGGTTTTCTGC-AAAATGAAAAAG
1 AAAATGGAGAAATGA-AAACATTTGAAAATGAATGAGGTTTTCT-CAAAAATGAAAAAG
* * * *
44782683 AAAATAGAGAAATGAAAACATTTGGAAATGAATGTGGTTTTCTCAAAAAATGAAAATG
1 AAAATGGAGAAATGAAAACATTTGAAAATGAATGAGGTTTTCTC-AAAAATGAAAAAG
44782741 AAAATG
1 AAAATG
44782747 AACTAGAAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
56 9 0.16
57 31 0.55
58 16 0.29
ACGTcount: A:0.51, C:0.05, G:0.20, T:0.24
Consensus pattern (57 bp):
AAAATGGAGAAATGAAAACATTTGAAAATGAATGAGGTTTTCTCAAAAATGAAAAAG
Found at i:44785096 original size:25 final size:24
Alignment explanation
Indices: 44785050--44785102 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 24
44785040 TTATTTAATC
* * *
44785050 TTAATTAATTAACTTAATTATTAT
1 TTAATTAAATAACTTAACTATTAA
*
44785074 TTAATTATAATAATTTAACTATTAA
1 TTAATTA-AATAACTTAACTATTAA
44785099 TTAA
1 TTAA
44785103 ACTAAATGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (24 bp):
TTAATTAAATAACTTAACTATTAA
Found at i:44788158 original size:30 final size:30
Alignment explanation
Indices: 44788108--44788172 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
44788098 TAAAAGAGTG
44788108 TGTGATATAATTGATATATGATA-TATGATA
1 TGTGATATAATTGATATATGA-AGTATGATA
*
44788138 TGTGATATGAA-T-ATAGTATGAAGTATGTTA
1 TGTGATAT-AATTGATA-TATGAAGTATGATA
44788168 TGTGA
1 TGTGA
44788173 AATTGTACAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
29 4 0.13
30 25 0.81
31 2 0.06
ACGTcount: A:0.37, C:0.00, G:0.22, T:0.42
Consensus pattern (30 bp):
TGTGATATAATTGATATATGAAGTATGATA
Found at i:44792988 original size:19 final size:20
Alignment explanation
Indices: 44792955--44792999 Score: 74
Period size: 19 Copynumber: 2.3 Consensus size: 20
44792945 CAGTAAAATG
44792955 TTTTCTGGAAAATGATTTCC
1 TTTTCTGGAAAATGATTTCC
*
44792975 TTTTCTGG-AAATGATTTGC
1 TTTTCTGGAAAATGATTTCC
44792994 TTTTCT
1 TTTTCT
44793000 TGTGTTTGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.20, C:0.13, G:0.16, T:0.51
Consensus pattern (20 bp):
TTTTCTGGAAAATGATTTCC
Found at i:44793115 original size:16 final size:17
Alignment explanation
Indices: 44793083--44793123 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
44793073 GTTTTTACAC
44793083 ATATTAATAAATTTTTAT
1 ATATTAATAAA-TTTTAT
44793101 ATATTAATAAA-TTTAT
1 ATATTAATAAATTTTAT
*
44793117 ATTTTAA
1 ATATTAA
44793124 ATTGTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 11 0.50
18 11 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATATTAATAAATTTTAT
Done.