Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167960.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_22, 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: 19587844
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 68000 characters in sequence are not A, C, G, or T
File 26 of 105
Found at i:5238227 original size:19 final size:20
Alignment explanation
Indices: 5238193--5238230 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
5238183 CATCCTTTGC
*
5238193 TATTATTTTAATTTTGGATT
1 TATTATTTTAAATTTGGATT
5238213 TATTA-TTTAAATTTGGAT
1 TATTATTTTAAATTTGGAT
5238231 AATAATTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.29, C:0.00, G:0.11, T:0.61
Consensus pattern (20 bp):
TATTATTTTAAATTTGGATT
Found at i:5238957 original size:32 final size:33
Alignment explanation
Indices: 5238913--5238985 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
5238903 TTAACAGTAT
* *
5238913 TTATATTAGAAAAACGTTGCTAAA-TTAGTGACA
1 TTATA-TAGAAAAACATTACTAAATTTAGTGACA
* *
5238946 TTATATAGAAAAATATTACTAAATTTAGTGATA
1 TTATATAGAAAAACATTACTAAATTTAGTGACA
*
5238979 TTTTATA
1 TTATATA
5238986 ATACAAACGT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
32 15 0.44
33 19 0.56
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.40
Consensus pattern (33 bp):
TTATATAGAAAAACATTACTAAATTTAGTGACA
Found at i:5240555 original size:161 final size:161
Alignment explanation
Indices: 5240232--5240912 Score: 703
Period size: 161 Copynumber: 4.2 Consensus size: 161
5240222 TATTTTGACC
* * * * * * * *
5240232 TTTCACACATATCAATCATGAAAATCAAATTCATTCATTTGGACAAGTTTAATTTTATGTATTGA
1 TTTCACACATATCAATTATGAAAACCAAGTTCAATCATTTGAAAAAGTTTAATATCATGTATTGA
* * * * * * *
5240297 AGCTATCCAACCTATT-AAACAGAACAATAATAGTAACTTTGTATTTTTGCCTTTTAATGATAAA
66 AGCTATCCAAACTGTTAAAATAGAACAATAATAGCAAATTTGTATTTTTGCCTTTTAACGACAAA
* * * * *
5240361 AAAAGTCTTAAACAAAGGTAATCAACAACTT
131 AAAAGTCCTAAACAAACGTAAACGATAACTT
* * * * *
5240392 TTTCACATATATCAATTGTGAAAACCAAGTTTAATCATTTGAAAAAATTTAATATTATGTATTGA
1 TTTCACACATATCAATTATGAAAACCAAGTTCAATCATTTGAAAAAGTTTAATATCATGTATTGA
* * * *
5240457 AGCTATCCAAATTGTTAAAATAAAACAATAACAGCAAATTTGTATTTTTGCCTTTTAACGACATG
66 AGCTATCCAAACTGTTAAAATAGAACAATAATAGCAAATTTGTATTTTTGCCTTTTAACGACA-A
* * * *
5240522 AAAAA-TCTTAAATAGAGGTAAAC-AGTAACTT
130 AAAAAGTCCTAAACAAACGTAAACGA-TAACTT
* * * *
5240553 TTTCACATATATTAATTACGGAAACCAAGTTCAATCATTTGAAAAAGTTTAATATCATGTATTGA
1 TTTCACACATATCAATTATGAAAACCAAGTTCAATCATTTGAAAAAGTTTAATATCATGTATTGA
* * *
5240618 AGCCATCCAAATTGTTAAAATAGAATAATAATAGCAAATTTGTATTTTTGCCTTTTAACGACAAA
66 AGCTATCCAAACTGTTAAAATAGAACAATAATAGCAAATTTGTATTTTTGCCTTTTAACGACAAA
* *
5240683 AATAA-TCCTAAATAAACATAAACGATAACTT
131 AA-AAGTCCTAAACAAACGTAAACGATAACTT
** * * * *
5240714 TTTCACACATATCAACCAT-AGAAACTAAGTTCAATCA-TTCAGATAAGCTTAATATCATGTATT
1 TTTCACACATATCAATTATGA-AAACCAAGTTCAATCATTTGA-AAAAGTTTAATATCATGTATT
* * ** * *
5240777 AAAGCTAT-CAAACTGTTAAAATAGAACAATAATATCAAATTTACA-TTTTACCTTTTAACGGCA
64 GAAGCTATCCAAACTGTTAAAATAGAACAATAATAGCAAATTTGTATTTTTGCCTTTTAACGACA
* * *
5240840 TAAAAAGTCCTAAACAGACGTAAACGTTAACTT
129 AAAAAAGTCCTAAACAAACGTAAACGATAACTT
* * * * *
5240873 TTTCACACATATCAACTGTGGAAATCAAGTTCAATTATTT
1 TTTCACACATATCAATTATGAAAACCAAGTTCAATCATTT
5240913 TGACAAGTAT
Statistics
Matches: 439, Mismatches: 72, Indels: 20
0.83 0.14 0.04
Matches are distributed among these distances:
158 2 0.00
159 71 0.16
160 108 0.25
161 252 0.57
162 6 0.01
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.34
Consensus pattern (161 bp):
TTTCACACATATCAATTATGAAAACCAAGTTCAATCATTTGAAAAAGTTTAATATCATGTATTGA
AGCTATCCAAACTGTTAAAATAGAACAATAATAGCAAATTTGTATTTTTGCCTTTTAACGACAAA
AAAAGTCCTAAACAAACGTAAACGATAACTT
Found at i:5242731 original size:124 final size:125
Alignment explanation
Indices: 5242499--5242730 Score: 301
Period size: 124 Copynumber: 1.9 Consensus size: 125
5242489 GTGACTTCCT
* * * * *
5242499 CTCCCATTATTTTGGAAGAATTATTCAAGGCATTTTTGTCTAAAAAATGCTTTAAATAATCTCTT
1 CTCCCATTATTTTGAAAGAATTATTCAAGGCATTTTTGGCCAAAAAATACCTTAAATAATCTCTT
* *
5242564 ACAAAAAATTGAATGGGGGTATTGAAGATGTTTCTGGCTAAAAATGACTTTAACAATTGC
66 ACAAAAAATTAAATGAGGGTATTGAAGATGTTTCTGGCTAAAAATGACTTTAACAATTGC
* * * * *
5242624 CTCCCATTATTTT-AAAGGATTATTGAAGGTATTTTTGGCCAAAAAATACCTTGAATAATTTCTT
1 CTCCCATTATTTTGAAAGAATTATTCAAGGCATTTTTGGCCAAAAAATACCTTAAATAATCTCTT
*
5242688 ACAAAAAATTAAAT-AGGGTATTTAAGGCAT-TTTCTGG-TAAAAA
66 ACAAAAAATTAAATGAGGGTATTGAA-G-ATGTTTCTGGCTAAAAA
5242731 AACACCTTCA
Statistics
Matches: 92, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
123 15 0.16
124 62 0.67
125 15 0.16
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (125 bp):
CTCCCATTATTTTGAAAGAATTATTCAAGGCATTTTTGGCCAAAAAATACCTTAAATAATCTCTT
ACAAAAAATTAAATGAGGGTATTGAAGATGTTTCTGGCTAAAAATGACTTTAACAATTGC
Found at i:5243768 original size:19 final size:19
Alignment explanation
Indices: 5243730--5243768 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
5243720 TATCATGTCA
*
5243730 TTTATATTATTTTTTAATT
1 TTTATATTATTTTTCAATT
5243749 TTTAT-TTATTTTTCATATT
1 TTTATATTATTTTTCA-ATT
5243768 T
1 T
5243769 CACTCTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTATATTATTTTTCAATT
Found at i:5246962 original size:13 final size:14
Alignment explanation
Indices: 5246944--5246988 Score: 58
Period size: 13 Copynumber: 3.4 Consensus size: 14
5246934 TAACCCTTTT
5246944 TATATTAATA-TAA
1 TATATTAATATTAA
5246957 TATATTAATATTAA
1 TATATTAATATTAA
*
5246971 -ATATTATTATTAA
1 TATATTAATATTAA
*
5246984 AATAT
1 TATAT
5246989 AATTTTTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 22 0.76
14 7 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TATATTAATATTAA
Found at i:5246969 original size:19 final size:19
Alignment explanation
Indices: 5246945--5246983 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5246935 AACCCTTTTT
5246945 ATATTAATATAATA-TATTA
1 ATATTAA-ATAATATTATTA
*
5246964 ATATTAAATATTATTATTA
1 ATATTAAATAATATTATTA
5246983 A
1 A
5246984 AATATAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATTAAATAATATTATTA
Found at i:5247012 original size:15 final size:15
Alignment explanation
Indices: 5246994--5247042 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 15
5246984 AATATAATTT
5246994 TTTTAATATTAATAA
1 TTTTAATATTAATAA
*
5247009 TTTTAATAATAAATAA
1 TTTTAAT-ATTAATAA
5247025 TTTCTACATATTTAATAA
1 TTT-TA-ATA-TTAATAA
5247043 AAATAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
15 7 0.25
16 10 0.36
17 3 0.11
18 8 0.29
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (15 bp):
TTTTAATATTAATAA
Found at i:5247050 original size:24 final size:25
Alignment explanation
Indices: 5247008--5247067 Score: 88
Period size: 24 Copynumber: 2.4 Consensus size: 25
5246998 AATATTAATA
*
5247008 ATTTTAATAATAAATAATTTCTACAT
1 ATTTTAATAATAAATAATTT-TAAAT
5247034 A-TTTAATAA-AAATAATTTTAAAT
1 ATTTTAATAATAAATAATTTTAAAT
5247057 ATTTTAATAAT
1 ATTTTAATAAT
5247068 TATGTTAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
23 5 0.16
24 17 0.55
25 8 0.26
26 1 0.03
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (25 bp):
ATTTTAATAATAAATAATTTTAAAT
Found at i:5256118 original size:13 final size:13
Alignment explanation
Indices: 5256100--5256124 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5256090 CTAGGCAAAC
5256100 TTTTTTGCACATT
1 TTTTTTGCACATT
5256113 TTTTTTGCACAT
1 TTTTTTGCACAT
5256125 GAGACATCCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.16, G:0.08, T:0.60
Consensus pattern (13 bp):
TTTTTTGCACATT
Found at i:5263928 original size:24 final size:25
Alignment explanation
Indices: 5263900--5263947 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
5263890 GCATATTATA
*
5263900 ATAGTTATATAAA-TTAATAATTTT
1 ATAGTTATATAAAGATAATAATTTT
* *
5263924 ATAGTTGTTTAAAGATAATAATTT
1 ATAGTTATATAAAGATAATAATTT
5263948 GTAAAATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (25 bp):
ATAGTTATATAAAGATAATAATTTT
Found at i:5265131 original size:17 final size:17
Alignment explanation
Indices: 5265105--5265140 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5265095 AAATCATGAG
5265105 TAATAAGATCACATTGA
1 TAATAAGATCACATTGA
* *
5265122 TAATACGATCACTTTGA
1 TAATAAGATCACATTGA
5265139 TA
1 TA
5265141 GTTACATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.33
Consensus pattern (17 bp):
TAATAAGATCACATTGA
Found at i:5265233 original size:34 final size:35
Alignment explanation
Indices: 5265203--5265272 Score: 87
Period size: 33 Copynumber: 2.1 Consensus size: 35
5265193 TATTTATATA
5265203 ATTTT-TTTTGGTTT-TTT-TTTATTCTGTTTATT
1 ATTTTGTTTTGGTTTATTTATTTATTCTGTTTATT
*
5265235 ATTTTGTTTTGTTTTATTTATTTATT-TG-TTACTT
1 ATTTTGTTTTGGTTTATTTATTTATTCTGTTTA-TT
5265269 ATTT
1 ATTT
5265273 ACTTGATCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
32 5 0.15
33 11 0.33
34 11 0.33
35 6 0.18
ACGTcount: A:0.13, C:0.03, G:0.09, T:0.76
Consensus pattern (35 bp):
ATTTTGTTTTGGTTTATTTATTTATTCTGTTTATT
Found at i:5265243 original size:27 final size:27
Alignment explanation
Indices: 5265208--5265260 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
5265198 ATATAATTTT
* *
5265208 TTTTGGTTTTTTTTTATTCTGTTTATTA
1 TTTTGGTTTTGTTTTATT-TATTTATTA
5265236 TTTT-GTTTTGTTTTATTTATTTATT
1 TTTTGGTTTTGTTTTATTTATTTATT
5265261 TGTTACTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 7 0.30
27 12 0.52
28 4 0.17
ACGTcount: A:0.11, C:0.02, G:0.09, T:0.77
Consensus pattern (27 bp):
TTTTGGTTTTGTTTTATTTATTTATTA
Found at i:5268011 original size:22 final size:22
Alignment explanation
Indices: 5267983--5268031 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
5267973 AGACGGGTTT
*
5267983 GTGTTAGATTTGCGTCAGATAC
1 GTGTTAGATTCGCGTCAGATAC
5268005 GTGTTAGATTCGCGTCAGATAC
1 GTGTTAGATTCGCGTCAGATAC
*
5268027 ATGTT
1 GTGTT
5268032 TAATATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.22, C:0.14, G:0.27, T:0.37
Consensus pattern (22 bp):
GTGTTAGATTCGCGTCAGATAC
Found at i:5269165 original size:19 final size:17
Alignment explanation
Indices: 5269108--5269156 Score: 66
Period size: 15 Copynumber: 2.9 Consensus size: 17
5269098 GATGATATTC
5269108 ATTTTCTCTTTTTTTTTA
1 ATTTT-TCTTTTTTTTTA
*
5269126 ATTTTTCTTTTTCTTT-
1 ATTTTTCTTTTTTTTTA
5269142 -TTTTTCTTTTTTTTT
1 ATTTTTCTTTTTTTTT
5269157 CAAATTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 14 0.48
17 10 0.34
18 5 0.17
ACGTcount: A:0.06, C:0.10, G:0.00, T:0.84
Consensus pattern (17 bp):
ATTTTTCTTTTTTTTTA
Found at i:5269300 original size:25 final size:26
Alignment explanation
Indices: 5269261--5269318 Score: 75
Period size: 24 Copynumber: 2.3 Consensus size: 26
5269251 CTCAATTTTC
5269261 TTTTTTTCCTTTTTTAATTTTT-A-A
1 TTTTTTTCCTTTTTTAATTTTTAACA
* *
5269285 TTTTTTTCTTTCTTTTTATTTTTAACA
1 TTTTTTTCCTT-TTTTAATTTTTAACA
5269312 TTTTTTT
1 TTTTTTT
5269319 ACTAAATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 10 0.34
25 10 0.34
26 1 0.03
27 8 0.28
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.78
Consensus pattern (26 bp):
TTTTTTTCCTTTTTTAATTTTTAACA
Found at i:5270343 original size:2 final size:2
Alignment explanation
Indices: 5270336--5270373 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
5270326 CACATGCCCC
*
5270336 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5270374 TTTTTAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5270744 original size:24 final size:24
Alignment explanation
Indices: 5270717--5270773 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
5270707 TTACCACTCC
* *
5270717 CCTCCAACTTCTGGAGGTGGTAGT
1 CCTCCAACATATGGAGGTGGTAGT
*
5270741 CCTCCATCATATGGAGGTGGTAGT
1 CCTCCAACATATGGAGGTGGTAGT
5270765 CCTCCAACA
1 CCTCCAACA
5270774 CCAGTCACTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.21, C:0.28, G:0.25, T:0.26
Consensus pattern (24 bp):
CCTCCAACATATGGAGGTGGTAGT
Found at i:5272416 original size:12 final size:11
Alignment explanation
Indices: 5272400--5272438 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
5272390 CAAAATAATT
5272400 TTTTTATTAAA
1 TTTTTATTAAA
5272411 TTTTT-TTATAA
1 TTTTTATTA-AA
5272422 TTTTTATTAAA
1 TTTTTATTAAA
*
5272433 ATTTTA
1 TTTTTA
5272439 AATCATATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
10 3 0.12
11 19 0.76
12 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTTTATTAAA
Found at i:5272717 original size:10 final size:10
Alignment explanation
Indices: 5272704--5272747 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
5272694 CTAAACTGAA
5272704 TTATATATTT
1 TTATATATTT
5272714 TTAT-TAGTTT
1 TTATATA-TTT
5272724 TTATATATTT
1 TTATATATTT
*
5272734 TT-TAAATTT
1 TTATATATTT
5272743 TTATA
1 TTATA
5272748 AAATAAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
9 10 0.33
10 18 0.60
11 2 0.07
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (10 bp):
TTATATATTT
Found at i:5274560 original size:33 final size:34
Alignment explanation
Indices: 5274523--5274610 Score: 88
Period size: 34 Copynumber: 2.6 Consensus size: 34
5274513 TTCAAATATT
* * * *
5274523 CATTTTCGAGAA-TCTTTAGGATTCTTGGAAATC
1 CATTTTCGAGAAGTCTTAAAGATTATCGGAAATC
* * *
5274556 CATTTTCAAGAAGTCTTAAAGCTTATCGGATATC
1 CATTTTCGAGAAGTCTTAAAGATTATCGGAAATC
**
5274590 CATTTTCGAGAAACCTTAAAG
1 CATTTTCGAGAAGTCTTAAAG
5274611 CTTTTTGAAT
Statistics
Matches: 44, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
33 11 0.25
34 33 0.75
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (34 bp):
CATTTTCGAGAAGTCTTAAAGATTATCGGAAATC
Found at i:5274640 original size:33 final size:34
Alignment explanation
Indices: 5274553--5274641 Score: 92
Period size: 34 Copynumber: 2.6 Consensus size: 34
5274543 ATTCTTGGAA
* ** *
5274553 ATCCATTTTCAAGAAGTCTTAAAGCTTATCGGAT
1 ATCCATTTTCGAGAAACCTTAAAGCTTATCGAAT
* *
5274587 ATCCATTTTCGAGAAACCTTAAAGCTTTTTGAAT
1 ATCCATTTTCGAGAAACCTTAAAGCTTATCGAAT
*
5274621 A-CCATTTTTGA-AAAGCCTTAA
1 ATCCATTTTCGAGAAA-CCTTAA
5274642 GTCTTCTTGA
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
32 3 0.06
33 15 0.32
34 29 0.62
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (34 bp):
ATCCATTTTCGAGAAACCTTAAAGCTTATCGAAT
Found at i:5274652 original size:33 final size:33
Alignment explanation
Indices: 5274555--5274652 Score: 83
Period size: 34 Copynumber: 2.9 Consensus size: 33
5274545 TCTTGGAAAT
* ** * * *
5274555 CCATTTTCAAGAAGTCTTAAAGCTTATCGGATA
1 CCATTTTCGAGAAACCTTAAAGCTTCTTGAATA
*
5274588 TCCATTTTCGAGAAACCTTAAAGCTTTTTGAATA
1 -CCATTTTCGAGAAACCTTAAAGCTTCTTGAATA
*
5274622 CCATTTTTGA-AAAGCCTT-AAGTCTTCTTGAA
1 CCATTTTCGAGAAA-CCTTAAAG-CTTCTTGAA
5274653 AATTCATTTC
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
32 6 0.11
33 21 0.39
34 27 0.50
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (33 bp):
CCATTTTCGAGAAACCTTAAAGCTTCTTGAATA
Found at i:5275164 original size:10 final size:10
Alignment explanation
Indices: 5275149--5275182 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
5275139 TTAAGTAATT
5275149 AATTAAAATA
1 AATTAAAATA
5275159 AATTAAAATA
1 AATTAAAATA
* *
5275169 AATTTAAGTA
1 AATTAAAATA
5275179 AATT
1 AATT
5275183 TATTATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (10 bp):
AATTAAAATA
Found at i:5284211 original size:27 final size:27
Alignment explanation
Indices: 5284173--5284239 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
5284163 ATACTTCCCT
5284173 ATGGCAAATTAATACTAGTTATCCATA
1 ATGGCAAATTAATACTAGTTATCCATA
*
5284200 ATGGCAAATTAATACTATTTATCCATA
1 ATGGCAAATTAATACTAGTTATCCATA
*
5284227 ATGACAAATTAAT
1 ATGGCAAATTAAT
5284240 CGATAATACT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.34
Consensus pattern (27 bp):
ATGGCAAATTAATACTAGTTATCCATA
Found at i:5284277 original size:42 final size:42
Alignment explanation
Indices: 5284225--5284309 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
5284215 TATTTATCCA
*
5284225 TAATGACAAATTAATCGATAATACTAACATTATCATGGGAAG
1 TAATGACAAATTAATCCATAATACTAACATTATCATGGGAAG
* *
5284267 TAATGGCAAATTAATCCATAATACTAACATTATCATGTGAAG
1 TAATGACAAATTAATCCATAATACTAACATTATCATGGGAAG
5284309 T
1 T
5284310 CATAATACCA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.31
Consensus pattern (42 bp):
TAATGACAAATTAATCCATAATACTAACATTATCATGGGAAG
Found at i:5284331 original size:16 final size:17
Alignment explanation
Indices: 5284310--5284349 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
5284300 CATGTGAAGT
5284310 CATAATAC-CATTGATC
1 CATAATACACATTGATC
*
5284326 CATAATACTATATTGATC
1 CATAATAC-ACATTGATC
5284344 CATAAT
1 CATAAT
5284350 GGCAAATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.38
18 13 0.62
ACGTcount: A:0.40, C:0.20, G:0.05, T:0.35
Consensus pattern (17 bp):
CATAATACACATTGATC
Found at i:5285411 original size:24 final size:25
Alignment explanation
Indices: 5285384--5285436 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 25
5285374 TTATTATTAC
* *
5285384 AATAATAAATTATTT-TAATATTTT
1 AATAATAAATAATTTGAAATATTTT
5285408 AATAATAAATAATTTGAAATATTTT
1 AATAATAAATAATTTGAAATATTTT
5285433 AATA
1 AATA
5285437 GTTATTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 14 0.54
25 12 0.46
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (25 bp):
AATAATAAATAATTTGAAATATTTT
Found at i:5285747 original size:3 final size:3
Alignment explanation
Indices: 5285739--5285784 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
5285729 TTATGACATT
5285739 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5285785 AGGTTGTAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5295203 original size:247 final size:247
Alignment explanation
Indices: 5294748--5295249 Score: 734
Period size: 247 Copynumber: 2.0 Consensus size: 247
5294738 GATTAGTAAA
* **
5294748 ACTTTCAAGCATAGTCTTTAAATTTTTGGGTAAAATTCGTAAGTTTTTTTAACTGAATTTATTTT
1 ACTTTCGAGCATAGTCTTTAAATTTTTGGGTAAAATTCGTAAGTTTTTCGAACTGAATTTATTTT
* * *
5294813 AGTGTTGAGATTTATAAGATCTCTAAACGTAATCTTTAAGTCCTCCAAGCAGGATTTATTAGTCT
66 AGTGTTAAGATTTATAAGATCTCTAAACATAATCTTTAAGTCCTCCAAGCAGGATTCATTAGTCT
* * *
5294878 TTCGAGCTAAATCTATTTTAGTATCCAAATTTGTAGGACCTTTGGACATAATCTCCAAGTTATTG
131 TTCGAGCTAAATCTATTTTAGTATCCAAATTTGTAAGACCTTCGGACATAATCTCAAAGTTATTG
* * * * *
5294943 TGTTACGTTTTTAAAAGTTGTGGAACCTCTAATAAGAAGAGCTTTTAAATTT
196 TGTTACATTTTTAAAAGTTATGGAACCTATAATAAAAAAAGCTTTTAAATTT
* * * *
5294995 ACTTTCGAGCATTGTCTTTAAGTTTTTGGGTAAAATTTGTAAGTTTTTCGAGCTGAATTTATTTT
1 ACTTTCGAGCATAGTCTTTAAATTTTTGGGTAAAATTCGTAAGTTTTTCGAACTGAATTTATTTT
* * * * * *
5295060 AGTGTTAAGATTTATAAGTTCTCTGAGCATAATCTTTAAGTCTTCTAGGCAGGATTCATTAGTCT
66 AGTGTTAAGATTTATAAGATCTCTAAACATAATCTTTAAGTCCTCCAAGCAGGATTCATTAGTCT
* * *
5295125 TTCTAGCTAAATCTATTTTAGTATCTAGATTTGTAAGACCTTCGGACATAATCTCAAAGTTATTG
131 TTCGAGCTAAATCTATTTTAGTATCCAAATTTGTAAGACCTTCGGACATAATCTCAAAGTTATTG
* *
5295190 TGTTATATTTTTAAAAGTTATGGAGCCTATAATAAAAAAAGCTTTTAAATTT
196 TGTTACATTTTTAAAAGTTATGGAACCTATAATAAAAAAAGCTTTTAAATTT
*
5295242 ATTTTCGA
1 ACTTTCGA
5295250 AAGTTGTGAA
Statistics
Matches: 225, Mismatches: 30, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
247 225 1.00
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (247 bp):
ACTTTCGAGCATAGTCTTTAAATTTTTGGGTAAAATTCGTAAGTTTTTCGAACTGAATTTATTTT
AGTGTTAAGATTTATAAGATCTCTAAACATAATCTTTAAGTCCTCCAAGCAGGATTCATTAGTCT
TTCGAGCTAAATCTATTTTAGTATCCAAATTTGTAAGACCTTCGGACATAATCTCAAAGTTATTG
TGTTACATTTTTAAAAGTTATGGAACCTATAATAAAAAAAGCTTTTAAATTT
Found at i:5295325 original size:18 final size:18
Alignment explanation
Indices: 5295304--5295343 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
5295294 AAAATCAATC
5295304 CAAAAAA-TAAAAAATAAA
1 CAAAAAACT-AAAAATAAA
*
5295322 CAAAAAACTGAAAATAAA
1 CAAAAAACTAAAAATAAA
5295340 CAAA
1 CAAA
5295344 GTTTGAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 19 0.95
19 1 0.05
ACGTcount: A:0.78, C:0.10, G:0.03, T:0.10
Consensus pattern (18 bp):
CAAAAAACTAAAAATAAA
Found at i:5297476 original size:18 final size:16
Alignment explanation
Indices: 5297453--5297500 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
5297443 ACCATTTCTT
5297453 TAAAAATAAATAAATAAA
1 TAAAAAT-AATAAA-AAA
5297471 TAAAAATAATAAAAAA
1 TAAAAATAATAAAAAA
*
5297487 TGAGAAA-AATAAAA
1 T-AAAAATAATAAAA
5297501 TTTTTATCCG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 11 0.39
17 10 0.36
18 7 0.25
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (16 bp):
TAAAAATAATAAAAAA
Found at i:5298754 original size:33 final size:35
Alignment explanation
Indices: 5298689--5298754 Score: 82
Period size: 33 Copynumber: 1.9 Consensus size: 35
5298679 TATTTTGATG
*
5298689 AAAATATTGATTTTTCAAAAAAAAATCTAAACACT
1 AAAATATTGATTTTTCAAAAAAAAATCCAAACACT
* **
5298724 AAAATA-T-ATTTTTCACAAAATCATCCAAACA
1 AAAATATTGATTTTTCAAAAAAAAATCCAAACA
5298755 ACAAAAGTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 20 0.74
34 1 0.04
35 6 0.22
ACGTcount: A:0.53, C:0.15, G:0.02, T:0.30
Consensus pattern (35 bp):
AAAATATTGATTTTTCAAAAAAAAATCCAAACACT
Found at i:5300348 original size:1 final size:1
Alignment explanation
Indices: 5300312--5300341 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
5300302 TTTACTCACG
*
5300312 TTTTGTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5300342 CATTTTTATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.03, T:0.97
Consensus pattern (1 bp):
T
Found at i:5307288 original size:11 final size:11
Alignment explanation
Indices: 5307272--5307296 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5307262 AACTAAGTCT
5307272 ATTTTATTTTA
1 ATTTTATTTTA
5307283 ATTTTATTTTA
1 ATTTTATTTTA
5307294 ATT
1 ATT
5307297 AGTTTACAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
ATTTTATTTTA
Found at i:5312616 original size:30 final size:30
Alignment explanation
Indices: 5312582--5312676 Score: 102
Period size: 30 Copynumber: 3.2 Consensus size: 30
5312572 TATTACATTT
* *
5312582 AAATAAACCTTTGACATTTAATTTGCATCC
1 AAATAAACCTTTAACATTTAATTTACATCC
* * * *
5312612 AAATAAGCCTTTAACATTTAGTTTATATTC
1 AAATAAACCTTTAACATTTAATTTACATCC
* *
5312642 AAATAAACCTTTTACTTTTAATTTACA-CC
1 AAATAAACCTTTAACATTTAATTTACATCC
5312671 TAAATA
1 -AAATA
5312677 CGAGTTTAAC
Statistics
Matches: 52, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.39, C:0.17, G:0.04, T:0.40
Consensus pattern (30 bp):
AAATAAACCTTTAACATTTAATTTACATCC
Found at i:5318672 original size:30 final size:31
Alignment explanation
Indices: 5318638--5318721 Score: 100
Period size: 31 Copynumber: 2.8 Consensus size: 31
5318628 CTTTTGGCCT
* *
5318638 AACAAGTGGTATCAG-GCTGTGGTGATTCCC
1 AACAAGTGGTATCAGAGCTATAGTGATTCCC
* * *
5318668 AACAAGTGATGTCAGAGCTATAGTGATTCCT
1 AACAAGTGGTATCAGAGCTATAGTGATTCCC
*
5318699 AACAAGTGGTATCATAGC-ATAGT
1 AACAAGTGGTATCAGAGCTATAGT
5318722 TTGATACATG
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
30 18 0.40
31 27 0.60
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (31 bp):
AACAAGTGGTATCAGAGCTATAGTGATTCCC
Found at i:5319658 original size:31 final size:31
Alignment explanation
Indices: 5319623--5319688 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
5319613 ATTTTAGCCT
* *
5319623 AACAAGTGATATCAGAGCTGTGGTGATTCTC
1 AACAAGTGATATCAGAGCTATAGTGATTCTC
* * *
5319654 AACAAGTGATGTTAGAGCTATAGTGATTCTT
1 AACAAGTGATATCAGAGCTATAGTGATTCTC
5319685 AACA
1 AACA
5319689 TAGCCTCCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (31 bp):
AACAAGTGATATCAGAGCTATAGTGATTCTC
Found at i:5322054 original size:61 final size:58
Alignment explanation
Indices: 5321921--5322135 Score: 261
Period size: 62 Copynumber: 3.6 Consensus size: 58
5321911 TTTTATGCAG
5321921 GAAAAATTGATACTTTCAACTTTTCCTCAAAAAAACCTTTTTTGAAAATTTATTCTTAA
1 GAAAAATTGATACTTTCAACTTTTCCT-AAAAAAACCTTTTTTGAAAATTTATTCTTAA
**** * *
5321980 GAAAAATTGATACTTTCAACTTTTCTCTAAAATATTTTTTTTTTGAAATTTTTAATT-TTGA
1 GAAAAATTGATACTTTCAACTTTTC-CTAAAA-AAACCTTTTTTGAAA-ATTT-ATTCTTAA
* *
5322041 GAAAAATTGATACTTTCAACTTTTCCTAAAAAAAAAAACTTTTTTTGAAAATTTATCCTTAA
1 GAAAAATTGATACTTTCAACTTTTCCT----AAAAAAACCTTTTTTGAAAATTTATTCTTAA
*
5322103 GGAAAATTGATACTTTCAACTTTTCCTAAAAAA
1 GAAAAATTGATACTTTCAACTTTTCCTAAAAAA
5322136 TATATATATT
Statistics
Matches: 134, Mismatches: 13, Indels: 19
0.81 0.08 0.11
Matches are distributed among these distances:
58 6 0.04
59 29 0.22
60 15 0.11
61 33 0.25
62 35 0.26
63 12 0.09
64 4 0.03
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (58 bp):
GAAAAATTGATACTTTCAACTTTTCCTAAAAAAACCTTTTTTGAAAATTTATTCTTAA
Found at i:5322118 original size:62 final size:58
Alignment explanation
Indices: 5321921--5322135 Score: 268
Period size: 61 Copynumber: 3.6 Consensus size: 58
5321911 TTTTATGCAG
* *
5321921 GAAAAATTGATACTTTCAACTTTTCCTCAAAAAAACCTTTTTTGAAAATTTATTCTTAA
1 GAAAAATTGATACTTTCAACTTTTCCTAAAAAAAACTTTTTTTGAAAATTTA-TCTTAA
* *** * * *
5321980 GAAAAATTGATACTTTCAACTTTTCTCTAAAATATTTTTTTTTTGAAATTTTTAATTTTGA
1 GAAAAATTGATACTTTCAACTTTTC-CTAAAAAAAACTTTTTTTGAAA-ATTT-ATCTTAA
5322041 GAAAAATTGATACTTTCAACTTTTCCTAAAAAAAAAAACTTTTTTTGAAAATTTATCCTTAA
1 GAAAAATTGATACTTTCAACTTTTCCT---AAAAAAAACTTTTTTTGAAAATTTAT-CTTAA
*
5322103 GGAAAATTGATACTTTCAACTTTTCCTAAAAAA
1 GAAAAATTGATACTTTCAACTTTTCCTAAAAAA
5322136 TATATATATT
Statistics
Matches: 132, Mismatches: 17, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
59 31 0.23
60 18 0.14
61 34 0.26
62 33 0.25
63 16 0.12
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (58 bp):
GAAAAATTGATACTTTCAACTTTTCCTAAAAAAAACTTTTTTTGAAAATTTATCTTAA
Found at i:5322194 original size:16 final size:16
Alignment explanation
Indices: 5322168--5322278 Score: 52
Period size: 16 Copynumber: 6.7 Consensus size: 16
5322158 AAAAAATGAA
*
5322168 AAAAAATAAAA-GAAT
1 AAAAAATAAAATAAAT
5322183 AAAAAATGAAAATAAAT
1 AAAAAAT-AAAATAAAT
*
5322200 -AAAAATAGAAAAAAATT
1 AAAAAATA-AAATAAA-T
* **
5322217 AAACAATCTCAATATAAT
1 AAAAAAT-AAAATA-AAT
*
5322235 -AATAAT-AAATAAAT
1 AAAAAATAAAATAAAT
5322249 AAAATAATTAAAA-AAATT
1 AAAA-AA-TAAAATAAA-T
5322267 AAAAAATGAAAA
1 AAAAAAT-AAAA
5322279 AAAAACCTGG
Statistics
Matches: 74, Mismatches: 9, Indels: 24
0.69 0.08 0.22
Matches are distributed among these distances:
14 3 0.04
15 14 0.19
16 19 0.26
17 19 0.26
18 17 0.23
19 2 0.03
ACGTcount: A:0.73, C:0.03, G:0.04, T:0.21
Consensus pattern (16 bp):
AAAAAATAAAATAAAT
Found at i:5322200 original size:17 final size:16
Alignment explanation
Indices: 5322168--5322281 Score: 65
Period size: 17 Copynumber: 6.9 Consensus size: 16
5322158 AAAAAATGAA
*
5322168 AAAAAAT-AAAAGAAT
1 AAAAAATGAAAAAAAT
5322183 AAAAAATGAAAATAAAT
1 AAAAAATGAAAA-AAAT
5322200 -AAAAATAGAAAAAAATT
1 AAAAAAT-GAAAAAAA-T
* * * *
5322217 AAACAATCTCAATATAAT
1 AAA-AA-ATGAAAAAAAT
* *
5322235 -AATAAT-AAATAAAT
1 AAAAAATGAAAAAAAT
*
5322249 AAAATAATTAAAAAAATT
1 AAAA-AATGAAAAAAA-T
5322267 AAAAAATGAAAAAAA
1 AAAAAATGAAAAAAA
5322282 AACCTGGGAA
Statistics
Matches: 75, Mismatches: 13, Indels: 20
0.69 0.12 0.19
Matches are distributed among these distances:
14 5 0.07
15 10 0.13
16 17 0.23
17 27 0.36
18 8 0.11
19 7 0.09
20 1 0.01
ACGTcount: A:0.74, C:0.03, G:0.04, T:0.20
Consensus pattern (16 bp):
AAAAAATGAAAAAAAT
Found at i:5322211 original size:25 final size:25
Alignment explanation
Indices: 5322158--5322213 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
5322148 CATTTTATTT
*
5322158 AAAAAATGAAAAAAAATAAAAGAAT
1 AAAAAATGAAAAAAAATAAAAGAAG
*
5322183 AAAAAATGAAAATAAATAAAA-ATAG
1 AAAAAATGAAAAAAAATAAAAGA-AG
5322208 AAAAAA
1 AAAAAA
5322214 ATTAAACAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 1 0.04
25 27 0.96
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.12
Consensus pattern (25 bp):
AAAAAATGAAAAAAAATAAAAGAAG
Found at i:5323165 original size:41 final size:41
Alignment explanation
Indices: 5323120--5323218 Score: 110
Period size: 41 Copynumber: 2.4 Consensus size: 41
5323110 CAAAATAAAA
* *
5323120 AATATTAATAGATAATTTAAAA-AAATAATCAAATAAATAAT
1 AATATTAATAGATAACTAAAAATAAATAAT-AAATAAATAAT
* * * *
5323161 AATATTAACAGATAACTAAAAATAAATACTAGATAAATTAT
1 AATATTAATAGATAACTAAAAATAAATAATAAATAAATAAT
5323202 AATATATAATCAGATAA
1 AATAT-TAAT-AGATAA
5323219 ATATATATAT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
41 33 0.69
42 9 0.19
43 6 0.12
ACGTcount: A:0.61, C:0.05, G:0.04, T:0.30
Consensus pattern (41 bp):
AATATTAATAGATAACTAAAAATAAATAATAAATAAATAAT
Found at i:5323184 original size:20 final size:20
Alignment explanation
Indices: 5323112--5323221 Score: 62
Period size: 21 Copynumber: 5.2 Consensus size: 20
5323102 AGAAAAAACA
*
5323112 AAATAAAAAATATTAATAGAT
1 AAAT-AAAAATATTAACAGAT
* * *
5323133 AATTTAAAAA-AATAATCAAAT
1 AA-ATAAAAATATTAA-CAGAT
*
5323154 AAATAATAATATTAACAGAT
1 AAATAAAAATATTAACAGAT
* *
5323174 AACTAAAAATA-AATACTAGAT
1 AAATAAAAATATTA-AC-AGAT
* *
5323195 AAATTATAATATATAATCAGAT
1 AAATAAAAATAT-TAA-CAGAT
5323217 AAATA
1 AAATA
5323222 TATATATAAA
Statistics
Matches: 65, Mismatches: 16, Indels: 15
0.68 0.17 0.16
Matches are distributed among these distances:
19 1 0.02
20 24 0.37
21 28 0.43
22 10 0.15
23 2 0.03
ACGTcount: A:0.63, C:0.05, G:0.04, T:0.29
Consensus pattern (20 bp):
AAATAAAAATATTAACAGAT
Found at i:5323682 original size:38 final size:39
Alignment explanation
Indices: 5323583--5323694 Score: 140
Period size: 38 Copynumber: 2.9 Consensus size: 39
5323573 TTCGAAAAAC
* *
5323583 ATAAACAAAGCTCTCTAATCAGAGGTC-ACGACTTTGAA
1 ATAAATAAAGCTCTCTAATCAGAGGTCAACGATTTTGAA
* * *
5323621 ATGAATAAAGCTCCTCTATTCAGAGCTCAACGATTTTGAAA
1 ATAAATAAAGCT-CTCTAATCAGAGGTCAACGATTTTG-AA
5323662 ATAAAT-AAG-TCTCTAATCAGAGGTCAACGATTT
1 ATAAATAAAGCTCTCTAATCAGAGGTCAACGATTT
5323695 GGATATAAGC
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
38 31 0.49
39 14 0.22
40 11 0.17
41 7 0.11
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (39 bp):
ATAAATAAAGCTCTCTAATCAGAGGTCAACGATTTTGAA
Found at i:5323787 original size:8 final size:8
Alignment explanation
Indices: 5323741--5323780 Score: 53
Period size: 8 Copynumber: 4.8 Consensus size: 8
5323731 TCGACAAGTA
5323741 TTTTTTGCT
1 TTTTTTG-T
5323750 TTTTTTAGT
1 TTTTTT-GT
*
5323759 TTTATTGT
1 TTTTTTGT
5323767 TTTTTTGT
1 TTTTTTGT
5323775 TTTTTT
1 TTTTTT
5323781 TTGTTTTGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 15 0.54
9 12 0.43
10 1 0.04
ACGTcount: A:0.05, C:0.03, G:0.10, T:0.82
Consensus pattern (8 bp):
TTTTTTGT
Found at i:5323972 original size:42 final size:42
Alignment explanation
Indices: 5323823--5324056 Score: 271
Period size: 42 Copynumber: 5.8 Consensus size: 42
5323813 CTTTAAGCAA
* * *
5323823 AGGCTC-ACGACTTAT-AAAAATTAAA--GCTCATCTAATTAG
1 AGGCTCAACGACTT-TGAAAAAGTAAATGGCTCCTCTAATCAG
*
5323862 -GACTCAACGACTTTGAAAAAGTAAATGGCT--TCTAAT--G
1 AGGCTCAACGACTTTGAAAAAGTAAATGGCTCCTCTAATCAG
*
5323899 AGGCTCATAC-AATTTG-AAAAGTAAATGGCTCCTCTAATCAG
1 AGGCTCA-ACGACTTTGAAAAAGTAAATGGCTCCTCTAATCAG
5323940 AGGCTCAACGACTTTGAAAAAGTAAATGGCTCCTCTAATCAG
1 AGGCTCAACGACTTTGAAAAAGTAAATGGCTCCTCTAATCAG
* *
5323982 AGGCTCAACAACTTTGGAAAA-TAAATGGCTCCTCTAATCAG
1 AGGCTCAACGACTTTGAAAAAGTAAATGGCTCCTCTAATCAG
5324023 AGGGCTCAACGACTTT-AGAAAA-TAAATGGCTCCT
1 A-GGCTCAACGACTTTGA-AAAAGTAAATGGCTCCT
5324057 TGATAATCAT
Statistics
Matches: 172, Mismatches: 9, Indels: 25
0.83 0.04 0.12
Matches are distributed among these distances:
37 15 0.09
38 15 0.09
39 30 0.17
40 2 0.01
41 37 0.22
42 73 0.42
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.26
Consensus pattern (42 bp):
AGGCTCAACGACTTTGAAAAAGTAAATGGCTCCTCTAATCAG
Found at i:5324022 original size:83 final size:82
Alignment explanation
Indices: 5323864--5324056 Score: 292
Period size: 83 Copynumber: 2.4 Consensus size: 82
5323854 CTAATTAGGA
5323864 CTCAACGACTTTGAAAAAGTAAATGGCT--TCTAATGAGGCTCATACAATTTGAAAAGTAAATGG
1 CTCAACGACTTTGAAAAAGTAAATGGCTCCTCTAATGAGGCTCATACAATTTGAAAAGTAAATGG
5323927 CTCCTCTAATCAGA-GG
66 CTCCTCTAATCAGAGGG
5323943 CTCAACGACTTTGAAAAAGTAAATGGCTCCTCTAATCAGAGGCTCA-ACAACTTTGGAAAA-TAA
1 CTCAACGACTTTGAAAAAGTAAATGGCTCCTCTAAT--GAGGCTCATACAA-TTT-GAAAAGTAA
5324006 ATGGCTCCTCTAATCAGAGGG
62 ATGGCTCCTCTAATCAGAGGG
5324027 CTCAACGACTTT-AGAAAA-TAAATGGCTCCT
1 CTCAACGACTTTGA-AAAAGTAAATGGCTCCT
5324057 TGATAATCAT
Statistics
Matches: 106, Mismatches: 0, Indels: 12
0.90 0.00 0.10
Matches are distributed among these distances:
79 28 0.26
81 6 0.06
82 4 0.04
83 45 0.42
84 23 0.22
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.25
Consensus pattern (82 bp):
CTCAACGACTTTGAAAAAGTAAATGGCTCCTCTAATGAGGCTCATACAATTTGAAAAGTAAATGG
CTCCTCTAATCAGAGGG
Found at i:5325082 original size:17 final size:18
Alignment explanation
Indices: 5325057--5325125 Score: 67
Period size: 18 Copynumber: 4.1 Consensus size: 18
5325047 TCTTTTTTCA
5325057 TTCACTTTTTTTTCTTTT
1 TTCACTTTTTTTTCTTTT
* *
5325075 TTCATTTTTTTTTCATTT
1 TTCACTTTTTTTTCTTTT
*
5325093 TT-A-TTTTTTTT-TATT
1 TTCACTTTTTTTTCTTTT
*
5325108 TTCA--TTATTTTCTTTT
1 TTCACTTTTTTTTCTTTT
5325124 TT
1 TT
5325126 TTAAGCATAG
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
15 10 0.23
16 14 0.33
17 1 0.02
18 18 0.42
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (18 bp):
TTCACTTTTTTTTCTTTT
Found at i:5325083 original size:18 final size:18
Alignment explanation
Indices: 5325057--5325109 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 18
5325047 TCTTTTTTCA
*
5325057 TTCACTTTTTTTTCTTTT
1 TTCATTTTTTTTTCTTTT
*
5325075 TTCATTTTTTTTTCATTT
1 TTCATTTTTTTTTCTTTT
*
5325093 TT-ATTTTTTTTTATTTT
1 TTCATTTTTTTTTCTTTT
5325110 CATTATTTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 13 0.42
18 18 0.58
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.81
Consensus pattern (18 bp):
TTCATTTTTTTTTCTTTT
Found at i:5325087 original size:22 final size:22
Alignment explanation
Indices: 5325047--5325127 Score: 57
Period size: 22 Copynumber: 3.8 Consensus size: 22
5325037 CCCTGATGAC
***
5325047 TCTTTTTTCATTCACTTTTTTT
1 TCTTTTTTCATTTTTTTTTTTT
5325069 TCTTTTTTCA----TTTTTTTT
1 TCTTTTTTCATTTTTTTTTTTT
*
5325087 TCATTTTT-ATTTTTTTTTATTT
1 TCTTTTTTCATTTTTTTTT-TTT
5325109 TCATTATTTTC-TTTTTTTT
1 TC-TT-TTTTCATTTTTTTT
5325128 AAGCATAGTA
Statistics
Matches: 48, Mismatches: 3, Indels: 14
0.74 0.05 0.22
Matches are distributed among these distances:
17 1 0.02
18 14 0.29
21 5 0.10
22 15 0.31
23 1 0.02
24 12 0.25
ACGTcount: A:0.10, C:0.11, G:0.00, T:0.79
Consensus pattern (22 bp):
TCTTTTTTCATTTTTTTTTTTT
Found at i:5325118 original size:18 final size:17
Alignment explanation
Indices: 5325057--5325127 Score: 67
Period size: 16 Copynumber: 4.1 Consensus size: 17
5325047 TCTTTTTTCA
5325057 TTCACTTTTTTTTCTT-TT
1 TTCA-TTTTTTTT-TTATT
*
5325075 TTCATTTTTTTTTCATT
1 TTCATTTTTTTTTTATT
*
5325092 TTTA-TTTTTTTTTATT
1 TTCATTTTTTTTTTATT
5325108 TTCATTATTTTCTTTT-TT
1 TTCATT-TTTT-TTTTATT
5325126 TT
1 TT
5325128 AAGCATAGTA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
16 15 0.33
17 14 0.31
18 12 0.27
19 4 0.09
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (17 bp):
TTCATTTTTTTTTTATT
Found at i:5325125 original size:16 final size:16
Alignment explanation
Indices: 5325064--5325125 Score: 65
Period size: 17 Copynumber: 3.9 Consensus size: 16
5325054 TCATTCACTT
5325064 TTTTTTCTT-TTTTCA
1 TTTTTTCTTATTTTCA
* *
5325079 TTTTTTTTTCATTTTTA
1 TTTTTTCTT-ATTTTCA
*
5325096 TTTTTTTTTATTTTCA
1 TTTTTTCTTATTTTCA
5325112 TTATTTTCTT-TTTT
1 TT-TTTTCTTATTTT
5325126 TTAAGCATAG
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
15 8 0.20
16 12 0.30
17 20 0.50
ACGTcount: A:0.10, C:0.08, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTTTCTTATTTTCA
Found at i:5325126 original size:17 final size:16
Alignment explanation
Indices: 5325057--5325118 Score: 70
Period size: 17 Copynumber: 3.6 Consensus size: 16
5325047 TCTTTTTTCA
*
5325057 TTCACTTTTTTTTCTTTT
1 TTCA-TTTTTTTT-TATT
5325075 TTCATTTTTTTTTCATT
1 TTCATTTTTTTTT-ATT
*
5325092 TTTATTTTTTTTTATT
1 TTCATTTTTTTTTATT
5325108 TTCATTATTTT
1 TTCATT-TTTT
5325119 CTTTTTTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
16 9 0.23
17 26 0.67
18 4 0.10
ACGTcount: A:0.11, C:0.10, G:0.00, T:0.79
Consensus pattern (16 bp):
TTCATTTTTTTTTATT
Found at i:5325127 original size:33 final size:33
Alignment explanation
Indices: 5325062--5325128 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 33
5325052 TTTCATTCAC
*
5325062 TTTTTTTTCTTTTTTCATTTTTTTTTCATTTTTA
1 TTTTTTTTCTATTTTCATTTTTTTTT-ATTTTTA
5325096 TTTTTTTT-TATTTTCATTATTTTCTTT-TTTTTA
1 TTTTTTTTCTATTTTCATT-TTTT-TTTATTTTTA
5325129 AGCATAGTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
33 15 0.50
34 12 0.40
35 3 0.10
ACGTcount: A:0.10, C:0.07, G:0.00, T:0.82
Consensus pattern (33 bp):
TTTTTTTTCTATTTTCATTTTTTTTTATTTTTA
Found at i:5336107 original size:33 final size:32
Alignment explanation
Indices: 5336056--5336133 Score: 84
Period size: 33 Copynumber: 2.4 Consensus size: 32
5336046 ATTTTCAATT
* ** * * *
5336056 TTTAAAAATATTAAAATTTGTATATTTGAAAGA
1 TTTAAAAATTTTTGAATTTATATA-TTAAAAAA
*
5336089 TTTAAAAGTTTTTGAATTTATATATTAAAAAA
1 TTTAAAAATTTTTGAATTTATATATTAAAAAA
5336121 TTTAAAAATTTTT
1 TTTAAAAATTTTT
5336134 ATAAGATATT
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
32 18 0.49
33 19 0.51
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.47
Consensus pattern (32 bp):
TTTAAAAATTTTTGAATTTATATATTAAAAAA
Found at i:5339629 original size:14 final size:14
Alignment explanation
Indices: 5339610--5339645 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
5339600 TTAAAATAGG
*
5339610 GAATGAAAGCGGAA
1 GAATGAAAGAGGAA
5339624 GAATGAAAGAGGAA
1 GAATGAAAGAGGAA
*
5339638 AAATGAAA
1 GAATGAAA
5339646 AATGTTCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.58, C:0.03, G:0.31, T:0.08
Consensus pattern (14 bp):
GAATGAAAGAGGAA
Found at i:5350868 original size:2 final size:2
Alignment explanation
Indices: 5350861--5350914 Score: 71
Period size: 2 Copynumber: 29.0 Consensus size: 2
5350851 TCAATATAAC
*
5350861 AT AT AT AT AT AT A- AT AT AG AT A- AT AT A- AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5350899 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
5350915 TCTACCACCC
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
1 4 0.09
2 42 0.91
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:5360300 original size:2 final size:2
Alignment explanation
Indices: 5360293--5360333 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
5360283 ACATGTATCA
5360293 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5360334 CCAAAACTCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5360941 original size:28 final size:29
Alignment explanation
Indices: 5360908--5360962 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
5360898 AATAAACTTT
*
5360908 TAACTTGTAA-TTGTATCCAAATAAGCCA
1 TAACTTGTAATTTATATCCAAATAAGCCA
* *
5360936 TAACTTTTAATTTATATCTAAATAAGC
1 TAACTTGTAATTTATATCCAAATAAGC
5360963 TCTTAACATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 9 0.39
29 14 0.61
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (29 bp):
TAACTTGTAATTTATATCCAAATAAGCCA
Found at i:5361074 original size:23 final size:24
Alignment explanation
Indices: 5361035--5361083 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
5361025 AAGAGCTTAT
5361035 TTTTATATAATAGAAAT-ATAAAA
1 TTTTATATAATAGAAATAATAAAA
*
5361058 TTTTATCTAAATA-AAATAATAAAA
1 TTTTATAT-AATAGAAATAATAAAA
5361082 TT
1 TT
5361084 CAATTACTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (24 bp):
TTTTATATAATAGAAATAATAAAA
Found at i:5364006 original size:20 final size:20
Alignment explanation
Indices: 5363978--5364015 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5363968 ACTACTTTTA
*
5363978 CACCCATATGCTGCATATAT
1 CACCCATATGCAGCATATAT
*
5363998 CACCTATATGCAGCATAT
1 CACCCATATGCAGCATAT
5364016 CTTTCAAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.29, G:0.11, T:0.29
Consensus pattern (20 bp):
CACCCATATGCAGCATATAT
Found at i:5368189 original size:24 final size:24
Alignment explanation
Indices: 5368141--5368190 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
5368131 TTGTTAAAAA
*
5368141 TAATTTTTAGTTTTTAATAAGATT
1 TAATTTTTAGTTTTTAATAAAATT
5368165 TAATTTTATA-TTTTT-ATCAAAATT
1 TAATTTT-TAGTTTTTAAT-AAAATT
5368189 TA
1 TA
5368191 TAAATATTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 2 0.09
24 19 0.83
25 2 0.09
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (24 bp):
TAATTTTTAGTTTTTAATAAAATT
Found at i:5369259 original size:28 final size:27
Alignment explanation
Indices: 5369227--5369317 Score: 77
Period size: 23 Copynumber: 3.4 Consensus size: 27
5369217 TAAGTAATTT
*
5369227 TTTTTTATAAATATATAGTAATATATATA
1 TTTTTAATAAA-ATATAGTAAT-TATATA
*
5369256 TTTTTAATAAAATATATTAATTATA-A
1 TTTTTAATAAAATATAGTAATTATATA
*
5369282 ---TTAATCAAAA-ATAATAATT-TATA
1 TTTTTAAT-AAAATATAGTAATTATATA
5369305 TTATTTAATAAAA
1 TT-TTTAATAAAA
5369318 AATTTATTTA
Statistics
Matches: 53, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
22 2 0.04
23 14 0.26
24 4 0.08
26 5 0.09
27 9 0.17
28 9 0.17
29 10 0.19
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (27 bp):
TTTTTAATAAAATATAGTAATTATATA
Found at i:5370542 original size:16 final size:17
Alignment explanation
Indices: 5370523--5370559 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
5370513 ACAGAGTAAA
*
5370523 AAAAAACCTA-CAAAAC
1 AAAAAACCTAGAAAAAC
5370539 AAAAAACCTAGAAAAAC
1 AAAAAACCTAGAAAAAC
5370556 AAAA
1 AAAA
5370560 GAATTTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.73, C:0.19, G:0.03, T:0.05
Consensus pattern (17 bp):
AAAAAACCTAGAAAAAC
Found at i:5371502 original size:32 final size:31
Alignment explanation
Indices: 5371464--5371550 Score: 93
Period size: 32 Copynumber: 2.7 Consensus size: 31
5371454 TCCTTTTTAC
*
5371464 AAAAAATTCCATATCATTTATAAGAAATTAAGT
1 AAAAAATTCCATATCATTTA-AAG-AATTAAAT
* **
5371497 AAAAATTTTTATATCAATTTAAAGAATTAAAT
1 AAAAAATTCCATATC-ATTTAAAGAATTAAAT
* *
5371529 AAAAAACTCCTTATCATTTAAA
1 AAAAAATTCCATATCATTTAAA
5371551 AAATATTAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
31 7 0.16
32 17 0.39
33 15 0.34
34 5 0.11
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (31 bp):
AAAAAATTCCATATCATTTAAAGAATTAAAT
Found at i:5373028 original size:21 final size:20
Alignment explanation
Indices: 5373002--5373062 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 20
5372992 AGATAAATTT
*
5373002 TTTTTTTTCATTTTTTATTAC
1 TTTTTTTT-ATTTTTTATTAA
*
5373023 TTTTTTTAATTTTTTAATTAA
1 TTTTTTTTATTTTTT-ATTAA
5373044 TTTTTATTTATTATTTTAT
1 TTTTT-TTTATT-TTTTAT
5373063 AACCAAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 7 0.21
21 16 0.47
22 7 0.21
23 4 0.12
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTTTTTTATTTTTTATTAA
Found at i:5373394 original size:21 final size:20
Alignment explanation
Indices: 5373370--5373418 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
5373360 AAATATTAAT
5373370 AATAAAATTAAAAATAACAAA
1 AATAAAATTAAAAA-AACAAA
* *
5373391 AATAATATTTAAAAAAATAAA
1 AATAA-AATTAAAAAAACAAA
5373412 AA-AAAAT
1 AATAAAAT
5373419 CACTTAAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 2 0.08
20 2 0.08
21 12 0.50
22 8 0.33
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (20 bp):
AATAAAATTAAAAAAACAAA
Found at i:5374705 original size:49 final size:51
Alignment explanation
Indices: 5374632--5375177 Score: 528
Period size: 50 Copynumber: 10.7 Consensus size: 51
5374622 TTTAAAATCT
* *
5374632 AAAAAAGGCTCATCTCAGCAGAGGCTTAACAACTTTAAAAATTCT-ATCTTG
1 AAAAAA-GCTCATCTCAGTAGAGGCTCAACAACTTTAAAAATTCTCATCTTG
* *
5374683 -AAAAAGCTCATCTAAGTAGAGGCTCAACAA-TTTTAAAA-TCTCATCTT-
1 AAAAAAGCTCATCTCAGTAGAGGCTCAACAACTTTAAAAATTCTCATCTTG
* * * *
5374730 AGAAAAAGCTCCTTTCCA-CAGAGGCTTAACAACTTT-AAAATTCT-ATCTTG
1 A-AAAAAGCTCATCT-CAGTAGAGGCTCAACAACTTTAAAAATTCTCATCTTG
* * * *
5374780 AAAAAAGCTTC-TCTCAATAGAGGTTCCACAACTTTAAAAATTTTCATCTTG
1 AAAAAAGC-TCATCTCAGTAGAGGCTCAACAACTTTAAAAATTCTCATCTTG
* * * * * *
5374831 AAAAAGGTTCCTCTCAGTAGAGGCTCAATAATTTTAAAAATTCT-ATCTCG
1 AAAAAAGCTCATCTCAGTAGAGGCTCAACAACTTTAAAAATTCTCATCTTG
* *
5374881 AAAAAAGCTCCTTTCAGTAGAGGCTCAACAACTTTAAAAAATTCTCATCTTG
1 AAAAAAGCTCATCTCAGTAGAGGCTCAACAACTTT-AAAAATTCTCATCTTG
* * * * *
5374933 AAAAAAAGTTC-TCTCAGCAAAGGCTCAATAATTTTAAAAATTCT-ATCTTG
1 -AAAAAAGCTCATCTCAGTAGAGGCTCAACAACTTTAAAAATTCTCATCTTG
* * * *
5374983 AAAAAAAGCTCATCTCAGTAAAAGCTCAATAACTTAAAAAAATTCTCATCTTG
1 -AAAAAAGCTCATCTCAGTAGAGGCTCAACAACTT-TAAAAATTCTCATCTTG
** *
5375036 -AAAAAGACTCATCTCAACAGAGGCTCAATAACTTTAAAAAATT-T-ATCTTG
1 AAAAAAG-CTCATCTCAGTAGAGGCTCAACAACTTT-AAAAATTCTCATCTTG
* * * * *
5375086 AAAAAAACTCATCTCAGCATAGCCTCAACAACTTTAAAAAATTTTCATCTTG
1 AAAAAAGCTCATCTCAGTAGAGGCTCAACAACTTT-AAAAATTCTCATCTTG
*
5375138 AAAAAAAAGCTCTTCTCAGTAGAGGCTCAACAACTTTAAA
1 --AAAAAAGCTCATCTCAGTAGAGGCTCAACAACTTTAAA
5375178 TTAAACCATT
Statistics
Matches: 414, Mismatches: 56, Indels: 48
0.80 0.11 0.09
Matches are distributed among these distances:
47 3 0.01
48 14 0.03
49 77 0.19
50 113 0.27
51 90 0.22
52 69 0.17
53 18 0.04
54 30 0.07
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.29
Consensus pattern (51 bp):
AAAAAAGCTCATCTCAGTAGAGGCTCAACAACTTTAAAAATTCTCATCTTG
Found at i:5374960 original size:102 final size:102
Alignment explanation
Indices: 5374644--5375177 Score: 579
Period size: 102 Copynumber: 5.3 Consensus size: 102
5374634 AAAAGGCTCA
* *
5374644 TCTCAGCAGAGGCTTAACAACTTTAAAAATTCTATCTTG-AAAAAGCTCATCTAAGTAGAGGCTC
1 TCTCAGCAGAGGCTCAACAACTTTAAAAATTCTATCTTGAAAAAAGCTCATCTCAGTAGAGGCTC
* * *
5374708 AACAA-TTT-TAAAA-TCTCATCTT-AGAAAAAGCTCC
66 AACAACTTTAAAAAATTCTCATCTTGAAAAAAAG-TTC
* * * *
5374742 TTTCCA-CAGAGGCTTAACAACTTT-AAAATTCTATCTTGAAAAAAGCTTC-TCTCAATAGAGGT
1 TCT-CAGCAGAGGCTCAACAACTTTAAAAATTCTATCTTGAAAAAAGC-TCATCTCAGTAGAGGC
* * *
5374804 TCCACAACTTT-AAAAATTTTCATCTTG-AAAAAGGTTCC
64 TCAACAACTTTAAAAAATTCTCATCTTGAAAAAAAGTT-C
* * * * * *
5374842 TCTCAGTAGAGGCTCAATAATTTTAAAAATTCTATCTCGAAAAAAGCTCCTTTCAGTAGAGGCTC
1 TCTCAGCAGAGGCTCAACAACTTTAAAAATTCTATCTTGAAAAAAGCTCATCTCAGTAGAGGCTC
5374907 AACAACTTTAAAAAATTCTCATCTTGAAAAAAAGTTC
66 AACAACTTTAAAAAATTCTCATCTTGAAAAAAAGTTC
* * * * *
5374944 TCTCAGCAAAGGCTCAATAATTTTAAAAATTCTATCTTGAAAAAAAGCTCATCTCAGTAAAAGCT
1 TCTCAGCAGAGGCTCAACAACTTTAAAAATTCTATCTTG-AAAAAAGCTCATCTCAGTAGAGGCT
* * * *
5375009 CAATAACTTAAAAAAATTCTCATCTTGAAAAAGA-CTC
65 CAACAACTTTAAAAAATTCTCATCTTGAAAAAAAGTTC
* * * * * *
5375046 ATCTCAACAGAGGCTCAATAACTTTAAAAAATT-TATCTTGAAAAAAACTCATCTCAGCATAGCC
1 -TCTCAGCAGAGGCTCAACAACTTT-AAAAATTCTATCTTGAAAAAAGCTCATCTCAGTAGAGGC
* *
5375110 TCAACAACTTTAAAAAATTTTCATCTTGAAAAAAAAGCTC
64 TCAACAACTTTAAAAAATTCTCATCTTG-AAAAAAAGTTC
*
5375150 TTCTCAGTAGAGGCTCAACAACTTTAAA
1 -TCTCAGCAGAGGCTCAACAACTTTAAA
5375178 TTAAACCATT
Statistics
Matches: 370, Mismatches: 49, Indels: 29
0.83 0.11 0.06
Matches are distributed among these distances:
97 14 0.04
98 43 0.12
99 14 0.04
100 32 0.09
101 41 0.11
102 98 0.26
103 97 0.26
104 31 0.08
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (102 bp):
TCTCAGCAGAGGCTCAACAACTTTAAAAATTCTATCTTGAAAAAAGCTCATCTCAGTAGAGGCTC
AACAACTTTAAAAAATTCTCATCTTGAAAAAAAGTTC
Found at i:5375192 original size:102 final size:98
Alignment explanation
Indices: 5374807--5375193 Score: 323
Period size: 103 Copynumber: 3.8 Consensus size: 98
5374797 TAGAGGTTCC
* * * * *
5374807 ACAACTTT-AAAAATTTTCATCTTG-AAAAAGGTTCCTCTCAGTAGAGGCTCAATAATTTTAAAA
1 ACAACTTTAAAAAATTCTCATCTTGAAAAAAAGCT-CTCTCAGCAGAGGCTCAATAACTTTAAAA
* * * * * * *
5374870 ATTCTATCTCGAAAAAAGCTCCTTTCAGTAGAGGCTCA
65 A-ACCAT-T-GAAAAAAACTCATCTCAG-AAAAGCTCA
* * *
5374908 ACAACTTTAAAAAATTCTCATCTTGAAAAAAAGTTCTCTCAGCAAAGGCTCAATAATTTTAAAAA
1 ACAACTTTAAAAAATTCTCATCTTGAAAAAAAGCTCTCTCAGCAGAGGCTCAATAACTTTAAAAA
* *
5374973 TTCTATCTTGAAAAAAAGCTCATCTCAGTAAAAGCTCA
66 -ACCA--TTGAAAAAAA-CTCATCTCAG-AAAAGCTCA
* * * *
5375011 ATAACTTAAAAAAATTCTCATCTTGAAAAAGA-CTCATCTCAACAGAGGCTCAATAACTTTAAAA
1 ACAACTTTAAAAAATTCTCATCTTGAAAAAAAGCTC-TCTCAGCAGAGGCTCAATAACTTTAAAA
** * *
5375075 AATTTATCTTGAAAAAAACTCATCTCAGCATAGCCTCA
65 AA-CCA--TTGAAAAAAACTCATCTCAGAAAAG-CTCA
* * *
5375113 ACAACTTTAAAAAATTTTCATCTTGAAAAAAAAGCTCTTCTCAGTAGAGGCTCAACAACTTTAAA
1 ACAACTTTAAAAAATTCTCATCTTG-AAAAAAAGCTC-TCTCAGCAGAGGCTCAATAACTTTAAA
5375178 TTAAACCATT-AAAAAA
64 --AAACCATTGAAAAAA
5375194 TAACTTCAAA
Statistics
Matches: 244, Mismatches: 30, Indels: 23
0.82 0.10 0.08
Matches are distributed among these distances:
101 11 0.05
102 99 0.41
103 102 0.42
104 28 0.11
105 1 0.00
106 3 0.01
ACGTcount: A:0.43, C:0.19, G:0.09, T:0.29
Consensus pattern (98 bp):
ACAACTTTAAAAAATTCTCATCTTGAAAAAAAGCTCTCTCAGCAGAGGCTCAATAACTTTAAAAA
ACCATTGAAAAAAACTCATCTCAGAAAAGCTCA
Found at i:5375504 original size:147 final size:147
Alignment explanation
Indices: 5375276--5375651 Score: 506
Period size: 147 Copynumber: 2.6 Consensus size: 147
5375266 ATGTCATCAC
*
5375276 CGAAGGAAACTCGAATATCACCATCGAGAAAATGCAATTCAAGCTTTAATACTCAGG-TATCACC
1 CGAAGAAAACTCGAATATCACCATCGAGAAAATGCAATTCAAGCTTTAATACTC-GGATATCACC
* * * * **
5375340 ACCGAGAAAATGCAAATGCAAATTCAAACTTTAAACTCGGATATCACCATTAAGAATATACAAAA
65 ATCGAGAGAATACAAATGCAAATTCAAACTTTAAACTCAGATATCACCACCAAGAATATACAAAA
* * *
5375405 GA-TTTCGGATATTGCCAT
130 AACTTT-GAATATCGCCAT
* * *
5375423 CGAAGAAAACTCGAATATCACCATCGAAAAAATGTAATTCAAGCATTAATACTCGGATATCACCA
1 CGAAGAAAACTCGAATATCACCATCGAGAAAATGCAATTCAAGCTTTAATACTCGGATATCACCA
* * * **
5375488 TTGAGAGAATATAAATGCAAATTCAACCTTTAAACTCAGATATCACCACCAAGAATATGTAAAAA
66 TCGAGAGAATACAAATGCAAATTCAAACTTTAAACTCAGATATCACCACCAAGAATATACAAAAA
5375553 ACTTTGAATATCGCCAT
131 ACTTTGAATATCGCCAT
* * * *
5375570 CGAA-AGAAACTCGAATATCCCCATCGAGAAAATGCAATTCAAACTTTAATACTTGGATATCATC
1 CGAAGA-AAACTCGAATATCACCATCGAGAAAATGCAATTCAAGCTTTAATACTCGGATATCACC
5375634 ATCGAGAGAATACAAATG
65 ATCGAGAGAATACAAATG
5375652 ACTTTTTTAA
Statistics
Matches: 199, Mismatches: 27, Indels: 6
0.86 0.12 0.03
Matches are distributed among these distances:
146 3 0.02
147 193 0.97
148 3 0.02
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.24
Consensus pattern (147 bp):
CGAAGAAAACTCGAATATCACCATCGAGAAAATGCAATTCAAGCTTTAATACTCGGATATCACCA
TCGAGAGAATACAAATGCAAATTCAAACTTTAAACTCAGATATCACCACCAAGAATATACAAAAA
ACTTTGAATATCGCCAT
Found at i:5375762 original size:82 final size:82
Alignment explanation
Indices: 5375668--5375955 Score: 335
Period size: 82 Copynumber: 3.3 Consensus size: 82
5375658 TTAATACTTG
* * *
5375668 GATATCACCACTGAGTGATTTTGAAAATGTCTTGGATTTCACCTCCAAGAAAATGCAAATGCAAA
1 GATATCACCACTGATTGATTTTGAAAATGTCTTGGATATCACCACCAAGAAAATGCAAATGCAAA
5375733 TTTAAACTTTAAACTCA
66 TTTAAACTTTAAACTCA
*
5375750 GATATCACCACTGATTGATTTTGAAAATGTCATGGATATCACCACCAAGAAAATGCAAATGCAAA
1 GATATCACCACTGATTGATTTTGAAAATGTCTTGGATATCACCACCAAGAAAATGCAAATGC--A
* *
5375815 AATGCAAGTGCAAA-TTTAAACTTTAAACTTG
64 AAT-----T-TAAACTTTAAAC--T---C--A
* * *
5375846 GATATTACCACTGATTGATTTTGAAAATATCTTGGATATCACCACCAAGAAAAAGCAAATGCAAA
1 GATATCACCACTGATTGATTTTGAAAATGTCTTGGATATCACCACCAAGAAAATGCAAATGCAAA
5375911 TTTAAACTTTAAACTCA
66 TTTAAACTTTAAACTCA
* *
5375928 TATATCACCACCGATTGATTTTGAAAAT
1 GATATCACCACTGATTGATTTTGAAAAT
5375956 AATTTATCAC
Statistics
Matches: 175, Mismatches: 15, Indels: 32
0.79 0.07 0.14
Matches are distributed among these distances:
82 83 0.47
84 5 0.03
87 1 0.01
88 3 0.02
89 16 0.09
90 3 0.02
91 1 0.01
94 5 0.03
96 58 0.33
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (82 bp):
GATATCACCACTGATTGATTTTGAAAATGTCTTGGATATCACCACCAAGAAAATGCAAATGCAAA
TTTAAACTTTAAACTCA
Found at i:5375818 original size:14 final size:14
Alignment explanation
Indices: 5375799--5375828 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5375789 CACCACCAAG
5375799 AAAATGCAAATGCA
1 AAAATGCAAATGCA
*
5375813 AAAATGCAAGTGCA
1 AAAATGCAAATGCA
5375827 AA
1 AA
5375829 TTTAAACTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.13, G:0.17, T:0.13
Consensus pattern (14 bp):
AAAATGCAAATGCA
Found at i:5375882 original size:96 final size:96
Alignment explanation
Indices: 5375717--5375910 Score: 325
Period size: 96 Copynumber: 2.0 Consensus size: 96
5375707 CACCTCCAAG
*
5375717 AAAATGCAAATGCAAATTTAAACTTTAAACTCAGATATCACCACTGATTGATTTTGAAAATGTCA
1 AAAATGCAAATGCAAATTTAAACTTTAAACTCAGATATCACCACTGATTGATTTTGAAAATATCA
*
5375782 TGGATATCACCACCAAGAAAATGCAAATGCA
66 TGGATATCACCACCAAGAAAAAGCAAATGCA
* ** * *
5375813 AAAATGCAAGTGCAAATTTAAACTTTAAACTTGGATATTACCACTGATTGATTTTGAAAATATCT
1 AAAATGCAAATGCAAATTTAAACTTTAAACTCAGATATCACCACTGATTGATTTTGAAAATATCA
5375878 TGGATATCACCACCAAGAAAAAGCAAATGCA
66 TGGATATCACCACCAAGAAAAAGCAAATGCA
5375909 AA
1 AA
5375911 TTTAAACTTT
Statistics
Matches: 91, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
96 91 1.00
ACGTcount: A:0.44, C:0.16, G:0.13, T:0.27
Consensus pattern (96 bp):
AAAATGCAAATGCAAATTTAAACTTTAAACTCAGATATCACCACTGATTGATTTTGAAAATATCA
TGGATATCACCACCAAGAAAAAGCAAATGCA
Found at i:5376150 original size:23 final size:23
Alignment explanation
Indices: 5376121--5376169 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
5376111 TTTATAAAGC
5376121 TTTTTGGAATTCAAATCCCAAAT
1 TTTTTGGAATTCAAATCCCAAAT
* * *
5376144 TTTTTGGGATTCAAATCTCATAT
1 TTTTTGGAATTCAAATCCCAAAT
5376167 TTT
1 TTT
5376170 CAACCGACGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.29, C:0.14, G:0.10, T:0.47
Consensus pattern (23 bp):
TTTTTGGAATTCAAATCCCAAAT
Found at i:5376349 original size:3 final size:3
Alignment explanation
Indices: 5376341--5376368 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5376331 ATATATATAT
5376341 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
5376369 ATACAAAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:5376605 original size:44 final size:44
Alignment explanation
Indices: 5376508--5376676 Score: 146
Period size: 44 Copynumber: 3.7 Consensus size: 44
5376498 TTCCAGAAGT
* * * *
5376508 TCAACAACATTTTTTAAAATTT-AAAACGCTCATCTGAGCAGAA-GC
1 TCAACAAC--TTTTAAAAATTTAAAAAGGCTCCTCTAAGCA-AAGGC
5376553 TCAACAACTTTTAAAAATTTAAAAAGGCTCCTCTAAGCAAAGGC
1 TCAACAACTTTTAAAAATTTAAAAAGGCTCCTCTAAGCAAAGGC
* * * *
5376597 TCAACAACTTTAAAATTCATCATCTTGGAAAA-GCTCCTCTAAGTAGAGGC
1 TCAACAACTTTTAAA---A--AT-TT-AAAAAGGCTCCTCTAAGCAAAGGC
*
5376647 TCAACAACTTTTAAAAATTTAATAAGGCTC
1 TCAACAACTTTTAAAAATTTAAAAAGGCTC
5376677 GAAATCAAGT
Statistics
Matches: 103, Mismatches: 11, Indels: 21
0.76 0.08 0.16
Matches are distributed among these distances:
43 16 0.16
44 37 0.36
45 10 0.10
47 2 0.02
49 2 0.02
50 32 0.31
51 4 0.04
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.28
Consensus pattern (44 bp):
TCAACAACTTTTAAAAATTTAAAAAGGCTCCTCTAAGCAAAGGC
Found at i:5388741 original size:12 final size:12
Alignment explanation
Indices: 5388726--5388755 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
5388716 TTTATTTTTC
5388726 TTATTTTTTTAA
1 TTATTTTTTTAA
5388738 TTA-TTTTTTAA
1 TTATTTTTTTAA
5388749 TTATTTT
1 TTATTTT
5388756 ATAAGATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTATTTTTTTAA
Found at i:5388915 original size:21 final size:21
Alignment explanation
Indices: 5388891--5388951 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
5388881 AAATATTAAT
*
5388891 AATAAAATTGAAAATAACAAA
1 AATAAAATTGAAAAAAACAAA
* * *
5388912 AATAATATTTAAAAAAATAAA
1 AATAAAATTGAAAAAAACAAA
*
5388933 AA-AAAACT-AAAAAAA-AAA
1 AATAAAATTGAAAAAAACAAA
5388951 A
1 A
5388952 TCACCTAAAC
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
18 4 0.12
19 7 0.21
20 4 0.12
21 19 0.56
ACGTcount: A:0.77, C:0.03, G:0.02, T:0.18
Consensus pattern (21 bp):
AATAAAATTGAAAAAAACAAA
Found at i:5389050 original size:21 final size:21
Alignment explanation
Indices: 5389024--5389072 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
5389014 TCGGGTTCAG
5389024 TGGTTTGGGGCATGTCCGACT
1 TGGTTTGGGGCATGTCCGACT
*
5389045 TGGTTTGGGGCATGTCCGTCT
1 TGGTTTGGGGCATGTCCGACT
*
5389066 CGGTTTG
1 TGGTTTG
5389073 TGTAGGGTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.06, C:0.18, G:0.39, T:0.37
Consensus pattern (21 bp):
TGGTTTGGGGCATGTCCGACT
Found at i:5389956 original size:10 final size:10
Alignment explanation
Indices: 5389943--5389976 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
5389933 TTTTCTTTCT
5389943 TTTTTTTGTA
1 TTTTTTTGTA
5389953 TTTTTTTGTA
1 TTTTTTTGTA
*
5389963 TTATTATTGTA
1 TT-TTTTTGTA
5389974 TTT
1 TTT
5389977 AATAATATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.15, C:0.00, G:0.09, T:0.76
Consensus pattern (10 bp):
TTTTTTTGTA
Found at i:5389956 original size:11 final size:11
Alignment explanation
Indices: 5389908--5389976 Score: 52
Period size: 11 Copynumber: 6.2 Consensus size: 11
5389898 TGTTTTTTCC
*
5389908 TTTTCTTGTAT
1 TTTTTTTGTAT
5389919 TTTTTGTT-TAT
1 TTTTT-TTGTAT
* *
5389930 CTTTTTTCTTTCT
1 -TTTTTT-TGTAT
5389943 TTTTTTTGTA-
1 TTTTTTTGTAT
5389953 TTTTTTTGTAT
1 TTTTTTTGTAT
* *
5389964 TATTATTGTAT
1 TTTTTTTGTAT
5389975 TT
1 TT
5389977 AATAATATTA
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
10 10 0.22
11 20 0.43
12 14 0.30
13 2 0.04
ACGTcount: A:0.10, C:0.06, G:0.07, T:0.77
Consensus pattern (11 bp):
TTTTTTTGTAT
Found at i:5395639 original size:49 final size:47
Alignment explanation
Indices: 5395576--5395720 Score: 129
Period size: 49 Copynumber: 3.1 Consensus size: 47
5395566 TCCAAACTTT
* * * *
5395576 ATAAATAATCAAACCCACTTGTTTAATGATGTTGTTATAACTTTGTACC
1 ATAAACAAT-AAACCAACTTGCTTAATGAT-TTGTCATAACTTTGTACC
* * *
5395625 ATAAACAATAAAACCTACTTGCTCAATGATTCTGTCACAAC-TT-T---
1 ATAAACAAT-AAACCAACTTGCTTAATGATT-TGTCATAACTTTGTACC
* *
5395669 ATAAACAATAAACCAACTTGCTTAATGATCATGTCATGACTTTGTACC
1 ATAAACAATAAACCAACTTGCTTAATGAT-TTGTCATAACTTTGTACC
5395717 ATAA
1 ATAA
5395721 TAGAGTGTTG
Statistics
Matches: 77, Mismatches: 12, Indels: 15
0.74 0.12 0.14
Matches are distributed among these distances:
43 25 0.32
44 11 0.14
45 1 0.01
47 1 0.01
48 7 0.09
49 32 0.42
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (47 bp):
ATAAACAATAAACCAACTTGCTTAATGATTTGTCATAACTTTGTACC
Found at i:5400294 original size:658 final size:658
Alignment explanation
Indices: 5399038--5400355 Score: 2447
Period size: 658 Copynumber: 2.0 Consensus size: 658
5399028 TCAGTTTAGA
5399038 ATATGAACTTGTTGGCATTGAAGTGTAAAGTTACAAAACTTATATTTTGTTGCCATTGGAAAGGA
1 ATATGAACTTGTTGGCATTGAAGTGTAAAGTTACAAAACTTATATTTTGTTGCCATTGGAAAGGA
*
5399103 AAATATGAACTTTATATGTATGGTATTTGCTAGCCAAGTGAAATATAACAAACTTGTTACAAAGT
66 AAATATGAACTTTATAAGTATGGTATTTGCTAGCCAAGTGAAATATAACAAACTTGTTACAAAGT
*
5399168 ACTATTTACTTATTGTATTTTGTTATGTTTTATATGGAATTTCATAATTTGTATTCTATATGTAA
131 ACTATTTACTTATTGTATTTTGTTATGTTTTATATGAAATTTCATAATTTGTATTCTATATGTAA
*
5399233 AAGAACATGCCAAGATCTATCCATTGATTATGCTATAAACACAAATTTAGGACTCAAATTAAAAC
196 AAGAACATGCCAAGATCTATCCATTGATTATGCTATAAACACAAATTTAAGACTCAAATTAAAAC
5399298 CTTATTTTTTAGGATGCTTCTATTTTCATAAACTAAAATAATTTAATTATAACAAATGTGTATTA
261 CTTATTTTTTAGGATGCTTCTATTTTCATAAACTAAAATAATTTAATTATAACAAATGTGTATTA
* *
5399363 ATACACAAACATAATCATATTACACAAATCTGTAAGTTTAGAATCATATCCAGCTTGCAATCGAC
326 ATACACAAACATAATCATATTACACAAATCTGTAAATTTAGAATCATATCCAGCTTGCAATCAAC
* * *
5399428 AGCATACATATTACAAGCCAATCACCCTAAACACTAGACTAAACTTTGTTCATTTTCTTTTCAAC
391 ACCATACATATTACAAGCCAATCACCCTAAACAATAGACTAAACTTTATTCATTTTCTTTTCAAC
*
5399493 ATCAACATAAAAATAACAACAAACAAATATATTGCAATCCACTTCCAACTTCTATTCTTGCGATT
456 ATCAACATAAAAATAACAACAAACAAACATATTGCAATCCACTTCCAACTTCTATTCTTGCGATT
* *
5399558 ACAATTGTTGTTGTTTGCATTTGCTTAAATGACTTGATTTTGGTGTTCCTTTCTTCACATCTTTC
521 ACAATTGTTGTTGTTTGCATTTGCTTAAATGACTTGATTTTGGTGTTCCTTTCTTCACATCCTCC
5399623 TTGATAAACCTAAAATGACTATCTTGCTGTATTCATCTATTAGAGGATTACACCATTGAAAAAAC
586 TTGATAAACCTAAAATGACTATCTTGCTGTATTCATCTATTAGAGGATTACACCATTGAAAAAAC
5399688 CTACATGC
651 CTACATGC
5399696 ATATGAACTTGTTGGCATTGAAGTGTAAAGTTACAAAACTTATATTTTGTTGCCATTGGAAAGGA
1 ATATGAACTTGTTGGCATTGAAGTGTAAAGTTACAAAACTTATATTTTGTTGCCATTGGAAAGGA
5399761 AAATATGAACTTTATAAGTATGGTATTTGCTAGCCAAGTGAAATATAACAAACTTGTTACAAAGT
66 AAATATGAACTTTATAAGTATGGTATTTGCTAGCCAAGTGAAATATAACAAACTTGTTACAAAGT
*
5399826 ACTATTTACTTATTGTATTTTGTTATGTTTTATATGAAATTTCATAATTTGTGTTCTATATGTAA
131 ACTATTTACTTATTGTATTTTGTTATGTTTTATATGAAATTTCATAATTTGTATTCTATATGTAA
*
5399891 AAGAACATGCCAAGATCTATCCATTGATTATGCTATGAACACAAATTTAAGACTCAAATTAAAAC
196 AAGAACATGCCAAGATCTATCCATTGATTATGCTATAAACACAAATTTAAGACTCAAATTAAAAC
5399956 CTTATTTTTTAGGATGCTTCTATTTTCATAAACTAAAATAATTTAATTATAACAAATGTGTATTA
261 CTTATTTTTTAGGATGCTTCTATTTTCATAAACTAAAATAATTTAATTATAACAAATGTGTATTA
* *
5400021 ATACACAAACATAATCATATTACATAAATTTGTAAATTTAGAATCATATCCAGCTTGCAATCAAC
326 ATACACAAACATAATCATATTACACAAATCTGTAAATTTAGAATCATATCCAGCTTGCAATCAAC
* *
5400086 ACCATATATATTACAAGCCAATTACCCTAAACAATAGACTAAACTTTATTCATTTTCTTTTCAAC
391 ACCATACATATTACAAGCCAATCACCCTAAACAATAGACTAAACTTTATTCATTTTCTTTTCAAC
* *
5400151 ATCAACATAAAAATAACAACAAACAAACATATTGCAATCCACTTCCAGCTTTTATTCTTGCGATT
456 ATCAACATAAAAATAACAACAAACAAACATATTGCAATCCACTTCCAACTTCTATTCTTGCGATT
*
5400216 ACAATTGTTGTTGTTTGCATTTGCTTAAATGACTTGATTTTGGTGTTCCTTTCTTCGCATCCTCC
521 ACAATTGTTGTTGTTTGCATTTGCTTAAATGACTTGATTTTGGTGTTCCTTTCTTCACATCCTCC
*
5400281 TTGATAAACCTAAAATGACTATCTTGTTGTATTCATCTATTAGAGGATTACACCATTGAAAAAAC
586 TTGATAAACCTAAAATGACTATCTTGCTGTATTCATCTATTAGAGGATTACACCATTGAAAAAAC
5400346 CTACATGC
651 CTACATGC
5400354 AT
1 AT
5400356 CAAGTTGTTG
Statistics
Matches: 639, Mismatches: 21, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
658 639 1.00
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (658 bp):
ATATGAACTTGTTGGCATTGAAGTGTAAAGTTACAAAACTTATATTTTGTTGCCATTGGAAAGGA
AAATATGAACTTTATAAGTATGGTATTTGCTAGCCAAGTGAAATATAACAAACTTGTTACAAAGT
ACTATTTACTTATTGTATTTTGTTATGTTTTATATGAAATTTCATAATTTGTATTCTATATGTAA
AAGAACATGCCAAGATCTATCCATTGATTATGCTATAAACACAAATTTAAGACTCAAATTAAAAC
CTTATTTTTTAGGATGCTTCTATTTTCATAAACTAAAATAATTTAATTATAACAAATGTGTATTA
ATACACAAACATAATCATATTACACAAATCTGTAAATTTAGAATCATATCCAGCTTGCAATCAAC
ACCATACATATTACAAGCCAATCACCCTAAACAATAGACTAAACTTTATTCATTTTCTTTTCAAC
ATCAACATAAAAATAACAACAAACAAACATATTGCAATCCACTTCCAACTTCTATTCTTGCGATT
ACAATTGTTGTTGTTTGCATTTGCTTAAATGACTTGATTTTGGTGTTCCTTTCTTCACATCCTCC
TTGATAAACCTAAAATGACTATCTTGCTGTATTCATCTATTAGAGGATTACACCATTGAAAAAAC
CTACATGC
Found at i:5401352 original size:25 final size:25
Alignment explanation
Indices: 5401308--5401356 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
5401298 TTAATTATCC
5401308 AATGATGAAATTTATAAAAATTTCA
1 AATGATGAAATTTATAAAAATTTCA
*
5401333 AATGAT-AAATTTTTATAAAATTTC
1 AATGATGAAATTTATA-AAAATTTC
5401357 TACGTGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.41
Consensus pattern (25 bp):
AATGATGAAATTTATAAAAATTTCA
Found at i:5401466 original size:13 final size:13
Alignment explanation
Indices: 5401448--5401473 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5401438 TTTAAAATAA
5401448 AAAAAATAAAAAT
1 AAAAAATAAAAAT
5401461 AAAAAATAAAAAT
1 AAAAAATAAAAAT
5401474 TTGGGTTGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:5402523 original size:21 final size:20
Alignment explanation
Indices: 5402499--5402567 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
5402489 CTTCCATATG
5402499 TCAACCCCTAACTCCTCTCTT
1 TCAACCCCTAACTCCTC-CTT
* ** *
5402520 TCAACACCTAGGTTCTCCCTT
1 TCAACCCCTAACTCCT-CCTT
* *
5402541 TCAACCCTTAACTCCTCATT
1 TCAACCCCTAACTCCTCCTT
5402561 TCAACCC
1 TCAACCC
5402568 TCAATTCCCT
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
20 10 0.27
21 26 0.70
22 1 0.03
ACGTcount: A:0.22, C:0.43, G:0.03, T:0.32
Consensus pattern (20 bp):
TCAACCCCTAACTCCTCCTT
Found at i:5402583 original size:21 final size:20
Alignment explanation
Indices: 5402539--5402585 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
5402529 AGGTTCTCCC
*
5402539 TTTCAACCCTTAACTCCTCA
1 TTTCAACCCTCAACTCCTCA
* *
5402559 TTTCAACCCTCAATTCCCTCT
1 TTTCAACCCTCAACT-CCTCA
5402580 TTTCAA
1 TTTCAA
5402586 ACTCCCTTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.23, C:0.38, G:0.00, T:0.38
Consensus pattern (20 bp):
TTTCAACCCTCAACTCCTCA
Found at i:5402649 original size:21 final size:20
Alignment explanation
Indices: 5402625--5402674 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 20
5402615 AAAATGAATC
*
5402625 TCCTCTTTTGATCTCCTTTGT
1 TCCTCTTTTGATCCCCTTT-T
5402646 TCCTTCTTTTGATCCCCTTTT
1 TCC-TCTTTTGATCCCCTTTT
*
5402667 TTCTCTTT
1 TCCTCTTT
5402675 AAGATCCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 5 0.19
21 6 0.23
22 15 0.58
ACGTcount: A:0.04, C:0.30, G:0.06, T:0.60
Consensus pattern (20 bp):
TCCTCTTTTGATCCCCTTTT
Found at i:5402984 original size:13 final size:13
Alignment explanation
Indices: 5402966--5402992 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5402956 CACATGTGCT
5402966 ACTTACTCTTTAC
1 ACTTACTCTTTAC
5402979 ACTTACTCTTTAC
1 ACTTACTCTTTAC
5402992 A
1 A
5402993 AAATTTATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.30, G:0.00, T:0.44
Consensus pattern (13 bp):
ACTTACTCTTTAC
Found at i:5403146 original size:21 final size:21
Alignment explanation
Indices: 5403108--5403149 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5403098 CAAAAAAACT
*
5403108 AAAATTTTAGTAACTAAATTA
1 AAAATTTTAATAACTAAATTA
**
5403129 AAAATTTTAATAGTTAAATTA
1 AAAATTTTAATAACTAAATTA
5403150 CTATTTTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.40
Consensus pattern (21 bp):
AAAATTTTAATAACTAAATTA
Found at i:5403508 original size:2 final size:2
Alignment explanation
Indices: 5403501--5403528 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5403491 AACAAATGCA
5403501 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5403529 GTACATTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5405489 original size:72 final size:72
Alignment explanation
Indices: 5405403--5405546 Score: 279
Period size: 72 Copynumber: 2.0 Consensus size: 72
5405393 ATAGACGAGA
*
5405403 ATGAAAAGATCAATTTCCTTCTTTTTGGAGTTCATATAAATTGGTCAGACATATGAATAGTTCAC
1 ATGAAAAGATCAATTTCCTTCATTTTGGAGTTCATATAAATTGGTCAGACATATGAATAGTTCAC
5405468 ATTATGC
66 ATTATGC
5405475 ATGAAAAGATCAATTTCCTTCATTTTGGAGTTCATATAAATTGGTCAGACATATGAATAGTTCAC
1 ATGAAAAGATCAATTTCCTTCATTTTGGAGTTCATATAAATTGGTCAGACATATGAATAGTTCAC
5405540 ATTATGC
66 ATTATGC
5405547 TTTTGCAAGT
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (72 bp):
ATGAAAAGATCAATTTCCTTCATTTTGGAGTTCATATAAATTGGTCAGACATATGAATAGTTCAC
ATTATGC
Found at i:5406556 original size:85 final size:85
Alignment explanation
Indices: 5406382--5406624 Score: 300
Period size: 81 Copynumber: 2.9 Consensus size: 85
5406372 ACACACATAT
* * *
5406382 ACACACACACACACGTGCGTATATACATATATTTATATCTTCACCTTATT-TTTT-ATGGAATTT
1 ACACACACACAAAC-AGCGTATATACATATATTTATATCTTCACTTTATTGTTTTGATGGAATTT
* *
5406445 ACTGATTGGGCACCATCAAAAC
65 ATTGATTGGGCAACATC-AAAC
*
5406467 ACACACACACAAACACGCGTGTATACATATATTTATATCTTCACTTTATTGTTTTGATGGAATTT
1 ACACACACACAAACA-GCGTATATACATATATTTATATCTTCACTTTATTGTTTTGATGGAATTT
**
5406532 ATTGATTGGGCAACAT-TGA-
65 ATTGATTGGGCAACATCAAAC
* * * *
5406551 A-ACACATACAAACA-CATATATAAATATATTTATATCTTCACTTTATTGTTTTGATAGAATTTA
1 ACACACACACAAACAGCGTATATACATATATTTATATCTTCACTTTATTGTTTTGATGGAATTTA
*
5406614 TTGATCGGGCA
66 TTGATTGGGCA
5406625 CCGTTGAAGG
Statistics
Matches: 141, Mismatches: 14, Indels: 10
0.85 0.08 0.06
Matches are distributed among these distances:
81 55 0.39
83 12 0.09
84 1 0.01
85 46 0.33
86 4 0.03
87 23 0.16
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.37
Consensus pattern (85 bp):
ACACACACACAAACAGCGTATATACATATATTTATATCTTCACTTTATTGTTTTGATGGAATTTA
TTGATTGGGCAACATCAAAC
Found at i:5406927 original size:208 final size:209
Alignment explanation
Indices: 5406563--5406962 Score: 676
Period size: 208 Copynumber: 1.9 Consensus size: 209
5406553 CACATACAAA
* * *
5406563 CACATATATAAATATATTTATATCTTCACTTTATTGTTTTGATAGAATTTATTGATCGGGCACCG
1 CACATATATAAAGATATTTATATCTTCACTTTATTGTTTTGATAGAATTTATTGATCGGACACCA
*
5406628 TTGAAGGCCCTAAGATGATGTTGTGAACATAAGATTGTCCATCTAATCTCCTCTTGGAGACTGAA
66 CTGAAGGCCCTAAGATGATGTTGTGAACATAAGATTGTCCATCTAATCTCCTCTTGGAGACTGAA
*
5406693 ATTATGATTCTGTAATTGAATAACAGAAATTATGTTCTTATTGT-GTTGTCTGTTTAAATGCTCT
131 ATTATGATTCTGTAATTGAATAACAGAAATTATGTTCTTACTGTAGTTGTCTGTTTAAATGCTCT
5406757 GATTCACACACTAG
196 GATTCACACACTAG
* * *
5406771 CACATATATACAGATATTTATATCTTCACTTTATTGTTTTGATGGAATTTATTGATTGGACACCA
1 CACATATATAAAGATATTTATATCTTCACTTTATTGTTTTGATAGAATTTATTGATCGGACACCA
* * *
5406836 CTGAAGGCCTTAAGATGATGTTGTGAACATAAGATTGTCCATCTCATCTCCTCTTGGAGATTGAA
66 CTGAAGGCCCTAAGATGATGTTGTGAACATAAGATTGTCCATCTAATCTCCTCTTGGAGACTGAA
* *
5406901 ATTATGATTCTGTAATTGAGTAACAGAAATTATGTTCTTACTGTATTTGTCTGTTTAAATGC
131 ATTATGATTCTGTAATTGAATAACAGAAATTATGTTCTTACTGTAGTTGTCTGTTTAAATGC
5406963 AATGCTCTGA
Statistics
Matches: 178, Mismatches: 13, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
208 162 0.91
209 16 0.09
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (209 bp):
CACATATATAAAGATATTTATATCTTCACTTTATTGTTTTGATAGAATTTATTGATCGGACACCA
CTGAAGGCCCTAAGATGATGTTGTGAACATAAGATTGTCCATCTAATCTCCTCTTGGAGACTGAA
ATTATGATTCTGTAATTGAATAACAGAAATTATGTTCTTACTGTAGTTGTCTGTTTAAATGCTCT
GATTCACACACTAG
Found at i:5409647 original size:16 final size:16
Alignment explanation
Indices: 5409626--5409657 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5409616 TTATTCTTCC
5409626 ACAAAAAAAAAAAAGA
1 ACAAAAAAAAAAAAGA
*
5409642 ACAAAAAGAAAAAAGA
1 ACAAAAAAAAAAAAGA
5409658 CATTAGTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.84, C:0.06, G:0.09, T:0.00
Consensus pattern (16 bp):
ACAAAAAAAAAAAAGA
Found at i:5413360 original size:17 final size:16
Alignment explanation
Indices: 5413344--5413382 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
5413334 TTAAAGATAT
5413344 TATATTAAAATTAATA
1 TATATTAAAATTAATA
* *
5413360 TATAATAAAATTTATAA
1 TATATTAAAATTAAT-A
5413377 TATATT
1 TATATT
5413383 TGACATTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TATATTAAAATTAATA
Found at i:5414150 original size:22 final size:21
Alignment explanation
Indices: 5414100--5414156 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
5414090 AAAAAGGCAT
*
5414100 AAAAACAA-TAAAAACAAAAAG
1 AAAAA-AATTAAAAACAAAAAC
* *
5414121 GAATAAATTGAAAAACAAAAAC
1 AAAAAAATT-AAAAACAAAAAC
5414143 AAAAAAATTAAAAA
1 AAAAAAATTAAAAA
5414157 TAAAGGAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 2 0.07
21 9 0.31
22 18 0.62
ACGTcount: A:0.77, C:0.07, G:0.05, T:0.11
Consensus pattern (21 bp):
AAAAAAATTAAAAACAAAAAC
Found at i:5414377 original size:20 final size:21
Alignment explanation
Indices: 5414332--5414382 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 21
5414322 CGACATTCAA
*
5414332 ATTAAATTTAAATATTAATAT
1 ATTAAATTTAAATATTAAAAT
*
5414353 CTTAAA-TTAAAGTA-TAAAAT
1 ATTAAATTTAAA-TATTAAAAT
*
5414373 ATTAACTTTA
1 ATTAAATTTA
5414383 TTAATATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (21 bp):
ATTAAATTTAAATATTAAAAT
Found at i:5414998 original size:11 final size:10
Alignment explanation
Indices: 5414973--5414997 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5414963 TATCTAAATT
5414973 AAAAATTAAC
1 AAAAATTAAC
5414983 AAAAATTAAC
1 AAAAATTAAC
5414993 AAAAA
1 AAAAA
5414998 AGAAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (10 bp):
AAAAATTAAC
Found at i:5415173 original size:16 final size:16
Alignment explanation
Indices: 5415120--5415191 Score: 64
Period size: 16 Copynumber: 4.8 Consensus size: 16
5415110 ATTATGTATA
5415120 AATATAAT-ATAT-TT
1 AATATAATAATATATT
* *
5415134 ATTA-AATTAAGATATT
1 AATATAA-TAATATATT
*
5415150 AA-ATAATAATTTATT
1 AATATAATAATATATT
*
5415165 AATATAATAATATATA
1 AATATAATAATATATT
5415181 AATATAA-AATA
1 AATATAATAATA
5415192 AAATAAATAA
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
13 2 0.04
14 4 0.09
15 17 0.37
16 23 0.50
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (16 bp):
AATATAATAATATATT
Found at i:5415175 original size:8 final size:8
Alignment explanation
Indices: 5415152--5415224 Score: 52
Period size: 8 Copynumber: 10.0 Consensus size: 8
5415142 AAGATATTAA
5415152 ATAATAAT
1 ATAATAAT
* *
5415160 TTATTAAT
1 ATAATAAT
5415168 ATAATAAT
1 ATAATAAT
5415176 AT-ATAA-
1 ATAATAAT
*
5415182 AT-ATAAA
1 ATAATAAT
5415189 ATAA-AAT
1 ATAATAAT
5415196 A-AATAAT
1 ATAATAAT
*
5415203 -TAAAAAT
1 ATAATAAT
*
5415210 ATAATTAT
1 ATAATAAT
5415218 AT-ATAAT
1 ATAATAAT
5415225 TGTGACAAGA
Statistics
Matches: 51, Mismatches: 9, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
6 8 0.16
7 21 0.41
8 22 0.43
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATAATAAT
Found at i:5421927 original size:94 final size:94
Alignment explanation
Indices: 5421765--5421950 Score: 329
Period size: 94 Copynumber: 2.0 Consensus size: 94
5421755 GAAAAACTCT
* *
5421765 CCCTTAAACAATGCTTGGCAAAACTCCTCATTAATTAATGCATCCTAATCCAACACAACTCAATA
1 CCCTTAAACAATGCATGGCAAAACTCCTCATTAATTAATGCATCCTAATCCAACACAACTCAACA
5421830 AACATATGTTACTCAAATATATGAACTGC
66 AACATATGTTACTCAAATATATGAACTGC
5421859 CCCTTAAACAATGCATGGCAAAACTCC-CTATTAATTAATGCATCCTAATCCAACACAACTCAAC
1 CCCTTAAACAATGCATGGCAAAACTCCTC-ATTAATTAATGCATCCTAATCCAACACAACTCAAC
*
5421923 AAACATATGTTAGTCAAATATATGAACT
65 AAACATATGTTACTCAAATATATGAACT
5421951 AAGCACAATC
Statistics
Matches: 88, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
93 1 0.01
94 87 0.99
ACGTcount: A:0.40, C:0.25, G:0.08, T:0.27
Consensus pattern (94 bp):
CCCTTAAACAATGCATGGCAAAACTCCTCATTAATTAATGCATCCTAATCCAACACAACTCAACA
AACATATGTTACTCAAATATATGAACTGC
Found at i:5428749 original size:13 final size:13
Alignment explanation
Indices: 5428731--5428778 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
5428721 ACATATATAT
5428731 AAATTAAAAATAA
1 AAATTAAAAATAA
**
5428744 AAATTATAGATGTAA
1 AAATTA-A-AAATAA
*
5428759 AAATTCAAAATAA
1 AAATTAAAAATAA
5428772 AAATTAA
1 AAATTAA
5428779 GTTTAATAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
13 16 0.59
14 2 0.07
15 9 0.33
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (13 bp):
AAATTAAAAATAA
Found at i:5429384 original size:38 final size:39
Alignment explanation
Indices: 5429304--5429384 Score: 91
Period size: 38 Copynumber: 2.2 Consensus size: 39
5429294 ATATTTGTTC
*
5429304 AAAAT-AAAAATTAAGATATTTATTTTACAATTTAATAT
1 AAAATAAAAAATTAAGATATTTATTTTACAATTCAATAT
*
5429342 -AAATAAAAAATT-ATATAATTTATTTTA-AA-TCACATAT
1 AAAATAAAAAATTAAGAT-ATTTATTTTACAATTCA-ATAT
5429379 AAAATA
1 AAAATA
5429385 CTTTTGTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
36 2 0.05
37 13 0.35
38 22 0.59
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.40
Consensus pattern (39 bp):
AAAATAAAAAATTAAGATATTTATTTTACAATTCAATAT
Found at i:5433352 original size:10 final size:10
Alignment explanation
Indices: 5433337--5433374 Score: 76
Period size: 10 Copynumber: 3.8 Consensus size: 10
5433327 GGTTGAGTTC
5433337 CTTTCCATTA
1 CTTTCCATTA
5433347 CTTTCCATTA
1 CTTTCCATTA
5433357 CTTTCCATTA
1 CTTTCCATTA
5433367 CTTTCCAT
1 CTTTCCAT
5433375 CAGTTATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.18, C:0.32, G:0.00, T:0.50
Consensus pattern (10 bp):
CTTTCCATTA
Found at i:5434641 original size:21 final size:19
Alignment explanation
Indices: 5434607--5434646 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
5434597 AAAAATTTAA
*
5434607 ATTAATTGAAATATATTTTT
1 ATTAATTAAAATAT-TTTTT
5434627 ATTAATATAAAATATTTTTT
1 ATTAAT-TAAAATATTTTTT
5434647 GGTTAAGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (19 bp):
ATTAATTAAAATATTTTTT
Found at i:5434912 original size:18 final size:18
Alignment explanation
Indices: 5434889--5434923 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5434879 GTTTTTAAGG
*
5434889 CATCTATAACTATTTGTT
1 CATCTATAACTAATTGTT
5434907 CATCTATAACTAATTGT
1 CATCTATAACTAATTGT
5434924 ATTTGGTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.06, T:0.46
Consensus pattern (18 bp):
CATCTATAACTAATTGTT
Found at i:5435600 original size:16 final size:16
Alignment explanation
Indices: 5435579--5435609 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5435569 TTATTTATTA
*
5435579 AAAATATTTTTAATAT
1 AAAATAATTTTAATAT
5435595 AAAATAATTTTAATA
1 AAAATAATTTTAATA
5435610 ATTTTTAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAAATAATTTTAATAT
Found at i:5435636 original size:26 final size:26
Alignment explanation
Indices: 5435559--5435636 Score: 74
Period size: 26 Copynumber: 3.1 Consensus size: 26
5435549 CCATTTTTGT
*
5435559 TAATTTTTAATTATTTATTAA--AAA
1 TAATTTTTAATTATTTATTAATTTAA
** *
5435583 T-ATTTTTAA-TATAAAATAATTTTAA
1 TAATTTTTAATTATTTATTAA-TTTAA
*
5435608 TAATTTTTAATTATTTATTAATTTCA
1 TAATTTTTAATTATTTATTAATTTAA
5435634 TAA
1 TAA
5435637 ATGACAAATA
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
22 7 0.17
23 8 0.20
24 1 0.02
25 3 0.07
26 15 0.37
27 7 0.17
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (26 bp):
TAATTTTTAATTATTTATTAATTTAA
Found at i:5435746 original size:17 final size:19
Alignment explanation
Indices: 5435704--5435746 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
5435694 CAAAACTTAA
* *
5435704 TTATATATTTTTATTAGTT
1 TTATATATTTTTATAAATT
5435723 TTATATATTTTT-TAAATT
1 TTATATATTTTTATAAATT
5435741 TT-TATA
1 TTATATA
5435747 AAATAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 4 0.18
18 6 0.27
19 12 0.55
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
TTATATATTTTTATAAATT
Found at i:5435802 original size:22 final size:23
Alignment explanation
Indices: 5435765--5435820 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
5435755 ATAATTATTT
* *
5435765 TATATATAAATTTATTTAAAT-A
1 TATATAAAAATTTATTAAAATAA
5435787 TAT-TAAAAATCTTATTAAAATAA
1 TATATAAAAAT-TTATTAAAATAA
5435810 TATATAAAAAT
1 TATATAAAAAT
5435821 AAAAAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 6 0.21
22 12 0.41
23 4 0.14
24 7 0.24
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
TATATAAAAATTTATTAAAATAA
Found at i:5439439 original size:40 final size:40
Alignment explanation
Indices: 5439390--5439470 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
5439380 GAAGTATGTG
* *
5439390 GAGCATGCTCTTTCCACACTTTGGTAGTATGTTCAGTATT
1 GAGCATGCTCTTTCCACACTTTGGTAGCATGTTCAGCATT
5439430 GAGCATGCTCTTTCCACACTTTGGTAGCATGTTCAGCATT
1 GAGCATGCTCTTTCCACACTTTGGTAGCATGTTCAGCATT
5439470 G
1 G
5439471 GAGTTAATCA
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:0.20, C:0.22, G:0.21, T:0.37
Consensus pattern (40 bp):
GAGCATGCTCTTTCCACACTTTGGTAGCATGTTCAGCATT
Found at i:5441271 original size:143 final size:143
Alignment explanation
Indices: 5441086--5441359 Score: 345
Period size: 143 Copynumber: 1.9 Consensus size: 143
5441076 TTAGGGATAT
* * ** * * *
5441086 TTTCATAATTTAGCCTTTTCAAGCTCAAATTTTTATGAAACTTTTTCAGATCTCACTTTTAAAAT
1 TTTCATAATTTAACCTTTTCAAGCTCAAATTTTCACAAAACTTTTT-AGATCTCAATTTCAAAAC
* * *
5441151 ATTTGATGATT-TTTTGTGCATTTAAAATCACAACAATACC-CCAAAATGTATGAAATTACCAAA
65 ATTTCATGATTGTTGT-TGCATTTAAAATCACAACAATACCTCCAAAATGTATAAAATTACCAAA
5441214 ATATCTTTAAAAGTA
129 ATATCTTTAAAAGTA
* * * *
5441229 TTTCATAATTTAATCTTTTCAAGCTCGAATTTTCACAAAACTTTTTAGATCTTAATTTCATAACA
1 TTTCATAATTTAACCTTTTCAAGCTCAAATTTTCACAAAACTTTTTAGATCTCAATTTCAAAACA
* * * * *
5441294 TTTCATGATTGTTGTTGCATTTGAAATCATAGCAATACCTCGAAAATGTATAAAATTACTAAAAT
66 TTTCATGATTGTTGTTGCATTTAAAATCACAACAATACCTCCAAAATGTATAAAATTACCAAAAT
5441359 A
131 A
5441360 CCCTTACAGA
Statistics
Matches: 110, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
142 44 0.40
143 66 0.60
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.40
Consensus pattern (143 bp):
TTTCATAATTTAACCTTTTCAAGCTCAAATTTTCACAAAACTTTTTAGATCTCAATTTCAAAACA
TTTCATGATTGTTGTTGCATTTAAAATCACAACAATACCTCCAAAATGTATAAAATTACCAAAAT
ATCTTTAAAAGTA
Found at i:5441374 original size:143 final size:142
Alignment explanation
Indices: 5441057--5441374 Score: 343
Period size: 143 Copynumber: 2.2 Consensus size: 142
5441047 GAGAGATATG
* * * *
5441057 AAATTACCAAAATACCCATTTAGGGATATTTTCATAATTTAGCCTTTTCAAGCTCAAATTTTTAT
1 AAATTACCAAAATACCC--TTA-AGATA-TTTCATAATTTAACCTTTTCAAGCTCAAATTTTCAC
* * * * * *
5441122 GAAACTTTTTCAGATCTCACTTTTAAAATATTTGATGATTTTTTGTGCATTTAAAATCACAACAA
62 AAAACTTTTTCAGATCTCAATTTCAAAACATTTCATGATTTTGTGTGCATTTAAAATCACAACAA
*
5441187 TACCCCAAAATGTATG
127 TACCCCAAAATGTATA
* * * * *
5441203 AAATTACCAAAATATCTTTAAAAGTATTTCATAATTTAATCTTTTCAAGCTCGAATTTTCACAAA
1 AAATTACCAAAATACCCTTAAGA-TATTTCATAATTTAACCTTTTCAAGCTCAAATTTTCACAAA
* * * * *
5441268 ACTTTTT-AGATCTTAATTTCATAACATTTCATGATTGTTGT-TGCATTTGAAATCATAGCAATA
65 ACTTTTTCAGATCTCAATTTCAAAACATTTCATGATT-TTGTGTGCATTTAAAATCACAACAATA
*
5441331 CCTCGAAAATGTATA
129 CC-CCAAAATGTATA
*
5441346 AAATTACTAAAATACCCTTACAGATATTT
1 AAATTACCAAAATACCCTTA-AGATATTT
5441375 TTATTTGGTT
Statistics
Matches: 142, Mismatches: 26, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
142 44 0.31
143 76 0.54
144 7 0.05
146 15 0.11
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (142 bp):
AAATTACCAAAATACCCTTAAGATATTTCATAATTTAACCTTTTCAAGCTCAAATTTTCACAAAA
CTTTTTCAGATCTCAATTTCAAAACATTTCATGATTTTGTGTGCATTTAAAATCACAACAATACC
CCAAAATGTATA
Found at i:5444612 original size:57 final size:56
Alignment explanation
Indices: 5444544--5444664 Score: 133
Period size: 56 Copynumber: 2.2 Consensus size: 56
5444534 CGAAAGAAAT
* *
5444544 AATA-TTTTATTTAAGTAAAATTTGATACTTACAATTTTTTCCT-TAACTA-TTTTTT-A
1 AATATTTTTATTTAA-TAAAAATTGATA-TTACAA-TTTTTCCTCCAA-TATTTTTTTGA
* **
5444600 AATATTTTTATTTTATAAAAATTGATATTTGAATTTTTCCTCCAATATTTTTTTGA
1 AATATTTTTATTTAATAAAAATTGATATTACAATTTTTCCTCCAATATTTTTTTGA
5444656 AATATTTTT
1 AATATTTTT
5444665 TTATTTAGAA
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
54 10 0.18
55 12 0.21
56 25 0.45
57 9 0.16
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.55
Consensus pattern (56 bp):
AATATTTTTATTTAATAAAAATTGATATTACAATTTTTCCTCCAATATTTTTTTGA
Found at i:5444881 original size:91 final size:91
Alignment explanation
Indices: 5444755--5445017 Score: 350
Period size: 91 Copynumber: 2.9 Consensus size: 91
5444745 TTTGATTTTT
* * * * * *
5444755 TTTTTTGTTTAAAGGAAAATCAATACTTCAACTTTTCTTCAAGAGAAACACTTTTT-AAATTTTA
1 TTTTTTATTTTAAGAAAAATTAATACTTCAACTTTTCTTC-A-AGAAATATTTTTTAAAATTTTA
5444819 TTTTTAAGGAAAATTATTTTTTT-GAGA
64 TTTTTAAGGAAAATTATTTTTTTGGAGA
* *
5444846 TTTTTTATTTTAAGAAAAATTAATACTTTAACTTTTCTTTAAGAAATATTTTTTGAAAATTTTAT
1 TTTTTTATTTTAAGAAAAATTAATACTTCAACTTTTCTTCAAGAAATATTTTTT-AAAATTTTAT
* * *
5444911 TTTTGAGAAAAATTATTTTTTTGGAGT
65 TTTTAAGGAAAATTATTTTTTTGGAGA
*
5444938 TTTTTTATTTTAAGAAAAATTGATACTTCAACTTTTCTTCAAGAAATATTTTTTAAAAATTTTTA
1 TTTTTTATTTTAAGAAAAATTAATACTTCAACTTTTCTTCAAGAAATATTTTTT-AAAA-TTTTA
*
5445003 TTTTTAAAGAAAATT
64 TTTTTAAGGAAAATT
5445018 GATACTTCAA
Statistics
Matches: 150, Mismatches: 18, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
89 11 0.07
90 1 0.01
91 63 0.42
92 58 0.39
93 17 0.11
ACGTcount: A:0.36, C:0.06, G:0.08, T:0.50
Consensus pattern (91 bp):
TTTTTTATTTTAAGAAAAATTAATACTTCAACTTTTCTTCAAGAAATATTTTTTAAAATTTTATT
TTTAAGGAAAATTATTTTTTTGGAGA
Done.