Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold11
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: 5230303
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 140504 characters in sequence are not A, C, G, or T
File 20 of 29
Found at i:3006716 original size:6 final size:6
Alignment explanation
Indices: 3006705--3006772 Score: 58
Period size: 6 Copynumber: 12.3 Consensus size: 6
3006695 TTGATTTAAA
* * * *
3006705 TAAATT TAAATT TAAA-- TAAATT TAAACT TAAA-- TAAAAT CAAATA
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
3006749 TAAA-- TAAATT TAAATT TAAATT TA
1 TAAATT TAAATT TAAATT TAAATT TA
3006773 TGGTCAATTA
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
4 12 0.24
6 39 0.76
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (6 bp):
TAAATT
Found at i:3007659 original size:18 final size:19
Alignment explanation
Indices: 3007638--3007677 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
3007628 TATATTAAAA
3007638 TATTAA-AAATTATATTTT
1 TATTAATAAATTATATTTT
**
3007656 TATTAATATTTTATATTTT
1 TATTAATAAATTATATTTT
3007675 TAT
1 TAT
3007678 AATTAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTAATAAATTATATTTT
Found at i:3008557 original size:17 final size:18
Alignment explanation
Indices: 3008535--3008568 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3008525 ATATAATCAT
3008535 ATTTAAAATTT-TAATAC
1 ATTTAAAATTTATAATAC
*
3008552 ATTTAATATTTATAATA
1 ATTTAAAATTTATAATA
3008569 TTATTTAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTTAAAATTTATAATAC
Found at i:3008837 original size:2 final size:2
Alignment explanation
Indices: 3008830--3008859 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3008820 AAAGTTAGTA
3008830 AT 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 AT
3008860 GTAAAACAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3011786 original size:20 final size:19
Alignment explanation
Indices: 3011741--3011783 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
3011731 ACTTTGTTAA
3011741 TAAA-TAATATTAATAATT
1 TAAATTAATATTAATAATT
*
3011759 TTAATTAATATTTAATAA-T
1 TAAATTAATA-TTAATAATT
3011778 TAAATT
1 TAAATT
3011784 TAAATATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 3 0.14
19 11 0.52
20 7 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TAAATTAATATTAATAATT
Found at i:3013036 original size:2 final size:2
Alignment explanation
Indices: 3013031--3013062 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3013021 TGAAATCAGG
3013031 AT AT 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 AT AT
3013063 CCTCAAGTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3013874 original size:98 final size:98
Alignment explanation
Indices: 3013658--3013849 Score: 377
Period size: 98 Copynumber: 2.0 Consensus size: 98
3013648 ACTAACAAAG
3013658 TATGAATAAACATATATTTTGCACCAACCTACCATTATGAATGACTACTAATTGCTCCTTAACCC
1 TATGAATAAACATATATTTTGCACCAACCTACCATTATGAATGACTACTAATTGCTCCTTAACCC
3013723 CAACTCTCTTCTTTTTCTTGTTATATTTTCAGA
66 CAACTCTCTTCTTTTTCTTGTTATATTTTCAGA
3013756 TATGAATAAACATATATTTTGCACCAACCTACCATTATGAATGACTACTAATTGCTCCTTAACCC
1 TATGAATAAACATATATTTTGCACCAACCTACCATTATGAATGACTACTAATTGCTCCTTAACCC
3013821 CAACTCTCTTCTTTTTCTTGTTAT-TTTTC
66 CAACTCTCTTCTTTTTCTTGTTATATTTTC
3013850 CTCTTCTATT
Statistics
Matches: 94, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
97 5 0.05
98 89 0.95
ACGTcount: A:0.29, C:0.24, G:0.07, T:0.41
Consensus pattern (98 bp):
TATGAATAAACATATATTTTGCACCAACCTACCATTATGAATGACTACTAATTGCTCCTTAACCC
CAACTCTCTTCTTTTTCTTGTTATATTTTCAGA
Found at i:3026704 original size:49 final size:49
Alignment explanation
Indices: 3026601--3026788 Score: 185
Period size: 49 Copynumber: 4.0 Consensus size: 49
3026591 TCTCTGATTG
* * * *
3026601 GAATAACTTTTTACTAAGTTATATGCGGTTTCCCCCGCATTTATGTATA
1 GAATAACTTTTTACTAAGTTACATGTGGTTTCCCCCGCATTCATATATA
* *
3026650 TAATAACTTTTTACTAAGTTACATGTGGTTTCCCCCGCATTCATATGTA
1 GAATAACTTTTTACTAAGTTACATGTGGTTTCCCCCGCATTCATATATA
** *
3026699 GAATAAC----T--T-AGTGCCATGTGGTTT-CCCTGCATTCATATATA
1 GAATAACTTTTTACTAAGTTACATGTGGTTTCCCCCGCATTCATATATA
* * ** **
3026740 GAATTACTTTTTACTTAGTCCCATGTGGTTTCCCTTGCATTCATATATA
1 GAATAACTTTTTACTAAGTTACATGTGGTTTCCCCCGCATTCATATATA
3026789 TATATGTATA
Statistics
Matches: 117, Mismatches: 14, Indels: 16
0.80 0.10 0.11
Matches are distributed among these distances:
41 21 0.18
42 13 0.11
43 1 0.01
45 2 0.02
47 1 0.01
48 14 0.12
49 65 0.56
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.41
Consensus pattern (49 bp):
GAATAACTTTTTACTAAGTTACATGTGGTTTCCCCCGCATTCATATATA
Found at i:3026742 original size:41 final size:43
Alignment explanation
Indices: 3026671--3026788 Score: 132
Period size: 48 Copynumber: 2.6 Consensus size: 43
3026661 TACTAAGTTA
* * *
3026671 CATGTGGTTTCCCCCGCATTCATATGTAGAA-TA-ACTTAGTGC
1 CATGTGGTTT-CCCTGCATTCATATATAGAATTATACTTAGTCC
3026713 CATGTGGTTTCCCTGCATTCATATATAGAATTACTTTTTACTTAGTCC
1 CATGTGGTTTCCCTGCATTCATATATAGAATTA-----TACTTAGTCC
3026761 CATGTGGTTTCCCTTGCATTCATATATA
1 CATGTGGTTTCCC-TGCATTCATATATA
3026789 TATATGTATA
Statistics
Matches: 65, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
41 18 0.28
42 12 0.18
48 21 0.32
49 14 0.22
ACGTcount: A:0.23, C:0.22, G:0.15, T:0.40
Consensus pattern (43 bp):
CATGTGGTTTCCCTGCATTCATATATAGAATTATACTTAGTCC
Found at i:3028077 original size:34 final size:34
Alignment explanation
Indices: 3028034--3028104 Score: 115
Period size: 34 Copynumber: 2.1 Consensus size: 34
3028024 GTTATTTCAG
* * *
3028034 TGTATATTTGGTATGTGTGGCATACTTATCAATT
1 TGTATATTTGGTAAGTGTGACATACATATCAATT
3028068 TGTATATTTGGTAAGTGTGACATACATATCAATT
1 TGTATATTTGGTAAGTGTGACATACATATCAATT
3028102 TGT
1 TGT
3028105 TGTGAAGTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.27, C:0.08, G:0.20, T:0.45
Consensus pattern (34 bp):
TGTATATTTGGTAAGTGTGACATACATATCAATT
Found at i:3031497 original size:25 final size:25
Alignment explanation
Indices: 3031463--3031512 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
3031453 GTCTTTACTT
3031463 ACCCTACAGTCTCTACTATGAATTC
1 ACCCTACAGTCTCTACTATGAATTC
3031488 ACCCTACAGTCTCTACTATGAATTC
1 ACCCTACAGTCTCTACTATGAATTC
3031513 TTCTCATTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.32, G:0.08, T:0.32
Consensus pattern (25 bp):
ACCCTACAGTCTCTACTATGAATTC
Found at i:3032423 original size:50 final size:50
Alignment explanation
Indices: 3032364--3032555 Score: 285
Period size: 50 Copynumber: 3.8 Consensus size: 50
3032354 ACTTAAAGTT
* * *
3032364 AACAATTACGGTCACCTCTTTCTATTATCAAAGGTTGGTGAAGAATAGTC
1 AACAATTACGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAATAGTC
*
3032414 AACAATTACGGTTACCTCTCTCGATTGTCAAAGGTTGGTGAAGAATAGTC
1 AACAATTACGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAATAGTC
* * * * *
3032464 AACAATTACGGTCACTTCTTTCGATTGTCAAAGGTTGGTGAAAAAAAATC
1 AACAATTACGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAATAGTC
* *
3032514 AATAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAA
1 AACAATTACGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAA
3032556 AGATAATCAA
Statistics
Matches: 128, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 128 1.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (50 bp):
AACAATTACGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAATAGTC
Found at i:3037020 original size:50 final size:51
Alignment explanation
Indices: 3036939--3037100 Score: 161
Period size: 50 Copynumber: 3.2 Consensus size: 51
3036929 AGTTGTTTAA
* * * *
3036939 AGTCAACAATTACGGCTACCTC-TCTCTATTGTCAAAAGTTGGTGAACAAT
1 AGTCAACAATTACGACCACATCTTCTCGATTGTCAAAAGTTGGTGAACAAT
* * ** *
3036989 AGTTAACAATTAC-AGTCACAT-TTCTCGATTGTCAATGGTTGGTGAAGAAT
1 AGTCAACAATTACGA-CCACATCTTCTCGATTGTCAAAAGTTGGTGAACAAT
* * *
3037039 AGTCAACAATTACGACCACCTCTT-TCGATTGTCAAAAGTTGGTAAAGAAT
1 AGTCAACAATTACGACCACATCTTCTCGATTGTCAAAAGTTGGTGAACAAT
* *
3037089 AATCAGCAATTA
1 AGTCAACAATTA
3037101 GTTTTGGTGA
Statistics
Matches: 91, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
50 88 0.97
51 3 0.03
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.30
Consensus pattern (51 bp):
AGTCAACAATTACGACCACATCTTCTCGATTGTCAAAAGTTGGTGAACAAT
Found at i:3040600 original size:25 final size:24
Alignment explanation
Indices: 3040552--3040600 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
3040542 TGGTTCAAAG
**
3040552 TTATTATTTTTTAAATATTTATAT
1 TTATTATTTTTTAAATATGAATAT
3040576 TTATTATATTTTTAAATATGAATAT
1 TTATTAT-TTTTTAAATATGAATAT
3040601 GAATACGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
TTATTATTTTTTAAATATGAATAT
Found at i:3040857 original size:2 final size:2
Alignment explanation
Indices: 3040850--3040877 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3040840 TAAGCCAGAT
3040850 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3040878 AAGAGAGAAA
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):
TA
Found at i:3041507 original size:3 final size:3
Alignment explanation
Indices: 3041499--3041529 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
3041489 CAAAACCTAG
3041499 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
3041530 CTCCTCATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:3043848 original size:18 final size:19
Alignment explanation
Indices: 3043827--3043870 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
3043817 CGAATTTTAA
* *
3043827 TATTTATAATTTAT-TTTT
1 TATTTATAAATTATAATTT
*
3043845 TATTTTTAAATTATAATTT
1 TATTTATAAATTATAATTT
3043864 TATTTAT
1 TATTTAT
3043871 TAAAACAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TATTTATAAATTATAATTT
Found at i:3043864 original size:20 final size:19
Alignment explanation
Indices: 3043819--3043874 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 19
3043809 TTAATATACG
* *
3043819 AATTTTAATATTTATAATTT
1 AATTTTTATTTTTA-AATTT
*
3043839 ATTTTTTATTTTTAAATTAT
1 AATTTTTATTTTTAAATT-T
3043859 AA-TTTTATTTATTAAA
1 AATTTTTATTT-TTAAA
3043875 ACAAATTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
AATTTTTATTTTTAAATTT
Found at i:3044398 original size:2 final size:2
Alignment explanation
Indices: 3044391--3044415 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3044381 ACCTCCGCAT
3044391 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3044416 GTAATTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3047763 original size:24 final size:24
Alignment explanation
Indices: 3047736--3047781 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
3047726 AAGTGAATAT
3047736 ATATAAT-TAAATAAAATATTAAAA
1 ATATAATATAAATAAAAT-TTAAAA
*
3047760 ATATAATATAATTAAAATTTAA
1 ATATAATATAAATAAAATTTAA
3047782 TTTTATATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (24 bp):
ATATAATATAAATAAAATTTAAAA
Found at i:3047776 original size:16 final size:16
Alignment explanation
Indices: 3047731--3047782 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 16
3047721 TATCAAAGTG
3047731 AATAT-ATATAATT-A
1 AATATAATATAATTAA
3047745 AATA-AA-AT-ATTAAA
1 AATATAATATAATT-AA
3047759 AATATAATATAATTAA
1 AATATAATATAATTAA
*
3047775 AATTTAAT
1 AATATAAT
3047783 TTTATATAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
12 3 0.10
13 2 0.06
14 10 0.32
15 2 0.06
16 11 0.35
17 3 0.10
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AATATAATATAATTAA
Found at i:3047811 original size:18 final size:18
Alignment explanation
Indices: 3047770--3047814 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
3047760 ATATAATATA
*
3047770 ATTAAAA-TTT-AATTTT
1 ATTAAAATTTTAAAATTT
*
3047786 A-TATAATTTTAAAATTT
1 ATTAAAATTTTAAAATTT
3047803 ATTAAAATTTTA
1 ATTAAAATTTTA
3047815 TTATTATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 4 0.17
16 4 0.17
17 6 0.26
18 9 0.39
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTAAAATTTTAAAATTT
Found at i:3048271 original size:13 final size:14
Alignment explanation
Indices: 3048243--3048275 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
3048233 TTACCAATTC
*
3048243 AATTAATTTAATAT
1 AATTAATTTAAGAT
3048257 AATTAA-TTAAGAT
1 AATTAATTTAAGAT
3048270 AATTAA
1 AATTAA
3048276 ATAATATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (14 bp):
AATTAATTTAAGAT
Found at i:3048956 original size:2 final size:2
Alignment explanation
Indices: 3048949--3048982 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3048939 CATTCTCTTC
*
3048949 AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3048983 GTATCACAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3049404 original size:2 final size:2
Alignment explanation
Indices: 3049369--3049395 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3049359 ATTATTGAAT
3049369 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3049396 TGTTATATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3053347 original size:2 final size:2
Alignment explanation
Indices: 3053340--3053376 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3053330 TGACTATGGA
3053340 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3053377 AGTTTAGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3053689 original size:2 final size:2
Alignment explanation
Indices: 3053682--3053716 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3053672 GGAATTTGAA
3053682 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 A
3053717 CATACACGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3055349 original size:18 final size:17
Alignment explanation
Indices: 3055313--3055351 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
3055303 ATTTTTTTAA
3055313 TTTTAACTTATATATTT
1 TTTTAACTTATATATTT
*
3055330 TTTTAACTGTA-ATAATT
1 TTTTAACT-TATATATTT
3055347 TTTTA
1 TTTTA
3055352 TTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 18 0.90
18 2 0.10
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.62
Consensus pattern (17 bp):
TTTTAACTTATATATTT
Found at i:3057189 original size:2 final size:2
Alignment explanation
Indices: 3057178--3057211 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3057168 TATTCCATTA
3057178 AT AT -T 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 A
3057212 AGCTGTTCAC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3057406 original size:16 final size:16
Alignment explanation
Indices: 3057385--3057415 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3057375 GATCATTTTA
*
3057385 AATATGATATAAAAAT
1 AATATGACATAAAAAT
3057401 AATATGACATAAAAA
1 AATATGACATAAAAA
3057416 ATTATTATAA
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:0.65, C:0.03, G:0.06, T:0.26
Consensus pattern (16 bp):
AATATGACATAAAAAT
Found at i:3065505 original size:4 final size:4
Alignment explanation
Indices: 3065496--3065536 Score: 59
Period size: 4 Copynumber: 10.5 Consensus size: 4
3065486 GTGCAGAATC
3065496 TGTA TGTA TGTA TGTA TGTA TGTA TGTA T-T- TGTA TTGTA TG
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA -TGTA TG
3065537 ATCAGAGCTG
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 1 0.03
3 2 0.06
4 27 0.79
5 4 0.12
ACGTcount: A:0.22, C:0.00, G:0.24, T:0.54
Consensus pattern (4 bp):
TGTA
Found at i:3066731 original size:2 final size:2
Alignment explanation
Indices: 3066726--3066773 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
3066716 TGTGTGTGTG
3066726 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
3066768 TG TA TA
1 TA TA TA
3066774 GGTTTCAATA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3067214 original size:2 final size:2
Alignment explanation
Indices: 3067207--3067265 Score: 86
Period size: 2 Copynumber: 30.5 Consensus size: 2
3067197 CAATTAAGGT
* *
3067207 TA TA TA TA T- TT TA TA TA TA TA TA TA TT TA TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3067247 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
3067266 TCAAGGATGG
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
1 2 0.04
2 50 0.96
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:3067696 original size:2 final size:2
Alignment explanation
Indices: 3067691--3067731 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
3067681 AAAGACTAGC
*
3067691 AG AG AG AG AG AG AG AG AG AG AA AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3067732 AAGATCATGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3069011 original size:4 final size:4
Alignment explanation
Indices: 3069002--3069032 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
3068992 GATGTTTCAC
3069002 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTC
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTC
3069033 AACAACTCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
TTCT
Found at i:3070635 original size:35 final size:36
Alignment explanation
Indices: 3070572--3070667 Score: 108
Period size: 35 Copynumber: 2.7 Consensus size: 36
3070562 TTAAAGTAAA
* * *
3070572 TTTTATATTTTTATTGT-ATTAAATAAGTT-TTTTAT
1 TTTTA-ATTTTTATTTTAAATAAATAAGTTGATTTAT
3070607 TATTTAATTTTTATTTTAAATAAA-AAGTTGATTTAT
1 T-TTTAATTTTTATTTTAAATAAATAAGTTGATTTAT
*
3070643 TTTTAATGTTTATTTTAATATAAAT
1 TTTTAATTTTTATTTTAA-ATAAAT
3070668 TAAAATTTGA
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
35 32 0.62
36 20 0.38
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.60
Consensus pattern (36 bp):
TTTTAATTTTTATTTTAAATAAATAAGTTGATTTAT
Found at i:3070705 original size:30 final size:30
Alignment explanation
Indices: 3070664--3070734 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
3070654 ATTTTAATAT
*
3070664 AAATT-AAAATTTGAT-TCAATATAAATTAA
1 AAATTAAAAATTT-ATCTCAATACAAATTAA
**
3070693 AAATTAAAAATTTATCTGGATACAAATTAA
1 AAATTAAAAATTTATCTCAATACAAATTAA
3070723 AAATTAAAAATT
1 AAATTAAAAATT
3070735 AATTTAATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 7 0.19
30 30 0.81
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.35
Consensus pattern (30 bp):
AAATTAAAAATTTATCTCAATACAAATTAA
Found at i:3071227 original size:22 final size:22
Alignment explanation
Indices: 3071202--3071248 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
3071192 ATTAAAATTA
*
3071202 AAAATATAATGTAAAAGT-TTTT
1 AAAATAT-ATGTAAAAATATTTT
*
3071224 AAAATATATTTAAAAATATTTT
1 AAAATATATGTAAAAATATTTT
3071246 AAA
1 AAA
3071249 CATGTGATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.40
Consensus pattern (22 bp):
AAAATATATGTAAAAATATTTT
Found at i:3071770 original size:22 final size:22
Alignment explanation
Indices: 3071713--3071783 Score: 81
Period size: 24 Copynumber: 3.1 Consensus size: 22
3071703 CATATATTTG
*
3071713 ATATTATTTTATTTAATTTTTATA
1 ATATT-TTTTATTTAAATTTTA-A
3071737 A-ATTTATATTATTTAAATTTTAA
1 ATATTT-T-TTATTTAAATTTTAA
*
3071760 ATATTTTTTATTTAAATATTAA
1 ATATTTTTTATTTAAATTTTAA
3071782 AT
1 AT
3071784 TTATTAATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
22 17 0.40
23 7 0.17
24 18 0.43
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
ATATTTTTTATTTAAATTTTAA
Found at i:3071795 original size:22 final size:21
Alignment explanation
Indices: 3071720--3071840 Score: 68
Period size: 22 Copynumber: 5.5 Consensus size: 21
3071710 TTGATATTAT
3071720 TTTATTTAATTTT--TA-TAAA
1 TTTA-TTAATTTTAATATTAAA
* * *
3071739 TTTATATTATTTAAATTTTAAA
1 TTTAT-TAATTTTAATATTAAA
* * *
3071761 TATTTTTTATTTAAATATTAAA
1 T-TTATTAATTTTAATATTAAA
*
3071783 TTTATTAATTTTAATATAAAA
1 TTTATTAATTTTAATATTAAA
* *
3071804 ATTAATAGATATTTAATATTTAAA
1 TTTATTA-AT-TTTAATA-TTAAA
3071828 TTTACTTTAATTT
1 TTTA--TTAATTT
3071841 AATTTTATAA
Statistics
Matches: 78, Mismatches: 14, Indels: 15
0.73 0.13 0.14
Matches are distributed among these distances:
18 1 0.01
19 9 0.12
21 22 0.28
22 23 0.29
23 10 0.13
24 9 0.12
25 2 0.03
26 2 0.03
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (21 bp):
TTTATTAATTTTAATATTAAA
Found at i:3071828 original size:23 final size:22
Alignment explanation
Indices: 3071768--3071829 Score: 56
Period size: 23 Copynumber: 2.8 Consensus size: 22
3071758 AAATATTTTT
*
3071768 TATTTAA-ATATTAAATTTATTAA
1 TATTTAATAT-TTAAA-TTAATAA
**
3071791 T-TTTAATATAAAAATTAATAGA
1 TATTTAATATTTAAATTAATA-A
3071813 TATTTAATATTTAAATT
1 TATTTAATATTTAAATT
3071830 TACTTTAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
21 5 0.16
22 10 0.32
23 16 0.52
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
TATTTAATATTTAAATTAATAA
Found at i:3073942 original size:13 final size:13
Alignment explanation
Indices: 3073912--3073936 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3073902 AATTAAAAAT
3073912 ATATAAAATATTA
1 ATATAAAATATTA
3073925 ATATAAAATATT
1 ATATAAAATATT
3073937 TTTATATTTT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATAAAATATTA
Found at i:3073991 original size:19 final size:19
Alignment explanation
Indices: 3073956--3073997 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
3073946 TAATATATTT
3073956 TAAAAAATAAACTTTTTACA
1 TAAAAAATAAAC-TTTTACA
*
3073976 TAAAAAATCAAA-TTTTAGA
1 TAAAAAAT-AAACTTTTACA
3073995 TAA
1 TAA
3073998 TTATTTTTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 9 0.45
20 8 0.40
21 3 0.15
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.33
Consensus pattern (19 bp):
TAAAAAATAAACTTTTACA
Found at i:3074931 original size:12 final size:13
Alignment explanation
Indices: 3074900--3074936 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
3074890 CTGTGATCTA
3074900 AAATTTTT-TTAT
1 AAATTTTTGTTAT
3074912 AAAGTTTTTGTT-T
1 AAA-TTTTTGTTAT
3074925 AAATTTTTGTTA
1 AAATTTTTGTTA
3074937 AGTCTATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 11 0.50
13 9 0.41
14 2 0.09
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
AAATTTTTGTTAT
Found at i:3077485 original size:2 final size:2
Alignment explanation
Indices: 3077473--3077505 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3077463 TAGAAACCTT
*
3077473 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3077506 CACTCTCACA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3085191 original size:22 final size:21
Alignment explanation
Indices: 3085166--3085227 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 21
3085156 TTATAATATT
3085166 TTTTATTAAATATAATAATAAA
1 TTTTATTAAATATAATAA-AAA
*
3085188 TTTTAATAAAT-TAA-AAAAA
1 TTTTATTAAATATAATAAAAA
*
3085207 TAATTTATTTAATATAATAAA
1 T--TTTATTAAATATAATAAA
3085228 TTTAAAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
19 4 0.12
20 2 0.06
21 11 0.33
22 13 0.39
23 3 0.09
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TTTTATTAAATATAATAAAAA
Found at i:3086192 original size:22 final size:22
Alignment explanation
Indices: 3086141--3086198 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 22
3086131 TTTAATTATT
*
3086141 AATTAATTAATAAAATATTTTTAA
1 AATTAATT-ATAAAATA-TTATAA
3086165 AA-TAATTATAAAATA-TATAA
1 AATTAATTATAAAATATTATAA
3086185 ATATTAA-TATAAAA
1 A-ATTAATTATAAAA
3086199 ATAAATTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 5 0.16
21 8 0.26
22 11 0.35
23 5 0.16
24 2 0.06
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AATTAATTATAAAATATTATAA
Found at i:3087849 original size:3 final size:3
Alignment explanation
Indices: 3087834--3087867 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
3087824 ACAACCTGCC
3087834 CTA CTA C-A GCTA CTA CTA CTA CTA CTA CTA CTA C
1 CTA CTA CTA -CTA CTA CTA CTA CTA CTA CTA CTA C
3087868 CAGACCCGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 1 0.03
3 27 0.93
4 1 0.03
ACGTcount: A:0.32, C:0.35, G:0.03, T:0.29
Consensus pattern (3 bp):
CTA
Found at i:3088120 original size:2 final size:2
Alignment explanation
Indices: 3088115--3088147 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
3088105 ATCTCTTTCC
3088115 TA TA TA TA TA TA TA TA T- TA -A TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3088148 TATGTAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3088139 original size:16 final size:16
Alignment explanation
Indices: 3088118--3088149 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3088108 TCTTTCCTAT
3088118 ATATATATATATATTA
1 ATATATATATATATTA
3088134 ATATATATATATATTA
1 ATATATATATATATTA
3088150 TGTAAAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATATATATATATATTA
Found at i:3088610 original size:8 final size:8
Alignment explanation
Indices: 3088595--3088630 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
3088585 GGTTCAGAAC
3088595 AGAAAAAA
1 AGAAAAAA
*
3088603 AAAAAAAA
1 AGAAAAAA
3088611 AGAAAAAA
1 AGAAAAAA
3088619 AGAAAAAGA
1 AGAAAAA-A
3088628 AGA
1 AGA
3088631 TCGAAAGGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
8 21 0.84
9 4 0.16
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (8 bp):
AGAAAAAA
Found at i:3088618 original size:14 final size:14
Alignment explanation
Indices: 3088599--3088628 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3088589 CAGAACAGAA
3088599 AAAAAAAAAAAAAG
1 AAAAAAAAAAAAAG
*
3088613 AAAAAAAGAAAAAG
1 AAAAAAAAAAAAAG
3088627 AA
1 AA
3088629 GATCGAAAGG
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:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAAG
Found at i:3088619 original size:17 final size:17
Alignment explanation
Indices: 3088597--3088630 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3088587 TTCAGAACAG
3088597 AAAAAAAAAAAAAAAGA
1 AAAAAAAAAAAAAAAGA
* *
3088614 AAAAAAGAAAAAGAAGA
1 AAAAAAAAAAAAAAAGA
3088631 TCGAAAGGGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAAAAAGA
Found at i:3089001 original size:2 final size:2
Alignment explanation
Indices: 3088994--3089027 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3088984 AATTAACGAG
3088994 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3089028 GAGAGAGAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3089032 original size:2 final size:2
Alignment explanation
Indices: 3089027--3089056 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3089017 ATATATATAT
3089027 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3089057 CAACAGATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3089654 original size:41 final size:41
Alignment explanation
Indices: 3089575--3089655 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
3089565 TTTACAGTAA
* * *
3089575 ACTTTGTCATGTATACAAACTAAAAATATTAACAAGTTTAT
1 ACTTTATCATGTAAACAAACTAAAAATATCAACAAGTTTAT
3089616 ACTTTATCATGTAAACAAACTAAAAATATCAACAAGTTTA
1 ACTTTATCATGTAAACAAACTAAAAATATCAACAAGTTTA
3089656 ATCAGCCATG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.47, C:0.14, G:0.06, T:0.33
Consensus pattern (41 bp):
ACTTTATCATGTAAACAAACTAAAAATATCAACAAGTTTAT
Found at i:3095575 original size:24 final size:25
Alignment explanation
Indices: 3095548--3095633 Score: 81
Period size: 24 Copynumber: 3.6 Consensus size: 25
3095538 ATTATCATTA
3095548 ATAAAATA-AAATAATAATTTATAT
1 ATAAAATATAAATAATAATTTATAT
* *
3095572 ATAAAATATAAA-AATAA-ATATAA
1 ATAAAATATAAATAATAATTTATAT
* * ** *
3095595 ATATAATA-GAATAATGGTTCATAT
1 ATAAAATATAAATAATAATTTATAT
3095619 ATAAAATATAAATAA
1 ATAAAATATAAATAA
3095634 ATTATATAAC
Statistics
Matches: 47, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
22 2 0.04
23 14 0.30
24 23 0.49
25 8 0.17
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (25 bp):
ATAAAATATAAATAATAATTTATAT
Found at i:3099030 original size:18 final size:18
Alignment explanation
Indices: 3099021--3099105 Score: 161
Period size: 18 Copynumber: 4.7 Consensus size: 18
3099011 ACATATATAT
*
3099021 ATATATATACATACATAC
1 ATATATATATATACATAC
3099039 ATATATATATATACATAC
1 ATATATATATATACATAC
3099057 ATATATATATATACATAC
1 ATATATATATATACATAC
3099075 ATATATATATATACATAC
1 ATATATATATATACATAC
3099093 ATATATATATATA
1 ATATATATATATA
3099106 TTACACACTC
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
18 66 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.39
Consensus pattern (18 bp):
ATATATATATATACATAC
Found at i:3099030 original size:22 final size:22
Alignment explanation
Indices: 3099004--3099106 Score: 151
Period size: 22 Copynumber: 4.9 Consensus size: 22
3098994 TTTCAATGTG
3099004 TATACATACATATATATATATA
1 TATACATACATATATATATATA
*
3099026 TATACATACATACATATATATA
1 TATACATACATATATATATATA
3099048 TATACATAC----ATATATATA
1 TATACATACATATATATATATA
3099066 TATACATACATATATATATATA
1 TATACATACATATATATATATA
* *
3099088 CATACATATATATATATAT
1 TATACATACATATATATAT
3099107 TACACACTCA
Statistics
Matches: 74, Mismatches: 3, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
18 18 0.24
22 56 0.76
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.40
Consensus pattern (22 bp):
TATACATACATATATATATATA
Found at i:3099100 original size:4 final size:4
Alignment explanation
Indices: 3099013--3099106 Score: 107
Period size: 4 Copynumber: 23.5 Consensus size: 4
3099003 GTATACATAC
* * * * *
3099013 ATAT ATAT ATAT ATAT ACAT ACAT ACAT ATAT ATAT ATAC ATAC ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * *
3099061 ATAT ATAT ACAT ACAT ATAT ATAT ATAC ATAC ATAT ATAT ATAT AT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT AT
3099107 TACACACTCA
Statistics
Matches: 82, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 82 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (4 bp):
ATAT
Found at i:3099191 original size:46 final size:45
Alignment explanation
Indices: 3099122--3099219 Score: 153
Period size: 46 Copynumber: 2.2 Consensus size: 45
3099112 ACTCATGTCT
*
3099122 ACTAGATACGTAAGTGTTACAAGCGACAAATGT-GTTGCTACTATA
1 ACTAGATACGTAAGTGTTACAAGCGACAAAT-TAGTTACTACTATA
3099167 ACTAGATACGTAAAGTGTTACAAGCGACAAATTAGTTACTACTATA
1 ACTAGATACGT-AAGTGTTACAAGCGACAAATTAGTTACTACTATA
*
3099213 ATTAGAT
1 ACTAGAT
3099220 TGTTTGGAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
45 12 0.24
46 37 0.76
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (45 bp):
ACTAGATACGTAAGTGTTACAAGCGACAAATTAGTTACTACTATA
Found at i:3102621 original size:193 final size:193
Alignment explanation
Indices: 3102292--3102682 Score: 782
Period size: 193 Copynumber: 2.0 Consensus size: 193
3102282 CCCGTACTCA
3102292 TGTTTAAATATGTGTCGAACAAAAGTACTTTAGAGAAAATGAAGAGTACAGGTACCATAGGATAT
1 TGTTTAAATATGTGTCGAACAAAAGTACTTTAGAGAAAATGAAGAGTACAGGTACCATAGGATAT
3102357 TAGCAGAAATTTGGTTTGCTTTTTGTCAATTTTGTTCTGTGTTATTTTTGTCAGTTTTGTAGATG
66 TAGCAGAAATTTGGTTTGCTTTTTGTCAATTTTGTTCTGTGTTATTTTTGTCAGTTTTGTAGATG
3102422 CAATCAGTGAGGACAGATTGCTTATTTACATTCATCTAGCTAATTAAAGCACAATTTCTTCTC
131 CAATCAGTGAGGACAGATTGCTTATTTACATTCATCTAGCTAATTAAAGCACAATTTCTTCTC
3102485 TGTTTAAATATGTGTCGAACAAAAGTACTTTAGAGAAAATGAAGAGTACAGGTACCATAGGATAT
1 TGTTTAAATATGTGTCGAACAAAAGTACTTTAGAGAAAATGAAGAGTACAGGTACCATAGGATAT
3102550 TAGCAGAAATTTGGTTTGCTTTTTGTCAATTTTGTTCTGTGTTATTTTTGTCAGTTTTGTAGATG
66 TAGCAGAAATTTGGTTTGCTTTTTGTCAATTTTGTTCTGTGTTATTTTTGTCAGTTTTGTAGATG
3102615 CAATCAGTGAGGACAGATTGCTTATTTACATTCATCTAGCTAATTAAAGCACAATTTCTTCTC
131 CAATCAGTGAGGACAGATTGCTTATTTACATTCATCTAGCTAATTAAAGCACAATTTCTTCTC
3102678 TGTTT
1 TGTTT
3102683 CCAGAGTGTC
Statistics
Matches: 198, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
193 198 1.00
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (193 bp):
TGTTTAAATATGTGTCGAACAAAAGTACTTTAGAGAAAATGAAGAGTACAGGTACCATAGGATAT
TAGCAGAAATTTGGTTTGCTTTTTGTCAATTTTGTTCTGTGTTATTTTTGTCAGTTTTGTAGATG
CAATCAGTGAGGACAGATTGCTTATTTACATTCATCTAGCTAATTAAAGCACAATTTCTTCTC
Found at i:3102938 original size:2 final size:2
Alignment explanation
Indices: 3102931--3102983 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
3102921 GATGTGTAAT
3102931 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3102973 TA TA TA TA TA T
1 TA TA TA TA TA T
3102984 TTGGGCATGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3105755 original size:7 final size:7
Alignment explanation
Indices: 3105743--3105770 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
3105733 TAGCAACTCT
3105743 TATGGTA
1 TATGGTA
3105750 TATGGTA
1 TATGGTA
3105757 TATGGTA
1 TATGGTA
3105764 TATGGTA
1 TATGGTA
3105771 ACATTCAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.43
Consensus pattern (7 bp):
TATGGTA
Found at i:3109068 original size:52 final size:52
Alignment explanation
Indices: 3108988--3109231 Score: 379
Period size: 52 Copynumber: 4.7 Consensus size: 52
3108978 AAAAGTTACT
* *
3108988 TGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAGATTTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
* *
3109040 TGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCT
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
*
3109092 TGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
3109144 TGCATGTATCGATACATTTTAA-AATGTATCGATACATCTGGGCAAA-TTGCC
1 TGCATGTATCGATACA-TTTAATAATGTATCGATACATCTGGGCAAATTTGCC
*
3109195 TGCATGTATCGATACA--AAGATCAATGTATCGATACAT
1 TGCATGTATCGATACATTTA-AT-AATGTATCGATACAT
3109232 TTGAGTAATG
Statistics
Matches: 179, Mismatches: 9, Indels: 9
0.91 0.05 0.05
Matches are distributed among these distances:
48 1 0.01
49 1 0.01
51 36 0.20
52 136 0.76
53 5 0.03
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (52 bp):
TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
Found at i:3109308 original size:33 final size:33
Alignment explanation
Indices: 3109271--3109337 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3109261 AGTAGCTTAA
3109271 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
3109304 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
3109337 A
1 A
3109338 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:3109311 original size:13 final size:13
Alignment explanation
Indices: 3109293--3109317 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3109283 CAAAAAAATA
3109293 TGTATCGATACAT
1 TGTATCGATACAT
3109306 TGTATCGATACA
1 TGTATCGATACA
3109318 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3111949 original size:23 final size:21
Alignment explanation
Indices: 3111917--3111978 Score: 63
Period size: 23 Copynumber: 2.9 Consensus size: 21
3111907 AGATCATTCA
*
3111917 TTTAA-ATTAAATAAATTTAT
1 TTTAATATTAAATAAATATAT
*
3111937 TTATAAATATTAAATGAATATAT
1 TT-T-AATATTAAATAAATATAT
*
3111960 TTTAATATGTAATTAAATA
1 TTTAATAT-TAAATAAATA
3111979 CGTTTCTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 2 0.06
21 6 0.18
22 11 0.32
23 15 0.44
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (21 bp):
TTTAATATTAAATAAATATAT
Found at i:3121074 original size:17 final size:16
Alignment explanation
Indices: 3121052--3121094 Score: 63
Period size: 17 Copynumber: 2.8 Consensus size: 16
3121042 ACTCGAACAA
3121052 AATATTTAATATAATAT
1 AATATTTAATATAA-AT
3121069 AATATTTAATA-AAAT
1 AATATTTAATATAAAT
3121084 -ATATTTAATAT
1 AATATTTAATAT
3121095 TTTAAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 10 0.40
15 2 0.08
16 2 0.08
17 11 0.44
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATATTTAATATAAAT
Found at i:3121100 original size:19 final size:19
Alignment explanation
Indices: 3121068--3121116 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
3121058 TAATATAATA
3121068 TAATATTTAATAAAATATATT
1 TAATATTT--TAAAATATATT
*
3121089 TAATATTTTAAAATATTTT
1 TAATATTTTAAAATATATT
*
3121108 TTATATTTT
1 TAATATTTT
3121117 TTTAAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 18 0.69
21 8 0.31
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TAATATTTTAAAATATATT
Found at i:3127564 original size:3 final size:3
Alignment explanation
Indices: 3127556--3127589 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
3127546 AGCCCAGAAA
3127556 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
3127590 AGGGGAAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:3133171 original size:2 final size:2
Alignment explanation
Indices: 3133164--3133191 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3133154 GGATTTTCTT
3133164 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3133192 ATATATAGAA
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:3135353 original size:3 final size:3
Alignment explanation
Indices: 3135345--3135370 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3135335 AATGAAGCTT
3135345 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
3135371 GATTTTACGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3137404 original size:7 final size:7
Alignment explanation
Indices: 3137392--3137459 Score: 52
Period size: 7 Copynumber: 9.6 Consensus size: 7
3137382 AACGTAAAAA
3137392 TTTATAT
1 TTTATAT
3137399 TTTATAT
1 TTTATAT
3137406 AATTTATAT
1 --TTTATAT
3137415 TTATATAAT
1 TT-TAT-AT
3137424 TTT-T-T
1 TTTATAT
* *
3137429 ATTAAAT
1 TTTATAT
3137436 TTTATAT
1 TTTATAT
3137443 TTTA-AT
1 TTTATAT
*
3137449 CTTATAT
1 TTTATAT
3137456 TTTA
1 TTTA
3137460 GTAATATAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 14
0.71 0.09 0.21
Matches are distributed among these distances:
5 3 0.06
6 5 0.10
7 25 0.52
8 4 0.08
9 11 0.23
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (7 bp):
TTTATAT
Found at i:3137419 original size:15 final size:16
Alignment explanation
Indices: 3137390--3137425 Score: 65
Period size: 15 Copynumber: 2.3 Consensus size: 16
3137380 TTAACGTAAA
3137390 AATTTATATTTTATAT
1 AATTTATATTTTATAT
3137406 AATTTATA-TTTATAT
1 AATTTATATTTTATAT
3137421 AATTT
1 AATTT
3137426 TTTATTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
AATTTATATTTTATAT
Found at i:3137937 original size:11 final size:10
Alignment explanation
Indices: 3137921--3137947 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
3137911 GTTTAATTTC
3137921 TTTTTTTTTG
1 TTTTTTTTTG
3137931 TTTTTTTTTG
1 TTTTTTTTTG
3137941 TTTTTTT
1 TTTTTTT
3137948 GTTTTGCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:3139700 original size:12 final size:12
Alignment explanation
Indices: 3139683--3139708 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3139673 ATCGAAGTAT
3139683 AACAAACTTGAA
1 AACAAACTTGAA
3139695 AACAAACTTGAA
1 AACAAACTTGAA
3139707 AA
1 AA
3139709 AAAAATTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.15, G:0.08, T:0.15
Consensus pattern (12 bp):
AACAAACTTGAA
Found at i:3140180 original size:25 final size:25
Alignment explanation
Indices: 3140151--3140200 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
3140141 TTAAAAAATT
*
3140151 TATTAAAATA-TTAATTTTATAATAA
1 TATTAAAATATTTAAATTTA-AATAA
*
3140176 TATTAATATATTTAAATTTAAATAA
1 TATTAAAATATTTAAATTTAAATAA
3140201 ATAATTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
TATTAAAATATTTAAATTTAAATAA
Found at i:3142759 original size:17 final size:16
Alignment explanation
Indices: 3142737--3142785 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
3142727 CAATGATGAG
*
3142737 AAAAGAGAAAGGAGAGA
1 AAAAGAGAAAAGA-AGA
3142754 AAAAGAGAAAAGAAG-
1 AAAAGAGAAAAGAAGA
*
3142769 AAAAGA-AAAAAAAGA
1 AAAAGAGAAAAGAAGA
3142784 AA
1 AA
3142786 GACAAAGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 7 0.24
15 8 0.28
16 2 0.07
17 12 0.41
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (16 bp):
AAAAGAGAAAAGAAGA
Found at i:3142780 original size:24 final size:23
Alignment explanation
Indices: 3142734--3142783 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
3142724 CAGCAATGAT
* *
3142734 GAGAAAAGAGAAAGGAGAGAAAAA
1 GAGAAAAGAGAAAAGA-AAAAAAA
3142758 GAGAAAAGAAGAAAAGAAAAAAAA
1 GAGAAAAG-AGAAAAGAAAAAAAA
3142782 GA
1 GA
3142784 AAGACAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (23 bp):
GAGAAAAGAGAAAAGAAAAAAAA
Found at i:3142932 original size:22 final size:22
Alignment explanation
Indices: 3142907--3142962 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
3142897 AGTTTACGTA
3142907 TTTATATTATATTCAT-ATTATT
1 TTTATATTATATT-ATAATTATT
*
3142929 TTTATATTATATTTTAATTATT
1 TTTATATTATATTATAATTATT
3142951 TTTAT-TTATATT
1 TTTATATTATATT
3142963 GTATTCATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
21 8 0.25
22 24 0.75
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTATATTATATTATAATTATT
Found at i:3142967 original size:11 final size:11
Alignment explanation
Indices: 3142905--3142962 Score: 66
Period size: 11 Copynumber: 5.4 Consensus size: 11
3142895 AAAGTTTACG
3142905 TATTTATATTA
1 TATTTATATTA
*
3142916 TATTCATATTA
1 TATTTATATTA
*
3142927 TTTTTATATTA
1 TATTTATATTA
3142938 TATTT-TAATTA
1 TATTTAT-ATTA
*
3142949 TTTTTAT-TTA
1 TATTTATATTA
3142959 TATT
1 TATT
3142963 GTATTCATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
10 7 0.18
11 31 0.79
12 1 0.03
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (11 bp):
TATTTATATTA
Found at i:3142973 original size:37 final size:37
Alignment explanation
Indices: 3142932--3143004 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 37
3142922 TATTATTTTT
*
3142932 ATATTATATTTTAA-TTATTTT-TATTTATATTGTATTC
1 ATATTATATCTTAATTTATTTTATATTT-T-TTGTATTC
* *
3142969 ATATTGTGTCTTAATTTATTTTATATTTTTTGTATT
1 ATATTATATCTTAATTTATTTTATATTTTTTGTATT
3143005 GTTAATAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
37 18 0.58
38 8 0.26
39 5 0.16
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (37 bp):
ATATTATATCTTAATTTATTTTATATTTTTTGTATTC
Found at i:3143762 original size:22 final size:21
Alignment explanation
Indices: 3143714--3143776 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
3143704 TAATAATGAT
3143714 TTAATATAATT-T-AATTTAAA
1 TTAATATAATTATAAATTT-AA
*
3143734 TTTATATAATTATAAATTTAA
1 TTAATATAATTATAAATTTAA
*
3143755 TTAA-ATATTTTATAAATATTAA
1 TTAATATA-ATTATAAAT-TTAA
3143777 AACATTTTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
20 13 0.36
21 14 0.39
22 9 0.25
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTAATATAATTATAAATTTAA
Found at i:3146947 original size:29 final size:29
Alignment explanation
Indices: 3146883--3146953 Score: 99
Period size: 29 Copynumber: 2.5 Consensus size: 29
3146873 TATTCCTGTT
*
3146883 AGTTTTACTATGAATATTATGTAGGACTG
1 AGTTTTACTATGAGTATTATGTAGGACTG
* *
3146912 AGATTTACTATGAGTATTATGTAGGATTG
1 AGTTTTACTATGAGTATTATGTAGGACTG
*
3146941 ATTTTTACT-TGAG
1 AGTTTTACTATGAG
3146954 AAATATAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 4 0.11
29 33 0.89
ACGTcount: A:0.30, C:0.06, G:0.21, T:0.44
Consensus pattern (29 bp):
AGTTTTACTATGAGTATTATGTAGGACTG
Found at i:3147996 original size:22 final size:21
Alignment explanation
Indices: 3147964--3148025 Score: 79
Period size: 22 Copynumber: 2.9 Consensus size: 21
3147954 AGTTAATAAA
*
3147964 ATATTCTAATATTTTAATGAT
1 ATATTATAATATTTTAATGAT
*
3147985 ATTTTTATAATATTTTAATGAT
1 A-TATTATAATATTTTAATGAT
*
3148007 ATATTAAATATATTTTAAT
1 ATATTATA-ATATTTTAAT
3148026 ATTAATATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 6 0.17
22 29 0.83
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (21 bp):
ATATTATAATATTTTAATGAT
Found at i:3148043 original size:24 final size:23
Alignment explanation
Indices: 3147971--3148063 Score: 77
Period size: 22 Copynumber: 4.0 Consensus size: 23
3147961 AAAATATTCT
* *
3147971 AATATTTTAATGAT-AT-TTTTAT
1 AATATTTTAAT-ATAATATTTAAA
3147993 AATATTTTAATGAT-ATA-TTAAA
1 AATATTTTAAT-ATAATATTTAAA
*
3148015 TATATTTTAATATTAATATTTAAA
1 AATATTTTAATA-TAATATTTAAA
* *
3148039 AATATATTAATAATATTATTTAAA
1 AATATTTTAAT-ATAATATTTAAA
3148063 A
1 A
3148064 TAAAATATTA
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
21 1 0.02
22 30 0.50
23 3 0.05
24 25 0.42
25 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
AATATTTTAATATAATATTTAAA
Found at i:3148053 original size:11 final size:11
Alignment explanation
Indices: 3147914--3148054 Score: 65
Period size: 11 Copynumber: 12.5 Consensus size: 11
3147904 AATAATAATC
3147914 TAATA-ATTAA
1 TAATATATTAA
*
3147924 TAATATATAAGAA
1 TAATATAT--TAA
*
3147937 GTAATGATTTTAA
1 -TAAT-ATATTAA
*
3147950 TAATA-GTTAA
1 TAATATATTAA
* *
3147960 TAAAATATT-C
1 TAATATATTAA
*
3147970 TAATATTTTAA
1 TAATATATTAA
* * *
3147981 TGATATTTTTA
1 TAATATATTAA
*
3147992 TAATATTTTAA
1 TAATATATTAA
*
3148003 TGATATATTAA
1 TAATATATTAA
*
3148014 -ATATATTTTAA
1 TA-ATATATTAA
*
3148025 TATTAATATTTAA
1 TAAT-ATA-TTAA
*
3148038 AAATATATTAA
1 TAATATATTAA
3148049 TAATAT
1 TAATAT
3148055 TATTTAAAAT
Statistics
Matches: 97, Mismatches: 23, Indels: 21
0.69 0.16 0.15
Matches are distributed among these distances:
10 20 0.21
11 50 0.52
12 10 0.10
13 10 0.10
14 4 0.04
15 3 0.03
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (11 bp):
TAATATATTAA
Found at i:3148966 original size:5 final size:5
Alignment explanation
Indices: 3148949--3148982 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
3148939 TCTTTAACTA
*
3148949 CTTTT CTTCT CTTTT CTTTT C-TTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT
3148983 GACGTAAAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (5 bp):
CTTTT
Found at i:3148975 original size:14 final size:15
Alignment explanation
Indices: 3148949--3148982 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
3148939 TCTTTAACTA
3148949 CTTTTCTTCTCTTTT
1 CTTTTCTTCTCTTTT
3148964 CTTTTCTT-TCTTTT
1 CTTTTCTTCTCTTTT
3148978 CTTTT
1 CTTTT
3148983 GACGTAAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (15 bp):
CTTTTCTTCTCTTTT
Found at i:3152187 original size:2 final size:2
Alignment explanation
Indices: 3152180--3152211 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3152170 GTGGTAACGG
3152180 AT AT 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 AT AT
3152212 CAATTTTTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3152422 original size:2 final size:2
Alignment explanation
Indices: 3152415--3152446 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3152405 CCCTGAGCAT
3152415 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3152447 AACTTTGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3156024 original size:148 final size:148
Alignment explanation
Indices: 3155824--3156107 Score: 550
Period size: 148 Copynumber: 1.9 Consensus size: 148
3155814 AAAATCCAAA
*
3155824 CTGTTCTTTTTTAGTAACAGCTAACTAGGCAGTCACTACTTCACATAATCCATTTAAAAACTCGC
1 CTGTTCCTTTTTAGTAACAGCTAACTAGGCAGTCACTACTTCACATAATCCATTTAAAAACTCGC
3155889 CAATTCTGATCAACCCAAAACCCAACGTTAGAAATCCAGCATGGTTATTAAAAAAAAGAGGCATT
66 CAATTCTGATCAACCCAAAACCCAACGTTAGAAATCCAGCATGGTTATTAAAAAAAAGAGGCATT
3155954 TTTCAACCCAAAACCCAG
131 TTTCAACCCAAAACCCAG
3155972 CTGTTCCTTTTTAGTAACAGCTAACTAGGCAGTCACTACTTCACATAATCCATTTAAAAACTCGC
1 CTGTTCCTTTTTAGTAACAGCTAACTAGGCAGTCACTACTTCACATAATCCATTTAAAAACTCGC
*
3156037 CAATTCTGATCAACCCAAAACCCAACGTTGGAAATCCAGCATGGTTATTAAAAAAAAGAGGCATT
66 CAATTCTGATCAACCCAAAACCCAACGTTAGAAATCCAGCATGGTTATTAAAAAAAAGAGGCATT
3156102 TTTCAA
131 TTTCAA
3156108 TCAAAACAAA
Statistics
Matches: 134, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
148 134 1.00
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (148 bp):
CTGTTCCTTTTTAGTAACAGCTAACTAGGCAGTCACTACTTCACATAATCCATTTAAAAACTCGC
CAATTCTGATCAACCCAAAACCCAACGTTAGAAATCCAGCATGGTTATTAAAAAAAAGAGGCATT
TTTCAACCCAAAACCCAG
Found at i:3159802 original size:8 final size:9
Alignment explanation
Indices: 3159778--3159806 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
3159768 AAATTTTATA
3159778 TTATTATTT
1 TTATTATTT
3159787 TTATTATTT
1 TTATTATTT
3159796 TTA-TATTT
1 TTATTATTT
3159804 TTA
1 TTA
3159807 CATAAATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (9 bp):
TTATTATTT
Found at i:3163170 original size:27 final size:28
Alignment explanation
Indices: 3163140--3163208 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 28
3163130 AAAGATAAAA
3163140 AAATTTAAAA-TTTTACTTACGTTATTT
1 AAATTTAAAAGTTTTACTTACGTTATTT
3163167 AAATTTAAAAATAAGTTTTACTTACGTTATTT
1 AAATTT---AA-AAGTTTTACTTACGTTATTT
3163199 AAATTTAAAA
1 AAATTTAAAA
3163209 ATAAATATCG
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
27 6 0.16
28 2 0.05
29 2 0.05
30 2 0.05
31 2 0.05
32 23 0.62
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.46
Consensus pattern (28 bp):
AAATTTAAAAGTTTTACTTACGTTATTT
Found at i:3163190 original size:32 final size:32
Alignment explanation
Indices: 3163150--3163212 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
3163140 AAATTTAAAA
3163150 TTTTACTTACGTTATTTAAATTTAAAAATAAG
1 TTTTACTTACGTTATTTAAATTTAAAAATAAG
3163182 TTTTACTTACGTTATTTAAATTTAAAAATAA
1 TTTTACTTACGTTATTTAAATTTAAAAATAA
3163213 ATATCGATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.48
Consensus pattern (32 bp):
TTTTACTTACGTTATTTAAATTTAAAAATAAG
Found at i:3163791 original size:26 final size:27
Alignment explanation
Indices: 3163757--3163833 Score: 81
Period size: 26 Copynumber: 2.9 Consensus size: 27
3163747 TTTAAATTAT
3163757 TATTTAATTAATAAAAATTTTATTT-A
1 TATTTAATTAATAAAAATTTTATTTAA
3163783 TATTTAATT-ATAAAAATATTT-TTTAAA
1 TATTTAATTAATAAAAAT-TTTATTT-AA
*
3163810 AATTTAA-TAATAAAATAATTTTAT
1 TATTTAATTAAT-AAA-AATTTTAT
3163834 ATATCAATTC
Statistics
Matches: 43, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
25 11 0.26
26 13 0.30
27 9 0.21
28 6 0.14
29 4 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
TATTTAATTAATAAAAATTTTATTTAA
Found at i:3163814 original size:27 final size:25
Alignment explanation
Indices: 3163758--3163833 Score: 73
Period size: 25 Copynumber: 2.8 Consensus size: 25
3163748 TTAAATTATT
*
3163758 ATTTAATTAATAAAAATTTTATTTAT
1 ATTTAATT-ATAAAAATTTTATTTAA
3163784 ATTTAATTATAAAAATATTT-TTTAAAA
1 ATTTAATTATAAAAAT-TTTATTT--AA
*
3163811 ATTTAATAATAAAATAATTTTAT
1 ATTTAATTAT-AAA-AATTTTAT
3163834 ATATCAATTC
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
25 11 0.26
26 11 0.26
27 10 0.24
28 6 0.14
29 4 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
ATTTAATTATAAAAATTTTATTTAA
Found at i:3164088 original size:31 final size:31
Alignment explanation
Indices: 3164053--3164139 Score: 174
Period size: 31 Copynumber: 2.8 Consensus size: 31
3164043 TTCAAGCGTA
3164053 TCATTTTTGGACTCTTTGACATTAGTTTACC
1 TCATTTTTGGACTCTTTGACATTAGTTTACC
3164084 TCATTTTTGGACTCTTTGACATTAGTTTACC
1 TCATTTTTGGACTCTTTGACATTAGTTTACC
3164115 TCATTTTTGGACTCTTTGACATTAG
1 TCATTTTTGGACTCTTTGACATTAG
3164140 CCAATCTGGT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 56 1.00
ACGTcount: A:0.20, C:0.18, G:0.14, T:0.48
Consensus pattern (31 bp):
TCATTTTTGGACTCTTTGACATTAGTTTACC
Found at i:3164620 original size:17 final size:17
Alignment explanation
Indices: 3164598--3164630 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3164588 ATGATTATTA
3164598 TTAAAAAATTATAATAT
1 TTAAAAAATTATAATAT
*
3164615 TTAAAAAATTTTAATA
1 TTAAAAAATTATAATA
3164631 ATATCACGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TTAAAAAATTATAATAT
Found at i:3167177 original size:29 final size:27
Alignment explanation
Indices: 3167132--3167186 Score: 83
Period size: 29 Copynumber: 2.0 Consensus size: 27
3167122 TAAGTAATCG
*
3167132 ATAATATTAAATATGATTAAAATAAAT
1 ATAATATTAAATATGATAAAAATAAAT
3167159 ATAATATTTATAATATGATAAAAATAAA
1 ATAATA-TTA-AATATGATAAAAATAAA
3167187 ATATGATGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 6 0.24
28 3 0.12
29 16 0.64
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (27 bp):
ATAATATTAAATATGATAAAAATAAAT
Found at i:3167290 original size:20 final size:21
Alignment explanation
Indices: 3167267--3167312 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
3167257 TAAAATATTT
*
3167267 TAAATATA-ATTATAATATA-A
1 TAAATATATATAATAATA-ACA
3167287 TAAA-ATATATAATAATAACA
1 TAAATATATATAATAATAACA
3167307 TAAATA
1 TAAATA
3167313 CATAAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 4 0.18
20 17 0.77
21 1 0.05
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAATATATATAATAATAACA
Found at i:3167674 original size:16 final size:15
Alignment explanation
Indices: 3167643--3167671 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3167633 TTTTAATGAT
3167643 AAAAATTTATATTTA
1 AAAAATTTATATTTA
3167658 AAAAATTTATATTT
1 AAAAATTTATATTT
3167672 TAATTAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AAAAATTTATATTTA
Found at i:3176177 original size:24 final size:27
Alignment explanation
Indices: 3176104--3176174 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
3176094 AAACAAGTCT
* *
3176104 CCATATTTGACAAACCCAAAGGA-AACCA
1 CCATTTTTGACAAACACAAA--ATAACCA
3176132 CCATTTTTGACAAACACAAAATAACCA
1 CCATTTTTGACAAACACAAAATAACCA
3176159 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
3176175 AATGGGTGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.45, C:0.27, G:0.07, T:0.21
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAATAACCA
Found at i:3181111 original size:19 final size:18
Alignment explanation
Indices: 3181087--3181135 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
3181077 TATATCCGTT
3181087 AAATATAATATTTGATTAA
1 AAATATAATATTT-ATTAA
* * *
3181106 AAATATATTAATTCTTAA
1 AAATATAATATTTATTAA
3181124 AAA-ATAATATTT
1 AAATATAATATTT
3181136 TATACATAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 7 0.28
18 7 0.28
19 11 0.44
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (18 bp):
AAATATAATATTTATTAA
Found at i:3181623 original size:2 final size:2
Alignment explanation
Indices: 3181616--3181641 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3181606 CAACCCAAAC
3181616 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
3181642 GAGAGAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3182972 original size:1 final size:1
Alignment explanation
Indices: 3182966--3182994 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
3182956 AAAAGAAAGG
3182966 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3182995 GGAAGAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3184321 original size:18 final size:18
Alignment explanation
Indices: 3184288--3184326 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
3184278 AAATATTTTT
**
3184288 AATTTTATTTTTTATTAA
1 AATTTTATTTGATATTAA
*
3184306 AATTTTATTTGATATTTA
1 AATTTTATTTGATATTAA
3184324 AAT
1 AAT
3184327 AAATTTTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
AATTTTATTTGATATTAA
Found at i:3184670 original size:2 final size:2
Alignment explanation
Indices: 3184663--3184692 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3184653 TGATAGTTAG
*
3184663 AT AT AT AT AT AT TT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3184693 TTGGGTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:3185182 original size:17 final size:18
Alignment explanation
Indices: 3185155--3185188 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3185145 ACTTTTATTT
*
3185155 AAAATATGAAAATAAATG
1 AAAATATGAAAACAAATG
3185173 AAAA-ATGAAAACAAAT
1 AAAATATGAAAACAAAT
3185189 TTAATATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.71, C:0.03, G:0.09, T:0.18
Consensus pattern (18 bp):
AAAATATGAAAACAAATG
Found at i:3185698 original size:2 final size:2
Alignment explanation
Indices: 3185693--3185726 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3185683 GTAAAAAAAC
3185693 AT AT AT 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 AT AT AT
3185727 CATGGGATTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3195583 original size:3 final size:3
Alignment explanation
Indices: 3195575--3195607 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3195565 AAAGCAGTAC
3195575 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3195608 AAACATGTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3195880 original size:24 final size:25
Alignment explanation
Indices: 3195844--3195896 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
3195834 AAAATAACTA
3195844 AAATATAATAAAATATAAATA-TAT
1 AAATATAATAAAATATAAATATTAT
* *
3195868 AAATAT-ATCAAAATTTATATATTAT
1 AAATATAAT-AAAATATAAATATTAT
3195893 AAAT
1 AAAT
3195897 TATTAACAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 2 0.08
24 16 0.64
25 7 0.28
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (25 bp):
AAATATAATAAAATATAAATATTAT
Found at i:3195881 original size:18 final size:16
Alignment explanation
Indices: 3195842--3195931 Score: 51
Period size: 16 Copynumber: 5.5 Consensus size: 16
3195832 AAAAAATAAC
3195842 TAAAATATAATAAAATA
1 TAAAATAT-ATAAAATA
3195859 T-AAATATATAAATATA
1 TAAAATATATAAA-ATA
* * *
3195875 TCAAAATTTATATATTA
1 T-AAAATATATAAAATA
*
3195892 TAAATTAT-TAACAAGT-
1 TAAAATATATAA-AA-TA
* *
3195908 TAAAATTTATAAATTA
1 TAAAATATATAAAATA
*
3195924 TATAATAT
1 TAAAATAT
3195932 CTTAAATATG
Statistics
Matches: 54, Mismatches: 12, Indels: 15
0.67 0.15 0.19
Matches are distributed among these distances:
15 8 0.15
16 29 0.54
17 8 0.15
18 9 0.17
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (16 bp):
TAAAATATATAAAATA
Found at i:3195938 original size:25 final size:24
Alignment explanation
Indices: 3195842--3195938 Score: 72
Period size: 25 Copynumber: 3.9 Consensus size: 24
3195832 AAAAAATAAC
* * *
3195842 TAAAATATAATAAAATATAAATATA
1 TAAATTAT-ATAAAATTTAAATTTA
*
3195867 TAAA-TATATCAAAATTTATATATTA
1 TAAATTATAT-AAAATTTAAAT-TTA
*
3195892 TAAATTAT-TAACAAGTTAAAATTTA
1 TAAATTATATAA-AA-TTTAAATTTA
*
3195917 TAAATTATATAATATCTTAAAT
1 TAAATTATATAAAAT-TTAAAT
3195939 ATGATTATAA
Statistics
Matches: 58, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
23 2 0.03
24 15 0.26
25 30 0.52
26 11 0.19
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (24 bp):
TAAATTATATAAAATTTAAATTTA
Found at i:3201589 original size:28 final size:26
Alignment explanation
Indices: 3201534--3201589 Score: 67
Period size: 28 Copynumber: 2.1 Consensus size: 26
3201524 ATTTATTTTT
* **
3201534 ATATTAATATTTAAAAAAAATATCGA
1 ATATAAATATTTAAAAAAAATAGAGA
3201560 ATATAAATATTTAAAAAAAAAATAGAGA
1 ATATAAATATTT--AAAAAAAATAGAGA
3201588 AT
1 AT
3201590 CAAAGCACCC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 11 0.44
28 14 0.56
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.30
Consensus pattern (26 bp):
ATATAAATATTTAAAAAAAATAGAGA
Found at i:3203809 original size:2 final size:2
Alignment explanation
Indices: 3203802--3203833 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3203792 TGATGACGCA
3203802 AT AT 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 AT AT
3203834 TAGTAGTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3204541 original size:41 final size:40
Alignment explanation
Indices: 3204482--3204582 Score: 116
Period size: 41 Copynumber: 2.5 Consensus size: 40
3204472 AATAATTTTG
*
3204482 TTTTAAAAATATAATATATGGATCGTTATCGA-ATGGATGTTT
1 TTTTAAAAA-ATAATATATGAATCGTTATCGAGA-GG-TGTTT
* * *
3204524 TTTTAAAAAATAATATATGAATGGTTATTGAGAGGTTTTT
1 TTTTAAAAAATAATATATGAATCGTTATCGAGAGGTGTTT
*
3204564 TTTTAAAAAA-AAAATATGA
1 TTTTAAAAAATAATATATGA
3204583 GTAGTTAAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
39 8 0.15
40 14 0.26
41 21 0.40
42 10 0.19
ACGTcount: A:0.42, C:0.02, G:0.15, T:0.42
Consensus pattern (40 bp):
TTTTAAAAAATAATATATGAATCGTTATCGAGAGGTGTTT
Found at i:3204641 original size:26 final size:29
Alignment explanation
Indices: 3204598--3204654 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 29
3204588 TAAAAAAAAT
*
3204598 AAAAATATGGGTAGTTTTCTTT-AG-AATA
1 AAAAATATGGGTACTTTT-TTTAAGTAATA
3204626 AAAAAT-TGGGT-CTTTTTTTAAGTAATA
1 AAAAATATGGGTACTTTTTTTAAGTAATA
3204653 AA
1 AA
3204655 TGTTGGTTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
25 3 0.12
26 6 0.23
27 11 0.42
28 6 0.23
ACGTcount: A:0.40, C:0.04, G:0.16, T:0.40
Consensus pattern (29 bp):
AAAAATATGGGTACTTTTTTTAAGTAATA
Found at i:3205819 original size:79 final size:79
Alignment explanation
Indices: 3205643--3205867 Score: 425
Period size: 79 Copynumber: 2.9 Consensus size: 79
3205633 ATTTTATAAT
* *
3205643 TAATAGGATAATTTTTCTTTTCATATGACTTAGCATAAAATATTGATTTG-TTTATAACTTTATA
1 TAATAGGATAATTTTTCTTTTTATATGACTTAGTATAAAATATTGATTTGATTTATAACTTTATA
3205707 TTTATATTAATTTG
66 TTTATATTAATTTG
3205721 TAATAGGATAATTTTTCTTTTTATATGACTTAGTATAAAATATTGATTTGATTTATAACTTTATA
1 TAATAGGATAATTTTTCTTTTTATATGACTTAGTATAAAATATTGATTTGATTTATAACTTTATA
3205786 TTTATATTAATTTG
66 TTTATATTAATTTG
3205800 TAATAGGATAATTTTTCTTTTTATATGACTTAGTATAAAATATTGATTTGATTTATAACTTTATA
1 TAATAGGATAATTTTTCTTTTTATATGACTTAGTATAAAATATTGATTTGATTTATAACTTTATA
3205865 TTT
66 TTT
3205868 TGCTTCTCAG
Statistics
Matches: 144, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
78 48 0.33
79 96 0.67
ACGTcount: A:0.34, C:0.05, G:0.09, T:0.52
Consensus pattern (79 bp):
TAATAGGATAATTTTTCTTTTTATATGACTTAGTATAAAATATTGATTTGATTTATAACTTTATA
TTTATATTAATTTG
Done.