Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 133 of 167
Found at i:44572533 original size:54 final size:55
Alignment explanation
Indices: 44572419--44572542 Score: 139
Period size: 54 Copynumber: 2.3 Consensus size: 55
44572409 AATTTTCTCG
* * *
44572419 CACACTTAGTGCTCAATAACCGATTTCGCACACTTAGTGCTCGGAAATCCAATTTG
1 CACACTTAGTGCTCAATAACCAACTTCGCACACTTAGTGCTC-GAAATCCAATTTA
* *
44572475 CACACTTAGTGCTTAA-AACCAACTT-GCACACTTAGTGCTC--AATGACCGATTTCA
1 CACACTTAGTGCTCAATAACCAACTTCGCACACTTAGTGCTCGAAAT--CCAATTT-A
44572529 CACACTTAGTGCTC
1 CACACTTAGTGCTC
44572543 GGTATCAAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
51 3 0.05
53 6 0.10
54 28 0.47
55 7 0.12
56 15 0.25
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (55 bp):
CACACTTAGTGCTCAATAACCAACTTCGCACACTTAGTGCTCGAAATCCAATTTA
Found at i:44582199 original size:20 final size:20
Alignment explanation
Indices: 44582171--44582209 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
44582161 TAATAATAAT
*
44582171 ATTATAAAAATTCTAAAAAA
1 ATTAAAAAAATTCTAAAAAA
*
44582191 ATTAAAAAAATTTTAAAAA
1 ATTAAAAAAATTCTAAAAA
44582210 TAAAAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (20 bp):
ATTAAAAAAATTCTAAAAAA
Found at i:44582217 original size:20 final size:20
Alignment explanation
Indices: 44582176--44582217 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
44582166 ATAATATTAT
*
44582176 AAAAATTCTAAAAAAATTAA
1 AAAAATTCTAAAAAAATAAA
*
44582196 AAAAATT-T-TAAAAATAAA
1 AAAAATTCTAAAAAAATAAA
44582214 AAAA
1 AAAA
44582218 TTTATTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 12 0.60
19 1 0.05
20 7 0.35
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAAATTCTAAAAAAATAAA
Found at i:44582227 original size:17 final size:17
Alignment explanation
Indices: 44582187--44582220 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
44582177 AAAATTCTAA
44582187 AAAAATTAAAAAAATTTT
1 AAAAA-TAAAAAAATTTT
44582205 AAAAATAAAAAAATTT
1 AAAAATAAAAAAATTT
44582221 ATTAAATTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAAATAAAAAAATTTT
Found at i:44582227 original size:26 final size:26
Alignment explanation
Indices: 44582184--44582234 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
44582174 ATAAAAATTC
*
44582184 TAAAAAAATTAAAAAAATTTTAAAAA
1 TAAAAAAATTAAAAAAATTCTAAAAA
* **
44582210 TAAAAAAATTTATTAAATTCTAAAA
1 TAAAAAAATTAAAAAAATTCTAAAA
44582235 TATATAATTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (26 bp):
TAAAAAAATTAAAAAAATTCTAAAAA
Found at i:44583780 original size:13 final size:13
Alignment explanation
Indices: 44583759--44583791 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
44583749 AAACTTTATT
*
44583759 ATTATTATTTTTA
1 ATTAATATTTTTA
44583772 ATTAATATTTTTA
1 ATTAATATTTTTA
44583785 ATTAATA
1 ATTAATA
44583792 AATATTTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
ATTAATATTTTTA
Found at i:44585772 original size:496 final size:485
Alignment explanation
Indices: 44584794--44585758 Score: 1341
Period size: 493 Copynumber: 2.0 Consensus size: 485
44584784 GGCATAACTT
* *
44584794 TCCATCAAATACTTAGATTGAAGGAGAATGTCAACAATTCTAAGTTTTTTTTTTTTGAGAAACTT
1 TCCATCAAATACTTACATTGAAGGAGAATGTCAACAATTCTAAG-TTTTTTTTGTTGAGAAACTT
* *
44584859 TGATTTGGTAATTAGTACTTCAATTTTGAAAGGTTGATTAAGCATGGTTATAAACAATTTTAGTT
65 TGATTTGATAATTAGTACTTCAATTCTGAAAGGTTGATTAAGCATGGTTATAAACAATTTTAGTT
* * *
44584924 AATAGACGTTATTGACGTTGCAATGTGGGTTTTGATAGTTGCGACAAAAGAATAAAAATAATAAG
130 AATAGACATTATTGACGTTGCAATGTGAGTTTTGATAGTTGCGACAAAAGAAT-AAAATAACAAG
* * **
44584989 ATAAAAGAAGATGGAGACCGAGAATTTGTTGATGCAATTCAATTCAACAATCTAACTCTGTGGGG
194 ATAAAAGAAGATAGAGACCGAAAATTTGTTGATGCAATTCAATTCAACAATCTAACTCTGTAAGG
* * * * * *
44585054 CTTTATCTAAATAACGAGTTCATTATACAAAATTTTCGCATTACAGATTTACTAGCCAACCCAAT
259 CCTTACCTAAATAACAAGTCCATTATACAAAATTTTCACATTACAGATTTACTAACCAACCCAAT
* * *
44585119 CTACTAAAGCTCACCAAGGATAATTACAATCACAAAGATCGTACAGCTTGTATACTCTCACTCTC
324 CTACCAAAGCTCACC-A-GATAATTACAACCACAAAGATCGGACAGCTTGTATACTCTCACTCTC
*
44585184 AATCCAAAACCTCCATATATAAAGCTAAAATTGATAATACGAATTGAGATGCATGTCAAATATGC
387 AATCCAAAACCTCCATATATAAAGCTAAAATGGATAATACGAATTGAGA--CATGTCAAATATGC
** *
44585249 TGGTAATGCTTTGACTGCATGTTTGGTATATTTGAC
450 TAATAATGCTTTGACTGCATGTTTGGTACATTTGAC
44585285 TCCATCAAATACTTACATTGAAGGAGAATGTCAACAATTCTAAG-TTTTTTTGTTGAGAAACTTT
1 TCCATCAAATACTTACATTGAAGGAGAATGTCAACAATTCTAAGTTTTTTTTGTTGAGAAACTTT
* ** * *
44585349 GATTTGATAATTAGAATCCTATCCTTTAATTCTGAAAGGTTGATTAAGTTTGGTTATAGACGATT
66 GATTTGATAATTAG-----TA--CTTCAATTCTGAAAGGTTGATTAAGCATGGTTATAAACAATT
* *
44585414 TTAGTTAGTAGACATTATTGATGTTGCAATGTGAGTTTTGATAGTTGCGGA-AAAAGAAT-AAA-
124 TTAGTTAATAGACATTATTGACGTTGCAATGTGAGTTTTGATAGTTGC-GACAAAAGAATAAAAT
* ** *
44585476 AACAAGATAAATGAAGATAGAGACCGAAAATTTGTTGATGCAATTCGTTTCAACAATCTACCTCT
188 AACAAGATAAAAGAAGATAGAGACCGAAAATTTGTTGATGCAATTCAATTCAACAATCTAACTCT
* * *
44585541 GTAAGGCCTTACCTAGATAACAAGTCCATTATACAAACTTTTCACATTACAGATTTGCTAACCAA
253 GTAAGGCCTTACCTAAATAACAAGTCCATTATACAAAATTTTCACATTACAGATTTACTAACCAA
* * *
44585606 CCCAATCTACCCAAGTTCACC-GATAATTACAACCACAAAGATCGGACAGCTTGTATGCTCTCAC
318 CCCAATCTACCAAAGCTCACCAGATAATTACAACCACAAAGATCGGACAGCTTGTATACTCTCAC
* * * *
44585670 TCTCAATCCAAAACCTCCCTATATAAGGCTAAAATGGATAATGCGTATTGA-A-ATGTCAAATAT
383 TCTCAATCCAAAACCTCCATATATAAAGCTAAAATGGATAATACGAATTGAGACATGTCAAATAT
*
44585733 GCTAATAATGCTTTGACTTCATGTTT
448 GCTAATAATGCTTTGACTGCATGTTT
44585759 TATATGTTTT
Statistics
Matches: 421, Mismatches: 45, Indels: 21
0.86 0.09 0.04
Matches are distributed among these distances:
486 34 0.08
489 33 0.08
490 86 0.20
491 43 0.10
493 130 0.31
494 5 0.01
496 88 0.21
497 2 0.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (485 bp):
TCCATCAAATACTTACATTGAAGGAGAATGTCAACAATTCTAAGTTTTTTTTGTTGAGAAACTTT
GATTTGATAATTAGTACTTCAATTCTGAAAGGTTGATTAAGCATGGTTATAAACAATTTTAGTTA
ATAGACATTATTGACGTTGCAATGTGAGTTTTGATAGTTGCGACAAAAGAATAAAATAACAAGAT
AAAAGAAGATAGAGACCGAAAATTTGTTGATGCAATTCAATTCAACAATCTAACTCTGTAAGGCC
TTACCTAAATAACAAGTCCATTATACAAAATTTTCACATTACAGATTTACTAACCAACCCAATCT
ACCAAAGCTCACCAGATAATTACAACCACAAAGATCGGACAGCTTGTATACTCTCACTCTCAATC
CAAAACCTCCATATATAAAGCTAAAATGGATAATACGAATTGAGACATGTCAAATATGCTAATAA
TGCTTTGACTGCATGTTTGGTACATTTGAC
Found at i:44592065 original size:28 final size:28
Alignment explanation
Indices: 44592023--44592086 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
44592013 ATTTACCTTA
* *
44592023 TCTAGTGGTTCAACCACACTTATCTGAT
1 TCTAGTGGCTCAACCACACTTATCTAAT
* **
44592051 TCTGGTGGCTCAACCACGTTTATCTAAT
1 TCTAGTGGCTCAACCACACTTATCTAAT
44592079 TCTAGTGG
1 TCTAGTGG
44592087 ATTACCGCAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.36
Consensus pattern (28 bp):
TCTAGTGGCTCAACCACACTTATCTAAT
Found at i:44594255 original size:61 final size:61
Alignment explanation
Indices: 44594142--44594267 Score: 173
Period size: 61 Copynumber: 2.1 Consensus size: 61
44594132 TTTTTGGATA
* * * * *
44594142 TTTTTAGGATTAGAATTAAATTGAAAAATTTTGTAAATATTGAAGGTCAAATTTATTGATT
1 TTTTTAGAATTAGAACTAAAATGAAAAATTTTGTAAATATTGAAGCTCAAATTTATTGAAT
* *
44594203 TTTTTAGAATTTGAACTAAAATGAAAAATTTTGTAAATATTGAAGACT-AAATTTGTTGAAT
1 TTTTTAGAATTAGAACTAAAATGAAAAATTTTGTAAATATTGAAG-CTCAAATTTATTGAAT
44594264 TTTT
1 TTTT
44594268 CATATTTAGG
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
61 56 0.98
62 1 0.02
ACGTcount: A:0.40, C:0.02, G:0.13, T:0.44
Consensus pattern (61 bp):
TTTTTAGAATTAGAACTAAAATGAAAAATTTTGTAAATATTGAAGCTCAAATTTATTGAAT
Found at i:44597097 original size:9 final size:9
Alignment explanation
Indices: 44597083--44597121 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
44597073 TAAAGTATTT
44597083 ATTAAACTA
1 ATTAAACTA
*
44597092 ATTAAATTA
1 ATTAAACTA
*
44597101 ATTAACCTAA
1 ATTAAACT-A
44597111 ATTAAACTA
1 ATTAAACTA
44597120 AT
1 AT
44597122 GGAATTTCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
9 17 0.68
10 8 0.32
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36
Consensus pattern (9 bp):
ATTAAACTA
Found at i:44601673 original size:37 final size:37
Alignment explanation
Indices: 44601574--44601683 Score: 123
Period size: 37 Copynumber: 3.0 Consensus size: 37
44601564 TAGAATTTTA
* * *
44601574 TCGATTGAACATCATTCAGTATAACAGTAAGGTTTGC
1 TCGATTGAGCTTCATTCAGTATAACGGTAAGGTTTGC
* * *
44601611 TCAATTGAGCTCCATTCAGTATAACGGTATGAG-TTGC
1 TCGATTGAGCTTCATTCAGTATAACGGTAAG-GTTTGC
* * *
44601648 TCGATTGAGCTTCATTCAATATAACGATAAGATTTG
1 TCGATTGAGCTTCATTCAGTATAACGGTAAGGTTTG
44601684 GCTTGATAGA
Statistics
Matches: 59, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
37 58 0.98
38 1 0.02
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (37 bp):
TCGATTGAGCTTCATTCAGTATAACGGTAAGGTTTGC
Found at i:44616844 original size:22 final size:21
Alignment explanation
Indices: 44616814--44616872 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
44616804 TCTCCGATTC
* *
44616814 AATTTTTAAATTATGTCAAAAT
1 AATTATTAAATTAT-TAAAAAT
44616836 AATTATTAAATTTATTAAAAAT
1 AATTATTAAA-TTATTAAAAAT
44616858 -A-TATTAAATTTATTA
1 AATTATTAAA-TTATTA
44616873 TTTTAACATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.41
21 1 0.03
22 15 0.44
23 4 0.12
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (21 bp):
AATTATTAAATTATTAAAAAT
Found at i:44616889 original size:20 final size:20
Alignment explanation
Indices: 44616862--44616927 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 20
44616852 AAAAATATAT
44616862 TAAA-TTTATTATTTTAACA
1 TAAATTTTATTATTTTAACA
* *
44616881 TAAATTTTAATATTTTTAATA
1 TAAATTTTATTA-TTTTAACA
*
44616902 TAATTTTAATAATTATTTTAACA
1 TAAATTT--T-ATTATTTTAACA
44616925 TAA
1 TAA
44616928 TTTAAAAATG
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
19 4 0.11
20 6 0.16
21 13 0.35
23 11 0.30
24 3 0.08
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
TAAATTTTATTATTTTAACA
Found at i:44616928 original size:23 final size:22
Alignment explanation
Indices: 44616868--44616930 Score: 85
Period size: 23 Copynumber: 2.9 Consensus size: 22
44616858 ATATTAAATT
44616868 TATTATTTTAACATAAATTTTAA
1 TATTATTTTAACAT-AATTTTAA
*
44616891 TA-T-TTTTAATATAATTTTAA
1 TATTATTTTAACATAATTTTAA
44616911 TAATTATTTTAACATAATTT
1 T-ATTATTTTAACATAATTT
44616931 AAAAATGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 9 0.26
21 9 0.26
22 2 0.06
23 15 0.43
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (22 bp):
TATTATTTTAACATAATTTTAA
Found at i:44620802 original size:7 final size:7
Alignment explanation
Indices: 44620778--44620810 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
44620768 AAAAAATATT
44620778 TATTTTA
1 TATTTTA
*
44620785 T-TTTAA
1 TATTTTA
44620791 TATTTTA
1 TATTTTA
44620798 TATTTTA
1 TATTTTA
44620805 TATTTT
1 TATTTT
44620811 TTGAAAGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TATTTTA
Found at i:44624238 original size:20 final size:20
Alignment explanation
Indices: 44624201--44624240 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
44624191 ATTTCTTTAG
*
44624201 ATCTTGCCAAATCGTTGATA
1 ATCTTGCCAAATCATTGATA
44624221 ATCTTGCCAAAAT-ATTGATA
1 ATCTTGCC-AAATCATTGATA
44624241 CCAATCGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (20 bp):
ATCTTGCCAAATCATTGATA
Found at i:44625639 original size:9 final size:9
Alignment explanation
Indices: 44625620--44625654 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
44625610 TTATCACACA
44625620 ACCACAAAGT
1 ACCA-AAAGT
*
44625630 ATCAAAAGT
1 ACCAAAAGT
44625639 ACCAAAAGT
1 ACCAAAAGT
44625648 ACCAAAA
1 ACCAAAA
44625655 TTCAAAGCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 20 0.87
10 3 0.13
ACGTcount: A:0.57, C:0.23, G:0.09, T:0.11
Consensus pattern (9 bp):
ACCAAAAGT
Found at i:44627757 original size:22 final size:22
Alignment explanation
Indices: 44627697--44627763 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
44627687 AAAAAACTTG
* *
44627697 AAATGTATATTTGAAATGTTTT
1 AAATATATATTTGAAATTTTTT
* *
44627719 ATAATAT-TTTTTAAAATTTTTT
1 A-AATATATATTTGAAATTTTTT
44627741 AAATATATATTTGAAATTATTTT
1 AAATATATATTTGAAATT-TTTT
44627764 TTTAAATTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
21 5 0.14
22 23 0.64
23 8 0.22
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (22 bp):
AAATATATATTTGAAATTTTTT
Found at i:44627777 original size:20 final size:21
Alignment explanation
Indices: 44627749--44627807 Score: 77
Period size: 20 Copynumber: 2.8 Consensus size: 21
44627739 TTAAATATAT
*
44627749 ATTTGAAATTATTTTTTT-AA
1 ATTTTAAATTATTTTTTTAAA
44627769 ATTTTAAA-TATTATTTTTAAA
1 ATTTTAAATTATT-TTTTTAAA
44627790 ATTTTAAATATATTTTTT
1 ATTTTAAAT-TATTTTTT
44627808 AATTATATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
19 4 0.12
20 12 0.35
21 10 0.29
22 4 0.12
23 4 0.12
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
ATTTTAAATTATTTTTTTAAA
Found at i:44627807 original size:21 final size:21
Alignment explanation
Indices: 44627749--44627809 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
44627739 TTAAATATAT
* *
44627749 ATTTGAAAT-TATTTTTTTAA
1 ATTTTAAATATATTTTTTAAA
44627769 ATTTTAAATAT-TATTTTTAAA
1 ATTTTAAATATAT-TTTTTAAA
44627790 ATTTTAAATATATTTTTTAA
1 ATTTTAAATATATTTTTTAA
44627810 TTATATAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
20 9 0.25
21 26 0.72
22 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
ATTTTAAATATATTTTTTAAA
Found at i:44627818 original size:21 final size:19
Alignment explanation
Indices: 44627761--44627824 Score: 67
Period size: 21 Copynumber: 3.2 Consensus size: 19
44627751 TTGAAATTAT
44627761 TTTTTTAAATTTTAAATATTA
1 TTTTTT-AATTTTAAATA-TA
*
44627782 TTTTTAAAATTTTAAATATA
1 TTTTT-TAATTTTAAATATA
44627802 TTTTTTAATTATATAAA-ATA
1 TTTTTTAATT-T-TAAATATA
44627822 TTT
1 TTT
44627825 AAAAATTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
19 4 0.11
20 14 0.37
21 20 0.53
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTTTAATTTTAAATATA
Found at i:44627935 original size:14 final size:14
Alignment explanation
Indices: 44627916--44627942 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
44627906 TTTACATATA
44627916 ATTTTTAAATTATG
1 ATTTTTAAATTATG
44627930 ATTTTTAAATTAT
1 ATTTTTAAATTAT
44627943 TTTTAAAGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (14 bp):
ATTTTTAAATTATG
Found at i:44628099 original size:20 final size:20
Alignment explanation
Indices: 44628076--44628129 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
44628066 ACTTTATTTA
44628076 AAAAATATATATTAAAAAGT
1 AAAAATATATATTAAAAAGT
* * * *
44628096 AAAAATTTAAATTAAAGATT
1 AAAAATATATATTAAAAAGT
*
44628116 AAAAACATATATTA
1 AAAAATATATATTA
44628130 TAACTGGTCA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (20 bp):
AAAAATATATATTAAAAAGT
Found at i:44630829 original size:30 final size:30
Alignment explanation
Indices: 44630739--44630835 Score: 108
Period size: 30 Copynumber: 3.2 Consensus size: 30
44630729 GTCGCAGAGC
* *
44630739 AGTTCATATC-ACTCGGACAT-GGACGGTTCA
1 AGTTCATATCAAC-CAGACATAGG-CGGTTCG
* * *
44630769 AGTTCATATCACCCAGACATGGGCGCTTCG
1 AGTTCATATCAACCAGACATAGGCGGTTCG
*
44630799 AGTTCATATCAACCAGACATAGGTGGTTCG
1 AGTTCATATCAACCAGACATAGGCGGTTCG
44630829 AGTTCAT
1 AGTTCAT
44630836 TTCACCTAGA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
30 54 0.95
31 3 0.05
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.27
Consensus pattern (30 bp):
AGTTCATATCAACCAGACATAGGCGGTTCG
Found at i:44632559 original size:9 final size:9
Alignment explanation
Indices: 44632535--44632611 Score: 55
Period size: 9 Copynumber: 7.8 Consensus size: 9
44632525 ATAATATATT
*
44632535 TTTAAAAAA
1 TTTAAAATA
*
44632544 TTAAAAATA
1 TTTAAAATA
44632553 TTTAAAATA
1 TTTAAAATA
*
44632562 TTATAAAACAA
1 TT-TAAAA-TA
*
44632573 ATTAAAATA
1 TTTAAAATA
44632582 TTTAAAAGATACA
1 TTT-AAA-AT--A
44632595 TTTAAAATA
1 TTTAAAATA
44632604 TTATAAAA
1 TT-TAAAA
44632612 CTAATAATAA
Statistics
Matches: 54, Mismatches: 7, Indels: 13
0.73 0.09 0.18
Matches are distributed among these distances:
9 23 0.43
10 18 0.33
11 6 0.11
12 3 0.06
13 4 0.07
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (9 bp):
TTTAAAATA
Found at i:44632568 original size:20 final size:21
Alignment explanation
Indices: 44632545--44632612 Score: 79
Period size: 20 Copynumber: 3.3 Consensus size: 21
44632535 TTTAAAAAAT
44632545 TAAAA-ATATTTAAAATATTA
1 TAAAACATATTTAAAATATTA
*
44632565 TAAAACA-AATTAAAATATT-
1 TAAAACATATTTAAAATATTA
*
44632584 TAAAAGATACATTTAAAATATTA
1 TAAAACAT--ATTTAAAATATTA
44632607 TAAAAC
1 TAAAAC
44632613 TAATAATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
19 6 0.15
20 16 0.41
21 1 0.03
22 11 0.28
23 5 0.13
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.34
Consensus pattern (21 bp):
TAAAACATATTTAAAATATTA
Found at i:44632622 original size:22 final size:22
Alignment explanation
Indices: 44632549--44632622 Score: 75
Period size: 22 Copynumber: 3.4 Consensus size: 22
44632539 AAAAATTAAA
44632549 AATATTTAAAATATTATAAAAC-
1 AATA-TTAAAATATTATAAAACT
*
44632571 AA-ATTAAAATATT-TAAAAGAT
1 AATATTAAAATATTATAAAA-CT
44632592 ACAT-TTAAAATATTATAAAACT
1 A-ATATTAAAATATTATAAAACT
*
44632614 AATAATAAA
1 AATATTAAA
44632623 TTTGAAAGGT
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
19 5 0.12
20 10 0.23
21 4 0.09
22 19 0.44
23 5 0.12
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.34
Consensus pattern (22 bp):
AATATTAAAATATTATAAAACT
Found at i:44632624 original size:79 final size:78
Alignment explanation
Indices: 44632473--44632624 Score: 166
Period size: 79 Copynumber: 1.9 Consensus size: 78
44632463 AAAAATATGC
* * * * **
44632473 ATTTAAAATATTATAAAACAAATAATAAATTTAAAATATCATATCTTTAAAAATAATATATTTTT
1 ATTTAAAATATTATAAAACAAATAATAAATTTAAAAGATCACA-CTTTAAAAATAATAAACTAAT
44632538 AAAAAATTAAAAAT
65 AAAAAATTAAAAAT
*
44632552 ATTTAAAATATTATAAAACAAATTAA-AATATTTAAAAGAT-ACA-TTTAAAATATTATAAAACT
1 ATTTAAAATATTATAAAACAAA-TAATAA-ATTTAAAAGATCACACTTTAAAA-ATAAT-AAACT
*
44632614 AATAATAAATT
62 AATAAAAAATT
44632625 TGAAAGGTCA
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
77 7 0.11
78 4 0.07
79 37 0.61
80 13 0.21
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.37
Consensus pattern (78 bp):
ATTTAAAATATTATAAAACAAATAATAAATTTAAAAGATCACACTTTAAAAATAATAAACTAATA
AAAAATTAAAAAT
Found at i:44632682 original size:22 final size:21
Alignment explanation
Indices: 44632657--44632707 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
44632647 ATTTAAATGT
* *
44632657 TTTATAATATTAAAAATATATA
1 TTTAAAATATTAAAAAAATA-A
*
44632679 TTTAAAATTTTAAAAAAATAA
1 TTTAAAATATTAAAAAAATAA
44632700 TTTCAAAA
1 TTT-AAAA
44632708 ATATATATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
TTTAAAATATTAAAAAAATAA
Found at i:44632708 original size:36 final size:37
Alignment explanation
Indices: 44632660--44632743 Score: 120
Period size: 36 Copynumber: 2.3 Consensus size: 37
44632650 TAAATGTTTT
44632660 ATAATATTAAAAATATATATTTAAAA-TTTTAAAAAA
1 ATAATATTAAAAATATATATTTAAAATTTTTAAAAAA
*
44632696 ATAAT-TTCAAAAATATATATTTAAAATTTTTTAAAAA
1 ATAATATT-AAAAATATATATTTAAAATTTTTAAAAAA
*
44632733 ATATTA-TAAAA
1 ATAATATTAAAA
44632744 TATTTCAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
35 2 0.05
36 27 0.63
37 14 0.33
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (37 bp):
ATAATATTAAAAATATATATTTAAAATTTTTAAAAAA
Found at i:44648572 original size:39 final size:39
Alignment explanation
Indices: 44648513--44648650 Score: 206
Period size: 39 Copynumber: 3.5 Consensus size: 39
44648503 ATCGTCATCT
* * *
44648513 GAAGCCCGAAGTCTAGCTGAACCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAACCACAAAAGTGCTAAACG
* *
44648552 GAAGCCCGAAGGCTAACTGAAGCACAAAAGTGTTAAACG
1 GAAGCCCGAAGGCTAACTGAACCACAAAAGTGCTAAACG
44648591 GAAGCCCGAAGGCTAACT-AACGCACAAAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAC-CACAAAAGTGCTAAACG
*
44648630 GAAGCCTGAAGGCTAACTGAA
1 GAAGCCCGAAGGCTAACTGAA
44648651 GCTCATCAGA
Statistics
Matches: 89, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
38 2 0.02
39 85 0.96
40 2 0.02
ACGTcount: A:0.39, C:0.23, G:0.25, T:0.13
Consensus pattern (39 bp):
GAAGCCCGAAGGCTAACTGAACCACAAAAGTGCTAAACG
Found at i:44652425 original size:120 final size:120
Alignment explanation
Indices: 44652115--44652431 Score: 368
Period size: 128 Copynumber: 2.6 Consensus size: 120
44652105 GAAGATTCAT
* * *
44652115 TAAAACAAAGGCAATATTCGATGTTTGGAAATTCGGGAAATAGTACCCTATCGTGTTGGGTTTCA
1 TAAAAC-AAGGCAATATTCGATGTTTGGAAATTCGGG-AATAGTGCCCTATCGTGCTGGGTTTCG
* * *
44652180 ATTTCCCGTTTGTTCAAAATAATCAAATATTCCTTTAGAATTTTACTCGTGTTTTTCCAAACA
64 ATTTCCCGTTTGTTCAAAATAATCAAATATTCCTATAGAATTTCACTAGTGTTTTT------A
* * *
44652243 CTAAAACAAGGCAATA-TCTGATGTTGGGAAATTCGGGGAATAGTGTCCTATCGTGCTAGGTTTC
1 -TAAAACAAGGCAATATTC-GATGTTTGGAAATTC-GGGAATAGTGCCCTATCGTGCTGGGTTTC
* *
44652307 GATTTCCCGTTTGTTCAAAATAATCGAATATTCCTATGGAATTTCACTAGTGTTTTT-
63 GATTTCCCGTTTGTTCAAAATAATCAAATATTCCTATAGAATTTCACTAGTGTTTTTA
* * * * *
44652364 TAAAGCGAGGCAATATTCAATGTTTGGAAATTCGAGGAATCGTGCCCTACCGTGCTGGGTTTCGA
1 TAAAACAAGGCAATATTCGATGTTTGGAAATTCG-GGAATAGTGCCCTATCGTGCTGGGTTTCGA
44652429 TTT
65 TTT
44652432 TTCATTGGAC
Statistics
Matches: 165, Mismatches: 19, Indels: 17
0.82 0.09 0.08
Matches are distributed among these distances:
119 1 0.01
120 55 0.33
121 2 0.01
127 2 0.01
128 96 0.58
129 9 0.05
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.35
Consensus pattern (120 bp):
TAAAACAAGGCAATATTCGATGTTTGGAAATTCGGGAATAGTGCCCTATCGTGCTGGGTTTCGAT
TTCCCGTTTGTTCAAAATAATCAAATATTCCTATAGAATTTCACTAGTGTTTTTA
Found at i:44653490 original size:17 final size:18
Alignment explanation
Indices: 44653450--44653490 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
44653440 ACTTTTATAA
44653450 TTCA-ATTCATATTTCAT
1 TTCATATTCATATTTCAT
*
44653467 TTC-TATTCA-ATTTCTT
1 TTCATATTCATATTTCAT
44653483 TTCATATT
1 TTCATATT
44653491 TCACTTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.24, C:0.17, G:0.00, T:0.59
Consensus pattern (18 bp):
TTCATATTCATATTTCAT
Found at i:44653879 original size:17 final size:17
Alignment explanation
Indices: 44653845--44653879 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
44653835 CGAAAGCTTC
*
44653845 TGTTTCTTTTCTCCTTT
1 TGTTTCTTTTCTCATTT
*
44653862 TGTTTCTTTTCTTATTT
1 TGTTTCTTTTCTCATTT
44653879 T
1 T
44653880 ACTTTATTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.03, C:0.17, G:0.06, T:0.74
Consensus pattern (17 bp):
TGTTTCTTTTCTCATTT
Found at i:44653927 original size:3 final size:3
Alignment explanation
Indices: 44653912--44653960 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
44653902 ATATGTTAGT
* *
44653912 TAA TAA TAT TAA TAA TAA TACA TTA TAA TAA TAA T-A TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
44653956 TAA TA
1 TAA TA
44653961 TTTAATTCAT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 4 0.10
3 33 0.85
4 2 0.05
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:44653942 original size:16 final size:16
Alignment explanation
Indices: 44653916--44653960 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
44653906 GTTAGTTAAT
44653916 AATATTAATAATAATAC
1 AATA-TAATAATAATAC
* *
44653933 ATTATAATAATAATAT
1 AATATAATAATAATAC
44653949 AATATAATAATA
1 AATATAATAATA
44653961 TTTAATTCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
16 22 0.88
17 3 0.12
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (16 bp):
AATATAATAATAATAC
Found at i:44653958 original size:13 final size:14
Alignment explanation
Indices: 44653912--44653961 Score: 61
Period size: 13 Copynumber: 3.6 Consensus size: 14
44653902 ATATGTTAGT
44653912 TAATAATATTAATAA
1 TAATAATA-TAATAA
44653927 TAATACAT-T-ATAA
1 TAATA-ATATAATAA
44653940 TAATAATATAAT-A
1 TAATAATATAATAA
44653953 TAATAATAT
1 TAATAATAT
44653962 TTAATTCATA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
12 2 0.06
13 20 0.62
14 3 0.09
15 5 0.16
16 2 0.06
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (14 bp):
TAATAATATAATAA
Found at i:44654094 original size:3 final size:3
Alignment explanation
Indices: 44654086--44654148 Score: 62
Period size: 3 Copynumber: 22.0 Consensus size: 3
44654076 TAAATTATTT
* *
44654086 TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA T-T TAA T-A TAA -AA CT-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA
*
44654131 TAA TAA TAA TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA
44654149 ATATCTATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
2 6 0.12
3 43 0.88
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:44654456 original size:12 final size:12
Alignment explanation
Indices: 44654407--44654462 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
44654397 ATTTTATTTC
*
44654407 ATAAT-ATAATA
1 ATAATAATAATT
*
44654418 ATAATAATATTT
1 ATAATAATAATT
* **
44654430 A-AATAAAAACC
1 ATAATAATAATT
44654441 ATAATAATAATT
1 ATAATAATAATT
44654453 ATAATAATAA
1 ATAATAATAA
44654463 ATTGATAACT
Statistics
Matches: 34, Mismatches: 9, Indels: 3
0.74 0.20 0.07
Matches are distributed among these distances:
11 12 0.35
12 22 0.65
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (12 bp):
ATAATAATAATT
Found at i:44655930 original size:14 final size:14
Alignment explanation
Indices: 44655899--44655950 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
44655889 AAATACTTTA
* *
44655899 TATGCAAATGTATA
1 TATGCAGATGTATG
*
44655913 TATGCAGATTTATG
1 TATGCAGATGTATG
*
44655927 TATGCGGATGTATG
1 TATGCAGATGTATG
* *
44655941 AATGCGGATG
1 TATGCAGATG
44655951 CACCAATTCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.31, C:0.08, G:0.27, T:0.35
Consensus pattern (14 bp):
TATGCAGATGTATG
Found at i:44660318 original size:13 final size:13
Alignment explanation
Indices: 44660300--44660326 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
44660290 TACAAAAAAA
44660300 TCATTTTATTTTT
1 TCATTTTATTTTT
44660313 TCATTTTATTTTT
1 TCATTTTATTTTT
44660326 T
1 T
44660327 TACCTCTTTT
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:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (13 bp):
TCATTTTATTTTT
Found at i:44661189 original size:14 final size:14
Alignment explanation
Indices: 44661159--44661217 Score: 57
Period size: 14 Copynumber: 4.3 Consensus size: 14
44661149 CGGAAGAGAG
* *
44661159 AAAGAA-AAGAGAG
1 AAAGAAGAAGAAAA
*
44661172 AAAGGAGAAGAAAA
1 AAAGAAGAAGAAAA
*
44661186 AAAGAAGAAGAGAA
1 AAAGAAGAAGAAAA
* *
44661200 GAAGAAGAAAAAAA
1 AAAGAAGAAGAAAA
44661214 AAAG
1 AAAG
44661218 GTAATGTATT
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
13 5 0.14
14 31 0.86
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (14 bp):
AAAGAAGAAGAAAA
Found at i:44661205 original size:25 final size:22
Alignment explanation
Indices: 44661151--44661213 Score: 72
Period size: 25 Copynumber: 2.6 Consensus size: 22
44661141 CCACACACCG
44661151 GAAGAGAGAAAGAAAAGAGAGAAA
1 GAAGA-AGAAA-AAAAGAGAGAAA
*
44661175 GGAGAAGAAAAAAAGAAGAAGAGAA
1 GAAGAAGAAAAAAAG-AG-AGA-AA
44661200 GAAGAAGAAAAAAA
1 GAAGAAGAAAAAAA
44661214 AAAGGTAATG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
22 5 0.15
23 7 0.21
24 7 0.21
25 15 0.44
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (22 bp):
GAAGAAGAAAAAAAGAGAGAAA
Found at i:44661443 original size:33 final size:33
Alignment explanation
Indices: 44661400--44661507 Score: 95
Period size: 33 Copynumber: 3.4 Consensus size: 33
44661390 GTTTTTTATA
*
44661400 ATTATTTTAAAATTAATTTGTTAGTAATTTAGG
1 ATTATGTTAAAATTAATTTGTTAGTAATTTAGG
*
44661433 ATTATGTTAAAATT-TTTTG-T-GT--TTGTA--
1 ATTATGTTAAAATTAATTTGTTAGTAATT-TAGG
* * *
44661460 ATTATTTTAAAATTAAATTATTAGTAATTTAGG
1 ATTATGTTAAAATTAATTTGTTAGTAATTTAGG
*
44661493 ATTAAGTTATAAATT
1 ATTATGTTA-AAATT
44661508 GTTGTGTTTA
Statistics
Matches: 58, Mismatches: 8, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
27 13 0.22
28 4 0.07
29 3 0.05
30 4 0.07
31 3 0.05
32 6 0.10
33 20 0.34
34 5 0.09
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (33 bp):
ATTATGTTAAAATTAATTTGTTAGTAATTTAGG
Found at i:44661484 original size:60 final size:61
Alignment explanation
Indices: 44661384--44661517 Score: 191
Period size: 60 Copynumber: 2.2 Consensus size: 61
44661374 GAATGTAATT
* * * *
44661384 TTTTTTGTTTTTTATAATTATTTTAAAATTAATTTGTTAGTAATTTAGGATTATGTTA-AAA
1 TTTTTTG-TGTTTATAATTATTTTAAAATTAAATTATTAGTAATTTAGGATTAAGTTATAAA
*
44661445 TTTTTTGTGTTTGTAATTATTTTAAAATTAAATTATTAGTAATTTAGGATTAAGTTATAAA
1 TTTTTTGTGTTTATAATTATTTTAAAATTAAATTATTAGTAATTTAGGATTAAGTTATAAA
*
44661506 -TTGTTGTGTTTA
1 TTTTTTGTGTTTA
44661518 GTTTAGTATT
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
60 55 0.85
61 10 0.15
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (61 bp):
TTTTTTGTGTTTATAATTATTTTAAAATTAAATTATTAGTAATTTAGGATTAAGTTATAAA
Found at i:44661587 original size:14 final size:14
Alignment explanation
Indices: 44661561--44661613 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
44661551 ATAAAAAATT
44661561 AAAANAGAA-AAGAG
1 AAAA-AGAAGAAGAG
* * *
44661575 AGAAAGGAGAAGAA
1 AAAAAGAAGAAGAG
44661589 AAAAAGAAGAAGAG
1 AAAAAGAAGAAGAG
*
44661603 AAGAAGAAGAA
1 AAAAAGAAGAA
44661614 AAAAAAAAGG
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
13 3 0.10
14 28 0.90
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.00
Consensus pattern (14 bp):
AAAAAGAAGAAGAG
Found at i:44661601 original size:28 final size:27
Alignment explanation
Indices: 44661561--44661622 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 27
44661551 ATAAAAAATT
* * *
44661561 AAAANAGAAAAGAG-AGAAAGGAGAAGA
1 AAAAAAGAAAAGAGAAG-AAGAAGAAAA
44661588 AAAAAAGAAGAAGAGAAGAAGAAGAAAA
1 AAAAAAGAA-AAGAGAAGAAGAAGAAAA
44661616 AAAAAAG
1 AAAAAAG
44661623 GTAATGTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 8 0.27
28 20 0.67
29 2 0.07
ACGTcount: A:0.73, C:0.00, G:0.26, T:0.00
Consensus pattern (27 bp):
AAAAAAGAAAAGAGAAGAAGAAGAAAA
Found at i:44661607 original size:405 final size:404
Alignment explanation
Indices: 44661159--44661972 Score: 1601
Period size: 405 Copynumber: 2.0 Consensus size: 404
44661149 CGGAAGAGAG
44661159 AAAGAAAAGAGAGAAAGGAGAAGAAAAAAAGAAGAAGAGAAGAAGAAGAAAAAAAAAAGGTAATG
1 AAAGAAAAGAGAGAAAGGAGAAGAAAAAAAGAAGAAGAGAAGAAGAAGAAAAAAAAAAGGTAATG
44661224 TATTAAAAAAAGGTAATGTCTTTTTTAGTAAATAATTTTGTTTATAATTTAAAGAGTTTAATTAA
66 TATTAAAAAAAGGTAATGTCTTTTTTAGTAAATAATTTTGTTTATAATTTAAAGAGTTTAATTAA
44661289 GATATTGTGGTTTTTTTTTGTTATTAATTATTAATTATAAAATATTTATGTTTAGTGTTTATAGT
131 GATATTGTGGTTTTTTTTTGTTATTAATTATTAATTATAAAATATTTATGTTTAGTGTTTATAGT
44661354 TTTGGATTAATATTTTGTATGAATGTAATTTTTTTTGTTTTTTATAATTATTTTAAAATTAATTT
196 TTTGGATTAATATTTTGTATGAATGTAATTTTTTTTGTTTTTTATAATTATTTTAAAATTAATTT
44661419 GTTAGTAATTTAGGATTATGTTAAAATTTTTTGTGTTTGTAATTATTTTAAAATTAAATTATTAG
261 GTTAGTAATTTAGGATTATGTTAAAATTTTTTGTGTTTGTAATTATTTTAAAATTAAATTATTAG
44661484 TAATTTAGGATTAAGTTATAAATTGTTGTGTTTAGTTTAGTATTTGGTGAGTTTAACATATAAGT
326 TAATTTAGGATTAAGTTATAAATTGTTGTGTTTAGTTTAGTATTTGGTGAGTTTAACATATAAGT
44661549 TTATAAAAAATTAA
391 TTATAAAAAATTAA
44661563 AANAGAAAAGAGAGAAAGGAGAAGAAAAAAAGAAGAAGAGAAGAAGAAGAAAAAAAAAAGGTAAT
1 AA-AGAAAAGAGAGAAAGGAGAAGAAAAAAAGAAGAAGAGAAGAAGAAGAAAAAAAAAAGGTAAT
44661628 GTATTAAAAAAAGGTAATGTCTTTTTTAGTAAATAATTTTGTTTATAATTTAAAGAGTTTAATTA
65 GTATTAAAAAAAGGTAATGTCTTTTTTAGTAAATAATTTTGTTTATAATTTAAAGAGTTTAATTA
44661693 AGATATTGTGGTTTTTTTTTGTTATTAATTATTAATTATAAAATATTTATGTTTAGTGTTTATAG
130 AGATATTGTGGTTTTTTTTTGTTATTAATTATTAATTATAAAATATTTATGTTTAGTGTTTATAG
44661758 TTTTGGATTAATATTTTGTATGAATGTAATTTTTTTTGTTTTTTATAATTATTTTAAAATTAATT
195 TTTTGGATTAATATTTTGTATGAATGTAATTTTTTTTGTTTTTTATAATTATTTTAAAATTAATT
44661823 TGTTAGTAATTTAGGATTATGTTAAAATTTTTTGTGTTTGTAATTATTTTAAAATTAAATTATTA
260 TGTTAGTAATTTAGGATTATGTTAAAATTTTTTGTGTTTGTAATTATTTTAAAATTAAATTATTA
44661888 GTAATTTAGGATTAAGTTATAAATTGTTGTGTTTAGTTTAGTATTTGGTGAGTTTAACATATAAG
325 GTAATTTAGGATTAAGTTATAAATTGTTGTGTTTAGTTTAGTATTTGGTGAGTTTAACATATAAG
44661953 TTTATAAAAAAAATTAA
390 TTTAT--AAAAAATTAA
44661970 AAA
1 AAA
44661973 TCATTTCATT
Statistics
Matches: 407, Mismatches: 0, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
404 2 0.00
405 392 0.96
406 1 0.00
407 12 0.03
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.44
Consensus pattern (404 bp):
AAAGAAAAGAGAGAAAGGAGAAGAAAAAAAGAAGAAGAGAAGAAGAAGAAAAAAAAAAGGTAATG
TATTAAAAAAAGGTAATGTCTTTTTTAGTAAATAATTTTGTTTATAATTTAAAGAGTTTAATTAA
GATATTGTGGTTTTTTTTTGTTATTAATTATTAATTATAAAATATTTATGTTTAGTGTTTATAGT
TTTGGATTAATATTTTGTATGAATGTAATTTTTTTTGTTTTTTATAATTATTTTAAAATTAATTT
GTTAGTAATTTAGGATTATGTTAAAATTTTTTGTGTTTGTAATTATTTTAAAATTAAATTATTAG
TAATTTAGGATTAAGTTATAAATTGTTGTGTTTAGTTTAGTATTTGGTGAGTTTAACATATAAGT
TTATAAAAAATTAA
Found at i:44661848 original size:33 final size:33
Alignment explanation
Indices: 44661805--44661912 Score: 95
Period size: 33 Copynumber: 3.4 Consensus size: 33
44661795 GTTTTTTATA
*
44661805 ATTATTTTAAAATTAATTTGTTAGTAATTTAGG
1 ATTATGTTAAAATTAATTTGTTAGTAATTTAGG
*
44661838 ATTATGTTAAAATT-TTTTG-T-GT--TTGTA--
1 ATTATGTTAAAATTAATTTGTTAGTAATT-TAGG
* * *
44661865 ATTATTTTAAAATTAAATTATTAGTAATTTAGG
1 ATTATGTTAAAATTAATTTGTTAGTAATTTAGG
*
44661898 ATTAAGTTATAAATT
1 ATTATGTTA-AAATT
44661913 GTTGTGTTTA
Statistics
Matches: 58, Mismatches: 8, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
27 13 0.22
28 4 0.07
29 3 0.05
30 4 0.07
31 3 0.05
32 6 0.10
33 20 0.34
34 5 0.09
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (33 bp):
ATTATGTTAAAATTAATTTGTTAGTAATTTAGG
Found at i:44661889 original size:60 final size:61
Alignment explanation
Indices: 44661789--44661922 Score: 191
Period size: 60 Copynumber: 2.2 Consensus size: 61
44661779 GAATGTAATT
* * * *
44661789 TTTTTTGTTTTTTATAATTATTTTAAAATTAATTTGTTAGTAATTTAGGATTATGTTA-AAA
1 TTTTTTG-TGTTTATAATTATTTTAAAATTAAATTATTAGTAATTTAGGATTAAGTTATAAA
*
44661850 TTTTTTGTGTTTGTAATTATTTTAAAATTAAATTATTAGTAATTTAGGATTAAGTTATAAA
1 TTTTTTGTGTTTATAATTATTTTAAAATTAAATTATTAGTAATTTAGGATTAAGTTATAAA
*
44661911 -TTGTTGTGTTTA
1 TTTTTTGTGTTTA
44661923 GTTTAGTATT
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
60 55 0.85
61 10 0.15
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (61 bp):
TTTTTTGTGTTTATAATTATTTTAAAATTAAATTATTAGTAATTTAGGATTAAGTTATAAA
Found at i:44665567 original size:17 final size:18
Alignment explanation
Indices: 44665545--44665588 Score: 65
Period size: 17 Copynumber: 2.5 Consensus size: 18
44665535 TCTTTCCCCC
44665545 AACTAAAATAAAA-AATA
1 AACTAAAATAAAATAATA
44665562 AACTAAAAATAAAATAATA
1 AACT-AAAATAAAATAATA
44665581 AAC-AAAAT
1 AACTAAAAT
44665589 TTACTTTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 9 0.36
18 9 0.36
19 7 0.28
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.18
Consensus pattern (18 bp):
AACTAAAATAAAATAATA
Found at i:44672533 original size:20 final size:19
Alignment explanation
Indices: 44672505--44672557 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
44672495 ATAAAATTGT
*
44672505 AATATTAAATAATTTATTAA
1 AATAATAAATAATTTATT-A
*
44672525 AATAATAAATTATATTATTA
1 AATAATAAATAAT-TTATTA
44672545 AAT-ATAAATAATT
1 AATAATAAATAATT
44672558 AAATATGCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 1 0.03
19 8 0.28
20 15 0.52
21 5 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AATAATAAATAATTTATTA
Found at i:44672544 original size:33 final size:31
Alignment explanation
Indices: 44672486--44672548 Score: 90
Period size: 33 Copynumber: 2.0 Consensus size: 31
44672476 TTGTTAATTT
*
44672486 TTTATTAAAATAAAATTGTAATATTAAATAA
1 TTTATTAAAATAAAATTATAATATTAAATAA
*
44672517 TTTATTAAAATAATAAATTATATTATTAAATA
1 TTTATTAAAAT-A-AAATTATAATATTAAATA
44672549 TAAATAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 11 0.39
32 1 0.04
33 16 0.57
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (31 bp):
TTTATTAAAATAAAATTATAATATTAAATAA
Found at i:44683100 original size:26 final size:26
Alignment explanation
Indices: 44683070--44683137 Score: 100
Period size: 26 Copynumber: 2.6 Consensus size: 26
44683060 CCATATAGGA
*
44683070 AAGCTCACAAAGAGCCTTTAATCCAG
1 AAGCTCACAAAGAGCCTTTAATACAG
**
44683096 AAGCTCACAAAGAGCCTTTAATAGGG
1 AAGCTCACAAAGAGCCTTTAATACAG
*
44683122 AAGCTCACGAAGAGCC
1 AAGCTCACAAAGAGCC
44683138 ATATAACGAG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.16
Consensus pattern (26 bp):
AAGCTCACAAAGAGCCTTTAATACAG
Found at i:44686198 original size:35 final size:35
Alignment explanation
Indices: 44686159--44686235 Score: 111
Period size: 35 Copynumber: 2.2 Consensus size: 35
44686149 ACCCCATCAG
*
44686159 AGATACAAATGCATATTCGGGCCCAAGCCCAT-TT
1 AGATACAAATACATATTCGGGCCCAAGCCCATCTT
* *
44686193 CAGATACAAATACATATTTGGGCCTAAGCCCATCTT
1 -AGATACAAATACATATTCGGGCCCAAGCCCATCTT
44686229 AGATACA
1 AGATACA
44686236 GATATAGATA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 36 0.95
36 2 0.05
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.25
Consensus pattern (35 bp):
AGATACAAATACATATTCGGGCCCAAGCCCATCTT
Found at i:44696031 original size:6 final size:6
Alignment explanation
Indices: 44696017--44696049 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
44696007 AAAAGAAATC
*
44696017 AAAAAG AAAAGG AAAAGG AAAAGG AAAAGG AAA
1 AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG AAA
44696050 GGTAGAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (6 bp):
AAAAGG
Found at i:44697600 original size:46 final size:44
Alignment explanation
Indices: 44697507--44697632 Score: 155
Period size: 46 Copynumber: 2.8 Consensus size: 44
44697497 TGATATGTGT
* *
44697507 GCTAGTGTAAGACATGTCTGGGACATGCATTAGCCATAACATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCA-TCGGCATAACA-GAGA
*
44697553 GCTAGTGTAAGGCATGTCTGGGACATGCATCGGCATTGAGACA-AGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCA-T-A-ACAGAGA
* *
44697599 GCTAGTTTAAGACATGTCTAGGACATGCATCGGC
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGC
44697633 CTCGCGATAT
Statistics
Matches: 71, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
45 4 0.06
46 63 0.89
47 1 0.01
48 3 0.04
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (44 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCATAACAGAGA
Found at i:44697752 original size:49 final size:49
Alignment explanation
Indices: 44697693--44697801 Score: 139
Period size: 49 Copynumber: 2.2 Consensus size: 49
44697683 TGTTGTGTGT
*
44697693 CAGTGTAAGACCTCTCTGGGACATGCCATCGACAC-CGATAAATGAGAGC
1 CAGTGTAAGACCTCTCTGGGACATGCCATCGAC-CTCGATAAATGAAAGC
* * * * **
44697742 CAGTGTAAGACCTGTCTGTGACATGGCATCGACCTCGCTGTATGAAAGC
1 CAGTGTAAGACCTCTCTGGGACATGCCATCGACCTCGATAAATGAAAGC
44697791 CAGTGTAAGAC
1 CAGTGTAAGAC
44697802 TATGTTTGAG
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
48 1 0.02
49 51 0.98
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.21
Consensus pattern (49 bp):
CAGTGTAAGACCTCTCTGGGACATGCCATCGACCTCGATAAATGAAAGC
Found at i:44701188 original size:21 final size:22
Alignment explanation
Indices: 44701149--44701189 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
44701139 CTTGCGTTTG
*
44701149 TTCATTTTTTCCCTCTATTTTC
1 TTCATTTTTTCACTCTATTTTC
*
44701171 TTCATTTTTTTACT-TATTT
1 TTCATTTTTTCACTCTATTT
44701190 CATGATATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.12, C:0.20, G:0.00, T:0.68
Consensus pattern (22 bp):
TTCATTTTTTCACTCTATTTTC
Found at i:44705068 original size:16 final size:16
Alignment explanation
Indices: 44705047--44705089 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
44705037 GGGGTTTTGG
44705047 GTTTTCTTTATGTTTT
1 GTTTTCTTTATGTTTT
44705063 GTTTTCTTTATGTTTT
1 GTTTTCTTTATGTTTT
*
44705079 GTTATCTTTAT
1 GTTTTCTTTAT
44705090 TCTTTTGAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.09, C:0.07, G:0.12, T:0.72
Consensus pattern (16 bp):
GTTTTCTTTATGTTTT
Found at i:44710739 original size:48 final size:49
Alignment explanation
Indices: 44710676--44710986 Score: 223
Period size: 49 Copynumber: 6.5 Consensus size: 49
44710666 AGAGCTAGTA
* * *
44710676 TAAGACATGTTTGGGACAT-GCATCGGCCTCGAGATATTTAAGCGAGTG
1 TAAGACATGTCTGGGACATGGCATCGGCCTCGAGATATGTAAGCCAGTG
* * * * *
44710724 TAAGACATGTCTGGGACAT-GCATCGGCATTGAGACAAG--AGCTAGTG
1 TAAGACATGTCTGGGACATGGCATCGGCCTCGAGATATGTAAGCCAGTG
* * * ** * ** *
44710770 TAAGACATGTCTAGAATAT-GCATCAACCTCGCGATATACAAGCTAGTG
1 TAAGACATGTCTGGGACATGGCATCGGCCTCGAGATATGTAAGCCAGTG
* * * ** *
44710818 TAAGACCTGTCTGGGACATGGCATCAG-CT--TG-T-TGTGTGTCAGTG
1 TAAGACATGTCTGGGACATGGCATCGGCCTCGAGATATGTAAGCCAGTG
* * * *
44710862 TAAGACCTGTCTGGGACATGGCATCGTCAC-CGATAGATG-AGAGCCAGTG
1 TAAGACATGTCTGGGACATGGCATCGGC-CTCGAGATATGTA-AGCCAGTG
* * ** *
44710911 TAAGACCTGTATGGGACATGGCATCGGCCTCGCTATATGAAAGCCAGTG
1 TAAGACATGTCTGGGACATGGCATCGGCCTCGAGATATGTAAGCCAGTG
44710960 TAAGACCATGTCTGGGACATGGCATCG
1 TAAGA-CATGTCTGGGACATGGCATCG
44710987 ACAACTTAAC
Statistics
Matches: 206, Mismatches: 44, Indels: 24
0.75 0.16 0.09
Matches are distributed among these distances:
44 31 0.15
45 1 0.00
46 36 0.17
48 58 0.28
49 60 0.29
50 20 0.10
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.24
Consensus pattern (49 bp):
TAAGACATGTCTGGGACATGGCATCGGCCTCGAGATATGTAAGCCAGTG
Found at i:44710775 original size:94 final size:95
Alignment explanation
Indices: 44710666--44710842 Score: 239
Period size: 94 Copynumber: 1.9 Consensus size: 95
44710656 CCACAGCATG
* * * ** **
44710666 AGAGCTAGTATAAGACATGTTTGGGACATGCATCGGCCTCGAGATATTTAAGCGAGTGTAAGACA
1 AGAGCTAGTATAAGACATGTCTAGAACATGCATCAACCTCGAGATATACAAGCGAGTGTAAGACA
44710731 TGTCTGGGACAT-GCATCGGCATTGAGACA
66 TGTCTGGGACATGGCATCGGCATTGAGACA
* * * * *
44710760 AGAGCTAGTGTAAGACATGTCTAGAATATGCATCAACCTCGCGATATACAAGCTAGTGTAAGACC
1 AGAGCTAGTATAAGACATGTCTAGAACATGCATCAACCTCGAGATATACAAGCGAGTGTAAGACA
44710825 TGTCTGGGACATGGCATC
66 TGTCTGGGACATGGCATC
44710843 AGCTTGTTGT
Statistics
Matches: 70, Mismatches: 12, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
94 65 0.93
95 5 0.07
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.24
Consensus pattern (95 bp):
AGAGCTAGTATAAGACATGTCTAGAACATGCATCAACCTCGAGATATACAAGCGAGTGTAAGACA
TGTCTGGGACATGGCATCGGCATTGAGACA
Found at i:44710781 original size:46 final size:47
Alignment explanation
Indices: 44710623--44710986 Score: 183
Period size: 48 Copynumber: 7.7 Consensus size: 47
44710613 TGATATGTGT
* * **
44710623 GCTAGTGTAAGACATATCTGGGATATGCATCAACCA-C-AG-CATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATC-GGCATCGAGACAT-AGA
* * * *
44710669 GCTAGTATAAGACATGTTTGGGACATGCATCGGCCTCGAGATATTTA-A
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGACA--TAGA
* *
44710717 GCGAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGACA-AGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGACATAGA
* * * ** * * * *
44710763 GCTAGTGTAAGACATGTCTAGAATATGCATCAACCTCGCGATATACAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGACATA-GA
* * * * *
44710811 GCTAGTGTAAGACCTGTCTGGGACATGGCATCAGC-TTGTTG---T-GT
1 GCTAGTGTAAGACATGTCTGGGACAT-GCATCGGCATCG-AGACATAGA
* * * * *
44710855 G-TCAGTGTAAGACCTGTCTGGGACATGGCATCGTCACCGATAGATGAGA
1 GCT-AGTGTAAGACATGTCTGGGACAT-GCATCGGCATCGAGACAT-AGA
* * * * ** * *
44710904 GCCAGTGTAAGACCTGTATGGGACATGGCATCGGCCTCGCTATATGAAA
1 GCTAGTGTAAGACATGTCTGGGACAT-GCATCGGCATCGAGACAT-AGA
*
44710953 GCCAGTGTAAGACCATGTCTGGGACATGGCATCG
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCG
44710987 ACAACTTAAC
Statistics
Matches: 248, Mismatches: 51, Indels: 34
0.74 0.15 0.10
Matches are distributed among these distances:
43 1 0.00
44 31 0.12
45 3 0.01
46 63 0.25
47 4 0.02
48 64 0.26
49 62 0.25
50 20 0.08
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (47 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGACATAGA
Found at i:44714705 original size:12 final size:13
Alignment explanation
Indices: 44714652--44714765 Score: 59
Period size: 12 Copynumber: 9.5 Consensus size: 13
44714642 TTTTTAAGTC
*
44714652 ATTTTTATAA-TA
1 ATTTTAATAATTA
*
44714664 ATTTCAA-AATTA
1 ATTTTAATAATTA
*
44714676 A-ATT-ATAATTA
1 ATTTTAATAATTA
*
44714687 TTTTTAATAA-TA
1 ATTTTAATAATTA
* * *
44714699 ATTTTAAAAAGTC
1 ATTTTAATAATTA
*
44714712 ATTTTTATAA-TA
1 ATTTTAATAATTA
*
44714724 ATTTGAA-AATTA
1 ATTTTAATAATTA
*
44714736 A-ATT-ATAATTA
1 ATTTTAATAATTA
*
44714747 TTTTTAATAA-TA
1 ATTTTAATAATTA
44714759 ATTTTAA
1 ATTTTAA
44714766 ATTGAATTAT
Statistics
Matches: 74, Mismatches: 19, Indels: 18
0.67 0.17 0.16
Matches are distributed among these distances:
10 2 0.03
11 16 0.22
12 39 0.53
13 17 0.23
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (13 bp):
ATTTTAATAATTA
Found at i:44714716 original size:60 final size:60
Alignment explanation
Indices: 44714647--44714766 Score: 231
Period size: 60 Copynumber: 2.0 Consensus size: 60
44714637 ATTCATTTTT
44714647 AAGTCATTTTTATAATAATTTCAAAATTAAATTATAATTATTTTTAATAATAATTTTAAA
1 AAGTCATTTTTATAATAATTTCAAAATTAAATTATAATTATTTTTAATAATAATTTTAAA
*
44714707 AAGTCATTTTTATAATAATTTGAAAATTAAATTATAATTATTTTTAATAATAATTTTAAA
1 AAGTCATTTTTATAATAATTTCAAAATTAAATTATAATTATTTTTAATAATAATTTTAAA
44714767 TTGAATTATA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.48
Consensus pattern (60 bp):
AAGTCATTTTTATAATAATTTCAAAATTAAATTATAATTATTTTTAATAATAATTTTAAA
Found at i:44714752 original size:34 final size:34
Alignment explanation
Indices: 44714712--44714781 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 34
44714702 TTAAAAAGTC
44714712 ATTTTT-ATAATAATTTGAAAATTAAATTATAATT
1 ATTTTTAATAATAATTT-AAAATTAAATTATAATT
* *
44714746 ATTTTTAATAATAATTTTAAATTGAATTATAATT
1 ATTTTTAATAATAATTTAAAATTAAATTATAATT
44714780 AT
1 AT
44714782 AATTATCACA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
34 23 0.70
35 10 0.30
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (34 bp):
ATTTTTAATAATAATTTAAAATTAAATTATAATT
Found at i:44714936 original size:23 final size:20
Alignment explanation
Indices: 44714881--44714949 Score: 61
Period size: 23 Copynumber: 3.4 Consensus size: 20
44714871 AAAATTTCTT
*
44714881 AATTA-ATAATTGTAAATTA
1 AATTATATAATTTTAAATTA
*
44714900 AATTATAAATATTTTAAATTGA
1 AATTATATA-ATTTTAAATT-A
*
44714922 TAATTATCATAATTTT-TATTA
1 -AATTAT-ATAATTTTAAATTA
44714943 AATTATA
1 AATTATA
44714950 ATTTTTTGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
19 6 0.15
20 8 0.20
21 10 0.24
22 4 0.10
23 11 0.27
24 2 0.05
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (20 bp):
AATTATATAATTTTAAATTA
Found at i:44718090 original size:30 final size:30
Alignment explanation
Indices: 44718048--44718105 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
44718038 TATATTCAAG
44718048 TTGAACGTTTGTAGCAATTTGTGTGTTTCA
1 TTGAACGTTTGTAGCAATTTGTGTGTTTCA
*
44718078 TTGAA-GTGTTGTAGCAATTTTTGTGTTT
1 TTGAACGT-TTGTAGCAATTTGTGTGTTT
44718106 TGTAAAAGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 2 0.08
30 24 0.92
ACGTcount: A:0.19, C:0.07, G:0.24, T:0.50
Consensus pattern (30 bp):
TTGAACGTTTGTAGCAATTTGTGTGTTTCA
Found at i:44718120 original size:30 final size:29
Alignment explanation
Indices: 44718054--44718122 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
44718044 CAAGTTGAAC
**
44718054 GTTTGTAGCAATTTGTGTGTTTCATTGAA
1 GTTTGTAGCAATTTGTGTGTTTCATAAAA
* **
44718083 GTGTTGTAGCAATTTTTGTGTTTTGTAAAA
1 GT-TTGTAGCAATTTGTGTGTTTCATAAAA
44718113 GGTTTGTAGC
1 -GTTTGTAGC
44718123 GACTTTCTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
29 2 0.06
30 29 0.88
31 2 0.06
ACGTcount: A:0.20, C:0.06, G:0.26, T:0.48
Consensus pattern (29 bp):
GTTTGTAGCAATTTGTGTGTTTCATAAAA
Found at i:44721602 original size:9 final size:10
Alignment explanation
Indices: 44721578--44721602 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
44721568 AAATAAAAAT
44721578 ATTTTTGAAA
1 ATTTTTGAAA
44721588 ATTTTTGAAA
1 ATTTTTGAAA
44721598 ATTTT
1 ATTTT
44721603 CCCTAAAAAC
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:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (10 bp):
ATTTTTGAAA
Found at i:44722191 original size:21 final size:21
Alignment explanation
Indices: 44722167--44722207 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
44722157 CTTCGTCTTC
44722167 TTCCTCAACTT-CTTCTTCCTT
1 TTCCTC-ACTTGCTTCTTCCTT
*
44722188 TTCCTCTCTTGCTTCTTCCT
1 TTCCTCACTTGCTTCTTCCT
44722208 CCTCTTCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.05, C:0.39, G:0.02, T:0.54
Consensus pattern (21 bp):
TTCCTCACTTGCTTCTTCCTT
Found at i:44744548 original size:35 final size:35
Alignment explanation
Indices: 44744502--44744570 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
44744492 AATGGTCATT
44744502 GTGGTTTGAGGAGTTTATACTCCTCATTCCTGCTG
1 GTGGTTTGAGGAGTTTATACTCCTCATTCCTGCTG
44744537 GTGGTTTGAGGAGTTTATACTCCTCATTCCTGCT
1 GTGGTTTGAGGAGTTTATACTCCTCATTCCTGCT
44744571 ATCAATCTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.41
Consensus pattern (35 bp):
GTGGTTTGAGGAGTTTATACTCCTCATTCCTGCTG
Found at i:44744660 original size:30 final size:30
Alignment explanation
Indices: 44744620--44744681 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
44744610 TACCTTAAAA
*
44744620 GTGCCAAACTTAGGATGACTCACATTCACC
1 GTGCCAAACTTAGGATGACTCACATCCACC
* * *
44744650 GTGCCGAACTTGGGATGACTCACCTCCACC
1 GTGCCAAACTTAGGATGACTCACATCCACC
44744680 GT
1 GT
44744682 ACTGAGTACC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.23
Consensus pattern (30 bp):
GTGCCAAACTTAGGATGACTCACATCCACC
Found at i:44749158 original size:19 final size:19
Alignment explanation
Indices: 44749114--44749163 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
44749104 CATTCTATAC
* *
44749114 CATCAAACATACTAGCAAA
1 CATCAATCATTCTAGCAAA
44749133 CATCAATCATTCTAGCAAA
1 CATCAATCATTCTAGCAAA
44749152 CATCAATCATTC
1 CATCAATCATTC
44749164 AAAGCTTCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.44, C:0.28, G:0.04, T:0.24
Consensus pattern (19 bp):
CATCAATCATTCTAGCAAA
Found at i:44749399 original size:31 final size:31
Alignment explanation
Indices: 44749364--44749425 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
44749354 CCTCAAACAA
* * *
44749364 AGACTTCCTAGGTACATGCCATTGCAAATTT
1 AGACTTCCTAGGCACATACCATTACAAATTT
44749395 AGACTTCCTAGGCACATACCATTACAAATTT
1 AGACTTCCTAGGCACATACCATTACAAATTT
44749426 TAACATCACC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.31
Consensus pattern (31 bp):
AGACTTCCTAGGCACATACCATTACAAATTT
Found at i:44751292 original size:30 final size:30
Alignment explanation
Indices: 44751258--44751320 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
44751248 ACTTAACAAG
44751258 CAAATG-CTTCTAAAATAATAAAAAAATTAA
1 CAAATGCCTT-TAAAATAATAAAAAAATTAA
*
44751288 CAAATGCCTTTAAAATAATAAGAAAATTAA
1 CAAATGCCTTTAAAATAATAAAAAAATTAA
44751318 CAA
1 CAA
44751321 TAAAATAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 28 0.90
31 3 0.10
ACGTcount: A:0.59, C:0.11, G:0.05, T:0.25
Consensus pattern (30 bp):
CAAATGCCTTTAAAATAATAAAAAAATTAA
Found at i:44756585 original size:27 final size:27
Alignment explanation
Indices: 44756348--44756573 Score: 452
Period size: 27 Copynumber: 8.4 Consensus size: 27
44756338 TCGTTTCCCA
44756348 CCAAAATTTTCTTTTAATATTTTTCCT
1 CCAAAATTTTCTTTTAATATTTTTCCT
44756375 CCAAAATTTTCTTTTAATATTTTTCCT
1 CCAAAATTTTCTTTTAATATTTTTCCT
44756402 CCAAAATTTTCTTTTAATATTTTTCCT
1 CCAAAATTTTCTTTTAATATTTTTCCT
44756429 CCAAAATTTTCTTTTAATATTTTTCCT
1 CCAAAATTTTCTTTTAATATTTTTCCT
44756456 CCAAAATTTTCTTTTAATATTTTTCCT
1 CCAAAATTTTCTTTTAATATTTTTCCT
44756483 CCAAAATTTTCTTTTAATATTTTTCCT
1 CCAAAATTTTCTTTTAATATTTTTCCT
44756510 CCAAAATTTTCTTTTAATATTTTTCCT
1 CCAAAATTTTCTTTTAATATTTTTCCT
44756537 CCAAAATTTTCTTTTAATATTTTTCCT
1 CCAAAATTTTCTTTTAATATTTTTCCT
44756564 CCAAAATTTT
1 CCAAAATTTT
44756574 ACTCCCCTAT
Statistics
Matches: 199, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 199 1.00
ACGTcount: A:0.27, C:0.19, G:0.00, T:0.55
Consensus pattern (27 bp):
CCAAAATTTTCTTTTAATATTTTTCCT
Found at i:44768180 original size:19 final size:20
Alignment explanation
Indices: 44768128--44768180 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
44768118 AAAATTATAA
*
44768128 AAAAGTTCAAAATAATTTTC
1 AAAAGTTCAAAATAATTTTT
* *
44768148 AAAATTTTAAAATAATTTTT
1 AAAAGTTCAAAATAATTTTT
44768168 AAAA-TTCAAAATA
1 AAAAGTTCAAAATA
44768181 TTTATATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 8 0.28
20 21 0.72
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.38
Consensus pattern (20 bp):
AAAAGTTCAAAATAATTTTT
Found at i:44768190 original size:20 final size:19
Alignment explanation
Indices: 44768167--44768206 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
44768157 AAATAATTTT
44768167 TAAAATTCAAAATATTTATA
1 TAAAATTCAAAA-ATTTATA
*
44768187 T-AAATTCCAAAATTTATA
1 TAAAATTCAAAAATTTATA
44768205 TA
1 TA
44768207 TTTTTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
18 8 0.44
19 9 0.50
20 1 0.06
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAAATTCAAAAATTTATA
Found at i:44768207 original size:20 final size:19
Alignment explanation
Indices: 44768156--44768206 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
44768146 TCAAAATTTT
*
44768156 AAAATAATTTTTA-AAATTC
1 AAAAT-ATTTATATAAATTC
44768175 AAAATATTTATATAAATTC
1 AAAATATTTATATAAATTC
*
44768194 CAAA-ATTTATATA
1 AAAATATTTATATA
44768207 TTTTTAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 15 0.52
19 14 0.48
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (19 bp):
AAAATATTTATATAAATTC
Found at i:44768705 original size:21 final size:19
Alignment explanation
Indices: 44768681--44768730 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 19
44768671 CATGTGTCAT
44768681 AAAAATAAAAAATATCATTTC
1 AAAAATAAAAAA-ATC-TTTC
*
44768702 AAAAATTAAAAAAATCTTTT
1 AAAAA-TAAAAAAATCTTTC
*
44768722 AAAAGTAAA
1 AAAAATAAA
44768731 GAATTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 4 0.15
20 7 0.27
21 8 0.31
22 7 0.27
ACGTcount: A:0.64, C:0.06, G:0.02, T:0.28
Consensus pattern (19 bp):
AAAAATAAAAAAATCTTTC
Found at i:44772881 original size:16 final size:17
Alignment explanation
Indices: 44772837--44772883 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
44772827 TTATTTTTCA
*
44772837 AAAAATAAAATTTTTTGT
1 AAAAAT-AATTTTTTTGT
**
44772855 TCAAATAATTTTTTTGT
1 AAAAATAATTTTTTTGT
44772872 AAAAAT-ATTTTT
1 AAAAATAATTTTT
44772884 CGAAAAATTA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
16 6 0.25
17 14 0.58
18 4 0.17
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (17 bp):
AAAAATAATTTTTTTGT
Found at i:44779461 original size:15 final size:15
Alignment explanation
Indices: 44779420--44779461 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
44779410 ACCTCTTAAA
44779420 ATAATTATATA-TAT
1 ATAATTATATATTAT
44779434 ATATATTATATATTAT
1 ATA-ATTATATATTAT
44779450 -TAATTATCATAT
1 ATAATTAT-ATAT
44779462 GATAATAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 8 0.32
15 14 0.56
16 3 0.12
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (15 bp):
ATAATTATATATTAT
Found at i:44783262 original size:32 final size:32
Alignment explanation
Indices: 44783222--44783288 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
44783212 AAATAAGCTG
*
44783222 AAAAATTATGCAGGGATGTAAGAAAGATTTCA
1 AAAAATTATACAGGGATGTAAGAAAGATTTCA
*
44783254 AAAAATTATACAGGGATGTTAGAAAGATTTCA
1 AAAAATTATACAGGGATGTAAGAAAGATTTCA
44783286 AAA
1 AAA
44783289 CTAATAAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.49, C:0.06, G:0.19, T:0.25
Consensus pattern (32 bp):
AAAAATTATACAGGGATGTAAGAAAGATTTCA
Found at i:44785264 original size:30 final size:30
Alignment explanation
Indices: 44785228--44785288 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
44785218 ATTTTATTGT
*
44785228 TAATTTTTTTATTATTTTA-AAGACATTTGC
1 TAATTTTGTTATTATTTTAGAAG-CATTTGC
44785258 TAATTTTGTTATTATTTTAGAAGCATTTGC
1 TAATTTTGTTATTATTTTAGAAGCATTTGC
44785288 T
1 T
44785289 TGTTAAATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 26 0.90
31 3 0.10
ACGTcount: A:0.28, C:0.07, G:0.10, T:0.56
Consensus pattern (30 bp):
TAATTTTGTTATTATTTTAGAAGCATTTGC
Found at i:44785440 original size:12 final size:12
Alignment explanation
Indices: 44785410--44785442 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
44785400 TATATATTTT
44785410 AAAATT-ATATA
1 AAAATTAATATA
44785421 AAAA-TAATATA
1 AAAATTAATATA
44785432 AAAATTAATAT
1 AAAATTAATAT
44785443 GGGCGGGTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:44785774 original size:17 final size:18
Alignment explanation
Indices: 44785744--44785781 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
44785734 AAATTTTATT
44785744 AATAAATTAATTTAATAC
1 AATAAATTAATTTAATAC
*
44785762 AATAAA-TATTTTAATAC
1 AATAAATTAATTTAATAC
44785779 AAT
1 AAT
44785782 TGGCATGCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (18 bp):
AATAAATTAATTTAATAC
Found at i:44794738 original size:25 final size:25
Alignment explanation
Indices: 44794685--44794739 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
44794675 TTGAGAAAGT
* *
44794685 TTACCGATATTTAGCTCGCATGAGT
1 TTACCGATATTCAGCTCGCATGAGC
* * *
44794710 TTACCGATATTCAGGTTGTATGAGC
1 TTACCGATATTCAGCTCGCATGAGC
44794735 TTACC
1 TTACC
44794740 TTTTACAACT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (25 bp):
TTACCGATATTCAGCTCGCATGAGC
Found at i:44796600 original size:30 final size:30
Alignment explanation
Indices: 44796564--44796624 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
44796554 ATTAAGTTAG
44796564 TATTAAAGTTTCGTCATAAAATTTTAACGT
1 TATTAAAGTTTCGTCATAAAATTTTAACGT
44796594 TATTAAAGTTTCGTCATAAAATTTTAACGT
1 TATTAAAGTTTCGTCATAAAATTTTAACGT
44796624 T
1 T
44796625 TTGATAGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (30 bp):
TATTAAAGTTTCGTCATAAAATTTTAACGT
Found at i:44797123 original size:16 final size:16
Alignment explanation
Indices: 44797099--44797129 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
44797089 TGAAGCTTTT
44797099 AATTCATTAAATGATG
1 AATTCATTAAATGATG
*
44797115 AATTTATTAAATGAT
1 AATTCATTAAATGAT
44797130 TTTAGTGAAA
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:0.45, C:0.03, G:0.10, T:0.42
Consensus pattern (16 bp):
AATTCATTAAATGATG
Found at i:44799515 original size:26 final size:25
Alignment explanation
Indices: 44799495--44799680 Score: 237
Period size: 26 Copynumber: 7.2 Consensus size: 25
44799485 TAATGCAAAT
44799495 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATG-TCCA
* *
44799521 TGATAATGGGTTAGATAAATGTTTCA
1 TGATAATGGGTTAGGTAAATG-TCCA
* *
44799547 TGATAATGAGTTAGGTATATGTTCCA
1 TGATAATGGGTTAGGTAAATG-TCCA
44799573 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATG-TCCA
* *
44799599 TGATAATGGGTTAGATAAATGTTTCA
1 TGATAATGGGTTAGGTAAATG-TCCA
* *
44799625 TGATAATGAGTTAGGTATATGTTCCA
1 TGATAATGGGTTAGGTAAATG-TCCA
44799651 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATG-TCCA
44799677 TGAT
1 TGAT
44799681 GGGAATTTCA
Statistics
Matches: 144, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 144 1.00
ACGTcount: A:0.32, C:0.06, G:0.25, T:0.37
Consensus pattern (25 bp):
TGATAATGGGTTAGGTAAATGTCCA
Found at i:44799552 original size:52 final size:52
Alignment explanation
Indices: 44799495--44799680 Score: 300
Period size: 52 Copynumber: 3.6 Consensus size: 52
44799485 TAATGCAAAT
* *
44799495 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGGTTAGATAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTCCA
* *
44799547 TGATAATGAGTTAGGTATATGTTCCATGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTCCA
* * * *
44799599 TGATAATGGGTTAGATAAATGTTTCATGATAATGAGTTAGGTATATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTCCA
44799651 TGATAATGGGTTAGGTAAATGTTCCATGAT
1 TGATAATGGGTTAGGTAAATGTTCCATGAT
44799681 GGGAATTTCA
Statistics
Matches: 122, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 122 1.00
ACGTcount: A:0.32, C:0.06, G:0.25, T:0.37
Consensus pattern (52 bp):
TGATAATGGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTCCA
Found at i:44799624 original size:78 final size:78
Alignment explanation
Indices: 44799495--44799680 Score: 372
Period size: 78 Copynumber: 2.4 Consensus size: 78
44799485 TAATGCAAAT
44799495 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGGTTAGATAAATGTTTCATGATAATGAGTTA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGGTTAGATAAATGTTTCATGATAATGAGTTA
44799560 GGTATATGTTCCA
66 GGTATATGTTCCA
44799573 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGGTTAGATAAATGTTTCATGATAATGAGTTA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGGTTAGATAAATGTTTCATGATAATGAGTTA
44799638 GGTATATGTTCCA
66 GGTATATGTTCCA
44799651 TGATAATGGGTTAGGTAAATGTTCCATGAT
1 TGATAATGGGTTAGGTAAATGTTCCATGAT
44799681 GGGAATTTCA
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 108 1.00
ACGTcount: A:0.32, C:0.06, G:0.25, T:0.37
Consensus pattern (78 bp):
TGATAATGGGTTAGGTAAATGTTCCATGATAATGGGTTAGATAAATGTTTCATGATAATGAGTTA
GGTATATGTTCCA
Found at i:44801586 original size:32 final size:34
Alignment explanation
Indices: 44801525--44801589 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 34
44801515 CTATGGGCCA
*
44801525 TATTGTTATCTGAATAATGGGCTAAGGCCCAGTT
1 TATTGTAATCTGAATAATGGGCTAAGGCCCAGTT
**
44801559 TATTGTAATCTGAA-AA-GGGCTCTGGCCCAGT
1 TATTGTAATCTGAATAATGGGCTAAGGCCCAGT
44801590 ACCACTGTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 13 0.46
33 2 0.07
34 13 0.46
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (34 bp):
TATTGTAATCTGAATAATGGGCTAAGGCCCAGTT
Found at i:44805734 original size:17 final size:17
Alignment explanation
Indices: 44805691--44805761 Score: 79
Period size: 17 Copynumber: 4.0 Consensus size: 17
44805681 CAATGATATG
* *
44805691 CAATCTTAGTTGTGATA
1 CAATCTTAGATATGATA
44805708 TGCAATCTTAGATATGATA
1 --CAATCTTAGATATGATA
* *
44805727 CTATCTTAGATATGATTG
1 CAATCTTAGATATGA-TA
44805745 CAATCTTAGATATGATA
1 CAATCTTAGATATGATA
44805762 TGCAATTTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
17 15 0.33
18 15 0.33
19 15 0.33
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.39
Consensus pattern (17 bp):
CAATCTTAGATATGATA
Found at i:44805752 original size:35 final size:36
Alignment explanation
Indices: 44805693--44805761 Score: 113
Period size: 35 Copynumber: 1.9 Consensus size: 36
44805683 ATGATATGCA
* *
44805693 ATCTTAGTTGTGATATGCAATCTTAGATATGATACT
1 ATCTTAGATATGATATGCAATCTTAGATATGATACT
44805729 ATCTTAGATATGAT-TGCAATCTTAGATATGATA
1 ATCTTAGATATGATATGCAATCTTAGATATGATA
44805762 TGCAATTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 19 0.61
36 12 0.39
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (36 bp):
ATCTTAGATATGATATGCAATCTTAGATATGATACT
Found at i:44805780 original size:17 final size:19
Alignment explanation
Indices: 44805683--44805773 Score: 125
Period size: 19 Copynumber: 4.9 Consensus size: 19
44805673 ATAATCTTCA
*
44805683 ATGATATGCAATCTTAGTT
1 ATGATATGCAATCTTAGAT
*
44805702 GTGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
44805721 ATGATA--CTATCTTAGAT
1 ATGATATGCAATCTTAGAT
44805738 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
44805756 ATGATATGCAATTTTAGA
1 ATGATATGCAATCTTAGA
44805774 AGATATGATT
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
17 15 0.24
18 15 0.24
19 33 0.52
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:44805799 original size:22 final size:22
Alignment explanation
Indices: 44805734--44805796 Score: 62
Period size: 23 Copynumber: 3.0 Consensus size: 22
44805724 ATACTATCTT
44805734 AGATATGAT-TGCAATCTT---
1 AGATATGATATGCAATCTTAGA
*
44805752 AGATATGATATGCAATTTTAGA
1 AGATATGATATGCAATCTTAGA
* *
44805774 AGATATGATTTTGTAATCTTAGA
1 AGATATGA-TATGCAATCTTAGA
44805797 GATTTAATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
18 9 0.25
19 8 0.22
22 8 0.22
23 11 0.31
ACGTcount: A:0.37, C:0.06, G:0.17, T:0.40
Consensus pattern (22 bp):
AGATATGATATGCAATCTTAGA
Found at i:44808490 original size:20 final size:20
Alignment explanation
Indices: 44808465--44808504 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
44808455 AGTCCGTAAA
*
44808465 TATTATTTAGTATTTACAAG
1 TATTATTTAATATTTACAAG
44808485 TATTATTTAATATTTACAAG
1 TATTATTTAATATTTACAAG
44808505 GTCAGTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (20 bp):
TATTATTTAATATTTACAAG
Found at i:44820102 original size:27 final size:27
Alignment explanation
Indices: 44820067--44820141 Score: 100
Period size: 26 Copynumber: 2.8 Consensus size: 27
44820057 AGTCTGCTAG
*
44820067 GACAATAAACATGGGGTAGTCCATCG-
1 GACAGTAAACATGGGGTAGTCCATCGA
*
44820093 GAACAGTAAA-ATAGGGTAGTCCATCGA
1 G-ACAGTAAACATGGGGTAGTCCATCGA
*
44820120 GATAGTAAACATGGGGTAGTCC
1 GACAGTAAACATGGGGTAGTCC
44820142 GCAGGGACAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
26 23 0.55
27 19 0.45
ACGTcount: A:0.36, C:0.16, G:0.28, T:0.20
Consensus pattern (27 bp):
GACAGTAAACATGGGGTAGTCCATCGA
Found at i:44820155 original size:27 final size:27
Alignment explanation
Indices: 44820066--44820157 Score: 98
Period size: 27 Copynumber: 3.4 Consensus size: 27
44820056 TAGTCTGCTA
44820066 GGACAATAAACATGGGGTAGTCCATCG
1 GGACAATAAACATGGGGTAGTCCATCG
* * *
44820093 GAACAGTAAA-ATAGGGTAGTCCATCG
1 GGACAATAAACATGGGGTAGTCCATCG
* * * *
44820119 AGATAGTAAACATGGGGTAGTCC-GCAG
1 GGACAATAAACATGGGGTAGTCCATC-G
44820146 GGACAATAAACA
1 GGACAATAAACA
44820158 CAAGGTAATC
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
26 23 0.44
27 29 0.56
ACGTcount: A:0.38, C:0.16, G:0.28, T:0.17
Consensus pattern (27 bp):
GGACAATAAACATGGGGTAGTCCATCG
Found at i:44828181 original size:17 final size:18
Alignment explanation
Indices: 44828156--44828199 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
44828146 AACCAAATTG
44828156 GGCGTGTGGG-CCACACA
1 GGCGTGTGGGCCCACACA
*
44828173 GGTGTGTGGGCCCACACA
1 GGCGTGTGGGCCCACACA
44828191 GGCGTGTGG
1 GGCGTGTGG
44828200 ATTCTTGGGC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.14, C:0.25, G:0.45, T:0.16
Consensus pattern (18 bp):
GGCGTGTGGGCCCACACA
Found at i:44828693 original size:24 final size:24
Alignment explanation
Indices: 44828661--44828720 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 24
44828651 CCCACATGAA
*
44828661 GTGT-AGGGATGGTCGGAGATGGT
1 GTGTAAGGGATGGTCAGAGATGGT
44828684 GTGTAAGGGATGGTCAGAGATGGT
1 GTGTAAGGGATGGTCAGAGATGGT
*
44828708 GTGTAAAGGATGG
1 GTGTAAGGGATGG
44828721 GGGTAGGATA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
23 4 0.12
24 30 0.88
ACGTcount: A:0.23, C:0.03, G:0.48, T:0.25
Consensus pattern (24 bp):
GTGTAAGGGATGGTCAGAGATGGT
Found at i:44833021 original size:18 final size:18
Alignment explanation
Indices: 44832984--44833028 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
44832974 CTTAGAATTT
* *
44832984 TGGGCCCACATGTCCTTG
1 TGGGCCCACATGCCCATG
*
44833002 TGGGCGCACATGCCCATG
1 TGGGCCCACATGCCCATG
44833020 T-GGCCCACA
1 TGGGCCCACA
44833029 CAGCCTGGCC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.16, C:0.36, G:0.29, T:0.20
Consensus pattern (18 bp):
TGGGCCCACATGCCCATG
Found at i:44835299 original size:27 final size:26
Alignment explanation
Indices: 44835263--44835400 Score: 106
Period size: 27 Copynumber: 5.2 Consensus size: 26
44835253 TGGAAATAAA
*
44835263 TATATGAAATGATTATATGAATTGGT
1 TATATGAAATGATTATATGAAATGGT
44835289 TATATGAAAATAGA-TATATGAAATGGT
1 TATATG-AAAT-GATTATATGAAATGGT
44835316 TATATGAAAAATGA-TATAT-ATAATGGT
1 TATATG--AAATGATTATATGA-AATGGT
* * *
44835343 TACATG-AATCAATTATATGAAAAAT-GA
1 TATATGAAAT-GATTATATG--AAATGGT
* * *
44835370 TATATGAAATGGTTATATGAATTAGT
1 TATATGAAATGATTATATGAAATGGT
44835396 TATAT
1 TATAT
44835401 ATAAACAGAT
Statistics
Matches: 92, Mismatches: 9, Indels: 22
0.75 0.07 0.18
Matches are distributed among these distances:
24 3 0.03
25 4 0.04
26 18 0.20
27 53 0.58
28 13 0.14
29 1 0.01
ACGTcount: A:0.45, C:0.01, G:0.16, T:0.38
Consensus pattern (26 bp):
TATATGAAATGATTATATGAAATGGT
Found at i:44835350 original size:40 final size:40
Alignment explanation
Indices: 44835306--44835416 Score: 122
Period size: 40 Copynumber: 2.8 Consensus size: 40
44835296 AAATAGATAT
*
44835306 ATGAAATGGTTATATGAAAAATGATATAT-ATAATGGTTAC
1 ATGAAATAGTTATATGAAAAATGATATATGA-AATGGTTAC
* *
44835346 ATG-AATCAATTATATGAAAAATGATATATGAAATGGTTAT
1 ATGAAAT-AGTTATATGAAAAATGATATATGAAATGGTTAC
*
44835386 ATGAATTAGTTATAT-ATAAACA-GATATATGA
1 ATGAAATAGTTATATGA-AAA-ATGATATATGA
44835417 TAACCGATTA
Statistics
Matches: 61, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
39 4 0.07
40 53 0.87
41 4 0.07
ACGTcount: A:0.47, C:0.03, G:0.15, T:0.35
Consensus pattern (40 bp):
ATGAAATAGTTATATGAAAAATGATATATGAAATGGTTAC
Found at i:44835397 original size:13 final size:13
Alignment explanation
Indices: 44835249--44835449 Score: 93
Period size: 13 Copynumber: 14.8 Consensus size: 13
44835239 GATAAATATC
**
44835249 TATATGGAAATAAA
1 TATAT-GAAATAGT
44835263 TATATGAAAT-GAT
1 TATATGAAATAG-T
* *
44835276 TATATGAATTGGT
1 TATATGAAATAGT
*
44835289 TATATGAAAATAGA
1 TATATG-AAATAGT
*
44835303 TATATGAAATGGT
1 TATATGAAATAGT
* *
44835316 TATATGAAAAATGA
1 TATATGAAATA-GT
*
44835330 TATAT-ATAATGGT
1 TATATGA-AATAGT
* *
44835343 TACATG-AATCAAT
1 TATATGAAAT-AGT
* *
44835356 TATATGAAAAATGA
1 TATATGAAATA-GT
*
44835370 TATATGAAATGGT
1 TATATGAAATAGT
*
44835383 TATATGAATTAGT
1 TATATGAAATAGT
* * *
44835396 TATATATAAACAGA
1 TATAT-GAAATAGT
**
44835410 TATATGATAACCGAT
1 TATATGA-AATAG-T
*
44835425 TATATGGAAATAGA
1 TATAT-GAAATAGT
44835439 TATATGAAATA
1 TATATGAAATA
44835450 AAACATTGGA
Statistics
Matches: 138, Mismatches: 36, Indels: 27
0.69 0.18 0.13
Matches are distributed among these distances:
12 3 0.02
13 72 0.52
14 53 0.38
15 8 0.06
16 2 0.01
ACGTcount: A:0.47, C:0.02, G:0.15, T:0.35
Consensus pattern (13 bp):
TATATGAAATAGT
Found at i:44837422 original size:42 final size:41
Alignment explanation
Indices: 44837314--44837422 Score: 128
Period size: 44 Copynumber: 2.6 Consensus size: 41
44837304 TTTCAGTACG
* * * *
44837314 TGATTTCGTGTAAGACCACGTCTGGGACGTTGGCATCAATT
1 TGATTTCGTGTAAGACCATGTCTCGGACATTGGCATCAATA
*
44837355 TGATATTTACGCGTAAGACCATGTCTCGGACATTGGCATCATATA
1 TG--ATTT-CGTGTAAGACCATGTCTCGGACATTGGCATCA-ATA
*
44837400 TGATTTCGTGTAAGACCTTGTCT
1 TGATTTCGTGTAAGACCATGTCT
44837423 GGGATAGTGG
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
41 2 0.04
42 15 0.26
43 8 0.14
44 28 0.49
45 4 0.07
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (41 bp):
TGATTTCGTGTAAGACCATGTCTCGGACATTGGCATCAATA
Found at i:44837434 original size:42 final size:43
Alignment explanation
Indices: 44837314--44837477 Score: 142
Period size: 42 Copynumber: 3.9 Consensus size: 43
44837304 TTTCAGTACG
*
44837314 TGATTTCGTGTAAGACCACGTCTGGGA-CGTTGGCATCA-ATT
1 TGATTTCGTGTAAGACCACGTCTGGGATAGTTGGCATCATATT
* * * * *
44837355 TGATATTTACGCGTAAGACCATGTCTCGGACA-TTGGCATCATATA
1 TG--ATTT-CGTGTAAGACCACGTCTGGGATAGTTGGCATCATATT
** *
44837400 TGATTTCGTGTAAGACCTTGTCTGGGATAG-TGGCATTGATATT
1 TGATTTCGTGTAAGACCACGTCTGGGATAGTTGGCA-TCATATT
* * *
44837443 TGATTAC-AGTAAGACCTCGTCTGGGAT-GTTGGCAT
1 TGATTTCGTGTAAGACCACGTCTGGGATAGTTGGCAT
44837478 TGTACGAGCT
Statistics
Matches: 101, Mismatches: 14, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
41 4 0.04
42 47 0.47
43 19 0.19
44 27 0.27
45 4 0.04
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.34
Consensus pattern (43 bp):
TGATTTCGTGTAAGACCACGTCTGGGATAGTTGGCATCATATT
Found at i:44842480 original size:18 final size:17
Alignment explanation
Indices: 44842432--44842482 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
44842422 ATTTATATAT
*
44842432 TATTTATTTTACTATAAA
1 TATTTATTATA-TATAAA
44842450 TA-TTATGTATATATAAA
1 TATTTAT-TATATATAAA
44842467 TGATTTATTATATATA
1 T-ATTTATTATATATA
44842483 TTATTTTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
17 11 0.38
18 14 0.48
19 4 0.14
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (17 bp):
TATTTATTATATATAAA
Found at i:44842561 original size:20 final size:22
Alignment explanation
Indices: 44842532--44842599 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 22
44842522 TAAGTTTTAT
44842532 TTATAT-ATTTTA-TA-ATATA
1 TTATATCATTTTACTATATATA
44842551 TTATATCATTTTACTATATATA
1 TTATATCATTTTACTATATATA
* * * *
44842573 TTAT-TCATTATATTATTTTTA
1 TTATATCATTTTACTATATATA
44842594 TTATAT
1 TTATAT
44842600 TTAATGTTAC
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
19 6 0.15
20 6 0.15
21 19 0.46
22 10 0.24
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.60
Consensus pattern (22 bp):
TTATATCATTTTACTATATATA
Found at i:44842596 original size:14 final size:14
Alignment explanation
Indices: 44842549--44842600 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
44842539 TTTTATAATA
*
44842549 TATTATATCA-TTT
1 TATTATATTATTTT
*
44842562 TACTATATATATTATT
1 TATTATAT-TATT-TT
*
44842578 CATTATATTATTTT
1 TATTATATTATTTT
44842592 TATTATATT
1 TATTATATT
44842601 TAATGTTACT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
13 7 0.23
14 11 0.35
15 5 0.16
16 8 0.26
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.62
Consensus pattern (14 bp):
TATTATATTATTTT
Found at i:44844275 original size:31 final size:31
Alignment explanation
Indices: 44844210--44844292 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 31
44844200 CTTCCTGCAT
* **
44844210 TAAAATCCAACCAAATACAACAAATATATTA
1 TAAAATCCAACCAAAAACAACAAATATAGCA
* * *
44844241 TAAAATGCAGCCAAAAACAACAAATTTAGCA
1 TAAAATCCAACCAAAAACAACAAATATAGCA
*
44844272 TAAAAAATACAACCAAAAACA
1 T--AAAATCCAACCAAAAACA
44844293 TTAATTCTAA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
31 26 0.62
33 16 0.38
ACGTcount: A:0.60, C:0.19, G:0.04, T:0.17
Consensus pattern (31 bp):
TAAAATCCAACCAAAAACAACAAATATAGCA
Found at i:44850175 original size:9 final size:9
Alignment explanation
Indices: 44850161--44850282 Score: 102
Period size: 9 Copynumber: 12.9 Consensus size: 9
44850151 ATGTATTAGT
44850161 TAAGTTATG
1 TAAGTTATG
44850170 TAAGTTGTTATG
1 TAA---GTTATG
44850182 TACA-TTATG
1 TA-AGTTATG
* *
44850191 TGAGCTATG
1 TAAGTTATG
*
44850200 TAAATTATG
1 TAAGTTATG
44850209 TAAGTTATG
1 TAAGTTATG
*
44850218 TAAATTATG
1 TAAGTTATG
44850227 TAAGTTGTTATG
1 TAA---GTTATG
*
44850239 TAAATTATG
1 TAAGTTATG
*
44850248 TAAGTTATA
1 TAAGTTATG
*
44850257 TGAGTTATG
1 TAAGTTATG
44850266 TAAGTTATG
1 TAAGTTATG
*
44850275 TAATTTAT
1 TAAGTTAT
44850283 TGAAGTAATG
Statistics
Matches: 90, Mismatches: 15, Indels: 16
0.74 0.12 0.13
Matches are distributed among these distances:
8 1 0.01
9 72 0.80
12 16 0.18
13 1 0.01
ACGTcount: A:0.34, C:0.02, G:0.19, T:0.46
Consensus pattern (9 bp):
TAAGTTATG
Found at i:44850226 original size:57 final size:57
Alignment explanation
Indices: 44850165--44850282 Score: 173
Period size: 57 Copynumber: 2.1 Consensus size: 57
44850155 ATTAGTTAAG
* * *
44850165 TTATGTAAGTTGTTATGTACATTATGTGAGCTATGTAAATTATGTAAGTTATGTAAA
1 TTATGTAAGTTGTTATGTAAATTATGTAAGCTATATAAATTATGTAAGTTATGTAAA
* * * *
44850222 TTATGTAAGTTGTTATGTAAATTATGTAAGTTATATGAGTTATGTAAGTTATGTAAT
1 TTATGTAAGTTGTTATGTAAATTATGTAAGCTATATAAATTATGTAAGTTATGTAAA
44850279 TTAT
1 TTAT
44850283 TGAAGTAATG
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.33, C:0.02, G:0.19, T:0.47
Consensus pattern (57 bp):
TTATGTAAGTTGTTATGTAAATTATGTAAGCTATATAAATTATGTAAGTTATGTAAA
Found at i:44850238 original size:48 final size:48
Alignment explanation
Indices: 44850186--44850277 Score: 121
Period size: 48 Copynumber: 1.9 Consensus size: 48
44850176 GTTATGTACA
* * *
44850186 TTATGTGAGCTATGTAAATTATGTAAGTTATGTAAATTATGTAAGTTG
1 TTATGTAAACTATGTAAATTATATAAGTTATGTAAATTATGTAAGTTG
* * * *
44850234 TTATGTAAATTATGTAAGTTATATGAGTTATGTAAGTTATGTAA
1 TTATGTAAACTATGTAAATTATATAAGTTATGTAAATTATGTAA
44850278 TTTATTGAAG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 37 1.00
ACGTcount: A:0.35, C:0.01, G:0.20, T:0.45
Consensus pattern (48 bp):
TTATGTAAACTATGTAAATTATATAAGTTATGTAAATTATGTAAGTTG
Found at i:44850239 original size:39 final size:39
Alignment explanation
Indices: 44850196--44850271 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 39
44850186 TTATGTGAGC
*
44850196 TATGTAAATTATGTAAGTTATGTAAATTATGTAAGTTGT
1 TATGTAAATTATGTAAGTTATATAAATTATGTAAGTTGT
* *
44850235 TATGTAAATTATGTAAGTTATATGAGTTATGTAAGTT
1 TATGTAAATTATGTAAGTTATATAAATTATGTAAGTT
44850272 ATGTAATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (39 bp):
TATGTAAATTATGTAAGTTATATAAATTATGTAAGTTGT
Found at i:44853932 original size:25 final size:25
Alignment explanation
Indices: 44853898--44853958 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
44853888 TGCGGAAGCG
* *
44853898 GAGAGCGACGGTGAAGGGACGCAGAA
1 GAGA-CGACGGTGAAGAGACGCAAAA
44853924 GAGACGACGGTGAAGAGACGCAAAA
1 GAGACGACGGTGAAGAGACGCAAAA
44853949 GAGACGACGG
1 GAGACGACGG
44853959 CGAACGACGA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
25 29 0.88
26 4 0.12
ACGTcount: A:0.38, C:0.16, G:0.43, T:0.03
Consensus pattern (25 bp):
GAGACGACGGTGAAGAGACGCAAAA
Found at i:44854491 original size:158 final size:157
Alignment explanation
Indices: 44854264--44854554 Score: 365
Period size: 158 Copynumber: 1.8 Consensus size: 157
44854254 CATTTATTTA
* * *
44854264 AAAAACGCCGCTAATCCCTATATACTCAACTAAAACGACGACGTGTACTATAAACTTGAATTATT
1 AAAAACGCCGCAAATCCCTATATACTCAACTAAAACGACGACGTGTACCATAAACTTGAATTATG
* * *
44854329 TTGCGGCATTTTTGAAAGCGCCACTAATACTCGT-AT-ATACTAAAACGGCGCCGTTTTCGTTAA
66 TTGCGGCATTTTTAAAAACGCCACTAATACTC-TAATAAT-CTAAAACGACGCCGTTTTCGTTAA
44854392 ACTAATCTGTATTTTGTGGCGTTTTCTAT
129 ACTAATCTGTATTTTGTGGCGTTTTCTAT
* * * * *
44854421 AAAAACGCCGCAAATCCCCTATATATTGAACTAAAACGACGACGCT-T-CCAGTACACTTTACTT
1 AAAAACGCCGCAAAT-CCCTATATACTCAACTAAAACGACGACG-TGTACCA-TAAACTTGAATT
* * *
44854484 CTGTTGCGGCATTTTTAAAAACGCCACTAGTACTCTAATCAATCTAAAACGACGCCGTTTTCTTT
63 ATGTTGCGGCATTTTTAAAAACGCCACTAATACTCTAAT-AATCTAAAACGACGCCGTTTTCGTT
*
44854549 CAACTA
127 AAACTA
44854555 TACTATTTTT
Statistics
Matches: 113, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
157 17 0.15
158 68 0.60
159 26 0.23
160 2 0.02
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.31
Consensus pattern (157 bp):
AAAAACGCCGCAAATCCCTATATACTCAACTAAAACGACGACGTGTACCATAAACTTGAATTATG
TTGCGGCATTTTTAAAAACGCCACTAATACTCTAATAATCTAAAACGACGCCGTTTTCGTTAAAC
TAATCTGTATTTTGTGGCGTTTTCTAT
Found at i:44854582 original size:158 final size:158
Alignment explanation
Indices: 44854262--44854588 Score: 362
Period size: 158 Copynumber: 2.1 Consensus size: 158
44854252 GGCATTTATT
* *
44854262 TAAAAAACGCCGCTAATCCCTATATACTCAACTAAAACGACGACGTGTACTATAAACTTGAATTA
1 TAAAAAACGCCGCAAATCCCTATATACTCAACTAAAACGACGACGTGTACCATAAACTTGAATTA
* * * *
44854327 TTTTGCGGCATTTTTGAAAGCGCCACTAATACTCGTATATACTAAAACGGCGCCGTTTTCGTTAA
66 TGTTGCGGCATTTTTAAAAACGCCACTAATACTCGTATATACTAAAACGACGCCGTTTTCGTTAA
* *
44854392 ACTAATCTGTATTTTGTGGCGTTTTCTA
131 ACTAATCTATATTTTGCGGCGTTTTCTA
* * * * *
44854420 T-AAAAACGCCGCAAATCCCCTATATATTGAACTAAAACGACGACGCT-T-CCAGTACACTTTAC
1 TAAAAAACGCCGCAAAT-CCCTATATACTCAACTAAAACGACGACG-TGTACCA-TAAACTTGAA
* *
44854482 TTCTGTTGCGGCATTTTTAAAAACGCCACTAGTACTC-TA-ATCAATCTAAAACGACGCCGTTTT
63 TTATGTTGCGGCATTTTTAAAAACGCCACTAATACTCGTATAT--A-CTAAAACGACGCCGTTTT
* * * * *
44854545 CTTTCAACT-ATACTATTTTTTGCGGTGTTTT-TT
125 CGTTAAACTAAT-CTATATTTTGCGGCGTTTTCTA
44854578 TAAAAAACGCC
1 TAAAAAACGCC
44854589 ACTAATCTCT
Statistics
Matches: 141, Mismatches: 20, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
156 2 0.01
157 18 0.13
158 72 0.51
159 49 0.35
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.33
Consensus pattern (158 bp):
TAAAAAACGCCGCAAATCCCTATATACTCAACTAAAACGACGACGTGTACCATAAACTTGAATTA
TGTTGCGGCATTTTTAAAAACGCCACTAATACTCGTATATACTAAAACGACGCCGTTTTCGTTAA
ACTAATCTATATTTTGCGGCGTTTTCTA
Done.