Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167882.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_15, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 22478863
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 61000 characters in sequence are not A, C, G, or T
File 27 of 106
Found at i:5031575 original size:28 final size:27
Alignment explanation
Indices: 5031486--5031627 Score: 92
Period size: 28 Copynumber: 5.1 Consensus size: 27
5031476 ATTATTATAA
* *
5031486 AATATTTTTTAATATTTTAATTATACAT
1 AATATTTTTTAATA-TTTAATAATAAAT
* * * *
5031514 -ATCACTATTTTAAAATTTATTAAT-GAT
1 AAT-A-TTTTTTAATATTTAATAATAAAT
5031541 AAATATTTTTTAAATATTTAATAATAAAT
1 -AATATTTTTT-AATATTTAATAATAAAT
** * * *
5031570 TGTATTATATTT-CTATTTAACAGTAAAT
1 AATATT-T-TTTAATATTTAATAATAAAT
*
5031598 AATATTTTGTAATATTTAATAATAAAT
1 AATATTTTTTAATATTTAATAATAAAT
5031625 AAT
1 AAT
5031628 TGTCATAATG
Statistics
Matches: 85, Mismatches: 20, Indels: 19
0.69 0.16 0.15
Matches are distributed among these distances:
26 2 0.02
27 26 0.31
28 41 0.48
29 13 0.15
30 3 0.04
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.50
Consensus pattern (27 bp):
AATATTTTTTAATATTTAATAATAAAT
Found at i:5043313 original size:25 final size:24
Alignment explanation
Indices: 5043279--5043337 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 24
5043269 ATACTAGAAG
5043279 CTTTTATTTTTATT-TTTTTATCGTT
1 CTTTTATTTTT-TTCTTTTT-TCGTT
*
5043304 CTTTTATTTTTTTCTTTTTTCTTT
1 CTTTTATTTTTTTCTTTTTTCGTT
*
5043328 CTTTTCTTTT
1 CTTTTATTTT
5043338 CTTATTCATG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
24 15 0.48
25 16 0.52
ACGTcount: A:0.07, C:0.12, G:0.02, T:0.80
Consensus pattern (24 bp):
CTTTTATTTTTTTCTTTTTTCGTT
Found at i:5043321 original size:24 final size:25
Alignment explanation
Indices: 5043279--5043337 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 25
5043269 ATACTAGAAG
*
5043279 CTTTTATTTTTATTTTTTTATCGTT
1 CTTTTATTTTTATTCTTTTATCGTT
* *
5043304 CTTTTATTTTT-TTCTTTTTTCTTT
1 CTTTTATTTTTATTCTTTTATCGTT
*
5043328 CTTTTCTTTT
1 CTTTTATTTT
5043338 CTTATTCATG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
24 19 0.63
25 11 0.37
ACGTcount: A:0.07, C:0.12, G:0.02, T:0.80
Consensus pattern (25 bp):
CTTTTATTTTTATTCTTTTATCGTT
Found at i:5045257 original size:16 final size:16
Alignment explanation
Indices: 5045236--5045266 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5045226 TAAATTACAT
*
5045236 GAATCTAATTATTCAC
1 GAATCTAACTATTCAC
5045252 GAATCTAACTATTCA
1 GAATCTAACTATTCA
5045267 TGAACTTAAC
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:0.39, C:0.19, G:0.06, T:0.35
Consensus pattern (16 bp):
GAATCTAACTATTCAC
Found at i:5047337 original size:3 final size:3
Alignment explanation
Indices: 5047316--5047353 Score: 51
Period size: 3 Copynumber: 12.3 Consensus size: 3
5047306 AAAATCACTA
5047316 TAT TATT TAT ATAT T-T TAT TAT TAT TAT TAT TAT TAT T
1 TAT TA-T TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT T
5047354 TACAAAAGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 2 0.06
3 24 0.75
4 6 0.19
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:5048572 original size:25 final size:25
Alignment explanation
Indices: 5048546--5048594 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
5048536 CATATCACTA
*
5048546 TTTTAAAATTTATTAATAATAAATAT
1 TTTTAAAATAT-TTAATAATAAATAT
*
5048572 TTTTTAAATATTTAATAATAAAT
1 TTTTAAAATATTTAATAATAAAT
5048595 TGTATTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
TTTTAAAATATTTAATAATAAATAT
Found at i:5048600 original size:28 final size:25
Alignment explanation
Indices: 5048558--5048649 Score: 71
Period size: 28 Copynumber: 3.5 Consensus size: 25
5048548 TTAAAATTTA
5048558 TTAATAATAAA-TATTTTTTAAATAT
1 TTAATAATAAATTATTTTTT-AATAT
*
5048583 TTAATAATAAATTGTATTATATTT-CTAT
1 TTAATAATAAA-T-TATT-T-TTTAATAT
* * *
5048611 TTAACAGTAAATAATATTTTGTAATAT
1 TTAATAATAAAT--TATTTTTTAATAT
5048638 TTAATAATAAAT
1 TTAATAATAAAT
5048650 AATTGTCATA
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
25 11 0.21
26 2 0.04
27 15 0.29
28 20 0.38
29 1 0.02
30 3 0.06
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (25 bp):
TTAATAATAAATTATTTTTTAATAT
Found at i:5049265 original size:12 final size:13
Alignment explanation
Indices: 5049238--5049263 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5049228 GTGTATTAAA
5049238 TATAAACCCTTTT
1 TATAAACCCTTTT
5049251 TATAAACCCTTTT
1 TATAAACCCTTTT
5049264 ATTTAAGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (13 bp):
TATAAACCCTTTT
Found at i:5055663 original size:17 final size:17
Alignment explanation
Indices: 5055641--5055673 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5055631 CTCAAAGCTA
5055641 TATTTCT-TCTTTCTTAT
1 TATTTCTGT-TTTCTTAT
5055658 TATTTCTGTTTTCTTA
1 TATTTCTGTTTTCTTA
5055674 AATTTTCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 14 0.93
18 1 0.07
ACGTcount: A:0.12, C:0.15, G:0.03, T:0.70
Consensus pattern (17 bp):
TATTTCTGTTTTCTTAT
Found at i:5056149 original size:3 final size:3
Alignment explanation
Indices: 5056141--5056183 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
5056131 CTTCTATAGT
*
5056141 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
5056184 ATTTTAGACG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:5063278 original size:34 final size:34
Alignment explanation
Indices: 5063205--5063278 Score: 82
Period size: 34 Copynumber: 2.2 Consensus size: 34
5063195 ATTGAAAATA
*
5063205 TAACCTTATCTTTTTATTTCTAAGGCTTAGATAG
1 TAACCTTATCTCTTTATTTCTAAGGCTTAGATAG
*
5063239 AAACCTTATACTCTTTACTTTCT-AGGC-TA-ACTAG
1 TAACCTTAT-CTCTTTA-TTTCTAAGGCTTAGA-TAG
5063273 TAACCT
1 TAACCT
5063279 CTCAATCTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
33 1 0.03
34 18 0.53
35 10 0.29
36 5 0.15
ACGTcount: A:0.28, C:0.20, G:0.09, T:0.42
Consensus pattern (34 bp):
TAACCTTATCTCTTTATTTCTAAGGCTTAGATAG
Found at i:5063793 original size:73 final size:72
Alignment explanation
Indices: 5063659--5063840 Score: 206
Period size: 73 Copynumber: 2.5 Consensus size: 72
5063649 TACCCAAACT
* ** *
5063659 CGATCGATCCTTTCCATGAAGGGATCAATTGTTTCATGTTTAGGTGCCATATACGCCTTTGAAAA
1 CGATCGATCCTTTCCATG-AGGGATCAATTGGTTCATGTTTAGGAACCATATACGCATTTGAAAA
5063724 T-CATGACC
65 TGC-TGACC
* * * * *
5063732 TGATCGATCCCTTCCATGAGGGAATCGATTGGTTCATGTTTTGGAACCA-ATTATGCATTTGAAA
1 CGATCGATCCTTTCCATGAGGG-ATCAATTGGTTCATGTTTAGGAACCATA-TACGCATTTGAAA
*
5063796 ATGCTTACC
64 ATGCTGACC
*
5063805 CGATCGATCCTTTCCTTGAGGGGATCAATTGGTTCA
1 CGATCGATCCTTTCCATGA-GGGATCAATTGGTTCA
5063841 AGGGGGTGAT
Statistics
Matches: 91, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
72 5 0.05
73 82 0.90
74 4 0.04
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.34
Consensus pattern (72 bp):
CGATCGATCCTTTCCATGAGGGATCAATTGGTTCATGTTTAGGAACCATATACGCATTTGAAAAT
GCTGACC
Found at i:5064636 original size:17 final size:17
Alignment explanation
Indices: 5064611--5064648 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
5064601 TAATGTTTTG
* *
5064611 TCAATATAAGGATCATT
1 TCAAAATAAGGATCAAT
5064628 TCAAAATAAGGATCAAT
1 TCAAAATAAGGATCAAT
5064645 TCAA
1 TCAA
5064649 GGCTAATAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.29
Consensus pattern (17 bp):
TCAAAATAAGGATCAAT
Found at i:5065034 original size:17 final size:17
Alignment explanation
Indices: 5064990--5065036 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 17
5064980 ACAACTCCAC
5064990 CTCT-TCTTT-TTTTCT
1 CTCTCTCTTTATTTTCT
*
5065005 CTCTCATTTTTTATTTTCT
1 CTCTC--TCTTTATTTTCT
5065024 CTCTCTCTTTATT
1 CTCTCTCTTTATT
5065037 GCTGCAACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 4 0.15
17 7 0.27
18 4 0.15
19 11 0.42
ACGTcount: A:0.06, C:0.26, G:0.00, T:0.68
Consensus pattern (17 bp):
CTCTCTCTTTATTTTCT
Found at i:5069262 original size:28 final size:27
Alignment explanation
Indices: 5069223--5069278 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
5069213 ACCCCATGAA
* *
5069223 CTTTTTTTTTTCATTTTTTTCTATTTT
1 CTTTTTTTTTTCAATTTGTTCTATTTT
*
5069250 CTTTTTGTTTTTCAATTTGTTCTTTTTT
1 CTTTTT-TTTTTCAATTTGTTCTATTTT
5069278 C
1 C
5069279 ATATTTAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 6 0.24
28 19 0.76
ACGTcount: A:0.07, C:0.12, G:0.04, T:0.77
Consensus pattern (27 bp):
CTTTTTTTTTTCAATTTGTTCTATTTT
Found at i:5069623 original size:21 final size:21
Alignment explanation
Indices: 5069599--5069638 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
5069589 AAATTAGATA
5069599 AATTTTGTAAAAAATAGTATG
1 AATTTTGTAAAAAATAGTATG
5069620 AATTTTGTAAAAAATAGTA
1 AATTTTGTAAAAAATAGTA
5069639 AATGCCTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (21 bp):
AATTTTGTAAAAAATAGTATG
Found at i:5077820 original size:2 final size:2
Alignment explanation
Indices: 5077813--5077853 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
5077803 TCTAGAAGAA
5077813 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C- CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5077854 ATTTCAGTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:5084511 original size:18 final size:18
Alignment explanation
Indices: 5084488--5084523 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
5084478 GGTAAATTAC
5084488 TAAAATTAGGCATCTAAG
1 TAAAATTAGGCATCTAAG
5084506 TAAAATTAGGCATCTAAG
1 TAAAATTAGGCATCTAAG
5084524 ATATATTTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.28
Consensus pattern (18 bp):
TAAAATTAGGCATCTAAG
Found at i:5084713 original size:17 final size:17
Alignment explanation
Indices: 5084691--5084735 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
5084681 TTAAAATTAG
5084691 AAAGTTACATAA-AATGA
1 AAAGTTAC-TAAGAATGA
*
5084708 AAAGTTACTAAGAATGG
1 AAAGTTACTAAGAATGA
*
5084725 AAAGTTTCTAA
1 AAAGTTACTAA
5084736 ACCCAATGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 22 0.88
ACGTcount: A:0.51, C:0.07, G:0.16, T:0.27
Consensus pattern (17 bp):
AAAGTTACTAAGAATGA
Found at i:5098522 original size:15 final size:15
Alignment explanation
Indices: 5098502--5098531 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5098492 AGTTACTTAG
*
5098502 ATTTACGTTTTTGCA
1 ATTTACATTTTTGCA
5098517 ATTTACATTTTTGCA
1 ATTTACATTTTTGCA
5098532 CTTTTTCTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.13, G:0.10, T:0.53
Consensus pattern (15 bp):
ATTTACATTTTTGCA
Found at i:5101695 original size:40 final size:39
Alignment explanation
Indices: 5101612--5101695 Score: 105
Period size: 40 Copynumber: 2.1 Consensus size: 39
5101602 AAAATTTGTG
* * *** *
5101612 TGAAGTCTTCTCATTTCATGAACATTCTAATTAGTTCTG
1 TGAAGTCTTCTCATTGCATGAAAATTCTAATTAACACTA
5101651 TGAAGTTCTTCTCATTGCATGAAAATTCTAATTAACACTA
1 TGAAG-TCTTCTCATTGCATGAAAATTCTAATTAACACTA
5101691 TGAAG
1 TGAAG
5101696 GTAAAATTTC
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
39 5 0.13
40 33 0.87
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (39 bp):
TGAAGTCTTCTCATTGCATGAAAATTCTAATTAACACTA
Found at i:5102132 original size:16 final size:14
Alignment explanation
Indices: 5102112--5102159 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 14
5102102 TATATAATAT
5102112 AAAAAAAAATCTAAA
1 AAAAAAAAAT-TAAA
5102127 ACAAAAAAAATTAAA
1 A-AAAAAAAATTAAA
*
5102142 AAAAACAAA--AAA
1 AAAAAAAAATTAAA
5102154 AAAAAA
1 AAAAAA
5102160 GAGCTCATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
12 8 0.27
14 7 0.23
15 6 0.20
16 9 0.30
ACGTcount: A:0.85, C:0.06, G:0.00, T:0.08
Consensus pattern (14 bp):
AAAAAAAAATTAAA
Found at i:5102141 original size:15 final size:15
Alignment explanation
Indices: 5102112--5102151 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 15
5102102 TATATAATAT
5102112 AAAAAAAAATCTAAA
1 AAAAAAAAATCTAAA
5102127 ACAAAAAAAAT-TAAA
1 A-AAAAAAAATCTAAA
5102142 AAAAACAAAA
1 AAAAA-AAAA
5102152 AAAAAAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 4 0.17
15 10 0.43
16 9 0.39
ACGTcount: A:0.82, C:0.07, G:0.00, T:0.10
Consensus pattern (15 bp):
AAAAAAAAATCTAAA
Found at i:5103705 original size:16 final size:15
Alignment explanation
Indices: 5103658--5103705 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
5103648 ATATTTTATT
*
5103658 AATATAATAAATATA
1 AATATAAAAAATATA
*
5103673 AATATAAAATAAAATA
1 AATATAAAA-AATATA
*
5103689 AATAATTAAAAATATA
1 AAT-ATAAAAAATATA
5103705 A
1 A
5103706 TTTTATATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 8 0.30
16 14 0.52
17 5 0.19
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AATATAAAAAATATA
Found at i:5113765 original size:19 final size:20
Alignment explanation
Indices: 5113743--5113780 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5113733 TTTATTTTTT
*
5113743 ATTTT-TTTTCAAAATTATA
1 ATTTTATTTACAAAATTATA
*
5113762 ATTTTATTTACAATATTAT
1 ATTTTATTTACAAAATTAT
5113781 TACCCCTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTTTATTTACAAAATTATA
Found at i:5126702 original size:3 final size:3
Alignment explanation
Indices: 5126694--5126719 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5126684 TAGGAAATGC
5126694 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
5126720 CATCATCATC
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:5127006 original size:13 final size:13
Alignment explanation
Indices: 5126988--5127012 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5126978 AATGGAAACC
5126988 TTTTCTTTTTTTT
1 TTTTCTTTTTTTT
5127001 TTTTCTTTTTTT
1 TTTTCTTTTTTT
5127013 AGTATAAGTT
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (13 bp):
TTTTCTTTTTTTT
Found at i:5132215 original size:15 final size:15
Alignment explanation
Indices: 5132192--5132226 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
5132182 TAATTGGTAT
*
5132192 TTAACTTTAATTTTC
1 TTAATTTTAATTTTC
*
5132207 TTAATTTTAATTTTT
1 TTAATTTTAATTTTC
5132222 TTAAT
1 TTAAT
5132227 AATAATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.66
Consensus pattern (15 bp):
TTAATTTTAATTTTC
Found at i:5132276 original size:3 final size:3
Alignment explanation
Indices: 5132223--5132261 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
5132213 TTAATTTTTT
5132223 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5132262 CAGCGGTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:5136289 original size:805 final size:807
Alignment explanation
Indices: 5134241--5137470 Score: 5289
Period size: 805 Copynumber: 4.0 Consensus size: 807
5134231 GGGAGGCCAA
*
5134241 GATTAAGACCTATTTTTGACAGTCACCCCTAATTACTTGATTTAGAAAGCAAAGTGTTCTAAAGA
1 GATTAAGACCTATTTTTGACAGTCACCCCTAATTACTTGATTTAGAAAGTAAAGTGTTCTAAAGA
* * * *
5134306 TGTTGTACTTCCTCCAGATGATTTTTCATTTCAATAAGTGAACCCGTGAGCAAAAGAACCATTGT
66 TATTGTGCTTCCTCCAGATGATTTTTCATTTCAACAAGTGAACCCATGAGCAAAAGAACCATTGT
* *
5134371 CGGAAGTTGAGCTTGTAAAGCAAGAACTTGAAGCAAAAAAAAAAATTGAAAAAGGAAAATTTAAG
131 CGGAAGTTGAGCTTGTAAAGCAAGAACTTGAAGC-AAAAAAAAAATTGAAAAAGAAAAATTTGAG
* *
5134436 ACT-CAAGAAAGAGATGGGACAATTAAAATATGAACCGAAAGCTTGAAAAAGCAAACTCAAAAAA
195 ACTCCAAG-AAGAGATGGGACAATTAAAATATGAAGCGAAAGCTTGAAAAAGCAAACTAAAAAAA
* *
5134500 ATAATGCAAGATCAAGATGTGACTCTAAATGATTTAAATGATTTGCATCAAGGAAACAAAAAAAT
259 ATAATGCAAGATCAAGATGTGACTCAAAATGATTTAAAGGATTTGCATCAAGGAAACAAAAAAAT
5134565 GCGAACCCAATTAAAA-AAGGGAAACGATGCTAGATTTAGTGTTAAGCAACAAAA-AGAAATGAT
324 GCGAACCCAATTAAAAGAA-GGAAACGATGCTAGATTTAGTGTTAAGCAACAAAAGA-AAATGAT
* *
5134628 TGAACTTCAAGAAGAGATGCAACATTGTAATGACAAAGCCAAGGAAAATGAAGAAAAAACCATCA
387 TGAACTTCAAGAAGAGATGCAACATTGTAACGACAAAGCCAAGGAAAATGAAGAAAAAGCCATCA
* *
5134693 GGATTTTTCCAGAACAGTAAGAGTGGAAGGTTTGTATTCAATAACTTCAGCAAGAGTGATGAAAT
452 GGATTTTTCGAGAACAGTAAGAGTGGAAGGTTTGTATTCAACAACTTCAGCAAGAGTGATGAAAT
5134758 GTCAAAAGGAGAATGCTAAATTGAAAGCACAGATCAAAGATGAAAAAAGAAAACACTATGAAATG
517 GTCAAAAGGAGAATGCTAAATTGAAAGCACAGATCAAAGATG-AAAAAGAAAACACTATGAAATG
*
5134823 CAAAAGGAGAAAGAATCGCTTTACCAAATAATTCAATAGATGGAACAGCAATTACAGAACCACAA
581 CAAAAGGAGAAAGAATCGCTTTACCAAGTAATTCAATAGATGGAACAGCAATTACAGAACCACAA
*
5134888 AGACCATATTTTCACAATTATCAAAGAATGGCAAAATAGAGAAGAAGATTGGAGATACACTTACG
646 AGACCATATTTTCATAATTATCAAAGAATGGCAAAATAGAGAAGAAGATTGGAGATACACTTACG
*
5134953 ATCTTAAAATGGATGCTCGTATGAAGTGGAAGGCAAAGAGCTTTGGAAGGCAACAATACATAGAG
711 ATCTTAAAATGGATGCTCGTATGAAGTGGAAGGCAGAGAGCTTTGGAAGGCAACAATACATAGAG
5135018 CATCTGGCTAGTCAAATTTGTAAAGCAGTAAG
776 CATCTGGCTAGTCAAATTTGTAAAGCAGTAAG
* * *
5135050 AATTAGGACCTATTTTTGACATTGACAGTCACCCCTAATTACTTGATTTAAAAAGTAAAGTGTTC
1 GATTAAGACCTA--TTT----TTGACAGTCACCCCTAATTACTTGATTTAGAAAGTAAAGTGTTC
* *
5135115 TAAAGATATTGTGCTTCCTCTAGATGATTTTTCATTTCAACAAGTGAACCTATGAGCAAAAGAAC
60 TAAAGATATTGTGCTTCCTCCAGATGATTTTTCATTTCAACAAGTGAACCCATGAGCAAAAGAAC
5135180 CATTGTCGGAAGTTGAGCTTGTAAAGCAAGAACTTGAAGCAAAAAAAAAATTG-AAAA-AAAAAT
125 CATTGTCGGAAGTTGAGCTTGTAAAGCAAGAACTTGAAGCAAAAAAAAAATTGAAAAAGAAAAAT
*
5135243 TTGAGACTCCAAGAAGAGATGGGACAATTAAAATATTAAGCGAAAGCTTGAAAAAGCAAACTAAA
190 TTGAGACTCCAAGAAGAGATGGGACAATTAAAATATGAAGCGAAAGCTTGAAAAAGCAAACTAAA
* *
5135308 AAAAACAATGCAAGATCAAGATGTGACTCAAAATGATTTAAAAGATTTGCATCAAGGAAACAAAA
255 AAAAATAATGCAAGATCAAGATGTGACTCAAAATGATTTAAAGGATTTGCATCAAGGAAACAAAA
* * *
5135373 AAATGCGAACCTAATTAAAAGAGGGAAACGATGCTAGATTTAGTGTTAAACAACAAAACG-AAAT
320 AAATGCGAACCCAATTAAAAGAAGGAAACGATGCTAGATTTAGTGTTAAGCAACAAAA-GAAAAT
* *
5135437 GATTGAACTTTAAGAAGAGATGCAACATTGTAACGACAAAACCAAGGAAAATGAAGAAAAAGCCA
384 GATTGAACTTCAAGAAGAGATGCAACATTGTAACGACAAAGCCAAGGAAAATGAAGAAAAAGCCA
*
5135502 TCAGGATTTTTTGAGAACAGTAAGAGTGGAAGGTTTGTATTCAACAACTTCAGCAAGAGTGATGA
449 TCAGGATTTTTCGAGAACAGTAAGAGTGGAAGGTTTGTATTCAACAACTTCAGCAAGAGTGATGA
*
5135567 AATGTCAAAAGGAGAATGCTAAATTGAAAGCACAGATCAAAGATG-AAAA-AAAATACTATGAAA
514 AATGTCAAAAGGAGAATGCTAAATTGAAAGCACAGATCAAAGATGAAAAAGAAAACACTATGAAA
* * * * *
5135630 TGCAAAAGGGGAAAGAATCGCTTTACCAAGTAATTTAATAAATGGAACAACAATTATAGAACCAC
579 TGCAAAAGGAGAAAGAATCGCTTTACCAAGTAATTCAATAGATGGAACAGCAATTACAGAACCAC
* *
5135695 AAAGATCATATTTTCATAATTATCAAAGAATGGCAAAATAGAGAAGAAGATTGGAGATACACTTG
644 AAAGACCATATTTTCATAATTATCAAAGAATGGCAAAATAGAGAAGAAGATTGGAGATACACTTA
*
5135760 CGATCTTAAAATGGATGCTCGTATGAAGTGAAAGGCAGAGAGCTTTGGAAGGCAACAATACATAG
709 CGATCTTAAAATGGATGCTCGTATGAAGTGGAAGGCAGAGAGCTTTGGAAGGCAACAATACATAG
*
5135825 AGCATCTGGCTAGTCAAATTTGTAAAGCAGTATG
774 AGCATCTGGCTAGTCAAATTTGTAAAGCAGTAAG
5135859 GATTAAGACCTATTTTTGACAGTCACCCCTAATTACTTGATTTAGAAAGTAAAGTGTTCTAAAGA
1 GATTAAGACCTATTTTTGACAGTCACCCCTAATTACTTGATTTAGAAAGTAAAGTGTTCTAAAGA
* *
5135924 TATTGTGCTTTCTCCAGATGATTTTTCATTTCAAAAAGTGAACCCATGAGCAAAAGAACCATTGT
66 TATTGTGCTTCCTCCAGATGATTTTTCATTTCAACAAGTGAACCCATGAGCAAAAGAACCATTGT
* * * * *
5135989 CAGAAGTTAAGCTTGTAAAGCAAGAACTTGAAGCAGAAAAAAAATTGAAAACGGAAAATTTGAGA
131 CGGAAGTTGAGCTTGTAAAGCAAGAACTTGAAGCAAAAAAAAAATTGAAAAAGAAAAATTTGAGA
*
5136054 CTCCAAGAAGAGATGGGACAATTAAAATATGAAGCGAAAGCTTGAAAAAGCAAACTCAAAAAAAT
196 CTCCAAGAAGAGATGGGACAATTAAAATATGAAGCGAAAGCTTGAAAAAGCAAACTAAAAAAAAT
* * *
5136119 AATGCAAGATCAAGATGTGACTCAAAATGATTTTAAGGATTTGTATCAAGAAAACAAAAAAATGC
261 AATGCAAGATCAAGATGTGACTCAAAATGATTTAAAGGATTTGCATCAAGGAAACAAAAAAATGC
* *
5136184 GAACCCAATTAAAAGAAAGAAACGGTGCTAGATTTAGTGTTAAGCAACAAAAGAAAATGATTGAA
326 GAACCCAATTAAAAGAAGGAAACGATGCTAGATTTAGTGTTAAGCAACAAAAGAAAATGATTGAA
*
5136249 CTTCAAGAAGAGATGCAACATTGTAACGACAAAGCCAAGGAAAATGAAGAAAAGGCCATCAGGAT
391 CTTCAAGAAGAGATGCAACATTGTAACGACAAAGCCAAGGAAAATGAAGAAAAAGCCATCAGGAT
* * * * *
5136314 TTTTGGAGAACAGTACGAATGAAAGGTTTGTATTCAACAACTTTAGCAAGAGTGATGAAATGTCA
456 TTTTCGAGAACAGTAAGAGTGGAAGGTTTGTATTCAACAACTTCAGCAAGAGTGATGAAATGTCA
*
5136379 AAAGGAGAATGCTAAATTGAAAGCACAAATCAAAGATGAAAAAGAAAACACTATGAAATGCAAAA
521 AAAGGAGAATGCTAAATTGAAAGCACAGATCAAAGATGAAAAAGAAAACACTATGAAATGCAAAA
* *
5136444 GGAGAAAGAATCGCTTTACCAAGTAATTCAATAGATGGAA-AGCAATTACAGAATCACAAAGATC
586 GGAGAAAGAATCGCTTTACCAAGTAATTCAATAGATGGAACAGCAATTACAGAACCACAAAGACC
* * *
5136508 ATATTTCCATAATTATCAAAGAATGGCAAAATAGAGAAGAAG-TTGGAGATACACTTGCAATCTT
651 ATATTTTCATAATTATCAAAGAATGGCAAAATAGAGAAGAAGATTGGAGATACACTTACGATCTT
* * ** ** *
5136572 AAAATGGATGTTTGTATGAAGTGGAAGGCAGAGAGCTTTGGAATACAACAATATGTAGAGCATAT
716 AAAATGGATGCTCGTATGAAGTGGAAGGCAGAGAGCTTTGGAAGGCAACAATACATAGAGCATCT
*
5136637 GGCTAGTCAAATTTGTAAAGCAGTAAA
781 GGCTAGTCAAATTTGTAAAGCAGTAAG
* *
5136664 GATTAGGACCTATTTTTGATC-GTCACCCCTAATTACTTGATTTAGAAAGGAAAGTGTTCTAAAG
1 GATTAAGACCTATTTTTGA-CAGTCACCCCTAATTACTTGATTTAGAAAGTAAAGTGTTCTAAAG
* * * **
5136728 ATATTTTGTTTCCTTCAGATGATTTTTCATTTCAACAAGTGAACCTGTGAGCAAAAGAACCATTG
65 ATATTGTGCTTCCTCCAGATGATTTTTCATTTCAACAAGTGAACCCATGAGCAAAAGAACCATTG
* * * * * *
5136793 TCGAAAGTTGAGCTTGTAAAGTAAGAACTTGAAG-TAGAAAAAAATTGAAAAAGAAAAATATGAA
130 TCGGAAGTTGAGCTTGTAAAGCAAGAACTTGAAGCAAAAAAAAAATTGAAAAAGAAAAATTTGAG
* *
5136857 ACTCCAAAAAGAGATGGGACAATAAAAATATGAAGCGAAAGCTTGAAAAAGCAAACTAAAAAAAA
195 ACTCCAAGAAGAGATGGGACAATTAAAATATGAAGCGAAAGCTTGAAAAAGCAAACTAAAAAAAA
* *
5136922 TAATGCAAGATCAAGATGTGACTCAAAATGATTTAAAGAATTTGCATCAAGGAAACAAAAAAATA
260 TAATGCAAGATCAAGATGTGACTCAAAATGATTTAAAGGATTTGCATCAAGGAAACAAAAAAATG
* * *
5136987 CGAACCCAATTAAAAGAGGGAAACGGTGCTAGATTTAGTGTTAAGCAACAAAAGAAAATTATTGA
325 CGAACCCAATTAAAAGAAGGAAACGATGCTAGATTTAGTGTTAAGCAACAAAAGAAAATGATTGA
* *
5137052 ACTTCAAGAAGAGATGCAACATTGTAACGACAAAGCCAAGAAAAATGAAGAAAAAGCCATTAGGA
390 ACTTCAAGAAGAGATGCAACATTGTAACGACAAAGCCAAGGAAAATGAAGAAAAAGCCATCAGGA
* *
5137117 TATTTCGAGAACAGTAAGAGTGGAAGGTTTGTATTCAACAACTTCAACAAGAGTGATGAAATGTC
455 TTTTTCGAGAACAGTAAGAGTGGAAGGTTTGTATTCAACAACTTCAGCAAGAGTGATGAAATGTC
*
5137182 AAAAGGAGAATGCTAAATTGAAAGCACAGATAAAAGATGAAAAAAGAAAACACTATG-AATGCAA
520 AAAAGGAGAATGCTAAATTGAAAGCACAGATCAAAGATG-AAAAAGAAAACACTATGAAATGCAA
* * *
5137246 AAGGAAAAAGAATCGCTTTACCAAGTAATTCAATAGATGGAACAGTAATTACAGAACCAAAAAGA
584 AAGGAGAAAGAATCGCTTTACCAAGTAATTCAATAGATGGAACAGCAATTACAGAACCACAAAGA
5137311 CCATATTTTCATAATTATCAAAGAATGGCAAAATAGAGAAGAAGATTGGAGATACACTTACGATC
649 CCATATTTTCATAATTATCAAAGAATGGCAAAATAGAGAAGAAGATTGGAGATACACTTACGATC
* * *
5137376 TTAAAATGGATGTTCGTATGAAGTGGAAGGCATAGAACTTTGGAAGGCAACAATACATAGAGCAT
714 TTAAAATGGATGCTCGTATGAAGTGGAAGGCAGAGAGCTTTGGAAGGCAACAATACATAGAGCAT
5137441 CTGGCTAGTCAAATTTGTAAAGCAGTAAG
779 CTGGCTAGTCAAATTTGTAAAGCAGTAAG
5137470 G
1 G
5137471 GAAGTATAGG
Statistics
Matches: 2249, Mismatches: 153, Indels: 41
0.92 0.06 0.02
Matches are distributed among these distances:
803 154 0.07
804 416 0.18
805 680 0.30
806 171 0.08
807 60 0.03
809 250 0.11
810 4 0.00
811 3 0.00
812 348 0.15
813 9 0.00
814 13 0.01
815 141 0.06
ACGTcount: A:0.45, C:0.13, G:0.19, T:0.23
Consensus pattern (807 bp):
GATTAAGACCTATTTTTGACAGTCACCCCTAATTACTTGATTTAGAAAGTAAAGTGTTCTAAAGA
TATTGTGCTTCCTCCAGATGATTTTTCATTTCAACAAGTGAACCCATGAGCAAAAGAACCATTGT
CGGAAGTTGAGCTTGTAAAGCAAGAACTTGAAGCAAAAAAAAAATTGAAAAAGAAAAATTTGAGA
CTCCAAGAAGAGATGGGACAATTAAAATATGAAGCGAAAGCTTGAAAAAGCAAACTAAAAAAAAT
AATGCAAGATCAAGATGTGACTCAAAATGATTTAAAGGATTTGCATCAAGGAAACAAAAAAATGC
GAACCCAATTAAAAGAAGGAAACGATGCTAGATTTAGTGTTAAGCAACAAAAGAAAATGATTGAA
CTTCAAGAAGAGATGCAACATTGTAACGACAAAGCCAAGGAAAATGAAGAAAAAGCCATCAGGAT
TTTTCGAGAACAGTAAGAGTGGAAGGTTTGTATTCAACAACTTCAGCAAGAGTGATGAAATGTCA
AAAGGAGAATGCTAAATTGAAAGCACAGATCAAAGATGAAAAAGAAAACACTATGAAATGCAAAA
GGAGAAAGAATCGCTTTACCAAGTAATTCAATAGATGGAACAGCAATTACAGAACCACAAAGACC
ATATTTTCATAATTATCAAAGAATGGCAAAATAGAGAAGAAGATTGGAGATACACTTACGATCTT
AAAATGGATGCTCGTATGAAGTGGAAGGCAGAGAGCTTTGGAAGGCAACAATACATAGAGCATCT
GGCTAGTCAAATTTGTAAAGCAGTAAG
Found at i:5145331 original size:14 final size:15
Alignment explanation
Indices: 5145306--5145353 Score: 64
Period size: 14 Copynumber: 3.3 Consensus size: 15
5145296 ACTTTGCCTG
5145306 AAAAGAAGACAAAA-A
1 AAAAGAA-ACAAAACA
5145321 AAAAGAAACAAAACA
1 AAAAGAAACAAAACA
*
5145336 AACA-AAACAAAACA
1 AAAAGAAACAAAACA
5145350 AAAA
1 AAAA
5145354 ACAAACAGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
14 19 0.63
15 11 0.37
ACGTcount: A:0.81, C:0.12, G:0.06, T:0.00
Consensus pattern (15 bp):
AAAAGAAACAAAACA
Found at i:5146401 original size:50 final size:50
Alignment explanation
Indices: 5146343--5146453 Score: 181
Period size: 50 Copynumber: 2.2 Consensus size: 50
5146333 GAAAAAAAAT
5146343 ATTTTTAAAGTTTCAAAG-CTTCTGTTT-GGGGGAAGCCATTTTCAAACAAG
1 ATTTTTAAAGTTTCAAAGCCTT-TGTTTAGGGGG-AGCCATTTTCAAACAAG
*
5146393 ATTTTTAAAGTTTTAAAGCCTTTGTTTAGGGGGAGCCATTTTCAAACAAG
1 ATTTTTAAAGTTTCAAAGCCTTTGTTTAGGGGGAGCCATTTTCAAACAAG
5146443 ATTTTTAAAGT
1 ATTTTTAAAGT
5146454 GTTTTAAACA
Statistics
Matches: 58, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
50 50 0.86
51 8 0.14
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.39
Consensus pattern (50 bp):
ATTTTTAAAGTTTCAAAGCCTTTGTTTAGGGGGAGCCATTTTCAAACAAG
Found at i:5146462 original size:23 final size:24
Alignment explanation
Indices: 5146431--5146478 Score: 89
Period size: 23 Copynumber: 2.0 Consensus size: 24
5146421 GGGGGAGCCA
5146431 TTTTCAAACAAGATTTTTAAAGTG
1 TTTTCAAACAAGATTTTTAAAGTG
5146455 TTTT-AAACAAGATTTTTAAAGTG
1 TTTTCAAACAAGATTTTTAAAGTG
5146478 T
1 T
5146479 CAAAGCTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.83
24 4 0.17
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (24 bp):
TTTTCAAACAAGATTTTTAAAGTG
Found at i:5146507 original size:73 final size:74
Alignment explanation
Indices: 5146381--5146525 Score: 222
Period size: 73 Copynumber: 2.0 Consensus size: 74
5146371 GGGGAAGCCA
* * *
5146381 TTTTCAAACAAGATTTTTAAAGTTTTAAAGCCTTTGTTTAGGGGGAGCCATTTTCAAACAAGATT
1 TTTTCAAACAAGATTTTTAAAGTGTCAAAGCCTTTGTTTAAGGGGAGCCATTTTCAAACAAGATT
5146446 TTTAAAGTG
66 TTTAAAGTG
* *
5146455 TTTT-AAACAAGATTTTTAAAGTGTCAAAG-CTTCTGTTTAAGGGGAGCTATTTTCAAATAAGAT
1 TTTTCAAACAAGATTTTTAAAGTGTCAAAGCCTT-TGTTTAAGGGGAGCCATTTTCAAACAAGAT
5146518 TTTTAAAG
65 TTTTAAAG
5146526 AGTCAAAGCC
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
72 3 0.05
73 58 0.89
74 4 0.06
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (74 bp):
TTTTCAAACAAGATTTTTAAAGTGTCAAAGCCTTTGTTTAAGGGGAGCCATTTTCAAACAAGATT
TTTAAAGTG
Found at i:5146562 original size:123 final size:123
Alignment explanation
Indices: 5146343--5146576 Score: 335
Period size: 123 Copynumber: 1.9 Consensus size: 123
5146333 GAAAAAAAAT
* * ** *
5146343 ATTTTTAAAGTTTCAAAGCTTCTGTTTGGGGGAAGCCATTTTCAAACAAGATTTTTAAAGTTTTA
1 ATTTTTAAAGTGTCAAAGCTTCTGTTTAGGGGAAGCCATTTTCAAACAAGATTTTTAAAGAGTCA
* * * * *
5146408 AAGCCTTTGTTTAGGGGGAGCCATTTTCAAACAAGATTTTTAAAGTGTTTTAAACAAG
66 AAGCCTATATTTAGGAGAAGCCATTTTCAAACAAAATTTTTAAAGTGTTTTAAACAAG
* *
5146466 ATTTTTAAAGTGTCAAAGCTTCTGTTTAAGGGG-AGCTATTTTCAAATAAGATTTTTAAAGAGTC
1 ATTTTTAAAGTGTCAAAGCTTCTGTTT-AGGGGAAGCCATTTTCAAACAAGATTTTTAAAGAGTC
*
5146530 AAAGCCTATATTTAGGAGAAGTCATTTTCAAACAAAATTTTTAAAGT
65 AAAGCCTATATTTAGGAGAAGCCATTTTCAAACAAAATTTTTAAAGT
5146577 TTCAAAGCCT
Statistics
Matches: 97, Mismatches: 13, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
123 93 0.96
124 4 0.04
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.38
Consensus pattern (123 bp):
ATTTTTAAAGTGTCAAAGCTTCTGTTTAGGGGAAGCCATTTTCAAACAAGATTTTTAAAGAGTCA
AAGCCTATATTTAGGAGAAGCCATTTTCAAACAAAATTTTTAAAGTGTTTTAAACAAG
Found at i:5146639 original size:52 final size:51
Alignment explanation
Indices: 5146466--5146649 Score: 205
Period size: 50 Copynumber: 3.6 Consensus size: 51
5146456 TTTAAACAAG
* *
5146466 ATTTTTAAAGTGTCAAAG-CTTCTGTTTA-AGGGGAG-CTATTTTCAAATAAG
1 ATTTTTAAAGTGTCAAAGCCTT-TGTTTAGAGGGAAGTC-ATTTTCAAATAAA
* * * * *
5146516 ATTTTTAAAGAGTCAAAGCCTATATTTAG-GAGAAGTCATTTTCAAACAAA
1 ATTTTTAAAGTGTCAAAGCCTTTGTTTAGAGGGAAGTCATTTTCAAATAAA
*
5146566 ATTTTTAAAGTTTCAAAGCCTTTGTTTAGAGGGAAGTCATTTTCAAATAAAA
1 ATTTTTAAAGTGTCAAAGCCTTTGTTTAGAGGGAAGTCATTTTCAAAT-AAA
* * * *
5146618 ACTTTTAAAGTTTCAATGCCTTTGATTAGAGG
1 ATTTTTAAAGTGTCAAAGCCTTTGTTTAGAGG
5146650 AGTATTCAAA
Statistics
Matches: 113, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
50 62 0.55
51 19 0.17
52 32 0.28
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (51 bp):
ATTTTTAAAGTGTCAAAGCCTTTGTTTAGAGGGAAGTCATTTTCAAATAAA
Found at i:5147488 original size:143 final size:145
Alignment explanation
Indices: 5147295--5147667 Score: 425
Period size: 143 Copynumber: 2.6 Consensus size: 145
5147285 GCCTTTTAGG
* * * * * *
5147295 GGGTATCTTCGTAATTTAGTC-TTTCTGAGCTGAAATTTTTATGAAACTTTTCAGATATTAATTT
1 GGGTATTTTCGTAATTT-GACATTTTTGAGCTCAGATTTTCATGAAACTTTTCAGATATTAATTT
*
5147359 CATAATATTTCATAATTTTTGATGCATTTGAAATCATAGCAATACC-TCAAAAGTATAAAATTAC
65 CATAATATTTCATAATTTTTGATGCATTTGAAATCATAGCAATACCATAAAAAGTATAAAATTAC
*
5147423 GAAAATACCATTAT-A
130 GAAAATACCACTATAA
* * * *
5147438 GGGTATTTTCGTTATTT-ACCATTTTTGAGCTCAGATTTTCATGAAACTTTTTAAATCTTAATTT
1 GGGTATTTTCGTAATTTGA-CATTTTTGAGCTCAGATTTTCATGAAACTTTTCAGATATTAATTT
* * * *
5147502 CATAATATTTCATAATTTTTGGTGCATTTGAAATCATAGTAGTACCATAAAAAGTATGAAATTAC
65 CATAATATTTCATAATTTTTGATGCATTTGAAATCATAGCAATACCATAAAAAGTATAAAATTAC
* *
5147567 TAAAATACCCCTATAA
130 GAAAATACCACTATAA
* * ** ** *
5147583 GGGTATTTTTGTAATTTGATATTTTCAAG-TTTGAATTTTCATGAAACTTTTCAGATATCAATAT
1 GGGTATTTTCGTAATTTGACATTTTTGAGCTCAG-ATTTTCATGAAACTTTTCAGATATTAAT-T
* *
5147647 T-ATAATATTTTATGATTTTTG
64 TCATAATATTTCATAATTTTTG
5147668 GTGTTTTAAA
Statistics
Matches: 192, Mismatches: 31, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
142 1 0.01
143 94 0.49
144 29 0.15
145 65 0.34
146 3 0.02
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.43
Consensus pattern (145 bp):
GGGTATTTTCGTAATTTGACATTTTTGAGCTCAGATTTTCATGAAACTTTTCAGATATTAATTTC
ATAATATTTCATAATTTTTGATGCATTTGAAATCATAGCAATACCATAAAAAGTATAAAATTACG
AAAATACCACTATAA
Found at i:5157366 original size:13 final size:13
Alignment explanation
Indices: 5157348--5157380 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
5157338 AATAATTTTC
5157348 AAATAAAAAAATA
1 AAATAAAAAAATA
5157361 AAATAAAAAAATA
1 AAATAAAAAAATA
5157374 AAA-AAAA
1 AAATAAAA
5157381 GGATGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.20
13 16 0.80
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAATAAAAAAATA
Found at i:5158043 original size:22 final size:22
Alignment explanation
Indices: 5158018--5158081 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 22
5158008 CAATTATTTA
5158018 GACTTGTTTTTAGTGCTTAAAT
1 GACTTGTTTTTAGTGCTTAAAT
**
5158040 GACTTAATTTTA---CTT--A-
1 GACTTGTTTTTAGTGCTTAAAT
*
5158056 GACTTGTTTTTAGTGCCTAAAT
1 GACTTGTTTTTAGTGCTTAAAT
5158078 GACT
1 GACT
5158082 GAATTTTACG
Statistics
Matches: 31, Mismatches: 5, Indels: 12
0.65 0.10 0.25
Matches are distributed among these distances:
16 10 0.32
17 1 0.03
19 5 0.16
21 1 0.03
22 14 0.45
ACGTcount: A:0.25, C:0.12, G:0.16, T:0.47
Consensus pattern (22 bp):
GACTTGTTTTTAGTGCTTAAAT
Found at i:5158066 original size:38 final size:38
Alignment explanation
Indices: 5158015--5158090 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
5158005 AAACAATTAT
* *
5158015 TTAGACTTGTTTTTAGTGCTTAAATGACTTAATTTTAC
1 TTAGACTTGTTTTTAGTGCCTAAATGACTGAATTTTAC
5158053 TTAGACTTGTTTTTAGTGCCTAAATGACTGAATTTTAC
1 TTAGACTTGTTTTTAGTGCCTAAATGACTGAATTTTAC
5158091 GTAGTTTTGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.47
Consensus pattern (38 bp):
TTAGACTTGTTTTTAGTGCCTAAATGACTGAATTTTAC
Found at i:5159483 original size:19 final size:20
Alignment explanation
Indices: 5159459--5159498 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
5159449 TAAATTCACC
5159459 TATTGTTTA-ATCTTTAATT
1 TATTGTTTACATCTTTAATT
*
5159478 TATTGTTTACATGTTTAATT
1 TATTGTTTACATCTTTAATT
5159498 T
1 T
5159499 TGCTAGGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.25, C:0.05, G:0.07, T:0.62
Consensus pattern (20 bp):
TATTGTTTACATCTTTAATT
Found at i:5161042 original size:20 final size:20
Alignment explanation
Indices: 5160994--5161045 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
5160984 TCAATCCAAG
*
5160994 AAAGACAAGTCATCAAGATT
1 AAAGACAAGTCAACAAGATT
** **
5161014 TTATCCAAGTCAACAAGATT
1 AAAGACAAGTCAACAAGATT
5161034 AAAGACAAGTCA
1 AAAGACAAGTCA
5161046 GATTAACATA
Statistics
Matches: 23, Mismatches: 9, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.48, C:0.17, G:0.13, T:0.21
Consensus pattern (20 bp):
AAAGACAAGTCAACAAGATT
Found at i:5161162 original size:12 final size:12
Alignment explanation
Indices: 5161145--5161177 Score: 57
Period size: 12 Copynumber: 2.7 Consensus size: 12
5161135 CAAGTCTACC
5161145 ATACCTCTTTAT
1 ATACCTCTTTAT
5161157 ATACCTCTTTAT
1 ATACCTCTTTAT
5161169 ATACTCTCT
1 ATAC-CTCT
5161178 AGGATTCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.48
Consensus pattern (12 bp):
ATACCTCTTTAT
Found at i:5168718 original size:13 final size:14
Alignment explanation
Indices: 5168700--5168733 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
5168690 TGCCACTCAT
5168700 TTTCTCCTCT-TTA
1 TTTCTCCTCTCTTA
*
5168713 TTTCTCCTCTCTTC
1 TTTCTCCTCTCTTA
5168727 TTTCTCC
1 TTTCTCC
5168734 GATCCAGCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.03, C:0.38, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTCTCCTCTCTTA
Found at i:5169820 original size:18 final size:18
Alignment explanation
Indices: 5169797--5169832 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
5169787 ACACATCACA
5169797 ACCAATCAAACATCCTAT
1 ACCAATCAAACATCCTAT
*
5169815 ACCAATCAACCATCCTAT
1 ACCAATCAAACATCCTAT
5169833 CCATGGGCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.36, G:0.00, T:0.22
Consensus pattern (18 bp):
ACCAATCAAACATCCTAT
Found at i:5172575 original size:2 final size:2
Alignment explanation
Indices: 5172568--5172594 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5172558 ACTTAAAGAT
5172568 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 A
5172595 AACAGAATAC
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5173172 original size:20 final size:20
Alignment explanation
Indices: 5173147--5173185 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5173137 TTTAAAATAT
5173147 TTAAAATAATATTTCTATTC
1 TTAAAATAATATTTCTATTC
* *
5173167 TTAAAATATTATTTTTATT
1 TTAAAATAATATTTCTATT
5173186 GATTTAATAA
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:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (20 bp):
TTAAAATAATATTTCTATTC
Found at i:5173344 original size:13 final size:13
Alignment explanation
Indices: 5173326--5173350 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5173316 ATATATACAT
5173326 TAAAAATAAAATA
1 TAAAAATAAAATA
5173339 TAAAAATAAAAT
1 TAAAAATAAAAT
5173351 TTTAAATTGA
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAAAATAAAATA
Found at i:5173797 original size:20 final size:20
Alignment explanation
Indices: 5173768--5173806 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5173758 TTTCACTTAA
5173768 ATTTAAATAAAAATATTTTT
1 ATTTAAATAAAAATATTTTT
* *
5173788 ATTTATATAATAATATTTT
1 ATTTAAATAAAAATATTTT
5173807 ATGTCGAGTA
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
ATTTAAATAAAAATATTTTT
Found at i:5173970 original size:20 final size:21
Alignment explanation
Indices: 5173927--5173972 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
5173917 TTATCTTTCT
*
5173927 TTTTTGAAAAAAAAAAGATAA
1 TTTTTGAAAAAAAAAACATAA
* *
5173948 TTTTT-AAAAAAAAAACTTGA
1 TTTTTGAAAAAAAAAACATAA
5173968 TTTTT
1 TTTTT
5173973 CGTTGTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (21 bp):
TTTTTGAAAAAAAAAACATAA
Found at i:5175745 original size:30 final size:29
Alignment explanation
Indices: 5175702--5175794 Score: 114
Period size: 32 Copynumber: 3.0 Consensus size: 29
5175692 ATGCAAAAAT
*
5175702 ATCATAATAAATCATGCAAATAAATTAAA
1 ATCATAAAAAATCATGCAAATAAATTAAA
*
5175731 TTCATAAAAAAATCATGCAAAAATAAATTAATA
1 ATCAT-AAAAAATCATGC--AAATAAATTAA-A
*
5175764 ATCATAAAAAATAATGCAAATAAAATTAAA
1 ATCATAAAAAATCATGCAAAT-AAATTAAA
5175794 A
1 A
5175795 CATGCAAATT
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
29 4 0.07
30 17 0.31
31 7 0.13
32 22 0.40
33 5 0.09
ACGTcount: A:0.62, C:0.09, G:0.03, T:0.26
Consensus pattern (29 bp):
ATCATAAAAAATCATGCAAATAAATTAAA
Found at i:5175937 original size:18 final size:18
Alignment explanation
Indices: 5175891--5175972 Score: 62
Period size: 18 Copynumber: 4.4 Consensus size: 18
5175881 ATAAATAAGC
*
5175891 AAATAAAATAAAAGATAGGAA
1 AAATAAAACAAAA-ATA--AA
5175912 AAAT-AAACAAACAA-AAA
1 AAATAAAACAAA-AATAAA
5175929 AAATAAAACAAAAATAAA
1 AAATAAAACAAAAATAAA
* * *
5175947 AAACAAAA-AGATATAGAA
1 AAATAAAACAAAAATA-AA
5175965 AAATAAAA
1 AAATAAAA
5175973 ACTTACGATT
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
17 13 0.25
18 26 0.50
19 1 0.02
20 7 0.13
21 5 0.10
ACGTcount: A:0.78, C:0.05, G:0.06, T:0.11
Consensus pattern (18 bp):
AAATAAAACAAAAATAAA
Found at i:5175941 original size:13 final size:13
Alignment explanation
Indices: 5175910--5175955 Score: 65
Period size: 14 Copynumber: 3.4 Consensus size: 13
5175900 AAAAGATAGG
5175910 AAAAATAAACAAAC
1 AAAAATAAA-AAAC
*
5175924 AAAAAAAATAAAAC
1 AAAAATAA-AAAAC
5175938 AAAAATAAAAAAC
1 AAAAATAAAAAAC
5175951 AAAAA
1 AAAAA
5175956 GATATAGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 10 0.34
14 18 0.62
15 1 0.03
ACGTcount: A:0.85, C:0.09, G:0.00, T:0.07
Consensus pattern (13 bp):
AAAAATAAAAAAC
Found at i:5176895 original size:11 final size:11
Alignment explanation
Indices: 5176879--5176908 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
5176869 AAAAATAATA
5176879 AAAATTAAACC
1 AAAATTAAACC
*
5176890 AAAATTAAACT
1 AAAATTAAACC
5176901 AAAATTAA
1 AAAATTAA
5176909 TGCAAATGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAATTAAACC
Found at i:5177200 original size:22 final size:22
Alignment explanation
Indices: 5177173--5177215 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
5177163 ACACTTTTCA
*
5177173 AAAGTTCCTAACTTGAAATTCC
1 AAAGTTCATAACTTGAAATTCC
*
5177195 AAAGTTCATAATTTGAAATTC
1 AAAGTTCATAACTTGAAATTC
5177216 AAGAATTCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (22 bp):
AAAGTTCATAACTTGAAATTCC
Found at i:5177316 original size:18 final size:19
Alignment explanation
Indices: 5177275--5177317 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
5177265 AAGGTCTCAA
**
5177275 AGCAAGAATTAAAAAATTC
1 AGCAAGAAACAAAAAATTC
5177294 A-CAAGAAACAAAAAATT-
1 AGCAAGAAACAAAAAATTC
5177311 AGCAAGA
1 AGCAAGA
5177318 TTTATAAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 1 0.05
18 19 0.90
19 1 0.05
ACGTcount: A:0.63, C:0.12, G:0.12, T:0.14
Consensus pattern (19 bp):
AGCAAGAAACAAAAAATTC
Found at i:5177415 original size:30 final size:29
Alignment explanation
Indices: 5177375--5177431 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
5177365 AAAAGTTTGC
*
5177375 AAAAGATTCAAGGTTAGTAAAAAATTTTA
1 AAAAGATTCAAGATTAGTAAAAAATTTTA
*
5177404 AAAATGATTCAAGATTTGTAAAAAATTT
1 AAAA-GATTCAAGATTAGTAAAAAATTT
5177432 AAAGATTCGC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.51, C:0.04, G:0.12, T:0.33
Consensus pattern (29 bp):
AAAAGATTCAAGATTAGTAAAAAATTTTA
Found at i:5177457 original size:18 final size:18
Alignment explanation
Indices: 5177404--5177490 Score: 70
Period size: 19 Copynumber: 4.7 Consensus size: 18
5177394 AAAAATTTTA
* *
5177404 AAAATGATTCAAGATTTGT
1 AAAA-GATTCAAAATTTGC
* * *
5177423 AAAAAATTTAAAGATTCGC
1 AAAAGATTCAAA-ATTTGC
*
5177442 AAAATATTCAAAA-TT-C
1 AAAAGATTCAAAATTTGC
5177458 ATAAAGATTCAAAAGTTTGC
1 A-AAAGATTCAAAA-TTTGC
5177478 AAAAGATTCAAAA
1 AAAAGATTCAAAA
5177491 ATAATTTTGA
Statistics
Matches: 54, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
16 2 0.04
17 12 0.22
18 6 0.11
19 32 0.59
20 2 0.04
ACGTcount: A:0.52, C:0.09, G:0.10, T:0.29
Consensus pattern (18 bp):
AAAAGATTCAAAATTTGC
Found at i:5177491 original size:10 final size:9
Alignment explanation
Indices: 5177441--5177490 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
5177431 TAAAGATTCG
*
5177441 CAAAATATT
1 CAAAAGATT
5177450 C-AAA-ATT
1 CAAAAGATT
5177457 CATAAAGATT
1 CA-AAAGATT
*
5177467 CAAAAGTTT
1 CAAAAGATT
5177476 GCAAAAGATT
1 -CAAAAGATT
5177486 CAAAA
1 CAAAA
5177491 ATAATTTTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
7 4 0.11
8 3 0.09
9 15 0.43
10 13 0.37
ACGTcount: A:0.54, C:0.12, G:0.08, T:0.26
Consensus pattern (9 bp):
CAAAAGATT
Found at i:5177570 original size:45 final size:44
Alignment explanation
Indices: 5177519--5177816 Score: 214
Period size: 45 Copynumber: 6.7 Consensus size: 44
5177509 AAATGAAGCT
* *
5177519 TCTAAAATTCAAAGATTCACATTCGAAAATTTTTTGAAATTCACA
1 TCTAAAATTCAAAGATTCACATTCGAAAA-ATTTAGAAATTCACA
*
5177564 TCTAAAATTTCAAA-ATTCAAATTCG-AAAATCTTAGAAATTCACA
1 TCTAAAA-TTCAAAGATTCACATTCGAAAAAT-TTAGAAATTCACA
* * * * * * *
5177608 TATAAGATTCAAAGGTTCATATTTGAAAAGTTTAGAGATTCACA
1 TCTAAAATTCAAAGATTCACATTCGAAAAATTTAGAAATTCACA
* * * *
5177652 T-TAAAAAATTAAAAAATTCTCATTTGAAAAATTTTA-AAGATTCACA
1 TCT--AAAATTCAAAGATTCACATTCGAAAAA-TTTAGAA-ATTCACA
* * * **
5177698 TTTAAAATTCAAATATTCTCATTTAAAAAATTTAGAAATTCACA
1 TCTAAAATTCAAAGATTCACATTCGAAAAATTTAGAAATTCACA
* * *
5177742 TTCAAAAATTCAAAGAGTCTA-ATTCAAAAAATTTTA-AATATTCACA
1 -TCTAAAATTCAAAGATTC-ACATTCGAAAAA-TTTAGAA-ATTCACA
* * *
5177788 TC-AAAATTTCAAAAATTCGCATTTGAAAA
1 TCTAAAA-TTCAAAGATTCACATTCGAAAA
5177817 TTTCAAAGAT
Statistics
Matches: 205, Mismatches: 32, Indels: 32
0.76 0.12 0.12
Matches are distributed among these distances:
43 8 0.04
44 56 0.27
45 111 0.54
46 29 0.14
47 1 0.00
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.34
Consensus pattern (44 bp):
TCTAAAATTCAAAGATTCACATTCGAAAAATTTAGAAATTCACA
Found at i:5177659 original size:23 final size:22
Alignment explanation
Indices: 5177645--5177842 Score: 98
Period size: 23 Copynumber: 8.8 Consensus size: 22
5177635 AAGTTTAGAG
*
5177645 ATTCACATTAAAAAATTAAAAA
1 ATTCACATTAAAAAATTTAAAA
* * *
5177667 ATTCTCATTTGAAAAATTTTAAAG
1 ATTCACA-TT-AAAAAATTTAAAA
* * *
5177691 ATTCACATT-TAAAATTCAAAT
1 ATTCACATTAAAAAATTTAAAA
* *
5177712 ATTCTCATTTAAAAAATTTAGAA
1 ATTCACA-TTAAAAAATTTAAAA
* * *
5177735 ATTCACATTCAAAAATTCAAAG
1 ATTCACATTAAAAAATTTAAAA
* *
5177757 AGTCTA-ATTCAAAAAATTTTAAAT
1 ATTC-ACATT-AAAAAA-TTTAAAA
*
5177781 ATTCACA-T-CAAAATTTCAAAA
1 ATTCACATTAAAAAATTT-AAAA
* ** *
5177802 ATTCGCATTTGAAAATTTCAAAG
1 ATTCACATTAAAAAATTT-AAAA
** *
5177825 ATTCTTATTTAAAAATTT
1 ATTCACATTAAAAAATTT
5177843 TAGAGATTCT
Statistics
Matches: 133, Mismatches: 32, Indels: 21
0.72 0.17 0.11
Matches are distributed among these distances:
20 3 0.02
21 27 0.20
22 26 0.20
23 52 0.39
24 25 0.19
ACGTcount: A:0.48, C:0.12, G:0.04, T:0.36
Consensus pattern (22 bp):
ATTCACATTAAAAAATTTAAAA
Found at i:5177732 original size:90 final size:90
Alignment explanation
Indices: 5177628--5177918 Score: 277
Period size: 90 Copynumber: 3.2 Consensus size: 90
5177618 AAAGGTTCAT
* *
5177628 ATTTGAAAAGTTTAGAGATTCACATTAAAAAATTAAAAAATTCTCATTTGAAAAATTTTAAAGAT
1 ATTTGAAAAATTTAGAGATTCACATTAAAAAATTAAAAGATTCTCATTT-AAAAATTTTAAAGAT
*
5177693 TCACATTTAAAA-TTCAAATATTCTC
65 TCACATTTAAAAGTTCAAAAATTCTC
* * * * * * * *
5177718 ATTTAAAAAATTTAGAAATTCACATTCAAAAATTCAAAGAGTCTAATTCAAAAAATTTTAAATAT
1 ATTTGAAAAATTTAGAGATTCACATTAAAAAATTAAAAGATTCTCATT-TAAAAATTTTAAAGAT
* * *
5177783 TCACA-TCAAAATTTCAAAAATTCGC
65 TCACATTTAAAAGTTCAAAAATTCTC
* ** * * * * * *
5177808 ATTTG-AAAATTTCAAAGATTCTTATTTAAAAATTTTAGAGATTCTCATCT-AATA-TTCAAAGA
1 ATTTGAAAAATTT-AGAGATTCACA-TTAAAAAATTAAAAGATTCTCATTTAAAAATTTTAAAGA
*
5177870 TTTACATTTGAAAAGTTCAAAAATTCTC
64 TTCACATTT-AAAAGTTCAAAAATTCTC
*
5177898 ATTTGAAAATTTTAGAGATTC
1 ATTTGAAAAATTTAGAGATTC
5177919 TTATCCAAAA
Statistics
Matches: 159, Mismatches: 35, Indels: 14
0.76 0.17 0.07
Matches are distributed among these distances:
88 11 0.07
89 16 0.10
90 109 0.69
91 23 0.14
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.37
Consensus pattern (90 bp):
ATTTGAAAAATTTAGAGATTCACATTAAAAAATTAAAAGATTCTCATTTAAAAATTTTAAAGATT
CACATTTAAAAGTTCAAAAATTCTC
Found at i:5177849 original size:23 final size:23
Alignment explanation
Indices: 5177652--5177939 Score: 96
Period size: 23 Copynumber: 12.8 Consensus size: 23
5177642 GAGATTCACA
* * * *
5177652 TTAAAAAATTAAAAAATTCTCAT
1 TTAAAAATTTCAAAGATTCTTAT
* **
5177675 TTGAAAAATTTTAAAGATTCACAT
1 TT-AAAAATTTCAAAGATTCTTAT
* *
5177699 TT-AAAA-TTCAAATATTCTCAT
1 TTAAAAATTTCAAAGATTCTTAT
**
5177720 TTAAAAAATTT-AGAA-ATTCACAT
1 TT-AAAAATTTCA-AAGATTCTTAT
* * *
5177743 TCAAAAA-TTCAAAGAGTCTAAT
1 TTAAAAATTTCAAAGATTCTTAT
* * * *
5177765 TCAAAAAATTTTAAATATTC--AC
1 T-TAAAAATTTCAAAGATTCTTAT
* * * **
5177787 ATCAAAATTTCAAAAATTCGCAT
1 TTAAAAATTTCAAAGATTCTTAT
*
5177810 TTGAAAATTTCAAAGATTCTTAT
1 TTAAAAATTTCAAAGATTCTTAT
* * *
5177833 TTAAAAATTTTAGAGATTCTCAT
1 TTAAAAATTTCAAAGATTCTTAT
* * *
5177856 CT-AATA-TTCAAAGATT-TACAT
1 TTAAAAATTTCAAAGATTCT-TAT
* * * *
5177877 TTGAAAAGTTCAAAAATTCTCAT
1 TTAAAAATTTCAAAGATTCTTAT
* * *
5177900 TTGAAAATTTTAGAGATTCTTA-
1 TTAAAAATTTCAAAGATTCTTAT
**
5177922 TCCAAAA-TTCAAAGATTC
1 TTAAAAATTTCAAAGATTC
5177940 GCATTAGAAA
Statistics
Matches: 202, Mismatches: 48, Indels: 32
0.72 0.17 0.11
Matches are distributed among these distances:
20 1 0.00
21 53 0.26
22 28 0.14
23 88 0.44
24 32 0.16
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.37
Consensus pattern (23 bp):
TTAAAAATTTCAAAGATTCTTAT
Found at i:5177866 original size:67 final size:67
Alignment explanation
Indices: 5177599--5177955 Score: 244
Period size: 67 Copynumber: 5.3 Consensus size: 67
5177589 AAAATCTTAG
* * * * * *
5177599 AAATTCACATAT-AAGA-TTCAAAGGTTCAT-ATTTGAAAAGTTTAGAGATTCACAT-TAAAAAA
1 AAATTCACATTTGAAAAGTTCAAAGATTC-TCATTTAAAAATTTTAGAGATTCTCATCT--AAAA
*
5177660 TTAAA
63 TTCAA
* * * * * * * *
5177665 AAATTCTCATTTGAAAAATTTTAAAGATTCACATTT-AAAA-TTCAAATATTCTCATTTAAAAAA
1 AAATTCACATTTG-AAAAGTTCAAAGATTCTCATTTAAAAATTTTAGAGATTCTCATCT--AAAA
* *
5177728 TTTAG
63 TTCAA
* * * * * * * *
5177733 AAATTCACA-TTCAAAAATTCAAAGAGTCTAATTCAAAAAATTTTAAATATTCACATC-AAAATT
1 AAATTCACATTTGAAAAGTTCAAAGATTCTCATT-TAAAAATTTTAGAGATTCTCATCTAAAA-T
5177796 TCAA
64 TCAA
* * * *
5177800 AAATTCGCATTTGAAAATTTCAAAGATTCTTATTTAAAAATTTTAGAGATTCTCATCTAATATTC
1 AAATTCACATTTGAAAAGTTCAAAGATTCTCATTTAAAAATTTTAGAGATTCTCATCTAAAATTC
5177865 AA
66 AA
* * * * * *
5177867 AGATTTACATTTGAAAAGTTCAAAAATTCTCATTTGAAAATTTTAGAGATTCTTATCCAAAATTC
1 AAATTCACATTTGAAAAGTTCAAAGATTCTCATTTAAAAATTTTAGAGATTCTCATCTAAAATTC
5177932 AA
66 AA
* * *
5177934 AGATTCGCATTAGAAAAGTTCA
1 AAATTCACATTTGAAAAGTTCA
5177956 CATCTAAAAT
Statistics
Matches: 232, Mismatches: 48, Indels: 21
0.77 0.16 0.07
Matches are distributed among these distances:
66 30 0.13
67 124 0.53
68 52 0.22
69 26 0.11
ACGTcount: A:0.45, C:0.12, G:0.08, T:0.36
Consensus pattern (67 bp):
AAATTCACATTTGAAAAGTTCAAAGATTCTCATTTAAAAATTTTAGAGATTCTCATCTAAAATTC
AA
Found at i:5183655 original size:13 final size:15
Alignment explanation
Indices: 5183629--5183661 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
5183619 ACACGTAAAG
5183629 ATCATGCAAAAAT-A
1 ATCATGCAAAAATAA
5183643 ATCATGC-AAAATAA
1 ATCATGCAAAAATAA
5183657 ATCAT
1 ATCAT
5183662 AATAAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.55, C:0.15, G:0.06, T:0.24
Consensus pattern (15 bp):
ATCATGCAAAAATAA
Found at i:5183751 original size:54 final size:55
Alignment explanation
Indices: 5183636--5183766 Score: 133
Period size: 55 Copynumber: 2.4 Consensus size: 55
5183626 AAGATCATGC
* * * *
5183636 AAAAATAATCATGCAAAATAAATCATAATAAATAATGCAAATAAATATACTTAATG
1 AAAAATCATTATGCAAAA-ATATCATAATAAATAATGCAAATAAATATAATTAATG
* * * * *
5183692 CAAAAT-ATTGTGTAAAAATATCATAATAAATCATGCAAAATAAAT-TAAATTCAT-
1 AAAAATCATTATGCAAAAATATCATAATAAATAATGC-AAATAAATAT-AATTAATG
5183746 AAAAATCATTATGCAAAAATA
1 AAAAATCATTATGCAAAAATA
5183767 AATTAATAAT
Statistics
Matches: 61, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
54 23 0.38
55 33 0.54
56 5 0.08
ACGTcount: A:0.57, C:0.09, G:0.05, T:0.28
Consensus pattern (55 bp):
AAAAATCATTATGCAAAAATATCATAATAAATAATGCAAATAAATATAATTAATG
Found at i:5183942 original size:17 final size:17
Alignment explanation
Indices: 5183896--5183946 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
5183886 TTAAAATAAT
*
5183896 AAATAAGAAAATAAA-AT
1 AAAT-AGAAAATAAACAA
5183913 AAAT--AAAAT-AACAA
1 AAATAGAAAATAAACAA
5183927 AAATAGAAAATAAACAA
1 AAATAGAAAATAAACAA
5183944 AAA
1 AAA
5183947 ATAAACAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
13 2 0.07
14 10 0.34
16 5 0.17
17 12 0.41
ACGTcount: A:0.78, C:0.04, G:0.04, T:0.14
Consensus pattern (17 bp):
AAATAGAAAATAAACAA
Found at i:5183959 original size:12 final size:11
Alignment explanation
Indices: 5183933--5183958 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5183923 ACAAAAATAG
5183933 AAAATAAACAA
1 AAAATAAACAA
5183944 AAAATAAACAA
1 AAAATAAACAA
5183955 AAAA
1 AAAA
5183959 AAATTTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.08, G:0.00, T:0.08
Consensus pattern (11 bp):
AAAATAAACAA
Found at i:5184160 original size:27 final size:27
Alignment explanation
Indices: 5184126--5184183 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
5184116 CTTTTCCTTC
5184126 TCTAGA-TTGGATTCTCTCC-TCTTTCTT
1 TCTAGATTTGG-TTCTC-CCATCTTTCTT
*
5184153 TCTAGATTTGGTTCTCCCATCTTTTTT
1 TCTAGATTTGGTTCTCCCATCTTTCTT
5184180 TCTA
1 TCTA
5184184 AAAATCCCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 2 0.07
27 22 0.79
28 4 0.14
ACGTcount: A:0.12, C:0.24, G:0.10, T:0.53
Consensus pattern (27 bp):
TCTAGATTTGGTTCTCCCATCTTTCTT
Found at i:5184992 original size:11 final size:11
Alignment explanation
Indices: 5184957--5184986 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
5184947 AAAATAATAA
*
5184957 AAAATTAAACC
1 AAAATTAAACT
5184968 AAAATTAAACT
1 AAAATTAAACT
5184979 AAAATTAA
1 AAAATTAA
5184987 CATAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAATTAAACT
Found at i:5185579 original size:3 final size:3
Alignment explanation
Indices: 5185571--5185611 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
5185561 AAATCTACCA
5185571 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5185612 CAATTTGTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5187654 original size:20 final size:20
Alignment explanation
Indices: 5187629--5187682 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 20
5187619 TTATTATTAA
5187629 AATTATTAATATTTAAAAAT
1 AATTATTAATATTTAAAAAT
5187649 AATTA-T-AT-TTTAAAAAT
1 AATTATTAATATTTAAAAAT
5187666 AA-TATTTAATA-TTAAAA
1 AATTA-TTAATATTTAAAA
5187683 TATTATGTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
16 2 0.07
17 11 0.37
18 3 0.10
19 9 0.30
20 5 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AATTATTAATATTTAAAAAT
Found at i:5187693 original size:19 final size:17
Alignment explanation
Indices: 5187661--5187700 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
5187651 TTATATTTTA
5187661 AAAATAATATTTAATATT
1 AAAATAATATTTAATA-T
*
5187679 AAAATATTATGTTAATAT
1 AAAATAATAT-TTAATAT
5187697 AAAA
1 AAAA
5187701 AGTACTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (17 bp):
AAAATAATATTTAATAT
Found at i:5187701 original size:19 final size:18
Alignment explanation
Indices: 5187659--5187701 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
5187649 AATTATATTT
5187659 TAAAAATAATATTTAATA
1 TAAAAATAATATTTAATA
* *
5187677 TTAAAATATTATGTTAATA
1 TAAAAATAATAT-TTAATA
5187696 TAAAAA
1 TAAAAA
5187702 GTACTTAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
TAAAAATAATATTTAATA
Found at i:5187744 original size:23 final size:23
Alignment explanation
Indices: 5187732--5187959 Score: 123
Period size: 23 Copynumber: 9.7 Consensus size: 23
5187722 TATTATTCTT
5187732 TATATTATTTATTAATATATTAA
1 TATATTATTTATTAATATATTAA
*
5187755 TATATTATTTATTCATAATATT-A
1 TATATTATTTATTAAT-ATATTAA
* * *
5187778 TAT-TTATTAATAAATA-ATATAC
1 TATATTATTTATTAATATAT-TAA
* * *
5187800 TATAATATATATTAGTATATT-A
1 TATATTATTTATTAATATATTAA
* *
5187822 TTTATTAATATATTATTATAATATTAA
1 TATATT-ATTTATTA--AT-ATATTAA
* *
5187849 TTAGTATAATATTTATTAATATAATAT
1 -TA-TAT--TATTTATTAATATATTAA
* *
5187876 TAT-TTATTAATTAAT-TAATAGTA
1 TATATTATTTATTAATATATTA--A
*
5187899 TATATT-TATTAATAATATATTAA
1 TATATTAT-TTATTAATATATTAA
* *
5187922 TATATTATTTATTAATAAAATT-T
1 TATATTATTTATTAAT-ATATTAA
5187945 TAT-TTATTTATTAAT
1 TATATTATTTATTAAT
5187960 TTAATATTAT
Statistics
Matches: 158, Mismatches: 26, Indels: 43
0.70 0.11 0.19
Matches are distributed among these distances:
20 2 0.01
21 7 0.04
22 38 0.24
23 57 0.36
24 21 0.13
25 6 0.04
26 7 0.04
27 6 0.04
28 3 0.02
29 3 0.02
30 7 0.04
31 1 0.01
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (23 bp):
TATATTATTTATTAATATATTAA
Found at i:5187750 original size:15 final size:15
Alignment explanation
Indices: 5187749--5187938 Score: 101
Period size: 15 Copynumber: 13.5 Consensus size: 15
5187739 TTTATTAATA
5187749 TATTAATATATTATT
1 TATTAATATATTATT
*
5187764 TATTCATAATATTATATT
1 TATTAAT-ATA-T-TATT
* *
5187782 TATTAATA-AATA-A
1 TATTAATATATTATT
* * *
5187795 TA-TACTATAATATA
1 TATTAATATATTATT
*
5187809 TATTAGTATATTATT
1 TATTAATATATTATT
5187824 TATTAATATATTA-T
1 TATTAATATATTATT
5187838 TA-T-A-ATATTA--
1 TATTAATATATTATT
* *
5187848 -ATTAGTATAATATT
1 TATTAATATATTATT
*
5187862 TATTAATATAATA-T
1 TATTAATATATTATT
*
5187876 TATT--TAT-TAATT
1 TATTAATATATTATT
*
5187888 AATTAATAGTATATATT
1 TATTAATA-TAT-TATT
5187905 TATTAATA-A-TA--
1 TATTAATATATTATT
5187916 TATTAATATATTATT
1 TATTAATATATTATT
5187931 TATTAATA
1 TATTAATA
5187939 AAATTTTATT
Statistics
Matches: 136, Mismatches: 17, Indels: 44
0.69 0.09 0.22
Matches are distributed among these distances:
9 1 0.01
10 1 0.01
11 15 0.11
12 18 0.13
13 11 0.08
14 15 0.11
15 48 0.35
16 5 0.04
17 12 0.09
18 10 0.07
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.53
Consensus pattern (15 bp):
TATTAATATATTATT
Found at i:5187775 original size:18 final size:18
Alignment explanation
Indices: 5187737--5187916 Score: 85
Period size: 18 Copynumber: 9.9 Consensus size: 18
5187727 TTCTTTATAT
5187737 TATTTATTAATATATTAATATA
1 TATTTATTAATA-A-T-AT-TA
*
5187759 TTATTTATTCATAATATTA
1 -TATTTATTAATAATATTA
*
5187778 TATTTATTAATAA-ATAA
1 TATTTATTAATAATATTA
*
5187795 TATACTA-TAATATATATTA
1 TAT-TTATTAATA-ATATTA
* *
5187814 GTATATTATT--TATTAATA
1 -TAT-TTATTAATAATATTA
5187832 TA-TTATT-ATAATATTA
1 TATTTATTAATAATATTA
*
5187848 -A-TTAGT-ATAATATT-
1 TATTTATTAATAATATTA
* *
5187862 TATTAATATAATATTATT-
1 TATTTAT-TAATAATATTA
*
5187880 TATTAATTAATTAATAGTATA
1 TATTTATTAA-TAATA-T-TA
5187901 TATTTATTAATAATAT
1 TATTTATTAATAATAT
5187917 ATTAATATAT
Statistics
Matches: 127, Mismatches: 16, Indels: 32
0.73 0.09 0.18
Matches are distributed among these distances:
15 19 0.15
16 8 0.06
17 17 0.13
18 37 0.29
19 9 0.07
20 14 0.11
21 11 0.09
22 1 0.01
23 11 0.09
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (18 bp):
TATTTATTAATAATATTA
Found at i:5187842 original size:38 final size:37
Alignment explanation
Indices: 5187749--5187938 Score: 139
Period size: 38 Copynumber: 5.2 Consensus size: 37
5187739 TTTATTAATA
* *
5187749 TATTAATATATTATTTATTCATAATATTA-TAT-TTATT
1 TATTAATATATTA-TTA-TAATATTATTAGTATATTATT
* * *
5187786 AATAAATA-ATATACTATAATATATATTAGTATATTATT
1 TATTAATATAT-TATTATAATAT-TATTAGTATATTATT
*
5187824 TATTAATATATTATTATAATATTAATTAGTATAATATT
1 TATTAATATATTATTATAATATT-ATTAGTATATTATT
* * * *
5187862 TATTAATATAATATTAT-TTATTA--ATTA-ATTA-A
1 TATTAATATATTATTATAATATTATTAGTATATTATT
* *
5187894 TAGT-ATATATTTATTAATAATA-TATTAATATATTATT
1 TATTAATATA-TTATT-ATAATATTATTAGTATATTATT
5187931 TATTAATA
1 TATTAATA
5187939 AAATTTTATT
Statistics
Matches: 119, Mismatches: 20, Indels: 27
0.72 0.12 0.16
Matches are distributed among these distances:
31 5 0.04
32 7 0.06
33 7 0.06
34 5 0.04
35 7 0.06
36 14 0.12
37 19 0.16
38 53 0.45
39 2 0.02
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.53
Consensus pattern (37 bp):
TATTAATATATTATTATAATATTATTAGTATATTATT
Found at i:5187914 original size:56 final size:51
Alignment explanation
Indices: 5187806--5187937 Score: 144
Period size: 56 Copynumber: 2.5 Consensus size: 51
5187796 ATACTATAAT
* *
5187806 ATATATTAGTATATTATTTATTAA-TATATTATTATAATATTAATTAGTATA
1 ATATATTAATATATTATTTATTAATTATATTAATATAATATTAATTAG-ATA
*
5187857 ATATTTATTAATATAATATTATTTATTAATTA-ATTAATAGTATATATTTATTA-ATA
1 ATA--TATT-A-AT-ATATTATTTATTAATTATATTAATA-TA-ATATTAATTAGATA
5187913 ATATATTAATATATTATTTATTAAT
1 ATATATTAATATATTATTTATTAAT
5187938 AAAATTTTAT
Statistics
Matches: 70, Mismatches: 3, Indels: 16
0.79 0.03 0.18
Matches are distributed among these distances:
51 18 0.26
52 2 0.03
53 5 0.07
54 5 0.07
55 1 0.01
56 26 0.37
57 4 0.06
58 9 0.13
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (51 bp):
ATATATTAATATATTATTTATTAATTATATTAATATAATATTAATTAGATA
Found at i:5187939 original size:26 final size:25
Alignment explanation
Indices: 5187802--5187968 Score: 139
Period size: 26 Copynumber: 6.5 Consensus size: 25
5187792 TAATATACTA
*
5187802 TAATATATATTAGTATATTATTTAT
1 TAATATATATTAATATATTATTTAT
*
5187827 TAATATATTATT-ATAATATTAATTAGT
1 TAATATA-TATTAAT-ATATTATTTA-T
*
5187854 ATAATATTTATTAATATAATATTATTTAT
1 -TAATATATATT-A-AT-ATATTATTTAT
5187883 TAAT-TA-ATTAATAGTATATATTTAT
1 TAATATATATTAATA-TAT-TATTTAT
5187908 TAATAATATATTAATATATTATTTAT
1 TAAT-ATATATTAATATATTATTTAT
* *
5187934 TAATA-AAATT-TTAT-TTATTTAT
1 TAATATATATTAATATATTATTTAT
*
5187956 TAATTTAATATTA
1 TAATAT-ATATTA
5187969 TTTATAGGTA
Statistics
Matches: 118, Mismatches: 9, Indels: 30
0.75 0.06 0.19
Matches are distributed among these distances:
22 12 0.10
23 4 0.03
24 13 0.11
25 21 0.18
26 27 0.23
27 11 0.09
28 17 0.14
29 1 0.01
30 12 0.10
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (25 bp):
TAATATATATTAATATATTATTTAT
Found at i:5187948 original size:69 final size:70
Alignment explanation
Indices: 5187829--5187965 Score: 190
Period size: 69 Copynumber: 2.0 Consensus size: 70
5187819 TTATTTATTA
* *
5187829 ATATATTATTATAATATTAATTAGTATAATATTTATTAATATAATATTATTTATTAATTAA-TTA
1 ATATATTATTATAATATTAATTAATATAATATTTATTAATAAAATATTATTTATTAATTAATTTA
5187893 ATAGT
66 ATAGT
* * *
5187898 ATATATTTATTAATAATA-T-ATTAATATATTATTTATTAATAAAATTTTATTTATTTATTAATT
1 ATATA-TTATT-ATAATATTAATTAATATAATATTTATTAATAAAATATTATTTATTAATTAATT
5187961 TAATA
64 TAATA
5187966 TTATTTATAG
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
69 42 0.70
70 12 0.20
71 6 0.10
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (70 bp):
ATATATTATTATAATATTAATTAATATAATATTTATTAATAAAATATTATTTATTAATTAATTTA
ATAGT
Found at i:5187968 original size:48 final size:50
Alignment explanation
Indices: 5187802--5187959 Score: 137
Period size: 56 Copynumber: 3.1 Consensus size: 50
5187792 TAATATACTA
* * * *
5187802 TAAT-ATATATTAGTATATTATTTATTAA-T-ATATTATTATAATATTAAT
1 TAATAATATATTAATATATTATTTATTAATTAATAATAGTAT-ATATTTAT
5187850 TAGTATAATATTTATTAATATAATATTATTTATTAATTAATTAATAGTATATATTTAT
1 TA--ATAATA--TATT-A-AT-ATATTATTTATTAATTAA-TAATAGTATATATTTAT
** *
5187908 TAATAATATATTAATATATTATTTATTAA-TAA-AATTTTATTTATTTAT
1 TAATAATATATTAATATATTATTTATTAATTAATAATAGTATATATTTAT
5187956 TAAT
1 TAAT
5187960 TTAATATTAT
Statistics
Matches: 92, Mismatches: 7, Indels: 22
0.76 0.06 0.18
Matches are distributed among these distances:
48 19 0.21
50 5 0.05
51 17 0.18
52 2 0.02
53 5 0.05
54 5 0.05
55 1 0.01
56 20 0.22
57 1 0.01
58 10 0.11
59 7 0.08
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (50 bp):
TAATAATATATTAATATATTATTTATTAATTAATAATAGTATATATTTAT
Found at i:5188520 original size:26 final size:26
Alignment explanation
Indices: 5188484--5188535 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
5188474 AATGGGCGAA
5188484 CACCACCAATGAGAATAACTTTAGAT
1 CACCACCAATGAGAATAACTTTAGAT
5188510 CACCACCAATGAGAATAACTTTAGAT
1 CACCACCAATGAGAATAACTTTAGAT
5188536 TCAACCTCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.23, G:0.12, T:0.23
Consensus pattern (26 bp):
CACCACCAATGAGAATAACTTTAGAT
Found at i:5189116 original size:8 final size:8
Alignment explanation
Indices: 5189105--5189142 Score: 60
Period size: 8 Copynumber: 4.8 Consensus size: 8
5189095 TTTCTCTTCT
5189105 TTTTTTCA
1 TTTTTTCA
5189113 TTTTTTCA
1 TTTTTTCA
5189121 TTTTTTCA
1 TTTTTTCA
5189129 TTTTCTT-A
1 TTTT-TTCA
5189137 TTTTTT
1 TTTTTT
5189143 TTACTTTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 2 0.07
8 25 0.86
9 2 0.07
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTTCA
Found at i:5189125 original size:35 final size:33
Alignment explanation
Indices: 5189086--5189183 Score: 85
Period size: 33 Copynumber: 2.9 Consensus size: 33
5189076 TCATATCATT
*
5189086 TTTTTTTCTTTTCTCTTCTTTTTTTCATTTTTTCA
1 TTTTTTTC-TTTCTCTTCTTTTTTTCACTTTTT-A
* * *
5189121 -TTTTTTCATTT-TCTTATTTTTTTTACTTTTTG
1 TTTTTTTC-TTTCTCTTCTTTTTTTCACTTTTTA
*
5189153 TTTTTCATTCTTTCACTTCTTTTTTTC-CTTT
1 TTTTT--TTCTTTCTCTTCTTTTTTTCACTTT
5189184 CTTTTGAAGG
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
33 21 0.41
34 17 0.33
35 13 0.25
ACGTcount: A:0.07, C:0.16, G:0.01, T:0.76
Consensus pattern (33 bp):
TTTTTTTCTTTCTCTTCTTTTTTTCACTTTTTA
Found at i:5189178 original size:22 final size:22
Alignment explanation
Indices: 5189145--5189187 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
5189135 TATTTTTTTT
*
5189145 ACTTTTTGTTTTTCATTCTTTC
1 ACTTTTTGTTTTCCATTCTTTC
*
5189167 ACTTCTTT-TTTTCCTTTCTTT
1 ACTT-TTTGTTTTCCATTCTTT
5189188 TGAAGGGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.07, C:0.21, G:0.02, T:0.70
Consensus pattern (22 bp):
ACTTTTTGTTTTCCATTCTTTC
Found at i:5189634 original size:21 final size:21
Alignment explanation
Indices: 5189608--5189661 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
5189598 TTTTCTTTTG
5189608 TTTTTTTTCTTTCCTTTTAT-T
1 TTTTTTTTCTTTCCTTTT-TCT
* *
5189629 TTTTTTCTCTTTTCTTTTTCT
1 TTTTTTTTCTTTCCTTTTTCT
5189650 TTTTTTTT-TTTC
1 TTTTTTTTCTTTC
5189662 GACATGCCCC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 4 0.14
21 24 0.86
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (21 bp):
TTTTTTTTCTTTCCTTTTTCT
Found at i:5189641 original size:26 final size:26
Alignment explanation
Indices: 5189612--5189661 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
5189602 CTTTTGTTTT
5189612 TTTTC-TTTCCTTTTATTTTTTTTCTC
1 TTTTCTTTTCCTTTT-TTTTTTTTCTC
*
5189638 TTTTCTTTTTCTTTTTTTTTTTTC
1 TTTTCTTTTCCTTTTTTTTTTTTC
5189662 GACATGCCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (26 bp):
TTTTCTTTTCCTTTTTTTTTTTTCTC
Found at i:5194396 original size:27 final size:26
Alignment explanation
Indices: 5194366--5194418 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
5194356 TATCTTTGGT
5194366 TTTAAGTAAAAATGT-TTTTATTTAAGA
1 TTTAA-TAAAAAT-TCTTTTATTTAAGA
* *
5194393 TTTAATAATAATTCTTTTTTTTAAGA
1 TTTAATAAAAATTCTTTTATTTAAGA
5194419 AAGAAAATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 1 0.04
26 17 0.74
27 5 0.22
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.53
Consensus pattern (26 bp):
TTTAATAAAAATTCTTTTATTTAAGA
Found at i:5195177 original size:20 final size:20
Alignment explanation
Indices: 5195154--5195192 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5195144 AGTTTTTCTT
*
5195154 AGGGTTTAGGGATTCACAAA
1 AGGGTTTAAGGATTCACAAA
*
5195174 AGGGTTTAAGGTTTCACAA
1 AGGGTTTAAGGATTCACAA
5195193 TTTTACCTAG
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:0.33, C:0.10, G:0.28, T:0.28
Consensus pattern (20 bp):
AGGGTTTAAGGATTCACAAA
Found at i:5195757 original size:11 final size:12
Alignment explanation
Indices: 5195738--5195770 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
5195728 ACTTAAGTTT
5195738 TTATTTATTTTA
1 TTATTTATTTTA
5195750 TT-TTTA-TTTA
1 TTATTTATTTTA
5195760 TTATTTATTTT
1 TTATTTATTTT
5195771 GTTTAATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 6 0.32
11 8 0.42
12 5 0.26
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (12 bp):
TTATTTATTTTA
Found at i:5197470 original size:17 final size:17
Alignment explanation
Indices: 5197439--5197541 Score: 57
Period size: 17 Copynumber: 5.9 Consensus size: 17
5197429 TGGTCAAAGC
*
5197439 TTTTTATTTAT-TTTAA
1 TTTTTATTTTTATTTAA
5197455 TTTTTATTTTTATTTATA
1 TTTTTATTTTTATTTA-A
* * *
5197473 TATATATTTTAATATTTTA
1 TTTTTATTTT--TATTTAA
* * *
5197492 TTTATATGTATT-TTGAA
1 TTTTTAT-TTTTATTTAA
* **
5197509 TTTTTATCTTTTATATGT
1 TTTTTAT-TTTTATTTAA
5197527 TTTTTATTTTTATTT
1 TTTTTATTTTTATTT
5197542 TTCAATAACG
Statistics
Matches: 65, Mismatches: 16, Indels: 11
0.71 0.17 0.12
Matches are distributed among these distances:
16 10 0.15
17 23 0.35
18 18 0.28
19 7 0.11
20 7 0.11
ACGTcount: A:0.24, C:0.01, G:0.03, T:0.72
Consensus pattern (17 bp):
TTTTTATTTTTATTTAA
Found at i:5197505 original size:47 final size:47
Alignment explanation
Indices: 5197439--5197541 Score: 113
Period size: 47 Copynumber: 2.2 Consensus size: 47
5197429 TGGTCAAAGC
* *
5197439 TTTTTATTTATTTTAATTTT-TATTTTTAT-TTATATATATATTTTAA
1 TTTTTATTTATTGTAATTTTGAATTTTTATCTTATATATAT-TTTTAA
* * *
5197485 TATTTTATTTATATGT-ATTTTGAATTTTTATCTTTTATATGTTTTTTA
1 T-TTTTATTTAT-TGTAATTTTGAATTTTTATCTTATATATATTTTTAA
5197533 TTTTTATTT
1 TTTTTATTT
5197542 TTCAATAACG
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
46 1 0.02
47 23 0.48
48 16 0.33
49 8 0.17
ACGTcount: A:0.24, C:0.01, G:0.03, T:0.72
Consensus pattern (47 bp):
TTTTTATTTATTGTAATTTTGAATTTTTATCTTATATATATTTTTAA
Found at i:5197535 original size:24 final size:24
Alignment explanation
Indices: 5197454--5197543 Score: 96
Period size: 23 Copynumber: 3.8 Consensus size: 24
5197444 ATTTATTTTA
* * *
5197454 ATTTTTATTTTTATTTATATATAT
1 ATTTTAATTTTTATTTTTATATGT
5197478 ATTTTAATATTTTA--TTTATATGT
1 ATTTTAAT-TTTTATTTTTATATGT
5197501 ATTTTGAATTTTTATCTTTTATATGT
1 ATTTT-AATTTTTAT-TTTTATATGT
*
5197527 -TTTTTATTTTTATTTTT
1 ATTTTAATTTTTATTTTT
5197544 CAATAACGGA
Statistics
Matches: 57, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
23 21 0.37
24 18 0.32
25 9 0.16
26 9 0.16
ACGTcount: A:0.24, C:0.01, G:0.03, T:0.71
Consensus pattern (24 bp):
ATTTTAATTTTTATTTTTATATGT
Found at i:5197542 original size:5 final size:6
Alignment explanation
Indices: 5197445--5197543 Score: 60
Period size: 6 Copynumber: 16.5 Consensus size: 6
5197435 AAGCTTTTTA
* * * * *
5197445 TTTATT TTAATT TTTATT TTTATT TATATA TATATT TTAATAT TTTA--
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTAT-T TTTATT
* * * * *
5197492 TTTATA TGTATT TTGAATT TTTATCT TTTATA TGT-TT TTTATT TTTATT
1 TTTATT TTTATT TT-TATT TTTAT-T TTTATT TTTATT TTTATT TTTATT
5197541 TTT
1 TTT
5197544 CAATAACGGA
Statistics
Matches: 70, Mismatches: 17, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
4 4 0.06
5 3 0.04
6 48 0.69
7 15 0.21
ACGTcount: A:0.24, C:0.01, G:0.03, T:0.72
Consensus pattern (6 bp):
TTTATT
Found at i:5197782 original size:41 final size:41
Alignment explanation
Indices: 5197735--5197813 Score: 131
Period size: 41 Copynumber: 1.9 Consensus size: 41
5197725 AAAAACAAAT
5197735 TTAAATTAAAAAAATAAAATATCTCAGATAAAATTAAGAAC
1 TTAAATTAAAAAAATAAAATATCTCAGATAAAATTAAGAAC
* * *
5197776 TTAAATTAAAAAAGTAAAATATCTCGGATAAAGTTAAG
1 TTAAATTAAAAAAATAAAATATCTCAGATAAAATTAAG
5197814 TGTCTATACT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.57, C:0.06, G:0.09, T:0.28
Consensus pattern (41 bp):
TTAAATTAAAAAAATAAAATATCTCAGATAAAATTAAGAAC
Found at i:5203344 original size:7 final size:7
Alignment explanation
Indices: 5203303--5203343 Score: 73
Period size: 7 Copynumber: 5.9 Consensus size: 7
5203293 TATAAAATCA
5203303 AAAATTC
1 AAAATTC
5203310 AAAATTC
1 AAAATTC
5203317 AAAATTC
1 AAAATTC
5203324 AAAATTC
1 AAAATTC
*
5203331 AAAATTT
1 AAAATTC
5203338 AAAATT
1 AAAATT
5203344 TTTAAAAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.32
Consensus pattern (7 bp):
AAAATTC
Found at i:5205642 original size:33 final size:33
Alignment explanation
Indices: 5205605--5205694 Score: 126
Period size: 33 Copynumber: 2.7 Consensus size: 33
5205595 GTAGATTTTT
* * *
5205605 GAAACCTTAAAATGAAACCTTAGATGAAAACTC
1 GAAACCTTAAAATGAAACCCTAAATAAAAACTC
*
5205638 GAAACCTTAAAATGAAACCCTAAATAAAAACTT
1 GAAACCTTAAAATGAAACCCTAAATAAAAACTC
* *
5205671 GAAACCCTAAAATTAAACCCTAAA
1 GAAACCTTAAAATGAAACCCTAAA
5205695 ATGTAAACCC
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.52, C:0.20, G:0.08, T:0.20
Consensus pattern (33 bp):
GAAACCTTAAAATGAAACCCTAAATAAAAACTC
Found at i:5205690 original size:13 final size:14
Alignment explanation
Indices: 5205672--5205709 Score: 69
Period size: 13 Copynumber: 2.8 Consensus size: 14
5205662 TAAAAACTTG
5205672 AAACCCTAAAAT-T
1 AAACCCTAAAATGT
5205685 AAACCCTAAAATGT
1 AAACCCTAAAATGT
5205699 AAACCCTAAAA
1 AAACCCTAAAA
5205710 CAAAACCTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.55, C:0.24, G:0.03, T:0.18
Consensus pattern (14 bp):
AAACCCTAAAATGT
Found at i:5205715 original size:13 final size:13
Alignment explanation
Indices: 5205672--5205716 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
5205662 TAAAAACTTG
*
5205672 AAACCCTAAAATT
1 AAACCCTAAAACT
*
5205685 AAACCCTAAAATGT
1 AAACCCTAAAA-CT
*
5205699 AAACCCTAAAACA
1 AAACCCTAAAACT
5205712 AAACC
1 AAACC
5205717 TTATGTGAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 16 0.57
14 12 0.43
ACGTcount: A:0.56, C:0.27, G:0.02, T:0.16
Consensus pattern (13 bp):
AAACCCTAAAACT
Found at i:5205741 original size:27 final size:29
Alignment explanation
Indices: 5205711--5205767 Score: 84
Period size: 27 Copynumber: 2.0 Consensus size: 29
5205701 ACCCTAAAAC
5205711 AAAACCTTATGTG-AGAACC-T-AAACCCT
1 AAAACCTTATGTGCA-AACCTTAAAACCCT
5205738 AAAACCTTATGTGCAAACCTTAAAACCCT
1 AAAACCTTATGTGCAAACCTTAAAACCCT
5205767 A
1 A
5205768 TGTGTAACCC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 17 0.63
28 2 0.07
29 8 0.30
ACGTcount: A:0.42, C:0.26, G:0.09, T:0.23
Consensus pattern (29 bp):
AAAACCTTATGTGCAAACCTTAAAACCCT
Found at i:5205755 original size:21 final size:21
Alignment explanation
Indices: 5205731--5205824 Score: 74
Period size: 19 Copynumber: 4.8 Consensus size: 21
5205721 GTGAGAACCT
*
5205731 AAACCCTAAAACCTTATGTGC
1 AAACCCTAAAACCCTATGTGC
* *
5205752 AAACCTTAAAACCCTATGTGT
1 AAACCCTAAAACCCTATGTGC
* * * *
5205773 AACCCCT--AATCCTAGGT-A
1 AAACCCTAAAACCCTATGTGC
5205791 AAACCCT-AAACCCTATGTG-
1 AAACCCTAAAACCCTATGTGC
*
5205810 AAATCCT-AAACCCTA
1 AAACCCTAAAACCCTA
5205825 AGTAAAACCT
Statistics
Matches: 59, Mismatches: 12, Indels: 6
0.77 0.16 0.08
Matches are distributed among these distances:
18 6 0.10
19 30 0.51
21 23 0.39
ACGTcount: A:0.38, C:0.30, G:0.09, T:0.23
Consensus pattern (21 bp):
AAACCCTAAAACCCTATGTGC
Found at i:5205805 original size:19 final size:19
Alignment explanation
Indices: 5205783--5205858 Score: 71
Period size: 19 Copynumber: 3.9 Consensus size: 19
5205773 AACCCCTAAT
5205783 CCTAGGTAAAACCCTAAAC
1 CCTAGGTAAAACCCTAAAC
* * *
5205802 CCTATGTGAAATCCTAAAC
1 CCTAGGTAAAACCCTAAAC
* *
5205821 CCTAAGTAAAACCTCGAAAC
1 CCTAGGTAAAACC-CTAAAC
* * *
5205841 CATAGTTCAAACCCTAAA
1 CCTAGGTAAAACCCTAAA
5205859 TGAAAATCTA
Statistics
Matches: 44, Mismatches: 12, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
19 30 0.68
20 14 0.32
ACGTcount: A:0.42, C:0.29, G:0.09, T:0.20
Consensus pattern (19 bp):
CCTAGGTAAAACCCTAAAC
Found at i:5205830 original size:38 final size:38
Alignment explanation
Indices: 5205760--5205833 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
5205750 GCAAACCTTA
* * *
5205760 AAACCCTATGTGTAACCCCTAATCCTAGGTAAAACCCT
1 AAACCCTATGTGTAAACCCTAACCCTAAGTAAAACCCT
*
5205798 AAACCCTATGTG-AAATCCTAAACCCTAAGTAAAACC
1 AAACCCTATGTGTAAACCCT-AACCCTAAGTAAAACC
5205834 TCGAAACCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 5 0.16
38 26 0.84
ACGTcount: A:0.39, C:0.30, G:0.09, T:0.22
Consensus pattern (38 bp):
AAACCCTATGTGTAAACCCTAACCCTAAGTAAAACCCT
Found at i:5205942 original size:16 final size:16
Alignment explanation
Indices: 5205921--5205964 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
5205911 TATTAAAAAT
*
5205921 AATAATTAAAAAATAA
1 AATAATAAAAAAATAA
5205937 AATAATAAAAAAATAA
1 AATAATAAAAAAATAA
*
5205953 AA-AACAAAAAAA
1 AATAATAAAAAAA
5205965 AGGTGGTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 9 0.35
16 17 0.65
ACGTcount: A:0.82, C:0.02, G:0.00, T:0.16
Consensus pattern (16 bp):
AATAATAAAAAAATAA
Found at i:5205955 original size:8 final size:8
Alignment explanation
Indices: 5205928--5205965 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
5205918 AATAATAATT
5205928 AAAAAATA
1 AAAAAATA
*
5205936 AAATAATA
1 AAAAAATA
5205944 AAAAAATA
1 AAAAAATA
5205952 AAAAACA-A
1 AAAAA-ATA
5205960 AAAAAA
1 AAAAAA
5205966 GGTGGTTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
7 1 0.04
8 25 0.93
9 1 0.04
ACGTcount: A:0.87, C:0.03, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAAAATA
Found at i:5206653 original size:5 final size:5
Alignment explanation
Indices: 5206643--5206693 Score: 54
Period size: 5 Copynumber: 10.2 Consensus size: 5
5206633 ATTTGGTATT
5206643 TTTTA TTTTA TTTTA TTTTA -TTTA -TTTA -TTTA GTTATTA TATTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TT-TTA T-TTTA
5206688 TTTTA T
1 TTTTA T
5206694 AAGTATTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
4 12 0.29
5 20 0.48
6 6 0.14
7 4 0.10
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:5206668 original size:4 final size:4
Alignment explanation
Indices: 5206639--5206690 Score: 52
Period size: 4 Copynumber: 12.2 Consensus size: 4
5206629 AGCCATTTGG
*
5206639 TATT T-TT TATTT TATTT TATTT TATT TATT TATT TAGT TATT ATATT
1 TATT TATT TA-TT TA-TT TA-TT TATT TATT TATT TATT TATT -TATT
5206686 TATT T
1 TATT T
5206691 TATAAGTATT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
3 3 0.07
4 22 0.51
5 18 0.42
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (4 bp):
TATT
Found at i:5206668 original size:9 final size:9
Alignment explanation
Indices: 5206643--5206693 Score: 52
Period size: 9 Copynumber: 5.7 Consensus size: 9
5206633 ATTTGGTATT
5206643 TTTTATTTTA
1 TTTTA-TTTA
5206653 TTTTATTT-
1 TTTTATTTA
5206661 TATTTATTTA
1 T-TTTATTTA
*
5206671 -TTTAGTTA
1 TTTTATTTA
*
5206679 TTATATTTA
1 TTTTATTTA
5206688 TTTTAT
1 TTTTAT
5206694 AAGTATTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
8 8 0.24
9 21 0.62
10 5 0.15
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.75
Consensus pattern (9 bp):
TTTTATTTA
Found at i:5206668 original size:26 final size:30
Alignment explanation
Indices: 5206639--5206693 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
5206629 AGCCATTTGG
5206639 TATTT-TTTA-TT-TTAT-TTTATTTTATT
1 TATTTATTTAGTTATTATATTTATTTTATT
5206665 TATTTATTTAGTTATTATATTTATTTTAT
1 TATTTATTTAGTTATTATATTTATTTTAT
5206694 AAGTATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 5 0.20
27 4 0.16
28 2 0.08
29 4 0.16
30 10 0.40
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.75
Consensus pattern (30 bp):
TATTTATTTAGTTATTATATTTATTTTATT
Found at i:5220578 original size:11 final size:11
Alignment explanation
Indices: 5220564--5220597 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
5220554 TTTTTGTTCC
5220564 ATTTTAAGTTT
1 ATTTTAAGTTT
5220575 ATTTTAAGTTT
1 ATTTTAAGTTT
*
5220586 GTTTTAATGTTT
1 ATTTTAA-GTTT
5220598 CCTTGCATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.65
Consensus pattern (11 bp):
ATTTTAAGTTT
Found at i:5221412 original size:20 final size:20
Alignment explanation
Indices: 5221374--5221412 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5221364 GGGTAATTTG
* * *
5221374 CAATTTTATTTCTTTTTGTT
1 CAATTTAATTTCATATTGTT
5221394 CAATTTAATTTCATATTGT
1 CAATTTAATTTCATATTGT
5221413 GCATGATTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.10, G:0.05, T:0.62
Consensus pattern (20 bp):
CAATTTAATTTCATATTGTT
Found at i:5222137 original size:15 final size:17
Alignment explanation
Indices: 5222112--5222147 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
5222102 GGATTTTTAT
5222112 AAATTCAATTTTTTG-A
1 AAATTCAATTTTTTGTA
5222128 AAATTC-ATTTTTTGTA
1 AAATTCAATTTTTTGTA
5222144 AAAT
1 AAAT
5222148 CCTTCAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.50
Consensus pattern (17 bp):
AAATTCAATTTTTTGTA
Found at i:5222243 original size:70 final size:67
Alignment explanation
Indices: 5222169--5222297 Score: 170
Period size: 67 Copynumber: 1.9 Consensus size: 67
5222159 TTGATAGGAT
5222169 TTTTATGAAATTAATTTTTAAAAAATTTTTATTTATAAACTT-ATATAATTCTATAATATTTTTG
1 TTTTATGAAATTAATTTTTAAAAAA---TTATTTATAAA-TTCATATAATTCTATAATATTTTTG
5222233 TAAGAA
62 TAAGAA
* * * * *
5222239 TTTTATGAAGTTAATTTTTCAAAAATTATTTTTAAATTCGTATAATTCTTTAATATTTT
1 TTTTATGAAATTAATTTTTAAAAAATTATTTATAAATTCATATAATTCTATAATATTTT
5222298 GATCAAATTT
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
66 2 0.04
67 28 0.53
70 23 0.43
ACGTcount: A:0.38, C:0.04, G:0.05, T:0.53
Consensus pattern (67 bp):
TTTTATGAAATTAATTTTTAAAAAATTATTTATAAATTCATATAATTCTATAATATTTTTGTAAG
AA
Found at i:5222330 original size:15 final size:15
Alignment explanation
Indices: 5222310--5222339 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5222300 TCAAATTTTA
5222310 TTTTTAAAAAATTAT
1 TTTTTAAAAAATTAT
*
5222325 TTTTTAAAAACTTAT
1 TTTTTAAAAAATTAT
5222340 AAAATCTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTTTAAAAAATTAT
Found at i:5222386 original size:13 final size:13
Alignment explanation
Indices: 5222365--5222398 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
5222355 TGTGGTAAGA
5222365 TTTATAAATTTTAT
1 TTTA-AAATTTTAT
5222379 TTTAAAATTTTAT
1 TTTAAAATTTTAT
5222392 TTTAAAA
1 TTTAAAA
5222399 AAGTTCTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TTTAAAATTTTAT
Found at i:5225319 original size:20 final size:20
Alignment explanation
Indices: 5225294--5225334 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
5225284 TTAGGTTCTT
5225294 AAAAATTG-ATAAGAGGAAAA
1 AAAAATTGCA-AAGAGGAAAA
*
5225314 AAAAATTGCAATGAGGAAAA
1 AAAAATTGCAAAGAGGAAAA
5225334 A
1 A
5225335 CAAAGAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.63, C:0.02, G:0.20, T:0.15
Consensus pattern (20 bp):
AAAAATTGCAAAGAGGAAAA
Found at i:5226792 original size:1 final size:1
Alignment explanation
Indices: 5226788--5226832 Score: 90
Period size: 1 Copynumber: 45.0 Consensus size: 1
5226778 TTTTGCCAAG
5226788 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5226833 CTCTTGTATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:5229157 original size:13 final size:13
Alignment explanation
Indices: 5229139--5229163 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5229129 GGTGTTGCTG
5229139 TTTATTATTATTA
1 TTTATTATTATTA
5229152 TTTATTATTATT
1 TTTATTATTATT
5229164 TCACTCAATA
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTATTATTATTA
Found at i:5231641 original size:17 final size:17
Alignment explanation
Indices: 5231616--5231667 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
5231606 AATGGAAAGT
5231616 TTACTAAAAATAGC-AG
1 TTACTAAAAATAGCAAG
*
5231632 TTATTAAAAATAGCAAG
1 TTACTAAAAATAGCAAG
*
5231649 TTACTAAAAATAGAAAG
1 TTACTAAAAATAGCAAG
5231666 TT
1 TT
5231668 GTAAATCCTA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
16 13 0.41
17 19 0.59
ACGTcount: A:0.52, C:0.08, G:0.12, T:0.29
Consensus pattern (17 bp):
TTACTAAAAATAGCAAG
Done.