Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold72
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: 5928628
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 261288 characters in sequence are not A, C, G, or T
File 38 of 39
Found at i:5648930 original size:14 final size:14
Alignment explanation
Indices: 5648872--5648946 Score: 62
Period size: 15 Copynumber: 5.0 Consensus size: 14
5648862 AACACACAAA
*
5648872 TTTTTTTATCTCTCT
1 TTTTTTT-TCTCTCC
*
5648887 TTTTTTTTCTTCTTC
1 TTTTTTTTC-TCTCC
*
5648902 TTTTCTTTCAT-TCC
1 TTTTTTTTC-TCTCC
5648916 TTTTTTTTCTCTCC
1 TTTTTTTTCTCTCC
5648930 TTTCCTTTCTTCTCTCC
1 TTT--TTT-TTCTCTCC
5648947 CTTCATGAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
13 1 0.02
14 18 0.37
15 19 0.39
16 3 0.06
17 8 0.16
ACGTcount: A:0.03, C:0.28, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTTTTTCTCTCC
Found at i:5649671 original size:15 final size:15
Alignment explanation
Indices: 5649651--5649683 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
5649641 AATAATTATT
5649651 ATTT-AATATAATATA
1 ATTTAAATAT-ATATA
5649666 ATTTAAATATATATA
1 ATTTAAATATATATA
5649681 ATT
1 ATT
5649684 ATTAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTTAAATATATATA
Found at i:5649687 original size:36 final size:35
Alignment explanation
Indices: 5649624--5649711 Score: 99
Period size: 36 Copynumber: 2.5 Consensus size: 35
5649614 TTTTAAATTA
*
5649624 TAAAAAATATTAAA-ATAAATAATTATT-ATTTAAT
1 TAAATAAT-TTAAATATAAATAATTATTAATTTAAT
*
5649658 ATAATATAATTTAAATATATATAATTATTAATTTAAT
1 -TAA-ATAATTTAAATATAAATAATTATTAATTTAAT
*
5649695 TAAATATTTATAAATAT
1 TAAATAATT-TAAATAT
5649712 TAAAAATCTG
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
35 13 0.28
36 26 0.57
37 7 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (35 bp):
TAAATAATTTAAATATAAATAATTATTAATTTAAT
Found at i:5649701 original size:22 final size:20
Alignment explanation
Indices: 5649655--5649701 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
5649645 ATTATTATTT
5649655 AATATAATATAATTTAAATA
1 AATATAATATAATTTAAATA
* *
5649675 TATATAATTATTAATTTAATTA
1 AATATAA-TA-TAATTTAAATA
5649697 AATAT
1 AATAT
5649702 TTATAAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 6 0.27
21 2 0.09
22 14 0.64
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AATATAATATAATTTAAATA
Found at i:5649706 original size:26 final size:27
Alignment explanation
Indices: 5649655--5649714 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 27
5649645 ATTATTATTT
5649655 AATA-TAATATAATTTAAATATATATA
1 AATATTAATATAATTTAAATATATATA
* * *
5649681 ATTATTAATTTAA-TTAAATATTTATA
1 AATATTAATATAATTTAAATATATATA
5649707 AATATTAA
1 AATATTAA
5649715 AAATCTGTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 22 0.76
27 7 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
AATATTAATATAATTTAAATATATATA
Found at i:5649745 original size:3 final size:3
Alignment explanation
Indices: 5649737--5649772 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
5649727 TTTTAATTTT
5649737 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5649773 CTACTATTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5650011 original size:25 final size:25
Alignment explanation
Indices: 5649983--5650042 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 25
5649973 GTTAATTATT
5649983 AAATATTATCA-TTTTTTAAATTTAA
1 AAATATT-TCATTTTTTTAAATTTAA
*
5650008 AAATAATTTTATTTTTTTAAATTTAA
1 AAAT-ATTTCATTTTTTTAAATTTAA
5650034 ATAATATTT
1 A-AATATTT
5650043 TTTTAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
25 6 0.19
26 22 0.71
27 3 0.10
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (25 bp):
AAATATTTCATTTTTTTAAATTTAA
Found at i:5650030 original size:26 final size:27
Alignment explanation
Indices: 5649994--5650044 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
5649984 AATATTATCA
5649994 TTTTTTAAATTTAAA-AATAATTTTAT
1 TTTTTTAAATTTAAATAATAATTTTAT
*
5650020 TTTTTTAAATTTAAATAATATTTTT
1 TTTTTTAAATTTAAATAATAATTTT
5650045 TTAAAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (27 bp):
TTTTTTAAATTTAAATAATAATTTTAT
Found at i:5650043 original size:21 final size:23
Alignment explanation
Indices: 5649994--5650049 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 23
5649984 AATATTATCA
5649994 TTTTTTAAATTTAAAAATAATTTTAT
1 TTTTTTAAATTT-AAAATAA--TTAT
5650020 TTTTTTAAATTT-AAATAA-TAT
1 TTTTTTAAATTTAAAATAATTAT
5650041 TTTTTTAAA
1 TTTTTTAAA
5650050 AAAATTAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
21 12 0.40
24 6 0.20
26 12 0.40
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TTTTTTAAATTTAAAATAATTAT
Found at i:5650058 original size:20 final size:20
Alignment explanation
Indices: 5650003--5650060 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
5649993 ATTTTTTAAA
*
5650003 TTTAAAAATAATT-TTATTTT
1 TTTAAAAA-AATTAATATTTT
*
5650023 TTTAAATTTAAA-TAATATTTT
1 TTTAAA--AAAATTAATATTTT
5650044 TTTAAAAAAATTAATAT
1 TTTAAAAAAATTAATAT
5650061 AAAATATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
19 3 0.10
20 13 0.42
21 14 0.45
22 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTAAAAAAATTAATATTTT
Found at i:5650443 original size:36 final size:36
Alignment explanation
Indices: 5650403--5650471 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 36
5650393 ATATTAATAT
** * *
5650403 ATTATGTTATTTATATTTAAAAATAAATAAATTATC
1 ATTATGTTATAAAAATTTAAAAATAAAGAAATTATC
*
5650439 ATTATTTTATAAAAATTTAAAAATAAAGAAATT
1 ATTATGTTATAAAAATTTAAAAATAAAGAAATT
5650472 GATTTAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.43
Consensus pattern (36 bp):
ATTATGTTATAAAAATTTAAAAATAAAGAAATTATC
Found at i:5650682 original size:24 final size:23
Alignment explanation
Indices: 5650635--5650689 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
5650625 TTATTATCAG
*
5650635 TAAATTTTAAATAATAATAATTAA
1 TAAA-TTTAAATAAAAATAATTAA
* *
5650659 TTAATTTAAATAAAAATATTTTAA
1 TAAATTTAAATAAAAATA-ATTAA
5650683 TAAATTT
1 TAAATTT
5650690 GTTTCAAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 13 0.50
24 13 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TAAATTTAAATAAAAATAATTAA
Found at i:5650963 original size:39 final size:40
Alignment explanation
Indices: 5650888--5650971 Score: 100
Period size: 39 Copynumber: 2.1 Consensus size: 40
5650878 TCTTACAAAC
* *
5650888 ATATTAATATGATTTTTTAAATATAATAAAATAAATTAAA
1 ATATAAATATGATTTTTTAAATATAATAAAACAAATTAAA
** *
5650928 ATATAAATAT-ATTTTTT-AATATCTTACAAACAAATTAAT
1 ATATAAATATGATTTTTTAAATATAATA-AAACAAATTAAA
5650967 ATATA
1 ATATA
5650972 TTTTGTAAGC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
38 7 0.18
39 22 0.58
40 9 0.24
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (40 bp):
ATATAAATATGATTTTTTAAATATAATAAAACAAATTAAA
Found at i:5650971 original size:33 final size:33
Alignment explanation
Indices: 5650868--5650975 Score: 94
Period size: 33 Copynumber: 3.1 Consensus size: 33
5650858 TTATCATAAT
*
5650868 TTTTTTAATATCTTACAAACATATTAATATGAT-
1 TTTTTTAATATCTTACAAACAAATTAATAT-ATA
* ** *
5650901 TTTTTAAATATAATA-AAATAAATTAAAATATAAATATA
1 TTTTTTAATATCTTACAAACAAATT---A-AT--ATATA
5650939 TTTTTTAATATCTTACAAACAAATTAATATATA
1 TTTTTTAATATCTTACAAACAAATTAATATATA
5650972 TTTT
1 TTTT
5650976 GTAAGCAATG
Statistics
Matches: 58, Mismatches: 9, Indels: 16
0.70 0.11 0.19
Matches are distributed among these distances:
32 7 0.12
33 21 0.36
35 3 0.05
36 3 0.05
37 2 0.03
38 14 0.24
39 8 0.14
ACGTcount: A:0.47, C:0.06, G:0.01, T:0.46
Consensus pattern (33 bp):
TTTTTTAATATCTTACAAACAAATTAATATATA
Found at i:5655150 original size:10 final size:10
Alignment explanation
Indices: 5655125--5655158 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
5655115 TATGCGTAAA
5655125 ATTATATTTAT
1 ATTAT-TTTAT
*
5655136 ATTATTTTTT
1 ATTATTTTAT
5655146 ATTATTTTAT
1 ATTATTTTAT
5655156 ATT
1 ATT
5655159 TAATTATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 16 0.76
11 5 0.24
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
ATTATTTTAT
Found at i:5655155 original size:15 final size:15
Alignment explanation
Indices: 5655132--5655227 Score: 72
Period size: 15 Copynumber: 6.4 Consensus size: 15
5655122 AAAATTATAT
* * *
5655132 TTATATTATTTTTTA
1 TTATTTTATATTTAA
5655147 TTATTTTATATTTAA
1 TTATTTTATATTTAA
*
5655162 TTATTTTA-AATT-A
1 TTATTTTATATTTAA
*
5655175 TTTTTTTATATATTAA
1 TTATTTTATAT-TTAA
*
5655191 TTTATTTTATATTTTA
1 -TTATTTTATATTTAA
* *
5655207 TATAATTTAT-TATAA
1 T-TATTTTATATTTAA
5655222 TTATTT
1 TTATTT
5655228 GATTTTGACT
Statistics
Matches: 64, Mismatches: 12, Indels: 11
0.74 0.14 0.13
Matches are distributed among these distances:
13 8 0.12
14 8 0.12
15 27 0.42
16 11 0.17
17 10 0.16
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TTATTTTATATTTAA
Found at i:5655174 original size:25 final size:26
Alignment explanation
Indices: 5655126--5655214 Score: 84
Period size: 25 Copynumber: 3.7 Consensus size: 26
5655116 ATGCGTAAAA
**
5655126 TTATATTTATATTATTTTTTATTATT
1 TTATATTTATATTATTTTAAATTATT
5655152 TTATATTTA-ATTATTTTAAATTA-T
1 TTATATTTATATTATTTTAAATTATT
*
5655176 TT-T-TTTATA-TA--TTAATTTATT
1 TTATATTTATATTATTTTAAATTATT
*
5655197 TTATATTTTATATAATTT
1 TTATA-TTTATATTATTT
5655215 ATTATAATTA
Statistics
Matches: 51, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
20 7 0.14
21 3 0.06
22 7 0.14
23 2 0.04
24 9 0.18
25 13 0.25
26 9 0.18
27 1 0.02
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (26 bp):
TTATATTTATATTATTTTAAATTATT
Found at i:5655225 original size:25 final size:23
Alignment explanation
Indices: 5655124--5655227 Score: 70
Period size: 25 Copynumber: 4.3 Consensus size: 23
5655114 TTATGCGTAA
* *
5655124 AATTATATTTATATTATTT-TTT
1 AATTATTTTTATATAATTTATTT
*
5655146 -ATTATTTTATATTTAA-TTATTTT
1 AATTATTTT-TATATAATTTA-TTT
* *
5655169 AAATTATTTTTTTATATATTAATTT
1 -AATTATTTTTATATA-ATTTATTT
*
5655194 ATTTTATATTTTATATAATTTATTAT
1 A-ATTAT-TTTTATATAATTTATT-T
5655220 AATTATTT
1 AATTATTT
5655228 GATTTTGACT
Statistics
Matches: 62, Mismatches: 10, Indels: 18
0.69 0.11 0.20
Matches are distributed among these distances:
21 9 0.15
22 5 0.08
23 3 0.05
24 7 0.11
25 26 0.42
26 12 0.19
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
AATTATTTTTATATAATTTATTT
Found at i:5656136 original size:16 final size:16
Alignment explanation
Indices: 5656115--5656168 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
5656105 GTTATAAGAA
* *
5656115 TTAAATCATTTTAGAT
1 TTAAATAATTTTAAAT
*
5656131 TTAAATAAATTTAAAT
1 TTAAATAATTTTAAAT
* *
5656147 TTATATTATTTTAAAT
1 TTAAATAATTTTAAAT
5656163 TTAAAT
1 TTAAAT
5656169 TTTATTTTAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (16 bp):
TTAAATAATTTTAAAT
Found at i:5658005 original size:26 final size:26
Alignment explanation
Indices: 5657976--5658025 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
5657966 AATAATCAAT
5657976 TTATATAAATTTATACTAATTTTTTA
1 TTATATAAATTTATACTAATTTTTTA
5658002 TTATATAAATTTATACTAATTTTT
1 TTATATAAATTTATACTAATTTTT
5658026 AAAAAGGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (26 bp):
TTATATAAATTTATACTAATTTTTTA
Found at i:5658036 original size:25 final size:26
Alignment explanation
Indices: 5657982--5658037 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
5657972 CAATTTATAT
* * *
5657982 AAATTTATACTAATTTTTTATTATAT
1 AAATTTATACTAATTTTTTATAAAAG
5658008 AAATTTATACTAA-TTTTTA-AAAAGG
1 AAATTTATACTAATTTTTTATAAAA-G
5658033 AAATT
1 AAATT
5658038 AAGAAGGCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 2 0.08
25 11 0.42
26 13 0.50
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.48
Consensus pattern (26 bp):
AAATTTATACTAATTTTTTATAAAAG
Found at i:5670655 original size:6 final size:6
Alignment explanation
Indices: 5670639--5670668 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
5670629 TCGTTCTTAG
*
5670639 CATAGC TATAGC CATAGC CATAGC CATAGC
1 CATAGC CATAGC CATAGC CATAGC CATAGC
5670669 AGGGGTCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.33, C:0.30, G:0.17, T:0.20
Consensus pattern (6 bp):
CATAGC
Found at i:5675516 original size:33 final size:33
Alignment explanation
Indices: 5675474--5675541 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
5675464 GAACATTACC
5675474 CTTCCCATCTACCTGGGGAGCGGAAGACAGCTG
1 CTTCCCATCTACCTGGGGAGCGGAAGACAGCTG
* *
5675507 CTTCCCATCTACCTGGGGAGTGGAAGCCAGCTG
1 CTTCCCATCTACCTGGGGAGCGGAAGACAGCTG
5675540 CT
1 CT
5675542 GGCTAGCTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.19, C:0.31, G:0.29, T:0.21
Consensus pattern (33 bp):
CTTCCCATCTACCTGGGGAGCGGAAGACAGCTG
Found at i:5678547 original size:15 final size:14
Alignment explanation
Indices: 5678505--5678581 Score: 66
Period size: 15 Copynumber: 5.1 Consensus size: 14
5678495 ATTTTAAGTA
5678505 TAAATTA-TTAATTT
1 TAAATTATTTAA-TT
5678519 TAAATTTAATTTAATT
1 TAAA-TT-ATTTAATT
*
5678535 TAAAATTATTTAAAAT
1 T-AAATTATTT-AATT
*
5678551 TATATTATTTAAATT
1 TAAATTATTT-AATT
5678566 TAAATTATTTTAATT
1 TAAATTA-TTTAATT
5678581 T
1 T
5678582 TGAATTATAA
Statistics
Matches: 53, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
14 4 0.08
15 29 0.55
16 13 0.25
17 7 0.13
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TAAATTATTTAATT
Found at i:5678587 original size:16 final size:16
Alignment explanation
Indices: 5678493--5678589 Score: 69
Period size: 16 Copynumber: 6.2 Consensus size: 16
5678483 TTGCATTTAT
* *
5678493 TTATTTTAAGTATAAA
1 TTATTTTAAATTTAAA
*
5678509 TTA--TTAATTTTAAA
1 TTATTTTAAATTTAAA
*
5678523 TTTAATTT-AATTTAAAA
1 -TTATTTTAAATTT-AAA
* *
5678540 TTA-TTTAAAATTATA
1 TTATTTTAAATTTAAA
5678555 TTA-TTTAAATTTAAA
1 TTATTTTAAATTTAAA
* *
5678570 TTATTTTAATTTTGAA
1 TTATTTTAAATTTAAA
5678586 TTAT
1 TTAT
5678590 AACAAGAATG
Statistics
Matches: 66, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
14 9 0.14
15 24 0.36
16 28 0.42
17 5 0.08
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (16 bp):
TTATTTTAAATTTAAA
Found at i:5678589 original size:31 final size:28
Alignment explanation
Indices: 5678505--5678589 Score: 73
Period size: 31 Copynumber: 2.8 Consensus size: 28
5678495 ATTTTAAGTA
5678505 TAAATTA-TTAATTTTAAATTTAATTTAATT
1 TAAATTATTTAATTTT-AA-TT-ATTTAATT
**
5678535 TAAAATTATTTAAAATTATATTATTTAAATT
1 T-AAATTATTTAATTTTA-ATTATTT-AATT
5678566 TAAATTATTTTAATTTTGAATTAT
1 TAAATTA-TTTAATTTT-AATTAT
5678590 AACAAGAATG
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
30 11 0.24
31 26 0.58
32 8 0.18
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (28 bp):
TAAATTATTTAATTTTAATTATTTAATT
Found at i:5679098 original size:2 final size:2
Alignment explanation
Indices: 5679091--5679138 Score: 69
Period size: 2 Copynumber: 23.0 Consensus size: 2
5679081 TGATGACTGC
*
5679091 AT AT AT AT AT AT AT AT AT AT AT TT GAT AT GAT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT -AT AT AT AT AT AT AT
5679135 AT AT
1 AT AT
5679139 GGTGTTATCG
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 39 0.93
3 3 0.07
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5679627 original size:23 final size:23
Alignment explanation
Indices: 5679597--5679658 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
5679587 TTATGAGCAT
* *
5679597 TAAATAAAAATGTGTATATATAA
1 TAAATAAAAATATATATATATAA
* *
5679620 TAAATAAAAATATATATTTATAT
1 TAAATAAAAATATATATATATAA
5679643 TAAATAATAAA-ATATA
1 TAAATAA-AAATATATA
5679659 AATAAAAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 31 0.91
24 3 0.09
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (23 bp):
TAAATAAAAATATATATATATAA
Found at i:5679679 original size:36 final size:36
Alignment explanation
Indices: 5679619--5679688 Score: 124
Period size: 36 Copynumber: 1.9 Consensus size: 36
5679609 TGTATATATA
5679619 ATAAATAAAAATATATATTTATATTAAATAATAAAAT
1 ATAAATAAAAATATATATTTATATTAAA-AATAAAAT
5679656 ATAAATAAAAAT-TATATTTATATTAAAAATAAA
1 ATAAATAAAAATATATATTTATATTAAAAATAAA
5679689 TTAATATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
35 6 0.18
36 15 0.45
37 12 0.36
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (36 bp):
ATAAATAAAAATATATATTTATATTAAAAATAAAAT
Found at i:5679686 original size:38 final size:37
Alignment explanation
Indices: 5679619--5679701 Score: 116
Period size: 38 Copynumber: 2.2 Consensus size: 37
5679609 TGTATATATA
5679619 ATAAATAAAAATATATATTTATATTAAAT-AATAAAAT
1 ATAAATAAAAATATATATTTATATTAAATAAAT-AAAT
*
5679656 ATAAATAAAAAT-TATATTTATATTAAAAATAAATTAAT
1 ATAAATAAAAATATATATTTATATT--AAATAAATAAAT
5679694 ATAAATAA
1 ATAAATAA
5679702 GTTAAAAATA
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
36 12 0.29
37 12 0.29
38 15 0.36
39 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (37 bp):
ATAAATAAAAATATATATTTATATTAAATAAATAAAT
Found at i:5679714 original size:14 final size:13
Alignment explanation
Indices: 5679677--5679725 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
5679667 TTATATTTAT
5679677 ATTAAAAAT-A-A
1 ATTAAAAATAATA
*
5679688 ATT-AATATAAATA
1 ATTAAAAAT-AATA
5679701 AGTTAAAAATAATA
1 A-TTAAAAATAATA
5679715 ATTAAAAATAA
1 ATTAAAAATAA
5679726 GGGTAAAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
10 4 0.13
11 3 0.10
12 1 0.03
13 12 0.39
14 7 0.23
15 4 0.13
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (13 bp):
ATTAAAAATAATA
Found at i:5679723 original size:24 final size:25
Alignment explanation
Indices: 5679678--5679726 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
5679668 TATATTTATA
*
5679678 TTAAAAATAAATTAATATAAATAAG
1 TTAAAAATAAATTAATAAAAATAAG
5679703 TTAAAAAT-AA-TAATTAAAAATAAG
1 TTAAAAATAAATTAA-TAAAAATAAG
5679727 GGTAAAATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 3 0.14
24 11 0.50
25 8 0.36
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (25 bp):
TTAAAAATAAATTAATAAAAATAAG
Found at i:5679732 original size:25 final size:25
Alignment explanation
Indices: 5679679--5679741 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 25
5679669 ATATTTATAT
* *
5679679 TAAAAATAAATTAATATAAATAAGT
1 TAAAAATAAATTAATAAAAATAAGG
5679704 TAAAAAT-AA-TAATTAAAAATAAGGG
1 TAAAAATAAATTAA-TAAAAATAA-GG
5679729 T-AAAATGAAATTA
1 TAAAAAT-AAATTA
5679742 CCCCTCCACC
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
23 3 0.10
24 15 0.48
25 9 0.29
26 2 0.06
27 2 0.06
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (25 bp):
TAAAAATAAATTAATAAAAATAAGG
Found at i:5680459 original size:13 final size:13
Alignment explanation
Indices: 5680443--5680513 Score: 56
Period size: 13 Copynumber: 5.2 Consensus size: 13
5680433 CCTTTATTTC
5680443 ATTATTTTAATAA
1 ATTATTTTAATAA
5680456 ATTATAATTTAATTAA
1 ATTAT--TTTAA-TAA
*
5680472 ATTAATTT-ATATA
1 ATTATTTTAATA-A
*
5680485 ATTATTTTTAAAAA
1 ATTA-TTTTAATAA
5680499 TATTA-TTTAATAA
1 -ATTATTTTAATAA
5680512 AT
1 AT
5680514 GTGATTAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 15
0.71 0.06 0.23
Matches are distributed among these distances:
12 4 0.09
13 18 0.38
14 7 0.15
15 11 0.23
16 7 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTATTTTAATAA
Found at i:5680502 original size:12 final size:14
Alignment explanation
Indices: 5680443--5680513 Score: 58
Period size: 14 Copynumber: 5.0 Consensus size: 14
5680433 CCTTTATTTC
5680443 ATTATTTTAATAAATT
1 ATTA-TTTAATAAA-T
*
5680459 ATAATTTAATTAAAT
1 ATTATTTAA-TAAAT
* *
5680474 -TAATTTATATAATT
1 ATTATTTA-ATAAAT
5680488 ATT-TTTAA-AAAT
1 ATTATTTAATAAAT
5680500 ATTATTTAATAAAT
1 ATTATTTAATAAAT
5680514 GTGATTAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
12 6 0.13
13 6 0.13
14 19 0.41
15 8 0.17
16 7 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATTATTTAATAAAT
Found at i:5680665 original size:11 final size:12
Alignment explanation
Indices: 5680637--5680675 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
5680627 AGTGTGTTTC
*
5680637 ATTTATATTTTT
1 ATTTAAATTTTT
5680649 ATTTAAATTTTT
1 ATTTAAATTTTT
*
5680661 ATTAAAATTTATT
1 ATTTAAATTT-TT
5680674 AT
1 AT
5680676 CATGAGTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 20 0.83
13 4 0.17
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATTTAAATTTTT
Found at i:5680949 original size:25 final size:26
Alignment explanation
Indices: 5680909--5680963 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
5680899 AAAATATTTT
5680909 TAAA-TTAAATTAAAATATAA-AAAA
1 TAAATTTAAATTAAAATATAATAAAA
* *
5680933 TAAATTTAAACTT-AAATTTAATAAAT
1 TAAATTTAAA-TTAAAATATAATAAAA
5680959 TAAAT
1 TAAAT
5680964 ATGTCGAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 4 0.15
25 12 0.46
26 10 0.38
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (26 bp):
TAAATTTAAATTAAAATATAATAAAA
Found at i:5681810 original size:2 final size:2
Alignment explanation
Indices: 5681805--5681843 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5681795 TTTTATCAAT
5681805 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
5681844 ATATTTATTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:5689077 original size:66 final size:65
Alignment explanation
Indices: 5688966--5689094 Score: 231
Period size: 66 Copynumber: 2.0 Consensus size: 65
5688956 ACCTGCTTAC
5688966 AAATATTTAGACCTGCTTTGCAAGCCTAACGCCTTCTTGTAGCTTTAGGTTGTAAAACTGATTAG
1 AAATATTTAGACCTGCTTTGCAAGCCTAACGCCTTCTTGTAGCTTTAGGTTGTAAAACTGATTAG
* *
5689031 AAATATTTAGACCTGCTTTGGCAAGCCTAACGCCTTTTTGTGGCTTTAGGTTGTAAAACTGATT
1 AAATATTTAGACCTGCTTT-GCAAGCCTAACGCCTTCTTGTAGCTTTAGGTTGTAAAACTGATT
5689095 GTTTACATTT
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
65 19 0.31
66 42 0.69
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.36
Consensus pattern (65 bp):
AAATATTTAGACCTGCTTTGCAAGCCTAACGCCTTCTTGTAGCTTTAGGTTGTAAAACTGATTAG
Found at i:5689179 original size:21 final size:21
Alignment explanation
Indices: 5689150--5689191 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
5689140 TTGCCAACTA
*
5689150 TTAGGGCATGCTGTAGAGGTT
1 TTAGAGCATGCTGTAGAGGTT
5689171 TTAGAGCATGCTGTAGAGGTT
1 TTAGAGCATGCTGTAGAGGTT
5689192 ACGGCATCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.10, G:0.36, T:0.33
Consensus pattern (21 bp):
TTAGAGCATGCTGTAGAGGTT
Found at i:5696655 original size:2 final size:2
Alignment explanation
Indices: 5696650--5696687 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
5696640 TCACACACAC
5696650 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5696688 CTAATTTTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5696974 original size:2 final size:2
Alignment explanation
Indices: 5696967--5696999 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5696957 TAAAAGTATC
5696967 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5697000 CTATCGATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5697191 original size:24 final size:24
Alignment explanation
Indices: 5697159--5697205 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
5697149 TTAACGAGTT
5697159 TTTTAAGTCGTTTGTGACCAAAAG
1 TTTTAAGTCGTTTGTGACCAAAAG
*
5697183 TTTTAAGTCGTTTTTGACCAAAA
1 TTTTAAGTCGTTTGTGACCAAAA
5697206 CAAAAGGGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (24 bp):
TTTTAAGTCGTTTGTGACCAAAAG
Found at i:5698468 original size:2 final size:2
Alignment explanation
Indices: 5698461--5698502 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
5698451 TGCTTGCATC
5698461 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5698503 TCAAGTATGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5698628 original size:2 final size:2
Alignment explanation
Indices: 5698621--5698655 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5698611 ATGGTATTAT
5698621 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5698656 GACATAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5699383 original size:8 final size:8
Alignment explanation
Indices: 5699369--5699411 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
5699359 GCATTAATAT
5699369 TATATACA
1 TATATACA
*
5699377 TACATACA
1 TATATACA
*
5699385 TATATATA
1 TATATACA
*
5699393 TATATATA
1 TATATACA
5699401 TATATACA
1 TATATACA
5699409 TAT
1 TAT
5699412 TTGTTAATGC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 31 1.00
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (8 bp):
TATATACA
Found at i:5699389 original size:2 final size:2
Alignment explanation
Indices: 5699365--5699411 Score: 51
Period size: 2 Copynumber: 24.0 Consensus size: 2
5699355 TAATGCATTA
* * *
5699365 AT AT -T AT AT AC AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
5699406 AC AT AT
1 AT AT AT
5699412 TTGTTAATGC
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:5699509 original size:2 final size:2
Alignment explanation
Indices: 5699491--5699531 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
5699481 GACAGGCTAA
* *
5699491 TC TC TC GC TC TC CC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
5699532 ATATATATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.51, G:0.02, T:0.46
Consensus pattern (2 bp):
TC
Found at i:5699536 original size:2 final size:2
Alignment explanation
Indices: 5699531--5699566 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5699521 TCTCTCTCTC
5699531 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5699567 CTTGTTCTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5701810 original size:2 final size:2
Alignment explanation
Indices: 5701803--5701838 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5701793 ACTGCCTTAT
5701803 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
5701839 TATATATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:5706667 original size:14 final size:14
Alignment explanation
Indices: 5706648--5706679 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
5706638 AGAAAAATAG
5706648 TTTTTTCTTTTCTT
1 TTTTTTCTTTTCTT
*
5706662 TTTTTTTTTTTCTT
1 TTTTTTCTTTTCTT
5706676 TTTT
1 TTTT
5706680 CCTACTCTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (14 bp):
TTTTTTCTTTTCTT
Found at i:5714671 original size:19 final size:19
Alignment explanation
Indices: 5714644--5714686 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
5714634 ATAATTTTTT
*
5714644 AATTAAAAT-TTTTAAGTTA
1 AATTAAAATAATTTAA-TTA
*
5714663 AATTTAAATAATTTAATTA
1 AATTAAAATAATTTAATTA
5714682 AATTA
1 AATTA
5714687 CAAACAAAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (19 bp):
AATTAAAATAATTTAATTA
Found at i:5716011 original size:132 final size:132
Alignment explanation
Indices: 5715774--5716022 Score: 327
Period size: 132 Copynumber: 1.9 Consensus size: 132
5715764 GACATTGTTA
* *
5715774 TTTGATTCACAAAATAATAATTTTTTAAAATAATTGATTTTAATTTTATTCTTCAAATTTTCAAA
1 TTTGATTCACAAAATAATAATTTTGTAAAATAATTGATTTCAATTTTATTCTTCAAATTTTCAAA
* * ** *
5715839 ATAATTATTTTATATATTTTTTATTAAATAATTATTTCGATCTTGAACGTAAATAGTGATATTAT
66 ATAATTATTTTACATATCTTCCATTAAATAATTATTTCGATCTTAAACGTAAATAGTGATATTAT
5715904 TG
131 TG
* * * * * *
5715906 TTTGATTCACGAAATAATAATTTTGTGAAATTATTGATTTCGATTTTATTTTTTAAATTTTCAAA
1 TTTGATTCACAAAATAATAATTTTGTAAAATAATTGATTTCAATTTTATTCTTCAAATTTTCAAA
* * * * * *
5715971 ATAGTTATTTTGCGTCTCTTCCGTTAAATAATTATTTCGATTTTAAACGTAA
66 ATAATTATTTTACATATCTTCCATTAAATAATTATTTCGATCTTAAACGTAA
5716023 TATAAAATTT
Statistics
Matches: 98, Mismatches: 19, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
132 98 1.00
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.49
Consensus pattern (132 bp):
TTTGATTCACAAAATAATAATTTTGTAAAATAATTGATTTCAATTTTATTCTTCAAATTTTCAAA
ATAATTATTTTACATATCTTCCATTAAATAATTATTTCGATCTTAAACGTAAATAGTGATATTAT
TG
Found at i:5720151 original size:35 final size:36
Alignment explanation
Indices: 5720080--5720151 Score: 85
Period size: 36 Copynumber: 2.0 Consensus size: 36
5720070 AAGATTTTTT
* * *
5720080 AAATTTAATCTTAAATTATATAAAATACTAATATAA
1 AAATTAAATCTTAAATTATATAAAATAATAAAATAA
*
5720116 AAATTAAATTTTAATATT-TAT-AAATAATAAAATAA
1 AAATTAAATCTTAA-ATTATATAAAATAATAAAATAA
5720151 A
1 A
5720152 CCTATTTGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
35 13 0.42
36 15 0.48
37 3 0.10
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (36 bp):
AAATTAAATCTTAAATTATATAAAATAATAAAATAA
Found at i:5724832 original size:26 final size:26
Alignment explanation
Indices: 5724795--5724845 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
5724785 TTGAGTTCTG
*
5724795 ATACCTCTTTGAGCTTTCTTTGGGTA
1 ATACCTCCTTGAGCTTTCTTTGGGTA
*
5724821 ATACCTCCTTGAGCTTTTTTTGGGT
1 ATACCTCCTTGAGCTTTCTTTGGGT
5724846 CTTGCAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.47
Consensus pattern (26 bp):
ATACCTCCTTGAGCTTTCTTTGGGTA
Found at i:5736727 original size:7 final size:7
Alignment explanation
Indices: 5736715--5736748 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
5736705 ATATTTCACA
5736715 AAAAAAT
1 AAAAAAT
5736722 AAAAAAT
1 AAAAAAT
*
5736729 TAAAAAT
1 AAAAAAT
5736736 AAAAAAGT
1 AAAAAA-T
5736744 AAAAA
1 AAAAA
5736749 CAGTGAGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (7 bp):
AAAAAAT
Found at i:5736735 original size:14 final size:14
Alignment explanation
Indices: 5736716--5736748 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
5736706 TATTTCACAA
*
5736716 AAAAATAAAAAATT
1 AAAAATAAAAAAGT
5736730 AAAAATAAAAAAGT
1 AAAAATAAAAAAGT
5736744 AAAAA
1 AAAAA
5736749 CAGTGAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (14 bp):
AAAAATAAAAAAGT
Found at i:5737863 original size:8 final size:8
Alignment explanation
Indices: 5737850--5737879 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
5737840 AATAATTTTT
5737850 AAAAATTA
1 AAAAATTA
5737858 AAAAATTA
1 AAAAATTA
*
5737866 AAAAATAA
1 AAAAATTA
5737874 AAAAAT
1 AAAAAT
5737880 AAATTTACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (8 bp):
AAAAATTA
Found at i:5737866 original size:15 final size:15
Alignment explanation
Indices: 5737848--5737882 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
5737838 GTAATAATTT
*
5737848 TTAAAAATTAAAAAA
1 TTAAAAAATAAAAAA
5737863 TTAAAAAATAAAAAA
1 TTAAAAAATAAAAAA
*
5737878 ATAAA
1 TTAAA
5737883 TTTACAATCC
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:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
TTAAAAAATAAAAAA
Found at i:5738136 original size:24 final size:24
Alignment explanation
Indices: 5738109--5738155 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
5738099 CACTTATTCT
*
5738109 TGAAGAAA-ATTAGAAAAGAAATGG
1 TGAAAAAATATTAGAAAA-AAATGG
*
5738133 TGAAAAAATATTTGAAAAAAATG
1 TGAAAAAATATTAGAAAAAAATG
5738156 AAGAATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.60, C:0.00, G:0.19, T:0.21
Consensus pattern (24 bp):
TGAAAAAATATTAGAAAAAAATGG
Found at i:5740816 original size:7 final size:7
Alignment explanation
Indices: 5740804--5740837 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
5740794 TTTTCATTTC
5740804 TTTTTAT
1 TTTTTAT
5740811 TTTTTAT
1 TTTTTAT
5740818 TTTTTAAT
1 TTTTT-AT
*
5740826 TTTTAAT
1 TTTTTAT
5740833 TTTTT
1 TTTTT
5740838 TTGGTAGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTTAT
Found at i:5740823 original size:14 final size:15
Alignment explanation
Indices: 5740804--5740837 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
5740794 TTTTCATTTC
*
5740804 TTTTT-ATTTTTTAT
1 TTTTTAATTTTTAAT
5740818 TTTTTAATTTTTAAT
1 TTTTTAATTTTTAAT
5740833 TTTTT
1 TTTTT
5740838 TTGGTAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTAATTTTTAAT
Found at i:5743071 original size:23 final size:23
Alignment explanation
Indices: 5743045--5743112 Score: 70
Period size: 23 Copynumber: 2.9 Consensus size: 23
5743035 TTAAATTATT
5743045 ATTTAATAAAAAATAATATTTAA
1 ATTTAATAAAAAATAATATTTAA
*
5743068 ATTTAATTATAAAAT-ATA--TAA
1 ATTTAA-TAAAAAATAATATTTAA
5743089 ATATTAATATAAAAATTAATATTT
1 AT-TTAATA-AAAAA-TAATATTT
5743113 TAATAATATA
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
21 7 0.19
22 8 0.22
23 10 0.28
24 10 0.28
26 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
ATTTAATAAAAAATAATATTTAA
Found at i:5743089 original size:21 final size:21
Alignment explanation
Indices: 5743059--5743141 Score: 63
Period size: 21 Copynumber: 4.1 Consensus size: 21
5743049 AATAAAAAAT
*
5743059 AATATTTAAAT-TTAATTATAA
1 AATATATAAATATTAA-TATAA
5743080 AATATATAAATATTAATATAA
1 AATATATAAATATTAATATAA
5743101 AA-AT-T-AATATT--T-TAA
1 AATATATAAATATTAATATAA
* *
5743116 TAATATAATAAATAATAAAATAA
1 -AATAT-ATAAATATTAATATAA
5743139 AAT
1 AAT
5743142 TTTAAATCGA
Statistics
Matches: 50, Mismatches: 3, Indels: 17
0.71 0.04 0.24
Matches are distributed among these distances:
15 3 0.06
16 3 0.06
17 2 0.04
18 6 0.12
19 2 0.04
20 7 0.14
21 17 0.34
22 7 0.14
23 3 0.06
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AATATATAAATATTAATATAA
Found at i:5743127 original size:47 final size:42
Alignment explanation
Indices: 5743047--5743134 Score: 97
Period size: 45 Copynumber: 2.0 Consensus size: 42
5743037 AAATTATTAT
5743047 TTAATAAAAAATAATATTTAAATTTAATTATAAAATATATAAATA
1 TTAATAAAAAATAATATTTAAA-TTAATTAT-AAATA-ATAAATA
*
5743092 TTAATATAAAAATTAATATTTTAA-TAATATAATAAATAATAAA
1 TTAATA-AAAAA-TAATATTTAAATTAAT-T-ATAAATAATAAA
5743135 ATAAAATTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
45 15 0.39
46 11 0.29
47 12 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (42 bp):
TTAATAAAAAATAATATTTAAATTAATTATAAATAATAAATA
Found at i:5744132 original size:2 final size:2
Alignment explanation
Indices: 5744125--5744159 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5744115 AATCGGACAC
5744125 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
5744160 AGGGATTGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5745555 original size:2 final size:2
Alignment explanation
Indices: 5745543--5745572 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5745533 CTATAGGTAC
*
5745543 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5745573 AACACAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:5745789 original size:1 final size:1
Alignment explanation
Indices: 5745742--5745771 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
5745732 ACCGACACAG
5745742 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
5745772 AAAAAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:5751777 original size:23 final size:25
Alignment explanation
Indices: 5751738--5751796 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 25
5751728 TACATTCATA
*
5751738 TTATA-TAAATTTAAAATA-TATAT
1 TTATATTATATTTAAAATATTATAT
* *
5751761 TT-TATTATATTTTAAATATTTTAT
1 TTATATTATATTTAAAATATTATAT
5751785 TTATATTATATT
1 TTATATTATATT
5751797 ATATTATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 2 0.07
23 13 0.43
24 6 0.20
25 9 0.30
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
TTATATTATATTTAAAATATTATAT
Found at i:5751803 original size:10 final size:10
Alignment explanation
Indices: 5751756--5751801 Score: 58
Period size: 10 Copynumber: 4.6 Consensus size: 10
5751746 ATTTAAAATA
5751756 TATATTTTAT
1 TATATTTTAT
5751766 TATATTTTA-
1 TATATTTTAT
*
5751775 AATATTTTATT
1 TATATTTTA-T
*
5751786 TATATTATAT
1 TATATTTTAT
5751796 TATATT
1 TATATT
5751802 ATTAATTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
9 8 0.26
10 16 0.52
11 7 0.23
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TATATTTTAT
Found at i:5753863 original size:30 final size:30
Alignment explanation
Indices: 5753827--5753903 Score: 118
Period size: 30 Copynumber: 2.6 Consensus size: 30
5753817 GTAGCAGATG
*
5753827 CTTGACCATAAGAATTTGCGTTACTTGTTA
1 CTTGACCATAAGAATTAGCGTTACTTGTTA
* *
5753857 CTTGACCATAATAATTAGCGTTACTTTTTA
1 CTTGACCATAAGAATTAGCGTTACTTGTTA
*
5753887 CTTGACCATGAGAATTA
1 CTTGACCATAAGAATTA
5753904 TTAACATTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (30 bp):
CTTGACCATAAGAATTAGCGTTACTTGTTA
Found at i:5755218 original size:24 final size:23
Alignment explanation
Indices: 5755180--5755233 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
5755170 TTTGAAATTA
5755180 ACTTTTT-TTTTAATTAATAAAAT
1 ACTTTTTATTTTAATT-ATAAAAT
*
5755203 A-TTTTTATTTGTAATTATATAAT
1 ACTTTTTATTT-TAATTATAAAAT
5755226 ACTTTTTA
1 ACTTTTTA
5755234 AAATATAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 5 0.19
23 11 0.41
24 11 0.41
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (23 bp):
ACTTTTTATTTTAATTATAAAAT
Found at i:5755262 original size:20 final size:21
Alignment explanation
Indices: 5755228--5755267 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5755218 TATATAATAC
*
5755228 TTTTTAAAATATAAATATTAT
1 TTTTTAAAATATAAAAATTAT
*
5755249 TTTTTAATAT-TAAAAATTA
1 TTTTTAAAATATAAAAATTA
5755268 AAGCGGACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTTTAAAATATAAAAATTAT
Found at i:5757309 original size:6 final size:6
Alignment explanation
Indices: 5757291--5757324 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
5757281 ATTAGGAGAA
* *
5757291 GGCTTT GCCTTT GGTTTT GGCTTT GGCTTT GGCT
1 GGCTTT GGCTTT GGCTTT GGCTTT GGCTTT GGCT
5757325 ATTGCATGGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.18, G:0.32, T:0.50
Consensus pattern (6 bp):
GGCTTT
Found at i:5757678 original size:3 final size:3
Alignment explanation
Indices: 5757664--5757700 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
5757654 TATCAACCCT
*
5757664 TTC TTC TCC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
5757701 CATCTCTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:5757914 original size:2 final size:2
Alignment explanation
Indices: 5757907--5757936 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5757897 TTTATCTGGG
5757907 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5757937 TTCTTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5768181 original size:5 final size:5
Alignment explanation
Indices: 5768163--5768212 Score: 64
Period size: 5 Copynumber: 10.0 Consensus size: 5
5768153 TTGCATCCGA
* * * *
5768163 TCCTA TCCTA TCCAT TCCAT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT
1 TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT
5768213 AAAAGTCCAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 42 1.00
ACGTcount: A:0.08, C:0.40, G:0.00, T:0.52
Consensus pattern (5 bp):
TCCTT
Found at i:5790409 original size:24 final size:21
Alignment explanation
Indices: 5790381--5790432 Score: 81
Period size: 20 Copynumber: 2.5 Consensus size: 21
5790371 ATTATGGTTA
5790381 TAAATAATATATTAATTAATTT
1 TAAATAAT-TATTAATTAATTT
5790403 TAAA-AATTATTAATTAATTT
1 TAAATAATTATTAATTAATTT
5790423 TAAA-AATTAT
1 TAAATAATTAT
5790433 CTTCCTCAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 23 0.77
21 3 0.10
22 4 0.13
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TAAATAATTATTAATTAATTT
Found at i:5790413 original size:20 final size:20
Alignment explanation
Indices: 5790390--5790432 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
5790380 ATAAATAATA
5790390 TATTAATTAATTTTAAAAAT
1 TATTAATTAATTTTAAAAAT
5790410 TATTAATTAATTTTAAAAAT
1 TATTAATTAATTTTAAAAAT
5790430 TAT
1 TAT
5790433 CTTCCTCAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TATTAATTAATTTTAAAAAT
Found at i:5797772 original size:2 final size:2
Alignment explanation
Indices: 5797765--5797803 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5797755 TGGGTTTGTT
5797765 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5797804 TAGTAAGTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5799957 original size:24 final size:23
Alignment explanation
Indices: 5799904--5799949 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
5799894 ACAAACCAAA
*
5799904 AAAGAAAAAAAAGAAGAAAGAGC
1 AAAGAAAAAAAAGAAAAAAGAGC
5799927 AAAGAAAAATAAAGAAAAAAGAG
1 AAAGAAAAA-AAAGAAAAAAGAG
5799950 GCATGAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (23 bp):
AAAGAAAAAAAAGAAAAAAGAGC
Found at i:5801087 original size:2 final size:2
Alignment explanation
Indices: 5801077--5801115 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
5801067 AGTGTGTGTG
*
5801077 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5801116 GAAGAAACAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5808953 original size:16 final size:16
Alignment explanation
Indices: 5808922--5808996 Score: 100
Period size: 16 Copynumber: 4.8 Consensus size: 16
5808912 TATTTAAATG
5808922 TAATTTAAATTTAAAAA
1 TAATTTAAATTT-AAAA
*
5808939 TAACTTAAA-TTAAAA
1 TAATTTAAATTTAAAA
*
5808954 T-ATTTATATTTAAAA
1 TAATTTAAATTTAAAA
5808969 TAATTTAAATTTAAAA
1 TAATTTAAATTTAAAA
*
5808985 TAATTAAAATTT
1 TAATTTAAATTT
5808997 GAACCTACTT
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
14 5 0.10
15 12 0.24
16 26 0.51
17 8 0.16
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (16 bp):
TAATTTAAATTTAAAA
Found at i:5808965 original size:31 final size:31
Alignment explanation
Indices: 5808924--5808992 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
5808914 TTTAAATGTA
5808924 ATTTAAATTTAAAAATAACTTAAA-TTAAAAT
1 ATTTAAATTT-AAAATAACTTAAATTTAAAAT
* *
5808955 ATTTATATTTAAAATAATTTAAATTTAAAAT
1 ATTTAAATTTAAAATAACTTAAATTTAAAAT
*
5808986 AATTAAA
1 ATTTAAA
5808993 ATTTGAACCT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 12 0.36
31 21 0.64
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (31 bp):
ATTTAAATTTAAAATAACTTAAATTTAAAAT
Found at i:5809158 original size:29 final size:30
Alignment explanation
Indices: 5809125--5809194 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
5809115 TTTTAAGTGA
* *
5809125 TTTTATATTTTTA-TTATAATTAAATAAGT
1 TTTTATATTTTAATTTATAATTAAATAAAT
* **
5809154 TTTTAAATTTTAATTTATGTTTAAATAAAT
1 TTTTATATTTTAATTTATAATTAAATAAAT
5809184 TTTTATTATTT
1 TTTTA-TATTT
5809195 AAGTATAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 11 0.33
30 18 0.55
31 4 0.12
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (30 bp):
TTTTATATTTTAATTTATAATTAAATAAAT
Found at i:5809872 original size:19 final size:19
Alignment explanation
Indices: 5809809--5809872 Score: 53
Period size: 19 Copynumber: 3.4 Consensus size: 19
5809799 AATCGTTATG
*
5809809 AAAAATCTTTTAAATTGAT
1 AAAAATATTTTAAATTGAT
*
5809828 AAAAATA-ATTACATATT--T
1 AAAAATATTTTA-A-ATTGAT
*
5809846 GAAGAATATTTTAAATTGAT
1 -AAAAATATTTTAAATTGAT
5809866 AAAAATA
1 AAAAATA
5809873 GTCATGATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 12
0.67 0.10 0.24
Matches are distributed among these distances:
18 7 0.21
19 20 0.59
20 7 0.21
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.38
Consensus pattern (19 bp):
AAAAATATTTTAAATTGAT
Found at i:5809963 original size:21 final size:21
Alignment explanation
Indices: 5809909--5809965 Score: 64
Period size: 22 Copynumber: 2.8 Consensus size: 21
5809899 ATTATCATCT
*
5809909 TAAATATTTTT-A-TTATAAA
1 TAAAAATTTTTAATTTATAAA
* *
5809928 TAAAATTTATTTAATTTATAAG
1 TAAAAATT-TTTAATTTATAAA
5809950 TAAAAATTTTTAATTT
1 TAAAAATTTTTAATTT
5809966 CACATTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 6 0.19
20 3 0.10
21 9 0.29
22 13 0.42
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
TAAAAATTTTTAATTTATAAA
Found at i:5815524 original size:2 final size:2
Alignment explanation
Indices: 5815517--5815550 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
5815507 CTTCACGTGC
5815517 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5815551 ACCTTGAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5815888 original size:3 final size:3
Alignment explanation
Indices: 5815880--5815911 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
5815870 GCAGATGATC
5815880 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
5815912 AGGAGCCTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:5816579 original size:6 final size:6
Alignment explanation
Indices: 5816568--5816603 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
5816558 TAATACAGTT
* *
5816568 GAAGGG GAAGGG GAAGGG GAAGGG AAAGGG AAAGGG
1 GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG
5816604 AGGGATTCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.39, C:0.00, G:0.61, T:0.00
Consensus pattern (6 bp):
GAAGGG
Found at i:5816775 original size:3 final size:3
Alignment explanation
Indices: 5816762--5816816 Score: 94
Period size: 3 Copynumber: 18.7 Consensus size: 3
5816752 TTTATACTAA
5816762 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
5816809 GAT AAT AA
1 AAT AAT AA
5816817 AGAAAAAGAA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 47 0.96
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5817267 original size:6 final size:6
Alignment explanation
Indices: 5817256--5817293 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
5817246 CATCAACTTG
5817256 TTTT-T TTTT-T TTTTGT TTTTGT TTTTGT TTTTGT TTTT
1 TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTT
5817294 ATCAACTACT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 9 0.28
6 23 0.72
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (6 bp):
TTTTGT
Found at i:5817596 original size:2 final size:2
Alignment explanation
Indices: 5817589--5817614 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5817579 ATTCTCATGC
5817589 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
5817615 CAATTCCCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5817620 original size:112 final size:112
Alignment explanation
Indices: 5817479--5817726 Score: 478
Period size: 112 Copynumber: 2.2 Consensus size: 112
5817469 TTCCACGTAC
5817479 ATATATATATATATATATATATATCAATTCCCTAAACCTTGTGAACATAATGATTGAGAATGTAT
1 ATATATATATATATATATATATATCAATTCCCTAAACCTTGTGAACATAATGATTGAGAATGTAT
5817544 GTAACTTTATATTCGATTTCAAATATCTTCTTATCATTCTCATGCAT
66 GTAACTTTATATTCGATTTCAAATATCTTCTTATCATTCTCATGCAT
* *
5817591 ATATATATATATATATATATATATCAATTCCCTAAACCTTTTGATCATAATGATTGAGAATGTAT
1 ATATATATATATATATATATATATCAATTCCCTAAACCTTGTGAACATAATGATTGAGAATGTAT
5817656 GTAACTTTATATTCGATTTCAAATATCTTCTTATCATTCTCATGCAT
66 GTAACTTTATATTCGATTTCAAATATCTTCTTATCATTCTCATGCAT
5817703 ATATATATATATATATATATATAT
1 ATATATATATATATATATATATAT
5817727 ATATATATAA
Statistics
Matches: 134, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
112 134 1.00
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.44
Consensus pattern (112 bp):
ATATATATATATATATATATATATCAATTCCCTAAACCTTGTGAACATAATGATTGAGAATGTAT
GTAACTTTATATTCGATTTCAAATATCTTCTTATCATTCTCATGCAT
Found at i:5817747 original size:2 final size:2
Alignment explanation
Indices: 5817701--5817735 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5817691 ATTCTCATGC
5817701 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5817736 AACATCATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5818721 original size:25 final size:26
Alignment explanation
Indices: 5818681--5818730 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
5818671 TTAATTAATA
5818681 TTTTATTATATTTTTTAAAAAATTTG
1 TTTTATTATATTTTTTAAAAAATTTG
*
5818707 TTTTA-TATATTTTTTATAAAATTT
1 TTTTATTATATTTTTTAAAAAATTT
5818731 AAAAATTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (26 bp):
TTTTATTATATTTTTTAAAAAATTTG
Found at i:5823267 original size:21 final size:21
Alignment explanation
Indices: 5823221--5823269 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
5823211 GTCTTTATTT
*
5823221 TTATTT-TATTTTTGAATTTA
1 TTATTTATATTTTTGAATTGA
** *
5823241 AAATTTATATTTTTTAATTGA
1 TTATTTATATTTTTGAATTGA
5823262 TTATTTAT
1 TTATTTAT
5823270 TAACAGTATT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (21 bp):
TTATTTATATTTTTGAATTGA
Found at i:5830843 original size:12 final size:12
Alignment explanation
Indices: 5830826--5830869 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
5830816 CTATTTTATG
5830826 AATAATAATAAC
1 AATAATAATAAC
5830838 AATAATAATAAC
1 AATAATAATAAC
*
5830850 ATTAATAATAAC
1 AATAATAATAAC
*
5830862 ATTAATAA
1 AATAATAA
5830870 CTTTTTTCCC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.30
Consensus pattern (12 bp):
AATAATAATAAC
Found at i:5834562 original size:2 final size:2
Alignment explanation
Indices: 5834557--5834581 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5834547 AAAAAAAATG
5834557 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5834582 TTAAAAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5836085 original size:11 final size:12
Alignment explanation
Indices: 5836059--5836091 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
5836049 GAGATTGAGA
*
5836059 TTTTGTTTTTTC
1 TTTTCTTTTTTC
5836071 TTTTCTTTTTT-
1 TTTTCTTTTTTC
5836082 TTTTCTTTTT
1 TTTTCTTTTT
5836092 CAAAATTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.00, C:0.09, G:0.03, T:0.88
Consensus pattern (12 bp):
TTTTCTTTTTTC
Found at i:5836085 original size:16 final size:17
Alignment explanation
Indices: 5836059--5836090 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
5836049 GAGATTGAGA
5836059 TTTTGTTTTTTCTTTTC
1 TTTTGTTTTTTCTTTTC
5836076 TTTT-TTTTTTCTTTT
1 TTTTGTTTTTTCTTTT
5836091 TCAAAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.00, C:0.09, G:0.03, T:0.88
Consensus pattern (17 bp):
TTTTGTTTTTTCTTTTC
Found at i:5842326 original size:3 final size:3
Alignment explanation
Indices: 5842311--5842344 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
5842301 CGTGTGTTTG
*
5842311 ATT ATT ATC ATT ATT ATT ATT ATT ATT ACTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT
5842345 TATCATAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:5843270 original size:2 final size:2
Alignment explanation
Indices: 5843263--5843290 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5843253 TCCAAAGAAT
5843263 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5843291 CATTGACGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5843836 original size:5 final size:5
Alignment explanation
Indices: 5843826--5843851 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
5843816 CAAGGGGGCC
5843826 CTCGA CTCGA CTCGA CTCGA CTCGA C
1 CTCGA CTCGA CTCGA CTCGA CTCGA C
5843852 CGCCAATTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.42, G:0.19, T:0.19
Consensus pattern (5 bp):
CTCGA
Found at i:5844603 original size:2 final size:2
Alignment explanation
Indices: 5844598--5844628 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5844588 TGTGTGTGTG
5844598 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5844629 TTCCTTTTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5846079 original size:2 final size:2
Alignment explanation
Indices: 5846067--5846102 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
5846057 CTTTTCTGCT
5846067 TC TC T- TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
5846103 ATATATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:5846107 original size:2 final size:2
Alignment explanation
Indices: 5846102--5846138 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5846092 TCTCTCTCTC
5846102 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5846139 TCAAAAGAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5846640 original size:2 final size:2
Alignment explanation
Indices: 5846633--5846658 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5846623 GAATAATTAA
5846633 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
5846659 TGCTCCCCGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5849315 original size:2 final size:2
Alignment explanation
Indices: 5849308--5849353 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
5849298 GGCTGTGGAC
5849308 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5849350 AG AG
1 AG AG
5849354 TTAATATTCT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5851050 original size:22 final size:22
Alignment explanation
Indices: 5851022--5851065 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
5851012 ATGTGTGCGC
5851022 GCTTGAATTGATGCATTGCAGT
1 GCTTGAATTGATGCATTGCAGT
5851044 GCTTGAATTGATGCATTGCAGT
1 GCTTGAATTGATGCATTGCAGT
5851066 TTGCAAACCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.14, G:0.27, T:0.36
Consensus pattern (22 bp):
GCTTGAATTGATGCATTGCAGT
Found at i:5852448 original size:3 final size:3
Alignment explanation
Indices: 5852424--5852479 Score: 78
Period size: 3 Copynumber: 19.0 Consensus size: 3
5852414 GAGGAACACG
* *
5852424 ATT ATT A-T ATC ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
5852471 ATG ATT ATT
1 ATT ATT ATT
5852480 TTTCCTAATG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:5854771 original size:18 final size:20
Alignment explanation
Indices: 5854734--5854774 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
5854724 TTAGTTGTGG
5854734 AAGTTGGTTACTAAGTTTGTT
1 AAGTTGGTTACT-AGTTTGTT
5854755 AAGTTGGTTA-T-GTTTGTT
1 AAGTTGGTTACTAGTTTGTT
5854773 AA
1 AA
5854775 TTTGTTAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 9 0.45
20 1 0.05
21 10 0.50
ACGTcount: A:0.24, C:0.02, G:0.24, T:0.49
Consensus pattern (20 bp):
AAGTTGGTTACTAGTTTGTT
Found at i:5854834 original size:2 final size:2
Alignment explanation
Indices: 5854827--5854870 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
5854817 AAGTCTTTAC
5854827 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5854869 TA
1 TA
5854871 CACACATACA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5855063 original size:8 final size:8
Alignment explanation
Indices: 5855041--5855097 Score: 69
Period size: 8 Copynumber: 6.9 Consensus size: 8
5855031 CTCAAAATTG
5855041 ACAAACTA
1 ACAAACTA
**
5855049 ATTAACTA
1 ACAAACTA
5855057 ACAAACTA
1 ACAAACTA
5855065 ACAAACTA
1 ACAAACTA
5855073 ACAAACATA
1 ACAAAC-TA
*
5855082 ACCAACTTA
1 ACAAAC-TA
5855091 ACAAACT
1 ACAAACT
5855098 TAGTAATCAA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
8 27 0.66
9 14 0.34
ACGTcount: A:0.58, C:0.25, G:0.00, T:0.18
Consensus pattern (8 bp):
ACAAACTA
Found at i:5855092 original size:9 final size:9
Alignment explanation
Indices: 5855055--5855099 Score: 58
Period size: 9 Copynumber: 5.2 Consensus size: 9
5855045 ACTAATTAAC
5855055 TAACAAAC-
1 TAACAAACT
5855063 TAACAAAC-
1 TAACAAACT
*
5855071 TAACAAACA
1 TAACAAACT
*
5855080 TAACCAACT
1 TAACAAACT
5855089 TAACAAACT
1 TAACAAACT
5855098 TA
1 TA
5855100 GTAATCAACT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
8 16 0.48
9 17 0.52
ACGTcount: A:0.58, C:0.24, G:0.00, T:0.18
Consensus pattern (9 bp):
TAACAAACT
Found at i:5865577 original size:155 final size:155
Alignment explanation
Indices: 5865295--5865607 Score: 608
Period size: 155 Copynumber: 2.0 Consensus size: 155
5865285 AAGCTTGTTC
5865295 GTGTGTTCGTAACTCCAATAATTGATTTGTGTTTCTGTTTTTATACATTCAGTTGTAATAAGATA
1 GTGTGTTCGTAACTCCAATAATTGATTTGTGTTTCTGTTTTTATACATTCAGTTGTAATAAGATA
5865360 TTGAAGCTGCTGCATGCTTACATAGCCGATAGGCATTCTCCGTTAAAGTAATTCCTGCCAAATTT
66 TTGAAGCTGCTGCATGCTTACATAGCCGATAGGCATTCTCCGTTAAAGTAATTCCTGCCAAATTT
*
5865425 TAAGTGCGTGAGTTGGGGAAGTTGA
131 TAAGTGCGTGAGCTGGGGAAGTTGA
5865450 GTGTGTTCGTAACTCCAATAATTGATTTGTGTTTCTGTTTTTATACATTCAGTTGTAATAAGATA
1 GTGTGTTCGTAACTCCAATAATTGATTTGTGTTTCTGTTTTTATACATTCAGTTGTAATAAGATA
*
5865515 TTGGAGCTGCTGCATGCTTACATAGCCGATAGGCATTCTCCGTTAAAGTAATTCCTGCCAAATTT
66 TTGAAGCTGCTGCATGCTTACATAGCCGATAGGCATTCTCCGTTAAAGTAATTCCTGCCAAATTT
5865580 TAAGTGCGTGAGCTGGGGAAGTTGA
131 TAAGTGCGTGAGCTGGGGAAGTTGA
5865605 GTG
1 GTG
5865608 ACGCCTAAAA
Statistics
Matches: 156, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
155 156 1.00
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (155 bp):
GTGTGTTCGTAACTCCAATAATTGATTTGTGTTTCTGTTTTTATACATTCAGTTGTAATAAGATA
TTGAAGCTGCTGCATGCTTACATAGCCGATAGGCATTCTCCGTTAAAGTAATTCCTGCCAAATTT
TAAGTGCGTGAGCTGGGGAAGTTGA
Found at i:5867543 original size:15 final size:14
Alignment explanation
Indices: 5867522--5867560 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
5867512 TTCTCGAGCC
5867522 AAAAAAATAAATAAA
1 AAAAAAATAAA-AAA
*
5867537 TAAAAAATAAAAAA
1 AAAAAAATAAAAAA
5867551 AAGAAAAATA
1 AA-AAAAATA
5867561 GGTTAGCAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.13
Consensus pattern (14 bp):
AAAAAAATAAAAAA
Found at i:5867723 original size:2 final size:2
Alignment explanation
Indices: 5867716--5867755 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
5867706 CAAATCAAGG
5867716 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5867756 GTACAGATTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5869685 original size:42 final size:42
Alignment explanation
Indices: 5869638--5869718 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 42
5869628 TATGCAGTTA
* *
5869638 ATCCATGTATTTATGCAAATTTACAGATTTA-ACTTTTTATCC
1 ATCCATCTATTTATGCAAACTTACAGATTTACA-TTTTTATCC
*
5869680 ATCCATCTATTTATGTAAACTTACAGATTTACATTTTTA
1 ATCCATCTATTTATGCAAACTTACAGATTTACATTTTTA
5869719 ATAATTAGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
42 34 0.97
43 1 0.03
ACGTcount: A:0.32, C:0.16, G:0.06, T:0.46
Consensus pattern (42 bp):
ATCCATCTATTTATGCAAACTTACAGATTTACATTTTTATCC
Found at i:5870013 original size:16 final size:16
Alignment explanation
Indices: 5869992--5870029 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
5869982 ACTGATCGAC
*
5869992 TCGAACCCGAAATGAT
1 TCGAACCCAAAATGAT
5870008 TCGAACCCAAAATGAT
1 TCGAACCCAAAATGAT
*
5870024 CCGAAC
1 TCGAAC
5870030 TTGAAATGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.29, G:0.16, T:0.16
Consensus pattern (16 bp):
TCGAACCCAAAATGAT
Done.