Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009643.1 Hibiscus syriacus cultivar Beakdansim tig00117056_pilon, 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: 8859806
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 41
Found at i:2034133 original size:16 final size:16
Alignment explanation
Indices: 2034112--2034153 Score: 52
Period size: 14 Copynumber: 2.7 Consensus size: 16
2034102 TCTTGATTGC
2034112 AATAAAATATTTTCTA
1 AATAAAATATTTTCTA
*
2034128 AAT-AAAT-TATTCTA
1 AATAAAATATTTTCTA
2034142 AATAGAAATATT
1 AATA-AAATATT
2034154 ACTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
14 9 0.43
15 4 0.19
16 7 0.33
17 1 0.05
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.40
Consensus pattern (16 bp):
AATAAAATATTTTCTA
Found at i:2034158 original size:16 final size:14
Alignment explanation
Indices: 2034112--2034164 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 14
2034102 TCTTGATTGC
2034112 AATAAAATATTTTCTA
1 AATAAAATA--TTCTA
*
2034128 AATAAATTATTCTA
1 AATAAAATATTCTA
2034142 AATAGAAATATTACTA
1 AATA-AAATATT-CTA
2034158 ATATAAA
1 A-ATAAA
2034165 CCTATTAGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 9 0.28
15 6 0.19
16 14 0.44
17 3 0.09
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.38
Consensus pattern (14 bp):
AATAAAATATTCTA
Found at i:2039663 original size:11 final size:11
Alignment explanation
Indices: 2039647--2039671 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2039637 TATAATTAAG
2039647 GAAAGTAAGAT
1 GAAAGTAAGAT
2039658 GAAAGTAAGAT
1 GAAAGTAAGAT
2039669 GAA
1 GAA
2039672 GGACTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.28, T:0.16
Consensus pattern (11 bp):
GAAAGTAAGAT
Found at i:2046683 original size:13 final size:13
Alignment explanation
Indices: 2046665--2046708 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
2046655 ATAAATAATA
*
2046665 AAAAAATTACAAT
1 AAAAAACTACAAT
* *
2046678 AAAAAAGTCCAAT
1 AAAAAACTACAAT
*
2046691 AAACAACTACAAT
1 AAAAAACTACAAT
2046704 AAAAA
1 AAAAA
2046709 GTACTAAATA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.68, C:0.14, G:0.02, T:0.16
Consensus pattern (13 bp):
AAAAAACTACAAT
Found at i:2048971 original size:9 final size:9
Alignment explanation
Indices: 2048957--2048992 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
2048947 TTAAGAAAAT
2048957 ATTAAATAA
1 ATTAAATAA
2048966 ATTAAAT-A
1 ATTAAATAA
*
2048974 CTTAAATAA
1 ATTAAATAA
2048983 ATTAAATAA
1 ATTAAATAA
2048992 A
1 A
2048993 AAATATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 7 0.29
9 17 0.71
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (9 bp):
ATTAAATAA
Found at i:2048980 original size:17 final size:16
Alignment explanation
Indices: 2048953--2048990 Score: 67
Period size: 17 Copynumber: 2.3 Consensus size: 16
2048943 GTAATTAAGA
2048953 AAATATTAAATAAATT
1 AAATATTAAATAAATT
2048969 AAATACTTAAATAAATT
1 AAATA-TTAAATAAATT
2048986 AAATA
1 AAATA
2048991 AAAAATATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (16 bp):
AAATATTAAATAAATT
Found at i:2048990 original size:26 final size:22
Alignment explanation
Indices: 2048952--2049015 Score: 67
Period size: 26 Copynumber: 2.7 Consensus size: 22
2048942 AGTAATTAAG
*
2048952 AAAATATTAAATAAATTAAATACTT
1 AAAAAATTAAATAAA--AAATA-TT
2048977 AAATAAATTAAATAAAAAATATT
1 AAA-AAATTAAATAAAAAATATT
2049000 AAAAAA-TATAATAAAA
1 AAAAAATTA-AATAAAA
2049016 TATACTTTAG
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
21 2 0.06
22 10 0.28
23 5 0.14
24 5 0.14
25 3 0.08
26 11 0.31
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (22 bp):
AAAAAATTAAATAAAAAATATT
Found at i:2049951 original size:54 final size:54
Alignment explanation
Indices: 2049887--2050004 Score: 143
Period size: 54 Copynumber: 2.2 Consensus size: 54
2049877 TAATATAAGA
*** *
2049887 TATTATATTTTATTTTAATAATATATAATAAATTATTAATAA-AATTTATATTATT
1 TATTATATTTTATAGAAATAATAT-TAATAAATTATTAATAAGAA-TAATATTATT
*
2049942 TATTA-ATTTTATAGAAATAATATTATTAAATTATTAATAATGAATAATATTATT
1 TATTATATTTTATAGAAATAATATTAATAAATTATTAATAA-GAATAATATTATT
2049996 TA-TATATTT
1 TATTATATTT
2050005 AATATTAATA
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
53 18 0.33
54 30 0.55
55 7 0.13
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (54 bp):
TATTATATTTTATAGAAATAATATTAATAAATTATTAATAAGAATAATATTATT
Found at i:2050014 original size:27 final size:27
Alignment explanation
Indices: 2049934--2050019 Score: 70
Period size: 27 Copynumber: 3.1 Consensus size: 27
2049924 AATAAAATTT
* *
2049934 ATATTATTTAT-TAATTTTATAGAAATA
1 ATATTATTTATAT-ATTTAATATAAATA
* *
2049961 ATATTA-TTAAAT-TATTAATAATGAATA
1 ATATTATTTATATAT-TTAAT-ATAAATA
2049988 ATATTATTTATATATTTAATATTAATATA
1 ATATTATTTATATATTTAATA-TAA-ATA
2050017 ATA
1 ATA
2050020 ACCTAATAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
25 1 0.02
26 7 0.15
27 19 0.41
28 12 0.26
29 7 0.15
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (27 bp):
ATATTATTTATATATTTAATATAAATA
Found at i:2050060 original size:23 final size:23
Alignment explanation
Indices: 2050034--2050078 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2050024 AATAATATTT
2050034 TAATAAAAATATTTAAAATATAC
1 TAATAAAAATATTTAAAATATAC
* * *
2050057 TAATTAATATTTTTAAAATATA
1 TAATAAAAATATTTAAAATATA
2050079 ATATAACATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
TAATAAAAATATTTAAAATATAC
Found at i:2050204 original size:18 final size:17
Alignment explanation
Indices: 2050174--2050211 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
2050164 TAATAAAATT
2050174 ATAAAAATAATATTTTA
1 ATAAAAATAATATTTTA
*
2050191 ATAATAAATTATATTTTA
1 ATAA-AAATAATATTTTA
2050209 ATA
1 ATA
2050212 TTTTAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATAAAAATAATATTTTA
Found at i:2050401 original size:13 final size:14
Alignment explanation
Indices: 2050372--2050398 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2050362 TGTAATTTAT
2050372 TTTACGGAAAAAAA
1 TTTACGGAAAAAAA
2050386 TTTACGGAAAAAA
1 TTTACGGAAAAAA
2050399 TTTTCAGTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.07, G:0.15, T:0.22
Consensus pattern (14 bp):
TTTACGGAAAAAAA
Found at i:2051855 original size:20 final size:20
Alignment explanation
Indices: 2051830--2051896 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
2051820 AATTCGTAAT
2051830 GCGAATAAGTAAATCGCAAC
1 GCGAATAAGTAAATCGCAAC
** * *
2051850 GCGAATTGGGAAATTCGCAAT
1 GCGAATAAGTAAA-TCGCAAC
2051871 GCGAATAAGTAAATCGCAAC
1 GCGAATAAGTAAATCGCAAC
2051891 GCGAAT
1 GCGAAT
2051897 TGGGAAAATC
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 22 0.58
21 16 0.42
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (20 bp):
GCGAATAAGTAAATCGCAAC
Found at i:2051865 original size:41 final size:41
Alignment explanation
Indices: 2051820--2051915 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
2051810 CGATTTTCCC
*
2051820 AATTCGTAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
2051861 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
2051902 AAATCGCAATGCGA
1 AATTCGCAATGCGA
2051916 TACTGACTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.40, C:0.17, G:0.24, T:0.20
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:2051869 original size:21 final size:20
Alignment explanation
Indices: 2051840--2051915 Score: 89
Period size: 21 Copynumber: 3.7 Consensus size: 20
2051830 GCGAATAAGT
2051840 AAATCGCAACGCGAATTGGG
1 AAATCGCAACGCGAATTGGG
* ** *
2051860 AAATTCGCAATGCGAATAAGT
1 AAA-TCGCAACGCGAATTGGG
2051881 AAATCGCAACGCGAATTGGG
1 AAATCGCAACGCGAATTGGG
*
2051901 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
2051916 TACTGACTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.17
Consensus pattern (20 bp):
AAATCGCAACGCGAATTGGG
Found at i:2051928 original size:41 final size:41
Alignment explanation
Indices: 2051842--2051976 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
2051832 GAATAAGTAA
* * *
2051842 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
2051883 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
2051924 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
2051965 TTCGCAACGCGA
1 ATCGCAACGCGA
2051977 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:2051929 original size:20 final size:20
Alignment explanation
Indices: 2051904--2051997 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
2051894 AATTGGGAAA
*
2051904 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
2051924 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
2051945 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
2051965 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
2051985 TTCGCAACGCGAT
1 ATCGCAACGCGAT
2051998 TTACTTAGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:2052565 original size:19 final size:19
Alignment explanation
Indices: 2052522--2052586 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
2052512 CGAGAATGAG
* *
2052522 AATCGCAACGCGGAAATGAC
1 AATCGCAACGC-GAAATAAA
*
2052542 TATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATAAA
**
2052561 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAATAAA
2052580 AATCGCA
1 AATCGCA
2052587 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
19 29 0.74
20 10 0.26
ACGTcount: A:0.45, C:0.26, G:0.18, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATAAA
Found at i:2052604 original size:19 final size:19
Alignment explanation
Indices: 2052582--2052784 Score: 210
Period size: 19 Copynumber: 11.1 Consensus size: 19
2052572 GAAACCAAAA
*
2052582 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2052601 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2052620 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
2052639 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
2052658 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
2052678 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
2052694 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
2052711 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
2052725 TCTCGTTGCGATAATCATT
1 TCGCGTTGCGATTTTCATT
*
2052744 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
2052764 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
2052784 T
1 T
2052785 TAACCAAAAG
Statistics
Matches: 156, Mismatches: 15, Indels: 26
0.79 0.08 0.13
Matches are distributed among these distances:
14 20 0.13
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 78 0.50
20 49 0.31
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2052701 original size:58 final size:57
Alignment explanation
Indices: 2052582--2052701 Score: 179
Period size: 58 Copynumber: 2.1 Consensus size: 57
2052572 GAAACCAAAA
* * * *
2052582 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATTTCGCGTTGCGATTTTCATTTCGCGTTGCGATTGTCATG
2052639 TCGCGTTGCGATTTTAATTTCGCGGTTGCGATTTTCATTTCGCGTTGCGATTGTC-TGG
1 TCGCGTTGCGATTTTAATTTCGC-GTTGCGATTTTCATTTCGCGTTGCGATTGTCAT-G
2052697 TCGCG
1 TCGCG
2052702 ATAGTCATTT
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
57 22 0.39
58 35 0.61
ACGTcount: A:0.11, C:0.21, G:0.24, T:0.44
Consensus pattern (57 bp):
TCGCGTTGCGATTTTAATTTCGCGTTGCGATTTTCATTTCGCGTTGCGATTGTCATG
Found at i:2052710 original size:33 final size:33
Alignment explanation
Indices: 2052673--2052760 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 33
2052663 GTTGCGATTT
* * *
2052673 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAA
*
2052706 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAA
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAA
2052739 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
2052761 ATTATCTCGT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 35 0.70
34 15 0.30
ACGTcount: A:0.12, C:0.25, G:0.24, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAA
Found at i:2054846 original size:42 final size:42
Alignment explanation
Indices: 2054786--2054908 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
2054776 GCCCGACTCG
* * *
2054786 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
2054828 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
2054870 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
2054909 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:2054866 original size:21 final size:21
Alignment explanation
Indices: 2054842--2054908 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2054832 TCATTCCTCG
2054842 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
2054863 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
2054884 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
2054905 AGAG
1 AGAG
2054909 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:2056286 original size:14 final size:14
Alignment explanation
Indices: 2056267--2056302 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2056257 ATTGTTTAAT
2056267 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
2056281 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
2056295 TGATTTGT
1 TGATTTGT
2056303 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:2056503 original size:19 final size:19
Alignment explanation
Indices: 2056481--2056600 Score: 80
Period size: 19 Copynumber: 6.7 Consensus size: 19
2056471 CGAAATTAAA
2056481 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
2056500 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
2056515 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
2056533 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
2056548 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
2056566 TTCGCATTGCGATTTTGTCGT
1 TTCGCGTTGCGA-TTT-TCAT
2056587 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
2056601 GGACATTAAG
Statistics
Matches: 75, Mismatches: 13, Indels: 24
0.67 0.12 0.21
Matches are distributed among these distances:
14 17 0.23
16 6 0.08
17 6 0.08
19 28 0.37
20 3 0.04
21 6 0.08
22 9 0.12
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.44
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:2056587 original size:33 final size:33
Alignment explanation
Indices: 2056485--2056579 Score: 181
Period size: 33 Copynumber: 2.9 Consensus size: 33
2056475 ATTAAATTCG
*
2056485 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
2056518 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
2056551 CGTTGCGATTTTCATTTCGCATTGCGATT
1 CGTTGCGATTTTCATTTCGCATTGCGATT
2056580 TTGTCGTTTC
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 61 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:2056600 original size:22 final size:20
Alignment explanation
Indices: 2056551--2056600 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 20
2056541 GCGATTCTCT
2056551 CGTTGCGA-TTTTCATTTCG
1 CGTTGCGATTTTTCATTTCG
* *
2056570 CATTGCGATTTTGTCGTTTCCG
1 CGTTGCGATTTT-TCATTT-CG
2056592 CGTTGCGAT
1 CGTTGCGAT
2056601 GGACATTAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 7 0.28
20 3 0.12
21 5 0.20
22 10 0.40
ACGTcount: A:0.10, C:0.22, G:0.24, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTTTTCATTTCG
Found at i:2058891 original size:12 final size:12
Alignment explanation
Indices: 2058874--2058898 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2058864 TCTTCGGGGA
2058874 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2058886 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2058898 C
1 C
2058899 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:2060396 original size:14 final size:14
Alignment explanation
Indices: 2060377--2060413 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2060367 CATCAATTAA
2060377 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
2060391 ACAAATCATCTTTT
1 ACAAATCAACATTT
2060405 ACAAATCAA
1 ACAAATCAA
2060414 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:2060982 original size:14 final size:14
Alignment explanation
Indices: 2060963--2060999 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2060953 CATCAATTAA
2060963 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
2060977 ACAAATCATCTTTT
1 ACAAATCAACATTT
2060991 ACAAATCAA
1 ACAAATCAA
2061000 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:2061466 original size:588 final size:589
Alignment explanation
Indices: 2060000--2061836 Score: 3556
Period size: 588 Copynumber: 3.1 Consensus size: 589
2059990 TTTAACAATT
2060000 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
2060065 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
66 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
2060130 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
131 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
* ** **
2060195 AATGCGAAAATGGTTATCACAACGAGAAAATCGCAATGCGAAATTTCATTTCGCATTGCGATTTT
196 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAA-TGAAAATCGCATTGCGATTTT
*
2060260 CTCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAA
260 CTCGTTGCGATAACCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAA
2060325 ATCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATT
325 ATCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATT
2060390 TACAAATCATCTTTTACAAATCAATTAAACAATC--AAAA-AATAATAATTCTTATTTCTTCATC
390 TACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATC
2060452 AATTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAG
455 AATTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAG
2060517 GATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAAC
520 GATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAAC
2060582 AGCAA
585 AGCAA
2060587 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
2060652 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
66 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
2060717 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
131 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
2060782 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
196 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
*
2060847 TCGTTGCGATAACCATTTCGCGTTACGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
261 TCGTTGCGATAACCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
2060912 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
326 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
2060977 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCA
391 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCA
2061042 ATTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGG
456 ATTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGG
2061107 ATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACA
521 ATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACA
2061172 GCAA
586 GCAA
2061176 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAAC-AAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
2061240 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
66 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
2061305 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
131 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
*
2061370 AACGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
196 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
2061435 TCGTTGCGATAACCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
261 TCGTTGCGATAACCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
2061500 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
326 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
2061565 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCA
391 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCA
2061630 ATTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGG
456 ATTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGG
2061695 ATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACA
521 ATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACA
*
2061760 ACAA
586 GCAA
2061764 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
2061829 CTTGCATT
66 CTTGCATT
2061837 TGACTTACCA
Statistics
Matches: 1236, Mismatches: 10, Indels: 6
0.99 0.01 0.00
Matches are distributed among these distances:
586 179 0.14
587 237 0.19
588 589 0.48
589 231 0.19
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (589 bp):
ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
TCGTTGCGATAACCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCA
ATTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGG
ATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACA
GCAA
Found at i:2061570 original size:14 final size:14
Alignment explanation
Indices: 2061551--2061587 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2061541 CATCAATTAA
2061551 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
2061565 ACAAATCATCTTTT
1 ACAAATCAACATTT
2061579 ACAAATCAA
1 ACAAATCAA
2061588 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:2063490 original size:20 final size:19
Alignment explanation
Indices: 2063454--2063575 Score: 112
Period size: 19 Copynumber: 6.7 Consensus size: 19
2063444 CGAAACTTAA
*
2063454 AATCGCAACGTGAAATGAC
1 AATCGCAACGCGAAATGAC
* *
2063473 TATCGCAACGCGGAAATGGC
1 AATCGCAACGC-GAAATGAC
* * *
2063493 TATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAC
2063512 AATCGCAACGCGAAATGA-
1 AATCGCAACGCGAAATGAC
*
2063530 AATCGCAA--CGACA--A-
1 AATCGCAACGCGAAATGAC
*
2063544 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAC
*
2063563 AATCGCAATGCGA
1 AATCGCAACGCGA
2063576 TTTTCATTTC
Statistics
Matches: 86, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
14 9 0.10
16 8 0.09
18 9 0.10
19 43 0.50
20 17 0.20
ACGTcount: A:0.42, C:0.22, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAC
Found at i:2063498 original size:39 final size:38
Alignment explanation
Indices: 2063455--2063528 Score: 103
Period size: 39 Copynumber: 1.9 Consensus size: 38
2063445 GAAACTTAAA
* **
2063455 ATCGCAACGTGAAATGACTATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGAAATGAAAATCGCAACGC-GAAATGGCT
*
2063494 ATCGCAATGCGAAATGAAAATCGCAACGCGAAATG
1 ATCGCAACGCGAAATGAAAATCGCAACGCGAAATG
2063529 AAATCGCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
38 6 0.19
39 25 0.81
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.16
Consensus pattern (38 bp):
ATCGCAACGCGAAATGAAAATCGCAACGCGAAATGGCT
Found at i:2063606 original size:14 final size:14
Alignment explanation
Indices: 2063587--2063644 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
2063577 TTTCATTTCG
2063587 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
2063601 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
*
2063617 CGCGTTGCGATGTTGT
1 --CGTTGCGATTTTGT
2063633 CGTTGCGATTTT
1 CGTTGCGATTTT
2063645 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.61
16 4 0.11
18 10 0.28
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:2063651 original size:33 final size:33
Alignment explanation
Indices: 2063571--2063660 Score: 155
Period size: 32 Copynumber: 2.8 Consensus size: 33
2063561 AAAATCGCAA
*
2063571 TGCGATTTTCATTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTCATTTCGCGTTGCGATGTTGTCGT
2063604 TGCGA-TTTCATTTCGCGTTGCGATGTTGTCGT
1 TGCGATTTTCATTTCGCGTTGCGATGTTGTCGT
*
2063636 TGCGATTTTCATTTCGCATTGCGAT
1 TGCGATTTTCATTTCGCGTTGCGAT
2063661 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 31 0.57
33 23 0.43
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATGTTGTCGT
Found at i:2063679 original size:20 final size:19
Alignment explanation
Indices: 2063645--2063699 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
2063635 TTGCGATTTT
*
2063645 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
2063664 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
2063684 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
2063700 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:2064198 original size:18 final size:18
Alignment explanation
Indices: 2064172--2064216 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
2064162 GTCGATCAGA
*
2064172 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
2064190 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
2064208 TGATGGCTC
1 TGATGGCTC
2064217 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:2065561 original size:20 final size:20
Alignment explanation
Indices: 2065536--2065573 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2065526 AATAGTTTCT
2065536 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
2065556 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
2065574 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:2065862 original size:22 final size:22
Alignment explanation
Indices: 2065837--2065880 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2065827 GATTTAGATA
2065837 GACGGATTTCGCCAGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
* *
2065859 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
2065881 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCAGAGATGGG
Found at i:2066093 original size:20 final size:20
Alignment explanation
Indices: 2066068--2066161 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
2066058 GATTATGTAT
2066068 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
2066088 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
2066108 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
2066129 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
2066149 TATCGCATTGCGA
1 TATCGCGTTGCGA
2066162 TTTTCTCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:2066133 original size:41 final size:42
Alignment explanation
Indices: 2066088--2066223 Score: 118
Period size: 41 Copynumber: 3.3 Consensus size: 42
2066078 CGAAAGTCAG
* * * *
2066088 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTAT
1 TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
* * *
2066129 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCTCAA
1 TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
** ** * *
2066171 T-TCGCGTTGCG-ATTTACTTATTCGCATTGCGAATTTCCCAA
1 TATCGCGTTGCGAAAGTAAGTA-TCGCATTGCGATTTTCTCAA
2066212 T-TCGCGTTGCGA
1 TATCGCGTTGCGA
2066224 TTTACTTATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
40 3 0.04
41 70 0.92
42 3 0.04
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (42 bp):
TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
Found at i:2066162 original size:20 final size:20
Alignment explanation
Indices: 2066048--2066162 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
2066038 CGCTTTGAAA
*
2066048 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
2066069 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
2066089 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
2066109 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
2066130 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
2066150 ATCGCATTGCGAT
1 ATCGCATTGCGAT
2066163 TTTCTCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:2066195 original size:20 final size:20
Alignment explanation
Indices: 2066151--2066243 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
2066141 ATAGTCAGTA
*
2066151 TCGCATTGCGATTTTCTCAAT
1 TCGCATTGCGATTTACT-AAT
* *
2066172 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
* *
2066192 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTAAT
* *
2066213 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
2066233 TCGCATTGCGA
1 TCGCATTGCGA
2066244 ATTGGGAAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.47
21 31 0.53
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTAAT
Found at i:2066224 original size:41 final size:41
Alignment explanation
Indices: 2066151--2066246 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
2066141 ATAGTCAGTA
* *
2066151 TCGCATTGCGATTTTCTCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
2066192 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
2066233 TCGCATTGCGAATT
1 TCGCATTGCGAATT
2066247 GGGAAAATCG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:2070023 original size:15 final size:15
Alignment explanation
Indices: 2070003--2070039 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
2069993 TAGGGCATAT
2070003 CACAACAGGCATGGA
1 CACAACAGGCATGGA
2070018 CACAACAGGCATGGA
1 CACAACAGGCATGGA
2070033 CACAACA
1 CACAACA
2070040 TCATTTGCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.43, C:0.30, G:0.22, T:0.05
Consensus pattern (15 bp):
CACAACAGGCATGGA
Found at i:2083655 original size:41 final size:41
Alignment explanation
Indices: 2083610--2083749 Score: 174
Period size: 42 Copynumber: 3.4 Consensus size: 41
2083600 GAGTAGACAT
* *
2083610 TTAGCGGTGTTT-TATCCAAAATGCCGTAATAGAGTGTTAAA
1 TTAGCGGCGTTTATA-CCAAAATGCCGTAATAGAGTGGTAAA
* *
2083651 TTAGCGGCGTTTATACCAAAAACGCCGTAATATAGTGGTAAA
1 TTAGCGGCGTTTATACC-AAAATGCCGTAATAGAGTGGTAAA
* *
2083693 TTAGCGGCGTTTATACCACAAATACCGTAATAGAATGGTAAA
1 TTAGCGGCGTTTATACCA-AAATGCCGTAATAGAGTGGTAAA
* *
2083735 TTAGAGGCATTTATA
1 TTAGCGGCGTTTATA
2083750 TGTAAAACGC
Statistics
Matches: 86, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
41 14 0.16
42 72 0.84
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (41 bp):
TTAGCGGCGTTTATACCAAAATGCCGTAATAGAGTGGTAAA
Found at i:2083726 original size:84 final size:83
Alignment explanation
Indices: 2083610--2083767 Score: 201
Period size: 84 Copynumber: 1.9 Consensus size: 83
2083600 GAGTAGACAT
* * * * * *
2083610 TTAGCGGTGTTTTATCCAAAATGCCGTAATAGAGTGTTAAATTAGCGGCGTTTATACCAAAAACG
1 TTAGCGGCGTTTTATCCAAAATACCGTAATAGAATGGTAAATTAGAGGCATTTATACCAAAAACG
*
2083675 CCGTAATATAGTGGTAAA
66 CCGCAATATAGTGGTAAA
***
2083693 TTAGCGGCG-TTTATACCACAAATACCGTAATAGAATGGTAAATTAGAGGCATTTATATGTAAAA
1 TTAGCGGCGTTTTAT-CCA-AAATACCGTAATAGAATGGTAAATTAGAGGCATTTATACCAAAAA
2083757 CGCCGCAATAT
64 CGCCGCAATAT
2083768 GGTTGTTTAA
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
82 5 0.08
83 11 0.17
84 47 0.75
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.29
Consensus pattern (83 bp):
TTAGCGGCGTTTTATCCAAAATACCGTAATAGAATGGTAAATTAGAGGCATTTATACCAAAAACG
CCGCAATATAGTGGTAAA
Found at i:2086655 original size:19 final size:22
Alignment explanation
Indices: 2086609--2086659 Score: 63
Period size: 19 Copynumber: 2.5 Consensus size: 22
2086599 CTTAATCTCT
*
2086609 TATATTCATATATATATATGCA
1 TATATTCATATATATATATACA
*
2086631 TTTATTCAT-TATATA-A-ACA
1 TATATTCATATATATATATACA
2086650 TATATTCATA
1 TATATTCATA
2086660 CAAGTCATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 10 0.40
20 1 0.04
21 6 0.24
22 8 0.32
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.47
Consensus pattern (22 bp):
TATATTCATATATATATATACA
Found at i:2094138 original size:24 final size:24
Alignment explanation
Indices: 2094108--2094157 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
2094098 TGGTGGTTGA
2094108 TTTAATGGT-TATTTGAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
2094132 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
2094156 TT
1 TT
2094158 GGTTCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.26, C:0.02, G:0.12, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:2094581 original size:16 final size:16
Alignment explanation
Indices: 2094560--2094592 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2094550 CACGTGAGGA
2094560 TTATTTTC-TTTTCATT
1 TTATTTTCATTTT-ATT
2094576 TTATTTTCATTTTATT
1 TTATTTTCATTTTATT
2094592 T
1 T
2094593 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCATTTTATT
Found at i:2094582 original size:11 final size:11
Alignment explanation
Indices: 2094562--2094592 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
2094552 CGTGAGGATT
*
2094562 ATTTTCTTTTC
1 ATTTTATTTTC
2094573 ATTTTATTTTC
1 ATTTTATTTTC
2094584 ATTTTATTT
1 ATTTTATTT
2094593 ACTGTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.74
Consensus pattern (11 bp):
ATTTTATTTTC
Found at i:2100960 original size:20 final size:21
Alignment explanation
Indices: 2100922--2100965 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2100912 TAACTTTTTC
*
2100922 TTTTTTCTTTCTTTATTAA-T
1 TTTTTTCTTTCATTATTAACT
2100942 TTTTTCTCTTTCATT-TTAACT
1 TTTTT-TCTTTCATTATTAACT
2100963 TTT
1 TTT
2100966 ACTTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTTTTCTTTCATTATTAACT
Found at i:2100965 original size:21 final size:20
Alignment explanation
Indices: 2100922--2100965 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2100912 TAACTTTTTC
*
2100922 TTTTTTCTTTCTTTATTAAT
1 TTTTTTCTTTCATTATTAAT
*
2100942 TTTTTCTCTTTCATT-TTAAC
1 TTTTT-TCTTTCATTATTAAT
2100962 TTTT
1 TTTT
2100966 ACTTTTTCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTTTTCTTTCATTATTAAT
Found at i:2104798 original size:16 final size:15
Alignment explanation
Indices: 2104777--2104814 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
2104767 CACGTGAGGA
2104777 TTATTTTC-TTTTCATT
1 TTATTTTCATTTT-A-T
2104793 TTATTTTCATTTTAT
1 TTATTTTCATTTTAT
2104808 TTATTTT
1 TTATTTT
2104815 TTTACCATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.38
16 9 0.43
17 4 0.19
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (15 bp):
TTATTTTCATTTTAT
Found at i:2104799 original size:11 final size:11
Alignment explanation
Indices: 2104779--2104809 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
2104769 CGTGAGGATT
*
2104779 ATTTTCTTTTC
1 ATTTTATTTTC
2104790 ATTTTATTTTC
1 ATTTTATTTTC
2104801 ATTTTATTT
1 ATTTTATTT
2104810 ATTTTTTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.74
Consensus pattern (11 bp):
ATTTTATTTTC
Found at i:2107943 original size:44 final size:44
Alignment explanation
Indices: 2107892--2107984 Score: 150
Period size: 44 Copynumber: 2.1 Consensus size: 44
2107882 TAAAAAAAAT
*
2107892 ACCGCAATATACCGTACATTTAGCAACGTTTATATACTAGAAAC
1 ACCGCAATATACCATACATTTAGCAACGTTTATATACTAGAAAC
* * *
2107936 GCCGCAATATACCATACATTTAGCATCGTTTTTATACTAGAAAC
1 ACCGCAATATACCATACATTTAGCAACGTTTATATACTAGAAAC
2107980 ACCGC
1 ACCGC
2107985 TAATTCTCAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.35, C:0.25, G:0.12, T:0.28
Consensus pattern (44 bp):
ACCGCAATATACCATACATTTAGCAACGTTTATATACTAGAAAC
Found at i:2108054 original size:43 final size:42
Alignment explanation
Indices: 2108007--2108142 Score: 137
Period size: 43 Copynumber: 3.2 Consensus size: 42
2107997 CTTATTGTGT
* *
2108007 CGTTTTCGATACAAACGCCGCTAAATCTAAAAACCTACTACGC
1 CGTTTTCGATA-AAACGCCGCTAAATCTCAAAACCTACTACGG
* ** * * *
2108050 CGTTTGTGGGGAAAACGTCGCAAAATATCAAAACCTACTACGG
1 CGTTT-TCGATAAAACGCCGCTAAATCTCAAAACCTACTACGG
** * *
2108093 CGTTTTTAAGTAAAACGCCGCTAAATCTCAACACCTACTGCGG
1 CGTTTTCGA-TAAAACGCCGCTAAATCTCAAAACCTACTACGG
2108136 CGTTTTC
1 CGTTTTC
2108143 CCTAAAAATA
Statistics
Matches: 73, Mismatches: 18, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
42 1 0.01
43 69 0.95
44 3 0.04
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (42 bp):
CGTTTTCGATAAAACGCCGCTAAATCTCAAAACCTACTACGG
Found at i:2108211 original size:43 final size:43
Alignment explanation
Indices: 2108061--2108226 Score: 138
Period size: 43 Copynumber: 3.9 Consensus size: 43
2108051 GTTTGTGGGG
* * * * ***
2108061 AAAACGTCGCAAAATATCAAAACCTACTACGGCGTTTTTAAGT-
1 AAAACGCCGCTAAATATCAACACCTACTGCGGCG-TTTTCCCTA
*
2108104 AAAACGCCGCTAAATCTCAACACCTACTGCGGCGTTTTCCCTA
1 AAAACGCCGCTAAATATCAACACCTACTGCGGCGTTTTCCCTA
*** * * * *
2108147 AAAATATCGTTAAACATCAACACCTATTGCGGCGTTTT-TCTGA
1 AAAACGCCGCTAAATATCAACACCTACTGCGGCGTTTTCCCT-A
* * *
2108190 CAAACGCCGCTAAATAACAACACCTAGTGCGGCGTTT
1 AAAACGCCGCTAAATATCAACACCTACTGCGGCGTTT
2108227 GTTATGTTGT
Statistics
Matches: 97, Mismatches: 24, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
42 7 0.07
43 90 0.93
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (43 bp):
AAAACGCCGCTAAATATCAACACCTACTGCGGCGTTTTCCCTA
Found at i:2112419 original size:29 final size:29
Alignment explanation
Indices: 2112383--2112479 Score: 95
Period size: 29 Copynumber: 3.3 Consensus size: 29
2112373 ATGATCACCC
*
2112383 AACTTTTAAAACTTACATTTTGGTCACTG
1 AACTTTTAAAACTTGCATTTTGGTCACTG
** **
2112412 AACTTTTAGGATGCTTGCATTTTGGTCACCC
1 AACTTTTA--AAACTTGCATTTTGGTCACTG
* * * *
2112443 AACTTTTAAAACTTGCAATATGGTTATTG
1 AACTTTTAAAACTTGCATTTTGGTCACTG
2112472 AACTTTTA
1 AACTTTTA
2112480 GTTCGTTTTC
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
29 29 0.55
31 24 0.45
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.41
Consensus pattern (29 bp):
AACTTTTAAAACTTGCATTTTGGTCACTG
Found at i:2114039 original size:25 final size:25
Alignment explanation
Indices: 2114011--2114071 Score: 122
Period size: 25 Copynumber: 2.4 Consensus size: 25
2114001 AAATCGACCC
2114011 ATAAATCTCATAACTATTTTCAATA
1 ATAAATCTCATAACTATTTTCAATA
2114036 ATAAATCTCATAACTATTTTCAATA
1 ATAAATCTCATAACTATTTTCAATA
2114061 ATAAATCTCAT
1 ATAAATCTCAT
2114072 TTTTGCTCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.39
Consensus pattern (25 bp):
ATAAATCTCATAACTATTTTCAATA
Found at i:2115417 original size:28 final size:28
Alignment explanation
Indices: 2115386--2115440 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
2115376 AATTCACGAT
2115386 TATATAAATGCAACTTGAAATTAACAAG
1 TATATAAATGCAACTTGAAATTAACAAG
2115414 TATATAAATGCAACTTGAAATTAACAA
1 TATATAAATGCAACTTGAAATTAACAA
2115441 AATATGAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (28 bp):
TATATAAATGCAACTTGAAATTAACAAG
Found at i:2122717 original size:20 final size:20
Alignment explanation
Indices: 2122666--2122719 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
2122656 TTGCAACCTT
* *
2122666 GATGCATGGATACATGGCAG
1 GATGCATCGATGCATGGCAG
*
2122686 GATGCATCGATGCATGGTAG
1 GATGCATCGATGCATGGCAG
2122706 GATGCATCGATGCA
1 GATGCATCGATGCA
2122720 CTAAGTGCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.28, C:0.17, G:0.33, T:0.22
Consensus pattern (20 bp):
GATGCATCGATGCATGGCAG
Found at i:2122771 original size:20 final size:19
Alignment explanation
Indices: 2122684--2122775 Score: 68
Period size: 20 Copynumber: 4.9 Consensus size: 19
2122674 GATACATGGC
*
2122684 AGGATGCATCGATGCATGG
1 AGGATGCATCGATGCATTG
*
2122703 TAGGATGCATCGATGCACT-
1 -AGGATGCATCGATGCATTG
* *
2122722 AAG-TGCATTCGATG-TTTG
1 AGGATGCA-TCGATGCATTG
*
2122740 A-G-TGCATGGATGCATTG
1 AGGATGCATCGATGCATTG
*
2122757 CATGATGCATCGATGCATT
1 -AGGATGCATCGATGCATT
2122776 AGTGCAGGTG
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
16 5 0.09
17 13 0.22
18 10 0.17
19 1 0.02
20 29 0.50
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.29
Consensus pattern (19 bp):
AGGATGCATCGATGCATTG
Found at i:2122810 original size:21 final size:20
Alignment explanation
Indices: 2122742--2122837 Score: 95
Period size: 21 Copynumber: 4.6 Consensus size: 20
2122732 GATGTTTGAG
* *
2122742 TGCATGGATGCATTGCATGA
1 TGCATGGATGCACTGCAGGA
* *
2122762 TGCATCGATGCATTAGTGCAGG-
1 TGCATGGATGC---ACTGCAGGA
2122784 TGCATGGATGCACTGCAGAGA
1 TGCATGGATGCACTGCAG-GA
2122805 TGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTGCA-GGA
*
2122826 TGCAGGGATGCA
1 TGCATGGATGCA
2122838 TGGATGCACT
Statistics
Matches: 64, Mismatches: 6, Indels: 11
0.79 0.07 0.14
Matches are distributed among these distances:
19 6 0.09
20 11 0.17
21 30 0.47
22 11 0.17
23 6 0.09
ACGTcount: A:0.25, C:0.18, G:0.34, T:0.23
Consensus pattern (20 bp):
TGCATGGATGCACTGCAGGA
Found at i:2122948 original size:29 final size:29
Alignment explanation
Indices: 2122927--2122983 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
2122917 AAACTTTGAA
2122927 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
*
2122956 TAAATTCAATTCAAGTCCAAAAATATTT
1 TAAATTCAATTCAAGTCCAAAAACATTT
2122984 TGCCTTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.46, C:0.14, G:0.05, T:0.35
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:2122974 original size:30 final size:29
Alignment explanation
Indices: 2122927--2122985 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 29
2122917 AAACTTTGAA
2122927 TAAATTCAATTAAGTCCAAAAACATTTTG
1 TAAATTCAATTAAGTCCAAAAACATTTTG
*
2122956 TAAATTCAATTCAAGTCCAAAAATATTTTG
1 TAAATTCAATT-AAGTCCAAAAACATTTTG
2122986 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 11 0.39
30 17 0.61
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.36
Consensus pattern (29 bp):
TAAATTCAATTAAGTCCAAAAACATTTTG
Found at i:2125260 original size:16 final size:16
Alignment explanation
Indices: 2125239--2125269 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2125229 ACGTTGTGTG
2125239 ATATGTATATATATAT
1 ATATGTATATATATAT
*
2125255 ATATGTATATGTATA
1 ATATGTATATATATA
2125270 CCTTACATTA
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:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (16 bp):
ATATGTATATATATAT
Found at i:2128900 original size:64 final size:64
Alignment explanation
Indices: 2128832--2128954 Score: 176
Period size: 64 Copynumber: 1.9 Consensus size: 64
2128822 ATTGTTCAAG
* * *
2128832 GTGTATCGATGCACATGAAATGTATCGATGCACTC-ATTTAAAATAAAAACATCGAATGTCATCA
1 GTGTATCGATGCACAAGAAATGCATCGATGCACCCGA-TTAAAATAAAAACATCGAATGTCATCA
* * *
2128896 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCGATTAAAATACAAACATCGAATGT
1 GTGTATCGATGCACAAGAAATGCATCGATGCACCCGATTAAAATAAAAACATCGAATGT
2128955 GATTTATGTA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
64 51 0.98
65 1 0.02
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (64 bp):
GTGTATCGATGCACAAGAAATGCATCGATGCACCCGATTAAAATAAAAACATCGAATGTCATCA
Found at i:2128972 original size:64 final size:65
Alignment explanation
Indices: 2128855--2128995 Score: 180
Period size: 64 Copynumber: 2.2 Consensus size: 65
2128845 CATGAAATGT
* * *
2128855 ATCGATGCACTC-ATTTAAAATAAAAACATCGAATGTCATCAGTGTATCGATGCACAAGTAGTGC
1 ATCGATGCACCCGATTTAAAATAAAAACATCGAATGTCATCAGTGTACCAATGCACAAGTAGTGC
* * * * *
2128919 ATCGATGCACCCGA-TTAAAATACAAACATCGAATGTGATTTA-TGTACCAATGCATAGGTAGTG
1 ATCGATGCACCCGATTTAAAATAAAAACATCGAATGTCA-TCAGTGTACCAATGCACAAGTAGTG
2128982 C
65 C
2128983 ATCGATGCACCCG
1 ATCGATGCACCCG
2128996 TCAAGGGATG
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
64 64 0.96
65 3 0.04
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (65 bp):
ATCGATGCACCCGATTTAAAATAAAAACATCGAATGTCATCAGTGTACCAATGCACAAGTAGTGC
Found at i:2136039 original size:3 final size:3
Alignment explanation
Indices: 2136031--2136085 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
2136021 GCATCTCTAA
2136031 AAT AAT 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
2136079 AAT AAT A
1 AAT AAT A
2136086 GTAGTAGCAG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2136590 original size:15 final size:15
Alignment explanation
Indices: 2136572--2136647 Score: 77
Period size: 15 Copynumber: 5.3 Consensus size: 15
2136562 GTGAAATTCT
2136572 AATTATTTAAATAAA
1 AATTATTTAAATAAA
*
2136587 AATTATTTATATAAA
1 AATTATTTAAATAAA
* **
2136602 AATTA-ATCGAT-AA
1 AATTATTTAAATAAA
*
2136615 TA-TATTTAAATAAA
1 AATTATTTAAATAAA
*
2136629 AATTATTTATATAAA
1 AATTATTTAAATAAA
2136644 AATT
1 AATT
2136648 CATCGATAAT
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
12 2 0.04
13 6 0.12
14 6 0.12
15 34 0.71
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (15 bp):
AATTATTTAAATAAA
Found at i:2136601 original size:19 final size:19
Alignment explanation
Indices: 2136574--2136643 Score: 52
Period size: 19 Copynumber: 3.5 Consensus size: 19
2136564 GAAATTCTAA
*
2136574 TTATTTAAATAAAAATTAT
1 TTATATAAATAAAAATTAT
*
2136593 TTATATAAA-AATTAATCGATAAT
1 TTATATAAATAA--AA---ATTAT
* *
2136616 ATATTTAAATAAAAATTAT
1 TTATATAAATAAAAATTAT
2136635 TTATATAAA
1 TTATATAAA
2136644 AATTCATCGA
Statistics
Matches: 38, Mismatches: 7, Indels: 12
0.67 0.12 0.21
Matches are distributed among these distances:
18 2 0.05
19 19 0.50
20 2 0.05
22 2 0.05
23 11 0.29
24 2 0.05
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (19 bp):
TTATATAAATAAAAATTAT
Found at i:2136604 original size:21 final size:21
Alignment explanation
Indices: 2136580--2136646 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
2136570 CTAATTATTT
2136580 AAATAAAAATTATTTATATAA
1 AAATAAAAATTATTTATATAA
* * * **
2136601 AAAT--TAATCGATAATATATTT
1 AAATAAAAAT-TAT-TTATATAA
2136622 AAATAAAAATTATTTATATAA
1 AAATAAAAATTATTTATATAA
2136643 AAAT
1 AAAT
2136647 TCATCGATAA
Statistics
Matches: 32, Mismatches: 10, Indels: 8
0.64 0.20 0.16
Matches are distributed among these distances:
19 3 0.09
20 2 0.06
21 22 0.69
22 2 0.06
23 3 0.09
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (21 bp):
AAATAAAAATTATTTATATAA
Found at i:2136622 original size:42 final size:42
Alignment explanation
Indices: 2136571--2136662 Score: 168
Period size: 42 Copynumber: 2.2 Consensus size: 42
2136561 AGTGAAATTC
2136571 TAAT-TATTTAAATAAAAATTATTTATATAAAAATTAATCGA
1 TAATATATTTAAATAAAAATTATTTATATAAAAATTAATCGA
*
2136612 TAATATATTTAAATAAAAATTATTTATATAAAAATTCATCGA
1 TAATATATTTAAATAAAAATTATTTATATAAAAATTAATCGA
2136654 TAATATATT
1 TAATATATT
2136663 ATTTTATTAT
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 4 0.08
42 45 0.92
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.42
Consensus pattern (42 bp):
TAATATATTTAAATAAAAATTATTTATATAAAAATTAATCGA
Found at i:2136690 original size:20 final size:21
Alignment explanation
Indices: 2136655--2136694 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
2136645 ATTCATCGAT
*
2136655 AATATATTATTTTATTATTTA
1 AATATATTATTGTATTATTTA
2136676 AATATA-TATTGTATTATTT
1 AATATATTATTGTATTATTT
2136695 TAATTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (21 bp):
AATATATTATTGTATTATTTA
Found at i:2136744 original size:37 final size:36
Alignment explanation
Indices: 2136701--2136784 Score: 87
Period size: 38 Copynumber: 2.3 Consensus size: 36
2136691 ATTTTAATTT
** *
2136701 TAATTAATATTAAATTTTACATAATTTATTTAAAAA
1 TAATTAATATTAAATTCAACATAATTTATATAAAAA
* * *
2136737 TATATTAAAATTTTACTTCAACATAATTTATATAAAAA
1 TA-ATTAATA-TTAAATTCAACATAATTTATATAAAAA
*
2136775 TAATTTATAT
1 TAATTAATAT
2136785 AAAAATATAT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
36 3 0.08
37 11 0.29
38 24 0.63
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (36 bp):
TAATTAATATTAAATTCAACATAATTTATATAAAAA
Found at i:2136777 original size:15 final size:15
Alignment explanation
Indices: 2136759--2136791 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
2136749 TTACTTCAAC
2136759 ATAATTTATATAAAA
1 ATAATTTATATAAAA
2136774 ATAATTTATATAAAA
1 ATAATTTATATAAAA
2136789 ATA
1 ATA
2136792 TATCATGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
ATAATTTATATAAAA
Found at i:2137623 original size:3 final size:3
Alignment explanation
Indices: 2137617--2137651 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
2137607 ATCATCACCA
* *
2137617 TCC TCC TCC TCC TCC TCC TCC TCA TCC TCG TCC TC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
2137652 TTTTGCCTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.03, C:0.60, G:0.03, T:0.34
Consensus pattern (3 bp):
TCC
Found at i:2140048 original size:2 final size:2
Alignment explanation
Indices: 2140041--2140068 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2140031 GACTATCTTT
2140041 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
2140069 AACTATTTTC
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:2140674 original size:16 final size:18
Alignment explanation
Indices: 2140638--2140677 Score: 73
Period size: 17 Copynumber: 2.3 Consensus size: 18
2140628 CGATATAATC
2140638 TTTATGTGATTAACTCTT
1 TTTATGTGATTAACTCTT
2140656 TTTATGT-ATTAACTCTT
1 TTTATGTGATTAACTCTT
2140673 TTTAT
1 TTTAT
2140678 CCTTTATATC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.23, C:0.10, G:0.07, T:0.60
Consensus pattern (18 bp):
TTTATGTGATTAACTCTT
Found at i:2147785 original size:26 final size:26
Alignment explanation
Indices: 2147754--2148030 Score: 168
Period size: 26 Copynumber: 11.0 Consensus size: 26
2147744 ACGCCTTAAT
*
2147754 GCATCCTTTCATTCATTTTAATTATG
1 GCATCCTTTCATGCATTTTAATTATG
* *
2147780 GCATCCTTCCATGC--CTT-A--AT-
1 GCATCCTTTCATGCATTTTAATTATG
2147800 GCATCCTTTCATGCATTTTAATTATG
1 GCATCCTTTCATGCATTTTAATTATG
2147826 GCATCCTTTCATGCATTTTAATTATG
1 GCATCCTTTCATGCATTTTAATTATG
* * *
2147852 GTATCCTTTCATGC--CTTAATGCACAT-
1 GCATCCTTTCATGCATTTTAAT---TATG
* * *
2147878 GCAT-TTTAATTATGGCATCCTTTCATGCCTTAAT-
1 GCATCCTT--TCAT-GCAT--TTT-A---ATT-ATG
2147912 GCATCCTTTCATGCATTTTAATTATG
1 GCATCCTTTCATGCATTTTAATTATG
* *
2147938 ACATCCTTTCATGC--CTT-A--AT-
1 GCATCCTTTCATGCATTTTAATTATG
2147958 GCATCCTTTCATGCATTTTAATTATG
1 GCATCCTTTCATGCATTTTAATTATG
2147984 GCATCCTTTCATGC--TTT-A--AT-
1 GCATCCTTTCATGCATTTTAATTATG
*
2148004 CCATCCTTTCATGCATTTTAATTATG
1 GCATCCTTTCATGCATTTTAATTATG
2148030 G
1 G
2148031 ATTCGATTTA
Statistics
Matches: 193, Mismatches: 23, Indels: 70
0.67 0.08 0.24
Matches are distributed among these distances:
20 39 0.20
21 6 0.03
22 7 0.04
23 6 0.03
24 12 0.06
25 10 0.05
26 83 0.43
27 5 0.03
28 2 0.01
29 1 0.01
30 3 0.02
32 6 0.03
33 4 0.02
34 6 0.03
35 2 0.01
36 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.44
Consensus pattern (26 bp):
GCATCCTTTCATGCATTTTAATTATG
Found at i:2147839 original size:46 final size:46
Alignment explanation
Indices: 2147710--2147839 Score: 199
Period size: 46 Copynumber: 2.8 Consensus size: 46
2147700 CGTATTAGCA
* * *
2147710 ATCCATTT-ATGCATTTAAATTATGGCATCATTTCACGCCTTAATGC
1 ATCC-TTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGC
* *
2147756 ATCCTTTCATTCATTTTAATTATGGCATCCTTCCATGCCTTAATGC
1 ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGC
2147802 ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGC
1 ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGC
2147840 ATTTTAATTA
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
45 3 0.04
46 73 0.96
ACGTcount: A:0.24, C:0.24, G:0.10, T:0.42
Consensus pattern (46 bp):
ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGC
Found at i:2147917 original size:20 final size:20
Alignment explanation
Indices: 2147892--2148017 Score: 117
Period size: 20 Copynumber: 5.7 Consensus size: 20
2147882 TTTAATTATG
*
2147892 GCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCTTTAAT
2147912 GCATCCTTTCATGCATTTTAATTAT
1 GCATCCTTTCATGC--TTT-A--AT
*
2147937 GACATCCTTTCATGCCTTAAT
1 G-CATCCTTTCATGCTTTAAT
2147958 GCATCCTTTCATGCATTTTAATTAT
1 GCATCCTTTCATGC--TTT-A--AT
2147983 GGCATCCTTTCATGCTTTAAT
1 -GCATCCTTTCATGCTTTAAT
*
2148004 CCATCCTTTCATGC
1 GCATCCTTTCATGC
2148018 ATTTTAATTA
Statistics
Matches: 90, Mismatches: 4, Indels: 24
0.76 0.03 0.20
Matches are distributed among these distances:
20 40 0.44
21 5 0.06
22 4 0.04
23 4 0.04
24 5 0.06
25 5 0.06
26 27 0.30
ACGTcount: A:0.21, C:0.26, G:0.10, T:0.43
Consensus pattern (20 bp):
GCATCCTTTCATGCTTTAAT
Found at i:2147943 original size:46 final size:46
Alignment explanation
Indices: 2147826--2148030 Score: 332
Period size: 46 Copynumber: 4.6 Consensus size: 46
2147816 TTTAATTATG
*
2147826 GCATCCTTTCATGCATTTTAATTATGGTATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAAT
2147872 GCA------CATGCATTTTAATTATGGCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAAT
*
2147912 GCATCCTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAAT
*
2147958 GCATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCTTTAAT
1 GCATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAAT
*
2148004 CCATCCTTTCATGCATTTTAATTATGG
1 GCATCCTTTCATGCATTTTAATTATGG
2148031 ATTCGATTTA
Statistics
Matches: 148, Mismatches: 5, Indels: 12
0.90 0.03 0.07
Matches are distributed among these distances:
40 39 0.26
46 109 0.74
ACGTcount: A:0.23, C:0.22, G:0.11, T:0.44
Consensus pattern (46 bp):
GCATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAAT
Found at i:2148454 original size:20 final size:20
Alignment explanation
Indices: 2148417--2148470 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
2148407 CCAAACTCAA
* *
2148417 TAGTATCGATACAACTATCC
1 TAGTACCGATACAACTATAC
**
2148437 TAGTACCGATACTTCTATAC
1 TAGTACCGATACAACTATAC
2148457 TATTGTACCGATAC
1 TA--GTACCGATAC
2148471 CCCCTTCCGG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 18 0.64
22 10 0.36
ACGTcount: A:0.31, C:0.24, G:0.11, T:0.33
Consensus pattern (20 bp):
TAGTACCGATACAACTATAC
Found at i:2148556 original size:22 final size:20
Alignment explanation
Indices: 2148512--2148567 Score: 76
Period size: 22 Copynumber: 2.7 Consensus size: 20
2148502 CGATGTTGCC
2148512 TGGTATCGATACCCATACCA
1 TGGTATCGATACCCATACCA
*
2148532 TGGTATCGATACTACCATACTA
1 TGGTATCGATAC--CCATACCA
*
2148554 TGGTACCGATACCC
1 TGGTATCGATACCC
2148568 TCTTCCAGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.44
22 18 0.56
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.27
Consensus pattern (20 bp):
TGGTATCGATACCCATACCA
Found at i:2148561 original size:95 final size:95
Alignment explanation
Indices: 2148443--2148618 Score: 289
Period size: 95 Copynumber: 1.9 Consensus size: 95
2148433 ATCCTAGTAC
* * * * *
2148443 CGATACTTCTATACTATTGTACCGATACCCCCTTCCGGTATCGATACTAATTTTAGATTCGATGT
1 CGATACTACCATACTATGGTACCGATACCCCCTTCCAGTATCGATACCAATTTTAGATTCGATGT
*
2148508 TGCCTGGTATCGATACCCATACCATGGTAT
66 TGCCTAGTATCGATACCCATACCATGGTAT
*
2148538 CGATACTACCATACTATGGTACCGATACCCTCTTCCAGTATCGATACCAATTTTAGATTCGATGT
1 CGATACTACCATACTATGGTACCGATACCCCCTTCCAGTATCGATACCAATTTTAGATTCGATGT
2148603 TGCCTAGTATCGATAC
66 TGCCTAGTATCGATAC
2148619 TACCTCGTCG
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
95 74 1.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.34
Consensus pattern (95 bp):
CGATACTACCATACTATGGTACCGATACCCCCTTCCAGTATCGATACCAATTTTAGATTCGATGT
TGCCTAGTATCGATACCCATACCATGGTAT
Found at i:2150265 original size:13 final size:13
Alignment explanation
Indices: 2150247--2150274 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2150237 TATTATTAAA
2150247 TAATGTATATTTT
1 TAATGTATATTTT
2150260 TAATGTATATTTT
1 TAATGTATATTTT
2150273 TA
1 TA
2150275 TACTTTCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (13 bp):
TAATGTATATTTT
Found at i:2151325 original size:16 final size:16
Alignment explanation
Indices: 2151304--2151346 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
2151294 GTACATCATC
2151304 TATCTAAAATTTTAAA
1 TATCTAAAATTTTAAA
* *
2151320 TATCTATAAACTTTAAT
1 TATCTA-AAATTTTAAA
2151337 TAT-TAAAATT
1 TATCTAAAATT
2151347 GTGATTGGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 4 0.17
16 8 0.35
17 11 0.48
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (16 bp):
TATCTAAAATTTTAAA
Found at i:2154818 original size:24 final size:24
Alignment explanation
Indices: 2154791--2154846 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
2154781 AAACGTATAT
*
2154791 ATCAGAAAACAAAACAG-ATTTCAG
1 ATCAGAAAACAAAACAGAATCT-AG
* * *
2154815 ATCAGATATCAGAACAGAATCTAG
1 ATCAGAAAACAAAACAGAATCTAG
2154839 ATCAGAAA
1 ATCAGAAA
2154847 TAAGATCAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.52, C:0.16, G:0.14, T:0.18
Consensus pattern (24 bp):
ATCAGAAAACAAAACAGAATCTAG
Found at i:2159559 original size:12 final size:12
Alignment explanation
Indices: 2159491--2159586 Score: 59
Period size: 12 Copynumber: 8.0 Consensus size: 12
2159481 GAAAACAAAA
*
2159491 CAGATTTCAGAT
1 CAGAATTCAGAT
*
2159503 CAG-ATATCAGAA
1 CAGAAT-TCAGAT
* *
2159515 CAGAATCCAGGT
1 CAGAATTCAGAT
* * * *
2159527 CAGAAATAATAA
1 CAGAATTCAGAT
*
2159539 CAAAATTCAGAT
1 CAGAATTCAGAT
*
2159551 CAGAATTCAGAA
1 CAGAATTCAGAT
*
2159563 CAGAATTCAAAT
1 CAGAATTCAGAT
* *
2159575 CGGAAATCAGAT
1 CAGAATTCAGAT
2159587 AAAACATTCA
Statistics
Matches: 59, Mismatches: 23, Indels: 4
0.69 0.27 0.05
Matches are distributed among these distances:
11 1 0.02
12 56 0.95
13 2 0.03
ACGTcount: A:0.47, C:0.17, G:0.16, T:0.21
Consensus pattern (12 bp):
CAGAATTCAGAT
Found at i:2159584 original size:24 final size:24
Alignment explanation
Indices: 2159477--2159585 Score: 110
Period size: 24 Copynumber: 4.5 Consensus size: 24
2159467 AAACGGATAT
* * *
2159477 ATCAGAAAACAAAACAGATTTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* *
2159501 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * * *
2159525 GTCAGAAATAATAACAAAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* *
2159549 ATCAGAATTCAGAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAG
*
2159573 ATCGGAAATCAGA
1 ATCAGAAATCAGA
2159586 TAAAACATTC
Statistics
Matches: 66, Mismatches: 19, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 66 1.00
ACGTcount: A:0.50, C:0.17, G:0.15, T:0.18
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:2164836 original size:22 final size:22
Alignment explanation
Indices: 2164761--2164842 Score: 96
Period size: 23 Copynumber: 3.8 Consensus size: 22
2164751 CCAGAACCCC
*
2164761 AGGGGGTATCGATTCCCC-T-A
1 AGGGGGAATCGATTCCCCTTCA
* *
2164781 GGGGGGAATCGGTTCCCCTTCA
1 AGGGGGAATCGATTCCCCTTCA
*
2164803 ATGGGGGAATCGGTTCCCCTTCA
1 A-GGGGGAATCGATTCCCCTTCA
*
2164826 AGGGGGTATCGATTCCC
1 AGGGGGAATCGATTCCC
2164843 TCTGCCCTAT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
20 15 0.28
21 1 0.02
22 15 0.28
23 22 0.42
ACGTcount: A:0.17, C:0.26, G:0.33, T:0.24
Consensus pattern (22 bp):
AGGGGGAATCGATTCCCCTTCA
Found at i:2171485 original size:22 final size:22
Alignment explanation
Indices: 2171460--2171512 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
2171450 ATTTGACTGG
2171460 GAATTTTGAGGCGTTTGGGTTC
1 GAATTTTGAGGCGTTTGGGTTC
*
2171482 GAATTTCGAGGCGTTTGGGTTC
1 GAATTTTGAGGCGTTTGGGTTC
2171504 GAATTTTGA
1 GAATTTTGA
2171513 AAAACGGACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.17, C:0.09, G:0.34, T:0.40
Consensus pattern (22 bp):
GAATTTTGAGGCGTTTGGGTTC
Found at i:2179447 original size:31 final size:32
Alignment explanation
Indices: 2179410--2179472 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
2179400 CGTTCTCAAT
2179410 AGTAAGT-AAAAACTTTTTTCTTCCAAGCCTA
1 AGTAAGTAAAAAACTTTTTTCTTCCAAGCCTA
2179441 AGTAAGTAAAAAACTTTTTTCTTCCAAGCCTA
1 AGTAAGTAAAAAACTTTTTTCTTCCAAGCCTA
2179473 TCCACTTTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 7 0.23
32 24 0.77
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.35
Consensus pattern (32 bp):
AGTAAGTAAAAAACTTTTTTCTTCCAAGCCTA
Found at i:2180013 original size:42 final size:42
Alignment explanation
Indices: 2179963--2180203 Score: 231
Period size: 42 Copynumber: 5.6 Consensus size: 42
2179953 TCAATATCTA
*
2179963 TAGCGGCGTTTTTGAAACAAACGCCGCAAAATGTGTCACATT
1 TAGCGGCGTTTTTGGAACAAACGCCGCAAAATGTGTCACATT
* **
2180005 TAGCGGCGTTTTTTGGAACAAATGCCGCAAAATGTCGAGATC-TT
1 TAGCGGCG-TTTTTGGAACAAACGCCGCAAAATGT-GTCA-CATT
* * * *
2180049 TAGCGGCATTTTTTGAACAAACGCCGCAAAATGTGTCATATA
1 TAGCGGCGTTTTTGGAACAAACGCCGCAAAATGTGTCACATT
* * *
2180091 TAGCGGCGTTTTTTGAACAAACGCCGTAAAATGTG--AGATCT
1 TAGCGGCGTTTTTGGAACAAACGCCGCAAAATGTGTCACAT-T
* * * *
2180132 ATAGTGGCATTTTTTTGGAGCAAACGCCGCAAAA-G-GTCAGATTT
1 -TAGCGGC--GTTTTTGGAACAAACGCCGCAAAATGTGTCACA-TT
2180176 ATAGCGGCGTTTTTGGAACAAACGCCGC
1 -TAGCGGCGTTTTTGGAACAAACGCCGC
2180204 TAATTACCTT
Statistics
Matches: 165, Mismatches: 23, Indels: 22
0.79 0.11 0.10
Matches are distributed among these distances:
40 3 0.02
42 69 0.42
43 49 0.30
44 42 0.25
45 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (42 bp):
TAGCGGCGTTTTTGGAACAAACGCCGCAAAATGTGTCACATT
Found at i:2180054 original size:86 final size:85
Alignment explanation
Indices: 2179958--2180203 Score: 322
Period size: 86 Copynumber: 2.9 Consensus size: 85
2179948 ATAGGTCAAT
*
2179958 ATCTATAGCGGC-GTTTTTGAAACAAACGCCGCAAAATGTGTCACATTTAGCGGCGTTTTTTGGA
1 ATCTATAGCGGCATTTTTTG-AACAAACGCCGCAAAATGTGTCACATTTAGCGGCGTTTTTTGGA
*
2180022 ACAAATGCCGCAAAATGTCGAG
65 ACAAACGCCGCAAAATGT-GAG
* * *
2180044 ATCTTTAGCGGCATTTTTTGAACAAACGCCGCAAAATGTGTCATATATAGCGGCGTTTTTT-GAA
1 ATCTATAGCGGCATTTTTTGAACAAACGCCGCAAAATGTGTCACATTTAGCGGCGTTTTTTGGAA
*
2180108 CAAACGCCGTAAAATGTGAG
66 CAAACGCCGCAAAATGTGAG
* * *
2180128 ATCTATAGTGGCATTTTTTTGGAGCAAACGCCGCAAAA-G-GTCAGATTTATAGCGGCG-TTTTT
1 ATCTATAGCGGCA-TTTTTT-GAACAAACGCCGCAAAATGTGTCACA-TT-TAGCGGCGTTTTTT
2180190 GGAACAAACGCCGC
62 GGAACAAACGCCGC
2180204 TAATTACCTT
Statistics
Matches: 142, Mismatches: 12, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
84 19 0.13
85 31 0.22
86 86 0.61
87 6 0.04
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (85 bp):
ATCTATAGCGGCATTTTTTGAACAAACGCCGCAAAATGTGTCACATTTAGCGGCGTTTTTTGGAA
CAAACGCCGCAAAATGTGAG
Found at i:2180181 original size:128 final size:127
Alignment explanation
Indices: 2179961--2180203 Score: 323
Period size: 128 Copynumber: 1.9 Consensus size: 127
2179951 GGTCAATATC
2179961 TATAGCGGCGTTTTTGAAACAAACGCCGCAAAATGTGTCACATTTAGCGGCGTTTTTTGGAACAA
1 TATAGCGGCGTTTTTGAAACAAACGCCGCAAAATGTG-CACATTTAGCGGCGTTTTTTGGAACAA
* * *
2180026 ATGCCGCAAAATGTCGAGATCTTTAGCGGCATTTTTTGAACAAACGCCGCAAAATGTGTCATA
65 ACGCCGCAAAAGGTCGAGATCTTTAGCGGCATTTTTGGAACAAACGCCGCAAAATGTGTCATA
* * * * *
2180089 TATAGCGGCGTTTTTTG-AACAAACGCCGTAAAATGTG-AGATCTATAGTGGCATTTTTTTGGAG
1 TATAGCGGCG-TTTTTGAAACAAACGCCGCAAAATGTGCACAT-T-TAGCGGC-GTTTTTTGGAA
*
2180152 CAAACGCCGCAAAAGGTC-AGAT-TTATAGCGGCGTTTTTGGAACAAACGCCGC
62 CAAACGCCGCAAAAGGTCGAGATCTT-TAGCGGCATTTTTGGAACAAACGCCGC
2180204 TAATTACCTT
Statistics
Matches: 101, Mismatches: 9, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
126 3 0.03
127 3 0.03
128 64 0.63
129 31 0.31
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (127 bp):
TATAGCGGCGTTTTTGAAACAAACGCCGCAAAATGTGCACATTTAGCGGCGTTTTTTGGAACAAA
CGCCGCAAAAGGTCGAGATCTTTAGCGGCATTTTTGGAACAAACGCCGCAAAATGTGTCATA
Found at i:2184395 original size:42 final size:41
Alignment explanation
Indices: 2184320--2184642 Score: 228
Period size: 42 Copynumber: 7.8 Consensus size: 41
2184310 TGGCTTTATT
** * *
2184320 TATTTAGTAGCGTTTATATAAATACGCCACTAAAGTATAAG
1 TATTTAGCGGCGTTTGTATAAAAACGCCACTAAAGTATAAG
* * * * *
2184361 TATTTGGCGGCGTTTGTGGTTAAAACGCCACTAAAATATTAG
1 TATTTAGCGGCGTTTGT-ATAAAAACGCCACTAAAGTATAAG
* * * * * *
2184403 TCTTTGGCGGTGTTT-TA-AGCAGAAACACCACTAAAGTA-CAT
1 TATTTAGCGGCGTTTGTATA--A-AAACGCCACTAAAGTATAAG
* * *
2184444 TATTTAGCGGCGTTTGTGCTTAAAACGCCACTAAAATATAA-
1 TATTTAGCGGCGTTTGT-ATAAAAACGCCACTAAAGTATAAG
* * * * * **
2184485 TATTTTAACAGCGTTTATATAAAAAATGCCACTAACGTACGAG
1 TA-TTTAGCGGCGTTTGTAT-AAAAACGCCACTAAAGTATAAG
* *
2184528 T-TTTAGCGGCGTTTGTACAAAAACGCCACTAAAGT-TTAG
1 TATTTAGCGGCGTTTGTATAAAAACGCCACTAAAGTATAAG
* * *
2184567 TATTTAGCTGCGTTTATATAAAAACGCCACTAAAGTACAAG
1 TATTTAGCGGCGTTTGTATAAAAACGCCACTAAAGTATAAG
* *
2184608 TATTTACCGGCGTTTAT-TCAAAAAACGCCACTAAA
1 TATTTAGCGGCGTTTGTAT--AAAAACGCCACTAAA
2184643 AATGCCGCTA
Statistics
Matches: 217, Mismatches: 50, Indels: 29
0.73 0.17 0.10
Matches are distributed among these distances:
39 3 0.01
40 47 0.22
41 75 0.35
42 91 0.42
43 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (41 bp):
TATTTAGCGGCGTTTGTATAAAAACGCCACTAAAGTATAAG
Found at i:2184517 original size:83 final size:82
Alignment explanation
Indices: 2184322--2184643 Score: 307
Period size: 83 Copynumber: 3.9 Consensus size: 82
2184312 GCTTTATTTA
* * * * * *
2184322 TTTAGTAGCGTTTATATAAATACGCCACTAAAGTATAAGTATTTGGCGGCGTTTGTGGTTAAAAC
1 TTTAGCAGCGTTTATATAAAAACGCCACTAAAGTACAAGTATTTAGCGGCGTTTGTGCTAAAAAC
2184387 GCCACTAAAATAT-TAGT
66 GCCACTAAAATATATA-T
* * * * * *
2184404 CTTTGGCGGTGTTT-TA-AGCAGAAACACCACTAAAGTAC-ATTATTTAGCGGCGTTTGTGCTTA
1 -TTTAGCAGCGTTTATATA--A-AAACGCCACTAAAGTACAAGTATTTAGCGGCGTTTGTGCTAA
2184466 AAACGCCACTAAAATATAATAT
62 AAACGCCACTAAAATAT-ATAT
* * * * *
2184488 TTTAACAGCGTTTATATAAAAAATGCCACTAACGTACGAGT-TTTAGCGGCGTTTGTAC-AAAAA
1 TTTAGCAGCGTTTATAT-AAAAACGCCACTAAAGTACAAGTATTTAGCGGCGTTTGTGCTAAAAA
* *
2184551 CGCCACTAAAGTTTAGTA-
65 CGCCACTAAAATATA-TAT
* * * * *
2184569 TTTAGCTGCGTTTATATAAAAACGCCACTAAAGTACAAGTATTTACCGGCGTTTATTCAAAAAAC
1 TTTAGCAGCGTTTATATAAAAACGCCACTAAAGTACAAGTATTTAGCGGCGTTTGTGCTAAAAAC
2184634 GCCACTAAAA
66 GCCACTAAAA
2184644 ATGCCGCTAA
Statistics
Matches: 196, Mismatches: 31, Indels: 25
0.78 0.12 0.10
Matches are distributed among these distances:
80 20 0.10
81 31 0.16
82 35 0.18
83 87 0.44
84 20 0.10
85 2 0.01
86 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (82 bp):
TTTAGCAGCGTTTATATAAAAACGCCACTAAAGTACAAGTATTTAGCGGCGTTTGTGCTAAAAAC
GCCACTAAAATATATAT
Found at i:2192292 original size:46 final size:46
Alignment explanation
Indices: 2192242--2192383 Score: 171
Period size: 46 Copynumber: 3.1 Consensus size: 46
2192232 CGAATCAGGC
* *
2192242 TGGTGCATCCTTTATGGGTGATAAATCCAATTATCGATATACAAGA
1 TGGTGCATCCTTTACGGATGATAAATCCAATTATCGATATACAAGA
* * * *
2192288 TGGTGCATCCTTTCCAGATGATAAATCCAATTA-CTGATATACATGC
1 TGGTGCATCCTTTACGGATGATAAATCCAATTATC-GATATACAAGA
* * *
2192334 TGGTGCATCC-TTACCGGATGATAAATCCAATTATCAATTTACAGGA
1 TGGTGCATCCTTTA-CGGATGATAAATCCAATTATCGATATACAAGA
2192380 TGGT
1 TGGT
2192384 AATATCCAAT
Statistics
Matches: 81, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
45 3 0.04
46 77 0.95
47 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Consensus pattern (46 bp):
TGGTGCATCCTTTACGGATGATAAATCCAATTATCGATATACAAGA
Found at i:2198231 original size:95 final size:95
Alignment explanation
Indices: 2198067--2198242 Score: 266
Period size: 95 Copynumber: 1.9 Consensus size: 95
2198057 TATAATATTA
* * *
2198067 TATACAATAAAGCTTGAGTTATCCCTCTAGAGCAATTGGTTAAACACCTCGGCTTTATGGATAAT
1 TATACAATAAAGCTTGAGCTATCCCTCTAGAGCAATTGGTTAAACACCTCGACTTTATGGATAAG
*
2198132 ATTCAGCTAGCCTGATAAAGGCGATTATAC
66 ATTCAGCTAACCTGATAAAGGCGATTATAC
* *
2198162 TATACAATAAAGCTTGAGCTGTCCCTTTA-AGGCAATTGGTTAAACACC-CTGACTTTATGGATA
1 TATACAATAAAGCTTGAGCTATCCCTCTAGA-GCAATTGGTTAAACACCTC-GACTTTATGGATA
2198225 AGATTCAGCTAACCTGAT
64 AGATTCAGCTAACCTGAT
2198243 GAAGAAATTT
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
94 2 0.03
95 71 0.97
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (95 bp):
TATACAATAAAGCTTGAGCTATCCCTCTAGAGCAATTGGTTAAACACCTCGACTTTATGGATAAG
ATTCAGCTAACCTGATAAAGGCGATTATAC
Found at i:2199627 original size:19 final size:19
Alignment explanation
Indices: 2199603--2199663 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
2199593 TTGAGACGTT
2199603 TCTCTTAAAACAATTTGTC
1 TCTCTTAAAACAATTTGTC
* *
2199622 TCTCTTGAGAC-A-TT-T-
1 TCTCTTAAAACAATTTGTC
2199637 TCTCTTAAAACAAATTTTGTC
1 TCTCTTAAAAC-AA-TTTGTC
2199658 TCTCTT
1 TCTCTT
2199664 GAGACAGTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
15 9 0.28
16 1 0.03
17 3 0.09
18 1 0.03
19 11 0.34
20 1 0.03
21 6 0.19
ACGTcount: A:0.26, C:0.21, G:0.07, T:0.46
Consensus pattern (19 bp):
TCTCTTAAAACAATTTGTC
Found at i:2199663 original size:36 final size:36
Alignment explanation
Indices: 2199582--2199685 Score: 162
Period size: 36 Copynumber: 3.0 Consensus size: 36
2199572 TTTGTCTACT
2199582 TTTTGTCTCTCTTGAGAC-GTTTCTCTTAAAAC-AA
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTAAAACAAA
*
2199616 -TTTGTCTCTCTTGAGACATTTTCTCTTAAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTAAAACAAA
*
2199651 TTTTGTCTCTCTTGAGACAGTTTC-CTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTAAAACAAA
2199686 AACTTTGAAT
Statistics
Matches: 64, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
33 17 0.27
34 13 0.20
35 12 0.19
36 22 0.34
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.42
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCTCTTAAAACAAA
Found at i:2199818 original size:39 final size:37
Alignment explanation
Indices: 2199699--2199819 Score: 149
Period size: 36 Copynumber: 3.3 Consensus size: 37
2199689 TTTGAATTGT
*
2199699 TTTC-CTT-AAACAAAGTTTTGTCTCTCTTGAGACAA
1 TTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
* *
2199734 TTTCTCTTAAAACAAA-TTTTGTCTCTCTTGAGACGG
1 TTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
* *
2199770 TTTCCCTTGAAACAAAGTTTTTAGGCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAAG-TTTT-GTCTCTCTTGAGACAG
*
2199809 TTTATCTTGAA
1 TTTCTCTTGAA
2199820 GCACCAATAT
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
35 4 0.05
36 35 0.48
37 7 0.10
38 4 0.05
39 23 0.32
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.40
Consensus pattern (37 bp):
TTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
Found at i:2199886 original size:34 final size:33
Alignment explanation
Indices: 2199829--2199919 Score: 148
Period size: 33 Copynumber: 2.8 Consensus size: 33
2199819 AGCACCAATA
2199829 TTTGAAATTGTTTC-CTTGAAACACAAAAAAAAC
1 TTTGAAATTGTTTCTCTTGAAACAC-AAAAAAAC
*
2199862 TTTGAAATTGTTTCTCTTGAAACACAAAAAACC
1 TTTGAAATTGTTTCTCTTGAAACACAAAAAAAC
*
2199895 TTTGAAAATGTTTCTCTTGAAACAC
1 TTTGAAATTGTTTCTCTTGAAACAC
2199920 CAAACCTTCG
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 45 0.82
34 10 0.18
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (33 bp):
TTTGAAATTGTTTCTCTTGAAACACAAAAAAAC
Found at i:2203114 original size:14 final size:13
Alignment explanation
Indices: 2203082--2203136 Score: 58
Period size: 13 Copynumber: 4.1 Consensus size: 13
2203072 AATAAAAAAG
2203082 ATAAAATATAAAT
1 ATAAAATATAAAT
2203095 ATAAAAT-TAAAT
1 ATAAAATATAAAT
**
2203107 ACATAAAAATATGTAT
1 --AT-AAAATATAAAT
2203123 ATAAAATATAAAT
1 ATAAAATATAAAT
2203136 A
1 A
2203137 ATTAATAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
12 5 0.15
13 17 0.50
14 4 0.12
15 5 0.15
16 3 0.09
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (13 bp):
ATAAAATATAAAT
Found at i:2203153 original size:25 final size:27
Alignment explanation
Indices: 2203120--2203180 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 27
2203110 TAAAAATATG
*
2203120 TATATAAAATATA-AATA-ATTAATAA
1 TATAAAAAATATATAATATATTAATAA
* *
2203145 TTTAAAAAATATATTTATATATTAATAA
1 TATAAAAAATATA-TAATATATTAATAA
2203173 TATAAAAA
1 TATAAAAA
2203181 TGAATATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 11 0.38
27 3 0.10
28 15 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (27 bp):
TATAAAAAATATATAATATATTAATAA
Found at i:2203187 original size:31 final size:28
Alignment explanation
Indices: 2203125--2203196 Score: 78
Period size: 31 Copynumber: 2.6 Consensus size: 28
2203115 ATATGTATAT
*
2203125 AAAATATA-A-ATA-ATTAATAATTTAA
1 AAAATATATATATATATTAATAATTAAA
*
2203150 AAAATATATTTATATATTAATAATATAAA
1 AAAATATATATATATATTAATAAT-TAAA
2203179 AATGAATATATATATATA
1 AA--AATATATATATATA
2203197 ATTTAGAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
25 8 0.21
27 3 0.08
28 9 0.24
29 5 0.13
31 13 0.34
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (28 bp):
AAAATATATATATATATTAATAATTAAA
Found at i:2203232 original size:26 final size:24
Alignment explanation
Indices: 2203172--2203232 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 24
2203162 TATATTAATA
*
2203172 ATATAAAAATGAATATATATATAT
1 ATATAAAAATGAAGATATATATAT
* *
2203196 AATTTAGAAATGTAAGATATATATAT
1 -ATATAAAAATG-AAGATATATATAT
2203222 ATATAATAAAT
1 ATATAA-AAAT
2203233 AATATTAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
25 13 0.45
26 16 0.55
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.38
Consensus pattern (24 bp):
ATATAAAAATGAAGATATATATAT
Found at i:2206805 original size:29 final size:29
Alignment explanation
Indices: 2206769--2206824 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
2206759 ATTAATTTAT
*
2206769 TTTTTGTTATTTATAATTT-TGCCTTTAAA
1 TTTTTGTTATTT-TAATTTATGCATTTAAA
2206798 TTTTTGTTATTTTAATTTATGCATTTA
1 TTTTTGTTATTTTAATTTATGCATTTA
2206825 CTTTCAGAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 6 0.24
29 19 0.76
ACGTcount: A:0.23, C:0.05, G:0.07, T:0.64
Consensus pattern (29 bp):
TTTTTGTTATTTTAATTTATGCATTTAAA
Found at i:2210813 original size:2 final size:2
Alignment explanation
Indices: 2210808--2210835 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2210798 TCAACATTGA
2210808 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
2210836 GTGTATTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2220716 original size:106 final size:105
Alignment explanation
Indices: 2220488--2220821 Score: 508
Period size: 106 Copynumber: 3.2 Consensus size: 105
2220478 TATTTCACGA
* * * *
2220488 CGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAA
1 CGAAGGATATTGGACTCAAGACAGCACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
* * *
2220553 CAACAA-CTTCCCAATCTCAGAGCCAATTTCAACTTCACAA
66 TAACAATC-TCCCAATTTCAGAGCCAATTTCAACTTCACAG
2220593 CGAAGGATATTGGACTCAAGACAGCACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
1 CGAAGGATATTGGACTCAAGACAGCACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
2220658 TAAGCAATCTCCCAATTTCAGAGCCAATTTCAACTTCACAG
66 TAA-CAATCTCCCAATTTCAGAGCCAATTTCAACTTCACAG
* *
2220699 CGAATGATATTGGACTCAAGGCAGCACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
1 CGAAGGATATTGGACTCAAGACAGCACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
* * *
2220764 TAAACAATTTCCCAGTTTCAGAGCCAACTTCAACTTCACAG
66 T-AACAATCTCCCAATTTCAGAGCCAATTTCAACTTCACAG
* *
2220805 CGGATGATATTGGACTC
1 CGAAGGATATTGGACTC
2220822 GGAACAATAC
Statistics
Matches: 213, Mismatches: 13, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
105 63 0.30
106 147 0.69
107 3 0.01
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.22
Consensus pattern (105 bp):
CGAAGGATATTGGACTCAAGACAGCACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
TAACAATCTCCCAATTTCAGAGCCAATTTCAACTTCACAG
Found at i:2222592 original size:2 final size:2
Alignment explanation
Indices: 2222585--2222614 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2222575 CAACATTTGA
2222585 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
2222615 TATTAATTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2224759 original size:29 final size:29
Alignment explanation
Indices: 2224724--2224805 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
2224714 CAACTAAATT
*
2224724 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
2224753 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
*
2224782 GATGTCATTGCTTGCATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
2224806 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:2229498 original size:29 final size:29
Alignment explanation
Indices: 2229443--2229523 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
2229433 AAACTAAATT
*
2229443 GATGTCATTACTTA-ATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
2229471 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
2229500 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
2229524 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
28 13 0.27
29 31 0.63
30 5 0.10
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:2230094 original size:19 final size:19
Alignment explanation
Indices: 2230072--2230111 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
2230062 TAAAATATTA
2230072 ATATTTGATTTATTAATCG
1 ATATTTGATTTATTAATCG
2230091 ATATTTGATTTATTAATCG
1 ATATTTGATTTATTAATCG
2230110 AT
1 AT
2230112 TAATTTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.53
Consensus pattern (19 bp):
ATATTTGATTTATTAATCG
Found at i:2231310 original size:29 final size:30
Alignment explanation
Indices: 2231265--2231338 Score: 93
Period size: 29 Copynumber: 2.5 Consensus size: 30
2231255 TAACCGTTGA
2231265 GTGACTAAAA-A-ATAAATTTTAAAAGCTA-
1 GTGACTAAAATAGA-AAATTTTAAAAGCTAT
*
2231293 GATGA-TAAAATTGAAAATTTTAAAAGCTAT
1 G-TGACTAAAATAGAAAATTTTAAAAGCTAT
2231323 GTGACTAAAATAGAAA
1 GTGACTAAAATAGAAA
2231339 CACAATAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
28 6 0.15
29 21 0.54
30 12 0.31
ACGTcount: A:0.53, C:0.05, G:0.14, T:0.28
Consensus pattern (30 bp):
GTGACTAAAATAGAAAATTTTAAAAGCTAT
Found at i:2232489 original size:21 final size:21
Alignment explanation
Indices: 2232451--2232490 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2232441 TGTTTTTTAA
* *
2232451 TATTTTTATATATGTTTAAAC
1 TATTTTTATAGATATTTAAAC
*
2232472 TATTTTTATAGGTATTTAA
1 TATTTTTATAGATATTTAA
2232491 TTTATAAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.57
Consensus pattern (21 bp):
TATTTTTATAGATATTTAAAC
Done.