Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 132 of 208
Found at i:43301657 original size:30 final size:30
Alignment explanation
Indices: 43301618--43301679 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
43301608 TACATGAAAT
43301618 ACATGGAAAT-GAT-ATTACATGATATATTGAA
1 ACATGGAAATGGATGA-TACATG-TATA-TGAA
43301649 ACAT-GAAATGGATGATACATGTATATGAA
1 ACATGGAAATGGATGATACATGTATATGAA
43301678 AC
1 AC
43301680 TTGCTTAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
29 6 0.21
30 9 0.31
31 13 0.45
32 1 0.03
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.29
Consensus pattern (30 bp):
ACATGGAAATGGATGATACATGTATATGAA
Found at i:43302047 original size:25 final size:25
Alignment explanation
Indices: 43302010--43302064 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
43302000 GTATAGGTTA
*
43302010 TTTTTTTGCTAA-TGTTGGCCTATATG
1 TTTTGTTGCTAATTG-TGGCC-ATATG
43302036 TTTTGTTG-TAATTGTGGCCATATG
1 TTTTGTTGCTAATTGTGGCCATATG
*
43302060 ATTTG
1 TTTTG
43302065 GATTATGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 9 0.35
25 8 0.31
26 9 0.35
ACGTcount: A:0.16, C:0.09, G:0.22, T:0.53
Consensus pattern (25 bp):
TTTTGTTGCTAATTGTGGCCATATG
Found at i:43302909 original size:250 final size:249
Alignment explanation
Indices: 43302449--43302952 Score: 807
Period size: 250 Copynumber: 2.0 Consensus size: 249
43302439 CATATGTTTA
*
43302449 AGGTTTGTTTATGCTTGATTTGGATGCCTTGCTATGGCTTGTAAGTTTGTGCAATTGTGGTTGTA
1 AGGTTTGTTTATGCTTGATTTCGATGCCTTGCTATGGCTTGTAAGTTTGTGCAATTGTGGTTGTA
* *
43302514 GGTACATGCCAAATTGGGTGAGAAAATGGCTTGTAAAATAGCCTATTTTCATCCACACAGGCAGA
66 GGTACATGCCAAATTGGGTGAGAAAATGACTAGTAAAATAGCCTATTTTCATCCACACAGGCAGA
* * *
43302579 GATACTGGTGTGTGTCTTAGTTGTGTGTGACACACAGCAGTGTGTCCCTTGTACCTTTCAAAGGT
131 GACACTGGTGTGTGTCTCAGTCGTGTGTGACACACAGCAGTGTGTCCCTTGTACCTTTCAAAGGT
*
43302644 TTCCAAGTTAGGCTGTTACACGACCTAGCACACAACCTGGCACACGGGCATGTG
196 TTCCAAGTCAGGCTGTTACACGACCTAGCACACAACCTGGCACACGGGCATGTG
*
43302698 AGGTTTGTTTATGCTTGATTTCGTTGCCTTGCTATGGCTTGTAAGTTTGTGCAATTGTGGTTGTA
1 AGGTTTGTTTATGCTTGATTTCGATGCCTTGCTATGGCTTGTAAGTTTGTGCAATTGTGGTTGTA
*
43302763 GGTACATGCCAAGTTGGGTGAGAAAAATGACTAGTAAAATAGCCTATTTTCATCCACACAGGCAG
66 GGTACATGCCAAATTGGGTGAG-AAAATGACTAGTAAAATAGCCTATTTTCATCCACACAGGCAG
*
43302828 AGACAC-GAGTGTGTGTCTCAGTCGTGTGTGACACACAGCCA-TGTGT-CCTCTGTAGCTTTCAA
130 AGACACTG-GTGTGTGTCTCAGTCGTGTGTGACACACAG-CAGTGTGTCCCT-TGTACCTTTCAA
* * *** *
43302890 AGGTTTGCAAGTCAGGCTGTTACACGGCCTAGCACATGGCCTGGCACACGGGCGTGTG
192 AGGTTTCCAAGTCAGGCTGTTACACGACCTAGCACACAACCTGGCACACGGGCATGTG
43302948 AGGTT
1 AGGTT
43302953 ACTTCAAAGG
Statistics
Matches: 235, Mismatches: 16, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
249 88 0.37
250 145 0.62
251 2 0.01
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (249 bp):
AGGTTTGTTTATGCTTGATTTCGATGCCTTGCTATGGCTTGTAAGTTTGTGCAATTGTGGTTGTA
GGTACATGCCAAATTGGGTGAGAAAATGACTAGTAAAATAGCCTATTTTCATCCACACAGGCAGA
GACACTGGTGTGTGTCTCAGTCGTGTGTGACACACAGCAGTGTGTCCCTTGTACCTTTCAAAGGT
TTCCAAGTCAGGCTGTTACACGACCTAGCACACAACCTGGCACACGGGCATGTG
Found at i:43309798 original size:30 final size:30
Alignment explanation
Indices: 43309764--43309843 Score: 115
Period size: 30 Copynumber: 2.7 Consensus size: 30
43309754 AACTAAAGTT
43309764 ATCCCTTTTCATAATTTGATGGTCGCCACC
1 ATCCCTTTTCATAATTTGATGGTCGCCACC
* ** *
43309794 ATCCCTTTTCATAGTTCAATGGTCGTCACC
1 ATCCCTTTTCATAATTTGATGGTCGCCACC
*
43309824 ATCCCATTTCATAATTTGAT
1 ATCCCTTTTCATAATTTGAT
43309844 AGCTGAAGCT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.23, C:0.28, G:0.11, T:0.39
Consensus pattern (30 bp):
ATCCCTTTTCATAATTTGATGGTCGCCACC
Found at i:43309858 original size:30 final size:30
Alignment explanation
Indices: 43309822--43309983 Score: 120
Period size: 30 Copynumber: 5.5 Consensus size: 30
43309812 ATGGTCGTCA
*
43309822 CCATCCCATTTCATAATTTGATAGCTGAAG
1 CCATCCCTTTTCATAATTTGATAGCTGAAG
* *
43309852 CTATCCCTTTTCATAGA-TTGATAGCCGAAG
1 CCATCCCTTTTCATA-ATTTGATAGCTGAAG
* * *
43309882 CCAT-CCTTTTCCATAGTTCGATAGCTAAAG
1 CCATCCCTTTT-CATAATTTGATAGCTGAAG
* * *
43309912 CCATCCC-TTTCATAGTTTGATGATCAT-CA-
1 CCATCCCTTTTCATAATTTGAT-AGC-TGAAG
* * *
43309941 CCATCCCTTTACATAA-TCGATAGCCGAAG
1 CCATCCCTTTTCATAATTTGATAGCTGAAG
* *
43309970 CTATTCCTTTTCAT
1 CCATCCCTTTTCAT
43309984 TTGTTGATGA
Statistics
Matches: 103, Mismatches: 20, Indels: 19
0.73 0.14 0.13
Matches are distributed among these distances:
28 3 0.03
29 38 0.37
30 58 0.56
31 4 0.04
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.35
Consensus pattern (30 bp):
CCATCCCTTTTCATAATTTGATAGCTGAAG
Found at i:43309858 original size:60 final size:59
Alignment explanation
Indices: 43309794--43309998 Score: 184
Period size: 60 Copynumber: 3.4 Consensus size: 59
43309784 GGTCGCCACC
* *
43309794 ATCCCTTTTCATAGTTCAATGGTCGTCACCATCCCATTT-CATAATTTGATAGCTGAAGCT
1 ATCCCTTTTCATAGTT-GATGGTCGTCACCATCCC-TTTACATAATTCGATAGCTGAAGCT
* * * * * * * *
43309854 ATCCCTTTTCATAGATTGATAGCCG-AAGCCATCCTTTTCCATAGTTCGATAGCTAAAGCC
1 ATCCCTTTTCATAG-TTGATGGTCGTCA-CCATCCCTTTACATAATTCGATAGCTGAAGCT
* * *
43309914 ATCCC-TTTCATAGTTTGATGATCATCACCATCCCTTTACATAA-TCGATAGCCGAAGCT
1 ATCCCTTTTCATAG-TTGATGGTCGTCACCATCCCTTTACATAATTCGATAGCTGAAGCT
* * *
43309972 ATTCCTTTTCATTTGTTGATGATCGTC
1 ATCCCTTTTCA-TAGTTGATGGTCGTC
43309999 GTCACGCCGT
Statistics
Matches: 115, Mismatches: 24, Indels: 13
0.76 0.16 0.09
Matches are distributed among these distances:
58 16 0.14
59 47 0.41
60 50 0.43
61 2 0.02
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (59 bp):
ATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTACATAATTCGATAGCTGAAGCT
Found at i:43309982 original size:59 final size:58
Alignment explanation
Indices: 43309797--43309983 Score: 153
Period size: 59 Copynumber: 3.2 Consensus size: 58
43309787 CGCCACCATC
** * * * *
43309797 CCTTTTCATAGTTCAATGGTCGTCACCATCCCATTTCATAATTTGATAGCTGAAGCTATC
1 CCTTTTCATAGTTTGATGATCATCACCATCCC-TTTCATAA-TCGATAGCTGAAGCTATT
* * *** * * * *
43309857 CCTTTTCATAGATTGAT-AGCCGAAGCCATCCTTTTCCATAGTTCGATAGCTAAAGCCA-T
1 CCTTTTCATAGTTTGATGATCATCA-CCATCCCTTT-CATA-ATCGATAGCTGAAGCTATT
* *
43309916 CCCTTTCATAGTTTGATGATCATCACCATCCCTTTACATAATCGATAGCCGAAGCTATT
1 CCTTTTCATAGTTTGATGATCATCACCATCCCTTT-CATAATCGATAGCTGAAGCTATT
43309975 CCTTTTCAT
1 CCTTTTCAT
43309984 TTGTTGATGA
Statistics
Matches: 95, Mismatches: 27, Indels: 11
0.71 0.20 0.08
Matches are distributed among these distances:
58 13 0.14
59 42 0.44
60 40 0.42
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.35
Consensus pattern (58 bp):
CCTTTTCATAGTTTGATGATCATCACCATCCCTTTCATAATCGATAGCTGAAGCTATT
Found at i:43311284 original size:24 final size:24
Alignment explanation
Indices: 43311257--43311316 Score: 104
Period size: 24 Copynumber: 2.5 Consensus size: 24
43311247 CTATTTTTGT
*
43311257 CCAAATTGTGGTTGTAGGTACGTG
1 CCAAATTGTGGTTGTAGGTACATG
43311281 CCAAATTGTGGTTGTAGGTACATG
1 CCAAATTGTGGTTGTAGGTACATG
43311305 CCAAATTG-GGTT
1 CCAAATTGTGGTT
43311317 ACAGAGCATT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
23 4 0.11
24 31 0.89
ACGTcount: A:0.23, C:0.13, G:0.30, T:0.33
Consensus pattern (24 bp):
CCAAATTGTGGTTGTAGGTACATG
Found at i:43311310 original size:93 final size:92
Alignment explanation
Indices: 43311099--43311315 Score: 362
Period size: 93 Copynumber: 2.3 Consensus size: 92
43311089 AAGTTTGTGC
*
43311099 AATTGTGGTTGTAGGTACATGCCAAATTAGGTGAGAAAAATAGCTTGTAAAATAGCCTATTTCGT
1 AATTGTGGTTGTAGGTACATGCCAAATTGGGTGAGAAAAATAGCTTGTAAAATAGCCTATTTCGT
43311164 CCAAATTATGGCTGTAGGTACGTGCCA
66 CCAAATTATGGCTGTAGGTACGTGCCA
* * * *
43311191 AATTGTTGTTGTAGGTACATGCCAAATTGGGTGAGAAAAATAGCTTGTAAAATTGTCTATTTTTG
1 AATTGTGGTTGTAGGTACATGCCAAATTGGGTGAGAAAAATAGCTTGTAAAATAGCCTA-TTTCG
* *
43311256 TCCAAATTGTGGTTGTAGGTACGTGCCA
65 TCCAAATTATGGCTGTAGGTACGTGCCA
43311284 AATTGTGGTTGTAGGTACATGCCAAATTGGGT
1 AATTGTGGTTGTAGGTACATGCCAAATTGGGT
43311316 TACAGAGCAT
Statistics
Matches: 116, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
92 55 0.47
93 61 0.53
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.34
Consensus pattern (92 bp):
AATTGTGGTTGTAGGTACATGCCAAATTGGGTGAGAAAAATAGCTTGTAAAATAGCCTATTTCGT
CCAAATTATGGCTGTAGGTACGTGCCA
Found at i:43313388 original size:25 final size:25
Alignment explanation
Indices: 43313334--43313401 Score: 70
Period size: 25 Copynumber: 2.7 Consensus size: 25
43313324 TATGCTCATT
*
43313334 CGAGCT-ATGAATCGGTATGCTCTCA
1 CGAGCTGA-GAATCGGTAAGCTCTCA
43313359 CGAGCTGTA-AATCGGTAAGCTCAT-A
1 CGAGCTG-AGAATCGGTAAGCTC-TCA
*
43313384 TGAGCTGAGAATCGGTAA
1 CGAGCTGAGAATCGGTAA
43313402 CCCTAATGAC
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
24 1 0.03
25 34 0.92
26 1 0.03
27 1 0.03
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.25
Consensus pattern (25 bp):
CGAGCTGAGAATCGGTAAGCTCTCA
Found at i:43317360 original size:27 final size:28
Alignment explanation
Indices: 43317325--43317377 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
43317315 CGAAATTCAT
*
43317325 ACTTTAATTA-TAAAATAATTAATTTGC
1 ACTTAAATTATTAAAATAATTAATTTGC
* *
43317352 ACTTAAATTATTAACATATTTAATTT
1 ACTTAAATTATTAAAATAATTAATTT
43317378 TAATTATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.47
Consensus pattern (28 bp):
ACTTAAATTATTAAAATAATTAATTTGC
Found at i:43320005 original size:50 final size:50
Alignment explanation
Indices: 43319947--43320188 Score: 317
Period size: 50 Copynumber: 4.8 Consensus size: 50
43319937 ATTTGGGTAA
* *
43319947 AGAGGTCCCATGTAAGACCATGTATGGGACATGGTGTTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
* * *
43319997 AGAGGTCCCATGTAAGACCATGCCTGGGACATGGCGTTTGCACTAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
* * *
43320047 AGAGGTCCCATGTAAGACCATGGCTGGGACACGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
* * * *
43320097 AGAGGTCCC-CGTAAGACCATGTCTGGGACATGGC-ATGAGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTG-GCACCAAGATG
** *
43320146 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
43320189 TGTTATTATC
Statistics
Matches: 169, Mismatches: 19, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
48 2 0.01
49 34 0.20
50 104 0.62
51 27 0.16
52 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.31, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
Found at i:43326835 original size:81 final size:81
Alignment explanation
Indices: 43326700--43326949 Score: 310
Period size: 81 Copynumber: 3.1 Consensus size: 81
43326690 ATTCATGGGC
* * *
43326700 AAATGACTGAAAGACCCCTGAAGGGTAAAATGACCGAAATACCACT-GAAGGGTAAAATGACTAA
1 AAATGACCGAAATACCCTTGAAGGGTAAAATGA-CGAAATACCACTCGAAGGGTAAAATGACTAA
43326764 AATACCCCCGAAGGGTA
65 AATACCCCCGAAGGGTA
* * * *
43326781 AAATGACCGAAATACCCTTGAAGAGTAAAATGATCAAAATA-CACTCGAAGGGTAAAATAACTGA
1 AAATGACCGAAATACCCTTGAAGGGTAAAATGA-CGAAATACCACTCGAAGGGTAAAATGACTAA
*
43326845 TATACCCCCGAAGGGTA
65 AATACCCCCGAAGGGTA
* * * *
43326862 AAATGATCGAAATACCCTTGAAGGGTAAAATGACTGAAATATC-CTCAAATGGTAAAATGACTAA
1 AAATGACCGAAATACCCTTGAAGGGTAAAATGAC-GAAATACCACTCGAAGGGTAAAATGACTAA
**
43326926 AATA-CCCTTATAGGGTA
65 AATACCCCCGA-AGGGTA
43326943 AAATGAC
1 AAATGAC
43326950 TTTTATACCT
Statistics
Matches: 145, Mismatches: 20, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
80 9 0.06
81 135 0.93
82 1 0.01
ACGTcount: A:0.44, C:0.18, G:0.19, T:0.19
Consensus pattern (81 bp):
AAATGACCGAAATACCCTTGAAGGGTAAAATGACGAAATACCACTCGAAGGGTAAAATGACTAAA
ATACCCCCGAAGGGTA
Found at i:43326950 original size:27 final size:26
Alignment explanation
Indices: 43326700--43326950 Score: 245
Period size: 27 Copynumber: 9.3 Consensus size: 26
43326690 ATTCATGGGC
*
43326700 AAATGACTGAAAGACCCCTGAAGGGTA
1 AAATGACTGAAATA-CCCTGAAGGGTA
*
43326727 AAATGACCGAAATACCACTGAAGGGTA
1 AAATGACTGAAATACC-CTGAAGGGTA
* *
43326754 AAATGACTAAAATACCCCCGAAGGGTA
1 AAATGACTGAAATA-CCCTGAAGGGTA
* *
43326781 AAATGACCGAAATACCCTTGAAGAGTA
1 AAATGACTGAAATACCC-TGAAGGGTA
* *
43326808 AAATGA-TCAAAATACACTCGAAGGGTA
1 AAATGACT-GAAATACCCT-GAAGGGTA
* * *
43326835 AAATAACTGATATACCCCCGAAGGGTA
1 AAATGACTGAAATA-CCCTGAAGGGTA
43326862 AAATGA-TCGAAATACCCTTGAAGGGTA
1 AAATGACT-GAAATACCC-TGAAGGGTA
* * *
43326889 AAATGACTGAAATATCCTCAAATGGTA
1 AAATGACTGAAATACCCT-GAAGGGTA
* *
43326916 AAATGACTAAAATACCCTTATAGGGTA
1 AAATGACTGAAATACCCTGA-AGGGTA
43326943 AAATGACT
1 AAATGACT
43326951 TTTATACCTC
Statistics
Matches: 184, Mismatches: 28, Indels: 24
0.78 0.12 0.10
Matches are distributed among these distances:
26 12 0.07
27 166 0.90
28 6 0.03
ACGTcount: A:0.44, C:0.18, G:0.19, T:0.20
Consensus pattern (26 bp):
AAATGACTGAAATACCCTGAAGGGTA
Found at i:43327153 original size:26 final size:26
Alignment explanation
Indices: 43327124--43327200 Score: 109
Period size: 26 Copynumber: 3.0 Consensus size: 26
43327114 TTGCCACGTA
* *
43327124 TACTGTTACTTGCAGCTTTACTGCGT
1 TACTGTTACTGGCAGCTTTGCTGCGT
*
43327150 TACTGTTACTGGCAGCTTTGGTGCGT
1 TACTGTTACTGGCAGCTTTGCTGCGT
* *
43327176 CACTATTACTGGCAGCTTTGCTGCG
1 TACTGTTACTGGCAGCTTTGCTGCG
43327201 ATATTGGTGT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 45 1.00
ACGTcount: A:0.14, C:0.23, G:0.25, T:0.38
Consensus pattern (26 bp):
TACTGTTACTGGCAGCTTTGCTGCGT
Found at i:43327356 original size:28 final size:28
Alignment explanation
Indices: 43327311--43327401 Score: 121
Period size: 28 Copynumber: 3.2 Consensus size: 28
43327301 ATTGCATTGA
43327311 TTACTGTATTGGGCTAAGGCCCCCACTG
1 TTACTGTATTGGGCTAAGGCCCCCACTG
* *
43327339 TTATTGTATTGGGATAAGGCCCACACACTG
1 TTACTGTATTGGGCTAAGGCCC-C-CACTG
* *
43327369 TTACTGTAATGGGCTAAGGCCCACACTG
1 TTACTGTATTGGGCTAAGGCCCCCACTG
43327397 -TACTG
1 TTACTG
43327402 ATACTATATA
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
27 5 0.09
28 25 0.45
29 1 0.02
30 24 0.44
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.29
Consensus pattern (28 bp):
TTACTGTATTGGGCTAAGGCCCCCACTG
Found at i:43327370 original size:30 final size:30
Alignment explanation
Indices: 43327311--43327394 Score: 127
Period size: 30 Copynumber: 2.9 Consensus size: 30
43327301 ATTGCATTGA
43327311 TTACTGTATTGGGCTAAGGCCC-C-CACTG
1 TTACTGTATTGGGCTAAGGCCCACACACTG
* *
43327339 TTATTGTATTGGGATAAGGCCCACACACTG
1 TTACTGTATTGGGCTAAGGCCCACACACTG
*
43327369 TTACTGTAATGGGCTAAGGCCCACAC
1 TTACTGTATTGGGCTAAGGCCCACAC
43327395 TGTACTGATA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
28 20 0.41
29 1 0.02
30 28 0.57
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27
Consensus pattern (30 bp):
TTACTGTATTGGGCTAAGGCCCACACACTG
Found at i:43331739 original size:28 final size:26
Alignment explanation
Indices: 43331685--43331765 Score: 74
Period size: 28 Copynumber: 3.0 Consensus size: 26
43331675 TTATGTGTTA
* * *
43331685 AATATGTTTTATTTCAATGCATGCATTT
1 AATATGTCTTAGTT-AATACATGCA-TT
43331713 AATATGTCTTAGTTAATACATGCCATT
1 AATATGTCTTAGTTAATACATG-CATT
* *
43331740 AATTTGTCTTAGCTTATTACAT-CATT
1 AATATGTCTTAG-TTAATACATGCATT
43331766 TTAATTTGCT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
26 4 0.09
27 20 0.43
28 22 0.48
ACGTcount: A:0.30, C:0.14, G:0.10, T:0.47
Consensus pattern (26 bp):
AATATGTCTTAGTTAATACATGCATT
Found at i:43331742 original size:27 final size:27
Alignment explanation
Indices: 43331685--43331766 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 27
43331675 TTATGTGTTA
* * *
43331685 AATATGTTTTATTTCAATGCATGCATTT
1 AATATGTCTTAGTT-AATACATGCATTT
43331713 AATATGTCTTAGTTAATACATGCCA-TT
1 AATATGTCTTAGTTAATACATG-CATTT
* *
43331740 AATTTGTCTTAGCTTATTACAT-CATTT
1 AATATGTCTTAG-TTAATACATGCATTT
43331767 TAATTTGCTT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
26 2 0.04
27 22 0.48
28 22 0.48
ACGTcount: A:0.29, C:0.13, G:0.10, T:0.48
Consensus pattern (27 bp):
AATATGTCTTAGTTAATACATGCATTT
Found at i:43332999 original size:11 final size:10
Alignment explanation
Indices: 43332975--43333008 Score: 52
Period size: 11 Copynumber: 3.4 Consensus size: 10
43332965 CGGAGTAAGT
43332975 AATT-AAAAA
1 AATTCAAAAA
43332984 AATTCAAAAA
1 AATTCAAAAA
43332994 ATATTCAAAAA
1 A-ATTCAAAAA
43333005 AATT
1 AATT
43333009 ATTATTTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 4 0.17
10 9 0.39
11 10 0.43
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (10 bp):
AATTCAAAAA
Found at i:43333056 original size:20 final size:20
Alignment explanation
Indices: 43333009--43333056 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
43332999 CAAAAAAATT
43333009 ATTATT-TTGTATTCAAGCA
1 ATTATTATTGTATTCAAGCA
43333028 ATTCA-TATTGTATTCAA-CA
1 ATT-ATTATTGTATTCAAGCA
43333047 AGTTATTATT
1 A-TTATTATT
43333057 AGAAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.48
Consensus pattern (20 bp):
ATTATTATTGTATTCAAGCA
Found at i:43336649 original size:28 final size:26
Alignment explanation
Indices: 43336595--43336675 Score: 74
Period size: 28 Copynumber: 3.0 Consensus size: 26
43336585 TTATGTGTTA
* * *
43336595 AATATGTTTTATTTCAATGCATGCATTT
1 AATATGTCTTAGTT-AATACATGCA-TT
43336623 AATATGTCTTAGTTAATACATGCCATT
1 AATATGTCTTAGTTAATACATG-CATT
* *
43336650 AATTTGTCTTAGCTTATTACAT-CATT
1 AATATGTCTTAG-TTAATACATGCATT
43336676 TTAATTTGCT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
26 4 0.09
27 20 0.43
28 22 0.48
ACGTcount: A:0.30, C:0.14, G:0.10, T:0.47
Consensus pattern (26 bp):
AATATGTCTTAGTTAATACATGCATT
Found at i:43336652 original size:27 final size:27
Alignment explanation
Indices: 43336595--43336676 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 27
43336585 TTATGTGTTA
* * *
43336595 AATATGTTTTATTTCAATGCATGCATTT
1 AATATGTCTTAGTT-AATACATGCATTT
43336623 AATATGTCTTAGTTAATACATGCCA-TT
1 AATATGTCTTAGTTAATACATG-CATTT
* *
43336650 AATTTGTCTTAGCTTATTACAT-CATTT
1 AATATGTCTTAG-TTAATACATGCATTT
43336677 TAATTTGCTT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
26 2 0.04
27 22 0.48
28 22 0.48
ACGTcount: A:0.29, C:0.13, G:0.10, T:0.48
Consensus pattern (27 bp):
AATATGTCTTAGTTAATACATGCATTT
Found at i:43338827 original size:136 final size:136
Alignment explanation
Indices: 43338572--43339126 Score: 826
Period size: 136 Copynumber: 4.1 Consensus size: 136
43338562 AAGAACATAG
*
43338572 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTAATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTATATATATTTTA--GAATTAATT
* * * * *
43338637 AATATAAACAGTTATATTAATTAAATTCGGTCAAAGTATAAAAAACATGAAAATTAATATTCTTT
64 AATATAAACAGTTATATTAATTAATTTCGATCAAAATATAAAAGACATGGAAATTAATATTCTTT
43338702 TGGAAAGA
129 TGGAAAGA
* * * *
43338710 ATAAAATTAATATATAAATTTTATTCATATAAAATATTAATTATATATATTATT-GAATTAATTA
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTATATATATT-TTAGAATTAATTA
*
43338774 ATATAAACAGTTATATTAATTAATTTCGATCAAAATATAAAAGGCATGGAAATTAATATTCTTTT
65 ATATAAACAGTTATATTAATTAATTTCGATCAAAATATAAAAGACATGGAAATTAATATTCTTTT
*
43338839 GGAAATA
130 GGAAAGA
*
43338846 ATATAATTAAT-TATGAATTTGATTCATACAAAATATTAATTTTATATATTTTACAGAATTAATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTATATATATTTT--AGAATTAATT
* * * * * *
43338910 AATGTAAACAGTTATAATAATTAATTTCGGTCCAAATATAAAAGACCTGGAGATTAATATTCTTT
64 AATATAAACAGTTATATTAATTAATTTCGATCAAAATATAAAAGACATGGAAATTAATATTCTTT
43338975 TGGAAAGA
129 TGGAAAGA
* * *
43338983 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTATATATATTATCGAATTTATTAA
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTATATATATTTTAGAATTAATTAA
* *
43339048 TATAAACATTTATATTAATTAATTTCGATCAAAATATAAAAGACATGGAAGTTAATATTCTTTTG
66 TATAAACAGTTATATTAATTAATTTCGATCAAAATATAAAAGACATGGAAATTAATATTCTTTTG
*
43339113 CAAAGA
131 GAAAGA
43339119 ATATAATT
1 ATATAATT
43339127 CATTTTTCTA
Statistics
Matches: 374, Mismatches: 38, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
134 2 0.01
135 35 0.09
136 165 0.44
137 85 0.23
138 85 0.23
139 2 0.01
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.40
Consensus pattern (136 bp):
ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTATATATATTTTAGAATTAATTAA
TATAAACAGTTATATTAATTAATTTCGATCAAAATATAAAAGACATGGAAATTAATATTCTTTTG
GAAAGA
Found at i:43339071 original size:273 final size:274
Alignment explanation
Indices: 43338572--43339126 Score: 907
Period size: 273 Copynumber: 2.0 Consensus size: 274
43338562 AAGAACATAG
*
43338572 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTAATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACAGAATTAATT
*
43338637 AATATAAACAGTTATATTAATTAAATTCGGTCAAAGTATAAAAAACATGAAAATTAATATTCTTT
66 AATATAAACAGTTATAATAATTAAATTCGGTCAAAGTATAAAAAACATGAAAATTAATATTCTTT
* * *
43338702 TGGAAAGAATAAAATTAATATATAAATTTTATTCATATAAAATATTAATTATATATATTATTGAA
131 TGGAAAGAATAAAATTAATATATAAATTTGATTCATACAAAATATTAATTATATATATTATCGAA
*
43338767 TTAATTAATATAAACAGTTATATTAATTAATTTCGATCAAAATATAAAAGGCATGGAAATTAATA
196 TTAATTAATATAAACAGTTATATTAATTAATTTCGATCAAAATATAAAAGACATGGAAATTAATA
* *
43338832 TTCTTTTGGAAATA
261 TTCTTTTGCAAAGA
*
43338846 ATATAATTAAT-TATGAATTTGATTCATACAAAATATTAATTTTATATATTTTACAGAATTAATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACAGAATTAATT
* * * * * *
43338910 AATGTAAACAGTTATAATAATTAATTTCGGTCCAAA-TATAAAAGACCTGGAGATTAATATTCTT
66 AATATAAACAGTTATAATAATTAAATTCGGT-CAAAGTATAAAAAACATGAAAATTAATATTCTT
* *
43338974 TTGGAAAGAATATAATTAATATATGAATTTGATTCATACAAAATATTAATTATATATATTATCGA
130 TTGGAAAGAATAAAATTAATATATAAATTTGATTCATACAAAATATTAATTATATATATTATCGA
* * *
43339039 ATTTATTAATATAAACATTTATATTAATTAATTTCGATCAAAATATAAAAGACATGGAAGTTAAT
195 ATTAATTAATATAAACAGTTATATTAATTAATTTCGATCAAAATATAAAAGACATGGAAATTAAT
43339104 ATTCTTTTGCAAAGA
260 ATTCTTTTGCAAAGA
43339119 ATATAATT
1 ATATAATT
43339127 CATTTTTCTA
Statistics
Matches: 260, Mismatches: 20, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
273 245 0.94
274 15 0.06
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.40
Consensus pattern (274 bp):
ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACAGAATTAATT
AATATAAACAGTTATAATAATTAAATTCGGTCAAAGTATAAAAAACATGAAAATTAATATTCTTT
TGGAAAGAATAAAATTAATATATAAATTTGATTCATACAAAATATTAATTATATATATTATCGAA
TTAATTAATATAAACAGTTATATTAATTAATTTCGATCAAAATATAAAAGACATGGAAATTAATA
TTCTTTTGCAAAGA
Found at i:43340652 original size:51 final size:51
Alignment explanation
Indices: 43340489--43340682 Score: 196
Period size: 51 Copynumber: 3.8 Consensus size: 51
43340479 GAAGTTGCTA
* *
43340489 GGTCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGAATG-ATA-
1 GGTCACATGTGTAGTACTATGTGTAGGCTACTACGTGTACC-GAATGAAAAT
* * * * ***
43340539 GGTCGCATGTGTAGTACTATGTGTAGGCTACTATGCGTACCGGAT-AGCTT
1 GGTCACATGTGTAGTACTATGTGTAGGCTACTACGTGTACCGAATGAAAAT
* * * * **
43340589 CGATCACGTGTGTAGTACTATGTGCAGACTACTACGTGTATTGAATGAAAAT
1 -GGTCACATGTGTAGTACTATGTGTAGGCTACTACGTGTACCGAATGAAAAT
* *
43340641 GGTCACATGTGTAGTACTATGTGTAGGCTACTATGTGAACCG
1 GGTCACATGTGTAGTACTATGTGTAGGCTACTACGTGTACCG
43340683 GCTATCATTT
Statistics
Matches: 111, Mismatches: 29, Indels: 7
0.76 0.20 0.05
Matches are distributed among these distances:
49 3 0.03
50 37 0.33
51 69 0.62
52 2 0.02
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (51 bp):
GGTCACATGTGTAGTACTATGTGTAGGCTACTACGTGTACCGAATGAAAAT
Found at i:43340683 original size:102 final size:101
Alignment explanation
Indices: 43340491--43340683 Score: 289
Period size: 102 Copynumber: 1.9 Consensus size: 101
43340481 AGTTGCTAGG
* * * *
43340491 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGAATGATAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGCAGACTACTACGTGTACCGGAATGAAAGGTCACATGTGTAGTAC
*
43340556 TATGTGTAGGCTACTATGCGTACCGGATAGCTTCGA
66 TATGTGTAGGCTACTATGCGAACCGGATAGCTTCGA
**
43340592 TCACGTGTGTAGTACTATGTGCAGACTACTACGTGTA-TTGAATGAAAATGGTCACATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGACTACTACGTGTACCGGAATG-AAA-GGTCACATGTGTAGT
*
43340656 ACTATGTGTAGGCTACTATGTGAACCGG
64 ACTATGTGTAGGCTACTATGCGAACCGG
43340684 CTATCATTTA
Statistics
Matches: 82, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
100 5 0.06
101 37 0.45
102 40 0.49
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (101 bp):
TCACGTGTGTAGTACTATGTGCAGACTACTACGTGTACCGGAATGAAAGGTCACATGTGTAGTAC
TATGTGTAGGCTACTATGCGAACCGGATAGCTTCGA
Found at i:43344271 original size:77 final size:77
Alignment explanation
Indices: 43344179--43344355 Score: 236
Period size: 77 Copynumber: 2.3 Consensus size: 77
43344169 TGAAAATTCA
* * *
43344179 TGAAGATAAAGTTTATATTAGCATATATCTTGCACATTTT-ATTTTT-TCAAAATTTATATA-TT
1 TGAAGATAAAATTTATATTAACATATATATTGCACATTTTAATTTTTATC--AATTTATATATTT
43344241 TCCGAATTTATCTTG
64 TCC-AATTTATCTTG
* * *
43344256 TGAAGATAAAATTTATATTAACATTTATATTGCATATTTTAATTTTTATCTATTTATATATTTTC
1 TGAAGATAAAATTTATATTAACATATATATTGCACATTTTAATTTTTATCAATTTATATATTTTC
43344321 CAATTTATCTTG
66 CAATTTATCTTG
*
43344333 TGAAGAT-AAATTTATATTGACAT
1 TGAAGATAAAATTTATATTAACAT
43344356 TTTCACATTG
Statistics
Matches: 90, Mismatches: 7, Indels: 7
0.87 0.07 0.07
Matches are distributed among these distances:
76 15 0.17
77 62 0.69
78 11 0.12
79 2 0.02
ACGTcount: A:0.34, C:0.08, G:0.08, T:0.49
Consensus pattern (77 bp):
TGAAGATAAAATTTATATTAACATATATATTGCACATTTTAATTTTTATCAATTTATATATTTTC
CAATTTATCTTG
Found at i:43344379 original size:77 final size:77
Alignment explanation
Indices: 43344179--43344378 Score: 207
Period size: 77 Copynumber: 2.6 Consensus size: 77
43344169 TGAAAATTCA
* * * * * *
43344179 TGAAGATAAAGTTTATATTAGCATATATC-TTGCACATTT-TATTTTT-TCAAAATTTATATATT
1 TGAAGATAAAATTTATATTAACATTTA-CATTGCATATTTGAATTTTTATC--TATTTATATATT
43344241 TCCGAATTTATCTTG
63 TCCGAATTTATCTTG
* *
43344256 TGAAGATAAAATTTATATTAACATTTATATTGCATATTTTAATTTTTATCTATTTATATATTTTC
1 TGAAGATAAAATTTATATTAACATTTACATTGCATATTTGAATTTTTATCTATTTATATA-TTTC
43344321 C-AATTTATCTTG
65 CGAATTTATCTTG
* *
43344333 TGAAGAT-AAATTTATATTGACATTTTCACATTG-GT-TTTGAATTTTT
1 TGAAGATAAAATTTATATTAACA-TTT-ACATTGCATATTTGAATTTTT
43344379 TCTTTATCCA
Statistics
Matches: 106, Mismatches: 11, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
76 24 0.23
77 64 0.60
78 16 0.15
79 2 0.02
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.51
Consensus pattern (77 bp):
TGAAGATAAAATTTATATTAACATTTACATTGCATATTTGAATTTTTATCTATTTATATATTTCC
GAATTTATCTTG
Found at i:43347409 original size:22 final size:24
Alignment explanation
Indices: 43347366--43347409 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
43347356 TGATTATATG
43347366 TTTTGATATAACAAATTAAAATGT
1 TTTTGATATAACAAATTAAAATGT
*
43347390 TTTTGA-ATAA-AAGTTAAAAT
1 TTTTGATATAACAAATTAAAAT
43347410 TGAACAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.48, C:0.02, G:0.09, T:0.41
Consensus pattern (24 bp):
TTTTGATATAACAAATTAAAATGT
Found at i:43351346 original size:3 final size:3
Alignment explanation
Indices: 43351338--43351375 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
43351328 ATTCTTGTAT
43351338 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
43351376 TACAAAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (3 bp):
TGA
Found at i:43352460 original size:20 final size:20
Alignment explanation
Indices: 43352409--43352461 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
43352399 AGCTACACCC
*
43352409 AAAATATCGATACTTTTATA
1 AAAATATCGATACTTGTATA
* *
43352429 AAAAAATTGATACTTGTATA
1 AAAATATCGATACTTGTATA
43352449 AAAATATCGATAC
1 AAAATATCGATAC
43352462 ATATTGGGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.49, C:0.09, G:0.08, T:0.34
Consensus pattern (20 bp):
AAAATATCGATACTTGTATA
Found at i:43354557 original size:22 final size:24
Alignment explanation
Indices: 43354517--43354560 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
43354507 TGATAATATG
43354517 TTTTGATATAAAAAATTAAAATGT
1 TTTTGATATAAAAAATTAAAATGT
*
43354541 TTTTGA-AT-AAAAGTTAAAAT
1 TTTTGATATAAAAAATTAAAAT
43354561 TGAAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
23 2 0.11
24 6 0.32
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (24 bp):
TTTTGATATAAAAAATTAAAATGT
Found at i:43359641 original size:21 final size:20
Alignment explanation
Indices: 43359615--43359666 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 20
43359605 TTTTTGCTGA
*
43359615 GTTGAGTAAGTGTGAATTTTG
1 GTTGAGGAA-TGTGAATTTTG
*
43359636 GTTGAGGAATGTGACTTTT-
1 GTTGAGGAATGTGAATTTTG
*
43359655 -TTGAGGCATGTG
1 GTTGAGGAATGTG
43359667 GTTTTTGTGG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 11 0.39
20 9 0.32
21 8 0.29
ACGTcount: A:0.21, C:0.04, G:0.35, T:0.40
Consensus pattern (20 bp):
GTTGAGGAATGTGAATTTTG
Found at i:43362895 original size:12 final size:12
Alignment explanation
Indices: 43362878--43362914 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
43362868 TGTTGTGGGA
*
43362878 CATGTGCCAGGC
1 CATGTGCTAGGC
*
43362890 CATGTGGTAGGC
1 CATGTGCTAGGC
43362902 CATGTGCTAGGC
1 CATGTGCTAGGC
43362914 C
1 C
43362915 GAGTGTTGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.16, C:0.27, G:0.35, T:0.22
Consensus pattern (12 bp):
CATGTGCTAGGC
Found at i:43365386 original size:13 final size:13
Alignment explanation
Indices: 43365349--43365410 Score: 88
Period size: 13 Copynumber: 4.8 Consensus size: 13
43365339 CTCTTCATTA
43365349 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
* *
43365362 CTGTGGAAAAGTG
1 CTTTTGAAAAGTG
*
43365375 CTTTTGAGAAGTG
1 CTTTTGAAAAGTG
*
43365388 CTTTTGAGAAGTG
1 CTTTTGAAAAGTG
43365401 CTTTTGAAAA
1 CTTTTGAAAA
43365411 ATTTGAGTGT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 43 1.00
ACGTcount: A:0.29, C:0.08, G:0.27, T:0.35
Consensus pattern (13 bp):
CTTTTGAAAAGTG
Found at i:43365661 original size:19 final size:19
Alignment explanation
Indices: 43365637--43365681 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
43365627 AATTATTTAT
43365637 TAAATT-TAATTAGAATATA
1 TAAATTATAATTA-AATATA
*
43365656 TAAATTATATTTAAATATA
1 TAAATTATAATTAAATATA
*
43365675 AAAATTA
1 TAAATTA
43365682 AACGTTTGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
TAAATTATAATTAAATATA
Found at i:43367702 original size:27 final size:27
Alignment explanation
Indices: 43367672--43367723 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
43367662 AAAACAAGGA
*
43367672 GAGAAAGGAAGATCGAAACAAGAAAGC
1 GAGAAAGGAAGATCAAAACAAGAAAGC
* *
43367699 GAGAAAGGAGGATTAAAACAAGAAA
1 GAGAAAGGAAGATCAAAACAAGAAA
43367724 AAAAAACCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.58, C:0.08, G:0.29, T:0.06
Consensus pattern (27 bp):
GAGAAAGGAAGATCAAAACAAGAAAGC
Found at i:43375235 original size:14 final size:14
Alignment explanation
Indices: 43375216--43375248 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
43375206 TCGAGCTACT
*
43375216 ATAAAATATAGAAA
1 ATAAAATAGAGAAA
43375230 ATAAAATAGAGAAA
1 ATAAAATAGAGAAA
43375244 ATAAA
1 ATAAA
43375249 CAGAGTAAGC
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:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (14 bp):
ATAAAATAGAGAAA
Found at i:43375928 original size:26 final size:26
Alignment explanation
Indices: 43375873--43375944 Score: 101
Period size: 26 Copynumber: 2.8 Consensus size: 26
43375863 GAGCCATATT
*
43375873 AGGAAGCTC-CGAAGGGCCATTAATC
1 AGGAAGCTCACGAAGAGCCATTAATC
* *
43375898 AGGAAGCTCACAAAGAGCCTTTAATC
1 AGGAAGCTCACGAAGAGCCATTAATC
*
43375924 GGGAAGCTCACGAAGAGCCAT
1 AGGAAGCTCACGAAGAGCCAT
43375945 ATATCGAGAT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
25 9 0.22
26 31 0.77
ACGTcount: A:0.35, C:0.24, G:0.26, T:0.15
Consensus pattern (26 bp):
AGGAAGCTCACGAAGAGCCATTAATC
Found at i:43375958 original size:26 final size:26
Alignment explanation
Indices: 43375900--43375959 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
43375890 CATTAATCAG
* *
43375900 GAAGCTCACAAAGAGCCTTTAATCGG
1 GAAGCTCACAAAGAGCCTATAATCGA
*
43375926 GAAGCTCACGAAGAGCC-ATATATCGA
1 GAAGCTCACAAAGAGCCTATA-ATCGA
*
43375952 GATGCTCA
1 GAAGCTCA
43375960 TAAGAGCTAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 2 0.07
26 27 0.93
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.18
Consensus pattern (26 bp):
GAAGCTCACAAAGAGCCTATAATCGA
Found at i:43380511 original size:21 final size:21
Alignment explanation
Indices: 43380487--43380532 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
43380477 TAGTATCACG
43380487 AGATCCAACAAATGAATATTC
1 AGATCCAACAAATGAATATTC
*
43380508 AGATCCAACAGATGAATATTC
1 AGATCCAACAAATGAATATTC
43380529 AGAT
1 AGAT
43380533 TTCCTACTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.46, C:0.17, G:0.13, T:0.24
Consensus pattern (21 bp):
AGATCCAACAAATGAATATTC
Found at i:43384012 original size:101 final size:102
Alignment explanation
Indices: 43383892--43384076 Score: 311
Period size: 101 Copynumber: 1.8 Consensus size: 102
43383882 AAAATGATGG
**
43383892 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACTGGAATGAT-A-GGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACTGG-ATGATAATGGTAACATGTGTAGT
43383955 ACTATGTGCAGGCTACTATGAGTACCGGATAGTTTCGA
65 ACTATGTGCAGGCTACTATGAGTACCGGATAGTTTCGA
* *
43383993 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATTGGATGGTAATGGTAACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACTGGATGATAATGGTAACATGTGTAGTA
43384058 CTATGTGCAGGCTACTATG
66 CTATGTGCAGGCTACTATG
43384077 TGAACCAAAC
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
100 4 0.05
101 41 0.53
102 33 0.42
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.32
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACTGGATGATAATGGTAACATGTGTAGTA
CTATGTGCAGGCTACTATGAGTACCGGATAGTTTCGA
Found at i:43384022 original size:51 final size:51
Alignment explanation
Indices: 43383888--43384074 Score: 227
Period size: 51 Copynumber: 3.7 Consensus size: 51
43383878 AGTGAAAATG
* *
43383888 ATGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACTGGA-A-TG
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACTGGATAGTA
* * * *
43383937 ATAGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGAGTACCGGATAGT-
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACTGGATAGTA
* * * * *
43383988 TTCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATTGGATGGTA
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACTGGATAGTA
*
43384040 ATGGTAACATGTGTAGTACTATGTGCAGGCTACTA
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTA
43384075 TGTGAACCAA
Statistics
Matches: 115, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
49 2 0.02
50 39 0.34
51 72 0.63
52 2 0.02
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.32
Consensus pattern (51 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACTGGATAGTA
Found at i:43384078 original size:26 final size:26
Alignment explanation
Indices: 43383998--43384078 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 26
43383988 TTCGATCACG
43383998 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
* *** *
43384024 CGTGTA-TTGGATG-GTAATGG-TAAC-A
1 TGTGTAGTACTATGTG-CA-GGCT-ACTA
43384049 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
43384075 TGTG
1 TGTG
43384079 AACCAAACAT
Statistics
Matches: 38, Mismatches: 10, Indels: 14
0.61 0.16 0.23
Matches are distributed among these distances:
24 1 0.03
25 16 0.42
26 20 0.53
27 1 0.03
ACGTcount: A:0.23, C:0.12, G:0.30, T:0.35
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGCTACTA
Found at i:43389120 original size:27 final size:27
Alignment explanation
Indices: 43389104--43389160 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
43389094 CCTAAAAGGA
*
43389104 TTTGGTATGTAGCAATGTCAGAAATGG
1 TTTGGTATGTAGCAATGCCAGAAATGG
*
43389131 TTTGGTATGTAGCAATGTCAGAAATGG
1 TTTGGTATGTAGCAATGCCAGAAATGG
43389158 TTT
1 TTT
43389161 ATGAATTAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.28, C:0.07, G:0.28, T:0.37
Consensus pattern (27 bp):
TTTGGTATGTAGCAATGCCAGAAATGG
Found at i:43391930 original size:16 final size:17
Alignment explanation
Indices: 43391902--43391933 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
43391892 AATATCATTT
43391902 ATTAAATTAATTTTCTA
1 ATTAAATTAATTTTCTA
43391919 ATTAAA-TAATTTTCT
1 ATTAAATTAATTTTCT
43391934 CAACCTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTAAATTAATTTTCTA
Found at i:43394491 original size:30 final size:30
Alignment explanation
Indices: 43394452--43394561 Score: 100
Period size: 30 Copynumber: 3.7 Consensus size: 30
43394442 TTGATATATC
* * *
43394452 TGGATGCCTTTATGGCTATTTAATAATGTG
1 TGGACGCCTTTATGGCTATCTAATAATGTA
* *
43394482 TGGTCGCCTTTATGGCTATCTAATGATGTA
1 TGGACGCCTTTATGGCTATCTAATAATGTA
* * *
43394512 TGGACGCCTCTGTGGCAATCTAAGTCAA-G--
1 TGGACGCCTTTATGGCTATCTAA-T-AATGTA
*
43394541 TGGACACCTTTATGGCTATCT
1 TGGACGCCTTTATGGCTATCT
43394562 TTTGATCTAA
Statistics
Matches: 64, Mismatches: 14, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
29 17 0.27
30 44 0.69
31 2 0.03
32 1 0.02
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (30 bp):
TGGACGCCTTTATGGCTATCTAATAATGTA
Found at i:43398712 original size:18 final size:18
Alignment explanation
Indices: 43398689--43398747 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
43398679 TTCCTAAAAT
43398689 CATCAAAATAAAGAAGTA
1 CATCAAAATAAAGAAGTA
* **
43398707 CATCAACCATTGATGGAA-T-
1 CATCAA--AAT-AAAGAAGTA
43398726 CATCAAAATAAAGAAGTA
1 CATCAAAATAAAGAAGTA
43398744 CATC
1 CATC
43398748 TACCATTGAT
Statistics
Matches: 30, Mismatches: 6, Indels: 10
0.65 0.13 0.22
Matches are distributed among these distances:
16 4 0.13
17 3 0.10
18 10 0.33
19 6 0.20
20 3 0.10
21 4 0.13
ACGTcount: A:0.51, C:0.17, G:0.12, T:0.20
Consensus pattern (18 bp):
CATCAAAATAAAGAAGTA
Found at i:43398736 original size:37 final size:37
Alignment explanation
Indices: 43398686--43398757 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
43398676 ATCTTCCTAA
43398686 AATCATCAAAATAAAGAAGTACATCAACCATTGATGG
1 AATCATCAAAATAAAGAAGTACATCAACCATTGATGG
*
43398723 AATCATCAAAATAAAGAAGTACATCTACCATTGAT
1 AATCATCAAAATAAAGAAGTACATCAACCATTGAT
43398758 TCAACTAACA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.49, C:0.17, G:0.11, T:0.24
Consensus pattern (37 bp):
AATCATCAAAATAAAGAAGTACATCAACCATTGATGG
Found at i:43406622 original size:48 final size:47
Alignment explanation
Indices: 43406552--43406642 Score: 137
Period size: 48 Copynumber: 1.9 Consensus size: 47
43406542 TTATCTGCGA
* * *
43406552 TTATGTGGCCATTATTGGCAATTATTTGGTGGTTTGTCCACAATGTG
1 TTATGTGGCCATTATTGACAATTATGTGGTGGCTTGTCCACAATGTG
*
43406599 TTATGTGGCCGTTTATTGACAATTATGTGGTGGCTTGTCCACAA
1 TTATGTGGCC-ATTATTGACAATTATGTGGTGGCTTGTCCACAA
43406643 ATGGTGTGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 10 0.26
48 29 0.74
ACGTcount: A:0.20, C:0.14, G:0.25, T:0.41
Consensus pattern (47 bp):
TTATGTGGCCATTATTGACAATTATGTGGTGGCTTGTCCACAATGTG
Found at i:43410362 original size:23 final size:24
Alignment explanation
Indices: 43410336--43410388 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
43410326 GAAAAACGAC
*
43410336 AGAAAATGG-GGAAG-AAAAGGAAA
1 AGAAAATGGTGG-AGCAAAAAGAAA
43410359 AGAAAATGGTGGAGCAAAAAGAAA
1 AGAAAATGGTGGAGCAAAAAGAAA
43410383 AGAAAA
1 AGAAAA
43410389 AACTATGCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 11 0.41
24 16 0.59
ACGTcount: A:0.62, C:0.02, G:0.30, T:0.06
Consensus pattern (24 bp):
AGAAAATGGTGGAGCAAAAAGAAA
Found at i:43410481 original size:37 final size:38
Alignment explanation
Indices: 43410430--43410505 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
43410420 GATAACTCCA
*
43410430 CAATCCCAT-TTTTCCTCCTAAAATCACTCCAACACTC
1 CAATCCCATATTTCCCTCCTAAAATCACTCCAACACTC
**
43410467 CAATCCCATATTTCCCTCCTAAAATCACTTTAACACTC
1 CAATCCCATATTTCCCTCCTAAAATCACTCCAACACTC
43410505 C
1 C
43410506 CCCACCACGC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
37 9 0.26
38 26 0.74
ACGTcount: A:0.30, C:0.39, G:0.00, T:0.30
Consensus pattern (38 bp):
CAATCCCATATTTCCCTCCTAAAATCACTCCAACACTC
Found at i:43411747 original size:27 final size:27
Alignment explanation
Indices: 43411717--43411772 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
43411707 TTTAAATGTT
* *
43411717 ATTTAAGGTACAATTTTTTATGTCAAG
1 ATTTAAGCTACAATTTTTGATGTCAAG
*
43411744 ATTTAAGCTACCATTTTTGATGTCAAG
1 ATTTAAGCTACAATTTTTGATGTCAAG
43411771 AT
1 AT
43411773 CACAAAACAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (27 bp):
ATTTAAGCTACAATTTTTGATGTCAAG
Found at i:43422293 original size:14 final size:14
Alignment explanation
Indices: 43422274--43422302 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
43422264 AAATAAAAAG
43422274 AATTATAAACAATC
1 AATTATAAACAATC
43422288 AATTATAAACAATC
1 AATTATAAACAATC
43422302 A
1 A
43422303 TCTCGAAGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.28
Consensus pattern (14 bp):
AATTATAAACAATC
Found at i:43423872 original size:15 final size:15
Alignment explanation
Indices: 43423829--43423863 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
43423819 GTTTTTTTAA
43423829 AAAGTTTATAATAAT
1 AAAGTTTATAATAAT
43423844 AAAGTTTATAATAAT
1 AAAGTTTATAATAAT
43423859 AAAGT
1 AAAGT
43423864 ATATCATAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (15 bp):
AAAGTTTATAATAAT
Found at i:43424500 original size:22 final size:22
Alignment explanation
Indices: 43424475--43424520 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
43424465 ATAATTTAAA
43424475 AATTAAAAGAAATT-AAAAAATT
1 AATTAAAA-AAATTAAAAAAATT
**
43424497 AATTTTAAAAATTAAAAAAATT
1 AATTAAAAAAATTAAAAAAATT
43424519 AA
1 AA
43424521 CCTAAAGTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (22 bp):
AATTAAAAAAATTAAAAAAATT
Found at i:43424518 original size:30 final size:29
Alignment explanation
Indices: 43424457--43424520 Score: 94
Period size: 31 Copynumber: 2.2 Consensus size: 29
43424447 TATATATCAT
*
43424457 ATTAATAAATAATTTAAAAATTAAAAGAA
1 ATTAAAAAATAATTTAAAAATTAAAAGAA
43424486 ATTAAAAAATTAATTTTAAAAATTAAAA-AA
1 ATTAAAAAA-TAA-TTTAAAAATTAAAAGAA
43424516 ATTAA
1 ATTAA
43424521 CCTAAAGTAC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 8 0.25
30 10 0.31
31 14 0.44
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (29 bp):
ATTAAAAAATAATTTAAAAATTAAAAGAA
Found at i:43424526 original size:21 final size:21
Alignment explanation
Indices: 43424484--43424526 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
43424474 AAATTAAAAG
**
43424484 AAATTAAAAAATTAATTTTAA
1 AAATTAAAAAATTAATCCTAA
43424505 AAATTAAAAAAATTAA-CCTAA
1 AAATT-AAAAAATTAATCCTAA
43424526 A
1 A
43424527 GTACATATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (21 bp):
AAATTAAAAAATTAATCCTAA
Found at i:43438215 original size:25 final size:25
Alignment explanation
Indices: 43438171--43438232 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 25
43438161 CAGCTCTTAT
* *
43438171 GAGCTTACCGATACTCAGCTCGGAG
1 GAGCTTACCGTTACTCAGCTCAGAG
* *
43438196 GAGCTTACCGTTATTTAGCTCAGAG
1 GAGCTTACCGTTACTCAGCTCAGAG
*
43438221 AAGCTTACCGTT
1 GAGCTTACCGTT
43438233 TATAACTCGT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.27
Consensus pattern (25 bp):
GAGCTTACCGTTACTCAGCTCAGAG
Found at i:43444099 original size:27 final size:27
Alignment explanation
Indices: 43444069--43444246 Score: 180
Period size: 27 Copynumber: 6.6 Consensus size: 27
43444059 ATATTGAGCC
* *
43444069 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * *
43444096 CGCACACTTAATGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
43444123 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** * *
43444151 CGCACACTTAGTGCCGCATGATCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
43444178 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
43444205 CGCACACTTAGTGCAACATAGTCAAAC-
1 CGCACACTTAGTGCTACATAATC-AACT
43444232 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
43444247 GTACAATTTA
Statistics
Matches: 125, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
27 101 0.81
28 24 0.19
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:43452320 original size:27 final size:27
Alignment explanation
Indices: 43452290--43452467 Score: 189
Period size: 27 Copynumber: 6.6 Consensus size: 27
43452280 ATATTGAGCC
* *
43452290 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
43452317 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
43452344 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** * *
43452372 CGCACACTTAGTGCCGCATGATCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
43452399 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
43452426 CGCACACTTAGTGCAACATAGTCAAAC-
1 CGCACACTTAGTGCTACATAATC-AACT
43452453 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
43452468 GTACAATTTA
Statistics
Matches: 127, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
27 103 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:43452429 original size:82 final size:81
Alignment explanation
Indices: 43452310--43452466 Score: 235
Period size: 82 Copynumber: 1.9 Consensus size: 81
43452300 GTGCTATATA
* *
43452310 ATCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGC
1 ATCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAAC-CGC
43452375 ACACTTAGTGCCGCATG
65 ACACTTAGTGCCGCATG
* * **
43452392 ATCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAACCGC
1 ATCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAACCGC
43452456 ACACTTAGTGC
65 ACACTTAGTGC
43452467 TGTACAATTT
Statistics
Matches: 68, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 53 0.78
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.26
Consensus pattern (81 bp):
ATCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAACCGCA
CACTTAGTGCCGCATG
Found at i:43461259 original size:50 final size:50
Alignment explanation
Indices: 43461142--43461317 Score: 185
Period size: 50 Copynumber: 3.5 Consensus size: 50
43461132 ACATGTCAAA
* * * * * * *
43461142 GCCATGTCCTAGACATGGTATTACATGGGATGTTTCTTGT-ATTGCAAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACGTTTCATATCAGTGCCAAT
* * *
43461191 GCCATATCCCAGATATGGTCTTACATGGGA-GTTCTCATATCAGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACGTT-TCATATCAGTGCCAAT
** * * * *
43461241 GCCATGTCCCAGACATGGTCTTACGGGGGACCTTTCATCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACGTTTCATATCAGTGCCAAT
43461291 GCCATGTCCCAGACATGGTCTTACATG
1 GCCATGTCCCAGACATGGTCTTACATG
43461318 AGATCTCTTT
Statistics
Matches: 104, Mismatches: 20, Indels: 5
0.81 0.16 0.04
Matches are distributed among these distances:
48 3 0.03
49 30 0.29
50 69 0.66
51 2 0.02
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.30
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACGTTTCATATCAGTGCCAAT
Found at i:43467479 original size:22 final size:22
Alignment explanation
Indices: 43467453--43467497 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
43467443 ATTATGATAA
43467453 TTGATATGT-TGAGATTGATATT
1 TTGATATGTATGAGATT-ATATT
*
43467475 TTGATATGTATGCGATTATATT
1 TTGATATGTATGAGATTATATT
43467497 T
1 T
43467498 GTGTTGATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.27, C:0.02, G:0.20, T:0.51
Consensus pattern (22 bp):
TTGATATGTATGAGATTATATT
Found at i:43477930 original size:59 final size:62
Alignment explanation
Indices: 43477852--43477968 Score: 154
Period size: 62 Copynumber: 1.9 Consensus size: 62
43477842 ATCACTTTAA
* * *
43477852 TATTAAATTAATATAATA-TT-TCT-CAAGATGAATATTAGAA-TAAATTTAATATTAAATCT
1 TATTAAATTAATAGAATATTTATCTACAAGATAAACATTA-AATTAAATTTAATATTAAATCT
43477911 TATTGAAA-TAATAGAATATTTATCTACAAGATAAACATTAAATTAAATTTAATATTAA
1 TATT-AAATTAATAGAATATTTATCTACAAGATAAACATTAAATTAAATTTAATATTAA
43477969 GATAATCATT
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
59 13 0.26
60 5 0.10
61 5 0.10
62 27 0.54
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (62 bp):
TATTAAATTAATAGAATATTTATCTACAAGATAAACATTAAATTAAATTTAATATTAAATCT
Found at i:43477994 original size:20 final size:18
Alignment explanation
Indices: 43477947--43478034 Score: 58
Period size: 19 Copynumber: 4.8 Consensus size: 18
43477937 CAAGATAAAC
43477947 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
43477964 ATTAAGA-TAATCATTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
**
43477984 ATTAAATTAATAAAATAAT
1 ATTAAATTAAT-ATTTAAT
*
43478003 ATT-AATATAAGTATTAAAT
1 ATTAAAT-TAA-TATTTAAT
*
43478022 -TTAATTTAATATT
1 ATTAAATTAATATT
43478035 AAGTTGTTAA
Statistics
Matches: 56, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
17 12 0.21
18 9 0.16
19 18 0.32
20 17 0.30
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:43479686 original size:43 final size:43
Alignment explanation
Indices: 43479625--43479834 Score: 251
Period size: 43 Copynumber: 4.9 Consensus size: 43
43479615 TTTATGTAAA
* * * *
43479625 AAACGCTGCTAAAGAACATGATCTTTAGTGGCGCTTCACCGAC
1 AAACGCCGCTAAAGAACATGACCTTTAGTGGCGCTTTACCCAC
* * * *
43479668 AAACGCCGCTAAAGAACATGATCTTTAGCGGTGCTTTTA-TCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGTGGCGC-TTTACCCAC
* * * *
43479711 AAACGCCGCTAAAGATCCTAACCTTTAGTGGCACTTTACCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGTGGCGCTTTACCCAC
** * *
43479754 AAACAACGCTAAAGAACATGACCTTTAGTGGCACTTTACCCAT
1 AAACGCCGCTAAAGAACATGACCTTTAGTGGCGCTTTACCCAC
*
43479797 AAACACCGCTAAAGAACATGACCTTTAGTGGCGCTTTA
1 AAACGCCGCTAAAGAACATGACCTTTAGTGGCGCTTTA
43479835 TGAAAAACGC
Statistics
Matches: 143, Mismatches: 22, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
42 4 0.03
43 136 0.95
44 3 0.02
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGACCTTTAGTGGCGCTTTACCCAC
Found at i:43485510 original size:21 final size:20
Alignment explanation
Indices: 43485486--43485528 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
43485476 TCTAACCCCT
*
43485486 AACCCTTAAACCTTAAATCCC
1 AACCCTTAAACCAT-AATCCC
43485507 AACCCTTAAACCATAATCCC
1 AACCCTTAAACCATAATCCC
43485527 AA
1 AA
43485529 ATCCATACTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.42, C:0.37, G:0.00, T:0.21
Consensus pattern (20 bp):
AACCCTTAAACCATAATCCC
Found at i:43485937 original size:41 final size:40
Alignment explanation
Indices: 43485892--43486156 Score: 185
Period size: 41 Copynumber: 6.5 Consensus size: 40
43485882 TAAAATGTTT
* **
43485892 TTAGCGGTGTTTTTGAAAAAATGCCGCTAAAACCCTTAGCA
1 TTAGCGGCGTTTTT-AAAAAATGCCGCTAAAACCCCCAGCA
* * * *
43485933 TTAGCAGCGCTTCTTCAAAAA-GCCGCTAAAACCCCGAGCA
1 TTAGCGGCG-TTTTTAAAAAATGCCGCTAAAACCCCCAGCA
* * * ***
43485973 TTAGCGGCACTTTTTCAAAAACGCCGCTAAAACCTTTAGCA
1 TTAGCGGC-GTTTTTAAAAAATGCCGCTAAAACCCCCAGCA
* * * ** *
43486014 TTAGCGACGCTTCTTCAAAAACACCGCTAAAACCCCGAGCA
1 TTAGCGGCG-TTTTTAAAAAATGCCGCTAAAACCCCCAGCA
* * * * *
43486055 TTAGCGATAC-TTCTTCAAAAATGCCGCTAAAGCTCCCAGCA
1 TTAGCG--GCGTTTTTAAAAAATGCCGCTAAAACCCCCAGCA
* *
43486096 TTAGCAGCGCTTCTTT-AAAAATGCCGCTAAAGCCCCCAGCA
1 TTAGCGGCG-TT-TTTAAAAAATGCCGCTAAAACCCCCAGCA
* *
43486137 TTAGCGGCGCTTTTGAAAAA
1 TTAGCGGCGTTTTTAAAAAA
43486157 GGTAAGAAAA
Statistics
Matches: 184, Mismatches: 30, Indels: 21
0.78 0.13 0.09
Matches are distributed among these distances:
39 4 0.02
40 40 0.22
41 132 0.72
42 6 0.03
43 2 0.01
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (40 bp):
TTAGCGGCGTTTTTAAAAAATGCCGCTAAAACCCCCAGCA
Found at i:43486056 original size:82 final size:81
Alignment explanation
Indices: 43485908--43486150 Score: 319
Period size: 82 Copynumber: 3.0 Consensus size: 81
43485898 GTGTTTTTGA
*
43485908 AAAAATGCCGCTAAAACCCTTAGCATTAGCAGCGCTTCTTCAAAAAGCCGCTAAAACCCCGAGCA
1 AAAAATGCCGCTAAAACCTTTAGCATTAGCAGCGCTTCTTCAAAAAGCCGCTAAAACCCCGAGCA
43485973 TTAGCGGCACTTTTTC
66 TTAGCGGCACTTTTTC
* *
43485989 AAAAACGCCGCTAAAACCTTTAGCATTAGC-GACGCTTCTTCAAAAACACCGCTAAAACCCCGAG
1 AAAAATGCCGCTAAAACCTTTAGCATTAGCAG-CGCTTCTTCAAAAA-GCCGCTAAAACCCCGAG
** *
43486053 CATTAGCGATACTTCTTC
64 CATTAGCGGCACTTTTTC
* ** * * *
43486071 AAAAATGCCGCT-AAAGCTCCCAGCATTAGCAGCGCTTCTTTAAAAATGCCGCTAAAGCCCCCAG
1 AAAAATGCCGCTAAAACCT-TTAGCATTAGCAGCGCTTCTTCAAAAA-GCCGCTAAAACCCCGAG
*
43486135 CATTAGCGGCGCTTTT
64 CATTAGCGGCACTTTT
43486151 GAAAAAGGTA
Statistics
Matches: 139, Mismatches: 19, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
80 1 0.01
81 47 0.34
82 90 0.65
83 1 0.01
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (81 bp):
AAAAATGCCGCTAAAACCTTTAGCATTAGCAGCGCTTCTTCAAAAAGCCGCTAAAACCCCGAGCA
TTAGCGGCACTTTTTC
Found at i:43486139 original size:123 final size:121
Alignment explanation
Indices: 43485915--43486156 Score: 292
Period size: 123 Copynumber: 2.0 Consensus size: 121
43485905 TGAAAAAATG
** * *
43485915 CCGCTAAAACCCTTAGCATTAGCAGCGCTTCTTCAAAAAGCCGCTAAAACCCCGAGCATTAGCGG
1 CCGCTAAAACCCCGAGCATTAGCAGCACTTCTTCAAAAAGCCGCTAAAACCCCGAGCATTAGCAG
***
43485980 CACTTTTTCAAAAACGCCGCTAAAACCTTTAGCATTAGCGACGCTTCTTCAAAAACA
66 CACTTTTTCAAAAACGCCGCTAAAACCCCCAGCATTAGCGACGCTT-TTCAAAAACA
* *
43486037 CCGCTAAAACCCCGAGCATTAGC-GATACTTCTTCAAAAATGCCGCTAAAGCTCCC-AGCATTAG
1 CCGCTAAAACCCCGAGCATTAGCAG-CACTTCTTCAAAAA-GCCGCTAAAAC-CCCGAGCATTAG
* * * * *
43486100 CAGCGCTTCTTT-AAAAATGCCGCTAAAGCCCCCAGCATTAGCGGCGCTTTTGAAAAA
63 CAGCACTT-TTTCAAAAACGCCGCTAAAACCCCCAGCATTAGCGACGCTTTTCAAAAA
43486157 GGTAAGAAAA
Statistics
Matches: 102, Mismatches: 14, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
121 1 0.01
122 40 0.39
123 55 0.54
124 6 0.06
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (121 bp):
CCGCTAAAACCCCGAGCATTAGCAGCACTTCTTCAAAAAGCCGCTAAAACCCCGAGCATTAGCAG
CACTTTTTCAAAAACGCCGCTAAAACCCCCAGCATTAGCGACGCTTTTCAAAAACA
Found at i:43486240 original size:25 final size:26
Alignment explanation
Indices: 43486200--43486250 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
43486190 TTGTAACATT
43486200 TTTTCAAAAATCGCCGCTAAAGCTCA
1 TTTTCAAAAATCGCCGCTAAAGCTCA
* *
43486226 TTTTGAAAAA-CGCCGCTAATGCTCA
1 TTTTCAAAAATCGCCGCTAAAGCTCA
43486251 ATCTTTAGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.27
Consensus pattern (26 bp):
TTTTCAAAAATCGCCGCTAAAGCTCA
Found at i:43492885 original size:25 final size:25
Alignment explanation
Indices: 43492851--43492901 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
43492841 TATACATGCC
43492851 ATAGCTCAAACATTGATCATCATAA
1 ATAGCTCAAACATTGATCATCATAA
43492876 ATAGCTCAAACATTGATCATCATAA
1 ATAGCTCAAACATTGATCATCATAA
43492901 A
1 A
43492902 ATATCGGACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.45, C:0.20, G:0.08, T:0.27
Consensus pattern (25 bp):
ATAGCTCAAACATTGATCATCATAA
Found at i:43493431 original size:50 final size:49
Alignment explanation
Indices: 43493375--43493488 Score: 120
Period size: 49 Copynumber: 2.3 Consensus size: 49
43493365 TATCCTAGAT
** * ** *
43493375 ATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATCTCCCGGAC
1 ATGGTCTTACATGGGACCTCTCATATCGGT-CCAACACCATCTCCCAGAC
** * * *
43493425 ATGGTCTTACGGGGGACCTCTCATCTCGGTCCAACACCATGTTCCAGAC
1 ATGGTCTTACATGGGACCTCTCATATCGGTCCAACACCATCTCCCAGAC
43493474 ATGGTCTTACATGGG
1 ATGGTCTTACATGGG
43493489 GCCATGTTCC
Statistics
Matches: 51, Mismatches: 13, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
49 26 0.51
50 25 0.49
ACGTcount: A:0.19, C:0.29, G:0.25, T:0.27
Consensus pattern (49 bp):
ATGGTCTTACATGGGACCTCTCATATCGGTCCAACACCATCTCCCAGAC
Found at i:43493504 original size:29 final size:29
Alignment explanation
Indices: 43493461--43493516 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
43493451 CGGTCCAACA
*
43493461 CCATGTTCCAGACATGGTCTTACATGGGG
1 CCATGTTCCAAACATGGTCTTACATGGGG
43493490 CCATGTTCCAAACATGGTCTTACATGG
1 CCATGTTCCAAACATGGTCTTACATGG
43493517 AATCTCTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.29
Consensus pattern (29 bp):
CCATGTTCCAAACATGGTCTTACATGGGG
Found at i:43507907 original size:18 final size:19
Alignment explanation
Indices: 43507870--43507909 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
43507860 GACAAATGCT
* *
43507870 TATGTTTAATTGATTTTAA
1 TATGGTTAACTGATTTTAA
43507889 TATGGTTAACTGA-TTTAA
1 TATGGTTAACTGATTTTAA
43507907 TAT
1 TAT
43507910 TATGATGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.33, C:0.03, G:0.12, T:0.53
Consensus pattern (19 bp):
TATGGTTAACTGATTTTAA
Found at i:43532379 original size:60 final size:60
Alignment explanation
Indices: 43532315--43532456 Score: 151
Period size: 60 Copynumber: 2.4 Consensus size: 60
43532305 GGCAAGCCAC
* * * *
43532315 CAATATTGCAAACAAGCTGCCAATATT-TTGGACAAACCACTAGTATTGTAAAAAAGCTGT
1 CAATATTGCAAACAAACTGCCAATATTGTAGG-CAAACCACCAGTATTGCAAAAAAGCTGT
* * * * * *
43532375 CAATATTGCAGATAAACTGTCAATATTGTAGGCAAGCCACCAGTATTGCAGATAAGCTGT
1 CAATATTGCAAACAAACTGCCAATATTGTAGGCAAACCACCAGTATTGCAAAAAAGCTGT
* * *
43532435 CAATATTGTAGACAAAATGCCA
1 CAATATTGCAAACAAACTGCCA
43532457 GTACTTCCTC
Statistics
Matches: 67, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
60 64 0.96
61 3 0.04
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26
Consensus pattern (60 bp):
CAATATTGCAAACAAACTGCCAATATTGTAGGCAAACCACCAGTATTGCAAAAAAGCTGT
Found at i:43532402 original size:40 final size:40
Alignment explanation
Indices: 43532358--43532444 Score: 102
Period size: 40 Copynumber: 2.2 Consensus size: 40
43532348 AAACCACTAG
***
43532358 TATTGTAAAAAAGCTGTCAATATTGCAGATAAACTGTCAA
1 TATTGTAAAAAAGCCACCAATATTGCAGATAAACTGTCAA
*** * *
43532398 TATTGTAGGCAAGCCACCAGTATTGCAGATAAGCTGTCAA
1 TATTGTAAAAAAGCCACCAATATTGCAGATAAACTGTCAA
43532438 TATTGTA
1 TATTGTA
43532445 GACAAAATGC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (40 bp):
TATTGTAAAAAAGCCACCAATATTGCAGATAAACTGTCAA
Found at i:43532432 original size:100 final size:100
Alignment explanation
Indices: 43532270--43532450 Score: 247
Period size: 100 Copynumber: 1.8 Consensus size: 100
43532260 TTGCAGACAC
* * * *
43532270 GCTGCCAATATTGCAGATAAACTATTCGTGTTGTGGGCAAGCCACCAATATTGCAAACAAGCTGC
1 GCTGCCAATATTGCAGATAAACTAGTCATATTGTAGGCAAGCCACCAATATTGCAAACAAGCTGC
* *
43532335 CAATATTTTGGACAAACCACTAGTATTGTAAAAAA
66 CAATATTGTAGACAAACCACTAGTATTGTAAAAAA
* * * *
43532370 GCTGTCAATATTGCAGATAAACT-GTCAATATTGTAGGCAAGCCACCAGTATTGCAGATAAGCTG
1 GCTGCCAATATTGCAGATAAACTAGTC-ATATTGTAGGCAAGCCACCAATATTGCAAACAAGCTG
*
43532434 TCAATATTGTAGACAAA
65 CCAATATTGTAGACAAA
43532451 ATGCCAGTAC
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
99 2 0.03
100 67 0.97
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.27
Consensus pattern (100 bp):
GCTGCCAATATTGCAGATAAACTAGTCATATTGTAGGCAAGCCACCAATATTGCAAACAAGCTGC
CAATATTGTAGACAAACCACTAGTATTGTAAAAAA
Found at i:43532441 original size:20 final size:20
Alignment explanation
Indices: 43532368--43532442 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
43532358 TATTGTAAAA
43532368 AAGCTGTCAATATTGCAGAT
1 AAGCTGTCAATATTGCAGAT
* * **
43532388 AAACTGTCAATATTGTAGGC
1 AAGCTGTCAATATTGCAGAT
*** *
43532408 AAGCCACCAGTATTGCAGAT
1 AAGCTGTCAATATTGCAGAT
43532428 AAGCTGTCAATATTG
1 AAGCTGTCAATATTG
43532443 TAGACAAAAT
Statistics
Matches: 39, Mismatches: 16, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (20 bp):
AAGCTGTCAATATTGCAGAT
Found at i:43535068 original size:27 final size:27
Alignment explanation
Indices: 43535037--43535301 Score: 141
Period size: 27 Copynumber: 9.9 Consensus size: 27
43535027 ATGCCCCTAA
43535037 AGGGTAAAATGACTGAAATACCCTCGAT
1 AGGGTAAAATGACTGAAATACCCTC-AT
* *
43535065 -GGGTAAAATGACTAAAATGCCCTCAT
1 AGGGTAAAATGACTGAAATACCCTCAT
* *
43535091 AGGGTAAAATGA-TCGAAATACCCCCGT
1 AGGGTAAAATGACT-GAAATACCCTCAT
* ** *
43535118 AGGGTAGAAT-ACAAAAATACCCCCAT
1 AGGGTAAAATGACTGAAATACCCTCAT
* * ** *
43535144 AGGGTACAATAACCAAAATACCC-CTGT
1 AGGGTAAAATGACTGAAATACCCTC-AT
* * * *
43535171 AGAGTAAAATGACTGTAATGCCC-CTGT
1 AGGGTAAAATGACTGAAATACCCTC-AT
** * **
43535198 AGAATAAAATGA-TCGTAATACCCTTGT
1 AGGGTAAAATGACT-GAAATACCCTCAT
* * * *
43535225 A-AGTAAAATGACCGTAATACCC-CTGT
1 AGGGTAAAATGACTGAAATACCCTC-AT
* * **
43535251 AGGGTAAAATGACCGTAATACCCTTTT
1 AGGGTAAAATGACTGAAATACCCTCAT
*
43535278 AGGGTAAAATGACTGTAATACCCT
1 AGGGTAAAATGACTGAAATACCCT
43535302 GGTGAGTAAA
Statistics
Matches: 196, Mismatches: 30, Indels: 23
0.79 0.12 0.09
Matches are distributed among these distances:
26 47 0.24
27 149 0.76
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.23
Consensus pattern (27 bp):
AGGGTAAAATGACTGAAATACCCTCAT
Found at i:43535095 original size:54 final size:53
Alignment explanation
Indices: 43535037--43535180 Score: 148
Period size: 53 Copynumber: 2.7 Consensus size: 53
43535027 ATGCCCCTAA
* * * *
43535037 AGGGTAAAATGA-CTGAAATACCCTCG-ATGGGTAAAATGACTAAAATGCCCTCAT
1 AGGGTAAAATGATC-GAAATACCCCCGTA-GGGTAAAAT-ACAAAAATACCCCCAT
*
43535091 AGGGTAAAATGATCGAAATACCCCCGTAGGGTAGAATACAAAAATACCCCCAT
1 AGGGTAAAATGATCGAAATACCCCCGTAGGGTAAAATACAAAAATACCCCCAT
* * * * * *
43535144 AGGGTACAATAACCAAAATACCCCTGTAGAGTAAAAT
1 AGGGTAAAATGATCGAAATACCCCCGTAGGGTAAAAT
43535181 GACTGTAATG
Statistics
Matches: 76, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
53 43 0.57
54 31 0.41
55 2 0.03
ACGTcount: A:0.42, C:0.20, G:0.19, T:0.19
Consensus pattern (53 bp):
AGGGTAAAATGATCGAAATACCCCCGTAGGGTAAAATACAAAAATACCCCCAT
Found at i:43535138 original size:26 final size:27
Alignment explanation
Indices: 43535106--43535172 Score: 91
Period size: 26 Copynumber: 2.5 Consensus size: 27
43535096 AAAATGATCG
*
43535106 AAATACCCCCGTAGGGTAGAAT-ACAA
1 AAATACCCCCGTAGGGTACAATAACAA
* *
43535132 AAATACCCCCATAGGGTACAATAACCA
1 AAATACCCCCGTAGGGTACAATAACAA
*
43535159 AAATACCCCTGTAG
1 AAATACCCCCGTAG
43535173 AGTAAAATGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
26 20 0.57
27 15 0.43
ACGTcount: A:0.42, C:0.27, G:0.15, T:0.16
Consensus pattern (27 bp):
AAATACCCCCGTAGGGTACAATAACAA
Found at i:43535232 original size:53 final size:54
Alignment explanation
Indices: 43535160--43535300 Score: 203
Period size: 53 Copynumber: 2.6 Consensus size: 54
43535150 CAATAACCAA
* * *
43535160 AATACCCCTGTAGAGTAAAATGACTGTAATGCCCCTGTAGAATAAAATGATCGT
1 AATACCCTTGTAGAGTAAAATGACTGTAATACCCCTGTAGAATAAAATGACCGT
* **
43535214 AATACCCTTGTA-AGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCGT
1 AATACCCTTGTAGAGTAAAATGACTGTAATACCCCTGTAGAATAAAATGACCGT
* *
43535267 AATACCCTTTTAGGGTAAAATGACTGTAATACCC
1 AATACCCTTGTAGAGTAAAATGACTGTAATACCC
43535301 TGGTGAGTAA
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
53 47 0.61
54 30 0.39
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (54 bp):
AATACCCTTGTAGAGTAAAATGACTGTAATACCCCTGTAGAATAAAATGACCGT
Found at i:43535244 original size:80 final size:80
Alignment explanation
Indices: 43535160--43535311 Score: 207
Period size: 80 Copynumber: 1.9 Consensus size: 80
43535150 CAATAACCAA
* * *
43535160 AATACCCCTGTAGAGTAAAATGACTGTAATGCCCCTGTAGAATAAAATGA-TCGTAATACCCTTG
1 AATACCCCTGTAGAGTAAAATGACCGTAATACCCCTGTAGAATAAAATGACT-GTAATACCCTGG
43535224 TAAGTAAAATGACCGT
65 TAAGTAAAATGACCGT
* * * **
43535240 AATACCCCTGTAGGGTAAAATGACCGTAATACCCTTTTAGGGTAAAATGACTGTAATACCCTGGT
1 AATACCCCTGTAGAGTAAAATGACCGTAATACCCCTGTAGAATAAAATGACTGTAATACCCTGGT
*
43535305 GAGTAAA
66 AAGTAAA
43535312 CTATATTTTC
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
80 61 0.98
81 1 0.02
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.26
Consensus pattern (80 bp):
AATACCCCTGTAGAGTAAAATGACCGTAATACCCCTGTAGAATAAAATGACTGTAATACCCTGGT
AAGTAAAATGACCGT
Found at i:43535393 original size:24 final size:24
Alignment explanation
Indices: 43535357--43535412 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
43535347 TATGTTGTTA
* *
43535357 AATGATTGATTTGTCTGTG-TTTGG
1 AATGACTGGTTTGTCTGTGATTT-G
*
43535381 TATGACTGGTTTGTCTGTGATTTG
1 AATGACTGGTTTGTCTGTGATTTG
43535405 AATGACTG
1 AATGACTG
43535413 ATTCTAAGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 24 0.89
25 3 0.11
ACGTcount: A:0.18, C:0.07, G:0.29, T:0.46
Consensus pattern (24 bp):
AATGACTGGTTTGTCTGTGATTTG
Found at i:43535626 original size:32 final size:33
Alignment explanation
Indices: 43535585--43535799 Score: 219
Period size: 32 Copynumber: 6.7 Consensus size: 33
43535575 GCTGCGATGC
* * *
43535585 TACTGATGGCTTTGTGTCAATCATAGT-ACTGT
1 TACTGATGGCTTTGTGCCGATCATATTCACTGT
* **
43535617 TACTGATGGCTTTGTGCTGATCATATT-ACAAT
1 TACTGATGGCTTTGTGCCGATCATATTCACTGT
* * * *
43535649 TACCGATGGCTGTGTGTCGATCAT-TTCATTGT
1 TACTGATGGCTTTGTGCCGATCATATTCACTGT
* *
43535681 TACTGATGGCTGTGTGCCGATCATA-TCACTGC
1 TACTGATGGCTTTGTGCCGATCATATTCACTGT
* *
43535713 TACTGATGGCTTTGTTCCGATCATATT-ACCGT
1 TACTGATGGCTTTGTGCCGATCATATTCACTGT
* *
43535745 TACTGATGGCTGTGTGCC-AGTCATA-TCACTGC
1 TACTGATGGCTTTGTGCCGA-TCATATTCACTGT
*
43535777 TACTGATGGCTTTGTGCCAATCA
1 TACTGATGGCTTTGTGCCGATCA
43535800 CATTATTGTA
Statistics
Matches: 151, Mismatches: 26, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
31 4 0.03
32 145 0.96
33 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.37
Consensus pattern (33 bp):
TACTGATGGCTTTGTGCCGATCATATTCACTGT
Found at i:43535753 original size:96 final size:96
Alignment explanation
Indices: 43535582--43535799 Score: 287
Period size: 96 Copynumber: 2.3 Consensus size: 96
43535572 TTTGCTGCGA
* * *
43535582 TGCTACTGATGGCTTTGTGTCAATCATAGTACTGTTACTGATGGCTTTGTGCTGATCATATTACA
1 TGCTACTGATGGCTTTGTGCCAATCATAGTACTGCTACTGATGGCTTTGTGCCGATCATATTACA
* * *
43535647 ATTACCGATGGCTGTGTGTC-GATCATTTCAT
66 ATTACCGATGGCTGTGTGCCAG-TCATATCAC
* * * *
43535678 TGTTACTGATGGCTGTGTGCCGATCATA-TCACTGCTACTGATGGCTTTGTTCCGATCATATTAC
1 TGCTACTGATGGCTTTGTGCCAATCATAGT-ACTGCTACTGATGGCTTTGTGCCGATCATATTAC
** *
43535742 CGTTACTGATGGCTGTGTGCCAGTCATATCAC
65 AATTACCGATGGCTGTGTGCCAGTCATATCAC
43535774 TGCTACTGATGGCTTTGTGCCAATCA
1 TGCTACTGATGGCTTTGTGCCAATCA
43535800 CATTATTGTA
Statistics
Matches: 104, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
95 1 0.01
96 102 0.98
97 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.37
Consensus pattern (96 bp):
TGCTACTGATGGCTTTGTGCCAATCATAGTACTGCTACTGATGGCTTTGTGCCGATCATATTACA
ATTACCGATGGCTGTGTGCCAGTCATATCAC
Found at i:43535841 original size:22 final size:21
Alignment explanation
Indices: 43535816--43535875 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 21
43535806 TGTACTTGTG
43535816 GCTTGTAGCCATTCTGTTTATA
1 GCTT-TAGCCATTCTGTTTATA
* *
43535838 GCTTATAGCTA-TCTTGTTTATG
1 GCTT-TAGCCATTC-TGTTTATA
43535860 GCTCTTAGCCATTCTG
1 GCT-TTAGCCATTCTG
43535876 ACTACTAGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
21 2 0.06
22 26 0.84
23 3 0.10
ACGTcount: A:0.17, C:0.20, G:0.18, T:0.45
Consensus pattern (21 bp):
GCTTTAGCCATTCTGTTTATA
Found at i:43538789 original size:14 final size:14
Alignment explanation
Indices: 43538770--43538818 Score: 71
Period size: 14 Copynumber: 3.5 Consensus size: 14
43538760 CTCCTTAAAA
43538770 GAAATTTTATCCTC
1 GAAATTTTATCCTC
*
43538784 GAAATTTTGTCCTC
1 GAAATTTTATCCTC
* *
43538798 AAAATTTCATCCTC
1 GAAATTTTATCCTC
43538812 GAAATTT
1 GAAATTT
43538819 ACCTGATACG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.31, C:0.20, G:0.08, T:0.41
Consensus pattern (14 bp):
GAAATTTTATCCTC
Found at i:43541966 original size:50 final size:49
Alignment explanation
Indices: 43541890--43542085 Score: 160
Period size: 50 Copynumber: 3.8 Consensus size: 49
43541880 CCTGTACTAC
* * *
43541890 CAATGTCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGT
1 CAATGCCATGTCCCAGACATGGTCTTACATGGGA-TTCTCATATCGGTGT
* *** * * * *
43541940 CGATGCCATGTCCCAGACATGGTCTTATGGGGGACCTATCATCTCGGTGC
1 CAATGCCATGTCCCAGACATGGTCTTACATGGGA-TTCTCATATCGGTGT
* * **
43541990 CAACGCCATGTCCCAGACATGGTCTTACATAGGATCTCTCATAACCTCAATAATGT
1 CAATGCCATGTCCCAGACATGGTCTTACATGGGAT-TCTCAT-A--TC---GGTGT
*
43542046 CAATGCAATGTCCCAGACATGGTCTTACATGGGA-TCTCAT
1 CAATGCCATGTCCCAGACATGGTCTTACATGGGATTCTCAT
43542086 TCCCTTAATG
Statistics
Matches: 112, Mismatches: 27, Indels: 10
0.75 0.18 0.07
Matches are distributed among these distances:
50 71 0.63
53 2 0.02
54 6 0.05
56 33 0.29
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.29
Consensus pattern (49 bp):
CAATGCCATGTCCCAGACATGGTCTTACATGGGATTCTCATATCGGTGT
Found at i:43544491 original size:20 final size:21
Alignment explanation
Indices: 43544444--43544494 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
43544434 GTATCATGAT
43544444 CTTTGCTT-CTTCTTTACTTA
1 CTTTGCTTACTTCTTTACTTA
* *
43544464 CTCT-CTTACTTGTTTACTTA
1 CTTTGCTTACTTCTTTACTTA
43544484 -TTTGCTTACTT
1 CTTTGCTTACTT
43544495 AAATAATTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.12, C:0.24, G:0.06, T:0.59
Consensus pattern (21 bp):
CTTTGCTTACTTCTTTACTTA
Found at i:43544841 original size:49 final size:50
Alignment explanation
Indices: 43544742--43544847 Score: 151
Period size: 49 Copynumber: 2.1 Consensus size: 50
43544732 ATGTTTCCTG
* * *
43544742 TCTCATATCGGTGCCCATGCCATGTCCCAGACATGGTCTTACGAGGGACC
1 TCTCATATCGGTGCCAACGCCATGTCCAAGACATGGTCTTACGAGGGACC
* *
43544792 TCTCATCTCGGTGCCAACGCCATGT-CAAGACATGGTCTTACGTGGGACC
1 TCTCATATCGGTGCCAACGCCATGTCCAAGACATGGTCTTACGAGGGACC
*
43544841 TTTCATA
1 TCTCATA
43544848 ACCTCAATAA
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
49 27 0.55
50 22 0.45
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26
Consensus pattern (50 bp):
TCTCATATCGGTGCCAACGCCATGTCCAAGACATGGTCTTACGAGGGACC
Found at i:43556096 original size:20 final size:19
Alignment explanation
Indices: 43556071--43556110 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
43556061 CAACTTGTGG
43556071 ACAAGCCACCAGTATTGCAA
1 ACAAG-CACCAGTATTGCAA
*
43556091 ACAAGCGCCAGTATTGCAA
1 ACAAGCACCAGTATTGCAA
43556110 A
1 A
43556111 TAAACTGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.40, C:0.28, G:0.17, T:0.15
Consensus pattern (19 bp):
ACAAGCACCAGTATTGCAA
Found at i:43556223 original size:20 final size:20
Alignment explanation
Indices: 43556200--43556282 Score: 71
Period size: 20 Copynumber: 4.2 Consensus size: 20
43556190 CAAGTTTTTG
*
43556200 GTATTGCAGATAAACTACCA
1 GTATTGCAGACAAACTACCA
43556220 GTATTGTC-GACAAGAC-ACCA
1 GTATTG-CAGACAA-ACTACCA
** * **
43556240 GTATTATAGACAAGCTGTCA
1 GTATTGCAGACAAACTACCA
*
43556260 GTATTGTAGACAAACTACCA
1 GTATTGCAGACAAACTACCA
43556280 GTA
1 GTA
43556283 CTTCCTCCTT
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
19 1 0.02
20 45 0.92
21 3 0.06
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.25
Consensus pattern (20 bp):
GTATTGCAGACAAACTACCA
Found at i:43563905 original size:21 final size:20
Alignment explanation
Indices: 43563848--43563906 Score: 66
Period size: 21 Copynumber: 3.0 Consensus size: 20
43563838 GAGTACATTA
43563848 TAAACAGAAGCCCG-AAGGC
1 TAAACAGAAGCCCGTAAGGC
* * *
43563867 TACACAGAAGCACATAAGTGC
1 TAAACAGAAGCCCGTAAG-GC
*
43563888 TAAACAGGAGCCCGTAAGG
1 TAAACAGAAGCCCGTAAGG
43563907 GTTGAACGGA
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
19 11 0.35
20 4 0.13
21 16 0.52
ACGTcount: A:0.41, C:0.24, G:0.25, T:0.10
Consensus pattern (20 bp):
TAAACAGAAGCCCGTAAGGC
Found at i:43563949 original size:42 final size:41
Alignment explanation
Indices: 43563902--43564049 Score: 161
Period size: 42 Copynumber: 3.5 Consensus size: 41
43563892 CAGGAGCCCG
* * *
43563902 TAAGGGTTGAACGGAAGCTCATAGAAGCTGAACGGAAACCCA
1 TAAGGGTTAAACTGAAGCTCATA-AAGCTGAACTGAAACCCA
* * * *
43563944 TAAGGGTTAATCTGAAGCTCAGAAGAGCTAAATTGAAACCCA
1 TAAGGGTTAAACTGAAGCTCATAA-AGCTGAACTGAAACCCA
* * *
43563986 TTAGGGTTAAACTGAAGCTCAAAAAAGCTGAACTAAAACCCA
1 TAAGGGTTAAACTGAAGCTC-ATAAAGCTGAACTGAAACCCA
* *
43564028 GAAAGGTTAAACTGAAGCTCAT
1 TAAGGGTTAAACTGAAGCTCAT
43564050 GAGAGTAAAA
Statistics
Matches: 87, Mismatches: 17, Indels: 5
0.80 0.16 0.05
Matches are distributed among these distances:
41 2 0.02
42 82 0.94
43 3 0.03
ACGTcount: A:0.41, C:0.18, G:0.22, T:0.19
Consensus pattern (41 bp):
TAAGGGTTAAACTGAAGCTCATAAAGCTGAACTGAAACCCA
Found at i:43571548 original size:20 final size:18
Alignment explanation
Indices: 43571524--43571589 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 18
43571514 TACAAAAGAC
43571524 ATTCAAAATAATTTTCAAA
1 ATTCAAAATAATTTT-AAA
43571543 ACTTCAAAATAAATTTTAAA
1 A-TTCAAAAT-AATTTTAAA
*
43571563 ATTTAAAAT-ATTTATAAAA
1 ATTCAAAATAATTT-T-AAA
43571582 ATTCAAAA
1 ATTCAAAA
43571590 ATTTCTATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
17 4 0.10
18 1 0.02
19 18 0.44
20 12 0.29
21 6 0.15
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (18 bp):
ATTCAAAATAATTTTAAA
Found at i:43575184 original size:85 final size:86
Alignment explanation
Indices: 43575041--43575233 Score: 212
Period size: 85 Copynumber: 2.3 Consensus size: 86
43575031 AAAAACGCCG
* * ** *
43575041 CTATAAATCATGACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTATAAACCAGGACCTTTAGCG
1 CTATAGATCAAGACCTTTAGCGGCGCTTTTTCCACAAAAACCACTATAAACCAGGACCTTTAGCG
* *
43575106 GCACTTTT-ACACAAACACTA
66 ACACTTTTCACACAAACACCA
* *
43575126 CTATAGATCAAGACCTTTAGTGGCGCTTTTTCCACAAAAACCACTAT-AGCTC-GAGACCTTTAG
1 CTATAGATCAAGACCTTTAGCGGCGCTTTTTCCACAAAAACCACTATAAAC-CAG-GACCTTTAG
* * ** *
43575189 CGACGCTTTTCCCACAAATGCCG
64 CGACACTTTTCACACAAACACCA
*
43575212 CTATAGCTCAAGACCTTTAGCG
1 CTATAGATCAAGACCTTTAGCG
43575234 ATGCTTCCTG
Statistics
Matches: 89, Mismatches: 16, Indels: 5
0.81 0.15 0.05
Matches are distributed among these distances:
84 3 0.03
85 59 0.66
86 27 0.30
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (86 bp):
CTATAGATCAAGACCTTTAGCGGCGCTTTTTCCACAAAAACCACTATAAACCAGGACCTTTAGCG
ACACTTTTCACACAAACACCA
Found at i:43575234 original size:43 final size:43
Alignment explanation
Indices: 43575033--43575233 Score: 208
Period size: 43 Copynumber: 4.7 Consensus size: 43
43575023 AACGCCGAAA
** *
43575033 AAACGCCGCTATAAATCATGACCTTTAGCGGCGCTTTTTCCAC
1 AAACGCCGCTATAGCTCAAGACCTTTAGCGGCGCTTTTTCCAC
* * * *
43575076 AAACGCCGCTATAAAC-CAGGACCTTTAGCGGCAC-TTTTACAC
1 AAACGCCGCTAT-AGCTCAAGACCTTTAGCGGCGCTTTTTCCAC
* ** * *
43575118 AAACACTACTATAGATCAAGACCTTTAGTGGCGCTTTTTCCAC
1 AAACGCCGCTATAGCTCAAGACCTTTAGCGGCGCTTTTTCCAC
** * * * *
43575161 AAAAACCACTATAGCTCGAGACCTTTAGCGACGCTTTTCCCAC
1 AAACGCCGCTATAGCTCAAGACCTTTAGCGGCGCTTTTTCCAC
*
43575204 AAATGCCGCTATAGCTCAAGACCTTTAGCG
1 AAACGCCGCTATAGCTCAAGACCTTTAGCG
43575234 ATGCTTCCTG
Statistics
Matches: 131, Mismatches: 24, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
41 1 0.01
42 31 0.24
43 97 0.74
44 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTATAGCTCAAGACCTTTAGCGGCGCTTTTTCCAC
Found at i:43575539 original size:118 final size:118
Alignment explanation
Indices: 43575406--43575642 Score: 474
Period size: 118 Copynumber: 2.0 Consensus size: 118
43575396 TTCTATGAAA
43575406 ATTTTAACTTTAAAACTAAATATAAAAATTAATGAATTTAGTTTTAGAATTTAAAATAATAAATT
1 ATTTTAACTTTAAAACTAAATATAAAAATTAATGAATTTAGTTTTAGAATTTAAAATAATAAATT
43575471 AATAACACAATTAAGAGATCAGCTAGCACATTAGGAAGGGAGAGAAGTGAGAG
66 AATAACACAATTAAGAGATCAGCTAGCACATTAGGAAGGGAGAGAAGTGAGAG
43575524 ATTTTAACTTTAAAACTAAATATAAAAATTAATGAATTTAGTTTTAGAATTTAAAATAATAAATT
1 ATTTTAACTTTAAAACTAAATATAAAAATTAATGAATTTAGTTTTAGAATTTAAAATAATAAATT
43575589 AATAACACAATTAAGAGATCAGCTAGCACATTAGGAAGGGAGAGAAGTGAGAG
66 AATAACACAATTAAGAGATCAGCTAGCACATTAGGAAGGGAGAGAAGTGAGAG
43575642 A
1 A
43575643 ATAACTTGAG
Statistics
Matches: 119, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
118 119 1.00
ACGTcount: A:0.49, C:0.07, G:0.15, T:0.30
Consensus pattern (118 bp):
ATTTTAACTTTAAAACTAAATATAAAAATTAATGAATTTAGTTTTAGAATTTAAAATAATAAATT
AATAACACAATTAAGAGATCAGCTAGCACATTAGGAAGGGAGAGAAGTGAGAG
Found at i:43576927 original size:20 final size:20
Alignment explanation
Indices: 43576902--43576941 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
43576892 TTAGAATTTA
43576902 AAATAATAAATTAATAACAC
1 AAATAATAAATTAATAACAC
43576922 AAATAATAAATTAATAACAC
1 AAATAATAAATTAATAACAC
43576942 GTACTTGCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.25
Consensus pattern (20 bp):
AAATAATAAATTAATAACAC
Found at i:43577539 original size:39 final size:39
Alignment explanation
Indices: 43577490--43577568 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
43577480 GCACTGGCAA
* *
43577490 TCATTGAATTTATACCAAAGGCCTATCCATCATAACATG
1 TCATAGAATTTATACCAAAGGCCCATCCATCATAACATG
* * *
43577529 TCATAGAATTTATACCATATGCCCATGCATCATAACATG
1 TCATAGAATTTATACCAAAGGCCCATCCATCATAACATG
43577568 T
1 T
43577569 TTGCATTTAG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.35, C:0.23, G:0.10, T:0.32
Consensus pattern (39 bp):
TCATAGAATTTATACCAAAGGCCCATCCATCATAACATG
Found at i:43579317 original size:205 final size:206
Alignment explanation
Indices: 43578965--43579375 Score: 729
Period size: 205 Copynumber: 2.0 Consensus size: 206
43578955 AAAATTATTT
*
43578965 TATTTTTGTATTTTAATTTTATTTTTTATAATTTGGTCCTTTCCAAAATAAATAATTATACCTAA
1 TATTTTTGTATTTTAATTTTATTTCTTATAATTTGGTCCTTTCCAAAATAAATAATTATACCTAA
43579030 ATATTCATATGAATCTATTACTTTTTTAAACTTATTTATTAATTCTATTTAAACTAATATTTAAA
66 ATATTCATATGAATCTATTACTTTTTTAAACTTATTTATTAATTCTATTTAAACTAATATTTAAA
* *
43579095 TATATCAAATGGTTTAGATTATAT-TTTTTTAAATATAAATGTATTAATTAATTGTATAAAATTT
131 TATATCAAATGGTTTAGATTAAATGTTTTTTAAATATAAAAGTATTAATTAATTGTATAAAATTT
**
43579159 TTTCATTTAAC
196 TACCATTTAAC
43579170 TATTTTTGTATTTTAATTTTATTTCTTATAATTTGGTCCTCTT-CAAAATAAATAATTATACCTA
1 TATTTTTGTATTTTAATTTTATTTCTTATAATTTGGTCCT-TTCCAAAATAAATAATTATACCTA
*
43579234 AATA-TCAATATGAATCTATTACTTTTTTTAACTTATTTATTAATTCTATTTAAACTAATATTTA
65 AATATTC-ATATGAATCTATTACTTTTTTAAACTTATTTATTAATTCTATTTAAACTAATATTTA
43579298 AATATATCAAATGGTTTAGATTAAATGTTTTTTAAATATAAAAGTATTAATTAATTGTATAAAAT
129 AATATATCAAATGGTTTAGATTAAATGTTTTTTAAATATAAAAGTATTAATTAATTGTATAAAAT
43579363 TTTACCATTTAAC
194 TTTACCATTTAAC
43579376 CAATCTCAAG
Statistics
Matches: 197, Mismatches: 6, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
204 2 0.01
205 145 0.74
206 50 0.25
ACGTcount: A:0.37, C:0.08, G:0.05, T:0.50
Consensus pattern (206 bp):
TATTTTTGTATTTTAATTTTATTTCTTATAATTTGGTCCTTTCCAAAATAAATAATTATACCTAA
ATATTCATATGAATCTATTACTTTTTTAAACTTATTTATTAATTCTATTTAAACTAATATTTAAA
TATATCAAATGGTTTAGATTAAATGTTTTTTAAATATAAAAGTATTAATTAATTGTATAAAATTT
TACCATTTAAC
Found at i:43579673 original size:14 final size:13
Alignment explanation
Indices: 43579649--43579692 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
43579639 CCCCTAACAC
*
43579649 CTAAACCTTAAAT
1 CTAATCCTTAAAT
43579662 CTCAATCCTTAAAT
1 CT-AATCCTTAAAT
*
43579676 CATAATCCTTATAT
1 C-TAATCCTTAAAT
43579690 CTA
1 CTA
43579693 TACTCCCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 4 0.15
14 22 0.81
15 1 0.04
ACGTcount: A:0.39, C:0.25, G:0.00, T:0.36
Consensus pattern (13 bp):
CTAATCCTTAAAT
Found at i:43579986 original size:7 final size:7
Alignment explanation
Indices: 43579974--43580012 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
43579964 CCTTAAACCG
43579974 TAATCCC
1 TAATCCC
43579981 TAATCCC
1 TAATCCC
43579988 TAATCCC
1 TAATCCC
*
43579995 TAAATCCA
1 T-AATCCC
*
43580003 TACTCCC
1 TAATCCC
43580010 TAA
1 TAA
43580013 ACCTTAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 21 0.78
8 6 0.22
ACGTcount: A:0.33, C:0.38, G:0.00, T:0.28
Consensus pattern (7 bp):
TAATCCC
Found at i:43580000 original size:15 final size:15
Alignment explanation
Indices: 43579974--43580013 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
43579964 CCTTAAACCG
*
43579974 TAATCCCT-AATCCC
1 TAATCCCTAAATCCA
43579988 TAATCCCTAAATCCA
1 TAATCCCTAAATCCA
*
43580003 TACTCCCTAAA
1 TAATCCCTAAA
43580014 CCTTAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.35
15 15 0.65
ACGTcount: A:0.35, C:0.38, G:0.00, T:0.28
Consensus pattern (15 bp):
TAATCCCTAAATCCA
Found at i:43580020 original size:22 final size:21
Alignment explanation
Indices: 43579879--43580020 Score: 72
Period size: 21 Copynumber: 6.7 Consensus size: 21
43579869 GCCCCTGAAT
* *
43579879 CCCTAAACCATAAATCCATAA
1 CCCTAAACCCTAAATCCATAC
** * * *
43579900 CATTAACCCCTAATGTCTA-AC
1 CCCTAAACCCTAA-ATCCATAC
* *
43579921 CCCTAAACCCCAAAGCCATAAC
1 CCCTAAACCCTAAATCCAT-AC
* **
43579943 CCCTAAACCTTAAATCCCGAC
1 CCCTAAACCCTAAATCCATAC
* * * *
43579964 CCTTAAACCGT-AATCCCTAAT
1 CCCTAAACCCTAAATCCAT-AC
*
43579985 CCCTAATCCCTAAATCCATAC
1 CCCTAAACCCTAAATCCATAC
*
43580006 TCCCTAAACCTTAAA
1 -CCCTAAACCCTAAA
43580021 ATAGTAACTC
Statistics
Matches: 85, Mismatches: 30, Indels: 11
0.67 0.24 0.09
Matches are distributed among these distances:
20 8 0.09
21 40 0.47
22 37 0.44
ACGTcount: A:0.37, C:0.38, G:0.03, T:0.22
Consensus pattern (21 bp):
CCCTAAACCCTAAATCCATAC
Found at i:43580508 original size:82 final size:81
Alignment explanation
Indices: 43580364--43580522 Score: 230
Period size: 82 Copynumber: 2.0 Consensus size: 81
43580354 TAAAATATTT
* * *
43580364 TTAGTGACGCTTTTTTAAAAACGCCGCCAAAGACCCCAGCATTAGCGGAGCTTTTCCTAAAACGC
1 TTAGTGACGCTTTCTCAAAAACGCCGCCAAAGACCCCAGCATTAGCGGAGCTTTTCCAAAAACGC
43580429 CGCTAAAGGCCCCAACA
66 CGCTAAA-GCCCCAACA
* * * *
43580446 TTAGTGGCGCTTTCTCAAAAACGCCGCTAAA-ACCCCGAGCATTAGCGGCGCTTTTTCAAAAACG
1 TTAGTGACGCTTTCTCAAAAACGCCGCCAAAGACCCC-AGCATTAGCGGAGCTTTTCCAAAAACG
43580510 CCGCTAAAGCCCC
65 CCGCTAAAGCCCC
43580523 GAAAGGTAAG
Statistics
Matches: 69, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 10 0.14
82 59 0.86
ACGTcount: A:0.29, C:0.31, G:0.19, T:0.21
Consensus pattern (81 bp):
TTAGTGACGCTTTCTCAAAAACGCCGCCAAAGACCCCAGCATTAGCGGAGCTTTTCCAAAAACGC
CGCTAAAGCCCCAACA
Found at i:43580524 original size:41 final size:40
Alignment explanation
Indices: 43580371--43580522 Score: 196
Period size: 41 Copynumber: 3.7 Consensus size: 40
43580361 TTTTTAGTGA
* *
43580371 CGCTTTTTTAAAAACGCCGCCAAAGACCCCAGCATTAGCGG
1 CGCTTTTTCAAAAACGCCGCTAAAG-CCCCAGCATTAGCGG
* * * * *
43580412 AGCTTTTCCTAAAACGCCGCTAAAGGCCCCAACATTAGTGG
1 CGCTTTTTCAAAAACGCCGCTAAA-GCCCCAGCATTAGCGG
* *
43580453 CGCTTTCTCAAAAACGCCGCTAAAACCCCGAGCATTAGCGG
1 CGCTTTTTCAAAAACGCCGCTAAAGCCCC-AGCATTAGCGG
43580494 CGCTTTTTCAAAAACGCCGCTAAAGCCCC
1 CGCTTTTTCAAAAACGCCGCTAAAGCCCC
43580523 GAAAGGTAAG
Statistics
Matches: 93, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 4 0.04
41 88 0.95
42 1 0.01
ACGTcount: A:0.29, C:0.33, G:0.18, T:0.20
Consensus pattern (40 bp):
CGCTTTTTCAAAAACGCCGCTAAAGCCCCAGCATTAGCGG
Found at i:43581055 original size:70 final size:70
Alignment explanation
Indices: 43580977--43581115 Score: 224
Period size: 70 Copynumber: 2.0 Consensus size: 70
43580967 AGTTGGAATA
* * ** *
43580977 AAATAATAGATTGATCGGTTCCAAATATGAAAATTCTTTTAGATGGTCATATAGTGGAGGCGGGT
1 AAATAATAGATTGATCAGTTCAAAATATGAAAATTCTTCAAGATGGTCATATAGTGGAGGCGAGT
43581042 GCTCC
66 GCTCC
*
43581047 AAATAATAGATTGATTAGTTCAAAATATGAAAATTCTTCAAGATGGTCATATAGTGGAGGCGAGT
1 AAATAATAGATTGATCAGTTCAAAATATGAAAATTCTTCAAGATGGTCATATAGTGGAGGCGAGT
43581112 GCTC
66 GCTC
43581116 TAGAAGAGAC
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
70 63 1.00
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.31
Consensus pattern (70 bp):
AAATAATAGATTGATCAGTTCAAAATATGAAAATTCTTCAAGATGGTCATATAGTGGAGGCGAGT
GCTCC
Found at i:43586500 original size:16 final size:16
Alignment explanation
Indices: 43586479--43586514 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
43586469 TAACTCAGGA
43586479 GCTGCAGGAGTACATG
1 GCTGCAGGAGTACATG
43586495 GCTGCAGGAGTACATG
1 GCTGCAGGAGTACATG
43586511 GCTG
1 GCTG
43586515 TGATTTCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.22, C:0.19, G:0.39, T:0.19
Consensus pattern (16 bp):
GCTGCAGGAGTACATG
Found at i:43587357 original size:120 final size:120
Alignment explanation
Indices: 43587231--43587520 Score: 485
Period size: 120 Copynumber: 2.4 Consensus size: 120
43587221 AATTATTTTA
* *
43587231 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTT-TCTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATATTAATTATTT-AAATTTATATTT
* *
43587295 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGACTATTAATTATTAAG
65 TACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* *
43587351 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATT-ATTATTTTAATTTATATTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAAT-ATTAATTATTTAAATTTATATTT
43587415 TACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
43587471 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTAT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATATTAATTAT
43587521 GTTTAAATAT
Statistics
Matches: 159, Mismatches: 8, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
119 7 0.04
120 149 0.94
121 3 0.02
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATATTAATTATTTAAATTTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:43587413 original size:15 final size:14
Alignment explanation
Indices: 43587361--43587416 Score: 55
Period size: 15 Copynumber: 4.1 Consensus size: 14
43587351 AATTTTATTA
43587361 AATTATA-TATTTT
1 AATTATATTATTTT
*
43587374 AATTATAATATATTT
1 AATTATATTAT-TTT
*
43587389 AATAATTATTATTTT
1 AATTA-TATTATTTT
43587404 AATT-TA-TATTTT
1 AATTATATTATTTT
43587416 A
1 A
43587417 CAGTATCATA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
12 7 0.19
13 9 0.24
14 3 0.08
15 13 0.35
16 5 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
AATTATATTATTTT
Found at i:43587477 original size:61 final size:61
Alignment explanation
Indices: 43587292--43587478 Score: 183
Period size: 61 Copynumber: 3.1 Consensus size: 61
43587282 TCAAATTTTC
*
43587292 TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGACTATTAATTATTAAGAA
1 TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAA
* * * * * * *
43587353 TTTTATTA-AATTATATATT-TTAATT-A-T-AATAT-ATTTAATAATTATT-ATT-TTAATTTA
1 TTTTA-TAGTATCATATATTATGATTTGAGTAAAT-TCATATAAGAA-TATTAATTATTAA--GA
43587410 TA
61 -A
*
43587412 TTTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAA
1 TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAA
43587473 TTTTAT
1 TTTTAT
43587479 TAAATTATAT
Statistics
Matches: 95, Mismatches: 17, Indels: 28
0.68 0.12 0.20
Matches are distributed among these distances:
56 4 0.04
57 12 0.13
58 8 0.08
59 16 0.17
60 8 0.08
61 21 0.22
62 9 0.09
63 13 0.14
64 4 0.04
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (61 bp):
TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAA
Found at i:43587500 original size:18 final size:17
Alignment explanation
Indices: 43587472--43587506 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
43587462 ATTATTAAGA
*
43587472 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
43587489 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
43587507 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:43587620 original size:147 final size:149
Alignment explanation
Indices: 43587460--43587734 Score: 509
Period size: 147 Copynumber: 1.9 Consensus size: 149
43587450 ATAAGAATAT
*
43587460 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
*
43587525 AAATATGATTAAATTATTTATTATTGAT-ATTAATAATCTTATTAAAATTTAAATAA-AATAATT
66 AAATATGATTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAACAATAATT
43587588 TACCAAAACAAATTTCTGC
131 TACCAAAACAAATTTCTGC
43587607 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
*
43587672 AAATATGATTAAATTATTTATTTTTGATAATAAATAATCTTATTAAAATTTAAATAACAATAA
66 AAATATGATTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAACAATAA
43587735 CAATAATCCT
Statistics
Matches: 123, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
147 91 0.74
148 27 0.22
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (149 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAACAATAATT
TACCAAAACAAATTTCTGC
Found at i:43587647 original size:18 final size:17
Alignment explanation
Indices: 43587619--43587653 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
43587609 ATTATTAAGA
*
43587619 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
43587636 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
43587654 TAAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:43587864 original size:44 final size:45
Alignment explanation
Indices: 43587815--43587909 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 45
43587805 TTACACCTCT
* * *
43587815 ATTACATTCAACCAAACA-CAGTTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACATCTATTCC
* *
43587859 ATTACATTCAACCAAACAGTAGATTTGCTATTACACATCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACATCTATTCC
43587904 ATTACA
1 ATTACA
43587910 CCTCTAATCC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.34
Consensus pattern (45 bp):
ATTACATTCAACCAAACAGCAGATTTACTATTACACATCTATTCC
Done.