Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 11 of 172
Found at i:3461186 original size:3 final size:3
Alignment explanation
Indices: 3461178--3461241 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
3461168 GAAAAATAAG
3461178 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
3461226 AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA A
3461242 AATGGAAGGA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:3468081 original size:14 final size:14
Alignment explanation
Indices: 3468059--3468088 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3468049 TTCTTTTTTG
3468059 TGTGAGAATGGAGT
1 TGTGAGAATGGAGT
*
3468073 TGTGTGAATGGAGT
1 TGTGAGAATGGAGT
3468087 TG
1 TG
3468089 ATAGGTTCGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.43, T:0.33
Consensus pattern (14 bp):
TGTGAGAATGGAGT
Found at i:3470283 original size:4 final size:4
Alignment explanation
Indices: 3470274--3470304 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
3470264 GTATTTTGTT
*
3470274 TTTA TTTA TTTG TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
3470305 TTGTCTTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:3470901 original size:9 final size:9
Alignment explanation
Indices: 3470887--3470920 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
3470877 ATACATGTGT
3470887 ATATATATA
1 ATATATATA
3470896 ATATATATA
1 ATATATATA
3470905 ATATATATA
1 ATATATATA
*
3470914 AAATATA
1 ATATATA
3470921 ATCTTTTCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
ATATATATA
Found at i:3477261 original size:20 final size:19
Alignment explanation
Indices: 3477204--3477263 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 19
3477194 TTTGTAATTT
3477204 ATAATAATTTAAATTAATAATG
1 ATAATAATTT-AATT--TAATG
*
3477226 ATAA-AATTATATTTTAACTG
1 ATAATAATT-TAATTTAA-TG
3477246 ATAATAATTTAATTTAAT
1 ATAATAATTTAATTTAAT
3477264 TCTTTAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
19 4 0.12
20 13 0.39
21 11 0.33
22 5 0.15
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (19 bp):
ATAATAATTTAATTTAATG
Found at i:3477922 original size:15 final size:15
Alignment explanation
Indices: 3477902--3477931 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3477892 TTAATTTATA
*
3477902 TATTTAAATTAATAT
1 TATTTAAAATAATAT
3477917 TATTTAAAATAATAT
1 TATTTAAAATAATAT
3477932 AACAAATTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTTAAAATAATAT
Found at i:3495644 original size:113 final size:113
Alignment explanation
Indices: 3495446--3495675 Score: 442
Period size: 113 Copynumber: 2.0 Consensus size: 113
3495436 CTTGCTGTCC
*
3495446 TTTTGGTTTCCCCACCTTTATCATGTCTTCTTGTGATGAACTTCTCTGTTCCAACCCTATTTATA
1 TTTTGGTTTCCCCACCTTTATCATGTCTTCTTGTGATAAACTTCTCTGTTCCAACCCTATTTATA
*
3495511 CTTTAGATCGAAGCAGCATGCTTGAGTTTATCCCATTTGACTCTTTTT
66 CTTTAGATCGAAGCAGCATGCTTGAGTTTAGCCCATTTGACTCTTTTT
3495559 TTTTGGTTTCCCCACCTTTATCATGTCTTCTTGTGATAAACTTCTCTGTTCCAACCCTATTTATA
1 TTTTGGTTTCCCCACCTTTATCATGTCTTCTTGTGATAAACTTCTCTGTTCCAACCCTATTTATA
3495624 CTTTAGATCGAAGCAGCATGCTTGAGTTTAGCCCATTTGACTCTTTTT
66 CTTTAGATCGAAGCAGCATGCTTGAGTTTAGCCCATTTGACTCTTTTT
3495672 TTTT
1 TTTT
3495676 AATGTGGGTG
Statistics
Matches: 115, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
113 115 1.00
ACGTcount: A:0.19, C:0.23, G:0.13, T:0.45
Consensus pattern (113 bp):
TTTTGGTTTCCCCACCTTTATCATGTCTTCTTGTGATAAACTTCTCTGTTCCAACCCTATTTATA
CTTTAGATCGAAGCAGCATGCTTGAGTTTAGCCCATTTGACTCTTTTT
Found at i:3499131 original size:30 final size:30
Alignment explanation
Indices: 3499097--3499155 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
3499087 TATTTTATTG
3499097 TTAATTTTGTTATTATTTTAAAGGCATTTC
1 TTAATTTTGTTATTATTTTAAAGGCATTTC
*
3499127 TTAATTTTGTTATTATTTTAGAGGCATTT
1 TTAATTTTGTTATTATTTTAAAGGCATTT
3499156 ACTTGTAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.25, C:0.05, G:0.12, T:0.58
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGGCATTTC
Found at i:3517915 original size:38 final size:38
Alignment explanation
Indices: 3517864--3517938 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 38
3517854 TCAAGAACAG
3517864 AGCTGCATTGATAGCACCGCCTTGACGACCGCCGGTAA
1 AGCTGCATTGATAGCACCGCCTTGACGACCGCCGGTAA
*
3517902 AGCTGCATTGATAGCACCGCCTTGGCGACCGCCGGTA
1 AGCTGCATTGATAGCACCGCCTTGACGACCGCCGGTA
3517939 TTTACCATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.21, C:0.32, G:0.28, T:0.19
Consensus pattern (38 bp):
AGCTGCATTGATAGCACCGCCTTGACGACCGCCGGTAA
Found at i:3521768 original size:19 final size:19
Alignment explanation
Indices: 3521739--3521776 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
3521729 CCGATTCAAT
3521739 TAAAAAATT-AATAAAAAA
1 TAAAAAATTAAATAAAAAA
3521757 TAAAAAATTTAAATAAAAAA
1 TAAAAAA-TTAAATAAAAAA
3521777 AACTTGGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
19 2 0.11
20 9 0.50
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (19 bp):
TAAAAAATTAAATAAAAAA
Found at i:3526654 original size:25 final size:25
Alignment explanation
Indices: 3526626--3526739 Score: 83
Period size: 25 Copynumber: 4.6 Consensus size: 25
3526616 CTTATGAGTA
*
3526626 TCCCGATACTTGGCTCTCACGAGCT
1 TCCCGATAATTGGCTCTCACGAGCT
*
3526651 TCCC-ATTATTTGGCTCTC-CGGAGCT
1 TCCCGA-TAATTGGCTCTCAC-GAGCT
* * *
3526676 TCCCGATAATAGGCTCTTATGAGCT
1 TCCCGATAATTGGCTCTCACGAGCT
* * * *
3526701 TCTCGATTAA-AGGTTCTC-CGAACT
1 TCCCGA-TAATTGGCTCTCACGAGCT
3526725 GTCCCGATAATTGGC
1 -TCCCGATAATTGGC
3526740 ATGCAATAGC
Statistics
Matches: 69, Mismatches: 13, Indels: 14
0.72 0.14 0.15
Matches are distributed among these distances:
24 9 0.13
25 56 0.81
26 4 0.06
ACGTcount: A:0.19, C:0.29, G:0.20, T:0.32
Consensus pattern (25 bp):
TCCCGATAATTGGCTCTCACGAGCT
Found at i:3526764 original size:25 final size:25
Alignment explanation
Indices: 3526747--3526821 Score: 89
Period size: 25 Copynumber: 3.0 Consensus size: 25
3526737 GGCATGCAAT
3526747 AGCTTCCCATTACATGGCTCACATG
1 AGCTTCCCATTACATGGCTCACATG
* * * *
3526772 AGCTTCCCGTTATATGGCTCAAAAG
1 AGCTTCCCATTACATGGCTCACATG
*
3526797 AGCTTCCCGATTACAT-GCTCGCATG
1 AGCTTCCC-ATTACATGGCTCACATG
3526822 GGCATACCTG
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
25 35 0.88
26 5 0.12
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (25 bp):
AGCTTCCCATTACATGGCTCACATG
Found at i:3528467 original size:25 final size:25
Alignment explanation
Indices: 3528356--3528471 Score: 66
Period size: 25 Copynumber: 4.8 Consensus size: 25
3528346 GAAGCTCATA
3528356 AGAG-GCCATA-ATCGAGAAG-TTC
1 AGAGAGCCATATATCGAGAAGCTTC
* * *
3528378 AAGCGAGCCA-ATATCGGGAAGCTCC
1 -AGAGAGCCATATATCGAGAAGCTTC
* * *
3528403 GGAGAGCCAT-TAAACAAGAAGC-TC
1 AGAGAGCCATAT-ATCGAGAAGCTTC
* * *
3528427 ATAAGAACC-TATTATCGGGAAGCTTC
1 A-GAGAGCCATA-TATCGAGAAGCTTC
3528453 AGAGAGCCATATATCGAGA
1 AGAGAGCCATATATCGAGA
3528472 CGCTCATAAG
Statistics
Matches: 65, Mismatches: 18, Indels: 18
0.64 0.18 0.18
Matches are distributed among these distances:
23 4 0.06
24 22 0.34
25 33 0.51
26 6 0.09
ACGTcount: A:0.37, C:0.21, G:0.25, T:0.17
Consensus pattern (25 bp):
AGAGAGCCATATATCGAGAAGCTTC
Found at i:3543149 original size:20 final size:19
Alignment explanation
Indices: 3543098--3543152 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
3543088 ATATATTTTA
3543098 ATATTTTTTATTTAAACATT
1 ATATTTTTT-TTTAAACATT
* *
3543118 ATATTATATTTTAAAC-TT
1 ATATTTTTTTTTAAACATT
3543136 GAGTATTTTTTTTTAAA
1 -A-TATTTTTTTTTAAA
3543153 GTTAGTTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 2 0.07
19 8 0.28
20 19 0.66
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (19 bp):
ATATTTTTTTTTAAACATT
Found at i:3551913 original size:3 final size:3
Alignment explanation
Indices: 3551905--3551956 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
3551895 ATCTTGTATC
* * *
3551905 ATT ATT ATT ATT ATT ATTT ATTT ATT ATT TTT ATT TTT ATT TTT ATT
1 ATT ATT ATT ATT ATT A-TT A-TT ATT ATT ATT ATT ATT ATT ATT ATT
*
3551952 TTT AT
1 ATT AT
3551957 ATTCATGTGC
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
3 33 0.82
4 7 0.17
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (3 bp):
ATT
Found at i:3552257 original size:8 final size:8
Alignment explanation
Indices: 3552244--3552268 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
3552234 TGTTATAACA
3552244 TATATATT
1 TATATATT
3552252 TATATATT
1 TATATATT
3552260 TATATATT
1 TATATATT
3552268 T
1 T
3552269 TTCTTTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TATATATT
Found at i:3556750 original size:16 final size:17
Alignment explanation
Indices: 3556721--3556752 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
3556711 TGAATTGATG
3556721 ATATGAAGTTATGTGAA
1 ATATGAAGTTATGTGAA
3556738 ATATGAA-TTATGTGA
1 ATATGAAGTTATGTGA
3556753 TTGCATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.38
Consensus pattern (17 bp):
ATATGAAGTTATGTGAA
Found at i:3571838 original size:21 final size:22
Alignment explanation
Indices: 3571809--3571855 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
3571799 CAGAAGGAGT
*
3571809 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
3571831 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
3571852 GAGT
1 GAGT
3571856 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:3575048 original size:21 final size:22
Alignment explanation
Indices: 3575019--3575065 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
3575009 CAGAAGGAGT
*
3575019 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
3575041 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
3575062 GAGT
1 GAGT
3575066 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:3576161 original size:18 final size:17
Alignment explanation
Indices: 3576138--3576173 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
3576128 ACATCCACCA
3576138 ATAATTATATCAGTCGTT
1 ATAATTATATCAGT-GTT
3576156 ATAATTATATCAGTGTT
1 ATAATTATATCAGTGTT
3576173 A
1 A
3576174 GTTTTTAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.44
Consensus pattern (17 bp):
ATAATTATATCAGTGTT
Found at i:3582970 original size:16 final size:16
Alignment explanation
Indices: 3582949--3582985 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
3582939 AAGCCCTCAT
3582949 TTCTTCAATCATAGCC
1 TTCTTCAATCATAGCC
3582965 TTCTTCAATCATAGCC
1 TTCTTCAATCATAGCC
3582981 TTCTT
1 TTCTT
3582986 TCATCTTGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.22, C:0.30, G:0.05, T:0.43
Consensus pattern (16 bp):
TTCTTCAATCATAGCC
Found at i:3585362 original size:22 final size:22
Alignment explanation
Indices: 3585334--3585375 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3585324 CATTCTGTAG
3585334 GAATATTCTGTAAATATTTTAA
1 GAATATTCTGTAAATATTTTAA
* *
3585356 GAATATTTTGTAGATATTTT
1 GAATATTCTGTAAATATTTT
3585376 CTTTATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.50
Consensus pattern (22 bp):
GAATATTCTGTAAATATTTTAA
Found at i:3589134 original size:22 final size:22
Alignment explanation
Indices: 3589106--3589150 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
3589096 AGGGGGAGTG
3589106 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
3589128 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
3589150 T
1 T
3589151 CTTTATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:3596965 original size:15 final size:15
Alignment explanation
Indices: 3596945--3596995 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
3596935 GTTCGAGCGT
3596945 AAAAATTATATTTAA
1 AAAAATTATATTTAA
** * *
3596960 AAAAATT-CCTTGAG
1 AAAAATTATATTTAA
3596974 AAAAATTATATTTAA
1 AAAAATTATATTTAA
3596989 AAAAATT
1 AAAAATT
3596996 CCTTGAGAAG
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
14 10 0.37
15 17 0.63
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (15 bp):
AAAAATTATATTTAA
Found at i:3596987 original size:29 final size:29
Alignment explanation
Indices: 3596945--3597004 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
3596935 GTTCGAGCGT
3596945 AAAAATTATATTTAAAAAAATTCCTTGAG
1 AAAAATTATATTTAAAAAAATTCCTTGAG
3596974 AAAAATTATATTTAAAAAAATTCCTTGAG
1 AAAAATTATATTTAAAAAAATTCCTTGAG
3597003 AA
1 AA
3597005 GTTGAAGTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (29 bp):
AAAAATTATATTTAAAAAAATTCCTTGAG
Found at i:3605379 original size:42 final size:42
Alignment explanation
Indices: 3605305--3605416 Score: 138
Period size: 42 Copynumber: 2.6 Consensus size: 42
3605295 TATAGGATTT
* *
3605305 TCGATATATGTTATCGTGTAAGACCACATCTGGGACATTGGCA
1 TCGATATGTGTTA-CGTGTAAGACCACATCTGGGACAGTGGCA
*
3605348 TCGACT-TGTGTTACGTGTAAGACC-CTGTCTGGGACAGTGGCA
1 TCGA-TATGTGTTACGTGTAAGACCAC-ATCTGGGACAGTGGCA
*
3605390 TCGATATGTGATTACATGTAAGACCAC
1 TCGATATGTG-TTACGTGTAAGACCAC
3605417 GCCAGGGACG
Statistics
Matches: 60, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
41 2 0.03
42 33 0.55
43 23 0.38
44 2 0.03
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (42 bp):
TCGATATGTGTTACGTGTAAGACCACATCTGGGACAGTGGCA
Found at i:3605432 original size:43 final size:42
Alignment explanation
Indices: 3605321--3605433 Score: 124
Period size: 42 Copynumber: 2.7 Consensus size: 42
3605311 TATGTTATCG
* * *
3605321 TGTAAGACCACATCTGGGACATTGGCATCGACTTGTGTTACG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTACA
3605363 TGTAAGACC-CTGTCTGGGACAG-TGGCATCGA-TATGTGATTACA
1 TGTAAGACCAC-GTCTGGGAC-GTTGGCATCGACT-TGTG-TTACA
* *
3605406 TGTAAGACCACGCCAGGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
3605434 TGTACGAGCT
Statistics
Matches: 60, Mismatches: 5, Indels: 11
0.79 0.07 0.14
Matches are distributed among these distances:
41 2 0.03
42 31 0.52
43 26 0.43
44 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (42 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTACA
Found at i:3606642 original size:87 final size:87
Alignment explanation
Indices: 3606531--3606704 Score: 312
Period size: 87 Copynumber: 2.0 Consensus size: 87
3606521 CAAAGATCAA
* **
3606531 TCATGAAATGGTTGTAATAACATACTTGATTTATCATGTTTATTAATATAAGGTGTTACCATTAT
1 TCATGAAATGGTTGTAATAACATACTTAATTTATCATGTTTATTAATATAAGACGTTACCATTAT
3606596 TATTTCAGTTTCTTTTCTGTGT
66 TATTTCAGTTTCTTTTCTGTGT
*
3606618 TCATGAGATGGTTGTAATAACATACTTAATTTATCATGTTTATTAATATAAGACGTTACCATTAT
1 TCATGAAATGGTTGTAATAACATACTTAATTTATCATGTTTATTAATATAAGACGTTACCATTAT
3606683 TATTTCAGTTTCTTTTCTGTGT
66 TATTTCAGTTTCTTTTCTGTGT
3606705 GTATAAATAA
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 83 1.00
ACGTcount: A:0.28, C:0.11, G:0.13, T:0.48
Consensus pattern (87 bp):
TCATGAAATGGTTGTAATAACATACTTAATTTATCATGTTTATTAATATAAGACGTTACCATTAT
TATTTCAGTTTCTTTTCTGTGT
Found at i:3615905 original size:5 final size:5
Alignment explanation
Indices: 3615895--3615919 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3615885 AGAAACTTGA
3615895 AAATT AAATT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT
3615920 CTACATCTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AAATT
Found at i:3619210 original size:56 final size:56
Alignment explanation
Indices: 3619148--3619261 Score: 228
Period size: 56 Copynumber: 2.0 Consensus size: 56
3619138 CCTAGATGAC
3619148 ATAACCAGTTTAATGGCAAACAAGGTGCAGTATGCAAAAAATTGCACTTACCACAA
1 ATAACCAGTTTAATGGCAAACAAGGTGCAGTATGCAAAAAATTGCACTTACCACAA
3619204 ATAACCAGTTTAATGGCAAACAAGGTGCAGTATGCAAAAAATTGCACTTACCACAA
1 ATAACCAGTTTAATGGCAAACAAGGTGCAGTATGCAAAAAATTGCACTTACCACAA
3619260 AT
1 AT
3619262 TTAAGAGACT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.43, C:0.19, G:0.16, T:0.22
Consensus pattern (56 bp):
ATAACCAGTTTAATGGCAAACAAGGTGCAGTATGCAAAAAATTGCACTTACCACAA
Found at i:3620291 original size:3 final size:3
Alignment explanation
Indices: 3620283--3620344 Score: 90
Period size: 3 Copynumber: 20.7 Consensus size: 3
3620273 ATGCAGGAAA
3620283 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG ATA-
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A-AG
* *
3620328 ATG ATG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AA
3620345 AATAGCCGAC
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
3 54 0.98
4 1 0.02
ACGTcount: A:0.65, C:0.00, G:0.31, T:0.05
Consensus pattern (3 bp):
AAG
Found at i:3620465 original size:3 final size:3
Alignment explanation
Indices: 3620457--3620491 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3620447 TCATTGGCCC
3620457 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
3620492 AACACAAGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:3626643 original size:11 final size:11
Alignment explanation
Indices: 3626627--3626653 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
3626617 TAGAAATTAG
3626627 TTTGTGAAACT
1 TTTGTGAAACT
3626638 TTTGTGAAACT
1 TTTGTGAAACT
3626649 TTTGT
1 TTTGT
3626654 ATTGATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.07, G:0.19, T:0.52
Consensus pattern (11 bp):
TTTGTGAAACT
Found at i:3628186 original size:93 final size:92
Alignment explanation
Indices: 3628054--3628248 Score: 286
Period size: 93 Copynumber: 2.1 Consensus size: 92
3628044 TTGATTTTAG
* *
3628054 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTA-TATAATTA
1 TAAATTCATATAAGAAAATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTA-AATTA
* *
3628118 TATTTAAT-ATTAATTATTTTAAATTGTA
65 TATGTAATAATT-ATTATTTTAAATTATA
* *
3628146 TAAATTCATATAAGAAAATTTTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTA
1 TAAATTCATATAAGAAAA-TTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTA
3628211 TATGTAATAATTATTATTTTAAATTATA
65 TATGTAATAATTATTATTTTAAATTATA
*
3628239 CAAATTCATA
1 TAAATTCATA
3628249 AACTATAATC
Statistics
Matches: 93, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
92 17 0.18
93 71 0.76
94 5 0.05
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (92 bp):
TAAATTCATATAAGAAAATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTAT
ATGTAATAATTATTATTTTAAATTATA
Found at i:3628296 original size:48 final size:52
Alignment explanation
Indices: 3628226--3628324 Score: 118
Period size: 52 Copynumber: 2.0 Consensus size: 52
3628216 AATAATTATT
3628226 ATTTTAAATTATACAAATTCATA-AACT-A-T-AATCATATTAGTTATAATA
1 ATTTTAAATTATACAAATTCATATAACTAATTAAATCATATTAGTTATAATA
* * **
3628274 ATTTTAAATTTTATTAAA-TCATATATTTAATTAAATCATATTAGTTATAAT
1 ATTTTAAATTATA-CAAATTCATATAACTAATTAAATCATATTAGTTATAAT
3628325 CATATATTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
48 17 0.40
49 5 0.12
50 1 0.02
51 1 0.02
52 18 0.43
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.46
Consensus pattern (52 bp):
ATTTTAAATTATACAAATTCATATAACTAATTAAATCATATTAGTTATAATA
Found at i:3628306 original size:17 final size:17
Alignment explanation
Indices: 3628281--3628314 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3628271 ATAATTTTAA
*
3628281 ATTTTATTAAATCATAT
1 ATTTAATTAAATCATAT
3628298 ATTTAATTAAATCATAT
1 ATTTAATTAAATCATAT
3628315 TAGTTATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAATTAAATCATAT
Found at i:3628331 original size:17 final size:16
Alignment explanation
Indices: 3628286--3628333 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
3628276 TTTAAATTTT
3628286 ATTAAATCATATATTTA
1 ATTAAATCATATA-TTA
3628303 ATTAAATC--ATATTA
1 ATTAAATCATATATTA
*
3628317 GTTATAATCATATATTA
1 ATTA-AATCATATATTA
3628334 TGATTTGAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 6 0.22
15 7 0.26
17 14 0.52
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (16 bp):
ATTAAATCATATATTA
Found at i:3628388 original size:54 final size:54
Alignment explanation
Indices: 3628330--3628508 Score: 137
Period size: 54 Copynumber: 3.1 Consensus size: 54
3628320 ATAATCATAT
3628330 ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
1 ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
* * * * * * * *
3628384 ATTATATATTTTAATTATATT-ATATTTAATAATAATTATGTTATTTTA-TATTTTACAGTATCA
1 ATTAT-GA-TTTGAGTAAATTCATA--TAAGAAT-ATTA-ATTA-TTAAGAATTTT--A-T-T-A
3628447 TA
54 -A
*
3628449 TATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
1 -ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
3628504 ATTAT
1 ATTAT
3628509 ATATTTTAAT
Statistics
Matches: 92, Mismatches: 17, Indels: 32
0.65 0.12 0.23
Matches are distributed among these distances:
54 10 0.11
55 5 0.05
56 10 0.11
57 7 0.08
58 5 0.05
59 9 0.10
60 6 0.07
61 9 0.10
62 5 0.05
63 7 0.08
64 10 0.11
65 4 0.04
66 5 0.05
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (54 bp):
ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
Found at i:3628391 original size:61 final size:61
Alignment explanation
Indices: 3628326--3628513 Score: 190
Period size: 61 Copynumber: 3.1 Consensus size: 61
3628316 AGTTATAATC
3628326 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
* * * * * * * * * * *
3628387 ATATATTTTAATTAT-ATTATATTTA-ATAATAATTATGTTATT-TT-A-TATTTTA-CAGTATC
1 ATATATTATGATT-TGAGTAAATTCATATAAGAA-TAT-TAATTATTAAGAATTTTATTA-AATT
*
3628446 ATATATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
3628507 ATATATT
1 ATATATT
3628514 TTAATTAAAA
Statistics
Matches: 94, Mismatches: 23, Indels: 20
0.69 0.17 0.15
Matches are distributed among these distances:
58 6 0.06
59 30 0.32
60 14 0.15
61 38 0.40
62 6 0.06
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (61 bp):
ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
Found at i:3628405 original size:18 final size:17
Alignment explanation
Indices: 3628374--3628408 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3628364 ATTATTAAGA
3628374 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
*
3628391 ATTTTAATTATATTATAT
1 ATTTT-ATTAAATTATAT
3628409 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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:3628447 original size:120 final size:119
Alignment explanation
Indices: 3628323--3628544 Score: 408
Period size: 120 Copynumber: 1.9 Consensus size: 119
3628313 ATTAGTTATA
3628323 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
1 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
* *
3628388 TATATTTTAATTATATTATATTTAATAATAATTATGTTATTTTATATTTTACAGT
66 TATATTTTAATTAAAATATATTT-ATAATAATTATGTTATTTTATATTTTACAGT
*
3628443 ATCATATATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
1 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
3628508 TATATTTTAATTAAAATATATTTATAATAATTATGTT
66 TATATTTTAATTAAAATATATTTATAATAATTATGTT
3628545 TAAATATGAT
Statistics
Matches: 99, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
119 14 0.14
120 85 0.86
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (119 bp):
ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
TATATTTTAATTAAAATATATTTATAATAATTATGTTATTTTATATTTTACAGT
Found at i:3628522 original size:18 final size:17
Alignment explanation
Indices: 3628494--3628528 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3628484 ATTATTAAGA
*
3628494 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
3628511 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
3628529 TTATAATAAT
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:3628528 original size:16 final size:17
Alignment explanation
Indices: 3628494--3628535 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
3628484 ATTATTAAGA
3628494 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA-TATAT
3628511 ATTTTAATTAAA-ATAT
1 ATTTTAATTAAATATAT
3628527 ATTTATAAT
1 ATTT-TAAT
3628536 AATTATGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 8 0.35
17 9 0.39
18 6 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTTAATTAAATATAT
Found at i:3628594 original size:77 final size:77
Alignment explanation
Indices: 3628513--3628751 Score: 178
Period size: 77 Copynumber: 3.2 Consensus size: 77
3628503 AATTATATAT
*
3628513 TTTAATTAAAATATATTTATAATAATTATGTTTAAATATGATTAAATTATTTATTATTGATATTA
1 TTTAAATAAAATATATTTATAATAATTATGTTTAAATATGATTAAATTATTTATTATTGATATTA
3628578 ATCTTATTAAAA
66 ATCTTATTAAAA
* * ** * * * ** *
3628590 TTTAAATAAAATA-ATTTACCAA-AA-CA-AATT---TCTG-CT-AATTATTAAGAATT-TTATT
1 TTTAAATAAAATATATTTA-TAATAATTATGTTTAAATATGATTAAATTATTTATTATTGATATT
* * *
3628645 AA-ATTA-TATAT
65 AATCTTATTAAAA
* * *
3628656 TTTAATTAAAATATATTAAATAATAATTATGTTTAAATATGATTAAATTATTTATTTTTGATAAT
1 TTTAAATAAAATATATT-TATAATAATTATGTTTAAATATGATTAAATTATTTATTATTGAT-AT
3628721 AAATAATCTTATTAAAA
64 ---TAATCTTATTAAAA
3628738 TTTAAATAACAATA
1 TTTAAATAA-AATA
3628752 ACAATAATCA
Statistics
Matches: 112, Mismatches: 31, Indels: 32
0.64 0.18 0.18
Matches are distributed among these distances:
66 15 0.13
67 8 0.07
68 9 0.08
69 12 0.11
70 3 0.03
71 3 0.03
73 3 0.03
74 3 0.03
75 11 0.10
76 8 0.07
77 16 0.14
80 3 0.03
81 3 0.03
82 11 0.10
83 4 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.46
Consensus pattern (77 bp):
TTTAAATAAAATATATTTATAATAATTATGTTTAAATATGATTAAATTATTTATTATTGATATTA
ATCTTATTAAAA
Found at i:3628643 original size:143 final size:147
Alignment explanation
Indices: 3628482--3628752 Score: 478
Period size: 143 Copynumber: 1.9 Consensus size: 147
3628472 ATAAGAATAT
*
3628482 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATT-TATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
3628546 AAATATGATTAAATTATTTATTATTGAT-AT-TAATCTTATTAAAATTTAAATAA-AATAATTTA
66 AAATATGATTAAATTATTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAATTTA
3628608 CCAAAACAAATTTCTGC
131 CCAAAACAAATTTCTGC
3628625 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
*
3628690 AAATATGATTAAATTATTTATTTTTGATAATAAATAATCTTATTAAAATTTAAATAACAATAA
66 AAATATGATTAAATTATTTATTATTGATAAT--ATAATCTTATTAAAATTTAAATAACAATAA
3628753 CAATAATCAT
Statistics
Matches: 120, Mismatches: 2, Indels: 6
0.94 0.02 0.05
Matches are distributed among these distances:
143 48 0.40
144 42 0.35
145 2 0.02
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (147 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAATTTA
CCAAAACAAATTTCTGC
Found at i:3628665 original size:18 final size:17
Alignment explanation
Indices: 3628637--3628671 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3628627 ATTATTAAGA
*
3628637 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
3628654 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
3628672 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:3628922 original size:45 final size:44
Alignment explanation
Indices: 3628833--3628927 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
3628823 TTACACCTCT
* *
3628833 ATTACATTCAACCAAACACAGTTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACACAGATTTACTATTACACCTCTATTCC
** *
3628877 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACA-CAGATTTACTATTACACCTCTATTCC
3628922 ATTACA
1 ATTACA
3628928 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:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (44 bp):
ATTACATTCAACCAAACACAGATTTACTATTACACCTCTATTCC
Found at i:3628927 original size:16 final size:16
Alignment explanation
Indices: 3628906--3628938 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3628896 TTGATTTGCT
*
3628906 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
3628922 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
3628938 A
1 A
3628939 ACCCAATACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.36, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:3630275 original size:21 final size:21
Alignment explanation
Indices: 3630249--3630301 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
3630239 ATTTGTTTCT
* *
3630249 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAATAACC
** *
3630270 AATCTCACTACTACAATAACT
1 AATCTCACCGCTACAATAACC
3630291 AATCTCACCGC
1 AATCTCACCGC
3630302 CACCGCTGTT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.36, G:0.06, T:0.25
Consensus pattern (21 bp):
AATCTCACCGCTACAATAACC
Found at i:3633484 original size:17 final size:17
Alignment explanation
Indices: 3633462--3633524 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
3633452 ATTAAATCAC
3633462 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
** * *
3633479 TACATAAGTCTTTGAATCAC
1 TACATAA---TTAAAAACAT
3633499 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
3633516 TACATAATT
1 TACATAATT
3633525 CTTGAAATTA
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
17 22 0.63
20 13 0.37
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.33
Consensus pattern (17 bp):
TACATAATTAAAAACAT
Found at i:3633498 original size:37 final size:37
Alignment explanation
Indices: 3633456--3633527 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
3633446 AACCGAATTA
3633456 AATCACTACATAATTAAAAACATTACATAAGTCTTTG
1 AATCACTACATAATTAAAAACATTACATAAGTCTTTG
*
3633493 AATCACTACATAATTAAAAACATTACATAATTCTT
1 AATCACTACATAATTAAAAACATTACATAAGTCTT
3633528 GAAATTAACA
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:0.47, C:0.17, G:0.03, T:0.33
Consensus pattern (37 bp):
AATCACTACATAATTAAAAACATTACATAAGTCTTTG
Found at i:3633541 original size:37 final size:37
Alignment explanation
Indices: 3633460--3633544 Score: 120
Period size: 37 Copynumber: 2.3 Consensus size: 37
3633450 GAATTAAATC
*
3633460 ACTACATAATTAAAAACATTACATAAGTCTTTGAATC
1 ACTACATAATTAAAAACATTACATAAGTCTTTGAATA
*
3633497 ACTACATAATTAAAAACATTACATAATTC-TTGAAATTA
1 ACTACATAATTAAAAACATTACATAAGTCTTTG-AA-TA
3633535 AC-ACATAATT
1 ACTACATAATT
3633545 GAAATGTAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
36 3 0.07
37 38 0.86
38 3 0.07
ACGTcount: A:0.48, C:0.15, G:0.04, T:0.33
Consensus pattern (37 bp):
ACTACATAATTAAAAACATTACATAAGTCTTTGAATA
Found at i:3633700 original size:38 final size:38
Alignment explanation
Indices: 3633656--3633732 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
3633646 TACTTAGAGT
*
3633656 TAGACTTTAGTTTTATTTTTATTGGGTTGGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGTAATTGGG
*
3633694 TAGACTTTAGTTTTAGTTTTATTGGGTTTGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGTAATTGGG
3633732 T
1 T
3633733 TGGGTTGGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.18, C:0.03, G:0.26, T:0.53
Consensus pattern (38 bp):
TAGACTTTAGTTTTAGTTTTATTGGGTTGGTAATTGGG
Found at i:3634132 original size:20 final size:20
Alignment explanation
Indices: 3634107--3634152 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
3634097 TAGTAAAGCT
3634107 TAACAACCTATTTAAAT-AA
1 TAACAACCTATTTAAATGAA
*
3634126 GTAACAACCTATTTGAATGAA
1 -TAACAACCTATTTAAATGAA
3634147 TAACAA
1 TAACAA
3634153 AATATTAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 22 0.92
21 2 0.08
ACGTcount: A:0.50, C:0.15, G:0.07, T:0.28
Consensus pattern (20 bp):
TAACAACCTATTTAAATGAA
Found at i:3634899 original size:14 final size:15
Alignment explanation
Indices: 3634868--3634900 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
3634858 AACGTTTATA
*
3634868 GATTATGGAATTAGG
1 GATTATGGAATCAGG
3634883 GATTATGG-ATCAGG
1 GATTATGGAATCAGG
3634897 GATT
1 GATT
3634901 CTGGTTTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (15 bp):
GATTATGGAATCAGG
Found at i:3636588 original size:147 final size:147
Alignment explanation
Indices: 3636417--3636865 Score: 370
Period size: 147 Copynumber: 3.1 Consensus size: 147
3636407 TTCCATGAAT
** * * * * * * **
3636417 CGCCGCAAAAATGTAATTATATTTATTGAAATGTTGTCGTTTTGTCTATGGTATTAGTGGCG-TT
1 CGCCGCAAAAATGTTCTAACATTTATTGAAACGCTGCCATTTTGTAAATGGTATTAGTGGCGTTT
* * * **
3636481 TTTCTGGAAACGCCACAAGCTTGA-GTTAGCTGTTGGGGAAACGACTTTG-TTTGAACTTATAGT
66 TTTC-GAAAACGCCACAAGCTTGAGGTAAG-TGTTGAGGAAACGACTGCGTTTTG-ACTTATAGT
3636544 TAGTGGCACTTTACTTAAAA
128 TAGTGGCACTTTACTTAAAA
* ** *
3636564 CGCCGCAAAATTGTTCTAACATTTACAGAAACGCTGCCATTTTGTAAATGTTATTAGTGGCGTTT
1 CGCCGCAAAAATGTTCTAACATTTATTGAAACGCTGCCATTTTGTAAATGGTATTAGTGGCGTTT
* ** * * *
3636629 TTTCGAAAACGCCGCGGGTTTGAGGTAAGTGTTGATGAAGCGACTGCGTTTTGACTTATAGTTAG
66 TTTCGAAAACGCCACAAGCTTGAGGTAAGTGTTGAGGAAACGACTGCGTTTTGACTTATAGTTAG
* *
3636694 TGGCGCTTTGCTTAAAA
131 TGGCACTTTACTTAAAA
* * ** * * * ** *
3636711 CGCCGCAAAAATGTTTTAACATTGATTGATGCGATGCCGTTTGGTTGTAT--TTTTAGTGGCGTT
1 CGCCGCAAAAATGTTCTAACATTTATTGAAACGCTGCCATTTTG-TAAATGGTATTAGTGGCGTT
* * * * * ** * *
3636774 TATTCAAAAACGCCACAGGTTTGAGCTATTTCTTGATGAAACGACTGCGTTTTGACTTATAGTTA
65 TTTTCGAAAACGCCACAAGCTTGAGGTAAGTGTTGAGGAAACGACTGCGTTTTGACTTATAGTTA
* *
3636839 GTGGCGCTTATA-TTCAAA
130 GTGGCACTT-TACTTAAAA
*
3636857 TGCCGCAAA
1 CGCCGCAAA
3636866 TGGTTAAATT
Statistics
Matches: 245, Mismatches: 52, Indels: 11
0.80 0.17 0.04
Matches are distributed among these distances:
146 90 0.37
147 138 0.56
148 17 0.07
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.36
Consensus pattern (147 bp):
CGCCGCAAAAATGTTCTAACATTTATTGAAACGCTGCCATTTTGTAAATGGTATTAGTGGCGTTT
TTTCGAAAACGCCACAAGCTTGAGGTAAGTGTTGAGGAAACGACTGCGTTTTGACTTATAGTTAG
TGGCACTTTACTTAAAA
Found at i:3636820 original size:146 final size:147
Alignment explanation
Indices: 3636530--3636865 Score: 399
Period size: 146 Copynumber: 2.3 Consensus size: 147
3636520 AACGACTTTG
* * *
3636530 TTTGAACTTATAGTTAGTGGCACTTTACTTAAAACGCCGCAAAATTGTTCTAACATTTACAGAAA
1 TTTG-ACTTATAGTTAGTGGCGCTTTACTTAAAACGCCGCAAAAATGTTCTAACATTGACAGAAA
* * * * * * * *
3636595 CGCTGCCATTTTGTAAATGTTATTAGTGGCGTTTTTTCGAAAACGCCGCGGGTTTGAGGTAAGTG
65 CGATGCCATTTGGTAAATGTTATTAGTGGCGTTTATTCAAAAACGCCACAGGTTTGAGCTAAGTC
*
3636660 TTGATGAAGCGACTGCGT
130 TTGATGAAACGACTGCGT
* * ** **
3636678 TTTGACTTATAGTTAGTGGCGCTTTGCTTAAAACGCCGCAAAAATGTTTTAACATTGATTGATGC
1 TTTGACTTATAGTTAGTGGCGCTTTACTTAAAACGCCGCAAAAATGTTCTAACATTGACAGAAAC
* ** **
3636743 GATGCCGTTTGGTTGTAT-TT-TTAGTGGCGTTTATTCAAAAACGCCACAGGTTTGAGCTATTTC
66 GATGCCATTTGG-TAAATGTTATTAGTGGCGTTTATTCAAAAACGCCACAGGTTTGAGCTAAGTC
3636806 TTGATGAAACGACTGCGT
130 TTGATGAAACGACTGCGT
* *
3636824 TTTGACTTATAGTTAGTGGCGCTTATA-TTCAAATGCCGCAAA
1 TTTGACTTATAGTTAGTGGCGCTT-TACTTAAAACGCCGCAAA
3636866 TGGTTAAATT
Statistics
Matches: 160, Mismatches: 26, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
146 89 0.56
147 64 0.40
148 7 0.04
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.35
Consensus pattern (147 bp):
TTTGACTTATAGTTAGTGGCGCTTTACTTAAAACGCCGCAAAAATGTTCTAACATTGACAGAAAC
GATGCCATTTGGTAAATGTTATTAGTGGCGTTTATTCAAAAACGCCACAGGTTTGAGCTAAGTCT
TGATGAAACGACTGCGT
Found at i:3639149 original size:13 final size:13
Alignment explanation
Indices: 3639133--3639298 Score: 120
Period size: 13 Copynumber: 12.5 Consensus size: 13
3639123 TTGCTAAAAT
*
3639133 TTACTTTAATATA
1 TTACTTAAATATA
*
3639146 TTACTTGAATATA
1 TTACTTAAATATA
*
3639159 TTACTTAAATAAA
1 TTACTTAAATATA
* *
3639172 TTAGTTAAATACA
1 TTACTTAAATATA
*
3639185 TTACTTACTAAAAT-
1 TTACTTA--AATATA
** *
3639199 TTGGTTAAATTTTA
1 TTACTTAAA-TATA
*
3639213 GTACTTAAATATA
1 TTACTTAAATATA
*
3639226 TTACTTAAATACA
1 TTACTTAAATATA
*
3639239 TTACTTACTAAAAT-
1 TTACTTA--AATATA
** *
3639253 TTGTTTAAATTTA
1 TTACTTAAATATA
*
3639266 TTACTTAAATATG
1 TTACTTAAATATA
*
3639279 TTACTTAAATACA
1 TTACTTAAATATA
3639292 TTACTTA
1 TTACTTA
3639299 CTAAAATTTA
Statistics
Matches: 116, Mismatches: 30, Indels: 14
0.73 0.19 0.09
Matches are distributed among these distances:
12 5 0.04
13 89 0.77
14 16 0.14
15 6 0.05
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.46
Consensus pattern (13 bp):
TTACTTAAATATA
Found at i:3639287 original size:80 final size:79
Alignment explanation
Indices: 3639134--3639288 Score: 170
Period size: 80 Copynumber: 1.9 Consensus size: 79
3639124 TGCTAAAATT
* * *
3639134 TACTTTAATATATTACTTGAATATATTACTTAAATAAATTAGTTAAATACATTACTTACTAAAAT
1 TACTTAAATATATTACTTAAATACATTACTTAAATAAATTAGTTAAATACATTACTTAC-AAAAT
**
3639199 TTGGTTAAATTTTAG
65 TTACTTAAATTTTAG
* * ** *
3639214 TACTTAAATATATTACTTAAATACATTACTT-ACTAAAATTTGTTTAAATTTATTACTTA-AATA
1 TACTTAAATATATTACTTAAATACATTACTTAAAT-AAATTAG-TTAAATACATTACTTACAAAA
3639277 TGTTACTTAAAT
64 T-TTACTTAAAT
3639289 ACATTACTTA
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
79 6 0.10
80 42 0.68
81 14 0.23
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (79 bp):
TACTTAAATATATTACTTAAATACATTACTTAAATAAATTAGTTAAATACATTACTTACAAAATT
TACTTAAATTTTAG
Found at i:3639294 original size:53 final size:54
Alignment explanation
Indices: 3639157--3639307 Score: 250
Period size: 54 Copynumber: 2.8 Consensus size: 54
3639147 TACTTGAATA
* *
3639157 TATTACTTAAATAAATTAGTTAAATACATTACTTACTAAAATTTGGTTAAATTT
1 TATTACTTAAATATATTACTTAAATACATTACTTACTAAAATTTGGTTAAATTT
* *
3639211 TAGTACTTAAATATATTACTTAAATACATTACTTACTAAAATTTGTTTAAA-TT
1 TATTACTTAAATATATTACTTAAATACATTACTTACTAAAATTTGGTTAAATTT
*
3639264 TATTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTT
1 TATTACTTAAATATATTACTTAAATACATTACTTACTAAAATTT
3639308 AAGTATTTAT
Statistics
Matches: 91, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
53 44 0.48
54 47 0.52
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (54 bp):
TATTACTTAAATATATTACTTAAATACATTACTTACTAAAATTTGGTTAAATTT
Found at i:3639685 original size:16 final size:16
Alignment explanation
Indices: 3639637--3639902 Score: 152
Period size: 16 Copynumber: 15.9 Consensus size: 16
3639627 TATAAACTTG
*
3639637 CATAACTTACGTAATAA
1 CATAACTTACATAAT-A
3639654 CATAACAACTTACATAATA
1 CAT---AACTTACATAATA
* *
3639673 CATAGCATACATAACTTA
1 CATAACTTACATAA--TA
3639691 CATAACTTACATAATA
1 CATAACTTACATAATA
*
3639707 CAAAACTTACATAACTTA
1 CATAACTTACATAA--TA
* * *
3639725 AATATCTTACACAACTTA
1 CATAACTTACATAA--TA
*
3639743 CATAACCTACATAATA
1 CATAACTTACATAATA
3639759 CATAACTTACATAATA
1 CATAACTTACATAATA
*
3639775 CATAA-TAAC-T--TA
1 CATAACTTACATAATA
3639787 C--AACTTACATGACATA
1 CATAACTTACAT-A-ATA
* **
3639803 CATTACTTTGATAACTTA
1 CATAACTTACATAA--TA
3639821 CATAACTTACATAATA
1 CATAACTTACATAATA
*
3639837 CATAACTTACATAGCTTA
1 CATAACTTACATA--ATA
*
3639855 CTTAA--TACATAACTTA
1 CATAACTTACATAA--TA
* * *
3639871 CATAACTTATACACGTA
1 CATAACTTACATA-ATA
3639888 CATAACTTACATAAT
1 CATAACTTACATAAT
3639903 TTACTTAATA
Statistics
Matches: 192, Mismatches: 33, Indels: 49
0.70 0.12 0.18
Matches are distributed among these distances:
10 2 0.01
11 3 0.02
12 4 0.02
14 1 0.01
15 3 0.02
16 78 0.41
17 17 0.09
18 69 0.36
19 4 0.02
20 11 0.06
ACGTcount: A:0.46, C:0.21, G:0.02, T:0.31
Consensus pattern (16 bp):
CATAACTTACATAATA
Found at i:3639692 original size:9 final size:9
Alignment explanation
Indices: 3639660--3639906 Score: 209
Period size: 9 Copynumber: 28.8 Consensus size: 9
3639650 ATAACATAAC
3639660 AACTTACAT
1 AACTTACAT
3639669 AA--TACAT
1 AACTTACAT
* *
3639676 AGCATACAT
1 AACTTACAT
3639685 AACTTACAT
1 AACTTACAT
3639694 AACTTACAT
1 AACTTACAT
*
3639703 AA--TACAA
1 AACTTACAT
3639710 AACTTACAT
1 AACTTACAT
*
3639719 AACTTAAAT
1 AACTTACAT
* *
3639728 ATCTTACAC
1 AACTTACAT
3639737 AACTTACAT
1 AACTTACAT
*
3639746 AACCTACAT
1 AACTTACAT
3639755 AA--TACAT
1 AACTTACAT
3639762 AACTTACAT
1 AACTTACAT
*
3639771 AATACATA-AT
1 -A-ACTTACAT
3639781 AACTTAC--
1 AACTTACAT
3639788 AACTTACAT
1 AACTTACAT
* *
3639797 GACATACAT
1 AACTTACAT
* **
3639806 TACTTTGAT
1 AACTTACAT
3639815 AACTTACAT
1 AACTTACAT
3639824 AACTTACAT
1 AACTTACAT
3639833 AA--TACAT
1 AACTTACAT
3639840 AACTTACAT
1 AACTTACAT
* *
3639849 AGCTTACTT
1 AACTTACAT
3639858 AA--TACAT
1 AACTTACAT
3639865 AACTTACAT
1 AACTTACAT
3639874 AACTT--AT
1 AACTTACAT
*
3639881 ACACGTACAT
1 A-ACTTACAT
3639891 AACTTACAT
1 AACTTACAT
*
3639900 AATTTAC
1 AACTTAC
3639907 TTAATACATA
Statistics
Matches: 190, Mismatches: 30, Indels: 36
0.74 0.12 0.14
Matches are distributed among these distances:
7 42 0.22
8 7 0.04
9 131 0.69
10 6 0.03
11 4 0.02
ACGTcount: A:0.45, C:0.21, G:0.02, T:0.32
Consensus pattern (9 bp):
AACTTACAT
Found at i:3639847 original size:25 final size:25
Alignment explanation
Indices: 3639631--3639917 Score: 240
Period size: 25 Copynumber: 11.1 Consensus size: 25
3639621 CTTATATATA
* *
3639631 AACTTGCATAACTTACGTAATAACAT
1 AACTTACATAACTTACATAAT-ACAT
3639657 AACAACTTACATAA--TACATAGCATACAT
1 ---AACTTACATAACTTACATA--ATACAT
*
3639685 AACTTACATAACTTACATAATACAA
1 AACTTACATAACTTACATAATACAT
* * *
3639710 AACTTACATAACTTAAATATCTTACAC
1 AACTTACATAACTTACATA--ATACAT
*
3639737 AACTTACATAACCTACATAATACAT
1 AACTTACATAACTTACATAATACAT
*
3639762 AACTTACATAA--TACATAATAACTTAC
1 AACTTACATAACTTACATAAT-AC--AT
* * * **
3639788 AACTTACATGACATACATTACTTTGAT
1 AACTTACATAACTTACA-TA-ATACAT
3639815 AACTTACATAACTTACATAATACAT
1 AACTTACATAACTTACATAATACAT
* *
3639840 AACTTACATAGCTTACTTAATACAT
1 AACTTACATAACTTACATAATACAT
* * *
3639865 AACTTACATAACTTATACACGTACAT
1 AACTTACATAACTTACATA-ATACAT
* *
3639891 AACTTACATAATTTACTTAATACAT
1 AACTTACATAACTTACATAATACAT
3639916 AA
1 AA
3639918 ATATATATCA
Statistics
Matches: 211, Mismatches: 33, Indels: 32
0.76 0.12 0.12
Matches are distributed among these distances:
23 8 0.04
24 2 0.01
25 97 0.46
26 33 0.16
27 48 0.23
28 8 0.04
29 14 0.07
30 1 0.00
ACGTcount: A:0.46, C:0.20, G:0.02, T:0.32
Consensus pattern (25 bp):
AACTTACATAACTTACATAATACAT
Found at i:3644841 original size:544 final size:544
Alignment explanation
Indices: 3643813--3644903 Score: 2164
Period size: 544 Copynumber: 2.0 Consensus size: 544
3643803 GTTTTCAACT
3643813 ATTTTATTTGTATTGCAGATAAAATGCCTAGAAGGAAAGTGCGAGAGCTAAGCATTTTTCAAGGT
1 ATTTTATTTGTATTGCAGATAAAATGCCTAGAAGGAAAGTGCGAGAGCTAAGCATTTTTCAAGGT
3643878 ACTCCAAACTCCGCGAAAACAAACAGCACTGAACAACAGACTACTGTTGGATATTCGAATGTCCC
66 ACTCCAAACTCCGCGAAAACAAACAGCACTGAACAACAGACTACTGTTGGATATTCGAATGTCCC
3643943 GACTACACCTGAAGAACCAATAGAAGTTCAAAGTAAATTAACATTTAATTTACATGCGCGTTGAC
131 GACTACACCTGAAGAACCAATAGAAGTTCAAAGTAAATTAACATTTAATTTACATGCGCGTTGAC
*
3644008 TTTTTGTTTATTTATTTTTAAAATTCTTATATTACAATATAACATTTTTCAGCTGAAAGTGGTGG
196 TTTTTGTTTATTTATTTTTAAAATTCTTATATTACAATATAACATTTTTCAGCTGAAAGTAGTGG
3644073 GACGCAGAGAGTTCGAGGACGTACGCTACTAAGGGATTTATACGAGCTAGATCCAGTCGAGCGTG
261 GACGCAGAGAGTTCGAGGACGTACGCTACTAAGGGATTTATACGAGCTAGATCCAGTCGAGCGTG
3644138 TCCAAGTATGCAGTAATAGCTTTGGTCAGCCTGTTGGATCAGAAGCTCGCCTTCTAGCAGGGTAC
326 TCCAAGTATGCAGTAATAGCTTTGGTCAGCCTGTTGGATCAGAAGCTCGCCTTCTAGCAGGGTAC
3644203 TTGGGCATTTTAGCACAGAATGCAAATATGTTGCCAATTAACTACGAGTCATGGCATAAAATGCC
391 TTGGGCATTTTAGCACAGAATGCAAATATGTTGCCAATTAACTACGAGTCATGGCATAAAATGCC
3644268 CGAGAGTAACAAGAACCAAGCTCTCGATGAGATTAAGGTAACAAAATGTTAGTGTCATTTATAGT
456 CGAGAGTAACAAGAACCAAGCTCTCGATGAGATTAAGGTAACAAAATGTTAGTGTCATTTATAGT
3644333 ACTTGGGTTTAAGTTTAATTTATA
521 ACTTGGGTTTAAGTTTAATTTATA
3644357 ATTTTATTTGTATTGCAGATAAAATGCCTAGAAGGAAAGTGCGAGAGCTAAGCATTTTTCAAGGT
1 ATTTTATTTGTATTGCAGATAAAATGCCTAGAAGGAAAGTGCGAGAGCTAAGCATTTTTCAAGGT
3644422 ACTCCAAACTCCGCGAAAACAAACAGCACTGAACAACAGACTACTGTTGGATATTCGAATGTCCC
66 ACTCCAAACTCCGCGAAAACAAACAGCACTGAACAACAGACTACTGTTGGATATTCGAATGTCCC
*
3644487 GACTACACCTGAAGAACCAATAGAAGTTCAAAGTAAATTAACATTTAATTTACATGCTCGTTGAC
131 GACTACACCTGAAGAACCAATAGAAGTTCAAAGTAAATTAACATTTAATTTACATGCGCGTTGAC
3644552 TTTTTGTTTATTTATTTTTAAAATTCTTATATTACAATATAACATTTTTCAGCTGAAAGTAGTGG
196 TTTTTGTTTATTTATTTTTAAAATTCTTATATTACAATATAACATTTTTCAGCTGAAAGTAGTGG
3644617 GACGCAGAGAGTTCGAGGACGTACGCTACTAAGGGATTTATACGAGCTAGATCCAGTCGAGCGTG
261 GACGCAGAGAGTTCGAGGACGTACGCTACTAAGGGATTTATACGAGCTAGATCCAGTCGAGCGTG
3644682 TCCAAGTATGCAGTAATAGCTTTGGTCAGCCTGTTGGATCAGAAGCTCGCCTTCTAGCAGGGTAC
326 TCCAAGTATGCAGTAATAGCTTTGGTCAGCCTGTTGGATCAGAAGCTCGCCTTCTAGCAGGGTAC
3644747 TTGGGCATTTTAGCACAGAATGCAAATATGTTGCCAATTAACTACGAGTCATGGCATAAAATGCC
391 TTGGGCATTTTAGCACAGAATGCAAATATGTTGCCAATTAACTACGAGTCATGGCATAAAATGCC
3644812 CGAGAGTAACAAGAACCAAGCTCTCGATGAGATTAAGGTAACAAAATGTTAGTGTCATTTATAGT
456 CGAGAGTAACAAGAACCAAGCTCTCGATGAGATTAAGGTAACAAAATGTTAGTGTCATTTATAGT
3644877 ACTTGGGTTTAAGTTTAATTTATA
521 ACTTGGGTTTAAGTTTAATTTATA
3644901 ATT
1 ATT
3644904 ACTTTCTTAA
Statistics
Matches: 545, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
544 545 1.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (544 bp):
ATTTTATTTGTATTGCAGATAAAATGCCTAGAAGGAAAGTGCGAGAGCTAAGCATTTTTCAAGGT
ACTCCAAACTCCGCGAAAACAAACAGCACTGAACAACAGACTACTGTTGGATATTCGAATGTCCC
GACTACACCTGAAGAACCAATAGAAGTTCAAAGTAAATTAACATTTAATTTACATGCGCGTTGAC
TTTTTGTTTATTTATTTTTAAAATTCTTATATTACAATATAACATTTTTCAGCTGAAAGTAGTGG
GACGCAGAGAGTTCGAGGACGTACGCTACTAAGGGATTTATACGAGCTAGATCCAGTCGAGCGTG
TCCAAGTATGCAGTAATAGCTTTGGTCAGCCTGTTGGATCAGAAGCTCGCCTTCTAGCAGGGTAC
TTGGGCATTTTAGCACAGAATGCAAATATGTTGCCAATTAACTACGAGTCATGGCATAAAATGCC
CGAGAGTAACAAGAACCAAGCTCTCGATGAGATTAAGGTAACAAAATGTTAGTGTCATTTATAGT
ACTTGGGTTTAAGTTTAATTTATA
Found at i:3646358 original size:43 final size:43
Alignment explanation
Indices: 3646297--3646449 Score: 166
Period size: 43 Copynumber: 3.5 Consensus size: 43
3646287 GCGTTTTTTC
* *
3646297 AAAAAATCGCCGCTAAAGGTCATGGTATTTTGC-AGCGTTTGTGG
1 AAAAAA-CGCCGCTAAAGGTCATGGTCTTTAGCGA-CGTTTGTGG
* * * *
3646341 AAAAAACGCCACTAAAGGTCACGGTCTTTAGCGCCGTTT-TTG
1 AAAAAACGCCGCTAAAGGTCATGGTCTTTAGCGACGTTTGTGG
* *
3646383 AGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGATGTTTGTGG
1 A-AAAAACGCCGCTAAAGGTCATGGTCTTTAGCGACGTTTGTGG
* * *
3646427 GAAAAGCGCCGCTAAAAGTCATG
1 AAAAAACGCCGCTAAAGGTCATG
3646450 ACCTTTGGCG
Statistics
Matches: 92, Mismatches: 14, Indels: 7
0.81 0.12 0.06
Matches are distributed among these distances:
42 3 0.03
43 81 0.88
44 8 0.09
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (43 bp):
AAAAAACGCCGCTAAAGGTCATGGTCTTTAGCGACGTTTGTGG
Found at i:3647450 original size:22 final size:22
Alignment explanation
Indices: 3647398--3647455 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
3647388 TTCAAATAAT
* *
3647398 AACAAGAAAATAGTAGTAATAT
1 AACAACAAAATAGTAGTAATAC
* *
3647420 AATAGCAAAATAGTAGTGAA-AC
1 AACAACAAAATAGTAGT-AATAC
3647442 AACAACAAAATAGT
1 AACAACAAAATAGT
3647456 TTATTTGGGT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
22 27 0.93
23 2 0.07
ACGTcount: A:0.59, C:0.09, G:0.14, T:0.19
Consensus pattern (22 bp):
AACAACAAAATAGTAGTAATAC
Found at i:3649094 original size:25 final size:25
Alignment explanation
Indices: 3649028--3649095 Score: 74
Period size: 24 Copynumber: 2.8 Consensus size: 25
3649018 TTTCTTTTTG
3649028 TATATTTGATTCTCTA-T-TTTTCA
1 TATATTTGATTCTCTATTATTTTCA
3649051 TATATGTT-ATTCTCT-TTATTTTC-
1 TATAT-TTGATTCTCTATTATTTTCA
*
3649074 TCATATTTGATTATCTATTATT
1 T-ATATTTGATTCTCTATTATT
3649096 ATATTTTCTA
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
23 16 0.42
24 17 0.45
25 5 0.13
ACGTcount: A:0.22, C:0.12, G:0.04, T:0.62
Consensus pattern (25 bp):
TATATTTGATTCTCTATTATTTTCA
Found at i:3662835 original size:16 final size:16
Alignment explanation
Indices: 3662812--3662857 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
3662802 CGTTTAGTTC
3662812 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
* **
3662828 GGTGTAATAAAATAGA
1 GCTGTAATGGAATAGA
*
3662844 GCTATAATGGAATA
1 GCTGTAATGGAATA
3662858 AATGAGTAAT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.43, C:0.04, G:0.26, T:0.26
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:3668224 original size:63 final size:62
Alignment explanation
Indices: 3668097--3668224 Score: 150
Period size: 63 Copynumber: 2.0 Consensus size: 62
3668087 ACAAGCATTC
* * * * * * *
3668097 TGATCGGTAGTGATCTTGCATGTGTTGCGGACTATCGCAGCTCTTTTTGAGTGTCTTGTTATA
1 TGATCGGTAGTGATCCTGCATATATTGCGGACTAACGCAACTCTTTGTGAGTGTCCTG-TATA
*
3668160 TGATCGGTTGTGATCCTGCATATATTGCGGACATAAACGCAACTCTTTGTGAGTGTCCTG-ATA
1 TGATCGGTAGTGATCCTGCATATATTGCGGAC-T-AACGCAACTCTTTGTGAGTGTCCTGTATA
3668223 TG
1 TG
3668225 GCTCGCTTGA
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
63 33 0.60
64 1 0.02
65 21 0.38
ACGTcount: A:0.20, C:0.17, G:0.26, T:0.38
Consensus pattern (62 bp):
TGATCGGTAGTGATCCTGCATATATTGCGGACTAACGCAACTCTTTGTGAGTGTCCTGTATA
Found at i:3670044 original size:26 final size:26
Alignment explanation
Indices: 3670015--3670070 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
3670005 TACTCTTTCA
3670015 AGCCATATAA-CAGGAAGCTCACAAAG
1 AGCCAT-TAATCAGGAAGCTCACAAAG
*
3670041 AGCCATTAATCGGGAAGCTCACAAAG
1 AGCCATTAATCAGGAAGCTCACAAAG
3670067 AGCC
1 AGCC
3670071 TATCAAGAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 3 0.11
26 25 0.89
ACGTcount: A:0.41, C:0.25, G:0.21, T:0.12
Consensus pattern (26 bp):
AGCCATTAATCAGGAAGCTCACAAAG
Found at i:3671563 original size:24 final size:26
Alignment explanation
Indices: 3671500--3671565 Score: 70
Period size: 24 Copynumber: 2.7 Consensus size: 26
3671490 ACTTTCATAG
*
3671500 AATATAAAG-TTAAATATATATAAAC
1 AATATAAAGAATAAATATATATAAAC
*
3671525 AA-ATATAGAA-AAA-ATA-ATAATAC
1 AATATAAAGAATAAATATATATAA-AC
3671548 AATATAAAGAATAAATAT
1 AATATAAAGAATAAATAT
3671566 GATAAAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
22 4 0.12
23 7 0.21
24 15 0.45
25 5 0.15
26 2 0.06
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.27
Consensus pattern (26 bp):
AATATAAAGAATAAATATATATAAAC
Found at i:3673361 original size:87 final size:87
Alignment explanation
Indices: 3673215--3673482 Score: 369
Period size: 87 Copynumber: 3.1 Consensus size: 87
3673205 ACTTGTAATC
** * * *
3673215 TTCGATCTGCTTCACTGTCGACGCAAG-AGAGTAAGATCTGCTATCTTTAACTAGCTCCACTGCA
1 TTCGATCTGCTTCACTGTTAACGCAGGAAG-GCAAGATCTGCTATCTTTAACCAGCTCCACTGCA
3673279 ACCGATGGAGGCAAGGCTTTGTT
65 ACCGATGGAGGCAAGGCTTTGTT
*
3673302 TTCGATCTGCTTCACTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACCGCAA
1 TTCGATCTGCTTCACTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
*
3673367 CCGATGGAGGCAAGGCTTTATT
66 CCGATGGAGGCAAGGCTTTGTT
* * * * **
3673389 TTCGATCTGTTTTATTGTTAACGCAGGAAGGCAAGATCTGCT-TCTTTAACCAGCTTCACTATAA
1 TTCGATCTGCTTCACTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
* * *
3673453 CCGATGAAGGCAAAGTTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
3673475 TTCGATCT
1 TTCGATCT
3673483 TCACTGATCT
Statistics
Matches: 162, Mismatches: 18, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
86 44 0.27
87 116 0.72
88 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (87 bp):
TTCGATCTGCTTCACTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
CCGATGGAGGCAAGGCTTTGTT
Found at i:3674713 original size:7 final size:7
Alignment explanation
Indices: 3674701--3674738 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
3674691 ATTTTTACTC
3674701 TTTCATT
1 TTTCATT
3674708 TTTCATT
1 TTTCATT
3674715 TTTCA-T
1 TTTCATT
*
3674721 TTTCACT
1 TTTCATT
3674728 TTTCATCT
1 TTTCAT-T
3674736 TTT
1 TTT
3674739 TTTTTACATC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
6 6 0.21
7 18 0.64
8 4 0.14
ACGTcount: A:0.13, C:0.18, G:0.00, T:0.68
Consensus pattern (7 bp):
TTTCATT
Found at i:3675115 original size:7 final size:6
Alignment explanation
Indices: 3675089--3675123 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
3675079 TGGCCTCTCC
3675089 TTTTC- TTTTCT TTTTCT TTTTCT TTTTCCT TTTTC
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTT-CT TTTTC
3675124 ATTCTGATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.18
6 17 0.61
7 6 0.21
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTCT
Found at i:3675202 original size:6 final size:6
Alignment explanation
Indices: 3675176--3675279 Score: 61
Period size: 6 Copynumber: 16.8 Consensus size: 6
3675166 TCTTTTTCTC
* * * *
3675176 ATTTTC ATTTTG ATCTTG ATTTTG ATTTT- -TTCTT- CTTTCTT ATTTTTG
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATT-TTG ATTT-TG A-TTTTG
* * * *
3675224 TTTTTG ATTTTG ATTTTTG ATTTTTTC ATTTTC ATTTTG ACTTTG ATTTTG
1 ATTTTG ATTTTG A-TTTTG A--TTTTG ATTTTG ATTTTG ATTTTG ATTTTG
3675275 ATTTT
1 ATTTT
3675280 TCTTTTTCTT
Statistics
Matches: 80, Mismatches: 11, Indels: 14
0.76 0.10 0.13
Matches are distributed among these distances:
4 2 0.03
5 3 0.04
6 59 0.74
7 7 0.09
8 9 0.11
ACGTcount: A:0.13, C:0.08, G:0.10, T:0.69
Consensus pattern (6 bp):
ATTTTG
Found at i:3679148 original size:15 final size:15
Alignment explanation
Indices: 3679128--3679157 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3679118 TTTGAATGAA
3679128 TTGGAAGATAAGGCT
1 TTGGAAGATAAGGCT
3679143 TTGGAAGATAAGGCT
1 TTGGAAGATAAGGCT
3679158 CATTTGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.27
Consensus pattern (15 bp):
TTGGAAGATAAGGCT
Found at i:3690716 original size:41 final size:39
Alignment explanation
Indices: 3690653--3690817 Score: 161
Period size: 41 Copynumber: 4.1 Consensus size: 39
3690643 GTGATTGAAT
* * *
3690653 ATAATACAGACGTTACGTCTAGCAGGCTTAATGCCGGTGA
1 ATAAT-CAGACTTTAAGTCTAGCAGGCTAAATGCCGGTGA
3690693 AGTAACTCAGACTTTAAGTCTAGCAGGCTAAATGCCGGTG-
1 A-TAA-TCAGACTTTAAGTCTAGCAGGCTAAATGCCGGTGA
* * *
3690733 ATACATTTCAGACTATATGTCTAGCAGGCTAAGTGCCGGTGTA
1 ATA-A--TCAGACTTTAAGTCTAGCAGGCTAAATGCCGGTG-A
* * * *
3690776 CTGAATCAGGCTTTAAGCCTAGCAGGCAAAATGCCGGTGA
1 AT-AATCAGACTTTAAGTCTAGCAGGCTAAATGCCGGTGA
3690816 AT
1 AT
3690818 CTGTTTAAAT
Statistics
Matches: 103, Mismatches: 15, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
39 2 0.02
40 5 0.05
41 92 0.89
42 1 0.01
43 2 0.02
44 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (39 bp):
ATAATCAGACTTTAAGTCTAGCAGGCTAAATGCCGGTGA
Found at i:3704829 original size:25 final size:25
Alignment explanation
Indices: 3704799--3704847 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
3704789 GACCCACAAC
3704799 TCGTGTGAGCATTCTGATTTACAGG
1 TCGTGTGAGCATTCTGATTTACAGG
*
3704824 TCGTGTGAGCATTTTGATTTACAG
1 TCGTGTGAGCATTCTGATTTACAG
3704848 CTCATGTAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.20, C:0.14, G:0.27, T:0.39
Consensus pattern (25 bp):
TCGTGTGAGCATTCTGATTTACAGG
Found at i:3704859 original size:25 final size:25
Alignment explanation
Indices: 3704806--3704860 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
3704796 AACTCGTGTG
* * *
3704806 AGCATTCTGATTTACAGGTCGTGTG
1 AGCATTCTGATTTACAGCTCATGTA
*
3704831 AGCATTTTGATTTACAGCTCATGTA
1 AGCATTCTGATTTACAGCTCATGTA
3704856 AGCAT
1 AGCAT
3704861 AAATGTACAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.36
Consensus pattern (25 bp):
AGCATTCTGATTTACAGCTCATGTA
Found at i:3707297 original size:29 final size:30
Alignment explanation
Indices: 3707247--3707305 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
3707237 CCTGTATTTG
*
3707247 GAATTTATATTTTTTATTTTTTGTTTTAAA
1 GAATTTATATTTTTTATTTTTTGATTTAAA
3707277 GAATTTAT-TTTTTTATTTTTTGATTTAAA
1 GAATTTATATTTTTTATTTTTTGATTTAAA
3707306 AATATAAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 20 0.71
30 8 0.29
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (30 bp):
GAATTTATATTTTTTATTTTTTGATTTAAA
Found at i:3719067 original size:29 final size:30
Alignment explanation
Indices: 3719016--3719072 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
3719006 CACGGGCTGC
3719016 CACATGGGCGTGTGGCCAACCCGTGTGGCT
1 CACATGGGCGTGTGGCCAACCCGTGTGGCT
*
3719046 CACA-GGGCGTGT-GCTCAGCCCGTGTGG
1 CACATGGGCGTGTGGC-CAACCCGTGTGG
3719073 GAATGGTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 2 0.08
29 19 0.76
30 4 0.16
ACGTcount: A:0.12, C:0.30, G:0.39, T:0.19
Consensus pattern (30 bp):
CACATGGGCGTGTGGCCAACCCGTGTGGCT
Found at i:3721362 original size:31 final size:31
Alignment explanation
Indices: 3721327--3721390 Score: 94
Period size: 32 Copynumber: 2.1 Consensus size: 31
3721317 TTTTTTTAAA
* *
3721327 TTTGAAAGGT-TTATTAAAATTTTTTCAAGAT
1 TTTGAAAGGTCTAATTAAAATTTTTACAA-AT
3721358 TTTGAAAGGTCTAATTAAAATTTTTACAAAT
1 TTTGAAAGGTCTAATTAAAATTTTTACAAAT
3721389 TT
1 TT
3721391 AAAGAGCCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 14 0.47
32 16 0.53
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.47
Consensus pattern (31 bp):
TTTGAAAGGTCTAATTAAAATTTTTACAAAT
Found at i:3721917 original size:16 final size:17
Alignment explanation
Indices: 3721883--3721921 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
3721873 AATATTTTAT
3721883 TATTATATAGTGAAATA
1 TATTATATAGTGAAATA
*
3721900 TATTATATAGT-TAATA
1 TATTATATAGTGAAATA
3721916 TATTAT
1 TATTAT
3721922 TTTGTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.49
Consensus pattern (17 bp):
TATTATATAGTGAAATA
Found at i:3722055 original size:34 final size:33
Alignment explanation
Indices: 3721988--3722058 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 33
3721978 TAAACATATT
*
3721988 ATATTTTATATAATTTATATCATAATTATAAAA
1 ATATTTTATATAATTTATATAATAATTATAAAA
3722021 ATATTTTA-ATAAATTGTATTATAAT-ATTATAAAA
1 ATATTTTATAT-AATT-TA-TATAATAATTATAAAA
3722055 ATAT
1 ATAT
3722059 AATAGGTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
32 2 0.06
33 12 0.35
34 15 0.44
35 5 0.15
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (33 bp):
ATATTTTATATAATTTATATAATAATTATAAAA
Found at i:3730146 original size:25 final size:25
Alignment explanation
Indices: 3730113--3730162 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
3730103 TTGTAAATCA
3730113 GAAAAATATCTTTAGA-AATTTTCT
1 GAAAAATATCTTTAGAGAATTTTCT
*
3730137 GAAATAATATGTTTAGAGAATTTTCT
1 GAAA-AATATCTTTAGAGAATTTTCT
3730163 CTCTACAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.17
25 11 0.48
26 8 0.35
ACGTcount: A:0.40, C:0.06, G:0.12, T:0.42
Consensus pattern (25 bp):
GAAAAATATCTTTAGAGAATTTTCT
Found at i:3730383 original size:37 final size:37
Alignment explanation
Indices: 3730300--3730391 Score: 100
Period size: 37 Copynumber: 2.5 Consensus size: 37
3730290 ATTTATCAAG
*
3730300 ATAAA-TATTAAGATAATCACTTTAATATTAAATTAAT
1 ATAAACTATTAAGATAAGCAC-TTAATATTAAATTAAT
*
3730337 AAAATACTATTAAGATAAGCA-TTAA-ATTAAATTTAAT
1 ATAA-ACTATTAAGATAAGCACTTAATATTAAA-TTAAT
*
3730374 ATTAAACTATTAAAATAA
1 A-TAAACTATTAAGATAA
3730392 TATTATTTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
36 6 0.13
37 25 0.53
38 3 0.06
39 13 0.28
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.37
Consensus pattern (37 bp):
ATAAACTATTAAGATAAGCACTTAATATTAAATTAAT
Found at i:3743346 original size:35 final size:35
Alignment explanation
Indices: 3743290--3743369 Score: 99
Period size: 35 Copynumber: 2.3 Consensus size: 35
3743280 ATATCTGTAA
* *
3743290 CTGTGTCTGCATCTGAAATGGG-CTCAGGCCCGAAT
1 CTGTATCTGTATCTGAAATGGGCCT-AGGCCCGAAT
*
3743325 CTGTATCTGTATCTGACATGGGCCTAGGCCCGAAT
1 CTGTATCTGTATCTGAAATGGGCCTAGGCCCGAAT
* *
3743360 ATGAATCTGT
1 CTGTATCTGT
3743370 CTCATTTGTG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
35 37 0.95
36 2 0.05
ACGTcount: A:0.21, C:0.24, G:0.26, T:0.29
Consensus pattern (35 bp):
CTGTATCTGTATCTGAAATGGGCCTAGGCCCGAAT
Found at i:3746711 original size:63 final size:63
Alignment explanation
Indices: 3746636--3746826 Score: 373
Period size: 63 Copynumber: 3.0 Consensus size: 63
3746626 TTGAGTTTTG
*
3746636 GAAGTCCAGTAAGGTAATGTAGTTTCTAACCCTAATTTATGATTTTTCTAATTTTGAAAATGT
1 GAAGTCCAGTAAGATAATGTAGTTTCTAACCCTAATTTATGATTTTTCTAATTTTGAAAATGT
3746699 GAAGTCCAGTAAGATAATGTAGTTTCTAACCCTAATTTATGATTTTTCTAATTTTGAAAATGT
1 GAAGTCCAGTAAGATAATGTAGTTTCTAACCCTAATTTATGATTTTTCTAATTTTGAAAATGT
3746762 GAAGTCCAGTAAGATAATGTAGTTTCTAACCCTAATTTATGATTTTTCTAATTTTGAAAATGT
1 GAAGTCCAGTAAGATAATGTAGTTTCTAACCCTAATTTATGATTTTTCTAATTTTGAAAATGT
3746825 GA
1 GA
3746827 TTTTAATGAT
Statistics
Matches: 127, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
63 127 1.00
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (63 bp):
GAAGTCCAGTAAGATAATGTAGTTTCTAACCCTAATTTATGATTTTTCTAATTTTGAAAATGT
Found at i:3752096 original size:23 final size:21
Alignment explanation
Indices: 3752057--3752121 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 21
3752047 TTCATATACA
* *
3752057 TTTTATATATTTAAAATTTAG
1 TTTTTTATTTTTAAAATTTAG
3752078 TGTTTTTATTTTTAGAAATTTAG
1 T-TTTTTATTTTTA-AAATTTAG
*
3752101 TTTCTTTATTTTTTAAATTTA
1 TTT-TTTATTTTTAAAATTTA
3752122 AAATTTTAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
21 1 0.03
22 19 0.50
23 18 0.47
ACGTcount: A:0.29, C:0.02, G:0.06, T:0.63
Consensus pattern (21 bp):
TTTTTTATTTTTAAAATTTAG
Found at i:3752112 original size:22 final size:22
Alignment explanation
Indices: 3752057--3752121 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 22
3752047 TTCATATACA
*
3752057 TTTTATATATTTAAAATTTAGTG
1 TTTT-TATTTTTAAAATTTAGTG
3752080 TTTTTATTTTTAGAAATTTAGT-
1 TTTTTATTTTTA-AAATTTAGTG
*
3752102 TTCTTTATTTTTTAAATTTA
1 TT-TTTATTTTTAAAATTTA
3752122 AAATTTTAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
22 16 0.42
23 22 0.58
ACGTcount: A:0.29, C:0.02, G:0.06, T:0.63
Consensus pattern (22 bp):
TTTTTATTTTTAAAATTTAGTG
Found at i:3752258 original size:33 final size:33
Alignment explanation
Indices: 3752216--3752288 Score: 130
Period size: 33 Copynumber: 2.2 Consensus size: 33
3752206 GCTTGGTATC
*
3752216 GATGT-AACATAAAAAATTACAATGAAAAGACT
1 GATGTGAACATAAAAAATTACAATGAAAAAACT
3752248 GATGTGAACATAAAAAATTACAATGAAAAAACT
1 GATGTGAACATAAAAAATTACAATGAAAAAACT
3752281 GATGTGAA
1 GATGTGAA
3752289 TTTTTCTTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
32 5 0.13
33 34 0.87
ACGTcount: A:0.55, C:0.08, G:0.15, T:0.22
Consensus pattern (33 bp):
GATGTGAACATAAAAAATTACAATGAAAAAACT
Found at i:3767105 original size:17 final size:19
Alignment explanation
Indices: 3767069--3767106 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3767059 TTGGCTGGTT
*
3767069 AGATGAAAGAAATGAAACA
1 AGATGAAAGAAATAAAACA
3767088 AGATGAAA-AAA-AAAACA
1 AGATGAAAGAAATAAAACA
3767105 AG
1 AG
3767107 TTTCTCTTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 3 0.17
19 8 0.44
ACGTcount: A:0.68, C:0.05, G:0.18, T:0.08
Consensus pattern (19 bp):
AGATGAAAGAAATAAAACA
Found at i:3770170 original size:34 final size:34
Alignment explanation
Indices: 3770128--3770197 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
3770118 TTAGGTTATC
3770128 TTACATTTAATAAAACAAACAACAAAATTTTACA
1 TTACATTTAATAAAACAAACAACAAAATTTTACA
3770162 TTACATTTAATAAAACAAACAACAAAATTTTACA
1 TTACATTTAATAAAACAAACAACAAAATTTTACA
3770196 TT
1 TT
3770198 TTAACAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.31
Consensus pattern (34 bp):
TTACATTTAATAAAACAAACAACAAAATTTTACA
Found at i:3782061 original size:10 final size:10
Alignment explanation
Indices: 3782048--3782103 Score: 67
Period size: 10 Copynumber: 5.6 Consensus size: 10
3782038 GATTAAAATA
*
3782048 TATACACATT
1 TATATACATT
3782058 TATATACATT
1 TATATACATT
*
3782068 TACATACATT
1 TATATACATT
*
3782078 CATATACATT
1 TATATACATT
* *
3782088 TACATGCATT
1 TATATACATT
3782098 TATATA
1 TATATA
3782104 AAATGGCATA
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
10 37 1.00
ACGTcount: A:0.39, C:0.16, G:0.02, T:0.43
Consensus pattern (10 bp):
TATATACATT
Found at i:3782082 original size:20 final size:20
Alignment explanation
Indices: 3782053--3782103 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
3782043 AAATATATAC
3782053 ACATTTATATACATTTACAT
1 ACATTTATATACATTTACAT
*
3782073 ACATTCATATACATTTACAT
1 ACATTTATATACATTTACAT
*
3782093 GCATTTATATA
1 ACATTTATATA
3782104 AAATGGCATA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.39, C:0.16, G:0.02, T:0.43
Consensus pattern (20 bp):
ACATTTATATACATTTACAT
Found at i:3791252 original size:18 final size:19
Alignment explanation
Indices: 3791209--3791253 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
3791199 CTCATCAATT
3791209 TTAAAAT-AATTTAATAAA
1 TTAAAATAAATTTAATAAA
3791227 --AAATATAAATTTAA-AAA
1 TTAAA-ATAAATTTAATAAA
3791244 TTAAAATAAA
1 TTAAAATAAA
3791254 CGAAAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
16 3 0.13
17 5 0.22
18 12 0.52
19 3 0.13
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TTAAAATAAATTTAATAAA
Found at i:3791275 original size:30 final size:32
Alignment explanation
Indices: 3791224--3791282 Score: 95
Period size: 30 Copynumber: 1.9 Consensus size: 32
3791214 ATAATTTAAT
*
3791224 AAAAAATATAAATTTAAAAATTAAAATAAACG
1 AAAAAATATAAATTAAAAAATTAAAATAAACG
3791256 AAAAAAT-TAAA-TAAAAAATTAAAATAA
1 AAAAAATATAAATTAAAAAATTAAAATAA
3791283 TTATTACTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 15 0.58
31 4 0.15
32 7 0.27
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (32 bp):
AAAAAATATAAATTAAAAAATTAAAATAAACG
Found at i:3800918 original size:69 final size:69
Alignment explanation
Indices: 3800833--3801192 Score: 184
Period size: 69 Copynumber: 5.2 Consensus size: 69
3800823 GGTAGCTGGA
* * * * ** *
3800833 AGCTTTACTCTAGCTAACTATTTTAAAGGTTGTAGTTTTTCACCTACGAACCTTAATATTACAAT
1 AGCTTTGCTCTTGCTAACTGTTTTAAAGGTTGCAACTTTTCACCTACGAACCTTAATATTACAAC
*
3800898 TAGG
66 TAAG
* * * * * * *
3800902 AGTTTTGCTCTTGCTAATTGTTTTAGAGGTTGCAACTTTTCACCTGCGGACCTTAATATTATAGC
1 AGCTTTGCTCTTGCTAACTGTTTTAAAGGTTGCAACTTTTCACCTACGAACCTTAATATTACAAC
3800967 TAAG
66 TAAG
* ** ** ** * * * *
3800971 AGCTTTGCTCTTACTAACTGTTTTGGAGGTTGCGGCTATTT-GTCTACGAATCTTAACATTATAG
1 AGCTTTGCTCTTGCTAACTGTTTTAAAGGTTGCAACT-TTTCACCTACGAACCTTAATATTACAA
* *
3801035 TTATG
65 CTAAG
* * * ** **** * * * * **
3801040 AGCTTTGCTCTCGTTAATTGTTTTGGAGGTTGTGGTTTTTCGCCTGCAAACCTTAATATGACAGT
1 AGCTTTGCTCTTGCTAACTGTTTTAAAGGTTGCAACTTTTCACCTACGAACCTTAATATTACAAC
*
3801105 TGAG
66 TAAG
* * * * * ** * * *
3801109 AGGTTTGCTCTCGCTAACTGTTTTAGAGGTTACAA-TTCTTCGCCTGTGAACCTTAATATGATAG
1 AGCTTTGCTCTTGCTAACTGTTTTAAAGGTTGCAACTT-TTCACCTACGAACCTTAATATTACAA
*
3801173 CTAGG
65 CTAAG
*
3801178 AGCTTTGCTTTTGCT
1 AGCTTTGCTCTTGCT
3801193 CACTATGTTG
Statistics
Matches: 227, Mismatches: 61, Indels: 6
0.77 0.21 0.02
Matches are distributed among these distances:
68 5 0.02
69 219 0.96
70 3 0.01
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.40
Consensus pattern (69 bp):
AGCTTTGCTCTTGCTAACTGTTTTAAAGGTTGCAACTTTTCACCTACGAACCTTAATATTACAAC
TAAG
Found at i:3801018 original size:138 final size:138
Alignment explanation
Indices: 3800876--3801139 Score: 312
Period size: 138 Copynumber: 1.9 Consensus size: 138
3800866 AGTTTTTCAC
* * *
3800876 CTACGAACCTTAATATTACAATTAGGAGTTTTGCTCTTGCTAATTGTTTTAGAGGTTGCAACTTT
1 CTACGAACCTTAACATTACAATTAGGAGCTTTGCTCTCGCTAATTGTTTTAGAGGTTGCAACTTT
** * * * *
3800941 TCACCTGCGGACCTTAATATTATAGCTAAGAGCTTTGCTCTTACTAACTGTTTTGGAGGTTGCGG
66 TCACCTGCAAACCTTAATATGACAGCTAAGAGCTTTGCTCTCACTAACTGTTTTAGAGGTTGCGG
3801006 CTATTTGT
131 CTATTTGT
* * * * * * ****
3801014 CTACGAATCTTAACATTATAGTTATGAGCTTTGCTCTCGTTAATTGTTTTGGAGGTTGTGGTTTT
1 CTACGAACCTTAACATTACAATTAGGAGCTTTGCTCTCGCTAATTGTTTTAGAGGTTGCAACTTT
* * * * *
3801079 TCGCCTGCAAACCTTAATATGACAGTTGAGAGGTTTGCTCTCGCTAACTGTTTTAGAGGTT
66 TCACCTGCAAACCTTAATATGACAGCTAAGAGCTTTGCTCTCACTAACTGTTTTAGAGGTT
3801140 ACAATTCTTC
Statistics
Matches: 102, Mismatches: 24, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
138 102 1.00
ACGTcount: A:0.22, C:0.17, G:0.21, T:0.40
Consensus pattern (138 bp):
CTACGAACCTTAACATTACAATTAGGAGCTTTGCTCTCGCTAATTGTTTTAGAGGTTGCAACTTT
TCACCTGCAAACCTTAATATGACAGCTAAGAGCTTTGCTCTCACTAACTGTTTTAGAGGTTGCGG
CTATTTGT
Found at i:3828905 original size:19 final size:19
Alignment explanation
Indices: 3828881--3828926 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
3828871 ATGTTTGAGC
*
3828881 ACTCAATTTAGTAAAAATG
1 ACTCAATTTAGTAAAAAGG
3828900 ACTCAATTTAGTAAAAAGG
1 ACTCAATTTAGTAAAAAGG
*
3828919 ACTAAATT
1 ACTCAATT
3828927 GCAATAGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.48, C:0.11, G:0.11, T:0.30
Consensus pattern (19 bp):
ACTCAATTTAGTAAAAAGG
Found at i:3831722 original size:24 final size:24
Alignment explanation
Indices: 3831695--3831757 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
3831685 AGAATCATTT
*
3831695 AGAATACACCATAAGACATCGTAC
1 AGAATACACCATAAGACATCATAC
* *
3831719 AGAA-ATCACCATAAGGCATCATAT
1 AGAATA-CACCATAAGACATCATAC
* *
3831743 AGAGTACGCCATAAG
1 AGAATACACCATAAG
3831758 GCTTCATAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
23 1 0.03
24 30 0.94
25 1 0.03
ACGTcount: A:0.44, C:0.22, G:0.16, T:0.17
Consensus pattern (24 bp):
AGAATACACCATAAGACATCATAC
Found at i:3833517 original size:28 final size:28
Alignment explanation
Indices: 3833477--3833540 Score: 128
Period size: 28 Copynumber: 2.3 Consensus size: 28
3833467 TTACGTTTTT
3833477 TTACACACATAGGCAGAGATTTACACAC
1 TTACACACATAGGCAGAGATTTACACAC
3833505 TTACACACATAGGCAGAGATTTACACAC
1 TTACACACATAGGCAGAGATTTACACAC
3833533 TTACACAC
1 TTACACAC
3833541 GCAAAGATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.39, C:0.27, G:0.12, T:0.22
Consensus pattern (28 bp):
TTACACACATAGGCAGAGATTTACACAC
Found at i:3834433 original size:16 final size:17
Alignment explanation
Indices: 3834412--3834470 Score: 63
Period size: 16 Copynumber: 3.6 Consensus size: 17
3834402 ATATTATATG
3834412 TTATATGATTATTT-TA
1 TTATATGATTATTTATA
*
3834428 TTATATG-TTATTTATT
1 TTATATGATTATTTATA
*
3834444 TTATAT-ATTATTACATA
1 TTATATGATTATT-TATA
3834461 TTATAT-ATTA
1 TTATATGATTA
3834471 CATATTTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
15 6 0.16
16 19 0.51
17 12 0.32
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (17 bp):
TTATATGATTATTTATA
Found at i:3834452 original size:23 final size:23
Alignment explanation
Indices: 3834367--3834454 Score: 71
Period size: 23 Copynumber: 3.9 Consensus size: 23
3834357 GCCCTATGTT
3834367 TTATTTAATTTTATA-A-T-TAT-
1 TTATTT-ATTTTATATATTATATG
*
3834387 TTATTTTATTTTCCTATATTATATG
1 TTA-TTTATTTT-ATATATTATATG
*
3834412 TTATATGATTATT-T-TATTATATG
1 TTAT-TTATT-TTATATATTATATG
3834435 TTATTTATTTTATATATTAT
1 TTATTTATTTTATATATTAT
3834455 TACATATTAT
Statistics
Matches: 55, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
20 8 0.15
21 7 0.13
22 6 0.11
23 20 0.36
24 5 0.09
25 7 0.13
26 2 0.04
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (23 bp):
TTATTTATTTTATATATTATATG
Found at i:3834454 original size:7 final size:7
Alignment explanation
Indices: 3834401--3834476 Score: 57
Period size: 7 Copynumber: 10.9 Consensus size: 7
3834391 TTTATTTTCC
3834401 TATATTA
1 TATATTA
*
3834408 TATGTTA
1 TATATTA
3834415 TATGATTA
1 TAT-ATTA
*
3834423 TTTTATTA
1 -TATATTA
*
3834431 TATGTTA
1 TATATTA
* *
3834438 TTTATTT
1 TATATTA
3834445 TATA-TA
1 TATATTA
3834451 T-TATTA
1 TATATTA
*
3834457 CATATTA
1 TATATTA
3834464 TATATTA
1 TATATTA
*
3834471 CATATT
1 TATATT
3834477 TTTATATATT
Statistics
Matches: 52, Mismatches: 13, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
5 2 0.04
6 4 0.08
7 37 0.71
8 7 0.13
9 2 0.04
ACGTcount: A:0.34, C:0.03, G:0.04, T:0.59
Consensus pattern (7 bp):
TATATTA
Found at i:3834481 original size:17 final size:17
Alignment explanation
Indices: 3834440--3834486 Score: 55
Period size: 14 Copynumber: 2.8 Consensus size: 17
3834430 ATATGTTATT
3834440 TATTTTATATATTATTACA
1 TATTTT-TATA-TATTACA
3834459 TA---TTATATATTACA
1 TATTTTTATATATTACA
3834473 TATTTTTATATATT
1 TATTTTTATATATT
3834487 TTGTATCTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
14 9 0.36
15 4 0.16
16 1 0.04
17 9 0.36
19 2 0.08
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (17 bp):
TATTTTTATATATTACA
Found at i:3843749 original size:40 final size:39
Alignment explanation
Indices: 3843651--3843913 Score: 278
Period size: 40 Copynumber: 6.6 Consensus size: 39
3843641 TCCTCGTTCA
* * * *
3843651 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
3843690 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
3843729 GAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
3843769 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
3843809 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
3843849 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
3843890 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
3843914 CAGCATTCAA
Statistics
Matches: 197, Mismatches: 21, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
39 40 0.20
40 145 0.74
41 12 0.06
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:3843873 original size:120 final size:119
Alignment explanation
Indices: 3843651--3843913 Score: 307
Period size: 120 Copynumber: 2.2 Consensus size: 119
3843641 TCCTCGTTCA
* * *
3843651 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATT
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATT
* * *
3843716 TAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAAC-TCGCAC
66 TAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAATAACTTAGCAC
* * * * *
3843769 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGA
1 -AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGACATAACCCGG-
* * ** * *
3843834 ATTT-GTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
63 ATTTAATAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATAATAACTTAGCAC
*
3843890 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
3843914 CAGCATTCAA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 37 0.31
120 75 0.62
121 9 0.07
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATT
TAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAATAACTTAGCAC
Found at i:3843922 original size:41 final size:41
Alignment explanation
Indices: 3843845--3843922 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
3843835 TTTGTATCTC
* * *
3843845 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
3843886 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
3843923 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:3850140 original size:87 final size:89
Alignment explanation
Indices: 3849958--3850141 Score: 225
Period size: 87 Copynumber: 2.1 Consensus size: 89
3849948 CGGAGAGTAG
* ** * *
3849958 ATCGAAGACATAGCAGATCTGACCTTTTGATGTTTTCACATCGAAGCAGATCCACGATGATTTGG
1 ATCGAAGACATAGCAGAGCTGACCTTCAGATGTTTACACATCGAAGCAGATCCAAGATGATTTGG
* *
3850023 CATTCTTGTGTTTACAAGGAGCAA
66 CATTCTTGTATTTACAAGGAACAA
* *
3850047 ATCGAAGACATAGCAGAGCTGACCTTCAGGTGTTTACAC-T-GAAGTAGATCCAAGATGATTTGG
1 ATCGAAGACATAGCAGAGCTGACCTTCAGATGTTTACACATCGAAGCAGATCCAAGATGATTTGG
3850110 CA-TCTCTGTATTGT-C-AGAGAACAA
66 CATTCT-TGTATT-TACAAG-GAACAA
3850134 ATCGAAGA
1 ATCGAAGA
3850142 AACAGATTTG
Statistics
Matches: 83, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
86 5 0.06
87 42 0.51
88 2 0.02
89 34 0.41
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (89 bp):
ATCGAAGACATAGCAGAGCTGACCTTCAGATGTTTACACATCGAAGCAGATCCAAGATGATTTGG
CATTCTTGTATTTACAAGGAACAA
Found at i:3850218 original size:220 final size:219
Alignment explanation
Indices: 3849836--3850615 Score: 1160
Period size: 220 Copynumber: 3.6 Consensus size: 219
3849826 AGGTTAAAGT
* * * * *
3849836 ATAGCAGATCTGGCCTTCAGGTGTTCACGCTGAAGCAGATCCAAGATGACTTGGCATCCCTGTAT
1 ATAGCAGATCTGACCTTCAGGTGTTTACACTGAAGCAGATCCAAGATGATTTGGCATCTCTGTAT
* * *
3849901 CGTCAGAGAACAAATCGAAGAAGCAGATTTGGCATCTCCATATTCGACGGAGAGTAGATCGAAGA
66 TGTCAGAGAACAAATCGAAGAAACAGATTTGGCATCTCCATATTCGACGGAGAGCAGATCG-AGA
* *
3849966 CATAGCAGATCTGACCTTTTGATGTTTTCACATCGAAGCAGATCCACGATGATTTGGCATTCTTG
130 CATAGCAGATCTGACCTTTAGATGTTTTCACATCGAAGCAGATCCAAGATGATTTGGCATTCTTG
3850031 TGTTTACAAGGAGCAAATCGAAGAC
195 TGTTTACAAGGAGCAAATCGAAGAC
* *
3850056 ATAGCAGAGCTGACCTTCAGGTGTTTACACTGAAGTAGATCCAAGATGATTTGGCATCTCTGTAT
1 ATAGCAGATCTGACCTTCAGGTGTTTACACTGAAGCAGATCCAAGATGATTTGGCATCTCTGTAT
*
3850121 TGTCAGAGAACAAATCGAAGAAACAGATTTGGCATCTCTATATTCGACGGAGAGCAGATCGTAGA
66 TGTCAGAGAACAAATCGAAGAAACAGATTTGGCATCTCCATATTCGACGGAGAGCAGATCG-AGA
3850186 CATAGCAGATCTGACCTTTAGATGTTTTCACATCGAAGCAGATCCAAGATGATTTGGCATTCTTG
130 CATAGCAGATCTGACCTTTAGATGTTTTCACATCGAAGCAGATCCAAGATGATTTGGCATTCTTG
3850251 TGTTTACAAGGAGCAAATCGAAGAC
195 TGTTTACAAGGAGCAAATCGAAGAC
3850276 ATAGCAGATCTGACCTTCAGGTGTTTACACTGAAGCAGATCCAAGATGATTTGGCATCTCTGTAT
1 ATAGCAGATCTGACCTTCAGGTGTTTACACTGAAGCAGATCCAAGATGATTTGGCATCTCTGTAT
* *
3850341 TGTCAGAGAACCAATTGAAGAAACAGATTTGGCATCTCCATATTCGACGGAGAGCAGA-C---AC
66 TGTCAGAGAACAAATCGAAGAAACAGATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAGAC
* * *
3850402 ATAGCAGATCTAACCTTCAGATGTTTAT-AC-T-GAAGCAGATCCAAGATGATTTGGCATCCTTG
131 ATAGCAGATCTGACCTTTAGATGTTT-TCACATCGAAGCAGATCCAAGATGATTTGGCATTCTTG
3850464 TGTTTACAAGGAGCAAATCGAAGAC
195 TGTTTACAAGGAGCAAATCGAAGAC
* * * * * * * *
3850489 ATAACAGATTTGGCTTTCATGTGTTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTGTAT
1 ATAGCAGATCTGACCTTCAGGTGTTTACACTGAAGCAGATCCAAGATGATTTGGCATCTCTGTAT
* * * * * * ** * *
3850554 TGTCAGGGAACAAATTGAATAAGCATATTTGGCGTCTCTGTGTTCGACAGAGAGCAGATCGA
66 TGTCAGAGAACAAATCGAAGAAACAGATTTGGCATCTCCATATTCGACGGAGAGCAGATCGA
3850616 AGATATCAAC
Statistics
Matches: 516, Mismatches: 40, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
213 160 0.31
214 2 0.00
215 28 0.05
216 1 0.00
219 1 0.00
220 324 0.63
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (219 bp):
ATAGCAGATCTGACCTTCAGGTGTTTACACTGAAGCAGATCCAAGATGATTTGGCATCTCTGTAT
TGTCAGAGAACAAATCGAAGAAACAGATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAGAC
ATAGCAGATCTGACCTTTAGATGTTTTCACATCGAAGCAGATCCAAGATGATTTGGCATTCTTGT
GTTTACAAGGAGCAAATCGAAGAC
Found at i:3850301 original size:89 final size:87
Alignment explanation
Indices: 3850172--3850332 Score: 259
Period size: 89 Copynumber: 1.8 Consensus size: 87
3850162 ATTCGACGGA
* * * *
3850172 GAGCAGATCGTAGACATAGCAGATCTGACCTTTAGATGTTTTCACATCGAAGCAGATCCAAGATG
1 GAGCAAATCGAAGACATAGCAGATCTGACCTTCAGATGTTTACAC-T-GAAGCAGATCCAAGATG
3850237 ATTTGGCATTCTTGTGTTTACAAG
64 ATTTGGCATTCTTGTGTTTACAAG
*
3850261 GAGCAAATCGAAGACATAGCAGATCTGACCTTCAGGTGTTTACACTGAAGCAGATCCAAGATGAT
1 GAGCAAATCGAAGACATAGCAGATCTGACCTTCAGATGTTTACACTGAAGCAGATCCAAGATGAT
3850326 TTGGCAT
66 TTGGCAT
3850333 CTCTGTATTG
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
87 26 0.39
88 1 0.01
89 40 0.60
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (87 bp):
GAGCAAATCGAAGACATAGCAGATCTGACCTTCAGATGTTTACACTGAAGCAGATCCAAGATGAT
TTGGCATTCTTGTGTTTACAAG
Found at i:3850924 original size:17 final size:17
Alignment explanation
Indices: 3850902--3850934 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3850892 AATAATTTTC
3850902 AAACCCAAACTTAAACT
1 AAACCCAAACTTAAACT
*
3850919 AAACCCACACTTAAAC
1 AAACCCAAACTTAAAC
3850935 CCGTTATACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.33, G:0.00, T:0.15
Consensus pattern (17 bp):
AAACCCAAACTTAAACT
Found at i:3851480 original size:28 final size:28
Alignment explanation
Indices: 3851448--3851510 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 28
3851438 TTACGTTTTT
3851448 TACACACATAGGCAGAGATTTACACACG
1 TACACACATAGGCAGAGATTTACACACG
*
3851476 TACACACATAGGCAGAGATTTACACACT
1 TACACACATAGGCAGAGATTTACACACG
3851504 TACACAC
1 TACACAC
3851511 GCAGAGATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.40, C:0.27, G:0.14, T:0.19
Consensus pattern (28 bp):
TACACACATAGGCAGAGATTTACACACG
Found at i:3851519 original size:24 final size:25
Alignment explanation
Indices: 3851459--3851520 Score: 81
Period size: 28 Copynumber: 2.4 Consensus size: 25
3851449 ACACACATAG
3851459 GCAGAGATTTACACACGTACACACATA
1 GCAGAGATTTACACACGTACACAC--A
*
3851486 GGCAGAGATTTACACACTTACACAC-
1 -GCAGAGATTTACACACGTACACACA
3851511 GCAGAGATTT
1 GCAGAGATTT
3851521 TTTCACACAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
24 10 0.30
28 23 0.70
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (25 bp):
GCAGAGATTTACACACGTACACACA
Found at i:3852403 original size:16 final size:14
Alignment explanation
Indices: 3852371--3852449 Score: 79
Period size: 14 Copynumber: 5.4 Consensus size: 14
3852361 TTTATTTTCT
* *
3852371 TATATTATATGTTA
1 TATATTATTTATTA
3852385 TATGATTATTTTATTA
1 TAT-ATTA-TTTATTA
*
3852401 TATGTTATTTATTTTA
1 TATATTATTTA--TTA
3852417 TATATTA-TTATTA
1 TATATTATTTATTA
*
3852430 CATATTATTTATTA
1 TATATTATTTATTA
3852444 TATATT
1 TATATT
3852450 TTATATATCA
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
13 9 0.17
14 18 0.33
15 10 0.19
16 17 0.31
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.62
Consensus pattern (14 bp):
TATATTATTTATTA
Found at i:3852422 original size:23 final size:22
Alignment explanation
Indices: 3852337--3852424 Score: 83
Period size: 23 Copynumber: 3.9 Consensus size: 22
3852327 GCCCTATGTT
*
3852337 TTATTTATTTTTATAAT-TAT-
1 TTATTTATTTTTATATTATATG
3852357 TTATTTTATTTTCTTATATTATATG
1 TTA-TTTA-TTT-TTATATTATATG
*
3852382 TTATATGATTATTT-TATTATATG
1 TTAT-TTATT-TTTATATTATATG
3852405 TTATTTATTTTATATATTAT
1 TTATTTATTTT-TATATTAT
3852425 TATTACATAT
Statistics
Matches: 56, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
20 3 0.05
21 6 0.11
22 8 0.14
23 25 0.45
24 8 0.14
25 6 0.11
ACGTcount: A:0.28, C:0.01, G:0.03, T:0.67
Consensus pattern (22 bp):
TTATTTATTTTTATATTATATG
Found at i:3852424 original size:7 final size:7
Alignment explanation
Indices: 3852371--3852455 Score: 64
Period size: 7 Copynumber: 11.7 Consensus size: 7
3852361 TTTATTTTCT
3852371 TATATTA
1 TATATTA
*
3852378 TATGTTA
1 TATATTA
3852385 TATGATTA
1 TAT-ATTA
*
3852393 TTTTATTA
1 -TATATTA
*
3852401 TATGTTA
1 TATATTA
*
3852408 TTTATTTTA
1 --TATATTA
3852417 TATATTA
1 TATATTA
3852424 T-TATTA
1 TATATTA
*
3852430 CATATTA
1 TATATTA
*
3852437 TTTATTA
1 TATATTA
*
3852444 TATATTT
1 TATATTA
3852451 TATAT
1 TATAT
3852456 ATCAATATTG
Statistics
Matches: 61, Mismatches: 12, Indels: 10
0.73 0.14 0.12
Matches are distributed among these distances:
6 5 0.08
7 41 0.67
8 7 0.11
9 8 0.13
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.62
Consensus pattern (7 bp):
TATATTA
Found at i:3852437 original size:29 final size:29
Alignment explanation
Indices: 3852372--3852453 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 29
3852362 TTATTTTCTT
* * *
3852372 ATATTATATGTTATATGATTATT-TTATTAT
1 ATATTATTTATTATAT-A-TATTATTATTAC
* *
3852402 ATGTTATTTATTTTATATATTATTATTAC
1 ATATTATTTATTATATATATTATTATTAC
*
3852431 ATATTATTTATTATATATTTTAT
1 ATATTATTTATTATATATATTAT
3852454 ATATCAATAT
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
28 4 0.09
29 27 0.63
30 12 0.28
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.62
Consensus pattern (29 bp):
ATATTATTTATTATATATATTATTATTAC
Found at i:3852463 original size:29 final size:29
Alignment explanation
Indices: 3852405--3852469 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
3852395 TTATTATATG
* *
3852405 TTATTTATTTTATATATTATTATTACATA
1 TTATTTATTATATATATTATTATCACATA
*
3852434 TTATTTATTATATATTTTATATATCA-ATA
1 TTATTTATTATATATATTAT-TATCACATA
3852463 TTGATTT
1 TT-ATTT
3852470 GGTGTTTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 23 0.74
30 8 0.26
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.62
Consensus pattern (29 bp):
TTATTTATTATATATATTATTATCACATA
Done.