Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167827.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_10, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 24162007
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 47000 characters in sequence are not A, C, G, or T
File 20 of 131
Found at i:5024954 original size:22 final size:22
Alignment explanation
Indices: 5024924--5024976 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
5024914 ATAAGAAAAA
*
5024924 AAAAGAAAGAAAGAAAGAACCTC
1 AAAA-AAAGAAAGAAACAACCTC
* *
5024947 AAAAAAAGCAAGCAACAACCTC
1 AAAAAAAGAAAGAAACAACCTC
*
5024969 AATAAAAG
1 AAAAAAAG
5024977 CTTTCAAACA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 22 0.85
23 4 0.15
ACGTcount: A:0.64, C:0.17, G:0.13, T:0.06
Consensus pattern (22 bp):
AAAAAAAGAAAGAAACAACCTC
Found at i:5027036 original size:2 final size:2
Alignment explanation
Indices: 5027029--5027059 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5027019 TATTTATCTG
*
5027029 TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5027060 TTTTCTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5027272 original size:34 final size:35
Alignment explanation
Indices: 5027228--5027306 Score: 133
Period size: 34 Copynumber: 2.3 Consensus size: 35
5027218 TATCTTTCTT
*
5027228 TTTACTTTATCTACTTTAATATAATTTTTTGATTA
1 TTTATTTTATCTACTTTAATATAATTTTTTGATTA
*
5027263 TTT-TTTTATCTACTTTAATATATTTTTTTGATTA
1 TTTATTTTATCTACTTTAATATAATTTTTTGATTA
5027297 TTTATTTTAT
1 TTTATTTTAT
5027307 GGATTGATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
34 32 0.78
35 9 0.22
ACGTcount: A:0.25, C:0.06, G:0.03, T:0.66
Consensus pattern (35 bp):
TTTATTTTATCTACTTTAATATAATTTTTTGATTA
Found at i:5028382 original size:10 final size:9
Alignment explanation
Indices: 5028358--5028399 Score: 54
Period size: 8 Copynumber: 4.9 Consensus size: 9
5028348 GTTCATTTGT
5028358 TTTA-TTTA
1 TTTATTTTA
5028366 TTTATTTTA
1 TTTATTTTA
5028375 TGTTATTTTA
1 T-TTATTTTA
5028385 -TTA-TTTA
1 TTTATTTTA
5028392 TTTATTTT
1 TTTATTTT
5028400 TGAAATATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
7 4 0.13
8 10 0.33
9 8 0.27
10 8 0.27
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.76
Consensus pattern (9 bp):
TTTATTTTA
Found at i:5029149 original size:14 final size:14
Alignment explanation
Indices: 5029113--5029142 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5029103 TTAGATATAT
5029113 TTTGATAAAAAAAA
1 TTTGATAAAAAAAA
*
5029127 TTTGATAAAAATAA
1 TTTGATAAAAAAAA
5029141 TT
1 TT
5029143 GATTAAATTT
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:0.57, C:0.00, G:0.07, T:0.37
Consensus pattern (14 bp):
TTTGATAAAAAAAA
Found at i:5034612 original size:20 final size:20
Alignment explanation
Indices: 5034589--5034629 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5034579 TAATTGTGGC
*
5034589 ATTGACTCTGCTGATATGAT
1 ATTGACTCTGCTGACATGAT
* *
5034609 ATTGACTTTGTTGACATGAT
1 ATTGACTCTGCTGACATGAT
5034629 A
1 A
5034630 ACATGAATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (20 bp):
ATTGACTCTGCTGACATGAT
Found at i:5034621 original size:289 final size:289
Alignment explanation
Indices: 5034032--5034624 Score: 954
Period size: 289 Copynumber: 2.1 Consensus size: 289
5034022 GTAAAGAGAG
* *
5034032 TTGATTTTGTTGACACAATAAATAGGTATAACAATTTGCATGTGTTCACCTCTCAGCCTTTTCTC
1 TTGATTTTGTTGACACAATAAATAAGTATAACAATTTGCATGTGTTCACCACTCAGCCTTTTCTC
**
5034097 TATAAAAATTTGTCTTTGGTCAAATTACGATAATAGTTTCTATTGTTTAACGAAATTTAAAATTT
66 TATAAAAATTTGTCTTTGGTCAAATTACGATAATAGTTTCTATAATTTAACGAAATTTAAAATTT
* * *
5034162 AATCTTTCTATTATAATTTATAAAAATATAATTCTCATATTTTTTTATTTAATAATTTTAATCAA
131 AATCTTTCTACTATAATCTATAAAAATATAATTATCATATTTTTTTATTTAATAATTTTAATCAA
* * * * *
5034227 ATTACTAATCTCATTAAATTTTTGTTGTTAAATATATTAATATAATTGTTGACTTGATGACATAA
196 ATCACTAATCTCATTAAATTTTTGTCGTTAAATATATTAATATAACTATTGACTTGATAACATAA
*
5034292 CTGTGGCATTGACTCTGCTAAACATGACG
261 CTGTGGCATTGACTCTGCTAAACATGACA
* **
5034321 TTGATTTTGTTGACACAATAAATAAGTTTAACAATTTGCATGTGTTCACCACTTTGCCTTTTCTC
1 TTGATTTTGTTGACACAATAAATAAGTATAACAATTTGCATGTGTTCACCACTCAGCCTTTTCTC
*
5034386 TATAAAAATTTGTCTTTGGTCAAATTACGATAATAGTTTTTATAATTTAACGAAATTTAAAATTT
66 TATAAAAATTTGTCTTTGGTCAAATTACGATAATAGTTTCTATAATTTAACGAAATTTAAAATTT
* *
5034451 AATCTTTTTACTATAATCTATAAAAATATAATTATTATATTTTTTTTATTTAATAATTTTAATCA
131 AATCTTTCTACTATAATCTATAAAAATATAATTATCATA-TTTTTTTATTTAATAATTTTAATCA
5034516 AATCACTAATCTCATTAAATTTTTGTCGTTAAATATATTAATATAACTATTGACTTGATAACATA
195 AATCACTAATCTCATTAAATTTTTGTCGTTAAATATATTAATATAACTATTGACTTGATAACATA
* * * *
5034581 ATTGTGGCATTGACTCTGCT-GATATGATA
260 ACTGTGGCATTGACTCTGCTAAACATGACA
*
5034610 TTGACTTTGTTGACA
1 TTGATTTTGTTGACA
5034625 TGATAACATG
Statistics
Matches: 279, Mismatches: 24, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
289 175 0.63
290 104 0.37
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.45
Consensus pattern (289 bp):
TTGATTTTGTTGACACAATAAATAAGTATAACAATTTGCATGTGTTCACCACTCAGCCTTTTCTC
TATAAAAATTTGTCTTTGGTCAAATTACGATAATAGTTTCTATAATTTAACGAAATTTAAAATTT
AATCTTTCTACTATAATCTATAAAAATATAATTATCATATTTTTTTATTTAATAATTTTAATCAA
ATCACTAATCTCATTAAATTTTTGTCGTTAAATATATTAATATAACTATTGACTTGATAACATAA
CTGTGGCATTGACTCTGCTAAACATGACA
Found at i:5035060 original size:27 final size:28
Alignment explanation
Indices: 5035020--5035075 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
5035010 AAAAAATTGA
*
5035020 ATTATATACAATTTT-TTTATTTTAAAAT
1 ATTATATACAATTTTAATT-TTTTAAAAT
*
5035048 ATTA-ATATAATTTTAATTTTTTAAAAT
1 ATTATATACAATTTTAATTTTTTAAAAT
5035075 A
1 A
5035076 ATATTTTAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 19 0.76
28 6 0.24
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (28 bp):
ATTATATACAATTTTAATTTTTTAAAAT
Found at i:5035081 original size:21 final size:22
Alignment explanation
Indices: 5035057--5035135 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 22
5035047 TATTAATATA
5035057 ATTTTAATTTTTT-AAAATAAT
1 ATTTTAATTTTTTAAAAATAAT
5035078 ATTTTAGAATTTTTATGAAAAATCAA-
1 ATTTT--AATTTTT-T-AAAAAT-AAT
*
5035104 A-TTTCATTTTTTAAAAATAAT
1 ATTTTAATTTTTTAAAAATAAT
5035125 -TTTTAATTTTT
1 ATTTTAATTTTT
5035136 AGAATTTTTA
Statistics
Matches: 48, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
20 2 0.04
21 20 0.42
22 1 0.02
23 13 0.27
24 1 0.02
25 3 0.06
26 6 0.12
27 2 0.04
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (22 bp):
ATTTTAATTTTTTAAAAATAAT
Found at i:5047000 original size:20 final size:19
Alignment explanation
Indices: 5046975--5047030 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 19
5046965 TGAAATTTAT
5046975 AAATTAATAAAATGATATAA
1 AAATTAATAAAAT-ATATAA
*
5046995 AAATTAATAACATATATAA
1 AAATTAATAAAATATATAA
*
5047014 ATAATTATTAAAA-ATAT
1 A-AATTAATAAAATATAT
5047031 TATTTACTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 11 0.34
20 21 0.66
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (19 bp):
AAATTAATAAAATATATAA
Found at i:5055535 original size:13 final size:12
Alignment explanation
Indices: 5055517--5055546 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
5055507 GTGAAAGTAG
5055517 AAAAAAAGGCAAA
1 AAAAAAAGG-AAA
5055530 AAAAAAAGGAAA
1 AAAAAAAGGAAA
5055542 AAAAA
1 AAAAA
5055547 GTTTAAATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.83, C:0.03, G:0.13, T:0.00
Consensus pattern (12 bp):
AAAAAAAGGAAA
Found at i:5057341 original size:15 final size:15
Alignment explanation
Indices: 5057323--5057392 Score: 81
Period size: 14 Copynumber: 4.7 Consensus size: 15
5057313 GTTTTTAGAA
5057323 TTTTGGATTTTAAGG
1 TTTTGGATTTTAAGG
*
5057338 TTTTAGATTTT-AGG
1 TTTTGGATTTTAAGG
* *
5057352 ATTTGGA-TTTAGGG
1 TTTTGGATTTTAAGG
*
5057366 GTTTGGATTTTAGAGG
1 TTTTGGATTTTA-AGG
5057382 TTTTGGATTTT
1 TTTTGGATTTT
5057393 TAGGGTTTTA
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
13 3 0.07
14 16 0.36
15 14 0.31
16 12 0.27
ACGTcount: A:0.19, C:0.00, G:0.29, T:0.53
Consensus pattern (15 bp):
TTTTGGATTTTAAGG
Found at i:5057459 original size:15 final size:14
Alignment explanation
Indices: 5057435--5057480 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
5057425 AAGTTTTGAA
*
5057435 GTTTGGATTTTAGG
1 GTTTTGATTTTAGG
* *
5057449 GTTTTGAATTTAAAG
1 GTTTTG-ATTTTAGG
5057464 GTTTTGATTTTAGG
1 GTTTTGATTTTAGG
5057478 GTT
1 GTT
5057481 AAGGTTTTGA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 14 0.54
15 12 0.46
ACGTcount: A:0.20, C:0.00, G:0.28, T:0.52
Consensus pattern (14 bp):
GTTTTGATTTTAGG
Found at i:5057866 original size:23 final size:22
Alignment explanation
Indices: 5057823--5057882 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 22
5057813 TATTTAATTC
* *
5057823 TTATTATAATTTTTAGTTTTTTA
1 TTATTATTA-TTTTAGATTTTTA
5057846 TTATTATTATTTTAGCATTTTTA
1 TTATTATTATTTTAG-ATTTTTA
*
5057869 ATA-TATTTATTTTA
1 TTATTA-TTATTTTA
5057883 ATATATATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 8 0.25
23 24 0.75
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (22 bp):
TTATTATTATTTTAGATTTTTA
Found at i:5057883 original size:14 final size:14
Alignment explanation
Indices: 5057864--5057902 Score: 60
Period size: 16 Copynumber: 2.6 Consensus size: 14
5057854 ATTTTAGCAT
5057864 TTTTAATATATTTA
1 TTTTAATATATTTA
5057878 TTTTAATATATATTTA
1 TTTT-A-ATATATTTA
5057894 TTTTAATAT
1 TTTTAATAT
5057903 TTTTTATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 8 0.35
15 2 0.09
16 13 0.57
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTAATATATTTA
Found at i:5057890 original size:16 final size:16
Alignment explanation
Indices: 5057869--5057911 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
5057859 AGCATTTTTA
5057869 ATATATTTATTTTAAT
1 ATATATTTATTTTAAT
5057885 ATATATTTATTTTAAT
1 ATATATTTATTTTAAT
*
5057901 AT-TTTTTATTT
1 ATATATTTATTT
5057912 ATTATTATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 8 0.31
16 18 0.69
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
ATATATTTATTTTAAT
Found at i:5057912 original size:14 final size:15
Alignment explanation
Indices: 5057864--5057920 Score: 73
Period size: 14 Copynumber: 3.9 Consensus size: 15
5057854 ATTTTAGCAT
5057864 TTTTAATA-TATTTA
1 TTTTAATATTATTTA
5057878 TTTTAATATATATTTA
1 TTTTAATAT-TATTTA
*
5057894 TTTTAATATTTTTTA
1 TTTTAATATTATTTA
*
5057909 -TTTATTATTATT
1 TTTTAATATTATT
5057921 AAAAATAATC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
14 18 0.47
15 5 0.13
16 15 0.39
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTTAATATTATTTA
Found at i:5058032 original size:8 final size:8
Alignment explanation
Indices: 5057987--5058032 Score: 56
Period size: 8 Copynumber: 5.5 Consensus size: 8
5057977 AAAAAAACTT
5057987 AAAATAACA
1 AAAATAA-A
*
5057996 AAAATAAT
1 AAAATAAA
*
5058004 AATATATAA
1 AAAATA-AA
5058013 AAAATAAA
1 AAAATAAA
5058021 AAAATAAA
1 AAAATAAA
5058029 AAAA
1 AAAA
5058033 AGTTTTTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
8 19 0.59
9 13 0.41
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.17
Consensus pattern (8 bp):
AAAATAAA
Found at i:5058032 original size:17 final size:17
Alignment explanation
Indices: 5057987--5058033 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
5057977 AAAAAAACTT
* *
5057987 AAAATAACAAAAATAAT
1 AAAATAAAAAAAATAAA
* *
5058004 AATATATAAAAAATAAA
1 AAAATAAAAAAAATAAA
5058021 AAAATAAAAAAAA
1 AAAATAAAAAAAA
5058034 GTTTTTTTAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.17
Consensus pattern (17 bp):
AAAATAAAAAAAATAAA
Found at i:5059124 original size:21 final size:21
Alignment explanation
Indices: 5059100--5059141 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
5059090 AATCGATATT
*
5059100 ATTATTAATATTATTATTAAA
1 ATTATTAATATTAATATTAAA
*
5059121 ATTATTACTATTAATATTAAA
1 ATTATTAATATTAATATTAAA
5059142 CTAAAACTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTATTAATATTAATATTAAA
Found at i:5059139 original size:12 final size:12
Alignment explanation
Indices: 5059095--5059127 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
5059085 AATTAAATCG
5059095 ATATTATTATTA
1 ATATTATTATTA
5059107 ATATTATTATTA
1 ATATTATTATTA
*
5059119 AAATTATTA
1 ATATTATTA
5059128 CTATTAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
ATATTATTATTA
Found at i:5059403 original size:38 final size:36
Alignment explanation
Indices: 5059305--5059403 Score: 83
Period size: 37 Copynumber: 2.7 Consensus size: 36
5059295 AGGTCAGGTG
* * * *
5059305 ATAAAGAAAATGATCGAGATGACATCGCGAGTTAAA
1 ATAAAAAAAATGATCGAGATAACAACGCAAGTTAAA
** * *
5059341 A-AATAAAAAATCGATTAAGGTAACAACGTAAGTTGAATA
1 ATAA-AAAAAAT-GATCGAGATAACAACGCAAGTT-AA-A
5059380 ATAAAAAAAATGATCGAGATAACA
1 ATAAAAAAAATGATCGAGATAACA
5059404 CCGCGAGTCA
Statistics
Matches: 47, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
35 2 0.04
36 7 0.15
37 15 0.32
38 12 0.26
39 9 0.19
40 2 0.04
ACGTcount: A:0.54, C:0.09, G:0.17, T:0.20
Consensus pattern (36 bp):
ATAAAAAAAATGATCGAGATAACAACGCAAGTTAAA
Found at i:5060136 original size:239 final size:238
Alignment explanation
Indices: 5059633--5060163 Score: 649
Period size: 239 Copynumber: 2.2 Consensus size: 238
5059623 ATTGTGACTT
* * * *
5059633 AAAAAATAAATAGACCAGGATTAAACCATGAGTCAGAGAATAACAACAATTGGGATTAAACTGCG
1 AAAAAATAAAGAGATCAGGATTAAACCACGAGTCAGAGAATAACAACAATCGGGATTAAACT-CG
* * * * * * *
5059698 ATTTTGAATTAAAGAGATCGAGATTGAATCATGAGTCGAAACATAAAGAGACTGAAATTAAATCA
65 ATTTTAAATTAAAAAGATCGAGATTAAATCATGAGTCAAAAAAAAAAGAGACTGAAATTAAACCA
* * *
5059763 CAAGTCAGAAAAATACTGAAGATCGGAAATAAATCACGAATCAGAGAATAAAAGACCAAGATTAA
130 CAAGTCAGAAAAAGAATGAAGATC-GAAATAAACCACGAATCAGAGAATAAAAGACCAAGATTAA
*
5059828 ACCATAAGTCAGAGAATAACGTTAACTTGGATTGAATCACAAGTC
194 ACCACAAGTCAGAGAATAACGTTAACTTGGATTGAATCACAAGTC
* * *
5059873 AGAAAATAAAGAGATCAGGATTAAATCACGAGTCAGAGAATAACAACGATCGGGATTAAA-TCAT
1 AAAAAATAAAGAGATCAGGATTAAACCACGAGTCAGAGAATAACAACAATCGGGATTAAACTC--
* * **
5059937 GATTTTAAATTAAAAAGATTGAGATTAAATCGTGAGT-AAAAAAAAAAGAGACTGGCATTAAACC
64 GATTTTAAATTAAAAAGATCGAGATTAAATCATGAGTCAAAAAAAAAAGAGACTGAAATTAAACC
** * ** *
5060001 GTAAGTCAGAGAAAGAATGAAGATC-AAGATTAAACCGTGAATCAGAGAATAAAGAGACCATGAT
129 ACAAGTCAGAAAAAGAATGAAGATCGAA-A-TAAACCACGAATCAGAGAATAAA-AGACCAAGAT
* * *
5060065 TAAATCGCAAGTCAGAGAA-AATGTTAACTTGGATTGAATCACAAGTC
191 TAAACCACAAGTCAGAGAATAACGTTAACTTGGATTGAATCACAAGTC
* * *
5060112 AAAAAATGAAGAGA-CTGAGATTAAACCACGAGTCTGAGAATAACAACAATCG
1 AAAAAATAAAGAGATCAG-GATTAAACCACGAGTCAGAGAATAACAACAATCG
5060164 AGACAAAATC
Statistics
Matches: 248, Mismatches: 37, Indels: 13
0.83 0.12 0.04
Matches are distributed among these distances:
237 2 0.01
238 4 0.02
239 132 0.53
240 110 0.44
ACGTcount: A:0.48, C:0.13, G:0.19, T:0.21
Consensus pattern (238 bp):
AAAAAATAAAGAGATCAGGATTAAACCACGAGTCAGAGAATAACAACAATCGGGATTAAACTCGA
TTTTAAATTAAAAAGATCGAGATTAAATCATGAGTCAAAAAAAAAAGAGACTGAAATTAAACCAC
AAGTCAGAAAAAGAATGAAGATCGAAATAAACCACGAATCAGAGAATAAAAGACCAAGATTAAAC
CACAAGTCAGAGAATAACGTTAACTTGGATTGAATCACAAGTC
Found at i:5060245 original size:239 final size:238
Alignment explanation
Indices: 5059633--5060252 Score: 630
Period size: 239 Copynumber: 2.6 Consensus size: 238
5059623 ATTGTGACTT
* * * * * **
5059633 AAAAAATAAATAGACCAGGATTAAACCATGAGTCAGAGAATAACAACAATTGGGATTAAA-C-TG
1 AAAAAATAAAGAGATCAGGATTAAACCACGAGTCAGAGAATAACAACAATCGAGACAAAATCAT-
* * * * *
5059696 CGATTTTGAATTAAAGAGATCGAGATTGAATCATGAGTCGAAACATAAAGAGACTGAAATTAAAT
65 -GA-TTTAAAGTAAAGAGATCGAGATTGAATCATGAGTTGAAACATAAAAAGACTGGAATTAAAT
** * * *
5059761 CACAAGTCAGAAAAATACTGAAGATCGGAAATAAATCACGAATCAGAGAATAAAAGACCAAGATT
128 CGTAAGTCAGAAAAAGAATGAAGATC-GAAATAAACCACGAATCAGAGAATAAAAGACCAAGATT
*
5059826 AAACCATAAGTCAGAGAATAACGTTAACTTGGATTGAATCACAAGTC
192 AAACCACAAGTCAGAGAATAACGTTAACTTGGATTGAATCACAAGTC
* * * * **
5059873 AGAAAATAAAGAGATCAGGATTAAATCACGAGTCAGAGAATAACAACGATCGGGATTAAATCATG
1 AAAAAATAAAGAGATCAGGATTAAACCACGAGTCAGAGAATAACAACAATCGAGACAAAATCATG
* * * * * * * * *
5059938 ATTTTAAATTAAAAAGATTGAGATTAAATCGTGAG-T-AAAAAAAAAAGAGACTGGCATTAAACC
66 A-TTTAAAGTAAAGAGATCGAGATTGAATCATGAGTTGAAACATAAAA-AGACTGGAATTAAATC
* ** *
5060001 GTAAGTCAGAGAAAGAATGAAGATC-AAGATTAAACCGTGAATCAGAGAATAAAGAGACCATGAT
129 GTAAGTCAGAAAAAGAATGAAGATCGAA-A-TAAACCACGAATCAGAGAATAAA-AGACCAAGAT
* * *
5060065 TAAATCGCAAGTCAGAGAA-AATGTTAACTTGGATTGAATCACAAGTC
191 TAAACCACAAGTCAGAGAATAACGTTAACTTGGATTGAATCACAAGTC
* * * *
5060112 AAAAAATGAAGAGA-CTGAGATTAAACCACGAGTCTGAGAATAACAACAATCGAGACAAAATCGT
1 AAAAAATAAAGAGATCAG-GATTAAACCACGAGTCAGAGAATAACAACAATCGAGACAAAATCAT
* * * *
5060176 GA-TTAGGAGTAAAGAGATCGGGATTGAACCACGAGTTGAAACATAAAAAGA-TCGGAATTAAAT
65 GATTTA-AAGTAAAGAGATCGAGATTGAATCATGAGTTGAAACATAAAAAGACT-GGAATTAAAT
5060239 CGTAAGTCA-AAAAA
128 CGTAAGTCAGAAAAA
5060253 TATCAACAGT
Statistics
Matches: 313, Mismatches: 56, Indels: 24
0.80 0.14 0.06
Matches are distributed among these distances:
237 5 0.02
238 35 0.11
239 154 0.49
240 117 0.37
241 1 0.00
242 1 0.00
ACGTcount: A:0.48, C:0.12, G:0.20, T:0.20
Consensus pattern (238 bp):
AAAAAATAAAGAGATCAGGATTAAACCACGAGTCAGAGAATAACAACAATCGAGACAAAATCATG
ATTTAAAGTAAAGAGATCGAGATTGAATCATGAGTTGAAACATAAAAAGACTGGAATTAAATCGT
AAGTCAGAAAAAGAATGAAGATCGAAATAAACCACGAATCAGAGAATAAAAGACCAAGATTAAAC
CACAAGTCAGAGAATAACGTTAACTTGGATTGAATCACAAGTC
Found at i:5060278 original size:101 final size:102
Alignment explanation
Indices: 5060150--5060339 Score: 240
Period size: 102 Copynumber: 1.9 Consensus size: 102
5060140 CGAGTCTGAG
* * * * **
5060150 AATAACAACAATCGAGACAAAATCGTGA-TTAGGAGTAAAGAGATCGGGATTGAACCACGAGTTG
1 AATAACAACAATCGAGACAAAACCGTGATTTAAGAGTAAAAAGATCGAGATTGAACCACGAGTCA
5060214 AAACATAAAAAGATC-GGAATTAAATCGTAAGTCAAAA
66 AAACATAAAAAGATCAGG-ATTAAATCGTAAGTCAAAA
* * * * ***
5060251 AATATCAACAGTCGAGACTAAACCGTGATTTAAGAGTAAAAAGATTGAGATTGAACTGTGAGTCA
1 AATAACAACAATCGAGACAAAACCGTGATTTAAGAGTAAAAAGATCGAGATTGAACCACGAGTCA
5060316 AAACATAAAAAGATCAGGATTAAA
66 AAACATAAAAAGATCAGGATTAAA
5060340 CCACAAGTTA
Statistics
Matches: 74, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
101 24 0.32
102 48 0.65
103 2 0.03
ACGTcount: A:0.47, C:0.12, G:0.20, T:0.21
Consensus pattern (102 bp):
AATAACAACAATCGAGACAAAACCGTGATTTAAGAGTAAAAAGATCGAGATTGAACCACGAGTCA
AAACATAAAAAGATCAGGATTAAATCGTAAGTCAAAA
Found at i:5060406 original size:33 final size:33
Alignment explanation
Indices: 5060363--5060514 Score: 110
Period size: 35 Copynumber: 4.5 Consensus size: 33
5060353 AAATTTTGAG
*
5060363 GATCGAGATTAAATCGTGAA-TCAGAGAATAAGA
1 GATCGAGATTAAATCGT-AAGTCAAAGAATAAGA
* *
5060396 GATCGGGATTAAATCGTAAGTCAAAGAATAACA
1 GATCGAGATTAAATCGTAAGTCAAAGAATAAGA
* * ** *
5060429 TTAACTTG-GATTAAATCACAAGTCAAAAAATAAGGA
1 --GA-TCGAGATTAAATCGTAAGTCAAAGAATAA-GA
* * * *
5060465 GATCGAGATTAAACCATGAGTCAAAGAATAACAA
1 GATCGAGATTAAATCGTAAGTCAAAGAATAA-GA
*
5060499 CAATCGAGATTAAATC
1 -GATCGAGATTAAATC
5060515 ACGATTTTGA
Statistics
Matches: 93, Mismatches: 19, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
32 2 0.02
33 29 0.31
34 23 0.25
35 36 0.39
36 3 0.03
ACGTcount: A:0.47, C:0.12, G:0.18, T:0.22
Consensus pattern (33 bp):
GATCGAGATTAAATCGTAAGTCAAAGAATAAGA
Found at i:5060510 original size:69 final size:68
Alignment explanation
Indices: 5060389--5060516 Score: 168
Period size: 69 Copynumber: 1.9 Consensus size: 68
5060379 TGAATCAGAG
* * * ** *
5060389 AATAAGAGATCGGGATTAAATCGTAAGTCAAAGAATAACATTAACTTGGATTAAATCACAAGTCA
1 AATAAGAGATCGAGATTAAACCATAAGTCAAAGAATAACAACAACTCGGATTAAATCACAAGTCA
5060454 AAA
66 AAA
*
5060457 AATAAGGAGATCGAGATTAAACCATGAGTCAAAGAATAACAACAA-TCGAGATTAAATCAC
1 AATAA-GAGATCGAGATTAAACCATAAGTCAAAGAATAACAACAACTCG-GATTAAATCAC
5060517 GATTTTGAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
68 7 0.14
69 44 0.86
ACGTcount: A:0.49, C:0.13, G:0.16, T:0.21
Consensus pattern (68 bp):
AATAAGAGATCGAGATTAAACCATAAGTCAAAGAATAACAACAACTCGGATTAAATCACAAGTCA
AAA
Found at i:5060589 original size:22 final size:22
Alignment explanation
Indices: 5060555--5060687 Score: 146
Period size: 22 Copynumber: 6.1 Consensus size: 22
5060545 ACAGCTAGTC
* *
5060555 GAAATTATGCTCGAAGTTCTTA
1 GAAATCATGCTCGAAGGTCTTA
* *
5060577 GAGATCATGCTCGAAGGTTTTA
1 GAAATCATGCTCGAAGGTCTTA
* *
5060599 GAGATTATGCTC-AGAGGTCTTA
1 GAAATCATGCTCGA-AGGTCTTA
* *
5060621 GAAATCATGCTTGAAAGTCTTA
1 GAAATCATGCTCGAAGGTCTTA
*
5060643 GAAATCATGC-CTGGAGGTCTTA
1 GAAATCATGCTC-GAAGGTCTTA
5060665 GAAATCAT-CTCGAAGGTCTTA
1 GAAATCATGCTCGAAGGTCTTA
5060686 GA
1 GA
5060688 GATTATGCCC
Statistics
Matches: 93, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
21 13 0.14
22 79 0.85
23 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (22 bp):
GAAATCATGCTCGAAGGTCTTA
Found at i:5060608 original size:44 final size:44
Alignment explanation
Indices: 5060558--5060695 Score: 165
Period size: 44 Copynumber: 3.2 Consensus size: 44
5060548 GCTAGTCGAA
* * *
5060558 ATTATGCTCGAAGTTCTTAGAGATCATGCTCGAAGGTTTTAGAG
1 ATTATGCTCGAAGGTCTTAGAAATCATGCTCGAAGGTCTTAGAG
* * *
5060602 ATTATGCTC-AGAGGTCTTAGAAATCATGCTTGAAAGTCTTAGAA
1 ATTATGCTCGA-AGGTCTTAGAAATCATGCTCGAAGGTCTTAGAG
* *
5060646 ATCATGC-CTGGAGGTCTTAGAAATCAT-CTCGAAGGTCTTAGAG
1 ATTATGCTC-GAAGGTCTTAGAAATCATGCTCGAAGGTCTTAGAG
5060689 ATTATGC
1 ATTATGC
5060696 CCAGAGGCCT
Statistics
Matches: 79, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
43 21 0.27
44 58 0.73
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (44 bp):
ATTATGCTCGAAGGTCTTAGAAATCATGCTCGAAGGTCTTAGAG
Found at i:5060893 original size:41 final size:41
Alignment explanation
Indices: 5060836--5060944 Score: 175
Period size: 41 Copynumber: 2.7 Consensus size: 41
5060826 ATCTGAAGAA
*
5060836 GGTTCCT-TCTAAACAGAGGCTTTGAAATCTTGATTGAAATT
1 GGTTCCTCT-TAAACAGAGGCTTTGAAATCTTGATTGAAAAT
5060877 GGTTCCTCTTAAACAGAGGCTTTGAAATCTTGATTGAAAAT
1 GGTTCCTCTTAAACAGAGGCTTTGAAATCTTGATTGAAAAT
* *
5060918 GGTTCCTCTTAAACATAGACTTTGAAA
1 GGTTCCTCTTAAACAGAGGCTTTGAAA
5060945 CTTTAAAAAC
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
41 63 0.98
42 1 0.02
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (41 bp):
GGTTCCTCTTAAACAGAGGCTTTGAAATCTTGATTGAAAAT
Found at i:5061297 original size:41 final size:41
Alignment explanation
Indices: 5061249--5061360 Score: 134
Period size: 41 Copynumber: 2.7 Consensus size: 41
5061239 TATACAAGTG
* *
5061249 CAAATGCAAGTGATGCAAATACGAATGTCTTTCTTGTGATA
1 CAAATGCAAGTGATGCAAATACAAATGTCCTTCTTGTGATA
* * * *
5061290 CAAATGCAAATGATGCAAATGCAAATGTCCTTCTTGTGGTG
1 CAAATGCAAGTGATGCAAATACAAATGTCCTTCTTGTGATA
* * * *
5061331 CAGATACAAGTGATGTAAATATAAATGTCC
1 CAAATGCAAGTGATGCAAATACAAATGTCC
5061361 CTTTCATGAT
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (41 bp):
CAAATGCAAGTGATGCAAATACAAATGTCCTTCTTGTGATA
Found at i:5061308 original size:15 final size:15
Alignment explanation
Indices: 5061285--5061316 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5061275 GTCTTTCTTG
5061285 TGATACAAATGCAAA
1 TGATACAAATGCAAA
*
5061300 TGATGCAAATGCAAA
1 TGATACAAATGCAAA
5061315 TG
1 TG
5061317 TCCTTCTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.12, G:0.19, T:0.22
Consensus pattern (15 bp):
TGATACAAATGCAAA
Found at i:5061699 original size:29 final size:28
Alignment explanation
Indices: 5061666--5061720 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
5061656 TTTTTTTTGA
* *
5061666 AGGCCAAATAAATTGGGCTTAAAGATTAG
1 AGGCCAAATAAAATGGGCAT-AAGATTAG
5061695 AGGCCAAATAAAATGGGCATAAGATT
1 AGGCCAAATAAAATGGGCATAAGATT
5061721 TTCTTAGGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.44, C:0.11, G:0.24, T:0.22
Consensus pattern (28 bp):
AGGCCAAATAAAATGGGCATAAGATTAG
Found at i:5061803 original size:33 final size:33
Alignment explanation
Indices: 5061759--5061837 Score: 140
Period size: 33 Copynumber: 2.4 Consensus size: 33
5061749 TAAAATTGGA
* *
5061759 GGCCAGATAAACTAGGCTTAAGATTTTCTTAAG
1 GGCCAGCTAAACTAGGCTTAAGATTTCCTTAAG
5061792 GGCCAGCTAAACTAGGCTTAAGATTTCCTTAAG
1 GGCCAGCTAAACTAGGCTTAAGATTTCCTTAAG
5061825 GGCCAGCTAAACT
1 GGCCAGCTAAACT
5061838 GGATTTAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.27
Consensus pattern (33 bp):
GGCCAGCTAAACTAGGCTTAAGATTTCCTTAAG
Found at i:5061890 original size:33 final size:33
Alignment explanation
Indices: 5061842--5061913 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
5061832 TAAACTGGAT
*
5061842 TTAAAACTTTATTGATGG-CAAGATAAATTAGGC
1 TTAAAACTTTATTGATGGTCAAG-TAAACTAGGC
* * *
5061875 TTAAATCTTTTTTGATGGTCAAGTAAACTGGGC
1 TTAAAACTTTATTGATGGTCAAGTAAACTAGGC
5061908 TTAAAA
1 TTAAAA
5061914 TTGAGGGCTA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
33 29 0.88
34 4 0.12
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (33 bp):
TTAAAACTTTATTGATGGTCAAGTAAACTAGGC
Found at i:5061934 original size:29 final size:29
Alignment explanation
Indices: 5061901--5061956 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
5061891 GGTCAAGTAA
*
5061901 ACTGGGCTTAAAATTGAGGGCTAGCTAAT
1 ACTGGGCTTAAAATTGAGGGCCAGCTAAT
5061930 ACTGGGCTTAAAATTGAGGGCCAGCTA
1 ACTGGGCTTAAAATTGAGGGCCAGCTA
5061957 CATTGGGCTT
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:0.30, C:0.16, G:0.29, T:0.25
Consensus pattern (29 bp):
ACTGGGCTTAAAATTGAGGGCCAGCTAAT
Found at i:5061970 original size:29 final size:28
Alignment explanation
Indices: 5061903--5061966 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 28
5061893 TCAAGTAAAC
*
5061903 TGGGCTTAAAATTGAGGGCTAGCTAATA
1 TGGGCTTAAAATTGAGGGCCAGCTAATA
5061931 CTGGGCTTAAAATTGAGGGCCAGCTACAT-
1 -TGGGCTTAAAATTGAGGGCCAGCTA-ATA
5061960 TGGGCTT
1 TGGGCTT
5061967 TAAACTTCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 7 0.21
29 24 0.73
30 2 0.06
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.28
Consensus pattern (28 bp):
TGGGCTTAAAATTGAGGGCCAGCTAATA
Found at i:5062003 original size:31 final size:31
Alignment explanation
Indices: 5061960--5062053 Score: 125
Period size: 31 Copynumber: 3.0 Consensus size: 31
5061950 CCAGCTACAT
*
5061960 TGGGCTTTAAACTTCATTGGTGCCAACTAAAC
1 TGGGC-TTAAACTTCATTGATGCCAACTAAAC
* * *
5061992 TGGGCTTAAACTTCATTGATGCCAAATCATC
1 TGGGCTTAAACTTCATTGATGCCAACTAAAC
*
5062023 TGGGCTTAAGACTTCATTGATGCCAGCTAAA
1 TGGGCTTAA-ACTTCATTGATGCCAACTAAA
5062054 TTAGGCTTGA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
31 31 0.58
32 22 0.42
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (31 bp):
TGGGCTTAAACTTCATTGATGCCAACTAAAC
Found at i:5062061 original size:32 final size:31
Alignment explanation
Indices: 5061949--5062061 Score: 120
Period size: 32 Copynumber: 3.6 Consensus size: 31
5061939 AAAATTGAGG
* * *
5061949 GCCAGCTACATTGGGCTTTAAACTTCATTGGT
1 GCCAACTAAATTGGGC-TTAAACTTCATTGAT
*
5061981 GCCAACTAAACTGGGCTTAAACTTCATTGAT
1 GCCAACTAAATTGGGCTTAAACTTCATTGAT
* *
5062012 GCCAAAT-CATCTGGGCTTAAGACTTCATTGAT
1 GCCAACTAAAT-TGGGCTTAA-ACTTCATTGAT
* *
5062044 GCCAGCTAAATTAGGCTT
1 GCCAACTAAATTGGGCTT
5062062 GATATTTTTT
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
30 1 0.01
31 29 0.43
32 35 0.52
33 2 0.03
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.31
Consensus pattern (31 bp):
GCCAACTAAATTGGGCTTAAACTTCATTGAT
Found at i:5063935 original size:15 final size:15
Alignment explanation
Indices: 5063917--5063970 Score: 76
Period size: 14 Copynumber: 3.7 Consensus size: 15
5063907 GTTTTTAGAA
5063917 TTTTGGATTTTAAGG
1 TTTTGGATTTTAAGG
5063932 TTTTGGATTTT-AGG
1 TTTTGGATTTTAAGG
*
5063946 ATTTGGA-TTTAAGG
1 TTTTGGATTTTAAGG
*
5063960 GTTTGGATTTT
1 TTTTGGATTTT
5063971 TAGGGTTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
13 3 0.09
14 18 0.51
15 14 0.40
ACGTcount: A:0.19, C:0.00, G:0.28, T:0.54
Consensus pattern (15 bp):
TTTTGGATTTTAAGG
Found at i:5063971 original size:29 final size:31
Alignment explanation
Indices: 5063908--5063979 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 31
5063898 GAATTTGGGG
* *
5063908 TTTTTAGAATTTTGGATTTTAAGGTTTTGGA
1 TTTTTAGGATTTTGGATTTTAAGGGTTTGGA
5063939 -TTTTAGGA-TTTGGA-TTTAAGGGTTTGGA
1 TTTTTAGGATTTTGGATTTTAAGGGTTTGGA
*
5063967 TTTTTAGGGTTTT
1 TTTTTAGGATTTT
5063980 AAAATTTTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 13 0.36
29 13 0.36
30 10 0.28
ACGTcount: A:0.19, C:0.00, G:0.26, T:0.54
Consensus pattern (31 bp):
TTTTTAGGATTTTGGATTTTAAGGGTTTGGA
Found at i:5064012 original size:22 final size:21
Alignment explanation
Indices: 5063974--5064024 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
5063964 GGATTTTTAG
*
5063974 GGTTTTAAAATTTTGGGTTTT
1 GGTTTTAAAATTTTGGGGTTT
*
5063995 GGTTTTGAAAGTTTTGGGGTTT
1 GGTTTT-AAAATTTTGGGGTTT
5064017 GGATTTTA
1 GG-TTTTA
5064025 GGATTTTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 6 0.23
22 16 0.62
23 4 0.15
ACGTcount: A:0.18, C:0.00, G:0.29, T:0.53
Consensus pattern (21 bp):
GGTTTTAAAATTTTGGGGTTT
Found at i:5066006 original size:5 final size:5
Alignment explanation
Indices: 5065998--5066026 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
5065988 ATAAAAGTTG
5065998 AAAAC AAAAC AAAAC AAAAC AAAAC AAAA
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAA
5066027 AATCTCAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:5066039 original size:12 final size:11
Alignment explanation
Indices: 5066023--5066052 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
5066013 AAAACAAAAC
5066023 AAAAAATCTCA
1 AAAAAATCTCA
5066034 ACAAAAATCTCA
1 A-AAAAATCTCA
5066046 AAAAAAT
1 AAAAAAT
5066053 ATTTTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.67, C:0.17, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAAAATCTCA
Found at i:5070748 original size:18 final size:20
Alignment explanation
Indices: 5070725--5070767 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
5070715 CCCGAAATTA
5070725 ATAAAATA-T-TTTTTTAAT
1 ATAAAATATTATTTTTTAAT
5070743 ATAAAATATTATTTTTTAAT
1 ATAAAATATTATTTTTTAAT
5070763 ATAAA
1 ATAAA
5070768 TAAAAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 8 0.35
19 1 0.04
20 14 0.61
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATAAAATATTATTTTTTAAT
Found at i:5075666 original size:20 final size:19
Alignment explanation
Indices: 5075628--5075666 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
5075618 AATATCAAGA
5075628 TAATATTAGAAAAAATGAC
1 TAATATTAGAAAAAATGAC
* *
5075647 TAATACTTATAAAAATTGAC
1 TAATA-TTAGAAAAAATGAC
5075667 ATGAGAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (19 bp):
TAATATTAGAAAAAATGAC
Found at i:5077200 original size:103 final size:102
Alignment explanation
Indices: 5077074--5077265 Score: 235
Period size: 103 Copynumber: 1.9 Consensus size: 102
5077064 AAGAAAAAAA
* *** * *
5077074 TTTTTAAAGTGGTTGAGCTTCTGCTTCGAAGAATTTTTTTGAGATA-AAATTTTTAAAGTTGTTT
1 TTTTTAAAGTGGTTGAGCTTCTGCTTAGAAGAATTTTTCCAAGA-AGAAATTTTTAAAGTGGTTA
5077138 AGCCTCTACCTAAAGAAGCCTTTTTTCAATATGAGACTT
65 AGCCTCTACCTAAAGAAG-CTTTTTTCAATATGAGACTT
* * *
5077177 TTTTTTAAGTTGTTGAG-TCTCTGCTTAGAAGAGTTTTTCCAAGAAGAAATTTTTAAAGTGGTTA
1 TTTTTAAAGTGGTTGAGCT-TCTGCTTAGAAGAATTTTTCCAAGAAGAAATTTTTAAAGTGGTTA
* * *
5077241 AGCCTCTGCTTAAAGGAGCTTTTTT
65 AGCCTCTACCTAAAGAAGCTTTTTT
5077266 AAAATAAAAT
Statistics
Matches: 75, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
102 9 0.12
103 66 0.88
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (102 bp):
TTTTTAAAGTGGTTGAGCTTCTGCTTAGAAGAATTTTTCCAAGAAGAAATTTTTAAAGTGGTTAA
GCCTCTACCTAAAGAAGCTTTTTTCAATATGAGACTT
Found at i:5077249 original size:49 final size:48
Alignment explanation
Indices: 5077071--5077354 Score: 151
Period size: 49 Copynumber: 5.7 Consensus size: 48
5077061 TTCAAGAAAA
* * * ***
5077071 AAATTTTTAAAGTGGTTGAGCTTCTGCTTCGAAGAATTTTTTTGAGATA-
1 AAATTTTTAAAGTGGTTGAGCCTCTGCTT-AAAGAGTTTTTCCAAGA-AG
* * * * * *
5077120 AAATTTTTAAAGTTGTTTAGCCTCTACCTAAAGAAGCCTTTTTTCAATATGAG
1 AAATTTTTAAAGTGGTTGAGCCTCTGCTTAAAG-AG--TTTTTCCAAGA--AG
** * * *
5077173 ACTTTTTTTTAAGTTGTTGAGTCTCTGCTTAGAAGAGTTTTTCCAAGAAG
1 A-AATTTTTAAAGTGGTTGAGCCTCTGCTTA-AAGAGTTTTTCCAAGAAG
* * *
5077223 AAATTTTTAAAGTGGTTAAGCCTCTGCTTAAAGGAGCTTTTT-TAA-AATA
1 AAATTTTTAAAGTGGTTGAGCCTCTGCTTAAA-GAG-TTTTTCCAAGAA-G
* ** * * *
5077272 AAATTTTTAATGTCATTGAGCCTCTACTTAAAAGAGCTTTTCCAAGATG
1 AAATTTTTAAAGTGGTTGAGCCTCTGCTT-AAAGAGTTTTTCCAAGAAG
* ** * *
5077321 AAAGTTTTAAAGTTATTGAGCATTTGCTTAAAGA
1 AAATTTTTAAAGTGGTTGAGCCTCTGCTTAAAGA
5077355 AACTTTTTCA
Statistics
Matches: 179, Mismatches: 43, Indels: 27
0.72 0.17 0.11
Matches are distributed among these distances:
48 16 0.09
49 105 0.59
50 12 0.07
51 8 0.04
52 10 0.06
53 1 0.01
54 24 0.13
55 3 0.02
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (48 bp):
AAATTTTTAAAGTGGTTGAGCCTCTGCTTAAAGAGTTTTTCCAAGAAG
Found at i:5077264 original size:152 final size:151
Alignment explanation
Indices: 5076974--5077328 Score: 364
Period size: 152 Copynumber: 2.4 Consensus size: 151
5076964 AAGATTTTTG
* *
5076974 TTTT-AAGTTGTTGAGCCTTTACCTAGAGGAACCTTTCTCAAGATGAAACTTTTTAAAATTGTTG
1 TTTTAAAGTTGTTGAGCCTCTACCTAGAAGAACCTTTCTCAAGATGAAACTTTTTAAAATTGTTG
* * * *
5077038 AGTCTCAACTTAGAGGAGCTTGTTTCAAGAAAAAAATTTTTAAAGTGGTTGAGCTTCTGCTTCGA
66 AGTCTCAACTTAGAAGAGCTTGTTTCAAGAAAAAAATTTTTAAAGTGGTTAAGCCTCTGCTTCAA
* * *
5077103 AGAATTTTTTTGAGATAAAAT
131 AGAACTTTTTTAAAATAAAAT
* * * * * *
5077124 TTTTAAAGTTGTTTAGCCTCTACCTA-AAGAAGCCTTTTTTCAATATGAGACTTTTTTTTAAGTT
1 TTTTAAAGTTGTTGAGCCTCTACCTAGAAGAA-CC-TTTCTCAAGATGAAAC--TTTTTAAAATT
** *
5077188 GTTGAGTCTCTGCTTAGAAGAG-TT-TTTCCAAG-AAGAAATTTTTAAAGTGGTTAAGCCTCTGC
62 GTTGAGTCTCAACTTAGAAGAGCTTGTTT-CAAGAAAAAAATTTTTAAAGTGGTTAAGCCTCTGC
*
5077250 TT-AAAGGAGCTTTTTTAAAATAAAAT
126 TTCAAA-GAACTTTTTTAAAATAAAAT
* ** * * * * *
5077276 TTTTAATGTCATTGAGCCTCTACTTAAAAGAGCTTTTC-CAAGATGAAAGTTTT
1 TTTTAAAGTTGTTGAGCCTCTACCTAGAAGAACCTTTCTCAAGATGAAACTTTT
5077329 AAAGTTATTG
Statistics
Matches: 167, Mismatches: 30, Indels: 18
0.78 0.14 0.08
Matches are distributed among these distances:
148 4 0.02
150 16 0.10
151 26 0.16
152 83 0.50
153 10 0.06
154 28 0.17
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39
Consensus pattern (151 bp):
TTTTAAAGTTGTTGAGCCTCTACCTAGAAGAACCTTTCTCAAGATGAAACTTTTTAAAATTGTTG
AGTCTCAACTTAGAAGAGCTTGTTTCAAGAAAAAAATTTTTAAAGTGGTTAAGCCTCTGCTTCAA
AGAACTTTTTTAAAATAAAAT
Found at i:5077463 original size:44 final size:42
Alignment explanation
Indices: 5077383--5077466 Score: 107
Period size: 43 Copynumber: 2.0 Consensus size: 42
5077373 AGTCTCTACT
*
5077383 TAAAAGAGCTTTTAAAATTTTTAAAATGATTGAGCCTCTGCA
1 TAAAAGAGCTTTTAAAATTTTTAAAATCATTGAGCCTCTGCA
* *
5077425 TAAAATAGCCTTTTTAAATTTTTAAAAGTCATCT-AGCCTCTG
1 TAAAAGAG-CTTTTAAAATTTTTAAAA-TCAT-TGAGCCTCTG
5077467 TTTAGAGAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
42 7 0.19
43 17 0.47
44 11 0.31
45 1 0.03
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (42 bp):
TAAAAGAGCTTTTAAAATTTTTAAAATCATTGAGCCTCTGCA
Found at i:5077686 original size:3 final size:3
Alignment explanation
Indices: 5077668--5077712 Score: 65
Period size: 3 Copynumber: 15.0 Consensus size: 3
5077658 TTCGGTATCA
*
5077668 ATT ACT ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT
5077713 TTTCTCTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:5077998 original size:19 final size:18
Alignment explanation
Indices: 5077956--5078003 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
5077946 GGAGGATCCA
*
5077956 TAAAAAAGAAAACCTGAT
1 TAAAAAAAAAAACCTGAT
* *
5077974 TGAAAAAAAAAACCTAGGT
1 TAAAAAAAAAAACCT-GAT
5077993 TAAAAAAAAAA
1 TAAAAAAAAAA
5078004 GCTTTCTGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 13 0.52
19 12 0.48
ACGTcount: A:0.67, C:0.08, G:0.10, T:0.15
Consensus pattern (18 bp):
TAAAAAAAAAAACCTGAT
Found at i:5078834 original size:21 final size:22
Alignment explanation
Indices: 5078817--5078857 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
5078807 AAAAAATTTT
5078817 AATAAATAATG-AATAAATAAA
1 AATAAATAATGAAATAAATAAA
5078838 AATAAATAATGAAATAAATA
1 AATAAATAATGAAATAAATA
5078858 GTTAAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (22 bp):
AATAAATAATGAAATAAATAAA
Found at i:5080071 original size:3 final size:3
Alignment explanation
Indices: 5080063--5080099 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
5080053 AATTATTTCT
5080063 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5080100 ATATAAGATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5081128 original size:15 final size:15
Alignment explanation
Indices: 5081105--5081143 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
5081095 CTTTAAAAAA
5081105 TTTTCTTTTCCTTTCC
1 TTTT-TTTTCCTTTCC
*
5081121 TTTTTTTTCTTTTCC
1 TTTTTTTTCCTTTCC
5081136 TTTCTTTT
1 TTT-TTTT
5081144 ATAAATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTTTTCCTTTCC
Found at i:5081128 original size:20 final size:19
Alignment explanation
Indices: 5081105--5081143 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
5081095 CTTTAAAAAA
5081105 TTTTCTTTTCCTTTCCTTTT
1 TTTTCTTTTCCTTT-CTTTT
5081125 TTTTCTTTTCCTTTCTTTT
1 TTTTCTTTTCCTTTCTTTT
5081144 ATAAATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTCTTTTCCTTTCTTTT
Found at i:5085349 original size:7 final size:7
Alignment explanation
Indices: 5085337--5085373 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
5085327 TTATTATGTG
5085337 TTTTATA
1 TTTTATA
5085344 TTTTATA
1 TTTTATA
5085351 TTTTTATA
1 -TTTTATA
5085359 TTTTAT-
1 TTTTATA
5085365 TTTTA-A
1 TTTTATA
5085371 TTT
1 TTT
5085374 ATTGAATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
6 8 0.29
7 13 0.46
8 7 0.25
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTATA
Found at i:5085357 original size:15 final size:14
Alignment explanation
Indices: 5085337--5085368 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
5085327 TTATTATGTG
5085337 TTTTATATTTTATAT
1 TTTTATATTTTAT-T
5085352 TTTTATATTTTATT
1 TTTTATATTTTATT
5085366 TTT
1 TTT
5085369 AATTTATTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTATATTTTATT
Found at i:5085367 original size:13 final size:14
Alignment explanation
Indices: 5085337--5085375 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
5085327 TTATTATGTG
5085337 TTTTATATTTTATAT
1 TTTTATA-TTTATAT
5085352 TTTTATATTT-TAT
1 TTTTATATTTATAT
5085365 TTTTA-ATTTAT
1 TTTTATATTTAT
5085376 TGAATTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 4 0.17
13 9 0.39
14 3 0.13
15 7 0.30
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTATATTTATAT
Found at i:5085523 original size:20 final size:18
Alignment explanation
Indices: 5085480--5085526 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 18
5085470 TTGTTACTAA
* *
5085480 TAATATAATAATATTTAT
1 TAATATAATAATAATTAC
5085498 TAATATAATATATTAATTAC
1 TAATATAATA-A-TAATTAC
5085518 TAATATAAT
1 TAATATAAT
5085527 TTTATTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 10 0.40
19 1 0.04
20 14 0.56
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
TAATATAATAATAATTAC
Found at i:5085536 original size:25 final size:25
Alignment explanation
Indices: 5085508--5085556 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
5085498 TAATATAATA
* *
5085508 TATTAATTACTAATATAATTTTATT
1 TATTAATTAATAAAATAATTTTATT
* *
5085533 TATTTATTAATAAAATATTTTTAT
1 TATTAATTAATAAAATAATTTTAT
5085557 AATAAAAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (25 bp):
TATTAATTAATAAAATAATTTTATT
Found at i:5085555 original size:17 final size:19
Alignment explanation
Indices: 5085535--5085585 Score: 63
Period size: 17 Copynumber: 2.8 Consensus size: 19
5085525 ATTTTATTTA
5085535 TTTATTAATAAAATA-T-T
1 TTTATTAATAAAATATTAT
5085552 TTTA-TAATAAAAATATTAT
1 TTTATTAAT-AAAATATTAT
*
5085571 TTTATTAATATAATA
1 TTTATTAATAAAATA
5085586 ATTGTAGTGC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
16 4 0.14
17 10 0.34
18 1 0.03
19 10 0.34
20 4 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTATTAATAAAATATTAT
Found at i:5089906 original size:23 final size:23
Alignment explanation
Indices: 5089863--5089915 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 23
5089853 GAAATATTAA
5089863 ATAAGAAATATTTTAAAATATTATTT
1 ATAA-AAA-ATTTTAAAATA-TATTT
*
5089889 -TAAAAAATTTTAATATATATTT
1 ATAAAAAATTTTAAAATATATTT
5089911 ATAAA
1 ATAAA
5089916 CATTTATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 5 0.20
23 14 0.56
24 3 0.12
25 3 0.12
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
ATAAAAAATTTTAAAATATATTT
Found at i:5090342 original size:30 final size:30
Alignment explanation
Indices: 5090301--5090365 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
5090291 GTTAAGGATA
*
5090301 TATTCAAATATAAATTAAGA-TATAAAAATT
1 TATTTAAATATAAATTAA-ATTATAAAAATT
*
5090331 TATTTAAATATAAATTAAATTTTAAAAATT
1 TATTTAAATATAAATTAAATTATAAAAATT
5090361 TATTT
1 TATTT
5090366 GGATGCAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 1 0.03
30 31 0.97
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (30 bp):
TATTTAAATATAAATTAAATTATAAAAATT
Found at i:5102869 original size:2 final size:2
Alignment explanation
Indices: 5102862--5102892 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5102852 AAGGTGATCT
5102862 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5102893 TGCGCAATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5112133 original size:3 final size:3
Alignment explanation
Indices: 5112120--5112149 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
5112110 TTGTATTTTT
*
5112120 TTA TTA ATA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5112150 ACTAATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:5112657 original size:51 final size:51
Alignment explanation
Indices: 5112591--5112691 Score: 159
Period size: 51 Copynumber: 2.0 Consensus size: 51
5112581 ATTTTTGGGT
*
5112591 CACCGAAAACTAAAAAAGTTTGAATTTTTTTGCCACCGTTGAATTTTTCGA
1 CACCGAAAACTAAAAAAGTGTGAATTTTTTTGCCACCGTTGAATTTTTCGA
**
5112642 CACC-AAAATCTAAAAAAGTGTGAATTTTTTTGTGACCGTTGAATTTTTCG
1 CACCGAAAA-CTAAAAAAGTGTGAATTTTTTTGCCACCGTTGAATTTTTCG
5112692 TCCATCGAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
50 4 0.09
51 42 0.91
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.37
Consensus pattern (51 bp):
CACCGAAAACTAAAAAAGTGTGAATTTTTTTGCCACCGTTGAATTTTTCGA
Found at i:5113023 original size:3 final size:3
Alignment explanation
Indices: 5113015--5113064 Score: 77
Period size: 3 Copynumber: 17.3 Consensus size: 3
5113005 TTTTATGTTA
*
5113015 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT -TT A-T ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5113061 ATT A
1 ATT A
5113065 CTGGTAATAA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 4 0.09
3 39 0.91
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:5113187 original size:20 final size:20
Alignment explanation
Indices: 5113164--5113218 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
5113154 AAAATTTAAT
5113164 AATAATAATTATTTAAAGCA
1 AATAATAATTATTTAAAGCA
*
5113184 AAT-A-AATTCTATTACAAGCA
1 AATAATAATTAT-TTA-AAGCA
5113204 AA-AAT-ATTATTTAAA
1 AATAATAATTATTTAAA
5113219 TTTTACCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
18 7 0.24
19 7 0.24
20 15 0.52
ACGTcount: A:0.55, C:0.07, G:0.04, T:0.35
Consensus pattern (20 bp):
AATAATAATTATTTAAAGCA
Found at i:5125527 original size:40 final size:40
Alignment explanation
Indices: 5125472--5125556 Score: 116
Period size: 40 Copynumber: 2.1 Consensus size: 40
5125462 ATCTCTCAAA
* * *
5125472 TTTTTAACATTTAAAGTTTGTTACCTCTAGTGATAGGAGC
1 TTTTTAACATTTAAAGTTCGTTACCTATAGTCATAGGAGC
* * *
5125512 TTTTTAACATTTAAAGTTCGTTGCCTATGGTCATAGGAGT
1 TTTTTAACATTTAAAGTTCGTTACCTATAGTCATAGGAGC
5125552 TTTTT
1 TTTTT
5125557 TTAATTTCAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.25, C:0.12, G:0.18, T:0.46
Consensus pattern (40 bp):
TTTTTAACATTTAAAGTTCGTTACCTATAGTCATAGGAGC
Found at i:5125753 original size:39 final size:39
Alignment explanation
Indices: 5125658--5125825 Score: 210
Period size: 39 Copynumber: 4.3 Consensus size: 39
5125648 AGCTTTTATC
* * *
5125658 ATTTAAAGTTTGTTGCCTTTGGTGAGAAGAGCCTTTTAA
1 ATTTAAAGTTTGTTGCCTCTAGTGAGAAGAGCCTTTTGA
* *
5125697 CATTTAAAGTTTGTTGCCTCTGGTGAGATGAGCCTTTTGA
1 -ATTTAAAGTTTGTTGCCTCTAGTGAGAAGAGCCTTTTGA
* * * * *
5125737 ATTTAAAGTTTTTTGCCTCTAATGAGAAAAGCTTTTTGG
1 ATTTAAAGTTTGTTGCCTCTAGTGAGAAGAGCCTTTTGA
* * *
5125776 ATTTAAAGTTTGTTGCCTCTAGTGAGAGGAGCTTTTTTA
1 ATTTAAAGTTTGTTGCCTCTAGTGAGAAGAGCCTTTTGA
5125815 ATTTAAAGTTT
1 ATTTAAAGTTT
5125826 CATAGCCTTT
Statistics
Matches: 112, Mismatches: 16, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
39 76 0.68
40 36 0.32
ACGTcount: A:0.25, C:0.11, G:0.21, T:0.43
Consensus pattern (39 bp):
ATTTAAAGTTTGTTGCCTCTAGTGAGAAGAGCCTTTTGA
Found at i:5126928 original size:23 final size:22
Alignment explanation
Indices: 5126897--5126950 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
5126887 TTTTGATTTT
* *
5126897 TTATGTTATT-TTTTTTATGATG
1 TTATTTTATTATTGTTT-TGATG
*
5126919 TTATTATTATTATTGTTTTGTTG
1 TTATT-TTATTATTGTTTTGATG
5126942 TTATTTTAT
1 TTATTTTAT
5126951 ATTATTAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 8 0.30
23 14 0.52
24 5 0.19
ACGTcount: A:0.19, C:0.00, G:0.11, T:0.70
Consensus pattern (22 bp):
TTATTTTATTATTGTTTTGATG
Found at i:5127187 original size:14 final size:14
Alignment explanation
Indices: 5127157--5127198 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 14
5127147 TTTTTGTTAA
5127157 AAAATAAAAAATTAT
1 AAAATAAAAAA-TAT
5127172 AAAATAAAATAA-AT
1 AAAATAAAA-AATAT
5127186 AAAATAAAAAATA
1 AAAATAAAAAATA
5127199 AATTGTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 2 0.08
14 12 0.48
15 9 0.36
16 2 0.08
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
AAAATAAAAAATAT
Found at i:5127201 original size:20 final size:20
Alignment explanation
Indices: 5127157--5127200 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
5127147 TTTTTGTTAA
* *
5127157 AAAATAAAAAATTATAAAAT
1 AAAATAAAAAAATAAAAAAT
5127177 AAAATAAATAAAATAAAAAAT
1 AAAATAAA-AAAATAAAAAAT
5127198 AAA
1 AAA
5127201 TTGTTTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (20 bp):
AAAATAAAAAAATAAAAAAT
Found at i:5131588 original size:21 final size:20
Alignment explanation
Indices: 5131553--5131638 Score: 86
Period size: 21 Copynumber: 4.2 Consensus size: 20
5131543 CGCATTAAAA
*
5131553 TAAAA-TTTCAAAAATTTTAT
1 TAAAAGTTTTAAAAATTTT-T
5131573 TAAAAGTTTTAAAAATTTTT
1 TAAAAGTTTTAAAAATTTTT
*
5131593 TAAAAAG-TCTAAAATATTTTT
1 T-AAAAGTTTTAAAA-ATTTTT
* * *
5131614 TAAAAATTATAAAAATTTAT
1 TAAAAGTTTTAAAAATTTTT
5131634 TAAAA
1 TAAAA
5131639 AATCCTAAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
20 27 0.47
21 30 0.53
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (20 bp):
TAAAAGTTTTAAAAATTTTT
Found at i:5131639 original size:20 final size:20
Alignment explanation
Indices: 5131562--5131639 Score: 84
Period size: 20 Copynumber: 3.8 Consensus size: 20
5131552 ATAAAATTTC
* *
5131562 AAAAATTTTATTAAAAGTTTT
1 AAAAA-TTTATTAAAAATTAT
* * *
5131583 AAAAATTTTTTAAAAAGTCT
1 AAAAATTTATTAAAAATTAT
*
5131603 AAAATATTTTTTAAAAATTAT
1 AAAA-ATTTATTAAAAATTAT
5131624 AAAAATTTATTAAAAA
1 AAAAATTTATTAAAAA
5131640 ATCCTAAAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
20 26 0.53
21 23 0.47
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (20 bp):
AAAAATTTATTAAAAATTAT
Found at i:5131647 original size:21 final size:19
Alignment explanation
Indices: 5131582--5131648 Score: 62
Period size: 21 Copynumber: 3.3 Consensus size: 19
5131572 TTAAAAGTTT
*
5131582 TAAAAATTTTTTAAAAAGTC
1 TAAAAA-TTTTTAAAAAATC
* *
5131602 TAAAATATTTTTTAAAAATTA
1 TAAAA-A-TTTTTAAAAAATC
5131623 TAAAAATTTATTAAAAAATCC
1 TAAAAATTT-TTAAAAAAT-C
5131644 TAAAA
1 TAAAA
5131649 TTCCAAAAGG
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
19 3 0.08
20 14 0.35
21 23 0.57
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.39
Consensus pattern (19 bp):
TAAAAATTTTTAAAAAATC
Found at i:5131648 original size:20 final size:19
Alignment explanation
Indices: 5131584--5131650 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 19
5131574 AAAAGTTTTA
*
5131584 AAAATTTTTTAAAAAGTCT
1 AAAATTTTTTAAAAAATCT
* *
5131603 AAAATATTTTTTAAAAATTAT
1 -AAA-ATTTTTTAAAAAATCT
*
5131624 AAAAATTTATTAAAAAATCCT
1 -AAAATTTTTTAAAAAAT-CT
5131645 AAAATT
1 AAAATT
5131651 CCAAAAGGTT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
20 21 0.52
21 19 0.47
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (19 bp):
AAAATTTTTTAAAAAATCT
Found at i:5131686 original size:20 final size:19
Alignment explanation
Indices: 5131659--5131697 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
5131649 TTCCAAAAGG
**
5131659 TTTCTTAAATTTTTTTAAA
1 TTTCTTAAAAATTTTTAAA
5131678 TTTCTTTAAAAATTTTTAAA
1 TTTC-TTAAAAATTTTTAAA
5131698 AATTCAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTCTTAAAAATTTTTAAA
Found at i:5131708 original size:20 final size:20
Alignment explanation
Indices: 5131685--5131816 Score: 99
Period size: 20 Copynumber: 6.4 Consensus size: 20
5131675 AAATTTCTTT
5131685 AAAAATTTTTAAAAATTC-A
1 AAAAATTTTTAAAAATTCTA
* *
5131704 AAAAAGATTTTAATAAATTCAA
1 AAAAA-TTTTTAA-AAATTCTA
5131726 AAAAATAATTCTTAAAAAATT-TA
1 AAAAAT--TT-TT-AAAAATTCTA
* * *
5131749 TAAAA-TTCTAAAAATTTTTA
1 AAAAATTTTTAAAAA-TTCTA
* * *
5131769 AAAACTTTTTAACAACTCTA
1 AAAAATTTTTAAAAATTCTA
*
5131789 AAAAATTTTTAAAAGTTCTA
1 AAAAATTTTTAAAAATTCTA
5131809 AAAAATTT
1 AAAAATTT
5131817 AAGAAAAGTT
Statistics
Matches: 88, Mismatches: 15, Indels: 19
0.72 0.12 0.16
Matches are distributed among these distances:
18 5 0.06
19 8 0.09
20 40 0.45
21 13 0.15
22 6 0.07
23 7 0.08
24 7 0.08
25 2 0.02
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAAATTTTTAAAAATTCTA
Found at i:5131713 original size:21 final size:20
Alignment explanation
Indices: 5131685--5131731 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 20
5131675 AAATTTCTTT
*
5131685 AAAAATTTTTAA-AAATTCA
1 AAAAAATTTTAATAAATTCA
5131704 AAAAAGATTTTAATAAATTCA
1 AAAAA-ATTTTAATAAATTCA
5131725 AAAAAAT
1 AAAAAAT
5131732 AATTCTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 5 0.20
20 8 0.32
21 12 0.48
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (20 bp):
AAAAAATTTTAATAAATTCA
Found at i:5131823 original size:10 final size:9
Alignment explanation
Indices: 5131737--5131834 Score: 52
Period size: 10 Copynumber: 10.1 Consensus size: 9
5131727 AAAATAATTC
5131737 TTAAAAAAT
1 TTAAAAAAT
*
5131746 TTATAAAAT
1 TTAAAAAAT
*
5131755 TCTAAAAATTT
1 T-TAAAAA-AT
*
5131766 TTAAAAACTTT
1 TTAAAAA--AT
* *
5131777 TTAACAACT
1 TTAAAAAAT
*
5131786 CTAAAAAATT
1 TTAAAAAA-T
* *
5131796 TTTAAAAGT
1 TTAAAAAAT
5131805 TCTAAAAAAT
1 T-TAAAAAAT
*
5131815 TTAAGAAAAG
1 TTAA-AAAAT
5131825 TTAAAAAAT
1 TTAAAAAAT
5131834 T
1 T
5131835 CCAAATATCT
Statistics
Matches: 68, Mismatches: 15, Indels: 12
0.72 0.16 0.13
Matches are distributed among these distances:
9 25 0.37
10 32 0.47
11 11 0.16
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.37
Consensus pattern (9 bp):
TTAAAAAAT
Found at i:5132029 original size:20 final size:20
Alignment explanation
Indices: 5131992--5132030 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5131982 AAAGTTTATA
* **
5131992 AAAAATTGTAAATTTTTTTT
1 AAAAATTCTAAAAATTTTTT
5132012 AAAAATTCTAAAAATTTTT
1 AAAAATTCTAAAAATTTTT
5132031 CATTTTTATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (20 bp):
AAAAATTCTAAAAATTTTTT
Found at i:5132069 original size:62 final size:63
Alignment explanation
Indices: 5132003--5132130 Score: 143
Period size: 63 Copynumber: 2.0 Consensus size: 63
5131993 AAAATTGTAA
* * * *
5132003 ATTTTTTTTAAAAATTCTAAAAA-TTTTT-CATTTTTATGAATCTTACATTTTTAATTTTTTCT
1 ATTTTTTTGAAAAATTC-AAAAAGTTTTTGAATTTTTATGAATCTTAAATTTTTAAGTTTTTCT
*** * * *
5132065 ATTTTTTTGAATTTTTCAAAAAGTTTTTGAATTTTTTTGGATTTTAAATTTTTAAGTTTTTCT
1 ATTTTTTTGAAAAATTCAAAAAGTTTTTGAATTTTTATGAATCTTAAATTTTTAAGTTTTTCT
5132128 ATT
1 ATT
5132131 GCTTATTTTT
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
61 5 0.09
62 18 0.33
63 31 0.57
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.61
Consensus pattern (63 bp):
ATTTTTTTGAAAAATTCAAAAAGTTTTTGAATTTTTATGAATCTTAAATTTTTAAGTTTTTCT
Found at i:5132150 original size:10 final size:10
Alignment explanation
Indices: 5132135--5132448 Score: 59
Period size: 10 Copynumber: 31.7 Consensus size: 10
5132125 TCTATTGCTT
5132135 ATTTTTTAAA
1 ATTTTTTAAA
**
5132145 ATTTTTTTTTA
1 A-TTTTTTAAA
* *
5132156 ATATTTTATA
1 ATTTTTTAAA
* *
5132166 A-TGTTTCAA
1 ATTTTTTAAA
5132175 ATTTTTT-AA
1 ATTTTTTAAA
*
5132184 ATTATTT--A
1 ATTTTTTAAA
**
5132192 ATTTTCCAAA
1 ATTTTTTAAA
* *
5132202 AATTTTTAGA
1 ATTTTTTAAA
*
5132212 ATTTTATAAA
1 ATTTTTTAAA
* *
5132222 A-ATTTTATAG
1 ATTTTTTA-AA
5132232 ATTTTTTCAAAA
1 ATTTTTT--AAA
* *
5132244 AATTTTT-AT
1 ATTTTTTAAA
5132253 ATTTTTT-AA
1 ATTTTTTAAA
**
5132262 ATTTTCAAAA
1 ATTTTTTAAA
**
5132272 ATTTTCCAAA
1 ATTTTTTAAA
* *
5132282 A-ATTTTAGA
1 ATTTTTTAAA
*
5132291 ATTTTTT-AG
1 ATTTTTTAAA
5132300 ATTTTTTGAAA
1 ATTTTTT-AAA
* *
5132311 AATTTTT-AG
1 ATTTTTTAAA
*
5132320 ATGTTTTAAA
1 ATTTTTTAAA
**
5132330 A-TTTTTATT
1 ATTTTTTAAA
*
5132339 ATTTTTTGAGA
1 ATTTTTT-AAA
**
5132350 A-TTTTTGGA
1 ATTTTTTAAA
5132359 A---TTTAAA
1 ATTTTTTAAA
**
5132366 ATTTTTTTGTTGA
1 A--TTTTT-TAAA
5132379 AT-TTTTAATA
1 ATTTTTTAA-A
*
5132389 A-TTTTTAGA
1 ATTTTTTAAA
*
5132398 ATTTTTTAGA
1 ATTTTTTAAA
5132408 ATTATTTTAAA
1 ATT-TTTTAAA
*
5132419 ATTTTTTTTAGA
1 A--TTTTTTAAA
5132431 ATTTTTTAGAA
1 ATTTTTTA-AA
5132442 ATTTTTT
1 ATTTTTT
5132449 TTTTATGCAT
Statistics
Matches: 215, Mismatches: 61, Indels: 55
0.65 0.18 0.17
Matches are distributed among these distances:
7 5 0.02
8 5 0.02
9 60 0.28
10 86 0.40
11 37 0.17
12 16 0.07
13 6 0.03
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.57
Consensus pattern (10 bp):
ATTTTTTAAA
Found at i:5132201 original size:26 final size:27
Alignment explanation
Indices: 5132149--5132220 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
5132139 TTTAAAATTT
5132149 TTTTTTAATATTTTATAATGTTTCAAA
1 TTTTTTAATATTTTATAATGTTTCAAA
5132176 TTTTTTAA-ATTATT-TAAT-TTTCCAAAA
1 TTTTTTAATATT-TTATAATGTTT-C-AAA
*
5132203 ATTTTTAGA-ATTTTATAA
1 TTTTTTA-ATATTTTATAA
5132221 AAATTTTATA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
25 3 0.08
26 8 0.21
27 21 0.54
28 7 0.18
ACGTcount: A:0.36, C:0.04, G:0.03, T:0.57
Consensus pattern (27 bp):
TTTTTTAATATTTTATAATGTTTCAAA
Found at i:5132256 original size:21 final size:21
Alignment explanation
Indices: 5132193--5132259 Score: 75
Period size: 20 Copynumber: 3.2 Consensus size: 21
5132183 AATTATTTAA
* *
5132193 TTTTCCAAAAATTTTTAGA-A
1 TTTTCAAAAAATTTTTAGATT
5132213 TTTT-ATAAAAATTTTATAGATT
1 TTTTCA-AAAAATTTT-TAGATT
*
5132235 TTTTCAAAAAATTTTTATATT
1 TTTTCAAAAAATTTTTAGATT
5132256 TTTT
1 TTTT
5132260 AAATTTTCAA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
20 13 0.32
21 13 0.32
22 13 0.32
23 1 0.03
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.55
Consensus pattern (21 bp):
TTTTCAAAAAATTTTTAGATT
Found at i:5132274 original size:69 final size:68
Alignment explanation
Indices: 5132177--5132334 Score: 169
Period size: 68 Copynumber: 2.3 Consensus size: 68
5132167 TGTTTCAAAT
* * * *
5132177 TTTTTAAATTATTT-AATTTTCCAAAAATTTT-TAGAATTTTATAAAAATTTTATAGATTTTTTC
1 TTTTTAAATTTTTTAAATTTTCCAAAAATTTTCCAAAAATTT-T-AAAATTTTATAGATTTTTT-
5132240 AAAAAA
63 AAAAAA
* * * *
5132246 TTTTTATATTTTTTAAATTTT-CAAAAATTTTCCAAAAATTTTAGAATTTTTTAGATTTTTTGAA
1 TTTTTAAATTTTTTAAATTTTCCAAAAATTTTCCAAAAATTTTAAAATTTTATAGATTTTTTAAA
5132310 AAA
66 AAA
* *
5132313 TTTTTAGATGTTTTAAAATTTT
1 TTTTTAAAT-TTTTTAAATTTT
5132335 TATTATTTTT
Statistics
Matches: 76, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
67 13 0.17
68 28 0.37
69 23 0.30
70 12 0.16
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (68 bp):
TTTTTAAATTTTTTAAATTTTCCAAAAATTTTCCAAAAATTTTAAAATTTTATAGATTTTTTAAA
AAA
Found at i:5132318 original size:20 final size:20
Alignment explanation
Indices: 5132293--5132347 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
5132283 ATTTTAGAAT
5132293 TTTTTAGATTTTTTGAAAAA
1 TTTTTAGATTTTTTGAAAAA
*
5132313 TTTTTAGATGTTTT--AAAA
1 TTTTTAGATTTTTTGAAAAA
*
5132331 TTTTTATTATTTTTTGA
1 TTTTTA-GATTTTTTGA
5132348 GAATTTTTGG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 10 0.34
19 6 0.21
20 13 0.45
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (20 bp):
TTTTTAGATTTTTTGAAAAA
Found at i:5132334 original size:30 final size:29
Alignment explanation
Indices: 5132256--5132335 Score: 74
Period size: 29 Copynumber: 2.8 Consensus size: 29
5132246 TTTTTATATT
* * **
5132256 TTTTA-AATTTTCAAAAATTTTCCAAAAA
1 TTTTAGAATTTTTAAAATTTTTTGAAAAA
* *
5132284 TTTTAGAATTTTTTAGATTTTTTGAAAAA
1 TTTTAGAATTTTTAAAATTTTTTGAAAAA
5132313 TTTTTAG-ATGTTTTAAAATTTTT
1 -TTTTAGAAT-TTTTAAAATTTTT
5132336 ATTATTTTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
28 5 0.12
29 19 0.46
30 17 0.41
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.54
Consensus pattern (29 bp):
TTTTAGAATTTTTAAAATTTTTTGAAAAA
Found at i:5132404 original size:20 final size:20
Alignment explanation
Indices: 5132293--5132405 Score: 65
Period size: 20 Copynumber: 5.8 Consensus size: 20
5132283 ATTTTAGAAT
*
5132293 TTTTTAG-ATTTTTTGAAAAA
1 TTTTTAGAATTTTTT-AATAA
*
5132313 TTTTTAG-ATGTTTTAA-AA
1 TTTTTAGAATTTTTTAATAA
** * *
5132331 TTTTTATTATTTTTTGAGAA
1 TTTTTAGAATTTTTTAATAA
* ** **
5132351 TTTTTGGAA-TTTAAAATTT
1 TTTTTAGAATTTTTTAATAA
*
5132370 TTTTGTTGAA-TTTTTAATAA
1 TTTT-TAGAATTTTTTAATAA
5132390 TTTTTAGAATTTTTTA
1 TTTTTAGAATTTTTTA
5132406 GAATTATTTT
Statistics
Matches: 70, Mismatches: 19, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
18 8 0.11
19 21 0.30
20 41 0.59
ACGTcount: A:0.30, C:0.00, G:0.10, T:0.60
Consensus pattern (20 bp):
TTTTTAGAATTTTTTAATAA
Found at i:5132429 original size:23 final size:23
Alignment explanation
Indices: 5132399--5132450 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
5132389 ATTTTTAGAA
5132399 TTTTTTAGAATTATTTTA-AAATT
1 TTTTTTAGAATT-TTTTAGAAATT
5132422 TTTTTTAGAATTTTTTAGAAATT
1 TTTTTTAGAATTTTTTAGAAATT
5132445 TTTTTT
1 TTTTTT
5132451 TTATGCATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 5 0.18
23 23 0.82
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (23 bp):
TTTTTTAGAATTTTTTAGAAATT
Found at i:5134837 original size:17 final size:18
Alignment explanation
Indices: 5134798--5134837 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
5134788 GTTGTAATGT
5134798 ATATATTAAATATGTATA
1 ATATATTAAATATGTATA
5134816 A-ATATTAACATAT-TA-A
1 ATATATTAA-ATATGTATA
5134832 ATATAT
1 ATATAT
5134838 ATTGTGCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
16 2 0.10
17 13 0.65
18 5 0.25
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (18 bp):
ATATATTAAATATGTATA
Found at i:5135274 original size:29 final size:28
Alignment explanation
Indices: 5135219--5135274 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 28
5135209 TGGGTTCAAA
* * * *
5135219 TACTTATTATTATATATTAATATTATTT
1 TACTTATTATCATATATAAAAAATATTT
5135247 TACTTATTAATCATATATAAAAAATATT
1 TACTTATT-ATCATATATAAAAAATATT
5135275 ACAAAATTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (28 bp):
TACTTATTATCATATATAAAAAATATTT
Found at i:5136613 original size:59 final size:59
Alignment explanation
Indices: 5136443--5137086 Score: 794
Period size: 59 Copynumber: 10.9 Consensus size: 59
5136433 TTTTGTTAAG
* * *
5136443 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTCTTGAAATTTTAATTTC-GA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAAATTT-ATTTCTAA
* *
5136501 GAAAAATTGATACTTTCAACTTTTCCTCAAAAATTTATTTTTTTTTTTGAAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAA--TA---TTTTTTTTGAAAATTTATTTCTAA
*
5136565 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAAATTTATTTCCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAAATTTATTTCTAA
* *
5136624 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA--TTTTTTGGAAATTTGGATTT-TCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAAATTT--ATTTCT-AA
* *** *
5136683 GGAAAATTGATACTTTCAACTTTTCCTCAAAAA-CCCTTTTTTG-AAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAAATTTATTTCTAA
* * *
5136740 GGAAAATTGATACTTTCGACTTTTCCCCAAAAATA-TTTTTTGGAAATTTTGATTT-TCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAAATTT-ATTTCT-AA
* * * *
5136799 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTTGAAATTTTGTTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA--TTTTTTTTGAAAATTTATTTCTAA
* * *
5136860 GGAAAATTGATACTTTCAACTTTTCCCCAAAAAT-GTTTTTTTG-GAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAAATTTATTTCTAA
* *
5136917 GGAAAATTGATACTCTCAACTTTTCCCTAAAAATATTTTTTTTGAAAATTTTAATTT-TCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAAA-TTT-ATTTCT-AA
*
5136978 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA--TTTTTTGGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAAATTTATTTCTAA
*
5137035 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGAAAATTT
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTTTGAAAATTT
5137087 TTATTTTTAT
Statistics
Matches: 518, Mismatches: 38, Indels: 58
0.84 0.06 0.09
Matches are distributed among these distances:
57 139 0.27
58 58 0.11
59 151 0.29
60 26 0.05
61 77 0.15
62 17 0.03
63 5 0.01
64 45 0.09
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (59 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAAATTTATTTCTAA
Found at i:5136890 original size:295 final size:294
Alignment explanation
Indices: 5136438--5137075 Score: 971
Period size: 295 Copynumber: 2.2 Consensus size: 294
5136428 TTTTTTTTTG
*
5136438 TTAAGGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTCTTGAAATTTTAATTTCGAGA
1 TTAA-GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTT-TTGAAATTTTAATTTCAAGA
5136503 AAAATTGATACTTTCAACTTTTCCTCAAAAATTTATTTTTTTTTTTGAAAATTTATTTCTAAGGA
64 AAAATTGATACTTTCAACTTTTCCTCAAAAA-TTATTTTTTTTTTTGAAAATTTATTTCTAAGGA
*
5136568 AAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAAATTTATTTCCAAGGAAAATTG
128 AAATTGATACTTTCAACTTTTCCCCAAAAAT-GTTTTTTTG-AAATTTATTTCCAAGGAAAATTG
* * *
5136633 ATACTTTCAACTTTTCCCTAAAAATA-TTTTTTGGAAATTTGGATTTTCAAGGAAAATTGATACT
191 ATACTCTCAACTTTTCCCTAAAAATATTTTTTTGAAAATTTGAATTTTCAAGGAAAATTGATACT
* *
5136697 TTCAACTTTTCCTCAAAAACCCTTTTTT-GAAATTTATTT
256 TTCAACTTTTCCCCAAAAA-CATTTTTTGGAAATTTATTT
* * *
5136736 TTAAGGAAAATTGATACTTTCGACTTTTCCCCAAAAATATTTTTTGGAAATTTTGATTTTCAAGG
1 TTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTT-GAAATTTT-AATTTCAAGA
* * *
5136801 AAAATTGATACTTTCAACTTTTCC-CTAAAAA-TA-TTTTTTTTTTGAAATTTTGTTTTTAAGGA
64 AAAATTGATACTTTCAACTTTTCCTC-AAAAATTATTTTTTTTTTTGAAAATTTATTTCTAAGGA
* **
5136863 AAATTGATACTTTCAACTTTTCCCCAAAAATGTTTTTTTGGAATTTATTTTTAAGGAAAATTGAT
128 AAATTGATACTTTCAACTTTTCCCCAAAAATGTTTTTTTGAAATTTATTTCCAAGGAAAATTGAT
*
5136928 ACTCTCAACTTTTCCCTAAAAATATTTTTTTTGAAAATTTTAATTTTCAAGGAAAATTGATACTT
193 ACTCTCAACTTTTCCCTAAAAATA-TTTTTTTGAAAATTTGAATTTTCAAGGAAAATTGATACTT
*
5136993 TCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTT
257 TCAACTTTTCCCCAAAAACATTTTTTGGAAATTTATTT
* *
5137031 CTAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTT
1 TTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTT
5137076 TTTGAAAATT
Statistics
Matches: 313, Mismatches: 21, Indels: 15
0.90 0.06 0.04
Matches are distributed among these distances:
293 45 0.14
294 14 0.04
295 163 0.52
296 4 0.01
297 47 0.15
298 40 0.13
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (294 bp):
TTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAATTTTAATTTCAAGAAA
AATTGATACTTTCAACTTTTCCTCAAAAATTATTTTTTTTTTTGAAAATTTATTTCTAAGGAAAA
TTGATACTTTCAACTTTTCCCCAAAAATGTTTTTTTGAAATTTATTTCCAAGGAAAATTGATACT
CTCAACTTTTCCCTAAAAATATTTTTTTGAAAATTTGAATTTTCAAGGAAAATTGATACTTTCAA
CTTTTCCCCAAAAACATTTTTTGGAAATTTATTT
Found at i:5137279 original size:5 final size:5
Alignment explanation
Indices: 5137266--5137297 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
5137256 GCGGCTTGGT
*
5137266 GGCTT GGCTC GGCTC GGCTC GGCTC GGCTC GG
1 GGCTC GGCTC GGCTC GGCTC GGCTC GGCTC GG
5137298 AGGGGCTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.44, T:0.22
Consensus pattern (5 bp):
GGCTC
Found at i:5137572 original size:20 final size:19
Alignment explanation
Indices: 5137522--5137573 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
5137512 CACCGGTGGG
*
5137522 ATTTCGCCGGATTCTGGAA
1 ATTTCGCCGGAATCTGGAA
*
5137541 ATTCTCGTCGGAATCTGGAAA
1 ATT-TCGCCGGAATCTGG-AA
5137562 ATTTCGCCGGAA
1 ATTTCGCCGGAA
5137574 GTTCGCCGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 3 0.11
20 20 0.71
21 5 0.18
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (19 bp):
ATTTCGCCGGAATCTGGAA
Found at i:5137580 original size:11 final size:11
Alignment explanation
Indices: 5137564--5137603 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
5137554 TCTGGAAAAT
5137564 TTCGCCGGAAG
1 TTCGCCGGAAG
5137575 TTCGCCGGAAG
1 TTCGCCGGAAG
*
5137586 TT-GCCGAAAG
1 TTCGCCGGAAG
*
5137596 ATCGCCGG
1 TTCGCCGG
5137604 TTTCTGGGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 8 0.32
11 17 0.68
ACGTcount: A:0.20, C:0.28, G:0.35, T:0.17
Consensus pattern (11 bp):
TTCGCCGGAAG
Found at i:5137646 original size:19 final size:20
Alignment explanation
Indices: 5137607--5137647 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
5137597 TCGCCGGTTT
5137607 CTGGGATTCTTCGCCGAAAA
1 CTGGGATTCTTCGCCGAAAA
* *
5137627 CTGGGATTGTT-GCCGGAAA
1 CTGGGATTCTTCGCCGAAAA
5137646 CT
1 CT
5137648 TCAAGTTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (20 bp):
CTGGGATTCTTCGCCGAAAA
Found at i:5137764 original size:25 final size:25
Alignment explanation
Indices: 5137717--5137770 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
5137707 AATCTGGAAA
*
5137717 TTTCCCAGAAATTTCCAGAAAATTT
1 TTTCCCAAAAATTTCCAGAAAATTT
*
5137742 TTTCGCCAAAAATTTCTAG-AAATTT
1 TTTC-CCAAAAATTTCCAGAAAATTT
5137767 TTTC
1 TTTC
5137771 TCACTCCCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 14 0.54
26 12 0.46
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.41
Consensus pattern (25 bp):
TTTCCCAAAAATTTCCAGAAAATTT
Found at i:5138131 original size:3 final size:3
Alignment explanation
Indices: 5138123--5138301 Score: 76
Period size: 3 Copynumber: 58.3 Consensus size: 3
5138113 GATAATTAAA
* **
5138123 AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AA- GAT AA- ACCC AAGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AA-T
*
5138167 ATAT ATT ACA- AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT
1 A-AT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
* *
5138213 ATAT AACT ATAT ACAT -AT AA- ATCT AAT -CT AA- AA- AAT AAAT AAAT
1 A-AT AA-T A-AT A-AT AAT AAT A-AT AAT AAT AAT AAT AAT -AAT -AAT
5138257 AAAT ATAT ACAT AAT AAT AAT AAT AAT AAT AA- AAT ACAT AA- AAT A
1 -AAT A-AT A-AT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT A
5138302 CAAAAGAAGA
Statistics
Matches: 141, Mismatches: 13, Indels: 44
0.71 0.07 0.22
Matches are distributed among these distances:
2 19 0.13
3 83 0.59
4 37 0.26
5 2 0.01
ACGTcount: A:0.64, C:0.06, G:0.01, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:5138491 original size:1 final size:1
Alignment explanation
Indices: 5138481--5138577 Score: 86
Period size: 1 Copynumber: 97.0 Consensus size: 1
5138471 CAACTCAACA
* ** *** * * * *
5138481 TTTTTATTTTTTGATTTTTTTTTTTAAATTTTTGTTTTTTTGTTTTTTGTTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
5138546 TGTTTTTTTTTTTGTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5138578 GTCGAAGCTC
Statistics
Matches: 77, Mismatches: 19, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 77 1.00
ACGTcount: A:0.05, C:0.00, G:0.07, T:0.88
Consensus pattern (1 bp):
T
Found at i:5138505 original size:15 final size:14
Alignment explanation
Indices: 5138481--5138579 Score: 103
Period size: 14 Copynumber: 7.0 Consensus size: 14
5138471 CAACTCAACA
*
5138481 TTTTTATTTTTTGAT
1 TTTTTTTTTTTTG-T
***
5138496 TTTTTTTTTTAAAT
1 TTTTTTTTTTTTGT
*
5138510 TTTTGTTTTTTTGT
1 TTTTTTTTTTTTGT
5138524 TTTTTGTTTTTTTGT
1 TTTTT-TTTTTTTGT
5138539 TTTTTTTTGTTTT-T
1 TTTTTTTT-TTTTGT
*
5138553 TTTTTTGTTTTT-T
1 TTTTTTTTTTTTGT
5138566 TTTTTTTTTTTTGT
1 TTTTTTTTTTTTGT
5138580 CGAAGCTCCT
Statistics
Matches: 70, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
13 16 0.23
14 27 0.39
15 27 0.39
ACGTcount: A:0.05, C:0.00, G:0.08, T:0.87
Consensus pattern (14 bp):
TTTTTTTTTTTTGT
Found at i:5138712 original size:42 final size:42
Alignment explanation
Indices: 5138584--5139119 Score: 717
Period size: 42 Copynumber: 13.0 Consensus size: 42
5138574 TTTTGTCGAA
* * * *
5138584 GCTCCTCTAAACAGAGACTCAACGACTTTTG-AAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
5138625 GCTCCTCTAAACAGAGGCA--ACGGACTTT-GAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCAC-GACTTTGGAAAAGTAAATT
*
5138665 GCTCCTCTCAACAGAGGCACCACGACTTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
* * *
5138707 GCTCCTCTCAACAGAGGTACCACGACTTTGAAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
5138749 GCTCCTCTAAACAGAGGCA--ACGGACTTTGG-AAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCAC-GACTTTGGAAAAGTAAATT
*
5138789 GCTCCTCTCAACAGAGGCACCACGACTTTGG-AAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
* *
5138830 GCTCCTCTCAACAGAGGCA--ACGGAACTTT-GAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCAC-G-ACTTTGGAAAAGTAAATT
*
5138871 GCTCCTCTAAACAGAGGCA--ACGAACTTTGAAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACG-ACTTTGGAAAAGTAAATT
* *
5138912 GCTCCTCTCAACAGAGGCACCACGACTTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
* *
5138954 GCTCCTCTAAACAGAGGCAACACGACTTTGGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
* *
5138996 GCTCCTCTAAACAGAGGCAACACGACTTTGGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
* *
5139038 GCTCCTCTAAACAGAGGTACCACGACTTT-GAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
5139079 GCTCCTCTAAACAGAGGCA--ACGGAACTTTGGAAAAGTAAAT
1 GCTCCTCTAAACAGAGGCACCAC-G-ACTTTGGAAAAGTAAAT
5139120 ACTCCTAGTC
Statistics
Matches: 454, Mismatches: 24, Indels: 33
0.89 0.05 0.06
Matches are distributed among these distances:
39 7 0.02
40 74 0.16
41 164 0.36
42 206 0.45
43 3 0.01
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.23
Consensus pattern (42 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
Found at i:5138720 original size:82 final size:79
Alignment explanation
Indices: 5138584--5139119 Score: 682
Period size: 82 Copynumber: 6.5 Consensus size: 79
5138574 TTTTGTCGAA
* *
5138584 GCTCCTCTAAACAGAGACTCAACGACTTTTG-AAAGTAAATTGCTCCTCTAAACAGAGGCAACGG
1 GCTCCTCTAAACAGAG--GCAACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCAAC-G
5138648 ACTTTGAAAAGTAAATT
63 ACTTTGAAAAGTAAATT
* * *
5138665 GCTCCTCTCAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTCAACAGAGGTACCAC
1 GCTCCTCTAAACAGAGGCA--ACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGG--CAAC
5138730 GACTTTGAAAAAGTAAATT
62 GACTTTG-AAAAGTAAATT
*
5138749 GCTCCTCTAAACAGAGGCAACGGACTTTGG-AAAGTAAATTGCTCCTCTCAACAGAGGCACCACG
1 GCTCCTCTAAACAGAGGCAAC-GACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCA--ACG
*
5138813 ACTTTGGAAAGTAAATT
63 ACTTTGAAAAGTAAATT
* *
5138830 GCTCCTCTCAACAGAGGCAACGGAACTTT-GAAAAATAAATTGCTCCTCTAAACAGAGGCAACGA
1 GCTCCTCTAAACAGAGGCAAC-G-ACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACG-
5138894 ACTTTGAAAAAGTAAATT
63 ACTTTG-AAAAGTAAATT
* *
5138912 GCTCCTCTCAACAGAGGCACCACGACTTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACAC
1 GCTCCTCTAAACAGAGGCA--ACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGC-A-AC
*
5138977 GACTTTGGAAAAATAAATT
62 GACTTT-GAAAAGTAAATT
* *
5138996 GCTCCTCTAAACAGAGGCAACACGACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGTACCAC
1 GCTCCTCTAAACAGAGGC-A-ACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGG--CAAC
*
5139061 GACTTTGAAAAATAAATT
62 GACTTTGAAAAGTAAATT
5139079 GCTCCTCTAAACAGAGGCAACGGAACTTTGGAAAAGTAAAT
1 GCTCCTCTAAACAGAGGCAAC-G-ACTTTGGAAAAGTAAAT
5139120 ACTCCTAGTC
Statistics
Matches: 412, Mismatches: 19, Indels: 46
0.86 0.04 0.10
Matches are distributed among these distances:
79 2 0.00
80 4 0.01
81 65 0.16
82 132 0.32
83 91 0.22
84 112 0.27
85 5 0.01
86 1 0.00
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.23
Consensus pattern (79 bp):
GCTCCTCTAAACAGAGGCAACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGACT
TTGAAAAGTAAATT
Found at i:5140156 original size:17 final size:18
Alignment explanation
Indices: 5140142--5140227 Score: 81
Period size: 17 Copynumber: 4.8 Consensus size: 18
5140132 TCACTTTTTC
*
5140142 TTTTTTCCATTTTTTCCA
1 TTTTTTTCATTTTTTCCA
5140160 TTTTTTTTTCA-TTTTT-CA
1 --TTTTTTTCATTTTTTCCA
*
5140178 TCATTTTTCATTTTTTCCA
1 T-TTTTTTCATTTTTTCCA
**
5140197 -TTTTTTCATTTTTTTTA
1 TTTTTTTCATTTTTTCCA
5140214 TTTTTTT-ATTTTTT
1 TTTTTTTCATTTTTT
5140228 TTGTATTTTT
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
16 1 0.02
17 28 0.49
18 13 0.23
19 7 0.12
20 8 0.14
ACGTcount: A:0.12, C:0.13, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTTTTCATTTTTTCCA
Found at i:5140167 original size:28 final size:27
Alignment explanation
Indices: 5140136--5140220 Score: 77
Period size: 28 Copynumber: 3.1 Consensus size: 27
5140126 TTTCATTCAC
*
5140136 TTTTTCTTTTTTCCAT-TTTTTCCATTTT
1 TTTTTCATTTTT-CATATTTTT-CATTTT
5140164 TTTTTCATTTTTCATCATTTTTCA--TT
1 TTTTTCATTTTTCAT-ATTTTTCATTTT
* * *
5140190 TTTTCCATTTTTTCATTTTTTTTATTTT
1 TTTTTCA-TTTTTCATATTTTTCATTTT
5140218 TTT
1 TTT
5140221 ATTTTTTTTG
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
26 14 0.29
27 11 0.23
28 18 0.38
29 5 0.10
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (27 bp):
TTTTTCATTTTTCATATTTTTCATTTT
Found at i:5140185 original size:11 final size:10
Alignment explanation
Indices: 5140142--5140227 Score: 52
Period size: 9 Copynumber: 9.6 Consensus size: 10
5140132 TCACTTTTTC
5140142 TTTTTTC-CA
1 TTTTTTCTCA
5140151 TTTTTTC-CA
1 TTTTTTCTCA
*
5140160 TTTTTTTTTCA
1 -TTTTTTCTCA
5140171 -TTTTTCATCA
1 TTTTTTC-TCA
5140181 --TTTT-TCA
1 TTTTTTCTCA
5140188 TTTTTTC-CA
1 TTTTTTCTCA
5140197 -TTTTT-TCA
1 TTTTTTCTCA
*
5140205 TTTTTT-TTA
1 TTTTTTCTCA
5140214 TTTTTT-T-A
1 TTTTTTCTCA
5140222 TTTTTT
1 TTTTTT
5140228 TTGTATTTTT
Statistics
Matches: 66, Mismatches: 3, Indels: 17
0.77 0.03 0.20
Matches are distributed among these distances:
7 3 0.05
8 14 0.21
9 38 0.58
10 9 0.14
11 2 0.03
ACGTcount: A:0.12, C:0.13, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTTTCTCA
Found at i:5140200 original size:46 final size:46
Alignment explanation
Indices: 5140124--5140212 Score: 146
Period size: 46 Copynumber: 1.9 Consensus size: 46
5140114 TGAGTCCTCC
5140124 TTTTTCATTCACTTTTTCTTTTTTCCATTTTTTCCATTTTTTTTTCA
1 TTTTTCATTCACTTTTTCTTTTTTCCATTTTTT-CATTTTTTTTTCA
5140171 TTTTTCA-TCA-TTTTTCATTTTTTCCATTTTTTCATTTTTTTT
1 TTTTTCATTCACTTTTTC-TTTTTTCCATTTTTTCATTTTTTTT
5140213 ATTTTTTTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
45 16 0.39
46 18 0.44
47 7 0.17
ACGTcount: A:0.11, C:0.17, G:0.00, T:0.72
Consensus pattern (46 bp):
TTTTTCATTCACTTTTTCTTTTTTCCATTTTTTCATTTTTTTTTCA
Found at i:5140228 original size:8 final size:8
Alignment explanation
Indices: 5140131--5140227 Score: 72
Period size: 8 Copynumber: 11.2 Consensus size: 8
5140121 TCCTTTTTCA
*
5140131 TTCACTTT
1 TTCATTTT
5140139 TTC-TTTT
1 TTCATTTT
5140146 TTCCATTTT
1 TT-CATTTT
5140155 TTCCATTTTTTT
1 TT-CA---TTTT
5140167 TTCA-TTT
1 TTCATTTT
5140174 TTCATCATTT
1 TTCAT--TTT
5140184 TTCATTTT
1 TTCATTTT
5140192 TTCCATTTT
1 TT-CATTTT
5140201 TTCATTTTT
1 TTCA-TTTT
*
5140210 TTTATTTT
1 TTCATTTT
*
5140218 TTTATTTT
1 TTCATTTT
5140226 TT
1 TT
5140228 TTGTATTTTT
Statistics
Matches: 77, Mismatches: 2, Indels: 20
0.78 0.02 0.20
Matches are distributed among these distances:
7 12 0.16
8 25 0.32
9 24 0.31
10 8 0.10
11 2 0.03
12 6 0.08
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.74
Consensus pattern (8 bp):
TTCATTTT
Found at i:5140228 original size:9 final size:9
Alignment explanation
Indices: 5140197--5140239 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
5140187 ATTTTTTCCA
*
5140197 TTTTTTCAT
1 TTTTTTTAT
5140206 TTTTTTTA-
1 TTTTTTTAT
5140214 TTTTTTTAT
1 TTTTTTTAT
*
5140223 TTTTTTTGT
1 TTTTTTTAT
5140232 ATTTTTTT
1 -TTTTTTT
5140240 CAAGCATAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
8 8 0.27
9 15 0.50
10 7 0.23
ACGTcount: A:0.09, C:0.02, G:0.02, T:0.86
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:5140236 original size:17 final size:18
Alignment explanation
Indices: 5140180--5140237 Score: 66
Period size: 17 Copynumber: 3.3 Consensus size: 18
5140170 ATTTTTCATC
**
5140180 ATTTTTCATTTTTTCCAT
1 ATTTTTCATTTTTTTTAT
5140198 -TTTTTCATTTTTTTTAT
1 ATTTTTCATTTTTTTTAT
* *
5140215 -TTTTTTATTTTTTTTGT
1 ATTTTTCATTTTTTTTAT
5140232 ATTTTT
1 ATTTTT
5140238 TTCAAGCATA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
17 30 0.86
18 5 0.14
ACGTcount: A:0.12, C:0.07, G:0.02, T:0.79
Consensus pattern (18 bp):
ATTTTTCATTTTTTTTAT
Found at i:5147457 original size:15 final size:15
Alignment explanation
Indices: 5147437--5147483 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
5147427 TTGTAAGTGT
5147437 AATGAATGAGAATGC
1 AATGAATGAGAATGC
*
5147452 AATGAATGAGAATGT
1 AATGAATGAGAATGC
5147467 AATGAATGAGAAATGC
1 AATGAATGAG-AATGC
5147483 A
1 A
5147484 TGTATGCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
15 24 0.83
16 5 0.17
ACGTcount: A:0.49, C:0.04, G:0.26, T:0.21
Consensus pattern (15 bp):
AATGAATGAGAATGC
Found at i:5150824 original size:58 final size:57
Alignment explanation
Indices: 5150635--5151265 Score: 894
Period size: 57 Copynumber: 11.1 Consensus size: 57
5150625 TTTTTTTTTG
*
5150635 TTAAGGGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTCTTGAAATTTTATT
1 TTAA-GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAA-TTTATT
** * *
5150693 TCGAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATTTTTTTTTTTGAAAATTTATT
1 TTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAA-TATTTTTTTTG-AAATTTATT
5150752 TCTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAATTTATT
1 T-TAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAATTTATT
* *
5150810 TCCAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATA--TTTTTTGAAATTTGATT
1 T-TAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAATTT-ATT
**
5150867 TTCAAGGAAAATTGATACTTTCAACTTTTCCCTC-AAAA-ACCTTTTTTGAAATTTATTT
1 TT-AAGGAAAATTGATACTTTCAACTTTTCCC-CAAAAATATTTTTTTTGAAATTTA-TT
*
5150925 TTAAGGAAAATTGATACTTTCAACTTTT-CCCAAAAATATTTTTTTGGAAATTTA-T
1 TTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAATTTATT
*
5150980 TTAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTT-TT
1 TTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAATTTATT
5151036 TTAAGGAAAATTGATACTTTCAACTTTT-CCC-AAAA-A-TTTTTTTGAAATTTATT
1 TTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAATTTATT
*
5151089 TTAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTTTATT
1 TTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTT-GAAA-TTTATT
*
5151148 TTCAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTGGAAATTTATT
1 TT-AAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAATTTATT
* *
5151205 TCTAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTAAAATTT-TT
1 T-TAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTTTGAAATTTATT
5151263 TTA
1 TTA
5151266 TTTTTATTTA
Statistics
Matches: 523, Mismatches: 25, Indels: 51
0.87 0.04 0.09
Matches are distributed among these distances:
52 14 0.03
53 31 0.06
54 6 0.01
55 36 0.07
56 73 0.14
57 162 0.31
58 79 0.15
59 50 0.10
60 72 0.14
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (57 bp):
TTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAATTTATT
Found at i:5151685 original size:20 final size:20
Alignment explanation
Indices: 5151660--5151697 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5151650 ACACCGGGTT
*
5151660 GCCGGATTCTGGAAATTTTC
1 GCCGGAATCTGGAAATTTTC
5151680 GCCGGAATCTGGAAATTT
1 GCCGGAATCTGGAAATTT
5151698 CACCGGAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (20 bp):
GCCGGAATCTGGAAATTTTC
Found at i:5151703 original size:19 final size:20
Alignment explanation
Indices: 5151661--5151705 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
5151651 CACCGGGTTG
* *
5151661 CCGGATTCTGGAAATTTTCG
1 CCGGAATCTGGAAATTTTCA
5151681 CCGGAATCTGGAAA-TTTCA
1 CCGGAATCTGGAAATTTTCA
5151700 CCGGAA
1 CCGGAA
5151706 GTTGGCCGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (20 bp):
CCGGAATCTGGAAATTTTCA
Found at i:5152360 original size:3 final size:3
Alignment explanation
Indices: 5152343--5152394 Score: 56
Period size: 3 Copynumber: 17.3 Consensus size: 3
5152333 ATCTAATCTG
5152343 AAT AA- AAT AAAT AAT AAT AA- AGAT -AT ACAT AAT AAT AAT AAT AAT
1 AAT AAT AAT -AAT AAT AAT AAT A-AT AAT A-AT AAT AAT AAT AAT AAT
5152388 AAT AAT A
1 AAT AAT A
5152395 GAATACATAA
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
2 5 0.12
3 32 0.74
4 6 0.14
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:5152377 original size:30 final size:30
Alignment explanation
Indices: 5152343--5152408 Score: 93
Period size: 30 Copynumber: 2.2 Consensus size: 30
5152333 ATCTAATCTG
5152343 AATAA-AATAAATAATAATAA-AGATATACAT
1 AATAATAAT-AATAATAATAATAGA-ATACAT
5152373 AATAATAATAATAATAATAATAGAATACAT
1 AATAATAATAATAATAATAATAGAATACAT
5152403 AA-AATA
1 AATAATA
5152409 CAAAAGAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
29 4 0.12
30 24 0.71
31 6 0.18
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.27
Consensus pattern (30 bp):
AATAATAATAATAATAATAATAGAATACAT
Found at i:5153575 original size:21 final size:20
Alignment explanation
Indices: 5153546--5153599 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
5153536 AAACCTAATC
*
5153546 TAAATAAATAAAAAAATAAAA
1 TAAA-AAATAAAAAAAGAAAA
*
5153567 TAAACAAATAAACAAAGAAAA
1 TAAA-AAATAAAAAAAGAAAA
5153588 -AAAAAA-AAAAAA
1 TAAAAAATAAAAAA
5153600 CCTGAGCGGC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 5 0.17
19 3 0.10
20 3 0.10
21 18 0.62
ACGTcount: A:0.83, C:0.04, G:0.02, T:0.11
Consensus pattern (20 bp):
TAAAAAATAAAAAAAGAAAA
Done.