Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 38 of 226
Found at i:16295136 original size:14 final size:13
Alignment explanation
Indices: 16295109--16295134 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16295099 TTTAATACAA
16295109 AAAATTTACTTTT
1 AAAATTTACTTTT
16295122 AAAATTTACTTTT
1 AAAATTTACTTTT
16295135 TATTTAAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
AAAATTTACTTTT
Found at i:16295211 original size:22 final size:22
Alignment explanation
Indices: 16295183--16295224 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
16295173 GGATAAAATA
16295183 TAGAATATATATATT-TAGAATT
1 TAGAATATATAT-TTATAGAATT
16295205 TAGAATATATATTTATAGAA
1 TAGAATATATATTTATAGAA
16295225 AAAGTCTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.43
Consensus pattern (22 bp):
TAGAATATATATTTATAGAATT
Found at i:16299677 original size:16 final size:16
Alignment explanation
Indices: 16299636--16299673 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
16299626 TTATTATAAT
16299636 CTATAATATAATAATAG
1 CTAT-ATATAATAATAG
*
16299653 CTATATATAATAGTAG
1 CTATATATAATAATAG
16299669 -TATAT
1 CTATAT
16299674 TATATATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 5 0.25
16 11 0.55
17 4 0.20
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.39
Consensus pattern (16 bp):
CTATATATAATAATAG
Found at i:16299930 original size:22 final size:21
Alignment explanation
Indices: 16299879--16299940 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 21
16299869 TCTATCTTTT
*
16299879 ATTATAATCTATAATA-TAATA
1 ATTAT-ATATATAATATTAATA
*
16299900 ATATTTATATATAATATTAATA
1 AT-TATATATATAATATTAATA
16299922 CATTATATAT-TACATATTA
1 -ATTATATATATA-ATATTA
16299941 TTATATATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
21 13 0.38
22 19 0.56
23 2 0.06
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTATATATATAATATTAATA
Found at i:16300135 original size:254 final size:250
Alignment explanation
Indices: 16299600--16300418 Score: 868
Period size: 254 Copynumber: 3.2 Consensus size: 250
16299590 TACTATATTA
* *
16299600 TATAATATCATGTAATACTATATATTTTATTATAATCTATAATATAATAATAGCTATATATAATA
1 TATAATATCATGTAATACTATATCTTTTATTATAATCTATAATATAATAATAGTTATATATAATA
* * * **
16299665 GTAGTATATTATATA-TA-A-ATTATTATACATTATTGTTTATTATTACACAAGGTTGAAATATG
66 GTAGTACATTATATATTACATATTATTATATATTATTGTTTATTATTATA-GTGGTTGAAATATG
* * * * *
16299727 CTCCAAGTCCCTATACTTTTTGTACATTTAAAAGTTAACCCTCCTACTATATTATATATATAATG
130 CTCTAAGTCTCTAT-CTTTTT-TGCATTTGAAAGTTAGCCCTCCTAC--TA-TAT-TATATAATG
* * * *
16299792 CTATATCATAT-AGAATATAATATATTA-ATAATT-T-TATACATGCATCAATGATTGAACAT
189 CTATATCATATCATAAT-TAATATTTTATATAATTATATATATATGCATCAATGATTAAACAT
* * ** * *
16299851 TAAAATATTATGTAATTTTCTATCTTTTATTATAATCTATAATATAATAATATTTATATATAATA
1 TATAATATCATGTAATACTATATCTTTTATTATAATCTATAATATAATAATAGTTATATATAATA
* * *
16299916 TTAATACATTATATATTACATATTATTATATATTATTGTTTATTATTATAGTGGTTGAAATTTGC
66 GTAGTACATTATATATTACATATTATTATATATTATTGTTTATTATTATAGTGGTTGAAATATGC
* * *
16299981 TCTAAGTTTCTATGCTTTTTATGCATTTGAAAGTTAGCCTTCCTACTATATTATATAATGCTATC
131 TCTAAGTCTCTAT-CTTTTT-TGCATTTGAAAGTTAGCCCTCCTACTATATTATATAATGCTATA
* *
16300046 TCATATCATATATTAATATTTTATATACATGTATATATATATGCATAAATGATT-AATAT
194 TCATATCATA-ATTAATATTTTATATA-AT-TATATATATATGCATCAATGATTAAACAT
* *
16300105 TATAATATCATGTAATACTATATTTTTTATTATAATCTATATTATAATAATAGTTATATATAATA
1 TATAATATCATGTAATACTATATCTTTTATTATAATCTATAATATAATAATAGTTATATATAATA
* * * * * * *
16300170 GTAGTACACTATATATTACTTATTATTGTATATTATTGTTTATTGTTATAGTAGTTAAAAAATGC
66 GTAGTACATTATATATTACATATTATTATATATTATTGTTTATTATTATAGTGGTTGAAATATGC
* * * * ** **
16300235 TTTAAGTCTCTATATTTTTCGTACTTCTGAAAGTTAGCCCTATTACTATATTATATAATATTATA
131 TCTAAGTCTCTATCTTTTTTGCA-TT-TGAAAGTTAGCCCTCCTACTATATTATATAATGCTATA
* * * * * *
16300300 TCATATCATAA--AATATATTAATGGTTTATATATATATATATGTATCGATAATTAAACAT
194 TCATATCATAATTAATAT-TTTAT--ATAAT-TATATATATATGCATCAATGATTAAACAT
* ** *
16300359 TACAATATCATGTAATTTTATATCTTTTATTATAATCTAT-ATGAAAATAATAGTTATATA
1 TATAATATCATGTAATACTATATCTTTTATTATAATCTATAAT-ATAATAATAGTTATATA
16300419 CGTGTTAATA
Statistics
Matches: 476, Mismatches: 75, Indels: 31
0.82 0.13 0.05
Matches are distributed among these distances:
249 19 0.04
250 14 0.03
251 81 0.17
252 10 0.02
253 81 0.17
254 254 0.53
255 17 0.04
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.46
Consensus pattern (250 bp):
TATAATATCATGTAATACTATATCTTTTATTATAATCTATAATATAATAATAGTTATATATAATA
GTAGTACATTATATATTACATATTATTATATATTATTGTTTATTATTATAGTGGTTGAAATATGC
TCTAAGTCTCTATCTTTTTTGCATTTGAAAGTTAGCCCTCCTACTATATTATATAATGCTATATC
ATATCATAATTAATATTTTATATAATTATATATATATGCATCAATGATTAAACAT
Found at i:16300168 original size:16 final size:17
Alignment explanation
Indices: 16300142--16300174 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
16300132 TATTATAATC
16300142 TATATTATAATAATAGT
1 TATATTATAATAATAGT
*
16300159 TATA-TATAATAGTAGT
1 TATATTATAATAATAGT
16300175 ACACTATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (17 bp):
TATATTATAATAATAGT
Found at i:16303628 original size:29 final size:27
Alignment explanation
Indices: 16303564--16303628 Score: 67
Period size: 29 Copynumber: 2.3 Consensus size: 27
16303554 AAATTTTGCA
* *
16303564 AAATTTTAATTTTTTTAAATTTTCATT
1 AAATTTTAATTTTTTAAAATTTTAATT
*
16303591 ATACCTTTTAATTTTTTAAAATATTTTAATT
1 A-A-ATTTTAATTTTTT-AAA-ATTTTAATT
16303622 AAATTTT
1 AAATTTT
16303629 CTTAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
27 1 0.03
28 1 0.03
29 16 0.53
30 3 0.10
31 9 0.30
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (27 bp):
AAATTTTAATTTTTTAAAATTTTAATT
Found at i:16307378 original size:251 final size:251
Alignment explanation
Indices: 16306935--16307439 Score: 965
Period size: 251 Copynumber: 2.0 Consensus size: 251
16306925 AATTCATGGC
*
16306935 TTTGTAACCCCCCTCTCTGTCACCCCCTTCCCAGAAATGTATGTAAAATGTGTCAAAGATATTTT
1 TTTGTAACCCCCCTCTCTGTCACCCCCTTCCCAGAAATATATGTAAAATGTGTCAAAGATATTTT
* *
16307000 GAGTATATAAGAGTTAATAAATATTGTAATGGCTCGAATTATCAATGTAGGTTATTAAATATTAT
66 GAGTATATAAGAGTTAATAAATATTGTAATGGCACAAATTATCAATGTAGGTTATTAAATATTAT
16307065 ACTAGTGCATATTCAAGGCCAAATAAGTTTTGGTACTTGCTTTTTTCCTATCCTATGTCATTTGG
131 ACTAGTGCATATTCAAGGCCAAATAAGTTTTGGTACTTGCTTTTTTCCTATCCTATGTCATTTGG
*
16307130 CTTATTTTTTCCGTTTTAATCTTTTCAAGTGAAGACCATTTCAATGGTTATATTGT
196 CTTATTTTTTCCGTTTCAATCTTTTCAAGTGAAGACCATTTCAATGGTTATATTGT
16307186 TTTGTAACCCCCCTCTCTGTCACCCCCTTCCCAGAAATATATGTAAAATGTGTCAAAGATATTTT
1 TTTGTAACCCCCCTCTCTGTCACCCCCTTCCCAGAAATATATGTAAAATGTGTCAAAGATATTTT
*
16307251 GAGTATATAAGAGTTGATAAATATTGTAATGGCACAAATTATCAATGTAGGTTATTAAATATTAT
66 GAGTATATAAGAGTTAATAAATATTGTAATGGCACAAATTATCAATGTAGGTTATTAAATATTAT
16307316 ACTAGTGCATATTCAAGGCCAAATAAGTTTTGGTACTTGCTTTTTTCCTATCCTATGTCATTTGG
131 ACTAGTGCATATTCAAGGCCAAATAAGTTTTGGTACTTGCTTTTTTCCTATCCTATGTCATTTGG
16307381 CTTATTTTTTCCGTTTCAATCTTTTCAAGTGAAGACCATTTCAATGGTTATATTGT
196 CTTATTTTTTCCGTTTCAATCTTTTCAAGTGAAGACCATTTCAATGGTTATATTGT
16307437 TTT
1 TTT
16307440 TTGTTACTGT
Statistics
Matches: 249, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
251 249 1.00
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (251 bp):
TTTGTAACCCCCCTCTCTGTCACCCCCTTCCCAGAAATATATGTAAAATGTGTCAAAGATATTTT
GAGTATATAAGAGTTAATAAATATTGTAATGGCACAAATTATCAATGTAGGTTATTAAATATTAT
ACTAGTGCATATTCAAGGCCAAATAAGTTTTGGTACTTGCTTTTTTCCTATCCTATGTCATTTGG
CTTATTTTTTCCGTTTCAATCTTTTCAAGTGAAGACCATTTCAATGGTTATATTGT
Found at i:16312201 original size:20 final size:20
Alignment explanation
Indices: 16312176--16312214 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
16312166 TGTAGGAACT
* *
16312176 TGCATTTTGGCTTTTTTTAG
1 TGCATTTTAGCTTGTTTTAG
16312196 TGCATTTTAGCTTGTTTTA
1 TGCATTTTAGCTTGTTTTA
16312215 TTTGTTTATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.10, G:0.18, T:0.59
Consensus pattern (20 bp):
TGCATTTTAGCTTGTTTTAG
Found at i:16314287 original size:20 final size:20
Alignment explanation
Indices: 16314237--16314291 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
16314227 TTAAAATTTT
*
16314237 ATAAAAATTTAT-AAAATTC
1 ATAAAAAATTATAAAAATTC
*
16314256 ATAAATAA-TATAATAAATTC
1 ATAAAAAATTATAA-AAATTC
16314276 -TAAAAAATTATAAAAA
1 ATAAAAAATTATAAAAA
16314292 AAGTCAACTC
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 3 0.10
19 16 0.53
20 11 0.37
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAAAAAATTATAAAAATTC
Found at i:16314292 original size:10 final size:10
Alignment explanation
Indices: 16314229--16314292 Score: 51
Period size: 10 Copynumber: 6.4 Consensus size: 10
16314219 AAACATATTT
*
16314229 AAAATTTTATA
1 AAAATTATA-A
*
16314240 AAAATT-TAT
1 AAAATTATAA
16314249 AAAATTCATAA
1 AAAATT-ATAA
*
16314260 ATAA-TATAA
1 AAAATTATAA
* *
16314269 TAAATTCTAA
1 AAAATTATAA
16314279 AAAATTATAA
1 AAAATTATAA
16314289 AAAA
1 AAAA
16314293 AGTCAACTCC
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
9 12 0.29
10 19 0.45
11 11 0.26
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (10 bp):
AAAATTATAA
Found at i:16321161 original size:18 final size:18
Alignment explanation
Indices: 16321138--16321176 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
16321128 TTTTATTATA
16321138 TAAATTAATAAATTTA-AT
1 TAAATT-ATAAATTTAGAT
*
16321156 TAAATTATTAATTTAGAT
1 TAAATTATAAATTTAGAT
16321174 TAA
1 TAA
16321177 GACCGGGTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (18 bp):
TAAATTATAAATTTAGAT
Found at i:16323278 original size:43 final size:42
Alignment explanation
Indices: 16323230--16323411 Score: 143
Period size: 48 Copynumber: 4.1 Consensus size: 42
16323220 TATCGTACAA
* *
16323230 ATGCCATGTCCCATACATGGTCTTACATGGAAATCTCATATCG
1 ATGCCATGTCCCATATATGGTCTTACA-CGAAATCTCATATCG
*
16323273 ATGCCAATAG-CCCAGT-TATGGTCTTACACGAAGTCTCATATCG
1 ATGCC-AT-GTCCCA-TATATGGTCTTACACGAAATCTCATATCG
* * *
16323316 ATGCCATATCCCAGATATGGTCTTATACGAAATCTCAAATCAATGCTG
1 ATGCCATGTCCCATATATGGTCTTACACGAAATCTC--AT--AT-C-G
* * * ** * *
16323364 ATGCCATATCCCAGATATGGTCTTATACGGGATATCAAATCG
1 ATGCCATGTCCCATATATGGTCTTACACGAAATCTCATATCG
16323406 ATGCCA
1 ATGCCA
16323412 ATGCCATATA
Statistics
Matches: 117, Mismatches: 11, Indels: 23
0.77 0.07 0.15
Matches are distributed among these distances:
42 32 0.27
43 24 0.21
44 21 0.18
45 2 0.02
46 3 0.03
47 1 0.01
48 34 0.29
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (42 bp):
ATGCCATGTCCCATATATGGTCTTACACGAAATCTCATATCG
Found at i:16323346 original size:42 final size:42
Alignment explanation
Indices: 16323230--16323411 Score: 175
Period size: 42 Copynumber: 4.1 Consensus size: 42
16323220 TATCGTACAA
* * * *
16323230 ATGCCATGTCCCATACATGGTCTTACATGGAAATCTCATATCG
1 ATGCCATATCCCAGATATGGTCTTACA-CGAAATCTCATATCG
* * *
16323273 ATGCCAATAGCCCAGTTATGGTCTTACACGAAGTCTCATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACACGAAATCTCATATCG
*
16323316 ATGCCATATCCCAGATATGGTCTTATACGAAATCTCAAATCAATGCTG
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTC--AT--AT-C-G
* ** * *
16323364 ATGCCATATCCCAGATATGGTCTTATACGGGATATCAAATCG
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
16323406 ATGCCA
1 ATGCCA
16323412 ATGCCATATA
Statistics
Matches: 117, Mismatches: 15, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
42 34 0.29
43 24 0.21
44 21 0.18
46 3 0.03
47 1 0.01
48 34 0.29
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
Found at i:16323386 original size:48 final size:48
Alignment explanation
Indices: 16323314--16323503 Score: 247
Period size: 48 Copynumber: 4.0 Consensus size: 48
16323304 AGTCTCATAT
16323314 CGATGCCATATCCCAGATATGGTCTTATACGAAATCTCAAATCAATGC
1 CGATGCCATATCCCAGATATGGTCTTATACGAAATCTCAAATCAATGC
* ** * *
16323362 TGATGCCATATCCCAGATATGGTCTTATACGGGATATCAAATCGATGC
1 CGATGCCATATCCCAGATATGGTCTTATACGAAATCTCAAATCAATGC
* * * ** *
16323410 CAATGCCATATACCAAATATGGTCTTATACGGGATCTCAAATCGATGC
1 CGATGCCATATCCCAGATATGGTCTTATACGAAATCTCAAATCAATGC
* *
16323458 CGATGCCATATCCCAGATATGATATTATAC-AAGATCTCAAATCAAT
1 CGATGCCATATCCCAGATATGGTCTTATACGAA-ATCTCAAATCAAT
16323504 TCGGCAATAT
Statistics
Matches: 123, Mismatches: 18, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
48 123 1.00
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.28
Consensus pattern (48 bp):
CGATGCCATATCCCAGATATGGTCTTATACGAAATCTCAAATCAATGC
Found at i:16323530 original size:30 final size:30
Alignment explanation
Indices: 16323495--16323587 Score: 107
Period size: 30 Copynumber: 3.1 Consensus size: 30
16323485 TACAAGATCT
16323495 CAAATCAATTCGGCAATATATATACATATA
1 CAAATCAATTCGGCAATATATATACATATA
* * *
16323525 CAAATCAATTCGACAATATATGTATCTACATA
1 CAAATCAATTCGGCAATATATATA-C-ATATA
* * *
16323557 TAAATCAATTTGGCAATATA-AAACATATA
1 CAAATCAATTCGGCAATATATATACATATA
16323586 CA
1 CA
16323588 TTTGAATTCA
Statistics
Matches: 51, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
29 5 0.10
30 23 0.45
31 2 0.04
32 21 0.41
ACGTcount: A:0.47, C:0.16, G:0.06, T:0.30
Consensus pattern (30 bp):
CAAATCAATTCGGCAATATATATACATATA
Found at i:16324823 original size:26 final size:26
Alignment explanation
Indices: 16324774--16324863 Score: 87
Period size: 26 Copynumber: 3.5 Consensus size: 26
16324764 ACAACTCTTA
* *
16324774 TGAGCTTCCCG-TTATATGGTTCTTCG
1 TGAGCTTCCCGATTA-AAGGCTCTTCG
* *
16324800 TAAGCTTCCCGATTAAAGGCTCTTTG
1 TGAGCTTCCCGATTAAAGGCTCTTCG
* *
16324826 TGAGCTTCCTGATTAATA-GCTCTCCG
1 TGAGCTTCCCGATTAA-AGGCTCTTCG
16324852 -GAGCTTCCCGAT
1 TGAGCTTCCCGAT
16324864 ATGGCTCGCT
Statistics
Matches: 53, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
25 11 0.21
26 38 0.72
27 4 0.08
ACGTcount: A:0.18, C:0.26, G:0.21, T:0.36
Consensus pattern (26 bp):
TGAGCTTCCCGATTAAAGGCTCTTCG
Found at i:16327191 original size:26 final size:27
Alignment explanation
Indices: 16327136--16327209 Score: 80
Period size: 30 Copynumber: 2.7 Consensus size: 27
16327126 TTTATATATA
*
16327136 TATATTTTTATATATTTTATTAAAAAT
1 TATATTTTTATATAATTTATTAAAAAT
*
16327163 TATATTTTTA-ATAATTTATTAGAACTTAT
1 TATATTTTTATATAATTTATTA-AA--AAT
16327192 TATGATTTTT-TATAATTT
1 TAT-ATTTTTATATAATTT
16327210 TATAATTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
26 10 0.25
27 12 0.30
29 5 0.12
30 13 0.32
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.59
Consensus pattern (27 bp):
TATATTTTTATATAATTTATTAAAAAT
Found at i:16327236 original size:7 final size:8
Alignment explanation
Indices: 16327199--16327237 Score: 53
Period size: 8 Copynumber: 4.8 Consensus size: 8
16327189 TATTATGATT
16327199 TTTTATAA
1 TTTTATAA
16327207 TTTTATAA
1 TTTTATAA
16327215 TTATTGATAA
1 TT-TT-ATAA
16327225 TTTTAT-A
1 TTTTATAA
16327232 TTTTAT
1 TTTTAT
16327238 TTGAATTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
7 7 0.24
8 12 0.41
9 4 0.14
10 6 0.21
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (8 bp):
TTTTATAA
Found at i:16327388 original size:19 final size:21
Alignment explanation
Indices: 16327366--16327409 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
16327356 TAATTAGAAT
16327366 TTTTTAT-AATATTTT-TTAG
1 TTTTTATGAATATTTTATTAG
*
16327385 TTTTTATGAATTTTTTATTAG
1 TTTTTATGAATATTTTATTAG
16327406 TTTT
1 TTTT
16327410 GTAAATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.32
20 7 0.32
21 8 0.36
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (21 bp):
TTTTTATGAATATTTTATTAG
Found at i:16327388 original size:20 final size:22
Alignment explanation
Indices: 16327365--16327409 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 22
16327355 TTAATTAGAA
16327365 TTTTTTAT-AATATTTT-TTAG
1 TTTTTTATGAATATTTTATTAG
*
16327385 -TTTTTATGAATTTTTTATTAG
1 TTTTTTATGAATATTTTATTAG
16327406 TTTT
1 TTTT
16327410 GTAAATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 7 0.33
20 7 0.33
21 4 0.19
22 3 0.14
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.71
Consensus pattern (22 bp):
TTTTTTATGAATATTTTATTAG
Found at i:16327937 original size:15 final size:16
Alignment explanation
Indices: 16327909--16327939 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
16327899 ACCAATTTGG
16327909 TTAATTTCAGTTAATT
1 TTAATTTCAGTTAATT
16327925 TTAATTT-AGTTAATT
1 TTAATTTCAGTTAATT
16327940 CGGTTAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.58
Consensus pattern (16 bp):
TTAATTTCAGTTAATT
Found at i:16328162 original size:12 final size:13
Alignment explanation
Indices: 16328140--16328168 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
16328130 AATATTAATT
16328140 CAATGCGATTAAC
1 CAATGCGATTAAC
16328153 CAAT-CGATTAAC
1 CAATGCGATTAAC
16328165 CAAT
1 CAAT
16328169 TAAACACCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.41, C:0.24, G:0.10, T:0.24
Consensus pattern (13 bp):
CAATGCGATTAAC
Found at i:16337866 original size:2 final size:2
Alignment explanation
Indices: 16337859--16337889 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
16337849 TAATGCTAAT
16337859 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
16337890 TAATCTACCA
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:16342610 original size:22 final size:22
Alignment explanation
Indices: 16342577--16342637 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
16342567 GCCCGGCCCG
* *
16342577 TTTTTAATTAAAATTAAAATTAT
1 TTTTTAA-TAAAATTAAAACTAA
16342600 TTTTTAATAAAATTAAAACTAA
1 TTTTTAATAAAATTAAAACTAA
* *
16342622 TTGTTATTAAAATTAA
1 TTTTTAATAAAATTAA
16342638 TTGTTAGTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 27 0.79
23 7 0.21
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
TTTTTAATAAAATTAAAACTAA
Found at i:16342650 original size:16 final size:16
Alignment explanation
Indices: 16342613--16342652 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
16342603 TTAATAAAAT
* *
16342613 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
16342629 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
16342645 TAAAATTA
1 TAAAATTA
16342653 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:16342758 original size:9 final size:9
Alignment explanation
Indices: 16342725--16342752 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
16342715 TTTATCAAAT
16342725 TATTAATTG
1 TATTAATTG
16342734 TATTAATTG
1 TATTAATTG
16342743 TATTAATTG
1 TATTAATTG
16342752 T
1 T
16342753 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:16342762 original size:68 final size:68
Alignment explanation
Indices: 16342641--16342850 Score: 388
Period size: 68 Copynumber: 3.1 Consensus size: 68
16342631 AAATTAATTG
*
16342641 TTAGTAAAATTATCAAATTATTAATTG--TTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
16342704 TGA
66 TGA
16342707 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
16342772 TGA
66 TGA
*
16342775 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
16342840 TGA
66 TGA
16342843 TTAGTAAA
1 TTAGTAAA
16342851 ACAAACTTGA
Statistics
Matches: 140, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
66 26 0.19
68 114 0.81
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.46
Consensus pattern (68 bp):
TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
TGA
Found at i:16342805 original size:9 final size:9
Alignment explanation
Indices: 16342793--16342820 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
16342783 TTTATCAAAT
16342793 TATTAATTG
1 TATTAATTG
16342802 TATTAATTG
1 TATTAATTG
16342811 TATTAATTG
1 TATTAATTG
16342820 T
1 T
16342821 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:16343889 original size:18 final size:19
Alignment explanation
Indices: 16343850--16343901 Score: 79
Period size: 18 Copynumber: 2.7 Consensus size: 19
16343840 ATTATATGAA
*
16343850 TTAAGTAAGAAAAGTCCAGG
1 TTAAGTAA-ACAAGTCCAGG
16343870 TTAAGTAAACAAGT-CAGG
1 TTAAGTAAACAAGTCCAGG
16343888 TTAAGTAAACAAGT
1 TTAAGTAAACAAGT
16343902 TTCGTTAACT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 18 0.58
19 5 0.16
20 8 0.26
ACGTcount: A:0.46, C:0.10, G:0.21, T:0.23
Consensus pattern (19 bp):
TTAAGTAAACAAGTCCAGG
Found at i:16344656 original size:17 final size:18
Alignment explanation
Indices: 16344628--16344662 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
16344618 AATCTTTAAA
16344628 AAAATAATATATTCATAT
1 AAAATAATATATTCATAT
*
16344646 AAAAT-ATATATTTATAT
1 AAAATAATATATTCATAT
16344663 CAATCATTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
AAAATAATATATTCATAT
Found at i:16347576 original size:2 final size:2
Alignment explanation
Indices: 16347571--16347595 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16347561 TCTACATTGA
16347571 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
16347596 GTTTTTGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:16352875 original size:12 final size:12
Alignment explanation
Indices: 16352858--16352882 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16352848 ATTTTCTAAC
16352858 ATGAGATATATA
1 ATGAGATATATA
16352870 ATGAGATATATA
1 ATGAGATATATA
16352882 A
1 A
16352883 CATTTCTTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (12 bp):
ATGAGATATATA
Found at i:16354502 original size:2 final size:2
Alignment explanation
Indices: 16354492--16354527 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
16354482 CTCTCTCTCT
*
16354492 CA CA AA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
16354528 AAAACAAACC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.47, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:16368718 original size:26 final size:26
Alignment explanation
Indices: 16368689--16368738 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
16368679 AAAACCTACT
16368689 TGTACCTAAAA-AAAG-TAAACAAATGA
1 TGTACC-AAAATAAAGCT-AACAAATGA
16368715 TGTACCAAAATAAAGCTAACAAAT
1 TGTACCAAAATAAAGCTAACAAAT
16368739 TAAGAGGTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 4 0.18
26 17 0.77
27 1 0.05
ACGTcount: A:0.56, C:0.14, G:0.10, T:0.20
Consensus pattern (26 bp):
TGTACCAAAATAAAGCTAACAAATGA
Found at i:16374328 original size:21 final size:23
Alignment explanation
Indices: 16374279--16374322 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
16374269 AATATGTTTA
*
16374279 ATAAGTATATTAATCTTTTTTAAG
1 ATAATTATATTAA-CTTTTTTAAG
16374303 ATAATTATATTAA-TTTTTTA
1 ATAATTATATTAACTTTTTTA
16374323 GTTAATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
24 12 0.63
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (23 bp):
ATAATTATATTAACTTTTTTAAG
Found at i:16375075 original size:44 final size:44
Alignment explanation
Indices: 16375025--16375115 Score: 146
Period size: 44 Copynumber: 2.1 Consensus size: 44
16375015 ATTCGTAGGT
* *
16375025 AAAATAATATTAAAATAACATATACTAATCAGAATTTAAGTGAG
1 AAAATAATATTAAAATAACATACACTAATCAAAATTTAAGTGAG
* *
16375069 AAAATAATATTAAAATAACTTACACTAATCAAAATTTATGTGAG
1 AAAATAATATTAAAATAACATACACTAATCAAAATTTAAGTGAG
16375113 AAA
1 AAA
16375116 CTAAAAACAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.30
Consensus pattern (44 bp):
AAAATAATATTAAAATAACATACACTAATCAAAATTTAAGTGAG
Found at i:16376616 original size:26 final size:26
Alignment explanation
Indices: 16376586--16376789 Score: 137
Period size: 24 Copynumber: 8.3 Consensus size: 26
16376576 GCAACTCTTA
*
16376586 TGAGCGTCCCGATATATGGCTCTTCG
1 TGAGCTTCCCGATATATGGCTCTTCG
* *
16376612 TGAGCTTCCCGAT-TAAAGGCTCTTTG
1 TGAGCTTCCCGATAT-ATGGCTCTTCG
*
16376638 TGAGCTTCCTGAT-TAATGGCTCTTCG
1 TGAGCTTCCCGATAT-ATGGCTCTTCG
* * *
16376664 -GAGCTTCTCG--ATATGGCTC-CCT
1 TGAGCTTCCCGATATATGGCTCTTCG
* * *
16376686 TGAACTTCCCGATATATGGCTATCCG
1 TGAGCTTCCCGATATATGGCTCTTCG
*
16376712 -GAGCTTCCCGTTA-ATGGCTCTTCG
1 TGAGCTTCCCGATATATGGCTCTTCG
* * * *
16376736 -GAGCTACCCGTTAT-TGGCTC-GCA
1 TGAGCTTCCCGATATATGGCTCTTCG
* * *
16376759 TGAGCTTCCTGA-ATATGACTCTT-A
1 TGAGCTTCCCGATATATGGCTCTTCG
16376783 TGAGCTT
1 TGAGCTT
16376790 TCTGTTATAC
Statistics
Matches: 142, Mismatches: 26, Indels: 22
0.75 0.14 0.12
Matches are distributed among these distances:
22 1 0.01
23 18 0.13
24 49 0.35
25 28 0.20
26 46 0.32
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (26 bp):
TGAGCTTCCCGATATATGGCTCTTCG
Found at i:16376718 original size:25 final size:25
Alignment explanation
Indices: 16376587--16376755 Score: 129
Period size: 26 Copynumber: 6.8 Consensus size: 25
16376577 CAACTCTTAT
*
16376587 GAGCGTCCCGATATATGGCTCTTCG
1 GAGCTTCCCGATATATGGCTCTTCG
* *
16376612 TGAGCTTCCCGAT-TAAAGGCTCTTTG
1 -GAGCTTCCCGATAT-ATGGCTCTTCG
*
16376638 TGAGCTTCCTGAT-TAATGGCTCTTCG
1 -GAGCTTCCCGATAT-ATGGCTCTTCG
*
16376664 GAGCTTCTCG--ATATGGCTCCCTT--
1 GAGCTTCCCGATATATGGCT--CTTCG
* * *
16376687 GAACTTCCCGATATATGGCTATCCG
1 GAGCTTCCCGATATATGGCTCTTCG
*
16376712 GAGCTTCCCGTTA-ATGGCTCTTCG
1 GAGCTTCCCGATATATGGCTCTTCG
* *
16376736 GAGCTACCCGTTAT-TGGCTC
1 GAGCTTCCCGATATATGGCTC
16376756 GCATGAGCTT
Statistics
Matches: 117, Mismatches: 17, Indels: 20
0.76 0.11 0.13
Matches are distributed among these distances:
23 15 0.13
24 28 0.24
25 31 0.26
26 43 0.37
ACGTcount: A:0.17, C:0.27, G:0.24, T:0.33
Consensus pattern (25 bp):
GAGCTTCCCGATATATGGCTCTTCG
Found at i:16376788 original size:72 final size:73
Alignment explanation
Indices: 16376638--16376789 Score: 164
Period size: 72 Copynumber: 2.1 Consensus size: 73
16376628 AGGCTCTTTG
* * * *
16376638 TGAGCTTCCTGATTAATGGCTCTTCGGAGCTTCTCGATATGGCTCCCTTGAACTTCCCGATATAT
1 TGAGCTTCCCGATTAATGGCTCTTCGGAGCTACCCGATATGGCTCCCATGAACTTCCCGATATAT
* *
16376703 GGCTATCC
66 GACTATCA
* * * * *
16376711 GGAGCTTCCCG-TTAATGGCTCTTCGGAGCTACCCGTTATTGGCTCGCATGAGCTTCCTGA-ATA
1 TGAGCTTCCCGATTAATGGCTCTTCGGAGCTACCCGATA-TGGCTCCCATGAACTTCCCGATATA
* *
16376774 TGACTCTTA
65 TGACTATCA
16376783 TGAGCTT
1 TGAGCTT
16376790 TCTGTTATAC
Statistics
Matches: 64, Mismatches: 14, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
72 38 0.59
73 26 0.41
ACGTcount: A:0.18, C:0.26, G:0.22, T:0.34
Consensus pattern (73 bp):
TGAGCTTCCCGATTAATGGCTCTTCGGAGCTACCCGATATGGCTCCCATGAACTTCCCGATATAT
GACTATCA
Found at i:16381293 original size:21 final size:20
Alignment explanation
Indices: 16381269--16381333 Score: 69
Period size: 21 Copynumber: 3.2 Consensus size: 20
16381259 GTGTTTTACT
*
16381269 TTCTATTCAGTTCTTACGAGC
1 TTCTGTTCAG-TCTTACGAGC
*
16381290 TTCTGTTAAGCTCTTACGAGC
1 TTCTGTTCAG-TCTTACGAGC
* *
16381311 TTTTGTTCAG-CTTTCGAGC
1 TTCTGTTCAGTCTTACGAGC
16381330 TTCT
1 TTCT
16381334 CTTGGCGTAT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
19 11 0.30
21 26 0.70
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (20 bp):
TTCTGTTCAGTCTTACGAGC
Found at i:16381330 original size:19 final size:21
Alignment explanation
Indices: 16381280--16381333 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
16381270 TCTATTCAGT
16381280 TCTTACGAGCTTCTGTTAAGC
1 TCTTACGAGCTTCTGTTAAGC
* *
16381301 TCTTACGAGCTTTTGTTCAGC
1 TCTTACGAGCTTCTGTTAAGC
16381322 T-TT-CGAGCTTCT
1 TCTTACGAGCTTCT
16381334 CTTGGCGTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 8 0.27
20 2 0.07
21 20 0.67
ACGTcount: A:0.15, C:0.24, G:0.19, T:0.43
Consensus pattern (21 bp):
TCTTACGAGCTTCTGTTAAGC
Found at i:16382824 original size:14 final size:12
Alignment explanation
Indices: 16382785--16382835 Score: 52
Period size: 12 Copynumber: 4.1 Consensus size: 12
16382775 AAAGTTAATA
16382785 TATATTATAATAT
1 TATATTAT-ATAT
16382798 TATATCT-TA-AT
1 TATAT-TATATAT
16382809 TATTAATTATATAT
1 TA-T-ATTATATAT
16382823 TATATTATATAT
1 TATATTATATAT
16382835 T
1 T
16382836 GTAATAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
11 4 0.12
12 13 0.39
13 11 0.33
14 5 0.15
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (12 bp):
TATATTATATAT
Found at i:16383273 original size:41 final size:41
Alignment explanation
Indices: 16383228--16383317 Score: 171
Period size: 41 Copynumber: 2.2 Consensus size: 41
16383218 AGAACTTATG
*
16383228 TGAAAATAGGGAGTTGAATTTATTCTAAAGTGGAATTTGCA
1 TGAAAATAGGGAGTTGAATTTATTCTAAAGTGAAATTTGCA
16383269 TGAAAATAGGGAGTTGAATTTATTCTAAAGTGAAATTTGCA
1 TGAAAATAGGGAGTTGAATTTATTCTAAAGTGAAATTTGCA
16383310 TGAAAATA
1 TGAAAATA
16383318 AAGAATTAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.40, C:0.04, G:0.22, T:0.33
Consensus pattern (41 bp):
TGAAAATAGGGAGTTGAATTTATTCTAAAGTGAAATTTGCA
Found at i:16383961 original size:40 final size:38
Alignment explanation
Indices: 16383877--16383978 Score: 116
Period size: 40 Copynumber: 2.7 Consensus size: 38
16383867 CTTTGGATTA
* **
16383877 ATTCGATGAGGCACTAGGTGTC-AATTTACTTCGGTTT
1 ATTCGATGAGACACTAGGTGTCAAATTTACTTCGAATT
**
16383914 AGCCGATGAGACACTAGGTGTCAAATTATTACTTCGAATT
1 ATTCGATGAGACACTAGGTGTCAAA-T-TTACTTCGAATT
* *
16383954 ATTCGATGAGACACTGGGTGCCAAA
1 ATTCGATGAGACACTAGGTGTCAAA
16383979 CTGATGTGTT
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
37 19 0.36
38 2 0.04
39 1 0.02
40 31 0.58
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (38 bp):
ATTCGATGAGACACTAGGTGTCAAATTTACTTCGAATT
Found at i:16384918 original size:12 final size:12
Alignment explanation
Indices: 16384901--16384933 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
16384891 ATTTCGAAAG
16384901 GGCACACGGCCT
1 GGCACACGGCCT
*
16384913 GGCACACGGTCT
1 GGCACACGGCCT
16384925 GGCACACGG
1 GGCACACGG
16384934 GCGTGTGGCT
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:0.18, C:0.36, G:0.36, T:0.09
Consensus pattern (12 bp):
GGCACACGGCCT
Found at i:16402645 original size:18 final size:18
Alignment explanation
Indices: 16402624--16402661 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
16402614 CACCCAAAAA
16402624 AAAAAAAAAGTA-AAAGAG
1 AAAAAAAAAG-ACAAAGAG
*
16402642 AAAAAAGAAGACAAAGAG
1 AAAAAAAAAGACAAAGAG
16402660 AA
1 AA
16402662 TCAAAGGCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (18 bp):
AAAAAAAAAGACAAAGAG
Found at i:16404244 original size:23 final size:24
Alignment explanation
Indices: 16404213--16404259 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
16404203 TAATATATGT
* * *
16404213 GAACGTAAAGATTTAAAT-TTTCA
1 GAACATAAAAATTGAAATGTTTCA
16404236 GAACATAAAAATTGAAATGTTTCA
1 GAACATAAAAATTGAAATGTTTCA
16404260 CAGCAACTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.32
Consensus pattern (24 bp):
GAACATAAAAATTGAAATGTTTCA
Found at i:16407930 original size:22 final size:22
Alignment explanation
Indices: 16407902--16407943 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
16407892 ATAGCTAATG
16407902 GAATTTATTCCAAAATTAAAAA
1 GAATTTATTCCAAAATTAAAAA
*
16407924 GAATTTATTTCAAAATTAAA
1 GAATTTATTCCAAAATTAAA
16407944 GCATATTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (22 bp):
GAATTTATTCCAAAATTAAAAA
Found at i:16412142 original size:2 final size:2
Alignment explanation
Indices: 16412135--16412187 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
16412125 ATGATATAAA
16412135 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16412177 AT AT AT AT AT A
1 AT AT AT AT AT A
16412188 AGAGGTTAGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16412523 original size:41 final size:41
Alignment explanation
Indices: 16412461--16412563 Score: 116
Period size: 41 Copynumber: 2.5 Consensus size: 41
16412451 GGCTATGTTC
* * * *
16412461 CTAGCAGGCTTGATGCAGGTGAAATAATTCAGACTTTACGT
1 CTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTATACGT
* * * *
16412502 CTAGCAGGCTTAATGCCGGTGATACATTTCGGACTATAGGT
1 CTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTATACGT
* *
16412543 CTAGCAGGCTAAAAGCCGGTG
1 CTAGCAGGCTTAATGCCGGTG
16412564 TACTGAATCA
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.26
Consensus pattern (41 bp):
CTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTATACGT
Found at i:16412873 original size:2 final size:2
Alignment explanation
Indices: 16412866--16412958 Score: 89
Period size: 2 Copynumber: 45.0 Consensus size: 2
16412856 TGTAATTGGG
16412866 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
16412908 AA AT GT ACT CAT TT AA AT GT AT AT GAT GA- AT AT GT AT AT AT AT
1 AT AT AT A-T -AT AT AT AT AT AT AT -AT -AT AT AT AT AT AT AT AT
16412951 AT AT AT AT
1 AT AT AT AT
16412959 TCGAATATAC
Statistics
Matches: 75, Mismatches: 12, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
1 1 0.01
2 67 0.89
3 6 0.08
4 1 0.01
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (2 bp):
AT
Found at i:16418382 original size:16 final size:17
Alignment explanation
Indices: 16418345--16418380 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
16418335 CATTTGTCAT
*
16418345 CTTT-TTTTTTTTTTTA
1 CTTTATTTTTATTTTTA
16418361 CTTTATTTTTATTTTTA
1 CTTTATTTTTATTTTTA
16418378 CTT
1 CTT
16418381 ATATATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.11, C:0.08, G:0.00, T:0.81
Consensus pattern (17 bp):
CTTTATTTTTATTTTTA
Found at i:16418402 original size:5 final size:5
Alignment explanation
Indices: 16418380--16418432 Score: 67
Period size: 5 Copynumber: 11.0 Consensus size: 5
16418370 TATTTTTACT
*
16418380 TATATA TATAA TACAA TATAA TATAA TATAA TATAA TA-AA -ATAA TAT-A
1 TATA-A TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
16418428 TATAA
1 TATAA
16418433 AACATAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
3 1 0.02
4 8 0.19
5 29 0.69
6 4 0.10
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (5 bp):
TATAA
Found at i:16423684 original size:5 final size:5
Alignment explanation
Indices: 16423672--16423725 Score: 76
Period size: 5 Copynumber: 11.2 Consensus size: 5
16423662 ATTTTTACTT
* *
16423672 ATATA ATACA ATACA ATATA ATATA ATATA ATATA ATATA AT-TA ATAT-
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
16423720 ATATA A
1 ATATA A
16423726 AACATAAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
4 8 0.18
5 37 0.82
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (5 bp):
ATATA
Found at i:16426831 original size:21 final size:21
Alignment explanation
Indices: 16426805--16426846 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
16426795 AATATATATA
*
16426805 TATGTTCTATAAGCTGAATTT
1 TATGTTCTATAAGCTAAATTT
16426826 TATGTTCTATAAGCTAAATTT
1 TATGTTCTATAAGCTAAATTT
16426847 GATTTTATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.48
Consensus pattern (21 bp):
TATGTTCTATAAGCTAAATTT
Found at i:16427178 original size:2 final size:2
Alignment explanation
Indices: 16427171--16427203 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
16427161 ATGATATGAA
16427171 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16427204 AGAGGTTAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16427561 original size:41 final size:41
Alignment explanation
Indices: 16427477--16427579 Score: 116
Period size: 41 Copynumber: 2.5 Consensus size: 41
16427467 GGCTATGTGC
* * *
16427477 CTAGCAGGCTTGATGCCGGTGAAATAATTCAGACTTTACGT
1 CTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTATACGT
* * * *
16427518 CTAGCAGGCTTAATGCCGGTGATACATTTCGGACTATAGGT
1 CTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTATACGT
* * *
16427559 CTAGTAGGCTAAAAGCCGGTG
1 CTAGCAGGCTTAATGCCGGTG
16427580 TACTGAATCA
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.27
Consensus pattern (41 bp):
CTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTATACGT
Found at i:16433534 original size:7 final size:7
Alignment explanation
Indices: 16433518--16433549 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
16433508 CTAAAGTTAC
*
16433518 CACTTAT
1 CACTTGT
16433525 CACTTGT
1 CACTTGT
16433532 CACTTGT
1 CACTTGT
16433539 CACTTGT
1 CACTTGT
16433546 CACT
1 CACT
16433550 GATCAGATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.19, C:0.31, G:0.09, T:0.41
Consensus pattern (7 bp):
CACTTGT
Found at i:16433538 original size:58 final size:58
Alignment explanation
Indices: 16433473--16433650 Score: 322
Period size: 58 Copynumber: 3.1 Consensus size: 58
16433463 ATCACATTTA
*
16433473 TCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGTTACCACTTATCACTTG
1 TCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
16433531 TCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
1 TCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
* *
16433589 TCACTTGTCACTTGTCACCGATCAAATAAGTGTAGCT-AAGCTACCACTTATCACTTG
1 TCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
16433646 TCACT
1 TCACT
16433651 GATCAGAAGT
Statistics
Matches: 117, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
57 25 0.21
58 92 0.79
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.33
Consensus pattern (58 bp):
TCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
Found at i:16433541 original size:14 final size:14
Alignment explanation
Indices: 16433518--16433554 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
16433508 CTAAAGTTAC
16433518 CACTTATCACTTGT
1 CACTTATCACTTGT
*
16433532 CACTTGTCACTTGT
1 CACTTATCACTTGT
*
16433546 CACTGATCA
1 CACTTATCA
16433555 GATAAGTGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.22, C:0.30, G:0.11, T:0.38
Consensus pattern (14 bp):
CACTTATCACTTGT
Found at i:16433592 original size:7 final size:7
Alignment explanation
Indices: 16433576--16433606 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
16433566 CTAAAGCTAC
*
16433576 CACTTAT
1 CACTTGT
16433583 CACTTGT
1 CACTTGT
16433590 CACTTGT
1 CACTTGT
16433597 CACTTGT
1 CACTTGT
16433604 CAC
1 CAC
16433607 CGATCAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.19, C:0.32, G:0.10, T:0.39
Consensus pattern (7 bp):
CACTTGT
Found at i:16506796 original size:15 final size:16
Alignment explanation
Indices: 16506773--16506804 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
16506763 AAAAAATTAT
16506773 AAAT-TTTTTTTAATA
1 AAATATTTTTTTAATA
16506788 AAATATTTTTTTAATA
1 AAATATTTTTTTAATA
16506804 A
1 A
16506805 TTTTTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
AAATATTTTTTTAATA
Found at i:16507061 original size:17 final size:17
Alignment explanation
Indices: 16507039--16507099 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 17
16507029 AAAAAAAAAA
16507039 AAGAGAGAAAGGAGAAG
1 AAGAGAGAAAGGAGAAG
16507056 AAGAGAAGGAGAAGGAGAAG
1 AAGAG-A-GA-AAGGAGAAG
16507076 AAGAG-GAAA--AGAAG
1 AAGAGAGAAAGGAGAAG
*
16507090 AAGAAAGAAA
1 AAGAGAGAAA
16507100 AAAAAAGAAG
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
14 9 0.23
15 4 0.10
16 2 0.05
17 7 0.18
18 1 0.03
19 2 0.05
20 14 0.36
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (17 bp):
AAGAGAGAAAGGAGAAG
Found at i:16507064 original size:14 final size:15
Alignment explanation
Indices: 16507042--16507096 Score: 58
Period size: 17 Copynumber: 3.5 Consensus size: 15
16507032 AAAAAAAAAG
16507042 AGAGAAAGGAGAAGA
1 AGAGAAAGGAGAAGA
*
16507057 AGAG-AAGGAGAAGG
1 AGAGAAAGGAGAAGA
*
16507071 AGAAGAAGAGGAAAAGA
1 AG-AGAA-AGGAGAAGA
16507088 AGAAGAAAG
1 AG-AGAAAG
16507097 AAAAAAAAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
14 11 0.32
15 6 0.18
16 3 0.09
17 14 0.41
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (15 bp):
AGAGAAAGGAGAAGA
Found at i:16507305 original size:18 final size:19
Alignment explanation
Indices: 16507278--16507456 Score: 132
Period size: 19 Copynumber: 9.0 Consensus size: 19
16507268 TTCTAAATTT
*
16507278 TTTTTGTATGAATTTTGTA
1 TTTTTGTATGAATATTGTA
16507297 TTTTT-TATGAATATTGTA
1 TTTTTGTATGAATATTGTA
* *
16507315 CTAATTTTATAATTAA-ATTTGTA
1 -T--TTTTGT-ATGAATA-TTGTA
* * * *
16507338 TTTATAGTTTTGGAT-TAGTA
1 TTT-TTG-TATGAATATTGTA
16507358 -TTTTGTATGAATATTGTAA
1 TTTTTGTATGAATATTGT-A
*
16507377 TTTTTTGTATGAATATTATA
1 -TTTTTGTATGAATATTGTA
*
16507397 ATTTTGTATGAATATTGTAA
1 TTTTTGTATGAATATTGT-A
16507417 TTTTTTTGTATGAATATTGTA
1 --TTTTTGTATGAATATTGTA
*
16507438 ATTTTGTATGAATATTGTA
1 TTTTTGTATGAATATTGTA
16507457 ATGTCGGGAT
Statistics
Matches: 127, Mismatches: 17, Indels: 32
0.72 0.10 0.18
Matches are distributed among these distances:
17 5 0.04
18 17 0.13
19 43 0.34
20 8 0.06
21 24 0.19
22 21 0.17
23 9 0.07
ACGTcount: A:0.30, C:0.01, G:0.13, T:0.56
Consensus pattern (19 bp):
TTTTTGTATGAATATTGTA
Found at i:16507383 original size:21 final size:21
Alignment explanation
Indices: 16507358--16507511 Score: 167
Period size: 19 Copynumber: 7.2 Consensus size: 21
16507348 TGGATTAGTA
16507358 TTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
*
16507379 TTTTGTATGAATATTATAA--
1 TTTTGTATGAATATTGTAATT
16507398 TTTTGTATGAATATTGTAATTT
1 TTTTGTATGAATATTGTAA-TT
16507420 TTTTGTATGAATATTGTAA--
1 TTTTGTATGAATATTGTAATT
16507439 TTTTGTATGAATATTGTAATGT
1 TTTTGTATGAATATTGTAAT-T
*
16507461 CGGGATATAT-TAT-AATATTGTAATT
1 -----T-TTTGTATGAATATTGTAATT
16507486 TTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
16507507 ATTTT
1 -TTTT
16507512 ATAATTAATT
Statistics
Matches: 114, Mismatches: 4, Indels: 29
0.78 0.03 0.20
Matches are distributed among these distances:
19 39 0.34
20 4 0.04
21 30 0.26
22 23 0.20
25 1 0.01
26 11 0.10
27 4 0.04
28 2 0.02
ACGTcount: A:0.31, C:0.01, G:0.14, T:0.55
Consensus pattern (21 bp):
TTTTGTATGAATATTGTAATT
Found at i:16507434 original size:41 final size:41
Alignment explanation
Indices: 16507357--16507458 Score: 188
Period size: 41 Copynumber: 2.5 Consensus size: 41
16507347 TTGGATTAGT
16507357 ATTTTGTATGAATATTGTAA-TTTTTTGTATGAATATTATA
1 ATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTATA
*
16507397 ATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTA
1 ATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTATA
16507438 ATTTTGTATGAATATTGTAAT
1 ATTTTGTATGAATATTGTAAT
16507459 GTCGGGATAT
Statistics
Matches: 60, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
40 20 0.33
41 40 0.67
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (41 bp):
ATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTATA
Found at i:16507566 original size:25 final size:24
Alignment explanation
Indices: 16507499--16507583 Score: 66
Period size: 26 Copynumber: 3.3 Consensus size: 24
16507489 TGTATGAATA
*
16507499 TTGTAATTATTTTATAATTAATTTG
1 TTGTAATTA-TTTAAAATTAATTTG
*
16507524 TTAGTAATT-TATATAAATT-ATTGTG
1 TT-GTAATTATTTA-AAATTAATT-TG
*
16507549 TGTGTAATTATTTAAAATTTAATTTA
1 T-TGTAATTATTTAAAA-TTAATTTG
16507575 TTAGTAATT
1 TT-GTAATT
16507584 TAGGATTAAG
Statistics
Matches: 48, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
24 6 0.12
25 19 0.40
26 20 0.42
27 3 0.06
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.55
Consensus pattern (24 bp):
TTGTAATTATTTAAAATTAATTTG
Found at i:16507696 original size:37 final size:37
Alignment explanation
Indices: 16507645--16507725 Score: 135
Period size: 37 Copynumber: 2.2 Consensus size: 37
16507635 CATATAAAGT
16507645 TTATAAAAAAATTAAAAATCATTTTATTAAAAGTTTAA
1 TTAT-AAAAAATTAAAAATCATTTTATTAAAAGTTTAA
* *
16507683 TTATAAAAAATTAAAATTTATTTTATTAAAAGTTTAA
1 TTATAAAAAATTAAAAATCATTTTATTAAAAGTTTAA
16507720 TTATAA
1 TTATAA
16507726 CTGACTTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
37 37 0.90
38 4 0.10
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.43
Consensus pattern (37 bp):
TTATAAAAAATTAAAAATCATTTTATTAAAAGTTTAA
Found at i:16507803 original size:15 final size:15
Alignment explanation
Indices: 16507762--16507803 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
16507752 GTTAACTCAT
*
16507762 TTAATTTTTATATAA
1 TTAAATTTTATATAA
*
16507777 TGTAACTTTTATATAA
1 T-TAAATTTTATATAA
16507793 TTAAATTTTAT
1 TTAAATTTTAT
16507804 TTGATTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (15 bp):
TTAAATTTTATATAA
Found at i:16508798 original size:24 final size:24
Alignment explanation
Indices: 16508766--16508832 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
16508756 AACCAAAATA
*
16508766 CCTTATTTTTTTCTTCTTTTCCTT
1 CCTTCTTTTTTTCTTCTTTTCCTT
* *
16508790 CCTTCTTTTCTTCTGC--TTCCTT
1 CCTTCTTTTTTTCTTCTTTTCCTT
*
16508812 CCTTC-TTATTTCTTCTGTTTC
1 CCTTCTTTTTTTCTTCT-TTTC
16508833 TCTAGTAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
21 7 0.21
22 11 0.32
24 16 0.47
ACGTcount: A:0.03, C:0.30, G:0.03, T:0.64
Consensus pattern (24 bp):
CCTTCTTTTTTTCTTCTTTTCCTT
Found at i:16508935 original size:27 final size:27
Alignment explanation
Indices: 16508914--16508986 Score: 146
Period size: 27 Copynumber: 2.7 Consensus size: 27
16508904 ACACCAATAA
16508914 TGGCGCCTCCCAGATAGGCACCACCAT
1 TGGCGCCTCCCAGATAGGCACCACCAT
16508941 TGGCGCCTCCCAGATAGGCACCACCAT
1 TGGCGCCTCCCAGATAGGCACCACCAT
16508968 TGGCGCCTCCCAGATAGGC
1 TGGCGCCTCCCAGATAGGC
16508987 GCTGATTAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.21, C:0.40, G:0.25, T:0.15
Consensus pattern (27 bp):
TGGCGCCTCCCAGATAGGCACCACCAT
Found at i:16515935 original size:22 final size:22
Alignment explanation
Indices: 16515909--16515955 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
16515899 ATACTTAACT
16515909 AAAGTATAAGGATTAAATTGTA
1 AAAGTATAAGGATTAAATTGTA
16515931 AAAGTATAAGGATTAAATTGTA
1 AAAGTATAAGGATTAAATTGTA
16515953 AAA
1 AAA
16515956 ATGATAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.30
Consensus pattern (22 bp):
AAAGTATAAGGATTAAATTGTA
Found at i:16520625 original size:18 final size:17
Alignment explanation
Indices: 16520592--16520630 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
16520582 TTGTATAAAT
16520592 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
16520610 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
16520627 TGTG
1 TGTG
16520631 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:16520748 original size:8 final size:8
Alignment explanation
Indices: 16520735--16520763 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
16520725 CACTAGAGAC
16520735 CAGTGTTA
1 CAGTGTTA
16520743 CAGTGTTA
1 CAGTGTTA
16520751 CAGTGTTA
1 CAGTGTTA
16520759 CAGTG
1 CAGTG
16520764 AGTCCCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:16520882 original size:23 final size:23
Alignment explanation
Indices: 16520851--16520926 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
16520841 GTGTTTATTG
16520851 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
16520874 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
16520897 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
16520920 ATCAGTG
1 ATCAGTG
16520927 TGGCACTTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:16521964 original size:40 final size:40
Alignment explanation
Indices: 16521916--16521991 Score: 143
Period size: 40 Copynumber: 1.9 Consensus size: 40
16521906 ACGCGCCAGG
*
16521916 AAATCGCGTCCACGTAAGCGTGATTTGCTGACGTGGACAC
1 AAATCGCGTCCACGTAAGCGCGATTTGCTGACGTGGACAC
16521956 AAATCGCGTCCACGTAAGCGCGATTTGCTGACGTGG
1 AAATCGCGTCCACGTAAGCGCGATTTGCTGACGTGG
16521992 CATGAACAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.24, C:0.25, G:0.29, T:0.22
Consensus pattern (40 bp):
AAATCGCGTCCACGTAAGCGCGATTTGCTGACGTGGACAC
Found at i:16526088 original size:18 final size:19
Alignment explanation
Indices: 16526065--16526102 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
16526055 TTAAAGTTTT
16526065 ATTTTAATATTT-TTATAC
1 ATTTTAATATTTATTATAC
*
16526083 ATTTTAATTTTTATTATAC
1 ATTTTAATATTTATTATAC
16526102 A
1 A
16526103 CACTTTAGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTAATATTTATTATAC
Found at i:16537694 original size:13 final size:14
Alignment explanation
Indices: 16537662--16537703 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
16537652 TTTATAGTTT
*
16537662 TATTATATAA-TTA
1 TATTATGTAATTTA
*
16537675 TATTATGTATTTTA
1 TATTATGTAATTTA
16537689 TA-TATGTAATTTA
1 TATTATGTAATTTA
16537702 TA
1 TA
16537704 ATACAAAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 20 0.80
14 5 0.20
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (14 bp):
TATTATGTAATTTA
Found at i:16539628 original size:115 final size:115
Alignment explanation
Indices: 16539426--16539662 Score: 440
Period size: 115 Copynumber: 2.1 Consensus size: 115
16539416 AATTACCGAA
* *
16539426 ATGTAGTGCCATAGACGGTGGCATACTAAGCAAGGACGTACCCCAAATCTTGTCCTCATTTTCCC
1 ATGTAGTGCCATAGACAGCGGCATACTAAGCAAGGACGTACCCCAAATCTTGTCCTCATTTTCCC
*
16539491 ACCAATCATTGTAGAATCAAAATTAAGATAAATAGCAAGGTTGCTTACTT
66 ACCAATCATTGTAGAATCAAAATTAAGATAAATAACAAGGTTGCTTACTT
16539541 ATGTAGTGCCATAGACAGCGGCATACTAAGCAAGGACGTACCCCAAATCTTGTCCTCATTTTCCC
1 ATGTAGTGCCATAGACAGCGGCATACTAAGCAAGGACGTACCCCAAATCTTGTCCTCATTTTCCC
16539606 ACCAATCATTGTAGAATCAAAATTAAGATAAATAACAAGGTTGCTTACTT
66 ACCAATCATTGTAGAATCAAAATTAAGATAAATAACAAGGTTGCTTACTT
16539656 AT-TAGTG
1 ATGTAGTG
16539663 AATAATGCAT
Statistics
Matches: 119, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
114 5 0.04
115 114 0.96
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.28
Consensus pattern (115 bp):
ATGTAGTGCCATAGACAGCGGCATACTAAGCAAGGACGTACCCCAAATCTTGTCCTCATTTTCCC
ACCAATCATTGTAGAATCAAAATTAAGATAAATAACAAGGTTGCTTACTT
Found at i:16547034 original size:24 final size:22
Alignment explanation
Indices: 16546986--16547034 Score: 53
Period size: 23 Copynumber: 2.1 Consensus size: 22
16546976 TAAAGCAGAT
* *
16546986 ATATTTAGTTAAAATTCAATAA
1 ATATTTAGGTAAAATTCAAAAA
*
16547008 ATATTTAAGGTAAAATTTAAAATA
1 ATATTT-AGGTAAAATTCAAAA-A
16547032 ATA
1 ATA
16547035 GTAGAAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 6 0.27
23 12 0.55
24 4 0.18
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.39
Consensus pattern (22 bp):
ATATTTAGGTAAAATTCAAAAA
Found at i:16548007 original size:2 final size:2
Alignment explanation
Indices: 16548000--16548035 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
16547990 TCACTCCCAA
16548000 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
16548036 ACACACACAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:16550028 original size:2 final size:2
Alignment explanation
Indices: 16550021--16550049 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
16550011 ACAAAGGACA
16550021 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16550050 GATTATGCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16551053 original size:2 final size:2
Alignment explanation
Indices: 16551046--16551070 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16551036 ATTTTACTAC
16551046 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
16551071 TATTGGCACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16558963 original size:2 final size:2
Alignment explanation
Indices: 16558958--16558991 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
16558948 TTTTCCCTTT
16558958 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16558992 NNNNNNNNNN
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16559324 original size:25 final size:25
Alignment explanation
Indices: 16559294--16559351 Score: 89
Period size: 26 Copynumber: 2.3 Consensus size: 25
16559284 CCCATTTTTT
* *
16559294 AATAAACATTAAAAAATATTTTAAA
1 AATAAAAAATAAAAAATATTTTAAA
16559319 AATAAAAAAATAAAAAATATTTTAAA
1 AAT-AAAAAATAAAAAATATTTTAAA
16559345 AATAAAA
1 AATAAAA
16559352 TATATATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 7 0.23
26 23 0.77
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.28
Consensus pattern (25 bp):
AATAAAAAATAAAAAATATTTTAAA
Found at i:16575643 original size:22 final size:23
Alignment explanation
Indices: 16575606--16575649 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
16575596 TACAAAAATG
*
16575606 TATTAAATTTGTATAAAATTAAT
1 TATTAAATGTGTATAAAATTAAT
*
16575629 TATT-AATGTGTATAAATTTAA
1 TATTAAATGTGTATAAAATTAA
16575650 ATAAATTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (23 bp):
TATTAAATGTGTATAAAATTAAT
Found at i:16578855 original size:12 final size:11
Alignment explanation
Indices: 16578809--16578851 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
16578799 AATAATAATT
*
16578809 AAAAATTTATA
1 AAAAAATTATA
16578820 AAAAAATTA-A
1 AAAAAATTATA
*
16578830 AAATAAAATATA
1 AAA-AAATTATA
16578842 AAAAAATTAT
1 AAAAAATTAT
16578852 TAAACTGATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 4 0.15
11 19 0.70
12 4 0.15
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AAAAAATTATA
Found at i:16579822 original size:2 final size:2
Alignment explanation
Indices: 16579815--16579855 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
16579805 TCATTTATGA
16579815 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
16579856 ACACACACAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:16590397 original size:54 final size:54
Alignment explanation
Indices: 16590315--16590417 Score: 197
Period size: 54 Copynumber: 1.9 Consensus size: 54
16590305 TAAGGGTTAG
16590315 CAACAAGGATCCGCCAGGTTGCCCACTTGACAACGAAAATTCTCCGACGTGAAC
1 CAACAAGGATCCGCCAGGTTGCCCACTTGACAACGAAAATTCTCCGACGTGAAC
*
16590369 CAACAAGGATCCGCCAGGTTGCCCACTTGGCAACGAAAATTCTCCGACG
1 CAACAAGGATCCGCCAGGTTGCCCACTTGACAACGAAAATTCTCCGACG
16590418 ATGTTCACGT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.30, C:0.32, G:0.21, T:0.17
Consensus pattern (54 bp):
CAACAAGGATCCGCCAGGTTGCCCACTTGACAACGAAAATTCTCCGACGTGAAC
Found at i:16594795 original size:3 final size:3
Alignment explanation
Indices: 16594789--16594835 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
16594779 TTAAAAACGC
16594789 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
16594836 GTTGATACAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:16613163 original size:24 final size:24
Alignment explanation
Indices: 16613126--16613172 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
16613116 TGAGAGAATT
16613126 TTTATTTTATTTAATATCAATATA
1 TTTATTTTATTTAATATCAATATA
*
16613150 TTTATATTTA-TTAATATTAATAT
1 TTTAT-TTTATTTAATATCAATAT
16613173 TAATATTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (24 bp):
TTTATTTTATTTAATATCAATATA
Found at i:16613167 original size:6 final size:6
Alignment explanation
Indices: 16613158--16613184 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
16613148 TATTTATATT
16613158 TATTAA TATTAA TATTAA TATTAA TAT
1 TATTAA TATTAA TATTAA TATTAA TAT
16613185 AAAATTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TATTAA
Found at i:16622137 original size:126 final size:126
Alignment explanation
Indices: 16621894--16622141 Score: 383
Period size: 127 Copynumber: 2.0 Consensus size: 126
16621884 AAATAAGGGT
*
16621894 TGAGAGATATTCATACTTTTTTCAAAAGATTGAAGATAACTTATTTTCTTGTTTTTAATAATAAT
1 TGAGAGATATTCATACTTTTTTCAAAAAATTGAAGATAACTTATTTTCTTGTTTTTAATAATAAT
* *
16621959 TTTAAAGAACGTTTATTTTTTTTCTATTTTTAATTTTTATTTGAATATTTTATTTTTGACA
66 TTTAAAGAACGCTTATTTTTTTTCTATTTTTAATTTTTATTTAAATATTTTATTTTTGACA
** * *
16622020 TGAGAGATAGTTCATTTTTTTTTCAAAAAATTGAAGATGATTTATTTTCTCT-TTTTTAATAATA
1 TGAGAGATA-TTCATACTTTTTTCAAAAAATTGAAGATAACTTATTTTCT-TGTTTTTAATAATA
* *
16622084 ATTTTAAAGAATGCTTA-TTTTTTTCTATTTTTAATTTTTATTTAAATTTTTTATTTTT
64 ATTTTAAAGAACGCTTATTTTTTTTCTATTTTTAATTTTTATTTAAATATTTTATTTTT
16622142 AAATTATTTT
Statistics
Matches: 111, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
126 48 0.43
127 62 0.56
128 1 0.01
ACGTcount: A:0.30, C:0.06, G:0.08, T:0.56
Consensus pattern (126 bp):
TGAGAGATATTCATACTTTTTTCAAAAAATTGAAGATAACTTATTTTCTTGTTTTTAATAATAAT
TTTAAAGAACGCTTATTTTTTTTCTATTTTTAATTTTTATTTAAATATTTTATTTTTGACA
Found at i:16622153 original size:16 final size:15
Alignment explanation
Indices: 16622103--16622154 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 15
16622093 AATGCTTATT
16622103 TTTTTCTATTTTT-AA
1 TTTTT-TATTTTTAAA
16622118 -TTTTTA--TTTAAA
1 TTTTTTATTTTTAAA
16622130 TTTTTTATTTTTAAA
1 TTTTTTATTTTTAAA
16622145 TTATTTTATT
1 TT-TTTTATT
16622155 GACATGACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
11 3 0.09
12 2 0.06
13 8 0.25
14 4 0.12
15 8 0.25
16 7 0.22
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTTTATTTTTAAA
Found at i:16622642 original size:29 final size:28
Alignment explanation
Indices: 16622609--16622666 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
16622599 AATTTAAAAG
*
16622609 TTAAA-ATATATTCTAAATTTTTATATTTT
1 TTAAATATAAATT-TAAATTTTT-TATTTT
*
16622638 TTAAATTTAAATTTAAATTTTTTATTTT
1 TTAAATATAAATTTAAATTTTTTATTTT
16622666 T
1 T
16622667 ATTTTTGATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 7 0.27
29 14 0.54
30 5 0.19
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (28 bp):
TTAAATATAAATTTAAATTTTTTATTTT
Found at i:16623809 original size:19 final size:17
Alignment explanation
Indices: 16623769--16623819 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
16623759 TAATTTTAAT
*
16623769 TTTAA-TTATAAAATATA
1 TTTAAGTTATAAAA-AAA
16623786 TTTAAAGTTATAAAAAAA
1 TTT-AAGTTATAAAAAAA
*
16623804 TGTTAAGTTAGAAAAA
1 T-TTAAGTTATAAAAA
16623820 GATCTTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
17 3 0.10
18 16 0.55
19 10 0.34
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (17 bp):
TTTAAGTTATAAAAAAA
Found at i:16625873 original size:4 final size:4
Alignment explanation
Indices: 16625864--16626150 Score: 556
Period size: 4 Copynumber: 71.8 Consensus size: 4
16625854 TACAATTCAA
* *
16625864 ATAC ATAC ATAC ATAC ATAC ATAC ATGC ATGC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
16625912 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
16625960 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
16626008 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
16626056 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
16626104 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
16626151 TAACACTCAT
Statistics
Matches: 281, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
4 281 1.00
ACGTcount: A:0.49, C:0.25, G:0.01, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:16630500 original size:8 final size:8
Alignment explanation
Indices: 16630487--16630511 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
16630477 ATCAACACTT
16630487 TTTCTTGC
1 TTTCTTGC
16630495 TTTCTTGC
1 TTTCTTGC
16630503 TTTCTTGC
1 TTTCTTGC
16630511 T
1 T
16630512 AGGTTGGGGT
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:0.00, C:0.24, G:0.12, T:0.64
Consensus pattern (8 bp):
TTTCTTGC
Found at i:16631741 original size:2 final size:2
Alignment explanation
Indices: 16631734--16631767 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
16631724 GCTTTATGTT
16631734 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
16631768 GAAGGAATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:16643581 original size:40 final size:38
Alignment explanation
Indices: 16643502--16643652 Score: 137
Period size: 40 Copynumber: 3.9 Consensus size: 38
16643492 ATTAAAAAAA
* * *
16643502 TAAAATTGT-AAAAA-ATTAAATATTTTTAAAAA-TATTT
1 TAAAATTTTAAAAAATATTAAA-AATTGTAAAAATTA-TT
* *
16643539 TAAAATTTTAAAAAGCTATTAAAAATTATAAAACATTATT
1 TAAAATTTTAAAAA-ATATTAAAAATTGTAAAA-ATTATT
*
16643579 TAAAAATTTTAAAAAATATTAAAAATTGTGAAAATTATT
1 T-AAAATTTTAAAAAATATTAAAAATTGTAAAAATTATT
* * *
16643618 AAAAAATTGAAAATAATTATTAAAAATTGTAAAAA
1 TAAAATTTTAAAA-AA-TATTAAAAATTGTAAAAA
16643653 CTATGAATCA
Statistics
Matches: 95, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
37 8 0.08
38 14 0.15
39 16 0.17
40 42 0.44
41 15 0.16
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.37
Consensus pattern (38 bp):
TAAAATTTTAAAAAATATTAAAAATTGTAAAAATTATT
Found at i:16643645 original size:10 final size:10
Alignment explanation
Indices: 16643446--16643645 Score: 92
Period size: 10 Copynumber: 20.8 Consensus size: 10
16643436 TTAGAAACCA
*
16643446 TAAAAAATACT
1 TAAAAATTA-T
16643457 TAAAAA-TAT
1 TAAAAATTAT
16643466 ATAAAAATTAT
1 -TAAAAATTAT
16643477 TAAAAA--AT
1 TAAAAATTAT
* *
16643485 T-TAGATTAT
1 TAAAAATTAT
*
16643494 TAAAAA--AA
1 TAAAAATTAT
*
16643502 T-AAAATT-G
1 TAAAAATTAT
16643510 TAAAAA--AT
1 TAAAAATTAT
* *
16643518 TAAATATTTT
1 TAAAAATTAT
16643528 TAAAAA-TATT
1 TAAAAATTA-T
*
16643538 TTAAAATT-T
1 TAAAAATTAT
*
16643547 TAAAAAGCTAT
1 TAAAAA-TTAT
16643558 TAAAAATTA-
1 TAAAAATTAT
16643567 TAAAACATTATT
1 TAAAA-ATTA-T
16643579 TAAAAATT-T
1 TAAAAATTAT
*
16643588 TAAAAAATAT
1 TAAAAATTAT
*
16643598 TAAAAATT-G
1 TAAAAATTAT
*
16643607 TGAAAATTAT
1 TAAAAATTAT
16643617 TAAAAA--AT
1 TAAAAATTAT
16643625 TGAAAATAATTAT
1 T--AAA-AATTAT
16643638 TAAAAATT
1 TAAAAATT
16643646 GTAAAAACTA
Statistics
Matches: 143, Mismatches: 21, Indels: 51
0.67 0.10 0.24
Matches are distributed among these distances:
7 6 0.04
8 14 0.10
9 35 0.24
10 55 0.38
11 25 0.17
12 5 0.03
13 3 0.02
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.36
Consensus pattern (10 bp):
TAAAAATTAT
Found at i:16643877 original size:22 final size:21
Alignment explanation
Indices: 16643851--16643974 Score: 73
Period size: 21 Copynumber: 6.0 Consensus size: 21
16643841 TTGTTAACTA
16643851 TTTACAATTTTTTAATAATTAT
1 TTTACAA-TTTTTAATAATTAT
*
16643873 TTTACGATTTTTAATAATT-T
1 TTTACAATTTTTAATAATTAT
* ** * *
16643893 TATA-AAAATTAAATAA-TGT
1 TTTACAATTTTTAATAATTAT
* *
16643912 TTTATAACTTTTAATAACTT-T
1 TTTACAATTTTTAATAA-TTAT
*
16643933 TTTA-AAATTTTAA-AA-TAT
1 TTTACAATTTTTAATAATTAT
*
16643951 TTTAAACAATATTTAATAATTAT
1 TTT--ACAATTTTTAATAATTAT
16643974 T
1 T
16643975 ATAATATTTA
Statistics
Matches: 79, Mismatches: 13, Indels: 19
0.71 0.12 0.17
Matches are distributed among these distances:
17 1 0.01
18 5 0.06
19 14 0.18
20 22 0.28
21 24 0.30
22 9 0.11
23 4 0.05
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (21 bp):
TTTACAATTTTTAATAATTAT
Found at i:16643924 original size:39 final size:38
Alignment explanation
Indices: 16643881--16643978 Score: 99
Period size: 39 Copynumber: 2.4 Consensus size: 38
16643871 ATTTTACGAT
*
16643881 TTTTAATAATTTTATAAAAATTAAATAATGTTTTATAAC-
1 TTTTAATAATTTTATAAAAATTAAA-AATATTTTA-AACA
* * *
16643920 TTTTAATAACTTTTTTAAAATTTTAAAATATTTTAAACAA
1 TTTTAATAA-TTTTATAAAAATTAAAAATATTTTAAAC-A
16643960 TATTTAATAATTATTATAA
1 T-TTTAATAATT-TTATAA
16643979 TATTTATTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
38 3 0.06
39 17 0.35
40 16 0.33
41 13 0.27
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (38 bp):
TTTTAATAATTTTATAAAAATTAAAAATATTTTAAACA
Found at i:16643943 original size:20 final size:19
Alignment explanation
Indices: 16643860--16643971 Score: 82
Period size: 20 Copynumber: 5.6 Consensus size: 19
16643850 ATTTACAATT
* *
16643860 TTTTAATAATTATTTTACGAT
1 TTTTAATAATT-TTTTA-AAA
*
16643881 TTTTAATAATTTTATAAAA
1 TTTTAATAATTTTTTAAAA
* * * *
16643900 ATTAAATAATGTTTTATAAC
1 TTTTAATAATTTTTTA-AAA
16643920 TTTTAATAACTTTTTTAAAA
1 TTTTAATAA-TTTTTTAAAA
*
16643940 TTTTAA-AATATTTTAAACAA
1 TTTTAATAAT-TTTTTAA-AA
16643960 TATTTAATAATT
1 T-TTTAATAATT
16643972 ATTATAATAT
Statistics
Matches: 72, Mismatches: 13, Indels: 12
0.74 0.13 0.12
Matches are distributed among these distances:
18 1 0.01
19 21 0.29
20 24 0.33
21 23 0.32
22 3 0.04
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.52
Consensus pattern (19 bp):
TTTTAATAATTTTTTAAAA
Found at i:16649364 original size:2 final size:2
Alignment explanation
Indices: 16649357--16649381 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16649347 CCCCTGCTCA
16649357 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
16649382 AATCTGGCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:16650689 original size:11 final size:11
Alignment explanation
Indices: 16650673--16650697 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
16650663 AAAAGGATAT
16650673 ATAAATAAATA
1 ATAAATAAATA
16650684 ATAAATAAATA
1 ATAAATAAATA
16650695 ATA
1 ATA
16650698 TATTGAAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
ATAAATAAATA
Found at i:16657446 original size:18 final size:19
Alignment explanation
Indices: 16657420--16657456 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
16657410 GAGCAAAGGT
16657420 AAATATAATATT-ATAAAA
1 AAATATAATATTAATAAAA
*
16657438 AAATTTAATATTAATAAAA
1 AAATATAATATTAATAAAA
16657457 TTAACATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
AAATATAATATTAATAAAA
Found at i:16677834 original size:18 final size:18
Alignment explanation
Indices: 16677808--16677842 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16677798 TCTTTATTTT
*
16677808 CATTTTCTCTCTATCTCC
1 CATTCTCTCTCTATCTCC
*
16677826 CATTCTCTCTCTCTCTC
1 CATTCTCTCTCTATCTC
16677843 TCTCTTTTGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.09, C:0.43, G:0.00, T:0.49
Consensus pattern (18 bp):
CATTCTCTCTCTATCTCC
Found at i:16691606 original size:29 final size:28
Alignment explanation
Indices: 16691530--16691609 Score: 83
Period size: 29 Copynumber: 2.8 Consensus size: 28
16691520 TAGATTTTTA
* * *
16691530 TAAT-TTTTTTATAATGTTTAATCAATTT
1 TAATATTTTTTATAAT-TTTATTAAAATT
16691558 TAA-ATATTTTTATATATTTTATTAAAATT
1 TAATAT-TTTTTATA-ATTTTATTAAAATT
16691587 TAATATTTTTTATAACTTTTATT
1 TAATATTTTTTATAA-TTTTATT
16691610 GATTTTTATC
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
28 5 0.11
29 35 0.80
30 4 0.09
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (28 bp):
TAATATTTTTTATAATTTTATTAAAATT
Found at i:16691617 original size:29 final size:28
Alignment explanation
Indices: 16691525--16691617 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 28
16691515 CCGGGTAGAT
* *
16691525 TTTTATAATTTTTTTATA-ATGTTTAATCAA
1 TTTT-TAATATTTTTATATAT-TTT-ATTAA
*
16691555 TTTTAAATATTTTTATATATTTTATTAA
1 TTTTTAATATTTTTATATATTTTATTAA
** *
16691583 AATTTAATATTTTT-TATAACTTTTATTGA
1 TTTTTAATATTTTTATAT-A-TTTTATTAA
16691612 TTTTTA
1 TTTTTA
16691618 TCCTTTATAA
Statistics
Matches: 51, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
27 3 0.06
28 16 0.31
29 26 0.51
30 6 0.12
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (28 bp):
TTTTTAATATTTTTATATATTTTATTAA
Found at i:16694185 original size:25 final size:25
Alignment explanation
Indices: 16694151--16694201 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
16694141 CCACTTAAGG
16694151 TTGTGTTGTTGGTGAGTGGAGATTT
1 TTGTGTTGTTGGTGAGTGGAGATTT
16694176 TTGTGTTGTTGGTGAGTGGAGATTT
1 TTGTGTTGTTGGTGAGTGGAGATTT
16694201 T
1 T
16694202 CATTTCAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.12, C:0.00, G:0.39, T:0.49
Consensus pattern (25 bp):
TTGTGTTGTTGGTGAGTGGAGATTT
Found at i:16700879 original size:24 final size:24
Alignment explanation
Indices: 16700846--16700895 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
16700836 TTTATTTATA
*
16700846 TATTTTTATATAAGAAATTAATAT
1 TATTTATATATAAGAAATTAATAT
** *
16700870 TATTTATATATTTGTAATTAATAT
1 TATTTATATATAAGAAATTAATAT
16700894 TA
1 TA
16700896 GCAATGTATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (24 bp):
TATTTATATATAAGAAATTAATAT
Found at i:16711872 original size:2 final size:2
Alignment explanation
Indices: 16711865--16711903 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
16711855 NNNNNNNNNG
16711865 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16711904 CTAATTTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16714428 original size:163 final size:163
Alignment explanation
Indices: 16714158--16714457 Score: 591
Period size: 163 Copynumber: 1.8 Consensus size: 163
16714148 GGTCGTACTT
16714158 AATGAAACCTAGAAATGATGATCTTCTCTAGTTGATGTTGTTTTTCGTCACCAGCTTGTCACTTA
1 AATGAAACCTAGAAATGATGATCTTCTCTAGTTGATGTTGTTTTTCGTCACCAGCTTGTCACTTA
16714223 TTGAAACCAAGGATTACAATATCGAATGCTTTGTGGCTAATTACTCTTGACTTTGTCAAGCCTGA
66 TTGAAACCAAGGATTACAATATCGAATGCTTTGTGGCTAATTACTCTTGACTTTGTCAAGCCTGA
16714288 GTGACTATTTAGTTAATTTCATAATTGATCACG
131 GTGACTATTTAGTTAATTTCATAATTGATCACG
*
16714321 AATGAAACCTAGAAATGATGATCTTCTCTAGTTGATGTTGTTTTTCGTCACCAGCTTGTCACTTT
1 AATGAAACCTAGAAATGATGATCTTCTCTAGTTGATGTTGTTTTTCGTCACCAGCTTGTCACTTA
16714386 TTGAAACCAAGGATTACAATATCGAATGCTTTGTGGCTAATTACTCTTGACTTTGTCAAGCCTGA
66 TTGAAACCAAGGATTACAATATCGAATGCTTTGTGGCTAATTACTCTTGACTTTGTCAAGCCTGA
16714451 GTGACTA
131 GTGACTA
16714458 ATTGATCACG
Statistics
Matches: 136, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
163 136 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.37
Consensus pattern (163 bp):
AATGAAACCTAGAAATGATGATCTTCTCTAGTTGATGTTGTTTTTCGTCACCAGCTTGTCACTTA
TTGAAACCAAGGATTACAATATCGAATGCTTTGTGGCTAATTACTCTTGACTTTGTCAAGCCTGA
GTGACTATTTAGTTAATTTCATAATTGATCACG
Found at i:16717291 original size:29 final size:29
Alignment explanation
Indices: 16717232--16717290 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
16717222 TTTGGTTTAC
* *
16717232 TGTGCAGTTTTATATATAAACTTTAATTT
1 TGTGCAATTTTATATAGAAACTTTAATTT
* *
16717261 TGTGCAATTTTATATAAGAAATTTTGATTT
1 TGTGCAATTTTATAT-AGAAACTTTAATTT
16717291 GATCTAATTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.51
Consensus pattern (29 bp):
TGTGCAATTTTATATAGAAACTTTAATTT
Found at i:16722494 original size:15 final size:16
Alignment explanation
Indices: 16722476--16722515 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
16722466 TCAAAGTCCT
16722476 AAAACAAAAAGAAA-A
1 AAAACAAAAAGAAAGA
*
16722491 AAAAAAAAAAGAAAGA
1 AAAACAAAAAGAAAGA
16722507 AAGAACAAA
1 AA-AACAAA
16722516 TCTGAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 13 0.62
16 3 0.14
17 5 0.24
ACGTcount: A:0.85, C:0.05, G:0.10, T:0.00
Consensus pattern (16 bp):
AAAACAAAAAGAAAGA
Found at i:16723030 original size:16 final size:15
Alignment explanation
Indices: 16723004--16723033 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
16722994 AATTATCACT
16723004 CCTTTCCTTGCCTTG
1 CCTTTCCTTGCCTTG
16723019 CCTTTGCCTTGCCTT
1 CCTTT-CCTTGCCTT
16723034 TCATTATCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.00, C:0.40, G:0.13, T:0.47
Consensus pattern (15 bp):
CCTTTCCTTGCCTTG
Found at i:16724822 original size:28 final size:30
Alignment explanation
Indices: 16724752--16724822 Score: 76
Period size: 28 Copynumber: 2.4 Consensus size: 30
16724742 TTTTTAAAAT
* *
16724752 TAAAAAATTAATAAAAAATGTACAAATTATTT
1 TAAAAAATT-A-AAAAAATGTAAAAATTATTA
*
16724784 TAAAAAA-TAAAAATAT-TAAAAATTA-TA
1 TAAAAAATTAAAAAAATGTAAAAATTATTA
16724811 TAAAAAATTAAA
1 TAAAAAATTAAA
16724823 TACTTTTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
27 8 0.23
28 12 0.34
29 6 0.17
30 1 0.03
31 1 0.03
32 7 0.20
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (30 bp):
TAAAAAATTAAAAAAATGTAAAAATTATTA
Done.