Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 109 of 125
Found at i:33183360 original size:15 final size:15
Alignment explanation
Indices: 33183327--33183361 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
33183317 GTTCATTTGG
**
33183327 TTTGGTTTAAATGGG
1 TTTGGTTTAAATGAA
33183342 TTTGGTTTAAATGAA
1 TTTGGTTTAAATGAA
33183357 TTTGG
1 TTTGG
33183362 GTTTGGTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.29, T:0.49
Consensus pattern (15 bp):
TTTGGTTTAAATGAA
Found at i:33183364 original size:21 final size:21
Alignment explanation
Indices: 33183338--33183405 Score: 118
Period size: 21 Copynumber: 3.2 Consensus size: 21
33183328 TTGGTTTAAA
33183338 TGGGTTTGGTTTAAATGAATT
1 TGGGTTTGGTTTAAATGAATT
*
33183359 TGGGTTTGGTTTAAATGAATG
1 TGGGTTTGGTTTAAATGAATT
33183380 TGGGTTTGGTTTAAATAGAATT
1 TGGGTTTGGTTTAAAT-GAATT
33183402 TGGG
1 TGGG
33183406 CTTAATGGGT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
21 36 0.82
22 8 0.18
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (21 bp):
TGGGTTTGGTTTAAATGAATT
Found at i:33183825 original size:18 final size:17
Alignment explanation
Indices: 33183796--33183843 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
33183786 GAAAATAGAA
33183796 AAGAAAAGAGAAA-GAAAT
1 AAGAAAA-AGAAATG-AAT
33183814 AAGAAATAAGAAATGAAT
1 AAGAAA-AAGAAATGAAT
*
33183832 GAGAAAAAGAAA
1 AAGAAAAAGAAA
33183844 AGAGAAAGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 6 0.22
18 19 0.70
19 2 0.07
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.08
Consensus pattern (17 bp):
AAGAAAAAGAAATGAAT
Found at i:33190333 original size:6 final size:7
Alignment explanation
Indices: 33190308--33190354 Score: 51
Period size: 7 Copynumber: 6.9 Consensus size: 7
33190298 TTTTTGAAAA
33190308 AGTCAAC
1 AGTCAAC
*
33190315 AGTTAAC
1 AGTCAAC
33190322 AGTCAA-
1 AGTCAAC
33190328 AGTCAAC
1 AGTCAAC
*
33190335 GGTCAAC
1 AGTCAAC
*
33190342 GGTCAAC
1 AGTCAAC
*
33190349 GGTCAA
1 AGTCAA
33190355 TCAACATCGA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
6 6 0.17
7 30 0.83
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.17
Consensus pattern (7 bp):
AGTCAAC
Found at i:33190339 original size:7 final size:7
Alignment explanation
Indices: 33190329--33190354 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
33190319 AACAGTCAAA
33190329 GTCAACG
1 GTCAACG
33190336 GTCAACG
1 GTCAACG
33190343 GTCAACG
1 GTCAACG
33190350 GTCAA
1 GTCAA
33190355 TCAACATCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.27, G:0.27, T:0.15
Consensus pattern (7 bp):
GTCAACG
Found at i:33190346 original size:20 final size:20
Alignment explanation
Indices: 33190306--33190347 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
33190296 TTTTTTTGAA
*
33190306 AAAGTCAACAGTTAACAGTC
1 AAAGTCAACAGTCAACAGTC
* *
33190326 AAAGTCAACGGTCAACGGTC
1 AAAGTCAACAGTCAACAGTC
33190346 AA
1 AA
33190348 CGGTCAATCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.43, C:0.21, G:0.19, T:0.17
Consensus pattern (20 bp):
AAAGTCAACAGTCAACAGTC
Found at i:33190380 original size:10 final size:10
Alignment explanation
Indices: 33190341--33190398 Score: 53
Period size: 10 Copynumber: 5.7 Consensus size: 10
33190331 CAACGGTCAA
33190341 CGGTCAACGGT
1 CGGTCAAC-GT
** *
33190352 CAATCAACAT
1 CGGTCAACGT
*
33190362 CGATCAACGT
1 CGGTCAACGT
*
33190372 CGGTCAACGC
1 CGGTCAACGT
*
33190382 CAGTCAACGT
1 CGGTCAACGT
33190392 CGGTCAA
1 CGGTCAA
33190399 TGGTTTGACT
Statistics
Matches: 37, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
10 31 0.84
11 6 0.16
ACGTcount: A:0.29, C:0.31, G:0.22, T:0.17
Consensus pattern (10 bp):
CGGTCAACGT
Found at i:33190455 original size:15 final size:15
Alignment explanation
Indices: 33190435--33190464 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
33190425 TGGTTCATTT
33190435 GGTTTGGTTCAAATG
1 GGTTTGGTTCAAATG
*
33190450 GGTTTGGTTTAAATG
1 GGTTTGGTTCAAATG
33190465 AATTTGGGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.03, G:0.33, T:0.43
Consensus pattern (15 bp):
GGTTTGGTTCAAATG
Found at i:33190474 original size:21 final size:21
Alignment explanation
Indices: 33190448--33190515 Score: 100
Period size: 21 Copynumber: 3.2 Consensus size: 21
33190438 TTGGTTCAAA
33190448 TGGGTTTGGTTTAAATGAATT
1 TGGGTTTGGTTTAAATGAATT
*
33190469 TGGGTTTGGTTTAAATGAATG
1 TGGGTTTGGTTTAAATGAATT
* *
33190490 TGAGTTTGGTTTAAATAGAGTT
1 TGGGTTTGGTTTAAAT-GAATT
33190512 TGGG
1 TGGG
33190516 CTTAATGGGT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
21 35 0.85
22 6 0.15
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (21 bp):
TGGGTTTGGTTTAAATGAATT
Found at i:33190908 original size:12 final size:11
Alignment explanation
Indices: 33190886--33190960 Score: 71
Period size: 11 Copynumber: 6.5 Consensus size: 11
33190876 AAGTGTGATT
33190886 AAAAGAGAAAG
1 AAAAGAGAAAG
*
33190897 AAAATAGAAAAG
1 AAAAGAG-AAAG
33190909 AAAAGAGAAAG
1 AAAAGAGAAAG
33190920 AAATA-AGAAATG
1 AAA-AGAGAAA-G
* *
33190932 AATGAGAAAAAG
1 AA-AAGAGAAAG
33190944 AAAAGAGAAAG
1 AAAAGAGAAAG
*
33190955 GAAAGA
1 AAAAGA
33190961 TGTGAGGCTT
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
11 30 0.58
12 18 0.35
13 4 0.08
ACGTcount: A:0.71, C:0.00, G:0.24, T:0.05
Consensus pattern (11 bp):
AAAAGAGAAAG
Found at i:33194330 original size:19 final size:17
Alignment explanation
Indices: 33194292--33194324 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
33194282 TAACATTGCA
*
33194292 TTTTAAATAATATAAAC
1 TTTTAAAAAATATAAAC
33194309 TTTTAAAAAATATAAA
1 TTTTAAAAAATATAAA
33194325 AACTTTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (17 bp):
TTTTAAAAAATATAAAC
Found at i:33195727 original size:51 final size:51
Alignment explanation
Indices: 33195623--33195735 Score: 129
Period size: 51 Copynumber: 2.2 Consensus size: 51
33195613 TTTTGTAAAT
* ** *
33195623 TAAATTTGATAAATCAAGACCAACTTGACAAAATGTGTAAATGTTGTGGGC
1 TAAATTTGTTAAATCAAGACCAACTTGACAAAATGTGTAAATGTTAAGAGC
* * * *
33195674 TAAATTTGTTAAATTAGGACCAAGTTGATAAAATGTGTAAACT-TTAAGAGC
1 TAAATTTGTTAAATCAAGACCAACTTGACAAAATGTGTAAA-TGTTAAGAGC
*
33195725 TAAATTGGTTA
1 TAAATTTGTTA
33195736 TTATATCAAT
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
51 51 0.98
52 1 0.02
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.33
Consensus pattern (51 bp):
TAAATTTGTTAAATCAAGACCAACTTGACAAAATGTGTAAATGTTAAGAGC
Found at i:33199419 original size:46 final size:44
Alignment explanation
Indices: 33199367--33199453 Score: 120
Period size: 46 Copynumber: 1.9 Consensus size: 44
33199357 CAACTAAAGT
* * *
33199367 TGTAACTAGCAATATTGACACATACATGTCTAATTGCAATCAACAC
1 TGTAACTAGCAACATTCACACATACATGACTAA-TG-AATCAACAC
*
33199413 TGTAACTAGCAACATTCACACATGCATGACTAATGAATCAA
1 TGTAACTAGCAACATTCACACATACATGACTAATGAATCAA
33199454 ATGCTGAAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
44 6 0.16
45 2 0.05
46 29 0.78
ACGTcount: A:0.40, C:0.22, G:0.11, T:0.26
Consensus pattern (44 bp):
TGTAACTAGCAACATTCACACATACATGACTAATGAATCAACAC
Found at i:33214688 original size:14 final size:14
Alignment explanation
Indices: 33214669--33214700 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
33214659 AACATACAAT
33214669 TATATATATATGTA
1 TATATATATATGTA
33214683 TATATATATATGTA
1 TATATATATATGTA
33214697 TATA
1 TATA
33214701 GAAGAGGTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (14 bp):
TATATATATATGTA
Found at i:33214872 original size:6 final size:6
Alignment explanation
Indices: 33214861--33214890 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
33214851 TAAACAGCAT
33214861 CTTTTG CTTTTG CTTTTG CTTTTG CTTTTG
1 CTTTTG CTTTTG CTTTTG CTTTTG CTTTTG
33214891 TATATCGCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.17, T:0.67
Consensus pattern (6 bp):
CTTTTG
Found at i:33218091 original size:17 final size:19
Alignment explanation
Indices: 33218069--33218105 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
33218059 TTTTATATAT
33218069 TCATAT-TAA-CATATTCA
1 TCATATATAATCATATTCA
*
33218086 TCATATATAATTATATTCA
1 TCATATATAATCATATTCA
33218105 T
1 T
33218106 TTCTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.35
18 3 0.18
19 8 0.47
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.46
Consensus pattern (19 bp):
TCATATATAATCATATTCA
Found at i:33221627 original size:20 final size:20
Alignment explanation
Indices: 33221581--33221623 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
33221571 TAATATTTTT
* *
33221581 AATATTTATAAAATCAAGTA
1 AATATTTATAAAATAAAATA
33221601 AATATTTA-AAAATAAAATA
1 AATATTTATAAAATAAAATA
33221620 AATA
1 AATA
33221624 ATTTTTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (20 bp):
AATATTTATAAAATAAAATA
Found at i:33229909 original size:30 final size:30
Alignment explanation
Indices: 33229868--33229926 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
33229858 ATATTCAAGA
*
33229868 TTTGGGACAAATATGTAACTAAAGGCGTTC
1 TTTGAGACAAATATGTAACTAAAGGCGTTC
33229898 TTTGAGACAAATATGTAACTAAAGGCGTT
1 TTTGAGACAAATATGTAACTAAAGGCGTT
33229927 GAAATCAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.31
Consensus pattern (30 bp):
TTTGAGACAAATATGTAACTAAAGGCGTTC
Found at i:33230190 original size:15 final size:15
Alignment explanation
Indices: 33230170--33230200 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
33230160 ACTAAAACGT
33230170 AACATTTCAAATATA
1 AACATTTCAAATATA
*
33230185 AACATTTTAAATATA
1 AACATTTCAAATATA
33230200 A
1 A
33230201 GTGACTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (15 bp):
AACATTTCAAATATA
Found at i:33233703 original size:16 final size:17
Alignment explanation
Indices: 33233663--33233703 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 17
33233653 ATATAATGAG
33233663 ATTAATAAAATATCAAA
1 ATTAATAAAATATCAAA
33233680 ATTGAATAAAAT-T-AAA
1 ATT-AATAAAATATCAAA
33233696 ATATAATA
1 AT-TAATA
33233704 TATATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 9 0.41
17 5 0.23
18 8 0.36
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.32
Consensus pattern (17 bp):
ATTAATAAAATATCAAA
Found at i:33242431 original size:17 final size:17
Alignment explanation
Indices: 33242409--33242447 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
33242399 GATGTGTAAG
33242409 AAAAAATAATAAA-AAAT
1 AAAAAATAA-AAATAAAT
*
33242426 AAAAAATAAAAATCAAT
1 AAAAAATAAAAATAAAT
33242443 AAAAA
1 AAAAA
33242448 TTGTACAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (17 bp):
AAAAAATAAAAATAAAT
Found at i:33242600 original size:29 final size:28
Alignment explanation
Indices: 33242519--33242608 Score: 85
Period size: 28 Copynumber: 3.2 Consensus size: 28
33242509 ATAAAATTTG
* * *
33242519 TAAAATTTATAAAAACCAT-AGAAAATCA
1 TAAAATATATAAAAA-TATAAGAAAATTA
*
33242547 TAAAATATATAAAAATATAAAAAAATTA
1 TAAAATATATAAAAATATAAGAAAATTA
* *
33242575 TAAAAT-TTTATAAAGTCATAAGAAAATTA
1 TAAAATATATA-AAAAT-ATAAGAAAATTA
33242604 TAAAA
1 TAAAA
33242609 AATGTAAAGA
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
27 5 0.10
28 31 0.60
29 16 0.31
ACGTcount: A:0.63, C:0.04, G:0.03, T:0.29
Consensus pattern (28 bp):
TAAAATATATAAAAATATAAGAAAATTA
Found at i:33242651 original size:20 final size:20
Alignment explanation
Indices: 33242597--33242651 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 20
33242587 AAGTCATAAG
*
33242597 AAAATTATAAAA-AATGTAA
1 AAAATTATAAAATTATGTAA
*
33242616 AGAAA-TA-AAAATTTATTTAA
1 A-AAATTATAAAA-TTATGTAA
33242636 AAAATTATAAAATTAT
1 AAAATTATAAAATTAT
33242652 CGTACCAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
18 4 0.14
19 6 0.21
20 15 0.52
21 4 0.14
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.33
Consensus pattern (20 bp):
AAAATTATAAAATTATGTAA
Found at i:33242863 original size:29 final size:30
Alignment explanation
Indices: 33242838--33242903 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 30
33242828 TATTTTTGTG
33242838 ATTTTTATA-AAATTTTAC-AATTTTTTAT
1 ATTTTTATATAAATTTTACTAATTTTTTAT
* * *
33242866 ATTTTT-TATATATTTTTCTAATTTTTTCT
1 ATTTTTATATAAATTTTACTAATTTTTTAT
33242895 AATTTTTAT
1 -ATTTTTAT
33242904 TGATTTTTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
27 2 0.06
28 13 0.42
29 9 0.29
30 6 0.19
31 1 0.03
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (30 bp):
ATTTTTATATAAATTTTACTAATTTTTTAT
Found at i:33242893 original size:10 final size:10
Alignment explanation
Indices: 33242839--33242901 Score: 58
Period size: 10 Copynumber: 6.4 Consensus size: 10
33242829 ATTTTTGTGA
*
33242839 TTTTTATAAA
1 TTTTTATAAT
* *
33242849 ATTTTACAAT
1 TTTTTATAAT
33242859 TTTTTAT-AT
1 TTTTTATAAT
33242868 TTTTTAT-AT
1 TTTTTATAAT
*
33242877 ATTTTTCTAAT
1 -TTTTTATAAT
*
33242888 TTTTTCTAAT
1 TTTTTATAAT
33242898 TTTT
1 TTTT
33242902 ATTGATTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
9 11 0.24
10 32 0.71
11 2 0.04
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:33242909 original size:29 final size:29
Alignment explanation
Indices: 33242838--33242927 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 29
33242828 TATTTTTGTG
* *
33242838 ATTTTTATAAAATTTTAC-AATTTTTTATA
1 ATTTTTAT-ATATTTTTCTAATTTTTTATA
* *
33242867 TTTTTTATATATTTTTCTAATTTTTTCTA
1 ATTTTTATATATTTTTCTAATTTTTTATA
*
33242896 ATTTTTAT-TGA-TTTT-T-ACTTTTTATA
1 ATTTTTATAT-ATTTTTCTAATTTTTTATA
33242922 ATTTTT
1 ATTTTT
33242928 TTACCACAAG
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
26 14 0.27
27 1 0.02
28 12 0.23
29 25 0.48
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.68
Consensus pattern (29 bp):
ATTTTTATATATTTTTCTAATTTTTTATA
Found at i:33242926 original size:9 final size:9
Alignment explanation
Indices: 33242822--33242927 Score: 63
Period size: 9 Copynumber: 11.4 Consensus size: 9
33242812 TTTTGATGCA
*
33242822 TTTTATTAT
1 TTTTATAAT
* *
33242831 TTTTGTGAT
1 TTTTATAAT
*
33242840 TTTTATAAAA
1 TTTTAT-AAT
*
33242850 TTTTACAATT
1 TTTTATAA-T
*
33242860 TTTTATATT
1 TTTTATAAT
33242869 TTTTATATAT
1 TTTTATA-AT
*
33242879 TTTTCTAATT
1 TTTTATAA-T
*
33242889 TTTTCTAAT
1 TTTTATAAT
*
33242898 TTTTATTGA-
1 TTTTA-TAAT
*
33242907 TTTT-TACT
1 TTTTATAAT
33242915 TTTTATAAT
1 TTTTATAAT
33242924 TTTT
1 TTTT
33242928 TTACCACAAG
Statistics
Matches: 74, Mismatches: 16, Indels: 14
0.71 0.15 0.13
Matches are distributed among these distances:
7 1 0.01
8 4 0.05
9 39 0.53
10 30 0.41
ACGTcount: A:0.25, C:0.04, G:0.03, T:0.69
Consensus pattern (9 bp):
TTTTATAAT
Found at i:33245081 original size:15 final size:16
Alignment explanation
Indices: 33245063--33245095 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
33245053 TAATTTTTTA
33245063 AAATTATAAAAAT-AT
1 AAATTATAAAAATGAT
*
33245078 AAATTATTAAAATGAT
1 AAATTATAAAAATGAT
33245094 AA
1 AA
33245096 TTTTATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (16 bp):
AAATTATAAAAATGAT
Found at i:33251007 original size:29 final size:30
Alignment explanation
Indices: 33250935--33251024 Score: 110
Period size: 30 Copynumber: 2.9 Consensus size: 30
33250925 TGTTTTAATA
*
33250935 ATGTATGAAAATTACACCAAATCAAAATTAC
1 ATGTAT-AAAATTACACAAAATCAAAATTAC
* **
33250966 ATGTATAAAATTACATAAAATCAATGTT-C
1 ATGTATAAAATTACACAAAATCAAAATTAC
33250995 ATGTATAAAATTACACATTAAATCAAAATT
1 ATGTATAAAATTACACA--AAATCAAAATT
33251025 TATACATAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
29 17 0.34
30 18 0.36
31 15 0.30
ACGTcount: A:0.51, C:0.12, G:0.06, T:0.31
Consensus pattern (30 bp):
ATGTATAAAATTACACAAAATCAAAATTAC
Found at i:33255101 original size:18 final size:17
Alignment explanation
Indices: 33255059--33255101 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
33255049 CAAAAATGAT
*
33255059 AAAAACAAATAATATTC
1 AAAAAAAAATAATATTC
33255076 AAATAAAAAATAATTAATTC
1 AAA-AAAAAATAA-T-ATTC
33255096 AAAAAA
1 AAAAAA
33255102 CTATAAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 3 0.14
18 8 0.36
19 4 0.18
20 7 0.32
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (17 bp):
AAAAAAAAATAATATTC
Found at i:33258599 original size:30 final size:31
Alignment explanation
Indices: 33258553--33258615 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 31
33258543 AAAAATAATT
* *
33258553 AACTTACAAATAGATAAATAAACATCCACAA
1 AACTTACAAAAAGATAAATAAACATCAACAA
*
33258584 AACTTA-AAAAAGATAAATGAACATCAACAA
1 AACTTACAAAAAGATAAATAAACATCAACAA
33258614 AA
1 AA
33258616 TCTAATTGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 23 0.79
31 6 0.21
ACGTcount: A:0.62, C:0.16, G:0.05, T:0.17
Consensus pattern (31 bp):
AACTTACAAAAAGATAAATAAACATCAACAA
Found at i:33261136 original size:11 final size:11
Alignment explanation
Indices: 33261102--33261127 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
33261092 TATTATCTTA
33261102 TATTATAATAT
1 TATTATAATAT
33261113 TATTATAATAT
1 TATTATAATAT
33261124 TATT
1 TATT
33261128 TTTATATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
TATTATAATAT
Found at i:33263585 original size:24 final size:23
Alignment explanation
Indices: 33263551--33263635 Score: 82
Period size: 24 Copynumber: 3.6 Consensus size: 23
33263541 TAGAAAACCT
* *
33263551 GGAGGCATGCCTGGTGGGTTTCCA
1 GGAGGAATGCCTGG-GGTTTTCCA
* *
33263575 GGTGGAATGCCTGGGGTTTTCCT
1 GGAGGAATGCCTGGGGTTTTCCA
* *
33263598 GGAGGTATGCCTGGAGGTTTTCCT
1 GGAGGAATGCCTGG-GGTTTTCCA
33263622 GGA-GATATGCCTGG
1 GGAGGA-ATGCCTGG
33263636 AGGAATGCCT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
23 20 0.38
24 32 0.62
ACGTcount: A:0.13, C:0.18, G:0.40, T:0.29
Consensus pattern (23 bp):
GGAGGAATGCCTGGGGTTTTCCA
Found at i:33263612 original size:12 final size:12
Alignment explanation
Indices: 33263581--33263672 Score: 78
Period size: 12 Copynumber: 7.8 Consensus size: 12
33263571 TCCAGGTGGA
33263581 ATGCCTGG-GGT
1 ATGCCTGGAGGT
* *
33263592 TTTCCTGGAGGT
1 ATGCCTGGAGGT
33263604 ATGCCTGGAGGT
1 ATGCCTGGAGGT
* * *
33263616 TTTCCTGGAGAT
1 ATGCCTGGAGGT
*
33263628 ATGCCTGGAGGA
1 ATGCCTGGAGGT
* *
33263640 ATGCCTGGTGGC
1 ATGCCTGGAGGT
* * *
33263652 ATGCCAGGTGGC
1 ATGCCTGGAGGT
33263664 ATGCCTGGA
1 ATGCCTGGA
33263673 AATGTTGATT
Statistics
Matches: 64, Mismatches: 16, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
11 6 0.09
12 58 0.91
ACGTcount: A:0.15, C:0.20, G:0.38, T:0.27
Consensus pattern (12 bp):
ATGCCTGGAGGT
Found at i:33263636 original size:24 final size:24
Alignment explanation
Indices: 33263581--33263638 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
33263571 TCCAGGTGGA
*
33263581 ATGCCTGG-GGTTTTCCTGGAGGT
1 ATGCCTGGAGGTTTTCCTGGAGAT
33263604 ATGCCTGGAGGTTTTCCTGGAGAT
1 ATGCCTGGAGGTTTTCCTGGAGAT
33263628 ATGCCTGGAGG
1 ATGCCTGGAGG
33263639 AATGCCTGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 8 0.24
24 25 0.76
ACGTcount: A:0.14, C:0.17, G:0.38, T:0.31
Consensus pattern (24 bp):
ATGCCTGGAGGTTTTCCTGGAGAT
Found at i:33271540 original size:2 final size:2
Alignment explanation
Indices: 33271535--33271563 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
33271525 TTTATGTGTG
33271535 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 T
33271564 CACCAGCTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33278575 original size:28 final size:26
Alignment explanation
Indices: 33278543--33278617 Score: 71
Period size: 28 Copynumber: 2.7 Consensus size: 26
33278533 ATTTCTATAA
33278543 ATTTTGTATATTTAAAATTT-ATTTTCT
1 ATTTT-TAT-TTTAAAATTTAATTTTCT
*
33278570 ATTTTTATTTTTAAAAATTTAATTTTTT
1 ATTTTTA-TTTT-AAAATTTAATTTTCT
*
33278598 ACTTTTCAATTTTAAAATTT
1 A-TTTT-TATTTTAAAATTT
33278618 CAGTCGTAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
26 5 0.12
27 13 0.32
28 14 0.34
29 8 0.20
30 1 0.02
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.63
Consensus pattern (26 bp):
ATTTTTATTTTAAAATTTAATTTTCT
Found at i:33278610 original size:29 final size:27
Alignment explanation
Indices: 33278556--33278614 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 27
33278546 TTGTATATTT
* *
33278556 AAAATTTATTTTCTATTTTTATTTTTA
1 AAAATTTATTTTCTATTTTCAATTTTA
*
33278583 AAAATTTAATTTTTTACTTTTCAATTTTA
1 AAAATTT-ATTTTCTA-TTTTCAATTTTA
33278612 AAA
1 AAA
33278615 TTTCAGTCGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 7 0.26
28 7 0.26
29 13 0.48
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (27 bp):
AAAATTTATTTTCTATTTTCAATTTTA
Found at i:33280790 original size:18 final size:18
Alignment explanation
Indices: 33280767--33280801 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
33280757 ACAAGAAAAT
33280767 GGAAACATATAAGGGTTA
1 GGAAACATATAAGGGTTA
*
33280785 GGAAACTTATAAGGGTT
1 GGAAACATATAAGGGTT
33280802 TTGATACGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.06, G:0.29, T:0.26
Consensus pattern (18 bp):
GGAAACATATAAGGGTTA
Found at i:33282369 original size:9 final size:9
Alignment explanation
Indices: 33282355--33282462 Score: 55
Period size: 9 Copynumber: 11.8 Consensus size: 9
33282345 GGCTATTCAC
33282355 ATAAAAATT
1 ATAAAAATT
*
33282364 ATAAAAAAT
1 ATAAAAATT
33282373 ATTAATTAAATT
1 A-TAA--AAATT
*
33282385 ATAAAAATA
1 ATAAAAATT
*
33282394 ATAAAAATA
1 ATAAAAATT
*
33282403 ATCAAATATT
1 AT-AAAAATT
*
33282413 ATTAAAAATA
1 A-TAAAAATT
* *
33282423 AT-TAAGTT
1 ATAAAAATT
33282431 ATAAAAA--
1 ATAAAAATT
33282438 ATAAAAA-T
1 ATAAAAATT
33282446 ATAATATAA-T
1 ATAA-A-AATT
33282456 ATAAAAA
1 ATAAAAA
33282463 AATAAAATTA
Statistics
Matches: 78, Mismatches: 12, Indels: 19
0.72 0.11 0.17
Matches are distributed among these distances:
7 7 0.09
8 11 0.14
9 29 0.37
10 22 0.28
11 4 0.05
12 5 0.06
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.31
Consensus pattern (9 bp):
ATAAAAATT
Found at i:33282472 original size:46 final size:47
Alignment explanation
Indices: 33282361--33282473 Score: 119
Period size: 46 Copynumber: 2.4 Consensus size: 47
33282351 TCACATAAAA
33282361 ATTATAAAAAATATTAATTAAATTATAAAAATAATAAAAATAATCAAAT
1 ATTATAAAAAATA--AATTAAATTATAAAAATAATAAAAATAATCAAAT
* *
33282410 ATTATTAAAAAT-AATTAAGTTAT-AAAA-AATAAAAAT-AT-AATAT
1 ATTATAAAAAATAAATTAAATTATAAAAATAATAAAAATAATCAA-AT
*
33282453 AATATAAAAAAATAAAATTAA
1 ATTAT-AAAAAAT-AAATTAA
33282474 CTCTTACCAT
Statistics
Matches: 56, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
42 2 0.04
43 8 0.14
44 15 0.27
45 4 0.07
46 16 0.29
49 11 0.20
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (47 bp):
ATTATAAAAAATAAATTAAATTATAAAAATAATAAAAATAATCAAAT
Found at i:33282595 original size:23 final size:22
Alignment explanation
Indices: 33282567--33282645 Score: 83
Period size: 23 Copynumber: 3.6 Consensus size: 22
33282557 TTTAGAGAAT
33282567 TTTAGAGAGAAATTTGTGTGAAA
1 TTTAGAGAGAAATTT-TGTGAAA
* **
33282590 TTT--AGAG-AATTTTGAGAGC
1 TTTAGAGAGAAATTTTGTGAAA
*
33282609 TTTAGAGAGGAATTTATGTGAAA
1 TTTAGAGAGAAATTT-TGTGAAA
33282632 TTTAGAGAGAAATT
1 TTTAGAGAGAAATT
33282646 AAGATAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
19 7 0.16
20 5 0.11
21 8 0.18
22 5 0.11
23 20 0.44
ACGTcount: A:0.38, C:0.01, G:0.25, T:0.35
Consensus pattern (22 bp):
TTTAGAGAGAAATTTTGTGAAA
Found at i:33283280 original size:17 final size:18
Alignment explanation
Indices: 33283249--33283282 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
33283239 AATAAATACA
33283249 AAATATAAAAAACCCAAT
1 AAATATAAAAAACCCAAT
*
33283267 AAAT-TAAAATACCCAA
1 AAATATAAAAAACCCAA
33283283 GTCCAGTACC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.65, C:0.18, G:0.00, T:0.18
Consensus pattern (18 bp):
AAATATAAAAAACCCAAT
Found at i:33283499 original size:29 final size:29
Alignment explanation
Indices: 33283466--33283521 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
33283456 TCAGACACTT
* *
33283466 GCAAAAAAGAGAAAGACAA-AAGACAAAAA
1 GCAAAAAA-ACAAACACAAGAAGACAAAAA
*
33283495 GCAAAGAAACAAACACAAGAAGACAAA
1 GCAAAAAAACAAACACAAGAAGACAAA
33283522 TGTAATCGGC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.70, C:0.14, G:0.16, T:0.00
Consensus pattern (29 bp):
GCAAAAAAACAAACACAAGAAGACAAAAA
Found at i:33284777 original size:12 final size:11
Alignment explanation
Indices: 33284761--33284831 Score: 54
Period size: 12 Copynumber: 5.9 Consensus size: 11
33284751 TTTTATTCAC
33284761 TTATTTATTTT
1 TTATTTATTTT
33284772 TGTATTTATTTT
1 T-TATTTATTTT
*
33284784 ATATACTATCATTTT
1 -T-TA-T-TTATTTT
*
33284799 TATATTCA-TTT
1 T-TATTTATTTT
33284810 TTATTTATTTAT
1 TTATTTATTT-T
33284822 TTATTTATTT
1 TTATTTATTT
33284832 CTTAGGTCAT
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
10 5 0.10
11 7 0.14
12 24 0.47
13 4 0.08
14 5 0.10
15 6 0.12
ACGTcount: A:0.24, C:0.04, G:0.01, T:0.70
Consensus pattern (11 bp):
TTATTTATTTT
Found at i:33285110 original size:30 final size:31
Alignment explanation
Indices: 33285074--33285136 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 31
33285064 ACTTATTGTT
33285074 AATATTT-TAA-TATATGAAATATTAATT-TTA
1 AATATTTCTAAGTA-AT-AAATATTAATTATTA
*
33285104 AATATTTCTAAGTAATTAATATTAATTATTA
1 AATATTTCTAAGTAATAAATATTAATTATTA
33285135 AA
1 AA
33285137 AAAATTAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 17 0.59
31 10 0.34
32 2 0.07
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (31 bp):
AATATTTCTAAGTAATAAATATTAATTATTA
Found at i:33285688 original size:198 final size:197
Alignment explanation
Indices: 33285340--33285736 Score: 611
Period size: 198 Copynumber: 2.0 Consensus size: 197
33285330 ATATATAAAA
* *
33285340 TATAAGTTAAAGAAAAGCCGCCGAGTTTACAAAAACCTGCTTGAAAATTGAAAAAAAGAAGAAAA
1 TATAAGCTAAAGAAAAGCCGCCGAGTTTAAAAAAACCTGCTTGAAAATTGAAAAAAAGAAGAAAA
*
33285405 TAGAAGGGGAGAAGGAAGGAAATAAAAGAGAAGAGAGCAAAAAAAATGGAAGAAAAAAGAAGAAG
66 TAGAAGGGGAGAAGGAAGGAAATAAAAGAGAAGACA-CAAAAAAAATGGAAGAAAAAAGAAGAAG
*
33285470 CAATTGATGTATTATGTAAAAGGTTAAAAAAGTAATCCACTTTCCTAAAAGTTCATTTGGAACTC
130 CAATTGATGTACTATGTAAAAGGTTAAAAAAGTAATCCACTTTCCTAAAAGTTCATTTGGAACTC
33285535 CAC
195 CAC
* * * *
33285538 TATAAGCTAAAGAAAAGCTGTCGAGTTTAGAAAAAACTTGTTTGAAAATTGAAAAAAAAAAGAAG
1 TATAAGCTAAAGAAAAGCCGCCGAGTTTA-AAAAAACCTGCTTGAAAATTG---AAAAAAAGAAG
33285603 AAAATAGAAGGGGAGAAGGAAGGAAATAAAAGAG-AG-CA-AAAAAAAATGGAAGAAAAAAGAAG
62 AAAATAGAAGGGGAGAAGGAAGGAAATAAAAGAGAAGACACAAAAAAAATGGAAGAAAAAAGAAG
* * * *
33285665 AAGCAATTGATGTACTGTGTAAAAGGTTAAAAAAGTAATTCATTTTTCTAAAAGTTCATTTGGAA
127 AAGCAATTGATGTACTATGTAAAAGGTTAAAAAAGTAATCCACTTTCCTAAAAGTTCATTTGGAA
*
33285730 TTCCAC
192 CTCCAC
33285736 T
1 T
33285737 GACCAAAATT
Statistics
Matches: 182, Mismatches: 13, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
198 116 0.64
199 18 0.10
200 1 0.01
201 2 0.01
202 45 0.25
ACGTcount: A:0.51, C:0.08, G:0.21, T:0.20
Consensus pattern (197 bp):
TATAAGCTAAAGAAAAGCCGCCGAGTTTAAAAAAACCTGCTTGAAAATTGAAAAAAAGAAGAAAA
TAGAAGGGGAGAAGGAAGGAAATAAAAGAGAAGACACAAAAAAAATGGAAGAAAAAAGAAGAAGC
AATTGATGTACTATGTAAAAGGTTAAAAAAGTAATCCACTTTCCTAAAAGTTCATTTGGAACTCC
AC
Found at i:33286063 original size:18 final size:20
Alignment explanation
Indices: 33286032--33286077 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 20
33286022 ATTAATTGTA
*
33286032 TTATTTATTAATG-T-TATT
1 TTATTTTTTAATGATATATT
*
33286050 TTATTTTTTTATGTATATATT
1 TTATTTTTTAATG-ATATATT
33286071 TTATTTT
1 TTATTTT
33286078 ATCATCATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 11 0.48
20 1 0.04
21 11 0.48
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (20 bp):
TTATTTTTTAATGATATATT
Found at i:33287159 original size:15 final size:14
Alignment explanation
Indices: 33287093--33287168 Score: 55
Period size: 14 Copynumber: 5.2 Consensus size: 14
33287083 CTTTGTTTTA
*
33287093 TTTATTTATTTATT
1 TTTATTTATTCATT
* *
33287107 TTTATATACCATCATT
1 TTTATTTA--TTCATT
*
33287123 TTT-TATATTCATT
1 TTTATTTATTCATT
*
33287136 TTTATTTATTTATT
1 TTTATTTATTCATT
*
33287150 TTTTTCTTATGTCATT
1 TTTAT-TTAT-TCATT
33287166 TTT
1 TTT
33287169 GTCCTTCTTA
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
13 8 0.16
14 19 0.39
15 8 0.16
16 14 0.29
ACGTcount: A:0.21, C:0.08, G:0.01, T:0.70
Consensus pattern (14 bp):
TTTATTTATTCATT
Found at i:33288519 original size:22 final size:22
Alignment explanation
Indices: 33288494--33288538 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
33288484 ATTTTTAAAA
*
33288494 TTTAAATT-ATATATTATATTAT
1 TTTAAATTCATA-ATCATATTAT
*
33288516 TTTAATTTCATAATCATATTAT
1 TTTAAATTCATAATCATATTAT
33288538 T
1 T
33288539 AATGAAATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTAAATTCATAATCATATTAT
Found at i:33289713 original size:18 final size:18
Alignment explanation
Indices: 33289682--33289740 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
33289672 CTTAAATTTA
* * *
33289682 AAAAATTCATAAATACAT
1 AAAAATTAAAAAATATAT
33289700 AAAAATTAAAAAAT-TAT
1 AAAAATTAAAAAATATAT
*
33289717 TAAAATTGATAAAAATATAT
1 AAAAATT-A-AAAAATATAT
33289737 AAAA
1 AAAA
33289741 TACTCAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
17 8 0.24
18 13 0.39
19 6 0.18
20 6 0.18
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (18 bp):
AAAAATTAAAAAATATAT
Found at i:33289738 original size:10 final size:9
Alignment explanation
Indices: 33289698--33289740 Score: 52
Period size: 10 Copynumber: 4.7 Consensus size: 9
33289688 TCATAAATAC
33289698 ATAAAAATT
1 ATAAAAATT
33289707 A-AAAAATT
1 ATAAAAATT
*
33289715 ATTAAAATT
1 ATAAAAATT
33289724 GATAAAAATAT
1 -ATAAAAAT-T
33289735 ATAAAA
1 ATAAAA
33289741 TACTCAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
8 8 0.28
9 7 0.24
10 13 0.45
11 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (9 bp):
ATAAAAATT
Found at i:33289761 original size:2 final size:2
Alignment explanation
Indices: 33289756--33289782 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
33289746 AAAAAATTAT
33289756 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 T
33289783 TTAATTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33291243 original size:29 final size:28
Alignment explanation
Indices: 33291211--33291278 Score: 91
Period size: 29 Copynumber: 2.4 Consensus size: 28
33291201 ATTTCGTATA
* * *
33291211 TTTAAAATTTACTTTTTCTTATTTTTATT
1 TTTAAAATTTAATTTTT-TTACTTTTAAT
33291240 TTTAAAAATTTAATTTTTTTACTTTTAAT
1 TTT-AAAATTTAATTTTTTTACTTTTAAT
33291269 TTTAAAATTT
1 TTTAAAATTT
33291279 CAACTGTAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
28 7 0.20
29 15 0.43
30 13 0.37
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (28 bp):
TTTAAAATTTAATTTTTTTACTTTTAAT
Found at i:33291250 original size:30 final size:29
Alignment explanation
Indices: 33291214--33291275 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 29
33291204 TCGTATATTT
* * ** *
33291214 AAAATTTACTTTTTCTTATTTTTATTTTTA
1 AAAATTTAATTTTTTTACTTTTAATTTT-A
33291244 AAAATTTAATTTTTTTACTTTTAATTTTA
1 AAAATTTAATTTTTTTACTTTTAATTTTA
33291273 AAA
1 AAA
33291276 TTTCAACTGT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 4 0.15
30 23 0.85
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (29 bp):
AAAATTTAATTTTTTTACTTTTAATTTTA
Found at i:33292763 original size:18 final size:18
Alignment explanation
Indices: 33292740--33292777 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
33292730 CTTCTAACAA
*
33292740 TATTTTTAAAGTAATTTT
1 TATTTTTAAAGTAAGTTT
*
33292758 TATTTTTAAATTAAGTTT
1 TATTTTTAAAGTAAGTTT
33292776 TA
1 TA
33292778 AATATTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (18 bp):
TATTTTTAAAGTAAGTTT
Found at i:33298164 original size:21 final size:21
Alignment explanation
Indices: 33298138--33298202 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
33298128 AACTAAATTT
33298138 TATAAATAAATATACAAAATA
1 TATAAATAAATATACAAAATA
* *
33298159 TATAAAAAAATTTACAAAATTA
1 TATAAATAAATATACAAAA-TA
* *
33298181 TAGAAATTAAATTAAACAAAAT
1 TATAAA-TAAA-TATACAAAAT
33298203 TTTGGCTGTA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 17 0.49
22 7 0.20
23 4 0.11
24 7 0.20
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.29
Consensus pattern (21 bp):
TATAAATAAATATACAAAATA
Found at i:33298360 original size:11 final size:10
Alignment explanation
Indices: 33298331--33298373 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
33298321 ATTTTTAAAT
33298331 AAAAATATT-
1 AAAAATATTA
33298340 -AAAATATTA
1 AAAAATATTA
*
33298349 AACAAATGTTA
1 AA-AAATATTA
33298360 AAAAATATTA
1 AAAAATATTA
33298370 AAAA
1 AAAA
33298374 TTGTAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
8 8 0.28
10 12 0.41
11 9 0.31
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (10 bp):
AAAAATATTA
Found at i:33298382 original size:20 final size:21
Alignment explanation
Indices: 33298340--33298385 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
33298330 TAAAAATATT
*
33298340 AAAATATTAAACAAATGTTAA
1 AAAATATTAAACAAATGTAAA
*
33298361 AAAATATTAAA-AATTGTAAA
1 AAAATATTAAACAAATGTAAA
33298381 AAAAT
1 AAAAT
33298386 TGTAAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.28
Consensus pattern (21 bp):
AAAATATTAAACAAATGTAAA
Found at i:33298392 original size:29 final size:28
Alignment explanation
Indices: 33298330--33298385 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 28
33298320 AATTTTTAAA
*
33298330 TAAAAATATTAAAATATTAAACAAATGT
1 TAAAAATATTAAAATATTAAAAAAATGT
33298358 TAAAAAATATTAAAA-ATTGTAAAAAAAT
1 T-AAAAATATTAAAATA-T-TAAAAAAAT
33298386 TGTAAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 2 0.08
29 14 0.58
30 8 0.33
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (28 bp):
TAAAAATATTAAAATATTAAAAAAATGT
Found at i:33305767 original size:19 final size:18
Alignment explanation
Indices: 33305743--33305806 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 18
33305733 ATCTCCTCAA
33305743 AAATTAACATTTAGTATTT
1 AAATTAA-ATTTAGTATTT
33305762 AAATTAAATTTA-TGATTT
1 AAATTAAATTTAGT-ATTT
*
33305780 AAGATTTAATTTAGTATTT
1 AA-ATTAAATTTAGTATTT
33305799 AAAATTAA
1 -AAATTAA
33305807 TTATTAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
17 1 0.03
18 11 0.28
19 24 0.62
20 3 0.08
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (18 bp):
AAATTAAATTTAGTATTT
Found at i:33306143 original size:29 final size:30
Alignment explanation
Indices: 33306101--33306159 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
33306091 TATGGTTTAA
* * *
33306101 TGTGTAATTATATACGTGAACT-TTGATTT
1 TGTGCAATTATATACATGAAATCTTGATTT
*
33306130 TGTGCAATTTTATACATGAAATCTTGATTT
1 TGTGCAATTATATACATGAAATCTTGATTT
33306160 GATCCAATTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.29, C:0.08, G:0.15, T:0.47
Consensus pattern (30 bp):
TGTGCAATTATATACATGAAATCTTGATTT
Found at i:33306372 original size:29 final size:30
Alignment explanation
Indices: 33306293--33306381 Score: 108
Period size: 31 Copynumber: 3.0 Consensus size: 30
33306283 GATTAAATCA
* * * *
33306293 AAATTAAAGTTTCAAGTATACATTTGAACC
1 AAATTAAAGTTTCATGTATATAATTGCACC
*
33306323 ACAATTAGAGTTTCATGTATATAATTGCACC
1 A-AATTAAAGTTTCATGTATATAATTGCACC
*
33306354 AAATTAAAG-TTCATTTATATAATTGCAC
1 AAATTAAAGTTTCATGTATATAATTGCAC
33306382 ATTAAATCAA
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
29 18 0.35
30 8 0.16
31 25 0.49
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.36
Consensus pattern (30 bp):
AAATTAAAGTTTCATGTATATAATTGCACC
Found at i:33307149 original size:16 final size:16
Alignment explanation
Indices: 33307128--33307159 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
33307118 TACACTTGAA
33307128 AAATAATAAATTAAAT
1 AAATAATAAATTAAAT
33307144 AAATAATAAATTAAAT
1 AAATAATAAATTAAAT
33307160 TGAAAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AAATAATAAATTAAAT
Found at i:33308025 original size:31 final size:30
Alignment explanation
Indices: 33307990--33308047 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
33307980 TAAAATAATG
*
33307990 ATTTAGCCCTTATAAAAAAGATAAAAATTTA
1 ATTTAACCCTT-TAAAAAAGATAAAAATTTA
* **
33308021 ATTTAATCCTTTAAAAATTATAAAAAT
1 ATTTAACCCTTTAAAAAAGATAAAAAT
33308048 ATAAGCTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
30 14 0.61
31 9 0.39
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (30 bp):
ATTTAACCCTTTAAAAAAGATAAAAATTTA
Found at i:33313346 original size:35 final size:33
Alignment explanation
Indices: 33313299--33313368 Score: 86
Period size: 35 Copynumber: 2.1 Consensus size: 33
33313289 ATTTCTTTAA
*
33313299 ATATATACAATTGAATCAAAATCAAATATATATAT
1 ATATATACAATTGAATCAAAA-CAAAAAT-TATAT
* * *
33313334 ATATATATAATTGGATGAAAACAAAAATTATAT
1 ATATATACAATTGAATCAAAACAAAAATTATAT
33313367 AT
1 AT
33313369 CAAATCACAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 7 0.23
34 6 0.19
35 18 0.58
ACGTcount: A:0.54, C:0.06, G:0.06, T:0.34
Consensus pattern (33 bp):
ATATATACAATTGAATCAAAACAAAAATTATAT
Found at i:33320441 original size:17 final size:18
Alignment explanation
Indices: 33320416--33320451 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
33320406 ATTTTTTTAG
*
33320416 AAATTAAAAAAAT-TAAA
1 AAATAAAAAAAATGTAAA
33320433 AAATAAAAAAAATGTAAA
1 AAATAAAAAAAATGTAAA
33320451 A
1 A
33320452 CACCATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATAAAAAAAATGTAAA
Found at i:33321430 original size:2 final size:2
Alignment explanation
Indices: 33321423--33321458 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
33321413 ATTATTCTTG
*
33321423 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33321459 CACTCCCAAC
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:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:33324041 original size:13 final size:14
Alignment explanation
Indices: 33324007--33324043 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
33323997 CCTCTTTCTC
*
33324007 CTTTATTTCTTCCA
1 CTTTATTTCTACCA
33324021 CTTT-TTTCTACCA
1 CTTTATTTCTACCA
33324034 -TTTATTTCTA
1 CTTTATTTCTA
33324044 TTTTCTCACT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
12 3 0.14
13 14 0.67
14 4 0.19
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.59
Consensus pattern (14 bp):
CTTTATTTCTACCA
Found at i:33325589 original size:3 final size:3
Alignment explanation
Indices: 33325581--33325606 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
33325571 GTTCTCACTG
33325581 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
33325607 ACTTAACAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:33338073 original size:25 final size:25
Alignment explanation
Indices: 33338039--33338098 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
33338029 GAAAAGATGG
*
33338039 TTAAATTAGGCTTAAAAGTCATTTTT
1 TTAATTTAGGCTTAAAAGT-ATTTTT
** *
33338065 TT-ATTTAGGCTTTTAAGTTTTTTT
1 TTAATTTAGGCTTAAAAGTATTTTT
33338089 TTAATTTAGG
1 TTAATTTAGG
33338099 AAAATATATC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 7 0.24
25 20 0.69
26 2 0.07
ACGTcount: A:0.27, C:0.05, G:0.13, T:0.55
Consensus pattern (25 bp):
TTAATTTAGGCTTAAAAGTATTTTT
Found at i:33349174 original size:26 final size:26
Alignment explanation
Indices: 33349115--33349165 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
33349105 ATATACCAAT
33349115 GAAACAATGCTACCTCAGAGCATACA
1 GAAACAATGCTACCTCAGAGCATACA
33349141 GAAACAATGCTACCTCAGAGCATAC
1 GAAACAATGCTACCTCAGAGCATAC
33349166 TATATCAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.41, C:0.27, G:0.16, T:0.16
Consensus pattern (26 bp):
GAAACAATGCTACCTCAGAGCATACA
Found at i:33358729 original size:6 final size:7
Alignment explanation
Indices: 33358707--33358732 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
33358697 ATAAATAAAA
33358707 TTTAATT
1 TTTAATT
33358714 TTTAATT
1 TTTAATT
33358721 TTTAATT
1 TTTAATT
33358728 TTTAA
1 TTTAA
33358733 AATAATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
TTTAATT
Found at i:33360742 original size:59 final size:59
Alignment explanation
Indices: 33360641--33360810 Score: 214
Period size: 59 Copynumber: 2.8 Consensus size: 59
33360631 GTACTTACGC
* * *
33360641 TTTTTCTTAATTTGGTATTTAAACTTTTTTTTGACCCAATTTGGTACTTAAACTTGATATT
1 TTTTTC-TAATTTGGTACTT-AATTTTTTTTTGACCCAATTTGGTACCTAAACTTGATATT
* * *
33360702 TTTTTCTAATTTGGTACTTAATTTTTTTTTGACCCTATTTGGTACCTGAACTTGGTATT
1 TTTTTCTAATTTGGTACTTAATTTTTTTTTGACCCAATTTGGTACCTAAACTTGATATT
* * * * **
33360761 TTTTCCTAATTTTGTACCTAATTTTTTTTAGATTCAATTTGGTACCTAAA
1 TTTTTCTAATTTGGTACTTAATTTTTTTTTGACCCAATTTGGTACCTAAA
33360811 TTTATTAAAT
Statistics
Matches: 95, Mismatches: 14, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
59 77 0.81
60 12 0.13
61 6 0.06
ACGTcount: A:0.23, C:0.13, G:0.11, T:0.54
Consensus pattern (59 bp):
TTTTTCTAATTTGGTACTTAATTTTTTTTTGACCCAATTTGGTACCTAAACTTGATATT
Found at i:33361067 original size:31 final size:31
Alignment explanation
Indices: 33361020--33361084 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
33361010 AAAGTTTAAG
*
33361020 ATTAAAAAAAATTGTCAAGTTT-AGGTACCAA
1 ATTAAAAAAAAGTGTCAAGTTTGA-GTACCAA
*
33361051 ATTAGAAAAAAGTGTCAAGTTTGAGTACCAA
1 ATTAAAAAAAAGTGTCAAGTTTGAGTACCAA
33361082 ATT
1 ATT
33361085 GAACCAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 30 0.97
32 1 0.03
ACGTcount: A:0.46, C:0.09, G:0.15, T:0.29
Consensus pattern (31 bp):
ATTAAAAAAAAGTGTCAAGTTTGAGTACCAA
Found at i:33361188 original size:9 final size:9
Alignment explanation
Indices: 33361168--33361211 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
33361158 TATCAAATCC
33361168 TTTTCTATAA
1 TTTT-TATAA
*
33361178 TTTTAATAA
1 TTTTTATAA
*
33361187 TTTTTATAT
1 TTTTTATAA
33361196 TTTTTATAA
1 TTTTTATAA
33361205 TTATTTA
1 TT-TTTA
33361212 AAAAATACGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
9 21 0.72
10 8 0.28
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (9 bp):
TTTTTATAA
Found at i:33362933 original size:30 final size:31
Alignment explanation
Indices: 33362869--33362926 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
33362859 TTTGGTGTCC
*
33362869 AAACTTGACATATTTTCTTAATTTGGTACCT
1 AAACTTGACATATTTTCTTAAGTTGGTACCT
*
33362900 AAACTTGATAT-TTTTCTTAAGTTGGTA
1 AAACTTGACATATTTTCTTAAGTTGGTA
33362927 TTTAAACCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (31 bp):
AAACTTGACATATTTTCTTAAGTTGGTACCT
Found at i:33363478 original size:60 final size:57
Alignment explanation
Indices: 33363397--33363566 Score: 155
Period size: 60 Copynumber: 2.9 Consensus size: 57
33363387 AATTGAGCCT
** * *
33363397 AAAAAAAGCTTAGATGCCAAATTAGAAAAAAATATCAAGTTTAAGTGTCAAATTGGGTCC
1 AAAAAAAATTTAGATACCAAATTAGAAAAAAATATCAAGTTTAAAT-TCAAATTGGG--C
* * * * * * * *
33363457 AAAAAAAGTTTA-AGTACCAAATTAGGAAAAAGTGTCAAATTCAAATACTGAATTGGGC
1 AAAAAAAATTTAGA-TACCAAATTAGAAAAAAATATCAAGTTTAAATTC-AAATTGGGC
*
33363515 AAAAAAAATTTAGATACCAAATTAAAAAAAAATA-CAAGTTTAAATATCAAAT
1 AAAAAAAATTTAGATACCAAATTAGAAAAAAATATCAAGTTTAAAT-TCAAAT
33363567 ATTATATTAA
Statistics
Matches: 87, Mismatches: 19, Indels: 11
0.74 0.16 0.09
Matches are distributed among these distances:
57 12 0.14
58 29 0.33
59 3 0.03
60 43 0.49
ACGTcount: A:0.52, C:0.10, G:0.13, T:0.25
Consensus pattern (57 bp):
AAAAAAAATTTAGATACCAAATTAGAAAAAAATATCAAGTTTAAATTCAAATTGGGC
Found at i:33363922 original size:15 final size:15
Alignment explanation
Indices: 33363902--33363951 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
33363892 ACCTGACATC
33363902 AGTGGCGGAACACCA
1 AGTGGCGGAACACCA
33363917 AGTGGC-G-ACACCA
1 AGTGGCGGAACACCA
* * *
33363930 A-TGGAGGAATATCA
1 AGTGGCGGAACACCA
33363944 AGTGGCGG
1 AGTGGCGG
33363952 CACTAAGGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
12 3 0.11
13 8 0.29
14 6 0.21
15 11 0.39
ACGTcount: A:0.32, C:0.20, G:0.36, T:0.12
Consensus pattern (15 bp):
AGTGGCGGAACACCA
Found at i:33364157 original size:4 final size:4
Alignment explanation
Indices: 33364139--33364200 Score: 54
Period size: 4 Copynumber: 15.0 Consensus size: 4
33364129 GGGGAAAAAA
* * *
33364139 AAAG AAAA AAGAG AAAG AAAG AAAG AAAG AAAG -AAG GAAG GAAG AAGGAG
1 AAAG AAAG AA-AG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AA--AG
*
33364189 AAAG AAAA AAAG
1 AAAG AAAG AAAG
33364201 TTAATGTGTT
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
3 3 0.06
4 39 0.80
5 3 0.06
6 4 0.08
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:33364575 original size:20 final size:21
Alignment explanation
Indices: 33364534--33364576 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
33364524 TAATTTACTT
33364534 TAATTTAATTTTGCTAGTTAG
1 TAATTTAATTTTGCTAGTTAG
* *
33364555 TAATTTTATTTTG-TTGTTAG
1 TAATTTAATTTTGCTAGTTAG
33364575 TA
1 TA
33364577 GTAGTAAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58
Consensus pattern (21 bp):
TAATTTAATTTTGCTAGTTAG
Found at i:33364720 original size:96 final size:91
Alignment explanation
Indices: 33364548--33364720 Score: 265
Period size: 96 Copynumber: 1.8 Consensus size: 91
33364538 TTAATTTTGC
* *
33364548 TAGTTAGTAATTTTATTTTGTTGTTAGTAGTAGTAAGTAAAAAATATTGTTTATATTTATTGATT
1 TAGTTAGTAATTCTATTTTGTTGTTAGTAGTAGTAAGTAAAAAATATTGTTCATATTTATTGATT
**
33364613 TAAAATTTAATAATGTTTAAAAAAAT
66 TAAAAAATAATAATGTTTAAAAAAAT
33364639 TAGTTAGTAATTCTATTTTGTTGTTAGTAAGTTGTAGTAAGTAAAAAAATATTGTTCATATTTAT
1 TAGTTAGTAATTCTATTTTGTTGTTAGT-A---GTAGTAAGT-AAAAAATATTGTTCATATTTAT
33364704 TGATTTAAAAAATAATA
61 TGATTTAAAAAATAATA
33364721 TAATAATTTA
Statistics
Matches: 73, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
91 27 0.37
92 1 0.01
95 9 0.12
96 36 0.49
ACGTcount: A:0.39, C:0.01, G:0.13, T:0.47
Consensus pattern (91 bp):
TAGTTAGTAATTCTATTTTGTTGTTAGTAGTAGTAAGTAAAAAATATTGTTCATATTTATTGATT
TAAAAAATAATAATGTTTAAAAAAAT
Found at i:33365899 original size:12 final size:13
Alignment explanation
Indices: 33365876--33365913 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
33365866 AATTCATATC
*
33365876 ACTTTCAATTTCA
1 ACTTTCACTTTCA
33365889 AC-TTCACTTTC-
1 ACTTTCACTTTCA
33365900 ACTTTCACTTTCA
1 ACTTTCACTTTCA
33365913 A
1 A
33365914 TTTTGATCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
11 2 0.09
12 17 0.77
13 3 0.14
ACGTcount: A:0.26, C:0.29, G:0.00, T:0.45
Consensus pattern (13 bp):
ACTTTCACTTTCA
Found at i:33366089 original size:22 final size:22
Alignment explanation
Indices: 33366063--33366108 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
33366053 TAAACATATA
33366063 ATATTTCACATATACATTGTTC
1 ATATTTCACATATACATTGTTC
33366085 ATATTTCACATATACATTGTTC
1 ATATTTCACATATACATTGTTC
33366107 AT
1 AT
33366109 CACATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.04, T:0.46
Consensus pattern (22 bp):
ATATTTCACATATACATTGTTC
Found at i:33366113 original size:18 final size:20
Alignment explanation
Indices: 33366067--33366116 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 20
33366057 CATATAATAT
33366067 TTCACATATACATTGTTCATA
1 TTCACATATACATTGTTCA-A
33366088 TTTCACATATACATTGTTC-A
1 -TTCACATATACATTGTTCAA
33366108 -TCACATATA
1 TTCACATATA
33366117 TATCATCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.32
20 1 0.04
22 18 0.64
ACGTcount: A:0.34, C:0.20, G:0.04, T:0.42
Consensus pattern (20 bp):
TTCACATATACATTGTTCAA
Found at i:33369744 original size:21 final size:21
Alignment explanation
Indices: 33369719--33369765 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
33369709 ACGAGCCACC
*
33369719 GCAATACTTTACTCCTCCCGGA
1 GCAATACTCTACTCCT-CCGGA
33369741 -CAATACTCTACTCCTCCGGA
1 GCAATACTCTACTCCTCCGGA
33369761 GCAAT
1 GCAAT
33369766 TGGACCCTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.26, C:0.36, G:0.13, T:0.26
Consensus pattern (21 bp):
GCAATACTCTACTCCTCCGGA
Found at i:33373027 original size:29 final size:28
Alignment explanation
Indices: 33372980--33373043 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 28
33372970 CACATTACCT
* *
33372980 TTCTTTCCTTCTTCTTTCTTTCCTCTCC
1 TTCTTTCATTCTTCATTCTTTCCTCTCC
*
33373008 TTCTTTCATTCATTCATTCTTTCCTCTCT
1 TTCTTTCATTC-TTCATTCTTTCCTCTCC
33373037 TTCTTTC
1 TTCTTTC
33373044 TCGTTTATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 10 0.31
29 22 0.69
ACGTcount: A:0.05, C:0.34, G:0.00, T:0.61
Consensus pattern (28 bp):
TTCTTTCATTCTTCATTCTTTCCTCTCC
Found at i:33373248 original size:27 final size:27
Alignment explanation
Indices: 33373218--33373269 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
33373208 CCCTTAGTGC
*
33373218 CGCCACTTGATATTCCTCCATTGGTAT
1 CGCCACTTGATATTCCTCCACTGGTAT
* *
33373245 CGCCACTTGGTGTTCCTCCACTGGT
1 CGCCACTTGATATTCCTCCACTGGT
33373270 GTCAGGTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.13, C:0.33, G:0.19, T:0.35
Consensus pattern (27 bp):
CGCCACTTGATATTCCTCCACTGGTAT
Found at i:33386600 original size:43 final size:42
Alignment explanation
Indices: 33386508--33386605 Score: 115
Period size: 43 Copynumber: 2.3 Consensus size: 42
33386498 TGCTAATGAT
* **
33386508 AACGCCGCTATAAAACATGTTCTTTAGCGGCGTTTTTCCCTCA
1 AACGCCGCTA-AAAACATGTTCTTTAGCGGCGCTTTTCCAACA
* * * *
33386551 AGCGCCGCTAAAGACCGTGTTCTTTAGCGGCGCTTTTCTAACA
1 AACGCCGCTAAA-AACATGTTCTTTAGCGGCGCTTTTCCAACA
33386594 AACGCCGCTAAA
1 AACGCCGCTAAA
33386606 TTAACAGATT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 2 0.04
43 44 0.96
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (42 bp):
AACGCCGCTAAAAACATGTTCTTTAGCGGCGCTTTTCCAACA
Found at i:33386957 original size:21 final size:21
Alignment explanation
Indices: 33386886--33386958 Score: 74
Period size: 21 Copynumber: 3.5 Consensus size: 21
33386876 CTTTCTTGTA
* * * *
33386886 GCCTCTGCTTCCCTTGCTGTT
1 GCCTCCGCTTGCCTCGCTGCT
* *
33386907 GTCTCCGCTTGCCTCGTTGCT
1 GCCTCCGCTTGCCTCGCTGCT
* *
33386928 GCTTTCGCTTGCCTCGCTGCT
1 GCCTCCGCTTGCCTCGCTGCT
33386949 GCCTCCGCTT
1 GCCTCCGCTT
33386959 TAAGTTGTAG
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.00, C:0.40, G:0.22, T:0.38
Consensus pattern (21 bp):
GCCTCCGCTTGCCTCGCTGCT
Found at i:33400308 original size:25 final size:25
Alignment explanation
Indices: 33400280--33400327 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
33400270 TAATCATGAC
33400280 ATTATTAATATAATACAAACAATGT
1 ATTATTAATATAATACAAACAATGT
33400305 ATTATTAATATAATACAAACAAT
1 ATTATTAATATAATACAAACAAT
33400328 TTAAGTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.54, C:0.08, G:0.02, T:0.35
Consensus pattern (25 bp):
ATTATTAATATAATACAAACAATGT
Found at i:33408231 original size:32 final size:31
Alignment explanation
Indices: 33408165--33408237 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
33408155 CATTTAAAAC
* *
33408165 AATAATTAAACTACTCCCATTAACAAATATT
1 AATAATTAAACTACTCCCATTAAAAAATACT
***
33408196 AATAATTAAACTACTCTTGTTAAAAAAATACT
1 AATAATTAAACTACTCCCATT-AAAAAATACT
33408228 AATAATTAAA
1 AATAATTAAA
33408238 TTTTTTTAAC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
31 18 0.50
32 18 0.50
ACGTcount: A:0.52, C:0.14, G:0.01, T:0.33
Consensus pattern (31 bp):
AATAATTAAACTACTCCCATTAAAAAATACT
Found at i:33412752 original size:30 final size:30
Alignment explanation
Indices: 33412692--33412785 Score: 104
Period size: 30 Copynumber: 3.1 Consensus size: 30
33412682 ACTTAACACG
*
33412692 TTTTCTTAATTTGGTACCTAAA-TT-ATTT
1 TTTTCTCAATTTGGTACCTAAACTTGATTT
* *
33412720 TTTGT-TCAGTTTGGTACTTAAACTTGATTT
1 TTT-TCTCAATTTGGTACCTAAACTTGATTT
*
33412750 TTTTCTTAATTTGGTACCTAAACTTGACATTT
1 TTTTCTCAATTTGGTACCTAAACTTG--ATTT
33412782 TTTT
1 TTTT
33412786 AATTTATTGG
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
28 17 0.31
29 4 0.07
30 25 0.46
32 8 0.15
ACGTcount: A:0.22, C:0.12, G:0.11, T:0.55
Consensus pattern (30 bp):
TTTTCTCAATTTGGTACCTAAACTTGATTT
Found at i:33412796 original size:32 final size:30
Alignment explanation
Indices: 33412692--33412806 Score: 103
Period size: 30 Copynumber: 3.8 Consensus size: 30
33412682 ACTTAACACG
* *
33412692 TTTTCTTAATTTGGTACCTAAA-TT-ATTT
1 TTTTATTAATTTGGTACTTAAACTTGATTT
* *
33412720 TTTGT-TCAGTTTGGTACTTAAACTTGATTT
1 TTT-TATTAATTTGGTACTTAAACTTGATTT
* *
33412750 TTTTCTTAATTTGGTACCTAAACTTGACATTT
1 TTTTATTAATTTGGTACTTAAACTTG--ATTT
*
33412782 TTTTAATTTA-TTGGTACTTAAACTT
1 TTTT-ATTAATTTGGTACTTAAACTT
33412807 TTGGGGGTTC
Statistics
Matches: 71, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
28 17 0.24
29 4 0.06
30 25 0.35
32 22 0.31
33 3 0.04
ACGTcount: A:0.24, C:0.11, G:0.10, T:0.54
Consensus pattern (30 bp):
TTTTATTAATTTGGTACTTAAACTTGATTT
Found at i:33412806 original size:62 final size:58
Alignment explanation
Indices: 33412692--33412806 Score: 151
Period size: 58 Copynumber: 1.9 Consensus size: 58
33412682 ACTTAACACG
* *
33412692 TTTTCTTAATTTGGTACCTAAATTATTTTTTGTTCAGTTTGGTACTTAAACTTGATTT
1 TTTTCTTAATTTGGTACCTAAATTAATTTTTGTTAAGTTTGGTACTTAAACTTGATTT
*
33412750 TTTTCTTAATTTGGTACCTAAACTTGACATTTTT-TTAATTTATTGGTACTTAAACTT
1 TTTTCTTAATTTGGTACCTAAA-TT-A-ATTTTTGTTAA-GT-TTGGTACTTAAACTT
33412807 TTGGGGGTTC
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
58 22 0.45
59 2 0.04
60 4 0.08
61 6 0.12
62 15 0.31
ACGTcount: A:0.24, C:0.11, G:0.10, T:0.54
Consensus pattern (58 bp):
TTTTCTTAATTTGGTACCTAAATTAATTTTTGTTAAGTTTGGTACTTAAACTTGATTT
Found at i:33413117 original size:60 final size:59
Alignment explanation
Indices: 33413009--33413197 Score: 202
Period size: 59 Copynumber: 3.2 Consensus size: 59
33412999 TAATTAATTT
* * * * * *
33413009 AGGTACCAAATTGAATCTAAAAAAAGCTTAGGTACCAAATTAGGAAAAAATGTTAAGTTC
1 AGGTACCAAATTGAGTC-AAAAAAAGTTTAGATATCAAATTAGGAAAAAATATCAAGTTC
* * *
33413069 AGGTACTAAATTGAGTCAAAAAAAGTTTAAATATCAAATTAGGAAAAAATATCAAGTTT
1 AGGTACCAAATTGAGTCAAAAAAAGTTTAGATATCAAATTAGGAAAAAATATCAAGTTC
* * * *
33413128 ACGTACCAAATT-AGATCAAAAAAAATTTAGATATCAAATTA-AAAAAATATATCAAATTC
1 AGGTACCAAATTGAG-TCAAAAAAAGTTTAGATATCAAATTAGGAAAAA-ATATCAAGTTC
**
33413187 AAATACCAAAT
1 AGGTACCAAAT
33413198 GTTTTACTAA
Statistics
Matches: 109, Mismatches: 18, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
58 7 0.06
59 87 0.80
60 15 0.14
ACGTcount: A:0.52, C:0.11, G:0.11, T:0.26
Consensus pattern (59 bp):
AGGTACCAAATTGAGTCAAAAAAAGTTTAGATATCAAATTAGGAAAAAATATCAAGTTC
Found at i:33415550 original size:30 final size:30
Alignment explanation
Indices: 33415516--33415578 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
33415506 TTTATTTTGG
33415516 GTAAATTCACTAGTAGTCACCTAATTATTA
1 GTAAATTCACTAGTAGTCACCTAATTATTA
*** **
33415546 GTAAATTTTTTTTTAGTCACCTAATTATTA
1 GTAAATTCACTAGTAGTCACCTAATTATTA
33415576 GTA
1 GTA
33415579 TTTTTTTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (30 bp):
GTAAATTCACTAGTAGTCACCTAATTATTA
Found at i:33415593 original size:29 final size:30
Alignment explanation
Indices: 33415529--33415595 Score: 118
Period size: 30 Copynumber: 2.3 Consensus size: 30
33415519 AATTCACTAG
33415529 TAGTCACCTAATTATTAGTAAATTTTTTTT
1 TAGTCACCTAATTATTAGTAAATTTTTTTT
*
33415559 TAGTCACCTAATTATTAGT-ATTTTTTTTT
1 TAGTCACCTAATTATTAGTAAATTTTTTTT
33415588 TAGTCACC
1 TAGTCACC
33415596 CAACTATGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 17 0.47
30 19 0.53
ACGTcount: A:0.27, C:0.13, G:0.07, T:0.52
Consensus pattern (30 bp):
TAGTCACCTAATTATTAGTAAATTTTTTTT
Found at i:33431253 original size:22 final size:22
Alignment explanation
Indices: 33431214--33431255 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
33431204 GAGGTGGTTA
* * *
33431214 ATTTTTATAAATTTTAAAAATT
1 ATTTTTAAAAAATATAAAAATT
33431236 ATTTTTAAAAAATATAAAAA
1 ATTTTTAAAAAATATAAAAA
33431256 CAAGTTAAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATTTTTAAAAAATATAAAAATT
Found at i:33431322 original size:22 final size:22
Alignment explanation
Indices: 33431289--33431333 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
33431279 ATTTATTAAA
*
33431289 ATAATAAAAAATATTAAAATTTT
1 ATAATAAAAAATAGT-AAATTTT
33431312 ATAA-AAAAAATAGTAAATTTT
1 ATAATAAAAAATAGTAAATTTT
33431333 A
1 A
33431334 AATTTTCTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.38
22 9 0.43
23 4 0.19
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (22 bp):
ATAATAAAAAATAGTAAATTTT
Found at i:33431329 original size:29 final size:28
Alignment explanation
Indices: 33431275--33431339 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 28
33431265 GGAAACTATA
* *
33431275 TAAAA-TTTATTAAAATAATAAAAAATAT
1 TAAAATTTTATAAAAAAAATAAAAAAT-T
**
33431303 TAAAATTTTATAAAAAAAATAGTAAATT
1 TAAAATTTTATAAAAAAAATAAAAAATT
*
33431331 TTAAATTTT
1 TAAAATTTT
33431340 CTATAGTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 14 0.45
29 17 0.55
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (28 bp):
TAAAATTTTATAAAAAAAATAAAAAATT
Found at i:33442828 original size:23 final size:23
Alignment explanation
Indices: 33442802--33442922 Score: 147
Period size: 23 Copynumber: 5.2 Consensus size: 23
33442792 ACACTAGCGC
*
33442802 GCTCTCTGATTAGCACTGTGTAT
1 GCTCTCTGATTAGCACTGTGTGT
* *
33442825 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
33442848 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
33442873 GCTCTCTGATTAGCACT-TCGTGT
1 GCTCTCTGATTAGCACTGT-GTGT
* *
33442896 TCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
33442919 GCTC
1 GCTC
33442923 AGTACTTTGT
Statistics
Matches: 85, Mismatches: 7, Indels: 12
0.82 0.07 0.12
Matches are distributed among these distances:
22 4 0.05
23 60 0.71
24 1 0.01
25 17 0.20
26 3 0.04
ACGTcount: A:0.12, C:0.25, G:0.21, T:0.41
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:33442894 original size:46 final size:47
Alignment explanation
Indices: 33442802--33442922 Score: 160
Period size: 48 Copynumber: 2.6 Consensus size: 47
33442792 ACACTAGCGC
* *
33442802 GCTCTCTG-ATTAGCACTGTGTATGCTCTCTGTTTAGCACGTCTCGT
1 GCTCTCTGTATTAGCACTGTGTGTGCTCTCTGATTAGCACGTCTCGT
33442848 GCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCAC-T-TCGT
1 GCTCTCTG-TATTAGCACTGTGTGTGCTCTCTGATTAGCACGTCTCGT
*
33442894 GTTCTCTCTG-ATTAGCACTTTGTGTGCTC
1 G--CTCTCTGTATTAGCACTGTGTGTGCTC
33442923 AGTACTTTGT
Statistics
Matches: 68, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
46 31 0.46
47 1 0.01
48 36 0.53
ACGTcount: A:0.12, C:0.25, G:0.21, T:0.41
Consensus pattern (47 bp):
GCTCTCTGTATTAGCACTGTGTGTGCTCTCTGATTAGCACGTCTCGT
Found at i:33442951 original size:39 final size:39
Alignment explanation
Indices: 33442887--33442961 Score: 116
Period size: 39 Copynumber: 1.9 Consensus size: 39
33442877 TCTGATTAGC
*
33442887 ACTTCGTGTTCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
*
33442926 ACTTTGTGTACTCTCT-ATTTAGCACTTTGTGTGCTC
1 ACTTCGTGTACTCTCTGA-TTAGCACTTTGTGTGCTC
33442962 TCTGTTGCCC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
38 1 0.03
39 32 0.97
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
Found at i:33444226 original size:18 final size:17
Alignment explanation
Indices: 33444190--33444223 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
33444180 ATGAATTTAT
33444190 TTGTATAATTGTGATAA
1 TTGTATAATTGTGATAA
33444207 TTGTATTAATT-TGATAA
1 TTGTA-TAATTGTGATAA
33444224 ATTTTAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (17 bp):
TTGTATAATTGTGATAA
Found at i:33448684 original size:6 final size:6
Alignment explanation
Indices: 33448674--33448703 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
33448664 ATTTTTTAGG
*
33448674 GCGGCG GCGGCA GCGGCA GCGGCA GCGGCA
1 GCGGCA GCGGCA GCGGCA GCGGCA GCGGCA
33448704 AACCGTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.13, C:0.33, G:0.53, T:0.00
Consensus pattern (6 bp):
GCGGCA
Found at i:33456094 original size:24 final size:22
Alignment explanation
Indices: 33456045--33456091 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
33456035 TTCATGACAT
33456045 AAATTTAATATATATAACTCTA
1 AAATTTAATATATATAACTCTA
33456067 AAATTTAATATATATAACTCTA
1 AAATTTAATATATATAACTCTA
33456089 AAA
1 AAA
33456092 AATGTACAAC
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:0.09, G:0.00, T:0.38
Consensus pattern (22 bp):
AAATTTAATATATATAACTCTA
Found at i:33463752 original size:16 final size:17
Alignment explanation
Indices: 33463716--33463752 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
33463706 TTTTATTTCT
*
33463716 TAAAAATTTAAAATTAA
1 TAAAAATTTAAAATAAA
33463733 -AAAAATTTAAAA-AAA
1 TAAAAATTTAAAATAAA
33463748 TAAAA
1 TAAAA
33463753 GTTTGTTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 2 0.11
16 16 0.89
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAAAATTTAAAATAAA
Found at i:33466597 original size:20 final size:20
Alignment explanation
Indices: 33466574--33466615 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
33466564 TAAAAAATTC
33466574 AAAAAAATATATAAAAATAT
1 AAAAAAATATATAAAAATAT
* * *
33466594 AAAAATATTTTTAAAAATAT
1 AAAAAAATATATAAAAATAT
33466614 AA
1 AA
33466616 TAATAAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAAAAATATATAAAAATAT
Found at i:33466620 original size:20 final size:20
Alignment explanation
Indices: 33466585--33466648 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
33466575 AAAAAATATA
33466585 TAAAAATATAAAAATATTTT
1 TAAAAATATAAAAATATTTT
* **
33466605 TAAAAATATAATAATAAATT
1 TAAAAATATAAAAATATTTT
*
33466625 TAAATATAATTAAAAATATTTT
1 TAAAAAT-A-TAAAAATATTTT
33466647 TA
1 TA
33466649 TATTAATATT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
20 23 0.66
21 1 0.03
22 11 0.31
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TAAAAATATAAAAATATTTT
Found at i:33467103 original size:5 final size:5
Alignment explanation
Indices: 33467093--33467120 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
33467083 AAGAGGAGGT
33467093 TTTTA TTTTA TTTTA TTTTA TTTTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTT
33467121 AATATTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:33487801 original size:21 final size:21
Alignment explanation
Indices: 33487771--33487825 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
33487761 TCTAAATTAT
*
33487771 TTATGATATTTAT-TTCTTTAA
1 TTATGTTATTTATGTT-TTTAA
33487792 TTATGTTATTTATGTTTTTAA
1 TTATGTTATTTATGTTTTTAA
*
33487813 TTATATTATTTAT
1 TTATGTTATTTAT
33487826 ACTTATATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 29 0.94
22 2 0.06
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.65
Consensus pattern (21 bp):
TTATGTTATTTATGTTTTTAA
Found at i:33489689 original size:42 final size:42
Alignment explanation
Indices: 33489630--33489712 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
33489620 CTAAATTCTT
*
33489630 CAAAAGTGTTAGAAGTTCTAAACTCTAATGGGTGTTACTAAC
1 CAAAAGTGTTAGAAGTTCTAAACTCTAATGAGTGTTACTAAC
33489672 CAAAAGTGTTAGAAGTTCTAAACTCTAATGAGTGTTACTAA
1 CAAAAGTGTTAGAAGTTCTAAACTCTAATGAGTGTTACTAA
33489713 TGAGTATATT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.31
Consensus pattern (42 bp):
CAAAAGTGTTAGAAGTTCTAAACTCTAATGAGTGTTACTAAC
Found at i:33489845 original size:24 final size:24
Alignment explanation
Indices: 33489813--33489884 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 24
33489803 TTGACTCAAG
*
33489813 CAAATAAACAAAATTTACTTGAAA
1 CAAATAAACAAAATTTAATTGAAA
33489837 CAAATAAACAAAATTTAATTGAAA
1 CAAATAAACAAAATTTAATTGAAA
* * * *
33489861 CAATTAAACAGAGTTTAACTGAAA
1 CAAATAAACAAAATTTAATTGAAA
33489885 GATTATTTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.57, C:0.11, G:0.07, T:0.25
Consensus pattern (24 bp):
CAAATAAACAAAATTTAATTGAAA
Found at i:33490168 original size:14 final size:14
Alignment explanation
Indices: 33490132--33490171 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
33490122 GGTTTTGATT
33490132 AAATAGGTAGGCAA
1 AAATAGGTAGGCAA
33490146 AAAT---T-GGCAA
1 AAATAGGTAGGCAA
33490156 AAATAGGTAGGCAA
1 AAATAGGTAGGCAA
33490170 AA
1 AA
33490172 GTGAAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 8
0.73 0.00 0.27
Matches are distributed among these distances:
10 9 0.41
11 1 0.05
13 1 0.05
14 11 0.50
ACGTcount: A:0.53, C:0.07, G:0.25, T:0.15
Consensus pattern (14 bp):
AAATAGGTAGGCAA
Found at i:33492723 original size:13 final size:13
Alignment explanation
Indices: 33492705--33492730 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
33492695 TTCAACACTT
33492705 ATAAAATTTAATA
1 ATAAAATTTAATA
33492718 ATAAAATTTAATA
1 ATAAAATTTAATA
33492731 CTTAATTTTT
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATAAAATTTAATA
Found at i:33504273 original size:53 final size:54
Alignment explanation
Indices: 33504215--33504318 Score: 165
Period size: 53 Copynumber: 1.9 Consensus size: 54
33504205 TTTTGGATTG
* * *
33504215 ATTATTTTTATGTTTAAATCAATTGTCATGTTGAAATACTG-TTTTTTTAATCA
1 ATTATTTATATGTTTAAATCAATTATCATGTTGAAATACTGCTTCTTTTAATCA
*
33504268 ATTATTTATATGTTTAAATCGATTATCATGTTGAAATACTGCTTCTTTTAA
1 ATTATTTATATGTTTAAATCAATTATCATGTTGAAATACTGCTTCTTTTAA
33504319 ATTGATTATT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
53 38 0.83
54 8 0.17
ACGTcount: A:0.31, C:0.09, G:0.10, T:0.51
Consensus pattern (54 bp):
ATTATTTATATGTTTAAATCAATTATCATGTTGAAATACTGCTTCTTTTAATCA
Found at i:33504348 original size:34 final size:34
Alignment explanation
Indices: 33504280--33504348 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
33504270 TATTTATATG
* *
33504280 TTTAAATCGATTATCATGTTGAAATACTGCTTCT
1 TTTAAATCGATTATCATGGTGAAATACTACTTCT
* * * *
33504314 TTTAAATTGATTATTATGGTGGAATACTATTTCT
1 TTTAAATCGATTATCATGGTGAAATACTACTTCT
33504348 T
1 T
33504349 CTTCTTTTGA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.29, C:0.10, G:0.13, T:0.48
Consensus pattern (34 bp):
TTTAAATCGATTATCATGGTGAAATACTACTTCT
Found at i:33505893 original size:25 final size:23
Alignment explanation
Indices: 33505865--33505910 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
33505855 GTTGAATCCA
33505865 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAA-TCTAAAAA-ATAATTTG
*
33505890 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
33505911 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTTG
Found at i:33511146 original size:14 final size:15
Alignment explanation
Indices: 33511123--33511153 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
33511113 AATCCTATTT
33511123 AAACTCTAAAAGATA
1 AAACTCTAAAAGATA
33511138 AAACT-TAAAAGATA
1 AAACTCTAAAAGATA
33511152 AA
1 AA
33511154 TATAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.65, C:0.10, G:0.06, T:0.19
Consensus pattern (15 bp):
AAACTCTAAAAGATA
Done.