Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
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: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 12 of 175
Found at i:3394216 original size:19 final size:19
Alignment explanation
Indices: 3394192--3394234 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
3394182 TGTTTTATGT
3394192 ATATATATAAT-ATAATATA
1 ATATAT-TAATGATAATATA
3394211 ATATATTAATGATAATATA
1 ATATATTAATGATAATATA
3394230 ATATA
1 ATATA
3394235 AAAACATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
ATATATTAATGATAATATA
Found at i:3394244 original size:24 final size:24
Alignment explanation
Indices: 3394198--3394263 Score: 71
Period size: 24 Copynumber: 2.7 Consensus size: 24
3394188 ATGTATATAT
* * *
3394198 ATAATATAATATAATATATTAATG
1 ATAATATAATATAATAAAATAATC
3394222 ATAATATAATATAA-AAACATAATC
1 ATAATATAATATAATAAA-ATAATC
*
3394246 ATTACTATAATATAATAA
1 A-TAATATAATATAATAA
3394264 TATTTTTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
23 2 0.06
24 19 0.54
25 12 0.34
26 2 0.06
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.36
Consensus pattern (24 bp):
ATAATATAATATAATAAAATAATC
Found at i:3395865 original size:4 final size:4
Alignment explanation
Indices: 3395858--3395908 Score: 50
Period size: 4 Copynumber: 12.5 Consensus size: 4
3395848 CATTCATTCG
* * *
3395858 TTTA TTTA TTT- TATTA TTTT TATTA TCTA TTTA TTTA TTTA TTTA CTTA
1 TTTA TTTA TTTA T-TTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA
3395907 TT
1 TT
3395909 ACTCATTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
3 1 0.03
4 33 0.87
5 4 0.11
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:3398897 original size:29 final size:31
Alignment explanation
Indices: 3398854--3398913 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
3398844 GAATTGGATC
*
3398854 AAATCAAAATTTCATGTATA-AAATTGCACA
1 AAATCAAAAGTTCATGTATACAAATTGCACA
*
3398884 AAATC-AAAGTTCATGTATACAATTTGCACA
1 AAATCAAAAGTTCATGTATACAAATTGCACA
3398914 TTAAACCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 13 0.48
30 14 0.52
ACGTcount: A:0.47, C:0.15, G:0.08, T:0.30
Consensus pattern (31 bp):
AAATCAAAAGTTCATGTATACAAATTGCACA
Found at i:3403357 original size:68 final size:68
Alignment explanation
Indices: 3403268--3403424 Score: 190
Period size: 68 Copynumber: 2.3 Consensus size: 68
3403258 GAGATGATAG
** * * * * *
3403268 ACGACGTCGAGACGAGCAAGGTGTAGTGCGTCAAGATGACGCAACGTCCTTGGCAACGAAGTAAG
1 ACGACGTCGAGACGAGCAAGGTGTAGCACGTCAAGATGACACAACATCCTTAGCAACCAAGCAAG
3403333 GCT
66 GCT
* * **
3403336 ACGATGTCGAGACGAGCAAGGTGTAGCACGTCGAGATGACATGACATCCTTAGCAACCAAGCAAG
1 ACGACGTCGAGACGAGCAAGGTGTAGCACGTCAAGATGACACAACATCCTTAGCAACCAAGCAAG
3403401 GCT
66 GCT
* *
3403404 ACGACATCGTGACGAG-AAGGT
1 ACGACGTCGAGACGAGCAAGGT
3403425 ATGCCACATC
Statistics
Matches: 75, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
67 5 0.07
68 70 0.93
ACGTcount: A:0.31, C:0.22, G:0.31, T:0.16
Consensus pattern (68 bp):
ACGACGTCGAGACGAGCAAGGTGTAGCACGTCAAGATGACACAACATCCTTAGCAACCAAGCAAG
GCT
Found at i:3406120 original size:20 final size:19
Alignment explanation
Indices: 3406087--3406126 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
3406077 TTCAATAATT
3406087 TTAATTAAAAATAATAAAAA
1 TTAATTAAAAATAA-AAAAA
**
3406107 TTAATTAATTATAAAAAAA
1 TTAATTAAAAATAAAAAAA
3406126 T
1 T
3406127 ATTTTAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TTAATTAAAAATAAAAAAA
Found at i:3411865 original size:31 final size:32
Alignment explanation
Indices: 3411802--3411868 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
3411792 ACTTAATAGC
* * *
3411802 CAATGACTTAAACAAAATTTTTTTGAATAATT
1 CAATGACTTAAACAAAATATTTCTAAATAATT
*
3411834 CAATGACTTAAATAAAA-ATTTCTAAATAATT
1 CAATGACTTAAACAAAATATTTCTAAATAATT
3411865 CAAT
1 CAAT
3411869 AATAGTGATA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 15 0.48
32 16 0.52
ACGTcount: A:0.48, C:0.10, G:0.04, T:0.37
Consensus pattern (32 bp):
CAATGACTTAAACAAAATATTTCTAAATAATT
Found at i:3413850 original size:16 final size:16
Alignment explanation
Indices: 3413829--3413868 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 16
3413819 TTATAATCAT
3413829 AATTAATATATT-AATA
1 AATTAAT-TATTGAATA
3413845 AATTAATTATTGAATA
1 AATTAATTATTGAATA
3413861 AATATAAT
1 AAT-TAAT
3413869 GATTATAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.18
16 14 0.64
17 4 0.18
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
AATTAATTATTGAATA
Found at i:3414439 original size:23 final size:23
Alignment explanation
Indices: 3414402--3414445 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
3414392 TAAATTTAAA
*
3414402 AAATTAAATATAAAAATATATAT
1 AAATTAAATAAAAAAATATATAT
* *
3414425 AAATTAATTAAAAAAGTATAT
1 AAATTAAATAAAAAAATATAT
3414446 TTTTTCACAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (23 bp):
AAATTAAATAAAAAAATATATAT
Found at i:3425512 original size:49 final size:48
Alignment explanation
Indices: 3425353--3425512 Score: 151
Period size: 49 Copynumber: 3.2 Consensus size: 48
3425343 TTATGTGTTC
* * * *
3425353 TGCATTTAATTAAGTCATGCATTAAAGCATCTCATATGTTCATAAAGTT
1 TGCATTTAATTATGTCATGCATT-AAGTAACTCATATGTTCATTAAGTT
** * * * *
3425402 TGTGTTTTAATTATGTCATGTATTAAGTAACTCCTATATTAATTAAG-T
1 TG-CATTTAATTATGTCATGCATTAAGTAACTCATATGTTCATTAAGTT
* * *
3425450 TGCATCTTAAATTATGTCATGCATTATGTAACTCATTTGTTCATTTAGTT
1 TGCAT-TT-AATTATGTCATGCATTAAGTAACTCATATGTTCATTAAGTT
3425500 TGCATTTCAATTA
1 TGCATTT-AATTA
3425513 AACCATGCAT
Statistics
Matches: 87, Mismatches: 20, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
47 1 0.01
48 5 0.06
49 58 0.67
50 23 0.26
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (48 bp):
TGCATTTAATTATGTCATGCATTAAGTAACTCATATGTTCATTAAGTT
Found at i:3446060 original size:30 final size:31
Alignment explanation
Indices: 3446004--3446066 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 31
3445994 AGATGCTCAC
3446004 TGAACTATTTGAAAGTTTTCATTTAAGTCAT
1 TGAACTATTTGAAAGTTTTCATTTAAGTCAT
*
3446035 TGAACTATTTGAAA-TTTTTATTTAAGTCAT
1 TGAACTATTTGAAAGTTTTCATTTAAGTCAT
3446065 TG
1 TG
3446067 GGATGTTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 17 0.55
31 14 0.45
ACGTcount: A:0.32, C:0.08, G:0.13, T:0.48
Consensus pattern (31 bp):
TGAACTATTTGAAAGTTTTCATTTAAGTCAT
Found at i:3460963 original size:21 final size:19
Alignment explanation
Indices: 3460925--3460966 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
3460915 TGGTTCATGC
3460925 TTATTTTTTTTATGAATTT
1 TTATTTTTTTTATGAATTT
*
3460944 TTATTTTTATCTTTTGAATTT
1 TTATTTTT-T-TTATGAATTT
3460965 TT
1 TT
3460967 TAAAATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
20 1 0.05
21 11 0.55
ACGTcount: A:0.19, C:0.02, G:0.05, T:0.74
Consensus pattern (19 bp):
TTATTTTTTTTATGAATTT
Found at i:3461838 original size:22 final size:22
Alignment explanation
Indices: 3461778--3461835 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 22
3461768 GATATGCAAT
3461778 GATATGCAATCTT---AGATAA
1 GATATGCAATCTTAGAAGATAA
3461797 GATATGCAATCTTAGAAGATAA
1 GATATGCAATCTTAGAAGATAA
* *
3461819 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
3461836 GATTTAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.39
22 8 0.24
23 12 0.36
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAA
Found at i:3462648 original size:24 final size:22
Alignment explanation
Indices: 3462621--3462826 Score: 105
Period size: 24 Copynumber: 8.8 Consensus size: 22
3462611 ATGTTTAAAC
3462621 TTATTATTAAATTTATCATTAATA
1 TTATT-TTAAATTTATCATT-ATA
**
3462645 TTATCTAAGTT-AATTTATTGTATATTA
1 TTAT-T---TTAAATTTATCAT-TA-TA
* * *
3462672 TTAATTTAGATTTATCACGTTTTA
1 TTATTTTAAATTTATCA--TTATA
*
3462696 TTATTTGT-AATTTATCAATATCA
1 TTATTT-TAAATTTATCATTAT-A
* * * *
3462719 TTATTTTAAATTCATCGTAACA
1 TTATTTTAAATTTATCATTATA
3462741 TTATTTTAAATTTATCATGTATA
1 TTATTTTAAATTTATCAT-TATA
3462764 TTTATTTTAAAATTTATCATTA-A
1 -TTATTTT-AAATTTATCATTATA
* *
3462787 -TATTTTAAAATTATTATGTACTA
1 TTATTTTAAATTTATCAT-TA-TA
**
3462810 TTATTTTGGATTTATCA
1 TTATTTTAAATTTATCA
3462827 CATATGTTTA
Statistics
Matches: 137, Mismatches: 27, Indels: 36
0.69 0.14 0.18
Matches are distributed among these distances:
20 9 0.07
21 8 0.06
22 20 0.15
23 21 0.15
24 46 0.34
25 14 0.10
26 11 0.08
27 8 0.06
ACGTcount: A:0.35, C:0.06, G:0.05, T:0.54
Consensus pattern (22 bp):
TTATTTTAAATTTATCATTATA
Found at i:3462721 original size:23 final size:23
Alignment explanation
Indices: 3462695--3462757 Score: 76
Period size: 22 Copynumber: 2.8 Consensus size: 23
3462685 ATCACGTTTT
*
3462695 ATTATTTGT-AATTTATCAATATC
1 ATTATTT-TAAATTTATCAATAAC
* *
3462718 ATTATTTTAAATTCATC-GTAAC
1 ATTATTTTAAATTTATCAATAAC
3462740 ATTATTTTAAATTTATCA
1 ATTATTTTAAATTTATCA
3462758 TGTATATTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
22 20 0.59
23 14 0.41
ACGTcount: A:0.37, C:0.10, G:0.03, T:0.51
Consensus pattern (23 bp):
ATTATTTTAAATTTATCAATAAC
Found at i:3482245 original size:59 final size:58
Alignment explanation
Indices: 3482181--3482489 Score: 234
Period size: 59 Copynumber: 5.2 Consensus size: 58
3482171 ATATATGTAA
*
3482181 ATTATATATTTCTATTAAATTATATTTAATAATTATTATTTTAAATTATATTTTATAGT
1 ATTATATATTT-TATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGT
* ** * * * * *
3482240 ATTATATATTATGATTTTAGTAAATTTATATAAGAA-TA-TTTAATATTAAGAATTTTATTA-A
1 ATTATATATT-TTATTAAATTATATTTA-ATAATAATTATTTTAA-ATT-A-TATTTTA-TAGT
3482301 ATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGT
1 ATTATATA-TTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGT
* ** * * * * * * *
3482360 ATTATATATTATGATTTTAGTAAATTCATATAAGAA-TA-TTTAATACTAAGAATTTTATTA-A
1 ATTATATATT-TTATTAAATTATATTTA-ATAATAATTATTTTAA-A-TTA-TATTTTA-TAGT
* * *
3482421 ATTATATATTTTAATTAAAATATATTTTATAATAATTATTTCAAATTATATTTTATAGT
1 ATTATATATTTT-ATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGT
*
3482480 ATCATATATT
1 ATTATATATT
3482490 ATGATTTTAG
Statistics
Matches: 190, Mismatches: 40, Indels: 40
0.70 0.15 0.15
Matches are distributed among these distances:
58 16 0.08
59 69 0.36
60 31 0.16
61 59 0.31
62 15 0.08
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (58 bp):
ATTATATATTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGT
Found at i:3482308 original size:61 final size:61
Alignment explanation
Indices: 3482240--3482550 Score: 282
Period size: 61 Copynumber: 5.2 Consensus size: 61
3482230 ATTTTATAGT
3482240 ATTATATATTATGATTTTAGTAAATTTATATAAGAATATTTAATATTAAGAATTTTATTAA
1 ATTATATATTATGATTTTAGTAAATTTATATAAGAATATTTAATATTAAGAATTTTATTAA
* * ** * * * * *
3482301 ATTATATATTTTTATTAAATTATATTTA-ATAATAATTATTTTAA-ATT-A-TATTTTA-TAGT
1 ATTATATATTATGATTTTAGTAAATTTATATAAGAA-TA-TTTAATATTAAGAATTTTATTA-A
* *
3482360 ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATACTAAGAATTTTATTAA
1 ATTATATATTATGATTTTAGTAAATTTATATAAGAATATTTAATATTAAGAATTTTATTAA
* * ** * * * * *
3482421 ATTATATATTTTAATTAAAATATATTT-TATAATAATTATTTCAA-ATT-A-TATTTTA-TAGT
1 ATTATATATTATGATTTTAGTAAATTTATATAAGAA-TATTT-AATATTAAGAATTTTATTA-A
* * * *
3482480 ATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAA
1 ATTATATATTATGATTTTAGTAAATTTATATAAGAATATTTAATATTAAGAATTTTATTAA
3482541 ATTATATATT
1 ATTATATATT
3482551 TTAATTAAAA
Statistics
Matches: 189, Mismatches: 45, Indels: 32
0.71 0.17 0.12
Matches are distributed among these distances:
58 10 0.05
59 63 0.33
60 30 0.16
61 75 0.40
62 11 0.06
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.51
Consensus pattern (61 bp):
ATTATATATTATGATTTTAGTAAATTTATATAAGAATATTTAATATTAAGAATTTTATTAA
Found at i:3482310 original size:120 final size:120
Alignment explanation
Indices: 3482178--3482585 Score: 683
Period size: 120 Copynumber: 3.4 Consensus size: 120
3482168 GCAATATATG
* *
3482178 TAAATTATATATTTCT-ATTAAATTATATTTAATAATTATTATTTTAAATTATATTTTATAGTAT
1 TAAATTATATATTT-TAATTAAAATATATTTAATAATAATTATTTTAAATTATATTTTATAGTAT
*
3482242 TATATATTATGATTTTAGTAAATTTATATAAGAATATTTAATATTAAGAATTTTAT
65 TATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTAT
* *
3482298 TAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATT
1 TAAATTATATATTTTAATTAAAATATATTTAATAATAATTATTTTAAATTATATTTTATAGTATT
*
3482363 ATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATACTAAGAATTTTAT
66 ATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTAT
* * *
3482418 TAAATTATATATTTTAATTAAAATATATTTTATAATAATTATTTCAAATTATATTTTATAGTATC
1 TAAATTATATATTTTAATTAAAATATATTTAATAATAATTATTTTAAATTATATTTTATAGTATT
* *
3482483 ATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTAT
66 ATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTAT
* *
3482538 TAAATTATATATTTTAATTAAAATATATTTAATAATAAATATGTTAAA
1 TAAATTATATATTTTAATTAAAATATATTTAATAATAATTATTTTAAA
3482586 ATATGATTAA
Statistics
Matches: 272, Mismatches: 15, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
119 1 0.00
120 271 1.00
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (120 bp):
TAAATTATATATTTTAATTAAAATATATTTAATAATAATTATTTTAAATTATATTTTATAGTATT
ATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTAT
Found at i:3482445 original size:16 final size:17
Alignment explanation
Indices: 3482411--3482449 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
3482401 AATACTAAGA
3482411 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA-TATAT
3482428 ATTTTAATTAAA-ATAT
1 ATTTTAATTAAATATAT
3482444 ATTTTA
1 ATTTTA
3482450 TAATAATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 10 0.48
17 5 0.24
18 6 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTAATTAAATATAT
Found at i:3482453 original size:18 final size:18
Alignment explanation
Indices: 3482411--3482445 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3482401 AATACTAAGA
*
3482411 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAAATATAT
3482428 ATTTTAATTAAAATATAT
1 ATTTTAATTAAAATATAT
3482446 TTTATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTTTAATTAAAATATAT
Found at i:3482559 original size:18 final size:17
Alignment explanation
Indices: 3482531--3482565 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3482521 ATTATTAAGA
*
3482531 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
3482548 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
3482566 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:3482791 original size:44 final size:45
Alignment explanation
Indices: 3482728--3482823 Score: 124
Period size: 44 Copynumber: 2.2 Consensus size: 45
3482718 TTATTACACC
* * *
3482728 TCCATTCCATTCAACCAAACACA-AGAA-TACTATTACGTCTCTAT
1 TCCATTACATTCAACCAAACA-ATAGAATTACTATTACGCCTCTAA
* *
3482772 TCCATTACATTCAACCAAACAATTGAATTGCTATTACGCCTCTAA
1 TCCATTACATTCAACCAAACAATAGAATTACTATTACGCCTCTAA
3482817 TCCATTA
1 TCCATTA
3482824 TGCATCTATT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
43 1 0.02
44 23 0.51
45 21 0.47
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.31
Consensus pattern (45 bp):
TCCATTACATTCAACCAAACAATAGAATTACTATTACGCCTCTAA
Found at i:3482831 original size:16 final size:16
Alignment explanation
Indices: 3482804--3482856 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
3482794 TTGAATTGCT
* *
3482804 ATTACGCCTCTAATCC
1 ATTACGCATCTATTCC
*
3482820 ATTATGCATCTATTCC
1 ATTACGCATCTATTCC
*
3482836 ATTACGCTTCTATTCC
1 ATTACGCATCTATTCC
3482852 ATTAC
1 ATTAC
3482857 AGCGAACCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.25, C:0.30, G:0.06, T:0.40
Consensus pattern (16 bp):
ATTACGCATCTATTCC
Found at i:3491421 original size:4 final size:4
Alignment explanation
Indices: 3491412--3491455 Score: 88
Period size: 4 Copynumber: 11.0 Consensus size: 4
3491402 ATAAAATGTA
3491412 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
3491456 ACGAAGATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:3493278 original size:95 final size:94
Alignment explanation
Indices: 3493150--3493350 Score: 305
Period size: 95 Copynumber: 2.1 Consensus size: 94
3493140 TATTGCGACC
* * * *
3493150 TCAGAGAGATAAGTTTGATATGATAAGATTTAATCCGACCCT-CTGCAGCTTCAAAGGTATAGGA
1 TCAGGGAGATAAATTTGATATGATAAGATTTAATCCGA-CCTACTGCAACTTCAAAGGTATAAGA
* *
3493214 TTCATTGTTTTAATCTGCTCCACTGCAACT
65 TTCATCGTTTTAATCCGCTCCACTGCAACT
*
3493244 TCAGGGAGATAATATTTGATATGATAAGATTTAATCCGACCTACTGCAACTTCAGAGGTATAAGA
1 TCAGGGAGATAA-ATTTGATATGATAAGATTTAATCCGACCTACTGCAACTTCAAAGGTATAAGA
*
3493309 TTCATCGTTTTAATCCGCTCTACTGCAACT
65 TTCATCGTTTTAATCCGCTCCACTGCAACT
3493339 TCAGGGAGATAA
1 TCAGGGAGATAA
3493351 GATTAGCTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
94 14 0.14
95 83 0.86
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Consensus pattern (94 bp):
TCAGGGAGATAAATTTGATATGATAAGATTTAATCCGACCTACTGCAACTTCAAAGGTATAAGAT
TCATCGTTTTAATCCGCTCCACTGCAACT
Found at i:3493336 original size:44 final size:41
Alignment explanation
Indices: 3493273--3493392 Score: 127
Period size: 41 Copynumber: 2.9 Consensus size: 41
3493263 TATGATAAGA
* *
3493273 TTTAATCCGAC-CTACTGCAACTTCAGAGG-TATAAGATTCATCGT
1 TTTAATCCG-CTCTACTGCAACTTCAG-GGAGATAAGATT-A--GC
3493317 TTTAATCCGCTCTACTGCAACTTCAGGGAGATAAGATTAGC
1 TTTAATCCGCTCTACTGCAACTTCAGGGAGATAAGATTAGC
* * * *
3493358 TTCAATCCACTCCACTGCAACTTCAGTGAGATAAG
1 TTTAATCCGCTCTACTGCAACTTCAGGGAGATAAG
3493393 GTTTGTTATC
Statistics
Matches: 68, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
41 32 0.47
43 4 0.06
44 32 0.47
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (41 bp):
TTTAATCCGCTCTACTGCAACTTCAGGGAGATAAGATTAGC
Found at i:3493676 original size:44 final size:45
Alignment explanation
Indices: 3493628--3493762 Score: 113
Period size: 44 Copynumber: 3.1 Consensus size: 45
3493618 AGGATTGGCT
3493628 TCTTCTG-TCTGCTCCTCTACTGCTTAGGGAGATAAGATCTACAA
1 TCTTCTGATCTGCTCCTCTACTGCTTAGGGAGATAAGATCTACAA
* * * * * **
3493672 TCTTC-GACCTACT-CTGCTACTGCTCAAGGAGATAAG-GCT--GG
1 TCTTCTGATCTGCTCCT-CTACTGCTTAGGGAGATAAGATCTACAA
* *
3493713 TGCTT-TCGATCTGCTCCACTACTGCTTAGGGGGATAAGATCTACAA
1 T-CTTCT-GATCTGCTCCTCTACTGCTTAGGGAGATAAGATCTACAA
3493759 TCTT
1 TCTT
3493763 TGACCTATTA
Statistics
Matches: 66, Mismatches: 16, Indels: 17
0.67 0.16 0.17
Matches are distributed among these distances:
41 1 0.02
42 3 0.05
43 28 0.42
44 30 0.45
45 3 0.05
46 1 0.02
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.32
Consensus pattern (45 bp):
TCTTCTGATCTGCTCCTCTACTGCTTAGGGAGATAAGATCTACAA
Found at i:3493782 original size:87 final size:87
Alignment explanation
Indices: 3493635--3493797 Score: 247
Period size: 87 Copynumber: 1.9 Consensus size: 87
3493625 GCTTCTTCTG
*
3493635 TCTGCTCCTCTACTGCTTAGGGAGATAAGATCTACAATCTTCGACCTACTCTGCTACTGCTCAAG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCGACCTACTCTGCTACTGCTCAAG
3493700 GAGATAAGGCTGGTGCTTTCGA
66 GAGATAAGGCTGGTGCTTTCGA
* * * * * *
3493722 TCTGCTCCACTACTGCTTAGGGGGATAAGATCTACAATCTTTGACCTATTAC-GTTGCTGCTCAG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCGACCTACT-CTGCTACTGCTCAA
3493786 GGAGATAAGGCT
65 GGAGATAAGGCT
3493798 AGTTTTTGAT
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
87 67 0.99
88 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (87 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCGACCTACTCTGCTACTGCTCAAG
GAGATAAGGCTGGTGCTTTCGA
Found at i:3493923 original size:89 final size:89
Alignment explanation
Indices: 3493805--3494020 Score: 297
Period size: 89 Copynumber: 2.4 Consensus size: 89
3493795 GCTAGTTTTT
* * * * * *
3493805 GATCTGCTTCACTGCCAGTATAAGAAGACAAGATCTGCTGCTTTTAGTCTGTTCCACTACAAACT
1 GATCTGCTTCGCTACCGGTACAGGAAGACAAGATCTGCTGCTTTTAGTCTGCTCCACTACAAACT
*
3493870 CAGGGAGGTAAAGCTTGTGTCTTC
66 CAGGGAGGCAAAGCTTGTGTCTTC
* * * *
3493894 GATCTGCTTCGCTACTGGTACAGGAAGACAAGATCTACTGCTTTTAGTCTGCTCCGCTGCAAACT
1 GATCTGCTTCGCTACCGGTACAGGAAGACAAGATCTGCTGCTTTTAGTCTGCTCCACTACAAACT
* *
3493959 TAGGGAGGCAAGGCTTGTGTCTTC
66 CAGGGAGGCAAAGCTTGTGTCTTC
* *
3493983 GATTTGCTTCGCTGCCGGTACAGGAAGACAAGATCTGC
1 GATCTGCTTCGCTACCGGTACAGGAAGACAAGATCTGC
3494021 AATCTTCAAC
Statistics
Matches: 110, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
89 110 1.00
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.29
Consensus pattern (89 bp):
GATCTGCTTCGCTACCGGTACAGGAAGACAAGATCTGCTGCTTTTAGTCTGCTCCACTACAAACT
CAGGGAGGCAAAGCTTGTGTCTTC
Found at i:3494440 original size:24 final size:24
Alignment explanation
Indices: 3494390--3494447 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
3494380 GGATTGCCCC
*
3494390 CCACTGTAATCTTTAAAGTTTAAT
1 CCACTGTAATCTTTAAAGGTTAAT
* *
3494414 CCATTGTAATC-TTCAAGGTTAAGT
1 CCACTGTAATCTTTAAAGGTTAA-T
3494438 CCACTGTAAT
1 CCACTGTAAT
3494448 TCTGGGACAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 9 0.31
24 20 0.69
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (24 bp):
CCACTGTAATCTTTAAAGGTTAAT
Found at i:3495389 original size:14 final size:14
Alignment explanation
Indices: 3495366--3495434 Score: 52
Period size: 14 Copynumber: 4.9 Consensus size: 14
3495356 TTGGCCTCTC
*
3495366 CTTTCATTTTTTTT
1 CTTTCTTTTTTTTT
*
3495380 CTTTC-TTTTTCTT
1 CTTTCTTTTTTTTT
*
3495393 CTTTTCTTTATCTTTT
1 C-TTTCTTT-TTTTTT
* *
3495409 C-TTCTTATTCTTT
1 CTTTCTTTTTTTTT
3495422 CTTTTCTTTTTTT
1 C-TTTCTTTTTTT
3495435 GAAATATTCT
Statistics
Matches: 42, Mismatches: 8, Indels: 9
0.71 0.14 0.15
Matches are distributed among these distances:
13 13 0.31
14 14 0.33
15 10 0.24
16 5 0.12
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (14 bp):
CTTTCTTTTTTTTT
Found at i:3495410 original size:25 final size:23
Alignment explanation
Indices: 3495376--3495431 Score: 69
Period size: 25 Copynumber: 2.4 Consensus size: 23
3495366 CTTTCATTTT
* *
3495376 TTTTC-TTTCTTTTTCTTCTTTTC
1 TTTTCTTTTCTTCTTATTC-TTTC
3495399 TTTATCTTTTCTTCTTATTCTTTC
1 TTT-TCTTTTCTTCTTATTCTTTC
3495423 TTTTCTTTT
1 TTTTCTTTT
3495432 TTTGAAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 9 0.31
24 9 0.31
25 11 0.38
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTTCTTTTCTTCTTATTCTTTC
Found at i:3495427 original size:18 final size:17
Alignment explanation
Indices: 3495376--3495433 Score: 73
Period size: 18 Copynumber: 3.2 Consensus size: 17
3495366 CTTTCATTTT
3495376 TTTTCTTTCTTTTTCTTC
1 TTTTCTTTC-TTTTCTTC
3495394 TTTTCTTTATCTTTTCTTC
1 TTTTC-TT-TCTTTTCTTC
3495413 TTATTCTTTCTTTTCTT-
1 TT-TTCTTTCTTTTCTTC
3495430 TTTT
1 TTTT
3495434 TGAAATATTC
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
16 2 0.05
17 2 0.05
18 14 0.38
19 14 0.38
20 5 0.14
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTCTTTCTTTTCTTC
Found at i:3495433 original size:25 final size:26
Alignment explanation
Indices: 3495373--3495434 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 26
3495363 CTCCTTTCAT
*
3495373 TTTTTTTCTTTCTTTTTCTTCTTTTC
1 TTTTTTTCTTTCTTATTCTTCTTTTC
3495399 TTTATCTTT-TCTTCTTATTCTTTCTTTTC
1 TTT-T-TTTCT-TTCTTATTC-TTCTTTTC
3495428 TTTTTTT
1 TTTTTTT
3495435 GAAATATTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
26 3 0.10
27 5 0.16
28 12 0.39
29 11 0.35
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (26 bp):
TTTTTTTCTTTCTTATTCTTCTTTTC
Found at i:3509001 original size:10 final size:11
Alignment explanation
Indices: 3508977--3509001 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3508967 ATTGACTATC
3508977 TTTTCAAACAT
1 TTTTCAAACAT
3508988 TTTTCAAACAT
1 TTTTCAAACAT
3508999 TTT
1 TTT
3509002 GAGGTACAAA
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:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (11 bp):
TTTTCAAACAT
Found at i:3516489 original size:18 final size:17
Alignment explanation
Indices: 3516468--3516524 Score: 55
Period size: 18 Copynumber: 3.4 Consensus size: 17
3516458 TGTAATAAGT
3516468 ATAATAATACCAATAATA
1 ATAATAATA-CAATAATA
* * *
3516486 ATAATAGTAGCAGTACTA
1 ATAATAATA-CAATAATA
3516504 ATAATAATA-AATAA-A
1 ATAATAATACAATAATA
3516519 ATAATA
1 ATAATA
3516525 TTAAACTATT
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
15 7 0.22
16 3 0.09
18 22 0.69
ACGTcount: A:0.60, C:0.07, G:0.05, T:0.28
Consensus pattern (17 bp):
ATAATAATACAATAATA
Found at i:3523691 original size:143 final size:143
Alignment explanation
Indices: 3523262--3524060 Score: 1100
Period size: 143 Copynumber: 5.6 Consensus size: 143
3523252 TAATTTCAAC
* * * * *
3523262 CTGCTCCACTACAACTTCAGGGAGATAAGGCTGGTGGCTTCAATATGCTCCACTGCGACTTCAGG
1 CTGCTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGTTCCACTGCAACTTCAGG
* *
3523327 AAGATAAGATCCGCCATAATTTGTAGCTTTAATCTGTTCAACTACAACGCTAGAGAAATAAGA-T
66 AAGATAAGATCCGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCTAGAGAAATAAGATT
3523391 CCACTGTCTTCAGT
131 CC-CTGTCTTCAGT
* * * * * * *
3523405 TTGCTCCGTTGCAACTTTAAGGAGATAAGGCTAGTGGCTTCAATCTGCTCCACTGCAACTTCA-A
1 CTGCTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGTTCCACTGCAACTTCAGG
* *
3523469 AAGATAAGATCCACCATAATTTGTAGCTTTAATCTGTTCTACTGCAACGCTAGAGAAATAAGATT
66 AAGATAAGATCCGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCTAGAGAAATAAGATT
*** *
3523534 TGTTGTATTCAGT
131 CCCTGTCTTCAGT
* * *
3523547 CTGCTCCGCTGCAACTTTAGGGAGATAAGGCTAGTGGCTTCAATATGTTCCACTGCAACTTCAGG
1 CTGCTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGTTCCACTGCAACTTCAGG
* * * *
3523612 AAGATAAGGTTCGCTATAATTTATAGCTTTAATCTGTTCCACTGCAACGCTAGAGAAATAAGATT
66 AAGATAAGATCCGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCTAGAGAAATAAGATT
*
3523677 CCCTGTCTTTAGT
131 CCCTGTCTTCAGT
* * * *
3523690 CTGCTCCGCTGTAACTTCAGGGAGATAAGGTTGGTGGCTTCAATCCGTTCCACTACAACTTCAGG
1 CTGCTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGTTCCACTGCAACTTCAGG
* * *
3523755 AAGATAAGATCTGCCATAATTTGTAGCTTTAATTTGTTCCACTGCAACGCTAGGGAAATAAGATT
66 AAGATAAGATCCGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCTAGAGAAATAAGATT
3523820 CCCTGTCTTCAGT
131 CCCTGTCTTCAGT
* * * *
3523833 CTGCTCCGTTGTAACTTCAGGGGGATAAGGCTGGTGGCTTCAATCTGCTT-CACTGCAACTTTAG
1 CTGCTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTG-TTCCACTGCAACTTCAG
* * * * *
3523897 AAAGATAAGATCCACCATAATTTGTAGCTTTAATCTGTTACACTGCAACGCCAGGGAAATAAGAT
65 GAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCTAGAGAAATAAGAT
* * *
3523962 TCGCTATCTTTAGT
130 TCCCTGTCTTCAGT
* * * *
3523976 CTGCTCCGCTGCAACTTCAGGGAGATAAGGTTGATTGCTTCAATTTGTTCCACTGCAACTTCAGG
1 CTGCTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGTTCCACTGCAACTTCAGG
3524041 AAGATAAGATCCGCCATAAT
66 AAGATAAGATCCGCCATAAT
3524061 GACTTTAATC
Statistics
Matches: 578, Mismatches: 74, Indels: 8
0.88 0.11 0.01
Matches are distributed among these distances:
142 129 0.22
143 447 0.77
144 2 0.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (143 bp):
CTGCTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGTTCCACTGCAACTTCAGG
AAGATAAGATCCGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCTAGAGAAATAAGATT
CCCTGTCTTCAGT
Found at i:3528150 original size:21 final size:20
Alignment explanation
Indices: 3528124--3528181 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
3528114 AGTAAACACC
3528124 AAAAAA-AATTTTAGAAAATTA
1 AAAAAAGAATTTTA-AAAA-TA
*
3528145 AAAAAAGTATTTTAAAAATA
1 AAAAAAGAATTTTAAAAATA
*
3528165 AAAAAAGTATTTTAAAA
1 AAAAAAGAATTTTAAAA
3528182 TATTTTTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 19 0.54
21 10 0.29
22 6 0.17
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (20 bp):
AAAAAAGAATTTTAAAAATA
Found at i:3528183 original size:19 final size:20
Alignment explanation
Indices: 3528131--3528181 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
3528121 ACCAAAAAAA
3528131 ATTTTAGAAAATTAAAAAAAGT
1 ATTTTA-AAAA-TAAAAAAAGT
3528153 ATTTTAAAAATAAAAAAAGT
1 ATTTTAAAAATAAAAAAAGT
3528173 ATTTTAAAA
1 ATTTTAAAA
3528182 TATTTTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 19 0.66
21 4 0.14
22 6 0.21
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (20 bp):
ATTTTAAAAATAAAAAAAGT
Found at i:3530261 original size:16 final size:17
Alignment explanation
Indices: 3530223--3530261 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
3530213 AATAAGATAC
*
3530223 ATAAATAAATAGTAATA
1 ATAAATAAATAGCAATA
3530240 AT-AATAAATA-CAATA
1 ATAAATAAATAGCAATA
3530255 ATAAATA
1 ATAAATA
3530262 TGGTACAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 6 0.30
16 12 0.60
17 2 0.10
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (17 bp):
ATAAATAAATAGCAATA
Found at i:3534977 original size:17 final size:17
Alignment explanation
Indices: 3534946--3534979 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3534936 AATTGATTTT
**
3534946 TTTTTTAATTTTTTAAA
1 TTTTTTAATGATTTAAA
3534963 TTTTTTAATGATTTAAA
1 TTTTTTAATGATTTAAA
3534980 CCTTTATAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
TTTTTTAATGATTTAAA
Found at i:3535992 original size:21 final size:21
Alignment explanation
Indices: 3535925--3535995 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
3535915 ATAAAAACAA
*
3535925 CAAAATAGTAACAATATAATAG
1 CAAAATAGTAGCAA-ATAATAG
* * ** *
3535947 TAAACTAGTAGCAAATAGCAA
1 CAAAATAGTAGCAAATAATAG
*
3535968 CAAAATAGTAGCAAACAATAG
1 CAAAATAGTAGCAAATAATAG
3535989 CAAAATA
1 CAAAATA
3535996 ACACTGAAAA
Statistics
Matches: 37, Mismatches: 12, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
21 26 0.70
22 11 0.30
ACGTcount: A:0.58, C:0.13, G:0.11, T:0.18
Consensus pattern (21 bp):
CAAAATAGTAGCAAATAATAG
Found at i:3535995 original size:32 final size:33
Alignment explanation
Indices: 3535925--3535995 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 33
3535915 ATAAAAACAA
* * * *
3535925 CAAAATAGTAACAATATAATAGTAAACTAGTAG
1 CAAAATAGCAACAAAATAATAGCAAACTAATAG
*
3535958 C-AAATAGCAACAAAATAGTAGCAAAC-AATAG
1 CAAAATAGCAACAAAATAATAGCAAACTAATAG
3535989 CAAAATA
1 CAAAATA
3535996 ACACTGAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
31 5 0.16
32 26 0.81
33 1 0.03
ACGTcount: A:0.58, C:0.13, G:0.11, T:0.18
Consensus pattern (33 bp):
CAAAATAGCAACAAAATAATAGCAAACTAATAG
Found at i:3543816 original size:31 final size:35
Alignment explanation
Indices: 3543755--3543817 Score: 89
Period size: 33 Copynumber: 1.9 Consensus size: 35
3543745 TACATTTGTA
*
3543755 TTATATATATAATTAGTAAAAATATATTTTATTAT
1 TTATATATATAATTAGTAAAAAGATATTTTATTAT
3543790 TTAT-TAT-TAATTAGT-AAAAGAT-TTTTAT
1 TTATATATATAATTAGTAAAAAGATATTTTAT
3543818 ATGATAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 6 0.22
32 6 0.22
33 8 0.30
34 3 0.11
35 4 0.15
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (35 bp):
TTATATATATAATTAGTAAAAAGATATTTTATTAT
Found at i:3544139 original size:11 final size:11
Alignment explanation
Indices: 3544125--3544166 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
3544115 ATAAAAGCAT
3544125 AAAAAGAAACA
1 AAAAAGAAACA
*
3544136 AAAAAGAAA-T
1 AAAAAGAAACA
*
3544146 AGAAAGAAACA
1 AAAAAGAAACA
*
3544157 AAATAGAAAC
1 AAAAAGAAAC
3544167 GAATAGGGAG
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
10 8 0.32
11 17 0.68
ACGTcount: A:0.76, C:0.07, G:0.12, T:0.05
Consensus pattern (11 bp):
AAAAAGAAACA
Found at i:3544399 original size:29 final size:29
Alignment explanation
Indices: 3544358--3544415 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
3544348 TTTTTTAGTA
3544358 GGGTTTATGTTGAAT-AAATGATTGAATTAG
1 GGGTTTATGTTG-ATGAAATGATTG-ATTAG
*
3544388 GGGTTTAT-TTGATGAAATTATTGATTAG
1 GGGTTTATGTTGATGAAATGATTGATTAG
3544416 AATTGATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 7 0.27
29 11 0.42
30 8 0.31
ACGTcount: A:0.31, C:0.00, G:0.26, T:0.43
Consensus pattern (29 bp):
GGGTTTATGTTGATGAAATGATTGATTAG
Found at i:3552587 original size:19 final size:19
Alignment explanation
Indices: 3552539--3552589 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 19
3552529 TACAATTTTG
3552539 TTTTTAATTTTGTCAAATT
1 TTTTTAATTTTGTCAAATT
3552558 TTTACTT-ATTTT-TCAAATT
1 TTT--TTAATTTTGTCAAATT
3552577 TTCTTTAATTTTG
1 TT-TTTAATTTTG
3552590 GACCAATCGA
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
18 2 0.07
19 17 0.63
20 6 0.22
21 2 0.07
ACGTcount: A:0.24, C:0.08, G:0.04, T:0.65
Consensus pattern (19 bp):
TTTTTAATTTTGTCAAATT
Found at i:3554570 original size:16 final size:16
Alignment explanation
Indices: 3554549--3554584 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
3554539 TTTGGTTCGC
*
3554549 TGTATTGGATTAGAGG
1 TGTATTGGATTAAAGG
3554565 TGTATTGGATTAAAGG
1 TGTATTGGATTAAAGG
3554581 TGTA
1 TGTA
3554585 ATAGCAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.33, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAAAGG
Found at i:3554648 original size:44 final size:44
Alignment explanation
Indices: 3554598--3554699 Score: 151
Period size: 39 Copynumber: 2.4 Consensus size: 44
3554588 GCAAATCAAC
3554598 TGTTTGGTTGAATGTAATGGAATAGAGGCGTAATAGTAATCTTA
1 TGTTTGGTTGAATGTAATGGAATAGAGGCGTAATAGTAATCTTA
* *
3554642 TGTTTGG-T---TG-AATGGAATAGAGGTGTAATAGTAATCTTG
1 TGTTTGGTTGAATGTAATGGAATAGAGGCGTAATAGTAATCTTA
3554681 TGTTTGGTTGAATGTAATG
1 TGTTTGGTTGAATGTAATG
3554700 TTAAGATCCG
Statistics
Matches: 51, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
39 34 0.67
40 3 0.06
43 3 0.06
44 11 0.22
ACGTcount: A:0.28, C:0.03, G:0.29, T:0.39
Consensus pattern (44 bp):
TGTTTGGTTGAATGTAATGGAATAGAGGCGTAATAGTAATCTTA
Found at i:3555384 original size:22 final size:22
Alignment explanation
Indices: 3555337--3555385 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
3555327 TTCCATTTGC
* * *
3555337 TCTCTTTTTCTTGATTTTGTAT
1 TCTCTTTTTCTTCATTTTCTAA
3555359 TCTCTTTTT-TTCATTTCTCTAA
1 TCTCTTTTTCTTCATTT-TCTAA
3555381 TCTCT
1 TCTCT
3555386 CTCCGCAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.10, C:0.20, G:0.04, T:0.65
Consensus pattern (22 bp):
TCTCTTTTTCTTCATTTTCTAA
Found at i:3558142 original size:32 final size:32
Alignment explanation
Indices: 3558098--3558171 Score: 139
Period size: 32 Copynumber: 2.3 Consensus size: 32
3558088 AGGTTCAAAT
*
3558098 CTTGTTGGTAACAATTTTAAATCTTTTTTGTA
1 CTTGTTGCTAACAATTTTAAATCTTTTTTGTA
3558130 CTTGTTGCTAACAATTTTAAATCTTTTTTGTA
1 CTTGTTGCTAACAATTTTAAATCTTTTTTGTA
3558162 CTTGTTGCTA
1 CTTGTTGCTA
3558172 TTGATGTAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.23, C:0.12, G:0.12, T:0.53
Consensus pattern (32 bp):
CTTGTTGCTAACAATTTTAAATCTTTTTTGTA
Found at i:3561358 original size:46 final size:47
Alignment explanation
Indices: 3561295--3561391 Score: 162
Period size: 47 Copynumber: 2.1 Consensus size: 47
3561285 ACATTTTCTT
*
3561295 ACAT-ACAGAGAC-TTTTTTGCCTAAAATTATACCCTCAATCATTTA
1 ACATCACAAAGACTTTTTTTGCCTAAAATTATACCCTCAATCATTTA
*
3561340 ACATCACAAAGACTTTTTTTGGCTAAAATTATACCCTCAATCATTTA
1 ACATCACAAAGACTTTTTTTGCCTAAAATTATACCCTCAATCATTTA
3561387 ACATC
1 ACATC
3561392 TCCTTTTCTT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
45 4 0.08
46 7 0.15
47 37 0.77
ACGTcount: A:0.36, C:0.23, G:0.06, T:0.35
Consensus pattern (47 bp):
ACATCACAAAGACTTTTTTTGCCTAAAATTATACCCTCAATCATTTA
Found at i:3568429 original size:114 final size:114
Alignment explanation
Indices: 3568229--3568457 Score: 458
Period size: 114 Copynumber: 2.0 Consensus size: 114
3568219 CTATTATATA
3568229 TAGTAACTTGTCTCTGTTTCCCAAATCTTTGTTGGCCATTGTAGCTTAAACAAAAGCTCAACACC
1 TAGTAACTTGTCTCTGTTTCCCAAATCTTTGTTGGCCATTGTAGCTTAAACAAAAGCTCAACACC
3568294 CGAGGTTTTAAGAAAAAAGGTTTGTTTTCCTTTTCTGCCTTCTCTTTTT
66 CGAGGTTTTAAGAAAAAAGGTTTGTTTTCCTTTTCTGCCTTCTCTTTTT
3568343 TAGTAACTTGTCTCTGTTTCCCAAATCTTTGTTGGCCATTGTAGCTTAAACAAAAGCTCAACACC
1 TAGTAACTTGTCTCTGTTTCCCAAATCTTTGTTGGCCATTGTAGCTTAAACAAAAGCTCAACACC
3568408 CGAGGTTTTAAGAAAAAAGGTTTGTTTTCCTTTTCTGCCTTCTCTTTTT
66 CGAGGTTTTAAGAAAAAAGGTTTGTTTTCCTTTTCTGCCTTCTCTTTTT
3568457 T
1 T
3568458 CCTTTTTGTC
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
114 115 1.00
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.41
Consensus pattern (114 bp):
TAGTAACTTGTCTCTGTTTCCCAAATCTTTGTTGGCCATTGTAGCTTAAACAAAAGCTCAACACC
CGAGGTTTTAAGAAAAAAGGTTTGTTTTCCTTTTCTGCCTTCTCTTTTT
Found at i:3572457 original size:16 final size:16
Alignment explanation
Indices: 3572427--3572460 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
3572417 TTTTTTCAAA
3572427 TTTATTAAAATATTAT
1 TTTATTAAAATATTAT
3572443 TTTA-TAAAATAATTAT
1 TTTATTAAAAT-ATTAT
3572459 TT
1 TT
3572461 CCATCCATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTATTAAAATATTAT
Found at i:3575591 original size:46 final size:45
Alignment explanation
Indices: 3575524--3575927 Score: 400
Period size: 46 Copynumber: 9.5 Consensus size: 45
3575514 AGTACTTCTA
* *
3575524 ATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTG
1 ATCAAGTGAAAAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTG
3575570 ATCAAGTGAAAAAGTGAT-A-----AG--T-GCTACACTTATCTG
1 ATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTG
* * * *
3575606 ATCAAGAGACAAAGTGATAACTGATAGCTTTAGCTACACTTATCTG
1 ATCAAGTGAAAAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTG
3575652 ATCAAGTGAAAAAGTGATAA---GT-GC-TA--T--ACTTATCTG
1 ATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTG
*
3575688 ATCAAGTGAAAAAGTGATAA-----A---T-GCTATACTTATCTG
1 ATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTG
* *
3575724 ATCAAGTGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTATCTG
1 ATCAAGTGAAAAAGTGATAAGTGGTAG-CTTAGCTACACTTATCTG
* *
3575770 ATCAAGTGAGAAAGTGATAAGTGGTAGCCTTAGTTACACTTATCTG
1 ATCAAGTGAAAAAGTGATAAGTGGTAG-CTTAGCTACACTTATCTG
* *
3575816 ATCAAGTGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTATCTG
1 ATCAAGTGAAAAAGTGATAAGTGGTAG-CTTAGCTACACTTATCTG
*
3575862 ATCAAGTGACAAAGTGATAAGTGGTAG-TCTAGCTACACTTATCTG
1 ATCAAGTGAAAAAGTGATAAGTGGTAGCT-TAGCTACACTTATCTG
* *
3575907 ATC-AG-GGACAAGTGATAAGTG
1 ATCAAGTGAAAAAGTGATAAGTG
3575928 ATCATACGTA
Statistics
Matches: 313, Mismatches: 19, Indels: 55
0.81 0.05 0.14
Matches are distributed among these distances:
33 1 0.00
34 1 0.00
36 87 0.28
37 2 0.01
38 1 0.00
40 4 0.01
41 1 0.00
42 4 0.01
43 14 0.04
44 3 0.01
45 22 0.07
46 173 0.55
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (45 bp):
ATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTG
Found at i:3575597 original size:36 final size:36
Alignment explanation
Indices: 3575556--3575746 Score: 238
Period size: 36 Copynumber: 5.0 Consensus size: 36
3575546 GGTAGCTTTA
3575556 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
3575592 GCTACACTTATCTGATCAAGAGACAAAGTGATAACTGATAGCTTT
1 GCTACACTTATCTGATCAAGTGAAAAAGTG---A-T-A-AG---T
3575637 AGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 -GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
3575674 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAAT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
3575710 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
3575746 G
1 G
3575747 TTAGCCTTAG
Statistics
Matches: 137, Mismatches: 8, Indels: 20
0.83 0.05 0.12
Matches are distributed among these distances:
36 97 0.71
37 1 0.01
39 1 0.01
40 3 0.02
41 2 0.01
42 3 0.02
43 1 0.01
45 1 0.01
46 28 0.20
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:3575661 original size:82 final size:82
Alignment explanation
Indices: 3575524--3575927 Score: 393
Period size: 82 Copynumber: 4.8 Consensus size: 82
3575514 AGTACTTCTA
* *
3575524 ATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATA
1 ATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATA
3575589 AGTGCTACACTTATCTG
66 AGTGCTACACTTATCTG
* * *
3575606 ATCAAGAGACAAAGTGATAACTGATAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATA
1 ATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATA
*
3575671 AGTGCTATACTTATCTG
66 AGTGCTACACTTATCTG
* * *
3575688 ATCAAGTGAAAAAGTGATAA-----A----T-GCTATACTTATCTGATCAAGTGACAAAGTGATA
1 ATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGTGAT-
3575743 AGTGTTAGCCTTAGCTACACTTATCTG
65 A-----AG---T-GCTACACTTATCTG
* * * *
3575770 ATCAAGTGAGAAAGTGATAAGTGGTAGCCTTAGTTACACTTATCTGATCAAGTGACAAAGTGATA
1 ATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGTGAT-
3575835 AGTGTTAGCCTTAGCTACACTTATCTG
65 A-----AG---T-GCTACACTTATCTG
* * *
3575862 ATCAAGTGACAAAGTGATAAGTGGTAG-TCTAGCTACACTTATCTGATC-AG-GGACAAGTGATA
1 ATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATA
3575924 AGTG
66 AGTG
3575928 ATCATACGTA
Statistics
Matches: 283, Mismatches: 19, Indels: 43
0.82 0.06 0.12
Matches are distributed among these distances:
72 30 0.11
73 2 0.01
77 1 0.00
78 2 0.01
79 1 0.00
80 1 0.00
81 1 0.00
82 128 0.45
83 2 0.01
87 1 0.00
88 1 0.00
89 8 0.03
90 2 0.01
91 19 0.07
92 84 0.30
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (82 bp):
ATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATA
AGTGCTACACTTATCTG
Found at i:3578190 original size:52 final size:52
Alignment explanation
Indices: 3578111--3578379 Score: 388
Period size: 52 Copynumber: 5.2 Consensus size: 52
3578101 TACTTCTGAT
* **
3578111 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGA
1 CAAGTGA-AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
* * *
3578164 CAAGTGGAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGA
1 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
3578216 C------AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
1 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
3578262 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
1 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
** *
3578314 CAAGTGAAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGA
1 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
*
3578366 CAAAGTGATAAGTG
1 C-AAGTGAAAAGTG
3578380 GCTACACTTA
Statistics
Matches: 197, Mismatches: 12, Indels: 14
0.88 0.05 0.06
Matches are distributed among these distances:
46 44 0.22
52 136 0.69
53 17 0.09
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (52 bp):
CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
Found at i:3578225 original size:98 final size:98
Alignment explanation
Indices: 3578105--3578379 Score: 415
Period size: 98 Copynumber: 2.7 Consensus size: 98
3578095 TTTGAGTACT
*
3578105 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
* *
3578170 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTACACTTA
**
3578203 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
3578268 AAAAGTGATAAGTGATAGCTTCGGCTACACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTACACTTA
*
3578301 TCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGA
1 TCTGATCAAGTGAC------AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGA
*
3578366 CAAAGTGATAAGTG
60 C-AAGTGAAAAGTG
3578380 GCTACACTTA
Statistics
Matches: 160, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
98 106 0.66
104 43 0.27
105 11 0.07
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.28
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTACACTTA
Found at i:3578387 original size:37 final size:37
Alignment explanation
Indices: 3578343--3578488 Score: 251
Period size: 37 Copynumber: 4.0 Consensus size: 37
3578333 GATAGCTTTA
3578343 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
3578380 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
* *
3578417 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
3578454 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
3578489 ATCATACGTA
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 89 0.86
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
Found at i:3579473 original size:439 final size:440
Alignment explanation
Indices: 3578649--3579527 Score: 1553
Period size: 439 Copynumber: 2.0 Consensus size: 440
3578639 AGGACGATGT
*
3578649 TGTTATTCAAACTAAAGTGATATTTTCATTGCTAAATTGAGAATTTCATAAATGTGTTATTGAAT
1 TGTTATTCAAACTAAAGTGATATTTTCATTGCAAAATTGAGAATTTCATAAATGTGTTATTGAAT
* *
3578714 GGTATAATCAATAAACATTGAGTTAAATGGTAAATACGTATTAGTTTTGAATTTGATGTCATTGA
66 GGTATAATCAATAAACATTGAGTTAAATGGTAAATACGTATTAGTGTTGAACTTGATGTCATTGA
* *
3578779 ATTGTACGTGAATTAAATGGAAATTTCTAGTGATATGATTTAAATTATGAGCATGAGAAATTGCG
131 ATTGTACGTGAATTAAATGGAAATTGCTAGTGATATGATCTAAATTATGAGCATGAGAAATTGCG
* *
3578844 AATTGAATGAAATGGAAATGAAGCATTAAATTGCATGAGTATGTATCGGGTCTCGCAGGCCCTAA
196 AATTGAAGGAAATGGAAATGAAGCATTAAATTGCATGAGTATGTATCGGGTCTCGCAAGCCCTAA
*
3578909 TTATTATGATTATAATATTTTGAGGATATATTGTGAAAAGTTATAGAAACATGTTAATTATTTTG
261 TTATTATGATTATAACATTTTGAGGATATATTGTGAAAAGTTATAGAAACATGTTAATTATTTTG
* *
3578974 AAAGTTTTAATTTTGATGAAATTTTATAACTCGGTTAAATACGTTTACAAGTGTATGTGTTTTGG
326 AAAGTTTTAATTTAGATGAAATTTTATAACTCGGTTAAATACGTTTACAAGTGCATGTGTTTTGG
* * *
3579039 TAATGCCTCGTACCCTATTCCGGTGTTGGATACGGGTAAGGGGTGTTACA
391 TAATGCATCGTACCCTATTCCGGTATTGAATACGGGTAAGGGGTGTTACA
*
3579089 TGTTATTCAAGCTAAAGTGATATTTTCATTGCAAAATTGAGAATTTCATAAATGT-TTATTGAAT
1 TGTTATTCAAACTAAAGTGATATTTTCATTGCAAAATTGAGAATTTCATAAATGTGTTATTGAAT
*
3579153 GGTATAATCAATAAACATTGAGTTAAATGGTAAATATGTATTAGTGTTGAACTTGATGTCATTGA
66 GGTATAATCAATAAACATTGAGTTAAATGGTAAATACGTATTAGTGTTGAACTTGATGTCATTGA
* *
3579218 ATTGTACGTGAGTTAAATGGAAATTGCTAGTGATATGATCTAAATTGTGAGCATGAGAAATTGCG
131 ATTGTACGTGAATTAAATGGAAATTGCTAGTGATATGATCTAAATTATGAGCATGAGAAATTGCG
* *
3579283 AATTGAAGGAAATGGAAATGAAGCATTGAATTGCATGAGTATGTATCGGGTCTCGTAAGCCCTAA
196 AATTGAAGGAAATGGAAATGAAGCATTAAATTGCATGAGTATGTATCGGGTCTCGCAAGCCCTAA
* *
3579348 TTATTATGATTATAACATTTTGAGGATATATTGTGAAAAGTTATAGGAGCATGTTAATTATTTTG
261 TTATTATGATTATAACATTTTGAGGATATATTGTGAAAAGTTATAGAAACATGTTAATTATTTTG
3579413 AAAGTTTTAATTTAGATGAAATTTTATAACTCGGTTAAATACGTTTACAAGTGCATGTGTTTTGG
326 AAAGTTTTAATTTAGATGAAATTTTATAACTCGGTTAAATACGTTTACAAGTGCATGTGTTTTGG
*
3579478 TAATGTATCGTACCCTATTCCGGTATTGAATACGGGTAAGGGGTGTTACA
391 TAATGCATCGTACCCTATTCCGGTATTGAATACGGGTAAGGGGTGTTACA
3579528 CCTGAACTCA
Statistics
Matches: 417, Mismatches: 22, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
439 364 0.87
440 53 0.13
ACGTcount: A:0.34, C:0.08, G:0.21, T:0.37
Consensus pattern (440 bp):
TGTTATTCAAACTAAAGTGATATTTTCATTGCAAAATTGAGAATTTCATAAATGTGTTATTGAAT
GGTATAATCAATAAACATTGAGTTAAATGGTAAATACGTATTAGTGTTGAACTTGATGTCATTGA
ATTGTACGTGAATTAAATGGAAATTGCTAGTGATATGATCTAAATTATGAGCATGAGAAATTGCG
AATTGAAGGAAATGGAAATGAAGCATTAAATTGCATGAGTATGTATCGGGTCTCGCAAGCCCTAA
TTATTATGATTATAACATTTTGAGGATATATTGTGAAAAGTTATAGAAACATGTTAATTATTTTG
AAAGTTTTAATTTAGATGAAATTTTATAACTCGGTTAAATACGTTTACAAGTGCATGTGTTTTGG
TAATGCATCGTACCCTATTCCGGTATTGAATACGGGTAAGGGGTGTTACA
Found at i:3579756 original size:21 final size:20
Alignment explanation
Indices: 3579732--3579783 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
3579722 GCACAAAAAT
*
3579732 AAAAAATGTTAACTTATGGA
1 AAAAAATGTTAAATTATGGA
* *
3579752 AAAAAATGATTAAATTTTGTAA
1 AAAAAATG-TTAAATTATG-GA
3579774 AAAAAATGTT
1 AAAAAATGTT
3579784 TGTTTATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 8 0.30
21 10 0.37
22 9 0.33
ACGTcount: A:0.54, C:0.02, G:0.12, T:0.33
Consensus pattern (20 bp):
AAAAAATGTTAAATTATGGA
Found at i:3581293 original size:22 final size:23
Alignment explanation
Indices: 3581268--3581310 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
3581258 GGTATTTTAA
3581268 ATATAAATATTTATTT-TATTTT
1 ATATAAATATTTATTTATATTTT
3581290 ATATAAATATTTATTTATATT
1 ATATAAATATTTATTTATATT
3581311 CATATTTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
ATATAAATATTTATTTATATTTT
Found at i:3581315 original size:22 final size:22
Alignment explanation
Indices: 3581268--3581315 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
3581258 GGTATTTTAA
*
3581268 ATATAAATATTTATTTTATTTT
1 ATATAAATATTTATTTTATTTC
3581290 ATATAAATATTTA-TTTATATTC
1 ATATAAATATTTATTTTAT-TTC
3581312 ATAT
1 ATAT
3581316 TTGTTGACTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
ATATAAATATTTATTTTATTTC
Found at i:3582631 original size:9 final size:9
Alignment explanation
Indices: 3582619--3582773 Score: 57
Period size: 9 Copynumber: 16.0 Consensus size: 9
3582609 AAAAATTAGA
3582619 ATAAAAATT
1 ATAAAAATT
3582628 ATAAAAA-T
1 ATAAAAATT
*
3582636 A-AAATTATT
1 ATAAA-AATT
3582645 AATATTAAAATT
1 -ATA--AAAATT
*
3582657 ATATAAACTT
1 ATA-AAAATT
*
3582667 CTAAAAATT
1 ATAAAAATT
3582676 ATAAAAAAATAT
1 AT--AAAAAT-T
3582688 ATAAAAA-T
1 ATAAAAATT
*
3582696 A-ATAAATT
1 ATAAAAATT
*
3582704 ATAATAAAATA
1 AT-A-AAAATT
3582715 ATAAAATATTTT
1 ATAAAA-A--TT
*
3582727 TTAAAAATAT
1 ATAAAAAT-T
* *
3582737 TTAAAATTTT
1 ATAAAA-ATT
3582747 ATAAAAATT
1 ATAAAAATT
* *
3582756 TTAAAAATC
1 ATAAAAATT
3582765 ATAAAAATT
1 ATAAAAATT
3582774 TGAATTGGAC
Statistics
Matches: 110, Mismatches: 18, Indels: 36
0.67 0.11 0.22
Matches are distributed among these distances:
7 7 0.06
8 7 0.06
9 34 0.31
10 30 0.27
11 18 0.16
12 12 0.11
13 2 0.02
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (9 bp):
ATAAAAATT
Found at i:3582711 original size:48 final size:48
Alignment explanation
Indices: 3582620--3582711 Score: 116
Period size: 48 Copynumber: 1.9 Consensus size: 48
3582610 AAAATTAGAA
** *
3582620 TAAAAATTATAAAAATAAAATTATTAATATTAAAATTATATAAACTTC
1 TAAAAATTATAAAAATAAAATTAAAAATAATAAAATTATATAAACTTC
*
3582668 TAAAAATTATAAAAA-AATATATAAAAATAAT-AAATTATAATAAA
1 TAAAAATTATAAAAATAAAAT-TAAAAATAATAAAATTAT-ATAAA
3582712 ATAATAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
47 11 0.29
48 27 0.71
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (48 bp):
TAAAAATTATAAAAATAAAATTAAAAATAATAAAATTATATAAACTTC
Found at i:3582712 original size:29 final size:28
Alignment explanation
Indices: 3582608--3582720 Score: 101
Period size: 28 Copynumber: 4.0 Consensus size: 28
3582598 TAAAAATATT
*
3582608 TAAAAATTAGAATAAAAAT-TATAAAAA
1 TAAAAATTATAATAAAAATATATAAAAA
**
3582635 T-AAAATTATTAATATTAAAATTATATAAACTTC
1 TAAAAATTA-TAATA--AAAA-TATATAAA--AA
3582668 TAAAAATTATAA-AAAAATATATAAAAA
1 TAAAAATTATAATAAAAATATATAAAAA
3582695 TAATAAATTATAAT-AAAATA-ATAAAA
1 TAA-AAATTATAATAAAAATATATAAAA
3582721 TATTTTTTAA
Statistics
Matches: 71, Mismatches: 5, Indels: 20
0.74 0.05 0.21
Matches are distributed among these distances:
26 7 0.10
27 14 0.20
28 15 0.21
29 12 0.17
30 5 0.07
31 6 0.08
32 1 0.01
33 4 0.06
34 7 0.10
ACGTcount: A:0.65, C:0.02, G:0.01, T:0.32
Consensus pattern (28 bp):
TAAAAATTATAATAAAAATATATAAAAA
Found at i:3582720 original size:48 final size:48
Alignment explanation
Indices: 3582618--3582720 Score: 111
Period size: 48 Copynumber: 2.1 Consensus size: 48
3582608 TAAAAATTAG
** * *
3582618 AATAAAAATTATAAAAATAAAATTATTAATATTAAAATTATATAAACT
1 AATAAAAATTATAAAAATAAAATTAAAAATAATAAAATTATATAAAAT
** *
3582666 TCTAAAAATTATAAAAA-AATATATAAAAATAAT-AAATTATAATAAAAT
1 AATAAAAATTATAAAAATAAAAT-TAAAAATAATAAAATTAT-ATAAAAT
3582714 AATAAAA
1 AATAAAA
3582721 TATTTTTTAA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
47 11 0.25
48 33 0.75
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (48 bp):
AATAAAAATTATAAAAATAAAATTAAAAATAATAAAATTATATAAAAT
Found at i:3582733 original size:21 final size:20
Alignment explanation
Indices: 3582668--3582754 Score: 63
Period size: 21 Copynumber: 4.3 Consensus size: 20
3582658 TATAAACTTC
* * *
3582668 TAAAAATTATAAAAAAATATA
1 TAAAAATAAT-AAAAATTTTA
*
3582689 TAAAAATAAT--AAATTATA
1 TAAAAATAATAAAAATTTTA
*
3582707 -ATAAAATAATAAAATATTTTT
1 TA-AAAATAATAAAA-ATTTTA
* *
3582728 TAAAAATATTTAAAATTTTA
1 TAAAAATAATAAAAATTTTA
3582748 TAAAAAT
1 TAAAAAT
3582755 TTTAAAAATC
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
17 1 0.02
18 15 0.28
20 14 0.26
21 23 0.43
22 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
TAAAAATAATAAAAATTTTA
Found at i:3582745 original size:20 final size:19
Alignment explanation
Indices: 3582722--3582774 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 19
3582712 ATAATAAAAT
*
3582722 ATTTTTTAAAAATATTTAAA
1 ATTTTATAAAAAT-TTTAAA
3582742 ATTTTATAAAAATTTTAAA
1 ATTTTATAAAAATTTTAAA
* *
3582761 A-ATCATAAAAATTT
1 ATTTTATAAAAATTT
3582775 GAATTGGACC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
18 11 0.37
19 7 0.23
20 12 0.40
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTTATAAAAATTTTAAA
Found at i:3586768 original size:54 final size:54
Alignment explanation
Indices: 3586710--3587092 Score: 430
Period size: 54 Copynumber: 7.1 Consensus size: 54
3586700 GCAACACCAG
* * * *
3586710 CAACAATGAAAATGCGGGTCAGGACGAGAAGAATGCCACTCAGAGTAACACTGA
1 CAACAATGAAAATGCGGGTCAGAACGAGAACAATGCTACTCAGAGCAACACTGA
* * *
3586764 CAACAATGAAAATGTGGGTCAGAATGAGAACAATGCTGCTCAGAGCAACACTGA
1 CAACAATGAAAATGCGGGTCAGAACGAGAACAATGCTACTCAGAGCAACACTGA
* * * * *
3586818 GAACAATGAAAATGCGGGTCAGAATGAGAGCAATGCTGCTCAGAGCAACACCGA
1 CAACAATGAAAATGCGGGTCAGAACGAGAACAATGCTACTCAGAGCAACACTGA
* ** * * *
3586872 GAACAATGAAAATGCAAGTCAGAACGAGAGCAATGCAACTCAGAGCAACACCGA
1 CAACAATGAAAATGCGGGTCAGAACGAGAACAATGCTACTCAGAGCAACACTGA
* * * * * * *
3586926 GAACAATCAGAATGCGGATCAGAACGAGCACAATGCTGCTCCA-AGTAACACTGA
1 CAACAATGAAAATGCGGGTCAGAACGAGAACAATGCTACT-CAGAGCAACACTGA
* * * * *
3586980 GAACAATGAGAATGCGGGTCAGAACGAGAACAATGCCACTCCA-AGTAACACCGA
1 CAACAATGAAAATGCGGGTCAGAACGAGAACAATGCTACT-CAGAGCAACACTGA
* *
3587034 CAACAATGAGAATGCAGGTCAGAACGAGAACAATG-TGACTCAGAGCAACACTGA
1 CAACAATGAAAATGCGGGTCAGAACGAGAACAATGCT-ACTCAGAGCAACACTGA
3587088 CAACA
1 CAACA
3587093 GCAACAGCAA
Statistics
Matches: 288, Mismatches: 38, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
53 2 0.01
54 284 0.99
55 2 0.01
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.13
Consensus pattern (54 bp):
CAACAATGAAAATGCGGGTCAGAACGAGAACAATGCTACTCAGAGCAACACTGA
Found at i:3586868 original size:162 final size:161
Alignment explanation
Indices: 3586687--3587092 Score: 496
Period size: 162 Copynumber: 2.5 Consensus size: 161
3586677 TTCAAATGAA
* * * *
3586687 AATGCTGCACAAAGCAACACCAGCAACAATGAAAATGCGGGTCAGGACGAGAAGAATGCCACTCA
1 AATGCTGCTC-AAGCAACACCAGCAACAATGAAAATGCAGGTCAGAACGAGAAGAATGCAACTCA
* * * * *
3586752 GAGTAACACTGACAACAATGAAAATGTGGGTCAGAATGAGAACAATGCTGCT-CAGAGCAACACT
65 GAGCAACACTGACAACAATCAAAATGCGGATCAGAACGAGAACAATGCTGCTCCA-AGCAACACT
* *
3586816 GAGAACAATGAAAATGCGGGTCAGAATGAGAGC
129 GAGAACAATGAAAATGCGGGTCAGAACGAGAAC
*
3586849 AATGCTGCTCAGAGCAACACCGAG-AACAATGAAAATGCAAGTCAGAACGAG-AGCAATGCAACT
1 AATGCTGCTCA-AGCAACACC-AGCAACAATGAAAATGCAGGTCAGAACGAGAAG-AATGCAACT
* * * * *
3586912 CAGAGCAACACCGAGAACAATCAGAATGCGGATCAGAACGAGCACAATGCTGCTCCAAGTAACAC
63 CAGAGCAACACTGACAACAATCAAAATGCGGATCAGAACGAGAACAATGCTGCTCCAAGCAACAC
*
3586977 TGAGAACAATGAGAATGCGGGTCAGAACGAGAAC
128 TGAGAACAATGAAAATGCGGGTCAGAACGAGAAC
** * * * **
3587011 AATGCCACTCCAAGTAACACC-GACAACAATGAGAATGCAGGTCAGAACGAGAACAATGTGACTC
1 AATGCTGCT-CAAGCAACACCAG-CAACAATGAAAATGCAGGTCAGAACGAGAAGAATGCAACTC
3587075 AGAGCAACACTGACAACA
64 AGAGCAACACTGACAACA
3587093 GCAACAGCAA
Statistics
Matches: 208, Mismatches: 28, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
160 1 0.00
161 3 0.01
162 197 0.95
163 7 0.03
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.13
Consensus pattern (161 bp):
AATGCTGCTCAAGCAACACCAGCAACAATGAAAATGCAGGTCAGAACGAGAAGAATGCAACTCAG
AGCAACACTGACAACAATCAAAATGCGGATCAGAACGAGAACAATGCTGCTCCAAGCAACACTGA
GAACAATGAAAATGCGGGTCAGAACGAGAAC
Found at i:3586899 original size:27 final size:27
Alignment explanation
Indices: 3586869--3587068 Score: 92
Period size: 27 Copynumber: 7.4 Consensus size: 27
3586859 AGAGCAACAC
*
3586869 CGAGAACAATGAAAATGCAAGTCAGAA
1 CGAGAACAATGAGAATGCAAGTCAGAA
* *
3586896 CGAGAGCAATGCA-ACT-CAGAG-CA-ACA
1 CGAGAACAATG-AGAATGCA-AGTCAGA-A
* *
3586922 CCGAGAACAATCAGAATGC-GGATCAGAA
1 -CGAGAACAATGAGAATGCAAG-TCAGAA
* * * *
3586950 CGAGCACAATGCTG-CTCCAAGT-A-ACA
1 CGAGAACAATG-AGAATGCAAGTCAGA-A
**
3586976 CTGAGAACAATGAGAATGCGGGTCAGAA
1 C-GAGAACAATGAGAATGCAAGTCAGAA
** * * * * *
3587004 CGAGAACAATGCCACTCCAAGTAACAC
1 CGAGAACAATGAGAATGCAAGTCAGAA
* *
3587031 CGACAACAATGAGAATGCAGGTCAGAA
1 CGAGAACAATGAGAATGCAAGTCAGAA
3587058 CGAGAACAATG
1 CGAGAACAATG
3587069 TGACTCAGAG
Statistics
Matches: 120, Mismatches: 37, Indels: 32
0.63 0.20 0.17
Matches are distributed among these distances:
25 2 0.02
26 11 0.09
27 95 0.79
28 10 0.08
29 2 0.02
ACGTcount: A:0.42, C:0.23, G:0.23, T:0.12
Consensus pattern (27 bp):
CGAGAACAATGAGAATGCAAGTCAGAA
Found at i:3587186 original size:51 final size:51
Alignment explanation
Indices: 3587104--3587202 Score: 146
Period size: 51 Copynumber: 1.9 Consensus size: 51
3587094 CAACAGCAAC
3587104 AACAACAACGAAAATGCAAGTCAAAACGAGAACAATGC-TGCTCAGAGCAGT
1 AACAACAACGAAAATGCAAGTCAAAACGAGAACAATGCAT-CTCAGAGCAGT
* ** *
3587155 AACAACAATGAAAATGCAAGTCAGGATGAGAACAATGCATCTCAGAGC
1 AACAACAACGAAAATGCAAGTCAAAACGAGAACAATGCATCTCAGAGC
3587203 TTCACCGACA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 42 0.98
52 1 0.02
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.13
Consensus pattern (51 bp):
AACAACAACGAAAATGCAAGTCAAAACGAGAACAATGCATCTCAGAGCAGT
Found at i:3587254 original size:63 final size:63
Alignment explanation
Indices: 3587155--3587286 Score: 210
Period size: 63 Copynumber: 2.1 Consensus size: 63
3587145 TCAGAGCAGT
* * * *
3587155 AACAACAATGAAAATGCAAGTCAGGATGAGAACAATGCATCTCAGAGCTTCACCGACACCACC
1 AACAACAATGAAAATGCAAGTCAGAACGAAAACAATGCATCTCAGAGCTACACCGACACCACC
*
3587218 AACAACAATGAAAATGCAAGTCAGAACGAAAACAATGCTTCTCAGAGCTACACCGACACCACC
1 AACAACAATGAAAATGCAAGTCAGAACGAAAACAATGCATCTCAGAGCTACACCGACACCACC
*
3587281 ACCAAC
1 AACAAC
3587287 GAGAGCAACG
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.43, C:0.29, G:0.15, T:0.13
Consensus pattern (63 bp):
AACAACAATGAAAATGCAAGTCAGAACGAAAACAATGCATCTCAGAGCTACACCGACACCACC
Found at i:3588988 original size:31 final size:31
Alignment explanation
Indices: 3588953--3589012 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
3588943 CTGAATTTAG
*
3588953 CAACTAGGTCCACTTTGGTAC-TTGAACTTGA
1 CAACTAGATCCACTTTGGT-CTTTGAACTTGA
*
3588984 CAACTAGATCCATTTTGGTCTTTGAACTT
1 CAACTAGATCCACTTTGGTCTTTGAACTT
3589013 AGATTCTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 1 0.04
31 25 0.96
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.37
Consensus pattern (31 bp):
CAACTAGATCCACTTTGGTCTTTGAACTTGA
Found at i:3595265 original size:23 final size:23
Alignment explanation
Indices: 3595239--3595286 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
3595229 TTAATTTTCA
3595239 AATTATTTAGTGATAATATTTAG
1 AATTATTTAGTGATAATATTTAG
*
3595262 AATTATTTAGTTATAATATTTAG
1 AATTATTTAGTGATAATATTTAG
3595285 AA
1 AA
3595287 AAAATCTAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (23 bp):
AATTATTTAGTGATAATATTTAG
Found at i:3596196 original size:13 final size:13
Alignment explanation
Indices: 3596124--3596200 Score: 57
Period size: 13 Copynumber: 5.6 Consensus size: 13
3596114 TTAAAAAATA
*
3596124 TTTTA-TTTATCT
1 TTTTATTTTATTT
*
3596136 ATTTATTTTATTT
1 TTTTATTTTATTT
*
3596149 TCTTAATTTTATTT
1 T-TTTATTTTATTT
**
3596163 TTGCATTTTCGAATATT
1 TTTTATTTT---AT-TT
3596180 TTTTATTTTATTT
1 TTTTATTTTATTT
3596193 TTTTATTT
1 TTTTATTT
3596201 CCCTATTTTA
Statistics
Matches: 51, Mismatches: 8, Indels: 11
0.73 0.11 0.16
Matches are distributed among these distances:
12 4 0.08
13 22 0.43
14 14 0.27
16 2 0.04
17 9 0.18
ACGTcount: A:0.19, C:0.05, G:0.03, T:0.73
Consensus pattern (13 bp):
TTTTATTTTATTT
Found at i:3604644 original size:76 final size:76
Alignment explanation
Indices: 3604518--3604668 Score: 284
Period size: 76 Copynumber: 2.0 Consensus size: 76
3604508 GGTTTGCCAG
*
3604518 AATTGTTTGTAATTACTTGTGCATTATAATCATTTTTTATTTTTAAGATTTGATTGTTTGTAATT
1 AATTGTTTGTAATTACTTGTACATTATAATCATTTTTTATTTTTAAGATTTGATTGTTTGTAATT
3604583 AAATTCAAATT
66 AAATTCAAATT
*
3604594 AATTGTTTGTAATTACTTGTATATTATAATCATTTTTTATTTTTAAGATTTGATTGTTTGTAATT
1 AATTGTTTGTAATTACTTGTACATTATAATCATTTTTTATTTTTAAGATTTGATTGTTTGTAATT
3604659 AAATTCAAAT
66 AAATTCAAAT
3604669 AAGTAATCTT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 73 1.00
ACGTcount: A:0.31, C:0.05, G:0.10, T:0.54
Consensus pattern (76 bp):
AATTGTTTGTAATTACTTGTACATTATAATCATTTTTTATTTTTAAGATTTGATTGTTTGTAATT
AAATTCAAATT
Found at i:3605404 original size:13 final size:13
Alignment explanation
Indices: 3605386--3605418 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
3605376 ATTTTTGAAT
3605386 TATTTAGCT-ATAA
1 TATTTAG-TGATAA
3605399 TATTTAGTGATAA
1 TATTTAGTGATAA
3605412 TATTTAG
1 TATTTAG
3605419 GAAAAATCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 1 0.05
13 18 0.95
ACGTcount: A:0.36, C:0.03, G:0.12, T:0.48
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:3606311 original size:12 final size:12
Alignment explanation
Indices: 3606296--3606326 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
3606286 TTTATTTTTG
3606296 TATTTTTGAATA
1 TATTTTTGAATA
3606308 TATTTTTGAATA
1 TATTTTTGAATA
3606320 TATTTTT
1 TATTTTT
3606327 ATTTTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (12 bp):
TATTTTTGAATA
Found at i:3612967 original size:23 final size:25
Alignment explanation
Indices: 3612932--3612986 Score: 71
Period size: 23 Copynumber: 2.3 Consensus size: 25
3612922 AAAATAAAAA
3612932 TATATAATAATTTTAT-ATTAATATT
1 TATATAATAATTTTATAATTAA-ATT
3612957 TATAT-AT-ATTTTATAATTAAATT
1 TATATAATAATTTTATAATTAAATT
*
3612980 TAAATAA
1 TATATAA
3612987 AAATATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 14 0.52
24 8 0.30
25 5 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
TATATAATAATTTTATAATTAAATT
Found at i:3613393 original size:34 final size:35
Alignment explanation
Indices: 3613349--3613415 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
3613339 CAGTAAAATA
*
3613349 TTTTCCGTAAAATGATTT-CGGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
3613383 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
3613416 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:3614069 original size:21 final size:20
Alignment explanation
Indices: 3614031--3614069 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
3614021 AAAAAATGAT
* *
3614031 AAAATTATATTTTTATTCAA
1 AAAATTATAATTTAATTCAA
3614051 AAAATTTATAATTTAATTC
1 AAAA-TTATAATTTAATTC
3614070 TTTCCTTTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (20 bp):
AAAATTATAATTTAATTCAA
Found at i:3621730 original size:16 final size:15
Alignment explanation
Indices: 3621703--3621734 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
3621693 TCCAAACGTT
3621703 TTCTTTTTTGATTTC
1 TTCTTTTTTGATTTC
3621718 TTCTTTCTTTGATTTC
1 TTCTTT-TTTGATTTC
3621734 T
1 T
3621735 GTTTGCTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.06, C:0.16, G:0.06, T:0.72
Consensus pattern (15 bp):
TTCTTTTTTGATTTC
Found at i:3622223 original size:40 final size:40
Alignment explanation
Indices: 3622168--3622257 Score: 135
Period size: 40 Copynumber: 2.2 Consensus size: 40
3622158 GGCGTGTGGC
* * *
3622168 TGGCCGTGTGTGAGACATGGCCGTGTGACTGTCGTAGGTG
1 TGGCCGTGTGCGAGACACGACCGTGTGACTGTCGTAGGTG
* *
3622208 TGGCTGTGTGCGAGACACGATCGTGTGACTGTCGTAGGTG
1 TGGCCGTGTGCGAGACACGACCGTGTGACTGTCGTAGGTG
3622248 TGGCCGTGTG
1 TGGCCGTGTG
3622258 ACGGAATGTA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.12, C:0.18, G:0.42, T:0.28
Consensus pattern (40 bp):
TGGCCGTGTGCGAGACACGACCGTGTGACTGTCGTAGGTG
Found at i:3629450 original size:44 final size:43
Alignment explanation
Indices: 3629340--3629454 Score: 133
Period size: 44 Copynumber: 2.7 Consensus size: 43
3629330 ATTTCGTACA
* * *
3629340 ATGCCAACGTCCCAGACGTGGTCTTATATGTAATTACATATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACATGTAATCACATATCG
* * ** *
3629383 ATGCCACTGTCCTAGACAAGGTCTTACATGTAAGTCACA-AGTTG
1 ATGCCAATGTCCCAGACGTGGTCTTACATGTAA-TCACATA-TCG
3629427 ATGCCAATGTCCCAGACGTGGTCTTACA
1 ATGCCAATGTCCCAGACGTGGTCTTACA
3629455 CGATAACACA
Statistics
Matches: 58, Mismatches: 12, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
43 28 0.48
44 30 0.52
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACGTGGTCTTACATGTAATCACATATCG
Found at i:3630080 original size:18 final size:17
Alignment explanation
Indices: 3630053--3630086 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3630043 CAAAGACAAA
*
3630053 ATATTTTAATCTTTCAC
1 ATATTTTAATATTTCAC
3630070 ATATCTTTAATATTTCA
1 ATAT-TTTAATATTTCA
3630087 TCATCAAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.32, C:0.15, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATTTTAATATTTCAC
Found at i:3638966 original size:40 final size:40
Alignment explanation
Indices: 3638916--3639021 Score: 122
Period size: 40 Copynumber: 2.6 Consensus size: 40
3638906 CTGTGGCTGG
* * *
3638916 CCGTGTGTGAGACACGGCCGTGTGACTGTCGTAAGTGTGA
1 CCGTGTGTGAGACACGACCGTGTGACTGTCATAAGTATGA
* * * * *
3638956 CCGTTTGTGAGACACGATCATGTGACTGTCATAGGTATGG
1 CCGTGTGTGAGACACGACCGTGTGACTGTCATAAGTATGA
* *
3638996 CCGTGCGCGAGACACGACCGTGTGAC
1 CCGTGTGTGAGACACGACCGTGTGAC
3639022 GGCAAATGTG
Statistics
Matches: 53, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.20, C:0.23, G:0.34, T:0.24
Consensus pattern (40 bp):
CCGTGTGTGAGACACGACCGTGTGACTGTCATAAGTATGA
Found at i:3642370 original size:32 final size:32
Alignment explanation
Indices: 3642334--3642441 Score: 103
Period size: 32 Copynumber: 3.2 Consensus size: 32
3642324 GTGATGAGAA
3642334 TTGAGTATGGTATGAAATGATGTATTCATGAG
1 TTGAGTATGGTATGAAATGATGTATTCATGAG
* * * * *
3642366 TTGAGTATTGAATGGCTAATGCCATTGTGA-TGA-GAA
1 TTGAGTATGGTAT-G-AAATG--A-TGT-ATTCATGAG
3642402 TTGAGTATGGTATGAAATGATGTATTCATGAG
1 TTGAGTATGGTATGAAATGATGTATTCATGAG
3642434 TTGAGTAT
1 TTGAGTAT
3642442 TGAATGGCTA
Statistics
Matches: 58, Mismatches: 10, Indels: 16
0.69 0.12 0.19
Matches are distributed among these distances:
30 1 0.02
31 5 0.09
32 22 0.38
33 1 0.02
34 8 0.14
35 1 0.02
36 14 0.24
37 5 0.09
38 1 0.02
ACGTcount: A:0.31, C:0.05, G:0.28, T:0.37
Consensus pattern (32 bp):
TTGAGTATGGTATGAAATGATGTATTCATGAG
Found at i:3642407 original size:68 final size:68
Alignment explanation
Indices: 3642324--3642461 Score: 276
Period size: 68 Copynumber: 2.0 Consensus size: 68
3642314 TATATAGCAA
3642324 GTGATGAGAATTGAGTATGGTATGAAATGATGTATTCATGAGTTGAGTATTGAATGGCTAATGCC
1 GTGATGAGAATTGAGTATGGTATGAAATGATGTATTCATGAGTTGAGTATTGAATGGCTAATGCC
3642389 ATT
66 ATT
3642392 GTGATGAGAATTGAGTATGGTATGAAATGATGTATTCATGAGTTGAGTATTGAATGGCTAATGCC
1 GTGATGAGAATTGAGTATGGTATGAAATGATGTATTCATGAGTTGAGTATTGAATGGCTAATGCC
3642457 ATT
66 ATT
3642460 GT
1 GT
3642462 ACAAACAAAT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 70 1.00
ACGTcount: A:0.30, C:0.06, G:0.28, T:0.36
Consensus pattern (68 bp):
GTGATGAGAATTGAGTATGGTATGAAATGATGTATTCATGAGTTGAGTATTGAATGGCTAATGCC
ATT
Found at i:3662220 original size:16 final size:15
Alignment explanation
Indices: 3662174--3662217 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
3662164 CTATAAATTA
3662174 AATCTTTGTATTTTT
1 AATCTTTGTATTTTT
*
3662189 -AT-TTAGTCATTTTT
1 AATCTTTGT-ATTTTT
3662203 AATCTTTGTATTTTT
1 AATCTTTGTATTTTT
3662218 TAAAATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
13 4 0.17
14 8 0.33
15 8 0.33
16 4 0.17
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.66
Consensus pattern (15 bp):
AATCTTTGTATTTTT
Found at i:3671174 original size:26 final size:26
Alignment explanation
Indices: 3671123--3671175 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
3671113 AACTTTTTTC
* *
3671123 AAATGTGGGTACCACATTGGATCAAA
1 AAATGTGAGTACCACATTAGATCAAA
3671149 AAATGATGAGTACCACATTAGA-CAAA
1 AAATG-TGAGTACCACATTAGATCAAA
3671175 A
1 A
3671176 GATATCAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 10 0.42
27 14 0.58
ACGTcount: A:0.45, C:0.15, G:0.19, T:0.21
Consensus pattern (26 bp):
AAATGTGAGTACCACATTAGATCAAA
Found at i:3682540 original size:18 final size:18
Alignment explanation
Indices: 3682506--3682544 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3682496 AAAAAGATTT
3682506 AATTTATAAAATGTTAACA
1 AATTTATAAAATGTTAA-A
*
3682525 AATTTA-AAAATTTTAAA
1 AATTTATAAAATGTTAAA
3682542 AAT
1 AAT
3682545 AATTAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 9 0.47
19 6 0.32
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (18 bp):
AATTTATAAAATGTTAAA
Found at i:3685185 original size:27 final size:27
Alignment explanation
Indices: 3685125--3685189 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
3685115 TAGAAGTGTT
3685125 TTATAAAAAATGACTCATTCCCGTAAC
1 TTATAAAAAATGACTCATTCCCGTAAC
* *
3685152 TTTTAAAAAATCGAC-CTATTTCCGTAA-
1 TTATAAAAAAT-GACTC-ATTCCCGTAAC
3685179 TTATAAAAAAT
1 TTATAAAAAAT
3685190 AATTTTATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 21 0.64
28 12 0.36
ACGTcount: A:0.43, C:0.17, G:0.06, T:0.34
Consensus pattern (27 bp):
TTATAAAAAATGACTCATTCCCGTAAC
Found at i:3692198 original size:18 final size:18
Alignment explanation
Indices: 3692164--3692198 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3692154 ACTATAAAAA
*
3692164 TTAAAAAATATGGAAATT
1 TTAAAAAATATAGAAATT
*
3692182 TTAAAAAATATATAAAT
1 TTAAAAAATATAGAAAT
3692199 AAAAATTCCA
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:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (18 bp):
TTAAAAAATATAGAAATT
Found at i:3696876 original size:3 final size:3
Alignment explanation
Indices: 3696868--3696898 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
3696858 TGCGAAATGT
3696868 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA G
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA G
3696899 CAACCTCATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:3704643 original size:17 final size:19
Alignment explanation
Indices: 3704610--3704645 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
3704600 TTAAAATTCA
3704610 TTAATAAATTAATTATTTT
1 TTAATAAATTAATTATTTT
3704629 TTAATAAA-T-ATTATTTT
1 TTAATAAATTAATTATTTT
3704646 AACCAATACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 1 0.06
19 8 0.47
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTAATAAATTAATTATTTT
Found at i:3708470 original size:20 final size:20
Alignment explanation
Indices: 3708433--3708471 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3708423 TTTTAGTTTC
** *
3708433 TTGATAAATTATATATTATT
1 TTGATAAAAAATAAATTATT
3708453 TTGATAAAAAATAAATTAT
1 TTGATAAAAAATAAATTAT
3708472 ACGTTATACA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (20 bp):
TTGATAAAAAATAAATTATT
Found at i:3709977 original size:31 final size:31
Alignment explanation
Indices: 3709942--3710009 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
3709932 AAAATATTTT
3709942 TTTAAAAAATAAAATATAATAATAAATAAGA
1 TTTAAAAAATAAAATATAATAATAAATAAGA
* ** * * *
3709973 TTTAAATAATTTAATATAATGATAAATGATA
1 TTTAAAAAATAAAATATAATAATAAATAAGA
3710004 TTTAAA
1 TTTAAA
3710010 TAGTTAATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (31 bp):
TTTAAAAAATAAAATATAATAATAAATAAGA
Found at i:3710010 original size:31 final size:30
Alignment explanation
Indices: 3709954--3710021 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 30
3709944 TAAAAAATAA
*
3709954 AATATAATAATAAATAAGATTTAAATAATTT
1 AATATAATAATAAATAAGATTTAAAT-AGTT
* * *
3709985 AATATAATGATAAATGATATTTAAATAGTT
1 AATATAATAATAAATAAGATTTAAATAGTT
3710015 AATATAA
1 AATATAA
3710022 ATAACGATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
30 10 0.30
31 23 0.70
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (30 bp):
AATATAATAATAAATAAGATTTAAATAGTT
Found at i:3714683 original size:30 final size:31
Alignment explanation
Indices: 3714630--3714687 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
3714620 ACCCAGTGGT
3714630 TTAAATAAAAACTTTCAAATAGTTCAGTAAC
1 TTAAATAAAAACTTTCAAATAGTTCAGTAAC
* *
3714661 TTAAATGAAAAC-TTCGAATAGTTCAGT
1 TTAAATAAAAACTTTCAAATAGTTCAGT
3714688 TGCCATTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (31 bp):
TTAAATAAAAACTTTCAAATAGTTCAGTAAC
Found at i:3715008 original size:59 final size:59
Alignment explanation
Indices: 3714884--3715008 Score: 134
Period size: 59 Copynumber: 2.1 Consensus size: 59
3714874 TTGGTACATG
*
3714884 ATTTTTT-TTATTAAATTTGATACTCGAGTTTTTTTTGTCTCAATTAAGTACCAAAGTT
1 ATTTTTTAATATTAAATTTGATACTCGAGTTTTTTTTGTCTCAATTAAGTACCAAAGTT
* * * *
3714942 -TGATTTTAATATTCAATTTGATAC-CTGAGCTTTTTTTATG-C-CAATTAAGTACCTATGTT
1 AT-TTTTTAATATTAAATTTGATACTC-GAG-TTTTTTT-TGTCTCAATTAAGTACCAAAGTT
3715001 ATTTTTTA
1 ATTTTTTA
3715009 TTAGAGCAAC
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
57 1 0.02
58 5 0.09
59 38 0.69
60 9 0.16
61 2 0.04
ACGTcount: A:0.27, C:0.11, G:0.10, T:0.51
Consensus pattern (59 bp):
ATTTTTTAATATTAAATTTGATACTCGAGTTTTTTTTGTCTCAATTAAGTACCAAAGTT
Found at i:3715111 original size:25 final size:25
Alignment explanation
Indices: 3715060--3715112 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
3715050 ATTTGGTTTG
* **
3715060 AGTACCAAATTGAACATTAAATTCA
1 AGTACCAAATTAAACATTAAAACCA
3715085 AGTACCAAATTAAACATTAAAACCA
1 AGTACCAAATTAAACATTAAAACCA
3715110 AGT
1 AGT
3715113 GCAGATACAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.51, C:0.17, G:0.08, T:0.25
Consensus pattern (25 bp):
AGTACCAAATTAAACATTAAAACCA
Found at i:3716305 original size:39 final size:39
Alignment explanation
Indices: 3716246--3716325 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
3716236 ACACTAAAGA
*
3716246 AAGAGAAATTTTTTTTCAAATAAAAACAACATATTCAAT
1 AAGAGAAATTTTTTTCCAAATAAAAACAACATATTCAAT
3716285 AAGAGAAATTTTTTTCCAAATAAAAACAACATATTCAAT
1 AAGAGAAATTTTTTTCCAAATAAAAACAACATATTCAAT
3716324 AA
1 AA
3716326 TTGATTTAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.53, C:0.11, G:0.05, T:0.31
Consensus pattern (39 bp):
AAGAGAAATTTTTTTCCAAATAAAAACAACATATTCAAT
Found at i:3718667 original size:20 final size:19
Alignment explanation
Indices: 3718624--3718669 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
3718614 ATGAAAACAC
*
3718624 AAATAAATAAACAAATAAA
1 AAATAAACAAACAAATAAA
3718643 AAATAAACAAA-AAATATAA
1 AAATAAACAAACAAATA-AA
3718662 AGAATAAA
1 A-AATAAA
3718670 AAGTACATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 5 0.21
19 13 0.54
20 6 0.25
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.15
Consensus pattern (19 bp):
AAATAAACAAACAAATAAA
Found at i:3720239 original size:13 final size:13
Alignment explanation
Indices: 3720221--3720258 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
3720211 TAAGGTTTTT
*
3720221 GCCACTATTTTGG
1 GCCACTGTTTTGG
3720234 GCCACTGTATTTGG
1 GCCACTGT-TTTGG
3720248 GCCACTGTTTT
1 GCCACTGTTTT
3720259 TGTATTTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.13, C:0.24, G:0.24, T:0.39
Consensus pattern (13 bp):
GCCACTGTTTTGG
Found at i:3726478 original size:13 final size:12
Alignment explanation
Indices: 3726462--3726494 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
3726452 AATATTTTAT
3726462 AAAAAAAAGAAA
1 AAAAAAAAGAAA
3726474 AAAAAAAAGAAA
1 AAAAAAAAGAAA
*
3726486 AACAAAAAG
1 AAAAAAAAG
3726495 GAGAGGTCAA
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:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGAAA
Found at i:3727510 original size:50 final size:45
Alignment explanation
Indices: 3727378--3727547 Score: 172
Period size: 44 Copynumber: 3.7 Consensus size: 45
3727368 TTATCATGGC
* *
3727378 GAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTGAAGCCACT-
1 GAATCTTATCTCCCTGAAGTTGTAGTGGAGCA-ATTGAAGCCACTA
* *
3727423 -AATCTTATAC-CCCTAAAGTTGTAGTGGGATG-AATTGAAGTCATCCTA
1 GAATCTTAT-CTCCCTGAAGTTGTAGT-GGA-GCAATTGAAGCCA--CTA
*
3727470 GTGAATCTTATCTCCCTGAAGATGTAGTGGAGCAATTTGAAGCCACTA
1 --GAATCTTATCTCCCTGAAGTTGTAGTGGAGCAA-TTGAAGCCACTA
3727518 G--TCTTATCTCCCTGAAGTTGTAGTGGAGCA
1 GAATCTTATCTCCCTGAAGTTGTAGTGGAGCA
3727548 GACTGAAGAT
Statistics
Matches: 105, Mismatches: 8, Indels: 25
0.76 0.06 0.18
Matches are distributed among these distances:
44 58 0.55
45 4 0.04
46 4 0.04
48 4 0.04
49 6 0.06
50 29 0.28
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.30
Consensus pattern (45 bp):
GAATCTTATCTCCCTGAAGTTGTAGTGGAGCAATTGAAGCCACTA
Found at i:3727510 original size:94 final size:94
Alignment explanation
Indices: 3727324--3727543 Score: 300
Period size: 94 Copynumber: 2.3 Consensus size: 94
3727314 GTCAGTAAAA
* * * * *
3727324 CCACAAATCCTATACCCCTAAAGTTGCAGTGGGATGAATTGAAGTTATCATGGCGAATCTTATCT
1 CCACTAATCTTATACCCCTAAAGTTGTAGTGGGATGAATTGAAGTCATCATAGCGAATCTTATCT
*
3727389 CCCTGAAGTTGCAGTGAAGCAGATTGAAG
66 CCCTGAAGATGCAGTGAAGCAGATTGAAG
* *
3727418 CCACTAATCTTATACCCCTAAAGTTGTAGTGGGATGAATTGAAGTCATCCTAGTGAATCTTATCT
1 CCACTAATCTTATACCCCTAAAGTTGTAGTGGGATGAATTGAAGTCATCATAGCGAATCTTATCT
* *
3727483 CCCTGAAGATGTAGTGGAGCA-ATTTGAAG
66 CCCTGAAGATGCAGTGAAGCAGA-TTGAAG
* *
3727512 CCACTAGTCTTAT-CTCCCTGAAGTTGTAGTGG
1 CCACTAATCTTATAC-CCCTAAAGTTGTAGTGG
3727544 AGCAGACTGA
Statistics
Matches: 112, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
93 2 0.02
94 110 0.98
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.30
Consensus pattern (94 bp):
CCACTAATCTTATACCCCTAAAGTTGTAGTGGGATGAATTGAAGTCATCATAGCGAATCTTATCT
CCCTGAAGATGCAGTGAAGCAGATTGAAG
Found at i:3727759 original size:44 final size:44
Alignment explanation
Indices: 3727666--3727779 Score: 120
Period size: 44 Copynumber: 2.6 Consensus size: 44
3727656 TTTTATCTTT
* *
3727666 CTGAAGTTGCAGTGGAACAGGTTAAAGATACCAATCTTATATCC
1 CTGAAGTTGCAGTGGAACAGATTAAAGATACCAATCCTATATCC
* ** * * ** *
3727710 TTGAAGTTGCAGTGGCGCAGATTGAAGCTATTAATCCTATCTCC
1 CTGAAGTTGCAGTGGAACAGATTAAAGATACCAATCCTATATCC
* *
3727754 CTGAAGTTGCAGTGGAGCGGATTAAA
1 CTGAAGTTGCAGTGGAACAGATTAAA
3727780 ATGATAAATC
Statistics
Matches: 56, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
44 56 1.00
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.28
Consensus pattern (44 bp):
CTGAAGTTGCAGTGGAACAGATTAAAGATACCAATCCTATATCC
Found at i:3727790 original size:44 final size:44
Alignment explanation
Indices: 3727666--3727823 Score: 112
Period size: 44 Copynumber: 3.6 Consensus size: 44
3727656 TTTTATCTTT
* *
3727666 CTGAAGTTGCAGTGGAACAGG-TT-AAA-GATACCAATCTTATATCC
1 CTGAAGTTGCAGTGGAGC-GGATTAAAATGATA--AATCCTATATCC
* * * ** * *
3727710 TTGAAGTTGCAGTGGCGCAGATTGAAGCT-ATTAATCCTATCTCC
1 CTGAAGTTGCAGTGGAGCGGATT-AAAATGATAAATCCTATATCC
*
3727754 CTGAAGTTGCAGTGGAGCGGATTAAAATGATAAATCCTTTA-CC
1 CTGAAGTTGCAGTGGAGCGGATTAAAATGATAAATCCTATATCC
* *
3727797 TCTGAGGTTGCAGTAGG-TCGGATTAAA
1 -CTGAAGTTGCAGT-GGAGCGGATTAAA
3727824 TCTATCATAG
Statistics
Matches: 88, Mismatches: 19, Indels: 14
0.73 0.16 0.12
Matches are distributed among these distances:
43 6 0.07
44 77 0.88
45 2 0.02
46 3 0.03
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (44 bp):
CTGAAGTTGCAGTGGAGCGGATTAAAATGATAAATCCTATATCC
Found at i:3727906 original size:44 final size:43
Alignment explanation
Indices: 3727830--3727952 Score: 113
Period size: 44 Copynumber: 2.7 Consensus size: 43
3727820 TAAATCTATC
* * * * **
3727830 ATAGCAAACCTTATCTCCCTGAAGTTACAGTGGAGTAGGTTGAAG
1 ATAGC-AATCTTATCT-CTTGAAGTTATAGTGGAGCAGACTGAAG
3727875 ATA-CAAGTCTTATCTCTGTGAAGTTATAGTGGAGCAGACTGAAG
1 ATAGCAA-TCTTATCTCT-TGAAGTTATAGTGGAGCAGACTGAAG
* *
3727919 ATAGTGAATCTTATTTTCTTGAAGTTATAGTGGA
1 ATAG-CAATCTTA-TCTCTTGAAGTTATAGTGGA
3727953 ACAAATTGAA
Statistics
Matches: 65, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
43 3 0.05
44 33 0.51
45 23 0.35
46 6 0.09
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.33
Consensus pattern (43 bp):
ATAGCAATCTTATCTCTTGAAGTTATAGTGGAGCAGACTGAAG
Found at i:3728078 original size:44 final size:46
Alignment explanation
Indices: 3728030--3728144 Score: 135
Period size: 49 Copynumber: 2.5 Consensus size: 46
3728020 CTTATCTCCC
* * *
3728030 TGAAGTTGCAATGGAGTAGGTTG-GA-GCTACAAATCTTATATTCT
1 TGAAGTTGCAGTGGAGCAGATTGAGAGGCTACAAATCTTATATTCT
* * *
3728074 TGAAGTTGTAGTGGGGCAGATTGAAGACGGGCTACAAATCTTATCTTCT
1 TGAAGTTGCAGTGGAGCAGATTG-AGA--GGCTACAAATCTTATATTCT
3728123 TGAAGTTGCAGTGGAGCAGATT
1 TGAAGTTGCAGTGGAGCAGATT
3728145 AAAGCCGCAA
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
44 18 0.31
46 2 0.03
49 38 0.66
ACGTcount: A:0.28, C:0.12, G:0.29, T:0.31
Consensus pattern (46 bp):
TGAAGTTGCAGTGGAGCAGATTGAGAGGCTACAAATCTTATATTCT
Found at i:3728282 original size:41 final size:41
Alignment explanation
Indices: 3728225--3728334 Score: 161
Period size: 41 Copynumber: 2.7 Consensus size: 41
3728215 ATTGCAGATA
*
3728225 TTATCTCTCTGAAGTTGTAGTAGAGCAGATCATA-TCAAACC
1 TTATCTCTCTGAAGTTGTAGTAGAGCAGATCAGAGT-AAACC
3728266 TTATCTCTCTGAAGTTGTAGTAGAGCAGATCAGAGTAAACC
1 TTATCTCTCTGAAGTTGTAGTAGAGCAGATCAGAGTAAACC
* *
3728307 TTATCTC-CTTGAAGTTGCAGTGGAGCAG
1 TTATCTCTC-TGAAGTTGTAGTAGAGCAG
3728335 GTTGAATATA
Statistics
Matches: 64, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
40 1 0.02
41 62 0.97
42 1 0.02
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (41 bp):
TTATCTCTCTGAAGTTGTAGTAGAGCAGATCAGAGTAAACC
Found at i:3728366 original size:44 final size:45
Alignment explanation
Indices: 3728306--3728464 Score: 144
Period size: 44 Copynumber: 3.6 Consensus size: 45
3728296 CAGAGTAAAC
* * ** *
3728306 CTTATCTCCTTGAAGTTGCAGTGGAGCAGGTTGAATA-TACCAAT
1 CTTATCTCCCTAAAGTTGCAGTGGAGCAAATTGAAAACTACCAAT
** *
3728350 CTTATCTCCCTAAAGTTGCAGTGGAGCTTATT-AAAATTA-CAAGT
1 CTTATCTCCCTAAAGTTGCAGTGGAGCAAATTGAAAACTACCAA-T
* * * * *
3728394 CTTATCTCTCTAAAGTTACAGTGGAGCAAATTGAAGACAACTAAT
1 CTTATCTCCCTAAAGTTGCAGTGGAGCAAATTGAAAACTACCAAT
* * *
3728439 CCTATCTCCTTGAAGTTGCAGTGGAG
1 CTTATCTCCCTAAAGTTGCAGTGGAG
3728465 TGGATTAAAA
Statistics
Matches: 92, Mismatches: 19, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
43 6 0.07
44 58 0.63
45 26 0.28
46 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31
Consensus pattern (45 bp):
CTTATCTCCCTAAAGTTGCAGTGGAGCAAATTGAAAACTACCAAT
Found at i:3732237 original size:89 final size:89
Alignment explanation
Indices: 3732086--3732264 Score: 340
Period size: 89 Copynumber: 2.0 Consensus size: 89
3732076 AATAAACCCC
*
3732086 TATCTTTAGCCAGTAGGCTTATAAATAAATGTTAGTGAAATATGTTAGAATGGGTCTGCTGGTCT
1 TATCTTTAGCCAGTAGGCTTATAAATAAATGTTAGTGAAATATGTTAGAATGGGCCTGCTGGTCT
*
3732151 GGTGGATAAATAGAGTGGCAAGTA
66 AGTGGATAAATAGAGTGGCAAGTA
3732175 TATCTTTAGCCAGTAGGCTTATAAATAAATGTTAGTGAAATATGTTAGAATGGGCCTGCTGGTCT
1 TATCTTTAGCCAGTAGGCTTATAAATAAATGTTAGTGAAATATGTTAGAATGGGCCTGCTGGTCT
3732240 AGTGGATAAATAGAGTGGCAAGTA
66 AGTGGATAAATAGAGTGGCAAGTA
3732264 T
1 T
3732265 CGGAGGTCTT
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 88 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (89 bp):
TATCTTTAGCCAGTAGGCTTATAAATAAATGTTAGTGAAATATGTTAGAATGGGCCTGCTGGTCT
AGTGGATAAATAGAGTGGCAAGTA
Found at i:3733677 original size:27 final size:27
Alignment explanation
Indices: 3733638--3733703 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
3733628 TCAAACTGAT
*
3733638 ATAAAATAACTGTTATGCCCCCACGTG
1 ATAAAATGACTGTTATGCCCCCACGTG
* * * *
3733665 GTAAAATGACTGTTATGCCCCTATGTT
1 ATAAAATGACTGTTATGCCCCCACGTG
3733692 ATAAAATGACTG
1 ATAAAATGACTG
3733704 CATACTCTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (27 bp):
ATAAAATGACTGTTATGCCCCCACGTG
Found at i:3735952 original size:22 final size:23
Alignment explanation
Indices: 3735900--3735953 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
3735890 CGGTTTTAAT
*
3735900 TAAAATTAAAATTATATCTGTAA
1 TAAAATTAAAACTATATCTGTAA
*
3735923 TAAAATTAAAACTA-AT-TGTTA
1 TAAAATTAAAACTATATCTGTAA
3735944 TCAAAATTAA
1 T-AAAATTAA
3735954 TTGTTATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 5 0.18
22 10 0.36
23 13 0.46
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.37
Consensus pattern (23 bp):
TAAAATTAAAACTATATCTGTAA
Found at i:3735954 original size:16 final size:16
Alignment explanation
Indices: 3735930--3735967 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
3735920 TAATAAAATT
*
3735930 AAAACTAATTGTTATC
1 AAAATTAATTGTTATC
*
3735946 AAAATTAATTGTTATT
1 AAAATTAATTGTTATC
3735962 AAAATT
1 AAAATT
3735968 GTATCAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (16 bp):
AAAATTAATTGTTATC
Done.