Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168270.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_5, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 27802247
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 124000 characters in sequence are not A, C, G, or T
File 3 of 147
Found at i:338702 original size:10 final size:9
Alignment explanation
Indices: 338687--338752 Score: 55
Period size: 10 Copynumber: 6.9 Consensus size: 9
338677 ATATATTTTC
338687 TTTTTATTCA
1 TTTTTATT-A
338697 TTTTTACTTA
1 TTTTTA-TTA
338707 TTTTTATGTA
1 TTTTTAT-TA
338717 -TTTTA-TA
1 TTTTTATTA
338724 TTTTTATTCCTA
1 TTTTTA-T--TA
*
338736 TTTTTATGA
1 TTTTTATTA
338745 TTTTTATT
1 TTTTTATT
338753 GTATTTTGGG
Statistics
Matches: 47, Mismatches: 2, Indels: 15
0.73 0.03 0.23
Matches are distributed among these distances:
7 2 0.04
8 5 0.11
9 14 0.30
10 15 0.32
11 3 0.06
12 8 0.17
ACGTcount: A:0.20, C:0.06, G:0.03, T:0.71
Consensus pattern (9 bp):
TTTTTATTA
Found at i:338720 original size:29 final size:27
Alignment explanation
Indices: 338696--338752 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
338686 CTTTTTATTC
*
338696 ATTTTTA-CTTATTTTTATGTATTTTAT
1 ATTTTTATCCTATTTTTATG-ATTTTAT
338723 ATTTTTATTCCTATTTTTATGATTTT-T
1 ATTTTTA-TCCTATTTTTATGATTTTAT
338750 ATT
1 ATT
338753 GTATTTTGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 11 0.41
28 5 0.19
29 11 0.41
ACGTcount: A:0.21, C:0.05, G:0.04, T:0.70
Consensus pattern (27 bp):
ATTTTTATCCTATTTTTATGATTTTAT
Found at i:338728 original size:37 final size:37
Alignment explanation
Indices: 338670--338759 Score: 103
Period size: 37 Copynumber: 2.4 Consensus size: 37
338660 TTTGGTATTT
* * *
338670 TTTTTATATATATTTTCTTTTTATT-C-ATTTTTACTTA
1 TTTTTATGTAT-TTTTATTTTTATTCCTATTTTTA-TGA
338707 TTTTTATGTATTTTATATTTTTATTCCTATTTTTATGA
1 TTTTTATGTATTTT-TATTTTTATTCCTATTTTTATGA
338745 TTTTTATTGTATTTT
1 TTTTTA-TGTATTTT
338760 GGGTGAATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
36 3 0.07
37 19 0.41
38 9 0.20
39 15 0.33
ACGTcount: A:0.20, C:0.06, G:0.03, T:0.71
Consensus pattern (37 bp):
TTTTTATGTATTTTTATTTTTATTCCTATTTTTATGA
Found at i:338757 original size:20 final size:19
Alignment explanation
Indices: 338687--338759 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 19
338677 ATATATTTTC
*
338687 TTTTTATT-CATTTTTACTTA
1 TTTTTATTGTATTTTTA--TA
338707 TTTTTA-TGTA-TTTTATA
1 TTTTTATTGTATTTTTATA
*
338724 TTTTTATTCCTATTTTTATGA
1 TTTTTATT-GTATTTTTAT-A
338745 TTTTTATTGTATTTT
1 TTTTTATTGTATTTT
338760 GGGTGAATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
17 8 0.18
18 1 0.02
19 8 0.18
20 19 0.42
21 9 0.20
ACGTcount: A:0.19, C:0.05, G:0.04, T:0.71
Consensus pattern (19 bp):
TTTTTATTGTATTTTTATA
Found at i:340299 original size:15 final size:15
Alignment explanation
Indices: 340279--340309 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
340269 TTTTTATTTC
*
340279 AATAAAATCAATAAA
1 AATAAAAACAATAAA
340294 AATAAAAACAATAAA
1 AATAAAAACAATAAA
340309 A
1 A
340310 TTACATCGAA
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:0.77, C:0.06, G:0.00, T:0.16
Consensus pattern (15 bp):
AATAAAAACAATAAA
Found at i:359154 original size:2 final size:2
Alignment explanation
Indices: 359149--359182 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
359139 AGTTTTTTTA
359149 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
359183 CTGAAAGCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:366933 original size:27 final size:27
Alignment explanation
Indices: 366895--366949 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
366885 GTCTCTACTT
366895 ACCTTTTTTTGTTTCAAGACTTATTGG
1 ACCTTTTTTTGTTTCAAGACTTATTGG
366922 ACCTTTTTTTGTTTCAAGACTTATTGG
1 ACCTTTTTTTGTTTCAAGACTTATTGG
366949 A
1 A
366950 TAATCCTGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.20, C:0.15, G:0.15, T:0.51
Consensus pattern (27 bp):
ACCTTTTTTTGTTTCAAGACTTATTGG
Found at i:367843 original size:2 final size:2
Alignment explanation
Indices: 367836--367862 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
367826 GCTCAAATTG
367836 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
367863 AGGATAAAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:368570 original size:2 final size:2
Alignment explanation
Indices: 368563--368587 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
368553 CAATTAATGA
368563 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
368588 AAATTAAGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:370607 original size:2 final size:2
Alignment explanation
Indices: 370600--370657 Score: 80
Period size: 2 Copynumber: 29.0 Consensus size: 2
370590 TGAAGGGATA
* * * *
370600 AT AT AT AT AT AT AT AT AT AT AT CT AT AT CT AT AT CT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
370642 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
370658 TAAAAGTAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:377548 original size:29 final size:29
Alignment explanation
Indices: 377515--377572 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
377505 CAATAAAATG
*
377515 TGATGGATGGATATTTTCCCACCAAACCA
1 TGATGGATGGATATTTTCCAACCAAACCA
377544 TGATGGATGGATATTTTCCAACCAAACCA
1 TGATGGATGGATATTTTCCAACCAAACCA
377573 AAAAATAGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (29 bp):
TGATGGATGGATATTTTCCAACCAAACCA
Found at i:378532 original size:6 final size:6
Alignment explanation
Indices: 378521--378545 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
378511 ATAAAAGAGA
378521 GGTTTT GGTTTT GGTTTT GGTTTT G
1 GGTTTT GGTTTT GGTTTT GGTTTT G
378546 CTAGGTGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.36, T:0.64
Consensus pattern (6 bp):
GGTTTT
Found at i:385796 original size:19 final size:19
Alignment explanation
Indices: 385772--385808 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
385762 TGATATTCTC
* *
385772 TCAAAAACAAAAACAAGAT
1 TCAAAAAAAAAAAAAAGAT
385791 TCAAAAAAAAAAAAAAGA
1 TCAAAAAAAAAAAAAAGA
385809 GGATAAAGCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.76, C:0.11, G:0.05, T:0.08
Consensus pattern (19 bp):
TCAAAAAAAAAAAAAAGAT
Found at i:388577 original size:20 final size:20
Alignment explanation
Indices: 388523--388579 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
388513 ATTGGTGTCG
*
388523 TATAAAATATTA-ATAATTTA
1 TATAAAA-ATTATATATTTTA
**
388543 TATAATTATGT-TATATTTTA
1 TATAAAAAT-TATATATTTTA
388563 TATAAAAATTATATATT
1 TATAAAAATTATATATT
388580 ATAATTTATA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
19 3 0.10
20 26 0.90
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
TATAAAAATTATATATTTTA
Found at i:388638 original size:21 final size:22
Alignment explanation
Indices: 388614--388655 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
388604 TAAAATTTAA
*
388614 TTATTTTTAA-TTTTATTAAAT
1 TTATTTATAATTTTTATTAAAT
388635 TTATTTATAATTTTTATTAAA
1 TTATTTATAATTTTTATTAAA
388656 ATTTTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TTATTTATAATTTTTATTAAAT
Found at i:390321 original size:13 final size:13
Alignment explanation
Indices: 390303--390344 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
390293 TTTTGTACTC
390303 AAATTTTTTATAT
1 AAATTTTTTATAT
* **
390316 ATATTTAATATAT
1 AAATTTTTTATAT
390329 AAATTTTTTAT-T
1 AAATTTTTTATAT
390341 AAAT
1 AAAT
390345 AATATAAAAT
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
12 5 0.22
13 18 0.78
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
AAATTTTTTATAT
Found at i:390435 original size:27 final size:29
Alignment explanation
Indices: 390374--390436 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 29
390364 ATTAATTAAA
390374 ATTAATATAT-T-TTTATTAAAAATATAT
1 ATTAATATATATATTTATTAAAAATATAT
*
390401 ATTGATATATATATTTA-TAAAAAT-TAT
1 ATTAATATATATATTTATTAAAAATATAT
390428 -TTAA-ATATA
1 ATTAATATATA
390437 CAAGTTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 5 0.16
26 3 0.09
27 12 0.38
28 8 0.25
29 4 0.12
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (29 bp):
ATTAATATATATATTTATTAAAAATATAT
Found at i:390933 original size:19 final size:17
Alignment explanation
Indices: 390914--390946 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
390904 ATCTTATTTA
390914 TTATA-ATATATAAAAT
1 TTATATATATATAAAAT
*
390930 TTATATATTTATAAAAT
1 TTATATATATATAAAAT
390947 ATTAAATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTATATATATATAAAAT
Found at i:396674 original size:24 final size:27
Alignment explanation
Indices: 396647--396701 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
396637 AAAATATTAT
396647 AAATCATAATTTT-A-A-ATATTAAAA
1 AAATCATAATTTTGAGACATATTAAAA
* *
396671 AAATTATAGTTTTGAGACATATTAAAA
1 AAATCATAATTTTGAGACATATTAAAA
396698 AAAT
1 AAAT
396702 AAATAAATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 11 0.42
25 1 0.04
26 1 0.04
27 13 0.50
ACGTcount: A:0.55, C:0.04, G:0.05, T:0.36
Consensus pattern (27 bp):
AAATCATAATTTTGAGACATATTAAAA
Found at i:397668 original size:36 final size:36
Alignment explanation
Indices: 397626--397696 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
397616 TATTCACTAA
*
397626 ATGAATAAAATTGATTTATTAAGATAAAAAATAATC
1 ATGAATAAAATTAATTTATTAAGATAAAAAATAATC
**
397662 ATGAATAAAATTAATTTATTAAGATTGAAAATAAT
1 ATGAATAAAATTAATTTATTAAGATAAAAAATAAT
397697 TTTGCTTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.55, C:0.01, G:0.08, T:0.35
Consensus pattern (36 bp):
ATGAATAAAATTAATTTATTAAGATAAAAAATAATC
Found at i:401941 original size:2 final size:2
Alignment explanation
Indices: 401934--401969 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
401924 TATATTATAA
401934 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
401970 AAGAATGATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:417993 original size:22 final size:21
Alignment explanation
Indices: 417927--417994 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 21
417917 ATTTTTTATT
*
417927 TTTTAATATTAAAATTCATGAAA
1 TTTTAATATTAAAA-T-ATTAAA
* *
417950 TTTTAATTTATAAAAATTTTAAA
1 TTTTAA--TATTAAAATATTAAA
417973 TTTTAATATTAAATATATTAAA
1 TTTTAATATTAAA-ATATTAAA
417995 ATTAATTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
21 6 0.16
22 7 0.19
23 16 0.43
24 1 0.03
25 7 0.19
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (21 bp):
TTTTAATATTAAAATATTAAA
Found at i:418509 original size:19 final size:19
Alignment explanation
Indices: 418476--418514 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
418466 TATATCTAAA
*
418476 TTTATATTAAAATATTATT
1 TTTATATTAAAATATGATT
* *
418495 TTTATATTCAGATATGATT
1 TTTATATTAAAATATGATT
418514 T
1 T
418515 AATTTGTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (19 bp):
TTTATATTAAAATATGATT
Found at i:418571 original size:22 final size:20
Alignment explanation
Indices: 418546--418590 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
418536 TTGATTTGAT
418546 TTAACTTGAAATTAATAAAATA
1 TTAACTTGAAA-T-ATAAAATA
* *
418568 TTAATTTTAAATATAAAATA
1 TTAACTTGAAATATAAAATA
418588 TTA
1 TTA
418591 TTTAATTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 11 0.52
21 1 0.05
22 9 0.43
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (20 bp):
TTAACTTGAAATATAAAATA
Found at i:418624 original size:19 final size:21
Alignment explanation
Indices: 418597--418636 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
418587 ATTATTTAAT
418597 TTAT-TTTTT-AATATAAATA
1 TTATCTTTTTAAATATAAATA
418616 TTATCTTTTTAAATATAAATA
1 TTATCTTTTTAAATATAAATA
418637 AATATATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.21
20 5 0.26
21 10 0.53
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (21 bp):
TTATCTTTTTAAATATAAATA
Found at i:418648 original size:49 final size:47
Alignment explanation
Indices: 418557--418649 Score: 109
Period size: 48 Copynumber: 1.9 Consensus size: 47
418547 TAACTTGAAA
* *
418557 TTAATAAAATATTAATTTTAAATATAAAATATTATTTAATTTATTTT
1 TTAATAAAATATTAATTTTAAATATAAAATAATATATAATTTATTTT
*
418604 TTAATATAAATATTATCTTTTTAAATAT-AAATAA-ATATATATTTAT
1 TTAATA-AAATATTA--ATTTTAAATATAAAATAATATATA-ATTTAT
418650 ATATATATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
47 6 0.15
48 12 0.31
49 11 0.28
50 10 0.26
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (47 bp):
TTAATAAAATATTAATTTTAAATATAAAATAATATATAATTTATTTT
Found at i:426701 original size:19 final size:18
Alignment explanation
Indices: 426650--426702 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
426640 TTATAATTAT
*
426650 TTATTAT-TTTAATCATA
1 TTATTATATTTATTCATA
* * *
426667 TTTTTGTATATATTCATA
1 TTATTATATTTATTCATA
426685 TTAATTATATTTATTCAT
1 TT-ATTATATTTATTCAT
426703 GTATATCCGA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
17 5 0.19
18 10 0.37
19 12 0.44
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (18 bp):
TTATTATATTTATTCATA
Found at i:429759 original size:256 final size:256
Alignment explanation
Indices: 429304--430072 Score: 1466
Period size: 256 Copynumber: 3.0 Consensus size: 256
429294 TTTGATTGTT
429304 GAAGGAATAGTGAAAACGAATTCGTTTCTAAGTTTTAGTGCCACCAGTGATTCGCAACTTGAAAA
1 GAAGGAATAGTGAAAACGAATTCGTTTCTAAGTTTTAGTGCCACCAGTGATTCGCAACTTGAAAA
*
429369 GTTTTTAGGCGACCTAACAGGGATTCTTTCCTCATATTCCAACAAGAGGAAGAGATCAAGCTCCT
66 GTTTTTAGGCAACCTAACAGGGATTCTTTCCTCATATTCCAACAAGAGGAAGAGATCAAGCTCCT
* *
429434 TCACATTGCAACGCTGCGCATAACTACTCCATGTATTGATGCGACGAAAAAATCTTTGTCGTTGG
131 TCACATTGCAACGCTGCGCATAGCTACTCCATGTATTGACGCGACGAAAAAATCTTTGTCGTTGG
429499 AAATCATAAAATCCCAGAGAGAATGTCTGAATATTTCTGGATCCACGAAGGCCAAGAACTC
196 AAATCATAAAATCCCAGAGAGAATGTCTGAATATTTCTGGATCCACGAAGGCCAAGAACTC
429560 GAAGGAATAGTGAAAACGAATTCGTTTCTAAGTTTTAGTGCCACCAGTGATTCGCAACTTGAAAA
1 GAAGGAATAGTGAAAACGAATTCGTTTCTAAGTTTTAGTGCCACCAGTGATTCGCAACTTGAAAA
*
429625 GTTTTTAGGCAACCTAACAGCGATTCTTTCCTCATATTCCAACAAGAGGAAGAGATCAAGCTCCT
66 GTTTTTAGGCAACCTAACAGGGATTCTTTCCTCATATTCCAACAAGAGGAAGAGATCAAGCTCCT
429690 TCACATTGCAACGCTGCGCATAGCTACTCCATGTATTGACGCGACGAAAAAATCTTTGTCGTTGG
131 TCACATTGCAACGCTGCGCATAGCTACTCCATGTATTGACGCGACGAAAAAATCTTTGTCGTTGG
* *
429755 AAATCATAACATCCCAGAGAGAATGTCTTAATATTTCTGGATCCACGAAGGCCAAGAACTC
196 AAATCATAAAATCCCAGAGAGAATGTCTGAATATTTCTGGATCCACGAAGGCCAAGAACTC
429816 GAAGGAATAGTGAAAACGAATTCGTTTCTAAGTTTTAGTGCCACCAGTGATTCGCAACTTGAAAA
1 GAAGGAATAGTGAAAACGAATTCGTTTCTAAGTTTTAGTGCCACCAGTGATTCGCAACTTGAAAA
429881 GTTTTTAGGCAACCTAACAGGGATTCTTTCCTCATATTCCAACAAGAGGAAGAGATCAAGCTCCT
66 GTTTTTAGGCAACCTAACAGGGATTCTTTCCTCATATTCCAACAAGAGGAAGAGATCAAGCTCCT
429946 TCACATTGCAACGCTGCGCATAGCTACTCCATGTATTGACGCGACGAAAAAATCTTTGTCGTTGG
131 TCACATTGCAACGCTGCGCATAGCTACTCCATGTATTGACGCGACGAAAAAATCTTTGTCGTTGG
* *
430011 AAATCATAAAATCCCAGAGAGAATGTCTGAATATTTCTGGATCCACAAAGGCCTAGAACTC
196 AAATCATAAAATCCCAGAGAGAATGTCTGAATATTTCTGGATCCACGAAGGCCAAGAACTC
430072 G
1 G
430073 GTCCACAAAG
Statistics
Matches: 502, Mismatches: 11, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
256 502 1.00
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.27
Consensus pattern (256 bp):
GAAGGAATAGTGAAAACGAATTCGTTTCTAAGTTTTAGTGCCACCAGTGATTCGCAACTTGAAAA
GTTTTTAGGCAACCTAACAGGGATTCTTTCCTCATATTCCAACAAGAGGAAGAGATCAAGCTCCT
TCACATTGCAACGCTGCGCATAGCTACTCCATGTATTGACGCGACGAAAAAATCTTTGTCGTTGG
AAATCATAAAATCCCAGAGAGAATGTCTGAATATTTCTGGATCCACGAAGGCCAAGAACTC
Found at i:434724 original size:23 final size:22
Alignment explanation
Indices: 434677--434734 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
434667 TTATTGAAAG
**
434677 AAATGTATTTCTTTGATTAAAT
1 AAATGTATTTCTTTGAACAAAT
*
434699 AAATGTATTTCATTTGAACAATT
1 AAATGTATTTC-TTTGAACAAAT
*
434722 AAA-GTAATTCTTT
1 AAATGTATTTCTTT
434735 CTCAATAACT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 17 0.55
23 11 0.35
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.47
Consensus pattern (22 bp):
AAATGTATTTCTTTGAACAAAT
Found at i:435197 original size:15 final size:15
Alignment explanation
Indices: 435177--435205 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
435167 TTGAGGTGAA
435177 TTTTATTAATTATTG
1 TTTTATTAATTATTG
435192 TTTTATTAATTATT
1 TTTTATTAATTATT
435206 TTACATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (15 bp):
TTTTATTAATTATTG
Found at i:437353 original size:21 final size:21
Alignment explanation
Indices: 437327--437377 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
437317 GACTTCATTT
437327 TATGCAAAACATGCATGTATG
1 TATGCAAAACATGCATGTATG
437348 TATGCAAAACATGCATGTATG
1 TATGCAAAACATGCATGTATG
437369 TATGCAAAA
1 TATGCAAAA
437378 GTACATTCGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (21 bp):
TATGCAAAACATGCATGTATG
Found at i:438207 original size:19 final size:20
Alignment explanation
Indices: 438183--438221 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
438173 TTCTCTTTTC
438183 TTTTCTTTA-TTTTTAGTTT
1 TTTTCTTTAGTTTTTAGTTT
438202 TTTTCTTTAGTTTTTAGTTT
1 TTTTCTTTAGTTTTTAGTTT
438222 AATTATTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.10, C:0.05, G:0.08, T:0.77
Consensus pattern (20 bp):
TTTTCTTTAGTTTTTAGTTT
Found at i:445240 original size:18 final size:18
Alignment explanation
Indices: 445217--445263 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
445207 GGAAAGAGGG
445217 AAATGCTTTTTGAACTTA
1 AAATGCTTTTTGAACTTA
*
445235 AAATGCTTTGTGAACTTA
1 AAATGCTTTTTGAACTTA
*
445253 AAATGATTTTT
1 AAATGCTTTTT
445264 AAAATTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.34, C:0.09, G:0.13, T:0.45
Consensus pattern (18 bp):
AAATGCTTTTTGAACTTA
Found at i:460998 original size:60 final size:60
Alignment explanation
Indices: 460905--461027 Score: 237
Period size: 60 Copynumber: 2.0 Consensus size: 60
460895 TAGCTAATCC
*
460905 TATATGGATAGATTATAGAAATTGAATGGTTATTATTATTTGTGTATTTTTTGGGATTTA
1 TATATGGATAAATTATAGAAATTGAATGGTTATTATTATTTGTGTATTTTTTGGGATTTA
460965 TATATGGATAAATTATAGAAATTGAATGGTTATTATTATTTGTGTATTTTTTGGGATTTA
1 TATATGGATAAATTATAGAAATTGAATGGTTATTATTATTTGTGTATTTTTTGGGATTTA
461025 TAT
1 TAT
461028 TTGATATATT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (60 bp):
TATATGGATAAATTATAGAAATTGAATGGTTATTATTATTTGTGTATTTTTTGGGATTTA
Found at i:464653 original size:17 final size:17
Alignment explanation
Indices: 464631--464683 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
464621 GATGAAAGCA
464631 AAGATGATCAAATGGCC
1 AAGATGATCAAATGGCC
*
464648 AAGATG---AAA--GCA
1 AAGATGATCAAATGGCC
464660 AAGATGATCAAATGGCC
1 AAGATGATCAAATGGCC
464677 AAGATGA
1 AAGATGA
464684 AATTCTAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
12 8 0.28
14 3 0.10
15 3 0.10
17 15 0.52
ACGTcount: A:0.47, C:0.13, G:0.25, T:0.15
Consensus pattern (17 bp):
AAGATGATCAAATGGCC
Found at i:464653 original size:29 final size:29
Alignment explanation
Indices: 464618--464685 Score: 136
Period size: 29 Copynumber: 2.3 Consensus size: 29
464608 ATGATTGAAT
464618 CAAGATGAAAGCAAAGATGATCAAATGGC
1 CAAGATGAAAGCAAAGATGATCAAATGGC
464647 CAAGATGAAAGCAAAGATGATCAAATGGC
1 CAAGATGAAAGCAAAGATGATCAAATGGC
464676 CAAGATGAAA
1 CAAGATGAAA
464686 TTCTAAGACT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.50, C:0.13, G:0.24, T:0.13
Consensus pattern (29 bp):
CAAGATGAAAGCAAAGATGATCAAATGGC
Found at i:468352 original size:18 final size:18
Alignment explanation
Indices: 468329--468366 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
468319 TGTGAGGGGG
*
468329 AATGCTTTTTGAACTTAA
1 AATGCTTTGTGAACTTAA
468347 AATGCTTTGTGAACTTAA
1 AATGCTTTGTGAACTTAA
468365 AA
1 AA
468367 CGATTTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (18 bp):
AATGCTTTGTGAACTTAA
Found at i:470108 original size:20 final size:20
Alignment explanation
Indices: 470083--470124 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
470073 ATCTCCCGTG
470083 TCCATTCAATTAAGACACAA
1 TCCATTCAATTAAGACACAA
470103 TCCATTCAATTAAGACACAA
1 TCCATTCAATTAAGACACAA
470123 TC
1 TC
470125 AAATAGGACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.26, G:0.05, T:0.26
Consensus pattern (20 bp):
TCCATTCAATTAAGACACAA
Found at i:471946 original size:20 final size:21
Alignment explanation
Indices: 471921--471963 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
471911 TAGTTATATT
471921 TTTTAATGA-ATTTTTACT-TA
1 TTTTAAT-ATATTTTTACTATA
471941 TTTTAATATATTTTTACTATA
1 TTTTAATATATTTTTACTATA
471962 TT
1 TT
471964 AATTCTATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 1 0.05
20 16 0.76
21 4 0.19
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (21 bp):
TTTTAATATATTTTTACTATA
Found at i:487363 original size:13 final size:14
Alignment explanation
Indices: 487335--487368 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
487325 TTTATATATA
*
487335 AAATTATAAATGAT
1 AAATTATAAATAAT
487349 AAATTA-AAATAAT
1 AAATTATAAATAAT
487362 AAATTAT
1 AAATTAT
487369 TGGTGTTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (14 bp):
AAATTATAAATAAT
Found at i:487570 original size:20 final size:21
Alignment explanation
Indices: 487533--487575 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
487523 TTATTACTGA
*
487533 TAAATATGTTTAAAAAAATTT
1 TAAATATGTCTAAAAAAATTT
*
487554 TAAA-ATGTCTAACAAAATTT
1 TAAATATGTCTAAAAAAATTT
487574 TA
1 TA
487576 CTTTTCAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.40
Consensus pattern (21 bp):
TAAATATGTCTAAAAAAATTT
Found at i:488045 original size:24 final size:23
Alignment explanation
Indices: 488012--488058 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
488002 ATCTAATAGT
488012 ATTATTCATATATAATCGTATTA
1 ATTATTCATATATAATCGTATTA
* *
488035 ATTATGTCATATCTTATCGTATTA
1 ATTAT-TCATATATAATCGTATTA
488059 TTTTGATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.34, C:0.11, G:0.06, T:0.49
Consensus pattern (23 bp):
ATTATTCATATATAATCGTATTA
Found at i:493432 original size:27 final size:27
Alignment explanation
Indices: 493394--493448 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
493384 ATTTATGGTG
*
493394 AGTAAAGAGACTTATTTAGCGAGTGCC
1 AGTAAAGAGACTTATTTAGCAAGTGCC
493421 AGTAAAGAGACTTATTTAGCAAGTGCC
1 AGTAAAGAGACTTATTTAGCAAGTGCC
493448 A
1 A
493449 AAGCACCACC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.25
Consensus pattern (27 bp):
AGTAAAGAGACTTATTTAGCAAGTGCC
Found at i:498386 original size:18 final size:20
Alignment explanation
Indices: 498365--498403 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
498355 TATTTAACAT
498365 TAAAATTT-AATTTTT-TAA
1 TAAAATTTAAATTTTTGTAA
498383 TAAAATTTAAATTTTTGTAA
1 TAAAATTTAAATTTTTGTAA
498403 T
1 T
498404 TTTTAATGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.42
19 7 0.37
20 4 0.21
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (20 bp):
TAAAATTTAAATTTTTGTAA
Found at i:498618 original size:25 final size:25
Alignment explanation
Indices: 498590--498638 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
498580 TTTGATTGGT
498590 TATAGGTAAATTAGAAACATATTAC
1 TATAGGTAAATTAGAAACATATTAC
498615 TATAGGTAAATTAGAAACATATTA
1 TATAGGTAAATTAGAAACATATTA
498639 ACATATACAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.49, C:0.06, G:0.12, T:0.33
Consensus pattern (25 bp):
TATAGGTAAATTAGAAACATATTAC
Found at i:500949 original size:2 final size:2
Alignment explanation
Indices: 500942--500976 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
500932 TGCATTATAA
500942 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
500977 AGAACTAGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:502576 original size:20 final size:20
Alignment explanation
Indices: 502553--502623 Score: 56
Period size: 20 Copynumber: 3.5 Consensus size: 20
502543 TACATATTTG
502553 ATATTAAAATTATAATTAAA
1 ATATTAAAATTATAATTAAA
* * **
502573 ATATT-TATTTGGAATTTAAA
1 ATATTAAAATTATAA-TTAAA
*
502593 ATATAAAAAATTATAATT-AA
1 ATAT-TAAAATTATAATTAAA
*
502613 ATATTTAAATT
1 ATATTAAAATT
502624 TGATTCCTAA
Statistics
Matches: 37, Mismatches: 11, Indels: 7
0.67 0.20 0.13
Matches are distributed among these distances:
19 10 0.27
20 20 0.54
21 2 0.05
22 5 0.14
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (20 bp):
ATATTAAAATTATAATTAAA
Found at i:505649 original size:19 final size:20
Alignment explanation
Indices: 505625--505670 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 20
505615 TTATTTTTAT
*
505625 TATATAAAAATTTA-AAAAA
1 TATATAAAAATTAATAAAAA
505644 TATATAAAAATTAATAAAAA
1 TATATAAAAATTAATAAAAA
505664 TATATAA
1 TATATAA
505671 TTTTGTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
TATATAAAAATTAATAAAAA
Found at i:505652 original size:10 final size:10
Alignment explanation
Indices: 505625--505670 Score: 60
Period size: 10 Copynumber: 4.7 Consensus size: 10
505615 TTATTTTTAT
505625 TATATAAAAA
1 TATATAAAAA
*
505635 TTTA-AAAAA
1 TATATAAAAA
505644 TATATAAAAA
1 TATATAAAAA
505654 T-TAATAAAAA
1 TAT-ATAAAAA
505664 TATATAA
1 TATATAA
505671 TTTTGTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
9 9 0.29
10 21 0.68
11 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
TATATAAAAA
Found at i:508088 original size:15 final size:15
Alignment explanation
Indices: 508068--508096 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
508058 GTTTCTAAAT
508068 CATCTTTGCCTCCTA
1 CATCTTTGCCTCCTA
508083 CATCTTTGCCTCCT
1 CATCTTTGCCTCCT
508097 GCAGCTAGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.41, G:0.07, T:0.41
Consensus pattern (15 bp):
CATCTTTGCCTCCTA
Found at i:510326 original size:11 final size:11
Alignment explanation
Indices: 510310--510334 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
510300 TATCAAAGAA
510310 GAAAAAGAAAG
1 GAAAAAGAAAG
510321 GAAAAAGAAAG
1 GAAAAAGAAAG
510332 GAA
1 GAA
510335 TATTTGCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (11 bp):
GAAAAAGAAAG
Found at i:512249 original size:2 final size:2
Alignment explanation
Indices: 512242--512270 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
512232 GACCTAGATT
512242 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
512271 AGATTATTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:515834 original size:30 final size:30
Alignment explanation
Indices: 515800--515893 Score: 179
Period size: 30 Copynumber: 3.1 Consensus size: 30
515790 TATATATGAA
515800 TTTATATTTGTTTATTGATTCACTTATTTC
1 TTTATATTTGTTTATTGATTCACTTATTTC
515830 TTTATATTTGTTTATTGATTCACTTATTTC
1 TTTATATTTGTTTATTGATTCACTTATTTC
*
515860 TTTATATTTGTTTATTGATTCACTTATTTG
1 TTTATATTTGTTTATTGATTCACTTATTTC
515890 TTTA
1 TTTA
515894 CATTCAAGTG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 63 1.00
ACGTcount: A:0.20, C:0.09, G:0.07, T:0.64
Consensus pattern (30 bp):
TTTATATTTGTTTATTGATTCACTTATTTC
Found at i:517985 original size:26 final size:25
Alignment explanation
Indices: 517914--517985 Score: 90
Period size: 26 Copynumber: 2.8 Consensus size: 25
517904 TCTGATTCGG
* *
517914 GCCTAATTGGGCTCATCTTGGGCTA
1 GCCTAGTTGGGCTCATCTTGGGCGA
* *
517939 GCCTAGTTAGGCCCATCTTGGGTCGA
1 GCCTAGTTGGGCTCATCTTGGG-CGA
*
517965 GCCTAGTTGGGCTCATTTTGG
1 GCCTAGTTGGGCTCATCTTGG
517986 TTAAACCCGA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
25 19 0.49
26 20 0.51
ACGTcount: A:0.14, C:0.24, G:0.31, T:0.32
Consensus pattern (25 bp):
GCCTAGTTGGGCTCATCTTGGGCGA
Found at i:519036 original size:42 final size:41
Alignment explanation
Indices: 518982--519071 Score: 110
Period size: 41 Copynumber: 2.2 Consensus size: 41
518972 TTATTTTTAG
518982 AAAAAAAGGAAAAAAGTATTCTATCTTTTTCAAAAAAAAAAA
1 AAAAAAAGGAAAAAAGTATTCTATC-TTTTCAAAAAAAAAAA
* * * * *
519024 AGAAAAAA-GAAAAAATTATTTTGTCTTTTCTAAAAAAAATA
1 A-AAAAAAGGAAAAAAGTATTCTATCTTTTCAAAAAAAAAAA
519065 AAAAAAA
1 AAAAAAA
519072 TTCTGAAAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
40 6 0.14
41 15 0.36
42 15 0.36
43 6 0.14
ACGTcount: A:0.62, C:0.06, G:0.07, T:0.26
Consensus pattern (41 bp):
AAAAAAAGGAAAAAAGTATTCTATCTTTTCAAAAAAAAAAA
Found at i:530232 original size:89 final size:88
Alignment explanation
Indices: 530151--530683 Score: 371
Period size: 89 Copynumber: 6.0 Consensus size: 88
530141 GACTAAGTCT
* ** * * *
530151 TGGTCATTTTATTTTGACTCGTGATTTCGTCTCGGTCACATGATTCATGGTTTCATTCTGATCAT
1 TGGTCACTTTATTTCAACTCGTGATTTCGTCCCGATCACATGATTCATGGTTTCATTCCGATCAT
*
530216 TCATTTTTCACATCGACTCGGTCC
66 TCATTTTTCAC-TCGACTCGATCC
* *** * * * ** ** ** *
530240 TGATTGTTTTATTTCGACTCATGGTTTAATCCTAATCACATGATTTGTGGTTTCATAT-TGATCA
1 TGGTCACTTTATTTCAACTCGTGATTTCGTCCCGATCACATGATTCATGGTTTCAT-TCCGATCA
* * * *
530304 TTCATTTTTGACCTTGACTTGATCT
65 TTCATTTTTCA-CTCGACTCGATCC
* * * * * * * *
530329 TAGTCACTTTATTTCAACTCATGATTTCGTTCTGATCACATGAGTCGTAGTTTCA-TCCCAGTCA
1 TGGTCACTTTATTTCAACTCGTGATTTCGTCCCGATCACATGATTCATGGTTTCATTCCGA-TCA
*
530393 TTCATTTTTGATCTCGACTCGATCC
65 TTCATTTTTCA-CTCGACTCGATCC
* * * *
530418 TGGTCACTTTATTTCAACTTGTGGTTTCATCCC-AGTCACATGATTCATGGTTTCA-TCCCAGTC
1 TGGTCACTTTATTTCAACTCGTGATTTCGTCCCGA-TCACATGATTCATGGTTTCATTCCGA-TC
530481 ATTCA-TTTTCAACCTCGACTCGATCC
64 ATTCATTTTTC-A-CTCGACTCGATCC
* * * * *
530507 TGATCACTTTATTTTAACTCGTGATTTCGTCCCGATCACATGATTTATGGTTTC-TCCCGGTCAT
1 TGGTCACTTTATTTCAACTCGTGATTTCGTCCCGATCACATGATTCATGGTTTCATTCCGATCAT
* * * *
530571 TCATTTTTGACCTTGACTTGGTCC
66 TCATTTTTCA-CTCGACTCGATCC
** * * ** * * * * *
530595 TGGTTGCTTTATTT-AGACTCATGGTTTCGTTTC-AACACATGATTCGTGATTTTATCCCGATCA
1 TGGTCACTTTATTTCA-ACTCGTGATTTCGTCCCGATCACATGATTCATGGTTTCATTCCGATCA
*
530658 TTCATTTTTTATCTCGACTCGATCC
65 TTCATTTTTCA-CTCGACTCGATCC
530683 T
1 T
530684 AGTCGCTTCA
Statistics
Matches: 351, Mismatches: 82, Indels: 23
0.77 0.18 0.05
Matches are distributed among these distances:
87 17 0.05
88 78 0.22
89 253 0.72
90 3 0.01
ACGTcount: A:0.19, C:0.23, G:0.15, T:0.43
Consensus pattern (88 bp):
TGGTCACTTTATTTCAACTCGTGATTTCGTCCCGATCACATGATTCATGGTTTCATTCCGATCAT
TCATTTTTCACTCGACTCGATCC
Found at i:530412 original size:178 final size:175
Alignment explanation
Indices: 530104--530621 Score: 513
Period size: 178 Copynumber: 2.9 Consensus size: 175
530094 ATTCCTCATT
* * * * * *
530104 ATTTGTGGTTTCATTTTGATCATTTATTCTCGATCTCGAC-TAAGTCTTGGTCATTTTATTTTGA
1 ATTTGTGGTTTCA-TTTGATCATTCATTTTCGACCTCGACTTGA-TCTT-GTCACTTTATTTTAA
* * * *
530168 CTCGTGATTTCG-TCTCGGTCACATGATTCATGGTTTCAT-TCTGATCATTCATTTTTCACATCG
63 CTCGTGATTTCGTTCT-GATCACATGATTCATGGTTTCATCCCAG-TCATTCATTTTTGAC-TCG
* * *
530231 ACTCGGTCCTGATTGTTTTATTTCGACTCATGGTTTAATCCTAATCACATG
125 ACTCGGTCCTGGTTGCTTTATTTCGACTCATGGTTTAATCCCAATCACATG
* * *
530282 ATTTGTGGTTTCATATTGATCATTCATTTTTGACCTTGACTTGATCTTAGTCACTTTATTTCAAC
1 ATTTGTGGTTTCAT-TTGATCATTCATTTTCGACCTCGACTTGATCTT-GTCACTTTATTTTAAC
* * * *
530347 TCATGATTTCGTTCTGATCACATGAGTCGTAGTTTCATCCCAGTCATTCATTTTTGATCTCGACT
64 TCGTGATTTCGTTCTGATCACATGATTCATGGTTTCATCCCAGTCATTCATTTTTGA-CTCGACT
* ** * ** * *
530412 CGATCCTGGTCACTTTATTTCAACTTGTGGTTTCATCCCAGTCACATG
128 CGGTCCTGGTTGCTTTATTTCGACTCATGGTTTAATCCCAATCACATG
** *** * * *
530460 ATTCATGGTTTCATCCCAGTCATTCATTTTCAACCTCGACTCGATCCTGATCACTTTATTTTAAC
1 ATTTGTGGTTTCATTTGA-TCATTCATTTTCGACCTCGACTTGATCTTG-TCACTTTATTTTAAC
* * * * *
530525 TCGTGATTTCGTCCCGATCACATGATTTATGGTTTC-TCCCGGTCATTCATTTTTGACCTTGACT
64 TCGTGATTTCGTTCTGATCACATGATTCATGGTTTCATCCCAGTCATTCATTTTTGA-CTCGACT
* *
530589 TGGTCCTGGTTGCTTTATTTAGACTCATGGTTT
128 CGGTCCTGGTTGCTTTATTTCGACTCATGGTTT
530622 CGTTTCAACA
Statistics
Matches: 275, Mismatches: 58, Indels: 15
0.79 0.17 0.04
Matches are distributed among these distances:
177 53 0.19
178 214 0.78
179 8 0.03
ACGTcount: A:0.19, C:0.22, G:0.15, T:0.44
Consensus pattern (175 bp):
ATTTGTGGTTTCATTTGATCATTCATTTTCGACCTCGACTTGATCTTGTCACTTTATTTTAACTC
GTGATTTCGTTCTGATCACATGATTCATGGTTTCATCCCAGTCATTCATTTTTGACTCGACTCGG
TCCTGGTTGCTTTATTTCGACTCATGGTTTAATCCCAATCACATG
Found at i:531008 original size:26 final size:26
Alignment explanation
Indices: 530957--531009 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
530947 ATCTCGACCC
* * *
530957 AATTGGGCCCATTTTGGTCTGGGCCT
1 AATTGAGCCCATTTAGGTCTGAGCCT
530983 AATTGAGCCCATCTTAGGT-TGAGCCT
1 AATTGAGCCCAT-TTAGGTCTGAGCCT
531009 A
1 A
531010 GCTGGGCCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.32
Consensus pattern (26 bp):
AATTGAGCCCATTTAGGTCTGAGCCT
Found at i:531081 original size:3 final size:3
Alignment explanation
Indices: 531073--531127 Score: 67
Period size: 3 Copynumber: 18.3 Consensus size: 3
531063 AATTAGATTC
* *
531073 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TTT TACT T-T TAT TTT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
*
531118 TAT TTT TAT T
1 TAT TAT TAT T
531128 TTTTTTGTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
2 2 0.05
3 40 0.91
4 2 0.05
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (3 bp):
TAT
Found at i:531130 original size:18 final size:18
Alignment explanation
Indices: 531075--531130 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 18
531065 TTAGATTCTA
* *
531075 TTATTATTATTATTATTA
1 TTATTATTATTTTTATTT
*
531093 TTATTATTATTTTTACTT
1 TTATTATTATTTTTATTT
*
531111 TTATTTTTATTTTTATTT
1 TTATTATTATTTTTATTT
531129 TT
1 TT
531131 TTTGTTTCCT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (18 bp):
TTATTATTATTTTTATTT
Found at i:531193 original size:6 final size:6
Alignment explanation
Indices: 531186--531229 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
531176 TCACCATATA
* * *
531186 TTATTA TTATTG TTATTT TTACTT TTATTT TTATTT TTATTT TT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TT
531230 TTTGTTTCCT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.77
Consensus pattern (6 bp):
TTATTT
Found at i:531259 original size:99 final size:99
Alignment explanation
Indices: 531085--531283 Score: 371
Period size: 99 Copynumber: 2.0 Consensus size: 99
531075 TTATTATTAT
531085 TATTATTATTATTATTATTTTTACTTTTATTTTTATTTTTATTTTTTTTGTTTCCTTTTCTACTC
1 TATTATTATTATTATTATTTTTACTTTTATTTTTATTTTTATTTTTTTTGTTTCCTTTTCTACTC
*
531150 AATCCGCACATGACCGTAGATCAAAATCACCATA
66 AATCCACACATGACCGTAGATCAAAATCACCATA
*
531184 TATTATTATTATTGTTATTTTTACTTTTATTTTTATTTTTATTTTTTTTGTTTCCTTTTCTACTC
1 TATTATTATTATTATTATTTTTACTTTTATTTTTATTTTTATTTTTTTTGTTTCCTTTTCTACTC
*
531249 AATCCACACATGACCGTAGATCAGAATCACCATA
66 AATCCACACATGACCGTAGATCAAAATCACCATA
531283 T
1 T
531284 TTTTTGGTTA
Statistics
Matches: 97, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
99 97 1.00
ACGTcount: A:0.25, C:0.16, G:0.06, T:0.54
Consensus pattern (99 bp):
TATTATTATTATTATTATTTTTACTTTTATTTTTATTTTTATTTTTTTTGTTTCCTTTTCTACTC
AATCCACACATGACCGTAGATCAAAATCACCATA
Found at i:532059 original size:9 final size:9
Alignment explanation
Indices: 532030--532071 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
532020 CGACCGCAGG
532030 TTTTT-TTT
1 TTTTTATTT
*
532038 TTTCTATTT
1 TTTTTATTT
532047 TTTTTATTT
1 TTTTTATTT
*
532056 TTTTAATTT
1 TTTTTATTT
532065 ATTTTTA
1 -TTTTTA
532072 ACCATATCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
8 4 0.14
9 19 0.68
10 5 0.18
ACGTcount: A:0.14, C:0.02, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTTTATTT
Found at i:532201 original size:43 final size:45
Alignment explanation
Indices: 532109--532192 Score: 136
Period size: 44 Copynumber: 1.9 Consensus size: 45
532099 TTTTTTAAGA
532109 AAAAAAGGAAAAAATTATTCTATCTTTTTCAAAAAAAAAAAGAAG
1 AAAAAAGGAAAAAATTATTCTATCTTTTTCAAAAAAAAAAAGAAG
* *
532154 AAAAAA-GAAAAAATTATTCTGTC-TTTTCTAAAAAAAAAA
1 AAAAAAGGAAAAAATTATTCTATCTTTTTCAAAAAAAAAAA
532193 TTCTAAAAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
43 15 0.41
44 16 0.43
45 6 0.16
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.26
Consensus pattern (45 bp):
AAAAAAGGAAAAAATTATTCTATCTTTTTCAAAAAAAAAAAGAAG
Found at i:536207 original size:15 final size:15
Alignment explanation
Indices: 536189--536219 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
536179 AAAAATATAA
*
536189 TTTAATTAATTTAAT
1 TTTAAATAATTTAAT
536204 TTTAAATAATTTAAT
1 TTTAAATAATTTAAT
536219 T
1 T
536220 CGAAATTAAC
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTAAATAATTTAAT
Found at i:538485 original size:23 final size:23
Alignment explanation
Indices: 538459--538534 Score: 73
Period size: 25 Copynumber: 3.1 Consensus size: 23
538449 GTGGGGAAGG
*
538459 AGAAAAGTAAAGAAGAAAAAAAA
1 AGAAAAGAAAAGAAGAAAAAAAA
538482 AG-AAAGAAAGAGAAGAGAGAAAAAA
1 AGAAAAGAAA-AGAAGA-A-AAAAAA
* *
538507 AAAAGAAGAAAAAAGAGAAAAAAAA
1 AGAA-AAGAAAAGA-AGAAAAAAAA
538532 AGA
1 AGA
538535 GATTTAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 6 0.14
23 8 0.19
24 1 0.02
25 15 0.35
26 4 0.09
27 9 0.21
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.01
Consensus pattern (23 bp):
AGAAAAGAAAAGAAGAAAAAAAA
Found at i:538490 original size:27 final size:26
Alignment explanation
Indices: 538462--538536 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 26
538452 GGGAAGGAGA
538462 AAAGTAAAGAAGAAAAAAAAAGA-AAG
1 AAAG-AAAGAAGAAAAAAAAAGAGAAG
538488 AAAGAGAAGAGAGAAAAAAAAA-AGAAG
1 AAAGA-AAGA-AGAAAAAAAAAGAGAAG
538515 AAA-AAAG-AGAAAAAAAAAGAGA
1 AAAGAAAGAAGAAAAAAAAAGAGA
538537 TTTAAAAAGT
Statistics
Matches: 45, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
23 11 0.24
24 3 0.07
25 4 0.09
26 10 0.22
27 17 0.38
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.01
Consensus pattern (26 bp):
AAAGAAAGAAGAAAAAAAAAGAGAAG
Found at i:538510 original size:30 final size:30
Alignment explanation
Indices: 538469--538525 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
538459 AGAAAAGTAA
*
538469 AGAAGAAAAAAA-AAGAAAGAAAGAGAAGAG
1 AGAAAAAAAAAAGAAGAAA-AAAGAGAAGAG
538499 AGAAAAAAAAAAGAAGAAAAAAGAGAA
1 AGAAAAAAAAAAGAAGAAAAAAGAGAA
538526 AAAAAAAGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 19 0.76
31 6 0.24
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (30 bp):
AGAAAAAAAAAAGAAGAAAAAAGAGAAGAG
Found at i:538525 original size:9 final size:10
Alignment explanation
Indices: 538467--538534 Score: 59
Period size: 10 Copynumber: 6.8 Consensus size: 10
538457 GGAGAAAAGT
538467 AAAGAAGAAA
1 AAAGAAGAAA
*
538477 AAAAAAGAAA
1 AAAGAAGAAA
*
538487 GAAAG-AGAAG
1 -AAAGAAGAAA
* *
538497 AGAGAAAAAAA
1 AAAG-AAGAAA
538508 AAAGAAGAAA
1 AAAGAAGAAA
538518 AAAG-AGAAA
1 AAAGAAGAAA
*
538527 AAAAAAGA
1 AAAGAAGA
538535 GATTTAAAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
9 11 0.24
10 25 0.56
11 9 0.20
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (10 bp):
AAAGAAGAAA
Found at i:538657 original size:22 final size:24
Alignment explanation
Indices: 538632--538679 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
538622 GTAAAAAAAA
*
538632 TTTGAAAAAT-AAA-AGAAAATTT
1 TTTGAAAAATCAAATAAAAAATTT
*
538654 TTTGAAAAGTCAAATAAAAAATTT
1 TTTGAAAAATCAAATAAAAAATTT
538678 TT
1 TT
538680 AAAAGTCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 9 0.41
23 3 0.14
24 10 0.45
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.35
Consensus pattern (24 bp):
TTTGAAAAATCAAATAAAAAATTT
Found at i:538683 original size:22 final size:22
Alignment explanation
Indices: 538609--538689 Score: 69
Period size: 23 Copynumber: 3.6 Consensus size: 22
538599 GAGAGATAGG
*
538609 TTTTAAAAG-CAAAGTAAAAAAAA
1 TTTTAAAAGTCAAA-T-AAAAAAT
* * *
538632 TTTGAAAAAT-AAA-AGAAAATT
1 TTTTAAAAGTCAAATA-AAAAAT
538653 TTTTGAAAAGTCAAATAAAAAAT
1 TTTT-AAAAGTCAAATAAAAAAT
538676 TTTTAAAAGTCAAA
1 TTTTAAAAGTCAAA
538690 AAATTTAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
20 1 0.02
21 7 0.15
22 15 0.33
23 22 0.48
24 1 0.02
ACGTcount: A:0.59, C:0.04, G:0.09, T:0.28
Consensus pattern (22 bp):
TTTTAAAAGTCAAATAAAAAAT
Found at i:538700 original size:17 final size:18
Alignment explanation
Indices: 538669--538708 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
538659 AAAGTCAAAT
*
538669 AAAAAATTTTTAAAAGTC
1 AAAAAATTTTAAAAAGTC
*
538687 AAAAAA-TTTAAAAAGTT
1 AAAAAATTTTAAAAAGTC
538704 AAAAA
1 AAAAA
538709 GAAAAACCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.28
Consensus pattern (18 bp):
AAAAAATTTTAAAAAGTC
Found at i:538793 original size:27 final size:26
Alignment explanation
Indices: 538763--538824 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 26
538753 TTGAAAAGTG
*
538763 AAAAAAAAACAACTTTGAAAAG-CCA
1 AAAAAAAAAAAACTTTGAAAAGTCCA
* * * *
538788 ACAAAAGAAAAAGCTTTGGAAAGTCTA
1 A-AAAAAAAAAAACTTTGAAAAGTCCA
538815 AAAAAAAAAA
1 AAAAAAAAAA
538825 GTTTAACTAG
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
25 1 0.03
26 25 0.86
27 3 0.10
ACGTcount: A:0.65, C:0.11, G:0.11, T:0.13
Consensus pattern (26 bp):
AAAAAAAAAAAACTTTGAAAAGTCCA
Found at i:539503 original size:23 final size:22
Alignment explanation
Indices: 539471--539570 Score: 68
Period size: 22 Copynumber: 4.5 Consensus size: 22
539461 AATTTTTAGT
539471 TTTCATTTGCATAATTTATTTG
1 TTTCATTTGCATAATTTATTTG
* *
539493 TTTCATGTTGCATTAATATAAAATTG
1 TTTCAT-TTGCA-TAAT-T-TATTTG
* *
539519 --TCA--AG-ATAATTT-TTAG
1 TTTCATTTGCATAATTTATTTG
539535 TTTTCATTTGCATAATTTATTTG
1 -TTTCATTTGCATAATTTATTTG
539558 TTTCATGTTGCAT
1 TTTCAT-TTGCAT
539571 TAATATAAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 23
0.65 0.09 0.26
Matches are distributed among these distances:
16 2 0.03
18 1 0.02
19 7 0.12
20 1 0.02
21 2 0.03
22 19 0.33
23 14 0.24
24 7 0.12
25 1 0.02
26 4 0.07
ACGTcount: A:0.27, C:0.09, G:0.11, T:0.53
Consensus pattern (22 bp):
TTTCATTTGCATAATTTATTTG
Found at i:539540 original size:65 final size:65
Alignment explanation
Indices: 539460--539589 Score: 260
Period size: 65 Copynumber: 2.0 Consensus size: 65
539450 TTGGTTGTTT
539460 TAATTTTTAGTTTTCATTTGCATAATTTATTTGTTTCATGTTGCATTAATATAAAATTGTCAAGA
1 TAATTTTTAGTTTTCATTTGCATAATTTATTTGTTTCATGTTGCATTAATATAAAATTGTCAAGA
539525 TAATTTTTAGTTTTCATTTGCATAATTTATTTGTTTCATGTTGCATTAATATAAAATTGTCAAGA
1 TAATTTTTAGTTTTCATTTGCATAATTTATTTGTTTCATGTTGCATTAATATAAAATTGTCAAGA
539590 AAAAAGAGAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.31, C:0.08, G:0.11, T:0.51
Consensus pattern (65 bp):
TAATTTTTAGTTTTCATTTGCATAATTTATTTGTTTCATGTTGCATTAATATAAAATTGTCAAGA
Found at i:539767 original size:15 final size:15
Alignment explanation
Indices: 539749--539796 Score: 78
Period size: 15 Copynumber: 3.2 Consensus size: 15
539739 TTAAAACTCG
539749 AAACCCTAAAATTCA
1 AAACCCTAAAATTCA
**
539764 AAACCCTAAAATTTG
1 AAACCCTAAAATTCA
539779 AAACCCTAAAATTCA
1 AAACCCTAAAATTCA
539794 AAA
1 AAA
539797 TCTTAGAACC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.54, C:0.23, G:0.02, T:0.21
Consensus pattern (15 bp):
AAACCCTAAAATTCA
Found at i:544641 original size:12 final size:12
Alignment explanation
Indices: 544620--544667 Score: 60
Period size: 13 Copynumber: 3.8 Consensus size: 12
544610 AATGTAAAAA
544620 AAAAAAAAAAGT
1 AAAAAAAAAAGT
* *
544632 AAAAAGAAAAGGC
1 AAAAA-AAAAAGT
544645 AAGAAAAAAAAGT
1 AA-AAAAAAAAGT
544658 AAAAAAAAAA
1 AAAAAAAAAA
544668 AAAAATGATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
12 13 0.43
13 14 0.47
14 3 0.10
ACGTcount: A:0.81, C:0.02, G:0.12, T:0.04
Consensus pattern (12 bp):
AAAAAAAAAAGT
Found at i:546737 original size:23 final size:24
Alignment explanation
Indices: 546683--546737 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 24
546673 CTATCAAGGA
** *
546683 AAAATAAAAGAAAGAGAATTTATC
1 AAAATAAAAGAAAGAGAAAATAGC
546707 AAAA-AAAAGAAAGA-AAAATAGC
1 AAAATAAAAGAAAGAGAAAATAGC
546729 AAAATAAAA
1 AAAATAAAA
546738 AAATGATCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 9 0.33
23 14 0.52
24 4 0.15
ACGTcount: A:0.73, C:0.04, G:0.11, T:0.13
Consensus pattern (24 bp):
AAAATAAAAGAAAGAGAAAATAGC
Found at i:546993 original size:57 final size:57
Alignment explanation
Indices: 546932--547039 Score: 171
Period size: 57 Copynumber: 1.9 Consensus size: 57
546922 AATTGGCACT
* * *
546932 TAAATTGTAGGCCCAGTTTAACTGACATTTAGATTTAAGCCTAGTTTAGCTACCATA
1 TAAATTGTAAGCCCAGTTTAACTGACATTTAAATTTAAGCCTAATTTAGCTACCATA
* *
546989 TAAATTTTAAGTCCAGTTTAACTGACATTTAAATTTAAGCCTAATTTAGCT
1 TAAATTGTAAGCCCAGTTTAACTGACATTTAAATTTAAGCCTAATTTAGCT
547040 GGCACTCATA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 46 1.00
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (57 bp):
TAAATTGTAAGCCCAGTTTAACTGACATTTAAATTTAAGCCTAATTTAGCTACCATA
Found at i:547021 original size:29 final size:29
Alignment explanation
Indices: 546908--547024 Score: 96
Period size: 29 Copynumber: 4.1 Consensus size: 29
546898 CAAGATAAGA
** * * *
546908 TTTAAGTTTAGTTTAATTGGCACTTAAAT
1 TTTAAGTCCAGTTTAACTGACATTTAAAT
* * * *
546937 TGTAGGCCCAGTTTAACTGACATTTAGA-
1 TTTAAGTCCAGTTTAACTGACATTTAAAT
* *
546965 TTTAAG-CCTAGTTTAGCT-ACCATATAAAT
1 TTTAAGTCC-AGTTTAACTGA-CATTTAAAT
546994 TTTAAGTCCAGTTTAACTGACATTTAAAT
1 TTTAAGTCCAGTTTAACTGACATTTAAAT
547023 TT
1 TT
547025 AAGCCTAATT
Statistics
Matches: 67, Mismatches: 16, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
27 3 0.04
28 18 0.27
29 43 0.64
30 3 0.04
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.41
Consensus pattern (29 bp):
TTTAAGTCCAGTTTAACTGACATTTAAAT
Found at i:547142 original size:28 final size:28
Alignment explanation
Indices: 547107--547207 Score: 98
Period size: 28 Copynumber: 3.6 Consensus size: 28
547097 GCACTTAGAC
*
547107 TTTAAGCCCAGTTTAGTTGGCATACAGT
1 TTTAAGCCCAGTTTAGCTGGCATACAGT
* * *
547135 TTTAAGCCCAGTTTAGCTAGCGTATAGAT
1 TTTAAGCCCAGTTTAGCTGGCATACAG-T
* * *
547164 TTTAAACCCAGTTTAGCT--AATACTTAGA
1 TTTAAGCCCAGTTTAGCTGGCATAC--AGT
547192 TTTAAGCCCAGTTTAG
1 TTTAAGCCCAGTTTAG
547208 TTGGTATTCA
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
27 2 0.03
28 38 0.63
29 20 0.33
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36
Consensus pattern (28 bp):
TTTAAGCCCAGTTTAGCTGGCATACAGT
Found at i:547196 original size:57 final size:56
Alignment explanation
Indices: 547076--547207 Score: 151
Period size: 57 Copynumber: 2.3 Consensus size: 56
547066 CTAGCACATG
* * * *
547076 GATTTAAGCTCAGTTTAGCTAGCACTTAGACTTTAAGCCCAGTTTAGTTGGCATACA
1 GATTTAAGCCCAGTTTAGCTAGCACTTAGACTTTAAACCCAGTTTAGCT-GAATACA
* * *
547133 GTTTTAAGCCCAGTTTAGCTAGC-GTATAGATTTTAAACCCAGTTTAGCT-AATACTTA
1 GATTTAAGCCCAGTTTAGCTAGCACT-TAGACTTTAAACCCAGTTTAGCTGAATAC--A
547190 GATTTAAGCCCAGTTTAG
1 GATTTAAGCCCAGTTTAG
547208 TTGGTATTCA
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
55 4 0.06
56 1 0.02
57 59 0.92
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (56 bp):
GATTTAAGCCCAGTTTAGCTAGCACTTAGACTTTAAACCCAGTTTAGCTGAATACA
Found at i:547222 original size:28 final size:27
Alignment explanation
Indices: 547107--547226 Score: 82
Period size: 28 Copynumber: 4.3 Consensus size: 27
547097 GCACTTAGAC
* *
547107 TTTAAGCCCAGTTTAGTTGGCA-TACAGT
1 TTTAAGCCCAGTTTAGTTGGTATTA-A-A
* *
547135 TTTAAGCCCAGTTTAGCTAGCGTA-TAGAT
1 TTTAAGCCCAGTTTAG-TTG-GTATTA-AA
* * ** *
547164 TTTAAACCCAGTTTAGCTAATACTTAGA
1 TTTAAGCCCAGTTTAGTTGGTA-TTAAA
547192 TTTAAGCCCAGTTTAGTTGGTATTCAAA
1 TTTAAGCCCAGTTTAGTTGGTATT-AAA
547220 TTTAAGC
1 TTTAAGC
547227 TCAATTTAAC
Statistics
Matches: 72, Mismatches: 15, Indels: 10
0.74 0.15 0.10
Matches are distributed among these distances:
27 4 0.06
28 43 0.60
29 20 0.28
30 5 0.07
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (27 bp):
TTTAAGCCCAGTTTAGTTGGTATTAAA
Found at i:547224 original size:85 final size:85
Alignment explanation
Indices: 546928--547226 Score: 260
Period size: 85 Copynumber: 3.5 Consensus size: 85
546918 GTTTAATTGG
* * ** * * * * * *
546928 CACTTAAATTGTAGGCCCAGTTTAACTGACATTTAGATTTAAGCCTAGTTTAGCTACCATATAAA
1 CACTTAGATT-TAAGCCCAGTTTAGTTGGCATTCAAATTTAAGCCCAGTTTAGCTAGCATATAGA
* * *
546993 TTTTAAGTCCAGTTTAACTGA
65 TTTTAAGCCCAGTTTAGCTAA
* * * * * * * * * * *
547014 CATTTAAATTTAAGCCTAATTTAGCTGGCACTCATATTTAAG-TCATGTCTAGCTAGCACATGGA
1 CACTTAGATTTAAGCCCAGTTTAGTTGGCATTCAAATTTAAGCCCA-GTTTAGCTAGCATATAGA
* *
547078 -TTTAAGCTCAGTTTAGCTAG
65 TTTTAAGCCCAGTTTAGCTAA
* ** *
547098 CACTTAGACTTTAAGCCCAGTTTAGTTGGCATACAGTTTTAAGCCCAGTTTAGCTAGCGTATAGA
1 CACTTAGA-TTTAAGCCCAGTTTAGTTGGCATTCAAATTTAAGCCCAGTTTAGCTAGCATATAGA
*
547163 TTTTAAACCCAGTTTAGCTAA
65 TTTTAAGCCCAGTTTAGCTAA
* *
547184 TACTTAGATTTAAGCCCAGTTTAGTTGGTATTCAAATTTAAGC
1 CACTTAGATTTAAGCCCAGTTTAGTTGGCATTCAAATTTAAGC
547227 TCAATTTAAC
Statistics
Matches: 166, Mismatches: 43, Indels: 9
0.76 0.20 0.04
Matches are distributed among these distances:
84 22 0.13
85 109 0.66
86 35 0.21
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (85 bp):
CACTTAGATTTAAGCCCAGTTTAGTTGGCATTCAAATTTAAGCCCAGTTTAGCTAGCATATAGAT
TTTAAGCCCAGTTTAGCTAA
Found at i:547747 original size:81 final size:81
Alignment explanation
Indices: 547598--547747 Score: 201
Period size: 81 Copynumber: 1.9 Consensus size: 81
547588 TTTTTGGTAG
** * * * * *
547598 AATATTTTAAATTTTAAAATTTCAAGGCATCTTTTTAGAGGAGTATTTGTAGATGTCGAGATTTA
1 AATATTTTAAAACTTAAAATTTCAAGGCATCTTTTTAGAAGAGCATTTATAGATGTCGAGACTCA
547663 TAAGTCCTATTGGCAA
66 TAAGTCCTATTGGCAA
* * * *
547679 AATATTTTAAAACTTAAAGTTTCAAGGCTTCTTTTTAGAAGAGCATTTATAGGTGTTGAGACTCA
1 AATATTTTAAAACTTAAAATTTCAAGGCATCTTTTTAGAAGAGCATTTATAGATGTCGAGACTCA
547744 TAAG
66 TAAG
547748 ACTTCTGAAC
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
81 58 1.00
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.39
Consensus pattern (81 bp):
AATATTTTAAAACTTAAAATTTCAAGGCATCTTTTTAGAAGAGCATTTATAGATGTCGAGACTCA
TAAGTCCTATTGGCAA
Found at i:547907 original size:3 final size:3
Alignment explanation
Indices: 547899--547941 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
547889 CTTATGGCAA
547899 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
547942 TGAAAAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:548138 original size:35 final size:35
Alignment explanation
Indices: 548051--548130 Score: 99
Period size: 35 Copynumber: 2.3 Consensus size: 35
548041 ATCCTAATCG
* *
548051 TTTTCATTTCTT-AACTCGTGATTCAGTCTCAGTTA
1 TTTTCA-TTCTTCAACTTGCGATTCAGTCTCAGTTA
* * *
548086 TTTTTATTCTTCAACTTGCGATTCATTCTTAGTTA
1 TTTTCATTCTTCAACTTGCGATTCAGTCTCAGTTA
548121 TTTTCATTCT
1 TTTTCATTCT
548131 CTGACTTGTG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
34 5 0.13
35 33 0.87
ACGTcount: A:0.19, C:0.19, G:0.09, T:0.54
Consensus pattern (35 bp):
TTTTCATTCTTCAACTTGCGATTCAGTCTCAGTTA
Found at i:548445 original size:27 final size:25
Alignment explanation
Indices: 548371--548445 Score: 60
Period size: 27 Copynumber: 2.8 Consensus size: 25
548361 TAATAATAAT
*
548371 AATTAAAAAAAGTACAAAACAAAAAAA
1 AATTAAAAAAA--AAAAAACAAAAAAA
* **
548398 AACCTAATAAAAAAAGGAACAAAAAAA
1 AA-TTAA-AAAAAAAAAAACAAAAAAA
548425 ACATTAAAAAAACAAAAAACA
1 A-ATTAAAAAAA-AAAAAACA
548446 TTAAAATTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
26 5 0.14
27 23 0.62
28 4 0.11
29 5 0.14
ACGTcount: A:0.76, C:0.11, G:0.04, T:0.09
Consensus pattern (25 bp):
AATTAAAAAAAAAAAAACAAAAAAA
Found at i:549956 original size:24 final size:22
Alignment explanation
Indices: 549929--549998 Score: 65
Period size: 24 Copynumber: 3.1 Consensus size: 22
549919 AGGAAAAAGG
549929 AAAAGTAAAGAAAAAGAAGAAGAA
1 AAAAG-AAAGAAAAAGAAGAA-AA
*
549953 AAAAGGAAAG-ATAAGAGAGAAAA
1 AAAA-GAAAGAAAAAGA-AGAAAA
*
549976 AAAA-AAGGAAAAAG-AGAAAA
1 AAAAGAAAGAAAAAGAAGAAAA
549996 AAA
1 AAA
549999 TTGAGAAAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
20 9 0.22
21 3 0.08
22 4 0.10
23 11 0.28
24 12 0.30
25 1 0.03
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (22 bp):
AAAAGAAAGAAAAAGAAGAAAA
Found at i:550123 original size:24 final size:22
Alignment explanation
Indices: 550096--550181 Score: 68
Period size: 21 Copynumber: 3.9 Consensus size: 22
550086 GGAAGGTAGG
550096 TTTGAAAAGTCAAGTCAAAAAAAT
1 TTTGAAAAGTCAAG--AAAAAAAT
* * *
550120 TTTGAAAAATAAAAGAAACAAAT
1 TTTGAAAAGT-CAAGAAAAAAAT
* *
550143 TTTGAAAAGTCAA-ATAAAAAC
1 TTTGAAAAGTCAAGAAAAAAAT
**
550164 TTCAAAAAGTCAA-AAAAA
1 TTTGAAAAGTCAAGAAAAA
550182 TGAAAAGTAA
Statistics
Matches: 50, Mismatches: 11, Indels: 5
0.76 0.17 0.08
Matches are distributed among these distances:
21 20 0.40
22 2 0.04
23 16 0.32
24 9 0.18
25 3 0.06
ACGTcount: A:0.60, C:0.08, G:0.09, T:0.22
Consensus pattern (22 bp):
TTTGAAAAGTCAAGAAAAAAAT
Found at i:550721 original size:30 final size:29
Alignment explanation
Indices: 550687--550748 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
550677 TGGAGCCTTA
*
550687 ACTTTTGAAAAGTAAA-AAATAAATAAAAAG
1 ACTTTTGAAAAATAAACAAA-AAA-AAAAAG
550717 AC-TTTGAAAAATAAACAAAAAAAAAAAG
1 ACTTTTGAAAAATAAACAAAAAAAAAAAG
550745 -CTTT
1 ACTTT
550749 AAAGTCCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
27 1 0.03
28 8 0.28
29 15 0.52
30 5 0.17
ACGTcount: A:0.63, C:0.06, G:0.08, T:0.23
Consensus pattern (29 bp):
ACTTTTGAAAAATAAACAAAAAAAAAAAG
Found at i:551622 original size:17 final size:16
Alignment explanation
Indices: 551600--551651 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 16
551590 AACCCTCAAG
551600 CTCAAAACTCTAAAACC
1 CTCAAAACTC-AAAACC
551617 CTCAAAACTCAAAACC
1 CTCAAAACTCAAAACC
551633 CT-AAAACCATCAAAACC
1 CTCAAAA-C-TCAAAACC
551650 CT
1 CT
551652 AAATTTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.12
16 9 0.27
17 20 0.61
ACGTcount: A:0.48, C:0.37, G:0.00, T:0.15
Consensus pattern (16 bp):
CTCAAAACTCAAAACC
Found at i:551627 original size:24 final size:24
Alignment explanation
Indices: 551587--551648 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
551577 AAAAAACCTT
* *
551587 TAAAACCCTC-AAGCTCAAAACTC
1 TAAAACCCTCAAAACTCAAAACCC
551610 TAAAACCCTCAAAACTCAAAACCC
1 TAAAACCCTCAAAACTCAAAACCC
*
551634 TAAAACCATCAAAAC
1 TAAAACCCTCAAAAC
551649 CCTAAATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
23 10 0.29
24 25 0.71
ACGTcount: A:0.50, C:0.34, G:0.02, T:0.15
Consensus pattern (24 bp):
TAAAACCCTCAAAACTCAAAACCC
Found at i:551640 original size:8 final size:8
Alignment explanation
Indices: 551603--551654 Score: 52
Period size: 8 Copynumber: 6.4 Consensus size: 8
551593 CCTCAAGCTC
*
551603 AAAACTCT
1 AAAACCCT
551611 AAAACCCT
1 AAAACCCT
*
551619 CAAAACTC-
1 -AAAACCCT
551627 AAAACCCT
1 AAAACCCT
*
551635 AAAACCAT
1 AAAACCCT
551643 CAAAACCCT
1 -AAAACCCT
551652 AAA
1 AAA
551655 TTTTAAAATC
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
7 6 0.17
8 17 0.47
9 13 0.36
ACGTcount: A:0.54, C:0.33, G:0.00, T:0.13
Consensus pattern (8 bp):
AAAACCCT
Found at i:551649 original size:9 final size:9
Alignment explanation
Indices: 551600--551651 Score: 58
Period size: 9 Copynumber: 6.2 Consensus size: 9
551590 AACCCTCAAG
*
551600 CTCAAAACT
1 CTCAAAACC
551609 CT-AAAACC
1 CTCAAAACC
551617 CTCAAAA--
1 CTCAAAACC
551624 CTCAAAACC
1 CTCAAAACC
551633 CT-AAAACC
1 CTCAAAACC
*
551641 ATCAAAACC
1 CTCAAAACC
551650 CT
1 CT
551652 AAATTTTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
7 7 0.19
8 14 0.39
9 15 0.42
ACGTcount: A:0.48, C:0.37, G:0.00, T:0.15
Consensus pattern (9 bp):
CTCAAAACC
Found at i:551667 original size:15 final size:15
Alignment explanation
Indices: 551610--551686 Score: 64
Period size: 15 Copynumber: 4.9 Consensus size: 15
551600 CTCAAAACTC
*
551610 TAAAACCCTCAAAACT
1 TAAAACCCT-AAAATT
* *
551626 CAAAACCCTAAAACCAT
1 TAAAACCCTAAAA--TT
* *
551643 CAAAACCCTAAATTT
1 TAAAACCCTAAAATT
*
551658 TAAAATCCTAAAATT
1 TAAAACCCTAAAATT
*
551673 TGAAACCCTAAAAT
1 TAAAACCCTAAAAT
551687 CCAAAATCTT
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
15 29 0.58
16 8 0.16
17 13 0.26
ACGTcount: A:0.51, C:0.26, G:0.01, T:0.22
Consensus pattern (15 bp):
TAAAACCCTAAAATT
Found at i:552944 original size:11 final size:10
Alignment explanation
Indices: 552923--552947 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
552913 AAAATACTTG
552923 TTTTCTTTTT
1 TTTTCTTTTT
552933 TTTTCTTTTT
1 TTTTCTTTTT
552943 TTTTC
1 TTTTC
552948 CGATCGAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:554806 original size:2 final size:2
Alignment explanation
Indices: 554799--554827 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
554789 TTATTTATTG
554799 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
554828 CACACTAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:558415 original size:26 final size:26
Alignment explanation
Indices: 558386--558437 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
558376 GCATGGAGTT
558386 GTCATTCTAGGTTATTTTTAGATGAA
1 GTCATTCTAGGTTATTTTTAGATGAA
558412 GTCATTCTAGGTTATTTTTAGATGAA
1 GTCATTCTAGGTTATTTTTAGATGAA
558438 TAGAGAGGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.08, G:0.19, T:0.46
Consensus pattern (26 bp):
GTCATTCTAGGTTATTTTTAGATGAA
Found at i:560096 original size:42 final size:42
Alignment explanation
Indices: 560049--560133 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
560039 ACTGATCACA
*
560049 TAAATGTAACTGATTGATATGTTTCAGGTTTTATATAAATTT
1 TAAATGTAACTGATTGATATGTTACAGGTTTTATATAAATTT
560091 TAAATGTAACTGATTGATATGTTACAGGTTTTATATAAATTT
1 TAAATGTAACTGATTGATATGTTACAGGTTTTATATAAATTT
560133 T
1 T
560134 TGGATTACTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.47
Consensus pattern (42 bp):
TAAATGTAACTGATTGATATGTTACAGGTTTTATATAAATTT
Found at i:565520 original size:2 final size:2
Alignment explanation
Indices: 565513--565557 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
565503 TTTGTAGATT
* *
565513 TA TA TA TA TC TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
565555 TA T
1 TA T
565558 TGATGACTCG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:568478 original size:2 final size:2
Alignment explanation
Indices: 568471--568499 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
568461 AAGATATCAC
568471 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
568500 TTGGCTTGAA
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:569630 original size:10 final size:10
Alignment explanation
Indices: 569608--569645 Score: 69
Period size: 10 Copynumber: 3.9 Consensus size: 10
569598 TGTAAAATTT
569608 AAATTTT-AA
1 AAATTTTAAA
569617 AAATTTTAAA
1 AAATTTTAAA
569627 AAATTTTAAA
1 AAATTTTAAA
569637 AAATTTTAA
1 AAATTTTAA
569646 TTAAATATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
9 7 0.25
10 21 0.75
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
AAATTTTAAA
Found at i:570421 original size:18 final size:18
Alignment explanation
Indices: 570398--570465 Score: 57
Period size: 22 Copynumber: 3.4 Consensus size: 18
570388 TTAATTTTAT
570398 TTTTTAATAATTTATAAA
1 TTTTTAATAATTTATAAA
570416 TTTTTAA-AATTTTATATTATAA
1 TTTTTAATAA--TT-TA-TA-AA
*
570438 TTTTTAATAGATTTATAAT
1 TTTTTAATA-ATTTATAAA
570457 TTTATTAAT
1 TTT-TTAAT
570466 TTTTTTTTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
17 2 0.05
18 7 0.17
19 6 0.15
20 9 0.22
21 4 0.10
22 11 0.27
23 1 0.02
24 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (18 bp):
TTTTTAATAATTTATAAA
Found at i:593057 original size:3 final size:3
Alignment explanation
Indices: 593042--593079 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
593032 CCGTCATGAA
* *
593042 CAT CAT CAA CAT CAT CAT CAT CAT CAT CAC CAT -AT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
593080 TCCTGTTGCC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.37, C:0.34, G:0.00, T:0.29
Consensus pattern (3 bp):
CAT
Found at i:593421 original size:17 final size:18
Alignment explanation
Indices: 593392--593425 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
593382 TGAGACTATT
593392 TTCAAGATTTTTTTCTTA
1 TTCAAGATTTTTTTCTTA
593410 TTCAAG-TTTTTTTCTT
1 TTCAAGATTTTTTTCTT
593426 TCTAGCATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.65
Consensus pattern (18 bp):
TTCAAGATTTTTTTCTTA
Found at i:596313 original size:11 final size:11
Alignment explanation
Indices: 596297--596327 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
596287 AATCTCATAA
596297 GAGATTTGTTT
1 GAGATTTGTTT
596308 GAGATTTGTTT
1 GAGATTTGTTT
*
596319 AAGATTTGT
1 GAGATTTGT
596328 CAGATATTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.52
Consensus pattern (11 bp):
GAGATTTGTTT
Found at i:596423 original size:52 final size:53
Alignment explanation
Indices: 596352--596501 Score: 187
Period size: 52 Copynumber: 2.8 Consensus size: 53
596342 GGATAAAAAG
* * * * *
596352 ACTTGTAAAAGAAGAATTCTAAGAGAAAGA-TGATTCTTAATAGGTAAGTTTA
1 ACTTGCAAAAAAAAAATTCTAAAAGAAAGAGGGATTCTTAATAGGTAAGTTTA
* *
596404 ACTTGCAAAAAAAAAATTCTAAAAGAAA-AGGGATTCTTAATAAGTAAGTTTG
1 ACTTGCAAAAAAAAAATTCTAAAAGAAAGAGGGATTCTTAATAGGTAAGTTTA
* *
596456 ACTTACAGAAAAAAAAATTCTAAAAAAAAAGAGGGATTCTTAATAG
1 ACTTGCA-AAAAAAAAATTCT-AAAAGAAAGAGGGATTCTTAATAG
596502 ACAAGTTTGT
Statistics
Matches: 84, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
51 1 0.01
52 49 0.58
53 13 0.15
54 7 0.08
55 14 0.17
ACGTcount: A:0.50, C:0.07, G:0.16, T:0.27
Consensus pattern (53 bp):
ACTTGCAAAAAAAAAATTCTAAAAGAAAGAGGGATTCTTAATAGGTAAGTTTA
Found at i:597113 original size:25 final size:25
Alignment explanation
Indices: 597048--597116 Score: 66
Period size: 25 Copynumber: 2.8 Consensus size: 25
597038 ATCATAACTG
* * **
597048 AAGGTTCGAAACGTGAGAAGAGTTA
1 AAGGTTCGAGACGTGAAAAGAGCCA
** * *
597073 AAAATTCAAGATGTGAAAAGAGCCA
1 AAGGTTCGAGACGTGAAAAGAGCCA
597098 AAGGTTCGAGACGTGAAAA
1 AAGGTTCGAGACGTGAAAA
597117 AGCTGAAAGT
Statistics
Matches: 32, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.45, C:0.10, G:0.28, T:0.17
Consensus pattern (25 bp):
AAGGTTCGAGACGTGAAAAGAGCCA
Found at i:597538 original size:52 final size:50
Alignment explanation
Indices: 597471--597627 Score: 179
Period size: 52 Copynumber: 3.0 Consensus size: 50
597461 TGGATAAAAA
* *
597471 GACTTATAAAAGAAGAATTCTAAGAGAAAGATGATTCTTAATAGGTAAGTTT
1 GACTTACAAGAGAAGAATTCTAA-AGAAAGA-GATTCTTAATAGGTAAGTTT
* * *
597523 GACTTGCAAGAGAAGAATTTTGAAAGAAAAAAGATTCTTAATAGGTAAGTTT
1 GACTTACAAGAGAAGAATTCT-AAAG-AAAGAGATTCTTAATAGGTAAGTTT
* * * *
597575 AACTTACAGGAAAAGAATTCTAAAAGAAAAGAGATTCTTAATGGGTAAGTTT
1 GACTTACAAGAGAAGAATTCT-AAAG-AAAGAGATTCTTAATAGGTAAGTTT
597627 G
1 G
597628 TATGGTTATA
Statistics
Matches: 89, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
52 83 0.93
53 6 0.07
ACGTcount: A:0.45, C:0.06, G:0.20, T:0.29
Consensus pattern (50 bp):
GACTTACAAGAGAAGAATTCTAAAGAAAGAGATTCTTAATAGGTAAGTTT
Found at i:597964 original size:74 final size:74
Alignment explanation
Indices: 597863--598011 Score: 226
Period size: 74 Copynumber: 2.0 Consensus size: 74
597853 AAGAGTTTGA
* * *
597863 GTTTGAGTTTATGTTTGTTTGTGTTGAGAATACTTCATAAGACTAGAGGAGATTGAGAGTGTCTT
1 GTTTGAGTTTATGTTTATTTGGGTTGAGAATACTTCATAAGACTAGAAGAGATTGAGAGTGTCTT
597928 ATAAGTATT
66 ATAAGTATT
* * * *
597937 GTTTGGGTTTGTGTTTATTTGGGTTGAGAATTCTTCATAGGACTAGAAGAGATTGAGAGTGTCTT
1 GTTTGAGTTTATGTTTATTTGGGTTGAGAATACTTCATAAGACTAGAAGAGATTGAGAGTGTCTT
*
598002 ATGAGTATT
66 ATAAGTATT
598011 G
1 G
598012 ATTGTTGAGT
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
74 67 1.00
ACGTcount: A:0.25, C:0.05, G:0.28, T:0.42
Consensus pattern (74 bp):
GTTTGAGTTTATGTTTATTTGGGTTGAGAATACTTCATAAGACTAGAAGAGATTGAGAGTGTCTT
ATAAGTATT
Found at i:598207 original size:2 final size:2
Alignment explanation
Indices: 598200--598261 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
598190 GCCCAACAGA
598200 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
598242 TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC
598262 CTTGTGTGAC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:600126 original size:27 final size:28
Alignment explanation
Indices: 600096--600148 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
600086 GTAAGTTATT
* *
600096 ATTAATTAATGATTTTAA-TTTAATAAA
1 ATTAATTAATAAATTTAATTTTAATAAA
*
600123 ATTAATTGATAAATTTAATTTTAATA
1 ATTAATTAATAAATTTAATTTTAATA
600149 CAAGACAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 15 0.68
28 7 0.32
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (28 bp):
ATTAATTAATAAATTTAATTTTAATAAA
Found at i:602065 original size:11 final size:11
Alignment explanation
Indices: 602045--602078 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
602035 CCATTACTAG
*
602045 TTAAAATATTT
1 TTAAATTATTT
602056 TTAAATTA-TT
1 TTAAATTATTT
602066 TTAAATTATTT
1 TTAAATTATTT
602077 TT
1 TT
602079 TTACTTAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTAAATTATTT
Found at i:607143 original size:51 final size:51
Alignment explanation
Indices: 607082--607203 Score: 226
Period size: 51 Copynumber: 2.4 Consensus size: 51
607072 TAGATAAAGG
607082 TAAGGGAAAGTTAATGAAGAATATTCAAAGCAAATCAAAATAGGCAAATGA
1 TAAGGGAAAGTTAATGAAGAATATTCAAAGCAAATCAAAATAGGCAAATGA
607133 TAAGGGAAAGTTAATGAAGAATATTCAAAGCAAATCAAAATAGGCAAATGA
1 TAAGGGAAAGTTAATGAAGAATATTCAAAGCAAATCAAAATAGGCAAATGA
* *
607184 GAAGGGAAAGTTAAAGAAGA
1 TAAGGGAAAGTTAATGAAGA
607204 TATGCATTAT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 69 1.00
ACGTcount: A:0.53, C:0.07, G:0.22, T:0.18
Consensus pattern (51 bp):
TAAGGGAAAGTTAATGAAGAATATTCAAAGCAAATCAAAATAGGCAAATGA
Found at i:614763 original size:3 final size:3
Alignment explanation
Indices: 614757--614819 Score: 119
Period size: 3 Copynumber: 21.3 Consensus size: 3
614747 TCTTTGAAAT
614757 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
614805 TAA TAA TAA T-A TAA T
1 TAA TAA TAA TAA TAA T
614820 CAAAGAGAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 57 0.97
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:615254 original size:12 final size:11
Alignment explanation
Indices: 615228--615253 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
615218 TTTTAAAATT
615228 AAAATTAAAGA
1 AAAATTAAAGA
615239 AAAATTAAAGA
1 AAAATTAAAGA
615250 AAAA
1 AAAA
615254 AATTTGCATG
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:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (11 bp):
AAAATTAAAGA
Found at i:616839 original size:19 final size:16
Alignment explanation
Indices: 616817--616859 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 16
616807 CCTGACAATT
616817 TATAATATGAAACCAATAA
1 TATAATAT-AAA--AATAA
616836 TATAATATAAAAATAA
1 TATAATATAAAAATAA
616852 TATGAATA
1 TAT-AATA
616860 AAAGATATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 8 0.35
17 4 0.17
18 3 0.13
19 8 0.35
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.30
Consensus pattern (16 bp):
TATAATATAAAAATAA
Found at i:622424 original size:8 final size:8
Alignment explanation
Indices: 622405--622434 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
622395 GAGTCTTTGC
622405 AAAAAGAGA
1 AAAAAGA-A
622414 AAAAAGAA
1 AAAAAGAA
622422 AAAAAGAA
1 AAAAAGAA
622430 AAAAA
1 AAAAA
622435 ACCAATCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 14 0.67
9 7 0.33
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:626558 original size:2 final size:2
Alignment explanation
Indices: 626551--626579 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
626541 AAAGAGAAAG
626551 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
626580 GGTATATGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.