Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold125
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: 3608436
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 25 characters in sequence are not A, C, G, or T
File 3 of 18
Found at i:338473 original size:59 final size:60
Alignment explanation
Indices: 338406--338543 Score: 192
Period size: 59 Copynumber: 2.3 Consensus size: 60
338396 TTACTTTTAG
* * *
338406 AATTTATTTGAATACAAATTAAAGATTAACAATTTATTTAAATA-CA-AATTAAAA-ATTAA
1 AATTTATTTAAATA-AAATTAAAGATTAACAATGTATTTAAATATAATAATTAAAATA-TAA
*
338465 AATTTATTTAAATATAAATTAAAGATTAATAATGTATTTAAATATAATAATTAAAATATAA
1 AATTTATTTAAATA-AAATTAAAGATTAACAATGTATTTAAATATAATAATTAAAATATAA
338526 AATTTATTTAAATAAAAT
1 AATTTATTTAAATAAAAT
338544 GATAAGGTTC
Statistics
Matches: 71, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
59 40 0.56
60 5 0.07
61 25 0.35
62 1 0.01
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (60 bp):
AATTTATTTAAATAAAATTAAAGATTAACAATGTATTTAAATATAATAATTAAAATATAA
Found at i:338512 original size:18 final size:17
Alignment explanation
Indices: 338491--338539 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 17
338481 AATTAAAGAT
338491 TAATAATGTATTTAAATA
1 TAATAAT-TATTTAAATA
338509 TAATAATTA---AAATA
1 TAATAATTATTTAAATA
338523 TAA-AATTTATTTAAATA
1 TAATAA-TTATTTAAATA
338540 AAATGATAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
13 2 0.07
14 11 0.41
17 7 0.26
18 7 0.26
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (17 bp):
TAATAATTATTTAAATA
Found at i:342150 original size:21 final size:21
Alignment explanation
Indices: 342126--342168 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
342116 AAAATATTTT
342126 TATATAAATA-TAATAATAAAA
1 TATATAAATATTAAT-ATAAAA
342147 TATATAAATATTAATATAAAA
1 TATATAAATATTAATATAAAA
342168 T
1 T
342169 TTGACGATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
TATATAAATATTAATATAAAA
Found at i:343207 original size:21 final size:22
Alignment explanation
Indices: 343151--343215 Score: 69
Period size: 21 Copynumber: 2.9 Consensus size: 22
343141 AAAGTAATTT
343151 TTATTTTAAAATTAATTATATATA
1 TTATTTT-AAA-TAATTATATATA
* *
343175 TTAATGTAAAATAATTATA-ATA
1 TT-ATTTTAAATAATTATATATA
*
343197 TTATTTTAAATAATGATAT
1 TTATTTTAAATAATTATAT
343216 GAATTTTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
21 13 0.38
22 5 0.15
23 8 0.24
24 5 0.15
25 3 0.09
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (22 bp):
TTATTTTAAATAATTATATATA
Found at i:343786 original size:19 final size:19
Alignment explanation
Indices: 343742--343787 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
343732 TTTTTGTAGG
*
343742 TTAAAATAAAAATGTAAAA
1 TTAAAATAAAAATATAAAA
*
343761 TTAAAATAAAAA-ATAATA
1 TTAAAATAAAAATATAAAA
343779 TTATAAATA
1 TTA-AAATA
343788 TGTAACACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (19 bp):
TTAAAATAAAAATATAAAA
Found at i:344256 original size:2 final size:2
Alignment explanation
Indices: 344249--344282 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
344239 AAGCAACATG
344249 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
344283 GAGAGAGAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:344287 original size:2 final size:2
Alignment explanation
Indices: 344282--344309 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
344272 ATATATATAT
344282 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
344310 TCAAATGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:346097 original size:22 final size:22
Alignment explanation
Indices: 346069--346113 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
346059 AAACATAATA
346069 ATAGTGATAATATTAATGTAAC
1 ATAGTGATAATATTAATGTAAC
346091 ATAGTGATAATATTAATGTAAC
1 ATAGTGATAATATTAATGTAAC
346113 A
1 A
346114 CACCATCTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.47, C:0.04, G:0.13, T:0.36
Consensus pattern (22 bp):
ATAGTGATAATATTAATGTAAC
Found at i:360617 original size:15 final size:15
Alignment explanation
Indices: 360597--360625 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
360587 GATGGGATAA
360597 TAAAGTAAGAGAGAT
1 TAAAGTAAGAGAGAT
360612 TAAAGTAAGAGAGA
1 TAAAGTAAGAGAGA
360626 CTCCGACCTT
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:0.55, C:0.00, G:0.28, T:0.17
Consensus pattern (15 bp):
TAAAGTAAGAGAGAT
Found at i:363240 original size:9 final size:8
Alignment explanation
Indices: 363213--363237 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
363203 TTATCTTTAT
363213 ATTTTAAA
1 ATTTTAAA
363221 ATTTTAAA
1 ATTTTAAA
363229 ATTTTAAA
1 ATTTTAAA
363237 A
1 A
363238 ATTATTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
ATTTTAAA
Found at i:363893 original size:14 final size:14
Alignment explanation
Indices: 363876--363905 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
363866 AAAAACTAAA
363876 AAAATTTAAATATG
1 AAAATTTAAATATG
*
363890 AAAATTTAAATTTG
1 AAAATTTAAATATG
363904 AA
1 AA
363906 TTACATTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37
Consensus pattern (14 bp):
AAAATTTAAATATG
Found at i:364771 original size:19 final size:19
Alignment explanation
Indices: 364747--364789 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
364737 ATATATATAT
*
364747 ATATATACTTAAT-AAAAAA
1 ATATATACAT-ATCAAAAAA
*
364766 ATATATCCATATCAAAAAA
1 ATATATACATATCAAAAAA
364785 ATATA
1 ATATA
364790 ACTATATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 2 0.10
19 19 0.90
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.30
Consensus pattern (19 bp):
ATATATACATATCAAAAAA
Found at i:364796 original size:19 final size:19
Alignment explanation
Indices: 364760--364796 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
364750 TATACTTAAT
*
364760 AAAAAAATATATCCATATC
1 AAAAAAATATAACCATATC
*
364779 AAAAAAATATAACTATAT
1 AAAAAAATATAACCATAT
364797 ATATATTTAT
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:0.62, C:0.11, G:0.00, T:0.27
Consensus pattern (19 bp):
AAAAAAATATAACCATATC
Found at i:367164 original size:3 final size:3
Alignment explanation
Indices: 367156--367181 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
367146 TCCTTTAGTA
367156 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
367182 GAAGAACAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:368575 original size:32 final size:36
Alignment explanation
Indices: 368534--368599 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 36
368524 TTAAATTCGA
368534 TTAAATTTAA-TTTAA-A-TAATA-AAAATATTTAT
1 TTAAATTTAATTTTAATATTAATATAAAATATTTAT
368566 TTAAATTTAATTTTAATATTAATATAAAATATTT
1 TTAAATTTAATTTTAATATTAATATAAAATATTT
368600 TTATTTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
32 10 0.33
33 5 0.17
34 1 0.03
35 5 0.17
36 9 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (36 bp):
TTAAATTTAATTTTAATATTAATATAAAATATTTAT
Found at i:368587 original size:12 final size:12
Alignment explanation
Indices: 368534--368598 Score: 50
Period size: 11 Copynumber: 5.8 Consensus size: 12
368524 TTAAATTCGA
368534 TTAAAT-TTAAT
1 TTAAATATTAAT
*
368545 TTAAATAATAA-
1 TTAAATATTAAT
*
368556 --AAATATTTAT
1 TTAAATATTAAT
368566 TTAAAT-TTAAT
1 TTAAATATTAAT
*
368577 TTTAATATTAAT
1 TTAAATATTAAT
*
368589 ATAAAATATT
1 -TTAAATATT
368599 TTTATTTTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
9 7 0.17
11 15 0.37
12 12 0.29
13 7 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
TTAAATATTAAT
Found at i:368961 original size:4 final size:4
Alignment explanation
Indices: 368947--369025 Score: 55
Period size: 4 Copynumber: 20.5 Consensus size: 4
368937 AATTTGATTA
*
368947 AATT AAATT AATT AAATT AATT TATT --TT AATT -ATT AA-T -ATT AATTT
1 AATT -AATT AATT -AATT AATT AATT AATT AATT AATT AATT AATT AA-TT
*
368993 AATT AATT AATTT AATT AATT -TTT AATT -ATT AA
1 AATT AATT AA-TT AATT AATT AATT AATT AATT AA
369026 AATATAAAAT
Statistics
Matches: 61, Mismatches: 3, Indels: 21
0.72 0.04 0.25
Matches are distributed among these distances:
2 3 0.05
3 10 0.16
4 32 0.52
5 16 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (4 bp):
AATT
Found at i:368994 original size:5 final size:5
Alignment explanation
Indices: 368931--369014 Score: 52
Period size: 5 Copynumber: 17.2 Consensus size: 5
368921 TCAAAAAAAA
* * * * * *
368931 TAATT AAATT TGA-T TAAAT TAAAT TAA-T TAAAT TAATT TATTT TAATTAT
1 TAATT TAATT TAATT TAATT TAATT TAATT TAATT TAATT TAATT TAA-T-T
368981 TAATAT TAATT TAA-T TAA-T TAATT TAA-T TAATT T
1 TAAT-T TAATT TAATT TAATT TAATT TAATT TAATT T
369015 TTAATTATTA
Statistics
Matches: 66, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
4 19 0.29
5 35 0.53
6 8 0.12
7 4 0.06
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (5 bp):
TAATT
Found at i:369012 original size:9 final size:9
Alignment explanation
Indices: 368931--369014 Score: 66
Period size: 9 Copynumber: 9.1 Consensus size: 9
368921 TCAAAAAAAA
368931 TAATTAAATT
1 TAATT-AATT
*
368941 TGATTAAATT
1 TAATT-AATT
*
368951 AAATTAATT
1 TAATTAATT
*
368960 AAATTAATT
1 TAATTAATT
*
368969 TATTTTAA-T
1 TA-ATTAATT
368978 T-ATTAATAT
1 TAATTAAT-T
368987 TAATTTAA-T
1 TAA-TTAATT
368996 TAATTAATT
1 TAATTAATT
369005 TAATTAATT
1 TAATTAATT
369014 T
1 T
369015 TTAATTATTA
Statistics
Matches: 62, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
7 4 0.06
8 4 0.06
9 33 0.53
10 17 0.27
11 4 0.06
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (9 bp):
TAATTAATT
Found at i:369020 original size:7 final size:7
Alignment explanation
Indices: 368953--369025 Score: 50
Period size: 7 Copynumber: 10.7 Consensus size: 7
368943 ATTAAATTAA
368953 ATTAATT
1 ATTAATT
368960 A--AATT
1 ATTAATT
*
368965 AATTTATT
1 -ATTAATT
368973 -TTAATT
1 ATTAATT
368979 ATTAA-T
1 ATTAATT
368985 ATTAA-T
1 ATTAATT
368991 -TTAATT
1 ATTAATT
368997 AATTAATTT
1 -ATTAA-TT
369006 AATTAATT
1 -ATTAATT
*
369014 TTTAATT
1 ATTAATT
369021 ATTAA
1 ATTAA
369026 AATATAAAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
5 8 0.15
6 14 0.26
7 15 0.28
8 9 0.17
9 8 0.15
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
ATTAATT
Found at i:369046 original size:45 final size:45
Alignment explanation
Indices: 368950--369080 Score: 106
Period size: 45 Copynumber: 2.9 Consensus size: 45
368940 TTGATTAAAT
* * **
368950 TAAATTAATTAAATTAATTTATTTTAATTATT--AATAT-TAATTTAA
1 TAAATTAATTTAATTAA--T-TTTTAATTATTAAAATATAAAATCGAA
*
368995 TTAATTAATTTAATTAATTTTTAATTATTAAAATATAAAATCGAA
1 TAAATTAATTTAATTAATTTTTAATTATTAAAATATAAAATCGAA
** * * *
369040 TAAATTAAAATAATTAAATTTAATATTTAATAAAATATAAA
1 TAAATTAATTTAATT-AATTT-TTAATTATTAAAATATAAA
369081 TTTAAATTTA
Statistics
Matches: 70, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
42 11 0.16
43 1 0.01
44 5 0.07
45 32 0.46
46 5 0.07
47 16 0.23
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.47
Consensus pattern (45 bp):
TAAATTAATTTAATTAATTTTTAATTATTAAAATATAAAATCGAA
Found at i:369064 original size:23 final size:22
Alignment explanation
Indices: 368929--369085 Score: 74
Period size: 23 Copynumber: 7.1 Consensus size: 22
368919 AATCAAAAAA
* * *
368929 AATAATTAAATTTGATTAAATTA
1 AATAATTAAA-ATAATTAAATTT
* * *
368952 AATTAATTAAATTAATTTATTTT
1 AA-TAATTAAAATAATTAAATTT
*
368975 AATTATT--AAT-ATT-AATTT
1 AATAATTAAAATAATTAAATTT
** *
368993 AATTAATTAATTTAATTAATTTTT
1 AA-TAATTAAAATAATTAA-ATTT
* * **
369017 AATTATTAAAAT-ATAAAATCG
1 AATAATTAAAATAATTAAATTT
369038 AATAAATTAAAATAATTAAATTT
1 AAT-AATTAAAATAATTAAATTT
*
369061 AATATTTAATAA-AATATAAATTT
1 AATAATTAA-AATAAT-TAAATTT
369084 AA
1 AA
369086 ATTTAAACTC
Statistics
Matches: 100, Mismatches: 23, Indels: 22
0.69 0.16 0.15
Matches are distributed among these distances:
18 6 0.06
19 7 0.07
20 2 0.02
21 5 0.05
22 27 0.27
23 40 0.40
24 13 0.13
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (22 bp):
AATAATTAAAATAATTAAATTT
Found at i:369069 original size:22 final size:21
Alignment explanation
Indices: 369040--369092 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
369030 TAAAATCGAA
369040 TAAA-TTAAAATAAT-TAAATT
1 TAAATTTAAAA-AATATAAATT
369060 TAATATTTAATAAAATATAAATT
1 TAA-ATTTAA-AAAATATAAATT
369083 TAAATTTAAA
1 TAAATTTAAA
369093 CTCATTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
20 3 0.10
21 2 0.07
22 13 0.45
23 11 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAATTTAAAAAATATAAATT
Found at i:369317 original size:27 final size:27
Alignment explanation
Indices: 369276--369329 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
369266 ATTATTTTGA
* *
369276 TTTAGATTTAAAATCGATTATTTCAAT
1 TTTAGATTTAAAATCAATTAATTCAAT
*
369303 TTTAGATTTAGAATCAATTAATTCAAT
1 TTTAGATTTAAAATCAATTAATTCAAT
369330 CAATTTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (27 bp):
TTTAGATTTAAAATCAATTAATTCAAT
Found at i:369359 original size:29 final size:29
Alignment explanation
Indices: 369318--369383 Score: 123
Period size: 29 Copynumber: 2.3 Consensus size: 29
369308 ATTTAGAATC
369318 AATTAATTCAATCAATTTTTTAATATTAA
1 AATTAATTCAATCAATTTTTTAATATTAA
*
369347 AATTAATTTAATCAATTTTTTAATATTAA
1 AATTAATTCAATCAATTTTTTAATATTAA
369376 AATTAATT
1 AATTAATT
369384 AAATTGATCA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (29 bp):
AATTAATTCAATCAATTTTTTAATATTAA
Found at i:369397 original size:29 final size:29
Alignment explanation
Indices: 369318--369397 Score: 88
Period size: 29 Copynumber: 2.8 Consensus size: 29
369308 ATTTAGAATC
* **
369318 AATTAATTCAATCAATTTTTTAATATTAA
1 AATTAATTAAATCAATCATTTAATATTAA
* **
369347 AATTAATTTAATCAATTTTTTAATATTAA
1 AATTAATTAAATCAATCATTTAATATTAA
**
369376 AATTAATTAAATTGATCATTTA
1 AATTAATTAAATCAATCATTTA
369398 TTTTATCATA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.45, C:0.05, G:0.01, T:0.49
Consensus pattern (29 bp):
AATTAATTAAATCAATCATTTAATATTAA
Found at i:369863 original size:2 final size:2
Alignment explanation
Indices: 369856--369886 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
369846 ATAGTAATAA
369856 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
369887 CACACGCATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:370920 original size:25 final size:25
Alignment explanation
Indices: 370877--370930 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
370867 AAGTGGGGCT
370877 TAAATTAATTTTTAATTATAATT-A
1 TAAATTAATTTTTAATTATAATTAA
* *
370901 TAAATTATTATTTTATTTATAATTAA
1 TAAATTAAT-TTTTAATTATAATTAA
370927 TAAA
1 TAAA
370931 ATTTTTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 8 0.31
25 13 0.50
26 5 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TAAATTAATTTTTAATTATAATTAA
Found at i:372278 original size:15 final size:15
Alignment explanation
Indices: 372235--372266 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
372225 AAACATGGAT
372235 GATGATGACGATGAC
1 GATGATGACGATGAC
*
372250 GATGATGAAGATGAC
1 GATGATGACGATGAC
372265 GA
1 GA
372267 GCTGGACGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.38, C:0.09, G:0.34, T:0.19
Consensus pattern (15 bp):
GATGATGACGATGAC
Found at i:372286 original size:9 final size:9
Alignment explanation
Indices: 372274--372298 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
372264 CGAGCTGGAC
372274 GATGAAGAG
1 GATGAAGAG
372283 GATGAAGAG
1 GATGAAGAG
372292 GATGAAG
1 GATGAAG
372299 GTGGTGATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.44, T:0.12
Consensus pattern (9 bp):
GATGAAGAG
Found at i:379645 original size:2 final size:2
Alignment explanation
Indices: 379638--379664 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
379628 CGAGAGCGAT
379638 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
379665 TACGAACACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:380158 original size:22 final size:22
Alignment explanation
Indices: 380112--380159 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
380102 ATTAATTTTT
*
380112 TTAAATTAGTAAAAATAATATA
1 TTAAATTAGTAAAAATAATAAA
380134 TTAAATATA-TAAAAA-AATTAAA
1 TTAAAT-TAGTAAAAATAA-TAAA
380156 TTAA
1 TTAA
380160 TAATTAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 2 0.09
22 19 0.83
23 2 0.09
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
TTAAATTAGTAAAAATAATAAA
Found at i:381234 original size:34 final size:34
Alignment explanation
Indices: 381172--381236 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
381162 ATTTAATTTA
* *
381172 ATTTAAATTATTATTAATTAATAAAAATATTTTT
1 ATTTAAATTATTATAAAATAATAAAAATATTTTT
*
381206 ATTTAAATTAATTATAAAAT-ATATAAATATT
1 ATTTAAATT-ATTATAAAATAATAAAAATATT
381237 ATATAAAACT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
34 19 0.70
35 8 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (34 bp):
ATTTAAATTATTATAAAATAATAAAAATATTTTT
Found at i:387844 original size:13 final size:14
Alignment explanation
Indices: 387828--387857 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
387818 ATTTTTTTAA
387828 AATATTTATAT-TT
1 AATATTTATATCTT
387841 AATATTTATATCTT
1 AATATTTATATCTT
387855 AAT
1 AAT
387858 TAAATTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (14 bp):
AATATTTATATCTT
Found at i:390349 original size:14 final size:14
Alignment explanation
Indices: 390313--390366 Score: 51
Period size: 14 Copynumber: 4.0 Consensus size: 14
390303 TTTATTTTAC
390313 TTTT-TATTA-TAT
1 TTTTATATTATTAT
*
390325 TTTTAAAATTATTAT
1 TTTT-ATATTATTAT
*
390340 TTTTATATTAATAT
1 TTTTATATTATTAT
*
390354 TTATATATT-TTAT
1 TTTTATATTATTAT
390367 AATTAAATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
12 4 0.12
13 3 0.09
14 20 0.59
15 7 0.21
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTATATTATTAT
Found at i:390353 original size:29 final size:29
Alignment explanation
Indices: 390295--390355 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
390285 TTAAATTGAA
*
390295 TTTTAAAATTTATTTTACTTTTTATTATAT
1 TTTTAAAATTTATTTTA-TTTATATTATAT
390325 TTTTAAAA-TTATTATT-TTTATATTAATAT
1 TTTTAAAATTTATT-TTATTTATATT-ATAT
390354 TT
1 TT
390356 ATATATTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
28 7 0.25
29 11 0.39
30 10 0.36
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (29 bp):
TTTTAAAATTTATTTTATTTATATTATAT
Found at i:393388 original size:3 final size:3
Alignment explanation
Indices: 393380--393405 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
393370 ATGCCAATTT
393380 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
393406 TTTTGTTGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:395096 original size:19 final size:19
Alignment explanation
Indices: 395056--395095 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
395046 TTAAATTTGA
395056 TTTAAATTAATATATAAAT
1 TTTAAATTAATATATAAAT
* *
395075 TTTAAATT-TTATTTAAAT
1 TTTAAATTAATATATAAAT
395093 TTT
1 TTT
395096 TTATATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTAAATTAATATATAAAT
Found at i:395143 original size:29 final size:28
Alignment explanation
Indices: 395094--395148 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
395084 TATTTAAATT
*
395094 TTTTATATTTATAAATAAATAATTTATAA
1 TTTTAAATTTATAAATAAAT-ATTTATAA
*
395123 TTTTAAATTTATTTAAT-AATATTTAT
1 TTTTAAATTTA-TAAATAAATATTTAT
395149 GGGTTGAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 6 0.26
29 13 0.57
30 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
TTTTAAATTTATAAATAAATATTTATAA
Found at i:395182 original size:16 final size:16
Alignment explanation
Indices: 395161--395247 Score: 52
Period size: 16 Copynumber: 5.3 Consensus size: 16
395151 GTTGAATCAG
395161 TAATTATTTAAATAAA
1 TAATTATTTAAATAAA
* *
395177 TAATTATTTTATATTAA
1 TAATTA-TTTAAATAAA
* * ** **
395194 TATTTATATATTTTTA
1 TAATTATTTAAATAAA
395210 TAATTAAATTTAAATAAA
1 TAATT--ATTTAAATAAA
395228 -AA-TATATTAAATAAA
1 TAATTAT-TTAAATAAA
395243 TAATT
1 TAATT
395248 GGACCCACCA
Statistics
Matches: 53, Mismatches: 12, Indels: 11
0.70 0.16 0.14
Matches are distributed among these distances:
14 2 0.04
15 9 0.17
16 20 0.38
17 16 0.30
18 6 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TAATTATTTAAATAAA
Found at i:395324 original size:35 final size:35
Alignment explanation
Indices: 395259--395327 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
395249 GACCCACCAA
*
395259 TACTCTTATTGAAGATGATTGAACAGGGCCCACAG
1 TACTCTTATTGAAGATGATTGAACAAGGCCCACAG
* **
395294 TACTCTTATTGAATATGATTGAGGAAGGCCCACA
1 TACTCTTATTGAAGATGATTGAACAAGGCCCACA
395328 TTCGATAATC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.28
Consensus pattern (35 bp):
TACTCTTATTGAAGATGATTGAACAAGGCCCACAG
Found at i:395519 original size:28 final size:28
Alignment explanation
Indices: 395488--395555 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
395478 AGTTAATTTA
395488 ATTTAAATTATTATTTAATAATAAAAAT
1 ATTTAAATTATTATTTAATAATAAAAAT
** *
395516 ATTTTTATT-TTAATTTAATTATAAAAAT
1 ATTTAAATTATT-ATTTAATAATAAAAAT
*
395544 ATATAAA-TATTA
1 ATTTAAATTATTA
395556 ATATAAAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
27 4 0.12
28 28 0.88
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (28 bp):
ATTTAAATTATTATTTAATAATAAAAAT
Found at i:395556 original size:28 final size:28
Alignment explanation
Indices: 395491--395566 Score: 75
Period size: 28 Copynumber: 2.8 Consensus size: 28
395481 TAATTTAATT
*
395491 TAAATTATT-ATTTAATAATAAAAATATT
1 TAAA-TATTAATTTAATAATAAAAATATA
** * *
395519 TTTATTTTAATTTAATTATAAAAATATA
1 TAAATATTAATTTAATAATAAAAATATA
*
395547 TAAATATTAATATAA-AATAA
1 TAAATATTAATTTAATAATAA
395567 TTTTTTCATT
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
27 7 0.19
28 30 0.81
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
TAAATATTAATTTAATAATAAAAATATA
Found at i:404291 original size:2 final size:2
Alignment explanation
Indices: 404284--404316 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
404274 TCTACCTATC
*
404284 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
404317 GTCCAAATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:407879 original size:21 final size:21
Alignment explanation
Indices: 407840--407880 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
407830 CAATCAAGCC
*
407840 ATAAATAAAAATGAACAAAAA
1 ATAAATAAAAATCAACAAAAA
*
407861 ATAAATAAAAATCATCAAAA
1 ATAAATAAAAATCAACAAAA
407881 TTTCATGCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.73, C:0.07, G:0.02, T:0.17
Consensus pattern (21 bp):
ATAAATAAAAATCAACAAAAA
Found at i:408777 original size:24 final size:23
Alignment explanation
Indices: 408733--408778 Score: 56
Period size: 25 Copynumber: 1.9 Consensus size: 23
408723 ATTTAATTAA
*
408733 AAATAATAAAATTATTAAAAATT
1 AAATAAAAAAATTATTAAAAATT
*
408756 AAATAAAAATAATTTTTTAAAAA
1 AAATAAAAA-AA-TTATTAAAAA
408779 AATTAATATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.42
24 2 0.11
25 9 0.47
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
AAATAAAAAAATTATTAAAAATT
Found at i:410505 original size:16 final size:17
Alignment explanation
Indices: 410474--410508 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
410464 AAATAAGTTA
*
410474 ATTTATGTTTACATATT
1 ATTTATGTTAACATATT
410491 ATTTAT-TTAACATATT
1 ATTTATGTTAACATATT
410507 AT
1 AT
410509 AATATCATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.57
Consensus pattern (17 bp):
ATTTATGTTAACATATT
Found at i:410549 original size:17 final size:16
Alignment explanation
Indices: 410528--410591 Score: 71
Period size: 17 Copynumber: 3.9 Consensus size: 16
410518 TAAAATAATA
410528 TATATTTATATAATTT
1 TATATTTATATAATTT
410544 TAATATATTA-ATAA-TT
1 T-ATAT-TTATATAATTT
410560 TATA-TTATATAATTTTT
1 TATATTTATATAA--TTT
410577 TATATTTATATAATT
1 TATATTTATATAATT
410592 ATATTATATT
Statistics
Matches: 41, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
13 3 0.07
14 4 0.10
15 3 0.07
16 6 0.15
17 14 0.34
18 11 0.27
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATATTTATATAATTT
Found at i:410571 original size:31 final size:31
Alignment explanation
Indices: 410521--410600 Score: 101
Period size: 31 Copynumber: 2.5 Consensus size: 31
410511 TATCATTTAA
*
410521 AATAATATATATTTATATAATTTTA-ATATATT
1 AATAATTTATA-TTATATAATTTTATATAT-TT
*
410553 AATAATTTATATTATATAATTTTTTATATTT
1 AATAATTTATATTATATAATTTTATATATTT
410584 ATATAA-TTATATTATAT
1 A-ATAATTTATATTATAT
410601 TTTAATTATT
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
31 26 0.59
32 18 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (31 bp):
AATAATTTATATTATATAATTTTATATATTT
Found at i:410617 original size:19 final size:19
Alignment explanation
Indices: 410572--410640 Score: 77
Period size: 19 Copynumber: 3.6 Consensus size: 19
410562 TATTATATAA
*
410572 TTTTTTATA-TTTATATAAT
1 TTTTTTATATTTTA-ATTAT
* *
410591 TATATTATATTTTAATTAT
1 TTTTTTATATTTTAATTAT
410610 TTTTTTATATTTTAATTAT
1 TTTTTTATATTTTAATTAT
*
410629 AATTTTTATATT
1 -TTTTTTATATT
410641 ATTTTTATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 28 0.67
20 14 0.33
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTTTATATTTTAATTAT
Found at i:410629 original size:49 final size:52
Alignment explanation
Indices: 410523--410643 Score: 123
Period size: 49 Copynumber: 2.4 Consensus size: 52
410513 TCATTTAAAA
410523 TAATATATATTTATATAATT-TTAATATATTAATAATTTATATTATATAATTT
1 TAAT-TATATTTATATAATTATTAATATATTAATAATTTATATTATATAATTT
* * *
410575 T--TTATATTTATATAATTATATTATATTTTAATTATTT-T-TT-TAT-ATTT
1 TAATTATATTTATATAATTAT-TAATATATTAATAATTTATATTATATAATTT
*
410622 TAATTATAATTTTTAT-ATTATT
1 TAATTAT-ATTTATATAATTATT
410644 TTTATATCAT
Statistics
Matches: 60, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
47 5 0.08
48 4 0.07
49 26 0.43
50 10 0.17
51 14 0.23
52 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (52 bp):
TAATTATATTTATATAATTATTAATATATTAATAATTTATATTATATAATTT
Found at i:410648 original size:11 final size:11
Alignment explanation
Indices: 410590--410650 Score: 63
Period size: 11 Copynumber: 5.5 Consensus size: 11
410580 ATTTATATAA
410590 TTATATTATATT
1 TTATATTAT-TT
410602 TTA-ATTATTT
1 TTATATTATTT
*
410612 TTTTA-TATTT
1 TTATATTATTT
* *
410622 TAATTATAATTT
1 TTA-TATTATTT
410634 TTATATTATTT
1 TTATATTATTT
410645 TTATAT
1 TTATAT
410651 CATTCAATCA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
10 10 0.25
11 21 0.52
12 9 0.22
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTATATTATTT
Found at i:410837 original size:21 final size:23
Alignment explanation
Indices: 410792--410840 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
410782 TATACCCATA
*
410792 TATTTATGAATCAATTCATATAT
1 TATTTATGAATCAATACATATAT
410815 TATTTATGAATCAA-ACA-ATAT
1 TATTTATGAATCAATACATATAT
410836 TATTT
1 TATTT
410841 TATTAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 9 0.36
22 2 0.08
23 14 0.56
ACGTcount: A:0.41, C:0.08, G:0.04, T:0.47
Consensus pattern (23 bp):
TATTTATGAATCAATACATATAT
Found at i:413143 original size:18 final size:18
Alignment explanation
Indices: 413106--413215 Score: 65
Period size: 18 Copynumber: 6.3 Consensus size: 18
413096 TGTTATTTTT
*
413106 ATATTATAATTATGTATATA
1 ATATTAT-A-TATTTATATA
413126 ATATTATATATTTATATA
1 ATATTATATATTTATATA
*
413144 ATTTTA-AGTA-TTA-ATA
1 ATATTATA-TATTTATATA
413160 AT-TTATAT-TTTATA-A
1 ATATTATATATTTATATA
* *
413175 ATTTTAATATGTTTATA-A
1 ATATT-ATATATTTATATA
* *
413193 AT-TTGTATATATATATA
1 ATATTATATATTTATATA
413210 TATATT
1 -ATATT
413216 GTTGTGTTTC
Statistics
Matches: 75, Mismatches: 5, Indels: 21
0.74 0.05 0.21
Matches are distributed among these distances:
15 10 0.13
16 17 0.23
17 11 0.15
18 27 0.36
19 3 0.04
20 7 0.09
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (18 bp):
ATATTATATATTTATATA
Found at i:413167 original size:31 final size:32
Alignment explanation
Indices: 413119--413181 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 32
413109 TTATAATTAT
413119 GTATATAATATTATATA-TTTATATAATTTTAA
1 GTATATAATATTATATATTTTATA-AATTTTAA
413151 GTAT-TAATAATT-TATATTTTATAAATTTTAA
1 GTATATAAT-ATTATATATTTTATAAATTTTAA
413182 TATGTTTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
31 16 0.55
32 13 0.45
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (32 bp):
GTATATAATATTATATATTTTATAAATTTTAA
Found at i:414810 original size:24 final size:25
Alignment explanation
Indices: 414777--414832 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 25
414767 AAATTATTAC
*
414777 TTAATAATAAAAAAATATTT-AAAT
1 TTAATTATAAAAAAATATTTAAAAT
* *
414801 TTAATTATAAAAATATTTTTAAAAAT
1 TTAATTATAAAAAAATATTT-AAAAT
414827 TTAATT
1 TTAATT
414833 TTTATTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 17 0.63
26 10 0.37
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
TTAATTATAAAAAAATATTTAAAAT
Found at i:415005 original size:21 final size:20
Alignment explanation
Indices: 414981--415040 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 20
414971 CCGTATTATT
414981 ATTTAATAATAAAATATTTAA
1 ATTTAAT-ATAAAATATTTAA
*
415002 ATTTAATTATAAAATATATAA
1 ATTTAA-TATAAAATATTTAA
*
415023 TTATTAATATAAAA-ATTT
1 AT-TTAATATAAAATATTT
415041 TTAAAATATT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 3 0.09
21 26 0.76
22 5 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTTAATATAAAATATTTAA
Found at i:421280 original size:21 final size:22
Alignment explanation
Indices: 421243--421294 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
421233 TTTAAAAACT
421243 TATTT-TATAATTAATAA-TAA
1 TATTTATATAATTAATAATTAA
* *
421263 TATTTATATATTTTATAATTAA
1 TATTTATATAATTAATAATTAA
*
421285 -ATTTAAATAA
1 TATTTATATAA
421295 AAAATTTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 5 0.19
21 18 0.69
22 3 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TATTTATATAATTAATAATTAA
Found at i:421696 original size:24 final size:21
Alignment explanation
Indices: 421672--421733 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
421662 ATAATACTAT
421672 TTATTATTAAAACATTAATTATA
1 TTATTATTAAAA-ATT-ATTATA
* *
421695 TTAATATT-TAAATTATTATAA
1 TTATTATTAAAAATTATTAT-A
*
421716 TTATTATTAAATATTATT
1 TTATTATTAAAAATTATT
421734 TCTATTAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
20 5 0.16
21 11 0.34
22 9 0.28
23 7 0.22
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (21 bp):
TTATTATTAAAAATTATTATA
Found at i:421746 original size:31 final size:32
Alignment explanation
Indices: 421696--421766 Score: 99
Period size: 31 Copynumber: 2.2 Consensus size: 32
421686 TTAATTATAT
** *
421696 TAATATTTAAATTATTATAATTATTATT-AAA
1 TAATATTTCTATTAATATAATTATTATTGAAA
*
421727 TATTATTTCTATTAATATAATTATTATTGAAA
1 TAATATTTCTATTAATATAATTATTATTGAAA
421759 TAATATTT
1 TAATATTT
421767 TTACTTTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 24 0.71
32 10 0.29
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (32 bp):
TAATATTTCTATTAATATAATTATTATTGAAA
Found at i:421754 original size:43 final size:43
Alignment explanation
Indices: 421672--421753 Score: 107
Period size: 43 Copynumber: 2.0 Consensus size: 43
421662 ATAATACTAT
421672 TTATTATTAAAACATTAATTATATTAATATTTAAATTATTATAA
1 TTATTATTAAAACATTAATTATATTAATATTT-AATTATTATAA
* * *
421716 TTATTATT-AAATATTATTTCTATTAATA--TAATTATTAT
1 TTATTATTAAAACATTAATTATATTAATATTTAATTATTAT
421754 TGAAATAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
40 9 0.26
41 1 0.03
43 17 0.49
44 8 0.23
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (43 bp):
TTATTATTAAAACATTAATTATATTAATATTTAATTATTATAA
Found at i:421761 original size:15 final size:14
Alignment explanation
Indices: 421712--421762 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 14
421702 TTAAATTATT
421712 ATAATTATTATTAA
1 ATAATTATTATTAA
421726 AT-ATTATTTCTATTAA
1 ATAATTA--T-TATTAA
421742 TATAATTATTATTGAA
1 -ATAATTATTATT-AA
421758 ATAAT
1 ATAAT
421763 ATTTTTACTT
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
13 4 0.13
14 2 0.06
15 10 0.32
16 9 0.29
17 2 0.06
18 4 0.13
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (14 bp):
ATAATTATTATTAA
Found at i:422517 original size:43 final size:44
Alignment explanation
Indices: 422469--422560 Score: 134
Period size: 43 Copynumber: 2.1 Consensus size: 44
422459 AATTCCACAA
* *
422469 GTTTAAAAAGTAAAAACCTATATTGCTCGAATTC-TTATTTTTT
1 GTTTAAAAAGTAAAAAACTATATTACTCGAATTCTTTATTTTTT
* *
422512 GTTTAAAAAGTAAAAAATTATATTACTTGAATTCTTTATTTTTT
1 GTTTAAAAAGTAAAAAACTATATTACTCGAATTCTTTATTTTTT
422556 -TTTAA
1 GTTTAA
422561 GTACTTTATA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
43 35 0.80
44 9 0.20
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.48
Consensus pattern (44 bp):
GTTTAAAAAGTAAAAAACTATATTACTCGAATTCTTTATTTTTT
Found at i:425059 original size:28 final size:28
Alignment explanation
Indices: 425028--425093 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
425018 TTTAGTGAGA
425028 ATTATTTATTTTTTA-CTT-TTTAAAAATT
1 ATTATTTATTTTTTATCTTGTTT--AAATT
*
425056 ATTATTTATAGTTTTATCTTGTTTAAATT
1 ATTATTTAT-TTTTTATCTTGTTTAAATT
425085 A-TATTTATT
1 ATTATTTATT
425094 GTTATTTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
28 16 0.48
29 11 0.33
30 3 0.09
31 3 0.09
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (28 bp):
ATTATTTATTTTTTATCTTGTTTAAATT
Found at i:426038 original size:3 final size:3
Alignment explanation
Indices: 426030--426054 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
426020 ATTAATGGAC
426030 CCA CCA CCA CCA CCA CCA CCA CCA C
1 CCA CCA CCA CCA CCA CCA CCA CCA C
426055 GCCCACAACG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.68, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:442199 original size:15 final size:15
Alignment explanation
Indices: 442179--442207 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
442169 GTAAATATTG
442179 AAATAAATAAAATTT
1 AAATAAATAAAATTT
442194 AAATAAATAAAATT
1 AAATAAATAAAATT
442208 ATCATTATCT
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAATAAATAAAATTT
Found at i:443022 original size:17 final size:16
Alignment explanation
Indices: 442971--443029 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 16
442961 GATAAATTTA
442971 AAATAAATTTTT-TAT
1 AAATAAATTTTTATAT
* * *
442986 AATTTAAATTATTATTT
1 AA-ATAAATTTTTATAT
443003 AAATAATATTTTTATAT
1 AAATAA-ATTTTTATAT
443020 AAATATAATT
1 AAATA-AATT
443030 ATAAAAATCT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
15 2 0.06
16 11 0.32
17 20 0.59
18 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AAATAAATTTTTATAT
Found at i:443030 original size:34 final size:33
Alignment explanation
Indices: 442966--443031 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
442956 AACTTGATAA
*
442966 ATTTAAAATAAATTTTTTATAATTTAAATTATT
1 ATTTAAAATAAATTTTTTATAATATAAATTATT
442999 ATTT-AAATAATATTTTTATATAA-ATATAATTAT
1 ATTTAAAATAA-ATTTTT-TATAATATA-AATTAT
443032 AAAAATCTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
32 6 0.21
33 12 0.41
34 11 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (33 bp):
ATTTAAAATAAATTTTTTATAATATAAATTATT
Found at i:444195 original size:23 final size:20
Alignment explanation
Indices: 444167--444220 Score: 56
Period size: 23 Copynumber: 2.6 Consensus size: 20
444157 AATATCATAA
444167 ATATAAATATTTAACTAACAAT
1 ATATAAATATTTAA-TAA-AAT
* *
444189 CATATAATTTTTTAATAAAAT
1 -ATATAAATATTTAATAAAAT
444210 AT-TAAATATTT
1 ATATAAATATTT
444221 TATCAATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
19 7 0.26
20 2 0.07
21 3 0.11
22 3 0.11
23 12 0.44
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (20 bp):
ATATAAATATTTAATAAAAT
Found at i:444420 original size:20 final size:20
Alignment explanation
Indices: 444383--444421 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
444373 TTGTAACTCA
* * *
444383 AATAATTTAATAATAATAAT
1 AATAAATTAAGAACAATAAT
444403 AATAAATTAAGAACAATAA
1 AATAAATTAAGAACAATAA
444422 ATGCATACCA
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:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (20 bp):
AATAAATTAAGAACAATAAT
Found at i:444854 original size:30 final size:30
Alignment explanation
Indices: 444810--444897 Score: 122
Period size: 30 Copynumber: 2.9 Consensus size: 30
444800 TATTAAATGC
* * ** *
444810 ATATATATAATTAAATTTTTATAAAATCTT
1 ATATATAAAATTAAAATCATATAAAATATT
*
444840 ATCTATAAAATTAAAATCATATAAAATATT
1 ATATATAAAATTAAAATCATATAAAATATT
444870 ATATATAAAATTAAAATCATATAAAATA
1 ATATATAAAATTAAAATCATATAAAATA
444898 GAATTAGCAT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (30 bp):
ATATATAAAATTAAAATCATATAAAATATT
Found at i:444864 original size:16 final size:16
Alignment explanation
Indices: 444843--444896 Score: 76
Period size: 16 Copynumber: 3.5 Consensus size: 16
444833 AAATCTTATC
444843 TATAAAATTAAAATCA
1 TATAAAATTAAAATCA
**
444859 TATAAAA-TATTAT-A
1 TATAAAATTAAAATCA
444873 TATAAAATTAAAATCA
1 TATAAAATTAAAATCA
444889 TATAAAAT
1 TATAAAAT
444897 AGAATTAGCA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
14 8 0.25
15 8 0.25
16 16 0.50
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (16 bp):
TATAAAATTAAAATCA
Found at i:444877 original size:14 final size:14
Alignment explanation
Indices: 444829--444880 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
444819 ATTAAATTTT
* *
444829 TATAAAATCTTATC
1 TATAAAATATTATA
**
444843 TATAAAATTAAAATCA
1 TATAAAA-TATTAT-A
444859 TATAAAATATTATA
1 TATAAAATATTATA
444873 TATAAAAT
1 TATAAAAT
444881 TAAAATCATA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
14 16 0.53
15 7 0.23
16 7 0.23
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (14 bp):
TATAAAATATTATA
Found at i:445305 original size:23 final size:25
Alignment explanation
Indices: 445267--445312 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
445257 CTATTAAATT
*
445267 TATTTTACGTTA-TTTTTTATATCA
1 TATTTTACATTATTTTTTTATATCA
445291 TATTTTA-ATTATTTTTTTATAT
1 TATTTTACATTATTTTTTTATAT
445313 GTAAATTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.67
Consensus pattern (25 bp):
TATTTTACATTATTTTTTTATATCA
Found at i:450281 original size:17 final size:16
Alignment explanation
Indices: 450255--450312 Score: 50
Period size: 17 Copynumber: 3.6 Consensus size: 16
450245 TATATATTTA
*
450255 TATAAATTTTAATAAT
1 TATAATTTTTAATAAT
*
450271 TAATAATTTTT-ATTA-
1 T-ATAATTTTTAATAAT
450286 TATAATTTTTAATATAT
1 TATAATTTTTAATA-AT
450303 T-TATATTTTT
1 TATA-ATTTTT
450313 TTTATTTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
14 9 0.26
15 3 0.09
16 7 0.21
17 15 0.44
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TATAATTTTTAATAAT
Found at i:450290 original size:31 final size:31
Alignment explanation
Indices: 450252--450317 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
450242 TATTATATAT
450252 TTATATAAATTTTAATA-ATTAATAATTTTTA
1 TTATATAAATTTTAATATATTAAT-ATTTTTA
* * *
450283 TTATATAATTTTTAATATATTTATATTTTTT
1 TTATATAAATTTTAATATATTAATATTTTTA
450314 TTAT
1 TTAT
450318 TTTATCATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
31 26 0.84
32 5 0.16
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (31 bp):
TTATATAAATTTTAATATATTAATATTTTTA
Found at i:450292 original size:14 final size:14
Alignment explanation
Indices: 450269--450302 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
450259 AATTTTAATA
450269 ATTA-ATAATTTTT
1 ATTATATAATTTTT
450282 ATTATATAATTTTT
1 ATTATATAATTTTT
*
450296 AATATAT
1 ATTATAT
450303 TTATATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTATATAATTTTT
Found at i:450313 original size:19 final size:20
Alignment explanation
Indices: 450291--450364 Score: 68
Period size: 19 Copynumber: 3.9 Consensus size: 20
450281 TATTATATAA
*
450291 TTTTTAATATATTTAT-A-T
1 TTTTTATTATATTTATAATT
*
450309 TTTTT-TTAT-TTTATCATAT
1 TTTTTATTATATTTATAAT-T
*
450328 TTTATATTATATTT-TAATT
1 TTTTTATTATATTTATAATT
*
450347 TTTTTATTATATTCATAA
1 TTTTTATTATATTTATAA
450365 GTTCTACTAC
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
16 5 0.11
17 4 0.09
18 5 0.11
19 18 0.40
20 10 0.22
21 3 0.07
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTTATTATATTTATAATT
Found at i:450338 original size:31 final size:32
Alignment explanation
Indices: 450298--450359 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
450288 TAATTTTTAA
*
450298 TATATTTATATTTT-TTTTATTTTATCATATTT
1 TATATTTATATTTTAATTT-TTTTATCATATTT
*
450330 TATA-TTATATTTTAATTTTTTTATTATATT
1 TATATTTATATTTTAATTTTTTTATCATATT
450360 CATAAGTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 20 0.74
32 7 0.26
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (32 bp):
TATATTTATATTTTAATTTTTTTATCATATTT
Found at i:450363 original size:37 final size:36
Alignment explanation
Indices: 450261--450363 Score: 110
Period size: 36 Copynumber: 3.0 Consensus size: 36
450251 TTTATATAAA
*
450261 TTTTAATA-ATTAATAA--TTTTTATTATAT-A-AT
1 TTTTAATATATTTATAATTTTTTTATTATATCATAT
* *
450292 TTTTAATATATTTATATTTTTTTTATTTTATCATAT
1 TTTTAATATATTTATAATTTTTTTATTATATCATAT
*
450328 TTTATATTATATTT-TAATTTTTTTATTATATTCATA
1 TTT-TAATATATTTATAATTTTTTTATTATA-TCATA
450364 AGTTCTACTA
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
31 8 0.14
32 6 0.10
34 11 0.19
35 1 0.02
36 19 0.32
37 14 0.24
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (36 bp):
TTTTAATATATTTATAATTTTTTTATTATATCATAT
Found at i:450615 original size:31 final size:32
Alignment explanation
Indices: 450577--450656 Score: 85
Period size: 33 Copynumber: 2.5 Consensus size: 32
450567 TTTTAAATAG
450577 TTTAAATTATTATTA-AT-AATA-AAAAAAATT
1 TTTAAATT-TTATTATATAAATATAAAAAAATT
* *
450607 ATTTAAATTTAATTATATAAATATAAAAATATT
1 -TTTAAATTTTATTATATAAATATAAAAAAATT
450640 TTTAAAATTTTTATTAT
1 TTT-AAA-TTTTATTAT
450657 TTTTTAATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
30 5 0.12
31 10 0.24
32 7 0.17
33 11 0.27
34 8 0.20
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (32 bp):
TTTAAATTTTATTATATAAATATAAAAAAATT
Found at i:450644 original size:32 final size:31
Alignment explanation
Indices: 450577--450645 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 31
450567 TTTTAAATAG
*
450577 TTTAAATTATTATTAATAATAAAAAAAATTA
1 TTTAAATTATAATTAATAATAAAAAAAATTA
*
450608 TTTAAATT-TAATTATATAAATATAAAAATATT-
1 TTTAAATTATAATTA-AT-AATA-AAAAAAATTA
450640 TTTAAA
1 TTTAAA
450646 ATTTTTATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
30 5 0.15
31 10 0.30
32 10 0.30
33 8 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (31 bp):
TTTAAATTATAATTAATAATAAAAAAAATTA
Found at i:450766 original size:2 final size:2
Alignment explanation
Indices: 450759--450784 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
450749 CTAAACAAAA
450759 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
450785 TAAAATCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:455866 original size:1 final size:1
Alignment explanation
Indices: 455860--455893 Score: 50
Period size: 1 Copynumber: 34.0 Consensus size: 1
455850 AAAGAAAGGT
* *
455860 AAAAAAAAAAAAAAAAGAAAAAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
455894 TGTATTTGCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (1 bp):
A
Found at i:455876 original size:19 final size:18
Alignment explanation
Indices: 455860--455893 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
455850 AAAGAAAGGT
455860 AAAAAAAAAAA-AAAAAG
1 AAAAAAAAAAAGAAAAAG
455877 AAAAAAAAAAAGAAAAA
1 AAAAAAAAAAAGAAAAA
455894 TGTATTTGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAAGAAAAAG
Found at i:455880 original size:12 final size:12
Alignment explanation
Indices: 455860--455893 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
455850 AAAGAAAGGT
455860 AAAAA-AAAAAA
1 AAAAAGAAAAAA
455871 AAAAAGAAAAAA
1 AAAAAGAAAAAA
455883 AAAAAGAAAAA
1 AAAAAGAAAAA
455894 TGTATTTGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 5 0.23
12 17 0.77
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAAA
Found at i:457785 original size:15 final size:17
Alignment explanation
Indices: 457749--457788 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 17
457739 AAATATATTT
457749 TTATA-TTTATTCTTAA
1 TTATATTTTATTCTTAA
457765 TT-TATTTTATT-TT-A
1 TTATATTTTATTCTTAA
457779 TTATATTTTA
1 TTATATTTTA
457789 AAATAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 3 0.14
15 11 0.50
16 8 0.36
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (17 bp):
TTATATTTTATTCTTAA
Found at i:457906 original size:20 final size:22
Alignment explanation
Indices: 457883--457924 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
457873 TACATATAAT
457883 ATTTAAA-TAAT-TTTTTATTA
1 ATTTAAATTAATATTTTTATTA
457903 ATTTAAATTTAATATTTTTATT
1 ATTTAAA-TTAATATTTTTATT
457925 TTAATTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.37
22 4 0.21
23 8 0.42
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
ATTTAAATTAATATTTTTATTA
Found at i:457928 original size:25 final size:26
Alignment explanation
Indices: 457883--457931 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
457873 TACATATAAT
457883 ATTTAAATAATTTTTTATTAATTTAA
1 ATTTAAATAATTTTTTATTAATTTAA
*
457909 ATTT-AAT-ATTTTTATTTTAATTT
1 ATTTAAATAATTTTT-TATTAATTT
457932 TTTCACATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 6 0.29
25 11 0.52
26 4 0.19
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (26 bp):
ATTTAAATAATTTTTTATTAATTTAA
Found at i:459035 original size:15 final size:16
Alignment explanation
Indices: 459014--459054 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
459004 TTATATATAA
459014 ATATAAATTTTAAAAT
1 ATATAAATTTTAAAAT
*
459030 -TATAAATATTAAAAT
1 ATATAAATTTTAAAAT
459045 ATAATAAATT
1 AT-ATAAATT
459055 ATTATTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 14 0.67
16 1 0.05
17 6 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATAAATTTTAAAAT
Found at i:459082 original size:13 final size:13
Alignment explanation
Indices: 459060--459089 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
459050 AAATTATTAT
459060 TAATTAAATTTAA
1 TAATTAAATTTAA
*
459073 TAATTTAATTTAA
1 TAATTAAATTTAA
459086 TAAT
1 TAAT
459090 CATATTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TAATTAAATTTAA
Found at i:459405 original size:20 final size:20
Alignment explanation
Indices: 459354--459412 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
459344 GAATAATTAG
*
459354 ATAATAAATATTTATTTTTA
1 ATAATAAATTTTTATTTTTA
*
459374 ATAAAATTAATTTATTATTTTT-
1 AT--AATAAATTT-TTATTTTTA
459396 ATAATAAATTTTT-TTTT
1 ATAATAAATTTTTATTTT
459413 CAAATATGCA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
18 4 0.12
19 2 0.06
20 10 0.30
22 9 0.27
23 8 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
ATAATAAATTTTTATTTTTA
Found at i:460675 original size:22 final size:20
Alignment explanation
Indices: 460650--460689 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
460640 ACATAAAATG
460650 AATATAAAAATAAAATCTTTCA
1 AATATAAAAA-AAAA-CTTTCA
*
460672 AATATATAAAAAAACTTT
1 AATATAAAAAAAAACTTT
460690 AAAAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 4 0.24
22 9 0.53
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (20 bp):
AATATAAAAAAAAACTTTCA
Found at i:462114 original size:14 final size:16
Alignment explanation
Indices: 462083--462116 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
462073 TTATATTAAT
462083 ATATTTCATTTAATAA
1 ATATTTCATTTAATAA
462099 ATATTTCA-TTAA-AA
1 ATATTTCATTTAATAA
462113 ATAT
1 ATAT
462117 AGTGATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.33
15 4 0.22
16 8 0.44
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (16 bp):
ATATTTCATTTAATAA
Found at i:462309 original size:27 final size:27
Alignment explanation
Indices: 462247--462318 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 27
462237 CAATTTATTT
* *
462247 TTTAATA-ATAATTAATTTATTTTAAA
1 TTTAATATATAATAAATTTATCTTAAA
** *
462273 TAAAAAATATAATAAATTTATCTTAAA
1 TTTAATATATAATAAATTTATCTTAAA
*
462300 TTTAATATATGATTAAATT
1 TTTAATATAT-AATAAATT
462319 AACAATAAAT
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
26 4 0.11
27 24 0.69
28 7 0.20
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (27 bp):
TTTAATATATAATAAATTTATCTTAAA
Found at i:464264 original size:15 final size:15
Alignment explanation
Indices: 464244--464273 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
464234 TGAATGAAGA
464244 GAATAAAATCTCAGC
1 GAATAAAATCTCAGC
464259 GAATAAAATCTCAGC
1 GAATAAAATCTCAGC
464274 AAATTCTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.20, G:0.13, T:0.20
Consensus pattern (15 bp):
GAATAAAATCTCAGC
Found at i:468202 original size:2 final size:2
Alignment explanation
Indices: 468195--468235 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
468185 GATATTAATT
468195 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
468236 GCTTTTAGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:472828 original size:29 final size:30
Alignment explanation
Indices: 472787--472958 Score: 137
Period size: 29 Copynumber: 5.8 Consensus size: 30
472777 ATTTTATCTC
* *
472787 ATTCGTAACATTTAAAAATTATATTT-TTT
1 ATTCATAATATTTAAAAATTATATTTATTT
**
472816 ATTCATAATATTTATTAA-TAT-TTTATTTTT
1 ATTCATAATATTTAAAAATTATATTTA--TTT
* * * *
472846 ATTTATAATTTTTAAAATTTATATTTATTC
1 ATTCATAATATTTAAAAATTATATTTATTT
472876 ATTCATAACT-TTTAAAAATTATATTTATCTT
1 ATTCATAA-TATTTAAAAATTATATTTAT-TT
*
472907 -TT-ATAATTTTTAAAAATTATATTTATCTT
1 ATTCATAATATTTAAAAATTATATTTAT-TT
472936 -TT-ATAACT-TTTAAAAATTTATAT
1 ATTCATAA-TATTTAAAAA-TTATAT
472959 CATACATCTA
Statistics
Matches: 120, Mismatches: 13, Indels: 19
0.79 0.09 0.12
Matches are distributed among these distances:
27 3 0.03
28 4 0.03
29 53 0.44
30 51 0.43
31 5 0.04
32 4 0.03
ACGTcount: A:0.38, C:0.05, G:0.01, T:0.56
Consensus pattern (30 bp):
ATTCATAATATTTAAAAATTATATTTATTT
Found at i:472847 original size:30 final size:29
Alignment explanation
Indices: 472797--472958 Score: 111
Period size: 30 Copynumber: 5.5 Consensus size: 29
472787 ATTCGTAACA
*
472797 TTTAAAAATTATATTTTTTATTCATAATATT
1 TTTAAAATTTATA-TTTTTATTCATAA-ATT
* *
472828 TATTAATATTT-TATTTTTATTTAT-AATT
1 T-TTAAAATTTATATTTTTATTCATAAATT
*
472856 TTTAAAATTTATATTTATTCATTCAT-AACT
1 TTTAAAATTTATATTT-TT-ATTCATAAATT
* *
472886 TTTAAAAATTATATTTATCT-TTTAT-AATT
1 TTTAAAATTTATATTT-T-TATTCATAAATT
* * *
472915 TTTAAAAATTATATTTATCT-TTTATAACTT
1 TTTAAAATTTATATTT-T-TATTCATAAATT
*
472945 TTAAAAATTTATAT
1 TTTAAAATTTATAT
472959 CATACATCTA
Statistics
Matches: 113, Mismatches: 12, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
27 8 0.07
28 9 0.08
29 35 0.31
30 50 0.44
31 4 0.04
32 7 0.06
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (29 bp):
TTTAAAATTTATATTTTTATTCATAAATT
Found at i:472910 original size:59 final size:58
Alignment explanation
Indices: 472797--472958 Score: 188
Period size: 59 Copynumber: 2.8 Consensus size: 58
472787 ATTCGTAACA
* * *
472797 TTTAAAAATTATATTT-TTTATTCATAA-TATTTATTAATATTTTATTTTTATTTATAATT
1 TTTAAAAATTATATTTATTCATTCATAACT-TTTA--AAAATTATATTTTTATTTATAATT
*
472856 TTTAAAATTTATATTTATTCATTCATAACTTTTAAAAATTATATTTATCT-TTTATAATT
1 TTTAAAAATTATATTTATTCATTCATAACTTTTAAAAATTATATTT-T-TATTTATAATT
* *
472915 TTTAAAAATTATATTTA-TCTTTTATAACTTTTAAAAATTTATAT
1 TTTAAAAATTATATTTATTCATTCATAACTTTTAAAAA-TTATAT
472959 CATACATCTA
Statistics
Matches: 91, Mismatches: 7, Indels: 10
0.84 0.06 0.09
Matches are distributed among these distances:
58 28 0.31
59 47 0.52
60 15 0.16
61 1 0.01
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (58 bp):
TTTAAAAATTATATTTATTCATTCATAACTTTTAAAAATTATATTTTTATTTATAATT
Found at i:472913 original size:89 final size:90
Alignment explanation
Indices: 472779--472958 Score: 219
Period size: 89 Copynumber: 2.0 Consensus size: 90
472769 TTCATAATAT
* * * *
472779 TTTATCTCATTCGTAACATTTAAAAATTATATTTTTTATTCATAATATTTATTAATATTTTATTT
1 TTTATCTCATTCATAACATTTAAAAATTATATTTTTTATTCATAAT-TTT-TAAAAATTATATTT
*
472844 -T-TATTTATAA-TTTTTAAAATTTATA
64 ATCT-TTTATAACTTTTAAAAATTTATA
*
472869 TTTAT-TCATTCATAACTTTTAAAAATTATATTTATCTT-TT-ATAATTTTTAAAAATTATATTT
1 TTTATCTCATTCATAACATTTAAAAATTATATTT-T-TTATTCATAATTTTTAAAAATTATATTT
472931 ATCTTTTATAACTTTTAAAAATTTATA
64 ATCTTTTATAACTTTTAAAAATTTATA
472958 T
1 T
472959 CATACATCTA
Statistics
Matches: 79, Mismatches: 6, Indels: 11
0.82 0.06 0.11
Matches are distributed among these distances:
87 11 0.14
88 11 0.14
89 47 0.59
90 8 0.10
91 2 0.03
ACGTcount: A:0.37, C:0.06, G:0.01, T:0.57
Consensus pattern (90 bp):
TTTATCTCATTCATAACATTTAAAAATTATATTTTTTATTCATAATTTTTAAAAATTATATTTAT
CTTTTATAACTTTTAAAAATTTATA
Found at i:474538 original size:16 final size:17
Alignment explanation
Indices: 474513--474547 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
474503 ATTATCTTTT
474513 AATTTATA-TTTAAATA
1 AATTTATATTTTAAATA
*
474529 AATTTTTATTTTAAATA
1 AATTTATATTTTAAATA
474546 AA
1 AA
474548 AAAGTTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
AATTTATATTTTAAATA
Found at i:474540 original size:28 final size:27
Alignment explanation
Indices: 474458--474542 Score: 80
Period size: 28 Copynumber: 3.0 Consensus size: 27
474448 AATTCTACTC
* * *
474458 TTTTATTTAAATAAACCTTGTATTTTTA
1 TTTTATTTAAATAAA-TTTTTATTTTAA
* * *
474486 TTTTAGTTACATAAATTATTATCTTTTAA
1 TTTTATTTAAATAAATT-TT-TATTTTAA
474515 TTTATATTTAAATAAATTTTTATTTTAA
1 TTT-TATTTAAATAAATTTTTATTTTAA
474543 ATAAAAAAGT
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
27 1 0.02
28 21 0.47
29 11 0.24
30 12 0.27
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (27 bp):
TTTTATTTAAATAAATTTTTATTTTAA
Found at i:479398 original size:15 final size:15
Alignment explanation
Indices: 479378--479448 Score: 60
Period size: 15 Copynumber: 4.9 Consensus size: 15
479368 ATTTGAATAG
479378 ATAAATTTAATTAAT
1 ATAAATTTAATTAAT
*
479393 ATAAATTAAATT--T
1 ATAAATTTAATTAAT
* **
479406 -TAAATATAATTTTT
1 ATAAATTTAATTAAT
479420 ATAAATTTATATTAA-
1 ATAAATTTA-ATTAAT
*
479435 ATTAATTTAATTAA
1 ATAAATTTAATTAA
479449 AATTATTATT
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
12 9 0.20
13 1 0.02
14 6 0.13
15 26 0.58
16 3 0.07
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATAAATTTAATTAAT
Found at i:479748 original size:2 final size:2
Alignment explanation
Indices: 479741--479767 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
479731 AAATGGCTTC
479741 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
479768 GTATTCTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:481556 original size:11 final size:11
Alignment explanation
Indices: 481540--481597 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
481530 AAATATGAAT
481540 ATATAAATATA
1 ATATAAATATA
*
481551 ATATAAAAATA
1 ATATAAATATA
481562 AT-TATAATATA
1 ATATA-AATATA
*
481573 ATA-AAATTTA
1 ATATAAATATA
*
481583 A-ATTAATATGA
1 ATATAAATAT-A
481594 ATAT
1 ATAT
481598 TTTAAAATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
9 1 0.03
10 12 0.32
11 22 0.59
12 2 0.05
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (11 bp):
ATATAAATATA
Found at i:482985 original size:23 final size:23
Alignment explanation
Indices: 482939--482982 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
482929 GTTTAACAAT
482939 TTAAAAATATTATAAATATTTTA
1 TTAAAAATATTATAAATATTTTA
* *
482962 TTAATAATATT-TATATATTTT
1 TTAAAAATATTATAAATATTTT
482983 TATAATTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TTAAAAATATTATAAATATTTTA
Found at i:482988 original size:22 final size:25
Alignment explanation
Indices: 482944--483015 Score: 66
Period size: 24 Copynumber: 3.0 Consensus size: 25
482934 ACAATTTAAA
482944 AATA-TTATAAATATTTTATTAA-T
1 AATATTTATAAATATTTTATTAATT
*
482967 AATATTTATATAT-TTTTA-TAATT
1 AATATTTATAAATATTTTATTAATT
*
482990 AA-ATTTAAGTAAA-ATATTATTAATT
1 AATATTT-A-TAAATATTTTATTAATT
483015 A
1 A
483016 TATAATAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
22 7 0.17
23 13 0.32
24 14 0.35
25 6 0.15
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (25 bp):
AATATTTATAAATATTTTATTAATT
Found at i:484985 original size:12 final size:12
Alignment explanation
Indices: 484968--485017 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
484958 CTTACTCTTT
484968 TATTA-TTATTAA
1 TATTATTTATT-A
484980 TATTATTTATT-
1 TATTATTTATTA
484991 TATTTATTTATTA
1 TA-TTATTTATTA
*
485004 TATTGATTGATTA
1 TATT-ATTTATTA
485017 T
1 T
485018 TATATTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
11 2 0.06
12 16 0.48
13 15 0.45
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (12 bp):
TATTATTTATTA
Found at i:485023 original size:21 final size:19
Alignment explanation
Indices: 484966--485023 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 19
484956 CTCTTACTCT
484966 TTTATT-ATTATTAATATTA
1 TTTATTGATTATT-ATATTA
*
484985 TTTATTTATTTATT-TATTA
1 TTTATTGA-TTATTATATTA
485004 TATTGATTGATTATTATATT
1 T-TT-ATTGATTATTATATT
485024 TTTTTGTGTC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
19 12 0.36
20 8 0.24
21 13 0.39
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (19 bp):
TTTATTGATTATTATATTA
Found at i:488597 original size:25 final size:25
Alignment explanation
Indices: 488569--488628 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
488559 TCATTTTAAA
488569 TAAAAATAATATA-ATATATTAAAAT
1 TAAAAATAATATATATA-ATTAAAAT
* * *
488594 TAAAATTAATATATATAATTGAATT
1 TAAAAATAATATATATAATTAAAAT
*
488619 TAATAATAAT
1 TAAAAATAAT
488629 TTTAAATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
25 26 0.90
26 3 0.10
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (25 bp):
TAAAAATAATATATATAATTAAAAT
Found at i:488845 original size:17 final size:18
Alignment explanation
Indices: 488813--488846 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
488803 TAACTTGATA
488813 GTAATTAAAAATAATTTT
1 GTAATTAAAAATAATTTT
488831 GTAATTAAAAA-AATTT
1 GTAATTAAAAATAATTT
488847 AGAAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (18 bp):
GTAATTAAAAATAATTTT
Found at i:489362 original size:12 final size:11
Alignment explanation
Indices: 489338--489370 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
489328 TAGGCATATC
489338 AAAA-AAAAAA
1 AAAAGAAAAAA
489348 AAAAGAAAAAGA
1 AAAAGAAAAA-A
489360 AAAAGAAAAAA
1 AAAAGAAAAAA
489371 GCAAACAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 4 0.19
11 6 0.29
12 11 0.52
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAA
Found at i:494266 original size:33 final size:34
Alignment explanation
Indices: 494183--494276 Score: 104
Period size: 33 Copynumber: 2.8 Consensus size: 34
494173 ATTTTGGATA
*
494183 TAATATTCATCTTTAATATTATTAAATTAGAAACG
1 TAATATTCATCTATAATATTATTAAATTAG-AACG
*
494218 -AA-ATTCATCTATAATATTATTAAATTAG-AGG
1 TAATATTCATCTATAATATTATTAAATTAGAACG
* * * *
494249 TAATATTCGTCTCTAATACTGTTAAATT
1 TAATATTCATCTATAATATTATTAAATT
494277 TAAAATAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
31 2 0.04
32 2 0.04
33 45 0.88
34 2 0.04
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (34 bp):
TAATATTCATCTATAATATTATTAAATTAGAACG
Found at i:507737 original size:33 final size:32
Alignment explanation
Indices: 507674--507781 Score: 103
Period size: 32 Copynumber: 3.2 Consensus size: 32
507664 ATAATAATAT
* **
507674 TTATATAAATTTTGATATATTAATAA-TTTATA
1 TTATATAAATTTTAATAT-TTTTTAATTTTATA
507706 TTATATAAATTTTAATATGTTTTTAATTTTATA
1 TTATATAAATTTTAATAT-TTTTTAATTTTATA
*
507739 TTATATATTATTTTATATTATTTTTTAATTATT-TA
1 TTATATA-AATTTTA-A-TATTTTTTAATT-TTATA
*
507774 TTTTATAA
1 TTATATAA
507782 TATATAGTTA
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
32 22 0.34
33 13 0.20
34 6 0.09
35 18 0.28
36 5 0.08
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (32 bp):
TTATATAAATTTTAATATTTTTTAATTTTATA
Found at i:507776 original size:15 final size:16
Alignment explanation
Indices: 507751--507798 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
507741 ATATATTATT
*
507751 TTATATTATTTTTTAA
1 TTATATTATTTTATAA
507767 TTAT-TTATTTTATAA
1 TTATATTATTTTATAA
*
507782 TATATAGTTATATTATA
1 T-TATA-TTATTTTATA
507799 TTTAAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 11 0.41
16 7 0.26
18 9 0.33
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (16 bp):
TTATATTATTTTATAA
Found at i:515436 original size:29 final size:31
Alignment explanation
Indices: 515386--515450 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 31
515376 TTATTTTAAT
* *
515386 TTTAATTTAAATAATATCATA-TATCTAA-A
1 TTTAATTTAAATAATATAATATTATCAAATA
*
515415 TTTAATTTAATTACATA-AATATTATCAAATA
1 TTTAATTTAAATA-ATATAATATTATCAAATA
515446 TTTAA
1 TTTAA
515451 ATTTTTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 15 0.50
30 9 0.30
31 6 0.20
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (31 bp):
TTTAATTTAAATAATATAATATTATCAAATA
Found at i:515976 original size:5 final size:5
Alignment explanation
Indices: 515961--516002 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
515951 CAGTTGAAAA
* *
515961 AAATT ATATT AAATT AGATT AAATT AAA-T AAATT AAAATT AA
1 AAATT AAATT AAATT AAATT AAATT AAATT AAATT -AAATT AA
516003 TATTTAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
4 4 0.13
5 22 0.71
6 5 0.16
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (5 bp):
AAATT
Found at i:516057 original size:16 final size:17
Alignment explanation
Indices: 516036--516082 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
516026 TTATAAAATT
516036 AAAATT-TTAAAAGAAA
1 AAAATTATTAAAAGAAA
*
516052 AAAATTGATTAAAA-TAA
1 AAAATT-ATTAAAAGAAA
516069 AAAATTGATTAAAA
1 AAAATT-ATTAAAA
516083 TTAAAATTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 6 0.21
17 16 0.57
18 6 0.21
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (17 bp):
AAAATTATTAAAAGAAA
Found at i:516065 original size:18 final size:17
Alignment explanation
Indices: 516042--516082 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
516032 AATTAAAATT
516042 TTAAAAGAAAAAAATTGA
1 TTAAAA-AAAAAAATTGA
*
516060 TTAAAATAAAAAATTGA
1 TTAAAAAAAAAAATTGA
516077 TTAAAA
1 TTAAAA
516083 TTAAAATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (17 bp):
TTAAAAAAAAAAATTGA
Done.