Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 140 of 182
Found at i:43552821 original size:13 final size:13
Alignment explanation
Indices: 43552803--43552840 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
43552793 TAAAAGGAAG
43552803 GAAAAATGAAAAA
1 GAAAAATGAAAAA
*
43552816 GAAAAAAGAAAAA
1 GAAAAATGAAAAA
43552829 GTAAAAAT-AAAA
1 G-AAAAATGAAAA
43552841 GTGAAATAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 17 0.77
14 5 0.23
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (13 bp):
GAAAAATGAAAAA
Found at i:43553069 original size:15 final size:17
Alignment explanation
Indices: 43553042--43553076 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
43553032 TCAAGTACTA
43553042 ATTTTAGATTTAACC-C
1 ATTTTAGATTTAACCAC
43553058 ATTTTA-ATTTAACCAC
1 ATTTTAGATTTAACCAC
43553074 ATT
1 ATT
43553077 CATCTAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.34, C:0.17, G:0.03, T:0.46
Consensus pattern (17 bp):
ATTTTAGATTTAACCAC
Found at i:43558401 original size:12 final size:12
Alignment explanation
Indices: 43558380--43558413 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
43558370 AAAACATAGT
*
43558380 AAACTTAAATTA
1 AAACTAAAATTA
43558392 AAACTAAAATTA
1 AAACTAAAATTA
43558404 AAACTAAAAT
1 AAACTAAAAT
43558414 CATCACAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (12 bp):
AAACTAAAATTA
Found at i:43558613 original size:8 final size:8
Alignment explanation
Indices: 43558593--43558628 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
43558583 TATTTTATAT
43558593 TTAAAATAA
1 TTAAAA-AA
43558602 TTAAAAAA
1 TTAAAAAA
43558610 TTAAAAAA
1 TTAAAAAA
*
43558618 TTGAAAAA
1 TTAAAAAA
43558626 TTA
1 TTA
43558629 TTTTATTAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
8 19 0.76
9 6 0.24
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (8 bp):
TTAAAAAA
Found at i:43558728 original size:7 final size:7
Alignment explanation
Indices: 43558712--43558763 Score: 95
Period size: 7 Copynumber: 7.4 Consensus size: 7
43558702 CATTTTGTAA
*
43558712 AAAAAAT
1 AAAAATT
43558719 AAAAATT
1 AAAAATT
43558726 AAAAATT
1 AAAAATT
43558733 AAAAATT
1 AAAAATT
43558740 AAAAATT
1 AAAAATT
43558747 AAAAATT
1 AAAAATT
43558754 AAAAATT
1 AAAAATT
43558761 AAA
1 AAA
43558764 TGTTAATATA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
7 44 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (7 bp):
AAAAATT
Found at i:43560555 original size:27 final size:26
Alignment explanation
Indices: 43560507--43560559 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 26
43560497 AAAATACAAA
43560507 TAAATATAATAAATATTTTATTTTAT
1 TAAATATAATAAATATTTTATTTTAT
*
43560533 TAAATATATATATATATTTTATTTTAT
1 TAAATATA-ATAAATATTTTATTTTAT
43560560 ATTTTGGGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 8 0.32
27 17 0.68
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
TAAATATAATAAATATTTTATTTTAT
Found at i:43563060 original size:46 final size:47
Alignment explanation
Indices: 43562974--43563062 Score: 108
Period size: 46 Copynumber: 1.9 Consensus size: 47
43562964 ATTTTTTTTT
* * *
43562974 ACCTTAAATCTAAAACCCTAAACCCAAAATTCGAATCCCGAACTCGA
1 ACCTTAAATCTAAAACCCTAAACCCAAAATCCCAAACCCGAACTCGA
* * * *
43563021 ACCTTAAA-CTCAAACCTTGAACCTAAAATCCCAAACCCGAAC
1 ACCTTAAATCTAAAACCCTAAACCCAAAATCCCAAACCCGAAC
43563063 ATTGAACCCA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
46 27 0.77
47 8 0.23
ACGTcount: A:0.43, C:0.34, G:0.06, T:0.18
Consensus pattern (47 bp):
ACCTTAAATCTAAAACCCTAAACCCAAAATCCCAAACCCGAACTCGA
Found at i:43563233 original size:31 final size:31
Alignment explanation
Indices: 43563173--43563233 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
43563163 TGTACATTTA
* *
43563173 AAATTTGAATTTTGGTTCATATGTGTACATG
1 AAATTTGAATTTTGATTCATATGTATACATG
43563204 AAATGTTG-ATTTTGATTCA-ATTGTATACAT
1 AAAT-TTGAATTTTGATTCATA-TGTATACAT
43563234 TTAAATAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
30 1 0.04
31 22 0.85
32 3 0.12
ACGTcount: A:0.31, C:0.07, G:0.16, T:0.46
Consensus pattern (31 bp):
AAATTTGAATTTTGATTCATATGTATACATG
Found at i:43565693 original size:13 final size:13
Alignment explanation
Indices: 43565677--43565701 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43565667 TTTTGGGATA
43565677 AAAAGTATTTTTT
1 AAAAGTATTTTTT
43565690 AAAAGTATTTTT
1 AAAAGTATTTTT
43565702 GAGTAAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (13 bp):
AAAAGTATTTTTT
Found at i:43567375 original size:14 final size:15
Alignment explanation
Indices: 43567356--43567384 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
43567346 TTAAAATAAG
43567356 ATTTATTTT-ATTTT
1 ATTTATTTTAATTTT
43567370 ATTTATTTTAATTTT
1 ATTTATTTTAATTTT
43567385 TTTTCATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
ATTTATTTTAATTTT
Found at i:43567672 original size:14 final size:15
Alignment explanation
Indices: 43567653--43567681 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
43567643 TTAAAATAAG
43567653 ATTTATTTT-ATTTT
1 ATTTATTTTAATTTT
43567667 ATTTATTTTAATTTT
1 ATTTATTTTAATTTT
43567682 TTTTCATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
ATTTATTTTAATTTT
Found at i:43567758 original size:297 final size:297
Alignment explanation
Indices: 43567170--43567769 Score: 1175
Period size: 297 Copynumber: 2.0 Consensus size: 297
43567160 TAAAATGAAT
43567170 TAATTATGGTCTAAATTTAAAGTAATGCCTTTTCGAGAGAGAAGGATTCTTTTAATGTTTTGAAA
1 TAATTATGGTCTAAATTTAAAGTAATGCCTTTTCGAGAGAGAAGGATTCTTTTAATGTTTTGAAA
43567235 TTTTGACCATACTTGATCGCATGATAAAATTTCAACTAAAATAACTAATTATATTTTATGTGAAG
66 TTTTGACCATACTTGATCGCATGATAAAATTTCAACTAAAATAACTAATTATATTTTATGTGAAG
43567300 GATAATGATAAAAAAAATATTTAGATAAATTACACCAACATTCACTTTAAAATAAGATTTATTTT
131 GATAATGATAAAAAAAATATTTAGATAAATTACACCAACATTCACTTTAAAATAAGATTTATTTT
43567365 ATTTTATTTATTTTAATTTTTTTTCATTTAGTCATTCAATTAAAATAATTATGCAAAATAGTCAC
196 ATTTTATTTATTTTAATTTTTTTTCATTTAGTCATTCAATTAAAATAATTATGCAAAATAGTCAC
43567430 TTTCGTTAAAAATTTTATTTTCCATTAATGGATTA-C
261 TTTCGTTAAAAATTTTATTTTCCATTAATGGATTACC
*
43567466 TAATTATGGTCTAAATTTAAAGTAATGCCTTTTCGAGAGAGAAGGATTTTTTTAATGTTTTGAAA
1 TAATTATGGTCTAAATTTAAAGTAATGCCTTTTCGAGAGAGAAGGATTCTTTTAATGTTTTGAAA
43567531 TTTTGACCATACTTGATCGCATGATAAAATTTCAACTAAAATAACTAATTATATTTTATGTGAAG
66 TTTTGACCATACTTGATCGCATGATAAAATTTCAACTAAAATAACTAATTATATTTTATGTGAAG
43567596 GATAATGATAAAAAAAAATATTTAGATAAATTACACCAACATTCACTTTAAAATAAGATTTATTT
131 GATAATGAT-AAAAAAAATATTTAGATAAATTACACCAACATTCACTTTAAAATAAGATTTATTT
43567661 TATTTTATTTATTTTAATTTTTTTTCATTTAGTCATTCAATTAAAATAATTATGCAAAATAGTCA
195 TATTTTATTTATTTTAATTTTTTTTCATTTAGTCATTCAATTAAAATAATTATGCAAAATAGTCA
43567726 CTTTCGTTAAAAATTTTATTTTCCATTAATGGATTACC
260 CTTTCGTTAAAAATTTTATTTTCCATTAATGGATTACC
43567764 TAATTA
1 TAATTA
43567770 GCAATCCACG
Statistics
Matches: 301, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
296 138 0.46
297 156 0.52
298 7 0.02
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (297 bp):
TAATTATGGTCTAAATTTAAAGTAATGCCTTTTCGAGAGAGAAGGATTCTTTTAATGTTTTGAAA
TTTTGACCATACTTGATCGCATGATAAAATTTCAACTAAAATAACTAATTATATTTTATGTGAAG
GATAATGATAAAAAAAATATTTAGATAAATTACACCAACATTCACTTTAAAATAAGATTTATTTT
ATTTTATTTATTTTAATTTTTTTTCATTTAGTCATTCAATTAAAATAATTATGCAAAATAGTCAC
TTTCGTTAAAAATTTTATTTTCCATTAATGGATTACC
Found at i:43570601 original size:23 final size:22
Alignment explanation
Indices: 43570546--43570603 Score: 62
Period size: 23 Copynumber: 2.6 Consensus size: 22
43570536 TAAATTTTTA
*
43570546 TTTTAAAAATAAAAATATAATT
1 TTTTAAAAATAAAAATAAAATT
* ***
43570568 GTTTGTTAATAAAAATTAAAATT
1 TTTTAAAAATAAAAA-TAAAATT
43570591 TTTTAAAAATAAA
1 TTTTAAAAATAAA
43570604 TTATATTATA
Statistics
Matches: 26, Mismatches: 9, Indels: 1
0.72 0.25 0.03
Matches are distributed among these distances:
22 11 0.42
23 15 0.58
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (22 bp):
TTTTAAAAATAAAAATAAAATT
Found at i:43571695 original size:28 final size:28
Alignment explanation
Indices: 43571671--43571769 Score: 81
Period size: 31 Copynumber: 3.4 Consensus size: 28
43571661 AGATTTTTCG
*
43571671 TTTAATTTAGAGTTAAATTAATTTTTAA
1 TTTAATTTAAAGTTAAATTAATTTTTAA
* * * *
43571699 TTTTATTTAAATTTAAATTTATTTTAAA
1 TTTAATTTAAAGTTAAATTAATTTTTAA
* * * *
43571727 TTTAAATTTAATTATTTAAATTTACTTTGAA
1 TTT-AATTTAA--AGTTAAATTAATTTTTAA
43571758 TTTAAATTTAAA
1 TTT-AATTTAAA
43571770 TAAAAATTAA
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
28 26 0.43
29 7 0.12
31 27 0.45
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (28 bp):
TTTAATTTAAAGTTAAATTAATTTTTAA
Found at i:43571712 original size:6 final size:6
Alignment explanation
Indices: 43571703--43571793 Score: 78
Period size: 6 Copynumber: 15.0 Consensus size: 6
43571693 TTTTAATTTT
*
43571703 ATTTAA ATTTAA ATTT-A TTTTAA ATTTAA ATTTAA TTATTTAA ATTT-A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA --ATTTAA ATTTAA
* * ** * *
43571751 CTTTGA ATTTAA ATTTAA ATAAAA ATTAAA ACATTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA A-TTTAA ATTTAA
43571794 CATTAAAAAA
Statistics
Matches: 69, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
5 8 0.12
6 51 0.74
7 4 0.06
8 6 0.09
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (6 bp):
ATTTAA
Found at i:43571717 original size:17 final size:17
Alignment explanation
Indices: 43571697--43571770 Score: 71
Period size: 17 Copynumber: 4.2 Consensus size: 17
43571687 ATTAATTTTT
43571697 AATTTTATTTAAATTTA
1 AATTTTATTTAAATTTA
43571714 AA-TTTATTTTAAATTTA
1 AATTTTA-TTTAAATTTA
43571731 AATTTAATTATTTAAATTT-
1 AA-TT--TTATTTAAATTTA
* *
43571750 ACTTTGAATTTAAATTTA
1 AATTT-TATTTAAATTTA
43571768 AAT
1 AAT
43571771 AAAAATTAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 13
0.75 0.05 0.21
Matches are distributed among these distances:
16 5 0.11
17 24 0.51
18 4 0.09
19 2 0.04
20 9 0.19
21 3 0.06
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (17 bp):
AATTTTATTTAAATTTA
Found at i:43573591 original size:25 final size:27
Alignment explanation
Indices: 43573557--43573608 Score: 81
Period size: 25 Copynumber: 2.0 Consensus size: 27
43573547 AGCTGTCACG
43573557 TGTCCCTTTT-TTTTT-ATTTATTTTA
1 TGTCCCTTTTATTTTTAATTTATTTTA
*
43573582 TGTCCCTTTTATTTTTAATTTGTTTTA
1 TGTCCCTTTTATTTTTAATTTATTTTA
43573609 ATTTAATCCC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 10 0.42
26 5 0.21
27 9 0.38
ACGTcount: A:0.13, C:0.12, G:0.06, T:0.69
Consensus pattern (27 bp):
TGTCCCTTTTATTTTTAATTTATTTTA
Found at i:43573958 original size:30 final size:30
Alignment explanation
Indices: 43573926--43574274 Score: 455
Period size: 30 Copynumber: 11.9 Consensus size: 30
43573916 TAAATGTCCA
43573926 AAAATTACATTTTGACCCCAAAACTTTT-C
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* *
43573955 AAAATTACATTTAG-CCCCAAAACTTTTCT
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* * *
43573984 ACAATTATATTTTTGACCTC-AAACTTTTCC
1 AAAATTACA-TTTTGACCCCAAAACTTTTCC
*
43574014 -AAATTACATTTTGACCCTAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
*
43574043 AAAATTACATTTTGACCCTAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
43574073 AAAATTACATTTTGA-CCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* * *
43574102 AAAATTATATTTTGACCCCGAAACTTTACC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
*
43574132 AAAATTACATTTCGACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* * *
43574162 AAAATTACATTTTAACCCCGAAACTTTTTC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
*
43574192 AAAATTACATTTTGACCCCAAAACTTTTCT
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* *
43574222 AAAATTA-TTTTTGACCCCGAAAC--TTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
*
43574249 AAAATTACTATTTT-ACCCCCAAACTT
1 AAAATTAC-ATTTTGACCCCAAAACTT
43574275 CCCTAAATCC
Statistics
Matches: 278, Mismatches: 32, Indels: 19
0.84 0.10 0.06
Matches are distributed among these distances:
27 10 0.04
28 30 0.11
29 81 0.29
30 154 0.55
31 3 0.01
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.36
Consensus pattern (30 bp):
AAAATTACATTTTGACCCCAAAACTTTTCC
Found at i:43574049 original size:59 final size:60
Alignment explanation
Indices: 43573926--43574274 Score: 464
Period size: 59 Copynumber: 5.9 Consensus size: 60
43573916 TAAATGTCCA
* * *
43573926 AAAATTACATTTTGACCCCAAAACTTTT-CAAAATTACATTTAG-CCCCAAAACTTTTCT
1 AAAATTACATTTTGACCCCGAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCC
* * * *
43573984 ACAATTATATTTTTGACCTC-AAACTTTTCC-AAATTACATTTTGACCCTAAAACTTTTCC
1 AAAATTACA-TTTTGACCCCGAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCC
**
43574043 AAAATTACATTTTGACCCTAAAACTTTTCCAAAATTACATTTTGA-CCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCGAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCC
* * *
43574102 AAAATTATATTTTGACCCCGAAACTTTACCAAAATTACATTTCGACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCGAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCC
* * *
43574162 AAAATTACATTTTAACCCCGAAACTTTTTCAAAATTACATTTTGACCCCAAAACTTTTCT
1 AAAATTACATTTTGACCCCGAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCC
* *
43574222 AAAATTA-TTTTTGACCCCGAAAC--TTCCAAAATTACTATTTT-ACCCCCAAACTT
1 AAAATTACATTTTGACCCCGAAACTTTTCCAAAATTAC-ATTTTGACCCCAAAACTT
43574275 CCCTAAATCC
Statistics
Matches: 258, Mismatches: 26, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
57 22 0.09
58 40 0.16
59 107 0.41
60 89 0.34
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.36
Consensus pattern (60 bp):
AAAATTACATTTTGACCCCGAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCC
Found at i:43586285 original size:31 final size:31
Alignment explanation
Indices: 43586250--43586361 Score: 125
Period size: 31 Copynumber: 3.5 Consensus size: 31
43586240 TCTTCATCTC
43586250 TGAAATTGAAGTAAGAGCAACGTCATCCCCT
1 TGAAATTGAAGTAAGAGCAACGTCATCCCCT
** * **
43586281 TGAAATTGAAGTAGAAGGATAACACGTCTTTACCT
1 TGAAATTGAAGT--AA-GAGCA-ACGTCATCCCCT
*
43586316 CTGAAATTGAAGTAAGAGCAACGTCATCCTCT
1 -TGAAATTGAAGTAAGAGCAACGTCATCCCCT
43586348 TGAAATTGAAGTAA
1 TGAAATTGAAGTAA
43586362 AGTTGGATAA
Statistics
Matches: 65, Mismatches: 11, Indels: 10
0.76 0.13 0.12
Matches are distributed among these distances:
31 26 0.40
32 8 0.12
33 5 0.08
34 5 0.08
35 9 0.14
36 12 0.18
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.26
Consensus pattern (31 bp):
TGAAATTGAAGTAAGAGCAACGTCATCCCCT
Found at i:43586679 original size:145 final size:144
Alignment explanation
Indices: 43586213--43587246 Score: 1389
Period size: 145 Copynumber: 7.3 Consensus size: 144
43586203 TCCAATCCGC
* * * * *
43586213 TGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCATCC
1 TGAAATTGAAGTAAACTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATCC
* * * * * * *
43586278 CCTTGAAATTGAAGTAGA--AGGATAACACGTCTTTACCTCTGAAATTGAAGTA--AG-AGCAAC
66 TCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAGGAGTAACATC
43586338 G--T-C-ATCCTCT
131 GTTTCCTATCCTCT
* * * * *
43586348 TGAAATTGAAGTAAAGTTGGATAACAAGTCTTCATCTC---AATTGAAGTAAGAAAAACATCGTT
1 TGAAATTGAAGTAAA-CTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAG---AGCAACG--
* * * * *
43586410 TCCTAT-CTCTTGAAATTGAAGTAAAATTGGATATCACGTCTTTATCTCTGAAATTGAAGTA--A
60 T-C-ATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAGGA
* *
43586472 G-AGCAACG--T-C-ATCC-CT
123 GTAACATCGTTTCCTATCCTCT
* * * * *
43586488 TGAAATTGAAGTAGAGTGGATAACACGTCCTTATCTCTGAAATTGAAGTAAGAGCAACGTCATCC
1 TGAAATTGAAGTAAACTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATCC
*
43586553 TCTCGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAGGAGTAACATC
66 TCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAGGAGTAACATC
43586618 GTTTCCTATCCTCT
131 GTTTCCTATCCTCT
43586632 TGAAATTGAAGTATAACTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATC
1 TGAAATTGAAGTA-AACTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATC
43586697 CTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAGGAGTAACAT
65 CTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAGGAGTAACAT
43586762 CGTTTCCTATCCTCT
130 CGTTTCCTATCCTCT
43586777 TGAAATTGAAGTATAACTGGATATCAAGTCTTTATCTCTGAAATTGAAG-AA-AG--ACGTCATC
1 TGAAATTGAAGTA-AACTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATC
43586838 CTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAGGAGTAACAT
65 CTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAGGAGTAACAT
43586903 CGTTTCCTATCCTCT
130 CGTTTCCTATCCTCT
43586918 TGAAATTGAAGTATAACTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATC
1 TGAAATTGAAGTA-AACTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATC
*
43586983 CTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGCAGGAGTAACAT
65 CTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAGGAGTAACAT
43587048 CGTTTCCTATCCTCT
130 CGTTTCCTATCCTCT
43587063 TGAAATTGAAGTATAACTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATC
1 TGAAATTGAAGTA-AACTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATC
* * * * * * *
43587128 CTCTTGAAATTGAAGTAGAGTTGGATAACACGCCTTTATCTCTGAAATTGAAATAAGAGCAAGAT
65 CTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAGGAGTAACAT
*
43587193 CATTTCCTATCCTCT
130 CGTTTCCTATCCTCT
* * *
43587208 AGAAATTGAAGTAAAGTTGGATAGTAAAGTCTTTATCTC
1 TGAAATTGAAGTAAA-CTGGATA-TCAAGTCTTTATCTC
43587247 CCTGAAGAGC
Statistics
Matches: 826, Mismatches: 44, Indels: 47
0.90 0.05 0.05
Matches are distributed among these distances:
133 12 0.01
135 16 0.02
136 75 0.09
137 1 0.00
138 3 0.00
139 46 0.06
140 18 0.02
141 184 0.22
142 15 0.02
143 8 0.01
144 19 0.02
145 415 0.50
146 14 0.02
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (144 bp):
TGAAATTGAAGTAAACTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATCC
TCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAGGAGTAACATC
GTTTCCTATCCTCT
Found at i:43586872 original size:286 final size:288
Alignment explanation
Indices: 43586213--43587246 Score: 1373
Period size: 286 Copynumber: 3.6 Consensus size: 288
43586203 TCCAATCCGC
* * * *
43586213 TGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCATCC
1 TGAAATTGAAGTAAACTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAG-AACGTCATCC
* * * * * * *
43586278 CCTTGAAATTGAAGTAGA--AGGATAACACGTCTTTACCTCTGAAATTGAAGTA--AG-AGCAAC
65 TCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAGGAGTAACATC
* * *
43586338 G--T-C-ATCCTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTCATCTC---AATTGAAGTA
130 GTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
* * * * * * *
43586396 AGAAAAACATCGTTTCCTAT-CTCTTGAAATTGAAGTAAAATTGGATATCACGTCTTTATCTCTG
195 AG---AGCAACG--T-C-ATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTG
* *
43586460 AAATTGAAGTA--AG-AGCAACG--T-C-ATCC-CT
253 AAATTGAAGTAGGAGTAACATCGTTTCCTATCCTCT
* * * *
43586488 TGAAATTGAAGTAGAGTGGATAACACGTCCTTATCTCTGAAATTGAAGTAAGAGCAACGTCATCC
1 TGAAATTGAAGTAAACTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAG-AACGTCATCC
*
43586553 TCTCGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAGGAGTAACATC
65 TCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAGGAGTAACATC
43586618 GTTTCCTATCCTCTTGAAATTGAAGTATAA-CTGGATATCAAGTCTTTATCTCTGAAATTGAAGT
130 GTTTCCTATCCTCTTGAAATTGAAGTA-AAGCTGGATATCAAGTCTTTATCTCTGAAATTGAAGT
43586682 AAGAGCAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTG
194 AAGAGCAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTG
43586747 AAGTAGGAGTAACATCGTTTCCTATCCTCT
259 AAGTAGGAGTAACATCGTTTCCTATCCTCT
*
43586777 TGAAATTGAAGTATAACTGGATATCAAGTCTTTATCTCTGAAATTGAAG-AA-AG-ACGTCATCC
1 TGAAATTGAAGTA-AACTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGAACGTCATCC
43586839 TCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAGGAGTAACATC
65 TCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAGGAGTAACATC
43586904 GTTTCCTATCCTCTTGAAATTGAAGTATAA-CTGGATATCAAGTCTTTATCTCTGAAATTGAAGT
130 GTTTCCTATCCTCTTGAAATTGAAGTA-AAGCTGGATATCAAGTCTTTATCTCTGAAATTGAAGT
43586968 AAGAGCAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTG
194 AAGAGCAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTG
*
43587033 AAGCAGGAGTAACATCGTTTCCTATCCTCT
259 AAGTAGGAGTAACATCGTTTCCTATCCTCT
*
43587063 TGAAATTGAAGTATAACTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATC
1 TGAAATTGAAGTA-AACTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAG-AACGTCATC
* * * * * * *
43587128 CTCTTGAAATTGAAGTAGAGTTGGATAACACGCCTTTATCTCTGAAATTGAAATAAGAGCAAGAT
64 CTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAGGAGTAACAT
* * * *
43587193 CATTTCCTATCCTCTAGAAATTGAAGTAAAGTTGGATAGTAAAGTCTTTATCTC
129 CGTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATA-TCAAGTCTTTATCTC
43587247 CCTGAAGAGC
Statistics
Matches: 690, Mismatches: 40, Indels: 42
0.89 0.05 0.05
Matches are distributed among these distances:
275 79 0.11
277 30 0.04
279 2 0.00
280 7 0.01
281 51 0.07
282 2 0.00
283 3 0.00
284 49 0.07
285 2 0.00
286 281 0.41
287 15 0.02
288 8 0.01
289 19 0.03
290 128 0.19
291 14 0.02
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (288 bp):
TGAAATTGAAGTAAACTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGAACGTCATCCT
CTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAGGAGTAACATCG
TTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAA
GAGCAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAA
GTAGGAGTAACATCGTTTCCTATCCTCT
Found at i:43587043 original size:431 final size:424
Alignment explanation
Indices: 43586213--43587246 Score: 1441
Period size: 431 Copynumber: 2.4 Consensus size: 424
43586203 TCCAATCCGC
* * * * *
43586213 TGAAATTGAAGTA-GAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCATC
1 TGAAATTGAAGTATAACTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATC
* * * * *
43586277 CCCTTGAAATTGAAGTAGA--AGGATAACACGTCTTTACCTCTGAAATTGAAGTA-AGAGCAACG
66 CTCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTTATCTCTGAAATTGAAGTAGAGAACATCG
* * *
43586339 --T-C-ATCCTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTCATCTCAATTGAAGTAAGAA
131 TTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCTC-A-TGAAATAAGAA
* * *
43586400 AAACATCGTTTCCTATCTCTTGAAATTGAAGTAAAATTGGATATCACGTCTTTATCTCTGAAATT
194 AAACATCG-TTCCTATCTCTTGAAATTGAAGTAAAATTGGATAACAAGTCTTCATCTCTGAAATT
* * * *
43586465 GAAGTAAGAGCAACGTCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCCTTATCTCTGAAA
258 GAAGTAAGAACAACGTCATCCCTTGAAATTGAAGTAAACTGGATAACAAGTCCTTATCTCTGAAA
43586530 TTGAAGTAAGAGCAACGTCATCCTCTCGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCT
323 TTGAAGTAAGAGCAACGTCATCCTCTCGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCT
*
43586595 GAAATTGAAGTAGGAGTAACATCGTTTCCTATCCTCT
388 GAAATTGAAGCAGGAGTAACATCGTTTCCTATCCTCT
43586632 TGAAATTGAAGTATAACTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATC
1 TGAAATTGAAGTATAACTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATC
* *
43586697 CTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAGGAGTAACAT
66 CTCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTTATCTCTGAAATTGAAGTA-GAG-AACAT
* *
43586762 CGTTTCCTATCCTCTTGAAATTGAAGTATAA-CTGGATATCAAGTCTTTATCTC-TGAAAT-TGA
129 CGTTTCCTATCCTCTTGAAATTGAAGTA-AAGTTGGATATCAAGTCTTTATCTCATGAAATAAGA
* * *
43586824 AGAAAGA-CG-T-C-ATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAA
193 A-AAACATCGTTCCTAT-CTCTTGAAATTGAAGTAAAATTGGATAACAAGTCTTCATCTCTGAAA
* * *
43586885 TTGAAGTAGGAGTAACATCGTTTCCTATCCTCTTGAAATTGAAGTATAACTGGATATCAAGTCTT
256 TTGAAGTA--AG-AACAACG--T-C-ATCC-CTTGAAATTGAAGTA-AACTGGATAACAAGTCCT
*
43586950 TATCTCTGAAATTGAAGTAAGAGCAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAG
312 TATCTCTGAAATTGAAGTAAGAGCAACGTCATCCTCTCGAAATTGAAGTAGAGTTGGATAACAAG
43587015 TCTTCATCTCTGAAATTGAAGCAGGAGTAACATCGTTTCCTATCCTCT
377 TCTTCATCTCTGAAATTGAAGCAGGAGTAACATCGTTTCCTATCCTCT
43587063 TGAAATTGAAGTATAACTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATC
1 TGAAATTGAAGTATAACTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATC
* * *
43587128 CTCTTGAAATTGAAGTAGAGTTGGATAACACGCCTTTATCTCTGAAATTGAAATAAGAGCAAGAT
66 CTCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTTATCTCTGAAATTGAAGT-AGAG-AACAT
* * *
43587193 CATTTCCTATCCTCTAGAAATTGAAGTAAAGTTGGATAGTAAAGTCTTTATCTC
129 CGTTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATA-TCAAGTCTTTATCTC
43587247 CCTGAAGAGC
Statistics
Matches: 548, Mismatches: 42, Indels: 37
0.87 0.07 0.06
Matches are distributed among these distances:
419 13 0.02
420 64 0.12
421 2 0.00
422 81 0.15
423 1 0.00
424 4 0.01
425 15 0.03
426 9 0.02
427 2 0.00
428 2 0.00
429 43 0.08
430 19 0.03
431 278 0.51
432 15 0.03
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (424 bp):
TGAAATTGAAGTATAACTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATC
CTCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTTATCTCTGAAATTGAAGTAGAGAACATCG
TTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCTCATGAAATAAGAAAA
ACATCGTTCCTATCTCTTGAAATTGAAGTAAAATTGGATAACAAGTCTTCATCTCTGAAATTGAA
GTAAGAACAACGTCATCCCTTGAAATTGAAGTAAACTGGATAACAAGTCCTTATCTCTGAAATTG
AAGTAAGAGCAACGTCATCCTCTCGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAA
ATTGAAGCAGGAGTAACATCGTTTCCTATCCTCT
Found at i:43587556 original size:28 final size:28
Alignment explanation
Indices: 43587524--43587578 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
43587514 TTTTCGTTTA
* *
43587524 ATTTAGAGTTAAATTGATTTTTAATTTT
1 ATTTAAAGTTAAATTGATTTTAAATTTT
* *
43587552 ATTTAAATTTAAATTTATTTTAAATTT
1 ATTTAAAGTTAAATTGATTTTAAATTT
43587579 AAATTTAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.58
Consensus pattern (28 bp):
ATTTAAAGTTAAATTGATTTTAAATTTT
Found at i:43587561 original size:6 final size:6
Alignment explanation
Indices: 43587552--43587642 Score: 78
Period size: 6 Copynumber: 15.0 Consensus size: 6
43587542 TTTTAATTTT
* *
43587552 ATTTAA ATTTAA ATTT-A TTTTAA ATTTAA ATTTAA TTATTAAA ATTT-A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA --ATTTAA ATTTAA
* ** * *
43587600 CTTTAA ATTTAA ATTTAA ATAAAA ATTAAA ACATTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA A-TTTAA ATTTAA
43587643 CATTAAAAAA
Statistics
Matches: 68, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
5 8 0.12
6 51 0.75
7 4 0.06
8 5 0.07
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (6 bp):
ATTTAA
Found at i:43587573 original size:17 final size:16
Alignment explanation
Indices: 43587543--43587616 Score: 89
Period size: 17 Copynumber: 4.6 Consensus size: 16
43587533 TAAATTGATT
*
43587543 TTTAATTTTATTTAAA
1 TTTAAATTTATTTAAA
43587559 TTTAAATTTATTTTAAA
1 TTTAAATTTA-TTTAAA
*
43587576 TTTAAATTTAATT--A
1 TTTAAATTTATTTAAA
*
43587590 TTAAAATTTACTTTAAA
1 TTTAAATTTA-TTTAAA
43587607 TTTAAATTTA
1 TTTAAATTTA
43587617 AATAAAAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
14 10 0.20
15 2 0.04
16 11 0.22
17 26 0.53
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTAAATTTATTTAAA
Found at i:43587637 original size:31 final size:30
Alignment explanation
Indices: 43587571--43587642 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 30
43587561 TAAATTTATT
* * *
43587571 TTAAATTTAAATTTAATTATTAAAATTTACT
1 TTAAATTTAAATTTAA-TATAAAAATTAACA
43587602 TTAAATTTAAATTTAA-ATAAAAATTAAAACA
1 TTAAATTTAAATTTAATATAAAAATT--AACA
43587633 TTAAATTTAA
1 TTAAATTTAA
43587643 CATTAAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 8 0.22
31 28 0.78
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (30 bp):
TTAAATTTAAATTTAATATAAAAATTAACA
Found at i:43588526 original size:10 final size:10
Alignment explanation
Indices: 43588497--43588540 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
43588487 ATATTTTTGG
*
43588497 TAATAGTAAA
1 TAATAATAAA
*
43588507 TAAATAATAAT
1 T-AATAATAAA
*
43588518 TATTAATAAA
1 TAATAATAAA
43588528 TAATAATAAA
1 TAATAATAAA
43588538 TAA
1 TAA
43588541 GTAAAGAGAG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
10 20 0.71
11 8 0.29
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (10 bp):
TAATAATAAA
Found at i:43589668 original size:162 final size:163
Alignment explanation
Indices: 43589391--43589684 Score: 457
Period size: 162 Copynumber: 1.8 Consensus size: 163
43589381 TTTTAATTTA
* * * *
43589391 ATCCTTTGACTGTTTGACTACATCAGAAGCTGCCATGTGTCACTTTTTTGGTTTATTTATGCATT
1 ATCCTTTAACTGTTTGACTACACCAGAAGCTGCCACGTGTCACTTTTTTGGTCTATTTATGCATT
* * *
43589456 TAGTCCCTTTTATTTTTAATTTGTTTTAATTTAATCCCTAAATCAACTTTTGTTTAATTACAAAA
66 TAGTCCCTTTTATTTCTAATTTGTTTTAATTTAATCCCTAAATCAACTTTTATTTAATTAAAAAA
43589521 TTAGCCCAAGAATTTTTCAAGGTTTATAAATTC
131 TTAGCCCAAGAATTTTTCAAGGTTTATAAATTC
* *
43589554 ATCCTTTAACTGTTTGACTGCACCAGAAGCTGCCACGTGTCAC-TTTTTGGTCTATTTATGTATT
1 ATCCTTTAACTGTTTGACTACACCAGAAGCTGCCACGTGTCACTTTTTTGGTCTATTTATGCATT
* * *
43589618 TAGT-CCTTTCTATTTCTAATTTGTTTTAATTTAGTCCTTAAATTAACTTTTATTTAATTAAAAA
66 TAGTCCCTTT-TATTTCTAATTTGTTTTAATTTAATCCCTAAATCAACTTTTATTTAATTAAAAA
43589682 ATT
130 ATT
43589685 GGTCCAAATT
Statistics
Matches: 118, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
161 5 0.04
162 74 0.63
163 39 0.33
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.47
Consensus pattern (163 bp):
ATCCTTTAACTGTTTGACTACACCAGAAGCTGCCACGTGTCACTTTTTTGGTCTATTTATGCATT
TAGTCCCTTTTATTTCTAATTTGTTTTAATTTAATCCCTAAATCAACTTTTATTTAATTAAAAAA
TTAGCCCAAGAATTTTTCAAGGTTTATAAATTC
Found at i:43589836 original size:30 final size:30
Alignment explanation
Indices: 43589800--43590124 Score: 467
Period size: 30 Copynumber: 10.9 Consensus size: 30
43589790 AAATTGTCCA
*
43589800 AAAATTACATTTTGACCCTAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
*
43589830 AAAATTACATTTTGACCCCAAAACTTTTCT
1 AAAATTACATTTTGACCCCAAAACTTTTCC
*
43589860 AAAATTACATTTTGACCCTAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
*
43589890 AAAATTACATTTTGACCCTAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* * *
43589920 AAAATTATATTTTAACCCCAAAACTTTACC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
*
43589950 AAAATTACATTTCGACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* *
43589980 ATAATTACATTTTGACCCCAAAACTTTTTC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* *
43590010 AAAATTACATTTTGACCCCGAAACTTTTCA
1 AAAATTACATTTTGACCCCAAAACTTTTCC
*
43590040 AAAATTACATTTTGACCCCAAAACTTTTCT
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* *
43590070 AAAATTATATTTTGACCCCGAAAC--TTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
*
43590098 AAAAATTACTATTTT-ACCCCCAAACTT
1 -AAAATTAC-ATTTTGACCCCAAAACTT
43590125 CCCTAAATCC
Statistics
Matches: 265, Mismatches: 26, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
28 3 0.01
29 16 0.06
30 246 0.93
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.35
Consensus pattern (30 bp):
AAAATTACATTTTGACCCCAAAACTTTTCC
Found at i:43593020 original size:39 final size:39
Alignment explanation
Indices: 43592976--43593087 Score: 161
Period size: 39 Copynumber: 2.9 Consensus size: 39
43592966 CCACATTAGG
*
43592976 AATATACTGAACTGGTAGTGACACTATAAACACTACGAT
1 AATATACTGAACTGGTAGTGACACTGTAAACACTACGAT
* * *
43593015 GATATACTGAACTGGCAGTGACACTGTAAACACTGCGAT
1 AATATACTGAACTGGTAGTGACACTGTAAACACTACGAT
* * *
43593054 AACATACTAAACTGGTAGTGACATTGTAAACACT
1 AATATACTGAACTGGTAGTGACACTGTAAACACT
43593088 GAAGTTGCTA
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 64 1.00
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (39 bp):
AATATACTGAACTGGTAGTGACACTGTAAACACTACGAT
Found at i:43593140 original size:79 final size:79
Alignment explanation
Indices: 43592978--43593167 Score: 203
Period size: 79 Copynumber: 2.4 Consensus size: 79
43592968 ACATTAGGAA
* * * * *
43592978 TATACTGAACTGGTAGTGACACTATAAACACTACGATGATATACTGAACTGGCAGTGACACTGTA
1 TATACTAAACTGGTAGTGACATTGTAAACACTAAGATGATATACCGAACTGGCAGTGACACTGTA
43593043 AACACTGCGATAAC
66 AACACTGCGATAAC
* * *
43593057 -ATACTAAACTGGTAGTGACATTGTAAACACTGAAGTTGCTATACCGAACTGGC-GATGACATTG
1 TATACTAAACTGGTAGTGACATTGTAAACACT-AAGATGATATACCGAACTGGCAG-TGACACTG
43593120 TAAACA-T-CGCA-AAGC
64 TAAACACTGCG-ATAA-C
* *
43593135 TATACTGAAGCT-GTAGTGAGATTGTAAACACTA
1 TATACT-AAACTGGTAGTGACATTGTAAACACTA
43593168 CAGGCTGTTA
Statistics
Matches: 95, Mismatches: 10, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
77 4 0.04
78 33 0.35
79 54 0.57
80 4 0.04
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.25
Consensus pattern (79 bp):
TATACTAAACTGGTAGTGACATTGTAAACACTAAGATGATATACCGAACTGGCAGTGACACTGTA
AACACTGCGATAAC
Found at i:43600102 original size:62 final size:62
Alignment explanation
Indices: 43600025--43600148 Score: 169
Period size: 62 Copynumber: 2.0 Consensus size: 62
43600015 AAACTTATTT
* * * *
43600025 ATTGGGCCTAAATTTTTTTTTTCAGTTACAATTTTT-TATTTTTTAAAACTTATAATAAATTA
1 ATTGGGCCTAAATTTTTTTTATCAATTAAAATTTTTCAATTTTTT-AAACTTATAATAAATTA
* * *
43600087 ATTGGGCCTTAATTTTTTTTATCAATTAAAATTTTTCAATTTTTTTAACTTATAATATATTA
1 ATTGGGCCTAAATTTTTTTTATCAATTAAAATTTTTCAATTTTTTAAACTTATAATAAATTA
43600149 CTTATCTTCA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
62 47 0.87
63 7 0.13
ACGTcount: A:0.32, C:0.08, G:0.06, T:0.54
Consensus pattern (62 bp):
ATTGGGCCTAAATTTTTTTTATCAATTAAAATTTTTCAATTTTTTAAACTTATAATAAATTA
Found at i:43605054 original size:12 final size:12
Alignment explanation
Indices: 43605039--43605072 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
43605029 TCGTTTAAAA
43605039 GCTCGTTTATTG
1 GCTCGTTTATTG
43605051 GCTCGTTTA-TG
1 GCTCGTTTATTG
*
43605062 ACTCGTTTATT
1 GCTCGTTTATT
43605073 TATTAATGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.12, C:0.18, G:0.21, T:0.50
Consensus pattern (12 bp):
GCTCGTTTATTG
Found at i:43605200 original size:24 final size:23
Alignment explanation
Indices: 43605173--43605226 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 23
43605163 ACATTTTTCG
43605173 TGAACATGTTCAATTATATATTCA
1 TGAACATGTTCAATTA-ATATTCA
* * *
43605197 TGAACATGTTCATTTAATGTTCG
1 TGAACATGTTCAATTAATATTCA
43605220 TGAACAT
1 TGAACAT
43605227 TAAACAAACG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 12 0.44
24 15 0.56
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (23 bp):
TGAACATGTTCAATTAATATTCA
Found at i:43614456 original size:39 final size:39
Alignment explanation
Indices: 43614413--43614553 Score: 165
Period size: 39 Copynumber: 3.6 Consensus size: 39
43614403 CTGAACTCGC
* *
43614413 AGTGACATTGTAAACATTGTAATGGCATACTAAACTGGT
1 AGTGACACTGTAAACATTGCAATGGCATACTAAACTGGT
* * * * * * *
43614452 AGTGACACAGTTAACACTGCGATGTCATACCAAACTGAT
1 AGTGACACTGTAAACATTGCAATGGCATACTAAACTGGT
* * *
43614491 AGTGACACTGTAAACATCGCAATGGTATACTGAACTGGT
1 AGTGACACTGTAAACATTGCAATGGCATACTAAACTGGT
*
43614530 AGTGACACTGTAAACACTGCAATG
1 AGTGACACTGTAAACATTGCAATG
43614554 CTATATTGGA
Statistics
Matches: 81, Mismatches: 21, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
39 81 1.00
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (39 bp):
AGTGACACTGTAAACATTGCAATGGCATACTAAACTGGT
Found at i:43614567 original size:39 final size:39
Alignment explanation
Indices: 43614400--43614567 Score: 137
Period size: 39 Copynumber: 4.3 Consensus size: 39
43614390 CCTTAGAAGA
* * * * *
43614400 ATACTGAACTCGCAGTGACATTGTAAACATTGTAATGGC-
1 ATACTGAACTGGTAGTGACACTGTAAACATCGCAAT-GCT
* * * *
43614439 ATACTAAACTGGTAGTGACACAGTTAACA-CTGCGATG-T
1 ATACTGAACTGGTAGTGACACTGTAAACATC-GCAATGCT
** * *
43614477 CATACCAAACTGATAGTGACACTGTAAACATCGCAATGGT
1 -ATACTGAACTGGTAGTGACACTGTAAACATCGCAATGCT
43614517 ATACTGAACTGGTAGTGACACTGTAAACA-CTGCAATGCT
1 ATACTGAACTGGTAGTGACACTGTAAACATC-GCAATGCT
* *
43614556 ATATTGGACTGG
1 ATACTGAACTGG
43614568 CGATAACACT
Statistics
Matches: 103, Mismatches: 20, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
38 2 0.02
39 99 0.96
40 2 0.02
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (39 bp):
ATACTGAACTGGTAGTGACACTGTAAACATCGCAATGCT
Found at i:43614577 original size:39 final size:39
Alignment explanation
Indices: 43614495--43614591 Score: 99
Period size: 39 Copynumber: 2.5 Consensus size: 39
43614485 ACTGATAGTG
* * *
43614495 ACACTGTAAACATCGCAATGGTATACTGAACTGGTAGTG
1 ACACTGTAAACATCGCAATGCTATACTGAACTGGGAGTA
* *
43614534 ACACTGTAAACA-CTGCAATGCTATATTGGACTGGCGA-TA
1 ACACTGTAAACATC-GCAATGCTATACTGAACTGG-GAGTA
* *
43614573 ACACTATAAATATCGCAAT
1 ACACTGTAAACATCGCAAT
43614592 ACTCTACTAA
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
38 1 0.02
39 45 0.94
40 2 0.04
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.26
Consensus pattern (39 bp):
ACACTGTAAACATCGCAATGCTATACTGAACTGGGAGTA
Found at i:43616554 original size:7 final size:8
Alignment explanation
Indices: 43616532--43616569 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
43616522 AAATATTTTA
43616532 TTATATTT
1 TTATATTT
43616540 TTATATTT
1 TTATATTT
43616548 TTA-ATTT
1 TTATATTT
*
43616555 TATATAATT
1 T-TATATTT
43616564 TTATAT
1 TTATAT
43616570 AATTTCTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
7 5 0.19
8 17 0.65
9 4 0.15
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (8 bp):
TTATATTT
Found at i:43616568 original size:10 final size:10
Alignment explanation
Indices: 43616549--43616605 Score: 64
Period size: 10 Copynumber: 5.6 Consensus size: 10
43616539 TTTATATTTT
43616549 TAATTTTATA
1 TAATTTTATA
43616559 TAATTTTATA
1 TAATTTTATA
*
43616569 TAATTTCT-TT
1 TAATTT-TATA
43616579 TAATTTTATA
1 TAATTTTATA
43616589 TTAATTTTGA-A
1 -TAATTTT-ATA
43616600 TAATTT
1 TAATTT
43616606 GTAATTACAA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
9 1 0.02
10 30 0.73
11 9 0.22
12 1 0.02
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (10 bp):
TAATTTTATA
Found at i:43616581 original size:30 final size:31
Alignment explanation
Indices: 43616546--43616605 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
43616536 ATTTTTATAT
43616546 TTTTAATTTTATA-TAATTTT-ATATAATTTC
1 TTTTAATTTTATATTAATTTTGA-ATAATTTC
43616576 TTTTAATTTTATATTAATTTTGAATAATTT
1 TTTTAATTTTATATTAATTTTGAATAATTT
43616606 GTAATTACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
30 13 0.46
31 14 0.50
32 1 0.04
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (31 bp):
TTTTAATTTTATATTAATTTTGAATAATTTC
Found at i:43616740 original size:17 final size:17
Alignment explanation
Indices: 43616704--43616742 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
43616694 TTTATATATA
* *
43616704 ATTTTAAAATTTTCATT
1 ATTTTAAAATTTTAAAT
*
43616721 ATTTTAACATTTTAAAT
1 ATTTTAAAATTTTAAAT
43616738 ATTTT
1 ATTTT
43616743 TTTACAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTAAAATTTTAAAT
Found at i:43616946 original size:17 final size:17
Alignment explanation
Indices: 43616921--43616964 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
43616911 TCAATTCTTT
*
43616921 TATATTTTTATAATTTA
1 TATAATTTTATAATTTA
* *
43616938 TATAATTTTGTCATTTA
1 TATAATTTTATAATTTA
43616955 TACTAATTTT
1 TA-TAATTTT
43616965 CTATAAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (17 bp):
TATAATTTTATAATTTA
Found at i:43622578 original size:21 final size:21
Alignment explanation
Indices: 43622554--43622605 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
43622544 TTGCAAAAAA
*
43622554 ATTAGGCTCGTCTAAAATTGG
1 ATTAGGCTCATCTAAAATTGG
43622575 ATTAGGCTCATCTAAAATTGG
1 ATTAGGCTCATCTAAAATTGG
43622596 ATTAGGCTCA
1 ATTAGGCTCA
43622606 AGCTCAAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (21 bp):
ATTAGGCTCATCTAAAATTGG
Found at i:43624723 original size:15 final size:15
Alignment explanation
Indices: 43624687--43624728 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
43624677 GGGGTCAAAA
*
43624687 TAAAATTTT-ACTTT
1 TAAAATTTTAAATTT
*
43624701 TATTAATTTTAAATTT
1 TA-AAATTTTAAATTT
43624717 TAAAATTTTAAA
1 TAAAATTTTAAA
43624729 AGGGTTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 2 0.09
15 15 0.65
16 6 0.26
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (15 bp):
TAAAATTTTAAATTT
Found at i:43626302 original size:20 final size:22
Alignment explanation
Indices: 43626259--43626307 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
43626249 TCCCTAAAAT
*
43626259 AAACAATATTGATCTATTTCTA
1 AAACAATATTGATATATTTCTA
*
43626281 AAACAAT-TT-ATATATTTTTA
1 AAACAATATTGATATATTTCTA
*
43626301 AAGCAAT
1 AAACAAT
43626308 GTACATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 15 0.62
21 2 0.08
22 7 0.29
ACGTcount: A:0.45, C:0.10, G:0.04, T:0.41
Consensus pattern (22 bp):
AAACAATATTGATATATTTCTA
Found at i:43629817 original size:31 final size:28
Alignment explanation
Indices: 43629757--43629821 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
43629747 TTTCGTATAA
* *
43629757 TTTGTAATATTATATATTAATTTTGATT
1 TTTGTATTTTTATATATTAATTTTGATT
*
43629785 TTGTGTATTTTTATATATTAAATTTTTTATT
1 TT-TGTATTTTTATATATT-AA-TTTTGATT
43629816 TTTGTA
1 TTTGTA
43629822 AATTATTAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
28 2 0.06
29 14 0.45
30 6 0.19
31 9 0.29
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.65
Consensus pattern (28 bp):
TTTGTATTTTTATATATTAATTTTGATT
Found at i:43638812 original size:33 final size:33
Alignment explanation
Indices: 43638765--43638830 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
43638755 ATCCCGACTT
43638765 TTTAAAATTCTTTTGCAAGTGACTTAAAAGAGA
1 TTTAAAATTCTTTTGCAAGTGACTTAAAAGAGA
* * * *
43638798 TTTAAAGTTTTTTTGCAATTGAGTTAAAAGAGA
1 TTTAAAATTCTTTTGCAAGTGACTTAAAAGAGA
43638831 CTCTTTTTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.39
Consensus pattern (33 bp):
TTTAAAATTCTTTTGCAAGTGACTTAAAAGAGA
Found at i:43643291 original size:30 final size:29
Alignment explanation
Indices: 43643252--43643319 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 29
43643242 ATAATATAAA
* * *
43643252 ATTAAAAATAACTTTAGTTTAATGTGTAAT
1 ATTATAAATAAATTTAGTTT-ATATGTAAT
* *
43643282 ATTATAAATAAATTTTGTTTTTATGTAAT
1 ATTATAAATAAATTTAGTTTATATGTAAT
*
43643311 TTTATAAAT
1 ATTATAAAT
43643320 GATATTTTGA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 15 0.47
30 17 0.53
ACGTcount: A:0.41, C:0.01, G:0.07, T:0.50
Consensus pattern (29 bp):
ATTATAAATAAATTTAGTTTATATGTAAT
Found at i:43645759 original size:16 final size:18
Alignment explanation
Indices: 43645740--43645774 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
43645730 TTACATTGAA
43645740 TAATATAAT-AA-ATTAT
1 TAATATAATCAATATTAT
43645756 TAATATAATCAATATTAT
1 TAATATAATCAATATTAT
43645774 T
1 T
43645775 TATTTTTACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 2 0.12
18 6 0.35
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
TAATATAATCAATATTAT
Found at i:43645853 original size:19 final size:19
Alignment explanation
Indices: 43645809--43645870 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
43645799 TTACAATTCT
43645809 ATTTTAATAATAAATTTT-A
1 ATTTTAATAAT-AATTTTAA
*
43645828 ATATTAATAATAATTTTAA
1 ATTTTAATAATAATTTTAA
*
43645847 ATTTT-A-AATATTTTTAA
1 ATTTTAATAATAATTTTAA
43645864 TATTTTA
1 -ATTTTA
43645871 TTGAAAATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
17 10 0.27
18 12 0.32
19 15 0.41
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTTTAATAATAATTTTAA
Found at i:43645861 original size:17 final size:18
Alignment explanation
Indices: 43645821--43645870 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
43645811 TTTAATAATA
*
43645821 AATTTTAATA-TTAATAAT
1 AATTTTAATATTTTA-AAT
43645839 AATTTTAA-ATTTTAAAT
1 AATTTTAATATTTTAAAT
*
43645856 ATTTTTAATATTTTA
1 AATTTTAATATTTTA
43645871 TTGAAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 11 0.39
18 17 0.61
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AATTTTAATATTTTAAAT
Found at i:43645864 original size:26 final size:24
Alignment explanation
Indices: 43645819--43645870 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
43645809 ATTTTAATAA
43645819 TAAATTTTAATATTAATAATAATTT
1 TAAATTTTAATATTAATAAT-ATTT
**
43645844 TAAATTTTAAATATTTTTAATATTT
1 TAAATTTT-AATATTAATAATATTT
43645869 TA
1 TA
43645871 TTGAAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 14 0.58
26 10 0.42
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TAAATTTTAATATTAATAATATTT
Found at i:43645865 original size:9 final size:9
Alignment explanation
Indices: 43645823--43645869 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
43645813 TAATAATAAA
43645823 TTTTAATAT
1 TTTTAATAT
** *
43645832 TAATAATAA
1 TTTTAATAT
43645841 TTTTAA-AT
1 TTTTAATAT
*
43645849 TTTAAATAT
1 TTTTAATAT
43645858 TTTTAATAT
1 TTTTAATAT
43645867 TTT
1 TTT
43645870 ATTGAAAATA
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
8 6 0.21
9 23 0.79
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
TTTTAATAT
Found at i:43646511 original size:21 final size:20
Alignment explanation
Indices: 43646468--43646514 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
43646458 CATTAAATTA
*
43646468 AAAAAATAAATCTTAGTTTT
1 AAAAAATAAATCTTAATTTT
43646488 AAAAAATAAATC-TAATTATCT
1 AAAAAATAAATCTTAATT-T-T
43646509 AAAAAA
1 AAAAAA
43646515 CTAACTCAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 4 0.17
20 13 0.54
21 7 0.29
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (20 bp):
AAAAAATAAATCTTAATTTT
Found at i:43647976 original size:60 final size:59
Alignment explanation
Indices: 43647875--43648035 Score: 189
Period size: 59 Copynumber: 2.7 Consensus size: 59
43647865 ATTGAATTTA
* * * *
43647875 AAAAAAAGCTTAGGTACCAAATTAGGAAAAAAATGCCAAGTTCAGATA-CTAAATTGGGTCC
1 AAAAAAAGTTTAGGTACCAAATTAAG-AAAAAATGTCAAGTTCAGATATC-AAATTAGG-CC
* * * *
43647936 AAAAAAAGTTTAGGTACTAAATTAAGAAAAAATGTTAAGTTCAGGTATCAAATTATGCC
1 AAAAAAAGTTTAGGTACCAAATTAAGAAAAAATGTCAAGTTCAGATATCAAATTAGGCC
* * *
43647995 AAAAAATGTTTAAGTACCAAATTAAAAAAAAATGTCAAGTT
1 AAAAAAAGTTTAGGTACCAAATTAAGAAAAAATGTCAAGTT
43648036 TAATTACCAA
Statistics
Matches: 86, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
59 38 0.44
60 24 0.28
61 24 0.28
ACGTcount: A:0.49, C:0.11, G:0.15, T:0.25
Consensus pattern (59 bp):
AAAAAAAGTTTAGGTACCAAATTAAGAAAAAATGTCAAGTTCAGATATCAAATTAGGCC
Found at i:43647982 original size:31 final size:33
Alignment explanation
Indices: 43647941--43648009 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 33
43647931 GGTCCAAAAA
*
43647941 AAGTTTAGGTA-CTAAATTAAG-AAAAAATG-TT
1 AAGTTCAGGTATC-AAATTAAGCAAAAAATGTTT
*
43647972 AAGTTCAGGTATCAAATTATGCCAAAAAATGTTT
1 AAGTTCAGGTATCAAATTAAG-CAAAAAATGTTT
43648006 AAGT
1 AAGT
43648010 ACCAAATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
31 17 0.53
32 1 0.03
33 8 0.25
34 6 0.19
ACGTcount: A:0.45, C:0.07, G:0.16, T:0.32
Consensus pattern (33 bp):
AAGTTCAGGTATCAAATTAAGCAAAAAATGTTT
Found at i:43653275 original size:119 final size:119
Alignment explanation
Indices: 43653064--43653301 Score: 422
Period size: 119 Copynumber: 2.0 Consensus size: 119
43653054 AATAGCATAC
*
43653064 AGTTTCTTCATTTCAATATCCAAGTCCCTTTGAGTTATATTATGCCAAATCAAATCATTTCAGTA
1 AGTTTCTTCATTTCAATATCCAAGTCCCTTTGAGTTATATTATGCCAAATCAAATCATTTCAATA
*
43653129 TCAAAGTCTCATATAAATATATTTAAAATATTATGACACAAAAAGCTAGTTTCT
66 TCAAAGTCTCATATAAATATATTTAAAATATTATGACACAAAAAGCCAGTTTCT
* *
43653183 AGTTTCTTCATTTCAATATCCATGTCCCTTTGAGTTATATTATGCCAAATCAAATCTTTTCAATA
1 AGTTTCTTCATTTCAATATCCAAGTCCCTTTGAGTTATATTATGCCAAATCAAATCATTTCAATA
* *
43653248 TCCAAGTCTCATATAAATATATTTAAAATATTATGACACCAAAAGCCAGTTTCT
66 TCAAAGTCTCATATAAATATATTTAAAATATTATGACACAAAAAGCCAGTTTCT
43653302 TCATTCTCCT
Statistics
Matches: 113, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
119 113 1.00
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (119 bp):
AGTTTCTTCATTTCAATATCCAAGTCCCTTTGAGTTATATTATGCCAAATCAAATCATTTCAATA
TCAAAGTCTCATATAAATATATTTAAAATATTATGACACAAAAAGCCAGTTTCT
Found at i:43654120 original size:6 final size:6
Alignment explanation
Indices: 43654109--43654143 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
43654099 CTTTCCCGTC
* *
43654109 TTCTTT TTCTTT TTCTTT TTCTTT TGCTTC TTCTT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTT
43654144 CATTTTCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (6 bp):
TTCTTT
Found at i:43654139 original size:21 final size:21
Alignment explanation
Indices: 43654115--43654154 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
43654105 CGTCTTCTTT
* *
43654115 TTCTTTTTCTTTTTCTTTTGC
1 TTCTTCTTCATTTTCTTTTGC
43654136 TTCTTCTTCATTTTCTTTT
1 TTCTTCTTCATTTTCTTTT
43654155 CCTTGTAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.03, C:0.20, G:0.03, T:0.75
Consensus pattern (21 bp):
TTCTTCTTCATTTTCTTTTGC
Found at i:43662513 original size:2 final size:2
Alignment explanation
Indices: 43662501--43662534 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
43662491 TTAATACTTA
*
43662501 AT AT TT 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
43662535 TGTAAATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:43663102 original size:17 final size:18
Alignment explanation
Indices: 43663067--43663105 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
43663057 ATAAAAATTC
* *
43663067 AAAATTTAAAAGATTATA
1 AAAATTCAAAAGATAATA
43663085 AAAATTCAAAA-ATAATA
1 AAAATTCAAAAGATAATA
43663102 AAAA
1 AAAA
43663106 ATAGCATGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAATTCAAAAGATAATA
Found at i:43663256 original size:30 final size:32
Alignment explanation
Indices: 43663191--43663262 Score: 80
Period size: 30 Copynumber: 2.3 Consensus size: 32
43663181 GTAAAAACAT
* *
43663191 AAATTTGACTATTTTTCAAAAGGTTAATGGTC
1 AAATTTGACTACTTTTCAAAAGATTAATGGTC
*
43663223 AAATTTGACT-CTTTT-AAAAGATTGA-GGTCC
1 AAATTTGACTACTTTTCAAAAGATTAATGGT-C
43663253 AAA-TTGACTA
1 AAATTTGACTA
43663263 AAGACGTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
29 9 0.26
30 12 0.34
31 4 0.11
32 10 0.29
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (32 bp):
AAATTTGACTACTTTTCAAAAGATTAATGGTC
Found at i:43663636 original size:29 final size:29
Alignment explanation
Indices: 43663574--43663637 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
43663564 AAAAAAAGAA
*
43663574 AAAAAAGAATGAAATTCAAGTATTTTCAT
1 AAAAAAGAATGAAATTCAAGTATTTCCAT
* *
43663603 GAAAAAGAATGAAGATATC-CGTA-TTCCAT
1 AAAAAAGAATGAA-AT-TCAAGTATTTCCAT
43663632 AAAAAA
1 AAAAAA
43663638 AGGTTGATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
29 22 0.76
30 5 0.17
31 2 0.07
ACGTcount: A:0.53, C:0.09, G:0.12, T:0.25
Consensus pattern (29 bp):
AAAAAAGAATGAAATTCAAGTATTTCCAT
Found at i:43670277 original size:2 final size:2
Alignment explanation
Indices: 43670265--43670314 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
43670255 TTCATTCAAG
* *
43670265 AT AT AT GT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
43670306 AT AT TT AT A
1 AT AT AT AT A
43670315 CTGGAACTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:43670979 original size:69 final size:66
Alignment explanation
Indices: 43670851--43670979 Score: 159
Period size: 69 Copynumber: 1.9 Consensus size: 66
43670841 AAATAATATA
* ** * *
43670851 ATGGTTTTGCCTTTTAACTTAATTGGTAAACATTTATCAAAATGATATAATTTTACCTTTAACTT
1 ATGGTTTTGACTTTTAACTTAAAAGGTAAACATTTATCAAAACGACATAATTTTACCTTTAACTT
43670916 G
66 G
* * *
43670917 ATGGTTTTGACTTTTAACTTTAGAAAAGGTAAACATTTATCAAAACGACGTAGTTTTGCCTTT
1 ATGGTTTTGACTTTTAAC-TT--AAAAGGTAAACATTTATCAAAACGACATAATTTTACCTTT
43670980 TCTTATTCAG
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
66 17 0.33
67 2 0.04
69 33 0.63
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (66 bp):
ATGGTTTTGACTTTTAACTTAAAAGGTAAACATTTATCAAAACGACATAATTTTACCTTTAACTT
G
Found at i:43693141 original size:14 final size:14
Alignment explanation
Indices: 43693124--43693166 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
43693114 TTTTTTTTTT
43693124 TTTATTATTTTTAG
1 TTTATTATTTTTAG
*
43693138 TTTATAATTTTTA-
1 TTTATTATTTTTAG
*
43693151 TTT-TTATTTTTGG
1 TTTATTATTTTTAG
43693164 TTT
1 TTT
43693167 TAGGTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
12 7 0.28
13 6 0.24
14 12 0.48
ACGTcount: A:0.19, C:0.00, G:0.07, T:0.74
Consensus pattern (14 bp):
TTTATTATTTTTAG
Found at i:43693155 original size:6 final size:6
Alignment explanation
Indices: 43693112--43693188 Score: 52
Period size: 6 Copynumber: 12.8 Consensus size: 6
43693102 ATCTCTGCAG
* *
43693112 ATTTTT -TTTTT TTTTATT ATTTTT AGTTTATA ATTTTT ATTTTT ATTTTT
1 ATTTTT ATTTTT ATTT-TT ATTTTT A-TTT-TT ATTTTT ATTTTT ATTTTT
** **
43693162 GGTTTT AGGTTT -TTTTT -TTTTT ATTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTT
43693189 AGGGTTTTTT
Statistics
Matches: 57, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
5 13 0.23
6 31 0.54
7 11 0.19
8 2 0.04
ACGTcount: A:0.14, C:0.00, G:0.06, T:0.79
Consensus pattern (6 bp):
ATTTTT
Found at i:43693174 original size:26 final size:26
Alignment explanation
Indices: 43693118--43693190 Score: 76
Period size: 26 Copynumber: 2.7 Consensus size: 26
43693108 GCAGATTTTT
43693118 TTTTTTTTTATTATTTTTAGTTTATAA
1 TTTTTTTTT-TTATTTTTAGTTTATAA
* * *
43693145 TTTTTATTTTTATTTTTGGTTT-TAGG
1 TTTTTTTTTTTATTTTTAGTTTATA-A
*
43693171 TTTTTTTTTTTTTATTTTAG
1 TTTTTTTTTTTAT-TTTTAG
43693191 GGTTTTTTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
25 2 0.05
26 23 0.61
27 13 0.34
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (26 bp):
TTTTTTTTTTTATTTTTAGTTTATAA
Found at i:43693175 original size:21 final size:22
Alignment explanation
Indices: 43693151--43693202 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
43693141 ATAATTTTTA
*
43693151 TTTTTATTTTTGGTTTTA-GGT
1 TTTTTATTTTTGATTTTAGGGT
* *
43693172 TTTTTTTTTTTTATTTTAGGGT
1 TTTTTATTTTTGATTTTAGGGT
43693194 TTTTTATTT
1 TTTTTATTT
43693203 ATTTTAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.10, C:0.00, G:0.13, T:0.77
Consensus pattern (22 bp):
TTTTTATTTTTGATTTTAGGGT
Found at i:43693198 original size:24 final size:24
Alignment explanation
Indices: 43693165--43693217 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
43693155 TATTTTTGGT
*
43693165 TTTA-GGTTTTTT-TTT-TTTTAT
1 TTTAGGGTTTTTTATTTATTTTAA
43693186 TTTAGGGTTTTTTATTTATTTTAA
1 TTTAGGGTTTTTTATTTATTTTAA
*
43693210 TTTGGGGT
1 TTTAGGGT
43693218 CGTGTAAGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 4 0.15
22 8 0.30
23 3 0.11
24 12 0.44
ACGTcount: A:0.13, C:0.00, G:0.17, T:0.70
Consensus pattern (24 bp):
TTTAGGGTTTTTTATTTATTTTAA
Found at i:43694479 original size:21 final size:19
Alignment explanation
Indices: 43694447--43694494 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
43694437 TTCTCATATT
**
43694447 TCTCACAATTCTCTCTTAATC
1 TCTCA-AATTCTCAATTAA-C
43694468 TCTCAAATTTCTCAATTAAC
1 TCTCAAA-TTCTCAATTAAC
43694488 TCTCAAA
1 TCTCAAA
43694495 AATCTCTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.31, C:0.29, G:0.00, T:0.40
Consensus pattern (19 bp):
TCTCAAATTCTCAATTAAC
Found at i:43694500 original size:20 final size:21
Alignment explanation
Indices: 43694462--43694500 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
43694452 CAATTCTCTC
**
43694462 TTAATCTCTCAAATTTCTCAA
1 TTAATCTCTCAAAAATCTCAA
43694483 TTAA-CTCTCAAAAATCTC
1 TTAATCTCTCAAAAATCTC
43694501 TCAAATTCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.36, C:0.26, G:0.00, T:0.38
Consensus pattern (21 bp):
TTAATCTCTCAAAAATCTCAA
Found at i:43695842 original size:17 final size:17
Alignment explanation
Indices: 43695820--43695857 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
43695810 AAGTTTTTTT
* *
43695820 TTTTTGTAATTTTGATG
1 TTTTTGGAATTTTGATA
43695837 TTTTTGGAATTTTGATA
1 TTTTTGGAATTTTGATA
43695854 TTTT
1 TTTT
43695858 AGTGTACATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.00, G:0.16, T:0.66
Consensus pattern (17 bp):
TTTTTGGAATTTTGATA
Found at i:43699646 original size:15 final size:15
Alignment explanation
Indices: 43699628--43699663 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
43699618 AATAATATAT
43699628 TTAACCCTAAATTAA
1 TTAACCCTAAATTAA
43699643 TTAACCCTAAATTAA
1 TTAACCCTAAATTAA
*
43699658 TAAACC
1 TTAACC
43699664 TTGAAACCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (15 bp):
TTAACCCTAAATTAA
Found at i:43699811 original size:20 final size:20
Alignment explanation
Indices: 43699783--43699821 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
43699773 TTTAATTTAA
43699783 TAAACACTTAAAACCCTAAT
1 TAAACACTTAAAACCCTAAT
* *
43699803 TAAATACTTAAAACTCTAA
1 TAAACACTTAAAACCCTAA
43699822 AAACCATGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.21, G:0.00, T:0.28
Consensus pattern (20 bp):
TAAACACTTAAAACCCTAAT
Found at i:43704172 original size:25 final size:25
Alignment explanation
Indices: 43704138--43704213 Score: 143
Period size: 25 Copynumber: 3.0 Consensus size: 25
43704128 GAGAAAGGGG
*
43704138 CTTTGATGAACATTAAAGTTGTCAT
1 CTTTGATGAACAATAAAGTTGTCAT
43704163 CTTTGATGAACAATAAAGTTGTCAT
1 CTTTGATGAACAATAAAGTTGTCAT
43704188 CTTTGATGAACAATAAAGTTGTCAT
1 CTTTGATGAACAATAAAGTTGTCAT
43704213 C
1 C
43704214 AAAATCAATG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 50 1.00
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (25 bp):
CTTTGATGAACAATAAAGTTGTCAT
Found at i:43718444 original size:2 final size:2
Alignment explanation
Indices: 43718437--43718470 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
43718427 TCAAACAATA
43718437 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
43718471 GTATGTATGT
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:43728835 original size:42 final size:42
Alignment explanation
Indices: 43728708--43728928 Score: 261
Period size: 42 Copynumber: 5.3 Consensus size: 42
43728698 TGATGTATAA
* * * * * *
43728708 AAAGGAAGACTCATGTCTTGGGTTGAGCATGAGGATTTG-TAT
1 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGAT-T
* * *
43728750 AAATGGAAGACTCGTGACTCG-GAATGA-ATATG-GATTATGATT
1 AAA-GGAAGACTCATGTCTCGAG-ATGAGA-ATGAGAATATGATT
43728792 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATT
1 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATT
* *
43728834 AAAGGAAGACTCATGTCTCGAGATGAGAATAAAAATATGATT
1 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATT
* *
43728876 AAAGGAAGACTCATGTTTCGGGATGAGAATGAGAATATGATT
1 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATT
43728918 AAAGGAAGACT
1 AAAGGAAGACT
43728929 TATGATTCAT
Statistics
Matches: 155, Mismatches: 17, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
41 22 0.14
42 112 0.72
43 21 0.14
ACGTcount: A:0.38, C:0.09, G:0.27, T:0.26
Consensus pattern (42 bp):
AAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATT
Found at i:43729625 original size:50 final size:50
Alignment explanation
Indices: 43729545--43729655 Score: 204
Period size: 50 Copynumber: 2.2 Consensus size: 50
43729535 GTTAGAATAC
* *
43729545 TAGTATCGGTAGAAGTTGCAAGGTAGGACTTCTTAGCTCTCTGGAGTTTT
1 TAGTATCGGTAAAAGTTGCAAGGTAAGACTTCTTAGCTCTCTGGAGTTTT
43729595 TAGTATCGGTAAAAGTTGCAAGGTAAGACTTCTTAGCTCTCTGGAGTTTT
1 TAGTATCGGTAAAAGTTGCAAGGTAAGACTTCTTAGCTCTCTGGAGTTTT
43729645 TAGTATCGGTA
1 TAGTATCGGTA
43729656 GAAGCATAAC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 59 1.00
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.36
Consensus pattern (50 bp):
TAGTATCGGTAAAAGTTGCAAGGTAAGACTTCTTAGCTCTCTGGAGTTTT
Found at i:43737048 original size:201 final size:195
Alignment explanation
Indices: 43736599--43737052 Score: 508
Period size: 201 Copynumber: 2.3 Consensus size: 195
43736589 TACCAGTACT
* * * * *
43736599 CGATGCTGCTCACATGAGCTGTCGAGGACTTGCAACGTATACGGTACC-CTAGCCATCGGTACGA
1 CGATGCTGCTCACACGAGCTGTTGAGGACTCGCAACATATACGGTACCTC-AGCCATCGATACGA
* * * *
43736663 TATTTGTCTGTACTATAAACTGTTTCCTAACGATGCTGCTCACACGAGCTGTTGAGAGTATGCAA
65 TATCTGTCTGCACTATAAACTGTTTCCTAACGATGCTGCTCACACGAGCTGTCGAGAATATGCAA
* *
43736728 TAAGCATAGTCCCAGCCATCGTAAGGCCTGTAATCCATTTAGGATCCATTTCTCTTTCCCAAGTC
130 TAAGCATAATCCCAGCCATCGTAAGGCCTGTAATCCATTTAGGATCCATTTCTCTTTCCCAACTC
43736793 A
195 A
* * * * * *
43736794 CGATGCTTCTCACACAAGTTGTTGAGGACTCGTAACATATGCGGTATCTCAGCCATCGATAC-AG
1 CGATGCTGCTCACACGAGCTGTTGAGGACTCGCAACATATACGGTACCTCAGCCATCGATACGA-
*
43736858 TATCTG-C-GCA-TAT-AACTG-TTCTCTAACGATGCTGTTCACACGAGCTGTCGAGAATATGCA
65 TATCTGTCTGCACTATAAACTGTTTC-CTAACGATGCTGCTCACACGAGCTGTCGAGAATATGCA
* * * * *
43736918 CTTATGCATAAATCTCAGCCATCGTAGGGCTTGTAATCCATTTAGGATCCATATTTCTTTTCTCA
129 -ATAAGCAT-AATCCCAGCCATCGTAAGGCCTGTAATCCATTTAGGATCC--A-----TTTCTC-
43736983 TTTCCCAACTCA
184 TTTCCCAACTCA
* * *
43736995 TGATGCTGCTCGCACGAGCTGTTGAGGACTCGCAACATATACGATACCTCAGCCATCG
1 CGATGCTGCTCACACGAGCTGTTGAGGACTCGCAACATATACGGTACCTCAGCCATCG
43737053 CGTCAGTTTC
Statistics
Matches: 214, Mismatches: 32, Indels: 20
0.80 0.12 0.08
Matches are distributed among these distances:
190 3 0.01
191 40 0.19
192 9 0.04
193 38 0.18
194 2 0.01
195 55 0.26
196 1 0.00
200 6 0.03
201 60 0.28
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (195 bp):
CGATGCTGCTCACACGAGCTGTTGAGGACTCGCAACATATACGGTACCTCAGCCATCGATACGAT
ATCTGTCTGCACTATAAACTGTTTCCTAACGATGCTGCTCACACGAGCTGTCGAGAATATGCAAT
AAGCATAATCCCAGCCATCGTAAGGCCTGTAATCCATTTAGGATCCATTTCTCTTTCCCAACTCA
Found at i:43739393 original size:18 final size:18
Alignment explanation
Indices: 43739370--43739411 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
43739360 TTGTGCTTTA
43739370 GAACATAGATTTTGTTTT
1 GAACATAGATTTTGTTTT
43739388 GAACATAGATTTTGTTTT
1 GAACATAGATTTTGTTTT
43739406 GAACAT
1 GAACAT
43739412 GGTTAGGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.31, C:0.07, G:0.17, T:0.45
Consensus pattern (18 bp):
GAACATAGATTTTGTTTT
Found at i:43741844 original size:33 final size:33
Alignment explanation
Indices: 43741802--43741864 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
43741792 GCTCGTGATT
*
43741802 CGATCTAACACTTTTTTCTTTCTAGTCTTTATC
1 CGATCTAACACTTTTTTCTTTCTAGACTTTATC
43741835 CGATCTAACACTTTTTTCTTTCTAGACTTT
1 CGATCTAACACTTTTTTCTTTCTAGACTTT
43741865 GAAAATGGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.19, C:0.24, G:0.06, T:0.51
Consensus pattern (33 bp):
CGATCTAACACTTTTTTCTTTCTAGACTTTATC
Found at i:43748156 original size:18 final size:17
Alignment explanation
Indices: 43748133--43748166 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
43748123 ACATATTATA
43748133 AAATATAACAAAAAAATT
1 AAATAT-ACAAAAAAATT
*
43748151 AAATATATAAAAAAAT
1 AAATATACAAAAAAAT
43748167 ATGATATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATATACAAAAAAATT
Found at i:43749259 original size:13 final size:14
Alignment explanation
Indices: 43749230--43749290 Score: 68
Period size: 14 Copynumber: 4.1 Consensus size: 14
43749220 ATAATTTAAA
43749230 TTCAACACTTAATTT
1 TTCAACACTT-ATTT
* **
43749245 TTTAGTACTTATTT
1 TTCAACACTTATTT
43749259 TTCAACACTTATTTTT
1 TTCAACACTTA--TTT
43749275 TTCAACACTTATTT
1 TTCAACACTTATTT
43749289 TT
1 TT
43749291 TTTTATTAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
14 17 0.45
15 7 0.18
16 14 0.37
ACGTcount: A:0.26, C:0.16, G:0.02, T:0.56
Consensus pattern (14 bp):
TTCAACACTTATTT
Found at i:43749260 original size:14 final size:14
Alignment explanation
Indices: 43749233--43749291 Score: 64
Period size: 15 Copynumber: 4.0 Consensus size: 14
43749223 ATTTAAATTC
43749233 AACACTTAATTTTTT
1 AACACTT-ATTTTTT
** *
43749248 AGTACTTATTTTTC
1 AACACTTATTTTTT
43749262 AACACTTATTTTTTT
1 AACACTTA-TTTTTT
43749277 CAACACTTATTTTTT
1 -AACACTTATTTTTT
43749292 TTTATTAAAC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
14 12 0.33
15 16 0.44
16 8 0.22
ACGTcount: A:0.27, C:0.15, G:0.02, T:0.56
Consensus pattern (14 bp):
AACACTTATTTTTT
Found at i:43749263 original size:29 final size:30
Alignment explanation
Indices: 43749230--43749290 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
43749220 ATAATTTAAA
**
43749230 TTCAACACTTAATTTTTT-AGTACTTATTT
1 TTCAACACTTAATTTTTTCAACACTTATTT
*
43749259 TTCAACACTTATTTTTTTCAACACTTATTT
1 TTCAACACTTAATTTTTTCAACACTTATTT
43749289 TT
1 TT
43749291 TTTTATTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.26, C:0.16, G:0.02, T:0.56
Consensus pattern (30 bp):
TTCAACACTTAATTTTTTCAACACTTATTT
Found at i:43749277 original size:16 final size:16
Alignment explanation
Indices: 43749230--43749292 Score: 78
Period size: 16 Copynumber: 4.1 Consensus size: 16
43749220 ATAATTTAAA
*
43749230 TTCAACACTTAATTTT
1 TTCAACACTTATTTTT
**
43749246 TT-AGTACTTA--TTT
1 TTCAACACTTATTTTT
43749259 TTCAACACTTATTTTT
1 TTCAACACTTATTTTT
43749275 TTCAACACTTATTTTT
1 TTCAACACTTATTTTT
43749291 TT
1 TT
43749293 TTATTAAACA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
13 5 0.12
14 6 0.15
15 6 0.15
16 23 0.57
ACGTcount: A:0.25, C:0.16, G:0.02, T:0.57
Consensus pattern (16 bp):
TTCAACACTTATTTTT
Found at i:43749505 original size:31 final size:30
Alignment explanation
Indices: 43749447--43749506 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
43749437 TTAAAATGGA
*
43749447 AAATTTTGATTTGATATAATTATATATATG
1 AAATTTTGATTTGATATAAATATATATATG
* *
43749477 AAATTTTGATTGTGGTTTAAATATATATAT
1 AAATTTTGATT-TGATATAAATATATATAT
43749507 AAAACTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (30 bp):
AAATTTTGATTTGATATAAATATATATATG
Found at i:43751429 original size:11 final size:11
Alignment explanation
Indices: 43751413--43751442 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
43751403 TATTGTAAAT
*
43751413 TAATAATATAA
1 TAATAAAATAA
43751424 TAATAAAATAA
1 TAATAAAATAA
43751435 TAATAAAA
1 TAATAAAA
43751443 AAAAATCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:43754433 original size:21 final size:22
Alignment explanation
Indices: 43754407--43754447 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
43754397 ACAAAAAAAT
*
43754407 TGCTATTTTTTTGTT-TTTTAA
1 TGCTATTTTCTTGTTGTTTTAA
43754428 TGCTATTTTCTTGTTGTTTT
1 TGCTATTTTCTTGTTGTTTT
43754448 CTCCCTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.10, C:0.07, G:0.12, T:0.71
Consensus pattern (22 bp):
TGCTATTTTCTTGTTGTTTTAA
Found at i:43754563 original size:30 final size:30
Alignment explanation
Indices: 43754529--43754593 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
43754519 ACTTATTTTC
*
43754529 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTACTATTTTAAAGGCAT
**
43754559 TTGTTAATTTTGTTACTATTTTTGAGGCAT
1 TTGTTAATTTTGTTACTATTTTAAAGGCAT
43754589 TTGTT
1 TTGTT
43754594 TGTTAAGTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.22, C:0.05, G:0.15, T:0.58
Consensus pattern (30 bp):
TTGTTAATTTTGTTACTATTTTAAAGGCAT
Found at i:43755387 original size:7 final size:7
Alignment explanation
Indices: 43755370--43755400 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
43755360 TATTGATTTT
43755370 TATATAAA
1 TATA-AAA
43755378 TATAAAA
1 TATAAAA
43755385 TATAAAA
1 TATAAAA
43755392 TATAAAA
1 TATAAAA
43755399 TA
1 TA
43755401 ATTTAGGGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 19 0.83
8 4 0.17
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
TATAAAA
Found at i:43759805 original size:29 final size:29
Alignment explanation
Indices: 43759765--43759855 Score: 89
Period size: 28 Copynumber: 3.1 Consensus size: 29
43759755 TACCTGGGGG
43759765 AAAATGGTAATTTTGGTGTAATCGGGGTTA
1 AAAATGGTAATTTTGGTG-AATCGGGGTTA
*** * *
43759795 AAAATGG-AATTTTAAAGATTCGGGGGT-
1 AAAATGGTAATTTTGGTGAATCGGGGTTA
43759822 AAAATGGTAATTTTCGGTGAAATC-GGGTTA
1 AAAATGGTAATTTT-GGTG-AATCGGGGTTA
43759852 AAAA
1 AAAA
43759856 CAGAATTTTA
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
27 7 0.15
28 14 0.30
29 12 0.26
30 14 0.30
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.32
Consensus pattern (29 bp):
AAAATGGTAATTTTGGTGAATCGGGGTTA
Found at i:43759829 original size:57 final size:58
Alignment explanation
Indices: 43759760--43759911 Score: 197
Period size: 57 Copynumber: 2.7 Consensus size: 58
43759750 ATGAATACCT
* **
43759760 GGGGG-AAAATGGTAATTTT-GGTGTAATCGGGGTTAAAAATGGAATTTT-AAAGATTC
1 GGGGGTAAAATGGTAATTTTCGGTGAAATC-GGGTTAAAAACAGAATTTTAAAAGATTC
*
43759816 GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGTTAAAAACAGAATTTTAAAAGCTTC
1 GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGTTAAAAACAGAATTTTAAAAGATTC
**
43759874 -GGGGTAAAATGGTAATTTTCAATG-AATCAGGGTTAAAA
1 GGGGGTAAAATGGTAATTTTCGGTGAAATC-GGGTTAAAA
43759912 TGTAATTTTT
Statistics
Matches: 86, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
56 9 0.10
57 62 0.72
58 15 0.17
ACGTcount: A:0.36, C:0.06, G:0.28, T:0.30
Consensus pattern (58 bp):
GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGTTAAAAACAGAATTTTAAAAGATTC
Found at i:43759954 original size:30 final size:30
Alignment explanation
Indices: 43759903--43760102 Score: 319
Period size: 30 Copynumber: 6.6 Consensus size: 30
43759893 CAATGAATCA
* *
43759903 GGGTTAAAATGTAATTTTTGGAAAAGTTTTG
1 GGGTCAAAATATAA-TTTTGGAAAAGTTTTG
*
43759934 GGGTCAAAATATAATTTTGGAAAAGTTTTA
1 GGGTCAAAATATAATTTTGGAAAAGTTTTG
* *
43759964 GGGTCAAAATGTAATTTTGGAAAAGTTTTA
1 GGGTCAAAATATAATTTTGGAAAAGTTTTG
*
43759994 GGGTCAAAATGTAATTTTGGAAAAGTTTTG
1 GGGTCAAAATATAATTTTGGAAAAGTTTTG
*
43760024 GTGTCAAAATATAATTTTGGAAAAGTTTTGG
1 GGGTCAAAATATAATTTTGGAAAAGTTTT-G
43760055 GGGTCAAAATATAATTTTGGAAAAGTTTTG
1 GGGTCAAAATATAATTTTGGAAAAGTTTTG
43760085 GGGTCAAAATATAATTTT
1 GGGTCAAAATATAATTTT
43760103 TGGACAATTT
Statistics
Matches: 160, Mismatches: 8, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
30 119 0.74
31 41 0.26
ACGTcount: A:0.36, C:0.03, G:0.23, T:0.38
Consensus pattern (30 bp):
GGGTCAAAATATAATTTTGGAAAAGTTTTG
Found at i:43760385 original size:159 final size:159
Alignment explanation
Indices: 43760197--43760505 Score: 419
Period size: 159 Copynumber: 1.9 Consensus size: 159
43760187 ATTTGAAAAT
* **
43760197 CTTGAAAAAATTTTGGACCAATTTTGTAATTATTA-AAAGTCGATTTAAGAATTAAATT-AAACA
1 CTTGAAAAAATTTTGGACCAATTTCGTAATTAAAATAAAGTCGATTT-AGAATTAAATTAAAACA
* * *
43760260 AATTAAAAATAAAAAGGACTAAATGCATAAAT-ATCCAAAAAATGACACGTGGCAGTCTCTGGTA
65 AA-TAAAAATAAAAAGGACTAAATGCATAAATAAT-CAAAAAATGACACATGGCAGCCTATGGTA
* *
43760324 TAGTCAAAGAGTCAAAGGACTAGTTTATAAAC
128 CAGTCAAACAGTCAAAGGACTAGTTTATAAAC
* * * *
43760356 CTTG-AAAAATTGTTGGGCCAATTTCGTAATTAAAATAAAGTTGATTTGGGATTAAATTAAAACA
1 CTTGAAAAAATT-TTGGACCAATTTCGTAATTAAAATAAAGTCGATTTAGAATTAAATTAAAACA
*
43760420 AATAAAAATAAAAAGGACTAAATGCATAAATAAATCAAAAAGTGACACATGGCAGCCTATGGTAC
65 AATAAAAATAAAAAGGACTAAATGCATAAAT-AATCAAAAAATGACACATGGCAGCCTATGGTAC
*
43760485 AGTCAAACAGTCAAATGACTA
129 AGTCAAACAGTCAAAGGACTA
43760506 AATTGAAAAG
Statistics
Matches: 131, Mismatches: 14, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
158 7 0.05
159 61 0.47
160 61 0.47
161 2 0.02
ACGTcount: A:0.46, C:0.12, G:0.15, T:0.27
Consensus pattern (159 bp):
CTTGAAAAAATTTTGGACCAATTTCGTAATTAAAATAAAGTCGATTTAGAATTAAATTAAAACAA
ATAAAAATAAAAAGGACTAAATGCATAAATAATCAAAAAATGACACATGGCAGCCTATGGTACAG
TCAAACAGTCAAAGGACTAGTTTATAAAC
Found at i:43761313 original size:17 final size:17
Alignment explanation
Indices: 43761293--43761326 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
43761283 TAAAACGTTT
*
43761293 ATTATTATTATTAATAC
1 ATTAATATTATTAATAC
43761310 ATTAATATTATTAATAC
1 ATTAATATTATTAATAC
43761327 TGACATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTAATATTATTAATAC
Found at i:43761381 original size:34 final size:35
Alignment explanation
Indices: 43761297--43761385 Score: 94
Period size: 34 Copynumber: 2.6 Consensus size: 35
43761287 ACGTTTATTA
* *
43761297 TTATTATTAATACATTAATATTATTAATACTGACAT
1 TTATTATT-ATACATTAATATCATTAATACAGACAT
* *
43761333 TTATTA-TA-ACCATTACTATCATTAATA-AGATAT
1 TTATTATTATA-CATTAATATCATTAATACAGACAT
*
43761366 TTATTATTATGCATTAATAT
1 TTATTATTATACATTAATAT
43761386 ACATGGGAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
33 11 0.25
34 26 0.59
35 1 0.02
36 6 0.14
ACGTcount: A:0.40, C:0.09, G:0.03, T:0.47
Consensus pattern (35 bp):
TTATTATTATACATTAATATCATTAATACAGACAT
Found at i:43761854 original size:20 final size:20
Alignment explanation
Indices: 43761821--43761877 Score: 80
Period size: 20 Copynumber: 2.8 Consensus size: 20
43761811 TGGCAGGGCA
43761821 TGGTGGACCAGCAGCAGGAGC
1 TGGTGG-CCAGCAGCAGGAGC
*
43761842 TGGTGGTCAGCAG-ATGGAGC
1 TGGTGGCCAGCAGCA-GGAGC
43761862 TGGTGGCCAGCAGCAG
1 TGGTGGCCAGCAGCAG
43761878 TAGGCACGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 1 0.03
20 24 0.75
21 7 0.22
ACGTcount: A:0.21, C:0.21, G:0.44, T:0.14
Consensus pattern (20 bp):
TGGTGGCCAGCAGCAGGAGC
Found at i:43762608 original size:69 final size:68
Alignment explanation
Indices: 43762466--43763464 Score: 1552
Period size: 68 Copynumber: 14.6 Consensus size: 68
43762456 TTCAATTCGG
* * * * * * * *
43762466 AGACTTGTTATCAACTCTTCTTTAATTTCAAGAGGATGACATTGCTCTTATTTCAATTTCAGAGG
1 AGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGA
*
43762531 TAA
66 TGA
* * * *
43762534 AGATGTGTTATCCACTCTACTTCAATTTCGAGGGGATGATGTTGCTTCTTATTTCAATTTCAGAG
1 AGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGC-TCTTACTTCAATTTCAGAG
* *
43762599 GTAA
65 ATGA
* *
43762603 AGATGTGTTATCCACTCTACTTCAATTTCGAGGGGATGACGTTGCTTCTCTTACTTCAATTTCAG
1 AGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTG---CTCTTACTTCAATTTCAG
43762668 AGATGA
63 AGATGA
*
43762674 AGACGTGTTATCCACTCTACTTCAATTTTAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGA
1 AGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGA
43762739 TGA
66 TGA
* *
43762742 AGATGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGA
1 AGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGA
43762807 TGA
66 TGA
*
43762810 AGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGA
1 AGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGA
43762875 TG-
66 TGA
*
43762877 AGACGTGTTATCCACTCTACTTCGATTTCAAGGGGATGACGTTGCTCTTTACTTCAATTTCAGAG
1 AGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTC-TTACTTCAATTTCAGAG
43762942 ATGA
65 ATGA
* * *
43762946 AGACGTGCTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTCCAATTTCAGAG
1 AGACGTGTTATCC-ACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAG
*
43763011 ATAA
65 ATGA
* * * *
43763015 AGACTTGATATCCAACTCTACTTCAATTTCAATGGGATGACATTGCTCTTACTTCAATTTCAGAG
1 AGACGTGTTATCC-ACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAG
43763080 ATGA
65 ATGA
*
43763084 AGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGA
1 AGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGA
43763149 TGA
66 TGA
*
43763152 AGACGTGTTATCCACTCTACTTCGATTTC-AGGGGATGACGTTGCTCTTACTTCAATTTCAGAGA
1 AGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGA
43763216 TGA
66 TGA
*
43763219 AGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGA
1 AGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGA
43763284 TGA
66 TGA
*
43763287 AGACGTGTTATCCACTCTACTTCGATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGA
1 AGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGA
43763352 TGA
66 TGA
* *
43763355 AGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTCCAATTTCAGAG
1 AGACGTGTTATCC-ACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAG
*
43763420 ATAA
65 ATGA
* *
43763424 AGACTTGATATCCAACTCTACTTCAATTTCAAGGGGATGAC
1 AGACGTGTTATCC-ACTCTACTTCAATTTCAAGGGGATGAC
43763465 ATTGGTGACC
Statistics
Matches: 870, Mismatches: 52, Indels: 17
0.93 0.06 0.02
Matches are distributed among these distances:
67 110 0.13
68 407 0.47
69 259 0.30
70 32 0.04
71 61 0.07
72 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (68 bp):
AGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGA
TGA
Found at i:43763410 original size:409 final size:410
Alignment explanation
Indices: 43762465--43763468 Score: 1676
Period size: 409 Copynumber: 2.4 Consensus size: 410
43762455 CTTCAATTCG
* * * ** * * *
43762465 GAGACTTGTTATCAACTCTTCTTTAATTTCAAGAGGATGACATTGCTCTTATTTCAATTTCAGAG
1 GAGACGTGTTATCCACTCTACTTCGATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAG
* * * * * * * *
43762530 GTAAAGATGTGTTATCC-ACTCTACTTCAATTTCGAGGGGATGATGTTGCTTCTTATTTCAATTT
66 ATGAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGC-TCTTACTCCAATTT
* * * *
43762594 CAGAGGTAAAGA-TGTGTTATCC-ACTCTACTTCAATTTCGAGGGGATGACGTTGCTTCTCTTAC
130 CAGAGATAAAGACT-TGATATCCAACTCTACTTCAATTTCAAGGGGATGACATTG--TCTCTTAC
* *
43762657 TTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTTAAGGGGATGACGTTGCTCT
192 TTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCTCT
*
43762722 TACTTCAATTTCAGAGATGAAGATGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGC
257 TACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGC
43762787 TCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGT
322 TCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGT
43762852 TGCTCTTACTTCAATTTCAGAGAT
387 TGCTCTTACTTCAATTTCAGAGAT
43762876 GAGACGTGTTATCCACTCTACTTCGATTTCAAGGGGATGACGTTGCTCTTTACTTCAATTTCAGA
1 GAGACGTGTTATCCACTCTACTTCGATTTCAAGGGGATGACGTTGCTC-TTACTTCAATTTCAGA
*
43762941 GATGAAGACGTGCTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTCCAATTT
65 GATGAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTCCAATTT
*
43763006 CAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAATGGGATGACATTG-CTCTTACTTC
130 CAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGGGGATGACATTGTCTCTTACTTC
43763070 AATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTAC
195 AATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTAC
* *
43763135 TTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCGATTTC-AGGGGATGACGTTGCTCT
260 TTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCTCT
43763199 TACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGC
325 TACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGC
43763264 TCTTACTTCAATTTCAGAGAT
390 TCTTACTTCAATTTCAGAGAT
43763285 GAAGACGTGTTATCCACTCTACTTCGATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGA
1 G-AGACGTGTTATCCACTCTACTTCGATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGA
43763350 GATGAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTCCAATTT
65 GATGAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTCCAATTT
43763415 CAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGGGGATGACATTG
130 CAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGGGGATGACATTG
43763469 GTGACCTGCA
Statistics
Matches: 559, Mismatches: 29, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
409 237 0.42
410 164 0.29
411 41 0.07
412 59 0.11
413 58 0.10
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (410 bp):
GAGACGTGTTATCCACTCTACTTCGATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAG
ATGAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTCCAATTTC
AGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGGGGATGACATTGTCTCTTACTTCA
ATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACT
TCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTT
ACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCT
CTTACTTCAATTTCAGAGAT
Found at i:43775441 original size:29 final size:28
Alignment explanation
Indices: 43775399--43775499 Score: 89
Period size: 29 Copynumber: 3.5 Consensus size: 28
43775389 ACCTAAGGGC
43775399 AAAATGGTAATTTTGGTGTAATCGGGGTTA
1 AAAATGG-AATTTTGGTG-AATCGGGGTTA
* *** *
43775429 AAAATAGAATTTTAAAGATTCGAGGG-T-
1 AAAATGGAATTTTGGTGAATCG-GGGTTA
43775456 AAAATGGTAAATTTTGGTGAAATCGGGGTTA
1 AAAATGG--AATTTTGGTG-AATCGGGGTTA
43775487 AAAATGGAATTTT
1 AAAATGGAATTTT
43775500 AGAAGCTTTG
Statistics
Matches: 55, Mismatches: 10, Indels: 13
0.71 0.13 0.17
Matches are distributed among these distances:
27 6 0.11
28 5 0.09
29 26 0.47
30 11 0.20
31 7 0.13
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.34
Consensus pattern (28 bp):
AAAATGGAATTTTGGTGAATCGGGGTTA
Found at i:43775549 original size:58 final size:57
Alignment explanation
Indices: 43775394--43775557 Score: 213
Period size: 58 Copynumber: 2.8 Consensus size: 57
43775384 TGGATACCTA
* * *
43775394 AGGGCAAAATGGTAATTTTGGTGTAATCGGGGTTAAAAATAGAATTTTAAAGATTCG
1 AGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAGATTCG
* *
43775451 AGGGTAAAATGGTAAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTTTG
1 AGGGTAAAATGGT-AATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTA-AAGATTCG
* * * *
43775510 GGGGTAAAATGGTAATTTTCGGTAAAATCAGGGTT-AAAATGTAATTTT
1 AGGGTAAAATGGTAATTTT-GGTGAAATCGGGGTTAAAAATGGAATTTT
43775558 GGAAAAGTTT
Statistics
Matches: 95, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
57 12 0.13
58 52 0.55
59 31 0.33
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.33
Consensus pattern (57 bp):
AGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAGATTCG
Found at i:43775573 original size:30 final size:30
Alignment explanation
Indices: 43775540--43776006 Score: 755
Period size: 30 Copynumber: 15.7 Consensus size: 30
43775530 GGTAAAATCA
* *
43775540 GGGTTAAAATGTAATTTTGGAAAAGTTTTA
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTG
*
43775570 GGGTCAAAATATAATTTTGGAAAAG-TTTG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTG
*
43775599 GGGTCAAAATGTAATTTTAGAAAAGTTTTG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTG
43775629 GGGTCAAAATGTAATTTTGGAAAAGTTTTG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTG
*
43775659 GGGTCAAAATATAATTTTGGAAAAGTTTTG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTG
43775689 GGGTCAAAATGTAATTTTGGAAAAGTTTTG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTG
43775719 GGGTCAAAATGTAATTTTGG-AAAGTTTTG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTG
*
43775748 GGGTCAAAATATAATTTTGGAAAAG-TTTG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTG
* *
43775777 GGGTCAAAATGTAA-TTTAGAAAAGTTTTA
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTG
43775806 GGGTCAAAATGTAATTTTGGAAAAGTTTTG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTG
*
43775836 GGGTCAAAATATAATTTTGGAAAAGTTTTG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTG
43775866 GGGTCAAAATGTAATTTTGGAAAAGTTTTG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTG
*
43775896 GGGTCAAAATATAATTTTGGAAAAGTTTTG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTG
* *
43775926 GGATCAAAATGTAATTTTGAAAAAGTTTTG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTG
*
43775956 GGGTCAAAATATAA-TTTGGAAAAGTTTTG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTG
* *
43775985 AGGTCAAAATATAATTTCTGGA
1 GGGTCAAAATGTAATTT-TGGA
43776007 TAATTTAGGG
Statistics
Matches: 407, Mismatches: 24, Indels: 11
0.92 0.05 0.02
Matches are distributed among these distances:
28 9 0.02
29 115 0.28
30 279 0.69
31 4 0.01
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.36
Consensus pattern (30 bp):
GGGTCAAAATGTAATTTTGGAAAAGTTTTG
Found at i:43776374 original size:158 final size:162
Alignment explanation
Indices: 43776098--43776408 Score: 438
Period size: 158 Copynumber: 1.9 Consensus size: 162
43776088 ATTTGAAAAT
* *
43776098 CTTGAAAAAATTTTGGACCAATTTTGTAATTAAATAAAAGTCGATTTATGGATTAAATTAAAACA
1 CTTGAAAAAATTTTGGACCAATTTCGTAATTAAATAAAAGTCGATTTAGGGATTAAATTAAAACA
* * *
43776163 AATTAAAAATAAAAAGGACTAAATGCATAAATAATCCAAAAAAATGACACGTGGCAGTCTCTGGT
66 AA-TAAAAATAAAAAGGACTAAATGCAGAAATAATCCAAAAAAATGACACGTGGCAGCCTATGGT
** *
43776228 GTAGTCAAAGAGTCAAAGGACTAGTTTTATAAC
130 ACAGTCAAACAGTCAAAGGACTAGTTTTATAAC
* *
43776261 CTTG-AAAAATTGTTGG-GCAATTTCGTAATTAAA-ATAAAGTTGATTT-GGGATTAAATTAAAA
1 CTTGAAAAAATT-TTGGACCAATTTCGTAATTAAATA-AAAGTCGATTTAGGGATTAAATTAAAA
*
43776322 C-AA-AAAAATAAAAAAGGACTAAATGCAGAAATAATCC-AAAAAGTGACACGTGGCAGCCTATG
64 CAAATAAAAAT-AAAAAGGACTAAATGCAGAAATAATCCAAAAAAATGACACGTGGCAGCCTATG
43776384 GTACAGTCAAACAGTCAAAGGACTA
128 GTACAGTCAAACAGTCAAAGGACTA
43776409 AATTGAAAAG
Statistics
Matches: 134, Mismatches: 11, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
158 50 0.37
159 26 0.19
160 2 0.01
161 16 0.12
162 32 0.24
163 8 0.06
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.26
Consensus pattern (162 bp):
CTTGAAAAAATTTTGGACCAATTTCGTAATTAAATAAAAGTCGATTTAGGGATTAAATTAAAACA
AATAAAAATAAAAAGGACTAAATGCAGAAATAATCCAAAAAAATGACACGTGGCAGCCTATGGTA
CAGTCAAACAGTCAAAGGACTAGTTTTATAAC
Found at i:43776623 original size:14 final size:16
Alignment explanation
Indices: 43776598--43776631 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
43776588 TAAATAACAT
43776598 TTTCAGATTTTTTT-A
1 TTTCAGATTTTTTTCA
43776613 TTTCA-ATTTTTTTCA
1 TTTCAGATTTTTTTCA
43776628 TTTC
1 TTTC
43776632 TTAAAATTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.18, C:0.12, G:0.03, T:0.68
Consensus pattern (16 bp):
TTTCAGATTTTTTTCA
Found at i:43777229 original size:17 final size:17
Alignment explanation
Indices: 43777209--43777242 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
43777199 TAAAACGTTT
*
43777209 ATTATTATTATTAATAC
1 ATTAATATTATTAATAC
43777226 ATTAATATTATTAATAC
1 ATTAATATTATTAATAC
43777243 TGACATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTAATATTATTAATAC
Found at i:43777297 original size:34 final size:35
Alignment explanation
Indices: 43777213--43777301 Score: 94
Period size: 34 Copynumber: 2.6 Consensus size: 35
43777203 ACGTTTATTA
* *
43777213 TTATTATTAATACATTAATATTATTAATACTGACAT
1 TTATTATT-ATACATTAATATCATTAATACAGACAT
* *
43777249 TTATTA-TA-ACCATTACTATCATTAATA-AGATAT
1 TTATTATTATA-CATTAATATCATTAATACAGACAT
*
43777282 TTATTATTATGCATTAATAT
1 TTATTATTATACATTAATAT
43777302 ACATGGGAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
33 11 0.25
34 26 0.59
35 1 0.02
36 6 0.14
ACGTcount: A:0.40, C:0.09, G:0.03, T:0.47
Consensus pattern (35 bp):
TTATTATTATACATTAATATCATTAATACAGACAT
Found at i:43777810 original size:20 final size:20
Alignment explanation
Indices: 43777755--43777812 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
43777745 AGCAGCAGCA
*
43777755 GGAGCTGGTGGTCAACAGAT
1 GGAGCTGGTGGTCAGCAGAT
43777775 GGAGCTGGTGGTCAGCAGAT
1 GGAGCTGGTGGTCAGCAGAT
*
43777795 GGAGCTGGTGGCCAGCAG
1 GGAGCTGGTGGTCAGCAG
43777813 CAGTAGGCAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.21, C:0.17, G:0.45, T:0.17
Consensus pattern (20 bp):
GGAGCTGGTGGTCAGCAGAT
Found at i:43779441 original size:21 final size:22
Alignment explanation
Indices: 43779417--43779463 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
43779407 AAAATTATTA
43779417 TTTTAGACATTTTTA-ACTTTTT
1 TTTTAGA-ATTTTTATACTTTTT
*
43779439 TTTTGGAATTTTTATACTTTTT
1 TTTTAGAATTTTTATACTTTTT
43779461 TTT
1 TTT
43779464 AAAAATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.68
Consensus pattern (22 bp):
TTTTAGAATTTTTATACTTTTT
Found at i:43785939 original size:31 final size:31
Alignment explanation
Indices: 43785912--43785974 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
43785902 ACTATATGCG
* *
43785912 TGAAATTTTTATTGTGATTCAAATATATACA
1 TGAAACTTTAATTGTGATTCAAATATATACA
* *
43785943 TGAAACTTTAATTTTGATTCAATTATATACA
1 TGAAACTTTAATTGTGATTCAAATATATACA
43785974 T
1 T
43785975 TTAAAAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (31 bp):
TGAAACTTTAATTGTGATTCAAATATATACA
Found at i:43786142 original size:29 final size:30
Alignment explanation
Indices: 43786098--43786175 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 30
43786088 AGAATTTGAT
43786098 TAAATCAAAATTTCATGTATAAAATTACATA
1 TAAATCAAAA-TTCATGTATAAAATTACATA
* * *
43786129 -AAATCAAAATTCATATATATAATTGCATA
1 TAAATCAAAATTCATGTATAAAATTACATA
* *
43786158 TTAAACCAAAGTTCATGT
1 -TAAATCAAAATTCATGT
43786176 GTATTAGGTC
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
29 17 0.44
30 9 0.23
31 13 0.33
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.35
Consensus pattern (30 bp):
TAAATCAAAATTCATGTATAAAATTACATA
Found at i:43787007 original size:21 final size:22
Alignment explanation
Indices: 43786978--43787024 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
43786968 ATGTCAAATT
43786978 TTATGTAATAATGT-AATATGAA
1 TTATGTAAT-ATGTAAATATGAA
* *
43787000 TTAT-TAATGTGTAAATATTAA
1 TTATGTAATATGTAAATATGAA
43787021 TTAT
1 TTAT
43787025 ATAAACGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 3 0.14
21 15 0.68
22 4 0.18
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.47
Consensus pattern (22 bp):
TTATGTAATATGTAAATATGAA
Found at i:43790848 original size:17 final size:17
Alignment explanation
Indices: 43790826--43790876 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
43790816 CAGTCAAAAT
43790826 AAATTTAAGAAAATAAC
1 AAATTTAAGAAAATAAC
**
43790843 AAATTT-AGTCAA-AAC
1 AAATTTAAGAAAATAAC
* *
43790858 AAAATTAATAAAATAAC
1 AAATTTAAGAAAATAAC
43790875 AA
1 AA
43790877 CTTTGAATAA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
15 8 0.31
16 7 0.27
17 11 0.42
ACGTcount: A:0.65, C:0.08, G:0.04, T:0.24
Consensus pattern (17 bp):
AAATTTAAGAAAATAAC
Found at i:43790871 original size:32 final size:33
Alignment explanation
Indices: 43790801--43790876 Score: 102
Period size: 32 Copynumber: 2.3 Consensus size: 33
43790791 CCTATTTACT
* *
43790801 TAAAATAA-ATAATTTCAGTCAAAATAAATTTAA
1 TAAAATAACA-AATTTCAGTCAAAACAAAATTAA
*
43790834 GAAAATAACAAATTT-AGTCAAAACAAAATTAA
1 TAAAATAACAAATTTCAGTCAAAACAAAATTAA
43790866 TAAAATAACAA
1 TAAAATAACAA
43790877 CTTTGAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 25 0.66
33 12 0.32
34 1 0.03
ACGTcount: A:0.62, C:0.08, G:0.04, T:0.26
Consensus pattern (33 bp):
TAAAATAACAAATTTCAGTCAAAACAAAATTAA
Found at i:43792836 original size:18 final size:18
Alignment explanation
Indices: 43792809--43792859 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
43792799 GTTTATAGAT
*
43792809 ATCCTTGGACTTACAGCA
1 ATCCTAGGACTTACAGCA
* * *
43792827 ATCCTCGGACTTGCAGCG
1 ATCCTAGGACTTACAGCA
43792845 ATCCTAGGACTTACA
1 ATCCTAGGACTTACA
43792860 TCGTTCATCA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.25
Consensus pattern (18 bp):
ATCCTAGGACTTACAGCA
Found at i:43793999 original size:297 final size:299
Alignment explanation
Indices: 43793451--43794045 Score: 1043
Period size: 297 Copynumber: 2.0 Consensus size: 299
43793441 ACCTGCATTT
* *
43793451 GACAATGGAGAAACCTTATCAAAAGAACTAAGATTCATTTCTGTTGACATGTCGATAGAAGCTTC
1 GACAATGGAG-AACCTTATCAAAAGAACGAAGATTCATTTCTGTTGACACGTCGATAGAAGCTTC
*
43793516 CTTGTCCATCGATAATAAGGAGACATCATCAATAGAAATAAGCTTAGAAGAAGCGGATGGCTCGA
65 CTTGTCCATCAATAATAAGGAGACATCATCAATAGAAATAAGCTTAGAAGAAGCGGATGGCTCGA
* *
43793581 TTTTGGTACTGGCTTGCTCCCAATGGAGTTCCTCCAAGCCATGTTGTTTCAAATCAGTAGATTCC
130 TTTTGGAACTGGCTTGCTCCCAATGGAGTTCCTCCAAGCCATGTTGTTTCAAATCAGCAGATTCC
*
43793646 GCTGGTATAGTCCCAAGAGGCTCAATGATGGCCGATTCTGATTCTGATTGTGAAATGAATATTGA
195 GCCGGTATAGTCCCAAGAGGCTCAATGATGGCCGATTCTGATTCTGATTGTGAAATGAATATTGA
43793711 AGGCTTAAGTGCAGAAACAGGATCCATGAATTTCTCTGTC
260 AGGCTTAAGTGCAGAAACAGGATCCATGAATTTCTCTGTC
*
43793751 GACAATGGAG-A-CTTATCAACAGAACGAAGATTCATTTCTGTTGACACGTCGATAGAAGCTTCC
1 GACAATGGAGAACCTTATCAAAAGAACGAAGATTCATTTCTGTTGACACGTCGATAGAAGCTTCC
*
43793814 TTGTCCATCAATGATAAAGG-GACATCATCAATAGAAATAAGCTTAGAAGAAGCGGATGGCTCGA
66 TTGTCCATCAATAAT-AAGGAGACATCATCAATAGAAATAAGCTTAGAAGAAGCGGATGGCTCGA
* *
43793878 TTTTGGAACTGGCTTGCTCCCAATTGAGTTCCTCCAAGCCATGTTGTTTCAAATCAGCAGATTCT
130 TTTTGGAACTGGCTTGCTCCCAATGGAGTTCCTCCAAGCCATGTTGTTTCAAATCAGCAGATTCC
* *
43793943 GCCGGTATAGTGCCAAGAGGCTCAATGATGGCTGATTCTGATTCTGATTGTGAAATGAATATTGA
195 GCCGGTATAGTCCCAAGAGGCTCAATGATGGCCGATTCTGATTCTGATTGTGAAATGAATATTGA
43794008 AGGCTTAAGTGCAGAAACAGGATCCATGAATTTCTCTG
260 AGGCTTAAGTGCAGAAACAGGATCCATGAATTTCTCTG
43794046 AAGCAAAATT
Statistics
Matches: 282, Mismatches: 12, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
297 267 0.95
298 5 0.02
300 10 0.04
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (299 bp):
GACAATGGAGAACCTTATCAAAAGAACGAAGATTCATTTCTGTTGACACGTCGATAGAAGCTTCC
TTGTCCATCAATAATAAGGAGACATCATCAATAGAAATAAGCTTAGAAGAAGCGGATGGCTCGAT
TTTGGAACTGGCTTGCTCCCAATGGAGTTCCTCCAAGCCATGTTGTTTCAAATCAGCAGATTCCG
CCGGTATAGTCCCAAGAGGCTCAATGATGGCCGATTCTGATTCTGATTGTGAAATGAATATTGAA
GGCTTAAGTGCAGAAACAGGATCCATGAATTTCTCTGTC
Found at i:43799128 original size:7 final size:7
Alignment explanation
Indices: 43799116--43799140 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
43799106 TTCTTGAATG
43799116 TTTCTCA
1 TTTCTCA
43799123 TTTCTCA
1 TTTCTCA
43799130 TTTCTCA
1 TTTCTCA
43799137 TTTC
1 TTTC
43799141 CTATTCATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (7 bp):
TTTCTCA
Found at i:43804590 original size:17 final size:17
Alignment explanation
Indices: 43804542--43804592 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
43804532 ATTCCAAAAA
43804542 TAATA-TTATTTAATAATT
1 TAATATTTATTT--TAATT
* *
43804560 TAATATTAAATTTAATT
1 TAATATTTATTTTAATT
43804577 TAATATTTATTTTAAT
1 TAATATTTATTTTAAT
43804593 AGTATTTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
17 19 0.68
18 5 0.18
19 4 0.14
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TAATATTTATTTTAATT
Done.