Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 141 of 150
Found at i:42548947 original size:20 final size:20
Alignment explanation
Indices: 42548922--42548966 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
42548912 ACACAATATG
* *
42548922 ATATGAAGTACATT-TAAAA
1 ATATGAACTAAATTGTAAAA
42548941 CATATGAACTAAATTGTAAAA
1 -ATATGAACTAAATTGTAAAA
42548962 ATATG
1 ATATG
42548967 TGTACTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.51, C:0.07, G:0.11, T:0.31
Consensus pattern (20 bp):
ATATGAACTAAATTGTAAAA
Found at i:42553787 original size:40 final size:41
Alignment explanation
Indices: 42553741--42553827 Score: 138
Period size: 41 Copynumber: 2.1 Consensus size: 41
42553731 TTAACCCGAA
*
42553741 TAAAAATGTTAAAACTCGAGCCTGACCCAACCTGTTCGTAT
1 TAAAATTGTTAAAACTCGAGCCTGACCCAACCTGTTCGTAT
* **
42553782 TAAAATTTTTTTAACTCGAGCCTGACCCAACCTGTTCGTAT
1 TAAAATTGTTAAAACTCGAGCCTGACCCAACCTGTTCGTAT
42553823 TAAAA
1 TAAAA
42553828 AATTTTTATG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (41 bp):
TAAAATTGTTAAAACTCGAGCCTGACCCAACCTGTTCGTAT
Found at i:42553834 original size:41 final size:41
Alignment explanation
Indices: 42553753--42553835 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
42553743 AAAATGTTAA
**
42553753 AACTCGAGCCTGACCCAACCTGTTCGTATTAAAATTTTTTT
1 AACTCGAGCCTGACCCAACCTGTTCGTATTAAAAAATTTTT
42553794 AACTCGAGCCTGACCCAACCTGTTCGTATTAAAAAATTTTT
1 AACTCGAGCCTGACCCAACCTGTTCGTATTAAAAAATTTTT
42553835 A
1 A
42553836 TGTAAAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (41 bp):
AACTCGAGCCTGACCCAACCTGTTCGTATTAAAAAATTTTT
Found at i:42561677 original size:30 final size:30
Alignment explanation
Indices: 42561641--42561700 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
42561631 ATTTTTAGAC
*
42561641 TAAAGTTTATACCAGACAATAATATACAAA
1 TAAAGTTCATACCAGACAATAATATACAAA
42561671 TAAAGTTCATACCAGACAATAATATACAAA
1 TAAAGTTCATACCAGACAATAATATACAAA
42561701 GAATGGAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.53, C:0.15, G:0.07, T:0.25
Consensus pattern (30 bp):
TAAAGTTCATACCAGACAATAATATACAAA
Found at i:42562710 original size:27 final size:27
Alignment explanation
Indices: 42562669--42562798 Score: 181
Period size: 27 Copynumber: 4.8 Consensus size: 27
42562659 TAGTATTGGC
* *
42562669 GCCTATCTGGAAGGCGCCAATGGTGGT
1 GCCTATTTGGGAGGCGCCAATGGTGGT
42562696 GCCTATTTGGGAGGCGCCAATGGTGGT
1 GCCTATTTGGGAGGCGCCAATGGTGGT
*
42562723 GCCTATTTGGGAGGCGCTAATGGTGGT
1 GCCTATTTGGGAGGCGCCAATGGTGGT
* * *
42562750 GCCTATCTAGGAGGCACCAATGGTGGT
1 GCCTATTTGGGAGGCGCCAATGGTGGT
*
42562777 GCC-ATATTAGGAGGCGCCAATG
1 GCCTAT-TTGGGAGGCGCCAATG
42562799 CTGTGATTTT
Statistics
Matches: 93, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
26 2 0.02
27 91 0.98
ACGTcount: A:0.19, C:0.20, G:0.37, T:0.24
Consensus pattern (27 bp):
GCCTATTTGGGAGGCGCCAATGGTGGT
Found at i:42562902 original size:18 final size:20
Alignment explanation
Indices: 42562860--42562906 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 20
42562850 AAAACGGAAG
42562860 AAAGAAGAAGGAAGGAAGCA
1 AAAGAAGAAGGAAGGAAGCA
* *
42562880 GAAGAA-AA-GAAGGAAGGA
1 AAAGAAGAAGGAAGGAAGCA
42562898 AAAGAAGAA
1 AAAGAAGAA
42562907 AAAAGTTAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 14 0.61
19 4 0.17
20 5 0.22
ACGTcount: A:0.64, C:0.02, G:0.34, T:0.00
Consensus pattern (20 bp):
AAAGAAGAAGGAAGGAAGCA
Found at i:42562909 original size:22 final size:23
Alignment explanation
Indices: 42562856--42562909 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
42562846 TACAAAAACG
*
42562856 GAAGAAAGAAGAAGGAAGGAAGCA
1 GAAGAAA-AAGAAGGAAGGAAGAA
42562880 GAAG-AAAAGAAGGAAGGAA-AA
1 GAAGAAAAAGAAGGAAGGAAGAA
42562901 GAAGAAAAA
1 GAAGAAAAA
42562910 AGTTAGGTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 5 0.18
22 17 0.61
23 2 0.07
24 4 0.14
ACGTcount: A:0.65, C:0.02, G:0.33, T:0.00
Consensus pattern (23 bp):
GAAGAAAAAGAAGGAAGGAAGAA
Found at i:42566248 original size:6 final size:6
Alignment explanation
Indices: 42566229--42566281 Score: 88
Period size: 6 Copynumber: 8.8 Consensus size: 6
42566219 AGAATGTAGT
* *
42566229 TCTGCC TCTCGC TCTGGC TCTGGC TCTGGC TCTGGC TCTGGC TCTGGC
1 TCTGGC TCTGGC TCTGGC TCTGGC TCTGGC TCTGGC TCTGGC TCTGGC
42566277 TCTGG
1 TCTGG
42566282 TGCATGATGC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.00, C:0.36, G:0.30, T:0.34
Consensus pattern (6 bp):
TCTGGC
Found at i:42567935 original size:16 final size:15
Alignment explanation
Indices: 42567904--42567945 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
42567894 ACAAAATCAA
*
42567904 ATAAAATTTAATTAT
1 ATAAAAGTTAATTAT
42567919 ATAAAAGTTACATTAT
1 ATAAAAGTTA-ATTAT
*
42567935 ATAAAAATTAA
1 ATAAAAGTTAA
42567946 ATAAGTTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (15 bp):
ATAAAAGTTAATTAT
Found at i:42568298 original size:22 final size:22
Alignment explanation
Indices: 42568273--42568685 Score: 239
Period size: 22 Copynumber: 18.2 Consensus size: 22
42568263 AATTAATTAT
*
42568273 AAAATAATCACAATATTCATAC
1 AAAATAATTACAATATTCATAC
*
42568295 AAAA-AATTACAATATTACAATAT
1 AAAATAATTACAATATT-C-ATAC
***
42568318 ATCCTCACATTACAATATTCATAC
1 AAAAT-A-ATTACAATATTCATAC
42568342 AAAATTACAAAATTACAATATTCATAC
1 AAAA-T----AATTACAATATTCATAC
* *
42568369 AAAAAAATTGCAATATTCATAC
1 AAAATAATTACAATATTCATAC
*
42568391 AAAATTATAATATTACAACATTCATAC
1 -AAA--AT-A-ATTACAATATTCATAC
* *
42568418 AAAA-AAATATAATATTCATAC
1 AAAATAATTACAATATTCATAC
42568439 AAAATTATAAAATTACAATATTCATAC
1 -AAA--AT--AATTACAATATTCATAC
* * *
42568466 AAAAAAATTGCAATATTCATCC
1 AAAATAATTACAATATTCATAC
42568488 AAAACTATAATATTACAATATTCATAC
1 -AAA--AT-A-ATTACAATATTCATAC
*
42568515 AAAA-AATTTATAATATTCATAC
1 AAAATAA-TTACAATATTCATAC
42568537 --AA-AATTACAATATTCATAC
1 AAAATAATTACAATATTCATAC
* *
42568556 AAAA-AATTACTA-ATCCA-A-
1 AAAATAATTACAATATTCATAC
* * * *
42568574 AACTATAAATACAA-ATTTAATTAT
1 AA-AATAATTACAATA-TTCA-TAC
42568598 AAAATAATTACAATATTCATAC
1 AAAATAATTACAATATTCATAC
*
42568620 --AA-CATTACAATATTCATA-
1 AAAATAATTACAATATTCATAC
*
42568638 AAAA-AATTATAATATTCATAC
1 AAAATAATTACAATATTCATAC
*
42568659 AAAA-AATTTAAAATATTCATAC
1 AAAATAA-TTACAATATTCATAC
42568681 AAAAT
1 AAAAT
42568686 TCTAATCTAA
Statistics
Matches: 308, Mismatches: 43, Indels: 79
0.72 0.10 0.18
Matches are distributed among these distances:
18 2 0.01
19 31 0.10
20 33 0.11
21 42 0.14
22 75 0.24
23 23 0.07
24 11 0.04
25 5 0.02
26 22 0.07
27 63 0.20
28 1 0.00
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
AAAATAATTACAATATTCATAC
Found at i:42568362 original size:27 final size:25
Alignment explanation
Indices: 42568326--42568541 Score: 188
Period size: 27 Copynumber: 8.8 Consensus size: 25
42568316 ATATCCTCAC
42568326 ATTACAATATTCATACAAAATTACAAA
1 ATTACAATATTCATACAAAA-TA-AAA
42568353 ATTACAATATTCATAC--AA-AAAA
1 ATTACAATATTCATACAAAATAAAA
* *
42568375 ATTGCAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAA-TA-AAA
*
42568402 ATTACAACATTCATAC--AA-AAAA
1 ATTACAATATTCATACAAAATAAAA
*
42568424 A-TATAATATTCATACAAAATTATAAA
1 ATTACAATATTCATACAAAA-TA-AAA
42568450 ATTACAATATTCATAC--AA-AAAA
1 ATTACAATATTCATACAAAATAAAA
* * *
42568472 ATTGCAATATTCATCCAAAACTATAAT
1 ATTACAATATTCATACAAAA-TA-AAA
42568499 ATTACAATATTCATAC--AA-AAAA
1 ATTACAATATTCATACAAAATAAAA
* *
42568521 TTTATAATATTCATACAAAAT
1 ATTACAATATTCATACAAAAT
42568542 TACAATATTC
Statistics
Matches: 154, Mismatches: 16, Indels: 40
0.73 0.08 0.19
Matches are distributed among these distances:
21 12 0.08
22 54 0.35
23 6 0.04
24 6 0.04
25 9 0.06
26 6 0.04
27 61 0.40
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.31
Consensus pattern (25 bp):
ATTACAATATTCATACAAAATAAAA
Found at i:42568396 original size:49 final size:49
Alignment explanation
Indices: 42568330--42568543 Score: 324
Period size: 49 Copynumber: 4.4 Consensus size: 49
42568320 CCTCACATTA
*
42568330 CAATATTCATACAAAATTACAAAATTACAATATTCATACAAAAAAATTG
1 CAATATTCATACAAAATTATAAAATTACAATATTCATACAAAAAAATTG
* *
42568379 CAATATTCATACAAAATTATAATATTACAACATTCATACAAAAAAATAT-
1 CAATATTCATACAAAATTATAAAATTACAATATTCATACAAAAAAAT-TG
42568428 -AATATTCATACAAAATTATAAAATTACAATATTCATACAAAAAAATTG
1 CAATATTCATACAAAATTATAAAATTACAATATTCATACAAAAAAATTG
* * * * *
42568476 CAATATTCATCCAAAACTATAATATTACAATATTCATACAAAAAATTTA
1 CAATATTCATACAAAATTATAAAATTACAATATTCATACAAAAAAATTG
*
42568525 TAATATTCATACAAAATTA
1 CAATATTCATACAAAATTA
42568544 CAATATTCAT
Statistics
Matches: 149, Mismatches: 13, Indels: 6
0.89 0.08 0.04
Matches are distributed among these distances:
47 1 0.01
48 44 0.30
49 103 0.69
50 1 0.01
ACGTcount: A:0.54, C:0.14, G:0.01, T:0.31
Consensus pattern (49 bp):
CAATATTCATACAAAATTATAAAATTACAATATTCATACAAAAAAATTG
Found at i:42568444 original size:97 final size:98
Alignment explanation
Indices: 42568331--42568546 Score: 380
Period size: 97 Copynumber: 2.2 Consensus size: 98
42568321 CTCACATTAC
*
42568331 AATATTCATACAAAATTACAAAATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAAT
1 AATATTCATACAAAATTACAAAATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAAC
42568396 TATAATATTACAACATTCATACAAAAAA-ATAT
66 TATAATATTACAACATTCATACAAAAAATATAT
* *
42568428 AATATTCATACAAAATTATAAAATTACAATATTCATACAAAAAAATTGCAATATTCATCCAAAAC
1 AATATTCATACAAAATTACAAAATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAAC
* *
42568493 TATAATATTACAATATTCATACAAAAAATTTAT
66 TATAATATTACAACATTCATACAAAAAATATAT
42568526 AATATTCATACAAAATTACAA
1 AATATTCATACAAAATTACAA
42568547 TATTCATACA
Statistics
Matches: 112, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
97 89 0.79
98 23 0.21
ACGTcount: A:0.55, C:0.13, G:0.01, T:0.31
Consensus pattern (98 bp):
AATATTCATACAAAATTACAAAATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAAC
TATAATATTACAACATTCATACAAAAAATATAT
Found at i:42568549 original size:49 final size:48
Alignment explanation
Indices: 42568273--42568550 Score: 321
Period size: 49 Copynumber: 5.7 Consensus size: 48
42568263 AATTAATTAT
* *
42568273 AAAATAATCACAATATTCATACAAAAAATTACAATATTACAATATATCCT-C
1 AAAA-AATTACAATATTCATAC--AAAATTACAATATTACAATAT-TCATAC
* *
42568324 ---ACATTACAATATTCATACAAAATTACAAAATTACAATATTCATAC
1 AAAAAATTACAATATTCATACAAAATTACAATATTACAATATTCATAC
* * *
42568369 AAAAAAATTGCAATATTCATACAAAATTATAATATTACAACATTCATAC
1 -AAAAAATTACAATATTCATACAAAATTACAATATTACAATATTCATAC
* * * *
42568418 AAAAAAATATAATATTCATACAAAATTATAAAATTACAATATTCATAC
1 AAAAAATTACAATATTCATACAAAATTACAATATTACAATATTCATAC
* * * *
42568466 AAAAAAATTGCAATATTCATCCAAAACTATAATATTACAATATTCATAC
1 -AAAAAATTACAATATTCATACAAAATTACAATATTACAATATTCATAC
*
42568515 AAAAAATTTATAATATTCATACAAAATTACAATATT
1 AAAAAA-TTACAATATTCATACAAAATTACAATATT
42568551 CATACAAAAA
Statistics
Matches: 195, Mismatches: 25, Indels: 16
0.83 0.11 0.07
Matches are distributed among these distances:
44 3 0.02
45 21 0.11
47 15 0.08
48 50 0.26
49 106 0.54
ACGTcount: A:0.54, C:0.14, G:0.01, T:0.31
Consensus pattern (48 bp):
AAAAAATTACAATATTCATACAAAATTACAATATTACAATATTCATAC
Found at i:42568627 original size:83 final size:83
Alignment explanation
Indices: 42568447--42568650 Score: 238
Period size: 83 Copynumber: 2.4 Consensus size: 83
42568437 ACAAAATTAT
*
42568447 AAAATTACAATATTCATACAAAAAAATTGCAATATTCATCCAAAACTATAATATTACAATATTCA
1 AAAATTACAATATTCATAC-AAAAAATT---ATA---ATCCAAAACTATAATATTACAATATTAA
*
42568512 TACAAAAAATTTATAATATTCATAC
59 TACAAAAAATTTACAATATTCATAC
*
42568537 AAAATTACAATATTCATACAAAAAATTACTAATCCAAAACTATAA-A-TACAA-ATTTAATTATA
1 AAAATTACAATATTCATACAAAAAATTA-TAATCCAAAACTATAATATTACAATA-TTAA-TACA
42568599 AAATAA-TTACAATATTCATAC
63 AAA-AATTTACAATATTCATAC
*
42568620 AACATTACAATATTCATA-AAAAAATTATAAT
1 AAAATTACAATATTCATACAAAAAATTATAAT
42568651 ATTCATACAA
Statistics
Matches: 106, Mismatches: 4, Indels: 17
0.83 0.03 0.13
Matches are distributed among these distances:
81 5 0.05
82 17 0.16
83 38 0.36
84 16 0.15
86 1 0.01
87 2 0.02
89 8 0.08
90 19 0.18
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.32
Consensus pattern (83 bp):
AAAATTACAATATTCATACAAAAAATTATAATCCAAAACTATAATATTACAATATTAATACAAAA
AATTTACAATATTCATAC
Found at i:42568685 original size:83 final size:84
Alignment explanation
Indices: 42568447--42568685 Score: 213
Period size: 83 Copynumber: 2.8 Consensus size: 84
42568437 ACAAAATTAT
** * *
42568447 AAAATTACAATATTCATACAAAAAAATTGCAATATTCATCCAAAACTATAATATTACAATATTCA
1 AAAATTACAATATTCAT--AAAAAAATTATAATATTCATAC-AAA--A-AAT-TTAAAATATTCA
*
42568512 TACAAAA-AATTTATAATATTCATAC
59 TACAAAATAATTTACAATATTCATAC
* * * * *
42568537 AAAATTACAATATTCATACAAAAAATTACT-A-ATCCAAAACTATAAA--TACAAAT-TTAATTA
1 AAAATTACAATATTCATA-AAAAAATTA-TAATATTC-ATACAAAAAATTTA-AAATATTCA-TA
*
42568597 TAAAATAA-TTACAATATTCATAC
61 CAAAATAATTTACAATATTCATAC
*
42568620 AACATTACAATATTCATAAAAAAATTATAATATTCATACAAAAAATTTAAAATATTCATACAAAA
1 AAAATTACAATATTCATAAAAAAATTATAATATTCATACAAAAAATTTAAAATATTCATACAAAA
42568685 T
66 T
42568686 TCTAATCTAA
Statistics
Matches: 120, Mismatches: 18, Indels: 29
0.72 0.11 0.17
Matches are distributed among these distances:
81 1 0.01
82 22 0.18
83 54 0.45
84 7 0.06
85 2 0.02
86 1 0.01
88 5 0.04
89 11 0.09
90 17 0.14
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (84 bp):
AAAATTACAATATTCATAAAAAAATTATAATATTCATACAAAAAATTTAAAATATTCATACAAAA
TAATTTACAATATTCATAC
Found at i:42568859 original size:3 final size:3
Alignment explanation
Indices: 42568853--42568885 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
42568843 TTTTTTTTCT
42568853 TTC TTC TTC TTC TTC -TC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
42568886 CCTTTCTCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:42568873 original size:14 final size:14
Alignment explanation
Indices: 42568849--42568882 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
42568839 ACCTTTTTTT
42568849 TTCTT-TCTTCTTC
1 TTCTTCTCTTCTTC
42568862 TTCTTCTCTTCTTC
1 TTCTTCTCTTCTTC
42568876 TTCTTCT
1 TTCTTCT
42568883 TCTCCTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (14 bp):
TTCTTCTCTTCTTC
Found at i:42568875 original size:17 final size:17
Alignment explanation
Indices: 42568849--42568886 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
42568839 ACCTTTTTTT
42568849 TTCT-TTCTTCTTCTTC
1 TTCTCTTCTTCTTCTTC
42568865 TTCTCTTCTTCTTCTTC
1 TTCTCTTCTTCTTCTTC
42568882 TTCTC
1 TTCTC
42568887 CTTTCTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (17 bp):
TTCTCTTCTTCTTCTTC
Found at i:42568897 original size:17 final size:17
Alignment explanation
Indices: 42568854--42568897 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
42568844 TTTTTTTCTT
*
42568854 TCTTCTTCTTCTTCTCT
1 TCTTCTTCTTCTTCTCC
42568871 TCTTCTTCTTCTTCTCC
1 TCTTCTTCTTCTTCTCC
42568888 T-TTCTCTCTT
1 TCTTCT-TCTT
42568898 TTTTTTTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 4 0.16
17 21 0.84
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (17 bp):
TCTTCTTCTTCTTCTCC
Found at i:42569630 original size:26 final size:27
Alignment explanation
Indices: 42569584--42569646 Score: 69
Period size: 26 Copynumber: 2.3 Consensus size: 27
42569574 TCAATTTTTT
42569584 ATATTAAATTTTTTTGGTTTAATT-AAA
1 ATATTAAATTTTTTTGGTTT-ATTAAAA
*
42569611 ATATT-AATTTTTTAT-TTTTATTAAAA
1 ATATTAAATTTTTT-TGGTTTATTAAAA
42569637 ATATTTAAAT
1 ATA-TTAAAT
42569647 ATAAATACAG
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
25 3 0.10
26 17 0.55
27 8 0.26
28 3 0.10
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (27 bp):
ATATTAAATTTTTTTGGTTTATTAAAA
Found at i:42569811 original size:20 final size:20
Alignment explanation
Indices: 42569786--42569844 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
42569776 GTTGCTACAC
*
42569786 CACCATGCTGCTGTCCCTTA
1 CACCATGCTACTGTCCCTTA
** *
42569806 CACCATGCTTTTGTCCCTTC
1 CACCATGCTACTGTCCCTTA
* *
42569826 CACCAGGCTACTATCCCTT
1 CACCATGCTACTGTCCCTT
42569845 CAATGGGAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.15, C:0.41, G:0.12, T:0.32
Consensus pattern (20 bp):
CACCATGCTACTGTCCCTTA
Found at i:42571329 original size:50 final size:50
Alignment explanation
Indices: 42571204--42571445 Score: 204
Period size: 50 Copynumber: 4.7 Consensus size: 50
42571194 GAATATAACA
* * * * * *
42571204 TGCCAAAGCTATGTCCCAAACATAGTCTTACATGGGATGTT-TCCTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-GTTCTCATAT-CGG
* * *
42571253 TGCCAATGCCATATCCCGGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
* * ** ** *
42571303 TGCCCATGCCATGTCCCAGACATGGTCTGACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
* * *
42571353 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGA-TCTCTCATAGTCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGT-TCTCATA---TC---GG
42571409 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
42571446 TCTTATCACC
Statistics
Matches: 153, Mismatches: 30, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
48 4 0.03
49 34 0.22
50 77 0.50
53 2 0.01
56 36 0.24
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
Found at i:42572747 original size:28 final size:33
Alignment explanation
Indices: 42572709--42572774 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
42572699 AGAAGAGAGA
*
42572709 AAGAAAAGAGAGAA-AAGAGAATAAA-AAAAAAAG
1 AAGAGAAGA-AGAAGAAGA-AATAAAGAAAAAAAG
42572742 AAGAGAAGAAGAAGAAGAAATAAAGAAAAAAAG
1 AAGAGAAGAAGAAGAAGAAATAAAGAAAAAAAG
42572775 GTAATGTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
32 10 0.33
33 20 0.67
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.03
Consensus pattern (33 bp):
AAGAGAAGAAGAAGAAGAAATAAAGAAAAAAAG
Found at i:42572754 original size:25 final size:26
Alignment explanation
Indices: 42572712--42572770 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 26
42572702 AGAGAGAAAG
*
42572712 AAAAG-AGAGAAAAGAGAATAAAAAA
1 AAAAGAAGAGAAAAGAGAAGAAAAAA
42572737 AAAAGAAGAGAAGAAGAAGAAGAAATAAA
1 AAAAGAAGAGAA-AAG-AGAAGAAA-AAA
42572766 GAAAA
1 -AAAA
42572771 AAAGGTAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 5 0.18
26 6 0.21
27 3 0.11
28 7 0.25
29 3 0.11
30 4 0.14
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (26 bp):
AAAAGAAGAGAAAAGAGAAGAAAAAA
Found at i:42572986 original size:60 final size:60
Alignment explanation
Indices: 42572921--42573054 Score: 205
Period size: 60 Copynumber: 2.2 Consensus size: 60
42572911 TGAATGTAAT
* * *
42572921 TTTTTTGCTTTTTATAATTATTTTAAAATTAATTTGTTAGTAATTTAGGATTATGTTATAA
1 TTTTTTG-TGTTTATAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAA
*
42572982 TTTTTTGTGTTTGTAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAA
1 TTTTTTGTGTTTATAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAA
* *
42573042 ATTGTTGTGTTTA
1 TTTTTTGTGTTTA
42573055 GTTTAGTTTT
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
60 59 0.89
61 7 0.11
ACGTcount: A:0.31, C:0.01, G:0.12, T:0.57
Consensus pattern (60 bp):
TTTTTTGTGTTTATAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAA
Found at i:42573223 original size:38 final size:39
Alignment explanation
Indices: 42573148--42573224 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
42573138 TTTTAATCAT
42573148 ATAGTTGCTGTTAACTCATTTAATTTTTTTTATATAAAC
1 ATAGTTGCTGTTAACTCATTTAATTTTTTTTATATAAAC
42573187 ATAGTTGCTGTTAACTCATTTAA-TTTTTTTATATAAAC
1 ATAGTTGCTGTTAACTCATTTAATTTTTTTTATATAAAC
42573225 TTGGATATCA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
38 15 0.39
39 23 0.61
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.51
Consensus pattern (39 bp):
ATAGTTGCTGTTAACTCATTTAATTTTTTTTATATAAAC
Found at i:42578685 original size:20 final size:20
Alignment explanation
Indices: 42578660--42578697 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
42578650 ACTAGATCTG
42578660 TTAAAAAAATTTCAAAATTC
1 TTAAAAAAATTTCAAAATTC
* *
42578680 TTAAAACAATTTCGAAAT
1 TTAAAAAAATTTCAAAAT
42578698 GCAAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.34
Consensus pattern (20 bp):
TTAAAAAAATTTCAAAATTC
Found at i:42579047 original size:27 final size:27
Alignment explanation
Indices: 42579017--42579091 Score: 114
Period size: 27 Copynumber: 2.8 Consensus size: 27
42579007 GCCTCTGAGT
*
42579017 TAGGCACAACTAGTCGCGCCTGTCAGA
1 TAGGCTCAACTAGTCGCGCCTGTCAGA
* *
42579044 TAGGCTCAACTAGTCGCGCCTTTGAGA
1 TAGGCTCAACTAGTCGCGCCTGTCAGA
*
42579071 TAGGCTCAACTAGTTGCGCCT
1 TAGGCTCAACTAGTCGCGCCT
42579092 CGTATCTATA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.24
Consensus pattern (27 bp):
TAGGCTCAACTAGTCGCGCCTGTCAGA
Found at i:42582832 original size:23 final size:23
Alignment explanation
Indices: 42582799--42582842 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
42582789 ATCAAATATA
*
42582799 CTTTTTTTTATATTT-TTTGTTTT
1 CTTTTTGTTAT-TTTATTTGTTTT
42582822 CTTTTTGTTATTTTATTTGTT
1 CTTTTTGTTATTTTATTTGTT
42582843 GACCTTGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.09, C:0.05, G:0.07, T:0.80
Consensus pattern (23 bp):
CTTTTTGTTATTTTATTTGTTTT
Found at i:42588151 original size:31 final size:29
Alignment explanation
Indices: 42588086--42588160 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 29
42588076 ATAACGTTTC
* *
42588086 AAATAAATAGAATATATATAAAAATTAGA
1 AAATAAATAGAATATATAGAAAAATTAAA
*
42588115 CAATAAATA-AATAATAATAGAAACAATTAAA
1 AAATAAATAGAAT-AT-ATAGAAA-AATTAAA
*
42588146 AAATAAATAGTATAT
1 AAATAAATAGAATAT
42588161 TTAAAATAGA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
28 3 0.08
29 10 0.27
30 6 0.16
31 16 0.43
32 2 0.05
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.27
Consensus pattern (29 bp):
AAATAAATAGAATATATAGAAAAATTAAA
Found at i:42588261 original size:2 final size:2
Alignment explanation
Indices: 42588254--42588284 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
42588244 ATAAGAAATG
42588254 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
42588285 AGAAAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42604821 original size:31 final size:29
Alignment explanation
Indices: 42604756--42604830 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 29
42604746 ATAACGTTTC
* *
42604756 AAATAAATAGAATATATATAAAAATTAGA
1 AAATAAATAGAATATATAGAAAAATTAAA
*
42604785 CAATAAATA-AATAATAATAGAAACAATTAAA
1 AAATAAATAGAAT-AT-ATAGAAA-AATTAAA
*
42604816 AAATAAATAGTATAT
1 AAATAAATAGAATAT
42604831 TTAAAATAGA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
28 3 0.08
29 10 0.27
30 6 0.16
31 16 0.43
32 2 0.05
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.27
Consensus pattern (29 bp):
AAATAAATAGAATATATAGAAAAATTAAA
Found at i:42604931 original size:2 final size:2
Alignment explanation
Indices: 42604924--42604954 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
42604914 ATAAGAAATG
42604924 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
42604955 AGAAAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42606792 original size:40 final size:41
Alignment explanation
Indices: 42606744--42606900 Score: 205
Period size: 40 Copynumber: 3.9 Consensus size: 41
42606734 GTGGTTTTAG
42606744 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CTGGATGTGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGATGTGA
* * *
42606784 TCTACTCCACTACTGCTTAGGG-GAATAAGATCTGTGGTTCTG-
1 TCTGCTCCACTACTGCTTAGGGAG-ATAAGATC--TGGATGTGA
* * *
42606826 TCTGCTCCACTATTGCTTAGGGAGATAAGA-CTTGATGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGATGTGA
42606866 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGG
42606901 TTTTCTTCAC
Statistics
Matches: 99, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
39 5 0.05
40 56 0.57
41 5 0.05
42 26 0.26
43 7 0.07
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (41 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGATGTGA
Found at i:42606830 original size:82 final size:83
Alignment explanation
Indices: 42606728--42606899 Score: 267
Period size: 82 Copynumber: 2.1 Consensus size: 83
42606718 CATGGGGATG
* * *
42606728 AGATTTGTGGTTTTAGTCTGCTCCACTACTGCTTAGGGAGATAAGACTGGATGTGATCTACTCCA
1 AGATCTGTGGTTCTAGTCTGCTCCACTACTGCTTAGGGAGATAAGACTGGATGCGATCTACTCCA
42606793 CTACTGCTTAGGG-GAATA
66 CTACTGCTTAGGGAG-ATA
* * *
42606811 AGATCTGTGGTTCT-GTCTGCTCCACTATTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCA
1 AGATCTGTGGTTCTAGTCTGCTCCACTACTGCTTAGGGAGATAAGACTGGATGCGATCTACTCCA
42606875 CTACTGCTTAGGGAGATA
66 CTACTGCTTAGGGAGATA
42606893 AGATCTG
1 AGATCTG
42606900 GTTTTCTTCA
Statistics
Matches: 82, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
82 69 0.84
83 13 0.16
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (83 bp):
AGATCTGTGGTTCTAGTCTGCTCCACTACTGCTTAGGGAGATAAGACTGGATGCGATCTACTCCA
CTACTGCTTAGGGAGATA
Found at i:42607276 original size:134 final size:134
Alignment explanation
Indices: 42606904--42607810 Score: 1593
Period size: 134 Copynumber: 6.7 Consensus size: 134
42606894 GATCTGGTTT
* * *
42606904 TCTTCACTCTATTCTACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGT
1 TCTTCAATCTATTCCACTGCC-AA-CCAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGT
*
42606969 AGTCACAGGGAGGTAAAATCTGCCATCTTCGATCTGTTTCGCTGCCAAATACAGGAAGGCAAGAT
64 AGTCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGAT
42607034 CTGCAA
129 CTGCAA
* * *
42607040 TCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAATTATCGACTTCAATGTACTCCACTGT
1 TCTTCAATCTATTCCACTGCC-AA-CCAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGT
42607105 AGTCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGAT
64 AGTCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGAT
*
42607170 CTGTAA
129 CTGCAA
*
42607176 TCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAGTTATCGGCTTCAATATACTCCACTGTAG
1 TCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAG
*
42607241 TCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCACTGCCAAATACAGGAAGGCAAGATCT
66 TCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCT
*
42607306 GTAA
131 GCAA
*
42607310 TCTTCAATATATTCCACTGCCAACCAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAG
1 TCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAG
42607375 TCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCT
66 TCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCT
42607440 GCAA
131 GCAA
* *
42607444 TCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCCTCAATGTACTCCACTGT
1 TCTTCAATCTATTCCACTGCC-AA-CCAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGT
42607509 AGTCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGAT
64 AGTCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGAT
*
42607574 CTGTAA
129 CTGCAA
42607580 TCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAG
1 TCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAG
42607645 TCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCT
66 TCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCT
42607710 GCAA
131 GCAA
*
42607714 TCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAGTTATCGGCTTCAATGTACTCCTCTGTAG
1 TCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAG
*
42607779 T--CAGGGAGGTAAAATCTGCCATCTTTGATCTG
66 TCACAGGGAGGTAAAATCTGCCATCTTCGATCTG
42607811 TTCTCTGGGG
Statistics
Matches: 745, Mismatches: 24, Indels: 8
0.96 0.03 0.01
Matches are distributed among these distances:
132 30 0.04
134 429 0.58
135 6 0.01
136 280 0.38
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (134 bp):
TCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAG
TCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCT
GCAA
Found at i:42607476 original size:270 final size:268
Alignment explanation
Indices: 42606904--42607810 Score: 1602
Period size: 270 Copynumber: 3.4 Consensus size: 268
42606894 GATCTGGTTT
* *
42606904 TCTTCACTCTATTCTACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGT
1 TCTTCAATCTATTCCACTGCC-AA-ACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGT
*
42606969 AGTCACAGGGAGGTAAAATCTGCCATCTTCGATCTGTTTCGCTGCCAAATACAGGAAGGCAAGAT
64 AGTCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGAT
* * * *
42607034 CTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAATTATCGACTTCAATGTACTC
129 CTGTAATCTTCAATCTATTCCACTGCC-AA-CCAGGGAGATAGAGTTATCGGCTTCAATGTACTC
42607099 CACTGTAGTCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGG
192 CACTGTAGTCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGG
*
42607164 CAAGATCTGTAA
257 CAAGATCTGCAA
* *
42607176 TCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAGTTATCGGCTTCAATATACTCCACTGTAG
1 TCTTCAATCTATTCCACTGCCAAACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAG
*
42607241 TCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCACTGCCAAATACAGGAAGGCAAGATCT
66 TCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCT
*
42607306 GTAATCTTCAATATATTCCACTGCCAACCAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACT
131 GTAATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACT
42607371 GTAGTCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAG
196 GTAGTCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAG
42607436 ATCTGCAA
261 ATCTGCAA
*
42607444 TCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCCTCAATGTACTCCACTGT
1 TCTTCAATCTATTCCACTGCC-AA-ACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGT
42607509 AGTCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGAT
64 AGTCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGAT
42607574 CTGTAATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAGTTATCGGCTTCAATGTACTCCA
129 CTGTAATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAGTTATCGGCTTCAATGTACTCCA
42607639 CTGTAGTCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCA
194 CTGTAGTCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCA
42607704 AGATCTGCAA
259 AGATCTGCAA
* *
42607714 TCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAGTTATCGGCTTCAATGTACTCCTCTGTAG
1 TCTTCAATCTATTCCACTGCCAAACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAG
*
42607779 T--CAGGGAGGTAAAATCTGCCATCTTTGATCTG
66 TCACAGGGAGGTAAAATCTGCCATCTTCGATCTG
42607811 TTCTCTGGGG
Statistics
Matches: 612, Mismatches: 21, Indels: 10
0.95 0.03 0.02
Matches are distributed among these distances:
266 30 0.05
268 168 0.27
269 6 0.01
270 387 0.63
271 2 0.00
272 19 0.03
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (268 bp):
TCTTCAATCTATTCCACTGCCAAACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAG
TCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCT
GTAATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACT
GTAGTCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAG
ATCTGCAA
Found at i:42607679 original size:404 final size:404
Alignment explanation
Indices: 42606930--42607810 Score: 1658
Period size: 404 Copynumber: 2.2 Consensus size: 404
42606920 CTGCCAAATA
42606930 CAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCAT
1 CAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCAT
*
42606995 CTTCGATCTGTTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGC
66 CTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGC
*
42607060 CAAATACAGGGAGATAGAATTATCGACTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATC
131 CAAATACAGGGAGATAGAATTATCGACCTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATC
42607125 TGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGTAATCTTCAATCTATTC
196 TGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGTAATCTTCAATCTATTC
42607190 CACTGCCAACCAGGGAGATAGAGTTATCGGCTTCAATATACTCCACTGTAGTCACAGGGAGGTAA
261 CACTGCCAACCAGGGAGATAGAGTTATCGGCTTCAATATACTCCACTGTAGTCACAGGGAGGTAA
*
42607255 AATCTGCCATCTTCGATCTGCTTCACTGCCAAATACAGGAAGGCAAGATCTGTAATCTTCAATAT
326 AATCTGCCATCTTCGATCTGCTTCACTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATAT
42607320 ATTCCACTGCCAAC
391 ATTCCACTGCCAAC
42607334 CAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCAT
1 CAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCAT
42607399 CTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGC
66 CTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGC
* *
42607464 CAAATACAGGGAGATAGAGTTATCGGCCTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATC
131 CAAATACAGGGAGATAGAATTATCGACCTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATC
42607529 TGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGTAATCTTCAATCTATTC
196 TGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGTAATCTTCAATCTATTC
*
42607594 CACTGCCAACCAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAA
261 CACTGCCAACCAGGGAGATAGAGTTATCGGCTTCAATATACTCCACTGTAGTCACAGGGAGGTAA
* *
42607659 AATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCT
326 AATCTGCCATCTTCGATCTGCTTCACTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATAT
42607724 ATTCCACTGCCAAC
391 ATTCCACTGCCAAC
*
42607738 CAGGGAGATAGAGTTATCGGCTTCAATGTACTCCTCTGTAGT--CAGGGAGGTAAAATCTGCCAT
1 CAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCAT
*
42607801 CTTTGATCTG
66 CTTCGATCTG
42607811 TTCTCTGGGG
Statistics
Matches: 467, Mismatches: 10, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
402 30 0.06
404 437 0.94
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (404 bp):
CAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCAT
CTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGC
CAAATACAGGGAGATAGAATTATCGACCTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATC
TGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGTAATCTTCAATCTATTC
CACTGCCAACCAGGGAGATAGAGTTATCGGCTTCAATATACTCCACTGTAGTCACAGGGAGGTAA
AATCTGCCATCTTCGATCTGCTTCACTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATAT
ATTCCACTGCCAAC
Found at i:42608414 original size:108 final size:108
Alignment explanation
Indices: 42608225--42608420 Score: 313
Period size: 108 Copynumber: 1.8 Consensus size: 108
42608215 GAAAAATGCT
42608225 TGAAAAAGATTATCAAAATGGAGAAAATGAAATTTTGTTGAGAGCAAAGCTCTAAACAAACAAAT
1 TGAAAAAGATTATCAAAATGGAGAAAATGAAATTTTGTTGAGAGCAAAGCTCTAAACAAACAAAT
42608290 CAATCAAGACAACAAATTTTGCTGAGATACGAGATGTATAAGA
66 CAATCAAGACAACAAATTTTGCTGAGATACGAGATGTATAAGA
* * **
42608333 TGAAAAAGATTATCACAATGGATAAAATGGAAA-TTTGTTGAGAGCAAAGCTCTAAATGAACAAA
1 TGAAAAAGATTATCAAAATGGAGAAAAT-GAAATTTTGTTGAGAGCAAAGCTCTAAACAAACAAA
* * *
42608397 TTAATCAAGATAGCAAATTTTGCT
65 TCAATCAAGACAACAAATTTTGCT
42608421 AGAATACAAA
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
108 76 0.95
109 4 0.05
ACGTcount: A:0.47, C:0.11, G:0.17, T:0.25
Consensus pattern (108 bp):
TGAAAAAGATTATCAAAATGGAGAAAATGAAATTTTGTTGAGAGCAAAGCTCTAAACAAACAAAT
CAATCAAGACAACAAATTTTGCTGAGATACGAGATGTATAAGA
Found at i:42608484 original size:45 final size:43
Alignment explanation
Indices: 42608386--42608486 Score: 103
Period size: 45 Copynumber: 2.3 Consensus size: 43
42608376 GCAAAGCTCT
* * * *
42608386 AAATGAACAAATTAATCAAGATAGCAAATTTTGCTAGAATACA
1 AAATGAATAAATTAATCAAGATAGCAAATTTCGCAAAAATACA
* **
42608429 AAATGAGAATAAATTAATCAAGATGGCGTATTTCGTCAAAAATACAA
1 AAAT--GAATAAATTAATCAAGATAGCAAATTTCG-CAAAAATAC-A
42608476 AAATGAATAAA
1 AAATGAATAAA
42608487 ATAGAAATAG
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
43 4 0.09
45 31 0.66
46 7 0.15
47 5 0.11
ACGTcount: A:0.52, C:0.10, G:0.13, T:0.25
Consensus pattern (43 bp):
AAATGAATAAATTAATCAAGATAGCAAATTTCGCAAAAATACA
Found at i:42608780 original size:8 final size:8
Alignment explanation
Indices: 42608757--42608786 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
42608747 TGGCCTCTCC
42608757 TTTTTCTT
1 TTTTTCTT
42608765 TTTGTTCTT
1 TTT-TTCTT
42608774 TTTTTCTT
1 TTTTTCTT
42608782 TTTTT
1 TTTTT
42608787 TGTTTCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.87
Consensus pattern (8 bp):
TTTTTCTT
Found at i:42609223 original size:1 final size:1
Alignment explanation
Indices: 42609217--42609334 Score: 65
Period size: 1 Copynumber: 118.0 Consensus size: 1
42609207 CCGGTAGAGG
* * * * * * * * * **
42609217 TTTTTTTCTTATTTTTTATTTTTTATTTTTTGTTTTTTTTCTTTTGTTTTCTCTTTTTTTTTGCT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* ** * * ** *
42609282 TCTTTTTTTTACTTTTTTTGTTTTTTTGTTTTTTACTTTTTTTTTATTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
42609335 GTTCTTTTGC
Statistics
Matches: 82, Mismatches: 35, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 82 1.00
ACGTcount: A:0.05, C:0.07, G:0.04, T:0.84
Consensus pattern (1 bp):
T
Found at i:42609266 original size:26 final size:25
Alignment explanation
Indices: 42609237--42609337 Score: 84
Period size: 26 Copynumber: 4.1 Consensus size: 25
42609227 ATTTTTTATT
42609237 TTTTATTTTTTGTTTTTTTTCTTTTG
1 TTTTATTTTTT-TTTTTTTTCTTTTG
* **
42609263 TTTTCTCTTTTTTTTTGCTTCTTTT-
1 TTTTAT-TTTTTTTTTTTTTCTTTTG
* *
42609288 TTTTACTTTTTTTGTTTTTT-TGTT-
1 TTTTA-TTTTTTTTTTTTTTCTTTTG
* *
42609312 TTTTACTTTTTTTTTATTT-TTTTG
1 TTTTATTTTTTTTTTTTTTCTTTTG
42609336 TT
1 TT
42609338 CTTTTGCCTC
Statistics
Matches: 60, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
23 14 0.23
24 10 0.17
25 14 0.23
26 17 0.28
27 5 0.08
ACGTcount: A:0.04, C:0.07, G:0.06, T:0.83
Consensus pattern (25 bp):
TTTTATTTTTTTTTTTTTTCTTTTG
Found at i:42609306 original size:59 final size:58
Alignment explanation
Indices: 42609222--42609334 Score: 144
Period size: 59 Copynumber: 1.9 Consensus size: 58
42609212 AGAGGTTTTT
*
42609222 TTCTTATTTTTTATTTTTTATTTTTTGTT-TTTTTT-CTTTTGTTTTCTCTTTTTTTTTGC
1 TTCTTATTTTTTATTTTTTATTTTTT-TTGTTTTTTACTTTT-TTTT-TATTTTTTTTTGC
42609281 TTCTT-TTTTTTACTTTTTT-TGTTTTTTTGTTTTTTACTTTTTTTTTATTTTTTT
1 TTCTTATTTTTTA-TTTTTTAT-TTTTTTTGTTTTTTACTTTTTTTTTATTTTTTT
42609335 GTTCTTTTGC
Statistics
Matches: 49, Mismatches: 1, Indels: 9
0.83 0.02 0.15
Matches are distributed among these distances:
58 18 0.37
59 26 0.53
60 5 0.10
ACGTcount: A:0.05, C:0.07, G:0.04, T:0.83
Consensus pattern (58 bp):
TTCTTATTTTTTATTTTTTATTTTTTTTGTTTTTTACTTTTTTTTTATTTTTTTTTGC
Found at i:42609308 original size:34 final size:32
Alignment explanation
Indices: 42609228--42609342 Score: 101
Period size: 35 Copynumber: 3.4 Consensus size: 32
42609218 TTTTTTCTTA
* * *
42609228 TTTTTTATTTTTTATTTTTTGTTTTTTTT-CT
1 TTTTTTGTTTTTTTTTTTTTCTTTTTTTTACT
42609259 TTTGTTT-TCTCTTTTTTTTTGCTTCTTTTTTTTACT
1 TTT-TTTGT-T-TTTTTTTTT--TTCTTTTTTTTACT
42609295 TTTTTTGTTTTTTTGTTTTTTACTTTTTTTTTA-T
1 TTTTTTGTTTTTTT-TTTTTT-C-TTTTTTTTACT
*
42609329 TTTTTTGTTCTTTT
1 TTTTTTGTTTTTTT
42609343 GCCTCCATTG
Statistics
Matches: 71, Mismatches: 3, Indels: 17
0.78 0.03 0.19
Matches are distributed among these distances:
31 4 0.06
32 4 0.06
33 10 0.14
34 20 0.28
35 27 0.38
36 6 0.08
ACGTcount: A:0.04, C:0.07, G:0.05, T:0.83
Consensus pattern (32 bp):
TTTTTTGTTTTTTTTTTTTTCTTTTTTTTACT
Found at i:42617518 original size:23 final size:23
Alignment explanation
Indices: 42617492--42617536 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
42617482 TTTGGAGAGG
*
42617492 TTAAAACATAATTTTATCATTTA
1 TTAAAACATAATTTCATCATTTA
**
42617515 TTAAATTATAATTTCATCATTT
1 TTAAAACATAATTTCATCATTT
42617537 TAAGGGACTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (23 bp):
TTAAAACATAATTTCATCATTTA
Found at i:42630425 original size:30 final size:30
Alignment explanation
Indices: 42630366--42630425 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
42630356 TCTTTCATTC
* * * *
42630366 TTTGTTTATTATTGTTTGGTATGACCTTTA
1 TTTGTATATTATTGTCTGGTATAAACTTTA
42630396 TTTGTATATTATTGTCTGGTATAAACTTTA
1 TTTGTATATTATTGTCTGGTATAAACTTTA
42630426 GTCCAAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.22, C:0.07, G:0.15, T:0.57
Consensus pattern (30 bp):
TTTGTATATTATTGTCTGGTATAAACTTTA
Found at i:42630767 original size:33 final size:33
Alignment explanation
Indices: 42630729--42630801 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
42630719 CAGTTTTTAT
**
42630729 AAAATATTTT-CAGAAAATTTGTCCAAACACAAG
1 AAAATATTTTACAG-AAATTCATCCAAACACAAG
* *
42630762 AAAATATTTTACAGAGATTCATCCAAACACTAG
1 AAAATATTTTACAGAAATTCATCCAAACACAAG
42630795 -AAATATT
1 AAAATATT
42630802 AACTTTTCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 7 0.20
33 25 0.71
34 3 0.09
ACGTcount: A:0.48, C:0.15, G:0.08, T:0.29
Consensus pattern (33 bp):
AAAATATTTTACAGAAATTCATCCAAACACAAG
Found at i:42633731 original size:30 final size:30
Alignment explanation
Indices: 42633695--42633760 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
42633685 CACGATGGTC
*
42633695 GATAATTGGGTGGTGGAGGAACAGACGACG
1 GATAATTGGGTGGCGGAGGAACAGACGACG
* *
42633725 GATAATTGGGTGGCGGGGGAACAGGCGACG
1 GATAATTGGGTGGCGGAGGAACAGACGACG
*
42633755 AATAAT
1 GATAAT
42633761 ATTGAGCTAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.30, C:0.11, G:0.42, T:0.17
Consensus pattern (30 bp):
GATAATTGGGTGGCGGAGGAACAGACGACG
Found at i:42633879 original size:108 final size:108
Alignment explanation
Indices: 42633732--42633945 Score: 338
Period size: 108 Copynumber: 2.0 Consensus size: 108
42633722 ACGGATAATT
* * *
42633732 GGGTGGCGGGGGAACAGGCGACGAATAATATTGAGCTACATAGCCAGGTGCATAAGGTTGTTGGT
1 GGGTGGCGGGGGAACAGACGACGAATAATATTGAACTACATAGCCAGGTGCATAAGCTTGTTGGT
*
42633797 ATGGTGGTGGATATCCATCAATAGGAGGATTTTGATGATAACC
66 ACGGTGGTGGATATCCATCAATAGGAGGATTTTGATGATAACC
* * * * *
42633840 GGGTGGTGGGGGAACAGATGGCGGATAATCTTGAACTACATAGCCAGGTGCATAAGCTTGTTGGT
1 GGGTGGCGGGGGAACAGACGACGAATAATATTGAACTACATAGCCAGGTGCATAAGCTTGTTGGT
*
42633905 ACGGTGGTGGATATCCATCCATAGGAGGATTTTGATGATAA
66 ACGGTGGTGGATATCCATCAATAGGAGGATTTTGATGATAA
42633946 TAGGTCCGCA
Statistics
Matches: 96, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
108 96 1.00
ACGTcount: A:0.27, C:0.13, G:0.34, T:0.26
Consensus pattern (108 bp):
GGGTGGCGGGGGAACAGACGACGAATAATATTGAACTACATAGCCAGGTGCATAAGCTTGTTGGT
ACGGTGGTGGATATCCATCAATAGGAGGATTTTGATGATAACC
Found at i:42634637 original size:28 final size:29
Alignment explanation
Indices: 42634587--42634641 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
42634577 TTTCATAATA
*
42634587 ATTTTTTGAATTTTATGAATTTTTTATAT
1 ATTTTTTAAATTTTATGAATTTTTTATAT
*
42634616 ATTTTTTAAATTTT-TGATTTTTTTAT
1 ATTTTTTAAATTTTATGAATTTTTTAT
42634642 TAATAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 11 0.46
29 13 0.54
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.69
Consensus pattern (29 bp):
ATTTTTTAAATTTTATGAATTTTTTATAT
Found at i:42635178 original size:23 final size:22
Alignment explanation
Indices: 42635147--42635192 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
42635137 CCCTCAAAAG
*
42635147 TTAAAAATTTTTAATTAAACCC
1 TTAAAAAATTTTAATTAAACCC
42635169 TTAAAAAATTTTAATTAAACCC
1 TTAAAAAATTTTAATTAAACCC
42635191 TT
1 TT
42635193 CCAAAACTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (22 bp):
TTAAAAAATTTTAATTAAACCC
Found at i:42636321 original size:29 final size:30
Alignment explanation
Indices: 42636287--42636343 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
42636277 TGGATTAAAT
* * *
42636287 TAGTCCCTCTATTATTAAATAG-ATCAATA
1 TAGTCCCTATACTATTAAAAAGAATCAATA
42636316 TAGTCCCTATACTATTAAAAAGAATCAA
1 TAGTCCCTATACTATTAAAAAGAATCAA
42636344 ATAAGTTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.33
Consensus pattern (30 bp):
TAGTCCCTATACTATTAAAAAGAATCAATA
Found at i:42636876 original size:13 final size:13
Alignment explanation
Indices: 42636858--42636885 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
42636848 AATTAAAATA
42636858 ATATGTATCTTTT
1 ATATGTATCTTTT
42636871 ATATGTATCTTTT
1 ATATGTATCTTTT
42636884 AT
1 AT
42636886 CCAAAACTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.07, G:0.07, T:0.61
Consensus pattern (13 bp):
ATATGTATCTTTT
Found at i:42638247 original size:10 final size:11
Alignment explanation
Indices: 42638221--42638246 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
42638211 GGCTCAAAAG
42638221 AAAAATTCTTC
1 AAAAATTCTTC
42638232 AAAAATTCTTC
1 AAAAATTCTTC
42638243 AAAA
1 AAAA
42638247 TAGAGATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (11 bp):
AAAAATTCTTC
Found at i:42640325 original size:47 final size:47
Alignment explanation
Indices: 42640230--42640325 Score: 129
Period size: 47 Copynumber: 2.0 Consensus size: 47
42640220 TAGGTTCTGG
* * **
42640230 TCATATTTAATTTTTTTGATACAATGCTTAGAACTACTCATAGTCCA
1 TCATATTTAATCTTTTTGAGACAATGCTTAGAACTACTCATAACCCA
* * *
42640277 TCATATTTGATCTTTTTGAGACAATGCTTAGAATTATTCATAACCCA
1 TCATATTTAATCTTTTTGAGACAATGCTTAGAACTACTCATAACCCA
42640324 TC
1 TC
42640326 CTCAACCCAT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.31, C:0.18, G:0.09, T:0.42
Consensus pattern (47 bp):
TCATATTTAATCTTTTTGAGACAATGCTTAGAACTACTCATAACCCA
Found at i:42647226 original size:29 final size:27
Alignment explanation
Indices: 42647187--42647241 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
42647177 ACTTTTTGGA
42647187 ATTTTAGAATTTAGT-CTCTATATTTTT
1 ATTTTAGAATTTAGTCCT-TATATTTTT
*
42647214 ATTTTCAGAAATTTTGTCCTTATATTTT
1 ATTTT-AG-AATTTAGTCCTTATATTTT
42647242 ATAGATTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 5 0.21
28 2 0.08
29 15 0.62
30 2 0.08
ACGTcount: A:0.25, C:0.09, G:0.07, T:0.58
Consensus pattern (27 bp):
ATTTTAGAATTTAGTCCTTATATTTTT
Found at i:42662603 original size:25 final size:27
Alignment explanation
Indices: 42662561--42662614 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
42662551 CAGGGTTTGG
42662561 AGTTTGTGGTTCATGGTTT-GAATTCA
1 AGTTTGTGGTTCATGGTTTAGAATTCA
*
42662587 AGTTTG-GGTTCGA-GGTTTAGGATTCA
1 AGTTTGTGGTTC-ATGGTTTAGAATTCA
42662613 AG
1 AG
42662615 ATTCGAGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 10 0.40
26 15 0.60
ACGTcount: A:0.20, C:0.07, G:0.31, T:0.41
Consensus pattern (27 bp):
AGTTTGTGGTTCATGGTTTAGAATTCA
Found at i:42663106 original size:21 final size:21
Alignment explanation
Indices: 42663082--42663123 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
42663072 CAAACTCAAA
42663082 CTCAAACCCTAAATCCTAAAC
1 CTCAAACCCTAAATCCTAAAC
**
42663103 CTCAAACTTTAAATCCTAAAC
1 CTCAAACCCTAAATCCTAAAC
42663124 TTGAATCCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.43, C:0.33, G:0.00, T:0.24
Consensus pattern (21 bp):
CTCAAACCCTAAATCCTAAAC
Found at i:42663602 original size:17 final size:16
Alignment explanation
Indices: 42663580--42663613 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
42663570 TAATAAAAAA
*
42663580 TATATTTTTATATTTTT
1 TATA-TTTTAAATTTTT
42663597 TATATTTTAAATTTTT
1 TATATTTTAAATTTTT
42663613 T
1 T
42663614 TTTATATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TATATTTTAAATTTTT
Found at i:42666185 original size:24 final size:22
Alignment explanation
Indices: 42666153--42666196 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
42666143 TATTTTATAT
*
42666153 TTTATATATCATTATATCAAATTA
1 TTTAAATATCATT-TA-CAAATTA
42666177 TTTAAATATCATTTACAAAT
1 TTTAAATATCATTTACAAAT
42666197 ATCTTTGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 2 0.11
24 12 0.63
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (22 bp):
TTTAAATATCATTTACAAATTA
Found at i:42668369 original size:19 final size:19
Alignment explanation
Indices: 42668343--42668389 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
42668333 TATATAAACT
42668343 TATAAAAATTATAATAAAAA
1 TATAAAAA-TATAATAAAAA
* * *
42668363 TATAAAAATATTATAATAC
1 TATAAAAATATAATAAAAA
42668382 TATAAAAA
1 TATAAAAA
42668390 ATTAAAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (19 bp):
TATAAAAATATAATAAAAA
Found at i:42668393 original size:18 final size:19
Alignment explanation
Indices: 42668363--42668398 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
42668353 ATAATAAAAA
*
42668363 TATAAAAATATTATAATAC
1 TATAAAAATATTAAAATAC
42668382 TATAAAAA-ATTAAAATA
1 TATAAAAATATTAAAATA
42668399 TAATTCTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (19 bp):
TATAAAAATATTAAAATAC
Found at i:42669439 original size:9 final size:9
Alignment explanation
Indices: 42669422--42669564 Score: 67
Period size: 9 Copynumber: 14.7 Consensus size: 9
42669412 TCTTATGATT
42669422 TTTTAATAA
1 TTTTAATAA
*
42669431 TTTTCATAA
1 TTTTAATAA
*
42669440 GTTTATATCAA
1 TTTTA-AT-AA
42669451 TTTTAAT-A
1 TTTTAATAA
42669459 TTTTAAATAA
1 TTTT-AATAA
*
42669469 TTTTTTATAA
1 -TTTTAATAA
*
42669479 GTTTTTAAGAA
1 --TTTTAATAA
*
42669490 TTTTAATACGT
1 TTTTAATA--A
*
42669501 TTTTATAAAA
1 TTTTA-ATAA
42669511 TTTTAAATAA
1 TTTT-AATAA
*
42669521 TTTAAAT-A
1 TTTTAATAA
42669529 TGTTTAATTAA
1 T-TTTAA-TAA
42669540 TTTT-ATAA
1 TTTTAATAA
*
42669548 TTTATTAAAAA
1 -TT-TTAATAA
42669559 TTTTAA
1 TTTTAA
42669565 ATATCATTTG
Statistics
Matches: 103, Mismatches: 15, Indels: 32
0.69 0.10 0.21
Matches are distributed among these distances:
8 10 0.10
9 35 0.34
10 27 0.26
11 29 0.28
12 2 0.02
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (9 bp):
TTTTAATAA
Found at i:42669462 original size:39 final size:39
Alignment explanation
Indices: 42669419--42669514 Score: 97
Period size: 39 Copynumber: 2.4 Consensus size: 39
42669409 AGTTCTTATG
*
42669419 ATTTTTTAATAATTTTCATAAGTTTATATCAATTTTAAT
1 ATTTTTTAATAATTTTCATAAGTTTATAACAATTTTAAT
* * * *
42669458 A-TTTTAAATAATTTTTTATAAGTTTTTAAGAATTTTAAT
1 ATTTTTTAATAA-TTTTCATAAGTTTATAACAATTTTAAT
42669497 ACGTTTTTATAA-AATTTT
1 A--TTTTT-TAATAATTTT
42669515 AAATAATTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
38 9 0.20
39 25 0.54
41 4 0.09
42 6 0.13
43 2 0.04
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.56
Consensus pattern (39 bp):
ATTTTTTAATAATTTTCATAAGTTTATAACAATTTTAAT
Found at i:42669493 original size:20 final size:20
Alignment explanation
Indices: 42669421--42669516 Score: 81
Period size: 20 Copynumber: 4.8 Consensus size: 20
42669411 TTCTTATGAT
*
42669421 TTTTTAATAATTTTCATAAG
1 TTTTTAATAATTTTAATAAG
*
42669441 TTTAT-ATCAATTTTAAT-A-
1 TTTTTAAT-AATTTTAATAAG
* *
42669459 TTTTAAATAATTTTTTATAAG
1 TTTTTAATAA-TTTTAATAAG
* *
42669480 TTTTTAAGAATTTTAATACG
1 TTTTTAATAATTTTAATAAG
*
42669500 TTTTTATAAAATTTTAA
1 TTTTTA-ATAATTTTAA
42669517 ATAATTTAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
18 5 0.08
19 11 0.18
20 27 0.45
21 17 0.28
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.55
Consensus pattern (20 bp):
TTTTTAATAATTTTAATAAG
Found at i:42669515 original size:30 final size:29
Alignment explanation
Indices: 42669422--42669517 Score: 86
Period size: 30 Copynumber: 3.2 Consensus size: 29
42669412 TCTTATGATT
* * *
42669422 TTTTAATAATTTTCATAAGTTTATAT-CAA
1 TTTTAA-AATTTTAATAAGTTTTTATAAAA
* * **
42669451 TTTTAATATTTTAAATAATTTTTTATAAGT
1 TTTTAAAATTTT-AATAAGTTTTTATAAAA
*
42669481 TTTTAAGAATTTTAATACGTTTTTATAAAA
1 TTTTAA-AATTTTAATAAGTTTTTATAAAA
42669511 TTTTAAA
1 TTTTAAA
42669518 TAATTTAAAT
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
28 5 0.10
29 17 0.33
30 25 0.48
31 5 0.10
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (29 bp):
TTTTAAAATTTTAATAAGTTTTTATAAAA
Found at i:42669522 original size:10 final size:10
Alignment explanation
Indices: 42669421--42669567 Score: 62
Period size: 10 Copynumber: 14.9 Consensus size: 10
42669411 TTCTTATGAT
*
42669421 TTTTTAATAA
1 TTTTAAATAA
*
42669431 TTTT-CATAA
1 TTTTAAATAA
* *
42669440 GTTTATATCAA
1 TTTTAAAT-AA
42669451 TTTT-AAT-A
1 TTTTAAATAA
42669459 TTTTAAATAA
1 TTTTAAATAA
**
42669469 TTTTTTATAA
1 TTTTAAATAA
* *
42669479 GTTTTTAAGAA
1 -TTTTAAATAA
*
42669490 TTTT-AATACGT
1 TTTTAAATA--A
42669501 TTTTATAA-AA
1 TTTTA-AATAA
42669511 TTTTAAATAA
1 TTTTAAATAA
42669521 -TTTAAAT-A
1 TTTTAAATAA
*
42669529 TGTTTAATTAA
1 T-TTTAAATAA
42669540 TTTT--ATAA
1 TTTTAAATAA
42669548 TTTATTAAA-AA
1 -TT-TTAAATAA
42669559 TTTTAAATA
1 TTTTAAATA
42669568 TCATTTGTAA
Statistics
Matches: 105, Mismatches: 14, Indels: 36
0.68 0.09 0.23
Matches are distributed among these distances:
8 9 0.09
9 29 0.28
10 42 0.40
11 21 0.20
12 2 0.02
13 2 0.02
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (10 bp):
TTTTAAATAA
Found at i:42671623 original size:2 final size:2
Alignment explanation
Indices: 42671616--42671644 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
42671606 ATTCTCGTTT
42671616 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
42671645 TCGGAACATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42674207 original size:29 final size:29
Alignment explanation
Indices: 42674161--42674230 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 29
42674151 AACGATAACG
42674161 TAAGTGATTAAAACGTAATATT-TTAAATA
1 TAAGTGATTAAAACGTAAT-TTATTAAATA
*
42674190 TAAGTGATTAAAATGTAATTTAAGTTAAATA
1 TAAGTGATTAAAACGTAATTT-A-TTAAATA
*
42674221 AAAGTGATTA
1 TAAGTGATTA
42674231 TTTTTAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
28 2 0.06
29 18 0.50
31 16 0.44
ACGTcount: A:0.49, C:0.01, G:0.13, T:0.37
Consensus pattern (29 bp):
TAAGTGATTAAAACGTAATTTATTAAATA
Found at i:42678541 original size:9 final size:9
Alignment explanation
Indices: 42678529--42678556 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
42678519 TTTATCAAAT
42678529 TATTAATTG
1 TATTAATTG
42678538 TATTAATTG
1 TATTAATTG
42678547 TATTAATTG
1 TATTAATTG
42678556 T
1 T
42678557 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:42679088 original size:65 final size:66
Alignment explanation
Indices: 42678966--42679091 Score: 175
Period size: 65 Copynumber: 1.9 Consensus size: 66
42678956 TCAATTTTAT
* * *
42678966 CTTTTTTGGTCACCCAACTATTTTAGATTTTTTGAAGTCTTCATTTTGGTGACCAAAAAAGGTAA
1 CTTTTTTGCTCACCCAACTATCTTAGATTTTTGGAAGTCTTCATTTTGGTGACCAAAAAAGGTAA
42679031 A
66 A
* * *
42679032 CTTTTTTTCTCACCCAACTATCTTGGA-TTTTGGATGT-TTCCATTTTGGTGACCAAAAAAG
1 CTTTTTTGCTCACCCAACTATCTTAGATTTTTGGAAGTCTT-CATTTTGGTGACCAAAAAAG
42679092 ACAAAATTGA
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
64 2 0.04
65 28 0.53
66 23 0.43
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.41
Consensus pattern (66 bp):
CTTTTTTGCTCACCCAACTATCTTAGATTTTTGGAAGTCTTCATTTTGGTGACCAAAAAAGGTAA
A
Found at i:42684359 original size:2 final size:2
Alignment explanation
Indices: 42684352--42684386 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
42684342 TTAGTAGGAT
42684352 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42684387 GCCAAAGTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:42687305 original size:21 final size:21
Alignment explanation
Indices: 42687279--42687333 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
42687269 AACAGCGGTG
*
42687279 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGGTACTGTA
*
42687300 GCGGTGAGATTGGGTACTGTA
1 GCGGTGAGATTAGGTACTGTA
42687321 GCGGTGAGATTAG
1 GCGGTGAGATTAG
42687334 AAACAATGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.22, C:0.09, G:0.40, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGGTACTGTA
Found at i:42703899 original size:12 final size:12
Alignment explanation
Indices: 42703882--42703906 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42703872 TTGCAGGAGA
42703882 TGTTTTCTTATT
1 TGTTTTCTTATT
42703894 TGTTTTCTTATT
1 TGTTTTCTTATT
42703906 T
1 T
42703907 TATCAGGTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.08, T:0.76
Consensus pattern (12 bp):
TGTTTTCTTATT
Found at i:42709178 original size:6 final size:6
Alignment explanation
Indices: 42709162--42709199 Score: 60
Period size: 6 Copynumber: 6.3 Consensus size: 6
42709152 TGGAAGAAAC
42709162 TTCTG- TTCTGT TTCTGT TTCTGT TTCTGT TTCATGT TT
1 TTCTGT TTCTGT TTCTGT TTCTGT TTCTGT TTC-TGT TT
42709200 TAAGTTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.16
6 21 0.68
7 5 0.16
ACGTcount: A:0.03, C:0.16, G:0.16, T:0.66
Consensus pattern (6 bp):
TTCTGT
Found at i:42722824 original size:23 final size:24
Alignment explanation
Indices: 42722777--42722822 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
42722767 GAAAAATATT
42722777 AAATATATATATATTTTATTTTTA
1 AAATATATATATATTTTATTTTTA
*
42722801 AAATATA-ATAGTTTTTTATTTT
1 AAATATATATA-TATTTTATTTT
42722823 AAGTTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (24 bp):
AAATATATATATATTTTATTTTTA
Found at i:42723031 original size:16 final size:16
Alignment explanation
Indices: 42723010--42723051 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
42723000 AATAATTTGA
42723010 TAATTTTACA-AACAAT
1 TAATTTTA-ATAACAAT
42723026 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
42723042 TAGTTTTAAT
1 TAATTTTAAT
42723052 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 1 0.04
16 23 0.96
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.45
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:42723050 original size:22 final size:23
Alignment explanation
Indices: 42723025--42723080 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
42723015 TTACAAACAA
* * *
42723025 TTAATTTTAAT-AACAATTAGTT
1 TTAATTTTAATAAAAAAATAATT
*
42723047 TTAATTTTATTAAAAAAATAATT
1 TTAATTTTAATAAAAAAATAATT
42723070 TTAATTTTAAT
1 TTAATTTTAAT
42723081 TTTAATTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
TTAATTTTAATAAAAAAATAATT
Found at i:42726374 original size:19 final size:20
Alignment explanation
Indices: 42726338--42726390 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
42726328 AAAAATTACA
*
42726338 AAAAAATCAAAATAATTT-T
1 AAAAATTCAAAATAATTTAT
42726357 CAAAAATTCAAAAT-ATTTAT
1 -AAAAATTCAAAATAATTTAT
42726377 AAAAATTCCAAAAT
1 AAAAATT-CAAAAT
42726391 TTATATTGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 11 0.37
20 19 0.63
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAAATTCAAAATAATTTAT
Found at i:42726380 original size:18 final size:18
Alignment explanation
Indices: 42726358--42726395 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
42726348 AATAATTTTC
42726358 AAAAATTCAAAATATTTAT
1 AAAAATTCAAAA-ATTTAT
*
42726377 AAAAATTCCAAAATTTAT
1 AAAAATTCAAAAATTTAT
42726395 A
1 A
42726396 TTGATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAAATTCAAAAATTTAT
Found at i:42726381 original size:20 final size:20
Alignment explanation
Indices: 42726337--42726424 Score: 63
Period size: 20 Copynumber: 4.2 Consensus size: 20
42726327 CAAAAATTAC
*
42726337 AAAAAAATCAAAATAATTT-T
1 AAAAAATTCAAAAT-ATTTAT
*
42726357 CAAAAATTCAAAATATTTAT
1 AAAAAATTCAAAATATTTAT
42726377 -AAAAATTCCAAAATTTATATTGAT
1 AAAAAATT-CAAAA--TAT-TT-AT
* *
42726401 AAAAAAATTCAAAAAATATAT
1 -AAAAAATTCAAAATATTTAT
42726422 AAA
1 AAA
42726425 TAAGTTAAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
19 11 0.20
20 21 0.38
21 2 0.04
22 4 0.07
23 4 0.07
24 2 0.04
25 5 0.09
26 7 0.12
ACGTcount: A:0.61, C:0.07, G:0.01, T:0.31
Consensus pattern (20 bp):
AAAAAATTCAAAATATTTAT
Found at i:42726710 original size:19 final size:19
Alignment explanation
Indices: 42726672--42726710 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
42726662 TTCGCTCGAC
* *
42726672 TCAATTTAAAAAAATTAAA
1 TCAAATTAAAAAAATAAAA
*
42726691 TCAAATTAAAATAATAAAA
1 TCAAATTAAAAAAATAAAA
42726710 T
1 T
42726711 AAAACTCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (19 bp):
TCAAATTAAAAAAATAAAA
Found at i:42727463 original size:9 final size:9
Alignment explanation
Indices: 42727449--42727524 Score: 91
Period size: 9 Copynumber: 8.4 Consensus size: 9
42727439 GTAGTGATTC
42727449 AATTCGGTT
1 AATTCGGTT
*
42727458 AATTCGGGT
1 AATTCGGTT
42727467 AATTCGGTT
1 AATTCGGTT
*
42727476 AATTCGGGT
1 AATTCGGTT
42727485 AA-TCAGGTT
1 AATTC-GGTT
* *
42727494 AATTCAGAT
1 AATTCGGTT
*
42727503 AATTCGGGT
1 AATTCGGTT
42727512 AATTCGGTT
1 AATTCGGTT
42727521 AATT
1 AATT
42727525 TTTAACCAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
8 2 0.04
9 52 0.93
10 2 0.04
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.38
Consensus pattern (9 bp):
AATTCGGTT
Found at i:42730539 original size:10 final size:11
Alignment explanation
Indices: 42730501--42730553 Score: 51
Period size: 10 Copynumber: 5.0 Consensus size: 11
42730491 TATCAATGAG
*
42730501 ATAAAAAAATT
1 ATAAAATAATT
42730512 ACTAAAAT-ATT
1 A-TAAAATAATT
42730523 AGT-AAATAATT
1 A-TAAAATAATT
42730534 A-AAAATAA-T
1 ATAAAATAATT
42730543 ATAAAATAATT
1 ATAAAATAATT
42730554 TCTAATATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
9 2 0.06
10 17 0.49
11 11 0.31
12 5 0.14
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (11 bp):
ATAAAATAATT
Found at i:42736873 original size:177 final size:176
Alignment explanation
Indices: 42736620--42737005 Score: 630
Period size: 177 Copynumber: 2.2 Consensus size: 176
42736610 TGTATGTAGA
42736620 GTTGGTGAAACATACAACGGAAA-GCCAGAGAATGCTCCAGCAGATAGGGAAGGCAAACCACAGC
1 GTTGGTGAAACATACAAC-GAAAGGCCAGAGAA-GCTCCAGCAGATAGGGAAGGCAAACCACAGC
* *
42736684 ACCATAAGAACCGATCCATCACTCTCGGGTCAGTTAAAGAATTCAATTTCGACAATATTAATGGA
64 ACCATAAGAACCGATCCATCACTCTCGGGTCACTTAAAGAATTCAATTTCGACAATATTAATGCA
* *
42736749 GAGATAGAAGAAAATGCTACTAAGTCAGTGGAAACTTATGAAGGTCGT
129 GAGATAGAAGAAAATGCTACCAAGTCAGTGGAAACTCATGAAGGTCGT
*
42736797 GTTGGTGAAACATGCAACGAAAGGCCAGAGCAAGCTCCAGCAGATAGGGAAGGCAAACCACAGCA
1 GTTGGTGAAACATACAACGAAAGGCCAGAG-AAGCTCCAGCAGATAGGGAAGGCAAACCACAGCA
* * *
42736862 CCATAAGAACCGATCCATCACTCTTGGGTCACTTAAAGAATTCAATTTCGACAATGTTAATGCCG
65 CCATAAGAACCGATCCATCACTCTCGGGTCACTTAAAGAATTCAATTTCGACAATATTAATGCAG
* *
42736927 AGATAGAAGAAAATGCTACCAAGTCGGTGGAAACTCATGAATGTCGT
130 AGATAGAAGAAAATGCTACCAAGTCAGTGGAAACTCATGAAGGTCGT
* *
42736974 GTTGGTGAAACATACAATGAAAGACCAGAGAA
1 GTTGGTGAAACATACAACGAAAGGCCAGAGAA
42737006 AGCTGAAGTA
Statistics
Matches: 194, Mismatches: 13, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
176 6 0.03
177 186 0.96
178 2 0.01
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.19
Consensus pattern (176 bp):
GTTGGTGAAACATACAACGAAAGGCCAGAGAAGCTCCAGCAGATAGGGAAGGCAAACCACAGCAC
CATAAGAACCGATCCATCACTCTCGGGTCACTTAAAGAATTCAATTTCGACAATATTAATGCAGA
GATAGAAGAAAATGCTACCAAGTCAGTGGAAACTCATGAAGGTCGT
Found at i:42739391 original size:18 final size:17
Alignment explanation
Indices: 42739368--42739405 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
42739358 TTTAAGAAAC
42739368 ATTTTTGAGACAAAAAGT
1 ATTTTTGAGACAAAAA-T
*
42739386 ATTTTTGAGATAAAAAT
1 ATTTTTGAGACAAAAAT
42739403 ATT
1 ATT
42739406 GTCAAACAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.45, C:0.03, G:0.13, T:0.39
Consensus pattern (17 bp):
ATTTTTGAGACAAAAAT
Found at i:42740671 original size:30 final size:32
Alignment explanation
Indices: 42740635--42740704 Score: 108
Period size: 32 Copynumber: 2.2 Consensus size: 32
42740625 ATTCATCAAA
*
42740635 ACAAAAAAC-AG-ATCTTGTAATAAAATGGTG
1 ACAAAAAACTAGAATCTTGTAATAAAATGATG
*
42740665 ACAAAAAACTCGAATCTTGTAATAAAATGATG
1 ACAAAAAACTAGAATCTTGTAATAAAATGATG
42740697 ACAAAAAA
1 ACAAAAAA
42740705 GTGAAGAACC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 9 0.25
31 1 0.03
32 26 0.72
ACGTcount: A:0.54, C:0.11, G:0.13, T:0.21
Consensus pattern (32 bp):
ACAAAAAACTAGAATCTTGTAATAAAATGATG
Found at i:42746827 original size:16 final size:16
Alignment explanation
Indices: 42746797--42746831 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
42746787 ATTTTTATCA
42746797 TTTTTAAATTAAAAAT
1 TTTTTAAATTAAAAAT
42746813 TTTTATAAATT-AAAAT
1 TTTT-TAAATTAAAAAT
42746829 TTT
1 TTT
42746832 ACTATTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTTTTAAATTAAAAAT
Found at i:42750412 original size:18 final size:17
Alignment explanation
Indices: 42750371--42750416 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
42750361 CTAAATAGTC
*
42750371 TTAAAAAAT-ATTATAT
1 TTAAAAAATAATTAAAT
42750387 TTATAAAAATAATTCAAAT
1 TTA-AAAAATAATT-AAAT
42750406 TT-AAAAATAAT
1 TTAAAAAATAAT
42750417 CACAAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 3 0.12
17 15 0.58
18 3 0.12
19 5 0.19
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (17 bp):
TTAAAAAATAATTAAAT
Found at i:42750607 original size:6 final size:7
Alignment explanation
Indices: 42750590--42750616 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
42750580 ACTGATATAC
42750590 AAAAAAG
1 AAAAAAG
42750597 AAAAAAG
1 AAAAAAG
42750604 AAAAAAG
1 AAAAAAG
42750611 AAAAAA
1 AAAAAA
42750617 AATTTGGGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:42751077 original size:108 final size:107
Alignment explanation
Indices: 42750926--42751324 Score: 336
Period size: 108 Copynumber: 3.6 Consensus size: 107
42750916 CAGTATACAA
* * * *
42750926 AAAAAGTAAAAAAAAAATTTCCCACAAAAAAGGTAGTGTCGGCCATTGGCAAACCAGCACAAAAA
1 AAAAAGTAAAAAAAAAATTTCCC-CAAAAAAGGTGGTGCCGGCCATTGGCAAGCCACCACAAAAA
* * * *
42750991 AAAATTTCTCCTTTTTTGGTATACTGATACATGCTATTGACACG
65 AAAATTTTTACTTTTTTAGTATATTGATAC-TGCTATTGACACG
* * * * *
42751035 AAACAAGTGAAAAAAAAATTT-CCGAAAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCACAA
1 AAA-AAGTAAAAAAAAAATTTCCCCAAAAAAGGTGGTGCCGGCCATTGGCAAGCCACCACAAAAA
*** ** * * * * **
42751099 ATTTTGTTTTTTTTTTTTACTTTTTTAGTATACTGATACCAGGACACG
65 AAAAT-TTTTACTTTTTTAGTATATT-G-ATACTGCTA--TTGACACG
* *
42751147 AAAAAAGTAAAAAAAAAATTTCCCCCAAAAAAGGTGGTGCCGGCCATTGGCAAGTCACCACAAAT
1 -AAAAAGTAAAAAAAAAATTT-CCCCAAAAAAGGTGGTGCCGGCCATTGGCAAGCCACCACAAAA
***** * *
42751212 TTTTTTTTTTACTTTTTTCGTATATTGATACTTGCAATTGACACG
64 AAAAATTTTTACTTTTTTAGTATATTGATAC-TGCTATTGACACG
* * *
42751257 AAAAGAGTGTAAAAAAAAA-TT-CTCAAAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACAAAA
1 AAAA-AGT-AAAAAAAAAATTTCCCCAAAAAAGGTGGTGCCGGCCATTGGCAAGCCACCACAAAA
42751320 AAAAA
64 AAAAA
42751325 CATTTTTTTT
Statistics
Matches: 226, Mismatches: 52, Indels: 25
0.75 0.17 0.08
Matches are distributed among these distances:
108 73 0.32
109 21 0.09
110 32 0.14
111 17 0.08
112 26 0.12
113 17 0.08
114 40 0.18
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26
Consensus pattern (107 bp):
AAAAAGTAAAAAAAAAATTTCCCCAAAAAAGGTGGTGCCGGCCATTGGCAAGCCACCACAAAAAA
AAATTTTTACTTTTTTAGTATATTGATACTGCTATTGACACG
Found at i:42751333 original size:222 final size:222
Alignment explanation
Indices: 42750925--42751334 Score: 547
Period size: 222 Copynumber: 1.8 Consensus size: 222
42750915 TCAGTATACA
* *
42750925 AAAAAAGTAAAAAAAAAATTTCCCACAAAAAAGGTAGTGTCGGCCATTGGCAAACCAGCACAAAA
1 AAAAAAGTAAAAAAAAAATTTCCCACAAAAAAGGTAGTGCCGGCCATTGGCAAACCACCACAAAA
* * *
42750990 AAAAATTTCTCCTTTTTTGGTATACTGATACATGCTATTGACACGAAACAAGTGAAAAAAAAATT
66 AAAAATTTCTACTTTTTTCGTATACTGATACATGCAATTGACACGAAACAAGTGAAAAAAAAATT
* * *****
42751055 TCCGAAAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCACAAATTTTGTTTTTTTTTTTTACT
131 TCCGAAAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACAAAAAAAAACATTTTTTTTTTTTACT
42751120 TTTTTAGTATACTGATACCAGGACACG
196 TTTTTAGTATACTGATACCAGGACACG
* * ** *
42751147 AAAAAAGTAAAAAAAAAATTTCCCCCAAAAAAGGTGGTGCCGGCCATTGGCAAGTCACCACAAAT
1 AAAAAAGTAAAAAAAAAATTTCCCACAAAAAAGGTAGTGCCGGCCATTGGCAAACCACCACAAAA
***** * * *
42751212 TTTTTTTTTTACTTTTTTCGTATATTGATACTTGCAATTGACACGAAA-AGAGTGTAAAAAAAAA
66 AAAAATTTCTACTTTTTTCGTATACTGATACATGCAATTGACACGAAACA-AGTG-AAAAAAAAA
42751276 -TTCTC-AAAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACAAAAAAAAACATTTTTTTT
129 TTTC-CGAAAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACAAAAAAAAACATTTTTTTT
42751335 ACTTTTTTCA
Statistics
Matches: 160, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
221 1 0.01
222 149 0.93
223 10 0.06
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (222 bp):
AAAAAAGTAAAAAAAAAATTTCCCACAAAAAAGGTAGTGCCGGCCATTGGCAAACCACCACAAAA
AAAAATTTCTACTTTTTTCGTATACTGATACATGCAATTGACACGAAACAAGTGAAAAAAAAATT
TCCGAAAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACAAAAAAAAACATTTTTTTTTTTTACT
TTTTTAGTATACTGATACCAGGACACG
Found at i:42755178 original size:48 final size:50
Alignment explanation
Indices: 42755090--42755192 Score: 147
Period size: 48 Copynumber: 2.1 Consensus size: 50
42755080 GTTTCTTCAT
42755090 CATCAAACTTAAAAAGCAACCACCAGCTTTTATGTTGTAACGTGGCAATCG
1 CATCAAACTTAAAAAGCAACCACCAGC-TTTATGTTGTAACGTGGCAATCG
* * * *
42755141 CATCAACCTT-AAATGCGACCACCAGC-TTATGTTGTAACGTGGCAATTG
1 CATCAAACTTAAAAAGCAACCACCAGCTTTATGTTGTAACGTGGCAATCG
42755189 CATC
1 CATC
42755193 TTCTTTAGCG
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
48 25 0.52
50 14 0.29
51 9 0.19
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (50 bp):
CATCAAACTTAAAAAGCAACCACCAGCTTTATGTTGTAACGTGGCAATCG
Found at i:42761260 original size:29 final size:29
Alignment explanation
Indices: 42761218--42761277 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
42761208 CAGATCTGGG
42761218 TATTAAGCATCTTTCAAGAAAAAAGGTTC
1 TATTAAGCATCTTTCAAGAAAAAAGGTTC
42761247 TATTAAGCATCTTTCAAGAAAAAAGGTTC
1 TATTAAGCATCTTTCAAGAAAAAAGGTTC
42761276 TA
1 TA
42761278 ACTTCGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (29 bp):
TATTAAGCATCTTTCAAGAAAAAAGGTTC
Found at i:42770056 original size:19 final size:17
Alignment explanation
Indices: 42770010--42770057 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 17
42770000 TTCAATTAAA
42770010 ATTTATTA-AAAATATT
1 ATTTATTACAAAATATT
42770026 ATTTTATATACAAAATAAATT
1 A-TTTAT-TACAAAAT--ATT
42770047 ATTTATTACAA
1 ATTTATTACAA
42770058 GGTTGTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 1 0.04
17 5 0.19
18 2 0.07
19 10 0.37
20 5 0.19
21 4 0.15
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (17 bp):
ATTTATTACAAAATATT
Found at i:42770470 original size:33 final size:34
Alignment explanation
Indices: 42770410--42770484 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 34
42770400 AATATAGTTG
* * * * *
42770410 ATATTTAATTAACTTGTGACGTTAATTTAAT-TA
1 ATATTTAATTAACTTCTCACATCAATTTAATCAA
*
42770443 ATATTTAATTAATTTCTCACATCAATTTAATCAA
1 ATATTTAATTAACTTCTCACATCAATTTAATCAA
42770477 ATATTTAA
1 ATATTTAA
42770485 GGTTGACTGA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
33 26 0.74
34 9 0.26
ACGTcount: A:0.40, C:0.09, G:0.04, T:0.47
Consensus pattern (34 bp):
ATATTTAATTAACTTCTCACATCAATTTAATCAA
Found at i:42771332 original size:16 final size:18
Alignment explanation
Indices: 42771293--42771326 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42771283 TAAGTTTATA
42771293 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
42771310 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
42771327 AATTTAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:42777297 original size:22 final size:20
Alignment explanation
Indices: 42777264--42777311 Score: 53
Period size: 22 Copynumber: 2.4 Consensus size: 20
42777254 ACTCCTTCAT
* *
42777264 TTATATAAATAAATTAATAA
1 TTATATAAATAAAATAAAAA
42777284 TTATATAATTATAAAATAAAAA
1 TTATATAA--ATAAAATAAAAA
42777306 -TATATA
1 TTATATA
42777312 TTCTTTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 8 0.33
21 6 0.25
22 10 0.42
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TTATATAAATAAAATAAAAA
Found at i:42784194 original size:18 final size:18
Alignment explanation
Indices: 42784171--42784235 Score: 67
Period size: 18 Copynumber: 3.4 Consensus size: 18
42784161 TAAATATATT
42784171 TATTTTTTAATTTTAAAA
1 TATTTTTTAATTTTAAAA
**
42784189 TATTTTTTACATACTTTTTTAA
1 TATTTTTT--A-A-TTTTAAAA
*
42784211 TTTTTTTTAATTTTAAAA
1 TATTTTTTAATTTTAAAA
42784229 TATTTTT
1 TATTTTT
42784236 AAAATACTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
18 20 0.54
19 1 0.03
20 2 0.05
21 1 0.03
22 13 0.35
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTTTTAATTTTAAAA
Found at i:42784225 original size:40 final size:40
Alignment explanation
Indices: 42784173--42784310 Score: 176
Period size: 40 Copynumber: 3.5 Consensus size: 40
42784163 AATATATTTA
42784173 TTTTTTAATTTTAAAATATTTTTTACATAC-TTTTTTAATT
1 TTTTTTAATTTTAAAATATTTTTTA-ATACTTTTTTTAATT
*
42784213 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTTAA-T
1 TTTTTTAATTTTAAAATATTTTT-TAATAC-TTTTTTTAATT
*
42784254 TTTTTTAATTTTAAAATA--TTTTAAAACTTTTTTTAATT
1 TTTTTTAATTTTAAAATATTTTTTAATACTTTTTTTAATT
**
42784292 TTTTAAAATTTTTAAAATA
1 TTTTTTAA-TTTTAAAATA
42784311 AAAATGGGCC
Statistics
Matches: 88, Mismatches: 5, Indels: 11
0.85 0.05 0.11
Matches are distributed among these distances:
37 9 0.10
38 11 0.12
39 13 0.15
40 27 0.31
41 20 0.23
42 8 0.09
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (40 bp):
TTTTTTAATTTTAAAATATTTTTTAATACTTTTTTTAATT
Found at i:42784284 original size:9 final size:10
Alignment explanation
Indices: 42784261--42784310 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
42784251 AATTTTTTTA
42784261 ATTTTAAAAT
1 ATTTTAAAAT
42784271 ATTTTAAAACT
1 ATTTTAAAA-T
**
42784282 -TTTTTTAAT
1 ATTTTAAAAT
*
42784291 TTTTTAAAAT
1 ATTTTAAAAT
42784301 -TTTTAAAAT
1 ATTTTAAAAT
42784310 A
1 A
42784311 AAAATGGGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
9 10 0.30
10 22 0.67
11 1 0.03
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (10 bp):
ATTTTAAAAT
Found at i:42784285 original size:28 final size:28
Alignment explanation
Indices: 42784253--42784308 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
42784243 TTTTTTTTAA
42784253 TTTTTTTAA-TTTTAAAATATTTTAAAAC
1 TTTTTTTAATTTTTAAAAT-TTTTAAAAC
42784281 TTTTTTTAATTTTTTAAAATTTTTAAAA
1 TTTTTTTAA-TTTTTAAAATTTTTAAAA
42784309 TAAAAATGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 9 0.35
29 8 0.31
30 9 0.35
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (28 bp):
TTTTTTTAATTTTTAAAATTTTTAAAAC
Found at i:42784303 original size:8 final size:9
Alignment explanation
Indices: 42784262--42784309 Score: 51
Period size: 9 Copynumber: 5.0 Consensus size: 9
42784252 ATTTTTTTAA
42784262 TTTTAAAAT
1 TTTTAAAAT
42784271 ATTTTAAAACTT
1 -TTTTAAAA--T
* *
42784283 TTTTTAATT
1 TTTTAAAAT
42784292 TTTTAAAAT
1 TTTTAAAAT
42784301 TTTTAAAAT
1 TTTTAAAAT
42784310 AAAAATGGGC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
9 17 0.53
10 8 0.25
11 6 0.19
12 1 0.03
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (9 bp):
TTTTAAAAT
Found at i:42786949 original size:38 final size:37
Alignment explanation
Indices: 42786905--42786989 Score: 125
Period size: 39 Copynumber: 2.2 Consensus size: 37
42786895 AAAAATTTAT
*
42786905 TTTAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA
1 TTTAAAAATT-AAAAAAGTATTTTAAAAA-AATTTAAAA
*
42786944 TTAAAAAAATTAAAAAAGTATTTTAAAAAAATTTAAAA
1 TT-TAAAAATTAAAAAAGTATTTTAAAAAAATTTAAAA
42786982 TTTAAAAA
1 TTTAAAAA
42786990 ATTTAAGTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
37 5 0.12
38 10 0.24
39 20 0.48
40 7 0.17
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (37 bp):
TTTAAAAATTAAAAAAGTATTTTAAAAAAATTTAAAA
Found at i:42786958 original size:8 final size:9
Alignment explanation
Indices: 42786940--42787030 Score: 51
Period size: 9 Copynumber: 9.2 Consensus size: 9
42786930 AAAATATTTT
42786940 AAAATTAAA
1 AAAATTAAA
42786949 AAAATTAAA
1 AAAATTAAA
42786958 AAAGTATTTTAAA
1 AAA--A--TTAAA
*
42786971 AAAATT-TA
1 AAAATTAAA
*
42786979 AAATTTAAA
1 AAAATTAAA
*
42786988 AAATTTAAGTA
1 AAAATTAA--A
42786999 TTTTAAAATTAAA
1 ----AAAATTAAA
42787012 AAAATTAAA
1 AAAATTAAA
42787021 AAAA-TAAA
1 AAAATTAAA
42787029 AA
1 AA
42787031 TATTTATTAT
Statistics
Matches: 67, Mismatches: 4, Indels: 23
0.71 0.04 0.24
Matches are distributed among these distances:
8 12 0.18
9 36 0.54
11 3 0.04
13 9 0.13
15 7 0.10
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (9 bp):
AAAATTAAA
Found at i:42786990 original size:38 final size:40
Alignment explanation
Indices: 42786903--42786992 Score: 139
Period size: 38 Copynumber: 2.3 Consensus size: 40
42786893 CCAAAAATTT
* *
42786903 ATTTTAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAA
1 ATTTAAAAAATTAAAAAAAGTATTTTAAAAATAATTTAAA
*
42786943 ATTAAAAAAATT-AAAAAAGTATTTTAAAAA-AATTTAAA
1 ATTTAAAAAATTAAAAAAAGTATTTTAAAAATAATTTAAA
42786981 ATTTAAAAAATT
1 ATTTAAAAAATT
42786993 TAAGTATTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
38 18 0.39
39 18 0.39
40 10 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (40 bp):
ATTTAAAAAATTAAAAAAAGTATTTTAAAAATAATTTAAA
Found at i:42792188 original size:33 final size:33
Alignment explanation
Indices: 42792151--42792217 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
42792141 GATCAATATG
42792151 AAAAAGCATGAACTTTTTATAAACCCAACACAT
1 AAAAAGCATGAACTTTTTATAAACCCAACACAT
42792184 AAAAAGCATGAACTTTTTATAAACCCAACACAT
1 AAAAAGCATGAACTTTTTATAAACCCAACACAT
42792217 A
1 A
42792218 TCCTACCATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.49, C:0.21, G:0.06, T:0.24
Consensus pattern (33 bp):
AAAAAGCATGAACTTTTTATAAACCCAACACAT
Found at i:42795924 original size:34 final size:34
Alignment explanation
Indices: 42795881--42795946 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
42795871 TCCCTCGTAA
*
42795881 GCACCCCACAACTTTGTTTCAACGCAAGCGAAAG
1 GCACCCCACAACTCTGTTTCAACGCAAGCGAAAG
42795915 GCACCCCACAACTCTGTTTCAACGCAAGCGAA
1 GCACCCCACAACTCTGTTTCAACGCAAGCGAA
42795947 GGGTTTCCAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.32, C:0.35, G:0.17, T:0.17
Consensus pattern (34 bp):
GCACCCCACAACTCTGTTTCAACGCAAGCGAAAG
Found at i:42803425 original size:14 final size:15
Alignment explanation
Indices: 42803401--42803433 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
42803391 ACATCTTTTA
42803401 ATAATTGCTTCATCC
1 ATAATTGCTTCATCC
42803416 ATAA-TGCTTCATCC
1 ATAATTGCTTCATCC
42803430 ATAA
1 ATAA
42803434 ATTTGAAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.33, C:0.24, G:0.06, T:0.36
Consensus pattern (15 bp):
ATAATTGCTTCATCC
Found at i:42808515 original size:22 final size:22
Alignment explanation
Indices: 42808485--42808530 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
42808475 GATATTATTG
* *
42808485 AATTGAATTTGAATAATTTTCA
1 AATTAAATTTGAATAATTTGCA
*
42808507 AATTAAATTTGAGTAATTTGCA
1 AATTAAATTTGAATAATTTGCA
42808529 AA
1 AA
42808531 CACAAATATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.41
Consensus pattern (22 bp):
AATTAAATTTGAATAATTTGCA
Found at i:42808802 original size:17 final size:18
Alignment explanation
Indices: 42808755--42808794 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
42808745 AATGTTTCTT
* *
42808755 AAAAGTGCTTTTGGGACA
1 AAAAGTACTTTTAGGACA
42808773 AAAAGTACTTTTAGGACA
1 AAAAGTACTTTTAGGACA
42808791 AAAA
1 AAAA
42808795 TATTTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.25
Consensus pattern (18 bp):
AAAAGTACTTTTAGGACA
Found at i:42812323 original size:20 final size:18
Alignment explanation
Indices: 42812285--42812337 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
42812275 GTACTTTGTG
*
42812285 TTAATATTTTTAAAT-TTT
1 TTAAT-TTTTTATATATTT
42812303 TATAATTCTTTTATATATTT
1 T-TAATT-TTTTATATATTT
*
42812323 TTTATTTTTTATATA
1 TTAATTTTTTATATA
42812338 AATTATTGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
18 11 0.37
19 15 0.50
20 4 0.13
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (18 bp):
TTAATTTTTTATATATTT
Found at i:42813114 original size:37 final size:37
Alignment explanation
Indices: 42813073--42813147 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
42813063 AGAATAATTC
*
42813073 TATAATAGCTAAATTGACCAAAAGTGTATACGTGAGG
1 TATAATAGCCAAATTGACCAAAAGTGTATACGTGAGG
**
42813110 TATAATAGCCAAATTGACTGAAAGTGTATACGTGAGG
1 TATAATAGCCAAATTGACCAAAAGTGTATACGTGAGG
42813147 T
1 T
42813148 CCACTAAAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.28
Consensus pattern (37 bp):
TATAATAGCCAAATTGACCAAAAGTGTATACGTGAGG
Found at i:42815429 original size:2 final size:2
Alignment explanation
Indices: 42815422--42815455 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
42815412 AGGCACATCA
42815422 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
42815456 TTCGGCATCG
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:42817623 original size:26 final size:27
Alignment explanation
Indices: 42817594--42817646 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
42817584 AACGTAAAAG
*
42817594 CTTTTAC-GTATTTTTTCACA-ATTTCA
1 CTTTTACAATATTTTTT-ACATATTTCA
42817620 CTTTTACAATATTTTTTACATATTTCA
1 CTTTTACAATATTTTTTACATATTTCA
42817647 TCATCTCATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 10 0.42
27 14 0.58
ACGTcount: A:0.26, C:0.17, G:0.02, T:0.55
Consensus pattern (27 bp):
CTTTTACAATATTTTTTACATATTTCA
Found at i:42818346 original size:17 final size:17
Alignment explanation
Indices: 42818320--42818354 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
42818310 CCTCCTCGCA
* *
42818320 CGTGTTGCGCCTGCGCG
1 CGTGTAGCGCCTCCGCG
42818337 CGTGTAGCGCCTCCGCG
1 CGTGTAGCGCCTCCGCG
42818354 C
1 C
42818355 CAAATCCACG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.03, C:0.40, G:0.37, T:0.20
Consensus pattern (17 bp):
CGTGTAGCGCCTCCGCG
Found at i:42819513 original size:2 final size:2
Alignment explanation
Indices: 42819508--42819559 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
42819498 TTTGTTCACG
* *
42819508 TA TA TA TT TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42819550 TA TA TA TA TA
1 TA TA TA TA TA
42819560 ATTAACCTCA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:42829390 original size:34 final size:35
Alignment explanation
Indices: 42829341--42829408 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 35
42829331 AACGTTCAAG
* * **
42829341 GTTTAGGGTTTGAGTTTGATGTTT-GGGGTCTAGT
1 GTTTAAGGTTCGAGTTCAATGTTTAGGGGTCTAGT
*
42829375 GTTTAAGGTTCGAGTTCAATGTTTAGGGTTCTAG
1 GTTTAAGGTTCGAGTTCAATGTTTAGGGGTCTAG
42829409 AGTTCGAAGT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 20 0.71
35 8 0.29
ACGTcount: A:0.16, C:0.06, G:0.34, T:0.44
Consensus pattern (35 bp):
GTTTAAGGTTCGAGTTCAATGTTTAGGGGTCTAGT
Done.