Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 125 of 198
Found at i:40048975 original size:150 final size:149
Alignment explanation
Indices: 40048714--40049165 Score: 584
Period size: 150 Copynumber: 3.0 Consensus size: 149
40048704 GAATCCTATC
* *
40048714 TCTTTGGCATTACAGTGGAACAGATTGAAGCTACAATAGCGAATCTTACTTCCCTGGTGATGTAG
1 TCTTTGGCATTACAGT-GAACAGATTGAAGCTACAATAGCGAATCTTACTTCCCTGGCGATGCAG
* *
40048779 TGGAACAGATTGAAGCTACAACAACGAATCTTACTTCCCCGACATTGCAGTTAAATAGATTGAAG
65 TGGAACAGATTGAAGCTACAACAGCGAATCTTACTTCCCCGACATTGCAGTTAAATAGATTAAAG
*
40048844 CTACGACAGCGAATCTTACT
130 CTACAACAGCGAATCTTACT
* * * *
40048864 TCTTTGGCATTACAGTAGAATAGATTGAAGCTACAACAGTGAATCTTACTTCCCTGGCGGTGCAG
1 TCTTTGGCATTACAGT-GAACAGATTGAAGCTACAATAGCGAATCTTACTTCCCTGGCGATGCAG
*
40048929 TGGAATAGATTGAAGCTACAACAGCGAATCTTACTTCCCCGACATTGCAGTTAAATAGATTAAAG
65 TGGAACAGATTGAAGCTACAACAGCGAATCTTACTTCCCCGACATTGCAGTTAAATAGATTAAAG
* *
40048994 CTACAACAACGAATCTTATT
130 CTACAACAGCGAATCTTACT
* * * * * * * *
40049014 TCCTTGGCGTTACAGTGAAGCAGATTAAAGCTACAATAACAAATCTTACTTCCCCGAC-ATTACA
1 TCTTTGGCATTACAGTGAA-CAGATTGAAGCTACAATAGCGAATCTTACTTCCCTGGCGA-TGCA
* * ** * * **
40049078 GT-GAAGCAGATTAAAGCTACAACAGCGAATCTTACTTACCCGATGTTACAGTGAAGCAGATTAA
64 GTGGAA-CAGATTGAAGCTACAACAGCGAATCTTACTTCCCCGACATTGCAGTTAAATAGATTAA
*
40049142 AGCTACAATAGCGAATCTTACT
128 AGCTACAACAGCGAATCTTACT
40049164 TC
1 TC
40049166 CTCGAAGTTG
Statistics
Matches: 262, Mismatches: 37, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
149 6 0.02
150 256 0.98
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (149 bp):
TCTTTGGCATTACAGTGAACAGATTGAAGCTACAATAGCGAATCTTACTTCCCTGGCGATGCAGT
GGAACAGATTGAAGCTACAACAGCGAATCTTACTTCCCCGACATTGCAGTTAAATAGATTAAAGC
TACAACAGCGAATCTTACT
Found at i:40054654 original size:14 final size:14
Alignment explanation
Indices: 40054632--40054668 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 14
40054622 GAAAAAAAAG
40054632 AGAGAAAGGAGAAGA
1 AGAG-AAGGAGAAGA
40054647 AGAGAAGGAGAAGA
1 AGAGAAGGAGAAGA
40054661 AGAAGAAG
1 AG-AGAAG
40054669 AAAGAAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (14 bp):
AGAGAAGGAGAAGA
Found at i:40054677 original size:17 final size:17
Alignment explanation
Indices: 40054629--40054678 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 17
40054619 AGAGAAAAAA
* *
40054629 AAGAGAGAAAGGAGAAG
1 AAGAAAGAAAGAAGAAG
40054646 AAGAGAAGGAGAAGAAGAAG
1 AAGA-AA-GA-AAGAAGAAG
40054666 AAGAAAGAAAGAA
1 AAGAAAGAAAGAA
40054679 AAAAGGTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
17 9 0.32
18 3 0.11
19 4 0.14
20 12 0.43
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (17 bp):
AAGAAAGAAAGAAGAAG
Found at i:40054909 original size:41 final size:43
Alignment explanation
Indices: 40054864--40055003 Score: 121
Period size: 41 Copynumber: 3.2 Consensus size: 43
40054854 TTTTAAATTT
40054864 TTGT-ATTTATAGTTTTG-GATTAGT-AATTTTTTGTATGAATA
1 TTGTAATTTATAGTTTTGAGATTA-TAAATTTTTTGTATGAATA
* *
40054905 TTGTAATTT-T-G-TATGAATATTATAAATTTTTTGTATGAATA
1 TTGTAATTTATAGTTTTG-AGATTATAAATTTTTTGTATGAATA
* **
40054946 TTGTAATATTATAGTTTTGTATGAATATTGCATTTTTTTTGTATGAATA
1 TTGTAAT-TTATAGTTTTG-A-GATTA-T--AAATTTTTTGTATGAATA
40054995 TTGTAATTT
1 TTGTAATTT
40055004 TGTAATTTTG
Statistics
Matches: 79, Mismatches: 8, Indels: 17
0.76 0.08 0.16
Matches are distributed among these distances:
39 3 0.04
40 2 0.03
41 33 0.42
42 6 0.08
43 1 0.01
44 1 0.01
45 4 0.05
46 3 0.04
47 1 0.01
48 2 0.03
49 23 0.29
ACGTcount: A:0.29, C:0.01, G:0.14, T:0.56
Consensus pattern (43 bp):
TTGTAATTTATAGTTTTGAGATTATAAATTTTTTGTATGAATA
Found at i:40054954 original size:49 final size:49
Alignment explanation
Indices: 40054901--40055265 Score: 334
Period size: 49 Copynumber: 7.6 Consensus size: 49
40054891 TTTTTGTATG
*
40054901 AATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGTAAATTTTTTGTATGAATATTGT
* * * **
40054950 AATATTATAGTTTTGTATGAATATTGCATTTTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGTAAATTTTTTGTATGAATATTGT
*
40054999 AATTTTGTAATTTTGTATGAATATTGTAATATTATAATTTTGTATGAATATTG-
1 AATATTGTAATTTTGTATGAATATTGTAA-A-T-T--TTTTGTATGAATATTGT
* *
40055052 CA-ATT-T--TTTTGTATGAATATTGT-AA--TTTTG--T-AATTTTGTAT
1 AATATTGTAATTTTGTATGAATATTGTAAATTTTTTGTATGAATATTG--T
* * *
40055093 GAATATTATAATTTTTTTATGAATATTGT-AA--TGTTGTATGAATATTGT
1 -AATATTGTAA-TTTTGTATGAATATTGTAAATTTTTTGTATGAATATTGT
* * *
40055141 AATATTATAATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGTAAATTTTTTGTATGAATATTGT
* ** *
40055190 AATATTGTAATTTTGTATGAATATTGT-AA-TGTGGGGAT--ATATTGT
1 AATATTGTAATTTTGTATGAATATTGTAAATTTTTTGTATGAATATTGT
40055235 AATATTGTAATTTTTTGTATGAATATTGTAA
1 AATATTGTAA--TTTTGTATGAATATTGTAA
40055266 TTATTTTATA
Statistics
Matches: 263, Mismatches: 30, Indels: 47
0.77 0.09 0.14
Matches are distributed among these distances:
38 6 0.02
39 1 0.00
41 5 0.02
42 1 0.00
43 3 0.01
44 1 0.00
45 17 0.06
46 15 0.06
47 56 0.21
48 4 0.02
49 126 0.48
50 6 0.02
51 2 0.01
52 3 0.01
53 1 0.00
54 16 0.06
ACGTcount: A:0.32, C:0.01, G:0.14, T:0.53
Consensus pattern (49 bp):
AATATTGTAATTTTGTATGAATATTGTAAATTTTTTGTATGAATATTGT
Found at i:40054969 original size:27 final size:27
Alignment explanation
Indices: 40054933--40055219 Score: 265
Period size: 27 Copynumber: 11.7 Consensus size: 27
40054923 ATTATAAATT
*
40054933 TTTTGTATGAATATTGTAATATTATAG
1 TTTTGTATGAATATTGTAATATTATAA
*
40054960 TTTTGTATGAATATTG-CAT-TT-T--
1 TTTTGTATGAATATTGTAATATTATAA
* *
40054982 TTTTGTATGAATATTGTAATTTTGTAA
1 TTTTGTATGAATATTGTAATATTATAA
40055009 TTTTGTATGAATATTGTAATATTATAA
1 TTTTGTATGAATATTGTAATATTATAA
*
40055036 TTTTGTATGAATATTG-CA-ATT-T--
1 TTTTGTATGAATATTGTAATATTATAA
* *
40055058 TTTTGTATGAATATTGTAATTTTGTAA
1 TTTTGTATGAATATTGTAATATTATAA
40055085 TTTTGTATGAATA-T-T-ATA--AT--
1 TTTTGTATGAATATTGTAATATTATAA
*
40055105 TTTTTTATGAATATTGT--------AA
1 TTTTGTATGAATATTGTAATATTATAA
*
40055124 TGTTGTATGAATATTGTAATATTATAA
1 TTTTGTATGAATATTGTAATATTATAA
*
40055151 TTTTGTATGAATATTG-CA-ATT-T--
1 TTTTGTATGAATATTGTAATATTATAA
*
40055173 TTTTGTATGAATATTGTAATATTGTAA
1 TTTTGTATGAATATTGTAATATTATAA
40055200 TTTTGTATGAATATTGTAAT
1 TTTTGTATGAATATTGTAAT
40055220 GTGGGGATAT
Statistics
Matches: 218, Mismatches: 15, Indels: 54
0.76 0.05 0.19
Matches are distributed among these distances:
19 15 0.07
20 12 0.06
21 1 0.00
22 50 0.23
23 4 0.02
24 12 0.06
25 12 0.06
26 5 0.02
27 107 0.49
ACGTcount: A:0.31, C:0.01, G:0.14, T:0.54
Consensus pattern (27 bp):
TTTTGTATGAATATTGTAATATTATAA
Found at i:40055023 original size:76 final size:74
Alignment explanation
Indices: 40054933--40055219 Score: 335
Period size: 76 Copynumber: 3.9 Consensus size: 74
40054923 ATTATAAATT
40054933 TTTTGTATGAATATTGTAATATTATAGTTTTGTATGAATATTGCATTTTTTTTGTATGAATATTG
1 TTTTGTATGAATATTGTAATATTAT--TTTTGTATGAATATTGCATTTTTTTTGTATGAATATTG
40054998 TAATTTTGTAA
64 TAATTTTGTAA
*
40055009 TTTTGTATGAATATTGTAATATTATAATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTG
1 TTTTGTATGAATATTGTAATATTAT--TTTTGTATGAATATTGCATTTTTTTTGTATGAATATTG
40055074 TAATTTTGTAA
64 TAATTTTGTAA
* ** *
40055085 TTTTGTATGAATA-T-T-ATA--ATTTTTTTATGAATATTG---TAATGTTGTATGAATATTGTA
1 TTTTGTATGAATATTGTAATATTATTTTTGTATGAATATTGCATTTTTTTTGTATGAATATTGTA
* *
40055142 ATATTATAA
66 ATTTTGTAA
* *
40055151 TTTTGTATGAATATTG-CA-ATT-TTTTTGTATGAATATTGTAATATTGTAATTTTGTATGAATA
1 TTTTGTATGAATATTGTAATATTATTTTTGTATGAATATTG-CAT-TT-T--TTTTGTATGAATA
40055213 TTGTAAT
61 TTGTAAT
40055220 GTGGGGATAT
Statistics
Matches: 186, Mismatches: 12, Indels: 26
0.83 0.05 0.12
Matches are distributed among these distances:
66 38 0.20
67 2 0.01
68 17 0.09
69 15 0.08
71 2 0.01
73 4 0.02
74 1 0.01
75 1 0.01
76 106 0.57
ACGTcount: A:0.31, C:0.01, G:0.14, T:0.54
Consensus pattern (74 bp):
TTTTGTATGAATATTGTAATATTATTTTTGTATGAATATTGCATTTTTTTTGTATGAATATTGTA
ATTTTGTAA
Found at i:40055171 original size:19 final size:19
Alignment explanation
Indices: 40055149--40055198 Score: 55
Period size: 22 Copynumber: 2.5 Consensus size: 19
40055139 GTAATATTAT
40055149 AATTTTGTATGAATATTGC
1 AATTTTGTATGAATATTGC
*
40055168 AATTTTTTTGTATGAATATTGT
1 AA---TTTTGTATGAATATTGC
*
40055190 AATATTGTA
1 AATTTTGTA
40055199 ATTTTGTATG
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
19 8 0.31
22 18 0.69
ACGTcount: A:0.32, C:0.02, G:0.14, T:0.52
Consensus pattern (19 bp):
AATTTTGTATGAATATTGC
Found at i:40055466 original size:38 final size:38
Alignment explanation
Indices: 40055415--40055495 Score: 146
Period size: 38 Copynumber: 2.2 Consensus size: 38
40055405 CATATAAAGT
40055415 TTAT-AAAAAATTAAAAATCATTTCATTAAAAGTTTAA
1 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
*
40055452 TTATAAAAAAATTAAAAATCATTTTATTAAAAGTTTAA
1 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
40055490 TTATAA
1 TTATAA
40055496 CTGACTTTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
37 4 0.10
38 38 0.90
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (38 bp):
TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
Found at i:40055573 original size:15 final size:15
Alignment explanation
Indices: 40055532--40055573 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
40055522 GTTAACTCAT
*
40055532 TTAATTTTTATATAA
1 TTAACTTTTATATAA
40055547 TGTAACTTTTATATAA
1 T-TAACTTTTATATAA
*
40055563 TTAAGTTTTAT
1 TTAACTTTTAT
40055574 TTGATTTTGT
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:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (15 bp):
TTAACTTTTATATAA
Found at i:40057719 original size:22 final size:21
Alignment explanation
Indices: 40057684--40057728 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
40057674 TATCTAATTT
*
40057684 TTTTCTTCTTTTCCTTCCTTC
1 TTTTCTTCTCTTCCTTCCTTC
40057705 TTTTCTTCTGCTTCCTTCCTTC
1 TTTTCTTCT-CTTCCTTCCTTC
40057727 TT
1 TT
40057729 ATTTCTTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTTCTTCTCTTCCTTCCTTC
Found at i:40057827 original size:27 final size:27
Alignment explanation
Indices: 40057789--40057864 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 27
40057779 AAAATAACAG
* *
40057789 CATTGGCGCCTCTCAGAGAGGCACCAT
1 CATTGGCGCCTCCCAGAGAGGCACCAC
40057816 CATTGGCGCCTCCCAG-GTAGGCACCAC
1 CATTGGCGCCTCCCAGAG-AGGCACCAC
*
40057843 CATTGGCGCCTCCCAGATAGGC
1 CATTGGCGCCTCCCAGAGAGGC
40057865 GCCAATACTA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
26 1 0.02
27 43 0.98
ACGTcount: A:0.20, C:0.37, G:0.26, T:0.17
Consensus pattern (27 bp):
CATTGGCGCCTCCCAGAGAGGCACCAC
Found at i:40065483 original size:45 final size:44
Alignment explanation
Indices: 40065398--40065697 Score: 198
Period size: 45 Copynumber: 6.7 Consensus size: 44
40065388 GAAAAATGAG
* * *
40065398 TAAGACCATAGCTGAAAGACA-TATGGCATCACAAATCAAACAAA
1 TAAGACCATAGTTGAAAGACACTATGGCA-CACGATTCAAACAAA
* ***
40065442 TAAGACCATAGTTGAAAGACGCTATGGCATCACGATTCAAACGTG
1 TAAGACCATAGTTGAAAGACACTATGGCA-CACGATTCAAACAAA
* * * * **
40065487 TAAGACCATAGTTGAAAGGCACTATGACACTA-TATTGAAAACGTA
1 TAAGACCATAGTTGAAAGACACTATGGCAC-ACGATT-CAAACAAA
* ** **
40065532 TAAGACCATAGTTGAAAGACACTATGGCAC-TGTATAGGAAACGTA
1 TAAGACCATAGTTGAAAGACACTATGGCACACG-AT-TCAAACAAA
* * * *
40065577 TAAGACCATAGTTGAAAAACATTATGGCA-AC-ATAACGAAAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGGCACACGAT-TC-AAACA--AA
* * * **
40065623 TAAGACCGTAGTTGAAAGACAATATGGCAACATGATGGAAA-ATGAA
1 TAAGACCATAGTTGAAAGACACTATGGC-ACACGATTCAAACA--AA
40065669 TAAGACCATAGTTGAAAGACACTATGGCA
1 TAAGACCATAGTTGAAAGACACTATGGCA
40065698 TCATTTCAGG
Statistics
Matches: 209, Mismatches: 34, Indels: 25
0.78 0.13 0.09
Matches are distributed among these distances:
43 3 0.01
44 26 0.12
45 116 0.56
46 57 0.27
47 4 0.02
48 1 0.00
49 2 0.01
ACGTcount: A:0.44, C:0.16, G:0.19, T:0.21
Consensus pattern (44 bp):
TAAGACCATAGTTGAAAGACACTATGGCACACGATTCAAACAAA
Found at i:40065548 original size:22 final size:22
Alignment explanation
Indices: 40065480--40065548 Score: 61
Period size: 21 Copynumber: 3.1 Consensus size: 22
40065470 ATCACGATTC
*
40065480 AAACGTGTAAGACCATAGTTGA
1 AAACGTATAAGACCATAGTTGA
* * *
40065502 AAGGCAC-TATGACACTATA-TTGA
1 AA---ACGTATAAGACCATAGTTGA
40065525 AAACGTATAAGACCATAGTTGA
1 AAACGTATAAGACCATAGTTGA
40065547 AA
1 AA
40065549 GACACTATGG
Statistics
Matches: 35, Mismatches: 7, Indels: 10
0.67 0.13 0.19
Matches are distributed among these distances:
20 2 0.06
21 9 0.26
22 8 0.23
23 6 0.17
24 8 0.23
25 2 0.06
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.23
Consensus pattern (22 bp):
AAACGTATAAGACCATAGTTGA
Found at i:40065574 original size:90 final size:90
Alignment explanation
Indices: 40065397--40065694 Score: 277
Period size: 90 Copynumber: 3.3 Consensus size: 90
40065387 TGAAAAATGA
* * * * * *
40065397 GTAAGACCATAGCTGAAAGACA-TATGGCATCACAA--ATCAAACAAATAAGACCATAGTTGAAA
1 GTAAGACCATAGTTGAAAGACACTATGACAACATAACGA-AAAACGAATAAGACCATAGTTGAAA
* * **
40065459 GACGCTATGGCATCACGATTCAAACGT
65 GACACTATGGCA-CATGATGGAAACGT
* ** *
40065486 GTAAGACCATAGTTGAAAGGCACTATGAC-ACTATATTG-AAAACGTATAAGACCATAGTTGAAA
1 GTAAGACCATAGTTGAAAGACACTATGACAAC-ATAACGAAAAACGAATAAGACCATAGTTGAAA
40065549 GACACTATGGCAC-TGTATAGGAAACGT
65 GACACTATGGCACATG-AT-GGAAACGT
* * * * * *
40065576 ATAAGACCATAGTTGAAAAACATTATGGCAACATAACGAAAAATGAATAAGACCGTAGTTGAAAG
1 GTAAGACCATAGTTGAAAGACACTATGACAACATAACGAAAAACGAATAAGACCATAGTTGAAAG
* *
40065641 ACAATATGGCAACATGATGGAAA-AT
66 ACACTATGGC-ACATGATGGAAACGT
40065666 GAATAAGACCATAGTTGAAAGACACTATG
1 G--TAAGACCATAGTTGAAAGACACTATG
40065695 GCATCATTTC
Statistics
Matches: 169, Mismatches: 28, Indels: 21
0.78 0.13 0.10
Matches are distributed among these distances:
88 1 0.01
89 24 0.14
90 75 0.44
91 39 0.23
92 28 0.17
93 2 0.01
ACGTcount: A:0.44, C:0.16, G:0.19, T:0.21
Consensus pattern (90 bp):
GTAAGACCATAGTTGAAAGACACTATGACAACATAACGAAAAACGAATAAGACCATAGTTGAAAG
ACACTATGGCACATGATGGAAACGT
Found at i:40072460 original size:22 final size:19
Alignment explanation
Indices: 40072434--40072482 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 19
40072424 AATAATACAT
40072434 TTTTTTAAATTATTATCAATA
1 TTTTTTAAA-T-TTATCAATA
*
40072455 TGTTTTAAATTTATCAATA
1 TTTTTTAAATTTATCAATA
40072474 TTATTTTAA
1 TT-TTTTAA
40072483 TATATATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 10 0.40
20 7 0.28
21 8 0.32
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (19 bp):
TTTTTTAAATTTATCAATA
Found at i:40072470 original size:19 final size:21
Alignment explanation
Indices: 40072436--40072474 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
40072426 TAATACATTT
40072436 TTTTAAATTATTATCAATATG
1 TTTTAAATTATTATCAATATG
40072457 TTTTAAA-T-TTATCAATAT
1 TTTTAAATTATTATCAATAT
40072475 TATTTTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
20 1 0.06
21 7 0.39
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (21 bp):
TTTTAAATTATTATCAATATG
Found at i:40078237 original size:26 final size:27
Alignment explanation
Indices: 40078186--40078239 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
40078176 AAACATAATA
*
40078186 CACACAATACATACAAATCATTAACAAC
1 CACACAATACATAAAAATCA-TAACAAC
40078214 CACA-AATACATCAAAAATCA-AACAAC
1 CACACAATACAT-AAAAATCATAACAAC
40078240 AATGCAGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 6 0.25
27 7 0.29
28 11 0.46
ACGTcount: A:0.57, C:0.28, G:0.00, T:0.15
Consensus pattern (27 bp):
CACACAATACATAAAAATCATAACAAC
Found at i:40081883 original size:36 final size:37
Alignment explanation
Indices: 40081843--40081917 Score: 125
Period size: 37 Copynumber: 2.1 Consensus size: 37
40081833 AATACACACT
* *
40081843 TAATCCAACCGA-AACATGCCAAATGCTCATAAGAGC
1 TAATCCAACCAATAACACGCCAAATGCTCATAAGAGC
40081879 TAATCCAACCAATAACACGCCAAATGCTCATAAGAGC
1 TAATCCAACCAATAACACGCCAAATGCTCATAAGAGC
40081916 TA
1 TA
40081918 TACATCTGCC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
36 11 0.31
37 25 0.69
ACGTcount: A:0.43, C:0.28, G:0.12, T:0.17
Consensus pattern (37 bp):
TAATCCAACCAATAACACGCCAAATGCTCATAAGAGC
Found at i:40083069 original size:48 final size:48
Alignment explanation
Indices: 40083005--40083101 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
40082995 CTTAATTCCT
40083005 TCCTCACTTAGTAATTAAGCTATTTGATCACCTAAATGCAATAATTAC
1 TCCTCACTTAGTAATTAAGCTATTTGATCACCTAAATGCAATAATTAC
* *
40083053 TCCTTACTTAGTAATTAAGCTATTTGATCACCTAAATGCAGTAATTAC
1 TCCTCACTTAGTAATTAAGCTATTTGATCACCTAAATGCAATAATTAC
40083101 T
1 T
40083102 ATCTTTTTCA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.37
Consensus pattern (48 bp):
TCCTCACTTAGTAATTAAGCTATTTGATCACCTAAATGCAATAATTAC
Found at i:40088792 original size:22 final size:22
Alignment explanation
Indices: 40088767--40088850 Score: 132
Period size: 22 Copynumber: 3.8 Consensus size: 22
40088757 GTATTATATC
* * *
40088767 CATGAGGGTTTAGTTCGTTAAA
1 CATGAGAGCTTAGTACGTTAAA
40088789 CATGAGAGCTTAGTACGTTAAA
1 CATGAGAGCTTAGTACGTTAAA
*
40088811 CATGAGAGCTTAGTACGTGAAA
1 CATGAGAGCTTAGTACGTTAAA
40088833 CATGAGAGCTTAGTACGT
1 CATGAGAGCTTAGTACGT
40088851 ACGGATTATT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 58 1.00
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAAA
Found at i:40089082 original size:21 final size:21
Alignment explanation
Indices: 40089058--40089097 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
40089048 ACTTAAACAT
* *
40089058 ACATTTCAGAAATTATCATAA
1 ACATATCAGAAATAATCATAA
*
40089079 ACATATCATAAATAATCAT
1 ACATATCAGAAATAATCAT
40089098 TCACATACAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.03, T:0.33
Consensus pattern (21 bp):
ACATATCAGAAATAATCATAA
Found at i:40093704 original size:20 final size:22
Alignment explanation
Indices: 40093679--40093728 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
40093669 CCAATCTGTC
40093679 AAAAATAA-T-CAAAATTCACT
1 AAAAATAATTGCAAAATTCACT
* *
40093699 AAAAATAATTGTAAAATTGACT
1 AAAAATAATTGCAAAATTCACT
40093721 AAAAATAA
1 AAAAATAA
40093729 ACATGTTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 8 0.31
21 1 0.04
22 17 0.65
ACGTcount: A:0.62, C:0.08, G:0.04, T:0.26
Consensus pattern (22 bp):
AAAAATAATTGCAAAATTCACT
Found at i:40101838 original size:21 final size:20
Alignment explanation
Indices: 40101814--40101859 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
40101804 CGGAATGCAA
40101814 TCAACCTAACACGAATTAAAT
1 TCAACCTAA-ACGAATTAAAT
* *
40101835 TCAACCTAAGCTAATTAAAT
1 TCAACCTAAACGAATTAAAT
40101855 T-AACC
1 TCAACC
40101860 ATTCCAATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 4 0.17
20 10 0.43
21 9 0.39
ACGTcount: A:0.46, C:0.24, G:0.04, T:0.26
Consensus pattern (20 bp):
TCAACCTAAACGAATTAAAT
Found at i:40104227 original size:112 final size:112
Alignment explanation
Indices: 40104030--40104257 Score: 393
Period size: 112 Copynumber: 2.0 Consensus size: 112
40104020 ATTAATTTTT
* *
40104030 AAGGTATGAGTTTATACCAATAGTATAATGCACCCGGTGATTGTGGTCCCGTGCTAGTTAGGTTA
1 AAGGTATGAGTTTATACCAATAGTATAATGCACCCGGTGATTGTGGTCCCGTGCCAGTTAAGTTA
* * *
40104095 CAAGGTAAGCTAGTTTGGAACTAATCGAATGTGAACTAGAAGAGTTA
66 CAAGGTAAGCTAGTTAGGAACTAATCGAATGTAAACTAAAAGAGTTA
*
40104142 AAGGTATGAGTTTATGCCAATAGTATAATGCACCCGGTGATTGTGGTCCCGTGCCAGTTAAGTTA
1 AAGGTATGAGTTTATACCAATAGTATAATGCACCCGGTGATTGTGGTCCCGTGCCAGTTAAGTTA
*
40104207 CAAGGTAAGCTGGTTAGGAACTAATCGAATGTAAACTAAAAGAGTTA
66 CAAGGTAAGCTAGTTAGGAACTAATCGAATGTAAACTAAAAGAGTTA
40104254 AAGG
1 AAGG
40104258 CTAAGGAGAT
Statistics
Matches: 109, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
112 109 1.00
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (112 bp):
AAGGTATGAGTTTATACCAATAGTATAATGCACCCGGTGATTGTGGTCCCGTGCCAGTTAAGTTA
CAAGGTAAGCTAGTTAGGAACTAATCGAATGTAAACTAAAAGAGTTA
Found at i:40107406 original size:43 final size:42
Alignment explanation
Indices: 40107358--40107442 Score: 143
Period size: 43 Copynumber: 2.0 Consensus size: 42
40107348 TTTTGGTAAA
40107358 TGTTGTTTTGTTATAGTTACGGTGTCTTTTGAAAGGCATATTG
1 TGTTGTTTTGTTATAGTTACGGTGTC-TTTGAAAGGCATATTG
**
40107401 TGTTGTTTTGTTATAGTTGTGGTGTCTTTGAAAGGCATATTG
1 TGTTGTTTTGTTATAGTTACGGTGTCTTTGAAAGGCATATTG
40107443 GTTAGGTGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
42 16 0.40
43 24 0.60
ACGTcount: A:0.18, C:0.06, G:0.27, T:0.49
Consensus pattern (42 bp):
TGTTGTTTTGTTATAGTTACGGTGTCTTTGAAAGGCATATTG
Found at i:40113317 original size:11 final size:11
Alignment explanation
Indices: 40113273--40113328 Score: 58
Period size: 11 Copynumber: 4.8 Consensus size: 11
40113263 GTAACATAGT
40113273 AAATAAACTTA
1 AAATAAACTTA
*
40113284 AAATCAAAATTA
1 AAAT-AAACTTA
40113296 AAACTTAAACTTA
1 AAA--TAAACTTA
*
40113309 AAATAAACTTC
1 AAATAAACTTA
*
40113320 AAATTAACT
1 AAATAAACT
40113329 AGGTAAAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
11 19 0.50
12 9 0.24
13 9 0.24
14 1 0.03
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (11 bp):
AAATAAACTTA
Found at i:40114996 original size:17 final size:18
Alignment explanation
Indices: 40114974--40115010 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
40114964 GGTTCGAAAT
40114974 AATTTA-TGATAT-TTTTA
1 AATTTATTGA-ATGTTTTA
40114991 AATTTATTGAATGTTTTA
1 AATTTATTGAATGTTTTA
40115009 AA
1 AA
40115011 GGTCTCCTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (18 bp):
AATTTATTGAATGTTTTA
Found at i:40116374 original size:25 final size:24
Alignment explanation
Indices: 40116346--40116392 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
40116336 TCACTTGCAT
40116346 TTATACA-TTATATATTTAATGTTAA
1 TTATACACTT-TAT-TTTAATGTTAA
*
40116371 TTATGCACTTTATTTTAATGTT
1 TTATACACTTTATTTTAATGTT
40116393 TTATATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 9 0.45
25 9 0.45
26 2 0.10
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.55
Consensus pattern (24 bp):
TTATACACTTTATTTTAATGTTAA
Found at i:40116450 original size:10 final size:10
Alignment explanation
Indices: 40116418--40116469 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
40116408 CTTGTATAAC
40116418 TTTTATTTAT
1 TTTTATTTAT
* *
40116428 TCTTATTTCT
1 TTTTATTTAT
40116438 TTTTATTTAT
1 TTTTATTTAT
*
40116448 TTTCATGTCTAT
1 TTTTAT-T-TAT
*
40116460 TTATATTTAT
1 TTTTATTTAT
40116470 ATATATATAT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
10 24 0.73
11 2 0.06
12 7 0.21
ACGTcount: A:0.19, C:0.08, G:0.02, T:0.71
Consensus pattern (10 bp):
TTTTATTTAT
Found at i:40116462 original size:20 final size:20
Alignment explanation
Indices: 40116419--40116463 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
40116409 TTGTATAACT
* *
40116419 TTTATTTATTCTTATTTCTT
1 TTTATTTATTCTTATGTCTA
40116439 TTTATTTATT-TTCATGTCTA
1 TTTATTTATTCTT-ATGTCTA
40116459 TTTAT
1 TTTAT
40116464 ATTTATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.18, C:0.09, G:0.02, T:0.71
Consensus pattern (20 bp):
TTTATTTATTCTTATGTCTA
Found at i:40116474 original size:2 final size:2
Alignment explanation
Indices: 40116461--40116497 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
40116451 CATGTCTATT
*
40116461 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
40116498 TTACACATTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:40122087 original size:32 final size:32
Alignment explanation
Indices: 40122046--40122106 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
40122036 TGGCCACTAC
*
40122046 GTCTTACGTGGCAGAGGGAATGCGAGCCCTGT
1 GTCTTACGTGGCAAAGGGAATGCGAGCCCTGT
40122078 GTCTTACGTGGCAAAGGGAATGCGAGCCC
1 GTCTTACGTGGCAAAGGGAATGCGAGCCC
40122107 CTAAGCTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.21, C:0.23, G:0.36, T:0.20
Consensus pattern (32 bp):
GTCTTACGTGGCAAAGGGAATGCGAGCCCTGT
Found at i:40127825 original size:42 final size:42
Alignment explanation
Indices: 40127778--40128158 Score: 478
Period size: 42 Copynumber: 9.1 Consensus size: 42
40127768 AAGGAGAACA
*
40127778 TTCATTGCATTTAAAGGCCCAAGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
*
40127820 TTCATTGCATTTAGAGGCCC-AGATGTGGAGGTCCATTCACTT
1 TTCATTGCATTTAGAGGCCCAAG-TGTGGAGGTCCATTTACTT
* * * *
40127862 TTCATTGCATTTAGAGACTCAATTGTGGAGGTCCATTGACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
* * ** *
40127904 TTCATTGCATTTAGAGGCCCAGGTGTTGAGGTTAATTCACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
* * *
40127946 TTCATTGCATTTAGAGGCCCAAGTATGGAGTTTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
* * *
40127988 TTCATTACATTTAGAGACCCAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
* * * *
40128030 TTCATTGCATTTAGAGGCCCAGGTGTTGAGGTTCATTCACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
* * *
40128072 TTCATTGCATTTAGAGACCCAAGTGTGGAGGTCCACTGACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
* * * *
40128114 TTCATTGCAGTTAGAGACCC-AGATATGGAGGTCCGTTTACTT
1 TTCATTGCATTTAGAGGCCCAAG-TGTGGAGGTCCATTTACTT
40128156 TTC
1 TTC
40128159 TAGTTTACTT
Statistics
Matches: 294, Mismatches: 42, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
41 4 0.01
42 289 0.98
43 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
Found at i:40128003 original size:126 final size:125
Alignment explanation
Indices: 40127778--40128158 Score: 539
Period size: 126 Copynumber: 3.0 Consensus size: 125
40127768 AAGGAGAACA
* * * * *
40127778 TTCATTGCATTTAAAGGCCCAAGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCC-AG
1 TTCATTGCATTTAGAGGCCCAGGTGTTGAGGTTCATTCACTTTTCATTGCATTTAGAGGCCCAAG
* *
40127842 ATGTGGAGGTCCATTCACTTTTCATTGCATTTAGAGACTCAATTGTGGAGGTCCATTGACTT
66 -TGTGGAGGTCCATTCACTTTTCATTGCATTTAGAGACCCAA-TGTGGAGGTCCATTTACTT
*
40127904 TTCATTGCATTTAGAGGCCCAGGTGTTGAGGTTAATTCACTTTTCATTGCATTTAGAGGCCCAAG
1 TTCATTGCATTTAGAGGCCCAGGTGTTGAGGTTCATTCACTTTTCATTGCATTTAGAGGCCCAAG
* * * * * *
40127969 TATGGAGTTTCATTTACTTTTCATTACATTTAGAGACCCAGGTGTGGAGGTCCATTTACTT
66 TGTGGAGGTCCATTCACTTTTCATTGCATTTAGAGACCCA-ATGTGGAGGTCCATTTACTT
*
40128030 TTCATTGCATTTAGAGGCCCAGGTGTTGAGGTTCATTCACTTTTCATTGCATTTAGAGACCCAAG
1 TTCATTGCATTTAGAGGCCCAGGTGTTGAGGTTCATTCACTTTTCATTGCATTTAGAGGCCCAAG
* * * * *
40128095 TGTGGAGGTCCACTGACTTTTCATTGCAGTTAGAGACCCAGATATGGAGGTCCGTTTACTT
66 TGTGGAGGTCCATTCACTTTTCATTGCATTTAGAGACCCA-ATGTGGAGGTCCATTTACTT
40128156 TTC
1 TTC
40128159 TAGTTTACTT
Statistics
Matches: 227, Mismatches: 26, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
126 225 0.99
127 2 0.01
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (125 bp):
TTCATTGCATTTAGAGGCCCAGGTGTTGAGGTTCATTCACTTTTCATTGCATTTAGAGGCCCAAG
TGTGGAGGTCCATTCACTTTTCATTGCATTTAGAGACCCAATGTGGAGGTCCATTTACTT
Found at i:40129392 original size:148 final size:147
Alignment explanation
Indices: 40128924--40129395 Score: 419
Period size: 148 Copynumber: 3.2 Consensus size: 147
40128914 GTTTTTTTTT
* * * * * * *
40128924 AAAGAGAAAGTTTAGATTTT---AACAAATAATT-TTTTTT-TGTTATTTTAAAGGAAAGTTTAA
1 AAAGAGAAACTTTAGATTTTGAAAAAAAAAAATTATTTTTTAAGTCATTTTAAAGGAAAATTCAA
* * * * *
40128984 ATTTTTAAAACAAAGTTTT-AATTTTTTTCAACTA-TATCAAAGT-AAAGATTTAATCTTTAAGA
66 AATTTTAAAACAAAGTTTTGATTTTTTTTCAACTACT-CCAAAATAAAAGCTTTAATCTTTAAGA
* * ****
40129046 AAAATAGTGATTTAAAAAAAAA
130 AAAATAATGGTTT----TTTCA
* * ** * *
40129068 AAAGGAGAAAGTTTAGTTTTTGAAAATTAAAAATCTATTTTTTTTTAGTCATTTTAAAGGAAAGT
1 AAA-GAGAAACTTTAGATTTTGAAAAAAAAAAAT-TA--TTTTTTAAGTCATTTTAAAGGAAAAT
40129133 TCAAAATTTTAAAACAAAGTTTTGATTTTTTTTCAACTACTCCAAAATAAAAGCTTTAATCTTTA
62 TCAAAATTTTAAAACAAAGTTTTGATTTTTTTTCAACTACTCCAAAATAAAAGCTTTAATCTTTA
* * **
40129198 AGAAAAATAGTGTTTTTTTTT
127 AGAAAAATAATGGTTTTTTCA
* * *
40129219 TAAGAGAAAGTTTAGATTTTGAAAAATAAAAAATTATTTTTTAAGTCATTTTAAAGGAAAATTTA
1 AAAGAGAAACTTTAGATTTTGAAAAA-AAAAAATTATTTTTTAAGTCATTTTAAAGGAAAATTCA
* * * * * *
40129284 AAATTTTAAAATAAAGTTTTGATTTTTTTT-AACTATTTCGAAAT-AAAGCTTTGATTTTTAAGA
65 AAATTTTAAAACAAAGTTTTGATTTTTTTTCAACTACTCCAAAATAAAAGCTTTAATCTTTAAGA
*
40129347 AAATTAATGGTTTTTTCA
130 AAAATAATGGTTTTTTCA
40129365 AAAGA-AAACTTTA-ATTTTGTAAAAAAAAAAA
1 AAAGAGAAACTTTAGATTTTG-AAAAAAAAAAA
40129396 AATTTGGCCA
Statistics
Matches: 276, Mismatches: 38, Indels: 28
0.81 0.11 0.08
Matches are distributed among these distances:
144 15 0.05
145 28 0.10
146 34 0.12
147 11 0.04
148 62 0.22
149 1 0.00
150 23 0.08
151 8 0.03
152 6 0.02
153 38 0.14
154 19 0.07
155 31 0.11
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (147 bp):
AAAGAGAAACTTTAGATTTTGAAAAAAAAAAATTATTTTTTAAGTCATTTTAAAGGAAAATTCAA
AATTTTAAAACAAAGTTTTGATTTTTTTTCAACTACTCCAAAATAAAAGCTTTAATCTTTAAGAA
AAATAATGGTTTTTTCA
Found at i:40130988 original size:21 final size:21
Alignment explanation
Indices: 40130945--40130988 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
40130935 GGTGTTACAA
* *
40130945 TTTTTAGGAAATTGATTGATT
1 TTTTTAAGAAATTGATAGATT
40130966 TTTTTAAGAAATTTGATAG-TT
1 TTTTTAAGAAA-TTGATAGATT
40130987 TT
1 TT
40130989 GGTATTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
TTTTTAAGAAATTGATAGATT
Found at i:40133433 original size:16 final size:16
Alignment explanation
Indices: 40133414--40133466 Score: 67
Period size: 16 Copynumber: 3.5 Consensus size: 16
40133404 GATCATACAA
40133414 AAATTAACTCAAAACC
1 AAATTAACTCAAAACC
* *
40133430 AAATTAACAC-GAA--
1 AAATTAACTCAAAACC
40133443 AAATTAACTCAAAACC
1 AAATTAACTCAAAACC
40133459 AAATTAAC
1 AAATTAAC
40133467 ATGAAGTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
13 9 0.30
14 2 0.07
15 2 0.07
16 17 0.57
ACGTcount: A:0.58, C:0.21, G:0.02, T:0.19
Consensus pattern (16 bp):
AAATTAACTCAAAACC
Found at i:40133447 original size:29 final size:29
Alignment explanation
Indices: 40133412--40133467 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
40133402 TGGATCATAC
40133412 AAAAATTAACTCAAAACCAAATTAACACG
1 AAAAATTAACTCAAAACCAAATTAACACG
40133441 AAAAATTAACTCAAAACCAAATTAACA
1 AAAAATTAACTCAAAACCAAATTAACA
40133468 TGAAGTGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.61, C:0.20, G:0.02, T:0.18
Consensus pattern (29 bp):
AAAAATTAACTCAAAACCAAATTAACACG
Found at i:40144735 original size:25 final size:26
Alignment explanation
Indices: 40144695--40144754 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
40144685 TTTAAAATAC
* * *
40144695 TTTTAAAATAATTTTTTATTTTTTAT
1 TTTTAAAACAATTTTTTAATGTTTAT
40144721 TTTTAAAACAATTTTTTAATGTTTAT
1 TTTTAAAACAATTTTTTAATGTTTAT
*
40144747 TTTAAAAA
1 TTTTAAAA
40144755 TGGGCCAGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (26 bp):
TTTTAAAACAATTTTTTAATGTTTAT
Found at i:40147838 original size:17 final size:17
Alignment explanation
Indices: 40147816--40147848 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
40147806 AATGTCCTTC
40147816 AATAGTAAAATTAAATA
1 AATAGTAAAATTAAATA
*
40147833 AATAGTAAGATTAAAT
1 AATAGTAAAATTAAAT
40147849 TCCTCGAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.09, T:0.30
Consensus pattern (17 bp):
AATAGTAAAATTAAATA
Found at i:40149453 original size:22 final size:24
Alignment explanation
Indices: 40149404--40149453 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 24
40149394 AAAGATTTTC
40149404 TAAATATATTTTCAATTTGTTCAA
1 TAAATATATTTTCAATTTGTTCAA
* *
40149428 -AAATAT-TTTTTAATTT-TTTAA
1 TAAATATATTTTCAATTTGTTCAA
40149449 TAAAT
1 TAAAT
40149454 TTGATGTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 4 0.17
22 13 0.57
23 6 0.26
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (24 bp):
TAAATATATTTTCAATTTGTTCAA
Found at i:40150140 original size:16 final size:16
Alignment explanation
Indices: 40150116--40150150 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
40150106 GGTTCATTGG
* *
40150116 AATAGAATAGAGCTGT
1 AATAAAATAAAGCTGT
40150132 AATAAAATAAAGCTGT
1 AATAAAATAAAGCTGT
40150148 AAT
1 AAT
40150151 CAGTAATTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.06, G:0.17, T:0.26
Consensus pattern (16 bp):
AATAAAATAAAGCTGT
Found at i:40150373 original size:16 final size:16
Alignment explanation
Indices: 40150354--40150437 Score: 55
Period size: 16 Copynumber: 4.9 Consensus size: 16
40150344 TAAAAATAAA
40150354 TAATTTAATTATATTT
1 TAATTTAATTATATTT
*
40150370 TAATATAATTATTATTAAAT
1 TAATTTAATTA-TATT---T
* *
40150390 ATAATTTAATAACATTT
1 -TAATTTAATTATATTT
*
40150407 TAATATAATTAT-TTT
1 TAATTTAATTATATTT
40150422 T-ATATTATATTATATT
1 TAAT-TTA-ATTATATT
40150438 AAAATGTTTT
Statistics
Matches: 52, Mismatches: 8, Indels: 15
0.69 0.11 0.20
Matches are distributed among these distances:
14 2 0.04
15 6 0.12
16 24 0.46
17 7 0.13
20 4 0.08
21 9 0.17
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (16 bp):
TAATTTAATTATATTT
Found at i:40167097 original size:3 final size:3
Alignment explanation
Indices: 40167084--40167114 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
40167074 TTTATATGTA
40167084 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
40167115 GGTAACAAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:40168098 original size:44 final size:45
Alignment explanation
Indices: 40167730--40168331 Score: 279
Period size: 44 Copynumber: 13.8 Consensus size: 45
40167720 TTAGTGCTGC
* * *
40167730 AGTCTACTCCACTGCAA-TGTCAGG-GAGATAAGATTTG-TCATCTTT
1 AGTCTGCTCCACTGCAACT-TCAGGAGAGATAAGACTTGCTTA-C-TT
* *
40167775 AGTCTGCCCCACTGCAACTTCAGGAG-GATAAGACTTGCTTAGTT
1 AGTCTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGCTTACTT
* * *
40167819 AGTCTGCCCCA-TGGAAACTTCAGGAG-GATAAGACTCGCTTACTT
1 AGTCTGCTCCACT-GCAACTTCAGGAGAGATAAGACTTGCTTACTT
* * * * *
40167863 AGTCTGCTCCACTGCAACTTCATG-GAGATAAGACTAG-ATGC-G
1 AGTCTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGCTTACTT
* * ** *
40167905 A-TCTGCT-CTCTACAACTTCA-GAGAGATAAGATCCAAGATT--TT
1 AGTCTGCTCCACTGCAACTTCAGGAGAGATAAGA--CTTGCTTACTT
* * * * * * *
40167947 AATCCGTTCCACTACAACTTTAGG-GAGATAGGATTATCGGC-T--TT
1 AGTCTGCTCCACTGCAACTTCAGGAGAGATAAGACT-T--GCTTACTT
** ** *
40167991 AACCTGCTCCACTGCAACTTCAGG-GAGATAAGGTTTGC-CATCTT
1 AGTCTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGCTTA-CTT
* *
40168035 CAGTCTGCCCCACTACAACTTCAGGAG-GATAAGACTTGCTTACTT
1 -AGTCTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGCTTACTT
* * * *
40168080 AGTCTGCTCCACTGCAACTTCAGG-GAGATAAGACTAG-ATGC-G
1 AGTCTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGCTTACTT
* * ** *
40168122 A-TCTGCT-CTCTGAAACTTCA-GAGAGATAAGATCCAAGATT--TT
1 AGTCTGCTCCACTGCAACTTCAGGAGAGATAAGA--CTTGCTTACTT
* * * * * * * *
40168164 AATCCGTTCCACTACAACTTTAGG-GAGATAGGA-TT-ATCGACTTT
1 AGTCTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGCT-TAC-TT
** * **
40168208 AACCTACTCCACTGCAACTTCAGG-GAGATAAGGTTTGCCTT-CTT
1 AGTCTGCTCCACTGCAACTTCAGGAGAGATAAGACTTG-CTTACTT
*
40168252 CAGTCTGC-CTCACTACAACTTCAGGAG-GATAAGACTTGCTTACTT
1 -AGTCTGCTC-CACTGCAACTTCAGGAGAGATAAGACTTGCTTACTT
*
40168297 AGTCTGCTCCACTGTAACTTCA-GAGAGATAAGACT
1 AGTCTGCTCCACTGCAACTTCAGGAGAGATAAGACT
40168332 AGATGCGATA
Statistics
Matches: 429, Mismatches: 83, Indels: 91
0.71 0.14 0.15
Matches are distributed among these distances:
39 2 0.00
40 42 0.10
41 14 0.03
42 10 0.02
43 21 0.05
44 231 0.54
45 101 0.24
46 7 0.02
47 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (45 bp):
AGTCTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGCTTACTT
Found at i:40168126 original size:217 final size:217
Alignment explanation
Indices: 40167834--40168417 Score: 999
Period size: 217 Copynumber: 2.7 Consensus size: 217
40167824 GCCCCATGGA
* *
40167834 AACTTCAGGAGGATAAGACTCGCTTACTTAGTCTGCTCCACTGCAACTTCATGGAGATAAGACTA
1 AACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTA
40167899 GATGCGATCTGCTCTCTACAACTTCAGAGAGATAAGATCCAAGATTTTAATCCGTTCCACTACAA
66 GATGCGATCTGCTCTCTACAACTTCAGAGAGATAAGATCCAAGATTTTAATCCGTTCCACTACAA
* *
40167964 CTTTAGGGAGATAGGATTATCGGCTTTAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGC
131 CTTTAGGGAGATAGGATTATCGACTTTAACCTACTCCACTGCAACTTCAGGGAGATAAGGTTTGC
40168029 CATCTTCAGTCTGCCCCACTAC
196 CATCTTCAGTCTGCCCCACTAC
40168051 AACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTA
1 AACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTA
40168116 GATGCGATCTGCTCTCTGA-AACTTCAGAGAGATAAGATCCAAGATTTTAATCCGTTCCACTACA
66 GATGCGATCTGCTCTCT-ACAACTTCAGAGAGATAAGATCCAAGATTTTAATCCGTTCCACTACA
40168180 ACTTTAGGGAGATAGGATTATCGACTTTAACCTACTCCACTGCAACTTCAGGGAGATAAGGTTTG
130 ACTTTAGGGAGATAGGATTATCGACTTTAACCTACTCCACTGCAACTTCAGGGAGATAAGGTTTG
* *
40168245 CCTTCTTCAGTCTGCCTCACTAC
195 CCATCTTCAGTCTGCCCCACTAC
* *
40168268 AACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGTAACTTCAGAGAGATAAGACTA
1 AACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTA
* * * * * *
40168333 GATGCGATATGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTAATCCGCTCCATTGCAA
66 GATGCGATCTGCTCTCTACAACTTCAGAGAGATAAGATCCAAGATTTTAATCCGTTCCACTACAA
* * *
40168398 CTTCAGAGAGATGGGATTAT
131 CTTTAGGGAGATAGGATTAT
40168418 TGGCCACGGA
Statistics
Matches: 348, Mismatches: 17, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
217 347 1.00
218 1 0.00
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (217 bp):
AACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTA
GATGCGATCTGCTCTCTACAACTTCAGAGAGATAAGATCCAAGATTTTAATCCGTTCCACTACAA
CTTTAGGGAGATAGGATTATCGACTTTAACCTACTCCACTGCAACTTCAGGGAGATAAGGTTTGC
CATCTTCAGTCTGCCCCACTAC
Found at i:40168235 original size:261 final size:261
Alignment explanation
Indices: 40167736--40168237 Score: 576
Period size: 261 Copynumber: 1.9 Consensus size: 261
40167726 CTGCAGTCTA
* * *
40167736 CTCCACTGCAATGTCAGGGAGATAAGATTTGTCATCTTTAGTCTGCCCCACTGCAACTTCAGGAG
1 CTCCACTGCAATGTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCCCACTACAACTTCAGGAG
* * * *
40167801 GATAAGACTTGCTTAGTTAGTCTGCCCCATGGAAACTTCAGGAGGATAAGACTCGCTTACTTAGT
66 GATAAGACTTGCTTACTTAGTCTGCCCCATGGAAACTTCAGGAGGATAAGACTAGCATACTGAGT
* * * * *
40167866 CTGCTCCACTGCAACTTCATGGAGATAAGACTAGATGCGATCTGCTCTCTACAACTTCAGAGAGA
131 CTGCTCCACTGAAACTTCATGGAGATAAGACAAGATGCAATCCGCTCACTACAACTTCAGAGAGA
* *
40167931 TAAGATCCAAGATTTTAATCCGTTCCACTACAACTTTAGGGAGATAGGATTATCGGCTTTAACCT
196 TAAGATCCAAGACTTTAATCCGTTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTTAACCT
40167996 G
261 G
*
40167997 CTCCACTGCAACT-TCAGGGAGATAAGGTTTGCCATCTTCAGTCTGCCCCACTACAACTTCAGGA
1 CTCCACTGCAA-TGTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCCCACTACAACTTCAGGA
* * *
40168061 GGATAAGACTTGCTTACTTAGTCTGCTCCACT-GCAACTTCAGG-GAGATAAGACTAG-ATGC-G
65 GGATAAGACTTGCTTACTTAGTCTGCCCCA-TGGAAACTTCAGGAG-GATAAGACTAGCATACTG
* ** *
40168122 A-TCTGCT-CTCTGAAACTTCA-GAGAGATAAGATCCAAGATTTTAATCCGTTCCACTACAACTT
128 AGTCTGCTCCACTGAAACTTCATG-GAGATAAGA--CAAGA-TGCAATCCGCT-CACTACAACTT
* * * * * *
40168184 TAGGGAGATAGGAT-TATCGACTTTAA-CC-TACTCCACTGCAACTTCAGGGAGATA
188 CAGAGAGATAAGATCCA-AGACTTTAATCCGT--TCCACTACAACTTCAGGGAGATA
40168238 AGGTTTGCCT
Statistics
Matches: 202, Mismatches: 28, Indels: 22
0.80 0.11 0.09
Matches are distributed among these distances:
256 1 0.00
257 20 0.10
258 6 0.03
259 6 0.03
260 12 0.06
261 155 0.77
262 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (261 bp):
CTCCACTGCAATGTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCCCACTACAACTTCAGGAG
GATAAGACTTGCTTACTTAGTCTGCCCCATGGAAACTTCAGGAGGATAAGACTAGCATACTGAGT
CTGCTCCACTGAAACTTCATGGAGATAAGACAAGATGCAATCCGCTCACTACAACTTCAGAGAGA
TAAGATCCAAGACTTTAATCCGTTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTTAACCT
G
Found at i:40173607 original size:27 final size:26
Alignment explanation
Indices: 40173559--40173610 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
40173549 ACGCGCCCTT
* * *
40173559 CTTCTTTCCTGTCTTTTTTCTAGCTC
1 CTTCTTTCCTGTCCTCTGTCTAGCTC
40173585 CTTCTTTCACTGTCCTCTGTCTAGCT
1 CTTCTTTC-CTGTCCTCTGTCTAGCT
40173611 TGTATCCTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 8 0.36
27 14 0.64
ACGTcount: A:0.06, C:0.33, G:0.10, T:0.52
Consensus pattern (26 bp):
CTTCTTTCCTGTCCTCTGTCTAGCTC
Found at i:40180432 original size:17 final size:17
Alignment explanation
Indices: 40180381--40180435 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
40180371 GTATCACATA
40180381 AAATAGC-AAAATAATAT
1 AAATAGCAAAAATAA-AT
* *
40180398 AAA-CG-AAAACACAAAT
1 AAATAGCAAAA-ATAAAT
40180414 AAATAGCAAAAATAAAT
1 AAATAGCAAAAATAAAT
40180431 AAATA
1 AAATA
40180436 AATAAATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
16 9 0.30
17 17 0.57
18 4 0.13
ACGTcount: A:0.69, C:0.09, G:0.05, T:0.16
Consensus pattern (17 bp):
AAATAGCAAAAATAAAT
Found at i:40182190 original size:16 final size:17
Alignment explanation
Indices: 40182169--40182211 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
40182159 ATAAAATTTA
40182169 AATATTTTATTAA-ATC
1 AATATTTTATTAAGATC
40182185 AATATTTTAATTAAGATC
1 AATATTTT-ATTAAGATC
40182203 -AT-TTTTATT
1 AATATTTTATT
40182212 TAATAAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 3 0.12
16 12 0.48
17 7 0.28
18 3 0.12
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (17 bp):
AATATTTTATTAAGATC
Found at i:40190259 original size:28 final size:28
Alignment explanation
Indices: 40190227--40190292 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 28
40190217 TTCCTTCCTA
40190227 AATTATCAATCCTCAAATTCCAATTTTC
1 AATTATCAATCCTCAAATTCCAATTTTC
* * * * *
40190255 TATTATAAATCTTCAATTTTCAATTTTC
1 AATTATCAATCCTCAAATTCCAATTTTC
*
40190283 AATTTTCAAT
1 AATTATCAAT
40190293 TTCCGATCCT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.35, C:0.18, G:0.00, T:0.47
Consensus pattern (28 bp):
AATTATCAATCCTCAAATTCCAATTTTC
Found at i:40190278 original size:7 final size:7
Alignment explanation
Indices: 40190247--40190294 Score: 60
Period size: 7 Copynumber: 6.9 Consensus size: 7
40190237 CCTCAAATTC
40190247 CAATTTT
1 CAATTTT
* *
40190254 CTATTAT
1 CAATTTT
* *
40190261 AAATCTT
1 CAATTTT
40190268 CAATTTT
1 CAATTTT
40190275 CAATTTT
1 CAATTTT
40190282 CAATTTT
1 CAATTTT
40190289 CAATTT
1 CAATTT
40190295 CCGATCCTCA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (7 bp):
CAATTTT
Found at i:40190343 original size:15 final size:16
Alignment explanation
Indices: 40190316--40190345 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
40190306 TTATTTTATT
40190316 AATTTTATTCTTTTCA
1 AATTTTATTCTTTTCA
40190332 AATTTT-TTCTTTTC
1 AATTTTATTCTTTTC
40190346 GTTATAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.20, C:0.13, G:0.00, T:0.67
Consensus pattern (16 bp):
AATTTTATTCTTTTCA
Found at i:40196269 original size:20 final size:20
Alignment explanation
Indices: 40196240--40196279 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
40196230 TTCACCTCAT
*
40196240 GCATCGCATCATATGCATTA
1 GCATCACATCATATGCATTA
40196260 GCATCACATCATATGCATTA
1 GCATCACATCATATGCATTA
40196280 AAGACCTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (20 bp):
GCATCACATCATATGCATTA
Found at i:40201921 original size:16 final size:16
Alignment explanation
Indices: 40201900--40201931 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
40201890 ATTCAGCATT
40201900 GGTGATATATCAGCTC
1 GGTGATATATCAGCTC
40201916 GGTGATATATCAGCTC
1 GGTGATATATCAGCTC
40201932 AGGGGTGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (16 bp):
GGTGATATATCAGCTC
Found at i:40204396 original size:46 final size:46
Alignment explanation
Indices: 40204340--40204492 Score: 128
Period size: 46 Copynumber: 3.2 Consensus size: 46
40204330 TGAATCCACA
40204340 ACGGCAGATCTTACTTAGCAGTGCAGTGGAACAGATTGAAGCTACG
1 ACGGCAGATCTTACTTAGCAGTGCAGTGGAACAGATTGAAGCTACG
* * * * * * * * * * * *
40204386 ACGGCGGATCTGGTTTCCCT-GATATTACAATTGAAAAGATTGTAGCCACA
1 ACGGCAGATC----TTACTTAG-CAGTGCAGTGGAACAGATTGAAGCTACG
*
40204436 ACGACAGATCTTACTTAGCAGTGCAGTGGAACAGATTGAAGCTACG
1 ACGGCAGATCTTACTTAGCAGTGCAGTGGAACAGATTGAAGCTACG
*
40204482 ACGGCGGATCT
1 ACGGCAGATCT
40204493 GGTTTCCCTG
Statistics
Matches: 74, Mismatches: 27, Indels: 12
0.65 0.24 0.11
Matches are distributed among these distances:
46 41 0.55
47 1 0.01
49 1 0.01
50 31 0.42
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (46 bp):
ACGGCAGATCTTACTTAGCAGTGCAGTGGAACAGATTGAAGCTACG
Found at i:40204491 original size:96 final size:96
Alignment explanation
Indices: 40204335--40204600 Score: 390
Period size: 96 Copynumber: 2.7 Consensus size: 96
40204325 AGGATTGAAT
40204335 CCACAACGGCAGATCTTACTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGT
1 CCACAACGGCAGATCTTACTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGT
40204400 TTCCCTGATATTACAATTGAAAAGATTGTA-G
66 TTCCCTGATATTACAATTGAAAAGATTG-AGG
*
40204431 CCACAACGACAGATCTTACTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGT
1 CCACAACGGCAGATCTTACTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGT
40204496 TTCCCTGATATTACAATTGAAAAGATTGAGG
66 TTCCCTGATATTACAATTGAAAAGATTGAGG
* * ** * * * * *
40204527 CCACAATGGCAGATCTTATTTCCCTAACGATGCGGCGGAATAGATTTAACCTACGACGGCGGATC
1 CCACAACGGCAGATCTTACTTAGC--A-G-TGCAGTGGAACAGATTGAAGCTACGACGGCGGATC
40204592 TGGTTTCCC
62 TGGTTTCCC
40204601 CAACATGGCA
Statistics
Matches: 154, Mismatches: 11, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
95 1 0.01
96 112 0.73
98 1 0.01
99 1 0.01
100 39 0.25
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (96 bp):
CCACAACGGCAGATCTTACTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGT
TTCCCTGATATTACAATTGAAAAGATTGAGG
Found at i:40211777 original size:12 final size:13
Alignment explanation
Indices: 40211744--40211774 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
40211734 ATGAAAAAGG
40211744 CTTGATTG-AAAA
1 CTTGATTGAAAAA
40211756 CTTGATTGAAAAA
1 CTTGATTGAAAAA
40211769 CTTGAT
1 CTTGAT
40211775 GAATGAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (13 bp):
CTTGATTGAAAAA
Found at i:40212202 original size:21 final size:21
Alignment explanation
Indices: 40212178--40212220 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
40212168 TTTTTAAAAT
40212178 TTACAAATGTTCTGAATTTGA
1 TTACAAATGTTCTGAATTTGA
40212199 TTACAAATGTTCTGAATTTGA
1 TTACAAATGTTCTGAATTTGA
40212220 T
1 T
40212221 CTTAATTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (21 bp):
TTACAAATGTTCTGAATTTGA
Found at i:40212494 original size:6 final size:6
Alignment explanation
Indices: 40212453--40212493 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
40212443 AATAAAAAAC
* * *
40212453 CCACTG CCACTG CCACCG CCACCG CCACCG CCACCC CCACC
1 CCACCG CCACCG CCACCG CCACCG CCACCG CCACCG CCACC
40212494 CTCGTCCCTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.17, C:0.66, G:0.12, T:0.05
Consensus pattern (6 bp):
CCACCG
Found at i:40213865 original size:6 final size:6
Alignment explanation
Indices: 40213818--40213855 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
40213808 ATATTTATTT
40213818 AATA-A AATATA AATATA AATATA AATATA AATATA AAT
1 AATATA AATATA AATATA AATATA AATATA AATATA AAT
40213856 TTTAAATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.12
6 28 0.88
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AATATA
Found at i:40213888 original size:21 final size:21
Alignment explanation
Indices: 40213840--40213900 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 21
40213830 ATATAAATAT
* * *
40213840 AAATATAAATATAAATTTTAA
1 AAATATTATTATAATTTTTAA
**
40213861 ATTTATTATTATAATTTTTAA
1 AAATATTATTATAATTTTTAA
40213882 AAATATTTATT-T-ATTTTTA
1 AAATA-TTATTATAATTTTTA
40213901 TATATTTTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
20 7 0.22
21 20 0.62
22 5 0.16
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
AAATATTATTATAATTTTTAA
Found at i:40213900 original size:10 final size:10
Alignment explanation
Indices: 40213864--40213940 Score: 66
Period size: 10 Copynumber: 7.8 Consensus size: 10
40213854 ATTTTAAATT
*
40213864 TATTATTATA
1 TATTTTTATA
*
40213874 -ATTTTTAAA
1 TATTTTTATA
* * *
40213883 AATATTTATT
1 TATTTTTATA
40213893 TATTTTTATA
1 TATTTTTATA
*
40213903 TATTTTTAAA
1 TATTTTTATA
* * *
40213913 AATATTTATT
1 TATTTTTATA
40213923 TATTTTTATA
1 TATTTTTATA
40213933 TATTTTTA
1 TATTTTTA
40213941 AAATTTATTG
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
9 7 0.14
10 43 0.86
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TATTTTTATA
Found at i:40213944 original size:29 final size:30
Alignment explanation
Indices: 40213861--40213943 Score: 150
Period size: 30 Copynumber: 2.8 Consensus size: 30
40213851 TAAATTTTAA
*
40213861 ATTTATTATTATA-ATTTTTAAAAATATTT
1 ATTTATTTTTATATATTTTTAAAAATATTT
40213890 ATTTATTTTTATATATTTTTAAAAATATTT
1 ATTTATTTTTATATATTTTTAAAAATATTT
40213920 ATTTATTTTTATATATTTTTAAAA
1 ATTTATTTTTATATATTTTTAAAA
40213944 TTTATTGTTG
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
29 12 0.23
30 40 0.77
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (30 bp):
ATTTATTTTTATATATTTTTAAAAATATTT
Found at i:40218419 original size:2 final size:2
Alignment explanation
Indices: 40218412--40218437 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40218402 ATGAATTTTA
40218412 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
40218438 TATTTTTGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40219354 original size:30 final size:29
Alignment explanation
Indices: 40219303--40219376 Score: 78
Period size: 31 Copynumber: 2.5 Consensus size: 29
40219293 CCGAGTATAA
*
40219303 TAAATATATATATTTTTA-TTTTTTAATTT
1 TAAA-ATATATTTTTTTATTTTTTTAATTT
* *
40219332 TAACATATATTTTTTTAAATTTTTTTATTTT
1 TAAAATATATTTTTTT--ATTTTTTTAATTT
*
40219363 TAAAATAAATTTTT
1 TAAAATATATTTTT
40219377 AGTGTTTTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 11 0.30
29 3 0.08
30 1 0.03
31 22 0.59
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (29 bp):
TAAAATATATTTTTTTATTTTTTTAATTT
Found at i:40220841 original size:11 final size:10
Alignment explanation
Indices: 40220814--40220843 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
40220804 ACTTGACTTC
40220814 AAATTTAAAT
1 AAATTTAAAT
40220824 AAATTTAAAT
1 AAATTTAAAT
40220834 ATAATTTAAA
1 A-AATTTAAA
40220844 ATTTTCAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.58
11 8 0.42
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
AAATTTAAAT
Found at i:40221417 original size:43 final size:42
Alignment explanation
Indices: 40221335--40221471 Score: 184
Period size: 43 Copynumber: 3.2 Consensus size: 42
40221325 ACGTCGCTAA
* * *
40221335 CTTTTGCGGCGCTTACAGAAAAAAACGCCGCTAACGATCATGTT
1 CTTTAGCGGCGC-TA-AGGAAAAAACGCCGCTAAAGATCATGTT
* *
40221379 CTTTAGCGGCGCTAAGGAAATACACGCCACTAAAGATCATGTT
1 CTTTAGCGGCGCTAAGGAAA-AAACGCCGCTAAAGATCATGTT
* *
40221422 CTTTAGCGGCGCTTATGAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTAAGGAAAAAACGCCGCTAAAGATCATGTT
40221464 CTTTAGCG
1 CTTTAGCG
40221472 TTAGCGGCGC
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
42 33 0.40
43 39 0.47
44 11 0.13
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (42 bp):
CTTTAGCGGCGCTAAGGAAAAAACGCCGCTAAAGATCATGTT
Found at i:40221461 original size:42 final size:42
Alignment explanation
Indices: 40221335--40221564 Score: 191
Period size: 42 Copynumber: 5.2 Consensus size: 42
40221325 ACGTCGCTAA
* * *
40221335 CTTTTGCGGCGCTTACAGAAAAAAACGCCGCTAACGATCATGTT
1 CTTTAGCGGCGCTTA-TG-AAAAAACGCCGCTAAAGATCATGTT
* * * *
40221379 CTTTAGCGGCGCTAAGGAAATACACGCCACTAAAGATCATGTT
1 CTTTAGCGGCGCTTATGAAA-AAACGCCGCTAAAGATCATGTT
40221422 CTTTAGCGGCGCTTATGAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTATGAAAAAACGCCGCTAAAGATCATGTT
*
40221464 CTTTAGCGTTAGCGGCGCTT-TGGAAGAAAACGCCTCTAAA-AGT-AGTGTT
1 C--T----TTAGCGGCGCTTAT-GAA-AAAACGCCGCTAAAGA-TCA-TGTT
* **
40221513 CTTTAGCGGCGCTTGTTCAAAAACGCCGCTAAA-AGT-AGTGTT
1 CTTTAGCGGCGCTTATGAAAAAACGCCGCTAAAGA-TCA-TGTT
40221555 CTTTAGCGGC
1 CTTTAGCGGC
40221565 ACTTGTTTCA
Statistics
Matches: 160, Mismatches: 14, Indels: 26
0.80 0.07 0.13
Matches are distributed among these distances:
42 56 0.35
43 51 0.32
44 15 0.09
47 2 0.01
48 17 0.11
49 19 0.12
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (42 bp):
CTTTAGCGGCGCTTATGAAAAAACGCCGCTAAAGATCATGTT
Found at i:40221570 original size:42 final size:43
Alignment explanation
Indices: 40221490--40221582 Score: 152
Period size: 42 Copynumber: 2.2 Consensus size: 43
40221480 GCTTTGGAAG
* *
40221490 AAAACGCCTCTAAAAGTAGTGTTCTTTAGCGGCGCTTG-TTCA
1 AAAACGCCGCTAAAAGTAGTGTTCTTTAGCGGCACTTGTTTCA
40221532 AAAACGCCGCTAAAAGTAGTGTTCTTTAGCGGCACTTGTTTCA
1 AAAACGCCGCTAAAAGTAGTGTTCTTTAGCGGCACTTGTTTCA
*
40221575 CAAACGCC
1 AAAACGCC
40221583 ACTGTTTTGA
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
42 36 0.77
43 11 0.23
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (43 bp):
AAAACGCCGCTAAAAGTAGTGTTCTTTAGCGGCACTTGTTTCA
Found at i:40222066 original size:21 final size:21
Alignment explanation
Indices: 40222004--40222072 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 21
40221994 GCTTCTATCG
* * *
40222004 CTGCTTCTCTCACTGCGGCCT
1 CTGCTTCTCTCGCTGCAGCTT
*
40222025 CTGCTTCTCTCGCTGTAGCTT
1 CTGCTTCTCTCGCTGCAGCTT
* *
40222046 CTGCTTCCCTCGCTGCCGCTT
1 CTGCTTCTCTCGCTGCAGCTT
*
40222067 GTGCTT
1 CTGCTT
40222073 TAAGTTGTTG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.03, C:0.39, G:0.20, T:0.38
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGCAGCTT
Found at i:40227556 original size:9 final size:9
Alignment explanation
Indices: 40227542--40227792 Score: 167
Period size: 9 Copynumber: 29.8 Consensus size: 9
40227532 AAGTTATTTA
40227542 TTATGTAAG
1 TTATGTAAG
40227551 TTATGTAAG
1 TTATGTAAG
* *
40227560 TTGTATAAG
1 TTATGTAAG
40227569 TTATGTAAG
1 TTATGTAAG
* *
40227578 CTGTGTAAG
1 TTATGTAAG
*
40227587 TTGTGT-A-
1 TTATGTAAG
* *
40227594 TTATGAAAC
1 TTATGTAAG
40227603 TTATGTAAG
1 TTATGTAAG
*
40227612 TTGTGT-A-
1 TTATGTAAG
40227619 TTATGTAAG
1 TTATGTAAG
*
40227628 TTATGTCAG
1 TTATGTAAG
*
40227637 TTGTGT-A-
1 TTATGTAAG
* *
40227644 TTATGAAAC
1 TTATGTAAG
40227653 TTATGTAAG
1 TTATGTAAG
*
40227662 TTATGT--C
1 TTATGTAAG
40227669 TTATGTAAG
1 TTATGTAAG
*
40227678 TTATGTAAA
1 TTATGTAAG
*
40227687 ATATGT-A-
1 TTATGTAAG
40227694 TTATGTAAG
1 TTATGTAAG
*
40227703 TTATGTCAG
1 TTATGTAAG
*
40227712 TTGTGT-A-
1 TTATGTAAG
*
40227719 TTATGTAAA
1 TTATGTAAG
40227728 TTATGT-A-
1 TTATGTAAG
40227735 TTATGTAAG
1 TTATGTAAG
*
40227744 TTATGTAAT
1 TTATGTAAG
*
40227753 TTGTGT-A-
1 TTATGTAAG
*
40227760 TTATGTAAC
1 TTATGTAAG
* *
40227769 TTATTTAAT
1 TTATGTAAG
*
40227778 TTGTGTAAG
1 TTATGTAAG
40227787 -TATGTA
1 TTATGTA
40227793 TTATTATGTA
Statistics
Matches: 190, Mismatches: 36, Indels: 33
0.73 0.14 0.13
Matches are distributed among these distances:
7 40 0.21
8 19 0.10
9 131 0.69
ACGTcount: A:0.30, C:0.03, G:0.20, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:40227560 original size:25 final size:25
Alignment explanation
Indices: 40227531--40227734 Score: 237
Period size: 25 Copynumber: 8.1 Consensus size: 25
40227521 GATTTAGGAA
* *
40227531 TAAGTTATTTATTATGTAAGTTATG
1 TAAGTTGTGTATTATGTAAGTTATG
* * *
40227556 TAAGTTGTATAAGTTATGTAAGCTGTG
1 TAAGTTGTGT-A-TTATGTAAGTTATG
* *
40227583 TAAGTTGTGTATTATGAAACTTATG
1 TAAGTTGTGTATTATGTAAGTTATG
40227608 TAAGTTGTGTATTATGTAAGTTATG
1 TAAGTTGTGTATTATGTAAGTTATG
* * *
40227633 TCAGTTGTGTATTATGAAACTTATG
1 TAAGTTGTGTATTATGTAAGTTATG
* *
40227658 TAAGTTATGTCTTATGTAAGTTATG
1 TAAGTTGTGTATTATGTAAGTTATG
** *
40227683 TAAAATATGTATTATGTAAGTTATG
1 TAAGTTGTGTATTATGTAAGTTATG
* *
40227708 TCAGTTGTGTATTATGTAAATTATG
1 TAAGTTGTGTATTATGTAAGTTATG
40227733 TA
1 TA
40227735 TTATGTAAGT
Statistics
Matches: 149, Mismatches: 28, Indels: 4
0.82 0.15 0.02
Matches are distributed among these distances:
25 126 0.85
26 2 0.01
27 21 0.14
ACGTcount: A:0.31, C:0.03, G:0.20, T:0.46
Consensus pattern (25 bp):
TAAGTTGTGTATTATGTAAGTTATG
Found at i:40227648 original size:41 final size:41
Alignment explanation
Indices: 40227603--40227772 Score: 187
Period size: 41 Copynumber: 4.3 Consensus size: 41
40227593 ATTATGAAAC
* *
40227603 TTATGTAAGTTGTGTATTATGTAAGTTATGTCAGTTGTGTA
1 TTATGTAAATTATGTATTATGTAAGTTATGTCAGTTGTGTA
* *
40227644 TTATG--AA--A---CTTATGTAAGTTATGTC--TTATGTAA
1 TTATGTAAATTATGTATTATGTAAGTTATGTCAGTTGTGT-A
*
40227677 GTTATGTAAAATATGTATTATGTAAGTTATGTCAGTTGTGTA
1 -TTATGTAAATTATGTATTATGTAAGTTATGTCAGTTGTGTA
* *
40227719 TTATGTAAATTATGTATTATGTAAGTTATGTAATTTGTGTA
1 TTATGTAAATTATGTATTATGTAAGTTATGTCAGTTGTGTA
*
40227760 TTATGTAACTTAT
1 TTATGTAAATTAT
40227773 TTAATTTGTG
Statistics
Matches: 108, Mismatches: 10, Indels: 22
0.77 0.07 0.16
Matches are distributed among these distances:
32 5 0.05
33 1 0.01
34 21 0.19
36 2 0.02
38 1 0.01
39 1 0.01
41 71 0.66
42 1 0.01
43 5 0.05
ACGTcount: A:0.30, C:0.03, G:0.19, T:0.48
Consensus pattern (41 bp):
TTATGTAAATTATGTATTATGTAAGTTATGTCAGTTGTGTA
Found at i:40227671 original size:16 final size:16
Alignment explanation
Indices: 40227603--40227750 Score: 124
Period size: 16 Copynumber: 9.0 Consensus size: 16
40227593 ATTATGAAAC
*
40227603 TTATGTAAGTTGTGTA
1 TTATGTAAGTTATGTA
40227619 TTATGTAAGTTATGTCA
1 TTATGTAAGTTATGT-A
* *
40227636 GTTGTGT-A-TTATGAAA
1 -TTATGTAAGTTATG-TA
*
40227652 CTTATGTAAGTTATGTC
1 -TTATGTAAGTTATGTA
40227669 TTATGTAAGTTATGTAAA
1 TTATGTAAGTTATGT--A
*
40227687 ATATGT-A-TTATGTAA
1 TTATGTAAGTTATGT-A
* *
40227702 GTTATGTCAGTTGTGTA
1 -TTATGTAAGTTATGTA
*
40227719 TTATGTAAATTATGTA
1 TTATGTAAGTTATGTA
40227735 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
40227751 ATTTGTGTAT
Statistics
Matches: 107, Mismatches: 15, Indels: 20
0.75 0.11 0.14
Matches are distributed among these distances:
15 2 0.02
16 79 0.74
17 6 0.06
18 20 0.19
ACGTcount: A:0.30, C:0.03, G:0.20, T:0.47
Consensus pattern (16 bp):
TTATGTAAGTTATGTA
Found at i:40227759 original size:25 final size:24
Alignment explanation
Indices: 40227690--40227806 Score: 79
Period size: 25 Copynumber: 5.0 Consensus size: 24
40227680 ATGTAAAATA
* *
40227690 TGTATTATGTAAGTTATGTCAGTTG
1 TGTATTATGTAA-TTATGTAATTTG
*
40227715 TGTATTATGTAAATTATGT-A-TTA
1 TGTATTATGT-AATTATGTAATTTG
40227738 TGTA--A-G---TTATGTAATTTG
1 TGTATTATGTAATTATGTAATTTG
*
40227756 TGTATTATGTAACTTATTTAATTTG
1 TGTATTATGTAA-TTATGTAATTTG
*
40227781 TGTAAGTATGTATTATTATGTAATTT
1 TGT-ATTATGTA--ATTATGTAATTT
40227807 ATTATGTAGG
Statistics
Matches: 74, Mismatches: 5, Indels: 24
0.72 0.05 0.23
Matches are distributed among these distances:
16 6 0.08
17 1 0.01
18 6 0.08
20 2 0.03
21 2 0.03
23 6 0.08
24 1 0.01
25 30 0.41
26 9 0.12
27 10 0.14
28 1 0.01
ACGTcount: A:0.29, C:0.02, G:0.17, T:0.52
Consensus pattern (24 bp):
TGTATTATGTAATTATGTAATTTG
Found at i:40227831 original size:48 final size:48
Alignment explanation
Indices: 40227779--40227874 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
40227769 TTATTTAATT
40227779 TGTGTAAGTATGTATTATTATGTAATTTATTATGTAGGATATTATCTA
1 TGTGTAAGTATGTATTATTATGTAATTTATTATGTAGGATATTATCTA
40227827 TGTGTAAGTATGTATTATTATGTAATTTATTATGTAGGATATTATCTA
1 TGTGTAAGTATGTATTATTATGTAATTTATTATGTAGGATATTATCTA
40227875 AGTTATGTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.31, C:0.02, G:0.17, T:0.50
Consensus pattern (48 bp):
TGTGTAAGTATGTATTATTATGTAATTTATTATGTAGGATATTATCTA
Found at i:40227869 original size:24 final size:24
Alignment explanation
Indices: 40227794--40227880 Score: 81
Period size: 24 Copynumber: 3.6 Consensus size: 24
40227784 AAGTATGTAT
*
40227794 TATTATGTAATTTATTATGTAGGA
1 TATTATCTAATTTATTATGTAGGA
* *
40227818 TATTATCT-ATGTGTAAGTATGTA--T
1 TATTATCTAAT-T-T-ATTATGTAGGA
*
40227842 TATTATGTAATTTATTATGTAGGA
1 TATTATCTAATTTATTATGTAGGA
*
40227866 TATTATCTAAGTTAT
1 TATTATCTAATTTAT
40227881 GTAAGTTTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
22 7 0.14
23 3 0.06
24 29 0.59
25 3 0.06
26 7 0.14
ACGTcount: A:0.32, C:0.02, G:0.15, T:0.51
Consensus pattern (24 bp):
TATTATCTAATTTATTATGTAGGA
Found at i:40227974 original size:24 final size:26
Alignment explanation
Indices: 40227931--40227985 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 26
40227921 TTATGTACGG
* *
40227931 TATGTGTTATTATGTAAGTTCTTTAT
1 TATGTGTTATTATGTAAGTTATGTAT
*
40227957 TATGT-TTGTTATGT-AGTTATGTAT
1 TATGTGTTATTATGTAAGTTATGTAT
40227981 TATGT
1 TATGT
40227986 ACGATATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 13 0.50
25 8 0.31
26 5 0.19
ACGTcount: A:0.22, C:0.02, G:0.18, T:0.58
Consensus pattern (26 bp):
TATGTGTTATTATGTAAGTTATGTAT
Found at i:40228179 original size:15 final size:15
Alignment explanation
Indices: 40228159--40228191 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
40228149 ATAATTATTT
*
40228159 ATAAATTTAATAGTA
1 ATAAATTTAATACTA
40228174 ATAAATTTAATACTA
1 ATAAATTTAATACTA
40228189 ATA
1 ATA
40228192 TAGAAACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (15 bp):
ATAAATTTAATACTA
Found at i:40229451 original size:24 final size:22
Alignment explanation
Indices: 40229392--40229448 Score: 69
Period size: 24 Copynumber: 2.5 Consensus size: 22
40229382 GGAAACTGGG
* *
40229392 GAAATAGGAATTGGGGGGAAAT
1 GAAATGGGAATTGGGGGGAAAC
40229414 GAAATCGGGGAATTGGGGGGAATAC
1 GAAAT--GGGAATTGGGGGGAA-AC
40229439 GAAATGGGAA
1 GAAATGGGAA
40229449 ATTAGGGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
22 5 0.17
23 5 0.17
24 14 0.47
25 6 0.20
ACGTcount: A:0.39, C:0.04, G:0.42, T:0.16
Consensus pattern (22 bp):
GAAATGGGAATTGGGGGGAAAC
Found at i:40230019 original size:22 final size:22
Alignment explanation
Indices: 40229985--40230037 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
40229975 ATAGGCCCCT
40229985 AACTTT-AACCCGTAACCTTCA
1 AACTTTAAACCCGTAACCTTCA
*
40230006 AACTTTAAACCCGTAACCTTTA
1 AACTTTAAACCCGTAACCTTCA
40230028 AACTTTAAAC
1 AACTTTAAAC
40230038 TCTTAAACCC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 6 0.20
22 24 0.80
ACGTcount: A:0.38, C:0.28, G:0.04, T:0.30
Consensus pattern (22 bp):
AACTTTAAACCCGTAACCTTCA
Found at i:40230037 original size:29 final size:29
Alignment explanation
Indices: 40229998--40230083 Score: 93
Period size: 29 Copynumber: 2.9 Consensus size: 29
40229988 TTTAACCCGT
*
40229998 AACCTTCAAACTTTAAACCCGTAACCTTTA
1 AACCTT-AAACTTTAAACCCGTAACCTTCA
* * *
40230028 AACTTTAAACTCTTAAACCC-TAAACTACA
1 AACCTTAAACT-TTAAACCCGTAACCTTCA
* *
40230057 AACCTTACACTCTAAACCCGTAACCTT
1 AACCTTAAACTTTAAACCCGTAACCTT
40230084 ACACTCAAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
28 7 0.16
29 25 0.56
30 13 0.29
ACGTcount: A:0.38, C:0.31, G:0.02, T:0.28
Consensus pattern (29 bp):
AACCTTAAACTTTAAACCCGTAACCTTCA
Found at i:40230051 original size:15 final size:14
Alignment explanation
Indices: 40230005--40230053 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
40229995 CGTAACCTTC
40230005 AAACTTTAAACCCGT
1 AAACTTTAAACCC-T
* **
40230020 AACCTTTAAACTTT
1 AAACTTTAAACCCT
40230034 AAACTCTTAAACCCT
1 AAACT-TTAAACCCT
40230049 AAACT
1 AAACT
40230054 ACAAACCTTA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
14 5 0.19
15 22 0.81
ACGTcount: A:0.41, C:0.27, G:0.02, T:0.31
Consensus pattern (14 bp):
AAACTTTAAACCCT
Found at i:40230953 original size:77 final size:76
Alignment explanation
Indices: 40230841--40230987 Score: 188
Period size: 77 Copynumber: 1.9 Consensus size: 76
40230831 TTTTCTAGTA
** *
40230841 AGCGCCACTAATATAAGTATACATCAAAATTAAAACTACGCGTTTTAGTTAAGATATTTTTGCGG
1 AGCGCCACTAATATAAGTATACATCAAAACCAAAACGACGCGTTTTAGTTAAGATA-TTTTGCGG
40230906 CGTTTTAACGTC
65 CGTTTTAACGTC
* * ** * *
40230918 AGCGCCACTAAT-TGAAGTATACATCGAGACCAAAACGGTGCGTTTTGGTTCAGATATTTTGCGG
1 AGCGCCACTAATAT-AAGTATACATCAAAACCAAAACGACGCGTTTTAGTTAAGATATTTTGCGG
40230982 CGTTTT
65 CGTTTT
40230988 CCTATAAGCG
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
76 15 0.25
77 45 0.75
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.33
Consensus pattern (76 bp):
AGCGCCACTAATATAAGTATACATCAAAACCAAAACGACGCGTTTTAGTTAAGATATTTTGCGGC
GTTTTAACGTC
Found at i:40231048 original size:266 final size:266
Alignment explanation
Indices: 40230631--40231425 Score: 1397
Period size: 266 Copynumber: 3.0 Consensus size: 266
40230621 GTATTTTGCT
*
40230631 TTTTTGCAGCGTTTTAACGTCAGCGCCACTAATTGAAGTATACATCGAGACCAAAACGGTGCGTT
1 TTTTTGCGGCGTTTTAACGTCAGCGCCACTAATTGAAGTATACATCGAGACCAAAACGGTGCGTT
*
40230696 TTGGTTCAGATATTTTGCGGCGTTTTCCTATAAGCGCCACTAAATGTAACATAGCTTAAGACAAA
66 TTGGTTCAGATATTTTGCGGCGTTTTCCTATAAGCGCCACTAAATGTAACATAGCTTAAGACCAA
*
40230761 ACACTGCGTTTTGTTAAGATACGTTGCGGCGCTTTGGATCAAGTGCCGCTAAAGCTATTCTTTAA
131 ACACTGCGTTTTGTTAAGATACGTTGCGGCGCTTTGGATCAAGCGCCGCTAAAGCTATTCTTTAA
40230826 CGGCGTTTTCTAGTAAGCGCCACTAATATAAGTATACATCAAAATTAAAACTACGCGTTTTAGTT
196 CGGCGTTTTCTAGTAAGCGCCACTAATATAAGTATACATCAAAATTAAAACTACGCGTTTTAGTT
40230891 AAGATA
261 AAGATA
40230897 TTTTTGCGGCGTTTTAACGTCAGCGCCACTAATTGAAGTATACATCGAGACCAAAACGGTGCGTT
1 TTTTTGCGGCGTTTTAACGTCAGCGCCACTAATTGAAGTATACATCGAGACCAAAACGGTGCGTT
40230962 TTGGTTCAGATATTTTGCGGCGTTTTCCTATAAGCGCCACTAAATGTAACATAGCTTAAGACCAA
66 TTGGTTCAGATATTTTGCGGCGTTTTCCTATAAGCGCCACTAAATGTAACATAGCTTAAGACCAA
*
40231027 ACACTGCGTTTTGTTAAGATACGTTGCGGCGCTTTGGCTCAAGCGCCGCTAAAGCTATTCTTTAA
131 ACACTGCGTTTTGTTAAGATACGTTGCGGCGCTTTGGATCAAGCGCCGCTAAAGCTATTCTTTAA
* **
40231092 CGGTGTTTTCTAGTAAGCGCCAC-----TAA-TATA-ATCAAAATTAAAACTACGCGTTTTACCT
196 CGGCGTTTTCTAGTAAGCGCCACTAATATAAGTATACATCAAAATTAAAACTACGCGTTTTAGTT
40231150 AAGATA
261 AAGATA
* * *
40231156 TTTTTGCGGTGTTTTAACGTCAGCGCCACTAATTGAAGTATACATCGAGACCAAAATGATGCGTT
1 TTTTTGCGGCGTTTTAACGTCAGCGCCACTAATTGAAGTATACATCGAGACCAAAACGGTGCGTT
* *
40231221 TTGGTTCAGATTTTTTGCGGCATTTTCCTATAAGCGCCACTAAATGTAACATAGCTTAAGACCAA
66 TTGGTTCAGATATTTTGCGGCGTTTTCCTATAAGCGCCACTAAATGTAACATAGCTTAAGACCAA
* *
40231286 ACACTGCGTTTTGTTAAGATACGTTGCGGCACTTTGGATCAAGCGCTGCTAAAGCTATTCTTTAA
131 ACACTGCGTTTTGTTAAGATACGTTGCGGCGCTTTGGATCAAGCGCCGCTAAAGCTATTCTTTAA
* *
40231351 CAGCGTTTTCTAGTAAGCGCCACTAATATAAGTATACATCAAAATTAAAACTACGCGTTTTAGTA
196 CGGCGTTTTCTAGTAAGCGCCACTAATATAAGTATACATCAAAATTAAAACTACGCGTTTTAGTT
40231416 AAGATA
261 AAGATA
40231422 TTTT
1 TTTT
40231426 GTGGCGCTTT
Statistics
Matches: 502, Mismatches: 20, Indels: 14
0.94 0.04 0.03
Matches are distributed among these distances:
259 240 0.48
260 4 0.01
261 3 0.01
264 3 0.01
265 4 0.01
266 248 0.49
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.32
Consensus pattern (266 bp):
TTTTTGCGGCGTTTTAACGTCAGCGCCACTAATTGAAGTATACATCGAGACCAAAACGGTGCGTT
TTGGTTCAGATATTTTGCGGCGTTTTCCTATAAGCGCCACTAAATGTAACATAGCTTAAGACCAA
ACACTGCGTTTTGTTAAGATACGTTGCGGCGCTTTGGATCAAGCGCCGCTAAAGCTATTCTTTAA
CGGCGTTTTCTAGTAAGCGCCACTAATATAAGTATACATCAAAATTAAAACTACGCGTTTTAGTT
AAGATA
Found at i:40231561 original size:116 final size:113
Alignment explanation
Indices: 40231405--40231645 Score: 261
Period size: 113 Copynumber: 2.1 Consensus size: 113
40231395 TTAAAACTAC
* * * * * **
40231405 GCGTTTTAGTAAAGATATTTTGTGGCGCTTTCTACGAAACGCCGCTAATACGGTGCTTTAGCGGC
1 GCGTTTTGGTTAAGATATTTTGCGGCGCTATCTACAAAACGCCGC-AA-A-GACGCTTTAGCGGC
*
40231470 G-CATATCACAAAGCGCCACTAAATCTAGGATACATCAACACCAAAAACGAT
63 GTCATATCA-AAAGCACCACTAAATCTAGGATACATCAACACCAAAAACGAT
* *
40231521 GCGTTTTGGTTAAGATATTTTGCGGCGCATATC-GCAAAACGCCGCAAAGACGCTTTCGCGGCGT
1 GCGTTTTGGTTAAGATATTTTGCGGCGC-TATCTACAAAACGCCGCAAAGACGCTTTAGCGGCGT
** * * * * * *
40231585 TTTTTTAGAAGCACCACTAATTCTAGGATACATCAGCACTAAAAACGAT
65 CATATCAAAAGCACCACTAAATCTAGGATACATCAACACCAAAAACGAT
40231634 GCGTTTTGGTTA
1 GCGTTTTGGTTA
40231646 GGAGAAATTA
Statistics
Matches: 105, Mismatches: 18, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
113 61 0.58
114 4 0.04
115 2 0.02
116 35 0.33
117 3 0.03
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.27
Consensus pattern (113 bp):
GCGTTTTGGTTAAGATATTTTGCGGCGCTATCTACAAAACGCCGCAAAGACGCTTTAGCGGCGTC
ATATCAAAAGCACCACTAAATCTAGGATACATCAACACCAAAAACGAT
Found at i:40231730 original size:114 final size:113
Alignment explanation
Indices: 40231480--40231781 Score: 324
Period size: 113 Copynumber: 2.7 Consensus size: 113
40231470 GCATATCACA
* * * * *
40231480 AAGCGCCACTAAATCTAGGATACATCAACACCAAAAACGATGCGTTTTGGTTAAGATATTTTGCG
1 AAGCGCCACTAATTCTAGGATACATCAGCA-CAAAAACGATGCGTTTTGGTTAGGAGAATTTGCG
* * * * * * *
40231545 GCGC-ATATCGCAAAACGCCGCAAAGACGCTTTCGCGGCGTTTTTTTAG
65 GCGCGTTGTTGTAAAACACCGCAAAGACACTTTAGCGGCGTTTTTTTAG
* * *
40231593 AAGCACCACTAATTCTAGGATACATCAGCACTAAAAACGATGCGTTTTGGTTAGGAGAAATTACG
1 AAGCGCCACTAATTCTAGGATACATCAGCAC-AAAAACGATGCGTTTTGGTTAGGAGAATTTGCG
* *
40231658 GCGCGTTGTTGTAAAACACCGCTAAGACACTTTAGTGGCGTGTTTTTT-G
65 GCGCGTTGTTGTAAAACACCGCAAAGACACTTTAGCGGCGT-TTTTTTAG
* * * * * *
40231707 AAGCGCCACTAATTCTTGCATACATAAAG-ACGAAAACGTTGCGTTTTGGATAGGAG-ATTTGCG
1 AAGCGCCACTAATTCTAGGATACAT-CAGCACAAAAACGATGCGTTTTGGTTAGGAGAATTTGCG
*
40231770 GCGCGTGGTTGT
65 GCGCGTTGTTGT
40231782 GAACGCCGCT
Statistics
Matches: 158, Mismatches: 27, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
112 17 0.11
113 81 0.51
114 52 0.33
115 8 0.05
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (113 bp):
AAGCGCCACTAATTCTAGGATACATCAGCACAAAAACGATGCGTTTTGGTTAGGAGAATTTGCGG
CGCGTTGTTGTAAAACACCGCAAAGACACTTTAGCGGCGTTTTTTTAG
Found at i:40232087 original size:8 final size:8
Alignment explanation
Indices: 40232076--40232103 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
40232066 ATTTATATAT
40232076 TTTTCAAA
1 TTTTCAAA
40232084 TTTTCAAA
1 TTTTCAAA
40232092 TTTTCAAA
1 TTTTCAAA
40232100 TTTT
1 TTTT
40232104 AATTTCAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.57
Consensus pattern (8 bp):
TTTTCAAA
Found at i:40238565 original size:11 final size:11
Alignment explanation
Indices: 40238523--40238663 Score: 106
Period size: 11 Copynumber: 13.5 Consensus size: 11
40238513 AATAAATACC
40238523 TAAAAACTATTT
1 TAAAAA-TATTT
*
40238535 T-AAAA-ATTA
1 TAAAAATATTT
*
40238544 AAAAAAGTATTT
1 TAAAAA-TATTT
40238556 TAAAAATATTT
1 TAAAAATATTT
40238567 TAAAAATATTT
1 TAAAAATATTT
40238578 T--AAA-A-TT
1 TAAAAATATTT
* *
40238585 AAAAAAAATTT
1 TAAAAATATTT
*
40238596 AAAAAAGTATTT
1 TAAAAA-TATTT
40238608 TAAAAATATTT
1 TAAAAATATTT
40238619 T--AAA-A-TT
1 TAAAAATATTT
*
40238626 TAAAAATA-AT
1 TAAAAATATTT
*
40238636 AAAAAAGTATTT
1 TAAAAA-TATTT
40238648 TAAAAATATTT
1 TAAAAATATTT
40238659 TAAAA
1 TAAAA
40238664 TTAAAAAAAT
Statistics
Matches: 105, Mismatches: 11, Indels: 27
0.73 0.08 0.19
Matches are distributed among these distances:
7 5 0.05
8 2 0.02
9 15 0.14
10 12 0.11
11 47 0.45
12 24 0.23
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.38
Consensus pattern (11 bp):
TAAAAATATTT
Found at i:40238588 original size:17 final size:17
Alignment explanation
Indices: 40238566--40238599 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40238556 TAAAAATATT
* *
40238566 TTAAAAATATTTTAAAA
1 TTAAAAAAAATTTAAAA
40238583 TTAAAAAAAATTTAAAA
1 TTAAAAAAAATTTAAAA
40238600 AAGTATTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TTAAAAAAAATTTAAAA
Found at i:40238601 original size:40 final size:40
Alignment explanation
Indices: 40238523--40238680 Score: 214
Period size: 40 Copynumber: 3.9 Consensus size: 40
40238513 AATAAATACC
*
40238523 TAAAAACTATTTTAAAAATTAAAAAAAGTATTTTAAAAA-TATTT
1 TAAAAA-TATTTT-AAAATTAAAAAAA--A-TTAAAAAAGTATTT
40238567 TAAAAATATTTTAAAATTAAAAAAAATTTAAAAAAGTATTT
1 TAAAAATATTTTAAAATTAAAAAAAA-TTAAAAAAGTATTT
*
40238608 TAAAAATATTTTAAAATTTAAAAATAA-TAAAAAAGTATTT
1 TAAAAATATTTTAAAA-TTAAAAAAAATTAAAAAAGTATTT
40238648 TAAAAATATTTTAAAATT-AAAAAAATTAAAAAA
1 TAAAAATATTTTAAAATTAAAAAAAATTAAAAAA
40238681 TAAATATATT
Statistics
Matches: 108, Mismatches: 3, Indels: 11
0.89 0.02 0.09
Matches are distributed among these distances:
38 6 0.06
39 9 0.08
40 38 0.35
41 21 0.19
42 22 0.20
43 6 0.06
44 6 0.06
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.36
Consensus pattern (40 bp):
TAAAAATATTTTAAAATTAAAAAAAATTAAAAAAGTATTT
Found at i:40238641 original size:52 final size:51
Alignment explanation
Indices: 40238536--40238663 Score: 163
Period size: 52 Copynumber: 2.5 Consensus size: 51
40238526 AAACTATTTT
* *
40238536 AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAAATATTTTAAAATTAAA
1 AAAAATTTAAAAAAGTATTTTAAAAATATTTT-AAAATATTTAAAAATTAAA
40238588 AAAAATTTAAAAAAGTATTTTAAAAATATTTT-AAA-ATTTAAAAATAATAAA
1 AAAAATTTAAAAAAGTATTTTAAAAATATTTTAAAATATTTAAAAAT--TAAA
* *
40238639 AAAGTATTTTAAAAA-TATTTTAAAA
1 AAA-AATTTAAAAAAGTATTTTAAAA
40238664 TTAAAAAAAT
Statistics
Matches: 69, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
49 9 0.13
50 3 0.04
51 17 0.25
52 40 0.58
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (51 bp):
AAAAATTTAAAAAAGTATTTTAAAAATATTTTAAAATATTTAAAAATTAAA
Found at i:40238853 original size:22 final size:22
Alignment explanation
Indices: 40238825--40238873 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
40238815 ATTTCGGGCG
40238825 GCCCGTCAGGCCGGGCCGCGCC
1 GCCCGTCAGGCCGGGCCGCGCC
40238847 GCCCGTCAGGCCGGGCCGCGCC
1 GCCCGTCAGGCCGGGCCGCGCC
40238869 GCCCG
1 GCCCG
40238874 GCCCATGAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.04, C:0.51, G:0.41, T:0.04
Consensus pattern (22 bp):
GCCCGTCAGGCCGGGCCGCGCC
Found at i:40239509 original size:3 final size:3
Alignment explanation
Indices: 40239501--40239545 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
40239491 CAACTTCACC
40239501 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
40239546 CATCATCATC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:40240197 original size:21 final size:24
Alignment explanation
Indices: 40240154--40240198 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
40240144 TAGAAACATT
40240154 AAAATAAATATTTCCCAACAAATTG
1 AAAATAAATATTT-CCAACAAATTG
40240179 AAAATAAAT-TTT-CAA-AAATT
1 AAAATAAATATTTCCAACAAATT
40240199 TGTATACTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 5 0.25
22 3 0.15
24 3 0.15
25 9 0.45
ACGTcount: A:0.56, C:0.11, G:0.02, T:0.31
Consensus pattern (24 bp):
AAAATAAATATTTCCAACAAATTG
Found at i:40241300 original size:36 final size:36
Alignment explanation
Indices: 40241260--40241511 Score: 116
Period size: 36 Copynumber: 7.1 Consensus size: 36
40241250 TGGTAGGACT
*
40241260 GAAAAATATGTGTGCCCAGCACTGGTCGATATAACC
1 GAAAAATATGTGTGCCCAGCACTGGTCGGTATAACC
** * * ** * *
40241296 G-AAAATAAATGCGCCCTGTGCTGGTCGGTAAAACT
1 GAAAAATATGTGTGCCCAGCACTGGTCGGTATAACC
* * * *
40241331 GAAAAATATGTGTACCTAGCACTGATCGGTGTAACC
1 GAAAAATATGTGTGCCCAGCACTGGTCGGTATAACC
** *** ** * * *
40241367 G-AAAATAAAATGTGCAGTGCGTTGGTTGGTAAAATC
1 GAAAAAT-ATGTGTGCCCAGCACTGGTCGGTATAACC
* * ** * *
40241403 GACAAATATGTGTACCCAAAACTAGTCGGTATAACT
1 GAAAAATATGTGTGCCCAGCACTGGTCGGTATAACC
* * * * ** *
40241439 G-ACAATAAGTGCGCCCTGTGCTGGTCGGTAAAACC
1 GAAAAATATGTGTGCCCAGCACTGGTCGGTATAACC
* *
40241474 -AACAAATATGTGTGCCTAGCACTGGTCGATATAACC
1 GAA-AAATATGTGTGCCCAGCACTGGTCGGTATAACC
40241510 GA
1 GA
40241512 TAATAAATGA
Statistics
Matches: 139, Mismatches: 71, Indels: 11
0.63 0.32 0.05
Matches are distributed among these distances:
35 54 0.39
36 80 0.58
37 5 0.04
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.24
Consensus pattern (36 bp):
GAAAAATATGTGTGCCCAGCACTGGTCGGTATAACC
Found at i:40241558 original size:71 final size:71
Alignment explanation
Indices: 40241263--40241558 Score: 304
Period size: 71 Copynumber: 4.2 Consensus size: 71
40241253 TAGGACTGAA
*
40241263 AAATATGTGTGCCCAGCACTGGTCGATATAACCGAAAATAAATGCGCCCTGTGCTGGTCGGTAAA
1 AAATATGTGTGCCCAGCACTGGTCGATATAACCGAAAATAAATGCGCCCTGCGCTGGTCGGTAAA
* *
40241328 ACTGAA
66 ACCGAC
* * * * * * ** * *
40241334 AAATATGTGTACCTAGCACTGATCGGTGTAACCGAAAATAAAATGTGCAGTGCGTTGGTTGGTAA
1 AAATATGTGTGCCCAGCACTGGTCGATATAACCGAAAAT-AAATGCGCCCTGCGCTGGTCGGTAA
*
40241399 AATCGAC
65 AACCGAC
* ** * * * * * *
40241406 AAATATGTGTACCCAAAACTAGTCGGTATAACTGACAATAAGTGCGCCCTGTGCTGGTCGGTAAA
1 AAATATGTGTGCCCAGCACTGGTCGATATAACCGAAAATAAATGCGCCCTGCGCTGGTCGGTAAA
*
40241471 ACCAAC
66 ACCGAC
* * * * * *
40241477 AAATATGTGTGCCTAGCACTGGTCGATATAACCGATAATAAATGAGCTCTACGCTGGTCGGTAGA
1 AAATATGTGTGCCCAGCACTGGTCGATATAACCGAAAATAAATGCGCCCTGCGCTGGTCGGTAAA
*
40241542 CCCGAC
66 ACCGAC
40241548 AAATATGTGTG
1 AAATATGTGTG
40241559 AAATCATTTC
Statistics
Matches: 177, Mismatches: 47, Indels: 2
0.78 0.21 0.01
Matches are distributed among these distances:
71 123 0.69
72 54 0.31
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (71 bp):
AAATATGTGTGCCCAGCACTGGTCGATATAACCGAAAATAAATGCGCCCTGCGCTGGTCGGTAAA
ACCGAC
Found at i:40250416 original size:40 final size:41
Alignment explanation
Indices: 40250331--40250417 Score: 115
Period size: 41 Copynumber: 2.1 Consensus size: 41
40250321 ACTAAAACAT
** *
40250331 AAATAAAATAAAATTCCTAAAATATACTAAAATTAACTTAT
1 AAATAAAATAAAATTCCTAAAATATACTAAAATTAAAATAC
*
40250372 AAATAAAATAAAA-TCCTAAAATCCTACTAAAA-TAAAATAC
1 AAATAAAATAAAATTCCTAAAAT-ATACTAAAATTAAAATAC
40250412 AAATAA
1 AAATAA
40250418 CTCTAAGATA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
40 20 0.49
41 21 0.51
ACGTcount: A:0.62, C:0.11, G:0.00, T:0.26
Consensus pattern (41 bp):
AAATAAAATAAAATTCCTAAAATATACTAAAATTAAAATAC
Found at i:40259518 original size:23 final size:23
Alignment explanation
Indices: 40259488--40259533 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
40259478 TAATAAAAAA
* *
40259488 GATTATCCCAACTTCCTATTATC
1 GATTATCCCAACTCCCCATTATC
*
40259511 GATTATCCTAACTCCCCATTATC
1 GATTATCCCAACTCCCCATTATC
40259534 TCATTAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.26, C:0.33, G:0.04, T:0.37
Consensus pattern (23 bp):
GATTATCCCAACTCCCCATTATC
Found at i:40263149 original size:67 final size:67
Alignment explanation
Indices: 40263040--40263171 Score: 210
Period size: 67 Copynumber: 2.0 Consensus size: 67
40263030 TTTCCAATTC
* * *
40263040 AGAGAGCATACTCTTGCGAACCTCATTTCTTATAGCGAGATTACCAGTCCAGGCTAAATCCCCTG
1 AGAGAGCACACTCCTGCGAACCTCATTTCTTACAGCGAGATTACCAGTCCAGGCTAAATCCCCTG
40263105 CA
66 CA
* * *
40263107 AGAGAGCACACTCCTGCGAACCTCATTTCTTACAGCGGGATTACTAGTCTAGGCTAAATCCCCTG
1 AGAGAGCACACTCCTGCGAACCTCATTTCTTACAGCGAGATTACCAGTCCAGGCTAAATCCCCTG
40263172 TAATATAAAC
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
67 59 1.00
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (67 bp):
AGAGAGCACACTCCTGCGAACCTCATTTCTTACAGCGAGATTACCAGTCCAGGCTAAATCCCCTG
CA
Found at i:40272866 original size:31 final size:31
Alignment explanation
Indices: 40272828--40272931 Score: 181
Period size: 31 Copynumber: 3.4 Consensus size: 31
40272818 TGGCCTAAAA
*
40272828 CCCACACGCCCGTGTGGCATACCCGTATAGG
1 CCCACACGCCCGTGTGGCATACCCGTGTAGG
*
40272859 CCCACACGCCTGTGTGGCATACCCGTGTAGG
1 CCCACACGCCCGTGTGGCATACCCGTGTAGG
*
40272890 CCCACATGCCCGTGTGGCATACCCGTGTAGG
1 CCCACACGCCCGTGTGGCATACCCGTGTAGG
40272921 CCCACACGCCC
1 CCCACACGCCC
40272932 AATCTTGCCT
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 68 1.00
ACGTcount: A:0.17, C:0.40, G:0.26, T:0.16
Consensus pattern (31 bp):
CCCACACGCCCGTGTGGCATACCCGTGTAGG
Found at i:40272903 original size:18 final size:18
Alignment explanation
Indices: 40272880--40272931 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 18
40272870 GTGTGGCATA
40272880 CCCGTGTAGGCCCACATG
1 CCCGTGTAGGCCCACATG
*
40272898 CCCGTGT-GG----CATA
1 CCCGTGTAGGCCCACATG
*
40272911 CCCGTGTAGGCCCACACG
1 CCCGTGTAGGCCCACATG
40272929 CCC
1 CCC
40272932 AATCTTGCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 10
0.67 0.08 0.26
Matches are distributed among these distances:
13 10 0.38
14 2 0.08
17 2 0.08
18 12 0.46
ACGTcount: A:0.15, C:0.42, G:0.27, T:0.15
Consensus pattern (18 bp):
CCCGTGTAGGCCCACATG
Found at i:40287232 original size:18 final size:18
Alignment explanation
Indices: 40287196--40287253 Score: 52
Period size: 17 Copynumber: 3.3 Consensus size: 18
40287186 ATTATTTGTA
*
40287196 ATTATTATATTTAAT-TTT
1 ATTATTA-ATTAAATATTT
40287214 ATTATTAATTAAATATTT
1 ATTATTAATTAAATATTT
*
40287232 AATT-TTAA-AAAATATTT
1 -ATTATTAATTAAATATTT
40287249 -TTATT
1 ATTATT
40287254 GATATTTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
15 2 0.06
16 2 0.06
17 14 0.40
18 14 0.40
19 3 0.09
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTATTAATTAAATATTT
Found at i:40288968 original size:24 final size:25
Alignment explanation
Indices: 40288910--40288969 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 25
40288900 AAAATACATT
* *
40288910 TTCTTAATTAAAAAATTAATTAAAA
1 TTCTTTATTAAAAAAATAATTAAAA
* * *
40288935 TTATTT-TTAAAAAAATCA-TAAAC
1 TTCTTTATTAAAAAAATAATTAAAA
40288958 TTCTTTATTAAA
1 TTCTTTATTAAA
40288970 TCAAGTGATG
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
23 9 0.32
24 15 0.54
25 4 0.14
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (25 bp):
TTCTTTATTAAAAAAATAATTAAAA
Found at i:40292598 original size:24 final size:25
Alignment explanation
Indices: 40292570--40292669 Score: 69
Period size: 25 Copynumber: 4.0 Consensus size: 25
40292560 GAGTTACCCG
*
40292570 TTAAGCTCACACGAGCTTTCTGTT-
1 TTAAGCTCACACGAGCTTCCTGTTA
** *
40292594 TTAAGCTCTTATGAGCTTCCTGTTA
1 TTAAGCTCACACGAGCTTCCTGTTA
* ** **
40292619 TTAAGCCCGGATAAGCTTCCTGTTA
1 TTAAGCTCACACGAGCTTCCTGTTA
* * *
40292644 -CATGGTTCACACGAGCTTCCTGTTA
1 TTA-AGCTCACACGAGCTTCCTGTTA
40292669 T
1 T
40292670 GTGGCTTGAG
Statistics
Matches: 57, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
24 21 0.37
25 36 0.63
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.37
Consensus pattern (25 bp):
TTAAGCTCACACGAGCTTCCTGTTA
Found at i:40293682 original size:133 final size:133
Alignment explanation
Indices: 40293444--40293840 Score: 749
Period size: 133 Copynumber: 3.0 Consensus size: 133
40293434 TATATTTGGT
40293444 AAGTTTGGACACTTGAACATATGTGATAATATGATATGCATAAGACTTGGTATTGGCTTAGTTTT
1 AAGTTTGGACACTTGAACATATGTGATAATATGATATGCATAAGACTTGGTATTGGCTTAGTTTT
* *
40293509 AATGTTTTGAATTGGTTGGTAAATGTATTTAAGTGTTTATGTAGGTGGAAGATAAGTTTGAGTGA
66 AATGTTTTGAATTGGTTGGTAAATGTATTTAAGTGTTTATGTAGGTGGAAGACAAGTTTGGGTGA
40293574 GAA
131 GAA
*
40293577 AAGTTTGGACACTTGAACATATGTGATAATATGATATGCATAAGACTTGATATTGGCTTAGTTTT
1 AAGTTTGGACACTTGAACATATGTGATAATATGATATGCATAAGACTTGGTATTGGCTTAGTTTT
40293642 AATGTTTTGAATTGGTTGGTAAATGTATTTAAGTGTTTATGTAGGTGGAAGACAAGTTTGGGTGA
66 AATGTTTTGAATTGGTTGGTAAATGTATTTAAGTGTTTATGTAGGTGGAAGACAAGTTTGGGTGA
40293707 GAA
131 GAA
*
40293710 AAGTTTGGACACTTGAACATATGTGATAAGATGATATGCATAAGACTTGGTATTGGCTTAGTTTT
1 AAGTTTGGACACTTGAACATATGTGATAATATGATATGCATAAGACTTGGTATTGGCTTAGTTTT
*
40293775 AATGTTTTGAATTGGTTGGTAAATGTATTTAAGTGTTTATGTAGGTGAAAGACAAGTTTGGGTGA
66 AATGTTTTGAATTGGTTGGTAAATGTATTTAAGTGTTTATGTAGGTGGAAGACAAGTTTGGGTGA
40293840 G
131 G
40293841 GAATAGGCTT
Statistics
Matches: 258, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
133 258 1.00
ACGTcount: A:0.30, C:0.05, G:0.26, T:0.39
Consensus pattern (133 bp):
AAGTTTGGACACTTGAACATATGTGATAATATGATATGCATAAGACTTGGTATTGGCTTAGTTTT
AATGTTTTGAATTGGTTGGTAAATGTATTTAAGTGTTTATGTAGGTGGAAGACAAGTTTGGGTGA
GAA
Found at i:40294560 original size:17 final size:17
Alignment explanation
Indices: 40294539--40294582 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
40294529 ATGGAATTAG
40294539 AATTTAGTTGAGAAAATT
1 AATTTAGTT-AGAAAATT
*
40294557 -ATTTAATTAGAAAATT
1 AATTTAGTTAGAAAATT
40294573 AATTTAGTTA
1 AATTTAGTTA
40294583 ATTTAGTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.45, C:0.00, G:0.11, T:0.43
Consensus pattern (17 bp):
AATTTAGTTAGAAAATT
Found at i:40294585 original size:9 final size:9
Alignment explanation
Indices: 40294571--40294603 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
40294561 AATTAGAAAA
40294571 TTAATTTAG
1 TTAATTTAG
40294580 TTAATTTAG
1 TTAATTTAG
*
40294589 TTAATTTAA
1 TTAATTTAG
40294598 TTAATT
1 TTAATT
40294604 AAAATAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (9 bp):
TTAATTTAG
Found at i:40300347 original size:20 final size:19
Alignment explanation
Indices: 40300307--40300370 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 19
40300297 TAATTTTTTT
*
40300307 AAAAATAAAAAATTATGAAA
1 AAAAATAAAAAATT-TTAAA
40300327 AAAAATAAAAAATCTTTAAA
1 AAAAATAAAAAAT-TTTAAA
*
40300347 ATTAAAAAAAAACAATTTTAAA
1 A--AAAATAAAA-AATTTTAAA
40300369 AA
1 AA
40300371 TATAAATATA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
20 19 0.50
21 1 0.03
22 15 0.39
23 3 0.08
ACGTcount: A:0.72, C:0.03, G:0.02, T:0.23
Consensus pattern (19 bp):
AAAAATAAAAAATTTTAAA
Found at i:40300370 original size:23 final size:25
Alignment explanation
Indices: 40300326--40300376 Score: 63
Period size: 23 Copynumber: 2.1 Consensus size: 25
40300316 AAATTATGAA
40300326 AAAAAATAAAAAATCTTTAAAAT-T
1 AAAAAATAAAAAATCTTTAAAATAT
*
40300350 AAAAAA-AAACAAT-TTTAAAAATAT
1 AAAAAATAAAAAATCTTT-AAAATAT
40300374 AAA
1 AAA
40300377 TATAAATTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 3 0.12
23 11 0.46
24 10 0.42
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (25 bp):
AAAAAATAAAAAATCTTTAAAATAT
Found at i:40302817 original size:51 final size:51
Alignment explanation
Indices: 40302762--40302880 Score: 132
Period size: 51 Copynumber: 2.3 Consensus size: 51
40302752 GGCCTTAAAG
* * * *
40302762 TTTACATATCCTGTCAATTTGATCTTGATTTAACAAATTTAG-CTCACAACA
1 TTTACACATCCTATCAATCTGATCATGATTTAACAAATTTAGCCT-ACAACA
* * * *
40302813 TTTACACGTTCTATCAATCTGGTCATGATTTAACAAATTTTGCCTACAACA
1 TTTACACATCCTATCAATCTGATCATGATTTAACAAATTTAGCCTACAACA
* *
40302864 TTTTCACATTCTATCAA
1 TTTACACATCCTATCAA
40302881 CATTTACAGA
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
51 55 0.96
52 2 0.04
ACGTcount: A:0.32, C:0.21, G:0.08, T:0.39
Consensus pattern (51 bp):
TTTACACATCCTATCAATCTGATCATGATTTAACAAATTTAGCCTACAACA
Found at i:40303835 original size:15 final size:15
Alignment explanation
Indices: 40303810--40303844 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
40303800 AACTCTATTT
*
40303810 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
40303824 TAATTAATATTAAGA
1 TAATTAATATTAAGA
40303839 TAATTA
1 TAATTA
40303845 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:40308460 original size:18 final size:18
Alignment explanation
Indices: 40308429--40308463 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
40308419 ATATGTAGAC
40308429 AAATATATAAACTAATAT
1 AAATATATAAACTAATAT
40308447 AAATA-ATAATACTAATA
1 AAATATATAA-ACTAATA
40308464 ATGATGATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (18 bp):
AAATATATAAACTAATAT
Found at i:40310260 original size:12 final size:12
Alignment explanation
Indices: 40310243--40310288 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
40310233 TTTAGTTTCC
40310243 TTACTTTATTTA
1 TTACTTTATTTA
40310255 TTACTTTATTT-
1 TTACTTTATTTA
**
40310266 TTTTTATTATTTA
1 TTACT-TTATTTA
40310279 TTAC-TTATTT
1 TTACTTTATTT
40310289 GGATATTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
11 9 0.32
12 17 0.61
13 2 0.07
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.72
Consensus pattern (12 bp):
TTACTTTATTTA
Found at i:40311329 original size:16 final size:16
Alignment explanation
Indices: 40311310--40311370 Score: 56
Period size: 16 Copynumber: 3.8 Consensus size: 16
40311300 TTCCTAAAGC
40311310 ATAAAAAATATAAATA
1 ATAAAAAATATAAATA
40311326 ATAAATAAATATAAATCA
1 ATAAA-AAATATAAAT-A
*
40311344 A-AATAAATA-AAA-A
1 ATAAAAAATATAAATA
*
40311357 AGAAAAAAATATAA
1 A-TAAAAAATATAA
40311371 TTTGGGGACT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
13 2 0.05
15 10 0.26
16 12 0.32
17 12 0.32
18 2 0.05
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (16 bp):
ATAAAAAATATAAATA
Found at i:40311356 original size:10 final size:10
Alignment explanation
Indices: 40311310--40311356 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
40311300 TTCCTAAAGC
*
40311310 ATAAAAA-AT
1 ATAAAAATAA
40311319 ATAAATAATAA
1 ATAAA-AATAA
*
40311330 ATAAATATAA
1 ATAAAAATAA
*
40311340 ATCAAAATAA
1 ATAAAAATAA
40311350 ATAAAAA
1 ATAAAAA
40311357 AGAAAAAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
9 5 0.16
10 20 0.65
11 6 0.19
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (10 bp):
ATAAAAATAA
Found at i:40313532 original size:40 final size:40
Alignment explanation
Indices: 40313483--40313573 Score: 137
Period size: 40 Copynumber: 2.3 Consensus size: 40
40313473 GAGTAAAATC
* * *
40313483 ATAGCTGAAAGATGTTATGGCATCATAAATGAGTAAGACT
1 ATAGTTGAAAGATGTTATGACATCATAAATGAGTAAGACA
*
40313523 ATAGTTGAAAGATGTTATGACATCTTAAATGAGTAAGACA
1 ATAGTTGAAAGATGTTATGACATCATAAATGAGTAAGACA
*
40313563 ATAGTTAAAAG
1 ATAGTTGAAAG
40313574 GCACTATAAC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.43, C:0.08, G:0.21, T:0.29
Consensus pattern (40 bp):
ATAGTTGAAAGATGTTATGACATCATAAATGAGTAAGACA
Found at i:40313586 original size:40 final size:40
Alignment explanation
Indices: 40313503--40313586 Score: 96
Period size: 40 Copynumber: 2.1 Consensus size: 40
40313493 GATGTTATGG
* * *** *
40313503 CATCATAAATGAGTAAGACTATAGTTGAAAGATGTTATGA
1 CATCATAAATGAGTAAGACAATAGTTAAAAGACACTATAA
* *
40313543 CATCTTAAATGAGTAAGACAATAGTTAAAAGGCACTATAA
1 CATCATAAATGAGTAAGACAATAGTTAAAAGACACTATAA
40313583 CATC
1 CATC
40313587 CTTTGATAGT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (40 bp):
CATCATAAATGAGTAAGACAATAGTTAAAAGACACTATAA
Done.