Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 39 of 204
Found at i:13551322 original size:11 final size:12
Alignment explanation
Indices: 13551287--13551338 Score: 52
Period size: 13 Copynumber: 4.2 Consensus size: 12
13551277 TGTATTTTTA
*
13551287 TCGTCTAAAATT
1 TCGTCGAAAATT
* *
13551299 TCATGGAAAAATT
1 TCGTCG-AAAATT
13551312 TCGT-GAAAATT
1 TCGTCGAAAATT
13551323 TCGTCCGAAAATT
1 TCGT-CGAAAATT
13551336 TCG
1 TCG
13551339 ACATTTGGGC
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
11 10 0.30
12 4 0.12
13 19 0.58
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (12 bp):
TCGTCGAAAATT
Found at i:13552434 original size:33 final size:33
Alignment explanation
Indices: 13552397--13552605 Score: 130
Period size: 33 Copynumber: 5.8 Consensus size: 33
13552387 TCCCCCAAGG
13552397 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* * * *
13552430 GGTTGCTAAGTGCTAATTTCACCGTATTTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGA-TTCCCCG-A--TT-CAT-TG---GT
13552472 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* * ** * *
13552505 GGTTGCTAAATACTGAACCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-TG---GT
* *
13552547 GGTTGCTAAGTGCTGATTCCCCGAATCACTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
*
13552580 GGTTGCTAAGTGCTGAATCCACCGAT
1 GGTTGCTAAGTGCTGATTCC-CCGAT
13552606 AACGGATAAC
Statistics
Matches: 133, Mismatches: 24, Indels: 37
0.69 0.12 0.19
Matches are distributed among these distances:
33 52 0.39
34 13 0.10
35 2 0.02
36 4 0.03
37 7 0.05
38 7 0.05
39 4 0.03
40 2 0.02
41 9 0.07
42 33 0.25
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
Found at i:13552528 original size:75 final size:75
Alignment explanation
Indices: 13552393--13552603 Score: 343
Period size: 75 Copynumber: 2.8 Consensus size: 75
13552383 TGATTCCCCC
*
13552393 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCT-AATTTCACCGTAT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGAA-TCCACCGTAT
*
13552457 TTTAAATGTGA
65 CTTAAATGTGA
* * *
13552468 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAATACTGAACCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGAATCCACCGTATC
13552533 TTAAATGTGA
66 TTAAATGTGA
* *
13552543 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGAATCCACCG
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGAATCCACCG
13552604 ATAACGGATA
Statistics
Matches: 125, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
75 123 0.98
76 2 0.02
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.31
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGAATCCACCGTATC
TTAAATGTGA
Found at i:13552666 original size:2 final size:2
Alignment explanation
Indices: 13552659--13552696 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
13552649 GAATAGGTGA
13552659 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13552697 GGTGGACAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13556560 original size:96 final size:97
Alignment explanation
Indices: 13556392--13556606 Score: 328
Period size: 96 Copynumber: 2.2 Consensus size: 97
13556382 AACAACTAGC
* *
13556392 TTTATTTGA-TTTTTCCATAAAAATCCTAAATACTAAACCCTAATCTAATTTTTTAAAAATTTAT
1 TTTATTTGATTTTTTCCTTAAAAATCCTAAACACTAAACCCTAATCTAATTTTTTAAAAATTTAT
* *
13556456 AATTAATTTACTCAAGTAACCCTAAACCCTAA
66 AATTAATTTAATCAAGAAACCCTAAACCCTAA
*
13556488 TTTATTTGATTTTTTCCTTAAAAA-CCATAAGCACTAAACCCTAATCTAATTTTTT-AAAATTTA
1 TTTATTTGATTTTTTCCTTAAAAATCC-TAAACACTAAACCCTAATCTAATTTTTTAAAAATTTA
* *
13556551 TAATTAATTTAATTAAGAAACCCTAAACCCTTA
65 TAATTAATTTAATCAAGAAACCCTAAACCCTAA
*
13556584 TTTATTTAATTTTTTCCTTAAAA
1 TTTATTTGATTTTTTCCTTAAAA
13556607 CCCTAAAATC
Statistics
Matches: 109, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
96 70 0.64
97 39 0.36
ACGTcount: A:0.39, C:0.16, G:0.02, T:0.42
Consensus pattern (97 bp):
TTTATTTGATTTTTTCCTTAAAAATCCTAAACACTAAACCCTAATCTAATTTTTTAAAAATTTAT
AATTAATTTAATCAAGAAACCCTAAACCCTAA
Found at i:13563559 original size:33 final size:33
Alignment explanation
Indices: 13563517--13563725 Score: 139
Period size: 33 Copynumber: 5.8 Consensus size: 33
13563507 ATATAAATGG
*
13563517 GGTTGCTAAGTGCTGATTTCCCGATTTATTGGC
1 GGTTGCTAAGTGCTGATTCCCCGATTTATTGGC
*
13563550 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A-TTT--AT-T---GGC
* *
13563592 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTTATTGGC
* *
13563625 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCG-AT-TT--AT-TG---GC
* * * * *
13563667 GGTTGCTAAGTGCTGATTCCCTGAATCACTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTTATTGGC
*
13563700 GGTTGCTAAGTGCTGAATTCACCGAT
1 GGTTGCTAAGTGCTG-ATTCCCCGAT
13563726 AACGGATAAC
Statistics
Matches: 141, Mismatches: 16, Indels: 37
0.73 0.08 0.19
Matches are distributed among these distances:
33 56 0.40
34 13 0.09
35 3 0.02
36 7 0.05
37 3 0.02
38 4 0.03
39 6 0.04
40 2 0.01
41 5 0.04
42 42 0.30
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGATTTATTGGC
Found at i:13563609 original size:42 final size:41
Alignment explanation
Indices: 13563550--13563686 Score: 164
Period size: 42 Copynumber: 3.5 Consensus size: 41
13563540 ATTTATTGGC
13563550 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCCACCGTA-TTTAAATGTGAAGGG
* *
13563592 GGTTGCTAAGTGCTGATTCC-CCG-A-TT-CAT-T---GGT
1 GGTTGCTAAGTGCTGATTCCACCGTATTTAAATGTGAAGGG
* *
13563625 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCGTAT-TTAAATGTGAAGGG
13563667 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
13563687 CTGAATCACT
Statistics
Matches: 79, Mismatches: 7, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
33 21 0.27
34 3 0.04
35 1 0.01
36 1 0.01
37 4 0.05
38 4 0.05
39 1 0.01
40 1 0.01
41 3 0.04
42 40 0.51
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.33
Consensus pattern (41 bp):
GGTTGCTAAGTGCTGATTCCACCGTATTTAAATGTGAAGGG
Found at i:13563638 original size:75 final size:75
Alignment explanation
Indices: 13563515--13563723 Score: 321
Period size: 75 Copynumber: 2.8 Consensus size: 75
13563505 GAATATAAAT
* * * *
13563515 GGGGTTGCTAAGTGCTGATTTCCCGATTTATTGGCGGTTGCTAAGTGCTGATTCCACCGTATTTT
1 GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTT
*
13563580 AAATGTGAAG
66 AAATGTGAAA
*
13563590 GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCTT
1 GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTT
13563655 AAATGTGAAA
66 AAATGTGAAA
* * *
13563665 GGGGTTGCTAAGTGCTGATTCCCTGAATCACTGGTGGTTGCTAAGTGCTGAATT-CACCG
1 GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTG-ATTCCACCG
13563724 ATAACGGATA
Statistics
Matches: 123, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
75 121 0.98
76 2 0.02
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.33
Consensus pattern (75 bp):
GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTT
AAATGTGAAA
Found at i:13570329 original size:42 final size:42
Alignment explanation
Indices: 13570270--13570406 Score: 139
Period size: 42 Copynumber: 3.5 Consensus size: 42
13570260 ATTTATTGGT
* *
13570270 GGTTGTTAAGTGCTGATTCCACCGTATTTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCCACCGTATATTAAATGTGAAGGG
* *
13570312 GGTTGCTAAGTGCTGATTCC-CC--A-ATT-CAT-T---GGT
1 GGTTGCTAAGTGCTGATTCCACCGTATATTAAATGTGAAGGG
* * * *
13570345 GGTTGCTAAATGCTGATCCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCGTATATTAAATGTGAAGGG
13570387 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
13570407 CCGAATCACT
Statistics
Matches: 74, Mismatches: 12, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
33 20 0.27
34 2 0.03
36 2 0.03
37 4 0.05
38 4 0.05
39 2 0.03
41 2 0.03
42 38 0.51
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (42 bp):
GGTTGCTAAGTGCTGATTCCACCGTATATTAAATGTGAAGGG
Found at i:13570359 original size:75 final size:75
Alignment explanation
Indices: 13570233--13570443 Score: 316
Period size: 75 Copynumber: 2.8 Consensus size: 75
13570223 TGATTCCCCC
* * * * *
13570233 AAGGGGTTGCTAAGTGATGATTCCCCGATTTATTGGTGGTTGTTAAGTGCTGATTCCACCGTATT
1 AAGGGGTTGCTAAGTGCTGATTCCCCAATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
13570298 TTAAATGTGA
66 TTAAATGTGA
* * *
13570308 AGGGGGTTGCTAAGTGCTGATTCCCCAATTCATTGGTGGTTGCTAAATGCTGATCCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCAATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
13570373 TTAAATGTGA
66 TTAAATGTGA
* *
13570383 AAGGGGTTGCTAAGTGCTGATTCCCCGAA-TCACTGGTGGTTGCTAAGTGCTGAATCCACCG
1 AAGGGGTTGCTAAGTGCTGATTCCCC-AATTCATTGGTGGTTGCTAAGTGCTGATTCCACCG
13570444 ATAACAGATA
Statistics
Matches: 122, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
75 120 0.98
76 2 0.02
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.32
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCAATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
TTAAATGTGA
Found at i:13575605 original size:19 final size:19
Alignment explanation
Indices: 13575558--13575610 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
13575548 ATCTTTAAGA
* *
13575558 ATATGCAATATTAAATATG
1 ATATGCAATCTTAGATATG
13575577 ATATGCAATCTTAGATATG
1 ATATGCAATCTTAGATATG
13575596 ATATGCAATCTTAGA
1 ATATGCAATCTTAGA
13575611 AGATATGATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (19 bp):
ATATGCAATCTTAGATATG
Found at i:13575636 original size:22 final size:22
Alignment explanation
Indices: 13575572--13575633 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 22
13575562 GCAATATTAA
13575572 ATATGATATGCAATCTT---AG
1 ATATGATATGCAATCTTAGAAG
13575591 ATATGATATGCAATCTTAGAAG
1 ATATGATATGCAATCTTAGAAG
* *
13575613 ATATGATTTTGTAATCTTAGA
1 ATATGA-TATGCAATCTTAGA
13575634 GATTTAATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
19 17 0.46
22 8 0.22
23 12 0.32
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (22 bp):
ATATGATATGCAATCTTAGAAG
Found at i:13576244 original size:37 final size:37
Alignment explanation
Indices: 13576168--13576244 Score: 86
Period size: 37 Copynumber: 2.1 Consensus size: 37
13576158 CATACATACG
*
13576168 TTTTATAATATATACATATACGTACACATTTTTTAATT
1 TTTTATAATATATACATATACG-ACACATTTTATAATT
* *
13576206 TTTTATAA-ATATATATATAC-ACATACTTTTATATATT
1 TTTTATAATATATACATATACGACACA-TTTTATA-ATT
13576243 TT
1 TT
13576245 CTATGTTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
35 4 0.12
36 6 0.18
37 16 0.47
38 8 0.24
ACGTcount: A:0.38, C:0.09, G:0.01, T:0.52
Consensus pattern (37 bp):
TTTTATAATATATACATATACGACACATTTTATAATT
Found at i:13576363 original size:23 final size:22
Alignment explanation
Indices: 13576336--13576379 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
13576326 ATAATTCACA
*
13576336 TACATATATATTTTTCTTATATG
1 TACATATATATATTT-TTATATG
13576359 TACATATATATATTTTTATAT
1 TACATATATATATTTTTATAT
13576380 TTTATAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (22 bp):
TACATATATATATTTTTATATG
Found at i:13581568 original size:21 final size:21
Alignment explanation
Indices: 13581516--13581595 Score: 65
Period size: 22 Copynumber: 3.8 Consensus size: 21
13581506 TTCAAGATCC
* *
13581516 AATTCAAAAAAAAAACCCAAA
1 AATTAAAAAAAAAAAACCAAA
*
13581537 AA-AACATAAAAAAAAAACCAAA
1 AATTA-A-AAAAAAAAAACCAAA
* *
13581559 AATTAAAAAAATTAAAATC-AA
1 AATTAAAAAAA-AAAAACCAAA
*
13581580 AATTAAAAAATAAAAA
1 AATTAAAAAAAAAAAA
13581596 TGACAAAAAG
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
20 4 0.09
21 20 0.43
22 22 0.47
23 1 0.02
ACGTcount: A:0.76, C:0.10, G:0.00, T:0.14
Consensus pattern (21 bp):
AATTAAAAAAAAAAAACCAAA
Found at i:13581587 original size:20 final size:21
Alignment explanation
Indices: 13581544--13581596 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
13581534 AAAAAAACAT
*
13581544 AAAAA-AAAAACCAAAAATTAA
1 AAAAATAAAAATC-AAAATTAA
*
13581565 AAAAATTAAAATCAAAATT-A
1 AAAAATAAAAATCAAAATTAA
13581585 AAAAATAAAAAT
1 AAAAATAAAAAT
13581597 GACAAAAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 12 0.43
21 11 0.39
22 5 0.18
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (21 bp):
AAAAATAAAAATCAAAATTAA
Found at i:13582958 original size:44 final size:44
Alignment explanation
Indices: 13582882--13583164 Score: 322
Period size: 44 Copynumber: 6.7 Consensus size: 44
13582872 AAAGCTTTAT
13582882 CTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTAC
1 CTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTAC
* * *
13582926 CTCCTTGGTTAGTAGTGGAATAGGTTGAAGATTGTAAGTCCTAC
1 CTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTAC
* * * *
13582970 CTCCCTGGTTAGTAGTGGAATAGGTTGAAGATTGTAAGTCTTAT
1 CTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTAC
* *
13583014 CTTCCTGGTCAGCAGTGGAATA----G--G--TG-AA-TCCTAT
1 CTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTAC
* *
13583048 CTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAATCCTAT
1 CTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTAC
*
13583092 CTCCCTGAG-CAGCAGTGGAATAGGTTGAAGATTGTGAA-TCCTAT
1 CTCCCTG-GTCAGCAGTGGAATAGGTTGAAGATTGT-AAGTCCTAC
**
13583136 CTCCCTGAG-CAGCAGTGGAGCAGGTTGAA
1 CTCCCTG-GTCAGCAGTGGAATAGGTTGAA
13583165 AATTACAGAT
Statistics
Matches: 214, Mismatches: 13, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
34 26 0.12
35 2 0.01
36 2 0.01
38 2 0.01
40 2 0.01
42 2 0.01
43 2 0.01
44 173 0.81
45 3 0.01
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (44 bp):
CTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTAC
Found at i:13583093 original size:78 final size:78
Alignment explanation
Indices: 13582964--13583116 Score: 236
Period size: 78 Copynumber: 2.0 Consensus size: 78
13582954 AGATTGTAAG
* * * * *
13582964 TCCTACCTCCCTGGTTAGTAGTGGAATAGGTTGAAGATTGTAAGTCTTATCTTCCTG-GTCAGCA
1 TCCTACCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAATCCTATCTCCCTGAG-CAGCA
13583028 GTGGAATAGGTGAA
65 GTGGAATAGGTGAA
*
13583042 TCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAATCCTATCTCCCTGAGCAGCAG
1 TCCTACCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAATCCTATCTCCCTGAGCAGCAG
13583107 TGGAATAGGT
66 TGGAATAGGT
13583117 TGAAGATTGT
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
78 67 0.99
79 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (78 bp):
TCCTACCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAATCCTATCTCCCTGAGCAGCAG
TGGAATAGGTGAA
Found at i:13583137 original size:122 final size:122
Alignment explanation
Indices: 13582920--13583154 Score: 332
Period size: 122 Copynumber: 1.9 Consensus size: 122
13582910 AGATTGTAAG
* * * * * *
13582920 TCCTACCTCCTTGGTTAGTAGTGGAATAGGTTGAAGATTGTAAGTCCTACCTCCCTGGTTAGTAG
1 TCCTACCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAATCCTACCTCCCTGGTCAGCAG
* *
13582985 TGGAATAGGTTGAAGATTGTAAGTCTTATCTTCCTG-GTCAGCAGTGGAATAGGTGAA
66 TGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTGAG-CAGCAGTGGAATAGGTGAA
* *
13583042 TCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAATCCTATCTCCCTGAG-CAGCA
1 TCCTACCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAATCCTACCTCCCTG-GTCAGCA
13583106 GTGGAATAGGTTGAAGATTGTGAA-TCCTATCTCCCTGAGCAGCAGTGGA
65 GTGGAATAGGTTGAAGATTGT-AAGTCCTATCTCCCTGAGCAGCAGTGGA
13583155 GCAGGTTGAA
Statistics
Matches: 100, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
122 96 0.96
123 4 0.04
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.30
Consensus pattern (122 bp):
TCCTACCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAATCCTACCTCCCTGGTCAGCAG
TGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTGAGCAGCAGTGGAATAGGTGAA
Found at i:13583180 original size:166 final size:166
Alignment explanation
Indices: 13582879--13583181 Score: 427
Period size: 166 Copynumber: 1.8 Consensus size: 166
13582869 CACAAAGCTT
* * * *
13582879 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTACCTCCTTGGTTAGTAGTGG
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAATCCTACCTCCCTGGTCAGCAGTGG
* * * *
13582944 AATAGGTTGAAGATTGTAAGTCCTACCTCCCTGGTTAGTAGTGGAATAGGTTGAAGATTGTAAGT
66 AATAGGTTGAAGATTGTAAGTCCTACCTCCCTGGTCAGCAGTGGAACAGGTTGAAGAATGTAAGT
13583009 CTTATCTTCCTGGTCAGCAGTGGAATAGGTGAATCC
131 CTTATCTTCCTGGTCAGCAGTGGAATAGGTGAATCC
*
13583045 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAATCCTATCTCCCTGAG-CAGCAGTG
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAATCCTACCTCCCTG-GTCAGCAGTG
* *
13583109 GAATAGGTTGAAGATTGTGAA-TCCTATCTCCCTGAG-CAGCAGTGGAGCAGGTTGAA-AAT-TA
65 GAATAGGTTGAAGATTGT-AAGTCCTACCTCCCTG-GTCAGCAGTGGAACAGGTTGAAGAATGTA
13583170 CAGATCTTATCT
128 -AG-TCTTATCT
13583182 CCCTAAGCAG
Statistics
Matches: 121, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
164 2 0.02
165 4 0.03
166 111 0.92
167 4 0.03
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.30
Consensus pattern (166 bp):
TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAATCCTACCTCCCTGGTCAGCAGTGG
AATAGGTTGAAGATTGTAAGTCCTACCTCCCTGGTCAGCAGTGGAACAGGTTGAAGAATGTAAGT
CTTATCTTCCTGGTCAGCAGTGGAATAGGTGAATCC
Found at i:13583181 original size:44 final size:43
Alignment explanation
Indices: 13583041--13583198 Score: 174
Period size: 44 Copynumber: 3.6 Consensus size: 43
13583031 GAATAGGTGA
* * *
13583041 ATCCTATCTCCCTG-GTCAGCAGTGGAATAGGTTGAAGATTGTAA
1 ATCCTATCTCCCTGAG-CAGCAGTGGAACAGGTTGAAGATT-CAG
* **
13583085 ATCCTATCTCCCTGAGCAGCAGTGGAATAGGTTGAAGATTGTG
1 ATCCTATCTCCCTGAGCAGCAGTGGAACAGGTTGAAGATTCAG
* *
13583128 AATCCTATCTCCCTGAGCAGCAGTGGAGCAGGTTGAAAATTACAG
1 -ATCCTATCTCCCTGAGCAGCAGTGGAACAGGTTGAAGATT-CAG
* * *
13583173 ATCTTATCTCCCTAAGCAGTAGTGGA
1 ATCCTATCTCCCTGAGCAGCAGTGGA
13583199 GCAGATCGAA
Statistics
Matches: 100, Mismatches: 11, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
44 98 0.98
45 2 0.02
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (43 bp):
ATCCTATCTCCCTGAGCAGCAGTGGAACAGGTTGAAGATTCAG
Found at i:13583191 original size:88 final size:88
Alignment explanation
Indices: 13583037--13583655 Score: 337
Period size: 88 Copynumber: 7.1 Consensus size: 88
13583027 AGTGGAATAG
** * ** * * *
13583037 GTGAATCCTATCTCCCTG-GTCAGCAGTGGAATAGGTTGAAGATTGTAAATCCTATCTCCCTGAG
1 GTGAATCCTATCTCCCTGAG-CAGCAGTGGAGCAGGTTGAAAATTACAGATCTTATCTCCCTAAG
* *
13583101 CAGCAGTGGAATAGGTTGAAGATT
65 CAGCAGTGGAGTAGGTCGAAGATT
13583125 GTGAATCCTATCTCCCTGAGCAGCAGTGGAGCAGGTTGAAAATTACAGATCTTATCTCCCTAAGC
1 GTGAATCCTATCTCCCTGAGCAGCAGTGGAGCAGGTTGAAAATTACAGATCTTATCTCCCTAAGC
* * * **
13583190 AGTAGTGGAGCAGATCGAAGACG
66 AGCAGTGGAGTAGGTCGAAGATT
* * ** * * * * * *** *
13583213 GCGAATCTTATCTTTCTAAGGTAGTAG-GGAAGCAGATT-TAAGCCACTAG-CCTTATCTCCCT-
1 GTGAATCCTATCTCCCTGA-GCAGCAGTGG-AGCAGGTTGAAAATTAC-AGATCTTATCTCCCTA
* * * *
13583274 GGTCAACAGTGGAATAGGTTGAAGATT
63 AG-CAGCAGTGGAGTAGGTCGAAGATT
** * *
13583301 GT-AAGTCCTATCTCCCT-AGTCAGCAGTGGAATAGG-TG--AA-T-C----C-TATTTCCCTTA
1 GTGAA-TCCTATCTCCCTGAG-CAGCAGTGGAGCAGGTTGAAAATTACAGATCTTATCTCCCTAA
** * *
13583354 TTAGCAGTGGAATAGGTAGAAGATT
64 GCAGCAGTGGAGTAGGTCGAAGATT
* * *
13583379 GTGAATCCTATCTCCCTGATCAGCAGTGGAGAAGGTTGAAAATTACAGATCTTATCTCTCTAAGC
1 GTGAATCCTATCTCCCTGAGCAGCAGTGGAGCAGGTTGAAAATTACAGATCTTATCTCCCTAAGC
* * * * **
13583444 AGTAGTGGAGCAGATCAAAGACG
66 AGCAGTGGAGTAGGTCGAAGATT
* ** * * * * * *** *
13583467 GCGAATATTATCTTCCC-AAGGTAGTAG-GGAAGCAGATT-TAAGCCACTAG-CCTTATCTCCCT
1 GTGAATCCTATC-TCCCTGA-GCAGCAGTGG-AGCAGGTTGAAAATTAC-AGATCTTATCTCCCT
* *
13583528 GAGCAGCAGTGGAGTAGGTTGAAGATT
62 AAGCAGCAGTGGAGTAGGTCGAAGATT
** *
13583555 GT-AGGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAG
1 GTGAATCC-TATCTCCCTGAGCAGCAGTGGAGCAGGTTGAAAATTACAGATCTTATCTCCCTAAG
* * **
13583619 CAGTAGTGGAGTAGATCGAAGACG
65 CAGCAGTGGAGTAGGTCGAAGATT
*
13583643 GTGAATCTTATCT
1 GTGAATCCTATCT
13583656 TCCCAAGGTA
Statistics
Matches: 382, Mismatches: 117, Indels: 64
0.68 0.21 0.11
Matches are distributed among these distances:
78 56 0.15
79 6 0.02
81 2 0.01
82 1 0.00
83 2 0.01
85 1 0.00
86 2 0.01
87 30 0.08
88 249 0.65
89 33 0.09
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (88 bp):
GTGAATCCTATCTCCCTGAGCAGCAGTGGAGCAGGTTGAAAATTACAGATCTTATCTCCCTAAGC
AGCAGTGGAGTAGGTCGAAGATT
Found at i:13583284 original size:132 final size:131
Alignment explanation
Indices: 13583133--13583585 Score: 402
Period size: 132 Copynumber: 3.5 Consensus size: 131
13583123 TTGTGAATCC
* *
13583133 TATCTCCCTGAGCAGCAGTGGAGCAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGCAGTGG
13583198 AGCAGATCGAAGACGGCGAATCTTATCTTTCTAAGGTAGTAGGGAAGCAGATTTAAGCCACTAGC
66 AGCAGATCGAAGACGGCGAAT-TTATCTTTCTAAGGTAGTAGGGAAGCAGATTTAAGCCACTAGC
13583263 CT
130 CT
* * * *
13583265 TATCTCCCTG-GTCAACAGTGGAATAGGTTGAAGATTGTA-AG-TCCTATCTCCCT-AGTCAGCA
1 TATCTCCCTGAG-CAGCAGTGGAGTAGGTTGAA-AAT-TACAGATCTTATCTCCCTAAG-CAGCA
** * * * ** * * * *
13583326 GTGGAATAGGT-GAA-TC--C-TATTTCCCTTAT-TAGCAGTGGAATA-GGTAGAAGATTGT--G
62 GTGGAGCAGATCGAAGACGGCGAATTTATCTT-TCTA--AG-GTAGTAGGGAAGCAGATT-TAAG
*
13583382 --A--ATCC-
122 CCACTAGCCT
* * * *
13583387 TATCTCCCTGATCAGCAGTGGAGAAGGTTGAAAATTACAGATCTTATCTCTCTAAGCAGTAGTGG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGCAGTGG
* * *
13583452 AGCAGATCAAAGACGGCGAATATTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACTAGC
66 AGCAGATCGAAGACGGCGAAT-TTATCTTTCTAAGGTAGTAGGGAAGCAGATTTAAGCCACTAGC
13583517 CT
130 CT
* ** ** *
13583519 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGGCCTTATCTCCCTGAGCAGCAGTGG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGCAGTGG
13583584 AG
66 AG
13583586 TAGGTTGAAA
Statistics
Matches: 242, Mismatches: 51, Indels: 56
0.69 0.15 0.16
Matches are distributed among these distances:
120 2 0.01
121 4 0.02
122 49 0.20
123 7 0.03
124 1 0.00
125 6 0.02
126 19 0.08
127 7 0.03
128 18 0.07
129 6 0.02
130 1 0.00
131 9 0.04
132 107 0.44
133 4 0.02
134 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (131 bp):
TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGCAGTGG
AGCAGATCGAAGACGGCGAATTTATCTTTCTAAGGTAGTAGGGAAGCAGATTTAAGCCACTAGCC
T
Found at i:13583328 original size:44 final size:43
Alignment explanation
Indices: 13583265--13583418 Score: 134
Period size: 44 Copynumber: 3.7 Consensus size: 43
13583255 CCACTAGCCT
* *
13583265 TATCTCCCTGGTCAACAGTGGAATAGGTTGAAGATTGTAAGTCC
1 TATCTCCCTAGTCAGCAGTGGAATAGGTTGAAGATTGTAA-TCC
13583309 TATCTCCCTAGTCAGCAGTGGAATA----G--G--TG-AATCC
1 TATCTCCCTAGTCAGCAGTGGAATAGGTTGAAGATTGTAATCC
* * *
13583343 TATTTCCCTTA-TTAGCAGTGGAATAGGTAGAAGATTGTGAATCC
1 TATCTCCC-TAGTCAGCAGTGGAATAGGTTGAAGATTGT-AATCC
13583387 TATCTCCCT-GATCAGCAGTGGAGA-AGGTTGAA
1 TATCTCCCTAG-TCAGCAGTGGA-ATAGGTTGAA
13583419 AATTACAGAT
Statistics
Matches: 89, Mismatches: 7, Indels: 28
0.72 0.06 0.23
Matches are distributed among these distances:
34 23 0.26
35 4 0.04
36 2 0.02
38 2 0.02
40 2 0.02
42 2 0.02
43 1 0.01
44 52 0.58
45 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (43 bp):
TATCTCCCTAGTCAGCAGTGGAATAGGTTGAAGATTGTAATCC
Found at i:13583344 original size:254 final size:254
Alignment explanation
Indices: 13583084--13583590 Score: 822
Period size: 254 Copynumber: 2.0 Consensus size: 254
13583074 GAAGATTGTA
*
13583084 AATCCTATCTCCCTGAGCAGCAGTGGAATAGGTTGAAGATTGTGAATCCTATCTCCCTGAGCAGC
1 AATCCTATCTCCCTGAGCAGCAGTGGAATAGGTAGAAGATTGTGAATCCTATCTCCCTGAGCAGC
* *
13583149 AGTGGAGCAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGG
66 AGTGGAGAAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGG
* * *
13583214 CGAATCTTATCTTTCTAAGGTAGTAGGGAAGCAGATTTAAGCCACTAGCCTTATCTCCCTG-GTC
131 CGAATATTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACTAGCCTTATCTCCCTGAG-C
*
13583278 AACAGTGGAATAGGTTGAAGATTGTAAGTCC-TATCTCCCT-AGTCAGCAGTGGAATAGGTG
195 AACAGTGGAATAGGTTGAAGATTGT-AGGCCTTATCTCCCTGAG-CAGCAGTGGAATAGGTG
* * ** *
13583338 AATCCTATTTCCCTTATTAGCAGTGGAATAGGTAGAAGATTGTGAATCCTATCTCCCTGATCAGC
1 AATCCTATCTCCCTGAGCAGCAGTGGAATAGGTAGAAGATTGTGAATCCTATCTCCCTGAGCAGC
*
13583403 AGTGGAGAAGGTTGAAAATTACAGATCTTATCTCTCTAAGCAGTAGTGGAGCAGATCAAAGACGG
66 AGTGGAGAAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGG
13583468 CGAATATTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACTAGCCTTATCTCCCTGAGCA
131 CGAATATTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACTAGCCTTATCTCCCTGAGCA
* * *
13583533 GCAGTGGAGTAGGTTGAAGATTGTAGGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGT
196 ACAGTGGAATAGGTTGAAGATTGTAGGCCTTATCTCCCTGAGCAGCAGTGGAATAGGT
13583591 TGAAAATTAC
Statistics
Matches: 234, Mismatches: 16, Indels: 6
0.91 0.06 0.02
Matches are distributed among these distances:
253 4 0.02
254 227 0.97
255 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.27
Consensus pattern (254 bp):
AATCCTATCTCCCTGAGCAGCAGTGGAATAGGTAGAAGATTGTGAATCCTATCTCCCTGAGCAGC
AGTGGAGAAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGG
CGAATATTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACTAGCCTTATCTCCCTGAGCA
ACAGTGGAATAGGTTGAAGATTGTAGGCCTTATCTCCCTGAGCAGCAGTGGAATAGGTG
Found at i:13583351 original size:34 final size:34
Alignment explanation
Indices: 13583306--13583370 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
13583296 AGATTGTAAG
13583306 TCCTATCTCCC-TAGTCAGCAGTGGAATAGGTGAA
1 TCCTATCTCCCTTA-TCAGCAGTGGAATAGGTGAA
* *
13583340 TCCTATTTCCCTTATTAGCAGTGGAATAGGT
1 TCCTATCTCCCTTATCAGCAGTGGAATAGGT
13583371 AGAAGATTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 26 0.93
35 2 0.07
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.32
Consensus pattern (34 bp):
TCCTATCTCCCTTATCAGCAGTGGAATAGGTGAA
Found at i:13583564 original size:44 final size:44
Alignment explanation
Indices: 13583515--13583632 Score: 173
Period size: 44 Copynumber: 2.7 Consensus size: 44
13583505 TAAGCCACTA
* **
13583515 GCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAG
1 GCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAG
13583559 GCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAG
1 GCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAG
** * *
13583603 ATCTTATCTCCCTAAGCAGTAGTGGAGTAG
1 GCCTTATCTCCCTGAGCAGCAGTGGAGTAG
13583633 ATCGAAGACG
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 67 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.27
Consensus pattern (44 bp):
GCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAG
Found at i:13583565 original size:298 final size:299
Alignment explanation
Indices: 13582939--13583594 Score: 688
Period size: 298 Copynumber: 2.2 Consensus size: 299
13582929 CTTGGTTAGT
* * * * *
13582939 AGTGGAATAGGTTGAAGATTGTAAGTCC-TACCTCCCTGGTTAGTAGTGGAATAGGTTGAAGATT
1 AGTGGAGTAGGTTGAAGATTGT-AGGCCTTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATT
* * * *
13583003 GTAAGTCTTATCTTCCTGGTCAGCAGTGGAATAGGTGAATCCTATCTCCCTGGTCAGCAGTGGAA
65 GTAAGTCCTATCTCCCTAGTCAGCAGTGGAATAGGTGAATCCTATCTCCCTGATCAGCAGTGGAA
* * **
13583068 TAGGTTGAAGATTGTAAATCCTATCTCCCTGAGCAGCAGTGGAATAGGTTGAAGATTGTGAATCC
130 TAGGTAGAAGATTGTAAATCCTATCTCCCTGAGCAGCAGTGGAATAGGTTGAAAATTCAGAATCC
* * * ** *
13583133 TATCTCCCTGAGCAGCAGTGGAGCAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGG
195 TATCTCCCTAAGCAGCAGTGGAGCAGGATCAAAACGACAGATATTATCTCCCTAAGCAGTAGTGG
** * ** * *
13583198 AGCAGATCGAAGACGGCGAATCTTATCTTTCTAAGGTAGT
260 AGCAGATCGAAGACCACGAACCTTATCTCCCTAAGGCAGC
* * * **** *
13583238 AG-GGAAGCAGATTTAAGCCACTA-GCCTTATCTCCCTGGTCAACAGTGGAATAGGTTGAAGATT
1 AGTGG-AGTAGGTTGAAGATTGTAGGCCTTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATT
* * *
13583301 GTAAGTCCTATCTCCCTAGTCAGCAGTGGAATAGGTGAATCCTATTTCCCTTATTAGCAGTGGAA
65 GTAAGTCCTATCTCCCTAGTCAGCAGTGGAATAGGTGAATCCTATCTCCCTGATCAGCAGTGGAA
* *
13583366 TAGGTAGAAGATTGTGAATCCTATCTCCCTGATCAGCAGTGGAGA-AGGTTGAAAATTACAG-AT
130 TAGGTAGAAGATTGTAAATCCTATCTCCCTGAGCAGCAGTGGA-ATAGGTTGAAAATT-CAGAAT
* * * * *
13583429 CTTATCTCTCTAAGCAGTAGTGGAGCA-GATCAAAGACGGC-GAATATTATCTTCCC-AAGGTAG
193 CCTATCTCCCTAAGCAGCAGTGGAGCAGGATCAAA-ACGACAG-ATATTATC-TCCCTAA-GCAG
** * * *
13583491 TAG-GGAAGCAGATTTAAG-CCACTAGCCTTATCTCCCTGA-GCAGC
254 TAGTGG-AGCAGATCGAAGACCACGAACCTTATCTCCCTAAGGCAGC
*
13583535 AGTGGAGTAGGTTGAAGATTGTAGGCCTTATCTCCCTGAG-CAGCAGTGGAGTAGGTTGAA
1 AGTGGAGTAGGTTGAAGATTGTAGGCCTTATCTCCCTG-GTCAGCAGTGGAATAGGTTGAA
13583595 AATTACAGAT
Statistics
Matches: 287, Mismatches: 58, Indels: 25
0.78 0.16 0.07
Matches are distributed among these distances:
297 24 0.08
298 229 0.80
299 34 0.12
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (299 bp):
AGTGGAGTAGGTTGAAGATTGTAGGCCTTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTG
TAAGTCCTATCTCCCTAGTCAGCAGTGGAATAGGTGAATCCTATCTCCCTGATCAGCAGTGGAAT
AGGTAGAAGATTGTAAATCCTATCTCCCTGAGCAGCAGTGGAATAGGTTGAAAATTCAGAATCCT
ATCTCCCTAAGCAGCAGTGGAGCAGGATCAAAACGACAGATATTATCTCCCTAAGCAGTAGTGGA
GCAGATCGAAGACCACGAACCTTATCTCCCTAAGGCAGC
Found at i:13583656 original size:176 final size:176
Alignment explanation
Indices: 13583356--13583726 Score: 618
Period size: 176 Copynumber: 2.1 Consensus size: 176
13583346 TTCCCTTATT
* * * *
13583356 AGCAGTGGAATAGGTAGAAGATTGTGAATCCTATCTCCCTGATCAGCAGTGGAGAAGGTTGAAAA
1 AGCAGTGGAGTAGGTTGAAGATTGTGAAGCCTATCTCCCTGAGCAGCAGTGGAGAAGGTTGAAAA
*
13583421 TTACAGATCTTATCTCTCTAAGCAGTAGTGGAGCAGATCAAAGACGGCGAATATTATCTTCCCAA
66 TTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCGAATATTATCTTCCCAA
13583486 GGTAGTAGGGAAGCAGATTTAAGCCACTAGCCTTATCTCCCTGAGC
131 GGTAGTAGGGAAGCAGATTTAAGCCACTAGCCTTATCTCCCTGAGC
* *
13583532 AGCAGTGGAGTAGGTTGAAGATTGT-AGGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAA
1 AGCAGTGGAGTAGGTTGAAGATTGTGAAGCC-TATCTCCCTGAGCAGCAGTGGAGAAGGTTGAAA
* * * *
13583596 ATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACGGTGAATCTTATCTTCCCA
65 ATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCGAATATTATCTTCCCA
13583661 AGGTAGTAGGGAAGCAGATTTAAGCCACTAGCCTTATCTCCCTGAGC
130 AGGTAGTAGGGAAGCAGATTTAAGCCACTAGCCTTATCTCCCTGAGC
*
13583708 AACAGTGGAGTAGGTTGAA
1 AGCAGTGGAGTAGGTTGAA
13583727 AATTATTGAT
Statistics
Matches: 182, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
175 3 0.02
176 179 0.98
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (176 bp):
AGCAGTGGAGTAGGTTGAAGATTGTGAAGCCTATCTCCCTGAGCAGCAGTGGAGAAGGTTGAAAA
TTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCGAATATTATCTTCCCAA
GGTAGTAGGGAAGCAGATTTAAGCCACTAGCCTTATCTCCCTGAGC
Found at i:13583697 original size:88 final size:88
Alignment explanation
Indices: 13583429--13583720 Score: 270
Period size: 88 Copynumber: 3.3 Consensus size: 88
13583419 AATTACAGAT
* * * * * *
13583429 CTTATCTCTCTAAGCAGTAGTGGAGCAGATCAAAGACGGCGAATATTATCTTCCCAAGGTAGTAG
1 CTTATCTCCCTAAGCAGCAGTGGAGTAGATCGAAGACGGTGAATCTTATCTTCCCAAGGTAGTAG
13583494 GGAAGCAGATTTAAGCCACTAGC
66 GGAAGCAGATTTAAGCCACTAGC
* * * ** ** * * *
13583517 CTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGT-AGGCCTTATC-TCCC-TGAGCAGC
1 CTTATCTCCCTAAGCAGCAGTGGAGTAGATCGAAGACGGTGA-ATCTTATCTTCCCAAG-GTAGT
* * * *** *
13583579 AGTGG-AGTAGGTTGAAAATTAC-AGAT
64 AG-GGAAGCAGATT-TAAGCCACTAG-C
*
13583605 CTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACGGTGAATCTTATCTTCCCAAGGTAGTAG
1 CTTATCTCCCTAAGCAGCAGTGGAGTAGATCGAAGACGGTGAATCTTATCTTCCCAAGGTAGTAG
13583670 GGAAGCAGATTTAAGCCACTAGC
66 GGAAGCAGATTTAAGCCACTAGC
* *
13583693 CTTATCTCCCTGAGCAACAGTGGAGTAG
1 CTTATCTCCCTAAGCAGCAGTGGAGTAG
13583721 GTTGAAAATT
Statistics
Matches: 150, Mismatches: 44, Indels: 20
0.70 0.21 0.09
Matches are distributed among these distances:
86 1 0.01
87 18 0.12
88 112 0.75
89 18 0.12
90 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.25
Consensus pattern (88 bp):
CTTATCTCCCTAAGCAGCAGTGGAGTAGATCGAAGACGGTGAATCTTATCTTCCCAAGGTAGTAG
GGAAGCAGATTTAAGCCACTAGC
Found at i:13583830 original size:44 final size:44
Alignment explanation
Indices: 13583738--13583843 Score: 117
Period size: 44 Copynumber: 2.4 Consensus size: 44
13583728 ATTATTGATT
* * ** *
13583738 TTATCTCCCT-AAGTTACAGTGGAGCAGATTGAAGCTAGTAATC
1 TTATCTCCCTGAAGTTGCAATGGAGCAGATTGAAAATAATAATC
* *
13583781 CTATCTCCCTGAAGTTGCAATGGAGCGGATT-AAAATAATAGATC
1 TTATCTCCCTGAAGTTGCAATGGAGCAGATTGAAAATAATA-ATC
*
13583825 TTATCTCTCTGAAGTTGCA
1 TTATCTCCCTGAAGTTGCA
13583844 GTAGAGTATA
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
43 15 0.29
44 37 0.71
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (44 bp):
TTATCTCCCTGAAGTTGCAATGGAGCAGATTGAAAATAATAATC
Found at i:13584453 original size:19 final size:19
Alignment explanation
Indices: 13584406--13584458 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
13584396 ATCTTCAAGA
* *
13584406 ATATGCAATATTAAATATG
1 ATATGCAATCTTAGATATG
13584425 ATATGCAATCTTAGATATG
1 ATATGCAATCTTAGATATG
13584444 ATATGCAATCTTAGA
1 ATATGCAATCTTAGA
13584459 AGATATGATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (19 bp):
ATATGCAATCTTAGATATG
Found at i:13584484 original size:22 final size:22
Alignment explanation
Indices: 13584420--13584481 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 22
13584410 GCAATATTAA
13584420 ATATGATATGCAATCTT---AG
1 ATATGATATGCAATCTTAGAAG
13584439 ATATGATATGCAATCTTAGAAG
1 ATATGATATGCAATCTTAGAAG
* *
13584461 ATATGATTTTGTAATCTTAGA
1 ATATGA-TATGCAATCTTAGA
13584482 GATTTAATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
19 17 0.46
22 8 0.22
23 12 0.32
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (22 bp):
ATATGATATGCAATCTTAGAAG
Found at i:13584729 original size:23 final size:23
Alignment explanation
Indices: 13584685--13584729 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
13584675 TCTTATTTTG
* *
13584685 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
13584708 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
13584730 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:13585091 original size:37 final size:37
Alignment explanation
Indices: 13585015--13585091 Score: 86
Period size: 37 Copynumber: 2.1 Consensus size: 37
13585005 CATACATACG
*
13585015 TTTTATAATATATACATATACGTACACATTTTTTAATT
1 TTTTATAATATATACATATACG-ACACATTTTATAATT
* *
13585053 TTTTATAA-ATATATATATAC-ACATACTTTTATATATT
1 TTTTATAATATATACATATACGACACA-TTTTATA-ATT
13585090 TT
1 TT
13585092 CTATGTTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
35 4 0.12
36 6 0.18
37 16 0.47
38 8 0.24
ACGTcount: A:0.38, C:0.09, G:0.01, T:0.52
Consensus pattern (37 bp):
TTTTATAATATATACATATACGACACATTTTATAATT
Found at i:13585387 original size:3 final size:3
Alignment explanation
Indices: 13585379--13585435 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
13585369 TTATCTTTTC
13585379 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
13585427 ATT ATT ATT
1 ATT ATT ATT
13585436 TTGTTCTTGA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:13587062 original size:33 final size:32
Alignment explanation
Indices: 13587018--13587169 Score: 115
Period size: 33 Copynumber: 4.6 Consensus size: 32
13587008 TAGTGTTTAT
*
13587018 ATGTAAGACCATAGCTCGGCTATGGCATTCTG
1 ATGTAAGACCATAGCTGGGCTATGGCATTCTG
* * * *
13587050 ATGATAAGACCATAACTGGGTTATGGCACTATG
1 ATG-TAAGACCATAGCTGGGCTATGGCATTCTG
* * * * * * * * *
13587083 AACGTAAGACAATGGTTGGACCATGACAGTGTTTAT
1 -ATGTAAGACCATAGCTGGGCTATGGCA-T-TCT-G
13587119 ATGTAAGACCATAGCTGGGCTATGGCATTCTG
1 ATGTAAGACCATAGCTGGGCTATGGCATTCTG
*
13587151 ATGATAAGACCATAACTGG
1 ATG-TAAGACCATAGCTGG
13587170 TTTATGACAC
Statistics
Matches: 87, Mismatches: 27, Indels: 11
0.70 0.22 0.09
Matches are distributed among these distances:
32 6 0.07
33 56 0.64
34 3 0.03
35 22 0.25
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (32 bp):
ATGTAAGACCATAGCTGGGCTATGGCATTCTG
Found at i:13587126 original size:101 final size:101
Alignment explanation
Indices: 13586952--13587190 Score: 363
Period size: 101 Copynumber: 2.4 Consensus size: 101
13586942 TGAATTGACG
* * * * * **
13586952 GATAATACCATAACT-GGTTATGGAACTATGAACATAAGACCATGGTTGTACCATGGTAGTGTTT
1 GATAAGACCATAACTGGGTTATGGCACTATGAACGTAAGACAATGGTTGGACCATGACAGTGTTT
13587016 ATATGTAAGACCATAGCTCGGCTATGGCATTCTGAT
66 ATATGTAAGACCATAGCTCGGCTATGGCATTCTGAT
13587052 GATAAGACCATAACTGGGTTATGGCACTATGAACGTAAGACAATGGTTGGACCATGACAGTGTTT
1 GATAAGACCATAACTGGGTTATGGCACTATGAACGTAAGACAATGGTTGGACCATGACAGTGTTT
*
13587117 ATATGTAAGACCATAGCTGGGCTATGGCATTCTGAT
66 ATATGTAAGACCATAGCTCGGCTATGGCATTCTGAT
* * * *
13587153 GATAAGACCATAACTGGTTTATGACACTACGAATGTAA
1 GATAAGACCATAACTGGGTTATGGCACTATGAACGTAA
13587191 AGGATGAATT
Statistics
Matches: 126, Mismatches: 12, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
100 14 0.11
101 112 0.89
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (101 bp):
GATAAGACCATAACTGGGTTATGGCACTATGAACGTAAGACAATGGTTGGACCATGACAGTGTTT
ATATGTAAGACCATAGCTCGGCTATGGCATTCTGAT
Found at i:13591480 original size:13 final size:14
Alignment explanation
Indices: 13591448--13591481 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
13591438 TCATGAATCT
13591448 ATGAAAATGTTTGAA
1 ATGAAAATGTTT-AA
13591463 ATGAAAATGTTT-A
1 ATGAAAATGTTTAA
13591476 ATGAAA
1 ATGAAA
13591482 GTATATCTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.37
15 12 0.63
ACGTcount: A:0.50, C:0.00, G:0.18, T:0.32
Consensus pattern (14 bp):
ATGAAAATGTTTAA
Found at i:13607366 original size:7 final size:7
Alignment explanation
Indices: 13607354--13607390 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
13607344 ATATGAAAGG
13607354 GATGGGA
1 GATGGGA
13607361 GATGGGA
1 GATGGGA
13607368 GATGGGA
1 GATGGGA
13607375 GATGGGA
1 GATGGGA
13607382 GATGGGA
1 GATGGGA
13607389 GA
1 GA
13607391 AGAAAGGGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.30, C:0.00, G:0.57, T:0.14
Consensus pattern (7 bp):
GATGGGA
Found at i:13610536 original size:16 final size:16
Alignment explanation
Indices: 13610492--13610541 Score: 56
Period size: 14 Copynumber: 3.4 Consensus size: 16
13610482 TAACACAATT
13610492 ATATTTAATGTTAAG-
1 ATATTTAATGTTAAGA
*
13610507 A-ATTT-AT-ATAAGA
1 ATATTTAATGTTAAGA
13610520 ATATTTAATGTTAAGA
1 ATATTTAATGTTAAGA
13610536 AT-TTTA
1 ATATTTA
13610542 TTAAATTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
12 4 0.14
13 3 0.10
14 8 0.28
15 7 0.24
16 7 0.24
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (16 bp):
ATATTTAATGTTAAGA
Found at i:13610657 original size:120 final size:120
Alignment explanation
Indices: 13610507--13611064 Score: 990
Period size: 120 Copynumber: 4.7 Consensus size: 120
13610497 TAATGTTAAG
* * * *
13610507 AATTTATATAAGAATATTTAATGTTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATT
1 AATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATT
* *
13610572 TAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTA
66 TAATAATAATTATTTCAAATTATATTTTATAGTATCATATATTATGATTTTAGTA
* *
13610627 AATTCATATAAGAATATTTAATACTAAGAATTTTATTAAATTATAAATTTTAATTAAAATATATT
1 AATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATT
*
13610692 TAATAATTATTATTTCAAATTATATTTTATAGTATCATATATTATGATTTTAGTA
66 TAATAATAATTATTTCAAATTATATTTTATAGTATCATATATTATGATTTTAGTA
*
13610747 AATTCATATAAGAATATTTAATACTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATT
1 AATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATT
13610812 TAATAATAATTATTTCAAATTATATTTTATAGTATCATATATTATGATTTTAGTA
66 TAATAATAATTATTTCAAATTATATTTTATAGTATCATATATTATGATTTTAGTA
* *
13610867 AATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATT
1 AATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATT
13610932 TAATAATAATTATTTCAAATTATATTTTATAGTATCATATATTATGATTTTAGTA
66 TAATAATAATTATTTCAAATTATATTTTATAGTATCATATATTATGATTTTAGTA
* *
13610987 AATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATT
1 AATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATT
13611052 TAATAATAATTAT
66 TAATAATAATTAT
13611065 GTTAAAATAT
Statistics
Matches: 424, Mismatches: 14, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 424 1.00
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.49
Consensus pattern (120 bp):
AATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATT
TAATAATAATTATTTCAAATTATATTTTATAGTATCATATATTATGATTTTAGTA
Found at i:13610677 original size:17 final size:18
Alignment explanation
Indices: 13610655--13610689 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
13610645 TAATACTAAG
*
13610655 AATTTT-ATTAAATTATA
1 AATTTTAATTAAAATATA
13610672 AATTTTAATTAAAATATA
1 AATTTTAATTAAAATATA
13610690 TTTAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AATTTTAATTAAAATATA
Found at i:13610802 original size:18 final size:17
Alignment explanation
Indices: 13610776--13610810 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
13610766 AATACTAAGA
*
13610776 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
13610793 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
13610811 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:13610924 original size:18 final size:17
Alignment explanation
Indices: 13610896--13610930 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
13610886 ATTATTAAGA
*
13610896 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
13610913 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
13610931 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:13611044 original size:18 final size:17
Alignment explanation
Indices: 13611016--13611050 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
13611006 ATTATTAAGA
*
13611016 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
13611033 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
13611051 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:13611270 original size:44 final size:45
Alignment explanation
Indices: 13611207--13611303 Score: 135
Period size: 44 Copynumber: 2.2 Consensus size: 45
13611197 CTATTACACC
* *
13611207 TCCATTCCATTCAACCAAACACA-AGAA-TACTATTACGCCTCTAT
1 TCCATTACATTCAACCAAACA-ATAGAATTACTATTACGCCTCTAA
* *
13611251 TCCATTACATTCAACCAAACAATTGAATTGCTATTACGCCTCTAA
1 TCCATTACATTCAACCAAACAATAGAATTACTATTACGCCTCTAA
13611296 TCCATTAC
1 TCCATTAC
13611304 GCCTCTATTC
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
43 1 0.02
44 23 0.49
45 23 0.49
ACGTcount: A:0.35, C:0.30, G:0.05, T:0.30
Consensus pattern (45 bp):
TCCATTACATTCAACCAAACAATAGAATTACTATTACGCCTCTAA
Found at i:13611304 original size:16 final size:16
Alignment explanation
Indices: 13611283--13611318 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
13611273 TTGAATTGCT
13611283 ATTACGCCTCTAATCC
1 ATTACGCCTCTAATCC
*
13611299 ATTACGCCTCTATTCC
1 ATTACGCCTCTAATCC
13611315 ATTA
1 ATTA
13611319 TAGCGAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.25, C:0.33, G:0.06, T:0.36
Consensus pattern (16 bp):
ATTACGCCTCTAATCC
Found at i:13615498 original size:19 final size:19
Alignment explanation
Indices: 13615474--13615512 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
13615464 TTAAGTAAAT
*
13615474 ATTGTTTGTATATATTTTA
1 ATTGTTGGTATATATTTTA
*
13615493 ATTGTTGGTATTTATTTTA
1 ATTGTTGGTATATATTTTA
13615512 A
1 A
13615513 GTAATTATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.13, T:0.62
Consensus pattern (19 bp):
ATTGTTGGTATATATTTTA
Found at i:13616552 original size:67 final size:67
Alignment explanation
Indices: 13616444--13616578 Score: 225
Period size: 67 Copynumber: 2.0 Consensus size: 67
13616434 GCCGGTGTGA
** *
13616444 TGCGATCACGGGTTCAAGTATAATCGGGGGCCAGTTGATGATCATTACGCAATCACGTGTTCAAG
1 TGCGATCACGGGTTCAAGTATAATCAAGGGCCAGTTGATGATCATTACACAATCACGTGTTCAAG
13616509 TT
66 TT
* *
13616511 TGCGATCGCGGGTTCGAGTATAATCAAGGGCCAGTTGATGATCATTACACAATCACGTGTTCAAG
1 TGCGATCACGGGTTCAAGTATAATCAAGGGCCAGTTGATGATCATTACACAATCACGTGTTCAAG
13616576 TT
66 TT
13616578 T
1 T
13616579 TTTGGATACC
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
67 63 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (67 bp):
TGCGATCACGGGTTCAAGTATAATCAAGGGCCAGTTGATGATCATTACACAATCACGTGTTCAAG
TT
Found at i:13618841 original size:18 final size:18
Alignment explanation
Indices: 13618820--13618866 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
13618810 AAGATGCAAA
*
13618820 TGAGGAACAAAATGC-AG
1 TGAGGAACAAAATACAAG
* *
13618837 CTGAGGAAGAAGATACAAG
1 -TGAGGAACAAAATACAAG
13618856 TGAGGAACAAA
1 TGAGGAACAAA
13618867 GGACAGCGAA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
18 21 0.91
19 2 0.09
ACGTcount: A:0.49, C:0.11, G:0.30, T:0.11
Consensus pattern (18 bp):
TGAGGAACAAAATACAAG
Found at i:13623216 original size:17 final size:17
Alignment explanation
Indices: 13623194--13623228 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
13623184 GTAAAGATTA
13623194 TGATACAAAAATTTTGG
1 TGATACAAAAATTTTGG
13623211 TGATACAAAAATTTTGG
1 TGATACAAAAATTTTGG
13623228 T
1 T
13623229 TAGTAAGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.37
Consensus pattern (17 bp):
TGATACAAAAATTTTGG
Found at i:13623523 original size:30 final size:30
Alignment explanation
Indices: 13623463--13623523 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
13623453 ACATATGGAT
*
13623463 TGGTTTTGTTGTAAATTTAATAAGTTTAAA
1 TGGTTTTGTTGTAAATTTAATAAGTCTAAA
*
13623493 TGGTTTTGTTGTTAATTTAATAA-TACTAAA
1 TGGTTTTGTTGTAAATTTAATAAGT-CTAAA
13623523 T
1 T
13623524 AAGTTTTGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 1 0.04
30 27 0.96
ACGTcount: A:0.33, C:0.02, G:0.15, T:0.51
Consensus pattern (30 bp):
TGGTTTTGTTGTAAATTTAATAAGTCTAAA
Found at i:13624637 original size:71 final size:71
Alignment explanation
Indices: 13624497--13624670 Score: 161
Period size: 71 Copynumber: 2.4 Consensus size: 71
13624487 TTCGACTAGT
* * * * * * *
13624497 GCTGGGTGCAAAACATTGTTGGTTTATCCGACTAGTGCAAGGCACATCTATCGTCAGTTTATCTA
1 GCTGGGCGCAAAATATTATCGGTTTATCCGACCAGTGCAAGGCACATCTATCATCAGTTTATCCA
*
13624562 GCCAAT
66 GCCAAC
* * * * *
13624568 GCTGGGCGTAAAATATTATCGGTTTATCTGACCAGTGCAGGGCACATCTATTATCGGTATTA-CC
1 GCTGGGCGCAAAATATTATCGGTTTATCCGACCAGTGCAAGGCACATCTATCATCAGT-TTATCC
*
13624632 GGCCAAC
65 AGCCAAC
* * *
13624639 GTTGGGCGCAAAACATTGTTACGGTTTATCCG
1 GCTGGGCGCAAAATATT-AT-CGGTTTATCCG
13624671 TCTAGCACTG
Statistics
Matches: 81, Mismatches: 19, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
71 67 0.83
72 4 0.05
73 10 0.12
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (71 bp):
GCTGGGCGCAAAATATTATCGGTTTATCCGACCAGTGCAAGGCACATCTATCATCAGTTTATCCA
GCCAAC
Found at i:13632519 original size:57 final size:56
Alignment explanation
Indices: 13632428--13632564 Score: 181
Period size: 57 Copynumber: 2.4 Consensus size: 56
13632418 CTATCATAGG
* *
13632428 TGGCCTGTCAATGGCCGGCACCGGTATAC-AAAAAAAA-TTTAGAAAAATTTCGGGTGC
1 TGGCCTGTCAATGGCTGGCACCAGTATACAAAAAAAAATTTTA-AAAAATTT--GGTGC
*
13632485 TGGCCTGTCAATGGCTGGCACCAGTATACGAAAAAAAAATTTTAAAAAATTTGGTGG
1 TGGCCTGTCAATGGCTGGCACCAGTATAC-AAAAAAAAATTTTAAAAAATTTGGTGC
13632542 TGGCCTGTCAATGG-TCGGCACCA
1 TGGCCTGTCAATGGCT-GGCACCA
13632565 CCTTTACGGC
Statistics
Matches: 73, Mismatches: 3, Indels: 8
0.87 0.04 0.10
Matches are distributed among these distances:
56 1 0.01
57 52 0.71
59 16 0.22
60 4 0.05
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (56 bp):
TGGCCTGTCAATGGCTGGCACCAGTATACAAAAAAAAATTTTAAAAAATTTGGTGC
Found at i:13632659 original size:90 final size:92
Alignment explanation
Indices: 13632501--13632676 Score: 275
Period size: 90 Copynumber: 1.9 Consensus size: 92
13632491 GTCAATGGCT
* *
13632501 GGCACCAGTATACGAAAAAAAAATTTTAAAAAATTTGGTGGTGGCCTGTCAATGGTCGGCACCAC
1 GGCACCAGTATACG--AAAAAAA-TTAAAAAAATTTGGTGGTGGCCTGTCAATGGCCGGCACCAC
*
13632566 CTTTACGGCAAAAAAATTTTTTTACAGGCC
63 CTTTACGGCAAAAAAAATTTTTTACAGGCC
13632596 GGCACCAGTATACG-AAAAAA-TAAAAAAATTTGGTGGTGGCCTGTCAATGGCCGGCACCACCTT
1 GGCACCAGTATACGAAAAAAATTAAAAAAATTTGGTGGTGGCCTGTCAATGGCCGGCACCACCTT
*
13632659 TACGGGAAAAAAAATTTT
66 TACGGCAAAAAAAATTTT
13632677 CAGGTGTTGG
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
90 57 0.74
92 6 0.08
95 14 0.18
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (92 bp):
GGCACCAGTATACGAAAAAAATTAAAAAAATTTGGTGGTGGCCTGTCAATGGCCGGCACCACCTT
TACGGCAAAAAAAATTTTTTACAGGCC
Found at i:13634778 original size:3 final size:3
Alignment explanation
Indices: 13634770--13634807 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
13634760 ATGTTATTAA
13634770 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
13634808 ATTGTGAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:13634947 original size:3 final size:3
Alignment explanation
Indices: 13634939--13635005 Score: 109
Period size: 3 Copynumber: 22.7 Consensus size: 3
13634929 GTGAATTAAA
*
13634939 TAT TAT TA- TAT GAT 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 TAT
*
13634986 TAT TAT CAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
13635006 ACTAATGCAT
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
2 2 0.03
3 57 0.97
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:13636206 original size:21 final size:20
Alignment explanation
Indices: 13636180--13636243 Score: 74
Period size: 21 Copynumber: 3.1 Consensus size: 20
13636170 GACTTTGCCG
13636180 ATCAGGCACTTTATGTGTCGT
1 ATCAGGCAC-TTATGTGTCGT
** *
13636201 ATCAGGCACCTCGTGCGTCGT
1 ATCAGGCA-CTTATGTGTCGT
*
13636222 TTCAGGCACTTATGTGTCGT
1 ATCAGGCACTTATGTGTCGT
13636242 AT
1 AT
13636244 ACTGATCAGG
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
20 10 0.29
21 23 0.68
22 1 0.03
ACGTcount: A:0.17, C:0.23, G:0.25, T:0.34
Consensus pattern (20 bp):
ATCAGGCACTTATGTGTCGT
Found at i:13638762 original size:14 final size:14
Alignment explanation
Indices: 13638743--13638782 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
13638733 TTGATTGCCA
13638743 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
13638757 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
13638771 GGAAAATGTTTT
1 GTAAAATGTTTT
13638783 ACTTTTCTGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:13638791 original size:20 final size:20
Alignment explanation
Indices: 13638766--13638803 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
13638756 CGTAAAATGA
*
13638766 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
13638786 TTTCTGGAAAATGATTTA
1 TTTCTGGAAAATGATTTA
13638804 TTAGATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.08, G:0.16, T:0.47
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:13639481 original size:58 final size:57
Alignment explanation
Indices: 13639308--13639593 Score: 251
Period size: 55 Copynumber: 5.2 Consensus size: 57
13639298 AAACAGACCC
* * ***
13639308 TTATTTCAATTTCATTTTAAATGG-CTGACACAC--TTTTTTTTTCATTC--CCCCAT
1 TTATTTCAAATTCATTTCAAA-GGCCTGACACACTTTTTTTTTTTCATTCAATTTCAT
* ***
13639361 TTATTTCAAA-TCATTTTCAAAGGCCTGACACACTTTTTTTTTGTCATTC--CCCCAT
1 TTATTTCAAATTCA-TTTCAAAGGCCTGACACACTTTTTTTTTTTCATTCAATTTCAT
* *
13639416 TTATTTCAAATTCATTTCAAAGGCCTCACACCCTTTTGTTTTTTTCATTCAATTTCAT
1 TTATTTCAAATTCATTTCAAAGGCCTGACACACTTTT-TTTTTTTCATTCAATTTCAT
** * *
13639474 TTATTTCAGTTTCATTTCAAAGGCCTGACAAAC---TTTTTTTTCATTCAATTTTAT
1 TTATTTCAAATTCATTTCAAAGGCCTGACACACTTTTTTTTTTTCATTCAATTTCAT
* * *
13639528 TTATTTCAATTTCATTTCAAAGGTCT-AGCACAC--TTTTTTTTTCATT-TATTTCAATT
1 TTATTTCAAATTCATTTCAAAGGCCTGA-CACACTTTTTTTTTTTCATTCAATTTC-A-T
13639584 TTATTTCAAA
1 TTATTTCAAA
13639594 GGCCTGACAC
Statistics
Matches: 200, Mismatches: 21, Indels: 21
0.83 0.09 0.09
Matches are distributed among these distances:
52 5 0.03
53 25 0.12
54 51 0.25
55 64 0.32
56 24 0.12
58 31 0.16
ACGTcount: A:0.25, C:0.20, G:0.06, T:0.49
Consensus pattern (57 bp):
TTATTTCAAATTCATTTCAAAGGCCTGACACACTTTTTTTTTTTCATTCAATTTCAT
Found at i:13639541 original size:54 final size:54
Alignment explanation
Indices: 13639308--13639638 Score: 305
Period size: 54 Copynumber: 6.2 Consensus size: 54
13639298 AAACAGACCC
* ***
13639308 TTATTTCAATTTCATTTTAAATGG-CTGACACACTTTTTTTTTCATTC-CCCCAT
1 TTATTTCAATTTCATTTCAAA-GGCCTGACACACTTTTTTTTTCATTCATTTCAT
* ***
13639361 TTATTTCAA-ATCATTTTCAAAGGCCTGACACACTTTTTTTTTGTCATTC-CCCCAT
1 TTATTTCAATTTCA-TTTCAAAGGCCTGACACAC-TTTTTTTT-TCATTCATTTCAT
* * *
13639416 TTATTTCAAATTCATTTCAAAGGCCTCACACCCTTTTGTTTTTTTCATTCAATTTCAT
1 TTATTTCAATTTCATTTCAAAGGCCTGACACAC--TT-TTTTTTTCATTC-ATTTCAT
* * *
13639474 TTATTTCAGTTTCATTTCAAAGGCCTGACAAAC-TTTTTTTTCATTCAATTTTAT
1 TTATTTCAATTTCATTTCAAAGGCCTGACACACTTTTTTTTTCATTC-ATTTCAT
*
13639528 TTATTTCAATTTCATTTCAAAGGTCT-AGCACAC-----TTTT--TT--TTTCAT
1 TTATTTCAATTTCATTTCAAAGGCCTGA-CACACTTTTTTTTTCATTCATTTCAT
*
13639573 TTATTTCAATTTTATTTCAAAGGCCTGACACACTTTTTTTTTCATTCAATTTCAT
1 TTATTTCAATTTCATTTCAAAGGCCTGACACACTTTTTTTTTCATTC-ATTTCAT
13639628 TTACTTTCAAT
1 TTA-TTTCAAT
13639639 GCAAATTTTT
Statistics
Matches: 236, Mismatches: 20, Indels: 41
0.79 0.07 0.14
Matches are distributed among these distances:
45 34 0.14
46 1 0.00
48 2 0.01
50 8 0.03
52 7 0.03
53 25 0.11
54 55 0.23
55 48 0.20
56 19 0.08
57 6 0.03
58 31 0.13
ACGTcount: A:0.24, C:0.21, G:0.06, T:0.49
Consensus pattern (54 bp):
TTATTTCAATTTCATTTCAAAGGCCTGACACACTTTTTTTTTCATTCATTTCAT
Found at i:13639583 original size:45 final size:45
Alignment explanation
Indices: 13639522--13639618 Score: 153
Period size: 45 Copynumber: 2.2 Consensus size: 45
13639512 TTTCATTCAA
*
13639522 TTTT-ATTTATTTCAATTTCATTTCAAAGGTCT-AGCACACTTTTT
1 TTTTCATTTATTTCAATTTCATTTCAAAGGCCTGA-CACACTTTTT
*
13639566 TTTTCATTTATTTCAATTTTATTTCAAAGGCCTGACACACTTTTT
1 TTTTCATTTATTTCAATTTCATTTCAAAGGCCTGACACACTTTTT
13639611 TTTTCATT
1 TTTTCATT
13639619 CAATTTCATT
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
44 4 0.08
45 44 0.90
46 1 0.02
ACGTcount: A:0.24, C:0.16, G:0.06, T:0.54
Consensus pattern (45 bp):
TTTTCATTTATTTCAATTTCATTTCAAAGGCCTGACACACTTTTT
Found at i:13639623 original size:40 final size:42
Alignment explanation
Indices: 13639529--13639629 Score: 127
Period size: 45 Copynumber: 2.4 Consensus size: 42
13639519 CAATTTTATT
*
13639529 TATTTCAATTTCATTTCAAAGGTCTAGCACACTTTTTTTTTC
1 TATTTCAATTTCATTTCAAAGGCCTAGCACACTTTTTTTTTC
*
13639571 ATTTATTTCAATTTTATTTCAAAGGCCT-GACACACTTTTTTTTTC
1 ---TATTTCAATTTCATTTCAAAGGCCTAG-CACACTTTTTTTTTC
13639616 -A-TTCAATTTCATTT
1 TATTTCAATTTCATTT
13639630 ACTTTCAATG
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
40 12 0.23
41 1 0.02
44 1 0.02
45 38 0.73
ACGTcount: A:0.25, C:0.18, G:0.06, T:0.51
Consensus pattern (42 bp):
TATTTCAATTTCATTTCAAAGGCCTAGCACACTTTTTTTTTC
Found at i:13642919 original size:57 final size:56
Alignment explanation
Indices: 13642819--13643140 Score: 235
Period size: 57 Copynumber: 5.7 Consensus size: 56
13642809 TCTGTAAAGG
** * * *
13642819 TGGTGCCGACCATTTCCAGGCCACCACC-TAA-TTTTTTTAATTTTTTTCGTATAC
1 TGGTGCCGACCATTGACAGGGCACAACCGAAATTTTTTTTAATTTTTTTCGTATAC
* *
13642873 TGGTGCCGACCATTGACAGGGCAGCAACCGAATTTTTTTTTTATTTTTTTCGTATAC
1 TGGTGCCGACCATTGACAGGGCA-CAACCGAAATTTTTTTTAATTTTTTTCGTATAC
* ** * * *
13642930 TGGTGTCGATAATTGACAGGACACCACCATAAATTTTTTTTAATTTTTTTCGTATA-
1 TGGTGCCGACCATTGACAGGGCACAACC-GAAATTTTTTTTAATTTTTTTCGTATAC
* * * *** * *** * *
13642986 TCGGTGCCGGCCTTTGACAGGGCAACATCCGAAAAAATATTT--TTTTCCCCGTAAAGG
1 T-GGTGCCGACCATTGACAGGGC-ACAACCGAAATTTTTTTTAATTTTTTTCGTATA-C
* *
13643043 TGGTGCC-AGCCATTGACAGGCCACCACC-AAATTTTTTTTTAATTTTTTTCGTATAC
1 TGGTGCCGA-CCATTGACAGGGCACAACCGAAA-TTTTTTTTAATTTTTTTCGTATAC
* * * *
13643099 TGGTGTCGGCCATTGACAGGTCAGCACCCGAAAATTTTTTTT
1 TGGTGCCGACCATTGACAGGGCA-CAACCG-AAATTTTTTTT
13643141 CCCGTAAAAG
Statistics
Matches: 201, Mismatches: 51, Indels: 28
0.72 0.18 0.10
Matches are distributed among these distances:
54 23 0.11
55 21 0.10
56 42 0.21
57 100 0.50
58 12 0.06
59 3 0.01
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (56 bp):
TGGTGCCGACCATTGACAGGGCACAACCGAAATTTTTTTTAATTTTTTTCGTATAC
Found at i:13643176 original size:108 final size:111
Alignment explanation
Indices: 13642941--13643190 Score: 339
Period size: 112 Copynumber: 2.3 Consensus size: 111
13642931 GGTGTCGATA
* *
13642941 ATTGACAGGA-CACCACCATAAATTTTTTTTAATTTTTTTCGTATATCGGTGCCGGCCTTTGACA
1 ATTGACA-GACCACCACCA-AATTTTTTTTTAATTTTTTTCGTATATCGGTGCCGGCCATTGACA
* * *
13643005 GGGCAACATCCGAAAAAATATTTTTTTCCCCGTAAAGGTGGTGCCAGCC
64 GGGCAACACCCG-AAAAATATTTTTTTCCCCGTAAAAGTAGTGCCAGCC
* *
13643054 ATTGACAGGCCACCACCAAATTTTTTTTTAATTTTTTTCGTATA-CTGGTGTCGGCCATTGACAG
1 ATTGACAGACCACCACCAAATTTTTTTTTAATTTTTTTCGTATATC-GGTGCCGGCCATTGACAG
* * *
13643118 GTCAGCACCCG-AAAAT-TTTTTTT-CCCGTAAAAGTAGTGCCGGCC
65 GGCAACACCCGAAAAATATTTTTTTCCCCGTAAAAGTAGTGCCAGCC
13643162 ATTGACAGACCACCACCAAATTTTTTTTT
1 ATTGACAGACCACCACCAAATTTTTTTTT
13643191 CTGTATACCA
Statistics
Matches: 124, Mismatches: 11, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
108 46 0.37
109 7 0.06
110 5 0.04
111 1 0.01
112 50 0.40
113 15 0.12
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (111 bp):
ATTGACAGACCACCACCAAATTTTTTTTTAATTTTTTTCGTATATCGGTGCCGGCCATTGACAGG
GCAACACCCGAAAAATATTTTTTTCCCCGTAAAAGTAGTGCCAGCC
Found at i:13643342 original size:16 final size:16
Alignment explanation
Indices: 13643321--13643373 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
13643311 ATATTATCAG
13643321 ATTATTTTAAAACTTA
1 ATTATTTTAAAACTTA
*
13643337 ATTATTTT---A-GTA
1 ATTATTTTAAAACTTA
13643349 ATTATTTTAAAACTTA
1 ATTATTTTAAAACTTA
13643365 AGTTATTTT
1 A-TTATTTT
13643374 TGTAAATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
12 10 0.33
13 1 0.03
15 1 0.03
16 11 0.37
17 7 0.23
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.55
Consensus pattern (16 bp):
ATTATTTTAAAACTTA
Found at i:13643353 original size:28 final size:29
Alignment explanation
Indices: 13643321--13643383 Score: 101
Period size: 28 Copynumber: 2.2 Consensus size: 29
13643311 ATATTATCAG
13643321 ATTATTTTAAAACTTAA-TTATTTTAGTA
1 ATTATTTTAAAACTTAAGTTATTTTAGTA
*
13643349 ATTATTTTAAAACTTAAGTTATTTTTGTA
1 ATTATTTTAAAACTTAAGTTATTTTAGTA
*
13643378 AATATT
1 ATTATT
13643384 AAATTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 17 0.53
29 15 0.47
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (29 bp):
ATTATTTTAAAACTTAAGTTATTTTAGTA
Found at i:13659024 original size:132 final size:132
Alignment explanation
Indices: 13658787--13659267 Score: 791
Period size: 132 Copynumber: 3.6 Consensus size: 132
13658777 ACCGGTGAAA
* *
13658787 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTATACATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
* * * *
13658852 GTAGTAGTGGAGCAGATCAAAGATGGCGAATCTTATCTTTCCAAGATAGTGGGAAGTAGATTTGA
66 GCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
13658917 GC
131 GC
* * * *
13658919 CACCAAGCCTTGTCTCCCTGAGCAGTAGTGGAGAAGGTTGAAGATTGTGGATCTTATCTCTCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
*
13658984 GCAGTAGTGGAGTAGATCGAAGATGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
13659049 GC
131 GC
*
13659051 CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
* *
13659116 GCAGTAGTGGAGTAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
13659181 GC
131 GC
* * * *
13659183 CACCAAGCCTTGTCTCCCTGAGTAGCAGCGGAGAAAGTTGAAGATTGTAGATCTTATTTCCTTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCT-A
13659248 AGCAGTAGTGGAGCAGATCG
65 AGCAGTAGTGGAGCAGATCG
13659268 TATCCAATCT
Statistics
Matches: 327, Mismatches: 21, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
132 307 0.94
133 20 0.06
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (132 bp):
CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
GCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
GC
Found at i:13659149 original size:44 final size:44
Alignment explanation
Indices: 13658837--13659153 Score: 150
Period size: 44 Copynumber: 7.2 Consensus size: 44
13658827 AAGATTATAC
* * **
13658837 ATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCAAAGATGGCGA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGATGGCGA
* *** *
13658881 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGTAGATTTG-AG-CCACCA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGTAGA-TTGAAGATGGCGA
* * * * * * * *
13658924 AGCCTTGTCTCCCTGAGCAGTAGTGGAGAAGGTTGAAGATTGTGG
1 A-TCTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGATGGCGA
* *
13658969 ATCTTATCTCTCTAAGCAGTAGTGGAGTAGATCGAAGATGGCGA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGATGGCGA
* * * *** *
13659013 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAG-CCACCA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGTAGATTGAAGATGGCGA
* * * * * * * *
13659056 AGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTG-TA
1 A-TCTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGATGGCGA
* *
13659100 GATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACGGCGA
1 -ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGATGGCGA
13659145 ATCTTATCT
1 ATCTTATCT
13659154 TTCCAAGATA
Statistics
Matches: 192, Mismatches: 61, Indels: 40
0.66 0.21 0.14
Matches are distributed among these distances:
42 8 0.04
43 21 0.11
44 141 0.73
45 15 0.08
46 7 0.04
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.27
Consensus pattern (44 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGATGGCGA
Found at i:13663625 original size:29 final size:30
Alignment explanation
Indices: 13663558--13663615 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
13663548 AAATATATAC
13663558 ATATAAATAT--GAAAATATTCATTAAAAA
1 ATATAAATATAGGAAAATATTCATTAAAAA
*
13663586 ATATAAATATAGGAAAATATTCGTTAAAAA
1 ATATAAATATAGGAAAATATTCATTAAAAA
13663616 TAAATATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 10 0.37
30 17 0.63
ACGTcount: A:0.59, C:0.03, G:0.07, T:0.31
Consensus pattern (30 bp):
ATATAAATATAGGAAAATATTCATTAAAAA
Found at i:13663679 original size:32 final size:32
Alignment explanation
Indices: 13663610--13663678 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
13663600 AAATATTCGT
* * * *
13663610 TAAAAATAAATATATACATGTACATATATATA
1 TAAAAATAATTATATACATATATATAGATATA
13663642 TAAAAATAATTATATACATATATATAGAT-TA
1 TAAAAATAATTATATACATATATATAGATATA
13663673 TAAAAA
1 TAAAAA
13663679 AGGATAATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
31 8 0.24
32 25 0.76
ACGTcount: A:0.58, C:0.04, G:0.03, T:0.35
Consensus pattern (32 bp):
TAAAAATAATTATATACATATATATAGATATA
Found at i:13664229 original size:23 final size:23
Alignment explanation
Indices: 13664202--13664246 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
13664192 AAGAGATTTG
*
13664202 AAATAAAAAATATACAAATCAAT
1 AAATAAAAAATACACAAATCAAT
**
13664225 AAATAAATTATACACAAATCAA
1 AAATAAAAAATACACAAATCAA
13664247 CAAAATAAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (23 bp):
AAATAAAAAATACACAAATCAAT
Found at i:13664462 original size:21 final size:21
Alignment explanation
Indices: 13664436--13664501 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
13664426 AAAGGGTATC
13664436 TACAAATAAAATCTCTAAGAT
1 TACAAATAAAATCTCTAAGAT
* *
13664457 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATAAAATC-TCTAAGAT
* ** *
13664480 TACATATATCATATCTAAGAT
1 TACAAATAAAATCTCTAAGAT
13664501 T
1 T
13664502 GCATATCATA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
21 12 0.33
22 13 0.36
23 11 0.31
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (21 bp):
TACAAATAAAATCTCTAAGAT
Found at i:13664479 original size:23 final size:24
Alignment explanation
Indices: 13664449--13664495 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
13664439 AAATAAAATC
13664449 TCTAAGATTACA-AAATCATATCT
1 TCTAAGATTACATAAATCATATCT
*
13664472 TCTAAGATTACATATATCATATCT
1 TCTAAGATTACATAAATCATATCT
13664496 AAGATTGCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.40, C:0.17, G:0.04, T:0.38
Consensus pattern (24 bp):
TCTAAGATTACATAAATCATATCT
Found at i:13664506 original size:21 final size:21
Alignment explanation
Indices: 13664449--13664526 Score: 81
Period size: 19 Copynumber: 3.7 Consensus size: 21
13664439 AAATAAAATC
*
13664449 TCTAAGATTACA-AAATCATA
1 TCTAAGATTACATATATCATA
13664469 TCTTCTAAGATTACATATATCATA
1 ---TCTAAGATTACATATATCATA
*
13664493 TCTAAGATTGC--ATATCATA
1 TCTAAGATTACATATATCATA
*
13664512 TCTACGATTACATAT
1 TCTAAGATTACATAT
13664527 CCTTGAAGAT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
19 17 0.35
21 12 0.25
23 12 0.25
24 7 0.15
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.37
Consensus pattern (21 bp):
TCTAAGATTACATATATCATA
Found at i:13664512 original size:24 final size:21
Alignment explanation
Indices: 13664449--13664514 Score: 55
Period size: 23 Copynumber: 3.0 Consensus size: 21
13664439 AAATAAAATC
13664449 TCTAAGATTACAAAATCATATCT
1 TCTAAGATT-C-AAATCATATCT
*
13664472 TCTAAGATT-ACAT-ATATCAT
1 TCTAAGATTCAAATCATATC-T
*
13664492 ATCTAAGATTGCATATCATATCT
1 -TCTAAGATT-CAAATCATATCT
13664515 ACGATTACAT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
19 5 0.14
20 4 0.11
21 9 0.25
23 13 0.36
24 5 0.14
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.38
Consensus pattern (21 bp):
TCTAAGATTCAAATCATATCT
Found at i:13666267 original size:113 final size:113
Alignment explanation
Indices: 13665796--13666271 Score: 649
Period size: 112 Copynumber: 4.2 Consensus size: 113
13665786 ATAATAAGCA
* * * * *
13665796 TTAGCGGCGTTTTATTAAAAGCGCCGCAAAAGACCTAAGGCCAACGACGCTGTTTTCTGTGTTTT
1 TTAGCGGCGTTTTCTGAAAAGCGCCGCAAAAAACCTAAGGCCAACGACGCCGTTTTCTGAGTTTT
* * * *
13665861 TGGGCCTGTAGCGACGTTTTTTGAAAAGCGCCGCTAATGCTCGGGGGAC-
66 TGGGCCTATAGCGGCGTTTTTTGAAAAGCGCCGCTAATGCTC--TGGCCT
* * *
13665910 TTAGCGGCGTTTTCTGAAAAGCGCCGCAAAAAACTTAAGGCC-A--ATGTCGTTTTCTGAGTTTT
1 TTAGCGGCGTTTTCTGAAAAGCGCCGCAAAAAACCTAAGGCCAACGACGCCGTTTTCTGAGTTTT
* * *
13665972 TGGGCCTGTAGCGGCGTTTTTTGAAAATCGCCGCTAATGCTCTTGCCT
66 TGGGCCTATAGCGGCGTTTTTTGAAAAGCGCCGCTAATGCTCTGGCCT
* *
13666020 TTAGCGACGTTTTCTGAAAAGCGCAGCAAAAAACCTAAGGCCAACGACGCCGTTTTCTGAGTTTT
1 TTAGCGGCGTTTTCTGAAAAGCGCCGCAAAAAACCTAAGGCCAACGACGCCGTTTTCTGAGTTTT
* * *
13666085 TGGGCCTATATCGGCG-TTTTTGAAAAGCGCCGCAAATGCTCTTGCCT
66 TGGGCCTATAGCGGCGTTTTTTGAAAAGCGCCGCTAATGCTCTGGCCT
**
13666132 TTAGCGGCGTTTTCTGAAAAGCGCCGCAAAAAACCTAAATCCAACGACGCCGTTTTCTGAGTTTT
1 TTAGCGGCGTTTTCTGAAAAGCGCCGCAAAAAACCTAAGGCCAACGACGCCGTTTTCTGAGTTTT
* * *
13666197 TGGGCCTATAGCGGCGTTTTTTAAAAAGCGCCACTAATGCTCCGGCCT
66 TGGGCCTATAGCGGCGTTTTTTGAAAAGCGCCGCTAATGCTCTGGCCT
*
13666245 TTAGCGGCGTTTT-TGAGGAAGCGCCGC
1 TTAGCGGCGTTTTCTGA-AAAGCGCCGC
13666272 TAATAGTAAT
Statistics
Matches: 323, Mismatches: 33, Indels: 13
0.88 0.09 0.04
Matches are distributed among these distances:
109 2 0.01
110 39 0.12
111 56 0.17
112 108 0.33
113 80 0.25
114 38 0.12
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.29
Consensus pattern (113 bp):
TTAGCGGCGTTTTCTGAAAAGCGCCGCAAAAAACCTAAGGCCAACGACGCCGTTTTCTGAGTTTT
TGGGCCTATAGCGGCGTTTTTTGAAAAGCGCCGCTAATGCTCTGGCCT
Found at i:13670085 original size:26 final size:26
Alignment explanation
Indices: 13670049--13670100 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
13670039 TTAAGGATGG
13670049 TTTAATGTTAAATTGAATTCATGAAA
1 TTTAATGTTAAATTGAATTCATGAAA
*
13670075 TTTAATGTTAAATTGTATTCATGAAA
1 TTTAATGTTAAATTGAATTCATGAAA
13670101 ATGACGCCGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.40, C:0.04, G:0.12, T:0.44
Consensus pattern (26 bp):
TTTAATGTTAAATTGAATTCATGAAA
Found at i:13670851 original size:19 final size:19
Alignment explanation
Indices: 13670829--13670873 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
13670819 CTCTCATCTC
*
13670829 CCCCAAATCCCTAAAATTT
1 CCCCAAATCCCTAAAAGTT
* *
13670848 CCCCTAATCCCTAACAGTT
1 CCCCAAATCCCTAAAAGTT
13670867 CCCCAAA
1 CCCCAAA
13670874 CCCAACATAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.33, C:0.42, G:0.02, T:0.22
Consensus pattern (19 bp):
CCCCAAATCCCTAAAAGTT
Found at i:13671237 original size:6 final size:6
Alignment explanation
Indices: 13671226--13671252 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
13671216 GAAATTTATA
13671226 TATATG TATATG TATATG TATATG TAT
1 TATATG TATATG TATATG TATATG TAT
13671253 TAAAACTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (6 bp):
TATATG
Found at i:13673303 original size:19 final size:19
Alignment explanation
Indices: 13673279--13673320 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
13673269 AAAATTTCTA
13673279 ATTACATAACATATATAAT
1 ATTACATAACATATATAAT
*
13673298 ATTACATAACTTATATAAT
1 ATTACATAACATATATAAT
13673317 ATTA
1 ATTA
13673321 AGATAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (19 bp):
ATTACATAACATATATAAT
Found at i:13673346 original size:225 final size:225
Alignment explanation
Indices: 13673075--13673560 Score: 911
Period size: 225 Copynumber: 2.2 Consensus size: 225
13673065 ACTTGCTTAA
* *
13673075 TACAAAACTTATATAATATTAAGATAAAATTTCAAAACTTGCAAAATCTTACGATCAGATTTCAT
1 TACATAACTTATATAATATTAAGATAAAATTTCTAAACTTGCAAAATCTTACGATCAGATTTCAT
13673140 AATTTATGTATTTTATGTAACTTACATAATATATAACTTACATAGCTTAAGTAACAGTAATTTCA
66 AATTTATGTATTTTATGTAACTTACATAATATATAACTTACATAGCTTAAGTAACAGTAATTTCA
13673205 GATCTACTTTCACAACTTACATAGCTTTTAGCAGGACACTTCATAACTTATATAAGATTAAGATA
131 GATCTACTTTCACAACTTACATAGCTTTTAGCAGGACACTTCATAACTTATATAAGATTAAGATA
13673270 AAATTTCTAATTACATAA-CATATATAATAT
196 AAATTTCTAATTACATAACCA-ATATAATAT
13673300 TACATAACTTATATAATATTAAGATAAAATTTCTAAACTTGCAAAATCTTACGATCAGATTTCAT
1 TACATAACTTATATAATATTAAGATAAAATTTCTAAACTTGCAAAATCTTACGATCAGATTTCAT
13673365 AATTTATGTATTTTATGTAACTTACATAATATATAACTTACATAGCTTAAGTAACAGTAATTTCA
66 AATTTATGTATTTTATGTAACTTACATAATATATAACTTACATAGCTTAAGTAACAGTAATTTCA
*
13673430 GATCTACTTTCACAACTTACATAGCTTTTAGCAGGACACTTCATAACTTATATAATATTAAGATA
131 GATCTACTTTCACAACTTACATAGCTTTTAGCAGGACACTTCATAACTTATATAAGATTAAGATA
*
13673495 AAATTTCTAATTACATAACCAATTTAATAT
196 AAATTTCTAATTACATAACCAATATAATAT
*
13673525 TACATAACTTATATAATATTAAGATAATATTTCTAA
1 TACATAACTTATATAATATTAAGATAAAATTTCTAA
13673561 TTACATAAAT
Statistics
Matches: 255, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
225 253 0.99
226 2 0.01
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.38
Consensus pattern (225 bp):
TACATAACTTATATAATATTAAGATAAAATTTCTAAACTTGCAAAATCTTACGATCAGATTTCAT
AATTTATGTATTTTATGTAACTTACATAATATATAACTTACATAGCTTAAGTAACAGTAATTTCA
GATCTACTTTCACAACTTACATAGCTTTTAGCAGGACACTTCATAACTTATATAAGATTAAGATA
AAATTTCTAATTACATAACCAATATAATAT
Found at i:13673541 original size:19 final size:19
Alignment explanation
Indices: 13673504--13673545 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
13673494 AAAATTTCTA
*
13673504 ATTACATAACCAATTTAAT
1 ATTACATAACCAATATAAT
**
13673523 ATTACATAACTTATATAAT
1 ATTACATAACCAATATAAT
13673542 ATTA
1 ATTA
13673546 AGATAATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (19 bp):
ATTACATAACCAATATAAT
Found at i:13673596 original size:16 final size:16
Alignment explanation
Indices: 13673577--13673776 Score: 115
Period size: 16 Copynumber: 13.0 Consensus size: 16
13673567 AAATAATATT
13673577 ATACATAACTTACATA
1 ATACATAACTTACATA
13673593 ATACATAAC-T---T-
1 ATACATAACTTACATA
*
13673604 -T-CATAACTTACATT
1 ATACATAACTTACATA
*
13673618 ATACACAACTTACAT-
1 ATACATAACTTACATA
* * *
13673633 A-GCTTAA-TTAACATT
1 ATACATAACTT-ACATA
13673648 ATACATAACTTACAT-
1 ATACATAACTTACATA
*
13673663 AT--ATAACTCACATA
1 ATACATAACTTACATA
* *
13673677 ACTTACATAGCTTACATT
1 A--TACATAACTTACATA
* *
13673695 CTACACAACTTACATAA
1 ATACATAACTTACAT-A
13673712 CATACATAA--TACATA
1 -ATACATAACTTACATA
*
13673727 ACTTACATAACTAACATA
1 A--TACATAACTTACATA
*
13673745 ATACATAGCTTACATA
1 ATACATAACTTACATA
*
13673761 ATACACAACTTACATA
1 ATACATAACTTACATA
13673777 GCTTACATAA
Statistics
Matches: 141, Mismatches: 21, Indels: 44
0.68 0.10 0.21
Matches are distributed among these distances:
9 6 0.04
10 2 0.01
12 1 0.01
13 13 0.09
14 9 0.06
15 7 0.05
16 80 0.57
17 2 0.01
18 21 0.15
ACGTcount: A:0.46, C:0.21, G:0.01, T:0.32
Consensus pattern (16 bp):
ATACATAACTTACATA
Found at i:13673613 original size:225 final size:224
Alignment explanation
Indices: 13673075--13673645 Score: 774
Period size: 225 Copynumber: 2.5 Consensus size: 224
13673065 ACTTGCTTAA
* * * ** * *
13673075 TACAAAACTTATATAATATTAAGATAAAATTTCAAAACTTGCAAAATCTTACGATCAGATTTCAT
1 TACATAACTTATATAATATTAAGATAAAATTTCTAAACTTACAAAATAATACGATCAAATTACAT
** * *
13673140 AATTTATGTATTTTATGTAACTTACATAATATATAACTTACATAGCTTAAGTAACAGTAATTTCA
66 AATACATGAATTTCA-GTAACTTACATAATATATAACTTACATAGCTTAAGTAACAGTAATTTCA
13673205 GATCTACTTTCACAACTTACATAGCTTTTAGCAGGACACTTCATAACTTATATAAGATTAAGATA
130 GATCTACTTTCACAACTTACATAGCTTTTAGCAGGACACTTCATAACTTATATAAGATTAAGATA
13673270 AAATTTCTAATTACATAACATATATAATAT
195 AAATTTCTAATTACATAACATATATAATAT
* ** * *
13673300 TACATAACTTATATAATATTAAGATAAAATTTCTAAACTTGCAAAATCTTACGATCAGATTTCAT
1 TACATAACTTATATAATATTAAGATAAAATTTCTAAACTTACAAAATAATACGATCAAATTACAT
** * *
13673365 AATTTATGTATTTTATGTAACTTACATAATATATAACTTACATAGCTTAAGTAACAGTAATTTCA
66 AATACATGAATTTCA-GTAACTTACATAATATATAACTTACATAGCTTAAGTAACAGTAATTTCA
*
13673430 GATCTACTTTCACAACTTACATAGCTTTTAGCAGGACACTTCATAACTTATATAATATTAAGATA
130 GATCTACTTTCACAACTTACATAGCTTTTAGCAGGACACTTCATAACTTATATAAGATTAAGATA
*
13673495 AAATTTCTAATTACATAACCA-ATTTAATAT
195 AAATTTCTAATTACATAA-CATATATAATAT
* **
13673525 TACATAACTTATATAATATTAAGATAATATTTCT-AA-TTACATAAATAATATTATACATAACTT
1 TACATAACTTATATAATATTAAGATAAAATTTCTAAACTTACA-AAATAATACGAT-CA-AA-TT
* * * *
13673588 ACATAATACAT-AACTTTCA-TAACTTACATTATACACAACTTACATAGCTTAATTAACA
62 ACATAATACATGAA-TTTCAGTAACTTACATAATATATAACTTACATAGCTTAAGTAACA
13673646 TTATACATAA
Statistics
Matches: 320, Mismatches: 20, Indels: 12
0.91 0.06 0.03
Matches are distributed among these distances:
223 4 0.01
224 10 0.03
225 288 0.90
226 4 0.01
227 14 0.04
ACGTcount: A:0.43, C:0.14, G:0.06, T:0.37
Consensus pattern (224 bp):
TACATAACTTATATAATATTAAGATAAAATTTCTAAACTTACAAAATAATACGATCAAATTACAT
AATACATGAATTTCAGTAACTTACATAATATATAACTTACATAGCTTAAGTAACAGTAATTTCAG
ATCTACTTTCACAACTTACATAGCTTTTAGCAGGACACTTCATAACTTATATAAGATTAAGATAA
AATTTCTAATTACATAACATATATAATAT
Found at i:13673620 original size:41 final size:41
Alignment explanation
Indices: 13673577--13673966 Score: 228
Period size: 41 Copynumber: 9.4 Consensus size: 41
13673567 AAATAATATT
* *
13673577 ATACATAACTTACATAATACATAACTTTCATAACTTACATT
1 ATACATAACTTACATAATACATAACTTACATAACTTACATA
* *
13673618 ATACACAACTTACATAGCTTA-ATTAACATTATACATAACTTACAT-
1 ATACATAACTTACATA--ATACA-TAAC--T-TACATAACTTACATA
* * * *
13673663 AT--ATAACTCACATAACTTACATAGCTTACAT-TC-TACACA
1 ATACATAACTTACATAA--TACATAACTTACATAACTTACATA
* *
13673702 ACTTACATAACATACATAATACATAACTTACATAACTAACATA
1 A--TACATAACTTACATAATACATAACTTACATAACTTACATA
* * *
13673745 ATACATAGCTTACATAATACACAACTTACATAGCTTACATA
1 ATACATAACTTACATAATACATAACTTACATAACTTACATA
* * * * * *
13673786 ATAAATAACTTACATAAAATACAACTTACATAGCTTACATG
1 ATACATAACTTACATAATACATAACTTACATAACTTACATA
* * *
13673827 ATATATAACTTACGA-AGCTTACATAA--TAAATAACTTACATA
1 ATACATAACTTAC-ATA--ATACATAACTTACATAACTTACATA
* * * * * * * *
13673868 AAATACAACTTACATAAAAAAGTTTA-TGACATAGCTTACATA
1 ATACATAACTTACATAATACA--TAACTTACATAACTTACATA
* *
13673910 ATACATAACTTACATAGCTTACATAA--TAAATAACTTACATA
1 ATACATAACTTACATA--ATACATAACTTACATAACTTACATA
* * *
13673951 AAATACAACTTACATA
1 ATACATAACTTACATA
13673967 GCAAATGGAA
Statistics
Matches: 269, Mismatches: 55, Indels: 50
0.72 0.15 0.13
Matches are distributed among these distances:
38 4 0.01
39 4 0.01
40 6 0.02
41 165 0.61
42 30 0.11
43 41 0.15
44 3 0.01
45 3 0.01
46 13 0.05
ACGTcount: A:0.47, C:0.19, G:0.03, T:0.31
Consensus pattern (41 bp):
ATACATAACTTACATAATACATAACTTACATAACTTACATA
Found at i:13673787 original size:25 final size:25
Alignment explanation
Indices: 13673578--13673802 Score: 136
Period size: 25 Copynumber: 9.3 Consensus size: 25
13673568 AATAATATTA
*
13673578 TACATAACTTACATAATACATAACT
1 TACATAACTTACATAATACACAACT
* *
13673603 TTCATAACTTACATTATACACAACT
1 TACATAACTTACATAATACACAACT
* *
13673628 TACATAGCTTA-AT--TA-AC-ATT
1 TACATAACTTACATAATACACAACT
*
13673648 ATACATAACTTACAT-AT--ATAACT
1 -TACATAACTTACATAATACACAACT
* * * *
13673671 CACATAACTTACATAGCT-TAC-ATT
1 TACATAACTTACATA-ATACACAACT
* *
13673695 CTACACAACTTACATAACATACATAA--
1 -TACATAACTTACAT-A-ATACACAACT
*
13673721 TACATAACTTACATAACTA-ACATA-A
1 TACATAACTTACATAA-TACACA-ACT
*
13673746 TACATAGCTTACATAATACACAACT
1 TACATAACTTACATAATACACAACT
* * *
13673771 TACATAGCTTACATAATAAATAACT
1 TACATAACTTACATAATACACAACT
13673796 TACATAA
1 TACATAA
13673803 AATACAACTT
Statistics
Matches: 158, Mismatches: 26, Indels: 32
0.73 0.12 0.15
Matches are distributed among these distances:
20 2 0.01
21 12 0.08
22 18 0.11
23 6 0.04
24 12 0.08
25 104 0.66
26 2 0.01
27 1 0.01
28 1 0.01
ACGTcount: A:0.46, C:0.21, G:0.02, T:0.32
Consensus pattern (25 bp):
TACATAACTTACATAATACACAACT
Found at i:13673799 original size:16 final size:16
Alignment explanation
Indices: 13673778--13673886 Score: 69
Period size: 16 Copynumber: 6.7 Consensus size: 16
13673768 ACTTACATAG
*
13673778 CTTACATAATAA-ATAA
1 CTTACATAA-AATACAA
13673794 CTTACATAAAATACAA
1 CTTACATAAAATACAA
*** *
13673810 CTTACATAGCTTACAT
1 CTTACATAAAATACAA
** * **
13673826 GATATATAACTTACGAA
1 CTTACATAAAATAC-AA
*
13673843 GCTTACATAATAA-ATAA
1 -CTTACATAA-AATACAA
13673860 CTTACATAAAATACAA
1 CTTACATAAAATACAA
13673876 CTTACATAAAA
1 CTTACATAAAA
13673887 AAGTTTATGA
Statistics
Matches: 71, Mismatches: 17, Indels: 10
0.72 0.17 0.10
Matches are distributed among these distances:
15 4 0.06
16 57 0.80
17 3 0.04
18 7 0.10
ACGTcount: A:0.50, C:0.17, G:0.04, T:0.29
Consensus pattern (16 bp):
CTTACATAAAATACAA
Found at i:13673808 original size:25 final size:25
Alignment explanation
Indices: 13673755--13673808 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
13673745 ATACATAGCT
* ***
13673755 TACATAATACACAACTTACATAGCT
1 TACATAATAAACAACTTACATAAAA
*
13673780 TACATAATAAATAACTTACATAAAA
1 TACATAATAAACAACTTACATAAAA
13673805 TACA
1 TACA
13673809 ACTTACATAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.52, C:0.19, G:0.02, T:0.28
Consensus pattern (25 bp):
TACATAATAAACAACTTACATAAAA
Found at i:13673822 original size:25 final size:25
Alignment explanation
Indices: 13673794--13673950 Score: 95
Period size: 25 Copynumber: 6.0 Consensus size: 25
13673784 TAATAAATAA
*
13673794 CTTACATAAAATACAACTTACATAG
1 CTTACATAAAATATAACTTACATAG
* *
13673819 CTTACATGATATATAACTTACGA-AG
1 CTTACATAAAATATAACTTAC-ATAG
*
13673844 CTTACATAATAA-ATAACTTACATAAAATACAA
1 CTTACATAA-AATATAACTTAC-----AT--AG
* *** *
13673876 CTTACATAAAAAAGTTTATGACATAG
1 CTTACATAAAATA-TAACTTACATAG
* *
13673902 CTTACATAATACATAACTTACATAG
1 CTTACATAAAATATAACTTACATAG
13673927 CTTACATAATAA-ATAACTTACATA
1 CTTACATAA-AATATAACTTACATA
13673951 AAATACAACT
Statistics
Matches: 101, Mismatches: 19, Indels: 24
0.70 0.13 0.17
Matches are distributed among these distances:
25 66 0.65
26 15 0.15
28 2 0.02
29 1 0.01
31 2 0.02
32 11 0.11
33 4 0.04
ACGTcount: A:0.48, C:0.17, G:0.05, T:0.31
Consensus pattern (25 bp):
CTTACATAAAATATAACTTACATAG
Found at i:13673869 original size:66 final size:66
Alignment explanation
Indices: 13673581--13673883 Score: 299
Period size: 66 Copynumber: 4.4 Consensus size: 66
13673571 AATATTATAC
* * * * * *
13673581 ATAACTTACATAATACATAACTTTCATAACTTACATTATACACAACTTACATAGCTTA-ATTAAC
1 ATAACTTACATAAAATACAACTTACATAGCTTACATAATACACAACTTACATAGCTTACA-T-A-
13673645 ATTATA
63 A-TA-A
** * *
13673651 CATAACTTACATATATAACTCACATAACTTACATAGCTTACATTCTACACAACTTACATAACATA
1 -ATAACTTACATA-A-AA-T-AC--AACTTACATAGCTTACATAATACACAACTTACATAGCTTA
*
13673716 CATAATAC
59 CATAATAA
* *
13673724 ATAACTTACAT-AACTAACATA-ATACATAGCTTACATAATACACAACTTACATAGCTTACATAA
1 ATAACTTACATAAAAT-ACA-ACTTACATAGCTTACATAATACACAACTTACATAGCTTACATAA
13673787 TAA
64 TAA
* * *
13673790 ATAACTTACATAAAATACAACTTACATAGCTTACATGATATATAACTTACGA-AGCTTACATAAT
1 ATAACTTACATAAAATACAACTTACATAGCTTACATAATACACAACTTAC-ATAGCTTACATAAT
13673854 AA
65 AA
13673856 ATAACTTACATAAAATACAACTTACATA
1 ATAACTTACATAAAATACAACTTACATA
13673884 AAAAAGTTTA
Statistics
Matches: 199, Mismatches: 22, Indels: 27
0.80 0.09 0.11
Matches are distributed among these distances:
65 1 0.01
66 121 0.61
67 5 0.03
68 3 0.02
69 1 0.01
70 1 0.01
71 12 0.06
72 12 0.06
73 1 0.01
74 2 0.01
75 2 0.01
76 1 0.01
77 36 0.18
78 1 0.01
ACGTcount: A:0.47, C:0.20, G:0.03, T:0.31
Consensus pattern (66 bp):
ATAACTTACATAAAATACAACTTACATAGCTTACATAATACACAACTTACATAGCTTACATAATA
A
Found at i:13673922 original size:83 final size:83
Alignment explanation
Indices: 13673813--13673966 Score: 274
Period size: 83 Copynumber: 1.9 Consensus size: 83
13673803 AATACAACTT
* *
13673813 ACATAGCTTACATGATATATAACTTACGA-AGCTTACATAATAAATAACTTACATAAAATACAAC
1 ACATAGCTTACATAATACATAACTTAC-ATAGCTTACATAATAAATAACTTACATAAAATACAAC
13673877 TTACATAAAAAAGTTTATG
65 TTACATAAAAAAGTTTATG
13673896 ACATAGCTTACATAATACATAACTTACATAGCTTACATAATAAATAACTTACATAAAATACAACT
1 ACATAGCTTACATAATACATAACTTACATAGCTTACATAATAAATAACTTACATAAAATACAACT
13673961 TACATA
66 TACATA
13673967 GCAAATGGAA
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
82 1 0.01
83 67 0.99
ACGTcount: A:0.49, C:0.16, G:0.05, T:0.30
Consensus pattern (83 bp):
ACATAGCTTACATAATACATAACTTACATAGCTTACATAATAAATAACTTACATAAAATACAACT
TACATAAAAAAGTTTATG
Found at i:13673948 original size:16 final size:16
Alignment explanation
Indices: 13673927--13673966 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
13673917 ACTTACATAG
*
13673927 CTTACATAATAA-ATAA
1 CTTACATAA-AATACAA
13673943 CTTACATAAAATACAA
1 CTTACATAAAATACAA
13673959 CTTACATA
1 CTTACATA
13673967 GCAAATGGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 2 0.09
16 20 0.91
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (16 bp):
CTTACATAAAATACAA
Found at i:13673957 original size:25 final size:25
Alignment explanation
Indices: 13673904--13673957 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
13673894 TGACATAGCT
* ***
13673904 TACATAATACATAACTTACATAGCT
1 TACATAATAAATAACTTACATAAAA
13673929 TACATAATAAATAACTTACATAAAA
1 TACATAATAAATAACTTACATAAAA
13673954 TACA
1 TACA
13673958 ACTTACATAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.52, C:0.17, G:0.02, T:0.30
Consensus pattern (25 bp):
TACATAATAAATAACTTACATAAAA
Found at i:13676079 original size:21 final size:21
Alignment explanation
Indices: 13676053--13676103 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
13676043 CTACAACTTA
*
13676053 AAGCAGAGGCGGCAGCAAGGG
1 AAGCAGAGGCGGCAGCAAGAG
* *
13676074 AAGCAGAGGCTGCAGCGAGAG
1 AAGCAGAGGCGGCAGCAAGAG
13676095 AAGCAGAGG
1 AAGCAGAGG
13676104 TTCAAAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.35, C:0.18, G:0.45, T:0.02
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCAAGAG
Found at i:13676564 original size:44 final size:44
Alignment explanation
Indices: 13676489--13676603 Score: 119
Period size: 44 Copynumber: 2.6 Consensus size: 44
13676479 ATTTTTTTAT
* * * *
13676489 AAAAGCGCCACTAAA-AGTCATGTTC-TATAGCGGCGTTTGTAAA
1 AAAAACGCCACTAAAGA-ACATGTTCTTTTAGCGCCGTTTGTAAA
* *
13676532 ATAAAACGCCGCTAAAGAACAT-TTCTTTTAGCGCCGTTTGTGAA
1 A-AAAACGCCACTAAAGAACATGTTCTTTTAGCGCCGTTTGTAAA
* *
13676576 AAAAGCGCCACTAAAGATCATGTTCTTT
1 AAAAACGCCACTAAAGAACATGTTCTTT
13676604 ACCGGCATTT
Statistics
Matches: 59, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
43 21 0.36
44 37 0.63
45 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (44 bp):
AAAAACGCCACTAAAGAACATGTTCTTTTAGCGCCGTTTGTAAA
Found at i:13676634 original size:42 final size:41
Alignment explanation
Indices: 13676578--13676788 Score: 217
Period size: 42 Copynumber: 5.0 Consensus size: 41
13676568 TTTGTGAAAA
* * * *
13676578 AAGCGCCACTAAAGATCATGTTCTTTACCGGCATTTTTTCTG
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCATTTTTT-TG
* * ***
13676620 AATCGCCGCTAAAGAACATGATCGTTAGCGGCATTTGTGAAG
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCATTT-TTTTG
* *
13676662 AAAGCGCCGCTAAAGAACATGATATTTAGCGACGTC-TTTTTTTT
1 -AAGCGCCGCTAAAGAACATGATCTTTAGCG--G-CATTTTTTTG
* *
13676706 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCC
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCATTTTTTT-G
*
13676748 AAGCGCCGCTAAAGAACATGACCTTTAGCGGCATTTATTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCATTT-TTTT
13676789 TGTAAACACT
Statistics
Matches: 141, Mismatches: 20, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
40 1 0.01
41 8 0.06
42 65 0.46
43 61 0.43
44 1 0.01
45 4 0.03
46 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.31
Consensus pattern (41 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCATTTTTTTG
Found at i:13676657 original size:85 final size:86
Alignment explanation
Indices: 13676538--13676737 Score: 242
Period size: 85 Copynumber: 2.3 Consensus size: 86
13676528 TAAAATAAAA
* * * * * *
13676538 CGCCGCTAAAGAACAT-TTCTTTTAGCGCCGTTTGTGAAAAAAGCGCCACTAAAGATCATGTTCT
1 CGCCGCTAAAGAACATGATC-TTTAGCGGCATTTGTGAAAAAAGCGCCACTAAAGAACATGATAT
* *
13676602 TTACCGGCAT-TTTTTCTGAAT
65 TTACCGACATCTTTTTCTGAAG
* * *
13676623 CGCCGCTAAAGAACATGATCGTTAGCGGCATTTGTGAAGAAAGCGCCGCTAAAGAACATGATATT
1 CGCCGCTAAAGAACATGATCTTTAGCGGCATTTGTGAAAAAAGCGCCACTAAAGAACATGATATT
* * * *
13676688 TAGCGACGTCTTTTTTTTAAG
66 TACCGACATCTTTTTCTGAAG
13676709 CGCCGCTAAAGAACATGATCTTTAGCGGC
1 CGCCGCTAAAGAACATGATCTTTAGCGGC
13676738 GTTTTTTTCC
Statistics
Matches: 97, Mismatches: 16, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
85 59 0.61
86 38 0.39
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.29
Consensus pattern (86 bp):
CGCCGCTAAAGAACATGATCTTTAGCGGCATTTGTGAAAAAAGCGCCACTAAAGAACATGATATT
TACCGACATCTTTTTCTGAAG
Found at i:13676691 original size:128 final size:128
Alignment explanation
Indices: 13676538--13676783 Score: 291
Period size: 128 Copynumber: 1.9 Consensus size: 128
13676528 TAAAATAAAA
* * * * *
13676538 CGCCGCTAAAGAACATTTCTTTTAGCGCCGT-TTGTGAAAAAAGCGCCACTAAAGATCATGTTCT
1 CGCCGCTAAAGAACATATCATTTAGCGACGTCTT-TGAAAAAAGCGCCACTAAAGAACATGATCT
* * *
13676602 TTACCGGCA-TTTTTTCTGAATCGCCGCTAAAGAACATGATCGTTAGCGGCATTTGTGAAGAAAG
65 TTACCGGCATTTTTTTC-CAAGCGCCGCTAAAGAACATGACCGTTAGCGGCATTTGTGAAGAAAG
***** *
13676666 CGCCGCTAAAGAACATGAT-ATTTAGCGACGTCTTTTTTTTAAGCGCCGCTAAAGAACATGATCT
1 CGCCGCTAAAGAACAT-ATCATTTAGCGACGTCTTTGAAAAAAGCGCCACTAAAGAACATGATCT
* * *
13676730 TTAGCGGCGTTTTTTTCCAAGCGCCGCTAAAGAACATGACCTTTAGCGGCATTT
65 TTACCGGCATTTTTTTCCAAGCGCCGCTAAAGAACATGACCGTTAGCGGCATTT
13676784 ATTTTTGTAA
Statistics
Matches: 98, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
128 88 0.90
129 10 0.10
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.30
Consensus pattern (128 bp):
CGCCGCTAAAGAACATATCATTTAGCGACGTCTTTGAAAAAAGCGCCACTAAAGAACATGATCTT
TACCGGCATTTTTTTCCAAGCGCCGCTAAAGAACATGACCGTTAGCGGCATTTGTGAAGAAAG
Found at i:13676920 original size:21 final size:22
Alignment explanation
Indices: 13676875--13676920 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
13676865 TTTAGCGGCA
**
13676875 CTAAAAAAGCGCCGCTAAAGGC
1 CTAAAAAAGCGCCGCTAAAAAC
13676897 CTAAAAAA-CGCCGCTAAAAAC
1 CTAAAAAAGCGCCGCTAAAAAC
13676918 CTA
1 CTA
13676921 TTTTGGTGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.46, C:0.28, G:0.15, T:0.11
Consensus pattern (22 bp):
CTAAAAAAGCGCCGCTAAAAAC
Found at i:13680252 original size:15 final size:16
Alignment explanation
Indices: 13680229--13680268 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
13680219 GTTGAGTCCG
*
13680229 TAGGATTTTT-TGGTT
1 TAGGATTTTTAGGGTT
*
13680244 TAGGGTTTTTAGGGTT
1 TAGGATTTTTAGGGTT
13680260 TAGGATTTT
1 TAGGATTTT
13680269 GTTAAAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.15, C:0.00, G:0.30, T:0.55
Consensus pattern (16 bp):
TAGGATTTTTAGGGTT
Found at i:13680328 original size:28 final size:31
Alignment explanation
Indices: 13680297--13680396 Score: 82
Period size: 34 Copynumber: 3.2 Consensus size: 31
13680287 TAGGGTGTAC
13680297 GGTTTA-AGAATTTTAAAA-AA-TAAATTAG
1 GGTTTAGAGAATTTTAAAATAATTAAATTAG
**
13680325 GGTTTAGAGTTTTTTAAAATTAATTAAATTAG
1 GGTTTAGAGAATTTTAAAA-TAATTAAATTAG
* **
13680357 GTTTTAG-GGGTTTTAAATCAATAAATTAAATTAG
1 GGTTTAGAGAATTTT-AA--AAT-AATTAAATTAG
13680391 GGTTTA
1 GGTTTA
13680397 AAGTTTTTAA
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
28 6 0.10
29 10 0.17
31 7 0.12
32 16 0.28
33 1 0.02
34 18 0.31
ACGTcount: A:0.40, C:0.01, G:0.17, T:0.42
Consensus pattern (31 bp):
GGTTTAGAGAATTTTAAAATAATTAAATTAG
Found at i:13680405 original size:34 final size:32
Alignment explanation
Indices: 13680317--13680440 Score: 117
Period size: 34 Copynumber: 3.8 Consensus size: 32
13680307 TTTTAAAAAA
* *
13680317 TAAATTAGGGTTTAGAGTTTTTTAAAATTAAT
1 TAAATTAGGGTTTAGAGTTTTTAAAAATAAAT
* * *
13680349 TAAATTAGGTTTTAGGGGTTTTAAATCAATAAAT
1 TAAATTAGGGTTTAGAGTTTTTAAA--AATAAAT
* *
13680383 TAAATTAGGGTTTAAAGTTTTTAAGAAAATTAAT
1 TAAATTAGGGTTTAGAGTTTTT-A-AAAATAAAT
* *
13680417 T-AATTAAGGTTTAG-TTTTTTAAAA
1 TAAATTAGGGTTTAGAGTTTTTAAAA
13680441 TGATTTTGTG
Statistics
Matches: 75, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
30 3 0.04
31 1 0.01
32 26 0.35
33 11 0.15
34 31 0.41
35 1 0.01
36 2 0.03
ACGTcount: A:0.40, C:0.01, G:0.15, T:0.44
Consensus pattern (32 bp):
TAAATTAGGGTTTAGAGTTTTTAAAAATAAAT
Found at i:13680815 original size:127 final size:126
Alignment explanation
Indices: 13680498--13680881 Score: 530
Period size: 127 Copynumber: 3.0 Consensus size: 126
13680488 ATGGATTTTG
* * * **
13680498 TTTTTTTTCTACATTAGTTTTAGAAAAATTAATTTT-AGGAAGACGGTTCTGAAA-AGATAATGT
1 TTTTTTTTCTACAGTAGTTTT-GAAAAAATAATTTTGA-GAAGACGGTTCT-AAACAAATGGTGT
* *
13680561 CAAAAACGCTTCAAACAGGATGCACTGTTAGCAAAATTACTGAAAAAAGCTCCCACGTGGA--C
63 CAAAAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGC
* *
13680623 --TTTTTTCTACAGTAGTTTCTGAAAAAATAATTTTGAAAAGACGGTTCTGAACAAATGGTGTCA
1 TTTTTTTTCTACAGTAGTTT-TGAAAAAATAATTTTGAGAAGACGGTTCTAAACAAATGGTGTCA
*
13680686 AAAACGCTTCAAGCAGGATGCACTGTCAGCAAAAATACTGAAAAAAGCTCCCACGTGGACGC
65 AAAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGC
13680748 TTTTTTTTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGACGGTTCTAAACAAATGGTGTCA
1 TTTTTTTTCTACAGTAGTT-TTGAAAAAATAATTTTGAGAAGACGGTTCTAAACAAATGGTGTCA
* * *
13680813 AAAATGCTTCAAGTAGGATGCACAGTCAGCAAAATTGA-TGAAAAAAGCTCCCACGTGGACACGC
65 AAAACGCTTCAAGCAGGATGCACTGTCAGCAAAATT-ACTGAAAAAAGCTCCCACGTGG--ACGC
13680877 TTTTT
1 TTTTT
13680882 CTATAATAGT
Statistics
Matches: 232, Mismatches: 16, Indels: 18
0.87 0.06 0.07
Matches are distributed among these distances:
122 2 0.01
123 105 0.45
124 2 0.01
125 1 0.00
127 111 0.48
128 2 0.01
129 9 0.04
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.29
Consensus pattern (126 bp):
TTTTTTTTCTACAGTAGTTTTGAAAAAATAATTTTGAGAAGACGGTTCTAAACAAATGGTGTCAA
AAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGC
Found at i:13681271 original size:16 final size:16
Alignment explanation
Indices: 13681250--13681284 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
13681240 TTTCACAAGA
13681250 TCATCCCAAGATGGAT
1 TCATCCCAAGATGGAT
13681266 TCATCCCAAGATGGAT
1 TCATCCCAAGATGGAT
13681282 TCA
1 TCA
13681285 AATGTGCTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (16 bp):
TCATCCCAAGATGGAT
Found at i:13682521 original size:24 final size:23
Alignment explanation
Indices: 13682465--13682521 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 23
13682455 AAGAACTTCT
*
13682465 ATTTTATTAAAAATATAAAAATA
1 ATTTTATTAAAAATATAAAAACA
13682488 ATTTACTATT-AAAATATTAAAAACA
1 ATTT--TATTAAAAATA-TAAAAACA
13682513 ACTTTTATT
1 A-TTTTATT
13682522 TTATTAAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
23 4 0.14
24 10 0.34
25 12 0.41
26 3 0.10
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (23 bp):
ATTTTATTAAAAATATAAAAACA
Found at i:13682961 original size:18 final size:18
Alignment explanation
Indices: 13682938--13682976 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
13682928 GGAAAATGAA
*
13682938 ACGTATAAGGGTTAAGAT
1 ACGTATAAGGGCTAAGAT
*
13682956 ACGTATAAGGGCTAGGAT
1 ACGTATAAGGGCTAAGAT
13682974 ACG
1 ACG
13682977 CACTTGGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.36, C:0.10, G:0.31, T:0.23
Consensus pattern (18 bp):
ACGTATAAGGGCTAAGAT
Found at i:13695973 original size:24 final size:24
Alignment explanation
Indices: 13695946--13696015 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 24
13695936 TTATTAACAT
13695946 TGTTCGTGAACATGTTCAATTAT-A
1 TGTTCGTGAACATGTTC-ATTATAA
* * * *
13695970 TGTTCATGAACATATTCGTTTTAA
1 TGTTCGTGAACATGTTCATTATAA
*
13695994 TATTCGTGAACATGTTCGATTA
1 TGTTCGTGAACATGTTC-ATTA
13696016 AGTTAAATGA
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
23 3 0.09
24 30 0.86
25 2 0.06
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.43
Consensus pattern (24 bp):
TGTTCGTGAACATGTTCATTATAA
Found at i:13699652 original size:19 final size:20
Alignment explanation
Indices: 13699628--13699669 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
13699618 ACTGAACTTG
*
13699628 AAAATTGAACTCGAG-ATCA
1 AAAATTGAACCCGAGAATCA
13699647 AAAATTGAACCCGAGAATCA
1 AAAATTGAACCCGAGAATCA
13699667 AAA
1 AAA
13699670 CCCGAGATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.52, C:0.17, G:0.14, T:0.17
Consensus pattern (20 bp):
AAAATTGAACCCGAGAATCA
Found at i:13700156 original size:13 final size:13
Alignment explanation
Indices: 13700138--13700172 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
13700128 GGGGTCATAC
13700138 GGCCGTGTGGCTA
1 GGCCGTGTGGCTA
13700151 GGCCGTGTGGCTA
1 GGCCGTGTGGCTA
13700164 GGCCGTGTG
1 GGCCGTGTG
13700173 ACTCACACGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.06, C:0.23, G:0.49, T:0.23
Consensus pattern (13 bp):
GGCCGTGTGGCTA
Found at i:13705315 original size:41 final size:41
Alignment explanation
Indices: 13705258--13705454 Score: 283
Period size: 41 Copynumber: 4.8 Consensus size: 41
13705248 AAATTATTCA
13705258 GACTATATGTCTAGCAGGCTAAGTGCCGGTGAACTGAATCG
1 GACTATATGTCTAGCAGGCTAAGTGCCGGTGAACTGAATCG
13705299 GACTATATGTCTAGCAGGCTAAGTGCCGGTGAACTGAATCG
1 GACTATATGTCTAGCAGGCTAAGTGCCGGTGAACTGAATCG
13705340 GACTATATGTCTAGCAGGCTAAGTGCCGGTGAACTGAATCAG
1 GACTATATGTCTAGCAGGCTAAGTGCCGGTGAACTGAATC-G
* * **
13705382 G-CTATAGGCCTAGCAGGCTAAGTGCCGGTGAAC-GAAATTA
1 GACTATATGTCTAGCAGGCTAAGTGCCGGTGAACTG-AATCG
* * *
13705422 GACTATAAGTCTATCAGG-TGAAGTGCCAGTGAA
1 GACTATATGTCTAGCAGGCT-AAGTGCCGGTGAA
13705455 TCTGTTTAAA
Statistics
Matches: 144, Mismatches: 8, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
40 3 0.02
41 139 0.97
42 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (41 bp):
GACTATATGTCTAGCAGGCTAAGTGCCGGTGAACTGAATCG
Found at i:13706951 original size:41 final size:40
Alignment explanation
Indices: 13706906--13707149 Score: 262
Period size: 41 Copynumber: 6.0 Consensus size: 40
13706896 CTTGTATAAA
* * * *
13706906 CACCGGCATAAAGCCTGCTAGGCACAAAGCCCGATACATT
1 CACCGGCATAAAGCCTGCTAGACATAAAGTCTGATACATT
* *
13706946 CCACCGGCACAAAGCCTGCTAGACATAAGGTCTGATACATTT
1 -CACCGGCATAAAGCCTGCTAGACATAAAGTCTGATACA-TT
13706988 CACCGGCACT-AAGCCTGCTAGACATAAAGTCTGAAGTA-ATT
1 CACCGGCA-TAAAGCCTGCTAGACATAAAGTCTG-A-TACATT
* *
13707029 CACCGGCATCAAGCCTGCTAGACGTAAAGTCTGAAATA-ATT
1 CACCGGCATAAAGCCTGCTAGACATAAAGTCTG--ATACATT
* *
13707070 CACCGGCATCAAGCCTGCTAGACGTAAAGTCTGAAATA-ATT
1 CACCGGCATAAAGCCTGCTAGACATAAAGTCTG--ATACATT
* * *
13707111 CACCGGCATCAAGCCTGCTAGACGTAAAGTCTGAAACAT
1 CACCGGCATAAAGCCTGCTAGACATAAAGTCTGATACAT
13707150 CTTATTTTCA
Statistics
Matches: 186, Mismatches: 10, Indels: 15
0.88 0.05 0.07
Matches are distributed among these distances:
39 2 0.01
40 3 0.02
41 173 0.93
42 6 0.03
43 2 0.01
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (40 bp):
CACCGGCATAAAGCCTGCTAGACATAAAGTCTGATACATT
Found at i:13707043 original size:82 final size:82
Alignment explanation
Indices: 13706906--13707149 Score: 316
Period size: 82 Copynumber: 3.0 Consensus size: 82
13706896 CTTGTATAAA
* * * * *
13706906 CACCGGCATAAAGCCTGCTAGGCACAAAGCCCG--ATACATTCCACCGGCA-CAAAGCCTGCTAG
1 CACCGGCATCAAGCCTGCTAGACATAAAGTCTGAAATA-ATT-CACCGGCATC-AAGCCTGCTAG
* * *
13706968 ACATAAGGTCTGATACATTT
63 ACGTAAAGTCTGAAACATTT
*
13706988 CACCGGCA-CTAAGCCTGCTAGACATAAAGTCTGAAGTAATTCACCGGCATCAAGCCTGCTAGAC
1 CACCGGCATC-AAGCCTGCTAGACATAAAGTCTGAAATAATTCACCGGCATCAAGCCTGCTAGAC
* *
13707052 GTAAAGTCTGAAATAATT
65 GTAAAGTCTGAAACATTT
*
13707070 CACCGGCATCAAGCCTGCTAGACGTAAAGTCTGAAATAATTCACCGGCATCAAGCCTGCTAGACG
1 CACCGGCATCAAGCCTGCTAGACATAAAGTCTGAAATAATTCACCGGCATCAAGCCTGCTAGACG
13707135 TAAAGTCTGAAACAT
66 TAAAGTCTGAAACAT
13707150 CTTATTTTCA
Statistics
Matches: 142, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
82 135 0.95
83 5 0.04
84 2 0.01
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (82 bp):
CACCGGCATCAAGCCTGCTAGACATAAAGTCTGAAATAATTCACCGGCATCAAGCCTGCTAGACG
TAAAGTCTGAAACATTT
Found at i:13707818 original size:16 final size:17
Alignment explanation
Indices: 13707797--13707831 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
13707787 ATCTAATAAT
13707797 TTATACAT-GTATATAC
1 TTATACATCGTATATAC
*
13707813 TTATACATCGTTTATAC
1 TTATACATCGTATATAC
13707830 TT
1 TT
13707832 CGACTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.31, C:0.14, G:0.06, T:0.49
Consensus pattern (17 bp):
TTATACATCGTATATAC
Found at i:13714274 original size:20 final size:19
Alignment explanation
Indices: 13714249--13714295 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
13714239 TTGGATGATA
13714249 TTTTTTCTCTTCTCTCTTCT
1 TTTTTTCTCTTCTCTCTT-T
* *
13714269 TTTTTTGTTTTCTCTCTTT
1 TTTTTTCTCTTCTCTCTTT
*
13714288 TATTTTCT
1 TTTTTTCT
13714296 TCCTTCGATC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.74
Consensus pattern (19 bp):
TTTTTTCTCTTCTCTCTTT
Found at i:13716931 original size:30 final size:30
Alignment explanation
Indices: 13716888--13716958 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 30
13716878 TTTAAGCAAA
13716888 AATATTAATTATTTATAACCATTAA-ATATTT
1 AATATT-ATTATTTATAA-CATTAATATATTT
* * *
13716919 AATATTATTATTTTTAATATTAATATTTTT
1 AATATTATTATTTATAACATTAATATATTT
13716949 AATATTATTA
1 AATATTATTA
13716959 ATAATATTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 5 0.14
30 25 0.69
31 6 0.17
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (30 bp):
AATATTATTATTTATAACATTAATATATTT
Found at i:13716969 original size:15 final size:15
Alignment explanation
Indices: 13716916--13716958 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
13716906 CCATTAAATA
13716916 TTTAATATTATTATT
1 TTTAATATTATTATT
*
13716931 TTTAATATTAATATT
1 TTTAATATTATTATT
13716946 TTTAATATTATTA
1 TTTAATATTATTA
13716959 ATAATATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTAATATTATTATT
Found at i:13716974 original size:12 final size:12
Alignment explanation
Indices: 13716914--13716974 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
13716904 AACCATTAAA
*
13716914 TATTTAATATTAT
1 TATTT-ATAATAT
*
13716927 TATTTTTAATATT
1 TATTTATAATA-T
*
13716940 AATATTTTTAATAT
1 --TATTTATAATAT
*
13716954 TATTAATAATAT
1 TATTTATAATAT
13716966 TATTTATAA
1 TATTTATAA
13716975 CCATTAATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
12 22 0.55
13 6 0.15
14 1 0.03
15 11 0.28
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TATTTATAATAT
Done.