Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008988.1 Hibiscus syriacus cultivar Beakdansim tig00112353_pilon, whole genome shotgun sequence
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: 339899
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:2443 original size:2 final size:2
Alignment explanation
Indices: 2436--2508 Score: 139
Period size: 2 Copynumber: 37.0 Consensus size: 2
2426 CTGGTTTCCA
2436 AT AT AT AT AT AT AT -T 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 AT AT
2477 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
2509 TTGTATCAGT
Statistics
Matches: 70, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 69 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:6064 original size:20 final size:16
Alignment explanation
Indices: 6024--6066 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 16
6014 CAGATGTAGT
6024 AATTTTTTTTTGTCTA
1 AATTTTTTTTTGTCTA
6040 AATTTATTTTTTGGTCATA
1 AATTT-TTTTTT-GTC-TA
6059 ATATTTTT
1 A-ATTTTT
6067 ATTTAAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 5 0.22
17 6 0.26
18 3 0.13
19 5 0.22
20 4 0.17
ACGTcount: A:0.23, C:0.05, G:0.07, T:0.65
Consensus pattern (16 bp):
AATTTTTTTTTGTCTA
Found at i:13505 original size:31 final size:31
Alignment explanation
Indices: 13467--13527 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
13457 ATTAAGAACA
13467 TACAGCTTTCATCATTAATCAAGTTTCTATT
1 TACAGCTTTCATCATTAATCAAGTTTCTATT
13498 TACAGCTTTCATCATTAATCAAGTTTCTAT
1 TACAGCTTTCATCATTAATCAAGTTTCTAT
13528 CTTGATGGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.44
Consensus pattern (31 bp):
TACAGCTTTCATCATTAATCAAGTTTCTATT
Found at i:16420 original size:68 final size:68
Alignment explanation
Indices: 16309--16446 Score: 267
Period size: 68 Copynumber: 2.0 Consensus size: 68
16299 TCTAACAATG
16309 AAACCATATACAACTGGACATGAGTTAACATTATTGATACAGTCTACTGCAACCCTGCAATCACT
1 AAACCATATACAACTGGACATGAGTTAACATTATTGATACAGTCTACTGCAACCCTGCAATCACT
16374 CTC
66 CTC
*
16377 AAACCATATACAACTGGACATGAGTTAACATTATTGATCCAGTCTACTGCAACCCTGCAATCACT
1 AAACCATATACAACTGGACATGAGTTAACATTATTGATACAGTCTACTGCAACCCTGCAATCACT
16442 CTC
66 CTC
16445 AA
1 AA
16447 CGATCAGCCT
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.36, C:0.27, G:0.12, T:0.26
Consensus pattern (68 bp):
AAACCATATACAACTGGACATGAGTTAACATTATTGATACAGTCTACTGCAACCCTGCAATCACT
CTC
Found at i:19683 original size:2 final size:2
Alignment explanation
Indices: 19678--19720 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
19668 TGTGTGTGTG
19678 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19720 T
1 T
19721 GTGTGTGTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:24016 original size:21 final size:21
Alignment explanation
Indices: 23992--24032 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
23982 GGTAAAAAAT
* *
23992 TACCTAAAATATTATTATTTC
1 TACCTAAAACATTAATATTTC
24013 TACCTAAAACATTAATATTT
1 TACCTAAAACATTAATATTT
24033 TTTAACATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (21 bp):
TACCTAAAACATTAATATTTC
Found at i:24514 original size:23 final size:23
Alignment explanation
Indices: 24490--24537 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
24480 TTTTTAGAAT
*
24490 AAAA-TATAATATATCTATTATATA
1 AAAAGTAT-ATATAT-TATTAAATA
24514 AAAAGTATATATATTATTAAATA
1 AAAAGTATATATATTATTAAATA
24537 A
1 A
24538 TAATTCAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 9 0.41
24 10 0.45
25 3 0.14
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
AAAAGTATATATATTATTAAATA
Found at i:37761 original size:27 final size:27
Alignment explanation
Indices: 37706--37769 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
37696 AAATTGACTT
* *
37706 AAGTATAGGGACCAATTTGACTCAAAA
1 AAGTGTAGGGACCAATTTGACCCAAAA
* *
37733 AATGTTTAGGG-CCAATTTGACCCAGAA
1 AA-GTGTAGGGACCAATTTGACCCAAAA
37760 AAGTGTAGGG
1 AAGTGTAGGG
37770 GGCATATTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 7 0.22
27 18 0.56
28 7 0.22
ACGTcount: A:0.38, C:0.14, G:0.25, T:0.23
Consensus pattern (27 bp):
AAGTGTAGGGACCAATTTGACCCAAAA
Found at i:39444 original size:27 final size:27
Alignment explanation
Indices: 39406--39457 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
39396 AGCTCCAGCT
*
39406 GGTGGAGGTGGAGGGCCAGGAGCTCCA
1 GGTGGAGGTGGAGGACCAGGAGCTCCA
39433 GGTGGAGGTGGAGGACCAGGAGCTC
1 GGTGGAGGTGGAGGACCAGGAGCTC
39458 GACCACCAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.19, C:0.17, G:0.52, T:0.12
Consensus pattern (27 bp):
GGTGGAGGTGGAGGACCAGGAGCTCCA
Found at i:39480 original size:42 final size:42
Alignment explanation
Indices: 39433--39577 Score: 202
Period size: 42 Copynumber: 3.5 Consensus size: 42
39423 AGGAGCTCCA
** * *
39433 GGTGGAGGTGGAGGACCAGGAGCTCGACCACCAGGAGGTGGT
1 GGTGGAGGTGGAGCTCCAGGAGCTCCACCACCAGCAGGTGGT
39475 GGTGGAGGT-GATGCTCCAGGAGCTCCACCACCAGCAGGTGGT
1 GGTGGAGGTGGA-GCTCCAGGAGCTCCACCACCAGCAGGTGGT
* * *
39517 GGGGGAGGTTGTGCTCCAGGAGCTCCACCACCAGCAGGTGGT
1 GGTGGAGGTGGAGCTCCAGGAGCTCCACCACCAGCAGGTGGT
*
39559 GGTGGAGGTGGTGCTCCAG
1 GGTGGAGGTGGAGCTCCAG
39578 ATGAGGGAGG
Statistics
Matches: 93, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
41 2 0.02
42 90 0.97
43 1 0.01
ACGTcount: A:0.18, C:0.23, G:0.43, T:0.16
Consensus pattern (42 bp):
GGTGGAGGTGGAGCTCCAGGAGCTCCACCACCAGCAGGTGGT
Found at i:39656 original size:36 final size:36
Alignment explanation
Indices: 39651--39842 Score: 294
Period size: 36 Copynumber: 5.2 Consensus size: 36
39641 ACGTTGGAGG
* *
39651 TGGAGGTGGGGGTGGGGGTGGAGGAGGAGCATCGGACGT
1 TGGAGGTGGAGGAGGGGGT-G--GAGGAGCATCGGACGT
*
39690 TGGAGGTGGAGGAGGGGGTGGAGGAACATCGGACGT
1 TGGAGGTGGAGGAGGGGGTGGAGGAGCATCGGACGT
* *
39726 TAGAGGTGGAGGAGGGGGTGGAGGAGCATTGGACGT
1 TGGAGGTGGAGGAGGGGGTGGAGGAGCATCGGACGT
*
39762 TGGAGGTGGAGGAGGGGGTGGAGGAGCATCGGATGT
1 TGGAGGTGGAGGAGGGGGTGGAGGAGCATCGGACGT
*
39798 TGGAGGTGGAGGAGGGGGTGGAGGAGCATTGGACGT
1 TGGAGGTGGAGGAGGGGGTGGAGGAGCATCGGACGT
39834 TGGAGGTGG
1 TGGAGGTGG
39843 TGGTGGAGAT
Statistics
Matches: 142, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
36 124 0.87
38 1 0.01
39 17 0.12
ACGTcount: A:0.19, C:0.06, G:0.58, T:0.16
Consensus pattern (36 bp):
TGGAGGTGGAGGAGGGGGTGGAGGAGCATCGGACGT
Found at i:40783 original size:18 final size:18
Alignment explanation
Indices: 40760--40894 Score: 220
Period size: 18 Copynumber: 7.6 Consensus size: 18
40750 CTAGGAGGGA
40760 TTGGCTGAGATACATCAC
1 TTGGCTGAGATACATCAC
*
40778 TTGGCTGAGATATATCAC
1 TTGGCTGAGATACATCAC
*
40796 TTGGCTGAGCT--ATCAC
1 TTGGCTGAGATACATCAC
* *
40812 TTGGCTGAGCTGCATCAC
1 TTGGCTGAGATACATCAC
40830 TTGGCTGAGATACATCAC
1 TTGGCTGAGATACATCAC
40848 TTGGCTGAGATACATCAC
1 TTGGCTGAGATACATCAC
40866 TTGGCTGAGATACATCAC
1 TTGGCTGAGATACATCAC
40884 TTGGCTGAGAT
1 TTGGCTGAGAT
40895 TGTCTTCTAA
Statistics
Matches: 111, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
16 16 0.14
18 95 0.86
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.30
Consensus pattern (18 bp):
TTGGCTGAGATACATCAC
Found at i:51442 original size:59 final size:60
Alignment explanation
Indices: 51324--51452 Score: 136
Period size: 59 Copynumber: 2.2 Consensus size: 60
51314 TATATATTTC
* * * **
51324 AATTTAATCCTTAAATGATGACCCTCATTCTAAATTAGTCCTTAAAATTTTGAAAATTCT
1 AATTTAATCCCTAAATGATAACCCTCATTATAAATTAGTCCACAAAATTTTGAAAATTCT
* * * **
51384 ATTTTAATCCCTAAAT-ATAACCCT-ATTTATAAATTGGTCCACAAACTTTTGACTATTCT
1 AATTTAATCCCTAAATGATAACCCTCA-TTATAAATTAGTCCACAAAATTTTGAAAATTCT
*
51443 AATTTCATCC
1 AATTTAATCC
51453 TCAATTTCAT
Statistics
Matches: 56, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
58 1 0.02
59 41 0.73
60 14 0.25
ACGTcount: A:0.35, C:0.19, G:0.05, T:0.40
Consensus pattern (60 bp):
AATTTAATCCCTAAATGATAACCCTCATTATAAATTAGTCCACAAAATTTTGAAAATTCT
Found at i:53924 original size:180 final size:182
Alignment explanation
Indices: 53626--53990 Score: 549
Period size: 181 Copynumber: 2.0 Consensus size: 182
53616 CGATACAAAT
* * * *
53626 TAAAAATGTATCGATCCATAGCAACATAACAAGTAAAAATATGATAAAACCGATGTCATTATGAT
1 TAAAAATGTATCGATCCATAGCAACATAACAAGTAAAAATATGACAAAACAGATCTCATAATGAT
* ** *
53691 AAAACCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTGTCGACACTT
66 AAAACCAGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTT
53756 TTGTAATTTAAAAGAGAAGAA-TTATAGCGTCT-AAAAGGTGTCGATACTTTA
131 TTGTAATTTAAAAGAGAAGAAGTTATAGCGTCTGAAAA-GTGTCGATACTTTA
* * * * * *
53807 TAAAAATGTATCGATTCATATCAATATAACAGGTAATAATATGACAAAACAGGTCTCGA-AATGA
1 TAAAAATGTATCGATCCATAGCAACATAACAAGTAAAAATATGACAAAACAGATCTC-ATAATGA
*
53871 T-AAATCAGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACT
65 TAAAACCAGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACT
53935 TTTGTAATTTAAAAGAGAAGAAGTTATAGCGTCTGAAAAGTGTCGATACTTTA
130 TTTGTAATTTAAAAGAGAAGAAGTTATAGCGTCTGAAAAGTGTCGATACTTTA
53988 TAA
1 TAA
53991 TTAATAATTC
Statistics
Matches: 166, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
180 80 0.48
181 81 0.49
182 5 0.03
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.29
Consensus pattern (182 bp):
TAAAAATGTATCGATCCATAGCAACATAACAAGTAAAAATATGACAAAACAGATCTCATAATGAT
AAAACCAGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTT
TTGTAATTTAAAAGAGAAGAAGTTATAGCGTCTGAAAAGTGTCGATACTTTA
Found at i:54030 original size:30 final size:30
Alignment explanation
Indices: 53989--54052 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
53979 GATACTTTAT
53989 AATTAATAATTCTTCAAAATTAGGTGACTA
1 AATTAATAATTCTTCAAAATTAGGTGACTA
*
54019 AATTGATAATTCTTCAAAATTAGGTGACTA
1 AATTAATAATTCTTCAAAATTAGGTGACTA
54049 AATT
1 AATT
54053 TCAAATTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (30 bp):
AATTAATAATTCTTCAAAATTAGGTGACTA
Found at i:54433 original size:18 final size:18
Alignment explanation
Indices: 54410--54447 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
54400 TCATACAAAC
54410 AAATATAAAACATAAAAA
1 AAATATAAAACATAAAAA
*
54428 AAATATAAATCATAAAAA
1 AAATATAAAACATAAAAA
54446 AA
1 AA
54448 TTCCTTATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.18
Consensus pattern (18 bp):
AAATATAAAACATAAAAA
Found at i:54447 original size:19 final size:19
Alignment explanation
Indices: 54398--54447 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 19
54388 TAGAAGAAAC
* *
54398 AATCATACAAACAAATATA
1 AATCATAAAAAAAAATATA
*
54417 AAACAT-AAAAAAAATATA
1 AATCATAAAAAAAAATATA
54435 AATCATAAAAAAA
1 AATCATAAAAAAA
54448 TTCCTTATGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 15 0.58
19 11 0.42
ACGTcount: A:0.72, C:0.10, G:0.00, T:0.18
Consensus pattern (19 bp):
AATCATAAAAAAAAATATA
Found at i:57958 original size:15 final size:17
Alignment explanation
Indices: 57938--57970 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
57928 TGTATTTTTT
57938 TTAAATT-TAAG-TAGA
1 TTAAATTGTAAGATAGA
57953 TTAAATTGTAAGATAGA
1 TTAAATTGTAAGATAGA
57970 T
1 T
57971 AAAAATACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 4 0.25
17 5 0.31
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.39
Consensus pattern (17 bp):
TTAAATTGTAAGATAGA
Found at i:66353 original size:173 final size:170
Alignment explanation
Indices: 66091--66438 Score: 594
Period size: 173 Copynumber: 2.0 Consensus size: 170
66081 GTTGACAATG
66091 ATACGTTGGTTGTCTTTTGCTACACCAAGAAATTGTTGACCAAGCTTAAACACATATCCAGTTGT
1 ATACGTTGGTTGTCTTTTGCTACACCAAGAAATTGTTGACCAAGCTTAAACACATATCCAGTTGT
66156 TGATCTCCTGGTGTCATGATCTCCTGCATAAT-CATCACAATAACCAA-AACTTGCAGTCTTCAC
66 TGATCTCCTGGTGTCATGATCTCCTGCATAATACATCACAATAACCAACAACTTGCAGTCTTCAC
66219 CTTTCTTGTACAAAAGACCATAGTCAATTGTATTCTTCACAT
131 C-TTCTTGTAC-AAAGACCATAGTCAATTGTATTCTTCACAT
66261 ATACGTTGGTTGTCTTTTGCTACACCAAGAAATTGTTCCGGAGCCAAGC-TAAACACATATCCAG
1 ATACGTTGGTTGTCTTTTGCTACACCAAGAAATTGTT---GA-CCAAGCTTAAACACATATCCAG
66325 TTGTTGATCTCCTGGTGTCATGATCTCCTGCATAATCAGCATCACAATAACCAACTAACTTGCAG
62 TTGTTGATCTCCTGGTGTCATGATCTCCTGCATAAT-A-CATCACAATAACCAAC-AACTTGCAG
66390 TCTTCACCTTCTTGTACAAAGACCATAGTCAATTGTATTCTTCACAT
124 TCTTCACCTTCTTGTACAAAGACCATAGTCAATTGTATTCTTCACAT
66437 AT
1 AT
66439 CTCAGTATTC
Statistics
Matches: 169, Mismatches: 0, Indels: 12
0.93 0.00 0.07
Matches are distributed among these distances:
170 37 0.22
173 53 0.31
174 6 0.04
176 47 0.28
177 9 0.05
178 17 0.10
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (170 bp):
ATACGTTGGTTGTCTTTTGCTACACCAAGAAATTGTTGACCAAGCTTAAACACATATCCAGTTGT
TGATCTCCTGGTGTCATGATCTCCTGCATAATACATCACAATAACCAACAACTTGCAGTCTTCAC
CTTCTTGTACAAAGACCATAGTCAATTGTATTCTTCACAT
Found at i:70235 original size:29 final size:29
Alignment explanation
Indices: 70193--70251 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
70183 ATTTTCACCT
70193 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
*
70222 AACTAAATTGATGTAAGCAATGGCATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
70251 A
1 A
70252 TTAATTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.47, C:0.14, G:0.15, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:72467 original size:12 final size:12
Alignment explanation
Indices: 72450--72474 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
72440 ACAAAGCACC
72450 ATTTGGTGCCTA
1 ATTTGGTGCCTA
72462 ATTTGGTGCCTA
1 ATTTGGTGCCTA
72474 A
1 A
72475 ATTATTTGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (12 bp):
ATTTGGTGCCTA
Found at i:84957 original size:18 final size:18
Alignment explanation
Indices: 84934--84973 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
84924 GGTTAATTTC
84934 CACCAATAATAACAAATT
1 CACCAATAATAACAAATT
84952 CACCAATAATAACAAATT
1 CACCAATAATAACAAATT
84970 CACC
1 CACC
84974 TTGAAAACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.53, C:0.28, G:0.00, T:0.20
Consensus pattern (18 bp):
CACCAATAATAACAAATT
Found at i:90685 original size:19 final size:19
Alignment explanation
Indices: 90661--90697 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
90651 TGATTAAATT
90661 AGCCG-CCCATTAATGTTGA
1 AGCCGCCCCATT-ATGTTGA
90680 AGCCGCCCCATTATGTTG
1 AGCCGCCCCATTATGTTG
90698 CTTTGATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.27
Consensus pattern (19 bp):
AGCCGCCCCATTATGTTGA
Found at i:98760 original size:24 final size:24
Alignment explanation
Indices: 98728--98780 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
98718 CATAAGATAA
98728 CTGCTCTGAGCCTTCAGAACTTAC
1 CTGCTCTGAGCCTTCAGAACTTAC
98752 CTGCTCTGAGCCTTCAGAACTTAC
1 CTGCTCTGAGCCTTCAGAACTTAC
98776 CTGCT
1 CTGCT
98781 GAGTATCCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.19, C:0.34, G:0.17, T:0.30
Consensus pattern (24 bp):
CTGCTCTGAGCCTTCAGAACTTAC
Found at i:105692 original size:6 final size:6
Alignment explanation
Indices: 105577--105690 Score: 155
Period size: 6 Copynumber: 19.7 Consensus size: 6
105567 ATTAAAAAAA
* *
105577 TTCTTC TTCTTC TTCTCC -T-T-C TTCTCC TTCTCC TTCTCC TTCTCC
1 TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC
105622 TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC TTCT-C
1 TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC
* * *
105669 TTCTTC TTCTTC TTCTTC TTCT
1 TTCTCC TTCTCC TTCTCC TTCT
105691 TCGAAGTACT
Statistics
Matches: 103, Mismatches: 1, Indels: 8
0.92 0.01 0.07
Matches are distributed among these distances:
3 1 0.01
4 2 0.02
5 7 0.07
6 93 0.90
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (6 bp):
TTCTCC
Found at i:107704 original size:17 final size:17
Alignment explanation
Indices: 107675--107710 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
107665 TTTAATATTA
107675 TAATTGTAAATATTTAT
1 TAATTGTAAATATTTAT
107692 TAATT-TAAGATATTTAT
1 TAATTGTAA-ATATTTAT
107709 TA
1 TA
107711 CTTTGAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 3 0.17
17 15 0.83
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
TAATTGTAAATATTTAT
Found at i:108820 original size:37 final size:37
Alignment explanation
Indices: 108778--108859 Score: 137
Period size: 37 Copynumber: 2.2 Consensus size: 37
108768 AACCGATGTA
* *
108778 GATTGAACCGGATTAGGCAACGGTTCCCGGTTGAATC
1 GATTGAACCGGATTAGACAACGATTCCCGGTTGAATC
*
108815 GATTGAACCGGATTAGACAACGATTTCCGGTTGAATC
1 GATTGAACCGGATTAGACAACGATTCCCGGTTGAATC
108852 GATTGAAC
1 GATTGAAC
108860 TGACCGATCC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.26
Consensus pattern (37 bp):
GATTGAACCGGATTAGACAACGATTCCCGGTTGAATC
Found at i:129515 original size:59 final size:59
Alignment explanation
Indices: 129423--129551 Score: 233
Period size: 59 Copynumber: 2.2 Consensus size: 59
129413 TTTGCTCTCC
129423 AAACAAATACCTAATAAAGAATCAATTATGCATACTATAATAAGACTA-CCACTTCAGTT
1 AAACAAATACCTAATAAAGAATCAATTATGCATACTATAATAAGAC-AGCCACTTCAGTT
*
129482 AAACAAATACCTAATAAAGAATCAATTATGCATACTATAATAAGGCAGCCACTTCAGTT
1 AAACAAATACCTAATAAAGAATCAATTATGCATACTATAATAAGACAGCCACTTCAGTT
129541 AAACAAATACC
1 AAACAAATACC
129552 AACAATTGAT
Statistics
Matches: 68, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
58 1 0.01
59 67 0.99
ACGTcount: A:0.48, C:0.19, G:0.08, T:0.25
Consensus pattern (59 bp):
AAACAAATACCTAATAAAGAATCAATTATGCATACTATAATAAGACAGCCACTTCAGTT
Found at i:131861 original size:11 final size:11
Alignment explanation
Indices: 131845--131869 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
131835 TTGATCTCGG
131845 CTACCAAGGTT
1 CTACCAAGGTT
131856 CTACCAAGGTT
1 CTACCAAGGTT
131867 CTA
1 CTA
131870 GTTTTACTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (11 bp):
CTACCAAGGTT
Found at i:135458 original size:18 final size:16
Alignment explanation
Indices: 135430--135473 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 16
135420 TGTTCGTAGG
*
135430 GAATTGAAATATGTGAA
1 GAATTGTAATATGT-AA
135447 GTAATTGTAATATGTAA
1 G-AATTGTAATATGTAA
*
135464 GAATTATAAT
1 GAATTGTAAT
135474 CTAAATTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 8 0.33
17 4 0.17
18 12 0.50
ACGTcount: A:0.45, C:0.00, G:0.18, T:0.36
Consensus pattern (16 bp):
GAATTGTAATATGTAA
Found at i:135473 original size:16 final size:18
Alignment explanation
Indices: 135437--135473 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
135427 AGGGAATTGA
*
135437 AATATGTGAAGTAATTGT
1 AATATGTGAAGTAATTAT
135455 AATATGT-AAG-AATTAT
1 AATATGTGAAGTAATTAT
135471 AAT
1 AAT
135474 CTAAATTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 8 0.44
17 3 0.17
18 7 0.39
ACGTcount: A:0.46, C:0.00, G:0.16, T:0.38
Consensus pattern (18 bp):
AATATGTGAAGTAATTAT
Found at i:147436 original size:16 final size:17
Alignment explanation
Indices: 147410--147454 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
147400 ATTTTGTTAG
*
147410 TAATTTATTTAACTATT
1 TAATTTATTTAAATATT
147427 TAATTT-TTTAAATATT
1 TAATTTATTTAAATATT
* *
147443 TTATTTAATTAA
1 TAATTTATTTAA
147455 TTTTTTTGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (17 bp):
TAATTTATTTAAATATT
Found at i:149692 original size:35 final size:32
Alignment explanation
Indices: 149652--149736 Score: 80
Period size: 35 Copynumber: 2.4 Consensus size: 32
149642 TTATTTTTGT
*
149652 TAATTTTGTTTATTATCATTTAATATCAGTTATTG
1 TAATTTTGTTTATTACCATTTAATA-C--TTATTG
*
149687 TAATTTGGTTATTATTTACCATTTAATACTTATTG
1 TAATTTTG-T-TTA-TTACCATTTAATACTTATTG
*
149722 TAAGTTTGTTGTATT
1 TAATTTTGTT-TATT
149737 TAAAATTATA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
33 3 0.07
34 3 0.07
35 19 0.45
36 1 0.02
37 4 0.10
38 12 0.29
ACGTcount: A:0.27, C:0.06, G:0.11, T:0.56
Consensus pattern (32 bp):
TAATTTTGTTTATTACCATTTAATACTTATTG
Found at i:155792 original size:21 final size:21
Alignment explanation
Indices: 155766--155818 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
155756 ATTCTGACTA
155766 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
155787 TCGCATTGTGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
155808 TCGCAATGCGA
1 TCGCATTGCGA
155819 ATATGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:155833 original size:20 final size:20
Alignment explanation
Indices: 155808--155858 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
155798 TTTTCCTAAT
155808 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATATGTAAA
155828 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATATGTAAA
*
155848 TCGCAACGCGA
1 TCGCAATGCGA
155859 TTCTGACTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATATGTAAA
Found at i:155870 original size:20 final size:20
Alignment explanation
Indices: 155847--155919 Score: 128
Period size: 20 Copynumber: 3.6 Consensus size: 20
155837 GAATATGTAA
155847 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
155867 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
155887 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
155907 ATCACAACGCGAT
1 ATCGCAACGCGAT
155920 GCTGTCGCAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:155871 original size:40 final size:40
Alignment explanation
Indices: 155827--155918 Score: 114
Period size: 40 Copynumber: 2.3 Consensus size: 40
155817 GAATATGTAA
*
155827 ATCGCAATGCGAATATGTA-AATCGCAACGCGATTCTGACT
1 ATCGCAACGCGAATATG-ACAATCGCAACGCGATTCTGACT
* * * *
155867 ATCGCAACGAGATTCTGACTATCGCAACGCGATTCTGACT
1 ATCGCAACGCGAATATGACAATCGCAACGCGATTCTGACT
*
155907 ATCACAACGCGA
1 ATCGCAACGCGA
155919 TGCTGTCGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
39 1 0.02
40 43 0.98
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.23
Consensus pattern (40 bp):
ATCGCAACGCGAATATGACAATCGCAACGCGATTCTGACT
Found at i:156802 original size:24 final size:24
Alignment explanation
Indices: 156749--156804 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
156739 CGATATTCGA
156749 ATTTTGATCTTGGTCAATACCCAG
1 ATTTTGATCTTGGTCAATACCCAG
* * *
156773 ACTTTGATCTTGGTCAATACTCGG
1 ATTTTGATCTTGGTCAATACCCAG
156797 ATTTTGAT
1 ATTTTGAT
156805 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41
Consensus pattern (24 bp):
ATTTTGATCTTGGTCAATACCCAG
Found at i:159082 original size:18 final size:18
Alignment explanation
Indices: 159059--159093 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
159049 AGAAAAAGGC
*
159059 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
159077 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
159094 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:159289 original size:20 final size:20
Alignment explanation
Indices: 159264--159374 Score: 126
Period size: 20 Copynumber: 5.8 Consensus size: 20
159254 TTACACATTC
159264 ATTTGAATATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
* *
159284 ATTTGACTATCGCAACGCGG
1 ATTTGAATATCGCAACGCGA
* *
159304 ATTTGATTATCGCAACTC-A
1 ATTTGAATATCGCAACGCGA
159323 A----AA-ATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
*
159338 ATTTGACTATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
*
159358 ATTTGATTATCGCAACG
1 ATTTGAATATCGCAACG
159375 GGTATTCGAC
Statistics
Matches: 76, Mismatches: 9, Indels: 12
0.78 0.09 0.12
Matches are distributed among these distances:
14 9 0.12
15 3 0.04
19 2 0.03
20 62 0.82
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (20 bp):
ATTTGAATATCGCAACGCGA
Found at i:159353 original size:74 final size:75
Alignment explanation
Indices: 159264--159443 Score: 226
Period size: 74 Copynumber: 2.4 Consensus size: 75
159254 TTACACATTC
* * **
159264 ATTTGAATATCGCAACGCGAATTTGACTATCGCAACGCGG-ATTTGATTATCGCAACTCA-AAAA
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACG-GGTATTCGACCATCGCAAC-CAGAAAA
*
159327 TCGCAACGCG-A
64 TCGCAAAGCGTA
* *
159338 ATTTGACTATCGCAACGCGAATTTGATTATCGCAACGGGTATTCGACCATCGCAACGAGAAAATC
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGGGTATTCGACCATCGCAACCAGAAAATC
159403 GCAAAGCGTA
66 GCAAAGCGTA
* *
159413 A-TAGACTATCGCAACGCGAA-TTGACTTTCGC
1 ATTTGACTATCGCAACGCGAATTTGACTATCGC
159444 GTTGCGATTT
Statistics
Matches: 93, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
73 12 0.13
74 79 0.85
75 2 0.02
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (75 bp):
ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGGGTATTCGACCATCGCAACCAGAAAATC
GCAAAGCGTA
Found at i:159629 original size:14 final size:14
Alignment explanation
Indices: 159592--159630 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
159582 TAAATATTAA
*
159592 ACAAATCAACTTTT
1 ACAAATCAATTTTT
159606 ACAAATCAATTTTT
1 ACAAATCAATTTTT
159620 ACAAATCAATT
1 ACAAATCAATT
159631 AAACAAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.36
Consensus pattern (14 bp):
ACAAATCAATTTTT
Found at i:161138 original size:42 final size:42
Alignment explanation
Indices: 161031--161140 Score: 107
Period size: 42 Copynumber: 2.6 Consensus size: 42
161021 TCTAGAATGT
* * *
161031 TGGGAG-GGACCTCTTCAACGATGACAGTGGCCTCTGGAACGG
1 TGGGAGAGG-CCTCTTGAACGATGACAGGGGCCTCTGGAACGA
* * ** * *
161073 TGGGAGTGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGA
1 TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTGGAACGA
161115 TAGGG-GAGGCCTCTTGAACGATGACA
1 T-GGGAGAGGCCTCTTGAACGATGACA
161141 AGTGAGTCGG
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
42 48 0.91
43 5 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.21
Consensus pattern (42 bp):
TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTGGAACGA
Found at i:161724 original size:20 final size:20
Alignment explanation
Indices: 161699--161744 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
161689 GATTCTTTCG
161699 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
161719 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
161739 TTGCGA
1 TTGCGA
161745 AAGTAAACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:161919 original size:18 final size:18
Alignment explanation
Indices: 161896--161941 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
161886 CTAAGCAATC
161896 TAAGTGAAATGGTTAATA
1 TAAGTGAAATGGTTAATA
*
161914 TAAGTGAAATGGTTAATC
1 TAAGTGAAATGGTTAATA
161932 TAAGTGAAAT
1 TAAGTGAAAT
161942 TACAAGTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.43, C:0.02, G:0.22, T:0.33
Consensus pattern (18 bp):
TAAGTGAAATGGTTAATA
Found at i:163694 original size:19 final size:20
Alignment explanation
Indices: 163658--163743 Score: 106
Period size: 19 Copynumber: 4.5 Consensus size: 20
163648 TATGAAACTT
163658 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
163678 AAAATCGCAAC-CGAAAATG
1 AAAATCGCAACACGAAAATG
** *
163697 ACTATCGCAACCCG-AAATG
1 AAAATCGCAACACGAAAATG
* *
163716 AAAATCGCAACGCGAAACT-
1 AAAATCGCAACACGAAAATG
163735 AAAATCGCA
1 AAAATCGCA
163744 TTGCGATTCT
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
19 42 0.72
20 16 0.28
ACGTcount: A:0.49, C:0.24, G:0.15, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:164156 original size:22 final size:22
Alignment explanation
Indices: 164125--164181 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
164115 GATGGAGATA
*
164125 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
* *
164147 GACTGATTTCGTCAGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
*
164169 GACGGATGTCGCC
1 GACGGATTTCGCC
164182 TTAGAGAGTG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.19, C:0.19, G:0.40, T:0.21
Consensus pattern (22 bp):
GACGGATTTCGCCAGAGATGGG
Found at i:164378 original size:20 final size:20
Alignment explanation
Indices: 164348--164421 Score: 121
Period size: 20 Copynumber: 3.7 Consensus size: 20
164338 GCGCTTTGAA
*
164348 AATCGCATTGCGATAGTTAG
1 AATCGCATTGCGATAGTCAG
* *
164368 CATCGCGTTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
164388 AATCGCATTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
164408 AATCGCATTGCGAT
1 AATCGCATTGCGAT
164422 TTACATATTC
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (20 bp):
AATCGCATTGCGATAGTCAG
Found at i:164433 original size:20 final size:20
Alignment explanation
Indices: 164410--164460 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
164400 ATAGTCAGAA
164410 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
164430 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
164450 TCGCATTGCGA
1 TCGCATTGCGA
164461 ATTCGGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:164481 original size:21 final size:21
Alignment explanation
Indices: 164457--164502 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
164447 TATTCGCATT
164457 GCGAATTCGGAAAATCGCAAC
1 GCGAATTCGGAAAATCGCAAC
* *
164478 GCGAATTTGGAAAATCGCAAT
1 GCGAATTCGGAAAATCGCAAC
164499 GCGA
1 GCGA
164503 TAATCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.37, C:0.20, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTCGGAAAATCGCAAC
Found at i:176601 original size:2 final size:2
Alignment explanation
Indices: 176590--176619 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
176580 TAATTAAAAA
*
176590 AT AT AG 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
176620 TAGAACTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:187845 original size:21 final size:21
Alignment explanation
Indices: 187819--187866 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
187809 TCAAGTAGGA
*
187819 GATTGTTGACAATTGCGCATG
1 GATTGTTGACAATTACGCATG
*
187840 GATTGTTGATAATTACGCATG
1 GATTGTTGACAATTACGCATG
187861 GCATTG
1 G-ATTG
187867 CATGGGATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.35
Consensus pattern (21 bp):
GATTGTTGACAATTACGCATG
Found at i:191352 original size:17 final size:18
Alignment explanation
Indices: 191315--191355 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
191305 ATATTATGTA
*
191315 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
191333 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
191350 TTTACT
1 TTTACT
191356 AATATAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:193061 original size:18 final size:18
Alignment explanation
Indices: 193034--193073 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
193024 ACAGCAGCCA
* *
193034 CCGCAGCCATTTATGATG
1 CCGCAACCATATATGATG
193052 CCGCAACCATATATGATG
1 CCGCAACCATATATGATG
193070 CCGC
1 CCGC
193074 CATCGCCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.25, C:0.33, G:0.20, T:0.23
Consensus pattern (18 bp):
CCGCAACCATATATGATG
Found at i:193623 original size:26 final size:24
Alignment explanation
Indices: 193552--193623 Score: 62
Period size: 26 Copynumber: 3.0 Consensus size: 24
193542 TTATATTTGT
193552 ATTTACTTTATTTTGTTAAATTGTA
1 ATTTACTTTATTTTGTTAAATT-TA
*
193577 ATTT--TTTATTATT-TCT-TATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
193599 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
193624 GTTGGACTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 15
0.69 0.04 0.28
Matches are distributed among these distances:
22 4 0.11
23 10 0.27
24 5 0.14
25 7 0.19
26 11 0.30
ACGTcount: A:0.26, C:0.06, G:0.04, T:0.64
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:200008 original size:23 final size:24
Alignment explanation
Indices: 199981--200025 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
199971 ACTCAAAAAT
199981 AAATA-TTAATTAA-AAATAATATA
1 AAATACTT-ATTAAGAAATAATATA
*
200004 AAATACTTCTTAAGAAATAATA
1 AAATACTTATTAAGAAATAATA
200026 ACATCCTCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATACTTATTAAGAAATAATATA
Found at i:200718 original size:18 final size:18
Alignment explanation
Indices: 200691--200734 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
200681 TTTTAAAATT
200691 TATAATATAATCAAAATAAA
1 TATAA-ATAAT-AAAATAAA
*
200711 T-TAAATAATAAAATGAA
1 TATAAATAATAAAATAAA
200728 TATAAAT
1 TATAAAT
200735 GGTTACAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 8 0.36
18 10 0.45
19 3 0.14
20 1 0.05
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (18 bp):
TATAAATAATAAAATAAA
Found at i:206002 original size:21 final size:20
Alignment explanation
Indices: 205976--206014 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
205966 ATTATATTTC
*
205976 AAAATATTATTTTTTTAAAGA
1 AAAATA-TATTTTTCTAAAGA
205997 AAAATATATTTTTCTAAA
1 AAAATATATTTTTCTAAA
206015 TTAATCGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (20 bp):
AAAATATATTTTTCTAAAGA
Found at i:210000 original size:29 final size:29
Alignment explanation
Indices: 209967--210037 Score: 133
Period size: 29 Copynumber: 2.4 Consensus size: 29
209957 ACATGACAGA
209967 CTCAACAAGGCTTAACTAACATACTGTTT
1 CTCAACAAGGCTTAACTAACATACTGTTT
*
209996 CTCAACTAGGCTTAACTAACATACTGTTT
1 CTCAACAAGGCTTAACTAACATACTGTTT
210025 CTCAACAAGGCTT
1 CTCAACAAGGCTT
210038 GCACAGAATG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.32, C:0.25, G:0.11, T:0.31
Consensus pattern (29 bp):
CTCAACAAGGCTTAACTAACATACTGTTT
Found at i:221031 original size:23 final size:23
Alignment explanation
Indices: 221005--221048 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
220995 TACCATTAAA
**
221005 TGTAACACCCTTAACCCATACCC
1 TGTAACACCCCCAACCCATACCC
221028 TGTAACACCCCCAACCCATAC
1 TGTAACACCCCCAACCCATAC
221049 TCGACCCGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.45, G:0.05, T:0.18
Consensus pattern (23 bp):
TGTAACACCCCCAACCCATACCC
Found at i:221852 original size:23 final size:23
Alignment explanation
Indices: 221818--221878 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
221808 CTCATATAAA
* **
221818 TGCACCGAAGTGCTGCGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
221841 TGCACCGTAGTGCCACGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
*
221864 TGCACCGTGGTGCCA
1 TGCACCGTAGTGCCA
221879 TATAATAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.23, C:0.26, G:0.30, T:0.21
Consensus pattern (23 bp):
TGCACCGTAGTGCCACGTAGAAT
Found at i:223521 original size:8 final size:8
Alignment explanation
Indices: 223488--223521 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
223478 TCGGTTCCCC
*
223488 TCTGGCAT
1 TCTGGAAT
223496 TCTGGAAT
1 TCTGGAAT
*
223504 TATGGAAT
1 TCTGGAAT
223512 TCTGGAAT
1 TCTGGAAT
223520 TC
1 TC
223522 CATGTTCGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.38
Consensus pattern (8 bp):
TCTGGAAT
Found at i:224193 original size:2 final size:2
Alignment explanation
Indices: 224186--224214 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
224176 TAATTTAGTG
224186 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
224215 TTAAAAATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:225207 original size:18 final size:19
Alignment explanation
Indices: 225171--225207 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
225161 GTCTTCCTTC
*
225171 GTTTTTTTTTCTCGTTTCT
1 GTTTTTTTTTCTCGGTTCT
225190 GTTTTTTTTT-TCGGTTCT
1 GTTTTTTTTTCTCGGTTCT
225208 TCCTCTCTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.00, C:0.14, G:0.14, T:0.73
Consensus pattern (19 bp):
GTTTTTTTTTCTCGGTTCT
Found at i:225583 original size:3 final size:3
Alignment explanation
Indices: 225575--225619 Score: 54
Period size: 3 Copynumber: 14.3 Consensus size: 3
225565 TATATATATT
* *
225575 TAA TAA TAAA TAA TAA TAA TAA TATA TTA TAT TAA TAA TAA TAA T
1 TAA TAA T-AA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA T
225620 TATTATTATG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
3 31 0.86
4 5 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:225596 original size:16 final size:16
Alignment explanation
Indices: 225575--225619 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
225565 TATATATATT
225575 TAATAATAAATAATAA
1 TAATAATAAATAATAA
* * *
225591 TAATAATATATTATAT
1 TAATAATAAATAATAA
225607 TAATAAT-AATAAT
1 TAATAATAAATAAT
225620 TATTATTATG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
15 4 0.17
16 20 0.83
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TAATAATAAATAATAA
Found at i:225610 original size:19 final size:19
Alignment explanation
Indices: 225588--225627 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
225578 TAATAAATAA
225588 TAATAATAATATATTA-TAT
1 TAATAATAATA-ATTATTAT
225607 TAATAATAATAATTATTAT
1 TAATAATAATAATTATTAT
225626 TA
1 TA
225628 TGAAAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TAATAATAATAATTATTAT
Found at i:225621 original size:13 final size:13
Alignment explanation
Indices: 225575--225621 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
225565 TATATATATT
*
225575 TAATAATAAATAA
1 TAATAATTAATAA
225588 TAATAA-TAAT-A
1 TAATAATTAATAA
*
225599 TATTATATTAATAA
1 TAATA-ATTAATAA
225613 TAATAATTA
1 TAATAATTA
225622 TTATTATGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
11 5 0.18
12 4 0.14
13 14 0.50
14 5 0.18
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TAATAATTAATAA
Found at i:226556 original size:23 final size:23
Alignment explanation
Indices: 226530--226596 Score: 134
Period size: 23 Copynumber: 2.9 Consensus size: 23
226520 AAGTACCGCA
226530 TAGAATTGCACCGTAGTGCCACG
1 TAGAATTGCACCGTAGTGCCACG
226553 TAGAATTGCACCGTAGTGCCACG
1 TAGAATTGCACCGTAGTGCCACG
226576 TAGAATTGCACCGTAGTGCCA
1 TAGAATTGCACCGTAGTGCCA
226597 TATAATAATG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.22
Consensus pattern (23 bp):
TAGAATTGCACCGTAGTGCCACG
Found at i:230079 original size:198 final size:197
Alignment explanation
Indices: 229442--230141 Score: 827
Period size: 199 Copynumber: 3.5 Consensus size: 197
229432 ACCTAAATAT
* * * *
229442 GTGTCGATACATTT-TCTAAAAGTATCGACCCAAAAAACATCAAAACCAATAATTATAATGTAAT
1 GTGTCGATACATTTAT-AAAAAGTATCGATCCAAAAAACATCGAAACCGATAATTATAATGTAAT
* * * * *
229506 AGGTAAATTAACAATGTAACCGGTATAAATATACCGG-TTAAT-TAGAAAACATGTAAACATAAT
65 AGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGT-GAAAATAGGT-CACATAAT
* * *
229569 GTATCGACACTTGTTTAGTTTGTGTCGATACTTATTGTCCAGAATGAATGCCCAAATGGGTGCAC
128 GTATCGACACTTATTTAATTTGTGTCGATACTT-TT-TCCAGAATGAATGCCCAAAAGGGTGCAC
229634 GCATAAA
191 GCATAAA
* * * * *
229641 ATGTCGATACAATTATTAAAAGTATCGATCCCAATAAA-ATCGAAACTGATAATTATAATGTAAT
1 GTGTCGATACATTTATAAAAAGTATCGAT-CCAAAAAACATCGAAACCGATAATTATAATGTAAT
* * * * *
229705 ATGTAAATTTACAATGTAACAGGTATAAATATACCGGTCTTATGAGAAAATAGGTCATCATAAAG
65 AGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGTGAAAATAGGTCA-CATAATG
* * * * * * * *
229770 TATCGATACTTATTAAATTTGTGTAGATATTTTTTTTCCATAATGAATG-CCAGACGGGTGCACT
129 TATCGACACTTATTTAATTTGTGTCGATA--CTTTTTCCAGAATGAATGCCCAAAAGGGTGCACG
229834 CATAAA
192 CATAAA
* *
229840 GTGTCGATACATTTTTAAAAAGTATCGATCCAAAAAACATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCAAAAAACATCGAAACCGATAATTATAATGTAATA
* * ** * ** *
229905 GGCAATTTTGTAATATAACCGGTATATTTATACCGGTTTTATGTGAGAATAGGTCTACATAATGT
66 GGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGTGAAAATAGGTC-ACATAATGT
* * *
229970 GTCGACACTT-TTTAATGTTGTGTCGATACTTTTTCCAGAATGAATGCCCAAAAAGGTGAACGCA
130 ATCGACACTTATTTAAT-TTGTGTCGATACTTTTTCCAGAATGAATGCCCAAAAGGGTGCACGCA
*
230034 TATA
194 TAAA
*
230038 GTGTCGATACATTTATAAAAAGTATCGATCCAAAAAACATCGAAGCCGATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCAAAAAACATCGAAACCGATAATTATAATGTAATA
* * *
230103 GGTAAATTTGCAATGTTACCGGTATAAATATACCAGTTT
66 GGTAAATTTACAATGTAACCGGTATAAATATACCGGTTT
230142 ACTTATAAAA
Statistics
Matches: 420, Mismatches: 70, Indels: 23
0.82 0.14 0.04
Matches are distributed among these distances:
197 16 0.04
198 120 0.29
199 218 0.52
200 62 0.15
201 2 0.00
202 2 0.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (197 bp):
GTGTCGATACATTTATAAAAAGTATCGATCCAAAAAACATCGAAACCGATAATTATAATGTAATA
GGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGTGAAAATAGGTCACATAATGTA
TCGACACTTATTTAATTTGTGTCGATACTTTTTCCAGAATGAATGCCCAAAAGGGTGCACGCATA
AA
Found at i:230264 original size:87 final size:86
Alignment explanation
Indices: 230159--230325 Score: 289
Period size: 87 Copynumber: 1.9 Consensus size: 86
230149 AAATAGGTCA
230159 ATATAAGCGCTACATATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACATATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
*
230224 TTGGTTAAATACATATTTTATT
66 TCGGTTAAATA-ATATTTTATT
* * *
230246 ATATAAGCGCTACCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATCTTT
1 ATATAAGCGCTACATATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
230311 TCGGTTAAATAATAT
66 TCGGTTAAATAATAT
230326 AACATAACCA
Statistics
Matches: 76, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
86 4 0.05
87 72 0.95
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.43
Consensus pattern (86 bp):
ATATAAGCGCTACATATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
TCGGTTAAATAATATTTTATT
Found at i:230293 original size:23 final size:23
Alignment explanation
Indices: 230243--230287 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
230233 TACATATTTT
*
230243 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
*
230266 ATTATATAAGCGTTACCTAATA
1 ATTATATAAGCGCTACCTAATA
230288 TGTTATTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.36
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:230810 original size:20 final size:19
Alignment explanation
Indices: 230770--230811 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
230760 ATTAGGAATA
* *
230770 TAATTAAATTATATTTTTT
1 TAATTAAATTATAATTATT
230789 TAATTAAAATTATAATTATT
1 TAATT-AAATTATAATTATT
230809 TAA
1 TAA
230812 GAATTTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TAATTAAATTATAATTATT
Found at i:242622 original size:28 final size:28
Alignment explanation
Indices: 242511--242614 Score: 199
Period size: 28 Copynumber: 3.7 Consensus size: 28
242501 GAGCATTACT
242511 TTACTTGATGAACAACGATAGGTTATCA
1 TTACTTGATGAACAACGATAGGTTATCA
242539 TTACTTGATGAACAACGATAGGTTATCA
1 TTACTTGATGAACAACGATAGGTTATCA
242567 TTACTTGATGAACAACGATAGGTTATCA
1 TTACTTGATGAACAACGATAGGTTATCA
*
242595 TTCCTTGATGAACAACGATA
1 TTACTTGATGAACAACGATA
242615 AATTATCACG
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
28 75 1.00
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (28 bp):
TTACTTGATGAACAACGATAGGTTATCA
Found at i:243749 original size:21 final size:21
Alignment explanation
Indices: 243715--243763 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
243705 CATGTCTTAT
*
243715 AGGGAAGCTCTTGGAAGAATGC
1 AGGG-AGCTATTGGAAGAATGC
* *
243737 AGGGAGCTATTGGAGGAGTGC
1 AGGGAGCTATTGGAAGAATGC
243758 AGGGAG
1 AGGGAG
243764 ATGAGGATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.29, C:0.10, G:0.45, T:0.16
Consensus pattern (21 bp):
AGGGAGCTATTGGAAGAATGC
Found at i:243826 original size:19 final size:19
Alignment explanation
Indices: 243802--243838 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
243792 CTTTAAACAT
243802 ACATATAAAGATAGTGCAG
1 ACATATAAAGATAGTGCAG
243821 ACATATAAAGATAGTGCA
1 ACATATAAAGATAGTGCA
243839 TCAGAAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.11, G:0.19, T:0.22
Consensus pattern (19 bp):
ACATATAAAGATAGTGCAG
Found at i:265836 original size:31 final size:32
Alignment explanation
Indices: 265795--265865 Score: 135
Period size: 31 Copynumber: 2.2 Consensus size: 32
265785 AACATGCATT
265795 CATTCATTCATGTTTATGGTCACAGAATATAA
1 CATTCATTCATGTTTATGGTCACAGAATATAA
265827 CA-TCATTCATGTTTATGGTCACAGAATATAA
1 CATTCATTCATGTTTATGGTCACAGAATATAA
265858 CATTCATT
1 CATTCATT
265866 TTTGTGATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
31 31 0.82
32 7 0.18
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (32 bp):
CATTCATTCATGTTTATGGTCACAGAATATAA
Found at i:270598 original size:27 final size:26
Alignment explanation
Indices: 270543--270599 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
270533 AAATTAAATC
* *
270543 TTAAACTATTTTAAATAAAATCATTA
1 TTAAACTATTTTAAATAAAATAATAA
*
270569 TTAAATTATGTTT-AATAAATATAATAA
1 TTAAACTAT-TTTAAATAAA-ATAATAA
270596 TTAA
1 TTAA
270600 TTGGTTTAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 14 0.54
27 12 0.46
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (26 bp):
TTAAACTATTTTAAATAAAATAATAA
Found at i:279459 original size:24 final size:23
Alignment explanation
Indices: 279427--279474 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
279417 AAAAATCAAA
*
279427 AGCTCGATTGAAACTCGAGACTCG
1 AGCTCGATTCAAACTCGA-ACTCG
*
279451 AGCTCGATTCAAGCTCGAACTCG
1 AGCTCGATTCAAACTCGAACTCG
279474 A
1 A
279475 TTCAAGCTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.29, C:0.27, G:0.23, T:0.21
Consensus pattern (23 bp):
AGCTCGATTCAAACTCGAACTCG
Found at i:279473 original size:17 final size:17
Alignment explanation
Indices: 279447--279645 Score: 247
Period size: 17 Copynumber: 11.6 Consensus size: 17
279437 AAACTCGAGA
*
279447 CTCGAGCTCGATTCAAG
1 CTCGAACTCGATTCAAG
279464 CTCGAACTCGATTCAAG
1 CTCGAACTCGATTCAAG
279481 CTCGAACTCGATTCAAG
1 CTCGAACTCGATTCAAG
* * *
279498 CTCAAACTCAAACTCGAA-
1 CTCGAACTC-GATTC-AAG
* * * *
279516 TTTGAGCTCGGTTCAAG
1 CTCGAACTCGATTCAAG
* *
279533 CTCAAACTCGATTTAAG
1 CTCGAACTCGATTCAAG
279550 CTCGAACTCGATTCAAG
1 CTCGAACTCGATTCAAG
279567 CTCGAACTCGATTCAAG
1 CTCGAACTCGATTCAAG
279584 CTCGAACTCGATTCAAG
1 CTCGAACTCGATTCAAG
* *
279601 CTCAAATTCGATTCAAG
1 CTCGAACTCGATTCAAG
*
279618 CTCAAACTCGATTCAAG
1 CTCGAACTCGATTCAAG
*
279635 CTAGAACTCGA
1 CTCGAACTCGA
279646 ACTCGAATTT
Statistics
Matches: 155, Mismatches: 24, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
16 2 0.01
17 143 0.92
18 8 0.05
19 2 0.01
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.25
Consensus pattern (17 bp):
CTCGAACTCGATTCAAG
Found at i:279531 original size:29 final size:28
Alignment explanation
Indices: 279499--279553 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
279489 CGATTCAAGC
*
279499 TCAAACTCAAACTCGAATTTGAGCTCGGT
1 TCAAACTCAAACTCG-ATTTAAGCTCGGT
*
279528 TCAAGCTCAAACTCGATTTAAGCTCG
1 TCAAACTCAAACTCGATTTAAGCTCG
279554 AACTCGATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 10 0.42
29 14 0.58
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.27
Consensus pattern (28 bp):
TCAAACTCAAACTCGATTTAAGCTCGGT
Found at i:282100 original size:7 final size:7
Alignment explanation
Indices: 282088--282184 Score: 94
Period size: 7 Copynumber: 13.9 Consensus size: 7
282078 GTGTATAAAT
282088 TAAACCA
1 TAAACCA
282095 TAAACCA
1 TAAACCA
282102 TAAACCA
1 TAAACCA
*
282109 TGAATCC-
1 T-AAACCA
282116 TAAACCA
1 TAAACCA
*
282123 TGAATCC-
1 T-AAACCA
282130 TAAACCA
1 TAAACCA
*
282137 TAAACCT
1 TAAACCA
282144 TAAATCC-
1 TAAA-CCA
282151 TAAACCA
1 TAAACCA
*
282158 TAAACCC
1 TAAACCA
282165 TAAAACC-
1 T-AAACCA
282172 TAAACCA
1 TAAACCA
282179 TAAACC
1 TAAACC
282185 CTATCATATA
Statistics
Matches: 76, Mismatches: 6, Indels: 16
0.78 0.06 0.16
Matches are distributed among these distances:
6 15 0.20
7 46 0.61
8 15 0.20
ACGTcount: A:0.49, C:0.30, G:0.02, T:0.19
Consensus pattern (7 bp):
TAAACCA
Found at i:282141 original size:35 final size:35
Alignment explanation
Indices: 282088--282187 Score: 130
Period size: 35 Copynumber: 2.9 Consensus size: 35
282078 GTGTATAAAT
* *
282088 TAAACCATAAACCATAAACCATGAATCCTAAACCA
1 TAAACCCTAAACCATAAACCATAAATCCTAAACCA
* * *
282123 TGAATCCTAAACCATAAACCTTAAATCCTAAACCA
1 TAAACCCTAAACCATAAACCATAAATCCTAAACCA
*
282158 TAAACCCTAAAACC-TAAACCATAAACCCTA
1 TAAACCCT-AAACCATAAACCATAAATCCTA
282188 TCATATAATT
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
35 50 0.91
36 5 0.09
ACGTcount: A:0.49, C:0.30, G:0.02, T:0.19
Consensus pattern (35 bp):
TAAACCCTAAACCATAAACCATAAATCCTAAACCA
Found at i:282187 original size:21 final size:21
Alignment explanation
Indices: 282088--282184 Score: 108
Period size: 21 Copynumber: 4.6 Consensus size: 21
282078 GTGTATAAAT
282088 TAAACCATAAACCAT-AAACC
1 TAAACCATAAACCATAAAACC
* * *
282108 ATGAATCC-TAAACCATGAATCC
1 -T-AAACCATAAACCATAAAACC
* *
282130 TAAACCATAAACCTTAAATCC
1 TAAACCATAAACCATAAAACC
*
282151 TAAACCATAAACCCTAAAACC
1 TAAACCATAAACCATAAAACC
282172 TAAACCATAAACC
1 TAAACCATAAACC
282185 CTATCATATA
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
20 4 0.06
21 54 0.82
22 8 0.12
ACGTcount: A:0.49, C:0.30, G:0.02, T:0.19
Consensus pattern (21 bp):
TAAACCATAAACCATAAAACC
Found at i:282284 original size:14 final size:14
Alignment explanation
Indices: 282265--282294 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
282255 TATAATTATC
*
282265 AATAATGTATTTTT
1 AATAATGTAATTTT
282279 AATAATGTAATTTT
1 AATAATGTAATTTT
282293 AA
1 AA
282295 AAAATCTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
AATAATGTAATTTT
Found at i:285887 original size:23 final size:23
Alignment explanation
Indices: 285854--285915 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
285844 CTCGTATAAA
*
285854 TGCACCTAAGTGCCATGTAGAAT
1 TGCACCGAAGTGCCATGTAGAAT
* **
285877 TGCACCGAAGTACCGCGTAGAAT
1 TGCACCGAAGTGCCATGTAGAAT
285900 TGCACCGAAGTGCCAT
1 TGCACCGAAGTGCCAT
285916 ACAAAATGTC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.29, C:0.26, G:0.24, T:0.21
Consensus pattern (23 bp):
TGCACCGAAGTGCCATGTAGAAT
Found at i:286854 original size:3 final size:3
Alignment explanation
Indices: 286784--286841 Score: 68
Period size: 3 Copynumber: 19.7 Consensus size: 3
286774 TTTATTTGAA
*
286784 TAT TAT T-T ATAT T-T TAT TAT TAT TAT TAT TAT AAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
286828 ATAT T-T TAT TAT TA
1 -TAT TAT TAT TAT TA
286842 ATAAATATTA
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
2 5 0.10
3 39 0.81
4 4 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:288591 original size:11 final size:13
Alignment explanation
Indices: 288553--288593 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 13
288543 TTTAATATAT
288553 ATATATATATATTA
1 ATATAT-TATATTA
*
288567 ATATATTATCTTA
1 ATATATTATATTA
288580 A-A-ATTATATTA
1 ATATATTATATTA
288591 ATA
1 ATA
288594 AACTTAACAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 9 0.38
12 2 0.08
13 7 0.29
14 6 0.25
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (13 bp):
ATATATTATATTA
Found at i:290993 original size:28 final size:27
Alignment explanation
Indices: 290951--291014 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
290941 AGAGTCGAGG
290951 GTTCTACGTGATCCTACAGGACATATGT
1 GTTCTACGTGATCCTACAGGACATA-GT
* * * *
290979 GTTCTATGTGGTCCTTCGGGACATAGT
1 GTTCTACGTGATCCTACAGGACATAGT
291006 GTTCCTACG
1 GTT-CTACG
291015 GGACAAATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 5 0.17
28 25 0.83
ACGTcount: A:0.19, C:0.22, G:0.25, T:0.34
Consensus pattern (27 bp):
GTTCTACGTGATCCTACAGGACATAGT
Found at i:292574 original size:15 final size:15
Alignment explanation
Indices: 292556--292589 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
292546 ACCTGAAATA
292556 TGTTATATGGTTACC
1 TGTTATATGGTTACC
292571 TGTTATATGGTTACC
1 TGTTATATGGTTACC
292586 TGTT
1 TGTT
292590 TCACTGTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.18, C:0.12, G:0.21, T:0.50
Consensus pattern (15 bp):
TGTTATATGGTTACC
Found at i:292743 original size:35 final size:35
Alignment explanation
Indices: 292694--292760 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
292684 TACAGTATGG
*
292694 AGGTTCAGCTCGATCAAATTGGTAATTCCTTATAT
1 AGGTTCAGCTCGATCAAACTGGTAATTCCTTATAT
* *
292729 AGGTTCAGAC-CGATCGAGCTGGTAATTCCTTA
1 AGGTTCAG-CTCGATCAAACTGGTAATTCCTTA
292761 CGGACCTAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 27 0.96
36 1 0.04
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (35 bp):
AGGTTCAGCTCGATCAAACTGGTAATTCCTTATAT
Found at i:294461 original size:23 final size:23
Alignment explanation
Indices: 294435--294512 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
294425 CACCACAGCT
294435 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
294458 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* * *
294481 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
294504 TATAATAAT
1 CAT-ATAAT
294513 GTCCATAAGG
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 41 0.91
24 4 0.09
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:294690 original size:103 final size:103
Alignment explanation
Indices: 294522--294839 Score: 555
Period size: 103 Copynumber: 3.1 Consensus size: 103
294512 TGTCCATAAG
* * * *
294522 GACCACATATCATTCCTTAATAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAACAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
* *
294587 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAT
66 TTCACACATGTTCCAAAGAATACATATATATCCCGAAA
294625 GACCACATATCATTCCTTAACAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAACAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
294690 TTCACACATGTTCCAAAGAATACATATATATCCCGAAA
66 TTCACACATGTTCCAAAGAATACATATATATCCCGAAA
*
294728 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAACAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
* *
294793 TTCACACATGTTCCAAAGAATACATATATATCTCGAAG
66 TTCACACATGTTCCAAAGAATACATATATATCCCGAAA
294831 GACCACATA
1 GACCACATA
294840 GACCCTCGAC
Statistics
Matches: 206, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 206 1.00
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (103 bp):
GACCACATATCATTCCTTAACAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
TTCACACATGTTCCAAAGAATACATATATATCCCGAAA
Found at i:295683 original size:64 final size:62
Alignment explanation
Indices: 295576--295695 Score: 168
Period size: 64 Copynumber: 1.9 Consensus size: 62
295566 TAATGAAGGT
* *
295576 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATACATTCGATGTTTATTTATTACTGGG
1 ATGCATCGATGCACTACTGATGCATCGATGCACAAAATACATTCGATG--TATTTATTACTGGG
* * * *
295640 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTATTTATT
1 ATGCATCGATGCACTACTGATGCATCGATGCACAAAATACATTCGATGTATTTATT
295696 TTAAAAGAGT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
62 8 0.16
64 42 0.84
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (62 bp):
ATGCATCGATGCACTACTGATGCATCGATGCACAAAATACATTCGATGTATTTATTACTGGG
Found at i:295709 original size:64 final size:64
Alignment explanation
Indices: 295576--295732 Score: 165
Period size: 64 Copynumber: 2.5 Consensus size: 64
295566 TAATGAAGGT
* * * * ** *
295576 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATACATTCGATGTTTATTTATTACTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAAATACATTCGATGTTTATTTATAAAAGAG
* * *
295640 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTATTTATTT-TAAAAGA
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAAATACATTCGATG--TTTATTTATAAAAGA
295704 G
64 G
* * *
295705 -TGCATCGATGCACTTCCTGTGCATCGAT
1 ATGCATCGATGCACTACTTATGCATCGAT
295733 ACACCTTCAA
Statistics
Matches: 78, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
64 67 0.86
65 4 0.05
66 7 0.09
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACAAAATACATTCGATGTTTATTTATAAAAGAG
Found at i:297916 original size:15 final size:16
Alignment explanation
Indices: 297889--297918 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
297879 AAAGACAACA
297889 TTTAAATTAAATAAAT
1 TTTAAATTAAATAAAT
297905 TTTAAATT-AATAAA
1 TTTAAATTAAATAAA
297919 GATTAAGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TTTAAATTAAATAAAT
Found at i:299758 original size:17 final size:17
Alignment explanation
Indices: 299736--299795 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
299726 GAAATATGAA
299736 TATATTATTTATAAATT
1 TATATTATTTATAAATT
* **
299753 TATATTTGATTAAATAAAAA
1 TATA-TT-ATT-TATAAATT
*
299773 TATATTATTTATGAATT
1 TATATTATTTATAAATT
299790 TATATT
1 TATATT
299796 CAATTAAAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
17 14 0.42
18 5 0.15
19 5 0.15
20 9 0.27
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TATATTATTTATAAATT
Found at i:299777 original size:37 final size:38
Alignment explanation
Indices: 299660--299833 Score: 178
Period size: 38 Copynumber: 4.6 Consensus size: 38
299650 AGGATAATGT
*
299660 TATATTATTTA-AGGATTTATATTCAATTGAAAT-TCAAA
1 TATATTATTTATA-AATTTATATTCAATTGAAATAT-AAA
* ** * *
299698 TATGTTATTTACGAATTTATATTCTATTGAAATATGAA
1 TATATTATTTATAAATTTATATTCAATTGAAATATAAA
** *
299736 TATATTATTTATAAATTTATATTTGATT-AAATAAAAA
1 TATATTATTTATAAATTTATATTCAATTGAAATATAAA
* * *
299773 TATATTATTTATGAATTTATATTCAATTAAAATATGAA
1 TATATTATTTATAAATTTATATTCAATTGAAATATAAA
299811 TATATTA-TTACT-AATTTATATTC
1 TATATTATTTA-TAAATTTATATTC
299834 GAGCAAAATA
Statistics
Matches: 115, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
37 46 0.40
38 68 0.59
39 1 0.01
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (38 bp):
TATATTATTTATAAATTTATATTCAATTGAAATATAAA
Found at i:299791 original size:75 final size:76
Alignment explanation
Indices: 299660--299833 Score: 221
Period size: 75 Copynumber: 2.3 Consensus size: 76
299650 AGGATAATGT
* ** * *
299660 TATATTATTTA-AGGATTTATATTCAATTGAAATTCAAATATGTTATTTACGAATTTATATTCTA
1 TATATTATTTATA-AATTTATATTCAATTGAAATAAAAATATATTATTTACGAATTTATATTCAA
*
299724 TTGAAATATGAA
65 TTAAAATATGAA
** *
299736 TATATTATTTATAAATTTATATTTGATT-AAATAAAAATATATTATTTATGAATTTATATTCAAT
1 TATATTATTTATAAATTTATATTCAATTGAAATAAAAATATATTATTTACGAATTTATATTCAAT
299800 TAAAATATGAA
66 TAAAATATGAA
299811 TATATTA-TTACT-AATTTATATTC
1 TATATTATTTA-TAAATTTATATTC
299834 GAGCAAAATA
Statistics
Matches: 86, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
74 13 0.15
75 49 0.57
76 23 0.27
77 1 0.01
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (76 bp):
TATATTATTTATAAATTTATATTCAATTGAAATAAAAATATATTATTTACGAATTTATATTCAAT
TAAAATATGAA
Found at i:299843 original size:37 final size:37
Alignment explanation
Indices: 299696--299835 Score: 140
Period size: 37 Copynumber: 3.8 Consensus size: 37
299686 TTGAAATTCA
* ** * *
299696 AATATGTTATTTACGAATTTATATTCTATTGAAATATG
1 AATATATTATTTATAAATTTATATTCGA-TAAAATATG
* * **
299734 AATATATTATTTATAAATTTATATTTGATTAAATAAA
1 AATATATTATTTATAAATTTATATTCGATAAAATATG
* *
299771 AATATATTATTTATGAATTTATATTCAATTAAAATATG
1 AATATATTATTTATAAATTTATATTCGA-TAAAATATG
299809 AATATATTA-TTACT-AATTTATATTCGA
1 AATATATTATTTA-TAAATTTATATTCGA
299836 GCAAAATACG
Statistics
Matches: 85, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
37 46 0.54
38 39 0.46
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.48
Consensus pattern (37 bp):
AATATATTATTTATAAATTTATATTCGATAAAATATG
Found at i:309906 original size:103 final size:103
Alignment explanation
Indices: 309727--310054 Score: 602
Period size: 103 Copynumber: 3.2 Consensus size: 103
309717 GTAGAGGGTC
*
309727 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGAAACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
309792 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
*
309830 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
309895 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
* *
309933 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAATAGGTGTGAGGTCTGTTAAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
309998 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
* *
310036 TATGTAGTCCTTAGGGACA
1 TATGTGGTCCTTCGGGACA
310055 ACTTTATATG
Statistics
Matches: 218, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 218 1.00
ACGTcount: A:0.26, C:0.12, G:0.25, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:310090 original size:23 final size:23
Alignment explanation
Indices: 310064--310131 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
310054 AACTTTATAT
*
310064 GGCACTTCGGTGCATTTCTATGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
310087 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
*
310110 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
310132 AGTTGTGGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.18, C:0.25, G:0.26, T:0.31
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:313738 original size:4 final size:4
Alignment explanation
Indices: 313729--313757 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
313719 TGGCATTCAT
313729 GAAA GAAA GAAA GAAA GAAA GAAA GAAA G
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA G
313758 GGTTTAACTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:323341 original size:10 final size:10
Alignment explanation
Indices: 323321--323414 Score: 53
Period size: 10 Copynumber: 9.4 Consensus size: 10
323311 TTTTCTTAGA
*
323321 GTTTATAAGG
1 GTTTACAAGG
*
323331 GTTTACGAGG
1 GTTTACAAGG
* *
323341 GTCTACAATG
1 GTTTACAAGG
* *
323351 GTTTACTAGA
1 GTTTACAAGG
** *
323361 GTTTTTAATG
1 GTTTACAAGG
*
323371 GTTTATAAGG
1 GTTTACAAGG
*
323381 GTTTACTAGG
1 GTTTACAAGG
* *
323391 GTTTATAAGA
1 GTTTACAAGG
* *
323401 ATTTACTAGG
1 GTTTACAAGG
323411 GTTT
1 GTTT
323415 TAAGGGGTTG
Statistics
Matches: 58, Mismatches: 26, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
10 58 1.00
ACGTcount: A:0.27, C:0.06, G:0.26, T:0.41
Consensus pattern (10 bp):
GTTTACAAGG
Found at i:323393 original size:20 final size:20
Alignment explanation
Indices: 323370--323593 Score: 120
Period size: 20 Copynumber: 11.3 Consensus size: 20
323360 AGTTTTTAAT
323370 GGTTTATAAGGGTTTACTAG
1 GGTTTATAAGGGTTTACTAG
**
323390 GGTTTATAAGAATTTACTAG
1 GGTTTATAAGGGTTTACTAG
* **
323410 GGTTT-TAAGGGGTTGTTAG
1 GGTTTATAAGGGTTTACTAG
**
323429 GGTTTA-ATAGGGTTTGTTAG
1 GGTTTATA-AGGGTTTACTAG
* *
323449 AGTTTACTAA-GGTTTCCTAG
1 GGTTTA-TAAGGGTTTACTAG
* * *
323469 GGTTTTTTAGGATTTA-TAGG
1 GGTTTATAAGGGTTTACTA-G
* * * *
323489 GGTTTGTTAGAGTTTACTAA
1 GGTTTATAAGGGTTTACTAG
* **
323509 GGTTTCCT-AGGGTTTTTTAG
1 GGTTT-ATAAGGGTTTACTAG
* * * *
323529 GATTTATAGGGGTTTGCTAT
1 GGTTTATAAGGGTTTACTAG
*
323549 GGTTTCT-AGGGTTTGA-TAG
1 GGTTTATAAGGGTTT-ACTAG
*
323568 GATTTATAAGGGTTTACTAG
1 GGTTTATAAGGGTTTACTAG
*
323588 GATTTA
1 GGTTTA
323594 CTTGGGTTTA
Statistics
Matches: 154, Mismatches: 38, Indels: 24
0.71 0.18 0.11
Matches are distributed among these distances:
19 34 0.22
20 115 0.75
21 4 0.03
22 1 0.01
ACGTcount: A:0.22, C:0.05, G:0.29, T:0.44
Consensus pattern (20 bp):
GGTTTATAAGGGTTTACTAG
Found at i:323394 original size:40 final size:41
Alignment explanation
Indices: 323298--323395 Score: 103
Period size: 40 Copynumber: 2.4 Consensus size: 41
323288 TTTGGGGTTT
* *
323298 AGGGTTTA-TAAGGTTTTCTTAGAGTTTATAAGGGTTTACG
1 AGGGTTTACTAAGGTTTACTTAGAGTTTATAAGGGTTTACA
* * * *
323338 AGGGTCTAC-AATGGTTTAC-TAGAGTTTTTAATGGTTTATA
1 AGGGTTTACTAA-GGTTTACTTAGAGTTTATAAGGGTTTACA
*
323378 AGGGTTTACTAGGGTTTA
1 AGGGTTTACTAAGGTTTA
323396 TAAGAATTTA
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
40 40 0.85
41 7 0.15
ACGTcount: A:0.26, C:0.06, G:0.27, T:0.42
Consensus pattern (41 bp):
AGGGTTTACTAAGGTTTACTTAGAGTTTATAAGGGTTTACA
Found at i:323470 original size:30 final size:30
Alignment explanation
Indices: 323436--323528 Score: 82
Period size: 30 Copynumber: 3.4 Consensus size: 30
323426 TAGGGTTTAA
323436 TAGGGTTTGTTAGAGTTTACTAAGGTTTCC
1 TAGGGTTTGTTAGAGTTTACTAAGGTTTCC
*
323466 TAGGGTTTTTTAG-GATTTA-T-A-G-----
1 TAGGGTTTGTTAGAG-TTTACTAAGGTTTCC
323488 --GGGTTTGTTAGAGTTTACTAAGGTTTCC
1 TAGGGTTTGTTAGAGTTTACTAAGGTTTCC
*
323516 TAGGGTTTTTTAG
1 TAGGGTTTGTTAG
323529 GATTTATAGG
Statistics
Matches: 48, Mismatches: 3, Indels: 24
0.64 0.04 0.32
Matches are distributed among these distances:
20 14 0.29
21 2 0.04
22 1 0.02
23 1 0.02
27 1 0.02
28 1 0.02
29 2 0.04
30 26 0.54
ACGTcount: A:0.19, C:0.06, G:0.28, T:0.46
Consensus pattern (30 bp):
TAGGGTTTGTTAGAGTTTACTAAGGTTTCC
Found at i:323500 original size:50 final size:50
Alignment explanation
Indices: 323425--323544 Score: 215
Period size: 50 Copynumber: 2.4 Consensus size: 50
323415 TAAGGGGTTG
*
323425 TTAGGGTTTAATA-GGGTTTGTTAGAGTTTACTAAGGTTTCCTAGGGTTTT
1 TTAGGATTT-ATAGGGGTTTGTTAGAGTTTACTAAGGTTTCCTAGGGTTTT
323475 TTAGGATTTATAGGGGTTTGTTAGAGTTTACTAAGGTTTCCTAGGGTTTT
1 TTAGGATTTATAGGGGTTTGTTAGAGTTTACTAAGGTTTCCTAGGGTTTT
323525 TTAGGATTTATAGGGGTTTG
1 TTAGGATTTATAGGGGTTTG
323545 CTATGGTTTC
Statistics
Matches: 68, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
49 3 0.04
50 65 0.96
ACGTcount: A:0.20, C:0.05, G:0.29, T:0.46
Consensus pattern (50 bp):
TTAGGATTTATAGGGGTTTGTTAGAGTTTACTAAGGTTTCCTAGGGTTTT
Found at i:323568 original size:10 final size:9
Alignment explanation
Indices: 323370--323603 Score: 67
Period size: 10 Copynumber: 23.7 Consensus size: 9
323360 AGTTTTTAAT
323370 GGTTTATAAG
1 GGTTTAT-AG
323380 GGTTTACTAG
1 GGTTTA-TAG
323390 GGTTTATAAG
1 GGTTTAT-AG
**
323400 AATTTACTAG
1 GGTTTA-TAG
323410 GGTTT-TAAGG
1 GGTTTAT-A-G
323420 GGTTGT-TAG
1 GGTT-TATAG
323429 GGTTTAATAG
1 GGTTT-ATAG
*
323439 GGTTTGTTAG
1 GGTTT-ATAG
* *
323449 AGTTTACTAA
1 GGTTTA-TAG
*
323459 GGTTTCCTAG
1 GGTTT-ATAG
*
323469 GGTTTTTTAG
1 GG-TTTATAG
*
323479 GATTTATAGG
1 GGTTTATA-G
*
323489 GGTTTGTTAG
1 GGTTT-ATAG
* *
323499 AGTTTACTAA
1 GGTTTA-TAG
*
323509 GGTTTCCTAG
1 GGTTT-ATAG
*
323519 GGTTTTTTAG
1 GG-TTTATAG
*
323529 GATTTATAGG
1 GGTTTATA-G
* *
323539 GGTTTGCTAT
1 GGTTT-ATAG
*
323549 GGTTTCTAG
1 GGTTTATAG
323558 GGTTTGATAG
1 GGTTT-ATAG
*
323568 GATTTATAAG
1 GGTTTAT-AG
323578 GGTTTACTAG
1 GGTTTA-TAG
* *
323588 GATTTACTTG
1 GGTTTA-TAG
323598 GGTTTA
1 GGTTTA
323604 GGGTTCAGGG
Statistics
Matches: 167, Mismatches: 36, Indels: 42
0.68 0.15 0.17
Matches are distributed among these distances:
8 2 0.01
9 27 0.16
10 123 0.74
11 15 0.09
ACGTcount: A:0.22, C:0.05, G:0.29, T:0.44
Consensus pattern (9 bp):
GGTTTATAG
Found at i:323569 original size:39 final size:40
Alignment explanation
Indices: 323500--323586 Score: 122
Period size: 39 Copynumber: 2.2 Consensus size: 40
323490 GTTTGTTAGA
** *
323500 GTTTACTAAGGTTTCCTAGGGTTTTTTAGGATTTATAGGG
1 GTTTACTAAGGTTTCCTAGGGTTTGATAGGATTTATAAGG
* *
323540 GTTTGCTATGGTTT-CTAGGGTTTGATAGGATTTATAAGG
1 GTTTACTAAGGTTTCCTAGGGTTTGATAGGATTTATAAGG
323579 GTTTACTA
1 GTTTACTA
323587 GGATTTACTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
39 29 0.71
40 12 0.29
ACGTcount: A:0.21, C:0.07, G:0.28, T:0.45
Consensus pattern (40 bp):
GTTTACTAAGGTTTCCTAGGGTTTGATAGGATTTATAAGG
Found at i:323613 original size:7 final size:7
Alignment explanation
Indices: 323597--323654 Score: 64
Period size: 7 Copynumber: 8.4 Consensus size: 7
323587 GGATTTACTT
*
323597 GGGTTTA
1 GGGTTCA
323604 GGGTTCA
1 GGGTTCA
323611 GGGTTCA
1 GGGTTCA
*
323618 GGGTTCT
1 GGGTTCA
323625 GGGTTC-
1 GGGTTCA
*
323631 GGGTTTA
1 GGGTTCA
*
323638 GGGTTTA
1 GGGTTCA
*
323645 GGGTTTA
1 GGGTTCA
323652 GGG
1 GGG
323655 CTCGGGCTCG
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
6 5 0.11
7 42 0.89
ACGTcount: A:0.10, C:0.07, G:0.47, T:0.36
Consensus pattern (7 bp):
GGGTTCA
Found at i:323640 original size:20 final size:21
Alignment explanation
Indices: 323604--323642 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
323594 CTTGGGTTTA
323604 GGGTTCAGGGTTCAGGGTTCT
1 GGGTTCAGGGTTCAGGGTTCT
*
323625 GGGTTC-GGGTTTAGGGTT
1 GGGTTCAGGGTTCAGGGTT
323643 TAGGGTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.08, C:0.10, G:0.46, T:0.36
Consensus pattern (21 bp):
GGGTTCAGGGTTCAGGGTTCT
Found at i:323659 original size:27 final size:27
Alignment explanation
Indices: 323604--323660 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
323594 CTTGGGTTTA
*
323604 GGGTTCAGGGTTCAGGGTTCTGGGTTC
1 GGGTTCAGGGTTCAGGGTTCTGGGCTC
* *
323631 GGGTTTAGGGTTTAGGGTT-TAGGGCTC
1 GGGTTCAGGGTTCAGGGTTCT-GGGCTC
323658 GGG
1 GGG
323661 CTCGGGGCCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 1 0.04
27 25 0.96
ACGTcount: A:0.09, C:0.11, G:0.47, T:0.33
Consensus pattern (27 bp):
GGGTTCAGGGTTCAGGGTTCTGGGCTC
Found at i:323899 original size:7 final size:7
Alignment explanation
Indices: 323604--323908 Score: 292
Period size: 7 Copynumber: 44.0 Consensus size: 7
323594 CTTGGGTTTA
*
323604 GGGTTCA
1 GGGTTCG
*
323611 GGGTTCA
1 GGGTTCG
*
323618 GGGTTCT
1 GGGTTCG
323625 GGGTTC-
1 GGGTTCG
**
323631 GGGTTTA
1 GGGTTCG
**
323638 GGGTTTA
1 GGGTTCG
**
323645 GGGTTTA
1 GGGTTCG
*
323652 GGGCTC-
1 GGGTTCG
*
323658 GGGCTCG
1 GGGTTCG
**
323665 GGGCCCG
1 GGGTTCG
*
323672 GGGCTC-
1 GGGTTCG
*
323678 GGGTCCG
1 GGGTTCG
*
323685 GGGCTCG
1 GGGTTCG
**
323692 GGGCCCG
1 GGGTTCG
*
323699 GGGTCCG
1 GGGTTCG
*
323706 GGGTCCG
1 GGGTTCG
*
323713 GGGTCCG
1 GGGTTCG
*
323720 GGGTCCG
1 GGGTTCG
323727 GGGTTCG
1 GGGTTCG
*
323734 GGGTCCG
1 GGGTTCG
*
323741 GGGTCCG
1 GGGTTCG
*
323748 GGGTCCG
1 GGGTTCG
*
323755 GGGTCCG
1 GGGTTCG
*
323762 GGGTCCG
1 GGGTTCG
*
323769 GGGTCCG
1 GGGTTCG
*
323776 GGGTCCG
1 GGGTTCG
*
323783 GGGTCCG
1 GGGTTCG
*
323790 GGGTCCG
1 GGGTTCG
*
323797 GGGTCCG
1 GGGTTCG
323804 GGGTTCG
1 GGGTTCG
323811 GGGTTCG
1 GGGTTCG
323818 GGGTTCG
1 GGGTTCG
323825 GGGTTCG
1 GGGTTCG
323832 GGGTTCG
1 GGGTTCG
323839 GGGTTCG
1 GGGTTCG
323846 GGGTTCG
1 GGGTTCG
323853 GGGTTCG
1 GGGTTCG
323860 GGGTTCG
1 GGGTTCG
323867 GGGTTCG
1 GGGTTCG
323874 GGGTTCG
1 GGGTTCG
323881 GGGTTCG
1 GGGTTCG
323888 GGGTTCG
1 GGGTTCG
*
323895 GGGTTCA
1 GGGTTCG
323902 GGGTTCG
1 GGGTTCG
323909 TGTTGAGTTA
Statistics
Matches: 278, Mismatches: 17, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
6 15 0.05
7 263 0.95
ACGTcount: A:0.02, C:0.21, G:0.54, T:0.23
Consensus pattern (7 bp):
GGGTTCG
Found at i:327335 original size:21 final size:21
Alignment explanation
Indices: 327309--327348 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
327299 CAGAACCCCA
*
327309 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
327330 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
327349 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:333495 original size:7 final size:7
Alignment explanation
Indices: 333483--333762 Score: 496
Period size: 7 Copynumber: 40.6 Consensus size: 7
333473 TGTTTCAACA
333483 GTTCGGG
1 GTTCGGG
333490 GTTCGGG
1 GTTCGGG
**
333497 GTTTAGG
1 GTTCGGG
333504 GTTCGGG
1 GTTCGGG
333511 GTTCGGG
1 GTTCGGG
333518 GTTCGGG
1 GTTCGGG
333525 GTTCGGG
1 GTTCGGG
333532 GTTCGGG
1 GTTCGGG
333539 GTTCGGG
1 GTTCGGG
333546 GTTCGGG
1 GTTCGGG
333553 GTTCGGG
1 GTTCGGG
333560 GTTCGGG
1 GTTCGGG
333567 GTTCGGG
1 GTTCGGG
333574 GTTC-GG
1 GTTCGGG
333580 GTTCGGG
1 GTTCGGG
333587 GTTCGGG
1 GTTCGGG
333594 GTTCGGG
1 GTTCGGG
333601 GTTCGGG
1 GTTCGGG
333608 GTTCGGG
1 GTTCGGG
333615 GTTCGGG
1 GTTCGGG
333622 GTTCGGG
1 GTTCGGG
333629 GTTCGGG
1 GTTCGGG
333636 GTTCGGG
1 GTTCGGG
333643 GTTCGGG
1 GTTCGGG
333650 GTTCGGG
1 GTTCGGG
333657 GTTCGGG
1 GTTCGGG
333664 GTTCGGG
1 GTTCGGG
333671 GTTC-GG
1 GTTCGGG
333677 GTTCGGG
1 GTTCGGG
333684 GTTCGGG
1 GTTCGGG
333691 GTTC-GG
1 GTTCGGG
333697 GTTCGGG
1 GTTCGGG
333704 GTTCGGG
1 GTTCGGG
333711 GTTCGGG
1 GTTCGGG
333718 GTTCGGG
1 GTTCGGG
333725 GTTCGGG
1 GTTCGGG
333732 GTTCGGG
1 GTTCGGG
333739 GTTC-GG
1 GTTCGGG
*
333745 GTTTGGG
1 GTTCGGG
*
333752 GTTCAGG
1 GTTCGGG
333759 GTTC
1 GTTC
333763 TCAGATTTAA
Statistics
Matches: 262, Mismatches: 7, Indels: 8
0.95 0.03 0.03
Matches are distributed among these distances:
6 23 0.09
7 239 0.91
ACGTcount: A:0.01, C:0.14, G:0.55, T:0.30
Consensus pattern (7 bp):
GTTCGGG
Found at i:336666 original size:10 final size:10
Alignment explanation
Indices: 336642--337539 Score: 509
Period size: 10 Copynumber: 90.9 Consensus size: 10
336632 TTTTTGAGGT
*
336642 TAGGATTTAC
1 TAGGGTTTAC
*
336652 CAGGGTTTAC
1 TAGGGTTTAC
*
336662 TAGGGTGTAC
1 TAGGGTTTAC
336672 TAGGGTTTAC
1 TAGGGTTTAC
**
336682 TAGATTTTA-
1 TAGGGTTTAC
**
336691 TACGCATTTAC
1 TA-GGGTTTAC
336702 TAGGGTTTA-
1 TAGGGTTTAC
* *
336711 TAATGATTTAC
1 T-AGGGTTTAC
336722 TACGGGTTTAC
1 TA-GGGTTTAC
* **
336733 TAGGATTTGT
1 TAGGGTTTAC
*
336743 TAGGATTTA-
1 TAGGGTTTAC
*
336752 TAAGGGTTTAT
1 T-AGGGTTTAC
* *
336763 TATGATTTAC
1 TAGGGTTTAC
*
336773 TAGGGTTTGC
1 TAGGGTTTAC
* *
336783 TAGGATTTAT
1 TAGGGTTTAC
*
336793 TAGGGTTTTTAA
1 TAGGG--TTTAC
*
336805 GAGGGTTT--
1 TAGGGTTTAC
*
336813 TAGGGTTT-T
1 TAGGGTTTAC
* *
336822 TAGGATTTAT
1 TAGGGTTTAC
*
336832 TAGGGTTTTC
1 TAGGGTTTAC
336842 TAGGGTTT-C
1 TAGGGTTTAC
336851 TTAGGGTTTAC
1 -TAGGGTTTAC
336862 TAGGGTTT-C
1 TAGGGTTTAC
336871 TAAGGGTTTA-
1 T-AGGGTTTAC
336881 TAAGGGATTT-C
1 T-AGGG-TTTAC
336892 TAGGGTTTA-
1 TAGGGTTTAC
336901 TAAGGGTTTAC
1 T-AGGGTTTAC
336912 TAGGGTTTAC
1 TAGGGTTTAC
* *
336922 AAGGGTTTAT
1 TAGGGTTTAC
* *
336932 TAGTGTTTGC
1 TAGGGTTTAC
*
336942 TAGGGTTTAT
1 TAGGGTTTAC
*
336952 TAGGGGTTA-
1 TAGGGTTTAC
* **
336961 TAAGGATTTGT
1 T-AGGGTTTAC
*
336972 TAGGGTTTGC
1 TAGGGTTTAC
**
336982 TAGGGTTTGT
1 TAGGGTTTAC
*
336992 TGGGGTTTA-
1 TAGGGTTTAC
*
337001 TCAGGGTTTAT
1 T-AGGGTTTAC
**
337012 TAGGGTTTGT
1 TAGGGTTTAC
*
337022 TATGGCTTT-C
1 TA-GGGTTTAC
* *
337032 TAAGGTTTCC
1 TAGGGTTTAC
*
337042 TAGGGTTTCC
1 TAGGGTTTAC
**
337052 TAGGGTTTGT
1 TAGGGTTTAC
* *
337062 TAAGATTTA-
1 TAGGGTTTAC
* *
337071 TAAGGATTTAT
1 T-AGGGTTTAC
337082 TAGGGTTTAC
1 TAGGGTTTAC
337092 TAGGGTTTA-
1 TAGGGTTTAC
337101 TAAGGGTTTA-
1 T-AGGGTTTAC
337111 -A-GGTTTA-
1 TAGGGTTTAC
*
337118 TAAGAG-TT--
1 T-AGGGTTTAC
*
337126 TAGGGTTTGC
1 TAGGGTTTAC
*
337136 TAGGATTTAC
1 TAGGGTTTAC
*
337146 TAGGGTATAC
1 TAGGGTTTAC
337156 TAGGGTTTAC
1 TAGGGTTTAC
337166 TAGGGTTTA-
1 TAGGGTTTAC
337175 TAAGGGTTTAC
1 T-AGGGTTTAC
337186 TAGGGTTTA-
1 TAGGGTTTAC
337195 TAAGGGTTTAC
1 T-AGGGTTTAC
*
337206 GAGGGTTTAC
1 TAGGGTTTAC
* **
337216 TAGGATTTGT
1 TAGGGTTTAC
*
337226 TAGGATTTA-
1 TAGGGTTTAC
*
337235 TAAGGGTTTAT
1 T-AGGGTTTAC
* *
337246 TATGATTTAC
1 TAGGGTTTAC
337256 TAGGGTTTAC
1 TAGGGTTTAC
337266 TAGGGTTTA-
1 TAGGGTTTAC
*
337275 TAAGGGTTTAA
1 T-AGGGTTTAC
337286 TAGGGTTTAC
1 TAGGGTTTAC
* *
337296 AAGGGTTTAT
1 TAGGGTTTAC
* *
337306 TAGTGTTTGTC
1 TAGGGTTT-AC
*
337317 TAGGGTTTAT
1 TAGGGTTTAC
337327 TAGGGTTTAC
1 TAGGGTTTAC
* *
337337 TAGTGTTTAT
1 TAGGGTTTAC
*
337347 TAGGGTTTAT
1 TAGGGTTTAC
* *
337357 TAGGATTT-T
1 TAGGGTTTAC
*
337366 TAGGGTTTAT
1 TAGGGTTTAC
337376 TAGGGTTTAC
1 TAGGGTTTAC
*
337386 TAGAG--TAC
1 TAGGGTTTAC
*
337394 TAGGGTTTAT
1 TAGGGTTTAC
337404 TAGGG-TT--
1 TAGGGTTTAC
*
337411 T--GGTTTGC
1 TAGGGTTTAC
*
337419 TAAGGTTTAC
1 TAGGGTTTAC
* *
337429 AAGGATTTAC
1 TAGGGTTTAC
337439 TAGGGTTTAC
1 TAGGGTTTAC
*
337449 AAGGGTTTAC
1 TAGGGTTTAC
*
337459 TAGTGTTTAGC
1 TAGGGTTTA-C
337470 TAGGGTTTAAC
1 TAGGGTTT-AC
* *
337481 TAGGATTTGC
1 TAGGGTTTAC
337491 TAGGGTTTAC
1 TAGGGTTTAC
* *
337501 AAGGGTTTAT
1 TAGGGTTTAC
* *
337511 TGGGGTTTAT
1 TAGGGTTTAC
*
337521 TAGGCTTTGA-
1 TAGGGTTT-AC
337531 TAGGGTTTA
1 TAGGGTTTA
337540 GGGTTTTTGA
Statistics
Matches: 703, Mismatches: 130, Indels: 111
0.74 0.14 0.12
Matches are distributed among these distances:
5 2 0.00
6 2 0.00
7 10 0.01
8 19 0.03
9 44 0.06
10 564 0.80
11 53 0.08
12 9 0.01
ACGTcount: A:0.22, C:0.06, G:0.29, T:0.43
Consensus pattern (10 bp):
TAGGGTTTAC
Found at i:337446 original size:30 final size:31
Alignment explanation
Indices: 337440--337509 Score: 56
Period size: 31 Copynumber: 2.3 Consensus size: 31
337430 AGGATTTACT
* * *
337440 AGGGTTTACAAGGGTTTA-CTAGTGTTTAGCT
1 AGGGTTTACAAGTGTTTAGCTAGGGTTTA-CA
*
337471 AGGGTTTAACTAG-GATTT-GCTAGGGTTTACA
1 AGGGTTT-ACAAGTG-TTTAGCTAGGGTTTACA
337502 AGGGTTTA
1 AGGGTTTA
337510 TTGGGGTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
30 1 0.03
31 16 0.48
32 16 0.48
ACGTcount: A:0.24, C:0.09, G:0.30, T:0.37
Consensus pattern (31 bp):
AGGGTTTACAAGTGTTTAGCTAGGGTTTACA
Found at i:337465 original size:153 final size:155
Alignment explanation
Indices: 337259--337539 Score: 381
Period size: 153 Copynumber: 1.8 Consensus size: 155
337249 GATTTACTAG
* * * *
337259 GGTTTACTAGGGTTTATAAGGGTTTAATAGGGTTTACAAGGGTTTATTAGTGTTT-GTCTAGGGT
1 GGTTTACTAAGGTTTACAAGGATTTAATAGGGTTTACAAGGGTTTACTAGTGTTTAG-CTAGGGT
* * * ** *
337323 TT-ATTAGGGTTTACTAGTGTTTATTAGGGTTTATTAGGATTT-TTAGGGTTT-ATTAGGGTTTA
65 TTAACTAGGATTTACTAGGGTTTACAAGGGTTTATTAGGATTTATTAGGCTTTGA-TAGGGTTTA
337385 CTAGAGTACTAGGGTTTATTAGGGTTT
129 CTAGAGTACTAGGGTTTATTAGGGTTT
* *
337412 GGTTTGCTAAGGTTTACAAGGATTTACTAGGGTTTACAAGGGTTTACTAGTGTTTAGCTAGGGTT
1 GGTTTACTAAGGTTTACAAGGATTTAATAGGGTTTACAAGGGTTTACTAGTGTTTAGCTAGGGTT
* * *
337477 TAACTAGGATTTGCTAGGGTTTACAAGGGTTTATTGGGGTTTATTAGGCTTTGATAGGGTTTA
66 TAACTAGGATTTACTAGGGTTTACAAGGGTTTATTAGGATTTATTAGGCTTTGATAGGGTTTA
337540 GGGTTTTTGA
Statistics
Matches: 109, Mismatches: 15, Indels: 6
0.84 0.12 0.05
Matches are distributed among these distances:
153 58 0.53
154 33 0.30
155 17 0.16
156 1 0.01
ACGTcount: A:0.22, C:0.06, G:0.29, T:0.43
Consensus pattern (155 bp):
GGTTTACTAAGGTTTACAAGGATTTAATAGGGTTTACAAGGGTTTACTAGTGTTTAGCTAGGGTT
TAACTAGGATTTACTAGGGTTTACAAGGGTTTATTAGGATTTATTAGGCTTTGATAGGGTTTACT
AGAGTACTAGGGTTTATTAGGGTTT
Found at i:339880 original size:7 final size:7
Alignment explanation
Indices: 339862--339899 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
339852 AAAACACAGA
339862 TGGGGTT
1 TGGGGTT
339869 T-GGGTT
1 TGGGGTT
339875 TGGGGTT
1 TGGGGTT
339882 TGGGGTT
1 TGGGGTT
339889 TGGGGTT
1 TGGGGTT
339896 TGGG
1 TGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.20
7 24 0.80
ACGTcount: A:0.00, C:0.00, G:0.58, T:0.42
Consensus pattern (7 bp):
TGGGGTT
Done.