Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014806.1 Kokia drynarioides strain JFW-HI SEQ_129848, 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: 395033
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 13 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:8169 original size:31 final size:31
Alignment explanation
Indices: 8129--8187 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
8119 GTGTAATTCA
*
8129 TATTTGAGTTAAACCGAAA-AACTTAATTTTT
1 TATTCGAGTTAAACC-AAATAACTTAATTTTT
*
8160 TATTCGAGTTAATCCAAATAACTTAATT
1 TATTCGAGTTAAACCAAATAACTTAATT
8188 AACTCAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 3 0.12
31 22 0.88
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (31 bp):
TATTCGAGTTAAACCAAATAACTTAATTTTT
Found at i:8825 original size:2 final size:2
Alignment explanation
Indices: 8818--8842 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8808 AATGAACAGC
8818 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 T
8843 TGATATAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13715 original size:23 final size:22
Alignment explanation
Indices: 13657--13717 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
13647 AGCGTTTCAT
*
13657 AAGGTAAAAAAAAACGTGCCAC
1 AAGGCAAAAAAAAACGTGCCAC
*
13679 AAGACAAAGAAAAAACGTGCCAC
1 AAGGCAAA-AAAAAACGTGCCAC
*
13702 AAAGGCAAATAAAAAC
1 -AAGGCAAAAAAAAAC
13718 TAAAAGAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 6 0.18
23 20 0.61
24 7 0.21
ACGTcount: A:0.59, C:0.18, G:0.16, T:0.07
Consensus pattern (22 bp):
AAGGCAAAAAAAAACGTGCCAC
Found at i:14152 original size:32 final size:32
Alignment explanation
Indices: 14116--14189 Score: 148
Period size: 32 Copynumber: 2.3 Consensus size: 32
14106 ATTAATTATA
14116 TAAAATTAAATTTAGAGTTGATTTTATTAGAT
1 TAAAATTAAATTTAGAGTTGATTTTATTAGAT
14148 TAAAATTAAATTTAGAGTTGATTTTATTAGAT
1 TAAAATTAAATTTAGAGTTGATTTTATTAGAT
14180 TAAAATTAAA
1 TAAAATTAAA
14190 AATCCTGAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.45, C:0.00, G:0.11, T:0.45
Consensus pattern (32 bp):
TAAAATTAAATTTAGAGTTGATTTTATTAGAT
Found at i:21262 original size:23 final size:23
Alignment explanation
Indices: 21198--21273 Score: 82
Period size: 23 Copynumber: 3.3 Consensus size: 23
21188 AATAAATGTG
* * *
21198 TTAAATATTAATGTGATTTGTTGC
1 TTAAATATTTATGCGATTT-ATGC
* *
21222 CTAAATATTTATGTGATTTATGC
1 TTAAATATTTATGCGATTTATGC
21245 TTAAAT-TTTACTGCGATTTATGC
1 TTAAATATTTA-TGCGATTTATGC
21268 TTAAAT
1 TTAAAT
21274 GTTAATATGA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
22 4 0.09
23 25 0.54
24 17 0.37
ACGTcount: A:0.30, C:0.08, G:0.13, T:0.49
Consensus pattern (23 bp):
TTAAATATTTATGCGATTTATGC
Found at i:21289 original size:23 final size:23
Alignment explanation
Indices: 21198--21289 Score: 67
Period size: 23 Copynumber: 4.0 Consensus size: 23
21188 AATAAATGTG
* * *
21198 TTAAATATTAATGTGATTTGTTGC
1 TTAAATGTTAATATGATTT-ATGC
* * * *
21222 CTAAATATTTATGTGATTTATGC
1 TTAAATGTTAATATGATTTATGC
* * **
21245 TTAAATTTTACTGCGATTTATGC
1 TTAAATGTTAATATGATTTATGC
*
21268 TTAAATGTTAATATGATGTATG
1 TTAAATGTTAATATGATTTATG
21290 TTTGTTCAGT
Statistics
Matches: 55, Mismatches: 13, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
23 38 0.69
24 17 0.31
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (23 bp):
TTAAATGTTAATATGATTTATGC
Found at i:23047 original size:14 final size:15
Alignment explanation
Indices: 23013--23061 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
23003 TTAAGGTTTG
23013 ATTAATTAAACTTA-A
1 ATTAATT-AACTTATA
*
23028 ATTAATTAA-TTATG
1 ATTAATTAACTTATA
23042 ATTAATTAACTTATA
1 ATTAATTAACTTATA
23057 ATTAA
1 ATTAA
23062 AGTATAAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 3 0.10
14 11 0.37
15 16 0.53
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (15 bp):
ATTAATTAACTTATA
Found at i:23468 original size:14 final size:14
Alignment explanation
Indices: 23449--23475 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
23439 TATAGATGGT
23449 AGAGGGGTGAAATA
1 AGAGGGGTGAAATA
23463 AGAGGGGTGAAAT
1 AGAGGGGTGAAAT
23476 TGATAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.44, T:0.15
Consensus pattern (14 bp):
AGAGGGGTGAAATA
Found at i:24894 original size:16 final size:16
Alignment explanation
Indices: 24873--24905 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
24863 TTTGAGGTTC
24873 AGTTTTGTGGGCATGT
1 AGTTTTGTGGGCATGT
24889 AGTTTTGTGGGCATGT
1 AGTTTTGTGGGCATGT
24905 A
1 A
24906 TATAGGCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.15, C:0.06, G:0.36, T:0.42
Consensus pattern (16 bp):
AGTTTTGTGGGCATGT
Found at i:28356 original size:91 final size:87
Alignment explanation
Indices: 28259--28477 Score: 273
Period size: 91 Copynumber: 2.5 Consensus size: 87
28249 AATTTTTTTC
* * * *
28259 AAAAAAAGCAATTAAGTCCCTACTTTTATTTTGCACTCATTTGGATGCTTGAACTTTCAAAATGC
1 AAAAAAAGCAATTAAG-CCCTACTTTTATTTTGCACTCAATTGCATACTTAAACTTTCAAAATGC
*
28324 ATAAAAAATACCCTCAAACTTTATA
65 ATAAAAAAGACCCTCAAAC-TT-TA
28349 ACAAAAAAGCAATTAAGCCACTACTTTTATTTTGCACTCAATTGCATACTTAAACTTTCAAAATG
1 A-AAAAAAGCAATTAAGCC-CTACTTTTATTTTGCACTCAATTGCATACTTAAACTTTCAAAATG
* **
28414 CATCAAAAAGGTCCTCAAACTTTA
64 CATAAAAAAGACCCTCAAACTTTA
* *
28438 AAAAAAA-CAATTAAGCCC--CTTATTTTTTTGCACTTAATTG
1 AAAAAAAGCAATTAAGCCCTACTT-TTATTTTGCACTCAATTG
28478 GGTAATTGAA
Statistics
Matches: 116, Mismatches: 10, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
84 3 0.03
85 16 0.14
86 1 0.01
87 10 0.09
88 6 0.05
89 3 0.03
90 5 0.04
91 72 0.62
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (87 bp):
AAAAAAAGCAATTAAGCCCTACTTTTATTTTGCACTCAATTGCATACTTAAACTTTCAAAATGCA
TAAAAAAGACCCTCAAACTTTA
Found at i:28640 original size:20 final size:21
Alignment explanation
Indices: 28602--28640 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
28592 TTCTAATTTT
* *
28602 AATTTTTTATATTTTTATTAA
1 AATTTATTATATTTCTATTAA
28623 AATTTATTA-ATTTCTATT
1 AATTTATTATATTTCTATT
28641 TTTTATAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (21 bp):
AATTTATTATATTTCTATTAA
Found at i:30472 original size:80 final size:80
Alignment explanation
Indices: 30339--30497 Score: 225
Period size: 80 Copynumber: 2.0 Consensus size: 80
30329 GGGCAAAACC
* *
30339 GTTGGTTAATCCAACTAGAACTGACTTCACTTATCGCTGTTTATCCCTTAGGCACTC-GGTGTCA
1 GTTGGTTAATCCAACTAGAACTGACTTCACTTATCGCGGTTTATCCCTTAGGCAC-CGGGTGCCA
30403 TGAATTGACGGATTTT
65 TGAATTGACGGATTTT
* * *
30419 GTTGGTTAATCCAACTAGAGCTGGGCTT-ACTTCTCGCGGTTTATCCGC-TAGGCACCGGGTGCC
1 GTTGGTTAATCCAACTAGAACT-GACTTCACTTATCGCGGTTTATCC-CTTAGGCACCGGGTGCC
30482 ATGAATTGACGGATTT
64 ATGAATTGACGGATTT
30498 GGATACAAGT
Statistics
Matches: 71, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
79 1 0.01
80 65 0.92
81 5 0.07
ACGTcount: A:0.21, C:0.22, G:0.24, T:0.33
Consensus pattern (80 bp):
GTTGGTTAATCCAACTAGAACTGACTTCACTTATCGCGGTTTATCCCTTAGGCACCGGGTGCCAT
GAATTGACGGATTTT
Found at i:31989 original size:20 final size:20
Alignment explanation
Indices: 31960--32001 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
31950 AAAAAAACGT
*
31960 AAAAAGTTAACTGTTTTTTA
1 AAAAAGTTAAATGTTTTTTA
* *
31980 AAAAATTTAAATTTTTTTTA
1 AAAAAGTTAAATGTTTTTTA
32000 AA
1 AA
32002 CCTATCCGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (20 bp):
AAAAAGTTAAATGTTTTTTA
Found at i:34731 original size:14 final size:15
Alignment explanation
Indices: 34702--34734 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
34692 TGCTGCAAAG
34702 AAGACACACCAAGCA
1 AAGACACACCAAGCA
*
34717 AAGAC-CACCACGCA
1 AAGACACACCAAGCA
34731 AAGA
1 AAGA
34735 GGAAAACGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.52, C:0.33, G:0.15, T:0.00
Consensus pattern (15 bp):
AAGACACACCAAGCA
Found at i:35104 original size:21 final size:21
Alignment explanation
Indices: 35080--35131 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
35070 CGAGATGATT
*
35080 CTACCGATAC-ATGTGATACAA
1 CTACCGATACAAT-TCATACAA
* * *
35101 CTACTGAAACAATTCATGCAA
1 CTACCGATACAATTCATACAA
35122 CTACCGATAC
1 CTACCGATAC
35132 CAAATATTCT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.38, C:0.27, G:0.12, T:0.23
Consensus pattern (21 bp):
CTACCGATACAATTCATACAA
Found at i:35898 original size:52 final size:52
Alignment explanation
Indices: 35820--36064 Score: 418
Period size: 52 Copynumber: 4.7 Consensus size: 52
35810 ATTTCATTTC
* *
35820 ATTCATATAGTCACGATGACACATAGCCACCGGACCTCATAATCCGTAAAGG
1 ATTCATATACTCACGATGACACATAGCCATCGGACCTCATAATCCGTAAAGG
* *
35872 ATTCATATGCTCACGATGACACATAGCCATCGGACCTCATAATCCATAAAGG
1 ATTCATATACTCACGATGACACATAGCCATCGGACCTCATAATCCGTAAAGG
35924 ATTCATATACTCACGATGACACATAGCCATCGGACCTCATAATCCGTAAAGG
1 ATTCATATACTCACGATGACACATAGCCATCGGACCTCATAATCCGTAAAGG
* *
35976 ATTCATATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAAG
1 ATTCATATACTCACGATGACACATAGCCATCGGACCTCATAATCCGTAAAGG
* *
36028 ATTCATATACTCACGAAGACACATAGTCATCGGACCT
1 ATTCATATACTCACGATGACACATAGCCATCGGACCT
36065 TTTTTCATTT
Statistics
Matches: 184, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 184 1.00
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.23
Consensus pattern (52 bp):
ATTCATATACTCACGATGACACATAGCCATCGGACCTCATAATCCGTAAAGG
Found at i:49232 original size:63 final size:63
Alignment explanation
Indices: 49133--49278 Score: 211
Period size: 63 Copynumber: 2.3 Consensus size: 63
49123 AATTAAATGT
* * *
49133 GTTTCAGTAGATGCGTTTTCAGCGAATAATAGTAATGAAAAGGTCTTCTGTGCTTGAAAACAC
1 GTTTCAGCAGATGCGTTTTCAGCGAATAATAATAATGAAAAGGTCTTATGTGCTTGAAAACAC
* * * *
49196 GTTTCAGCAGATGCGTTTTTATCGAATAATAATAATGAAATGGTTTTATGTGCTTGAAAACAC
1 GTTTCAGCAGATGCGTTTTCAGCGAATAATAATAATGAAAAGGTCTTATGTGCTTGAAAACAC
* *
49259 GTTTCAGCAAATGCATTTTC
1 GTTTCAGCAGATGCGTTTTC
49279 GTCGAAGTCA
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
63 73 1.00
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.35
Consensus pattern (63 bp):
GTTTCAGCAGATGCGTTTTCAGCGAATAATAATAATGAAAAGGTCTTATGTGCTTGAAAACAC
Found at i:49284 original size:63 final size:63
Alignment explanation
Indices: 49133--49299 Score: 210
Period size: 63 Copynumber: 2.6 Consensus size: 63
49123 AATTAAATGT
* * *
49133 GTTTCAGTAGATGCGTTTTCAG-CGAATAATAGTAATGAAAAGGTCTTCTGTGCTTGAAAACAC
1 GTTTCAGCAGATGCGTTTTC-GTCGAATAATAATAATGAAAAGGTCTTATGTGCTTGAAAACAC
** * *
49196 GTTTCAGCAGATGCGTTTTTATCGAATAATAATAATGAAATGGTTTTATGTGCTTGAAAACAC
1 GTTTCAGCAGATGCGTTTTCGTCGAATAATAATAATGAAAAGGTCTTATGTGCTTGAAAACAC
* * * *
49259 GTTTCAGCAAATGCATTTTCGTCGAAGTCACAATAATGAAA
1 GTTTCAGCAGATGCGTTTTCGTCGAA-TAATAATAATGAAA
49300 GGGGTACCCG
Statistics
Matches: 89, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
63 77 0.87
64 12 0.13
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.33
Consensus pattern (63 bp):
GTTTCAGCAGATGCGTTTTCGTCGAATAATAATAATGAAAAGGTCTTATGTGCTTGAAAACAC
Found at i:53419 original size:22 final size:23
Alignment explanation
Indices: 53389--53435 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
53379 TTTCAATCTC
*
53389 AAAATCCTAAA-CAATAAAACTCT
1 AAAATCCTAAACCAA-AAAACCCT
53412 AAAA-CCTAAACCAAAAAACCCT
1 AAAATCCTAAACCAAAAAACCCT
53434 AA
1 AA
53436 CCCTATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.60, C:0.26, G:0.00, T:0.15
Consensus pattern (23 bp):
AAAATCCTAAACCAAAAAACCCT
Found at i:58059 original size:13 final size:12
Alignment explanation
Indices: 58026--58055 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
58016 TAATTTTAAT
58026 ATTTTTAATGAA
1 ATTTTTAATGAA
58038 ATTTTTAATGAA
1 ATTTTTAATGAA
58050 ATTTTT
1 ATTTTT
58056 TAATTTTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (12 bp):
ATTTTTAATGAA
Found at i:59040 original size:34 final size:35
Alignment explanation
Indices: 59002--59069 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 35
58992 TTGAGAGAAC
* *
59002 TTTATAAGAGCTAGGGTTTTATTTTTGGA-TTTGT
1 TTTATAAGAGCTAAGGCTTTATTTTTGGAGTTTGT
* * *
59036 TTTATGAGAGTTAAGGCTTTGTTTTTGGAGTTTG
1 TTTATAAGAGCTAAGGCTTTATTTTTGGAGTTTG
59070 GGTTTGTACA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 24 0.86
35 4 0.14
ACGTcount: A:0.19, C:0.03, G:0.26, T:0.51
Consensus pattern (35 bp):
TTTATAAGAGCTAAGGCTTTATTTTTGGAGTTTGT
Found at i:64851 original size:29 final size:29
Alignment explanation
Indices: 64810--64867 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
64800 AAACATTCCC
* * * *
64810 CTAGTTTTTATGGCTTAAATTGAAACCCT
1 CTAGCTTTAATGGCTCAAATAGAAACCCT
*
64839 CTAGCTTTAATGGCTCAAGTAGAAACCCT
1 CTAGCTTTAATGGCTCAAATAGAAACCCT
64868 TTACAATTCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (29 bp):
CTAGCTTTAATGGCTCAAATAGAAACCCT
Found at i:76097 original size:14 final size:16
Alignment explanation
Indices: 76066--76097 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
76056 GATCCTTTTC
76066 AATATTATAAAAATAA
1 AATATTATAAAAATAA
76082 AATATTA-AAAAA-AA
1 AATATTATAAAAATAA
76096 AA
1 AA
76098 ACCAGAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.25
15 5 0.31
16 7 0.44
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (16 bp):
AATATTATAAAAATAA
Found at i:76511 original size:15 final size:15
Alignment explanation
Indices: 76479--76527 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
76469 AAGTTATAAA
76479 TTTAA-TCT-ATATTT
1 TTTAATTCTGATA-TT
76493 TTTAATT-TGATTATT
1 TTTAATTCTGA-TATT
*
76508 TTTAATTCTTATATT
1 TTTAATTCTGATATT
76523 TTTAA
1 TTTAA
76528 AGTTTTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
14 6 0.20
15 20 0.67
16 4 0.13
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (15 bp):
TTTAATTCTGATATT
Found at i:80412 original size:15 final size:14
Alignment explanation
Indices: 80384--80430 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
80374 TAACTAAACA
80384 ATAATATAAATTTT
1 ATAATATAAATTTT
*
80398 ATAATTATAATTTTT
1 ATAA-TATAAATTTT
*
80413 ATAA-ATAAGGTTTT
1 ATAATATAA-ATTTT
80427 ATAA
1 ATAA
80431 ACTATTCAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 4 0.14
14 12 0.41
15 13 0.45
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (14 bp):
ATAATATAAATTTT
Found at i:87839 original size:19 final size:18
Alignment explanation
Indices: 87815--87853 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
87805 TTGTCAAAGT
*
87815 AAATTAAAAATGTTATTAA
1 AAATTAAAAATCTTA-TAA
*
87834 AAATTATAAATCTTATAA
1 AAATTAAAAATCTTATAA
87852 AA
1 AA
87854 GAAATCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (18 bp):
AAATTAAAAATCTTATAA
Found at i:89463 original size:30 final size:30
Alignment explanation
Indices: 89408--89484 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
89398 ACTCAATTTT
* * * **
89408 TTTTTTAAAAGATTGATGGTTAAATTTGAC
1 TTTTTTAAAAGATTAATGATCAAATTCAAC
*
89438 TTTTTTAAAAGATTAATGATCAAATTCAAT
1 TTTTTTAAAAGATTAATGATCAAATTCAAC
89468 TCTTTTTAAAAGATTAA
1 T-TTTTTAAAAGATTAA
89485 GAATTAAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
30 25 0.62
31 15 0.38
ACGTcount: A:0.39, C:0.05, G:0.10, T:0.45
Consensus pattern (30 bp):
TTTTTTAAAAGATTAATGATCAAATTCAAC
Found at i:89535 original size:24 final size:26
Alignment explanation
Indices: 89489--89536 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
89479 GATTAAGAAT
89489 TAAATTTAACTAAAAAAAAATAAAAC
1 TAAATTTAACTAAAAAAAAATAAAAC
*
89515 TAAA-TTAA-TAAAAAAATATAAA
1 TAAATTTAACTAAAAAAAAATAAA
89537 CATTAAACGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 13 0.62
25 4 0.19
26 4 0.19
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (26 bp):
TAAATTTAACTAAAAAAAAATAAAAC
Found at i:89811 original size:27 final size:29
Alignment explanation
Indices: 89781--89842 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
89771 AATCATGTTA
*
89781 AATTTTT-T-TATTTAATCTATATATTCT
1 AATTTTTATATATATAATCTATATATTCT
* *
89808 AATTTTTATATATATAATTTATTTATTCT
1 AATTTTTATATATATAATCTATATATTCT
*
89837 ACTTTT
1 AATTTT
89843 ATGATGTCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 7 0.24
28 1 0.03
29 21 0.72
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (29 bp):
AATTTTTATATATATAATCTATATATTCT
Found at i:92653 original size:58 final size:58
Alignment explanation
Indices: 92588--92737 Score: 187
Period size: 57 Copynumber: 2.6 Consensus size: 58
92578 TTCTAATAAG
* * *
92588 ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATTATATTTTAACGTA
1 ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATAACATTTTAACATA
* * *
92646 ATTATTATTAAATACAATTTAAT-AAAATAATATATAATTTAATAACATTTTAATATA
1 ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATAACATTTTAACATA
* * *
92703 ATAATTATTAAAATATGAA-TTAGTAAAAATCATAA
1 ATTATTATT-AAATAT-AATTTAATAAAAATAATAA
92738 TATATAATAT
Statistics
Matches: 78, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
57 37 0.47
58 31 0.40
59 10 0.13
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (58 bp):
ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATAACATTTTAACATA
Found at i:99265 original size:17 final size:18
Alignment explanation
Indices: 99243--99278 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
99233 AAAATTCTTT
*
99243 AAATTAA-AATAGTAAAA
1 AAATTAACAATAATAAAA
99260 AAATTAACAATAATAAAA
1 AAATTAACAATAATAAAA
99278 A
1 A
99279 CGCATAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.22
Consensus pattern (18 bp):
AAATTAACAATAATAAAA
Found at i:103719 original size:3 final size:3
Alignment explanation
Indices: 103707--103752 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
103697 ATAACGTGTT
103707 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
103753 GATGATGATG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:103757 original size:3 final size:3
Alignment explanation
Indices: 103751--103789 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
103741 AATAATAATA
103751 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
103790 TAAAGAACAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:105104 original size:20 final size:19
Alignment explanation
Indices: 105081--105142 Score: 74
Period size: 20 Copynumber: 3.3 Consensus size: 19
105071 TTTTTTATTT
*
105081 AAAATAATTAAAAATTATA
1 AAAATAATTAAAAAATATA
* *
105100 GAAAATCATAAAAAAATATA
1 -AAAATAATTAAAAAATATA
105120 AAAA-AATTAAAAAA-ATA
1 AAAATAATTAAAAAATATA
105137 AAAATA
1 AAAATA
105143 TACAGAGAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
17 7 0.19
18 9 0.25
19 4 0.11
20 16 0.44
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.23
Consensus pattern (19 bp):
AAAATAATTAAAAAATATA
Found at i:105191 original size:18 final size:18
Alignment explanation
Indices: 105157--105191 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
105147 GAGAAGTGAA
*
105157 AAAATTGTAGAAGTATAG
1 AAAATTGTAAAAGTATAG
*
105175 AAAATTGTAAAATTATA
1 AAAATTGTAAAAGTATA
105192 TAAATTATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.14, T:0.31
Consensus pattern (18 bp):
AAAATTGTAAAAGTATAG
Found at i:105278 original size:28 final size:28
Alignment explanation
Indices: 105229--105297 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 28
105219 AAAATTATGT
105229 AAATTATAAAAGAATAAGAAAATTGTA-A
1 AAATTATAAAAGAATAAGAAAATT-TACA
**
105257 AAATTATGAAAA-AATATTAAAATTTACAA
1 AAATTAT-AAAAGAATAAGAAAATTTAC-A
105286 AATATTATAAAA
1 AA-ATTATAAAA
105298 AAACCATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
27 2 0.06
28 17 0.49
29 11 0.31
30 5 0.14
ACGTcount: A:0.64, C:0.01, G:0.06, T:0.29
Consensus pattern (28 bp):
AAATTATAAAAGAATAAGAAAATTTACA
Found at i:106700 original size:22 final size:21
Alignment explanation
Indices: 106661--106701 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
106651 AATAAGAGAT
*
106661 AAAAAAATATTAATTTAAAAC
1 AAAAAAATATTAAATTAAAAC
*
106682 AAAACAATATTTAAATTAAA
1 AAAAAAATA-TTAAATTAAA
106702 TAAAAGGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (21 bp):
AAAAAAATATTAAATTAAAAC
Found at i:106706 original size:21 final size:21
Alignment explanation
Indices: 106659--106706 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
106649 AAAATAAGAG
*
106659 ATAAAAAAATATTAATTTAAA
1 ATAAAAAAATATTAAATTAAA
* *
106680 ACAAAACAATATTTAAATT-AA
1 ATAAAAAAATA-TTAAATTAAA
106701 ATAAAA
1 ATAAAA
106707 GGAATCAAGG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (21 bp):
ATAAAAAAATATTAAATTAAA
Found at i:108211 original size:21 final size:22
Alignment explanation
Indices: 108173--108224 Score: 88
Period size: 21 Copynumber: 2.4 Consensus size: 22
108163 AACGTGGTGT
*
108173 TGACGTGACGATGACATGGCAC
1 TGACGTGGCGATGACATGGCAC
108195 TGACGTGGCGA-GACATGGCAC
1 TGACGTGGCGATGACATGGCAC
108216 TGACGTGGC
1 TGACGTGGC
108225 AATGCTAACG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 19 0.66
22 10 0.34
ACGTcount: A:0.23, C:0.23, G:0.37, T:0.17
Consensus pattern (22 bp):
TGACGTGGCGATGACATGGCAC
Found at i:108983 original size:49 final size:48
Alignment explanation
Indices: 108881--109254 Score: 179
Period size: 49 Copynumber: 7.6 Consensus size: 48
108871 TAATATTTTC
* * * * * * **
108881 CATTGCGGCTTCAATCTTTCCCTTTATGTCTTC-GCGTTACTAGATTCAC
1 CATTGTGGCTTAAATCTTTCCCTTCATG-CTTCTGAGGTAC-AGGTTCGT
*
108930 CATTGTGGCTTAAATCTTTCCCTTCGTGCTTCTGAGGTACAAGGTTCGT
1 CATTGTGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTAC-AGGTTCGT
* * * * *
108979 CATTGTGACTTAAACCTTTCCC-TCAATTATCTT-TGTGGTACTGGATTCGT
1 CATTGTGGCTTAAATCTTTCCCTTC-A-T-GCTTCTGAGGTACAGG-TTCGT
* *
109029 CGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACGAGGTTCGT
1 CATTGTGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTAC-AGGTTCGT
** ** * * * **
109078 CATTACGATTTAAA-CTTTTCCCTCCATTACCTTC-GTGGTATTGGATTC-T
1 CATTGTGGCTTAAATC-TTTCCCTTCA-T-GCTTCTGAGGTACAGG-TTCGT
* * * * *
109127 CCGTTGCGACTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTTGC
1 -CATTGTGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTAC-AGGTTCGT
* * * * * * *
109177 CGTTGCGACTTAAACCTTTCCCTTCATTATCTTC-GTGGTACTGGATTCG-
1 CATTGTGGCTTAAATCTTTCCCTTCA-T-GCTTCTGAGGTACAGG-TTCGT
* *
109226 CTGTTGCGGCTTAAATCTTTCCCTTCATG
1 C-ATTGTGGCTTAAATCTTTCCCTTCATG
109255 TCTTTATGGT
Statistics
Matches: 254, Mismatches: 50, Indels: 43
0.73 0.14 0.12
Matches are distributed among these distances:
48 14 0.06
49 128 0.50
50 98 0.39
51 14 0.06
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (48 bp):
CATTGTGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAGGTTCGT
Found at i:109044 original size:99 final size:98
Alignment explanation
Indices: 108936--109254 Score: 462
Period size: 99 Copynumber: 3.2 Consensus size: 98
108926 TCACCATTGT
* *
108936 GGCTTAAATCTTTCCCTTCGTGCTTCTGAGGTACAAGGTTCGTCATTGTGACTTAAACCTTTCCC
1 GGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGTCATTGCGACTTAAACCTTTCCC
*
109001 TCAATTATCTTTGTGGTACTGGATTCGTCGTTGC
66 TC-ATTATCTTCGTGGTACTGGATTCGTCGTTGC
* * * *
109035 GGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACGAGGTTCGTCATTACGATTTAAACTTTTCCC
1 GGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGTCATTGCGACTTAAACCTTTCCC
* *
109100 TCCATTACCTTCGTGGTATTGGATTC-TCCGTTGC
66 T-CATTATCTTCGTGGTACTGGATTCGT-CGTTGC
* * * *
109134 GACTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTTGCCGTTGCGACTTAAACCTTTCCC
1 GGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGTCATTGCGACTTAAACCTTTCCC
109199 TTCATTATCTTCGTGGTACTGGATTCG-CTGTTGC
66 -TCATTATCTTCGTGGTACTGGATTCGTC-GTTGC
109233 GGCTTAAATCTTTCCCTTCATG
1 GGCTTAAATCTTTCCCTTCATG
109255 TCTTTATGGT
Statistics
Matches: 195, Mismatches: 20, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
98 2 0.01
99 191 0.98
100 2 0.01
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.39
Consensus pattern (98 bp):
GGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGTCATTGCGACTTAAACCTTTCCC
TCATTATCTTCGTGGTACTGGATTCGTCGTTGC
Found at i:109250 original size:50 final size:50
Alignment explanation
Indices: 108985--109253 Score: 207
Period size: 50 Copynumber: 5.4 Consensus size: 50
108975 TCGTCATTGT
* * *
108985 GACTTAAACCTTTCCC-TCAATTATCTTTGTGGTACTGGATTCG-TCGTTGC
1 GACTTAAATCTTTCCCTTC-ATTAGCTTCGTGGTACTGGATTCGCT-GTTGC
* * * * *
109035 GGCTTAAATCTTTCCCTTCA-T-GCTTCTGAGGTAC-GAGGTTCG-TCATTAC
1 GACTTAAATCTTTCCCTTCATTAGCTTC-GTGGTACTG-GATTCGCT-GTTGC
* * * * * *
109084 GATTTAAA-CTTTTCCCTCCATTACCTTCGTGGTATTGGATTCTCCGTTGC
1 GACTTAAATC-TTTCCCTTCATTAGCTTCGTGGTACTGGATTCGCTGTTGC
* * * *
109134 GACTTAAATCTTTCCCTTCA-T-GCTTCTGAGGTACAAGG-TTTGCCGTTGC
1 GACTTAAATCTTTCCCTTCATTAGCTTC-GTGGTAC-TGGATTCGCTGTTGC
* *
109183 GACTTAAACCTTTCCCTTCATTATCTTCGTGGTACTGGATTCGCTGTTGC
1 GACTTAAATCTTTCCCTTCATTAGCTTCGTGGTACTGGATTCGCTGTTGC
*
109233 GGCTTAAATCTTTCCCTTCAT
1 GACTTAAATCTTTCCCTTCAT
109254 GTCTTTATGG
Statistics
Matches: 170, Mismatches: 35, Indels: 28
0.73 0.15 0.12
Matches are distributed among these distances:
48 9 0.05
49 68 0.40
50 81 0.48
51 12 0.07
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.39
Consensus pattern (50 bp):
GACTTAAATCTTTCCCTTCATTAGCTTCGTGGTACTGGATTCGCTGTTGC
Found at i:120983 original size:30 final size:31
Alignment explanation
Indices: 120947--121025 Score: 103
Period size: 30 Copynumber: 2.6 Consensus size: 31
120937 AAAAGGCAAG
120947 GGGTCAAAAATA-AATTTTT-AGAAAGTCTAA
1 GGGTCAAAAATATAATTTTTGA-AAAGTCTAA
* *
120977 GTGTC-AAAATATAATTTTTGAAAAGTCTAG
1 GGGTCAAAAATATAATTTTTGAAAAGTCTAA
121007 GGGT-AAAAATATAATTTTT
1 GGGTCAAAAATATAATTTTT
121026 TGGGAAGTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
29 6 0.14
30 36 0.84
31 1 0.02
ACGTcount: A:0.43, C:0.05, G:0.16, T:0.35
Consensus pattern (31 bp):
GGGTCAAAAATATAATTTTTGAAAAGTCTAA
Found at i:121047 original size:31 final size:31
Alignment explanation
Indices: 120952--121054 Score: 97
Period size: 31 Copynumber: 3.4 Consensus size: 31
120942 GCAAGGGGTC
* *
120952 AAAAATA-AATTTTTAG-AAAGTCTAAG-TGT
1 AAAAATATAATTTTTTGAAAAGTCT-AGCGGT
* *
120981 CAAAATATAA-TTTTTGAAAAGTCTAGGGGT
1 AAAAATATAATTTTTTGAAAAGTCTAGCGGT
** *
121011 AAAAATATAATTTTTTGGGAAGTTTAGCGGT
1 AAAAATATAATTTTTTGAAAAGTCTAGCGGT
*
121042 TAAAATATAATTT
1 AAAAATATAATTT
121055 CTCAATGAAA
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
29 13 0.21
30 20 0.33
31 28 0.46
ACGTcount: A:0.43, C:0.04, G:0.17, T:0.37
Consensus pattern (31 bp):
AAAAATATAATTTTTTGAAAAGTCTAGCGGT
Found at i:123522 original size:15 final size:16
Alignment explanation
Indices: 123498--123535 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
123488 TTTTTTCCCA
123498 TCTTTACCTTTCTCTAT
1 TCTTT-CCTTTCTCTAT
*
123515 T-TTTCCTTTCTTTAT
1 TCTTTCCTTTCTCTAT
123530 TCTTTC
1 TCTTTC
123536 TTCTTTTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 11 0.58
16 7 0.37
17 1 0.05
ACGTcount: A:0.08, C:0.26, G:0.00, T:0.66
Consensus pattern (16 bp):
TCTTTCCTTTCTCTAT
Found at i:123543 original size:26 final size:24
Alignment explanation
Indices: 123483--123543 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 24
123473 CACGAGTAAG
123483 TTTCT-TTTTTTCCCATCTTTACC
1 TTTCTCTTTTTTCCCATCTTTACC
** *
123506 TTTCTCTATTTTTCCTTTCTTTATTC
1 TTTCTCT-TTTTTCCCATCTTTA-CC
123532 TTTCTTCTTTTT
1 TTTC-TCTTTTT
123544 GTTTTTGCTG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 5 0.16
24 1 0.03
25 13 0.42
26 9 0.29
27 3 0.10
ACGTcount: A:0.07, C:0.25, G:0.00, T:0.69
Consensus pattern (24 bp):
TTTCTCTTTTTTCCCATCTTTACC
Found at i:128220 original size:84 final size:84
Alignment explanation
Indices: 128123--128291 Score: 304
Period size: 84 Copynumber: 2.0 Consensus size: 84
128113 AGAAGATTTC
128123 TTTCTGACAATTAAAAATCATGGTTGTGTTGGTGTTGTTTTGTTAACTTTTTGTATATGTAATAT
1 TTTCTGACAATTAAAAATCATGGTTGTGTTGGTGTTGTTTTGTTAACTTTTTGTATATGTAATAT
*
128188 TTGGATGATAAGATGTCAT
66 TTGGATGATAAGATGCCAT
128207 TTTCTGATC-ATTAAAAATCATGGTTGTGTTGGTGTTGTTTTGTTAACTTTTTGTATATGTAATA
1 TTTCTGA-CAATTAAAAATCATGGTTGTGTTGGTGTTGTTTTGTTAACTTTTTGTATATGTAATA
*
128271 TTTGGATGGTAAGATGCCAT
65 TTTGGATGATAAGATGCCAT
128291 T
1 T
128292 GATAGAATGT
Statistics
Matches: 82, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
84 81 0.99
85 1 0.01
ACGTcount: A:0.25, C:0.07, G:0.21, T:0.48
Consensus pattern (84 bp):
TTTCTGACAATTAAAAATCATGGTTGTGTTGGTGTTGTTTTGTTAACTTTTTGTATATGTAATAT
TTGGATGATAAGATGCCAT
Found at i:128699 original size:58 final size:57
Alignment explanation
Indices: 128536--128704 Score: 218
Period size: 58 Copynumber: 2.9 Consensus size: 57
128526 TAATATTATA
* * *
128536 TATTATAATTTTTACT-AATTCATATTTTAATAATAATTATATTAAAAATATTATTAAAT
1 TATTATTATTTTTATTAAATT-ATA-TTTAATAATAATTATATT-AAAATATAATTAAAT
*
128595 TATATATTA-TTTTATTAAATTATATTTAATAATAATTATGTTAAAATATAATTAAAT
1 TAT-TATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAAT
*
128652 TAATTATTATTTTTATTAAATTATATTTAATAATAATCT-TATTAAAATTTAAT
1 T-ATTATTATTTTTATTAAATTATATTTAATAATAAT-TATATTAAAATATAAT
128705 AACAATAATC
Statistics
Matches: 99, Mismatches: 6, Indels: 11
0.85 0.05 0.09
Matches are distributed among these distances:
57 20 0.20
58 58 0.59
59 13 0.13
60 8 0.08
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.52
Consensus pattern (57 bp):
TATTATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAAT
Found at i:128881 original size:16 final size:16
Alignment explanation
Indices: 128860--128913 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
128850 TGAATTACTG
128860 ATTACAG-TCTTATTCC
1 ATTACAGTTC-TATTCC
**
128876 ATTACAGTTCTATTTT
1 ATTACAGTTCTATTCC
*
128892 ATTACAATTCTATTCC
1 ATTACAGTTCTATTCC
128908 ATTACA
1 ATTACA
128914 ACGAATCAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
16 30 0.94
17 2 0.06
ACGTcount: A:0.30, C:0.20, G:0.04, T:0.46
Consensus pattern (16 bp):
ATTACAGTTCTATTCC
Found at i:129392 original size:20 final size:21
Alignment explanation
Indices: 129361--129399 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
129351 TAAAATTCTA
129361 ATTTTATTATTATTATAAACT
1 ATTTTATTATTATTATAAACT
129382 ATTTT-TTATTATTATAAA
1 ATTTTATTATTATTATAAA
129400 TGGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (21 bp):
ATTTTATTATTATTATAAACT
Found at i:133759 original size:31 final size:30
Alignment explanation
Indices: 133694--133764 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 30
133684 GTTACATTTA
* *
133694 ACAAAACAATCACTCAACTTTGAAAATGTG
1 ACAAAACAGTCACTAAACTTTGAAAATGTG
*
133724 ACAAAACAGTCACTAAAGTTATCGAAAA-GTG
1 ACAAAACAGTCACTAAACTT-T-GAAAATGTG
133755 ACAAAACAGT
1 ACAAAACAGT
133765 GCTCTTGGCT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 17 0.47
31 14 0.39
32 5 0.14
ACGTcount: A:0.49, C:0.18, G:0.13, T:0.20
Consensus pattern (30 bp):
ACAAAACAGTCACTAAACTTTGAAAATGTG
Found at i:134593 original size:31 final size:30
Alignment explanation
Indices: 134555--134626 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
134545 GTAAGTAGAG
* *
134555 GACTGTTTTGTCA-TTTTTCGATAACTTTAGT
1 GACTGTTTTGTCACATTTTC-A-AACTTGAGT
* *
134586 GACTGTTTTATCACATTTTCAAAGTTGAGT
1 GACTGTTTTGTCACATTTTCAAACTTGAGT
134616 GACTGTTTTGT
1 GACTGTTTTGT
134627 TAAATGTAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
30 17 0.49
31 13 0.37
32 5 0.14
ACGTcount: A:0.21, C:0.12, G:0.18, T:0.49
Consensus pattern (30 bp):
GACTGTTTTGTCACATTTTCAAACTTGAGT
Found at i:137309 original size:17 final size:17
Alignment explanation
Indices: 137287--137331 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
137277 AATCATTTAA
137287 ATAATTATTTTTG-AATT
1 ATAATTATTTTTGTAA-T
*
137304 ATAATTATTTATGTAAT
1 ATAATTATTTTTGTAAT
137321 -TAATTATTTTT
1 ATAATTATTTTT
137332 TGGGTCATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 10 0.40
17 13 0.52
18 2 0.08
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (17 bp):
ATAATTATTTTTGTAAT
Found at i:146833 original size:18 final size:18
Alignment explanation
Indices: 146793--146835 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
146783 TTTTCAGTTG
146793 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
* *
146811 CAATTAA-TTAAATTTATT
1 TAATTAATTTAAAATT-TT
146829 TAATTAA
1 TAATTAA
146836 AAACCATTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAATTTAAAATTTT
Found at i:147541 original size:44 final size:44
Alignment explanation
Indices: 147491--147583 Score: 159
Period size: 44 Copynumber: 2.1 Consensus size: 44
147481 CATTTAAAAG
*
147491 TTTATTTTATTAGGGTGTTTTTAATACTGTTAAATAAATATATT
1 TTTATTTTATTAGGGCGTTTTTAATACTGTTAAATAAATATATT
* *
147535 TTTATTTTATTATGGCGTTTTTAATACTGTTAGATAAATATATT
1 TTTATTTTATTAGGGCGTTTTTAATACTGTTAAATAAATATATT
147579 TTTAT
1 TTTAT
147584 GCAATCGTCC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.30, C:0.03, G:0.11, T:0.56
Consensus pattern (44 bp):
TTTATTTTATTAGGGCGTTTTTAATACTGTTAAATAAATATATT
Found at i:149457 original size:23 final size:23
Alignment explanation
Indices: 149412--149476 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
149402 GATTTAAAAC
*
149412 ATATTCATATTTATATTATTAAA
1 ATATTCATATTTATACTATTAAA
* *
149435 ATATTCATATTTTGTACTATAAAAA
1 ATATTCATA-TTTATACTAT-TAAA
149460 ATTATTACATATTTATA
1 A-TATT-CATATTTATA
149477 AATTGTAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
23 9 0.26
24 8 0.24
25 4 0.12
26 9 0.26
27 4 0.12
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (23 bp):
ATATTCATATTTATACTATTAAA
Found at i:150315 original size:31 final size:30
Alignment explanation
Indices: 150244--150316 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 30
150234 TTGTATATAT
150244 AAATTTTAATTTGGTGCAATTATACACGTG
1 AAATTTTAATTTGGTGCAATTATACACGTG
* * *
150274 AAACTCTAATTGTGGTTCAAATGTATAC-C-TG
1 AAATTTTAATT-TGGTGC-AAT-TATACACGTG
150305 AAATTTTAATTT
1 AAATTTTAATTT
150317 TGATTTAATC
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
30 10 0.29
31 16 0.46
32 4 0.11
33 5 0.14
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (30 bp):
AAATTTTAATTTGGTGCAATTATACACGTG
Found at i:151786 original size:2 final size:2
Alignment explanation
Indices: 151779--151812 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
151769 TCAACCATGC
151779 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
151813 ATCCAGCAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:157626 original size:66 final size:66
Alignment explanation
Indices: 157515--157646 Score: 246
Period size: 66 Copynumber: 2.0 Consensus size: 66
157505 ACGTTGTTTA
*
157515 TCTCTGACTGATTTTGCCACGTGAACCAATTATGTGTAGACACGTGACAAGGACAAGCTGAAGGG
1 TCTCTGACTAATTTTGCCACGTGAACCAATTATGTGTAGACACGTGACAAGGACAAGCTGAAGGG
157580 G
66 G
*
157581 TCTCTGACTAATTTTGCCACGTGAACCAATTATGTGTAGATACGTGACAAGGACAAGCTGAAGGG
1 TCTCTGACTAATTTTGCCACGTGAACCAATTATGTGTAGACACGTGACAAGGACAAGCTGAAGGG
157646 G
66 G
157647 CATTTTAACA
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.25
Consensus pattern (66 bp):
TCTCTGACTAATTTTGCCACGTGAACCAATTATGTGTAGACACGTGACAAGGACAAGCTGAAGGG
G
Found at i:157739 original size:33 final size:33
Alignment explanation
Indices: 157702--157780 Score: 130
Period size: 30 Copynumber: 2.5 Consensus size: 33
157692 TTCCCCTCAC
157702 TTTTTCATTATTATTTTTTTATTTGATAGGTTA
1 TTTTTCATTATTATTTTTTTATTTGATAGGTTA
157735 TTTTTC---ATTATTTTTTTATTTGATAGGTTA
1 TTTTTCATTATTATTTTTTTATTTGATAGGTTA
157765 TTTTTCATTATT-TTTT
1 TTTTTCATTATTATTTT
157781 AAACACCCAT
Statistics
Matches: 43, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
30 30 0.70
32 4 0.09
33 9 0.21
ACGTcount: A:0.19, C:0.04, G:0.08, T:0.70
Consensus pattern (33 bp):
TTTTTCATTATTATTTTTTTATTTGATAGGTTA
Found at i:157745 original size:30 final size:30
Alignment explanation
Indices: 157711--157780 Score: 140
Period size: 30 Copynumber: 2.3 Consensus size: 30
157701 CTTTTTCATT
157711 ATTATTTTTTTATTTGATAGGTTATTTTTC
1 ATTATTTTTTTATTTGATAGGTTATTTTTC
157741 ATTATTTTTTTATTTGATAGGTTATTTTTC
1 ATTATTTTTTTATTTGATAGGTTATTTTTC
157771 ATTATTTTTT
1 ATTATTTTTT
157781 AAACACCCAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.20, C:0.03, G:0.09, T:0.69
Consensus pattern (30 bp):
ATTATTTTTTTATTTGATAGGTTATTTTTC
Found at i:159136 original size:24 final size:23
Alignment explanation
Indices: 159094--159141 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
159084 ACTTTTATTC
159094 TCTCTCAAAAATTTGTTCTTGTTT
1 TCTCTCAAAAATTTGTTC-TGTTT
*
159118 TCTCTCAAATA-TTGCTTCTGTTT
1 TCTCTCAAAAATTTG-TTCTGTTT
159141 T
1 T
159142 TTAGTGATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.19, C:0.19, G:0.08, T:0.54
Consensus pattern (23 bp):
TCTCTCAAAAATTTGTTCTGTTT
Found at i:159450 original size:7 final size:7
Alignment explanation
Indices: 159440--159466 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
159430 GAAAATAATA
159440 AGTTGAG
1 AGTTGAG
159447 AGTTGAG
1 AGTTGAG
159454 AGTTGAG
1 AGTTGAG
159461 AGTTGA
1 AGTTGA
159467 ATTGAATAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.41, T:0.30
Consensus pattern (7 bp):
AGTTGAG
Found at i:160581 original size:21 final size:22
Alignment explanation
Indices: 160557--160609 Score: 92
Period size: 21 Copynumber: 2.5 Consensus size: 22
160547 ATTAATCAAA
160557 TTAATCGAACCTT-TTAAACTT
1 TTAATCGAACCTTCTTAAACTT
160578 TTAATCGAA-CTTCTTAAACTT
1 TTAATCGAACCTTCTTAAACTT
160599 TTAATCGAACC
1 TTAATCGAACC
160610 GAATTGAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 3 0.10
21 26 0.87
22 1 0.03
ACGTcount: A:0.34, C:0.21, G:0.06, T:0.40
Consensus pattern (22 bp):
TTAATCGAACCTTCTTAAACTT
Found at i:173932 original size:117 final size:117
Alignment explanation
Indices: 173789--174023 Score: 470
Period size: 117 Copynumber: 2.0 Consensus size: 117
173779 CGATCCGGCC
173789 CGAATTTGTAATAATGATTTTATTTTTTATTATTAATACCATTTTTTTACTTCAAATTTTAAAAA
1 CGAATTTGTAATAATGATTTTATTTTTTATTATTAATACCATTTTTTTACTTCAAATTTTAAAAA
173854 TTACTAAAAAAATTAATAATTTGTGTTACTACTTACTGTCTACGTCTTCTCT
66 TTACTAAAAAAATTAATAATTTGTGTTACTACTTACTGTCTACGTCTTCTCT
173906 CGAATTTGTAATAATGATTTTATTTTTTATTATTAATACCATTTTTTTACTTCAAATTTTAAAAA
1 CGAATTTGTAATAATGATTTTATTTTTTATTATTAATACCATTTTTTTACTTCAAATTTTAAAAA
173971 TTACTAAAAAAATTAATAATTTGTGTTACTACTTACTGTCTACGTCTTCTCT
66 TTACTAAAAAAATTAATAATTTGTGTTACTACTTACTGTCTACGTCTTCTCT
174023 C
1 C
174024 CTCCCCTTAG
Statistics
Matches: 118, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
117 118 1.00
ACGTcount: A:0.33, C:0.12, G:0.06, T:0.49
Consensus pattern (117 bp):
CGAATTTGTAATAATGATTTTATTTTTTATTATTAATACCATTTTTTTACTTCAAATTTTAAAAA
TTACTAAAAAAATTAATAATTTGTGTTACTACTTACTGTCTACGTCTTCTCT
Found at i:174111 original size:20 final size:20
Alignment explanation
Indices: 174086--174123 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
174076 AAAACCTAAA
*
174086 TGCTTCCATCCATTGCTAGG
1 TGCTTCCATCAATTGCTAGG
174106 TGCTTCCATCAATTGCTA
1 TGCTTCCATCAATTGCTA
174124 AGTCCTTTCA
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:0.18, C:0.29, G:0.16, T:0.37
Consensus pattern (20 bp):
TGCTTCCATCAATTGCTAGG
Found at i:174135 original size:20 final size:20
Alignment explanation
Indices: 174088--174141 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
174078 AACCTAAATG
* * *
174088 CTTCCATCCATTGCTAGGTG
1 CTTCCATCAATTGCTAAGTC
174108 CTTCCATCAATTGCTAAGTC
1 CTTCCATCAATTGCTAAGTC
* *
174128 CTTTCATCAGTTGC
1 CTTCCATCAATTGC
174142 AAATCGCAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.19, C:0.30, G:0.15, T:0.37
Consensus pattern (20 bp):
CTTCCATCAATTGCTAAGTC
Found at i:177058 original size:18 final size:18
Alignment explanation
Indices: 177035--177089 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 18
177025 TTAATAGGGT
177035 TGATTTGGGTGAAGATTA
1 TGATTTGGGTGAAGATTA
*
177053 TGATTTAGGTGAAGATTA
1 TGATTTGGGTGAAGATTA
* * *
177071 TGATTAGAGTGATGATTA
1 TGATTTGGGTGAAGATTA
177089 T
1 T
177090 AAACGGTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.29, T:0.40
Consensus pattern (18 bp):
TGATTTGGGTGAAGATTA
Found at i:177747 original size:23 final size:23
Alignment explanation
Indices: 177686--177748 Score: 85
Period size: 22 Copynumber: 2.8 Consensus size: 23
177676 TTTTGCAGGT
*
177686 TGTTTTTGGTGTAGA-TTTGGTAC
1 TGTTTTTGGT-TCGATTTTGGTAC
*
177709 TGTTTTTGGTGC-ATTTTGGTAC
1 TGTTTTTGGTTCGATTTTGGTAC
177731 TGTTTTTGGTTCGATTTT
1 TGTTTTTGGTTCGATTTT
177749 AGTAGTATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.03
22 19 0.54
23 15 0.43
ACGTcount: A:0.10, C:0.06, G:0.27, T:0.57
Consensus pattern (23 bp):
TGTTTTTGGTTCGATTTTGGTAC
Found at i:177759 original size:23 final size:22
Alignment explanation
Indices: 177705--177759 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
177695 TGTAGATTTG
* *
177705 GTACTGTTTTTGGTGCATTTTG
1 GTACTATTTTTGGTGCATTTTA
* *
177727 GTACTGTTTTTGGTTCGATTTTA
1 GTACTATTTTTGGTGC-ATTTTA
*
177750 GTAGTATTTT
1 GTACTATTTT
177760 CAGTGCTGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 15 0.54
23 13 0.46
ACGTcount: A:0.13, C:0.07, G:0.24, T:0.56
Consensus pattern (22 bp):
GTACTATTTTTGGTGCATTTTA
Found at i:178226 original size:11 final size:12
Alignment explanation
Indices: 178210--178241 Score: 57
Period size: 11 Copynumber: 2.8 Consensus size: 12
178200 ATAAAGCTTG
178210 ACCCGAACCC-A
1 ACCCGAACCCGA
178221 ACCCGAACCCGA
1 ACCCGAACCCGA
178233 ACCCGAACC
1 ACCCGAACC
178242 ATAATCACCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.34, C:0.53, G:0.12, T:0.00
Consensus pattern (12 bp):
ACCCGAACCCGA
Found at i:178229 original size:6 final size:6
Alignment explanation
Indices: 178210--178241 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
178200 ATAAAGCTTG
178210 ACCCGA ACCC-A ACCCGA ACCCGA ACCCGA ACC
1 ACCCGA ACCCGA ACCCGA ACCCGA ACCCGA ACC
178242 ATAATCACCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.34, C:0.53, G:0.12, T:0.00
Consensus pattern (6 bp):
ACCCGA
Found at i:179235 original size:18 final size:17
Alignment explanation
Indices: 179212--179249 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
179202 CTTTAGATTT
179212 TTTTTAAAAAAATATAAA
1 TTTTTAAAAAAATA-AAA
*
179230 TTTTTAAAAATATAAAA
1 TTTTTAAAAAAATAAAA
179247 TTT
1 TTT
179250 GGAATTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTTTAAAAAAATAAAA
Found at i:185377 original size:24 final size:24
Alignment explanation
Indices: 185350--185409 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
185340 TAAAAATAAT
* *
185350 TATATTAAAAATATTATTAAATTA
1 TATATTAATAATATTATTAAAATA
* *
185374 TATATTATTAATTTTATTAAAATA
1 TATATTAATAATATTATTAAAATA
185398 TAT-TTAATAATA
1 TATATTAATAATA
185410 ATCTTATTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 7 0.23
24 23 0.77
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TATATTAATAATATTATTAAAATA
Found at i:185609 original size:16 final size:17
Alignment explanation
Indices: 185588--185630 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
185578 ATTATTAATT
185588 ACAATTTTATTCCT-TC
1 ACAATTTTATTCCTATC
*
185604 ACAATTTT-TTCCTATT
1 ACAATTTTATTCCTATC
*
185620 ACAACTTTATT
1 ACAATTTTATT
185631 TCATTATAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 5 0.22
16 16 0.70
17 2 0.09
ACGTcount: A:0.28, C:0.21, G:0.00, T:0.51
Consensus pattern (17 bp):
ACAATTTTATTCCTATC
Found at i:186180 original size:24 final size:21
Alignment explanation
Indices: 186142--186190 Score: 62
Period size: 24 Copynumber: 2.2 Consensus size: 21
186132 AAAAAATTAT
186142 AAAATATAATATAATAAAATA
1 AAAATATAATATAATAAAATA
*
186163 AAAATATATACTATTAATAAGATA
1 AAAATATA-A-TA-TAATAAAATA
186187 AAAA
1 AAAA
186191 ATTGAGACTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 8 0.33
22 1 0.04
23 2 0.08
24 13 0.54
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (21 bp):
AAAATATAATATAATAAAATA
Found at i:190189 original size:109 final size:110
Alignment explanation
Indices: 190062--190268 Score: 265
Period size: 109 Copynumber: 1.9 Consensus size: 110
190052 TCAGTTAATT
** *
190062 TGACTAGTGCCAGGCACACAAATTGTCGGTTTAATTGACTAGCGCAGGGTGCAACA-TCGTTGGT
1 TGACTAGTGCCAGGCACACAAATTGTCGGTTTAACCGACTAGCGCAGGGCGCAACATTCGTTGGT
* *
190126 TTATCCAACTAGAGCTGGGCTTACCTTTTATATCGTCAGTATAGC
66 ATATCCAACTAGAGCTGGGCTCACCTTTTATATCGTCAGTATAGC
* * * * * * * * *
190171 TGACTAGTG-CACGTCACACCATTTTTCGGTTTAACCGACTAGTGCTGGGCGTAATATTTGTTGG
1 TGACTAGTGCCA-GGCACACAAATTGTCGGTTTAACCGACTAGCGCAGGGCGCAACATTCGTTGG
190235 TATATCCAACTAGAGCTGGGCTCACCTTTTATAT
65 TATATCCAACTAGAGCTGGGCTCACCTTTTATAT
190269 TATTGGTTTA
Statistics
Matches: 82, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
108 2 0.02
109 42 0.51
110 38 0.46
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (110 bp):
TGACTAGTGCCAGGCACACAAATTGTCGGTTTAACCGACTAGCGCAGGGCGCAACATTCGTTGGT
ATATCCAACTAGAGCTGGGCTCACCTTTTATATCGTCAGTATAGC
Found at i:194240 original size:56 final size:56
Alignment explanation
Indices: 194170--194454 Score: 412
Period size: 56 Copynumber: 5.1 Consensus size: 56
194160 AAAATATTTA
* * * *
194170 AACCTTTACATTGATATCCTTTTAGACATCTCTTCTCATAATATCCTTACGGGTAT
1 AACCTTTACATTGATATCCTTTTGGACATCCCTTTTCATAATATCCTTACGGATAT
* * * *
194226 AACCTTTACGTTGATATTCTTTTGAACATCCCTTTTCATAATATCCTTACGTATAT
1 AACCTTTACATTGATATCCTTTTGGACATCCCTTTTCATAATATCCTTACGGATAT
* *
194282 AACCTTTACATTGATATCCTTTCGGACATCCCTTTTCATAATATCCTTACGTATAT
1 AACCTTTACATTGATATCCTTTTGGACATCCCTTTTCATAATATCCTTACGGATAT
* * *
194338 AACCTTTACATTGATATCCTTTCGCATATCCCTTTTCATAATATCCTTACGGATAT
1 AACCTTTACATTGATATCCTTTTGGACATCCCTTTTCATAATATCCTTACGGATAT
* *
194394 AACCTTAACATTGATAAT-CTTTCGGACATCCCTTTTCATAATATCCTTAC-GATAT
1 AACCTTTACATTGAT-ATCCTTTTGGACATCCCTTTTCATAATATCCTTACGGATAT
194449 AACCTT
1 AACCTT
194455 CACAAAGTAT
Statistics
Matches: 210, Mismatches: 18, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
55 11 0.05
56 197 0.94
57 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.07, T:0.41
Consensus pattern (56 bp):
AACCTTTACATTGATATCCTTTTGGACATCCCTTTTCATAATATCCTTACGGATAT
Found at i:198984 original size:52 final size:52
Alignment explanation
Indices: 198802--198987 Score: 234
Period size: 52 Copynumber: 3.6 Consensus size: 52
198792 AATTCATATT
* * *
198802 CTCACGATGACA-TTGAGTCATCGGA-CCTTTAATCCAT-CATGGATTCATTTA
1 CTCACGATGACACTT-AGTCATCGGACCCTTTAATCCGTAAAT-GATTCGTTTA
* * ** *
198853 CTCACGATGACACTTAGTCATTGGACCTTTTAATTTGTAAAGGATTCGTTTA
1 CTCACGATGACACTTAGTCATCGGACCCTTTAATCCGTAAATGATTCGTTTA
* *
198905 CTCACGATGACACTTTGTCATCAGACCCTTTAATCCGTAAATGATTCGTTTA
1 CTCACGATGACACTTAGTCATCGGACCCTTTAATCCGTAAATGATTCGTTTA
*
198957 CTCACTATGACACTTAGTCATCGGACCCTTT
1 CTCACGATGACACTTAGTCATCGGACCCTTT
198988 CGTTTATAGC
Statistics
Matches: 114, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
51 21 0.18
52 92 0.81
53 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (52 bp):
CTCACGATGACACTTAGTCATCGGACCCTTTAATCCGTAAATGATTCGTTTA
Found at i:200216 original size:53 final size:53
Alignment explanation
Indices: 200136--200241 Score: 203
Period size: 53 Copynumber: 2.0 Consensus size: 53
200126 TACCATTGAA
200136 ATCGAGCTGTTACATTTCTAATCTATAACTACAGACACTTTCTCGGATCTACC
1 ATCGAGCTGTTACATTTCTAATCTATAACTACAGACACTTTCTCGGATCTACC
*
200189 ATCGAGCTGTTACATTTCTAATCTATAACTGCAGACACTTTCTCGGATCTACC
1 ATCGAGCTGTTACATTTCTAATCTATAACTACAGACACTTTCTCGGATCTACC
200242 CTAATACCTT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.34
Consensus pattern (53 bp):
ATCGAGCTGTTACATTTCTAATCTATAACTACAGACACTTTCTCGGATCTACC
Found at i:204012 original size:56 final size:56
Alignment explanation
Indices: 203943--204098 Score: 215
Period size: 56 Copynumber: 2.8 Consensus size: 56
203933 TTATTTAAAT
* * * * * *
203943 CTTTAAATTGATATGCTTTTAGACATCCCTTCTCATATTATCCTTA-GGCGTGTAAC
1 CTTTACATTGATATCCTTTTAGACATCCCTTTTCATAATATCCTTACGG-ATATAAC
* *
203999 CTTTACGTTGATATCCTTTTGGACATCCCTTTTCATAATATCCTTACGGATATAAC
1 CTTTACATTGATATCCTTTTAGACATCCCTTTTCATAATATCCTTACGGATATAAC
*
204055 CTTTACATTGATATCCTTTCAGACATCCCTTTTCATAATATCCT
1 CTTTACATTGATATCCTTTTAGACATCCCTTTTCATAATATCCT
204099 AATATCCTTA
Statistics
Matches: 88, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
56 86 0.98
57 2 0.02
ACGTcount: A:0.25, C:0.24, G:0.10, T:0.42
Consensus pattern (56 bp):
CTTTACATTGATATCCTTTTAGACATCCCTTTTCATAATATCCTTACGGATATAAC
Found at i:204042 original size:27 final size:27
Alignment explanation
Indices: 204009--204098 Score: 99
Period size: 27 Copynumber: 3.3 Consensus size: 27
203999 CTTTACGTTG
*
204009 ATATCCTTTTGGACATCCCTTTTCATA
1 ATATCCTTTCGGACATCCCTTTTCATA
* * * * *
204036 ATATCCTTACGGATATAACCTTTACATTG
1 ATATCCTTTCGGACAT-CCCTTTTCA-TA
*
204065 ATATCCTTTCAGACATCCCTTTTCATA
1 ATATCCTTTCGGACATCCCTTTTCATA
204092 ATATCCT
1 ATATCCT
204099 AATATCCTTA
Statistics
Matches: 49, Mismatches: 12, Indels: 4
0.75 0.18 0.06
Matches are distributed among these distances:
27 21 0.43
28 14 0.29
29 14 0.29
ACGTcount: A:0.27, C:0.26, G:0.07, T:0.41
Consensus pattern (27 bp):
ATATCCTTTCGGACATCCCTTTTCATA
Found at i:204188 original size:28 final size:28
Alignment explanation
Indices: 204157--204212 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
204147 TTCAGACATC
* *
204157 CCTTTTCATAATATCCTTAG-GGATATAA
1 CCTTTACAAAATATCCTT-GCGGATATAA
204185 CCTTTACAAAATATCCTTGCGGATATAA
1 CCTTTACAAAATATCCTTGCGGATATAA
204213 AAAAATCAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 1 0.04
28 24 0.96
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.36
Consensus pattern (28 bp):
CCTTTACAAAATATCCTTGCGGATATAA
Found at i:206403 original size:20 final size:22
Alignment explanation
Indices: 206374--206419 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
206364 TTAGCATACA
206374 TGTTTAACA-TTTC-ATACTTAG
1 TGTTTAACATTTTCTA-ACTTAG
206395 TGTTT-ACATTTTCTAACTTAG
1 TGTTTAACATTTTCTAACTTAG
206416 TGTT
1 TGTT
206420 ATACGATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 3 0.13
21 19 0.83
22 1 0.04
ACGTcount: A:0.24, C:0.13, G:0.11, T:0.52
Consensus pattern (22 bp):
TGTTTAACATTTTCTAACTTAG
Found at i:216915 original size:21 final size:21
Alignment explanation
Indices: 216881--216937 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 21
216871 TTTAGCATGC
216881 ATGTTTAGCA-TTTC-ATACTTA
1 ATGTTTA-CATTTTCTA-ACTTA
216902 ATGTTTACATTTTCTAACTTA
1 ATGTTTACATTTTCTAACTTA
*
216923 GTGTTATACAGTTTT
1 ATGTT-TACA-TTTT
216938 AATTCTTTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
20 2 0.06
21 20 0.65
22 5 0.16
23 4 0.13
ACGTcount: A:0.26, C:0.12, G:0.11, T:0.51
Consensus pattern (21 bp):
ATGTTTACATTTTCTAACTTA
Found at i:221234 original size:12 final size:12
Alignment explanation
Indices: 221217--221241 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
221207 TATATATATA
221217 TGTGTGTGTGTT
1 TGTGTGTGTGTT
221229 TGTGTGTGTGTT
1 TGTGTGTGTGTT
221241 T
1 T
221242 TAATATGATG
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:0.00, C:0.00, G:0.40, T:0.60
Consensus pattern (12 bp):
TGTGTGTGTGTT
Found at i:224576 original size:81 final size:81
Alignment explanation
Indices: 224441--224602 Score: 315
Period size: 81 Copynumber: 2.0 Consensus size: 81
224431 GATGACTGAG
*
224441 ATTTATGCTTGTTTGCATATTCTCGTCTGTTTAGTGCGAGCAGCATCGTAGGGAATATATATACC
1 ATTTATGCTTGTTTGCATATTCTCGTCTGCTTAGTGCGAGCAGCATCGTAGGGAATATATATACC
224506 GTATCGATGGCTAATA
66 GTATCGATGGCTAATA
224522 ATTTATGCTTGTTTGCATATTCTCGTCTGCTTAGTGCGAGCAGCATCGTAGGGAATATATATACC
1 ATTTATGCTTGTTTGCATATTCTCGTCTGCTTAGTGCGAGCAGCATCGTAGGGAATATATATACC
224587 GTATCGATGGCTAATA
66 GTATCGATGGCTAATA
224603 CTAGCATCGT
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 80 1.00
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (81 bp):
ATTTATGCTTGTTTGCATATTCTCGTCTGCTTAGTGCGAGCAGCATCGTAGGGAATATATATACC
GTATCGATGGCTAATA
Found at i:224682 original size:36 final size:36
Alignment explanation
Indices: 224628--224726 Score: 162
Period size: 36 Copynumber: 2.8 Consensus size: 36
224618 AGTAACATGT
224628 ATGACCTTTGGGTCAATAGGGAGTAAAATAAGCATC
1 ATGACCTTTGGGTCAATAGGGAGTAAAATAAGCATC
* * *
224664 ATGACCTTGGGGTTAATAGGGAGTAAAATGAGCATC
1 ATGACCTTTGGGTCAATAGGGAGTAAAATAAGCATC
*
224700 ATGACATTTGGGTCAATAGGGAGTAAA
1 ATGACCTTTGGGTCAATAGGGAGTAAA
224727 TCATATATCG
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 57 1.00
ACGTcount: A:0.35, C:0.11, G:0.28, T:0.25
Consensus pattern (36 bp):
ATGACCTTTGGGTCAATAGGGAGTAAAATAAGCATC
Found at i:226041 original size:21 final size:21
Alignment explanation
Indices: 226017--226102 Score: 118
Period size: 21 Copynumber: 4.1 Consensus size: 21
226007 ATATATACAG
* * *
226017 TTCATAATATGTAGATTACAA
1 TTCACAATATATAGATCACAA
* *
226038 TTCACAATATACATATCACAA
1 TTCACAATATATAGATCACAA
226059 TTCACAATATATAGATCACAA
1 TTCACAATATATAGATCACAA
*
226080 TTCACAATATACAGATCACAA
1 TTCACAATATATAGATCACAA
226101 TT
1 TT
226103 TGCAAGCAAT
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 57 1.00
ACGTcount: A:0.45, C:0.19, G:0.05, T:0.31
Consensus pattern (21 bp):
TTCACAATATATAGATCACAA
Found at i:226080 original size:42 final size:42
Alignment explanation
Indices: 225990--226102 Score: 138
Period size: 42 Copynumber: 2.6 Consensus size: 42
225980 GATTTGCAAT
* * * * *
225990 ACAATTCACAAT-TCACCATATATACAGTTCATAATATGTAGATT
1 ACAATTCACAATAT-A-CATAT-CACAATTCACAATATATAGATC
226034 ACAATTCACAATATACATATCACAATTCACAATATATAGATC
1 ACAATTCACAATATACATATCACAATTCACAATATATAGATC
*
226076 ACAATTCACAATATACAGATCACAATT
1 ACAATTCACAATATACATATCACAATT
226103 TGCAAGCAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
42 43 0.69
43 5 0.08
44 13 0.21
45 1 0.02
ACGTcount: A:0.45, C:0.20, G:0.04, T:0.30
Consensus pattern (42 bp):
ACAATTCACAATATACATATCACAATTCACAATATATAGATC
Found at i:226592 original size:31 final size:31
Alignment explanation
Indices: 226557--226619 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
226547 TTAGGATTGG
*
226557 AAAAATTGAAATTTTCTTACGAAGAATGACA
1 AAAAATTGAAATTTTCTTACAAAGAATGACA
* *
226588 AAAAATTGTATTTTTCTTACAAAGAATGACA
1 AAAAATTGAAATTTTCTTACAAAGAATGACA
226619 A
1 A
226620 CAGTTTTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.48, C:0.10, G:0.11, T:0.32
Consensus pattern (31 bp):
AAAAATTGAAATTTTCTTACAAAGAATGACA
Found at i:226797 original size:67 final size:67
Alignment explanation
Indices: 226713--226847 Score: 252
Period size: 67 Copynumber: 2.0 Consensus size: 67
226703 TGTCAATTGA
* *
226713 ACTAAACCTCAATCGACTTTCAACCTTTATCTTTTACTAACCTTCTTTTAGGTTATTCATAAATA
1 ACTAAAACTCAATCGACTTTCAACCTTTATCTTTTACTAACCTTCTTTTAGGTTATTAATAAATA
226778 TT
66 TT
226780 ACTAAAACTCAATCGACTTTCAACCTTTATCTTTTACTAACCTTCTTTTAGGTTATTAATAAATA
1 ACTAAAACTCAATCGACTTTCAACCTTTATCTTTTACTAACCTTCTTTTAGGTTATTAATAAATA
226845 TT
66 TT
226847 A
1 A
226848 TATTTTAGCC
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.32, C:0.21, G:0.04, T:0.43
Consensus pattern (67 bp):
ACTAAAACTCAATCGACTTTCAACCTTTATCTTTTACTAACCTTCTTTTAGGTTATTAATAAATA
TT
Found at i:228419 original size:20 final size:22
Alignment explanation
Indices: 228385--228424 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
228375 TAAACAAAAA
228385 AAATAAAATTTA-TTTGATCTC
1 AAATAAAATTTATTTTGATCTC
228406 AAATAAAA-TTATTTTGATC
1 AAATAAAATTTATTTTGATC
228425 CGAATCCAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (22 bp):
AAATAAAATTTATTTTGATCTC
Found at i:248072 original size:52 final size:53
Alignment explanation
Indices: 247965--248138 Score: 144
Period size: 51 Copynumber: 3.4 Consensus size: 53
247955 TTGAAGACTA
* * * * * *
247965 GCTCGTAATGAGCGATATTCTGAACTGGCTTGTAATGAGTGATATTCTGATTG
1 GCTCGTAATGAGTGATATTCTGAACTAGCTCGTAATGAGCGATATTCTAACTG
* *
248018 GCTTGTAA-GAGTGATATTCTGAACTAGCTCG-CATGAGCGATATTCTAAACTG
1 GCTCGTAATGAGTGATATTCTGAACTAGCTCGTAATGAGCGATATTCT-AACTG
* * * * * * *
248070 GCTCG-AATGAGTGATATTTTG-ATTGGCTCATAA-GAGTGATATTTTGAATTG
1 GCTCGTAATGAGTGATATTCTGAACTAGCTCGTAATGAGCGATATTCT-AACTG
*
248121 GCTCGT-ATGAGCGATATT
1 GCTCGTAATGAGTGATATT
248139 TTGATAGGCT
Statistics
Matches: 98, Mismatches: 19, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
51 51 0.52
52 40 0.41
53 7 0.07
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.35
Consensus pattern (53 bp):
GCTCGTAATGAGTGATATTCTGAACTAGCTCGTAATGAGCGATATTCTAACTG
Found at i:248097 original size:77 final size:78
Alignment explanation
Indices: 247961--248138 Score: 250
Period size: 77 Copynumber: 2.3 Consensus size: 78
247951 ACATTTGAAG
* * **
247961 ACTAGCTCGTAATGAGCGATATTCTGAACTGGCTTGTAATGAGTGATATTCTGATTGGCTTGTAA
1 ACTAGCTCG-AATGAGCGATATTCTAAACTGGCTCGTAATGAGTGATATTCTGATTGGCTCATAA
248026 GAGTGATATTCTGA
65 GAGTGATATTCTGA
* *
248040 ACTAGCTCGCATGAGCGATATTCTAAACTGGCTCG-AATGAGTGATATTTTGATTGGCTCATAAG
1 ACTAGCTCGAATGAGCGATATTCTAAACTGGCTCGTAATGAGTGATATTCTGATTGGCTCATAAG
*
248104 AGTGATATTTTGA
66 AGTGATATTCTGA
* * *
248117 ATTGGCTCGTATGAGCGATATT
1 ACTAGCTCGAATGAGCGATATT
248139 TTGATAGGCT
Statistics
Matches: 89, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
77 57 0.64
78 23 0.26
79 9 0.10
ACGTcount: A:0.27, C:0.13, G:0.25, T:0.35
Consensus pattern (78 bp):
ACTAGCTCGAATGAGCGATATTCTAAACTGGCTCGTAATGAGTGATATTCTGATTGGCTCATAAG
AGTGATATTCTGA
Found at i:248136 original size:26 final size:26
Alignment explanation
Indices: 247965--248157 Score: 167
Period size: 26 Copynumber: 7.5 Consensus size: 26
247955 TTGAAGACTA
*
247965 GCTCGTAATGAGCGATATTCTGAACTG
1 GCTCGT-ATGAGCGATATTCTGAATTG
* *
247992 GCTTGTAATGAGTGATATTCTG-ATTG
1 GCTCGT-ATGAGCGATATTCTGAATTG
* * * * *
248018 GCTTGTAAGAGTGATATTCTGAACTA
1 GCTCGTATGAGCGATATTCTGAATTG
* * *
248044 GCTCGCATGAGCGATATTCTAAACTG
1 GCTCGTATGAGCGATATTCTGAATTG
* * *
248070 GCTCGAATGAGTGATATTTTG-ATTG
1 GCTCGTATGAGCGATATTCTGAATTG
* * * *
248095 GCTCATAAGAGTGATATTTTGAATTG
1 GCTCGTATGAGCGATATTCTGAATTG
* *
248121 GCTCGTATGAGCGATATTTTG-ATAG
1 GCTCGTATGAGCGATATTCTGAATTG
248146 GCTCGTATGAGC
1 GCTCGTATGAGC
248158 TAAATTCCTT
Statistics
Matches: 140, Mismatches: 24, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
25 50 0.36
26 70 0.50
27 20 0.14
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.35
Consensus pattern (26 bp):
GCTCGTATGAGCGATATTCTGAATTG
Found at i:265261 original size:82 final size:81
Alignment explanation
Indices: 265087--265262 Score: 217
Period size: 82 Copynumber: 2.2 Consensus size: 81
265077 AACGCAACCA
* * *
265087 CTCACACAAGCTGATGATAATCCGCAATGTATACAGGAACTCAGCCATCGATACCGTCCATATTA
1 CTCACACAAGCTGATGAGAATCCACAATGTATACAGGAACTCAGCCATCGATACCGTCCATACTA
*
265152 CCCACGAATGATGCTG
66 CCCACGAACGATGCTG
* * * * * * * *
265168 CTCACACAAGCTGATGAGAATCCATAATGTATGCAGGAAACTCAGTCATTGCTACGGTCTATGCT
1 CTCACACAAGCTGATGAGAATCCACAATGTATACAGG-AACTCAGCCATCGATACCGTCCATACT
**
265233 ACCCACTCACGATGCTG
65 ACCCACGAACGATGCTG
265250 CTCACACAAGCTG
1 CTCACACAAGCTG
265263 TCAAGAATTC
Statistics
Matches: 80, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
81 33 0.41
82 47 0.59
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (81 bp):
CTCACACAAGCTGATGAGAATCCACAATGTATACAGGAACTCAGCCATCGATACCGTCCATACTA
CCCACGAACGATGCTG
Found at i:266770 original size:55 final size:54
Alignment explanation
Indices: 266658--266834 Score: 261
Period size: 55 Copynumber: 3.3 Consensus size: 54
266648 ATAACATTCA
*
266658 ATTTAAACACATAAACAATCGATTCAAAAG--TAGTATTCCAACATGACAATCG
1 ATTTAAACATATAAACAATCGATTCAAAAGAATAGTATTCCAACATGACAATCG
* *
266710 ATTTAAACATATAAACAATTGATTCAAAAGAAATAATATTCCAACATGA-ATATCG
1 ATTTAAACATATAAACAATCGATTCAAAAG-AATAGTATTCCAACATGACA-ATCG
* *
266765 ATTTAAACATATAAACAATCGATTCAAAAGAAGCAGTATTCCAATATGACAATCG
1 ATTTAAACATATAAACAATCGATTCAAAAGAA-TAGTATTCCAACATGACAATCG
266820 ATTTAAACATATAAA
1 ATTTAAACATATAAA
266835 AAAATCATAA
Statistics
Matches: 112, Mismatches: 7, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
52 28 0.25
54 3 0.03
55 80 0.71
56 1 0.01
ACGTcount: A:0.49, C:0.15, G:0.08, T:0.27
Consensus pattern (54 bp):
ATTTAAACATATAAACAATCGATTCAAAAGAATAGTATTCCAACATGACAATCG
Found at i:269806 original size:27 final size:27
Alignment explanation
Indices: 269768--269875 Score: 110
Period size: 27 Copynumber: 4.0 Consensus size: 27
269758 CGAACATAGT
*
269768 GAAGTGCAAGATGTCTCCACAAGTGGT
1 GAAGTGCAAGATGTCTCCACAAGTGGC
* *
269795 GAACTGCGAGATGTCTCCACAAGTGGC
1 GAAGTGCAAGATGTCTCCACAAGTGGC
* * *
269822 G-AGTTGCAAGAAGTCTCCATAACTGGC
1 GAAG-TGCAAGATGTCTCCACAAGTGGC
* * *
269849 AAAGTGCGAGATGTCTCTACGAAGTGG
1 GAAGTGCAAGATGTCTCCAC-AAGTGG
269876 AGAGCTTTAA
Statistics
Matches: 64, Mismatches: 14, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
26 1 0.02
27 56 0.88
28 7 0.11
ACGTcount: A:0.29, C:0.20, G:0.30, T:0.21
Consensus pattern (27 bp):
GAAGTGCAAGATGTCTCCACAAGTGGC
Found at i:269830 original size:54 final size:56
Alignment explanation
Indices: 269772--269893 Score: 142
Period size: 54 Copynumber: 2.2 Consensus size: 56
269762 CATAGTGAAG
* ** *
269772 TGCAAGATGTCTCCACAAGTGGTGAACTGCGAGATGTCTCCAC-AAGTGGCGAG-T
1 TGCAAGATGTCTCCACAACTGGCAAACTGCGAGATGTCTCCACGAAGTGGAGAGCT
* * * *
269826 TGCAAGAAGTCTCCATAACTGGCAAAGTGCGAGATGTCTCTACGAAGTGGAGAGCT
1 TGCAAGATGTCTCCACAACTGGCAAACTGCGAGATGTCTCCACGAAGTGGAGAGCT
*
269882 T-TAAGATGTCTC
1 TGCAAGATGTCTC
269894 TGCAAAGTGG
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
54 36 0.64
55 18 0.32
56 2 0.04
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (56 bp):
TGCAAGATGTCTCCACAACTGGCAAACTGCGAGATGTCTCCACGAAGTGGAGAGCT
Found at i:272304 original size:15 final size:16
Alignment explanation
Indices: 272284--272313 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
272274 AGCTTGCAGC
272284 TCTCAATTCA-AAGCA
1 TCTCAATTCACAAGCA
272299 TCTCAATTCACAAGC
1 TCTCAATTCACAAGC
272314 TAGCAGTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.37, C:0.30, G:0.07, T:0.27
Consensus pattern (16 bp):
TCTCAATTCACAAGCA
Found at i:277947 original size:34 final size:34
Alignment explanation
Indices: 277904--277968 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
277894 GGTTCTTGTT
277904 TGTGGACAATATGGCTTATGAAAAATGAGGTGTC
1 TGTGGACAATATGGCTTATGAAAAATGAGGTGTC
*
277938 TGTGGACAATGTGGCTTATGAAAAATGAGGT
1 TGTGGACAATATGGCTTATGAAAAATGAGGT
277969 TGCTTTTCAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.32, C:0.08, G:0.31, T:0.29
Consensus pattern (34 bp):
TGTGGACAATATGGCTTATGAAAAATGAGGTGTC
Found at i:288635 original size:16 final size:16
Alignment explanation
Indices: 288614--288658 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
288604 AATGGAATGA
288614 AAATAAATTTTTAATT
1 AAATAAATTTTTAATT
288630 AAATAAA--TTTAATT
1 AAATAAATTTTTAATT
*
288644 AATTAAAATTTTTAA
1 AAAT-AAATTTTTAA
288659 ATCCTAAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 10 0.40
15 3 0.12
16 7 0.28
17 5 0.20
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATAAATTTTTAATT
Found at i:289117 original size:50 final size:51
Alignment explanation
Indices: 289061--289161 Score: 177
Period size: 50 Copynumber: 2.0 Consensus size: 51
289051 TTCCATTTTA
*
289061 GCTGCCAGAGTTATTTTCCATTTTCTTCCATTTTTCTC-ATTTTCTTCACT
1 GCTGCCAAAGTTATTTTCCATTTTCTTCCATTTTTCTCTATTTTCTTCACT
*
289111 GCTGCCAAAGTTATTTTCCATTTTCTTCCATTTTTTTCTATTTTCTTCACT
1 GCTGCCAAAGTTATTTTCCATTTTCTTCCATTTTTCTCTATTTTCTTCACT
289162 ACAAAAATCC
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
50 36 0.75
51 12 0.25
ACGTcount: A:0.15, C:0.25, G:0.07, T:0.53
Consensus pattern (51 bp):
GCTGCCAAAGTTATTTTCCATTTTCTTCCATTTTTCTCTATTTTCTTCACT
Found at i:292393 original size:72 final size:72
Alignment explanation
Indices: 292302--292490 Score: 299
Period size: 72 Copynumber: 2.6 Consensus size: 72
292292 ATGTTAAATT
*
292302 AGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTAAATTTATGTTCTACTTATTTATGT
1 AGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTAAATTTATGTTCTACTTATTTATGA
292367 GTAATCC
66 GTAATCC
* *
292374 AGTTTTACCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTATGA
1 AGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTAAATTTATGTTCTACTTATTTATGA
**
292439 GTAATTT
66 GTAATCC
* * *
292446 AGTTTTATCAATAGTTGTTTATATTT-GATTTTGGATATAAAATTT
1 AGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTAAATTT
292491 GTTTATAGGT
Statistics
Matches: 107, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
71 16 0.15
72 91 0.85
ACGTcount: A:0.25, C:0.05, G:0.15, T:0.54
Consensus pattern (72 bp):
AGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTAAATTTATGTTCTACTTATTTATGA
GTAATCC
Found at i:294802 original size:62 final size:63
Alignment explanation
Indices: 294677--294806 Score: 147
Period size: 62 Copynumber: 2.1 Consensus size: 63
294667 CAAGGTTGGT
* * * * * *
294677 TTCAATTCACATTTGGTAACTCACGATGACACGGAGTCATCGGACCTTTAATCCGTAATAGGA
1 TTCATTTCACATTTGATAACTCACGATGACACAGAGTCATCGAACCTATAATCCGTAAAAGGA
* * * *
294740 TTCATTTCTCATTTGAT-ACTCACGATGACACATAGTTATCGAACCTCATAATTCG-AAAAGGA
1 TTCATTTCACATTTGATAACTCACGATGACACAGAGTCATCGAACCT-ATAATCCGTAAAAGGA
294802 TTCAT
1 TTCAT
294807 ATGCTCACGA
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
62 36 0.64
63 20 0.36
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.32
Consensus pattern (63 bp):
TTCATTTCACATTTGATAACTCACGATGACACAGAGTCATCGAACCTATAATCCGTAAAAGGA
Found at i:294843 original size:52 final size:52
Alignment explanation
Indices: 294755--294995 Score: 333
Period size: 52 Copynumber: 4.6 Consensus size: 52
294745 TTCTCATTTG
* *
294755 ATACTCACGATGACACATAGTTATCGAACCTCATAATTCGAAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGAACCTTATAATTCGAAAAGGATTCAT
* * * * *
294807 ATGCTCACGATGACACATAGTCATCGGACCTTATAATAT-GTAAAGAATTAAT
1 ATACTCACGATGACACATAGTCATCGAACCTTATAAT-TCGAAAAGGATTCAT
*
294859 ATACTCACGATGACACATAGTCATCGGACCTTATAA-TCTGTAAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGAACCTTATAATTC-G-AAAAGGATTCAT
* * * *
294912 ATACTCACGATGACACATAGTCATCGAACATCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGAACCTTATAATTCGAAAAGGATTCAT
294964 ATACTCACGATGACACATAGTCATCGAACCTT
1 ATACTCACGATGACACATAGTCATCGAACCTT
294996 TTGCATTTAC
Statistics
Matches: 166, Mismatches: 18, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
50 1 0.01
52 120 0.72
53 44 0.27
54 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGAACCTTATAATTCGAAAAGGATTCAT
Found at i:294936 original size:105 final size:104
Alignment explanation
Indices: 294755--294995 Score: 358
Period size: 105 Copynumber: 2.3 Consensus size: 104
294745 TTCTCATTTG
* * *
294755 ATACTCACGATGACACATAGTTATCGAACCTCATAATTCGAAAAGGATTCATATGCTCACGATGA
1 ATACTCACGATGACACATAGTCATCGAACCTTATAATTCGAAAAGGATTCATATACTCACGATGA
* * * *
294820 CACATAGTCATCGGACCTTATAATATGTAAAGAATTAAT
66 CACATAGTCATCGAACATCATAATACGTAAAGAATTAAT
*
294859 ATACTCACGATGACACATAGTCATCGGACCTTATAA-TCTGTAAAAGGATTCATATACTCACGAT
1 ATACTCACGATGACACATAGTCATCGAACCTTATAATTC-G-AAAAGGATTCATATACTCACGAT
* * *
294923 GACACATAGTCATCGAACATCATAATCCGTAAAGGATTCAT
64 GACACATAGTCATCGAACATCATAATACGTAAAGAATTAAT
294964 ATACTCACGATGACACATAGTCATCGAACCTT
1 ATACTCACGATGACACATAGTCATCGAACCTT
294996 TTGCATTTAC
Statistics
Matches: 123, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
103 2 0.02
104 34 0.28
105 87 0.71
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (104 bp):
ATACTCACGATGACACATAGTCATCGAACCTTATAATTCGAAAAGGATTCATATACTCACGATGA
CACATAGTCATCGAACATCATAATACGTAAAGAATTAAT
Found at i:295980 original size:16 final size:16
Alignment explanation
Indices: 295956--295988 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
295946 TCCTTACAAA
*
295956 TTTATTTCTTTAACAT
1 TTTAGTTCTTTAACAT
295972 TTTAGTTCTTTAACAT
1 TTTAGTTCTTTAACAT
295988 T
1 T
295989 AAAATCATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.12, G:0.03, T:0.61
Consensus pattern (16 bp):
TTTAGTTCTTTAACAT
Found at i:300150 original size:52 final size:52
Alignment explanation
Indices: 300062--300249 Score: 304
Period size: 52 Copynumber: 3.6 Consensus size: 52
300052 TTCTCATTTG
* * * * *
300062 ATACTCACGATGACACATAATTATCGAACCTCATAATCCGAAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTATAATCCGTAAAGGATTCAT
*
300114 ATGCTCACGATGACACATAGTCATCGGACCTTATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTATAATCCGTAAAGGATTCAT
* *
300166 ATACTCATGATGACACATAGTCATCGGACCTTATAATCTGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTATAATCCGTAAAGGATTCAT
300218 ATACTCACGATGACACATAGTCATCGGACCTT
1 ATACTCACGATGACACATAGTCATCGGACCTT
300250 TTGCATTTAC
Statistics
Matches: 126, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 126 1.00
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTTATAATCCGTAAAGGATTCAT
Found at i:300820 original size:18 final size:16
Alignment explanation
Indices: 300789--300824 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
300779 CCTCAATACC
300789 ATTTCATTTCAATTTA
1 ATTTCATTTCAATTTA
300805 ATTTCATTCCTCAATTTA
1 ATTTCATT--TCAATTTA
300823 AT
1 AT
300825 ATTTAGTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
18 10 0.56
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTCATTTCAATTTA
Found at i:301262 original size:16 final size:16
Alignment explanation
Indices: 301238--301270 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
301228 TCCTTACAAA
*
301238 TTTATTCCTTTAACAT
1 TTTAGTCCTTTAACAT
301254 TTTAGTCCTTTAACAT
1 TTTAGTCCTTTAACAT
301270 T
1 T
301271 AAAATCCTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.18, G:0.03, T:0.55
Consensus pattern (16 bp):
TTTAGTCCTTTAACAT
Found at i:303538 original size:53 final size:53
Alignment explanation
Indices: 303464--303724 Score: 319
Period size: 53 Copynumber: 4.9 Consensus size: 53
303454 TTCACATTTG
* * ***
303464 ATAACTCACGATGACACAGAGTAATC-AGACCTTTAATCTGTAATAGGATTTGT
1 ATAACTCACGATGACACAGAGTCATCGA-ACCTTTAATCCGTAATAGGATTCAA
* * *
303517 ATAACTCACAATGACACAGAGTCATCGGACCTTTAATCCGTAATAGGATCCAA
1 ATAACTCACGATGACACAGAGTCATCGAACCTTTAATCCGTAATAGGATTCAA
**
303570 ATAACTCACGATGACACAGAGTCATCGAACCTTT-ATCCACAATAGGATTCAA
1 ATAACTCACGATGACACAGAGTCATCGAACCTTTAATCCGTAATAGGATTCAA
* * * *
303622 ATAACTCACGATGACACAGAGTCATTGAACCTTTAATCCGTGATAAGATTCAT
1 ATAACTCACGATGACACAGAGTCATCGAACCTTTAATCCGTAATAGGATTCAA
* * * * * *
303675 ATAACTCACGATGACATAGAATTATCGAACATTTAATCCATGATAGGATT
1 ATAACTCACGATGACACAGAGTCATCGAACCTTTAATCCGTAATAGGATT
303725 TATTTCTCAT
Statistics
Matches: 180, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
52 48 0.27
53 132 0.73
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.27
Consensus pattern (53 bp):
ATAACTCACGATGACACAGAGTCATCGAACCTTTAATCCGTAATAGGATTCAA
Found at i:303654 original size:105 final size:106
Alignment explanation
Indices: 303464--303724 Score: 328
Period size: 105 Copynumber: 2.5 Consensus size: 106
303454 TTCACATTTG
** ***
303464 ATAACTCACGATGACACAGAGTAATC-AGACCTTTAATCTGTAATAGGATTTGTATAACTCACAA
1 ATAACTCACGATGACACAGAGTAATCGA-ACCTTTAATCCATAATAGGATTCAAATAACTCACAA
* *
303528 TGACACAGAGTCATCGGACCTTTAATCCGTAATAGGATCCAA
65 TGACACAGAGTCATCGAACCTTTAATCCGTAATAAGATCCAA
* * *
303570 ATAACTCACGATGACACAGAGTCATCGAACCTTT-ATCCACAATAGGATTCAAATAACTCACGAT
1 ATAACTCACGATGACACAGAGTAATCGAACCTTTAATCCATAATAGGATTCAAATAACTCACAAT
* * * *
303634 GACACAGAGTCATTGAACCTTTAATCCGTGATAAGATTCAT
66 GACACAGAGTCATCGAACCTTTAATCCGTAATAAGATCCAA
* * * * *
303675 ATAACTCACGATGACATAGAATTATCGAACATTTAATCCATGATAGGATT
1 ATAACTCACGATGACACAGAGTAATCGAACCTTTAATCCATAATAGGATT
303725 TATTTCTCAT
Statistics
Matches: 133, Mismatches: 20, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
105 88 0.66
106 44 0.33
107 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.27
Consensus pattern (106 bp):
ATAACTCACGATGACACAGAGTAATCGAACCTTTAATCCATAATAGGATTCAAATAACTCACAAT
GACACAGAGTCATCGAACCTTTAATCCGTAATAAGATCCAA
Found at i:304803 original size:14 final size:15
Alignment explanation
Indices: 304784--304816 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
304774 ACTAACTTCT
*
304784 AATTCACTAATT-AA
1 AATTCACCAATTCAA
304798 AATTCACCAATTCAA
1 AATTCACCAATTCAA
304813 AATT
1 AATT
304817 TTCATATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.33
Consensus pattern (15 bp):
AATTCACCAATTCAA
Found at i:308831 original size:6 final size:6
Alignment explanation
Indices: 308816--308849 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
308806 TAAGAAACTG
*
308816 CCATGA CCATGC CCATGC CCATGC CCATGC CCAT
1 CCATGC CCATGC CCATGC CCATGC CCATGC CCAT
308850 CTCCAAGACA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.21, C:0.47, G:0.15, T:0.18
Consensus pattern (6 bp):
CCATGC
Found at i:309697 original size:10 final size:10
Alignment explanation
Indices: 309682--309706 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
309672 AGTTTTTGAA
309682 ATAAAATATT
1 ATAAAATATT
309692 ATAAAATATT
1 ATAAAATATT
309702 ATAAA
1 ATAAA
309707 TTCAAATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
ATAAAATATT
Found at i:310489 original size:28 final size:28
Alignment explanation
Indices: 310452--310505 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
310442 AAAATAAAAC
310452 TTTGTAGGGGGAAGTAAAAGTTTTTGGGG
1 TTTGTA-GGGGAAGTAAAAGTTTTTGGGG
**
310481 TTTG-AGGGGAAGTAAATTTTTTTGG
1 TTTGTAGGGGAAGTAAAAGTTTTTGG
310506 AGGAACGTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 18 0.78
28 1 0.04
29 4 0.17
ACGTcount: A:0.24, C:0.00, G:0.37, T:0.39
Consensus pattern (28 bp):
TTTGTAGGGGAAGTAAAAGTTTTTGGGG
Found at i:311759 original size:37 final size:37
Alignment explanation
Indices: 311709--311847 Score: 215
Period size: 37 Copynumber: 3.8 Consensus size: 37
311699 TAAATAGGGC
* * *
311709 TATGTGCTTAGCAGGCTTCGTGCCGGTGTATTTGGGA
1 TATGTGCCTAGCAGGCTTCGTGCCGGTGTATTCGGGT
311746 TATGTGCCTAGCAGGCTTCGTGCCGGTGTATTCGGGT
1 TATGTGCCTAGCAGGCTTCGTGCCGGTGTATTCGGGT
* *
311783 TATGTGCCTAGCAGGCTTCGTGCTGGTGTATTCGGTT
1 TATGTGCCTAGCAGGCTTCGTGCCGGTGTATTCGGGT
* *
311820 TATGTACCTAGCAGGCTTTGTGCCGGTG
1 TATGTGCCTAGCAGGCTTCGTGCCGGTG
311848 ATTAAAGAAT
Statistics
Matches: 94, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 94 1.00
ACGTcount: A:0.12, C:0.19, G:0.34, T:0.35
Consensus pattern (37 bp):
TATGTGCCTAGCAGGCTTCGTGCCGGTGTATTCGGGT
Found at i:314500 original size:37 final size:36
Alignment explanation
Indices: 314444--314538 Score: 129
Period size: 37 Copynumber: 2.6 Consensus size: 36
314434 AAGTAAATCA
*
314444 GGCTATGTGCCTAGCAAGCTTCGTGCTAGTGTATTC
1 GGCTATGTGCCTAGCAAGCTTAGTGCTAGTGTATTC
314480 GAGCTATGTGCCTA-CTAAGCTTAGTGCTAGTGTATTC
1 G-GCTATGTGCCTAGC-AAGCTTAGTGCTAGTGTATTC
* *
314517 GGCTTATGTACCTAGCAGGCTT
1 GGC-TATGTGCCTAGCAAGCTT
314539 TATGCCGATG
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
36 4 0.08
37 47 0.90
38 1 0.02
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.34
Consensus pattern (36 bp):
GGCTATGTGCCTAGCAAGCTTAGTGCTAGTGTATTC
Done.