Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015024.1 Kokia drynarioides strain JFW-HI SEQ_130068, 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: 224678
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 257 characters in sequence are not A, C, G, or T
Found at i:27 original size:3 final size:3
Alignment explanation
Indices: 14--97 Score: 53
Period size: 3 Copynumber: 28.0 Consensus size: 3
4 TTTTTTATAT
* * * * *
14 TTA TTA ATA TTA TTA TAA TTA TTA ATA -TA TTA TTA TTTA ATG TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
* * * ** *
59 TTA GTA TTA TTA TTA ATG TTA TTA TGG CTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
98 CTAATGATAT
Statistics
Matches: 58, Mismatches: 21, Indels: 4
0.70 0.25 0.05
Matches are distributed among these distances:
2 2 0.03
3 53 0.91
4 3 0.05
ACGTcount: A:0.36, C:0.01, G:0.06, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:792 original size:29 final size:28
Alignment explanation
Indices: 760--828 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 28
750 TTATTTATTT
* * *
760 TAAATTTATAATAATTTTAAAT-TTGAAAG
1 TAAATTTAAAATAAATTT-AATCTT-AAAA
789 TAAATTTAAAATAAATTTAATCTTAAAA
1 TAAATTTAAAATAAATTTAATCTTAAAA
817 TAAATTTAAAAT
1 TAAATTTAAAAT
829 GAGTTTGTAC
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 18 0.50
29 18 0.50
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (28 bp):
TAAATTTAAAATAAATTTAATCTTAAAA
Found at i:15895 original size:4 final size:4
Alignment explanation
Indices: 15886--15936 Score: 57
Period size: 4 Copynumber: 12.8 Consensus size: 4
15876 ATCTGCATAT
* * * * *
15886 ATGC ATGC ATGC ATGC ATGC ATGC ATGG ATAC ATGG ATGT ATGT ATGC
1 ATGC ATGC ATGC ATGC ATGC ATGC ATGC ATGC ATGC ATGC ATGC ATGC
15934 ATG
1 ATG
15937 TGCTAGCAGT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.29
Consensus pattern (4 bp):
ATGC
Found at i:16343 original size:158 final size:157
Alignment explanation
Indices: 16054--16369 Score: 580
Period size: 158 Copynumber: 2.0 Consensus size: 157
16044 TGATTCAATG
16054 TGAAACGATAATATATGAAATTTGATTTTTTTTGCAATTTTATACTTTGGCATTTTGATTTGACT
1 TGAAACGATAATATATGAAATTTGATTTTTTTTGCAATTTTATACTTTGGCATTTTGATTTGACT
*
16119 AAATTTTTATAAATTTAGATAAAATAAATTGATGTATTCATTTATTTAAATATGAATCATTGGAT
66 AAATTTTTATAAATTAAGATAAAATAAATTGATGTATTCATTTATTTAAATATGAATCATTGGAT
16184 CAAAATTAAAGATTTATGTAT-AATTT
131 CAAAATTAAAGATTTATGTATAAATTT
16210 TGAAACGATAATATATGAAATTTGATTTTTTTTTGCAATTTTATACTTTGGCATTTTGATTTGAC
1 TGAAACGATAATATATGAAATTTGA-TTTTTTTTGCAATTTTATACTTTGGCATTTTGATTTGAC
* *
16275 TAAATTTTTATAAATTCAATATAAAATAAATTTATGTATTCATTTATTTAAATATGAATCATTGG
65 TAAATTTTTATAAATT-AAGATAAAATAAATTGATGTATTCATTTATTTAAATATGAATCATTGG
16340 ATCAAAATTAAAGATTTATGTATAAATTT
129 ATCAAAATTAAAGATTTATGTATAAATTT
16369 T
1 T
16370 ATGTATAATT
Statistics
Matches: 154, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
156 25 0.16
157 55 0.36
158 68 0.44
159 6 0.04
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.47
Consensus pattern (157 bp):
TGAAACGATAATATATGAAATTTGATTTTTTTTGCAATTTTATACTTTGGCATTTTGATTTGACT
AAATTTTTATAAATTAAGATAAAATAAATTGATGTATTCATTTATTTAAATATGAATCATTGGAT
CAAAATTAAAGATTTATGTATAAATTT
Found at i:21294 original size:7 final size:7
Alignment explanation
Indices: 21282--21310 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
21272 GGATATAAAC
21282 GGAGTTG
1 GGAGTTG
21289 GGAGTTG
1 GGAGTTG
21296 GGAGTTG
1 GGAGTTG
21303 GGAGTTG
1 GGAGTTG
21310 G
1 G
21311 TGAGATTCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.59, T:0.28
Consensus pattern (7 bp):
GGAGTTG
Found at i:30963 original size:21 final size:22
Alignment explanation
Indices: 30939--30988 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
30929 AGAAATCATA
30939 TATAATTTC-TATATCAA-TTTT
1 TATAATTTCATATAT-AATTTTT
*
30960 TATAAATTCATTATATAATTTTT
1 TATAATTTCA-TATATAATTTTT
30983 TATAAT
1 TATAAT
30989 AATAAGATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 8 0.33
22 2 0.08
23 14 0.58
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (22 bp):
TATAATTTCATATATAATTTTT
Found at i:30963 original size:23 final size:23
Alignment explanation
Indices: 30937--30988 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 23
30927 CTAGAAATCA
30937 TATATAATTTC-TATATCAATTTT
1 TATATAATTTCATATAT-AATTTT
30960 TATA-AA-TTCATTATATAATTTT
1 TATATAATTTCA-TATATAATTTT
30982 T-TATAAT
1 TATATAAT
30989 AATAAGATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
21 5 0.20
22 11 0.44
23 9 0.36
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (23 bp):
TATATAATTTCATATATAATTTT
Found at i:37792 original size:57 final size:57
Alignment explanation
Indices: 37729--37838 Score: 175
Period size: 57 Copynumber: 1.9 Consensus size: 57
37719 AAAAAATTCT
*
37729 TGTTTGCCACCCAATGGCTTACACTACATTTTCCAAATTTAAAAATATTTTTTTAAG
1 TGTTTGCCACCCAATGACTTACACTACATTTTCCAAATTTAAAAATATTTTTTTAAG
* * * *
37786 TGTTTGCTACCCAATGACTTACATTACTTTTTTCAAATTTAAAAATATTTTTT
1 TGTTTGCCACCCAATGACTTACACTACATTTTCCAAATTTAAAAATATTTTTT
37839 GGATATTGTT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 48 1.00
ACGTcount: A:0.31, C:0.17, G:0.07, T:0.45
Consensus pattern (57 bp):
TGTTTGCCACCCAATGACTTACACTACATTTTCCAAATTTAAAAATATTTTTTTAAG
Found at i:38066 original size:57 final size:57
Alignment explanation
Indices: 37984--38206 Score: 206
Period size: 57 Copynumber: 3.9 Consensus size: 57
37974 AAAAATGACT
* * *
37984 TACACCATTTTTTCCAGATTTAAAAATATTTTTTTTAGTGTTTGTCACCCAATGATC
1 TACATCATCTTTTCCAGATTTAAAAATATTTTTTTTAGTGTTTGCCACCCAATGATC
* * * *
38041 TACATCATCTTTTCCAGATTGAAAAATATTTTTTTTTTA-TGTTTGTCACCCAATGGTT
1 TACATCATCTTTTCCAGATTTAAAAATA--TTTTTTTTAGTGTTTGCCACCCAATGATC
* * * *
38099 TACACTACAT-TTTT-CAAATTTAAAAATA-TTTTTTAAGTATTTGCCACCCAACGA-C
1 TACA-T-CATCTTTTCCAGATTTAAAAATATTTTTTTTAGTGTTTGCCACCCAATGATC
* * * * *
38154 ATACATTA-CTTTTCTTAGATTTAAAAATATTGTTTTGAGTGTTTACCACCCAA
1 -TACATCATCTTTTC-CAGATTTAAAAATATTTTTTTTAGTGTTTGCCACCCAA
38207 AAGCCTACAC
Statistics
Matches: 136, Mismatches: 20, Indels: 20
0.77 0.11 0.11
Matches are distributed among these distances:
54 5 0.04
55 8 0.06
56 29 0.21
57 44 0.32
58 33 0.24
59 14 0.10
60 3 0.02
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.44
Consensus pattern (57 bp):
TACATCATCTTTTCCAGATTTAAAAATATTTTTTTTAGTGTTTGCCACCCAATGATC
Found at i:38124 original size:58 final size:58
Alignment explanation
Indices: 37992--38132 Score: 191
Period size: 58 Copynumber: 2.4 Consensus size: 58
37982 CTTACACCAT
37992 TTTTTCCAGATTTAAAAATA--TTTTTTTTAGTGTTTGTCACCCAATGATCTACATCA
1 TTTTTCCAGATTTAAAAATATTTTTTTTTTAGTGTTTGTCACCCAATGATCTACATCA
* * *
38048 TCTTTTCCAGATTGAAAAATATTTTTTTTTTA-TGTTTGTCACCCAATGGTTTACACTACA
1 T-TTTTCCAGATTTAAAAATATTTTTTTTTTAGTGTTTGTCACCCAATGATCTACA-T-CA
*
38108 TTTTT-CAAATTTAAAAATATTTTTT
1 TTTTTCCAGATTTAAAAATATTTTTT
38133 AAGTATTTGC
Statistics
Matches: 75, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
56 1 0.01
57 18 0.24
58 39 0.52
59 14 0.19
60 3 0.04
ACGTcount: A:0.29, C:0.14, G:0.08, T:0.49
Consensus pattern (58 bp):
TTTTTCCAGATTTAAAAATATTTTTTTTTTAGTGTTTGTCACCCAATGATCTACATCA
Found at i:38391 original size:11 final size:12
Alignment explanation
Indices: 38327--38391 Score: 53
Period size: 11 Copynumber: 5.2 Consensus size: 12
38317 TTAAAAAGTA
*
38327 TTTAAATTGTTT
1 TTTAAATTATTT
38339 TTT-AATTATTT
1 TTTAAATTATTT
*
38350 TAATTCAATTATAATT
1 T--TTAAATTAT--TT
*
38366 TTTAAATTATGT
1 TTTAAATTATTT
38378 TTT-AATTATTT
1 TTTAAATTATTT
38389 TTT
1 TTT
38392 TTAAATTTTG
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
11 18 0.41
12 7 0.16
13 2 0.05
14 14 0.32
16 3 0.07
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.65
Consensus pattern (12 bp):
TTTAAATTATTT
Found at i:38587 original size:57 final size:55
Alignment explanation
Indices: 38439--38588 Score: 149
Period size: 56 Copynumber: 2.7 Consensus size: 55
38429 TAAACATTCA
* * *
38439 AAAAAAATATTTTTATATCTAGAAAAAGTGGTGTAGACCATCGGATGGTAAACACC
1 AAAAAAATATTTTTAAATCTAGAAAAA-TGGTGTAGACCATCGGATAGCAAACACC
* * * * * * *
38495 AAAAAAATGTTTTTAAATTTA-AAAAATGTGATGTAGGCCATTGGGTAGCAAACGCTT
1 AAAAAAATATTTTTAAATCTAGAAAAATG-G-TGTAGACCATCGGATAGCAAACAC-C
*
38552 AAAAAAATATTTTTAAATCTGAGAAAGATGGTGTAGA
1 AAAAAAATATTTTTAAATCT-AGAAAAATGGTGTAGA
38589 TCATTAGGTG
Statistics
Matches: 75, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
54 2 0.03
55 6 0.08
56 36 0.48
57 23 0.31
58 2 0.03
59 6 0.08
ACGTcount: A:0.43, C:0.09, G:0.19, T:0.29
Consensus pattern (55 bp):
AAAAAAATATTTTTAAATCTAGAAAAATGGTGTAGACCATCGGATAGCAAACACC
Found at i:38603 original size:57 final size:55
Alignment explanation
Indices: 38439--38622 Score: 165
Period size: 57 Copynumber: 3.3 Consensus size: 55
38429 TAAACATTCA
* * *
38439 AAAAAAATATTTTTATATCTAGAAAAAGTGGTGTAGACCA-TCGGATGGTAAACACC
1 AAAAAAATATTTTTAAATCTAGAAAAA-TGGTGTAGACCATTAGG-TGGCAAACACC
* * * * * * *
38495 AAAAAAATGTTTTTAAATTTA-AAAAATGTGATGTAGGCCATTGGGTAGCAAACGCTT
1 AAAAAAATATTTTTAAATCTAGAAAAATG-G-TGTAGACCATTAGGTGGCAAACAC-C
* * * *
38552 AAAAAAATATTTTTAAATCTGAGAAAGATGGTGTAGATCATTAGGTGGCAAATATCG
1 AAAAAAATATTTTTAAATCT-AGAAAAATGGTGTAGACCATTAGGTGGCAAACA-CC
38609 AAAAAAATATTTTT
1 AAAAAAATATTTTT
38623 TTATTCGTAT
Statistics
Matches: 102, Mismatches: 19, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
54 2 0.02
55 6 0.06
56 33 0.32
57 52 0.51
58 3 0.03
59 6 0.06
ACGTcount: A:0.43, C:0.09, G:0.18, T:0.30
Consensus pattern (55 bp):
AAAAAAATATTTTTAAATCTAGAAAAATGGTGTAGACCATTAGGTGGCAAACACC
Found at i:42291 original size:39 final size:36
Alignment explanation
Indices: 42265--42339 Score: 114
Period size: 36 Copynumber: 2.1 Consensus size: 36
42255 CTGTAGATGG
*
42265 TGAGCGAGTAATAGGAGAGGATGGTCTTGTATAAGA
1 TGAGCGACTAATAGGAGAGGATGGTCTTGTATAAGA
* * *
42301 TGATCGACTAATGGGAGAGGATGGTCCTGTATAAGA
1 TGAGCGACTAATAGGAGAGGATGGTCTTGTATAAGA
42337 TGA
1 TGA
42340 CACAGAAGCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.32, C:0.08, G:0.35, T:0.25
Consensus pattern (36 bp):
TGAGCGACTAATAGGAGAGGATGGTCTTGTATAAGA
Found at i:44829 original size:16 final size:16
Alignment explanation
Indices: 44808--44839 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
44798 TATTTTTAGT
*
44808 TACAAATTTGTCTCAA
1 TACAAATCTGTCTCAA
44824 TACAAATCTGTCTCAA
1 TACAAATCTGTCTCAA
44840 AACTTGAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.22, G:0.06, T:0.34
Consensus pattern (16 bp):
TACAAATCTGTCTCAA
Found at i:47686 original size:22 final size:22
Alignment explanation
Indices: 47644--47686 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
47634 GACAAACAAT
* *
47644 TTAAATAATTATATAATATAAA
1 TTAAATAATTATAAAACATAAA
47666 TTAAATAATT-TAAAAACATAA
1 TTAAATAATTAT-AAAACATAA
47687 TTATATTCCG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (22 bp):
TTAAATAATTATAAAACATAAA
Found at i:68550 original size:31 final size:32
Alignment explanation
Indices: 68513--68575 Score: 103
Period size: 31 Copynumber: 2.0 Consensus size: 32
68503 CTCAAAAAGA
68513 TTAAGTACCAACTTA-AGAAAAAA-TGTCAAGT
1 TTAAGTACCAACTTAGA-AAAAAATTGTCAAGT
68544 TTAAGTACCAACTTAGAAAAAAATTGTCAAGT
1 TTAAGTACCAACTTAGAAAAAAATTGTCAAGT
68576 CTGAGTATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
31 21 0.70
32 9 0.30
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.27
Consensus pattern (32 bp):
TTAAGTACCAACTTAGAAAAAAATTGTCAAGT
Found at i:73525 original size:3 final size:3
Alignment explanation
Indices: 73512--73543 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
73502 TCATGTTGTA
*
73512 TAT TCT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
73544 AAGATGCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:87465 original size:24 final size:24
Alignment explanation
Indices: 87438--87487 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
87428 TAAAACATTA
* *
87438 TTTTGTATTTGGTGAAAATACCTC
1 TTTTATATTTGGTAAAAATACCTC
87462 TTTTATATTTGGTAAAAATACCTC
1 TTTTATATTTGGTAAAAATACCTC
87486 TT
1 TT
87488 AATTTTGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.48
Consensus pattern (24 bp):
TTTTATATTTGGTAAAAATACCTC
Found at i:87673 original size:41 final size:41
Alignment explanation
Indices: 87628--87710 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
87618 TTAGATACTG
* *
87628 ATCAAATTAGTCCTTTTCAAATTTTTAAAACATCGAGGTTA
1 ATCAAATTAGTCCTTTTCAAAATTTTAAAAAATCGAGGTTA
*
87669 ATCAAATTGGTCCTTTTCAAAATTTTAAAAAATCGAGGTTA
1 ATCAAATTAGTCCTTTTCAAAATTTTAAAAAATCGAGGTTA
87710 A
1 A
87711 ATTTCTAATC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (41 bp):
ATCAAATTAGTCCTTTTCAAAATTTTAAAAAATCGAGGTTA
Found at i:88185 original size:48 final size:48
Alignment explanation
Indices: 88114--88211 Score: 178
Period size: 48 Copynumber: 2.0 Consensus size: 48
88104 CACAACCTTA
* *
88114 ACATCAAATTCCTCTTTTATAGGAACCTAATCAAATTATAATCTCTCT
1 ACATCAAATTCCTCTTTTATAGGAACCTAATCAAATTACAATCTATCT
88162 ACATCAAATTCCTCTTTTATAGGAACCTAATCAAATTACAATCTATCT
1 ACATCAAATTCCTCTTTTATAGGAACCTAATCAAATTACAATCTATCT
88210 AC
1 AC
88212 TTTTAAATGA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.37, C:0.23, G:0.04, T:0.36
Consensus pattern (48 bp):
ACATCAAATTCCTCTTTTATAGGAACCTAATCAAATTACAATCTATCT
Found at i:88303 original size:22 final size:23
Alignment explanation
Indices: 88278--88320 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
88268 TTAAATCAAC
*
88278 ATTTGCTGATTAA-AAAATTATA
1 ATTTACTGATTAACAAAATTATA
*
88300 ATTTACTGTTTAACAAAATTA
1 ATTTACTGATTAACAAAATTA
88321 ATATTTATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (23 bp):
ATTTACTGATTAACAAAATTATA
Found at i:90716 original size:14 final size:14
Alignment explanation
Indices: 90697--90725 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
90687 AAAAACATAT
90697 TACTTGCACTAACA
1 TACTTGCACTAACA
90711 TACTTGCACTAACA
1 TACTTGCACTAACA
90725 T
1 T
90726 TTAGAAAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.28, G:0.07, T:0.31
Consensus pattern (14 bp):
TACTTGCACTAACA
Found at i:95630 original size:5 final size:5
Alignment explanation
Indices: 95622--95651 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
95612 ATCAAAAACC
95622 CAGGA CAGGA CAGGA CAGGA CAGGA CAGGA
1 CAGGA CAGGA CAGGA CAGGA CAGGA CAGGA
95652 AGCAGGGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.20, G:0.40, T:0.00
Consensus pattern (5 bp):
CAGGA
Found at i:97294 original size:27 final size:26
Alignment explanation
Indices: 97249--97303 Score: 83
Period size: 27 Copynumber: 2.1 Consensus size: 26
97239 TTAAAGAAAA
97249 AAGATGAGAAAAAGTGGTAGCGGATG
1 AAGATGAGAAAAAGTGGTAGCGGATG
* *
97275 AAGATGAGGAATAAGTGGTAGTGGATG
1 AAGATGA-GAAAAAGTGGTAGCGGATG
97302 AA
1 AA
97304 AAAGGAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 7 0.27
27 19 0.73
ACGTcount: A:0.42, C:0.02, G:0.38, T:0.18
Consensus pattern (26 bp):
AAGATGAGAAAAAGTGGTAGCGGATG
Found at i:98956 original size:2 final size:2
Alignment explanation
Indices: 98949--98973 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
98939 TTTCCTAATC
98949 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
98974 GGAATTTGTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:106327 original size:28 final size:29
Alignment explanation
Indices: 106270--106328 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
106260 TTTTTATCCA
*
106270 TGTTCTTCAACAAAGTTTTTAATTTGTTT
1 TGTTCTTCAACAAAGTTTTTAATTTCTTT
106299 TGTTCTTCAACAAAGTTTTT-ATTTCTTT
1 TGTTCTTCAACAAAGTTTTTAATTTCTTT
106327 TG
1 TG
106329 AAAGGGTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 9 0.31
29 20 0.69
ACGTcount: A:0.22, C:0.12, G:0.10, T:0.56
Consensus pattern (29 bp):
TGTTCTTCAACAAAGTTTTTAATTTCTTT
Found at i:106634 original size:21 final size:21
Alignment explanation
Indices: 106595--106634 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
106585 TTATATTCAA
*
106595 AAAATAATTTAAATTAATTTT
1 AAAATAATTTAAATAAATTTT
106616 AAAATATATTT-AATAAATT
1 AAAATA-ATTTAAATAAATT
106635 ATATTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AAAATAATTTAAATAAATTTT
Found at i:106637 original size:14 final size:12
Alignment explanation
Indices: 106602--106644 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 12
106592 CAAAAAATAA
106602 TTTAAATTA-AT
1 TTTAAATTATAT
*
106613 TTTAAAATATAT
1 TTTAAATTATAT
106625 TTAATAAATTATAT
1 TT--TAAATTATAT
106639 TTTAAA
1 TTTAAA
106645 AAATAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 8 0.30
12 8 0.30
14 11 0.41
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
TTTAAATTATAT
Found at i:106644 original size:26 final size:25
Alignment explanation
Indices: 106593--106654 Score: 83
Period size: 26 Copynumber: 2.5 Consensus size: 25
106583 TTTTATATTC
106593 AAAAAATAATT--TAAATTAATTTT
1 AAAAAATAATTAATAAATTAATTTT
* *
106616 AAAATATATTTAATAAATTATATTTT
1 AAAAAATAATTAATAAATTA-ATTTT
106642 AAAAAATAATTAA
1 AAAAAATAATTAA
106655 AATTTTGCTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
23 9 0.28
25 7 0.22
26 16 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
AAAAAATAATTAATAAATTAATTTT
Found at i:107144 original size:25 final size:27
Alignment explanation
Indices: 107089--107145 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 27
107079 GCATTTAATA
*
107089 ATTTTAATACAATGTAATTATTTCATT
1 ATTTTAATAAAATGTAATTATTTCATT
* *
107116 -TTTTATTAAAAT-TAATTATTT-TTT
1 ATTTTAATAAAATGTAATTATTTCATT
107140 ATTTTA
1 ATTTTA
107146 CTTTCATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 2 0.08
25 14 0.54
26 10 0.38
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (27 bp):
ATTTTAATAAAATGTAATTATTTCATT
Found at i:109626 original size:2 final size:2
Alignment explanation
Indices: 109619--109667 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
109609 TTTGGTCATT
109619 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
109661 TA TA TA T
1 TA TA TA T
109668 TGCATAAATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:115457 original size:36 final size:35
Alignment explanation
Indices: 115405--115512 Score: 180
Period size: 36 Copynumber: 3.0 Consensus size: 35
115395 CCCTTCTTCT
115405 AGTCCAAGTCAGCCTCGAATTCGCAGCCCCAGACCC
1 AGTCCAAGTCAGCCTCGAATTCGCAGCCCCAG-CCC
* *
115441 AGTCTAAGTCAGCCTCGAATTCGCAGCCCTAGCCCC
1 AGTCCAAGTCAGCCTCGAATTCGCAGCCCCAG-CCC
115477 AGTCCAAGTCAGCCTCGAATTCGCAGCCCCAGCCC
1 AGTCCAAGTCAGCCTCGAATTCGCAGCCCCAGCCC
115512 A
1 A
115513 TGCCGCCAAC
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
35 4 0.06
36 63 0.94
ACGTcount: A:0.24, C:0.41, G:0.19, T:0.16
Consensus pattern (35 bp):
AGTCCAAGTCAGCCTCGAATTCGCAGCCCCAGCCC
Found at i:127651 original size:6 final size:6
Alignment explanation
Indices: 127640--127667 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
127630 TTCTTTTCCG
127640 CCCGCA CCCGCA CCCGCA CCCGCA CCCG
1 CCCGCA CCCGCA CCCGCA CCCGCA CCCG
127668 TATCCGTATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.68, G:0.18, T:0.00
Consensus pattern (6 bp):
CCCGCA
Found at i:127765 original size:7 final size:7
Alignment explanation
Indices: 127753--127780 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
127743 ACTCATGCTT
127753 TACTTTC
1 TACTTTC
127760 TACTTTC
1 TACTTTC
127767 TACTTTC
1 TACTTTC
127774 TACTTTC
1 TACTTTC
127781 ACTACAGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.29, G:0.00, T:0.57
Consensus pattern (7 bp):
TACTTTC
Found at i:129071 original size:17 final size:17
Alignment explanation
Indices: 129034--129067 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
129024 TTGAAATATG
*
129034 TAATTATTATTTTATCA
1 TAATTATTATTTTATAA
129051 TAATT-TTATTTTATAA
1 TAATTATTATTTTATAA
129067 T
1 T
129068 TAATAGAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
TAATTATTATTTTATAA
Found at i:131564 original size:29 final size:28
Alignment explanation
Indices: 131525--131730 Score: 161
Period size: 29 Copynumber: 7.1 Consensus size: 28
131515 AAGGTCCCTA
131525 AACTGTCCAAAAATTACCATTTTACTCCCG
1 AACT-TCCAAAAATTACCATTTTAC-CCCG
* *
131555 AACTTCCAAAAATCA-CATTTTTACCCCAA
1 AACTTCCAAAAATTACCA-TTTTACCCC-G
*
131584 AACTTCTAAAAATTACCA-TTTACCCCTG
1 AACTTCCAAAAATTACCATTTTACCCC-G
* *
131612 AACTTCCAAAAA-TCCCATTTTTGACCTCG
1 AACTTCCAAAAATTACCA-TTTT-ACCCCG
*
131641 AAACTTCTAAAAATTACCATTTTACCCCCG
1 -AACTTCCAAAAATTACCATTTTA-CCCCG
* *
131671 AACTCCCAAAAATT--CATTTTTGACCCTG
1 AACTTCCAAAAATTACCA-TTTT-ACCCCG
* * *
131699 AAACATCCAAAGATTACTATTTTACTCCCG
1 -AACTTCCAAAAATTACCATTTTAC-CCCG
131729 AA
1 AA
131731 TGTCCGAAGA
Statistics
Matches: 141, Mismatches: 20, Indels: 31
0.73 0.10 0.16
Matches are distributed among these distances:
27 6 0.04
28 32 0.23
29 62 0.44
30 36 0.26
31 5 0.04
ACGTcount: A:0.36, C:0.29, G:0.05, T:0.30
Consensus pattern (28 bp):
AACTTCCAAAAATTACCATTTTACCCCG
Found at i:131645 original size:58 final size:59
Alignment explanation
Indices: 131524--131779 Score: 267
Period size: 58 Copynumber: 4.4 Consensus size: 59
131514 GAAGGTCCCT
* * * *
131524 AAACTGTCCAAAAATTACCATTTTACTCCCGAACTTCCAAAAATCACATTTTT-ACCCCA
1 AAACT-TCTAAAAATTACCATTTTACTCCCGAACTTCCAAAAATCCCATTTTTGACCTCG
131583 AAACTTCTAAAAATTACCA-TTTAC-CCCTGAACTTCCAAAAATCCCATTTTTGACCTCG
1 AAACTTCTAAAAATTACCATTTTACTCCC-GAACTTCCAAAAATCCCATTTTTGACCTCG
* * *
131641 AAACTTCTAAAAATTACCATTTTACCCCCGAACTCCCAAAAAT-TCATTTTTGACC-CTG
1 AAACTTCTAAAAATTACCATTTTACTCCCGAACTTCCAAAAATCCCATTTTTGACCTC-G
* * * * * * *
131699 AAACATCCAAAGATTACTATTTTACTCCCGAA-TGTCCGAAGA-CTCCATTTTCGACCTCG
1 AAACTTCTAAAAATTACCATTTTACTCCCGAACT-TCCAAAAATC-CCATTTTTGACCTCG
* *
131758 AAAC-TCTCAAAATTGCCATTTT
1 AAACTTCTAAAAATTACCATTTT
131780 TACCCTCGAA
Statistics
Matches: 167, Mismatches: 21, Indels: 19
0.81 0.10 0.09
Matches are distributed among these distances:
56 3 0.02
57 29 0.17
58 93 0.56
59 38 0.23
60 4 0.02
ACGTcount: A:0.34, C:0.29, G:0.06, T:0.30
Consensus pattern (59 bp):
AAACTTCTAAAAATTACCATTTTACTCCCGAACTTCCAAAAATCCCATTTTTGACCTCG
Found at i:134934 original size:27 final size:26
Alignment explanation
Indices: 134904--134984 Score: 69
Period size: 27 Copynumber: 3.0 Consensus size: 26
134894 TTCATGTTTA
134904 AAAATTTAATAAAATAAAATAAAATAT
1 AAAATTTAATAAAATAAAATAAAA-AT
*
134931 AAAA-TT-ATTAAATACTAAATAAAAAT
1 AAAATTTAATAAAATA--AAATAAAAAT
* *
134957 ATACTTTAA-AAAATAAAAATAATAAAT
1 AAAATTTAATAAAAT-AAAATAA-AAAT
134984 A
1 A
134985 CAGATTAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
25 7 0.16
26 12 0.27
27 23 0.52
28 2 0.05
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (26 bp):
AAAATTTAATAAAATAAAATAAAAAT
Found at i:135391 original size:21 final size:21
Alignment explanation
Indices: 135362--135402 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
135352 ATAAATAATA
*
135362 TAATAGTTTTGCCTTTTAACT
1 TAATAGTTTTGACTTTTAACT
*
135383 TAATGGTTTTGACTTTTAAC
1 TAATAGTTTTGACTTTTAAC
135403 ATTAGGAAAT
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:0.24, C:0.12, G:0.12, T:0.51
Consensus pattern (21 bp):
TAATAGTTTTGACTTTTAACT
Found at i:136520 original size:19 final size:20
Alignment explanation
Indices: 136507--136545 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
136497 TCCCATTATC
136507 ATCTCTAAACCCCAAAATCA
1 ATCTCTAAACCCCAAAATCA
136527 ATCT-TAAACCCCAAAATCA
1 ATCTCTAAACCCCAAAATCA
136546 TTCGTACCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.46, C:0.33, G:0.00, T:0.21
Consensus pattern (20 bp):
ATCTCTAAACCCCAAAATCA
Found at i:136608 original size:2 final size:2
Alignment explanation
Indices: 136601--136628 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
136591 TCTATTTTTA
136601 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
136629 TGTAAGGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:143026 original size:30 final size:30
Alignment explanation
Indices: 142990--143061 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
142980 TTAATACATG
*
142990 AACTTTAATTTGGTGCA-AT-TATACACATAC
1 AACTTTAATTTGGTGCATATGTAT--ACATAA
*
143020 AACTTTAATTATGGTTCATATGTATACATAA
1 AACTTTAATT-TGGTGCATATGTATACATAA
143051 AACTTTAATTT
1 AACTTTAATTT
143062 TAATTTAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
30 11 0.30
31 21 0.57
32 2 0.05
33 3 0.08
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (30 bp):
AACTTTAATTTGGTGCATATGTATACATAA
Found at i:143628 original size:27 final size:29
Alignment explanation
Indices: 143570--143629 Score: 70
Period size: 31 Copynumber: 2.1 Consensus size: 29
143560 TCAACTACAT
*
143570 ATGAATTTTAATTTAAGAAGCAATTTGATAC
1 ATGAATTTTAATTT-AGAAGCAA-TTCATAC
*
143601 ATGAATTTTAATTT-GATGCAA-TCATAC
1 ATGAATTTTAATTTAGAAGCAATTCATAC
143628 AT
1 AT
143630 ATACAACTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 7 0.26
29 6 0.22
31 14 0.52
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (29 bp):
ATGAATTTTAATTTAGAAGCAATTCATAC
Found at i:143735 original size:17 final size:17
Alignment explanation
Indices: 143713--143797 Score: 64
Period size: 17 Copynumber: 4.8 Consensus size: 17
143703 GTCATTTTGG
*
143713 GTTTAAATTTGATTTAA
1 GTTTAAATTTAATTTAA
**
143730 GTTTAAACTTTTCTTTTAAA
1 GTTTAAA--TTTAATTT-AA
* *
143750 GCTTAAATTTAAATTAA
1 GTTTAAATTTAATTTAA
*
143767 GTTTAAATTTAAATTGAA
1 GTTTAAATTT-AATTTAA
*
143785 -TTTAAATTGAATT
1 GTTTAAATTTAATT
143798 AAAGAAGTTC
Statistics
Matches: 54, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
16 4 0.07
17 26 0.48
18 10 0.19
19 6 0.11
20 8 0.15
ACGTcount: A:0.39, C:0.04, G:0.08, T:0.49
Consensus pattern (17 bp):
GTTTAAATTTAATTTAA
Found at i:143763 original size:6 final size:6
Alignment explanation
Indices: 143752--143792 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
143742 CTTTTAAAGC
* *
143752 TTAAAT TTAAA- TTAAGT TTAAAT TTAAA- TTGAAT TTAAAT T
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT T
143793 GAATTAAAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
5 8 0.28
6 21 0.72
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (6 bp):
TTAAAT
Found at i:143793 original size:11 final size:11
Alignment explanation
Indices: 143772--143797 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
143762 ATTAAGTTTA
143772 AATTTAAATTG
1 AATTTAAATTG
143783 AATTTAAATTG
1 AATTTAAATTG
143794 AATT
1 AATT
143798 AAAGAAGTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (11 bp):
AATTTAAATTG
Found at i:144460 original size:12 final size:12
Alignment explanation
Indices: 144441--144550 Score: 64
Period size: 12 Copynumber: 8.8 Consensus size: 12
144431 GTTTCTAAAA
144441 TAATAATAACAT
1 TAATAATAACAT
* *
144453 TTATAATAAACAA
1 TAATAAT-AACAT
*
144466 TAATAATAATAT
1 TAATAATAACAT
144478 TAATAATAA-A-
1 TAATAATAACAT
* *
144488 TAATATTAGCAT
1 TAATAATAACAT
*
144500 TAATATTAATAACAG
1 T-A-A-TAATAACAT
144515 TAATAATAA-AT
1 TAATAATAACAT
*
144526 GTGACATTAATAATAT
1 -T-A-A-TAATAACAT
144542 TAATAATAA
1 TAATAATAA
144551 AATAAAAGGA
Statistics
Matches: 76, Mismatches: 11, Indels: 22
0.70 0.10 0.20
Matches are distributed among these distances:
10 7 0.09
11 3 0.04
12 32 0.42
13 14 0.18
14 4 0.05
15 14 0.18
16 2 0.03
ACGTcount: A:0.56, C:0.05, G:0.04, T:0.35
Consensus pattern (12 bp):
TAATAATAACAT
Found at i:144467 original size:25 final size:25
Alignment explanation
Indices: 144439--144492 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
144429 TTGTTTCTAA
*
144439 AATAATAATAACATTTATAATAAAC
1 AATAATAATAACATTAATAATAAAC
* *
144464 AATAATAATAATATTAATAATAAAT
1 AATAATAATAACATTAATAATAAAC
144489 AATA
1 AATA
144493 TTAGCATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (25 bp):
AATAATAATAACATTAATAATAAAC
Found at i:145674 original size:29 final size:28
Alignment explanation
Indices: 145637--145922 Score: 220
Period size: 29 Copynumber: 9.8 Consensus size: 28
145627 CCCTAATCTA
*
145637 TCCATAAATTACATTTTTACCCTCAAACT
1 TCCAAAAATTACATTTTTACCC-CAAACT
145666 TCCAAAAATT-CAATTTTTAACCCCTAAACT
1 TCCAAAAATTAC-ATTTTT-ACCCC-AAACT
*
145696 TTCAAAAATTACA-TTTTACCCCCAAACT
1 TCCAAAAATTACATTTTTA-CCCCAAACT
* * *
145724 TCCAAAATTTCCATTTTTTGACACCGAAACT
1 TCCAAAAATTACA-TTTTT-AC-CCCAAACT
* * *
145755 TTCAAAAATTACATTTTTACTCCGAACT
1 TCCAAAAATTACATTTTTACCCCAAACT
**
145783 TCCAAAAA-TATCATTTTTGACCTTGAAACT
1 TCCAAAAATTA-CATTTTT-ACC-CCAAACT
*** *
145813 TTTGAAAATTACATTTTTATCCCCTAACT
1 TCCAAAAATTACATTTTTA-CCCCAAACT
* * * *
145842 TCCAAAAATTCCATTTTGACCCAAAAATT
1 TCCAAAAATTACATTTTTACCC-CAAACT
* *
145871 TCCAAGAATTACAATTTTACCCCTAAACT
1 TCCAAAAATTACATTTTTACCCC-AAACT
*
145900 TTCAAAAATTACCA-TTTTACCCC
1 TCCAAAAATTA-CATTTTTACCCC
145923 TGAATGTCCA
Statistics
Matches: 201, Mismatches: 39, Indels: 34
0.73 0.14 0.12
Matches are distributed among these distances:
27 2 0.01
28 39 0.19
29 90 0.45
30 49 0.24
31 21 0.10
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (28 bp):
TCCAAAAATTACATTTTTACCCCAAACT
Found at i:145722 original size:58 final size:58
Alignment explanation
Indices: 145642--145909 Score: 283
Period size: 58 Copynumber: 4.6 Consensus size: 58
145632 ATCTATCCAT
* *
145642 AAATTACATTTTTACCCTCAAACTTCCAAAAATTCAATTTTTAACCCCTAAACTTTCAA
1 AAATTACATTTTTACCCCCAAACTTCCAAAAATTCAATTTTTGA-CCCTAAACTTTCAA
* * *
145701 AAATTACA-TTTTACCCCCAAACTTCCAAAATTTCCATTTTTTGACACCGAAACTTTCAA
1 AAATTACATTTTTACCCCCAAACTTCCAAAAATT-CAATTTTTGAC-CCTAAACTTTCAA
* * * **
145760 AAATTACATTTTTA-CTCCGAACTTCCAAAAATATC-ATTTTTGACCTTGAAACTTTTGA
1 AAATTACATTTTTACCCCCAAACTTCCAAAAAT-TCAATTTTTGACCCT-AAACTTTCAA
* * * * *
145818 AAATTACATTTTTATCCCCTAACTTCCAAAAATTCCA-TTTTGACCCAAAAATTTCCAA
1 AAATTACATTTTTACCCCCAAACTTCCAAAAATTCAATTTTTGACCCTAAACTTT-CAA
* * * *
145876 GAATTACAATTTTACCCCTAAACTTTCAAAAATT
1 AAATTACATTTTTACCCCCAAACTTCCAAAAATT
145910 ACCATTTTAC
Statistics
Matches: 175, Mismatches: 26, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
57 7 0.04
58 93 0.53
59 69 0.39
60 6 0.03
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.36
Consensus pattern (58 bp):
AAATTACATTTTTACCCCCAAACTTCCAAAAATTCAATTTTTGACCCTAAACTTTCAA
Found at i:145934 original size:29 final size:29
Alignment explanation
Indices: 145817--146063 Score: 93
Period size: 29 Copynumber: 8.5 Consensus size: 29
145807 GAAACTTTTG
145817 AAAATTA-CATTTTTATCCCCT-AACT-TCCA
1 AAAATTACCA-TTTTA-CCCCTGAA-TGTCCA
*** *
145846 AAAATT-CCATTTTGACCCAAAAATTTCCA
1 AAAATTACCATTTT-ACCCCTGAATGTCCA
* * * *
145875 AGAATTACAATTTTACCCCTAAACT-TTCA
1 AAAATTACCATTTTACCCCTGAA-TGTCCA
145904 AAAATTACCATTTTACCCCTGAATGTCCA
1 AAAATTACCATTTTACCCCTGAATGTCCA
* * * * *
145933 AAAATT-CAATTTTTTATCCC-GATTTTTCTA
1 AAAATTACCA--TTTTACCCCTGA-ATGTCCA
* * * **
145963 AAATTTACCATTTTACCCTTGGATGT-TT
1 AAAATTACCATTTTACCCCTGAATGTCCA
** * *
145991 AAAATTA-CATTTTTATCCCCAAAACTTTCCT
1 AAAATTACCA-TTTTA-CCCCTGAA-TGTCCA
*
146022 AAAATTACCATTTTGCCCCTGAGA-GTCC-
1 AAAATTACCATTTTACCCCTGA-ATGTCCA
*
146050 AAAATTACGATTTT
1 AAAATTACCATTTT
146064 GCCCTCAGGC
Statistics
Matches: 164, Mismatches: 36, Indels: 37
0.69 0.15 0.16
Matches are distributed among these distances:
27 2 0.01
28 36 0.22
29 77 0.47
30 32 0.20
31 15 0.09
32 2 0.01
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCTGAATGTCCA
Found at i:146054 original size:59 final size:59
Alignment explanation
Indices: 145637--146063 Score: 214
Period size: 59 Copynumber: 7.3 Consensus size: 59
145627 CCCTAATCTA
* * *
145637 TCCATAAATTACATTTTTA-CCCTCAAAC-TTCCAAAAATT-CAATTTTTAACCCCT-AAACTT
1 TCCA-AAATTACATTTTTATCCC-CAAACTTTCCAAAAATTACCA-TTTT-ACCCCTGAGA-TG
* * * * * *
145697 TCAAAAATTACA-TTTTACCCCCAAAC-TTCC-AAAATTTCCATTTTTTGACACC-GAAACTT
1 TCCAAAATTACATTTTTATCCCCAAACTTTCCAAAAATTACCA--TTTT-ACCCCTGAGA-TG
* * * * * * *
145756 TCAAAAATTACATTTTTA-CTCCGAAC-TTCCAAAAA-TATCATTTTTGA-CCTTGAAACTT
1 TCCAAAATTACATTTTTATCCCCAAACTTTCCAAAAATTACCA-TTTT-ACCCCTGAGA-TG
** * ** * *
145814 TTGAAAATTACATTTTTATCCCCTAAC-TTCCAAAAATT-CCATTTTGA-CCCAAAAATT
1 TCCAAAATTACATTTTTATCCCCAAACTTTCCAAAAATTACCATTTT-ACCCCTGAGATG
*
145871 TCCAAGAATTACAATTTTA-CCCCTAAACTTT-CAAAAATTACCATTTTACCCCTGA-ATG
1 TCCAA-AATTACATTTTTATCCCC-AAACTTTCCAAAAATTACCATTTTACCCCTGAGATG
* ** * * *
145929 TCCAAAAATT-CAATTTTTTAT-CCCGATTTTTCTAAAATTTACCATTTTACCCTTG-GATG
1 TCC-AAAATTAC-A-TTTTTATCCCCAAACTTTCCAAAAATTACCATTTTACCCCTGAGATG
** * *
145988 TTTAAAATTACATTTTTATCCCCAAAACTTTCCTAAAATTACCATTTTGCCCCTGAGA-G
1 TCCAAAATTACATTTTTATCCCC-AAACTTTCCAAAAATTACCATTTTACCCCTGAGATG
146047 TCCAAAATTACGATTTT
1 TCCAAAATTAC-ATTTT
146064 GCCCTCAGGC
Statistics
Matches: 298, Mismatches: 44, Indels: 50
0.76 0.11 0.13
Matches are distributed among these distances:
57 24 0.08
58 105 0.35
59 149 0.50
60 20 0.07
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.37
Consensus pattern (59 bp):
TCCAAAATTACATTTTTATCCCCAAACTTTCCAAAAATTACCATTTTACCCCTGAGATG
Found at i:147723 original size:6 final size:6
Alignment explanation
Indices: 147712--147760 Score: 62
Period size: 6 Copynumber: 8.2 Consensus size: 6
147702 ATCCCCCTTG
* * * *
147712 CCTCTT CCTCTT CCTCTT CCTCTT CATCTT CATCTT CTTCTT CTTCTT
1 CCTCTT CCTCTT CCTCTT CCTCTT CCTCTT CCTCTT CCTCTT CCTCTT
147760 C
1 C
147761 ACCGCCAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.04, C:0.43, G:0.00, T:0.53
Consensus pattern (6 bp):
CCTCTT
Found at i:159967 original size:3 final size:3
Alignment explanation
Indices: 159961--160001 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
159951 ACTTCTTCTT
* * *
159961 CAC CAC CAC CAC CAT CAC CAT CAT CAC CAC CAC CAC CAC CA
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
160002 AAGTCAACTC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.34, C:0.59, G:0.00, T:0.07
Consensus pattern (3 bp):
CAC
Found at i:166028 original size:18 final size:18
Alignment explanation
Indices: 166001--166041 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
165991 CCAAATTATG
* *
166001 TTCTATATTTTAAATTAA
1 TTCTAAATTTTAAAATAA
166019 TTCTAAATTTTAAAATAA
1 TTCTAAATTTTAAAATAA
166037 -TCTAA
1 TTCTAA
166042 TTGAGTTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (18 bp):
TTCTAAATTTTAAAATAA
Found at i:176648 original size:13 final size:14
Alignment explanation
Indices: 176632--176660 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
176622 TTTGGCCATC
176632 ATTT-TTTTTTTTA
1 ATTTGTTTTTTTTA
176645 ATTTGTTTTTTTTA
1 ATTTGTTTTTTTTA
176659 AT
1 AT
176661 AGATTTTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.79
Consensus pattern (14 bp):
ATTTGTTTTTTTTA
Found at i:183268 original size:27 final size:27
Alignment explanation
Indices: 183202--183276 Score: 84
Period size: 27 Copynumber: 2.8 Consensus size: 27
183192 AATAATATTA
*
183202 ATAATT-TATGAAAATCAAAATTTATAT
1 ATAATTATAT-AAAATTAAAATTTATAT
*
183229 GTAATTATATAAAATTAAAATTTATAT
1 ATAATTATATAAAATTAAAATTTATAT
*
183256 ATTA-TATACT-AAATTAAAATT
1 ATAATTATA-TAAAATTAAAATT
183277 AATGTGTAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
26 15 0.36
27 24 0.57
28 3 0.07
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.43
Consensus pattern (27 bp):
ATAATTATATAAAATTAAAATTTATAT
Found at i:184113 original size:131 final size:134
Alignment explanation
Indices: 183964--184207 Score: 336
Period size: 132 Copynumber: 1.8 Consensus size: 134
183954 ATTAGTTAGA
** * * * *
183964 TGATTAAATGTTAGTAATTTTATC-TTAAGTCTCAAGTTCAATT-TCTCTTCT-ACTTACATTTG
1 TGATTAAATAATAATAATTTCATCTTTAAGTCCCAAGTTCAATTCT-TCTCCTAAC-TACATTTG
* * * *
184026 TATTTTTTTTTTTATGTTGTTTT-A-ATTTTTTTTTATTTTTAATTAATAGTTTTAACATATCAA
64 TAATTTTTATTTCACGTTGTTTTAAGATTTTTTTTTATTTTTAATTAATAGTTTTAACATATCAA
184089 CTCCAT
129 CTCCAT
*
184095 TGATTAAATAATAATAATTTCATCTTTGAGTCCCAAGTTCAATTCTTCTCCTAACTACATTTGTA
1 TGATTAAATAATAATAATTTCATCTTTAAGTCCCAAGTTCAATTCTTCTCCTAACTACATTTGTA
184160 ATTTTTATTTCACGTTGTTTTAAGATTTTTTTTTATTTTTAATTAATA
66 ATTTTTATTTCACGTTGTTTTAAGATTTTTTTTTATTTTTAATTAATA
184208 AATATATTGT
Statistics
Matches: 97, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
131 20 0.21
132 49 0.51
133 4 0.04
134 24 0.25
ACGTcount: A:0.27, C:0.11, G:0.07, T:0.54
Consensus pattern (134 bp):
TGATTAAATAATAATAATTTCATCTTTAAGTCCCAAGTTCAATTCTTCTCCTAACTACATTTGTA
ATTTTTATTTCACGTTGTTTTAAGATTTTTTTTTATTTTTAATTAATAGTTTTAACATATCAACT
CCAT
Found at i:198460 original size:54 final size:54
Alignment explanation
Indices: 198378--198486 Score: 209
Period size: 54 Copynumber: 2.0 Consensus size: 54
198368 GATAACATAA
198378 GTTGATTTAAATTGCACCCAACACCTTTCAATTTTTTTAACTTCATAAAGCATT
1 GTTGATTTAAATTGCACCCAACACCTTTCAATTTTTTTAACTTCATAAAGCATT
*
198432 GTTGATTTAAATTGCACTCAACACCTTTCAATTTTTTTAACTTCATAAAGCATT
1 GTTGATTTAAATTGCACCCAACACCTTTCAATTTTTTTAACTTCATAAAGCATT
198486 G
1 G
198487 AAGAGTAAGT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.31, C:0.19, G:0.08, T:0.41
Consensus pattern (54 bp):
GTTGATTTAAATTGCACCCAACACCTTTCAATTTTTTTAACTTCATAAAGCATT
Found at i:202762 original size:15 final size:16
Alignment explanation
Indices: 202742--202775 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
202732 AATTCTTTAA
202742 AAATTATAAAAAT-AT
1 AAATTATAAAAATAAT
*
202757 AAATTATTAAAATAAT
1 AAATTATAAAAATAAT
202773 AAA
1 AAA
202776 ATTACATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATTATAAAAATAAT
Found at i:204292 original size:14 final size:15
Alignment explanation
Indices: 204249--204290 Score: 84
Period size: 15 Copynumber: 2.8 Consensus size: 15
204239 AAAACTTTCG
204249 AAAATTTTAAAAATA
1 AAAATTTTAAAAATA
204264 AAAATTTTAAAAATA
1 AAAATTTTAAAAATA
204279 AAAATTTTAAAA
1 AAAATTTTAAAA
204291 TATTCATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAATTTTAAAAATA
Found at i:209911 original size:23 final size:21
Alignment explanation
Indices: 209880--209926 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
209870 AAAAACTCGA
209880 TTAAATCAAATAATTCGAATTAT
1 TTAAATC-AA-AATTCGAATTAT
* *
209903 TTAATTCAAAATTCGAATTTT
1 TTAAATCAAAATTCGAATTAT
209924 TTA
1 TTA
209927 TCGAATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 14 0.64
22 2 0.09
23 6 0.27
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.45
Consensus pattern (21 bp):
TTAAATCAAAATTCGAATTAT
Found at i:212937 original size:30 final size:31
Alignment explanation
Indices: 212903--212974 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 31
212893 AATTTTATGA
* * *
212903 TAAAATTTTATTTTTACTTTTCTT-AAAATT
1 TAAAATTTTATTCTAACTTTTCTTCAAAAAT
* *
212933 TAAAATTTAATTCTAACTTTTTTTCAAAAAT
1 TAAAATTTTATTCTAACTTTTCTTCAAAAAT
*
212964 AAAAATTTTAT
1 TAAAATTTTAT
212975 AGTTTAATTT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
30 20 0.59
31 14 0.41
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (31 bp):
TAAAATTTTATTCTAACTTTTCTTCAAAAAT
Found at i:213742 original size:19 final size:20
Alignment explanation
Indices: 213695--213744 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
213685 AACTCATTTA
* *
213695 TTATTTGATTATTATGTAAT
1 TTATTTTATTTTTATGTAAT
* *
213715 TTGTTTTATTTTTATGT-GT
1 TTATTTTATTTTTATGTAAT
213734 TTATTTTATTT
1 TTATTTTATTT
213745 ATTTATAGTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.20, C:0.00, G:0.10, T:0.70
Consensus pattern (20 bp):
TTATTTTATTTTTATGTAAT
Found at i:221748 original size:19 final size:18
Alignment explanation
Indices: 221724--221774 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
221714 GAGAAAGAAG
221724 GAAAAATAAAGG-AATAACA
1 GAAAAATAAAGGAAAT-A-A
*
221743 GAAAAA-AGAGGAAATAA
1 GAAAAATAAAGGAAATAA
*
221760 GAAAAATAAAAGAAA
1 GAAAAATAAAGGAAA
221775 GAAAATGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
17 7 0.26
18 11 0.41
19 9 0.33
ACGTcount: A:0.73, C:0.02, G:0.18, T:0.08
Consensus pattern (18 bp):
GAAAAATAAAGGAAATAA
Done.