Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 32 of 318
Found at i:11900933 original size:3 final size:3
Alignment explanation
Indices: 11900919--11900957 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
11900909 AGTAACCAAT
*
11900919 AAC AAT AAC AAC AAC AAC AAC AAC AAC AAC AAC ATAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC A-AC AA
11900958 AAGAATCAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.67, C:0.28, G:0.00, T:0.05
Consensus pattern (3 bp):
AAC
Found at i:11901271 original size:15 final size:15
Alignment explanation
Indices: 11901247--11901281 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
11901237 TATCGAAGAG
*
11901247 CTTCCGGCTCTTAAA
1 CTTCCGGCTCGTAAA
*
11901262 CTTCCTGCTCGTAAA
1 CTTCCGGCTCGTAAA
11901277 CTTCC
1 CTTCC
11901282 CCGTAAACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.17, C:0.37, G:0.11, T:0.34
Consensus pattern (15 bp):
CTTCCGGCTCGTAAA
Found at i:11903173 original size:22 final size:22
Alignment explanation
Indices: 11903135--11903179 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
11903125 GAATATCTTA
11903135 TTTTTTTAAAGATATTTTAATT
1 TTTTTTTAAAGATATTTTAATT
*
11903157 TTTTTATTAAATA-ATTTTAATT
1 TTTTT-TTAAAGATATTTTAATT
11903179 T
1 T
11903180 AAAGTTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
TTTTTTTAAAGATATTTTAATT
Found at i:11905271 original size:64 final size:64
Alignment explanation
Indices: 11905178--11905303 Score: 234
Period size: 64 Copynumber: 2.0 Consensus size: 64
11905168 CGGAATTTGC
*
11905178 TTAATGATGAGTTGTATTTATGAAGATTGATGAAGAGTATCTTACATATTTAAGTAGAATTTAT
1 TTAATGATGAGTTGTATTTATGAAGATTGATGAAGAGTATCTTACATAATTAAGTAGAATTTAT
*
11905242 TTAATGATGAGTTGTATTTATGAAGATTGATGAAGAGTATCTTACATAATTAAGTAGTATTT
1 TTAATGATGAGTTGTATTTATGAAGATTGATGAAGAGTATCTTACATAATTAAGTAGAATTT
11905304 TATAATTGAG
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 60 1.00
ACGTcount: A:0.36, C:0.03, G:0.19, T:0.42
Consensus pattern (64 bp):
TTAATGATGAGTTGTATTTATGAAGATTGATGAAGAGTATCTTACATAATTAAGTAGAATTTAT
Found at i:11911087 original size:65 final size:65
Alignment explanation
Indices: 11910968--11911090 Score: 160
Period size: 65 Copynumber: 1.9 Consensus size: 65
11910958 TTTGATAAAT
* * * *
11910968 TTAAATTTTATAAGCGTTGAATCTATATTAGAAATGTATTTGATAAATTTAAATTTTAAATGCGG
1 TTAAATTTTATAAGCGTTGAATCTATATTAAAAATGTACTTGACAAATTCAAATTTTAAATGCGG
* *
11911033 TTAAATTTTATAAGTGTTGAATTTATATTAAAAAT-TACTTGACCCAAA-TCAAATTTTA
1 TTAAATTTTATAAGCGTTGAATCTATATTAAAAATGTACTTGA--CAAATTCAAATTTTA
11911091 TGTTTTCATT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
64 6 0.12
65 41 0.82
66 3 0.06
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.43
Consensus pattern (65 bp):
TTAAATTTTATAAGCGTTGAATCTATATTAAAAATGTACTTGACAAATTCAAATTTTAAATGCGG
Found at i:11918204 original size:9 final size:9
Alignment explanation
Indices: 11918174--11918232 Score: 54
Period size: 9 Copynumber: 7.0 Consensus size: 9
11918164 AATTATATAT
11918174 TTTTTAAT-
1 TTTTTAATA
*
11918182 TTTTTAACA
1 TTTTTAATA
*
11918191 ATTTTAATA
1 TTTTTAATA
*
11918200 TTTTT-ATG
1 TTTTTAATA
*
11918208 TTTTTAAAA
1 TTTTTAATA
11918217 TTTTTAA-A
1 TTTTTAATA
11918225 -TTTTAATA
1 TTTTTAATA
11918233 AATTAATTAA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
7 6 0.15
8 16 0.39
9 19 0.46
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (9 bp):
TTTTTAATA
Found at i:11918205 original size:26 final size:25
Alignment explanation
Indices: 11918147--11918228 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 25
11918137 TATTTAATTA
* **
11918147 ATTTTTAA-ATTTTAAAAAATTATAT
1 ATTTTTAATTTTTTAAAATTTTA-AT
11918172 ATTTTTTAATTTTTTAACAATTTTAAT
1 A-TTTTTAATTTTTTAA-AATTTTAAT
11918199 ATTTTT-ATGTTTTTAAAATTTTTAA-
1 ATTTTTAAT-TTTTTAAAA-TTTTAAT
11918224 ATTTT
1 ATTTT
11918229 AATAAATTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
25 10 0.20
26 25 0.51
27 9 0.18
28 5 0.10
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (25 bp):
ATTTTTAATTTTTTAAAATTTTAAT
Found at i:11918228 original size:17 final size:17
Alignment explanation
Indices: 11918146--11918228 Score: 67
Period size: 17 Copynumber: 4.8 Consensus size: 17
11918136 ATATTTAATT
*
11918146 AATTTTTAAATTTTAAA
1 AATTTTTAAATTTTTAA
* * * *
11918163 AAATTATATATTTTTTA
1 AATTTTTAAATTTTTAA
* *
11918180 ATTTTTTAACAATTTTAA
1 AATTTTTAA-ATTTTTAA
* **
11918198 TATTTTTATGTTTTTAA
1 AATTTTTAAATTTTTAA
11918215 AATTTTTAAATTTT
1 AATTTTTAAATTTT
11918229 AATAAATTAA
Statistics
Matches: 46, Mismatches: 19, Indels: 2
0.69 0.28 0.03
Matches are distributed among these distances:
17 34 0.74
18 12 0.26
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (17 bp):
AATTTTTAAATTTTTAA
Found at i:11921690 original size:35 final size:34
Alignment explanation
Indices: 11921624--11921700 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 34
11921614 ACCTGACACT
* *
11921624 TTTTTTTTTCATACTTCTTTTGTTCTTTTTTTTCC
1 TTTTATTTTCATACTTCTTTTGTTCTTTTTTTT-A
*
11921659 TTTTATTTTCATATTTCTTTT-TT-TTACTTTTTTA
1 TTTTATTTTCATACTTCTTTTGTTCTT--TTTTTTA
11921693 TTTTATTT
1 TTTTATTT
11921701 CTTAATAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
33 2 0.05
34 10 0.27
35 25 0.68
ACGTcount: A:0.10, C:0.12, G:0.01, T:0.77
Consensus pattern (34 bp):
TTTTATTTTCATACTTCTTTTGTTCTTTTTTTTA
Found at i:11921737 original size:16 final size:16
Alignment explanation
Indices: 11921715--11921754 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
11921705 ATAAATTGTC
*
11921715 TTTTTATTTT-TTTCT
1 TTTTTATTTTGTTTAT
11921730 TATTTTATTTTGTTTAT
1 T-TTTTATTTTGTTTAT
11921747 TTTTTATT
1 TTTTTATT
11921755 ATTAACTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 16 0.73
17 5 0.23
ACGTcount: A:0.12, C:0.03, G:0.03, T:0.82
Consensus pattern (16 bp):
TTTTTATTTTGTTTAT
Found at i:11921793 original size:21 final size:21
Alignment explanation
Indices: 11921767--11921812 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
11921757 TAACTTTAAA
11921767 AAAATTGTAATGTA-TATTTTT
1 AAAATTGTAAT-TATTATTTTT
*
11921788 AAAATTTTAATTATTATTTTT
1 AAAATTGTAATTATTATTTTT
11921809 AAAA
1 AAAA
11921813 GTATTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (21 bp):
AAAATTGTAATTATTATTTTT
Found at i:11921915 original size:14 final size:14
Alignment explanation
Indices: 11921898--11921924 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11921888 TTTTTTAAAA
11921898 TTTTAAATATTAAT
1 TTTTAAATATTAAT
11921912 TTTTAAATATTAA
1 TTTTAAATATTAA
11921925 CCATATTTTT
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTTAAATATTAAT
Found at i:11921924 original size:37 final size:35
Alignment explanation
Indices: 11921783--11921924 Score: 144
Period size: 37 Copynumber: 4.0 Consensus size: 35
11921773 GTAATGTATA
* *
11921783 TTTTTAAAATTTTAATTATTATTTTTAAAAGT-AT
1 TTTTTAAAATTTTAAATATTATTTTTAAAATTAAT
* * * *
11921817 TTTTT-TAATTTTAGATATATATTTGTGAAATTAAT
1 TTTTTAAAATTTTAAATAT-TATTTTTAAAATTAAT
* * *
11921852 TTTTTATATATTTTAAAAATGTATTTTTCAAATTAAT
1 TTTTTA-AAATTTTAAATAT-TATTTTTAAAATTAAT
11921889 TTTTTAAAATTTTAAATATTAATTTTTAAATATTAA
1 TTTTTAAAATTTTAAATATT-ATTTTTAAA-ATTAA
11921925 CCATATTTTT
Statistics
Matches: 86, Mismatches: 16, Indels: 9
0.77 0.14 0.08
Matches are distributed among these distances:
33 10 0.12
34 15 0.17
35 8 0.09
36 19 0.22
37 34 0.40
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.57
Consensus pattern (35 bp):
TTTTTAAAATTTTAAATATTATTTTTAAAATTAAT
Found at i:11921931 original size:23 final size:23
Alignment explanation
Indices: 11921883--11921924 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
11921873 TATTTTTCAA
*
11921883 ATTAATTTTTTAAAATTTTAAAT
1 ATTAATTTTTTAAAATATTAAAT
11921906 ATTAA-TTTTT-AAATATTAA
1 ATTAATTTTTTAAAATATTAA
11921925 CCATATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 5 0.28
23 5 0.28
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
ATTAATTTTTTAAAATATTAAAT
Found at i:11922078 original size:20 final size:19
Alignment explanation
Indices: 11922049--11922095 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
11922039 TATATTTTTT
11922049 AAAAATTAAAAA-AAAGTTA
1 AAAAATTAAAAAGAAA-TTA
11922068 AAAAATGTAAAAAGAAATTA
1 AAAAAT-TAAAAAGAAATTA
11922088 AAGAAATT
1 AA-AAATT
11922096 GTATTTACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 6 0.24
20 12 0.48
21 7 0.28
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (19 bp):
AAAAATTAAAAAGAAATTA
Found at i:11922177 original size:14 final size:14
Alignment explanation
Indices: 11922158--11922196 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
11922148 TAATATTTAA
11922158 AAATTTTAAAAAAT
1 AAATTTTAAAAAAT
*
11922172 AAA-TTTGAAAAAT
1 AAATTTTAAAAAAT
11922185 AAATTTTTAAAA
1 AAA-TTTTAAAA
11922197 TATATAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
13 12 0.57
14 3 0.14
15 6 0.29
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (14 bp):
AAATTTTAAAAAAT
Found at i:11922206 original size:36 final size:34
Alignment explanation
Indices: 11922165--11922256 Score: 85
Period size: 36 Copynumber: 2.6 Consensus size: 34
11922155 TAAAAATTTT
* * *
11922165 AAAAAATAAATTTGAAAAATAAATTTTTAAAATATA
1 AAAAAAT-AATTTCAAAAATAAATATCTAAAAT-TA
* * *
11922201 TAAAAATTAATTTCACAAATATATATCTAAAATTA
1 -AAAAAATAATTTCAAAAATAAATATCTAAAATTA
* *
11922236 AAAAAATATTTTTAAAAATAA
1 AAAAAATAATTTCAAAAATAA
11922257 TAATTAAAAT
Statistics
Matches: 44, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
34 16 0.36
35 2 0.05
36 20 0.45
37 6 0.14
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (34 bp):
AAAAAATAATTTCAAAAATAAATATCTAAAATTA
Found at i:11922274 original size:22 final size:22
Alignment explanation
Indices: 11922245--11922291 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
11922235 AAAAAAATAT
11922245 TTTTAAAAATAATA-ATTA-AAA
1 TTTTAAAAAT-ATACATTACAAA
11922266 TTTTAAAAATATACATTACAAA
1 TTTTAAAAATATACATTACAAA
11922288 TTTT
1 TTTT
11922292 TTAAAGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 3 0.12
21 14 0.58
22 7 0.29
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTTAAAAATATACATTACAAA
Found at i:11922399 original size:27 final size:27
Alignment explanation
Indices: 11922369--11922434 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 27
11922359 ACAATTTATT
*
11922369 AAGAAATA-AAATAAAAAAGTAAAAAAA
1 AAGAAATAGAAA-AAAAAAGGAAAAAAA
*
11922396 AAGAAATATGAAAATAAAAGGAAAAAAA
1 AAGAAATA-GAAAAAAAAAGGAAAAAAA
*
11922424 AACAAA-AGAAA
1 AAGAAATAGAAA
11922435 TATGAAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 4 0.12
27 9 0.26
28 18 0.53
29 3 0.09
ACGTcount: A:0.79, C:0.02, G:0.11, T:0.09
Consensus pattern (27 bp):
AAGAAATAGAAAAAAAAAGGAAAAAAA
Found at i:11922430 original size:21 final size:22
Alignment explanation
Indices: 11922406--11922447 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
11922396 AAGAAATATG
*
11922406 AAAATAAA-AGGAAAAAAAAAC
1 AAAAGAAATAGGAAAAAAAAAC
*
11922427 AAAAGAAATATGAAAAAAAAA
1 AAAAGAAATAGGAAAAAAAAA
11922448 GTGTCAGGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.81, C:0.02, G:0.10, T:0.07
Consensus pattern (22 bp):
AAAAGAAATAGGAAAAAAAAAC
Found at i:11926583 original size:15 final size:15
Alignment explanation
Indices: 11926560--11926589 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
11926550 ACTAAATAAT
11926560 TAATAAATCAAAATA
1 TAATAAATCAAAATA
*
11926575 TAATGAATCAAAATA
1 TAATAAATCAAAATA
11926590 AATCTAGATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.07, G:0.03, T:0.27
Consensus pattern (15 bp):
TAATAAATCAAAATA
Found at i:11928402 original size:3 final size:3
Alignment explanation
Indices: 11928396--11928444 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
11928386 ATTTTGGATT
11928396 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
11928444 A
1 A
11928445 CAAACAAAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:11931697 original size:18 final size:21
Alignment explanation
Indices: 11931669--11931707 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
11931659 ATATTGCATC
11931669 AAAAATAAATA-TTT-ATATT
1 AAAAATAAATACTTTAATATT
11931688 AAAAAT-AATACTTTAATATT
1 AAAAATAAATACTTTAATATT
11931708 TGTTTATACA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 9 0.50
20 5 0.28
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (21 bp):
AAAAATAAATACTTTAATATT
Found at i:11934025 original size:22 final size:22
Alignment explanation
Indices: 11934000--11934041 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
11933990 TTTTAATGTG
11934000 TTGATAATAATA-TCAATATTAA
1 TTGA-AATAATATTCAATATTAA
*
11934022 TTGAATTAATATTCAATATT
1 TTGAAATAATATTCAATATT
11934042 TTCAAACTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (22 bp):
TTGAAATAATATTCAATATTAA
Found at i:11935195 original size:17 final size:18
Alignment explanation
Indices: 11935159--11935195 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
11935149 AATTTTAAAA
11935159 ATTAAAAATATGTTTTATT
1 ATTAAAAATATG-TTTATT
11935178 ATTAAAAATATG-TTATT
1 ATTAAAAATATGTTTATT
11935195 A
1 A
11935196 GTACTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
19 12 0.67
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (18 bp):
ATTAAAAATATGTTTATT
Found at i:11938688 original size:52 final size:51
Alignment explanation
Indices: 11938617--11938819 Score: 272
Period size: 52 Copynumber: 4.0 Consensus size: 51
11938607 ATCAAGTGAC
* **
11938617 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGT-G
* *
11938669 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC-----
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
*
11938715 AAAGTGATAAGTGATAGTTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
* *
11938766 AAAAGTGATAAGTGATAGCTTCGGCTACATTTATCTGATCAAAGTGATAAGTG
1 -AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATC-AAGTGACAAGTG
11938819 A
1 A
11938820 TAGCTTCGGC
Statistics
Matches: 133, Mismatches: 11, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
46 43 0.32
52 79 0.59
53 11 0.08
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (51 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
Found at i:11938723 original size:98 final size:98
Alignment explanation
Indices: 11938603--11938962 Score: 547
Period size: 98 Copynumber: 3.7 Consensus size: 98
11938593 TTTGAGTACT
*
11938603 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
* *
11938668 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
*
11938701 TCTGATCAAGTGACAAAGTGATAAGTGATAG-TTTCGGCTACACTTATCTGATCAAGTGACAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTT-AGCTACACTTATCTGATCAAGTGACAAGT
* *
11938765 GAAAAGTGATAAGTGATAGCTTCGGCTACATTTA
65 GAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
**
11938799 TCTG----A-T--CAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
11938857 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
* *
11938890 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGAC-AAGT
*
11938955 GATAAGTG
65 GAAAAGTG
11938963 GCTACACTTA
Statistics
Matches: 238, Mismatches: 14, Indels: 19
0.88 0.05 0.07
Matches are distributed among these distances:
91 83 0.35
92 2 0.01
93 1 0.00
94 1 0.00
95 1 0.00
97 3 0.01
98 136 0.57
99 11 0.05
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.29
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
Found at i:11938821 original size:39 final size:39
Alignment explanation
Indices: 11938767--11938857 Score: 157
Period size: 39 Copynumber: 2.4 Consensus size: 39
11938757 TGACAAGTGA
*
11938767 AAAGTGATAAGTGATAGCTTCGGCTACATTTATCTGATC
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATC
11938806 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATC
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATC
*
11938845 -AAGTGACAAGTGA
1 AAAGTGATAAGTGA
11938858 AAAGTGATAA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 12 0.24
39 38 0.76
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (39 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATC
Found at i:11938867 original size:52 final size:52
Alignment explanation
Indices: 11938806--11938962 Score: 218
Period size: 52 Copynumber: 3.1 Consensus size: 52
11938796 TTATCTGATC
*
11938806 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGACAAGTGA
*
11938858 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC------
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGACAAGTGA
**
11938904 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGTGA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGAC-AAGTGA
*
11938957 TAAGTG
1 AAAGTG
11938963 GCTACACTTA
Statistics
Matches: 92, Mismatches: 6, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
46 43 0.47
52 44 0.48
53 5 0.05
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.27
Consensus pattern (52 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGACAAGTGA
Found at i:11938932 original size:189 final size:190
Alignment explanation
Indices: 11938616--11938962 Score: 590
Period size: 189 Copynumber: 1.8 Consensus size: 190
11938606 GATCAAGTGA
* * *
11938616 CAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGT
1 CAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGT
* *
11938681 AATAGCTTCGGCTATACTTATCTGATCAAGTGACAAAGTGATAAGTGATAGTTTCGGCTACACTT
66 AATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGTTTCAGCTACACTT
*
11938746 ATCTGATCAAGTGAC-AAGTGAAAAGTGATAAGTGATAGCTTCGGCTACATTTATCTGAT
131 ATCTGATCAAGAGACAAAGTGAAAAGTGATAAGTGATAGCTTCGGCTACATTTATCTGAT
*
11938805 CAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGT
1 CAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGT
*
11938870 GATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTT-AGCTACACT
66 AATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAG-TTTCAGCTACACT
*
11938934 TATCTGATCAAGAGACAAAGTGATAAGTG
130 TATCTGATCAAGAGACAAAGTGAAAAGTG
11938963 GCTACACTTA
Statistics
Matches: 147, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
189 133 0.90
190 14 0.10
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (190 bp):
CAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGT
AATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGTTTCAGCTACACTT
ATCTGATCAAGAGACAAAGTGAAAAGTGATAAGTGATAGCTTCGGCTACATTTATCTGAT
Found at i:11938952 original size:46 final size:44
Alignment explanation
Indices: 11938858--11939073 Score: 199
Period size: 37 Copynumber: 5.3 Consensus size: 44
11938848 TGACAAGTGA
*
11938858 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC
1 AAAGTGATAAGTGATAGCTT--GCTACACTTATCTGATCAAGAGAC
11938904 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC
1 AAAGTGATAAGTGATAGC-TT-GCTACACTTATCTGATCAAGAGAC
*
11938950 AAAGTGATAA--G-T-G---GCTACACTTATCTGATCAAGAAAC
1 AAAGTGATAAGTGATAGCTTGCTACACTTATCTGATCAAGAGAC
*
11938987 AAAGTGATAA--G-T-G---GCTACACTTATCTGATCAAGAAAC
1 AAAGTGATAAGTGATAGCTTGCTACACTTATCTGATCAAGAGAC
*
11939024 AAAGTGAT-AG-G-T-G---GCTACACTTATCTGATC-AGGGAC
1 AAAGTGATAAGTGATAGCTTGCTACACTTATCTGATCAAGAGAC
11939060 -AAGTGATAAGTGAT
1 AAAGTGATAAGTGAT
11939074 CATACGTAAG
Statistics
Matches: 160, Mismatches: 5, Indels: 18
0.87 0.03 0.10
Matches are distributed among these distances:
35 7 0.04
36 7 0.04
37 89 0.56
38 1 0.01
42 1 0.01
43 1 0.01
44 1 0.01
46 51 0.32
47 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (44 bp):
AAAGTGATAAGTGATAGCTTGCTACACTTATCTGATCAAGAGAC
Found at i:11938970 original size:37 final size:37
Alignment explanation
Indices: 11938926--11939071 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
11938916 GATAGCTTTA
*
11938926 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
11938963 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
11939000 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
11939037 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
11939072 ATCATACGTA
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 89 0.86
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:11948850 original size:8 final size:8
Alignment explanation
Indices: 11948831--11948877 Score: 62
Period size: 8 Copynumber: 6.0 Consensus size: 8
11948821 TTACTTTACT
11948831 ATATATATA
1 ATATA-ATA
11948840 ATATAATA
1 ATATAATA
11948848 ATATAATA
1 ATATAATA
11948856 ATATAATA
1 ATATAATA
*
11948864 AAAT-ATA
1 ATATAATA
11948871 ATA-AATA
1 ATATAATA
11948878 TCTTTATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
7 8 0.23
8 22 0.63
9 5 0.14
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
ATATAATA
Found at i:11948853 original size:13 final size:13
Alignment explanation
Indices: 11948835--11948874 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
11948825 TTTACTATAT
11948835 ATATAATATAATA
1 ATATAATATAATA
11948848 ATATAATA-ATATA
1 ATATAATATA-ATA
*
11948861 ATAAAATATAATA
1 ATATAATATAATA
11948874 A
1 A
11948875 ATATCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 1 0.04
13 22 0.92
14 1 0.04
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
ATATAATATAATA
Found at i:11960354 original size:7 final size:7
Alignment explanation
Indices: 11960342--11960387 Score: 74
Period size: 7 Copynumber: 6.6 Consensus size: 7
11960332 AGGATGGAAA
11960342 TTAAATT
1 TTAAATT
11960349 TTAAATT
1 TTAAATT
11960356 TTAAATT
1 TTAAATT
11960363 TTAAATT
1 TTAAATT
*
11960370 TAAAATT
1 TTAAATT
*
11960377 TAAAATT
1 TTAAATT
11960384 TTAA
1 TTAA
11960388 TAATTATTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
TTAAATT
Found at i:11960367 original size:21 final size:21
Alignment explanation
Indices: 11960344--11960412 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 21
11960334 GATGGAAATT
* *
11960344 AAATTTTAAATTTTAAATTTT
1 AAATTTTAAATTTAAAATTTA
*
11960365 AAATTTAAAATTTAAAATTTTA
1 AAATTTTAAATTTAAAA-TTTA
** *
11960387 ATAATTATTATTTTTATAATTTA
1 A-AATT-TTAAATTTAAAATTTA
11960410 AAA
1 AAA
11960413 GAAATAAATT
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
21 15 0.39
22 6 0.16
23 9 0.24
24 8 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
AAATTTTAAATTTAAAATTTA
Found at i:11960461 original size:30 final size:30
Alignment explanation
Indices: 11960395--11960471 Score: 79
Period size: 30 Copynumber: 2.6 Consensus size: 30
11960385 TAATAATTAT
* * *
11960395 TATTTTTA-TAATTTAAAAGAAATAAATTA
1 TATTTTTATTATTTTTAAAGAAATAAAATA
*
11960424 -ATTTTTTATTATTTTTAAAGAGATAAAATA
1 TA-TTTTTATTATTTTTAAAGAAATAAAATA
11960454 TATTTTTATT-TTTATTAA
1 TATTTTTATTATTT-TTAA
11960472 TTTAAATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
28 1 0.03
29 9 0.22
30 29 0.73
31 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (30 bp):
TATTTTTATTATTTTTAAAGAAATAAAATA
Found at i:11963097 original size:22 final size:22
Alignment explanation
Indices: 11963057--11963099 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
11963047 ATATTTTGTA
*
11963057 ATGAATATTTTACGTATATAAT
1 ATGAATATTTTACATATATAAT
11963079 ATGAATATTTTA-ATAATATAA
1 ATGAATATTTTACAT-ATATAA
11963100 AAATATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (22 bp):
ATGAATATTTTACATATATAAT
Found at i:11976023 original size:43 final size:43
Alignment explanation
Indices: 11975972--11976058 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
11975962 AATAAAAAGG
11975972 ACTTGAAACAAACAATTTTCACAACAAAACAATCTTAGCCATC
1 ACTTGAAACAAACAATTTTCACAACAAAACAATCTTAGCCATC
11976015 ACTTGAAACAAACAATTTTCACAACAAAACAATCTTAGCCATC
1 ACTTGAAACAAACAATTTTCACAACAAAACAATCTTAGCCATC
11976058 A
1 A
11976059 ATCATAATGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.47, C:0.25, G:0.05, T:0.23
Consensus pattern (43 bp):
ACTTGAAACAAACAATTTTCACAACAAAACAATCTTAGCCATC
Found at i:11984680 original size:37 final size:37
Alignment explanation
Indices: 11984639--11984720 Score: 128
Period size: 37 Copynumber: 2.2 Consensus size: 37
11984629 AAATATTTAT
* * *
11984639 TAATCAATGTTCAAACTTTGAACATGCTTTATTAAAC
1 TAATCAATGCTAAAACTTTGAACATGCTTTAATAAAC
*
11984676 TAATCAATGCTAAAACTTTGAACATGCTTTAATGAAC
1 TAATCAATGCTAAAACTTTGAACATGCTTTAATAAAC
11984713 TAATCAAT
1 TAATCAAT
11984721 ATATTTATAC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (37 bp):
TAATCAATGCTAAAACTTTGAACATGCTTTAATAAAC
Found at i:11984800 original size:33 final size:33
Alignment explanation
Indices: 11984763--11984834 Score: 135
Period size: 33 Copynumber: 2.2 Consensus size: 33
11984753 TTAAAACTTG
*
11984763 AATTATACATATACCAACAATTAATTTTAGGTC
1 AATTATACATACACCAACAATTAATTTTAGGTC
11984796 AATTATACATACACCAACAATTAATTTTAGGTC
1 AATTATACATACACCAACAATTAATTTTAGGTC
11984829 AATTAT
1 AATTAT
11984835 CCATGCTTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.43, C:0.15, G:0.06, T:0.36
Consensus pattern (33 bp):
AATTATACATACACCAACAATTAATTTTAGGTC
Found at i:11988271 original size:121 final size:119
Alignment explanation
Indices: 11987859--11988601 Score: 1310
Period size: 121 Copynumber: 6.2 Consensus size: 119
11987849 TTTTCAAGTT
*
11987859 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
* *
11987924 TAATATAAGAATATTAATTATTAAGAATTTTTTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTATTAAATTATATATTTTAATTAAA
* *
11987978 ATACATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
* *
11988043 TAATATAAGAATATTAATTATTAAGAATTTTTTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTATTAAATTATATATTTTAATTAAA
11988097 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
*
11988162 TAATATAAGAATATT-ATCCAATTAAGAATTTCATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAAT--TATTAAGAATTT-ATTAAATTATATATTTTAATTAAA
11988218 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
*
11988283 TAATATAAGAATATT-ATCCAATTAAGAATTTCATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAAT--TATTAAGAATTT-ATTAAATTATATATTTTAATTAAA
11988339 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
11988404 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAA-TTTATTAAATTATATATTTTAATTAAA
11988459 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
*
11988524 TAATATAAGAATATTAACTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAA-TTTATTAAATTATATATTTTAATTAAA
11988579 ATATATTTAATAATAATTATGTT
1 ATATATTTAATAATAATTATGTT
11988602 TAAATATGAT
Statistics
Matches: 611, Mismatches: 8, Indels: 9
0.97 0.01 0.01
Matches are distributed among these distances:
118 2 0.00
119 196 0.32
120 185 0.30
121 226 0.37
122 2 0.00
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (119 bp):
ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
TAATATAAGAATATTAATTATTAAGAATTTATTAAATTATATATTTTAATTAAA
Found at i:11988458 original size:18 final size:17
Alignment explanation
Indices: 11988430--11988464 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
11988420 ATTATTAAGA
*
11988430 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
11988447 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
11988465 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:11988549 original size:361 final size:359
Alignment explanation
Indices: 11987859--11988601 Score: 1346
Period size: 361 Copynumber: 2.1 Consensus size: 359
11987849 TTTTCAAGTT
*
11987859 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
* *
11987924 TAATATAAGAATATTAATTATTAAGAATTTTTTAAATTATATAGTTTAATTAAAATACATTTAAT
66 TAATATAAGAATATTAATAATTAAGAATTTATTAAATTATATAGTTTAATTAAAATACATTTAAT
*
11987989 AATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAA
131 AATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAA
11988054 TATTAATTATTAAGAATTTTTTAAATTATATAGTTTAATTAAAATATATTTAATAATAATTATGT
196 TATTAATTATTAAGAATTTTTTAAATTATATAGTTTAATTAAAATATATTTAATAATAATTATGT
*
11988119 TAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTATCCAAT
261 TAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTATACAAT
11988184 TAAGAATTTCATTAAATTATATATTTTAATTAAA
326 TAAGAATTTCATTAAATTATATATTTTAATTAAA
11988218 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
* *
11988283 TAATATAAGAATATT-ATCCAATTAAGAATTTCATTAAATTATATATTTTAATTAAAATATATTT
66 TAATATAAGAATATTAAT--AATTAAGAATTT-ATTAAATTATATAGTTTAATTAAAATACATTT
11988347 AATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAA
128 AATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAA
*
11988412 GAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATT
193 GAATATTAATTATTAAGAATTTT-TTAAATTATATAGTTTAATTAAAATATATTTAATAATAATT
11988477 ATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTA-A
257 ATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTATA
* *
11988541 CTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
322 CAATTAAGAATTTCATTAAATTATATATTTTAATTAAA
11988579 ATATATTTAATAATAATTATGTT
1 ATATATTTAATAATAATTATGTT
11988602 TAAATATGAT
Statistics
Matches: 370, Mismatches: 10, Indels: 6
0.96 0.03 0.02
Matches are distributed among these distances:
358 2 0.01
359 79 0.21
360 11 0.03
361 175 0.47
362 103 0.28
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (359 bp):
ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
TAATATAAGAATATTAATAATTAAGAATTTATTAAATTATATAGTTTAATTAAAATACATTTAAT
AATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAA
TATTAATTATTAAGAATTTTTTAAATTATATAGTTTAATTAAAATATATTTAATAATAATTATGT
TAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTATACAAT
TAAGAATTTCATTAAATTATATATTTTAATTAAA
Found at i:11988578 original size:18 final size:17
Alignment explanation
Indices: 11988550--11988584 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
11988540 ACTATTAAGA
*
11988550 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
11988567 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
11988585 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:11988798 original size:44 final size:45
Alignment explanation
Indices: 11988749--11988839 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
11988739 ACCTCTATTC
* * *
11988749 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
11988793 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
11988838 CA
1 CA
11988840 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:11988854 original size:17 final size:16
Alignment explanation
Indices: 11988820--11988872 Score: 97
Period size: 16 Copynumber: 3.2 Consensus size: 16
11988810 GATTAGCTAT
11988820 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
11988836 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
11988853 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
11988869 TACA
1 TACA
11988873 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
16 20 0.56
17 16 0.44
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:12001495 original size:13 final size:14
Alignment explanation
Indices: 12001463--12001498 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
12001453 ATAAAAAATT
12001463 AAATTAAATAATAA
1 AAATTAAATAATAA
*
12001477 AAATTAAATAA-AG
1 AAATTAAATAATAA
12001490 AAATTAAAT
1 AAATTAAAT
12001499 TTCATTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (14 bp):
AAATTAAATAATAA
Found at i:12012623 original size:25 final size:25
Alignment explanation
Indices: 12012594--12012641 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
12012584 TTATGATTTT
* *
12012594 TAATTATTATTATAGATTTTTTTCA
1 TAATTATTAATATAAATTTTTTTCA
* *
12012619 TAATTTTTAATCTAAATTTTTTT
1 TAATTATTAATATAAATTTTTTT
12012642 AGTTTTCTTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (25 bp):
TAATTATTAATATAAATTTTTTTCA
Found at i:12013507 original size:17 final size:17
Alignment explanation
Indices: 12013458--12013512 Score: 53
Period size: 16 Copynumber: 3.3 Consensus size: 17
12013448 TTTAGCGTTG
*
12013458 ATTATATTACAAAATTTT
1 ATTAT-TTATAAAATTTT
*
12013476 -CTATTT-TAAATATTTT
1 ATTATTTATAAA-ATTTT
12013492 ATTATTTATAAAA-TTT
1 ATTATTTATAAAATTTT
12013508 ATTAT
1 ATTAT
12013513 GTTTATAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 3 0.10
16 15 0.48
17 9 0.29
18 4 0.13
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTATTTATAAAATTTT
Found at i:12014890 original size:9 final size:9
Alignment explanation
Indices: 12014876--12014905 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
12014866 TTAAAATTTG
12014876 ATAATTTTT
1 ATAATTTTT
12014885 ATAATTTTT
1 ATAATTTTT
12014894 ATTAATTTTT
1 A-TAATTTTT
12014904 AT
1 AT
12014906 TGTTATAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
ATAATTTTT
Found at i:12014899 original size:10 final size:10
Alignment explanation
Indices: 12014877--12014906 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
12014867 TAAAATTTGA
12014877 TAATTTTTA-
1 TAATTTTTAT
12014886 TAATTTTTAT
1 TAATTTTTAT
12014896 TAATTTTTAT
1 TAATTTTTAT
12014906 T
1 T
12014907 GTTATAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TAATTTTTAT
Found at i:12014922 original size:14 final size:15
Alignment explanation
Indices: 12014896--12014926 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
12014886 TAATTTTTAT
12014896 TAATTTTTATTGTTA
1 TAATTTTTATTGTTA
12014911 TAATTTTT-TTGTTA
1 TAATTTTTATTGTTA
12014925 TA
1 TA
12014927 TATCACATCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TAATTTTTATTGTTA
Found at i:12020856 original size:6 final size:6
Alignment explanation
Indices: 12020845--12020879 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
12020835 GTAGTTGTTG
12020845 TCATTA TCATTA TCATTA TCATTA TCATTA TCATT
1 TCATTA TCATTA TCATTA TCATTA TCATTA TCATT
12020880 TAGCCCAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.51
Consensus pattern (6 bp):
TCATTA
Found at i:12034461 original size:29 final size:30
Alignment explanation
Indices: 12034406--12034462 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
12034396 ATTAGACTAA
**
12034406 AATTTTTAAATTTAAAAAGTAGGAGGATTG
1 AATTTTTAAATTTAAAAAGTAAAAGGATTG
* *
12034436 AATTTTTAACTTT-TAAAGTAAAAGGAT
1 AATTTTTAAATTTAAAAAGTAAAAGGAT
12034463 CAAATCTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 11 0.48
30 12 0.52
ACGTcount: A:0.44, C:0.02, G:0.16, T:0.39
Consensus pattern (30 bp):
AATTTTTAAATTTAAAAAGTAAAAGGATTG
Found at i:12042044 original size:5 final size:5
Alignment explanation
Indices: 12042018--12042075 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
12042008 ATGTGTTAAA
* *
12042018 ATATAT ATATT AAATT ATTATT ATATT ATAGT ATATT ATATTAT ATATT
1 ATAT-T ATATT ATATT A-TATT ATATT ATATT ATATT ATA-T-T ATATT
12042067 ATATT ATAT
1 ATATT ATAT
12042076 AAATAAGTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
5 31 0.69
6 10 0.22
7 4 0.09
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (5 bp):
ATATT
Found at i:12042054 original size:10 final size:9
Alignment explanation
Indices: 12042019--12042076 Score: 61
Period size: 8 Copynumber: 6.7 Consensus size: 9
12042009 TGTGTTAAAA
12042019 TATATATAT
1 TATATATAT
*
12042028 TAAAT-TAT
1 TATATATAT
12042036 TAT-TATAT
1 TATATATAT
12042044 TATAGTATAT
1 TATA-TATAT
12042054 TATAT-TA-
1 TATATATAT
12042061 TATATTATAT
1 TATA-TATAT
12042071 TATATA
1 TATATA
12042077 AATAAGTAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
7 5 0.12
8 14 0.34
9 9 0.22
10 13 0.32
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (9 bp):
TATATATAT
Found at i:12042066 original size:12 final size:12
Alignment explanation
Indices: 12042021--12042076 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
12042011 TGTTAAAATA
*
12042021 TATATATTAAAT
1 TATATATTATAT
12042033 TAT-TATTATATT
1 TATATATTATA-T
12042045 ATAGTATATTATAT
1 -TA-TATATTATAT
12042059 TATATATTATAT
1 TATATATTATAT
12042071 TATATA
1 TATATA
12042077 AATAAGTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 6 0.15
12 20 0.51
13 4 0.10
14 2 0.05
15 7 0.18
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:12043329 original size:46 final size:46
Alignment explanation
Indices: 12043302--12043461 Score: 212
Period size: 46 Copynumber: 3.3 Consensus size: 46
12043292 CACTTTCCAC
12043302 TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACT
1 TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACT
* ** ** *
12043348 TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCAATTTCCAC
1 TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATC-A----C-T
12043400 TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACT
1 TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACT
12043446 TTGTCACTTGATCAGA
1 TTGTCACTTGATCAGA
12043462 AGTACTCAAA
Statistics
Matches: 96, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
46 54 0.56
47 2 0.02
51 2 0.02
52 38 0.40
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (46 bp):
TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACT
Found at i:12043334 original size:52 final size:52
Alignment explanation
Indices: 12043250--12043447 Score: 255
Period size: 52 Copynumber: 3.9 Consensus size: 52
12043240 ATAGGGCACT
* **
12043250 TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCAC
1 TTGTCACTTGATCAGATAAGTATAGCCAAAGCTACCACTTATCACTTTCCAC
* *
12043302 TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC--T----
1 TTGTCACTTGATCAGATAAGTATAGCCAAAGCTACCACTTATCACTTTCCAC
* ** *
12043348 TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCAATTTCCAC
1 TTGTCACTTGATCAGATAAGTATAGCCAAAGCTACCACTTATCACTTTCCAC
* *
12043400 TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTT
1 TTGTCACTTGATCAGATAAGTATAGCCAAAGCTACCACTTATCACTTT
12043448 GTCACTTGAT
Statistics
Matches: 123, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
46 39 0.32
48 1 0.01
50 1 0.01
52 82 0.67
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (52 bp):
TTGTCACTTGATCAGATAAGTATAGCCAAAGCTACCACTTATCACTTTCCAC
Found at i:12043415 original size:98 final size:98
Alignment explanation
Indices: 12043246--12043461 Score: 423
Period size: 98 Copynumber: 2.2 Consensus size: 98
12043236 CGGAATAGGG
*
12043246 CACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTTGTCACTT
1 CACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCAATTTCCACTTGTCACTT
12043311 GATCAGATAAGTGTAGCTAAAGCTACCACTTAT
66 GATCAGATAAGTGTAGCTAAAGCTACCACTTAT
12043344 CACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCAATTTCCACTTGTCACTT
1 CACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCAATTTCCACTTGTCACTT
12043409 GATCAGATAAGTGTAGCTAAAGCTACCACTTAT
66 GATCAGATAAGTGTAGCTAAAGCTACCACTTAT
12043442 CACTTTGTCACTTGATCAGA
1 CACTTTGTCACTTGATCAGA
12043462 AGTACTCAAA
Statistics
Matches: 117, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
98 117 1.00
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (98 bp):
CACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCAATTTCCACTTGTCACTT
GATCAGATAAGTGTAGCTAAAGCTACCACTTAT
Found at i:12045686 original size:18 final size:19
Alignment explanation
Indices: 12045663--12045701 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
12045653 ATATATAGAT
12045663 ATATATATTGAATA-TTGA
1 ATATATATTGAATATTTGA
*
12045681 ATATATATTGATTATTTGA
1 ATATATATTGAATATTTGA
12045700 AT
1 AT
12045702 TGAATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
ATATATATTGAATATTTGA
Found at i:12046050 original size:39 final size:39
Alignment explanation
Indices: 12045940--12046074 Score: 103
Period size: 39 Copynumber: 3.4 Consensus size: 39
12045930 GACCTCGAGT
* * * * *
12045940 CGATAAGACACTGGGTGTCACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCA-AATATTACTTCGGCTAG-TC
** ** * *
12045981 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
* *
12046019 CGATGAGACACTGGGTGTCAAATATTGCTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAAATATTACTTCG-GCTAGTC
*
12046058 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
12046075 CCATATTGGT
Statistics
Matches: 72, Mismatches: 20, Indels: 6
0.73 0.20 0.06
Matches are distributed among these distances:
38 18 0.25
39 35 0.49
40 4 0.06
41 15 0.21
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
Found at i:12046218 original size:18 final size:19
Alignment explanation
Indices: 12046197--12046237 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
12046187 AATGAAATGA
12046197 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
12046215 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
12046234 GAAA
1 GAAA
12046238 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:12049429 original size:21 final size:21
Alignment explanation
Indices: 12049397--12049437 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
12049387 TCATAAAGTT
12049397 TGTTTATATTTTAATTAATCA
1 TGTTTATATTTTAATTAATCA
12049418 TGTTT-TAGTTTTAATTAATC
1 TGTTTATA-TTTTAATTAATC
12049438 TTAATTTACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.29, C:0.05, G:0.07, T:0.59
Consensus pattern (21 bp):
TGTTTATATTTTAATTAATCA
Found at i:12049445 original size:21 final size:20
Alignment explanation
Indices: 12049403--12049462 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
12049393 AGTTTGTTTA
* **
12049403 TATTTTAATTAATCATGTTT
1 TATTTTAATTAATCTTAATT
12049423 TAGTTTTAATTAATCTTAATT
1 TA-TTTTAATTAATCTTAATT
* *
12049444 TA-CTTAATTAAGCTTAATT
1 TATTTTAATTAATCTTAATT
12049463 GTTTTTTTAC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
19 15 0.44
20 2 0.06
21 17 0.50
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (20 bp):
TATTTTAATTAATCTTAATT
Found at i:12049478 original size:27 final size:26
Alignment explanation
Indices: 12049442--12049492 Score: 93
Period size: 27 Copynumber: 1.9 Consensus size: 26
12049432 TTAATCTTAA
12049442 TTTACTTAATTAAGCTTAATTGTTTT
1 TTTACTTAATTAAGCTTAATTGTTTT
12049468 TTTACCTTAATTAAGCTTAATTGTT
1 TTTA-CTTAATTAAGCTTAATTGTT
12049493 AATTTCATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.27, C:0.10, G:0.08, T:0.55
Consensus pattern (26 bp):
TTTACTTAATTAAGCTTAATTGTTTT
Found at i:12050343 original size:15 final size:15
Alignment explanation
Indices: 12050323--12050352 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
12050313 GTAAAATAAT
12050323 AAAAAATATTTTACA
1 AAAAAATATTTTACA
12050338 AAAAAATATTTTACA
1 AAAAAATATTTTACA
12050353 TACAAAGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAAAATATTTTACA
Found at i:12052447 original size:32 final size:32
Alignment explanation
Indices: 12052406--12052471 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
12052396 TTGAGATAAA
12052406 ATGCTTATCAATGCTTTTTGTTAGGTTATGTG
1 ATGCTTATCAATGCTTTTTGTTAGGTTATGTG
12052438 ATGCTTATCAATGCTTTTTGTTAGGTTATGTG
1 ATGCTTATCAATGCTTTTTGTTAGGTTATGTG
12052470 AT
1 AT
12052472 TTAATGGAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.20, C:0.09, G:0.21, T:0.50
Consensus pattern (32 bp):
ATGCTTATCAATGCTTTTTGTTAGGTTATGTG
Found at i:12053088 original size:354 final size:354
Alignment explanation
Indices: 12052439--12053145 Score: 1414
Period size: 354 Copynumber: 2.0 Consensus size: 354
12052429 GGTTATGTGA
12052439 TGCTTATCAATGCTTTTTGTTAGGTTATGTGATTTAATGGAGAGTACTCATTAAGAAAAAGGTAG
1 TGCTTATCAATGCTTTTTGTTAGGTTATGTGATTTAATGGAGAGTACTCATTAAGAAAAAGGTAG
12052504 ATTGAGATCAACTAGTACATCTGTGGAAACCATTGAAAAGGACTTTGCTATTATTTTACCTGGGA
66 ATTGAGATCAACTAGTACATCTGTGGAAACCATTGAAAAGGACTTTGCTATTATTTTACCTGGGA
12052569 TGTTAGTCCTAAACAGAACAAAATGGTGAAATTTTACTCTACACCATGGGAGAAGGCTTTATTGT
131 TGTTAGTCCTAAACAGAACAAAATGGTGAAATTTTACTCTACACCATGGGAGAAGGCTTTATTGT
12052634 TGTTATTGTTCTATGTACTTTTTGGCTATTTAAGGTGGTGCTCTGATTCCTATGAACTCTTAGCA
196 TGTTATTGTTCTATGTACTTTTTGGCTATTTAAGGTGGTGCTCTGATTCCTATGAACTCTTAGCA
12052699 AGTTCTGTCATTTTGAAAGAGAGTCTTGCCAAGATGTTTATTGTACTTGGCATAAGTTCAATGTG
261 AGTTCTGTCATTTTGAAAGAGAGTCTTGCCAAGATGTTTATTGTACTTGGCATAAGTTCAATGTG
12052764 TCTCTCTGAATTTATGTGAATATTATCTC
326 TCTCTCTGAATTTATGTGAATATTATCTC
12052793 TGCTTATCAATGCTTTTTGTTAGGTTATGTGATTTAATGGAGAGTACTCATTAAGAAAAAGGTAG
1 TGCTTATCAATGCTTTTTGTTAGGTTATGTGATTTAATGGAGAGTACTCATTAAGAAAAAGGTAG
12052858 ATTGAGATCAACTAGTACATCTGTGGAAACCATTGAAAAGGACTTTGCTATTATTTTACCTGGGA
66 ATTGAGATCAACTAGTACATCTGTGGAAACCATTGAAAAGGACTTTGCTATTATTTTACCTGGGA
12052923 TGTTAGTCCTAAACAGAACAAAATGGTGAAATTTTACTCTACACCATGGGAGAAGGCTTTATTGT
131 TGTTAGTCCTAAACAGAACAAAATGGTGAAATTTTACTCTACACCATGGGAGAAGGCTTTATTGT
12052988 TGTTATTGTTCTATGTACTTTTTGGCTATTTAAGGTGGTGCTCTGATTCCTATGAACTCTTAGCA
196 TGTTATTGTTCTATGTACTTTTTGGCTATTTAAGGTGGTGCTCTGATTCCTATGAACTCTTAGCA
12053053 AGTTCTGTCATTTTGAAAGAGAGTCTTGCCAAGATGTTTATTGTACTTGGCATAAGTTCAATGTG
261 AGTTCTGTCATTTTGAAAGAGAGTCTTGCCAAGATGTTTATTGTACTTGGCATAAGTTCAATGTG
12053118 TCTCTCTGAATTTATGTGAATATTATCT
326 TCTCTCTGAATTTATGTGAATATTATCT
12053146 TGTGTCTAAC
Statistics
Matches: 353, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
354 353 1.00
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.38
Consensus pattern (354 bp):
TGCTTATCAATGCTTTTTGTTAGGTTATGTGATTTAATGGAGAGTACTCATTAAGAAAAAGGTAG
ATTGAGATCAACTAGTACATCTGTGGAAACCATTGAAAAGGACTTTGCTATTATTTTACCTGGGA
TGTTAGTCCTAAACAGAACAAAATGGTGAAATTTTACTCTACACCATGGGAGAAGGCTTTATTGT
TGTTATTGTTCTATGTACTTTTTGGCTATTTAAGGTGGTGCTCTGATTCCTATGAACTCTTAGCA
AGTTCTGTCATTTTGAAAGAGAGTCTTGCCAAGATGTTTATTGTACTTGGCATAAGTTCAATGTG
TCTCTCTGAATTTATGTGAATATTATCTC
Found at i:12061883 original size:6 final size:6
Alignment explanation
Indices: 12061872--12061896 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
12061862 TCTCCTCTGA
12061872 CAAACC CAAACC CAAACC CAAACC C
1 CAAACC CAAACC CAAACC CAAACC C
12061897 TGTCAAATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (6 bp):
CAAACC
Found at i:12069899 original size:39 final size:39
Alignment explanation
Indices: 12069854--12069933 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
12069844 ATTAAATTGA
12069854 CATTAAAAATAATTTATTATATTACTAATCACTATGTGG
1 CATTAAAAATAATTTATTATATTACTAATCACTATGTGG
12069893 CATTAAAAATAATTTATTATATTACTAATCACTATGTGG
1 CATTAAAAATAATTTATTATATTACTAATCACTATGTGG
12069932 CA
1 CA
12069934 ATAATTAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.40
Consensus pattern (39 bp):
CATTAAAAATAATTTATTATATTACTAATCACTATGTGG
Found at i:12072772 original size:11 final size:11
Alignment explanation
Indices: 12072758--12072782 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
12072748 TTCAGCTGAT
12072758 GAAAATGAAGA
1 GAAAATGAAGA
12072769 GAAAATGAAGA
1 GAAAATGAAGA
12072780 GAA
1 GAA
12072783 TTCTAGATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.28, T:0.08
Consensus pattern (11 bp):
GAAAATGAAGA
Found at i:12073096 original size:146 final size:143
Alignment explanation
Indices: 12072891--12073183 Score: 435
Period size: 146 Copynumber: 2.0 Consensus size: 143
12072881 TTGCTGCTTA
* * * *
12072891 AAATATCTCTTTTGGGATTATTTTCACTTTAGGTCATTCCTCATTTGACAATTGAGCTATTTAAT
1 AAATATCTCCTTTGGGATTATTTACACTTTAGGTCATTCCTCATTTGAAAATTGAGCTATTCAAT
* *
12072956 CCTTTTAGCAACTTTTACACCTTTTTTTTAATTTAGTCCTTTTTATTTAATTAATCACCCAAACG
66 CCTTCTAGCAACTTTTACACC---TTTTCAATTTAGTCCTTTTTATTTAATTAATCACCCAAACG
12073021 TCAAAATTTTCTAACG
128 TCAAAATTTTCTAACG
* * *
12073037 AAATATCTCCTTTGGGCTTATTTACACTTTAGGTTC-TTTCTCATTTGAAAATTGAGCTATTCGA
1 AAATATCTCCTTTGGGATTATTTACACTTTAGG-TCATTCCTCATTTGAAAATTGAGCTATTCAA
* * *
12073101 TCCTTCTATCAGCTTTTACACCTTTTCAATTTAGTCCTTTTTATTTAATTAATCACCCAAACTTC
65 TCCTTCTAGCAACTTTTACACCTTTTCAATTTAGTCCTTTTTATTTAATTAATCACCCAAACGTC
12073166 AAAATTTTCTAACG
130 AAAATTTTCTAACG
12073180 AAAT
1 AAAT
12073184 TTTAATACTA
Statistics
Matches: 134, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
143 59 0.44
146 73 0.54
147 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.08, T:0.45
Consensus pattern (143 bp):
AAATATCTCCTTTGGGATTATTTACACTTTAGGTCATTCCTCATTTGAAAATTGAGCTATTCAAT
CCTTCTAGCAACTTTTACACCTTTTCAATTTAGTCCTTTTTATTTAATTAATCACCCAAACGTCA
AAATTTTCTAACG
Found at i:12074416 original size:17 final size:17
Alignment explanation
Indices: 12074382--12074417 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
12074372 TGTTTTAGTA
*
12074382 TAGTTTTTATAGCGTTT
1 TAGTTTTTATAGCATTT
*
12074399 TAGTTTTTATTGCATTT
1 TAGTTTTTATAGCATTT
12074416 TA
1 TA
12074418 TACAATATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.19, C:0.06, G:0.14, T:0.61
Consensus pattern (17 bp):
TAGTTTTTATAGCATTT
Found at i:12085496 original size:13 final size:13
Alignment explanation
Indices: 12085478--12085505 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
12085468 AGTATACTAA
12085478 ACTTAAAGTAGTT
1 ACTTAAAGTAGTT
12085491 ACTTAAAGTAGTT
1 ACTTAAAGTAGTT
12085504 AC
1 AC
12085506 CATTGCCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (13 bp):
ACTTAAAGTAGTT
Found at i:12091449 original size:21 final size:21
Alignment explanation
Indices: 12091423--12091463 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
12091413 AGACGAGCGA
* *
12091423 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
12091444 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
12091464 TTGAGCAGAT
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:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:12097019 original size:14 final size:14
Alignment explanation
Indices: 12097000--12097029 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12096990 TTATATCGAG
12097000 ACCAATCCAAATCA
1 ACCAATCCAAATCA
*
12097014 ACCAATCCAATTCA
1 ACCAATCCAAATCA
12097028 AC
1 AC
12097030 ATATTTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.37, G:0.00, T:0.17
Consensus pattern (14 bp):
ACCAATCCAAATCA
Found at i:12110080 original size:44 final size:45
Alignment explanation
Indices: 12110032--12110118 Score: 158
Period size: 46 Copynumber: 1.9 Consensus size: 45
12110022 TTGACGAGCT
12110032 CATCAATCATGG-TATATATTATTGATACATGGAAATTATTGATA
1 CATCAATCATGGATATATATTATTGATACATGGAAATTATTGATA
12110076 CATCAATCATGGTATATATATTATTGATACATGGAAATTATTG
1 CATCAATCATGG-ATATATATTATTGATACATGGAAATTATTG
12110119 TACTAACTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
44 12 0.29
46 29 0.71
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.39
Consensus pattern (45 bp):
CATCAATCATGGATATATATTATTGATACATGGAAATTATTGATA
Found at i:12111426 original size:30 final size:30
Alignment explanation
Indices: 12111385--12111445 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
12111375 TATGATAAAC
*
12111385 TAGATTCAATAAGCTTTAATTCCATATTTT
1 TAGACTCAATAAGCTTTAATTCCATATTTT
12111415 TAGACTCAATAAGCTTTAATTCCATATTTT
1 TAGACTCAATAAGCTTTAATTCCATATTTT
12111445 T
1 T
12111446 TTCATCTTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.46
Consensus pattern (30 bp):
TAGACTCAATAAGCTTTAATTCCATATTTT
Found at i:12113043 original size:131 final size:129
Alignment explanation
Indices: 12112900--12113500 Score: 562
Period size: 131 Copynumber: 4.6 Consensus size: 129
12112890 AGATTTGATA
*
12112900 TTTGACAATTCGCGGAATCGTGCCCTAACGTGCTGGGTTGCAATTTCGCGTTTGCTCAAAATAAT
1 TTTGACAATTCG-GGAATCGTGCCCTATCGTGCTGGGTTGCAATTTCGCGTTTGCTCAAAATAAT
** * * *
12112965 CGAATATCATTTCAAAATTTCACTCATGTCTTTTAAAAATCCCTT-AAACGAAGGCGATGTGCGA
65 CGAATATCCCTTCAAAATTTCACTCATGT-TTTTAAAAA-CCCTTAAAACGAAAGCAATGTTCGA
*
12113029 TA
128 TG
* * * * *
12113031 TTTGGCAATTCGCGGAATCGTACCCTAACGTGTTGAGTTGCAATTTCGCGTTTGCTCAAAATAAT
1 TTTGACAATTCG-GGAATCGTGCCCTATCGTGCTGGGTTGCAATTTCGCGTTTGCTCAAAATAAT
* * * * * **
12113096 CAAATATCCCTTCAAAATTTCACTCAGGTCTTCTAAAAATCCTTTAAAACGAAGGCAATACTC-A
65 CGAATATCCCTTCAAAATTTCACTCATGT-TTTTAAAAA-CCCTTAAAACGAAAGCAATGTTCGA
12113160 GTG
128 -TG
* ** * *
12113163 TTTGACAATTCGGGAATCATGCCCTATCGTGCTGGGTTGTGATTTCTCGTTTGCTCAAAACAATC
1 TTTGACAATTCGGGAATCGTGCCCTATCGTGCTGGGTTGCAATTTCGCGTTTGCTCAAAATAATC
* * *** * * *
12113228 GAATATTCCTTTAGGTTTTCACTCATGTTTATTAAAAACCTTTCAAAAC-AAAG-GATGTTCGAG
66 GAATATCCCTTCAAAATTTCACTCATGTTT-TTAAAAACCCTT-AAAACGAAAGCAATGTTCGAT
12113291 G
129 G
* * * * ** ** * * * **
12113292 TTTGGCGATTTGAGAATCGTGCCCTATCGTGCTGGGTTGCGCTTTTTCATTTGTTCTAAACGATC
1 TTTGACAATTCGGGAATCGTGCCCTATCGTGCTGGGTTGCAATTTCGCGTTTGCTCAAAATAATC
* ** * * *
12113357 GAAGATCCCTTCGGAATTTCACTCATGTTTTCTAAAAACCCTTTAAAACGAAAGAAATATTCAAT
66 GAATATCCCTTCAAAATTTCACTCATGTTTT-TAAAAACCC-TTAAAACGAAAGCAATGTTCGAT
12113422 G
129 G
* * * *
12113423 TTTGACAATTCGGGGAATAGTACCCTATCGTGCTGGGTTGCAATTTCCCGTTTGTTCAAAATAAT
1 TTTGACAATTC-GGGAATCGTGCCCTATCGTGCTGGGTTGCAATTTCGCGTTTGCTCAAAATAAT
*
12113488 CGAATATCTCTTC
65 CGAATATCCCTTC
12113501 GGAGTTTCAC
Statistics
Matches: 383, Mismatches: 77, Indels: 19
0.80 0.16 0.04
Matches are distributed among these distances:
128 1 0.00
129 95 0.25
130 17 0.04
131 192 0.50
132 78 0.20
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (129 bp):
TTTGACAATTCGGGAATCGTGCCCTATCGTGCTGGGTTGCAATTTCGCGTTTGCTCAAAATAATC
GAATATCCCTTCAAAATTTCACTCATGTTTTTAAAAACCCTTAAAACGAAAGCAATGTTCGATG
Found at i:12113433 original size:260 final size:263
Alignment explanation
Indices: 12112900--12113494 Score: 675
Period size: 260 Copynumber: 2.3 Consensus size: 263
12112890 AGATTTGATA
* * *
12112900 TTTGACAATTCGCGGAATCGTGCCCTAACGTGCTGGGTTGCAATTTCGCGTTTGCTCAAAATAAT
1 TTTGACAATTCG-GGAATCATGCCCTATCGTGCTGGGTTGCAATTTCCCGTTTGCTCAAAATAAT
*
12112965 CGAATA-TCATTTCAAAATTTCACTCATGTCTTTTAAAAATCCCTTAAACGAAGGCGATGTGCGA
65 CGAATATTCATTTCAAAATTTCACTCATGTCTTTTAAAAATCCCTTAAACGAAAGCGATGTGCGA
* * * * *
12113029 TATTTGGCAATTCGCGGAATCGTACCCTAACGTGTTGAGTTGCAATTTCGCGTTTGCTCAAAATA
130 GATTTGGCAATTCGCAGAATCGTACCCTAACGTGCTGAGTTGCAATTTCGCATTTGCTCAAAACA
* * * *
12113094 ATCAAATATCCCTTCAAAATTTCACTCAGGTCTTCTAAAAATCCTTTAAAACGAAGGCAATACTC
195 ATCAAAGATCCCTTCAAAATTTCACTCAGGTCTTCTAAAAACCCTTTAAAACGAAAGAAATACTC
*
12113159 AGTG
260 AATG
** * *
12113163 TTTGACAATTCGGGAATCATGCCCTATCGTGCTGGGTTGTGATTTCTCGTTTGCTCAAAACAATC
1 TTTGACAATTCGGGAATCATGCCCTATCGTGCTGGGTTGCAATTTCCCGTTTGCTCAAAATAATC
* *** * *
12113228 GAATATTCCTTT-AGGTTTTCACTCATGT-TTATTAAAAA-CCTTTCAAAAC-AAAG-GATGTTC
66 GAATATTCATTTCAAAATTTCACTCATGTCTT-TTAAAAATCCCTT--AAACGAAAGCGATGTGC
* * * * * * ** ** * *
12113288 GAGGTTTGGCGATTTG-AGAATCGTGCCCTATCGTGCTGGGTTGCGCTTTTTCATTTGTTCTAAA
128 GAGATTTGGCAATTCGCAGAATCGTACCCTAACGTGCTGAGTTGCAATTTCGCATTTGCTCAAAA
* * ** * * *
12113352 CGATCGAAGATCCCTTCGGAATTTCACTCATGTTTTCTAAAAACCCTTTAAAACGAAAGAAATAT
193 CAATCAAAGATCCCTTCAAAATTTCACTCAGGTCTTCTAAAAACCCTTTAAAACGAAAGAAATAC
12113417 TCAATG
258 TCAATG
* *
12113423 TTTGACAATTCGGGGAAT-AGTACCCTATCGTGCTGGGTTGCAATTTCCCGTTTGTTCAAAATAA
1 TTTGACAATTC-GGGAATCA-TGCCCTATCGTGCTGGGTTGCAATTTCCCGTTTGCTCAAAATAA
12113487 TCGAATAT
64 TCGAATAT
12113495 CTCTTCGGAG
Statistics
Matches: 278, Mismatches: 48, Indels: 14
0.82 0.14 0.04
Matches are distributed among these distances:
260 106 0.38
261 76 0.27
262 75 0.27
263 21 0.08
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (263 bp):
TTTGACAATTCGGGAATCATGCCCTATCGTGCTGGGTTGCAATTTCCCGTTTGCTCAAAATAATC
GAATATTCATTTCAAAATTTCACTCATGTCTTTTAAAAATCCCTTAAACGAAAGCGATGTGCGAG
ATTTGGCAATTCGCAGAATCGTACCCTAACGTGCTGAGTTGCAATTTCGCATTTGCTCAAAACAA
TCAAAGATCCCTTCAAAATTTCACTCAGGTCTTCTAAAAACCCTTTAAAACGAAAGAAATACTCA
ATG
Found at i:12126049 original size:72 final size:74
Alignment explanation
Indices: 12125956--12126098 Score: 177
Period size: 73 Copynumber: 2.0 Consensus size: 74
12125946 TATTTAAGTT
* * ** * *
12125956 TTTTTTACTAAATTATTATTTAAATGTTA-TTTTGTGTTAATTTA-CTAAATTAAAT-TAAAAAT
1 TTTTTTACCAAATTAATATTTAAATACTATTTTTATATTAATTTATC-AAATT-AATCTAAAAAT
12126018 ATTATCAAATA
64 ATTATCAAATA
*
12126029 TTTTTTACCAAA-TAATATTTAGATACTATTTTTATATTAATTTATCAAATTAATCTAAAAATAT
1 TTTTTTACCAAATTAATATTTAAATACTATTTTTATATTAATTTATCAAATTAATCTAAAAATAT
12126093 TATCAA
66 TATCAA
12126099 TTTTGATATA
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
72 15 0.25
73 44 0.73
74 1 0.02
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.49
Consensus pattern (74 bp):
TTTTTTACCAAATTAATATTTAAATACTATTTTTATATTAATTTATCAAATTAATCTAAAAATAT
TATCAAATA
Found at i:12127903 original size:10 final size:10
Alignment explanation
Indices: 12127887--12127954 Score: 52
Period size: 10 Copynumber: 6.7 Consensus size: 10
12127877 TTTTTTAATA
12127887 AAATTTTTAT
1 AAATTTTTAT
*
12127897 TAATTTTTAT
1 AAATTTTTAT
12127907 AAATTTTGTTTAT
1 AAA--TT-TTTAT
*
12127920 AAATTTCT-T
1 AAATTTTTAT
12127929 -AATTTTTAT
1 AAATTTTTAT
*
12127938 AATAATTTT-T
1 AA-ATTTTTAT
12127948 AAATTTT
1 AAATTTT
12127955 AAAAGGGCTT
Statistics
Matches: 46, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
8 6 0.13
9 6 0.13
10 17 0.37
11 7 0.15
12 2 0.04
13 8 0.17
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (10 bp):
AAATTTTTAT
Found at i:12127952 original size:20 final size:19
Alignment explanation
Indices: 12127887--12127954 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 19
12127877 TTTTTTAATA
12127887 AAATTTTTAT-TAATTTTTAT
1 AAATTTTTATATAA-TTTT-T
*
12127907 AAATTTTGTTTATAAATTTCTT
1 AAATTTT-TATAT-AATTT-TT
12127929 -AATTTTTATAATAATTTTT
1 AAATTTTTAT-ATAATTTTT
12127948 AAATTTT
1 AAATTTT
12127955 AAAAGGGCTT
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
19 2 0.05
20 20 0.50
21 10 0.25
22 5 0.12
23 3 0.08
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (19 bp):
AAATTTTTATATAATTTTT
Found at i:12129442 original size:14 final size:15
Alignment explanation
Indices: 12129423--12129453 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
12129413 AATATCGCGA
12129423 TTTTTAATA-AATAT
1 TTTTTAATATAATAT
12129437 TTTTTAATATAATAT
1 TTTTTAATATAATAT
12129452 TT
1 TT
12129454 AAAATTATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTTTAATATAATAT
Found at i:12142227 original size:43 final size:43
Alignment explanation
Indices: 12142178--12142329 Score: 241
Period size: 43 Copynumber: 3.5 Consensus size: 43
12142168 GCATTACGCC
12142178 TGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAAGCT
1 TGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAAGCT
* * * * *
12142221 TGCTAGGCACGAAAGCCCAAATACACATCATTGGCACGATGCC
1 TGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAAGCT
* *
12142264 TGCTAGGCACGAAGGCCCGAATACACATCACCAGCACGAAGCT
1 TGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAAGCT
12142307 TGCTAGGCACGAAGGCCCGAATA
1 TGCTAGGCACGAAGGCCCGAATA
12142330 TAATACCAGC
Statistics
Matches: 97, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 97 1.00
ACGTcount: A:0.32, C:0.30, G:0.24, T:0.14
Consensus pattern (43 bp):
TGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAAGCT
Found at i:12142372 original size:38 final size:38
Alignment explanation
Indices: 12142322--12142429 Score: 153
Period size: 38 Copynumber: 2.8 Consensus size: 38
12142312 GGCACGAAGG
* * * *
12142322 CCCGAATATAATACCAGCACTAGGCCTGCGGGATTTAT
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
12142360 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
** *
12142398 CCCGGATATTTTACCAGCACGAAGCCTACGGG
1 CCCGGATATAATACCAGCACGAAGCCTGCGGG
12142430 TCTTTAAGCT
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 63 1.00
ACGTcount: A:0.29, C:0.28, G:0.23, T:0.20
Consensus pattern (38 bp):
CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
Found at i:12145310 original size:30 final size:30
Alignment explanation
Indices: 12145276--12145338 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
12145266 ACTTAACAAG
12145276 CAAATG-CTTCCAAAATAATAAAAAAATTAA
1 CAAATGCCTT-CAAAATAATAAAAAAATTAA
* *
12145306 CAAATGCCTTTAAAATAATAAGAAAATTAA
1 CAAATGCCTTCAAAATAATAAAAAAATTAA
12145336 CAA
1 CAA
12145339 TAAAATAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 27 0.90
31 3 0.10
ACGTcount: A:0.59, C:0.13, G:0.05, T:0.24
Consensus pattern (30 bp):
CAAATGCCTTCAAAATAATAAAAAAATTAA
Found at i:12145821 original size:26 final size:27
Alignment explanation
Indices: 12145790--12145875 Score: 88
Period size: 26 Copynumber: 3.3 Consensus size: 27
12145780 GTTAAGAATG
*
12145790 TTATTAAATTTTATTTAATAGTAATTA
1 TTATTAAATTATATTTAATAGTAATTA
* * * *
12145817 -TATTAAAATATAATTAA-ATTATTTA
1 TTATTAAATTATATTTAATAGTAATTA
* *
12145842 TTATTAAATTATATTTAATAAT-ATTC
1 TTATTAAATTATATTTAATAGTAATTA
12145868 TTATTAAA
1 TTATTAAA
12145876 ATTTAGTAAC
Statistics
Matches: 47, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
25 6 0.13
26 39 0.83
27 2 0.04
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (27 bp):
TTATTAAATTATATTTAATAGTAATTA
Found at i:12146768 original size:30 final size:31
Alignment explanation
Indices: 12146732--12146800 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
12146722 TAAAAATATA
*
12146732 ATTTTTAAAG-GATTAAATTAAAATTTTATT
1 ATTTTTAAAGAGATTAAAGTAAAATTTTATT
*
12146762 ATTTTTAAAGAGATTAAAGTATAATTTTATT
1 ATTTTTAAAGAGATTAAAGTAAAATTTTATT
12146793 -TTTATTAA
1 ATTT-TTAA
12146801 TTTAAAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
30 13 0.37
31 22 0.63
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (31 bp):
ATTTTTAAAGAGATTAAAGTAAAATTTTATT
Found at i:12147569 original size:17 final size:18
Alignment explanation
Indices: 12147549--12147596 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
12147539 TTGATCTGTC
12147549 AAATTAAAAATATGCT-T
1 AAATTAAAAATATGCTAT
12147566 AAA-TATAAAATATGCTAT
1 AAATTA-AAAATATGCTAT
*
12147584 GAATTAAATAATA
1 AAATTAAA-AATA
12147597 AAATAATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 2 0.08
17 13 0.50
18 5 0.19
19 6 0.23
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.33
Consensus pattern (18 bp):
AAATTAAAAATATGCTAT
Found at i:12175929 original size:54 final size:54
Alignment explanation
Indices: 12175858--12175966 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
12175848 AGGAAAAAAG
12175858 AAAAGATCAAGCCCGGATAAACCTTAATTGATTAAAAAAAGTAAGGAATCAATC
1 AAAAGATCAAGCCCGGATAAACCTTAATTGATTAAAAAAAGTAAGGAATCAATC
12175912 AAAAGATCAAGCCCGGATAAACCTTAATTGATTAAAAAAAGTAAGGAATCAATC
1 AAAAGATCAAGCCCGGATAAACCTTAATTGATTAAAAAAAGTAAGGAATCAATC
12175966 A
1 A
12175967 CTCAAGATCG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.20
Consensus pattern (54 bp):
AAAAGATCAAGCCCGGATAAACCTTAATTGATTAAAAAAAGTAAGGAATCAATC
Found at i:12179944 original size:30 final size:31
Alignment explanation
Indices: 12179908--12179968 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 31
12179898 GTGGAGGTGC
12179908 CAACTTGAGA-AAAA-AAATAGTTTAGGTACA
1 CAACTTGAGACAAAAGAAA-AGTTTAGGTACA
*
12179938 CAACTTGTGACCAAAAGAAAAGTTTAGGTAC
1 CAACTTGAGA-CAAAAGAAAAGTTTAGGTAC
12179969 CAATACGGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 9 0.33
32 15 0.56
33 3 0.11
ACGTcount: A:0.46, C:0.13, G:0.18, T:0.23
Consensus pattern (31 bp):
CAACTTGAGACAAAAGAAAAGTTTAGGTACA
Found at i:12184236 original size:232 final size:235
Alignment explanation
Indices: 12183786--12184268 Score: 830
Period size: 232 Copynumber: 2.1 Consensus size: 235
12183776 CCATATCAAT
* *
12183786 AATAC-AAAAGTTCATCTATGAAAATTAGCTAGAGTACAGTAACAGATAAAAACTAATTACATAA
1 AATACTAAAACTTAATCTATGAAAATTAGCTAGAGTACAGTAACAGATAAAAACTAATTACATAA
*
12183850 AAATCAGTCTAAAAGAAGAGAGAAAAAGAAAAAGGAGTAAAACACACCAGTCAAAATTCTACTTT
66 AAATCAGTCTAAAAGAAGAGAGAAAAAGAAAAAGGAGTAAAACACACAAGTCAAAATTCTACTTT
12183915 TCACTAAATATTTTTTTTCTTAAAAATGGGGAAAGGGGAGGACTTCCAGCGATGTGCAGAAAATC
131 TCACTAAATATTTTTTTTCTTAAAAATGGGGAAAGGGGAGGACTTCCAGCGATGTGCAGAAAATC
*
12183980 TTCAGATGTTGCTACTGCCGACAAGTTCTTACAATATGTA
196 TTCACATGTTGCTACTGCCGACAAGTTCTTACAATATGTA
* * **
12184020 AATACTAAAATTTAATCTATGAGAATTAGCTAGAGTACAGTATTAGATAAAAACTAATTACATAA
1 AATACTAAAACTTAATCTATGAAAATTAGCTAGAGTACAGTAACAGATAAAAACTAATTACATAA
12184085 AAATCAGTCTAAAAG-A-AGAGAAAAAGAAAAAGGAGTAAAACACACAAGTCAAAATTCTACTTT
66 AAATCAGTCTAAAAGAAGAGAGAAAAAGAAAAAGGAGTAAAACACACAAGTCAAAATTCTACTTT
* * *
12184148 TCACTAAATA-TTTTTTTCTTAAATATGGGGGAAGGGGAGGACTTCCAGCGATGTGTAGAAAATC
131 TCACTAAATATTTTTTTTCTTAAAAATGGGGAAAGGGGAGGACTTCCAGCGATGTGCAGAAAATC
*
12184212 TTCACATGTTGCTACTGCCGACAAGTTCTTCCAATATGTA
196 TTCACATGTTGCTACTGCCGACAAGTTCTTACAATATGTA
12184252 AATACTAAAACTTAATC
1 AATACTAAAACTTAATC
12184269 GTGAAGTATA
Statistics
Matches: 236, Mismatches: 12, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
232 105 0.44
233 56 0.24
234 6 0.03
235 69 0.29
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (235 bp):
AATACTAAAACTTAATCTATGAAAATTAGCTAGAGTACAGTAACAGATAAAAACTAATTACATAA
AAATCAGTCTAAAAGAAGAGAGAAAAAGAAAAAGGAGTAAAACACACAAGTCAAAATTCTACTTT
TCACTAAATATTTTTTTTCTTAAAAATGGGGAAAGGGGAGGACTTCCAGCGATGTGCAGAAAATC
TTCACATGTTGCTACTGCCGACAAGTTCTTACAATATGTA
Found at i:12186786 original size:15 final size:15
Alignment explanation
Indices: 12186766--12186796 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
12186756 AGGTCTCTCG
12186766 CTTCTCTATATGTTT
1 CTTCTCTATATGTTT
12186781 CTTCTCTATATGTTT
1 CTTCTCTATATGTTT
12186796 C
1 C
12186797 AAATTGTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.23, G:0.06, T:0.58
Consensus pattern (15 bp):
CTTCTCTATATGTTT
Found at i:12188092 original size:68 final size:70
Alignment explanation
Indices: 12188001--12188130 Score: 171
Period size: 68 Copynumber: 1.9 Consensus size: 70
12187991 TAAAAATATT
* *
12188001 AAATTTTATATAAACTTAAAAAAA-ATATGTATAAAAT-CAT-AACAATTTATAAATATTATAAA
1 AAATTTTATATAAACTTAAAAAAATA-AT-AAAAAAATCCATCAA-AATTTATAAATATTATAAA
12188063 CCCTATAA
63 CCCTATAA
*
12188071 AAATTTTA-ATAAA-TTACAAAAATAATAAAAAAATCCATCAAAATTTATAAATATTATAAA
1 AAATTTTATATAAACTTAAAAAAATAATAAAAAAATCCATCAAAATTTATAAATATTATAAA
12188131 AACTTATAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
67 6 0.11
68 32 0.59
69 8 0.15
70 8 0.15
ACGTcount: A:0.58, C:0.08, G:0.01, T:0.33
Consensus pattern (70 bp):
AAATTTTATATAAACTTAAAAAAATAATAAAAAAATCCATCAAAATTTATAAATATTATAAACCC
TATAA
Found at i:12188150 original size:19 final size:19
Alignment explanation
Indices: 12188110--12188150 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
12188100 AAAATCCATC
* * *
12188110 AAAATTTATAAATATTATA
1 AAAACTTATAAATATAAAA
12188129 AAAACTTATAAATATAAAA
1 AAAACTTATAAATATAAAA
12188148 AAA
1 AAA
12188151 TCATACTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAACTTATAAATATAAAA
Found at i:12203002 original size:21 final size:21
Alignment explanation
Indices: 12202961--12203002 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
12202951 CTTCCTCCAT
*
12202961 CTCCTCTTCATCAATTTCTTC
1 CTCCTCTTCATCAATTACTTC
12202982 CTCCTCTTCATC-ATATACTTC
1 CTCCTCTTCATCAAT-TACTTC
12203003 TTCTTCTACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.17, C:0.38, G:0.00, T:0.45
Consensus pattern (21 bp):
CTCCTCTTCATCAATTACTTC
Found at i:12204380 original size:322 final size:321
Alignment explanation
Indices: 12203787--12204388 Score: 961
Period size: 322 Copynumber: 1.9 Consensus size: 321
12203777 AAATATTAAT
* * **
12203787 TAATTTTTAATCTCAACGTTTATGTAGCAAACATTAAATTACGAAATGTGAACAGTTTAATAAAA
1 TAATTCTTAATCTCAACGTTTATGTAGCAAACATTAAATTACGAAATGTAAACAACTTAATAAAA
* * *
12203852 AATATTAAAATAAACGTCAATAGAAAATTTTATTAAATAAAAGGTTGAATAACACCTTATTAATT
66 AATATTAAAATAAACGACAATAAAAAATTTTATTAAATAAAAAGTTGAATAACACCTTATTAATT
* * * *
12203917 TTATTATATATCAAAGGTACACACGAAATGTAAAACAAAATTTCGAGTTAAGGTTATTGCACTTT
131 CTATCATATATCAAAGGGACACACGAAATATAAAACAAAATTTCGAGTTAAGGTTATTGCACTTT
* * *
12203982 GTGATAGCAGAAGAATGCAAGTAGTTTTCAAGAAATAATATGAAAACTTGGAAAAGGAAAACAGT
196 GTGATAGCAGAAGAATGCAAGTAGTTTTCAAGAAATAATATGAAAAATTAGAAAAGAAAAACAGT
* *
12204047 TGATGGATATAAGAAGAAATTTGATTAAACGAGGAAGTTTTTACTAACCGAAATTAAGGTTC
261 TAATAGATATAAGAA-AAATTTGATTAAACGAGGAAGTTTTTACTAACCGAAATTAAGGTTC
* *
12204109 TAATTCTTAATCTCAACGTTTATGTAGTAAACATTAAATTGCGAAATGTAAACAACTTAATAAAA
1 TAATTCTTAATCTCAACGTTTATGTAGCAAACATTAAATTACGAAATGTAAACAACTTAATAAAA
*
12204174 AATATTGAAATAAACGACAATAAAAAATTTTATTAAATAAAAAGTTGAATAACACCTTATTAATT
66 AATATTAAAATAAACGACAATAAAAAATTTTATTAAATAAAAAGTTGAATAACACCTTATTAATT
* * *
12204239 CTATCATATATCAAAGGGACACACGAAATATAGAATAAAATTTCGAGTTAAGGTTATTGTACTTT
131 CTATCATATATCAAAGGGACACACGAAATATAAAACAAAATTTCGAGTTAAGGTTATTGCACTTT
** * *
12204304 GTGATAGCAGGGGAATTCAAGTAGTTTTCAAGAAATAATATGAAAAATTAGAAAATAAAAACAGT
196 GTGATAGCAGAAGAATGCAAGTAGTTTTCAAGAAATAATATGAAAAATTAGAAAAGAAAAACAGT
12204369 TAATAGATATAAGAAAAATT
261 TAATAGATATAAGAAAAATT
12204389 ATAAATGAGA
Statistics
Matches: 254, Mismatches: 26, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
321 5 0.02
322 249 0.98
ACGTcount: A:0.46, C:0.09, G:0.14, T:0.31
Consensus pattern (321 bp):
TAATTCTTAATCTCAACGTTTATGTAGCAAACATTAAATTACGAAATGTAAACAACTTAATAAAA
AATATTAAAATAAACGACAATAAAAAATTTTATTAAATAAAAAGTTGAATAACACCTTATTAATT
CTATCATATATCAAAGGGACACACGAAATATAAAACAAAATTTCGAGTTAAGGTTATTGCACTTT
GTGATAGCAGAAGAATGCAAGTAGTTTTCAAGAAATAATATGAAAAATTAGAAAAGAAAAACAGT
TAATAGATATAAGAAAAATTTGATTAAACGAGGAAGTTTTTACTAACCGAAATTAAGGTTC
Found at i:12225343 original size:23 final size:21
Alignment explanation
Indices: 12225314--12225396 Score: 85
Period size: 21 Copynumber: 3.9 Consensus size: 21
12225304 TGATCAGTAT
*
12225314 ACGACACATAAAGTGCCTGAA
1 ACGACACACAAAGTGCCTGAA
* * *
12225335 ACGACACACGAGGTGCCTGAT
1 ACGACACACAAAGTGCCTGAA
* *
12225356 ACGACACACGAGGTGCCTGAAA
1 ACGACACACAAAGTGCCTG-AA
*
12225378 TACGACACATAAAGTGCCT
1 -ACGACACACAAAGTGCCT
12225397 AATCAGTAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
21 36 0.69
22 1 0.02
23 15 0.29
ACGTcount: A:0.36, C:0.27, G:0.23, T:0.14
Consensus pattern (21 bp):
ACGACACACAAAGTGCCTGAA
Found at i:12226379 original size:13 final size:14
Alignment explanation
Indices: 12226363--12226398 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
12226353 CAATCTCATA
12226363 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
12226376 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
12226389 TCTC-ATTTCA
1 TCTCAATTTCA
12226399 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:12226388 original size:18 final size:19
Alignment explanation
Indices: 12226350--12226390 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
12226340 TGGTTCATGT
12226350 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
12226369 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
12226387 TTTC
1 TTTC
12226391 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:12226580 original size:39 final size:38
Alignment explanation
Indices: 12226513--12226647 Score: 94
Period size: 39 Copynumber: 3.4 Consensus size: 38
12226503 ACCAATATGG
* * * *
12226513 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATATTTGA
1 CACCCAGTGTCTCATCGGCTAG-CCGAAGAAATATTTGA
* * *
12226552 CACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGTCTCATCGG-CTAGCCGAAGAAATATTTGA
* * * * *
12226590 TACCCAGT-ACTTCATCGAATCTATCCGAAGAAATATAGTGA
1 CACCCAGTGTC-TCATCG--GCTAGCCGAAGAAATAT-TTGA
12226631 CACCCAGTGTCTCATCG
1 CACCCAGTGTCTCATCG
12226648 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 16, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
37 1 0.01
38 17 0.23
39 35 0.48
40 4 0.05
41 15 0.21
42 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.24
Consensus pattern (38 bp):
CACCCAGTGTCTCATCGGCTAGCCGAAGAAATATTTGA
Found at i:12226913 original size:18 final size:19
Alignment explanation
Indices: 12226887--12226925 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
12226877 TTTCAATTCA
12226887 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
12226906 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
12226924 AT
1 AT
12226926 ATCTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:12228256 original size:5 final size:5
Alignment explanation
Indices: 12228246--12228302 Score: 53
Period size: 5 Copynumber: 11.0 Consensus size: 5
12228236 TTACTTATTT
* * *
12228246 ATATA ATATAA TATATA ATATA ATATA GTATA ATGTA ATAATA ATTTA
1 ATATA ATAT-A -ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA
12228294 ATAT- ATATA
1 ATATA ATATA
12228303 TTTTAACACA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
4 4 0.10
5 28 0.67
6 6 0.14
7 4 0.10
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:12228262 original size:12 final size:12
Alignment explanation
Indices: 12228245--12228300 Score: 60
Period size: 12 Copynumber: 4.5 Consensus size: 12
12228235 TTTACTTATT
12228245 TATATAATATAA
1 TATATAATATAA
12228257 TATATAATATAATA
1 TATATAATAT-A-A
*
12228271 TAGTATAATGTAA
1 TA-TATAATATAA
*
12228284 TA-ATAATTTAA
1 TATATAATATAA
12228295 TATATA
1 TATATA
12228301 TATTTTAACA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
11 10 0.26
12 13 0.34
13 4 0.11
14 4 0.11
15 7 0.18
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (12 bp):
TATATAATATAA
Found at i:12233063 original size:18 final size:18
Alignment explanation
Indices: 12233037--12233071 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12233027 GGTATTTTTT
*
12233037 TATTATATATTTTATATC
1 TATTATATAGTTTATATC
*
12233055 TATTTTATAGTTTATAT
1 TATTATATAGTTTATAT
12233072 TCGAATTTTG
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:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (18 bp):
TATTATATAGTTTATATC
Found at i:12240476 original size:36 final size:36
Alignment explanation
Indices: 12240429--12240500 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
12240419 AAAGAGATGA
12240429 AATATTGACAAAAAGTAATGCAAATGGCTTCAACTT
1 AATATTGACAAAAAGTAATGCAAATGGCTTCAACTT
12240465 AATATTGACAAAAAGTAATGCAAATGGCTTCAACTT
1 AATATTGACAAAAAGTAATGCAAATGGCTTCAACTT
12240501 TGATATGAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (36 bp):
AATATTGACAAAAAGTAATGCAAATGGCTTCAACTT
Found at i:12242746 original size:15 final size:15
Alignment explanation
Indices: 12242728--12242771 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
12242718 TTAGAATAAT
*
12242728 CATATTTCAAAAACA
1 CATATTTAAAAAACA
12242743 CATATTTAAAATAACA
1 CATATTTAAAA-AACA
12242759 -AT-TTTAAAAAACA
1 CATATTTAAAAAACA
12242772 ACCATTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 4 0.15
14 7 0.26
15 12 0.44
16 4 0.15
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.30
Consensus pattern (15 bp):
CATATTTAAAAAACA
Found at i:12243489 original size:24 final size:24
Alignment explanation
Indices: 12243462--12243513 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
12243452 TTAGTAAGTC
*
12243462 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
12243486 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
12243510 AAAT
1 AAAT
12243514 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:12245458 original size:24 final size:24
Alignment explanation
Indices: 12245431--12245482 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
12245421 TTAGTAAGTC
*
12245431 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
12245455 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
12245479 AAAT
1 AAAT
12245483 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:12247437 original size:30 final size:29
Alignment explanation
Indices: 12247403--12247460 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
12247393 TTTACAATTA
*
12247403 ATAAAATTACACTTTAATCTTTTAAAAATG
1 ATAAAATTACAATTTAAT-TTTTAAAAATG
**
12247433 ATAAAATTTTAATTTAATTTTTAAAAAT
1 ATAAAATTACAATTTAATTTTTAAAAAT
12247461 TATAGACATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (29 bp):
ATAAAATTACAATTTAATTTTTAAAAATG
Found at i:12248819 original size:40 final size:40
Alignment explanation
Indices: 12248775--12248854 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
12248765 AGTACATCAA
12248775 ATATTCTTCATAATGTGCTCTTAAATAAAGAGGTTAGATG
1 ATATTCTTCATAATGTGCTCTTAAATAAAGAGGTTAGATG
12248815 ATATTCTTCATAATGTGCTCTTAAATAAAGAGGTTAGATG
1 ATATTCTTCATAATGTGCTCTTAAATAAAGAGGTTAGATG
12248855 CTTCGCATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (40 bp):
ATATTCTTCATAATGTGCTCTTAAATAAAGAGGTTAGATG
Found at i:12256792 original size:96 final size:96
Alignment explanation
Indices: 12256624--12256817 Score: 275
Period size: 96 Copynumber: 2.0 Consensus size: 96
12256614 TCGCTTCTTT
*
12256624 TTGCTCCTTTTAGCCCTCTTGGCTTCGGCTTTACCCTTGCTCGAACCAAGCTTCTTGGGCTCCTT
1 TTGCTCCTTTTAGCCCTCTTGGCTTCGGCTTTACCCTTGCTCGAACCAAGCTTCCTGGGCTCCTT
* * * *
12256689 GTCTGCTCCATCGTTCCCTTCGATGACAGAC
66 ATCTGCTCCATCATTCCCATCGATAACAGAC
* *
12256720 TTGCTCCTCTTT-GCCCTCTTGGCTTCGGCTTTTCTCTTGCTCGAACCAAGCTTCCTGGGCT-CT
1 TTGCTCCT-TTTAGCCCTCTTGGCTTCGGCTTTACCCTTGCTCGAACCAAGCTTCCTGGGCTCCT
* *
12256783 GTATTTGCTCGATCATTCCCATCGATAACAGAC
65 -TATCTGCTCCATCATTCCCATCGATAACAGAC
12256816 TT
1 TT
12256818 CCTCGGACAC
Statistics
Matches: 87, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
95 2 0.02
96 82 0.94
97 3 0.03
ACGTcount: A:0.12, C:0.33, G:0.18, T:0.37
Consensus pattern (96 bp):
TTGCTCCTTTTAGCCCTCTTGGCTTCGGCTTTACCCTTGCTCGAACCAAGCTTCCTGGGCTCCTT
ATCTGCTCCATCATTCCCATCGATAACAGAC
Found at i:12264970 original size:46 final size:44
Alignment explanation
Indices: 12264911--12265025 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
12264901 ACAGGACAGA
* *
12264911 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
12264957 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
12265001 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
12265026 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:12265006 original size:44 final size:45
Alignment explanation
Indices: 12264911--12265044 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
12264901 ACAGGACAGA
* *
12264911 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
12264957 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
12265001 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
12265045 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:12280183 original size:27 final size:27
Alignment explanation
Indices: 12280136--12280201 Score: 64
Period size: 27 Copynumber: 2.4 Consensus size: 27
12280126 TCAATTTAAT
*
12280136 TTTTTTCTTTTATGTTATTTTAACTT-TC
1 TTTTTT-TTTTCTGTTATTTTAA-TTCTC
*
12280164 TTTTTTTTTTCT-TTATTTTTCATTCTC
1 TTTTTTTTTTCTGTTA-TTTTAATTCTC
*
12280191 TTTTGTTTTTC
1 TTTTTTTTTTC
12280202 CCTTTGTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
26 5 0.15
27 22 0.67
28 6 0.18
ACGTcount: A:0.09, C:0.12, G:0.03, T:0.76
Consensus pattern (27 bp):
TTTTTTTTTTCTGTTATTTTAATTCTC
Found at i:12282277 original size:30 final size:30
Alignment explanation
Indices: 12282243--12282305 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
12282233 ACTTATTTTA
*
12282243 TTGTTCATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
*
12282273 TTGTTAATTTTGTTATTATTTTAGAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
12282303 TTG
1 TTG
12282306 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.05, G:0.13, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:12282406 original size:17 final size:19
Alignment explanation
Indices: 12282379--12282425 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 19
12282369 TTGTTAGGAA
*
12282379 ATATTTATTTTGATGT-TT
1 ATATATATTTTGATGTATT
* *
12282397 TTA-ATATTTTTATGTATT
1 ATATATATTTTGATGTATT
12282415 ATATATATTTT
1 ATATATATTTT
12282426 AAAATTATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 10 0.43
18 6 0.26
19 7 0.30
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (19 bp):
ATATATATTTTGATGTATT
Done.