Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr8
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: 70076365
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3341059 characters in sequence are not A, C, G, or T
File 33 of 210
Found at i:11666352 original size:241 final size:242
Alignment explanation
Indices: 11665911--11666400 Score: 964
Period size: 241 Copynumber: 2.0 Consensus size: 242
11665901 ATGTATACTT
11665911 AAATAACATTAAGATAGATGCAATTTAACAAACAAATACCTGTAAAATAATAACAAAATTAACAA
1 AAAT-ACATTAAGATAGATGCAATTTAACAAACAAATACCTGTAAAATAATAACAAAATTAACAA
11665976 TCAAATTAAACAAGTGTCCTACAATATCTAAACAATAACAACAAAATAATAGTAACGTAATATTA
65 TCAAATTAAACAAGTGTCCTACAATATCTAAACAATAACAACAAAATAATAGTAACGTAATATTA
11666041 AAATGGTAGTAAAACAGGGAGAAAACAAGAAAATAATATTAAAACAACAAAAAATAGTAGATTTT
130 AAATGGTAGTAAAACAGGGAGAAAACAAGAAAATAATATTAAAACAACAAAAAATAGTAGATTTT
11666106 TTTTTTGTTTTTTTTTTGTGAATTTGGGTTGAGCCGAGCCAGAACAAA
195 TTTTTTGTTTTTTTTTTGTGAATTTGGGTTGAGCCGAGCCAGAACAAA
11666154 AAATACATTAAGATAG-TGCAATTTAACAAACAAATACCTGTAAAATAATAACAAAATTAACAAT
1 AAATACATTAAGATAGATGCAATTTAACAAACAAATACCTGTAAAATAATAACAAAATTAACAAT
11666218 CAAATTAAACAAGTGTCCTACAATATCTAAACAATAACAACAAAATAATAGTAACGTAATATTAA
66 CAAATTAAACAAGTGTCCTACAATATCTAAACAATAACAACAAAATAATAGTAACGTAATATTAA
11666283 AATGGTAGTAAAACAGGGAGAAAACAAGAAAATAATATTAAAACAACAAAAAATAGTAGATTTTT
131 AATGGTAGTAAAACAGGGAGAAAACAAGAAAATAATATTAAAACAACAAAAAATAGTAGATTTTT
11666348 TTTTTGTTTTTTTTTTGTGAATTTGGGTTGAGCCGAGCCAGAACAAA
196 TTTTTGTTTTTTTTTTGTGAATTTGGGTTGAGCCGAGCCAGAACAAA
11666395 AAATAC
1 AAATAC
11666401 CTTACTCGAG
Statistics
Matches: 247, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
241 231 0.94
242 12 0.05
243 4 0.02
ACGTcount: A:0.49, C:0.11, G:0.12, T:0.28
Consensus pattern (242 bp):
AAATACATTAAGATAGATGCAATTTAACAAACAAATACCTGTAAAATAATAACAAAATTAACAAT
CAAATTAAACAAGTGTCCTACAATATCTAAACAATAACAACAAAATAATAGTAACGTAATATTAA
AATGGTAGTAAAACAGGGAGAAAACAAGAAAATAATATTAAAACAACAAAAAATAGTAGATTTTT
TTTTTGTTTTTTTTTTGTGAATTTGGGTTGAGCCGAGCCAGAACAAA
Found at i:11675767 original size:27 final size:26
Alignment explanation
Indices: 11675715--11675768 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
11675705 CTATGACACC
* *
11675715 ATCAAATAAAAAAATATTTTTTAAAA
1 ATCAAATAAAAAAATATATTTAAAAA
11675741 ATCAAGATAAATAAAA-ATATTTAAAAA
1 ATCAA-ATAAA-AAAATATATTTAAAAA
11675768 A
1 A
11675769 ATCTAACATC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 5 0.21
27 15 0.62
28 4 0.17
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.30
Consensus pattern (26 bp):
ATCAAATAAAAAAATATATTTAAAAA
Found at i:11675784 original size:28 final size:28
Alignment explanation
Indices: 11675715--11675784 Score: 65
Period size: 28 Copynumber: 2.5 Consensus size: 28
11675705 CTATGACACC
**
11675715 ATCAA-AT-AAAAAAATATTTTTTAAAA
1 ATCAACATAAAAAAAATATTTTAAAAAA
*
11675741 ATCAAGATAAATAAAAATA-TTTAAAAAA
1 ATCAACATAAA-AAAAATATTTTAAAAAA
*
11675769 ATCTAACATCAAAAAA
1 ATC-AACATAAAAAAA
11675785 CAAAAGTGGC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
26 5 0.14
27 2 0.06
28 16 0.44
29 13 0.36
ACGTcount: A:0.64, C:0.07, G:0.01, T:0.27
Consensus pattern (28 bp):
ATCAACATAAAAAAAATATTTTAAAAAA
Found at i:11676114 original size:5 final size:5
Alignment explanation
Indices: 11676104--11676128 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
11676094 TAATCTATCT
11676104 AACCC AACCC AACCC AACCC AACCC
1 AACCC AACCC AACCC AACCC AACCC
11676129 CAACATTGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.60, G:0.00, T:0.00
Consensus pattern (5 bp):
AACCC
Found at i:11683933 original size:16 final size:16
Alignment explanation
Indices: 11683891--11683933 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
11683881 ATTAAACTAA
*
11683891 AAATTAACATAAATATC
1 AAATTAA-AAAAATATC
*
11683908 ATATTAAAAAAATATC
1 AAATTAAAAAAATATC
11683924 AAATTTAAAA
1 AAA-TTAAAA
11683934 TTGAAATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATTAAAAAAATATC
Found at i:11684211 original size:14 final size:16
Alignment explanation
Indices: 11684192--11684227 Score: 58
Period size: 14 Copynumber: 2.4 Consensus size: 16
11684182 AATATTGAGG
11684192 TTAAAATTT-AGAA-T
1 TTAAAATTTAAGAATT
11684206 TTAAAATTTAAGAATT
1 TTAAAATTTAAGAATT
11684222 TTAAAA
1 TTAAAA
11684228 AAATTATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 9 0.45
15 4 0.20
16 7 0.35
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.42
Consensus pattern (16 bp):
TTAAAATTTAAGAATT
Found at i:11686176 original size:9 final size:9
Alignment explanation
Indices: 11686162--11686198 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
11686152 NNNNNNNNNN
11686162 TATTCGAAT
1 TATTCGAAT
11686171 TATTCGAAT
1 TATTCGAAT
*
11686180 TATTCGAGT
1 TATTCGAAT
11686189 TATTCGAAT
1 TATTCGAAT
11686198 T
1 T
11686199 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:11689692 original size:108 final size:108
Alignment explanation
Indices: 11689503--11689714 Score: 415
Period size: 108 Copynumber: 2.0 Consensus size: 108
11689493 AGTCCCAATG
11689503 AGGATGGCTTCTCCGCTTCTTTGCGCGGAGGAGGAGGGAGGAGGAAATGGGTTTCAATGGGCAGA
1 AGGATGGCTTCTCCGCTTCTTTGCGCGGAGGAGGAGGGAGGAGGAAATGGGTTTCAATGGGCAGA
11689568 TGGATAGGCCTATTCATCACCTTCGGAAACTGAGATGCAGATA
66 TGGATAGGCCTATTCATCACCTTCGGAAACTGAGATGCAGATA
*
11689611 AGGATGGCTTCTCCGCTTCTTTGCGCGGAGGAGGAGGGAGGAGGAAATGGGTTTCAATGGGCGGA
1 AGGATGGCTTCTCCGCTTCTTTGCGCGGAGGAGGAGGGAGGAGGAAATGGGTTTCAATGGGCAGA
11689676 TGGATAGGCCTATTCATCACCTTCGGAAACTGAGATGCA
66 TGGATAGGCCTATTCATCACCTTCGGAAACTGAGATGCA
11689715 TCTCTATGGG
Statistics
Matches: 103, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
108 103 1.00
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.23
Consensus pattern (108 bp):
AGGATGGCTTCTCCGCTTCTTTGCGCGGAGGAGGAGGGAGGAGGAAATGGGTTTCAATGGGCAGA
TGGATAGGCCTATTCATCACCTTCGGAAACTGAGATGCAGATA
Found at i:11695665 original size:21 final size:21
Alignment explanation
Indices: 11695639--11695698 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
11695629 TGGGTGGATC
11695639 AGCTCTTACGAGCTTCTGTTA
1 AGCTCTTACGAGCTTCTGTTA
* * *
11695660 AGCTCTTACAAGCTTTTGTTC
1 AGCTCTTACGAGCTTCTGTTA
11695681 AGCT-TT-CGAGCTTCTGTT
1 AGCTCTTACGAGCTTCTGTT
11695699 GGCGTATTCG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
19 10 0.29
20 2 0.06
21 22 0.65
ACGTcount: A:0.17, C:0.23, G:0.18, T:0.42
Consensus pattern (21 bp):
AGCTCTTACGAGCTTCTGTTA
Found at i:11697114 original size:18 final size:18
Alignment explanation
Indices: 11697091--11697137 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 18
11697081 AATAACATAA
11697091 TTTATAATATATTTACT-T
1 TTTATAATATATTTA-TAT
*
11697109 TTTATATTTATATTTATAT
1 TTTATA-ATATATTTATAT
11697128 TTATATAATA
1 TT-TATAATA
11697138 AGTTTAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 7 0.29
19 13 0.54
20 4 0.17
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTATAATATATTTATAT
Found at i:11697120 original size:6 final size:6
Alignment explanation
Indices: 11697098--11697133 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
11697088 TAATTTATAA
*
11697098 TATATT TACTTTT TATATT TATATT TATATT TATAT
1 TATATT TA-TATT TATATT TATATT TATATT TATAT
11697134 AATAAGTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 22 0.81
7 5 0.19
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (6 bp):
TATATT
Found at i:11702875 original size:11 final size:11
Alignment explanation
Indices: 11702859--11702909 Score: 68
Period size: 11 Copynumber: 4.7 Consensus size: 11
11702849 TCAATTATTT
* *
11702859 TCTCAATTTCC
1 TCTCAAATTGC
11702870 TCTCAAATTGC
1 TCTCAAATTGC
11702881 TCTCAAATTGC
1 TCTCAAATTGC
*
11702892 TCTC-AATTTC
1 TCTCAAATTGC
11702902 TCTCAAAT
1 TCTCAAAT
11702910 CCATATTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
10 9 0.25
11 27 0.75
ACGTcount: A:0.25, C:0.29, G:0.04, T:0.41
Consensus pattern (11 bp):
TCTCAAATTGC
Found at i:11702904 original size:21 final size:22
Alignment explanation
Indices: 11702855--11702909 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 22
11702845 TTTCTCAATT
*
11702855 ATTT-TCTCAATTTCCTCTCAA
1 ATTTCTCTCAAATTCCTCTCAA
* *
11702876 ATTGCTCTCAAATTGCTCTC-A
1 ATTTCTCTCAAATTCCTCTCAA
11702897 ATTTCTCTCAAAT
1 ATTTCTCTCAAAT
11702910 CCATATTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 16 0.55
22 13 0.45
ACGTcount: A:0.25, C:0.27, G:0.04, T:0.44
Consensus pattern (22 bp):
ATTTCTCTCAAATTCCTCTCAA
Found at i:11705282 original size:49 final size:49
Alignment explanation
Indices: 11705229--11705372 Score: 270
Period size: 49 Copynumber: 2.9 Consensus size: 49
11705219 TATATTAATG
*
11705229 TAATAAAATACAAAATAGTTTAATTTGAATATTTTGATATTATTTGATA
1 TAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTGATA
*
11705278 TAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTGATG
1 TAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTGATA
11705327 TAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
1 TAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
11705373 CTCAAAAGCG
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 93 1.00
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (49 bp):
TAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTGATA
Found at i:11705639 original size:16 final size:16
Alignment explanation
Indices: 11705612--11705651 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
11705602 AATTTTTTCT
*
11705612 CCAAAACTCTAAAAAC
1 CCAAAACCCTAAAAAC
*
11705628 CCTAAACCCTAAAAAC
1 CCAAAACCCTAAAAAC
11705644 CCAAAACC
1 CCAAAACC
11705652 TAACGTGGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.53, C:0.38, G:0.00, T:0.10
Consensus pattern (16 bp):
CCAAAACCCTAAAAAC
Found at i:11711045 original size:17 final size:17
Alignment explanation
Indices: 11711002--11711046 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
11710992 TATAATTAAA
11711002 AATTAAAAATTATTTAT
1 AATTAAAAATTATTTAT
* **
11711019 TATTTTAAATTATTTAT
1 AATTAAAAATTATTTAT
11711036 AATTAAAAATT
1 AATTAAAAATT
11711047 TCTAGTAATA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
AATTAAAAATTATTTAT
Found at i:11712538 original size:24 final size:25
Alignment explanation
Indices: 11712488--11712539 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
11712478 TTTTTAGTTA
* *
11712488 ATTTTTTTTAGTTTTATATAATTTT
1 ATTTTTTTTAGTTTTATAAAATATT
11712513 ATTTTGTTTT-GTTTT-TAAAATATT
1 ATTTT-TTTTAGTTTTATAAAATATT
11712537 ATT
1 ATT
11712540 AATTAAGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 10 0.42
25 10 0.42
26 4 0.17
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (25 bp):
ATTTTTTTTAGTTTTATAAAATATT
Found at i:11713021 original size:284 final size:285
Alignment explanation
Indices: 11712510--11713078 Score: 1131
Period size: 284 Copynumber: 2.0 Consensus size: 285
11712500 TTTATATAAT
11712510 TTTATTTTGTTTTGTTTTTAAAATATTATTAATTAAGTTAAAATTTTAATATTACTAATTATTCC
1 TTTATTTTGTTTTGTTTTTAAAATATTATTAATTAAGTTAAAATTTTAATATTACTAATTATTCC
11712575 AATTAAAATGTTGATATAAAACTTTTCTTTACAACATACCTTCAAACGTTATAAAAAAGTATGTT
66 AATTAAAATGTTGATATAAAACTTTTCTTTACAACATACCTTCAAACGTTATAAAAAAGTATGTT
11712640 AGGATGATGAGTTTGAGGTTTTTTTTTTTTAAATCACAAATCTTGAACATTAGCCAAACATAAAA
131 AGGATGATGAGTTTGAGGTTTTTTTTTTTTAAATCACAAATCTTGAACATTAGCCAAACATAAAA
11712705 GATAAAAAAAAAAAAGAACTAGTTAGATAAACTAATAGCATTATAAAAGTAAAAGATAAAATTAT
196 GATAAAAAAAAAAAAGAACTAGTTAGATAAACTAATAGCATTATAAAAGTAAAAGATAAAATTAT
11712770 CTCAAATTAAAGTATTAAAGTATAC
261 CTCAAATTAAAGTATTAAAGTATAC
11712795 TTTATTTTG-TTTGTTTTTAAAATATTATTAATTAAGTTAAAATTTTAATATTACTAATTATTCC
1 TTTATTTTGTTTTGTTTTTAAAATATTATTAATTAAGTTAAAATTTTAATATTACTAATTATTCC
11712859 AATTAAAATGTTGATATAAAACTTTTCTTTACAACATACCTTCAAACGTTATAAAAAAGTATGTT
66 AATTAAAATGTTGATATAAAACTTTTCTTTACAACATACCTTCAAACGTTATAAAAAAGTATGTT
11712924 AGGATGATGAGTTTGAGGTTTTTTTTTTTTAAATCACAAATCTTGAACATTAGCCAAACATAAAA
131 AGGATGATGAGTTTGAGGTTTTTTTTTTTTAAATCACAAATCTTGAACATTAGCCAAACATAAAA
11712989 GATAAAAAAAAAAAAGAACTAGTTAGATAAACTAATAGCATTATAAAAGTAAAAGATAAAATTAT
196 GATAAAAAAAAAAAAGAACTAGTTAGATAAACTAATAGCATTATAAAAGTAAAAGATAAAATTAT
11713054 CTCAAATTAAAGTATTAAAGTATAC
261 CTCAAATTAAAGTATTAAAGTATAC
11713079 GAACTAAATT
Statistics
Matches: 284, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
284 275 0.97
285 9 0.03
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.38
Consensus pattern (285 bp):
TTTATTTTGTTTTGTTTTTAAAATATTATTAATTAAGTTAAAATTTTAATATTACTAATTATTCC
AATTAAAATGTTGATATAAAACTTTTCTTTACAACATACCTTCAAACGTTATAAAAAAGTATGTT
AGGATGATGAGTTTGAGGTTTTTTTTTTTTAAATCACAAATCTTGAACATTAGCCAAACATAAAA
GATAAAAAAAAAAAAGAACTAGTTAGATAAACTAATAGCATTATAAAAGTAAAAGATAAAATTAT
CTCAAATTAAAGTATTAAAGTATAC
Found at i:11723720 original size:75 final size:75
Alignment explanation
Indices: 11723629--11723838 Score: 321
Period size: 75 Copynumber: 2.8 Consensus size: 75
11723619 TGATTCCCCC
* * *
11723629 AAGGGGTTGCTAAGTGCTGGTTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCATCGTATT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
11723694 TTAAATGTGA
66 TTAAATGTGA
* * * *
11723704 AGGGGGTTGCTAAGTGCTTATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
11723769 TTAAATGTGA
66 TTAAATGTGA
* * * *
11723779 AAGGGGTTGTTAAGTGCTGATTCCCCAAATCACTGGTGGTTGCTAAGTGCTGAATCCACC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACC
11723839 AATAACGGAC
Statistics
Matches: 120, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
75 120 1.00
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
TTAAATGTGA
Found at i:11728930 original size:5 final size:5
Alignment explanation
Indices: 11728920--11728949 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
11728910 ATATTTTATA
11728920 TGATT TGATT TGATT TGATT TGATT TGATT
1 TGATT TGATT TGATT TGATT TGATT TGATT
11728950 ATGTAAATTG
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:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (5 bp):
TGATT
Found at i:11728962 original size:13 final size:13
Alignment explanation
Indices: 11728944--11728968 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11728934 TTGATTTGAT
11728944 TTGATTATGTAAA
1 TTGATTATGTAAA
11728957 TTGATTATGTAA
1 TTGATTATGTAA
11728969 TCTTGTAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (13 bp):
TTGATTATGTAAA
Found at i:11730328 original size:14 final size:13
Alignment explanation
Indices: 11730301--11730342 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
11730291 ATTATTTATT
11730301 ATTTTTTAAA-AA
1 ATTTTTTAAATAA
11730313 ATATTTTTAAATAA
1 AT-TTTTTAAATAA
* *
11730327 ATTTCTTGAATAA
1 ATTTTTTAAATAA
11730340 ATT
1 ATT
11730343 GACATGGAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 2 0.08
13 20 0.77
14 4 0.15
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (13 bp):
ATTTTTTAAATAA
Found at i:11731560 original size:115 final size:116
Alignment explanation
Indices: 11731383--11731614 Score: 448
Period size: 115 Copynumber: 2.0 Consensus size: 116
11731373 ACTTAAATTA
*
11731383 AAAAAATATGTAATAACTCTTATAAAAAATAAAATTCCTATCCAACATTACATAAATAACAAAAA
1 AAAAAATATGTAATAACTCTTATAAAAAAAAAAATTCCTATCCAACATTACATAAATAACAAAAA
11731448 AAAAGAATGTAATAAAATATTTATTTAATAAATAAATTTAATCTCTAAATC
66 AAAAGAATGTAATAAAATATTTATTTAATAAATAAATTTAATCTCTAAATC
11731499 AAAAAATATGT-ATAACTCTTATAAAAAAAAAAATTCCTATCCAACATTACATAAATAACAAAAA
1 AAAAAATATGTAATAACTCTTATAAAAAAAAAAATTCCTATCCAACATTACATAAATAACAAAAA
11731563 AAAAGAATGTAATAAAATATTTATTTAATAAATAAATTTAATCTCTAAATC
66 AAAAGAATGTAATAAAATATTTATTTAATAAATAAATTTAATCTCTAAATC
11731614 A
1 A
11731615 TAGTATTTCT
Statistics
Matches: 115, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
115 104 0.90
116 11 0.10
ACGTcount: A:0.56, C:0.10, G:0.03, T:0.31
Consensus pattern (116 bp):
AAAAAATATGTAATAACTCTTATAAAAAAAAAAATTCCTATCCAACATTACATAAATAACAAAAA
AAAAGAATGTAATAAAATATTTATTTAATAAATAAATTTAATCTCTAAATC
Found at i:11737598 original size:13 final size:13
Alignment explanation
Indices: 11737569--11737614 Score: 65
Period size: 14 Copynumber: 3.4 Consensus size: 13
11737559 AAATGCTCAG
*
11737569 AAATTCTTTTAAAA
1 AAATTATTTT-AAA
11737583 AAATTATTTTAAA
1 AAATTATTTTAAA
11737596 AAATTATTTTTAAA
1 AAATTA-TTTTAAA
11737610 AAATT
1 AAATT
11737615 CACGTTCATT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 9 0.30
14 21 0.70
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (13 bp):
AAATTATTTTAAA
Found at i:11738888 original size:39 final size:39
Alignment explanation
Indices: 11738797--11738887 Score: 119
Period size: 39 Copynumber: 2.3 Consensus size: 39
11738787 AAAATTTATA
* * *
11738797 TTTAATACAATAAAATATTTATTATATTTATTTGTGTTT
1 TTTAATATAATAAAACATTTATTATATTTATTAGTGTTT
*
11738836 TTTAATATAATAAAACATTTATTATATTTATGGTAGTTTTTT
1 TTTAATATAATAAAACATTTATTATATTTAT--TAG-TGTTT
11738878 TTTAATATAA
1 TTTAATATAA
11738888 ATACTTTTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
39 29 0.64
41 2 0.04
42 14 0.31
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.55
Consensus pattern (39 bp):
TTTAATATAATAAAACATTTATTATATTTATTAGTGTTT
Found at i:11749724 original size:17 final size:17
Alignment explanation
Indices: 11749704--11749737 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
11749694 TAAGAGATTA
11749704 TAAATAAAAATAAACAT
1 TAAATAAAAATAAACAT
* *
11749721 TAAATCAAAATATACAT
1 TAAATAAAAATAAACAT
11749738 ACATCTTAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (17 bp):
TAAATAAAAATAAACAT
Found at i:11762742 original size:24 final size:24
Alignment explanation
Indices: 11762710--11762761 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
11762700 GCGACATTGG
*
11762710 CAGCCGCAGCCGCAGCCT-TTGCAA
1 CAGCAGCAGCCGCAG-CTATTGCAA
* *
11762734 CAGCAGCAGCTGCTGCTATTGCAA
1 CAGCAGCAGCCGCAGCTATTGCAA
11762758 CAGC
1 CAGC
11762762 TGCGGAAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.23, C:0.37, G:0.25, T:0.15
Consensus pattern (24 bp):
CAGCAGCAGCCGCAGCTATTGCAA
Found at i:11780046 original size:25 final size:25
Alignment explanation
Indices: 11779977--11780108 Score: 89
Period size: 25 Copynumber: 5.4 Consensus size: 25
11779967 TGGTTCCTAC
* *
11779977 AAGCTTCCC-ATTTTTGGCTCTTCG
1 AAGCTTCCCGATTTATGGCTCTTTG
*
11780001 GAGCTTCCCGATAATTA--GCTCTTTG
1 AAGCTTCCCGAT--TTATGGCTCTTTG
**
11780026 AAGCTTCCCGATTTATGGCTCTCCG
1 AAGCTTCCCGATTTATGGCTCTTTG
* * * *
11780051 GAGCTTCCTGATAT-TGGCTCGCTTG
1 AAGCTTCCCGATTTATGGCTC-TTTG
*
11780076 AA-CTTCCC-AATTATGGCTCTTATG
1 AAGCTTCCCGATTTATGGCTCTT-TG
11780100 -AGCTTCCCG
1 AAGCTTCCCG
11780109 TTACATGGCT
Statistics
Matches: 81, Mismatches: 17, Indels: 19
0.69 0.15 0.16
Matches are distributed among these distances:
23 7 0.09
24 33 0.41
25 39 0.48
27 2 0.02
ACGTcount: A:0.17, C:0.28, G:0.20, T:0.36
Consensus pattern (25 bp):
AAGCTTCCCGATTTATGGCTCTTTG
Found at i:11780056 original size:50 final size:49
Alignment explanation
Indices: 11779977--11780144 Score: 153
Period size: 49 Copynumber: 3.4 Consensus size: 49
11779967 TGGTTCCTAC
* * *
11779977 AAGCTTCCCATTTTTGGCTCTTCGGAGCTTCCCGATAATTAGCTC-TTTG
1 AAGCTTCCCATTTATGGCTCTCCGGAGCTTCCCGAT-ATTAGCTCGCTTG
* *
11780026 AAGCTTCCCGATTTATGGCTCTCCGGAGCTTCCTGATATTGGCTCGCTTG
1 AAGCTTCCC-ATTTATGGCTCTCCGGAGCTTCCCGATATTAGCTCGCTTG
* *** * * * * *
11780076 AA-CTTCCCAATTATGGCTCTTATGAGCTTCCCGTTACATGGCTCACAT-
1 AAGCTTCCCATTTATGGCTCTCCGGAGCTTCCCGATA-TTAGCTCGCTTG
11780124 AAGCTTCCCATTATATGGCTC
1 AAGCTTCCCATT-TATGGCTC
11780145 GAAAGAGCTT
Statistics
Matches: 99, Mismatches: 15, Indels: 9
0.80 0.12 0.07
Matches are distributed among these distances:
48 24 0.24
49 38 0.38
50 37 0.37
ACGTcount: A:0.18, C:0.28, G:0.18, T:0.35
Consensus pattern (49 bp):
AAGCTTCCCATTTATGGCTCTCCGGAGCTTCCCGATATTAGCTCGCTTG
Found at i:11780118 original size:25 final size:25
Alignment explanation
Indices: 11780088--11780175 Score: 79
Period size: 25 Copynumber: 3.5 Consensus size: 25
11780078 CTTCCCAATT
*
11780088 ATGGCTCTTATGAGCTTCCCGTTAC
1 ATGGCTCGTATGAGCTTCCCGTTAC
** * * *
11780113 ATGGCTCACATAAGCTTCCCATTAT
1 ATGGCTCGTATGAGCTTCCCGTTAC
* * *
11780138 ATGGCTCGAAAGAGCTTCTCGTTTAC
1 ATGGCTCGTATGAGCTTCCCG-TTAC
11780164 AT-GCTCGTATGA
1 ATGGCTCGTATGA
11780176 ACATTCTCGG
Statistics
Matches: 48, Mismatches: 14, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
25 43 0.90
26 5 0.10
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (25 bp):
ATGGCTCGTATGAGCTTCCCGTTAC
Found at i:11781827 original size:99 final size:99
Alignment explanation
Indices: 11781702--11781899 Score: 369
Period size: 99 Copynumber: 2.0 Consensus size: 99
11781692 GCTTTCACCA
11781702 CTAAGACAAAGAGTGATCCATCGAGTAGGAGACACAAGACAAGATATATAGCCTACACTATTCTA
1 CTAAGACAAAGAGTGATCCATCGAGTAGGAGACACAAGACAAGATATATAGCCTACACTATTCTA
11781767 AAGTATCATCTCAACTTAGAGAAGTCACCATATT
66 AAGTATCATCTCAACTTAGAGAAGTCACCATATT
* *
11781801 CTAAGACAAAGAGTGATCGATCGAGTAGGAGACACAAGACAAGATATATAGTCTACACTATTCTA
1 CTAAGACAAAGAGTGATCCATCGAGTAGGAGACACAAGACAAGATATATAGCCTACACTATTCTA
*
11781866 AAGTATCATCTCAACTTTGAGAAGTCACCATATT
66 AAGTATCATCTCAACTTAGAGAAGTCACCATATT
11781900 GAGCATCTCT
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
99 96 1.00
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (99 bp):
CTAAGACAAAGAGTGATCCATCGAGTAGGAGACACAAGACAAGATATATAGCCTACACTATTCTA
AAGTATCATCTCAACTTAGAGAAGTCACCATATT
Found at i:11783321 original size:25 final size:25
Alignment explanation
Indices: 11783293--11783346 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 25
11783283 CACAAACGTA
11783293 GCTC-TTTATAAGCTTCCTAATATAG
1 GCTCTTTTATAAGCTTCCTAATAT-G
* *
11783318 GCTCTTTTGTGAGCTTCCTAATATG
1 GCTCTTTTATAAGCTTCCTAATATG
11783343 GCTC
1 GCTC
11783347 GTTTGAACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 9 0.35
26 17 0.65
ACGTcount: A:0.20, C:0.22, G:0.17, T:0.41
Consensus pattern (25 bp):
GCTCTTTTATAAGCTTCCTAATATG
Found at i:11783351 original size:25 final size:26
Alignment explanation
Indices: 11783303--11783351 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
11783293 GCTCTTTATA
*
11783303 AGCTTCCTAATATAGGCTCTTTTGTG
1 AGCTTCCTAATATAGGCTCGTTTGTG
11783329 AGCTTCCTAATAT-GGCTCGTTTG
1 AGCTTCCTAATATAGGCTCGTTTG
11783352 AACTTCCTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.41
Consensus pattern (26 bp):
AGCTTCCTAATATAGGCTCGTTTGTG
Found at i:11783735 original size:16 final size:16
Alignment explanation
Indices: 11783707--11783747 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
11783697 TAAATGGAAA
11783707 TATG-ATATGAAAAGAT
1 TATGTATATGAAAAG-T
11783723 TATGTATAT-AAAAGT
1 TATGTATATGAAAAGT
11783738 TAT-TATATGA
1 TATGTATATGA
11783748 TGAGCTCATC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 5 0.22
15 5 0.22
16 9 0.39
17 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.39
Consensus pattern (16 bp):
TATGTATATGAAAAGT
Found at i:11785698 original size:42 final size:42
Alignment explanation
Indices: 11785630--11785712 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
11785620 GTCCATACGG
*
11785630 GCGTGTGTCTCAACCGTGTGTAACACACGACCACACGCACGA
1 GCGTGTGTCTCAACCATGTGTAACACACGACCACACGCACGA
* * * * *
11785672 GCGTGTGTCTCAGCCATGTTTGACACACGGCCACGCGCACG
1 GCGTGTGTCTCAACCATGTGTAACACACGACCACACGCACG
11785713 GGCTGGTGGT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.22, C:0.34, G:0.27, T:0.18
Consensus pattern (42 bp):
GCGTGTGTCTCAACCATGTGTAACACACGACCACACGCACGA
Found at i:11787437 original size:21 final size:21
Alignment explanation
Indices: 11787396--11787437 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
11787386 ATATAAATAT
*
11787396 TAATATAAAAATTTTAACTAA
1 TAATATAAAAATTTGAACTAA
11787417 TAATAT-AAAATTTGAATCTAA
1 TAATATAAAAATTTGAA-CTAA
11787438 CCCGAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (21 bp):
TAATATAAAAATTTGAACTAA
Found at i:11791879 original size:40 final size:39
Alignment explanation
Indices: 11791824--11791958 Score: 139
Period size: 40 Copynumber: 3.4 Consensus size: 39
11791814 ACCAGTTTGG
* *
11791824 CACCCAGTGCCTCATCGGATAATTCGAAGTAATAATTTAA
1 CACCCAGTGCCTCATCGGATAATCCGAAGTAATAA-TTGA
* * * *
11791864 CACCCAGTGTCTCATCGGCTAAACCGAAGT-A-AATTGG
1 CACCCAGTGCCTCATCGGATAATCCGAAGTAATAATTGA
* *
11791901 CACCCAGTGCCTCATCGAATTAATCCGAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCGGA-TAATCCGAAGTAAT-AATTGA
* *
11791942 CACTCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
11791959 ACTCAAAGTC
Statistics
Matches: 77, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
37 18 0.23
38 12 0.16
39 1 0.01
40 26 0.34
41 20 0.26
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAATCCGAAGTAATAATTGA
Found at i:11791950 original size:41 final size:40
Alignment explanation
Indices: 11791824--11791959 Score: 134
Period size: 41 Copynumber: 3.5 Consensus size: 40
11791814 ACCAGTTTGG
* * * * *
11791824 CACCCAGTGCCTCATCGGATAATTCGAAGTAATAATTTAA
1 CACCCAGTGCCTCATCGAATAATCCGAAGTAGTAAATTGA
* ** * *
11791864 CACCCAGTGTCTCATCGGCTAAACCG-A--AGTAAATTGG
1 CACCCAGTGCCTCATCGAATAATCCGAAGTAGTAAATTGA
11791901 CACCCAGTGCCTCATCGAATTAATCCGAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCGAA-TAATCCGAAGTAGTAAATTGA
* *
11791942 CACTCAGTGTCTCATCGA
1 CACCCAGTGCCTCATCGA
11791960 CTCAAAGTCG
Statistics
Matches: 77, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
37 22 0.29
38 6 0.08
39 2 0.03
40 22 0.29
41 25 0.32
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.25
Consensus pattern (40 bp):
CACCCAGTGCCTCATCGAATAATCCGAAGTAGTAAATTGA
Found at i:11792401 original size:21 final size:20
Alignment explanation
Indices: 11792376--11792419 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
11792366 TCTTGGTTCG
11792376 TTTCTATTCTGTTTCTTTCTA
1 TTTCTATTCTGTTTCTTT-TA
* *
11792397 TTTCTTTTTTGTTTCTTTTA
1 TTTCTATTCTGTTTCTTTTA
11792417 TTT
1 TTT
11792420 ATTATATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.07, C:0.14, G:0.05, T:0.75
Consensus pattern (20 bp):
TTTCTATTCTGTTTCTTTTA
Found at i:11793554 original size:29 final size:29
Alignment explanation
Indices: 11793470--11793558 Score: 83
Period size: 29 Copynumber: 3.0 Consensus size: 29
11793460 AATTGAATTA
* *
11793470 AAATCAAAGTTTCATGTA-CACATATGAACC
1 AAATCAAAG-TTCATGTATCAAAT-TGCACC
* *
11793500 ACAATTCAAATTTCATGTGT-ATAATTGCACC
1 A-AA-TCAAAGTTCATGTATCA-AATTGCACC
11793531 AAATCAAAGTTCATGTATCAAATTGCAC
1 AAATCAAAGTTCATGTATCAAATTGCAC
11793559 ATTAGACCAA
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
29 21 0.44
30 4 0.08
31 16 0.33
32 7 0.15
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.30
Consensus pattern (29 bp):
AAATCAAAGTTCATGTATCAAATTGCACC
Found at i:11794338 original size:13 final size:13
Alignment explanation
Indices: 11794310--11794348 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
11794300 GGATGTTGTT
*
11794310 ATTATAAGTGAAAA
1 ATTATAA-TAAAAA
11794324 ATTATAATAAAAA
1 ATTATAATAAAAA
*
11794337 ATTAAAATAAAA
1 ATTATAATAAAA
11794349 CATAAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 16 0.70
14 7 0.30
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (13 bp):
ATTATAATAAAAA
Found at i:11796735 original size:17 final size:18
Alignment explanation
Indices: 11796703--11796741 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
11796693 TTTAAGAAGT
11796703 ATTTTTGAGACGAAAAAC
1 ATTTTTGAGACGAAAAAC
* *
11796721 ATTTTTGGGAC-AAAAGC
1 ATTTTTGAGACGAAAAAC
11796738 ATTT
1 ATTT
11796742 CTAAACACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.33
Consensus pattern (18 bp):
ATTTTTGAGACGAAAAAC
Found at i:11796824 original size:19 final size:19
Alignment explanation
Indices: 11796797--11796842 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
11796787 TTAGAAGCTG
* *
11796797 AAAATTTTAGCTTTTCTTC
1 AAAAGTTTAGCTTCTCTTC
11796816 AAAAGTTTAGCTTCTCTTC
1 AAAAGTTTAGCTTCTCTTC
11796835 AAAAGTTT
1 AAAAGTTT
11796843 TTTGTGTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.30, C:0.15, G:0.09, T:0.46
Consensus pattern (19 bp):
AAAAGTTTAGCTTCTCTTC
Found at i:11797320 original size:17 final size:17
Alignment explanation
Indices: 11797298--11797330 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
11797288 TCTAGATATT
11797298 AAAATGATTTTTTCCCC
1 AAAATGATTTTTTCCCC
11797315 AAAATGATTTTTTCCC
1 AAAATGATTTTTTCCC
11797331 TCTAGATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.21, G:0.06, T:0.42
Consensus pattern (17 bp):
AAAATGATTTTTTCCCC
Found at i:11797537 original size:18 final size:19
Alignment explanation
Indices: 11797499--11797555 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 19
11797489 ATAATAGATT
11797499 AAAATAATTTAAAAATATA
1 AAAATAATTTAAAAATATA
*
11797518 AAAAT-ATTTAAAAA-ATT
1 AAAATAATTTAAAAATATA
* *
11797535 AAATTAAATTAAAAATA-A
1 AAAATAATTTAAAAATATA
11797553 AAA
1 AAA
11797556 GTTCATGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
17 6 0.19
18 20 0.62
19 6 0.19
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAATAATTTAAAAATATA
Found at i:11832728 original size:17 final size:18
Alignment explanation
Indices: 11832706--11832750 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 18
11832696 AATAACTAAG
11832706 ATAAATAAAA-TAGAACA
1 ATAAATAAAATTAGAACA
11832723 ATAAATTAAAATTTAGAACA
1 ATAAA-TAAAA-TTAGAACA
11832743 ATAAATAA
1 ATAAATAA
11832751 GAAAATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.20
18 5 0.20
19 3 0.12
20 12 0.48
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.24
Consensus pattern (18 bp):
ATAAATAAAATTAGAACA
Found at i:11840976 original size:16 final size:17
Alignment explanation
Indices: 11840955--11840989 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
11840945 GGGTCCGGAT
11840955 ATTTAAAATGAA-AAAA
1 ATTTAAAATGAATAAAA
*
11840971 ATTTAAAATTAATAAAA
1 ATTTAAAATGAATAAAA
11840988 AT
1 AT
11840990 AAAACTACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (17 bp):
ATTTAAAATGAATAAAA
Found at i:11843266 original size:31 final size:30
Alignment explanation
Indices: 11843219--11843281 Score: 99
Period size: 31 Copynumber: 2.1 Consensus size: 30
11843209 TATTTTATTA
11843219 TTAATTTTGTTATTATTTTAAAGACATTTG
1 TTAATTTTGTTATTATTTTAAAGACATTTG
* *
11843249 TTAATTTTTTTTATTATTTTAGAGACATTTG
1 TTAA-TTTTGTTATTATTTTAAAGACATTTG
11843280 TT
1 TT
11843282 TGTTAAGTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 4 0.13
31 26 0.87
ACGTcount: A:0.27, C:0.03, G:0.10, T:0.60
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGACATTTG
Found at i:11843382 original size:24 final size:24
Alignment explanation
Indices: 11843353--11843399 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
11843343 ATGTTATAAC
11843353 TTTTTTTATTTACCAAAAAATATA
1 TTTTTTTATTTACCAAAAAATATA
*
11843377 TTTTTTTATTTACCAAAATATAT
1 TTTTTTTATTTACCAAAAAATAT
11843400 CAAAAAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (24 bp):
TTTTTTTATTTACCAAAAAATATA
Found at i:11843556 original size:4 final size:4
Alignment explanation
Indices: 11843547--11843693 Score: 117
Period size: 4 Copynumber: 36.0 Consensus size: 4
11843537 GAAGGAGAGG
* *
11843547 GAAA GAAA GAAA GAAA GAAA AAAA GAAA GAAA GGAGAT GAAA GAAA G-AA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA -GA-AA GAAA GAAA GAAA
* * *
11843596 -AAA GAAG GAAA GAAAA GGAAA G-GA GAAGA GAAA AAAA GAAA GAAA GAAA
1 GAAA GAAA GAAA G-AAA -GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA
*
11843645 G-AA G-AA GAAAA GGAAA GGAGAA GAAA -AAA GAAA GAAA GAAG GAAA
1 GAAA GAAA G-AAA -GAAA -GA-AA GAAA GAAA GAAA GAAA GAAA GAAA
11843690 GAAA
1 GAAA
11843694 TAAAAAGGAG
Statistics
Matches: 118, Mismatches: 12, Indels: 26
0.76 0.08 0.17
Matches are distributed among these distances:
3 15 0.13
4 74 0.63
5 24 0.20
6 5 0.04
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.01
Consensus pattern (4 bp):
GAAA
Found at i:11843589 original size:30 final size:29
Alignment explanation
Indices: 11843547--11843758 Score: 131
Period size: 30 Copynumber: 7.1 Consensus size: 29
11843537 GAAGGAGAGG
11843547 GAAA-GAAAGAAAGAAAGAAAAAAAGAAA
1 GAAAGGAAAGAAAGAAAGAAAAAAAGAAA
*
11843575 GAAAGGAGATGAAAGAAAGAAAAAGAAGGAAA
1 GAAAGGA-AAGAAAGAAAGAAAAA-AA-GAAA
*
11843607 GAAAAGGAAAG-GAGAAGAGAAAAAAAGAAA
1 G-AAAGGAAAGAAAGAA-AGAAAAAAAGAAA
11843637 GAAA-GAAAG-AAG-AAGAAAAGGAAAGGAGAA
1 GAAAGGAAAGAAAGAAAGAAAA--AAA-GA-AA
**
11843667 GAAA--AAAGAAAGAAAGAAGGAAAGAAA
1 GAAAGGAAAGAAAGAAAGAAAAAAAGAAA
*
11843694 TAAA--AAGGAGAAGAGAAA-AAAAAAAGAAGAA
1 GAAAGGAA--AGAA-AGAAAGAAAAAAAG-A-AA
* * *
11843725 GAAGAGGGAAGGAAGGAA-AAAAAAAGAAAA
1 GAA-AGGAAAGAAAGAAAGAAAAAAAG-AAA
11843755 GAAA
1 GAAA
11843759 ATGTATTTTT
Statistics
Matches: 151, Mismatches: 13, Indels: 39
0.74 0.06 0.19
Matches are distributed among these distances:
26 6 0.04
27 8 0.05
28 16 0.11
29 25 0.17
30 40 0.26
31 31 0.21
32 18 0.12
33 6 0.04
34 1 0.01
ACGTcount: A:0.71, C:0.00, G:0.28, T:0.01
Consensus pattern (29 bp):
GAAAGGAAAGAAAGAAAGAAAAAAAGAAA
Found at i:11843608 original size:44 final size:42
Alignment explanation
Indices: 11843552--11843721 Score: 126
Period size: 41 Copynumber: 4.1 Consensus size: 42
11843542 AGAGGGAAAG
11843552 AAAGAAAGAAAGAAAAAAAGAAAGAAAGGAGATGAAAGAAAGAA
1 AAAGAAAGAAAGAAAAAAAGAAAGAAAGGAGA-GAAA-AAAGAA
* * * * *
11843596 AAAGAAGGAAAG--AAAAGGAAAG-GAGAAGAGAAAAAA-AG
1 AAAGAAAGAAAGAAAAAAAGAAAGAAAGGAGAGAAAAAAGAA
* *
11843634 AAAGAAAGAAAGAAGAAGAA-AAGGAAAGGAGAAGAAAAAAG--
1 AAAGAAAGAAAGAA-AAAAAGAAAGAAAGGAG-AGAAAAAAGAA
* * *
11843675 AAAGAAAGAAGGAAAGAAA-TAA-AAAGGAGAAGAGAAAAA-AA
1 AAAGAAAGAAAGAAAAAAAGAAAGAAAGGAG-AGA-AAAAAGAA
11843716 AAAGAA
1 AAAGAA
11843722 GAAGAAGAGG
Statistics
Matches: 101, Mismatches: 16, Indels: 21
0.73 0.12 0.15
Matches are distributed among these distances:
38 12 0.12
39 14 0.14
40 16 0.16
41 31 0.31
42 17 0.17
44 11 0.11
ACGTcount: A:0.72, C:0.00, G:0.27, T:0.01
Consensus pattern (42 bp):
AAAGAAAGAAAGAAAAAAAGAAAGAAAGGAGAGAAAAAAGAA
Found at i:11843674 original size:62 final size:60
Alignment explanation
Indices: 11843548--11843722 Score: 150
Period size: 62 Copynumber: 2.9 Consensus size: 60
11843538 AAGGAGAGGG
* *
11843548 AAAGAAAGAAAGAAAGAAAAAAAGAAAGAAAGGAGATGAAAGAAAGAAAAAGAAGGAAAGA
1 AAAGAAAG-GAGAAAGAAAAAAAGAAAGAAAGGAGAAGAAAGAAAGAAAAAGAAGGAAAGA
*
11843609 AAAGGAAAGGAGAAGAGAAAAAAAGAAAGAAA-GA-AAG-AAG-AAGAAAAGGAAAGGAGAAG-
1 AAA-GAAAGGAGAA-AGAAAAAAAGAAAGAAAGGAGAAGAAAGAAAGAAAAAG-AAGGA-AAGA
* ** *
11843668 AAA-AAAGAAAGAAAGAAGGAAAGAAATAAAAAGGAGAAGAGAA-AAA-AAAAAGAAG
1 AAAGAAAG-GAGAAAGAAAAAAAG-AA-AGAAAGGAGAAGA-AAGAAAGAAAAAGAAG
11843723 AAGAAGAGGG
Statistics
Matches: 94, Mismatches: 8, Indels: 24
0.75 0.06 0.19
Matches are distributed among these distances:
57 12 0.13
58 14 0.15
59 15 0.16
60 7 0.07
61 15 0.16
62 27 0.29
63 4 0.04
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.01
Consensus pattern (60 bp):
AAAGAAAGGAGAAAGAAAAAAAGAAAGAAAGGAGAAGAAAGAAAGAAAAAGAAGGAAAGA
Found at i:11843677 original size:49 final size:48
Alignment explanation
Indices: 11843585--11843693 Score: 139
Period size: 49 Copynumber: 2.2 Consensus size: 48
11843575 GAAAGGAGAT
* * *
11843585 GAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAA
1 GAAAGAAAGAAAAAGAAGAAAAGAAAAGGAAAGGAAAAAAGAAAAAAA
* *
11843633 GAAAGAAAGAAAGAAGAAGAAAAGGAAAGGAGAA-GAAAAAAGAAAGAAA
1 GAAAGAAAGAAA-AAGAAGAAAAGAAAAGGA-AAGGAAAAAAGAAAAAAA
*
11843682 GAAGGAAAGAAA
1 GAAAGAAAGAAA
11843694 TAAAAAGGAG
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
48 12 0.23
49 39 0.74
50 2 0.04
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (48 bp):
GAAAGAAAGAAAAAGAAGAAAAGAAAAGGAAAGGAAAAAAGAAAAAAA
Found at i:11843724 original size:44 final size:44
Alignment explanation
Indices: 11843549--11843728 Score: 157
Period size: 44 Copynumber: 4.2 Consensus size: 44
11843539 AGGAGAGGGA
* * * ** *
11843549 AAGAAAGAAAGAAAGAAAAAAAGAAAGA-AAGGAGATGAAAGAAAG
1 AAGAAAGAAGGAAAGAAAAGAA-AAGGAGAA-GAGAAAAAAAAAAG
*
11843594 AA-AAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAGAAAG
1 AAGAAAGAAGGAAAGAAAAGAAAAGGAGAAGAGAAAAAAA-AAAG
* *
11843638 AAAGAAAGAA-G-AAGAAAAGGAAAGGAG-A-AG--AAAAAAGA-
1 -AAGAAAGAAGGAAAGAAAAGAAAAGGAGAAGAGAAAAAAAAAAG
11843676 AAGAAAGAAGGAAAGAAATA-AAAAGGAGAAGAGAAAAAAAAAAG
1 AAGAAAGAAGGAAAGAAA-AGAAAAGGAGAAGAGAAAAAAAAAAG
11843720 AAG-AAGAAG
1 AAGAAAGAAG
11843729 AGGGAAGGAA
Statistics
Matches: 113, Mismatches: 10, Indels: 26
0.76 0.07 0.17
Matches are distributed among these distances:
37 9 0.08
38 1 0.01
39 15 0.13
40 7 0.06
41 2 0.02
42 2 0.02
43 25 0.22
44 41 0.36
45 5 0.04
46 6 0.05
ACGTcount: A:0.71, C:0.00, G:0.28, T:0.01
Consensus pattern (44 bp):
AAGAAAGAAGGAAAGAAAAGAAAAGGAGAAGAGAAAAAAAAAAG
Found at i:11844296 original size:16 final size:15
Alignment explanation
Indices: 11844271--11844300 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
11844261 GTACTGAAAT
11844271 AATATAAAATAATAA
1 AATATAAAATAATAA
11844286 AATACTAAAATAATA
1 AATA-TAAAATAATA
11844301 TATTTTTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (15 bp):
AATATAAAATAATAA
Found at i:11845421 original size:3 final size:3
Alignment explanation
Indices: 11845413--11845459 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
11845403 TATGTATTAA
*
11845413 AAT AAT AAT AATT AAT -AT AAT AAT AAT AGT AAT ATAT AAT -AT AAT
1 AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT
11845458 AA
1 AA
11845460 CAAAGATAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
2 4 0.11
3 28 0.74
4 6 0.16
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:11845432 original size:15 final size:15
Alignment explanation
Indices: 11845408--11845453 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
11845398 ATATATATGT
*
11845408 ATTAAAATAATAATA
1 ATTAATATAATAATA
11845423 ATTAATATAATAATA
1 ATTAATATAATAATA
11845438 ATAGTAATAT-ATAATA
1 AT--TAATATAATAATA
11845454 TAATAACAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 16 0.57
16 6 0.21
17 6 0.21
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (15 bp):
ATTAATATAATAATA
Found at i:11845439 original size:21 final size:19
Alignment explanation
Indices: 11845413--11845459 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
11845403 TATGTATTAA
*
11845413 AATAATAATAATTA-ATAT
1 AATAATAATAATAATATAT
*
11845431 AATAATAATAGTAATATAT
1 AATAATAATAATAATATAT
11845450 AAT-ATAATAA
1 AATAATAATAA
11845460 CAAAGATAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (19 bp):
AATAATAATAATAATATAT
Found at i:11845445 original size:24 final size:24
Alignment explanation
Indices: 11845413--11845459 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
11845403 TATGTATTAA
11845413 AATAATAATA-ATTAATATAATAAT
1 AATAATAATATA-TAATATAATAAT
*
11845437 AATAGTAATATATAATATAATAA
1 AATAATAATATATAATATAATAA
11845460 CAAAGATAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (24 bp):
AATAATAATATATAATATAATAAT
Found at i:11845838 original size:141 final size:141
Alignment explanation
Indices: 11845584--11845868 Score: 534
Period size: 141 Copynumber: 2.0 Consensus size: 141
11845574 AAATCAAATT
* *
11845584 AAAATAGAGGATGAATTTGCAAAATGCGTGCAACATGAAGGGTCAAAAGGGAAATTAATCCCTCC
1 AAAATAGAGGATGAATTTGCAAAATGCGTGCAACATGAAGGGTCAAAAAGGAAATTAATCCCGCC
*
11845649 TCTCCCAAAGTGCTGTGCAGCACTGGATTAAAATCAAACAAATTTAATGTTTTAGGGAAAAATTT
66 TCTCCCAAAGTGCTGCGCAGCACTGGATTAAAATCAAACAAATTTAATGTTTTAGGGAAAAATTT
11845714 GAAAATAGCAA
131 GAAAATAGCAA
11845725 AAAATAGAGGATGAATTTGCAAAATGCGTGCAACATGAAGGGTCAAAAAGGAAATTAATCCCGCC
1 AAAATAGAGGATGAATTTGCAAAATGCGTGCAACATGAAGGGTCAAAAAGGAAATTAATCCCGCC
*
11845790 TCTCCCAAAGTGCTGCGTAGCACTGGATTAAAATCAAACAAATTTAATGTTTTAGGGAAAAATTT
66 TCTCCCAAAGTGCTGCGCAGCACTGGATTAAAATCAAACAAATTTAATGTTTTAGGGAAAAATTT
11845855 GAAAATAGCAA
131 GAAAATAGCAA
11845866 AAA
1 AAA
11845869 CAGTGGTTTT
Statistics
Matches: 140, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
141 140 1.00
ACGTcount: A:0.42, C:0.15, G:0.20, T:0.24
Consensus pattern (141 bp):
AAAATAGAGGATGAATTTGCAAAATGCGTGCAACATGAAGGGTCAAAAAGGAAATTAATCCCGCC
TCTCCCAAAGTGCTGCGCAGCACTGGATTAAAATCAAACAAATTTAATGTTTTAGGGAAAAATTT
GAAAATAGCAA
Found at i:11846956 original size:83 final size:83
Alignment explanation
Indices: 11846859--11847220 Score: 238
Period size: 83 Copynumber: 4.3 Consensus size: 83
11846849 TATTCTGTCT
* *
11846859 GCTCCACTACAACTTCAGGGAGATAAGACTGGATACGATCTGCT-TTCTGCAACCTCAGAAAGAT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTGGATACGATCTGCTCCTCTGCAACCTCAGAAAGAT
11846923 AAGATCTGGATGTTAATCC
66 AAGATCTGGAT-TTAATCC
* * * ** * * * * *
11846942 GCTCCACTGTAACTTTAGGGAGATAGGA-TTAATTTCTTCTG-TCTGCTCCACTGTAACTTCAGG
1 GCTCCACTGCAACTTCAGGGAGATAAGACTGGA----TAC-GATCTGCTCCTCTGCAACCTCAGA
* *** *
11847005 GAGATAAGA-CTGGATACGATCT
61 AAGATAAGATCTGGATTTAATCC
* * ** *** * * * *
11847027 GCT-CTCTGCAACCTCAGAAAGATAAGATCTGGATGTTAATCCGCTCCGCTGCAACTTCAGGGAA
1 GCTCCACTGCAACTTCAGGGAGATAAGA-CTGGAT-ACGATCTGCTCCTCTGCAACCTCA-GAAA
* **
11847091 -ATAGGAT-T-GATTTCTTCTGTC
63 GATAAGATCTGGATTTAATC---C
*
11847112 TACTCCACTGCAACTTCAGGGAGATAAGACTGGATACGATCTGCT-CTCTGCAACCTCAGAAAGA
1 -GCTCCACTGCAACTTCAGGGAGATAAGACTGGATACGATCTGCTCCTCTGCAACCTCAGAAAGA
11847176 TAAGATCTGGATGTTAATCC
65 TAAGATCTGGAT-TTAATCC
*
11847196 GCTCCACTGTAACTTCAGGGAGATA
1 GCTCCACTGCAACTTCAGGGAGATA
11847221 GGATTGATTT
Statistics
Matches: 203, Mismatches: 55, Indels: 42
0.68 0.18 0.14
Matches are distributed among these distances:
82 8 0.04
83 74 0.36
84 38 0.19
85 13 0.06
86 27 0.13
87 43 0.21
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (83 bp):
GCTCCACTGCAACTTCAGGGAGATAAGACTGGATACGATCTGCTCCTCTGCAACCTCAGAAAGAT
AAGATCTGGATTTAATCC
Found at i:11847004 original size:127 final size:127
Alignment explanation
Indices: 11846831--11847270 Score: 772
Period size: 127 Copynumber: 3.5 Consensus size: 127
11846821 CTGCCACTCT
* * * *
11846831 AGGGAGATAAGATTGGTTTATTCTGTCTGCTCCACTACAACTTCAGGGAGATAAGACTGGATACG
1 AGGGAGATAGGATTGATTTCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATACG
* *
11846896 ATCTGCTTTCTGCAACCTCAGAAAGATAAGATCTGGATGTTAATCCGCTCCACTGTAACTTT
66 ATCTGCTCTCTGCAACCTCAGAAAGATAAGATCTGGATGTTAATCCGCTCCACTGTAACTTC
* *
11846958 AGGGAGATAGGATTAATTTCTTCTGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTGGATACG
1 AGGGAGATAGGATTGATTTCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATACG
* *
11847023 ATCTGCTCTCTGCAACCTCAGAAAGATAAGATCTGGATGTTAATCCGCTCCGCTGCAACTTC
66 ATCTGCTCTCTGCAACCTCAGAAAGATAAGATCTGGATGTTAATCCGCTCCACTGTAACTTC
* *
11847085 AGGGAAATAGGATTGATTTCTTCTGTCTACTCCACTGCAACTTCAGGGAGATAAGACTGGATACG
1 AGGGAGATAGGATTGATTTCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATACG
11847150 ATCTGCTCTCTGCAACCTCAGAAAGATAAGATCTGGATGTTAATCCGCTCCACTGTAACTTC
66 ATCTGCTCTCTGCAACCTCAGAAAGATAAGATCTGGATGTTAATCCGCTCCACTGTAACTTC
11847212 AGGGAGATAGGATTGATTTCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTG
1 AGGGAGATAGGATTGATTTCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTG
11847271 AAGTTTCACC
Statistics
Matches: 295, Mismatches: 18, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
127 295 1.00
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.29
Consensus pattern (127 bp):
AGGGAGATAGGATTGATTTCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATACG
ATCTGCTCTCTGCAACCTCAGAAAGATAAGATCTGGATGTTAATCCGCTCCACTGTAACTTC
Found at i:11847177 original size:40 final size:41
Alignment explanation
Indices: 11847006--11847187 Score: 113
Period size: 40 Copynumber: 4.3 Consensus size: 41
11846996 AACTTCAGGG
11847006 AGATAAGACTGGATACGATCTGCT-CTCTGCAACCTCAGAA
1 AGATAAGACTGGATACGATCTGCTACTCTGCAACCTCAGAA
*** * * * * *
11847046 AGATAAGATCTGGATGTTAATCCGCTCCGCTGCAACTTCAGGGA
1 AGATAAGA-CTGGAT-ACGATCTGCTACTCTGCAACCTCA-GAA
* * * * * **
11847090 A-ATAGGA-TTGATTTC-TTCTGTCTACTCCACTGCAACTTCAGGG
1 AGATAAGACTGGA-TACGATCTG-CTACT---CTGCAACCTCAGAA
11847133 AGATAAGACTGGATACGATCTGCT-CTCTGCAACCTCAGAA
1 AGATAAGACTGGATACGATCTGCTACTCTGCAACCTCAGAA
11847173 AGATAAGATCTGGAT
1 AGATAAGA-CTGGAT
11847188 GTTAATCCGC
Statistics
Matches: 107, Mismatches: 22, Indels: 25
0.69 0.14 0.16
Matches are distributed among these distances:
40 30 0.28
41 19 0.18
42 7 0.07
43 21 0.20
44 23 0.21
45 7 0.07
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (41 bp):
AGATAAGACTGGATACGATCTGCTACTCTGCAACCTCAGAA
Found at i:11857980 original size:41 final size:42
Alignment explanation
Indices: 11857918--11858000 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 42
11857908 AGACAACTTT
11857918 GAATATACTTAAGGGTGAATAATGAAACTTTAGAAAATGTTA
1 GAATATACTTAAGGGTGAATAATGAAACTTTAGAAAATGTTA
11857960 GAATATACTT-AGGGTGAATAATGAAACTTTAGAAAATGTTA
1 GAATATACTTAAGGGTGAATAATGAAACTTTAGAAAATGTTA
11858001 TTTCTAAAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 31 0.76
42 10 0.24
ACGTcount: A:0.45, C:0.05, G:0.19, T:0.31
Consensus pattern (42 bp):
GAATATACTTAAGGGTGAATAATGAAACTTTAGAAAATGTTA
Found at i:11859251 original size:3 final size:3
Alignment explanation
Indices: 11859243--11859289 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
11859233 TATGTATTAA
*
11859243 AAT AAT AAT AATT AAT -AT AAT AAT AAT AGT AAT ATAT AAT -AT AAT
1 AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT
11859288 AA
1 AA
11859290 CAAAGATAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
2 4 0.11
3 28 0.74
4 6 0.16
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:11859262 original size:15 final size:15
Alignment explanation
Indices: 11859238--11859283 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
11859228 ATATATATGT
*
11859238 ATTAAAATAATAATA
1 ATTAATATAATAATA
11859253 ATTAATATAATAATA
1 ATTAATATAATAATA
11859268 ATAGTAATAT-ATAATA
1 AT--TAATATAATAATA
11859284 TAATAACAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 16 0.57
16 6 0.21
17 6 0.21
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (15 bp):
ATTAATATAATAATA
Found at i:11859269 original size:21 final size:19
Alignment explanation
Indices: 11859243--11859289 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
11859233 TATGTATTAA
*
11859243 AATAATAATAATTA-ATAT
1 AATAATAATAATAATATAT
*
11859261 AATAATAATAGTAATATAT
1 AATAATAATAATAATATAT
11859280 AAT-ATAATAA
1 AATAATAATAA
11859290 CAAAGATAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (19 bp):
AATAATAATAATAATATAT
Found at i:11859275 original size:24 final size:24
Alignment explanation
Indices: 11859243--11859289 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
11859233 TATGTATTAA
11859243 AATAATAATA-ATTAATATAATAAT
1 AATAATAATATA-TAATATAATAAT
*
11859267 AATAGTAATATATAATATAATAA
1 AATAATAATATATAATATAATAA
11859290 CAAAGATAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (24 bp):
AATAATAATATATAATATAATAAT
Found at i:11860377 original size:25 final size:25
Alignment explanation
Indices: 11860343--11860390 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
11860333 ATGTTATAAG
11860343 TTTTTTTATTTACCAAAATATATGT
1 TTTTTTTATTTACCAAAATATATGT
11860368 TTTTTTTATTTACCAAAATATAT
1 TTTTTTTATTTACCAAAATATAT
11860391 CAAAAAAACG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.33, C:0.08, G:0.02, T:0.56
Consensus pattern (25 bp):
TTTTTTTATTTACCAAAATATATGT
Found at i:11865835 original size:3 final size:3
Alignment explanation
Indices: 11865827--11865867 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
11865817 TCTTAATACT
11865827 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
11865868 TAATAATAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:11865872 original size:3 final size:3
Alignment explanation
Indices: 11865866--11865900 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
11865856 CAACAACAAC
*
11865866 AAT AAT AAT AAT AAT AAT AAT AAT ACT AACT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT A
11865901 CTATTANNNN
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:11868554 original size:27 final size:28
Alignment explanation
Indices: 11868519--11868589 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 28
11868509 AATTAAAAAA
*
11868519 TTACCAAAATGT-TATACA-TTTTTTTAT
1 TTACCAAAATATATATA-ATTTTTTTTAT
11868546 TTACCAAAATATATATAATTTTTTTTTAT
1 TTACCAAAATATATATAA-TTTTTTTTAT
11868575 TTACCAAAATATATA
1 TTACCAAAATATATA
11868590 AAAAAAACAG
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
27 12 0.30
28 4 0.10
29 24 0.60
ACGTcount: A:0.39, C:0.10, G:0.01, T:0.49
Consensus pattern (28 bp):
TTACCAAAATATATATAATTTTTTTTAT
Found at i:11868676 original size:27 final size:27
Alignment explanation
Indices: 11868637--11868714 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 27
11868627 TCCCTGGGTG
11868637 AAGGGAACACTGTTGGCGGCACCAAAC
1 AAGGGAACACTGTTGGCGGCACCAAAC
* *
11868664 AAGGGAACCCTGTTGGTGGCACCAAAC
1 AAGGGAACACTGTTGGCGGCACCAAAC
* *
11868691 AA-GGATTCTCTGTTGGCGGCACCA
1 AAGGGA-ACACTGTTGGCGGCACCA
11868715 CTCGTGTTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
26 3 0.07
27 42 0.93
ACGTcount: A:0.28, C:0.26, G:0.29, T:0.17
Consensus pattern (27 bp):
AAGGGAACACTGTTGGCGGCACCAAAC
Found at i:11872735 original size:38 final size:38
Alignment explanation
Indices: 11872656--11872851 Score: 231
Period size: 38 Copynumber: 5.2 Consensus size: 38
11872646 NNNNNNNNNN
* * *
11872656 TTTTCTTTTTTTTCCT-TCCTTCCCTCTTC-TT-CTTCT
1 TTTTC-TTTCTTTCCTCTCCTTTCCTTTTCTTTCCTTCT
* * *
11872692 TTTTTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTAT
1 TTTTCTTTCTTTC-C-TCTCCTTTCCTTTTCTTTCCTTCT
11872732 TTTTCTTTCTTTCCTC-CCATTTCCTTTTCTTTCCTTCT
1 TTTTCTTTCTTTCCTCTCC-TTTCCTTTTCTTTCCTTCT
* *
11872770 TTTTCTTTCTTTCCTCCCCTTTCCTTTTCATTCCTTCT
1 TTTTCTTTCTTTCCTCTCCTTTCCTTTTCTTTCCTTCT
* *
11872808 TTTTCTTTCTTTCCTCTCCTTTCCTTTTCCTT-CTTTT
1 TTTTCTTTCTTTCCTCTCCTTTCCTTTTCTTTCCTTCT
11872845 TTTTCTT
1 TTTTCTT
11872852 CGTTTATTTC
Statistics
Matches: 142, Mismatches: 11, Indels: 13
0.86 0.07 0.08
Matches are distributed among these distances:
35 8 0.06
36 5 0.04
37 14 0.10
38 95 0.67
39 5 0.04
40 15 0.11
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.67
Consensus pattern (38 bp):
TTTTCTTTCTTTCCTCTCCTTTCCTTTTCTTTCCTTCT
Found at i:11873052 original size:27 final size:27
Alignment explanation
Indices: 11873016--11873087 Score: 110
Period size: 27 Copynumber: 2.6 Consensus size: 27
11873006 TCTGTTTTTT
11873016 TTTATATATTTTGGTAAAT-AAAAAAA
1 TTTATATATTTTGGTAAATAAAAAAAA
11873042 TTATATATATTTTGGTAAATAAAAAAAA
1 TT-TATATATTTTGGTAAATAAAAAAAA
*
11873070 TTTATAACATTTTGGTAA
1 TTTAT-ATATTTTGGTAA
11873088 TTTTTATTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
26 2 0.05
27 20 0.48
28 20 0.48
ACGTcount: A:0.47, C:0.01, G:0.08, T:0.43
Consensus pattern (27 bp):
TTTATATATTTTGGTAAATAAAAAAAA
Found at i:11882696 original size:45 final size:42
Alignment explanation
Indices: 11882624--11882718 Score: 136
Period size: 45 Copynumber: 2.2 Consensus size: 42
11882614 TAAAACCAAG
*
11882624 ATTTCTTTTAAGATTTTTAATTCTTTATAGCTATATCTTATATTTT
1 ATTT-TTTTAAGATTTTTAATTCTTTATAACTATAT-TT-TA-TTT
*
11882670 ATTTTTTTAAGATTTTTAATTGTTTATAACTATATTTTATTT
1 ATTTTTTTAAGATTTTTAATTCTTTATAACTATATTTTATTT
11882712 ATTTTTT
1 ATTTTTT
11882719 AATAATTTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
42 10 0.21
43 2 0.04
44 2 0.04
45 29 0.62
46 4 0.09
ACGTcount: A:0.26, C:0.05, G:0.04, T:0.64
Consensus pattern (42 bp):
ATTTTTTTAAGATTTTTAATTCTTTATAACTATATTTTATTT
Found at i:11911486 original size:5 final size:5
Alignment explanation
Indices: 11911476--11911510 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
11911466 ACTCTTGGTG
11911476 CTTTT CTTTT CTTTT CTTTT CTTTT GCTTTT -TTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT -CTTTT CTTTT
11911511 TTATATAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
4 4 0.14
5 20 0.69
6 5 0.17
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (5 bp):
CTTTT
Found at i:11931810 original size:42 final size:42
Alignment explanation
Indices: 11931761--11931849 Score: 169
Period size: 42 Copynumber: 2.1 Consensus size: 42
11931751 TTGCCTAGCT
11931761 GTGTGTCACACACAGCTGAGACACACGCCTGTGTCTCTGCCC
1 GTGTGTCACACACAGCTGAGACACACGCCTGTGTCTCTGCCC
*
11931803 GTGTGTCACACACAGCTGAGACACATGCCTGTGTCTCTGCCC
1 GTGTGTCACACACAGCTGAGACACACGCCTGTGTCTCTGCCC
11931845 GTGTG
1 GTGTG
11931850 GACGAAATAG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.18, C:0.33, G:0.26, T:0.24
Consensus pattern (42 bp):
GTGTGTCACACACAGCTGAGACACACGCCTGTGTCTCTGCCC
Found at i:11933932 original size:25 final size:23
Alignment explanation
Indices: 11933855--11933945 Score: 107
Period size: 22 Copynumber: 4.0 Consensus size: 23
11933845 TGCATTAATG
*
11933855 AACAGAGAGCACAGATGTGCTAT
1 AACAGAGAGCACAGACGTGCTAT
*
11933878 -ACAGAGAGCACAGATGTGCTA-
1 AACAGAGAGCACAGACGTGCTAT
*
11933899 AACAGAGAGCACTGACGTGCTAGT
1 AACAGAGAGCACAGACGTGCTA-T
11933923 AATCAGAGAGCACCA-ACGTGCTA
1 AA-CAGAGAGCA-CAGACGTGCTA
11933946 ATAATCATAG
Statistics
Matches: 60, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
22 40 0.67
24 2 0.03
25 17 0.28
26 1 0.02
ACGTcount: A:0.37, C:0.21, G:0.26, T:0.15
Consensus pattern (23 bp):
AACAGAGAGCACAGACGTGCTAT
Found at i:11933957 original size:27 final size:25
Alignment explanation
Indices: 11933901--11933958 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
11933891 ATGTGCTAAA
** *
11933901 CAGAGAGCACTGACGTGCTAGTAAT
1 CAGAGAGCACCAACGTGCTAATAAT
11933926 CAGAGAGCACCAACGTGCTAATAAT
1 CAGAGAGCACCAACGTGCTAATAAT
*
11933951 CATAGAGC
1 CAGAGAGC
11933959 GCGCTAAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.17
Consensus pattern (25 bp):
CAGAGAGCACCAACGTGCTAATAAT
Found at i:11936138 original size:39 final size:40
Alignment explanation
Indices: 11936072--11936152 Score: 146
Period size: 39 Copynumber: 2.0 Consensus size: 40
11936062 CACTTCTTTC
11936072 CTATGAAAGTAGACTCTTTCAGATTTAATTTCATATCTCA
1 CTATGAAAGTAGACTCTTTCAGATTTAATTTCATATCTCA
*
11936112 CTATGAAAGTA-ACTCTTTCAGCTTTAATTTCATATCTCA
1 CTATGAAAGTAGACTCTTTCAGATTTAATTTCATATCTCA
11936151 CT
1 CT
11936153 CAACTTATAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
39 29 0.73
40 11 0.28
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.41
Consensus pattern (40 bp):
CTATGAAAGTAGACTCTTTCAGATTTAATTTCATATCTCA
Found at i:11941060 original size:22 final size:22
Alignment explanation
Indices: 11941032--11941112 Score: 90
Period size: 22 Copynumber: 3.5 Consensus size: 22
11941022 GCACTAATGA
11941032 ACAGAGAGCACTGAAGTGCTAT
1 ACAGAGAGCACTGAAGTGCTAT
* * *
11941054 ACAGAGAGCACAGATGTGCTAA
1 ACAGAGAGCACTGAAGTGCTAT
* *
11941076 ACAGGGAGCACTGACGTGCTAGT
1 ACAGAGAGCACTGAAGTGCTA-T
11941099 AATCAGAGAGCACT
1 -A-CAGAGAGCACT
11941113 AACGTACTAA
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
22 37 0.77
24 1 0.02
25 10 0.21
ACGTcount: A:0.36, C:0.20, G:0.28, T:0.16
Consensus pattern (22 bp):
ACAGAGAGCACTGAAGTGCTAT
Found at i:11941111 original size:25 final size:24
Alignment explanation
Indices: 11941033--11941159 Score: 118
Period size: 25 Copynumber: 5.3 Consensus size: 24
11941023 CACTAATGAA
*
11941033 CAGAGAGCACTGAAGTGCTAT-A-
1 CAGAGAGCACTGACGTGCTATAAT
* *
11941055 CAGAGAGCACAGATGTGCTA-AA-
1 CAGAGAGCACTGACGTGCTATAAT
*
11941077 CAGGGAGCACTGACGTGCTAGTAAT
1 CAGAGAGCACTGACGTGCTA-TAAT
* *
11941102 CAGAGAGCACTAACGTACTAATAAT
1 CAGAGAGCACTGACGTGCT-ATAAT
**
11941127 CAGAGAGCACCAACGTGCTAATAAT
1 CAGAGAGCACTGACGTGCT-ATAAT
*
11941152 TAGAGAGC
1 CAGAGAGC
11941160 GCGCTAAAGT
Statistics
Matches: 89, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
22 36 0.40
24 2 0.02
25 50 0.56
26 1 0.01
ACGTcount: A:0.38, C:0.20, G:0.25, T:0.17
Consensus pattern (24 bp):
CAGAGAGCACTGACGTGCTATAAT
Found at i:11941739 original size:9 final size:9
Alignment explanation
Indices: 11941725--11941780 Score: 60
Period size: 9 Copynumber: 6.1 Consensus size: 9
11941715 TTTGGTTAAA
11941725 AATTACCCG
1 AATTACCCG
11941734 AATTACCCG
1 AATTACCCG
* *
11941743 AATTAACCA
1 AATTACCCG
11941752 AATTA-CCG
1 AATTACCCG
*
11941760 AAAAATACCCG
1 --AATTACCCG
11941771 AATTACCCG
1 AATTACCCG
11941780 A
1 A
11941781 TTTTTTTTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
8 2 0.05
9 30 0.77
10 4 0.10
11 3 0.08
ACGTcount: A:0.43, C:0.29, G:0.09, T:0.20
Consensus pattern (9 bp):
AATTACCCG
Found at i:11942728 original size:5 final size:5
Alignment explanation
Indices: 11942718--11942785 Score: 129
Period size: 5 Copynumber: 13.8 Consensus size: 5
11942708 TTATTTCTTT
11942718 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
11942768 TATAA TAT-A TATAA TATA
1 TATAA TATAA TATAA TATA
11942786 TAACTTAACT
Statistics
Matches: 62, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.06
5 58 0.94
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:11947161 original size:14 final size:14
Alignment explanation
Indices: 11947142--11947172 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
11947132 AATGTATATG
*
11947142 TATATGTAAATACA
1 TATATGTAAAAACA
11947156 TATATGTAAAAACA
1 TATATGTAAAAACA
11947170 TAT
1 TAT
11947173 GTTTTTGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.35
Consensus pattern (14 bp):
TATATGTAAAAACA
Found at i:11947280 original size:75 final size:78
Alignment explanation
Indices: 11947169--11947375 Score: 199
Period size: 80 Copynumber: 2.7 Consensus size: 78
11947159 ATGTAAAAAC
* * * * * *
11947169 ATATGTTTTTGTATTGAGTTTGGGTATAATTTTTATATAAGTTTATATGA-AGTTCGGA-A-ATA
1 ATATGTTTTTGTATTGAATTTAGGTATGA-TATTATATAAGTTTATATGAGA-CTCGAATATATA
11947231 CAAATATA-AT-TGA
64 CAAATATATATATGA
* * * *
11947244 ATATGTTTTTGTGTTAAATTTAGGTATGACTATTATATAAAGTATGTATGAGACTCGAATATATA
1 ATATGTTTTTGTATTGAATTTAGGTATGA-TATTATAT-AAGTTTATATGAGACTCGAATATATA
* *
11947309 CAAATTTATATATGT
64 CAAATATATATATGA
* * *
11947324 ACATGTTTATGTATTGAATTTAGGTATGATAATTATATAAGTTTATGTGAGA
1 ATATGTTTTTGTATTGAATTTAGGTATGAT-ATTATATAAGTTTATATGAGA
11947376 TTCAATTATG
Statistics
Matches: 105, Mismatches: 20, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
75 31 0.30
76 14 0.13
77 2 0.02
78 10 0.10
79 14 0.13
80 34 0.32
ACGTcount: A:0.35, C:0.03, G:0.17, T:0.44
Consensus pattern (78 bp):
ATATGTTTTTGTATTGAATTTAGGTATGATATTATATAAGTTTATATGAGACTCGAATATATACA
AATATATATATGA
Found at i:11947763 original size:41 final size:41
Alignment explanation
Indices: 11947718--11947864 Score: 217
Period size: 41 Copynumber: 3.6 Consensus size: 41
11947708 CAGTGATATG
11947718 TTTCAGACTTTAAGTCTAGCAGGCTTGACGCTGGTGAAACA
1 TTTCAGACTTTAAGTCTAGCAGGCTTGACGCTGGTGAAACA
* * *
11947759 TTTCAGACTTTAACTCTAGCAGGC-TCAAGCCT-GTGAAACA
1 TTTCAGACTTTAAGTCTAGCAGGCTTGACG-CTGGTGAAACA
* *
11947799 TTTCAGACTTTAAGTCTAGCAGGCTTGACGCCGGTAAAACA
1 TTTCAGACTTTAAGTCTAGCAGGCTTGACGCTGGTGAAACA
*
11947840 TTTCAGACTTTATGTCTAGCAGGCT
1 TTTCAGACTTTAAGTCTAGCAGGCT
11947865 AAGTGCCAGT
Statistics
Matches: 94, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
40 35 0.37
41 59 0.63
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (41 bp):
TTTCAGACTTTAAGTCTAGCAGGCTTGACGCTGGTGAAACA
Found at i:11948187 original size:56 final size:56
Alignment explanation
Indices: 11948120--11948232 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
11948110 TTCAGATAGA
11948120 TGTATGTGAGAAATCTATATATGCATTTTGGTAAGTATAAATGTATTTGGTTATAT
1 TGTATGTGAGAAATCTATATATGCATTTTGGTAAGTATAAATGTATTTGGTTATAT
11948176 TGTATGTGAGAAATCTATATATGCATTTTGGTAAGTATAAATGTATTTGGTTATAT
1 TGTATGTGAGAAATCTATATATGCATTTTGGTAAGTATAAATGTATTTGGTTATAT
11948232 T
1 T
11948233 CGTCTAATGT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.32, C:0.04, G:0.19, T:0.45
Consensus pattern (56 bp):
TGTATGTGAGAAATCTATATATGCATTTTGGTAAGTATAAATGTATTTGGTTATAT
Found at i:11951303 original size:24 final size:24
Alignment explanation
Indices: 11951276--11951340 Score: 58
Period size: 25 Copynumber: 2.7 Consensus size: 24
11951266 CAAAAGAGTG
*
11951276 TCCCGTTATTAGCTCTCATGAGCT
1 TCCCGTTATTAGCTCTCACGAGCT
* * * **
11951300 TCCCATTATATGGTTCTTGCGAGCT
1 TCCCGTTAT-TAGCTCTCACGAGCT
*
11951325 TCCCGTTAATAGCTCT
1 TCCCGTTATTAGCTCT
11951341 TTGGAGCATC
Statistics
Matches: 30, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
24 13 0.43
25 17 0.57
ACGTcount: A:0.17, C:0.28, G:0.17, T:0.38
Consensus pattern (24 bp):
TCCCGTTATTAGCTCTCACGAGCT
Found at i:11951347 original size:24 final size:24
Alignment explanation
Indices: 11951276--11951353 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
11951266 CAAAAGAGTG
* *
11951276 TCCCGTTATTAGCTCTCAT-GAGCT
1 TCCCGTTAATAGCTCT-TTGGAGCT
* * *
11951300 TCCCATTATATGGTTC-TTGCGAGCT
1 TCCCGTTA-ATAGCTCTTTG-GAGCT
*
11951325 TCCCGTTAATAGCTCTTTGGAGCA
1 TCCCGTTAATAGCTCTTTGGAGCT
11951349 TCCCG
1 TCCCG
11951354 ATTGGTTGTG
Statistics
Matches: 41, Mismatches: 9, Indels: 8
0.71 0.16 0.14
Matches are distributed among these distances:
23 1 0.02
24 21 0.51
25 19 0.46
ACGTcount: A:0.17, C:0.28, G:0.19, T:0.36
Consensus pattern (24 bp):
TCCCGTTAATAGCTCTTTGGAGCT
Found at i:11951459 original size:27 final size:27
Alignment explanation
Indices: 11951425--11951493 Score: 129
Period size: 27 Copynumber: 2.6 Consensus size: 27
11951415 TGGCTCTTTG
11951425 GAGCTTCTCGATTAAAGGCTCTTTCAT
1 GAGCTTCTCGATTAAAGGCTCTTTCAT
11951452 GAGCTTCTCGATTAAAGGCTCTTTCAT
1 GAGCTTCTCGATTAAAGGCTCTTTCAT
*
11951479 GAGCTTCCCGATTAA
1 GAGCTTCTCGATTAA
11951494 TTGGCTCTCT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (27 bp):
GAGCTTCTCGATTAAAGGCTCTTTCAT
Found at i:11951565 original size:24 final size:26
Alignment explanation
Indices: 11951414--11951562 Score: 121
Period size: 27 Copynumber: 5.8 Consensus size: 26
11951404 GTCCTGATAT
* *
11951414 ATGGCTCTT-TGGAGCTTCTCGATTA
1 ATGGCTCTTCAGGAGCTTCCCGATTA
* * *
11951439 AAGGCTCTTTCATGAGCTTCTCGATTA
1 ATGGCTC-TTCAGGAGCTTCCCGATTA
* *
11951466 AAGGCTCTTTCATGAGCTTCCCGATTA
1 ATGGCTC-TTCAGGAGCTTCCCGATTA
* *
11951493 ATTGGCTC-TCTGGAGCTTCTCGA-TA
1 A-TGGCTCTTCAGGAGCTTCCCGATTA
* * *
11951518 TTGGCTCGT-ATGAGCTTCCCG-TTA
1 ATGGCTCTTCAGGAGCTTCCCGATTA
11951542 ATGGCTCTTC-GGAGCTTCCCG
1 ATGGCTCTTCAGGAGCTTCCCG
11951563 TTACATAGCT
Statistics
Matches: 103, Mismatches: 15, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
24 34 0.33
25 9 0.09
26 14 0.14
27 41 0.40
28 5 0.05
ACGTcount: A:0.17, C:0.25, G:0.23, T:0.36
Consensus pattern (26 bp):
ATGGCTCTTCAGGAGCTTCCCGATTA
Found at i:11951581 original size:25 final size:25
Alignment explanation
Indices: 11951527--11951589 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 25
11951517 ATTGGCTCGT
* *
11951527 ATGAGCTTCCCGTTAATGGCTCTTC
1 ATGAGCTTCCCGTTAATAGCTCTAC
*
11951552 -GGAGCTTCCCGTTACATAGCTC-AC
1 ATGAGCTTCCCGTTA-ATAGCTCTAC
*
11951576 ATGAGCTTCTCGTT
1 ATGAGCTTCCCGTT
11951590 TATGTGTTGT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
24 14 0.45
25 17 0.55
ACGTcount: A:0.17, C:0.29, G:0.21, T:0.33
Consensus pattern (25 bp):
ATGAGCTTCCCGTTAATAGCTCTAC
Found at i:11951584 original size:49 final size:49
Alignment explanation
Indices: 11951476--11951589 Score: 124
Period size: 49 Copynumber: 2.3 Consensus size: 49
11951466 AAGGCTCTTT
* * * *
11951476 CATGAGCTTCCCGATTAATTGGCTCTCTGGAGCTTCTCGATATTGGCTCG
1 CATGAGCTTCCCG-TTAATTGGCTCTCTGGAGCTTCCCGATAATAGCTCA
* *
11951526 TATGAGCTTCCCGTTAA-TGGCTCT-TCGGAGCTTCCCGTTACATAGCTCA
1 CATGAGCTTCCCGTTAATTGGCTCTCT-GGAGCTTCCCGATA-ATAGCTCA
*
11951575 CATGAGCTTCTCGTT
1 CATGAGCTTCCCGTT
11951590 TATGTGTTGT
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
47 1 0.02
48 19 0.35
49 22 0.41
50 12 0.22
ACGTcount: A:0.17, C:0.27, G:0.22, T:0.34
Consensus pattern (49 bp):
CATGAGCTTCCCGTTAATTGGCTCTCTGGAGCTTCCCGATAATAGCTCA
Found at i:11953174 original size:25 final size:26
Alignment explanation
Indices: 11953136--11953190 Score: 87
Period size: 25 Copynumber: 2.2 Consensus size: 26
11953126 TATGTCCATA
*
11953136 CGAG-CATGTAAATGGGAAGCTCTTT
1 CGAGCCATGTAAATGGGAAGCTCTTG
11953161 CGAGCCATGT-AATGGGAAGCTCTTG
1 CGAGCCATGTAAATGGGAAGCTCTTG
11953186 CGAGC
1 CGAGC
11953191 TAATTATCGG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 23 0.82
26 5 0.18
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (26 bp):
CGAGCCATGTAAATGGGAAGCTCTTG
Found at i:11953202 original size:25 final size:25
Alignment explanation
Indices: 11953136--11953207 Score: 78
Period size: 25 Copynumber: 2.9 Consensus size: 25
11953126 TATGTCCATA
*
11953136 CGAGC-ATGTAAATGGGAAGCTCTTT
1 CGAGCAATGT-AATGGGAAGCTCTTG
*
11953161 CGAGCCATGTAATGGGAAGCTCTTG
1 CGAGCAATGTAATGGGAAGCTCTTG
11953186 CGAGCTAAT-T-ATCGGGAAGCTC
1 CGAGC-AATGTAAT-GGGAAGCTC
11953208 ATACGAGCCA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
24 2 0.05
25 34 0.81
26 6 0.14
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.25
Consensus pattern (25 bp):
CGAGCAATGTAATGGGAAGCTCTTG
Found at i:11953214 original size:25 final size:25
Alignment explanation
Indices: 11953170--11953314 Score: 93
Period size: 25 Copynumber: 5.9 Consensus size: 25
11953160 TCGAGCCATG
* ** *
11953170 TAAT-GGGAAGCTCTTGCGAGCTAA
1 TAATCGGGAAGCTCATAAGAGCCAA
* *
11953194 TTATCGGGAAGCTCATACGAGCC-A
1 TAATCGGGAAGCTCATAAGAGCCAA
* *
11953218 TAAACGGGAAGCTCA-AGAGAGCCAC
1 TAATCGGGAAGCTCATA-AGAGCCAA
**
11953243 TAATCGAAAAGCTCATAAGAGCCAA
1 TAATCGGGAAGCTCATAAGAGCCAA
* * *
11953268 -ATATCGGGAAGCTCGTGAGAGCCAT
1 TA-ATCGGGAAGCTCATAAGAGCCAA
* *
11953293 TAAACGAGATA-CTCATAAGAGC
1 TAATCGGGA-AGCTCATAAGAGC
11953315 TAAATAATGG
Statistics
Matches: 93, Mismatches: 21, Indels: 13
0.73 0.17 0.10
Matches are distributed among these distances:
23 1 0.01
24 23 0.25
25 66 0.71
26 3 0.03
ACGTcount: A:0.37, C:0.21, G:0.25, T:0.18
Consensus pattern (25 bp):
TAATCGGGAAGCTCATAAGAGCCAA
Found at i:11953288 original size:50 final size:50
Alignment explanation
Indices: 11953202--11953320 Score: 136
Period size: 50 Copynumber: 2.4 Consensus size: 50
11953192 AATTATCGGG
* *
11953202 AAGCTCATACGAGCCATAA-ACGGGAAGCTCAAGAGAGCCACTAATCGA-A
1 AAGCTCATAAGAGCCA-AATACGGGAAGCTCAAGAGAGCCACTAAACGAGA
** *
11953251 AAGCTCATAAGAGCCAAATATCGGGAAGCTCGTGAGAGCCATTAAACGAGA
1 AAGCTCATAAGAGCCAAATA-CGGGAAGCTCAAGAGAGCCACTAAACGAGA
* *
11953302 TA-CTCATAAGAGCTAAATA
1 AAGCTCATAAGAGCCAAATA
11953321 ATGGAACACT
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
48 2 0.03
49 16 0.27
50 40 0.67
51 2 0.03
ACGTcount: A:0.41, C:0.21, G:0.22, T:0.16
Consensus pattern (50 bp):
AAGCTCATAAGAGCCAAATACGGGAAGCTCAAGAGAGCCACTAAACGAGA
Found at i:11961318 original size:12 final size:12
Alignment explanation
Indices: 11961301--11961325 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11961291 ATAATCTCTT
11961301 TAAAATTAAAAA
1 TAAAATTAAAAA
11961313 TAAAATTAAAAA
1 TAAAATTAAAAA
11961325 T
1 T
11961326 GTAGATATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
TAAAATTAAAAA
Found at i:11963723 original size:16 final size:16
Alignment explanation
Indices: 11963702--11963732 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11963692 TATACCTCAA
*
11963702 TTATACATAAATATAT
1 TTATACAAAAATATAT
11963718 TTATACAAAAATATA
1 TTATACAAAAATATA
11963733 AATTTTAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (16 bp):
TTATACAAAAATATAT
Found at i:11969518 original size:15 final size:17
Alignment explanation
Indices: 11969485--11969519 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
11969475 TTGTTATGTG
11969485 TTTGTTTTATTTAAATA
1 TTTGTTTTATTTAAATA
11969502 TTTGTTTT-TTT-AATA
1 TTTGTTTTATTTAAATA
11969517 TTT
1 TTT
11969520 TATTATACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
16 3 0.17
17 8 0.44
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (17 bp):
TTTGTTTTATTTAAATA
Found at i:11971449 original size:30 final size:30
Alignment explanation
Indices: 11971397--11971472 Score: 75
Period size: 29 Copynumber: 2.5 Consensus size: 30
11971387 GCGTCATGTC
*
11971397 ATTTTATATATTTTTTAATTATTTAATA-AT-
1 ATTTTA-ATAATTTTTAATTA-TTAATACATA
*
11971427 ATTTTAATAATTTTTATGTTATTAATACATA
1 ATTTTAATAATTTTTA-ATTATTAATACATA
**
11971458 ATTTTGGTAATTTTT
1 ATTTTAATAATTTTT
11971473 TTTACCTAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
29 15 0.38
30 11 0.28
31 13 0.33
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.61
Consensus pattern (30 bp):
ATTTTAATAATTTTTAATTATTAATACATA
Found at i:11977247 original size:173 final size:174
Alignment explanation
Indices: 11977042--11977389 Score: 689
Period size: 173 Copynumber: 2.0 Consensus size: 174
11977032 AAAAATAAAT
11977042 ACTTGAATATAATATAAAAATATACAATTATTTTATTCTATAAAAAAATACTTTAAGTGATATAA
1 ACTTGAATATAATATAAAAATATACAATTATTTTATTCTATAAAAAAATACTTTAAGTGATATAA
11977107 TATTATTTAATAATTCTGCACTACTCTAAGTATATATATATTTTTTGTAAAAAGGCTAACTACTC
66 TATTATTTAATAATTCTGCACTACTCTAAGTATATATATATTTTTTGTAAAAAGGCTAACTACTC
11977172 AACAAATCTTCAATTTTTTAATGTAACAAGTTGCAAATAGTGAC
131 AACAAATCTTCAATTTTTTAATGTAACAAGTTGCAAATAGTGAC
11977216 ACTTGAATAT-ATATAAAAATATACAATTATTTTATTCTATAAAAAAATACTTTAAGTGATATAA
1 ACTTGAATATAATATAAAAATATACAATTATTTTATTCTATAAAAAAATACTTTAAGTGATATAA
11977280 TATTATTTAATAATTCTGCACTACTCTAAGTATATATATATTTTTTGTAAAAAGGCTAACTACTC
66 TATTATTTAATAATTCTGCACTACTCTAAGTATATATATATTTTTTGTAAAAAGGCTAACTACTC
11977345 AACAAATCTTCAATTTTTTAATGTAACAAGTTGCAAATAGTGAC
131 AACAAATCTTCAATTTTTTAATGTAACAAGTTGCAAATAGTGAC
11977389 A
1 A
11977390 TGTTAGGAAA
Statistics
Matches: 174, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
173 164 0.94
174 10 0.06
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.39
Consensus pattern (174 bp):
ACTTGAATATAATATAAAAATATACAATTATTTTATTCTATAAAAAAATACTTTAAGTGATATAA
TATTATTTAATAATTCTGCACTACTCTAAGTATATATATATTTTTTGTAAAAAGGCTAACTACTC
AACAAATCTTCAATTTTTTAATGTAACAAGTTGCAAATAGTGAC
Found at i:11977915 original size:6 final size:6
Alignment explanation
Indices: 11977904--11977932 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
11977894 GTTGAAATAA
11977904 ATTTGG ATTTGG ATTTGG ATTTGG ATTTG
1 ATTTGG ATTTGG ATTTGG ATTTGG ATTTG
11977933 TAAATGTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.31, T:0.52
Consensus pattern (6 bp):
ATTTGG
Found at i:11981960 original size:2 final size:2
Alignment explanation
Indices: 11981955--11981991 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
11981945 ATGCACACAC
11981955 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
11981992 ATGTACCATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:11982474 original size:3 final size:3
Alignment explanation
Indices: 11982466--11982490 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
11982456 AGAGACAGAG
11982466 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
11982491 CCTCCAATGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:11989369 original size:30 final size:30
Alignment explanation
Indices: 11989307--11989368 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
11989297 TTTTTATTGG
* * *
11989307 AACATTTTTATATTAATTAATTATGAAAAA
1 AACATGTTTATATTAAATAATAATGAAAAA
*
11989337 AACATGTTTATATTAAATATATAATGAGAAA
1 AACATGTTTATATTAAATA-ATAATGAAAAA
11989368 A
1 A
11989369 CCTTTTTTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 17 0.63
31 10 0.37
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (30 bp):
AACATGTTTATATTAAATAATAATGAAAAA
Found at i:11995908 original size:124 final size:124
Alignment explanation
Indices: 11995688--11995953 Score: 399
Period size: 124 Copynumber: 2.1 Consensus size: 124
11995678 CCACGAGGGC
* *
11995688 GCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCCTACATGACCAATTGTAGCG
1 GCGATTTGACACTATTTGCTAAGAAACGTCAAAAAAAATTATTTCCTACATGACCAACTGTAGCG
* * * **
11995753 AAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCATATAGCATCCTGGTATCA
66 AAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
* * * *
11995812 GCGATTTTATACTATTTGCTAAGAAAACGTCAAAAAAAATTATTTCTTGCATGACC-ACTGTAGC
1 GCGATTTGACACTATTTGCTAAG-AAACGTCAAAAAAAATTATTTCCTACATGACCAACTGTAGC
11995876 GAAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
65 GAAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
**
11995936 GCGATTTCCCACTATTTG
1 GCGATTTGACACTATTTG
11995954 ACCAGATACG
Statistics
Matches: 127, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
124 97 0.76
125 30 0.24
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.30
Consensus pattern (124 bp):
GCGATTTGACACTATTTGCTAAGAAACGTCAAAAAAAATTATTTCCTACATGACCAACTGTAGCG
AAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
Found at i:12012322 original size:30 final size:30
Alignment explanation
Indices: 12012260--12012321 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
12012250 TTTTTATTGG
* * *
12012260 AACATTTTTATATTAATTAATTATGAAAAA
1 AACATGTTTATATTAAATAATAATGAAAAA
*
12012290 AACATGTTTATATTAAATATATAATGAGAAA
1 AACATGTTTATATTAAATA-ATAATGAAAAA
12012321 A
1 A
12012322 CCTTTTTTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 17 0.63
31 10 0.37
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (30 bp):
AACATGTTTATATTAAATAATAATGAAAAA
Found at i:12012535 original size:10 final size:10
Alignment explanation
Indices: 12012520--12012544 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
12012510 TAACCCTTCA
12012520 TATATATATT
1 TATATATATT
12012530 TATATATATT
1 TATATATATT
12012540 TATAT
1 TATAT
12012545 TAATTACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TATATATATT
Found at i:12015917 original size:22 final size:22
Alignment explanation
Indices: 12015892--12015961 Score: 122
Period size: 22 Copynumber: 3.2 Consensus size: 22
12015882 AAATTCAATA
12015892 TCAATTTCCTTCAAAAATTCTC
1 TCAATTTCCTTCAAAAATTCTC
*
12015914 TCAATTCCCTTCAAAAATTCTC
1 TCAATTTCCTTCAAAAATTCTC
*
12015936 TCAATTTCCTTCCAAAATTCTC
1 TCAATTTCCTTCAAAAATTCTC
12015958 TCAA
1 TCAA
12015962 ACTCTCAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.31, C:0.30, G:0.00, T:0.39
Consensus pattern (22 bp):
TCAATTTCCTTCAAAAATTCTC
Found at i:12015968 original size:52 final size:51
Alignment explanation
Indices: 12015911--12016013 Score: 136
Period size: 52 Copynumber: 2.0 Consensus size: 51
12015901 TTCAAAAATT
* * *
12015911 CTCTC-AATTCCCTTCAAAAATTCTCTCAATTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAAATTCCCTTC-AAAATCCTCTCAATTTCCTTCAAAAAATCTC-CAAA
* *
12015963 CTCTCAAATTCCTTTCAAAATCCTTTCAATTTCCTTCAAAAAATCTCCAAA
1 CTCTCAAATTCCCTTCAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
12016014 TCCATATTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
51 4 0.09
52 32 0.71
53 9 0.20
ACGTcount: A:0.33, C:0.31, G:0.00, T:0.36
Consensus pattern (51 bp):
CTCTCAAATTCCCTTCAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
Found at i:12016102 original size:30 final size:30
Alignment explanation
Indices: 12016046--12016102 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
12016036 ATTAAATTTC
*
12016046 ATTTTTTTAAGAAAATTTTAATTTTTTTTT
1 ATTTTTTTAAGAAAATTTTAAATTTTTTTT
* *
12016076 ATTTTTTTAA-ATAATTTTAAAATTTTT
1 ATTTTTTTAAGAAAATTTTAAATTTTTT
12016103 AATATTTTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 14 0.58
30 10 0.42
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (30 bp):
ATTTTTTTAAGAAAATTTTAAATTTTTTTT
Found at i:12016109 original size:30 final size:30
Alignment explanation
Indices: 12016046--12016110 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
12016036 ATTAAATTTC
* **
12016046 ATTTTTTTAAGAAAATTTTAATTTTTTTTT
1 ATTTTTTTAAGAAAATTTTAAATTTTTAAT
*
12016076 ATTTTTTTAA-ATAATTTTAAAATTTTTAAT
1 ATTTTTTTAAGAAAATTTT-AAATTTTTAAT
12016106 ATTTT
1 ATTTT
12016111 CAACAATGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 7 0.23
30 23 0.77
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.65
Consensus pattern (30 bp):
ATTTTTTTAAGAAAATTTTAAATTTTTAAT
Found at i:12017635 original size:18 final size:18
Alignment explanation
Indices: 12017602--12017636 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12017592 AGGTATGTTT
* *
12017602 CCTAACCCTTATATGTAC
1 CCTAACCCGTACATGTAC
12017620 CCTAACCCGTACATGTA
1 CCTAACCCGTACATGTA
12017637 TCCTTTTTCG
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:0.29, C:0.34, G:0.09, T:0.29
Consensus pattern (18 bp):
CCTAACCCGTACATGTAC
Found at i:12018143 original size:29 final size:29
Alignment explanation
Indices: 12018101--12018170 Score: 122
Period size: 29 Copynumber: 2.4 Consensus size: 29
12018091 TTTTGACATT
*
12018101 ATTTGATTAAAAACCCTAACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
*
12018130 ATTTAGTTAAAAACCCTAACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
12018159 ATTTAATTAAAA
1 ATTTAATTAAAA
12018171 TTNNNNNNNN
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.44, C:0.23, G:0.03, T:0.30
Consensus pattern (29 bp):
ATTTAATTAAAAACCCTAACCCTAACCTA
Found at i:12022500 original size:28 final size:28
Alignment explanation
Indices: 12022461--12022615 Score: 178
Period size: 29 Copynumber: 5.6 Consensus size: 28
12022451 NNNNNNNTAT
*
12022461 TTTAATTAAAAACCCTAACCTAATTTAA
1 TTTAATTAAAAACCCTAACCTAACTTAA
* *
12022489 TTTAATTAAAAACCCTAACCCTAACCTAT
1 TTTAATTAAAAACCCTAA-CCTAACTTAA
* * *
12022518 TTTACA-TGAAAACCCTAACCCTAACATAT
1 TTTA-ATTAAAAACCCTAA-CCTAACTTAA
*
12022547 TTTAATTAAAATCCCTAACCTAAC----
1 TTTAATTAAAAACCCTAACCTAACTTAA
12022571 -TTAATTAAAAACCCTAACCTAACTTAA
1 TTTAATTAAAAACCCTAACCTAACTTAA
12022598 TTTAATTAAAAACCCTAA
1 TTTAATTAAAAACCCTAA
12022616 TTTAATTAAA
Statistics
Matches: 111, Mismatches: 8, Indels: 16
0.82 0.06 0.12
Matches are distributed among these distances:
23 22 0.20
28 42 0.38
29 46 0.41
30 1 0.01
ACGTcount: A:0.45, C:0.23, G:0.01, T:0.32
Consensus pattern (28 bp):
TTTAATTAAAAACCCTAACCTAACTTAA
Found at i:12022562 original size:23 final size:23
Alignment explanation
Indices: 12022534--12022599 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
12022524 TGAAAACCCT
**
12022534 AACCCTAACATATTTTAATTAAA
1 AACCCTAACATAACTTAATTAAA
* *
12022557 ATCCCTAACCTAACTTAATTAAA
1 AACCCTAACATAACTTAATTAAA
*
12022580 AACCCTAACCTAACTTAATT
1 AACCCTAACATAACTTAATT
12022600 TAATTAAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (23 bp):
AACCCTAACATAACTTAATTAAA
Done.