Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 80 of 226
Found at i:29091630 original size:15 final size:15
Alignment explanation
Indices: 29091573--29091636 Score: 51
Period size: 15 Copynumber: 4.4 Consensus size: 15
29091563 CTTTAATTTT
* *
29091573 TAAAATAATAAAATT
1 TAAAATATTAAAATA
* *
29091588 TTAAATTTTAAAA-A
1 TAAAATATTAAAATA
* *
29091602 -AAATTATAAAAATA
1 TAAAATATTAAAATA
29091616 TAAAATATTAAAATA
1 TAAAATATTAAAATA
*
29091631 TTAAAT
1 TAAAAT
29091637 TGCATTTTAA
Statistics
Matches: 36, Mismatches: 11, Indels: 4
0.71 0.22 0.08
Matches are distributed among these distances:
13 8 0.22
14 1 0.03
15 27 0.75
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
TAAAATATTAAAATA
Found at i:29093479 original size:141 final size:141
Alignment explanation
Indices: 29093225--29093506 Score: 546
Period size: 141 Copynumber: 2.0 Consensus size: 141
29093215 AATTATTTTT
29093225 ATCTTGAGCTACAGAACTCTAAATTAGGATCCGCTAATTTTCCCTAAAACTAGACTTACATATAT
1 ATCTTGAGCTACAGAACTCTAAATTAGGATCCGCTAATTTTCCCTAAAACTAGACTTACATATAT
29093290 TCTTACCATAAAATTTTCAAAATTTTTGGTTTAGCCAATAAGTACAGTTTATTCTTTAAAGTCAC
66 TCTTACCATAAAATTTTCAAAATTTTTGGTTTAGCCAATAAGTACAGTTTATTCTTTAAAGTCAC
29093355 CTCTGTTCTGC
131 CTCTGTTCTGC
29093366 ATCTTGAGCTACAGAACTCTAAATTAGGATCCGCTAATTTTCCCTAAAACTAGACTTACATATAT
1 ATCTTGAGCTACAGAACTCTAAATTAGGATCCGCTAATTTTCCCTAAAACTAGACTTACATATAT
* *
29093431 TCTTACCATAAAATTTTCAAAATTTTTGGTTTAGTCAATAAGTGCAGTTTATTCTTTAAAGTCAC
66 TCTTACCATAAAATTTTCAAAATTTTTGGTTTAGCCAATAAGTACAGTTTATTCTTTAAAGTCAC
29093496 CTCTGTTCTGC
131 CTCTGTTCTGC
29093507 TGTCTAACAG
Statistics
Matches: 139, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
141 139 1.00
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.38
Consensus pattern (141 bp):
ATCTTGAGCTACAGAACTCTAAATTAGGATCCGCTAATTTTCCCTAAAACTAGACTTACATATAT
TCTTACCATAAAATTTTCAAAATTTTTGGTTTAGCCAATAAGTACAGTTTATTCTTTAAAGTCAC
CTCTGTTCTGC
Found at i:29098105 original size:22 final size:23
Alignment explanation
Indices: 29098056--29098105 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
29098046 AAACTTGAAT
*
29098056 TATAAATTTTTAAAAATAAAGAA
1 TATAAATTCTTAAAAATAAAGAA
*
29098079 T-TAAATTCTTAAAAATAGA-AA
1 TATAAATTCTTAAAAATAAAGAA
29098100 TATAAA
1 TATAAA
29098106 AATTAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 3 0.12
22 20 0.83
23 1 0.04
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (23 bp):
TATAAATTCTTAAAAATAAAGAA
Found at i:29108219 original size:69 final size:67
Alignment explanation
Indices: 29108078--29108207 Score: 152
Period size: 69 Copynumber: 1.9 Consensus size: 67
29108068 GATTTCGAAT
* * * * ** *
29108078 TGTCCCAACCTCCAATCCATGCCCCCAACATGCTTCCACGCTCTCTTTCTTATTTGTGGATCGGA
1 TGTCCCAACCTCCAATCCATGCCCCAAACATGCTCCCACCCTCTCTTTCTCATTTGTACATAGGA
29108143 AG
66 AG
* * *
29108145 TTGTCCCAAGCTCCAATCCATGTCGCCAAACATGCTCCCTCCCTCTCTTTCTCATTTGTACAT
1 -TGTCCCAACCTCCAATCCATG-CCCCAAACATGCTCCCACCCTCTCTTTCTCATTTGTACAT
29108208 TAGTGAATGT
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
68 20 0.38
69 32 0.62
ACGTcount: A:0.19, C:0.37, G:0.12, T:0.32
Consensus pattern (67 bp):
TGTCCCAACCTCCAATCCATGCCCCAAACATGCTCCCACCCTCTCTTTCTCATTTGTACATAGGA
AG
Found at i:29112452 original size:22 final size:22
Alignment explanation
Indices: 29112426--29112471 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
29112416 TTGGGTTTTG
*
29112426 TTTGAAGAGAAAAATATTGGGT
1 TTTGAAGAGAAAAATAATGGGT
* *
29112448 TTTGATGAGAAAATTAATGGGT
1 TTTGAAGAGAAAAATAATGGGT
29112470 TT
1 TT
29112472 GGAGGGAACT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.26, T:0.37
Consensus pattern (22 bp):
TTTGAAGAGAAAAATAATGGGT
Found at i:29117366 original size:18 final size:18
Alignment explanation
Indices: 29117333--29117367 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29117323 TGGAAAGGTC
*
29117333 ATATATATATGTATGTAT
1 ATATATATATGCATGTAT
*
29117351 ATATATATTTGCATGTA
1 ATATATATATGCATGTA
29117368 CAAGGAAAGA
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:0.37, C:0.03, G:0.11, T:0.49
Consensus pattern (18 bp):
ATATATATATGCATGTAT
Found at i:29121240 original size:38 final size:38
Alignment explanation
Indices: 29121187--29121263 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
29121177 GGTTGAGGAA
29121187 AGGGAAAAAAAAGCAATTACTTTACCAAAATGGATCCC
1 AGGGAAAAAAAAGCAATTACTTTACCAAAATGGATCCC
*
29121225 AGGGAAAAAAGAGCAATTACTTTACCAAAATGGATCCC
1 AGGGAAAAAAAAGCAATTACTTTACCAAAATGGATCCC
29121263 A
1 A
29121264 ATACAAGAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.47, C:0.18, G:0.17, T:0.18
Consensus pattern (38 bp):
AGGGAAAAAAAAGCAATTACTTTACCAAAATGGATCCC
Found at i:29124161 original size:14 final size:14
Alignment explanation
Indices: 29124128--29124165 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
29124118 GGATTTTGTA
29124128 TTTTA-TTTTAATT
1 TTTTATTTTTAATT
*
29124141 TAATTATTTTTAATT
1 T-TTTATTTTTAATT
29124156 TTTTATTTTT
1 TTTTATTTTT
29124166 CGAATTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
13 1 0.05
14 11 0.52
15 9 0.43
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTATTTTTAATT
Found at i:29124224 original size:30 final size:30
Alignment explanation
Indices: 29124188--29124244 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
29124178 TTTTAGCTCT
*
29124188 AAATAAATTATATTTATTAAATTCATTAAA
1 AAATAAATGATATTTATTAAATTCATTAAA
*
29124218 AAATAAATGGTATTTATTAAATTCATT
1 AAATAAATGATATTTATTAAATTCATT
29124245 GAATTAAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.44
Consensus pattern (30 bp):
AAATAAATGATATTTATTAAATTCATTAAA
Found at i:29126055 original size:10 final size:10
Alignment explanation
Indices: 29126037--29126101 Score: 51
Period size: 11 Copynumber: 6.3 Consensus size: 10
29126027 AAAAAAACAT
29126037 AATTGTTTAAA
1 AATT-TTTAAA
29126048 AATTTTTAAAA
1 AATTTTT-AAA
*
29126059 AATTTATAAA
1 AATTTTTAAA
* *
29126069 AATTATTAGA
1 AATTTTTAAA
*
29126079 AA-TTGTAAA
1 AATTTTTAAA
*
29126088 ATATTATTAAA
1 A-ATTTTTAAA
29126099 AAT
1 AAT
29126102 AGTAAAAATT
Statistics
Matches: 42, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
9 5 0.12
10 18 0.43
11 19 0.45
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.42
Consensus pattern (10 bp):
AATTTTTAAA
Found at i:29126081 original size:20 final size:21
Alignment explanation
Indices: 29126037--29126109 Score: 71
Period size: 20 Copynumber: 3.6 Consensus size: 21
29126027 AAAAAAACAT
* *
29126037 AATTGTTTAAAAATTTTTAAAA
1 AATTGTATAAAAATTATT-AAA
*
29126059 AATT-TATAAAAATTATTAGA
1 AATTGTATAAAAATTATTAAA
*
29126079 AATTGTA-AAATATTATTAAA
1 AATTGTATAAAAATTATTAAA
*
29126099 AATAGTA-AAAA
1 AATTGTATAAAA
29126110 TTGTTATTGG
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 26 0.60
21 13 0.30
22 4 0.09
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (21 bp):
AATTGTATAAAAATTATTAAA
Found at i:29126110 original size:29 final size:28
Alignment explanation
Indices: 29126057--29126113 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
29126047 AAATTTTTAA
* *
29126057 AAAATTTATAAAAATTATTAGAAATTGT
1 AAAATTTATAAAAATTAGTAAAAATTGT
29126085 AAAATATTATTAAAAA-TAGTAAAAATTGT
1 AAAAT-TTA-TAAAAATTAGTAAAAATTGT
29126114 TATTGGATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 5 0.20
29 14 0.56
30 6 0.24
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (28 bp):
AAAATTTATAAAAATTAGTAAAAATTGT
Found at i:29126359 original size:16 final size:15
Alignment explanation
Indices: 29126313--29126360 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 15
29126303 CATTTTTCTA
29126313 ATTTTTAGTAATTTTT
1 ATTTTT-GTAATTTTT
*
29126329 ATATTTTATATATTTTGT
1 AT-TTTTGTA-ATTTT-T
29126347 ATTTTTGTAATTTT
1 ATTTTTGTAATTTT
29126361 AAAAGATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
16 9 0.33
17 15 0.56
18 3 0.11
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (15 bp):
ATTTTTGTAATTTTT
Found at i:29127367 original size:13 final size:14
Alignment explanation
Indices: 29127349--29127377 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
29127339 CCAAAAATAA
29127349 TTTTATT-TTTATT
1 TTTTATTGTTTATT
29127362 TTTTATTGTTTATT
1 TTTTATTGTTTATT
29127376 TT
1 TT
29127378 GGGTTTGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.83
Consensus pattern (14 bp):
TTTTATTGTTTATT
Found at i:29127644 original size:2 final size:2
Alignment explanation
Indices: 29127637--29127679 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
29127627 GATTTATTTA
29127637 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29127679 A
1 A
29127680 AAGTTCTTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29133373 original size:14 final size:15
Alignment explanation
Indices: 29133354--29133382 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
29133344 GGGATTTTTC
29133354 TATATAT-ATATTTG
1 TATATATGATATTTG
29133368 TATATATGATATTTG
1 TATATATGATATTTG
29133383 AATAAACATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (15 bp):
TATATATGATATTTG
Found at i:29142794 original size:4 final size:4
Alignment explanation
Indices: 29142787--29142811 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
29142777 TAAGTATCTG
29142787 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
29142812 ATAGTACATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:29148604 original size:5 final size:5
Alignment explanation
Indices: 29148596--29148622 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
29148586 ATTATTTGAT
29148596 TTAAA TTAAA TTAAA TTAAA TTAAA TT
1 TTAAA TTAAA TTAAA TTAAA TTAAA TT
29148623 TTTTTAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (5 bp):
TTAAA
Found at i:29154292 original size:32 final size:32
Alignment explanation
Indices: 29154248--29154311 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
29154238 TTAAGTTAGT
29154248 TAAGTTATAATTTATTTAGATCAAGAACGGAA
1 TAAGTTATAATTTATTTAGATCAAGAACGGAA
29154280 TAAGTT-TGAATTTATTTAGATCAAGAACGGAA
1 TAAGTTAT-AATTTATTTAGATCAAGAACGGAA
29154312 GAAAACAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 1 0.03
32 30 0.97
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.34
Consensus pattern (32 bp):
TAAGTTATAATTTATTTAGATCAAGAACGGAA
Found at i:29154323 original size:32 final size:32
Alignment explanation
Indices: 29154256--29154323 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
29154246 GTTAAGTTAT
* ****
29154256 AATTTATTTAGATCAAGAACGGAATAAGTTTG
1 AATTTATTTAGATCAAGAACGGAAGAAAACAG
29154288 AATTTATTTAGATCAAGAACGGAAGAAAACAG
1 AATTTATTTAGATCAAGAACGGAAGAAAACAG
29154320 AATT
1 AATT
29154324 ATATCGGGGG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.46, C:0.07, G:0.18, T:0.29
Consensus pattern (32 bp):
AATTTATTTAGATCAAGAACGGAAGAAAACAG
Found at i:29156125 original size:15 final size:15
Alignment explanation
Indices: 29156105--29156133 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
29156095 ACGTATTTTC
29156105 TTCATTCAATTCAAT
1 TTCATTCAATTCAAT
29156120 TTCATTCAATTCAA
1 TTCATTCAATTCAA
29156134 ATCACTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (15 bp):
TTCATTCAATTCAAT
Found at i:29156923 original size:16 final size:17
Alignment explanation
Indices: 29156896--29156928 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
29156886 TTGTTTATTA
29156896 TTTAATAGATATAATAT
1 TTTAATAGATATAATAT
29156913 TTTAATA-ATATAATAT
1 TTTAATAGATATAATAT
29156929 AATAATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
TTTAATAGATATAATAT
Found at i:29156934 original size:16 final size:17
Alignment explanation
Indices: 29156898--29156935 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
29156888 GTTTATTATT
**
29156898 TAATAGATATAATATTT
1 TAATAGATATAATATAA
29156915 TAATA-ATATAATATAA
1 TAATAGATATAATATAA
29156931 TAATA
1 TAATA
29156936 TTTTATTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
TAATAGATATAATATAA
Found at i:29157479 original size:43 final size:43
Alignment explanation
Indices: 29157384--29157491 Score: 121
Period size: 43 Copynumber: 2.5 Consensus size: 43
29157374 GCGTCATTAC
* * *
29157384 ACCACGTCTGGGACGTTGGCATCGATTTGTGTTTACATGTAAG
1 ACCACGTCTGGGACGTTGGCATCGATATGTGATTACACGTAAG
* *
29157427 AGCC-TGTCTGGGACAG-TGGCATCGATATGTGATTACACGTAAT
1 A-CCACGTCTGGGAC-GTTGGCATCGATATGTGATTACACGTAAG
* *
29157470 ACCACGTCTGGAATGTTGGCAT
1 ACCACGTCTGGGACGTTGGCAT
29157492 TGTACGAGCC
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
42 3 0.06
43 47 0.89
44 3 0.06
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (43 bp):
ACCACGTCTGGGACGTTGGCATCGATATGTGATTACACGTAAG
Found at i:29163480 original size:18 final size:18
Alignment explanation
Indices: 29163459--29163496 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
29163449 AAACAATTCA
*
29163459 ATTTATCACATACCATAT
1 ATTTATCACATAACATAT
29163477 ATTTATCACATAACATAT
1 ATTTATCACATAACATAT
29163495 AT
1 AT
29163497 ATATTAACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.39
Consensus pattern (18 bp):
ATTTATCACATAACATAT
Found at i:29166598 original size:14 final size:14
Alignment explanation
Indices: 29166579--29166605 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29166569 AGAAGAGAAC
29166579 GAAAAAAAAGAAAA
1 GAAAAAAAAGAAAA
29166593 GAAAAAAAAGAAA
1 GAAAAAAAAGAAA
29166606 GTTCAAAGAA
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:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (14 bp):
GAAAAAAAAGAAAA
Found at i:29168798 original size:11 final size:11
Alignment explanation
Indices: 29168782--29168811 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
29168772 CATTATTTAT
29168782 TAAATAAAATA
1 TAAATAAAATA
29168793 TAAATAAAATA
1 TAAATAAAATA
29168804 TAATATAA
1 TAA-ATAA
29168812 TTAAGACTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
TAAATAAAATA
Found at i:29178323 original size:21 final size:21
Alignment explanation
Indices: 29178297--29178355 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
29178287 CACCATTGTT
*
29178297 TTTAATCTCATTGCTACAGTA
1 TTTAATCTCATCGCTACAGTA
* *
29178318 TTTAATCTCACCGCTATAGTA
1 TTTAATCTCATCGCTACAGTA
**
29178339 ACTAATCTCATCGCTAC
1 TTTAATCTCATCGCTAC
29178356 CGCTGTTTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.37
Consensus pattern (21 bp):
TTTAATCTCATCGCTACAGTA
Found at i:29186069 original size:103 final size:103
Alignment explanation
Indices: 29185890--29186096 Score: 333
Period size: 103 Copynumber: 2.0 Consensus size: 103
29185880 TCTATAGATA
* **
29185890 TATAAAGAAGGGTAAATTATAAAAATAGTCACTTTTGTTTATTTCAGATTACATTTTAGTCATTT
1 TATAAAAAAGGGTAAATTATAAAAATAGTCACTTTTGTTTACCTCAGATTACATTTTAGTCATTT
*
29185955 ATGTTTGAAATGTTATGTTTTAGTCACTTACATTATCG
66 ATGTTTAAAATGTTATGTTTTAGTCACTTACATTATCG
* * *
29185993 TATAAAAAAGGGTAAATTGTGAAAATAGTCACTTTTGTTTGCCTCAGATTACATTTTAGTCATTT
1 TATAAAAAAGGGTAAATTATAAAAATAGTCACTTTTGTTTACCTCAGATTACATTTTAGTCATTT
**
29186058 ATGTTTAAAATGTTATGTTTTAGTCACTTATGTTATCG
66 ATGTTTAAAATGTTATGTTTTAGTCACTTACATTATCG
29186096 T
1 T
29186097 TTTGTTACGA
Statistics
Matches: 95, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
103 95 1.00
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.44
Consensus pattern (103 bp):
TATAAAAAAGGGTAAATTATAAAAATAGTCACTTTTGTTTACCTCAGATTACATTTTAGTCATTT
ATGTTTAAAATGTTATGTTTTAGTCACTTACATTATCG
Found at i:29187062 original size:22 final size:21
Alignment explanation
Indices: 29187036--29187080 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
29187026 TGGATGGTAC
29187036 ATTTTTTGTGA-ATATTATTTAA
1 ATTTTTT-TGATATATT-TTTAA
*
29187058 ATTTTTTTTATATATTTTTAA
1 ATTTTTTTGATATATTTTTAA
29187079 AT
1 AT
29187081 GATTTATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (21 bp):
ATTTTTTTGATATATTTTTAA
Found at i:29187063 original size:21 final size:21
Alignment explanation
Indices: 29187038--29187080 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
29187028 GATGGTACAT
29187038 TTTTTGTGA-ATATTATTTAAA
1 TTTTTGTGATATATT-TTTAAA
* *
29187059 TTTTTTTTATATATTTTTAAA
1 TTTTTGTGATATATTTTTAAA
29187080 T
1 T
29187081 GATTTATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (21 bp):
TTTTTGTGATATATTTTTAAA
Found at i:29188755 original size:3 final size:3
Alignment explanation
Indices: 29188735--29188777 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
29188725 AAAACGACAG
* *
29188735 AGA AGG AGA AGG AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
29188778 ATGGACACAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:29191212 original size:18 final size:19
Alignment explanation
Indices: 29191189--29191237 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
29191179 GTTGTAAAGT
*
29191189 TTTATTTTTATTTATTTA-
1 TTTATTTTTATTTACTTAG
29191207 TTTATTTATT-TTTACTTAG
1 TTTATTT-TTATTTACTTAG
29191226 TTTAATTTTTAT
1 TTT-ATTTTTAT
29191238 GTAAATATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 14 0.54
19 7 0.27
20 5 0.19
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTATTTTTATTTACTTAG
Found at i:29191217 original size:22 final size:22
Alignment explanation
Indices: 29191188--29191237 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
29191178 AGTTGTAAAG
* *
29191188 TTTTATTTTTATTTA-TTTATT
1 TTTTATTTTTACTTAGTTTAAT
29191209 TATTTATTTTTACTTAGTTTAAT
1 T-TTTATTTTTACTTAGTTTAAT
29191232 TTTTAT
1 TTTTAT
29191238 GTAAATATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 18 0.72
23 6 0.24
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTATTTTTACTTAGTTTAAT
Found at i:29193223 original size:18 final size:19
Alignment explanation
Indices: 29193200--29193238 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
29193190 TATTAAATAC
29193200 AATATATAAAATTT-TTAA
1 AATATATAAAATTTATTAA
* *
29193218 AATATATTATATTTATTAA
1 AATATATAAAATTTATTAA
29193237 AA
1 AA
29193239 ATCATATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AATATATAAAATTTATTAA
Found at i:29194088 original size:31 final size:29
Alignment explanation
Indices: 29194024--29194089 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
29194014 ATGATAACGT
* *
29194024 AAGTGACTAAAATGTAACATATCAAACAC
1 AAGTGACTAAAATGTAACATAACAAACAA
29194053 AAGTGACTAAAATGTAATC-TAAGACAAACAA
1 AAGTGACTAAAATGTAA-CAT-A-ACAAACAA
29194084 AAGTGA
1 AAGTGA
29194090 TTATTTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 18 0.56
30 2 0.06
31 12 0.38
ACGTcount: A:0.53, C:0.14, G:0.14, T:0.20
Consensus pattern (29 bp):
AAGTGACTAAAATGTAACATAACAAACAA
Found at i:29194687 original size:32 final size:35
Alignment explanation
Indices: 29194634--29194706 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 35
29194624 TTATTATAAA
* *
29194634 ATAA-ATTTTGATTGTTAAAAGAA-AAT-TATATT
1 ATAATATTTTGATTGTTAAAAGAATAATATAAAAT
29194666 ATAATATTTTG-TT-TTACAAAGAATAATATAAAAT
1 ATAATATTTTGATTGTTA-AAAGAATAATATAAAAT
29194700 ATAATAT
1 ATAATAT
29194707 ATAAAATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
31 3 0.09
32 12 0.34
33 9 0.26
34 11 0.31
ACGTcount: A:0.49, C:0.01, G:0.07, T:0.42
Consensus pattern (35 bp):
ATAATATTTTGATTGTTAAAAGAATAATATAAAAT
Found at i:29195529 original size:42 final size:41
Alignment explanation
Indices: 29195471--29195605 Score: 148
Period size: 42 Copynumber: 3.2 Consensus size: 41
29195461 TAGATGTTAC
* *
29195471 TTAGTATTATTGTTAGTAAAAAACTAATATTATTATTATGG
1 TTAGTATTATTTTTAGTAAAAAACTAATATTATTGTTATGG
**
29195512 TTAGTTATTATTTTTAGTAAAACCCTAATTATTATTGTTA--G
1 TTAG-TATTATTTTTAGTAAAAAACTAA-TATTATTGTTATGG
* * *
29195553 TTAGTATTATTTTGAGTATAAAACTATTATTATTGTTATTGTG
1 TTAGTATTATTTTTAGTAAAAAACTAATATTATTGTTA-TG-G
29195596 TTAGTTATTA
1 TTAG-TATTA
29195606 GGATTAGTGG
Statistics
Matches: 78, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
39 11 0.14
40 18 0.23
41 9 0.12
42 20 0.26
43 15 0.19
44 5 0.06
ACGTcount: A:0.33, C:0.04, G:0.12, T:0.51
Consensus pattern (41 bp):
TTAGTATTATTTTTAGTAAAAAACTAATATTATTGTTATGG
Found at i:29197431 original size:12 final size:11
Alignment explanation
Indices: 29197416--29197449 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
29197406 AAAAAATTAT
29197416 AAAAATGATAAA
1 AAAAAT-ATAAA
*
29197428 AAAAATCTAAA
1 AAAAATATAAA
29197439 AAAAATATAAA
1 AAAAATATAAA
29197450 GCAAGTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (11 bp):
AAAAATATAAA
Found at i:29200154 original size:14 final size:16
Alignment explanation
Indices: 29200120--29200155 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
29200110 AAACAACTTA
*
29200120 ATATAAGCAAATATTT
1 ATATAAACAAATATTT
29200136 ATATAAACAAATATTT
1 ATATAAACAAATATTT
29200152 ATAT
1 ATAT
29200156 TTATGTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.39
Consensus pattern (16 bp):
ATATAAACAAATATTT
Found at i:29206848 original size:117 final size:117
Alignment explanation
Indices: 29206640--29206850 Score: 359
Period size: 117 Copynumber: 1.8 Consensus size: 117
29206630 TTTGATTTGT
* * * *
29206640 TGGTTATTTGTGATTTATTATTGCAATTTTAGTGCCATAATGTAGGGTTTGTTTTGTCGATTTTT
1 TGGTTAATTGTGATTTATTATTGCAATTTCAGTGCCACAATGTAGGGTTTGTTTTGTCGATTTGT
* * *
29206705 GATGCGATAGTGGTCCCGATGTTGTTGATAAAACTGTTGTCAAAATTGTAGA
66 GATGCAAAAGTGGTCCCGATGATGTTGATAAAACTGTTGTCAAAATTGTAGA
29206757 TGGTTAATTGTGATTTATTATTGCAATTTCAGTGCCACAATGTAGGGTTTGTTTTGTCGATTTGT
1 TGGTTAATTGTGATTTATTATTGCAATTTCAGTGCCACAATGTAGGGTTTGTTTTGTCGATTTGT
29206822 GATGCAAAAGTGGTCCCGATGATGTTGAT
66 GATGCAAAAGTGGTCCCGATGATGTTGAT
29206851 TTCTGTTACC
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
117 87 1.00
ACGTcount: A:0.23, C:0.09, G:0.25, T:0.43
Consensus pattern (117 bp):
TGGTTAATTGTGATTTATTATTGCAATTTCAGTGCCACAATGTAGGGTTTGTTTTGTCGATTTGT
GATGCAAAAGTGGTCCCGATGATGTTGATAAAACTGTTGTCAAAATTGTAGA
Found at i:29211924 original size:37 final size:37
Alignment explanation
Indices: 29211874--29211958 Score: 100
Period size: 37 Copynumber: 2.3 Consensus size: 37
29211864 TGACAAAGGT
* * ** * * *
29211874 CAAAACCACAATTAATTTTGATGGTAATGGGTTGGAA
1 CAAAAACACAATTAACTTCAATGGCAATGAGTTGAAA
29211911 CAAAAACACAATTAACTTCAATGGCAATGAGTTGAAA
1 CAAAAACACAATTAACTTCAATGGCAATGAGTTGAAA
29211948 CAAAAAC-CAAT
1 CAAAAACACAAT
29211959 GCATTGAAAC
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
36 4 0.10
37 37 0.90
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (37 bp):
CAAAAACACAATTAACTTCAATGGCAATGAGTTGAAA
Found at i:29212176 original size:18 final size:19
Alignment explanation
Indices: 29212153--29212190 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
29212143 ATGTCTCAAA
*
29212153 TATATACAAA-ATATGCTT
1 TATATACAAAGATATACTT
29212171 TATATACAAAGATATACTT
1 TATATACAAAGATATACTT
29212190 T
1 T
29212191 TTCATAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.45, C:0.11, G:0.05, T:0.39
Consensus pattern (19 bp):
TATATACAAAGATATACTT
Found at i:29213233 original size:17 final size:17
Alignment explanation
Indices: 29213211--29213249 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
29213201 TTTACCTTTT
*
29213211 AACTTAATTAATGGGTA
1 AACTTAATTAATGGGAA
*
29213228 AACTTAATTGATGGGAA
1 AACTTAATTAATGGGAA
29213245 AACTT
1 AACTT
29213250 TTATCAAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.33
Consensus pattern (17 bp):
AACTTAATTAATGGGAA
Found at i:29216006 original size:20 final size:20
Alignment explanation
Indices: 29215975--29216017 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
29215965 AAAGAAAAAC
29215975 TTTGTAAAAATGTAAAGATTA
1 TTTGTAAAAATGTAAAG-TTA
*
29215996 TTTGT-AAAATGTCAAGTTA
1 TTTGTAAAAATGTAAAGTTA
29216015 TTT
1 TTT
29216018 ATAGTGTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.29
20 10 0.48
21 5 0.24
ACGTcount: A:0.40, C:0.02, G:0.14, T:0.44
Consensus pattern (20 bp):
TTTGTAAAAATGTAAAGTTA
Found at i:29222203 original size:6 final size:6
Alignment explanation
Indices: 29222192--29222218 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
29222182 AGAAGAAAGT
29222192 AAGTGA AAGTGA AAGTGA AAGTGA AAG
1 AAGTGA AAGTGA AAGTGA AAGTGA AAG
29222219 CAAATAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.33, T:0.15
Consensus pattern (6 bp):
AAGTGA
Found at i:29230324 original size:25 final size:28
Alignment explanation
Indices: 29230279--29230333 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
29230269 TTAAGAACAC
*
29230279 ATATATATTATATAAAGAAAT-ATGTAT
1 ATATATACTATATAAAGAAATCATGTAT
29230306 ATATATACTATAT-AA-AAATGCATGTAT
1 ATATATACTATATAAAGAAAT-CATGTAT
29230333 A
1 A
29230334 AGTTTAGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 4 0.16
26 2 0.08
27 19 0.76
ACGTcount: A:0.51, C:0.04, G:0.07, T:0.38
Consensus pattern (28 bp):
ATATATACTATATAAAGAAATCATGTAT
Found at i:29231005 original size:13 final size:12
Alignment explanation
Indices: 29230987--29231025 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
29230977 TATTTCAGGT
29230987 AAAATAAAATGAA
1 AAAATAAAA-GAA
29231000 AAAATAAAAGAA
1 AAAATAAAAGAA
*
29231012 AATAAAAAAAGAA
1 AA-AATAAAAGAA
29231025 A
1 A
29231026 TATGTAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 5 0.21
13 19 0.79
ACGTcount: A:0.82, C:0.00, G:0.08, T:0.10
Consensus pattern (12 bp):
AAAATAAAAGAA
Found at i:29231021 original size:18 final size:18
Alignment explanation
Indices: 29230986--29231021 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
29230976 TTATTTCAGG
* *
29230986 TAAAATAAAATGAAAAAA
1 TAAAAGAAAATAAAAAAA
29231004 TAAAAGAAAATAAAAAAA
1 TAAAAGAAAATAAAAAAA
29231022 GAAATATGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.14
Consensus pattern (18 bp):
TAAAAGAAAATAAAAAAA
Found at i:29232635 original size:30 final size:30
Alignment explanation
Indices: 29232600--29232663 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
29232590 GGCAAAAAAT
29232600 TCTCAAATTTCTCCCTAAATTTCTCAAAGC
1 TCTCAAATTTCTCCCTAAATTTCTCAAAGC
*
29232630 TCTCAAATTTCTCCTTAAATTTCTCAAAGC
1 TCTCAAATTTCTCCCTAAATTTCTCAAAGC
29232660 TCTC
1 TCTC
29232664 TTTAATTAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.28, C:0.30, G:0.03, T:0.39
Consensus pattern (30 bp):
TCTCAAATTTCTCCCTAAATTTCTCAAAGC
Found at i:29234410 original size:18 final size:18
Alignment explanation
Indices: 29234387--29234429 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
29234377 TGCTAGATGC
*
29234387 GTATCCTAGCCCTTATAT
1 GTATCCTAACCCTTATAT
29234405 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
29234423 GTTTCCT
1 GTATCCT
29234430 TTTCCCAGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.28, G:0.09, T:0.42
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:29234855 original size:24 final size:22
Alignment explanation
Indices: 29234828--29234883 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 22
29234818 TATTTAATAA
29234828 AATAAATATTGTTTTTA-ATATTTT
1 AATAAA-ATT-TTTTTATAT-TTTT
29234852 AATAGTAAATTTTTTTATATTTTT
1 AATA--AAATTTTTTTATATTTTT
29234876 AATAAAAT
1 AATAAAAT
29234884 AGAAGTTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
22 4 0.14
24 18 0.62
25 5 0.17
26 2 0.07
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (22 bp):
AATAAAATTTTTTTATATTTTT
Found at i:29238098 original size:125 final size:126
Alignment explanation
Indices: 29237874--29238266 Score: 535
Period size: 125 Copynumber: 3.1 Consensus size: 126
29237864 GGCCAAACAT
* * * *
29237874 GAACTACTGCAGAAAAAGAGCGTCTACAT-AGGAGC-TTTTTCA-TCAATTTTGCTGACAGTGCA
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGA-GAGCTTTTTTCAGT-AATTTTGCTAACAGTGCA
** * *
29237936 TCCTATTTGAAGCGTTTTTGACACTATTTGTTTAGAAAAGTCTTCTCAAAATTA-TTTTTCAG
64 TCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAAAGTCTTCTCAAAATTATTTTTTCAA
29237998 GAACTACTGTAGAAAAAGAGCGTCCACGTGAGAGCTTTTTTCAGTAATTTTGCTAACAGTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGAGAGCTTTTTTCAGTAATTTTGCTAACAGTGCATC
** *
29238063 CTGCTTGAAGCGTTTTTGACACTAACTGTTCAGAAACGTCTTCTCAAAATTATTTTTTCAA
66 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAAAGTCTTCTCAAAATTATTTTTTCAA
* *
29238124 GAACTACTGTAGAAAAAGAGCGTCCATGTG-GAGCTTGTTTCAGTAATTTTGCTAACAGTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGAGAGCTTTTTTCAGTAATTTTGCTAACAGTGCATC
* * * * ** * *
29238188 CTGCTTGAAGCGCTTTTCAAATTATTTGTTCAGAACGGTATTCTCAAAATTATTTTTTTTAA
66 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAAAGTCTTCTCAAAATTA-TTTTTTCAA
29238250 GAACTACTGTAGAAAAA
1 GAACTACTGTAGAAAAA
29238267 AAAAACAAAA
Statistics
Matches: 241, Mismatches: 23, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
124 30 0.12
125 149 0.62
126 62 0.26
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (126 bp):
GAACTACTGTAGAAAAAGAGCGTCCACGTGAGAGCTTTTTTCAGTAATTTTGCTAACAGTGCATC
CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAAAGTCTTCTCAAAATTATTTTTTCAA
Found at i:29238448 original size:34 final size:34
Alignment explanation
Indices: 29238329--29238458 Score: 104
Period size: 34 Copynumber: 3.9 Consensus size: 34
29238319 TAGAATGTTA
* *
29238329 TTTTAAAAAAAA-ACTAAACCCTTATTTAATTAA
1 TTTTAAAAAAAACACTAAACCCTGATTTAATTAT
*** * *
29238362 TTTTCTTAAAAACATTAAACTCTGATTTAATTTAT
1 TTTTAAAAAAAACACTAAACCCTGATTTAA-TTAT
* ** * *
29238397 TTATT--TAAAGCCCCTAAACCCTAATTTAATTAT
1 TT-TTAAAAAAAACACTAAACCCTGATTTAATTAT
*
29238430 TTTTAAAAAAAACACTAAATCCTGATTTA
1 TTTTAAAAAAAACACTAAACCCTGATTTA
29238459 TTTTTTAAAA
Statistics
Matches: 73, Mismatches: 19, Indels: 9
0.72 0.19 0.09
Matches are distributed among these distances:
32 2 0.03
33 15 0.21
34 49 0.67
35 5 0.07
36 2 0.03
ACGTcount: A:0.43, C:0.15, G:0.02, T:0.40
Consensus pattern (34 bp):
TTTTAAAAAAAACACTAAACCCTGATTTAATTAT
Found at i:29242596 original size:48 final size:49
Alignment explanation
Indices: 29242486--29242598 Score: 117
Period size: 48 Copynumber: 2.3 Consensus size: 49
29242476 ATCTGGGCTG
* * *
29242486 TATAACAGGAAGCTCATAAGAGCCATATTCAGGAAGCTCCGGATAGCCA
1 TATATCAGGAAGCTCATAAGAGCCATATTCAGGAAGCTCCGAAAAGCCA
* * *
29242535 TATATC-GGAAAGCTCA-AGCGAGCTATA-TCGGGAAGCTCCGAAAAGCCA
1 TATATCAGG-AAGCTCATA-AGAGCCATATTCAGGAAGCTCCGAAAAGCCA
29242583 T-TAATCAGGAAGCTCA
1 TAT-ATCAGGAAGCTCA
29242599 CAAATAGCCT
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
47 1 0.02
48 32 0.59
49 21 0.39
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.19
Consensus pattern (49 bp):
TATATCAGGAAGCTCATAAGAGCCATATTCAGGAAGCTCCGAAAAGCCA
Found at i:29242612 original size:26 final size:26
Alignment explanation
Indices: 29242565--29242635 Score: 83
Period size: 26 Copynumber: 2.8 Consensus size: 26
29242555 AGCTATATCG
29242565 GGAAGCTC-CGAAA-AGCCATTAATCA
1 GGAAGCTCAC-AAATAGCCATTAATCA
* **
29242590 GGAAGCTCACAAATAGCCTTTAATTG
1 GGAAGCTCACAAATAGCCATTAATCA
*
29242616 GGAAGCTCACTAATAGCCAT
1 GGAAGCTCACAAATAGCCAT
29242636 ATATCGAAAC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
25 11 0.28
26 28 0.72
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.21
Consensus pattern (26 bp):
GGAAGCTCACAAATAGCCATTAATCA
Found at i:29242723 original size:24 final size:23
Alignment explanation
Indices: 29242696--29242778 Score: 67
Period size: 24 Copynumber: 3.4 Consensus size: 23
29242686 CACAACCGAT
*
29242696 CGGGATGCTCCGAAGAGCTATTAA
1 CGGGAAGCT-CGAAGAGCTATTAA
* * *
29242720 CGGGAAGCTCGCAGGAACCATATAA
1 CGGGAAGCTCG-AAGAGCTAT-TAA
* *
29242745 CGGGAAGCTCGAGAGGGCTAATAA
1 CGGGAAGCTCGA-AGAGCTATTAA
*
29242769 CGGGATGCTC
1 CGGGAAGCTC
29242779 TTTCGAGCTG
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
23 2 0.04
24 27 0.59
25 17 0.37
ACGTcount: A:0.30, C:0.22, G:0.33, T:0.16
Consensus pattern (23 bp):
CGGGAAGCTCGAAGAGCTATTAA
Found at i:29243660 original size:17 final size:16
Alignment explanation
Indices: 29243630--29243674 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
29243620 AAATGATGAT
*
29243630 ATTTTCTTTATTTTATC
1 ATTTTCATT-TTTTATC
*
29243647 ATTTATCATTTTTTATT
1 ATTT-TCATTTTTTATC
29243664 ATTTTCATTTT
1 ATTTTCATTTT
29243675 CCAATTTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 7 0.28
17 14 0.56
18 4 0.16
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (16 bp):
ATTTTCATTTTTTATC
Found at i:29244718 original size:13 final size:13
Alignment explanation
Indices: 29244700--29244725 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29244690 ATTTAAAATA
29244700 TAAATTAGATTTT
1 TAAATTAGATTTT
29244713 TAAATTAGATTTT
1 TAAATTAGATTTT
29244726 ACAAATAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
TAAATTAGATTTT
Found at i:29245128 original size:12 final size:12
Alignment explanation
Indices: 29245107--29245145 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
29245097 TGACGTGGCA
*
29245107 GAGGAGGACGAT
1 GAGGACGACGAT
*
29245119 GAGGACGACGAA
1 GAGGACGACGAT
*
29245131 GAGGATGACGAT
1 GAGGACGACGAT
29245143 GAG
1 GAG
29245146 CTTTATGGCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.36, C:0.10, G:0.46, T:0.08
Consensus pattern (12 bp):
GAGGACGACGAT
Found at i:29245266 original size:12 final size:12
Alignment explanation
Indices: 29245251--29245278 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
29245241 GGAAGAAGAT
29245251 GAGGGAGAGGGA
1 GAGGGAGAGGGA
29245263 GAGGGAGAGGGA
1 GAGGGAGAGGGA
29245275 GAGG
1 GAGG
29245279 ACGATTTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (12 bp):
GAGGGAGAGGGA
Found at i:29253494 original size:123 final size:126
Alignment explanation
Indices: 29253341--29253623 Score: 317
Period size: 126 Copynumber: 2.3 Consensus size: 126
29253331 TTTGTTTTTC
* * * * *
29253341 GTTGCACTTTCAATGTATACTAATGATGATTCCTTT-CTGTTTTTACGCAATTTGTT-ACATGTC
1 GTTGCACTTTTAATGTATACTAATGATGATTCCTTTCCGGTTCTTACACAATTTGTTCACATATC
* * * * *
29253404 GTTATTCATTT-CATATCTCGATTTTAATGTTC-ACATGTTCTTCATTGCATTAGAATTGTG
66 GTTATTCATTTGCATATCTCGAGTTTAATG-CCGACACGTTCTTCATTGCATTAGAATAGCG
* * *
29253464 GTTGCACTTTTGATGTATACTAGTGATGATT-CTTTCCGGTTCTTACACAATTTGTTGCATATAT
1 GTTGCACTTTTAATGTATACTAATGATGATTCCTTTCCGGTTCTTACACAATTTGTT-CACATAT
* * * * * **
29253528 GGTTATTCGTTTGTATATCTTGAGTTTAATGCCGATACGTTCTTCATTGCATTATCATAGCG
65 CGTTATTCATTTGCATATCTCGAGTTTAATGCCGACACGTTCTTCATTGCATTAGAATAGCG
*
29253590 ATTGCAC-TTTAATGTATACTAATGATGATTCCTT
1 GTTGCACTTTTAATGTATACTAATGATGATTCCTT
29253624 ATAGTTCTTA
Statistics
Matches: 131, Mismatches: 23, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
122 4 0.03
123 45 0.34
125 36 0.27
126 46 0.35
ACGTcount: A:0.23, C:0.16, G:0.16, T:0.46
Consensus pattern (126 bp):
GTTGCACTTTTAATGTATACTAATGATGATTCCTTTCCGGTTCTTACACAATTTGTTCACATATC
GTTATTCATTTGCATATCTCGAGTTTAATGCCGACACGTTCTTCATTGCATTAGAATAGCG
Found at i:29253640 original size:125 final size:123
Alignment explanation
Indices: 29253342--29253712 Score: 365
Period size: 125 Copynumber: 3.0 Consensus size: 123
29253332 TTGTTTTTCG
* * * *
29253342 TTGCACTTTCAATGTATACTAATGATGATTCCTTTCTGTTTTTACGCAATTTGTT--ACATGTCG
1 TTGCACTTT-AATGTATACTAATGATGATTCCTTT-AGTTCTTACACAATTTGTTGCATATGTCG
* * * * * * * *
29253405 TTATTCATTTCATATCTCGATTTTAATGTTC-ACATGTTCTTCATTGCATTAGAATTGTGG
64 TTATTCGTTTCATATCTTGAGTTTAATG-TCGATATGTTCTTCATTGCATTAGCATAGCGA
* * * * *
29253465 TTGCACTTTTGATGTATACTAGTGATGATT-CTTTCCGGTTCTTACACAATTTGTTGCATATATG
1 TTGCAC-TTTAATGTATACTAATGATGATTCCTTT--AGTTCTTACACAATTTGTTGCATATGTC
* * * *
29253529 GTTATTCGTTTGTATATCTTGAGTTTAATGCCGATACGTTCTTCATTGCATTATCATAGCGA
63 GTTATTCGTTT-CATATCTTGAGTTTAATGTCGATATGTTCTTCATTGCATTAGCATAGCGA
* **
29253591 TTGCACTTTAATGTATACTAATGATGATTCCTTATAGTTCTTACTCAATTT-TCTGCATATGTTA
1 TTGCACTTTAATGTATACTAATGATGATTCCTT-TAGTTCTTACACAATTTGT-TGCATATGTCG
* * * *
29253655 TTATTTGTTTACATATCTTGAGTTTAATGTTGATATGTTCTTCAATGCACTAGCATAG
64 TTATTCGTTT-CATATCTTGAGTTTAATGTCGATATGTTCTTCATTGCATTAGCATAG
29253713 GATAGCAGCG
Statistics
Matches: 203, Mismatches: 36, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
122 4 0.02
123 41 0.20
124 4 0.02
125 107 0.53
126 46 0.23
127 1 0.00
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.46
Consensus pattern (123 bp):
TTGCACTTTAATGTATACTAATGATGATTCCTTTAGTTCTTACACAATTTGTTGCATATGTCGTT
ATTCGTTTCATATCTTGAGTTTAATGTCGATATGTTCTTCATTGCATTAGCATAGCGA
Found at i:29259997 original size:45 final size:45
Alignment explanation
Indices: 29259936--29260024 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
29259926 ATGAAAAAAT
*
29259936 TATAAAATATACATAAAATCAACACTAGCACTAACAACATGTTTA
1 TATAAAATATACATAAAATCAACACTAACACTAACAACATGTTTA
*
29259981 TATAAAATATACATAAAATCAACACTAACGCTAACAACATGTTT
1 TATAAAATATACATAAAATCAACACTAACACTAACAACATGTTT
29260025 GGTTGAGGGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.51, C:0.18, G:0.04, T:0.27
Consensus pattern (45 bp):
TATAAAATATACATAAAATCAACACTAACACTAACAACATGTTTA
Found at i:29262404 original size:22 final size:22
Alignment explanation
Indices: 29262377--29262421 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
29262367 CGTTTGTTTC
29262377 TCACGTACTAAGCTCTCATGTT
1 TCACGTACTAAGCTCTCATGTT
29262399 TCACGTACTAAGCTCTCATGTT
1 TCACGTACTAAGCTCTCATGTT
29262421 T
1 T
29262422 GAACAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.27, G:0.13, T:0.38
Consensus pattern (22 bp):
TCACGTACTAAGCTCTCATGTT
Found at i:29262899 original size:13 final size:13
Alignment explanation
Indices: 29262881--29262905 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29262871 GTTTTCATCC
29262881 AAAATTCTTTAAT
1 AAAATTCTTTAAT
29262894 AAAATTCTTTAA
1 AAAATTCTTTAA
29262906 ACATCCATTA
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
AAAATTCTTTAAT
Found at i:29264198 original size:27 final size:28
Alignment explanation
Indices: 29264142--29264212 Score: 67
Period size: 29 Copynumber: 2.6 Consensus size: 28
29264132 AATACATCAA
*
29264142 AAAATTCAAAAA-ATCAT-AAATTATAAT
1 AAAATTCAAAAATA-AATGAAATTATAAT
* **
29264169 -AAATTCTAAAATAAATGAAATTATTTT
1 AAAATTCAAAAATAAATGAAATTATAAT
29264196 AAAAATTCAAAAATAAA
1 -AAAATTCAAAAATAAA
29264213 AAATTGAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
26 12 0.34
27 9 0.26
29 14 0.40
ACGTcount: A:0.62, C:0.06, G:0.01, T:0.31
Consensus pattern (28 bp):
AAAATTCAAAAATAAATGAAATTATAAT
Found at i:29281503 original size:10 final size:10
Alignment explanation
Indices: 29281488--29281577 Score: 55
Period size: 10 Copynumber: 9.3 Consensus size: 10
29281478 AATTAGAAAT
*
29281488 AAAAATCATA
1 AAAAATTATA
*
29281498 AAAAATACATA
1 AAAAAT-TATA
29281509 TAAAAATTATA
1 -AAAAATTATA
**
29281520 AAATTTTAT-
1 AAAAATTATA
**
29281529 AAAAATCGT-
1 AAAAATTATA
29281538 AAAAATTATA
1 AAAAATTATA
*
29281548 AAATA-TAT-
1 AAAAATTATA
*
29281556 AGAAA-TATA
1 AAAAATTATA
29281565 AAAAATTATA
1 AAAAATTATA
29281575 AAA
1 AAA
29281578 TTTTATAAAG
Statistics
Matches: 62, Mismatches: 13, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
8 6 0.10
9 19 0.31
10 24 0.39
11 7 0.11
12 6 0.10
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (10 bp):
AAAAATTATA
Found at i:29281524 original size:8 final size:8
Alignment explanation
Indices: 29281511--29281579 Score: 50
Period size: 8 Copynumber: 7.8 Consensus size: 8
29281501 AATACATATA
29281511 AAAATTAT
1 AAAATTAT
29281519 AAAATTTTAT
1 AAAA--TTAT
29281529 AAAAATCGTA-
1 -AAAAT--TAT
29281539 AAAATTAT
1 AAAATTAT
29281547 AAAATATAT
1 AAAAT-TAT
*
29281556 AGAAATATAA
1 A-AAAT-TAT
29281566 AAAATTAT
1 AAAATTAT
29281574 AAAATT
1 AAAATT
29281580 TTATAAAGTC
Statistics
Matches: 51, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
7 2 0.04
8 17 0.33
9 14 0.27
10 12 0.24
11 6 0.12
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.33
Consensus pattern (8 bp):
AAAATTAT
Found at i:29281556 original size:27 final size:26
Alignment explanation
Indices: 29281506--29281578 Score: 92
Period size: 27 Copynumber: 2.7 Consensus size: 26
29281496 TAAAAAATAC
*
29281506 ATATAAAAATTATAAAATTTTATAAAA
1 ATATAAAAATTATAAAA-TATATAAAA
* *
29281533 ATCGTAAAAATTATAAAATATATAGAA
1 AT-ATAAAAATTATAAAATATATAAAA
29281560 ATATAAAAAATTATAAAAT
1 ATAT-AAAAATTATAAAAT
29281579 TTTATAAAGT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
26 1 0.03
27 25 0.62
28 14 0.35
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (26 bp):
ATATAAAAATTATAAAATATATAAAA
Found at i:29281626 original size:55 final size:53
Alignment explanation
Indices: 29281506--29281624 Score: 141
Period size: 55 Copynumber: 2.1 Consensus size: 53
29281496 TAAAAAATAC
*
29281506 ATATAAAAATTATAAAATTTTATAAAAATCGTAAAAATTATAAAATATATAGAA
1 ATAT-AAAATTATAAAATTTTATAAAAATCGTAAAAATTATAAAATATAAAGAA
* *
29281560 ATATAAAAAATTATAAAATTTTAT-AAAGTCGTAAGAAGATTATACAAAATGTAAAGAA
1 ATAT--AAAATTATAAAATTTTATAAAAATCGTAA-AA-ATTAT--AAAATATAAAGAA
29281618 ATATAAA
1 ATATAAA
29281625 TTTCGTAAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
54 13 0.23
55 21 0.37
56 8 0.14
58 15 0.26
ACGTcount: A:0.60, C:0.03, G:0.07, T:0.31
Consensus pattern (53 bp):
ATATAAAATTATAAAATTTTATAAAAATCGTAAAAATTATAAAATATAAAGAA
Found at i:29282189 original size:90 final size:87
Alignment explanation
Indices: 29281914--29282200 Score: 299
Period size: 89 Copynumber: 3.2 Consensus size: 87
29281904 TAATAAGAGC
* *
29281914 AGGGGCTTAATTGCTTTTTTAAAAAATTTTGAGGGTCTTTTTTATGCATTTTGAAAGTTCAAGTA
1 AGGGGCTTAATTGCTTTTTTAAAAAGTTTT-AGGGTCTTTTTTATGCATTTTGAAAGTTCAAATA
29281979 CTCAATTAAGTGAAAAAAAAAT-
65 CTCAATTAAGTGAAAAAAAAATG
*** * * * * *
29282001 AGGGGCTTAATTGCTTTTTTTTTTTTAAGTTTGAGAGCCTTTTTGATGCATTTTGAATGTTCAAA
1 AGGGGCTTAATTGC---TTTTTTAAAAAGTTTTAGGGTCTTTTTTATGCATTTTGAAAGTTCAAA
* *
29282066 TACCCAGTTAAGTGAAAAAAAAA-G
63 TACTCAATTAAGTGAAAAAAAAATG
* * * *
29282090 TAGGGGCTTAATTGCTTTTCTTGAAAAAGTTTTAGGGTTTTTTTTATGTATTTTAAAAGTTCAAT
1 -AGGGGCTTAATTGCTTTT-TT-AAAAAGTTTTAGGGTCTTTTTTATGCATTTTGAAAGTTCAAA
* *
29282155 TGCTCAATTATGTGCAAAAAAAAATG
63 TACTCAATTAAGTG-AAAAAAAAATG
** *
29282181 AGAAGCTTAATTGTTTTTTT
1 AGGGGCTTAATTGCTTTTTT
29282201 TCTTTTTTTA
Statistics
Matches: 160, Mismatches: 31, Indels: 16
0.77 0.15 0.08
Matches are distributed among these distances:
87 18 0.11
88 2 0.01
89 90 0.56
90 49 0.31
91 1 0.01
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (87 bp):
AGGGGCTTAATTGCTTTTTTAAAAAGTTTTAGGGTCTTTTTTATGCATTTTGAAAGTTCAAATAC
TCAATTAAGTGAAAAAAAAATG
Found at i:29282424 original size:29 final size:30
Alignment explanation
Indices: 29282368--29282423 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
29282358 ACTGTATTAA
29282368 ATACCTATTTTCATAATTAATCTATTTTCC
1 ATACCTATTTTCATAATTAATCTATTTTCC
29282398 ATACC-ATTTTCATAATTAAT-TATTTT
1 ATACCTATTTTCATAATTAATCTATTTT
29282424 TATATTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 6 0.23
29 15 0.58
30 5 0.19
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (30 bp):
ATACCTATTTTCATAATTAATCTATTTTCC
Found at i:29284819 original size:16 final size:16
Alignment explanation
Indices: 29284798--29284872 Score: 82
Period size: 16 Copynumber: 4.8 Consensus size: 16
29284788 TATTTTATAT
29284798 ATTTTTATAAATTTTA
1 ATTTTTATAAATTTTA
29284814 ATTTTT-TAAATTTTA
1 ATTTTTATAAATTTTA
* *
29284829 AGTTTTTTTTAATTTTA
1 A-TTTTTATAAATTTTA
* **
29284846 ATTTATATATTTTTTA
1 ATTTTTATAAATTTTA
29284862 ATTTTTA-AAAT
1 ATTTTTATAAAT
29284873 CATGATCAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
15 12 0.25
16 27 0.56
17 9 0.19
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.65
Consensus pattern (16 bp):
ATTTTTATAAATTTTA
Found at i:29284867 original size:32 final size:31
Alignment explanation
Indices: 29284788--29284872 Score: 82
Period size: 32 Copynumber: 2.7 Consensus size: 31
29284778 AATTTTTGAG
* *
29284788 TATTTTATATATTTTTATAAATTTTAATTTTT
1 TATTTTTTA-ATTTTTATAAATTTTAATTTTA
** * *
29284820 TAAATTTTAAGTTTTTTTTAATTTTAATTTATA
1 TATTTTTTAA-TTTTTATAAATTTTAATTT-TA
29284853 TATTTTTTAATTTTTA-AAAT
1 TATTTTTTAATTTTTATAAAT
29284873 CATGATCAAA
Statistics
Matches: 41, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
31 4 0.10
32 28 0.68
33 9 0.22
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (31 bp):
TATTTTTTAATTTTTATAAATTTTAATTTTA
Found at i:29285074 original size:31 final size:30
Alignment explanation
Indices: 29285027--29285101 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 30
29285017 TTTTAACGAT
* *
29285027 AGAGTGGCT-AAATTGACAACTTATCTAATG
1 AGAGTGACTAAAATTGACAACTTATCTAA-C
29285057 AGAGTGACTAAAATTGACAACTTATCTAAC
1 AGAGTGACTAAAATTGACAACTTATCTAAC
29285087 ATGAGTGACTAAAAT
1 A-GAGTGACTAAAAT
29285102 AATAAATTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
30 9 0.22
31 32 0.78
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.28
Consensus pattern (30 bp):
AGAGTGACTAAAATTGACAACTTATCTAAC
Found at i:29287233 original size:2 final size:2
Alignment explanation
Indices: 29287226--29287257 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
29287216 CTAACTTTAA
29287226 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29287258 TCAAAGAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29289177 original size:22 final size:22
Alignment explanation
Indices: 29289135--29289177 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
29289125 ACAACTGAAG
**
29289135 AAAATAATAAATTGTGGATATT
1 AAAATAATAAATTGTAAATATT
29289157 AAAATAA-AAATGTGTAAATAT
1 AAAATAATAAAT-TGTAAATAT
29289178 ATCAAAATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.33
Consensus pattern (22 bp):
AAAATAATAAATTGTAAATATT
Found at i:29290029 original size:16 final size:16
Alignment explanation
Indices: 29290008--29290038 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29289998 TTGTGTATGG
*
29290008 TTTTAATATTAAATAT
1 TTTTAAGATTAAATAT
29290024 TTTTAAGATTAAATA
1 TTTTAAGATTAAATA
29290039 ACATTAATAA
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:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (16 bp):
TTTTAAGATTAAATAT
Found at i:29299357 original size:2 final size:2
Alignment explanation
Indices: 29299350--29299388 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
29299340 TTAGGTAAGA
29299350 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29299389 GTAGTTAGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29299714 original size:2 final size:2
Alignment explanation
Indices: 29299707--29299744 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
29299697 NNNNNNNNNN
29299707 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29299745 GAGTTTAGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29314521 original size:21 final size:22
Alignment explanation
Indices: 29314497--29314542 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
29314487 CATTTTTAAT
29314497 ATTTT-TAATTTTTAAAAATAG
1 ATTTTATAATTTTTAAAAATAG
29314518 ATTTTATAATTTTTAAAAATAG
1 ATTTTATAATTTTTAAAAATAG
29314540 ATT
1 ATT
29314543 AAATATTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (22 bp):
ATTTTATAATTTTTAAAAATAG
Found at i:29317039 original size:16 final size:16
Alignment explanation
Indices: 29317018--29317048 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29317008 TAATTATTTT
29317018 TAAAAAATATATATTC
1 TAAAAAATATATATTC
*
29317034 TAAAAATTATATATT
1 TAAAAAATATATATT
29317049 TGCTTATGAA
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:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAAAAATATATATTC
Found at i:29319742 original size:63 final size:63
Alignment explanation
Indices: 29319591--29319782 Score: 206
Period size: 63 Copynumber: 3.0 Consensus size: 63
29319581 TGGTCCACAT
* *
29319591 GGCTTGGACACACGCTCATGTCTCT-GACCCGTGTGACTCAAATTCCAAACCAGTGAGTTACAC
1 GGCTTGGACACACGCCCATGTCTCTAG-CCCGTGTGACTCAAATTCCAAAACAGTGAGTTACAC
* * * * * * * **
29319654 AGCCTGGACACACGTCCGTGCCTCTAGCTCGTTTGACTCAAATTTTAAAACAGTGAGTTACAC
1 GGCTTGGACACACGCCCATGTCTCTAGCCCGTGTGACTCAAATTCCAAAACAGTGAGTTACAC
* * * * * **
29319717 GGCTTGGACACACACCCATATCTCTAGCCCGTGTGAATCTAATTCCAAAATAGTTTGTTACAC
1 GGCTTGGACACACGCCCATGTCTCTAGCCCGTGTGACTCAAATTCCAAAACAGTGAGTTACAC
29319780 GGC
1 GGC
29319783 CTGCCACACG
Statistics
Matches: 101, Mismatches: 27, Indels: 2
0.78 0.21 0.02
Matches are distributed among these distances:
63 100 0.99
64 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (63 bp):
GGCTTGGACACACGCCCATGTCTCTAGCCCGTGTGACTCAAATTCCAAAACAGTGAGTTACAC
Found at i:29320831 original size:29 final size:30
Alignment explanation
Indices: 29320789--29320847 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
29320779 TACGATTTAA
*
29320789 TGTGAAATTGTATACAT-AAACTTTGATTT
1 TGTGAAATTGTATACATGAAAATTTGATTT
* * *
29320818 TGTGCAATTTTATATATGAAAATTTGATTT
1 TGTGAAATTGTATACATGAAAATTTGATTT
29320848 GATCCAATTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.47
Consensus pattern (30 bp):
TGTGAAATTGTATACATGAAAATTTGATTT
Found at i:29322168 original size:19 final size:19
Alignment explanation
Indices: 29322119--29322171 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
29322109 GGGTTTAAGA
* *
29322119 TTTTTAAAATTTTAT-ATT
1 TTTTTAAAATTTAATAATG
* **
29322137 TTTTTTATTTTTAATAATG
1 TTTTTAAAATTTAATAATG
29322156 TTTTTAAAATTTAATA
1 TTTTTAAAATTTAATA
29322172 GTATTTATAA
Statistics
Matches: 26, Mismatches: 8, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
18 11 0.42
19 15 0.58
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
TTTTTAAAATTTAATAATG
Found at i:29324614 original size:46 final size:46
Alignment explanation
Indices: 29324542--29324910 Score: 594
Period size: 46 Copynumber: 8.0 Consensus size: 46
29324532 ATAATGCTAT
* * * * *
29324542 AACTTAGTATGATTTTCTTTACTGAAACACCATATCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
*
29324588 AACTCAGTATGGTTTTCTTCATTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
*
29324634 AACTCAGTATGGTTTTCCTCATTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
* *
29324680 AACTCAGTATGGTTTTCTTTACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
* * *
29324726 AACTCAGTATGGTTTTGTTCATTGAAATATCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
* * *
29324772 AACTCAGTATGATTTTCTTCATTGAAATACTATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
*
29324818 AACTCAGTATGGTTTTCTTCATTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
29324864 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
29324910 A
1 A
29324911 CTTTGCCATG
Statistics
Matches: 300, Mismatches: 23, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 300 1.00
ACGTcount: A:0.29, C:0.24, G:0.08, T:0.39
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
Found at i:29329023 original size:13 final size:13
Alignment explanation
Indices: 29329005--29329042 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
29328995 CTAAATCATA
29329005 ATTTTAGTAAAAT
1 ATTTTAGTAAAAT
*
29329018 ATTTTAGTAAAAC
1 ATTTTAGTAAAAT
29329031 ATTTT-GTAAAAT
1 ATTTTAGTAAAAT
29329043 CAAGAGTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 6 0.26
13 17 0.74
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.45
Consensus pattern (13 bp):
ATTTTAGTAAAAT
Found at i:29333311 original size:17 final size:20
Alignment explanation
Indices: 29333269--29333306 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
29333259 TTTTCATTAC
*
29333269 GATATTTGATTTTTTTTCCA
1 GATATTTGATTTTTTCTCCA
29333289 GATATTTG-TTTTTTCTCC
1 GATATTTGATTTTTTCTCC
29333307 GTATTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.16, C:0.13, G:0.11, T:0.61
Consensus pattern (20 bp):
GATATTTGATTTTTTCTCCA
Found at i:29345887 original size:42 final size:42
Alignment explanation
Indices: 29345798--29345943 Score: 188
Period size: 42 Copynumber: 3.5 Consensus size: 42
29345788 TGATTCAGTA
* * *
29345798 CACCGGCACTT-AGCATGCTAGACATATAGTCTGA-AATGTTT
1 CACCGGCA-TTAAGCCTGCTAGACATAAAGTCTGATATTGTTT
* **
29345839 CACCGGCATTAAGCCTACTAGATGTAAAGTCTGATATTGTTT
1 CACCGGCATTAAGCCTGCTAGACATAAAGTCTGATATTGTTT
29345881 CACCGGCATTAAGCCTGCTAGACATAAAGTCTGATATTGTTT
1 CACCGGCATTAAGCCTGCTAGACATAAAGTCTGATATTGTTT
** *
29345923 CACTAGCAATAAGCCTGCTAG
1 CACCGGCATTAAGCCTGCTAG
29345944 GCGCTAAGCC
Statistics
Matches: 91, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
40 2 0.02
41 26 0.29
42 63 0.69
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.29
Consensus pattern (42 bp):
CACCGGCATTAAGCCTGCTAGACATAAAGTCTGATATTGTTT
Found at i:29349924 original size:19 final size:19
Alignment explanation
Indices: 29349900--29350012 Score: 163
Period size: 19 Copynumber: 5.8 Consensus size: 19
29349890 AATTTTTGAG
29349900 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
29349919 GATATGCAATCCAAGATAT
1 GATATGCAATCTTAGATAT
29349938 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
*
29349959 GATATGCAATATTAGATAT
1 GATATGCAATCTTAGATAT
**
29349978 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
29349997 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
29350013 ATATATGATT
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
19 65 0.79
21 17 0.21
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:29349945 original size:40 final size:40
Alignment explanation
Indices: 29349901--29350007 Score: 173
Period size: 40 Copynumber: 2.7 Consensus size: 40
29349891 ATTTTTGAGG
29349901 ATATGCAATCTTAGATATGATATGCAATCCAAGATATGAT
1 ATATGCAATCTTAGATATGATATGCAATCCAAGATATGAT
***
29349941 ATATGCAATCTTAGATATGATATGCAATATTAGATATGAT
1 ATATGCAATCTTAGATATGATATGCAATCCAAGATATGAT
29349981 ATAT--AATCTTAGATATGATATGCAATC
1 ATATGCAATCTTAGATATGATATGCAATC
29350008 TTAGAATATA
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
38 22 0.35
40 41 0.65
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (40 bp):
ATATGCAATCTTAGATATGATATGCAATCCAAGATATGAT
Found at i:29349967 original size:59 final size:56
Alignment explanation
Indices: 29349900--29350019 Score: 161
Period size: 59 Copynumber: 2.1 Consensus size: 56
29349890 AATTTTTGAG
* *
29349900 GATATGCAATCTTAGATATGATATGCAATCCAAGATATGATATATGCAATCTTAGATAT
1 GATATGCAATATTAGATATGATATACAATCCAAGATATG--ATATGCAATCTTAGA-AT
* **
29349959 GATATGCAATATTAGATATGATATATAATCTTAGATATGATATGCAATCTTAGAAT
1 GATATGCAATATTAGATATGATATACAATCCAAGATATGATATGCAATCTTAGAAT
29350015 -ATATG
1 GATATG
29350020 ATTTTGTAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
55 5 0.09
56 2 0.04
57 15 0.27
59 34 0.61
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (56 bp):
GATATGCAATATTAGATATGATATACAATCCAAGATATGATATGCAATCTTAGAAT
Found at i:29351196 original size:94 final size:94
Alignment explanation
Indices: 29351090--29351271 Score: 355
Period size: 94 Copynumber: 1.9 Consensus size: 94
29351080 AAAAATCGTA
29351090 AAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTT
1 AAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTT
29351155 AAATCTTGGATAAGCGGATGTTCTTGGAT
66 AAATCTTGGATAAGCGGATGTTCTTGGAT
29351184 AAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTT
1 AAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTT
*
29351249 AAATCTTGGATAAGTGGATGTTC
66 AAATCTTGGATAAGCGGATGTTC
29351272 CTTTAAAGTT
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
94 87 1.00
ACGTcount: A:0.27, C:0.13, G:0.26, T:0.34
Consensus pattern (94 bp):
AAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTT
AAATCTTGGATAAGCGGATGTTCTTGGAT
Found at i:29357205 original size:3 final size:3
Alignment explanation
Indices: 29357197--29357223 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
29357187 AATGCTATGT
29357197 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
29357224 AAAAATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:29358983 original size:14 final size:15
Alignment explanation
Indices: 29358964--29358992 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
29358954 ATATTTGGTG
29358964 AAATTATT-TTTAAA
1 AAATTATTATTTAAA
29358978 AAATTATTATTTAAA
1 AAATTATTATTTAAA
29358993 TATTACCACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AAATTATTATTTAAA
Found at i:29363349 original size:19 final size:19
Alignment explanation
Indices: 29363320--29363385 Score: 75
Period size: 19 Copynumber: 3.5 Consensus size: 19
29363310 CCAAATTTTT
29363320 TTTTAAAAAATAAAAAAGTA
1 TTTT-AAAAATAAAAAAGTA
29363340 TTTTAAAAATAAAAAA--A
1 TTTTAAAAATAAAAAAGTA
**
29363357 -TAAAAAAATAAAAAAAGTA
1 TTTTAAAAAT-AAAAAAGTA
29363376 TTTTAAAAAT
1 TTTTAAAAAT
29363386 TTTAAAAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
16 7 0.18
17 7 0.18
19 13 0.34
20 11 0.29
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (19 bp):
TTTTAAAAATAAAAAAGTA
Found at i:29363355 original size:8 final size:8
Alignment explanation
Indices: 29363344--29363372 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
29363334 AAAGTATTTT
29363344 AAAAATAA
1 AAAAATAA
29363352 AAAAATAA
1 AAAAATAA
29363360 AAAAATAA
1 AAAAATAA
29363368 AAAAA
1 AAAAA
29363373 GTATTTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAATAA
Found at i:29363368 original size:35 final size:37
Alignment explanation
Indices: 29363324--29363399 Score: 120
Period size: 36 Copynumber: 2.1 Consensus size: 37
29363314 ATTTTTTTTT
29363324 AAAAAAT-AAAAAAGTATTTTAAAAA-TAAAAAAATA
1 AAAAAATAAAAAAAGTATTTTAAAAATTAAAAAAATA
**
29363359 AAAAAATAAAAAAAGTATTTTAAAAATTTTAAAAATA
1 AAAAAATAAAAAAAGTATTTTAAAAATTAAAAAAATA
29363396 AAAA
1 AAAA
29363400 TAAAAATATT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 7 0.19
36 18 0.49
37 12 0.32
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (37 bp):
AAAAAATAAAAAAAGTATTTTAAAAATTAAAAAAATA
Found at i:29364024 original size:19 final size:18
Alignment explanation
Indices: 29363996--29364031 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
29363986 TTGCTTTTAT
*
29363996 TCAAAAAAAACCTTTGAA
1 TCAAAAAAAAACTTTGAA
29364014 TCAAGAAAAAAACTTTGA
1 TCAA-AAAAAAACTTTGA
29364032 TGTATGGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.56, C:0.14, G:0.08, T:0.22
Consensus pattern (18 bp):
TCAAAAAAAAACTTTGAA
Found at i:29364491 original size:2 final size:2
Alignment explanation
Indices: 29364442--29364475 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
29364432 TAATTAAAAG
*
29364442 AT AT AA AT AT AT AT AT AT AT AT AT AT AT ACT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A
29364476 GAAATAGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:29366343 original size:17 final size:17
Alignment explanation
Indices: 29366300--29366663 Score: 248
Period size: 17 Copynumber: 20.7 Consensus size: 17
29366290 AAAAAAAAAA
*
29366300 TTTGAAACACGAGAATTT
1 TTTGAAACACGA-AAATT
* *
29366318 TTTAAAACACGAAGATT
1 TTTGAAACACGAAAATT
*
29366335 TTTGGAACACGCAAAA-T
1 TTTGAAACACG-AAAATT
*
29366352 TTTGAAAACATGAAAATT
1 TTTG-AAACACGAAAATT
*
29366370 TTTGAAATACGAAAATT
1 TTTGAAACACGAAAATT
*
29366387 TTAGAAACACGAAAATT
1 TTTGAAACACGAAAATT
* *
29366404 TTTAAAACACGACAA-T
1 TTTGAAACACGAAAATT
**
29366420 TTTGAAACACGGTCAATT
1 TTTGAAACAC-GAAAATT
* *
29366438 TTTGAAAATACGACAATT
1 TTTG-AAACACGAAAATT
* * *
29366456 TTTGAAATATGAGAATTTT
1 TTTGAAACACGA-AA-ATT
* * *
29366475 TTTAAAACATGGAAATTTT
1 TTTGAAACA-CGAAA-ATT
*
29366494 TTTGAAAACAAGAAAATT
1 TTTG-AAACACGAAAATT
** * * *
29366512 TTCAAAATATGAGAATT
1 TTTGAAACACGAAAATT
*
29366529 TTTGAAAACACGGGAAATTTT
1 TTTG-AAACAC--GAAA-ATT
*
29366550 TTTAAAAACACGAAAATT
1 TTT-GAAACACGAAAATT
* *
29366568 TTTGAAACACTAGAATT
1 TTTGAAACACGAAAATT
* *
29366585 TTTAAAACACGAAGATT
1 TTTGAAACACGAAAATT
29366602 TTTGAAACACGAAAATT
1 TTTGAAACACGAAAATT
* **
29366619 TTAGAAACGTGAAAATT
1 TTTGAAACACGAAAATT
* *
29366636 TTTAAAACACGACAA-T
1 TTTGAAACACGAAAATT
29366652 TTTGAAACACGA
1 TTTGAAACACGA
29366664 TTTTTTTAAA
Statistics
Matches: 272, Mismatches: 59, Indels: 32
0.75 0.16 0.09
Matches are distributed among these distances:
16 22 0.08
17 145 0.53
18 53 0.19
19 31 0.11
20 10 0.04
21 11 0.04
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (17 bp):
TTTGAAACACGAAAATT
Found at i:29366476 original size:19 final size:19
Alignment explanation
Indices: 29366454--29366531 Score: 63
Period size: 19 Copynumber: 4.2 Consensus size: 19
29366444 AATACGACAA
*
29366454 TTTTTGAAATATGAGAATT
1 TTTTTAAAATATGAGAATT
*
29366473 TTTTTAAAACATG-GAAATT
1 TTTTTAAAATATGAG-AATT
* **
29366492 TTTTTGAAAACA--AGAAAA
1 TTTTT-AAAATATGAGAATT
*
29366510 TTTTCAAAATATGAGAATT
1 TTTTTAAAATATGAGAATT
29366529 TTT
1 TTT
29366532 GAAAACACGG
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
17 5 0.11
18 7 0.15
19 28 0.61
20 6 0.13
ACGTcount: A:0.42, C:0.04, G:0.12, T:0.42
Consensus pattern (19 bp):
TTTTTAAAATATGAGAATT
Found at i:29366494 original size:20 final size:20
Alignment explanation
Indices: 29366469--29366513 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
29366459 GAAATATGAG
* *
29366469 AATTTTTTT-AAAACATGGA
1 AATTTTTTTGAAAACAAGAA
29366488 AATTTTTTTGAAAACAAGAA
1 AATTTTTTTGAAAACAAGAA
29366508 AATTTT
1 AATTTT
29366514 CAAAATATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.42
Consensus pattern (20 bp):
AATTTTTTTGAAAACAAGAA
Found at i:29366512 original size:56 final size:57
Alignment explanation
Indices: 29366391--29366646 Score: 204
Period size: 56 Copynumber: 4.8 Consensus size: 57
29366381 AAAATTTTAG
* * * * **
29366391 AAACACGAAAATTTTTAAAACACGACAA--TTTTG-AAACACGGTCAA--TTTTTGA
1 AAACACGAAAATTTTTGAAATATGAGAATTTTTTGAAAACACGGGAAATTTTTTTGA
* * * *
29366443 AAATACGACAATTTTTGAAATATGAGAATTTTTTTAAAACA-TGGAAATTTTTTTGA
1 AAACACGAAAATTTTTGAAATATGAGAATTTTTTGAAAACACGGGAAATTTTTTTGA
* ** *
29366499 AAACAAGAAAATTTTCAAAATATGAGAA-TTTTTGAAAACACGGGAAATTTTTTTAA
1 AAACACGAAAATTTTTGAAATATGAGAATTTTTTGAAAACACGGGAAATTTTTTTGA
*
29366555 AAACACGAAAATTTTTGAAACACT-AGAA-TTTTT-AAAACAC--GAAGA--TTTTTG-
1 AAACACGAAAATTTTTGAAATA-TGAGAATTTTTTGAAAACACGGGAA-ATTTTTTTGA
* ** *
29366606 AAACACGAAAATTTTAGAAACGTGA-AAATTTTT-AAAACACG
1 AAACACGAAAATTTTTGAAATATGAGAATTTTTTGAAAACACG
29366647 ACAATTTTGA
Statistics
Matches: 168, Mismatches: 25, Indels: 22
0.78 0.12 0.10
Matches are distributed among these distances:
50 3 0.02
51 33 0.20
52 27 0.16
53 3 0.02
54 8 0.05
55 23 0.14
56 70 0.42
57 1 0.01
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.32
Consensus pattern (57 bp):
AAACACGAAAATTTTTGAAATATGAGAATTTTTTGAAAACACGGGAAATTTTTTTGA
Found at i:29366557 original size:21 final size:20
Alignment explanation
Indices: 29366527--29366570 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
29366517 AATATGAGAA
* *
29366527 TTTTTGAAAACACGGGAAATT
1 TTTTTAAAAACAC-GAAAATT
29366548 TTTTTAAAAACACGAAAATT
1 TTTTTAAAAACACGAAAATT
29366568 TTT
1 TTT
29366571 GAAACACTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (20 bp):
TTTTTAAAAACACGAAAATT
Found at i:29366964 original size:5 final size:5
Alignment explanation
Indices: 29366954--29366978 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
29366944 TAAAATTATT
29366954 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
29366979 ATTGAAGTAA
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:29367247 original size:7 final size:7
Alignment explanation
Indices: 29367235--29367262 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
29367225 CCCCTTCTTC
29367235 TTCTTTT
1 TTCTTTT
29367242 TTCTTTT
1 TTCTTTT
29367249 TTCTTTT
1 TTCTTTT
29367256 TTCTTTT
1 TTCTTTT
29367263 CTTTTTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TTCTTTT
Found at i:29367345 original size:19 final size:19
Alignment explanation
Indices: 29367314--29367377 Score: 67
Period size: 24 Copynumber: 3.2 Consensus size: 19
29367304 GGGTCTGGCT
29367314 TGCTGGG-TGCGCTGGGTC
1 TGCTGGGCTGCGCTGGGTC
29367332 TGCTGGGCTGCGCTGGGCCTGGCC
1 TGCTGGGCTGCGCTGGG--T---C
*
29367356 TGCTGGGCTGCGCTGGGCC
1 TGCTGGGCTGCGCTGGGTC
29367375 TGC
1 TGC
29367378 CCTACTGGGC
Statistics
Matches: 39, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
18 7 0.18
19 13 0.33
21 1 0.03
24 18 0.46
ACGTcount: A:0.00, C:0.30, G:0.47, T:0.23
Consensus pattern (19 bp):
TGCTGGGCTGCGCTGGGTC
Found at i:29367358 original size:24 final size:24
Alignment explanation
Indices: 29367331--29367401 Score: 124
Period size: 24 Copynumber: 3.0 Consensus size: 24
29367321 TGCGCTGGGT
*
29367331 CTGCTGGGCTGCGCTGGGCCTGGC
1 CTGCTGGGCTGCGCTGGGCCTGCC
29367355 CTGCTGGGCTGCGCTGGGCCTGCC
1 CTGCTGGGCTGCGCTGGGCCTGCC
*
29367379 CTACTGGGCTGCGCTGGGCCTGC
1 CTGCTGGGCTGCGCTGGGCCTGC
29367402 TGAAAATGGC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.01, C:0.35, G:0.42, T:0.21
Consensus pattern (24 bp):
CTGCTGGGCTGCGCTGGGCCTGCC
Found at i:29367446 original size:22 final size:21
Alignment explanation
Indices: 29367413--29367456 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
29367403 GAAAATGGCC
29367413 TGTTTTCTTTTTTTTTTTGCTT
1 TGTTTTCTTTTTTTTTTT-CTT
29367435 TGTTCTTC-TTTTTTTTTTCTT
1 TGTT-TTCTTTTTTTTTTTCTT
29367456 T
1 T
29367457 TTGGGCTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 4 0.19
22 14 0.67
23 3 0.14
ACGTcount: A:0.00, C:0.11, G:0.07, T:0.82
Consensus pattern (21 bp):
TGTTTTCTTTTTTTTTTTCTT
Found at i:29367595 original size:17 final size:18
Alignment explanation
Indices: 29367573--29367665 Score: 80
Period size: 19 Copynumber: 4.8 Consensus size: 18
29367563 TTACAAAATA
29367573 TTTTCTT-TTTTTTCTTT
1 TTTTCTTCTTTTTTCTTT
*
29367590 TTTTCTGTCTTTCTTCTTCT
1 TTTTCT-TCTTTTTTCTT-T
*
29367610 TCTTCCTTCTTTCTTTCTCTT
1 T-TTTCTTCTTT-TTTCT-TT
*
29367631 CTTTCTTCTTTTTTCTTCT
1 TTTTCTTCTTTTTTCTT-T
*
29367650 TCTTCTTCTTCTTTTC
1 TTTTCTTCTT-TTTTC
29367666 CGTTCGGTCT
Statistics
Matches: 61, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
17 6 0.10
18 2 0.03
19 22 0.36
20 21 0.34
21 9 0.15
22 1 0.02
ACGTcount: A:0.00, C:0.26, G:0.01, T:0.73
Consensus pattern (18 bp):
TTTTCTTCTTTTTTCTTT
Found at i:29367606 original size:3 final size:3
Alignment explanation
Indices: 29367600--29367662 Score: 69
Period size: 3 Copynumber: 20.7 Consensus size: 3
29367590 TTTTCTGTCT
29367600 TTC TTC TTC TTC TTCC TTC TTTC TT- TCTC TTC TTTC TTC TT- TT- TTC
1 TTC TTC TTC TTC TT-C TTC -TTC TTC T-TC TTC -TTC TTC TTC TTC TTC
29367646 TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TT
29367663 TTCCGTTCGG
Statistics
Matches: 54, Mismatches: 0, Indels: 12
0.82 0.00 0.18
Matches are distributed among these distances:
2 5 0.09
3 39 0.72
4 10 0.19
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TTC
Found at i:29367622 original size:20 final size:19
Alignment explanation
Indices: 29367575--29367659 Score: 86
Period size: 20 Copynumber: 4.4 Consensus size: 19
29367565 ACAAAATATT
* *
29367575 TTCTT-TTTTTTCTT-TTT
1 TTCTTCTTTCTTCTTCTTC
29367592 TTCTGTCTTTCTTCTTCTTC
1 TTCT-TCTTTCTTCTTCTTC
29367612 TTCCTTCTTTCTT-TCTCTTC
1 TT-CTTCTTTCTTCT-TCTTC
*
29367632 TTTCTTCTTTTTTCTTCTTC
1 -TTCTTCTTTCTTCTTCTTC
29367652 TTCTTCTT
1 TTCTTCTT
29367660 CTTTTCCGTT
Statistics
Matches: 58, Mismatches: 3, Indels: 12
0.79 0.04 0.16
Matches are distributed among these distances:
17 4 0.07
18 1 0.02
19 17 0.29
20 31 0.53
21 5 0.09
ACGTcount: A:0.00, C:0.26, G:0.01, T:0.73
Consensus pattern (19 bp):
TTCTTCTTTCTTCTTCTTC
Found at i:29368068 original size:30 final size:30
Alignment explanation
Indices: 29368014--29368182 Score: 171
Period size: 30 Copynumber: 5.7 Consensus size: 30
29368004 AAATACAGCA
* * **
29368014 AAAGTTTTGGGGCCAAAACATAATTTTGAG
1 AAAGTTTAGGGGTCAAAATGTAATTTTGAG
* * * *
29368044 AAAGCTTAAGGGTCCAAATGTAATTTTAAG
1 AAAGTTTAGGGGTCAAAATGTAATTTTGAG
*
29368074 AAAGTTTAGGGGTCAAAATGTAATTTAGA-
1 AAAGTTTAGGGGTCAAAATGTAATTTTGAG
** *
29368103 AAAGTTTAGGGGTTGAACTGTAATTTTGAG
1 AAAGTTTAGGGGTCAAAATGTAATTTTGAG
* * *
29368133 AAAGTTTATGGGTTAAAATGCAATTTT-AG
1 AAAGTTTAGGGGTCAAAATGTAATTTTGAG
*
29368162 AAAAGTTTAGTGGTCAAAATG
1 -AAAGTTTAGGGGTCAAAATG
29368183 CAAAAAAATT
Statistics
Matches: 113, Mismatches: 24, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
29 27 0.24
30 86 0.76
ACGTcount: A:0.38, C:0.06, G:0.24, T:0.33
Consensus pattern (30 bp):
AAAGTTTAGGGGTCAAAATGTAATTTTGAG
Found at i:29368588 original size:76 final size:77
Alignment explanation
Indices: 29368465--29368973 Score: 744
Period size: 77 Copynumber: 6.6 Consensus size: 77
29368455 CGACATGTGC
* * ** *
29368465 CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTCAAAAAACATAAATTTAAAAGAAA
1 CCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTTGAAAAACAGAAATTTAAAAGAAA
*
29368530 TACCTCGGCATGG
65 TACCTCGGCATGA
* * * *
29368543 TCTGAGGCTCAACTCACATCTGTATTATGAGTTGA-TTTTTGAAAAACGGAAATTTAAAAGAAAT
1 CCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAACAGAAATTTAAAAGAAAT
29368607 ACCTCGGCATGA
66 ACCTCGGCATGA
29368619 CCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAC-GAAAATTTAAAAGAAA
1 CCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAACAG-AAATTTAAAAGAAA
*
29368683 TACCTCGGCATAA
65 TACCTCGGCATGA
*
29368696 CCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTTGAAAAACGGAAATTTAAAAGAAAT
1 CCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAACAGAAATTTAAAAGAAAT
*
29368760 ACCTTGGCATGA
66 ACCTCGGCATGA
29368772 CCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAACAGAAA-TTAAAA-AA
1 CCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTG--AAAAACAGAAATTTAAAAGAA
* *
29368835 ATACCTCAGCGTGA
64 ATACCTCGGCATGA
*
29368849 CCGGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAAGCAGAAA-TTAAAA-A
1 CCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTG--AAAAA-CAGAAATTTAAAAGA
* *
29368912 AATACCTCAGCGTGA
63 AATACCTCGGCATGA
29368927 CCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAA
1 CCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAA
29368974 AAACAGAATT
Statistics
Matches: 402, Mismatches: 22, Indels: 16
0.91 0.05 0.04
Matches are distributed among these distances:
76 146 0.36
77 153 0.38
78 93 0.23
79 10 0.02
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.28
Consensus pattern (77 bp):
CCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAACAGAAATTTAAAAGAAAT
ACCTCGGCATGA
Found at i:29368655 original size:153 final size:152
Alignment explanation
Indices: 29368392--29368989 Score: 735
Period size: 153 Copynumber: 3.9 Consensus size: 152
29368382 GCGTGAAACA
* * * * * * *
29368392 CGAGGCTCAACTCACCTCTTGGATTATGATTTGATCTTCGAAAAAC-AAAAATT--GA-AAATAC
1 CGAGGCTCAACTCACCTC-TGTATTATGAGTTGATTTTTGAAAAACGGAAATTTAAAAGAAATAC
* * * * * *
29368453 CCCGACATGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTCAAAAAACATAA
65 CTCGGCA--TGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTAAAAAAACA-AA
**
29368518 ATTTAAAAGAAATACCTCGGCATGGTC
126 ATTTAAAAGAAATACCTCGGCATGACC
* *
29368545 TGAGGCTCAACTCACATCTGTATTATGAGTTGATTTTTGAAAAACGGAAATTTAAAAGAAATACC
1 CGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACGGAAATTTAAAAGAAATACC
**
29368610 TCGGCATGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAACGAAAATTT
66 TCGGCATGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAAC-AAAATTT
*
29368675 AAAAGAAATACCTCGGCATAACC
130 AAAAGAAATACCTCGGCATGACC
29368698 CGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACGGAAATTTAAAAGAAATACC
1 CGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACGGAAATTTAAAAGAAATACC
*
29368763 TTGGCATGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAACAGAAA-
66 TCGGCATGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTT-AAAAAAACA-AAAT
* *
29368827 TTAAAA-AAATACCTCAGCGTGACC
128 TTAAAAGAAATACCTCGGCATGACC
* *
29368851 GGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAAGCAGAAA-TTAAAA-AAA
1 CGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTTG--AAAAA-CGGAAATTTAAAAGAAA
* *
29368914 TACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAAACA
62 TACCTCGGCATGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTT--AAAAAAACA
*
29368979 GAATTTTAAAA
124 -AAATTTAAAA
29368990 ATATTTCTTG
Statistics
Matches: 397, Mismatches: 34, Indels: 24
0.87 0.07 0.05
Matches are distributed among these distances:
152 23 0.06
153 223 0.56
154 42 0.11
155 64 0.16
156 34 0.09
157 11 0.03
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (152 bp):
CGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACGGAAATTTAAAAGAAATACC
TCGGCATGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAACAAAATTTA
AAAGAAATACCTCGGCATGACC
Found at i:29369947 original size:21 final size:21
Alignment explanation
Indices: 29369923--29369974 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 21
29369913 CGGGTTTTCA
29369923 TCTTGATTTTTC-TTTTTCTTT
1 TCTTG-TTTTTCTTTTTTCTTT
29369944 TCTTTGTTTTTTCTTTTTTCTTT
1 TC-TTG-TTTTTCTTTTTTCTTT
29369967 T-TTGTTTT
1 TCTTGTTTT
29369975 GTTTTTGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 4 0.14
21 5 0.18
22 9 0.32
23 10 0.36
ACGTcount: A:0.02, C:0.12, G:0.06, T:0.81
Consensus pattern (21 bp):
TCTTGTTTTTCTTTTTTCTTT
Found at i:29369964 original size:18 final size:19
Alignment explanation
Indices: 29369941--29369980 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
29369931 TTTCTTTTTC
29369941 TTTTCTTTGTT-TTTTCTT
1 TTTTCTTTGTTGTTTTCTT
* *
29369959 TTTTCTTTTTTGTTTTGTT
1 TTTTCTTTGTTGTTTTCTT
29369978 TTT
1 TTT
29369981 GTTTTGTTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.85
Consensus pattern (19 bp):
TTTTCTTTGTTGTTTTCTT
Found at i:29369969 original size:16 final size:16
Alignment explanation
Indices: 29369935--29370006 Score: 56
Period size: 16 Copynumber: 4.3 Consensus size: 16
29369925 TTGATTTTTC
*
29369935 TTTTTCTTTTCTT-TGT
1 TTTTTCTTTT-TTGTTT
*
29369951 TTTTTCTTTTTTCTTT
1 TTTTTCTTTTTTGTTT
*
29369967 TTTGTTTTGTTTTTGTTT
1 TTT-TTCT-TTTTTGTTT
* *
29369985 TGTTCCTTTTTTGTTGT
1 TTTTTCTTTTTTGTT-T
29370002 TTTTT
1 TTTTT
29370007 TTAAGCATAA
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
15 2 0.05
16 23 0.52
17 9 0.20
18 10 0.23
ACGTcount: A:0.00, C:0.08, G:0.10, T:0.82
Consensus pattern (16 bp):
TTTTTCTTTTTTGTTT
Done.