Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold355
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: 530098
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
File 3 of 4
Found at i:289669 original size:20 final size:20
Alignment explanation
Indices: 289626--289677 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
289616 CTTAACTGTT
*
289626 TGTATCGATACA-CACAATA
1 TGTATCGATACATCACAAAA
*
289645 TGTATCGATACATCCCAAAA
1 TGTATCGATACATCACAAAA
289665 TGTATCGATACAT
1 TGTATCGATACAT
289678 TGGCTTGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (20 bp):
TGTATCGATACATCACAAAA
Found at i:295829 original size:13 final size:13
Alignment explanation
Indices: 295810--295848 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
295800 ACAGCTTTCT
295810 GTGTATCGATACA
1 GTGTATCGATACA
*
295823 TTGTATCGATACA
1 GTGTATCGATACA
295836 GTGTATCGATACA
1 GTGTATCGATACA
295849 AAGGGTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (13 bp):
GTGTATCGATACA
Found at i:296538 original size:230 final size:230
Alignment explanation
Indices: 296195--296663 Score: 938
Period size: 230 Copynumber: 2.0 Consensus size: 230
296185 TTTTGCATCG
296195 AAAATGTCCCATTTTCAAAATCAAAGCCTCCAAAGTAGTGACCACCACCTGTTCGGCAAAAGGCC
1 AAAATGTCCCATTTTCAAAATCAAAGCCTCCAAAGTAGTGACCACCACCTGTTCGGCAAAAGGCC
296260 TGAACCAAAGTCCTCTAGGCAGCACCTACAGGTCGCGACCGGCACCCCCAAGTCGCAACCGGGCA
66 TGAACCAAAGTCCTCTAGGCAGCACCTACAGGTCGCGACCGGCACCCCCAAGTCGCAACCGGGCA
296325 GCCCTCACACTAGCAGCCTAGAACATCCGAAACACCTCAGTTTTGTACCAAAACACTTCAAATTC
131 GCCCTCACACTAGCAGCCTAGAACATCCGAAACACCTCAGTTTTGTACCAAAACACTTCAAATTC
296390 ATTCTGATGGCTCCTCGGATGAAATTAACCGCTCA
196 ATTCTGATGGCTCCTCGGATGAAATTAACCGCTCA
296425 AAAATGTCCCATTTTCAAAATCAAAGCCTCCAAAGTAGTGACCACCACCTGTTCGGCAAAAGGCC
1 AAAATGTCCCATTTTCAAAATCAAAGCCTCCAAAGTAGTGACCACCACCTGTTCGGCAAAAGGCC
296490 TGAACCAAAGTCCTCTAGGCAGCACCTACAGGTCGCGACCGGCACCCCCAAGTCGCAACCGGGCA
66 TGAACCAAAGTCCTCTAGGCAGCACCTACAGGTCGCGACCGGCACCCCCAAGTCGCAACCGGGCA
296555 GCCCTCACACTAGCAGCCTAGAACATCCGAAACACCTCAGTTTTGTACCAAAACACTTCAAATTC
131 GCCCTCACACTAGCAGCCTAGAACATCCGAAACACCTCAGTTTTGTACCAAAACACTTCAAATTC
296620 ATTCTGATGGCTCCTCGGATGAAATTAACCGCTCA
196 ATTCTGATGGCTCCTCGGATGAAATTAACCGCTCA
296655 AAAATGTCC
1 AAAATGTCC
296664 TCGAGATGCC
Statistics
Matches: 239, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
230 239 1.00
ACGTcount: A:0.31, C:0.32, G:0.17, T:0.19
Consensus pattern (230 bp):
AAAATGTCCCATTTTCAAAATCAAAGCCTCCAAAGTAGTGACCACCACCTGTTCGGCAAAAGGCC
TGAACCAAAGTCCTCTAGGCAGCACCTACAGGTCGCGACCGGCACCCCCAAGTCGCAACCGGGCA
GCCCTCACACTAGCAGCCTAGAACATCCGAAACACCTCAGTTTTGTACCAAAACACTTCAAATTC
ATTCTGATGGCTCCTCGGATGAAATTAACCGCTCA
Found at i:298551 original size:13 final size:13
Alignment explanation
Indices: 298529--298559 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
298519 CGATACAGAT
298529 TACATAGTATCGA
1 TACATAGTATCGA
*
298542 TACATTGTATCGA
1 TACATAGTATCGA
298555 TACAT
1 TACAT
298560 GGCCAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATAGTATCGA
Found at i:298684 original size:20 final size:20
Alignment explanation
Indices: 298641--298725 Score: 87
Period size: 20 Copynumber: 4.7 Consensus size: 20
298631 CTTAACTGTT
* *
298641 TGTATCGATACA-CACAATA
1 TGTATCGATACATCCCAAAA
298660 TGTATCGATACATCCCAAAA
1 TGTATCGATACATCCCAAAA
298680 TGTATCGATACAT-------
1 TGTATCGATACATCCCAAAA
*
298693 TGTATCGATACATCCTAAAA
1 TGTATCGATACATCCCAAAA
298713 TGTATCGATACAT
1 TGTATCGATACAT
298726 TGGCTTGTAA
Statistics
Matches: 56, Mismatches: 2, Indels: 15
0.77 0.03 0.21
Matches are distributed among these distances:
13 13 0.23
19 12 0.21
20 31 0.55
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.31
Consensus pattern (20 bp):
TGTATCGATACATCCCAAAA
Found at i:298698 original size:13 final size:13
Alignment explanation
Indices: 298680--298705 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
298670 CATCCCAAAA
298680 TGTATCGATACAT
1 TGTATCGATACAT
298693 TGTATCGATACAT
1 TGTATCGATACAT
298706 CCTAAAATGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:298702 original size:33 final size:33
Alignment explanation
Indices: 298660--298727 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
298650 ACACACAATA
298660 TGTATCGATACATCCCAAAATGTATCGATACAT
1 TGTATCGATACATCCCAAAATGTATCGATACAT
*
298693 TGTATCGATACATCCTAAAATGTATCGATACAT
1 TGTATCGATACATCCCAAAATGTATCGATACAT
298726 TG
1 TG
298728 GCTTGTAACG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.32
Consensus pattern (33 bp):
TGTATCGATACATCCCAAAATGTATCGATACAT
Found at i:314166 original size:38 final size:38
Alignment explanation
Indices: 314115--314188 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
314105 AATGCGTTTC
314115 TTGAAGTTGTGTATCAGATTACAGGTTATGAATTATAT
1 TTGAAGTTGTGTATCAGATTACAGGTTATGAATTATAT
*
314153 TTGAAGTTGTGTATCCGATTACAGGTTATGAATTAT
1 TTGAAGTTGTGTATCAGATTACAGGTTATGAATTAT
314189 GTTGATACAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.30, C:0.07, G:0.22, T:0.42
Consensus pattern (38 bp):
TTGAAGTTGTGTATCAGATTACAGGTTATGAATTATAT
Found at i:314682 original size:13 final size:13
Alignment explanation
Indices: 314664--314703 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
314654 ACATTTTGCT
*
314664 TTGTATCAATACA
1 TTGTATCGATACA
*
314677 TTGTATCGATGCA
1 TTGTATCGATACA
314690 TTGTATCGATACA
1 TTGTATCGATACA
314703 T
1 T
314704 GATCATTGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:314712 original size:19 final size:18
Alignment explanation
Indices: 314688--314744 Score: 78
Period size: 19 Copynumber: 3.0 Consensus size: 18
314678 TGTATCGATG
314688 CATTGTATCGATACATGA
1 CATTGTATCGATACATGA
314706 TCATTGTATCGATACATGGA
1 -CATTGTATCGATACAT-GA
*
314726 CAAATGTATCGATACATGA
1 C-ATTGTATCGATACATGA
314745 AACTGGCAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
19 19 0.54
20 16 0.46
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.32
Consensus pattern (18 bp):
CATTGTATCGATACATGA
Found at i:314735 original size:20 final size:20
Alignment explanation
Indices: 314691--314743 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
314681 ATCGATGCAT
*
314691 TGTATCGATACAT-GATCAT
1 TGTATCGATACATGGATCAA
314710 TGTATCGATACATGGA-CAAA
1 TGTATCGATACATGGATC-AA
314730 TGTATCGATACATG
1 TGTATCGATACATG
314744 AAACTGGCAG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (20 bp):
TGTATCGATACATGGATCAA
Found at i:314797 original size:20 final size:20
Alignment explanation
Indices: 314772--314825 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
314762 CTACCACTAT
*
314772 TTGTATTGATACAT-AGGACA
1 TTGTATCGATACATGAGGA-A
*
314792 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGAGGAA
314812 TTGTATCGATACAT
1 TTGTATCGATACAT
314826 TGCTTGTAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 28 0.90
21 3 0.10
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGAGGAA
Found at i:316717 original size:65 final size:65
Alignment explanation
Indices: 316634--316767 Score: 241
Period size: 65 Copynumber: 2.1 Consensus size: 65
316624 ACAAATTTTT
* * *
316634 TAATGTCATTACATACTTGGCCAAATGTTAAAGAACTTGTTTGCAATTTTTTATAATTTATTTCA
1 TAATGTCAGTACATACTTGGCCAAATGTTAAAGAACTTATTTGCAAATTTTTATAATTTATTTCA
316699 TAATGTCAGTACATACTTGGCCAAATGTTAAAGAACTTATTTGCAAATTTTTATAATTTATTTCA
1 TAATGTCAGTACATACTTGGCCAAATGTTAAAGAACTTATTTGCAAATTTTTATAATTTATTTCA
316764 TAAT
1 TAAT
316768 TTTGGGTTAC
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.43
Consensus pattern (65 bp):
TAATGTCAGTACATACTTGGCCAAATGTTAAAGAACTTATTTGCAAATTTTTATAATTTATTTCA
Found at i:322153 original size:13 final size:13
Alignment explanation
Indices: 322135--322159 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
322125 CATTATGCTT
322135 TGTATCGATACAA
1 TGTATCGATACAA
322148 TGTATCGATACA
1 TGTATCGATACA
322160 TGTTCATTAT
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:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:322174 original size:19 final size:20
Alignment explanation
Indices: 322150--322200 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
322140 CGATACAATG
**
322150 TATCGATACATGTTC-ATTA
1 TATCGATACATGGACAATTA
*
322169 TATCGATACATGGACAATTG
1 TATCGATACATGGACAATTA
322189 TATCGATACATG
1 TATCGATACATG
322201 AAATTGGCAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (20 bp):
TATCGATACATGGACAATTA
Found at i:322194 original size:20 final size:20
Alignment explanation
Indices: 322144--322200 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 20
322134 TTGTATCGAT
*
322144 ACAA-TGTATCGATACATGT
1 ACAATTGTATCGATACATGG
* *
322163 TC-ATTATATCGATACATGG
1 ACAATTGTATCGATACATGG
322182 ACAATTGTATCGATACATG
1 ACAATTGTATCGATACATG
322201 AAATTGGCAG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 1 0.03
19 15 0.48
20 15 0.48
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (20 bp):
ACAATTGTATCGATACATGG
Found at i:322266 original size:13 final size:13
Alignment explanation
Indices: 322245--322287 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
322235 CGATACATGG
*
322245 TACATTGTATCGA
1 TACAATGTATCGA
322258 TACAATGTATCGA
1 TACAATGTATCGA
*
322271 TATAATGTATCGA
1 TACAATGTATCGA
322284 TACA
1 TACA
322288 TGATGAATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (13 bp):
TACAATGTATCGA
Found at i:322301 original size:20 final size:21
Alignment explanation
Indices: 322229--322308 Score: 83
Period size: 20 Copynumber: 3.7 Consensus size: 21
322219 CTACTACTTT
*
322229 TTGTATCGATACATGGT-ACA
1 TTGTATCGATACATGATGACA
*
322249 TTGTATCGATACAATGTATCGATA
1 TTGTATCGATAC-ATG-AT-GACA
322273 TAATGTATCGATACATGATGA-A
1 T--TGTATCGATACATGATGACA
322295 TTGTATCGATACAT
1 TTGTATCGATACAT
322309 TGCTTCTAAC
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
20 25 0.48
21 3 0.06
22 3 0.06
23 2 0.04
24 5 0.10
25 3 0.06
26 11 0.21
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.36
Consensus pattern (21 bp):
TTGTATCGATACATGATGACA
Found at i:326667 original size:4 final size:4
Alignment explanation
Indices: 326658--326690 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
326648 GATTTATGTA
326658 ATTT ATTT ATTT ATTT ATTT ATTT -TTT ATTT AT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT AT
326691 ACTTTGATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.11
4 25 0.89
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
ATTT
Found at i:328629 original size:15 final size:14
Alignment explanation
Indices: 328595--328628 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
328585 CAAGTTTAGG
328595 TTTTTTAAACTTGA
1 TTTTTTAAACTTGA
* *
328609 TTTTTTCAATTTGA
1 TTTTTTAAACTTGA
328623 TTTTTT
1 TTTTTT
328629 TATAAGTTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.21, C:0.06, G:0.06, T:0.68
Consensus pattern (14 bp):
TTTTTTAAACTTGA
Found at i:329580 original size:22 final size:21
Alignment explanation
Indices: 329508--329592 Score: 65
Period size: 20 Copynumber: 4.1 Consensus size: 21
329498 AAAGAGGTTG
329508 ATATAAATTATAA-T-TAAATT
1 ATATAAATT-TAATTATAAATT
329528 AT-T--ATTTAATTAATAAAATT
1 ATATAAATTTAATT-AT-AAATT
*
329548 -TTTAAATTTAATTATAAATT
1 ATATAAATTTAATTATAAATT
*
329568 ATATAAATATTAATTTAAAAATT
1 ATATAAAT-TTAA-TTATAAATT
329591 AT
1 AT
329593 TTTTTATTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 17
0.74 0.03 0.24
Matches are distributed among these distances:
16 3 0.06
17 4 0.08
19 3 0.06
20 13 0.25
21 8 0.15
22 12 0.23
23 10 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
ATATAAATTTAATTATAAATT
Found at i:329601 original size:7 final size:7
Alignment explanation
Indices: 329589--329618 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
329579 AATTTAAAAA
329589 TTATTTT
1 TTATTTT
329596 TTA-TTT
1 TTATTTT
329602 TTATTTT
1 TTATTTT
329609 TTATTTT
1 TTATTTT
329616 TTA
1 TTA
329619 AATATTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (7 bp):
TTATTTT
Found at i:329607 original size:13 final size:13
Alignment explanation
Indices: 329589--329616 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
329579 AATTTAAAAA
329589 TTATTTTTTATTT
1 TTATTTTTTATTT
329602 TTATTTTTTATTT
1 TTATTTTTTATTT
329615 TT
1 TT
329617 TAAATATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (13 bp):
TTATTTTTTATTT
Found at i:332387 original size:2 final size:2
Alignment explanation
Indices: 332380--332420 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
332370 ATGAATCTTT
332380 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
332421 TTGTAGAAGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:335983 original size:22 final size:23
Alignment explanation
Indices: 335958--336003 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
335948 TTATTGAAAG
*
335958 TAAAAATAATAATATA-ATATGA
1 TAAAAATAAAAATATATATATGA
*
335980 TAAAATTAAAAATATATATATGA
1 TAAAAATAAAAATATATATATGA
336003 T
1 T
336004 TGCAATCACT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (23 bp):
TAAAAATAAAAATATATATATGA
Found at i:341735 original size:31 final size:31
Alignment explanation
Indices: 341700--341760 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
341690 AAATAATTAA
*
341700 AATATAATAAAAATTA-ATATATATCATAAAT
1 AATATAATAAAAATTATATAAATAT-ATAAAT
* *
341731 AATATATTAAAATTTATATAAATATATAAA
1 AATATAATAAAAATTATATAAATATATAAA
341761 ATATAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 19 0.73
32 7 0.27
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (31 bp):
AATATAATAAAAATTATATAAATATATAAAT
Found at i:341764 original size:45 final size:45
Alignment explanation
Indices: 341686--341813 Score: 116
Period size: 45 Copynumber: 2.7 Consensus size: 45
341676 TGGACATAAG
*
341686 ATAAAAATAAT-TAAAATATAATAAAAATTAATATATATCATAAATAATAT
1 ATAAAAATAATAT-AAATATAAT-AAAA-T-ATATATAT-A-ATATAATAT
* * * * *
341736 ATTAAAATTTATATAAATAT-ATAAAATATAAAATATAATTTAATTT
1 A-TAAAAATAATATAAATATAATAAAATAT-ATATATAATATAATAT
341782 ATAAAAATAATATAAATATAATAAAATATATA
1 ATAAAAATAATATAAATATAATAAAATATATA
341814 AATTCTTAAT
Statistics
Matches: 65, Mismatches: 9, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
45 18 0.28
46 16 0.25
47 3 0.05
48 6 0.09
49 4 0.06
50 3 0.05
51 14 0.22
52 1 0.02
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (45 bp):
ATAAAAATAATATAAATATAATAAAATATATATATAATATAATAT
Found at i:341771 original size:36 final size:38
Alignment explanation
Indices: 341689--341817 Score: 117
Period size: 36 Copynumber: 3.4 Consensus size: 38
341679 ACATAAGATA
* *
341689 AAAATA-ATTAAAATATAATAAAAATTAATATATATCATAA-
1 AAAATATATT-AAAT-TTATAAAAA-TAATATAAAT-ATAAT
* *
341729 ATAATATATTAAAATTTATATAAAT-ATATAAA-AT-AT
1 AAAATATATT-AAATTTATAAAAATAATATAAATATAAT
*
341765 AAAATATAATTTAATTTATAAAAATAATATAAATATAAT
1 AAAATAT-ATTAAATTTATAAAAATAATATAAATATAAT
341804 AAAATATA-TAAATT
1 AAAATATATTAAATT
341818 CTTAATAAAT
Statistics
Matches: 75, Mismatches: 8, Indels: 15
0.77 0.08 0.15
Matches are distributed among these distances:
35 1 0.01
36 20 0.27
37 15 0.20
38 9 0.12
39 10 0.13
40 12 0.16
41 8 0.11
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (38 bp):
AAAATATATTAAATTTATAAAAATAATATAAATATAAT
Found at i:342454 original size:28 final size:28
Alignment explanation
Indices: 342415--342473 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
342405 ATTCAAAAAA
342415 TTTTAAAATTTTGTAAGGTATAAATATT
1 TTTTAAAATTTTGTAAGGTATAAATATT
* *
342443 TTTTAAATTTTTTTAAGGTATAAATATT
1 TTTTAAAATTTTGTAAGGTATAAATATT
342471 TTT
1 TTT
342474 AATTTCGATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (28 bp):
TTTTAAAATTTTGTAAGGTATAAATATT
Found at i:342949 original size:2 final size:2
Alignment explanation
Indices: 342942--342976 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
342932 TATACACATT
342942 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
342977 CTTTTTTTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:343904 original size:17 final size:17
Alignment explanation
Indices: 343826--343905 Score: 51
Period size: 15 Copynumber: 4.5 Consensus size: 17
343816 GAATTGAAAA
343826 TTATATTTTATTTAA-A-
1 TTATATTTT-TTTAATAT
*
343842 -TATATTTTGTTTGAATGT
1 TTATATTTT-TTT-AATAT
343860 TGTATTATTTATTTTAATTAT
1 T-TA-TATTT-TTTTAA-TAT
*
343881 TTA-ATTTTTTTAATCT
1 TTATATTTTTTTAATAT
343897 TTATATTTT
1 TTATATTTT
343906 GATTTATAGT
Statistics
Matches: 51, Mismatches: 4, Indels: 17
0.71 0.06 0.24
Matches are distributed among these distances:
15 11 0.22
16 7 0.14
17 11 0.22
18 4 0.08
20 6 0.12
21 11 0.22
22 1 0.02
ACGTcount: A:0.28, C:0.01, G:0.05, T:0.66
Consensus pattern (17 bp):
TTATATTTTTTTAATAT
Found at i:347881 original size:27 final size:27
Alignment explanation
Indices: 347831--347882 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
347821 TCATACTATA
* *
347831 TTTATATTATTTTTTGTGTTGTATTAT
1 TTTATATTATTTTTTATGTAGTATTAT
347858 TTTA-ATTATTTTTCTATGTAGTATT
1 TTTATATTATTTTT-TATGTAGTATT
347883 TATATCATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.21, C:0.02, G:0.10, T:0.67
Consensus pattern (27 bp):
TTTATATTATTTTTTATGTAGTATTAT
Found at i:348084 original size:32 final size:32
Alignment explanation
Indices: 348012--348095 Score: 93
Period size: 32 Copynumber: 2.6 Consensus size: 32
348002 TTTCAGAGTG
348012 TTATATA-TTTATATAAATTTTGATATATTTA
1 TTATATATTTTATATAAATTTTGATATATTTA
* *
348043 TTATTTATTTTATGTAAATTTT-AT-TATTATA
1 TTATATATTTTATATAAATTTTGATATATT-TA
348074 TTATCATATTTGTATTATAAAT
1 TTAT-ATATTT-TA-TATAAAT
348096 ATATTAAGAG
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
30 4 0.09
31 14 0.32
32 18 0.41
33 2 0.05
34 6 0.14
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.60
Consensus pattern (32 bp):
TTATATATTTTATATAAATTTTGATATATTTA
Found at i:352900 original size:15 final size:15
Alignment explanation
Indices: 352877--352932 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
352867 AAATATATCT
352877 TATTAATAATAAAAA
1 TATTAATAATAAAAA
* *
352892 TATTTATAATAATAA
1 TATTAATAATAAAAA
*
352907 T-TTAAAAAATAATAAA
1 TATT-AATAATAA-AAA
*
352923 TATTTATAAT
1 TATTAATAAT
352933 TATTTTTATC
Statistics
Matches: 31, Mismatches: 7, Indels: 5
0.72 0.16 0.12
Matches are distributed among these distances:
14 2 0.06
15 20 0.65
16 7 0.23
17 2 0.06
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TATTAATAATAAAAA
Found at i:352913 original size:22 final size:21
Alignment explanation
Indices: 352855--352913 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 21
352845 AATAAAAAAA
352855 TTATT-ATAATTTAAATATATC
1 TTATTAATAATTTAAA-ATATC
*
352876 TTATTAATAA-TAAAAATAT-
1 TTATTAATAATTTAAAATATC
352895 TTATAATAATAATTTAAAA
1 TTAT--TAATAATTTAAAA
352914 AATAATAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
19 4 0.12
20 4 0.12
21 15 0.47
22 9 0.28
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
TTATTAATAATTTAAAATATC
Found at i:352987 original size:31 final size:34
Alignment explanation
Indices: 352932--352996 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 34
352922 ATATTTATAA
352932 TTATTTTTATCAACTTAAAAATTATATA-TATTT
1 TTATTTTTATCAACTTAAAAATTATATATTATTT
*
352965 TTATTTTTAT-ATA-TT-AAAATTATTTATTATTT
1 TTATTTTTATCA-ACTTAAAAATTATATATTATTT
352997 AATAATAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
31 10 0.34
32 8 0.28
33 11 0.38
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (34 bp):
TTATTTTTATCAACTTAAAAATTATATATTATTT
Found at i:353243 original size:16 final size:16
Alignment explanation
Indices: 353205--353254 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
353195 AATTTTTTAT
* *
353205 TTAAAATTTATTTTAA
1 TTAAAATTTAATATAA
* *
353221 TTTAATTTTAA-ATAA
1 TTAAAATTTAATATAA
353236 TTAAAATTTAATATAA
1 TTAAAATTTAATATAA
353252 TTA
1 TTA
353255 CTAAATATTA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
15 12 0.44
16 15 0.56
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAAAATTTAATATAA
Found at i:354263 original size:26 final size:26
Alignment explanation
Indices: 354218--354268 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
354208 AATATATATA
** *
354218 TATATATATATATATTATTCGTTATC
1 TATATATATATATAGGATTCATTATC
*
354244 TATATATATGTATAGGATTCATTAT
1 TATATATATATATAGGATTCATTAT
354269 TCGTGAATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.51
Consensus pattern (26 bp):
TATATATATATATAGGATTCATTATC
Found at i:355732 original size:19 final size:19
Alignment explanation
Indices: 355708--355745 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
355698 ATACTTTATA
355708 TATCGAATATGAATAAATG
1 TATCGAATATGAATAAATG
355727 TATCGAATATGAATAAATG
1 TATCGAATATGAATAAATG
355746 GTTATAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.05, G:0.16, T:0.32
Consensus pattern (19 bp):
TATCGAATATGAATAAATG
Found at i:356490 original size:2 final size:2
Alignment explanation
Indices: 356485--356514 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
356475 TCTCTCTCTC
356485 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
356515 CCTTGGTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:356748 original size:16 final size:15
Alignment explanation
Indices: 356727--356776 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
356717 TCAGTTTTGA
356727 TAATTAAACTTAATTT
1 TAATTAAA-TTAATTT
356743 TAATTAAAGTT-A-TT
1 TAATTAAA-TTAATTT
*
356757 AAATATAAATTAATTT
1 TAAT-TAAATTAATTT
356773 TAAT
1 TAAT
356777 AGCAAATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 7 0.25
15 6 0.21
16 15 0.54
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (15 bp):
TAATTAAATTAATTT
Found at i:357683 original size:12 final size:10
Alignment explanation
Indices: 357662--357717 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 10
357652 TTGCTCAACA
357662 TTTTTTCTTT
1 TTTTTTCTTT
357672 CTTTTTTGCTTT
1 -TTTTTT-CTTT
*
357684 TTTTTCCTTT
1 TTTTTTCTTT
*
357694 TTTTTT-TTC
1 TTTTTTCTTT
* *
357703 ATTTTGCTTT
1 TTTTTTCTTT
357713 TTTTT
1 TTTTT
357718 AATATAATGA
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
9 6 0.17
10 15 0.42
11 11 0.31
12 4 0.11
ACGTcount: A:0.02, C:0.12, G:0.04, T:0.82
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:357707 original size:22 final size:21
Alignment explanation
Indices: 357662--357707 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
357652 TTGCTCAACA
*
357662 TTTTTTCTTTCTTTTTTGCTT
1 TTTTTTCTTTCTTTTTTGCAT
* *
357683 TTTTTTCCTTTTTTTTTTTCAT
1 TTTTTT-CTTTCTTTTTTGCAT
357705 TTT
1 TTT
357708 GCTTTTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.02, C:0.13, G:0.02, T:0.83
Consensus pattern (21 bp):
TTTTTTCTTTCTTTTTTGCAT
Found at i:358280 original size:2 final size:2
Alignment explanation
Indices: 358273--358310 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
358263 ATAATTATTC
*
358273 AT AT AT AT AT AT AT AT AT TT 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
358311 TACAAAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:367414 original size:78 final size:78
Alignment explanation
Indices: 367304--367509 Score: 234
Period size: 78 Copynumber: 2.6 Consensus size: 78
367294 GAGATAATAA
* * * * * * * *
367304 CGGGGTTGGAGTGTTCCCTTGAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCAAT-A
*
367369 -TTAGAAAAAAAAT
65 TTTAGAAAAAAAAC
* *
367382 CGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAAAAATCAATAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCAATA-
* * * *
367447 TTTGGGAATAAAGC
65 TTTAGAAAAAAAAC
* *
367461 CGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGAT
367510 GAAATAACAA
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
77 1 0.01
78 53 0.50
79 53 0.50
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.24
Consensus pattern (78 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCAATAT
TTAGAAAAAAAAC
Found at i:367517 original size:28 final size:28
Alignment explanation
Indices: 367461--367532 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
367451 GGAATAAAGC
** *
367461 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
367489 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
**
367517 CAAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
367533 TCGACTGTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:367733 original size:51 final size:52
Alignment explanation
Indices: 367612--367741 Score: 154
Period size: 51 Copynumber: 2.5 Consensus size: 52
367602 AGTGTTTCGA
* * * * *
367612 AAATAAAACCAGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAG
1 AAATAAAACCGGGGTTGGAGTATCCCCGATTATGGAAAAATCAATATTTTAG
* * * *
367664 CAATAAAACCGGGATTGGAATATCCCCGATTAT-GAAAAATCAATATTTTGG
1 AAATAAAACCGGGGTTGGAGTATCCCCGATTATGGAAAAATCAATATTTTAG
**
367715 AAATAAAGTCGGGGTTGGAGTATCCCC
1 AAATAAAACCGGGGTTGGAGTATCCCC
367742 TCGAAAATAA
Statistics
Matches: 64, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
51 36 0.56
52 28 0.44
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (52 bp):
AAATAAAACCGGGGTTGGAGTATCCCCGATTATGGAAAAATCAATATTTTAG
Found at i:367739 original size:263 final size:263
Alignment explanation
Indices: 367410--367910 Score: 751
Period size: 263 Copynumber: 1.9 Consensus size: 263
367400 TCGAAAATAA
* * *
367410 CGGGGTTGGAGTATCCCCAATTATGAAAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAGTAT
1 CGGGATTGGAATATCCCCAATTATGAAAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTAT
* * * *
367475 CCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAAT-AACAAGGTTGGAGTATCCTCGACT
66 CCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATG--ATCAACAAGGTTAGAGTATCCCCGACT
* *
367539 GTGAA-AAATTGGT-ATTTTTGGAAATAAAATTGGAGTTGGAGTATCCTCGATTAAAGGAAAATT
129 GTGAAGAAATTGGTGATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAA-GAAAATT
*
367602 AGTGT-TTCGAAAATAAAACCAGG-GTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGC
193 AGTGTCTT-GAAAATAAAACC-GGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAGC
367665 AATAAAAC
256 AATAAAAC
* *
367673 CGGGATTGGAATATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGGGGTTGGAGTAT
1 CGGGATTGGAATATCCCCAATTATGAAAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTAT
* ** *
367738 CCCCTCGAAAATAACGGGGTTGGAGTATCTCCGATGATCAACGGGGTTAGAGTATCCCCGATTGT
66 CCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGATCAACAAGGTTAGAGTATCCCCGACTGT
* *
367803 GAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTATAGAAAATTAGT
131 GAAGAAATTGGTGATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGAAAATTAGT
*
367868 GTCTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGGA
196 GTCTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGA
367911 GAATTGAGAA
Statistics
Matches: 214, Mismatches: 19, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
261 2 0.01
262 26 0.12
263 146 0.68
264 40 0.19
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (263 bp):
CGGGATTGGAATATCCCCAATTATGAAAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTAT
CCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGATCAACAAGGTTAGAGTATCCCCGACTGT
GAAGAAATTGGTGATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGAAAATTAGT
GTCTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAA
AAC
Found at i:367758 original size:28 final size:28
Alignment explanation
Indices: 367724--367796 Score: 87
Period size: 27 Copynumber: 2.6 Consensus size: 28
367714 GAAATAAAGT
367724 CGGGGTTGGAGTATCCCCTCGAAAAT-AA
1 CGGGGTTGGAGTATCCCC-CGAAAATCAA
* **
367752 CGGGGTTGGAGTAT-CTCCGATGATCAA
1 CGGGGTTGGAGTATCCCCCGAAAATCAA
*
367779 CGGGGTTAGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
367797 GATTGTGAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
26 5 0.13
27 17 0.45
28 16 0.42
ACGTcount: A:0.23, C:0.22, G:0.32, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCCGAAAATCAA
Found at i:367850 original size:54 final size:51
Alignment explanation
Indices: 367787--367913 Score: 157
Period size: 51 Copynumber: 2.4 Consensus size: 51
367777 AACGGGGTTA
* * *
367787 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTGTG-AGAAATTAGTG--TCTTGAAAATAAAATCGGAGTTG
*
367841 GAGTATCCCCGATTAT-AGAAAATTAGTGTCTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTGTGAG-AAATTAGTGTCTTGAAAATAAAATCGGAGTTG
*
367892 GAATATCCCCGATTGTGGAGAA
1 GAGTATCCCCGATTGT-GAGAA
367914 TTGAGAAACT
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
51 35 0.55
52 4 0.06
53 10 0.16
54 15 0.23
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (51 bp):
GAGTATCCCCGATTGTGAGAAATTAGTGTCTTGAAAATAAAATCGGAGTTG
Found at i:367888 original size:51 final size:51
Alignment explanation
Indices: 367555--367905 Score: 178
Period size: 52 Copynumber: 6.7 Consensus size: 51
367545 AATTGGTATT
* * * * *
367555 TTTGGAAATAAAATTGGAGTTGGAGTATCCTCGATTAAAGGAAAATTAGTG
1 TTTGAAAATAAAATCGGAGTTGGAGTATCCCCGATTATAGAAAAATTAGTG
* * *
367606 TTTCGAAAATAAAACCAGG-GTTGGAGTATCCCCGATTGTGGAAAAATTAGTG
1 TTT-GAAAATAAAATC-GGAGTTGGAGTATCCCCGATTATAGAAAAATTAGTG
* * * * * * *
367658 TTTTAGCAATAAAACCGG-GATTGGAATATCCCCGATTAT-GAAAAATCAATAT
1 TTTGA-AAATAAAATCGGAG-TTGGAGTATCCCCGATTATAGAAAAATTAGT-G
* * * ** **** *
367710 TTTGGAAATAAAGTCGGGGTTGGAGTATCCCCTCGAAAATA-ACGGGGTTGGAGTA
1 TTTGAAAATAAAATCGGAGTTGGAGTAT-CCC-CGATTATAGA-AAAATT--AGTG
* ** * * * * *
367765 TCTCCGATGAT-CAA-CGGGGTTAGAGTATCCCCGATTGT-GAAGAAATTGGTG
1 T-T-TGAAAATAAAATCGGAGTTGGAGTATCCCCGATTATAGAA-AAATTAGTG
*
367816 TTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTATAG-AAAATTAGTG
1 ---TTTGAAAATAAAATCGGAGTTGGAGTATCCCCGATTATAGAAAAATTAGTG
*
367869 TCTTGAAAATAAAATCGGAGTTGGAATATCCCCGATT
1 T-TTGAAAATAAAATCGGAGTTGGAGTATCCCCGATT
367906 GTGGAGAATT
Statistics
Matches: 220, Mismatches: 57, Indels: 46
0.68 0.18 0.14
Matches are distributed among these distances:
50 1 0.00
51 68 0.31
52 76 0.35
53 26 0.12
54 27 0.12
55 15 0.07
56 4 0.02
57 3 0.01
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.29
Consensus pattern (51 bp):
TTTGAAAATAAAATCGGAGTTGGAGTATCCCCGATTATAGAAAAATTAGTG
Found at i:370348 original size:19 final size:18
Alignment explanation
Indices: 370324--370423 Score: 103
Period size: 19 Copynumber: 5.9 Consensus size: 18
370314 CAGTAGCTAA
370324 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
370343 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
370358 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
370375 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
370390 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
370407 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
370424 TTGTTGAATT
Statistics
Matches: 69, Mismatches: 0, Indels: 25
0.73 0.00 0.27
Matches are distributed among these distances:
13 22 0.32
14 2 0.03
16 4 0.06
18 5 0.07
19 36 0.52
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:370364 original size:13 final size:13
Alignment explanation
Indices: 370346--370402 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
370336 ACAATACTTA
370346 TGTATCGATACAT
1 TGTATCGATACAT
370359 TGTATCGATACAAAACTT
1 TGTATCGATAC---A--T
370377 ATGTATCGATACAT
1 -TGTATCGATACAT
370391 TGTATCGATACA
1 TGTATCGATACA
370403 AAACTTATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
14 1 0.03
16 2 0.05
18 1 0.03
19 11 0.29
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:370368 original size:32 final size:32
Alignment explanation
Indices: 370327--370421 Score: 181
Period size: 32 Copynumber: 3.0 Consensus size: 32
370317 TAGCTAATTA
*
370327 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
370359 TGTATCGATACAAAACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
370391 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
370422 AATTGTTGAA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 62 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:370503 original size:21 final size:21
Alignment explanation
Indices: 370479--370535 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
370469 CATTTGTAGG
*
370479 ATGTTTCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
370500 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
370521 ATGTATCGATACATT
1 ATGTATCGATACATT
370536 TGGATTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:370555 original size:8 final size:8
Alignment explanation
Indices: 370542--370588 Score: 53
Period size: 7 Copynumber: 5.9 Consensus size: 8
370532 CATTTGGATT
370542 TTTTTTTA
1 TTTTTTTA
370550 -TTTTTTA
1 TTTTTTTA
370557 -TTTTTTA
1 TTTTTTTA
370564 TTTTTTTTAA
1 -TTTTTTT-A
*
370574 TTTTTTAA
1 TTTTTTTA
370582 TTTTTTT
1 TTTTTTT
370589 TTCAAACACT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
7 14 0.41
8 7 0.21
9 12 0.35
10 1 0.03
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTTTTTA
Found at i:370561 original size:17 final size:17
Alignment explanation
Indices: 370539--370590 Score: 70
Period size: 17 Copynumber: 3.0 Consensus size: 17
370529 ATACATTTGG
370539 ATTTTTT-TTTATTTTTT
1 ATTTTTTATTT-TTTTTT
*
370556 ATTTTTTATTTTTTTTA
1 ATTTTTTATTTTTTTTT
370573 ATTTTTTAATTTTTTTTT
1 ATTTTTT-ATTTTTTTTT
370591 CAAACACTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
17 19 0.61
18 12 0.39
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (17 bp):
ATTTTTTATTTTTTTTT
Found at i:370566 original size:24 final size:25
Alignment explanation
Indices: 370539--370587 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 25
370529 ATACATTTGG
*
370539 ATTTTTTTTTATTTTTT-ATTTTTT
1 ATTTTTTTTAATTTTTTAATTTTTT
370563 ATTTTTTTTAATTTTTTAATTTTTT
1 ATTTTTTTTAATTTTTTAATTTTTT
370588 TTTCAAACAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (25 bp):
ATTTTTTTTAATTTTTTAATTTTTT
Found at i:370586 original size:7 final size:7
Alignment explanation
Indices: 370543--370569 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
370533 ATTTGGATTT
370543 TTTTTTA
1 TTTTTTA
370550 TTTTTTA
1 TTTTTTA
370557 TTTTTTA
1 TTTTTTA
370564 TTTTTT
1 TTTTTT
370570 TTAATTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTA
Found at i:371395 original size:55 final size:54
Alignment explanation
Indices: 371311--372119 Score: 882
Period size: 55 Copynumber: 14.4 Consensus size: 54
371301 ATAAAGTGTA
* * *
371311 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-AAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
371366 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTAAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
371421 TCCTGCTCTTTGAGAACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT--AAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
371476 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACT-AAAAGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
371531 TCCTGCTCTTTGAGAACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT--AAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* * * *
371586 TCCTACTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGACGTG
1 TCCTGCTCTTTGAGGACT-AAAAGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
371641 TCCTGCT-TTTGAGGATTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-AAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
371695 TCCTGCTCTTTGAGGATTGGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT--AAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
371750 TCTTGCTCTTTGAGGATTGGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT--AAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
371805 TCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT--AAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* * **
371860 TCCTGCTCTTTGAGGATTGGAAAA-TGCCACCAACTTGTGTGGGCTTTGTAGAGAAAAAGCA
1 TCCTGCTCTTTGAGGACT--AAAAGTGCCACCAACTTGTGTGGGC-TT-T---G-AAAGGTG
* * * *
371921 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGGGTGGGCTTTAAGAGAAAAAGTG
1 TCCTGCTCTTTGAGGACTAAAAGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGTG
* * * *
371980 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTAAAAGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGTG
* * * *
372039 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTAAAAGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGTG
*
372098 TCCTGCTCTTTGAGAACTAAAA
1 TCCTGCTCTTTGAGGACTAAAA
372120 AGCGGAAGAA
Statistics
Matches: 689, Mismatches: 43, Indels: 40
0.89 0.06 0.05
Matches are distributed among these distances:
54 64 0.09
55 418 0.61
56 15 0.02
57 5 0.01
58 1 0.00
59 145 0.21
60 20 0.03
61 21 0.03
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (54 bp):
TCCTGCTCTTTGAGGACTAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:371504 original size:110 final size:110
Alignment explanation
Indices: 371311--372086 Score: 1048
Period size: 110 Copynumber: 6.9 Consensus size: 110
371301 ATAAAGTGTA
* * * *
371311 TCCTGCTCATTGAGGAGT-AAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGTGTCCTGCTCT
1 TCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCT
*
371375 TTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
65 TTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
371421 TCCTGCTCTTTGAGAACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
*
371486 TGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
66 TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
371531 TCCTGCTCTTTGAGAACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTACTCTT
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
* *
371596 TGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGACGTG
66 TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
371641 TCCTGCT-TTTGAGGATTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
* *
371705 TGAGGATTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
66 TGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
371750 TCTTGCTCTTTGAGGATTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
*
371815 TGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
66 TGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* * **
371860 TCCTGCTCTTTGAGGATTGGAAAATGCCACCAACTTGTGTGGGCTTTGTAGAGAAAAAGCATCCT
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGC-TT-T---G-AAAGGTGTCCT
*
371925 GCTCTTTGAGGACTG-AAGGTGCCACCAACTTGGGTGGGCTTTAAGAGAAAAAGTG
60 GCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAG-----GTG
* ** * *
371980 TCCCGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGAAAAGGCGTCCCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT----G-AAAGGTGTCCTG
372044 CTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAA
61 CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAA
372087 AAGAAAAGGC
Statistics
Matches: 614, Mismatches: 34, Indels: 28
0.91 0.05 0.04
Matches are distributed among these distances:
109 92 0.15
110 362 0.59
111 6 0.01
112 1 0.00
114 4 0.01
115 26 0.04
116 22 0.04
117 1 0.00
118 58 0.09
119 23 0.04
120 19 0.03
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.29
Consensus pattern (110 bp):
TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
Found at i:371826 original size:274 final size:273
Alignment explanation
Indices: 371331--372087 Score: 1006
Period size: 274 Copynumber: 2.7 Consensus size: 273
371321 TGAGGAGTAA
* *
371331 AAAGTGCCACCAACTCGTGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGAGGACT-AAAAGGTGCC
1 AAAGTGCCACCAACTTGTGTGGGCTTT-AAGAAGTGTCCTGCTCTTTGAGGACTGAAAA-GTGCC
*
371394 ACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGAGAACTGGAAAATGCCACCAACTTG
64 ACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTG
*
371458 TGTGGGCTTTGAAAGGTGTCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT
128 TGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTT
371523 AAGAGGTGTCCTGCTCTTTGAGAACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTC
192 AA-AGGTGTCCTGCTCTTTGAGAACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTC
*
371588 CTACTCTTTGGGGACT-G
256 CTACTCTTTGAGGACTGG
* * *
371605 AAAGGTGCCACCAACTTGTGTGGGCTTTAAGACGTGTCCTGCT-TTTGAGGATTGAAAAATGCCA
1 AAA-GTGCCACCAACTTGTGTGGGCTTTAAGAAGTGTCCTGCTCTTTGAGGACTGAAAAGTGCCA
*
371669 CCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGATTGGAAAATGCCACCAACTTGTG
65 CCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTG
* * *
371734 TGGGCTTTGAAAGGTGTCTTGCTCTTTGAGGATTGGAAAATGCCACCAACTTGTGTGGGCTTTGA
130 TGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTT-A
*
371799 AAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCT
193 AAGGTGTCCTGCTCTTTGAGAACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCT
* *
371864 GCTCTTTGAGGATTGG
258 ACTCTTTGAGGACTGG
* ** *
371880 AAAATGCCACCAACTTGTGTGGGCTTTGTAGAGAAAAAGCATCCTGCTCTTTGAGGACTG-AAGG
1 AAAGTGCCACCAACTTGTGTGGGC-TT-TA-AG---AAGTGTCCTGCTCTTTGAGGACTGAAAAG
* * * **
371944 TGCCACCAACTTGGGTGGGCTTTAAGAGAAAAAGTGTCCCGCTCTTTGAGGACT-GAAGGTGCCA
60 TGCCACCAACTTGTGTGGGCTTT----G-AAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCA
* * *
372008 CCAACTTGTGTGGGCTTTAAGAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACT
120 CCAACTTGTGTGGGCTTT----G-AAAGGTGTCCTGCTCTTTGAGGACTGAAAGTGCCACCAACT
372073 TGTGTGGGCTTTAAA
180 TGTGTGGGCTTTAAA
372088 AGAAAAGGCG
Statistics
Matches: 426, Mismatches: 33, Indels: 35
0.86 0.07 0.07
Matches are distributed among these distances:
274 227 0.53
275 52 0.12
276 2 0.00
277 2 0.00
280 33 0.08
281 10 0.02
284 27 0.06
285 22 0.05
287 3 0.01
288 27 0.06
289 21 0.05
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.29
Consensus pattern (273 bp):
AAAGTGCCACCAACTTGTGTGGGCTTTAAGAAGTGTCCTGCTCTTTGAGGACTGAAAAGTGCCAC
CAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGT
GGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAAG
GTGTCCTGCTCTTTGAGAACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTACT
CTTTGAGGACTGG
Found at i:373105 original size:1 final size:1
Alignment explanation
Indices: 373101--373157 Score: 51
Period size: 1 Copynumber: 57.0 Consensus size: 1
373091 CTTTTCTCTC
* * * * * * *
373101 TTTTTCTTTGTTTTGTTTTTTGTTTTTTTTGTTTTTTTTTGTTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
373158 GAAGAGAAGG
Statistics
Matches: 42, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.00, C:0.02, G:0.11, T:0.88
Consensus pattern (1 bp):
T
Found at i:373114 original size:9 final size:9
Alignment explanation
Indices: 373101--373158 Score: 59
Period size: 9 Copynumber: 6.7 Consensus size: 9
373091 CTTTTCTCTC
*
373101 TTTTTCTTT
1 TTTTTGTTT
*
373110 GTTTTG-TT
1 TTTTTGTTT
373118 -TTTTGTTT
1 TTTTTGTTT
373126 TTTTTGTTTT
1 TTTTTG-TTT
373136 TTTTTGTTT
1 TTTTTGTTT
*
373145 TTGTT-TTT
1 TTTTTGTTT
373153 TTTTTG
1 TTTTTG
373159 AAGAGAAGGT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
7 5 0.12
8 11 0.27
9 16 0.39
10 9 0.22
ACGTcount: A:0.00, C:0.02, G:0.12, T:0.86
Consensus pattern (9 bp):
TTTTTGTTT
Found at i:373120 original size:16 final size:15
Alignment explanation
Indices: 373101--373156 Score: 76
Period size: 16 Copynumber: 3.6 Consensus size: 15
373091 CTTTTCTCTC
*
373101 TTTTTCTTTGTTTTG
1 TTTTTTTTTGTTTTG
*
373116 TTTTTTGTTTTTTTTG
1 TTTTTT-TTTGTTTTG
373132 TTTTTTTTTGTTTTTG
1 TTTTTTTTTG-TTTTG
373148 TTTTTTTTT
1 TTTTTTTTT
373157 TGAAGAGAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
15 8 0.22
16 28 0.78
ACGTcount: A:0.00, C:0.02, G:0.11, T:0.88
Consensus pattern (15 bp):
TTTTTTTTTGTTTTG
Found at i:373130 original size:26 final size:24
Alignment explanation
Indices: 373101--373157 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 24
373091 CTTTTCTCTC
*
373101 TTTTTCTTTGTTTTGTTTTTTGTTT
1 TTTTTTTTTGTTTTG-TTTTTGTTT
*
373126 TTTTTGTTTTTTTTTGTTTTTGTTT
1 TTTTT-TTTTGTTTTGTTTTTGTTT
373151 TTTTTTT
1 TTTTTTT
373158 GAAGAGAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 2 0.07
25 19 0.66
26 8 0.28
ACGTcount: A:0.00, C:0.02, G:0.11, T:0.88
Consensus pattern (24 bp):
TTTTTTTTTGTTTTGTTTTTGTTT
Found at i:385663 original size:78 final size:78
Alignment explanation
Indices: 385553--385758 Score: 234
Period size: 78 Copynumber: 2.6 Consensus size: 78
385543 GAGATAATAA
* * * * * * *
385553 CGGGGTTGGAGTGTTCCCTTGAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-A
*
385618 -TTAGAAAAAAAAT
65 TTTAGAAAAAAAAC
* *
385631 CGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATA-
* * * *
385696 TTTGGGAATAAAGC
65 TTTAGAAAAAAAAC
* * *
385710 CGGGGTTGGAGTATCCCTTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGAT
385759 GAAATAACAA
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
77 1 0.01
78 54 0.50
79 52 0.49
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.25
Consensus pattern (78 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
TTAGAAAAAAAAC
Found at i:385743 original size:79 final size:78
Alignment explanation
Indices: 385553--385755 Score: 230
Period size: 79 Copynumber: 2.6 Consensus size: 78
385543 GAGATAATAA
* * ** * *
385553 CGGGGTTGGAGTGTTCCCTT-GAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATG
1 CGGGGTTGGAGT-ATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATG
*
385617 ATTAGAAAAAAAAT
65 ATTAGAAAAAAAAC
* *
385631 CGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAAT-A
1 CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATGA
* * * *
385695 TTTTGGGAATAAAGC
66 --TTAGAAAAAAAAC
* *
385710 CGGGGTTGGAGTATCCCTTCGGAAGTAACGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCC
385756 GATGAAATAA
Statistics
Matches: 105, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
77 6 0.06
78 49 0.47
79 50 0.48
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.25
Consensus pattern (78 bp):
CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATGA
TTAGAAAAAAAAC
Found at i:385766 original size:28 final size:27
Alignment explanation
Indices: 385710--385781 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 27
385700 GGAATAAAGC
*
385710 CGGGGTTGGAGTATCCCTTCGGAAGTAA
1 CGGGGTTGGAGTATCCC-TCGGAAATAA
385738 CGGGGTTGGAGTATCCC-CGATGAAATAA
1 CGGGGTTGGAGTATCCCTCG--GAAATAA
**
385766 CAAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
385782 TTGACTATGA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
26 2 0.05
28 37 0.95
ACGTcount: A:0.25, C:0.18, G:0.33, T:0.24
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCTCGGAAATAA
Found at i:385982 original size:51 final size:51
Alignment explanation
Indices: 385769--386154 Score: 215
Period size: 52 Copynumber: 7.4 Consensus size: 51
385759 GAAATAACAA
** * * * *
385769 GGTTGGAGTATCCTTGACTATGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGT-GTTTTGGAAATAAAACCGG
* * * * * * *
385821 AGTTGGAGTATCCTCGATTAAAGGAAAATTAGTGTTTCGAAAATAAAACCAG
1 GGTTGGAGTATCCCCGATT-ATGAAAAATTAGTGTTTTGGAAATAAAACCGG
* * *
385873 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTAT-GAAAAATTAGTGTTTTGGAAATAAAACCGG
* * * * * **
385925 GATTGGAATATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAACCGG
** * * * **** *
385976 GGTTGGAGTATCCCC---TCGGAAATAACGGGGTTGGAGTATCCCCAATGATCAA-CGG
1 GGTTGGAGTATCCCCGATTATGAAA-AA-----TTAGTGTTTTGGAAAT-A-AAACCGG
* * * *
386031 GGTTAGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAA-AAATTAGTG--TTTTGGAAATAAAACCGG
* * * *
386085 AGTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTCTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGA-AAAATTAGTGTTTTGGAAATAAAACCGG
* *
386136 AGTTGGAATATCCCCGATT
1 GGTTGGAGTATCCCCGATT
386155 GTGGAGAATT
Statistics
Matches: 252, Mismatches: 64, Indels: 37
0.71 0.18 0.10
Matches are distributed among these distances:
48 5 0.02
49 2 0.01
51 70 0.28
52 89 0.35
53 26 0.10
54 29 0.12
55 23 0.09
56 1 0.00
58 6 0.02
59 1 0.00
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAACCGG
Found at i:386004 original size:263 final size:263
Alignment explanation
Indices: 385659--386159 Score: 733
Period size: 263 Copynumber: 1.9 Consensus size: 263
385649 TCGAAAATAA
* * * *
385659 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAGTAT
1 CGGGATTGGAATATCCCCAATTATGAAAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTAT
* * * * **
385724 CCCTTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAAT-AACAAGGTTGGAGTATCCTTGACT
66 CCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATG--ATCAACAAGGTTAGAGTATCCCCGACT
*
385788 ATGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGAGTTGGAGTATCCTCGATTAAAGGAAAATT
129 ATGAAGAAATTGGTGATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAA-GAAAATT
*
385851 AGTGT-TTCGAAAATAAAACCAGG-GTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGC
193 AGTGTCTT-GAAAATAAAACC-GGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAGC
385914 AATAAAAC
256 AATAAAAC
* *
385922 CGGGATTGGAATATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGGGGTTGGAGTAT
1 CGGGATTGGAATATCCCCAATTATGAAAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTAT
** * *
385987 CCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATGATCAACGGGGTTAGAGTATCCCCGATTGT
66 CCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATGATCAACAAGGTTAGAGTATCCCCGACTAT
* *
386052 GAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTATAGAAAATTAGT
131 GAAGAAATTGGTGATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGAAAATTAGT
*
386117 GTCTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGGA
196 GTCTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGA
386160 GAATTGAGAA
Statistics
Matches: 212, Mismatches: 21, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
261 2 0.01
262 24 0.11
263 145 0.68
264 41 0.19
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (263 bp):
CGGGATTGGAATATCCCCAATTATGAAAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTAT
CCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATGATCAACAAGGTTAGAGTATCCCCGACTAT
GAAGAAATTGGTGATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGAAAATTAGT
GTCTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAA
AAC
Found at i:386099 original size:54 final size:51
Alignment explanation
Indices: 386036--386162 Score: 157
Period size: 51 Copynumber: 2.4 Consensus size: 51
386026 AACGGGGTTA
* * *
386036 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTGTG-AGAAATTAGTG--TCTTGAAAATAAAATCGGAGTTG
*
386090 GAGTATCCCCGATTAT-AGAAAATTAGTGTCTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTGTGAG-AAATTAGTGTCTTGAAAATAAAATCGGAGTTG
*
386141 GAATATCCCCGATTGTGGAGAA
1 GAGTATCCCCGATTGT-GAGAA
386163 TTGAGAAACT
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
51 35 0.55
52 4 0.06
53 10 0.16
54 15 0.23
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (51 bp):
GAGTATCCCCGATTGTGAGAAATTAGTGTCTTGAAAATAAAATCGGAGTTG
Found at i:388544 original size:13 final size:13
Alignment explanation
Indices: 388526--388551 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
388516 ACAAAGATCC
388526 ATGTATCGATACA
1 ATGTATCGATACA
388539 ATGTATCGATACA
1 ATGTATCGATACA
388552 CAGAAAAATA
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:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:388566 original size:33 final size:33
Alignment explanation
Indices: 388505--388571 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
388495 AAAATTTCCA
*** *
388505 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATATATCGATAC
*
388538 AATGTATCGATACACAGAAAAATATATCGATAC
1 AATGTATCGATACAAAGAAAAATATATCGATAC
388571 A
1 A
388572 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATATATCGATAC
Found at i:388615 original size:19 final size:18
Alignment explanation
Indices: 388591--388690 Score: 103
Period size: 19 Copynumber: 5.9 Consensus size: 18
388581 CAGTAGCTAA
388591 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
388610 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
388625 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
388642 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
388657 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
388674 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
388691 TTGTTGAATT
Statistics
Matches: 69, Mismatches: 0, Indels: 25
0.73 0.00 0.27
Matches are distributed among these distances:
13 22 0.32
14 2 0.03
16 4 0.06
18 5 0.07
19 36 0.52
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:388631 original size:13 final size:13
Alignment explanation
Indices: 388613--388669 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
388603 ACAATACTTA
388613 TGTATCGATACAT
1 TGTATCGATACAT
388626 TGTATCGATACAAAACTT
1 TGTATCGATAC---A--T
388644 ATGTATCGATACAT
1 -TGTATCGATACAT
388658 TGTATCGATACA
1 TGTATCGATACA
388670 AAACTTATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
14 1 0.03
16 2 0.05
18 1 0.03
19 11 0.29
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:388635 original size:32 final size:32
Alignment explanation
Indices: 388594--388688 Score: 181
Period size: 32 Copynumber: 3.0 Consensus size: 32
388584 TAGCTAATTA
*
388594 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
388626 TGTATCGATACAAAACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
388658 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
388689 AATTGTTGAA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 62 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:388770 original size:21 final size:21
Alignment explanation
Indices: 388746--388802 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
388736 CATTTGTAGG
388746 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
388767 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
388788 ATGTATCGATACATT
1 ATGTATCGATACATT
388803 TGGATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:388827 original size:11 final size:10
Alignment explanation
Indices: 388806--388855 Score: 66
Period size: 10 Copynumber: 5.0 Consensus size: 10
388796 ATACATTTGG
388806 ATTTTTTTTT
1 ATTTTTTTTT
388816 ATTTTATTTTT
1 ATTTT-TTTTT
388827 ATTTTTTTTT
1 ATTTTTTTTT
* *
388837 A-ATTTTTTA
1 ATTTTTTTTT
388846 ATTTTTTTTT
1 ATTTTTTTTT
388856 TCAAACACTC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
9 7 0.21
10 17 0.50
11 10 0.29
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (10 bp):
ATTTTTTTTT
Found at i:388830 original size:21 final size:19
Alignment explanation
Indices: 388806--388855 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
388796 ATACATTTGG
* *
388806 ATTTTTTTTTATTTTATTTTT
1 ATTTTTTTTTA-ATT-TTTTA
388827 ATTTTTTTTTAATTTTTTA
1 ATTTTTTTTTAATTTTTTA
388846 ATTTTTTTTT
1 ATTTTTTTTT
388856 TCAAACACTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 14 0.52
20 2 0.07
21 11 0.41
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (19 bp):
ATTTTTTTTTAATTTTTTA
Found at i:388833 original size:18 final size:19
Alignment explanation
Indices: 388810--388856 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
388800 ATTTGGATTT
388810 TTTTTTATTTTA-TTTTT-A
1 TTTTTT-TTTTATTTTTTAA
*
388828 TTTTTTTTTAATTTTTTAA
1 TTTTTTTTTTATTTTTTAA
388847 TTTTTTTTTT
1 TTTTTTTTTT
388857 CAAACACTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 4 0.16
18 11 0.44
19 10 0.40
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (19 bp):
TTTTTTTTTTATTTTTTAA
Found at i:388856 original size:21 final size:21
Alignment explanation
Indices: 388806--388856 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
388796 ATACATTTGG
*
388806 ATTTTTTTTTATTTTATTTTT
1 ATTTTTTTTTATTTTATTATT
*
388827 ATTTTTTTTTAATTTT-TTAAT
1 ATTTTTTTTT-ATTTTATTATT
388848 -TTTTTTTTT
1 ATTTTTTTTT
388857 CAAACACTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 9 0.33
21 13 0.48
22 5 0.19
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (21 bp):
ATTTTTTTTTATTTTATTATT
Found at i:391319 original size:29 final size:31
Alignment explanation
Indices: 391287--391344 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
391277 ACTGAAATGA
391287 AACT-ATTGGTCAAA-AAAATAACTAAGGTG
1 AACTAATTGGTCAAAGAAAATAACTAAGGTG
*
391316 AACTAATTGGTCAAAGAAAATGACTAAGG
1 AACTAATTGGTCAAAGAAAATAACTAAGG
391345 CGAAACCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 4 0.15
30 10 0.38
31 12 0.46
ACGTcount: A:0.48, C:0.10, G:0.19, T:0.22
Consensus pattern (31 bp):
AACTAATTGGTCAAAGAAAATAACTAAGGTG
Found at i:391342 original size:31 final size:31
Alignment explanation
Indices: 391269--391350 Score: 98
Period size: 30 Copynumber: 2.7 Consensus size: 31
391259 ATAACTATCG
*
391269 AGAAAATGACTGAA-ATGAAACTATTGGTCAA
1 AGAAAATGACT-AAGGTGAAACTATTGGTCAA
*
391300 A-AAAATAACTAAGGTG-AACTAATTGGTCAA
1 AGAAAATGACTAAGGTGAAACT-ATTGGTCAA
*
391330 AGAAAATGACTAAGGCGAAAC
1 AGAAAATGACTAAGGTGAAAC
391351 CAAATAGTTG
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
29 6 0.14
30 20 0.47
31 14 0.33
32 3 0.07
ACGTcount: A:0.50, C:0.11, G:0.20, T:0.20
Consensus pattern (31 bp):
AGAAAATGACTAAGGTGAAACTATTGGTCAA
Found at i:391474 original size:31 final size:31
Alignment explanation
Indices: 391439--391568 Score: 77
Period size: 31 Copynumber: 4.2 Consensus size: 31
391429 GATTAGGGCA
* *
391439 AAACCAATTACTCAAGAAAATGACTAAGATG
1 AAACCAACTAATCAAGAAAATGACTAAGATG
**
391470 AAACC-ACTAATCGAA-AAAATGACTAAGGCG
1 AAACCAACTAATC-AAGAAAATGACTAAGATG
* * * * * * *
391500 AAACCTATTAGTAAAAGGAAATGACTAGGGTG
1 AAACCAACTAAT-CAAGAAAATGACTAAGATG
* * * *
391532 AAACAAACTATTCGAGAAGATGA-TCAAGATG
1 AAACCAACTAATCAAGAAAATGACT-AAGATG
391563 AAACCA
1 AAACCA
391569 TCAGTTGGAA
Statistics
Matches: 73, Mismatches: 21, Indels: 10
0.70 0.20 0.10
Matches are distributed among these distances:
30 24 0.33
31 29 0.40
32 20 0.27
ACGTcount: A:0.49, C:0.15, G:0.18, T:0.18
Consensus pattern (31 bp):
AAACCAACTAATCAAGAAAATGACTAAGATG
Found at i:392597 original size:15 final size:14
Alignment explanation
Indices: 392571--392610 Score: 62
Period size: 15 Copynumber: 2.8 Consensus size: 14
392561 TTCAGGTTTT
392571 TCTTTTTTTTTCTC
1 TCTTTTTTTTTCTC
*
392585 TCTTTTTTCTTTCTT
1 TCTTTTTT-TTTCTC
392600 TCTTTTTTTTT
1 TCTTTTTTTTT
392611 ATTTTTCTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (14 bp):
TCTTTTTTTTTCTC
Found at i:392615 original size:25 final size:25
Alignment explanation
Indices: 392569--392616 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
392559 CTTTCAGGTT
*
392569 TTTCTTTTTTTTTCTCTCTTTTTTC
1 TTTCTTTTTTTTTCTCTATTTTTTC
*
392594 TTTCTTTCTTTTTT-TTTATTTTT
1 TTTCTTT-TTTTTTCTCTATTTTT
392617 CTCATATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (25 bp):
TTTCTTTTTTTTTCTCTATTTTTTC
Found at i:396143 original size:18 final size:19
Alignment explanation
Indices: 396103--396144 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
396093 GAGATTTTTG
*
396103 TTTTTATTTTTATTTCCTA
1 TTTTTATCTTTATTTCCTA
*
396122 -TTTTATCTTTA-TTCTTA
1 TTTTTATCTTTATTTCCTA
396139 TTTTTA
1 TTTTTA
396145 ATTCATACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTTATCTTTATTTCCTA
Found at i:397325 original size:28 final size:30
Alignment explanation
Indices: 397262--397325 Score: 69
Period size: 30 Copynumber: 2.2 Consensus size: 30
397252 TGATATATTG
** *
397262 ATAATATATAAATTTATATATTATCAATACG
1 ATAA-ATATAAATTTATATATTAAAAATACA
*
397293 TTAAATATAAATTTATAT-TTAAAAATA-A
1 ATAAATATAAATTTATATATTAAAAATACA
397321 ATAAA
1 ATAAA
397326 AAAAGCTTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
28 4 0.14
29 7 0.25
30 14 0.50
31 3 0.11
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.41
Consensus pattern (30 bp):
ATAAATATAAATTTATATATTAAAAATACA
Found at i:397540 original size:11 final size:11
Alignment explanation
Indices: 397518--397553 Score: 54
Period size: 11 Copynumber: 3.1 Consensus size: 11
397508 TCACAATAGA
397518 CTTTTCTTTTTT
1 CTTTT-TTTTTT
397530 CTTTTTTTTTT
1 CTTTTTTTTTT
397541 CTTTTTGTTTTT
1 CTTTTT-TTTTT
397553 C
1 C
397554 GTCTAAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 12 0.52
12 11 0.48
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.83
Consensus pattern (11 bp):
CTTTTTTTTTT
Found at i:399453 original size:18 final size:18
Alignment explanation
Indices: 399419--399454 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
399409 GTAAAACAGA
*
399419 TACTCGAATTTGAAAAAT
1 TACTCGAATATGAAAAAT
399437 TACTCGAATATGTAAAAA
1 TACTCGAATATG-AAAAA
399455 ATCTAAAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.31
Consensus pattern (18 bp):
TACTCGAATATGAAAAAT
Found at i:399977 original size:16 final size:16
Alignment explanation
Indices: 399938--399977 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
399928 CTTAAGCTGA
*
399938 AAAATGACTAGAATAT
1 AAAATGATTAGAATAT
*
399954 AAAATGATTAGAATTT
1 AAAATGATTAGAATAT
399970 AAAATGAT
1 AAAATGAT
399978 CTGAACTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.55, C:0.03, G:0.12, T:0.30
Consensus pattern (16 bp):
AAAATGATTAGAATAT
Found at i:406823 original size:57 final size:59
Alignment explanation
Indices: 406749--406960 Score: 196
Period size: 64 Copynumber: 3.4 Consensus size: 59
406739 TTCCTTATAA
*
406749 CACACAAGCGAGCAACAAAGTTGCCATGCA-T-A-AAGACTAAAACAAGTTATCACAAAG
1 CACACAAGCGAGCAACAAAGTTGCCATGCAGTCACAAGACTAAAACAAG-CATCACAAAG
* **
406806 CACACAAGCGAGTAACAAAGTTGCCACACATAAGTGCCACAAGACTAAAACAAGCATCACAAAG
1 CACACAAGCGAGCAACAAAGTTGCCATGC---AGT--CACAAGACTAAAACAAGCATCACAAAG
* * *
406870 CACACAAGCGAGCAACAAAGTTGCCATGCAAAAAAGCCACAAGATTAAAACAAGCTATTACAAAG
1 CACACAAGCGAGCAACAAAGTTGCCATGC-----AGTCACAAGACTAAAACAAGC-ATCACAAAG
* * * *
406935 CATACAAACAAGCAACTAAGTTGCCA
1 CACACAAGCGAGCAACAAAGTTGCCA
406961 CGCATAAGTG
Statistics
Matches: 129, Mismatches: 15, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
57 26 0.20
60 1 0.01
61 1 0.01
64 53 0.41
65 44 0.34
66 4 0.03
ACGTcount: A:0.48, C:0.25, G:0.15, T:0.13
Consensus pattern (59 bp):
CACACAAGCGAGCAACAAAGTTGCCATGCAGTCACAAGACTAAAACAAGCATCACAAAG
Found at i:406887 original size:64 final size:64
Alignment explanation
Indices: 406781--406971 Score: 247
Period size: 64 Copynumber: 3.0 Consensus size: 64
406771 GCCATGCATA
* * *
406781 AAGACTAAAACAAGTTATCACAAAGCACACAAGCGAGTAACAAAGTTGCCACACATAAGTGCCAC
1 AAGACTAAAACAAG-CATCACAAAGCACACAAGCGAGCAACAAAGTTGCCACGCATAAGTGCCAC
* * **
406846 AAGACTAAAACAAGCATCACAAAGCACACAAGCGAGCAACAAAGTTGCCATGCAAAAAAGCCAC
1 AAGACTAAAACAAGCATCACAAAGCACACAAGCGAGCAACAAAGTTGCCACGCATAAGTGCCAC
* * * * * *
406910 AAGATTAAAACAAGCTATTACAAAGCATACAAACAAGCAACTAAGTTGCCACGCATAAGTGC
1 AAGACTAAAACAAGC-ATCACAAAGCACACAAGCGAGCAACAAAGTTGCCACGCATAAGTGC
406972 TATAAAGTCT
Statistics
Matches: 108, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
64 57 0.53
65 51 0.47
ACGTcount: A:0.48, C:0.24, G:0.15, T:0.13
Consensus pattern (64 bp):
AAGACTAAAACAAGCATCACAAAGCACACAAGCGAGCAACAAAGTTGCCACGCATAAGTGCCAC
Found at i:406987 original size:129 final size:121
Alignment explanation
Indices: 406749--406996 Score: 275
Period size: 129 Copynumber: 2.0 Consensus size: 121
406739 TTCCTTATAA
* * *
406749 CACACAAGCGAGCAACAAAGTTGCCATGCATAAAGACTAAAACAAGTTATCACAAAGCACACAAG
1 CACACAAGCGAGCAACAAAGTTGCCATGCAAAAAGACTAAAACAAGCTATCACAAAGCACACAAA
* * *
406814 CGAGTAACAAAGTTGCCACACATAAGTGCCACAAGACTAAAAC-AAGCATCACAAAG
66 CAAGCAACAAAGTTGCCACACATAAGTGCCAAAAGACTAAAACAAAGCAT-ACAAAG
*
406870 CACACAAGCGAGCAACAAAGTTGCCATGCAAAAAAGCCACAAGATTAAAACAAGCTATTACAAAG
1 CACACAAGCGAGCAACAAAGTTGCCATGC-AAAAAG--AC-----TAAAACAAGCTATCACAAAG
* * * * * *
406935 CATACAAACAAGCAACTAAGTTGCCACGCATAAGTGCTATAAAGTCT-GAACAAAGCATACAA
58 CACACAAACAAGCAACAAAGTTGCCACACATAAGTGCCA-AAAGACTAAAACAAAGCATACAA
406997 GCGAGCAACA
Statistics
Matches: 104, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
121 29 0.28
122 5 0.05
124 2 0.02
129 57 0.55
130 11 0.11
ACGTcount: A:0.47, C:0.24, G:0.15, T:0.14
Consensus pattern (121 bp):
CACACAAGCGAGCAACAAAGTTGCCATGCAAAAAGACTAAAACAAGCTATCACAAAGCACACAAA
CAAGCAACAAAGTTGCCACACATAAGTGCCAAAAGACTAAAACAAAGCATACAAAG
Found at i:410126 original size:22 final size:23
Alignment explanation
Indices: 410098--410153 Score: 105
Period size: 22 Copynumber: 2.5 Consensus size: 23
410088 TGGACATGTT
410098 AAAAATGCATGAAACATAAT-AA
1 AAAAATGCATGAAACATAATAAA
410120 AAAAATGCATGAAACATAATAAA
1 AAAAATGCATGAAACATAATAAA
410143 AAAAATGCATG
1 AAAAATGCATG
410154 GTCAAAGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 20 0.61
23 13 0.39
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (23 bp):
AAAAATGCATGAAACATAATAAA
Found at i:411093 original size:20 final size:19
Alignment explanation
Indices: 411068--411138 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
411058 AGACATAATG
411068 TATCGATACATTGTAGAATA
1 TATCGATACATTGTA-AATA
* * *
411088 TATCGATACATTCATACATG
1 TATCGATACATT-GTAAATA
* *
411108 TATCGATATATTGAAAAATA
1 TATCGATACATTG-TAAATA
411128 TATCGATACAT
1 TATCGATACAT
411139 CAGGGTATGA
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
20 38 0.95
21 2 0.05
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.35
Consensus pattern (19 bp):
TATCGATACATTGTAAATA
Found at i:411128 original size:40 final size:39
Alignment explanation
Indices: 411061--411138 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
411051 GGTAAAAAGA
* *
411061 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
*
411100 CATACATGTATCGATATATTGAAAAATATATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
411139 CAGGGTATGA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:411670 original size:32 final size:32
Alignment explanation
Indices: 411621--413182 Score: 2685
Period size: 32 Copynumber: 48.8 Consensus size: 32
411611 AAAATGGTGA
* * ** *
411621 TTTGAAAAGGGTTGCCACTGACTTGCATAGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
411653 TTTTAAATGGGTTGCCACCGACTTGTGTGCGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
411685 TTTGAAATGAGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
411717 TTTGGAATGGGTTGCCACCGACTTGTGTGGGT
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
411749 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
411781 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
411813 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
411845 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
411877 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
411909 TTTGAAATGGGTTGCCACCGGCTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
411941 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
411973 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
412005 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
412037 TTTGAAATGAGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
412069 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
412101 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
412133 TTTGAAATAGGTTGCCACCAACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
412165 TTTGAAATGGGTTGCCACCGACTTATGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
412197 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
412229 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
412261 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
412293 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
412325 TTTGGAATGGGTTGCCACCGACTGGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
412357 TTTGAAATGAGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
412389 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
412421 TTTGAAATAGGTTGCCACCGCCTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
412453 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
412485 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
412517 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
412549 TTTGAAATGAGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
412581 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
412613 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
412645 TTTGAAATAGGTTGCCACCAACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
412677 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
412709 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
412741 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
412773 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
412805 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
412837 TTTGAAATGAGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
412869 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
412901 TTTGGAATGGGTTACCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
412933 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
412965 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
412997 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
413029 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
413061 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
413093 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
413125 TTTGAAATGGGTTGCCACTGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
413157 TTTGAAATGGG-TGCCACGGAGTTGTG
1 TTTGAAATGGGTTGCCACCGACTTGTG
413183 GATTTAAAAG
Statistics
Matches: 1460, Mismatches: 70, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
31 13 0.01
32 1447 0.99
ACGTcount: A:0.15, C:0.19, G:0.35, T:0.31
Consensus pattern (32 bp):
TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
Found at i:413199 original size:27 final size:27
Alignment explanation
Indices: 413165--413902 Score: 1181
Period size: 27 Copynumber: 27.0 Consensus size: 27
413155 GCTTTGAAAT
*
413165 GGGTGCCACGGAGTTGTGGATTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
413192 GGATGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
413219 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
413246 GGGTGCCACGGAGTTGTGGTCTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
413273 GGGATGCCACGGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
413301 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
413328 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
413355 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
413382 GAGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
413409 AGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
**
413436 GGGTGCCACAAAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
413463 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
413490 GAGATGCCACGGAGTTGTGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
413518 GGGATGCCACGGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
413546 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
413573 GGGTGCCACGGAGTTGTGGACTTAAAGA
1 GGGTGCCACGGAGTTGTGGACTTAAA-A
413601 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
* * *
413629 GAGCGCTACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
413656 GGGTGCCACGGAGTTGTGGACTTTGAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
413684 -GGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
413710 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
* **
413738 GAGTGCCACGGAGTTGTGGACTTTGAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
413765 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
413792 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
413820 GAGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
* * *
413848 GAGTGCCACAGAGTTGTGGATTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
413875 GGGTGCCACAGAGTTGTGGGCTTCAAAA
1 GGGTGCCACGGAGTTGTGGACTT-AAAA
413903 AGAAATGCCA
Statistics
Matches: 664, Mismatches: 37, Indels: 19
0.92 0.05 0.03
Matches are distributed among these distances:
26 5 0.01
27 447 0.67
28 207 0.31
29 5 0.01
ACGTcount: A:0.27, C:0.14, G:0.35, T:0.23
Consensus pattern (27 bp):
GGGTGCCACGGAGTTGTGGACTTAAAA
Found at i:413300 original size:82 final size:81
Alignment explanation
Indices: 413165--413902 Score: 1181
Period size: 82 Copynumber: 9.0 Consensus size: 81
413155 GCTTTGAAAT
* *
413165 GGGTGCCACGGAGTTGTGGATTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
413230 AGTTGTGGACTTAAAA
66 AGTTGTGGACTTAAAA
*
413246 GGGTGCCACGGAGTTGTGGTCTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
413311 GAGTTGTGGACTTAAAA
65 GAGTTGTGGACTTAAAA
*
413328 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGAGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
413393 AGTTGTGGACTTAAAA
66 AGTTGTGGACTTAAAA
* **
413409 AGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAAAGTTGTGGACTTAAAAGGGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
413474 AGTTGTGGACTTAAAA
66 AGTTGTGGACTTAAAA
*
413490 GAGATGCCACGGAGTTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCAC
1 G-GGTGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCAC
413555 GGAGTTGTGGACTTAAAA
64 GGAGTTGTGGACTTAAAA
* * *
413573 GGGTGCCACGGAGTTGTGGACTTAAAGAGGGTGCCACGGAGTTGTGGACTTTAAAAGAGCGCTAC
1 GGGTGCCACGGAGTTGTGGACTTAAA-AGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCAC
413638 GGAGTTGTGGACTTAAAA
64 GGAGTTGTGGACTTAAAA
* *
413656 GGGTGCCACGGAGTTGTGGACTTTGAAA-GGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACG
1 GGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
413720 GAGTTGTGGACTTTAAAA
65 GAGTTGTGGAC-TTAAAA
* **
413738 GAGTGCCACGGAGTTGTGGACTTTGAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
413803 AGTTGTGGACTTTAAAA
66 AGTTGTGGAC-TTAAAA
* * * * *
413820 GAGTGCCACGGAGTTGTGGACTTTAAAAGAGTGCCACAGAGTTGTGGATTTAAAAGGGTGCCACA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
*
413885 GAGTTGTGGGCTTCAAAA
65 GAGTTGTGGACTT-AAAA
413903 AGAAATGCCA
Statistics
Matches: 614, Mismatches: 33, Indels: 18
0.92 0.05 0.03
Matches are distributed among these distances:
81 182 0.30
82 271 0.44
83 157 0.26
84 4 0.01
ACGTcount: A:0.27, C:0.14, G:0.35, T:0.23
Consensus pattern (81 bp):
GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
AGTTGTGGACTTAAAA
Found at i:421438 original size:22 final size:23
Alignment explanation
Indices: 421410--421465 Score: 105
Period size: 22 Copynumber: 2.5 Consensus size: 23
421400 TGGACATGTT
421410 AAAAATGCATGAAACATAAT-AA
1 AAAAATGCATGAAACATAATAAA
421432 AAAAATGCATGAAACATAATAAA
1 AAAAATGCATGAAACATAATAAA
421455 AAAAATGCATG
1 AAAAATGCATG
421466 GTCAAAGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 20 0.61
23 13 0.39
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (23 bp):
AAAAATGCATGAAACATAATAAA
Found at i:422405 original size:20 final size:19
Alignment explanation
Indices: 422380--422450 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
422370 AGACATAATG
422380 TATCGATACATTGTAGAATA
1 TATCGATACATTGTA-AATA
* * *
422400 TATCGATACATTCATACATG
1 TATCGATACATT-GTAAATA
* *
422420 TATCGATATATTGAAAAATA
1 TATCGATACATTG-TAAATA
422440 TATCGATACAT
1 TATCGATACAT
422451 CAGGGTATGA
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
20 38 0.95
21 2 0.05
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.35
Consensus pattern (19 bp):
TATCGATACATTGTAAATA
Found at i:422440 original size:40 final size:39
Alignment explanation
Indices: 422373--422450 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
422363 GGTAAAAAGA
* *
422373 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
*
422412 CATACATGTATCGATATATTGAAAAATATATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
422451 CAGGGTATGA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:424907 original size:21 final size:21
Alignment explanation
Indices: 424881--424934 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
424871 CTGGTTCTAT
*
424881 TCGACAACAACCAATTCCTAG
1 TCGACAACAACCAATTCATAG
* * *
424902 TCGACATA-AAACTATTCATGG
1 TCGACA-ACAACCAATTCATAG
424923 TCGACAACAACC
1 TCGACAACAACC
424935 TTTTCGTGGT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
20 1 0.04
21 24 0.92
22 1 0.04
ACGTcount: A:0.39, C:0.30, G:0.11, T:0.20
Consensus pattern (21 bp):
TCGACAACAACCAATTCATAG
Found at i:425739 original size:16 final size:15
Alignment explanation
Indices: 425714--425745 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
425704 AAATTAAATC
425714 ATTTATTTAAATTTA
1 ATTTATTTAAATTTA
425729 ATTTGATTTAAATTTA
1 ATTT-ATTTAAATTTA
425745 A
1 A
425746 CATTAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (15 bp):
ATTTATTTAAATTTA
Found at i:426447 original size:16 final size:18
Alignment explanation
Indices: 426408--426448 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
426398 TTAAAATTAA
426408 ATTTAAATAATAATAACT
1 ATTTAAATAATAATAACT
*
426426 -TTTAAATAA-AA-AATT
1 ATTTAAATAATAATAACT
426441 ATTTAAAT
1 ATTTAAAT
426449 CGAGTTCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 3 0.14
16 9 0.43
17 9 0.43
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTTAAATAATAATAACT
Found at i:427063 original size:39 final size:38
Alignment explanation
Indices: 427020--427093 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
427010 ATTCAAAGTA
* * * *
427020 AAATTAAATTATTATAATAAATTATATAAAATATAAGAT
1 AAATTAAAATATGATAA-AAATAATATAAAAAATAAGAT
*
427059 AAATTAAAATATGATAAAAATAATTTAAAAAATAA
1 AAATTAAAATATGATAAAAATAATATAAAAAATAA
427094 TTAAAATATT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
38 15 0.50
39 15 0.50
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.34
Consensus pattern (38 bp):
AAATTAAAATATGATAAAAATAATATAAAAAATAAGAT
Found at i:427099 original size:21 final size:21
Alignment explanation
Indices: 427035--427101 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
427025 AAATTATTAT
427035 AATAAATTATATAAAAT-AT-AA
1 AATAAATTA-A-AAAATAATAAA
* * *
427056 GATAAATTAAAATATGATAAA
1 AATAAATTAAAAAATAATAAA
* *
427077 AATAATTTAAAAAATAATTAA
1 AATAAATTAAAAAATAATAAA
427098 AATA
1 AATA
427102 TTATATGACA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.11
20 3 0.08
21 30 0.81
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (21 bp):
AATAAATTAAAAAATAATAAA
Found at i:427855 original size:6 final size:5
Alignment explanation
Indices: 427771--427852 Score: 53
Period size: 5 Copynumber: 16.2 Consensus size: 5
427761 TTAAATAATT
* *
427771 ATTTA ATTTA ATTTA ATTTA ATTT- ATATTA TATTAA ATTTAA ATTTT
1 ATTTA ATTTA ATTTA ATTTA ATTTA AT-TTA -ATTTA ATTT-A ATTTA
* * * *
427818 ATTT- -TTATT ATTAA AATTA ATTTG ATTTA ATTTA A
1 ATTTA ATT-TA ATTTA ATTTA ATTTA ATTTA ATTTA A
427853 ATTATTATTT
Statistics
Matches: 60, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
3 2 0.03
4 3 0.05
5 44 0.73
6 9 0.15
7 2 0.03
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (5 bp):
ATTTA
Found at i:427875 original size:41 final size:42
Alignment explanation
Indices: 427803--427898 Score: 119
Period size: 41 Copynumber: 2.4 Consensus size: 42
427793 TTATATTATA
* * *
427803 TTAAATTTAAATT-TTATTTTTATTATTAAAATTAA-TTTGAT
1 TTAAATTTAAATTATTATTTATA-TAATAAAAATAATTTTGAT
*
427844 TT-AATTTAAATTATTATTTATATAATAAAAATAATTTTTAT
1 TTAAATTTAAATTATTATTTATATAATAAAAATAATTTTGAT
427885 TTAAATTT-AATTAT
1 TTAAATTTAAATTAT
427899 AAAAATATAT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
40 20 0.42
41 23 0.48
42 5 0.10
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (42 bp):
TTAAATTTAAATTATTATTTATATAATAAAAATAATTTTGAT
Found at i:429882 original size:77 final size:77
Alignment explanation
Indices: 429748--429893 Score: 233
Period size: 77 Copynumber: 1.9 Consensus size: 77
429738 CAACGTTACT
* *
429748 TTAAAGTGTATTTAAAAAATTAATAAATAAATAAATAGACTATGTATCACCTCACTAA-TCCCGT
1 TTAAAGCGTATTTAAAAAATTAATAAATAAATAAATAGAATATGTATCACCTCACTAACT-CCGT
429812 TTGTAAATGTCAC
65 TTGTAAATGTCAC
*
429825 TTAAAGCGTATTTAAAAAATTAATAAATAGATAAATAGAATATGTATCATCCT-ACTAACTCCGT
1 TTAAAGCGTATTTAAAAAATTAATAAATAAATAAATAGAATATGTATCA-CCTCACTAACTCCGT
429889 TTGTA
65 TTGTA
429894 GAGTTTTTAT
Statistics
Matches: 64, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
77 60 0.94
78 4 0.06
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.34
Consensus pattern (77 bp):
TTAAAGCGTATTTAAAAAATTAATAAATAAATAAATAGAATATGTATCACCTCACTAACTCCGTT
TGTAAATGTCAC
Found at i:430466 original size:2 final size:2
Alignment explanation
Indices: 430459--430496 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
430449 AAGTATTAAA
430459 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
430497 GGGGTACATG
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:442095 original size:1 final size:1
Alignment explanation
Indices: 442089--442165 Score: 91
Period size: 1 Copynumber: 77.0 Consensus size: 1
442079 AAATCTTCAC
* * ** * * *
442089 TTTTTTTTTGTTTTTTTTTTTGTTTTTTTTTTTGGTTTTTTTCTTTTTTTTTTGTTTTGTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
442154 TTTTTTTTTTTT
1 TTTTTTTTTTTT
442166 CCAATTGCCA
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 64 1.00
ACGTcount: A:0.00, C:0.01, G:0.08, T:0.91
Consensus pattern (1 bp):
T
Found at i:442106 original size:12 final size:12
Alignment explanation
Indices: 442089--442165 Score: 113
Period size: 12 Copynumber: 6.4 Consensus size: 12
442079 AAATCTTCAC
442089 TTTTTTTTTGTT
1 TTTTTTTTTGTT
442101 TTTTTTTTTGTT
1 TTTTTTTTTGTT
442113 TTTTTTTTTGGTT
1 TTTTTTTTT-GTT
442126 TTTTTCTTTT-TT
1 TTTTT-TTTTGTT
*
442138 TTTTGTTTTGTT
1 TTTTTTTTTGTT
442150 TTTTTTTTT-TT
1 TTTTTTTTTGTT
442161 TTTTT
1 TTTTT
442166 CCAATTGCCA
Statistics
Matches: 60, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
11 11 0.18
12 37 0.62
13 8 0.13
14 4 0.07
ACGTcount: A:0.00, C:0.01, G:0.08, T:0.91
Consensus pattern (12 bp):
TTTTTTTTTGTT
Found at i:453666 original size:14 final size:15
Alignment explanation
Indices: 453638--453666 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
453628 ATCTCTGAAC
453638 TTGTCTTCTAACAAT
1 TTGTCTTCTAACAAT
453653 TTGTCTTC-AACAAT
1 TTGTCTTCTAACAAT
453667 ACCCTTTACC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.28, C:0.21, G:0.07, T:0.45
Consensus pattern (15 bp):
TTGTCTTCTAACAAT
Found at i:455374 original size:2 final size:2
Alignment explanation
Indices: 455367--455391 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
455357 ATTATTGGTA
455367 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
455392 ATTTTAACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:457236 original size:13 final size:14
Alignment explanation
Indices: 457217--457249 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
457207 AAAATATCAA
*
457217 AATATTAGTATTTT
1 AATATTAATATTTT
457231 -ATATTAATATTTT
1 AATATTAATATTTT
457244 AATATT
1 AATATT
457250 TTAAAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (14 bp):
AATATTAATATTTT
Found at i:458247 original size:15 final size:16
Alignment explanation
Indices: 458227--458256 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
458217 TATTCATAAT
458227 GCTTCTAATT-GATTA
1 GCTTCTAATTAGATTA
458242 GCTTCTAATTAGATT
1 GCTTCTAATTAGATT
458257 GATTTAGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (16 bp):
GCTTCTAATTAGATTA
Found at i:460138 original size:2 final size:2
Alignment explanation
Indices: 460131--460177 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
460121 TTAGAAGTTC
460131 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
460173 AT AT A
1 AT AT A
460178 ACCAGAAATT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.