Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold150
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: 1465027
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.31
Warning! 98465 characters in sequence are not A, C, G, or T
File 2 of 9
Found at i:159906 original size:124 final size:123
Alignment explanation
Indices: 159736--160094 Score: 353
Period size: 125 Copynumber: 2.9 Consensus size: 123
159726 ATTTTTAATA
* * * * *
159736 AAAAATAGTATTTAATTAACTATAAAGAAATTTATATTAAAAATTAAACTATTAA-ACTT-T-TT
1 AAAAATAATATTTAATTAAGTTTAAA-AAATTTACATTAAAAATTAAAATATTAATA-TTATGTT
* * * *
159798 TTGA-AATAA-AAAAAATTAAATAAAAATAAAAAGGGCTTATTATTATTATTTTTTA-ATAAAAT
64 TTGATAAAAATAAAAAATT---TAAAAATAAAAAAGACTTATTATTA-TAATTTTTAGA-AAAAT
*
159860 CAAAAATAAAATTTAATTAAGTTTAAAAAA-TTACATTAATAAATTAAAATA-TAATTATTATGT
1 -AAAAATAATATTTAATTAAGTTTAAAAAATTTACATTAA-AAATTAAAATATTAA-TATTATGT
* * * *
159923 TTTTATAAAAATAAAAAATTTTAAAATAAAAAAGATTTTTTATTATAATTTTTAGAAAAAT
63 TTTGATAAAAATAAAAAATTTAAAAATAAAAAAGACTTATTATTATAATTTTTAGAAAAAT
159984 AAAAATAATATTTAATTAAGTTTAAAAAATTTACATTAACAAATTAAAATATTAATTATTATGTT
1 AAAAATAATATTTAATTAAGTTTAAAAAATTTACATTAA-AAATTAAAATATTAA-TATTATGTT
* * * ** *
160049 TT--TTAAAATAAAAAATTT-AGATTAAAAAAGGGTTTTTATTATAATT
64 TTGATAAAAATAAAAAATTTAAAAATAAAAAAGACTTATTATTATAATT
160095 GAAAGCTTAT
Statistics
Matches: 203, Mismatches: 21, Indels: 23
0.82 0.09 0.09
Matches are distributed among these distances:
122 24 0.12
123 54 0.27
124 48 0.24
125 60 0.30
126 5 0.02
127 4 0.02
128 8 0.04
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (123 bp):
AAAAATAATATTTAATTAAGTTTAAAAAATTTACATTAAAAATTAAAATATTAATATTATGTTTT
GATAAAAATAAAAAATTTAAAAATAAAAAAGACTTATTATTATAATTTTTAGAAAAAT
Found at i:160005 original size:123 final size:123
Alignment explanation
Indices: 159820--160094 Score: 380
Period size: 123 Copynumber: 2.2 Consensus size: 123
159810 AAATTAAATA
* * *
159820 AAAAT-AAAAAGGGCTTATTATTATTATTTTTTAATAAAATCAAAAATAAAATTTAATTAAGTTT
1 AAAATAAAAAAGAG-TTTTTATTA-TAATTTTTAATAAAATCAAAAATAAAATTTAATTAAGTTT
*
159884 AAAAAA-TTACATTAATAAATTAAAATA-TAATTATTATGTTTTTATAAAAATAAAAAATTTT
64 AAAAAATTTACATTAACAAATTAAAATATTAATTATTATGTTTTT-T-AAAATAAAAAA-TTT
* *
159945 AAAATAAAAAAGATTTTTTATTATAATTTTTAGA-AAAAT-AAAAATAATATTTAATTAAGTTTA
1 AAAATAAAAAAGAGTTTTTATTATAATTTTTA-ATAAAATCAAAAATAAAATTTAATTAAGTTTA
160008 AAAAATTTACATTAACAAATTAAAATATTAATTATTATGTTTTTTAAAATAAAAAATTT
65 AAAAATTTACATTAACAAATTAAAATATTAATTATTATGTTTTTTAAAATAAAAAATTT
* * *
160067 AGATTAAAAAAGGGTTTTTATTATAATT
1 AAAATAAAAAAGAGTTTTTATTATAATT
160095 GAAAGCTTAT
Statistics
Matches: 136, Mismatches: 10, Indels: 11
0.87 0.06 0.07
Matches are distributed among these distances:
122 27 0.20
123 39 0.29
124 34 0.25
125 30 0.22
126 6 0.04
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (123 bp):
AAAATAAAAAAGAGTTTTTATTATAATTTTTAATAAAATCAAAAATAAAATTTAATTAAGTTTAA
AAAATTTACATTAACAAATTAAAATATTAATTATTATGTTTTTTAAAATAAAAAATTT
Found at i:160881 original size:19 final size:20
Alignment explanation
Indices: 160838--160888 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
160828 TACAAGCCAA
**
160838 TGTATCGATACATTTTATGG
1 TGTATCGATACATACTATGG
*
160858 TGTATCGATACATACTGT-G
1 TGTATCGATACATACTATGG
160877 TGTATCGATACA
1 TGTATCGATACA
160889 AGTTTGGCTA
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:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATACTATGG
Found at i:163429 original size:13 final size:13
Alignment explanation
Indices: 163411--163449 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
163401 ATAATCCCGC
*
163411 TGTATCGATACAG
1 TGTATCGATACAA
163424 TGTATCGATACAA
1 TGTATCGATACAA
163437 TGTATCGATACAA
1 TGTATCGATACAA
163450 GGAATTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:168007 original size:9 final size:9
Alignment explanation
Indices: 167993--168023 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
167983 TCTGAGTCAC
*
167993 CATCATCAT
1 CATCATCTT
168002 CATCATCTT
1 CATCATCTT
168011 CATCATCTT
1 CATCATCTT
168020 CATC
1 CATC
168024 GTCCTTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.26, C:0.35, G:0.00, T:0.39
Consensus pattern (9 bp):
CATCATCTT
Found at i:169637 original size:20 final size:20
Alignment explanation
Indices: 169612--169649 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
169602 TACAAGCCAA
*
169612 TGTATCGATACATTTTATGG
1 TGTATCGATACAATTTATGG
169632 TGTATCGATACAATTTAT
1 TGTATCGATACAATTTAT
169650 CGATACATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.45
Consensus pattern (20 bp):
TGTATCGATACAATTTATGG
Found at i:169656 original size:33 final size:32
Alignment explanation
Indices: 169609--169676 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 32
169599 CGTTACAAGC
**
169609 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATACTAT-GTGTATCGATA
* *
169642 CAATTTATCGATACATACTGTGTGTATCGATA
1 CAATGTATCGATACATACTATGTGTATCGATA
169674 CAA
1 CAA
169677 GTTTGGCTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 14 0.45
33 17 0.55
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (32 bp):
CAATGTATCGATACATACTATGTGTATCGATA
Found at i:170401 original size:23 final size:23
Alignment explanation
Indices: 170327--170401 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 23
170317 GAATAGAGGG
*
170327 TTTTTT-ATTTGAATAATGATAAAT
1 TTTTTTAATTTG-TTAATG-TAAAT
** *
170351 TTTTTTAATTCCTTAAATGT-TAT
1 TTTTTTAATTTGTT-AATGTAAAT
*
170374 ATTTTTAATTTGTTAATGTAAAT
1 TTTTTTAATTTGTTAATGTAAAT
170397 TTTTT
1 TTTTT
170402 ACATTTAATT
Statistics
Matches: 39, Mismatches: 9, Indels: 7
0.71 0.16 0.13
Matches are distributed among these distances:
22 5 0.13
23 19 0.49
24 8 0.21
25 7 0.18
ACGTcount: A:0.31, C:0.03, G:0.07, T:0.60
Consensus pattern (23 bp):
TTTTTTAATTTGTTAATGTAAAT
Found at i:170561 original size:112 final size:116
Alignment explanation
Indices: 170376--170661 Score: 309
Period size: 119 Copynumber: 2.5 Consensus size: 116
170366 AATGTTATAT
* * * * *
170376 TTTTAATTTGTTAATGTAAATTTTTTACATTTAATTAAATATCATTTTTTATTTTATTAAAAAAA
1 TTTTAATTTGTTAATGTAATTTTTTTAAACTTAATTAAATATTATTTTTAATTTTATTAAAAAAA
*
170441 TTTAAATAA-AAA-ATGCTT-TTT-A-TTTTTA-TAAAAACATATAATTAATA
66 TATAAATAATAAACATGCTTATTTAATTTTTTATTAAAAA-A-ATAATTAATA
*
170488 TTTTAATTTGTAAATGTAATTTTTTTTAAACTTAATTAAATATTATTTTTAATTTTATTAAAAAA
1 TTTTAATTTGTTAATGTAA-TTTTTTTAAACTTAATTAAATATTATTTTTAATTTTATTAAAAAA
* ** *
170553 CA-AT-AATAATAAACCCTTTTTAATTTAATTTTTTATTTTAAAAAATAATTAATA
65 -ATATAAATAATAAA-CATGCTT-ATTTAATTTTTTA-TTAAAAAAATAATTAATA
* * *
170607 TTTTAATTTATTAATATAAATTTTTTTAAAGTTAATTAAATATTATTTTTTAATT
1 TTTTAATTTGTTAATGT-AATTTTTTTAAACTTAATTAAATATTA-TTTTTAATT
170662 AAAAATAATA
Statistics
Matches: 146, Mismatches: 15, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
112 23 0.16
113 44 0.30
114 1 0.01
115 3 0.02
117 3 0.02
118 1 0.01
119 54 0.37
120 12 0.08
121 5 0.03
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (116 bp):
TTTTAATTTGTTAATGTAATTTTTTTAAACTTAATTAAATATTATTTTTAATTTTATTAAAAAAA
TATAAATAATAAACATGCTTATTTAATTTTTTATTAAAAAAATAATTAATA
Found at i:170657 original size:72 final size:68
Alignment explanation
Indices: 170580--170713 Score: 180
Period size: 68 Copynumber: 1.9 Consensus size: 68
170570 TTTTAATTTA
* * *
170580 ATTTTTTATTTTAAAA-AATAATTAATATTTTAATTTATTAATATAAATTTTTTTAAAGTTAATT
1 ATTTTTTAATTAAAAATAATAATTAATATATT-A-TTATTAAT-TAAA-TTTTTTAAAGTTAATT
170644 AAATATT
62 AAATATT
* *
170651 ATTTTTTAATTAAAAATAATAATTAATATATTATTATTTATTAAATTTTTTAAATTTAATTAA
1 ATTTTTTAATTAAAAATAATAATTAATATATTATTATTAATTAAATTTTTTAAAGTTAATTAA
170714 TTTATAAAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
68 17 0.30
69 4 0.07
70 7 0.12
71 15 0.26
72 14 0.25
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (68 bp):
ATTTTTTAATTAAAAATAATAATTAATATATTATTATTAATTAAATTTTTTAAAGTTAATTAAAT
ATT
Found at i:170715 original size:72 final size:71
Alignment explanation
Indices: 170580--170713 Score: 168
Period size: 71 Copynumber: 1.9 Consensus size: 71
170570 TTTTAATTTA
* * * * *
170580 ATTTTTTATTTTAAAAAATAATTAATATTTTAATTTATTAATATAAATTTTTTTAAAGTTAATTA
1 ATTTTTTAATTAAAAAAATAATTAATATATTAATTTATTAATATAAATTTTTTAAAAATTAATTA
170645 AATATT
66 AATATT
* *
170651 ATTTTTTAATTAAAAATAATAATTAATATATT-A-TTATTTAT-TAAATTTTTT-AAATTTAATT
1 ATTTTTTAATTAAAAA-AATAATTAATATATTAATTTATTAATATAAATTTTTTAAAAATTAATT
170712 AA
65 AA
170714 TTTATAAAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
68 11 0.19
69 10 0.18
70 7 0.12
71 15 0.26
72 14 0.25
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (71 bp):
ATTTTTTAATTAAAAAAATAATTAATATATTAATTTATTAATATAAATTTTTTAAAAATTAATTA
AATATT
Found at i:171790 original size:19 final size:19
Alignment explanation
Indices: 171752--171803 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
171742 TTCATGCTCC
* *
171752 AATGTATTGATAATTTTCAT
1 AATGTATCGAT-ACTTTCAT
171772 AATGTATCGATACTTTCAT
1 AATGTATCGATACTTTCAT
171791 AATGTATCGATAC
1 AATGTATCGATAC
171804 ATGCATTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 20 0.67
20 10 0.33
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.42
Consensus pattern (19 bp):
AATGTATCGATACTTTCAT
Found at i:175222 original size:12 final size:12
Alignment explanation
Indices: 175191--175229 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
175181 AAGGAAGAAG
* *
175191 AATCAAAATAGA
1 AATCAAAGTAAA
*
175203 AATCAAAGTATA
1 AATCAAAGTAAA
175215 AATCAAAGTAAA
1 AATCAAAGTAAA
175227 AAT
1 AAT
175230 AAAAAAGGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.64, C:0.08, G:0.08, T:0.21
Consensus pattern (12 bp):
AATCAAAGTAAA
Found at i:179548 original size:21 final size:22
Alignment explanation
Indices: 179524--179567 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
179514 AATTTAGTCT
179524 TTACATAATTA-AAACAT-AAAA
1 TTACA-AATTAGAAACATCAAAA
*
179545 TTACACATTAGAAACATCAAAA
1 TTACAAATTAGAAACATCAAAA
179567 T
1 T
179568 CAGCATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 4 0.20
21 11 0.55
22 5 0.25
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.27
Consensus pattern (22 bp):
TTACAAATTAGAAACATCAAAA
Found at i:179889 original size:21 final size:21
Alignment explanation
Indices: 179865--179906 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
179855 ATAAAATGTC
*
179865 AAAAATGCCTAAAACATGTTT
1 AAAAATGCATAAAACATGTTT
*
179886 AAAAATGCATGAAACATGTTT
1 AAAAATGCATAAAACATGTTT
179907 TACATAACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.29
Consensus pattern (21 bp):
AAAAATGCATAAAACATGTTT
Found at i:180211 original size:18 final size:18
Alignment explanation
Indices: 180188--180223 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
180178 ACTATTACAC
*
180188 CACATATGTTCATGAAGA
1 CACATATGTTCAAGAAGA
180206 CACATATGTTCAAGAAGA
1 CACATATGTTCAAGAAGA
180224 TTATGTCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.25
Consensus pattern (18 bp):
CACATATGTTCAAGAAGA
Found at i:181618 original size:13 final size:13
Alignment explanation
Indices: 181600--181625 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
181590 TACAACAAGT
181600 ATGTATCGATACA
1 ATGTATCGATACA
181613 ATGTATCGATACA
1 ATGTATCGATACA
181626 CAAAAAATTG
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:182474 original size:13 final size:13
Alignment explanation
Indices: 182456--182481 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
182446 CAATTTGTCC
182456 ATGTATCGATACA
1 ATGTATCGATACA
182469 ATGTATCGATACA
1 ATGTATCGATACA
182482 TCTGGGTGTG
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:183844 original size:21 final size:22
Alignment explanation
Indices: 183820--183863 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
183810 TAATCGGAGT
183820 TACTG-AGGGTC-GAGTATTATG
1 TACTGAAGGGTCGGAGTA-TATG
*
183841 TACTGAATGGTCGGAGTATATG
1 TACTGAAGGGTCGGAGTATATG
183863 T
1 T
183864 GTGATAAGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 10 0.50
23 5 0.25
ACGTcount: A:0.25, C:0.09, G:0.32, T:0.34
Consensus pattern (22 bp):
TACTGAAGGGTCGGAGTATATG
Found at i:184934 original size:13 final size:13
Alignment explanation
Indices: 184916--184944 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
184906 AAATAGTACC
184916 CAATGTATCGATA
1 CAATGTATCGATA
184929 CAATGTATCGATA
1 CAATGTATCGATA
184942 CAA
1 CAA
184945 GGAATGTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:191096 original size:20 final size:20
Alignment explanation
Indices: 191071--191123 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 20
191061 GTTACAAGCT
191071 ATGTATCGATACATT-T-CTTC
1 ATGTATCGATACATTGTAC--C
191091 ATGTATCGATACATTGTACC
1 ATGTATCGATACATTGTACC
191111 ATGTATCGATACA
1 ATGTATCGATACA
191124 AATAGTGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 29 0.94
21 1 0.03
22 1 0.03
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATTGTACC
Found at i:191193 original size:13 final size:13
Alignment explanation
Indices: 191175--191201 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
191165 CAATTTGTCC
191175 ATGTATCGATACA
1 ATGTATCGATACA
191188 ATGTATCGATACA
1 ATGTATCGATACA
191201 A
1 A
191202 AGCAGCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:196370 original size:59 final size:57
Alignment explanation
Indices: 196239--196372 Score: 178
Period size: 59 Copynumber: 2.3 Consensus size: 57
196229 GGCTATTTAT
* * * **
196239 GTTATTTTACATAATCTAGGGCTTTTCAGATATTTCCATTCATTTTAGGGCATTTAG
1 GTTATTTTACATAATCTAGGGCTTTTCAGAAATTTCCATGCATTTTAAGGCAAATAG
* * *
196296 GTTATTTTACATAATCTAGAGTCTTTTTAGAAATTTTCATGCATTTTAAAGGCAAATAG
1 GTTATTTTACATAATCTAG-GGCTTTTCAGAAATTTCCATGCATTTT-AAGGCAAATAG
196355 GTTATTTTACATAATCTA
1 GTTATTTTACATAATCTA
196373 ATGTCATTTT
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
57 19 0.28
58 22 0.33
59 26 0.39
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.45
Consensus pattern (57 bp):
GTTATTTTACATAATCTAGGGCTTTTCAGAAATTTCCATGCATTTTAAGGCAAATAG
Found at i:196383 original size:59 final size:57
Alignment explanation
Indices: 196233--196506 Score: 254
Period size: 58 Copynumber: 4.8 Consensus size: 57
196223 ACATAAGGCT
* * *
196233 ATTTATGTTATTTTACATAATCT-AGGGC-TTTTCAGATATTTCCATTCATTTTAGGGC
1 ATTTAGGTTATTTTACATAATCTAAGGTCATTTT-AGAAATTTCCA-TCATTTTAGGGC
* * *
196290 ATTTAGGTTATTTTACATAATCT-AGAGTCTTTTTAGAAATTTTCATGCATTTTAAAGGC
1 ATTTAGGTTATTTTACATAATCTAAG-GTCATTTTAGAAATTTCCAT-CATTTT-AGGGC
** * * * *
196349 AAATAGGTTATTTTACATAATCTAATGTCATTTTAATAAATTT-CATTATTTTTGGGCC
1 ATTTAGGTTATTTTACATAATCTAAGGTCATTTT-AGAAATTTCCATCATTTTAGGG-C
* *
196407 ATTTAGGTTATTTTACATAATTTAAGGTCATTTTAGCAAA-TTCCATCATTTTAAGGCC
1 ATTTAGGTTATTTTACATAATCTAAGGTCATTTTAG-AAATTTCCATCATTTT-AGGGC
* * * * *
196465 ATTTCGATTATTTCACATAATCTTAGGTCATTTCAG-AATTTC
1 ATTTAGGTTATTTTACATAATCTAAGGTCATTTTAGAAATTTC
196507 TGCCACCTTA
Statistics
Matches: 179, Mismatches: 27, Indels: 22
0.79 0.12 0.10
Matches are distributed among these distances:
56 2 0.01
57 33 0.18
58 95 0.53
59 41 0.23
60 8 0.04
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.46
Consensus pattern (57 bp):
ATTTAGGTTATTTTACATAATCTAAGGTCATTTTAGAAATTTCCATCATTTTAGGGC
Found at i:196423 original size:117 final size:115
Alignment explanation
Indices: 196239--196460 Score: 281
Period size: 117 Copynumber: 1.9 Consensus size: 115
196229 GGCTATTTAT
* *
196239 GTTATTTTACATAATCTAGGGCTTTTCAGATATTTCCATTCATTTTAGGGCATTTAGGTTATTTT
1 GTTATTTTACATAATCTAGGGCTTTTAAGAAATTTCCATTCATTTTAGGGCATTTAGGTTATTTT
* *
196304 ACATAATCT-AGAGTCTTTTTAG-AAATTTTCATGCATTTTAAAGGCAAATAG
66 ACATAATCTAAG-GTCATTTTAGCAAA-TTCCAT-CATTTTAAAGGCAAATAG
* * * *
196355 GTTATTTTACATAATCTAATGTCATTTTAATAAATTT-CATT-ATTTTTGGGCCATTTAGGTTAT
1 GTTATTTTACATAATCT-AGGGC-TTTTAAGAAATTTCCATTCATTTTAGGG-CATTTAGGTTAT
*
196418 TTTACATAATTTAAGGTCATTTTAGCAAATTCCATCATTTTAA
63 TTTACATAATCTAAGGTCATTTTAGCAAATTCCATCATTTTAA
196461 GGCCATTTCG
Statistics
Matches: 92, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
116 33 0.36
117 44 0.48
118 15 0.16
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.46
Consensus pattern (115 bp):
GTTATTTTACATAATCTAGGGCTTTTAAGAAATTTCCATTCATTTTAGGGCATTTAGGTTATTTT
ACATAATCTAAGGTCATTTTAGCAAATTCCATCATTTTAAAGGCAAATAG
Found at i:196476 original size:116 final size:117
Alignment explanation
Indices: 196240--196497 Score: 287
Period size: 116 Copynumber: 2.2 Consensus size: 117
196230 GCTATTTATG
* * *
196240 TTATTTTACATAATCTAGGGC-TTTTCAGATATTTCCATTCATTTTAGGGCATTTAGGTTATTTT
1 TTATTTTACATAATCTAGGTCATTTTAAGAAATTTCCATTCATTTTAGGGCATTTAGGTTATTTT
* * *
196304 ACATAATCTAGAGTCTTTTTAGAAATTTTCATGCATTTTAAAGGCAAATAGG
66 ACATAATCTAGAGTCATTTTAGAAATTTCCATGCATTTTAAAGGCAAATAGA
* * *
196356 TTATTTTACATAATCTAATGTCATTTTAATAAATTT-CATT-ATTTTTGGGCCATTTAGGTTATT
1 TTATTTTACATAATCT-AGGTCATTTTAAGAAATTTCCATTCATTTTAGGG-CATTTAGGTTATT
* ** *
196419 TTACATAATTTA-AGGTCATTTTAGCAAA-TTCCAT-CATTTT-AAGGCCATTTCGA
64 TTACATAATCTAGA-GTCATTTTAG-AAATTTCCATGCATTTTAAAGG-CAAATAGA
*
196472 TTATTTCACATAATCTTAGGTCATTT
1 TTATTTTACATAATC-TAGGTCATTT
196498 CAGAATTTCT
Statistics
Matches: 120, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
115 4 0.03
116 57 0.47
117 46 0.38
118 13 0.11
ACGTcount: A:0.29, C:0.13, G:0.12, T:0.46
Consensus pattern (117 bp):
TTATTTTACATAATCTAGGTCATTTTAAGAAATTTCCATTCATTTTAGGGCATTTAGGTTATTTT
ACATAATCTAGAGTCATTTTAGAAATTTCCATGCATTTTAAAGGCAAATAGA
Found at i:196648 original size:48 final size:48
Alignment explanation
Indices: 196581--196826 Score: 194
Period size: 49 Copynumber: 5.1 Consensus size: 48
196571 GTTTCATGAG
* * *
196581 AAAATTAAA-CCTTTAGGGTTAGTTTTGTACTTTTGTTAAAATTAACC
1 AAAATTAAATCTTTTAGGGTTAGTTTTGTACTTTTATTAAAATCAACC
** * * **
196628 AAAATTAAATCTTTTAGGGTTAACTTTGTACTTTTCA-TCAAATCGATT
1 AAAATTAAATCTTTTAGGGTTAGTTTTGTACTTTT-ATTAAAATCAACC
* ** * * * *
196676 GAAACCAAATCTTTT-GAAGTTAGTTTTGTACTGTTTGTTAAAATCGATC
1 AAAATTAAATCTTTTAG-GGTTAGTTTTGTACT-TTTATTAAAATCAACC
* * *
196725 GAAATCAAATCTTTTAAGGTTAGTTTTGTACTTTTCATTAAAAAT-AACC
1 AAAATTAAATCTTTTAGGGTTAGTTTTGTACTTTT-ATT-AAAATCAACC
* * * * *
196774 AAAATTAAGTTTTTTAGGATTAGTTTTATACTTTTCATCAAAATCAACC
1 AAAATTAAATCTTTTAGGGTTAGTTTTGTACTTTT-ATTAAAATCAACC
196823 AAAA
1 AAAA
196827 CCAAGCCTCT
Statistics
Matches: 158, Mismatches: 32, Indels: 16
0.77 0.16 0.08
Matches are distributed among these distances:
47 10 0.06
48 60 0.38
49 83 0.53
50 5 0.03
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.41
Consensus pattern (48 bp):
AAAATTAAATCTTTTAGGGTTAGTTTTGTACTTTTATTAAAATCAACC
Found at i:196766 original size:49 final size:48
Alignment explanation
Indices: 196592--196767 Score: 176
Period size: 48 Copynumber: 3.6 Consensus size: 48
196582 AAATTAAACC
* * ** * * *
196592 TTTAGGGTTAGTTTTGTACTTTTGTTAAAATTAACCAAAATTAAATCT
1 TTTAAGGTTAGTTTTGTACTTTTATTAAAATCGATCGAAATCAAATCT
* ** * * *
196640 TTTAGGGTTAACTTTGTACTTTTCA-TCAAATCGATTGAAACCAAATCT
1 TTTAAGGTTAGTTTTGTACTTTT-ATTAAAATCGATCGAAATCAAATCT
*
196688 TTTGAA-GTTAGTTTTGTACTGTTTGTTAAAATCGATCGAAATCAAATCT
1 TTT-AAGGTTAGTTTTGTACT-TTTATTAAAATCGATCGAAATCAAATCT
196737 TTTAAGGTTAGTTTTGTACTTTTCATTAAAA
1 TTTAAGGTTAGTTTTGTACTTTT-ATTAAAA
196768 ATAACCAAAA
Statistics
Matches: 103, Mismatches: 19, Indels: 11
0.77 0.14 0.08
Matches are distributed among these distances:
48 56 0.54
49 47 0.46
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.44
Consensus pattern (48 bp):
TTTAAGGTTAGTTTTGTACTTTTATTAAAATCGATCGAAATCAAATCT
Found at i:197837 original size:28 final size:28
Alignment explanation
Indices: 197797--197862 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 28
197787 AAACGGGATC
* *
197797 GGAGTACCCCCTCAGAAATAATAGGGTT
1 GGAGTATCCCCTCAAAAATAATAGGGTT
*
197825 GGAGTATCCCCTCAAAAATAATGGGGTT
1 GGAGTATCCCCTCAAAAATAATAGGGTT
*
197853 GTAGTATCCC
1 GGAGTATCCC
197863 TGATTATGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.24
Consensus pattern (28 bp):
GGAGTATCCCCTCAAAAATAATAGGGTT
Found at i:197911 original size:79 final size:79
Alignment explanation
Indices: 197821--198558 Score: 823
Period size: 79 Copynumber: 9.3 Consensus size: 79
197811 GAAATAATAG
* * * * *
197821 GGTTGGAGTATCCCCTCAAAAATAATGGGGTT-GTAGTATCCCTGATTATGAAAAATTGATATTT
1 GGTTGGAGTATCCCCTCGAAAATAACGGGGTTAG-AGTATCCCCGATTGTGAAAAATTGATGTTT
*
197885 TGGAAATAAAACCGA
65 TAGAAATAAAACCGA
* *
197900 GGTTGGAGTATCCTCTCGAAAATAACGGGGTTAGAGTATCCCCGATTATGAAAAATT-AGTGTTT
1 GGTTGGAGTATCCCCTCGAAAATAACGGGGTTAGAGTATCCCCGATTGTGAAAAATTGA-TGTTT
* * * *
197964 TAAAAATAAGATCGG
65 TAGAAATAAAACCGA
* * *
197979 GGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCTCGATTGTGAAAAA-TCAGTGTTT
1 GGTTGGAGTATCCCCTCGAAAATAACGGGGTTAGAGTATCCCCGATTGTGAAAAATTGA-TGTTT
* *
198043 TAGAAATAAAATCGG
65 TAGAAATAAAACCGA
*
198058 GGTTGGAGTATCCCCTCGAAAATAACGGGGTTAGAGTATCCCCGATTGTGAAAAAAT-AGTGTTT
1 GGTTGGAGTATCCCCTCGAAAATAACGGGGTTAGAGTATCCCCGATTGTGAAAAATTGA-TGTTT
*
198122 TAAAAATAAAACCGA
65 TAGAAATAAAACCGA
* * * ** * * * *
198137 GTTTGAAATATCCCCTC-AGAAATAGTGGGGTTGGAGTATTCCCGATTGTGAAAAATTAATATTT
1 GGTTGGAGTATCCCCTCGA-AAATAACGGGGTTAGAGTATCCCCGATTGTGAAAAATTGATGTTT
*
198201 TGGAAATAAAACCGA
65 TAGAAATAAAACCGA
* * * *
198216 GGTTGGAGTATCCTCTCGAAAATAACGGGGTTAGAGTATTCCCAATTGTGAAAAATTGGTGTTTT
1 GGTTGGAGTATCCCCTCGAAAATAACGGGGTTAGAGTATCCCCGATTGTGAAAAATTGATGTTTT
* *
198281 AGAAATAAGATC-A
66 AGAAATAAAACCGA
** * *
198294 GGTTTGGAGTATCCCCTTAAAAATAACAGGGTTAGAGTATCCCCGATTGTG-AAAA-TCAGTGTT
1 GG-TTGGAGTATCCCCTCGAAAATAACGGGGTTAGAGTATCCCCGATTGTGAAAAATTGA-TGTT
* *
198357 TTCA-AAATAAAATCGG
64 TT-AGAAATAAAACCGA
* *
198373 GGTTGGAGTATCCCCTCGAACATAACGAGGTTAGAGTATCCCCGATTGTGAAAAATCTG-TGTTT
1 GGTTGGAGTATCCCCTCGAAAATAACGGGGTTAGAGTATCCCCGATTGTGAAAAAT-TGATGTTT
*
198437 TAGAAATAAAACCGG
65 TAGAAATAAAACCGA
* * *
198452 GGTTGGAGTATCCCCTC-AGAAATAACGGGGTTGGAGTATCCTCCCCAATTGTGAAAAATCGATG
1 GGTTGGAGTATCCCCTCGA-AAATAACGGGGTTAGAGTA---TCCCCGATTGTGAAAAATTGATG
* *
198516 TTTTGGGAATAAAACCGA
62 TTTTAGAAATAAAACCGA
* *
198534 GGTTGGAGTATTCCCTCGGAAATAA
1 GGTTGGAGTATCCCCTCGAAAATAA
198559 AAACATGAAT
Statistics
Matches: 565, Mismatches: 73, Indels: 39
0.83 0.11 0.06
Matches are distributed among these distances:
77 1 0.00
78 70 0.12
79 432 0.76
80 4 0.01
81 2 0.00
82 56 0.10
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.28
Consensus pattern (79 bp):
GGTTGGAGTATCCCCTCGAAAATAACGGGGTTAGAGTATCCCCGATTGTGAAAAATTGATGTTTT
AGAAATAAAACCGA
Found at i:201006 original size:99 final size:100
Alignment explanation
Indices: 200896--201075 Score: 247
Period size: 99 Copynumber: 1.8 Consensus size: 100
200886 AATGCCTGAA
* ** *
200896 TGTATCGATAC-ATTAAGAAATGTATTTATACATCTGGGTAAAACCCAAAATGTAT-GATACAAT
1 TGTATCGATACAATGAA-AAATGTATCGATACATCTAGGTAAAACCCAAAATGTATCGATACAAT
200959 GAAAAATATATCGATACGTCTGGATAAAATTGAGAT
65 GAAAAATATATCGATACGTCTGGATAAAATTGAGAT
* * * *
200995 TGTATCGATACAATGAACAATGTATCGATACATCTAGGTAAAATCTAGAATGTATCGATACAATG
1 TGTATCGATACAATGAAAAATGTATCGATACATCTAGGTAAAACCCAAAATGTATCGATACAATG
* *
201060 AACAATGTATCGATAC
66 AAAAATATATCGATAC
201076 AAATTGTGAA
Statistics
Matches: 69, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
99 42 0.61
100 27 0.39
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (100 bp):
TGTATCGATACAATGAAAAATGTATCGATACATCTAGGTAAAACCCAAAATGTATCGATACAATG
AAAAATATATCGATACGTCTGGATAAAATTGAGAT
Found at i:201018 original size:20 final size:20
Alignment explanation
Indices: 200995--201077 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
200985 AAATTGAGAT
200995 TGTATCGATACAATGAACAA
1 TGTATCGATACAATGAACAA
*
201015 TGTATCGATACATCTAGGTAAAATCTAGA
1 TGTATCGATACA---A--T-GAA-C-A-A
201044 ATGTATCGATACAATGAACAA
1 -TGTATCGATACAATGAACAA
201065 TGTATCGATACAA
1 TGTATCGATACAA
201078 ATTGTGAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 20
0.70 0.03 0.27
Matches are distributed among these distances:
20 25 0.49
21 1 0.02
22 1 0.02
23 2 0.04
24 2 0.04
25 2 0.04
26 2 0.04
27 2 0.04
28 1 0.02
29 1 0.02
30 12 0.24
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (20 bp):
TGTATCGATACAATGAACAA
Found at i:201021 original size:50 final size:50
Alignment explanation
Indices: 200893--201076 Score: 205
Period size: 50 Copynumber: 3.7 Consensus size: 50
200883 AAAAATGCCT
* * ** * * *
200893 GAATGTATCGATAC-ATTAAGAAATGTATTTATACATCTGGGTAAAACCCA
1 GAATGTATCGATACAATGAA-CAATGTATCGATACATCTAGGTAAAATCTA
* * * *
200943 AAATGTAT-GATACAATGAAAAATATATCGATACGTCT-GGATAAAAT-TGA
1 GAATGTATCGATACAATGAACAATGTATCGATACATCTAGG-TAAAATCT-A
*
200992 GATTGTATCGATACAATGAACAATGTATCGATACATCTAGGTAAAATCTA
1 GAATGTATCGATACAATGAACAATGTATCGATACATCTAGGTAAAATCTA
201042 GAATGTATCGATACAATGAACAATGTATCGATACA
1 GAATGTATCGATACAATGAACAATGTATCGATACA
201077 AATTGTGAAA
Statistics
Matches: 114, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
48 2 0.02
49 31 0.27
50 78 0.68
51 3 0.03
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.29
Consensus pattern (50 bp):
GAATGTATCGATACAATGAACAATGTATCGATACATCTAGGTAAAATCTA
Found at i:202184 original size:32 final size:33
Alignment explanation
Indices: 202138--202208 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 33
202128 AATTAATTAG
*
202138 TTTTAATCAGTATTT-AATTATAATT-TCCTCTT
1 TTTTAATCAGTATTTGAA-TATAATTCTCCTATT
*
202170 TTTTAAT-AGTTATTTGAATATAATTCTCTTATT
1 TTTTAATCAG-TATTTGAATATAATTCTCCTATT
202203 TTTTAA
1 TTTTAA
202209 AAAACAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
31 2 0.06
32 19 0.56
33 13 0.38
ACGTcount: A:0.30, C:0.08, G:0.04, T:0.58
Consensus pattern (33 bp):
TTTTAATCAGTATTTGAATATAATTCTCCTATT
Found at i:209336 original size:2 final size:2
Alignment explanation
Indices: 209329--209379 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
209319 ATGTGTCATA
*
209329 AT AT AT AT GT 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
209371 AT AT AT AT A
1 AT AT AT AT A
209380 CACACGATAT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:210253 original size:21 final size:21
Alignment explanation
Indices: 210212--210254 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
210202 ACTTACCAAA
* *
210212 AAAATAACAATAATAGTAATG
1 AAAATAACAATAACAGAAATG
210233 AAAATAA-AATTAACAGAAATG
1 AAAATAACAA-TAACAGAAATG
210254 A
1 A
210255 TTTTTTCTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.65, C:0.05, G:0.09, T:0.21
Consensus pattern (21 bp):
AAAATAACAATAACAGAAATG
Found at i:213262 original size:2 final size:2
Alignment explanation
Indices: 213255--213281 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
213245 TGAACTTAAA
213255 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
213282 CTTACTAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:214322 original size:36 final size:36
Alignment explanation
Indices: 214279--214366 Score: 115
Period size: 37 Copynumber: 2.4 Consensus size: 36
214269 AATTTTAAAT
214279 TTAAAAAATAAAAATAACAAC-CCTTCAGTTTTAGAC
1 TTAAAAAA-AAAAATAACAACTCCTTCAGTTTTAGAC
* * *
214315 TTGAAAAACAAAAATAATAACTCTTTCAGTTTTAGAC
1 TT-AAAAAAAAAAATAACAACTCCTTCAGTTTTAGAC
214352 TTAAATAAAAAAAAT
1 TTAAA-AAAAAAAAT
214367 TCCAATTGAT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
36 16 0.36
37 29 0.64
ACGTcount: A:0.52, C:0.12, G:0.06, T:0.30
Consensus pattern (36 bp):
TTAAAAAAAAAAATAACAACTCCTTCAGTTTTAGAC
Found at i:214470 original size:13 final size:15
Alignment explanation
Indices: 214440--214469 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
214430 TTTTTTGAGA
214440 ATTCAGATATTATAT
1 ATTCAGATATTATAT
214455 ATTCAGATATTATAT
1 ATTCAGATATTATAT
214470 TTATCATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (15 bp):
ATTCAGATATTATAT
Found at i:214707 original size:17 final size:17
Alignment explanation
Indices: 214673--214708 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
214663 AGAAAATTTG
**
214673 ATTTAATGAATTTGAAT
1 ATTTAATGAATTCAAAT
214690 ATTTAATGAATTCAAAT
1 ATTTAATGAATTCAAAT
214707 AT
1 AT
214709 CCGATGAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.44
Consensus pattern (17 bp):
ATTTAATGAATTCAAAT
Found at i:215695 original size:31 final size:30
Alignment explanation
Indices: 215659--215737 Score: 83
Period size: 32 Copynumber: 2.6 Consensus size: 30
215649 ATTTAATATT
*
215659 TTATTTTATTATTAATAATTAGATTAAAATA
1 TTATTTTATTATTAATAATTA-AATAAAATA
* *
215690 TTATTTTTATAATTAA-ATTTAAATAAAATA
1 TTA-TTTTATTATTAATAATTAAATAAAATA
215720 -T-TTTTATTATTAAATAAT
1 TTATTTTATTATT-AATAAT
215738 AATTGAAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
27 9 0.22
28 2 0.05
29 3 0.08
30 8 0.20
31 7 0.17
32 11 0.28
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (30 bp):
TTATTTTATTATTAATAATTAAATAAAATA
Found at i:215713 original size:25 final size:26
Alignment explanation
Indices: 215664--215734 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 26
215654 ATATTTTATT
* *
215664 TTATTATTAATAATTAGATTAAAAT-A
1 TTATT-TTTATAATTAAATTAAAATAA
*
215690 TTATTTTTATAATTAAATTTAAATAAA
1 TTATTTTTATAATTAAATTAAAAT-AA
* *
215717 ATATTTTTATTATTAAAT
1 TTATTTTTATAATTAAAT
215735 AATAATTGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
25 16 0.42
26 5 0.13
27 17 0.45
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (26 bp):
TTATTTTTATAATTAAATTAAAATAA
Found at i:217883 original size:2 final size:2
Alignment explanation
Indices: 217876--217907 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
217866 TAAATTATTT
217876 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
217908 ATTGGCTAAA
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):
TA
Found at i:221142 original size:15 final size:15
Alignment explanation
Indices: 221122--221168 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
221112 GAATCACTAT
221122 TATTATTATTTATTA
1 TATTATTATTTATTA
*
221137 TATTATTATTTATGA
1 TATTATTATTTATTA
* *
221152 TGATAAATATTTATTA
1 T-ATTATTATTTATTA
221168 T
1 T
221169 TATAAATCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
15 15 0.56
16 12 0.44
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (15 bp):
TATTATTATTTATTA
Found at i:221627 original size:29 final size:29
Alignment explanation
Indices: 221571--221628 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
221561 AAATAAAAAA
* *
221571 TATATTTTTAATTTATTTAAATATATTTT
1 TATATTTTTAATTTATTTAAAAAAATTTT
221600 TATATTTTT-ATTATATTTAAAAAAATTTT
1 TATATTTTTAATT-TATTTAAAAAAATTTT
221629 ATTTAATAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 23 0.88
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (29 bp):
TATATTTTTAATTTATTTAAAAAAATTTT
Found at i:221866 original size:7 final size:7
Alignment explanation
Indices: 221854--221878 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
221844 TATTTAGATA
221854 AATTTTT
1 AATTTTT
221861 AATTTTT
1 AATTTTT
221868 AATTTTT
1 AATTTTT
221875 AATT
1 AATT
221879 ATAGTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
AATTTTT
Found at i:221904 original size:18 final size:18
Alignment explanation
Indices: 221859--221915 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
221849 AGATAAATTT
* *
221859 TTAATTTTTAATTTTTAA
1 TTAATTTTTAACTTTAAA
*
221877 TTATAGTTTTATA-TTTAAA
1 TTA-ATTTTTA-ACTTTAAA
221896 TTAATTTTTAACTTTAAA
1 TTAATTTTTAACTTTAAA
221914 TT
1 TT
221916 TATATTTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 1 0.03
18 17 0.52
19 14 0.42
20 1 0.03
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (18 bp):
TTAATTTTTAACTTTAAA
Found at i:221935 original size:18 final size:18
Alignment explanation
Indices: 221883--221943 Score: 53
Period size: 18 Copynumber: 3.7 Consensus size: 18
221873 TTAATTATAG
*
221883 TTTTATATTTAAATTAAT
1 TTTTATATTTAAATAAAT
*
221901 TTTTA-ACTT---TAAA-
1 TTTTATATTTAAATAAAT
221914 -TTTATATTTAAATAAAT
1 TTTTATATTTAAATAAAT
221931 TTTTAATATTTAA
1 TTTT-ATATTTAA
221944 TTTTTATCTA
Statistics
Matches: 33, Mismatches: 3, Indels: 13
0.67 0.06 0.27
Matches are distributed among these distances:
12 4 0.12
13 3 0.09
14 3 0.09
16 4 0.12
17 3 0.09
18 8 0.24
19 8 0.24
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTATATTTAAATAAAT
Found at i:221957 original size:30 final size:29
Alignment explanation
Indices: 221868--221959 Score: 103
Period size: 30 Copynumber: 3.1 Consensus size: 29
221858 TTTAATTTTT
* * *
221868 AATTTTTAATTATAGTTTTATATTTAAATT
1 AATTTTTAATTTTAATTTT-TATTTAAATA
* *
221898 AATTTTTAACTTTAAATTTATATTTAAATA
1 AATTTTTAA-TTTTAATTTTTATTTAAATA
*
221928 AATTTTTAATATTTAATTTTTATCTAAATA
1 AATTTTTAAT-TTTAATTTTTATTTAAATA
221958 AA
1 AA
221960 CTTATAATAT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
29 1 0.02
30 45 0.87
31 6 0.12
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.55
Consensus pattern (29 bp):
AATTTTTAATTTTAATTTTTATTTAAATA
Found at i:221968 original size:30 final size:30
Alignment explanation
Indices: 221912--221969 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
221902 TTTAACTTTA
* * *
221912 AATTTATATTTAAATAAATTTTTAATATTT
1 AATTTATATCTAAATAAACTTATAATATTT
*
221942 AATTTTTATCTAAATAAACTTATAATAT
1 AATTTATATCTAAATAAACTTATAATAT
221970 AAATCTATAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (30 bp):
AATTTATATCTAAATAAACTTATAATATTT
Found at i:222226 original size:23 final size:23
Alignment explanation
Indices: 222200--222285 Score: 57
Period size: 27 Copynumber: 3.5 Consensus size: 23
222190 ATCCTATAAA
222200 TATAA-AATTTAAATTTTATTATT
1 TATAATAATTTAAATTTTATT-TT
* * *
222223 TATAATATTTTTATTTTTATTTT
1 TATAATAATTTAAATTTTATTTT
* *
222246 TATATTATAATTTTTTATTTTTATTTT
1 TATA--ATAA--TTTAAATTTTATTTT
222273 TATATTATAATTT
1 TATA--ATAATTT
222286 TTTATAAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
23 11 0.20
24 12 0.22
25 6 0.11
27 25 0.46
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
TATAATAATTTAAATTTTATTTT
Found at i:222239 original size:6 final size:6
Alignment explanation
Indices: 222228--222275 Score: 60
Period size: 6 Copynumber: 7.5 Consensus size: 6
222218 TTATTTATAA
*
222228 TATTTT TATTTT TATTTT TATATTAT AATTTTT TATTTT TATTTT TAT
1 TATTTT TATTTT TATTTT TAT-TT-T TA-TTTT TATTTT TATTTT TAT
222276 ATTATAATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
6 28 0.76
7 4 0.11
8 4 0.11
9 1 0.03
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (6 bp):
TATTTT
Found at i:222260 original size:27 final size:27
Alignment explanation
Indices: 222218--222290 Score: 130
Period size: 27 Copynumber: 2.7 Consensus size: 27
222208 TTAAATTTTA
222218 TTAT-TTATAATATTTTTATTTTTATTT
1 TTATATTATAAT-TTTTTATTTTTATTT
222245 TTATATTATAATTTTTTATTTTTATTT
1 TTATATTATAATTTTTTATTTTTATTT
222272 TTATATTATAATTTTTTAT
1 TTATATTATAATTTTTTAT
222291 AAAAAATTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
27 38 0.84
28 7 0.16
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (27 bp):
TTATATTATAATTTTTTATTTTTATTT
Found at i:222566 original size:21 final size:19
Alignment explanation
Indices: 222537--222581 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
222527 AGTTACGGTT
* *
222537 AAATTTAAATTATTATTTAA
1 AAATTTAAAATATTA-ATAA
222557 AAATATTAAAATATTAATAA
1 AAAT-TTAAAATATTAATAA
222577 AAATT
1 AAATT
222582 ATTTTATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 1 0.05
20 11 0.50
21 10 0.45
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATTTAAAATATTAATAA
Found at i:224059 original size:32 final size:31
Alignment explanation
Indices: 223966--224093 Score: 125
Period size: 32 Copynumber: 4.0 Consensus size: 31
223956 TGATGTATAA
* *
223966 TATAAATTTATAAAAAATTTAAATTAATATTAAT
1 TATAAA-TT-TAATAAATTTAAA-TAAAATTAAT
* * *
224000 TATAAATTAAATAAA-TTAAATATAATTATT
1 TATAAATTTAATAAATTTAAATAAAATTAAT
*
224030 TATAAGTTTAATAAATATTAAATAAAATTAAT
1 TATAAATTTAATAAAT-TTAAATAAAATTAAT
* *
224062 TATAAATTTAATAATTATTAAA-AAATTTAAT
1 TATAAATTTAATAAAT-TTAAATAAAATTAAT
224093 T
1 T
224094 TTATTTTTTA
Statistics
Matches: 80, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
30 20 0.25
31 14 0.17
32 38 0.47
33 2 0.03
34 6 0.08
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (31 bp):
TATAAATTTAATAAATTTAAATAAAATTAAT
Found at i:224083 original size:16 final size:16
Alignment explanation
Indices: 223996--224083 Score: 60
Period size: 16 Copynumber: 5.7 Consensus size: 16
223986 AAATTAATAT
*
223996 TAATTA-TAAATTAAA
1 TAATTATTAAATTTAA
*
224011 TAA--ATTAAATATAA
1 TAATTATTAAATTTAA
* *
224025 TTATT-TATAAGTTTAA
1 TAATTAT-TAAATTTAA
* **
224041 TAAATATTAAATAAAA
1 TAATTATTAAATTTAA
224057 TTAATTA-TAAATTTAA
1 -TAATTATTAAATTTAA
224073 TAATTATTAAA
1 TAATTATTAAA
224084 AAATTTAATT
Statistics
Matches: 53, Mismatches: 13, Indels: 13
0.67 0.16 0.16
Matches are distributed among these distances:
13 1 0.02
14 9 0.17
15 10 0.19
16 27 0.51
17 6 0.11
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (16 bp):
TAATTATTAAATTTAA
Found at i:224193 original size:5 final size:5
Alignment explanation
Indices: 224183--224216 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
224173 TATATGAAAG
224183 TTATT TTATT TTATT TTA-T TTATT TTATAT TTAT
1 TTATT TTATT TTATT TTATT TTATT TTAT-T TTAT
224217 AAATATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.15
5 18 0.67
6 5 0.19
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (5 bp):
TTATT
Found at i:224198 original size:10 final size:10
Alignment explanation
Indices: 224183--224216 Score: 52
Period size: 9 Copynumber: 3.4 Consensus size: 10
224173 TATATGAAAG
224183 TTATTTTATT
1 TTATTTTATT
224193 TTATTTTA-T
1 TTATTTTATT
224202 TTATTTTATAT
1 TTATTTTAT-T
224213 TTAT
1 TTAT
224217 AAATATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.41
10 8 0.36
11 5 0.23
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
TTATTTTATT
Found at i:224203 original size:15 final size:16
Alignment explanation
Indices: 224183--224216 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
224173 TATATGAAAG
224183 TTATTTTATTTTAT-T
1 TTATTTTATTTTATAT
224198 TTA-TTTATTTTATAT
1 TTATTTTATTTTATAT
224213 TTAT
1 TTAT
224217 AAATATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTATTTTATAT
Found at i:224747 original size:27 final size:29
Alignment explanation
Indices: 224684--224747 Score: 80
Period size: 27 Copynumber: 2.3 Consensus size: 29
224674 ATTTTTATGT
224684 AATTTTT-TATATGTTATATCAAATTTAA
1 AATTTTTATATATGTTATATCAAATTTAA
* * *
224712 AAGTGTTATATAT-TTATAT-AAATTTTA
1 AATTTTTATATATGTTATATCAAATTTAA
224739 AATTTTTAT
1 AATTTTTAT
224748 CTAATTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
27 14 0.47
28 11 0.37
29 5 0.17
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (29 bp):
AATTTTTATATATGTTATATCAAATTTAA
Found at i:224755 original size:66 final size:64
Alignment explanation
Indices: 224672--224803 Score: 219
Period size: 64 Copynumber: 2.0 Consensus size: 64
224662 TTGCCATGTG
* *
224672 AAATTTTTATGTAATTTTTTATATGTTATATCAAATTTAAAAGTGTTATATATTTATATAAATTT
1 AAATTTTTATCTAATTTTTTATATG-TATATCAAATTTAAAA-TATTATATATTTATATAAATTT
224737 T
64 T
*
224738 AAATTTTTATCTAATTTTTTATTTGTATATCAAATTTAAAATATTATATATTTATATAAATTTT
1 AAATTTTTATCTAATTTTTTATATGTATATCAAATTTAAAATATTATATATTTATATAAATTTT
224802 AA
1 AA
224804 TAAATTAATG
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
64 24 0.38
65 16 0.25
66 23 0.37
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (64 bp):
AAATTTTTATCTAATTTTTTATATGTATATCAAATTTAAAATATTATATATTTATATAAATTTT
Found at i:224898 original size:28 final size:31
Alignment explanation
Indices: 224862--224924 Score: 87
Period size: 28 Copynumber: 2.1 Consensus size: 31
224852 GTCATATTTA
224862 ATTTTTTATATTATA-TCATAT-TT-TAATT
1 ATTTTTTATATTATATTCATATCTTATAATT
* *
224890 ATTTTTTATATTGTATTTATATCTTATAATT
1 ATTTTTTATATTATATTCATATCTTATAATT
224921 ATTT
1 ATTT
224925 GATGTTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 14 0.47
29 5 0.17
30 2 0.07
31 9 0.30
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.65
Consensus pattern (31 bp):
ATTTTTTATATTATATTCATATCTTATAATT
Found at i:225683 original size:23 final size:25
Alignment explanation
Indices: 225651--225704 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
225641 ATTTGTATCG
225651 TATTTGAATT-TTGTATT-ATATTA
1 TATTTGAATTATTGTATTCATATTA
* * *
225674 TATTTTAATTATTTTTTTCATATTA
1 TATTTGAATTATTGTATTCATATTA
225699 TATTTG
1 TATTTG
225705 TATCGTATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 9 0.36
24 5 0.20
25 11 0.44
ACGTcount: A:0.28, C:0.02, G:0.06, T:0.65
Consensus pattern (25 bp):
TATTTGAATTATTGTATTCATATTA
Found at i:226043 original size:11 final size:11
Alignment explanation
Indices: 226027--226052 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
226017 TTGTGTTATT
226027 TTATATTAAAA
1 TTATATTAAAA
226038 TTATATTAAAA
1 TTATATTAAAA
226049 TTAT
1 TTAT
226053 TATATATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TTATATTAAAA
Found at i:227667 original size:17 final size:17
Alignment explanation
Indices: 227640--227681 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
227630 TTAAATTTTA
* *
227640 AAATAATTATATAAATTT
1 AAAT-ATTATAAAAATAT
227658 AAATATTATAAAAATAT
1 AAATATTATAAAAATAT
227675 AAATATT
1 AAATATT
227682 CGATCTGCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATATTATAAAAATAT
Found at i:228364 original size:16 final size:16
Alignment explanation
Indices: 228343--228395 Score: 56
Period size: 15 Copynumber: 3.3 Consensus size: 16
228333 CAAAAACTTG
*
228343 AATAAAAATATTAAAA
1 AATAAAAATAATAAAA
*
228359 AAT-AAAATAATGAAA
1 AATAAAAATAATAAAA
228374 AATAAATAAATAA-AAAA
1 AAT-AA-AAATAATAAAA
228391 AATAA
1 AATAA
228396 GAAGAGCAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 13 0.42
16 5 0.16
17 7 0.23
18 6 0.19
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (16 bp):
AATAAAAATAATAAAA
Found at i:230148 original size:27 final size:27
Alignment explanation
Indices: 230118--230204 Score: 74
Period size: 28 Copynumber: 3.3 Consensus size: 27
230108 ACTAAAAAAT
230118 TATTTTATAATTTATATATTTATATAA
1 TATTTTATAATTTATATATTTATATAA
* * *
230145 TATTCATATATTTTAT-TA-TTATA-AT
1 TATT-TTATAATTTATATATTTATATAA
* *
230170 TATATTTAAAATATTATATATTTAAATAA
1 TAT-TTTATAAT-TTATATATTTATATAA
230199 -ATTTTA
1 TATTTTA
230205 ATGTATTAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
25 8 0.17
26 10 0.22
27 12 0.26
28 15 0.33
29 1 0.02
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (27 bp):
TATTTTATAATTTATATATTTATATAA
Found at i:230158 original size:35 final size:35
Alignment explanation
Indices: 230118--230192 Score: 93
Period size: 35 Copynumber: 2.1 Consensus size: 35
230108 ACTAAAAAAT
230118 TATTTTATAATT-T-A-TATATTTATATAATATTCATA
1 TATTTTATAATTATAATTATATTTA-A-AATATT-ATA
*
230153 TATTTTATTATTATAATTATATTTAAAATATTATA
1 TATTTTATAATTATAATTATATTTAAAATATTATA
230188 TATTT
1 TATTT
230193 AAATAAATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
35 19 0.53
36 7 0.19
37 2 0.06
38 8 0.22
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (35 bp):
TATTTTATAATTATAATTATATTTAAAATATTATA
Found at i:230300 original size:25 final size:23
Alignment explanation
Indices: 230259--230304 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
230249 ATTTACATTA
230259 TATTTTAATTTTATATCATATTT
1 TATTTTAATTTTATATCATATTT
*
230282 TATTTATATTTTTAGTATCATAT
1 TATTT-TAATTTTA-TATCATAT
230305 GCAAAGTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 7 0.35
25 8 0.40
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.63
Consensus pattern (23 bp):
TATTTTAATTTTATATCATATTT
Found at i:233367 original size:11 final size:11
Alignment explanation
Indices: 233349--233417 Score: 76
Period size: 11 Copynumber: 6.6 Consensus size: 11
233339 TAAATATTTA
233349 TATATTTATAT
1 TATATTTATAT
* *
233360 TGTATTTATAA
1 TATATTTATAT
233371 TATATTTATA-
1 TATATTTATAT
233381 TATATATTATAT
1 TATAT-TTATAT
233393 T-TATTTA-AT
1 TATATTTATAT
233402 T-T-TTTATAT
1 TATATTTATAT
233411 TATATTT
1 TATATTT
233418 TAATTATTGT
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
8 4 0.08
9 7 0.14
10 9 0.18
11 29 0.58
12 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (11 bp):
TATATTTATAT
Found at i:233380 original size:28 final size:29
Alignment explanation
Indices: 233336--233396 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 29
233326 AGCATGTGAA
* *
233336 TTATAAATATTTATATATTTATATTGTAT
1 TTATAAATATTTATATATATATATTATAT
233365 TTAT-AATATATT-TATATATATATTATAT
1 TTATAAATAT-TTATATATATATATTATAT
233393 TTAT
1 TTAT
233397 TTAATTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 23 0.79
29 6 0.21
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (29 bp):
TTATAAATATTTATATATATATATTATAT
Found at i:234360 original size:18 final size:21
Alignment explanation
Indices: 234320--234361 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
234310 TCTAAATTCA
*
234320 ATTATATATATTAATTTTGAT
1 ATTATATATATTAATGTTGAT
234341 ATTA-ATATATT-ATGTT-AT
1 ATTATATATATTAATGTTGAT
234359 ATT
1 ATT
234362 TATTTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 5 0.25
19 4 0.20
20 7 0.35
21 4 0.20
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (21 bp):
ATTATATATATTAATGTTGAT
Found at i:234830 original size:18 final size:17
Alignment explanation
Indices: 234801--234843 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
234791 AAATATTTTT
234801 AAATAAAAATAATAATA
1 AAATAAAAATAATAATA
234818 AAATAATAAATAATAAT-
1 AAATAA-AAATAATAATA
*
234835 TAATAAAAA
1 AAATAAAAA
234844 GTTTATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 3 0.12
17 11 0.46
18 10 0.42
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
AAATAAAAATAATAATA
Found at i:234991 original size:30 final size:29
Alignment explanation
Indices: 234886--234996 Score: 98
Period size: 30 Copynumber: 3.6 Consensus size: 29
234876 GAATAATGAC
* *
234886 TTAAAAAGTTAAATATATTTTTGATCAAATT
1 TTAAAAA--TAAATATATTTTTTATAAAATT
*
234917 TTAAAAATATAAGTGAATATTTTTTA-AATATT
1 TTAAAAATA-AA-T--ATATTTTTTATAAAATT
**
234949 AAAAAAATAAATATATTTTTTATAAAATT
1 TTAAAAATAAATATATTTTTTATAAAATT
*
234978 TTAAAGGATAAATATATTT
1 TTAAA-AATAAATATATTT
234997 ACTTTTTTTT
Statistics
Matches: 65, Mismatches: 9, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
28 10 0.15
29 10 0.15
30 15 0.23
31 10 0.15
32 11 0.17
33 9 0.14
ACGTcount: A:0.50, C:0.01, G:0.05, T:0.44
Consensus pattern (29 bp):
TTAAAAATAAATATATTTTTTATAAAATT
Found at i:236192 original size:17 final size:18
Alignment explanation
Indices: 236167--236200 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
236157 CATAGAATTT
*
236167 AAAATATAATA-TAATAC
1 AAAAAATAATATTAATAC
236184 AAAAAATAATATTAATA
1 AAAAAATAATATTAATA
236201 TAAATATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAAAATAATATTAATAC
Found at i:236233 original size:33 final size:33
Alignment explanation
Indices: 236196--236284 Score: 92
Period size: 32 Copynumber: 2.6 Consensus size: 33
236186 AAAATAATAT
236196 TAATATAAATATATAAATAT-TTCAAAATTTATA
1 TAATATAAATATATAAATATATT-AAAATTTATA
* * *
236229 TAATATAAAT-TATTAATGTATTAATATTTATA
1 TAATATAAATATATAAATATATTAAAATTTATA
*
236261 TAAATATAAAATATCTTAAATATA
1 T-AATAT-AAATAT-ATAAATATA
236285 ATTATAACAT
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
32 17 0.38
33 17 0.38
34 4 0.09
35 1 0.02
36 6 0.13
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (33 bp):
TAATATAAATATATAAATATATTAAAATTTATA
Found at i:236506 original size:22 final size:21
Alignment explanation
Indices: 236475--236522 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 21
236465 TAATTATTTT
*
236475 AAAATCAATAAGTGAATGATTAA
1 AAAATCAATAA-TAAAT-ATTAA
236498 AAAAT-AATAATAAATATTAA
1 AAAATCAATAATAAATATTAA
236518 AAAAT
1 AAAAT
236523 TTAATAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 10 0.42
21 4 0.17
22 5 0.21
23 5 0.21
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (21 bp):
AAAATCAATAATAAATATTAA
Found at i:238793 original size:16 final size:17
Alignment explanation
Indices: 238752--238796 Score: 67
Period size: 16 Copynumber: 2.8 Consensus size: 17
238742 ATATTTTAAG
238752 TTATATTTTAAA-TTTT
1 TTATATTTTAAATTTTT
*
238768 TTATAATTTAAATTTTT
1 TTATATTTTAAATTTTT
238785 TTAT-TTTTAAAT
1 TTATATTTTAAAT
238797 AATATATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 18 0.69
17 8 0.31
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATATTTTAAATTTTT
Found at i:239454 original size:26 final size:25
Alignment explanation
Indices: 239399--239457 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 25
239389 TTCAATTAAA
*
239399 AAAATAAAATAAATAAATATAGATT
1 AAAATAAAATAAATAAATATAGATC
*
239424 TAAATAATAAT-AATAAATAATAGATC
1 AAAATAA-AATAAATAAAT-ATAGATC
239450 AAAATAAA
1 AAAATAAA
239458 TTCTAAGATA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 14 0.48
26 15 0.52
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (25 bp):
AAAATAAAATAAATAAATATAGATC
Found at i:239620 original size:17 final size:18
Alignment explanation
Indices: 239600--239647 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
239590 GTTTTAAGTT
*
239600 TAAAAAAT-AGATTTATG
1 TAAAAAATAAAATTTATG
239617 TAAAAAATAAAATTTAT-
1 TAAAAAATAAAATTTATG
*
239634 TTAAAAATAAAATT
1 TAAAAAATAAAATT
239648 ATTTTTAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 21 0.75
18 7 0.25
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.35
Consensus pattern (18 bp):
TAAAAAATAAAATTTATG
Found at i:239649 original size:16 final size:17
Alignment explanation
Indices: 239619--239651 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
239609 GATTTATGTA
239619 AAAAATAAAATTTATTT
1 AAAAATAAAATTTATTT
239636 AAAAATAAAA-TTATTT
1 AAAAATAAAATTTATTT
239652 TTAATTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAAAATAAAATTTATTT
Found at i:239794 original size:28 final size:28
Alignment explanation
Indices: 239754--239807 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
239744 AATTTTATTT
*
239754 TATAAAAAATAAATATA-TAATATTATAA
1 TATAAAAAATAAAAATATTAA-ATTATAA
* *
239782 TATAAATATTAAAAATATTAAATTAT
1 TATAAAAAATAAAAATATTAAATTAT
239808 TTATATTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
28 19 0.86
29 3 0.14
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (28 bp):
TATAAAAAATAAAAATATTAAATTATAA
Found at i:239871 original size:13 final size:13
Alignment explanation
Indices: 239853--239887 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
239843 AATGATTAAA
*
239853 TTTAAAAAAATAT
1 TTTAAAAAAATAC
239866 TTTAAAAAAATAC
1 TTTAAAAAAATAC
*
239879 ATTAAAAAA
1 TTTAAAAAA
239888 TATAAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (13 bp):
TTTAAAAAAATAC
Found at i:240357 original size:21 final size:21
Alignment explanation
Indices: 240331--240423 Score: 61
Period size: 21 Copynumber: 4.4 Consensus size: 21
240321 TAAAAATATT
240331 TTATATTTTTAATAAATTT-TA
1 TTATATTTTTAAT-AATTTATA
240352 TTATA---TTAATAATTTATA
1 TTATATTTTTAATAATTTATA
* * *
240370 TTATATTTATATTATTTTATA
1 TTATATTTTTAATAATTTATA
* *
240391 -TATTATATTTAATTAACTTTTATG
1 TTA-TATTTTTAA-TAA--TTTATA
240415 TTATATTTT
1 TTATATTTT
240424 GATCATTTAA
Statistics
Matches: 54, Mismatches: 9, Indels: 15
0.69 0.12 0.19
Matches are distributed among these distances:
17 5 0.09
18 12 0.22
20 2 0.04
21 21 0.39
22 2 0.04
24 10 0.19
25 2 0.04
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (21 bp):
TTATATTTTTAATAATTTATA
Found at i:240360 original size:18 final size:17
Alignment explanation
Indices: 240317--240395 Score: 61
Period size: 18 Copynumber: 4.4 Consensus size: 17
240307 TTTATTAAAA
*
240317 ATATTAAAAATATTTTAT
1 ATATTAATAA-ATTTTAT
*
240335 ATTTTTAATAAATTTTATT
1 A-TATTAATAAATTTTA-T
240354 ATATTAAT-AATTTATATT
1 ATATTAATAAATTT-TA-T
* *
240372 ATATTTATATTATTTTAT
1 ATATTAATA-AATTTTAT
240390 ATATTA
1 ATATTA
240396 TATTTAATTA
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
17 5 0.10
18 30 0.60
19 11 0.22
20 4 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATATTAATAAATTTTAT
Found at i:240392 original size:23 final size:22
Alignment explanation
Indices: 240350--240422 Score: 75
Period size: 23 Copynumber: 3.5 Consensus size: 22
240340 TAATAAATTT
240350 TATTATA-TTAA-TAA--TTTA
1 TATTATATTTAATTAACTTTTA
*
240368 TATTATATTTATATT-ATTTTATA
1 TATTATATTTA-ATTAACTTT-TA
240391 TATTATATTTAATTAACTTTTA
1 TATTATATTTAATTAACTTTTA
*
240413 TGTTATATTT
1 TATTATATTT
240423 TGATCATTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
18 7 0.15
19 3 0.07
20 2 0.04
21 1 0.02
22 16 0.35
23 17 0.37
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (22 bp):
TATTATATTTAATTAACTTTTA
Found at i:240904 original size:30 final size:29
Alignment explanation
Indices: 240870--240987 Score: 110
Period size: 30 Copynumber: 3.8 Consensus size: 29
240860 CATGATAAGC
*
240870 GTATAGTTTAAGTTATGATAAAGGGCTCTG
1 GTATAGTTCAAGTTATGATAAAGGG-TCTG
*
240900 GTATAGTTCAAGTTATGATAAAGAGTCATG
1 GTATAGTTCAAGTTATGATAAAGGGTC-TG
*
240930 ATAAACGTATAGTTTAAGTTATGATAAAGGGTTCTG
1 ------GTATAGTTCAAGTTATGATAAAGGG-TCTG
* *
240966 TTATAGTTCAAGTTTTGATAAA
1 GTATAGTTCAAGTTATGATAAA
240988 AGGTTGGGGT
Statistics
Matches: 73, Mismatches: 7, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
29 2 0.03
30 44 0.60
36 25 0.34
37 2 0.03
ACGTcount: A:0.35, C:0.06, G:0.22, T:0.37
Consensus pattern (29 bp):
GTATAGTTCAAGTTATGATAAAGGGTCTG
Found at i:240927 original size:66 final size:66
Alignment explanation
Indices: 240857--240987 Score: 226
Period size: 66 Copynumber: 2.0 Consensus size: 66
240847 GTAAAGTCGA
*
240857 AGTCATGATAAGCGTATAGTTTAAGTTATGATAAAGGGCTCTGGTATAGTTCAAGTTATGATAAA
1 AGTCATGATAAACGTATAGTTTAAGTTATGATAAAGGGCTCTGGTATAGTTCAAGTTATGATAAA
240922 G
66 G
* * *
240923 AGTCATGATAAACGTATAGTTTAAGTTATGATAAAGGGTTCTGTTATAGTTCAAGTTTTGATAAA
1 AGTCATGATAAACGTATAGTTTAAGTTATGATAAAGGGCTCTGGTATAGTTCAAGTTATGATAAA
240988 AGGTTGGGGT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.35, C:0.07, G:0.22, T:0.36
Consensus pattern (66 bp):
AGTCATGATAAACGTATAGTTTAAGTTATGATAAAGGGCTCTGGTATAGTTCAAGTTATGATAAA
G
Found at i:240949 original size:36 final size:35
Alignment explanation
Indices: 240857--240958 Score: 117
Period size: 30 Copynumber: 3.0 Consensus size: 35
240847 GTAAAGTCGA
240857 AGTCATGATAAGCGTATAGTTTAAGTTATGATAAAG
1 AGTCATGATAA-CGTATAGTTTAAGTTATGATAAAG
* *
240893 GGCTC-TG-----GTATAGTTCAAGTTATGATAAAG
1 AG-TCATGATAACGTATAGTTTAAGTTATGATAAAG
240923 AGTCATGATAAACGTATAGTTTAAGTTATGATAAAG
1 AGTCATGAT-AACGTATAGTTTAAGTTATGATAAAG
240959 GGTTCTGTTA
Statistics
Matches: 54, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
29 2 0.04
30 25 0.46
36 25 0.46
37 2 0.04
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (35 bp):
AGTCATGATAACGTATAGTTTAAGTTATGATAAAG
Found at i:241220 original size:93 final size:96
Alignment explanation
Indices: 240995--241232 Score: 311
Period size: 98 Copynumber: 2.5 Consensus size: 96
240985 AAAAGGTTGG
* * **
240995 GGTCTTGGAAGAGATGTAGTATTATGAGGTATTCGTAATAAGTTTTGAGTGGGAGCTATATTCGT
1 GGTCTTAGAAGAGATGTAGTATTATGAGCTATTCGTAATAAGTTTTGAGTACGAGC-ATATTCGT
* *
241060 AGTAAGTTTTAAGTTACGATAAAGGAAGTTTCT
65 AGTAAGTTCTAAGTTACGATAAAGG-AGTCTCT
* *
241093 GGGCCTAGAAGAGATGTAGTATTATGAGCTATTCGTAATAAGTTTTGAGTACGAGC-TATTCGTA
1 GGTCTTAGAAGAGATGTAGTATTATGAGCTATTCGTAATAAGTTTTGAGTACGAGCATATTCGTA
* *
241157 GTAAGTTCTAAGTTATGATAATGG-GTCT-T
66 GTAAGTTCTAAGTTACGATAAAGGAGTCTCT
* * * *
241186 GGTCTTAGAAGAGATGTAGCATTATAAGCTATTCGTAGTAAATTTTG
1 GGTCTTAGAAGAGATGTAGTATTATGAGCTATTCGTAATAAGTTTTG
241233 TATGGGATGT
Statistics
Matches: 124, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
93 42 0.34
94 3 0.02
96 29 0.23
98 50 0.40
ACGTcount: A:0.30, C:0.08, G:0.26, T:0.36
Consensus pattern (96 bp):
GGTCTTAGAAGAGATGTAGTATTATGAGCTATTCGTAATAAGTTTTGAGTACGAGCATATTCGTA
GTAAGTTCTAAGTTACGATAAAGGAGTCTCT
Found at i:243397 original size:20 final size:19
Alignment explanation
Indices: 243372--243431 Score: 75
Period size: 20 Copynumber: 3.1 Consensus size: 19
243362 AATAGATGTT
243372 AGTAAAGGGAAAGAAAGAAA
1 AGTAAA-GGAAAGAAAGAAA
* *
243392 AGTAAAAGAAAGAAAAAAAA
1 AGTAAAGGAAAG-AAAGAAA
*
243412 AGTAAAGGAAGGAAAGAAA
1 AGTAAAGGAAAGAAAGAAA
243431 A
1 A
243432 TGATTCATCT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
19 12 0.35
20 22 0.65
ACGTcount: A:0.70, C:0.00, G:0.25, T:0.05
Consensus pattern (19 bp):
AGTAAAGGAAAGAAAGAAA
Found at i:243418 original size:15 final size:15
Alignment explanation
Indices: 243381--243418 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
243371 TAGTAAAGGG
*
243381 AAAGAAAGAAAAGTA
1 AAAGAAAGAAAAGAA
243396 AAAGAAAGAAAA-AA
1 AAAGAAAGAAAAGAA
243410 AAAGTAAAG
1 AAAG-AAAG
243419 GAAGGAAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.05
Consensus pattern (15 bp):
AAAGAAAGAAAAGAA
Found at i:244641 original size:22 final size:21
Alignment explanation
Indices: 244616--244674 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
244606 ATAATTTTTA
* *
244616 ATTTTAAAGTTTTATGTAAACG
1 ATTTTGAAGTTTTATATAAA-G
*
244638 ATTTTGAAGTTTTATATAAAT
1 ATTTTGAAGTTTTATATAAAG
244659 AGTTTTGAAGTTTTAT
1 A-TTTTGAAGTTTTAT
244675 TTTCAAACAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 1 0.03
22 32 0.97
ACGTcount: A:0.34, C:0.02, G:0.14, T:0.51
Consensus pattern (21 bp):
ATTTTGAAGTTTTATATAAAG
Found at i:245180 original size:14 final size:14
Alignment explanation
Indices: 245161--245191 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
245151 AAAGAATACC
245161 GTGTAAGAATGCGT
1 GTGTAAGAATGCGT
245175 GTGTAAGAATGCGT
1 GTGTAAGAATGCGT
245189 GTG
1 GTG
245192 CTTATTTGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.26, C:0.06, G:0.39, T:0.29
Consensus pattern (14 bp):
GTGTAAGAATGCGT
Found at i:245244 original size:39 final size:39
Alignment explanation
Indices: 245190--245345 Score: 285
Period size: 39 Copynumber: 4.0 Consensus size: 39
245180 AGAATGCGTG
*
245190 TGCTTATTTGCTTTAAGTAACGTATGTCAAATTTTGGAT
1 TGCTTATTTGCTTTAAGCAACGTATGTCAAATTTTGGAT
*
245229 TGCTTATTTGCTTTAAGCAACGTATGTCAAATTTTGGAG
1 TGCTTATTTGCTTTAAGCAACGTATGTCAAATTTTGGAT
*
245268 TGCTTATTTGCTTTAAGTAACGTATGTCAAATTTTGGAT
1 TGCTTATTTGCTTTAAGCAACGTATGTCAAATTTTGGAT
245307 TGCTTATTTGCTTTAAGCAACGTATGTCAAATTTTGGAT
1 TGCTTATTTGCTTTAAGCAACGTATGTCAAATTTTGGAT
245346 AAGCAACGTA
Statistics
Matches: 112, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 112 1.00
ACGTcount: A:0.26, C:0.12, G:0.19, T:0.44
Consensus pattern (39 bp):
TGCTTATTTGCTTTAAGCAACGTATGTCAAATTTTGGAT
Found at i:245348 original size:25 final size:25
Alignment explanation
Indices: 245320--245370 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
245310 TTATTTGCTT
245320 TAAGCAACGTATGTCAAATTTTGGA
1 TAAGCAACGTATGTCAAATTTTGGA
245345 TAAGCAACGTATGTCAAATTTTGGA
1 TAAGCAACGTATGTCAAATTTTGGA
245370 T
1 T
245371 GGACATTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (25 bp):
TAAGCAACGTATGTCAAATTTTGGA
Found at i:245948 original size:29 final size:29
Alignment explanation
Indices: 245902--245962 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
245892 CAATTTTAGT
* * *
245902 TTTGAAGTTTTACATAAATGGTTTTGAAG
1 TTTGAAGTTTTACATAAACGATTTTAAAG
**
245931 TTTGAAGTTTTATGTAAACGATTTTAAAG
1 TTTGAAGTTTTACATAAACGATTTTAAAG
245960 TTT
1 TTT
245963 TATTTAAATG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.18, T:0.48
Consensus pattern (29 bp):
TTTGAAGTTTTACATAAACGATTTTAAAG
Found at i:245980 original size:22 final size:22
Alignment explanation
Indices: 245935--245980 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
245925 TTGAAGTTTG
**
245935 AAGTTTTATGTAAACGATTTTA
1 AAGTTTTATGTAAACGATAATA
* *
245957 AAGTTTTATTTAAATGATAATA
1 AAGTTTTATGTAAACGATAATA
245979 AA
1 AA
245981 ATTAAAATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.43
Consensus pattern (22 bp):
AAGTTTTATGTAAACGATAATA
Found at i:246369 original size:77 final size:77
Alignment explanation
Indices: 246242--246401 Score: 257
Period size: 77 Copynumber: 2.1 Consensus size: 77
246232 CAATTTAGTT
* * **
246242 TGGAAATTTTTTGTAAATCTTTTAACTTTCTTACTATCTTTTTAATCCAATCATAATATGGCTCT
1 TGGAAATTTTATGTAAATCTTTTAACTTTCTTACCATCCCTTTAATCCAATCATAATATGGCTCT
**
246307 TTCCAAGTTTTA
66 CCCCAAGTTTTA
*
246319 TGGAAATTTTATGTAAATCTTTTAATTTTCTTACCATCCCTTTAATCCAATCATAATATGGCTCT
1 TGGAAATTTTATGTAAATCTTTTAACTTTCTTACCATCCCTTTAATCCAATCATAATATGGCTCT
246384 CCCCAAGTTTTA
66 CCCCAAGTTTTA
246396 TGGAAA
1 TGGAAA
246402 CACATTATTT
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
77 76 1.00
ACGTcount: A:0.29, C:0.17, G:0.09, T:0.45
Consensus pattern (77 bp):
TGGAAATTTTATGTAAATCTTTTAACTTTCTTACCATCCCTTTAATCCAATCATAATATGGCTCT
CCCCAAGTTTTA
Found at i:246604 original size:22 final size:22
Alignment explanation
Indices: 246540--246605 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
246530 TTCAATTTTA
* *
246540 GTTTTGAAGTTTTATGTAAACG
1 GTTTTAAAGTTTTATGTAAATG
* *
246562 ATTTTTAAGTTTTATGTAAATG
1 GTTTTAAAGTTTTATGTAAATG
*
246584 GTTTTAAAGTTTTATTTAAATG
1 GTTTTAAAGTTTTATGTAAATG
246606 AATAATAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.30, C:0.02, G:0.17, T:0.52
Consensus pattern (22 bp):
GTTTTAAAGTTTTATGTAAATG
Found at i:247979 original size:30 final size:29
Alignment explanation
Indices: 247941--247998 Score: 89
Period size: 30 Copynumber: 2.0 Consensus size: 29
247931 CAATTTTAGT
*
247941 TTTAAAGTTTTATGTAAATGGTTTTGAAG
1 TTTAAAGTTTTATGTAAATAGTTTTGAAG
*
247970 TTTAGAAGTTTTTTGTAAATAGTTTTGAA
1 TTTA-AAGTTTTATGTAAATAGTTTTGAA
247999 ATTTTATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (29 bp):
TTTAAAGTTTTATGTAAATAGTTTTGAAG
Found at i:247993 original size:22 final size:22
Alignment explanation
Indices: 247968--248011 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
247958 ATGGTTTTGA
*
247968 AGTTTAGAAGTTTT-TTGTAAAT
1 AGTTTAGAAATTTTATT-TAAAT
*
247990 AGTTTTGAAATTTTATTTAAAT
1 AGTTTAGAAATTTTATTTAAAT
248012 GATAATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (22 bp):
AGTTTAGAAATTTTATTTAAAT
Found at i:248473 original size:21 final size:21
Alignment explanation
Indices: 248444--248485 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
248434 TTTTAAAGTT
*
248444 TGAATTTTTATATAAATGATA
1 TGAAGTTTTATATAAATGATA
*
248465 TGAAGTTTTATTTAAATGATA
1 TGAAGTTTTATATAAATGATA
248486 ATACAGCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (21 bp):
TGAAGTTTTATATAAATGATA
Found at i:248639 original size:27 final size:27
Alignment explanation
Indices: 248609--248663 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
248599 CTTTCTCCAA
248609 ACTTACATGGAAGAGTATCTACATTTC
1 ACTTACATGGAAGAGTATCTACATTTC
* *
248636 ACTTATATGGAAGAGTATTTACATTTC
1 ACTTACATGGAAGAGTATCTACATTTC
248663 A
1 A
248664 AATTTATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (27 bp):
ACTTACATGGAAGAGTATCTACATTTC
Found at i:249146 original size:17 final size:17
Alignment explanation
Indices: 249120--249176 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 17
249110 TTTATTTTAT
249120 TTTTAA-ATAAATAATA
1 TTTTAATATAAATAATA
249136 TTTTAATATAAACATAAT-
1 TTTTAATAT-AA-ATAATA
* *
249154 TTTTAATTTTAATAAATA
1 TTTTAATATAAAT-AATA
249172 TTTTA
1 TTTTA
249177 TTATTTAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
16 8 0.24
17 6 0.18
18 15 0.44
19 5 0.15
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTTAATATAAATAATA
Found at i:249216 original size:25 final size:24
Alignment explanation
Indices: 249171--249217 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
249161 TTTAATAAAT
*
249171 ATTTTATTATTTAATATAAATATA
1 ATTTTATTATTTAATAAAAATATA
**
249195 ATTTTAATTATTTTTTAAAAATA
1 ATTTT-ATTATTTAATAAAAATA
249218 AACATAATTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 5 0.26
25 14 0.74
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
ATTTTATTATTTAATAAAAATATA
Found at i:249232 original size:64 final size:65
Alignment explanation
Indices: 249172--249336 Score: 199
Period size: 64 Copynumber: 2.5 Consensus size: 65
249162 TTAATAAATA
*
249172 TTTTATTATTTAATATAAATATAATTTTAATTATTT-TTTAAAAATAAACATAATTCAATAATTT
1 TTTTATTATTTAATATAAATATAATTTTAATTATTTATATAAAAATAAACATAATTCAATAATTT
* * * * * *
249236 TTTTAGTATTTAATGTAAATATAATTTT-ATTATTTAATATAAATATAGATATAATTTAATAATT
1 TTTTATTATTTAATATAAATATAATTTTAATTATTT-ATATAAAAATAAACATAATTCAATAATT
249300 T
65 T
* * *
249301 TTAATTATTATTCAACATAAATATAATTTTATTTAT
1 TT--TTATTATTTAATATAAATATAATTTTAATTAT
249337 ATTTAATTAT
Statistics
Matches: 84, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
63 7 0.08
64 26 0.31
65 25 0.30
67 22 0.26
68 4 0.05
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (65 bp):
TTTTATTATTTAATATAAATATAATTTTAATTATTTATATAAAAATAAACATAATTCAATAATTT
Found at i:249263 original size:24 final size:24
Alignment explanation
Indices: 249236--249282 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
249226 TCAATAATTT
*
249236 TTTTAGTATTTAATGTAAATATAA
1 TTTTAGTATTTAATATAAATATAA
*
249260 TTTTATTATTTAATATAAATATA
1 TTTTAGTATTTAATATAAATATA
249283 GATATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (24 bp):
TTTTAGTATTTAATATAAATATAA
Found at i:249328 original size:29 final size:29
Alignment explanation
Indices: 249294--249373 Score: 79
Period size: 35 Copynumber: 2.6 Consensus size: 29
249284 ATATAATTTA
249294 ATAATTTTTAATTATTATTCAACATAAAT
1 ATAATTTTTAATTATTATTCAACATAAAT
* *
249323 ATAATTTTATTTATATTTAATTATTTAATATAAAT
1 ATAA--TT-TTTA-A-TT-ATTATTCAACATAAAT
*
249358 ATATTTTTTAATTATT
1 ATAATTTTTAATTATT
249374 TATTTTATAT
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
29 7 0.17
30 2 0.05
31 3 0.07
32 8 0.19
33 3 0.07
34 2 0.05
35 17 0.40
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (29 bp):
ATAATTTTTAATTATTATTCAACATAAAT
Found at i:249384 original size:30 final size:29
Alignment explanation
Indices: 249298--249399 Score: 87
Period size: 30 Copynumber: 3.3 Consensus size: 29
249288 AATTTAATAA
* *
249298 TTTTTAATTATTATTCAACATAAATATAATT
1 TTTTTAATTATTATTTAATATAAATAT-A-T
249329 TTATTTATATTTAATTATTTAATATAAATATAT
1 TT-TTTA-A-TT-ATTATTTAATATAAATATAT
* * *
249362 TTTTTAATTATTTATTTTATATATATACAT
1 TTTTTAATTA-TTATTTAATATAAATATAT
*
249392 ATTTTAAT
1 TTTTTAAT
249400 CAAATATTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
29 1 0.02
30 25 0.42
31 3 0.05
32 8 0.13
33 4 0.07
34 3 0.05
35 16 0.27
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (29 bp):
TTTTTAATTATTATTTAATATAAATATAT
Found at i:251471 original size:25 final size:23
Alignment explanation
Indices: 251443--251498 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 23
251433 TTGCTAATAA
251443 TGATTTTTTATTT-TTATCTTTTTT
1 TGATTTTTT-TTTATT-TCTTTTTT
251467 CTGATTTCTTTTTTATTTCTTTTTT
1 -TGATTT-TTTTTTATTTCTTTTTT
251492 T-ATTTTT
1 TGATTTTT
251499 ATCATGTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
22 2 0.07
23 4 0.14
24 1 0.03
25 17 0.59
26 5 0.17
ACGTcount: A:0.11, C:0.07, G:0.04, T:0.79
Consensus pattern (23 bp):
TGATTTTTTTTTATTTCTTTTTT
Found at i:251490 original size:12 final size:12
Alignment explanation
Indices: 251459--251496 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
251449 TTTATTTTTA
251459 TCTTTTTTCTGATT
1 TCTTTTTT-T-ATT
251473 TC-TTTTTTATT
1 TCTTTTTTTATT
251484 TCTTTTTTTATT
1 TCTTTTTTTATT
251496 T
1 T
251497 TTATCATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 5 0.22
12 11 0.48
13 5 0.22
14 2 0.09
ACGTcount: A:0.08, C:0.11, G:0.03, T:0.79
Consensus pattern (12 bp):
TCTTTTTTTATT
Found at i:254716 original size:81 final size:78
Alignment explanation
Indices: 254588--254767 Score: 197
Period size: 81 Copynumber: 2.3 Consensus size: 78
254578 ATCGCCATAT
* *
254588 TGGCATCAATATTATCAGTGACGCTGAGTCACTCTGATCCTACTCGCCACCATAGCTTCAC-CAT
1 TGGCACCAATATTATCAGTGACGCTGAGTCACTCCGATCCTACTCGCCACCA-A--TTCACTC-T
254652 GATCCTGATCGCCACCG
62 GATCCTGATCGCCACCG
* * * *
254669 TGGCACTAATATTATCAGTGATGTTGAGTC-TTCGCGATCCTGA-TCGCCACCAATTCACTCTGA
1 TGGCACCAATATTATCAGTGACGCTGAGTCACTC-CGATCCT-ACTCGCCACCAATTCACTCTGA
* *
254732 TCTTGATCGCCACCT
64 TCCTGATCGCCACCG
*
254747 TGGCACCAATATTGT-AGTGAC
1 TGGCACCAATATTATCAGTGAC
254768 ACCAAGTCGT
Statistics
Matches: 85, Mismatches: 11, Indels: 10
0.80 0.10 0.09
Matches are distributed among these distances:
77 5 0.06
78 34 0.40
79 1 0.01
80 3 0.04
81 41 0.48
82 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.18, T:0.29
Consensus pattern (78 bp):
TGGCACCAATATTATCAGTGACGCTGAGTCACTCCGATCCTACTCGCCACCAATTCACTCTGATC
CTGATCGCCACCG
Found at i:259392 original size:17 final size:19
Alignment explanation
Indices: 259370--259412 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 19
259360 TCAATTCAGT
259370 TTAAAATAATAT-T-TTTA
1 TTAAAATAATATATCTTTA
259387 TTAAAATAATATATCTTTA
1 TTAAAATAATATATCTTTA
*
259406 TTTAAAT
1 TTAAAAT
259413 CTAATTATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 12 0.52
18 1 0.04
19 10 0.43
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
TTAAAATAATATATCTTTA
Found at i:260554 original size:2 final size:2
Alignment explanation
Indices: 260547--260582 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
260537 ACAAAATAAT
*
260547 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
260583 CCAACTTCGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:266836 original size:20 final size:21
Alignment explanation
Indices: 266797--266836 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
266787 TTATTTGTTA
*
266797 TGTTTAATTTTTTTTAATGAT
1 TGTTTAATTTTTCTTAATGAT
*
266818 TGTTTAA-TTTTCTTCATGA
1 TGTTTAATTTTTCTTAATGA
266837 AAGATTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.23, C:0.05, G:0.10, T:0.62
Consensus pattern (21 bp):
TGTTTAATTTTTCTTAATGAT
Found at i:267387 original size:9 final size:9
Alignment explanation
Indices: 267373--267398 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
267363 GTGATTTTTG
267373 TAATTATTT
1 TAATTATTT
267382 TAATTATTT
1 TAATTATTT
267391 TAATTATT
1 TAATTATT
267399 AGTATTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
TAATTATTT
Found at i:267421 original size:13 final size:15
Alignment explanation
Indices: 267386--267424 Score: 57
Period size: 13 Copynumber: 2.8 Consensus size: 15
267376 TTATTTTAAT
267386 TATTTTAATTATTAG
1 TATTTTAATTATTAG
267401 TA-TTTAATT-TT-G
1 TATTTTAATTATTAG
267413 TATTTTAATTAT
1 TATTTTAATTAT
267425 ATAAGAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 3 0.14
13 9 0.41
14 8 0.36
15 2 0.09
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (15 bp):
TATTTTAATTATTAG
Found at i:267736 original size:9 final size:8
Alignment explanation
Indices: 267680--267735 Score: 55
Period size: 9 Copynumber: 6.9 Consensus size: 8
267670 ATATAAACTA
267680 TAAA-TAT
1 TAAATTAT
267687 TAAATT-T
1 TAAATTAT
267694 TAAATT-T
1 TAAATTAT
267701 TAAATTTAT
1 TAAA-TTAT
267710 TATAATTAT
1 TA-AATTAT
267719 ATAAATTAAT
1 -TAAATT-AT
267729 TAAATTA
1 TAAATTA
267736 AATAGGAGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
7 16 0.37
8 4 0.09
9 17 0.40
10 6 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
TAAATTAT
Found at i:268840 original size:17 final size:16
Alignment explanation
Indices: 268818--268863 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
268808 AAAAATATAT
268818 TATAATTTATTTATAAA
1 TATAATTT-TTTATAAA
* *
268835 TATAA-TTTTAATATA
1 TATAATTTTTTATAAA
268850 TATAATTTTTTATA
1 TATAATTTTTTATA
268864 TAAATTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
15 11 0.44
16 9 0.36
17 5 0.20
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATAATTTTTTATAAA
Done.