Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold356
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: 432500
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 2 of 4
Found at i:145540 original size:28 final size:29
Alignment explanation
Indices: 145487--145545 Score: 68
Period size: 31 Copynumber: 2.0 Consensus size: 29
145477 TACGTATGAA
*
145487 TTAAATAAAAATATTATTATCTATAATAATT
1 TTAAATAAAAATATTATTA--TATAAAAATT
145518 TTAAA-AAAAATACTTATTA-ATAAAAATT
1 TTAAATAAAAATA-TTATTATATAAAAATT
145546 ATTTTATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
28 8 0.31
30 7 0.27
31 11 0.42
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (29 bp):
TTAAATAAAAATATTATTATATAAAAATT
Found at i:145732 original size:16 final size:16
Alignment explanation
Indices: 145711--145762 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
145701 TGATGATATC
145711 TTATATAAATTAATTT
1 TTATATAAATTAATTT
*
145727 TTATATAAA--AA-AT
1 TTATATAAATTAATTT
145740 TTA-AGTAAATTAATTT
1 TTATA-TAAATTAATTT
145756 TTATATA
1 TTATATA
145763 TTTAAAAGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
12 1 0.03
13 8 0.28
14 2 0.07
15 2 0.07
16 15 0.52
17 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (16 bp):
TTATATAAATTAATTT
Found at i:145777 original size:31 final size:29
Alignment explanation
Indices: 145716--145779 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 29
145706 ATATCTTATA
* *
145716 TAAATTAATTTTTATATAAAAAATTTAAG
1 TAAATTAATTTTTATATAAAAAAGTAAAG
*
145745 TAAATTAATTTTTATATATTTAAAAGTAAAG
1 TAAATTAATTTTTATATA--AAAAAGTAAAG
145776 TAAA
1 TAAA
145780 AAGGTAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 18 0.60
31 12 0.40
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.44
Consensus pattern (29 bp):
TAAATTAATTTTTATATAAAAAAGTAAAG
Found at i:145937 original size:32 final size:31
Alignment explanation
Indices: 145871--145938 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
145861 ATTAATAACT
* *
145871 TTAAAAAATTTTTAAATATAAACTTTTATTA
1 TTAAAAAATTTTTAAAGATAAACTTTTATCA
* * *
145902 TTAAGAAATTTTTAAAGGTAAATTTTTTATCA
1 TTAAAAAATTTTTAAAGATAAA-CTTTTATCA
145934 TTAAA
1 TTAAA
145939 TATATTATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
31 19 0.63
32 11 0.37
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (31 bp):
TTAAAAAATTTTTAAAGATAAACTTTTATCA
Found at i:146360 original size:12 final size:11
Alignment explanation
Indices: 146339--146380 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
146329 AATTAAAAAA
146339 TAATTTTATAT
1 TAATTTTATAT
146350 TAATATTTATA-
1 TAAT-TTTATAT
*
146361 TATTTTTATAAT
1 TAATTTTAT-AT
146373 TAATTTTA
1 TAATTTTA
146381 AATAAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 5 0.19
11 8 0.31
12 13 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TAATTTTATAT
Found at i:146677 original size:36 final size:32
Alignment explanation
Indices: 146592--146677 Score: 75
Period size: 35 Copynumber: 2.5 Consensus size: 32
146582 GATCGATTTA
*
146592 AAAATTTATTTTATTATTTAAAATAAAAATAT
1 AAAATTTATTTTAATATTTAAAATAAAAATAT
*
146624 AAATGATTTTATATTAATATTTATAAATAAATTTAA-AT
1 AAA--A-TTTATTTTAATATTTA-AAATAAA---AATAT
146662 AAAATTATATTTTAAT
1 AAAATT-TATTTTAAT
146678 TATGTGATAG
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
32 3 0.07
34 1 0.02
35 16 0.37
36 16 0.37
38 5 0.12
39 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (32 bp):
AAAATTTATTTTAATATTTAAAATAAAAATAT
Found at i:148847 original size:22 final size:22
Alignment explanation
Indices: 148795--148847 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
148785 GTAATAATTT
*
148795 TATTTAAAT-TTATTATAAAAA
1 TATTTAAATATTAATATAAAAA
*
148816 TATATAAATATTAATATAAAAA
1 TATTTAAATATTAATATAAAAA
*
148838 TATTTTAATA
1 TATTTAAATA
148848 ATTTTGTGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 8 0.30
22 19 0.70
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TATTTAAATATTAATATAAAAA
Found at i:151525 original size:2 final size:2
Alignment explanation
Indices: 151512--151543 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
151502 GTTAAACCGA
*
151512 AT AT AA 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
151544 TTGCAAATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:156057 original size:27 final size:26
Alignment explanation
Indices: 156008--156097 Score: 94
Period size: 25 Copynumber: 3.3 Consensus size: 26
155998 TTTTACTGCC
156008 ATTAATTTTGATTTGAATATAAAAATTTA
1 ATTAA-TTT-ATTT-AATATAAAAATTTA
**
156037 ATTAATTTATTTAA-ATTTAAATTTA
1 ATTAATTTATTTAATATAAAAATTTA
*
156062 ATTAAATCTTATTTAATATAAAAAATTA
1 ATT-AAT-TTATTTAATATAAAAATTTA
156090 A-TAATTTA
1 ATTAATTTA
156098 AAATCAATTA
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
25 15 0.28
26 8 0.15
27 13 0.25
28 12 0.23
29 5 0.09
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (26 bp):
ATTAATTTATTTAATATAAAAATTTA
Found at i:156115 original size:21 final size:20
Alignment explanation
Indices: 156091--156152 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 20
156081 AAAAAATTAA
156091 TAATTTAAAATCAATTAATTT
1 TAATTTAAAAT-AATTAATTT
*
156112 TAATTT-TAA-AA-TAATTT
1 TAATTTAAAATAATTAATTT
* *
156129 AAATTTAAAATAATTAAATT
1 TAATTTAAAATAATTAATTT
156149 TAAT
1 TAAT
156153 AAATTTAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
17 11 0.33
18 4 0.12
19 2 0.06
20 10 0.30
21 6 0.18
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
TAATTTAAAATAATTAATTT
Found at i:156119 original size:22 final size:22
Alignment explanation
Indices: 156094--156136 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
156084 AAATTAATAA
*
156094 TTTAAAATCAA-TTAATTTTAAT
1 TTTAAAAT-AATTTAAATTTAAT
156116 TTTAAAATAATTTAAATTTAA
1 TTTAAAATAATTTAAATTTAA
156137 AATAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTAAAATAATTTAAATTTAAT
Found at i:156128 original size:17 final size:17
Alignment explanation
Indices: 156106--156151 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 17
156096 TAAAATCAAT
*
156106 TAATTTTAATTTTAAAA
1 TAATTTTAAATTTAAAA
156123 TAA-TTTAAATTTAAAA
1 TAATTTTAAATTTAAAA
156139 TAA--TTAAATTTAA
1 TAATTTTAAATTTAA
156152 TAAATTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 10 0.36
16 15 0.54
17 3 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TAATTTTAAATTTAAAA
Found at i:156147 original size:15 final size:16
Alignment explanation
Indices: 156110--156162 Score: 74
Period size: 15 Copynumber: 3.4 Consensus size: 16
156100 ATCAATTAAT
*
156110 TTTAATTTTAAAATAA
1 TTTAAATTTAAAATAA
156126 TTTAAATTTAAAATAA
1 TTTAAATTTAAAATAA
*
156142 -TTAAATTTAATA-AA
1 TTTAAATTTAAAATAA
156156 TTTAAAT
1 TTTAAAT
156163 ATTTAATCTA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
14 2 0.06
15 17 0.50
16 15 0.44
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTAAATTTAAAATAA
Found at i:156278 original size:16 final size:16
Alignment explanation
Indices: 156236--156282 Score: 53
Period size: 17 Copynumber: 3.0 Consensus size: 16
156226 ATTATTCAAA
156236 TTAAAATT--AATAAT
1 TTAAAATTAAAATAAT
* *
156250 TTTAAATACAAAATAAT
1 TTAAAAT-TAAAATAAT
156267 TTAAAATTAAAATAAT
1 TTAAAATTAAAATAAT
156283 CTGAACTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 6 0.23
16 8 0.31
17 12 0.46
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (16 bp):
TTAAAATTAAAATAAT
Found at i:156751 original size:16 final size:16
Alignment explanation
Indices: 156732--156773 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
156722 ATATTAAATC
*
156732 AATTTTAATTATTTTA
1 AATTTAAATTATTTTA
*
156748 AATTTGAATTATTTTA
1 AATTTAAATTATTTTA
156764 AATTTAAATT
1 AATTTAAATT
156774 TTTAATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (16 bp):
AATTTAAATTATTTTA
Found at i:158087 original size:20 final size:20
Alignment explanation
Indices: 158064--158102 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
158054 CAAAACTCTT
158064 TTTTAATATTTAAA-AAATAG
1 TTTTAATA-TTAAATAAATAG
158084 TTTTAATATTAAATAAATA
1 TTTTAATATTAAATAAATA
158103 TTAACTATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (20 bp):
TTTTAATATTAAATAAATAG
Found at i:160798 original size:31 final size:31
Alignment explanation
Indices: 160760--160822 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
160750 AGACTTTTTT
160760 AGTGGATGTAATAATCTTGAATACGATTTGA
1 AGTGGATGTAATAATCTTGAATACGATTTGA
160791 AGTGGATGTAATAATCTTGAATACGATTTGA
1 AGTGGATGTAATAATCTTGAATACGATTTGA
160822 A
1 A
160823 TATGATATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.37, C:0.06, G:0.22, T:0.35
Consensus pattern (31 bp):
AGTGGATGTAATAATCTTGAATACGATTTGA
Found at i:163188 original size:7 final size:7
Alignment explanation
Indices: 163178--163217 Score: 66
Period size: 7 Copynumber: 6.0 Consensus size: 7
163168 TAAATAATAA
163178 AAAATTT
1 AAAATTT
163185 AAAATTT
1 AAAATTT
163192 --AATTT
1 AAAATTT
163197 AAAATTT
1 AAAATTT
163204 AAAATTT
1 AAAATTT
163211 AAAATTT
1 AAAATTT
163218 GATTTTAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 5 0.16
7 26 0.84
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (7 bp):
AAAATTT
Found at i:163194 original size:19 final size:19
Alignment explanation
Indices: 163172--163212 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
163162 TGAGTTTAAA
163172 TAATAAAAAATTTAAAATT
1 TAATAAAAAATTTAAAATT
**
163191 TAATTTAAAATTTAAAATT
1 TAATAAAAAATTTAAAATT
163210 TAA
1 TAA
163213 AATTTGATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TAATAAAAAATTTAAAATT
Found at i:163318 original size:25 final size:26
Alignment explanation
Indices: 163290--163342 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 26
163280 ATTAAATTTA
*
163290 TTTATAAAAAATTTTATT-TTTATAT
1 TTTATAAAAAATTTAATTATTTATAT
***
163315 TTTATTTTAAATTTAATTATTTATAT
1 TTTATAAAAAATTTAATTATTTATAT
163341 TT
1 TT
163343 AAATTTGAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (26 bp):
TTTATAAAAAATTTAATTATTTATAT
Found at i:163335 original size:20 final size:21
Alignment explanation
Indices: 163315--163353 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
163305 ATTTTTATAT
163315 TTTAT-TTTAAATTT-AATTA
1 TTTATATTTAAATTTGAATTA
163334 TTTATATTTAAATTTGAATT
1 TTTATATTTAAATTTGAATT
163354 TGATTTTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 9 0.50
21 4 0.22
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (21 bp):
TTTATATTTAAATTTGAATTA
Found at i:163353 original size:26 final size:25
Alignment explanation
Indices: 163298--163360 Score: 72
Period size: 26 Copynumber: 2.5 Consensus size: 25
163288 TATTTATAAA
* * *
163298 AAATTTTATTTTTATATTTTATTTT
1 AAATTTAATTTTTATATTTAAATTT
163323 AAATTTAATTATTTATATTTAAATTT
1 AAATTTAATT-TTTATATTTAAATTT
* *
163349 GAATTTGATTTT
1 AAATTTAATTTT
163361 GAATTGAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
25 11 0.34
26 21 0.66
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (25 bp):
AAATTTAATTTTTATATTTAAATTT
Found at i:167899 original size:35 final size:33
Alignment explanation
Indices: 167832--167899 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
167822 TTTAAAATAT
* *
167832 TATATATTTTAAATATTAATAATTTATGTTATA
1 TATAAATTTTAAATATTAATAATTTATATTATA
*
167865 TATAAATTTTAATATATTTATATATTTATATTATA
1 TATAAATTTTAA-ATATTAATA-ATTTATATTATA
167900 ATTTTATTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 11 0.37
34 8 0.27
35 11 0.37
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (33 bp):
TATAAATTTTAAATATTAATAATTTATATTATA
Found at i:167903 original size:30 final size:31
Alignment explanation
Indices: 167828--167929 Score: 86
Period size: 31 Copynumber: 3.2 Consensus size: 31
167818 TGAATTTAAA
* *
167828 ATATTATATATTTTAA-ATATTAATAATTTATGT
1 ATATTATAAATTTTAATATATT--TAATATAT-T
167861 -TATATATAAATTTTAATATATTT-ATATATTT
1 ATAT-TATAAATTTTAATATATTTAATATA-TT
* *
167892 ATATTAT-AATTTTATTATTTTTAATATATT
1 ATATTATAAATTTTAATATATTTAATATATT
167922 ATAATTAT
1 AT-ATTAT
167930 TTTAATTTGC
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
30 17 0.29
31 18 0.31
32 8 0.14
33 11 0.19
34 5 0.08
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (31 bp):
ATATTATAAATTTTAATATATTTAATATATT
Found at i:167919 original size:20 final size:19
Alignment explanation
Indices: 167871--167932 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
167861 TATATATAAA
167871 TTTTAATATA-TTTATATAT
1 TTTTAATATATTTTAT-TAT
* *
167890 TTATATTATAATTTTATTAT
1 TTTTAATAT-ATTTTATTAT
*
167910 TTTTAATATATTATAATTAT
1 TTTTAATATATT-TTATTAT
167930 TTT
1 TTT
167933 AATTTGCTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
19 10 0.29
20 20 0.57
21 5 0.14
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTAATATATTTTATTAT
Found at i:170799 original size:25 final size:27
Alignment explanation
Indices: 170756--170824 Score: 67
Period size: 25 Copynumber: 2.7 Consensus size: 27
170746 TATAAAAAAT
*
170756 ATATAAATATTTTAA-AATT-T-ATATA
1 ATATAAATA-ATTAATAATTATAATATA
170781 ATATAAATAATTAATAATTATAATATA
1 ATATAAATAATTAATAATTATAATATA
*
170808 A-A-AAATAAAATAATAAT
1 ATATAAAT-AATTAATAAT
170825 AAAAATACAC
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
24 4 0.11
25 17 0.45
26 11 0.29
27 6 0.16
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (27 bp):
ATATAAATAATTAATAATTATAATATA
Found at i:171351 original size:21 final size:21
Alignment explanation
Indices: 171327--171374 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
171317 TCTTTATAAA
171327 TTAAATTATAA-TTAATTTAAT
1 TTAAATTA-AATTTAATTTAAT
* *
171348 TTAAATTAAATTTTATTTATT
1 TTAAATTAAATTTAATTTAAT
171369 TTAAAT
1 TTAAAT
171375 AAAAATTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTAAATTAAATTTAATTTAAT
Found at i:171453 original size:41 final size:40
Alignment explanation
Indices: 171408--171497 Score: 94
Period size: 41 Copynumber: 2.2 Consensus size: 40
171398 TTTTATTAAT
*
171408 TTAAAAATAAAT-ATT-TATTTATATATTATAAAAATTATAAA
1 TTAAAAATAAATAATTAAATTTA-AT-TTA-AAAAATTATAAA
* *
171449 TTAAATAAAAAATAATTAAATTTAATTTAAATAATTATAAA
1 TTAAA-AATAAATAATTAAATTTAATTTAAAAAATTATAAA
*
171490 TAAAAAAT
1 TTAAAAAT
171498 CAAACGGAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
40 2 0.05
41 20 0.49
42 9 0.22
43 5 0.12
44 5 0.12
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (40 bp):
TTAAAAATAAATAATTAAATTTAATTTAAAAAATTATAAA
Found at i:171461 original size:19 final size:20
Alignment explanation
Indices: 171437--171490 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
171427 TATATATTAT
171437 AAAAATTATAAATTAA-ATA
1 AAAAATTATAAATTAATATA
* *
171456 AAAAATAATTAAATTTAATTTA
1 AAAAATTA-TAAA-TTAATATA
*
171478 AATAATTATAAAT
1 AAAAATTATAAAT
171491 AAAAAATCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
19 7 0.25
20 5 0.18
21 8 0.29
22 8 0.29
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAAATTATAAATTAATATA
Found at i:172914 original size:20 final size:20
Alignment explanation
Indices: 172868--172942 Score: 69
Period size: 20 Copynumber: 3.5 Consensus size: 20
172858 TTTTTAACTT
*
172868 TTTATATAAATATTATATTTAAA
1 TTTAAATAAATA--ATATTT-AA
172891 TTTAAATAAATAATATTTAA
1 TTTAAATAAATAATATTTAA
* * * *
172911 TTTAAATTATTAAAATTAAA
1 TTTAAATAAATAATATTTAA
172931 TTTAATATAAAT
1 TTTAA-ATAAAT
172943 TAAATTTGTC
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 23 0.52
21 10 0.23
23 11 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TTTAAATAAATAATATTTAA
Found at i:172933 original size:25 final size:26
Alignment explanation
Indices: 172873--172944 Score: 76
Period size: 25 Copynumber: 2.7 Consensus size: 26
172863 AACTTTTTAT
172873 ATAAATATTATATTTAAATT-TAAATAA
1 ATAAAT-TTA-ATTTAAATTATAAATAA
*
172900 ATAATATTTAATTTAAATTATTAA-AA
1 ATAA-ATTTAATTTAAATTATAAATAA
* *
172926 TTAAATTTAATATAAATTA
1 ATAAATTTAATTTAAATTA
172945 AATTTGTCAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
25 14 0.35
26 14 0.35
27 10 0.25
28 2 0.05
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
ATAAATTTAATTTAAATTATAAATAA
Found at i:173647 original size:21 final size:19
Alignment explanation
Indices: 173627--173687 Score: 51
Period size: 21 Copynumber: 3.3 Consensus size: 19
173617 TATAAAAAAT
173627 TATTATAAATATGATATAAA
1 TATTAT-AATATGATATAAA
173647 TATATATTAATAT-AT-TAAA
1 TAT-TA-TAATATGATATAAA
173666 -ATT-T-ATATGATATAAA
1 TATTATAATATGATATAAA
173682 TTATTA
1 -TATTA
173688 AATTATTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 15
0.69 0.00 0.31
Matches are distributed among these distances:
14 4 0.12
15 3 0.09
16 4 0.12
17 1 0.03
18 5 0.15
19 4 0.12
20 5 0.15
21 7 0.21
22 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
TATTATAATATGATATAAA
Found at i:173677 original size:35 final size:31
Alignment explanation
Indices: 173635--173701 Score: 89
Period size: 35 Copynumber: 2.0 Consensus size: 31
173625 ATTATTATAA
*
173635 ATATGATATAAATATATATTAATATATTAAAATTT
1 ATATGATATAAAT-TAT-TAAAT-TATT-AAATTT
173670 ATATGATATAAATTATTAAATTATTAAATTT
1 ATATGATATAAATTATTAAATTATTAAATTT
173701 A
1 A
173702 AAATTTATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 7 0.23
32 4 0.13
33 4 0.13
34 3 0.10
35 13 0.42
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (31 bp):
ATATGATATAAATTATTAAATTATTAAATTT
Found at i:174056 original size:2 final size:2
Alignment explanation
Indices: 174049--174082 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
174039 CAAATGCTTT
174049 TA 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 TA
174083 CTTGTAATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:174642 original size:29 final size:31
Alignment explanation
Indices: 174599--174658 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
174589 TTAATGGGTA
174599 TTTATGATTTTTAAAATGA-AAAAAATAATT
1 TTTATGATTTTTAAAATGATAAAAAATAATT
*
174629 TTTAT-ATTTTTAAAATTATAAAAAATAATT
1 TTTATGATTTTTAAAATGATAAAAAATAATT
174659 AATTTAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 12 0.43
30 16 0.57
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (31 bp):
TTTATGATTTTTAAAATGATAAAAAATAATT
Found at i:174714 original size:10 final size:10
Alignment explanation
Indices: 174666--174713 Score: 55
Period size: 9 Copynumber: 4.8 Consensus size: 10
174656 ATTAATTTAA
*
174666 TATAAAAAAT
1 TATAAATAAT
174676 TATAAA-AAT
1 TATAAATAAT
174685 TATAAATAAT
1 TATAAATAAT
174695 TA-AAATATATT
1 TATAAATA-A-T
174706 TATAAATA
1 TATAAATA
174714 TACGTTAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
9 14 0.41
10 12 0.35
11 3 0.09
12 5 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
TATAAATAAT
Found at i:174836 original size:40 final size:37
Alignment explanation
Indices: 174782--174857 Score: 116
Period size: 40 Copynumber: 2.0 Consensus size: 37
174772 ACATTTTAAA
174782 TAAAAAAATAATATTAAAAATAATATAAATATATTTTC
1 TAAAAAAATAATATTAAAAATAATATAAATA-ATTTTC
*
174820 TAAATAAAATATATATTAAAATTAATATAAATAATTTT
1 TAAA-AAAATA-ATATTAAAAATAATATAAATAATTTT
174858 TTATATTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
38 4 0.11
39 11 0.31
40 20 0.57
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (37 bp):
TAAAAAAATAATATTAAAAATAATATAAATAATTTTC
Found at i:174851 original size:22 final size:22
Alignment explanation
Indices: 174787--174852 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 22
174777 TTAAATAAAA
*
174787 AAATA-ATATTAAAAATAATAT
1 AAATATATATTAAAATTAATAT
** *
174808 AAATATAT-TT--TCTAAATA-
1 AAATATATATTAAAATTAATAT
174826 AAATATATATTAAAATTAATAT
1 AAATATATATTAAAATTAATAT
174848 AAATA
1 AAATA
174853 ATTTTTTATA
Statistics
Matches: 33, Mismatches: 7, Indels: 9
0.67 0.14 0.18
Matches are distributed among these distances:
18 8 0.24
19 6 0.18
21 12 0.36
22 7 0.21
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
AAATATATATTAAAATTAATAT
Found at i:174894 original size:19 final size:18
Alignment explanation
Indices: 174861--174908 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
174851 TAATTTTTTA
*
174861 TATTTATATTATATTAAT
1 TATTTATAATATATTAAT
174879 TATTTATTAATATATTAA-
1 TATTTA-TAATATATTAAT
*
174897 AATTTA-AATATA
1 TATTTATAATATA
174909 ATACTATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 6 0.22
18 11 0.41
19 10 0.37
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TATTTATAATATATTAAT
Found at i:177052 original size:34 final size:34
Alignment explanation
Indices: 176979--177045 Score: 93
Period size: 32 Copynumber: 2.0 Consensus size: 34
176969 TATTATAATT
* * *
176979 ATATTTAAAATATTTTTTGTTTATATTAATTTTA
1 ATATTTAAAATAATTTTTGATTATATAAATTTTA
177013 ATATTT-AAATAATTTTT-ATTATATAAATTTTA
1 ATATTTAAAATAATTTTTGATTATATAAATTTTA
177045 A
1 A
177046 AATATTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 14 0.47
33 10 0.33
34 6 0.20
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (34 bp):
ATATTTAAAATAATTTTTGATTATATAAATTTTA
Found at i:177086 original size:28 final size:29
Alignment explanation
Indices: 176958--177097 Score: 96
Period size: 27 Copynumber: 4.8 Consensus size: 29
176948 TTTTATTTAT
176958 ATATTTTATTATATTATAATTATA-TTTAAA
1 ATATTTTA-TATATTAT-ATTATATTTTAAA
* *
176988 ATATTTTTTGT-TTATATTA-ATTTT--A
1 ATATTTTATATATTATATTATATTTTAAA
* * *
177013 ATATTTAAATAATTTTTATTATATAAATTTTAAA
1 ATATTT-TAT-A-TATTA-TAT-TATATTTTAAA
* *
177047 ATATTTTTTATATTATATTATATTTT-TA
1 ATATTTTATATATTATATTATATTTTAAA
*
177075 ATATTTTATATA-TAAATTATATT
1 ATATTTTATATATTATATTATATT
177098 CATATGACCG
Statistics
Matches: 88, Mismatches: 12, Indels: 23
0.72 0.10 0.19
Matches are distributed among these distances:
25 7 0.08
26 2 0.02
27 17 0.19
28 17 0.19
29 12 0.14
30 13 0.15
31 6 0.07
32 6 0.07
33 1 0.01
34 7 0.08
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (29 bp):
ATATTTTATATATTATATTATATTTTAAA
Found at i:177094 original size:60 final size:59
Alignment explanation
Indices: 176982--177096 Score: 144
Period size: 60 Copynumber: 1.9 Consensus size: 59
176972 TATAATTATA
* * **
176982 TTTAAAATATTTTTTGTTTATATTAATTTTAATATTTAAATAATTTTTATTATATAAAT
1 TTTAAAATATTTTTTATTTATATTAATTTTAATATTTAAATAATATAAATTATATAAAT
*
177041 TTTAAAATATTTTTTATATTATATTATATTTTTAATATTT-TAT-ATATAAATTATAT
1 TTTAAAATATTTTTTAT-TTATATTA-A-TTTTAATATTTAAATAATATAAATTATAT
177097 TCATATGACC
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
59 16 0.33
60 18 0.38
61 3 0.06
62 11 0.23
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (59 bp):
TTTAAAATATTTTTTATTTATATTAATTTTAATATTTAAATAATATAAATTATATAAAT
Found at i:177630 original size:18 final size:17
Alignment explanation
Indices: 177603--177641 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
177593 AAAACATCTT
177603 ATTAAATTAATTTAAACA
1 ATTAAATTAATTTAAA-A
*
177621 ATTAAGTTAATTTAAAA
1 ATTAAATTAATTTAAAA
177638 ATTA
1 ATTA
177642 TCATTCACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (17 bp):
ATTAAATTAATTTAAAA
Found at i:181629 original size:51 final size:51
Alignment explanation
Indices: 181569--181670 Score: 186
Period size: 51 Copynumber: 2.0 Consensus size: 51
181559 AGGCAACTTA
* *
181569 AAAGATGGTTACGTTGTCACTGTACGATTGCATGCGGCACACTTGGCAGAT
1 AAAGATGGTTACGTTGTCACTGTACGATGGCATGCGGCAAACTTGGCAGAT
181620 AAAGATGGTTACGTTGTCACTGTACGATGGCATGCGGCAAACTTGGCAGAT
1 AAAGATGGTTACGTTGTCACTGTACGATGGCATGCGGCAAACTTGGCAGAT
181671 CGCAGTTGCT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.26
Consensus pattern (51 bp):
AAAGATGGTTACGTTGTCACTGTACGATGGCATGCGGCAAACTTGGCAGAT
Found at i:184984 original size:39 final size:39
Alignment explanation
Indices: 184909--184986 Score: 93
Period size: 39 Copynumber: 2.0 Consensus size: 39
184899 TAATTTTTTT
* *
184909 TATAAAAATATATATGTCTAATATATATTTAAATATAAA
1 TATAAAAATATAAATGTCTAAAATATATTTAAATATAAA
* * * * *
184948 TATAAAAATATAAATTTTTAAAATTTTTTTATATATAAA
1 TATAAAAATATAAATGTCTAAAATATATTTAAATATAAA
184987 AATATTTTAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (39 bp):
TATAAAAATATAAATGTCTAAAATATATTTAAATATAAA
Found at i:188197 original size:6 final size:6
Alignment explanation
Indices: 188186--188238 Score: 61
Period size: 6 Copynumber: 8.8 Consensus size: 6
188176 TCTACTGTTT
* * * * *
188186 AGAGAG AGAGAG AAAGAG AGAGAG AGCGAG ACAGAG AGACAG AGAGAC
1 AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG
188234 AGAGA
1 AGAGA
188239 ATGGTTTTAA
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.51, C:0.08, G:0.42, T:0.00
Consensus pattern (6 bp):
AGAGAG
Found at i:188203 original size:8 final size:8
Alignment explanation
Indices: 188186--188238 Score: 61
Period size: 8 Copynumber: 6.6 Consensus size: 8
188176 TCTACTGTTT
*
188186 AGAGAGAG
1 AGAGAGAC
* *
188194 AGAGAAAG
1 AGAGAGAC
*
188202 AGAGAGAG
1 AGAGAGAC
*
188210 AGCGAGAC
1 AGAGAGAC
188218 AGAGAGAC
1 AGAGAGAC
188226 AGAGAGAC
1 AGAGAGAC
188234 AGAGA
1 AGAGA
188239 ATGGTTTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 40 1.00
ACGTcount: A:0.51, C:0.08, G:0.42, T:0.00
Consensus pattern (8 bp):
AGAGAGAC
Found at i:188207 original size:16 final size:16
Alignment explanation
Indices: 188186--188238 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
188176 TCTACTGTTT
* *
188186 AGAGAGAGAGAGAAAG
1 AGAGAGAGAGAGAGAC
*
188202 AGAGAGAGAGCGAGAC
1 AGAGAGAGAGAGAGAC
*
188218 AGAGAGACAGAGAGAC
1 AGAGAGAGAGAGAGAC
188234 AGAGA
1 AGAGA
188239 ATGGTTTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.51, C:0.08, G:0.42, T:0.00
Consensus pattern (16 bp):
AGAGAGAGAGAGAGAC
Found at i:188496 original size:20 final size:21
Alignment explanation
Indices: 188473--188524 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
188463 TTAATTTTTA
188473 TATTTAATTTTAAATTT-AAT
1 TATTTAATTTTAAATTTAAAT
*
188493 TATTT-TTATTTAAATTTAAAT
1 TATTTAAT-TTTAAATTTAAAT
188514 TAATTTAATTT
1 T-ATTTAATTT
188525 GAGTTTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
19 1 0.04
20 14 0.54
21 4 0.15
22 6 0.23
23 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTTAATTTTAAATTTAAAT
Found at i:188510 original size:26 final size:25
Alignment explanation
Indices: 188432--188519 Score: 88
Period size: 26 Copynumber: 3.4 Consensus size: 25
188422 TACATTAATT
* * *
188432 AATTAAATTTATTTATTTAAGGTTTA
1 AATTTAATTTTTTTATTTAA-ATTTA
* *
188458 TAAGTTTAATTTTTATATTTAATTTTA
1 -AA-TTTAATTTTTTTATTTAAATTTA
188485 AATTTAATTATTTTTATTTAAATTTA
1 AATTTAATT-TTTTTATTTAAATTTA
188511 AA-TTAATTT
1 AATTTAATTT
188520 AATTTGAGTT
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
24 1 0.02
25 13 0.25
26 18 0.34
27 6 0.11
28 15 0.28
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (25 bp):
AATTTAATTTTTTTATTTAAATTTA
Found at i:188655 original size:24 final size:24
Alignment explanation
Indices: 188627--188686 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
188617 ATAATTTTTG
188627 GATAAAAATAAGCTATTCTATATC
1 GATAAAAATAAGCTATTCTATATC
188651 GATAAAAATAAGCTATTCTATATC
1 GATAAAAATAAGCTATTCTATATC
*
188675 AATGAAAAATAA
1 GAT-AAAAATAA
188687 TATTTTTATG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 26 0.76
25 8 0.24
ACGTcount: A:0.52, C:0.10, G:0.08, T:0.30
Consensus pattern (24 bp):
GATAAAAATAAGCTATTCTATATC
Found at i:188770 original size:16 final size:15
Alignment explanation
Indices: 188751--188802 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 15
188741 TGTAATATCT
188751 ATATAAATAAAATATA
1 ATATAAAT-AAATATA
*
188767 ATAT-AATTAATA-A
1 ATATAAATAAATATA
188780 AT-TAAATAAATATAA
1 ATATAAATAAATAT-A
188795 ATATAAAT
1 ATATAAAT
188803 CACATAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
12 1 0.03
13 10 0.33
14 4 0.13
15 6 0.20
16 9 0.30
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
ATATAAATAAATATA
Found at i:188829 original size:16 final size:15
Alignment explanation
Indices: 188753--188834 Score: 67
Period size: 16 Copynumber: 5.1 Consensus size: 15
188743 TAATATCTAT
188753 ATAAATA-AAATATAA
1 ATAAATATAAAT-TAA
*
188768 TATAATTAATAAATTAA
1 -ATAAAT-ATAAATTAA
188785 ATAAATATAAATATAA
1 ATAAATATAAAT-TAA
* *
188801 ATCACATAAAAATTAA
1 AT-AAATATAAATTAA
*
188817 AAAATATATAAATTAA
1 ATAA-ATATAAATTAA
188833 AT
1 AT
188835 TAATTTTATA
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
15 7 0.13
16 30 0.57
17 12 0.23
18 4 0.08
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (15 bp):
ATAAATATAAATTAA
Found at i:189179 original size:18 final size:19
Alignment explanation
Indices: 189147--189187 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
189137 TTTTAATATT
*
189147 ATTTTAAATTGTAATATAA
1 ATTTTAAAATGTAATATAA
*
189166 ATTTTAAAAT-TAATTTAA
1 ATTTTAAAATGTAATATAA
189184 ATTT
1 ATTT
189188 GAATAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
ATTTTAAAATGTAATATAA
Found at i:189389 original size:24 final size:23
Alignment explanation
Indices: 189362--189414 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 23
189352 TATGATCGAT
189362 ATATATTTAAATATAAATAT-AAAA
1 ATATATTTAAA-A-AAATATAAAAA
*
189386 ATATTTTTTAAAAAAATATAAAAA
1 ATA-TATTTAAAAAAATATAAAAA
189410 ATATA
1 ATATA
189415 AAAAATTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 11 0.44
25 7 0.28
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
ATATATTTAAAAAAATATAAAAA
Found at i:189410 original size:9 final size:9
Alignment explanation
Indices: 189396--189424 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
189386 ATATTTTTTA
189396 AAAAAATAT
1 AAAAAATAT
189405 AAAAAATAT
1 AAAAAATAT
189414 AAAAAAT-T
1 AAAAAATAT
189422 AAA
1 AAA
189425 TATATTGGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.20
9 16 0.80
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AAAAAATAT
Found at i:189866 original size:6 final size:6
Alignment explanation
Indices: 189857--189883 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
189847 CTAAAAATAA
189857 ATATTT ATATTT ATATTT ATATTT ATA
1 ATATTT ATATTT ATATTT ATATTT ATA
189884 ATTAATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (6 bp):
ATATTT
Found at i:196834 original size:2 final size:2
Alignment explanation
Indices: 196822--196861 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
196812 TTACATATGC
*
196822 AT AT AT GT AT AT AT AT AT AT AT AT AT AT -T AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
196862 TTGAATTTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:197257 original size:13 final size:15
Alignment explanation
Indices: 197229--197260 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
197219 CATAGACATG
197229 AATTATATGTATTTT
1 AATTATATGTATTTT
197244 AATTAT-TG-ATTTT
1 AATTATATGTATTTT
197257 AATT
1 AATT
197261 TTTATTGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
14 2 0.12
15 6 0.35
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.59
Consensus pattern (15 bp):
AATTATATGTATTTT
Found at i:197267 original size:16 final size:17
Alignment explanation
Indices: 197246--197279 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
197236 TGTATTTTAA
197246 TTATTGAT-TTTAATTT
1 TTATTGATATTTAATTT
197262 TTATTGATATTTAATTT
1 TTATTGATATTTAATTT
197279 T
1 T
197280 ATTATAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (17 bp):
TTATTGATATTTAATTT
Found at i:206506 original size:2 final size:2
Alignment explanation
Indices: 206494--206535 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
206484 TTACATATGC
*
206494 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
206534 AT
1 AT
206536 TTGAATTTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:206930 original size:13 final size:15
Alignment explanation
Indices: 206902--206933 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
206892 CATAGACATG
206902 AATTATATGTATTTT
1 AATTATATGTATTTT
206917 AATTAT-TG-ATTTT
1 AATTATATGTATTTT
206930 AATT
1 AATT
206934 TTTATTGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
14 2 0.12
15 6 0.35
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.59
Consensus pattern (15 bp):
AATTATATGTATTTT
Found at i:206940 original size:16 final size:17
Alignment explanation
Indices: 206919--206952 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
206909 TGTATTTTAA
206919 TTATTGAT-TTTAATTT
1 TTATTGATATTTAATTT
206935 TTATTGATATTTAATTT
1 TTATTGATATTTAATTT
206952 T
1 T
206953 ATTATAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (17 bp):
TTATTGATATTTAATTT
Found at i:207268 original size:19 final size:21
Alignment explanation
Indices: 207244--207296 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
207234 TATTTAAAAA
207244 ATATTAAAATTT-TAT-TTTT
1 ATATTAAAATTTATATATTTT
*
207263 ATATTAATATTTATATATTTT
1 ATATTAAAATTTATATATTTT
207284 ATAATT-AAATTTA
1 AT-ATTAAAATTTA
207297 AATAAAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 11 0.38
20 3 0.10
21 12 0.41
22 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
ATATTAAAATTTATATATTTT
Found at i:207323 original size:20 final size:20
Alignment explanation
Indices: 207300--207341 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
207290 AAATTTAAAT
207300 AAAATATATTATTTT-AATTA
1 AAAAT-TATTATTTTAAATTA
207320 AAAATTATTATTTTAAATTA
1 AAAATTATTATTTTAAATTA
207340 AA
1 AA
207342 CTAATATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AAAATTATTATTTTAAATTA
Found at i:207649 original size:27 final size:27
Alignment explanation
Indices: 207595--207650 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
207585 TTTATATTAT
* * *
207595 TTTTATATTTTATTATATTATAAAATA
1 TTTTATATTTAAATAAATTATAAAATA
* *
207622 TTTTATATTTAAATAAATTTTAATATA
1 TTTTATATTTAAATAAATTATAAAATA
207649 TT
1 TT
207651 AATAATATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (27 bp):
TTTTATATTTAAATAAATTATAAAATA
Found at i:207720 original size:25 final size:26
Alignment explanation
Indices: 207686--207769 Score: 77
Period size: 25 Copynumber: 3.2 Consensus size: 26
207676 GAAATATTTA
*
207686 TTTATATATATTATA-TTATAATTAT
1 TTTAAATATATTATATTTATAATTAT
207711 TTTAAATATATTATATTTTTATAATTAT
1 TTTAAATATATTATA--TTTATAATTAT
*
207739 ATTTAACAT-TATTA-AGTT-TAATTAT
1 -TTTAA-ATATATTATATTTATAATTAT
*
207764 ATTAAA
1 TTTAAA
207770 AATCCAGTTA
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
23 1 0.02
24 4 0.08
25 21 0.41
26 2 0.04
28 11 0.22
29 10 0.20
30 2 0.04
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (26 bp):
TTTAAATATATTATATTTATAATTAT
Found at i:207908 original size:2 final size:2
Alignment explanation
Indices: 207901--207938 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
207891 TTCTTGACTA
*
207901 AT AT AT AT AT AT AT AT AC 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
207939 GTTTAAACCT
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:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:208666 original size:31 final size:32
Alignment explanation
Indices: 208631--208697 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 32
208621 CGATTCAATT
208631 TAAATTACT-AT-TAAAATAATTATAAAATATA
1 TAAATTACTAATATAAAATAATT-TAAAATATA
* * *
208662 TAAA-TATTAATATAAAATAATTTTAAATATT
1 TAAATTACTAATATAAAATAATTTAAAATATA
208693 TAAAT
1 TAAAT
208698 ATATTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
30 3 0.10
31 17 0.57
32 10 0.33
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (32 bp):
TAAATTACTAATATAAAATAATTTAAAATATA
Found at i:208698 original size:31 final size:32
Alignment explanation
Indices: 208642--208717 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
208632 AAATTACTAT
*
208642 TAAAATAATTATAAAATATATAAATAT-TAATA
1 TAAAATAATT-TTAAATATATAAATATATAATA
* **
208674 TAAAATAATTTTAAATATTTAAATATATTTTA
1 TAAAATAATTTTAAATATATAAATATATAATA
*
208706 TGAAATAATTTT
1 TAAAATAATTTT
208718 TAAACTTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
31 14 0.37
32 24 0.63
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (32 bp):
TAAAATAATTTTAAATATATAAATATATAATA
Found at i:208790 original size:2 final size:2
Alignment explanation
Indices: 208783--208812 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
208773 TAGTAATTTG
208783 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
208813 CTTTATATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:209043 original size:13 final size:13
Alignment explanation
Indices: 209021--209099 Score: 56
Period size: 13 Copynumber: 6.0 Consensus size: 13
209011 TTTTAATATT
*
209021 TTTATTATTAATA
1 TTTATAATTAATA
209034 TTTATAATTAATA
1 TTTATAATTAATA
209047 -TT-TAATATAATTA
1 TTTATAAT-TAA-TA
*
209060 ATTATAA-TAATA
1 TTTATAATTAATA
*
209072 TTTAATATATTTATA
1 TTT-ATA-ATTAATA
* *
209087 ATTATAATAAATA
1 TTTATAATTAATA
209100 GGATATAATT
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
11 4 0.08
12 9 0.17
13 25 0.47
14 6 0.11
15 9 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTTATAATTAATA
Found at i:209055 original size:16 final size:16
Alignment explanation
Indices: 209036--209090 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
209026 TATTAATATT
*
209036 TATAATTAATATTTAA
1 TATAATTAATATATAA
209052 TATAATTAAT-TATAA
1 TATAATTAATATATAA
* *
209067 TAATATTTAATATAT-T
1 T-ATAATTAATATATAA
209083 TATAATTA
1 TATAATTA
209091 TAATAAATAG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
15 11 0.33
16 19 0.58
17 3 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TATAATTAATATATAA
Found at i:209070 original size:25 final size:27
Alignment explanation
Indices: 209035--209096 Score: 92
Period size: 25 Copynumber: 2.3 Consensus size: 27
209025 TTATTAATAT
209035 TTATAATTAATATTTAATATA-AT-TAA
1 TTATAA-TAATATTTAATATATATATAA
*
209061 TTATAATAATATTTAATATATTTATAA
1 TTATAATAATATTTAATATATATATAA
209088 TTATAATAA
1 TTATAATAA
209097 ATAGGATATA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
25 14 0.42
26 7 0.21
27 12 0.36
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
TTATAATAATATTTAATATATATATAA
Found at i:209347 original size:13 final size:13
Alignment explanation
Indices: 209329--209358 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
209319 ATTTTTAAAA
*
209329 ATATTTATATTTT
1 ATATTTATATTTG
209342 ATATTTATATTTG
1 ATATTTATATTTG
209355 ATAT
1 ATAT
209359 ATATTTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (13 bp):
ATATTTATATTTG
Found at i:210053 original size:13 final size:13
Alignment explanation
Indices: 210017--210057 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
210007 AATAAAAAAT
*
210017 TATATGTATATTAA
1 TATATG-ATATTTA
210031 T-TAT-ATATTTA
1 TATATGATATTTA
210042 TATATGATATTTA
1 TATATGATATTTA
210055 TAT
1 TAT
210058 TTAAATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
11 7 0.29
12 3 0.12
13 13 0.54
14 1 0.04
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (13 bp):
TATATGATATTTA
Found at i:210717 original size:9 final size:9
Alignment explanation
Indices: 210700--210753 Score: 58
Period size: 9 Copynumber: 6.0 Consensus size: 9
210690 CATGTTAATA
210700 TAAAATTTT
1 TAAAATTTT
210709 T-AAATTTT
1 TAAAATTTT
*
210717 TAAAACTTT
1 TAAAATTTT
210726 TAAAA-TTT
1 TAAAATTTT
*
210734 TAAATTCTTTT
1 TAAA--ATTTT
210745 TAAAATTTT
1 TAAAATTTT
210754 CATGATGACT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
8 15 0.39
9 16 0.42
11 7 0.18
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.56
Consensus pattern (9 bp):
TAAAATTTT
Found at i:210720 original size:17 final size:17
Alignment explanation
Indices: 210700--210753 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
210690 CATGTTAATA
* *
210700 TAAAATTTTTAAATTTT
1 TAAAACTTTTAAAATTT
210717 TAAAACTTTTAAAATTT
1 TAAAACTTTTAAAATTT
*
210734 TAAATTCTTTTTAAAATTT
1 TAAA-AC-TTTTAAAATTT
210753 T
1 T
210754 CATGATGACT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
17 19 0.59
18 1 0.03
19 12 0.38
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.56
Consensus pattern (17 bp):
TAAAACTTTTAAAATTT
Found at i:211412 original size:22 final size:22
Alignment explanation
Indices: 211384--211427 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
211374 TATTTAAAAA
* *
211384 TATTTTATCATATTTATCTTAT
1 TATTTTATCAAATTTATATTAT
*
211406 TATTTTATTAAATTTATATTAT
1 TATTTTATCAAATTTATATTAT
211428 ATCATATTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.64
Consensus pattern (22 bp):
TATTTTATCAAATTTATATTAT
Found at i:211612 original size:2 final size:2
Alignment explanation
Indices: 211605--211629 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
211595 AAGTAAATGA
211605 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
211630 ACGAATTTAA
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:212195 original size:12 final size:13
Alignment explanation
Indices: 212175--212212 Score: 60
Period size: 12 Copynumber: 3.0 Consensus size: 13
212165 TTATTTAAAT
212175 TTATTTATAATTA
1 TTATTTATAATTA
*
212188 TT-TTTATATTTA
1 TTATTTATAATTA
212200 TTATTTATAATTA
1 TTATTTATAATTA
212213 ATAAAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TTATTTATAATTA
Found at i:212590 original size:19 final size:18
Alignment explanation
Indices: 212560--212595 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
212550 ATTAAGATAA
212560 TTTTAAATTAATAAATAT
1 TTTTAAATTAATAAATAT
212578 TTTTAATATTAATAAATA
1 TTTTAA-ATTAATAAATA
212596 ATTGATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTTAAATTAATAAATAT
Found at i:215619 original size:16 final size:17
Alignment explanation
Indices: 215600--215632 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
215590 TAAATCATTG
215600 TTTAATTA-ATAAAAAT
1 TTTAATTATATAAAAAT
*
215616 TTTATTTATATAAAAAT
1 TTTAATTATATAAAAAT
215633 ATAAAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTAATTATATAAAAAT
Found at i:215675 original size:8 final size:8
Alignment explanation
Indices: 215658--215694 Score: 65
Period size: 8 Copynumber: 4.6 Consensus size: 8
215648 TCAAATGAGT
*
215658 TTTTAGTA
1 TTTTAATA
215666 TTTTAATA
1 TTTTAATA
215674 TTTTAATA
1 TTTTAATA
215682 TTTTAATA
1 TTTTAATA
215690 TTTTA
1 TTTTA
215695 TAAATAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (8 bp):
TTTTAATA
Found at i:220523 original size:31 final size:31
Alignment explanation
Indices: 220465--220523 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
220455 GTTTGGGAGA
*
220465 AAAATTTTCTATTTTTTTAATTTTTATTTAT
1 AAAATTTTCTATTTTTTTAATTATTATTTAT
220496 AAAATTTTCT-TTTATTATT-ATTATTATT
1 AAAATTTTCTATTT-TT-TTAATTATTATT
220524 ATTATTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 3 0.12
31 20 0.80
32 2 0.08
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (31 bp):
AAAATTTTCTATTTTTTTAATTATTATTTAT
Found at i:221324 original size:18 final size:18
Alignment explanation
Indices: 221296--221364 Score: 65
Period size: 18 Copynumber: 3.9 Consensus size: 18
221286 ATTGTATTTA
221296 AAATATTTTATATTTATAT
1 AAAT-TTTTATATTTATAT
* *
221315 AAATTTTTATATGTAAAT
1 AAATTTTTATATTTATAT
221333 -AA--TTTAT-TTTATAT
1 AAATTTTTATATTTATAT
221347 AAATTTTGATATATTTAT
1 AAATTTT--TATATTTAT
221365 GTATTTATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
14 5 0.12
15 7 0.17
17 4 0.10
18 12 0.30
19 7 0.17
20 5 0.12
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
AAATTTTTATATTTATAT
Found at i:221349 original size:32 final size:33
Alignment explanation
Indices: 221296--221358 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
221286 ATTGTATTTA
* *
221296 AAATATTTTATATTTATATAAATTTTTATATGT
1 AAATAATTTATATTTATATAAATTTTGATATGT
221329 AAATAATTTAT-TTTATATAAATTTTGATAT
1 AAATAATTTATATTTATATAAATTTTGATAT
221359 ATTTATGTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 18 0.64
33 10 0.36
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (33 bp):
AAATAATTTATATTTATATAAATTTTGATATGT
Found at i:221384 original size:11 final size:11
Alignment explanation
Indices: 221368--221431 Score: 58
Period size: 12 Copynumber: 5.5 Consensus size: 11
221358 TATTTATGTA
221368 TTTATATTATT
1 TTTATATTATT
221379 TTTATATTATTT
1 TTTATATTA-TT
*
221391 TTTATATCATATA
1 TTTATAT--TATT
221404 TTTA-ATTATTCT
1 TTTATATTA-T-T
*
221416 TTTATATTATA
1 TTTATATTATT
221427 TTTAT
1 TTTAT
221432 GTAATCGTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
10 2 0.05
11 15 0.34
12 16 0.36
13 9 0.20
14 2 0.05
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTATATTATT
Found at i:221405 original size:27 final size:25
Alignment explanation
Indices: 221379--221430 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
221369 TTATATTATT
221379 TTTATATTATT-TTTTATATCATATA
1 TTTA-ATTATTCTTTTATATCATATA
221404 TTTAATTATTCTTTTATAT--TATA
1 TTTAATTATTCTTTTATATCATATA
221427 TTTA
1 TTTA
221431 TGTAATCGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
23 8 0.31
24 6 0.23
25 12 0.46
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (25 bp):
TTTAATTATTCTTTTATATCATATA
Found at i:221407 original size:25 final size:24
Alignment explanation
Indices: 221368--221431 Score: 87
Period size: 23 Copynumber: 2.7 Consensus size: 24
221358 TATTTATGTA
*
221368 TTTATATTATTTTTATATTATT-T
1 TTTATATTATATTTATATTATTCT
221391 TTTATATCATATATTTA-ATTATTCT
1 TTTATAT--TATATTTATATTATTCT
221416 TTTATATTATATTTAT
1 TTTATATTATATTTAT
221432 GTAATCGTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
23 15 0.42
24 6 0.17
25 15 0.42
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (24 bp):
TTTATATTATATTTATATTATTCT
Found at i:221599 original size:17 final size:18
Alignment explanation
Indices: 221566--221604 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
221556 TTATCAATTG
*
221566 AATAAATATAAATTATTA
1 AATAAATATAAAATATTA
221584 AATAAAT-TAAAATATTA
1 AATAAATATAAAATATTA
221601 AATA
1 AATA
221605 TGAATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AATAAATATAAAATATTA
Found at i:221615 original size:2 final size:2
Alignment explanation
Indices: 221608--221639 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
221598 TTAAATATGA
221608 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
221640 TAAACTTAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:222562 original size:12 final size:12
Alignment explanation
Indices: 222545--222574 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
222535 GACTTTTATA
222545 TTTTAATTTGAT
1 TTTTAATTTGAT
222557 TTTTAATTTGAT
1 TTTTAATTTGAT
*
222569 ATTTAA
1 TTTTAA
222575 AAAAAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (12 bp):
TTTTAATTTGAT
Found at i:222768 original size:18 final size:17
Alignment explanation
Indices: 222738--222771 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
222728 TTTAAGTATC
*
222738 AAATTGAACATTAAATT
1 AAATTGAAAATTAAATT
222755 AAATATGAAAATTAAAT
1 AAAT-TGAAAATTAAAT
222772 GAATATTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (17 bp):
AAATTGAAAATTAAATT
Found at i:224273 original size:13 final size:13
Alignment explanation
Indices: 224230--224273 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
224220 AAACTATTTG
224230 ATAATTTTATTTTT
1 ATAATTTT-TTTTT
**
224244 ATAATTTTTTTAA
1 ATAATTTTTTTTT
224257 ATAATTTTTTTTT
1 ATAATTTTTTTTT
224270 ATAA
1 ATAA
224274 ATATTGGGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
13 18 0.69
14 8 0.31
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
ATAATTTTTTTTT
Found at i:225022 original size:18 final size:18
Alignment explanation
Indices: 224999--225033 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
224989 TATCGTGCTT
* *
224999 ATATTATTTTTTTATTTA
1 ATATTATGTTTTAATTTA
225017 ATATTATGTTTTAATTT
1 ATATTATGTTTTAATTT
225034 TTTTTATATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (18 bp):
ATATTATGTTTTAATTTA
Found at i:227481 original size:12 final size:12
Alignment explanation
Indices: 227464--227489 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
227454 TTCGAATTGA
227464 TTTTTTAGTTTC
1 TTTTTTAGTTTC
227476 TTTTTTAGTTTC
1 TTTTTTAGTTTC
227488 TT
1 TT
227490 GAGTTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.08, T:0.77
Consensus pattern (12 bp):
TTTTTTAGTTTC
Found at i:229757 original size:20 final size:20
Alignment explanation
Indices: 229734--229802 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
229724 TGTAAATATA
*
229734 TTATATAATAATATAATAAT
1 TTATATAATAATATTATAAT
* * *
229754 TTATATATTTATCTTATAA-
1 TTATATAATAATATTATAAT
*
229773 TTATATAAATATTATTATATAT
1 TTATAT-AATAATATTATA-AT
229795 TTATATAA
1 TTATATAA
229803 ATTTGATATA
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
19 6 0.16
20 23 0.61
21 3 0.08
22 6 0.16
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (20 bp):
TTATATAATAATATTATAAT
Found at i:229779 original size:31 final size:33
Alignment explanation
Indices: 229737--229798 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
229727 AAATATATTA
229737 TATAATAATAT-AATAAT-TTATATATTTATCT
1 TATAATAATATAAATAATATTATATATTTATCT
* *
229768 TATAATTATATAAATATTATTATATATTTAT
1 TATAATAATATAAATAATATTATATATTTAT
229799 ATAAATTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 10 0.37
32 5 0.19
33 12 0.44
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (33 bp):
TATAATAATATAAATAATATTATATATTTATCT
Found at i:229876 original size:7 final size:7
Alignment explanation
Indices: 229849--229904 Score: 66
Period size: 7 Copynumber: 8.6 Consensus size: 7
229839 AAATCATATT
229849 TATTTTA
1 TATTTTA
*
229856 T-TTTTT
1 TATTTTA
*
229862 TATATTA
1 TATTTTA
229869 TATTTTA
1 TATTTTA
229876 TATTTTA
1 TATTTTA
229883 TATTTTA
1 TATTTTA
229890 TA--TTA
1 TATTTTA
229895 T-TTTTA
1 TATTTTA
229901 TATT
1 TATT
229905 ATATGCGTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 4 0.10
6 9 0.22
7 28 0.68
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TATTTTA
Found at i:237365 original size:2 final size:2
Alignment explanation
Indices: 237358--237390 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
237348 TTCTCAATGC
237358 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
237391 GTATCCTGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:238336 original size:24 final size:24
Alignment explanation
Indices: 238284--238334 Score: 84
Period size: 25 Copynumber: 2.1 Consensus size: 24
238274 AAAAAAAGAC
*
238284 AAAGAAAAAAGAACCCTATGTATG
1 AAAGAAAAAAGAACCCTATGCATG
238308 AAAGAATAAAAGAACCCTATGCATG
1 AAAGAA-AAAAGAACCCTATGCATG
238333 AA
1 AA
238335 GAACTCTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 6 0.24
25 19 0.76
ACGTcount: A:0.55, C:0.14, G:0.16, T:0.16
Consensus pattern (24 bp):
AAAGAAAAAAGAACCCTATGCATG
Found at i:241668 original size:15 final size:15
Alignment explanation
Indices: 241650--241689 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 15
241640 TTATTATATC
241650 TATAATTATAA-TAAA
1 TATAA-TATAATTAAA
241665 TATAATATAATTAAA
1 TATAATATAATTAAA
241680 TATATATATA
1 TATA-ATATA
241690 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 5 0.22
15 13 0.57
16 5 0.22
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TATAATATAATTAAA
Found at i:241686 original size:2 final size:2
Alignment explanation
Indices: 241644--241706 Score: 57
Period size: 2 Copynumber: 34.5 Consensus size: 2
241634 TAATATTTAT
* * *
241644 TA TA TC TA TA -A T- TA TA -A TA AA TA TA -A TA TA -A T- TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
241680 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 T
241707 GATCATAATT
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
1 6 0.12
2 43 0.88
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:243445 original size:24 final size:22
Alignment explanation
Indices: 243417--243496 Score: 63
Period size: 22 Copynumber: 3.4 Consensus size: 22
243407 TCCAATTTTG
243417 AATATAAATTTTTAAATTTAAATT
1 AATATAAATTTTT--ATTTAAATT
* * *
243441 AATATATATTATTATTTAATAAT
1 AATATAAATTTTTATTTAA-ATT
*
243464 AA-ATATATTTTTCATTTAAAATT
1 AATATAAATTTTT-ATTT-AAATT
243487 AATTATAAAT
1 AA-TATAAAT
243497 AATTTTTAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
22 15 0.33
23 12 0.27
24 13 0.29
25 5 0.11
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (22 bp):
AATATAAATTTTTATTTAAATT
Found at i:243459 original size:22 final size:23
Alignment explanation
Indices: 243432--243493 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
243422 AAATTTTTAA
243432 ATTTAAATTAATATATATTATT-
1 ATTTAAATTAATATATATTATTC
* *
243454 ATTTAATAATAA-ATATATTTTTC
1 ATTTAA-ATTAATATATATTATTC
243477 ATTTAAAATTAAT-TATA
1 ATTT-AAATTAATATATA
243494 AATAATTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
22 15 0.45
23 16 0.48
24 2 0.06
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
ATTTAAATTAATATATATTATTC
Found at i:243854 original size:19 final size:18
Alignment explanation
Indices: 243814--243861 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 18
243804 TTTATAATAA
243814 AATTTAAATAAAAACATT
1 AATTTAAATAAAAACATT
*
243832 --TTTAAATAATAAATATT
1 AATTTAAATAA-AAACATT
243849 AATTTAAACTAAA
1 AATTTAAA-TAAA
243862 TTAAATCAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 9 0.36
17 6 0.24
19 7 0.28
20 3 0.12
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTTAAATAAAAACATT
Found at i:247493 original size:27 final size:26
Alignment explanation
Indices: 247457--247534 Score: 88
Period size: 26 Copynumber: 3.0 Consensus size: 26
247447 ATCGAAAATA
*
247457 TATTTTAAATCATATTAAAT-TTATTT
1 TATTTTAAAT-ATAATAAATATTATTT
247483 TATTTATAAATATAATAAATATTA-TT
1 TATTT-TAAATATAATAAATATTATTT
* * *
247509 TAGTTTAATTAAAATAAATATTATTT
1 TATTTTAAATATAATAAATATTATTT
247535 AATAATTAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
25 16 0.36
26 21 0.47
27 8 0.18
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (26 bp):
TATTTTAAATATAATAAATATTATTT
Found at i:247863 original size:15 final size:14
Alignment explanation
Indices: 247845--247879 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
247835 ATAAATATTT
247845 ATATATTTTATATAA
1 ATATATTTTAT-TAA
*
247860 ATATAATTTATTAA
1 ATATATTTTATTAA
247874 ATATAT
1 ATATAT
247880 ATATTTATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
ATATATTTTATTAA
Found at i:247894 original size:19 final size:19
Alignment explanation
Indices: 247870--247906 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
247860 ATATAATTTA
247870 TTAAATATATATATTTATG
1 TTAAATATATATATTTATG
247889 TTAAATATATATATTTAT
1 TTAAATATATATATTTAT
247907 ATTCAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (19 bp):
TTAAATATATATATTTATG
Found at i:248400 original size:155 final size:155
Alignment explanation
Indices: 248091--248396 Score: 551
Period size: 155 Copynumber: 2.0 Consensus size: 155
248081 ATCACCATAA
* * * **
248091 TTTAAATACTAAAAGAAGTTGCTGGATTTGCCATTGTTGGTGAGCTGTTAGGTGTTGCCTAAAGT
1 TTTAAATACTAAAAGAAATTGATGGATTTGCCACTGTTACTGAGCTGTTAGGTGTTGCCTAAAGT
248156 CAAAAGTTCCTTCCTTTCACGTTTACGCATATGATATCGCACATGAGAATTAGTTCCATCAATTC
66 CAAAAGTTCCTTCCTTTCACGTTTACGCATATGATATCGCACATGAGAATTAGTTCCATCAATTC
248221 TAATCTGAAGCAAGAGTACTTTGAG
131 TAATCTGAAGCAAGAGTACTTTGAG
*
248246 TTTAAATACTAAAAGAAATTGATGGATTTGCCACTGTTACTGAGCTGTTAGTTGTTGCCTAAAGT
1 TTTAAATACTAAAAGAAATTGATGGATTTGCCACTGTTACTGAGCTGTTAGGTGTTGCCTAAAGT
248311 CAAAAGTTCCTTCC-TTCACGTTTACGCATATGATATCGCACATGAGAATTAGTTCCATCAATTC
66 CAAAAGTTCCTTCCTTTCACGTTTACGCATATGATATCGCACATGAGAATTAGTTCCATCAATTC
248375 TAATCTGAAGCAAGAGTACTTT
131 TAATCTGAAGCAAGAGTACTTT
248397 TGAGCTTGAA
Statistics
Matches: 145, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
154 72 0.50
155 73 0.50
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (155 bp):
TTTAAATACTAAAAGAAATTGATGGATTTGCCACTGTTACTGAGCTGTTAGGTGTTGCCTAAAGT
CAAAAGTTCCTTCCTTTCACGTTTACGCATATGATATCGCACATGAGAATTAGTTCCATCAATTC
TAATCTGAAGCAAGAGTACTTTGAG
Found at i:248976 original size:23 final size:23
Alignment explanation
Indices: 248950--248995 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
248940 CGATGTGCGT
248950 TCCAACCTTCAATGCTTAAGTCA
1 TCCAACCTTCAATGCTTAAGTCA
*
248973 TCCAATCTTCAATGCTTAAGTCA
1 TCCAACCTTCAATGCTTAAGTCA
248996 GTATTTGAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.30, C:0.28, G:0.09, T:0.33
Consensus pattern (23 bp):
TCCAACCTTCAATGCTTAAGTCA
Found at i:250347 original size:16 final size:16
Alignment explanation
Indices: 250326--250359 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
250316 TCCGAAGTCC
250326 ATGGTTGGTAAGAAAG
1 ATGGTTGGTAAGAAAG
250342 ATGGTTGGTAAGAAAG
1 ATGGTTGGTAAGAAAG
250358 AT
1 AT
250360 CCTTCGGATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.35, T:0.26
Consensus pattern (16 bp):
ATGGTTGGTAAGAAAG
Found at i:250509 original size:20 final size:21
Alignment explanation
Indices: 250486--250551 Score: 68
Period size: 20 Copynumber: 3.3 Consensus size: 21
250476 AATATAAATT
* *
250486 TAAATTATTATTT-TATTAAA
1 TAAATAATTATTTAAATTAAA
250506 TAAATAATTATTTAAATTAAA
1 TAAATAATTATTTAAATTAAA
*
250527 TCAAATCA--ATTTAAATTAAA
1 T-AAATAATTATTTAAATTAAA
250547 -AAATA
1 TAAATA
250552 TAAATATAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
18 4 0.10
20 24 0.60
21 7 0.17
22 5 0.12
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAATAATTATTTAAATTAAA
Found at i:250510 original size:32 final size:31
Alignment explanation
Indices: 250465--250524 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
250455 AAATTTATAT
*
250465 TTTTATAATTAAAT-ATAAATTTAAATTATTA
1 TTTTATAAATAAATAAT-AATTTAAATTATTA
*
250496 TTTTATTAAATAAATAATTATTTAAATTA
1 TTTTA-TAAATAAATAATAATTTAAATTA
250525 AATCAAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 5 0.20
32 18 0.72
33 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (31 bp):
TTTTATAAATAAATAATAATTTAAATTATTA
Found at i:250746 original size:11 final size:12
Alignment explanation
Indices: 250717--250796 Score: 51
Period size: 13 Copynumber: 6.6 Consensus size: 12
250707 AGATATAATA
*
250717 ATTTATATATTT
1 ATTTATAAATTT
250729 ATATTATAAATTT
1 AT-TTATAAATTT
250742 -TTTAT-AATTAT
1 ATTTATAAATT-T
*
250753 ATTTA-AAATAT
1 ATTTATAAATTT
*
250764 -TTTATAAATATA
1 ATTTATAAAT-TT
*
250776 ATTTATATATTAT
1 ATTTATAAATT-T
250789 AATTTATA
1 -ATTTATA
250797 TTATATAAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
10 8 0.15
11 10 0.19
12 11 0.21
13 17 0.32
14 7 0.13
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTTATAAATTT
Found at i:250752 original size:22 final size:22
Alignment explanation
Indices: 250722--250840 Score: 72
Period size: 22 Copynumber: 5.5 Consensus size: 22
250712 TAATAATTTA
*
250722 TATATTTATATTATAAATTTTT
1 TATAATTATATTATAAATTTTT
*
250744 TATAATTATATT-TAAAATATTT
1 TATAATTATATTAT-AAATTTTT
* * *
250766 TATAAATATAATT-T--ATATAT
1 TATAATTAT-ATTATAAATTTTT
*
250786 TATAATTTATATTATATAAATTTT
1 TATAA-TTATATTATA-AATTTTT
* *
250810 AATAATATATATTAT--A-TTTA
1 TATAAT-TATATTATAAATTTTT
250830 TATAATTATAT
1 TATAATTATAT
250841 ATCTAAACTT
Statistics
Matches: 78, Mismatches: 11, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
19 5 0.06
20 21 0.27
21 6 0.08
22 26 0.33
23 5 0.06
24 15 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TATAATTATATTATAAATTTTT
Found at i:250765 original size:24 final size:23
Alignment explanation
Indices: 250713--250840 Score: 66
Period size: 23 Copynumber: 5.9 Consensus size: 23
250703 TGATAGATAT
* *
250713 AATAATTTATATATTTATATTATA
1 AATATTTTATATAATTATATTA-A
250737 AAT-TTTT-TATAATTATATTTAA
1 AATATTTTATATAATTATA-TTAA
250759 AATATTTTATA-AA-TATAATT--
1 AATATTTTATATAATTAT-ATTAA
* * *
250779 TATATATTATA-ATTTATATTATA
1 AATATTTTATATAATTATATTA-A
250802 TAA-ATTTTA-ATAATATATATT--
1 -AATATTTTATATAAT-TATATTAA
250823 -ATA-TTTATATAATTATAT
1 AATATTTTATATAATTATAT
250841 ATCTAAACTT
Statistics
Matches: 83, Mismatches: 8, Indels: 31
0.68 0.07 0.25
Matches are distributed among these distances:
19 10 0.12
20 19 0.23
21 3 0.04
22 19 0.23
23 20 0.24
24 12 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
AATATTTTATATAATTATATTAA
Found at i:250767 original size:10 final size:11
Alignment explanation
Indices: 250732--250774 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
250722 TATATTTATA
*
250732 TTATAAATTTT
1 TTATAAATATT
*
250743 TTATAATTATAT
1 TTATAAATAT-T
250755 TTA-AAATATT
1 TTATAAATATT
250765 TTATAAATAT
1 TTATAAATAT
250775 AATTTATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 4 0.15
11 19 0.70
12 4 0.15
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TTATAAATATT
Found at i:250809 original size:43 final size:43
Alignment explanation
Indices: 250743--250847 Score: 110
Period size: 43 Copynumber: 2.4 Consensus size: 43
250733 TATAAATTTT
250743 TTATAA-TTATATTTAAAATATTTT-ATAA-ATATAATTTATATA
1 TTATAATTTATATTTAAAATATTTTAATAATATAT-A-TTATATA
* *
250785 TTATAATTTATATTATATAA-ATTTTAATAATATATATTATATT
1 TTATAATTTATATT-TAAAATATTTTAATAATATATATTATATA
*
250828 TATATAATTATATATCTAAA
1 T-TATAATT-TATATTTAAA
250848 CTTATTAAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
42 6 0.11
43 19 0.36
44 19 0.36
45 9 0.17
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (43 bp):
TTATAATTTATATTTAAAATATTTTAATAATATATATTATATA
Done.