Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold477
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: 400253
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
File 2 of 3
Found at i:106984 original size:41 final size:38
Alignment explanation
Indices: 106925--107001 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 38
106915 ATTTTATAAA
*
106925 TTTTAATATATTTATATATTTATAATTTATTTATATTATTT
1 TTTTAATATATATATATATTT-TAA-TT-TTTATATTATTT
106966 TTTTAATAT-TATATTATATTTTAATTTTTATATTAT
1 TTTTAATATATATA-TATATTTTAATTTTTATATTAT
107002 ATTTATCTCG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
38 10 0.29
39 2 0.06
40 6 0.18
41 16 0.47
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (38 bp):
TTTTAATATATATATATATTTTAATTTTTATATTATTT
Found at i:106999 original size:19 final size:19
Alignment explanation
Indices: 106939--107005 Score: 73
Period size: 19 Copynumber: 3.4 Consensus size: 19
106929 AATATATTTA
106939 TATATTTATAATTTATTTATAT
1 TATATTT-TAA-TT-TTTATAT
* *
106961 TATTTTTTTAA-TATTATAT
1 TA-TATTTTAATTTTTATAT
106980 TATATTTTAATTTTTATAT
1 TATATTTTAATTTTTATAT
106999 TATATTT
1 TATATTT
107006 ATCTCGTATT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
18 7 0.18
19 22 0.56
20 1 0.03
22 5 0.13
23 4 0.10
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TATATTTTAATTTTTATAT
Found at i:108923 original size:2 final size:2
Alignment explanation
Indices: 108918--108961 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
108908 TCAACAAAAT
*
108918 TA TA TA -A TA TC 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 TA TA TA TA
108959 TA T
1 TA T
108962 TGCTAACGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:111170 original size:19 final size:20
Alignment explanation
Indices: 111146--111187 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
111136 ATTTTCTTAG
*
111146 TTTTATATTGT-TAAATATA
1 TTTTATATTATATAAATATA
*
111165 TTTTATATTATATTAATATA
1 TTTTATATTATATAAATATA
111185 TTT
1 TTT
111188 ATTTTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTTATATTATATAAATATA
Found at i:115212 original size:2 final size:2
Alignment explanation
Indices: 115205--115238 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
115195 TATGAGTTAC
115205 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
115239 CCTTTTTCAC
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):
AT
Found at i:116759 original size:2 final size:2
Alignment explanation
Indices: 116752--116786 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
116742 TCAAGGATAC
* *
116752 AT AT AT AT AT AT AT AT AT AC AT AT AT AA AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
116787 GGGGATTGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:118159 original size:19 final size:15
Alignment explanation
Indices: 118120--118169 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 15
118110 GTGAATTTTC
118120 AAAAATTAATATATA
1 AAAAATTAATATATA
*
118135 AAAAATTAAT-TATT
1 AAAAATTAATATATA
*
118149 ATAAATT-A-A-ATA
1 AAAAATTAATATATA
118161 AAAAATTAA
1 AAAAATTAA
118170 ATCAATTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
12 8 0.28
13 2 0.07
14 9 0.31
15 10 0.34
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAAAATTAATATATA
Found at i:118223 original size:32 final size:32
Alignment explanation
Indices: 118160--118223 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
118150 TAAATTAAAT
** *
118160 AAAAAATTAAATCAATTATTTCACTATAATAA
1 AAAAAATTAAATCAACAATTTCACTAGAATAA
*
118192 AAAAAATT-AATCATACAATTTGACTAGAATAA
1 AAAAAATTAAATCA-ACAATTTCACTAGAATAA
118224 TTTATCCATG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 5 0.19
32 22 0.81
ACGTcount: A:0.56, C:0.09, G:0.03, T:0.31
Consensus pattern (32 bp):
AAAAAATTAAATCAACAATTTCACTAGAATAA
Found at i:118606 original size:16 final size:16
Alignment explanation
Indices: 118572--118671 Score: 56
Period size: 16 Copynumber: 6.1 Consensus size: 16
118562 GATTATAAAT
*
118572 TTAATAAATCAAATATAA
1 TTAAT-AAT-AAATTTAA
*
118590 TTACTAATAAATTTAA
1 TTAATAATAAATTTAA
* * **
118606 TAAATATTAAATAAAA
1 TTAATAATAAATTTAA
* *
118622 TTATTTATAAATTTAA
1 TTAATAATAAATTTAA
* * *
118638 TGAATATTAAATATAA
1 TTAATAATAAATTTAA
* * *
118654 TTACTTATAATTTTAA
1 TTAATAATAAATTTAA
118670 TT
1 TT
118672 GTCATTAAAA
Statistics
Matches: 58, Mismatches: 24, Indels: 2
0.69 0.29 0.02
Matches are distributed among these distances:
16 51 0.88
17 3 0.05
18 4 0.07
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (16 bp):
TTAATAATAAATTTAA
Found at i:118624 original size:32 final size:31
Alignment explanation
Indices: 118564--118670 Score: 144
Period size: 32 Copynumber: 3.4 Consensus size: 31
118554 TAAAATTTGA
*
118564 TTATAAATTTAATAA-ATCAAATATAATTAC
1 TTATAAATTTAATAATATTAAATATAATTAC
* * *
118594 TAATAAATTTAATAAATATTAAATAAAATTAT
1 TTATAAATTTAAT-AATATTAAATATAATTAC
118626 TTATAAATTTAATGAATATTAAATATAATTAC
1 TTATAAATTTAAT-AATATTAAATATAATTAC
*
118658 TTATAATTTTAAT
1 TTATAAATTTAAT
118671 TGTCATTAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
30 12 0.18
31 2 0.03
32 52 0.79
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (31 bp):
TTATAAATTTAATAATATTAAATATAATTAC
Found at i:120227 original size:21 final size:21
Alignment explanation
Indices: 120186--120227 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
120176 AAATATTATT
* *
120186 TTTATATTAATATTTATATAA
1 TTTATATTAATATATAAATAA
120207 TTTATAATTAA-ATATAAATAA
1 TTTAT-ATTAATATATAAATAA
120228 AATATATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TTTATATTAATATATAAATAA
Found at i:124772 original size:15 final size:15
Alignment explanation
Indices: 124740--124784 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
124730 AAATACCATG
*
124740 ATTTAATGAATTTAAA
1 ATTTAAT-AATTTTAA
124756 ATTTAATAATTTTAA
1 ATTTAATAATTTTAA
*
124771 ATTTTA-AATTTTAA
1 ATTTAATAATTTTAA
124785 TGTCATAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
14 8 0.30
15 12 0.44
16 7 0.26
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
ATTTAATAATTTTAA
Found at i:125301 original size:17 final size:17
Alignment explanation
Indices: 125279--125357 Score: 56
Period size: 17 Copynumber: 4.7 Consensus size: 17
125269 TTCATGTTAA
125279 AAAATTAATAAATAATT
1 AAAATTAATAAATAATT
* *
125296 AAAATTGATTAAA-ATTT
1 AAAATT-AATAAATAATT
***
125313 TGTATATAA-AAATAATT
1 AAAAT-TAATAAATAATT
**
125330 -TTATTAATAAATAATT
1 AAAATTAATAAATAATT
125346 AAAATTAATAAA
1 AAAATTAATAAA
125358 AAATAATTGT
Statistics
Matches: 47, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
15 3 0.06
16 14 0.30
17 24 0.51
18 6 0.13
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
AAAATTAATAAATAATT
Found at i:126592 original size:18 final size:18
Alignment explanation
Indices: 126565--126627 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 18
126555 TTTATTAAAT
126565 TTAAAA-TTTAAAATATA
1 TTAAAATTTTAAAATATA
126582 TTAAAATTTTAAAAATTAATA
1 TTAAAATTTT-AAAA-T-ATA
*
126603 TAAAATATTTTAATAATATA
1 TTAAA-ATTTTAA-AATATA
126623 TTAAA
1 TTAAA
126628 CATAATAATC
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
17 6 0.16
18 3 0.08
19 4 0.11
20 8 0.21
21 10 0.26
22 7 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TTAAAATTTTAAAATATA
Found at i:126996 original size:19 final size:18
Alignment explanation
Indices: 126967--127024 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 18
126957 ATAACAAATA
126967 AAAAAATTATTAATAGTGTT
1 AAAAAA-TATTAATA-TGTT
*
126987 AAAAAATATTTAA-ATATT
1 AAAAAATA-TTAATATGTT
127005 AATAAAATATTAATATGTT
1 AA-AAAATATTAATATGTT
127024 A
1 A
127025 TATGATGTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
18 9 0.27
19 14 0.42
20 10 0.30
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (18 bp):
AAAAAATATTAATATGTT
Found at i:127536 original size:34 final size:31
Alignment explanation
Indices: 127436--127536 Score: 102
Period size: 28 Copynumber: 3.2 Consensus size: 31
127426 CATTAATTTT
* *
127436 AAATATAATATAAAAAT-TAAA-ATA-TATA
1 AAATATAACATAAATATATAAATATATTATA
127464 AAATATAACATAAATATATAAATATATTA-A
1 AAATATAACATAAATATATAAATATATTATA
*
127494 AATTATATAACATATAATATTTTAAATATAATTATA
1 AA--ATATAACATA-AATA-TATAAATAT-ATTATA
127530 AAATATA
1 AAATATA
127537 TATAATTCAA
Statistics
Matches: 61, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
28 15 0.25
29 4 0.07
30 6 0.10
31 2 0.03
32 10 0.16
33 4 0.07
34 13 0.21
35 4 0.07
36 3 0.05
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (31 bp):
AAATATAACATAAATATATAAATATATTATA
Found at i:127538 original size:9 final size:9
Alignment explanation
Indices: 127443--127509 Score: 59
Period size: 9 Copynumber: 7.3 Consensus size: 9
127433 TTTAAATATA
127443 ATATAAAA-
1 ATATAAAAT
127451 AT-TAAAAT
1 ATATAAAAT
127459 ATATAAAAT
1 ATATAAAAT
*
127468 ATAACATAAAT
1 AT-ATA-AAAT
127479 ATAT-AAAT
1 ATATAAAAT
127487 ATATTAAAATT
1 ATA-TAAAA-T
*
127498 ATATAACAT
1 ATATAAAAT
127507 ATA
1 ATA
127510 ATATTTTAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
7 5 0.10
8 11 0.22
9 13 0.27
10 10 0.20
11 10 0.20
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (9 bp):
ATATAAAAT
Found at i:134466 original size:2 final size:2
Alignment explanation
Indices: 134461--134496 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
134451 GGGGGGGGAG
* *
134461 GA GA GA GA GA GA GG GA GA GA GA GA GA GA GA AA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
134497 AACAGAGTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:137377 original size:11 final size:12
Alignment explanation
Indices: 137341--137387 Score: 53
Period size: 11 Copynumber: 4.1 Consensus size: 12
137331 AATTAAAATT
*
137341 ATTTATATTTAT
1 ATTTATATTTAA
*
137353 ATTTATATTAAA
1 ATTTATATTTAA
137365 ATTT-TATTTAA
1 ATTTATATTTAA
*
137376 ATATA-ATTTAA
1 ATTTATATTTAA
137387 A
1 A
137388 AATTAAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 16 0.53
12 14 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
ATTTATATTTAA
Found at i:137395 original size:30 final size:30
Alignment explanation
Indices: 137359--137446 Score: 115
Period size: 30 Copynumber: 2.9 Consensus size: 30
137349 TTATATTTAT
*
137359 ATTAAAATTTTATTTAAATATAATTTAAAA
1 ATTAAAATTTTATTTAAATATAAATTAAAA
* * *
137389 ATTAAAATTTTATATAATTATAAATTAATA
1 ATTAAAATTTTATTTAAATATAAATTAAAA
*
137419 ATTAATAA-TATATTTAAATATAAATTAA
1 ATTAA-AATTTTATTTAAATATAAATTAA
137447 TATTATTTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
30 48 0.96
31 2 0.04
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
ATTAAAATTTTATTTAAATATAAATTAAAA
Found at i:137403 original size:24 final size:24
Alignment explanation
Indices: 137376--137421 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
137366 TTTTATTTAA
137376 ATATAATTTAAAAATTAA-AATTTT
1 ATATAA-TTAAAAATTAATAATTTT
*
137400 ATATAATTATAAATTAATAATT
1 ATATAATTAAAAATTAATAATT
137422 AATAATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
ATATAATTAAAAATTAATAATTTT
Found at i:137447 original size:30 final size:30
Alignment explanation
Indices: 137325--137448 Score: 114
Period size: 30 Copynumber: 4.3 Consensus size: 30
137315 TACTATATTT
* *
137325 AATTAA-AATTAAAA-T-TATTTATATTTA
1 AATTAATAATTAAAATTATATTTAAATATA
* * *
137352 TATTTAT-ATTAAAATTTTATTTAAATATA
1 AATTAATAATTAAAATTATATTTAAATATA
* * * * *
137381 ATTTAAAAATTAAAATTTTATATAATTATA
1 AATTAATAATTAAAATTATATTTAAATATA
137411 AATTAATAATTAATAA-TATATTTAAATATA
1 AATTAATAATTAA-AATTATATTTAAATATA
137441 AATTAATA
1 AATTAATA
137449 TTATTTTTAA
Statistics
Matches: 77, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
27 11 0.14
28 1 0.01
29 13 0.17
30 50 0.65
31 2 0.03
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (30 bp):
AATTAATAATTAAAATTATATTTAAATATA
Found at i:138206 original size:2 final size:2
Alignment explanation
Indices: 138194--138235 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
138184 TCTTCAAATC
*
138194 TA TA AA TA 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 TA TA TA TA
138236 ATGAACTACA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:138318 original size:16 final size:17
Alignment explanation
Indices: 138299--138347 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
138289 AGAAAGAGAG
*
138299 AAAGAATGAAAAAAA-A
1 AAAGAAAGAAAAAAATA
138315 AAAGAAAGAAAAAAATA
1 AAAGAAAGAAAAAAATA
*
138332 AAA-AGAGATAAAAAAT
1 AAAGAAAGA-AAAAAAT
138348 TTATAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 18 0.62
17 11 0.38
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (17 bp):
AAAGAAAGAAAAAAATA
Found at i:138322 original size:20 final size:18
Alignment explanation
Indices: 138297--138337 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
138287 ATAGAAAGAG
138297 AGAAAGAATGAAAAAAAAAA
1 AGAAAGAA--AAAAAAAAAA
*
138317 AGAAAGAAAAAAATAAAA
1 AGAAAGAAAAAAAAAAAA
138335 AGA
1 AGA
138338 GATAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 12 0.60
20 8 0.40
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (18 bp):
AGAAAGAAAAAAAAAAAA
Found at i:138344 original size:17 final size:17
Alignment explanation
Indices: 138307--138347 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
138297 AGAAAGAATG
138307 AAAAAA-AAAAAGAAAGA
1 AAAAAATAAAAAG-AAGA
138324 AAAAAATAAAAAG-AGA
1 AAAAAATAAAAAGAAGA
138340 TAAAAAAT
1 -AAAAAAT
138348 TTATAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 3 0.14
17 13 0.59
18 6 0.27
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (17 bp):
AAAAAATAAAAAGAAGA
Found at i:138461 original size:32 final size:32
Alignment explanation
Indices: 138425--138490 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
138415 ATATTATAAA
138425 TTTATATAACATTT-ATAAATATTTTTTATATT
1 TTTATAT-ACATTTCATAAATATTTTTTATATT
* ** *
138457 TTTATATTCATTTCATATTTATTTTTTGTATT
1 TTTATATACATTTCATAAATATTTTTTATATT
138489 TT
1 TT
138491 ATTTTAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 5 0.17
32 24 0.83
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.65
Consensus pattern (32 bp):
TTTATATACATTTCATAAATATTTTTTATATT
Found at i:139986 original size:18 final size:18
Alignment explanation
Indices: 139963--140016 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
139953 TGTATTATCT
139963 TATTTAAATAAAATAATA
1 TATTTAAATAAAATAATA
**
139981 TATTTAAATAATTTAATA
1 TATTTAAATAAAATAATA
*
139999 TTTTTAAAATAAAA-AATA
1 TATTT-AAATAAAATAATA
140017 ATAATAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 24 0.80
19 6 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TATTTAAATAAAATAATA
Found at i:143290 original size:11 final size:11
Alignment explanation
Indices: 143252--143320 Score: 59
Period size: 11 Copynumber: 6.0 Consensus size: 11
143242 AATAAATAAA
143252 TTTT-TAAATT
1 TTTTATAAATT
*
143262 TTTTATAAATAAAA
1 TTTTATAAAT---T
*
143276 TTTTATTAATT
1 TTTTATAAATT
*
143287 TTTTATAAATAA
1 TTTTATAAAT-T
*
143299 TTTTATTAATT
1 TTTTATAAATT
143310 TTTTATAAATT
1 TTTTATAAATT
143321 AAATTTTTTA
Statistics
Matches: 46, Mismatches: 8, Indels: 9
0.73 0.13 0.14
Matches are distributed among these distances:
10 4 0.09
11 24 0.52
12 9 0.20
14 9 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTTATAAATT
Found at i:143292 original size:25 final size:24
Alignment explanation
Indices: 143243--143327 Score: 129
Period size: 23 Copynumber: 3.5 Consensus size: 24
143233 TTTAGGGTGA
*
143243 ATAAATAAATTTT-TAAATTTTTT
1 ATAAATAAATTTTATTAATTTTTT
143266 ATAAATAAAATTTTATTAATTTTTT
1 ATAAAT-AAATTTTATTAATTTTTT
143291 ATAAAT-AATTTTATTAATTTTTT
1 ATAAATAAATTTTATTAATTTTTT
143314 ATAAATTAAATTTT
1 ATAAA-TAAATTTT
143328 TTATAATTAA
Statistics
Matches: 57, Mismatches: 1, Indels: 6
0.89 0.02 0.09
Matches are distributed among these distances:
23 28 0.49
24 8 0.14
25 21 0.37
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
ATAAATAAATTTTATTAATTTTTT
Found at i:143327 original size:16 final size:15
Alignment explanation
Indices: 143306--143337 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
143296 TAATTTTATT
143306 AATTTTTTATAAATTA
1 AATTTTTTAT-AATTA
143322 AATTTTTTATAATTA
1 AATTTTTTATAATTA
143337 A
1 A
143338 TAGTGATAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
AATTTTTTATAATTA
Found at i:147325 original size:16 final size:16
Alignment explanation
Indices: 147306--147340 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
147296 AAAAATAATT
147306 TAAAAAATATAAA-AAA
1 TAAAAAATA-AAATAAA
147322 TAAAAAATAAAATAAA
1 TAAAAAATAAAATAAA
147338 TAA
1 TAA
147341 TGTAAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 3 0.17
16 15 0.83
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (16 bp):
TAAAAAATAAAATAAA
Found at i:147337 original size:28 final size:28
Alignment explanation
Indices: 147294--147351 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
147284 AAAATTTTTT
**
147294 TAAAAAATAATTTAAAAAATATAAAAAA
1 TAAAAAATAAAATAAAAAATATAAAAAA
* * *
147322 TAAAAAATAAAATAAATAATGTAAATAA
1 TAAAAAATAAAATAAAAAATATAAAAAA
147350 TA
1 TA
147352 TAATGAATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (28 bp):
TAAAAAATAAAATAAAAAATATAAAAAA
Found at i:147679 original size:14 final size:15
Alignment explanation
Indices: 147654--147682 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
147644 GTTAAACATA
147654 TTGATTTAATTCGAT
1 TTGATTTAATTCGAT
147669 TTGATTT-ATTCGAT
1 TTGATTTAATTCGAT
147683 AGCAAATTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.24, C:0.07, G:0.14, T:0.55
Consensus pattern (15 bp):
TTGATTTAATTCGAT
Found at i:147847 original size:22 final size:23
Alignment explanation
Indices: 147807--147851 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
147797 ATTTAAATTA
147807 TTATTTAATTATTAAAAATATTT
1 TTATTTAATTATTAAAAATATTT
*
147830 TTATTTTATTA-TAAAAATATTT
1 TTATTTAATTATTAAAAATATTT
147852 ATAAAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TTATTTAATTATTAAAAATATTT
Found at i:147853 original size:20 final size:22
Alignment explanation
Indices: 147807--147851 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
147797 ATTTAAATTA
147807 TTATTTAATTATTAAAAATATTT
1 TTATTTAATTATTAAAAATA-TT
*
147830 TTATTTTATTA-TAAAAATATT
1 TTATTTAATTATTAAAAATATT
147851 T
1 T
147852 ATAAAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 3 0.14
22 8 0.38
23 10 0.48
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTATTTAATTATTAAAAATATT
Found at i:147855 original size:12 final size:12
Alignment explanation
Indices: 147838--147865 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
147828 TTTTATTTTA
147838 TTATAAAAATAT
1 TTATAAAAATAT
147850 TTATAAAAATAT
1 TTATAAAAATAT
147862 TTAT
1 TTAT
147866 TTTTTTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
TTATAAAAATAT
Found at i:148760 original size:3 final size:3
Alignment explanation
Indices: 148752--148779 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
148742 GGCGCAGACA
148752 ACG ACG ACG ACG ACG ACG ACG ACG ACG A
1 ACG ACG ACG ACG ACG ACG ACG ACG ACG A
148780 TAAGGCATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.32, G:0.32, T:0.00
Consensus pattern (3 bp):
ACG
Found at i:150371 original size:12 final size:12
Alignment explanation
Indices: 150354--150378 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
150344 TTATGTTCTG
150354 AAAACAATATTA
1 AAAACAATATTA
150366 AAAACAATATTA
1 AAAACAATATTA
150378 A
1 A
150379 TAGGTGAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAACAATATTA
Found at i:156733 original size:11 final size:11
Alignment explanation
Indices: 156719--156744 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
156709 AAAGATAATA
156719 AAAATATATGT
1 AAAATATATGT
156730 AAAATATATGT
1 AAAATATATGT
156741 AAAA
1 AAAA
156745 GTTAAAAAAA
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:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (11 bp):
AAAATATATGT
Found at i:157151 original size:24 final size:24
Alignment explanation
Indices: 157124--157248 Score: 82
Period size: 24 Copynumber: 5.2 Consensus size: 24
157114 TGAAAGAAAA
157124 AATAAAAATTTAGTAAATGTGATT
1 AATAAAAATTTAGTAAATGTGATT
* * **
157148 AAT-AATATGTT-GTTAAATAG-AAAA
1 AATAAAAAT-TTAG-TAAAT-GTGATT
157172 AATAAAAATTTAGTAAATGTGATT
1 AATAAAAATTTAGTAAATGTGATT
* * **
157196 AAT-AATATGTT-GTTAAATAG-AAAA
1 AATAAAAAT-TTAG-TAAAT-GTGATT
157220 AATAAAAATTTAGTAAATGTGATT
1 AATAAAAATTTAGTAAATGTGATT
157244 AATAA
1 AATAA
157249 TATGTTGTTA
Statistics
Matches: 73, Mismatches: 16, Indels: 24
0.65 0.14 0.21
Matches are distributed among these distances:
23 12 0.16
24 49 0.67
25 12 0.16
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (24 bp):
AATAAAAATTTAGTAAATGTGATT
Found at i:157172 original size:48 final size:48
Alignment explanation
Indices: 157118--157262 Score: 290
Period size: 48 Copynumber: 3.0 Consensus size: 48
157108 GTTAGCTGAA
157118 AGAAAAAATAAAAATTTAGTAAATGTGATTAATAATATGTTGTTAAAT
1 AGAAAAAATAAAAATTTAGTAAATGTGATTAATAATATGTTGTTAAAT
157166 AGAAAAAATAAAAATTTAGTAAATGTGATTAATAATATGTTGTTAAAT
1 AGAAAAAATAAAAATTTAGTAAATGTGATTAATAATATGTTGTTAAAT
157214 AGAAAAAATAAAAATTTAGTAAATGTGATTAATAATATGTTGTTAAAT
1 AGAAAAAATAAAAATTTAGTAAATGTGATTAATAATATGTTGTTAAAT
157262 A
1 A
157263 CTAAGTTATC
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 97 1.00
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.35
Consensus pattern (48 bp):
AGAAAAAATAAAAATTTAGTAAATGTGATTAATAATATGTTGTTAAAT
Found at i:157260 original size:24 final size:24
Alignment explanation
Indices: 157137--157261 Score: 82
Period size: 24 Copynumber: 5.2 Consensus size: 24
157127 AAAAATTTAG
157137 TAAATGTGATTAATAATATGTTGT
1 TAAATGTGATTAATAATATGTTGT
* ** *
157161 TAAATAG-AAAAAATAAAAAT-TTAG-
1 TAAAT-GTGATTAAT-AATATGTT-GT
157185 TAAATGTGATTAATAATATGTTGT
1 TAAATGTGATTAATAATATGTTGT
* ** *
157209 TAAATAG-AAAAAATAAAAAT-TTAG-
1 TAAAT-GTGATTAAT-AATATGTT-GT
157233 TAAATGTGATTAATAATATGTTGT
1 TAAATGTGATTAATAATATGTTGT
157257 TAAAT
1 TAAAT
157262 ACTAAGTTAT
Statistics
Matches: 73, Mismatches: 16, Indels: 24
0.65 0.14 0.21
Matches are distributed among these distances:
23 12 0.16
24 49 0.67
25 12 0.16
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.38
Consensus pattern (24 bp):
TAAATGTGATTAATAATATGTTGT
Found at i:162310 original size:32 final size:32
Alignment explanation
Indices: 162269--162337 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
162259 CAATGATTTG
*
162269 TATCGATACATAAGTGTTGTATCGATACAATA
1 TATCGATACATAAGTGTTGTATCGATAAAATA
* *
162301 TATCGATACATAAGTTTTGTATCGATAAAATG
1 TATCGATACATAAGTGTTGTATCGATAAAATA
162333 TATCG
1 TATCG
162338 CTAGGAAGCT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (32 bp):
TATCGATACATAAGTGTTGTATCGATAAAATA
Found at i:162325 original size:19 final size:19
Alignment explanation
Indices: 162265--162327 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
162255 ATTTCAATGA
162265 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
162284 GTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
*
162299 --TATATCGATACATAAGT
1 TTTGTATCGATACATAAGT
162316 TTTGTATCGATA
1 TTTGTATCGATA
162328 AAATGTATCG
Statistics
Matches: 35, Mismatches: 3, Indels: 12
0.70 0.06 0.24
Matches are distributed among these distances:
13 10 0.29
15 2 0.06
17 2 0.06
19 21 0.60
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:166200 original size:13 final size:13
Alignment explanation
Indices: 166182--166208 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
166172 GAACATAACT
166182 AATGTATCGATAC
1 AATGTATCGATAC
166195 AATGTATCGATAC
1 AATGTATCGATAC
166208 A
1 A
166209 TTAAATAATG
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):
AATGTATCGATAC
Found at i:167729 original size:2 final size:2
Alignment explanation
Indices: 167722--167746 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
167712 GTTATCTCTT
167722 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 T
167747 TCATGCATTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:168621 original size:12 final size:12
Alignment explanation
Indices: 168604--168628 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
168594 TTTTGAGCTC
168604 CCCTCAAAATAG
1 CCCTCAAAATAG
168616 CCCTCAAAATAG
1 CCCTCAAAATAG
168628 C
1 C
168629 TATTCAATGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.36, G:0.08, T:0.16
Consensus pattern (12 bp):
CCCTCAAAATAG
Found at i:171024 original size:283 final size:282
Alignment explanation
Indices: 170496--171039 Score: 782
Period size: 282 Copynumber: 1.9 Consensus size: 282
170486 CACCCTTTCT
* * * **
170496 TTTTTTTTTCTTTCTTGTTAGGCCTAGGTCACCACTCTACAAGCAATTATTTTGTAAGCCACCAC
1 TTTTTTTTTCTTTCTTGTTAGGCCCAAGTCACCACTCTACAAGCAATCATTCCGTAAGCCACCAC
* * * *
170561 TTCAAGTGTTGAGCCTTGTAAGATGGAGCTGACTCTGATACCAATTGGCACAGACCTTTGGAGAA
66 TTCAAGTGTTAAGCCTTGTAAGATGGAGCTGACTCTGATACAAATTGGCACAAACCTTTGGAAAA
* * *
170626 CCACCCCTAAAAGCTAGCTACTGAGGTGTAAGAGCCTAGGTCTATATATACCCATAAAGAAAGCT
131 CCACCCCTAAAAGCTAGCTACTGAGGTGGAAGAGCCTAGATCTATATATACCCACAAAGAAAGCT
* * * * *
170691 TTTTTATTTTAATATAAAATCTAAGTGGATCATAACAATACCCTACGCTTGAAGGACCAACGTCC
196 TTTCTATTTCAATATAAAATCCAAGTAGATCATAACAATACCCCACGCTTGAAGGACCAACGTCC
170756 TATTTGGTCATGGTTAGCACCC
261 TATTTGGTCATGGTTAGCACCC
* * * * *
170778 TTTTTTTTTCTTTCTTGTTAGGCCCAAGTCACCACTCTGCAGGCCATCATTCCGTGAGCCACCAT
1 TTTTTTTTTCTTTCTTGTTAGGCCCAAGTCACCACTCTACAAGCAATCATTCCGTAAGCCACCAC
* * * *
170843 TTCGAGTTTTAAGCCTTGTAAGATGGAGCTGGCTCTGATACAAATTGGCATAAACCTTTGGAAAA
66 TTCAAGTGTTAAGCCTTGTAAGATGGAGCTGACTCTGATACAAATTGGCACAAACCTTTGGAAAA
* *
170908 CCACACCCTAAAAGCTAGCTATTGAGGTGGGAGAGCCTAGATCTATATATACCCACAAAGAAAGC
131 CCAC-CCCTAAAAGCTAGCTACTGAGGTGGAAGAGCCTAGATCTATATATACCCACAAAGAAAGC
* * * * *
170973 TTTTCTATTTCAATGTGAGATCCAAGTAGATCATAGCAATACCCCACGCTTGAAGGACTAACGTC
195 TTTTCTATTTCAATATAAAATCCAAGTAGATCATAACAATACCCCACGCTTGAAGGACCAACGTC
171038 CT
260 CT
171040 CGTTAGTCAC
Statistics
Matches: 228, Mismatches: 33, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
282 116 0.51
283 112 0.49
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (282 bp):
TTTTTTTTTCTTTCTTGTTAGGCCCAAGTCACCACTCTACAAGCAATCATTCCGTAAGCCACCAC
TTCAAGTGTTAAGCCTTGTAAGATGGAGCTGACTCTGATACAAATTGGCACAAACCTTTGGAAAA
CCACCCCTAAAAGCTAGCTACTGAGGTGGAAGAGCCTAGATCTATATATACCCACAAAGAAAGCT
TTTCTATTTCAATATAAAATCCAAGTAGATCATAACAATACCCCACGCTTGAAGGACCAACGTCC
TATTTGGTCATGGTTAGCACCC
Found at i:172329 original size:21 final size:21
Alignment explanation
Indices: 172290--172329 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
172280 GAAAGTTTTC
* *
172290 GATTTTCTTGCGCAGGAGAGT
1 GATTTTCTTGCGAAAGAGAGT
*
172311 GATTTTCTTGGGAAAGAGA
1 GATTTTCTTGCGAAAGAGA
172330 ACGTCGATAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.10, G:0.33, T:0.33
Consensus pattern (21 bp):
GATTTTCTTGCGAAAGAGAGT
Found at i:172571 original size:3 final size:3
Alignment explanation
Indices: 172563--172591 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
172553 AGTTATTACT
172563 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
172592 TTTTATTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:172948 original size:2 final size:2
Alignment explanation
Indices: 172941--172990 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
172931 TTTTCAGTAT
172941 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
172983 GA GA GA GA
1 GA GA GA GA
172991 ATATGTTTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:176565 original size:2 final size:2
Alignment explanation
Indices: 176558--176701 Score: 198
Period size: 2 Copynumber: 72.0 Consensus size: 2
176548 ACACCCATAC
* *
176558 AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AC 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
* * **
176600 AT AT AT AT AC AT AT AT AT AT AT AC AT AT AT AT AT AT GC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * **
176642 AT AT AT AT AT AT AC AT AT AT AT AT AT AC AT AT AT AT AT AT GC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
176684 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
176702 GCATGCTTGT
Statistics
Matches: 122, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 122 1.00
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.44
Consensus pattern (2 bp):
AT
Found at i:177860 original size:4 final size:4
Alignment explanation
Indices: 177851--177879 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
177841 CTTTAGGCCT
177851 TGGC TGGC TGGC TGGC TGGC TGGC TGGC T
1 TGGC TGGC TGGC TGGC TGGC TGGC TGGC T
177880 ACGAACAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.00, C:0.24, G:0.48, T:0.28
Consensus pattern (4 bp):
TGGC
Found at i:180517 original size:2 final size:2
Alignment explanation
Indices: 180510--180535 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
180500 TATCTATCAC
180510 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
180536 TTAAGCTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:181489 original size:16 final size:16
Alignment explanation
Indices: 181459--181504 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
181449 TATAAAAAAT
*
181459 TATATCATTTAATTAAA
1 TATAT-ATTTTATTAAA
181476 TATATATTTTATTAAA
1 TATATATTTTATTAAA
* *
181492 TATTTATTATATT
1 TATATATTTTATT
181505 TTTAAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 21 0.81
17 5 0.19
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (16 bp):
TATATATTTTATTAAA
Found at i:181502 original size:21 final size:22
Alignment explanation
Indices: 181474--181524 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
181464 CATTTAATTA
**
181474 AATATATATTTTATTAAATATTT
1 AATATAT-TTTTAAAAAATATTT
*
181497 ATTATATTTTTAAAAAATATTT
1 AATATATTTTTAAAAAATATTT
181519 AATATA
1 AATATA
181525 ACTATTATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
AATATATTTTTAAAAAATATTT
Found at i:185880 original size:31 final size:28
Alignment explanation
Indices: 185845--185902 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
185835 TAAAAAAATT
*
185845 ACTTATAATTTTAAGTAAGATTATTTATTTG
1 ACTTATAA-TTT-A-TAAAATTATTTATTTG
*
185876 ACTTATCATTTATAAAATTATTTATTT
1 ACTTATAATTTATAAAATTATTTATTT
185903 AATGTACTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 14 0.56
29 1 0.04
30 3 0.12
31 7 0.28
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.53
Consensus pattern (28 bp):
ACTTATAATTTATAAAATTATTTATTTG
Found at i:186772 original size:16 final size:16
Alignment explanation
Indices: 186753--186808 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 16
186743 TATATCATAA
186753 TTATATTTAAAATATT
1 TTATATTTAAAATATT
186769 TTATATTTACGTAAAT-TT
1 TTATATTTA---AAATATT
186787 TTATATATTAAAA-A-T
1 TTATAT-TTAAAATATT
186802 TTATATT
1 TTATATT
186809 ATATAAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
14 1 0.03
15 7 0.20
16 12 0.34
18 8 0.23
19 7 0.20
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (16 bp):
TTATATTTAAAATATT
Found at i:187145 original size:12 final size:12
Alignment explanation
Indices: 187128--187152 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
187118 CTTGAAAATA
187128 ATAATAATAATT
1 ATAATAATAATT
187140 ATAATAATAATT
1 ATAATAATAATT
187152 A
1 A
187153 AAATCCAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAATAATAATT
Found at i:187395 original size:2 final size:2
Alignment explanation
Indices: 187388--187414 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
187378 ATTATGGAGC
187388 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
187415 ACTTCAGCTT
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:189439 original size:10 final size:10
Alignment explanation
Indices: 189424--189456 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
189414 AAAGATTTGG
189424 ATTTATATAT
1 ATTTATATAT
189434 ATTTATATAT
1 ATTTATATAT
*
189444 ATATATATAT
1 ATTTATATAT
189454 ATT
1 ATT
189457 AAAAAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
ATTTATATAT
Found at i:190173 original size:21 final size:21
Alignment explanation
Indices: 190134--190173 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
190124 CATTGGTTGG
**
190134 ATGAAAAAATATATTTTTTGA
1 ATGAAAAAATATAACTTTTGA
*
190155 ATGAAAAAATGTAACTTTT
1 ATGAAAAAATATAACTTTT
190174 ATGATCAAAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.10, T:0.40
Consensus pattern (21 bp):
ATGAAAAAATATAACTTTTGA
Found at i:191046 original size:16 final size:16
Alignment explanation
Indices: 190984--191046 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
190974 ATGTTAATAA
* * *
190984 TTTATTATATATAAAT
1 TTTATAATATTTATAT
*
191000 TTTAAAATATTTACATAT
1 TTTATAATATTT--ATAT
*
191018 TTATATCATATTTATAT
1 TT-TATAATATTTATAT
191035 TTTATAATATTT
1 TTTATAATATTT
191047 TTATATCATA
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
16 18 0.49
17 6 0.16
18 5 0.14
19 8 0.22
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTATAATATTTATAT
Found at i:191049 original size:18 final size:18
Alignment explanation
Indices: 190998--191052 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
190988 TTATATATAA
* **
190998 ATTTTAAAATATTTACAT
1 ATTTTATAATATTTTTAT
*
191016 A-TTTAT-ATCATATTTAT
1 ATTTTATAAT-ATTTTTAT
191033 ATTTTATAATATTTTTAT
1 ATTTTATAATATTTTTAT
191051 AT
1 AT
191053 CATATTTATA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
16 2 0.07
17 10 0.34
18 15 0.52
19 2 0.07
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTTTATAATATTTTTAT
Found at i:191527 original size:16 final size:16
Alignment explanation
Indices: 191506--191546 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
191496 TAATTTTTTT
191506 TTTTAGATTTAAATTA
1 TTTTAGATTTAAATTA
*
191522 TTTTAGATTTGAATTA
1 TTTTAGATTTAAATTA
191538 TTTTAGATT
1 TTTTAGATT
191547 CGTATCATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.59
Consensus pattern (16 bp):
TTTTAGATTTAAATTA
Found at i:191556 original size:16 final size:16
Alignment explanation
Indices: 191506--191557 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
191496 TAATTTTTTT
** *
191506 TTTTAGATTTAAATTA
1 TTTTAGATTCGAATCA
* *
191522 TTTTAGATTTGAATTA
1 TTTTAGATTCGAATCA
*
191538 TTTTAGATTCGTATCA
1 TTTTAGATTCGAATCA
191554 TTTT
1 TTTT
191558 GAATTCAGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.29, C:0.04, G:0.10, T:0.58
Consensus pattern (16 bp):
TTTTAGATTCGAATCA
Found at i:191557 original size:32 final size:31
Alignment explanation
Indices: 191506--191620 Score: 97
Period size: 32 Copynumber: 3.6 Consensus size: 31
191496 TAATTTTTTT
** *
191506 TTTTAGATTTAAATTATTTTAGATTTGAATTA
1 TTTTAGATTCGAATCATTTT-GATTTGAATTA
* * *
191538 TTTTAGATTCGTATCATTTTGAATTCAGATTA
1 TTTTAGATTCGAATCATTTTGATTTGA-ATTA
* *
191570 TTTT-GAGTTCGGATCATTTTGAGTTTGAGTTA
1 TTTTAGA-TTCGAATCATTTTGA-TTTGAATTA
* *
191602 TTTCAGATTTGAATCATTT
1 TTTTAGATTCGAATCATTT
191621 CAAGTTCGAG
Statistics
Matches: 66, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
31 7 0.11
32 54 0.82
33 5 0.08
ACGTcount: A:0.27, C:0.06, G:0.15, T:0.52
Consensus pattern (31 bp):
TTTTAGATTCGAATCATTTTGATTTGAATTA
Found at i:191592 original size:16 final size:16
Alignment explanation
Indices: 191545--191594 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
191535 TTATTTTAGA
* *
191545 TTCGTATCATTTTGAA
1 TTCGGATCATTTTGAG
* *
191561 TTCAGATTATTTTGAG
1 TTCGGATCATTTTGAG
191577 TTCGGATCATTTTGAG
1 TTCGGATCATTTTGAG
191593 TT
1 TT
191595 TGAGTTATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.22, C:0.10, G:0.18, T:0.50
Consensus pattern (16 bp):
TTCGGATCATTTTGAG
Found at i:191604 original size:16 final size:16
Alignment explanation
Indices: 191534--191594 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
191524 TTAGATTTGA
*
191534 ATTATTTT-AGATTCGT
1 ATTATTTTGAG-TTCGG
* * *
191550 ATCATTTTGAATTCAG
1 ATTATTTTGAGTTCGG
191566 ATTATTTTGAGTTCGG
1 ATTATTTTGAGTTCGG
*
191582 ATCATTTTGAGTT
1 ATTATTTTGAGTT
191595 TGAGTTATTT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
16 35 0.97
17 1 0.03
ACGTcount: A:0.25, C:0.08, G:0.16, T:0.51
Consensus pattern (16 bp):
ATTATTTTGAGTTCGG
Found at i:192723 original size:31 final size:32
Alignment explanation
Indices: 192678--192761 Score: 107
Period size: 31 Copynumber: 2.7 Consensus size: 32
192668 CGGATTAATT
192678 ATTCAGGTCATTTCGAGTTCGAATCATTTCAG
1 ATTCAGGTCATTTCGAGTTCGAATCATTTCAG
* * * *
192710 ATTCGGGTC-TTTCGGGTTCGAGTCATTTCGG
1 ATTCAGGTCATTTCGAGTTCGAATCATTTCAG
* *
192741 ATTCAGATCATTTCTAGTTCG
1 ATTCAGGTCATTTCGAGTTCG
192762 GGTCATTCTG
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
31 26 0.60
32 17 0.40
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (32 bp):
ATTCAGGTCATTTCGAGTTCGAATCATTTCAG
Found at i:192729 original size:15 final size:16
Alignment explanation
Indices: 192684--192768 Score: 66
Period size: 16 Copynumber: 5.4 Consensus size: 16
192674 AATTATTCAG
*
192684 GTCATTTCGAGTTCGA
1 GTCATTTCGGGTTCGA
* * * *
192700 ATCATTTCAGATTCGG
1 GTCATTTCGGGTTCGA
192716 GTC-TTTCGGGTTCGA
1 GTCATTTCGGGTTCGA
*
192731 GTCATTTCGGATTC-A
1 GTCATTTCGGGTTCGA
** *
192746 GATCATTTCTAGTTCGG
1 G-TCATTTCGGGTTCGA
192763 GTCATT
1 GTCATT
192769 CTGGATTTGA
Statistics
Matches: 52, Mismatches: 14, Indels: 6
0.72 0.19 0.08
Matches are distributed among these distances:
15 14 0.27
16 37 0.71
17 1 0.02
ACGTcount: A:0.18, C:0.19, G:0.24, T:0.40
Consensus pattern (16 bp):
GTCATTTCGGGTTCGA
Found at i:192738 original size:47 final size:48
Alignment explanation
Indices: 192684--192798 Score: 130
Period size: 47 Copynumber: 2.4 Consensus size: 48
192674 AATTATTCAG
* *
192684 GTCATTTCGAGTTCGAATCATTTC-AGATTCGGGTCTTTC-GGGTTCGA
1 GTCATTTCGAGTTCGAATCATTTCTAG-TTCGGGTCATTCTGGATTCGA
*
192731 GTCATTTCG-GATTC-AGATCATTTCTAGTTCGGGTCATTCTGGATTTGA
1 GTCATTTCGAG-TTCGA-ATCATTTCTAGTTCGGGTCATTCTGGATTCGA
* *
192779 GTTATTTCGAGTTCGGATCA
1 GTCATTTCGAGTTCGAATCA
192799 ATTCGAATTT
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
46 2 0.04
47 31 0.54
48 23 0.40
49 1 0.02
ACGTcount: A:0.18, C:0.17, G:0.24, T:0.40
Consensus pattern (48 bp):
GTCATTTCGAGTTCGAATCATTTCTAGTTCGGGTCATTCTGGATTCGA
Found at i:192982 original size:3 final size:3
Alignment explanation
Indices: 192974--193017 Score: 54
Period size: 3 Copynumber: 14.3 Consensus size: 3
192964 ATAAATTTTA
*
192974 ATT ATT ATT ATT ATT ATT ATT ATT ATCT -TT AATT ATA ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT -ATT ATT ATT ATT A
193018 CGTTATATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
2 1 0.03
3 32 0.89
4 3 0.08
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:193736 original size:13 final size:14
Alignment explanation
Indices: 193708--193738 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
193698 AATTCAAGCC
193708 TTATATATTATACT
1 TTATATATTATACT
193722 TTATATATT-TACT
1 TTATATATTATACT
193735 TTAT
1 TTAT
193739 GTTTGACATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.61
Consensus pattern (14 bp):
TTATATATTATACT
Found at i:193900 original size:25 final size:28
Alignment explanation
Indices: 193867--193921 Score: 80
Period size: 25 Copynumber: 2.1 Consensus size: 28
193857 TGAAGAAAAT
*
193867 ATATAAAAATTAAATTAAA-A-TTTTAA
1 ATATAAAAATAAAATTAAATATTTTTAA
193893 ATAT-AAAATAAAATTAAATATTTTTAA
1 ATATAAAAATAAAATTAAATATTTTTAA
193920 AT
1 AT
193922 TTTTAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 13 0.50
26 5 0.19
27 8 0.31
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (28 bp):
ATATAAAAATAAAATTAAATATTTTTAA
Found at i:193932 original size:7 final size:8
Alignment explanation
Indices: 193912--193936 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
193902 AAAATTAAAT
193912 ATTTTTAA
1 ATTTTTAA
193920 ATTTTTAA
1 ATTTTTAA
193928 ATTTTTAA
1 ATTTTTAA
193936 A
1 A
193937 AAATAATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
ATTTTTAA
Found at i:193949 original size:15 final size:14
Alignment explanation
Indices: 193927--193960 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
193917 TAAATTTTTA
193927 AATTTTTAAAAAAT
1 AATTTTTAAAAAAT
193941 AATTATTTAAAAAAT
1 AATT-TTTAAAAAAT
*
193956 TATTT
1 AATTT
193961 GTATCTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AATTTTTAAAAAAT
Found at i:194037 original size:18 final size:18
Alignment explanation
Indices: 194015--194054 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
194005 ACTATTTTTT
194015 ATTTTTAAAATAA-AATA
1 ATTTTTAAAATAATAATA
194032 ATTTTTAAAATAATAAT-
1 ATTTTTAAAATAATAATA
194049 ATTTTT
1 ATTTTT
194055 TTACTCTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 19 0.86
18 3 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTTTTAAAATAATAATA
Found at i:194528 original size:16 final size:17
Alignment explanation
Indices: 194499--194531 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
194489 TTGAATTGGT
194499 AAAAAATTAATTAATTTA
1 AAAAAATT-ATTAATTTA
194517 AAAAAATT-TTAATTT
1 AAAAAATTATTAATTT
194532 TATATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAAAAATTATTAATTTA
Found at i:194542 original size:15 final size:15
Alignment explanation
Indices: 194522--194603 Score: 67
Period size: 15 Copynumber: 5.0 Consensus size: 15
194512 ATTTAAAAAA
194522 ATTTTAATTTTATAT
1 ATTTTAATTTTATAT
*
194537 ATTTTAATTTTATAA
1 ATTTTAATTTTATAT
194552 ATTTTATTTATATTTAATAAT
1 ATTTTA---AT-TTT-AT-AT
*
194573 ATTTAAATATTTA-AGT
1 ATTTTAAT-TTTATA-T
194589 ATTTTAATTTTATAT
1 ATTTTAATTTTATAT
194604 TAAAAAGTAT
Statistics
Matches: 55, Mismatches: 4, Indels: 16
0.73 0.05 0.21
Matches are distributed among these distances:
15 26 0.47
16 9 0.16
17 1 0.02
18 8 0.15
19 3 0.05
20 2 0.04
21 6 0.11
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (15 bp):
ATTTTAATTTTATAT
Found at i:194566 original size:20 final size:20
Alignment explanation
Indices: 194539--194576 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
194529 TTTTATATAT
*
194539 TTTAATTTTATAA-ATTTTA
1 TTTAATTTAATAATATTTTA
194558 TTTATATTTAATAATATTT
1 TTTA-ATTTAATAATATTT
194577 AAATATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 8 0.50
21 4 0.25
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTAATTTAATAATATTTTA
Found at i:197043 original size:22 final size:23
Alignment explanation
Indices: 197000--197048 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
196990 TGTTTAGATT
* * *
197000 TGTTTGTTTATTGTTTATGAACA
1 TGTTTGTTAATTGTTCACGAACA
197023 TGTTT-TTAATTGTTCACGAACA
1 TGTTTGTTAATTGTTCACGAACA
197045 TGTT
1 TGTT
197049 CATTTGGTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.22, C:0.08, G:0.16, T:0.53
Consensus pattern (23 bp):
TGTTTGTTAATTGTTCACGAACA
Found at i:207502 original size:28 final size:28
Alignment explanation
Indices: 207449--207502 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
207439 AAAAAAGTAT
*
207449 TTATTAGTAAAATAAAAGTAGAAATTCA
1 TTATTAGTAAAATAAAAGAAGAAATTCA
*
207477 TTATTAGTAAAATTAAAA-AAGGAATT
1 TTATTAGTAAAA-TAAAAGAAGAAATT
207503 TATACCACAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 18 0.78
29 5 0.22
ACGTcount: A:0.54, C:0.02, G:0.11, T:0.33
Consensus pattern (28 bp):
TTATTAGTAAAATAAAAGAAGAAATTCA
Found at i:212414 original size:8 final size:8
Alignment explanation
Indices: 212403--212430 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
212393 TATTTTAATT
212403 TTAAAATA
1 TTAAAATA
212411 TTAAAATA
1 TTAAAATA
212419 TTAAAATA
1 TTAAAATA
212427 TTAA
1 TTAA
212431 TATAAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
TTAAAATA
Found at i:212442 original size:14 final size:14
Alignment explanation
Indices: 212397--212438 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 14
212387 ATTTAATATT
*
212397 TTAATTTTAAAATA
1 TTAATATTAAAATA
212411 TTAAAATATTAAAATA
1 TT--AATATTAAAATA
212427 TTAATA-TAAAAT
1 TTAATATTAAAAT
212439 TATTTTATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 6 0.24
14 6 0.24
16 13 0.52
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAATATTAAAATA
Found at i:212549 original size:27 final size:27
Alignment explanation
Indices: 212459--212537 Score: 79
Period size: 26 Copynumber: 2.8 Consensus size: 27
212449 GTATAATTTT
* * *
212459 TAATATTTATATTTTGAATATTATTAAACA
1 TAATATTTAAATTTT-AATAATA-T-AATA
212489 TACATATTTAAATTTTAATAATATAATA
1 TA-ATATTTAAATTTTAATAATATAATA
*
212517 TAATATTT-ATTTTTAATAATA
1 TAATATTTAAATTTTAATAATA
212538 AATCATTTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
26 12 0.27
27 6 0.14
28 5 0.11
29 1 0.02
30 8 0.18
31 12 0.27
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.51
Consensus pattern (27 bp):
TAATATTTAAATTTTAATAATATAATA
Found at i:212841 original size:29 final size:27
Alignment explanation
Indices: 212797--212860 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 27
212787 AATATTTTAA
212797 AATA-TTTAATGTTTTAATAATAAATAGT
1 AATATTTTAATGTTTTAAT-ATAAATA-T
* *
212825 ATTATTTTAAT-TATTTAATATTAATAT
1 AATATTTTAATGT-TTTAATATAAATAT
212852 AATATTTTA
1 AATATTTTA
212861 GTATTAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
27 9 0.29
28 10 0.32
29 12 0.39
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (27 bp):
AATATTTTAATGTTTTAATATAAATAT
Found at i:212865 original size:26 final size:28
Alignment explanation
Indices: 212797--212872 Score: 70
Period size: 26 Copynumber: 2.8 Consensus size: 28
212787 AATATTTTAA
*
212797 AATA-TTTAATGT-TTTAATAATAAATAGT
1 AATATTTTAA-GTATTTAAT-ATTAATAGT
* *
212825 ATTATTTTAATTATTTAATATTAATA-T
1 AATATTTTAAGTATTTAATATTAATAGT
*
212852 AATATTTT-AGTATTAAATATT
1 AATATTTTAAGTATTTAATATT
212873 TTTATTAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
26 11 0.28
27 8 0.20
28 10 0.25
29 11 0.28
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (28 bp):
AATATTTTAAGTATTTAATATTAATAGT
Found at i:212994 original size:11 final size:11
Alignment explanation
Indices: 212978--213082 Score: 56
Period size: 11 Copynumber: 9.5 Consensus size: 11
212968 AAATTGTAAC
212978 ATAATATTTTA
1 ATAATATTTTA
*
212989 ATAATATTATA
1 ATAATATTTTA
* * **
213000 TTATTATTAAA
1 ATAATATTTTA
* * *
213011 ATATTAGTATAA
1 ATAATA-TTTTA
213023 ATAATATTTTA
1 ATAATATTTTA
*
213034 ATAAT-TATT-
1 ATAATATTTTA
213043 ATAATATTTT-
1 ATAATATTTTA
*
213053 A-AATATTTAA
1 ATAATATTTTA
213063 ATAATTGATGTTTA
1 ATAA-T-AT-TTTA
213077 ATAATA
1 ATAATA
213083 AATAGTATAT
Statistics
Matches: 73, Mismatches: 14, Indels: 13
0.73 0.14 0.13
Matches are distributed among these distances:
9 12 0.16
10 8 0.11
11 33 0.45
12 10 0.14
13 3 0.04
14 7 0.10
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.50
Consensus pattern (11 bp):
ATAATATTTTA
Found at i:213042 original size:12 final size:11
Alignment explanation
Indices: 212978--213048 Score: 61
Period size: 11 Copynumber: 6.3 Consensus size: 11
212968 AAATTGTAAC
*
212978 ATAATATTTTA
1 ATAATATTATA
212989 ATAATATTATA
1 ATAATATTATA
* * *
213000 TTATTATTAAA
1 ATAATATTATA
* *
213011 ATATTAGTATAA
1 ATAATATTAT-A
*
213023 ATAATATTTTA
1 ATAATATTATA
213034 ATAATTATTATA
1 ATAA-TATTATA
213046 ATA
1 ATA
213049 TTTTAAATAT
Statistics
Matches: 47, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
11 30 0.64
12 17 0.36
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (11 bp):
ATAATATTATA
Found at i:213066 original size:20 final size:19
Alignment explanation
Indices: 213020--213105 Score: 66
Period size: 21 Copynumber: 4.2 Consensus size: 19
213010 AATATTAGTA
*
213020 TAAATAATATTTTAATAAT
1 TAAATAATATTTTAATATT
*
213039 TATTATAATATTTTAAATATT
1 TA-AATAATATTTT-AATATT
*
213060 TAAATAATTGATGTTTAATA-A
1 TAAATAA-T-AT-TTTAATATT
213081 TAAATAGTATATTTTAAATATT
1 TAAATA--ATATTTT-AATATT
213103 TAA
1 TAA
213106 TATTAATATA
Statistics
Matches: 53, Mismatches: 5, Indels: 15
0.73 0.07 0.21
Matches are distributed among these distances:
19 2 0.04
20 17 0.32
21 20 0.38
22 10 0.19
23 4 0.08
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (19 bp):
TAAATAATATTTTAATATT
Found at i:216200 original size:2 final size:2
Alignment explanation
Indices: 216193--216235 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
216183 CGAGCTAACG
216193 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
216235 T
1 T
216236 TGCTCTCATG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:217278 original size:17 final size:17
Alignment explanation
Indices: 217256--217297 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
217246 TTTAAATTTT
217256 TATTATATTCTATA-TAA
1 TATTATATT-TATATTAA
217273 TATTAT-TTTATATTAA
1 TATTATATTTATATTAA
217289 TATTTATAT
1 TA-TTATAT
217298 ATTTTTATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 4 0.18
16 7 0.32
17 10 0.45
18 1 0.05
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (17 bp):
TATTATATTTATATTAA
Found at i:231130 original size:12 final size:12
Alignment explanation
Indices: 231113--231138 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
231103 GTATCAAGTT
231113 ATTACCTTACTA
1 ATTACCTTACTA
231125 ATTACCTTACTA
1 ATTACCTTACTA
231137 AT
1 AT
231139 GCTGATGAAC
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:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (12 bp):
ATTACCTTACTA
Found at i:240702 original size:17 final size:17
Alignment explanation
Indices: 240682--240721 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
240672 ATGATTATTT
240682 TTAAA-ATTAAATTAAAA
1 TTAAATATTAAA-TAAAA
*
240699 TTAAATATTATATAAAA
1 TTAAATATTAAATAAAA
240716 TTAAAT
1 TTAAAT
240722 TGATTTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TTAAATATTAAATAAAA
Found at i:240862 original size:11 final size:11
Alignment explanation
Indices: 240846--240870 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
240836 TTTTTATTTT
240846 ATAAAAATTAA
1 ATAAAAATTAA
240857 ATAAAAATTAA
1 ATAAAAATTAA
240868 ATA
1 ATA
240871 TAATTTGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
ATAAAAATTAA
Found at i:241587 original size:17 final size:17
Alignment explanation
Indices: 241565--241597 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
241555 ATATTATATA
241565 AAATATGAAATAAAATG
1 AAATATGAAATAAAATG
*
241582 AAATATGATATAAAAT
1 AAATATGAAATAAAAT
241598 ATTATATGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (17 bp):
AAATATGAAATAAAATG
Found at i:242621 original size:13 final size:13
Alignment explanation
Indices: 242605--242629 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
242595 TGAGGATATT
242605 ATTAAAAAAATTA
1 ATTAAAAAAATTA
242618 ATTAAAAAAATT
1 ATTAAAAAAATT
242630 TAAAATTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTAAAAAAATTA
Found at i:243714 original size:21 final size:20
Alignment explanation
Indices: 243690--243732 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
243680 AATTTTTAAC
*
243690 TTTTTATTGATTTAAATAAAA
1 TTTTAATTGATTTAAA-AAAA
**
243711 TTTTAATTTTTTTAAAAAAA
1 TTTTAATTGATTTAAAAAAA
243731 TT
1 TT
243733 ATATTTAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTTAATTGATTTAAAAAAA
Found at i:243939 original size:15 final size:15
Alignment explanation
Indices: 243919--243970 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 15
243909 AAATTTTTTA
243919 TTAATTAAATTAATT
1 TTAATTAAATTAATT
243934 TTAATTAAATTTAATTTT
1 TTAATTAAA-TTAA--TT
243952 TTATATT-AATTAATT
1 TTA-ATTAAATTAATT
243967 TTAA
1 TTAA
243971 ATTATTTCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
14 1 0.03
15 14 0.42
16 4 0.12
17 4 0.12
18 7 0.21
19 3 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTAATTAAATTAATT
Found at i:244324 original size:19 final size:20
Alignment explanation
Indices: 244298--244346 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
244288 AAATTTTAAG
*
244298 ATATTTTATAGTG-ATTTTCA
1 ATATTTTATAATGTATTTT-A
*
244318 A-ATTTTAAAATGTATTTTA
1 ATATTTTATAATGTATTTTA
244337 ATATTTTATA
1 ATATTTTATA
244347 TCAATTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.55
Consensus pattern (20 bp):
ATATTTTATAATGTATTTTA
Found at i:244716 original size:20 final size:22
Alignment explanation
Indices: 244693--244733 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
244683 AAACTAAAAC
244693 ATAA-TTAAA-AATTTTATACT
1 ATAATTTAAATAATTTTATACT
244713 ATAATTTAAATTAATTTTATA
1 ATAATTTAAA-TAATTTTATA
244734 AATATTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 5 0.28
23 9 0.50
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
ATAATTTAAATAATTTTATACT
Found at i:244959 original size:14 final size:12
Alignment explanation
Indices: 244929--244971 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
244919 AAATATTTAA
*
244929 TTTTTTTACTTT
1 TTTTTTTTCTTT
*
244941 TTTTTTCTCTTT
1 TTTTTTTTCTTT
*
244953 TTATTTTTCTTT
1 TTTTTTTTCTTT
244965 TTGTTTT
1 TT-TTTT
244972 CTCTATTAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 22 0.88
13 3 0.12
ACGTcount: A:0.05, C:0.09, G:0.02, T:0.84
Consensus pattern (12 bp):
TTTTTTTTCTTT
Found at i:244972 original size:11 final size:11
Alignment explanation
Indices: 244929--244973 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
244919 AAATATTTAA
*
244929 TTTTTTTACTT
1 TTTTTTTTCTT
244940 TTTTTTTCTCTT
1 TTTTTTT-TCTT
244952 TTTATTTTTCTT
1 TTT-TTTTTCTT
*
244964 TTTGTTTTCT
1 TTTTTTTTCT
244974 CTATTAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 13 0.43
12 13 0.43
13 4 0.13
ACGTcount: A:0.04, C:0.11, G:0.02, T:0.82
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:245280 original size:15 final size:15
Alignment explanation
Indices: 245260--245297 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
245250 ATTTATAAAT
*
245260 ATAAAAAGGAAAAAG
1 ATAAAAAAGAAAAAG
245275 ATAAAAAAGAAAAA-
1 ATAAAAAAGAAAAAG
245289 AGTAAAAAA
1 A-TAAAAAA
245298 CTCAAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 1 0.05
15 20 0.95
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (15 bp):
ATAAAAAAGAAAAAG
Found at i:245283 original size:16 final size:15
Alignment explanation
Indices: 245262--245297 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
245252 TTATAAATAT
*
245262 AAAAAGGAAAAAGATA
1 AAAAAGAAAAAAG-TA
245278 AAAAAGAAAAAAGTA
1 AAAAAGAAAAAAGTA
245293 AAAAA
1 AAAAA
245298 CTCAAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.06
Consensus pattern (15 bp):
AAAAAGAAAAAAGTA
Found at i:246728 original size:91 final size:91
Alignment explanation
Indices: 246573--246754 Score: 337
Period size: 91 Copynumber: 2.0 Consensus size: 91
246563 GCTGAAAGTA
*
246573 AAAGTAAATTTCCATGAAAAACAAGTCGGCCATATTAATATCACTTACCCATTTTCTCAAAATCC
1 AAAGTAAATTTCCATGAAAAACAAGTCGGCCATAGTAATATCACTTACCCATTTTCTCAAAATCC
246638 AAACTCAATTTCCAATTGCCTTAGTT
66 AAACTCAATTTCCAATTGCCTTAGTT
* *
246664 AAAGTAAATTTCCATGAAAAACGAGTCGGCCATAGTAATATTACTTACCCATTTTCTCAAAATCC
1 AAAGTAAATTTCCATGAAAAACAAGTCGGCCATAGTAATATCACTTACCCATTTTCTCAAAATCC
246729 AAACTCAATTTCCAATTGCCTTAGTT
66 AAACTCAATTTCCAATTGCCTTAGTT
246755 TATGTGATCA
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
91 88 1.00
ACGTcount: A:0.37, C:0.23, G:0.09, T:0.32
Consensus pattern (91 bp):
AAAGTAAATTTCCATGAAAAACAAGTCGGCCATAGTAATATCACTTACCCATTTTCTCAAAATCC
AAACTCAATTTCCAATTGCCTTAGTT
Found at i:246823 original size:2 final size:2
Alignment explanation
Indices: 246816--246851 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
246806 TGCTTGTTTA
246816 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
246852 TTATTAGTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:247288 original size:22 final size:22
Alignment explanation
Indices: 247260--247305 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
247250 TTCAAAAACA
*
247260 TTTAATAAATTTAAATT-TAAAT
1 TTTAATAAA-TAAAATTATAAAT
*
247282 TTTAATATATAAAATTATAAAT
1 TTTAATAAATAAAATTATAAAT
247304 TT
1 TT
247306 ATTTTTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTAATAAATAAAATTATAAAT
Found at i:248798 original size:3 final size:3
Alignment explanation
Indices: 248792--248829 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
248782 ATCATCATTG
248792 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
248830 TATAGAAGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:250622 original size:21 final size:20
Alignment explanation
Indices: 250598--250644 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
250588 TATATTAAAA
250598 ATATATTATTAAATTAAATAT
1 ATATATTATT-AATTAAATAT
* *
250619 ATATTTTATTAAGTAAATAT
1 ATATATTATTAATTAAATAT
250639 -TATATT
1 ATATATT
250645 TAATATTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 5 0.22
20 9 0.39
21 9 0.39
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
ATATATTATTAATTAAATAT
Found at i:250629 original size:16 final size:16
Alignment explanation
Indices: 250590--250650 Score: 50
Period size: 16 Copynumber: 3.6 Consensus size: 16
250580 TTTAATTATA
*
250590 TATTAAAAATATATTAT
1 TATTAAATATATATT-T
250607 TAAATTAAATATATATTT
1 T--ATTAAATATATATTT
* * *
250625 TATTAAGTAAATATTA
1 TATTAAATATATATTT
*
250641 TATTTAATAT
1 TATTAAATAT
250651 TTATATAACA
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
16 19 0.54
17 1 0.03
18 2 0.06
19 13 0.37
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
TATTAAATATATATTT
Found at i:250645 original size:21 final size:21
Alignment explanation
Indices: 250598--250645 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
250588 TATATTAAAA
* *
250598 ATATATTATTAAATTAAATAT
1 ATATTTTATTAAAGTAAATAT
250619 ATATTTTATT-AAGTAAATATT
1 ATATTTTATTAAAGTAAATA-T
250640 ATATTT
1 ATATTT
250646 AATATTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
ATATTTTATTAAAGTAAATAT
Found at i:251201 original size:21 final size:22
Alignment explanation
Indices: 251175--251216 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
251165 GATTTTGATT
251175 TATTAATTTA-TATTATATTTA
1 TATTAATTTATTATTATATTTA
*
251196 TATTAATTTATTTTTATATTT
1 TATTAATTTATTATTATATTT
251217 GTATAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
TATTAATTTATTATTATATTTA
Found at i:251285 original size:18 final size:19
Alignment explanation
Indices: 251248--251286 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
251238 TATTATATTT
* *
251248 TTATATAAATTTTCATATA
1 TTATATAAATATTAATATA
251267 TTATATAAA-ATTAATATA
1 TTATATAAATATTAATATA
251285 TT
1 TT
251287 TTTTTTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (19 bp):
TTATATAAATATTAATATA
Found at i:251295 original size:11 final size:12
Alignment explanation
Indices: 251281--251310 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
251271 ATAAAATTAA
251281 TATATTTTTT-T
1 TATATTTTTTAT
251292 TATATTTTTTAT
1 TATATTTTTTAT
251304 TATATTT
1 TATATTT
251311 AAATTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TATATTTTTTAT
Found at i:251311 original size:18 final size:20
Alignment explanation
Indices: 251290--251339 Score: 50
Period size: 22 Copynumber: 2.5 Consensus size: 20
251280 ATATATTTTT
251290 TTTATATTTTTT-AT-TATA
1 TTTATATTTTTTGATATATA
*
251308 TTTAAATTATTTTGATCATATA
1 TTTATATT-TTTTGAT-ATATA
*
251330 ATTATATTTT
1 TTTATATTTT
251340 ATTTAAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 7 0.28
19 4 0.16
20 2 0.08
21 2 0.08
22 10 0.40
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (20 bp):
TTTATATTTTTTGATATATA
Found at i:255482 original size:22 final size:22
Alignment explanation
Indices: 255450--255510 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 22
255440 AATATCTTTG
*
255450 TTAAATGTGTTAGGTAAACATA
1 TTAAGTGTGTTAGGTAAACATA
* * *
255472 TTAGGTGTGTTAGGTGAGCATA
1 TTAAGTGTGTTAGGTAAACATA
255494 TTAAGTGTGTTAGGTAA
1 TTAAGTGTGTTAGGTAA
255511 CGTGTTAGGT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.31, C:0.03, G:0.28, T:0.38
Consensus pattern (22 bp):
TTAAGTGTGTTAGGTAAACATA
Found at i:260943 original size:22 final size:21
Alignment explanation
Indices: 260911--261053 Score: 114
Period size: 22 Copynumber: 6.8 Consensus size: 21
260901 GATAAACTAC
*
260911 TGATAAAATAATAGTATATAAT
1 TGAT-AAATAATAGTAAATAAT
260933 TGATAACATAATAGTAAAT--T
1 TGATAA-ATAATAGTAAATAAT
* * *
260953 T-ATAATTAAAAATAAATAA-
1 TGATAAATAATAGTAAATAAT
* *
260972 TGATAAGATAATAGTATATGAT
1 TGATAA-ATAATAGTAAATAAT
** * *
260994 AAATAAAATAATAATAAATTAT
1 TGAT-AAATAATAGTAAATAAT
261016 TGATAAATAATAGTAAATAAT
1 TGATAAATAATAGTAAATAAT
*
261037 TAATAATATAATAGTAA
1 TGATAA-ATAATAGTAA
261054 CTAACGAAAT
Statistics
Matches: 94, Mismatches: 19, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
18 9 0.10
19 5 0.05
20 6 0.06
21 31 0.33
22 41 0.44
23 2 0.02
ACGTcount: A:0.57, C:0.01, G:0.08, T:0.34
Consensus pattern (21 bp):
TGATAAATAATAGTAAATAAT
Done.