Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 2 of 235
Found at i:230725 original size:13 final size:13
Alignment explanation
Indices: 230707--230731 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
230697 CAAGAAATAT
230707 ATTATAATAAAAA
1 ATTATAATAAAAA
230720 ATTATAATAAAA
1 ATTATAATAAAA
230732 TAAGAAACAG
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):
ATTATAATAAAAA
Found at i:233697 original size:12 final size:12
Alignment explanation
Indices: 233677--233749 Score: 52
Period size: 12 Copynumber: 6.6 Consensus size: 12
233667 ATTTAGGATT
*
233677 ATTTCGATTTCA
1 ATTTTGATTTCA
*
233689 ATTTTGATTTCG
1 ATTTTGATTTCA
*
233701 ATTCTGA--T--
1 ATTTTGATTTCA
*
233709 -TTT-GATTTCG
1 ATTTTGATTTCA
233719 ATTTCT-ATTTCA
1 ATTT-TGATTTCA
233731 ATTTTGATTTCA
1 ATTTTGATTTCA
233743 ATTTTGA
1 ATTTTGA
233750 AACACTCATT
Statistics
Matches: 48, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
6 2 0.04
7 2 0.04
8 1 0.02
10 1 0.02
11 4 0.08
12 38 0.79
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.56
Consensus pattern (12 bp):
ATTTTGATTTCA
Found at i:233700 original size:18 final size:18
Alignment explanation
Indices: 233677--233749 Score: 85
Period size: 18 Copynumber: 4.1 Consensus size: 18
233667 ATTTAGGATT
233677 ATTTCGATTTCAATTTTG
1 ATTTCGATTTCAATTTTG
*
233695 ATTTCGA-TTCTGATTTTG
1 ATTTCGATTTC-AATTTTG
* **
233713 ATTTCGATTTCTATTTCA
1 ATTTCGATTTCAATTTTG
*
233731 ATTTTGATTTCAATTTTG
1 ATTTCGATTTCAATTTTG
233749 A
1 A
233750 AACACTCATT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
17 3 0.07
18 39 0.87
19 3 0.07
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.56
Consensus pattern (18 bp):
ATTTCGATTTCAATTTTG
Found at i:233782 original size:18 final size:18
Alignment explanation
Indices: 233760--233836 Score: 75
Period size: 18 Copynumber: 4.3 Consensus size: 18
233750 AACACTCATT
*
233760 GATTTTGATTTTGATTTCA
1 GATTTAGATTTTGATTT-A
* * *
233779 -ATTTCGATCTCGATTTA
1 GATTTAGATTTTGATTTA
* *
233796 GCTTTAGATTTAGATTTA
1 GATTTAGATTTTGATTTA
*
233814 GATTTAGATTTTGATTTT
1 GATTTAGATTTTGATTTA
233832 GATTT
1 GATTT
233837 GGGGTTATTT
Statistics
Matches: 47, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
17 1 0.02
18 46 0.98
ACGTcount: A:0.23, C:0.06, G:0.16, T:0.55
Consensus pattern (18 bp):
GATTTAGATTTTGATTTA
Found at i:233852 original size:6 final size:6
Alignment explanation
Indices: 233790--233836 Score: 67
Period size: 6 Copynumber: 7.8 Consensus size: 6
233780 TTTCGATCTC
* * *
233790 GATTTA GCTTTA GATTTA GATTTA GATTTA GATTTT GATTTT GATTT
1 GATTTA GATTTA GATTTA GATTTA GATTTA GATTTA GATTTA GATTT
233837 GGGGTTATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.26, C:0.02, G:0.17, T:0.55
Consensus pattern (6 bp):
GATTTA
Found at i:233949 original size:48 final size:48
Alignment explanation
Indices: 233888--234064 Score: 255
Period size: 48 Copynumber: 3.6 Consensus size: 48
233878 GCCATGTGCA
* * *
233888 TGATATTTATTGTTTTTATCTGCCATTGTATGGATGTCATTATCAAAC
1 TGATGTTTATTGTTTGTATCTGCCATTGTATGGATGCCATTATCAAAC
233936 TGATGTTTATTGTTTGTATCTGCCATTGTATGGATGCCATTATCAAAC
1 TGATGTTTATTGTTTGTATCTGCCATTGTATGGATGCCATTATCAAAC
* *
233984 TGATGTTTGTTTATTGTTTGTATCTGTCATTATATGGATGCCATTATCAAAC
1 TGA----TGTTTATTGTTTGTATCTGCCATTGTATGGATGCCATTATCAAAC
* *
234036 TGATGTTTATTGTGTATATCTGCCATTGT
1 TGATGTTTATTGTTTGTATCTGCCATTGT
234065 TTGTATCCAA
Statistics
Matches: 116, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
48 70 0.60
52 46 0.40
ACGTcount: A:0.23, C:0.12, G:0.18, T:0.47
Consensus pattern (48 bp):
TGATGTTTATTGTTTGTATCTGCCATTGTATGGATGCCATTATCAAAC
Found at i:234020 original size:52 final size:52
Alignment explanation
Indices: 233893--234043 Score: 238
Period size: 52 Copynumber: 3.0 Consensus size: 52
233883 GTGCATGATA
* *
233893 TTTATTGTTTTTATCTGCCATTGTATGGATGTCATTATCAAACTGA----TG
1 TTTATTGTTTGTATCTGCCATTGTATGGATGCCATTATCAAACTGATGTTTG
233941 TTTATTGTTTGTATCTGCCATTGTATGGATGCCATTATCAAACTGATGTTTG
1 TTTATTGTTTGTATCTGCCATTGTATGGATGCCATTATCAAACTGATGTTTG
* *
233993 TTTATTGTTTGTATCTGTCATTATATGGATGCCATTATCAAACTGATGTTT
1 TTTATTGTTTGTATCTGCCATTGTATGGATGCCATTATCAAACTGATGTTT
234044 ATTGTGTATA
Statistics
Matches: 95, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
48 44 0.46
52 51 0.54
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.48
Consensus pattern (52 bp):
TTTATTGTTTGTATCTGCCATTGTATGGATGCCATTATCAAACTGATGTTTG
Found at i:235675 original size:27 final size:27
Alignment explanation
Indices: 235645--235705 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 27
235635 GACATCTCTA
235645 TTTTTTCTCTTCTCCT-TCTCT-TTCTTC
1 TTTTTTCTC--CTCCTATCTCTCTTCTTC
* *
235672 -TTTTTCTCCTCCTATTTTTCTTCTTC
1 TTTTTTCTCCTCCTATCTCTCTTCTTC
235698 TTTTTTCT
1 TTTTTTCT
235706 TTTTCTCTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 5 0.17
25 3 0.10
26 14 0.48
27 7 0.24
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.69
Consensus pattern (27 bp):
TTTTTTCTCCTCCTATCTCTCTTCTTC
Found at i:247371 original size:39 final size:36
Alignment explanation
Indices: 247300--247397 Score: 90
Period size: 39 Copynumber: 2.6 Consensus size: 36
247290 AAAAAATAAA
* *
247300 ATAT-ATATTTATATTATTTTTAATTTTTAATTTAAT
1 ATATAATAATTATA-TATTTTTTATTTTTAATTTAAT
* *
247336 ATTTAATAATTATATATTTTTTATTTATTAAAATTTTAT
1 ATATAATAATTATATATTTTTTATTT-TT--AATTTAAT
* *
247375 ATATAGTAATTTTAATATTTTTT
1 ATATAATAATTAT-ATATTTTTT
247398 GAATGTTTAC
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
36 14 0.28
37 10 0.20
39 17 0.34
40 9 0.18
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (36 bp):
ATATAATAATTATATATTTTTTATTTTTAATTTAAT
Found at i:259402 original size:20 final size:21
Alignment explanation
Indices: 259373--259417 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
259363 TTTATTATGT
259373 TATATCATATGAAAAT-TAAA
1 TATATCATATGAAAATCTAAA
* * *
259393 TATATTATATTATAATCTAAA
1 TATATCATATGAAAATCTAAA
259414 TATA
1 TATA
259418 AAAAATATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.42
Consensus pattern (21 bp):
TATATCATATGAAAATCTAAA
Found at i:264785 original size:33 final size:31
Alignment explanation
Indices: 264747--264810 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
264737 GACACTACAG
*
264747 ATATTACTAGACAGTAATGGATTGTCAAAATAT
1 ATATTACTAGACAG--ATGGATTATCAAAATAT
* * *
264780 ATATTAGTTGATAGATGGATTATCAAAATAT
1 ATATTACTAGACAGATGGATTATCAAAATAT
264811 TTGATTGTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 16 0.59
33 11 0.41
ACGTcount: A:0.42, C:0.06, G:0.16, T:0.36
Consensus pattern (31 bp):
ATATTACTAGACAGATGGATTATCAAAATAT
Found at i:269051 original size:2 final size:2
Alignment explanation
Indices: 269044--269093 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
269034 TTCGATGAAA
269044 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
269086 TG TG TG TG
1 TG TG TG TG
269094 AGAGAGAGAG
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:269098 original size:2 final size:2
Alignment explanation
Indices: 269093--269131 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
269083 GTGTGTGTGT
269093 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
269132 GAAGAGGAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:269400 original size:29 final size:31
Alignment explanation
Indices: 269350--269414 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 31
269340 AACTGGATCT
* *
269350 AATTTTTGAAATCTGAAAAATAGAAAAACTA
1 AATTTTTGAAATATGAAAAATACAAAAACTA
*
269381 AATTTTT-AAATAT-AAAAATACAAAAATTA
1 AATTTTTGAAATATGAAAAATACAAAAACTA
269410 AATTT
1 AATTT
269415 CAAAATTTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 19 0.61
30 5 0.16
31 7 0.23
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.34
Consensus pattern (31 bp):
AATTTTTGAAATATGAAAAATACAAAAACTA
Found at i:269420 original size:29 final size:29
Alignment explanation
Indices: 269365--269420 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
269355 TTGAAATCTG
* **
269365 AAAAATAGAAAAACTAAATTTTTAAATAT
1 AAAAATACAAAAACTAAATTTCAAAATAT
*
269394 AAAAATACAAAAATTAAATTTCAAAAT
1 AAAAATACAAAAACTAAATTTCAAAAT
269421 TTTCAAGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (29 bp):
AAAAATACAAAAACTAAATTTCAAAATAT
Found at i:269689 original size:8 final size:9
Alignment explanation
Indices: 269645--269669 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
269635 AAATATCACG
269645 TTAATAAAT
1 TTAATAAAT
269654 TTAATAAAT
1 TTAATAAAT
269663 TTAATAA
1 TTAATAA
269670 TTAAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
TTAATAAAT
Found at i:269698 original size:27 final size:28
Alignment explanation
Indices: 269649--269701 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
269639 ATCACGTTAA
** *
269649 TAAATTTAATAAATTTAATAATTAAAAT
1 TAAATTTAATAAATGAAAAAATTAAAAT
269677 TAAATTTAA-AAATGAAAAAATTAAA
1 TAAATTTAATAAATGAAAAAATTAAA
269702 TTCTGAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 13 0.59
28 9 0.41
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (28 bp):
TAAATTTAATAAATGAAAAAATTAAAAT
Found at i:269718 original size:21 final size:20
Alignment explanation
Indices: 269658--269718 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 20
269648 ATAAATTTAA
*
269658 TAAATTTAATAATT-AAAAT
1 TAAATTTAAAAATTAAAAAT
*
269677 TAAATTTAAAAATGAAAAAAT
1 TAAATTTAAAAAT-TAAAAAT
*
269698 TAAATTCTGAAAATTAAAAAT
1 TAAATT-TAAAAATTAAAAAT
269719 ACAAAATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
19 12 0.34
21 17 0.49
22 6 0.17
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (20 bp):
TAAATTTAAAAATTAAAAAT
Found at i:270838 original size:13 final size:14
Alignment explanation
Indices: 270820--270852 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
270810 TTTAATTTTC
*
270820 AAAATTTCAAAA-A
1 AAAATTTAAAAATA
270833 AAAATTTAAAAATA
1 AAAATTTAAAAATA
270847 AAAATT
1 AAAATT
270853 GCATTTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (14 bp):
AAAATTTAAAAATA
Found at i:270882 original size:30 final size:31
Alignment explanation
Indices: 270848--270933 Score: 113
Period size: 30 Copynumber: 2.8 Consensus size: 31
270838 TTAAAAATAA
*
270848 AAATTGCATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
270878 AAATTTCATTTTGACCCTTAAAC-TTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
270908 AAATTTCACTTAGACCCCTAAACTTT
1 AAATTTCATTTTGACCCCTAAACTTT
270934 CATTAAATTT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
29 4 0.08
30 42 0.88
31 2 0.04
ACGTcount: A:0.29, C:0.24, G:0.05, T:0.42
Consensus pattern (31 bp):
AAATTTCATTTTGACCCCTAAACTTTTCTCT
Found at i:270934 original size:30 final size:30
Alignment explanation
Indices: 270860--270943 Score: 107
Period size: 30 Copynumber: 2.8 Consensus size: 30
270850 ATTGCATTTT
* * *
270860 GACCCCTAAACTTT-TCCTAAATTTCATTTT
1 GACCCCTAAACTTTCT-TTAAATTTCACTTA
*
270890 GACCCTTAAACTTTCTTTAAATTTCACTTA
1 GACCCCTAAACTTTCTTTAAATTTCACTTA
*
270920 GACCCCTAAACTTTCATTAAATTT
1 GACCCCTAAACTTTCTTTAAATTT
270944 TAATCCTAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 46 0.98
31 1 0.02
ACGTcount: A:0.30, C:0.25, G:0.04, T:0.42
Consensus pattern (30 bp):
GACCCCTAAACTTTCTTTAAATTTCACTTA
Found at i:271335 original size:3 final size:3
Alignment explanation
Indices: 271327--271372 Score: 58
Period size: 3 Copynumber: 15.0 Consensus size: 3
271317 GCTAGACTTT
*
271327 GAA GAA GAA GAA GGAA GAA GAA GGAA GAA GAA -AA GAG GAA GAA GAA
1 GAA GAA GAA GAA -GAA GAA GAA -GAA GAA GAA GAA GAA GAA GAA GAA
271373 AGAAAAAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 2 0.05
3 30 0.79
4 6 0.16
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:271345 original size:10 final size:10
Alignment explanation
Indices: 271330--271358 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
271320 AGACTTTGAA
271330 GAAGAAGAAG
1 GAAGAAGAAG
271340 GAAGAAGAAG
1 GAAGAAGAAG
271350 GAAGAAGAA
1 GAAGAAGAA
271359 AAGAGGAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (10 bp):
GAAGAAGAAG
Found at i:271345 original size:13 final size:13
Alignment explanation
Indices: 271327--271372 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
271317 GCTAGACTTT
271327 GAAGAAGAAGAAG
1 GAAGAAGAAGAAG
271340 GAAGAAGAAGGAA-
1 GAAGAAGAA-GAAG
271353 GAAGAA-AAG-AG
1 GAAGAAGAAGAAG
271364 GAAGAAGAA
1 GAAGAAGAA
271373 AGAAAAAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 1 0.03
11 7 0.23
12 4 0.13
13 15 0.50
14 3 0.10
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (13 bp):
GAAGAAGAAGAAG
Found at i:271386 original size:24 final size:24
Alignment explanation
Indices: 271328--271384 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 24
271318 CTAGACTTTG
* *
271328 AAGAAGAAGAAGGAAGAAGAAGGAAG
1 AAGAA-AAG-AGGAAGAAGAAGAAAA
271354 AAGAAAAGAGGAAGAAGAAAGAAAA
1 AAGAAAAGAGGAAGAAG-AAGAAAA
271379 AAGAAA
1 AAGAAA
271385 GAAAAATCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 9 0.32
25 14 0.50
26 5 0.18
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (24 bp):
AAGAAAAGAGGAAGAAGAAGAAAA
Found at i:271511 original size:19 final size:20
Alignment explanation
Indices: 271461--271514 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
271451 CCGACCCAGC
271461 AGCCCAAGAAAAAAACAACA
1 AGCCCAAGAAAAAAACAACA
***
271481 AAAACAA-AAAAAAGA-AACA
1 AGCCCAAGAAAAAA-ACAACA
271500 AGCCCAAGAAAAAAA
1 AGCCCAAGAAAAAAA
271515 AAGAAGAGCA
Statistics
Matches: 26, Mismatches: 6, Indels: 5
0.70 0.16 0.14
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.72, C:0.19, G:0.09, T:0.00
Consensus pattern (20 bp):
AGCCCAAGAAAAAAACAACA
Found at i:271706 original size:20 final size:22
Alignment explanation
Indices: 271681--271723 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
271671 TCGGGTTTCG
271681 AAATTT-TCGTG-TCTTCAAAA
1 AAATTTCTCGTGTTCTTCAAAA
*
271701 AAATTTCTCGTGTTTTTCAAAA
1 AAATTTCTCGTGTTCTTCAAAA
271723 A
1 A
271724 TAAGGTAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 5 0.25
22 9 0.45
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (22 bp):
AAATTTCTCGTGTTCTTCAAAA
Found at i:271880 original size:36 final size:35
Alignment explanation
Indices: 271827--271895 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 35
271817 TAAAAATCGG
* *
271827 AAAATTTTTCGTGTTTTCAAAAATTCCCGTGTTGC
1 AAAAATTTTCATGTTTTCAAAAATTCCCGTGTTGC
*
271862 AAAAATTTTCATGTTTTTCAAAAATTCTCGTGTT
1 AAAAATTTTCATG-TTTTCAAAAATTCCCGTGTT
271896 TTCAAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 11 0.37
36 19 0.63
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (35 bp):
AAAAATTTTCATGTTTTCAAAAATTCCCGTGTTGC
Found at i:271967 original size:17 final size:17
Alignment explanation
Indices: 271827--272179 Score: 178
Period size: 17 Copynumber: 19.9 Consensus size: 17
271817 TAAAAATCGG
*
271827 AAAATTTTTCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
** *
271845 AAAAATTCCCGTGTTGC
1 AAAAATTTTCGTGTTTC
*
271862 AAAAATTTTCATGTTTTTC
1 AAAAATTTTC--GTGTTTC
*
271881 AAAAATTCTCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
* * *
271899 AAAAAAATTCCAAT-TTTC
1 -AAAAATTTTC-GTGTTTC
*
271917 AAAATTTTTCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
**
271935 TAAAAAACTTCTGTGTTTC
1 -AAAAATTTTC-GTGTTTC
271954 AAAAATTTTCGTGTTTC
1 AAAAATTTTCGTGTTTC
* *
271971 TAAAATTTTCGTATTTC
1 AAAAATTTTCGTGTTTC
*
271988 AAAAATTTTCTTGTTTTC
1 AAAAATTTTCGTG-TTTC
* * *
272006 -AAATTTTTCGTATTTAA
1 AAAAATTTTCGTGTTT-C
**
272023 AAAAATCCTCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
*
272041 -AAAA-TTCCAGTGTTTC
1 AAAAATTTTC-GTGTTTC
* *
272057 AAAATTTTTCGTGTTTAAAA
1 AAAAATTTTCGTGTTT---C
**
272077 AAAAATTCCCGT-TTTCC
1 AAAAATTTTCGTGTTT-C
* ** *
272094 AAAAACTTTCACGTTTT
1 AAAAATTTTCGTGTTTC
**
272111 AAGAAATTGACCGTGTTTC
1 AA-AAATT-TTCGTGTTTC
*
272130 ATAAATTTTCGTGTTTC
1 AAAAATTTTCGTGTTTC
* *
272147 AAAGAAATCTCGTGTTTC
1 AAA-AATTTTCGTGTTTC
272165 -AAAATTTTCGTGTTT
1 AAAAATTTTCGTGTTT
272180 TTTTTTTTAA
Statistics
Matches: 244, Mismatches: 68, Indels: 48
0.68 0.19 0.13
Matches are distributed among these distances:
16 20 0.08
17 98 0.40
18 69 0.28
19 44 0.18
20 13 0.05
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.44
Consensus pattern (17 bp):
AAAAATTTTCGTGTTTC
Found at i:281807 original size:19 final size:20
Alignment explanation
Indices: 281783--281820 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
281773 TCATGATAGG
*
281783 TTTTTTATTTATT-TTTTGT
1 TTTTTTATTAATTATTTTGT
281802 TTTTTTATTAATTATTTTG
1 TTTTTTATTAATTATTTTG
281821 AATATCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.79
Consensus pattern (20 bp):
TTTTTTATTAATTATTTTGT
Found at i:282546 original size:21 final size:21
Alignment explanation
Indices: 282507--282546 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
282497 AAAAAAAATT
*
282507 GGTTCAGAGTTTGAAGTTTGA
1 GGTTCAGAGTTTCAAGTTTGA
* *
282528 GGTTCAGGGTTTCAGGTTT
1 GGTTCAGAGTTTCAAGTTT
282547 AGCGTTCGTA
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:0.17, C:0.07, G:0.35, T:0.40
Consensus pattern (21 bp):
GGTTCAGAGTTTCAAGTTTGA
Found at i:283417 original size:31 final size:31
Alignment explanation
Indices: 283382--283440 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
283372 AATGTTAAGT
**
283382 AAGTTTACATTTTGGTCATTAAATTATTAGA
1 AAGTTTACATTTAAGTCATTAAATTATTAGA
* *
283413 AAGTTTCCATTTAAGTTATTAAATTATT
1 AAGTTTACATTTAAGTCATTAAATTATT
283441 TGAGGGTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.36, C:0.07, G:0.10, T:0.47
Consensus pattern (31 bp):
AAGTTTACATTTAAGTCATTAAATTATTAGA
Found at i:286658 original size:13 final size:13
Alignment explanation
Indices: 286637--286680 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 13
286627 TAATACTTAT
286637 TTTTC-TTTAAAA
1 TTTTCATTTAAAA
286649 TTTTCATTTAAAA
1 TTTTCATTTAAAA
*
286662 TTATGTCATATAAAA
1 TT-T-TCATTTAAAA
286677 TTTT
1 TTTT
286681 TAACAGTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 5 0.18
13 10 0.36
14 2 0.07
15 11 0.39
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (13 bp):
TTTTCATTTAAAA
Found at i:291910 original size:20 final size:19
Alignment explanation
Indices: 291882--291919 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
291872 CCCAAAAATA
291882 AAAAAGAGAAAAAGATTAAC
1 AAAAAGAGAAAAA-ATTAAC
*
291902 AAAAGGAGAAAAAATTAA
1 AAAAAGAGAAAAAATTAA
291920 ATTAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.71, C:0.03, G:0.16, T:0.11
Consensus pattern (19 bp):
AAAAAGAGAAAAAATTAAC
Found at i:296929 original size:29 final size:29
Alignment explanation
Indices: 296896--296955 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
296886 AAATTTTGAC
*
296896 TTAATAAAATTTAAACTACTTAATATCAA
1 TTAATAAAATTTAAACTAATTAATATCAA
* *
296925 TTAATGAAATTTAAATTAATTAATATCAA
1 TTAATAAAATTTAAACTAATTAATATCAA
296954 TT
1 TT
296956 TAAAACTAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.42
Consensus pattern (29 bp):
TTAATAAAATTTAAACTAATTAATATCAA
Found at i:304874 original size:22 final size:22
Alignment explanation
Indices: 304828--304870 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
304818 ATATAGTTAT
*
304828 TAAATATTAAAATAATATAATA
1 TAAATATTAAAATAATATAAAA
304850 TAAATATTTAAAA-AAT-TAAAA
1 TAAATA-TTAAAATAATATAAAA
304871 ATAATATGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 4 0.21
22 9 0.47
23 6 0.32
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
TAAATATTAAAATAATATAAAA
Found at i:306398 original size:19 final size:20
Alignment explanation
Indices: 306366--306409 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
306356 TAAAAAACTC
306366 AAAATTCCTTTAAAATAT-AAA
1 AAAATTCC-TTAAAA-ATGAAA
306387 AAAATTCC-TAAAAATGAAA
1 AAAATTCCTTAAAAATGAAA
306406 AAAA
1 AAAA
306410 AAAACCCATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 2 0.09
19 12 0.55
21 8 0.36
ACGTcount: A:0.64, C:0.09, G:0.02, T:0.25
Consensus pattern (20 bp):
AAAATTCCTTAAAAATGAAA
Found at i:306400 original size:20 final size:21
Alignment explanation
Indices: 306366--306410 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
306356 TAAAAAACTC
*
306366 AAAATTCCTTTAAAAT-ATAAA
1 AAAATTCCTTAAAAATGA-AAA
306387 AAAATTCC-TAAAAATGAAAA
1 AAAATTCCTTAAAAATGAAAA
306407 AAAA
1 AAAA
306411 AAACCCATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.64, C:0.09, G:0.02, T:0.24
Consensus pattern (21 bp):
AAAATTCCTTAAAAATGAAAA
Found at i:307943 original size:22 final size:21
Alignment explanation
Indices: 307870--307939 Score: 67
Period size: 21 Copynumber: 3.3 Consensus size: 21
307860 TTTCTTTGGA
307870 ATTAATTT-AATATTTTAAAAT
1 ATTAATTTAAATA-TTTAAAAT
307891 -TATAATTTCAAAT-TTTAAAAT
1 AT-TAATTT-AAATATTTAAAAT
307912 ATTTTAA-TTAAATATTTAAAAT
1 A--TTAATTTAAATATTTAAAAT
307934 ATTAAT
1 ATTAAT
307940 ATTATATCAA
Statistics
Matches: 41, Mismatches: 0, Indels: 16
0.72 0.00 0.28
Matches are distributed among these distances:
20 5 0.12
21 18 0.44
22 11 0.27
23 6 0.15
24 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTAATTTAAATATTTAAAAT
Found at i:312621 original size:21 final size:21
Alignment explanation
Indices: 312595--312635 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
312585 ATCTGCTCAA
* *
312595 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
312616 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
312636 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:317401 original size:21 final size:21
Alignment explanation
Indices: 317375--317415 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
317365 ATCTGCTCAA
* *
317375 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
317396 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
317416 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:322899 original size:3 final size:3
Alignment explanation
Indices: 322891--323176 Score: 88
Period size: 3 Copynumber: 92.3 Consensus size: 3
322881 CTATTTTACC
* * * *
322891 ATT ATT ATT ATT ATC ATT ATT -TGT ATC CTT ATT AAT A-T ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT
* ** * * *
322935 ATT GTT -TCCT CCT ATT ATT ATT AACCT ATT ATT ATT CTT ATT AGT A-T
1 ATT ATT AT--T ATT ATT ATT ATT -A-TT ATT ATT ATT ATT ATT ATT ATT
*
322982 ATT ATT ATT -TCCT ATT CTT -TAT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT AT--T ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT
** * *
323028 ATT CATGT ATT -TCCT CCT ATT ATT ATT AACCT ATT ATT ATT CTT ATT
1 ATT -AT-T ATT AT--T ATT ATT ATT ATT -A-TT ATT ATT ATT ATT ATT
* * *
323075 AGT A-T ATT ATT AACGT ATAT ATT ATT ATT -TAT ATT ATT GTT ATT ATT
1 ATT ATT ATT ATT -A-TT AT-T ATT ATT ATT AT-T ATT ATT ATT ATT ATT
* * * * * * * * *
323122 AAT ACT CTT ATC GTT ACT ATT GTT TTT ATT CCTT -TT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT
323167 ATT ATT ATT A
1 ATT ATT ATT A
323177 CAATTAACAT
Statistics
Matches: 210, Mismatches: 44, Indels: 58
0.67 0.14 0.19
Matches are distributed among these distances:
2 14 0.07
3 170 0.81
4 21 0.10
5 5 0.02
ACGTcount: A:0.28, C:0.10, G:0.03, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:323231 original size:23 final size:23
Alignment explanation
Indices: 323205--323283 Score: 65
Period size: 20 Copynumber: 3.4 Consensus size: 23
323195 TACGGTCACC
323205 ATTATATTTTTTATTTTATTATT
1 ATTATATTTTTTATTTTATTATT
*
323228 ATTACTAATTTTTTATTATCATTATT
1 ATTA-T-ATTTTTTATT-TTATTATT
* * * *
323254 ACTATA-GTATTA--TTATTACT
1 ATTATATTTTTTATTTTATTATT
323274 ATTATATTTT
1 ATTATATTTT
323284 CATCTACATA
Statistics
Matches: 43, Mismatches: 9, Indels: 10
0.69 0.15 0.16
Matches are distributed among these distances:
20 11 0.26
21 1 0.02
23 8 0.19
24 2 0.05
25 11 0.26
26 10 0.23
ACGTcount: A:0.30, C:0.05, G:0.01, T:0.63
Consensus pattern (23 bp):
ATTATATTTTTTATTTTATTATT
Found at i:323240 original size:26 final size:23
Alignment explanation
Indices: 323210--323257 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
323200 TCACCATTAT
*
323210 ATTTTTTATTTTATTATTATTACTA
1 ATTTTTTA--TTATCATTATTACTA
323235 ATTTTTTATTATCATTATTACTA
1 ATTTTTTATTATCATTATTACTA
323258 TAGTATTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 14 0.64
25 8 0.36
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (23 bp):
ATTTTTTATTATCATTATTACTA
Found at i:324082 original size:28 final size:28
Alignment explanation
Indices: 324039--324094 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
324029 GCAAGCTCAT
324039 TCTCAAAAGTTCGAGATATCGTGTCCTA
1 TCTCAAAAGTTCGAGATATCGTGTCCTA
* *
324067 TCTCAAAAGTTTGAGATGTCGTGTCCTA
1 TCTCAAAAGTTCGAGATATCGTGTCCTA
324095 ACTTACTGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (28 bp):
TCTCAAAAGTTCGAGATATCGTGTCCTA
Found at i:327456 original size:21 final size:21
Alignment explanation
Indices: 327430--327481 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
327420 TCACTTCGTT
327430 TCTTTTTGTCCAAATTACTTC
1 TCTTTTTGTCCAAATTACTTC
* *
327451 TCTTTTTGTCCAAGTTGCTTC
1 TCTTTTTGTCCAAATTACTTC
327472 TCTTTTTGTC
1 TCTTTTTGTC
327482 TAACTCAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.12, C:0.23, G:0.10, T:0.56
Consensus pattern (21 bp):
TCTTTTTGTCCAAATTACTTC
Found at i:327897 original size:40 final size:39
Alignment explanation
Indices: 327856--327970 Score: 117
Period size: 40 Copynumber: 2.9 Consensus size: 39
327846 CATTTGGATA
*
327856 AAAAACGCCACTAAAAATAAGCATTAGCGGCGCTTTTAT
1 AAAAACGCCGCTAAAAATAAGCATTAGCGGCGCTTTTAT
* ** * * *
327895 AAAAACACCGCTAAAGGTCGAGCATTAGCAGCACTTTT-T
1 AAAAACGCCGCTAAAAAT-AAGCATTAGCGGCGCTTTTAT
* *
327934 GGAAAACGCCGCTAAAAATAAGCATTACCGGCG-TTTT
1 -AAAAACGCCGCTAAAAATAAGCATTAGCGGCGCTTTT
327971 CAAAAAAGTG
Statistics
Matches: 59, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
38 4 0.07
39 25 0.42
40 30 0.51
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.23
Consensus pattern (39 bp):
AAAAACGCCGCTAAAAATAAGCATTAGCGGCGCTTTTAT
Found at i:328082 original size:41 final size:41
Alignment explanation
Indices: 328025--328227 Score: 316
Period size: 41 Copynumber: 5.0 Consensus size: 41
328015 TGAGTTTTTG
* *
328025 GGGCCTTTAGTGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* *
328066 GGGCCTTTAGCGGCGTTTTGGAAGAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* *
328107 AGGCCTTTAGCGGCGTTTTTGAATAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* * * *
328148 TGACCTTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGCTT
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
328189 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
328228 CCGCTTTTGA
Statistics
Matches: 149, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 149 1.00
ACGTcount: A:0.19, C:0.23, G:0.29, T:0.29
Consensus pattern (41 bp):
GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
Found at i:328691 original size:14 final size:15
Alignment explanation
Indices: 328663--328695 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
328653 AAGGTTTATA
328663 GATTATGGAATTAGG
1 GATTATGGAATTAGG
328678 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
328692 GATT
1 GATT
328696 CTGGTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:328933 original size:14 final size:14
Alignment explanation
Indices: 328914--328987 Score: 69
Period size: 14 Copynumber: 5.3 Consensus size: 14
328904 TAAATAAGAT
*
328914 TTAGGGGTTAGTAG
1 TTAGGGGTTAGGAG
*
328928 TTAGGGGTTAGGGG
1 TTAGGGGTTAGGAG
*
328942 TTAGGGGTTAGGGG
1 TTAGGGGTTAGGAG
**
328956 TTAAAGGTTA-GAGG
1 TTAGGGGTTAGGA-G
* *
328970 TTAGAGGTTAAGAG
1 TTAGGGGTTAGGAG
328984 TTAG
1 TTAG
328988 TGATTTAGGG
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
13 1 0.02
14 49 0.94
15 2 0.04
ACGTcount: A:0.24, C:0.00, G:0.45, T:0.31
Consensus pattern (14 bp):
TTAGGGGTTAGGAG
Found at i:328937 original size:7 final size:7
Alignment explanation
Indices: 328914--328979 Score: 78
Period size: 7 Copynumber: 9.4 Consensus size: 7
328904 TAAATAAGAT
328914 TTAGGGG
1 TTAGGGG
**
328921 TTAGTAG
1 TTAGGGG
328928 TTAGGGG
1 TTAGGGG
328935 TTAGGGG
1 TTAGGGG
328942 TTAGGGG
1 TTAGGGG
328949 TTAGGGG
1 TTAGGGG
**
328956 TTAAAGG
1 TTAGGGG
*
328963 TTAGAGG
1 TTAGGGG
*
328970 TTAGAGG
1 TTAGGGG
328977 TTA
1 TTA
328980 AGAGTTAGTG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 52 1.00
ACGTcount: A:0.23, C:0.00, G:0.45, T:0.32
Consensus pattern (7 bp):
TTAGGGG
Found at i:328986 original size:21 final size:21
Alignment explanation
Indices: 328927--328987 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
328917 GGGGTTAGTA
* * *
328927 GTTAGGGGTTAGGGGTTAGGG
1 GTTAGGGGTTAAGAGTTAGAG
328948 GTTAGGGGTTAA-AGGTTAGAG
1 GTTAGGGGTTAAGA-GTTAGAG
*
328969 GTTAGAGGTTAAGAGTTAG
1 GTTAGGGGTTAAGAGTTAG
328988 TGATTTAGGG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
21 33 0.97
22 1 0.03
ACGTcount: A:0.25, C:0.00, G:0.46, T:0.30
Consensus pattern (21 bp):
GTTAGGGGTTAAGAGTTAGAG
Found at i:333467 original size:43 final size:43
Alignment explanation
Indices: 333407--333497 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
333397 CTTTGAGTTC
* * * *
333407 ATTA-CAAGATTTCCTTGATTAAGTAAATGTATTATATCTTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATATTTT
*
333449 ATTACCAAGATTTACTTGATTAAGAAAATGCATTGTATATTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATATTTT
333492 ATTACC
1 ATTACC
333498 TTGCATATGT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 4 0.09
43 39 0.91
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.44
Consensus pattern (43 bp):
ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATATTTT
Found at i:333842 original size:43 final size:43
Alignment explanation
Indices: 333772--334038 Score: 284
Period size: 43 Copynumber: 6.3 Consensus size: 43
333762 AAGATATATT
* **
333772 TTTAGTGGCGTTTGTGTTAAAAGCGCCGCTAAAGGTCTAT-TC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTATGTC
* * * * *
333814 TATAGCGGCATTTGTGGGAAAAAGCGCCGCTAAAGCTCAATATC
1 TTTAGCGGCGTTTGTGGG-AAAAGCGCCGCTAAAGGTCTATGTC
*
333858 -TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCT-TGGTT
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTAT-GTC
*
333900 TTTAGCGGCGTTTGCGAGG--AAGCGCCGCTAAAGGTCT-TGGTC
1 TTTAGCGGCGTTTGTG-GGAAAAGCGCCGCTAAAGGTCTAT-GTC
* * *
333942 TTTAGTGGC-TTTTTGGG-GAAGCGCCGCTAAAGGTC-ATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTAT-GTC
*
333983 TTTAGCGGCGTTTGTGGGAAAAACGCCGCTAAAGGTCT-TAGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTAT-GTC
334026 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
334039 ATTTATAAAA
Statistics
Matches: 192, Mismatches: 23, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
40 2 0.01
41 35 0.18
42 69 0.36
43 82 0.43
44 4 0.02
ACGTcount: A:0.21, C:0.18, G:0.31, T:0.30
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTATGTC
Found at i:333987 original size:83 final size:83
Alignment explanation
Indices: 333792--334030 Score: 254
Period size: 84 Copynumber: 2.8 Consensus size: 83
333782 TTTGTGTTAA
* * * * *
333792 AAGCGCCGCTAAAGGTCTAT--TCTATAGCGGCATTTGTGGGAAAAAGCGCCGCTAAAGCTCAAT
1 AAGCGCCGCTAAAGGTC-ATGGTCTTTAGCGGCGTTTGCGGG-AAAA-CGCCGCTAAAGGTC-TT
* * *
333855 A-TC-TTAGCGGCGTTTGTGGGAA
62 AGTCTTTAGTGGC-TTTTTGGG-G
* * * *
333877 AAGCGCCGCTAAAGGTCTTGGTTTTTAGCGGCGTTTGCGAGG-AAGCGCCGCTAAAGGTCTTGGT
1 AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGCG-GGAAAACGCCGCTAAAGGTCTTAGT
333941 CTTTAGTGGCTTTTTGGGG
65 CTTTAGTGGCTTTTTGGGG
*
333960 AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAACGCCGCTAAAGGTCTTAGT
1 AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGCGGG-AAAACGCCGCTAAAGGTCTTAGT
334025 CTTTAG
65 CTTTAG
334031 CGGCGTTTAT
Statistics
Matches: 130, Mismatches: 17, Indels: 15
0.80 0.10 0.09
Matches are distributed among these distances:
82 2 0.02
83 37 0.28
84 49 0.38
85 26 0.20
86 14 0.11
87 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.28
Consensus pattern (83 bp):
AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGCGGGAAAACGCCGCTAAAGGTCTTAGTC
TTTAGTGGCTTTTTGGGG
Found at i:334164 original size:22 final size:21
Alignment explanation
Indices: 334130--334174 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
334120 TTTAGTGGCG
* *
334130 CTAAAAAATGCCGCTAAAGGC
1 CTAAAAAACGCCGCTAAAAGC
*
334151 CTAAAAAAGCGCCGTTAAAAGC
1 CTAAAAAA-CGCCGCTAAAAGC
334173 CT
1 CT
334175 GTTTTGGTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.42, C:0.24, G:0.18, T:0.16
Consensus pattern (21 bp):
CTAAAAAACGCCGCTAAAAGC
Found at i:335176 original size:29 final size:28
Alignment explanation
Indices: 335114--335169 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
335104 TGTATTGATA
* * *
335114 AATTAGACTTGGTTTACGTAAAAATATC
1 AATTAGACTTGGTTTACCTAAAAAAAAC
335142 AATTAGACTTGGTTTACCTAAAAAAAAC
1 AATTAGACTTGGTTTACCTAAAAAAAAC
335170 TGATTAGGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (28 bp):
AATTAGACTTGGTTTACCTAAAAAAAAC
Found at i:338979 original size:11 final size:11
Alignment explanation
Indices: 338963--338987 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
338953 AAACAAGTAA
338963 ATTATAAATAT
1 ATTATAAATAT
338974 ATTATAAATAT
1 ATTATAAATAT
338985 ATT
1 ATT
338988 CCTTTAAACA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
ATTATAAATAT
Found at i:340857 original size:12 final size:12
Alignment explanation
Indices: 340840--340868 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
340830 TAAATTTTAT
340840 TTATTATATATA
1 TTATTATATATA
340852 TTATTATATATA
1 TTATTATATATA
340864 TTATT
1 TTATT
340869 TTTTTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTATTATATATA
Found at i:347932 original size:13 final size:12
Alignment explanation
Indices: 347893--347946 Score: 53
Period size: 13 Copynumber: 4.7 Consensus size: 12
347883 CTTAATCCTA
347893 AAATAATAAAAT
1 AAATAATAAAAT
347905 -AA-AATAATAAT
1 AAATAATAA-AAT
347916 AAATAATAAAACT
1 AAATAATAAAA-T
*
347929 AAATAA-AACA-
1 AAATAATAAAAT
347939 AAATAATA
1 AAATAATA
347947 TATTCTATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
10 11 0.31
11 6 0.17
12 7 0.19
13 12 0.33
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (12 bp):
AAATAATAAAAT
Found at i:347942 original size:23 final size:23
Alignment explanation
Indices: 347892--347946 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
347882 GCTTAATCCT
347892 AAAATAATAAAATAAAATAATAA
1 AAAATAATAAAATAAAATAATAA
*
347915 TAAATAATAAAACT-AAATAA-AA
1 AAAATAATAAAA-TAAAATAATAA
347937 CAAAATAATA
1 -AAAATAATA
347947 TATTCTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 2 0.07
23 25 0.89
24 1 0.04
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.22
Consensus pattern (23 bp):
AAAATAATAAAATAAAATAATAA
Found at i:348245 original size:17 final size:18
Alignment explanation
Indices: 348213--348246 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
348203 AGTTTTAAAT
*
348213 ATTTTTATAAAGTATTTA
1 ATTTTTATAAAATATTTA
348231 ATTTTTA-AAAATATTT
1 ATTTTTATAAAATATTT
348247 TTAGACAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (18 bp):
ATTTTTATAAAATATTTA
Found at i:354921 original size:42 final size:43
Alignment explanation
Indices: 354875--354965 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 43
354865 AGATATAGTA
* *
354875 TAATAATGAAAATATAAATA-GATAAAAATCATAATA-AATGAG
1 TAATAATGAAAATAAAAATATAATAAAAATCATAATACAATG-G
* *
354917 TAATAA-GAAAATAAAAATATAATAATAGTCATAATACAATGG
1 TAATAATGAAAATAAAAATATAATAAAAATCATAATACAATGG
354959 TAATAAT
1 TAATAAT
354966 AATTACAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
41 12 0.29
42 26 0.62
43 4 0.10
ACGTcount: A:0.60, C:0.03, G:0.09, T:0.27
Consensus pattern (43 bp):
TAATAATGAAAATAAAAATATAATAAAAATCATAATACAATGG
Found at i:354939 original size:19 final size:19
Alignment explanation
Indices: 354873--354941 Score: 52
Period size: 19 Copynumber: 3.4 Consensus size: 19
354863 ATAGATATAG
*
354873 TATAATAATGAAAATATAAA
1 TATAATAA-GAAAATAAAAA
*
354893 TA-GATAA-AAATCATAATAAA
1 TATAATAAGAAA--ATAA-AAA
354913 TGAGTAATAAGAAAATAAAAA
1 T-A-TAATAAGAAAATAAAAA
354934 TATAATAA
1 TATAATAA
354942 TAGTCATAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 15
0.68 0.05 0.26
Matches are distributed among these distances:
17 3 0.08
19 13 0.33
20 7 0.18
21 5 0.13
22 4 0.10
23 4 0.10
24 3 0.08
ACGTcount: A:0.65, C:0.01, G:0.07, T:0.26
Consensus pattern (19 bp):
TATAATAAGAAAATAAAAA
Found at i:355171 original size:14 final size:14
Alignment explanation
Indices: 355152--355195 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
355142 AAAATAATAC
355152 TATATATAAATATA
1 TATATATAAATATA
*
355166 TATATATACATATA
1 TATATATAAATATA
* * *
355180 TGTACATAAAAATA
1 TATATATAAATATA
355194 TA
1 TA
355196 CCCTAATATA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.39
Consensus pattern (14 bp):
TATATATAAATATA
Found at i:355254 original size:141 final size:141
Alignment explanation
Indices: 355024--355364 Score: 349
Period size: 141 Copynumber: 2.4 Consensus size: 141
355014 AAAATAATAC
* * * *
355024 TATATATAAATATATATATATAATGAAAATACACACTACTATATAATAATAATAACAATAATAAT
1 TATATATATATACATATATATAATAAAAATACACACTAATATATAATAATAATAACAATAATAAT
* *
355089 AATATAAAAATACAAAGAGCAAATAT-A-ATAA-A-AATATTAAATTAAAGTAATAAAAAATAAT
66 AATATAAAAATACAAAAAGCAAATATAATATAATAGAATATTAAAATAAAGTAAT-AAAAATAAT
355150 ACTATATATAAA
130 ACTATATATAAA
* * * **
355162 TATATATATATACATATATGTACATAAAAATATACCCTAATATATATGATAATAATAGTAATAAT
1 TATATATATATACATATATATA-ATAAAAATACACACTAATATATA--ATAATAATAACAATAAT
* * * * *
355227 AATAGTATTAAAATGCAAAAAGTAAATATAATATAATAGTAATATTAAAATAAAGTAATTAAAAT
63 AATAATATAAAAATACAAAAAGCAAATATAATATAATAG-AATATTAAAATAAAGTAATAAAAAT
*
355292 AGTACTATATATAAA
127 AATACTATATATAAA
* * * * *
355307 -A-ATGTATATACGTACATATGTAATAAAACATACA-TC-AATAT-TAATAGTAATAACAATA
1 TATATATATATAC--ATATATATAATAAAA-ATACACACTAATATATAATAATAATAACAATA
355365 GAAGTGATAA
Statistics
Matches: 168, Mismatches: 24, Indels: 20
0.79 0.11 0.09
Matches are distributed among these distances:
138 19 0.11
139 19 0.11
140 12 0.07
141 39 0.23
142 3 0.02
143 18 0.11
144 9 0.05
145 31 0.18
146 18 0.11
ACGTcount: A:0.57, C:0.06, G:0.05, T:0.32
Consensus pattern (141 bp):
TATATATATATACATATATATAATAAAAATACACACTAATATATAATAATAATAACAATAATAAT
AATATAAAAATACAAAAAGCAAATATAATATAATAGAATATTAAAATAAAGTAATAAAAATAATA
CTATATATAAA
Found at i:355283 original size:16 final size:17
Alignment explanation
Indices: 355245--355285 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
355235 TAAAATGCAA
*
355245 AAAGTAA-ATATAATAT
1 AAAGTAATATATAAAAT
355261 AATAGTAATAT-TAAAAT
1 AA-AGTAATATATAAAAT
355278 AAAGTAAT
1 AAAGTAAT
355286 TAAAATAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 8 0.36
17 12 0.55
18 2 0.09
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (17 bp):
AAAGTAATATATAAAAT
Found at i:356827 original size:24 final size:24
Alignment explanation
Indices: 356780--356827 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
356770 TTTTGAGTAA
* **
356780 TTTAATTTTTTTCTTTTATGTTCT
1 TTTAATTTTTTTATTTTACATTCT
*
356804 TTTAATTTTTTTATTTTCCATTCT
1 TTTAATTTTTTTATTTTACATTCT
356828 CTTCTACTTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.15, C:0.10, G:0.02, T:0.73
Consensus pattern (24 bp):
TTTAATTTTTTTATTTTACATTCT
Found at i:358743 original size:27 final size:27
Alignment explanation
Indices: 358711--358762 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
358701 ATAACCATCC
*
358711 AAAATTGCCATGGCTTTGAAGTCTTCA
1 AAAATTGCCATGGCTTTGAACTCTTCA
*
358738 AAAATTGCCATGGTTTTGAACTCTT
1 AAAATTGCCATGGCTTTGAACTCTT
358763 TGAAACCTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (27 bp):
AAAATTGCCATGGCTTTGAACTCTTCA
Found at i:360599 original size:77 final size:78
Alignment explanation
Indices: 360451--360600 Score: 223
Period size: 77 Copynumber: 1.9 Consensus size: 78
360441 AAAACTGACG
* * * *
360451 TAAAATTGACTTAGTATATAATAATTTATTTTTTGTCGATCTATTTTTGAAAAATTAATTAATGA
1 TAAAATTCACTTAGCATATAATAATTTATTTTTTGTCAATCTATATTTGAAAAATTAATTAATGA
360516 TTTAAATTATAAT
66 TTTAAATTATAAT
* *
360529 TAAAATTCACTTAGCATATAATTA-TTATTTTTT-TCAATCTATATTTGAAAAAATTAATTGATG
1 TAAAATTCACTTAGCATATAATAATTTATTTTTTGTCAATCTATATTTG-AAAAATTAATTAATG
360592 ATTTAAATT
65 ATTTAAATT
360601 GGGATAAATT
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
76 12 0.18
77 32 0.49
78 21 0.32
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.48
Consensus pattern (78 bp):
TAAAATTCACTTAGCATATAATAATTTATTTTTTGTCAATCTATATTTGAAAAATTAATTAATGA
TTTAAATTATAAT
Found at i:364514 original size:28 final size:28
Alignment explanation
Indices: 364482--364546 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
364472 ATTTACTAGA
*
364482 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
*
364510 ATACCCCTATGTATGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
364538 ATACCCCTA
1 ATACCCCTA
364547 GGGTTAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.34, C:0.28, G:0.08, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:364710 original size:27 final size:27
Alignment explanation
Indices: 364652--364741 Score: 119
Period size: 28 Copynumber: 3.2 Consensus size: 27
364642 AGGAAGCGTC
364652 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
* *
364680 CTGGTGGCCCTGCCACATATATCTGTT
1 CTGGTGGCACTGCCACAAATATCTGTT
364707 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCAC-AAATATCTGT-T
364736 CTGGTG
1 CTGGTG
364742 ACTCTGTCAC
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
27 23 0.42
28 25 0.45
29 7 0.13
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.32
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:364760 original size:55 final size:56
Alignment explanation
Indices: 364652--364766 Score: 146
Period size: 55 Copynumber: 2.1 Consensus size: 56
364642 AGGAAGCGTC
* *
364652 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACATATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
* * *
364707 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTGTCACAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACATATATCTGTAT
364763 CTGG
1 CTGG
364767 CAGCCATGCT
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
54 1 0.02
55 30 0.58
56 21 0.40
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
Found at i:365765 original size:54 final size:53
Alignment explanation
Indices: 365692--365799 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 53
365682 TGTTACATTT
365692 AGTGGTATCAGAGCCAAGTTGCAACAACTCGGCTGTGGAATGGGTTTACAAAA
1 AGTGGTATCAGAGCCAAGTTGCAACAACTCGGCTGTGGAATGGGTTTACAAAA
365745 ANGTGGTATCAGAGCCAAGTTGCAACAACTCGGCTGTGGAATGGGTTTACAAAA
1 A-GTGGTATCAGAGCCAAGTTGCAACAACTCGGCTGTGGAATGGGTTTACAAAA
365799 A
1 A
365800 CAAAGATCTT
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
53 1 0.02
54 53 0.98
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.22
Consensus pattern (53 bp):
AGTGGTATCAGAGCCAAGTTGCAACAACTCGGCTGTGGAATGGGTTTACAAAA
Found at i:365909 original size:11 final size:10
Alignment explanation
Indices: 365881--365914 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
365871 AGCCTGTAAG
365881 TATTCTGAAT
1 TATTCTGAAT
*
365891 TTTTCTGAAT
1 TATTCTGAAT
365901 ATATTCTGAAT
1 -TATTCTGAAT
365912 TAT
1 TAT
365915 CTGTCTGTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.53
Consensus pattern (10 bp):
TATTCTGAAT
Found at i:379108 original size:26 final size:28
Alignment explanation
Indices: 379046--379108 Score: 69
Period size: 26 Copynumber: 2.3 Consensus size: 28
379036 AACTAATCAG
* *
379046 AATATTTTATCATTGTACATTTAAATAC
1 AATATTTTATCATGGTACATTCAAATAC
*
379074 AATCA-TTTAT-A-GGTACATTCATATAC
1 AAT-ATTTTATCATGGTACATTCAAATAC
379100 AATATTTTA
1 AATATTTTA
379109 AGCATATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
25 1 0.03
26 19 0.63
27 1 0.03
28 8 0.27
29 1 0.03
ACGTcount: A:0.40, C:0.11, G:0.05, T:0.44
Consensus pattern (28 bp):
AATATTTTATCATGGTACATTCAAATAC
Found at i:387669 original size:19 final size:19
Alignment explanation
Indices: 387645--387683 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
387635 CAGCTTAGTA
387645 GGGAAAAGATCCGATCTTG
1 GGGAAAAGATCCGATCTTG
*
387664 GGGAAAGGATCCGATCTTG
1 GGGAAAAGATCCGATCTTG
387683 G
1 G
387684 AAGGACTTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.15, G:0.36, T:0.21
Consensus pattern (19 bp):
GGGAAAAGATCCGATCTTG
Found at i:392916 original size:65 final size:65
Alignment explanation
Indices: 392844--392974 Score: 244
Period size: 65 Copynumber: 2.0 Consensus size: 65
392834 TCAATAGTTC
*
392844 TTTTTATTATTATCTTTAATATGTATATATTGTATATATATCATCATTGATTTTTAATATACTTG
1 TTTTTATTATTATCTTTAATATGTATATATTGTACATATATCATCATTGATTTTTAATATACTTG
*
392909 TTTTTATTATTATCTTTAATATGTATATATTGTGCATATATCATCATTGATTTTTAATATACTTG
1 TTTTTATTATTATCTTTAATATGTATATATTGTACATATATCATCATTGATTTTTAATATACTTG
392974 T
1 T
392975 CACACTTATA
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (65 bp):
TTTTTATTATTATCTTTAATATGTATATATTGTACATATATCATCATTGATTTTTAATATACTTG
Found at i:393871 original size:44 final size:45
Alignment explanation
Indices: 393818--393920 Score: 127
Period size: 44 Copynumber: 2.3 Consensus size: 45
393808 TGTCTTTGAC
* * *
393818 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATA-TATAAT
1 ATGGACTTACATGAATCAATCCTGTCTCCAAAGCCATATTATAAT
** *
393862 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGAATCAATCCTGTCTCCAAAGCCATA-TTATAAT
*
393908 CTGGACTTACATG
1 ATGGACTTACATG
393921 GCTCATTTCT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
44 33 0.66
46 17 0.34
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (45 bp):
ATGGACTTACATGAATCAATCCTGTCTCCAAAGCCATATTATAAT
Found at i:408618 original size:16 final size:15
Alignment explanation
Indices: 408592--408626 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
408582 TGATGTGAAT
408592 AATATAAAATATTAA
1 AATATAAAATATTAA
*
408607 AATATCAAAATATTAG
1 AATAT-AAAATATTAA
408623 AATA
1 AATA
408627 ATAATAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (15 bp):
AATATAAAATATTAA
Found at i:408844 original size:22 final size:24
Alignment explanation
Indices: 408781--408845 Score: 80
Period size: 25 Copynumber: 2.8 Consensus size: 24
408771 CGTGATAATA
*
408781 TTAAAAATATGTACATAATATAGTG
1 TTAAAAATATATACATAATATAG-G
*
408806 TTAAAAATACATACATAATATA-G
1 TTAAAAATATATACATAATATAGG
*
408829 TT-AAGATATATACATAA
1 TTAAAAATATATACATAA
408846 GATAACATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 13 0.36
23 3 0.08
25 20 0.56
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34
Consensus pattern (24 bp):
TTAAAAATATATACATAATATAGG
Found at i:408902 original size:25 final size:25
Alignment explanation
Indices: 408866--408997 Score: 93
Period size: 25 Copynumber: 5.6 Consensus size: 25
408856 AAAAAAATAT
*
408866 ATATATAAATAATATAATATTAAAG
1 ATATATACATAATATAATATTAAAG
* * *
408891 ATATATACATAAAATAGTA-TAATAT
1 ATATATACATAATATAATATTAA-AG
* *
408916 ATATATACGTAATATAGA-ATTTAA-
1 ATATATACATAATATA-ATATTAAAG
* *
408940 A-ATATACCTAATAT-AT-TAAAAG
1 ATATATACATAATATAATATTAAAG
*
408962 A-ATATATATAATATAATATT-AAG
1 ATATATACATAATATAATATTAAAG
*
408985 AAATATA-ATAATA
1 ATATATACATAATA
408998 AAAAAAAAAG
Statistics
Matches: 85, Mismatches: 14, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
21 4 0.05
22 12 0.14
23 24 0.28
24 10 0.12
25 33 0.39
26 2 0.02
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.36
Consensus pattern (25 bp):
ATATATACATAATATAATATTAAAG
Found at i:409527 original size:30 final size:30
Alignment explanation
Indices: 409484--409613 Score: 190
Period size: 30 Copynumber: 4.3 Consensus size: 30
409474 TAGGTACAAG
* *
409484 TGGTGGTGTAGCAAGTGTGGCTAGTGAAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
* *
409514 AGGTAGTGGAGCAAGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
409544 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
* *
409574 TGGTGGTGGA-AAAGGAGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAA-GTGTGGCTAGTGGAGT
409604 TGGTGGTGGA
1 TGGTGGTGGA
409614 AAAGGAGTGG
Statistics
Matches: 91, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
29 2 0.02
30 89 0.98
ACGTcount: A:0.20, C:0.05, G:0.48, T:0.26
Consensus pattern (30 bp):
TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
Found at i:409540 original size:18 final size:18
Alignment explanation
Indices: 409517--409572 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
409507 GTGAAGTAGG
409517 TAGTGGAGCAAGTGTGGC
1 TAGTGGAGCAAGTGTGGC
409535 TAGT-G-G--AGT-TGG-
1 TAGTGGAGCAAGTGTGGC
*
409547 TGGTGGAGCAAGTGTGGC
1 TAGTGGAGCAAGTGTGGC
409565 TAGTGGAG
1 TAGTGGAG
409573 TTGGTGGTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 12
0.68 0.05 0.27
Matches are distributed among these distances:
12 3 0.10
13 4 0.13
14 4 0.13
16 4 0.13
17 4 0.13
18 11 0.37
ACGTcount: A:0.20, C:0.07, G:0.48, T:0.25
Consensus pattern (18 bp):
TAGTGGAGCAAGTGTGGC
Found at i:409638 original size:33 final size:30
Alignment explanation
Indices: 409530--409628 Score: 155
Period size: 30 Copynumber: 3.3 Consensus size: 30
409520 TGGAGCAAGT
* *
409530 GTGGCTAGTGGAGTTGGTGGTGGAGCAA-GT
1 GTGGCTAGTGGAGTTGGTGGTGGA-AAAGGA
409560 GTGGCTAGTGGAGTTGGTGGTGGAAAAGGA
1 GTGGCTAGTGGAGTTGGTGGTGGAAAAGGA
409590 GTGGCTAGTGGAGTTGGTGGTGGAAAAGGA
1 GTGGCTAGTGGAGTTGGTGGTGGAAAAGGA
409620 GTGGGCTAG
1 GT-GGCTAG
409629 GATTTAGTTG
Statistics
Matches: 65, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
29 2 0.03
30 57 0.88
31 6 0.09
ACGTcount: A:0.20, C:0.05, G:0.51, T:0.24
Consensus pattern (30 bp):
GTGGCTAGTGGAGTTGGTGGTGGAAAAGGA
Found at i:410450 original size:87 final size:86
Alignment explanation
Indices: 410254--410569 Score: 257
Period size: 88 Copynumber: 3.6 Consensus size: 86
410244 TGATTCTTTA
* * * * * *
410254 CTCGGCATGTGATCCTGA-GCTCAACTCATTTCTCGCAATATGAATTGACTCTTTAAAACTAGAC
1 CTCGGCACGTGA-CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGA-TTTTTAAAAC-AGAA
* ** *
410318 ATTAAAAACAAAAATTGAAAATAG
63 ATTGAAAACAAATTTTGAAAATAC
* * *
410342 CTCAGCACGTGAGCCAAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAACA-AAATT
1 CTCGGCACGTGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAACAGAAA-T
*
410406 TGTAAAACAGATTTTGAAAATAC
65 TG-AAAACAAATTTTGAAAATAC
* * * * * *
410429 CTCGGTATGTGACCCGAGGCTCAACTCATTTCTCGTAATATGAGTTGATTCTTGAAAAGCATAAA
1 CTCGGCACGTGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATT-TTTAAAA-CAGAAA
410494 TTGAAAA-AACATTAATT-AAAACTAC
64 TTGAAAACAA-ATT--TTGAAAA-TAC
* * * * * *
410519 CTC--AACGTGTCCTGAGGCTCAACTCACCTCTCGTAACATGAGTTGATTTTT
1 CTCGGCACGTGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTT
410570 TTGAAAAAGA
Statistics
Matches: 187, Mismatches: 31, Indels: 21
0.78 0.13 0.09
Matches are distributed among these distances:
85 2 0.01
86 3 0.02
87 73 0.39
88 89 0.48
89 9 0.05
90 11 0.06
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (86 bp):
CTCGGCACGTGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAACAGAAATT
GAAAACAAATTTTGAAAATAC
Found at i:410551 original size:88 final size:86
Alignment explanation
Indices: 410332--410568 Score: 239
Period size: 87 Copynumber: 2.7 Consensus size: 86
410322 AAAACAAAAA
* * * * * *
410332 TTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAA
1 TTGAAAATACCTC-GAACGTGACCCGAGGCTCAACTCACTTCTCGTAATATGAGTTGATTTTGAA
* *
410397 AACAAAATTTGTAAAACAGATT
65 AACAAAATTTGTAAAAAACATT
* * *
410419 TTGAAAATACCTCGGTATGTGACCCGAGGCTCAACTCATTTCTCGTAATATGAGTTGATTCTTGA
1 TTGAAAATACCTC-GAACGTGACCCGAGGCTCAACTCACTTCTCGTAATATGAGTTGATT-TTGA
410484 AAAGCATAAA-TTG-AAAAAACATT
64 AAA-CA-AAATTTGTAAAAAACATT
* * * *
410507 AATT-AAAACTACCTC-AACGTGTCCTGAGGCTCAACTCACCTCTCGTAACATGAGTTGATTTT
1 --TTGAAAA-TACCTCGAACGTGACCCGAGGCTCAACTCACTTCTCGTAATATGAGTTGATTTT
410569 TTTGAAAAAG
Statistics
Matches: 126, Mismatches: 18, Indels: 12
0.81 0.12 0.08
Matches are distributed among these distances:
87 54 0.43
88 52 0.41
89 9 0.07
90 11 0.09
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (86 bp):
TTGAAAATACCTCGAACGTGACCCGAGGCTCAACTCACTTCTCGTAATATGAGTTGATTTTGAAA
ACAAAATTTGTAAAAAACATT
Found at i:410624 original size:77 final size:77
Alignment explanation
Indices: 410511--410949 Score: 687
Period size: 77 Copynumber: 5.8 Consensus size: 77
410501 AACATTAATT
* * * *
410511 AAAACTACCTCAACGTGT--CCTGAGGCTCAACTCACCTCTCGTAACATGAGTTGATTTTTTTGA
1 AAAAC-ACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGA
410574 AAAAGAGAAGTTG
65 AAAAGAGAAGTTG
410587 AAAACACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAA
1 AAAACACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAA
410652 AAAGAGAAGTTG
66 AAAGAGAAGTTG
410664 AAAACACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAA
1 AAAACACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAA
410729 AAAGAGAAGTTG
66 AAAGAGAAGTTG
410741 AAAACACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAA
1 AAAACACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAA
410806 AAAGAGAAGTTG
66 AAAGAGAAGTTG
410818 AAAACACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTG--
1 AAAACACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAA
* * *
410880 -ATGATAAATTG
66 AAAGAGAAGTTG
* * ** * * *
410891 AAAATACCTCA--ATGTGACTTGAGGTTCAACTCACCTCTTGCAATATGAGTTAATTTTTT
1 AAAACACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
410950 GAATTAAAAC
Statistics
Matches: 346, Mismatches: 14, Indels: 10
0.94 0.04 0.03
Matches are distributed among these distances:
71 36 0.10
72 5 0.01
73 18 0.05
75 11 0.03
76 12 0.03
77 264 0.76
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (77 bp):
AAAACACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAA
AAAGAGAAGTTG
Found at i:411451 original size:75 final size:73
Alignment explanation
Indices: 411297--411560 Score: 325
Period size: 75 Copynumber: 3.6 Consensus size: 73
411287 TCGACATGTG
* * * * **
411297 ATCC-GAGGCTCCACTCAACTCTCACAATATGAGTTGATTTTTGAAA-ACAGATATCAAAATTAC
1 ATCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAGACAGAAATTGAAATTAC
411360 CTCAGCGT
66 CTCAGCGT
* * *
411368 GTCCTGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTATTTTGAAAGACAAAAATTGAAATT
1 ATCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-T-TTTTGAAAGACAGAAATTGAAATT
411433 ACCTCAGCGT
64 ACCTCAGCGT
* *
411443 ATCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAGGCAGAAATTGAAAATAC
1 ATCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAGACAGAAATTGAAATTAC
* *
411508 CTCAACAT
66 CTCAGCGT
* * * *
411516 GTCAGTCAAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTT
1 ATC-CT-GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
411561 TTGAACCGTA
Statistics
Matches: 167, Mismatches: 20, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
71 3 0.02
72 29 0.17
73 32 0.19
74 10 0.06
75 93 0.56
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (73 bp):
ATCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAGACAGAAATTGAAATTAC
CTCAGCGT
Found at i:411576 original size:150 final size:146
Alignment explanation
Indices: 411297--411565 Score: 369
Period size: 147 Copynumber: 1.8 Consensus size: 146
411287 TCGACATGTG
* *
411297 ATCCGAGGCTCCACTCAACTCTCACAATATGAGTTGATTTTTGAAAACAGATATCAAAATTACCT
1 ATCCGAGGCTCAACTCAACTCTCACAATATGAGTTGATTTTTGAAAACAGAAATCAAAATTACCT
* * * * *
411362 CAGCGTGTCCTGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTATTTTGAAAGACAAAAATT
66 CAACATGTCCTAAGGCTCAACTCACCTCTCGCAATATGAGCTGATTATTTTGAAAGACAAAAATT
411427 GAAATTACCTCAGCGT
131 GAAATTACCTCAGCGT
* * * *
411443 ATCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAGGCAGAAATTGAAAA-TA
1 ATCC-GAGGCTCAACTCAACTCTCACAATATGAGTTGATTTTTGAAA-ACAGAAA-TCAAAATTA
* *
411507 CCTCAACATGTCAGTCAAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTGAA
63 CCTCAACATGTC-CT-AAGGCTCAACTCACCTCTCGCAATATGAGCTGATTATTTTGAA
411566 CCGTAGAAAT
Statistics
Matches: 105, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
146 4 0.04
147 39 0.37
148 17 0.16
149 6 0.06
150 39 0.37
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.29
Consensus pattern (146 bp):
ATCCGAGGCTCAACTCAACTCTCACAATATGAGTTGATTTTTGAAAACAGAAATCAAAATTACCT
CAACATGTCCTAAGGCTCAACTCACCTCTCGCAATATGAGCTGATTATTTTGAAAGACAAAAATT
GAAATTACCTCAGCGT
Found at i:418877 original size:9 final size:9
Alignment explanation
Indices: 418863--418906 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
418853 TATTCCAATT
418863 TTATTATTA
1 TTATTATTA
418872 TTATTATTA
1 TTATTATTA
418881 TTTATT-TTA
1 -TTATTATTA
418890 TT-TTATT-
1 TTATTATTA
418897 TTATT-TTA
1 TTATTATTA
418905 TT
1 TT
418907 TCTTTTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
7 6 0.19
8 8 0.26
9 12 0.39
10 5 0.16
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (9 bp):
TTATTATTA
Found at i:418891 original size:5 final size:5
Alignment explanation
Indices: 418860--418907 Score: 60
Period size: 5 Copynumber: 8.8 Consensus size: 5
418850 AAGTATTCCA
418860 ATTTT ATTATT ATTATT ATTATTT ATTTT ATTTT ATTTT ATTTT ATTT
1 ATTTT ATT-TT ATT-TT A-T-TTT ATTTT ATTTT ATTTT ATTTT ATTT
418908 CTTTTTTTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
5 25 0.62
6 10 0.25
7 4 0.10
8 1 0.03
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (5 bp):
ATTTT
Found at i:419285 original size:46 final size:45
Alignment explanation
Indices: 419217--419308 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 45
419207 ATTACCAAAA
419217 GAAAATATACATCACCAAAAGTTTGCTGAAGTCGGGTCTGGCTTT
1 GAAAATATACATCACCAAAAGTTTGCTGAAGTCGGGTCTGGCTTT
*
419262 GNAAAATATACATCACGAAAAGTTTGCTGAAGTCGGGTCTGGCTTT
1 G-AAAATATACATCACCAAAAGTTTGCTGAAGTCGGGTCTGGCTTT
419308 G
1 G
419309 GATGCTGGTT
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
45 1 0.02
46 44 0.98
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.28
Consensus pattern (45 bp):
GAAAATATACATCACCAAAAGTTTGCTGAAGTCGGGTCTGGCTTT
Found at i:419748 original size:6 final size:6
Alignment explanation
Indices: 419737--419767 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
419727 ACAAATCCGA
*
419737 AACAGT AACAGT AACAGT AACGGT AACAGT A
1 AACAGT AACAGT AACAGT AACAGT AACAGT A
419768 TTCGACACAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.16, G:0.19, T:0.16
Consensus pattern (6 bp):
AACAGT
Found at i:419807 original size:12 final size:12
Alignment explanation
Indices: 419790--419814 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
419780 AGTGTCGAAT
419790 CGGTAACAGTAA
1 CGGTAACAGTAA
419802 CGGTAACAGTAA
1 CGGTAACAGTAA
419814 C
1 C
419815 AGTAGTCGGC
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:0.20, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTAACAGTAA
Found at i:426057 original size:16 final size:15
Alignment explanation
Indices: 426031--426065 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
426021 TGATGTGAAT
426031 AATATAAAATATTAA
1 AATATAAAATATTAA
*
426046 AATATCAAAATATTAG
1 AATAT-AAAATATTAA
426062 AATA
1 AATA
426066 ATAATNNNNN
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (15 bp):
AATATAAAATATTAA
Found at i:426656 original size:30 final size:30
Alignment explanation
Indices: 426615--426713 Score: 162
Period size: 30 Copynumber: 3.3 Consensus size: 30
426605 TAGGTACAAG
426615 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
* * *
426645 AGGTAGTGGAGCAAGTGTGGCTAGTGGAAT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
*
426675 TGGTGGTGGAGCAAGTGTGGCTAGAGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
426705 TGGTGGTGG
1 TGGTGGTGG
426714 TAAAGACTAG
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 62 1.00
ACGTcount: A:0.19, C:0.06, G:0.49, T:0.25
Consensus pattern (30 bp):
TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
Found at i:427299 original size:27 final size:27
Alignment explanation
Indices: 427259--427315 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
427249 TCCACCAACG
*
427259 CTCCTCCAGCTCTAAAATACTCTCTAA
1 CTCCTCAAGCTCTAAAATACTCTCTAA
*
427286 CTCCTCAAGGTCTAAAATACTCTCTAA
1 CTCCTCAAGCTCTAAAATACTCTCTAA
427313 CTC
1 CTC
427316 AGTTCTGAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.30, C:0.35, G:0.05, T:0.30
Consensus pattern (27 bp):
CTCCTCAAGCTCTAAAATACTCTCTAA
Found at i:429118 original size:40 final size:40
Alignment explanation
Indices: 429072--429153 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
429062 AAATTTATGA
*
429072 TTATCTTTGTGAACAATATAATCCTTAAAATTTGAATATT
1 TTATCTTTCTGAACAATATAATCCTTAAAATTTGAATATT
*
429112 TTATCTTTCTGAATAATATAATCCTTAAAATTTGAATATT
1 TTATCTTTCTGAACAATATAATCCTTAAAATTTGAATATT
429152 TT
1 TT
429154 TATATATAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.48
Consensus pattern (40 bp):
TTATCTTTCTGAACAATATAATCCTTAAAATTTGAATATT
Found at i:429148 original size:23 final size:23
Alignment explanation
Indices: 429081--429149 Score: 60
Period size: 23 Copynumber: 3.3 Consensus size: 23
429071 ATTATCTTTG
*
429081 TGAACAATATAATCCTTAAAATT
1 TGAATAATATAATCCTTAAAATT
* * *
429104 TGAAT-ATTTTAT-CTT----TC
1 TGAATAATATAATCCTTAAAATT
429121 TGAATAATATAATCCTTAAAATT
1 TGAATAATATAATCCTTAAAATT
429144 TGAATA
1 TGAATA
429150 TTTTTATATA
Statistics
Matches: 33, Mismatches: 7, Indels: 12
0.63 0.13 0.23
Matches are distributed among these distances:
17 6 0.18
18 5 0.15
19 3 0.09
21 3 0.09
22 5 0.15
23 11 0.33
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (23 bp):
TGAATAATATAATCCTTAAAATT
Found at i:434602 original size:43 final size:43
Alignment explanation
Indices: 434551--434791 Score: 268
Period size: 43 Copynumber: 5.6 Consensus size: 43
434541 TTATTTAAAA
* * *
434551 AAACGCTGCTAAAGACCATAACCTTTACCGGCGCTTTTTTCAC
1 AAACGCCGCTAAAGACCATAACCTTTAGCGGCGCTTTTCTCAC
* * * *
434594 AACCGCTGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCATAACCTTTAGCGGCGCTTTTCTCAC
* * * * *
434637 AAATGCCGCTAAAGACCATGACCTTTAGCGGCACTTTTCCCGC
1 AAACGCCGCTAAAGACCATAACCTTTAGCGGCGCTTTTCTCAC
* * * * *
434680 AAACGCCGCTAAAAACCATGACCTTTAGCGGCACTTTTTTTAC
1 AAACGCCGCTAAAGACCATAACCTTTAGCGGCGCTTTTCTCAC
* * * *
434723 AAACGCCGCTATAGAACA-AACCTTTAGCGACGCTTTTGTCAC
1 AAACGCCGCTAAAGACCATAACCTTTAGCGGCGCTTTTCTCAC
**
434765 AAACGCCGCTAAAGAATATAACCTTTA
1 AAACGCCGCTAAAGACCATAACCTTTA
434792 AAAATATATA
Statistics
Matches: 171, Mismatches: 26, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
42 35 0.20
43 136 0.80
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCATAACCTTTAGCGGCGCTTTTCTCAC
Found at i:447187 original size:14 final size:14
Alignment explanation
Indices: 447168--447198 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
447158 AAAAAATTTT
*
447168 AAAAATTTAAATTA
1 AAAAATTTAAATGA
447182 AAAAATTTAAATGA
1 AAAAATTTAAATGA
447196 AAA
1 AAA
447199 TTTTTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (14 bp):
AAAAATTTAAATGA
Found at i:456035 original size:29 final size:29
Alignment explanation
Indices: 455982--456037 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
455972 TTTGATTCTT
**
455982 TTTAATAGTACAAGGACTACTTTGATCCA
1 TTTAATAGTACAAGGACTAAATTGATCCA
* *
456011 TTTAATAGTGCATGGACTAAATTGATC
1 TTTAATAGTACAAGGACTAAATTGATC
456038 AAGTTCCTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (29 bp):
TTTAATAGTACAAGGACTAAATTGATCCA
Found at i:461561 original size:46 final size:44
Alignment explanation
Indices: 461456--461563 Score: 135
Period size: 44 Copynumber: 2.4 Consensus size: 44
461446 TGTCTTTGAC
** * * *
461456 ATAGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATAGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
* *
461500 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATAGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
461546 ATAGACTTACATGGCTCA
1 ATAGACTTACATGGCTCA
461564 TTTCTGCTCT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
44 32 0.59
46 22 0.41
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.33
Consensus pattern (44 bp):
ATAGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:463241 original size:21 final size:21
Alignment explanation
Indices: 463211--463259 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
463201 GGGGCCTACG
*
463211 CGCCCATGTGAAGGCCACACA
1 CGCCCGTGTGAAGGCCACACA
* * * *
463232 TGCCCGTGTGGATGCCACATA
1 CGCCCGTGTGAAGGCCACACA
463253 CGCCCGT
1 CGCCCGT
463260 ATAGATAGCA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.20, C:0.37, G:0.27, T:0.16
Consensus pattern (21 bp):
CGCCCGTGTGAAGGCCACACA
Found at i:466827 original size:51 final size:51
Alignment explanation
Indices: 466767--466870 Score: 199
Period size: 51 Copynumber: 2.0 Consensus size: 51
466757 TATTTTATAG
*
466767 GAACTCGGTGAAAGGAAAAATCCACACTAAGAATTTATTTTTTGTTTCAAT
1 GAACTCGGTGAAAGGAAAAATCCACACTAAGAATTTATTTTTTATTTCAAT
466818 GAACTCGGTGAAAGGAAAAATCCACACTAAGAATTTATTTTTTATTTCAAT
1 GAACTCGGTGAAAGGAAAAATCCACACTAAGAATTTATTTTTTATTTCAAT
466869 GA
1 GA
466871 GCTAACAGAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.33
Consensus pattern (51 bp):
GAACTCGGTGAAAGGAAAAATCCACACTAAGAATTTATTTTTTATTTCAAT
Found at i:468848 original size:71 final size:72
Alignment explanation
Indices: 468731--468876 Score: 276
Period size: 71 Copynumber: 2.0 Consensus size: 72
468721 TTATAAGAGA
468731 TAGTTTGATAAAAAAAACTTGACCCGCTATCTATGCAAGATAGGAACCAGAGGTAAGGTTAAACA
1 TAGTTTGATAAAAAAAACTTGACCCGCTATCTATGCAAGATAGGAACCAGAGGTAAGGTTAAACA
*
468796 CCACATT
66 CCACACT
468803 TAGTTTGAT-AAAAAAACTTGACCCGCTATCTATGCAAGATAGGAACCAGAGGTAAGGTTAAACA
1 TAGTTTGATAAAAAAAACTTGACCCGCTATCTATGCAAGATAGGAACCAGAGGTAAGGTTAAACA
468867 CCACACT
66 CCACACT
468874 TAG
1 TAG
468877 AAAAGTGATA
Statistics
Matches: 73, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
71 64 0.88
72 9 0.12
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.23
Consensus pattern (72 bp):
TAGTTTGATAAAAAAAACTTGACCCGCTATCTATGCAAGATAGGAACCAGAGGTAAGGTTAAACA
CCACACT
Found at i:472881 original size:26 final size:24
Alignment explanation
Indices: 472851--472900 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
472841 AAATAAAAAA
*
472851 ATTTAAAAATATAATAAATCAAATAT
1 ATTTAAAAACATAA-AAA-CAAATAT
472877 ATTTAAAAACATAAAAACAAATAT
1 ATTTAAAAACATAAAAACAAATAT
472901 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (24 bp):
ATTTAAAAACATAAAAACAAATAT
Found at i:493080 original size:21 final size:21
Alignment explanation
Indices: 493054--493094 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
493044 AACATATGGC
493054 TGGAGGGGAGCAGAAAAAGGG
1 TGGAGGGGAGCAGAAAAAGGG
493075 TGGAGGGGAGCAGAAAAAGG
1 TGGAGGGGAGCAGAAAAAGG
493095 CTGGCGGTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.05, G:0.51, T:0.05
Consensus pattern (21 bp):
TGGAGGGGAGCAGAAAAAGGG
Found at i:496121 original size:19 final size:19
Alignment explanation
Indices: 496097--496134 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
496087 ATTCTTTTGC
496097 GTATTAGTTTCCTATTATT
1 GTATTAGTTTCCTATTATT
*
496116 GTATTATTTTCCTATTATT
1 GTATTAGTTTCCTATTATT
496135 AAACCAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.11, G:0.08, T:0.61
Consensus pattern (19 bp):
GTATTAGTTTCCTATTATT
Found at i:497665 original size:42 final size:42
Alignment explanation
Indices: 497617--497703 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
497607 AAATATAGCC
497617 CTTGATGTTACTCTTGATTATAAAAGTGAGTAATATAGTTTT
1 CTTGATGTTACTCTTGATTATAAAAGTGAGTAATATAGTTTT
497659 CTTGATGTTACTCTTGATTATAAAAGTGAGTAATATAGTTTT
1 CTTGATGTTACTCTTGATTATAAAAGTGAGTAATATAGTTTT
497701 CTT
1 CTT
497704 TCTTACATTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.30, C:0.08, G:0.16, T:0.46
Consensus pattern (42 bp):
CTTGATGTTACTCTTGATTATAAAAGTGAGTAATATAGTTTT
Found at i:505360 original size:49 final size:49
Alignment explanation
Indices: 505288--505385 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
505278 TTGGGGGGAC
505288 TAAATTGGATCCCCCACTTATCAGTGCTTTAGTCAAAAGATGAGACCAG
1 TAAATTGGATCCCCCACTTATCAGTGCTTTAGTCAAAAGATGAGACCAG
505337 TAAATTGGATCCCCCACTTATCAGTGCTTTAGTCAAAAGATGAGACCAG
1 TAAATTGGATCCCCCACTTATCAGTGCTTTAGTCAAAAGATGAGACCAG
505386 AGACACACAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (49 bp):
TAAATTGGATCCCCCACTTATCAGTGCTTTAGTCAAAAGATGAGACCAG
Found at i:506913 original size:63 final size:63
Alignment explanation
Indices: 506792--506932 Score: 151
Period size: 63 Copynumber: 2.2 Consensus size: 63
506782 CATACACTCA
* * * * * * *
506792 TTCCCGCATCAACACATTTAGCTCCGGTTTATTTTACATAAGCACCATAACGCGCACAA-CTAT
1 TTCCTGCATCAACACATTGAACTCCGGTTTATTTTACACAAGCACCACAACACACACAATC-AT
* *
506855 TTCCTGCATCAACACATTGAACAT-CGGTTTATTTTATACAAGCATCACAACACACACAATCAT
1 TTCCTGCATCAACACATTGAAC-TCCGGTTTATTTTACACAAGCACCACAACACACACAATCAT
* *
506918 TCCCTACATCAACAC
1 TTCCTGCATCAACAC
506933 CTTCTATAGG
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
63 63 0.97
64 2 0.03
ACGTcount: A:0.33, C:0.30, G:0.09, T:0.28
Consensus pattern (63 bp):
TTCCTGCATCAACACATTGAACTCCGGTTTATTTTACACAAGCACCACAACACACACAATCAT
Found at i:508588 original size:43 final size:44
Alignment explanation
Indices: 508487--508601 Score: 137
Period size: 43 Copynumber: 2.6 Consensus size: 44
508477 ATGTTTTTTC
** *
508487 TGTAAGACCACATTTGGGACGTTGGCATCGACTTATGATTTACA
1 TGTAAGACCATGTCTGGGACGTTGGCATCGACTTATGATTTACA
* *
508531 TGTAAGACCCTGTCTGGGACAG-TGGCATCGA-TATTTGA-TTACA
1 TGTAAGACCATGTCTGGGAC-GTTGGCATCGACT-TATGATTTACA
*
508574 TGTAAGACCATGTCTGGGACGTTAGCAT
1 TGTAAGACCATGTCTGGGACGTTGGCAT
508602 TGTACGAGCT
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
42 1 0.02
43 30 0.49
44 29 0.48
45 1 0.02
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.30
Consensus pattern (44 bp):
TGTAAGACCATGTCTGGGACGTTGGCATCGACTTATGATTTACA
Found at i:519075 original size:20 final size:20
Alignment explanation
Indices: 519024--519076 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
519014 AATTTGATCT
*
519024 TAATTCTAAAAAATTCAAAGA
1 TAATT-TAAAAAATACAAAGA
519045 -AATTTATAAAAATACATAA-A
1 TAATTTA-AAAAATACA-AAGA
519065 TAATTTAAAAAA
1 TAATTTAAAAAA
519077 AGTATAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
19 2 0.07
20 18 0.64
21 8 0.29
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.30
Consensus pattern (20 bp):
TAATTTAAAAAATACAAAGA
Found at i:519107 original size:20 final size:21
Alignment explanation
Indices: 519052--519108 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
519042 AGAAATTTAT
* * *
519052 AAAAATACATAAATAATTTAA
1 AAAAATAAATTAATAAATTAA
519073 AAAAAGTATAA-TAATAAATT-A
1 AAAAA-TA-AATTAATAAATTAA
519094 AAAAATAAATTAATA
1 AAAAATAAATTAATA
519109 TTAATATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
19 2 0.07
20 7 0.23
21 11 0.37
22 9 0.30
23 1 0.03
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (21 bp):
AAAAATAAATTAATAAATTAA
Found at i:519117 original size:24 final size:24
Alignment explanation
Indices: 519081--519152 Score: 85
Period size: 24 Copynumber: 3.0 Consensus size: 24
519071 AAAAAAAGTA
*
519081 TAATAATAA-ATTAAAAAATAAAT
1 TAATATTAATATTAAAAAATAAAT
*
519104 TAATATTAATATTAAATAAATATAT
1 TAATATTAATATTAAA-AAATAAAT
519129 T-ATATTAATATTAAATAAAATAAA
1 TAATATTAATATT-AA-AAAATAAA
519153 AATCCTCTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
23 8 0.19
24 17 0.40
25 16 0.38
26 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
TAATATTAATATTAAAAAATAAAT
Found at i:519125 original size:17 final size:18
Alignment explanation
Indices: 519099--519136 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
519089 AATTAAAAAA
*
519099 TAAATTAATAT-TAATAT
1 TAAATAAATATATAATAT
*
519116 TAAATAAATATATTATAT
1 TAAATAAATATATAATAT
519134 TAA
1 TAA
519137 TATTAAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAATAAATATATAATAT
Found at i:522458 original size:28 final size:29
Alignment explanation
Indices: 522417--522471 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
522407 CTTTATTCCG
*
522417 ATTGCACTACGGTG-TCCTCTGTTCTGAC
1 ATTGCACTACGGTGCACCTCTGTTCTGAC
* *
522445 ATTGTACTTCGGTGCACCTCTGTTCTG
1 ATTGCACTACGGTGCACCTCTGTTCTG
522472 TTAATGCACT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.13, C:0.27, G:0.22, T:0.38
Consensus pattern (29 bp):
ATTGCACTACGGTGCACCTCTGTTCTGAC
Found at i:522482 original size:29 final size:29
Alignment explanation
Indices: 522419--522495 Score: 75
Period size: 29 Copynumber: 2.7 Consensus size: 29
522409 TTATTCCGAT
* * *
522419 TGCACTACGGTG-TCCTCTGTTCTGACAT
1 TGCACTTCGGTGCACCTCTGTTCTGACAA
* **
522447 TGTACTTCGGTGCACCTCTGTTCTGTTAA
1 TGCACTTCGGTGCACCTCTGTTCTGACAA
* *
522476 TGCACTTTGGTGCAACTCTG
1 TGCACTTCGGTGCACCTCTG
522496 CATTTGTTTC
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
28 10 0.26
29 29 0.74
ACGTcount: A:0.14, C:0.26, G:0.22, T:0.38
Consensus pattern (29 bp):
TGCACTTCGGTGCACCTCTGTTCTGACAA
Done.