Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold320
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: 2598547
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 499 characters in sequence are not A, C, G, or T
File 3 of 17
Found at i:328527 original size:20 final size:20
Alignment explanation
Indices: 328499--328536 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
328489 CTATATTTTC
328499 AAATATGTATCGATACATCA
1 AAATATGTATCGATACATCA
*
328519 AAATTTGTATCGATACAT
1 AAATATGTATCGATACAT
328537 TTACACGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (20 bp):
AAATATGTATCGATACATCA
Found at i:329373 original size:20 final size:21
Alignment explanation
Indices: 329333--329388 Score: 87
Period size: 20 Copynumber: 2.7 Consensus size: 21
329323 ATAAAAGTTA
329333 CATTCTTTCATCCAAAAAAATG
1 CATT-TTTCATCCAAAAAAATG
*
329355 CATTTTTCATCC-CAAAAATG
1 CATTTTTCATCCAAAAAAATG
329375 CATTTTTCATCCAA
1 CATTTTTCATCCAA
329389 GTACACTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
20 19 0.61
21 8 0.26
22 4 0.13
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.36
Consensus pattern (21 bp):
CATTTTTCATCCAAAAAAATG
Found at i:330293 original size:20 final size:20
Alignment explanation
Indices: 330263--330318 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
330253 TTTTACCTAG
330263 ATGTATCGATACATTCCTCA
1 ATGTATCGATACATTCCTCA
* * *
330283 TTGTATTGATACATTTCTCA
1 ATGTATCGATACATTCCTCA
330303 ATGTATCGATACATTC
1 ATGTATCGATACATTC
330319 AAGCATTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTCCTCA
Found at i:332794 original size:79 final size:78
Alignment explanation
Indices: 332664--333060 Score: 437
Period size: 79 Copynumber: 5.1 Consensus size: 78
332654 TCATTGATGT
* * * * *
332664 TTTTATTTCTGAAACATCGATTTTCCACAATTGGGGATACTCCAACCCCGTTATTTTCAAAGGGA
1 TTTTATTTCTAAAACATCGATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTTCAGAGGGA
*
332729 TACTTCAATCCCAG
66 TACTCCAA-CCCAG
* * *
332743 TTTTATTTCTAAAACATCGATTTTTCACAATCGGAGATACTCCAACCCCGTTA-TTTCTGAGAGG
1 TTTTATTTCTAAAACATCGATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTTCAGAG-GG
*
332807 ATACTCCAACCCCAA
65 ATACTCCAA-CCCAG
* * * * * *
332822 TTTTCTTTCCAAAACATCGATTTTTTACCATCGAGAATACTCCAACCCCGTT-TATTTCTGAGAG
1 TTTTATTTCTAAAACATCGATTTTTCACCATCGGGGATACTCCAACCCCGTTAT-TTTCAGAG-G
*
332886 GATACTCCAACCCCG
64 GATACTCCAACCCAG
*
332901 ATTTTATTTCTAAAACATCGATTTTTCTCCATCGGGGATACTCCAACCCCGTTATTTT-AGAAGG
1 -TTTTATTTCTAAAACATCGATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTTCAG-AGG
*
332965 GATACTCCAATCTC-G
64 GATACTCCAA-CCCAG
* * * * * *
332980 ATTTTATTTTTAAAATACCAATTTTTCACCATTGGGGATACTCCAACCCCATT-TTTTC-GAGGG
1 -TTTTATTTCTAAAACATCGATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTTCAGAGGG
*
333043 ATACTCCAACCCCG
65 ATACTCCAACCCAG
333057 TTTT
1 TTTT
333061 TATCTCCAAA
Statistics
Matches: 275, Mismatches: 34, Indels: 21
0.83 0.10 0.06
Matches are distributed among these distances:
76 6 0.02
77 14 0.05
78 11 0.04
79 170 0.62
80 73 0.27
81 1 0.00
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.35
Consensus pattern (78 bp):
TTTTATTTCTAAAACATCGATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTTCAGAGGGA
TACTCCAACCCAG
Found at i:332968 original size:159 final size:159
Alignment explanation
Indices: 332700--333063 Score: 438
Period size: 159 Copynumber: 2.3 Consensus size: 159
332690 ACAATTGGGG
* * * *
332700 ATACTCCAACCCCG-TTATTT-TCAAAGGGATACTTCAATCCC-AGTTTTATTTCTAAAACATCG
1 ATACTCCAACCCCGTTTATTTCTGAGA-GGATACTCCAACCCCGA-TTTTATTTCTAAAACATCG
*
332762 ATTTTTCACAATCGGAGATACTCCAACCCCGTTATTTCTGAGAGGATACTCCAACCCCAATTTTC
64 ATTTTTCACAATCGGAGATACTCCAACCCCGTTATTTCTGAGAGGATACTCCAACCCCAATTTTA
* * *
332827 TTTCCAAAACATCGATTTTTTACCATCGAGA
129 TTTCCAAAACACCAATTTTTCACCATCGAGA
332858 ATACTCCAACCCCGTTTATTTCTGAGAGGATACTCCAACCCCGATTTTATTTCTAAAACATCGAT
1 ATACTCCAACCCCGTTTATTTCTGAGAGGATACTCCAACCCCGATTTTATTTCTAAAACATCGAT
* * * * * *
332923 TTTTCTCCATCGGGGATACTCCAACCCCGTTATTT-T-AGAAGGGATACTCCAATCTCGATTTTA
66 TTTTCACAATCGGAGATACTCCAACCCCGTTATTTCTGAG-A-GGATACTCCAACCCCAATTTTA
** * * * *
332986 TTTTTAAAATACCAATTTTTCACCATTGGGG
129 TTTCCAAAACACCAATTTTTCACCATCGAGA
* *
333017 ATACTCCAACCCCATTT-TTTC-GAG-GGATACTCCAACCCCGTTTTTAT
1 ATACTCCAACCCCGTTTATTTCTGAGAGGATACTCCAACCCCGATTTTAT
333064 CTCCAAAATA
Statistics
Matches: 179, Mismatches: 22, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
156 22 0.12
157 5 0.03
158 20 0.11
159 128 0.72
160 4 0.02
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34
Consensus pattern (159 bp):
ATACTCCAACCCCGTTTATTTCTGAGAGGATACTCCAACCCCGATTTTATTTCTAAAACATCGAT
TTTTCACAATCGGAGATACTCCAACCCCGTTATTTCTGAGAGGATACTCCAACCCCAATTTTATT
TCCAAAACACCAATTTTTCACCATCGAGA
Found at i:334196 original size:14 final size:14
Alignment explanation
Indices: 334160--334204 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
334150 AAATTTAATA
*
334160 TATAAATTTATGTAT
1 TATAAATTTAT-TTT
*
334175 TATTAATTTATTTT
1 TATAAATTTATTTT
*
334189 TATAAATTTATATT
1 TATAAATTTATTTT
334203 TA
1 TA
334205 ATACATTGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
14 16 0.62
15 10 0.38
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (14 bp):
TATAAATTTATTTT
Found at i:335105 original size:23 final size:23
Alignment explanation
Indices: 335060--335106 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
335050 TTAAAAGCTT
*
335060 TAATATATATTTATATATTAAAA
1 TAATATATATTTATATATAAAAA
*
335083 TAAT-TATATTTTTAGTATAAAAA
1 TAATATATATTTATA-TATAAAAA
335106 T
1 T
335107 TAAATATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TAATATATATTTATATATAAAAA
Found at i:335479 original size:3 final size:3
Alignment explanation
Indices: 335473--335511 Score: 69
Period size: 3 Copynumber: 12.7 Consensus size: 3
335463 ATTATTTATG
335473 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATAA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA AT
335512 TTTGATTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:337226 original size:13 final size:12
Alignment explanation
Indices: 337185--337239 Score: 51
Period size: 13 Copynumber: 4.6 Consensus size: 12
337175 TATATAATGG
*
337185 TTTTAATAATTT
1 TTTTTATAATTT
*
337197 ATTTT-TAA-TT
1 TTTTTATAATTT
*
337207 ATTTTATAATATT
1 TTTTTATAAT-TT
337220 TTTTTATAATTT
1 TTTTTATAATTT
337232 TTATTTAT
1 TT-TTTAT
337240 GTGTTGTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
10 7 0.19
11 6 0.17
12 7 0.19
13 16 0.44
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTTATAATTT
Found at i:337290 original size:14 final size:15
Alignment explanation
Indices: 337246--337282 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
337236 TTATGTGTTG
*
337246 TTATAAA-AATATTT
1 TTATAAATAATTTTT
337260 TTATAAATAATTTTT
1 TTATAAATAATTTTT
337275 TTA-AAATA
1 TTATAAATA
337283 TTTATTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TTATAAATAATTTTT
Found at i:338148 original size:25 final size:24
Alignment explanation
Indices: 338119--338168 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
338109 GACTGTTCGC
*
338119 TAAATTTTAA-TTAAATTAATCTAT
1 TAAAATTTAATTTAAATTAAT-TAT
*
338143 TAAAATTTAATTTAATTTAATTAT
1 TAAAATTTAATTTAAATTAATTAT
338167 TA
1 TA
338169 GTTAATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (24 bp):
TAAAATTTAATTTAAATTAATTAT
Found at i:340463 original size:11 final size:11
Alignment explanation
Indices: 340449--340517 Score: 61
Period size: 11 Copynumber: 6.3 Consensus size: 11
340439 TTAAATAATT
340449 ATATAATATAA
1 ATATAATATAA
340460 ATATAATATAA
1 ATATAATATAA
*
340471 AAATAAT-TAAA
1 ATATAATAT-AA
*
340482 ATATGATAT-A
1 ATATAATATAA
* *
340492 ATATAAAATTTA
1 ATATAATA-TAA
*
340504 ATATAAAATAA
1 ATATAATATAA
340515 ATA
1 ATA
340518 CATAAATTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
10 8 0.17
11 30 0.62
12 10 0.21
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (11 bp):
ATATAATATAA
Found at i:340480 original size:38 final size:38
Alignment explanation
Indices: 340434--340511 Score: 106
Period size: 39 Copynumber: 2.1 Consensus size: 38
340424 TGATAATTTT
*
340434 AAATATT-AAATAATTATATAATAT-AAATATAATATAA
1 AAATATTAAAAT-ATGATATAATATAAAATATAATATAA
*
340471 AAATAATTAAAATATGATATAATATAAAATTTAATATAA
1 AAAT-ATTAAAATATGATATAATATAAAATATAATATAA
340510 AA
1 AA
340512 TAAATACATA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
37 4 0.11
38 14 0.39
39 18 0.50
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (38 bp):
AAATATTAAAATATGATATAATATAAAATATAATATAA
Found at i:340569 original size:32 final size:33
Alignment explanation
Indices: 340495--340574 Score: 99
Period size: 32 Copynumber: 2.4 Consensus size: 33
340485 TGATATAATA
* *
340495 TAAAATTTAATATAAAATAAATACATAAATTTTT
1 TAAAATTT-ATATAAAATAAATACATAAACTTAT
* **
340529 TAAAATTTATATAAAATAAAT-TATTGACTTAT
1 TAAAATTTATATAAAATAAATACATAAACTTAT
340561 TAAAATTTATATAA
1 TAAAATTTATATAA
340575 TTATATAATA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
32 20 0.49
33 13 0.32
34 8 0.20
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (33 bp):
TAAAATTTATATAAAATAAATACATAAACTTAT
Found at i:340618 original size:27 final size:26
Alignment explanation
Indices: 340558--340618 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
340548 ATTATTGACT
*
340558 TATTA-AAATTTATATAATTATATAA
1 TATTATAAATTTATATAAATATATAA
*
340583 TATTTTAAATTTAATATAAATATATAA
1 TATTATAAATTT-ATATAAATATATAA
340610 -ATATATAAA
1 TAT-TATAAA
340619 AAATTAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 4 0.13
26 8 0.27
27 18 0.60
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
TATTATAAATTTATATAAATATATAA
Found at i:344495 original size:23 final size:25
Alignment explanation
Indices: 344449--344495 Score: 71
Period size: 23 Copynumber: 1.9 Consensus size: 25
344439 ATTTAACAAT
344449 AATATTATATTAAATGTAATTTTTTA
1 AATATTATATTAAA-GTAATTTTTTA
344475 AATATTA-ATTAAA-TAATTTTT
1 AATATTATATTAAAGTAATTTTT
344496 AATTAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 8 0.38
25 6 0.29
26 7 0.33
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (25 bp):
AATATTATATTAAAGTAATTTTTTA
Found at i:344503 original size:25 final size:25
Alignment explanation
Indices: 344448--344505 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
344438 AATTTAACAA
344448 TAATATTATATTAAATGTAATTTTTT
1 TAATATTATATTAAA-GTAATTTTTT
*
344474 AAATATTA-ATTAAA-TAATTTTTAAT
1 TAATATTATATTAAAGTAATTTTT--T
344499 TAATATT
1 TAATATT
344506 TATAGATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
23 8 0.29
25 13 0.46
26 7 0.25
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (25 bp):
TAATATTATATTAAAGTAATTTTTT
Found at i:344884 original size:10 final size:9
Alignment explanation
Indices: 344856--344940 Score: 53
Period size: 8 Copynumber: 10.0 Consensus size: 9
344846 TTTTAATTAA
*
344856 ATTTTATAA
1 ATTTTATAT
344865 ATTTTA-AT
1 ATTTTATAT
344873 ATATTTATAT
1 AT-TTTATAT
344883 A-TTTATAT
1 ATTTTATAT
*
344891 CATGTTATAT
1 -ATTTTATAT
344901 -TTTTAT-T
1 ATTTTATAT
344908 ATATTTA-A-
1 AT-TTTATAT
344916 ATTTT-T-T
1 ATTTTATAT
344923 ATTATTAT-T
1 ATT-TTATAT
344932 ATTTTATAT
1 ATTTTATAT
344941 GATATAATCA
Statistics
Matches: 61, Mismatches: 3, Indels: 24
0.69 0.03 0.27
Matches are distributed among these distances:
7 7 0.11
8 24 0.39
9 21 0.34
10 9 0.15
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (9 bp):
ATTTTATAT
Found at i:344890 original size:16 final size:16
Alignment explanation
Indices: 344871--344914 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 16
344861 ATAAATTTTA
344871 ATATATTTATATATTT
1 ATATATTTATATATTT
*
344887 ATATCATGTTATATTTTT
1 ATAT-AT-TTATATATTT
344905 ATTATATTTA
1 A-TATATTTA
344915 AATTTTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 4 0.17
17 5 0.21
18 12 0.50
19 3 0.12
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (16 bp):
ATATATTTATATATTT
Found at i:345041 original size:28 final size:28
Alignment explanation
Indices: 345010--345070 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
345000 TTATTTTTAG
*
345010 TTATTACAAAAAT-GATATAATTTTTTTT
1 TTATTACAAAAATAG-TATAATTTTATTT
* * *
345038 TTATTTCAATAATAGTATCATTTTATTT
1 TTATTACAAAAATAGTATAATTTTATTT
345066 TTATT
1 TTATT
345071 TGGTATGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 27 0.96
29 1 0.04
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.57
Consensus pattern (28 bp):
TTATTACAAAAATAGTATAATTTTATTT
Found at i:350520 original size:22 final size:22
Alignment explanation
Indices: 350492--350533 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
350482 ATAAGGAGAG
* *
350492 AGAAAGAAGGAAAATGAAAAAA
1 AGAAAGAAAGAAAAAGAAAAAA
350514 AGAAAGAAAGAAAAAGAAAA
1 AGAAAGAAAGAAAAAGAAAA
350534 GAAATGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.02
Consensus pattern (22 bp):
AGAAAGAAAGAAAAAGAAAAAA
Found at i:350545 original size:18 final size:17
Alignment explanation
Indices: 350489--350546 Score: 50
Period size: 18 Copynumber: 3.5 Consensus size: 17
350479 TCAATAAGGA
* *
350489 GAGAGAAAGAAGGAAAAT
1 GAGAAAAAGAAAG-AAAT
*
350507 GAAAAAAAGAAAG-AA-
1 GAGAAAAAGAAAGAAAT
350522 -AGAAAAAGAAAAGAAAT
1 GAGAAAAAG-AAAGAAAT
350539 GAGAAAAA
1 GAGAAAAA
350547 ATTTTACGTG
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 7 0.22
15 4 0.12
16 4 0.12
18 17 0.53
ACGTcount: A:0.72, C:0.00, G:0.24, T:0.03
Consensus pattern (17 bp):
GAGAAAAAGAAAGAAAT
Found at i:350833 original size:11 final size:11
Alignment explanation
Indices: 350819--350856 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
350809 ATATCATGTG
350819 TATATTATTTT
1 TATATTATTTT
350830 TATATTATATTT
1 TATATTAT-TTT
350842 TA-ATTATTTT
1 TATATTATTTT
350852 T-TATT
1 TATATT
350857 TATGTTATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 7 0.28
11 13 0.52
12 5 0.20
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TATATTATTTT
Found at i:351680 original size:26 final size:27
Alignment explanation
Indices: 351629--351688 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 27
351619 ATAATTATTT
351629 AATA-TAATTTAACTTAAATTTATATA
1 AATATTAATTTAACTTAAATTTATATA
*
351655 ATTATTAATTTAA-TTAAATATT-TATA
1 AATATTAATTTAACTTAAAT-TTATATA
351681 AATATTAA
1 AATATTAA
351689 AATCTCGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 20 0.67
27 10 0.33
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (27 bp):
AATATTAATTTAACTTAAATTTATATA
Found at i:352175 original size:17 final size:17
Alignment explanation
Indices: 352153--352185 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
352143 TATTTTTATA
352153 TTTATTTTAA-AAAATAG
1 TTTA-TTTAATAAAATAG
352170 TTTATTTAATAAAATA
1 TTTATTTAATAAAATA
352186 TATATTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
TTTATTTAATAAAATAG
Found at i:352329 original size:52 final size:52
Alignment explanation
Indices: 352252--352362 Score: 168
Period size: 52 Copynumber: 2.1 Consensus size: 52
352242 AAGTAAAACA
* *
352252 AAAAAATTGATCTTCTAAATATATGATCTATCTCTTTTCGAAATAAAATGAT
1 AAAAAATTGATATTCTAAATATATGATCTATCTCTTTTCGAAATAAAATGAC
* * * *
352304 AAAAAATTGATATTTTAAGTGTATGATTTATCTCTTTTCGAAATAAAATGAC
1 AAAAAATTGATATTCTAAATATATGATCTATCTCTTTTCGAAATAAAATGAC
352356 AAAAAAT
1 AAAAAAT
352363 CAATTAAGTA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (52 bp):
AAAAAATTGATATTCTAAATATATGATCTATCTCTTTTCGAAATAAAATGAC
Found at i:352375 original size:46 final size:50
Alignment explanation
Indices: 352273--352378 Score: 139
Period size: 52 Copynumber: 2.2 Consensus size: 50
352263 CTTCTAAATA
* * *
352273 TATGATCTATCTCTTTTCGAAATAAAATGATAAAAAATTGATATTTTAAGTG
1 TATGATTTATCTCTTTTCGAAATAAAATGACAAAAAATTCATA-TTTAAG-G
352325 TATGATTTATCTCTTTTCGAAATAAAATGACAAAAAA-TCA-A-TTAA-G
1 TATGATTTATCTCTTTTCGAAATAAAATGACAAAAAATTCATATTTAAGG
352371 TATGATTT
1 TATGATTT
352379 CCTAAAACTG
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
46 9 0.18
48 4 0.08
50 1 0.02
51 2 0.04
52 35 0.69
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.40
Consensus pattern (50 bp):
TATGATTTATCTCTTTTCGAAATAAAATGACAAAAAATTCATATTTAAGG
Found at i:352915 original size:41 final size:41
Alignment explanation
Indices: 352839--352916 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 41
352829 AAATAACAAT
* *
352839 TTTTTTAAAAAATATGAATAAATTAAAACAGATTTGAATTA
1 TTTTTTAAAAAATATGAACAAATTAAAACAAATTTGAATTA
* * *
352880 TTTTTT-ATAAATATGAACGAATTTAAACTAAATTTGA
1 TTTTTTAAAAAATATGAACAAATTAAAAC-AAATTTGA
352917 GCCATATTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
40 18 0.58
41 13 0.42
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.41
Consensus pattern (41 bp):
TTTTTTAAAAAATATGAACAAATTAAAACAAATTTGAATTA
Found at i:353426 original size:2 final size:2
Alignment explanation
Indices: 353413--353445 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
353403 TATTCAACAA
*
353413 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
353446 ACAATGTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:360886 original size:23 final size:23
Alignment explanation
Indices: 360860--360904 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
360850 TTACACACAT
360860 GGGTTGGGGTGAATTTTTCTCTG
1 GGGTTGGGGTGAATTTTTCTCTG
360883 GGGTTGGGGTGAATTTTTCTCT
1 GGGTTGGGGTGAATTTTTCTCT
360905 ACATTGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.09, C:0.09, G:0.38, T:0.44
Consensus pattern (23 bp):
GGGTTGGGGTGAATTTTTCTCTG
Found at i:361113 original size:18 final size:18
Alignment explanation
Indices: 361090--361125 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
361080 AGCTCATGTA
361090 ATTTGGCTTGTCTGTAGG
1 ATTTGGCTTGTCTGTAGG
361108 ATTTGGCTTGTCTGTAGG
1 ATTTGGCTTGTCTGTAGG
361126 CAGCGGCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.33, T:0.44
Consensus pattern (18 bp):
ATTTGGCTTGTCTGTAGG
Found at i:362173 original size:12 final size:12
Alignment explanation
Indices: 362156--362185 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
362146 GACAGACTAG
362156 AGAGAATAGAGA
1 AGAGAATAGAGA
362168 AGAGAATAGAGA
1 AGAGAATAGAGA
*
362180 GGAGAA
1 AGAGAA
362186 ATTAGATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.37, T:0.07
Consensus pattern (12 bp):
AGAGAATAGAGA
Found at i:366810 original size:21 final size:22
Alignment explanation
Indices: 366781--366824 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
366771 TCATTACCAC
*
366781 AATAATA-TTAATTTTATTAAA
1 AATAATATTTAATTTTACTAAA
*
366802 AATATTATTTAATTTTACTAAA
1 AATAATATTTAATTTTACTAAA
366824 A
1 A
366825 TCAATCTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
AATAATATTTAATTTTACTAAA
Found at i:367469 original size:12 final size:12
Alignment explanation
Indices: 367452--367491 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
367442 AAATTATATA
367452 TTTATATAAATT
1 TTTATATAAATT
*
367464 TTTATA-ATATAT
1 TTTATATAAAT-T
367476 TTTATATAAATT
1 TTTATATAAATT
367488 TTTA
1 TTTA
367492 CATATTCGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 3 0.12
12 18 0.75
13 3 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTATATAAATT
Found at i:367541 original size:30 final size:29
Alignment explanation
Indices: 367507--367571 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 29
367497 TCGTTATATA
*
367507 TTTATACCGTATTACTATATTT-A-TATTATT
1 TTTATACCATATTA-TA-ATTTCATTATT-TT
*
367537 TTTATATCATATTATAATTTCATTATTTT
1 TTTATACCATATTATAATTTCATTATTTT
367566 TTTATA
1 TTTATA
367572 TTATATTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 4 0.13
29 11 0.35
30 16 0.52
ACGTcount: A:0.31, C:0.08, G:0.02, T:0.60
Consensus pattern (29 bp):
TTTATACCATATTATAATTTCATTATTTT
Found at i:367552 original size:27 final size:24
Alignment explanation
Indices: 367522--367583 Score: 72
Period size: 27 Copynumber: 2.5 Consensus size: 24
367512 ACCGTATTAC
367522 TATATTTATATTATTTTTATATCATAT
1 TATATTTATATTATTTTT-T-T-ATAT
*
367549 TATAATTT-CATTATTTTTTTATAT
1 TAT-ATTTATATTATTTTTTTATAT
367573 TATATTTATAT
1 TATATTTATAT
367584 CATATAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
23 4 0.13
24 9 0.29
25 1 0.03
26 1 0.03
27 12 0.39
28 4 0.13
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (24 bp):
TATATTTATATTATTTTTTTATAT
Found at i:367586 original size:27 final size:30
Alignment explanation
Indices: 367530--367586 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
367520 ACTATATTTA
*
367530 TATTATTTTTATATCATATTATAATTTCAT
1 TATTATTTTTATATCATATTATAATATCAT
*
367560 TATT-TTTTTATATTATATT-T-ATATCAT
1 TATTATTTTTATATCATATTATAATATCAT
367587 ATAATTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 6 0.24
28 1 0.04
29 14 0.56
30 4 0.16
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (30 bp):
TATTATTTTTATATCATATTATAATATCAT
Found at i:367602 original size:40 final size:40
Alignment explanation
Indices: 367526--367602 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
367516 TATTACTATA
* * * *
367526 TTTATATTATTTTTATATCATATTATAATTTCATTATTTT
1 TTTATATTATATTTATATCATATAATAATATAATTATTTT
*
367566 TTTATATTATATTTATATCATATAATTATATAATTAT
1 TTTATATTATATTTATATCATATAATAATATAATTAT
367603 AGTTTACATT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (40 bp):
TTTATATTATATTTATATCATATAATAATATAATTATTTT
Found at i:367679 original size:17 final size:16
Alignment explanation
Indices: 367658--367754 Score: 69
Period size: 16 Copynumber: 6.0 Consensus size: 16
367648 ATCAAATCAA
367658 TATTAAATTTAAATTT
1 TATTAAATTTAAATTT
367674 TAATT-AATTTAAATTT
1 T-ATTAAATTTAAATTT
367690 T-TATAAATTTTAAAATATT
1 TAT-TAAA-TTT-AAAT-TT
* * **
367709 TA-AAAATTTCGAATAG
1 TATTAAATTT-AAATTT
367725 TATTAAATTTAAA-TT
1 TATTAAATTTAAATTT
367740 T-TTAAATTTAAATTT
1 TATTAAATTTAAATTT
367755 CCTCATATAC
Statistics
Matches: 63, Mismatches: 9, Indels: 19
0.69 0.10 0.21
Matches are distributed among these distances:
14 12 0.19
15 4 0.06
16 19 0.30
17 18 0.29
18 7 0.11
19 3 0.05
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (16 bp):
TATTAAATTTAAATTT
Found at i:367746 original size:14 final size:14
Alignment explanation
Indices: 367727--367754 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
367717 TCGAATAGTA
367727 TTAAATTTAAATTT
1 TTAAATTTAAATTT
367741 TTAAATTTAAATTT
1 TTAAATTTAAATTT
367755 CCTCATATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTAAATTTAAATTT
Found at i:375740 original size:21 final size:21
Alignment explanation
Indices: 375671--375742 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
375661 CGAATAGACG
375671 ATAAAATTAATT-TTGATAA-A
1 ATAAAATTAATTATT-ATAATA
* * * *
375691 ATTAAAAATAATAATGATTATA
1 A-TAAAATTAATTATTATAATA
375713 ATAAAATTAATTATTATAATA
1 ATAAAATTAATTATTATAATA
375734 ATAAAATTA
1 ATAAAATTA
375743 TATACTATAA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
20 1 0.02
21 37 0.90
22 3 0.07
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (21 bp):
ATAAAATTAATTATTATAATA
Found at i:375751 original size:21 final size:21
Alignment explanation
Indices: 375710--375752 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
375700 AATAATGATT
*
375710 ATAATAAAATTAATTATTATA
1 ATAATAAAATTAATTACTATA
375731 ATAATAAAATT-ATATACTATA
1 ATAATAAAATTAAT-TACTATA
375752 A
1 A
375753 AAGTGAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
ATAATAAAATTAATTACTATA
Found at i:375888 original size:16 final size:16
Alignment explanation
Indices: 375858--375903 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
375848 ATAAAAAATA
*
375858 ATTAAA-AATATTTAT
1 ATTAAATAATAATTAT
375873 ATTAAATAATAATTAT
1 ATTAAATAATAATTAT
* *
375889 GTTGAATAATAATTA
1 ATTAAATAATAATTA
375904 AAAATTAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 6 0.22
16 21 0.78
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.43
Consensus pattern (16 bp):
ATTAAATAATAATTAT
Found at i:375934 original size:37 final size:38
Alignment explanation
Indices: 375875--375975 Score: 89
Period size: 42 Copynumber: 2.6 Consensus size: 38
375865 ATATTTATAT
* * * * *
375875 TAAATAATAATTATGTTGAATAATA-ATTAAAAATTAA
1 TAAATTATATTTATATTAAATAATATATTAAAAACTAA
*
375912 TAAATTATATTTATATTAAATAAAAAAATATATTTAAAACTAA
1 TAAATTATATTTATATTAAAT-----AATATATTAAAAACTAA
375955 -AAATTATATTTATATTAAATA
1 TAAATTATATTTATATTAAATA
375976 TTATTTATAT
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
37 18 0.35
42 24 0.46
43 10 0.19
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (38 bp):
TAAATTATATTTATATTAAATAATATATTAAAAACTAA
Found at i:375962 original size:42 final size:42
Alignment explanation
Indices: 375896--375975 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
375886 TATGTTGAAT
*
375896 AATAATTAAAAATTAATAAATTATATTTATATTAAATAAAAA
1 AATAATTAAAAACTAATAAATTATATTTATATTAAATAAAAA
*
375938 AATATATTTAAAACTAA-AAATTATATTTATATTAAATA
1 AATA-ATTAAAAACTAATAAATTATATTTATATTAAATA
375976 TTATTTATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 25 0.71
43 10 0.29
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (42 bp):
AATAATTAAAAACTAATAAATTATATTTATATTAAATAAAAA
Found at i:378866 original size:41 final size:41
Alignment explanation
Indices: 378809--378891 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
378799 ATAAAGAGAC
378809 TTTCATATTAGTTGTCCATGGATCAACTGCTTCTATGAAAA
1 TTTCATATTAGTTGTCCATGGATCAACTGCTTCTATGAAAA
* *
378850 TTTCATATTAGTTGTCCATGGATCAAGTGCTTTTATGAAAA
1 TTTCATATTAGTTGTCCATGGATCAACTGCTTCTATGAAAA
378891 T
1 T
378892 GGGATCTCCT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (41 bp):
TTTCATATTAGTTGTCCATGGATCAACTGCTTCTATGAAAA
Found at i:382447 original size:34 final size:34
Alignment explanation
Indices: 382401--382585 Score: 257
Period size: 34 Copynumber: 5.5 Consensus size: 34
382391 GTAAAAACCA
*
382401 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
382435 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
382469 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
382503 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
382537 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
382570 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
382586 TCTCCCACTT
Statistics
Matches: 135, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
33 18 0.13
34 113 0.84
35 4 0.03
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:386678 original size:19 final size:19
Alignment explanation
Indices: 386651--386713 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
386641 TCACGTGTAC
* *
386651 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
386670 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
**
386689 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTGAAT
386708 AGTACC
1 AGTACC
386714 TCGACAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:387067 original size:34 final size:34
Alignment explanation
Indices: 387021--387203 Score: 199
Period size: 34 Copynumber: 5.4 Consensus size: 34
387011 GTAAAAACCA
*
387021 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
387055 TCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* * *
387089 CCATTTAATCAATAATGATAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
387123 CCATTTAATCAACAATGGTAAGCTACCAAATTTT
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * ** * *
387157 TCATTTAGTCAACAATAATAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
387190 CCATTTAATCAACA
1 CCATTTAATCAACA
387204 CGTGCAAAAT
Statistics
Matches: 124, Mismatches: 23, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
33 15 0.12
34 105 0.85
35 4 0.03
ACGTcount: A:0.42, C:0.25, G:0.06, T:0.27
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:387507 original size:27 final size:29
Alignment explanation
Indices: 387415--387507 Score: 86
Period size: 29 Copynumber: 3.2 Consensus size: 29
387405 CTCAATTCAG
*
387415 TTTTAA-TTGTATTAATCT-ATCAAAATAAA
1 TTTTAATTTG-ATTAAT-TGATTAAAATAAA
* * *
387444 ATTTAATTTTATTAATTGATTAATCAAAAAA
1 TTTTAATTTGATTAATTGATTAA--AATAAA
387475 TTTTAATTTGATT-ATTGATT-AAATAAA
1 TTTTAATTTGATTAATTGATTAAAATAAA
387502 TTTTAA
1 TTTTAA
387508 AATTTTGATT
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
27 11 0.21
28 1 0.02
29 16 0.30
30 9 0.17
31 16 0.30
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.48
Consensus pattern (29 bp):
TTTTAATTTGATTAATTGATTAAAATAAA
Found at i:387585 original size:20 final size:20
Alignment explanation
Indices: 387560--387598 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
387550 TAAAAATATT
* *
387560 ATATTTTTAATTTTTATTAA
1 ATATTTTAAATTTTAATTAA
387580 ATATTTTAAATTTTAATTA
1 ATATTTTAAATTTTAATTA
387599 TCGATTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
ATATTTTAAATTTTAATTAA
Found at i:388802 original size:16 final size:16
Alignment explanation
Indices: 388781--388813 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
388771 GATAAATATT
388781 AATTTAAAAATATAAA
1 AATTTAAAAATATAAA
*
388797 AATTTATAAATATAAA
1 AATTTAAAAATATAAA
388813 A
1 A
388814 TAAATATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AATTTAAAAATATAAA
Found at i:390337 original size:20 final size:20
Alignment explanation
Indices: 390299--390341 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
390289 TTCCCAAAAA
*
390299 AAAAAAAAACTCAGAAATTGC
1 AAAAAAAAACTAAGAAATT-C
*
390320 AAAAAAAAAC-AAGCAATTC
1 AAAAAAAAACTAAGAAATTC
390339 AAA
1 AAA
390342 TTCCCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.20
20 6 0.30
21 10 0.50
ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12
Consensus pattern (20 bp):
AAAAAAAAACTAAGAAATTC
Found at i:390745 original size:2 final size:2
Alignment explanation
Indices: 390738--390768 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
390728 TGAGAATAGA
390738 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
390769 CGCACCTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:390984 original size:20 final size:19
Alignment explanation
Indices: 390939--391008 Score: 58
Period size: 18 Copynumber: 3.7 Consensus size: 19
390929 AAATTACAAT
390939 AATTAAAATATTA-A-A-A
1 AATTAAAATATTAGACATA
*
390955 AATTTTAAAATATTAGAGTATA
1 AA--TTAAAATATTAGA-CATA
*
390977 AATTAAAAATATTTGACATA
1 AATT-AAAATATTAGACATA
390997 AATTAAAA-ATTA
1 AATTAAAATATTA
391009 AAAGTTAATT
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
16 2 0.05
18 14 0.32
19 5 0.11
20 9 0.20
21 11 0.25
22 3 0.07
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.36
Consensus pattern (19 bp):
AATTAAAATATTAGACATA
Found at i:390987 original size:21 final size:20
Alignment explanation
Indices: 390961--391006 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
390951 AAAAAATTTT
*
390961 AAAATATTAGAGTATAAATTA
1 AAAATATTAGA-CATAAATTA
*
390982 AAAATATTTGACATAAATTA
1 AAAATATTAGACATAAATTA
391002 AAAAT
1 AAAAT
391007 TAAAAGTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.33
Consensus pattern (20 bp):
AAAATATTAGACATAAATTA
Found at i:391035 original size:28 final size:27
Alignment explanation
Indices: 390973--391035 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
390963 AATATTAGAG
*
390973 TATAAATTAAAAATATTTGACATAAAT
1 TATAAATTAAAAATAATTGACATAAAT
* * *
391000 TAAAAATTAAAAGTTAATTGATA-AAAT
1 TATAAATTAAAA-ATAATTGACATAAAT
391027 ATATAAATT
1 -TATAAATT
391036 TTAATTTTAG
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 15 0.52
28 14 0.48
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.37
Consensus pattern (27 bp):
TATAAATTAAAAATAATTGACATAAAT
Found at i:393017 original size:19 final size:20
Alignment explanation
Indices: 392992--393039 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
392982 AAATATATGC
392992 ATAGTTTTTA-AGGGCAAT-G
1 ATAGTTTTTACAGGG-AATAG
*
393011 TTAGTTTTTACAGGGAATAG
1 ATAGTTTTTACAGGGAATAG
393031 ATAGTTTTT
1 ATAGTTTTT
393040 TTTCCCTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.29, C:0.04, G:0.23, T:0.44
Consensus pattern (20 bp):
ATAGTTTTTACAGGGAATAG
Found at i:393401 original size:3 final size:3
Alignment explanation
Indices: 393393--393419 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
393383 GTAGAGACGG
393393 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
393420 AGAAAGAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:395756 original size:2 final size:2
Alignment explanation
Indices: 395707--395742 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
395697 TCAAGTGACC
* *
395707 AT AT CT AT AT AT 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
395743 CAAAAGTTTA
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:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:397618 original size:3 final size:3
Alignment explanation
Indices: 397610--397656 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
397600 CCATGCACCT
*
397610 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATG ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
397657 TCTCTTTCAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:401570 original size:23 final size:24
Alignment explanation
Indices: 401526--401574 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
401516 ATTATATTTA
*
401526 TTTAAATTATAAAAAAATTAAAAT
1 TTTAAAATATAAAAAAATTAAAAT
*
401550 TTTAAAATATAAATAAA-TAAAAT
1 TTTAAAATATAAAAAAATTAAAAT
401573 TT
1 TT
401575 AATTAATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
TTTAAAATATAAAAAAATTAAAAT
Found at i:402097 original size:16 final size:16
Alignment explanation
Indices: 402076--402108 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
402066 GATGAATATT
402076 AATTTAAAAATATAAA
1 AATTTAAAAATATAAA
*
402092 AATTTATAAATATAAA
1 AATTTAAAAATATAAA
402108 A
1 A
402109 TAAATATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AATTTAAAAATATAAA
Found at i:402151 original size:19 final size:20
Alignment explanation
Indices: 402124--402161 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
402114 ATAATTTTAA
402124 GAAAAATT-AATTTTTAATT
1 GAAAAATTAAATTTTTAATT
*
402143 GAAATATTAAATTTTTAAT
1 GAAAAATTAAATTTTTAAT
402162 ATTGATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (20 bp):
GAAAAATTAAATTTTTAATT
Found at i:403029 original size:15 final size:17
Alignment explanation
Indices: 403011--403042 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
403001 GATTTGAGGG
403011 GATTTA-ATT-TAATTT
1 GATTTATATTATAATTT
403026 GATTTATATTATAATTT
1 GATTTATATTATAATTT
403043 ATAAAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 3 0.20
17 6 0.40
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.59
Consensus pattern (17 bp):
GATTTATATTATAATTT
Found at i:403339 original size:31 final size:31
Alignment explanation
Indices: 403280--403343 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
403270 CTCATTAACT
* *
403280 ATTAATAAAAATAATAAATTTTATAAATAAA
1 ATTAATAAAAATAATAAATTTAAAAAATAAA
*
403311 ATTAAT-ATAATAATAAATTTAAGAAAATAAA
1 ATTAATAAAAATAATAAATTTAA-AAAATAAA
403342 AT
1 AT
403344 ATATGATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 14 0.48
31 15 0.52
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (31 bp):
ATTAATAAAAATAATAAATTTAAAAAATAAA
Found at i:404089 original size:2 final size:2
Alignment explanation
Indices: 404082--404108 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
404072 ATAATTGAGA
404082 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
404109 GTAAATACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:404702 original size:18 final size:18
Alignment explanation
Indices: 404679--404713 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
404669 GTTACAATAA
404679 TTAAAATATTAAAATATT
1 TTAAAATATTAAAATATT
*
404697 TTAAAATATTTAAATAT
1 TTAAAATATTAAAATAT
404714 AAATTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTAAAATATTAAAATATT
Found at i:404722 original size:20 final size:20
Alignment explanation
Indices: 404677--404742 Score: 84
Period size: 20 Copynumber: 3.4 Consensus size: 20
404667 AAGTTACAAT
404677 AATTAAAATA-TTAAA-ATA
1 AATTAAAATATTTAAATATA
**
404695 TTTTAAAATATTTAAATATA
1 AATTAAAATATTTAAATATA
404715 AATTAAAAATATTT-AATATA
1 AATT-AAAATATTTAAATATA
404735 AATTAAAA
1 AATTAAAA
404743 ATTAAAAGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
18 8 0.20
19 9 0.22
20 15 0.37
21 9 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AATTAAAATATTTAAATATA
Found at i:404743 original size:20 final size:21
Alignment explanation
Indices: 404699--404744 Score: 85
Period size: 20 Copynumber: 2.2 Consensus size: 21
404689 AAAATATTTT
404699 AAAATATTTAAATATAAATTA
1 AAAATATTTAAATATAAATTA
404720 AAAATATTT-AATATAAATTA
1 AAAATATTTAAATATAAATTA
404740 AAAAT
1 AAAAT
404745 TAAAAGTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 16 0.64
21 9 0.36
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
AAAATATTTAAATATAAATTA
Found at i:411878 original size:52 final size:51
Alignment explanation
Indices: 411791--412157 Score: 308
Period size: 52 Copynumber: 6.9 Consensus size: 51
411781 GATAAGAATA
* * * * *
411791 ATGATAAAAGTGCCAATATGTTGATTCAAGGCCAGCAATATTATGCTTAAAG
1 ATGACAAAAGTGCCAATGTGCTGATTCAAGGCCAGCGATATT-GGCTTAAAG
* * * * *
411843 GTGACAAATGTGCCAATGTGCTGATTCAAGTCCAGCGACATTGGGCTTAAAA
1 ATGACAAAAGTGCCAATGTGCTGATTCAAGGCCAGCGATATT-GGCTTAAAG
*
411895 ATGACAAAAGTGCCAATGTACTGATTCAAGGCCAGCGATATTGGACTT-AAG
1 ATGACAAAAGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGG-CTTAAAG
* * *
411946 ATGACAAAGGTGCCAATGTGCTTATTCAAGGCCAGCGACATTGGACTTAAAG
1 ATGACAAAAGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGG-CTTAAAG
* * ** * **
411998 ATGATAAGAGCACCAATATGCTGATTCAAGGCCAAAGATATTGGACTT-AAG
1 ATGACAAAAGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGG-CTTAAAG
* * *
412049 AAAGA-AAAAGGTGCCAATGTGCTGATTCAAGGCCAGTGACATTGGACTTAGAAAG
1 -ATGACAAAA-GTGCCAATGTGCTGATTCAAGGCCAGCGATATTGG-CTT--AAAG
* * * * *
412104 AAAAGACTTAATAAGTGCCTATGTGTTGATTCAAGGCCAACGACATTGGGCTTA
1 --ATGAC--AA-AAGTGCCAATGTGCTGATTCAAGGCCAGCGATATT-GGCTTA
412158 GAAAGAGATG
Statistics
Matches: 259, Mismatches: 43, Indels: 21
0.80 0.13 0.07
Matches are distributed among these distances:
51 54 0.21
52 158 0.61
55 3 0.01
56 5 0.02
57 1 0.00
59 34 0.13
60 4 0.02
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (51 bp):
ATGACAAAAGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGCTTAAAG
Found at i:411995 original size:103 final size:103
Alignment explanation
Indices: 411790--412098 Score: 404
Period size: 103 Copynumber: 3.0 Consensus size: 103
411780 AGATAAGAAT
* * * * *
411790 AATGATAAAAGTGCCAATATGTTGATTCAAGGCCAGCAATATTATG-CTTAAAGGTGACAAATGT
1 AATGATAAAAGTGCCAATATGCTGATTCAAGGCCAGCGATATT-GGACTT-AAGATGACAAAGGT
* *
411854 GCCAATGTGCTGATTCAAGTCCAGCGACATTGGGCTTAAA
64 GCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAA
* * *
411894 AATGACAAAAGTGCCAATGTACTGATTCAAGGCCAGCGATATTGGACTTAAGATGACAAAGGTGC
1 AATGATAAAAGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAGATGACAAAGGTGC
*
411959 CAATGTGCTTATTCAAGGCCAGCGACATTGGACTTAAA
66 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAA
* * ** ** * *
411997 GATGATAAGAGCACCAATATGCTGATTCAAGGCCAAAGATATTGGACTTAAGAAAGAAAAAGGTG
1 AATGATAAAAGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAG-ATGACAAAGGTG
*
412062 CCAATGTGCTGATTCAAGGCCAGTGACATTGGACTTA
65 CCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTA
412099 GAAAGAAAAG
Statistics
Matches: 179, Mismatches: 24, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
103 93 0.52
104 86 0.48
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.24
Consensus pattern (103 bp):
AATGATAAAAGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAGATGACAAAGGTGC
CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAA
Found at i:412607 original size:65 final size:65
Alignment explanation
Indices: 412170--412975 Score: 797
Period size: 65 Copynumber: 12.5 Consensus size: 65
412160 AAGAGATGCA
* * * * * *
412170 ACCGACTTGTATGGGCTTT-TAAGAGGGTTGCTACCGATTTGTGTAGGCTTTTGA-AA-GGTTGC
1 ACCGACTTGTGTGGGCTTTAGAAGA-GGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTGC
412232 C
65 C
* * * * *
412233 ACCAACTTGGGTGGGCTTTAG-AGAATGGTTTCCATCGACTTGTGTGGGATTT--AGAAGAGGTT
1 ACCGACTTGTGTGGGCTTTAGAAG-A-GGTTGCCACCGACTTGTGTGGGCTTTAGAGAAG-GGTT
***
412295 TTT
63 GCC
* *
412298 ACCGACTTGTGTGGGCTTTAGAAGAGGTTGCCACCAACTTGTATGGGCTTTA-AGAAGGGTTGCC
1 ACCGACTTGTGTGGGCTTTAGAAGAGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTGCC
* * * *
412362 ATCGACTTGTGTGGGCTTTAAGAAG-GGTTGCCACCGACTTGTGTGGCCTTTTGA-AAAGGTTGC
1 ACCGACTTGTGTGGGCTTT-AGAAGAGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTGC
412425 C
65 C
* *** *
412426 ACCGACTTATGTGGGCTTTAGAA-AGAGTTGCTGTCGACTTGTGTGGGCTTTAAAG-A-GGTTGC
1 ACCGACTTGTGTGGGCTTTAGAAGAG-GTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTGC
412488 C
65 C
* * *
412489 ACTGACTTGTGTAGGCTTTGGAGAAG-GGTTGCCACTGACTTGTGTGGGCTTTAGAGAAGGGTTG
1 ACCGACTTGTGTGGGCTTT--AGAAGAGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTG
412553 CC
64 CC
* * * * **
412555 ACCGACTTGTGTGGGTTTTTGAAGAGGTTGTCACCGATTTGTGTAAGCTTTAGAGAAGGGTTGCC
1 ACCGACTTGTGTGGGCTTTAGAAGAGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTGCC
*** *
412620 ATTAACTTGTGTGGGCTTTAGAA-AGGGTTGCCACCGACTTGTGTGGGCTTTAGTGAAGGGTTGC
1 ACCGACTTGTGTGGGCTTTAGAAGA-GGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTGC
412684 C
65 C
* * * *
412685 ACCGACTTGTGTAGGCTTTTGAAGAGGTTGCCACCAACTTGTGTGGGCTTTAGA-AA-GGTTGTC
1 ACCGACTTGTGTGGGCTTTAGAAGAGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTGCC
** * * * * * * * *
412748 ATTGACTTGTGTGAGCTTT-GAAGAGGTTACTACCGACTTGTATGGACTTTGGAGAAAGATTGCC
1 ACCGACTTGTGTGGGCTTTAGAAGAGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTGCC
* * *
412812 ACCAACTTGTGTGGGCTTTACGAA-AGGTTGCCACCGACTTGTATGGGCTTTAGAGAAGGGGTGC
1 ACCGACTTGTGTGGGCTTTA-GAAGAGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTGC
412876 C
65 C
* *
412877 ACTGACTTGTGTGGGCTTTATAGAAG-GGTTGCCACCAACTTGTGTGGGCTTTAGAGAA-GGTTG
1 ACCGACTTGTGTGGGC-TT-TAGAAGAGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTG
412940 CC
64 CC
* * * * * *
412942 ATCAATTTGTTTGGGCTTTAGAAAAGGGTGCCAC
1 ACCGACTTGTGTGGGCTTTAGAAGAGGTTGCCAC
412976 GAAGTTGTGG
Statistics
Matches: 607, Mismatches: 108, Indels: 55
0.79 0.14 0.07
Matches are distributed among these distances:
62 29 0.05
63 76 0.13
64 197 0.32
65 239 0.39
66 64 0.11
67 2 0.00
ACGTcount: A:0.21, C:0.16, G:0.32, T:0.32
Consensus pattern (65 bp):
ACCGACTTGTGTGGGCTTTAGAAGAGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTGCC
Found at i:412961 original size:32 final size:32
Alignment explanation
Indices: 412170--412975 Score: 760
Period size: 32 Copynumber: 25.1 Consensus size: 32
412160 AAGAGATGCA
* * *
412170 ACCGACTTGTATGGGCTTTTA-AGAGGGTTGCT
1 ACCGACTTGTGTGGGC-TTTAGAGAAGGTTGCC
* * *
412202 ACCGATTTGTGTAGGCTTTTGA-AAGGTTGCC
1 ACCGACTTGTGTGGGCTTTAGAGAAGGTTGCC
* * *
412233 ACCAACTTGGGTGGGCTTTAGAGAATGGTTTCC
1 ACCGACTTGTGTGGGCTTTAGAGAA-GGTTGCC
* * ***
412266 ATCGACTTGTGTGGGATTTAGA-AGAGGTTTTT
1 ACCGACTTGTGTGGGCTTTAGAGA-AGGTTGCC
412298 ACCGACTTGTGTGGGCTTTAGA-AGAGGTTGCC
1 ACCGACTTGTGTGGGCTTTAGAGA-AGGTTGCC
* *
412330 ACCAACTTGTATGGGCTTTA-AGAAGGGTTGCC
1 ACCGACTTGTGTGGGCTTTAGAGAA-GGTTGCC
*
412362 ATCGACTTGTGTGGGCTTTA-AGAAGGGTTGCC
1 ACCGACTTGTGTGGGCTTTAGAGAA-GGTTGCC
* * *
412394 ACCGACTTGTGTGGCCTTTTGAAAAGGTTGCC
1 ACCGACTTGTGTGGGCTTTAGAGAAGGTTGCC
* *
412426 ACCGACTTATGTGGGCTTTAGA-AAGAGTTGCT
1 ACCGACTTGTGTGGGCTTTAGAGAAG-GTTGCC
** *
412458 GTCGACTTGTGTGGGCTTTAAAG-AGGTTGCC
1 ACCGACTTGTGTGGGCTTTAGAGAAGGTTGCC
* * *
412489 ACTGACTTGTGTAGGCTTTGGAGAAGGGTTGCC
1 ACCGACTTGTGTGGGCTTTAGAGAA-GGTTGCC
*
412522 ACTGACTTGTGTGGGCTTTAGAGAAGGGTTGCC
1 ACCGACTTGTGTGGGCTTTAGAGAA-GGTTGCC
* * *
412555 ACCGACTTGTGTGGGTTTTTGA-AGAGGTTGTC
1 ACCGACTTGTGTGGGCTTTAGAGA-AGGTTGCC
* **
412587 ACCGATTTGTGTAAGCTTTAGAGAAGGGTTGCC
1 ACCGACTTGTGTGGGCTTTAGAGAA-GGTTGCC
***
412620 ATTAACTTGTGTGGGCTTTAGA-AAGGGTTGCC
1 ACCGACTTGTGTGGGCTTTAGAGAA-GGTTGCC
*
412652 ACCGACTTGTGTGGGCTTTAGTGAAGGGTTGCC
1 ACCGACTTGTGTGGGCTTTAGAGAA-GGTTGCC
* *
412685 ACCGACTTGTGTAGGCTTTTGA-AGAGGTTGCC
1 ACCGACTTGTGTGGGCTTTAGAGA-AGGTTGCC
* *
412717 ACCAACTTGTGTGGGCTTTAGA-AAGGTTGTC
1 ACCGACTTGTGTGGGCTTTAGAGAAGGTTGCC
** * * *
412748 ATTGACTTGTGTGAGCTTT-GA-AGAGGTTACT
1 ACCGACTTGTGTGGGCTTTAGAGA-AGGTTGCC
* * * *
412779 ACCGACTTGTATGGACTTTGGAGAAAGATTGCC
1 ACCGACTTGTGTGGGCTTTAGAG-AAGGTTGCC
*
412812 ACCAACTTGTGTGGGCTTTACGA-AAGGTTGCC
1 ACCGACTTGTGTGGGCTTTA-GAGAAGGTTGCC
* *
412844 ACCGACTTGTATGGGCTTTAGAGAAGGGGTGCC
1 ACCGACTTGTGTGGGCTTTAGAGAA-GGTTGCC
* *
412877 ACTGACTTGTGTGGGCTTTATAGAAGGGTTGCC
1 ACCGACTTGTGTGGGCTTTAGAGAA-GGTTGCC
*
412910 ACCAACTTGTGTGGGCTTTAGAGAAGGTTGCC
1 ACCGACTTGTGTGGGCTTTAGAGAAGGTTGCC
* * * * * *
412942 ATCAATTTGTTTGGGCTTTAGAAAAGGGTGCC
1 ACCGACTTGTGTGGGCTTTAGAGAAGGTTGCC
412974 AC
1 AC
412976 GAAGTTGTGG
Statistics
Matches: 639, Mismatches: 112, Indels: 46
0.80 0.14 0.06
Matches are distributed among these distances:
30 3 0.00
31 97 0.15
32 319 0.50
33 217 0.34
34 3 0.00
ACGTcount: A:0.21, C:0.16, G:0.32, T:0.32
Consensus pattern (32 bp):
ACCGACTTGTGTGGGCTTTAGAGAAGGTTGCC
Found at i:412999 original size:33 final size:33
Alignment explanation
Indices: 412962--413377 Score: 229
Period size: 33 Copynumber: 12.9 Consensus size: 33
412952 TTGGGCTTTA
*
412962 GAAAAGGGTGCCACGAAGTTGTGGACTTTGAAG
1 GAAAAGGGTGCCACGAAGTTGTGGACTTTAAAG
** * * *
412995 GAAAACAGTGCCATGGAGTTATGGA-TTTAAAAGG
1 GAAAAGGGTGCCACGAAGTTGTGGACTTT-AAA-G
* * *
413029 GAAAA-GCTGCCACGAAGTTGTCGACTTAAAAG
1 GAAAAGGGTGCCACGAAGTTGTGGACTTTAAAG
** * * * *
413061 GAAATA--GTGCCAAAAAATTATGGACTTAAAAA
1 GAAA-AGGGTGCCACGAAGTTGTGGACTTTAAAG
* *
413093 GAAAAAGATGCCAC-AGAGTTGTGGAC-TT----
1 GAAAAGGGTGCCACGA-AGTTGTGGACTTTAAAG
* * * *
413121 -AAAAGTGTGCCACGAAGTTGTGGACGTAAAAA
1 GAAAAGGGTGCCACGAAGTTGTGGACTTTAAAG
* * * * ** *
413153 GTAAAGAGTGCTACAAAGTCATGGACTTTAGA-
1 GAAAAGGGTGCCACGAAGTTGTGGACTTTAAAG
* * *
413185 GAAAAAGGTGCCA-TAGAGTTGTGGACTTAAAAG
1 GAAAAGGGTGCCACGA-AGTTGTGGACTTTAAAG
*
413218 GAAAAGGGTGCCACCG-AGTCGTGGACTTTAAAG
1 GAAAAGGGTGCCA-CGAAGTTGTGGACTTTAAAG
* ** * * * *
413251 AAAAAAAGTGTCATGGAGTTGTGG-GTTTAAAAG
1 GAAAAGGGTGCCACGAAGTTGTGGACTTT-AAAG
*
413284 GAAAAGGGTGCCA-TAGAGTTGTGGACTTTAAA-
1 GAAAAGGGTGCCACGA-AGTTGTGGACTTTAAAG
* * *
413316 GAAAAAGGTGCCACGGAGTTGTGGACTTAAAAG
1 GAAAAGGGTGCCACGAAGTTGTGGACTTTAAAG
*
413349 GAAAAGGGTGCCAC-AGAGTCGTGGACTTT
1 GAAAAGGGTGCCACGA-AGTTGTGGACTTT
413378 TAAAAAAAGA
Statistics
Matches: 285, Mismatches: 73, Indels: 50
0.70 0.18 0.12
Matches are distributed among these distances:
27 20 0.07
28 2 0.01
31 2 0.01
32 85 0.30
33 165 0.58
34 11 0.04
ACGTcount: A:0.37, C:0.12, G:0.29, T:0.22
Consensus pattern (33 bp):
GAAAAGGGTGCCACGAAGTTGTGGACTTTAAAG
Found at i:413188 original size:92 final size:92
Alignment explanation
Indices: 413036--413217 Score: 240
Period size: 92 Copynumber: 2.0 Consensus size: 92
413026 AGGGAAAAGC
* * *
413036 TGCCACGAAGTTGTCGACTTAAAAGGAAATAGTGCCAAAAAATTATGGACTTAAAAAGAAAAAGA
1 TGCCACGAAGTTGTCGACTAAAAAGGAAAGAGTGCCAAAAAATCATGGACTTAAAAAGAAAAAGA
413101 TGCCACAGAGTTGTGGACTTAAAAGTG
66 TGCCACAGAGTTGTGGACTTAAAAGTG
* * * * * * *
413128 TGCCACGAAGTTGTGGACGTAAAAAGTAAAGAGTGCTACAAAGTCATGGACTT-TAGAGAAAAAG
1 TGCCACGAAGTTGTCGAC-TAAAAAGGAAAGAGTGCCAAAAAATCATGGACTTAAAAAGAAAAAG
* *
413192 GTGCCATAGAGTTGTGGACTTAAAAG
65 ATGCCACAGAGTTGTGGACTTAAAAG
413218 GAAAAGGGTG
Statistics
Matches: 77, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
92 50 0.65
93 27 0.35
ACGTcount: A:0.40, C:0.13, G:0.25, T:0.22
Consensus pattern (92 bp):
TGCCACGAAGTTGTCGACTAAAAAGGAAAGAGTGCCAAAAAATCATGGACTTAAAAAGAAAAAGA
TGCCACAGAGTTGTGGACTTAAAAGTG
Found at i:413205 original size:65 final size:65
Alignment explanation
Indices: 412962--413386 Score: 352
Period size: 65 Copynumber: 6.6 Consensus size: 65
412952 TTGGGCTTTA
* * * *
412962 GAAAAGGGTGCCAC-GAAGTTGTGGACTTTGAAGGAAAACA-GTGCCATGGAGTTATGGATTTAA
1 GAAAAGGGTGCCACAG-AGTCGTGGACTTT-AAAGAAAA-AGGTGCCATGGAGTTGTGGACTTAA
413025 AAGG
63 AA-G
* * * * * *** * *
413029 GAAAA-GCTGCCAC-GAAGTTGTCGACTTAAAAGGAAATA-GTGCCAAAAAATTATGGACTTAAA
1 GAAAAGGGTGCCACAG-AGTCGTGGACTTTAAA-GAAAAAGGTGCCATGGAGTTGTGGACTTAAA
*
413091 AA
64 AG
* * * * * *
413093 GAAAAAGATGCCACAGAGTTGTGGAC-TT-----AAAAGTGTGCCACGAAGTTGTGGACGTAAAA
1 GAAAAGGGTGCCACAGAGTCGTGGACTTTAAAGAAAAAG-GTGCCATGGAGTTGTGGACTTAAAA
*
413152 A
65 G
* * * * * * *
413153 GTAAAGAGTGCTACAAAGTCATGGACTTTAGAGAAAAAGGTGCCATAGAGTTGTGGACTTAAAAG
1 GAAAAGGGTGCCACAGAGTCGTGGACTTTAAAGAAAAAGGTGCCATGGAGTTGTGGACTTAAAAG
* * * **
413218 GAAAAGGGTGCCACCGAGTCGTGGACTTTAAAGAAAAAAAGTGTCATGGAGTTGTGGGTTTAAAA
1 GAAAAGGGTGCCACAGAGTCGTGGACTTTAAAG-AAAAAGGTGCCATGGAGTTGTGGACTTAAAA
413283 G
65 G
* * *
413284 GAAAAGGGTGCCATAGAGTTGTGGACTTTAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAAG
1 GAAAAGGGTGCCACAGAGTCGTGGACTTTAAAGAAAAAGGTGCCATGGAGTTGTGGACTTAAAAG
*
413349 GAAAAGGGTGCCACAGAGTCGTGGACTTTTAA-AAAAAG
1 GAAAAGGGTGCCACAGAGTCGTGGACTTTAAAGAAAAAG
413387 ATTTAAAGGA
Statistics
Matches: 290, Mismatches: 56, Indels: 27
0.78 0.15 0.07
Matches are distributed among these distances:
58 3 0.01
60 39 0.13
61 2 0.01
64 12 0.04
65 142 0.49
66 87 0.30
67 5 0.02
ACGTcount: A:0.38, C:0.12, G:0.29, T:0.21
Consensus pattern (65 bp):
GAAAAGGGTGCCACAGAGTCGTGGACTTTAAAGAAAAAGGTGCCATGGAGTTGTGGACTTAAAAG
Found at i:414425 original size:51 final size:51
Alignment explanation
Indices: 414370--414488 Score: 150
Period size: 51 Copynumber: 2.3 Consensus size: 51
414360 GGGATAACAA
** *
414370 CGGGGTTGGAGTATCTCC-GATTATGGAAAATCGGTGTTTTGGAAATAAAAT
1 CGGGGTTGGAGTATC-CCTGATTATGGAAAATCGACGTTTTGAAAATAAAAT
* * *
414421 CGGGGTTGGAATATCCCTGATTATTGAAAATTGACGTTTTGAAAATAAAAT
1 CGGGGTTGGAGTATCCCTGATTATGGAAAATCGACGTTTTGAAAATAAAAT
* *
414472 CGGGATTAGAGTATCCC
1 CGGGGTTGGAGTATCCC
414489 CTCGAAAATA
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
50 2 0.03
51 56 0.97
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.31
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCTGATTATGGAAAATCGACGTTTTGAAAATAAAAT
Found at i:414546 original size:79 final size:80
Alignment explanation
Indices: 414463--414630 Score: 196
Period size: 79 Copynumber: 2.1 Consensus size: 80
414453 GACGTTTTGA
* * * *
414463 AAATAAAATCGGGATTAGAGTATCCCCTCGAAAATAACGGGGTCGGAGTAT-CTCCGATTGTGAA
1 AAATAAAATCGGGATTAGAGTATCACCTCGAAAATAACAGGATCGAAGTATCCT-CGATTGTGAA
414527 AA-ATCGATGCTTTAG
65 AAGATCGATGCTTTAG
** * * * *
414542 AAATAAAGCCGGGGTTGGAGTATCACCTCGAAAATAACAGGATTGAAGTATCCTTGATTGTGAAA
1 AAATAAAATCGGGATTAGAGTATCACCTCGAAAATAACAGGATCGAAGTATCCTCGATTGTGAAA
* * *
414607 AGATTGGTGTTTTAG
66 AGATCGATGCTTTAG
414622 AAATAAAAT
1 AAATAAAAT
414631 TGAGGTTGAA
Statistics
Matches: 72, Mismatches: 15, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
79 53 0.74
80 19 0.26
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (80 bp):
AAATAAAATCGGGATTAGAGTATCACCTCGAAAATAACAGGATCGAAGTATCCTCGATTGTGAAA
AGATCGATGCTTTAG
Found at i:414662 original size:131 final size:130
Alignment explanation
Indices: 414509--414759 Score: 310
Period size: 131 Copynumber: 1.9 Consensus size: 130
414499 ACGGGGTCGG
* * * * *
414509 AGTATCTCCGATTGTGAAAAATCGATGCTTTAGAAATAAAGCCGG-GGTTGGAGTATCACCTCGA
1 AGTATCTCCGATTGTGAAAAATCAATACTTTAGAAATAAAACCGGAAGTTAGAGTATCACCTCGA
* * * *
414573 AAATAACAG-GATTGAAGTATCCTTGATTGTGAAAAGATTGGTGTTTTAGAAATAAAATTGAGGT
66 AAATAA-AGAGATTGAAGTATCCTCGATTATGAAAA-ATTGATGTTTT-GAAAAAAAATTGAGGT
414637 TGA
128 TGA
* * *
414640 AGTATC-CTCGATTGTGAGAAATCAATATTTTAGAAATAAAACCGGAAGTTAGAGTATCGCCTCG
1 AGTATCTC-CGATTGTGAAAAATCAATACTTTAGAAATAAAACCGGAAGTTAGAGTATCACCTCG
* * *
414704 AAAATAAGGAGATTGGAGTATCCTCGATTATGAGAAATTGATGTTTTGAAAAAAAA
65 AAAATAAAGAGATTGAAGTATCCTCGATTATGAAAAATTGATGTTTTGAAAAAAAA
414760 AACCAGGGTT
Statistics
Matches: 102, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
130 9 0.09
131 49 0.48
132 44 0.43
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (130 bp):
AGTATCTCCGATTGTGAAAAATCAATACTTTAGAAATAAAACCGGAAGTTAGAGTATCACCTCGA
AAATAAAGAGATTGAAGTATCCTCGATTATGAAAAATTGATGTTTTGAAAAAAAATTGAGGTTGA
Found at i:414776 original size:132 final size:131
Alignment explanation
Indices: 414493--414782 Score: 302
Period size: 132 Copynumber: 2.2 Consensus size: 131
414483 TATCCCCTCG
* * * * * * *
414493 AAAATAACGGGGTCGGAGTAT-CTCCGATTGTGAAAAATCGATGCTTTAGAAATAAAGCCGGGGT
1 AAAAAAACAGGGTTGGAGTATCCTCCGATTGTGAAAAATCAATACTTTAGAAATAAAACCGGAGT
* * * * *
414557 TGGAGTATCACCTCGAAAATAACAGGATTGAAGTATCCTTGATTGTGAAAAGATTGGTGTTTTAG
66 TAGAGTATCACCTCGAAAATAACAGGATTGAAGTATCCTCGATTATGAAAAGATTGATGTTTTAA
414622 A
131 A
* ** * * *
414623 AATAAAATTGAGGTTGAAGTATCCT-CGATTGTGAGAAATCAATATTTTAGAAATAAAACCGGAA
1 AAAAAAACAG-GGTTGGAGTATCCTCCGATTGTGAAAAATCAATACTTTAGAAATAAAACCGG-A
* * * *
414687 GTTAGAGTATCGCCTCGAAAATAA-GGAGATTGGAGTATCCTCGATTATGAGAA-ATTGATGTTT
64 GTTAGAGTATCACCTCGAAAATAACAG-GATTGAAGTATCCTCGATTATGAAAAGATTGATGTTT
414750 TGAAA
128 T-AAA
414755 AAAAAAACCAGGGTTGGAGTAT-CTCCGA
1 AAAAAAA-CAGGGTTGGAGTATCCTCCGA
414783 GATGAAAAAT
Statistics
Matches: 128, Mismatches: 25, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
130 6 0.05
131 54 0.42
132 67 0.52
133 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.28
Consensus pattern (131 bp):
AAAAAAACAGGGTTGGAGTATCCTCCGATTGTGAAAAATCAATACTTTAGAAATAAAACCGGAGT
TAGAGTATCACCTCGAAAATAACAGGATTGAAGTATCCTCGATTATGAAAAGATTGATGTTTTAA
A
Found at i:417148 original size:13 final size:13
Alignment explanation
Indices: 417130--417159 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
417120 GTAAACCTAG
417130 AATGTATCGATAC
1 AATGTATCGATAC
417143 AATGTATCGATAC
1 AATGTATCGATAC
417156 AATG
1 AATG
417160 AATAATGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:417178 original size:62 final size:63
Alignment explanation
Indices: 417081--417207 Score: 184
Period size: 62 Copynumber: 2.0 Consensus size: 63
417071 AAAATGCGTA
* * * *
417081 AATGTATTGATACATTGAAAAATGTATCGATACATCTGGGT-AAACCTAGAATGTATCGATAC
1 AATGTATCGATACAATGAAAAATGTATCGATACATCTAGGTAAAACCCAGAATGTATCGATAC
* * *
417143 AATGTATCGATACAATGAATAATGTATTGATACATCTAGGTAAAACCCAGAATGTATCGTTAC
1 AATGTATCGATACAATGAAAAATGTATCGATACATCTAGGTAAAACCCAGAATGTATCGATAC
417206 AA
1 AA
417208 ATTGTGAATG
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
62 36 0.63
63 21 0.37
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (63 bp):
AATGTATCGATACAATGAAAAATGTATCGATACATCTAGGTAAAACCCAGAATGTATCGATAC
Found at i:423389 original size:2 final size:2
Alignment explanation
Indices: 423377--423412 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
423367 CTTAATTACT
* *
423377 TA TA TA CA TA TA TA CA 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
423413 AATACCTAAA
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:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:424615 original size:19 final size:18
Alignment explanation
Indices: 424591--424628 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
424581 TATTAAAGCT
*
424591 TATTTTGTTTTAGATTTAA
1 TATTTTGATTTA-ATTTAA
424610 TATTTTGATTTAATTTAA
1 TATTTTGATTTAATTTAA
424628 T
1 T
424629 TAAAGTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (18 bp):
TATTTTGATTTAATTTAA
Found at i:428007 original size:14 final size:14
Alignment explanation
Indices: 427988--428020 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
427978 ATGAAACAAC
*
427988 TCAAAAAGTAAACA
1 TCAAAAAGAAAACA
428002 TCAAAAAGAAAACA
1 TCAAAAAGAAAACA
428016 TCAAA
1 TCAAA
428021 GTTGATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.67, C:0.15, G:0.06, T:0.12
Consensus pattern (14 bp):
TCAAAAAGAAAACA
Found at i:428833 original size:2 final size:2
Alignment explanation
Indices: 428826--428858 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
428816 ATTGTTAGTG
428826 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
428859 GTGGTTTTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:429345 original size:20 final size:20
Alignment explanation
Indices: 429322--429380 Score: 61
Period size: 18 Copynumber: 3.1 Consensus size: 20
429312 TTTAATATTT
429322 ATATTTTATAATTAAATAAA
1 ATATTTTATAATTAAATAAA
* *
429342 ATATTTTATTA-TAAA-ATA
1 ATATTTTATAATTAAATAAA
* *
429360 ATAATTTA-AATTAAATTAA
1 ATATTTTATAATTAAATAAA
429379 AT
1 AT
429381 TAAATTAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
17 1 0.03
18 13 0.42
19 7 0.23
20 10 0.32
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATATTTTATAATTAAATAAA
Found at i:429373 original size:5 final size:5
Alignment explanation
Indices: 429365--429389 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
429355 AAATAATAAT
429365 TTAAA TTAAA TTAAA TTAAA TTAAA
1 TTAAA TTAAA TTAAA TTAAA TTAAA
429390 AAAATTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TTAAA
Found at i:431408 original size:15 final size:16
Alignment explanation
Indices: 431384--431416 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
431374 ATGTTGACTT
*
431384 TTTTATTTTTATA-AA
1 TTTTAATTTTATATAA
431399 TTTTAATTTTATATAA
1 TTTTAATTTTATATAA
431415 TT
1 TT
431417 AAAAATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTAATTTTATATAA
Found at i:431422 original size:23 final size:23
Alignment explanation
Indices: 431391--431447 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
431381 CTTTTTTATT
* * * *
431391 TTTATAAATTTTAATTTTATATA
1 TTTAAAAATTATAAATTTATAAA
* *
431414 ATTAAAAATAATAAATTTATAAA
1 TTTAAAAATTATAAATTTATAAA
431437 TTTAAAAATTA
1 TTTAAAAATTA
431448 AAAAAATCTT
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TTTAAAAATTATAAATTTATAAA
Found at i:431429 original size:30 final size:30
Alignment explanation
Indices: 431394--431451 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
431384 TTTTATTTTT
* *
431394 ATAAATTT-TAATTTTATATAATTAAAAATA
1 ATAAATTTATAAATTTA-AAAATTAAAAATA
431424 ATAAATTTATAAATTTAAAAATTAAAAA
1 ATAAATTTATAAATTTAAAAATTAAAAA
431452 AATCTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 18 0.72
31 7 0.28
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (30 bp):
ATAAATTTATAAATTTAAAAATTAAAAATA
Found at i:431895 original size:16 final size:16
Alignment explanation
Indices: 431887--431922 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
431877 TTAAATTTTT
431887 TTAAATTTAAATTAAA
1 TTAAATTTAAATTAAA
431903 TTAAATTTAAA-TAAA
1 TTAAATTTAAATTAAA
431918 TTAAA
1 TTAAA
431923 AAATAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TTAAATTTAAATTAAA
Found at i:431931 original size:23 final size:22
Alignment explanation
Indices: 431900--431942 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
431890 AATTTAAATT
* *
431900 AAATTAAATTTAAATAAATTAAA
1 AAATAAAATATAAA-AAATTAAA
431923 AAATAAAATATAAAAAATTA
1 AAATAAAATATAAAAAATTA
431943 TTTTATATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (22 bp):
AAATAAAATATAAAAAATTAAA
Found at i:431955 original size:16 final size:18
Alignment explanation
Indices: 431930--431969 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
431920 AAAAAATAAA
* *
431930 ATATAAAAAATTATTT-T
1 ATATTAAAATTTATTTAT
431947 ATATTAAAATTTATTTAT
1 ATATTAAAATTTATTTAT
431965 ATATT
1 ATATT
431970 TTATAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATTAAAATTTATTTAT
Found at i:432036 original size:19 final size:20
Alignment explanation
Indices: 432012--432051 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
432002 TAACTGATAA
432012 TAATTTAAATT-AAATAAAT
1 TAATTTAAATTAAAATAAAT
432031 TAATTTAAATTAAAATAAAT
1 TAATTTAAATTAAAATAAAT
432051 T
1 T
432052 TTAAATTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TAATTTAAATTAAAATAAAT
Found at i:434687 original size:26 final size:25
Alignment explanation
Indices: 434658--434781 Score: 76
Period size: 26 Copynumber: 4.8 Consensus size: 25
434648 CGTAATCTTT
434658 AATATTAATATATTGTATTAATATTA
1 AATATTAATATATT-TATTAATATTA
* * *
434684 AATATTTATATATTTTTTATTATTAA
1 AATATTAATATATTTATTAATATT-A
*
434710 AACATTAAT-TA--TA-TAGATATTTAA
1 AATATTAATATATTTATTA-ATA-TT-A
* *
434734 AATATTAAAATAATTATTAAAATATTA
1 AATATTAATATATTTATT--AATATTA
*
434761 TTTATATTAATATATTTATTA
1 --AATATTAATATATTTATTA
434782 CTAGATTAAT
Statistics
Matches: 75, Mismatches: 12, Indels: 21
0.69 0.11 0.19
Matches are distributed among these distances:
22 2 0.03
23 3 0.04
24 11 0.15
25 12 0.16
26 21 0.28
27 4 0.05
28 3 0.04
29 18 0.24
30 1 0.01
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.51
Consensus pattern (25 bp):
AATATTAATATATTTATTAATATTA
Found at i:434769 original size:20 final size:20
Alignment explanation
Indices: 434693--434769 Score: 52
Period size: 20 Copynumber: 3.8 Consensus size: 20
434683 AAATATTTAT
434693 ATATT-TTT-TATTATTAAA
1 ATATTATTTATATTATTAAA
* *
434711 ACATTAATTATATAGATATTTAAA
1 ATATT-ATT-TATA-TTA-TTAAA
**
434735 ATATTA-AAATAATTATTAAA
1 ATATTATTTAT-ATTATTAAA
434755 ATATTATTTATATTA
1 ATATTATTTATATTA
434770 ATATATTTAT
Statistics
Matches: 43, Mismatches: 8, Indels: 14
0.66 0.12 0.22
Matches are distributed among these distances:
18 4 0.09
20 17 0.40
21 7 0.16
22 3 0.07
23 3 0.07
24 9 0.21
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (20 bp):
ATATTATTTATATTATTAAA
Found at i:434790 original size:73 final size:73
Alignment explanation
Indices: 434713--434859 Score: 267
Period size: 73 Copynumber: 2.0 Consensus size: 73
434703 TTATTAAAAC
*
434713 ATTAATTATATAGATATTTAAAATATTAAAATAATTATTAAAATATTATTTATATTAATATATTT
1 ATTAATTATATAGATATTTAAAATATTAAAATAATTATTAAAATATTATTTATAGTAATATATTT
434778 ATTACTAG
66 ATTACTAG
*
434786 ATTAATTATATAGATATTTAAAATATTAAAATAATTATTAAAGTATTATTTATAGTAATATATTT
1 ATTAATTATATAGATATTTAAAATATTAAAATAATTATTAAAATATTATTTATAGTAATATATTT
*
434851 ATTATTAG
66 ATTACTAG
434859 A
1 A
434860 ATATTATTAT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.48
Consensus pattern (73 bp):
ATTAATTATATAGATATTTAAAATATTAAAATAATTATTAAAATATTATTTATAGTAATATATTT
ATTACTAG
Found at i:435074 original size:54 final size:56
Alignment explanation
Indices: 435002--435115 Score: 137
Period size: 55 Copynumber: 2.1 Consensus size: 56
434992 ATAGTTATTT
* *
435002 AAATACTTAAAATAATAATATTTAGT-AT-TAAAACATTAGTTATATAAATATTT-TA
1 AAATACTTAAAATAATAATAATTAGTAATAAAAAACATTA-TTAT-TAAATATTTATA
* * *
435057 AAATATTTAGAAT-ATAATAATTATTAATAAAAAACATTATTATTAAATATTTATA
1 AAATACTTAAAATAATAATAATTAGTAATAAAAAACATTATTATTAAATATTTATA
435112 AAAT
1 AAAT
435116 TTGTTATTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
54 19 0.37
55 23 0.45
56 9 0.18
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (56 bp):
AAATACTTAAAATAATAATAATTAGTAATAAAAAACATTATTATTAAATATTTATA
Found at i:435652 original size:17 final size:17
Alignment explanation
Indices: 435620--435662 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
435610 AAGGAGCTAA
435620 AAAATATTTA-AACAAT
1 AAAATATTTATAACAAT
*
435636 AAAATATTTATACCAAT
1 AAAATATTTATAACAAT
*
435653 ATAA-ATTTAT
1 AAAATATTTAT
435663 TGTATTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (17 bp):
AAAATATTTATAACAAT
Found at i:435703 original size:19 final size:20
Alignment explanation
Indices: 435679--435722 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
435669 ATTTGTTTTT
**
435679 AATTATTTATTAAATTTA-A
1 AATTATTTAAAAAATTTACA
435698 AATTATTTAAAAAATTTACA
1 AATTATTTAAAAAATTTACA
435718 AATTA
1 AATTA
435723 AACTAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
AATTATTTAAAAAATTTACA
Found at i:444532 original size:103 final size:103
Alignment explanation
Indices: 444350--444573 Score: 268
Period size: 103 Copynumber: 2.2 Consensus size: 103
444340 ATTTCTTATT
* * * **
444350 CATGGGTATACTCCAACCCTGACCTTTTAAATGGATACTCTAACCCCACTTTTTGAAATTTGTCA
1 CATGGGAATACTCCAACCCTGACCTTTCAAAGGGATACTCTAACCCCACTTTTCAAAATTTGTCA
* * *
444415 GGATTGGAAGTTTTCTTTTGTCAAAATCATTGGTCATC
66 AGATTGGAACTTTTCCTTTGTCAAAATCATTGGTCATC
* * * * **
444453 CATGGGGATACCCCAACCCTGACCTTTCGAAGGGATACTCTAACTCTGCTTTTCAAAATTTGTCA
1 CATGGGAATACTCCAACCCTGACCTTTCAAAGGGATACTCTAACCCCACTTTTCAAAATTTGTCA
* * * *
444518 AGATTTGAACTTTTCCTTTGTTAAAATTATTTGTCATC
66 AGATTGGAACTTTTCCTTTGTCAAAATCATTGGTCATC
* *
444556 AACGGGAATACTCCAACC
1 CATGGGAATACTCCAACC
444574 TTATTTTTTC
Statistics
Matches: 100, Mismatches: 21, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
103 100 1.00
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (103 bp):
CATGGGAATACTCCAACCCTGACCTTTCAAAGGGATACTCTAACCCCACTTTTCAAAATTTGTCA
AGATTGGAACTTTTCCTTTGTCAAAATCATTGGTCATC
Found at i:444584 original size:103 final size:102
Alignment explanation
Indices: 444357--444600 Score: 238
Period size: 103 Copynumber: 2.4 Consensus size: 102
444347 ATTCATGGGT
* ** * ** *
444357 ATACTCCAACCCTGACCTTTTAAATGGATACTCTAACCCCACTTTTTGAAATTTGTCAGGATTGG
1 ATACCCCAACCCTGACC-TTTCGAGGGATACTCTAACCCCACTTTTCAAAATTTGTCAAGATTGG
* * * * *
444422 AAGTTTTCTTTTGTCAAAATCATTGGTCATCCATGGGG
65 AACTTTTCCTTTGTCAAAATCATTGGTCATCAACGGGA
* ** *
444460 ATACCCCAACCCTGACCTTTCGAAGGGATACTCTAACTCTGCTTTTCAAAATTTGTCAAGATTTG
1 ATACCCCAACCCTGACCTTTCG-AGGGATACTCTAACCCCACTTTTCAAAATTTGTCAAGATTGG
* * *
444525 AACTTTTCCTTTGTTAAAATTATTTGTCATCAACGGGA
65 AACTTTTCCTTTGTCAAAATCATTGGTCATCAACGGGA
* * **
444563 ATACTCCAA-CCTTATTTTTTCGAGGAGATACTCTAACC
1 ATACCCCAACCCTGA-CCTTTCGAGG-GATACTCTAACC
444601 TCGCCTTTCA
Statistics
Matches: 114, Mismatches: 24, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
102 10 0.09
103 104 0.91
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (102 bp):
ATACCCCAACCCTGACCTTTCGAGGGATACTCTAACCCCACTTTTCAAAATTTGTCAAGATTGGA
ACTTTTCCTTTGTCAAAATCATTGGTCATCAACGGGA
Found at i:450186 original size:79 final size:79
Alignment explanation
Indices: 450093--450315 Score: 236
Period size: 79 Copynumber: 2.8 Consensus size: 79
450083 TCATTCATGT
* * **
450093 TTTTATTTCCAAAACACCAATTTTTTTACAATCGAAATACTCCAACCCCGTTATTTCCGAGGGGA
1 TTTTATTTTCAAAACACCAATTTTTTTACAATCGAAATACTCCAACCCCGTTATTTCCAAAAGGA
450158 TACTCCAACCCCGG
66 TACTCCAACCCCGG
* * * ** **
450172 TTTTATTTTCAAAACACCAATTTTTCATA-ATTGGGGATACTCCAACCTTGTTATTTCCAAAAGG
1 TTTTATTTTCAAAACACCAATTTTT-TTACAATCGAAATACTCCAACCCCGTTATTTCCAAAAGG
450236 ATACTCCAACCCCGG
65 ATACTCCAACCCCGG
* ** *
450251 TTTTA-TTTCTAAAACATCAA-TTTTTTACAATCGGGGATACTCTAACCCCGATTTTATTTCCAA
1 TTTTATTTTC-AAAACACCAATTTTTTTACAATC-GAAATACTCCAACCCCG---TTATTTCCAA
450314 AA
61 AA
450316 CATCAATTTT
Statistics
Matches: 119, Mismatches: 18, Indels: 11
0.80 0.12 0.07
Matches are distributed among these distances:
77 2 0.02
78 10 0.08
79 93 0.78
80 2 0.02
82 12 0.10
ACGTcount: A:0.30, C:0.25, G:0.10, T:0.35
Consensus pattern (79 bp):
TTTTATTTTCAAAACACCAATTTTTTTACAATCGAAATACTCCAACCCCGTTATTTCCAAAAGGA
TACTCCAACCCCGG
Found at i:450310 original size:51 final size:51
Alignment explanation
Indices: 450234--450362 Score: 172
Period size: 51 Copynumber: 2.6 Consensus size: 51
450224 ATTTCCAAAA
* * * **
450234 GGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTTACAATCGG
1 GGATACTCTAACCCCGATTTTATTTCCAAAACATCAATTTTCCACAATCGG
*
450285 GGATACTCTAACCCCGATTTTATTTCCAAAACATCAATTTTCCACCATCGG
1 GGATACTCTAACCCCGATTTTATTTCCAAAACATCAATTTTCCACAATCGG
* *
450336 GGATACTCTAATCCC-A-GTTATTTCCAA
1 GGATACTCTAACCCCGATTTTATTTCCAA
450363 GGGGATACTC
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
49 10 0.14
50 1 0.01
51 59 0.84
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.33
Consensus pattern (51 bp):
GGATACTCTAACCCCGATTTTATTTCCAAAACATCAATTTTCCACAATCGG
Found at i:450437 original size:51 final size:51
Alignment explanation
Indices: 450382--450478 Score: 140
Period size: 51 Copynumber: 1.9 Consensus size: 51
450372 CCAACCCTAG
* * *
450382 TTTTATTTCTAAAACATCAATTTTCCACAATTGGGGATACTGTAACTTCGA
1 TTTTATTTCCAAAACATCAATTTTCCACAATCGGGGATACTCTAACTTCGA
* * *
450433 TTTTATTTCCAAAACATCGATTTTTCACCATCGGGGATACTCTAAC
1 TTTTATTTCCAAAACATCAATTTTCCACAATCGGGGATACTCTAAC
450479 CCCGTTATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 40 1.00
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (51 bp):
TTTTATTTCCAAAACATCAATTTTCCACAATCGGGGATACTCTAACTTCGA
Found at i:450507 original size:28 final size:30
Alignment explanation
Indices: 450466--450524 Score: 86
Period size: 28 Copynumber: 2.0 Consensus size: 30
450456 TTCACCATCG
*
450466 GGGATACTCTAACCCC-G-TTATTTCTAAA
1 GGGATACTCCAACCCCGGTTTATTTCTAAA
450494 GGGATACTCCAACCCCGGTTTTATTTCTAAA
1 GGGATACTCCAACCCCGG-TTTATTTCTAAA
450525 AAATCAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 15 0.56
29 1 0.04
31 11 0.41
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.32
Consensus pattern (30 bp):
GGGATACTCCAACCCCGGTTTATTTCTAAA
Found at i:450549 original size:130 final size:130
Alignment explanation
Indices: 450153--450640 Score: 672
Period size: 130 Copynumber: 3.7 Consensus size: 130
450143 TTATTTCCGA
* ** * * * * *
450153 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTTCATAATTGGGGATACTCCAAC
1 GGGGATACTCTAACTTCGATTTTATTTCCAAAACATCAATTTTTCACAATCGGGGATACTCCAAC
** * **
450218 CTTGTTATTTCCAAAAGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTTACAATC
66 CCAGTTATTTCCAAAGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTCCACAATC
** * * *
450283 GGGGATACTCTAACCCCGATTTTATTTCCAAAACATCAATTTTCCACCATCGGGGATACTCTAAT
1 GGGGATACTCTAACTTCGATTTTATTTCCAAAACATCAATTTTTCACAATCGGGGATACTCCAA-
* **
450348 CCCAGTTATTTCCAAGGGGATACTCCAACCCTAGTTTTATTTCTAAAACATCAATTTTCCACAAT
65 CCCAGTTATTTCCAAAGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTCCACAAT
*
450413 T
130 C
* * * *
450414 GGGGATACTGTAACTTCGATTTTATTTCCAAAACATCGATTTTTCACCATCGGGGATACTCTAAC
1 GGGGATACTCTAACTTCGATTTTATTTCCAAAACATCAATTTTTCACAATCGGGGATACTCCAAC
* * *
450479 CCCGTTATTTCTAAAGGGATACTCCAACCCCGGTTTTATTTCTAAAAAATCAATTTTCCACAATC
66 CCAGTTATTTCCAAAGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTCCACAATC
*
450544 GGGGATACTCTAACTTCGATTTTATTTCCAAAACATCAATTTTTCACAATCGAGGATACTCCAAC
1 GGGGATACTCTAACTTCGATTTTATTTCCAAAACATCAATTTTTCACAATCGGGGATACTCCAAC
*
450609 CCAGTTATTT-CATTAGGGATACTCCAACCCCG
66 CCAGTTATTTCCA-AAGGGATACTCCAACCCCG
450641 TTATTTCTGA
Statistics
Matches: 318, Mismatches: 38, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
129 1 0.00
130 201 0.63
131 116 0.36
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (130 bp):
GGGGATACTCTAACTTCGATTTTATTTCCAAAACATCAATTTTTCACAATCGGGGATACTCCAAC
CCAGTTATTTCCAAAGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTCCACAATC
Found at i:450567 original size:51 final size:51
Alignment explanation
Indices: 450494--450610 Score: 162
Period size: 51 Copynumber: 2.3 Consensus size: 51
450484 TATTTCTAAA
* *
450494 GGGATACTCCAACCCCGGTTTTATTTCTAAAAAATCAATTTTCCACAATCG
1 GGGATACTCCAACCCCGATTTTATTTCCAAAAAATCAATTTTCCACAATCG
* ** * *
450545 GGGATACTCTAACTTCGATTTTATTTCCAAAACATCAATTTTTCACAATCG
1 GGGATACTCCAACCCCGATTTTATTTCCAAAAAATCAATTTTCCACAATCG
*
450596 AGGATACTCCAACCC
1 GGGATACTCCAACCC
450611 AGTTATTTCA
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.32
Consensus pattern (51 bp):
GGGATACTCCAACCCCGATTTTATTTCCAAAAAATCAATTTTCCACAATCG
Found at i:450667 original size:28 final size:28
Alignment explanation
Indices: 450597--450670 Score: 105
Period size: 28 Copynumber: 2.6 Consensus size: 28
450587 TCACAATCGA
* *
450597 GGATACTCCAACCCAGTTATTTCATTAG
1 GGATACTCCAACCCCGTTATTTCATGAG
450625 GGATACTCCAACCCCGTTATTTC-TGAGG
1 GGATACTCCAACCCCGTTATTTCATGA-G
*
450653 GGATACTCCAGCCCCGTT
1 GGATACTCCAACCCCGTT
450671 GTTATCTCCA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
27 2 0.05
28 40 0.95
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTATTTCATGAG
Found at i:452703 original size:52 final size:51
Alignment explanation
Indices: 452641--452776 Score: 157
Period size: 51 Copynumber: 2.6 Consensus size: 51
452631 AATTTATTGG
* ** * *
452641 ATGTATCGATACATTGAAGAATGTATCGATACCCTTAGG-TCAAAAACCTATA
1 ATGTATCGATACAATGAAGAATGTATCGATACAATT-GGATC-AAAACCCAGA
* *
452693 ATGTATCGATACAATGATGAATGGATCGATACAATTGGATCAAAACCCAGA
1 ATGTATCGATACAATGAAGAATGTATCGATACAATTGGATCAAAACCCAGA
* * *
452744 ATGCATCGATACAATGAAAAATGTATCAATACA
1 ATGTATCGATACAATGAAGAATGTATCGATACA
452777 TTTATTTCCA
Statistics
Matches: 71, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
51 38 0.54
52 33 0.46
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (51 bp):
ATGTATCGATACAATGAAGAATGTATCGATACAATTGGATCAAAACCCAGA
Found at i:456836 original size:20 final size:20
Alignment explanation
Indices: 456813--456864 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
456803 TTGCAAAATG
456813 TATTGATACATTACT-ATTTA
1 TATTGATACATTACTCA-TTA
*
456833 TATTGATACATTATTCATTA
1 TATTGATACATTACTCATTA
*
456853 TATCGATACATT
1 TATTGATACATT
456865 CTGGGTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.48
Consensus pattern (20 bp):
TATTGATACATTACTCATTA
Found at i:461346 original size:31 final size:31
Alignment explanation
Indices: 461239--461469 Score: 151
Period size: 31 Copynumber: 7.5 Consensus size: 31
461229 GCCTTAGAAT
* * * **
461239 GTCAAAGCCCACACAAGTTAGTGACACCTTG
1 GTCAAAGCCCGCACGAGTTGGTGACACCTAA
* * * * * *
461270 GACAAAGCCTGCACAAGCTGGCGACACCTGA
1 GTCAAAGCCCGCACGAGTTGGTGACACCTAA
* * *
461301 GTTACAA-CCCGCACTAGTTGGTGGCATCCT-A
1 GTCA-AAGCCCGCACGAGTTGGTGACA-CCTAA
* * * * *
461332 GTCAAAGCCCGCACTAGCTGATGACACTTGA
1 GTCAAAGCCCGCACGAGTTGGTGACACCTAA
* * **
461363 GTCTAAGCTCGCACGAGTTGGTGGTACCTAA
1 GTCAAAGCCCGCACGAGTTGGTGACACCTAA
* *
461394 GTCAAAGCCCGCACAAGCTGGTGACACCTAA
1 GTCAAAGCCCGCACGAGTTGGTGACACCTAA
* ** * *
461425 GTCTAAGCCTACACGAGTTGGCGACACCTGA
1 GTCAAAGCCCGCACGAGTTGGTGACACCTAA
*
461456 GCCAAAGCCCGCAC
1 GTCAAAGCCCGCAC
461470 AAACTAGCGG
Statistics
Matches: 150, Mismatches: 46, Indels: 8
0.74 0.23 0.04
Matches are distributed among these distances:
30 4 0.03
31 141 0.94
32 5 0.03
ACGTcount: A:0.28, C:0.30, G:0.24, T:0.18
Consensus pattern (31 bp):
GTCAAAGCCCGCACGAGTTGGTGACACCTAA
Found at i:461533 original size:31 final size:31
Alignment explanation
Indices: 461393--461567 Score: 89
Period size: 31 Copynumber: 5.6 Consensus size: 31
461383 GTGGTACCTA
* ** * *
461393 AGTCAAAGCCCGCACAAGCTGGTGACACCTA
1 AGTCAAAGCCCGCACAAGTTGGCAACACTTG
* ** * * *
461424 AGTCTAAGCCTACACGAGTTGGCGACACCTG
1 AGTCAAAGCCCGCACAAGTTGGCAACACTTG
* ** * ** *
461455 AGCCAAAGCCCGCACAAACTAGCGGCACCTG
1 AGTCAAAGCCCGCACAAGTTGGCAACACTTG
* * ** *
461486 AGGCTAAGCCTACACAAGTTGGCAACTCTTG
1 AGTCAAAGCCCGCACAAGTTGGCAACACTTG
* **
461517 AGTCAAAGCCCGCACAAGCTGGCGGCACTTG
1 AGTCAAAGCCCGCACAAGTTGGCAACACTTG
* * *
461548 ATTCTAAGCCCGCATAAGTT
1 AGTCAAAGCCCGCACAAGTT
461568 AGCGCAAACT
Statistics
Matches: 105, Mismatches: 39, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
31 105 1.00
ACGTcount: A:0.29, C:0.31, G:0.23, T:0.17
Consensus pattern (31 bp):
AGTCAAAGCCCGCACAAGTTGGCAACACTTG
Found at i:461567 original size:62 final size:62
Alignment explanation
Indices: 461272--461557 Score: 218
Period size: 62 Copynumber: 4.6 Consensus size: 62
461262 ACACCTTGGA
* * * ** * ***
461272 CAAAGCCTGCACAAGCTGGCGACACCTGAGT-TACAACCCGCACTAGTTGGTGGCATCCT-AGT
1 CAAAGCCCGCACAAGCTGGCGGCACCTGAGTCTA-AGCCTACACAAGTTGGCAACA-CCTGAGT
* ** * * * * **** *
461334 CAAAGCCCGCACTAGCTGATGACACTTGAGTCTAAG-CTCGCACGAGTTGGTGGTACCTAAGT
1 CAAAGCCCGCACAAGCTGGCGGCACCTGAGTCTAAGCCT-ACACAAGTTGGCAACACCTGAGT
* * * * * *
461396 CAAAGCCCGCACAAGCTGGTGACACCTAAGTCTAAGCCTACACGAGTTGGCGACACCTGAGC
1 CAAAGCCCGCACAAGCTGGCGGCACCTGAGTCTAAGCCTACACAAGTTGGCAACACCTGAGT
* * * * *
461458 CAAAGCCCGCACAAACTAGCGGCACCTGAGGCTAAGCCTACACAAGTTGGCAACTCTTGAGT
1 CAAAGCCCGCACAAGCTGGCGGCACCTGAGTCTAAGCCTACACAAGTTGGCAACACCTGAGT
* *
461520 CAAAGCCCGCACAAGCTGGCGGCACTTGATTCTAAGCC
1 CAAAGCCCGCACAAGCTGGCGGCACCTGAGTCTAAGCC
461558 CGCATAAGTT
Statistics
Matches: 185, Mismatches: 35, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
61 4 0.02
62 177 0.96
63 4 0.02
ACGTcount: A:0.28, C:0.30, G:0.24, T:0.18
Consensus pattern (62 bp):
CAAAGCCCGCACAAGCTGGCGGCACCTGAGTCTAAGCCTACACAAGTTGGCAACACCTGAGT
Found at i:461633 original size:31 final size:31
Alignment explanation
Indices: 461595--461659 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
461585 CCTAAGTTTG
** *
461595 AGTCAAAGCCTGCACAAGTTGATGGCACCTA
1 AGTCAAAGCCCACACAAGCTGATGGCACCTA
*
461626 AGTCAAAGCCCACACAAGCTGGTGGCACCTA
1 AGTCAAAGCCCACACAAGCTGATGGCACCTA
461657 AGT
1 AGT
461660 TCGAGTCAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.32, C:0.28, G:0.23, T:0.17
Consensus pattern (31 bp):
AGTCAAAGCCCACACAAGCTGATGGCACCTA
Found at i:461772 original size:31 final size:30
Alignment explanation
Indices: 461725--461902 Score: 124
Period size: 31 Copynumber: 5.8 Consensus size: 30
461715 TCAAAGCCTA
* *
461725 CACGAGCTGGCGGCACCTGAGTCTAAGCTCG
1 CACGAGTTGGCGGCACCTAAGTCTAAGC-CG
* * * *
461756 CACGAGTTGGCAGCACCAAAGTCAAAGCCCA
1 CACGAGTTGGCGGCACCTAAGTCTAAG-CCG
* ** *
461787 CACAAGTTGGTTGCACCTGAGTCTAAGCCCG
1 CACGAGTTGGCGGCACCTAAGTCTAAG-CCG
* * * *
461818 TATGAGTTGGTGGCACCCT-AGTCAAAGCCTG
1 CACGAGTTGGCGGCA-CCTAAGTCTAAGCC-G
* * *
461849 CACAAGCTGACGGCACCTAAGTCTAAGCCTG
1 CACGAGTTGGCGGCACCTAAGTCTAAGCC-G
* *
461880 CACGAGTTGGTGGCATCTAAGTC
1 CACGAGTTGGCGGCACCTAAGTC
461903 AAATCCCACA
Statistics
Matches: 113, Mismatches: 30, Indels: 8
0.75 0.20 0.05
Matches are distributed among these distances:
30 5 0.04
31 104 0.92
32 4 0.04
ACGTcount: A:0.25, C:0.29, G:0.27, T:0.19
Consensus pattern (30 bp):
CACGAGTTGGCGGCACCTAAGTCTAAGCCG
Found at i:461811 original size:62 final size:61
Alignment explanation
Indices: 461714--461926 Score: 228
Period size: 62 Copynumber: 3.4 Consensus size: 61
461704 GCCTTAGAAT
* * **
461714 GTCAAAGCCTACACGAGCTGGCGGCACCTGAGTCTAAGCTCGCACGAGTTGGCAGCACCAAA
1 GTCAAAGCCCACACAAGCTGGCGGCACCTGAGTCTAAGC-CGCACGAGTTGGTGGCACCAAA
* ** * * **
461776 GTCAAAGCCCACACAAGTTGGTTGCACCTGAGTCTAAGCCCGTATGAGTTGGTGGCACCCTA
1 GTCAAAGCCCACACAAGCTGGCGGCACCTGAGTCTAAG-CCGCACGAGTTGGTGGCACCAAA
** * * * *
461838 GTCAAAGCCTGCACAAGCTGACGGCACCTAAGTCTAAGCCTGCACGAGTTGGTGGCATCTAA
1 GTCAAAGCCCACACAAGCTGGCGGCACCTGAGTCTAAGCC-GCACGAGTTGGTGGCACCAAA
* *
461900 GTCAAATCCCACACAAGCTGGTGGCAC
1 GTCAAAGCCCACACAAGCTGGCGGCAC
461927 GTAAGTTCGA
Statistics
Matches: 121, Mismatches: 28, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
61 2 0.02
62 118 0.98
63 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.26, T:0.18
Consensus pattern (61 bp):
GTCAAAGCCCACACAAGCTGGCGGCACCTGAGTCTAAGCCGCACGAGTTGGTGGCACCAAA
Found at i:462060 original size:86 final size:87
Alignment explanation
Indices: 461900--462071 Score: 249
Period size: 86 Copynumber: 2.0 Consensus size: 87
461890 TGGCATCTAA
* * * * *
461900 GTCAAATCCCACACAAGCTGGTGGCACGTAAGTTCGAGTCAAGTCCATATTAGTTGGCACCTATC
1 GTCAAAGCCCACACAAGCTAGTGGCACCTAAGATCGAGTCAAGTCCACATTAGTTGGCACCTATC
461965 TGAAGAGGTCAAGCCTTAGAAT
66 TGAAGAGGTCAAGCCTTAGAAT
* * *
461987 GTCAAAGCCCACACAAGCTAGTGGCACCTAA-ATCGAGTTAAGTTCACATTAGTTGGCACCTGTC
1 GTCAAAGCCCACACAAGCTAGTGGCACCTAAGATCGAGTCAAGTCCACATTAGTTGGCACCTATC
462051 T-AAGAAGGTCAAGCCTTAGAA
66 TGAAG-AGGTCAAGCCTTAGAA
462072 CACCAAAACC
Statistics
Matches: 76, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
85 3 0.04
86 45 0.59
87 28 0.37
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.23
Consensus pattern (87 bp):
GTCAAAGCCCACACAAGCTAGTGGCACCTAAGATCGAGTCAAGTCCACATTAGTTGGCACCTATC
TGAAGAGGTCAAGCCTTAGAAT
Done.