Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold374
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: 461091
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 4 of 4
Found at i:424410 original size:6 final size:7
Alignment explanation
Indices: 424391--424446 Score: 71
Period size: 7 Copynumber: 8.3 Consensus size: 7
424381 CTTGAAAAAG
424391 AATTTTT
1 AATTTTT
424398 AATTTTT
1 AATTTTT
424405 AATTTTT
1 AATTTTT
424412 AA-TTTT
1 AATTTTT
424418 AATTTTT
1 AATTTTT
* *
424425 CAGTTTT
1 AATTTTT
*
424432 -GTTTTT
1 AATTTTT
424438 AATTTTT
1 AATTTTT
424445 AA
1 AA
424447 CTCTCGTTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
6 10 0.24
7 32 0.76
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.68
Consensus pattern (7 bp):
AATTTTT
Found at i:424410 original size:14 final size:14
Alignment explanation
Indices: 424391--424446 Score: 71
Period size: 13 Copynumber: 4.1 Consensus size: 14
424381 CTTGAAAAAG
424391 AATTTTTAATTTTT
1 AATTTTTAATTTTT
424405 AATTTTTAA-TTTT
1 AATTTTTAATTTTT
* *
424418 AATTTTTCAGTTTT
1 AATTTTTAATTTTT
*
424432 -GTTTTTAATTTTT
1 AATTTTTAATTTTT
424445 AA
1 AA
424447 CTCTCGTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
13 22 0.63
14 13 0.37
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.68
Consensus pattern (14 bp):
AATTTTTAATTTTT
Found at i:424419 original size:20 final size:20
Alignment explanation
Indices: 424394--424446 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
424384 GAAAAAGAAT
*
424394 TTTTAATTTTTAATTTTTAA
1 TTTTAATTTTTAAGTTTTAA
* **
424414 TTTTAATTTTTCAGTTTTGT
1 TTTTAATTTTTAAGTTTTAA
424434 TTTTAATTTTTAA
1 TTTTAATTTTTAA
424447 CTCTCGTTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.70
Consensus pattern (20 bp):
TTTTAATTTTTAAGTTTTAA
Found at i:429240 original size:26 final size:26
Alignment explanation
Indices: 429210--429262 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
429200 ACGAATATTT
*
429210 AATATATTAAAATTTATATA-AATATA
1 AATAT-TTAAAATTTAAATATAATATA
*
429236 AATATTTTAAATTTAAATATAATATA
1 AATATTTAAAATTTAAATATAATATA
429262 A
1 A
429263 TAAAATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 12 0.50
26 12 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
AATATTTAAAATTTAAATATAATATA
Found at i:429252 original size:32 final size:31
Alignment explanation
Indices: 429183--429270 Score: 83
Period size: 32 Copynumber: 2.8 Consensus size: 31
429173 ATAAAATTGT
*
429183 TTTAAAATGTATATAATACGAATATTTAATA
1 TTTAAAATGTATATAATACAAATATTTAATA
* *
429214 TATTAAAATTTATATAAATATAAATATTTTAA-A
1 T-TTAAAATGTATAT-AATACAAATA-TTTAATA
*
429247 TTTAAATAT-AATATAATA-AAATAT
1 TTTAAA-ATGTATATAATACAAATAT
429271 ATAAATACGA
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
29 1 0.02
30 5 0.10
31 5 0.10
32 21 0.43
33 12 0.24
34 5 0.10
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.43
Consensus pattern (31 bp):
TTTAAAATGTATATAATACAAATATTTAATA
Found at i:433931 original size:27 final size:25
Alignment explanation
Indices: 433865--433932 Score: 68
Period size: 24 Copynumber: 2.7 Consensus size: 25
433855 AAACACCCGT
*
433865 AAATATAAAAGA-T-ATTAAAACTTA
1 AAATATAAAA-ATTAATTAAAAATTA
433889 AAATATAAAAATTAATTAAAAATTA
1 AAATATAAAAATTAATTAAAAATTA
* *
433914 CATATACTAAAATTTAATT
1 -AAATA-TAAAAATTAATT
433933 TCTTAATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
23 1 0.03
24 11 0.30
25 10 0.27
26 4 0.11
27 11 0.30
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.34
Consensus pattern (25 bp):
AAATATAAAAATTAATTAAAAATTA
Found at i:434075 original size:3 final size:3
Alignment explanation
Indices: 434067--434102 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
434057 AAGCAAAGTT
434067 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
434103 AAGGCGGTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:434931 original size:28 final size:31
Alignment explanation
Indices: 434868--434932 Score: 75
Period size: 28 Copynumber: 2.2 Consensus size: 31
434858 TATTTTTTTA
*
434868 AAATATGTTTTTAATTTAATTTATAATAATT
1 AAATATGTTTTTAATTAAATTTATAATAATT
*
434899 TAATAT-TTTTT-ATTAAATTT-TAA-AATAT
1 AAATATGTTTTTAATTAAATTTATAATAAT-T
434927 AAATAT
1 AAATAT
434933 ATTTCTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
27 3 0.10
28 9 0.30
29 8 0.27
30 5 0.17
31 5 0.17
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (31 bp):
AAATATGTTTTTAATTAAATTTATAATAATT
Found at i:434994 original size:24 final size:25
Alignment explanation
Indices: 434950--434997 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
434940 TATATTAATA
*
434950 ATATAATATAATATATTTATTTTTT
1 ATATAATATAATATATATATTTTTT
*
434975 ATATCATAT-ATATATATATTTTT
1 ATATAATATAATATATATATTTTT
434998 AATGATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (25 bp):
ATATAATATAATATATATATTTTTT
Found at i:435251 original size:13 final size:13
Alignment explanation
Indices: 435233--435257 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
435223 TTAAGACACC
435233 CATTTTTCATTAA
1 CATTTTTCATTAA
435246 CATTTTTCATTA
1 CATTTTTCATTA
435258 TCCAAATATA
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:0.28, C:0.16, G:0.00, T:0.56
Consensus pattern (13 bp):
CATTTTTCATTAA
Found at i:435710 original size:9 final size:9
Alignment explanation
Indices: 435698--435749 Score: 56
Period size: 9 Copynumber: 6.0 Consensus size: 9
435688 GGTATAAAAA
435698 TAATATATT
1 TAATATATT
435707 TAATATATAT
1 TAATATAT-T
*
435717 T--TTTATT
1 TAATATATT
*
435724 TAAAAT-TT
1 TAATATATT
435732 TAATATATT
1 TAATATATT
435741 TAATATATT
1 TAATATATT
435750 ATTATTTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
7 2 0.06
8 11 0.31
9 20 0.57
10 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
TAATATATT
Found at i:435759 original size:17 final size:17
Alignment explanation
Indices: 435705--435760 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
435695 AAATAATATA
*
435705 TTTAATATA-TATTTTT
1 TTTAATATATTATTATT
* * * *
435721 ATTTAAAATTTTAATATA
1 -TTTAATATATTATTATT
435739 TTTAATATATTATTATT
1 TTTAATATATTATTATT
435756 TTTAA
1 TTTAA
435761 ATTTATAAAA
Statistics
Matches: 29, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
17 25 0.86
18 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTAATATATTATTATT
Found at i:435816 original size:16 final size:17
Alignment explanation
Indices: 435770--435807 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
435760 AATTTATAAA
*
435770 AAATATAAAATATAATAT
1 AAATATATAA-ATAATAT
435788 AAATATATAAATAAT-T
1 AAATATATAAATAATAT
435804 AAAT
1 AAAT
435808 TTATTAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 5 0.26
18 9 0.47
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAATATATAAATAATAT
Found at i:436171 original size:5 final size:5
Alignment explanation
Indices: 436161--436207 Score: 51
Period size: 5 Copynumber: 9.0 Consensus size: 5
436151 TTTATTTTTT
*
436161 ATATA ATATA A-ATTA TATATC ATATA TATATA ATATA ATATA ATATA
1 ATATA ATATA ATA-TA -ATATA ATATA -ATATA ATATA ATATA ATATA
436208 TAATTAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
4 1 0.03
5 27 0.75
6 7 0.19
7 1 0.03
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (5 bp):
ATATA
Found at i:436280 original size:26 final size:26
Alignment explanation
Indices: 436242--436298 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
436232 AACGTTAAAA
*
436242 TTAAAATTTTATTTAAATTT-ATTTT
1 TTAAAATTATATTTAAATTTAATTTT
**
436267 TTAAAATTAATATTTTTATTTAATTTT
1 TTAAAATT-ATATTTAAATTTAATTTT
436294 TTAAA
1 TTAAA
436299 TAATAAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 8 0.30
26 9 0.33
27 10 0.37
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (26 bp):
TTAAAATTATATTTAAATTTAATTTT
Found at i:436302 original size:25 final size:26
Alignment explanation
Indices: 436258--436312 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
436248 TTTTATTTAA
**
436258 ATTTATTTTTTAAAATTAATATTTTT
1 ATTTATTTTTTAAAATTAATAAATTT
436284 ATTTAATTTTTT-AAA-TAATAAATTT
1 ATTT-ATTTTTTAAAATTAATAAATTT
436309 ATTT
1 ATTT
436313 TCAAACTCGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 12 0.46
26 7 0.27
27 7 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (26 bp):
ATTTATTTTTTAAAATTAATAAATTT
Found at i:436308 original size:27 final size:26
Alignment explanation
Indices: 436258--436308 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
436248 TTTTATTTAA
*
436258 ATTTATTTTTTAAAATTAATATTTTT
1 ATTTATTTTTTAAAAATAATATTTTT
436284 ATTTAATTTTTTAAATAATAA-ATTT
1 ATTT-ATTTTTTAAA-AATAATATTT
436309 ATTTTCAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 4 0.18
27 14 0.64
28 4 0.18
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (26 bp):
ATTTATTTTTTAAAAATAATATTTTT
Found at i:436565 original size:17 final size:17
Alignment explanation
Indices: 436533--436566 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
436523 CAACCATATG
* *
436533 AATAATTATTTCATGTA
1 AATAATTAATTAATGTA
436550 AATAATTAATTAATGTA
1 AATAATTAATTAATGTA
436567 TAGCCTAATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (17 bp):
AATAATTAATTAATGTA
Found at i:436913 original size:16 final size:16
Alignment explanation
Indices: 436890--436922 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
436880 TATTTATATG
436890 AAAATATAAAT-TTTA
1 AAAATATAAATATTTA
436905 AAAATTATAAATATTTA
1 AAAA-TATAAATATTTA
436922 A
1 A
436923 TATTTAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 7 0.44
17 5 0.31
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AAAATATAAATATTTA
Found at i:439451 original size:18 final size:18
Alignment explanation
Indices: 439428--439463 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
439418 AATTACCTCT
439428 TTCACTGGCGTAATGACA
1 TTCACTGGCGTAATGACA
439446 TTCACTGGCGTAATGACA
1 TTCACTGGCGTAATGACA
439464 GTTGAATATG
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:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (18 bp):
TTCACTGGCGTAATGACA
Found at i:440763 original size:18 final size:18
Alignment explanation
Indices: 440740--440802 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
440730 AGATTGGGAG
440740 GGAGAAGAGAAACTAGAT
1 GGAGAAGAGAAACTAGAT
* * * *
440758 GGAGAACTAGAACCATGGGAG
1 GGAGAA-GAGAAAC-T-AGAT
440779 GGAGAAGAGAAACTAGAT
1 GGAGAAGAGAAACTAGAT
*
440797 GCAGAA
1 GGAGAA
440803 CTAGTACCAA
Statistics
Matches: 33, Mismatches: 9, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
18 13 0.39
19 6 0.18
20 6 0.18
21 8 0.24
ACGTcount: A:0.46, C:0.10, G:0.35, T:0.10
Consensus pattern (18 bp):
GGAGAAGAGAAACTAGAT
Found at i:440788 original size:39 final size:39
Alignment explanation
Indices: 440734--440811 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
440724 AAAAGCAGAT
*
440734 TGGGAGGGAGAAGAGAAACTAGATGGAGAACTAGAACCA
1 TGGGAGGGAGAAGAGAAACTAGATGCAGAACTAGAACCA
*
440773 TGGGAGGGAGAAGAGAAACTAGATGCAGAACTAGTACCA
1 TGGGAGGGAGAAGAGAAACTAGATGCAGAACTAGAACCA
440812 AATAACCCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.42, C:0.12, G:0.35, T:0.12
Consensus pattern (39 bp):
TGGGAGGGAGAAGAGAAACTAGATGCAGAACTAGAACCA
Found at i:441333 original size:29 final size:29
Alignment explanation
Indices: 441265--441322 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
441255 ATTAGATTTA
*
441265 AATAAAATTTTTTATAATTTAAATTAAAT
1 AATAAAATTATTTATAATTTAAATTAAAT
441294 AATAAAAATTATTT-TAATTTAAATATAAA
1 AAT-AAAATTATTTATAATTTAAAT-TAAA
441323 CATAAATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
AATAAAATTATTTATAATTTAAATTAAAT
Found at i:441338 original size:18 final size:17
Alignment explanation
Indices: 441315--441349 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
441305 TTTTAATTTA
*
441315 AATATAAACATAAATATT
1 AATATAAAAAT-AATATT
441333 AATATAAAAATAATATT
1 AATATAAAAATAATATT
441350 TTAATTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (17 bp):
AATATAAAAATAATATT
Found at i:441696 original size:3 final size:3
Alignment explanation
Indices: 441688--441713 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
441678 CTAAAAATAA
441688 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
441714 AATAAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:441950 original size:15 final size:16
Alignment explanation
Indices: 441932--441963 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
441922 GTTTTTTTCC
441932 TTTTTTCT-TTTCTTT
1 TTTTTTCTATTTCTTT
441947 TTTTTTCTATTTCTTT
1 TTTTTTCTATTTCTTT
441963 T
1 T
441964 ACTAAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTTCTATTTCTTT
Found at i:444465 original size:20 final size:20
Alignment explanation
Indices: 444437--444507 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
444427 TCATACCCTG
444437 ATGTATCGATATATTTTTCA
1 ATGTATCGATATATTTTTCA
* * * * *
444457 ATATATCGATACATGTATGA
1 ATGTATCGATATATTTTTCA
* *
444477 ATGTATCGATATATTCTACA
1 ATGTATCGATATATTTTTCA
444497 ATGTATCGATA
1 ATGTATCGATA
444508 CATTATGTCT
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.41
Consensus pattern (20 bp):
ATGTATCGATATATTTTTCA
Found at i:444504 original size:40 final size:39
Alignment explanation
Indices: 444437--444514 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
444427 TCATACCCTG
* *
444437 ATGTATCGATATATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATATATTCTACAATATATCGATACAT-TATGA
*
444477 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATATATTCTACAATATATCGATACATTATG
444515 TCTTTTTACC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.41
Consensus pattern (39 bp):
ATGTATCGATATATTCTACAATATATCGATACATTATGA
Found at i:456567 original size:28 final size:28
Alignment explanation
Indices: 456363--457055 Score: 143
Period size: 28 Copynumber: 24.7 Consensus size: 28
456353 AAAAGGGTTG
*
456363 GCCCCTGTACTTGCTGGGCTTTTGAAA-GAAT
1 GCCCCTG-ACTTG-TGGGC--TTGAAACGAGT
* * * *
456394 GCCACTAACTCGTGGGCTTGAAAGGAG-
1 GCCCCTGACTTGTGGGCTTGAAACGAGT
* *
456421 G-CCCTGACTTGTGGGTTTG-AAGGAGT
1 GCCCCTGACTTGTGGGCTTGAAACGAGT
* * *
456447 GGTCACTGACTTGTGTGCTTTGAAA-G-GT
1 -GCCCCTGACTTGTGGGC-TTGAAACGAGT
* * * *
456475 ACCCCTGACTTGCGTGAGCTTTAAATGAGT
1 GCCCCTGACTT--GTGGGCTTGAAACGAGT
* *
456505 GCCACCTGACTTGTGTGGCGTCTTTAAACGGGT
1 GCC-CCTGAC-T-TGTGG-G-CTTGAAACGAGT
456538 GCCCCTTGACTTGTGGGCTTGAAA-GAGT
1 GCCCC-TGACTTGTGGGCTTGAAACGAGT
* * * *
456566 GCCACTGA-ATGTGGGCCTTCGCAA--TGT
1 GCCCCTGACTTGTGGG-CTT-GAAACGAGT
* *
456593 G-CACTGACTTCGTGGGCTTCGAAA-GGGT
1 GCCCCTGACTT-GTGGGCTT-GAAACGAGT
*
456621 G-CCATGACTTGTGGGCTTCTGAAA-G-G-
1 GCCCCTGACTTGTGGGC-T-TGAAACGAGT
* * *
456647 G-CACTAAACTTG-GGGCTTTGAAA-GGGT
1 GCCCCT-GACTTGTGGGC-TTGAAACGAGT
* *
456674 G-CCATGA-TT-TGGGCTTGAAAAGAGT
1 GCCCCTGACTTGTGGGCTTGAAACGAGT
* * *
456699 G--CCTGATTTGCGGGTTTGAAACGAGT
1 GCCCCTGACTTGTGGGCTTGAAACGAGT
* *
456725 GCACACTGACTTGTGGTGCTTTGAAAGGAGT
1 GC-CCCTGACTTGTGG-GC-TTGAAACGAGT
* * * *
456756 GCCAAC-GA-TTGTGTGCTTTGCAA-GGGT
1 GCC-CCTGACTTGTGGGC-TTGAAACGAGT
* *
456783 G-CCCTAACTT-TGTGGTTTGGACAACGAGT
1 GCCCCTGACTTGTG-GGCTT-GA-AACGAGT
* **
456812 G--CCTGATTTTGTGGGCTTTGAAAATAGT
1 GCCCCTGA-CTTGTGGGC-TTGAAACGAGT
* * *
456840 GCCACTGACTCGTGGGCTTTGAAAGGAG-
1 GCCCCTGACTTGTGGGC-TTGAAACGAGT
**
456868 GCCAATGACTTGTGGGCTTTGAAA-G-GT
1 GCCCCTGACTTGTGGGC-TTGAAACGAGT
* * * *
456895 GACACTGAGTTGTGGGCTTTTCGAAA-GGGT
1 GCCCCTGACTTGTGGGC--TT-GAAACGAGT
* * *
456925 G-CCATGACTTGTGGGATTTGAAAAGAGT
1 GCCCCTGACTTGTGGG-CTTGAAACGAGT
** * * *
456953 GCCATTGATTTGTGGGCTTTAACAAAGAGT
1 GCCCCTGACTTGTGGGC-TTGA-AACGAGT
* *
456983 GCCACTGACTTGT-GGCTTTGAAAGGAGT
1 GCCCCTGACTTGTGGGC-TTGAAACGAGT
* * * *
457011 GCCACTGA-TTGTTGGCTTTAAA-GGGT
1 GCCCCTGACTTGTGGGCTTGAAACGAGT
*
457037 GCCACTGACTTGT-GGCTTG
1 GCCCCTGACTTGTGGGCTTG
457056 CAAGGGATGC
Statistics
Matches: 516, Mismatches: 88, Indels: 121
0.71 0.12 0.17
Matches are distributed among these distances:
24 10 0.02
25 25 0.05
26 74 0.14
27 88 0.17
28 120 0.23
29 99 0.19
30 44 0.09
31 33 0.06
32 5 0.01
33 18 0.03
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (28 bp):
GCCCCTGACTTGTGGGCTTGAAACGAGT
Found at i:456612 original size:27 final size:27
Alignment explanation
Indices: 456544--457248 Score: 252
Period size: 27 Copynumber: 25.5 Consensus size: 27
456534 GGGTGCCCCT
*
456544 TGACTTGTGGGCTT-GAAAGAGTGCCA
1 TGACTTGTGGGCTTCGAAAGGGTGCCA
* * *
456570 CTGA-ATGTGGGCCTTCGCAA-TGTG-CA
1 -TGACTTGTGGG-CTTCGAAAGGGTGCCA
456596 CTGACTTCGTGGGCTTCGAAAGGGTGCCA
1 -TGACTT-GTGGGCTTCGAAAGGGTGCCA
** *
456625 TGACTTGTGGGCTTCTGAAAGGGCACTA
1 TGACTTGTGGGCTTC-GAAAGGGTGCCA
* *
456653 -AACTTG-GGGCTTTGAAAGGGTGCCA
1 TGACTTGTGGGCTTCGAAAGGGTGCCA
*
456678 TGA-TT-TGGGCTT-GAAAAGAGTGCC-
1 TGACTTGTGGGCTTCG-AAAGGGTGCCA
* * * *
456702 TGATTTGCGGG-TTTGAAACGAGTGCACA
1 TGACTTGTGGGCTTCGAAA-GGGTGC-CA
*
456730 CTGACTTGTGGTGCTTTGAAAGGAGTGCCAA
1 -TGACTTGTGG-GCTTCGAAAGG-GTGCC-A
* * * * *
456761 CGA-TTGTGTGCTTTGCAAGGGTGCCC
1 TGACTTGTGGGCTTCGAAAGGGTGCCA
* * * *
456787 TAACTT-TGTGGTTTGGACAACGAGTGCC-
1 TGACTTGTG-GGCTTCGA-AA-GGGTGCCA
* * **
456815 TGATTTTGTGGGCTTTGAAAATAGTGCCA
1 TGA-CTTGTGGGCTTCG-AAAGGGTGCCA
* *
456844 CTGACTCGTGGGCTTTGAAAGGAG-GCCAA
1 -TGACTTGTGGGCTTCGAAAGG-GTGCC-A
* *
456873 TGACTTGTGGGCTTTGAAA-GGTGACA
1 TGACTTGTGGGCTTCGAAAGGGTGCCA
*
456899 CTGAGTTGTGGGCTTTTCGAAAGGGTGCCA
1 -TGACTTGTGGGC--TTCGAAAGGGTGCCA
* * *
456929 TGACTTGTGGGATTTGAAAAGAGTGCCA
1 TGACTTGTGGGCTTCG-AAAGGGTGCCA
* *
456957 TTGATTTGTGGGCTTTAAC-AAAGAGTGCCA
1 -TGACTTGTGGGC-TT--CGAAAGGGTGCCA
*
456987 CTGACTTGT-GGCTTTGAAAGGAGTGCCA
1 -TGACTTGTGGGCTTCGAAAGG-GTGCCA
* *
457015 CTGA-TTGTTGGCTT-TAAAGGGTGCCA
1 -TGACTTGTGGGCTTCGAAAGGGTGCCA
*
457041 CTGACTTGT-GGCTT-GCAAGGGATGCCA
1 -TGACTTGTGGGCTTCGAAAGGG-TGCCA
457068 CTGAC-T-T-GGCTT-GAAAGGGTG-CA
1 -TGACTTGTGGGCTTCGAAAGGGTGCCA
* * *
457091 CTGGACTTGTGGGCTTTGGCCAAGAGTGCCA
1 -T-GACTTGTGGGC-TTCG-AAAGGGTGCCA
457122 TGACTTGCTGGG-TT-GAAAGTGGTGCCA
1 TGACTTG-TGGGCTTCGAAAG-GGTGCCA
* *
457149 CTGA-TTGTTGG-TT-GCAAGGGTGCCAAA
1 -TGACTTGTGGGCTTCGAAAGGGTGCC--A
* * * *
457176 CTTGCCTTTTGGGCTTTGAAAGAGTGCCA
1 --TGACTTGTGGGCTTCGAAAGGGTGCCA
* * *
457205 CTGA-TTATGGGCTTTGAAAGCGTGCCCA
1 -TGACTTGTGGGCTTCGAAAGGGTG-CCA
457233 CTGAACTTGTGGGCTT
1 -TG-ACTTGTGGGCTT
457249 TGGAACGGGA
Statistics
Matches: 534, Mismatches: 77, Indels: 131
0.72 0.10 0.18
Matches are distributed among these distances:
23 4 0.01
24 9 0.02
25 52 0.10
26 68 0.13
27 119 0.22
28 114 0.21
29 86 0.16
30 59 0.11
31 23 0.04
ACGTcount: A:0.21, C:0.17, G:0.32, T:0.29
Consensus pattern (27 bp):
TGACTTGTGGGCTTCGAAAGGGTGCCA
Found at i:456705 original size:24 final size:26
Alignment explanation
Indices: 456659--456726 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 26
456649 ACTAAACTTG
*
456659 GGGCTTTG-AAAGGGTGCCATGATTT-
1 GGGC-TTGAAAAGAGTGCCATGATTTC
456684 GGGCTTGAAAAGAGTGCC-TGATTTGC
1 GGGCTTGAAAAGAGTGCCATGATTT-C
* *
456710 GGGTTTGAAACGAGTGC
1 GGGCTTGAAAAGAGTGC
456727 ACACTGACTT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
24 9 0.24
25 13 0.35
26 15 0.41
ACGTcount: A:0.22, C:0.13, G:0.37, T:0.28
Consensus pattern (26 bp):
GGGCTTGAAAAGAGTGCCATGATTTC
Found at i:456908 original size:84 final size:81
Alignment explanation
Indices: 456371--457250 Score: 411
Period size: 84 Copynumber: 10.5 Consensus size: 81
456361 TGGCCCCTGT
* * *
456371 ACTTGCTGGGCTTTTGAAAGAATGCCACTAACTCGTGGGC-TTGAAAGGAG-GCC-CTGACTTGT
1 ACTTG-TGGGC-TTTGAAAGAGTG-CACTGACTTGTGGGCTTTGAAA-GAGTGCCACTGA-TTGT
*
456433 GGG-TTTG-AAGGAGTGGTCACTG
61 GGGCTTTGAAAGG-GT-GCCA-TG
* * * *
456455 ACTTGTGTGCTTTGAAAG-GTACCCCTGACTTGCGTGAGCTTT-AAATGAGTGCCACCTGACTTG
1 ACTTGTGGGCTTTGAAAGAGT-GCACTGACTT--GTGGGCTTTGAAA-GAGTGCCA-CTGA-TTG
* *
456518 TGTGGCGTCTTTAAACGGGTGCCCCTTG
60 TG-GGC-T-TTGAAA-GGGTG--CCATG
* * * *
456546 ACTTGTGGGC-TTGAAAGAGTGCCACTGA-ATGTGGGCCTTCGCAA-TGTG-CACTGACTTCGTG
1 ACTTGTGGGCTTTGAAAGAGTG-CACTGACTTGTGGG-CTTTGAAAGAGTGCCACTGA-TT-GTG
*
456607 GGCTTCGAAAGGGTGCCATG
62 GGCTTTGAAAGGGTGCCATG
* *
456627 ACTTGTGGGCTTCTGAAAG-G-GCACTAAACTTG-GGGCTTTGAAAGGGTGCCA-TGATT-TGGG
1 ACTTGTGGGCTT-TGAAAGAGTGCACT-GACTTGTGGGCTTTGAAAGAGTGCCACTGATTGTGGG
*
456687 C-TTGAAAAGAGTGCC-TG
64 CTTTG-AAAGGGTGCCATG
* *
456704 ATTTGCGGG-TTTGAAACGAGTGCACACTGACTTGTGGTGCTTTGAAAGGAGTGCCAAC-GATTG
1 ACTTGTGGGCTTTGAAA-GAGTG--CACTGACTTGTGG-GCTTTGAAA-GAGTGCC-ACTGATTG
* * * *
456767 TGTGCTTTGCAAGGGTGCCCTA
60 TGGGCTTTGAAAGGGTGCCATG
* * *
456789 ACTT-TGTGG-TTTGGACAACGAGTGC-CTGATTTTGTGGGCTTTGAAAATAGTGCCACTGACTC
1 ACTTGTG-GGCTTT-GA-AA-GAGTGCACTGA-CTTGTGGGCTTTG-AAAGAGTGCCACTGA-TT
456851 GTGGGCTTTGAAAGGAG-GCCAATG
59 GTGGGCTTTGAAAGG-GTGCC-ATG
* *
456875 ACTTGTGGGCTTTGAAAG-GTGACACTGAGTTGTGGGCTTTTCGAAAGGGTGCCA-TGACTTGTG
1 ACTTGTGGGCTTTGAAAGAGTG-CACTGACTTGTGGGC-TTT-GAAAGAGTGCCACTGA-TTGTG
* *
456938 GGATTTGAAAAGAGTGCCATTG
62 GGCTTTG-AAAGGGTGCCA-TG
* * *
456960 ATTTGTGGGCTTTAACAAAGAGTGCCACTGACTTGT-GGCTTTGAAAGGAGTGCCACTGATTGTT
1 ACTTGTGGGCTTT--GAAAGAGTG-CACTGACTTGTGGGCTTTGAAA-GAGTGCCACTGATTGTG
457024 GGCTTT-AAAGGGTGCCACTG
62 GGCTTTGAAAGGGTGCCA-TG
* * *
457044 ACTTGT-GGC-TTGCAAGGGATGCCACTGAC-T-T-GGC-TTGAAAGGGTG-CACTGGACTTGTG
1 ACTTGTGGGCTTTGAAAGAG-TG-CACTGACTTGTGGGCTTTGAAAGAGTGCCACT-GA-TTGTG
* *
457102 GGCTTTGGCCAAGAGTGCCATG
62 GGCTTT-G-AAAGGGTGCCATG
* * * * *
457124 ACTTGCTGGG--TTGAAAGTGGTGCCACTGA-TTGTTGG--TTGCAAGGGTGCCAAACTTGCCTT
1 ACTTG-TGGGCTTTGAAAG-AGTG-CACTGACTTGTGGGCTTTGAAAGAGTGCC--AC-TG-ATT
* *
457184 TTGGGCTTTGAAAGAGTGCCACTG
59 GTGGGCTTTGAAAGGGTGCCA-TG
* *
457208 A-TTATGGGCTTTGAAAGCGTGCCCACTGAACTTGTGGGCTTTG
1 ACTTGTGGGCTTTGAAAGAGTG--CACTG-ACTTGTGGGCTTTG
457251 GAACGGGATG
Statistics
Matches: 631, Mismatches: 77, Indels: 172
0.72 0.09 0.20
Matches are distributed among these distances:
75 5 0.01
76 7 0.01
77 18 0.03
78 31 0.05
79 9 0.01
80 30 0.05
81 77 0.12
82 41 0.06
83 57 0.09
84 105 0.17
85 97 0.15
86 59 0.09
87 30 0.05
88 23 0.04
89 4 0.01
90 13 0.02
91 22 0.03
92 3 0.00
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (81 bp):
ACTTGTGGGCTTTGAAAGAGTGCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGATTGTGGGCT
TTGAAAGGGTGCCATG
Found at i:456927 original size:113 final size:111
Alignment explanation
Indices: 456377--457108 Score: 417
Period size: 113 Copynumber: 6.6 Consensus size: 111
456367 CTGTACTTGC
* * * *
456377 TGGGCTTTTG-AAAGAATGCCACTAACTCGTGGGC-TTGAAAGGAG-GCC-CTGACTTGTGGG-T
1 TGGGC-TTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCAATGACTTGTGGGCT
* * * * *
456437 TTGAAGGAGTGGTCACTGACTTGTGTGCTTT-GAAAG-GTACCCCTGACTTGCG
65 TTGAAAG-GT-GCCACTGA-TTGTGGGCTTTCGAAAGAGT--GCCTGA-TT-TG
* * * **
456489 TGAGCTTT-AAATGAGTGCCACCTGACTTGTGTGGCGTCTTTAAACGG-GTGCCCCTTGACTTGT
1 TGGGCTTTGAAAAGAGTGCCA-CTGACTTGTG-GGC-T-TTGAAA-GGAGTG-CCAATGACTTGT
* * * * *
456552 GGGC-TTGAAAGAGTGCCACTGAATGTGGGCCTTCGCAA-TGTGCACTGACTTCG
60 GGGCTTTGAAAG-GTGCCACTGATTGTGGGCTTTCGAAAGAGTGC-CTGA-TTTG
* * ** *
456605 TGGGCTTCG-AAAGGGTGCCA-TGACTTGTGGGCTTCTGAAAGG-GCACTAA--ACTTG-GGGCT
1 TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTT-TGAAAGGAGTGCCAATGACTTGTGGGCT
456664 TTGAAAGGGTGCCA-TGATT-TGGGC-TT-GAAAAGAGTGCCTGATTTG
65 TTGAAA-GGTGCCACTGATTGTGGGCTTTCG-AAAGAGTGCCTGATTTG
* * * *
456709 CGGG-TTTGAAACGAGTGCACACTGACTTGTGGTGCTTTGAAAGGAGTGCCAACGA-TTGTGTGC
1 TGGGCTTTGAAAAGAGTGC-CACTGACTTGTGG-GCTTTGAAAGGAGTGCCAATGACTTGTGGGC
* * *
456772 TTTGCAAGGGTGCC-CTAACTT-TGTGG-TTTGGACAACGAGTGCCTGATTTTG
64 TTTG-AAAGGTGCCACTGA-TTGTG-GGCTTTCGA-AA-GAGTGCCTGA-TTTG
* *
456823 TGGGCTTTGAAAATAGTGCCACTGACTCGTGGGCTTTGAAAGGAG-GCCAATGACTTGTGGGCTT
1 TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCAATGACTTGTGGGCTT
* * *
456887 TGAAAGGTGACACTGAGTTGTGGGCTTTTCGAAAGGGTGCCATGACTTG
66 TGAAAGGTGCCACTGA-TTGTGGGC-TTTCGAAAGAGTGCC-TGATTTG
* * * * * *
456936 TGGGATTTGAAAAGAGTGCCATTGATTTGTGGGCTTTAACAAAGAGTGCCACTGACTTGT-GGCT
1 TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGA-AAGGAGTGCCAATGACTTGTGGGCT
* * *
457000 TTGAAAGGAGTGCCACTGATTGTTGGCTTT--AAAGGGTGCCACTGACTTG
65 TTGAAA-G-GTGCCACTGATTGTGGGCTTTCGAAAGAGTG-C-CTGATTTG
* * *
457049 T-GGC-TTG-CAAGGGATGCCACTGAC-T-T-GGC-TTGAAAGG-GTG-CACTGGACTTGTGGGC
1 TGGGCTTTGAAAAGAG-TGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCAAT-GACTTGTGGGC
457105 TTTG
64 TTTG
457109 GCCAAGAGTG
Statistics
Matches: 499, Mismatches: 68, Indels: 112
0.73 0.10 0.16
Matches are distributed among these distances:
103 3 0.01
104 18 0.04
105 20 0.04
106 36 0.07
107 19 0.04
108 23 0.05
109 18 0.04
110 12 0.02
111 32 0.06
112 44 0.09
113 98 0.20
114 54 0.11
115 37 0.07
116 33 0.07
117 18 0.04
118 14 0.03
119 20 0.04
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (111 bp):
TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCAATGACTTGTGGGCTT
TGAAAGGTGCCACTGATTGTGGGCTTTCGAAAGAGTGCCTGATTTG
Found at i:457003 original size:58 final size:56
Alignment explanation
Indices: 456345--457249 Score: 341
Period size: 56 Copynumber: 16.1 Consensus size: 56
456335 CATTGCTTGC
* * * * *
456345 TGGGCTTTAAAAGGGTTGGCCCCTGTACTTGCTGGGCTTTTG-AAAGAATGCCACTAACTCG
1 TGGGCTTTAAAAGAG-T-GCCACTG-ACTTG-TGGGC-TTTGAAAAGAGTGCCACTGA-TTG
* * * *
456406 TGGGCTTGAAAGGAG-GCC-CTGACTTGTGGG-TTTG-AAGGAGTGGTCACTGACTTG
1 TGGGCTTTAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGT-GCCACTGA-TTG
* * * * * *
456460 TGTGCTTTGAAAG-GTACCCCTGACTTGCGTGAGCTTT-AAATGAGTGCCACCTGACTTGTG
1 TGGGCTTTAAAAGAGTGCCACTGACTT--GTGGGCTTTGAAAAGAGTGCCA-CTGA--T-TG
* * * *
456520 TGGCGTCTTTAAACGGGTGCCCCTTGACTTGTGGGC-TTG-AAAGAGTGCCACTGAATG
1 TGG-G-CTTTAAAAGAGTGCCAC-TGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTG
*** * * *
456577 TGGGCCTTCGCAA-TGTG-CACTGACTTCGTGGGCTTCG-AAAGGGTGCCA-TGACTTG
1 TGGG-CTTTAAAAGAGTGCCACTGACTT-GTGGGCTTTGAAAAGAGTGCCACTGA-TTG
* * *
456632 TGGGCTTCTGAAAG-G-G-CACTAAACTTG-GGGCTTTG-AAAGGGTGCCA-TGATT-
1 TGGGCTT-TAAAAGAGTGCCACT-GACTTGTGGGCTTTGAAAAGAGTGCCACTGATTG
* * * *
456683 TGGGCTTGAAAAGAGTG-C-CTGATTTGCGGG-TTTGAAACGAGTGCACACTGACTTG
1 TGGGCTTTAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGC-CACTGA-TTG
* * * * *
456738 TGGTGCTTTGAAAGGAGTGCCAAC-GA-TTGTGTGCTTTG-CAAGGGTGCC-CTAACTT-
1 TGG-GCTTT-AAAAGAGTGCC-ACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGA-TTG
* * * *
456793 TGTGG-TTTGGACAACGAGTG-C-CTGATTTTGTGGGCTTTGAAAATAGTGCCACTGACTCG
1 TG-GGCTTT--A-AAAGAGTGCCACTGA-CTTGTGGGCTTTGAAAAGAGTGCCACTGA-TTG
* * *
456852 TGGGCTTTGAAAGGAG-GCCAATGACTTGTGGGCTTTG-AAAG-GTGACACTGAGTTG
1 TGGGCTTT-AAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGA-TTG
* * * *
456907 TGGGCTTTTCGAAAGGGTGCCA-TGACTTGTGGGATTTGAAAAGAGTGCCATTGATTTG
1 TGGGC-TTT-AAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGA-TTG
*
456965 TGGGCTTTAACAAAGAGTGCCACTGACTTGT-GGCTTTGAAAGGAGTGCCACTGATTG
1 TGGGCTTT-A-AAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTG
* * * * *
457022 TTGGCTTT-AAAGGGTGCCACTGACTTGT-GGC-TTG-CAAGGGATGCCACTGACT-
1 TGGGCTTTAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAG-TGCCACTGATTG
* * **
457074 T-GGC-TTGAAAGGGTG-CACTGGACTTGTGGGCTTTGGCCAAGAGTGCCA-TGACTTG
1 TGGGCTTTAAAAGAGTGCCACT-GACTTGTGGGCTTT-GAAAAGAGTGCCACTGA-TTG
* * * * * * *
457129 CTGGG--TTGAAAGTGGTGCCACTGA-TTGTTGG--TTG-CAAGGGTGCCAAACTTGCCTTT
1 -TGGGCTTTAAAAG-AGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCC--AC-TG-ATTG
* * *
457185 TGGGCTTTGAAAGAGTGCCACTGA-TTATGGGCTTTG-AAAGCGTGCCCACTGAACTTG
1 TGGGCTTTAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTG-CCACTG-A-TTG
457242 TGGGCTTT
1 TGGGCTTT
457250 GGAACGGGAT
Statistics
Matches: 667, Mismatches: 100, Indels: 158
0.72 0.11 0.17
Matches are distributed among these distances:
50 18 0.03
51 38 0.06
52 22 0.03
53 60 0.09
54 79 0.12
55 74 0.11
56 100 0.15
57 97 0.15
58 99 0.15
59 22 0.03
60 9 0.01
61 25 0.04
62 12 0.02
63 6 0.01
64 6 0.01
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (56 bp):
TGGGCTTTAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTG
Found at i:457098 original size:51 final size:53
Alignment explanation
Indices: 456820--457108 Score: 191
Period size: 58 Copynumber: 5.2 Consensus size: 53
456810 GTGCCTGATT
** * *
456820 TTGTGGGCTTTGAAAATAGTGCCACTGACTCGTGGGCTTTGAAAGGAG-GCCAATGAC
1 TTGT-GGCTTTGAAAGGAGTGCCACTGA-TC-TTGGC-TTGAAAGG-GTGCCACTGAC
*
456877 TTGTGGGCTTTGAAA-G-GTGACACTGAGT-TGTGGGCTTTTCGAAAGGGTGCCA-TGAC
1 TTGT-GGCTTTGAAAGGAGTGCCACTGA-TCT-T-GGC--TT-GAAAGGGTGCCACTGAC
* * * * * *
456933 TTGTGGGATTTGAAAAGAGTGCCATTGATTTGTGGGCTTTAACAAAGAGTGCCACTGAC
1 TTGT-GGCTTTGAAAGGAGTGCCACTGATCT-T-GGC-TT--GAAAGGGTGCCACTGAC
* *
456992 TTGTGGCTTTGAAAGGAGTGCCACTGATTGTTGGCTTTAAAGGGTGCCACTGAC
1 TTGTGGCTTTGAAAGGAGTGCCACTGA-TCTTGGCTTGAAAGGGTGCCACTGAC
*
457046 TTGTGGC-TTGCAAGG-GATGCCACTGA-CTTGGCTTGAAAGGGTG-CACTGGAC
1 TTGTGGCTTTGAAAGGAG-TGCCACTGATCTTGGCTTGAAAGGGTGCCACT-GAC
457097 TTGTGGGCTTTG
1 TTGT-GGCTTTG
457109 GCCAAGAGTG
Statistics
Matches: 198, Mismatches: 19, Indels: 34
0.79 0.08 0.14
Matches are distributed among these distances:
50 4 0.02
51 22 0.11
52 4 0.02
53 20 0.10
54 22 0.11
55 13 0.07
56 24 0.12
57 33 0.17
58 46 0.23
59 10 0.05
ACGTcount: A:0.21, C:0.16, G:0.33, T:0.30
Consensus pattern (53 bp):
TTGTGGCTTTGAAAGGAGTGCCACTGATCTTGGCTTGAAAGGGTGCCACTGAC
Found at i:458470 original size:8 final size:8
Alignment explanation
Indices: 458448--458508 Score: 52
Period size: 8 Copynumber: 7.5 Consensus size: 8
458438 TCTAGACTTC
458448 TCTTTTTT
1 TCTTTTTT
*
458456 GCATTTTTT
1 TC-TTTTTT
458465 TCTTTTTT
1 TCTTTTTT
*
458473 TGTTTTTT
1 TCTTTTTT
* *
458481 TGTTTGTT
1 TCTTTTTT
458489 T-TTTTTT
1 TCTTTTTT
*
458496 TGTTTTTCT
1 TCTTTTT-T
458505 TCTT
1 TCTT
458509 GGGGTAAAGG
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
7 6 0.14
8 27 0.61
9 11 0.25
ACGTcount: A:0.02, C:0.08, G:0.08, T:0.82
Consensus pattern (8 bp):
TCTTTTTT
Found at i:458479 original size:17 final size:18
Alignment explanation
Indices: 458445--458504 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 18
458435 TTATCTAGAC
*
458445 TTCTCTTTTTTGCATTTTT
1 TTCTCTTTTTTG-TTTTTT
458464 TTCT-TTTTTTGTTTTTT
1 TTCTCTTTTTTGTTTTTT
* * *
458481 TGTTTGTTTTTTTTTTGTTT
1 T-TCTCTTTTTTGTTT-TTT
458501 TTCT
1 TTCT
458505 TCTTGGGGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
17 6 0.18
18 9 0.26
19 15 0.44
20 4 0.12
ACGTcount: A:0.02, C:0.08, G:0.08, T:0.82
Consensus pattern (18 bp):
TTCTCTTTTTTGTTTTTT
Done.