Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold110
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: 1159294
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
File 3 of 6
Found at i:282374 original size:16 final size:17
Alignment explanation
Indices: 282346--282389 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
282336 TAACCTTAGG
282346 TTTG-AATTATTTTAAA
1 TTTGAAATTATTTTAAA
*
282362 TTT-AAATTTTTTTAAA
1 TTTGAAATTATTTTAAA
282378 TTTGAAA-TATTT
1 TTTGAAATTATTT
282390 CAGATTTAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 21 0.88
17 3 0.12
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (17 bp):
TTTGAAATTATTTTAAA
Found at i:283798 original size:27 final size:26
Alignment explanation
Indices: 283768--283819 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
283758 ACTTGTGACA
283768 TAAGTGATA-AAAAATATTATTTTTAAG
1 TAAGT-ATATAAAAATA-TATTTTTAAG
*
283795 TAAGTTTATAAAAATATATTTTTAA
1 TAAGTATATAAAAATATATTTTTAA
283820 TTATATTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (26 bp):
TAAGTATATAAAAATATATTTTTAAG
Found at i:283903 original size:19 final size:18
Alignment explanation
Indices: 283862--283906 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
283852 GCAACAAAAA
*
283862 ATATAAATTTAATTTGTT
1 ATATAAAATTAATTTGTT
*
283880 ATATAAAATTAATTTTTT
1 ATATAAAATTAATTTGTT
283898 ATTATAAAA
1 A-TATAAAA
283907 AATAATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
ATATAAAATTAATTTGTT
Found at i:285473 original size:13 final size:13
Alignment explanation
Indices: 285455--285480 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
285445 CAATTTTTTG
285455 TGTATCGATACAT
1 TGTATCGATACAT
285468 TGTATCGATACAT
1 TGTATCGATACAT
285481 ATTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:285491 original size:32 final size:33
Alignment explanation
Indices: 285435--285498 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
285425 TACAAGCCAA
* *
285435 TGTATTGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATATTTTGTGTATCGATACAT
285468 TGTATCGATAC-ATATTTTGTGTATCGATACA
1 TGTATCGATACAATATTTTGTGTATCGATACA
285499 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 19 0.66
33 10 0.34
ACGTcount: A:0.28, C:0.11, G:0.16, T:0.45
Consensus pattern (33 bp):
TGTATCGATACAATATTTTGTGTATCGATACAT
Found at i:287230 original size:16 final size:16
Alignment explanation
Indices: 287176--287234 Score: 64
Period size: 16 Copynumber: 3.7 Consensus size: 16
287166 TGACCTGAAT
* *
287176 CCGAAATGACCCGATC
1 CCGAAATGATCCGAAC
* * *
287192 CCTAAATAATCCGAAT
1 CCGAAATGATCCGAAC
*
287208 CCAAAATGATCCGAAC
1 CCGAAATGATCCGAAC
287224 CCGAAATGATC
1 CCGAAATGATC
287235 TAAACTTAAA
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.39, C:0.31, G:0.14, T:0.17
Consensus pattern (16 bp):
CCGAAATGATCCGAAC
Found at i:289873 original size:22 final size:22
Alignment explanation
Indices: 289834--289889 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
289824 TTATATATAT
* *
289834 AATAAAATAGTAATTTATCAAAA
1 AATAAATTA-TAACTTATCAAAA
289857 AATAAATTATAACTTATCAAAA
1 AATAAATTATAACTTATCAAAA
*
289879 AGTAAATTATA
1 AATAAATTATA
289890 TCATGAGATT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 22 0.73
23 8 0.27
ACGTcount: A:0.59, C:0.05, G:0.04, T:0.32
Consensus pattern (22 bp):
AATAAATTATAACTTATCAAAA
Found at i:299532 original size:11 final size:11
Alignment explanation
Indices: 299516--299540 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
299506 ATTATAGGAA
299516 AAAAAAAGAGG
1 AAAAAAAGAGG
299527 AAAAAAAGAGG
1 AAAAAAAGAGG
299538 AAA
1 AAA
299541 CTCTATGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAGG
Found at i:300288 original size:16 final size:16
Alignment explanation
Indices: 300267--300299 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
300257 GTGCGTTAAT
300267 TAAATTTAGATTTTAG
1 TAAATTTAGATTTTAG
300283 TAAATTTAGATTTTAG
1 TAAATTTAGATTTTAG
300299 T
1 T
300300 CTTGTATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (16 bp):
TAAATTTAGATTTTAG
Found at i:300525 original size:6 final size:6
Alignment explanation
Indices: 300516--300559 Score: 56
Period size: 6 Copynumber: 7.3 Consensus size: 6
300506 TTTTTATATA
300516 TTTAAT TTT-AT TTTATAT TTT-AT TTTAATT TTTAAT TTTAAT TT
1 TTTAAT TTTAAT TTTA-AT TTTAAT TTTAA-T TTTAAT TTTAAT TT
300560 AATAATTGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
5 10 0.29
6 13 0.38
7 11 0.32
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (6 bp):
TTTAAT
Found at i:300531 original size:19 final size:20
Alignment explanation
Indices: 300507--300559 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
300497 TTAAAATTAT
300507 TTTTATATATTTAATTTT-A
1 TTTTATATATTTAATTTTAA
300526 TTTTATAT-TTT-ATTTTAA
1 TTTTATATATTTAATTTTAA
300544 TTTT-TA-ATTTTAATTT
1 TTTTATATA-TTTAATTT
300560 AATAATTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 7 0.23
18 11 0.37
19 12 0.40
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTATATATTTAATTTTAA
Found at i:300534 original size:17 final size:18
Alignment explanation
Indices: 300512--300547 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
300502 ATTATTTTTA
300512 TATATTTAATTTT-ATTT
1 TATATTTAATTTTAATTT
*
300529 TATATTTTATTTTAATTT
1 TATATTTAATTTTAATTT
300547 T
1 T
300548 TAATTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
TATATTTAATTTTAATTT
Found at i:300560 original size:18 final size:19
Alignment explanation
Indices: 300505--300562 Score: 75
Period size: 18 Copynumber: 3.1 Consensus size: 19
300495 TTTTAAAATT
*
300505 ATTTTTATATATTTAATTTT
1 ATTTTTATAT-TTTAATTTA
*
300525 A-TTTTATATTTTATTTTA
1 ATTTTTATATTTTAATTTA
300543 ATTTTTA-ATTTTAATTTA
1 ATTTTTATATTTTAATTTA
300561 AT
1 AT
300563 AATTGATAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
18 20 0.59
19 13 0.38
20 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
ATTTTTATATTTTAATTTA
Found at i:300858 original size:19 final size:18
Alignment explanation
Indices: 300818--300860 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
300808 AAAGTATTGA
300818 AAATTTTAAAATAAATAAT
1 AAATTTTAAAATAAAT-AT
300837 AAATTTTAAATATTAAAT-T
1 AAATTTTAAA-A-TAAATAT
300856 AAATT
1 AAATT
300861 CTTGAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 16 0.73
20 1 0.05
21 5 0.23
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATTTTAAAATAAATAT
Found at i:309226 original size:2 final size:2
Alignment explanation
Indices: 309219--309243 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
309209 GCCAACCCTA
309219 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
309244 CATGATTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:313496 original size:20 final size:20
Alignment explanation
Indices: 313454--313509 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
313444 TTCAACGATC
***
313454 TGTATCGATACATAAAATGT
1 TGTATCGATACATATTTTGT
*
313474 TGTATCGATACATATTTTTT
1 TGTATCGATACATATTTTGT
313494 TGTATCGATACA-ATTT
1 TGTATCGATACATATTT
313510 AAGCTACTGC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 4 0.12
20 28 0.88
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (20 bp):
TGTATCGATACATATTTTGT
Found at i:313566 original size:13 final size:13
Alignment explanation
Indices: 313548--313572 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
313538 ATTACTCAAA
313548 TGTATCGATACAT
1 TGTATCGATACAT
313561 TGTATCGATACA
1 TGTATCGATACA
313573 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:313674 original size:52 final size:52
Alignment explanation
Indices: 313581--313708 Score: 215
Period size: 52 Copynumber: 2.5 Consensus size: 52
313571 CACTGATCTT
* *
313581 TGTATCGATACATGCAGG-TAATTTGCCCAGATGTATCGATACA-TTTTAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATT-AAA
313632 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
313684 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
313709 TCATATTTCG
Statistics
Matches: 73, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
51 18 0.25
52 52 0.71
53 3 0.04
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
Found at i:319879 original size:33 final size:33
Alignment explanation
Indices: 319842--319910 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
319832 CCGTTAGAAG
*
319842 CAATGTATAGATACAAT-TCATCATGTATCGATA
1 CAATGTATAGATACAATGT-ACCATGTATCGATA
* *
319875 CAATGTATCGATACAATGTACCATGTATTGATA
1 CAATGTATAGATACAATGTACCATGTATCGATA
319908 CAA
1 CAA
319911 ACAGTGGTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (33 bp):
CAATGTATAGATACAATGTACCATGTATCGATA
Found at i:319882 original size:13 final size:13
Alignment explanation
Indices: 319864--319894 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
319854 ACAATTCATC
319864 ATGTATCGATACA
1 ATGTATCGATACA
319877 ATGTATCGATACA
1 ATGTATCGATACA
319890 ATGTA
1 ATGTA
319895 CCATGTATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:319983 original size:19 final size:19
Alignment explanation
Indices: 319939--319994 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
319929 CTGCCAGTTT
* **
319939 CATGTATCGATGCAATTGTC
1 CATGTATCGATACAA-TGAA
319959 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
319978 CATGTATCGACACAATG
1 CATGTATCGATACAATG
319995 TATCGATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:320513 original size:13 final size:13
Alignment explanation
Indices: 320495--320521 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
320485 ACATTATGCT
320495 TTGTATCGATACA
1 TTGTATCGATACA
320508 TTGTATCGATACA
1 TTGTATCGATACA
320521 T
1 T
320522 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:320554 original size:20 final size:19
Alignment explanation
Indices: 320505--320557 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
320495 TTGTATCGAT
* *
320505 ACATTGTATCGATACATGT
1 ACATAGTATCGATACATGG
* *
320524 TCATTGTATCGATACATGG
1 ACATAGTATCGATACATGG
320543 ACAATAGTATCGATA
1 AC-ATAGTATCGATA
320558 TATGAAATTG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (19 bp):
ACATAGTATCGATACATGG
Found at i:322255 original size:12 final size:12
Alignment explanation
Indices: 322240--322264 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
322230 TGAAGAGGAA
322240 GATGATAATGAT
1 GATGATAATGAT
322252 GATGATAATGAT
1 GATGATAATGAT
322264 G
1 G
322265 GTGACTCGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.28, T:0.32
Consensus pattern (12 bp):
GATGATAATGAT
Found at i:328660 original size:22 final size:22
Alignment explanation
Indices: 328635--328676 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
328625 TTTTTAAAGA
328635 TTTGACAAAGGGGGAGAAATGC
1 TTTGACAAAGGGGGAGAAATGC
*
328657 TTTGATAAAGGGGGAGAAAT
1 TTTGACAAAGGGGGAGAAAT
328677 ATGTTTATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.36, T:0.21
Consensus pattern (22 bp):
TTTGACAAAGGGGGAGAAATGC
Found at i:329274 original size:13 final size:13
Alignment explanation
Indices: 329256--329282 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
329246 ACATTATGCT
329256 TTGTATCGATACA
1 TTGTATCGATACA
329269 TTGTATCGATACA
1 TTGTATCGATACA
329282 T
1 T
329283 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:329407 original size:20 final size:20
Alignment explanation
Indices: 329382--329436 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
329372 TTATCGATAC
329382 ATTGTATCGATACATAATGA
1 ATTGTATCGATACATAATGA
*
329402 ATTGTATCGATACATGATGA
1 ATTGTATCGATACATAATGA
*
329422 ATTGCATCGATACAT
1 ATTGTATCGATACAT
329437 TGCTTGTAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (20 bp):
ATTGTATCGATACATAATGA
Found at i:336995 original size:9 final size:9
Alignment explanation
Indices: 336981--337014 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
336971 TCCGAGTCAC
336981 CATCATTAT
1 CATCATTAT
336990 CATCATTAT
1 CATCATTAT
336999 CATC-TTCAT
1 CATCATT-AT
337008 CATCATT
1 CATCATT
337015 GATGGTTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 2 0.09
9 19 0.83
10 2 0.09
ACGTcount: A:0.29, C:0.26, G:0.00, T:0.44
Consensus pattern (9 bp):
CATCATTAT
Found at i:338731 original size:19 final size:19
Alignment explanation
Indices: 338687--338742 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
338677 CTGCCAGTTT
**
338687 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
338707 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
338726 CATGTATCGATACAATG
1 CATGTATCGATACAATG
338743 TATTGATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:339002 original size:18 final size:18
Alignment explanation
Indices: 338979--339015 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
338969 GAGTGTTTTT
338979 GAATAAAACTTGTTTACG
1 GAATAAAACTTGTTTACG
338997 GAATAAAACTTGTTTACG
1 GAATAAAACTTGTTTACG
339015 G
1 G
339016 TTTTTCAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (18 bp):
GAATAAAACTTGTTTACG
Found at i:339376 original size:13 final size:13
Alignment explanation
Indices: 339358--339384 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
339348 ACATGTTGCT
339358 TTGTATCGATACA
1 TTGTATCGATACA
339371 TTGTATCGATACA
1 TTGTATCGATACA
339384 T
1 T
339385 GTTCAATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:339381 original size:33 final size:32
Alignment explanation
Indices: 339339--339403 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 32
339329 CACACCCAGA
**
339339 TGTATCGATACATGTTGCTTTGTATCGATACAT
1 TGTATCGATACATGTT-CAATGTATCGATACAT
339372 TGTATCGATACATGTTCAATGTATCGATACAT
1 TGTATCGATACATGTTCAATGTATCGATACAT
339404 GGACAAATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.47
33 16 0.53
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATGTTCAATGTATCGATACAT
Found at i:339396 original size:19 final size:21
Alignment explanation
Indices: 339370--339425 Score: 80
Period size: 19 Copynumber: 2.8 Consensus size: 21
339360 GTATCGATAC
**
339370 ATTGTATCGATACATGTTC-A
1 ATTGTATCGATACATGGACAA
339390 A-TGTATCGATACATGGACAA
1 ATTGTATCGATACATGGACAA
339410 ATTGTATCGATACATG
1 ATTGTATCGATACATG
339426 AAATTGGCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 15 0.47
20 3 0.09
21 14 0.44
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (21 bp):
ATTGTATCGATACATGGACAA
Found at i:347551 original size:18 final size:19
Alignment explanation
Indices: 347521--347559 Score: 71
Period size: 18 Copynumber: 2.1 Consensus size: 19
347511 ATAAATTTTT
347521 TATAAAAAGGGGGAGAAGA
1 TATAAAAAGGGGGAGAAGA
347540 TATAAAAA-GGGGAGAAGA
1 TATAAAAAGGGGGAGAAGA
347558 TA
1 TA
347560 ATCGTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.54, C:0.00, G:0.33, T:0.13
Consensus pattern (19 bp):
TATAAAAAGGGGGAGAAGA
Found at i:347613 original size:41 final size:40
Alignment explanation
Indices: 347549--347671 Score: 166
Period size: 37 Copynumber: 3.1 Consensus size: 40
347539 ATATAAAAAG
347549 GGGAGAAGATAATCGTTTAAAGGGGGAGAATTTTTTTTAAGA
1 GGGA-AAGATAATCGTTT-AAGGGGGAGAATTTTTTTTAAGA
*
347591 GGGAAAAGATAATTGTTTAAGGGGGAGAATTTTTTTTAAGA
1 GGG-AAAGATAATCGTTTAAGGGGGAGAATTTTTTTTAAGA
347632 -GG--AGATAATCGTTTAA-GGGGAGAATATTTTTTTAAG-
1 GGGAAAGATAATCGTTTAAGGGGGAGAAT-TTTTTTTAAGA
347668 GGGA
1 GGGA
347672 GAAAAACGAA
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
36 9 0.12
37 25 0.33
40 2 0.03
41 23 0.31
42 15 0.20
43 1 0.01
ACGTcount: A:0.35, C:0.02, G:0.31, T:0.33
Consensus pattern (40 bp):
GGGAAAGATAATCGTTTAAGGGGGAGAATTTTTTTTAAGA
Found at i:347630 original size:19 final size:19
Alignment explanation
Indices: 347571--347674 Score: 88
Period size: 19 Copynumber: 5.4 Consensus size: 19
347561 TCGTTTAAAG
347571 GGGGAGAAT-TTTTTTTAA
1 GGGGAGAATATTTTTTTAA
* * *
347589 GAGGGAAAAGATAATTGTTTAA
1 G-GGG-AGA-ATATTTTTTTAA
347611 GGGGGAGAAT-TTTTTTTAA
1 -GGGGAGAATATTTTTTTAA
* * **
347630 GAGGAG-ATAATCGTTTAA
1 GGGGAGAATATTTTTTTAA
347648 GGGGAGAATATTTTTTTAA
1 GGGGAGAATATTTTTTTAA
347667 GGGGAGAA
1 GGGGAGAA
347675 AAACGAAAAC
Statistics
Matches: 65, Mismatches: 14, Indels: 13
0.71 0.15 0.14
Matches are distributed among these distances:
17 2 0.03
18 17 0.26
19 27 0.42
20 4 0.06
21 4 0.06
22 10 0.15
23 1 0.02
ACGTcount: A:0.35, C:0.01, G:0.31, T:0.34
Consensus pattern (19 bp):
GGGGAGAATATTTTTTTAA
Found at i:348255 original size:19 final size:21
Alignment explanation
Indices: 348231--348282 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
348221 CGATACATTA
**
348231 TATCGATACATGTTC-AA-TG
1 TATCGATACATGGACAAATTG
348250 TATCGATACATGGACAAATTG
1 TATCGATACATGGACAAATTG
348271 TATCGATACATG
1 TATCGATACATG
348283 AAATTGGCAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.45
20 2 0.07
21 14 0.48
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (21 bp):
TATCGATACATGGACAAATTG
Found at i:348257 original size:32 final size:33
Alignment explanation
Indices: 348198--348260 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
348188 CACCCAAATG
**
348198 TATCGATACATGCTGCTTTGTATCGATACATTA
1 TATCGATACATGCTGCAATGTATCGATACATTA
*
348231 TATCGATACATG-TTCAATGTATCGATACAT
1 TATCGATACATGCTGCAATGTATCGATACAT
348261 GGACAAATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 15 0.56
33 12 0.44
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.38
Consensus pattern (33 bp):
TATCGATACATGCTGCAATGTATCGATACATTA
Found at i:348354 original size:33 final size:32
Alignment explanation
Indices: 348310--348373 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 32
348300 CCTATATTAT
348310 TTGTATCGATACATG-GTACAATGTATCGATACA
1 TTGTATCGATACATGAG-A-AATGTATCGATACA
*
348343 TTGTATTGATACATGAAGAAATGTATCGATA
1 TTGTATCGATACATG-AGAAATGTATCGATA
348374 TATAGCTTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 26 0.93
34 1 0.04
35 1 0.04
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (32 bp):
TTGTATCGATACATGAGAAATGTATCGATACA
Found at i:350798 original size:8 final size:8
Alignment explanation
Indices: 350785--350819 Score: 70
Period size: 8 Copynumber: 4.4 Consensus size: 8
350775 TTTTTTTCAA
350785 AAACAACC
1 AAACAACC
350793 AAACAACC
1 AAACAACC
350801 AAACAACC
1 AAACAACC
350809 AAACAACC
1 AAACAACC
350817 AAA
1 AAA
350820 AATATTTTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.66, C:0.34, G:0.00, T:0.00
Consensus pattern (8 bp):
AAACAACC
Found at i:356554 original size:20 final size:20
Alignment explanation
Indices: 356526--356583 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
356516 TTGATACAAC
* *
356526 AAGTTAATGTATCAATACAT
1 AAGTAAATGTATCGATACAT
* *
356546 AAGTGAATGTATCGATATAT
1 AAGTAAATGTATCGATACAT
356566 AAGTAAATGTATCGATAC
1 AAGTAAATGTATCGATAC
356584 TGGACCATGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.33
Consensus pattern (20 bp):
AAGTAAATGTATCGATACAT
Found at i:356745 original size:21 final size:20
Alignment explanation
Indices: 356697--356748 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
356687 AACCCAAATA
*
356697 TATCGATACATTCTTCAAAG
1 TATCGATACATGCTTCAAAG
* * *
356717 TATTGATACATGCTTGTAATG
1 TATCGATACATGCTT-CAAAG
356738 TATCGATACAT
1 TATCGATACAT
356749 TATTCATTGT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (20 bp):
TATCGATACATGCTTCAAAG
Found at i:356757 original size:93 final size:91
Alignment explanation
Indices: 356625--356795 Score: 236
Period size: 93 Copynumber: 1.9 Consensus size: 91
356615 AAAAGAAATT
*
356625 GTATTGATACATAAGTGAATGTATCGTACATTTCTCATTGTATTGATACATTCTGGGTTTTTAAC
1 GTATTGATACATAAGTGAATGTATCGTACATTTCTCATTGTATCGATACATTCTGGGTTTTTAAC
356690 CCAAATATATCGATACATTCTTCAAA
66 CCAAATATATCGATACATTCTTCAAA
*** * *
356716 GTATTGATACATGCTTGTAATGTATCGATACATTAT-TCATTGTATCGATGCATTCTGGTTTTTT
1 GTATTGATACATAAGTG-AATGTATCG-TACATT-TCTCATTGTATCGATACATTCTGGGTTTTT
* *
356780 GACCCAAATGTATCGA
63 AACCCAAATATATCGA
356796 AAATTTTTTA
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
91 14 0.20
92 9 0.13
93 45 0.65
94 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.40
Consensus pattern (91 bp):
GTATTGATACATAAGTGAATGTATCGTACATTTCTCATTGTATCGATACATTCTGGGTTTTTAAC
CCAAATATATCGATACATTCTTCAAA
Found at i:357355 original size:52 final size:51
Alignment explanation
Indices: 357293--357467 Score: 145
Period size: 52 Copynumber: 3.4 Consensus size: 51
357283 TGGACTTTAC
* * * *
357293 ACTAGCAAATTTTATTAGGCAAAACAAGTTACGTTGGGCTTTGACTCTTAAT
1 ACTAGCAAATTTCACTAGG-AAAACAAGTTATGTTGGGCTTTGACTCTTGAT
* * * **
357345 ACTAGCAAATTTCACTAGGTGAAACTAGTTTTGTTATGCTTTGACTCTTGAT
1 ACTAGCAAATTTCACTAGG-AAAACAAGTTATGTTGGGCTTTGACTCTTGAT
* * * * * *
357397 ACTAACCAATTTCATTAGATGAAACCAA-TTATGTTGGGCTTTAAATCTTGAT
1 ACTAGCAAATTTCACTAG--GAAAACAAGTTATGTTGGGCTTTGACTCTTGAT
* * *
357449 ACTGGCCAATTTTACTAGG
1 ACTAGCAAATTTCACTAGG
357468 TAGAACTAGC
Statistics
Matches: 96, Mismatches: 25, Indels: 6
0.76 0.20 0.05
Matches are distributed among these distances:
50 1 0.01
52 90 0.94
53 4 0.04
54 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.37
Consensus pattern (51 bp):
ACTAGCAAATTTCACTAGGAAAACAAGTTATGTTGGGCTTTGACTCTTGAT
Found at i:357828 original size:53 final size:53
Alignment explanation
Indices: 357763--357892 Score: 152
Period size: 53 Copynumber: 2.4 Consensus size: 53
357753 AGTTAAATTT
* * ** *
357763 GGCTTGACTCTTGGTGTAGGCCAATTAGCTAAAACTTTCTTGCCGAAATCATTG
1 GGCTT-ACTCTTGGTATAGGCCAATTAGCCAAAACTAGCCTGCCGAAATCATTG
* * *
357817 GGCTTACTCTTGGTATGGGCCAATTAGCCAAAACTAGCCTGTCGACATCATTG
1 GGCTTACTCTTGGTATAGGCCAATTAGCCAAAACTAGCCTGCCGAAATCATTG
* * *
357870 AGCTTACTCTTGGAATGGGCCAA
1 GGCTTACTCTTGGTATAGGCCAA
357893 CTTCACTGGG
Statistics
Matches: 66, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
53 61 0.92
54 5 0.08
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (53 bp):
GGCTTACTCTTGGTATAGGCCAATTAGCCAAAACTAGCCTGCCGAAATCATTG
Found at i:363761 original size:20 final size:20
Alignment explanation
Indices: 363733--363773 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
363723 TACATACTGC
363733 TAAGGAAATGTATCGATACA
1 TAAGGAAATGTATCGATACA
*
363753 TAAGTAAATGTATCGATACA
1 TAAGGAAATGTATCGATACA
363773 T
1 T
363774 TTTCTATCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.10, G:0.17, T:0.29
Consensus pattern (20 bp):
TAAGGAAATGTATCGATACA
Found at i:366525 original size:28 final size:30
Alignment explanation
Indices: 366485--366541 Score: 73
Period size: 28 Copynumber: 1.9 Consensus size: 30
366475 CCACCATCAA
**
366485 GGATACTTGAACCTC-A-TTATTTTTAAGG
1 GGATACTCCAACCTCGATTTATTTTTAAGG
366513 GGATACTCCAACCTCGATTTTATTTTTAA
1 GGATACTCCAACCTCGA-TTTATTTTTAA
366542 AACACTAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 13 0.54
29 1 0.04
31 10 0.42
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (30 bp):
GGATACTCCAACCTCGATTTATTTTTAAGG
Found at i:366728 original size:237 final size:238
Alignment explanation
Indices: 366214--366763 Score: 594
Period size: 237 Copynumber: 2.3 Consensus size: 238
366204 TCATTGATGT
* * * * *
366214 TTTTATTTCTTACACATCGAT-TTTTCACTATCGGGGATACTCCAACCACGCTATTTTCGAGGGG
1 TTTTATTTCTAAAACATCGATCTTTTCACCATCGGGGATACTCCAACCACACTATTTTCAAGGGG
* * * *
366278 ATGCTCTAACCCTGGTTTTATTTCTAAAACACCAATCTTCCACCATCGAGGATACTCTAACCCTG
66 ATACTCCAACCCTGATTTTATTTCTAAAACACCAATCTTCCACCATAGAGGATACTCTAACCCTG
* * *
366343 TTATTTTCAAGGGGATACTCCAACCTCAGTTTTATTTCTAAAACATCAATTTTCCACCAACGGGG
131 TTATTTTCAAGGGGATACTCCAACCCCAGTTTTATTTCTAAAACATCAATTTCCCACCAACAGGG
* * * * *
366408 ATACTCCAACCCCATTATTTTTTAGGAGATATTCCAACCTCGA
196 ACACTCCAACCCCATTATTTCTGAGGAGATACTCCAACCCCGA
* ** ** * * *
366451 TTTTATTTCTAAAACATCGATC-TTCCACCATCAAGGATACTTGAACCTCATTATTTTTAAGGGG
1 TTTTATTTCTAAAACATCGATCTTTTCACCATCGGGGATACTCCAACCACACTATTTTCAAGGGG
* * *
366515 ATACTCCAA-CCTCGATTTTATTTTTAAAACACTAATTTTCCACCATTAG-GGATACTCTAA-CC
66 ATACTCCAACCCT-GATTTTATTTCTAAAACACCAATCTTCCACCA-TAGAGGATACTCTAACCC
** * * * *
366577 TCGTTATTTTTGAGGGGGTACTCCAACCCCGGTTTTATTTTTAAAACA-CTAATTTCCCACCATC
129 T-GTTATTTTCAAGGGGATACTCCAACCCCAGTTTTATTTCTAAAACATC-AATTTCCCACCAAC
* ** *
366641 AGGGACACTCCAACTCTGTTATTTCTGAGGAGATACTGCAACCCCGA
192 AGGGACACTCCAACCCCATTATTTCTGAGGAGATACTCCAACCCCGA
* * * ** *
366688 TTTTATTTTTAAAATAT-TATCTTTTCACCATCGGGGATACTCCAACTC-CGTTGTTTTCAAGGG
1 TTTTATTTCTAAAACATCGATCTTTTCACCATCGGGGATACTCCAAC-CACACTATTTTCAAGGG
*
366751 GATACTCTAACCC
65 GATACTCCAACCC
366764 CATTTTCATC
Statistics
Matches: 255, Mismatches: 50, Indels: 15
0.80 0.16 0.05
Matches are distributed among these distances:
236 10 0.04
237 240 0.94
238 5 0.02
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.35
Consensus pattern (238 bp):
TTTTATTTCTAAAACATCGATCTTTTCACCATCGGGGATACTCCAACCACACTATTTTCAAGGGG
ATACTCCAACCCTGATTTTATTTCTAAAACACCAATCTTCCACCATAGAGGATACTCTAACCCTG
TTATTTTCAAGGGGATACTCCAACCCCAGTTTTATTTCTAAAACATCAATTTCCCACCAACAGGG
ACACTCCAACCCCATTATTTCTGAGGAGATACTCCAACCCCGA
Found at i:366763 original size:79 final size:78
Alignment explanation
Indices: 366233--366769 Score: 465
Period size: 79 Copynumber: 6.8 Consensus size: 78
366223 TTACACATCG
* * * * * * * *
366233 ATTTTTCACTATCGGGGATACTCCAACCACGCTATTTTCGAGGGGATGCTCTAACCCTGGTTTTA
1 ATTTTCCACCATCGGGGATACTCCAACC-CGTTATTTTCAAGGGGATACTCCAACCCCGATTTTA
*
366298 TTTCTAAAACACCA
65 TTTCTAAAACACTA
* * * *
366312 ATCTTCCACCATCGAGGATACTCTAACCCTGTTATTTTCAAGGGGATACTCCAACCTC-AGTTTT
1 ATTTTCCACCATCGGGGATACTCCAACCC-GTTATTTTCAAGGGGATACTCCAACCCCGA-TTTT
366376 ATTTCTAAAACA-TCA
64 ATTTCTAAAACACT-A
* * ** * * *
366391 ATTTTCCACCAACGGGGATACTCCAACCCCATTATTTTTTAGGAGATATTCCAACCTCGATTTTA
1 ATTTTCCACCATCGGGGATACTCCAA-CCCGTTATTTTCAAGGGGATACTCCAACCCCGATTTTA
*
366456 TTTCTAAAACA-TCG
65 TTTCTAAAACACT-A
* ** ** * * *
366470 ATCTTCCACCATCAAGGATACTTGAACCTCATTATTTTTAAGGGGATACTCCAACCTCGATTTTA
1 ATTTTCCACCATCGGGGATACTCCAACC-CGTTATTTTCAAGGGGATACTCCAACCCCGATTTTA
*
366535 TTTTTAAAACACTA
65 TTTCTAAAACACTA
** * ** * *
366549 ATTTTCCACCATTAGGGATACTCTAACCTCGTTATTTTTGAGGGGGTACTCCAACCCCGGTTTTA
1 ATTTTCCACCATCGGGGATACTCCAACC-CGTTATTTTCAAGGGGATACTCCAACCCCGATTTTA
*
366614 TTTTTAAAACACTA
65 TTTCTAAAACACTA
* * * * * * *
366628 ATTTCCCACCATCAGGGACACTCCAACTCTGTTA-TTTCTGAGGAGATACTGCAACCCCGATTTT
1 ATTTTCCACCATCGGGGATACTCCAAC-CCGTTATTTTC-AAGGGGATACTCCAACCCCGATTTT
* * *
366692 ATTTTTAAAATA-TT
64 ATTTCTAAAACACTA
* * *
366706 ATCTTTTCACCATCGGGGATACTCCAACTCCGTTGTTTTCAAGGGGATACTCTAACCCC-ATTTT
1 AT-TTTCCACCATCGGGGATACTCCAAC-CCGTTATTTTCAAGGGGATACTCCAACCCCGATTTT
366770 CATCTCCAAA
Statistics
Matches: 381, Mismatches: 66, Indels: 23
0.81 0.14 0.05
Matches are distributed among these distances:
78 14 0.04
79 357 0.94
80 10 0.03
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.34
Consensus pattern (78 bp):
ATTTTCCACCATCGGGGATACTCCAACCCGTTATTTTCAAGGGGATACTCCAACCCCGATTTTAT
TTCTAAAACACTA
Found at i:375683 original size:89 final size:89
Alignment explanation
Indices: 375515--375685 Score: 202
Period size: 89 Copynumber: 1.9 Consensus size: 89
375505 ATTTTTAACA
** *
375515 TTTTAAATTTTCATTATCATTAAAAAGTAAATAAATTTATTTTGTACAAAAAAAGTTAAAACTTA
1 TTTTAAATTTTCATTATCATTAAAAAGTAAATAAATTTATTTAATACAAAAAAAGCTAAAACTTA
*
375580 CATCCAACTTATTTATTGTTGTAC
66 CATCCAAATTATTTATTGTTGTAC
* * * * * **
375604 TTTTAATTTTTCATTAAT-TTTAAAGAGTACATAAATTTATTTAATATAAAAGGAGCTAAAACTT
1 TTTTAAATTTTCATT-ATCATTAAAAAGTAAATAAATTTATTTAATACAAAAAAAGCTAAAACTT
*
375668 ACAT-TAAATTCATTTATT
65 ACATCCAAATT-ATTTATT
375686 TTCACACTTT
Statistics
Matches: 68, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
88 4 0.06
89 62 0.91
90 2 0.03
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.44
Consensus pattern (89 bp):
TTTTAAATTTTCATTATCATTAAAAAGTAAATAAATTTATTTAATACAAAAAAAGCTAAAACTTA
CATCCAAATTATTTATTGTTGTAC
Found at i:375695 original size:89 final size:87
Alignment explanation
Indices: 375496--375702 Score: 193
Period size: 89 Copynumber: 2.3 Consensus size: 87
375486 TTTTACAGTC
* **
375496 AATTATTTTATTTTTAACATTTTAAATTTTCATTATCATTAAAAAGTAAATAAATTTATTTTGTA
1 AATTA-TTTA-TTTTAAC-TTTTAATTTTTCATTATCATTAAAAAGTAAATAAATTTATTTAATA
*
375561 CAAAAAAAGTTAAAACTTACATCCA
63 CAAAAAAAGCTAAAACTTACATCCA
* * * * *
375586 ACTTATTTATTGTTGTACTTTTAATTTTTCATTAAT-TTTAAAGAGTACATAAATTTATTTAATA
1 AATTATTTATT-TT-AACTTTTAATTTTTCATT-ATCATTAAAAAGTAAATAAATTTATTTAATA
* ** *
375650 TAAAAGGAGCTAAAACTTACAT-TA
63 CAAAAAAAGCTAAAACTTACATCCA
*
375674 AATTCATTTATTTTCACACTTTTAGTTTT
1 AATT-ATTTATTTT-A-ACTTTTAATTTT
375703 ATATTAACAT
Statistics
Matches: 95, Mismatches: 17, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
88 8 0.08
89 79 0.83
90 8 0.08
ACGTcount: A:0.39, C:0.09, G:0.05, T:0.46
Consensus pattern (87 bp):
AATTATTTATTTTAACTTTTAATTTTTCATTATCATTAAAAAGTAAATAAATTTATTTAATACAA
AAAAAGCTAAAACTTACATCCA
Found at i:380192 original size:13 final size:13
Alignment explanation
Indices: 380174--380198 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
380164 ATTCAAATAA
380174 AAATAAATTAAAT
1 AAATAAATTAAAT
380187 AAATAAATTAAA
1 AAATAAATTAAA
380199 GACAAAATAA
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATAAATTAAAT
Found at i:386418 original size:20 final size:20
Alignment explanation
Indices: 386393--386451 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 20
386383 TGCTAGTTTC
386393 ATGTATCGATACAATTCGTT
1 ATGTATCGATACAATTCGTT
* *
386413 ATGTATTGATACCAA---GATC
1 ATGTATCGATA-CAATTCG-TT
386432 ATGTATCGATACAATTCGTT
1 ATGTATCGATACAATTCGTT
386452 GTATATTGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
18 4 0.13
19 11 0.37
20 11 0.37
21 4 0.13
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACAATTCGTT
Found at i:386437 original size:19 final size:19
Alignment explanation
Indices: 386413--386482 Score: 63
Period size: 19 Copynumber: 3.6 Consensus size: 19
386403 ACAATTCGTT
*
386413 ATGTATTGATACCAAGATC
1 ATGTATCGATACCAAGATC
*
386432 ATGTATCGATA-CAA-TTC
1 ATGTATCGATACCAAGATC
* *
386449 GTTGTATATTGATACCAAGATC
1 -ATG--TATCGATACCAAGATC
386471 ATGTATCGATAC
1 ATGTATCGATAC
386483 AGTGTATCGA
Statistics
Matches: 39, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
17 2 0.05
18 5 0.13
19 18 0.46
20 7 0.18
21 5 0.13
22 2 0.05
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (19 bp):
ATGTATCGATACCAAGATC
Found at i:386443 original size:39 final size:39
Alignment explanation
Indices: 386391--386483 Score: 168
Period size: 39 Copynumber: 2.4 Consensus size: 39
386381 ACTGCTAGTT
*
386391 TCATGTATCGATACAATTCGTTATGTATTGATACCAAGA
1 TCATGTATCGATACAATTCGTTATATATTGATACCAAGA
*
386430 TCATGTATCGATACAATTCGTTGTATATTGATACCAAGA
1 TCATGTATCGATACAATTCGTTATATATTGATACCAAGA
386469 TCATGTATCGATACA
1 TCATGTATCGATACA
386484 GTGTATCGAT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.35
Consensus pattern (39 bp):
TCATGTATCGATACAATTCGTTATATATTGATACCAAGA
Found at i:386476 original size:21 final size:21
Alignment explanation
Indices: 386416--386476 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
386406 ATTCGTTATG
386416 TATTGATACCAAGATCATG--
1 TATTGATACCAAGATCATGTA
* * *
386435 TATCGATA-CAA-TTCGTTGTA
1 TATTGATACCAAGATC-ATGTA
386455 TATTGATACCAAGATCATGTA
1 TATTGATACCAAGATCATGTA
386476 T
1 T
386477 CGATACAGTG
Statistics
Matches: 31, Mismatches: 6, Indels: 8
0.69 0.13 0.18
Matches are distributed among these distances:
17 2 0.06
18 5 0.16
19 7 0.23
20 7 0.23
21 8 0.26
22 2 0.06
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (21 bp):
TATTGATACCAAGATCATGTA
Found at i:386490 original size:13 final size:13
Alignment explanation
Indices: 386472--386496 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
386462 ACCAAGATCA
386472 TGTATCGATACAG
1 TGTATCGATACAG
386485 TGTATCGATACA
1 TGTATCGATACA
386497 AAGCAATATG
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:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:387037 original size:22 final size:22
Alignment explanation
Indices: 387011--387092 Score: 107
Period size: 23 Copynumber: 3.7 Consensus size: 22
387001 CAAATTATAA
387011 CTCCCCTTTAATAAAAATTTTT
1 CTCCCCTTTAATAAAAATTTTT
387033 CTCCCCTTTAATAAAAAATTTTT
1 CTCCCCTTTAAT-AAAAATTTTT
*
387056 CTCCCCCTTAAT--AAA-TTTT
1 CTCCCCTTTAATAAAAATTTTT
387075 CTCTCCCTCTTAATAAAA
1 CTC-CCCT-TTAATAAAA
387093 TTTCTTCCCT
Statistics
Matches: 53, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
19 7 0.13
20 6 0.11
21 5 0.09
22 12 0.23
23 23 0.43
ACGTcount: A:0.32, C:0.27, G:0.00, T:0.41
Consensus pattern (22 bp):
CTCCCCTTTAATAAAAATTTTT
Found at i:387096 original size:21 final size:22
Alignment explanation
Indices: 387014--387102 Score: 89
Period size: 21 Copynumber: 4.2 Consensus size: 22
387004 ATTATAACTC
*
387014 CCCT-TTAATAAAAATTTTTCT
1 CCCTCTTAATAAAAATTTCTCT
*
387035 CCC-CTTTAATAAAAAATTTTTCT
1 CCCTC-TTAAT-AAAAATTTCTCT
* *
387058 CCCCCTTAAT-AAATTTTCTCT
1 CCCTCTTAATAAAAATTTCTCT
387079 CCCTCTTAAT-AAAATTTCT-T
1 CCCTCTTAATAAAAATTTCTCT
387099 CCCT
1 CCCT
387103 TAAAAATATC
Statistics
Matches: 60, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
20 5 0.08
21 29 0.48
22 5 0.08
23 20 0.33
24 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.00, T:0.44
Consensus pattern (22 bp):
CCCTCTTAATAAAAATTTCTCT
Found at i:387120 original size:18 final size:19
Alignment explanation
Indices: 387055--387121 Score: 68
Period size: 18 Copynumber: 3.6 Consensus size: 19
387045 AAAAAATTTT
*
387055 TCTC-CCCCTTAATAAATTT
1 TCTCTCCCCTTAATAAA-TA
387074 TCTCTCCCTCTTAATAAA-A
1 TCTCTCCC-CTTAATAAATA
* *
387093 TTTCTTCCCTTAA-AAATA
1 TCTCTCCCCTTAATAAATA
387111 TCTCTCCCCTT
1 TCTCTCCCCTT
387122 TTTTTTTCCA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
17 3 0.08
18 15 0.38
19 10 0.25
20 3 0.08
21 9 0.22
ACGTcount: A:0.25, C:0.33, G:0.00, T:0.42
Consensus pattern (19 bp):
TCTCTCCCCTTAATAAATA
Found at i:387184 original size:45 final size:44
Alignment explanation
Indices: 387105--387208 Score: 165
Period size: 45 Copynumber: 2.4 Consensus size: 44
387095 TCTTCCCTTA
*
387105 AAAAT-ATCTCTCCCCTTTTTTTTTCCAAAATAATCTCTTTTAT
1 AAAATAATCTCTCCTCTTTTTTTTTCCAAAATAATCTCTTTTAT
*
387148 AAAATAATCTCTCCTTTTTTTTGTTTCCAAAATAATCTCTTTTAT
1 AAAATAATCTCTCCTCTTTTTT-TTTCCAAAATAATCTCTTTTAT
*
387193 AAAATAATCTTTCCTC
1 AAAATAATCTCTCCTC
387209 CATTTTCAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
43 5 0.09
44 14 0.25
45 36 0.65
ACGTcount: A:0.30, C:0.21, G:0.01, T:0.48
Consensus pattern (44 bp):
AAAATAATCTCTCCTCTTTTTTTTTCCAAAATAATCTCTTTTAT
Found at i:389094 original size:13 final size:13
Alignment explanation
Indices: 389076--389110 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
389066 AGTGCCTTTT
*
389076 TATCGATGCAATG
1 TATCGATACAATG
389089 TATCGATACAATG
1 TATCGATACAATG
*
389102 TATCAATAC
1 TATCGATAC
389111 TAAGATCCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.31
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:393218 original size:15 final size:16
Alignment explanation
Indices: 393200--393235 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
393190 TCTAGTTCAT
393200 AATTTTC-TTTTCAAC
1 AATTTTCATTTTCAAC
393215 AA-TTTCATTTTCAAC
1 AATTTTCATTTTCAAC
393230 AATTTT
1 AATTTT
393236 TGATTTATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 4 0.21
15 12 0.63
16 3 0.16
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (16 bp):
AATTTTCATTTTCAAC
Found at i:395448 original size:20 final size:21
Alignment explanation
Indices: 395425--395463 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
395415 CAAAGCAATA
395425 TGTATCGATAC-TTCTAGGCC
1 TGTATCGATACTTTCTAGGCC
395445 TGTATCGATACTTTCTAGG
1 TGTATCGATACTTTCTAGG
395464 GTTTTGACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (21 bp):
TGTATCGATACTTTCTAGGCC
Found at i:396251 original size:13 final size:13
Alignment explanation
Indices: 396235--396259 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
396225 ATAATACACA
396235 GTATCGATACATT
1 GTATCGATACATT
396248 GTATCGATACAT
1 GTATCGATACAT
396260 GACCACTGTA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:396256 original size:33 final size:32
Alignment explanation
Indices: 396214--396276 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
396204 CACCTTTAGA
396214 TGTATCGATACATAATACACAGTATCGATACAT
1 TGTATCGATACATAA-ACACAGTATCGATACAT
* * *
396247 TGTATCGATACATGACCACTGTATCGATAC
1 TGTATCGATACATAAACACAGTATCGATAC
396277 TTGCAAAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (32 bp):
TGTATCGATACATAAACACAGTATCGATACAT
Found at i:396369 original size:32 final size:33
Alignment explanation
Indices: 396328--396395 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
396318 CCTTAACTGT
*
396328 TTGTATCGATACAT-A-CAAGATGTATCAATACA
1 TTGTATCGATACATGACCAA-ACGTATCAATACA
*
396360 TTGTATCGATACATGACCAAACGTATCGATACA
1 TTGTATCGATACATGACCAAACGTATCAATACA
396393 TTG
1 TTG
396396 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
32 14 0.44
33 15 0.47
34 3 0.09
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.31
Consensus pattern (33 bp):
TTGTATCGATACATGACCAAACGTATCAATACA
Found at i:397976 original size:24 final size:24
Alignment explanation
Indices: 397944--397991 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
397934 TATCAATACA
397944 TTTGGTTAAAATGTGCATTTTACT
1 TTTGGTTAAAATGTGCATTTTACT
397968 TTTGGTTAAAATGTGCATTTTACT
1 TTTGGTTAAAATGTGCATTTTACT
397992 CACCTTAGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.08, G:0.17, T:0.50
Consensus pattern (24 bp):
TTTGGTTAAAATGTGCATTTTACT
Found at i:399034 original size:21 final size:21
Alignment explanation
Indices: 399008--399083 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
398998 CTGCCAAGAA
399008 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
****
399029 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
399049 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
399070 ATGTATCGATACAT
1 ATGTATCGATACAT
399084 TGCAACATGT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:399053 original size:20 final size:20
Alignment explanation
Indices: 399028--399101 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
399018 ACATCTTTTT
399028 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
****
399048 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGCAA
399069 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
399089 CATGTATCGATAC
1 CATGTATCGATAC
399102 TTTGAATTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (20 bp):
CATGTATCGATACATTGCAA
Found at i:399065 original size:41 final size:41
Alignment explanation
Indices: 399008--399101 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
398998 CTGCCAAGAA
399008 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
399049 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
399090 ATGTATCGATAC
1 ATGTATCGATAC
399102 TTTGAATTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:401570 original size:13 final size:13
Alignment explanation
Indices: 401552--401590 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
401542 ATAATCACCC
* *
401552 TGTATCGATATAG
1 TGTATCGATACAA
401565 TGTATCGATACAA
1 TGTATCGATACAA
401578 TGTATCGATACAA
1 TGTATCGATACAA
401591 AGAAAAATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:405532 original size:21 final size:21
Alignment explanation
Indices: 405503--405547 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
405493 AAGTTTTCAT
*
405503 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
405523 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
405545 TTT
1 TTT
405548 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:407779 original size:13 final size:13
Alignment explanation
Indices: 407761--407786 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
407751 CAATTTTTTG
407761 TGTATCGATACAT
1 TGTATCGATACAT
407774 TGTATCGATACAT
1 TGTATCGATACAT
407787 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:410913 original size:13 final size:13
Alignment explanation
Indices: 410895--410919 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
410885 AGGCTTTGGG
410895 ATTAGTTTAGTTT
1 ATTAGTTTAGTTT
410908 ATTAGTTTAGTT
1 ATTAGTTTAGTT
410920 AGTGGCTTTG
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:0.24, C:0.00, G:0.16, T:0.60
Consensus pattern (13 bp):
ATTAGTTTAGTTT
Found at i:415092 original size:28 final size:28
Alignment explanation
Indices: 415052--415107 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
415042 AAAAATTTCG
*
415052 TAAACTACTTTTATTATTCTGTTAATGA
1 TAAACTACCTTTATTATTCTGTTAATGA
*
415080 TAAACTACCTTTATTATTTTGTTAATGA
1 TAAACTACCTTTATTATTCTGTTAATGA
415108 GAAAATCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.32, C:0.11, G:0.07, T:0.50
Consensus pattern (28 bp):
TAAACTACCTTTATTATTCTGTTAATGA
Found at i:416647 original size:20 final size:20
Alignment explanation
Indices: 416624--416697 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
416614 ACAATTCAAA
416624 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
416644 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
416665 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
416685 GTATCGATACATG
1 GTATCGATACATG
416698 AAAAAGATGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:416668 original size:21 final size:21
Alignment explanation
Indices: 416642--416717 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
416632 ACATGTTGCA
416642 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
416663 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
416683 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
416704 ATGTATCGATACAT
1 ATGTATCGATACAT
416718 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:416675 original size:41 final size:41
Alignment explanation
Indices: 416624--416717 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
416614 ACAATTCAAA
416624 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
416665 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
416706 GTATCGATACAT
1 GTATCGATACAT
416718 TTCTTGGCAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
Found at i:419028 original size:21 final size:21
Alignment explanation
Indices: 418995--419039 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
418985 TTGCAAGTTG
*
418995 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
419017 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
419037 AAA
1 AAA
419040 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:422961 original size:13 final size:13
Alignment explanation
Indices: 422943--422981 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
422933 ACATTTTTCT
422943 TTGTATCGATACA
1 TTGTATCGATACA
422956 TTGTATCGATACA
1 TTGTATCGATACA
*
422969 CTGTATCGATACA
1 TTGTATCGATACA
422982 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:425542 original size:13 final size:13
Alignment explanation
Indices: 425524--425549 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
425514 TACAGCAAGT
425524 ATGTATCGATACA
1 ATGTATCGATACA
425537 ATGTATCGATACA
1 ATGTATCGATACA
425550 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:426438 original size:26 final size:26
Alignment explanation
Indices: 426402--426451 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
426392 TCATTGCTCC
426402 AAAGTTTGGCCATGACATATGATCCT
1 AAAGTTTGGCCATGACATATGATCCT
*
426428 AAAGTTTGGCCATGACATTTGATC
1 AAAGTTTGGCCATGACATATGATC
426452 ATGGCCATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (26 bp):
AAAGTTTGGCCATGACATATGATCCT
Found at i:427109 original size:41 final size:42
Alignment explanation
Indices: 427062--427147 Score: 138
Period size: 42 Copynumber: 2.1 Consensus size: 42
427052 TTTTAATGAG
* *
427062 AAAAGGTTCATGTAGAAATT-AAAACAGAAGAAATGAATAAA
1 AAAAGGTTCATGTAGAAATTAAAAACAAAAGAAATAAATAAA
*
427103 AAAAGGTTCATGTAGAATTTAAAAACAAAAGAAATAAATAAA
1 AAAAGGTTCATGTAGAAATTAAAAACAAAAGAAATAAATAAA
427145 AAA
1 AAA
427148 TAAACTTGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 19 0.46
42 22 0.54
ACGTcount: A:0.62, C:0.05, G:0.14, T:0.20
Consensus pattern (42 bp):
AAAAGGTTCATGTAGAAATTAAAAACAAAAGAAATAAATAAA
Found at i:427760 original size:13 final size:13
Alignment explanation
Indices: 427742--427768 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
427732 ACATTATGCT
427742 TTGTATCGATACA
1 TTGTATCGATACA
427755 TTGTATCGATACA
1 TTGTATCGATACA
427768 T
1 T
427769 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:427798 original size:20 final size:19
Alignment explanation
Indices: 427752--427812 Score: 68
Period size: 19 Copynumber: 3.1 Consensus size: 19
427742 TTGTATCGAT
**
427752 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATAA
*
427771 TCATTGTATCGATACATAA
1 ACATTGTATCGATACATAA
*
427790 ACAATTGTATCAATACATGAA
1 AC-ATTGTATCGATACAT-AA
427811 AC
1 AC
427813 TGGCAGTAGC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
19 17 0.49
20 14 0.40
21 4 0.11
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.33
Consensus pattern (19 bp):
ACATTGTATCGATACATAA
Found at i:427862 original size:20 final size:20
Alignment explanation
Indices: 427837--427890 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
427827 CTACCACTAT
*
427837 TTGTATCGATACATGGT-ACA
1 TTGTATCGATACATGATGA-A
427857 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGATGAA
427877 TTGTATCGATACAT
1 TTGTATCGATACAT
427891 TGCTTGTAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGATGAA
Found at i:428402 original size:13 final size:13
Alignment explanation
Indices: 428384--428409 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
428374 TTGCCTTAAA
428384 GGTAATCAATTCT
1 GGTAATCAATTCT
428397 GGTAATCAATTCT
1 GGTAATCAATTCT
428410 AGTAGTGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
GGTAATCAATTCT
Found at i:433280 original size:142 final size:142
Alignment explanation
Indices: 433108--433414 Score: 451
Period size: 142 Copynumber: 2.2 Consensus size: 142
433098 AAAATCATGG
* * * * *
433108 GATACGAAAGGTTTTGAAAATTTCTATACCCTTACGGAAAACCACAGGAATATTAGAAATCTTGA
1 GATACAAAAAGTTTTGAAAATTTCTATACCCCTACAGAAAACCACAGGAATATTAGAAATCTAGA
* *
433173 AAAATTATGTTAATAATTTTTATTTAA-TTTTTAA-TTTCAAAAAAAATTCATTTCATACTTTAA
66 AAAATTAAGATAATAATTTTTATTTAATTTTTTAATTTTC--AAAAAATTCATTTCATACTTTAA
433236 TGGAAAACCGAAAA
129 TGGAAAACCGAAAA
* *
433250 GATACAAAAAGTTTT-AAAGATTTCTATACCCCTATAGAAAACCATAGGAATATTAGAAATCTAG
1 GATACAAAAAGTTTTGAAA-ATTTCTATACCCCTACAGAAAACCACAGGAATATTAGAAATCTAG
433314 AAAAATTAAGATAATAATTTTTATTTAATTTTTTAATTTTCAAAAAATTCATTTCATACTTTAAT
65 AAAAATTAAGATAATAATTTTTATTTAATTTTTTAATTTTCAAAAAATTCATTTCATACTTTAAT
* *
433379 GGAGAACTGAAAA
130 GGAAAACCGAAAA
433392 GATACGAAAAA-TTTTGAAAATTT
1 GATAC-AAAAAGTTTTGAAAATTT
433415 TCATATCCCC
Statistics
Matches: 149, Mismatches: 11, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
141 3 0.02
142 127 0.85
143 15 0.10
144 4 0.03
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (142 bp):
GATACAAAAAGTTTTGAAAATTTCTATACCCCTACAGAAAACCACAGGAATATTAGAAATCTAGA
AAAATTAAGATAATAATTTTTATTTAATTTTTTAATTTTCAAAAAATTCATTTCATACTTTAATG
GAAAACCGAAAA
Found at i:433459 original size:142 final size:140
Alignment explanation
Indices: 433108--433480 Score: 409
Period size: 142 Copynumber: 2.6 Consensus size: 140
433098 AAAATCATGG
* * * * * * *
433108 GATACGAAAGGTTTTGAAA-ATTTCTATACCCTTACGGAAAACCACAGGAATATTAGAAATCTTG
1 GATACAAAAAGTTTT-AAAGATTTCTATACCCCTACAGAAAACCATAGAAATATTAAAAATC-TG
* *
433172 AAAAATTATGTTAATAATTTTTATTTAATTTTTAATTTCAAAAAAAATTCATTTCATACTTTAAT
64 AAAAATTAAGATAATAATTTTTATTTAATTTTTAATTTC-AAAAAAATTCATTTCATACTTTAAT
433237 GGAAAACCGAAAA
128 GGAAAACCGAAAA
* * *
433250 GATACAAAAAGTTTTAAAGATTTCTATACCCCTATAGAAAACCATAGGAATATTAGAAATCTAGA
1 GATACAAAAAGTTTTAAAGATTTCTATACCCCTACAGAAAACCATAGAAATATTAAAAATCT-GA
433315 AAAATTAAGATAATAATTTTTATTTAATTTTTTAATTTTC-AAAAAATTCATTTCATACTTTAAT
65 AAAATTAAGATAATAATTTTTATTTAA-TTTTTAA-TTTCAAAAAAATTCATTTCATACTTTAAT
* *
433379 GGAGAACTGAAAA
128 GGAAAACCGAAAA
* * * *
433392 GATACGAAAAA-TTTTGAAA-ATTT-TCATATCCCC-ACGGATAGCCAT-GAAAATTTTAAAAAT
1 GATAC-AAAAAGTTTT-AAAGATTTCT-ATA-CCCCTACAGAAAACCATAG-AAATATTAAAAA-
* *
433452 TCTGAAAAATTAGGATGATAATTTTTATT
60 TCTGAAAAATTAAGATAATAATTTTTATT
433481 GAATAAAATA
Statistics
Matches: 202, Mismatches: 19, Indels: 20
0.84 0.08 0.08
Matches are distributed among these distances:
141 6 0.03
142 170 0.84
143 22 0.11
144 4 0.02
ACGTcount: A:0.43, C:0.11, G:0.10, T:0.35
Consensus pattern (140 bp):
GATACAAAAAGTTTTAAAGATTTCTATACCCCTACAGAAAACCATAGAAATATTAAAAATCTGAA
AAATTAAGATAATAATTTTTATTTAATTTTTAATTTCAAAAAAATTCATTTCATACTTTAATGGA
AAACCGAAAA
Found at i:433521 original size:18 final size:19
Alignment explanation
Indices: 433494--433537 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
433484 TAAAATAATA
433494 TTTA-TTTATT-CTTTTAC
1 TTTATTTTATTACTTTTAC
* *
433511 TTTATTTTATTATTTTTAT
1 TTTATTTTATTACTTTTAC
433530 TTTATTTT
1 TTTATTTT
433538 CAAAAATTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 6 0.26
19 13 0.57
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTATTTTATTACTTTTAC
Found at i:434384 original size:12 final size:12
Alignment explanation
Indices: 434367--434411 Score: 58
Period size: 11 Copynumber: 3.9 Consensus size: 12
434357 CCTTAATTTT
434367 TCTTTTTTTCTC
1 TCTTTTTTTCTC
434379 TC-TTTTTTCT-
1 TCTTTTTTTCTC
*
434389 TTTTTTTTTCTC
1 TCTTTTTTTCTC
*
434401 TTTTTTTTTCT
1 TCTTTTTTTCT
434412 TACTTGCCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
10 1 0.03
11 16 0.53
12 13 0.43
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (12 bp):
TCTTTTTTTCTC
Found at i:434392 original size:20 final size:19
Alignment explanation
Indices: 434363--434406 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 19
434353 TTTGCCTTAA
434363 TTTTTCTTTTTTTCTCTCT
1 TTTTTCTTTTTTTCTCTCT
*
434382 TTTTTCTTTTTTTTTTCTCT
1 TTTTTC-TTTTTTTCTCTCT
434402 TTTTT
1 TTTTT
434407 TTTCTTACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (19 bp):
TTTTTCTTTTTTTCTCTCT
Found at i:434397 original size:13 final size:13
Alignment explanation
Indices: 434381--434409 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
434371 TTTTTCTCTC
434381 TTTTT-TCTTTTT
1 TTTTTCTCTTTTT
434393 TTTTTCTCTTTTT
1 TTTTTCTCTTTTT
434406 TTTT
1 TTTT
434410 CTTACTTGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTTCTCTTTTT
Found at i:435329 original size:166 final size:169
Alignment explanation
Indices: 434973--435329 Score: 390
Period size: 166 Copynumber: 2.1 Consensus size: 169
434963 ATGTATTATA
* * ** * * *
434973 AAAATTTTAAA--TAGAAGAAAATCCCCCTGAAAATATTTATGGGATAGAAAATTCAGTTTTTTT
1 AAAATTTTAAACCAAGAA-AAAA-CCCCGTGAAAACCTTTACGGAATAGAAAACTCAGTTTTTTT
* * * * *
435036 TTAAAAATAAGGGTATTTTAAGGAAAAAATTAAAAAACTCATGAAAATAAATGAATTTTTCAAAA
64 TCAAAAAT-AGGGAATTTCAAGGAAAAAATTAAAAAACTAATGAAAATAAAGGAATTTTTCAAAA
* *
435101 CTGATTTACTATAAATTAAATGATGATATTTGATGAATTTTG
128 CTAATTTACTATAAATTAAATAATGATATTTGATGAATTTTG
* *
435143 AAAATTTTGAACCGAGAAAAAACCCCGTGAAAACCTTTACGGAATAGAAAACTCAG-TTTTTTTC
1 AAAATTTTAAACCAAGAAAAAACCCCGTGAAAACCTTTACGGAATAGAAAACTCAGTTTTTTTTC
* * *
435207 AAAAAT-GGGAAATTTCAAGGAAAAAA-TGAAAAATTAAT-AAAATAAAAGGAATTTTT-TAAAC
66 AAAAATAGGG-AATTTCAAGGAAAAAATTAAAAAACTAATGAAAAT-AAAGGAATTTTTCAAAAC
* * *
435268 TAATTTATTATGAGTTAAATAAT-ACTATTTGATGAATTTT-
129 TAATTTACTATAAATTAAATAATGA-TATTTGATGAATTTTG
435308 AAAATTTATAAACCAAGAAAAA
1 AAAATTT-TAAACCAAGAAAAA
435330 TCATCCCAAA
Statistics
Matches: 158, Mismatches: 23, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
165 8 0.05
166 54 0.34
167 23 0.15
168 14 0.09
169 13 0.08
170 38 0.24
171 4 0.03
172 4 0.03
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.32
Consensus pattern (169 bp):
AAAATTTTAAACCAAGAAAAAACCCCGTGAAAACCTTTACGGAATAGAAAACTCAGTTTTTTTTC
AAAAATAGGGAATTTCAAGGAAAAAATTAAAAAACTAATGAAAATAAAGGAATTTTTCAAAACTA
ATTTACTATAAATTAAATAATGATATTTGATGAATTTTG
Found at i:439987 original size:21 final size:21
Alignment explanation
Indices: 439954--440003 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
439944 TTGCAAGTTG
*
439954 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
439976 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
439997 AAATAAA
1 AAATAAA
440004 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:441819 original size:15 final size:15
Alignment explanation
Indices: 441799--441829 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
441789 TAAAAATGTC
*
441799 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
441814 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
441829 C
1 C
441830 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:443929 original size:13 final size:13
Alignment explanation
Indices: 443911--443948 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
443901 CATTTTTCTT
443911 TGTATCGATACAA
1 TGTATCGATACAA
*
443924 TGTATCGATACAC
1 TGTATCGATACAA
443937 TGTATCGATACA
1 TGTATCGATACA
443949 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:445601 original size:23 final size:21
Alignment explanation
Indices: 445559--445602 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
445549 GTTTAATGTT
**
445559 TTTGCTTGACTTTGTGTTTTA
1 TTTGCTTGACTTTGAATTTTA
445580 TTTGCATTGTACTTTGAATTTTA
1 TTTGC-TTG-ACTTTGAATTTTA
445603 ATCTATAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
22 3 0.16
23 11 0.58
ACGTcount: A:0.16, C:0.09, G:0.16, T:0.59
Consensus pattern (21 bp):
TTTGCTTGACTTTGAATTTTA
Found at i:446518 original size:32 final size:34
Alignment explanation
Indices: 446477--446539 Score: 103
Period size: 32 Copynumber: 1.9 Consensus size: 34
446467 TAGCCAAACT
*
446477 TGTATCGATACAC-AAAATA-TGTATCGATATAA
1 TGTATCGATACACAAAAAAATTGTATCGATATAA
446509 TGTATCGATACACAAAAAAATTGTATCGATA
1 TGTATCGATACACAAAAAAATTGTATCGATA
446540 CATTGGCTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 13 0.46
33 5 0.18
34 10 0.36
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (34 bp):
TGTATCGATACACAAAAAAATTGTATCGATATAA
Found at i:448555 original size:20 final size:20
Alignment explanation
Indices: 448519--448556 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
448509 TACATTTTTC
**
448519 ATTTTTATGAATTTTTTGAG
1 ATTTTTATGAAAATTTTGAG
448539 ATTTTTATGAAAATTTTG
1 ATTTTTATGAAAATTTTG
448557 GAAAGTTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (20 bp):
ATTTTTATGAAAATTTTGAG
Found at i:454896 original size:19 final size:20
Alignment explanation
Indices: 454872--454922 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
454862 CAATTCAGTG
*
454872 TGTATCGATACTAAG-AACA
1 TGTATCGATACAAAGCAACA
454891 TGTATCGATACAAAGCAACA
1 TGTATCGATACAAAGCAACA
454911 TGTATCGATACA
1 TGTATCGATACA
454923 TCTGGGTGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.25
Consensus pattern (20 bp):
TGTATCGATACAAAGCAACA
Found at i:455650 original size:15 final size:15
Alignment explanation
Indices: 455632--455660 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
455622 ATACTCCCCC
455632 TTTTTGTAATCCCTT
1 TTTTTGTAATCCCTT
455647 TTTTTGTAATCCCT
1 TTTTTGTAATCCCT
455661 CTTTATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.07, T:0.59
Consensus pattern (15 bp):
TTTTTGTAATCCCTT
Found at i:463557 original size:19 final size:19
Alignment explanation
Indices: 463529--463590 Score: 73
Period size: 19 Copynumber: 3.6 Consensus size: 19
463519 TATAATTCAG
*
463529 TGTATTGATACCAAGAACA
1 TGTATCGATACCAAGAACA
463548 TGTATCGATA-C----A-A
1 TGTATCGATACCAAGAACA
463561 TGTATCGATACCAAGAACA
1 TGTATCGATACCAAGAACA
463580 TGTATCGATAC
1 TGTATCGATAC
463591 AATATATTGA
Statistics
Matches: 36, Mismatches: 1, Indels: 12
0.73 0.02 0.24
Matches are distributed among these distances:
13 11 0.31
14 2 0.06
18 2 0.06
19 21 0.58
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (19 bp):
TGTATCGATACCAAGAACA
Found at i:463565 original size:13 final size:13
Alignment explanation
Indices: 463547--463571 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
463537 TACCAAGAAC
463547 ATGTATCGATACA
1 ATGTATCGATACA
463560 ATGTATCGATAC
1 ATGTATCGATAC
463572 CAAGAACATG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:463571 original size:32 final size:32
Alignment explanation
Indices: 463529--463624 Score: 147
Period size: 32 Copynumber: 3.0 Consensus size: 32
463519 TATAATTCAG
463529 TGTATTGATACCAAGAACATGTATCGATACAA
1 TGTATTGATACCAAGAACATGTATCGATACAA
*
463561 TGTATCGATACCAAGAACATGTATCGATACAA
1 TGTATTGATACCAAGAACATGTATCGATACAA
* * *
463593 TATATTGATACAAAGCAATATGTATCGATACA
1 TGTATTGATACCAAG-AACATGTATCGATACA
463625 TCTGGGTGTG
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
32 43 0.74
33 15 0.26
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.28
Consensus pattern (32 bp):
TGTATTGATACCAAGAACATGTATCGATACAA
Found at i:464442 original size:51 final size:52
Alignment explanation
Indices: 464365--464464 Score: 148
Period size: 51 Copynumber: 1.9 Consensus size: 52
464355 AATTTTTTAG
* **
464365 AGATGAAAAATTTGGTGTTTTGGAAGTAAAAATGGGGTTGGAGTATCCCTAT
1 AGATGAAAAATTTGATGTTTTGGAAGTAAAAACAGGGTTGGAGTATCCCTAT
* *
464417 AGATGAAAATTTTGAT-TTTTGGAAGTAAAAACAGGGTTGTAGTATCCC
1 AGATGAAAAATTTGATGTTTTGGAAGTAAAAACAGGGTTGGAGTATCCC
464465 CATGGATATG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
51 29 0.67
52 14 0.33
ACGTcount: A:0.34, C:0.07, G:0.26, T:0.33
Consensus pattern (52 bp):
AGATGAAAAATTTGATGTTTTGGAAGTAAAAACAGGGTTGGAGTATCCCTAT
Found at i:464490 original size:28 final size:29
Alignment explanation
Indices: 464450--464522 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 29
464440 AGTAAAAACA
* * *
464450 GGGTTGTAGTATCCCCAT-GGATATGGTG
1 GGGTTGGAGTATCCCCATAGAAGATGGTG
*
464478 GGGTTGGAGTAT-CCCTTAGAAGATGGTG
1 GGGTTGGAGTATCCCCATAGAAGATGGTG
464506 GGGTTGGAGTATCCCCA
1 GGGTTGGAGTATCCCCA
464523 AAGATGAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
27 4 0.11
28 31 0.82
29 3 0.08
ACGTcount: A:0.19, C:0.15, G:0.37, T:0.29
Consensus pattern (29 bp):
GGGTTGGAGTATCCCCATAGAAGATGGTG
Found at i:466507 original size:12 final size:14
Alignment explanation
Indices: 466490--466521 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
466480 GTCTCTCTTC
466490 TCCTCTT-TGG-AA
1 TCCTCTTCTGGAAA
466502 TCCTCTTCTGGAAA
1 TCCTCTTCTGGAAA
466516 TCCTCT
1 TCCTCT
466522 CCTTTTTGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.39
13 3 0.17
14 8 0.44
ACGTcount: A:0.16, C:0.31, G:0.12, T:0.41
Consensus pattern (14 bp):
TCCTCTTCTGGAAA
Found at i:466997 original size:52 final size:52
Alignment explanation
Indices: 466940--467080 Score: 174
Period size: 52 Copynumber: 2.7 Consensus size: 52
466930 AATTGCCTGC
* * * * *
466940 ATGTATCGATACATTGAAGAATGTATCGATACATTTGGGTCAAAAACCCAGA
1 ATGTATCAATACAATAAAAAATGTATCGATACATTTAGGTCAAAAACCCAGA
* *
466992 ATGTATCAATATAATAAAAAATGTATCGATACATTTAGGTCAAAAACCTAGA
1 ATGTATCAATACAATAAAAAATGTATCGATACATTTAGGTCAAAAACCCAGA
* * * *
467044 ATGTATTAATAAAATGAAAAAAAGCATCGATACATTT
1 ATGTATCAATACAAT-AAAAAATGTATCGATACATTT
467081 TCTTTTTTGA
Statistics
Matches: 77, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
52 58 0.75
53 19 0.25
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.28
Consensus pattern (52 bp):
ATGTATCAATACAATAAAAAATGTATCGATACATTTAGGTCAAAAACCCAGA
Found at i:467184 original size:21 final size:20
Alignment explanation
Indices: 467136--467190 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
467126 ATATTTTAGA
* *
467136 TATGTATTGATACGTTCACT
1 TATGTATCGATACATTCACT
467156 TATGTATCGATACATTCACT
1 TATGTATCGATACATTCACT
*
467176 TATTGTATCAATACA
1 TA-TGTATCGATACA
467191 AATTATAGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
20 20 0.65
21 11 0.35
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (20 bp):
TATGTATCGATACATTCACT
Found at i:471662 original size:19 final size:21
Alignment explanation
Indices: 471619--471670 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
471609 TTCAATAATT
471619 TGTATCGATACAAACAGTAAA
1 TGTATCGATACAAACAGTAAA
*
471640 TGTATCGATACATA-AGT-AA
1 TGTATCGATACAAACAGTAAA
471659 TGTATCGATACA
1 TGTATCGATACA
471671 GTGTATCGCT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 14 0.47
20 3 0.10
21 13 0.43
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.29
Consensus pattern (21 bp):
TGTATCGATACAAACAGTAAA
Found at i:474471 original size:79 final size:77
Alignment explanation
Indices: 474261--474506 Score: 261
Period size: 79 Copynumber: 3.2 Consensus size: 77
474251 TTCACAATTA
* * * *
474261 GGGATACTCCAACCCCATTATTTCCT-AGGGGACACTCCAACCCCGATTTTATTTCCAAAACATC
1 GGGATACTCCAACCCCATTATTT-CTGAGGGGATACTCCAACCCAG-TTTTATTT-CTAAACATT
*
474325 AATTT-T--TCATCG
63 AATTTCTCATAATCG
* * * *
474337 GGGATACTCCAACCCCATTA-TTCCGAGGGGATACCCCAACCCCAGCTTTACTTCTAAACTATTA
1 GGGATACTCCAACCCCATTATTTCTGAGGGGATACTCCAA-CCCAGTTTTATTTCTAAAC-ATTA
474401 ATTTCTCATAATCG
64 ATTTCTCATAATCG
* * * *
474415 GGGATACTCCAATCTCGTTATTTCTGAGGGGATACTCCAACCCTAGTTTTATTTCTAAAACACTA
1 GGGATACTCCAACCCCATTATTTCTGAGGGGATACTCCAACCC-AGTTTTATTTCT-AAACATTA
474480 A-TTCTCCATAATCG
64 ATTTCT-CATAATCG
474494 GGGATACTCCAAC
1 GGGATACTCCAAC
474507 TCCGATTTTA
Statistics
Matches: 142, Mismatches: 18, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
74 6 0.04
75 27 0.19
76 25 0.18
78 29 0.20
79 51 0.36
80 4 0.03
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.30
Consensus pattern (77 bp):
GGGATACTCCAACCCCATTATTTCTGAGGGGATACTCCAACCCAGTTTTATTTCTAAACATTAAT
TTCTCATAATCG
Found at i:474518 original size:51 final size:51
Alignment explanation
Indices: 474442--474555 Score: 167
Period size: 51 Copynumber: 2.2 Consensus size: 51
474432 TTATTTCTGA
* * *
474442 GGGGATACTCCAACCCTAGTTTTATTTCTAAAACACTAATTCTCCATAATC
1 GGGGATACTCCAACCCGAGTTTTATTTCCAAAACACTAATTCTCCACAATC
* *
474493 GGGGATACTCCAACTCCGA-TTTTATTTCCAAAACACTAATTTTTCACAATC
1 GGGGATACTCCAAC-CCGAGTTTTATTTCCAAAACACTAATTCTCCACAATC
474544 GGGGATACTCCA
1 GGGGATACTCCA
474556 GCCCTGTTAT
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
51 54 0.95
52 3 0.05
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACCCGAGTTTTATTTCCAAAACACTAATTCTCCACAATC
Found at i:474577 original size:28 final size:28
Alignment explanation
Indices: 474541--474614 Score: 103
Period size: 28 Copynumber: 2.6 Consensus size: 28
474531 ATTTTTCACA
* *
474541 ATCGGGGATACTCCAGCCCTGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
474569 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
***
474597 CGAGGGGATACTCCAACC
1 ATCGGGGATACTCCAACC
474615 TCAGCTTTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.22, C:0.31, G:0.22, T:0.26
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATTTC
Found at i:474647 original size:107 final size:107
Alignment explanation
Indices: 474493--474700 Score: 285
Period size: 107 Copynumber: 1.9 Consensus size: 107
474483 CTCCATAATC
* * * *
474493 GGGGATACTCCAACTCCGATTTTATTTCCAAAACACTAATTTTTCACAATCGGGGATACTCCAGC
1 GGGGATACTCCAACTCAGACTTTATTTCCAAAACACTAATTTCTCACAATCGGGGATACTCCAAC
* * *
474558 CCTGTTA-TTTCATCGGGGATACTCCAACCCCGTTATTTCCGA
66 CCCGTTATTTTCA-AGGGGAAACTCCAACCCCGTTATTTCCGA
** * *
474600 GGGGATACTCCAACCTCAG-CTTTATTTCTGAAATACTGATTTCTCACAATCGGGGATACTCCAA
1 GGGGATACTCCAA-CTCAGACTTTATTTCCAAAACACTAATTTCTCACAATCGGGGATACTCCAA
474664 CCCCGTTATTTTCAAGGGGAAACTCCAACCCCGTTAT
65 CCCCGTTATTTTCAAGGGGAAACTCCAACCCCGTTAT
474701 GATCTCCAAA
Statistics
Matches: 88, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
107 79 0.90
108 9 0.10
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.30
Consensus pattern (107 bp):
GGGGATACTCCAACTCAGACTTTATTTCCAAAACACTAATTTCTCACAATCGGGGATACTCCAAC
CCCGTTATTTTCAAGGGGAAACTCCAACCCCGTTATTTCCGA
Found at i:479464 original size:150 final size:150
Alignment explanation
Indices: 479310--479667 Score: 382
Period size: 150 Copynumber: 2.4 Consensus size: 150
479300 GTACCTGGAG
* *
479310 ATCCTAGGGGACCT-AAAAAGATAAAAACAAACCTACTCCTAATTCATACTTTTGGCATAAAAAT
1 ATCCTAGGGGACTTGAAAAAGATAAAAACAAACCTACTCCTAATTCATACCTTTGGCATAAAAAT
* * * ** **
479374 AGACCCGGTAGTTTTATAGGACTAGGTTTTGAAGAAAATTGCTAAAAGGTCCCTAAGGCCTACCA
66 AGACCCGGTAATTTCATAGGACTAGG-TTTCAAGAAAAAAGCTAAAACATCCCTAAGGCCTACCA
*
479439 TCGACTTA-AGAATGCC-CGGTC
130 TCAACTTATA-AATGCCTC-GTC
* * * * * *
479460 ATCCTAAGGGACTTGGAAAAGATAAAAATAAACCTACTCCTAATTCATACCTTTAGCGTAAAAGT
1 ATCCTAGGGGACTTGAAAAAGATAAAAACAAACCTACTCCTAATTCATACCTTTGGCATAAAAAT
* ** ** * **
479525 GGACTTGGTAATTTCATAGGGTTAGGTTTCAGGAAAAAAGCTAAAACATCCCTAAGGTTTACCAT
66 AGACCCGGTAATTTCATAGGACTAGGTTTCAAGAAAAAAGCTAAAACATCCCTAAGGCCTACCAT
* *
479590 CAACTTATAAGTGCCTCGTG
131 CAACTTATAAATGCCTCGTC
* * * * *
479610 ATCTTAGGGGACTTGAAAAAG-CAAAAGCAAACCTACTCCTGATTCATACCTTCGGCAT
1 ATCCTAGGGGACTTGAAAAAGATAAAAACAAACCTACTCCTAATTCATACCTTTGGCAT
479668 TGAAGCAGAT
Statistics
Matches: 169, Mismatches: 36, Indels: 7
0.80 0.17 0.03
Matches are distributed among these distances:
149 30 0.18
150 74 0.44
151 65 0.38
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (150 bp):
ATCCTAGGGGACTTGAAAAAGATAAAAACAAACCTACTCCTAATTCATACCTTTGGCATAAAAAT
AGACCCGGTAATTTCATAGGACTAGGTTTCAAGAAAAAAGCTAAAACATCCCTAAGGCCTACCAT
CAACTTATAAATGCCTCGTC
Found at i:480375 original size:3 final size:3
Alignment explanation
Indices: 480362--480413 Score: 88
Period size: 3 Copynumber: 17.7 Consensus size: 3
480352 TAAACAATAT
*
480362 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA CTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
480409 TTA TT
1 TTA TT
480414 TATGTCTCAA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:481458 original size:13 final size:13
Alignment explanation
Indices: 481440--481465 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
481430 CAATTTTTGG
481440 TGTATCGATACAT
1 TGTATCGATACAT
481453 TGTATCGATACAT
1 TGTATCGATACAT
481466 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:481477 original size:32 final size:33
Alignment explanation
Indices: 481420--481483 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
481410 TACAAGCCAA
**
481420 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
481453 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
481484 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Done.