Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008268.1 Hibiscus syriacus cultivar Beakdansim tig00110925_pilon, whole genome shotgun sequence
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: 492505
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:387935 original size:30 final size:31
Alignment explanation
Indices: 387863--387940 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
387853 AATAAGAGTT
* *
387863 TAACATTTT-TAAATCTATTTAAATAATGGTC
1 TAACATTTTAT-AATCTATTTAAATAAAGATC
*
387894 TAACATTTTATAATTTATTTAAATAAAGAT-
1 TAACATTTTATAATCTATTTAAATAAAGATC
* *
387924 TAACGTTTTATATTCTA
1 TAACATTTTATAATCTA
387941 CTCAAACATG
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
30 14 0.35
31 25 0.62
32 1 0.03
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.47
Consensus pattern (31 bp):
TAACATTTTATAATCTATTTAAATAAAGATC
Found at i:388043 original size:19 final size:20
Alignment explanation
Indices: 388000--388045 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
387990 ACTTAAGAAG
388000 ATTTAAAATGTTAAACCTTTT
1 ATTTAAAATGTTAAA-CTTTT
388021 -TTTAAAA-GTTAAA-TTCTT
1 ATTTAAAATGTTAAACTT-TT
388039 ATTTAAA
1 ATTTAAA
388046 CATTTGGTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
17 2 0.09
18 2 0.09
19 12 0.52
20 7 0.30
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (20 bp):
ATTTAAAATGTTAAACTTTT
Found at i:389758 original size:34 final size:33
Alignment explanation
Indices: 389673--389771 Score: 171
Period size: 33 Copynumber: 3.0 Consensus size: 33
389663 ATTTGGCAAG
389673 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
*
389706 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
*
389739 TTGGAAAATTCATCTTTGGTAGGTGGCCAACTT
1 TTGGAAAATTCATC-TTGGTTGGTGGCCAACTT
389772 TGCACATTGG
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
33 45 0.73
34 17 0.27
ACGTcount: A:0.23, C:0.15, G:0.24, T:0.37
Consensus pattern (33 bp):
TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
Found at i:395420 original size:64 final size:63
Alignment explanation
Indices: 395352--395581 Score: 230
Period size: 64 Copynumber: 3.6 Consensus size: 63
395342 TTGGAATACT
* ***
395352 TGATGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCC
** * **
395416 TGATGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCC
* * * * * *
395480 AGAGTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATG-TTCAATTAAT-TC
1 TGA-TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAA--AATAGC
*
395543 A
63 C
*
395544 TCGATGCATCGATGCATGGACTGATGCATCGATGCATG
1 T-GATGCATCGATGCATGGAGTG-TGCATCGATGCATG
395582 CCTTTGAATA
Statistics
Matches: 137, Mismatches: 23, Indels: 11
0.80 0.13 0.06
Matches are distributed among these distances:
63 4 0.03
64 70 0.51
65 63 0.46
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (63 bp):
TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCC
Found at i:395504 original size:19 final size:19
Alignment explanation
Indices: 395480--395530 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
395470 GAAAATATTC
395480 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
395499 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
395518 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
395531 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:395572 original size:65 final size:64
Alignment explanation
Indices: 395374--395581 Score: 239
Period size: 65 Copynumber: 3.2 Consensus size: 64
395364 GCACCAAGTG
* *
395374 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTGATGCATCGATGCATGG-CTTG
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAAT-TCATGATGCATCGATGCATGGAC-TG
395438 -
64 A
*
395438 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA-GAGTGCATCGATGCATGGA--
1 TGCATCGATGCATGAAATGCATTCGATG-TTTGAAAA-ATTCATGA-TGCATCGATGCATGGACT
395500 GA
63 GA
* * * *
395502 GTGCATCGGTGCATGGAATGCATTCGATG-TTCAATTAATTCATCGATGCATCGATGCATGGACT
1 -TGCATCGATGCATGAAATGCATTCGATGTTTGAA-AAATTCAT-GATGCATCGATGCATGGACT
395566 GA
63 GA
395568 TGCATCGATGCATG
1 TGCATCGATGCATG
395582 CCTTTGAATA
Statistics
Matches: 124, Mismatches: 9, Indels: 21
0.81 0.06 0.14
Matches are distributed among these distances:
63 10 0.08
64 46 0.37
65 64 0.52
66 4 0.03
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (64 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATTCATGATGCATCGATGCATGGACTGA
Found at i:402026 original size:22 final size:21
Alignment explanation
Indices: 401984--402023 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
401974 GAGTTTGTTT
*
401984 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
402005 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
402024 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:404019 original size:64 final size:63
Alignment explanation
Indices: 403951--404180 Score: 212
Period size: 64 Copynumber: 3.6 Consensus size: 63
403941 TTGGAACACT
* ***
403951 TGATGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCC
* ** * **
404015 TGATGCATTGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCC
* * * * * *
404079 AGAGTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATG-TTCAATTAAT-TC
1 TGA-TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAA--AATAGC
*
404142 A
63 C
* *
404143 TCGATGCATCGATGCATGGACTGATGCATCGGTGCATG
1 T-GATGCATCGATGCATGGAGTG-TGCATCGATGCATG
404181 CCTTTGAATA
Statistics
Matches: 136, Mismatches: 24, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
63 4 0.03
64 69 0.51
65 63 0.46
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (63 bp):
TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCC
Found at i:404103 original size:19 final size:19
Alignment explanation
Indices: 404079--404129 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
404069 GAAAATATTC
404079 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
404098 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
404117 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
404130 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:404171 original size:65 final size:64
Alignment explanation
Indices: 403973--404180 Score: 221
Period size: 65 Copynumber: 3.2 Consensus size: 64
403963 GCACCAAGTG
* * *
403973 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTGATGCATTGATGCATGG-CTTG
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAAT-TCATGATGCATCGATGCATGGAC-TG
404037 -
64 A
*
404037 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA-GAGTGCATCGATGCATGGA--
1 TGCATCGATGCATGAAATGCATTCGATG-TTTGAAAA-ATTCATGA-TGCATCGATGCATGGACT
404099 GA
63 GA
* * * *
404101 GTGCATCGGTGCATGGAATGCATTCGATG-TTCAATTAATTCATCGATGCATCGATGCATGGACT
1 -TGCATCGATGCATGAAATGCATTCGATGTTTGAA-AAATTCAT-GATGCATCGATGCATGGACT
404165 GA
63 GA
*
404167 TGCATCGGTGCATG
1 TGCATCGATGCATG
404181 CCTTTGAATA
Statistics
Matches: 124, Mismatches: 9, Indels: 21
0.81 0.06 0.14
Matches are distributed among these distances:
63 10 0.08
64 46 0.37
65 64 0.52
66 4 0.03
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.30
Consensus pattern (64 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATTCATGATGCATCGATGCATGGACTGA
Found at i:404810 original size:18 final size:18
Alignment explanation
Indices: 404784--404818 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
404774 TCTCTTAAGG
404784 GTGTCGTATAAGAGAAAC
1 GTGTCGTATAAGAGAAAC
* *
404802 GTGTTGTATGAGAGAAA
1 GTGTCGTATAAGAGAAA
404819 GGTGCAATTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.06, G:0.31, T:0.26
Consensus pattern (18 bp):
GTGTCGTATAAGAGAAAC
Found at i:407045 original size:19 final size:19
Alignment explanation
Indices: 407018--407064 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
407008 AAAGGCCAAT
407018 GGAGCAGATGAGAACGTGA
1 GGAGCAGATGAGAACGTGA
* *
407037 GGAGAAGATGAGAATGTGA
1 GGAGCAGATGAGAACGTGA
407056 GGAGCAGAT
1 GGAGCAGAT
407065 TTATCTAGCC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.38, C:0.06, G:0.43, T:0.13
Consensus pattern (19 bp):
GGAGCAGATGAGAACGTGA
Found at i:408241 original size:21 final size:19
Alignment explanation
Indices: 408213--408258 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
408203 TCATTGAATC
408213 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
408233 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
408252 ACTTAGT
1 A-TTAGT
408259 AGGATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:413311 original size:14 final size:14
Alignment explanation
Indices: 413294--413321 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
413284 TAATATATTC
413294 AAAATAAAAATAAT
1 AAAATAAAAATAAT
413308 AAAATAAAAATAAT
1 AAAATAAAAATAAT
413322 TATTTTGGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
AAAATAAAAATAAT
Found at i:426886 original size:16 final size:17
Alignment explanation
Indices: 426865--426897 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
426855 GATTTTGTTT
426865 ATTTTTTA-TTATTTTG
1 ATTTTTTATTTATTTTG
426881 ATTTTTTATTTATTTTG
1 ATTTTTTATTTATTTTG
426898 GTTCCTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (17 bp):
ATTTTTTATTTATTTTG
Found at i:427832 original size:50 final size:47
Alignment explanation
Indices: 427713--427832 Score: 125
Period size: 50 Copynumber: 2.4 Consensus size: 47
427703 GTAAAGCGTT
427713 CCCCCTGAACCGCGCTATACGCTGATTTGGCGCCACGTAGGTATAGCG
1 CCCCCT-AACCGCGCTATACGCTGATTTGGCGCCACGTAGGTATAGCG
** * *
427761 CGCCCCTTGCCTCGCGATATACAG-TGATTTGGCGCCACGTGGGTATAGCATG
1 C-CCCC-TAAC-CGCGCTATAC-GCTGATTTGGCGCCACGTAGGTATAGC--G
427813 CCCCCTAATCCGCGCTATAC
1 CCCCCTAA-CCGCGCTATAC
427833 CTGGTTATCT
Statistics
Matches: 58, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
48 1 0.02
49 5 0.09
50 44 0.76
51 6 0.10
52 2 0.03
ACGTcount: A:0.18, C:0.34, G:0.25, T:0.23
Consensus pattern (47 bp):
CCCCCTAACCGCGCTATACGCTGATTTGGCGCCACGTAGGTATAGCG
Found at i:427977 original size:10 final size:10
Alignment explanation
Indices: 427959--427997 Score: 69
Period size: 10 Copynumber: 3.9 Consensus size: 10
427949 TCACACCAAA
427959 TTCTCTCAAT
1 TTCTCTCAAT
*
427969 TTCTTTCAAT
1 TTCTCTCAAT
427979 TTCTCTCAAT
1 TTCTCTCAAT
427989 TTCTCTCAA
1 TTCTCTCAA
427998 ATACTCTCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.21, C:0.28, G:0.00, T:0.51
Consensus pattern (10 bp):
TTCTCTCAAT
Found at i:428004 original size:20 final size:20
Alignment explanation
Indices: 427955--428005 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
427945 TTTATCACAC
*
427955 CAAATTCTCTCAATTTCTTT
1 CAAATTCTCTCAATTTCTCT
*
427975 CAATTTCTCTCAATTTCTCT
1 CAAATTCTCTCAATTTCTCT
*
427995 CAAATACTCTC
1 CAAATTCTCTC
428006 TCTTTTTAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.25, C:0.29, G:0.00, T:0.45
Consensus pattern (20 bp):
CAAATTCTCTCAATTTCTCT
Found at i:428084 original size:17 final size:18
Alignment explanation
Indices: 428047--428087 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
428037 ATATTATGTA
*
428047 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
428065 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
428082 TTTACT
1 TTTACT
428088 AATATAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:428351 original size:111 final size:111
Alignment explanation
Indices: 428157--428370 Score: 419
Period size: 111 Copynumber: 1.9 Consensus size: 111
428147 ATATATGTCT
*
428157 ACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
1 ACACTTTGCTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATTAGTAATAATTAGT
428222 TGATTTATTTAATGCATGATTATTAGATTAAGAATTAAATATCTCG
66 TGATTTATTTAATGCATGATTATTAGATTAAGAATTAAATATCTCG
428268 ACACTTTGCTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATTAGTAATAATTAGT
1 ACACTTTGCTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATTAGTAATAATTAGT
428333 TGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
428371 TTTTTGTAAT
Statistics
Matches: 102, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
111 102 1.00
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.44
Consensus pattern (111 bp):
ACACTTTGCTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATTAGTAATAATTAGT
TGATTTATTTAATGCATGATTATTAGATTAAGAATTAAATATCTCG
Found at i:430435 original size:24 final size:24
Alignment explanation
Indices: 430408--430479 Score: 58
Period size: 24 Copynumber: 2.9 Consensus size: 24
430398 TTATATTTGT
430408 ATTTACTTTATTTTGTTAAATTGA
1 ATTTACTTTATTTTGTTAAATTGA
** * *
430432 ATTTTTTTTATTATT-TCT-CATTTA
1 ATTTACTTTATT-TTGT-TAAATTGA
430456 ATACTTACTTTATTTTGTTAAATT
1 AT--TTACTTTATTTTGTTAAATT
430480 TGTTGGACTT
Statistics
Matches: 35, Mismatches: 7, Indels: 10
0.67 0.13 0.19
Matches are distributed among these distances:
24 17 0.49
25 6 0.17
26 12 0.34
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.62
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTGA
Found at i:430548 original size:35 final size:33
Alignment explanation
Indices: 430509--430593 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 33
430499 GTATTTCAGT
430509 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAATA-C--TTATTG
*
430544 TAATTTGGTTATCATTTACCATTTAATACTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATACTTATTG
* *
430579 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
430594 TAAAATTATA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.56
36 1 0.02
37 2 0.05
38 13 0.30
ACGTcount: A:0.27, C:0.08, G:0.11, T:0.54
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATACTTATTG
Found at i:434119 original size:182 final size:182
Alignment explanation
Indices: 433811--434258 Score: 722
Period size: 182 Copynumber: 2.5 Consensus size: 182
433801 TTTACTATAG
* *
433811 GTTTTGTCCTTTCGAGATCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACAT
1 GTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACAT
* * *
433876 TTTTATAAAGTATCGAA-ACTTTATTGGCGCTATAACTTCTTTTCTTTTAAATTCTAAAAGTGTC
66 TTTTATAAAGTATC-AACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTC
* *
433940 GATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGC-TCTTTACCT
130 GATACTTATAATAAAGTATCGACAATATCAACATATACGGTAGCGT-TTTACCT
*
433993 GTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATATAT
1 GTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACAT
434058 TTTTATAAAGTATCAACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCG
66 TTTTATAAAGTATCAACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCG
434123 ATACTTATAATAAAGTATCGACAATATCAACATATACGGTAGCGTTTTACCT
131 ATACTTATAATAAAGTATCGACAATATCAACATATACGGTAGCGTTTTACCT
* ** * *
434175 GTTTTGTCATATATAGACCAATTTTGTCAT-TTTTTACCTGTTTTATTGTTATGGATCGATACAT
1 GTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACAT
* *
434239 TTTTATAAAATATCGACACT
66 TTTTATAAAGTATCAACACT
434259 ATCAACATAT
Statistics
Matches: 248, Mismatches: 16, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
181 52 0.21
182 195 0.79
183 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (182 bp):
GTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACAT
TTTTATAAAGTATCAACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCG
ATACTTATAATAAAGTATCGACAATATCAACATATACGGTAGCGTTTTACCT
Found at i:434466 original size:111 final size:112
Alignment explanation
Indices: 434132--434703 Score: 880
Period size: 111 Copynumber: 5.1 Consensus size: 112
434122 GATACTTATA
* * * * * * *
434132 ATAAAGTATCGACAATATCAACATATACGGTAGCGTTTTACCTGTTTTGTCATATATAGACCAAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
*
434197 TTTGTCA-TTTTTTACCTGTTTTATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* * * * *
434243 ATAAAATATCGACACTATCAACATATCCGTTAGCGCTTTACCTGTTTTGTCATTTATAGATCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
*
434308 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACAATTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
*
434355 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTT-TCATTTATAGATCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
434419 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
** * *
434466 ATAAAGTATCGACACTTTCAATATATCCAATAGCACTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
* * *
434531 TTTGTCA-TTTTTTACCTATTATATTGTTATGGATAGATATATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
*
434577 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
** * *
434642 TTTGTCATTTTTTTATTTGTTATATTGTTATGGATCAATATATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
434689 ATAAAGTATCGACAC
1 ATAAAGTATCGACAC
434704 AAACCGACAA
Statistics
Matches: 427, Mismatches: 31, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
111 276 0.65
112 151 0.35
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
Found at i:434520 original size:223 final size:223
Alignment explanation
Indices: 434132--434703 Score: 887
Period size: 223 Copynumber: 2.6 Consensus size: 223
434122 GATACTTATA
* * * * * * *
434132 ATAAAGTATCGACAATATCAACATATACGGTAGCGTTTTACCTGTTTTGTCATATATAGACCAAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
* *
434197 TTTGTCA-TTTTTTACCTGTTTTATTGTTATGGATCGATACATTTTTATAAAATATCGACACTAT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTAT
** * *
434261 CAACATATCCGTTAGCGCTTTACCTGTTTTGTCATTTATAGATCGATTTTGTCATTTTTTTACCT
131 CAACATATCCAATAGCACTTTACCTGTTTTGTCATTTATAGACCGATTTTGTCA-TTTTTTACCT
* *
434326 GTTATATTGTTATGGATCGATACAATTTT
195 ATTATATTGTTATGGATAGATACAATTTT
*
434355 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTT-TCATTTATAGATCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
*
434419 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTAT
* *
434484 CAATATATCCAATAGCACTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTACCTA
131 CAACATATCCAATAGCACTTTACCTGTTTTGTCATTTATAGACCGATTTTGTCATTTTTTACCTA
* *
434549 TTATATTGTTATGGATAGATATATTTTT
196 TTATATTGTTATGGATAGATACAATTTT
*
434577 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
** * *
434642 TTTGTCATTTTTTTATTTGTTATATTGTTATGGATCAATATATTTTTATAAAGTATCGACAC
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACAC
434704 AAACCGACAA
Statistics
Matches: 320, Mismatches: 27, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
222 103 0.32
223 217 0.68
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (223 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTAT
CAACATATCCAATAGCACTTTACCTGTTTTGTCATTTATAGACCGATTTTGTCATTTTTTACCTA
TTATATTGTTATGGATAGATACAATTTT
Found at i:435590 original size:3 final size:3
Alignment explanation
Indices: 435582--435649 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
435572 TTTACAAAGA
435582 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
435630 AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
435650 AGTAAAAGCA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:436733 original size:20 final size:21
Alignment explanation
Indices: 436705--436743 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
436695 GTTGTGACCG
*
436705 TTTATAGCCGTT-GGGGATGA
1 TTTAGAGCCGTTCGGGGATGA
436725 TTTAGAGCCGTTCGGGGAT
1 TTTAGAGCCGTTCGGGGAT
436744 TTTTTTCTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.18, C:0.13, G:0.36, T:0.33
Consensus pattern (21 bp):
TTTAGAGCCGTTCGGGGATGA
Found at i:437871 original size:30 final size:30
Alignment explanation
Indices: 437826--437955 Score: 118
Period size: 30 Copynumber: 4.3 Consensus size: 30
437816 AACACTGAAA
* *
437826 GGACTTAAAATAACAAAAATAGAAACTTAAG
1 GGAC-TAAAACAACAAAAACAGAAACTTAAG
* * *
437857 GGACTAAAACAACAAAAACATATAGTTAAG
1 GGACTAAAACAACAAAAACAGAAACTTAAG
* * *
437887 GGACTAAAACCATAAAAATAGAAACTTAAAG
1 GGACTAAAACAACAAAAACAGAAACTT-AAG
* ** *
437918 GGA-TAAAATAGTAAAAACCAAAAACTTAAG
1 GGACTAAAACAACAAAAA-CAGAAACTTAAG
437948 GGACTAAA
1 GGACTAAA
437956 TAGTAAATAA
Statistics
Matches: 80, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
30 59 0.74
31 21 0.26
ACGTcount: A:0.58, C:0.12, G:0.14, T:0.17
Consensus pattern (30 bp):
GGACTAAAACAACAAAAACAGAAACTTAAG
Found at i:437934 original size:60 final size:61
Alignment explanation
Indices: 437840--437955 Score: 155
Period size: 60 Copynumber: 1.9 Consensus size: 61
437830 TTAAAATAAC
* * *
437840 AAAAATAGAAACTTAAGGGACTAAAACAACAAAAA-CATATAGTTAAGGGACTAAAACCAT
1 AAAAATAGAAACTTAAGGGACTAAAACAACAAAAACCAAAAACTTAAGGGACTAAAACCAT
* **
437900 AAAAATAGAAACTTAAAGGGA-TAAAATAGTAAAAACCAAAAACTTAAGGGACTAAA
1 AAAAATAGAAACTT-AAGGGACTAAAACAACAAAAACCAAAAACTTAAGGGACTAAA
437956 TAGTAAATAA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
60 25 0.52
61 23 0.48
ACGTcount: A:0.59, C:0.11, G:0.14, T:0.16
Consensus pattern (61 bp):
AAAAATAGAAACTTAAGGGACTAAAACAACAAAAACCAAAAACTTAAGGGACTAAAACCAT
Found at i:439636 original size:3 final size:3
Alignment explanation
Indices: 439628--439678 Score: 70
Period size: 3 Copynumber: 17.3 Consensus size: 3
439618 AAAATAACAA
*
439628 AAT AAT AAT AAT AA- ACAT AAT AAT AAT AAT AAT AAT AAT AA- ATT
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT
439672 AAT AAT A
1 AAT AAT A
439679 TTTTTGATAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 2 0.05
3 40 0.93
4 1 0.02
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:439644 original size:18 final size:18
Alignment explanation
Indices: 439623--439659 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
439613 AATTAAAAAT
439623 AACAAAATAATAATAATA
1 AACAAAATAATAATAATA
*
439641 AACATAATAATAATAATA
1 AACAAAATAATAATAATA
439659 A
1 A
439660 TAATAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.24
Consensus pattern (18 bp):
AACAAAATAATAATAATA
Found at i:439952 original size:9 final size:9
Alignment explanation
Indices: 439938--439970 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
439928 TCGAATTATT
439938 TTTGAAAAC
1 TTTGAAAAC
439947 TTTGAAAAC
1 TTTGAAAAC
*
439956 TTTGAGAAC
1 TTTGAAAAC
439965 TTTGAA
1 TTTGAA
439971 TAAATTCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.36
Consensus pattern (9 bp):
TTTGAAAAC
Found at i:441266 original size:20 final size:20
Alignment explanation
Indices: 441230--441268 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
441220 TCTAAATCAT
*
441230 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATTCCATTTTGG
441250 TTTTCAAAA-TCCAATTTTG
1 TTTTCAAAATTCC-ATTTTG
441269 CTTTCAATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.28, C:0.13, G:0.08, T:0.51
Consensus pattern (20 bp):
TTTTCAAAATTCCATTTTGG
Found at i:444275 original size:18 final size:18
Alignment explanation
Indices: 444254--444288 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
444244 ACACTTACCA
444254 CGATAACACCACTTGTCG
1 CGATAACACCACTTGTCG
*
444272 CGATAACATCACTTGTC
1 CGATAACACCACTTGTC
444289 ACGGCAACTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.31, G:0.14, T:0.26
Consensus pattern (18 bp):
CGATAACACCACTTGTCG
Found at i:445229 original size:21 final size:21
Alignment explanation
Indices: 445205--445364 Score: 113
Period size: 21 Copynumber: 7.6 Consensus size: 21
445195 CCATATTCTC
*
445205 GTCCACCACCGTATTCTTTAT
1 GTCCACCACCGTATCCTTTAT
* ** *
445226 GTCCTCCACCGTATCCTCCAC
1 GTCCACCACCGTATCCTTTAT
* *
445247 CTCCACTACCGTATCCTTTAT
1 GTCCACCACCGTATCCTTTAT
* ** *
445268 GTCCACCATCGTATCCTCCAC
1 GTCCACCACCGTATCCTTTAT
* * ** *
445289 CTCCACTACCGTATCCTCCAC
1 GTCCACCACCGTATCCTTTAT
* ** *
445310 CTCCACCACCGTATCCTCCAC
1 GTCCACCACCGTATCCTTTAT
* *
445331 CTCCACCACCGTATCATTTAT
1 GTCCACCACCGTATCCTTTAT
*
445352 GCCCACCACCGTA
1 GTCCACCACCGTA
445365 ATTTCCACCG
Statistics
Matches: 112, Mismatches: 27, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 112 1.00
ACGTcount: A:0.19, C:0.46, G:0.07, T:0.27
Consensus pattern (21 bp):
GTCCACCACCGTATCCTTTAT
Found at i:445258 original size:42 final size:42
Alignment explanation
Indices: 445206--445381 Score: 219
Period size: 42 Copynumber: 4.2 Consensus size: 42
445196 CATATTCTCG
* * *
445206 TCCACCACCGTATTCTTTATGTCCTCCACCGTATCCTCCACC
1 TCCACTACCGTATCCTTTATGTCCACCACCGTATCCTCCACC
*
445248 TCCACTACCGTATCCTTTATGTCCACCATCGTATCCTCCACC
1 TCCACTACCGTATCCTTTATGTCCACCACCGTATCCTCCACC
** **
445290 TCCACTACCGTATCCTCCACCTCCACCACCGTATCCTCCACC
1 TCCACTACCGTATCCTTTATGTCCACCACCGTATCCTCCACC
* * * *
445332 TCCACCACCGTATCATTTATGCCCACCACCGTAAT-TTCCACC
1 TCCACTACCGTATCCTTTATGTCCACCACCGT-ATCCTCCACC
*
445374 GCCACTAC
1 TCCACTAC
445382 TGGAACTTCC
Statistics
Matches: 114, Mismatches: 19, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
42 112 0.98
43 2 0.02
ACGTcount: A:0.20, C:0.47, G:0.07, T:0.27
Consensus pattern (42 bp):
TCCACTACCGTATCCTTTATGTCCACCACCGTATCCTCCACC
Found at i:445274 original size:63 final size:63
Alignment explanation
Indices: 445204--445381 Score: 180
Period size: 63 Copynumber: 2.8 Consensus size: 63
445194 ACCATATTCT
* **
445204 CGTCCACCACCGTATTCTTTATGTCCTCCACCGTATCCTCCACCTCCACTACCGTATCCTTTA
1 CGTCCACCACCGTATTCTTTATGTCCACCACCGTATCCTCCACCTCCACTACCGTATCCTCCA
* * * ** ** * *
445267 TGTCCACCATCGTATCCTCCACCTCCACTACCGTATCCTCCACCTCCACCACCGTATCCTCCA
1 CGTCCACCACCGTATTCTTTATGTCCACCACCGTATCCTCCACCTCCACTACCGTATCCTCCA
* * * *
445330 CCTCCACCACCGTA-TCATTTATGCCCACCACCGTAAT-TTCCACCGCCACTAC
1 CGTCCACCACCGTATTC-TTTATGTCCACCACCGT-ATCCTCCACCTCCACTAC
445382 TGGAACTTCC
Statistics
Matches: 88, Mismatches: 25, Indels: 4
0.75 0.21 0.03
Matches are distributed among these distances:
62 1 0.01
63 85 0.97
64 2 0.02
ACGTcount: A:0.20, C:0.47, G:0.07, T:0.26
Consensus pattern (63 bp):
CGTCCACCACCGTATTCTTTATGTCCACCACCGTATCCTCCACCTCCACTACCGTATCCTCCA
Found at i:445449 original size:18 final size:18
Alignment explanation
Indices: 445389--445449 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
445379 TACTGGAACT
* * *
445389 TCCATGTCTATCGCATCC
1 TCCATGTTTACCGTATCC
* *
445407 TCCATGTTTACCACCATATCT
1 TCCATGTTT---ACCGTATCC
445428 TCCATGTTTACCGTATCC
1 TCCATGTTTACCGTATCC
445446 TCCA
1 TCCA
445450 CCATAACCGT
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
18 19 0.58
21 14 0.42
ACGTcount: A:0.20, C:0.36, G:0.08, T:0.36
Consensus pattern (18 bp):
TCCATGTTTACCGTATCC
Found at i:454411 original size:2 final size:2
Alignment explanation
Indices: 454404--454441 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
454394 AAGGGTTTTA
454404 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
454442 CACATAATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:455899 original size:14 final size:13
Alignment explanation
Indices: 455861--455901 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 13
455851 ACTTGACCGA
455861 ATCCGATTACCCG
1 ATCCGATTACCCG
*
455874 ATCTGATTACCCG
1 ATCCGATTACCCG
455887 ATCCGATTTACCCG
1 ATCCGA-TTACCCG
455901 A
1 A
455902 CCCAATACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 17 0.68
14 8 0.32
ACGTcount: A:0.24, C:0.34, G:0.15, T:0.27
Consensus pattern (13 bp):
ATCCGATTACCCG
Found at i:462092 original size:27 final size:27
Alignment explanation
Indices: 462046--462133 Score: 122
Period size: 27 Copynumber: 3.3 Consensus size: 27
462036 AGGCACAGCG
** *
462046 TCCTCCATAACCACCACGTCCTCTGTA
1 TCCTCCATTCCCACCGCGTCCTCTGTA
**
462073 TCCTCCATTCCCTTCGCGTCCTCTGTA
1 TCCTCCATTCCCACCGCGTCCTCTGTA
*
462100 TCCTCCATTCCCACCGCGCCCTCTGTA
1 TCCTCCATTCCCACCGCGTCCTCTGTA
462127 TCCTCCA
1 TCCTCCA
462134 CGTCCACCGT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.14, C:0.48, G:0.09, T:0.30
Consensus pattern (27 bp):
TCCTCCATTCCCACCGCGTCCTCTGTA
Found at i:462149 original size:27 final size:27
Alignment explanation
Indices: 462064--462149 Score: 84
Period size: 27 Copynumber: 3.2 Consensus size: 27
462054 AACCACCACG
* ** *
462064 TCCTCTGTATCCTCCATTCCCTTCGCG
1 TCCTCTGTATCCTCCAGTCCCACCGCA
* *
462091 TCCTCTGTATCCTCCATTCCCACCGCG
1 TCCTCTGTATCCTCCAGTCCCACCGCA
* *
462118 CCCTCTGTATCCTCCACGT-CCACCGTA
1 TCCTCTGTATCCTCCA-GTCCCACCGCA
462145 TCCTC
1 TCCTC
462150 CATAACCTCC
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
27 50 0.98
28 1 0.02
ACGTcount: A:0.10, C:0.48, G:0.10, T:0.31
Consensus pattern (27 bp):
TCCTCTGTATCCTCCAGTCCCACCGCA
Found at i:463774 original size:13 final size:13
Alignment explanation
Indices: 463756--463786 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
463746 CGATACAAGT
463756 GTGTTTCATGATG
1 GTGTTTCATGATG
463769 GTGTTTCATGATG
1 GTGTTTCATGATG
463782 GTGTT
1 GTGTT
463787 ACATTACGAT
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:0.13, C:0.06, G:0.32, T:0.48
Consensus pattern (13 bp):
GTGTTTCATGATG
Found at i:464141 original size:39 final size:39
Alignment explanation
Indices: 464073--464240 Score: 230
Period size: 39 Copynumber: 4.3 Consensus size: 39
464063 GTTATGACTT
* *
464073 GTAAGTCCTTTACCACAGGCTCCTC-GCTTTGTGCTCAGG
1 GTAAGTCC-TTACCGCAGACTCCTCGGCTTTGTGCTCAGG
**
464112 GTAAGTCCTTACCGCAGACTCCTCGGCTTTGTGCTCATA
1 GTAAGTCCTTACCGCAGACTCCTCGGCTTTGTGCTCAGG
* *
464151 GTAAGTCCTTACCGCAGGCTCCTCGACTTTGTGCTCAGG
1 GTAAGTCCTTACCGCAGACTCCTCGGCTTTGTGCTCAGG
* * *
464190 GTAAGTCCTTACCGCAGACTCCTCTGCTTTGTGCACATG
1 GTAAGTCCTTACCGCAGACTCCTCGGCTTTGTGCTCAGG
*
464229 TTAAGTCCTTAC
1 GTAAGTCCTTAC
464241 TGCATGTCCT
Statistics
Matches: 114, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
38 14 0.12
39 100 0.88
ACGTcount: A:0.17, C:0.30, G:0.21, T:0.31
Consensus pattern (39 bp):
GTAAGTCCTTACCGCAGACTCCTCGGCTTTGTGCTCAGG
Found at i:464202 original size:78 final size:76
Alignment explanation
Indices: 464072--464240 Score: 275
Period size: 78 Copynumber: 2.2 Consensus size: 76
464062 AGTTATGACT
464072 TGTAAGTCCTTTACCACAGGCTCCTCGCTTTGTGCTCAGGGTAAGTCCTTACCGCAGACTCCTCG
1 TGTAAGTCC-TTACCACAGGCTCCTCGCTTTGTGCTCAGGGTAAGTCCTTACCGCAGACTCCTCG
*
464137 GCTTTGTGCTCA
65 GCTTTGTGCACA
*
464149 TAGTAAGTCCTTACCGCAGGCTCCTCGACTTTGTGCTCAGGGTAAGTCCTTACCGCAGACTCCTC
1 T-GTAAGTCCTTACCACAGGCTCCTCG-CTTTGTGCTCAGGGTAAGTCCTTACCGCAGACTCCTC
*
464214 TGCTTTGTGCACA
64 GGCTTTGTGCACA
464227 TGTTAAGTCCTTAC
1 TG-TAAGTCCTTAC
464241 TGCATGTCCT
Statistics
Matches: 86, Mismatches: 3, Indels: 5
0.91 0.03 0.05
Matches are distributed among these distances:
77 18 0.21
78 68 0.79
ACGTcount: A:0.17, C:0.30, G:0.21, T:0.31
Consensus pattern (76 bp):
TGTAAGTCCTTACCACAGGCTCCTCGCTTTGTGCTCAGGGTAAGTCCTTACCGCAGACTCCTCGG
CTTTGTGCACA
Found at i:468607 original size:2 final size:2
Alignment explanation
Indices: 468600--468624 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
468590 GGTTACTCTC
468600 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
468625 CTTACTCGAT
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:474189 original size:23 final size:23
Alignment explanation
Indices: 474163--474226 Score: 110
Period size: 23 Copynumber: 2.8 Consensus size: 23
474153 TTTTTAAAGG
*
474163 TTTAGATAAGAATAAAAAATATT
1 TTTAAATAAGAATAAAAAATATT
474186 TTTAAATAAGAATAAAAAATATT
1 TTTAAATAAGAATAAAAAATATT
*
474209 TTTAAATAAAAATAAAAA
1 TTTAAATAAGAATAAAAA
474227 TAAAATTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (23 bp):
TTTAAATAAGAATAAAAAATATT
Found at i:474453 original size:29 final size:28
Alignment explanation
Indices: 474396--474450 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 28
474386 CGTGCAAAAA
474396 AATAAAATATT-TTTAAATTAAGTTAAT
1 AATAAAATATTATTTAAATTAAGTTAAT
474423 AATAAAATATATATTT-AA-TAAGTTAAT
1 AATAAAATAT-TATTTAAATTAAGTTAAT
474450 A
1 A
474451 TAACAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 20 0.77
28 3 0.12
29 3 0.12
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (28 bp):
AATAAAATATTATTTAAATTAAGTTAAT
Found at i:474461 original size:27 final size:29
Alignment explanation
Indices: 474399--474461 Score: 78
Period size: 27 Copynumber: 2.2 Consensus size: 29
474389 GCAAAAAAAT
*
474399 AAAATATTTTTAAATTAAGTTAATAATAA
1 AAAATATATTTAAATTAAGTTAATAATAA
*
474428 AATATATATTT-AA-TAAGTTAAT-ATAA
1 AAAATATATTTAAATTAAGTTAATAATAA
474454 CAAAATAT
1 -AAAATAT
474462 TTATTACAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 4 0.13
27 15 0.50
28 2 0.07
29 9 0.30
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.40
Consensus pattern (29 bp):
AAAATATATTTAAATTAAGTTAATAATAA
Found at i:483678 original size:9 final size:9
Alignment explanation
Indices: 483664--483756 Score: 78
Period size: 10 Copynumber: 9.7 Consensus size: 9
483654 GCTGCTGGAA
483664 ACCGGTTTG
1 ACCGGTTTG
*
483673 ACCGGTTTTCA
1 ACCGG-TTT-G
483684 ACCGGTTCTG
1 ACCGGTT-TG
483694 ACCGGTTTG
1 ACCGGTTTG
* *
483703 ACCGATTTCA
1 ACCGGTTT-G
*
483713 ACCGGTTCG
1 ACCGGTTTG
483722 AACCGGTTTG
1 -ACCGGTTTG
*
483732 ACCGGTCTG
1 ACCGGTTTG
*
483741 AATCGGTTTG
1 -ACCGGTTTG
483751 ACCGGT
1 ACCGGT
483757 CCGACCCGAC
Statistics
Matches: 66, Mismatches: 12, Indels: 12
0.73 0.13 0.13
Matches are distributed among these distances:
9 27 0.41
10 33 0.50
11 6 0.09
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:483735 original size:19 final size:19
Alignment explanation
Indices: 483663--483756 Score: 86
Period size: 19 Copynumber: 4.8 Consensus size: 19
483653 GGCTGCTGGA
483663 AACCGGTTTGACCGGTTTTC-
1 AACCGGTTTGACCGG--TTCG
*
483683 AACCGGTTCTGACCGGTTTG
1 AACCGGTT-TGACCGGTTCG
* *
483703 -ACCGATTTCAACCGGTTCG
1 AACCGGTTT-GACCGGTTCG
483722 AACCGGTTTGACCGG-TCTG
1 AACCGGTTTGACCGGTTC-G
*
483741 AATCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
483757 CCGACCCGAC
Statistics
Matches: 61, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
18 3 0.05
19 36 0.59
20 15 0.25
21 7 0.11
ACGTcount: A:0.17, C:0.26, G:0.28, T:0.30
Consensus pattern (19 bp):
AACCGGTTTGACCGGTTCG
Found at i:483747 original size:29 final size:28
Alignment explanation
Indices: 483664--483756 Score: 114
Period size: 29 Copynumber: 3.2 Consensus size: 28
483654 GCTGCTGGAA
483664 ACCGGTTTGACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TTTCAACCGGTTC-G
*
483694 ACCGGTTTGACCGATTTCAACCGGTTCG
1 ACCGGTTTGACCGGTTTCAACCGGTTCG
* * * *
483722 AACCGGTTTGACCGGTCTGAATCGGTTTG
1 -ACCGGTTTGACCGGTTTCAACCGGTTCG
483751 ACCGGT
1 ACCGGT
483757 CCGACCCGAC
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
28 7 0.12
29 36 0.64
30 13 0.23
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (28 bp):
ACCGGTTTGACCGGTTTCAACCGGTTCG
Found at i:484780 original size:63 final size:63
Alignment explanation
Indices: 484678--484801 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
484668 CTAATGTGAC
* ** * *
484678 TCTTAGGTAGGCTCTGCGGCCCTGAGATCATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCATTCTCGGGTAGGCCCT-CAGGCCCTAAGATGTGT
* *
484741 TCTTAGGTAGGCCCCACGGCCCCGAAATC-TATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCAT-TCTCGGGTAGGCCCTCAGGCCCTAAGATGT
484802 TCCCTTAGGG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 50 0.96
ACGTcount: A:0.17, C:0.28, G:0.29, T:0.26
Consensus pattern (63 bp):
TCTTAGGTAGGCCCCACGGCCCCGAAATCATTCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:490991 original size:9 final size:9
Alignment explanation
Indices: 490977--491059 Score: 76
Period size: 10 Copynumber: 8.7 Consensus size: 9
490967 GCTGCTGGAA
490977 ACCGGTTTG
1 ACCGGTTTG
*
490986 ACCGGTTTTCA
1 ACCGG-TTT-G
490997 ACCGGTTTG
1 ACCGGTTTG
*
491006 ACCGGTTTCA
1 ACCGGTTT-G
*
491016 ACCGGTTCG
1 ACCGGTTTG
491025 AACCGGTTTG
1 -ACCGGTTTG
*
491035 ACCGGTCTG
1 ACCGGTTTG
*
491044 AATCGGTTTG
1 -ACCGGTTTG
491054 ACCGGT
1 ACCGGT
491060 CCGACCCGAC
Statistics
Matches: 59, Mismatches: 10, Indels: 10
0.75 0.13 0.13
Matches are distributed among these distances:
9 26 0.44
10 28 0.47
11 5 0.08
ACGTcount: A:0.16, C:0.25, G:0.29, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:491001 original size:20 final size:20
Alignment explanation
Indices: 490976--491033 Score: 91
Period size: 20 Copynumber: 2.9 Consensus size: 20
490966 GGCTGCTGGA
490976 AACCGGTTTGACCGGTTTTC
1 AACCGGTTTGACCGGTTTTC
490996 AACCGGTTTGACCGG-TTTC
1 AACCGGTTTGACCGGTTTTC
*
491015 AACCGGTTCGAACCGGTTT
1 AACCGGTTTG-ACCGGTTT
491034 GACCGGTCTG
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
19 13 0.37
20 20 0.57
21 2 0.06
ACGTcount: A:0.17, C:0.26, G:0.26, T:0.31
Consensus pattern (20 bp):
AACCGGTTTGACCGGTTTTC
Found at i:491038 original size:19 final size:19
Alignment explanation
Indices: 490997--491059 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
490987 CCGGTTTTCA
* *
490997 ACCGGTTTG-ACCGGTTTCA
1 ACCGGTTCGAACCGGTTT-G
491016 ACCGGTTCGAACCGGTTTG
1 ACCGGTTCGAACCGGTTTG
*
491035 ACCGG-TCTGAATCGGTTTG
1 ACCGGTTC-GAACCGGTTTG
491054 ACCGGT
1 ACCGGT
491060 CCGACCCGAC
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
18 2 0.05
19 28 0.74
20 8 0.21
ACGTcount: A:0.16, C:0.25, G:0.30, T:0.29
Consensus pattern (19 bp):
ACCGGTTCGAACCGGTTTG
Found at i:491050 original size:29 final size:29
Alignment explanation
Indices: 490996--491059 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
490986 ACCGGTTTTC
*
490996 AACCGGTTTGACCGGTTTCAACCGGTTCG
1 AACCGGTTTGACCGGTCTCAACCGGTTCG
* * *
491025 AACCGGTTTGACCGGTCTGAATCGGTTTG
1 AACCGGTTTGACCGGTCTCAACCGGTTCG
491054 -ACCGGT
1 AACCGGT
491060 CCGACCCGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 6 0.19
29 25 0.81
ACGTcount: A:0.17, C:0.25, G:0.30, T:0.28
Consensus pattern (29 bp):
AACCGGTTTGACCGGTCTCAACCGGTTCG
Found at i:492077 original size:63 final size:63
Alignment explanation
Indices: 491975--492098 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
491965 CTAATGTGAC
* ** * *
491975 TCTTAGGTAGGCTCTGCGGCCCTGAGATCATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCATTCTCGGGTAGGCCCT-CAGGCCCTAAGATGTGT
* *
492038 TCTTAGGTAGGCCCCACGGCCCCGAAATC-TATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCAT-TCTCGGGTAGGCCCTCAGGCCCTAAGATGT
492099 TCCCTTAGGG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 50 0.96
ACGTcount: A:0.17, C:0.28, G:0.29, T:0.26
Consensus pattern (63 bp):
TCTTAGGTAGGCCCCACGGCCCCGAAATCATTCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Done.