Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008912.1 Hibiscus syriacus cultivar Beakdansim tig00112215_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: 3753803
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 18
Found at i:501135 original size:22 final size:22
Alignment explanation
Indices: 501110--501160 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
501100 TTGTGTTTGG
501110 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
501132 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
501154 TCAAAGG
1 TCAAAGG
501161 ATTGATGGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:501795 original size:20 final size:20
Alignment explanation
Indices: 501770--501807 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
501760 TTTTGTCCCC
*
501770 TTTTTTTATTTTTGTTTTCT
1 TTTTTTTATTCTTGTTTTCT
*
501790 TTTTTTTGTTCTTGTTTT
1 TTTTTTTATTCTTGTTTT
501808 TTCCTTTTTT
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:0.03, C:0.05, G:0.08, T:0.84
Consensus pattern (20 bp):
TTTTTTTATTCTTGTTTTCT
Found at i:501809 original size:22 final size:22
Alignment explanation
Indices: 501784--501836 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
501774 TTTATTTTTG
* *
501784 TTTTCTTTTTTTTGTTCTTGTT
1 TTTTCTTTTTTTTCTTCTTCTT
*
501806 TTTTCCTTTTTTTCTTCTTCTT
1 TTTTCTTTTTTTTCTTCTTCTT
501828 TTTTCTTTT
1 TTTTCTTTT
501837 GCCCTTTTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.00, C:0.15, G:0.04, T:0.81
Consensus pattern (22 bp):
TTTTCTTTTTTTTCTTCTTCTT
Found at i:505411 original size:2 final size:2
Alignment explanation
Indices: 505393--505432 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
505383 ATAATAATAA
*
505393 AT AT AT A- AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
505433 CTTTAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:505955 original size:36 final size:37
Alignment explanation
Indices: 505906--505975 Score: 108
Period size: 36 Copynumber: 1.9 Consensus size: 37
505896 AACATAGAAA
*
505906 AATTCTATTCTATTTTT-AGGAG-TTGAATCCTAGCAG
1 AATTCTATCCTATTTTTGA-GAGTTTGAATCCTAGCAG
505942 AATTCTATCCTATTTTTGAGAGTTTGAATCCTAG
1 AATTCTATCCTATTTTTGAGAGTTTGAATCCTAG
505976 TAGGACGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
36 19 0.61
37 12 0.39
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (37 bp):
AATTCTATCCTATTTTTGAGAGTTTGAATCCTAGCAG
Found at i:512890 original size:15 final size:16
Alignment explanation
Indices: 512862--512891 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
512852 TTTTTTTATC
512862 TTTTTTTTCGTCTTCT
1 TTTTTTTTCGTCTTCT
512878 TTTTTTTTC-TCTTC
1 TTTTTTTTCGTCTTC
512892 AGGCCAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTTTTTTCGTCTTCT
Found at i:513756 original size:24 final size:24
Alignment explanation
Indices: 513729--513794 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
513719 AACTCGTATA
513729 AATTTGCACCGAAGTGCCACGTAG
1 AATTTGCACCGAAGTGCCACGTAG
*
513753 AATTTGTC-CCGAAG-GACCCCGTAG
1 AATTTG-CACCGAAGTG-CCACGTAG
* *
513777 AA-ATGCACCGTAGTGCCA
1 AATTTGCACCGAAGTGCCA
513795 TATAAGATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
22 1 0.03
23 10 0.29
24 22 0.65
25 1 0.03
ACGTcount: A:0.29, C:0.27, G:0.24, T:0.20
Consensus pattern (24 bp):
AATTTGCACCGAAGTGCCACGTAG
Found at i:517860 original size:23 final size:23
Alignment explanation
Indices: 517830--517873 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
517820 AATACATATA
517830 TGTCCCGAAGGACCACGTAGAAT
1 TGTCCCGAAGGACCACGTAGAAT
*
517853 TGTCCCGAAGGACCGCGTAGA
1 TGTCCCGAAGGACCACGTAGA
517874 CCCTCTACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.27, G:0.30, T:0.16
Consensus pattern (23 bp):
TGTCCCGAAGGACCACGTAGAAT
Found at i:525502 original size:16 final size:16
Alignment explanation
Indices: 525481--525512 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
525471 AAAATACTTT
525481 GTTGTGGCATGTTAAG
1 GTTGTGGCATGTTAAG
525497 GTTGTGGCATGTTAAG
1 GTTGTGGCATGTTAAG
525513 CTTGCATCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.38, T:0.38
Consensus pattern (16 bp):
GTTGTGGCATGTTAAG
Found at i:531212 original size:21 final size:23
Alignment explanation
Indices: 531174--531224 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
531164 TTTTCTAGAA
*
531174 TGCTACAGGTGTATCGATACCC-
1 TGCTACAGGTGTACCGATACCCT
531196 TGCTACA-GTGTACCGATACCCT
1 TGCTACAGGTGTACCGATACCCT
531218 TGCTACA
1 TGCTACA
531225 ATAATTTCGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 13 0.48
22 14 0.52
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (23 bp):
TGCTACAGGTGTACCGATACCCT
Found at i:532903 original size:23 final size:23
Alignment explanation
Indices: 532871--532945 Score: 98
Period size: 23 Copynumber: 3.2 Consensus size: 23
532861 TCAGGTAAAT
* *
532871 TATCATATCATAATCCTGGTCAG
1 TATCAGATCAAAATCCTGGTCAG
532894 TATCAGATCAAAATCCAT-GTCAG
1 TATCAGATCAAAATCC-TGGTCAG
*
532917 TATCAGATCAAAATCCAGGTCAGG
1 TATCAGATCAAAATCCTGGTCA-G
532941 TATCA
1 TATCA
532946 TAACAGAATT
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
23 39 0.85
24 7 0.15
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (23 bp):
TATCAGATCAAAATCCTGGTCAG
Found at i:536431 original size:24 final size:23
Alignment explanation
Indices: 536380--536442 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 23
536370 TCCAAGTTAC
* *
536380 GTATCAGATCAAAAATCAATGTCA
1 GTATCAGATC-AGAATCAAGGTCA
*
536404 GTATCAGATCAGAATCCAGGTCA
1 GTATCAGATCAGAATCAAGGTCA
* *
536427 GGTATCATAACAGAAT
1 -GTATCAGATCAGAAT
536443 TCAAATCAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
23 10 0.30
24 23 0.70
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.24
Consensus pattern (23 bp):
GTATCAGATCAGAATCAAGGTCA
Found at i:540282 original size:14 final size:14
Alignment explanation
Indices: 540265--540291 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
540255 ACCGATGCGG
540265 GTAACCCGATCCGT
1 GTAACCCGATCCGT
540279 GTAACCCGATCCG
1 GTAACCCGATCCG
540292 ATCCAGGAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.37, G:0.22, T:0.19
Consensus pattern (14 bp):
GTAACCCGATCCGT
Found at i:540832 original size:2 final size:2
Alignment explanation
Indices: 540827--540891 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
540817 CACACACACG
540827 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
540869 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
540892 GAACACTACC
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:541139 original size:23 final size:24
Alignment explanation
Indices: 541082--541158 Score: 93
Period size: 24 Copynumber: 3.2 Consensus size: 24
541072 TTCAGGACAA
* * *
541082 GTATTAGATCAGAATCCAGGTCAT
1 GTATCAGATCAGAATCCAGGTTAG
* *
541106 GTATCATATCAGAATCCATGTTA-
1 GTATCAGATCAGAATCCAGGTTAG
*
541129 GTATCAGATCATAATCCAGGTTAG
1 GTATCAGATCAGAATCCAGGTTAG
541153 GTATCA
1 GTATCA
541159 TAACATAATT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 20 0.44
24 25 0.56
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (24 bp):
GTATCAGATCAGAATCCAGGTTAG
Found at i:541165 original size:24 final size:23
Alignment explanation
Indices: 541089--541167 Score: 86
Period size: 24 Copynumber: 3.3 Consensus size: 23
541079 CAAGTATTAG
* *
541089 ATCAGAATCCAGGTCATGTATCAT
1 ATCATAATCCAGGTTA-GTATCAT
* * *
541113 ATCAGAATCCATGTTAGTATCAG
1 ATCATAATCCAGGTTAGTATCAT
541136 ATCATAATCCAGGTTAGGTATCAT
1 ATCATAATCCAGGTTA-GTATCAT
*
541160 AACATAAT
1 ATCATAAT
541168 TCAAATTAGA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
23 20 0.43
24 27 0.57
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (23 bp):
ATCATAATCCAGGTTAGTATCAT
Found at i:543508 original size:65 final size:65
Alignment explanation
Indices: 543421--543563 Score: 161
Period size: 65 Copynumber: 2.2 Consensus size: 65
543411 GATGCATTTC
* * *
543421 ATGCATCGATGCA-CATACCATGCATTGATGCACTCAGAG-T-TTTATGAAAACATCAAATGCGT
1 ATGCATCGATGCACCATAACATGCATCGATGCACTCAG-GCTATTT-TG-AAACATCAAACGCGT
543483 TTGT
63 TT-T
* *
543487 -TGCATCGATGCACCA-AACATGCATCGATGTACTCAGGCTATTTTGAAACATCGAACGCGTTTT
1 ATGCATCGATGCACCATAACATGCATCGATGCACTCAGGCTATTTTGAAACATCAAACGCGTTTT
*
543550 ATGCATCTATGCAC
1 ATGCATCGATGCAC
543564 TCTTAGTGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
63 1 0.01
64 28 0.42
65 33 0.49
66 5 0.07
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.29
Consensus pattern (65 bp):
ATGCATCGATGCACCATAACATGCATCGATGCACTCAGGCTATTTTGAAACATCAAACGCGTTTT
Found at i:549443 original size:23 final size:23
Alignment explanation
Indices: 549374--549454 Score: 96
Period size: 23 Copynumber: 3.7 Consensus size: 23
549364 ACACCTAACA
*
549374 GTGCATCGATGCA-TCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
* * *
549396 GTGCATTGAT--ACACCATGAAG
1 GTGCATCGATGCACACCTTGAAT
*
549417 GTGCATCGATGCACGCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
549440 GTGCATCGATGCACA
1 GTGCATCGATGCACA
549455 AGGTCATGCA
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
20 1 0.02
21 15 0.32
22 9 0.19
23 22 0.47
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26
Consensus pattern (23 bp):
GTGCATCGATGCACACCTTGAAT
Found at i:549465 original size:43 final size:43
Alignment explanation
Indices: 549373--549473 Score: 116
Period size: 43 Copynumber: 2.3 Consensus size: 43
549363 TACACCTAAC
* * * *
549373 AGTGCATCGATGCA-TCCTTGAATGTGCATTGATACACCATGA
1 AGTGCATCGATGCACGCCTTGAATGTGCATCGATACACAAGGA
* *
549415 AGGTGCATCGATGCACGCCTTGAATGTGCATCGATGCACAAGGTC
1 A-GTGCATCGATGCACGCCTTGAATGTGCATCGATACACAAGG-A
549460 A-TGCATCGATGCAC
1 AGTGCATCGATGCAC
549474 AAGGTCATAC
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
42 1 0.02
43 26 0.52
44 22 0.44
45 1 0.02
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.25
Consensus pattern (43 bp):
AGTGCATCGATGCACGCCTTGAATGTGCATCGATACACAAGGA
Found at i:549466 original size:20 final size:20
Alignment explanation
Indices: 549441--549512 Score: 126
Period size: 20 Copynumber: 3.6 Consensus size: 20
549431 GCCTTGAATG
549441 TGCATCGATGCACAAGGTCA
1 TGCATCGATGCACAAGGTCA
549461 TGCATCGATGCACAAGGTCA
1 TGCATCGATGCACAAGGTCA
* *
549481 TACATCGATGTACAAGGTCA
1 TGCATCGATGCACAAGGTCA
549501 TGCATCGATGCA
1 TGCATCGATGCA
549513 TCGGTCGGGT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.22
Consensus pattern (20 bp):
TGCATCGATGCACAAGGTCA
Found at i:554416 original size:2 final size:2
Alignment explanation
Indices: 554409--554462 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
554399 CATTTAAGAC
554409 AT AT 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 AT AT
554451 AT AT AT AT AT AT
1 AT AT AT AT AT AT
554463 GAACACTACC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:559006 original size:24 final size:24
Alignment explanation
Indices: 558979--559042 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 24
558969 TATATCAAAA
* *
558979 ATCAAAACATAATTCATGTCAAGT
1 ATCATAACATAATTCAGGTCAAGT
* * * *
559003 ATCATATCAGAATCCAGGTCAGGT
1 ATCATAACATAATTCAGGTCAAGT
559027 ATCATAACATAATTCA
1 ATCATAACATAATTCA
559043 AATAGGAAAT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.28
Consensus pattern (24 bp):
ATCATAACATAATTCAGGTCAAGT
Found at i:566706 original size:26 final size:27
Alignment explanation
Indices: 566625--566691 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
566615 AAATCTGTTG
*
566625 TTGAAGATTACCTAAAAGGTTGAGATC
1 TTGAAGATTGCCTAAAAGGTTGAGATC
566652 TTGAAGATTGCCTAAAAGGTTGAGATC
1 TTGAAGATTGCCTAAAAGGTTGAGATC
566679 TTGAAGATTGCCT
1 TTGAAGATTGCCT
566692 TATGGTTGTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (27 bp):
TTGAAGATTGCCTAAAAGGTTGAGATC
Found at i:567357 original size:29 final size:29
Alignment explanation
Indices: 567324--567384 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
567314 AAAAGAGGAT
* *
567324 GAATAAATTGAATACTTTATTTATGATAA
1 GAATAAACTGAAGACTTTATTTATGATAA
567353 GAATAAACTGAAGACTTTATTTATGATAA
1 GAATAAACTGAAGACTTTATTTATGATAA
567382 GAA
1 GAA
567385 AATAACCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.46, C:0.05, G:0.13, T:0.36
Consensus pattern (29 bp):
GAATAAACTGAAGACTTTATTTATGATAA
Found at i:571095 original size:59 final size:59
Alignment explanation
Indices: 570999--571119 Score: 179
Period size: 59 Copynumber: 2.1 Consensus size: 59
570989 AATAGATGGA
* * * *
570999 TAAGTGTCCTATCGAACCCTCCTGGTCGCAATAAAAAGGCAAACTCGATAATATGGCTC
1 TAAGTGTCCTATCCAACCCTCCTAGTCACAATAAAAAGGCAAACTCGACAATATGGCTC
* * *
571058 TAAGTGTCCTATCCAATCCTCCTAGTCACAATGAAAAGGTAAACTCGACAATATGGCTC
1 TAAGTGTCCTATCCAACCCTCCTAGTCACAATAAAAAGGCAAACTCGACAATATGGCTC
571117 TAA
1 TAA
571120 CCAACCCTCC
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.25
Consensus pattern (59 bp):
TAAGTGTCCTATCCAACCCTCCTAGTCACAATAAAAAGGCAAACTCGACAATATGGCTC
Found at i:585081 original size:94 final size:93
Alignment explanation
Indices: 584940--585139 Score: 314
Period size: 94 Copynumber: 2.2 Consensus size: 93
584930 GATTCAATCA
* *
584940 GTATCGATACC-TACTAGGTAGTATTGATACCATGGTAAGGGTATCGATACAAGGAAACATCGAA
1 GTATCGGTACCATAATAGGTAGTATTGATACCATGGTAAGGGTATCGATACAAGGAAACATCGAA
585004 TCT-AAATCGATATCGATACTGTAAGGGG
66 TCTAAAATCGATATCGATACTGTAA-GGG
585032 GTATCGGTACCATAATATGGTAGTATTGATACCATGGTAAGGGTATCGATACAAGGAAACATCGA
1 GTATCGGTACCATAATA-GGTAGTATTGATACCATGGTAAGGGTATCGATACAAGGAAACATCGA
* * *
585097 ATTTAAAATTGGTATCGATACTGTAAGGG
65 ATCTAAAATCGATATCGATACTGTAAGGG
*
585126 GTATCTGTACCATA
1 GTATCGGTACCATA
585140 GTATAGAAGT
Statistics
Matches: 99, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
92 10 0.10
93 4 0.04
94 66 0.67
95 19 0.19
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.28
Consensus pattern (93 bp):
GTATCGGTACCATAATAGGTAGTATTGATACCATGGTAAGGGTATCGATACAAGGAAACATCGAA
TCTAAAATCGATATCGATACTGTAAGGG
Found at i:585151 original size:94 final size:94
Alignment explanation
Indices: 584959--585177 Score: 307
Period size: 94 Copynumber: 2.3 Consensus size: 94
584949 CCTACTAGGT
584959 AGTATTGATACCATGGTAAGGGTATCGATACAAGGAAACATCGAATCTAAATCGATATCGATACT
1 AGTATTGATACCATGGTAAGGGTATCGATACAAGGAAACATCGAATCTAAATCGATATCGATACT
* *
585024 GTAAGGGGGTATCGGTACCATAATATGGT
66 GTAAGGGGGTATCGGTACCATAATATAGA
* * *
585053 AGTATTGATACCATGGTAAGGGTATCGATACAAGGAAACATCGAATTTAAAATTGGTATCGATAC
1 AGTATTGATACCATGGTAAGGGTATCGATACAAGGAAACATCGAATCT-AAATCGATATCGATAC
* *
585118 TGTAA-GGGGTATCTGTACCATAGTATAGA
65 TGTAAGGGGGTATCGGTACCATAATATAGA
* * * *
585147 AGTATCGGTACCAGGGT-AGTAGTATCGATAC
1 AGTATTGATACCATGGTAAG-GGTATCGATAC
585178 TATTAAGCTT
Statistics
Matches: 112, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
93 2 0.02
94 91 0.81
95 19 0.17
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.27
Consensus pattern (94 bp):
AGTATTGATACCATGGTAAGGGTATCGATACAAGGAAACATCGAATCTAAATCGATATCGATACT
GTAAGGGGGTATCGGTACCATAATATAGA
Found at i:585576 original size:20 final size:20
Alignment explanation
Indices: 585551--585909 Score: 117
Period size: 20 Copynumber: 15.8 Consensus size: 20
585541 TAGTATGTAA
*
585551 AATGCATGAAATAATGCATT
1 AATGCATGAAATGATGCATT
*
585571 AATGCATGAAAGGATGTCATAATT
1 AATGCATGAAATGATG-C---ATT
585595 AAAATGCATGAAATGATGCATT
1 --AATGCATGAAATGATGCATT
* * *
585617 AAAGCATGAAAGGATACCATAATT
1 AATGCATGAAATGAT-GC---ATT
585641 AAAATGCATGAAATGATGCATT
1 --AATGCATGAAATGATGCATT
* * *
585663 AAGGCATGAAAGGATTCCACAATT
1 AATGCATGAAATGA-T--GC-ATT
585687 AAAATGCATGAAATGATGCATT
1 --AATGCATGAAATGATGCATT
* * *
585709 AAGGCATGACAGGATGCCATAATT
1 AATGCATGAAATGATG-C---ATT
*
585733 AAAATGCATGAAAGGATGCATT
1 --AATGCATGAAATGATGCATT
* *
585755 AAGGCATGAAAGGATGCCATAATT
1 AATGCATGAAATGATG-C---ATT
*
585779 AAAATGCATGAAAGGATGCATT
1 --AATGCATGAAATGATGCATT
* *
585801 AAGGCATGAAAGGATGCCATAATT
1 AATGCATGAAATGATG-C---ATT
585825 AAAATGCATGAAA-GAATGCATT
1 --AATGCATGAAATG-ATGCATT
* *
585847 AAGGCATGAAAGGATGCCATAATTAT
1 AATGCATGAAATGATG-C---A-T-T
* *
585873 AATGCATGAAAGGTTGCATT
1 AATGCATGAAATGATGCATT
* *
585893 AAGGTATGAAATGATGC
1 AATGCATGAAATGATGC
585910 CATAATTATA
Statistics
Matches: 264, Mismatches: 31, Indels: 88
0.69 0.08 0.23
Matches are distributed among these distances:
20 109 0.41
21 9 0.03
22 19 0.07
23 2 0.01
24 19 0.07
25 9 0.03
26 97 0.37
ACGTcount: A:0.43, C:0.11, G:0.21, T:0.24
Consensus pattern (20 bp):
AATGCATGAAATGATGCATT
Found at i:585615 original size:46 final size:46
Alignment explanation
Indices: 585548--586119 Score: 856
Period size: 46 Copynumber: 12.4 Consensus size: 46
585538 CTATAGTATG
** * *
585548 TAAAATGCATGAAATAATGCATTAATGCATGAAAGGATGTCATAAT
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAT
* * *
585594 TAAAATGCATGAAATGATGCATTAAAGCATGAAAGGATACCATAAT
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAT
* * *
585640 TAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATTCCACAAT
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAT
* *
585686 TAAAATGCATGAAATGATGCATTAAGGCATGACAGGATGCCATAAT
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAT
585732 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAT
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAT
585778 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAT
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAT
*
585824 TAAAATGCATGAAAGAATGCATTAAGGCATGAAAGGATGCCATAAT
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAT
* * * *
585870 TATAATGCATGAAAGGTTGCATTAAGGTATGAAATGATGCCATAAT
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAT
* * * * * *
585916 TATAATGTATGAAAGGATGCATTAATGTATGAAAGAATTCCATAAT
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAT
* *
585962 TAAAATGCATGAAAGGGTGCATTAAGTCATGAAAGGATGCCATAAT
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAT
* * * * *
586008 TAAAATACATGAAAGGATACATTAAGGAAAGAAAGGATGACATAAT
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAT
* *
586054 TAAAATGCATGAAAGGATGCATTAAGGCATGAAATGATGCTATAAT
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAT
586100 TAAAATGCATGAAAGGATGC
1 TAAAATGCATGAAAGGATGC
586120 CATAATTTAA
Statistics
Matches: 480, Mismatches: 46, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 480 1.00
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.25
Consensus pattern (46 bp):
TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAT
Found at i:585961 original size:20 final size:19
Alignment explanation
Indices: 585917--585961 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
585907 TGCCATAATT
* *
585917 ATAATGTATGAAAGGATGC
1 ATAATGTATGAAAGAATCC
585936 ATTAATGTATGAAAGAATTCC
1 A-TAATGTATGAAAGAA-TCC
585957 ATAAT
1 ATAAT
585962 TAAAATGCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 1 0.05
20 18 0.82
21 3 0.14
ACGTcount: A:0.44, C:0.07, G:0.18, T:0.31
Consensus pattern (19 bp):
ATAATGTATGAAAGAATCC
Found at i:601105 original size:21 final size:21
Alignment explanation
Indices: 601076--601115 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
601066 ATATTTAATG
601076 AAAAAGATACCAATTGTTATC
1 AAAAAGATACCAATTGTTATC
* *
601097 AAAAGGATATCAATTGTTA
1 AAAAAGATACCAATTGTTA
601116 AAAATATATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.30
Consensus pattern (21 bp):
AAAAAGATACCAATTGTTATC
Found at i:601124 original size:18 final size:19
Alignment explanation
Indices: 601103--601144 Score: 68
Period size: 18 Copynumber: 2.2 Consensus size: 19
601093 TATCAAAAGG
601103 ATATCAATTGTT-AAAAAT
1 ATATCAATTGTTAAAAAAT
601121 ATATCAATTGTTGAAAAAAT
1 ATATCAATTGTT-AAAAAAT
601141 ATAT
1 ATAT
601145 GAAAATGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 12 0.55
20 10 0.45
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (19 bp):
ATATCAATTGTTAAAAAAT
Found at i:602677 original size:21 final size:19
Alignment explanation
Indices: 602652--602715 Score: 67
Period size: 21 Copynumber: 3.3 Consensus size: 19
602642 ATATTTAATG
602652 AAAAAAGATACCAATTGTT
1 AAAAAAGATACCAATTGTT
**
602671 AACAAAAGGATGTCAATTGTT
1 AA-AAAA-GATACCAATTGTT
*
602692 -AAAAAGATACAAATTGTT
1 AAAAAAGATACCAATTGTT
*
602710 AGAAAA
1 AAAAAA
602716 TATATGAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
18 10 0.28
19 10 0.28
20 5 0.14
21 11 0.31
ACGTcount: A:0.53, C:0.08, G:0.14, T:0.25
Consensus pattern (19 bp):
AAAAAAGATACCAATTGTT
Found at i:602706 original size:18 final size:18
Alignment explanation
Indices: 602654--602715 Score: 54
Period size: 18 Copynumber: 3.2 Consensus size: 18
602644 ATTTAATGAA
602654 AAAAGATACCAATTGTTAAC
1 AAAAGATA-CAATTGTT-AC
*
602674 AAAAGGATGTCAATTGTTA-
1 AAAA-GAT-ACAATTGTTAC
*
602693 AAAAGATACAAATTGTTAG
1 AAAAGATAC-AATTGTTAC
602712 AAAA
1 AAAA
602716 TATATGAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
17 1 0.03
18 11 0.31
19 8 0.22
20 5 0.14
21 11 0.31
ACGTcount: A:0.52, C:0.08, G:0.15, T:0.26
Consensus pattern (18 bp):
AAAAGATACAATTGTTAC
Found at i:604737 original size:20 final size:20
Alignment explanation
Indices: 604712--604750 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
604702 ACACTTACCC
*
604712 TCTTC-TCATCTTTCTTCCTA
1 TCTTCTTCATATTT-TTCCTA
604732 TCTTCTTCATATTTTTCCT
1 TCTTCTTCATATTTTTCCT
604751 TTCAAGCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.10, C:0.31, G:0.00, T:0.59
Consensus pattern (20 bp):
TCTTCTTCATATTTTTCCTA
Found at i:612436 original size:2 final size:2
Alignment explanation
Indices: 612429--612473 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
612419 ACGAAGATTG
612429 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
612471 TA T
1 TA T
612474 TCATGGAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:622393 original size:21 final size:21
Alignment explanation
Indices: 622367--622422 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
622357 ACAAAACTTG
*
622367 CTGAAAATCCTGCAGCCACTA
1 CTGAAAATCCTACAGCCACTA
*
622388 CTGAAAATCCTACAGCCACTG
1 CTGAAAATCCTACAGCCACTA
622409 CTGAAAATCCTACA
1 CTGAAAATCCTACA
622423 ACCATTTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.36, C:0.32, G:0.12, T:0.20
Consensus pattern (21 bp):
CTGAAAATCCTACAGCCACTA
Found at i:630034 original size:2 final size:2
Alignment explanation
Indices: 630029--630053 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
630019 AATGTGTGTG
630029 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
630054 TCAACTTGTC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:636263 original size:24 final size:24
Alignment explanation
Indices: 636216--636263 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
636206 TTCACTGCTT
* *
636216 GACCCGGTTCCTCCTATTTTGCTC
1 GACCCGGTTCCTCATATTTCGCTC
*
636240 GACCCGGTTCCTCATGTTTCGCTC
1 GACCCGGTTCCTCATATTTCGCTC
636264 TTCCCCGAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.08, C:0.38, G:0.19, T:0.35
Consensus pattern (24 bp):
GACCCGGTTCCTCATATTTCGCTC
Found at i:649675 original size:19 final size:20
Alignment explanation
Indices: 649647--649687 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
649637 AGATATTTTA
649647 TTATA-GTTTTATCTTTTGT
1 TTATATGTTTTATCTTTTGT
* *
649666 TTATATTTTTTATTTTTTGT
1 TTATATGTTTTATCTTTTGT
649686 TT
1 TT
649688 TCTTTTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.15, C:0.02, G:0.07, T:0.76
Consensus pattern (20 bp):
TTATATGTTTTATCTTTTGT
Found at i:652919 original size:21 final size:21
Alignment explanation
Indices: 652891--652966 Score: 107
Period size: 21 Copynumber: 3.6 Consensus size: 21
652881 TATAAAATTA
*
652891 TCCCGAAGGACCTCATATATG
1 TCCCGAAGGACCTCGTATATG
* *
652912 TTCCGAAGGACGTCGTATATG
1 TCCCGAAGGACCTCGTATATG
652933 TCCCGAAGGACCTCGTATATG
1 TCCCGAAGGACCTCGTATATG
* *
652954 TCCCAAAGAACCT
1 TCCCGAAGGACCT
652967 TGTAGAACCC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (21 bp):
TCCCGAAGGACCTCGTATATG
Found at i:656410 original size:18 final size:18
Alignment explanation
Indices: 656366--656432 Score: 95
Period size: 18 Copynumber: 3.9 Consensus size: 18
656356 ACCGATCAAC
**
656366 GGTCAACGGGTCGGAACG
1 GGTCAACGGGTCGGGTCG
656384 GGT---CGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
656399 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
656417 GGTCAACGGGTCGGGT
1 GGTCAACGGGTCGGGT
656433 AAACGGGTCG
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
15 13 0.30
18 31 0.70
ACGTcount: A:0.12, C:0.21, G:0.51, T:0.16
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:656432 original size:5 final size:5
Alignment explanation
Indices: 656372--656420 Score: 53
Period size: 5 Copynumber: 9.2 Consensus size: 5
656362 CAACGGTCAA
**
656372 CGGGT CGGAA CGGGT CGGGT CGGGT CGGGT CAACGGGT CGGGT CGGGT
1 CGGGT CGGGT CGGGT CGGGT CGGGT CGGGT ---CGGGT CGGGT CGGGT
656420 C
1 C
656421 AACGGGTCGG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
5 32 0.86
8 5 0.14
ACGTcount: A:0.08, C:0.22, G:0.53, T:0.16
Consensus pattern (5 bp):
CGGGT
Found at i:656437 original size:13 final size:13
Alignment explanation
Indices: 656410--656442 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
656400 GTCAACGGGT
*
656410 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
656423 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
656436 CGGGTCG
1 CGGGTCG
656443 TGACCGGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.15, C:0.21, G:0.48, T:0.15
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:656452 original size:31 final size:31
Alignment explanation
Indices: 656392--656453 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
656382 CGGGTCGGGT
* * *
656392 CGGGTCGGGTCAACGGGTCGGGTCGGGTCAA
1 CGGGTCGGGTAAACGGGTCGGGACCGGTCAA
*
656423 CGGGTCGGGTAAACGGGTCGTGACCGGTCAA
1 CGGGTCGGGTAAACGGGTCGGGACCGGTCAA
656454 ACCGGTCAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.16, C:0.23, G:0.45, T:0.16
Consensus pattern (31 bp):
CGGGTCGGGTAAACGGGTCGGGACCGGTCAA
Found at i:656465 original size:10 final size:10
Alignment explanation
Indices: 656445--656480 Score: 56
Period size: 11 Copynumber: 3.6 Consensus size: 10
656435 ACGGGTCGTG
656445 ACCGGTC-AA
1 ACCGGTCAAA
656454 ACCGGTCAAA
1 ACCGGTCAAA
656464 ACCGGTTCAAA
1 ACCGG-TCAAA
656475 ACCGGT
1 ACCGGT
656481 TTCCAGCGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 7 0.28
10 8 0.32
11 10 0.40
ACGTcount: A:0.33, C:0.31, G:0.22, T:0.14
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:663644 original size:13 final size:13
Alignment explanation
Indices: 663628--663660 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
663618 GTCAACGGGT
*
663628 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
663641 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
663654 CGGGTCG
1 CGGGTCG
663661 TGACCGGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.15, C:0.21, G:0.48, T:0.15
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:663683 original size:10 final size:10
Alignment explanation
Indices: 663663--663717 Score: 69
Period size: 10 Copynumber: 5.6 Consensus size: 10
663653 ACGGGTCGTG
663663 ACCGGTC-AA
1 ACCGGTCAAA
663672 ACCGGTCAAA
1 ACCGGTCAAA
663682 ACCGGTTCAAA
1 ACCGG-TCAAA
* *
663693 ACTGGT-TAA
1 ACCGGTCAAA
663702 ACCGGTCAAA
1 ACCGGTCAAA
663712 ACCGGT
1 ACCGGT
663718 TTCCAGCGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
9 14 0.36
10 16 0.41
11 9 0.23
ACGTcount: A:0.35, C:0.27, G:0.22, T:0.16
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:663703 original size:20 final size:19
Alignment explanation
Indices: 663663--663718 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
663653 ACGGGTCGTG
*
663663 ACCGGTC-AAACCGGTCAAA
1 ACCGGTCAAAACCGGT-TAA
*
663682 ACCGGTTCAAAACTGGTTAA
1 ACCGG-TCAAAACCGGTTAA
663702 ACCGGTCAAAACCGGTT
1 ACCGGTCAAAACCGGTT
663719 TCCAGCGTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 16 0.50
20 9 0.28
21 7 0.22
ACGTcount: A:0.34, C:0.27, G:0.21, T:0.18
Consensus pattern (19 bp):
ACCGGTCAAAACCGGTTAA
Found at i:665281 original size:9 final size:9
Alignment explanation
Indices: 665267--665350 Score: 63
Period size: 9 Copynumber: 9.7 Consensus size: 9
665257 ATACGTATAC
*
665267 TATATAGTT
1 TATATACTT
665276 TATATA-TT
1 TATATACTT
*
665284 T-TATAGTT
1 TATATACTT
*
665292 TATATAATT
1 TATATACTT
665301 TATATACTT
1 TATATACTT
665310 ATATTTATACTT
1 -TA--TATACTT
*
665322 TAT-T-GTT
1 TATATACTT
665329 TATATAC-T
1 TATATACTT
665337 T-TATACTT
1 TATATACTT
665345 TATATA
1 TATATA
665351 TATATATAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
7 14 0.23
8 12 0.19
9 25 0.40
10 2 0.03
11 2 0.03
12 7 0.11
ACGTcount: A:0.33, C:0.05, G:0.04, T:0.58
Consensus pattern (9 bp):
TATATACTT
Found at i:665288 original size:16 final size:16
Alignment explanation
Indices: 665269--665351 Score: 76
Period size: 16 Copynumber: 4.9 Consensus size: 16
665259 ACGTATACTA
665269 TATAGTTTATATATTT
1 TATAGTTTATATATTT
665285 TATAGTTTATATAATTT
1 TATAGTTTATAT-ATTT
* *
665302 ATATACTTATATTTATACTT
1 -TATAGTT-TA--TATATTT
* *
665322 TATTGTTTATATACTT
1 TATAGTTTATATATTT
*
665338 TATACTTTATATAT
1 TATAGTTTATATAT
665352 ATATATAATA
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
16 30 0.55
17 4 0.07
18 8 0.15
19 7 0.13
20 3 0.05
21 3 0.05
ACGTcount: A:0.33, C:0.05, G:0.04, T:0.59
Consensus pattern (16 bp):
TATAGTTTATATATTT
Found at i:667399 original size:23 final size:24
Alignment explanation
Indices: 667365--667445 Score: 148
Period size: 23 Copynumber: 3.5 Consensus size: 24
667355 ATGCTTCATG
667365 GTATCGGTACCACTGTGTAAAGTA
1 GTATCGGTACCACTGTGTAAAGTA
667389 GTATC-GTACCACTGTGTAAAGTA
1 GTATCGGTACCACTGTGTAAAGTA
667412 GTATC-GTACCACTGTGTAAAGTA
1 GTATCGGTACCACTGTGTAAAGTA
667435 GTATCGGTACC
1 GTATCGGTACC
667446 TATTTTGTAT
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
23 46 0.82
24 10 0.18
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (24 bp):
GTATCGGTACCACTGTGTAAAGTA
Found at i:667796 original size:9 final size:9
Alignment explanation
Indices: 667751--667911 Score: 89
Period size: 9 Copynumber: 18.7 Consensus size: 9
667741 TAGTTCAACA
*
667751 TATACACTT
1 TATATACTT
667760 ATATATAC-T
1 -TATATACTT
667769 TATATAC--
1 TATATACTT
667776 T-TATAC--
1 TATATACTT
*
667782 TATATAGTT
1 TATATACTT
667791 TATATA-TT
1 TATATACTT
*
667799 T-TATAGTT
1 TATATACTT
*
667807 TATATAATT
1 TATATACTT
667816 TATATACTT
1 TATATACTT
667825 ATATTTATACTT
1 -TA--TATACTT
*
667837 TAT-T-GTT
1 TATATACTT
667844 TATATAC-T
1 TATATACTT
667852 T-TATACTT
1 TATATACTT
*
667860 TATATAATT
1 TATATACTT
667869 TATATACTT
1 TATATACTT
*
667878 ATATCTATACTG
1 -TA--TATACTT
*
667890 TAT-T-GTT
1 TATATACTT
667897 TATATACTT
1 TATATACTT
667906 TATATA
1 TATATA
667912 TATATATATA
Statistics
Matches: 122, Mismatches: 12, Indels: 35
0.72 0.07 0.21
Matches are distributed among these distances:
6 6 0.05
7 23 0.19
8 21 0.17
9 45 0.37
10 10 0.08
11 4 0.03
12 13 0.11
ACGTcount: A:0.34, C:0.08, G:0.03, T:0.55
Consensus pattern (9 bp):
TATATACTT
Found at i:667796 original size:16 final size:16
Alignment explanation
Indices: 667777--667923 Score: 64
Period size: 16 Copynumber: 8.7 Consensus size: 16
667767 CTTATATACT
667777 TATACTATATAGTTTA
1 TATACTATATAGTTTA
* *
667793 TATATTTTATAGTTTA
1 TATACTATATAGTTTA
* *
667809 TATAATTTATATACTTATA
1 TAT-A-CTATATAGTT-TA
* *
667828 TTTATACTTTATTGTTTA
1 --TATACTATATAGTTTA
* *
667846 TATACTTTATACTTTA
1 TATACTATATAGTTTA
* *
667862 TATAATTTATATACTTATA
1 TAT-A-CTATATAGTT-TA
* *
667881 TCTATACTGTATTGTTTA
1 --TATACTATATAGTTTA
* *
667899 TATACTTTATA-TATA
1 TATACTATATAGTTTA
667914 TATA-TATATA
1 TATACTATATA
667924 TAAGTATAAT
Statistics
Matches: 101, Mismatches: 20, Indels: 22
0.71 0.14 0.15
Matches are distributed among these distances:
14 5 0.05
15 7 0.07
16 43 0.43
17 2 0.02
18 20 0.20
19 16 0.16
20 2 0.02
21 6 0.06
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.56
Consensus pattern (16 bp):
TATACTATATAGTTTA
Found at i:667846 original size:53 final size:52
Alignment explanation
Indices: 667761--667925 Score: 224
Period size: 53 Copynumber: 3.1 Consensus size: 52
667751 TATACACTTA
* *
667761 TATATACTTATATACTTATACTATATAGTTTATATATTTTATAGTTTATATAATT
1 TATATACTTATAT--TTATACTATATTGTTTATATACTTTATA-TTTATATAATT
*
667816 TATATACTTATATTTATACTTTATTGTTTATATACTTTATACTTTATATAATT
1 TATATACTTATATTTATACTATATTGTTTATATACTTTATA-TTTATATAATT
* * * *
667869 TATATACTTATATCTATACTGTATTGTTTATATACTTTATATATATAT-ATA
1 TATATACTTATATTTATACTATATTGTTTATATACTTTATATTTATATAATT
667920 TATATA
1 TATATA
667926 AGTATAATAT
Statistics
Matches: 102, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 8 0.08
52 6 0.06
53 75 0.74
55 13 0.13
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (52 bp):
TATATACTTATATTTATACTATATTGTTTATATACTTTATATTTATATAATT
Found at i:673143 original size:14 final size:15
Alignment explanation
Indices: 673124--673153 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
673114 CCAAAGTCCA
673124 ATCATAACAAA-AAT
1 ATCATAACAAACAAT
673138 ATCATAACAAACAAT
1 ATCATAACAAACAAT
673153 A
1 A
673154 ATAGGACTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.63, C:0.17, G:0.00, T:0.20
Consensus pattern (15 bp):
ATCATAACAAACAAT
Found at i:673700 original size:10 final size:10
Alignment explanation
Indices: 673685--673721 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
673675 TTTGCCTGCT
673685 AGAGAGAAAG
1 AGAGAGAAAG
673695 AGAGAGAAAG
1 AGAGAGAAAG
673705 -G-GAGAAAG
1 AGAGAGAAAG
673713 AGAGAGAAA
1 AGAGAGAAA
673722 ATTCTCTCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 7 0.28
9 2 0.08
10 16 0.64
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (10 bp):
AGAGAGAAAG
Found at i:674509 original size:3 final size:3
Alignment explanation
Indices: 674475--674534 Score: 66
Period size: 3 Copynumber: 20.0 Consensus size: 3
674465 TGTAATTAAT
* * * * * *
674475 TAA TAT TAA TAA AAA TAA CAA CAA CAA CAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
674523 TAA TAA TAA TAA
1 TAA TAA TAA TAA
674535 ATTAAAATAA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (3 bp):
TAA
Found at i:674945 original size:134 final size:134
Alignment explanation
Indices: 674723--675085 Score: 476
Period size: 134 Copynumber: 2.7 Consensus size: 134
674713 GAAGAGTTCA
* * * * ** * **
674723 GGTTGTCTAAGGGCGACACAGCTCCTACGTGATGAGGAAATCTGGTTAAG-GGATGGCAATGCTC
1 GGTTATCTAAGGGTGACACGGCTCCTACGTGATGAGGAGATCTGG-TCGGTGGATGACACGGCTC
* *
674787 ATACGTGATGAAGAGTTCTGGTCATCTTTAGGAAGGGTGATAACTCAGTTCCTACGCGATGAGGA
65 ATACGTGATGAAGAGTTCTGGTCATCTTTAGGAAGGGCGATAACACAGTTCCTACGCGATGAGGA
* *
674852 TGGCT
130 CGACT
* *
674857 GGTTATCTAGGGGTGACACGGCTCCTACGTGATGAAGAGATCTGGTCGGTGGATGACACGGCTCA
1 GGTTATCTAAGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACACGGCTCA
* *
674922 TACGTGATGAAGAGTTCTGGTCATCTTTAGGAAGGGCGATAACACGGTTCCTACGTGATGAGGAC
66 TACGTGATGAAGAGTTCTGGTCATCTTTAGGAAGGGCGATAACACAGTTCCTACGCGATGAGGAC
674987 GACT
131 GACT
* * * * * * *
674991 AGTTATCTATGGTTGACACGGCTCCTACATGATGAGGAGGTATGTTCGGTGGATGACACGGCTCA
1 GGTTATCTAAGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACACGGCTCA
* *
675056 TACTTGATGAAGAGTTCTGGCCATCTTTAG
66 TACGTGATGAAGAGTTCTGGTCATCTTTAG
675086 TGATTATGGT
Statistics
Matches: 201, Mismatches: 27, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
133 2 0.01
134 199 0.99
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (134 bp):
GGTTATCTAAGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACACGGCTCA
TACGTGATGAAGAGTTCTGGTCATCTTTAGGAAGGGCGATAACACAGTTCCTACGCGATGAGGAC
GACT
Found at i:675329 original size:32 final size:34
Alignment explanation
Indices: 675282--675413 Score: 117
Period size: 38 Copynumber: 3.8 Consensus size: 34
675272 CAAAGATCGG
*
675282 TGTTTCGAGAGAAACAAACTCAAAGATG-T-TTT
1 TGTTTCAAGAGAAACAAACTCAAAGATGTTGTTT
* *
675314 TGTTTCAAGAAAAACATACTCAAAGATTTTGTTTGTTT
1 TGTTTCAAGAGAAACAAACTCAAAGA---TG-TTGTTT
* **
675352 TGTTTCAAGGGAAACAAACTCAAAGATGGTAAATTT
1 TGTTTCAAGAGAAACAAACTCAAAGAT-GT-TGTTT
*
675388 TGTTTCCAA-AGAAACAGACTCAAAGA
1 TGTTT-CAAGAGAAACAAACTCAAAGA
675414 ATTTTCTCAA
Statistics
Matches: 81, Mismatches: 10, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
32 23 0.28
35 4 0.05
36 24 0.30
37 4 0.05
38 26 0.32
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (34 bp):
TGTTTCAAGAGAAACAAACTCAAAGATGTTGTTT
Found at i:675767 original size:31 final size:31
Alignment explanation
Indices: 675685--675759 Score: 91
Period size: 31 Copynumber: 2.4 Consensus size: 31
675675 GTCAAATTCG
*
675685 TTTCAAGGGAAAC-GACTCAAAGATGGTTTTA
1 TTTCAAGGGAAACAAACTCAAAGAT-GTTTTA
675716 TTTCAAGGGAAACAAACTCAAAGAT-TTTGTA
1 TTTCAAGGGAAACAAACTCAAAGATGTTT-TA
* *
675747 TTTCTAGTGAAAC
1 TTTCAAGGGAAAC
675760 TATCTCAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
30 3 0.08
31 26 0.67
32 10 0.26
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (31 bp):
TTTCAAGGGAAACAAACTCAAAGATGTTTTA
Found at i:675941 original size:62 final size:61
Alignment explanation
Indices: 675883--676000 Score: 141
Period size: 61 Copynumber: 1.9 Consensus size: 61
675873 TGTTTCAAGT
*
675883 GAAACAGACTCACAAATAGC-AAATGTTGTT-TCCAAAGAAACAGACTCAAAGATTTTTCAAAA
1 GAAACAGACTCA-AAAGA-CAAAATGTTGTTAT-CAAAGAAACAGACTCAAAGATTTTTCAAAA
*** * *
675945 GAAACTTTCTCAAAAGACAAAATTTTGTTATCAAAGAAACATACTCAAAGATTTTT
1 GAAACAGACTCAAAAGACAAAATGTTGTTATCAAAGAAACAGACTCAAAGATTTTT
676001 TTCATTTTGT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
60 1 0.02
61 37 0.77
62 10 0.21
ACGTcount: A:0.46, C:0.16, G:0.11, T:0.27
Consensus pattern (61 bp):
GAAACAGACTCAAAAGACAAAATGTTGTTATCAAAGAAACAGACTCAAAGATTTTTCAAAA
Found at i:676140 original size:36 final size:36
Alignment explanation
Indices: 676100--676195 Score: 111
Period size: 36 Copynumber: 2.6 Consensus size: 36
676090 ATAATTTGGA
*
676100 AAATTGTCTCAAGTGAGACAACATTTGTTTTTAGAG
1 AAATTGTCTCAAGTGAGACAACAATTGTTTTTAGAG
* ** *
676136 AAATTGTTTCAAACGAGACAAAAATTGTTTTTAGAG
1 AAATTGTCTCAAGTGAGACAACAATTGTTTTTAGAG
**
676172 AAAACGATCTCAAGTGAGATCAAC
1 AAATTG-TCTCAAGTGAGA-CAAC
676196 TTTATTTAAT
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
36 35 0.74
37 9 0.19
38 3 0.06
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (36 bp):
AAATTGTCTCAAGTGAGACAACAATTGTTTTTAGAG
Found at i:676328 original size:35 final size:36
Alignment explanation
Indices: 676237--676344 Score: 130
Period size: 35 Copynumber: 3.0 Consensus size: 36
676227 TATCTCAAAG
* * * *
676237 GAAAAGTGTCTCAAGTGAGACGAAATTTTTTTTTTCA
1 GAAAATTGTCTCAAGCGAGAC-AAAATTTGTTTTTCA
* *
676274 -AGAAATTGTCTAAAACGAGACAAAATTTGTTTTT-A
1 GA-AAATTGTCTCAAGCGAGACAAAATTTGTTTTTCA
676309 GAAAATTGTCTCAAGCGAGACAAAATTTGTTTTTCA
1 GAAAATTGTCTCAAGCGAGACAAAATTTGTTTTTCA
676345 AAAGAAGTTG
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
35 31 0.52
36 14 0.23
37 15 0.25
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (36 bp):
GAAAATTGTCTCAAGCGAGACAAAATTTGTTTTTCA
Found at i:679141 original size:51 final size:52
Alignment explanation
Indices: 679062--679176 Score: 178
Period size: 51 Copynumber: 2.2 Consensus size: 52
679052 GTTTCTAAGG
*
679062 CCCCGTTTGGTTCAAGGAATGTTATATTACCGGGAGAATGAAATCCTTA-TT
1 CCCCGTTTGGTTCAAGGAATGTTATATTACCGGGAGAATGAAATCCTCATTT
* * *
679113 CCCCGTTTGGTTCAAGGAATGTTGTATTATCGGGGGAATGAAATCCTCATTT
1 CCCCGTTTGGTTCAAGGAATGTTATATTACCGGGAGAATGAAATCCTCATTT
*
679165 CCCTGTTTGGTT
1 CCCCGTTTGGTT
679177 GGCCGGTAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
51 45 0.78
52 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (52 bp):
CCCCGTTTGGTTCAAGGAATGTTATATTACCGGGAGAATGAAATCCTCATTT
Found at i:679960 original size:25 final size:26
Alignment explanation
Indices: 679932--679980 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
679922 ACTTTTTGTC
*
679932 CAACACTTTTCAAAGTTCA-TTTCTA
1 CAACACTTTTAAAAGTTCACTTTCTA
679957 CAACACTTTTAAAAGTTCACTTTC
1 CAACACTTTTAAAAGTTCACTTTC
679981 AAAAACTATG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.39
Consensus pattern (26 bp):
CAACACTTTTAAAAGTTCACTTTCTA
Found at i:681096 original size:13 final size:13
Alignment explanation
Indices: 681080--681106 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
681070 ACAGATTCAT
681080 AAAATGAAAGAAA
1 AAAATGAAAGAAA
681093 AAAATGAAAGAAA
1 AAAATGAAAGAAA
681106 A
1 A
681107 GTGGTGTTAT
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:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (13 bp):
AAAATGAAAGAAA
Found at i:686590 original size:2 final size:2
Alignment explanation
Indices: 686583--687070 Score: 191
Period size: 2 Copynumber: 247.5 Consensus size: 2
686573 GATTTGTTAC
686583 AT AT 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 AT AT
* * *
686625 AT AT ACT -T AT AT AT GT ACT -T AT GT AT AT ACT -T AT AT AT GT
1 AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT
** * * * * *
686665 ACT -T GG AT AT AT AC ACT -T AT GT CT AT ACT -T TT GT AT AT AT
1 A-T AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT
* * * * * *
686705 AC AT AT AT GT AC AT AC AT CAC AT AT AT AT ACT -T AT AT AT AT AC
1 AT AT AT AT AT AT AT AT AT -AT AT AT AT AT A-T AT AT AT AT AT AT
* * * * * * * *
686748 AT AC AT AT AT AT AC AT GT AT A- AC AT AT ACG AC AT AC AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
* * * * * *
686790 A- AT AT AT AT AT AT AT AT AT AC AT GT AT A- AG AT AT AG AC AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * **
686830 AC AC AC AT A- AGT AT AT AC AT GC AT A- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
686871 AT AT AT AT AT AT AT AT AT AT AT ACT -T AT AT AT -T AT AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
* *
686912 ACT -T AT AT AT ACT -T AT ACT AT AT AT -T TT AT AT ACT TT AT AGT
1 A-T AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT A-T AT AT A-T
* * * *
686954 TT AT AT A- AT TT AT AT AT TT AT ACT TT AT AT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
* * * *
686995 AT AT A- AGT AT A- AT AT AT AT AT AT AT AT AC AC AT GT GT CAT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
*
687037 -T AT AT -T AT -T AT AT A- AT AT AT AT AC AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
687071 ATTATTTCAA
Statistics
Matches: 368, Mismatches: 73, Indels: 90
0.69 0.14 0.17
Matches are distributed among these distances:
1 26 0.07
2 324 0.88
3 18 0.05
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.44
Consensus pattern (2 bp):
AT
Found at i:686805 original size:49 final size:48
Alignment explanation
Indices: 686737--686846 Score: 148
Period size: 49 Copynumber: 2.2 Consensus size: 48
686727 TATATATACT
* *
686737 TATATATATACATACATATATATACATGTATAACATATACGACATACACA
1 TATA-ATATATATACATATATATACATGTATAACATATA-GACACACACA
* *
686787 TATAATATATATATATATATATACATGTATAAGATATAGACACACACA
1 TATAATATATATACATATATATACATGTATAACATATAGACACACACA
*
686835 CATAAGTATATA
1 TATAA-TATATA
686847 CATGCATAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
48 13 0.24
49 37 0.69
50 4 0.07
ACGTcount: A:0.49, C:0.13, G:0.05, T:0.33
Consensus pattern (48 bp):
TATAATATATATACATATATATACATGTATAACATATAGACACACACA
Found at i:686958 original size:25 final size:24
Alignment explanation
Indices: 686917--686994 Score: 88
Period size: 25 Copynumber: 3.2 Consensus size: 24
686907 TATACACTTA
*
686917 TATATACTTATAC--TATATATTT
1 TATATATTTATACTTTATATATTT
* *
686939 TATATACTTTATAGTTTATATAATT
1 TATATA-TTTATACTTTATATATTT
*
686964 TATATATTTATACTTTATATATATA
1 TATATATTTATACTTTATATAT-TT
686989 TATATA
1 TATATA
686995 ATATAAGTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
22 6 0.13
23 5 0.11
24 14 0.30
25 21 0.46
ACGTcount: A:0.38, C:0.05, G:0.01, T:0.55
Consensus pattern (24 bp):
TATATATTTATACTTTATATATTT
Found at i:689660 original size:20 final size:20
Alignment explanation
Indices: 689635--689677 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
689625 CCATTATTCC
* *
689635 ATAACCATATACCATAGACA
1 ATAACCATAAACAATAGACA
*
689655 ATAACCATAAATAATAGACA
1 ATAACCATAAACAATAGACA
689675 ATA
1 ATA
689678 GCCCAATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.56, C:0.19, G:0.05, T:0.21
Consensus pattern (20 bp):
ATAACCATAAACAATAGACA
Found at i:692442 original size:45 final size:45
Alignment explanation
Indices: 692378--692469 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
692368 CCATACTTAT
692378 TTAATTTTAAAAGATTTTATTTTCTTTATAGGACATGTATGTTCC
1 TTAATTTTAAAAGATTTTATTTTCTTTATAGGACATGTATGTTCC
692423 TTAATTTTAAAAGATTTTATTTTCTTTATAGGACATGTATGTTCC
1 TTAATTTTAAAAGATTTTATTTTCTTTATAGGACATGTATGTTCC
692468 TT
1 TT
692470 GTGACCATGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.28, C:0.09, G:0.11, T:0.52
Consensus pattern (45 bp):
TTAATTTTAAAAGATTTTATTTTCTTTATAGGACATGTATGTTCC
Found at i:694698 original size:20 final size:20
Alignment explanation
Indices: 694673--694710 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
694663 TTATTGTTCT
694673 TATAGTATCGGTACTATTTA
1 TATAGTATCGGTACTATTTA
694693 TATAGTATCGGTACTATT
1 TATAGTATCGGTACTATT
694711 CATCCAATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.45
Consensus pattern (20 bp):
TATAGTATCGGTACTATTTA
Found at i:697458 original size:20 final size:20
Alignment explanation
Indices: 697433--697479 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
697423 TACTGTTCGT
*
697433 TACTATTCACACATTATC-G
1 TACTATTCACACAATATCAG
*
697452 ATACTATTCATACAATATCAG
1 -TACTATTCACACAATATCAG
697473 TACTATT
1 TACTATT
697480 TGTTGTTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.36, C:0.21, G:0.04, T:0.38
Consensus pattern (20 bp):
TACTATTCACACAATATCAG
Found at i:697476 original size:50 final size:50
Alignment explanation
Indices: 697418--697530 Score: 147
Period size: 50 Copynumber: 2.3 Consensus size: 50
697408 TTTTTTGAGC
*
697418 ATCAGTACTGTTCGTTACTATTCACACATTATCGATACTATTCATACAAT
1 ATCAGTACTATTCGTTACTATTCACACATTATCGATACTATTCATACAAT
* ** * * *
697468 ATCAGTACTATTTGTTGTTGTTCACACATTATCGGTACTATTCATACAGT
1 ATCAGTACTATTCGTTACTATTCACACATTATCGATACTATTCATACAAT
*
697518 A-CAATACTATTCG
1 ATCAGTACTATTCG
697531 CAAAAACATT
Statistics
Matches: 54, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
49 10 0.19
50 44 0.81
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (50 bp):
ATCAGTACTATTCGTTACTATTCACACATTATCGATACTATTCATACAAT
Found at i:698032 original size:9 final size:9
Alignment explanation
Indices: 698010--698076 Score: 57
Period size: 9 Copynumber: 7.2 Consensus size: 9
698000 TATATATACT
698010 TATACTTATA
1 TATACTT-TA
*
698020 TATAGTTTA
1 TATACTTTA
*
698029 TATAATTTA
1 TATACTTTA
698038 TATACTTATA
1 TATACTT-TA
698048 TTTATACTTTA
1 --TATACTTTA
*
698059 T-T-GTTTA
1 TATACTTTA
698066 TATACTTTA
1 TATACTTTA
698075 TA
1 TA
698077 CTATATTATA
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
7 5 0.11
8 2 0.04
9 23 0.49
10 8 0.17
11 2 0.04
12 7 0.15
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.57
Consensus pattern (9 bp):
TATACTTTA
Found at i:698074 original size:23 final size:22
Alignment explanation
Indices: 698016--698093 Score: 70
Period size: 23 Copynumber: 3.4 Consensus size: 22
698006 TACTTATACT
698016 TATATATAGTTTATA-TA-ATTTA
1 TATATATA-TTTATACTATA-TTA
* *
698038 TATACTTATATTTATACTTTATTG
1 TATA--TATATTTATACTATATTA
*
698062 TTTATATACTTTATACTATATTA
1 TATATATA-TTTATACTATATTA
698085 TATATATAT
1 TATATATAT
698094 ATAAATACAT
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
22 9 0.20
23 25 0.56
24 10 0.22
25 1 0.02
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (22 bp):
TATATATATTTATACTATATTA
Found at i:698132 original size:18 final size:18
Alignment explanation
Indices: 698111--698145 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
698101 CATTATAACA
698111 TATATACATAT-TATATTT
1 TATATA-ATATATATATTT
698129 TATATAATATATATATT
1 TATATAATATATATATT
698146 ATAATTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
TATATAATATATATATTT
Found at i:700718 original size:42 final size:42
Alignment explanation
Indices: 700659--700743 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
700649 AAATCTCGCC
*
700659 GGTGTGGGATGCACTCTTAACTAGCTTGATTTCCAAAGCTCT
1 GGTGTGCGATGCACTCTTAACTAGCTTGATTTCCAAAGCTCT
*
700701 GGTGTGCGATGCACTCTTAACTAGCTTGATTTCCATAGCTCT
1 GGTGTGCGATGCACTCTTAACTAGCTTGATTTCCAAAGCTCT
700743 G
1 G
700744 TTCGTTTCCC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.34
Consensus pattern (42 bp):
GGTGTGCGATGCACTCTTAACTAGCTTGATTTCCAAAGCTCT
Found at i:701264 original size:13 final size:16
Alignment explanation
Indices: 701228--701259 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
701218 TTATGAAACA
701228 AAAC-TAAATAATAAT
1 AAACTTAAATAATAAT
701243 AAACTTAAATAA-AAT
1 AAACTTAAATAATAAT
701258 AA
1 AA
701260 TTAAAATAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (16 bp):
AAACTTAAATAATAAT
Found at i:702997 original size:32 final size:31
Alignment explanation
Indices: 702961--703036 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
702951 GGGGCCGTGA
*
702961 GGCCTACCTAAGAACACATCTTAGGGCCGCAG
1 GGCCTACCTAAGAA-ACATCTCAGGGCCGCAG
** **
702993 GGCCTACCCGAGAATGATCTCAGGGCCGCAG
1 GGCCTACCTAAGAAACATCTCAGGGCCGCAG
* *
703024 AGACTACCTAAGA
1 GGCCTACCTAAGA
703037 GTTACATTAG
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.66
32 12 0.34
ACGTcount: A:0.29, C:0.30, G:0.26, T:0.14
Consensus pattern (31 bp):
GGCCTACCTAAGAAACATCTCAGGGCCGCAG
Found at i:706384 original size:3 final size:3
Alignment explanation
Indices: 706376--706402 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
706366 TTTTCTCACA
706376 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
706403 GTTGTTGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:709375 original size:13 final size:13
Alignment explanation
Indices: 709357--709389 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
709347 TTGACTCTTA
709357 ATGAGAAAGTACC
1 ATGAGAAAGTACC
709370 ATGAGAAAGTACC
1 ATGAGAAAGTACC
709383 ATGAGAA
1 ATGAGAA
709390 TTCGTACCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.48, C:0.12, G:0.24, T:0.15
Consensus pattern (13 bp):
ATGAGAAAGTACC
Found at i:711088 original size:15 final size:15
Alignment explanation
Indices: 711068--711097 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
711058 ATGTTTTGAA
711068 TTTTAAAAAATATGT
1 TTTTAAAAAATATGT
*
711083 TTTTAAAATATATGT
1 TTTTAAAAAATATGT
711098 ATCTTTAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (15 bp):
TTTTAAAAAATATGT
Found at i:714817 original size:26 final size:26
Alignment explanation
Indices: 714788--714844 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
714778 GATTCATGTT
*
714788 TCTCTGCCTGATAAAATTCTCCAGTA
1 TCTCTGCCTGATAAAATTATCCAGTA
*
714814 TCTCTGCCTGATAAGATTATCCAGTA
1 TCTCTGCCTGATAAAATTATCCAGTA
714840 TCTCT
1 TCTCT
714845 TAATAATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.25, C:0.26, G:0.12, T:0.37
Consensus pattern (26 bp):
TCTCTGCCTGATAAAATTATCCAGTA
Found at i:715444 original size:12 final size:12
Alignment explanation
Indices: 715427--715467 Score: 82
Period size: 12 Copynumber: 3.4 Consensus size: 12
715417 CTTCCCAAAG
715427 CTCACTCTGTTA
1 CTCACTCTGTTA
715439 CTCACTCTGTTA
1 CTCACTCTGTTA
715451 CTCACTCTGTTA
1 CTCACTCTGTTA
715463 CTCAC
1 CTCAC
715468 CTTTTCAGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.17, C:0.37, G:0.07, T:0.39
Consensus pattern (12 bp):
CTCACTCTGTTA
Found at i:717094 original size:13 final size:13
Alignment explanation
Indices: 717078--717102 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
717068 CAAATTCATA
717078 AAATGAAAGAAAT
1 AAATGAAAGAAAT
717091 AAATGAAAGAAA
1 AAATGAAAGAAA
717103 AGTGATGTTA
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:0.16, T:0.12
Consensus pattern (13 bp):
AAATGAAAGAAAT
Found at i:717230 original size:14 final size:15
Alignment explanation
Indices: 717205--717236 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
717195 TATTTAGCTC
717205 TTTATCCCCCATAGG
1 TTTATCCCCCATAGG
717220 TTTAT-CCCCATAGG
1 TTTATCCCCCATAGG
717234 TTT
1 TTT
717237 TCATCACACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.19, C:0.28, G:0.12, T:0.41
Consensus pattern (15 bp):
TTTATCCCCCATAGG
Found at i:718171 original size:6 final size:5
Alignment explanation
Indices: 718162--718204 Score: 50
Period size: 6 Copynumber: 7.8 Consensus size: 5
718152 ATTAATACTT
718162 TATATA TATAA TATAA GTATAA TATAA TTATAA TATATA TATA
1 TATA-A TATAA TATAA -TATAA TATAA -TATAA TATA-A TATA
718205 TATGTGTGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
5 15 0.44
6 19 0.56
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (5 bp):
TATAA
Found at i:718204 original size:11 final size:11
Alignment explanation
Indices: 718168--718198 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
718158 ACTTTATATA
718168 TATAATATAAG
1 TATAATATAAG
*
718179 TATAATATAAT
1 TATAATATAAG
718190 TATAATATA
1 TATAATATA
718199 TATATATATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (11 bp):
TATAATATAAG
Found at i:720788 original size:18 final size:18
Alignment explanation
Indices: 720765--720801 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
720755 CATTATTCAT
* *
720765 AACCATATACCATAGACA
1 AACCATAAACAATAGACA
720783 AACCATAAACAATAGACA
1 AACCATAAACAATAGACA
720801 A
1 A
720802 TAGCCCAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.24, G:0.05, T:0.14
Consensus pattern (18 bp):
AACCATAAACAATAGACA
Found at i:724369 original size:20 final size:20
Alignment explanation
Indices: 724329--724370 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
724319 GTTCATATAG
*
724329 TATCGGTACTATTTATACAA
1 TATCGGTACTATTCATACAA
*
724349 TATCGGTACTATTCATCCAA
1 TATCGGTACTATTCATACAA
724369 TA
1 TA
724371 CAATATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (20 bp):
TATCGGTACTATTCATACAA
Found at i:727113 original size:20 final size:20
Alignment explanation
Indices: 727085--727132 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
727075 TACTGTTCGT
* *
727085 TACTGTTCACACATTATCCA-
1 TACTATTCACACAATAT-CAG
*
727105 TACTATTCATACAATATCAG
1 TACTATTCACACAATATCAG
727125 TACTATTC
1 TACTATTC
727133 GTTGTTGTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.38
Consensus pattern (20 bp):
TACTATTCACACAATATCAG
Found at i:727145 original size:50 final size:50
Alignment explanation
Indices: 727070--727182 Score: 158
Period size: 50 Copynumber: 2.3 Consensus size: 50
727060 TTTTTTGAGC
*
727070 ATCAGTACTGTTCGTTACTGTTCACACATTATCCA-TACTATTCATACAAT
1 ATCAGTACTATTCGTTACTGTTCACACATTAT-CAGTACTATTCATACAAT
** *
727120 ATCAGTACTATTCGTTGTTGTTCACACATTATCAGTACTATTCATACAGT
1 ATCAGTACTATTCGTTACTGTTCACACATTATCAGTACTATTCATACAAT
*
727170 A-CAATACTATTCG
1 ATCAGTACTATTCG
727183 CAAAAACATT
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
49 13 0.23
50 44 0.77
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.38
Consensus pattern (50 bp):
ATCAGTACTATTCGTTACTGTTCACACATTATCAGTACTATTCATACAAT
Found at i:727662 original size:14 final size:14
Alignment explanation
Indices: 727643--727723 Score: 51
Period size: 14 Copynumber: 5.6 Consensus size: 14
727633 TTCAACATAC
727643 ACTTATATACTTAT
1 ACTTATATACTTAT
*
727657 ACTTATATATAGTTTATAT
1 AC-T-TATATA--CT-TAT
*
727676 AATTTATATACTTAT
1 ACT-TATATACTTAT
727691 A-TT-TATACTTAT
1 ACTTATATACTTAT
**
727703 TGTTATATACTTAT
1 ACTTATATACTTAT
727717 AC-TATAT
1 ACTTATAT
727724 TATTATATAT
Statistics
Matches: 53, Mismatches: 7, Indels: 15
0.71 0.09 0.20
Matches are distributed among these distances:
12 9 0.17
13 8 0.15
14 12 0.23
15 5 0.09
16 7 0.13
18 8 0.15
19 4 0.08
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.53
Consensus pattern (14 bp):
ACTTATATACTTAT
Found at i:727734 original size:2 final size:2
Alignment explanation
Indices: 727714--727752 Score: 55
Period size: 2 Copynumber: 20.0 Consensus size: 2
727704 GTTATATACT
727714 TA TA CTA TA T- TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
727753 CATTATAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 2 0.06
2 30 0.88
3 2 0.06
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:730359 original size:40 final size:41
Alignment explanation
Indices: 730304--730383 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 41
730294 AAATCTCGCC
*
730304 GGTGTGGGATGCACTCTTAACTAGCTTGATTTCCA-AGCTT
1 GGTGTGCGATGCACTCTTAACTAGCTTGATTTCCATAGCTT
730344 GGTGTGCGATGCACTCTTAACTAGCTTGATTTCCATAGCT
1 GGTGTGCGATGCACTCTTAACTAGCTTGATTTCCATAGCT
730384 CTGTTCGTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 34 0.89
41 4 0.11
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.35
Consensus pattern (41 bp):
GGTGTGCGATGCACTCTTAACTAGCTTGATTTCCATAGCTT
Found at i:732681 original size:13 final size:16
Alignment explanation
Indices: 732645--732676 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
732635 ATTATGAACA
732645 AAAC-TAAATAATAAT
1 AAACTTAAATAATAAT
732660 AAACTTAAATAA-AAT
1 AAACTTAAATAATAAT
732675 AA
1 AA
732677 TTAAAATAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (16 bp):
AAACTTAAATAATAAT
Found at i:738274 original size:3 final size:3
Alignment explanation
Indices: 738266--738292 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
738256 TTTTCTCACA
738266 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
738293 GTTGTTGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:745409 original size:12 final size:12
Alignment explanation
Indices: 745392--745420 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
745382 CTTCCCAAAG
745392 CTCACTCTGTTA
1 CTCACTCTGTTA
745404 CTCACTCTGTTA
1 CTCACTCTGTTA
745416 CTCAC
1 CTCAC
745421 CTTTTCAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.38, G:0.07, T:0.38
Consensus pattern (12 bp):
CTCACTCTGTTA
Found at i:747200 original size:14 final size:14
Alignment explanation
Indices: 747181--747210 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
747171 TTTAGCTCTT
747181 TTATCCCCCATAGG
1 TTATCCCCCATAGG
747195 TTATCCCCCATAGG
1 TTATCCCCCATAGG
747209 TT
1 TT
747211 TTCATCACAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.33
Consensus pattern (14 bp):
TTATCCCCCATAGG
Found at i:748336 original size:370 final size:366
Alignment explanation
Indices: 747639--748392 Score: 1154
Period size: 370 Copynumber: 2.0 Consensus size: 366
747629 ACCTCTTCAT
*
747639 AAGAAAAGGTAAGAGTTCTATGCCTTTGGTATACCTCTTCATATAATCAATCGTCCATGTATGAT
1 AAGAAAAGGTAAGAGTTCTATGCCTTTGGTATACCTCTTCATATAATCAATCATCCATGTATGAT
*
747704 TGTATATAAAGGAAATGGTCTTTTTACTTGGTCTATACATTTTTTGCACATTTGTATAAAAATTA
66 TGTATATAAAGGAAATGGTCTTTTTACTTGGTCTATACATTTTTCGCACATTTGTATAAAAATTA
747769 ATTAATAATATATAAAAATATTATTATTATTTTATCAGTTTACTTATTATATAAAATAGAAAAAG
131 ATTAATAATATATAAAAATATTATTATTATTTTATCAGTTTACTTATTATATAAAATAGAAAAAG
747834 CACCACGGAAGAAAGAATCCACATGGAGAAGCAATAACAAGTATTTGGCATTTATATGTTGCTAA
196 CACCACGGAAGAAAGAATCCACATGGAGAAGCAATAACAAGTATTTGGCATTTATATGTTGCTAA
**
747899 CCCCAAAATTATAATATGATATATACACTTATGTCTACTTTTGTATATAACATATATGTACATAC
261 CCCCAAAATTATAATATGATATATACACTTATGTCTACTACTGTATAT-A-ATATA-GTA-ATAC
747964 ATAACATATGTACTTTTATATATACATACACATATACATGTATCA
322 ATAACATATGTACTTTTATATATACATACACATATACATGTATCA
748009 AAGAAAAGGTAAGAGTTCTATGCCTTTGGTATACCTCTTCATATAATCAATCATCCATGTATGAT
1 AAGAAAAGGTAAGAGTTCTATGCCTTTGGTATACCTCTTCATATAATCAATCATCCATGTATGAT
* * * *
748074 TGTATAT-AAGGAAGTGGTATTTTTTAGTTGGTCTAATACATTTTTCGCACATTTTTATAAAAAT
66 TGTATATAAAGGAAATGGT-CTTTTTACTTGGTCT-ATACATTTTTCGCACATTTGTATAAAAAT
748138 TAATTAATAATATATAAAAAAATATTATTATTATTATTTTATCAGTTTACTTATTTATATAAAAT
129 TAATTAATAATATAT---AAAA-A-TATTATTATTATTTTATCAGTTTACTTA-TTATATAAAAT
*
748203 AGAAAAAGCA-CATCGGAAGAAAGAATCCCACATGGAGAAGCAATAGCAAGTATTTGGCATTTAT
188 AGAAAAAGCACCA-CGGAAGAAAGAAT-CCACATGGAGAAGCAATAACAAGTATTTGGCA-TT-T
*
748267 ATATGTTGCTAACCCCAAAATTAATAATCTGATATATACACTTATGTCTA-TACTTTTGTATATA
249 ATATGTTGCTAACCCCAAAATT-ATAATATGATATATACACTTATGTCTACTAC---TG--TATA
748331 TACATATATGTACATACATAACATATGTACTTTTATATATACATACACATATATACATGTAT
308 TA-ATATA-GTA-ATACATAACATATGTACTTTTATATATACATACAC--ATATACATGTAT
748393 AACATTTATG
Statistics
Matches: 354, Mismatches: 10, Indels: 24
0.91 0.03 0.06
Matches are distributed among these distances:
369 10 0.03
370 84 0.24
371 42 0.12
374 4 0.01
375 1 0.00
376 30 0.08
377 34 0.10
378 31 0.09
379 2 0.01
380 24 0.07
381 26 0.07
383 2 0.01
384 47 0.13
385 5 0.01
386 12 0.03
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (366 bp):
AAGAAAAGGTAAGAGTTCTATGCCTTTGGTATACCTCTTCATATAATCAATCATCCATGTATGAT
TGTATATAAAGGAAATGGTCTTTTTACTTGGTCTATACATTTTTCGCACATTTGTATAAAAATTA
ATTAATAATATATAAAAATATTATTATTATTTTATCAGTTTACTTATTATATAAAATAGAAAAAG
CACCACGGAAGAAAGAATCCACATGGAGAAGCAATAACAAGTATTTGGCATTTATATGTTGCTAA
CCCCAAAATTATAATATGATATATACACTTATGTCTACTACTGTATATAATATAGTAATACATAA
CATATGTACTTTTATATATACATACACATATACATGTATCA
Found at i:748395 original size:43 final size:41
Alignment explanation
Indices: 748317--748397 Score: 99
Period size: 43 Copynumber: 1.9 Consensus size: 41
748307 CTTATGTCTA
* * *
748317 TACTTTTGTATATATACATATATGTACATACATAACATATG
1 TACTTTTATATATATACACATATATACATACATAACATATG
**
748358 TACTTTTATATATACATACACATATATACATGTATAACAT
1 TACTTTTATATAT--ATACACATATATACATACATAACAT
748398 TTATGATATA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
41 12 0.36
43 21 0.64
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.41
Consensus pattern (41 bp):
TACTTTTATATATATACACATATATACATACATAACATATG
Found at i:748423 original size:2 final size:2
Alignment explanation
Indices: 748411--748461 Score: 61
Period size: 2 Copynumber: 26.5 Consensus size: 2
748401 TGATATACAC
* *
748411 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT GT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
748451 AC AT AT AT AT A
1 AT AT AT AT AT A
748462 CACACACTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (2 bp):
AT
Found at i:748442 original size:57 final size:58
Alignment explanation
Indices: 748364--748501 Score: 160
Period size: 57 Copynumber: 2.4 Consensus size: 58
748354 TATGTACTTT
* * * * *
748364 TATATATACATACACATATATACATGTATAACATTTATGATATACACA-TATAA-TATA-
1 TATATATATATATATATATATACATGTATAACATATAT-ATACACACACT-TAAGTATAC
748421 TATATATATATATATATATATACATGTATAACATATATATACACACACTTAAGTATAC
1 TATATATATATATATATATATACATGTATAACATATATATACACACACTTAAGTATAC
748479 TGCATA-ATATAT-TATATATATAC
1 T--ATATATATATATATATATATAC
748502 TTATACTATA
Statistics
Matches: 71, Mismatches: 5, Indels: 9
0.84 0.06 0.11
Matches are distributed among these distances:
56 11 0.15
57 39 0.55
58 12 0.17
59 6 0.08
60 3 0.04
ACGTcount: A:0.46, C:0.12, G:0.04, T:0.38
Consensus pattern (58 bp):
TATATATATATATATATATATACATGTATAACATATATATACACACACTTAAGTATAC
Found at i:748524 original size:16 final size:16
Alignment explanation
Indices: 748503--748537 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
748493 TATATATACT
*
748503 TATACTATATATTTTA
1 TATACTATATAGTTTA
*
748519 TATACTTTATAGTTTA
1 TATACTATATAGTTTA
748535 TAT
1 TAT
748538 CATTCATACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.57
Consensus pattern (16 bp):
TATACTATATAGTTTA
Found at i:748567 original size:2 final size:2
Alignment explanation
Indices: 748560--748615 Score: 66
Period size: 2 Copynumber: 29.5 Consensus size: 2
748550 TATTAATACT
*
748560 TA TA TA TA TA TA -A TA TA -A GTA TA -A TA CA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
748599 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
748616 GTGTGTGTGT
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
1 4 0.09
2 42 0.89
3 1 0.02
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:748682 original size:17 final size:15
Alignment explanation
Indices: 748639--748682 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
748629 TGTGTGTGTC
748639 ATATTATATTATTAT
1 ATATTATATTATTAT
*
748654 ATAATATA-TATTCAT
1 ATATTATATTATT-AT
748669 ATATTATAATTATT
1 ATATTAT-ATTATT
748683 TCCATTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 4 0.17
15 15 0.62
16 1 0.04
17 4 0.17
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (15 bp):
ATATTATATTATTAT
Found at i:750979 original size:20 final size:20
Alignment explanation
Indices: 750954--750996 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
750944 CCATTATTCC
* *
750954 ATAACCATATACCATAGACA
1 ATAACCATAAACAATAGACA
750974 ATAACCATAAACAATAGACA
1 ATAACCATAAACAATAGACA
750994 ATA
1 ATA
750997 GCCCAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.56, C:0.21, G:0.05, T:0.19
Consensus pattern (20 bp):
ATAACCATAAACAATAGACA
Found at i:753043 original size:17 final size:18
Alignment explanation
Indices: 753021--753058 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
753011 TTTTGTCATT
753021 AAAT-AAATCCATTTATG
1 AAATAAAATCCATTTATG
* *
753038 AAATAAAATTCATTTGTG
1 AAATAAAATCCATTTATG
753056 AAA
1 AAA
753059 GAATCACCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.34
Consensus pattern (18 bp):
AAATAAAATCCATTTATG
Found at i:755890 original size:18 final size:18
Alignment explanation
Indices: 755867--755902 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
755857 TTATTGTTCA
*
755867 TATAGTATCGGTACTATT
1 TATAGTATCGATACTATT
755885 TATAGTATCGATACTATT
1 TATAGTATCGATACTATT
755903 CATCCAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.44
Consensus pattern (18 bp):
TATAGTATCGATACTATT
Found at i:758621 original size:34 final size:34
Alignment explanation
Indices: 758581--758645 Score: 130
Period size: 34 Copynumber: 1.9 Consensus size: 34
758571 CGTCACTAAC
758581 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGTA
758615 AGTAAGGCCCTGAGCACACAGCCGAGGAACC
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACC
758646 TCCAAGTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.32, C:0.31, G:0.29, T:0.08
Consensus pattern (34 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGTA
Found at i:758755 original size:24 final size:24
Alignment explanation
Indices: 758728--758817 Score: 121
Period size: 23 Copynumber: 3.8 Consensus size: 24
758718 CATAATTCAA
758728 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCATATCAGAATCCAG
* *
758752 GTCATGTATCATATCAGAATCCAT
1 GTCAAGTATCATATCAGAATCCAG
*
758776 GTCAA-TATCAGATCAGAATCCAG
1 GTCAAGTATCATATCAGAATCCAG
* *
758799 GTC-AGGATCATAACAGAAT
1 GTCAAGTATCATATCAGAAT
758818 TCAAGTCGGA
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
22 1 0.02
23 30 0.53
24 26 0.46
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.26
Consensus pattern (24 bp):
GTCAAGTATCATATCAGAATCCAG
Found at i:758835 original size:47 final size:47
Alignment explanation
Indices: 758711--758824 Score: 140
Period size: 47 Copynumber: 2.4 Consensus size: 47
758701 ATATATCAAA
* * * * *
758711 ATCAAAACATAATTCAAGTCAAGTATCATATCAGAATCCAGGTCATGT
1 ATCATAACAGAATCCAAGTCAA-TATCAGATCAGAATCCAGGTCATGG
* *
758759 ATCATATCAGAATCCATGTCAATATCAGATCAGAATCCAGGTCA-GG
1 ATCATAACAGAATCCAAGTCAATATCAGATCAGAATCCAGGTCATGG
*
758805 ATCATAACAGAATTCAAGTC
1 ATCATAACAGAATCCAAGTC
758825 GGAAATCAGA
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
46 18 0.32
47 21 0.38
48 17 0.30
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.25
Consensus pattern (47 bp):
ATCATAACAGAATCCAAGTCAATATCAGATCAGAATCCAGGTCATGG
Found at i:759461 original size:162 final size:163
Alignment explanation
Indices: 759187--759511 Score: 643
Period size: 162 Copynumber: 2.0 Consensus size: 163
759177 TCTAGGGTAT
759187 TTACTCTTTAATACCACAAATTCTTGTCCGTAGACCATTTTCGGAATTATCGCTGAATAAATCTT
1 TTACTCTTTAATACCACAAATTCTTGTCCGTAGACCATTTTCGGAATTATCGCTGAATAAATCTT
759252 CCAATGACTTTATTTCATTTCCACGCTTCCACAATATCATGAAATGTTGACGTACTTGATTAATT
66 CCAATGACTTTATTTCATTTCCACGCTTCCACAATATCATGAAATGTTGACGTACTTGATTAATT
759317 TGTTCATAACCCATTGTAATTGTACACTACGTA
131 TGTTCATAACCCATTGTAATTGTACACTACGTA
759350 TTACTC-TTAATACCACAAATTCTTGTCCGTAGACCATTTTCGGAATTATCGCTGAATAAATCTT
1 TTACTCTTTAATACCACAAATTCTTGTCCGTAGACCATTTTCGGAATTATCGCTGAATAAATCTT
759414 CCAATGACTTTATTTCATTTCCACGCTTCCACAATATCATGAAATGTTGACGTACTTGATTAATT
66 CCAATGACTTTATTTCATTTCCACGCTTCCACAATATCATGAAATGTTGACGTACTTGATTAATT
759479 TGTTCATAACCCATTGTAATTGTACACTACGTA
131 TGTTCATAACCCATTGTAATTGTACACTACGTA
759512 AACTCATCAG
Statistics
Matches: 162, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
162 156 0.96
163 6 0.04
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.38
Consensus pattern (163 bp):
TTACTCTTTAATACCACAAATTCTTGTCCGTAGACCATTTTCGGAATTATCGCTGAATAAATCTT
CCAATGACTTTATTTCATTTCCACGCTTCCACAATATCATGAAATGTTGACGTACTTGATTAATT
TGTTCATAACCCATTGTAATTGTACACTACGTA
Found at i:760142 original size:18 final size:18
Alignment explanation
Indices: 760121--760156 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
760111 CTTCCATCCG
*
760121 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
760139 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
760157 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:761469 original size:15 final size:15
Alignment explanation
Indices: 761449--761482 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
761439 GGTCAACTCC
761449 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
761464 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
761479 GGTC
1 GGTC
761483 GGGTCATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.24, C:0.26, G:0.35, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:761482 original size:8 final size:7
Alignment explanation
Indices: 761448--761479 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
761438 TGGTCAACTC
761448 CGGTCAA
1 CGGTCAA
761455 CGGTCAA
1 CGGTCAA
761462 CGGGTCAA
1 C-GGTCAA
761470 CGGTCAA
1 CGGTCAA
761477 CGG
1 CGG
761480 GTCGGGTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:763420 original size:35 final size:35
Alignment explanation
Indices: 763347--763421 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
763337 CGTCACTAAC
**
763347 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
*
763382 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
763417 AGTAA
1 AGTAA
763422 TCTTCCTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.29, G:0.28, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:763558 original size:23 final size:23
Alignment explanation
Indices: 763498--763572 Score: 105
Period size: 24 Copynumber: 3.2 Consensus size: 23
763488 CATAATTCAA
*
763498 GTCAAGTATCATATCAGAATCCAG
1 GTCAA-TATCAGATCAGAATCCAG
* *
763522 GTCATGTATCAGATCAGAATCCAT
1 GTCA-ATATCAGATCAGAATCCAG
763546 GTCAATATCAGATCAGAATCCAG
1 GTCAATATCAGATCAGAATCCAG
763569 GTCA
1 GTCA
763573 GGATCATAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
23 21 0.47
24 24 0.53
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.25
Consensus pattern (23 bp):
GTCAATATCAGATCAGAATCCAG
Done.