Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008199.1 Hibiscus syriacus cultivar Beakdansim tig00110819_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: 2638622
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 11
Found at i:781123 original size:19 final size:20
Alignment explanation
Indices: 781089--781128 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
781079 GTGTTATCAC
* *
781089 TTAATTTGAGATTAAATTTA
1 TTAAATTGAGATTAAAATTA
781109 TTAAATTGA-ATTAAAATTA
1 TTAAATTGAGATTAAAATTA
781128 T
1 T
781129 GACCAAATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (20 bp):
TTAAATTGAGATTAAAATTA
Found at i:783644 original size:29 final size:29
Alignment explanation
Indices: 783609--783690 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
783599 AAACTAAATT
*
783609 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
783638 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
783667 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
783691 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:787713 original size:29 final size:29
Alignment explanation
Indices: 787678--787759 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
787668 AAACTAAATT
*
787678 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
787707 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
787736 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
787760 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:797296 original size:60 final size:60
Alignment explanation
Indices: 797203--797323 Score: 161
Period size: 60 Copynumber: 2.0 Consensus size: 60
797193 TAGTTGGGTA
** * *
797203 ATCATTTTGTAACTTTTAATAGTCAAGTGACTCAACAAAGCAACACCCTATAGTCGAAGG
1 ATCATTTTGTAACTTTTAATAGTCAAGAAACTCAACAAAGAAACACCCTATAATCGAAGG
*** * *
797263 ATCATTTTGTAACTTTTAATAGTTGGGAAACTCAACAAAGAAATATCCTATAATCGAAGG
1 ATCATTTTGTAACTTTTAATAGTCAAGAAACTCAACAAAGAAACACCCTATAATCGAAGG
797323 A
1 A
797324 CCATCGTGTA
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.30
Consensus pattern (60 bp):
ATCATTTTGTAACTTTTAATAGTCAAGAAACTCAACAAAGAAACACCCTATAATCGAAGG
Found at i:802843 original size:20 final size:18
Alignment explanation
Indices: 802806--802864 Score: 55
Period size: 19 Copynumber: 3.0 Consensus size: 18
802796 AAATCATTTA
*
802806 ATTTATTTTTTCTAAATT
1 ATTTATTTTTTATAAATT
802824 ATTTAGTTTTTTATATAATT
1 ATTTA-TTTTTTATA-AATT
*
802844 AAAATTTATTTTTTAAAAATT
1 ---ATTTATTTTTTATAAATT
802865 TAAAACAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
18 5 0.15
19 8 0.24
20 4 0.12
21 4 0.12
22 8 0.24
23 5 0.15
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (18 bp):
ATTTATTTTTTATAAATT
Found at i:802867 original size:22 final size:23
Alignment explanation
Indices: 802824--802869 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
802814 TTTCTAAATT
*
802824 ATTTAGTTTTTTATATAATTAAA
1 ATTTAGTTTTTTATAAAATTAAA
802847 ATTTA-TTTTTTA-AAAATTTAAA
1 ATTTAGTTTTTTATAAAA-TTAAA
802869 A
1 A
802870 CAATTCATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 3 0.14
22 13 0.62
23 5 0.24
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (23 bp):
ATTTAGTTTTTTATAAAATTAAA
Found at i:803765 original size:15 final size:17
Alignment explanation
Indices: 803740--803771 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
803730 ATTTATATAA
803740 AATACAAAC-AAAGCAT
1 AATACAAACAAAAGCAT
803756 AATA-AAACAAAAGCAT
1 AATACAAACAAAAGCAT
803772 TTGTACAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.66, C:0.16, G:0.06, T:0.12
Consensus pattern (17 bp):
AATACAAACAAAAGCAT
Found at i:807502 original size:24 final size:24
Alignment explanation
Indices: 807448--807503 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
807438 AGCTCGATTA
* *
807448 AAGCTCAAGACTTGAACTCAATTG
1 AAGCTCGAGACTTGAACTAAATTG
*
807472 AAGCTCGAGACTTGAGCTAAATTG
1 AAGCTCGAGACTTGAACTAAATTG
807496 AAGCTCGA
1 AAGCTCGA
807504 TTCAAGCTCG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (24 bp):
AAGCTCGAGACTTGAACTAAATTG
Found at i:807510 original size:11 final size:11
Alignment explanation
Indices: 807496--807534 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
807486 AGCTAAATTG
807496 AAGCTCGATTC
1 AAGCTCGATTC
*
807507 AAGCTCGTTTC
1 AAGCTCGATTC
*
807518 AAGCTCGATTT
1 AAGCTCGATTC
807529 AAGCTC
1 AAGCTC
807535 ACAGGTTTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.31
Consensus pattern (11 bp):
AAGCTCGATTC
Found at i:808974 original size:7 final size:7
Alignment explanation
Indices: 808964--809072 Score: 58
Period size: 7 Copynumber: 15.3 Consensus size: 7
808954 TTTTATATTT
808964 AACCCTA
1 AACCCTA
808971 AACCCTA
1 AACCCTA
*
808978 ACCCCT-
1 AACCCTA
*
808984 AACACATA
1 AAC-CCTA
808992 AACCCTA
1 AACCCTA
*
808999 AATCCTA
1 AACCCTA
**
809006 AAATCTA
1 AACCCTA
*
809013 AACCATA
1 AACCCTA
*
809020 AACTCTA
1 AACCCTA
**
809027 AACATTA
1 AACCCTA
*
809034 AACCATA
1 AACCCTA
*
809041 AACTCTAA
1 AACCCT-A
*
809049 AACCTTA
1 AACCCTA
*
809056 AATCCTTA
1 AA-CCCTA
*
809064 AACTCTA
1 AACCCTA
809071 AA
1 AA
809073 ACCTTAAATC
Statistics
Matches: 76, Mismatches: 22, Indels: 8
0.72 0.21 0.08
Matches are distributed among these distances:
6 2 0.03
7 59 0.78
8 15 0.20
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.22
Consensus pattern (7 bp):
AACCCTA
Found at i:809013 original size:28 final size:28
Alignment explanation
Indices: 808964--809029 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 28
808954 TTTTATATTT
**
808964 AACCCTAAACCCTAACCCCT-AACACATA
1 AACCCTAAACCCTAAAACCTAAAC-CATA
* *
808992 AACCCTAAATCCTAAAATCTAAACCATA
1 AACCCTAAACCCTAAAACCTAAACCATA
*
809020 AACTCTAAAC
1 AACCCTAAAC
809030 ATTAAACCAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
28 28 0.90
29 3 0.10
ACGTcount: A:0.47, C:0.35, G:0.00, T:0.18
Consensus pattern (28 bp):
AACCCTAAACCCTAAAACCTAAACCATA
Found at i:809014 original size:21 final size:21
Alignment explanation
Indices: 808990--809073 Score: 91
Period size: 21 Copynumber: 3.9 Consensus size: 21
808980 CCCTAACACA
*
808990 TAAACCCTAAA-TCCTAAAATC
1 TAAACCATAAACT-CTAAAATC
809011 TAAACCATAAACTCTAAACAT-
1 TAAACCATAAACTCTAAA-ATC
*
809032 TAAACCATAAACTCTAAAACC
1 TAAACCATAAACTCTAAAATC
*
809053 TTAAATCCTTAAACTCTAAAA
1 -TAAA-CCATAAACTCTAAAA
809074 CCTTAAATCC
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
20 1 0.02
21 33 0.60
22 7 0.13
23 14 0.25
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (21 bp):
TAAACCATAAACTCTAAAATC
Found at i:809069 original size:23 final size:23
Alignment explanation
Indices: 809018--809084 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
809008 ATCTAAACCA
* *
809018 TAAACTCT-AAACATTAAA-CCA
1 TAAACTCTAAAACCTTAAATCCT
809039 TAAACTCTAAAACCTTAAATCCT
1 TAAACTCTAAAACCTTAAATCCT
809062 TAAACTCTAAAACCTTAAATCCT
1 TAAACTCTAAAACCTTAAATCCT
809085 ATCACATAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
21 8 0.19
22 9 0.21
23 25 0.60
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAACTCTAAAACCTTAAATCCT
Found at i:809111 original size:29 final size:29
Alignment explanation
Indices: 809062--809142 Score: 110
Period size: 29 Copynumber: 2.8 Consensus size: 29
809052 CTTAAATCCT
*
809062 TAAACTCTAAAACCTTAAATCCTATCACA
1 TAAACTCTAAACCCTTAAATCCTATCACA
* * *
809091 TAAGCTTTAAACCCTTAAATCATATCACA
1 TAAACTCTAAACCCTTAAATCCTATCACA
*
809120 TAAACTCTAAACCC-TAAACCCTA
1 TAAACTCTAAACCCTTAAATCCTA
809143 AATCTTATCA
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 7 0.16
29 37 0.84
ACGTcount: A:0.43, C:0.28, G:0.01, T:0.27
Consensus pattern (29 bp):
TAAACTCTAAACCCTTAAATCCTATCACA
Found at i:809871 original size:14 final size:14
Alignment explanation
Indices: 809854--809894 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
809844 TTTATTCATC
809854 AATAATGTATTTTT
1 AATAATGTATTTTT
809868 AAT-A--TATTTTT
1 AATAATGTATTTTT
*
809879 AATAATGTAATTTT
1 AATAATGTATTTTT
809893 AA
1 AA
809895 AAATCTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
11 10 0.43
12 1 0.04
13 1 0.04
14 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (14 bp):
AATAATGTATTTTT
Found at i:813328 original size:21 final size:21
Alignment explanation
Indices: 813304--813353 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
813294 AAATTTATAA
*
813304 ATTAATATTATAAATATAAAT
1 ATTAAAATTATAAATATAAAT
* *
813325 ATTAAAATTATAATTATAAAC
1 ATTAAAATTATAAATATAAAT
813346 ATATAAAA
1 AT-TAAAA
813354 AAATTATAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
ATTAAAATTATAAATATAAAT
Found at i:813360 original size:19 final size:17
Alignment explanation
Indices: 813336--813370 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 17
813326 TTAAAATTAT
813336 AATTATAAACATATAAAAA
1 AATTAT-AACATA-AAAAA
813355 AATTATAACATAAAAA
1 AATTATAACATAAAAA
813371 TATTTTAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 6 0.38
19 6 0.38
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.26
Consensus pattern (17 bp):
AATTATAACATAAAAAA
Found at i:813366 original size:18 final size:18
Alignment explanation
Indices: 813336--813387 Score: 56
Period size: 16 Copynumber: 3.0 Consensus size: 18
813326 TTAAAATTAT
813336 AATTATAAACATATAAAAA
1 AATTATAAACATA-AAAAA
813355 AATTAT-AACAT-AAAAA
1 AATTATAAACATAAAAAA
* *
813371 TATTTTAAACA-AAAAAA
1 AATTATAAACATAAAAAA
813388 TTATACATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
16 9 0.31
17 9 0.31
18 5 0.17
19 6 0.21
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (18 bp):
AATTATAAACATAAAAAA
Found at i:813369 original size:16 final size:15
Alignment explanation
Indices: 813348--813392 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
813338 TTATAAACAT
813348 ATAAAAAAATTATAA
1 ATAAAAAAATTATAA
* *
813363 CATAAAAATATTTTAA
1 -ATAAAAAAATTATAA
*
813379 ACAAAAAAATTATA
1 ATAAAAAAATTATA
813393 CATTTGACTA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (15 bp):
ATAAAAAAATTATAA
Found at i:819616 original size:24 final size:24
Alignment explanation
Indices: 819584--819639 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
819574 GTTGGATAAT
*
819584 GAATATGTCATGTTTTCAACTGAA
1 GAATCTGTCATGTTTTCAACTGAA
819608 GAATCTGTCATGTTTTCAACTGAA
1 GAATCTGTCATGTTTTCAACTGAA
819632 GAATCTGT
1 GAATCTGT
819640 TCCAGCTCAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (24 bp):
GAATCTGTCATGTTTTCAACTGAA
Found at i:819804 original size:33 final size:33
Alignment explanation
Indices: 819767--819846 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
819757 TAAGGATAAT
* *
819767 TAGTAGGGATGATGCTCCTTTAAGTCAGACATG
1 TAGTAGGGATGATGCTCCTTTAAGCCAGACAAG
*
819800 TAGTAGGGATGATACTCCTTTAAGCCAGACAAG
1 TAGTAGGGATGATGCTCCTTTAAGCCAGACAAG
*
819833 TAGTAGGAATGATG
1 TAGTAGGGATGATG
819847 AGCCTATGAG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.28
Consensus pattern (33 bp):
TAGTAGGGATGATGCTCCTTTAAGCCAGACAAG
Found at i:820829 original size:201 final size:200
Alignment explanation
Indices: 820537--821580 Score: 937
Period size: 201 Copynumber: 5.2 Consensus size: 200
820527 GCTAGACCCC
* ** * *
820537 TACATCAAGTTGCTCTGACGCAATAAGTTCAACACCAAATGTTTCGGATTATTCTGATGACAAAG
1 TACATCAAGTTGCTCTGAAGCTTTAAGTTCAACACCAAATGTTTCGGATTATTCTGGTGTCAAAG
* * * * * *
820602 AAATAGATGGTAGGAACTCTATTCCCTCTGGTGTTAAAGAAATGGATACTAGGTATTGCACTTCC
66 AAATGGATGTTAGGAACTCCATTCCCTCTGGTGTTAAAGAAATGGATACTAGGAACT-CATTTCC
* * * *
820667 TCGTCTCCAGAACTCATAAATGTTGTGAGGGTTGAATTGGATATGAGAACCATGACTAGTCCAGT
130 TCATCTCCAGAACCCATAAATGTTGTGAGGGATGAATTCGATATGAGAACCATGACTAGTCCAGT
* *
820732 GGCTCT
195 GACACT
** * * * * * *
820738 TATGTCAAGTTGCTCTGAAGCTTTAAGCTCAAGACCAAATGCTTCAGATTGTTCTGGTGTCGAAG
1 TACATCAAGTTGCTCTGAAGCTTTAAGTTCAACACCAAATGTTTCGGATTATTCTGGTGTCAAAG
* * * * *
820803 AACTGGATGTTAGGAACTCCATTCCCTCTGGTGTTAAAGAAATGGATATTAGGAATTCTTTTTCT
66 AAATGGATGTTAGGAACTCCATTCCCTCTGGTGTTAAAGAAATGGATACTAGGAACTC-ATTTCC
* * * * * * * * * * * ** *
820868 TCATCTCCAAAACACTTAAATGTCGCGAAGGATGAACTGGATTTGACAAACACAACTAGTCCGGT
130 TCATCTCCAGAACCCATAAATGTTGTGAGGGATGAATTCGATATGAGAACCATGACTAGTCCAGT
*
820933 GACAGT
195 GACACT
* * * * * * * **
820939 TTCATCAAATTTCATC-GGAGCTTTAAGTTCAACGCCAAATG-TTCTGGGTTATTCCGGTGTCGG
1 TACATCAAGTTGC-TCTGAAGCTTTAAGTTCAACACCAAATGTTTC-GGATTATTCTGGTGTCAA
** * * *
821002 AGAAATGGATGTTAGGAACTCCGCTCTCTCTGGTGTTAAAGAAATGGATATTGGGAACTCCATTT
64 AGAAATGGATGTTAGGAACTCCATTCCCTCTGGTGTTAAAGAAATGGATACTAGGAACT-CATTT
** * * * * *
821067 TTTCATCTCCAGAACCCATTGAA-GTTGGGAGGGATGAATTAGATATGAGAAACTTGACTAGTCC
128 CCTCATCTCCAGAACCCA-TAAATGTTGTGAGGGATGAATTCGATATGAGAACCATGACTAGTCC
*
821131 AGTGACAGT
192 AGTGACACT
* * * * * * *
821140 TACACCAAATTTCTCTGAAACTTCAAGTTCAACACCAAATATTTCGGATTATTCTGGTGTCAACG
1 TACATCAAGTTGCTCTGAAGCTTTAAGTTCAACACCAAATGTTTCGGATTATTCTGGTGTCAAAG
* * * * * *
821205 AAATGGATGTCAGGAACTCCTTTCCCTCTGGTGTTCAACAAATGGAT-GTCATGAACTCGATTTC
66 AAATGGATGTTAGGAACTCCATTCCCTCTGGTGTTAAAGAAATGGATACT-AGGAACTC-ATTTC
* ** * * * *
821269 CTCATCTCCAGGACCCATCGATGTTGTGAGAGATGAATTCAATATGAGAACCATGGCTAATCCAG
129 CTCATCTCCAGAACCCATAAATGTTGTGAGGGATGAATTCGATATGAGAACCATGACTAGTCCAG
*
821334 TGACCCT
194 TGACACT
** * * * * * * *
821341 GGCATCAAGCTGCTCTGAAGCTTTAAGTTCAACACCAAATGGTCCGGAATATTATGGTCTTAAAG
1 TACATCAAGTTGCTCTGAAGCTTTAAGTTCAACACCAAATGTTTCGGATTATTCTGGTGTCAAAG
* * * * * * *
821406 AAATGGATGTTAGGGACTCAATGCCCTCCGGTGTTAAATAAAGGGATACTGGGAACTCCATTTCC
66 AAATGGATGTTAGGAACTCCATTCCCTCTGGTGTTAAAGAAATGGATACTAGGAACT-CATTTCC
* ** *
821471 TCGTCTCCAGAACCCATCGATGTTGTGAGAGATGAATTCGATATGAGAACCATGACTAGT-CATG
130 TCATCTCCAGAACCCATAAATGTTGTGAGGGATGAATTCGATATGAGAACCATGACTAGTCCA-G
*
821535 TGACCCT
194 TGACACT
** * * *
821542 GGCATCAAGCTCCTCTGAAGCTTCAAGTTCAACACCAAA
1 TACATCAAGTTGCTCTGAAGCTTTAAGTTCAACACCAAA
821581 CGTCTCTGAT
Statistics
Matches: 682, Mismatches: 148, Indels: 26
0.80 0.17 0.03
Matches are distributed among these distances:
200 12 0.02
201 659 0.97
202 11 0.02
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (200 bp):
TACATCAAGTTGCTCTGAAGCTTTAAGTTCAACACCAAATGTTTCGGATTATTCTGGTGTCAAAG
AAATGGATGTTAGGAACTCCATTCCCTCTGGTGTTAAAGAAATGGATACTAGGAACTCATTTCCT
CATCTCCAGAACCCATAAATGTTGTGAGGGATGAATTCGATATGAGAACCATGACTAGTCCAGTG
ACACT
Found at i:821269 original size:40 final size:39
Alignment explanation
Indices: 821192--821269 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
821182 TTCGGATTAT
*
821192 TCTGGTGTCAACGAAATGGATGTCAGGAACTCCTTTCCC
1 TCTGGTGTCAACGAAATGGATGTCAGGAACTCATTTCCC
*
821231 TCTGGTGTTCAAC-AAATGGATGTCATGAACTCGATTTCC
1 TCTGGTG-TCAACGAAATGGATGTCAGGAACTC-ATTTCC
821270 TCATCTCCAG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
39 25 0.71
40 10 0.29
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.31
Consensus pattern (39 bp):
TCTGGTGTCAACGAAATGGATGTCAGGAACTCATTTCCC
Found at i:833645 original size:21 final size:22
Alignment explanation
Indices: 833610--833650 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
833600 TTTAAATATT
* *
833610 ATATTATACTTTATATAAATAA
1 ATATGATACTTTATAAAAATAA
833632 ATATGATA-TTTATAAAAAT
1 ATATGATACTTTATAAAAAT
833651 TATTTAAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (22 bp):
ATATGATACTTTATAAAAATAA
Found at i:838002 original size:50 final size:50
Alignment explanation
Indices: 837884--838006 Score: 131
Period size: 50 Copynumber: 2.5 Consensus size: 50
837874 TAAAGCGAGC
* ** *
837884 CCCCTGAACTGCGCTATACGCTGATTTAGCGCCACGTGGGTATAGCGCGT
1 CCCCTGAACTGCGCTATACGCTGATCTAGCGCCACGTAAGTATAGCGCGG
* * ** * * *
837934 TCCATGCCCCGCGATATACGGTGATCTAGCGCCACGTAAGTATAGCGCGG
1 CCCCTGAACTGCGCTATACGCTGATCTAGCGCCACGTAAGTATAGCGCGG
*
837984 CCCCTGATCTGCGCTATAC-CTGA
1 CCCCTGAACTGCGCTATACGCTGA
838007 GTATCTGACA
Statistics
Matches: 55, Mismatches: 18, Indels: 1
0.74 0.24 0.01
Matches are distributed among these distances:
49 3 0.05
50 52 0.95
ACGTcount: A:0.20, C:0.32, G:0.26, T:0.23
Consensus pattern (50 bp):
CCCCTGAACTGCGCTATACGCTGATCTAGCGCCACGTAAGTATAGCGCGG
Found at i:838140 original size:10 final size:10
Alignment explanation
Indices: 838125--838164 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
838115 TTTATCATAC
838125 CAAATTCTCT
1 CAAATTCTCT
838135 CAAATTCTCT
1 CAAATTCTCT
838145 -AAATTTCTCT
1 CAAA-TTCTCT
*
838155 CAAATACTCT
1 CAAATTCTCT
838165 ATTTTTTAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 21 0.78
11 3 0.11
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:838482 original size:111 final size:111
Alignment explanation
Indices: 838288--838620 Score: 630
Period size: 111 Copynumber: 3.0 Consensus size: 111
838278 TGGAAATCAT
* *
838288 ATATCTCTACACTTTGCTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
838353 TATTTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
838399 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
838464 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
838510 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
838575 TAATTAGTTGATTTATTTAATGCATGATTATTAGAGTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
838621 TTTTTGTAAT
Statistics
Matches: 218, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
111 218 1.00
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.44
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:844288 original size:12 final size:12
Alignment explanation
Indices: 844255--844291 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
844245 ATTTATAAGA
*
844255 GAGGAGAGATGC
1 GAGGAGAGATGT
844267 GA-G-GAGATGT
1 GAGGAGAGATGT
844277 GAGGAGAGATGT
1 GAGGAGAGATGT
844289 GAG
1 GAG
844292 AACGGGAGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
10 8 0.36
11 2 0.09
12 12 0.55
ACGTcount: A:0.32, C:0.03, G:0.51, T:0.14
Consensus pattern (12 bp):
GAGGAGAGATGT
Found at i:844539 original size:49 final size:49
Alignment explanation
Indices: 844438--844560 Score: 135
Period size: 49 Copynumber: 2.5 Consensus size: 49
844428 CCCCTACGTG
*
844438 GCGTATAGCGCGG-AGCAGGGGGCACGCTATACCCCACGTGTAACTCAGTCA
1 GCGTATAGCGCGGTA-CAGGGGG--CGCTATACCCCACGTGTAACTCAATCA
* *
844489 GCGTATAGCGCGGTACAGGGGGCGCTATACTCCACGTGGT-GC-CAAATCA
1 GCGTATAGCGCGGTACAGGGGGCGCTATACCCCACGT-GTAACTC-AATCA
* *
844538 GCATATAGCGCGGTTCAGGGGGC
1 GCGTATAGCGCGGTACAGGGGGC
844561 ACGCTTTACT
Statistics
Matches: 64, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
48 1 0.02
49 40 0.62
50 2 0.03
51 20 0.31
52 1 0.02
ACGTcount: A:0.22, C:0.27, G:0.34, T:0.17
Consensus pattern (49 bp):
GCGTATAGCGCGGTACAGGGGGCGCTATACCCCACGTGTAACTCAATCA
Found at i:846130 original size:29 final size:29
Alignment explanation
Indices: 846092--846157 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
846082 GTTCCATAAT
*
846092 TTTAATAATTATTTTATAATTTCT-AACAC
1 TTTAATAATTATTTTATAACTTCTGAA-AC
*
846121 TTTAATAATTATTTTATAACTTCTGGAAC
1 TTTAATAATTATTTTATAACTTCTGAAAC
846150 TTTAATAA
1 TTTAATAA
846158 CAAAAAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 33 0.97
30 1 0.03
ACGTcount: A:0.38, C:0.09, G:0.03, T:0.50
Consensus pattern (29 bp):
TTTAATAATTATTTTATAACTTCTGAAAC
Found at i:847293 original size:37 final size:36
Alignment explanation
Indices: 847218--847293 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
847208 TTTTTATATT
*
847218 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
847254 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
847291 TTT
1 TTT
847294 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:847973 original size:16 final size:17
Alignment explanation
Indices: 847943--847975 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
847933 AAATCGATCC
847943 AAAAAACCGATAACCGA
1 AAAAAACCGATAACCGA
*
847960 AAAAAATCGA-AACCGA
1 AAAAAACCGATAACCGA
847976 TTTGGTGTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.61, C:0.21, G:0.12, T:0.06
Consensus pattern (17 bp):
AAAAAACCGATAACCGA
Found at i:850119 original size:61 final size:61
Alignment explanation
Indices: 849999--850120 Score: 149
Period size: 61 Copynumber: 2.0 Consensus size: 61
849989 CTTAAGTTAT
* * * *
849999 AATTATAATTTATATATTCATATGACAATAACTTAAATAAACTAATATAATGCATAAATAA
1 AATTATAATTAATATATTCATATGACAATAAATTAAATAAACTAATACAATGCACAAATAA
* * *
850060 AATTATAATTAATATATTCATAT-A-ATTACAATTAAAATAAACTATTACAATGTACAAATAA
1 AATTATAATTAATATATTCATATGACAATA-AATT-AAATAAACTAATACAATGCACAAATAA
850121 TGAACTGATA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
59 3 0.06
60 4 0.08
61 45 0.87
ACGTcount: A:0.53, C:0.08, G:0.02, T:0.36
Consensus pattern (61 bp):
AATTATAATTAATATATTCATATGACAATAAATTAAATAAACTAATACAATGCACAAATAA
Found at i:855430 original size:23 final size:23
Alignment explanation
Indices: 855381--855449 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
855371 CCAAACGACC
* *
855381 GAAAAATGTAATATAAATA-CAGA
1 GAAAAATGTACTATAAA-AGCAAA
** *
855404 -AAAAATGTGTTATAAAGGCAAA
1 GAAAAATGTACTATAAAAGCAAA
855426 GAAAAATGTACTATAAAAGCAAA
1 GAAAAATGTACTATAAAAGCAAA
855449 G
1 G
855450 TTATTAAACA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
22 17 0.46
23 20 0.54
ACGTcount: A:0.58, C:0.06, G:0.16, T:0.20
Consensus pattern (23 bp):
GAAAAATGTACTATAAAAGCAAA
Found at i:858860 original size:2 final size:2
Alignment explanation
Indices: 858853--858924 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
858843 TGCATTGATG
858853 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
858895 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
858925 GTTGTGAAAT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:859221 original size:17 final size:16
Alignment explanation
Indices: 859195--859228 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
859185 TTTCACTAAT
*
859195 AGAGGAAATATTACAA
1 AGAGGAAATAATACAA
859211 AGAGAGAAATAATACAA
1 AGAG-GAAATAATACAA
859228 A
1 A
859229 TAGCCTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.62, C:0.06, G:0.18, T:0.15
Consensus pattern (16 bp):
AGAGGAAATAATACAA
Found at i:862449 original size:23 final size:23
Alignment explanation
Indices: 862431--862490 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
862421 CTCGTATAAA
862431 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
862454 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
*
862477 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
862491 ATATAATGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.23, C:0.32, G:0.27, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCCCGTAGAAT
Found at i:863214 original size:67 final size:67
Alignment explanation
Indices: 863114--863250 Score: 238
Period size: 67 Copynumber: 2.0 Consensus size: 67
863104 GGAATCGGTT
* *
863114 CCCCCCTGGGGGTATCGATTCCCCACTAGCATTCTGGAATTCATATTCGTTGAGGGGGTATCGGT
1 CCCCCCTGGGGGTATCGATTCCCCACTAGCATTCTGGAAATCATATTCGTTGAAGGGGTATCGGT
863179 CC
66 CC
*
863181 CCCCCCTGGGGGTATCGATTCCCCTCTAGCATTCTGGAAATCATATTCGTTGAAGGGGTATCGGT
1 CCCCCCTGGGGGTATCGATTCCCCACTAGCATTCTGGAAATCATATTCGTTGAAGGGGTATCGGT
*
863246 TC
66 CC
863248 CCC
1 CCC
863251 TTGAATGGGT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.17, C:0.29, G:0.26, T:0.28
Consensus pattern (67 bp):
CCCCCCTGGGGGTATCGATTCCCCACTAGCATTCTGGAAATCATATTCGTTGAAGGGGTATCGGT
CC
Found at i:863260 original size:21 final size:21
Alignment explanation
Indices: 863230--863272 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
863220 ATCATATTCG
* *
863230 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
863251 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
863272 T
1 T
863273 AGCCCGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:869328 original size:23 final size:23
Alignment explanation
Indices: 869310--869369 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
869300 CTCGTATAAA
869310 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
*
869333 TACACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
*
869356 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
869370 ATATAATGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.25, C:0.32, G:0.25, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCCCGTAGAAT
Found at i:870091 original size:66 final size:66
Alignment explanation
Indices: 869982--870153 Score: 247
Period size: 66 Copynumber: 2.6 Consensus size: 66
869972 TTTTTCTCAT
* * *
869982 GGGGGAATCGGTTCCCCCCCTGGGGGTATCGATTCCCCACTAGCATTCTGGAATTCATATTCGTT
1 GGGGGTATCGG-TCCCCCCCTGGGGGTATCGATTCCCCTCTAGCATTCTGGAAATCATATTCGTT
870047 GA
65 GA
870049 GGGGGTATCGGTCCCCCCCTGGGGGTATCGATTCCCCTCTAGCATTCTGGAAATCATATTCGTTG
1 GGGGGTATCGGTCCCCCCCTGGGGGTATCGATTCCCCTCTAGCATTCTGGAAATCATATTCGTTG
870114 A
66 A
* * * *
870115 AGGGGTATCGGT-TCCCCTTGAATGGGTATCGATTCCCCT
1 GGGGGTATCGGTCCCCCCCTG--GGGGTATCGATTCCCCT
870154 AGCCCGAAAA
Statistics
Matches: 96, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
65 6 0.06
66 64 0.67
67 26 0.27
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (66 bp):
GGGGGTATCGGTCCCCCCCTGGGGGTATCGATTCCCCTCTAGCATTCTGGAAATCATATTCGTTG
A
Found at i:870141 original size:21 final size:21
Alignment explanation
Indices: 870111--870153 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
870101 ATCATATTCG
*
870111 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
870132 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
870153 T
1 T
870154 AGCCCGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.23, G:0.28, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:872855 original size:17 final size:16
Alignment explanation
Indices: 872829--872862 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
872819 TTTCACTAAT
*
872829 AGAGGAAATATTACAA
1 AGAGGAAATAATACAA
872845 AGAGAGAAATAATACAA
1 AGAG-GAAATAATACAA
872862 A
1 A
872863 TAGCCTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.62, C:0.06, G:0.18, T:0.15
Consensus pattern (16 bp):
AGAGGAAATAATACAA
Found at i:881466 original size:31 final size:30
Alignment explanation
Indices: 881415--881472 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
881405 TTAGTTAATT
*
881415 TTGATAATGAATTGAAGTTTATCATGTAAG
1 TTGATAATGAATTGAAGTTTAGCATGTAAG
*
881445 TTGATTAATGAA-TGCATGTTTAGCATGT
1 TTGA-TAATGAATTG-AAGTTTAGCATGT
881473 GTCTAGAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 6 0.25
31 18 0.75
ACGTcount: A:0.33, C:0.05, G:0.21, T:0.41
Consensus pattern (30 bp):
TTGATAATGAATTGAAGTTTAGCATGTAAG
Found at i:887397 original size:18 final size:17
Alignment explanation
Indices: 887376--887434 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 17
887366 AATTATTCAT
887376 CTTTATTCATTTATATTC
1 CTTTATT-ATTTATATTC
* *
887394 CTTTAGTTATTCATATTT
1 CTTTA-TTATTTATATTC
*
887412 ATTTATTTATTTATATTC
1 CTTTA-TTATTTATATTC
*
887430 TTTTA
1 CTTTA
887435 GTTAGTGGAT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
18 31 0.94
19 2 0.06
ACGTcount: A:0.24, C:0.10, G:0.02, T:0.64
Consensus pattern (17 bp):
CTTTATTATTTATATTC
Found at i:887420 original size:22 final size:22
Alignment explanation
Indices: 887378--887425 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
887368 TTATTCATCT
*
887378 TTATTCATTTATATTCCTTTAG
1 TTATTCATTTATATTCATTTAG
* *
887400 TTATTCATATT-TATTTATTTAT
1 TTATTCAT-TTATATTCATTTAG
887422 TTAT
1 TTAT
887426 ATTCTTTTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.25, C:0.08, G:0.02, T:0.65
Consensus pattern (22 bp):
TTATTCATTTATATTCATTTAG
Found at i:889371 original size:52 final size:52
Alignment explanation
Indices: 889293--889397 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 52
889283 CATCATAGGC
*
889293 TGTAGGAAAAGTTCACACCTAACATAAAATTTTGCGTTTGTCTATGATTATA
1 TGTAGGAAAAGTTCACACCTAACATAAAATTTTGCGTTCGTCTATGATTATA
889345 TGTAGGAAAAGTTCACACCTAACATAAAATTTTGCGTTCGTCTATGATTATA
1 TGTAGGAAAAGTTCACACCTAACATAAAATTTTGCGTTCGTCTATGATTATA
889397 T
1 T
889398 TGACGTTGTT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.36
Consensus pattern (52 bp):
TGTAGGAAAAGTTCACACCTAACATAAAATTTTGCGTTCGTCTATGATTATA
Found at i:901866 original size:6 final size:6
Alignment explanation
Indices: 901855--901880 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
901845 GTTAGAGCAT
901855 CTTTTC CTTTTC CTTTTC CTTTTC CT
1 CTTTTC CTTTTC CTTTTC CTTTTC CT
901881 ATTTGACAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (6 bp):
CTTTTC
Found at i:903637 original size:19 final size:19
Alignment explanation
Indices: 903571--903646 Score: 100
Period size: 19 Copynumber: 3.8 Consensus size: 19
903561 AGGGTGTCAA
903571 AGTGCATCCATACGC-CCTGC
1 AGTGCATCCAT--GCACCTGC
903591 AGTGCATCCATGCACCTGTAC
1 AGTGCATCCATGCACCTG--C
903612 TAGTGCATCCATGCACCTGC
1 -AGTGCATCCATGCACCTGC
903632 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
903647 TCAAACACCG
Statistics
Matches: 52, Mismatches: 0, Indels: 9
0.85 0.00 0.15
Matches are distributed among these distances:
18 2 0.04
19 19 0.37
20 12 0.23
21 1 0.02
22 18 0.35
ACGTcount: A:0.22, C:0.36, G:0.20, T:0.22
Consensus pattern (19 bp):
AGTGCATCCATGCACCTGC
Found at i:903711 original size:21 final size:20
Alignment explanation
Indices: 903667--903722 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 20
903657 AATGCAATTA
***
903667 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCAGGCT
903687 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATC-AGGCT
*
903708 GTGCATCGATACATC
1 GTGCATCGATGCATC
903723 TTGCTATGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.21, C:0.27, G:0.23, T:0.29
Consensus pattern (20 bp):
GTGCATCGATGCATCAGGCT
Found at i:903714 original size:41 final size:41
Alignment explanation
Indices: 903667--903749 Score: 107
Period size: 41 Copynumber: 2.0 Consensus size: 41
903657 AATGCAATTA
* * *
903667 GTGCATCGATGCATCCTT-CTGTGCATCGATGCATC-AAGGCT
1 GTGCATCGATACAT-CTTGCTATGCATCCATGCA-CGAAGGCT
903708 GTGCATCGATACATCTTGCTATGCATCCATGCACGAAGGCT
1 GTGCATCGATACATCTTGCTATGCATCCATGCACGAAGGCT
903749 G
1 G
903750 CAACGGCTAG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
40 4 0.11
41 33 0.89
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.28
Consensus pattern (41 bp):
GTGCATCGATACATCTTGCTATGCATCCATGCACGAAGGCT
Found at i:903734 original size:20 final size:20
Alignment explanation
Indices: 903667--903740 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
903657 AATGCAATTA
903667 GTGCATCGATGCATCCTT-CT
1 GTGCATCGATGCAT-CTTGCT
**
903687 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATC-TTGCT
*
903708 GTGCATCGATACATCTTGCT
1 GTGCATCGATGCATCTTGCT
* *
903728 ATGCATCCATGCA
1 GTGCATCGATGCA
903741 CGAAGGCTGC
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
19 1 0.02
20 27 0.61
21 16 0.36
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.30
Consensus pattern (20 bp):
GTGCATCGATGCATCTTGCT
Found at i:903872 original size:21 final size:21
Alignment explanation
Indices: 903843--903882 Score: 64
Period size: 20 Copynumber: 1.9 Consensus size: 21
903833 TTTGAGTAGG
903843 AAAATCATCTCCAAACGGCTCC
1 AAAATCATCTCC-AACGGCTCC
903865 AAAA-CATCTCCAACGGCT
1 AAAATCATCTCCAACGGCT
903883 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.35, G:0.10, T:0.17
Consensus pattern (21 bp):
AAAATCATCTCCAACGGCTCC
Found at i:907053 original size:29 final size:30
Alignment explanation
Indices: 906984--907042 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
906974 CAATTTAAGG
*
906984 CAAAATATTTTTGGACTTAAATTGAATTTA
1 CAAAATGTTTTTGGACTTAAATTGAATTTA
907014 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTAAATTGAATTTA
907043 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 11 0.39
30 17 0.61
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.44
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTAAATTGAATTTA
Found at i:907148 original size:21 final size:21
Alignment explanation
Indices: 907122--907220 Score: 87
Period size: 21 Copynumber: 4.7 Consensus size: 21
907112 AGGGTGTCAA
* *
907122 AGTGCATTCATGTACCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
907143 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
907164 AGCGCATCCATGCA--CCTGCAC
1 AGTGCATCCATGCACCCCTG--C
* * *
907185 TAGTGCATCGATGCA-TCATGC
1 -AGTGCATCCATGCACCCCTGC
907206 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
907221 TCAAACACCG
Statistics
Matches: 65, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
19 4 0.06
20 13 0.20
21 33 0.51
22 12 0.18
23 3 0.05
ACGTcount: A:0.22, C:0.34, G:0.20, T:0.23
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:907285 original size:21 final size:20
Alignment explanation
Indices: 907241--907296 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 20
907231 AATGCAATTA
***
907241 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCAGGCT
907261 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATC-AGGCT
907282 GTGCATCGATGCATC
1 GTGCATCGATGCATC
907297 CTACTATGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.29
Consensus pattern (20 bp):
GTGCATCGATGCATCAGGCT
Found at i:907288 original size:41 final size:41
Alignment explanation
Indices: 907241--907323 Score: 123
Period size: 41 Copynumber: 2.0 Consensus size: 41
907231 AATGCAATTA
* * *
907241 GTGCATCGATGCATCCTTCTGTGCATCGATGCATC-AAGGCT
1 GTGCATCGATGCATCCTACTATGCATCCATGCA-CGAAGGCT
907282 GTGCATCGATGCATCCTACTATGCATCCATGCACGAAGGCT
1 GTGCATCGATGCATCCTACTATGCATCCATGCACGAAGGCT
907323 G
1 G
907324 CAACGACTAG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 1 0.03
41 37 0.97
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.27
Consensus pattern (41 bp):
GTGCATCGATGCATCCTACTATGCATCCATGCACGAAGGCT
Found at i:907308 original size:20 final size:20
Alignment explanation
Indices: 907241--907314 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
907231 AATGCAATTA
*
907241 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTACT
*
907261 GTGCATCGATGCAT-CAAGGCT
1 GTGCATCGATGCATCCTA--CT
907282 GTGCATCGATGCATCCTACT
1 GTGCATCGATGCATCCTACT
* *
907302 ATGCATCCATGCA
1 GTGCATCGATGCA
907315 CGAAGGCTGC
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
19 1 0.02
20 27 0.59
21 16 0.35
22 2 0.04
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (20 bp):
GTGCATCGATGCATCCTACT
Found at i:907456 original size:21 final size:21
Alignment explanation
Indices: 907427--907466 Score: 64
Period size: 20 Copynumber: 1.9 Consensus size: 21
907417 TTTGAGTAGA
907427 AAAATCATCTCCAAACGGCTCC
1 AAAATCATCTCC-AACGGCTCC
907449 AAAA-CATCTCCAACGGCT
1 AAAATCATCTCCAACGGCT
907467 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.35, G:0.10, T:0.17
Consensus pattern (21 bp):
AAAATCATCTCCAACGGCTCC
Found at i:907720 original size:35 final size:35
Alignment explanation
Indices: 907680--907773 Score: 136
Period size: 35 Copynumber: 2.7 Consensus size: 35
907670 CCTTTTGTAA
*
907680 AGGGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCT
1 AGGGGAAAAGTTCTAGCTTATCCCGTGTAAAAGCT
*
907715 AGGGGAAAAGTTATAGCTTATCCCGTGTAAAAGCT
1 AGGGGAAAAGTTCTAGCTTATCCCGTGTAAAAGCT
* * *
907750 A-GGGAAATGTTCTAGTTTAGCCCG
1 AGGGGAAAAGTTCTAGCTTATCCCG
907774 GAAAAACTAG
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 19 0.36
35 34 0.64
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.27
Consensus pattern (35 bp):
AGGGGAAAAGTTCTAGCTTATCCCGTGTAAAAGCT
Found at i:910245 original size:22 final size:19
Alignment explanation
Indices: 910176--910265 Score: 90
Period size: 19 Copynumber: 4.4 Consensus size: 19
910166 AACGCAATTT
910176 TGAAAAATGTGTTGCGATAG
1 TGAAAAA-GTGTTGCGATAG
* * *
910196 TTAAAATGTGTTGCGAGAG
1 TGAAAAAGTGTTGCGATAG
910215 TTTGAAAAACGTGTTATTGCGATAG
1 --TGAAAAA-GTG---TTGCGATAG
910240 TGAAAAAGTGTTGCGATAG
1 TGAAAAAGTGTTGCGATAG
910259 TGAAAAA
1 TGAAAAA
910266 TCCAAAATAA
Statistics
Matches: 58, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
19 27 0.47
20 5 0.09
21 5 0.09
22 6 0.10
23 7 0.12
25 8 0.14
ACGTcount: A:0.37, C:0.06, G:0.28, T:0.30
Consensus pattern (19 bp):
TGAAAAAGTGTTGCGATAG
Found at i:915443 original size:13 final size:13
Alignment explanation
Indices: 915396--915443 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
915386 ATTTATATTG
*
915396 AAAATATTAATTT
1 AAAATATTAATAT
* *
915409 AAATTATAAATACT
1 AAAATATTAATA-T
915423 AAATATATTAATAT
1 AAA-ATATTAATAT
915437 AAAATAT
1 AAAATAT
915444 ATATATATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
13 13 0.46
14 8 0.29
15 7 0.25
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATATTAATAT
Found at i:915445 original size:2 final size:2
Alignment explanation
Indices: 915440--915486 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
915430 TTAATATAAA
915440 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
915482 -T AT AT
1 AT AT AT
915487 GTAATGTAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:921766 original size:56 final size:56
Alignment explanation
Indices: 921699--921809 Score: 213
Period size: 56 Copynumber: 2.0 Consensus size: 56
921689 AAGGGAAGAT
921699 TGAAGGGATAAGTGAGCTAAGATCATTGCTTATCCTAAACAAGGCAATTGATTGAC
1 TGAAGGGATAAGTGAGCTAAGATCATTGCTTATCCTAAACAAGGCAATTGATTGAC
*
921755 TGAAGGGATAAGTGAGCTAAGATCATTGCTTATCCTATACAAGGCAATTGATTGA
1 TGAAGGGATAAGTGAGCTAAGATCATTGCTTATCCTAAACAAGGCAATTGATTGA
921810 ACCCGACTAC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (56 bp):
TGAAGGGATAAGTGAGCTAAGATCATTGCTTATCCTAAACAAGGCAATTGATTGAC
Found at i:926021 original size:29 final size:30
Alignment explanation
Indices: 925984--926041 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
925974 TCATCAAGCG
*
925984 AATATAAT-AATAAAAA-TATATATTTTTCT
1 AATAAAATAAATAAAAATTA-ATATTTTTCT
926013 AATAAAATAAAATAAAAATTAATATTTTT
1 AATAAAAT-AAATAAAAATTAATATTTTT
926042 AAAGAACGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 7 0.28
31 16 0.64
32 2 0.08
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (30 bp):
AATAAAATAAATAAAAATTAATATTTTTCT
Found at i:927483 original size:2 final size:2
Alignment explanation
Indices: 927476--927535 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
927466 AAAATTTTGC
927476 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
927518 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
927536 GCATATTATT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:935055 original size:15 final size:15
Alignment explanation
Indices: 935037--935066 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
935027 CCACGGTGCT
935037 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
935052 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
935067 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:939269 original size:21 final size:21
Alignment explanation
Indices: 939229--939269 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
939219 TTGCTGGAGT
*
939229 ACTTGTCTTAGAAACTGCTTC
1 ACTTGTCTTAGAAACGGCTTC
939250 ACTTGTCTTA-AAACAGGCTT
1 ACTTGTCTTAGAAAC-GGCTT
939270 ATGTTCAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.37
Consensus pattern (21 bp):
ACTTGTCTTAGAAACGGCTTC
Found at i:939364 original size:3 final size:3
Alignment explanation
Indices: 939356--939391 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
939346 TTTCATTTAT
939356 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
939392 CCCTTTACAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:942794 original size:19 final size:19
Alignment explanation
Indices: 942770--942820 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 19
942760 CATACTAAAT
*
942770 TTTTTTATAATTTTTCTGA
1 TTTTTTATAATTTTTATGA
* *
942789 TTTTTTGTATTTTTTATGA
1 TTTTTTATAATTTTTATGA
* *
942808 ATTTTTAAAATTT
1 TTTTTTATAATTT
942821 AAGTAGATTA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.24, C:0.02, G:0.06, T:0.69
Consensus pattern (19 bp):
TTTTTTATAATTTTTATGA
Found at i:943213 original size:20 final size:19
Alignment explanation
Indices: 943175--943213 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
943165 CACAGGTTAG
*
943175 TGATAAAATTATAAGAGAA
1 TGATAAAATTAAAAGAGAA
*
943194 TGATCAAAATTAAAATAGAA
1 TGAT-AAAATTAAAAGAGAA
943214 CTAAATATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.59, C:0.03, G:0.13, T:0.26
Consensus pattern (19 bp):
TGATAAAATTAAAAGAGAA
Found at i:943541 original size:17 final size:18
Alignment explanation
Indices: 943495--943541 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
943485 TGTTTATGAG
943495 GGAATTGAAATCTGTGAA
1 GGAATTGAAATCTGTGAA
* *
943513 GAAATTGAAATCTGT-CA
1 GGAATTGAAATCTGTGAA
*
943530 GGAATTGGAATC
1 GGAATTGAAATC
943542 CAATTCCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.38, C:0.09, G:0.26, T:0.28
Consensus pattern (18 bp):
GGAATTGAAATCTGTGAA
Found at i:954350 original size:29 final size:28
Alignment explanation
Indices: 954308--954391 Score: 132
Period size: 29 Copynumber: 2.9 Consensus size: 28
954298 TGCAACGTGG
954308 GTAGGTCGCCAGGGAATCCCAGCGACATT
1 GTAGGTCGCCAGGG-ATCCCAGCGACATT
954337 GTAGGTCGCCAGGGCATCCCAGCGACATT
1 GTAGGTCGCCAGGG-ATCCCAGCGACATT
*
954366 GTAGGTCGCCAAGGGATCCCAACGAC
1 GTAGGTCGCC-AGGGATCCCAGCGAC
954392 CTATGCCTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
29 48 0.92
30 4 0.08
ACGTcount: A:0.24, C:0.30, G:0.31, T:0.15
Consensus pattern (28 bp):
GTAGGTCGCCAGGGATCCCAGCGACATT
Found at i:954474 original size:12 final size:11
Alignment explanation
Indices: 954454--954489 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
954444 GAAATCAACT
954454 GCATTATTGCA
1 GCATTATTGCA
*
954465 GCACTTATTGCT
1 GCA-TTATTGCA
954477 GCATTATTGCA
1 GCATTATTGCA
954488 GC
1 GC
954490 CCGTGAACGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.36
Consensus pattern (11 bp):
GCATTATTGCA
Found at i:954831 original size:28 final size:27
Alignment explanation
Indices: 954792--954844 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
954782 TATATTAAAA
954792 AATAATTAATTAGTGTGTTAGTTAGTCT
1 AATAATTAATTAGTGTG-TAGTTAGTCT
* *
954820 AATATTTAATTAGTTTGTAGTTAGT
1 AATAATTAATTAGTGTGTAGTTAGT
954845 TAAATAGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.32, C:0.02, G:0.17, T:0.49
Consensus pattern (27 bp):
AATAATTAATTAGTGTGTAGTTAGTCT
Found at i:954850 original size:27 final size:29
Alignment explanation
Indices: 954791--954855 Score: 82
Period size: 27 Copynumber: 2.3 Consensus size: 29
954781 ATATATTAAA
954791 AAATAATTAATTAGTGTGTTAGTTAGTCT
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
* *
954820 -AATATTTAATTAGTTTG-TAGTTAGT-T
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
*
954846 AAATAGTTAA
1 AAATAATTAA
954856 GTTATATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 1 0.03
27 16 0.50
28 15 0.47
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.46
Consensus pattern (29 bp):
AAATAATTAATTAGTGTGTTAGTTAGTCT
Found at i:954994 original size:18 final size:18
Alignment explanation
Indices: 954971--955025 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
954961 AATAATTATT
954971 TAAATTAGTTTATTGTTA
1 TAAATTAGTTTATTGTTA
954989 TAAATTA--TTA--G-T-
1 TAAATTAGTTTATTGTTA
*
955001 T-AATTAGTTTATTATTA
1 TAAATTAGTTTATTGTTA
955018 TAAATTAG
1 TAAATTAG
955026 GGTAAAACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
11 5 0.17
12 1 0.03
13 4 0.14
14 1 0.03
16 4 0.14
17 1 0.03
18 13 0.45
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (18 bp):
TAAATTAGTTTATTGTTA
Found at i:955078 original size:21 final size:21
Alignment explanation
Indices: 955053--955092 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
955043 GTTAATTAGT
955053 TTGTTAGTTTAAGTTATATTA
1 TTGTTAGTTTAAGTTATATTA
955074 TTGTTAGTTTAAGTTATAT
1 TTGTTAGTTTAAGTTATAT
955093 CATATAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (21 bp):
TTGTTAGTTTAAGTTATATTA
Found at i:955339 original size:30 final size:30
Alignment explanation
Indices: 955271--955374 Score: 106
Period size: 30 Copynumber: 3.4 Consensus size: 30
955261 ATTAGTTAAT
* *
955271 TAGTTTTTTAGTAGTAAATTATAATTAAA-AA
1 TAGTTTATTAGT-TTAAATTAT-ATTAAAGAA
*
955302 TCA-TTTATTAGTTTAATTTATATTAAAGAA
1 T-AGTTTATTAGTTTAAATTATATTAAAGAA
* *
955332 TAGTTTATTAG-TTAACGTTATATTAAAGAC
1 TAGTTTATTAGTTTAA-ATTATATTAAAGAA
955362 TAGTTTATTAGTT
1 TAGTTTATTAGTT
955375 GTTTAAGGGA
Statistics
Matches: 63, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
29 11 0.17
30 41 0.65
31 10 0.16
32 1 0.02
ACGTcount: A:0.38, C:0.03, G:0.11, T:0.48
Consensus pattern (30 bp):
TAGTTTATTAGTTTAAATTATATTAAAGAA
Found at i:957705 original size:14 final size:14
Alignment explanation
Indices: 957686--957733 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
957676 TTCAAGTCGT
957686 AAATCATTACTATC
1 AAATCATTACTATC
957700 AAATCATTAC--T-
1 AAATCATTACTATC
*
957711 AAATCATTAATATC
1 AAATCATTACTATC
957725 AAATCATTA
1 AAATCATTA
957734 AATATTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 9 0.30
12 1 0.03
13 1 0.03
14 19 0.63
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATCATTACTATC
Found at i:957713 original size:25 final size:25
Alignment explanation
Indices: 957685--957733 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
957675 GTTCAAGTCG
*
957685 TAAATCATTACTATCAAATCATTAC
1 TAAATCATTAATATCAAATCATTAC
957710 TAAATCATTAATATCAAATCATTA
1 TAAATCATTAATATCAAATCATTA
957734 AATATTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (25 bp):
TAAATCATTAATATCAAATCATTAC
Found at i:957749 original size:21 final size:22
Alignment explanation
Indices: 957685--957743 Score: 75
Period size: 25 Copynumber: 2.6 Consensus size: 22
957675 GTTCAAGTCG
*
957685 TAAATCATTACTATCAAATCATT
1 TAAATCATTAATATCAAATCA-T
957708 ACTAAATCATTAATATCAAATCAT
1 --TAAATCATTAATATCAAATCAT
957732 TAAAT-ATTAATA
1 TAAATCATTAATA
957744 ATAAATTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
21 7 0.21
22 5 0.15
24 1 0.03
25 20 0.61
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAATCATTAATATCAAATCAT
Found at i:957754 original size:21 final size:22
Alignment explanation
Indices: 957685--957754 Score: 63
Period size: 21 Copynumber: 3.1 Consensus size: 22
957675 GTTCAAGTCG
* *
957685 TAAATCATTACTATCAAATCATTAC
1 TAAATCATTAATATC-AA--ATTAT
*
957710 TAAATCATTAATATCAAATCAT
1 TAAATCATTAATATCAAATTAT
957732 TAAAT-ATTAATAAT-AAATTAT
1 TAAATCATTAAT-ATCAAATTAT
957753 TA
1 TA
957755 TTACTAATCT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
21 14 0.35
22 10 0.25
24 2 0.05
25 14 0.35
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (22 bp):
TAAATCATTAATATCAAATTAT
Found at i:957758 original size:49 final size:49
Alignment explanation
Indices: 957705--958688 Score: 438
Period size: 49 Copynumber: 18.4 Consensus size: 49
957695 CTATCAAATC
* * *
957705 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATT-ATT
1 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
*
957754 ATTACTAATCTTTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
* * *
957803 ATTACTAATCATTACTATTAAATCATTAAAAAGTAATAATAATTTAATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
* *
957852 ATTACTAATAATTACTATCAAATCATTAAAAATTAACAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
* *
957901 ATTACTAATCATTACTAAATCATTAAT-ATCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACT--ATCA--AATCATTAAA-AATT--A-A-TAA---TAATTTCATT
957961 ATTACTAATCATTACTAATCATTGCTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATC---A-T--T-A---CTATCAAATCATTAAAAATTAATAATAATTTCATT
*
958020 ATTACTAATAATTACTAAATTATTTTTATCAAATCATTAAAAATTAATAATGATTTTATTATTAC
1 ATTAC---TAA-T-C---ATTA---CTATCAAATCATTAAAAATTAATAAT-A----A-T-TT-C
*
958085 TAATC
47 --ATT
958090 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
* *
958140 ATTACTAATCATTACTAAATCATTAAT-ATCAAATCATTAAATATTAATAATAATTTCATTATTA
1 ATTACTAATCATTACT--ATCA--AATCATTAAA-AATT--A-A-TAA---TAATTTC---A-T-
958204 CTAAT
49 ----T
*
958209 CATTACTAATCATTACTATCAAATCATTAAAAATTAATAATATTTTCATT
1 -ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
958259 ATTACTAATCATTACTAAATCATTATTATCAAATCATTAAAAATTAATAATGATTTCATTATTAC
1 ATTACTAATCA-T--T--A-C-----TATCAAATCATTAAAAATTAATAAT-A----A-T-TT-C
*
958324 TAATC
47 --ATT
958329 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
* * * * *
958379 ATTACTAATCATTAATATCAAATCATT-AATATCAAATTATTAA-AT-ATT
1 ATTACTAATCATTACTATCAAATCATTAAAAAT-TAA-TAATAATTTCATT
* * * * * * *
958427 AATAATAATTTCATTATTA-CTAATCATTACTAATATTACT-ATCAA-ATCATT
1 ATTACTAA--TCATTACTATCAAATCATTA--AAAATTAATAAT-AATTTCATT
** * * * * * ** * * * *
958478 AAAAATTAAT-AATAATTTC--ATTATTACTAATCATTACTAA-ATCATT
1 -ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
* * * * * * * * * *
958524 ATTATCAAATCATTA--A--AAATTAATAATGATTTCATTATTA-TTAATC
1 ATTA-CTAATCATTACTATCAAATCATTAA-AAATTAATAATAATTTCATT
* *
958570 ATTACTAAATCATTACTATCAAATTATTAAAAATTAATAATAATTTAATT
1 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
*
958620 ATAACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
*
958669 ATTACTAATCATAACTATCA
1 ATTACTAATCATTACTATCA
958689 GATTACTATC
Statistics
Matches: 736, Mismatches: 91, Indels: 216
0.71 0.09 0.21
Matches are distributed among these distances:
45 9 0.01
46 35 0.05
47 4 0.01
48 55 0.07
49 237 0.32
50 57 0.08
51 12 0.02
52 24 0.03
53 16 0.02
54 3 0.00
55 6 0.01
56 3 0.00
57 5 0.01
59 23 0.03
60 130 0.18
61 3 0.00
62 9 0.01
63 10 0.01
64 6 0.01
65 2 0.00
66 17 0.02
67 17 0.02
68 13 0.02
69 1 0.00
70 34 0.05
71 5 0.01
ACGTcount: A:0.47, C:0.11, G:0.01, T:0.41
Consensus pattern (49 bp):
ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
Found at i:957934 original size:60 final size:60
Alignment explanation
Indices: 957847--958636 Score: 1275
Period size: 60 Copynumber: 13.2 Consensus size: 60
957837 AATAATAATT
* * *
957847 TAATTATTACT-AATAATTACTATCAAATCATTAAAAATTAACAATAATTTCATTATTAC
1 TAATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTAC
* *
957906 TAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTAC
1 TAATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTAC
*
957966 TAATCATTACT-AATCATTGCTATCAAATCATTAAAAATTAATAATAATTTCATTATTAC
1 TAATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTAC
* * ** * *
958025 TAATAATTACTAAATTATTTTTATCAAATCATTAAAAATTAATAATGATTTTATTATTAC
1 TAATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTAC
958085 TAATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTAC
1 TAATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTAC
* *
958145 TAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTAC
1 TAATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTAC
*
958205 TAATCATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATATTTTCATTATTAC
1 TAATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTAC
* *
958264 TAATCATTACTAAATCATTATTATCAAATCATTAAAAATTAATAATGATTTCATTATTAC
1 TAATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTAC
958324 TAATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTAC
1 TAATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTAC
* * * *
958384 TAATCATTAATATCAAATCATTAATATCAAATTATTAAATATTAATAATAATTTCATTATTAC
1 TAATCATT-A-CT-AAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTAC
958447 TAATCATTACT-AAT-ATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTAC
1 TAATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTAC
* * *
958505 TAATCATTACTAAATCATTATTATCAAATCATTAAAAATTAATAATGATTTCATTATTAT
1 TAATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTAC
* * *
958565 TAATCATTACTAAATCATTACTATCAAATTATTAAAAATTAATAATAATTTAATTATAAC
1 TAATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTAC
958625 TAATCATTACTA
1 TAATCATTACTA
958637 TCAAATCATT
Statistics
Matches: 676, Mismatches: 47, Indels: 15
0.92 0.06 0.02
Matches are distributed among these distances:
58 52 0.08
59 127 0.19
60 439 0.65
61 2 0.00
62 2 0.00
63 54 0.08
ACGTcount: A:0.46, C:0.12, G:0.01, T:0.42
Consensus pattern (60 bp):
TAATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTAC
Found at i:958061 original size:179 final size:180
Alignment explanation
Indices: 957847--958736 Score: 1357
Period size: 179 Copynumber: 5.0 Consensus size: 180
957837 AATAATAATT
* * *
957847 TAATTATTACT-AATAATTACTATCAAATCATTAAAAATTAACAATAATTTCATTATTACTAATC
1 TAATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
* *
957911 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC
66 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
*
957976 T-AATCATTGCTATCAAATCATTAAAAATTAATAATAATTTCATTATTAC
131 TAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTAC
* * ** * *
958025 TAATAATTACTAAATTATTTTTATCAAATCATTAAAAATTAATAATGATTTTATTATTACTAATC
1 TAATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
958090 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
66 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
* *
958155 TAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTAC
131 TAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTAC
*
958205 TAATCATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATATTTTCATTATTACTAATC
1 TAATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
* *
958269 ATTACTAAATCATTATTATCAAATCATTAAAAATTAATAATGATTTCATTATTACTAATCATTAC
66 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
958334 TAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTAC
131 TAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTAC
* * * *
958384 TAATCATTAATATCAAATCATTAATATCAAATTATTAAATATTAATAATAATTTCATTATTACTA
1 TAATCATT-A-CT-AAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTA
958449 ATCATTACT-AAT-ATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCAT
63 ATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCAT
* * *
958512 TACTAAATCATTATTATCAAATCATTAAAAATTAATAATGATTTCATTATTAT
128 TACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTAC
*
958565 TAATCATTACTAAATCATTACTATCAAATTATTAAAAATTAATAATAATTT-A--A-T--T-AT-
1 TAATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
*
958622 A--ACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATAAC
66 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
* *
958684 T--ATCAGATTACTATCAAATCATTAAATATTAATAATAATTTCATCATTAC
131 TAAATC--ATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTAC
958734 TAA
1 TAA
958737 ATCTTATAAA
Statistics
Matches: 661, Mismatches: 42, Indels: 27
0.91 0.06 0.04
Matches are distributed among these distances:
167 3 0.00
168 6 0.01
169 96 0.15
170 1 0.00
171 2 0.00
172 1 0.00
174 1 0.00
175 1 0.00
177 1 0.00
178 48 0.07
179 278 0.42
180 57 0.09
181 108 0.16
182 3 0.00
183 55 0.08
ACGTcount: A:0.46, C:0.12, G:0.01, T:0.41
Consensus pattern (180 bp):
TAATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
TAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTAC
Found at i:958140 original size:239 final size:239
Alignment explanation
Indices: 957701--958736 Score: 1525
Period size: 239 Copynumber: 4.5 Consensus size: 239
957691 ATTACTATCA
957701 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAAT-A----A--ATTA-T--T-A
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
*
957755 TTACTAATCTTTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCA-T--T-
66 TTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTA
* * *
957816 -A-C--TA-T-T-AAATCATTAAAAAGTAATAATAATTT-A--ATTA-T--T-A---CT-AATAA
131 AATCATTATTATCAAATCATTAAAAATTAATAATGATTTCATTATTACTAATCATTACTAAATCA
*
957863 TTACTATCAAATCATTAAAAATTAACAATAATTTCATTATTACT
196 TTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
957907 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
* *
957972 TTACTAATCATTGCTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATAATTACTA
66 TTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTA
* * *
958037 AATTATTTTTATCAAATCATTAAAAATTAATAATGATTTTATTATTACTAATCATTACTAAATCA
131 AATCATTATTATCAAATCATTAAAAATTAATAATGATTTCATTATTACTAATCATTACTAAATCA
958102 TTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
196 TTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
958146 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
*
958211 TTACTAATCATTACTATCAAATCATTAAAAATTAATAATATTTTCATTATTACTAATCATTACTA
66 TTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTA
958276 AATCATTATTATCAAATCATTAAAAATTAATAATGATTTCATTATTACTAATCATTACTAAATCA
131 AATCATTATTATCAAATCATTAAAAATTAATAATGATTTCATTATTACTAATCATTACTAAATCA
958341 TTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
196 TTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
* *
958385 AATCATTAATATCAAATCATTAATATCAAATTATTAAATATTAATAATAATTTCATTATTACTAA
1 AATCATT-A-CT-AAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAA
958450 TCATTACTAAT-ATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTA
63 TCATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTA
*
958514 CTAAATCATTATTATCAAATCATTAAAAATTAATAATGATTTCATTATTATTAATCATTACTAAA
128 CTAAATCATTATTATCAAATCATTAAAAATTAATAATGATTTCATTATTACTAATCATTACTAAA
*
958579 TCATTACTATCAAATTATTAAAAATTAATAATAATTT-A--A-T--T
193 TCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
* *
958620 -AT-A--ACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCA
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
* * *
958680 TAACT-ATCAGATTACTATCAAATCATTAAATATTAATAATAATTTCATCATTACTAA
66 TTACTAATC--ATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAA
958737 ATCTTATAAA
Statistics
Matches: 764, Mismatches: 27, Indels: 55
0.90 0.03 0.07
Matches are distributed among these distances:
206 45 0.06
207 1 0.00
211 1 0.00
213 4 0.01
214 1 0.00
216 1 0.00
217 57 0.07
218 1 0.00
220 1 0.00
222 1 0.00
225 1 0.00
226 3 0.00
227 56 0.07
228 24 0.03
229 47 0.06
230 1 0.00
231 4 0.01
232 1 0.00
233 1 0.00
234 3 0.00
235 2 0.00
237 1 0.00
238 3 0.00
239 287 0.38
240 2 0.00
241 153 0.20
242 62 0.08
ACGTcount: A:0.47, C:0.11, G:0.01, T:0.41
Consensus pattern (239 bp):
AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
TTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTA
AATCATTATTATCAAATCATTAAAAATTAATAATGATTTCATTATTACTAATCATTACTAAATCA
TTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
Found at i:958215 original size:10 final size:10
Alignment explanation
Indices: 958200--958226 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
958190 TAATTTCATT
958200 ATTACTAATC
1 ATTACTAATC
958210 ATTACTAATC
1 ATTACTAATC
958220 ATTACTA
1 ATTACTA
958227 TCAAATCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (10 bp):
ATTACTAATC
Found at i:958302 original size:24 final size:24
Alignment explanation
Indices: 958254--958302 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
958244 AATAATATTT
* *
958254 TCATTATTACTAATCATTACTAAA
1 TCATTATTACAAATCATTACAAAA
958278 TCATTATTATCAAATCATTA-AAAA
1 TCATTATTA-CAAATCATTACAAAA
958302 T
1 T
958303 TAATAATGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (24 bp):
TCATTATTACAAATCATTACAAAA
Found at i:958391 original size:35 final size:35
Alignment explanation
Indices: 958350--958455 Score: 102
Period size: 35 Copynumber: 3.2 Consensus size: 35
958340 ATTACTATCA
958350 AATCATTAAAAATTAATAATAATTTCATTATTACT
1 AATCATTAAAAATTAATAATAATTTCATTATTACT
* * *
958385 AATCATT---AA-T-ATCA-AA--TCATTAATATCA
1 AATCATTAAAAATTAATAATAATTTCATTATTA-CT
* *
958413 AATTATTAAATATTAATAATAATTTCATTATTACT
1 AATCATTAAAAATTAATAATAATTTCATTATTACT
958448 AATCATTA
1 AATCATTA
958456 CTAATATTAC
Statistics
Matches: 53, Mismatches: 9, Indels: 18
0.66 0.11 0.22
Matches are distributed among these distances:
27 8 0.15
28 7 0.13
29 2 0.04
30 3 0.06
31 2 0.04
32 3 0.06
33 3 0.06
34 2 0.04
35 15 0.28
36 8 0.15
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.42
Consensus pattern (35 bp):
AATCATTAAAAATTAATAATAATTTCATTATTACT
Found at i:958404 original size:14 final size:14
Alignment explanation
Indices: 958385--958421 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
958375 CATTATTACT
958385 AATCATTAATATCA
1 AATCATTAATATCA
958399 AATCATTAATATCA
1 AATCATTAATATCA
*
958413 AATTATTAA
1 AATCATTAA
958422 ATATTAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (14 bp):
AATCATTAATATCA
Found at i:958450 original size:18 final size:18
Alignment explanation
Indices: 958423--958508 Score: 50
Period size: 18 Copynumber: 4.6 Consensus size: 18
958413 AATTATTAAA
*
958423 TATTAATAATAATTTCAT
1 TATTACTAATAATTTCAT
* * *
958441 TATTACTAATCATTACTAA
1 TATTACTAATAATTTC-AT
*
958460 TATTACT-ATCAA-ATCAT
1 TATTACTAAT-AATTTCAT
*
958477 TAAAAATTAATAATAATTTCAT
1 T----ATTACTAATAATTTCAT
958499 TATTACTAAT
1 TATTACTAAT
958509 CATTACTAAA
Statistics
Matches: 49, Mismatches: 11, Indels: 16
0.64 0.14 0.21
Matches are distributed among these distances:
17 2 0.04
18 24 0.49
19 9 0.18
21 7 0.14
22 7 0.14
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.44
Consensus pattern (18 bp):
TATTACTAATAATTTCAT
Found at i:958543 original size:24 final size:24
Alignment explanation
Indices: 958495--958543 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
958485 AATAATAATT
* *
958495 TCATTATTACTAATCATTACTAAA
1 TCATTATTACAAATCATTACAAAA
958519 TCATTATTATCAAATCATTA-AAAA
1 TCATTATTA-CAAATCATTACAAAA
958543 T
1 T
958544 TAATAATGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (24 bp):
TCATTATTACAAATCATTACAAAA
Found at i:958682 original size:21 final size:21
Alignment explanation
Indices: 958653--958736 Score: 52
Period size: 21 Copynumber: 4.1 Consensus size: 21
958643 CATTAAAAAT
958653 TAATAATAATTTCATTATTAC
1 TAATAATAATTTCATTATTAC
* * *
958674 TAATCATAACTATCA-GATTAC
1 TAATAATAA-TTTCATTATTAC
* * *
958695 T-ATCA-AA--TCATTAAATAT
1 TAATAATAATTTCATT-ATTAC
*
958713 TAATAATAATTTCATCATTAC
1 TAATAATAATTTCATTATTAC
958734 TAA
1 TAA
958737 ATCTTATAAA
Statistics
Matches: 46, Mismatches: 10, Indels: 14
0.66 0.14 0.20
Matches are distributed among these distances:
16 3 0.07
18 4 0.09
19 5 0.11
20 6 0.13
21 20 0.43
22 8 0.17
ACGTcount: A:0.45, C:0.13, G:0.01, T:0.40
Consensus pattern (21 bp):
TAATAATAATTTCATTATTAC
Found at i:958736 original size:109 final size:108
Alignment explanation
Indices: 958505--958736 Score: 340
Period size: 109 Copynumber: 2.1 Consensus size: 108
958495 TCATTATTAC
* * *
958505 TAATCATTACTAAATCATTATTATCAAATCATTAAAAATTAATAATGATTTCATTATTATTAATC
1 TAATCATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
* *
958570 ATTACTAAATCATTACTATCAAATTATTAAAAATTAATAATAATT
65 ATAACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATT
* *
958615 TAATTATAACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCA
1 TAATCATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCA
*
958680 TAACT-ATCAGATTACTATCAAATCATTAAATATTAATAATAATT
66 TAACTAATC--ATTACTATCAAATCATTAAAAATTAATAATAATT
*
958724 TCATCATTACTAA
1 TAATCATTACTAA
958737 ATCTTATAAA
Statistics
Matches: 109, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
107 3 0.03
109 97 0.89
110 9 0.08
ACGTcount: A:0.47, C:0.12, G:0.01, T:0.41
Consensus pattern (108 bp):
TAATCATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCA
TAACTAATCATTACTATCAAATCATTAAAAATTAATAATAATT
Found at i:961839 original size:28 final size:28
Alignment explanation
Indices: 961808--961861 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
961798 ATAATCTAAT
*
961808 ATATAACTTAAACTAACAAATTAATATA
1 ATATAACTTAAACTAACAAACTAATATA
961836 ATATAACTTAAACTAACAAACTAATA
1 ATATAACTTAAACTAACAAACTAATA
961862 ATTTATACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (28 bp):
ATATAACTTAAACTAACAAACTAATATA
Found at i:961868 original size:28 final size:28
Alignment explanation
Indices: 961804--961868 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
961794 TTATATAATC
*
961804 TAATATATAACTTAAACTAACAAATTAA
1 TAATATATAACTTAAACTAACAAACTAA
961832 T-ATAATATAACTTAAACTAACAAACTAA
1 TAAT-ATATAACTTAAACTAACAAACTAA
*
961860 TAATTTATA
1 TAATATATA
961869 CTAACAAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 29 0.88
29 2 0.06
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (28 bp):
TAATATATAACTTAAACTAACAAACTAA
Found at i:961871 original size:21 final size:21
Alignment explanation
Indices: 961838--961886 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
961828 TTAATATAAT
961838 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
961859 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
961880 ATTAACT
1 A-TAACT
961887 AAAATTATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:962630 original size:29 final size:29
Alignment explanation
Indices: 962526--962661 Score: 85
Period size: 29 Copynumber: 4.6 Consensus size: 29
962516 GGACGCCGGC
* * *
962526 GTGCATGGCAACCTATAAGGTCGCTGGGC
1 GTGCATGGCGACCTACAAGGTCGCTGGGA
* * *
962555 GTACATGGCGACCTACCATCTTGGTCG-TCGGTA
1 GTGCATGGCGACCTA-CA---AGGTCGCT-GGGA
* * *
962588 TTGCTTGGCAACCTACAAGGTCGCTGGGA
1 GTGCATGGCGACCTACAAGGTCGCTGGGA
* *** *
962617 GTGCATGGTGACCTTGTAGGTCGCTTGGA
1 GTGCATGGCGACCTACAAGGTCGCTGGGA
*
962646 GTGCTTGGCGACCTAC
1 GTGCATGGCGACCTAC
962662 GGCCAGCTGT
Statistics
Matches: 77, Mismatches: 24, Indels: 12
0.68 0.21 0.11
Matches are distributed among these distances:
29 54 0.70
30 2 0.03
32 3 0.04
33 18 0.23
ACGTcount: A:0.18, C:0.24, G:0.32, T:0.26
Consensus pattern (29 bp):
GTGCATGGCGACCTACAAGGTCGCTGGGA
Found at i:967911 original size:13 final size:13
Alignment explanation
Indices: 967893--967918 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
967883 ATGTTGATCA
967893 AACTTTGATCGAG
1 AACTTTGATCGAG
967906 AACTTTGATCGAG
1 AACTTTGATCGAG
967919 TCATTTTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
AACTTTGATCGAG
Found at i:975205 original size:32 final size:32
Alignment explanation
Indices: 975132--975206 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
975122 ATTAGACGTG
* *
975132 AATTTATAAAATTTTAGGAGGTGAAAATAGAG
1 AATTTATAAAATTTTAGGACGTGAAAATAGAA
** ** *
975164 AATCAATAAAATTTTAGGACGTGAATTTATAA
1 AATTTATAAAATTTTAGGACGTGAAAATAGAA
975196 AATTTATAAAA
1 AATTTATAAAA
975207 AGTCAAAGAG
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.49, C:0.03, G:0.15, T:0.33
Consensus pattern (32 bp):
AATTTATAAAATTTTAGGACGTGAAAATAGAA
Found at i:981993 original size:31 final size:31
Alignment explanation
Indices: 981934--982007 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 31
981924 GAGTAATCAA
* *
981934 TTTGTTACAAATCAATAATATTAGTGACCGG
1 TTTGTTACAAATCAATAACATTAATGACCGG
* * * **
981965 TTTGTTTCACATCGATAACATTAATGACCAA
1 TTTGTTACAAATCAATAACATTAATGACCGG
*
981996 TTTATTACAAAT
1 TTTGTTACAAAT
982008 TGATAATATT
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (31 bp):
TTTGTTACAAATCAATAACATTAATGACCGG
Found at i:990338 original size:35 final size:36
Alignment explanation
Indices: 990285--990364 Score: 117
Period size: 35 Copynumber: 2.2 Consensus size: 36
990275 GGCAACCAAT
* *
990285 TTTGAAAAATTGGTTTTCAAAGTTTGATAAATGTTTC
1 TTTG-AAAATTGGGTTTCAAAGTTTGATAAATGTTTA
*
990322 TTTGAAAA-TGGGTTTCAAAGTTTGGTAAATGTTTA
1 TTTGAAAATTGGGTTTCAAAGTTTGATAAATGTTTA
990357 TTTGAAAA
1 TTTGAAAA
990365 AATAGTTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 32 0.80
36 4 0.10
37 4 0.10
ACGTcount: A:0.34, C:0.04, G:0.19, T:0.44
Consensus pattern (36 bp):
TTTGAAAATTGGGTTTCAAAGTTTGATAAATGTTTA
Found at i:990844 original size:18 final size:17
Alignment explanation
Indices: 990806--990839 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
990796 ATTTATTACT
990806 ATTTACGTGAATAGTAA
1 ATTTACGTGAATAGTAA
990823 ATTT-CGTGAATAGTAA
1 ATTTACGTGAATAGTAA
990839 A
1 A
990840 AATTTTGTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.41, C:0.06, G:0.18, T:0.35
Consensus pattern (17 bp):
ATTTACGTGAATAGTAA
Found at i:994895 original size:35 final size:35
Alignment explanation
Indices: 994845--994960 Score: 162
Period size: 35 Copynumber: 3.3 Consensus size: 35
994835 TGGCAACCAA
994845 CTTTGAAAAATTGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAA-TGGTTTTCAAAGTTTGGTAAATGTTT
994882 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* * *
994917 CTATGAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
*
994953 -GTTGAAAA
1 CTTTGAAAA
994961 ATGATAATGT
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
35 41 0.56
36 27 0.37
37 5 0.07
ACGTcount: A:0.31, C:0.05, G:0.20, T:0.44
Consensus pattern (35 bp):
CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:996830 original size:17 final size:17
Alignment explanation
Indices: 996782--996830 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 17
996772 ATGATATCAC
996782 ATGTATCCCAAAACCCG
1 ATGTATCCCAAAACCCG
* * *
996799 ATATAGATACCAAAATCCG
1 ATGT--ATCCCAAAACCCG
996818 ATGTATCCCAAAA
1 ATGTATCCCAAAA
996831 ACTCTCTCAA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
17 11 0.44
19 14 0.56
ACGTcount: A:0.43, C:0.27, G:0.10, T:0.20
Consensus pattern (17 bp):
ATGTATCCCAAAACCCG
Found at i:999079 original size:28 final size:26
Alignment explanation
Indices: 999023--999086 Score: 67
Period size: 28 Copynumber: 2.4 Consensus size: 26
999013 CCATATAACT
* *
999023 TTTTTTTTTTCATTGCACAATCTCTC
1 TTTTTTTTTCCTTTGCACAATCTCTC
*
999049 TTTCTTTATTTCCTTTGCACAAT-TTTAC
1 TTT-TTT-TTTCCTTTGCACAATCTCT-C
999077 TTTTTTTTTC
1 TTTTTTTTTC
999087 TCATTTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
26 7 0.22
27 8 0.25
28 17 0.53
ACGTcount: A:0.14, C:0.20, G:0.03, T:0.62
Consensus pattern (26 bp):
TTTTTTTTTCCTTTGCACAATCTCTC
Found at i:1000307 original size:25 final size:28
Alignment explanation
Indices: 1000277--1000327 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
1000267 AAGGAAAAAT
*
1000277 AAAATA-AAA-TAA-AATAAAAAGAACG
1 AAAATAGAAATTAATAAAAAAAAGAACG
1000302 AAAATAGAAATTAATAAAAAAAAGAA
1 AAAATAGAAATTAATAAAAAAAAGAA
1000328 AAATTGGGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 6 0.27
26 3 0.14
27 3 0.14
28 10 0.45
ACGTcount: A:0.76, C:0.02, G:0.08, T:0.14
Consensus pattern (28 bp):
AAAATAGAAATTAATAAAAAAAAGAACG
Found at i:1010025 original size:29 final size:30
Alignment explanation
Indices: 1009982--1010049 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
1009972 TATAATTATT
1009982 TTTGAAAAATAATTT-ATGTAAAATAAATTA-
1 TTTG-AAAATAATTTAAT-TAAAATAAATTAC
* *
1010012 TTTGAAAATGATTTAATTAAAATGAATTAC
1 TTTGAAAATAATTTAATTAAAATAAATTAC
*
1010042 ATTGAAAA
1 TTTGAAAA
1010050 ATAGTTTTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 20 0.61
30 13 0.39
ACGTcount: A:0.51, C:0.01, G:0.09, T:0.38
Consensus pattern (30 bp):
TTTGAAAATAATTTAATTAAAATAAATTAC
Found at i:1010595 original size:16 final size:18
Alignment explanation
Indices: 1010563--1010595 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
1010553 GAAAACAGTA
1010563 AATAATATTAGTTATATT
1 AATAATATTAGTTATATT
1010581 AATAAT-TTA-TTATAT
1 AATAATATTAGTTATAT
1010596 ATTATTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 3 0.20
18 6 0.40
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (18 bp):
AATAATATTAGTTATATT
Found at i:1010676 original size:19 final size:18
Alignment explanation
Indices: 1010652--1010696 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
1010642 GAGTATATAT
1010652 TAATATAATATTAAAAATA
1 TAATAT-ATATTAAAAATA
*
1010671 TAATAT-TATTAAAATTA
1 TAATATATATTAAAAATA
*
1010688 TATTATATA
1 TAATATATA
1010697 AATACATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 15 0.65
18 2 0.09
19 6 0.26
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TAATATATATTAAAAATA
Found at i:1011118 original size:6 final size:7
Alignment explanation
Indices: 1011096--1011121 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1011086 CTTAATTTGA
1011096 TTTAATT
1 TTTAATT
1011103 TTTAATT
1 TTTAATT
1011110 TTTAATT
1 TTTAATT
1011117 TTTAA
1 TTTAA
1011122 ATATACTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
TTTAATT
Found at i:1018922 original size:16 final size:15
Alignment explanation
Indices: 1018892--1018930 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
1018882 ATGTGTATTA
*
1018892 ATAAAATAT-TTTAT
1 ATAAATTATGTTTAT
1018906 ATACAATTATGTTTAT
1 ATA-AATTATGTTTAT
1018922 ATAAATTAT
1 ATAAATTAT
1018931 CTCAATGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 3 0.14
15 11 0.50
16 8 0.36
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (15 bp):
ATAAATTATGTTTAT
Found at i:1024277 original size:4 final size:4
Alignment explanation
Indices: 1024268--1024295 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
1024258 TGGAATTTTC
1024268 TTAT TTAT TTAT TTAT TTAT TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT
1024296 CATTTCTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTAT
Found at i:1027321 original size:20 final size:20
Alignment explanation
Indices: 1027298--1027347 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1027288 GCGAAATTGG
1027298 AAATCGCAACGCGAATATGT
1 AAATCGCAACGCGAATATGT
* *
1027318 AAATCGCAACGCGTATCTGT
1 AAATCGCAACGCGAATATGT
*
1027338 AATTCGCAAC
1 AAATCGCAAC
1027348 ACAGAAGTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (20 bp):
AAATCGCAACGCGAATATGT
Found at i:1027550 original size:22 final size:22
Alignment explanation
Indices: 1027525--1027571 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1027515 GGCGACATCT
*
1027525 GTCCCCATCTCCGACGAAATCC
1 GTCCCCATCTCCGACAAAATCC
* *
1027547 GTCCCCATCTTCGGCAAAATCC
1 GTCCCCATCTCCGACAAAATCC
1027569 GTC
1 GTC
1027572 TATCTCCATC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.21, C:0.43, G:0.15, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACAAAATCC
Found at i:1028930 original size:30 final size:30
Alignment explanation
Indices: 1028894--1028956 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
1028884 ACCTAAATGC
1028894 ATGTAACCTATTTCCGTGGGGTTCATATCT
1 ATGTAACCTATTTCCGTGGGGTTCATATCT
*
1028924 ATGTAACCTGTTTCCGTGGGGTTCATATCT
1 ATGTAACCTATTTCCGTGGGGTTCATATCT
1028954 ATG
1 ATG
1028957 AAAAAGTTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (30 bp):
ATGTAACCTATTTCCGTGGGGTTCATATCT
Found at i:1029633 original size:21 final size:21
Alignment explanation
Indices: 1029606--1029655 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
1029596 ATTAGGGGAG
* *
1029606 TTACGTGATGAGGTCAATGCT
1 TTACGTGAGGAGGTCAATACT
* *
1029627 TTGCGTGAGGAGGTCGATACT
1 TTACGTGAGGAGGTCAATACT
1029648 TTACGTGA
1 TTACGTGA
1029656 AGACAATGAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.14, G:0.32, T:0.32
Consensus pattern (21 bp):
TTACGTGAGGAGGTCAATACT
Found at i:1029696 original size:21 final size:21
Alignment explanation
Indices: 1029672--1029721 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1029662 TGATGCATGG
*
1029672 CGTGATGAGGTA-CGGTCTTTA
1 CGTGATGAGGTAGAGGT-TTTA
*
1029693 CGTGGTGAGGTAGAGGTTTTA
1 CGTGATGAGGTAGAGGTTTTA
*
1029714 CGCGATGA
1 CGTGATGA
1029722 CAATGGTGCT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.20, C:0.12, G:0.38, T:0.30
Consensus pattern (21 bp):
CGTGATGAGGTAGAGGTTTTA
Found at i:1030132 original size:42 final size:42
Alignment explanation
Indices: 1030065--1030156 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
1030055 CCTGTCATCT
*
1030065 TTCAAGAGGCCCCTATCATCCTTCAAGAGGCCCCTCCCACCG
1 TTCAAGAGGCCCCTATCAACCTTCAAGAGGCCCCTCCCACCG
* * * *
1030107 TTCAAGAGGCCCCTGTCAACGTTCAAGAGGTCCCTCCCACGG
1 TTCAAGAGGCCCCTATCAACCTTCAAGAGGCCCCTCCCACCG
1030149 TTCAAGAG
1 TTCAAGAG
1030157 CCCGATTCAC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.23, C:0.37, G:0.21, T:0.20
Consensus pattern (42 bp):
TTCAAGAGGCCCCTATCAACCTTCAAGAGGCCCCTCCCACCG
Done.