Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008122.1 Hibiscus syriacus cultivar Beakdansim tig00110676_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: 2511854
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 8
Found at i:328 original size:6 final size:6
Alignment explanation
Indices: 317--363 Score: 80
Period size: 6 Copynumber: 8.2 Consensus size: 6
307 GACACGTATT
317 ACCACG ACCACG ACCACG ACCACG ACCACG A-C-CG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
363 A
1 A
364 TCCGAGCCGA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
4 3 0.08
5 2 0.05
6 34 0.87
ACGTcount: A:0.34, C:0.49, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:373 original size:22 final size:22
Alignment explanation
Indices: 317--363 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 22
307 GACACGTATT
317 ACCACGACCACGACCACGACCACG
1 ACCACGA-C-CGACCACGACCACG
341 ACCACGACCGACCACGACCACG
1 ACCACGACCGACCACGACCACG
363 A
1 A
364 TCCGAGCCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 15 0.65
23 1 0.04
24 7 0.30
ACGTcount: A:0.34, C:0.49, G:0.17, T:0.00
Consensus pattern (22 bp):
ACCACGACCGACCACGACCACG
Found at i:6195 original size:5 final size:5
Alignment explanation
Indices: 6185--6248 Score: 92
Period size: 5 Copynumber: 12.8 Consensus size: 5
6175 ACCACGACCA
* *
6185 CGAGC CGAGC CGAGC CGAGC CGTGC CGTGC CGAGC CGAGC CGAGC CGAGC
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC
* *
6235 CGAGA CGAGA CGAG
1 CGAGC CGAGC CGAG
6249 ACGGACGGAC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 56 1.00
ACGTcount: A:0.20, C:0.36, G:0.41, T:0.03
Consensus pattern (5 bp):
CGAGC
Found at i:11164 original size:57 final size:57
Alignment explanation
Indices: 11076--11190 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
11066 AGCCAATTTC
11076 TTTTATAATAGTTTCCCATCTTTATCCTTCTTTGTCTTCACAAATTTCCATTAACTT
1 TTTTATAATAGTTTCCCATCTTTATCCTTCTTTGTCTTCACAAATTTCCATTAACTT
11133 TTTTATAATAGTTTCCCATCTTTATCCTTCTTTGTCTTCACAAATTTCCATTAACTT
1 TTTTATAATAGTTTCCCATCTTTATCCTTCTTTGTCTTCACAAATTTCCATTAACTT
11190 T
1 T
11191 CTATTGCACC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.23, C:0.23, G:0.03, T:0.51
Consensus pattern (57 bp):
TTTTATAATAGTTTCCCATCTTTATCCTTCTTTGTCTTCACAAATTTCCATTAACTT
Found at i:21441 original size:2 final size:2
Alignment explanation
Indices: 21434--21466 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
21424 CCGGCAATTC
21434 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
21467 TTATTCATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21579 original size:16 final size:16
Alignment explanation
Indices: 21539--21569 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21529 AATTGTTTTT
*
21539 TTATAATATAATATAG
1 TTATAAAATAATATAG
21555 TTATAAAATAATATA
1 TTATAAAATAATATA
21570 TGTTTGAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
TTATAAAATAATATAG
Found at i:24906 original size:24 final size:24
Alignment explanation
Indices: 24872--24927 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
24862 TAAGCAAGGG
* *
24872 TGCAAATATTTATTTCCTGTACGA
1 TGCAAAGATTTATTTCCCGTACGA
24896 TGCAAAGATTTATTTCCCGTACGA
1 TGCAAAGATTTATTTCCCGTACGA
24920 TGCAAAGA
1 TGCAAAGA
24928 GACTTACTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (24 bp):
TGCAAAGATTTATTTCCCGTACGA
Found at i:27763 original size:24 final size:24
Alignment explanation
Indices: 27718--27763 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
27708 GGTTTTGGAT
*
27718 TGGGTTTAGAGAGGAAGGAGAGAG
1 TGGGTTTAGAGAGGAAGAAGAGAG
*
27742 TGGGTTTTAGAG-GGGAGAAGAG
1 TGGG-TTTAGAGAGGAAGAAGAG
27764 GAGGCGCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.30, C:0.00, G:0.50, T:0.20
Consensus pattern (24 bp):
TGGGTTTAGAGAGGAAGAAGAGAG
Found at i:27909 original size:4 final size:4
Alignment explanation
Indices: 27900--27927 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
27890 CCTCTTCCAA
27900 TTAT TTAT TTAT TTAT TTAT TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT
27928 ATCTCTTCAA
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:32717 original size:22 final size:23
Alignment explanation
Indices: 32663--32721 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
32653 TCTACAAAAA
*
32663 TATTTTATTATATTATATATATAG
1 TATTTTATTAT-TAATATATATAG
**
32687 TATTATTATTATTAATATAT-TTT
1 TATT-TTATTATTAATATATATAG
32710 TATTTTATTATT
1 TATTTTATTATT
32722 TTGCAGGCCC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
22 8 0.26
23 5 0.16
24 11 0.35
25 7 0.23
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (23 bp):
TATTTTATTATTAATATATATAG
Found at i:32811 original size:33 final size:33
Alignment explanation
Indices: 32770--32858 Score: 126
Period size: 33 Copynumber: 2.7 Consensus size: 33
32760 TTAAGAAAAT
32770 AAACCAATGTATTTGAGTCCAATTGAAACACTA
1 AAACCAATGTATTTGAGTCCAATTGAAACACTA
* * *
32803 AAATCAATGTATTTGAATCCTATTGAAACACTA
1 AAACCAATGTATTTGAGTCCAATTGAAACACTA
32836 AAACCGAA-GTATTTTGAGTCCAA
1 AAACC-AATGTA-TTTGAGTCCAA
32859 GTCTCTAAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
33 37 0.77
34 11 0.23
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (33 bp):
AAACCAATGTATTTGAGTCCAATTGAAACACTA
Found at i:38829 original size:16 final size:17
Alignment explanation
Indices: 38802--38836 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
38792 TATCGTCGAC
38802 CGAAATTTCACTATTCA
1 CGAAATTTCACTATTCA
38819 CGAAA-TTCACTATTCA
1 CGAAATTTCACTATTCA
38835 CG
1 CG
38837 TGAATAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.31
Consensus pattern (17 bp):
CGAAATTTCACTATTCA
Found at i:52045 original size:29 final size:30
Alignment explanation
Indices: 51977--52049 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 30
51967 AAATTTGAGG
* * * *
51977 ACCAATTTAGAATGTATTCATAGTTTAAGA
1 ACCAATTTAAAATGTATTAAAAGTGTAAGA
*
52007 ACGGAA-TTAAAATGT-TTAAAAGTGTAAGA
1 AC-CAATTTAAAATGTATTAAAAGTGTAAGA
52036 ACCAATTTAAAATG
1 ACCAATTTAAAATG
52050 AGGGTCATAG
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
28 2 0.06
29 21 0.60
30 10 0.29
31 2 0.06
ACGTcount: A:0.45, C:0.08, G:0.15, T:0.32
Consensus pattern (30 bp):
ACCAATTTAAAATGTATTAAAAGTGTAAGA
Found at i:52679 original size:17 final size:18
Alignment explanation
Indices: 52646--52680 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
52636 TTTATCCCCA
52646 TTTTCTTCTCAATAATTT
1 TTTTCTTCTCAATAATTT
*
52664 TTTTTTTCTCAA-AATTT
1 TTTTCTTCTCAATAATTT
52681 ATTCGAAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.23, C:0.14, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTCTTCTCAATAATTT
Found at i:64662 original size:31 final size:31
Alignment explanation
Indices: 64627--64688 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
64617 TTGGGCATTG
64627 GCATCAAACTCTTTCACACACTTAAAACAAA
1 GCATCAAACTCTTTCACACACTTAAAACAAA
64658 GCATCAAACTCTTTCACACACTTAAAACAAA
1 GCATCAAACTCTTTCACACACTTAAAACAAA
64689 CTTTACAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.45, C:0.29, G:0.03, T:0.23
Consensus pattern (31 bp):
GCATCAAACTCTTTCACACACTTAAAACAAA
Found at i:69942 original size:62 final size:62
Alignment explanation
Indices: 69814--69966 Score: 186
Period size: 62 Copynumber: 2.5 Consensus size: 62
69804 TGAATGTATA
* * *
69814 CATCGATGCACTACTGTGCATCGGTGCATAAAATGCATTCGATGTTTTTATTTAATGGGATG
1 CATCGATGCACTACTGTGCATCGATGCATAAAATCCATTCGATGTTTTTATTTAATGGCATG
* * *
69876 CATCGATGCACTCCTTATGCATCGATGCAT-AAATCCTATTCGATGTTTTCTA-TTAAT-TCATG
1 CATCGATGCACTAC-TGTGCATCGATGCATAAAATCC-ATTCGATGTTTT-TATTTAATGGCATG
*
69938 CATCGATGCACTGCATGTGCATCGATGCA
1 CATCGATGCACTAC-TGTGCATCGATGCA
69967 CCTTAAACAA
Statistics
Matches: 79, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
62 47 0.59
63 30 0.38
64 2 0.03
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (62 bp):
CATCGATGCACTACTGTGCATCGATGCATAAAATCCATTCGATGTTTTTATTTAATGGCATG
Found at i:72624 original size:31 final size:30
Alignment explanation
Indices: 72586--72679 Score: 91
Period size: 30 Copynumber: 3.1 Consensus size: 30
72576 GAACCTCGGC
*
72586 AACTGTCCATAGGTCCCAAAGAACCTAGGTA
1 AACTGTCCATA-GTCCCAAAGAACATAGGTA
* * **
72617 AACTGTCCATATTTCCTTAGAACATAGGTA
1 AACTGTCCATAGTCCCAAAGAACATAGGTA
* *
72647 TACTGTCCATATGTCTCGAAAG-ACATAGGTA
1 AACTGTCCATA-GTC-CCAAAGAACATAGGTA
72678 AA
1 AA
72680 ACCCTCGACT
Statistics
Matches: 49, Mismatches: 12, Indels: 4
0.75 0.18 0.06
Matches are distributed among these distances:
30 24 0.49
31 22 0.45
32 3 0.06
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (30 bp):
AACTGTCCATAGTCCCAAAGAACATAGGTA
Found at i:72845 original size:17 final size:19
Alignment explanation
Indices: 72813--72848 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
72803 CATATATCTC
72813 ATATCATATCACATGTATT
1 ATATCATATCACATGTATT
72832 ATAT-ATAT-ACATGTATT
1 ATATCATATCACATGTATT
72849 CATGTAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (19 bp):
ATATCATATCACATGTATT
Found at i:73463 original size:59 final size:58
Alignment explanation
Indices: 73356--73468 Score: 140
Period size: 59 Copynumber: 1.9 Consensus size: 58
73346 GCACTACTTG
* * *
73356 TGCATCGGTGCATAAAATGCATTCGATGTTTTTATTTAATGGGGATGCATCGATCCTTA
1 TGCATCGATGCATAAAATCCATTCGATGTTTTTATTTAAT-GGCATGCATCGATCCTTA
*
73415 TGCATCGATGCAT-AAATCCTATTCGATGTTTTCTATTTAAAT-TCATGCATCGAT
1 TGCATCGATGCATAAAATCC-ATTCGATGTTTT-TATTT-AATGGCATGCATCGAT
73469 ACACTGCATG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
58 5 0.11
59 34 0.72
60 5 0.11
61 3 0.06
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.39
Consensus pattern (58 bp):
TGCATCGATGCATAAAATCCATTCGATGTTTTTATTTAATGGCATGCATCGATCCTTA
Found at i:75902 original size:13 final size:13
Alignment explanation
Indices: 75884--75957 Score: 94
Period size: 13 Copynumber: 5.3 Consensus size: 13
75874 GTCACAACCC
75884 GACCCGACCCGTT
1 GACCCGACCCGTT
75897 GACCCGACCCGTT
1 GACCCGACCCGTT
75910 GACCCGACCCGACCCGTT
1 -----GACCCGACCCGTT
*
75928 TACCCGACCCGTT
1 GACCCGACCCGTT
75941 GACCCGACCCGTT
1 GACCCGACCCGTT
75954 GACC
1 GACC
75958 GTTGACCCAT
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
13 41 0.76
18 13 0.24
ACGTcount: A:0.16, C:0.47, G:0.22, T:0.15
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:75916 original size:31 final size:31
Alignment explanation
Indices: 75880--75951 Score: 135
Period size: 31 Copynumber: 2.3 Consensus size: 31
75870 ACCGGTCACA
75880 ACCCGACCCGACCCGTTGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTGACCCGACCCGTTG
*
75911 ACCCGACCCGACCCGTTTACCCGACCCGTTG
1 ACCCGACCCGACCCGTTGACCCGACCCGTTG
75942 ACCCGACCCG
1 ACCCGACCCG
75952 TTGACCGTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.17, C:0.50, G:0.21, T:0.12
Consensus pattern (31 bp):
ACCCGACCCGACCCGTTGACCCGACCCGTTG
Found at i:75951 original size:18 final size:18
Alignment explanation
Indices: 75897--75938 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
75887 CCGACCCGTT
75897 GACCCGACCCGTTGACCC
1 GACCCGACCCGTTGACCC
*
75915 GACCCGACCCGTTTACCC
1 GACCCGACCCGTTGACCC
75933 GACCCG
1 GACCCG
75939 TTGACCCGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.17, C:0.50, G:0.21, T:0.12
Consensus pattern (18 bp):
GACCCGACCCGTTGACCC
Found at i:75970 original size:15 final size:15
Alignment explanation
Indices: 75946--75979 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
75936 CCGTTGACCC
*
75946 GACCCGTTGACCGTT
1 GACCCATTGACCGTT
75961 GACCCATTGACCGTT
1 GACCCATTGACCGTT
75976 GACC
1 GACC
75980 ACTGTTGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.35, G:0.24, T:0.24
Consensus pattern (15 bp):
GACCCATTGACCGTT
Found at i:77288 original size:18 final size:18
Alignment explanation
Indices: 77262--77297 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
77252 TCGAAAGGAC
*
77262 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
77280 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
77298 CGGATGGAAG
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:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:78469 original size:23 final size:23
Alignment explanation
Indices: 78443--78516 Score: 96
Period size: 23 Copynumber: 3.2 Consensus size: 23
78433 AATTCTATTA
*
78443 TGATCCTGACCTGGATTCTGATC
1 TGATCATGACCTGGATTCTGATC
*
78466 TGAT-ATTGACATGGATTCTGATC
1 TGATCA-TGACCTGGATTCTGATC
*
78489 TGATACATGACCTGGATTCTGATA
1 TGAT-CATGACCTGGATTCTGATC
78513 TGAT
1 TGAT
78517 ACTTGACTTG
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
23 24 0.55
24 19 0.43
25 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (23 bp):
TGATCATGACCTGGATTCTGATC
Found at i:78504 original size:24 final size:24
Alignment explanation
Indices: 78449--78523 Score: 116
Period size: 24 Copynumber: 3.2 Consensus size: 24
78439 ATTATGATCC
78449 TGACCTGGATTCTGATCTGATA-T
1 TGACCTGGATTCTGATCTGATACT
* *
78472 TGACATGGATTCTGATCTGATACA
1 TGACCTGGATTCTGATCTGATACT
*
78496 TGACCTGGATTCTGATATGATACT
1 TGACCTGGATTCTGATCTGATACT
78520 TGAC
1 TGAC
78524 TTGAATTATG
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 21 0.46
24 25 0.54
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.36
Consensus pattern (24 bp):
TGACCTGGATTCTGATCTGATACT
Found at i:80719 original size:18 final size:18
Alignment explanation
Indices: 80713--80767 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
80703 CCGACCCGTT
80713 GACCCGACCCGTTGA--C
1 GACCCGACCCGTTGACCC
80729 --CC-GACCCGTTGACCC
1 GACCCGACCCGTTGACCC
*
80744 GACCCGACCCGTTTACCC
1 GACCCGACCCGTTGACCC
80762 GACCCG
1 GACCCG
80768 TTGACCGTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
13 10 0.30
14 2 0.06
15 1 0.03
17 2 0.06
18 18 0.55
ACGTcount: A:0.16, C:0.49, G:0.22, T:0.13
Consensus pattern (18 bp):
GACCCGACCCGTTGACCC
Found at i:80732 original size:31 final size:28
Alignment explanation
Indices: 80696--80767 Score: 81
Period size: 31 Copynumber: 2.4 Consensus size: 28
80686 ACCGGTCACA
80696 ACCCGACCCGACCCGTTGACCCGACCCGTTG
1 ACCCGACCCGACCC---GACCCGACCCGTTG
*
80727 ACCCGACCCGTTGACCCGACCCGACCCGTTT
1 ACCCGACCC---GACCCGACCCGACCCGTTG
80758 ACCCGACCCG
1 ACCCGACCCG
80768 TTGACCGTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
28 1 0.03
31 31 0.84
34 5 0.14
ACGTcount: A:0.17, C:0.50, G:0.21, T:0.12
Consensus pattern (28 bp):
ACCCGACCCGACCCGACCCGACCCGTTG
Found at i:80762 original size:26 final size:24
Alignment explanation
Indices: 80696--80754 Score: 86
Period size: 26 Copynumber: 2.5 Consensus size: 24
80686 ACCGGTCACA
80696 ACCC-GACCCGACCCGTTGACCCG
1 ACCCTGACCCGACCCGTTGACCCG
80719 ACCCGTTGACCCGACCCGTTGACCCG
1 ACCC--TGACCCGACCCGTTGACCCG
80745 ACCC-GACCCG
1 ACCCTGACCCG
80755 TTTACCCGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
23 10 0.30
26 23 0.70
ACGTcount: A:0.17, C:0.51, G:0.22, T:0.10
Consensus pattern (24 bp):
ACCCTGACCCGACCCGTTGACCCG
Found at i:80768 original size:31 final size:31
Alignment explanation
Indices: 80713--80773 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
80703 CCGACCCGTT
80713 GACCCGACCCGTTGACCCGACCCGTTGACCC
1 GACCCGACCCGTTGACCCGACCCGTTGACCC
*
80744 GACCCGACCCGTTTACCCGACCCGTTGACC
1 GACCCGACCCGTTGACCCGACCCGTTGACC
80774 GTTGACCCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.16, C:0.48, G:0.21, T:0.15
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGTTGACCC
Found at i:80769 original size:13 final size:13
Alignment explanation
Indices: 80700--80749 Score: 100
Period size: 13 Copynumber: 3.8 Consensus size: 13
80690 GTCACAACCC
80700 GACCCGACCCGTT
1 GACCCGACCCGTT
80713 GACCCGACCCGTT
1 GACCCGACCCGTT
80726 GACCCGACCCGTT
1 GACCCGACCCGTT
80739 GACCCGACCCG
1 GACCCGACCCG
80750 ACCCGTTTAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.16, C:0.48, G:0.24, T:0.12
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:80786 original size:15 final size:15
Alignment explanation
Indices: 80762--80795 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
80752 CCGTTTACCC
*
80762 GACCCGTTGACCGTT
1 GACCCATTGACCGTT
80777 GACCCATTGACCGTT
1 GACCCATTGACCGTT
80792 GACC
1 GACC
80796 ACTGTTGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.35, G:0.24, T:0.24
Consensus pattern (15 bp):
GACCCATTGACCGTT
Found at i:82107 original size:18 final size:18
Alignment explanation
Indices: 82081--82116 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
82071 TCGAAAGGAC
*
82081 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
82099 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
82117 CGGATGGAAG
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:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:83288 original size:23 final size:23
Alignment explanation
Indices: 83262--83335 Score: 96
Period size: 23 Copynumber: 3.2 Consensus size: 23
83252 AATTCTATTA
*
83262 TGATCCTGACCTGGATTCTGATC
1 TGATCATGACCTGGATTCTGATC
*
83285 TGAT-ATTGACATGGATTCTGATC
1 TGATCA-TGACCTGGATTCTGATC
*
83308 TGATACATGACCTGGATTCTGATA
1 TGAT-CATGACCTGGATTCTGATC
83332 TGAT
1 TGAT
83336 ACTTGACTTG
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
23 24 0.55
24 19 0.43
25 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (23 bp):
TGATCATGACCTGGATTCTGATC
Found at i:83323 original size:24 final size:24
Alignment explanation
Indices: 83268--83342 Score: 116
Period size: 24 Copynumber: 3.2 Consensus size: 24
83258 ATTATGATCC
83268 TGACCTGGATTCTGATCTGATA-T
1 TGACCTGGATTCTGATCTGATACT
* *
83291 TGACATGGATTCTGATCTGATACA
1 TGACCTGGATTCTGATCTGATACT
*
83315 TGACCTGGATTCTGATATGATACT
1 TGACCTGGATTCTGATCTGATACT
83339 TGAC
1 TGAC
83343 TTGAATTATG
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 21 0.46
24 25 0.54
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.36
Consensus pattern (24 bp):
TGACCTGGATTCTGATCTGATACT
Found at i:90485 original size:13 final size:13
Alignment explanation
Indices: 90467--90502 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
90457 TCATAACCCG
90467 ACCCGACCCGTTT
1 ACCCGACCCGTTT
90480 ACCCGACCCGTTT
1 ACCCGACCCGTTT
90493 ACCCGACCCG
1 ACCCGACCCG
90503 GCCCGTTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.17, C:0.50, G:0.17, T:0.17
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:90507 original size:18 final size:17
Alignment explanation
Indices: 90462--90509 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 17
90452 ACTGGTCATA
90462 ACCCGACCCGACCCGTTT
1 ACCCGACCCG-CCCGTTT
90480 ACCCGA----CCCGTTT
1 ACCCGACCCGCCCGTTT
90493 ACCCGACCCGGCCCGTT
1 ACCCGACCC-GCCCGTT
90510 GACTAGTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 10
0.71 0.00 0.29
Matches are distributed among these distances:
13 13 0.52
18 12 0.48
ACGTcount: A:0.15, C:0.50, G:0.19, T:0.17
Consensus pattern (17 bp):
ACCCGACCCGCCCGTTT
Found at i:93104 original size:24 final size:24
Alignment explanation
Indices: 92998--93104 Score: 88
Period size: 24 Copynumber: 4.5 Consensus size: 24
92988 ATATTTTATC
* *
92998 TGATTTCTGATTTGAATTCTGTTT
1 TGATTTCTGATCTGAATTATGTTT
** * * *
93022 TGACATCTGATCTGAAATCTGTTC
1 TGATTTCTGATCTGAATTATGTTT
* * * * *
93046 TGATTCCTAACCTGGATTATGTTA
1 TGATTTCTGATCTGAATTATGTTT
*
93070 TGATATCTGATCTGAATTATGTTT
1 TGATTTCTGATCTGAATTATGTTT
*
93094 TGATTTTTGAT
1 TGATTTCTGAT
93105 ATCTCCGTTT
Statistics
Matches: 61, Mismatches: 22, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
24 61 1.00
ACGTcount: A:0.22, C:0.12, G:0.17, T:0.49
Consensus pattern (24 bp):
TGATTTCTGATCTGAATTATGTTT
Found at i:93278 original size:2 final size:2
Alignment explanation
Indices: 93271--93305 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
93261 GGGATGGGGG
93271 TA TA TA TA TA 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 TA TA TA TA TA T
93306 GTTTTAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:96385 original size:18 final size:19
Alignment explanation
Indices: 96362--96400 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
96352 ATTTATAACT
96362 ATATGA-GGTAAAAAAATA
1 ATATGATGGTAAAAAAATA
* *
96380 ATATGATTGTAAAAATATA
1 ATATGATGGTAAAAAAATA
96399 AT
1 AT
96401 TATTTAAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.56, C:0.00, G:0.13, T:0.31
Consensus pattern (19 bp):
ATATGATGGTAAAAAAATA
Found at i:96508 original size:17 final size:17
Alignment explanation
Indices: 96486--96521 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
96476 CGAGATCATA
*
96486 ATATTATTTTTTATATT
1 ATATTATATTTTATATT
*
96503 ATATTATATTTTATTTT
1 ATATTATATTTTATATT
96520 AT
1 AT
96522 GTAAATAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:108208 original size:9 final size:8
Alignment explanation
Indices: 108186--108211 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
108176 ACGATATAAT
108186 TGTTTTTA
1 TGTTTTTA
108194 TGTTTTTA
1 TGTTTTTA
108202 TGTTTTTA
1 TGTTTTTA
108210 TG
1 TG
108212 CTATAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.15, T:0.73
Consensus pattern (8 bp):
TGTTTTTA
Found at i:114427 original size:28 final size:30
Alignment explanation
Indices: 114387--114473 Score: 79
Period size: 30 Copynumber: 3.0 Consensus size: 30
114377 AAATCTAGGC
* *
114387 AACTTTCAAAAATC-AT-CGTGTTCCAAAT
1 AACTTTTAGAAATCGATGCGTGTTCCAAAT
* * *
114415 AACTTTTAGAAATCGTTGTGTGTTCTAAAT
1 AACTTTTAGAAATCGATGCGTGTTCCAAAT
* * * *
114445 AACTTTTAGAAGTCGTTGTGTGATCCAAA
1 AACTTTTAGAAATCGATGCGTGTTCCAAA
114474 CGACTGCCAG
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
28 12 0.24
29 1 0.02
30 36 0.73
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (30 bp):
AACTTTTAGAAATCGATGCGTGTTCCAAAT
Found at i:114445 original size:30 final size:30
Alignment explanation
Indices: 114404--114473 Score: 113
Period size: 30 Copynumber: 2.3 Consensus size: 30
114394 AAAAATCATC
114404 GTGTTCCAAATAACTTTTAGAAATCGTTGT
1 GTGTTCCAAATAACTTTTAGAAATCGTTGT
* *
114434 GTGTTCTAAATAACTTTTAGAAGTCGTTGT
1 GTGTTCCAAATAACTTTTAGAAATCGTTGT
*
114464 GTGATCCAAA
1 GTGTTCCAAA
114474 CGACTGCCAG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.39
Consensus pattern (30 bp):
GTGTTCCAAATAACTTTTAGAAATCGTTGT
Found at i:121754 original size:23 final size:23
Alignment explanation
Indices: 121728--121778 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
121718 GAAGGGGCCA
121728 ATTCCATTAATGAGGAATTTGGT
1 ATTCCATTAATGAGGAATTTGGT
121751 ATTCCATTAATGAGGAATTTGGT
1 ATTCCATTAATGAGGAATTTGGT
121774 ATTCC
1 ATTCC
121779 TCAGATTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (23 bp):
ATTCCATTAATGAGGAATTTGGT
Found at i:130607 original size:133 final size:132
Alignment explanation
Indices: 130436--130702 Score: 516
Period size: 133 Copynumber: 2.0 Consensus size: 132
130426 AGTAAAATAC
130436 ATTCTTTTGAGAAGACAAATAACATATCTTATAGCTAAGCTCATCGAATGATCATTAGAGGACAT
1 ATTCTTTTGAGAAGACAAATAACATATCTTATAGCTAAGCTCATCGAATGATCATTAGAGGACAT
130501 ATGAACATTAGGATGTATTTTAGTCGATTTTGAGAAAGTAGTCATTGAGCACATTAACACTGATC
66 ATGAACATTAGGATGTATTTTAGTCGATTTTGAGAAAGTAGTCATTGAGCACATTAACACTGATC
130566 AG
131 AG
130568 ATTCTTTTTGAGAAGACAAATAACATATCTTATAGCTAAGCTCATCGAATGATCATTAGAGGACA
1 ATTC-TTTTGAGAAGACAAATAACATATCTTATAGCTAAGCTCATCGAATGATCATTAGAGGACA
*
130633 TATGAACATTAGGGTGTATTTTAGTCGATTTTGAGAAAGTAGTCATTGAGCACATTAACACTGAT
65 TATGAACATTAGGATGTATTTTAGTCGATTTTGAGAAAGTAGTCATTGAGCACATTAACACTGAT
130698 CAG
130 CAG
130701 AT
1 AT
130703 GTTAGCTGAT
Statistics
Matches: 133, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
132 4 0.03
133 129 0.97
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.32
Consensus pattern (132 bp):
ATTCTTTTGAGAAGACAAATAACATATCTTATAGCTAAGCTCATCGAATGATCATTAGAGGACAT
ATGAACATTAGGATGTATTTTAGTCGATTTTGAGAAAGTAGTCATTGAGCACATTAACACTGATC
AG
Found at i:132683 original size:16 final size:17
Alignment explanation
Indices: 132650--132683 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
132640 TCTTCTATTT
*
132650 TTATTTTATATTTTAAA
1 TTATTTTATATATTAAA
132667 TTATTTT-TATATTAAA
1 TTATTTTATATATTAAA
132683 T
1 T
132684 AATAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTTTATATATTAAA
Found at i:159775 original size:27 final size:24
Alignment explanation
Indices: 159732--159822 Score: 103
Period size: 27 Copynumber: 3.5 Consensus size: 24
159722 AAATTGAACG
*
159732 ACCGGTTTTTTTACCGGATTAAAA
1 ACCGGTTTTTTTACCGGATAAAAA
159756 ACCGGTTTTTTTCAAACCGGATAAAAA
1 ACCGGTTTTTTT---ACCGGATAAAAA
159783 ACCGG-TTTTTTATCCGGATAAAAAAAA
1 ACCGGTTTTTTTA-CCGGAT---AAAAA
159810 ACCGGTTTTTTTA
1 ACCGGTTTTTTTA
159823 AAAAACCGGT
Statistics
Matches: 58, Mismatches: 1, Indels: 12
0.82 0.01 0.17
Matches are distributed among these distances:
23 1 0.02
24 18 0.31
26 6 0.10
27 26 0.45
28 7 0.12
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.35
Consensus pattern (24 bp):
ACCGGTTTTTTTACCGGATAAAAA
Found at i:174612 original size:83 final size:82
Alignment explanation
Indices: 174445--174838 Score: 364
Period size: 83 Copynumber: 4.8 Consensus size: 82
174435 TAGTATGCAC
* * * *
174445 CTTTCATTTAGATAGG-ATGGAACACTATGACATAGCAGATATTCTCTGAATAATAATGGAAAAT
1 CTTTCATTTAGAT-GGAATGAAACACTATGACATGGCAGAGATTCTCTTAATAATAATGGAAAAT
* * *
174509 GTTTTCCCTGGAATGCGT
65 GTTTCCCCTAGAATGTGT
* * * *
174527 CTTTCATTTCAGATGGGATGAAACACTATGACATTGTAGAGGTTCTCTTAATAATAATGGAAAAT
1 CTTTCATTT-AGATGGAATGAAACACTATGACATGGCAGAGATTCTCTTAATAATAATGGAAAAT
*
174592 ATTTCCCCTAG-ATCGTGT
65 GTTTCCCCTAGAAT-GTGT
* * * * * * *
174610 CTTTCATTTTGGATGGAATGAAACATTATAAAATGGTAGAGGTTCTCTTAATAAT-ATGGAAAAC
1 CTTTCA-TTTAGATGGAATGAAACACTATGACATGGCAGAGATTCTCTTAATAATAATGGAAAAT
*
174674 GCTTCCCCTAGAATGTGT
65 GTTTCCCCTAGAATGTGT
* * * * * *
174692 TTTTCATTTATGATGGAATGAAACATTATGAGATGGCAGAAATTCTCTAAATAATAATGGAAAAC
1 CTTTCATTTA-GATGGAATGAAACACTATGACATGGCAGAGATTCTCTTAATAATAATGGAAAAT
* * * * ***
174757 GCTTCTCGTATAATGCAC
65 GTTTCCCCTAGAATGTGT
* * * *
174775 CTTTCATTTCGGATGGGATTAAACAATATGACATGGCAGAGATTCT-TTGAATAATAATGGAAAA
1 CTTTCATTT-AGATGGAATGAAACACTATGACATGGCAGAGATTCTCTT-AATAATAATGGAAAA
174839 CACTATGACA
Statistics
Matches: 262, Mismatches: 41, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
81 3 0.01
82 78 0.30
83 178 0.68
84 3 0.01
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (82 bp):
CTTTCATTTAGATGGAATGAAACACTATGACATGGCAGAGATTCTCTTAATAATAATGGAAAATG
TTTCCCCTAGAATGTGT
Found at i:176706 original size:24 final size:24
Alignment explanation
Indices: 176652--176706 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
176642 ATTATTGTCA
*
176652 TCATCATTCTCGTCCTCATCATCG
1 TCATCATTCTCCTCCTCATCATCG
* * * *
176676 TCCTCATTCTCCTTCTCATTATTG
1 TCATCATTCTCCTCCTCATCATCG
176700 TCATCAT
1 TCATCAT
176707 CACTCTCAAC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.16, C:0.35, G:0.05, T:0.44
Consensus pattern (24 bp):
TCATCATTCTCCTCCTCATCATCG
Found at i:178638 original size:15 final size:15
Alignment explanation
Indices: 178618--178647 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
178608 CCTAACAAAT
178618 AAATTTTAACCATTA
1 AAATTTTAACCATTA
*
178633 AAATTTTAACTATTA
1 AAATTTTAACCATTA
178648 TTTCAAAATT
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:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (15 bp):
AAATTTTAACCATTA
Found at i:178678 original size:14 final size:14
Alignment explanation
Indices: 178661--178690 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
178651 CAAAATTATT
178661 TAAATAAATTCAAA
1 TAAATAAATTCAAA
*
178675 TAAATAAATTCTAA
1 TAAATAAATTCAAA
178689 TA
1 TA
178691 TTTTAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (14 bp):
TAAATAAATTCAAA
Found at i:179794 original size:245 final size:247
Alignment explanation
Indices: 179345--179830 Score: 769
Period size: 245 Copynumber: 2.0 Consensus size: 247
179335 GTCTGTCAGT
* * *
179345 GAGAGATGTTTTTTTGAATTTTGAAGACAAATTTCGTGACATGTGCGGCACGTGCCGTGTGGGTG
1 GAGAGATGTTTTTTTGAATTTTGAAGACAAATTCCGAGACATGTGCGGCACGTGCCGTGTGGGTA
* *
179410 AAATGAAAGGGAACGGAAGACTTAAAACGGTGGCGTATCGTAGCTTGGTCGCAATAGTGGTGGAT
66 AAATGAAAGGGAACGGAAGACTTAAAACGGCGGCGTATAGTAGCTTGGTCGCAATAGTGGTGGAT
* * * *
179475 CTAGTGGGCCGTAAATTGGTACAATGGATGTTTTCTTAAGAATGGGCCAATCATCAACCAGTATC
131 CCAGTGGGCCGTAAATTGGTACAATGGATGTTTTCTTAAGAACGGGCCAATCAGCAACCAGCATC
* * *
179540 CCACATGGTGGGGCCCCGTAGAAATTAGTCCGTTGCGTGGTCGGTTTTTCTC
196 CCACATGGTGGGGCCCCGAAGAAATTAGTCCGTTGCGCGGCCGGTTTTTCTC
* *
179592 GAGAGATGTTTTTTT-ATTTTTGAAGACAGATTCCGAGACATGTGCGGCACGTGCCGTGTGGGTA
1 GAGAGATGTTTTTTTGAATTTTGAAGACAAATTCCGAGACATGTGCGGCACGTGCCGTGTGGGTA
* * ** * *
179656 AAATGAAAGGGAGCGGAAGACTTAAAACGGCGTCGTATAGTTTCTT-GTTGCGATAGTGGTGGAT
66 AAATGAAAGGGAACGGAAGACTTAAAACGGCGGCGTATAGTAGCTTGGTCGCAATAGTGGTGGAT
*
179720 CCAGTGGGCCGTAAATTGGTACAGTGGATGTTTTCTTAAGAACGGGCCAATCAGCAACCAGCATC
131 CCAGTGGGCCGTAAATTGGTACAATGGATGTTTTCTTAAGAACGGGCCAATCAGCAACCAGCATC
179785 CCACATGGTGGGGCCCCGAAGAAATTAGTCCGTTGCGCGGCCGGTT
196 CCACATGGTGGGGCCCCGAAGAAATTAGTCCGTTGCGCGGCCGGTT
179831 CTTGAGCCTT
Statistics
Matches: 218, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
245 119 0.55
246 84 0.39
247 15 0.07
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.27
Consensus pattern (247 bp):
GAGAGATGTTTTTTTGAATTTTGAAGACAAATTCCGAGACATGTGCGGCACGTGCCGTGTGGGTA
AAATGAAAGGGAACGGAAGACTTAAAACGGCGGCGTATAGTAGCTTGGTCGCAATAGTGGTGGAT
CCAGTGGGCCGTAAATTGGTACAATGGATGTTTTCTTAAGAACGGGCCAATCAGCAACCAGCATC
CCACATGGTGGGGCCCCGAAGAAATTAGTCCGTTGCGCGGCCGGTTTTTCTC
Found at i:184960 original size:16 final size:16
Alignment explanation
Indices: 184939--184970 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
184929 CAAATCATAG
*
184939 TCAAGTAGCGTGAGAA
1 TCAAGTAGCATGAGAA
184955 TCAAGTAGCATGAGAA
1 TCAAGTAGCATGAGAA
184971 AACTATCTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.12, G:0.28, T:0.19
Consensus pattern (16 bp):
TCAAGTAGCATGAGAA
Found at i:185387 original size:12 final size:12
Alignment explanation
Indices: 185370--185395 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
185360 TACTAAAAAT
185370 TCAAATTTTAAA
1 TCAAATTTTAAA
185382 TCAAATTTTAAA
1 TCAAATTTTAAA
185394 TC
1 TC
185396 TTGAAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (12 bp):
TCAAATTTTAAA
Found at i:192385 original size:23 final size:23
Alignment explanation
Indices: 192341--192385 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
192331 TTTCCAATAA
**
192341 ATTTACATGTATGACATGTTTTT
1 ATTTACATGTATGACACATTTTT
* *
192364 ATTTACCTTTATGACACATTTT
1 ATTTACATGTATGACACATTTT
192386 CTTATTATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.13, G:0.09, T:0.51
Consensus pattern (23 bp):
ATTTACATGTATGACACATTTTT
Found at i:192667 original size:16 final size:18
Alignment explanation
Indices: 192632--192672 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
192622 TTTGTGGTTC
192632 ATTTGTTTATATGATCAT
1 ATTTGTTTATATGATCAT
*
192650 ATTTGTTTGTAT-AT-AT
1 ATTTGTTTATATGATCAT
192666 ATTTGTT
1 ATTTGTT
192673 CGAGTTTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.41
17 2 0.09
18 11 0.50
ACGTcount: A:0.24, C:0.02, G:0.12, T:0.61
Consensus pattern (18 bp):
ATTTGTTTATATGATCAT
Found at i:201021 original size:42 final size:43
Alignment explanation
Indices: 200912--201174 Score: 216
Period size: 42 Copynumber: 6.2 Consensus size: 43
200902 AAAAATGATT
* * *
200912 AAATTAGGGGGTATAAATTATAAAAGTAAAAAGTGGGATTGAAAA
1 AAATTA-GGGGTCTCAATTATAAAAGTAAAAAGTGAGATT-AAAA
* * * *
200957 AAATTAGGGAT-TGAATTATAAAGGTAAAAAGTGAGA-TAATA
1 AAATTAGGGGTCTCAATTATAAAAGTAAAAAGTGAGATTAAAA
* *
200998 AAATTAGGGGTCTCAATTATAAAGGT-AAAAGTGAGATTAAGA
1 AAATTAGGGGTCTCAATTATAAAAGTAAAAAGTGAGATTAAAA
* * *
201040 AAACTAGGAGCCTCAATTATAAAAGTAAAAAGTGAGATTAAAAA
1 AAATTAGGGGTCTCAATTATAAAAGTAAAAAGTGAGATT-AAAA
* * * ** * *
201084 AAAATAGGGG-CTTCATTTGT-AAAGTAGGAAGTGAGATTGAAC
1 AAATTAGGGGTC-TCAATTATAAAAGTAAAAAGTGAGATTAAAA
* * * * *
201126 AAATTAGAGG-CTTCAATTATAAATGAAAAAAATGAG-TTGAAA
1 AAATTAGGGGTC-TCAATTATAAAAGTAAAAAGTGAGATTAAAA
201168 AAATTAG
1 AAATTAG
201175 AGACTCCAAT
Statistics
Matches: 181, Mismatches: 31, Indels: 15
0.80 0.14 0.07
Matches are distributed among these distances:
41 23 0.13
42 70 0.39
43 61 0.34
44 21 0.12
45 6 0.03
ACGTcount: A:0.49, C:0.04, G:0.22, T:0.25
Consensus pattern (43 bp):
AAATTAGGGGTCTCAATTATAAAAGTAAAAAGTGAGATTAAAA
Found at i:201142 original size:86 final size:84
Alignment explanation
Indices: 200927--201170 Score: 228
Period size: 86 Copynumber: 2.9 Consensus size: 84
200917 AGGGGGTATA
* * * * *
200927 AATTATAAAAGTAAAAAGTGGGATTGAAAAAAATTAGGGATTGAATTATAAAGGTAAAAAGTGAG
1 AATTATAAAGGT-AAAAGTGAGATTG-AAAAAATTAGGGCTTCAATTATAAAAGTAAAAAGTGAG
* *
200992 A-TAATAAAATTAGGGGTCTC
64 ATTAAAAAAAATAGGGGTCTC
* *
201012 AATTATAAAGGTAAAAGTGAGATT-AAGAAAACTAGGAGCCTCAATTATAAAAGTAAAAAGTGAG
1 AATTATAAAGGTAAAAGTGAGATTGAA-AAAATTAGG-GCTTCAATTATAAAAGTAAAAAGTGAG
201076 ATTAAAAAAAAATAGGGG-CTTC
64 ATT-AAAAAAAATAGGGGTC-TC
* * * * * * *
201098 ATTTGTAAA-GTAGGAAGTGAGATTGAACAAATTAGAGGCTTCAATTATAAATGAAAAAAATGAG
1 AATTATAAAGGTA-AAAGTGAGATTGAAAAAATTAG-GGCTTCAATTATAAAAGTAAAAAGTGAG
*
201162 -TTGAAAAAA
64 ATTAAAAAAA
201171 TTAGAGACTC
Statistics
Matches: 132, Mismatches: 19, Indels: 17
0.79 0.11 0.10
Matches are distributed among these distances:
82 2 0.02
83 8 0.06
84 41 0.31
85 18 0.14
86 60 0.45
87 3 0.02
ACGTcount: A:0.50, C:0.05, G:0.21, T:0.25
Consensus pattern (84 bp):
AATTATAAAGGTAAAAGTGAGATTGAAAAAATTAGGGCTTCAATTATAAAAGTAAAAAGTGAGAT
TAAAAAAAATAGGGGTCTC
Found at i:210483 original size:20 final size:20
Alignment explanation
Indices: 210458--210502 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
210448 GTCATCTAAT
210458 TTTTTAAACCCCAGACCGGA
1 TTTTTAAACCCCAGACCGGA
*
210478 TTTTTAAACCTCAGACCGGA
1 TTTTTAAACCCCAGACCGGA
210498 TTTTT
1 TTTTT
210503 TTCCGGATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (20 bp):
TTTTTAAACCCCAGACCGGA
Found at i:212949 original size:2 final size:2
Alignment explanation
Indices: 212944--212985 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
212934 CCCCCCACAT
212944 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
212986 CTTATAAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:213478 original size:23 final size:23
Alignment explanation
Indices: 213427--213478 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
213417 TAACCCATTT
* *
213427 TATTATATAAGTGCTACCTATTA
1 TATTATATAAGCGCTACCTAATA
**
213450 CGTTATATAAGCGCTACCTAATA
1 TATTATATAAGCGCTACCTAATA
213473 TATTAT
1 TATTAT
213479 TGTGTTTGAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (23 bp):
TATTATATAAGCGCTACCTAATA
Found at i:213794 original size:23 final size:23
Alignment explanation
Indices: 213744--213788 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
213734 AACATATTTT
*
213744 ATTATATAACCGCTACCTATTAC
1 ATTATATAACCGCTACCTAATAC
*
213767 ATTATATAAGCGCTACCTAATA
1 ATTATATAACCGCTACCTAATA
213789 TGTTATTGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.22, G:0.07, T:0.33
Consensus pattern (23 bp):
ATTATATAACCGCTACCTAATAC
Found at i:213813 original size:158 final size:158
Alignment explanation
Indices: 213284--213813 Score: 774
Period size: 158 Copynumber: 3.4 Consensus size: 158
213274 ATAATGTGCA
* * * * * * *
213284 ACCTATTATGTTACATAAGCTCTACCAAATATATTATTATGCTTGATAATATTTTCAATAATTAA
1 ACCTATTACGTTATATAAGCGCTACCTAATATATTATTGTGCTTGATAATATTTCCAGTAATTAA
* *
213349 CCGGTTATGTTATCATTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGT
66 CTGGTTATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGT
* *
213414 AATTAACCCATTTTATTATATAAGTGCT
131 AATTAACCTATTTTATTATATAAGCGCT
* * * *
213442 ACCTATTACGTTATATAAGCGCTACCTAATATATTATTGTGTTTGATAATGTTTCTAGTAAATAA
1 ACCTATTACGTTATATAAGCGCTACCTAATATATTATTGTGCTTGATAATATTTCCAGTAATTAA
213507 CCT-GTTATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAG
66 -CTGGTTATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAG
*
213571 TAATTAACCTATTTTATTATATAAGCGTT
130 TAATTAACCTATTTTATTATATAAGCGCT
* * * *
213600 ACCTATTACGCTATATAAGTGTTACCTAATATGTTATTGTGCTTGATAATATTTCCAGTAATTAA
1 ACCTATTACGTTATATAAGCGCTACCTAATATATTATTGTGCTTGATAATATTTCCAGTAATTAA
* * * *
213665 CTGGTTATGCTATCCTTGGAAACATTTTGGGCGTTTACCTAATATTTTGTAATAACAAATTAAGT
66 CTGGTTATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGT
* *
213730 AATTAACATATTTTATTATATAACCGCT
131 AATTAACCTATTTTATTATATAAGCGCT
* * **
213758 ACCTATTACATTATATAAGCGCTACCTAATATGTTATTGCACTTGATAATATTTCC
1 ACCTATTACGTTATATAAGCGCTACCTAATATATTATTGTGCTTGATAATATTTCC
213814 GGTTAAATGA
Statistics
Matches: 333, Mismatches: 37, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
157 2 0.01
158 330 0.99
159 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (158 bp):
ACCTATTACGTTATATAAGCGCTACCTAATATATTATTGTGCTTGATAATATTTCCAGTAATTAA
CTGGTTATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGT
AATTAACCTATTTTATTATATAAGCGCT
Found at i:217623 original size:3 final size:3
Alignment explanation
Indices: 217573--217608 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
217563 CTTCATTAGA
217573 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
217609 CAACAAGTCA
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:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:217725 original size:21 final size:21
Alignment explanation
Indices: 217699--217738 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
217689 GGTTAAGATT
*
217699 TTCGTCTCCCTCATCTTCAGC
1 TTCGTCGCCCTCATCTTCAGC
217720 TTCGTCGCCCTCATCTTCA
1 TTCGTCGCCCTCATCTTCA
217739 TCATCATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.10, C:0.42, G:0.10, T:0.38
Consensus pattern (21 bp):
TTCGTCGCCCTCATCTTCAGC
Found at i:219144 original size:14 final size:14
Alignment explanation
Indices: 219125--219164 Score: 80
Period size: 14 Copynumber: 2.9 Consensus size: 14
219115 TGAATGATTG
219125 AAATAAATGATTTA
1 AAATAAATGATTTA
219139 AAATAAATGATTTA
1 AAATAAATGATTTA
219153 AAATAAATGATT
1 AAATAAATGATT
219165 CTTTTATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.35
Consensus pattern (14 bp):
AAATAAATGATTTA
Found at i:232045 original size:8 final size:9
Alignment explanation
Indices: 232017--232044 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
232007 TAAATGATCT
232017 AATTAAAAA
1 AATTAAAAA
232026 AATTAAAAA
1 AATTAAAAA
232035 AATTAAAAA
1 AATTAAAAA
232044 A
1 A
232045 TCGATAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AATTAAAAA
Found at i:232779 original size:25 final size:25
Alignment explanation
Indices: 232751--232806 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
232741 GTTAATTTCA
232751 GTCATATGTTTTCATTCATCCAACG
1 GTCATATGTTTTCATTCATCCAACG
*
232776 GTCAGATGTTTTCATTCATCCAACG
1 GTCATATGTTTTCATTCATCCAACG
232801 GTCATA
1 GTCATA
232807 AATCTGTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (25 bp):
GTCATATGTTTTCATTCATCCAACG
Found at i:235366 original size:2 final size:2
Alignment explanation
Indices: 235361--235406 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
235351 TGTGTGTGTG
* *
235361 TA TA TA TA TA TA TA TA TA TA CA TA TA CA 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
235403 TA TA
1 TA TA
235407 AATTTTTATT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:248162 original size:31 final size:31
Alignment explanation
Indices: 248099--248190 Score: 123
Period size: 31 Copynumber: 3.0 Consensus size: 31
248089 TGTCGGATTA
* *
248099 AAGGGTTAAATTGATATTTTATTTAAAGTTTT
1 AAGGGTCAAATTGATATTTT-TTTAAAATTTT
248131 AAGGGTCAAATTGATATTTTTTTAAAATTTT
1 AAGGGTCAAATTGATATTTTTTTAAAATTTT
* * *
248162 AAGGGTCAACTAG-TATTTTTTTTAAATTT
1 AAGGGTCAAATTGATATTTTTTTAAAATTT
248191 AGGAGTTAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
30 15 0.27
31 21 0.38
32 19 0.35
ACGTcount: A:0.34, C:0.03, G:0.14, T:0.49
Consensus pattern (31 bp):
AAGGGTCAAATTGATATTTTTTTAAAATTTT
Found at i:256011 original size:26 final size:25
Alignment explanation
Indices: 255982--256032 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
255972 TGTATATAAC
*
255982 TTAAAAATATTTTTTATATTAACTTA
1 TTAAAAATATTTTAT-TATTAACTTA
*
256008 TTAAACATATTTTATTATTAACTTA
1 TTAAAAATATTTTATTATTAACTTA
256033 ATTTAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (25 bp):
TTAAAAATATTTTATTATTAACTTA
Found at i:256026 original size:25 final size:23
Alignment explanation
Indices: 255963--256033 Score: 81
Period size: 25 Copynumber: 3.0 Consensus size: 23
255953 TTAAATTCAT
*
255963 AATATTTTATGTATATAACTTAAA
1 AATATTTTATATAT-TAACTTAAA
*
255987 AATATTTTTTATATTAACTTATTAA
1 AATATTTTATATATTAACTTA--AA
256012 ACATATTTTAT-TATTAACTTAA
1 A-ATATTTTATATATTAACTTAA
256034 TTTAATTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
23 8 0.20
24 12 0.29
25 13 0.32
26 8 0.20
ACGTcount: A:0.42, C:0.06, G:0.01, T:0.51
Consensus pattern (23 bp):
AATATTTTATATATTAACTTAAA
Found at i:256048 original size:25 final size:25
Alignment explanation
Indices: 255967--256032 Score: 73
Period size: 24 Copynumber: 2.6 Consensus size: 25
255957 ATTCATAATA
* *
255967 TTTTATGTATATAACTTA-AAAATATT
1 TTTTAT-TAT-TAACTTATTAAACATT
*
255993 TTTTA-TATTAACTTATTAAACATA
1 TTTTATTATTAACTTATTAAACATT
256017 TTTTATTATTAACTTA
1 TTTTATTATTAACTTA
256033 ATTTAATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
23 7 0.20
24 13 0.37
25 10 0.29
26 5 0.14
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.53
Consensus pattern (25 bp):
TTTTATTATTAACTTATTAAACATT
Found at i:268326 original size:24 final size:24
Alignment explanation
Indices: 268299--268371 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 24
268289 CGTTCATTTA
268299 CGTTC-GTGAACGTTCGGTTATGTT
1 CGTTCGGT-AACGTTCGGTTATGTT
* * *
268323 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
* * * *
268347 CGTTCGATTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
268371 C
1 C
268372 ATTCATTTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
24 42 0.95
25 2 0.05
ACGTcount: A:0.11, C:0.15, G:0.25, T:0.49
Consensus pattern (24 bp):
CGTTCGGTAACGTTCGGTTATGTT
Found at i:268328 original size:14 final size:14
Alignment explanation
Indices: 268309--268364 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
268299 CGTTCGTGAA
268309 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
268323 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
268337 CG-T---TTATGTT
1 CGTTCGGTTATGTT
*
268347 CGTTCGATTATGTT
1 CGTTCGGTTATGTT
268361 CGTT
1 CGTT
268365 TATGTTCATT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 27 0.71
ACGTcount: A:0.09, C:0.14, G:0.25, T:0.52
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:268381 original size:24 final size:23
Alignment explanation
Indices: 268310--268384 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 23
268300 GTTCGTGAAC
* *
268310 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTC-ATTAT
268334 GTTCGTTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCGTTC-ATTAT
*
268358 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGTTTATGTTCGTTCA-TTAT
268382 GTT
1 GTT
268385 TAACCCAATC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
23 1 0.02
24 46 0.98
ACGTcount: A:0.12, C:0.12, G:0.21, T:0.55
Consensus pattern (23 bp):
GTTCGTTTATGTTCGTTCATTAT
Found at i:269135 original size:16 final size:16
Alignment explanation
Indices: 269114--269180 Score: 93
Period size: 16 Copynumber: 4.3 Consensus size: 16
269104 GTCTCCAACG
*
269114 TTTATGTTCGTGTTTA
1 TTTATGTTCGTGTTCA
*
269130 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
*
269146 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
269162 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
269176 TTTAT
1 TTTAT
269181 TAAATGAACG
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
14 5 0.10
15 2 0.04
16 41 0.85
ACGTcount: A:0.10, C:0.09, G:0.19, T:0.61
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:269153 original size:32 final size:32
Alignment explanation
Indices: 269112--269172 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
269102 GGGTCTCCAA
*
269112 CGTTTATGTTCGTGTTTATTTATGTTCGTGTT
1 CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
*
269144 CGTTTATGTTCGTGTTCGTTTATGTTCGT
1 CGTTTATGTTCGTGTTCATTTATGTTCGT
269173 TTATTTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.08, C:0.11, G:0.23, T:0.57
Consensus pattern (32 bp):
CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
Found at i:269232 original size:16 final size:16
Alignment explanation
Indices: 269211--269243 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
269201 AAAAAAATTT
269211 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
269227 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
269243 T
1 T
269244 CTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:269256 original size:71 final size:71
Alignment explanation
Indices: 269140--269271 Score: 255
Period size: 71 Copynumber: 1.9 Consensus size: 71
269130 TTTATGTTCG
*
269140 TGTTCGTTTATGTTCGTGTTCGTTTATGTTCGTTTATTTATTAAATGAACGAACATGAACAAAAA
1 TGTTCGTTTATGTTCGTGTTCGTTTATGTTCGTCTATTTATTAAATGAACGAACATGAACAAAAA
269205 AAATTT
66 AAATTT
269211 TGTTCGTTTATGTTCGTGTTCGTTTATGTTCGTCTATTTATTAAATGAACGAACATGAACA
1 TGTTCGTTTATGTTCGTGTTCGTTTATGTTCGTCTATTTATTAAATGAACGAACATGAACA
269272 TACATCCGTT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
71 60 1.00
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.44
Consensus pattern (71 bp):
TGTTCGTTTATGTTCGTGTTCGTTTATGTTCGTCTATTTATTAAATGAACGAACATGAACAAAAA
AAATTT
Found at i:271766 original size:2 final size:2
Alignment explanation
Indices: 271761--271804 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
271751 TTTAACTAGC
271761 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
271803 AT
1 AT
271805 GGGGTTTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:276287 original size:90 final size:88
Alignment explanation
Indices: 276135--276304 Score: 295
Period size: 90 Copynumber: 1.9 Consensus size: 88
276125 ACACACCCTT
*
276135 TTATAGTCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
1 TTATAGTCAAGTCACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
*
276200 ATTAATTAGAATTTAATAATCCTC
66 ATTAATT-GAAATTAATAATCCTC
*
276224 TTATATTCAAGTCACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATATTT
1 TTATAGTCAAGTCACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTATATTT
276289 AATTAATTGAAATTAA
65 AATTAATTGAAATTAA
276305 ATATTCAGGA
Statistics
Matches: 77, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
89 36 0.47
90 41 0.53
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.45
Consensus pattern (88 bp):
TTATAGTCAAGTCACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
ATTAATTGAAATTAATAATCCTC
Found at i:277365 original size:14 final size:14
Alignment explanation
Indices: 277348--277375 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
277338 TAATGTCTTC
277348 AAAGCAATGATATT
1 AAAGCAATGATATT
277362 AAAGCAATGATATT
1 AAAGCAATGATATT
277376 GTTTTATATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.14, T:0.29
Consensus pattern (14 bp):
AAAGCAATGATATT
Found at i:281960 original size:2 final size:2
Alignment explanation
Indices: 281953--282010 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
281943 AGTTTAATCA
281953 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
281995 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
282011 TAGTATTTTA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:282945 original size:83 final size:83
Alignment explanation
Indices: 282854--283095 Score: 259
Period size: 83 Copynumber: 2.9 Consensus size: 83
282844 TAGCGGCGTT
* ** * * * *
282854 TTTTTCAACAAACGCCGTGATAGAGTAGTATTTTAGCGGCGTTTGTGTAAAAACGCCGCAATAGG
1 TTTTTCAACAAACGCAGCAATAAAGTAGTACTTTAGCGGCGTTTTTATAAAAACGCCGCAATAGG
*
282919 GTTAATCTATAGTGACGC
66 GTTCATCTATAGTGACGC
** * * * * *
282937 TTTTTCAACAAATACTGCAATAAAATAGTACTTTAGCGGCGTTTTTATACAAATGTCGCAATAGG
1 TTTTTCAACAAACGCAGCAATAAAGTAGTACTTTAGCGGCGTTTTTATAAAAACGCCGCAATAGG
* * * **
283002 ATTCATCTATGGTGGCTT
66 GTTCATCTATAGTGACGC
* * * *
283020 TTTTTTAACAAAGGCAGCAATAAAGTAATACTTTAGCGGCGTTTTTATAAAAACGCCGTAATAGG
1 TTTTTCAACAAACGCAGCAATAAAGTAGTACTTTAGCGGCGTTTTTATAAAAACGCCGCAATAGG
*
283085 GGTCATCTATA
66 GTTCATCTATA
283096 TAGATGCTAA
Statistics
Matches: 127, Mismatches: 32, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
83 127 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.33
Consensus pattern (83 bp):
TTTTTCAACAAACGCAGCAATAAAGTAGTACTTTAGCGGCGTTTTTATAAAAACGCCGCAATAGG
GTTCATCTATAGTGACGC
Found at i:291670 original size:12 final size:12
Alignment explanation
Indices: 291653--291706 Score: 72
Period size: 12 Copynumber: 4.4 Consensus size: 12
291643 TTGTTCAAAC
291653 ATTATAAAAAAA
1 ATTATAAAAAAA
**
291665 ATTATAAAAGATT
1 ATTATAAAA-AAA
291678 ATTATAAAAAAA
1 ATTATAAAAAAA
*
291690 ATTATAAAAAAT
1 ATTATAAAAAAA
291702 ATTAT
1 ATTAT
291707 CTGTCCTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
12 26 0.72
13 10 0.28
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (12 bp):
ATTATAAAAAAA
Found at i:291684 original size:25 final size:24
Alignment explanation
Indices: 291653--291706 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 24
291643 TTGTTCAAAC
*
291653 ATTATAAAAAAAATTATAAAAGATT
1 ATTATAAAAAAAATTATAAAA-AAT
291678 ATTATAAAAAAAATTATAAAAAAT
1 ATTATAAAAAAAATTATAAAAAAT
291702 ATTAT
1 ATTAT
291707 CTGTCCTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 7 0.25
25 21 0.75
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (24 bp):
ATTATAAAAAAAATTATAAAAAAT
Found at i:299081 original size:28 final size:28
Alignment explanation
Indices: 299049--299104 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
299039 AACAAATCAA
299049 CCATAGCATACAAAAGATTGCATTCATT
1 CCATAGCATACAAAAGATTGCATTCATT
299077 CCATAGCATACAAAAGATTGCATTCATT
1 CCATAGCATACAAAAGATTGCATTCATT
299105 ACAATGTATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (28 bp):
CCATAGCATACAAAAGATTGCATTCATT
Found at i:304024 original size:103 final size:103
Alignment explanation
Indices: 303845--304045 Score: 305
Period size: 103 Copynumber: 2.0 Consensus size: 103
303835 TGTATATTAT
* * * * *
303845 TAAAAGAAAAATAAGAGCTCATTTAATTAAGCACTTTTTAGATTACACCCTAAGCCCTAAGTCTT
1 TAAAAGAAAAATAAAAGCTCATTTAATTAAGAACATGTTAGATTACACCCTAAACCCTAAGTCTT
*
303910 GAACCCTAAACCCTTAATTCAATTATGTGATAGGGTAC
66 GAACCCTAAACCCTTAATTCAATTATATGATAGGGTAC
303948 TAAAAGAAAAATAAAAGCTCATTTAATTAAGAACATGTTAGATTACACCCTAAACCCTAAGTCTT
1 TAAAAGAAAAATAAAAGCTCATTTAATTAAGAACATGTTAGATTACACCCTAAACCCTAAGTCTT
* **
304013 -AAGTCCTAAACCCTTAATTTGATTATATGATAG
66 GAA-CCCTAAACCCTTAATTCAATTATATGATAG
304046 TGTTAAGTTA
Statistics
Matches: 88, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
102 2 0.02
103 86 0.98
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.30
Consensus pattern (103 bp):
TAAAAGAAAAATAAAAGCTCATTTAATTAAGAACATGTTAGATTACACCCTAAACCCTAAGTCTT
GAACCCTAAACCCTTAATTCAATTATATGATAGGGTAC
Found at i:305329 original size:18 final size:18
Alignment explanation
Indices: 305308--305359 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
305298 TAATTCAAAA
305308 TCGAGCTTTAATCGAGTT
1 TCGAGCTTTAATCGAGTT
*
305326 TCGAG-TTTGAATTGAGTT
1 TCGAGCTTT-AATCGAGTT
* *
305344 TGGAGCTTGAATCGAG
1 TCGAGCTTTAATCGAG
305360 CTCAGAATCG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 3 0.11
18 23 0.82
19 2 0.07
ACGTcount: A:0.23, C:0.12, G:0.29, T:0.37
Consensus pattern (18 bp):
TCGAGCTTTAATCGAGTT
Found at i:305936 original size:16 final size:16
Alignment explanation
Indices: 305906--305936 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
305896 TAATATTGAA
*
305906 ACTTGAACTCAAAAAG
1 ACTTGAACTAAAAAAG
305922 ACTTGAACTAAAAAA
1 ACTTGAACTAAAAAA
305937 AAAATTTAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.16, G:0.10, T:0.19
Consensus pattern (16 bp):
ACTTGAACTAAAAAAG
Found at i:306423 original size:22 final size:21
Alignment explanation
Indices: 306398--306438 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
306388 TATAAAAAAT
306398 TATTTTTATTAAATATTTTTGA
1 TATTTTTATTAAAT-TTTTTGA
*
306420 TATTTTTATTTAATTTTTT
1 TATTTTTATTAAATTTTTT
306439 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (21 bp):
TATTTTTATTAAATTTTTTGA
Found at i:311917 original size:25 final size:25
Alignment explanation
Indices: 311889--311938 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
311879 TGATGATGTG
311889 ATATTTTTTAT-TATTTAATTAATTA
1 ATATTTTTTATATATTT-ATTAATTA
*
311914 ATATTTTTTATATATTTTTTAATTA
1 ATATTTTTTATATATTTATTAATTA
311939 TCTCTTACCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (25 bp):
ATATTTTTTATATATTTATTAATTA
Found at i:316383 original size:18 final size:19
Alignment explanation
Indices: 316356--316395 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
316346 CTTCTGAAAA
316356 TTTAAATTTTTTGTATG-T
1 TTTAAATTTTTTGTATGAT
* *
316374 TTTAATTTTTTTTTATGAT
1 TTTAAATTTTTTGTATGAT
316393 TTT
1 TTT
316396 TTTATTGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.72
Consensus pattern (19 bp):
TTTAAATTTTTTGTATGAT
Found at i:322405 original size:2 final size:2
Alignment explanation
Indices: 322398--322429 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
322388 CTGACTTTAG
322398 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
322430 TTGAATAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:324761 original size:21 final size:21
Alignment explanation
Indices: 324718--324757 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
324708 TAATAATTTT
324718 TATTTTTATATTATTAAAATA
1 TATTTTTATATTATTAAAATA
324739 TATTATTTA-ATTA-TAAAAT
1 TATT-TTTATATTATTAAAAT
324758 TATAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 8 0.44
22 4 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TATTTTTATATTATTAAAATA
Found at i:324817 original size:19 final size:20
Alignment explanation
Indices: 324727--324814 Score: 67
Period size: 19 Copynumber: 4.4 Consensus size: 20
324717 TTATTTTTAT
* **
324727 ATTATTAAAATATATTATTTA
1 ATTA-TAAAATATAATAAATA
324748 ATTATAAAATTATAA-AAAT-
1 ATTATAAAA-TATAATAAATA
* *
324767 ATTATAAAATATTAATTTAACA
1 ATTATAAAATA-TAA-TAAATA
324789 ATT-T-AAATATAATAAATA
1 ATTATAAAATATAATAAATA
324807 ATTATAAA
1 ATTATAAA
324815 TATTATTTTA
Statistics
Matches: 53, Mismatches: 7, Indels: 15
0.71 0.09 0.20
Matches are distributed among these distances:
18 9 0.17
19 16 0.30
20 14 0.26
21 11 0.21
22 3 0.06
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (20 bp):
ATTATAAAATATAATAAATA
Found at i:328403 original size:23 final size:22
Alignment explanation
Indices: 328360--328403 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
328350 GTGATGGGAA
*
328360 ATTTAATTGTATGTCTATTGAG
1 ATTTAATTGTATGTATATTGAG
328382 ATTTATATTGTAT-TATACTTGA
1 ATTTA-ATTGTATGTATA-TTGA
328404 TTTTTGTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.30, C:0.05, G:0.14, T:0.52
Consensus pattern (22 bp):
ATTTAATTGTATGTATATTGAG
Found at i:328454 original size:53 final size:53
Alignment explanation
Indices: 328390--328496 Score: 137
Period size: 53 Copynumber: 2.0 Consensus size: 53
328380 AGATTTATAT
* * * *
328390 TGTATTATACTTGATTTTTGTTAATGTTT-AAAAAGATTTTGAT-GAGTGAATGA
1 TGTATGATACTTGA-TTTTGATAATATTTGAAAAAGATTCTGATAG-GTGAATGA
*
328443 TGTATGATACTTGATTTTGATGATATTTGAAAAAGATTCTGATAGGTGAATGA
1 TGTATGATACTTGATTTTGATAATATTTGAAAAAGATTCTGATAGGTGAATGA
328496 T
1 T
328497 AAATGATTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
52 11 0.23
53 35 0.74
54 1 0.02
ACGTcount: A:0.33, C:0.03, G:0.21, T:0.44
Consensus pattern (53 bp):
TGTATGATACTTGATTTTGATAATATTTGAAAAAGATTCTGATAGGTGAATGA
Found at i:328634 original size:49 final size:49
Alignment explanation
Indices: 328559--328723 Score: 285
Period size: 49 Copynumber: 3.4 Consensus size: 49
328549 GAGGTGGAGC
* ** *
328559 ATTTAACACGTCTGACGTCTTTGTGACTATGGTGCTACGATTGATGATG
1 ATTTAGCACGTCTGACGTCTTTGTGACGGTGGTGCTATGATTGATGATG
*
328608 ATTTAGCACGTCTGACGTCTTCGTGACGGTGGTGCTATGATTGATGATG
1 ATTTAGCACGTCTGACGTCTTTGTGACGGTGGTGCTATGATTGATGATG
328657 ATTTAGCACGTCTGACGTCTTTGTGACGGTGGTGCTATGATTGATGATG
1 ATTTAGCACGTCTGACGTCTTTGTGACGGTGGTGCTATGATTGATGATG
328706 ATTTAGCACGTCTGACGT
1 ATTTAGCACGTCTGACGT
328724 TACAGATGTA
Statistics
Matches: 110, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 110 1.00
ACGTcount: A:0.20, C:0.16, G:0.28, T:0.36
Consensus pattern (49 bp):
ATTTAGCACGTCTGACGTCTTTGTGACGGTGGTGCTATGATTGATGATG
Found at i:328742 original size:52 final size:48
Alignment explanation
Indices: 328588--328746 Score: 214
Period size: 49 Copynumber: 3.2 Consensus size: 48
328578 TTTGTGACTA
*
328588 TGGTGCTACGATTGATGATGATTTAGCACGTCTGACGTCTTCGTG-ACGG
1 TGGTGCTATGATTGATGATGATTTAGCACGTCTGACG--TTCGTGTACGG
*
328637 TGGTGCTATGATTGATGATGATTTAGCACGTCTGACG-TCTTTGTGACGG
1 TGGTGCTATGATTGATGATGATTTAGCACGTCTGACGTTC-GTGT-ACGG
328686 TGGTGCTATGATTGATGATGATTTAGCACGTCTGACGTTACAGATGTAACGG
1 TGGTGCTATGATTGATGATGATTTAGCACGTCTGACGTT-C-G-TGT-ACGG
328738 TGGTGCTAT
1 TGGTGCTAT
328747 TTATGTGTAT
Statistics
Matches: 99, Mismatches: 5, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
46 2 0.02
47 2 0.02
49 77 0.78
50 1 0.01
51 1 0.01
52 16 0.16
ACGTcount: A:0.20, C:0.15, G:0.30, T:0.35
Consensus pattern (48 bp):
TGGTGCTATGATTGATGATGATTTAGCACGTCTGACGTTCGTGTACGG
Found at i:332275 original size:43 final size:43
Alignment explanation
Indices: 332186--332354 Score: 175
Period size: 43 Copynumber: 3.9 Consensus size: 43
332176 TAGATGCTTT
* *
332186 AATTATAAAAGTAAAAAGTAAAATTGAAAAAAATTAGGGAAT-TC
1 AATTATAAAAGTAAAAAGTAAGATT-AAAAAAATTAGGG-GTCTC
* *
332230 AATTAT-AAAGATAAAAAGTGAGATTTAAAAAATTAGGGGTCTC
1 AATTATAAAAG-TAAAAAGTAAGATTAAAAAAATTAGGGGTCTC
* * * *
332273 AATTATAAAAGTAAAAAATAAGGTTGAAAAAATTAAGGG-CGTC
1 AATTATAAAAGTAAAAAGTAAGATTAAAAAAATTAGGGGTC-TC
* *
332316 AATTATAAATA-TAAAAGGTAGGATTAAAAAAATTAGGGG
1 AATTATAAA-AGTAAAAAGTAAGATTAAAAAAATTAGGGG
332355 CCATAATTGT
Statistics
Matches: 105, Mismatches: 15, Indels: 11
0.80 0.11 0.08
Matches are distributed among these distances:
42 2 0.02
43 80 0.76
44 23 0.22
ACGTcount: A:0.54, C:0.03, G:0.18, T:0.25
Consensus pattern (43 bp):
AATTATAAAAGTAAAAAGTAAGATTAAAAAAATTAGGGGTCTC
Found at i:332352 original size:86 final size:87
Alignment explanation
Indices: 332186--332354 Score: 227
Period size: 86 Copynumber: 2.0 Consensus size: 87
332176 TAGATGCTTT
* *
332186 AATTATAAAAGTAAAAAGTAAAATTGAAAAAAATTAGGGAATTCAATTATAAAGATAAAAAGTGA
1 AATTATAAAAGTAAAAAATAAAATTGAAAAAAATTAGGGAAGTCAATTATAAAGATAAAAAGTGA
*
332251 GATTTAAAAAATTAGGGGTCTC
66 GATTAAAAAAATTAGGGGTCTC
** * * *
332273 AATTATAAAAGTAAAAAATAAGGTTG-AAAAAATTAAGGG-CGTCAATTATAAATATAAAAGGT-
1 AATTATAAAAGTAAAAAATAAAATTGAAAAAAATT-AGGGAAGTCAATTATAAAGATAAAAAGTG
332335 AGGATTAAAAAAATTAGGGG
65 A-GATTAAAAAAATTAGGGG
332355 CCATAATTGT
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
85 1 0.01
86 44 0.61
87 27 0.38
ACGTcount: A:0.54, C:0.03, G:0.18, T:0.25
Consensus pattern (87 bp):
AATTATAAAAGTAAAAAATAAAATTGAAAAAAATTAGGGAAGTCAATTATAAAGATAAAAAGTGA
GATTAAAAAAATTAGGGGTCTC
Found at i:334617 original size:19 final size:19
Alignment explanation
Indices: 334589--334627 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
334579 TTTAATACTT
*
334589 ATTATGCTTATAAAAAATA
1 ATTATACTTATAAAAAATA
334608 ATTATACTTATAAAAAATA
1 ATTATACTTATAAAAAATA
334627 A
1 A
334628 AAATATTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (19 bp):
ATTATACTTATAAAAAATA
Found at i:337422 original size:61 final size:62
Alignment explanation
Indices: 337336--337451 Score: 157
Period size: 61 Copynumber: 1.9 Consensus size: 62
337326 TTTGATACGA
* * *
337336 GGATTTTTAAATATTATAAAGTAATTATTA-ATTTTT-T-AAATGATTATAAAATGATCCTT
1 GGATTTTTAAATATTATAAAATAATTAATATATTTTTATCAAATAATTATAAAATGATCCTT
*
337395 GGATTTATTAAATTATTATAAAATAATTAATATATTTTTATCTAATAATTATAAAAT
1 GGATTT-TTAAA-TATTATAAAATAATTAATATATTTTTATCAAATAATTATAAAAT
337452 CATTAATAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
59 6 0.12
60 5 0.10
61 17 0.35
62 6 0.12
63 1 0.02
64 13 0.27
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (62 bp):
GGATTTTTAAATATTATAAAATAATTAATATATTTTTATCAAATAATTATAAAATGATCCTT
Found at i:340211 original size:40 final size:41
Alignment explanation
Indices: 340131--340223 Score: 118
Period size: 40 Copynumber: 2.3 Consensus size: 41
340121 ACAAAATGAC
* * *
340131 ACTTTAGAGGCGTTTTTTAAACAAACGCTGCTATAGAGTAGT
1 ACTTTAGTGGCGTTTTTT-AACAAACGCCGCTATAAAGTAGT
*
340173 ACTTTAGTGGCGTTTTTT-ATAAACGCCG-TAATAAAGTAGT
1 ACTTTAGTGGCGTTTTTTAACAAACGCCGCT-ATAAAGTAGT
340213 ACTTTAGTGGC
1 ACTTTAGTGGC
340224 ATTTGTGCTA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
39 1 0.02
40 28 0.61
42 17 0.37
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (41 bp):
ACTTTAGTGGCGTTTTTTAACAAACGCCGCTATAAAGTAGT
Found at i:340285 original size:12 final size:14
Alignment explanation
Indices: 340249--340285 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
340239 CGCCGCGATC
340249 TTTAGCGGCGCTAT
1 TTTAGCGGCGCTAT
340263 TTTCAGCGGCGCT-T
1 TTT-AGCGGCGCTAT
340277 TTT-GCGGCG
1 TTTAGCGGCG
340286 TTTGTCATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 6 0.27
14 7 0.32
15 9 0.41
ACGTcount: A:0.08, C:0.24, G:0.32, T:0.35
Consensus pattern (14 bp):
TTTAGCGGCGCTAT
Found at i:340552 original size:27 final size:27
Alignment explanation
Indices: 340522--340573 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
340512 TGAGAACGTA
*
340522 TAAGACTCGTACAACATGCAATATATG
1 TAAGACTCATACAACATGCAATATATG
*
340549 TAAGACTCATGCAACATGCAATATA
1 TAAGACTCATACAACATGCAATATA
340574 CAATACGAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.25
Consensus pattern (27 bp):
TAAGACTCATACAACATGCAATATATG
Found at i:340627 original size:71 final size:73
Alignment explanation
Indices: 340540--340691 Score: 238
Period size: 74 Copynumber: 2.1 Consensus size: 73
340530 GTACAACATG
* *
340540 CAATATATGTAAGACTCATGCAACATG-CA-ATATACAATACGA-AGAACCCATTTTTAAATTTC
1 CAATATATATAAGACTCATGCAACATGAAATATATACAATACGATA-AACCCATTTTTAAATTTC
*
340602 TATATCCGT
65 TATATCCAT
340611 CAATATATATAAGACTCATGCAACATGTAAATATATACAATACGATAAACCCATTTTTAAATTTC
1 CAATATATATAAGACTCATGCAACATG-AAATATATACAATACGATAAACCCATTTTTAAATTTC
340676 TATATCCAT
65 TATATCCAT
340685 CAATATA
1 CAATATA
340692 CAACATGTAA
Statistics
Matches: 74, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
71 26 0.35
73 1 0.01
74 46 0.62
75 1 0.01
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.32
Consensus pattern (73 bp):
CAATATATATAAGACTCATGCAACATGAAATATATACAATACGATAAACCCATTTTTAAATTTCT
ATATCCAT
Found at i:352001 original size:14 final size:14
Alignment explanation
Indices: 351982--352036 Score: 73
Period size: 14 Copynumber: 4.2 Consensus size: 14
351972 GTTCGTGAAT
351982 GTTCGGTTATGTTC
1 GTTCGGTTATGTTC
351996 GTTCGGTTA---T-
1 GTTCGGTTATGTTC
*
352006 GTTCGATTATGTTC
1 GTTCGGTTATGTTC
352020 GTTCGGTTATGTTC
1 GTTCGGTTATGTTC
352034 GTT
1 GTT
352037 TATGTTCATT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
10 8 0.23
11 1 0.03
13 1 0.03
14 25 0.71
ACGTcount: A:0.09, C:0.13, G:0.27, T:0.51
Consensus pattern (14 bp):
GTTCGGTTATGTTC
Found at i:352053 original size:24 final size:24
Alignment explanation
Indices: 351980--352043 Score: 110
Period size: 24 Copynumber: 2.7 Consensus size: 24
351970 ACGTTCGTGA
*
351980 ATGTTCGGTTATGTTCGTTCGGTT
1 ATGTTCGATTATGTTCGTTCGGTT
352004 ATGTTCGATTATGTTCGTTCGGTT
1 ATGTTCGATTATGTTCGTTCGGTT
*
352028 ATGTTCGTTTATGTTC
1 ATGTTCGATTATGTTC
352044 ATTCATTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.11, C:0.12, G:0.25, T:0.52
Consensus pattern (24 bp):
ATGTTCGATTATGTTCGTTCGGTT
Found at i:356668 original size:2 final size:2
Alignment explanation
Indices: 356581--356659 Score: 65
Period size: 2 Copynumber: 39.0 Consensus size: 2
356571 ATTAAGTGTG
*
356581 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A GTA CA 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
* * *
356623 TA AA GTA TA -A GTA TA TA AA CTA TA T- TG TA TA TA TA TA
1 TA TA -TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA
356660 AAGTATATAA
Statistics
Matches: 63, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
1 3 0.05
2 56 0.89
3 4 0.06
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (2 bp):
TA
Found at i:356681 original size:29 final size:29
Alignment explanation
Indices: 356585--356686 Score: 95
Period size: 29 Copynumber: 3.5 Consensus size: 29
356575 AGTGTGTATA
* *
356585 TATATA-TATATATATATA-TATATATAAG
1 TATATAGTATATATATAAAGTATATA-AAC
* *
356613 TACATA-TATATAAAGTATAAGTATATAAAC
1 TATATAGTATATATA-TA-AAGTATATAAAC
*
356643 TATATTGTATATATATAAAGTATATAAAC
1 TATATAGTATATATATAAAGTATATAAAC
356672 TATGA-AGTATATATA
1 TAT-ATAGTATATATA
356687 CATAAATAAG
Statistics
Matches: 61, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
28 12 0.20
29 26 0.43
30 10 0.16
31 13 0.21
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (29 bp):
TATATAGTATATATATAAAGTATATAAAC
Found at i:356916 original size:2 final size:2
Alignment explanation
Indices: 356911--356991 Score: 72
Period size: 2 Copynumber: 39.0 Consensus size: 2
356901 TCAATCTACT
* ** *
356911 TA TA TA TA TA TA TA TA TA AA GG TA TA AA GTA TA TA GTA 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
* * *
356955 TA TA AA GTA TA TA CA TA AA 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
356992 AGTATAGCAT
Statistics
Matches: 63, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
2 59 0.94
3 4 0.06
ACGTcount: A:0.52, C:0.01, G:0.06, T:0.41
Consensus pattern (2 bp):
TA
Found at i:357280 original size:147 final size:148
Alignment explanation
Indices: 357013--357307 Score: 556
Period size: 147 Copynumber: 2.0 Consensus size: 148
357003 AAACATAAGT
*
357013 GATTAAAATAAAATATTCTAAAATTAGCATTCACATTTAATTACTATAATTAGAATGTATACATG
1 GATTAAAATAAAATATTCTAAAATTAGCATTCACATTTAATTACTAGAATTAGAATGTATACATG
357078 ACTAAATTGCATTGAATTAAAAATTAAATAAATCAGCTGACCCTTATTCCCATATGTAATAGGGT
66 ACTAAATTGCATTGAATTAAAAATTAAATAAATCAGCTGACCCTTATTCCCATATGTAATAGGGT
357143 AA-GGGGAGGTAAGATAG
131 AAGGGGGAGGTAAGATAG
357160 GATTAAAATAAAATATTCTAAAATTAGCATTCACATTTAATTACTAGAATTAGAATGTATACATG
1 GATTAAAATAAAATATTCTAAAATTAGCATTCACATTTAATTACTAGAATTAGAATGTATACATG
* *
357225 ACTAAATTGCATTGAATTAAAAATTAAATAAATTAGCTGACCCTTATTCTCATATGTAATAGGGT
66 ACTAAATTGCATTGAATTAAAAATTAAATAAATCAGCTGACCCTTATTCCCATATGTAATAGGGT
357290 AAGGGGGAGGTAAGATAG
131 AAGGGGGAGGTAAGATAG
357308 TAGGCTGCCC
Statistics
Matches: 144, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
147 129 0.90
148 15 0.10
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (148 bp):
GATTAAAATAAAATATTCTAAAATTAGCATTCACATTTAATTACTAGAATTAGAATGTATACATG
ACTAAATTGCATTGAATTAAAAATTAAATAAATCAGCTGACCCTTATTCCCATATGTAATAGGGT
AAGGGGGAGGTAAGATAG
Found at i:357781 original size:26 final size:25
Alignment explanation
Indices: 357718--357781 Score: 94
Period size: 24 Copynumber: 2.5 Consensus size: 25
357708 TTCTTTTAAA
357718 ATTTTAAATATTTATCTTTTATATAT
1 ATTTTAAAT-TTTATCTTTTATATAT
*
357744 ATATTAAA-TTTATCTTTTATATAT
1 ATTTTAAATTTTATCTTTTATATAT
357768 ATTTTAAAATTTTA
1 ATTTT-AAATTTTA
357782 AATTAAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 20 0.59
25 3 0.09
26 11 0.32
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTTTAAATTTTATCTTTTATATAT
Found at i:357886 original size:15 final size:17
Alignment explanation
Indices: 357868--357907 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
357858 TTATATAATA
*
357868 TAATAAAAT-CA-TGTT
1 TAATAAAATACATTATT
357883 TAAT-AAATACATTATT
1 TAATAAAATACATTATT
357899 TAATAAAAT
1 TAATAAAAT
357908 TAAATAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 4 0.19
15 6 0.29
16 7 0.33
17 4 0.19
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.40
Consensus pattern (17 bp):
TAATAAAATACATTATT
Found at i:366210 original size:17 final size:18
Alignment explanation
Indices: 366181--366214 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
366171 TATTTTAGAG
366181 TTTAAATAAAAAAATTAT
1 TTTAAATAAAAAAATTAT
366199 TTTAAA-AAAAAAATTA
1 TTTAAATAAAAAAATTA
366215 ATTGATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TTTAAATAAAAAAATTAT
Found at i:368318 original size:26 final size:26
Alignment explanation
Indices: 368282--368359 Score: 147
Period size: 26 Copynumber: 3.0 Consensus size: 26
368272 CCAAAGATAA
368282 CATGTAACACAAAGCAACAAGGCTCT
1 CATGTAACACAAAGCAACAAGGCTCT
368308 CATGTAACACAAAGCAACAAGGCTCT
1 CATGTAACACAAAGCAACAAGGCTCT
*
368334 CATGTAACACAAAGCAAAAAGGCTCT
1 CATGTAACACAAAGCAACAAGGCTCT
368360 TTATTATATG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 51 1.00
ACGTcount: A:0.44, C:0.26, G:0.15, T:0.15
Consensus pattern (26 bp):
CATGTAACACAAAGCAACAAGGCTCT
Done.