Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007708.1 Hibiscus syriacus cultivar Beakdansim tig00109923_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: 882274
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:795989 original size:38 final size:38
Alignment explanation
Indices: 795947--796109 Score: 105
Period size: 38 Copynumber: 4.4 Consensus size: 38
795937 ATATCTATAA
* *
795947 TATATTATATTTATTT-TTTTTTTGAT-TATTTTACTTAT
1 TATATTATATTT-TTTACTTTTTT-ATATATTTTACTCAT
795985 TATA-TATATGTTTTTACTTTTTTATATATTTTACTCAT
1 TATATTATAT-TTTTTACTTTTTTATATATTTTACTCAT
* * ** *
796023 T-TATTATATTTTATA-TTTATCCTATATTTTA-T-GT
1 TATATTATATTTTTTACTTTTTTATATATTTTACTCAT
*
796057 T-T-TTATATTCTTTTACTTGTTTTATTTATTTT--TACAT
1 TATATTATATT-TTTTACTT-TTTTATATATTTTACT-CAT
*
796094 TATCATTTTATTTTTT
1 TAT-ATTATATTTTTT
796110 TAGTGTTTGC
Statistics
Matches: 99, Mismatches: 14, Indels: 23
0.73 0.10 0.17
Matches are distributed among these distances:
33 7 0.07
34 7 0.07
35 4 0.04
36 22 0.22
37 19 0.19
38 30 0.30
39 4 0.04
40 6 0.06
ACGTcount: A:0.23, C:0.06, G:0.02, T:0.68
Consensus pattern (38 bp):
TATATTATATTTTTTACTTTTTTATATATTTTACTCAT
Found at i:795998 original size:20 final size:20
Alignment explanation
Indices: 795975--796013 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
795965 TTTTTGATTA
795975 TTTTACTTATTATATATATGT
1 TTTTACTT-TTATATATATGT
*
795996 TTTTACTTTTTTATATAT
1 TTTTACTTTTATATATAT
796014 TTTACTCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.67
Consensus pattern (20 bp):
TTTTACTTTTATATATATGT
Found at i:796016 original size:18 final size:18
Alignment explanation
Indices: 795975--796091 Score: 64
Period size: 17 Copynumber: 6.3 Consensus size: 18
795965 TTTTTGATTA
*
795975 TTTTACTTATTATATATATGT
1 TTTTACTT-TT-T-TATATAT
795996 TTTTACTTTTTTATATA-
1 TTTTACTTTTTTATATAT
**
796013 TTTTACTCATTTATTATAT
1 TTTTACTTTTTTA-TATAT
* **
796032 TTTATA-TTTATCCTATA-
1 TTT-TACTTTTTTATATAT
796049 TTTTA-TGTTTTTATAT-T
1 TTTTACT-TTTTTATATAT
*
796066 CTTTTACTTGTTTTATTTAT
1 -TTTTACTT-TTTTATATAT
796086 TTTTAC
1 TTTTAC
796092 ATTATCATTT
Statistics
Matches: 75, Mismatches: 12, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
16 3 0.04
17 20 0.27
18 19 0.25
19 20 0.27
20 5 0.07
21 8 0.11
ACGTcount: A:0.23, C:0.08, G:0.03, T:0.67
Consensus pattern (18 bp):
TTTTACTTTTTTATATAT
Found at i:796029 original size:20 final size:19
Alignment explanation
Indices: 795973--796053 Score: 57
Period size: 18 Copynumber: 4.4 Consensus size: 19
795963 TTTTTTTGAT
795973 TATTTTACT-TATTATATATA
1 TATTTTACTAT-TTAT-TATA
*
795993 TGTTTTTACT-TTT-TTATA
1 T-ATTTTACTATTTATTATA
796011 TATTTTACTCATTTA-T-TA
1 TATTTTACT-ATTTATTATA
**
796029 TATTTTA-TATTTATCCTA
1 TATTTTACTATTTATTATA
796047 TATTTTA
1 TATTTTA
796054 TGTTTTTATA
Statistics
Matches: 52, Mismatches: 3, Indels: 14
0.75 0.04 0.20
Matches are distributed among these distances:
16 5 0.10
17 8 0.15
18 23 0.44
19 5 0.10
20 3 0.06
21 8 0.15
ACGTcount: A:0.27, C:0.07, G:0.01, T:0.64
Consensus pattern (19 bp):
TATTTTACTATTTATTATA
Found at i:800613 original size:66 final size:66
Alignment explanation
Indices: 800514--800639 Score: 225
Period size: 66 Copynumber: 1.9 Consensus size: 66
800504 TGGAATTTAA
* * *
800514 GCAATTTGGAAAACAACTGGTAATATCGATACTACTTAGAGAGTATCGATACTTCTCTTAATTTG
1 GCAATTTGGAAAACAACTGGTAATATCGATACTACCTAGAGAATATCGATACTGCTCTTAATTTG
800579 T
66 T
800580 GCAATTTGGAAAACAACTGGTAATATCGATACTACCTAGAGAATATCGATACTGCTCTTA
1 GCAATTTGGAAAACAACTGGTAATATCGATACTACCTAGAGAATATCGATACTGCTCTTA
800640 CCTTTGGTAT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 57 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Consensus pattern (66 bp):
GCAATTTGGAAAACAACTGGTAATATCGATACTACCTAGAGAATATCGATACTGCTCTTAATTTG
T
Found at i:802036 original size:2 final size:2
Alignment explanation
Indices: 802029--802058 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
802019 GTCACTTGTC
*
802029 AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
802059 TCCAATCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:810211 original size:16 final size:16
Alignment explanation
Indices: 810190--810229 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
810180 ATCTTATTAG
810190 ATCAAATAAAATTTAA
1 ATCAAATAAAATTTAA
810206 ATCAAATAAAATTTAA
1 ATCAAATAAAATTTAA
810222 ATCAAATA
1 ATCAAATA
810230 CCCATCTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.30
Consensus pattern (16 bp):
ATCAAATAAAATTTAA
Found at i:819952 original size:7 final size:7
Alignment explanation
Indices: 819936--819973 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
819926 GTCAAAGAAA
*
819936 GTCAATG
1 GTCAACG
819943 GTCAACG
1 GTCAACG
819950 GTCAACG
1 GTCAACG
819957 GTCAACG
1 GTCAACG
819964 GTCAACG
1 GTCAACG
819971 GTC
1 GTC
819974 GGGTCGGGTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.18
Consensus pattern (7 bp):
GTCAACG
Found at i:819980 original size:5 final size:5
Alignment explanation
Indices: 819970--820049 Score: 70
Period size: 5 Copynumber: 14.8 Consensus size: 5
819960 AACGGTCAAC
* * *
819970 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GTTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
*
820019 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTC
820050 AGACCGGTCA
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
5 50 0.82
7 11 0.18
ACGTcount: A:0.07, C:0.23, G:0.50, T:0.20
Consensus pattern (5 bp):
GGTCG
Found at i:819991 original size:22 final size:22
Alignment explanation
Indices: 819963--820049 Score: 165
Period size: 22 Copynumber: 4.0 Consensus size: 22
819953 AACGGTCAAC
819963 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
819985 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
820007 GGTCAACGTTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
820029 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
820050 AGACCGGTCA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 63 1.00
ACGTcount: A:0.09, C:0.23, G:0.48, T:0.20
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:820064 original size:9 final size:9
Alignment explanation
Indices: 820046--820144 Score: 81
Period size: 9 Copynumber: 10.3 Consensus size: 9
820036 GGTCGGGTCG
*
820046 GGTCAGACC
1 GGTCAAACC
820055 GGTCAAACC
1 GGTCAAACC
* *
820064 GATTCAGACC
1 G-GTCAAACC
820074 GGTCAAACC
1 GGTCAAACC
*
820083 GGTTCGAACC
1 GG-TCAAACC
*
820093 GGTTGAAACC
1 GG-TCAAACC
820103 GGTCAAACC
1 GGTCAAACC
820112 GGTCAGAACC
1 GGTCA-AACC
*
820122 GGTTGAAAACC
1 GG-T-CAAACC
*
820133 GGTTAAACC
1 GGTCAAACC
820142 GGT
1 GGT
820145 TTCCAGCAGC
Statistics
Matches: 74, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
9 36 0.49
10 30 0.41
11 7 0.09
12 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:820103 original size:29 final size:31
Alignment explanation
Indices: 820071--820145 Score: 120
Period size: 29 Copynumber: 2.5 Consensus size: 31
820061 ACCGATTCAG
820071 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
820100 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
820130 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
820146 TCCAGCAGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.57
30 15 0.36
31 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:820123 original size:19 final size:19
Alignment explanation
Indices: 820046--820144 Score: 80
Period size: 19 Copynumber: 5.2 Consensus size: 19
820036 GGTCGGGTCG
820046 GGTCAG-ACCGGTCAAACC
1 GGTCAGAACCGGTCAAACC
*
820064 GATTCAG-ACCGGTCAAACC
1 G-GTCAGAACCGGTCAAACC
*
820083 GGTTC-GAACCGGTTGAAACC
1 GG-TCAGAACCGG-TCAAACC
820103 GGTCA-AACCGGTCAGAACC
1 GGTCAGAACCGGTCA-AACC
* * *
820122 GGTTGAAAACCGGTTAAACC
1 GG-TCAGAACCGGTCAAACC
820142 GGT
1 GGT
820145 TTCCAGCAGC
Statistics
Matches: 67, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
18 4 0.06
19 39 0.58
20 16 0.24
21 8 0.12
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.16
Consensus pattern (19 bp):
GGTCAGAACCGGTCAAACC
Found at i:827319 original size:5 final size:5
Alignment explanation
Indices: 827309--827349 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
827299 AACGGTCAAC
*
827309 GGTCG GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTC
827350 AGACCGGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 28 0.88
7 4 0.12
ACGTcount: A:0.05, C:0.22, G:0.54, T:0.20
Consensus pattern (5 bp):
GGTCG
Found at i:827393 original size:19 final size:19
Alignment explanation
Indices: 827352--827415 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
827342 GTCGGGTCAG
*
827352 ACCGGTCAAACCGATTC-A
1 ACCGGTCAAACCGGTTCGA
827370 GACCGGTCAAACCGGTTCGA
1 -ACCGGTCAAACCGGTTCGA
*
827390 ACCGGTTGAAACCGG-TCAGA
1 ACCGG-TCAAACCGGTTC-GA
827410 ACCGGT
1 ACCGGT
827416 TGAAAACCGG
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
19 24 0.60
20 16 0.40
ACGTcount: A:0.28, C:0.30, G:0.27, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAACCGGTTCGA
Found at i:827403 original size:20 final size:21
Alignment explanation
Indices: 827378--827436 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
827368 CAGACCGGTC
827378 AAACCGGTTCGAACCGGTTG-
1 AAACCGGTTCGAACCGGTTGA
827398 AAACCGG-TCAGAACCGGTTGA
1 AAACCGGTTC-GAACCGGTTGA
*
827419 AAACCGGTT-AAACCGGTT
1 AAACCGGTTCGAACCGGTT
827437 TCCAGCAGCC
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
19 2 0.06
20 25 0.71
21 7 0.20
22 1 0.03
ACGTcount: A:0.31, C:0.24, G:0.27, T:0.19
Consensus pattern (21 bp):
AAACCGGTTCGAACCGGTTGA
Found at i:828751 original size:22 final size:22
Alignment explanation
Indices: 828726--828777 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
828716 CTGTACAAAT
828726 TTAATGAATAGTACTATGAACA
1 TTAATGAATAGTACTATGAACA
*
828748 TTAATGAATAGTACTGTGAACA
1 TTAATGAATAGTACTATGAACA
*
828770 GTAATGAA
1 TTAATGAA
828778 CAATACCGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.44, C:0.08, G:0.17, T:0.31
Consensus pattern (22 bp):
TTAATGAATAGTACTATGAACA
Found at i:828847 original size:21 final size:21
Alignment explanation
Indices: 828821--828879 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
828811 CAGGAGTATT
828821 GATACCCTGCTACAGTATACC
1 GATACCCTGCTACAGTATACC
*
828842 GATACCCTGCTACAGTATACT
1 GATACCCTGCTACAGTATACC
*
828863 GATACCCTGTTACAGTA
1 GATACCCTGCTACAGTA
828880 ATTTCGGTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (21 bp):
GATACCCTGCTACAGTATACC
Found at i:832644 original size:17 final size:17
Alignment explanation
Indices: 832622--832656 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
832612 TTCCTAATAT
832622 ATATTA-AACTAAACCTA
1 ATATTAGAA-TAAACCTA
832639 ATATTAGAATAAACCTA
1 ATATTAGAATAAACCTA
832656 A
1 A
832657 CTACAAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.88
18 2 0.12
ACGTcount: A:0.54, C:0.14, G:0.03, T:0.29
Consensus pattern (17 bp):
ATATTAGAATAAACCTA
Found at i:833849 original size:53 final size:53
Alignment explanation
Indices: 833787--833993 Score: 285
Period size: 53 Copynumber: 3.9 Consensus size: 53
833777 TTCAACCAGT
*
833787 GGGTTCGCTCCCTCTTACTTCAAGGAGTATAACTCGAACAATCTTCTGCTTAC
1 GGGTTCGCTCCCTCTTACTTCAAGGAGTAGAACTCGAACAATCTTCTGCTTAC
* * * * *
833840 GGGTTCGCTCCCTCTTGCTTCAAGGAGTAGAACTC-AAAATATCTTCTTCCTAA
1 GGGTTCGCTCCCTCTTACTTCAAGGAGTAGAACTCGAACA-ATCTTCTGCTTAC
*
833893 GGGTTCGCTCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTG-TCTAC
1 GGGTTCGCTCCCTCTTACTTCAAGGAGTAGAACTCGAACAATCTTCTGCT-TAC
* *
833946 GGGTTCGCT-CCTCCTTACTTCAGGGAGTATAACTCGAACAATCTTCTG
1 GGGTTCGCTCCCT-CTTACTTCAAGGAGTAGAACTCGAACAATCTTCTG
833994 GTGTGATTCT
Statistics
Matches: 137, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
52 6 0.04
53 128 0.93
54 3 0.02
ACGTcount: A:0.22, C:0.28, G:0.19, T:0.31
Consensus pattern (53 bp):
GGGTTCGCTCCCTCTTACTTCAAGGAGTAGAACTCGAACAATCTTCTGCTTAC
Found at i:834446 original size:42 final size:42
Alignment explanation
Indices: 834388--834602 Score: 155
Period size: 42 Copynumber: 4.9 Consensus size: 42
834378 CGGAGGACTT
* *
834388 ATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTC
1 ATCATCATGCTCGAAAGACTTACTGATGACCCGAAGGATTTC
* * * *
834430 ATCATCATGCTTGAAAGACTTACTGATGGCACTTACTGATGGGTTTGC
1 ATCATCATGCTCGAAAGACTTACTGAT-G-AC---CCGAAGGATTT-C
* * * ** * ** *
834478 TTCA-CTACT-CTTCCGTGAAGGCTTACAAATTACCTTAAGGATTTA
1 ATCATC-A-TGC-T-CG-AAAGACTTACTGATGACCCGAAGGATTTC
*
834523 ATCATCATGCTCGAAAGACTTACTGATGACCCAAAGGATTTC
1 ATCATCATGCTCGAAAGACTTACTGATGACCCGAAGGATTTC
* *
834565 ATCATCATGCTCGAAAGACTTATTGATGGCCCGAAGGA
1 ATCATCATGCTCGAAAGACTTACTGATGACCCGAAGGA
834603 CTTGTAAATT
Statistics
Matches: 131, Mismatches: 29, Indels: 26
0.70 0.16 0.14
Matches are distributed among these distances:
42 80 0.61
43 3 0.02
44 4 0.03
45 5 0.04
46 9 0.07
47 9 0.07
48 6 0.05
49 4 0.03
50 1 0.01
51 10 0.08
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (42 bp):
ATCATCATGCTCGAAAGACTTACTGATGACCCGAAGGATTTC
Found at i:834465 original size:13 final size:13
Alignment explanation
Indices: 834447--834471 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
834437 TGCTTGAAAG
834447 ACTTACTGATGGC
1 ACTTACTGATGGC
834460 ACTTACTGATGG
1 ACTTACTGATGG
834472 GTTTGCTTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (13 bp):
ACTTACTGATGGC
Found at i:834858 original size:42 final size:42
Alignment explanation
Indices: 834804--834902 Score: 135
Period size: 42 Copynumber: 2.4 Consensus size: 42
834794 CTTACAAATT
* *
834804 ACCCGAATGACTTAATTATCATGCTCAAAAGACTTACTGATG
1 ACCCGAAGGACTTAATCATCATGCTCAAAAGACTTACTGATG
* * *
834846 GCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATG
1 ACCCGAAGGACTTAATCATCATGCTCAAAAGACTTACTGATG
* *
834888 ACACTAAGGACTTAA
1 ACCCGAAGGACTTAA
834903 ATTGCTTACT
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.25
Consensus pattern (42 bp):
ACCCGAAGGACTTAATCATCATGCTCAAAAGACTTACTGATG
Found at i:834879 original size:22 final size:21
Alignment explanation
Indices: 834807--834881 Score: 55
Period size: 22 Copynumber: 3.5 Consensus size: 21
834797 ACAAATTACC
* *
834807 CGAATGACTTAATTATCATGCT
1 CGAAAGACTT-ATCATCATGCT
* * *
834829 CAAAAGACTTA-C-TGATGGCC
1 CGAAAGACTTATCATCAT-GCT
*
834849 CGAAGGACTTCATCATCATGCT
1 CGAAAGACTT-ATCATCATGCT
834871 CGAAAGACTTA
1 CGAAAGACTTA
834882 CTGATGACAC
Statistics
Matches: 39, Mismatches: 10, Indels: 9
0.67 0.17 0.16
Matches are distributed among these distances:
19 3 0.08
20 10 0.26
21 3 0.08
22 20 0.51
23 3 0.08
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (21 bp):
CGAAAGACTTATCATCATGCT
Found at i:843698 original size:17 final size:17
Alignment explanation
Indices: 843678--843730 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
843668 CCTAATATAT
843678 ATATTAAACTAAACCTA
1 ATATTAAACTAAACCTA
*
843695 ATATTAAAATAAACCTA
1 ATATTAAACTAAACCTA
*
843712 ACTA-TAAAC-AAAACTA
1 A-TATTAAACTAAACCTA
843728 ATA
1 ATA
843731 GCTGTTCCTC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 2 0.06
16 7 0.22
17 21 0.66
18 2 0.06
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.26
Consensus pattern (17 bp):
ATATTAAACTAAACCTA
Found at i:845521 original size:31 final size:31
Alignment explanation
Indices: 845494--845564 Score: 115
Period size: 31 Copynumber: 2.3 Consensus size: 31
845484 TCGGGGACCA
*
845494 TATTGCAAACGGACTAAATGTTGGGGGACTG
1 TATTGCAAACAGACTAAATGTTGGGGGACTG
* *
845525 TATTGCAATCATACTAAATGTTGGGGGACTG
1 TATTGCAAACAGACTAAATGTTGGGGGACTG
845556 TATTGCAAA
1 TATTGCAAA
845565 TTTTAAAAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.30
Consensus pattern (31 bp):
TATTGCAAACAGACTAAATGTTGGGGGACTG
Found at i:846104 original size:13 final size:13
Alignment explanation
Indices: 846086--846113 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
846076 GTATCAAATT
846086 TTATAAAATTTCA
1 TTATAAAATTTCA
846099 TTATAAAATTTCA
1 TTATAAAATTTCA
846112 TT
1 TT
846114 CTTAAAAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (13 bp):
TTATAAAATTTCA
Found at i:856078 original size:81 final size:81
Alignment explanation
Indices: 855986--856137 Score: 286
Period size: 81 Copynumber: 1.9 Consensus size: 81
855976 CAACAGCCTG
*
855986 CATAATTAACTCTTAAAGAACCTCAAACCATGACACGTGGTAAAATAATATCACAAAATATCCTG
1 CATAATTAACTCTTAAAGAACCTCAAACCATGACACGTGATAAAATAATATCACAAAATATCCTG
856051 ATCCTTAAAGCATAAA
66 ATCCTTAAAGCATAAA
*
856067 CATAATTAACTCTTAAAGAACCTCAAACCATGACACGTGATATAATAATATCACAAAATATCCTG
1 CATAATTAACTCTTAAAGAACCTCAAACCATGACACGTGATAAAATAATATCACAAAATATCCTG
856132 ATCCTT
66 ATCCTT
856138 CAAAAGCCTA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
81 69 1.00
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (81 bp):
CATAATTAACTCTTAAAGAACCTCAAACCATGACACGTGATAAAATAATATCACAAAATATCCTG
ATCCTTAAAGCATAAA
Found at i:856781 original size:2 final size:2
Alignment explanation
Indices: 856774--856808 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
856764 CAAACAAACA
856774 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
856809 ATTTGAAGTA
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:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:873629 original size:20 final size:20
Alignment explanation
Indices: 873606--873698 Score: 87
Period size: 21 Copynumber: 4.5 Consensus size: 20
873596 ATTTTCCAAT
873606 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
873626 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
873646 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* * ** *
873667 TCGTAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
873688 TCGCAATGCGA
1 TCGCAATGCGA
873699 TACTGACTAT
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.46
21 30 0.54
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:873648 original size:41 final size:41
Alignment explanation
Indices: 873603--873698 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
873593 GCGATTTTCC
873603 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
873644 AATTCGCAATGCGAATAAGTAAATCGTAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
873685 AAATCGCAATGCGA
1 AATTCGCAATGCGA
873699 TACTGACTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.40, C:0.17, G:0.24, T:0.20
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:873652 original size:21 final size:20
Alignment explanation
Indices: 873606--873698 Score: 87
Period size: 20 Copynumber: 4.5 Consensus size: 20
873596 ATTTTCCAAT
*
873606 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
873626 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
873646 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* * **
873667 TCGTAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
873688 TCGCAATGCGA
1 TCGCAATGCGA
873699 TACTGACTAT
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 28 0.50
21 28 0.50
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:873712 original size:20 final size:20
Alignment explanation
Indices: 873687--873779 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
873677 AATTGGGAAA
*
873687 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
873707 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
873728 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
873748 -TCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
873767 TTCGCAACGCGAT
1 ATCGCAACGCGAT
873780 TTACTTAGCA
Statistics
Matches: 59, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
19 17 0.29
20 28 0.47
21 14 0.24
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:873729 original size:41 final size:40
Alignment explanation
Indices: 873684--873760 Score: 109
Period size: 41 Copynumber: 1.9 Consensus size: 40
873674 GCGAATTGGG
* * *
873684 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACT-TCGCAACGCGATAATAA
*
873725 AAAATCGCAACGAGATACTTACTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTGACTTCGCAACGCGATA
873761 CTGACTTTCG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
40 12 0.38
41 20 0.62
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.21
Consensus pattern (40 bp):
AAAATCGCAACGAGATACTGACTTCGCAACGCGATAATAA
Found at i:873753 original size:19 final size:20
Alignment explanation
Indices: 873729--873775 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
873719 TAATAAAAAA
*
873729 TCGCAACGAGATACTTAC-T
1 TCGCAACGAGATACTGACTT
*
873748 TCGCAACGCGATACTGACTT
1 TCGCAACGAGATACTGACTT
873768 TCGCAACG
1 TCGCAACG
873776 CGATTTACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (20 bp):
TCGCAACGAGATACTGACTT
Found at i:874360 original size:19 final size:19
Alignment explanation
Indices: 874336--874380 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
874326 GCAACGAGAT
*
874336 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
874355 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
874374 AATCGCA
1 AATCGCA
874381 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:874398 original size:19 final size:19
Alignment explanation
Indices: 874376--874525 Score: 152
Period size: 20 Copynumber: 8.1 Consensus size: 19
874366 GAAACCAAAA
*
874376 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
874395 TCGCATTGCGA-TTTCATT
1 TCGCGTTGCGATTTTCATT
*
874413 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
874432 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
874452 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
874466 TCTCGTTGCGATAGTCATTT
1 TCGCGTTGCGATTTTCA-TT
*
874486 TCGCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
874505 ATCTCGTTGCGA-TTTCATT
1 -TCGCGTTGCGATTTTCATT
874524 TC
1 TC
874526 AACCAAAAGA
Statistics
Matches: 112, Mismatches: 10, Indels: 19
0.79 0.07 0.13
Matches are distributed among these distances:
14 10 0.09
16 2 0.02
17 3 0.03
18 19 0.17
19 36 0.32
20 42 0.38
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:874484 original size:33 final size:34
Alignment explanation
Indices: 874437--874501 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
874427 TAATTTCGCG
**
874437 GTTGCGATTTTCA-TTTCGCGTTGCGATTCTCTC
1 GTTGCGATAGTCATTTTCGCGTTGCGATTCTCTC
874470 GTTGCGATAGTCATTTTCGCGTTGCGATTCTC
1 GTTGCGATAGTCATTTTCGCGTTGCGATTCTC
874502 ATTATCTCGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 11 0.38
34 18 0.62
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.43
Consensus pattern (34 bp):
GTTGCGATAGTCATTTTCGCGTTGCGATTCTCTC
Found at i:874523 original size:39 final size:37
Alignment explanation
Indices: 874376--874525 Score: 157
Period size: 37 Copynumber: 4.1 Consensus size: 37
874366 GAAACCAAAA
* *
874376 TCGCATTGCGATTTTCATTTCGCATTGCGATTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTCATT
*
874413 TCGCGTTGCGATTTTAATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGA-TTTCATT
* *
874452 TCGCGTTGCGA--TTC---TCTCGTTGCGATAGTCATTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGAT-TTCA-TT
* *
874486 TCGCGTTGCGATTCTCATTATCTCGTTGCGATTTCATT
1 TCGCGTTGCGATTTTCATT-TCGCGTTGCGATTTCATT
874524 TC
1 TC
874526 AACCAAAAGA
Statistics
Matches: 95, Mismatches: 8, Indels: 19
0.78 0.07 0.16
Matches are distributed among these distances:
32 1 0.01
33 10 0.11
34 16 0.17
36 2 0.02
37 23 0.24
38 10 0.11
39 21 0.22
40 12 0.13
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.45
Consensus pattern (37 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTCATT
Found at i:876593 original size:21 final size:21
Alignment explanation
Indices: 876569--876635 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
876559 TCATTCCTCG
876569 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
876590 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
876611 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
876632 AGAG
1 AGAG
876636 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:877985 original size:13 final size:14
Alignment explanation
Indices: 877977--878013 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
877967 GATTGTTTAA
877977 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
*
877991 GTGATTTGTAAAAG
1 TTGATTTGTAAAAG
878005 TTGATTTGT
1 TTGATTTGT
878014 TTAATTGATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.24, T:0.46
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:878179 original size:19 final size:19
Alignment explanation
Indices: 878157--878274 Score: 76
Period size: 19 Copynumber: 6.7 Consensus size: 19
878147 CGAAATTAAA
878157 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
878176 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
878191 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
878209 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
878224 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
878242 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
878261 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
878275 GGATTAAGAG
Statistics
Matches: 73, Mismatches: 15, Indels: 21
0.67 0.14 0.19
Matches are distributed among these distances:
14 17 0.23
16 6 0.08
17 6 0.08
19 34 0.47
20 10 0.14
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:878203 original size:33 final size:33
Alignment explanation
Indices: 878161--878254 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
878151 ATTAAATTCG
878161 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
878194 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
878227 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
878255 AGTAATTTCC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:881936 original size:14 final size:14
Alignment explanation
Indices: 881917--881953 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
881907 CGTCAATTAA
881917 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
881931 ACAAATCATCTTTT
1 ACAAATCAACATTT
881945 ACAAATCAA
1 ACAAATCAA
881954 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Done.