Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002960.1 Hibiscus syriacus cultivar Beakdansim tig00006128_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: 82957
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:930 original size:36 final size:36
Alignment explanation
Indices: 902--1130 Score: 350
Period size: 36 Copynumber: 6.4 Consensus size: 36
892 TGAAGTCAAC
* * *
902 GATCAAGATGATGAGCTTGTATCAGATGAATTTGAT
1 GATCAGGATGATGTGCTTGTATCGGATGAATTTGAT
* * * * *
938 GATCCGGACGATGAGCTTGTACCAGATGAATTTGAT
1 GATCAGGATGATGTGCTTGTATCGGATGAATTTGAT
*
974 GATCAGGATGATGTGCTTGTGTCGGATGAATTTGAT
1 GATCAGGATGATGTGCTTGTATCGGATGAATTTGAT
* *
1010 GATCAGGATGATGTGCTTGTATCTGATGGATTTGAT
1 GATCAGGATGATGTGCTTGTATCGGATGAATTTGAT
*
1046 GATCAGGATGTTGTGCTTGTATCGGATGAATTTGAT
1 GATCAGGATGATGTGCTTGTATCGGATGAATTTGAT
1082 GATCAGGATGATGTGCTTGTATCGGATGAATTTGAT
1 GATCAGGATGATGTGCTTGTATCGGATGAATTTGAT
1118 GATCAGGATGATG
1 GATCAGGATGATG
1131 AGTTTGATGG
Statistics
Matches: 176, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 176 1.00
ACGTcount: A:0.26, C:0.10, G:0.30, T:0.34
Consensus pattern (36 bp):
GATCAGGATGATGTGCTTGTATCGGATGAATTTGAT
Found at i:1442 original size:84 final size:85
Alignment explanation
Indices: 1274--1442 Score: 182
Period size: 84 Copynumber: 2.0 Consensus size: 85
1264 GGATCTTGAG
* *
1274 AAAAGGCTACTTGCTAGAGGAAAACAACAAAGAGTTCCAAAAGAGCAAAAAGGTCAAAAGCTAGA
1 AAAAGGCTACTTGCTAAACGAAAACAACAAAGAGTTCCAAAAGAGCAAAAAGGTCAAAAGCTAGA
*** *
1339 AAGAGTTGGGTCTATTAAGA
66 AAGACCAGGGTCTACTAAGA
* * *
1359 AAAAGG-TACTTGCTAAACGAAACCAACCAAA-AGTTCTAAAAGAGC-AAAAGGTTCAAAAGCTT
1 AAAAGGCTACTTGCTAAACGAAAACAA-CAAAGAGTTCCAAAAGAGCAAAAAGG-TCAAAAGCTA
* ** *
1421 GATATTCCAGGGTCTGCTAAGA
64 GAAAGACCAGGGTCTACTAAGA
1443 GGTATTTATG
Statistics
Matches: 69, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
83 6 0.09
84 53 0.77
85 10 0.14
ACGTcount: A:0.45, C:0.15, G:0.21, T:0.18
Consensus pattern (85 bp):
AAAAGGCTACTTGCTAAACGAAAACAACAAAGAGTTCCAAAAGAGCAAAAAGGTCAAAAGCTAGA
AAGACCAGGGTCTACTAAGA
Found at i:11362 original size:21 final size:21
Alignment explanation
Indices: 11338--11381 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
11328 TATTACATTA
* * *
11338 AAATATTGTAGATTGTTATGT
1 AAATATTATAAATTGTCATGT
*
11359 AAATTTTATAAATTGTCATGT
1 AAATATTATAAATTGTCATGT
11380 AA
1 AA
11382 GCATCGTGAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.02, G:0.14, T:0.45
Consensus pattern (21 bp):
AAATATTATAAATTGTCATGT
Found at i:12714 original size:22 final size:20
Alignment explanation
Indices: 12686--12727 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
12676 TTTTATTATC
12686 TTAAATTGATATATATTTAATT
1 TTAAATT-ATAT-TATTTAATT
*
12708 TTAAATTTTATTATTTAATT
1 TTAAATTATATTATTTAATT
12728 CAATACTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 3 0.16
22 7 0.37
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TTAAATTATATTATTTAATT
Found at i:13760 original size:10 final size:10
Alignment explanation
Indices: 13739--13784 Score: 55
Period size: 9 Copynumber: 5.0 Consensus size: 10
13729 TTTATTAGTC
13739 AAAGTA-ATT
1 AAAGTATATT
13748 AAAGTATATT
1 AAAGTATATT
13758 AAAGTAT-TT
1 AAAGTATATT
*
13767 AAAATAT-TT
1 AAAGTATATT
13776 AAAGT-TATT
1 AAAGTATATT
13785 TTCATTTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
8 1 0.03
9 22 0.67
10 10 0.30
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (10 bp):
AAAGTATATT
Found at i:13784 original size:19 final size:19
Alignment explanation
Indices: 13739--13785 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
13729 TTTATTAGTC
* *
13739 AAAGTAATTAAAGTATATT
1 AAAGTATTTAAAATATATT
13758 AAAGTATTTAAAATAT-TT
1 AAAGTATTTAAAATATATT
13776 AAAGTTATTT
1 AAAG-TATTT
13786 TCATTTTAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (19 bp):
AAAGTATTTAAAATATATT
Found at i:14991 original size:30 final size:30
Alignment explanation
Indices: 14942--15000 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
14932 TAATGAAAAC
* * *
14942 TTCACTTTGGTCTCCAAATTTAT-TTAAAT
1 TTCACTTTAGTCTCAAAATTAATATTAAAT
14971 TTCACTTTAGTCCTCAAAATTAATATTAAA
1 TTCACTTTAGT-CTCAAAATTAATATTAAA
15001 AAAATTAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 10 0.40
30 10 0.40
31 5 0.20
ACGTcount: A:0.34, C:0.17, G:0.05, T:0.44
Consensus pattern (30 bp):
TTCACTTTAGTCTCAAAATTAATATTAAAT
Found at i:17197 original size:152 final size:151
Alignment explanation
Indices: 16913--17214 Score: 489
Period size: 152 Copynumber: 2.0 Consensus size: 151
16903 CGTCAAGACA
* * *
16913 CTAGACCTCTTAAGCAAGGTCAGGGATTCAAATCCTCACGATTATTAATGAAGTAAACTAAGTTA
1 CTAGACCCCTTAAGCAAGGTCAGGGATTCAAATCCTCACGATTATGAATGAAGCAAACTAAGTTA
* * * *
16978 GGAGGGTCGTACTTATCTTTACAGTAACTGACTCAGATTAATCAATTAATAGATTAGATACCGAT
66 GAAGAGTCGTACTTATCTCTACAGTAACTGACTCAGATTAATCAATTAATAGATTAAATACCGAT
17043 GATTATAAAAAAAATTAAACC
131 GATTATAAAAAAAATTAAACC
* *
17064 CTAGACCCCCTTAAGTAAGGTCAGAGG-TTCAAATCCTCACGATTATGAATGAAGCAAACTGAGT
1 CTAGA-CCCCTTAAGCAAGGTCAG-GGATTCAAATCCTCACGATTATGAATGAAGCAAACTAAGT
*
17128 TAGAAGAGTCGTACTTATCTCTACAGTAACTGACTCAGATTAATCAATTAATATATTAAATACCG
64 TAGAAGAGTCGTACTTATCTCTACAGTAACTGACTCAGATTAATCAATTAATAGATTAAATACCG
17193 ATGATTATAAAAAAAATTAAAC
129 ATGATTATAAAAAAAATTAAAC
17215 TCTAACATAA
Statistics
Matches: 139, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
151 5 0.04
152 132 0.95
153 2 0.01
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (151 bp):
CTAGACCCCTTAAGCAAGGTCAGGGATTCAAATCCTCACGATTATGAATGAAGCAAACTAAGTTA
GAAGAGTCGTACTTATCTCTACAGTAACTGACTCAGATTAATCAATTAATAGATTAAATACCGAT
GATTATAAAAAAAATTAAACC
Found at i:27723 original size:31 final size:31
Alignment explanation
Indices: 27688--27762 Score: 116
Period size: 31 Copynumber: 2.4 Consensus size: 31
27678 GGTATTTATA
27688 GTTAAAGCTTT-GGGACTAATATTGTAAATAG
1 GTTAAAG-TTTAGGGACTAATATTGTAAATAG
27719 GTTAAAGTTTAGGGACTAATATTGTAAATAG
1 GTTAAAGTTTAGGGACTAATATTGTAAATAG
**
27750 CCTAAAGTTTAGG
1 GTTAAAGTTTAGG
27763 AAGTAATTAG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
30 3 0.07
31 38 0.93
ACGTcount: A:0.36, C:0.07, G:0.23, T:0.35
Consensus pattern (31 bp):
GTTAAAGTTTAGGGACTAATATTGTAAATAG
Found at i:31316 original size:11 final size:11
Alignment explanation
Indices: 31293--31325 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
31283 AATTTTAAAA
31293 TTATA-ATTATT
1 TTATATATT-TT
31304 TTATATATTTT
1 TTATATATTTT
31315 TTATATATTTT
1 TTATATATTTT
31326 CACCCCTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 18 0.86
12 3 0.14
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TTATATATTTT
Found at i:32486 original size:14 final size:14
Alignment explanation
Indices: 32467--32493 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
32457 AATATAAAAT
32467 TATTTTTTAAATTG
1 TATTTTTTAAATTG
32481 TATTTTTTAAATT
1 TATTTTTTAAATT
32494 TATAATTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.67
Consensus pattern (14 bp):
TATTTTTTAAATTG
Found at i:32507 original size:23 final size:23
Alignment explanation
Indices: 32481--32524 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
32471 TTTTAAATTG
32481 TATTTTTTAAATTTATAATTTAT
1 TATTTTTTAAATTTATAATTTAT
*
32504 TATTTTTTAAATTTGTAATTT
1 TATTTTTTAAATTTATAATTT
32525 TATGACTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (23 bp):
TATTTTTTAAATTTATAATTTAT
Found at i:32534 original size:23 final size:23
Alignment explanation
Indices: 32485--32535 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
32475 AAATTGTATT
* *
32485 TTTTAAATTTATAATTTATTATT
1 TTTTAAATTTATAATTTATGATC
*
32508 TTTTAAATTTGTAATTTTATGA-C
1 TTTTAAATTTATAA-TTTATGATC
32531 TTTTA
1 TTTTA
32536 TTTATTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 18 0.75
24 6 0.25
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (23 bp):
TTTTAAATTTATAATTTATGATC
Found at i:42199 original size:25 final size:25
Alignment explanation
Indices: 42166--42214 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
42156 TAGTTCATCG
* *
42166 TTCAGATGGAAGAGAACTGGTATCA
1 TTCAAATGGAAAAGAACTGGTATCA
42191 TTCAAATGGAAAAGAACTGGTATC
1 TTCAAATGGAAAAGAACTGGTATC
42215 CTAATAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.24
Consensus pattern (25 bp):
TTCAAATGGAAAAGAACTGGTATCA
Found at i:42667 original size:13 final size:13
Alignment explanation
Indices: 42649--42673 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42639 CTTTTAAGTA
42649 GGGATTTATTTAC
1 GGGATTTATTTAC
42662 GGGATTTATTTA
1 GGGATTTATTTA
42674 TATATTTATT
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:0.04, G:0.24, T:0.48
Consensus pattern (13 bp):
GGGATTTATTTAC
Found at i:42909 original size:21 final size:21
Alignment explanation
Indices: 42879--42940 Score: 97
Period size: 21 Copynumber: 3.0 Consensus size: 21
42869 ACTGTGATTG
*
42879 CGACCGTCGCGAGCGCTATTA
1 CGACCTTCGCGAGCGCTATTA
42900 CGACCTTCGCGAGCGCTATTA
1 CGACCTTCGCGAGCGCTATTA
* *
42921 CGATCTTCGCGAGAGCTATT
1 CGACCTTCGCGAGCGCTATT
42941 GCGGCCGTCG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.19, C:0.31, G:0.26, T:0.24
Consensus pattern (21 bp):
CGACCTTCGCGAGCGCTATTA
Found at i:42951 original size:21 final size:21
Alignment explanation
Indices: 42879--42952 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
42869 ACTGTGATTG
42879 CGACCGTCGCGAGCGCTATTA
1 CGACCGTCGCGAGCGCTATTA
*
42900 CGACCTTCGCGAGCGCTATTA
1 CGACCGTCGCGAGCGCTATTA
* * * *
42921 CGATCTTCGCGAGAGCTATTG
1 CGACCGTCGCGAGCGCTATTA
*
42942 CGGCCGTCGCG
1 CGACCGTCGCG
42953 GATAACTAGG
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.16, C:0.32, G:0.30, T:0.22
Consensus pattern (21 bp):
CGACCGTCGCGAGCGCTATTA
Found at i:45800 original size:21 final size:21
Alignment explanation
Indices: 45776--45836 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
45766 TCAACTTTGA
45776 AAATGGTTTTTAAAGTTTGGT
1 AAATGGTTTTTAAAGTTTGGT
*
45797 AAAT-G-TTTT----TTT-GA
1 AAATGGTTTTTAAAGTTTGGT
*
45811 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTTAAAGTTTGGT
45832 AAATG
1 AAATG
45837 TTTCTTGGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 14
0.64 0.06 0.30
Matches are distributed among these distances:
14 5 0.17
15 4 0.13
16 3 0.10
19 4 0.13
20 4 0.13
21 10 0.33
ACGTcount: A:0.31, C:0.02, G:0.21, T:0.46
Consensus pattern (21 bp):
AAATGGTTTTTAAAGTTTGGT
Found at i:45810 original size:35 final size:35
Alignment explanation
Indices: 45770--45920 Score: 205
Period size: 35 Copynumber: 4.3 Consensus size: 35
45760 TTGCAATCAA
45770 CTTTGAAAATGGTTTTTAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTTAAAGTTTGGTAAATGTTT
* *
45805 TTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTTAAAGTTTGGTAAATGTTT
* *
45840 CTTGGAAAATTGTTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTT-AAAGTTTGGTAAATGTTT
* * *
45876 CTTTGAAAAATGTTTTTTAAAATTTGGTAGATGTTT
1 CTTTG-AAAATGGTTTTTAAAGTTTGGTAAATGTTT
*
45912 -GTTGAAAAT
1 CTTTGAAAAT
45921 AGGAATGTGT
Statistics
Matches: 102, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
34 5 0.05
35 49 0.48
36 38 0.37
37 10 0.10
ACGTcount: A:0.30, C:0.03, G:0.19, T:0.48
Consensus pattern (35 bp):
CTTTGAAAATGGTTTTTAAAGTTTGGTAAATGTTT
Found at i:45864 original size:36 final size:36
Alignment explanation
Indices: 45770--45920 Score: 200
Period size: 36 Copynumber: 4.3 Consensus size: 36
45760 TTGCAATCAA
*
45770 CTTTGAAAATGGTTTTT-AAAGTTTGGTAAATGTTT
1 CTTTGAAAATTGTTTTTCAAAGTTTGGTAAATGTTT
* *
45805 TTTTGAAAA-TGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATTGTTTTTCAAAGTTTGGTAAATGTTT
*
45840 CTTGGAAAATTGTTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATTGTTTTTCAAAGTTTGGTAAATGTTT
* * * *
45876 CTTTGAAAAATGTTTTTTAAAATTTGGTAGATGTTT
1 CTTTGAAAATTGTTTTTCAAAGTTTGGTAAATGTTT
*
45912 -GTTGAAAAT
1 CTTTGAAAAT
45921 AGGAATGTGT
Statistics
Matches: 101, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
34 5 0.05
35 40 0.40
36 56 0.55
ACGTcount: A:0.30, C:0.03, G:0.19, T:0.48
Consensus pattern (36 bp):
CTTTGAAAATTGTTTTTCAAAGTTTGGTAAATGTTT
Found at i:45869 original size:71 final size:70
Alignment explanation
Indices: 45772--45920 Score: 210
Period size: 71 Copynumber: 2.1 Consensus size: 70
45762 GCAATCAACT
* *
45772 TTGAAAATGGTTTTTAAAGTTTGGTAAATGTTTTTTTG-AAAATGGTTTTCAAAGTTTGGTAAAT
1 TTGAAAATGGTTTTTAAAGTTTGGTAAATGTTTCTTTGAAAAATGGTTTTCAAAATTTGGTAAAT
45836 GTTTC
66 GTTTC
* * * *
45841 TTGGAAAATTGTTTTTCAAAGTTTGGTAAATGTTTCTTTGAAAAATGTTTTTTAAAATTTGGTAG
1 TT-GAAAATGGTTTTT-AAAGTTTGGTAAATGTTTCTTTGAAAAATGGTTTTCAAAATTTGGTAA
*
45906 ATGTTTG
64 ATGTTTC
45913 TTGAAAAT
1 TTGAAAAT
45921 AGGAATGTGT
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
69 2 0.03
70 12 0.17
71 28 0.40
72 28 0.40
ACGTcount: A:0.30, C:0.03, G:0.19, T:0.48
Consensus pattern (70 bp):
TTGAAAATGGTTTTTAAAGTTTGGTAAATGTTTCTTTGAAAAATGGTTTTCAAAATTTGGTAAAT
GTTTC
Found at i:46471 original size:20 final size:22
Alignment explanation
Indices: 46446--46485 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
46436 AGTCATATCT
46446 AGCCG-TTGGGAATG-TTTTGG
1 AGCCGTTTGGGAATGATTTTGG
46466 AGCCGTTTGGGAATGATTTT
1 AGCCGTTTGGGAATGATTTT
46486 TCAGCAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.17, C:0.10, G:0.35, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGAATGATTTTGG
Found at i:46630 original size:19 final size:19
Alignment explanation
Indices: 46580--46646 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
46570 GAGCCTCGGG
* * *
46580 TTACTGTTCAAACAATGAT
1 TTACTGTTCAAATAGTAAT
46599 TTACTGTTCAAATAGTAAT
1 TTACTGTTCAAATAGTAAT
*
46618 TTACTGTTCAAATAGTAAA
1 TTACTGTTCAAATAGTAAT
*
46637 TTACTATTCA
1 TTACTGTTCA
46647 TAAAAACATT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 43 1.00
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.40
Consensus pattern (19 bp):
TTACTGTTCAAATAGTAAT
Found at i:46743 original size:29 final size:31
Alignment explanation
Indices: 46711--46770 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
46701 AAATTTTGAA
*
46711 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
46740 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
46771 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:48052 original size:19 final size:19
Alignment explanation
Indices: 48009--48056 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
47999 TCTAAATCCT
*
48009 TTTTCAAAATTTCATTTTG
1 TTTTCAAAATCTCATTTTG
48028 TCTTTCAAAATCT-ATTTTTG
1 T-TTTCAAAATCTCA-TTTTG
48048 TTTTCAAAA
1 TTTTCAAAA
48057 GAAAATCATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.29, C:0.12, G:0.04, T:0.54
Consensus pattern (19 bp):
TTTTCAAAATCTCATTTTG
Found at i:49287 original size:21 final size:21
Alignment explanation
Indices: 49261--49302 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
49251 CCAGAATGGG
*
49261 GGGAATCGATACCCCTTCATA
1 GGGAATCAATACCCCTTCATA
49282 GGGAATCAATACCCCTTCATA
1 GGGAATCAATACCCCTTCATA
49303 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.24
Consensus pattern (21 bp):
GGGAATCAATACCCCTTCATA
Found at i:49433 original size:19 final size:19
Alignment explanation
Indices: 49409--49475 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
49399 GAGCCTCGGG
*
49409 TTACTGTTCAAACAGTGAT
1 TTACTGTTCAAACAGTAAT
*
49428 TTACTGTTCAAATAGTAAT
1 TTACTGTTCAAACAGTAAT
* *
49447 TTACTGTTCAAATAGTAAA
1 TTACTGTTCAAACAGTAAT
*
49466 TTACTATTCA
1 TTACTGTTCA
49476 TAAAAACATT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.40
Consensus pattern (19 bp):
TTACTGTTCAAACAGTAAT
Found at i:49572 original size:29 final size:31
Alignment explanation
Indices: 49540--49599 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
49530 AAATTTTGAA
*
49540 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
49569 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
49600 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:50853 original size:15 final size:15
Alignment explanation
Indices: 50829--50860 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
50819 AGGCAGATCG
*
50829 AAATCCAGAACGGGA
1 AAATCAAGAACGGGA
50844 AAATCAAGAACGGGA
1 AAATCAAGAACGGGA
50859 AA
1 AA
50861 GAAATATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.16, G:0.25, T:0.06
Consensus pattern (15 bp):
AAATCAAGAACGGGA
Found at i:54161 original size:21 final size:21
Alignment explanation
Indices: 54137--54197 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
54127 CCAACTTTGA
54137 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
54158 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
*
54172 AAATGGTTTTCAAAGTTTGAT
1 AAATGGTTTTCAAAGTTTGGT
54193 AAATG
1 AAATG
54198 TTTCTTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 14
0.64 0.06 0.30
Matches are distributed among these distances:
14 5 0.17
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 9 0.30
ACGTcount: A:0.33, C:0.05, G:0.20, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:54218 original size:36 final size:35
Alignment explanation
Indices: 54131--54245 Score: 178
Period size: 35 Copynumber: 3.3 Consensus size: 35
54121 TGGCAACCAA
54131 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
54166 CTTTGAAAATGGTTTTCAAAGTTTGATAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
54201 CTTTGAAAAATGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
54237 -GTTGAAAAT
1 CTTTGAAAAT
54246 ATGAATGGGT
Statistics
Matches: 74, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
34 5 0.07
35 42 0.57
36 27 0.36
ACGTcount: A:0.30, C:0.05, G:0.19, T:0.45
Consensus pattern (35 bp):
CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:55609 original size:16 final size:16
Alignment explanation
Indices: 55584--55614 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
55574 CTTCTAAATT
*
55584 TTTTTTGAGTTCAAGC
1 TTTTTCGAGTTCAAGC
55600 TTTTTCGAGTTCAAG
1 TTTTTCGAGTTCAAG
55615 TTTCAATATT
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:0.19, C:0.13, G:0.19, T:0.48
Consensus pattern (16 bp):
TTTTTCGAGTTCAAGC
Found at i:73989 original size:38 final size:36
Alignment explanation
Indices: 73909--73989 Score: 90
Period size: 38 Copynumber: 2.2 Consensus size: 36
73899 TAACAAGTTG
* * *
73909 AAAAATATTTATATATTTTCTTAAAAAATTTAAATT
1 AAAAAAATTTATATATTTTCTTAAAAAATTGAAAAT
* *
73945 AAAAAAATTTATATAATTTTTTTTACAAAATTGAAAAT
1 AAAAAAATTTATAT-A-TTTTCTTAAAAAATTGAAAAT
*
73983 ATAAAAA
1 AAAAAAA
73990 GGTTTAATGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
36 13 0.35
37 1 0.03
38 23 0.62
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.42
Consensus pattern (36 bp):
AAAAAAATTTATATATTTTCTTAAAAAATTGAAAAT
Found at i:75395 original size:51 final size:50
Alignment explanation
Indices: 75280--75398 Score: 139
Period size: 50 Copynumber: 2.4 Consensus size: 50
75270 ATGTATATAT
* * * *
75280 TTACATCGGTGTAAGTATTTATTAAGTAATACATTATTTATTTTATTTAC
1 TTACACCGGTGTAAGTATTTATTAAGTAATACATTATTTATTTTACTAAA
* * * * *
75330 TTACACTGGCGTAAGTATTTATTAAGTGATACGTTTTTTTATTTTACTAAA
1 TTACACCGGTGTAAGTATTTATTAAGTAATAC-ATTATTTATTTTACTAAA
*
75381 TTACACCGATGTAAGTAT
1 TTACACCGGTGTAAGTAT
75399 ATGTTTTGTG
Statistics
Matches: 56, Mismatches: 12, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
50 28 0.50
51 28 0.50
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.46
Consensus pattern (50 bp):
TTACACCGGTGTAAGTATTTATTAAGTAATACATTATTTATTTTACTAAA
Done.