Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002922.1 Hibiscus syriacus cultivar Beakdansim tig00006039_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: 65793
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:5405 original size:5 final size:5
Alignment explanation
Indices: 5389--5418 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
5379 GGTAGTGTAT
5389 ATATA TATATA ATATA ATATA ATATA ATAT
1 ATATA -ATATA ATATA ATATA ATATA ATAT
5419 GTAATGAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
ATATA
Found at i:6886 original size:26 final size:26
Alignment explanation
Indices: 6836--6886 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
6826 AGGTACAATA
* * *
6836 CCCTTTGTTGTGAAGTTGTGGATGAC
1 CCCTTCGTTGTGAAGTTGAGCATGAC
6862 CCCTTCGTTGTGAAGTTGAGCATGA
1 CCCTTCGTTGTGAAGTTGAGCATGA
6887 GAATTATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.18, C:0.18, G:0.29, T:0.35
Consensus pattern (26 bp):
CCCTTCGTTGTGAAGTTGAGCATGAC
Found at i:7125 original size:106 final size:106
Alignment explanation
Indices: 6940--7478 Score: 783
Period size: 106 Copynumber: 5.0 Consensus size: 106
6930 GTACTGTTCT
* * *
6940 GAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACAA
7005 CCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
*
7046 GAGTCCAATATACTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACAA
*
7111 CCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTC
66 CCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
* * *
7152 GAGTCCAATATCATTCGCTGTGAAGTTGAAACTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACAA
*
7217 CCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
* * * * * *
7258 GAGTCCAATATCCTTTGATGTGAAGTTGAAATTGGCTCTAAAATTAGGAAGTTGTTTTGTTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTG-TTTGTTGACA
* *
7323 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
65 ACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
* * * * *
7365 GAGTCTAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAATGAAACT-GAAAAGTGATTTATT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC----TGAAACTGGGAAATTG-TTTGTT
* * * *
7429 GACAACCAGCCGTCCCTTCATCGTGAAGTTGAACTTGGGTTGTCTC
61 GACAACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
7475 GAGT
1 GAGT
7479 GGCGCGATAT
Statistics
Matches: 396, Mismatches: 32, Indels: 6
0.91 0.07 0.01
Matches are distributed among these distances:
106 248 0.63
107 87 0.22
110 56 0.14
111 5 0.01
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACAA
CCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
Found at i:18930 original size:16 final size:15
Alignment explanation
Indices: 18901--18930 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
18891 AATAGAAATA
18901 AAATAAAAAATAATC
1 AAATAAAAAATAATC
18916 AAATAAAATAATAAT
1 AAATAAAA-AATAAT
18931 AAAGGGTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.23
Consensus pattern (15 bp):
AAATAAAAAATAATC
Found at i:25660 original size:24 final size:23
Alignment explanation
Indices: 25602--25663 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
25592 AAATAAATCA
25602 ATATTA-AAAATAAATATAGTCC
1 ATATTACAAAATAAATATAGTCC
* * *
25624 AT-GTCCATTAATAAATAATAGTCC
1 ATATTACA-AAATAAAT-ATAGTCC
25648 ATATTACAAAATAAAT
1 ATATTACAAAATAAAT
25664 GTCCATTTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
21 1 0.03
22 3 0.10
23 7 0.23
24 16 0.53
25 3 0.10
ACGTcount: A:0.52, C:0.11, G:0.05, T:0.32
Consensus pattern (23 bp):
ATATTACAAAATAAATATAGTCC
Found at i:25688 original size:39 final size:36
Alignment explanation
Indices: 25624--25695 Score: 90
Period size: 39 Copynumber: 1.9 Consensus size: 36
25614 AATATAGTCC
* *
25624 ATGTCCATTAATAAATAATAGTCCATATTACAAAATAA
1 ATGTCCATTAATAAATAAAAATCC--ATTACAAAATAA
*
25662 ATGTCCATTTTATAAATAAAAATCCATTACAAAA
1 ATGTCCA-TTAATAAATAAAAATCCATTACAAAA
25696 CTAAGCTCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
37 9 0.30
38 7 0.23
39 14 0.47
ACGTcount: A:0.50, C:0.14, G:0.04, T:0.32
Consensus pattern (36 bp):
ATGTCCATTAATAAATAAAAATCCATTACAAAATAA
Found at i:26151 original size:17 final size:17
Alignment explanation
Indices: 26131--26196 Score: 66
Period size: 16 Copynumber: 4.1 Consensus size: 17
26121 TTACTAAATT
*
26131 ATTTTTATTATATATTT
1 ATTTTTATTATATATTA
* *
26148 ATTTTT-TAATAAATTA
1 ATTTTTATTATATATTA
* *
26164 AATTTTACTATA-ATTA
1 ATTTTTATTATATATTA
26180 ATTTTTA-TATATATTA
1 ATTTTTATTATATATTA
26196 A
1 A
26197 AAAAATTAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
15 4 0.10
16 27 0.68
17 9 0.22
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTTATTATATATTA
Found at i:26155 original size:32 final size:32
Alignment explanation
Indices: 26119--26185 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
26109 TAAATATATA
* * * *
26119 TTTTACTAAATT-ATTTTTATTATATATTTATT
1 TTTTAATAAATTAAATTTTACTATA-ATTAATT
26151 TTTTAATAAATTAAATTTTACTATAATTAATT
1 TTTTAATAAATTAAATTTTACTATAATTAATT
26183 TTT
1 TTT
26186 ATATATATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 20 0.67
33 10 0.33
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (32 bp):
TTTTAATAAATTAAATTTTACTATAATTAATT
Found at i:26190 original size:15 final size:15
Alignment explanation
Indices: 26138--26196 Score: 57
Period size: 15 Copynumber: 3.8 Consensus size: 15
26128 ATTATTTTTA
* *
26138 TTATATATTTATTTT
1 TTATATAATTAATTT
*
26153 TTA-ATAAATTAAATT
1 TTATAT-AATTAATTT
26168 TTACTATAATTAATTT
1 TTA-TATAATTAATTT
26184 TTATATATATTAA
1 TTATATA-ATTAA
26197 AAAAATTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
14 2 0.06
15 16 0.44
16 16 0.44
17 2 0.06
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (15 bp):
TTATATAATTAATTT
Found at i:27603 original size:17 final size:17
Alignment explanation
Indices: 27583--27619 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
27573 TTTTAATTTT
* *
27583 TTATTAAATGTGTTTAA
1 TTATTAAATATGATTAA
27600 TTATTAAATATGATTAA
1 TTATTAAATATGATTAA
27617 TTA
1 TTA
27620 AAAATATTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (17 bp):
TTATTAAATATGATTAA
Found at i:34470 original size:32 final size:31
Alignment explanation
Indices: 34430--34508 Score: 95
Period size: 32 Copynumber: 2.5 Consensus size: 31
34420 TTATCACTCC
34430 TGTACATTATATGAATAAAACACTGACTCTGT
1 TGTACATTATATGAATAAAACACTGACT-TGT
* * * **
34462 TGTGCATTATCTAAATGCAACACTGACTTGT
1 TGTACATTATATGAATAAAACACTGACTTGT
*
34493 TGTACATTATTTGAAT
1 TGTACATTATATGAAT
34509 GTAACATTGA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
31 16 0.41
32 23 0.59
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (31 bp):
TGTACATTATATGAATAAAACACTGACTTGT
Found at i:34933 original size:13 final size:13
Alignment explanation
Indices: 34917--34955 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
34907 AGTACCCTTG
34917 AACAGTGAACAGT
1 AACAGTGAACAGT
*
34930 AACAGTGAATAGT
1 AACAGTGAACAGT
* *
34943 AATAGTGCACAGT
1 AACAGTGAACAGT
34956 GATGATGAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.44, C:0.13, G:0.23, T:0.21
Consensus pattern (13 bp):
AACAGTGAACAGT
Found at i:34938 original size:20 final size:20
Alignment explanation
Indices: 34900--34938 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
34890 TTTTTTAAAT
* **
34900 AGTGAACAGTACCCTTGAAC
1 AGTGAACAGTAACAGTGAAC
34920 AGTGAACAGTAACAGTGAA
1 AGTGAACAGTAACAGTGAA
34939 TAGTAATAGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.18
Consensus pattern (20 bp):
AGTGAACAGTAACAGTGAAC
Found at i:35063 original size:12 final size:12
Alignment explanation
Indices: 35046--35079 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
35036 TTTACTATTC
35046 ACTGCTACAGTA
1 ACTGCTACAGTA
35058 ACTGCTACAGTA
1 ACTGCTACAGTA
35070 A--GCTACAGTA
1 ACTGCTACAGTA
35080 CTTCCGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 9 0.41
12 13 0.59
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.24
Consensus pattern (12 bp):
ACTGCTACAGTA
Found at i:42929 original size:23 final size:22
Alignment explanation
Indices: 42873--42931 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 22
42863 GTCATAACCA
42873 TATTTTGAAAAATAATTAAATAT
1 TATTTT-AAAAATAATTAAATAT
* *
42896 TATTTAAAAAAATAATTATGACT-T
1 TATTT-TAAAAATAATTA--AATAT
42920 TATTTTAAAAAT
1 TATTTTAAAAAT
42932 TTTGTCGGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
23 22 0.73
24 6 0.20
25 2 0.07
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (22 bp):
TATTTTAAAAATAATTAAATAT
Found at i:45287 original size:3 final size:3
Alignment explanation
Indices: 45279--45304 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
45269 AATTAAATTT
45279 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
45305 TATTTTTAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:45852 original size:131 final size:131
Alignment explanation
Indices: 45492--45831 Score: 441
Period size: 131 Copynumber: 2.6 Consensus size: 131
45482 GTTATGGTAG
* ** *
45492 TCTAAGGGTGACACAACTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACACGGTTCCTACTA
1 TCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGTGGATGACACGGTTCCTAC--
* *
45557 GAGATGAGGATGACAGGCCATTTTTAGGGAGGGTGATAACACGGTTCCTACGCGATGAGGACGGC
64 GAGATGAGGATGACAGGCCATCTTTAGGGA---TGATAACACGATTCCTACGCGATGAGGACGGC
45622 TGGTTA
126 TGGTTA
* * * * *
45628 TCTAGAGGTGACACGGCTCCTACATGATGAGGAAGTCTAGTCGGTGGATGACACGGTTCTTAC-A
1 TCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGTGGATGACACGGTTCCTACGA
* * *
45692 TGATGAGGATGACAGGCCATCTTTAGGGATGGTAACACGATTCCTATGTGATGAGGACGGCTGGT
66 -GATGAGGATGACAGGCCATCTTTAGGGATGATAACACGATTCCTACGCGATGAGGACGGCTGGT
45757 TA
130 TA
* * *
45759 TCTAGGGGTGACACGGCTTCTATGTGATGAGGAGGTCTGGTCGG-GAGATGATACGGTTCCTACG
1 TCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGTG-GATGACACGGTTCCTACG
*
45823 CGATGAGGA
65 AGATGAGGA
45832 CGGATGTCCA
Statistics
Matches: 178, Mismatches: 23, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
130 1 0.01
131 95 0.53
133 1 0.01
134 27 0.15
136 54 0.30
ACGTcount: A:0.24, C:0.18, G:0.34, T:0.25
Consensus pattern (131 bp):
TCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGTGGATGACACGGTTCCTACGA
GATGAGGATGACAGGCCATCTTTAGGGATGATAACACGATTCCTACGCGATGAGGACGGCTGGTT
A
Found at i:45968 original size:67 final size:68
Alignment explanation
Indices: 45856--46179 Score: 388
Period size: 67 Copynumber: 4.8 Consensus size: 68
45846 TAGGGATTTA
* * * * *
45856 TTTCAAGAGAAATTGTCTCAAGGGAGAAAAAACTTTGTTTCAAGGGAAATAGACTTAAAGA-TTT
1 TTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGATTTT
45920 TTG
66 TTG
* * * * *
45923 TTTCAAGGGAAACTGTGTCAAGAGAGACAAAACTTTGTTTTAAGGGAAACAAACTCAAAGA-CTT
1 TTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGATTTT
45987 TTG
66 TTG
* * *
45990 TTTCAAAAGAAATTGTCTCAAGAGTGACACAAA--TTGTTTCAAGGCAAACAAACTCAAAGATCT
1 TTTCAAGAGAAATTGTCTCAAGAGAGACA-AAACTTTGTTTCAAGGGAAACAAACTCAAAGAT-T
46053 TTTTACG
64 TTTT--G
* *
46060 TTTCAAGATAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAGACTCAAAGATTTT
1 TTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGA-TTT
46125 TTTG
65 TTTG
* * * * *
46129 TTTCAAGAGAAACTGTCCCAAGGGAGACACAAC-TTGTTTCAAGAGAAACAA
1 TTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAA
46180 TCTCCAAGTT
Statistics
Matches: 219, Mismatches: 30, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
66 25 0.11
67 81 0.37
68 23 0.11
69 32 0.15
70 27 0.12
71 30 0.14
72 1 0.00
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (68 bp):
TTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGATTTT
TTG
Found at i:46099 original size:137 final size:133
Alignment explanation
Indices: 45856--46179 Score: 391
Period size: 137 Copynumber: 2.4 Consensus size: 133
45846 TAGGGATTTA
* * * *
45856 TTTCAAGAGAAATTGTCTCAAGGGAGA-AAAAACTTTGTTTCAAGGGAAATAGACTTAAAGATTT
1 TTTCAAGAGAAATTGTCTCAAGGGAGACACAAA--TTGTTTCAA-GGAAACAAACTCAAAGATTT
* * *
45920 TTGTTTCAAGGGAAACTGTGTCAAGAGAGACAAAACTTTGTTTTAAGGGAAACAAACTCAAAGA-
63 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGAT
45984 CTTTTG
128 CTTTTG
* * *
45990 TTTCAAAAGAAATTGTCTCAAGAGTGACACAAATTGTTTCAAGGCAAACAAACTCAAAGATCTTT
1 TTTCAAGAGAAATTGTCTCAAGGGAGACACAAATTGTTTCAAGG-AAACAAACTCAAAGA--TTT
* * *
46055 TTACGTTTCAAGATAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAGACTCAAAG
63 TT--GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAG
*
46120 ATTTTTTTG
126 A-TCTTTTG
* * *
46129 TTTCAAGAGAAACTGTCCCAAGGGAGACACAACTTGTTTCAAGAGAAACAA
1 TTTCAAGAGAAATTGTCTCAAGGGAGACACAAATTGTTTCAAG-GAAACAA
46180 TCTCCAAGTT
Statistics
Matches: 161, Mismatches: 20, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
132 2 0.01
133 21 0.13
134 24 0.15
135 9 0.06
137 56 0.35
139 48 0.30
140 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (133 bp):
TTTCAAGAGAAATTGTCTCAAGGGAGACACAAATTGTTTCAAGGAAACAAACTCAAAGATTTTTG
TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGATCTT
TTG
Found at i:55882 original size:206 final size:206
Alignment explanation
Indices: 55508--55918 Score: 743
Period size: 207 Copynumber: 2.0 Consensus size: 206
55498 CTCAGCCTCT
55508 TCTACAACCTTTTGCAACGAAGTCTTGATTTGACCCCTTACAAAGCCTCGCCACAACCAGGAGTC
1 TCTACAACCTTTTGCAACGAAGTCTTGATTTGACCCCTTACAAAGCCTCGCCACAACCAGGAGTC
*
55573 ACCATCATGTTCTTGACTCCATTACCCCTCTGCTTGCCTACACCAGATGATGGCATCTCCATCGC
66 ACCATCATGTTCTTGACTCCATTACCCCTCTGCTTACCTACACCAGATGATGGCATCTCCATCGC
55638 AACCCCAAAAATGGGTGAAAGAATCATTTGTTAATTCATTAAAAGCAGACCTTTCTTGAATATGA
131 AACCCCAAAAATGGGTGAAAGAATCATTTGTTAATTCATTAAAAGCAGACCTTTCTTGAATATGA
55703 TTCCCATTTCC
196 TTCCCATTTCC
*
55714 TCTACAATCTTTTGCAACGAAGTCTTGATTTGACCCCTTAACAAAGCCTCGCCACAACCAGGAGT
1 TCTACAACCTTTTGCAACGAAGTCTTGATTTGACCCCTT-ACAAAGCCTCGCCACAACCAGGAGT
*
55779 CACCATCATGTTCTTGACTCCATTACCCCTCTGCTTACCTACACCAGATGATGGCGTCTCCATCG
65 CACCATCATGTTCTTGACTCCATTACCCCTCTGCTTACCTACACCAGATGATGGCATCTCCATCG
* * *
55844 CAACCCCGAAAATGGGTG-AAGAATCATTTGTTAATTCATTAAAAGCAGACTTTTCTTGAATCTG
130 CAACCCCAAAAATGGGTGAAAGAATCATTTGTTAATTCATTAAAAGCAGACCTTTCTTGAATATG
*
55908 TTTCCCATTTC
195 ATTCCCATTTC
55919 TTGTTCTTGT
Statistics
Matches: 197, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
206 92 0.47
207 105 0.53
ACGTcount: A:0.27, C:0.29, G:0.14, T:0.29
Consensus pattern (206 bp):
TCTACAACCTTTTGCAACGAAGTCTTGATTTGACCCCTTACAAAGCCTCGCCACAACCAGGAGTC
ACCATCATGTTCTTGACTCCATTACCCCTCTGCTTACCTACACCAGATGATGGCATCTCCATCGC
AACCCCAAAAATGGGTGAAAGAATCATTTGTTAATTCATTAAAAGCAGACCTTTCTTGAATATGA
TTCCCATTTCC
Found at i:59258 original size:24 final size:25
Alignment explanation
Indices: 59214--59288 Score: 68
Period size: 25 Copynumber: 3.0 Consensus size: 25
59204 TTATGTCAAT
**
59214 ATTATTATTAAAAT-ATTATATCTATA
1 ATTATTA-TAAAATAAAAATAT-TATA
59240 ATT-TTAT-AAATAAAAATATTA-A
1 ATTATTATAAAATAAAAATATTATA
*
59262 TATTATTATAAAATAAAATTATTATA
1 -ATTATTATAAAATAAAAATATTATA
59288 A
1 A
59289 ATTACATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
22 1 0.02
23 9 0.22
24 10 0.24
25 17 0.41
26 4 0.10
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (25 bp):
ATTATTATAAAATAAAAATATTATA
Found at i:59328 original size:42 final size:41
Alignment explanation
Indices: 59281--59411 Score: 133
Period size: 42 Copynumber: 3.2 Consensus size: 41
59271 AAAATAAAAT
59281 TATTATAAATTACATTAATTATTTATTAAAATAAGAATAATA
1 TATTATAAATTA-ATTAATTATTTATTAAAATAAGAATAATA
* * * * *
59323 AATTATTAATTATATTAATTAGTTATTAAATTAATAAT-AT-
1 TATTATAAATTA-ATTAATTATTTATTAAAATAAGAATAATA
* * *
59363 TATTAAAATATTAA-AAATTATTATATTAAAATAAGAATATTA
1 TATTATAA-ATTAATTAATTATT-TATTAAAATAAGAATAATA
59405 TATTATA
1 TATTATA
59412 TTTTAAGAAA
Statistics
Matches: 70, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
39 6 0.09
40 19 0.27
41 7 0.10
42 38 0.54
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (41 bp):
TATTATAAATTAATTAATTATTTATTAAAATAAGAATAATA
Found at i:59374 original size:11 final size:12
Alignment explanation
Indices: 59161--59375 Score: 67
Period size: 11 Copynumber: 17.9 Consensus size: 12
59151 AACAAAATAA
* *
59161 TAATATTATTTT
1 TAATAATATTAT
59173 TAA-AATATTA-
1 TAATAATATTAT
*
59183 GAATAAT-TTATT
1 TAATAATATTA-T
*
59195 TAATATTATTTAT
1 TAATAATA-TTAT
*
59208 GTCAATATTATTAT
1 -T-AATAATATTAT
59222 TAA-AATATTAT
1 TAATAATATTAT
* *
59233 ATCTATAATTTTAT
1 -T-AATAATATTAT
* * *
59247 AAATAAAAATAT
1 TAATAATATTAT
*
59259 TAATATTATTAT
1 TAATAATATTAT
* *
59271 AAAATAAAATTAT
1 -TAATAATATTAT
59284 T-ATAA-ATTACAT
1 TAATAATATT--AT
*
59296 TAATTAT-TTAT
1 TAATAATATTAT
** *
59307 TAA-AATAAGAA
1 TAATAATATTAT
59318 TAATAA-ATTAT
1 TAATAATATTAT
*
59329 TAATTATATTAAT
1 TAATAATATT-AT
*
59342 TAGT--TATTAAAT
1 TAATAATATT--AT
59354 TAATAATATTAT
1 TAATAATATTAT
59366 TAA-AATATTA
1 TAATAATATTA
59376 AAAATTATTA
Statistics
Matches: 149, Mismatches: 32, Indels: 45
0.66 0.14 0.20
Matches are distributed among these distances:
10 10 0.07
11 46 0.31
12 45 0.30
13 22 0.15
14 19 0.13
15 7 0.05
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.47
Consensus pattern (12 bp):
TAATAATATTAT
Found at i:59550 original size:18 final size:17
Alignment explanation
Indices: 59527--59569 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
59517 AAAATTATAA
*
59527 AATTATATATAATAATAT
1 AATTATATACAATAA-AT
59545 AATTATA-ACAATAAAT
1 AATTATATACAATAAAT
59561 ATATTATAT
1 A-ATTATAT
59570 TATATTAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 3 0.14
17 12 0.55
18 7 0.32
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTATATACAATAAAT
Found at i:59635 original size:28 final size:27
Alignment explanation
Indices: 59604--59666 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
59594 AATAATTAAT
* *
59604 AAATAATATTTTTATA-AAAATGATACTA
1 AAATAATATATTAATATAAAAT-ATA-TA
*
59632 AAATAATATATTAATATTAAATATATA
1 AAATAATATATTAATATAAAATATATA
59659 AAATAATA
1 AAATAATA
59667 ATGTTTTGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 10 0.32
28 17 0.55
29 4 0.13
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (27 bp):
AAATAATATATTAATATAAAATATATA
Found at i:63004 original size:21 final size:21
Alignment explanation
Indices: 62976--63027 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
62966 GGATGAACTA
* *
62976 TATCGATATTGATGTAATTAG
1 TATCGATACTGATGCAATTAG
*
62997 TATTGATACTGATGCAATTAG
1 TATCGATACTGATGCAATTAG
63018 TATCGATACT
1 TATCGATACT
63028 AAGAGAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (21 bp):
TATCGATACTGATGCAATTAG
Found at i:63548 original size:54 final size:54
Alignment explanation
Indices: 63460--64004 Score: 763
Period size: 54 Copynumber: 10.1 Consensus size: 54
63450 CTATGTATAA
* * * * *
63460 TATCGACACTAAGTGTGCAACCCACGGAACTCATAATATGTTTATGAATGATCG
1 TATCGGCACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCG
* *
63514 TATCGGCACTAAGTGTGCAACCCACAAAATTCATAATATGTTTATGAACGATCG
1 TATCGGCACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCG
*
63568 TATCGGCACTAAGTGTGCAACCCACGGAATTCATAATATGTTTATGAACGACCG
1 TATCGGCACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCG
* * * *
63622 TATCAGC-CTTAAGTGTGCAACCTACGGAATTCATAATATGTTTATGAACGACTG
1 TATCGGCAC-TAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCG
* * *
63676 TATCGACACTAAGTGTGCAACCCGC-GAAATTCATAATATGTTTATGAACGGCCG
1 TATCGGCACTAAGTGTGCAACCCACAG-AATTCATAATATGTTTATGAACGACCG
* * * *
63730 TATTC-ACACTAAGTGTGCAACCCACAAAATTCATAATATGTTTATGAATGACTG
1 TA-TCGGCACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCG
* * *
63784 TATCGGTACTAAGTGTGCAACCCACAAAAGTCATAATATGTTTATGAACGACCG
1 TATCGGCACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCG
* * *
63838 TATCGGCACTAAGTGTTCAACCCACGGAATTCATAATATGTTTATGAACGACCT
1 TATCGGCACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCG
* * * **
63892 TATTGGCACTAAGTGTGTAACCCACAGAATTCATAATAGGTTTATGAACGACAT
1 TATCGGCACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCG
*
63946 TATCGGCACTAAGTGTGAAACCCACAGAATTCATAATATGTTTATGAACGACCG
1 TATCGGCACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCG
64000 TATCG
1 TATCG
64005 ACACGTGTGC
Statistics
Matches: 441, Mismatches: 44, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
53 4 0.01
54 434 0.98
55 3 0.01
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (54 bp):
TATCGGCACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCG
Done.