Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003209.1 Hibiscus syriacus cultivar Beakdansim tig00006755_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: 53754
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Found at i:932 original size:18 final size:19
Alignment explanation
Indices: 913--968 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
903 AAGTGTTTAA
913 ATGATTTTTGAATATTAAAT
1 ATGATTTTT-AATATTAAAT
*
933 ATGATTTTTAATAATTATAAA
1 ATGATTTTTAAT-ATTA-AAT
* *
954 ATAATGTTTAATATT
1 ATGATTTTTAATATT
969 TGACTAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 3 0.10
20 16 0.52
21 12 0.39
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (19 bp):
ATGATTTTTAATATTAAAT
Found at i:2092 original size:20 final size:20
Alignment explanation
Indices: 2069--2118 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
2059 AATAATTTAA
2069 ATATTAA-AATTAAAATTGAT
1 ATATTAATAATT-AAATTGAT
* *
2089 ATATTAATTATTAAATTTAT
1 ATATTAATAATTAAATTGAT
2109 ATATT-ATAAT
1 ATATTAATAAT
2119 ATTAATAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 4 0.15
20 19 0.73
21 3 0.12
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
ATATTAATAATTAAATTGAT
Found at i:4227 original size:10 final size:12
Alignment explanation
Indices: 4198--4222 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4188 GATTATACAT
4198 ATACACTTTGAA
1 ATACACTTTGAA
4210 ATACACTTTGAA
1 ATACACTTTGAA
4222 A
1 A
4223 CACTTATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (12 bp):
ATACACTTTGAA
Found at i:4422 original size:12 final size:12
Alignment explanation
Indices: 4365--4427 Score: 53
Period size: 12 Copynumber: 5.3 Consensus size: 12
4355 ACCAATATGC
4365 ATCAC-TTTCA-
1 ATCACATTTCAT
4375 A-CACATATTCA-
1 ATCACAT-TTCAT
*
4386 ATACACATGTCAT
1 AT-CACATTTCAT
*
4399 ATTCAAATTTCAT
1 A-TCACATTTCAT
4412 ATCACATTTCAT
1 ATCACATTTCAT
4424 ATCA
1 ATCA
4428 ATTATGTGCA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
9 3 0.07
10 2 0.05
11 5 0.12
12 17 0.40
13 15 0.35
14 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.02, T:0.37
Consensus pattern (12 bp):
ATCACATTTCAT
Found at i:5973 original size:17 final size:17
Alignment explanation
Indices: 5948--6021 Score: 87
Period size: 17 Copynumber: 4.3 Consensus size: 17
5938 TTGATACTGT
5948 AATATCTGATAACT-TA
1 AATATCTGATAACTATA
*
5964 AATCATCTGATAATTATA
1 AAT-ATCTGATAACTATA
**
5982 AATATCTGATAACGGTGA
1 AATATCTGATAACTAT-A
*
6000 AATGTCTGATAACTATA
1 AATATCTGATAACTATA
6017 AATAT
1 AATAT
6022 TTAGAATTCA
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
16 3 0.06
17 25 0.53
18 19 0.40
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.35
Consensus pattern (17 bp):
AATATCTGATAACTATA
Found at i:6017 original size:35 final size:34
Alignment explanation
Indices: 5948--6021 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 34
5938 TTGATACTGT
* *
5948 AATATCTGATAACTTAAATCATCTGATAATTATA
1 AATATCTGATAACTGAAATCATCTGATAACTATA
*
5982 AATATCTGATAACGGTGAAAT-GTCTGATAACTATA
1 AATATCTGATAAC--TGAAATCATCTGATAACTATA
6017 AATAT
1 AATAT
6022 TTAGAATTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
34 13 0.37
35 17 0.49
36 5 0.14
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.35
Consensus pattern (34 bp):
AATATCTGATAACTGAAATCATCTGATAACTATA
Found at i:9381 original size:22 final size:22
Alignment explanation
Indices: 9355--9407 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
9345 TTTCCGAATA
9355 TCTTTCATCTTTGTTGGGAAAG
1 TCTTTCATCTTTGTTGGGAAAG
9377 TCTTTCATCTTTGTTGGGAAAG
1 TCTTTCATCTTTGTTGGGAAAG
9399 TCTTTCATC
1 TCTTTCATC
9408 AAATCTTACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.17, C:0.17, G:0.19, T:0.47
Consensus pattern (22 bp):
TCTTTCATCTTTGTTGGGAAAG
Found at i:13945 original size:20 final size:20
Alignment explanation
Indices: 13907--13945 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
13897 CATTGCAGGA
13907 ATTTATGGCCTCAACAAAAG
1 ATTTATGGCCTCAACAAAAG
*
13927 ATTTCATGGCTTCAA-AAAA
1 ATTT-ATGGCCTCAACAAAA
13946 AACCTTGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.28
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:20674 original size:20 final size:22
Alignment explanation
Indices: 20627--20680 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
20617 CCGGAAGGGT
*
20627 GTATCGGTACCATGGTATAGTA
1 GTATCGATACCATGGTATAGTA
*
20649 GTATCGATACCATGGTA-AG-G
1 GTATCGATACCATGGTATAGTA
20669 GTATCGATACCA
1 GTATCGATACCA
20681 AGAACCATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 12 0.40
21 2 0.07
22 16 0.53
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.28
Consensus pattern (22 bp):
GTATCGATACCATGGTATAGTA
Found at i:20731 original size:95 final size:95
Alignment explanation
Indices: 20551--20773 Score: 252
Period size: 95 Copynumber: 2.3 Consensus size: 95
20541 TACCGATGAG
* * * *
20551 GTAGTATCGATGCCATGGTAAGGGTATCGATGCCAAGAAACATCGAATCTAAAATTACTATCAAA
1 GTAGTATCGATACCATGGTAAGGGTATCGATACCAAGAAACATCAAATCTAAAAGTACTATCAAA
* * *
20616 ACCGGAAGGGTGTATCGGTACCATGGTATA
66 ACAGAAAGGGTGTATCGGTACCATAGTATA
* ** * *
20646 GTAGTATCGATACCATGGTAAGGGTATCGATACCAAGAACCATCAAATCTAAAAGTGGTATCGAT
1 GTAGTATCGATACCATGGTAAGGGTATCGATACCAAGAAACATCAAATCTAAAAGTACTATCAAA
*
20711 ACAGAAAGAGG-GTATTGGTACCATAGTATA
66 ACAGAAAG-GGTGTATCGGTACCATAGTATA
* * * * *
20741 GAAGTATTGGTACCAGGGT-AGTAGTATCGATAC
1 GTAGTATCGATACCATGGTAAG-GGTATCGATAC
20774 AATTGAGCTT
Statistics
Matches: 108, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
94 2 0.02
95 104 0.96
96 2 0.02
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25
Consensus pattern (95 bp):
GTAGTATCGATACCATGGTAAGGGTATCGATACCAAGAAACATCAAATCTAAAAGTACTATCAAA
ACAGAAAGGGTGTATCGGTACCATAGTATA
Found at i:21201 original size:20 final size:20
Alignment explanation
Indices: 21176--21241 Score: 96
Period size: 20 Copynumber: 3.3 Consensus size: 20
21166 ATTAAAATTG
*
21176 ATGAAAGGATGCATTAAGGT
1 ATGAAAGGATGCATTAAGGC
* *
21196 ATGAAAGGATGCGTTACGGC
1 ATGAAAGGATGCATTAAGGC
*
21216 AAGAAAGGATGCATTAAGGC
1 ATGAAAGGATGCATTAAGGC
21236 ATGAAA
1 ATGAAA
21242 AGATACCATA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.41, C:0.09, G:0.30, T:0.20
Consensus pattern (20 bp):
ATGAAAGGATGCATTAAGGC
Found at i:21337 original size:20 final size:20
Alignment explanation
Indices: 21312--21385 Score: 85
Period size: 20 Copynumber: 3.4 Consensus size: 20
21302 TAATTAAAAT
21312 GCATGAAATGATGCATTAAG
1 GCATGAAATGATGCATTAAG
*
21332 GCATGAAATGATGTCATAATTAAAAT
1 GCATGAAATGATG-C---ATT--AAG
21358 GCATGAAATGATGCATTAAG
1 GCATGAAATGATGCATTAAG
21378 GCATGAAA
1 GCATGAAA
21386 GGATACCATA
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
20 23 0.50
21 1 0.02
22 3 0.07
24 3 0.07
25 1 0.02
26 15 0.33
ACGTcount: A:0.43, C:0.09, G:0.22, T:0.26
Consensus pattern (20 bp):
GCATGAAATGATGCATTAAG
Found at i:21350 original size:46 final size:46
Alignment explanation
Indices: 21218--21412 Score: 239
Period size: 46 Copynumber: 4.1 Consensus size: 46
21208 GTTACGGCAA
* *
21218 GAAAGGATGCATTAAGGCATGAAAAGATACCATAATTAAAATGCAT
1 GAAATGATGCATTAAGGCATGAAAGGATACCATAATTAAAATGCAT
* * *
21264 GAAAGGATGCCATCATTAAAATGCATGAAAGGATTCCATAATTAAAATGCAT
1 GAAATGATG----CATT--AAGGCATGAAAGGATACCATAATTAAAATGCAT
* **
21316 GAAATGATGCATTAAGGCATGAAATGATGTCATAATTAAAATGCAT
1 GAAATGATGCATTAAGGCATGAAAGGATACCATAATTAAAATGCAT
* *
21362 GAAATGATGCATTAAGGCATGAAAGGATACCATAATTTAAATGTAT
1 GAAATGATGCATTAAGGCATGAAAGGATACCATAATTAAAATGCAT
21408 -AAATG
1 GAAATG
21413 GATGTGTTAA
Statistics
Matches: 130, Mismatches: 13, Indels: 13
0.83 0.08 0.08
Matches are distributed among these distances:
45 5 0.04
46 79 0.61
48 4 0.03
50 4 0.03
52 38 0.29
ACGTcount: A:0.45, C:0.10, G:0.19, T:0.26
Consensus pattern (46 bp):
GAAATGATGCATTAAGGCATGAAAGGATACCATAATTAAAATGCAT
Found at i:21362 original size:26 final size:26
Alignment explanation
Indices: 21234--21371 Score: 162
Period size: 26 Copynumber: 5.5 Consensus size: 26
21224 ATGCATTAAG
* *
21234 GCATGAAAAGATACCATAATTAAAAT
1 GCATGAAATGATGCCATAATTAAAAT
* *
21260 GCATGAAAGGATGCCATCATTAAAAT
1 GCATGAAATGATGCCATAATTAAAAT
* *
21286 GCATGAAAGGATTCCATAATTAAAAT
1 GCATGAAATGATGCCATAATTAAAAT
*
21312 GCATGAAATGATG-C---ATT--AAG
1 GCATGAAATGATGCCATAATTAAAAT
*
21332 GCATGAAATGATGTCATAATTAAAAT
1 GCATGAAATGATGCCATAATTAAAAT
21358 GCATGAAATGATGC
1 GCATGAAATGATGC
21372 ATTAAGGCAT
Statistics
Matches: 96, Mismatches: 10, Indels: 12
0.81 0.08 0.10
Matches are distributed among these distances:
20 15 0.16
21 1 0.01
22 3 0.03
24 3 0.03
25 1 0.01
26 73 0.76
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.25
Consensus pattern (26 bp):
GCATGAAATGATGCCATAATTAAAAT
Found at i:29675 original size:40 final size:40
Alignment explanation
Indices: 29609--29839 Score: 140
Period size: 40 Copynumber: 5.7 Consensus size: 40
29599 CAAATGCCGG
* *
29609 TAAATACTCGTACTTTAGTGGTGTTTTTATATAAACACAGC
1 TAAATACT-ATACTTTAGTGGCGTTTTTATATAAACACAGC
* * * *
29650 TAAATATTATAGTTTAGTGGCGTTTTCATATAAACACCGC
1 TAAATACTATACTTTAGTGGCGTTTTTATATAAACACAGC
* * * * *
29690 TAATTACTATACTTTAGCGGCGTTTTTGTACAAACGCCA-C
1 TAAATACTATACTTTAGTGGCGTTTTTATATAAAC-ACAGC
* * * * * * * * *
29730 TAAAAACTCGTACTCTAGCGGCGTTTTAAGCACAAACGCCGC
1 TAAATACT-ATACTTTAGTGGCGTTTTTA-TATAAACACAGC
** ** * * *
29772 TAAAGGCCCGTACATTAGTGGCGTTTTCATATAAACACCGC
1 TAAA-TACTATACTTTAGTGGCGTTTTTATATAAACACAGC
* **
29813 TAATTACTATACTTTAGCAGCGTTTTT
1 TAAATACTATACTTTAGTGGCGTTTTT
29840 GTGCAAACGC
Statistics
Matches: 142, Mismatches: 43, Indels: 11
0.72 0.22 0.06
Matches are distributed among these distances:
40 77 0.54
41 37 0.26
42 27 0.19
43 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (40 bp):
TAAATACTATACTTTAGTGGCGTTTTTATATAAACACAGC
Found at i:29775 original size:42 final size:42
Alignment explanation
Indices: 29580--29984 Score: 279
Period size: 42 Copynumber: 9.8 Consensus size: 42
29570 AAAATGGGCT
* ** * * *
29580 TTTAGCGACGTTTTTTGAACAAATGCCGGTAAATACTCGTAC
1 TTTAGCGGCGTTTTAAGTACAAACGCCGCTAAATACTCGTAC
* * * * * * ** *
29622 TTTAGTGGTGTTTTTA-TATAAACACAGCTAAATA-TTATAG
1 TTTAGCGGCGTTTTAAGTACAAACGCCGCTAAATACTCGTAC
* * * * * *
29662 TTTAGTGGCGTTTTCA-TATAAACACCGCTAATTACT-ATAC
1 TTTAGCGGCGTTTTAAGTACAAACGCCGCTAAATACTCGTAC
* * *
29702 TTTAGCGGCGTTTT-TGTACAAACGCCACTAAAAACTCGTAC
1 TTTAGCGGCGTTTTAAGTACAAACGCCGCTAAATACTCGTAC
* * ** *
29743 TCTAGCGGCGTTTTAAGCACAAACGCCGCTAAAGGCCCGTAC
1 TTTAGCGGCGTTTTAAGTACAAACGCCGCTAAATACTCGTAC
* * * * * * *
29785 ATTAGTGGCGTTTTCA-TATAAACACCGCTAATTACT-ATAC
1 TTTAGCGGCGTTTTAAGTACAAACGCCGCTAAATACTCGTAC
* * * * *
29825 TTTAGCAGCGTTTT-TGTGCAAACGCCGCTAAAAACTCATAC
1 TTTAGCGGCGTTTTAAGTACAAACGCCGCTAAATACTCGTAC
* *
29866 TTTAGCGGCATTTTAAGTACAAACGCCGCTAAAGTACTTGTA-
1 TTTAGCGGCGTTTTAAGTACAAACGCCGCTAAA-TACTCGTAC
* * * *
29908 TTTAGCGGCATTTTAAGCACAAACGCCGCTAAATGCTTGTAC
1 TTTAGCGGCGTTTTAAGTACAAACGCCGCTAAATACTCGTAC
* * **
29950 TTTAGCAGCGTTTTAAGCACATGCGCCGCTAAATA
1 TTTAGCGGCGTTTTAAGTACAAACGCCGCTAAATA
29985 AATATACTTT
Statistics
Matches: 286, Mismatches: 68, Indels: 18
0.77 0.18 0.05
Matches are distributed among these distances:
40 93 0.33
41 65 0.23
42 123 0.43
43 5 0.02
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (42 bp):
TTTAGCGGCGTTTTAAGTACAAACGCCGCTAAATACTCGTAC
Found at i:29810 original size:123 final size:123
Alignment explanation
Indices: 29663--29899 Score: 411
Period size: 123 Copynumber: 1.9 Consensus size: 123
29653 ATATTATAGT
*
29663 TTAGTGGCGTTTTCATATAAACACCGCTAATTACTATACTTTAGCGGCGTTTTTGTACAAACGCC
1 TTAGTGGCGTTTTCATATAAACACCGCTAATTACTATACTTTAGCAGCGTTTTTGTACAAACGCC
* *
29728 ACTAAAAACTCGTACTCTAGCGGCGTTTTAAGCACAAACGCCGCTAAAGGCCCGTACA
66 ACTAAAAACTCATACTCTAGCGGCATTTTAAGCACAAACGCCGCTAAAGGCCCGTACA
*
29786 TTAGTGGCGTTTTCATATAAACACCGCTAATTACTATACTTTAGCAGCGTTTTTGTGCAAACGCC
1 TTAGTGGCGTTTTCATATAAACACCGCTAATTACTATACTTTAGCAGCGTTTTTGTACAAACGCC
* * *
29851 GCTAAAAACTCATACTTTAGCGGCATTTTAAGTACAAACGCCGCTAAAG
66 ACTAAAAACTCATACTCTAGCGGCATTTTAAGCACAAACGCCGCTAAAG
29900 TACTTGTATT
Statistics
Matches: 107, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
123 107 1.00
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (123 bp):
TTAGTGGCGTTTTCATATAAACACCGCTAATTACTATACTTTAGCAGCGTTTTTGTACAAACGCC
ACTAAAAACTCATACTCTAGCGGCATTTTAAGCACAAACGCCGCTAAAGGCCCGTACA
Found at i:30002 original size:84 final size:84
Alignment explanation
Indices: 29843--30004 Score: 184
Period size: 84 Copynumber: 1.9 Consensus size: 84
29833 CGTTTTTGTG
* * ** *
29843 CAAACGCCGCTAAAAACTCATACTTTAGCGGCATTTTAAGTACAAACGCCGCTAAAGTACTTGTA
1 CAAACGCCGCTAAAAACTCATACTTTAGCAGCATTTTAAGCACAAACGCCGCTAAAGTAAATATA
29908 TTTAGCGGCATTTTAAGCA
66 TTTAGCGGCATTTTAAGCA
** ** * **
29927 CAAACGCCGCTAAATGCTTGTACTTTAGCAGCGTTTTAAGCACATGCGCCGCTAAA-TAAATATA
1 CAAACGCCGCTAAAAACTCATACTTTAGCAGCATTTTAAGCACAAACGCCGCTAAAGTAAATATA
29991 CTTTA-CTGGCATTT
66 -TTTAGC-GGCATTT
30005 GTATATAAAC
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
83 6 0.09
84 58 0.91
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (84 bp):
CAAACGCCGCTAAAAACTCATACTTTAGCAGCATTTTAAGCACAAACGCCGCTAAAGTAAATATA
TTTAGCGGCATTTTAAGCA
Found at i:33082 original size:11 final size:11
Alignment explanation
Indices: 33066--33093 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
33056 AAAACATCGT
33066 TCAATACACAA
1 TCAATACACAA
33077 TCAATACACAA
1 TCAATACACAA
33088 TCAATA
1 TCAATA
33094 TCGGCGTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.54, C:0.25, G:0.00, T:0.21
Consensus pattern (11 bp):
TCAATACACAA
Found at i:33149 original size:43 final size:43
Alignment explanation
Indices: 33079--33263 Score: 190
Period size: 43 Copynumber: 4.1 Consensus size: 43
33069 ATACACAATC
* * *
33079 AATACACAATCAATATCGGCGTTTGTAAAGAAAAACGCCGCTA
1 AATACACAGTCAATAGCGGCGTTTATAAAGAAAAACGCCGCTA
* * * *
33122 AATGCATAGTCAATAGCAGCGTTTGTAAAGACAAACGCACAAACGCCGCTA
1 AATACACAGTCAATAGCGGCGTTTATAAAG----A---A-AAACGCCGCTA
*
33173 AATACACAGTCAATAGCGGCGTTTATAAAGACAAACGCCGCTA
1 AATACACAGTCAATAGCGGCGTTTATAAAGAAAAACGCCGCTA
* * * *
33216 AATACACAGTCAATAGCGGCATGTATAAAGACAGACGCCGCTA
1 AATACACAGTCAATAGCGGCGTTTATAAAGAAAAACGCCGCTA
33259 AATAC
1 AATAC
33264 CAATACCTAT
Statistics
Matches: 121, Mismatches: 13, Indels: 16
0.81 0.09 0.11
Matches are distributed among these distances:
43 81 0.67
47 2 0.02
50 1 0.01
51 37 0.31
ACGTcount: A:0.41, C:0.23, G:0.18, T:0.18
Consensus pattern (43 bp):
AATACACAGTCAATAGCGGCGTTTATAAAGAAAAACGCCGCTA
Found at i:33170 original size:51 final size:51
Alignment explanation
Indices: 33111--33210 Score: 164
Period size: 51 Copynumber: 2.0 Consensus size: 51
33101 TTGTAAAGAA
* * *
33111 AAACGCCGCTAAATGCATAGTCAATAGCAGCGTTTGTAAAGACAAACGCAC
1 AAACGCCGCTAAATACACAGTCAATAGCAGCGTTTATAAAGACAAACGCAC
*
33162 AAACGCCGCTAAATACACAGTCAATAGCGGCGTTTATAAAGACAAACGC
1 AAACGCCGCTAAATACACAGTCAATAGCAGCGTTTATAAAGACAAACGC
33211 CGCTAAATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.40, C:0.24, G:0.19, T:0.17
Consensus pattern (51 bp):
AAACGCCGCTAAATACACAGTCAATAGCAGCGTTTATAAAGACAAACGCAC
Found at i:33245 original size:94 final size:94
Alignment explanation
Indices: 33079--33253 Score: 251
Period size: 94 Copynumber: 1.9 Consensus size: 94
33069 ATACACAATC
* * * * *
33079 AATACACAATCAATATCGGCGTTTGTAAAGAAAAACGCCGCTAAATGCATAGTCAATAGCAGCGT
1 AATACACAATCAATAGCGGCGTTTATAAAGAAAAACGCCGCTAAATACACAGTCAATAGCAGCAT
* *
33144 TTGTAAAGACAAACGCACAAACGCCGCTA
66 GTATAAAGACAAACGCACAAACGCCGCTA
* * *
33173 AATACACAGTCAATAGCGGCGTTTATAAAGACAAACGCCGCTAAATACACAGTCAATAGCGGCAT
1 AATACACAATCAATAGCGGCGTTTATAAAGAAAAACGCCGCTAAATACACAGTCAATAGCAGCAT
*
33238 GTATAAAGACAGACGC
66 GTATAAAGACAAACGC
33254 CGCTAAATAC
Statistics
Matches: 70, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
94 70 1.00
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.18
Consensus pattern (94 bp):
AATACACAATCAATAGCGGCGTTTATAAAGAAAAACGCCGCTAAATACACAGTCAATAGCAGCAT
GTATAAAGACAAACGCACAAACGCCGCTA
Found at i:34986 original size:49 final size:49
Alignment explanation
Indices: 34903--35381 Score: 617
Period size: 49 Copynumber: 9.8 Consensus size: 49
34893 GAATACCATG
* * *
34903 AGTGGCACCTTTTATAACGAAAATGCACAGTTATGCATTTAATTTTCATT
1 AGTGGCACCTTTTAT-GCCAAAATGCACCGTTATGCATTTAATTTTCATT
* * * *
34953 AGTGGTACATTTTATGCCAAAGTGCACCGTTATGCATTTAACTTTCATT
1 AGTGGCACCTTTTATGCCAAAATGCACCGTTATGCATTTAATTTTCATT
* * *
35002 AGTGGCACCTTTTATGTCAAAATGCACCATTATGCATTTAACTTT-ATT
1 AGTGGCACCTTTTATGCCAAAATGCACCGTTATGCATTTAATTTTCATT
*
35050 AGTGGCACCTTTTATGCCAAAAT-AATCCGTTATGCATTTAATTTTCATT
1 AGTGGCACCTTTTATGCCAAAATGCA-CCGTTATGCATTTAATTTTCATT
* **
35099 ATTGGCACCTTTTATGCCAAAATGCACTATTATGCATTTAAATTTT-ATT
1 AGTGGCACCTTTTATGCCAAAATGCACCGTTATGCATTT-AATTTTCATT
* * *
35148 AGTGGTACCTTTTATGCCAAATTGCACCGTTATGCATTTAACTTTCATT
1 AGTGGCACCTTTTATGCCAAAATGCACCGTTATGCATTTAATTTTCATT
35197 AGTGGCACCTTTTATGCCAAAATGCACCGTTATGCATTTAACTTTT-ATT
1 AGTGGCACCTTTTATGCCAAAATGCACCGTTATGCATTTAA-TTTTCATT
** * *
35246 AGTGGCACCTTTTATGCCAAAATGTTCCGTTGTGCATTTAACTTTCATT
1 AGTGGCACCTTTTATGCCAAAATGCACCGTTATGCATTTAATTTTCATT
* * * ** *
35295 AGGGGCACCCTTTATACCAAAATAAACCGTTATGCATTTAACTTTT-ACT
1 AGTGGCACCTTTTATGCCAAAATGCACCGTTATGCATTTAA-TTTTCATT
* *
35344 AGTGGCACATTTTATGCCAAAATGCACCATTATGCATT
1 AGTGGCACCTTTTATGCCAAAATGCACCGTTATGCATT
35382 CATTTTATAG
Statistics
Matches: 372, Mismatches: 49, Indels: 17
0.85 0.11 0.04
Matches are distributed among these distances:
47 1 0.00
48 50 0.13
49 295 0.79
50 26 0.07
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (49 bp):
AGTGGCACCTTTTATGCCAAAATGCACCGTTATGCATTTAATTTTCATT
Found at i:41518 original size:49 final size:49
Alignment explanation
Indices: 40990--41518 Score: 693
Period size: 49 Copynumber: 10.8 Consensus size: 49
40980 TTAATGAATA
* * * * * *
40990 TCATGAGTGTCACCTTTTATAACGAAAATGTACCATTATGCATTTAACTT
1 TCATTAGTGGCACCTTTTAT-GCCAAAATGCACCGTTATGCATTTAACTT
* * *
41040 TCATTAGTGGCACCTTTTATGCCAAAATGCACTGTTATGCGTTTAGCTT
1 TCATTAGTGGCACCTTTTATGCCAAAATGCACCGTTATGCATTTAACTT
* * * *
41089 TCATTAATGGCACCTTTTATGCCAAAATACATCGTTATGCATTTAGCTT
1 TCATTAGTGGCACCTTTTATGCCAAAATGCACCGTTATGCATTTAACTT
* * *
41138 TTATTAGCGGCACATTTTATGCCAAAATGCACCGTTATGCATTTAACTT
1 TCATTAGTGGCACCTTTTATGCCAAAATGCACCGTTATGCATTTAACTT
* * * * *
41187 TCATTAGTGGCATCTTTTATGCCAAAATGAATCATTATGCATTTAAGTT
1 TCATTAGTGGCACCTTTTATGCCAAAATGCACCGTTATGCATTTAACTT
41236 TCATTAGTGGCACCTTTTATGCCAAAATGCACCGTTATGCATTTAACTT
1 TCATTAGTGGCACCTTTTATGCCAAAATGCACCGTTATGCATTTAACTT
* * *
41285 TCATTAATGGCACATTTTATGCCAAAATGCACCGTTATGTATTTAACTT
1 TCATTAGTGGCACCTTTTATGCCAAAATGCACCGTTATGCATTTAACTT
* *
41334 TCATTGGTGGCACCTTTTATGCCAAAATGCACCTTTATGCATTTAACTT
1 TCATTAGTGGCACCTTTTATGCCAAAATGCACCGTTATGCATTTAACTT
* * * * *
41383 TTATTAGTGG-ACCTATTAAGCTAAAATGCACCGTTATCCATTTAACTT
1 TCATTAGTGGCACCTTTTATGCCAAAATGCACCGTTATGCATTTAACTT
* * * *
41431 TCATTAGTGGTATCC-TTTATGCCAAAATACATCGTTATGTATTTAACTT
1 TCATTAGTGGCA-CCTTTTATGCCAAAATGCACCGTTATGCATTTAACTT
* *
41480 TTATTAGTGGCACCTTTTATGCCAAAATGCACCATTATG
1 TCATTAGTGGCACCTTTTATGCCAAAATGCACCGTTATG
41519 AATTCATTTT
Statistics
Matches: 414, Mismatches: 62, Indels: 7
0.86 0.13 0.01
Matches are distributed among these distances:
48 44 0.11
49 350 0.85
50 20 0.05
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (49 bp):
TCATTAGTGGCACCTTTTATGCCAAAATGCACCGTTATGCATTTAACTT
Found at i:43526 original size:3 final size:3
Alignment explanation
Indices: 43513--43561 Score: 62
Period size: 3 Copynumber: 16.3 Consensus size: 3
43503 AAAAATAAAA
* * * *
43513 AAT ATT AAT AAT AAT AGT AAT AGT AAT AGT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
43561 A
1 A
43562 TAAATTATAA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:43533 original size:12 final size:12
Alignment explanation
Indices: 43513--43561 Score: 71
Period size: 12 Copynumber: 4.1 Consensus size: 12
43503 AAAAATAAAA
*
43513 AATATTAATAAT
1 AATAGTAATAAT
*
43525 AATAGTAATAGT
1 AATAGTAATAAT
43537 AATAGTAATAAT
1 AATAGTAATAAT
*
43549 AATAATAATAAT
1 AATAGTAATAAT
43561 A
1 A
43562 TAAATTATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (12 bp):
AATAGTAATAAT
Found at i:43946 original size:134 final size:132
Alignment explanation
Indices: 43741--44171 Score: 443
Period size: 134 Copynumber: 3.2 Consensus size: 132
43731 TCGAGAAATG
* * * * **
43741 TTGACTCATTCCAGTATTCTTCAGGGAAATTGAATCGATGTAGACTTCCTCCACT-ATCACTCAG
1 TTGATTCATTCCACTATTCTTCAGGGAAATTAAATCGAAGTAGACTTGTTCCACTGAT-ACTCAG
* * * *
43805 GGAATATCAAATCTTGAAAGAGATGGATCTATTTCGCTTCTTCTTGAGGGAAAATCAGATCTGAT
65 GGAATATCAAATCTTGAAAGAGAGGGATATGTTTCGCTTATTCTTGAGGGAAAATCAGATCTGAT
*
43870 ATTT
130 A-TA
* * *
43874 TTAATTCATTCCACTATTCTTTAGGGAAGATTAAATCGAAGTAGACTTGTTCCACTGGTACTCAG
1 TTGATTCATTCCACTATTCTTCAGGGAA-ATTAAATCGAAGTAGACTTGTTCCACTGATACTCAG
* * * *
43939 GGAATATCAAATCTTGAAAAAGAGGGATATGTTTCGCTTATTCTTGAGGGAAAATAAGATTTGGG
65 GGAATATCAAATCTTGAAAGAGAGGGATATGTTTCGCTTATTCTTGAGGGAAAATCAGATCT-GA
*
44004 TACA
129 TATA
* * * * * * * * *
44008 TTGATTGATTCCATTGTTCTTCATGGAATATTAAATCGAGGAAGACTTGTTCCACTGTTATTAAG
1 TTGATTCATTCCACTATTCTTCAGGGAA-ATTAAATCGAAGTAGACTTGTTCCACTGATACTCAG
* * * * * *
44073 GGAATATCAAATCTAT-AAAGAGAGGGATTTGTTCCGCTTTTTCTTAAGGAAAAATCAGATCCGA
65 GGAATATCAAATCT-TGAAAGAGAGGGATATGTTTCGCTTATTCTTGAGGGAAAATCAGATCTG-
* *
44137 AAATG
128 ATATA
*
44142 TTGATTCATTCCACTGTTCTTTCAGGGAAA
1 TTGATTCATTCCACTATTC-TTCAGGGAAA
44172 ATTGGGTCGA
Statistics
Matches: 245, Mismatches: 47, Indels: 11
0.81 0.16 0.04
Matches are distributed among these distances:
133 25 0.10
134 207 0.84
135 13 0.05
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (132 bp):
TTGATTCATTCCACTATTCTTCAGGGAAATTAAATCGAAGTAGACTTGTTCCACTGATACTCAGG
GAATATCAAATCTTGAAAGAGAGGGATATGTTTCGCTTATTCTTGAGGGAAAATCAGATCTGATA
TA
Found at i:45477 original size:17 final size:17
Alignment explanation
Indices: 45422--45476 Score: 92
Period size: 17 Copynumber: 3.2 Consensus size: 17
45412 CTTTCTTCCT
*
45422 TTTTTATTCATTTTTTC
1 TTTTCATTCATTTTTTC
45439 TTTTCATTCATTTTTTC
1 TTTTCATTCATTTTTTC
45456 TTTTCATTCATTTTTTTC
1 TTTTCATTCA-TTTTTTC
45474 TTT
1 TTT
45477 CTTCTTTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
17 26 0.72
18 10 0.28
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTCATTCATTTTTTC
Found at i:45487 original size:34 final size:35
Alignment explanation
Indices: 45422--45493 Score: 87
Period size: 34 Copynumber: 2.1 Consensus size: 35
45412 CTTTCTTCCT
*
45422 TTTTTATTCATTTTTTCTTTTCATTC-ATTTTTTC
1 TTTTCATTCATTTTTTCTTTTCATTCTATTTTTTC
*
45456 TTTTCATTCATTTTTT-TCTTTC-TTCTTTTTTTTTC
1 TTTTCATTCATTTTTTCT-TTTCATTC-TATTTTTTC
45491 TTT
1 TTT
45494 GTTCAGGCGA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
33 4 0.12
34 19 0.58
35 10 0.30
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.76
Consensus pattern (35 bp):
TTTTCATTCATTTTTTCTTTTCATTCTATTTTTTC
Found at i:49618 original size:33 final size:34
Alignment explanation
Indices: 49571--49634 Score: 121
Period size: 33 Copynumber: 1.9 Consensus size: 34
49561 ATCCCATTCG
49571 GGTGCAGTTGGACAACCTAGGCTTATATCATCTC
1 GGTGCAGTTGGACAACCTAGGCTTATATCATCTC
49605 GGTG-AGTTGGACAACCTAGGCTTATATCAT
1 GGTGCAGTTGGACAACCTAGGCTTATATCAT
49635 TCTCCCCTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 26 0.87
34 4 0.13
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (34 bp):
GGTGCAGTTGGACAACCTAGGCTTATATCATCTC
Found at i:51993 original size:21 final size:22
Alignment explanation
Indices: 51964--52004 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
51954 CATAGCCCTA
* *
51964 ATTTATTCTTCCAGTTGTTTCC
1 ATTTATTCTTCAAATTGTTTCC
51986 ATTT-TTCTTCAAATTGTTT
1 ATTTATTCTTCAAATTGTTT
52005 GTTCGGCTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.17, C:0.17, G:0.07, T:0.59
Consensus pattern (22 bp):
ATTTATTCTTCAAATTGTTTCC
Found at i:53503 original size:21 final size:21
Alignment explanation
Indices: 53478--53525 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
53468 GTTTATTAAT
53478 TCCTATAAA-ATAA-TAATCTGA
1 TCCTATAAAGATAATTAATC--A
53499 TCCTA-AAAGATAATTAATCA
1 TCCTATAAAGATAATTAATCA
53519 TCCTATA
1 TCCTATA
53526 TTATATTACA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
20 9 0.38
21 10 0.42
22 5 0.21
ACGTcount: A:0.46, C:0.17, G:0.04, T:0.33
Consensus pattern (21 bp):
TCCTATAAAGATAATTAATCA
Done.