Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002664.1 Hibiscus syriacus cultivar Beakdansim tig00005470_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: 93542
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:6112 original size:37 final size:39
Alignment explanation
Indices: 6069--6161 Score: 118
Period size: 37 Copynumber: 2.4 Consensus size: 39
6059 TACTCTAAGA
* *
6069 AAATTAAATAAAAACATTACAAACTAAATAATAA-AAA-
1 AAATTAAATAAAAACATTAAAAACTAAACAATAAGAAAC
* * *
6106 TAATTAAATAGAAACATTAAAAACTAAACATTAAGAAAC
1 AAATTAAATAAAAACATTAAAAACTAAACAATAAGAAAC
*
6145 AAAATAAATAAAAACAT
1 AAATTAAATAAAAACAT
6162 AATTTATTAC
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
37 29 0.63
38 3 0.07
39 14 0.30
ACGTcount: A:0.68, C:0.09, G:0.02, T:0.22
Consensus pattern (39 bp):
AAATTAAATAAAAACATTAAAAACTAAACAATAAGAAAC
Found at i:8602 original size:14 final size:14
Alignment explanation
Indices: 8583--8616 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
8573 AGACCAAAAC
8583 AATAAAAAAATAAA
1 AATAAAAAAATAAA
* *
8597 AATAAAATAATAAT
1 AATAAAAAAATAAA
8611 AATAAA
1 AATAAA
8617 TAATATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
AATAAAAAAATAAA
Found at i:8611 original size:17 final size:18
Alignment explanation
Indices: 8591--8633 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
8581 ACAATAAAAA
8591 AATAAAAATAAAATA-AT
1 AATAAAAATAAAATATAT
*
8608 AATAATAAATAATATATAT
1 AATAA-AAATAAAATATAT
8627 ACATAAA
1 A-ATAAA
8634 TATTTTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 5 0.23
18 9 0.41
19 4 0.18
20 4 0.18
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (18 bp):
AATAAAAATAAAATATAT
Found at i:8713 original size:69 final size:69
Alignment explanation
Indices: 8631--8855 Score: 235
Period size: 69 Copynumber: 3.2 Consensus size: 69
8621 ATATATACAT
* * *
8631 AAATATTTTCAAAAACATAATATAAAATTTCAAAATGTTTT-TAAACTATATAATATATGAATTT
1 AAATGTTTTCAAAAACATAATATAAAATTTCAAAATGTTTTAAAAACTATATAATATAT-AATGT
8695 TTTCA
65 TTTCA
* * * * * *
8700 ACATGTTTTCAAAAAAAGATTATAAAATATCCAAAACGTTTTAAAAACTATATAATATA-AATGT
1 AAATGTTTTCAAAAACATAATATAAAAT-TTCAAAATGTTTTAAAAACTATATAATATATAATGT
8764 TTTCA
65 TTTCA
** *
8769 AAATGTTTTC-AAAACTATAATATATATGTTTTCAAAAATGTTTTCAAAACTATATATATATATA
1 AAATGTTTTCAAAAAC-ATAATATA-A-AATTTC-AAAATGTTTTAAAAACTATATA-ATATATA
8833 A-GTTTTCA
61 ATGTTTTCA
8841 AAATGATTTT-AAAAA
1 AAATG-TTTTCAAAAA
8856 TTATATATTA
Statistics
Matches: 128, Mismatches: 18, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
68 4 0.03
69 47 0.37
70 14 0.11
71 36 0.28
72 17 0.13
73 10 0.08
ACGTcount: A:0.48, C:0.08, G:0.05, T:0.40
Consensus pattern (69 bp):
AAATGTTTTCAAAAACATAATATAAAATTTCAAAATGTTTTAAAAACTATATAATATATAATGTT
TTCA
Found at i:8774 original size:11 final size:11
Alignment explanation
Indices: 8758--8782 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
8748 TATATAATAT
8758 AAATGTTTTCA
1 AAATGTTTTCA
8769 AAATGTTTTCA
1 AAATGTTTTCA
8780 AAA
1 AAA
8783 CTATAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:8777 original size:36 final size:36
Alignment explanation
Indices: 8658--8884 Score: 179
Period size: 35 Copynumber: 6.4 Consensus size: 36
8648 TAATATAAAA
* *
8658 TTTCAAAATGTTTT-TAAACTATATAATATATGAATTT
1 TTTCAAAATGTTTTAAAAACTATATAATATA--AATGT
* * * *
8695 TTTCAACATGTTTTCAAAAA--A-AGATTATAAA-AT
1 TTTCAAAATGTTTT-AAAAACTATATAATATAAATGT
* * *
8728 ATCCAAAACGTTTTAAAAACTATATAATATAAATGT
1 TTTCAAAATGTTTTAAAAACTATATAATATAAATGT
* *
8764 TTTCAAAATGTTTTCAAAAC--TATAATATATATGT
1 TTTCAAAATGTTTTAAAAACTATATAATATAAATGT
*
8798 TTTCAAAAATGTTTTCAAAACTATATATATATATAA-GT
1 TTTC-AAAATGTTTTAAAAACTATATA-ATATA-AATGT
* *
8836 TTTCAAAATGATTTTAAAAATTATAT-AT-TATAT-T
1 TTTCAAAATG-TTTTAAAAACTATATAATATAAATGT
8870 TTTCTAAAATGTTTT
1 TTTC-AAAATGTTTT
8885 TTTTAAAACT
Statistics
Matches: 155, Mismatches: 21, Indels: 31
0.75 0.10 0.15
Matches are distributed among these distances:
32 5 0.03
33 11 0.07
34 30 0.19
35 32 0.21
36 25 0.16
37 24 0.15
38 24 0.15
39 4 0.03
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (36 bp):
TTTCAAAATGTTTTAAAAACTATATAATATAAATGT
Found at i:8798 original size:34 final size:34
Alignment explanation
Indices: 8731--8884 Score: 168
Period size: 34 Copynumber: 4.3 Consensus size: 34
8721 ATAAAATATC
* *
8731 CAAAACGTTTTAAAAACTATATAATATAAATGTTTT
1 CAAAATGTTTTAAAAAC--TATAATATATATGTTTT
*
8767 CAAAATGTTTTCAAAACTATAATATATATGTTTT
1 CAAAATGTTTTAAAAACTATAATATATATGTTTT
*
8801 CAAAAATGTTTTCAAAACTATATATATATATAAGTTTT
1 C-AAAATGTTTTAAAAACTATA-ATATATAT--GTTTT
*
8839 CAAAATGATTTTAAAAATTAT-ATATTATAT-TTTT
1 CAAAATG-TTTTAAAAACTATAATA-TATATGTTTT
8873 CTAAAATGTTTT
1 C-AAAATGTTTT
8885 TTTTAAAACT
Statistics
Matches: 106, Mismatches: 5, Indels: 16
0.83 0.04 0.13
Matches are distributed among these distances:
34 26 0.25
35 26 0.25
36 26 0.25
37 11 0.10
38 17 0.16
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (34 bp):
CAAAATGTTTTAAAAACTATAATATATATGTTTT
Found at i:8818 original size:71 final size:69
Alignment explanation
Indices: 8658--8884 Score: 223
Period size: 71 Copynumber: 3.2 Consensus size: 69
8648 TAATATAAAA
* * * *
8658 TTTCAAAATGTTTTTAAACTATATAATATATGAATTTTTTCAACATGTTTTCAAAA-A-AAGATT
1 TTTCAAAATGTTTTAAAACTATATAATATAT-AATGTTTTCAAAATGTTTTCAAAATATAATATT
*
8721 ATAAAAT
65 AT--ATT
* * *
8728 ATCCAAAACGTTTTAAAAACTATATAATATA-AATGTTTTCAAAATGTTTTCAAAACTATAATA-
1 TTTCAAAATGTTTT-AAAACTATATAATATATAATGTTTTCAAAATGTTTTCAAAA-TATAATAT
8791 TATATGT
64 TATAT-T
*
8798 TTTCAAAAATGTTTTCAAAACTATATATATATATAA-GTTTTCAAAATGATTTTAAAAAT-TATA
1 TTTC-AAAATGTTTT-AAAACTATATA-ATATATAATGTTTTCAAAATG-TTTTCAAAATATA-A
8861 TATTATATT
61 TATTATATT
8870 TTTCTAAAATGTTTT
1 TTTC-AAAATGTTTT
8885 TTTTAAAACT
Statistics
Matches: 132, Mismatches: 14, Indels: 20
0.80 0.08 0.12
Matches are distributed among these distances:
69 23 0.17
70 14 0.11
71 41 0.31
72 39 0.30
73 15 0.11
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (69 bp):
TTTCAAAATGTTTTAAAACTATATAATATATAATGTTTTCAAAATGTTTTCAAAATATAATATTA
TATT
Found at i:8844 original size:72 final size:71
Alignment explanation
Indices: 8732--8884 Score: 204
Period size: 72 Copynumber: 2.1 Consensus size: 71
8722 TAAAATATCC
* *
8732 AAAACGTTTTAAAAACTATATAATATAAATGTTTTCAAAATG-TTTTCAAAACTATA-ATATATA
1 AAAATGTTTTAAAAACTATATAATATAAATGTTTTCAAAATGATTTTAAAAACTATATAT-TATA
8795 TGTTTTCA
65 T-TTTTCA
* *
8803 AAAATGTTTTCAAAACTATATATATATATAA-GTTTTCAAAATGATTTTAAAAATTATATATTAT
1 AAAATGTTTTAAAAACTATATA-ATATA-AATGTTTTCAAAATGATTTTAAAAACTATATATTAT
*
8867 ATTTTTCT
64 ATTTTTCA
8875 AAAATGTTTT
1 AAAATGTTTT
8885 TTTTAAAACT
Statistics
Matches: 73, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
71 20 0.27
72 32 0.44
73 19 0.26
74 2 0.03
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (71 bp):
AAAATGTTTTAAAAACTATATAATATAAATGTTTTCAAAATGATTTTAAAAACTATATATTATAT
TTTTCA
Found at i:8898 original size:37 final size:35
Alignment explanation
Indices: 8658--8950 Score: 192
Period size: 37 Copynumber: 8.3 Consensus size: 35
8648 TAATATAAAA
* *
8658 TTTCAAAATGTTTT-TAAACTATATAATATATGAATTT
1 TTTCAAAATGTTTTCAAAACTATAT-ATATAT--ATAT
* ** * *
8695 TTTCAACATGTTTTCAAAAAAAGAT-TATA-AAAT
1 TTTCAAAATGTTTTCAAAACTATATATATATATAT
* * * * * *
8728 ATCCAAAACGTTTTAAAAACTATATAATATAAATGT
1 TTTCAAAATGTTTTCAAAACTATAT-ATATATATAT
*
8764 TTTCAAAATGTTTTCAAAACTATA-ATATATATGT
1 TTTCAAAATGTTTTCAAAACTATATATATATATAT
8798 TTTCAAAAATGTTTTCAAAACTATATATATATATAAGT
1 TTTC-AAAATGTTTTCAAAACTATATATATATAT-A-T
* *
8836 TTTCAAAATGATTTTAAAAATTATATAT-TATAT-T
1 TTTCAAAATG-TTTTCAAAACTATATATATATATAT
*
8870 TTTCTAAAATGTTTTTTTTAAAACTATATAT-TATA-A-
1 TTTC-AAAATG---TTTTCAAAACTATATATATATATAT
** * * *
8906 TTT-AAAAACTATTAAAAACTATATATATATACGTAG
1 TTTCAAAATGTTTTCAAAACTATATATATATA--TAT
8942 TTTCAAAAT
1 TTTCAAAAT
8951 ATGTATATAT
Statistics
Matches: 204, Mismatches: 33, Indels: 38
0.74 0.12 0.14
Matches are distributed among these distances:
31 15 0.07
32 4 0.02
33 19 0.09
34 22 0.11
35 31 0.15
36 40 0.20
37 47 0.23
38 26 0.13
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.43
Consensus pattern (35 bp):
TTTCAAAATGTTTTCAAAACTATATATATATATAT
Found at i:8905 original size:72 final size:70
Alignment explanation
Indices: 8732--8906 Score: 192
Period size: 72 Copynumber: 2.4 Consensus size: 70
8722 TAAAATATCC
* * *
8732 AAAACGTTTTAAAAACTATATAATATAAATGTTTTCAAAATGTTTTCAAAACTATAATATATATG
1 AAAATGTTTTAAAAACTATATATTAT-AATGTTTTCAAAATGTTTTAAAAACTATAATATATATG
8797 TTTTCA
65 TTTTCA
* * *
8803 AAAATGTTTTCAAAACTATATATATATATAAGTTTTCAAAATGATTTTAAAAATTAT-ATATTAT
1 AAAATGTTTTAAAAACTATATAT-TATA-ATGTTTTCAAAATG-TTTTAAAAACTATAATA-TAT
*
8867 AT-TTTTCT
62 ATGTTTTCA
*
8875 AAAATGTTTTTTTTAAAACTATATATTATAAT
1 AAAATG---TTTTAAAAACTATATATTATAAT
8907 TTAAAAACTA
Statistics
Matches: 88, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
71 21 0.24
72 30 0.34
73 17 0.19
74 4 0.05
75 16 0.18
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (70 bp):
AAAATGTTTTAAAAACTATATATTATAATGTTTTCAAAATGTTTTAAAAACTATAATATATATGT
TTTCA
Found at i:9626 original size:81 final size:80
Alignment explanation
Indices: 9512--10034 Score: 487
Period size: 81 Copynumber: 6.4 Consensus size: 80
9502 TTATTGACAA
* * * * * * * *
9512 ATAGCCCTTCTTGCCATGAGCTATGTTGTAAATGATATGACCTCGAAGTTGAGTGTAATCGAACT
1 ATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATATG-CCTTGAAGCTGAGCGTAATCGAACT
*
9577 CG-GGAGTCTTTGGCAG
65 CGAAG-GTCTTTGGCAG
* *
9593 ATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTC
1 ATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATATGCCTTGAAGCTGAGCGTAATCGAACTC
9658 GAAGGTCTTTGATTGGCAG
66 GAAGGTC--T--TTGGCAG
* ** *
9677 ATA-CCCTTCTTGACTTAAGTTATGCTGCAAATGATGCGCCCTCGAAGCTGAGCGTAATCGAACT
1 ATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATATG-CCTTGAAGCTGAGCGTAATCGAACT
**
9741 CGGGGGTCTTTGGCAG
65 CGAAGGTCTTTGGCAG
* * * * *
9757 ATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
1 ATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATATGCCTTGAAGCTGAGCGTAATCGAACTC
* *
9822 AAAGGTCTTTGCTAACAG
66 GAAGGTCTTTG---GCAG
* * * * * * * *
9840 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACT
1 ATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATATG-CCTTGAAGCTGAGCGTAATCGAACT
*
9905 -TAAGGGTCTTTGGCAG
65 CGAA-GGTCTTTGGCAG
* * * * * *
9921 ATAGCTCTTCTCGACTTAAGCTATACTGC-AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
1 ATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATATGCCTTGAAGCTGAGCGTAATCGAACTC
* *
9985 AAAGGTTTTGGTGGCAG
66 GAAGGTCTT--TGGCAG
* * * *
10002 ATAGCCCTTCTGGCCTTGAGCTAAGCTGCAAAT
1 ATAGCCCTTCTTGACTTAAGCTATGCTGCAAAT
10035 AGTTTGTTTA
Statistics
Matches: 361, Mismatches: 65, Indels: 31
0.79 0.14 0.07
Matches are distributed among these distances:
79 27 0.07
80 75 0.21
81 119 0.33
82 5 0.01
83 67 0.19
84 68 0.19
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (80 bp):
ATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATATGCCTTGAAGCTGAGCGTAATCGAACTC
GAAGGTCTTTGGCAG
Found at i:9788 original size:164 final size:163
Alignment explanation
Indices: 9541--10012 Score: 669
Period size: 164 Copynumber: 2.9 Consensus size: 163
9531 GCTATGTTGT
* * * * *
9541 AAATGATATGACCTCGAAGTTGAGTGTAATCGAACTCGGGAGTCTTTGGCAGATAGCCCTTCTTG
1 AAATGATACGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
* * * *
9606 ACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGAT
66 ACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTG-C
*
9671 TGGCAGATACCCTTCTTGACTTAAGTTATGCTGC
130 TGGCAGATACCCTTCTAGACTTAAGTTATGCTGC
* *
9705 AAATGATGCGCCCTCGAAGCTGAGCGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
1 AAATGATACGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
*
9770 ACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCT
66 ACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCT
** * * *
9835 AACAGATAACCCTTCTAGCCTTGAGTTATGCTGT
131 GGCAGAT-ACCCTTCTAGACTTAAGTTATGCTGC
* * * *** *
9869 AAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAGCTCTTCTCG
1 AAATGATACGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
*
9934 ACTTAAGCTATACTGC-AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGT-TTTGGT
66 ACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCT
9997 GGCAGATAGCCCTTCT
131 GGCAGATA-CCCTTCT
10013 GGCCTTGAGC
Statistics
Matches: 276, Mismatches: 30, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
161 1 0.00
162 17 0.06
163 47 0.17
164 211 0.76
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (163 bp):
AAATGATACGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
ACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCT
GGCAGATACCCTTCTAGACTTAAGTTATGCTGC
Found at i:13354 original size:19 final size:18
Alignment explanation
Indices: 13330--13365 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
13320 GTGAATGCAA
13330 AAAATAACAAAATGCAAAG
1 AAAATAA-AAAATGCAAAG
*
13349 AAAATAAGAAATGCAAA
1 AAAATAAAAAATGCAAA
13366 ATGTCTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.69, C:0.08, G:0.11, T:0.11
Consensus pattern (18 bp):
AAAATAAAAAATGCAAAG
Found at i:14973 original size:6 final size:6
Alignment explanation
Indices: 14956--14992 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
14946 TTTAATTGCG
* *
14956 AAAATT AGAATT TAAATT AAAATT AAAATT AAAATT A
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT A
14993 TTCGATCCGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (6 bp):
AAAATT
Found at i:16504 original size:36 final size:36
Alignment explanation
Indices: 16415--16685 Score: 157
Period size: 37 Copynumber: 7.4 Consensus size: 36
16405 CAAAATGTTT
* *
16415 AAACTATATAATATATGAATTTTTTC-AACATGTTTTCAA
1 AAACTATATAATATA--AA--TTTTCAAAAATGTTTTTAA
** * * *
16454 AAAAAAGATTATATAAATTTTCCAAAAACG-TTTTAA
1 AAACTATATAATATAAATTTT-CAAAAATGTTTTTAA
*
16490 AAACTATATAATATAAATGTTTTC--AAATG-TTTTCA
1 AAACTATATAATATAAA--TTTTCAAAAATGTTTTTAA
**
16525 AAACTATA-ATATATATGTTTTCAAAAATGTTTTTCAA
1 AAACTATATA-ATATAAATTTTCAAAAATGTTTTT-AA
*
16562 AAACTATATATATATATAAGTTTTC-AAAATGATTTTAA
1 AAACTATATA-ATATA-AA-TTTTCAAAAATGTTTTTAA
* * * * **
16600 AAATTATATATTATATATTTTCTAAAATGTTTTTTTT
1 AAACTATATAATATAAATTTTCAAAAATG-TTTTTAA
* * *
16637 AAACTATATATTATATAATTTT-AAAAA--CTATTAA
1 AAACTATATAATATA-AATTTTCAAAAATGTTTTTAA
*
16671 AAACTATATATTATA
1 AAACTATATAATATA
16686 TACGTAGTTT
Statistics
Matches: 185, Mismatches: 32, Indels: 35
0.73 0.13 0.14
Matches are distributed among these distances:
33 5 0.03
34 19 0.10
35 36 0.19
36 30 0.16
37 42 0.23
38 27 0.15
39 21 0.11
40 5 0.03
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (36 bp):
AAACTATATAATATAAATTTTCAAAAATGTTTTTAA
Found at i:16627 original size:75 final size:74
Alignment explanation
Indices: 16465--16687 Score: 234
Period size: 75 Copynumber: 3.1 Consensus size: 74
16455 AAAAAGATTA
* * *
16465 TATAAATTTTCCAAAAACG-TTTTAAAAACTATATA-ATATA-AATGTTTTC-AAATG-TTTTCA
1 TATATATTTT-CAAAAATGTTTTTAAAAACTATATATATATATAA-GTTTTCAAAATGATTTTAA
16525 AAACTATA-AT
64 AAACTATATAT
*
16535 ATATATGTTTTCAAAAATGTTTTTCAAAAACTATATATATATATAAGTTTTCAAAATGATTTTAA
1 -TATATATTTTCAAAAATGTTTTT-AAAAACTATATATATATATAAGTTTTCAAAATGATTTTAA
*
16600 AAATTATATAT
64 AAACTATATAT
* ** *
16611 TATATATTTTCTAAAATGTTTTTTTTAAACTATATAT-TATATAA-TTTT-AAAA--ACTATTAA
1 TATATATTTTCAAAAATG-TTTTTAAAAACTATATATATATATAAGTTTTCAAAATGA-TTTTAA
16671 AAACTATATAT
64 AAACTATATAT
16682 TATATA
1 TATATA
16688 CGTAGTTTCA
Statistics
Matches: 132, Mismatches: 11, Indels: 18
0.82 0.07 0.11
Matches are distributed among these distances:
70 8 0.06
71 33 0.25
72 16 0.12
73 15 0.11
74 14 0.11
75 39 0.30
76 7 0.05
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.45
Consensus pattern (74 bp):
TATATATTTTCAAAAATGTTTTTAAAAACTATATATATATATAAGTTTTCAAAATGATTTTAAAA
ACTATATAT
Found at i:16645 original size:37 final size:38
Alignment explanation
Indices: 16484--16687 Score: 164
Period size: 37 Copynumber: 5.6 Consensus size: 38
16474 TCCAAAAACG
* *
16484 TTTTAAAAACTATATA-ATATAAATGTTT-TCAAATG--
1 TTTTAAAAACTATATATATATATAT-TTTCTAAAATGTT
* * *
16519 TTTTCAAAACTATA-ATATATATGTTTTCAAAAATGTT
1 TTTTAAAAACTATATATATATATATTTTCTAAAATGTT
* *
16556 TTTCAAAAACTATATATATATATAAGTTTTC-AAAATG-A
1 TTTTAAAAACTATATATATATAT-A-TTTTCTAAAATGTT
*
16594 TTTTAAAAATTATATAT-TATATATTTTCTAAAATGTT
1 TTTTAAAAACTATATATATATATATTTTCTAAAATGTT
** * **
16631 TTTTTTAAACTATATAT-TATATAATTT-TAAAA--AC
1 TTTTAAAAACTATATATATATATATTTTCTAAAATGTT
*
16665 TATTAAAAACTATATAT-TATATA
1 TTTTAAAAACTATATATATATATA
16688 CGTAGTTTCA
Statistics
Matches: 139, Mismatches: 21, Indels: 19
0.78 0.12 0.11
Matches are distributed among these distances:
34 24 0.17
35 29 0.21
36 12 0.09
37 40 0.29
38 23 0.17
39 6 0.04
40 5 0.04
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (38 bp):
TTTTAAAAACTATATATATATATATTTTCTAAAATGTT
Found at i:22719 original size:14 final size:14
Alignment explanation
Indices: 22697--22729 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
22687 CGTTCGTGAA
*
22697 CGTTCGGTTATGTT
1 CGTTTGGTTATGTT
22711 CGTTTGGTTATGTT
1 CGTTTGGTTATGTT
22725 CGTTT
1 CGTTT
22730 ATGTTCATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.12, G:0.27, T:0.55
Consensus pattern (14 bp):
CGTTTGGTTATGTT
Found at i:22725 original size:24 final size:24
Alignment explanation
Indices: 22718--22772 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
22708 GTTCGTTTGG
22718 TTATGTTCGTTTATGTTCATTCAA
1 TTATGTTCGTTTATGTTCATTCAA
*
22742 TTATGTTCGTTTATGTTCATTCAT
1 TTATGTTCGTTTATGTTCATTCAA
22766 TTATGTT
1 TTATGTT
22773 TAACCCAATC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.18, C:0.11, G:0.13, T:0.58
Consensus pattern (24 bp):
TTATGTTCGTTTATGTTCATTCAA
Found at i:23525 original size:16 final size:16
Alignment explanation
Indices: 23500--23555 Score: 94
Period size: 16 Copynumber: 3.5 Consensus size: 16
23490 CCAACGTTTA
23500 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
* *
23516 AGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
23532 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
23548 TGTTCGTT
1 TGTTCGTT
23556 ATTTATTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.09, C:0.12, G:0.23, T:0.55
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:23644 original size:16 final size:16
Alignment explanation
Indices: 23623--23655 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
23613 AAAAAAAATT
23623 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
23639 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
23655 T
1 T
23656 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:38841 original size:71 final size:71
Alignment explanation
Indices: 38753--38897 Score: 281
Period size: 71 Copynumber: 2.0 Consensus size: 71
38743 CTCAATATGA
38753 AGTCAGATATTTTATTTTGAGAATTACGACATTTGTTACAGTAACTTGAAACTGGCTAAATAGGT
1 AGTCAGATATTTTATTTTGAGAATTACGACATTTGTTACAGTAACTTGAAACTGGCTAAATAGGT
38818 ATGACG
66 ATGACG
*
38824 AGTCAGATATTTTATTTTGAGAATTACGACATTTGTTATAGTAACTTGAAACTGGCTAAATAGGT
1 AGTCAGATATTTTATTTTGAGAATTACGACATTTGTTACAGTAACTTGAAACTGGCTAAATAGGT
38889 ATGACG
66 ATGACG
38895 AGT
1 AGT
38898 TTTAATAGAA
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 73 1.00
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.36
Consensus pattern (71 bp):
AGTCAGATATTTTATTTTGAGAATTACGACATTTGTTACAGTAACTTGAAACTGGCTAAATAGGT
ATGACG
Found at i:41634 original size:14 final size:15
Alignment explanation
Indices: 41610--41642 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
41600 TAAGAGTCAT
*
41610 TTTTCTCTCTCTTGA
1 TTTTCTCTCTCTTCA
41625 TTTT-TCTCTCTTCA
1 TTTTCTCTCTCTTCA
41639 TTTT
1 TTTT
41643 GGTTGAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.06, C:0.24, G:0.03, T:0.67
Consensus pattern (15 bp):
TTTTCTCTCTCTTCA
Found at i:43831 original size:2 final size:2
Alignment explanation
Indices: 43824--43858 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
43814 CGTTTTTATT
43824 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
43859 GGATAGATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:50446 original size:11 final size:11
Alignment explanation
Indices: 50430--50454 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
50420 TGCACTCCAC
50430 TCTTTTTTTTT
1 TCTTTTTTTTT
50441 TCTTTTTTTTT
1 TCTTTTTTTTT
50452 TCT
1 TCT
50455 GATTTTAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TCTTTTTTTTT
Found at i:61649 original size:64 final size:63
Alignment explanation
Indices: 61564--61723 Score: 189
Period size: 64 Copynumber: 2.5 Consensus size: 63
61554 TTGTTTAAGG
* * * *
61564 TGCATCGATGCACATGCAGTGCATCGATGCA-AGAATTTAAATAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCACACAA-TTAAATA-AAAACATCGAATAGGATTTA
* * *
61628 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCA-CACAATTAAATAAAAACATCGAATAGGATTTA
*
61692 TGCATCGATGCAT-GGTGTAGTGCATCGATGCA
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCA
61724 TACCTTCATT
Statistics
Matches: 84, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
63 1 0.01
64 61 0.73
65 21 0.25
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (63 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCACACAATTAAATAAAAACATCGAATAGGATTTA
Found at i:61724 original size:65 final size:65
Alignment explanation
Indices: 61600--61724 Score: 200
Period size: 64 Copynumber: 1.9 Consensus size: 65
61590 ATGCAAGAAT
61600 TTAAATAGAAAACATCGAATAGGATTTATGCATCGATGCATAAGGAGTGCATCGATGCATCCCCA
1 TTAAATAGAAAACATCGAATAGGATTTATGCATCGATGCATAAGGAGTGCATCGATGCATCCCCA
* *
61665 TTAAATA-CAAACATCGAATAGGATTTATGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TTAAATAGAAAACATCGAATAGGATTTATGCATCGATGCATAAG-G-AGTGCATCGATGCAT
61725 ACCTTCATTA
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
63 1 0.02
64 33 0.59
65 22 0.39
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (65 bp):
TTAAATAGAAAACATCGAATAGGATTTATGCATCGATGCATAAGGAGTGCATCGATGCATCCCCA
Found at i:63071 original size:22 final size:21
Alignment explanation
Indices: 63017--63080 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
63007 AGTCGAGGGT
63017 TTCATAGGTCCTTCGGGACAA
1 TTCATAGGTCCTTCGGGACAA
*
63038 CTCATAGGTCCTTCGGGACATA
1 TTCATAGGTCCTTCGGGACA-A
*
63060 TTCACAGGTCCTTCGGGACAA
1 TTCATAGGTCCTTCGGGACAA
63081 ATTTCATATG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
21 20 0.51
22 19 0.49
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (21 bp):
TTCATAGGTCCTTCGGGACAA
Found at i:83544 original size:15 final size:17
Alignment explanation
Indices: 83511--83544 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
83501 AATCTAAATT
83511 TAAATAATAAAAGTCTA
1 TAAATAATAAAAGTCTA
83528 TAAA-AATAAAA-TCTA
1 TAAATAATAAAAGTCTA
83543 TA
1 TA
83545 TCAAACTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 7 0.41
17 4 0.24
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.29
Consensus pattern (17 bp):
TAAATAATAAAAGTCTA
Found at i:85404 original size:63 final size:63
Alignment explanation
Indices: 85281--85440 Score: 216
Period size: 63 Copynumber: 2.5 Consensus size: 63
85271 TTGTTTAAGG
* * * * *
85281 TGCATCGATGCACATGCAGTGCATCGATGCA-AGAATTAAATAGAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATACAATTAAATACAAACATCGAATAGGATTTA
* *
85343 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATACAATTAAATACAAACATCGAATAGGATTTA
*
85406 TGCATCGATGCAT-GGTGTAGTGCATCGATGCATAC
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCATAC
85441 CTTCATTAAA
Statistics
Matches: 86, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
62 29 0.34
63 41 0.48
64 16 0.19
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (63 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATACAATTAAATACAAACATCGAATAGGATTTA
Found at i:86752 original size:21 final size:21
Alignment explanation
Indices: 86726--86786 Score: 95
Period size: 22 Copynumber: 2.9 Consensus size: 21
86716 TCGAGGGTTT
86726 ATAGGTCCTTCGGGACAACTC
1 ATAGGTCCTTCGGGACAACTC
*
86747 ATAGGTCCTTCGGGACATATTC
1 ATAGGTCCTTCGGGACA-ACTC
*
86769 ACAGGTCCTTCGGGACAA
1 ATAGGTCCTTCGGGACAA
86787 ATTTCATATG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 18 0.49
22 19 0.51
ACGTcount: A:0.25, C:0.26, G:0.25, T:0.25
Consensus pattern (21 bp):
ATAGGTCCTTCGGGACAACTC
Found at i:92076 original size:66 final size:67
Alignment explanation
Indices: 91944--92077 Score: 200
Period size: 66 Copynumber: 2.0 Consensus size: 67
91934 TTTGCAGTAC
* * *
91944 TCATTGATATTTATATTATCTAACATAGCTGTCAATGAACCTTTCTTTCAGGTTCATTTGTTAGC
1 TCATTGATATTAATATTATCTAACATAGCTGTCAATGAACCTTTCTTTCAGGTTCATGTGTCAGC
92009 TG
66 TG
* *
92011 TCATTGATA-TAATCTTATCTAACATTGCTGTCAATGAACCTTTCTTTCAGGTTCGA-GTGTCAG
1 TCATTGATATTAATATTATCTAACATAGCTGTCAATGAACCTTTCTTTCAGGTTC-ATGTGTCAG
92074 CTG
65 CTG
92077 T
1 T
92078 TTACTAATGG
Statistics
Matches: 61, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
66 51 0.84
67 10 0.16
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.43
Consensus pattern (67 bp):
TCATTGATATTAATATTATCTAACATAGCTGTCAATGAACCTTTCTTTCAGGTTCATGTGTCAGC
TG
Done.