Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006173.1 Hibiscus syriacus cultivar Beakdansim tig00014675_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: 51103
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:1195 original size:2 final size:2
Alignment explanation
Indices: 1188--1214 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1178 TTTTTAAATA
1188 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1215 ATTATCCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1356 original size:2 final size:2
Alignment explanation
Indices: 1349--1380 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1339 TATTATTAAA
1349 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1381 GAATAGATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1727 original size:40 final size:40
Alignment explanation
Indices: 1672--1750 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
1662 TGTGTGGTAA
1672 TACAGTACAGTGAGAAAAGTTTGACATTAGAATTAGCAAG
1 TACAGTACAGTGAGAAAAGTTTGACATTAGAATTAGCAAG
**
1712 TACAGTAGTGTGAGAAAAGTTTGACATTAGAATTAGCAA
1 TACAGTACAGTGAGAAAAGTTTGACATTAGAATTAGCAA
1751 AAAAAAGTCC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.27
Consensus pattern (40 bp):
TACAGTACAGTGAGAAAAGTTTGACATTAGAATTAGCAAG
Found at i:6709 original size:38 final size:34
Alignment explanation
Indices: 6651--6957 Score: 151
Period size: 38 Copynumber: 8.5 Consensus size: 34
6641 TTTTTAATAG
*
6651 TTTTTAAAATTATATAATATATAGTTTTAAAAGAAAACA
1 TTTTGAAAA-TATAT-ATATATAGTTTT---AGAAAACA
* *
6690 TTTTAGAAAATATATATATATAATTTTTA-AAATCA
1 TTTT-GAAAATATATATATAT-AGTTTTAGAAAACA
*
6725 TTTTGAAAACTTATATATATATATAGTTTTTGAAAACA
1 TTTTG-AAA---ATATATATATATAGTTTTAGAAAACA
*
6763 TTTTTGAAAACATATAT-TATAGTTTT-GAAAACA
1 -TTTTGAAAATATATATATATAGTTTTAGAAAACA
* * * *
6796 TTTTGAAAACATTTATATTATAGTTTT-TAAAACG
1 TTTTGAAAATATATATA-TATAGTTTTAGAAAACA
* * ** *
6830 TTTTGGGAAAATTTATATAATCTTTTTTTTTTGAAAACA
1 TTTT--GAAAA--TATAT-ATATATAGTTTTAGAAAACA
*
6869 TGTTGAAAAAATTCATATATTATATAG-TTTA-AAAACA
1 TTTTG--AAAA-T-ATATA-TATATAGTTTTAGAAAACA
* * *
6906 TTTTG-AAATTTATATATTATATGTTTTTGAAAATA
1 TTTTGAAAATATATATA-TATA-GTTTTAGAAAACA
* *
6941 TTTATGTATATATATAT
1 TTT-TGAAAATATATAT
6958 TATTATTATT
Statistics
Matches: 212, Mismatches: 30, Indels: 54
0.72 0.10 0.18
Matches are distributed among these distances:
31 2 0.01
32 23 0.11
33 9 0.04
34 34 0.16
35 27 0.13
36 8 0.04
37 24 0.11
38 41 0.19
39 40 0.19
40 4 0.02
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.46
Consensus pattern (34 bp):
TTTTGAAAATATATATATATAGTTTTAGAAAACA
Found at i:6733 original size:34 final size:33
Alignment explanation
Indices: 6684--6848 Score: 152
Period size: 34 Copynumber: 4.7 Consensus size: 33
6674 GTTTTAAAAG
6684 AAAACATTTTAGAAAATATATATATATAATTTTT
1 AAAACATTTT-GAAAATATATATATATAATTTTT
6718 AAAATCATTTTGAAAACTTATATATATATATAGTTTTT
1 AAAA-CATTTTGAAAA--TATATATATATA-A-TTTTT
* * *
6756 GAAAACATTTTTGAAAACATATAT-TATAGTTTTG
1 -AAAACA-TTTTGAAAATATATATATATAATTTTT
* * *
6790 AAAACATTTTGAAAACATTTATATTATAGTTTTT
1 AAAACATTTTGAAAATATATATA-TATAATTTTT
* *
6824 AAAACGTTTTGGGAAAATTTATATA
1 AAAACATTTT--GAAAATATATATA
6849 ATCTTTTTTT
Statistics
Matches: 111, Mismatches: 9, Indels: 20
0.79 0.06 0.14
Matches are distributed among these distances:
32 15 0.14
33 6 0.05
34 31 0.28
35 6 0.05
36 26 0.23
37 7 0.06
38 7 0.06
39 13 0.12
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.44
Consensus pattern (33 bp):
AAAACATTTTGAAAATATATATATATAATTTTT
Found at i:6768 original size:12 final size:12
Alignment explanation
Indices: 6751--6775 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6741 ATATATATAG
6751 TTTTTGAAAACA
1 TTTTTGAAAACA
6763 TTTTTGAAAACA
1 TTTTTGAAAACA
6775 T
1 T
6776 ATATTATAGT
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:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TTTTTGAAAACA
Found at i:6801 original size:11 final size:11
Alignment explanation
Indices: 6785--6809 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
6775 TATATTATAG
6785 TTTTGAAAACA
1 TTTTGAAAACA
6796 TTTTGAAAACA
1 TTTTGAAAACA
6807 TTT
1 TTT
6810 ATATTATAGT
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:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:6933 original size:73 final size:72
Alignment explanation
Indices: 6656--6943 Score: 229
Period size: 73 Copynumber: 3.9 Consensus size: 72
6646 AATAGTTTTT
* * *
6656 AAAATTATATAATATATAGTTTTAAAAGAAAACATTTTAGAAAATATATA-TATATAATTTTT-A
1 AAAATTATATATTATATAGTTTT---A-AAAACATTTTGGAAAATATATATTATAT-GTTTTTGA
6719 AAATCATTTTG-A
61 AAA-CATTTTGAA
* * * *
6731 AAACTTATATATATATATAGTTTTTGAAAACATTTTTGAAAACATATATTATA-G-TTTTGAAAA
1 AAAATTATATAT-TATATAG-TTTTAAAAACATTTTGGAAAATATATATTATATGTTTTTGAAAA
6794 CATTTTGAA
64 CATTTTGAA
* * * * *
6803 AACATT-TATA-T-TATAGTTTTTAAAACGTTTTGGGAAAATTTATATAATCT-TTTTTTTTTGA
1 AAAATTATATATTATATAGTTTTAAAAACATTTT-GGAAAA--TATAT-AT-TATATGTTTTTGA
*
6864 AAACATGTTGAA
61 AAACATTTTGAA
*
6876 AAAATTCATATATTATATAG-TTTAAAAACATTTT-GAAATTTATATATTATATGTTTTTGAAAA
1 AAAATT-ATATATTATATAGTTTTAAAAACATTTTGGAAA-ATATATATTATATGTTTTTGAAAA
*
6939 TATTT
64 CATTT
6944 ATGTATATAT
Statistics
Matches: 172, Mismatches: 23, Indels: 39
0.74 0.10 0.17
Matches are distributed among these distances:
67 13 0.08
68 10 0.06
69 1 0.01
70 4 0.02
71 19 0.11
72 27 0.16
73 47 0.27
74 8 0.05
75 14 0.08
76 20 0.12
77 9 0.05
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (72 bp):
AAAATTATATATTATATAGTTTTAAAAACATTTTGGAAAATATATATTATATGTTTTTGAAAACA
TTTTGAA
Found at i:6950 original size:24 final size:24
Alignment explanation
Indices: 6906--6951 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
6896 TTTAAAAACA
*
6906 TTTTGAAATTTATATATTATATGT
1 TTTTGAAATATATATATTATATGT
*
6930 TTTTGAAA-ATATTTATGTATAT
1 TTTTGAAATATATATAT-TATAT
6952 ATATATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.57
Consensus pattern (24 bp):
TTTTGAAATATATATATTATATGT
Found at i:6975 original size:15 final size:16
Alignment explanation
Indices: 6957--6992 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
6947 TATATATATA
6957 TTATTATTA-TTTATT
1 TTATTATTATTTTATT
*
6972 TTATTTTTATTTTATT
1 TTATTATTATTTTATT
6988 TTATT
1 TTATT
6993 GTTTTGGTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (16 bp):
TTATTATTATTTTATT
Found at i:6982 original size:11 final size:11
Alignment explanation
Indices: 6955--6989 Score: 52
Period size: 11 Copynumber: 3.0 Consensus size: 11
6945 TGTATATATA
6955 TATTATTATTATT
1 TATT-TTATT-TT
6968 TATTTTATTTT
1 TATTTTATTTT
6979 TATTTTATTTT
1 TATTTTATTTT
6990 ATTGTTTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 13 0.59
12 5 0.23
13 4 0.18
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (11 bp):
TATTTTATTTT
Found at i:8170 original size:24 final size:24
Alignment explanation
Indices: 8118--8176 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
8108 AATTTTATCT
*
8118 TTATTTTTTT-ATTTTACTTTTAAA
1 TTATTTTTTTAATTTAACTTTT-AA
*
8142 ATATTTTTTTAATTTAACCTTTT-A
1 TTATTTTTTTAATTTAA-CTTTTAA
*
8166 TTATTATTTTA
1 TTATTTTTTTA
8177 TTATTTCTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 19 0.66
25 5 0.17
26 5 0.17
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (24 bp):
TTATTTTTTTAATTTAACTTTTAA
Found at i:8177 original size:8 final size:8
Alignment explanation
Indices: 8166--8224 Score: 50
Period size: 8 Copynumber: 7.2 Consensus size: 8
8156 TAACCTTTTA
8166 TTATTATT
1 TTATTATT
8174 TTATTATT
1 TTATTATT
*
8182 TCT-TTCTT
1 T-TATTATT
*
8190 TCATTATT
1 TTATTATT
8198 ATTATTATT
1 -TTATTATT
8207 TT-TATATT
1 TTAT-TATT
*
8215 TTTTTATT
1 TTATTATT
8223 TT
1 TT
8225 TTAGCATTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
7 1 0.02
8 32 0.76
9 9 0.21
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (8 bp):
TTATTATT
Found at i:13595 original size:164 final size:164
Alignment explanation
Indices: 13353--13996 Score: 923
Period size: 164 Copynumber: 3.9 Consensus size: 164
13343 TCCTGCCACC
13353 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
*
13418 AAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAG
66 AAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAG
*
13483 CATAACTCAAGGCTAGAAGGGTTATCTGTTAGAA
131 CATAACTCAAGGCAAGAAGGGTTATCTGTTAGAA
* *
13517 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
* * *
13582 AAGAGCTATCTGCCAAAGACCCTTAAGTTTGATTACACTCAGCTTCAAGGGCATAACATTTACAG
66 AAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAG
* *
13647 CATAACTCAAGGCTAGAAGGGTTATCTGTTAGCA
131 CATAACTCAAGGCAAGAAGGGTTATCTGTTAGAA
*
13681 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
* * * * ** * *
13746 AAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACGCTCAGCTTCGAGGGCGCATCATTTGCAG
66 AAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAG
* * **
13811 CATAACTTAAGTCAAGAAGGGTTATCTGCCA-ATCA
131 CATAACTCAAGGCAAGAAGGGTTATCTGTTAGA--A
* * * *
13846 AAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAGCTTAAGTCAAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
* * * * * * *
13911 AAGGGCCATCTGCCAAAGACTCC-CGAGTTCAATTACACTCAACTTCGAGGTCATATCATTTACA
66 AAGGGCTATCTGCCAAAGAC-CCTCAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACA
* * *
13975 ACATAGCTCATGGCAAGAAGGG
130 GCATAACTCAAGGCAAGAAGGG
13997 CTATTTGTCA
Statistics
Matches: 436, Mismatches: 41, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
164 303 0.69
165 131 0.30
166 2 0.00
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.25
Consensus pattern (164 bp):
AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
AAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAG
CATAACTCAAGGCAAGAAGGGTTATCTGTTAGAA
Found at i:13909 original size:84 final size:81
Alignment explanation
Indices: 13312--13930 Score: 595
Period size: 81 Copynumber: 7.6 Consensus size: 81
13302 TAAACAAACT
* * * * *
13312 ATTTGCAGCTTAGCTCAAGGCCAGAAGGGCT-TCCTGCCACCAAGACCTTCGAGTTCGACTACGC
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTAT-CTG-CACAAAGACCTTCGAGTTCGACTACGC
13376 TCAGCTCCAAGGCACATC
64 TCAGCTCCAAGGCACATC
* * * *
13394 ATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGC-CAAAGACCCTT-AAGTTCGATTACACT
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCACAAAGA-CCTTCGAGTTCGACTACGCT
* * *
13457 CAGCTTCAAGGGCATAAC
65 CAGCTCCAA-GGCACATC
* * * * * * * * *
13475 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTAGAAAAGACCTTTGAGTTCGACTACGC
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-CA-CAAAGACCTTCGAGTTCGACTACGC
13540 TCAGCTCCAAGGCACATC
64 TCAGCTCCAAGGCACATC
* * * * * *
13558 ATTTGCAGTATAGCTTAAGTCGAGAAGAGCTATCTGC-CAAAGACCCTT-AAGTTTGATTACACT
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCACAAAGA-CCTTCGAGTTCGACTACGCT
* * *
13621 CAGCTTCAAGGGCATAAC
65 CAGCTCCAA-GGCACATC
* * * * * * * *
13639 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGC
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-CA-CAAAGACCTTCGAGTTCGACTACGC
13704 TCAGCTCCAAGGCACATC
64 TCAGCTCCAAGGCACATC
* ** *
13722 ATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGC-CAAAGACCCCCGAGTTCGATTACGCTC
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCACAAAGACCTTCGAGTTCGACTACGCTC
* * *
13786 AGCTTCGAGGGCGCATC
66 AGC-TCCAAGGCACATC
* * * *
13803 ATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAATCAAAGACCTTCGAGTTTGACTACG
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C-A-CAAAGACCTTCGAGTTCGACTACG
*
13868 CTCAGCTCCAAGGCATATC
63 CTCAGCTCCAAGGCACATC
* *
13887 ATTTGCAGCATAGCTTAAGTCAAGAAGGGCCATCTGC-CAAAGAC
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCACAAAGAC
13931 TCCCGAGTTC
Statistics
Matches: 429, Mismatches: 90, Indels: 38
0.77 0.16 0.07
Matches are distributed among these distances:
80 82 0.19
81 120 0.28
82 30 0.07
83 79 0.18
84 92 0.21
85 26 0.06
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (81 bp):
ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCACAAAGACCTTCGAGTTCGACTACGCTC
AGCTCCAAGGCACATC
Found at i:14726 original size:36 final size:35
Alignment explanation
Indices: 14654--14914 Score: 221
Period size: 37 Copynumber: 7.3 Consensus size: 35
14644 GTTTTAAAAG
* *
14654 AAAACATTTTAGAAAACATATATAATATATAATTTTT
1 AAAACATTTT-GAAAACTTATAT-ATATATAGTTTTT
14691 AAAATCATTTTGAAAACTTATATATATATAGTTTTT
1 AAAA-CATTTTGAAAACTTATATATATATAGTTTTT
* *
14727 GAAAACATTTTTGAAAACATATATAT-TATAGTTTTG
1 -AAAACA-TTTTGAAAACTTATATATATATAGTTTTT
14763 AAAACATTTTGAAAACATT-TATATTATATAGTTTTT
1 AAAACATTTTGAAAAC-TTATATA-TATATAGTTTTT
* * * **
14799 AAAACGTTTTGGGAAAATTTATATA-ATCTTTTTTTT
1 AAAACATTTT--GAAAACTTATATATATATAGTTTTT
* * *
14835 GAAAACATGTTGAAAAAATTCATATATTATATAG-TTTA
1 -AAAACATTTTG-AAAACTT-ATATA-TATATAGTTTTT
*
14873 AAAACATTTTG-AAATTTATAT-TATAT-GTTTTT
1 AAAACATTTTGAAAACTTATATATATATAGTTTTT
*
14905 GAAAATATTT
1 -AAAACATTT
14915 ATGTATATAT
Statistics
Matches: 186, Mismatches: 22, Indels: 36
0.76 0.09 0.15
Matches are distributed among these distances:
31 1 0.01
32 8 0.04
33 8 0.04
34 18 0.10
35 14 0.08
36 55 0.30
37 61 0.33
38 18 0.10
39 3 0.02
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.45
Consensus pattern (35 bp):
AAAACATTTTGAAAACTTATATATATATAGTTTTT
Found at i:14739 original size:37 final size:37
Alignment explanation
Indices: 14621--14914 Score: 217
Period size: 37 Copynumber: 8.1 Consensus size: 37
14611 TTTTTAATAG
*
14621 TTTTT-AAAA-TTATATAATATATAGTTTTAAAAGAAAACA
1 TTTTTGAAAACTTATAT-ATATATAGTTTT---TGAAAACA
* * *
14660 TTTTAGAAAACATATATAATATATAATTTTT-AAAATCA
1 TTTTTGAAAACTTATAT-ATATATAGTTTTTGAAAA-CA
14698 -TTTTGAAAACTTATATATATATAGTTTTTGAAAACA
1 TTTTTGAAAACTTATATATATATAGTTTTTGAAAACA
*
14734 TTTTTGAAAACATATATAT-TATAG-TTTTGAAAACA
1 TTTTTGAAAACTTATATATATATAGTTTTTGAAAACA
*
14769 -TTTTGAAAACATT-TATATTATATAGTTTTT-AAAACG
1 TTTTTGAAAAC-TTATATA-TATATAGTTTTTGAAAACA
* * * **
14805 TTTTGGGAAAATTTATATA-ATCTTTTTTTTGAAAACA
1 TTTT-TGAAAACTTATATATATATAGTTTTTGAAAACA
* * *
14842 -TGTTGAAAAAATTCATATATTATATAG--TTTAAAAACA
1 TTTTTG-AAAACTT-ATATA-TATATAGTTTTTGAAAACA
* *
14879 -TTTTG-AAATTTATAT-TATAT-GTTTTTGAAAATA
1 TTTTTGAAAACTTATATATATATAGTTTTTGAAAACA
14912 TTT
1 TTT
14915 ATGTATATAT
Statistics
Matches: 208, Mismatches: 27, Indels: 45
0.74 0.10 0.16
Matches are distributed among these distances:
31 1 0.00
32 5 0.02
33 8 0.04
34 20 0.10
35 19 0.09
36 45 0.22
37 71 0.34
38 11 0.05
39 7 0.03
40 4 0.02
41 17 0.08
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.45
Consensus pattern (37 bp):
TTTTTGAAAACTTATATATATATAGTTTTTGAAAACA
Found at i:14774 original size:11 final size:11
Alignment explanation
Indices: 14758--14782 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
14748 TATATTATAG
14758 TTTTGAAAACA
1 TTTTGAAAACA
14769 TTTTGAAAACA
1 TTTTGAAAACA
14780 TTT
1 TTT
14783 ATATTATATA
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:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:14904 original size:73 final size:72
Alignment explanation
Indices: 14703--14893 Score: 194
Period size: 73 Copynumber: 2.6 Consensus size: 72
14693 AATCATTTTG
* * * ** **
14703 AAAACTTATATATATATAGTTTTTGAAAACATTTTTGAAAACATATAT-AT-TATAGTTTTGAAA
1 AAAATTTATAT-TATATAG-TTTTAAAAACATTTTGGAAAATTTATATAATCT-TTTTTTTGAAA
*
14766 ACATTTTGAA
63 ACATGTTGAA
* * *
14776 AACATTTATATTATATAGTTTTTAAAACGTTTTGGGAAAATTTATATAATCTTTTTTTTGAAAAC
1 AAAATTTATATTATATAGTTTTAAAAACATTTT-GGAAAATTTATATAATCTTTTTTTTGAAAAC
14841 ATGTTGAA
65 ATGTTGAA
14849 AAAATTCATATATTATATAG-TTTAAAAACATTTT-G-AAATTTATAT
1 AAAATT--TATATTATATAGTTTTAAAAACATTTTGGAAAATTTATAT
14894 TATATGTTTT
Statistics
Matches: 100, Mismatches: 13, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
71 23 0.23
72 18 0.18
73 34 0.34
74 13 0.13
75 12 0.12
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (72 bp):
AAAATTTATATTATATAGTTTTAAAAACATTTTGGAAAATTTATATAATCTTTTTTTTGAAAACA
TGTTGAA
Found at i:14948 original size:5 final size:5
Alignment explanation
Indices: 14938--14963 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
14928 TTATTTATTA
14938 TTTAT TTTAT TTTAT TTTAT TTTAT T
1 TTTAT TTTAT TTTAT TTTAT TTTAT T
14964 GTTTTGGTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:16142 original size:24 final size:25
Alignment explanation
Indices: 16090--16148 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
16080 AATTTTATCT
* *
16090 TTATTTTTTT-ATTTTACTTTTTAA
1 TTATTTTTTTAATTTAACCTTTTAA
*
16114 ATATTTTTTTAATTTAACCTTTT-A
1 TTATTTTTTTAATTTAACCTTTTAA
*
16138 TTATTATTTTA
1 TTATTTTTTTA
16149 TTATTTCTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
24 19 0.66
25 10 0.34
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.69
Consensus pattern (25 bp):
TTATTTTTTTAATTTAACCTTTTAA
Found at i:16149 original size:8 final size:8
Alignment explanation
Indices: 16138--16196 Score: 50
Period size: 8 Copynumber: 7.2 Consensus size: 8
16128 TAACCTTTTA
16138 TTATTATT
1 TTATTATT
16146 TTATTATT
1 TTATTATT
*
16154 TCT-TTCTT
1 T-TATTATT
*
16162 TCATTATT
1 TTATTATT
16170 ATTATTATT
1 -TTATTATT
16179 TT-TTATAT
1 TTATTAT-T
*
16187 TTTTTATT
1 TTATTATT
16195 TT
1 TT
16197 TTAGCATTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
7 4 0.10
8 26 0.62
9 12 0.29
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (8 bp):
TTATTATT
Found at i:16762 original size:18 final size:17
Alignment explanation
Indices: 16732--16765 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
16722 GAAGATTGAC
16732 TTTAAAATATATATTTT
1 TTTAAAATATATATTTT
*
16749 TTTATAAATTTATATTT
1 TTTA-AAATATATATTT
16766 GATGCATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTAAAATATATATTTT
Found at i:17146 original size:2 final size:2
Alignment explanation
Indices: 17139--17175 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
17129 ATAGAATTTT
17139 TA 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 TA T
17176 TTAATCTCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18898 original size:60 final size:60
Alignment explanation
Indices: 18834--18948 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
18824 TAACCCTAAG
* * * *
18834 ACTATAGGGTATTATTTTGTCGAGTTCT-TCAACTATTAAAAGTTACAAAACGATCCTTTA
1 ACTATAAGGCATTATTTTGTCAAG-TCTACCAACTATTAAAAGTTACAAAACGATCCTTTA
* * * *
18894 ACTATAATGCATTATTTTGTTAAGTCTACCGACTATTAAAAGTTACAAAATGATC
1 ACTATAAGGCATTATTTTGTCAAGTCTACCAACTATTAAAAGTTACAAAACGATC
18949 ACTCGACTAT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
59 3 0.07
60 43 0.93
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (60 bp):
ACTATAAGGCATTATTTTGTCAAGTCTACCAACTATTAAAAGTTACAAAACGATCCTTTA
Found at i:25824 original size:17 final size:17
Alignment explanation
Indices: 25802--25834 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
25792 CAAATAATTT
25802 TAAAATTAA-TAATAATA
1 TAAAA-TAAGTAATAATA
25819 TAAAATAAGTAATAAT
1 TAAAATAAGTAATAAT
25835 TATTTTATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
TAAAATAAGTAATAATA
Found at i:27612 original size:33 final size:34
Alignment explanation
Indices: 27570--27643 Score: 123
Period size: 33 Copynumber: 2.2 Consensus size: 34
27560 ACATAAAGAA
27570 AAAAAAAGTTAACTACAACAATAAGCAAATG-AC
1 AAAAAAAGTTAACTACAACAATAAGCAAATGAAC
* *
27603 AAAAAAAGTTTACTACAACAATAAGCAAATGAAG
1 AAAAAAAGTTAACTACAACAATAAGCAAATGAAC
27637 AAAAAAA
1 AAAAAAA
27644 CACATGTTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 30 0.79
34 8 0.21
ACGTcount: A:0.64, C:0.12, G:0.09, T:0.15
Consensus pattern (34 bp):
AAAAAAAGTTAACTACAACAATAAGCAAATGAAC
Found at i:31217 original size:17 final size:18
Alignment explanation
Indices: 31186--31223 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
31176 TCTGGTTAAG
*
31186 AAAACTAAATTTATACAT
1 AAAACTAAATATATACAT
31204 AAAA-TAAATATATACAT
1 AAAACTAAATATATACAT
31221 AAA
1 AAA
31224 GCAAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAACTAAATATATACAT
Found at i:45710 original size:19 final size:20
Alignment explanation
Indices: 45686--45732 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
45676 CACCGATCGA
45686 GATACCAAGG-CATGGTATC
1 GATACCAAGGCCATGGTATC
45705 GATACCAAGGCCATGGTATC
1 GATACCAAGGCCATGGTATC
*
45725 AATACCAA
1 GATACCAA
45733 AAAGCCTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.19
Consensus pattern (20 bp):
GATACCAAGGCCATGGTATC
Found at i:46775 original size:2 final size:2
Alignment explanation
Indices: 46770--46818 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
46760 TCCATCCATC
46770 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
46810 TA TA TA TA T
1 TA TA TA TA T
46819 CAAAAAATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 43 0.96
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:47096 original size:23 final size:22
Alignment explanation
Indices: 47066--47108 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
47056 TTGGTGCTGG
47066 AAACAAGATAAAAAATAAGATTA
1 AAACAAGATAAAAAA-AAGATTA
*
47089 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAAAAAAGAT
47109 AAGAATTGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.70, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAAAAAAGATTA
Done.