Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005257.1 Hibiscus syriacus cultivar Beakdansim tig00011894_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: 82813
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:3510 original size:21 final size:20
Alignment explanation
Indices: 3482--3525 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
3472 GAGTAACACC
3482 TTTTCATACATGCATTTGCA
1 TTTTCATACATGCATTTGCA
** *
3502 TTTTGCATATTTGCATTTTCA
1 TTTT-CATACATGCATTTGCA
3523 TTT
1 TTT
3526 ATACTTTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.20, C:0.16, G:0.09, T:0.55
Consensus pattern (20 bp):
TTTTCATACATGCATTTGCA
Found at i:6370 original size:17 final size:15
Alignment explanation
Indices: 6341--6389 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 15
6331 ATTATACTTG
6341 AAGAAGAGAAAAAAAA
1 AAGAAG-GAAAAAAAA
6357 AAGAAAAGGAAAAAAAGA
1 AAG--AAGGAAAAAAA-A
*
6375 ATGAAGGAAAAAAAA
1 AAGAAGGAAAAAAAA
6390 TTGAATCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 1 0.03
16 14 0.48
17 8 0.28
18 6 0.21
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (15 bp):
AAGAAGGAAAAAAAA
Found at i:6395 original size:19 final size:16
Alignment explanation
Indices: 6352--6388 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
6342 AGAAGAGAAA
6352 AAAAAAAGAA--AAGG
1 AAAAAAAGAATGAAGG
6366 AAAAAAAGAATGAAGG
1 AAAAAAAGAATGAAGG
6382 AAAAAAA
1 AAAAAAA
6389 ATTGAATCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 10 0.48
16 11 0.52
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (16 bp):
AAAAAAAGAATGAAGG
Found at i:6886 original size:32 final size:32
Alignment explanation
Indices: 6845--6905 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
6835 TCTGGAAATA
* *
6845 AGAAGTATCTCTACGAGATGAGCATAACAATG
1 AGAAGTATCTCTACCAGATAAGCATAACAATG
6877 AGAAGTATCTCTACCAGATAAGCATAACA
1 AGAAGTATCTCTACCAGATAAGCATAACA
6906 TCATTTCTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.21
Consensus pattern (32 bp):
AGAAGTATCTCTACCAGATAAGCATAACAATG
Found at i:9536 original size:74 final size:75
Alignment explanation
Indices: 9383--9552 Score: 209
Period size: 74 Copynumber: 2.3 Consensus size: 75
9373 TAACAAAAAG
* *
9383 CAAATGATGGGGCATGCTGAAAGCCCATTTCAATCAAAATCAAGAATGTTGACTCATTTTGAACA
1 CAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAAAATCAAGAATGTTGACTCATTTGGAACA
* *
9448 TTTGTATCAG
66 TCTGTATCAA
* * * * *
9458 CAAATGTTGGGGCATGCTGAAAGCCC-TTTTAATTAGAATCAGGAATGTTG-GTGCATTTGGAAC
1 CAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAAAATCAAGAATGTTGACT-CATTTGGAAC
*
9521 GTCTGTATCAA
65 ATCTGTATCAA
* *
9532 CAAATGTTAGGGCATGTTGAA
1 CAAATGTTGGGGCATGCTGAA
9553 GACCCATATA
Statistics
Matches: 82, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
73 1 0.01
74 56 0.68
75 25 0.30
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (75 bp):
CAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAAAATCAAGAATGTTGACTCATTTGGAACA
TCTGTATCAA
Found at i:10543 original size:55 final size:52
Alignment explanation
Indices: 10423--10585 Score: 184
Period size: 55 Copynumber: 3.0 Consensus size: 52
10413 TTGATCAGAA
* *
10423 ATCTGTGCAGAAACCACAGAAAATGATGAATGTGTTGTCAAATGCTTTACAAAC
1 ATCT-TGCAGAAACCACAG-AAATGATGAATGTGTTGTCAAATGTTTTACGAAC
* * * *
10477 AT-TTGGCCAGAAGCCACAAGAAAGGATGAATGTGTTATCTAATGTTTTTACGAAC
1 ATCTT-G-CAGAAACCAC-AGAAATGATGAATGTGTTGTCAAATG-TTTTACGAAC
*
10532 ATCTATGCAGAAACCACGAGAAATGATGAATGTATTGTCAAATGTTTTACGAAC
1 ATCT-TGCAGAAACCAC-AGAAATGATGAATGTGTTGTCAAATGTTTTACGAAC
10586 CAGTGATTAT
Statistics
Matches: 91, Mismatches: 12, Indels: 12
0.79 0.10 0.10
Matches are distributed among these distances:
52 1 0.01
53 2 0.02
54 42 0.46
55 43 0.47
56 2 0.02
57 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (52 bp):
ATCTTGCAGAAACCACAGAAATGATGAATGTGTTGTCAAATGTTTTACGAAC
Found at i:10982 original size:22 final size:22
Alignment explanation
Indices: 10951--11008 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
10941 CTACATCTAT
10951 ACTCTTCAAAGATGATAAATTC
1 ACTCTTCAAAGATGATAAATTC
* * *
10973 ACTCTCCAAAGATAATAGATTC
1 ACTCTTCAAAGATGATAAATTC
*
10995 TCT-TTCAAAGATGA
1 ACTCTTCAAAGATGA
11009 AAGCTTTATT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 9 0.30
22 21 0.70
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (22 bp):
ACTCTTCAAAGATGATAAATTC
Found at i:11792 original size:45 final size:45
Alignment explanation
Indices: 11743--11889 Score: 258
Period size: 45 Copynumber: 3.3 Consensus size: 45
11733 AAGCTTTTTA
*
11743 ATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCAGG
1 ATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCAGG
* *
11788 ATGTTTTCAAAACCTTCGGGTTATCTGTAAGCCCTTCAGTGCATG
1 ATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCAGG
*
11833 ATGTTTTCAAAACCATCGGGTCATCTGTAAGCCCTTCAGTGCAGG
1 ATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCAGG
11878 ATGTTTTCAAAA
1 ATGTTTTCAAAA
11890 AACCTTCAGG
Statistics
Matches: 96, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 96 1.00
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (45 bp):
ATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCAGG
Found at i:11960 original size:45 final size:45
Alignment explanation
Indices: 11907--12777 Score: 1215
Period size: 45 Copynumber: 19.3 Consensus size: 45
11897 AGGAGCTTTT
* *
11907 TGATGTTTTTAAAACTTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
11952 TGATGTTTTCAAAACCTTCGGGTCATTTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
11997 TGATGTTTTCAAAACCTTCGGGTCATTTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
12042 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
12087 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
12132 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * *
12177 TGATGTTTTCAAAACCTTTGGGTCATCTGTAAGCCCTTTAGTACA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
12222 TGATGTTTTCAAAACCTTCGGGTCATCTGTAATCCCTTTAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
12267 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGCGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
12312 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
12357 TGATGTTTTCAAAACCTTCAGGTCATCTGTAAGCCTTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
12402 TGATGTTTTCAAAATCTTCGGGTCATCTGTAAGCCCTTCAGTGCAA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGC-A
*
12448 T-ATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * * ** *
12492 TGATGCTTTCGAAACTTTCGGGTCATCTGTAAGATCTTCATTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
** * * * *
12537 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACGGTGTA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* ** * *
12582 TGATGTTTTCAAAACCTTCAGGTCATCCATAAGACCTACAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
** *
12627 TGATGTTTTCAAAACCTTCGGGTCATCCATAAG-ACTTACAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTT-CAGTGCA
* * ** *
12672 GGTTGTTTTCAAAAAGCCTTTAGGTCATCTGTAAGACCTTCAGTGCA
1 TGATGTTTTC-AAAA-CCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * * ** * ** **
12719 GGATGTTTTTAAAGTCCTTCAAGCCATCCATAAGATCTTCAGTGCA
1 TGATGTTTTCAAA-ACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
12765 TGATGTTTTCAAA
1 TGATGTTTTCAAA
12778 GGAGATTTTA
Statistics
Matches: 753, Mismatches: 66, Indels: 13
0.91 0.08 0.02
Matches are distributed among these distances:
44 4 0.01
45 671 0.89
46 45 0.06
47 30 0.04
48 3 0.00
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:12059 original size:25 final size:24
Alignment explanation
Indices: 11941--12194 Score: 71
Period size: 25 Copynumber: 11.2 Consensus size: 24
11931 ATCTGTAAGC
11941 CCTTCAGTGCATGATGTTTTCAAAA
1 CCTTCAGTGCATGAT-TTTTCAAAA
* * * **
11966 CCTTC-G-G-GTCATTTGT-AAGC
1 CCTTCAGTGCATGATTTTTCAAAA
11986 CCTTCAGTGCATGATGTTTTCAAAA
1 CCTTCAGTGCATGAT-TTTTCAAAA
* * * **
12011 CCTTC-G-G-GTCATTTGT-AAGC
1 CCTTCAGTGCATGATTTTTCAAAA
12031 CCTTCAGTGCATGATATTTTCAAAA
1 CCTTCAGTGCATGAT-TTTTCAAAA
* * * * **
12056 CCTTC-G-G-GTCATCTGT-AAGT
1 CCTTCAGTGCATGATTTTTCAAAA
12076 CCTTCAGTGCATGATGTTTTCAAAA
1 CCTTCAGTGCATGAT-TTTTCAAAA
* * * * **
12101 CCTTC-G-G-GTCATCTGT-AAGC
1 CCTTCAGTGCATGATTTTTCAAAA
12121 CCTTCAGTGCATGATGTTTTCAAAA
1 CCTTCAGTGCATGAT-TTTTCAAAA
* * * * *
12146 CCTTC-G-G-GTCATCTGT-AAGA
1 CCTTCAGTGCATGATTTTTCAAAA
12166 CCTTCAGTGCATGATGTTTTCAAAA
1 CCTTCAGTGCATGAT-TTTTCAAAA
12191 CCTT
1 CCTT
12195 TGGGTCATCT
Statistics
Matches: 150, Mismatches: 54, Indels: 50
0.59 0.21 0.20
Matches are distributed among these distances:
20 36 0.24
21 17 0.11
22 20 0.13
23 20 0.13
24 17 0.11
25 40 0.27
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (24 bp):
CCTTCAGTGCATGATTTTTCAAAA
Found at i:15770 original size:17 final size:18
Alignment explanation
Indices: 15748--15781 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
15738 TTTTTCGAAT
15748 CTTTCTTCCTTT-TTTTC
1 CTTTCTTCCTTTGTTTTC
*
15765 CTTTCTTTCTTTGTTTT
1 CTTTCTTCCTTTGTTTT
15782 TTTGTTCGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.00, C:0.24, G:0.03, T:0.74
Consensus pattern (18 bp):
CTTTCTTCCTTTGTTTTC
Found at i:25697 original size:17 final size:18
Alignment explanation
Indices: 25637--25697 Score: 56
Period size: 17 Copynumber: 3.3 Consensus size: 18
25627 TTTCATGTCT
25637 TTTTTTTTTCTTTCGAACA
1 TTTTTTTTT-TTTCGAACA
*
25656 -GTTTTTTTTTTCGAAC-
1 TTTTTTTTTTTTCGAACA
25672 TGCTATTTTTTTTTTC-AACA
1 T--T-TTTTTTTTTTCGAACA
25692 TTTTTT
1 TTTTTT
25698 GTGATGGAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
17 12 0.34
18 8 0.23
19 3 0.09
20 12 0.34
ACGTcount: A:0.15, C:0.13, G:0.07, T:0.66
Consensus pattern (18 bp):
TTTTTTTTTTTTCGAACA
Found at i:27756 original size:13 final size:13
Alignment explanation
Indices: 27738--27763 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27728 ATGGTCGAAC
27738 AAAAATAAAAATT
1 AAAAATAAAAATT
27751 AAAAATAAAAATT
1 AAAAATAAAAATT
27764 TAACGGAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AAAAATAAAAATT
Found at i:46088 original size:12 final size:12
Alignment explanation
Indices: 46071--46095 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
46061 GCATATCATA
46071 AGCTCAAACCCG
1 AGCTCAAACCCG
46083 AGCTCAAACCCG
1 AGCTCAAACCCG
46095 A
1 A
46096 TTTACCTAAG
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:0.36, C:0.40, G:0.16, T:0.08
Consensus pattern (12 bp):
AGCTCAAACCCG
Found at i:46739 original size:40 final size:40
Alignment explanation
Indices: 46695--46772 Score: 140
Period size: 40 Copynumber: 1.9 Consensus size: 40
46685 CAGTGTTCAT
46695 ACCTAGTCCGAGTACAGGCAGATGTCG-TTCAGAGACAGAG
1 ACCTAGTCCGAGTACAGGCAGATG-CGATTCAGAGACAGAG
46735 ACCTAGTCCGAGTACAGGCAGATGCGATTCAGAGACAG
1 ACCTAGTCCGAGTACAGGCAGATGCGATTCAGAGACAG
46773 CCTTGTCACT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
39 2 0.05
40 35 0.95
ACGTcount: A:0.31, C:0.23, G:0.29, T:0.17
Consensus pattern (40 bp):
ACCTAGTCCGAGTACAGGCAGATGCGATTCAGAGACAGAG
Found at i:54212 original size:20 final size:21
Alignment explanation
Indices: 54182--54258 Score: 77
Period size: 22 Copynumber: 3.7 Consensus size: 21
54172 TTTTTTGAAA
* *
54182 TTTTGGCTTTTTTTGGCTCTT
1 TTTTTGCTTTTTTTGGCTTTT
* *
54203 TTTTTGTTTTTTTTGCCGTTTT
1 TTTTTGCTTTTTTTGGC-TTTT
* *
54225 TTTTTGCCTTTTTT-GTTTTT
1 TTTTTGCTTTTTTTGGCTTTT
54245 TTTTTG-TTTTTTTG
1 TTTTTGCTTTTTTTG
54259 AAAAAAAATA
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
19 6 0.13
20 10 0.22
21 14 0.31
22 15 0.33
ACGTcount: A:0.00, C:0.09, G:0.14, T:0.77
Consensus pattern (21 bp):
TTTTTGCTTTTTTTGGCTTTT
Found at i:54217 original size:31 final size:30
Alignment explanation
Indices: 54182--54247 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 30
54172 TTTTTTGAAA
54182 TTTTG-GCTTTTTTTGGCTCTTTTTTTGTTTT
1 TTTTGCGCTTTTTTTGGC-C-TTTTTTGTTTT
* *
54213 TTTTGCCGTTTTTTTTTGCCTTTTTTGTTTT
1 TTTTG-CGCTTTTTTTGGCCTTTTTTGTTTT
54244 TTTT
1 TTTT
54248 TTGTTTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 20 0.65
32 1 0.03
33 10 0.32
ACGTcount: A:0.00, C:0.11, G:0.14, T:0.76
Consensus pattern (30 bp):
TTTTGCGCTTTTTTTGGCCTTTTTTGTTTT
Found at i:54225 original size:13 final size:12
Alignment explanation
Indices: 54189--54238 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
54179 AAATTTTGGC
* *
54189 TTTTTTTGGCTC
1 TTTTTTTGCCTT
54201 TTTTTTTG---T
1 TTTTTTTGCCTT
54210 TTTTTTTGCCGTT
1 TTTTTTTGCC-TT
54223 TTTTTTTGCCTT
1 TTTTTTTGCCTT
54235 TTTT
1 TTTT
54239 GTTTTTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
9 8 0.24
12 14 0.42
13 11 0.33
ACGTcount: A:0.00, C:0.12, G:0.12, T:0.76
Consensus pattern (12 bp):
TTTTTTTGCCTT
Found at i:58223 original size:174 final size:174
Alignment explanation
Indices: 57933--58287 Score: 624
Period size: 174 Copynumber: 2.0 Consensus size: 174
57923 CCAAAATTTA
57933 TAAATCCTTCGGGTCATCCATAAGACCTTCGGGCAGGATGTTTTCACATGAGAAAGGTTTCTAAT
1 TAAATCCTTCGGGTCATCCATAAGACCTTCGGGCAGGATGTTTTCACATGAGAAAGGTTTCTAAT
* *
57998 TTAAATATAAAATTAAATTTTTTGAAAAGTAAGAAAGGTTTCTTACCTAGTAAATTATTTCCAAA
66 TTAAATATAAAATTAAATTTTTTAAAAAGTAAGAAAGGTTTCTTACCTAGTAAACTATTTCCAAA
*
58063 ATTAAATCCTTCGGGTCATCAGTAAGTCTTCCGAGCATGATGCT
131 ATTAAATCCTTCGGGTCATCAGTAAGTCTTCCGAGCATGATGAT
* *
58107 TAAATCCTTCTGGTCATCCATAAGACCTTCGGGCAGGATGTTTTCACATGAGAAAGGTTTCTCAT
1 TAAATCCTTCGGGTCATCCATAAGACCTTCGGGCAGGATGTTTTCACATGAGAAAGGTTTCTAAT
58172 TTAAAT-TGAAAATTGAAA-TTTTTAAAAAGTAAGAAAGGTTTCTTACCTAGTAAACTATTTCCA
66 TTAAATAT-AAAATT-AAATTTTTTAAAAAGTAAGAAAGGTTTCTTACCTAGTAAACTATTTCCA
58235 AAATTAAATCCTTCGGGTCATCAGTAAGTCTTCCGAGCATGATGAT
129 AAATTAAATCCTTCGGGTCATCAGTAAGTCTTCCGAGCATGATGAT
*
58281 CAAATCC
1 TAAATCC
58288 ATCAGTAAGT
Statistics
Matches: 173, Mismatches: 6, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
173 1 0.01
174 169 0.98
175 3 0.02
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (174 bp):
TAAATCCTTCGGGTCATCCATAAGACCTTCGGGCAGGATGTTTTCACATGAGAAAGGTTTCTAAT
TTAAATATAAAATTAAATTTTTTAAAAAGTAAGAAAGGTTTCTTACCTAGTAAACTATTTCCAAA
ATTAAATCCTTCGGGTCATCAGTAAGTCTTCCGAGCATGATGAT
Found at i:58291 original size:34 final size:34
Alignment explanation
Indices: 58253--58380 Score: 202
Period size: 34 Copynumber: 3.8 Consensus size: 34
58243 TCCTTCGGGT
58253 CATCAGTAAGTCTTCCGAGCATGATGATCAAATC
1 CATCAGTAAGTCTTCCGAGCATGATGATCAAATC
58287 CATCAGTAAGTCTTCCGAGCATGATGATCAAATC
1 CATCAGTAAGTCTTCCGAGCATGATGATCAAATC
** *
58321 CATCAGTAAGTCTTATGAGTATGATGATCAAATC
1 CATCAGTAAGTCTTCCGAGCATGATGATCAAATC
* * *
58355 CATCTGTAAGTATTTCGAGCATGATG
1 CATCAGTAAGTCTTCCGAGCATGATG
58381 CTTAAATATT
Statistics
Matches: 86, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 86 1.00
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.30
Consensus pattern (34 bp):
CATCAGTAAGTCTTCCGAGCATGATGATCAAATC
Found at i:58519 original size:37 final size:37
Alignment explanation
Indices: 58475--58552 Score: 111
Period size: 37 Copynumber: 2.1 Consensus size: 37
58465 GTCCTCCGGG
**
58475 CCATTTTAAGCCTTCAATGAAGAGTAGTGAAGAAAAT
1 CCATTTTAAGCCTTCAACAAAGAGTAGTGAAGAAAAT
* * *
58512 CCATTTTAAGCCTTCACCAAAGAGTTGTGAAGCAAAT
1 CCATTTTAAGCCTTCAACAAAGAGTAGTGAAGAAAAT
58549 CCAT
1 CCAT
58553 CAGTAAGCCT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (37 bp):
CCATTTTAAGCCTTCAACAAAGAGTAGTGAAGAAAAT
Found at i:58605 original size:116 final size:116
Alignment explanation
Indices: 58396--58629 Score: 355
Period size: 116 Copynumber: 2.0 Consensus size: 116
58386 ATATTTTGGG
* * *
58396 CCATCTTAAGCTTTCACCGAAGTATAGTGAAGCAAATCCATCAGTAAGCCTTTCGAGCATGACGA
1 CCATCTTAAGCCTTCACCAAAGTATAGTGAAGCAAATCCATCAGTAAGCCTTCCGAGCATGACGA
* * *
58461 TTAAGTCCTCCGGGCCATTTTAAGCCTTCA-ATGAAGAGTAGTGAAGAAAAT
66 TGAAGTCCTCCGGGCCATCTTAAGCCTTCACA-GAAGAATAGTGAAGAAAAT
* *
58512 CCATTTTAAGCCTTCACCAAAG-AGTTGTGAAGCAAATCCATCAGTAAGCCTTCCGAGCATGACG
1 CCATCTTAAGCCTTCACCAAAGTA-TAGTGAAGCAAATCCATCAGTAAGCCTTCCGAGCATGACG
*
58576 ATGAAGTCCTCCGGGCCATCTTAAGCCTTCACAGAAGAATAGTGAAGCAAAT
65 ATGAAGTCCTCCGGGCCATCTTAAGCCTTCACAGAAGAATAGTGAAGAAAAT
58628 CC
1 CC
58630 TTCTATATGA
Statistics
Matches: 107, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
115 1 0.01
116 105 0.98
117 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (116 bp):
CCATCTTAAGCCTTCACCAAAGTATAGTGAAGCAAATCCATCAGTAAGCCTTCCGAGCATGACGA
TGAAGTCCTCCGGGCCATCTTAAGCCTTCACAGAAGAATAGTGAAGAAAAT
Found at i:58874 original size:134 final size:134
Alignment explanation
Indices: 58634--59071 Score: 696
Period size: 134 Copynumber: 3.3 Consensus size: 134
58624 AAATCCTTCT
* * * *
58634 ATATGATATTTCCTTCAGAAGAAGTGGAACAAATCACTCTTTTTCAAGATTTGATGTTCCCTGAG
1 ATATGATATTCCCTTCAGAAGAAGTGGAACAAATCATTCTCTTTCAAGATTTGATATTCCCTGAG
* * *
58699 TGACAGCGGAACAAGTCTACCATGATTCAATCTTCCCTGAGTGATAGTGGAATGGATCAACTCAT
66 TGACAGCGGAACAAGTCTACCACGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACTCAT
58764 CCAG
131 CCAG
* *
58768 ATATGATATTCCCTTCAGAAGAAGTGGAACATATCATTCTCTTTCAAGATTTGATATTCCCTTAG
1 ATATGATATTCCCTTCAGAAGAAGTGGAACAAATCATTCTCTTTCAAGATTTGATATTCCCTGAG
* *
58833 TGACAGCGGAACAAGTCTACCAGGATTCAATCTTCCCTGAGTGACAGCAGAATGGATCAACTCAT
66 TGACAGCGGAACAAGTCTACCACGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACTCAT
58898 CCAG
131 CCAG
* * *
58902 ATCTGATATTCCCTTCAGAAGAGGCGGAACAAATCATTCTCTTTCAAGATTTGATATTCCCTGAG
1 ATATGATATTCCCTTCAGAAGAAGTGGAACAAATCATTCTCTTTCAAGATTTGATATTCCCTGAG
* * *
58967 TGACAGCGAAACAAGTCTACCACGATTCAATCTTCCATGAGTGACAACGGAATGGATCAACTCAT
66 TGACAGCGGAACAAGTCTACCACGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACTCAT
59032 CCAG
131 CCAG
* * *
59036 ATCTGATATTCCATTCAGAAGAAGTGGAACAGATCA
1 ATATGATATTCCCTTCAGAAGAAGTGGAACAAATCA
59072 CTCATCCCTA
Statistics
Matches: 280, Mismatches: 24, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
134 280 1.00
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (134 bp):
ATATGATATTCCCTTCAGAAGAAGTGGAACAAATCATTCTCTTTCAAGATTTGATATTCCCTGAG
TGACAGCGGAACAAGTCTACCACGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACTCAT
CCAG
Found at i:63828 original size:2 final size:2
Alignment explanation
Indices: 63823--63883 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
63813 TATATATATA
63823 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
63865 TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG T
63884 CGGTGATATG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:78965 original size:13 final size:12
Alignment explanation
Indices: 78939--78974 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 12
78929 ATTTTAGAAC
78939 TTCATATTCATTT
1 TTCAT-TTCATTT
78952 TTCATTTCATTT
1 TTCATTTCATTT
78964 TTCACTTTCAT
1 TTCA-TTTCAT
78975 GTTCGTTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.61
Consensus pattern (12 bp):
TTCATTTCATTT
Found at i:78998 original size:13 final size:13
Alignment explanation
Indices: 78939--79000 Score: 56
Period size: 13 Copynumber: 4.9 Consensus size: 13
78929 ATTTTAGAAC
* *
78939 TTCATATTCATTT
1 TTCATTTTCATAT
*
78952 TTCA-TTTCATTT
1 TTCATTTTCATAT
* *
78964 TTCACTTTCAT-G
1 TTCATTTTCATAT
*
78976 TTCGTTTTCATAT
1 TTCATTTTCATAT
78989 TTCATTTTCATA
1 TTCATTTTCATA
79001 ACCAATATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
12 20 0.49
13 21 0.51
ACGTcount: A:0.19, C:0.18, G:0.03, T:0.60
Consensus pattern (13 bp):
TTCATTTTCATAT
Found at i:79055 original size:19 final size:19
Alignment explanation
Indices: 79033--79098 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
79023 ATTCATTCTG
79033 AGATTCATAACTT-TTTTC
1 AGATTCATAACTTATTTTC
79051 TAGATTCATAACTTATTTTC
1 -AGATTCATAACTTATTTTC
* * *
79071 ATATTCATAGCTTAATTTC
1 AGATTCATAACTTATTTTC
79090 AGATTCATA
1 AGATTCATA
79099 GCTAAACTTC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
19 37 0.88
20 5 0.12
ACGTcount: A:0.32, C:0.15, G:0.06, T:0.47
Consensus pattern (19 bp):
AGATTCATAACTTATTTTC
Found at i:79099 original size:19 final size:19
Alignment explanation
Indices: 79033--79119 Score: 86
Period size: 19 Copynumber: 4.6 Consensus size: 19
79023 ATTCATTCTG
* *
79033 AGATTCATAACTT-TTTTC
1 AGATTCATAGCTTAATTTC
* *
79051 TAGATTCATAACTTATTTTC
1 -AGATTCATAGCTTAATTTC
*
79071 ATATTCATAGCTTAATTTC
1 AGATTCATAGCTTAATTTC
* *
79090 AGATTCATAGCTAAACTTC
1 AGATTCATAGCTTAATTTC
*
79109 AAATTCATAGC
1 AGATTCATAGC
79120 CCAATGCATA
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
19 55 0.92
20 5 0.08
ACGTcount: A:0.33, C:0.17, G:0.07, T:0.43
Consensus pattern (19 bp):
AGATTCATAGCTTAATTTC
Found at i:81653 original size:27 final size:27
Alignment explanation
Indices: 81623--81684 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
81613 TGATTAACCA
81623 AATTTTTACCAGACTTTAACACTTTAT
1 AATTTTTACCAGACTTTAACACTTTAT
81650 AATTTTTACCAGACTTTAACACTTTAT
1 AATTTTTACCAGACTTTAACACTTTAT
*
81677 AGTTTTTA
1 AATTTTTA
81685 ACATAATAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.32, C:0.16, G:0.05, T:0.47
Consensus pattern (27 bp):
AATTTTTACCAGACTTTAACACTTTAT
Found at i:82245 original size:2 final size:2
Alignment explanation
Indices: 82238--82273 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
82228 ATAAATTATG
82238 AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
82274 TATTTATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.