Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000706.1 Hibiscus syriacus cultivar Beakdansim tig00001372_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: 103608
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:2034 original size:13 final size:13
Alignment explanation
Indices: 2016--2049 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
2006 GTTTAAAACA
2016 AAATATAATTCCT
1 AAATATAATTCCT
2029 AAATATAATTCCT
1 AAATATAATTCCT
*
2042 AAAAATAA
1 AAATATAA
2050 AAAAAAAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATATAATTCCT
Found at i:2145 original size:23 final size:23
Alignment explanation
Indices: 2119--2164 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
2109 TGATTGAATC
*
2119 TTTTAGAAGCTGCTGACTGGGCA
1 TTTTAGAAACTGCTGACTGGGCA
*
2142 TTTTAGAAACTGTTGACTGGGCA
1 TTTTAGAAACTGCTGACTGGGCA
2165 CCACATCAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (23 bp):
TTTTAGAAACTGCTGACTGGGCA
Found at i:10598 original size:22 final size:22
Alignment explanation
Indices: 10573--10622 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 22
10563 GGGGTTTTGG
10573 TAAAAAGAT-ATTTAAA-TAATAA
1 TAAAAA-ATGATTTAAAGTAA-AA
10595 T-AAAAATGATTTAAAGTAAAA
1 TAAAAAATGATTTAAAGTAAAA
10616 TAAAAAA
1 TAAAAAA
10623 AATTAAAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 2 0.08
21 14 0.56
22 9 0.36
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (22 bp):
TAAAAAATGATTTAAAGTAAAA
Found at i:10606 original size:21 final size:21
Alignment explanation
Indices: 10582--10621 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
10572 GTAAAAAGAT
10582 ATTTAAA-TAATAATAAAAATG
1 ATTTAAAGTAA-AATAAAAATG
10603 ATTTAAAGTAAAATAAAAA
1 ATTTAAAGTAAAATAAAAA
10622 AAATTAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (21 bp):
ATTTAAAGTAAAATAAAAATG
Found at i:18122 original size:52 final size:53
Alignment explanation
Indices: 18042--18232 Score: 296
Period size: 53 Copynumber: 3.6 Consensus size: 53
18032 ATGAGGGATC
* * * **
18042 TGCTTCAGGGAGTATAACTCGAATAATCTTCT-ACTTACGGGTTCGGTCCCTCT
1 TGCTTCAGGGAGTAGAACTCGAACAATCTTCTGTC-TACGGGTTCACTCCCTCT
18095 TGCTTCAGGG-GTAGAACTCGAACAATCTTCTGTCTACGGGTTCACTCCCTCT
1 TGCTTCAGGGAGTAGAACTCGAACAATCTTCTGTCTACGGGTTCACTCCCTCT
*
18147 TGCTTCAGGGAGTAGAACTCGAACAATCTTCTGTCTATGGGTTCACTCCCTCT
1 TGCTTCAGGGAGTAGAACTCGAACAATCTTCTGTCTACGGGTTCACTCCCTCT
*
18200 TGCTTCAGGGAGTAGAACTTGAACAATCTTCTG
1 TGCTTCAGGGAGTAGAACTCGAACAATCTTCTG
18233 GTGTGATTCT
Statistics
Matches: 129, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
52 45 0.35
53 84 0.65
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.32
Consensus pattern (53 bp):
TGCTTCAGGGAGTAGAACTCGAACAATCTTCTGTCTACGGGTTCACTCCCTCT
Found at i:18763 original size:42 final size:42
Alignment explanation
Indices: 18717--18923 Score: 292
Period size: 42 Copynumber: 4.9 Consensus size: 42
18707 AAATGACCCG
18717 AATGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCA
1 AATGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCA
*
18759 AATGATTTAATCATCATGCTCGAAAGACTTACTGATGACCCGA
1 AATGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCC-A
* * *
18802 AA-GACTTCATCATCATGCTCGAAAGACTTACTGATGGCCCG
1 AATGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCA
* ** * * *
18843 AAGGGCTTCATCGTCATGCTCGAAAGACTTACTGA-GGACCCG
1 AATGATTTAATCATCATGCTCGAAAGACTTACTGATGG-CCCA
18885 AATGATTTAATCATCATGCTCGAAAGACTTACTGATGGC
1 AATGATTTAATCATCATGCTCGAAAGACTTACTGATGGC
18924 ACTTACTGAT
Statistics
Matches: 149, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
41 4 0.03
42 140 0.94
43 5 0.03
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (42 bp):
AATGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCA
Found at i:18787 original size:84 final size:84
Alignment explanation
Indices: 18691--19055 Score: 358
Period size: 84 Copynumber: 4.2 Consensus size: 84
18681 TTTATTATCT
* ***
18691 TGCTCGAAAGACTCAAAAATGACCCGAATGATTTAATCATCATGCTCGAAAGACTTACTGATGGC
1 TGCTCGAAAGACTTACTGATGACCCGAATGATTTAATCATCATGCTCGAAAGACTTACTGATGGC
* *
18756 CCAAATGATTTAATCATCA
66 CCAAAGGACTTAATCATCA
* * *
18775 TGCTCGAAAGACTTACTGATGACCCGAAAGACTTCATCATCATGCTCGAAAGACTTACTGATGGC
1 TGCTCGAAAGACTTACTGATGACCCGAATGATTTAATCATCATGCTCGAAAGACTTACTGATGGC
* * * *
18840 CCGAAGGGCTTCATCGTCA
66 CCAAAGGACTTAATCATCA
*
18859 TGCTCGAAAGACTTACTGAGGACCCGAATGATTTAATCATCATGCTCGAAAGACTTACTGATGGC
1 TGCTCGAAAGACTTACTGATGACCCGAATGATTTAATCATCATGCTCGAAAGACTTACTGATGGC
* * * **
18924 ACTTACTGATGGATTTTCTTCATTACTA
66 -C---C-AAAGGA-CTTAATCA-T-C-A
* * ** * *
18952 TTTGGT-G-AAGGCTTACAAATTACCTGAATGATTTAATCATCATGCTCGAAAGACTTACT-ATG
1 --TGCTCGAAAGACTTACTGATGACCCGAATGATTTAATCATCATGCTCGAAAGACTTACTGATG
** *
19014 GCCTGAAGGACTTCATCATCA
64 GCCCAAAGGACTTAATCATCA
19035 TGCTCGAAAGACTTACTGATG
1 TGCTCGAAAGACTTACTGATG
19056 GCACTTACTG
Statistics
Matches: 230, Mismatches: 38, Indels: 27
0.78 0.13 0.09
Matches are distributed among these distances:
81 3 0.01
82 1 0.00
83 11 0.05
84 133 0.58
85 2 0.01
86 6 0.03
87 5 0.02
88 1 0.00
89 4 0.02
90 5 0.02
91 2 0.01
92 6 0.03
93 47 0.20
94 1 0.00
95 3 0.01
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (84 bp):
TGCTCGAAAGACTTACTGATGACCCGAATGATTTAATCATCATGCTCGAAAGACTTACTGATGGC
CCAAAGGACTTAATCATCA
Found at i:18804 original size:20 final size:19
Alignment explanation
Indices: 18732--18921 Score: 85
Period size: 20 Copynumber: 9.2 Consensus size: 19
18722 TTTAATCATC
*
18732 ATGCTCGAAAGACTTACTG
1 ATGCCCGAAAGACTTACTG
* *
18751 ATGGCCC-AAATGATTTAATCATC
1 AT-GCCCGAAA-GACTT-A-C-TG
*
18774 ATGCTCGAAAGACTTACTG
1 ATGCCCGAAAGACTTACTG
*
18793 ATGACCCGAAAGACTTCATCATC
1 ATG-CCCGAAAGACTT-A-C-TG
*
18816 ATGCTCGAAAGACTTACTG
1 ATGCCCGAAAGACTTACTG
* * *
18835 ATGGCCCGAAGGGCTTCATCGTC
1 AT-GCCCGAAAGACTT-A-C-TG
*
18858 ATGCTCGAAAGACTTACTG
1 ATGCCCGAAAGACTTACTG
* * * *
18877 AGGACCCGAATGATTTAATCATC
1 ATG-CCCGAAAGACTT-A-C-TG
*
18900 ATGCTCGAAAGACTTACTG
1 ATGCCCGAAAGACTTACTG
18919 ATG
1 ATG
18922 GCACTTACTG
Statistics
Matches: 125, Mismatches: 28, Indels: 36
0.66 0.15 0.19
Matches are distributed among these distances:
19 19 0.15
20 41 0.33
21 8 0.06
22 41 0.33
23 16 0.13
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (19 bp):
ATGCCCGAAAGACTTACTG
Found at i:18929 original size:13 final size:13
Alignment explanation
Indices: 18911--18935 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18901 TGCTCGAAAG
18911 ACTTACTGATGGC
1 ACTTACTGATGGC
18924 ACTTACTGATGG
1 ACTTACTGATGG
18936 ATTTTCTTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (13 bp):
ACTTACTGATGGC
Found at i:19058 original size:134 final size:135
Alignment explanation
Indices: 18856--19184 Score: 439
Period size: 134 Copynumber: 2.4 Consensus size: 135
18846 GGCTTCATCG
* * *
18856 TCATGCTCGAAAGACTTACTGA-GGACCCGAATGATTTAATCATCATGCTCGAAAGACTTACTGA
1 TCATGCTCGAAAGACTTACTGATGG-CCTGAAGGATTTCATCATCATGCTCGAAAGACTTACTGA
* * * * *
18920 TGGCACTTACTGATGGATTTTCTTCATTACTATTTGGTGAAGGCTTACAAATTACCTGAATGATT
65 TGGCACTTACTGATGGATTTGCTTCACTACTATTCGGTGAAGGCTTACAAATTACCTGAAAGACT
18985 TAATCA
130 TAATCA
*
18991 TCATGCTCGAAAGACTTACT-ATGGCCTGAAGGACTTCATCATCATGCTCGAAAGACTTACTGAT
1 TCATGCTCGAAAGACTTACTGATGGCCTGAAGGATTTCATCATCATGCTCGAAAGACTTACTGAT
* * * *
19055 GGCACTTACTGATGGGTTTGCTTCACTACTCTTCGGTGAAGGCTTATAAATTTCCTGAAAGACTT
66 GGCACTTACTGATGGATTTGCTTCACTACTATTCGGTGAAGGCTTACAAATTACCTGAAAGACTT
19120 AATCA
131 AATCA
* ** * * * *
19125 TCATGATCGAAATCCTTACTGATGG-ATCAAAGGATTTCATCATCATGATCAAAAGACTTA
1 TCATGCTCGAAAGACTTACTGATGGCCT-GAAGGATTTCATCATCATGCTCGAAAGACTTA
19185 TTAAGTGCGA
Statistics
Matches: 170, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
134 116 0.68
135 54 0.32
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (135 bp):
TCATGCTCGAAAGACTTACTGATGGCCTGAAGGATTTCATCATCATGCTCGAAAGACTTACTGAT
GGCACTTACTGATGGATTTGCTTCACTACTATTCGGTGAAGGCTTACAAATTACCTGAAAGACTT
AATCA
Found at i:19063 original size:13 final size:13
Alignment explanation
Indices: 19045--19069 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19035 TGCTCGAAAG
19045 ACTTACTGATGGC
1 ACTTACTGATGGC
19058 ACTTACTGATGG
1 ACTTACTGATGG
19070 GTTTGCTTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (13 bp):
ACTTACTGATGGC
Found at i:23615 original size:6 final size:6
Alignment explanation
Indices: 23604--23642 Score: 60
Period size: 6 Copynumber: 6.3 Consensus size: 6
23594 AAATACATAT
*
23604 AATGCA AATGCA AATGCA AATGTCA AATGCA AATACA AA
1 AATGCA AATGCA AATGCA AATG-CA AATGCA AATGCA AA
23643 AGGTGTCATT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.54, C:0.15, G:0.13, T:0.18
Consensus pattern (6 bp):
AATGCA
Found at i:23630 original size:19 final size:18
Alignment explanation
Indices: 23604--23642 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
23594 AAATACATAT
*
23604 AATGCAAATGCAAATGCA
1 AATGCAAATGCAAATACA
23622 AATGTCAAATGCAAATACA
1 AATG-CAAATGCAAATACA
23641 AA
1 AA
23643 AGGTGTCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.54, C:0.15, G:0.13, T:0.18
Consensus pattern (18 bp):
AATGCAAATGCAAATACA
Found at i:33520 original size:146 final size:144
Alignment explanation
Indices: 33248--33635 Score: 485
Period size: 146 Copynumber: 2.6 Consensus size: 144
33238 TATATCACTG
* * * *
33248 AAGTTGTTGGTATTTTTTGGCATGG-GCAATATTAATGGCATTTTCTGAAGATTATTAATGGCCA
1 AAGTTGTTGGCATTTTCTGGCATGGTGCATTATTAATGGCATTTTCTAAAGATTATTAATGGCCA
** **
33312 GTTATTGGGAGTTTCGGGCTGAAGCATTATTAGACATTACATTTCACTGAAAAGTTACTGAAGAT
66 -TT-TTGACA-TTTCGGGCTGAAGC-TTATTAGACACAACATTTCACTGAAAAGTTACTGAAGAT
*
33377 GATT-AATGGGGCACTGAA
127 AATTGAA-GGGGCACTGAA
*
33395 AATTTGTTGGCATTTTCTGGCATGGTGCATTATTAATGGCATTTTCTAAAGATTATTAATGGCCC
1 AAGTTGTTGGCATTTTCTGGCATGGTGCATTATTAATGGCATTTTCTAAAGATTATTAATGG-CC
* * *
33460 ATTTTGACATTTCGGGATGAAGCTTTATTAGACACAACATTTCATTGAAAAG-TAGTTGAAGATA
65 ATTTTGACATTTCGGGCTGAAGC-TTATTAGACACAACATTTCACTGAAAAGTTA-CTGAAGATA
*
33524 ATTGAAGGGGCATTGAA
128 ATTGAAGGGGCACTGAA
* * * *
33541 AAGTTGCTAGCATTTTCTAGCATGGTGCATTATTAATGGCATTTTATAAAGATTATTAATGGTCC
1 AAGTTGTTGGCATTTTCTGGCATGGTGCATTATTAATGGCATTTTCTAAAGATTATTAATGG-CC
* *
33606 GTTTTGACATCTTCGAGCTGAAGCTTATTA
65 ATTTTGACAT-TTCGGGCTGAAGCTTATTA
33636 AATTAGCTTA
Statistics
Matches: 212, Mismatches: 24, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
145 2 0.01
146 132 0.62
147 39 0.18
148 36 0.17
149 3 0.01
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (144 bp):
AAGTTGTTGGCATTTTCTGGCATGGTGCATTATTAATGGCATTTTCTAAAGATTATTAATGGCCA
TTTTGACATTTCGGGCTGAAGCTTATTAGACACAACATTTCACTGAAAAGTTACTGAAGATAATT
GAAGGGGCACTGAA
Found at i:35496 original size:31 final size:31
Alignment explanation
Indices: 35458--35611 Score: 256
Period size: 31 Copynumber: 5.0 Consensus size: 31
35448 CCCGAAGGAC
* *
35458 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
35489 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
35520 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
35551 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
35582 CAGTCCATATGTTCCGAAGAACATAGGTAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAA
35612 CCCTCGACCC
Statistics
Matches: 116, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:35816 original size:23 final size:24
Alignment explanation
Indices: 35790--35836 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
35780 ATATACTTGT
*
35790 TTTCACATATATA-TTTCATATCA
1 TTTCACATATACACTTTCATATCA
35813 TTTCACATATACACTTTCATATCA
1 TTTCACATATACACTTTCATATCA
35837 CATGCCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTCACATATACACTTTCATATCA
Found at i:36381 original size:21 final size:21
Alignment explanation
Indices: 36355--36400 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
36345 AATTCTGTCG
* *
36355 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
36376 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
36397 CTTG
1 CTTG
36401 CCCAGAACTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.15, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:38402 original size:28 final size:28
Alignment explanation
Indices: 38370--38435 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
38360 ATCAATAAGA
38370 ATATATTTAACTAAAATCAAATTCATAC
1 ATATATTTAACTAAAATCAAATTCATAC
* *
38398 ATATATTTAACTAAACTTAAATTCATAC
1 ATATATTTAACTAAAATCAAATTCATAC
38426 ATATATTTAA
1 ATATATTTAA
38436 AACATTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (28 bp):
ATATATTTAACTAAAATCAAATTCATAC
Found at i:48414 original size:11 final size:11
Alignment explanation
Indices: 48400--48428 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
48390 ATAGGCCTTT
48400 AATATCTTCGG
1 AATATCTTCGG
48411 AATATCTTCGG
1 AATATCTTCGG
48422 AATATCT
1 AATATCT
48429 CTCTCAATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (11 bp):
AATATCTTCGG
Found at i:49012 original size:185 final size:185
Alignment explanation
Indices: 48691--49081 Score: 617
Period size: 185 Copynumber: 2.1 Consensus size: 185
48681 ATTAAATTTT
* * *
48691 AAATTTTAAATATATTATATATAACATATGGGCTTAGCCTAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
*
48756 TTTAAGATCTAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTATATAAATTTTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTATATAAA-TTTT
**
48821 TTATTTTATAATTATATATTATTTAAATTAATTGTAAAC-TGGTTTTTTAATTAAA
130 TTATTTTATAATTATATATTATTTAAATTAATCATAAACTTGGTTTTTTAATTAAA
*
48876 AAATATTATATATATTATATATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
*
48941 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATCTGAAA-TT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAA-TTATAT-AAATTT
**
49005 TTTATTTTATAATTATATATTATTTAAATTAATCATAAACTTTTTTTTTTAATTAAA
129 TTTATTTTATAATTATATATTATTTAAATTAATCATAAACTTGGTTTTTTAATTAAA
* * *
49062 AAACATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
49082 AATTAGAAAA
Statistics
Matches: 189, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
185 159 0.84
186 27 0.14
187 3 0.02
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.43
Consensus pattern (185 bp):
AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTATATAAATTTTT
TATTTTATAATTATATATTATTTAAATTAATCATAAACTTGGTTTTTTAATTAAA
Found at i:49229 original size:15 final size:14
Alignment explanation
Indices: 49209--49241 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
49199 AAAAAAGTTT
49209 GGTTAATTCGGTTAC
1 GGTTAATTCGGTT-C
49224 GGTTAATTCGGTTC
1 GGTTAATTCGGTTC
49238 GGTT
1 GGTT
49242 CGGTTTTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.15, C:0.12, G:0.30, T:0.42
Consensus pattern (14 bp):
GGTTAATTCGGTTC
Found at i:55409 original size:19 final size:19
Alignment explanation
Indices: 55382--55430 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
55372 ATCGAAATAG
* *
55382 GGTATCGATACCATGAAAT
1 GGTACCGATACCATCAAAT
*
55401 GGTACCGATACCATCAGAT
1 GGTACCGATACCATCAAAT
55420 GGTACCGATAC
1 GGTACCGATAC
55431 TACTATATAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (19 bp):
GGTACCGATACCATCAAAT
Found at i:58156 original size:23 final size:22
Alignment explanation
Indices: 58113--58174 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
58103 TCGAAGAAAA
*
58113 AAAAAGAAAAAACAACAGTTCG
1 AAAAAGAAAAAAAAACAGTTCG
*
58135 AAAAAGAAAAAAAAAGATGTTCG
1 AAAAAGAAAAAAAAACA-GTTCG
*
58158 AGAAAAAAAAGAAAAAA
1 A-AAAAGAAA-AAAAAA
58175 TACATGAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 15 0.44
23 6 0.18
24 7 0.21
25 6 0.18
ACGTcount: A:0.71, C:0.06, G:0.15, T:0.08
Consensus pattern (22 bp):
AAAAAGAAAAAAAAACAGTTCG
Found at i:66942 original size:24 final size:24
Alignment explanation
Indices: 66909--66954 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
66899 AAATGAGACA
* *
66909 CATACTTAACTCTCACCTAACTTT
1 CATACCTAACTCTAACCTAACTTT
*
66933 CATACCTAACTTTAACCTAACT
1 CATACCTAACTCTAACCTAACT
66955 AATTTGATGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.35
Consensus pattern (24 bp):
CATACCTAACTCTAACCTAACTTT
Found at i:66952 original size:11 final size:13
Alignment explanation
Indices: 66923--66954 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
66913 CTTAACTCTC
66923 ACCTAACTTTCAT
1 ACCTAACTTTCAT
66936 ACCTAACTTT-A-
1 ACCTAACTTTCAT
66947 ACCTAACT
1 ACCTAACT
66955 AATTTGATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 1 0.05
13 10 0.53
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (13 bp):
ACCTAACTTTCAT
Found at i:70402 original size:24 final size:24
Alignment explanation
Indices: 70369--70426 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
70359 ATTGTTGTAA
*
70369 TTCCAGCCTCATCCACGATTGTGAC
1 TTCCA-CCTCATCCACGATTGCGAC
* * *
70394 TTCCACCTCGTCTATGATTGCGAC
1 TTCCACCTCATCCACGATTGCGAC
70418 TTCCACCTC
1 TTCCACCTC
70427 GTTTATGGCT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 24 0.83
25 5 0.17
ACGTcount: A:0.17, C:0.38, G:0.14, T:0.31
Consensus pattern (24 bp):
TTCCACCTCATCCACGATTGCGAC
Found at i:70427 original size:24 final size:24
Alignment explanation
Indices: 70385--70433 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
70375 CCTCATCCAC
*
70385 GATTGTGACTTCCACCTCGTCTAT
1 GATTGCGACTTCCACCTCGTCTAT
*
70409 GATTGCGACTTCCACCTCGTTTAT
1 GATTGCGACTTCCACCTCGTCTAT
70433 G
1 G
70434 GCTTTACCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.16, C:0.29, G:0.18, T:0.37
Consensus pattern (24 bp):
GATTGCGACTTCCACCTCGTCTAT
Found at i:82570 original size:43 final size:42
Alignment explanation
Indices: 82523--82720 Score: 177
Period size: 42 Copynumber: 4.7 Consensus size: 42
82513 AATAGGTGTG
*
82523 GACATTTAGCGGCGTTTTTTGTATAAACGCCGCAACTGATTAT
1 GACATTTAGCGGC-TTTTTTGTATAAACGCCGCAACAGATTAT
* * * *
82566 GACATTTAGCGACTTTTTTTGTTTAAATGCAGCAACAGATTAT
1 GACATTTAGCGGC-TTTTTTGTATAAACGCCGCAACAGATTAT
* * * *
82609 GACATTTAGCGGCATTTTTGTTTAAACGTCGCAATA-AGTTAT
1 GACATTTAGCGGCTTTTTTGTATAAACGCCGCAACAGA-TTAT
* ** * *
82651 GATATTTAGCAACTTGTTTGTATAAACGCCG-AACCAGGTTAT
1 GACATTTAGCGGCTTTTTTGTATAAACGCCGCAA-CAGATTAT
* * *
82693 GATATTTAGTGG-TGTTTTTATATAAACG
1 GACATTTAGCGGCT-TTTTTGTATAAACG
82721 GCAAATGTGT
Statistics
Matches: 125, Mismatches: 26, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
41 4 0.03
42 72 0.58
43 49 0.39
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (42 bp):
GACATTTAGCGGCTTTTTTGTATAAACGCCGCAACAGATTAT
Found at i:82651 original size:42 final size:42
Alignment explanation
Indices: 82523--82660 Score: 138
Period size: 43 Copynumber: 3.2 Consensus size: 42
82513 AATAGGTGTG
* *
82523 GACATTTAGCGGCGTTTTTTGTATAAACGCCGCAACTGA-TTAT
1 GACATTTAGCGGCGTTTTTTGTTTAAACG-CGCAA-TAAGTTAT
* * * *
82566 GACATTTAGCGACTTTTTTTGTTTAAATGCAGCAA-CAGATTAT
1 GACATTTAGCGGCGTTTTTTGTTTAAACGC-GCAATAAG-TTAT
*
82609 GACATTTAGCGGC-ATTTTTGTTTAAACGTCGCAATAAGTTAT
1 GACATTTAGCGGCGTTTTTTGTTTAAACG-CGCAATAAGTTAT
*
82651 GATATTTAGC
1 GACATTTAGC
82661 AACTTGTTTG
Statistics
Matches: 80, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
41 1 0.01
42 31 0.39
43 48 0.60
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (42 bp):
GACATTTAGCGGCGTTTTTTGTTTAAACGCGCAATAAGTTAT
Found at i:82939 original size:27 final size:27
Alignment explanation
Indices: 82903--82971 Score: 104
Period size: 27 Copynumber: 2.6 Consensus size: 27
82893 AACCATTCAA
*
82903 GTAATGTAGTTCAACATTAAGTCAAAT
1 GTAATATAGTTCAACATTAAGTCAAAT
*
82930 GTAATATAGTTCAACATTAAGTGAAAT
1 GTAATATAGTTCAACATTAAGTCAAAT
*
82957 GT-ACATAGTTCAACA
1 GTAATATAGTTCAACA
82972 ACTATAATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
26 12 0.31
27 27 0.69
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (27 bp):
GTAATATAGTTCAACATTAAGTCAAAT
Found at i:85250 original size:12 final size:12
Alignment explanation
Indices: 85220--85254 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
85210 ATCTTTTTAT
85220 TTATCTTGTTT-
1 TTATCTTGTTTC
*
85231 TAATCTTGTTTC
1 TTATCTTGTTTC
85243 TTATCTTGTTTC
1 TTATCTTGTTTC
85255 CAGCACACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.11, C:0.14, G:0.09, T:0.66
Consensus pattern (12 bp):
TTATCTTGTTTC
Found at i:89072 original size:2 final size:2
Alignment explanation
Indices: 89065--89101 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
89055 CCAAACGCCC
89065 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
89102 GGGTAGCGTA
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:89585 original size:13 final size:13
Alignment explanation
Indices: 89567--89604 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
89557 ATAGATAAGT
89567 CTAACTAACTAGC
1 CTAACTAACTAGC
89580 CTAACTAACTAGC
1 CTAACTAACTAGC
* *
89593 CCAACTGACTAG
1 CTAACTAACTAG
89605 AAATTGGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.37, C:0.32, G:0.11, T:0.21
Consensus pattern (13 bp):
CTAACTAACTAGC
Found at i:91433 original size:15 final size:15
Alignment explanation
Indices: 91413--91451 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
91403 AAGGTGGAGG
*
91413 TGGAGGTGGTAATGA
1 TGGAGGTGGTAAGGA
91428 TGGAGGTGGTAAGGA
1 TGGAGGTGGTAAGGA
91443 TGGAGGTGG
1 TGGAGGTGG
91452 AGATGGTGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.23, C:0.00, G:0.54, T:0.23
Consensus pattern (15 bp):
TGGAGGTGGTAAGGA
Found at i:91452 original size:21 final size:21
Alignment explanation
Indices: 91398--91458 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
91388 GTGGTGGTTA
91398 TGGTAAAGG-TGGAGGTGGAGG
1 TGGT-AAGGATGGAGGTGGAGG
91419 TGGT-A--AT-GA--TGGAGG
1 TGGTAAGGATGGAGGTGGAGG
*
91434 TGGTAAGGATGGAGGTGGAGA
1 TGGTAAGGATGGAGGTGGAGG
91455 TGGT
1 TGGT
91459 GATAGAGATG
Statistics
Matches: 32, Mismatches: 1, Indels: 14
0.68 0.02 0.30
Matches are distributed among these distances:
15 10 0.31
16 1 0.03
17 2 0.06
18 3 0.09
19 3 0.09
21 13 0.41
ACGTcount: A:0.25, C:0.00, G:0.52, T:0.23
Consensus pattern (21 bp):
TGGTAAGGATGGAGGTGGAGG
Found at i:94544 original size:44 final size:44
Alignment explanation
Indices: 94471--94595 Score: 144
Period size: 44 Copynumber: 2.8 Consensus size: 44
94461 AAAGGAACAA
**
94471 CAAAGACGCAGTATGCCAGAACAACCGAGAACAGTAAATGCAAAC
1 CAAAGA-GCAGTATGCCAGAACAACCGAGAACAGTAAACACAAAC
* * ** *
94516 CAAAGAGCAGTATGCCAGACCAATCGAGAACAAAAAACACAAAT
1 CAAAGAGCAGTATGCCAGAACAACCGAGAACAGTAAACACAAAC
** *
94560 C-AAGAGCAGTATGCCAGATTAACCAAGAACAGTAAA
1 CAAAGAGCAGTATGCCAGAACAACCGAGAACAGTAAA
94596 GGAGCAATCT
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
43 29 0.43
44 32 0.48
45 6 0.09
ACGTcount: A:0.49, C:0.22, G:0.18, T:0.10
Consensus pattern (44 bp):
CAAAGAGCAGTATGCCAGAACAACCGAGAACAGTAAACACAAAC
Done.