Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001914.1 Hibiscus syriacus cultivar Beakdansim tig00003875_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: 83547
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:2023 original size:36 final size:35
Alignment explanation
Indices: 1959--2063 Score: 124
Period size: 36 Copynumber: 2.9 Consensus size: 35
1949 TGAATCCTCA
*
1959 AAGCCTTCACCGAA-G-AGTGAAGAAAATCCATCCT
1 AAGCCTTCACCGAAGGTAGTGAAG-CAATCCATCCT
* *
1993 AAGCCTTCATCGAAGGGTAGTGAAGCAATCCATCTT
1 AAGCCTTCACCGAA-GGTAGTGAAGCAATCCATCCT
*
2029 AAGCCTTCACCTAAGAGTAGTGAAGCAAATCCATC
1 AAGCCTTCACCGAAG-GTAGTGAAGC-AATCCATC
2064 AGTAAGTCTT
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
34 13 0.21
35 1 0.02
36 32 0.52
37 15 0.25
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (35 bp):
AAGCCTTCACCGAAGGTAGTGAAGCAATCCATCCT
Found at i:2267 original size:42 final size:42
Alignment explanation
Indices: 2190--2272 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
2180 ATCAATAAGT
* *
2190 GCCACCAGTAAGTCTTTCGAGCATGATTATGAAATCCTTCGA
1 GCCACCAGTAAGTCTTTCGAACATGATGATGAAATCCTTCGA
* * *
2232 GCCATCAGTAAGTCTTTCGAACGTGATGATTAAATCCTTCG
1 GCCACCAGTAAGTCTTTCGAACATGATGATGAAATCCTTCG
2273 GGTAATTTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (42 bp):
GCCACCAGTAAGTCTTTCGAACATGATGATGAAATCCTTCGA
Found at i:2324 original size:135 final size:132
Alignment explanation
Indices: 2063--2316 Score: 370
Period size: 135 Copynumber: 1.9 Consensus size: 132
2053 GCAAATCCAT
* * * * *
2063 CAGTAAGTCTTTCGAGCATGATGAAATCTTTTGGGCCATCAGTAAGTCTTTCGAGCTTGATGATT
1 CAGTAAGTCTTTCGAGCATGATGAAATCCTTCGAGCCATCAGTAAGTCTTTCGAACGTGATGATT
*
2128 AAACCCTTCGGGTAATTTGTAAGCTTTCAGGAAATAGTAGTGAAGCAAATCCATCAATAAGTGCC
66 AAACCCTTCGGGTAATTTATAAGCTTTCAGGAAATAGTAGTGAAGCAAATCCATCAATAAGTGCC
2193 AC
131 AC
2195 CAGTAAGTCTTTCGAGCATGATTATGAAATCCTTCGAGCCATCAGTAAGTCTTTCGAACGTGATG
1 CAGTAAGTCTTTCGAGCATG---ATGAAATCCTTCGAGCCATCAGTAAGTCTTTCGAACGTGATG
*
2260 ATTAAATCCTTCGGGTAATTTATAAG-TCTTCACGGAAGA-A-TAGTGAAGCAAATCCAT
63 ATTAAACCCTTCGGGTAATTTATAAGCT-TTCA-GGAA-ATAGTAGTGAAGCAAATCCAT
2317 TAGTAAGTCT
Statistics
Matches: 109, Mismatches: 7, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
132 20 0.18
134 1 0.01
135 82 0.75
136 5 0.05
137 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.30
Consensus pattern (132 bp):
CAGTAAGTCTTTCGAGCATGATGAAATCCTTCGAGCCATCAGTAAGTCTTTCGAACGTGATGATT
AAACCCTTCGGGTAATTTATAAGCTTTCAGGAAATAGTAGTGAAGCAAATCCATCAATAAGTGCC
AC
Found at i:3186 original size:55 final size:54
Alignment explanation
Indices: 2766--3554 Score: 828
Period size: 54 Copynumber: 14.6 Consensus size: 54
2756 CACACCAGAA
* * *
2766 GTTCGAGTTCCTACACCCTAAAG-AA-AGGAAGTGAACCCGTAGGCAGAAGATT
1 GTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGCAGAAGATT
*
2818 GTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGTGAACCCGTAGGCAGAAGATT
1 GTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGCAGAAGATT
* * * **
2872 GATCGAG----TACTGCCTAAAGAAAGAGGGAGCAAACCCGTAGATAGAAGATT
1 GTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGCAGAAGATT
* * * *
2922 ATTCAAGATCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGACAGAAGATT
1 GTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGCAGAAGATT
* *
2976 GTTCGAGTTCCTACTCCTTAAAGAAAGAGGGAGCGAACTCGTAGGCAGAAGATT
1 GTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGCAGAAGATT
* * * * * * *
3030 GTTTGAATTCCTACTTCCTAAAGAAAGAGGGAACGAACCTGTAAGCA-AATATT
1 GTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGCAGAAGATT
* *** *
3083 GTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGTGAATATGTAAGCAGAAGATT
1 GTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGCAGAAGATT
* * *
3137 GATCGAGTTCCTACTCCCTGAAAGAAAGAGGGAGCGAACCCGTTGGCAGAATATT
1 GTTCGAGTTCCTACTCCCT-AAAGAAAGAGGGAGCGAACCCGTAGGCAGAAGATT
* * * *
3192 GTTTGAGTTTCTACCCCCTGAAAGAAA-AGGGGAGCGAACACGTAGGCAGAAGATT
1 GTTCGAGTTCCTACTCCCT-AAAGAAAGA-GGGAGCGAACCCGTAGGCAGAAGATT
* ** * * *
3247 GTTTGAGTTCCTACTCCCTGAAAGAAAGAGGGAATGAACCCATGGGCAGAAGAAT
1 GTTCGAGTTCCTACTCCCT-AAAGAAAGAGGGAGCGAACCCGTAGGCAGAAGATT
* * * *
3302 ATTCGAGTTCCTACTCCCTGAAAGAAAGAGGGAACGAACCCATTGGCAGAAGATT
1 GTTCGAGTTCCTACTCCCT-AAAGAAAGAGGGAGCGAACCCGTAGGCAGAAGATT
* * * *
3357 GTTCAAGTT-CTACTCCCTAAAGAAAGAGGAAGTGAACCCGTAAGCAGAAGATT
1 GTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGCAGAAGATT
* * * *
3410 ATTCGAGTT-CTACTCCCTGAAGCAAGAGGGAGCGAACCCGTATGCAGAAGATT
1 GTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGCAGAAGATT
* * * * **
3463 GTTTGAGGGACGAGTT-CTACTACCTGAAGCAAGAGGGAGTGAACCCGTATACAGAAGATT
1 G-TT------CGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGCAGAAGATT
* * * *
3523 GTTTGAGTT-CTACTCCCTGAAGCAAGATGGAG
1 GTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAG
3555 AACTTGTTGA
Statistics
Matches: 633, Mismatches: 87, Indels: 33
0.84 0.12 0.04
Matches are distributed among these distances:
50 42 0.07
52 22 0.03
53 148 0.23
54 194 0.31
55 176 0.28
56 1 0.00
59 2 0.00
60 48 0.08
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (54 bp):
GTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGCAGAAGATT
Found at i:3507 original size:60 final size:60
Alignment explanation
Indices: 3413--3529 Score: 207
Period size: 60 Copynumber: 1.9 Consensus size: 60
3403 GAAGATTATT
* *
3413 CGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTATGCAGAAGATTGTTTGAGGGA
1 CGAGTTCTACTACCTGAAGCAAGAGGGAGCGAACCCGTATACAGAAGATTGTTTGAGGGA
*
3473 CGAGTTCTACTACCTGAAGCAAGAGGGAGTGAACCCGTATACAGAAGATTGTTTGAG
1 CGAGTTCTACTACCTGAAGCAAGAGGGAGCGAACCCGTATACAGAAGATTGTTTGAG
3530 TTCTACTCCC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.30, C:0.19, G:0.30, T:0.21
Consensus pattern (60 bp):
CGAGTTCTACTACCTGAAGCAAGAGGGAGCGAACCCGTATACAGAAGATTGTTTGAGGGA
Found at i:5600 original size:37 final size:36
Alignment explanation
Indices: 5525--5600 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
5515 TTTTTATATT
*
5525 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
5561 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
5598 TTT
1 TTT
5601 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:7835 original size:17 final size:17
Alignment explanation
Indices: 7775--7842 Score: 68
Period size: 17 Copynumber: 4.0 Consensus size: 17
7765 ATTCATGCAT
7775 CTAGTTCATTGAAT-AAA
1 CTAGTTCATT-AATCAAA
* *
7792 GTCAGTTCATTAATTAAA
1 CT-AGTTCATTAATCAAA
*
7810 CTA-TTCATTCATCAAA
1 CTAGTTCATTAATCAAA
*
7826 CTAGTTCATTTATCAAA
1 CTAGTTCATTAATCAAA
7843 TTAACTCTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
16 14 0.33
17 17 0.40
18 12 0.28
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.38
Consensus pattern (17 bp):
CTAGTTCATTAATCAAA
Found at i:9682 original size:14 final size:15
Alignment explanation
Indices: 9663--9691 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
9653 CATTAGAGTG
9663 TATTGGTGA-GATTT
1 TATTGGTGATGATTT
9677 TATTGGTGATGATTT
1 TATTGGTGATGATTT
9692 AAATCTTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.52
Consensus pattern (15 bp):
TATTGGTGATGATTT
Found at i:11707 original size:17 final size:17
Alignment explanation
Indices: 11681--11726 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
11671 TTCATTAATT
*
11681 AACTAGTTCATTCATCA
1 AACTAATTCATTCATCA
* *
11698 AACTAATTCATTTATTA
1 AACTAATTCATTCATCA
*
11715 AACTAACTCATT
1 AACTAATTCATT
11727 TGTTTCATGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.39, C:0.20, G:0.02, T:0.39
Consensus pattern (17 bp):
AACTAATTCATTCATCA
Found at i:14083 original size:31 final size:29
Alignment explanation
Indices: 14048--14122 Score: 71
Period size: 31 Copynumber: 2.5 Consensus size: 29
14038 CATATGAATT
14048 ATAACTTTTAATAATCTAAAGAATTAATGAA
1 ATAACTTTTAATAATCTAAAG-ATT-ATGAA
* * ***
14079 ATAACATCTT-ATAATTTAAAGATTATTTT
1 ATAAC-TTTTAATAATCTAAAGATTATGAA
14108 ATAACTTTTAATAAT
1 ATAACTTTTAATAAT
14123 AAAAAATTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
28 3 0.08
29 12 0.33
30 3 0.08
31 15 0.42
32 3 0.08
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.43
Consensus pattern (29 bp):
ATAACTTTTAATAATCTAAAGATTATGAA
Found at i:15468 original size:20 final size:20
Alignment explanation
Indices: 15446--15533 Score: 113
Period size: 20 Copynumber: 4.4 Consensus size: 20
15436 GGTCTGTCAG
*
15446 TATCGATACTGGAAAAACAG
1 TATCGATACTGGAAAAACAA
*
15466 TATCGATACTGGAAGAACAA
1 TATCGATACTGGAAAAACAA
* *
15486 TATCGATACTGAAAAAATAA
1 TATCGATACTGGAAAAACAA
* * *
15506 TATCGACACTAGAAGAACAA
1 TATCGATACTGGAAAAACAA
15526 TATCGATA
1 TATCGATA
15534 TTATTCTTCA
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 57 1.00
ACGTcount: A:0.48, C:0.15, G:0.16, T:0.22
Consensus pattern (20 bp):
TATCGATACTGGAAAAACAA
Found at i:15492 original size:40 final size:40
Alignment explanation
Indices: 15446--15533 Score: 131
Period size: 40 Copynumber: 2.2 Consensus size: 40
15436 GGTCTGTCAG
* * * *
15446 TATCGATACTGGAAAAACAGTATCGATACTGGAAGAACAA
1 TATCGATACTGAAAAAACAATATCGACACTAGAAGAACAA
*
15486 TATCGATACTGAAAAAATAATATCGACACTAGAAGAACAA
1 TATCGATACTGAAAAAACAATATCGACACTAGAAGAACAA
15526 TATCGATA
1 TATCGATA
15534 TTATTCTTCA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.48, C:0.15, G:0.16, T:0.22
Consensus pattern (40 bp):
TATCGATACTGAAAAAACAATATCGACACTAGAAGAACAA
Found at i:21761 original size:27 final size:27
Alignment explanation
Indices: 21731--21793 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
21721 AAAATATTGC
21731 TATTCGGATCAGACATCACATATACGT
1 TATTCGGATCAGACATCACATATACGT
** *
21758 TATTCAAATCAGACATCAGATATACGT
1 TATTCGGATCAGACATCACATATACGT
21785 TATTCGGAT
1 TATTCGGAT
21794 ATATGTAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (27 bp):
TATTCGGATCAGACATCACATATACGT
Found at i:21877 original size:22 final size:24
Alignment explanation
Indices: 21849--21905 Score: 91
Period size: 22 Copynumber: 2.5 Consensus size: 24
21839 GTCCGAGTAA
*
21849 TATTAATATTATATATTTTTATA-
1 TATTAATATTATATATTTTAATAT
21872 T-TTAATATTATATATTTTAATAT
1 TATTAATATTATATATTTTAATAT
21895 TATTAATATTA
1 TATTAATATTA
21906 AATAATATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
22 20 0.65
23 2 0.06
24 9 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TATTAATATTATATATTTTAATAT
Found at i:29867 original size:17 final size:19
Alignment explanation
Indices: 29845--29879 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
29835 TTGATGCATT
29845 CATAAAAA-CAT-CATTTG
1 CATAAAAATCATGCATTTG
29862 CATAAAAATCATGCATTT
1 CATAAAAATCATGCATTT
29880 CATTGATACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 3 0.19
19 5 0.31
ACGTcount: A:0.46, C:0.17, G:0.06, T:0.31
Consensus pattern (19 bp):
CATAAAAATCATGCATTTG
Found at i:30161 original size:20 final size:20
Alignment explanation
Indices: 30136--30209 Score: 103
Period size: 20 Copynumber: 3.7 Consensus size: 20
30126 TATTTCCCAC
30136 CATTTGTAAAACCTCCGGGT
1 CATTTGTAAAACCTCCGGGT
*
30156 CATTTGTAAAGCCTCCGGGT
1 CATTTGTAAAACCTCCGGGT
* *
30176 CATTTGTAAAGCCTCCGAGT
1 CATTTGTAAAACCTCCGGGT
**
30196 CATAGGTAAAACCT
1 CATTTGTAAAACCT
30210 TTGGATAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.28
Consensus pattern (20 bp):
CATTTGTAAAACCTCCGGGT
Found at i:30581 original size:174 final size:172
Alignment explanation
Indices: 30284--30710 Score: 624
Period size: 174 Copynumber: 2.5 Consensus size: 172
30274 TCAAATTAAA
* * *
30284 CTTCACGGAAGAGTAGTGAAGAAAAAATAAGATAAAAATTAGATCTCCACGGAAGAGTAGTGGAA
1 CTTCACGGAAGAGTAGTGAAG-CAAAACAAGATAAAAATCAGATCTCCACGGAAGAGTAGTGGAA
* * *
30349 CGGATTTTTCAACAAAGTATGAAGCTTTCATGAAAAAGTAATGAAGTAATGAAAATTCAGCCTTC
65 CGAATTTTTCAACAAAGTATGAAGCCTTCATGAAAAAGTAATGAAGTAATGAAAATTCAACCTTC
30414 ACAGAAGAGTAGTGAAGCAAGTCATTTGCAAATCATATTCAGC
130 ACAGAAGAGTAGTGAAGCAAGTCATTTGCAAATCATATTCAGC
*
30457 CTTCAGGGAAGAGTAGTGAAGCAAAAGCAAGATAAAAAATCAGATCTCCACGGAAGAGTAGTGGA
1 CTTCACGGAAGAGTAGTGAAGCAAAA-CAAGAT-AAAAATCAGATCTCCACGGAAGAGTAGTGGA
* *
30522 ACGAATTTTTCAGCAAAGTATGAAGCCTTCATGAAAGAGTAATGAAGTAAT-ACAAATTCAACCT
64 ACGAATTTTTCAACAAAGTATGAAGCCTTCATGAAAAAGTAATGAAGTAATGA-AAATTCAACCT
* * *
30586 TCACAGAAGAGTAGTGAAGTAAGTCATTTGCAAGTCATCTTCAGC
128 TCACAGAAGAGTAGTGAAGCAAGTCATTTGCAAATCATATTCAGC
** ** *
30631 CTTCACAAAAGAGTAGTGAAGCAAGAACAAGATCAAAGTTC-GATCTCCACGAAAGAGTAGTGGA
1 CTTCACGGAAGAGTAGTGAAGCAA-AACAAGAT-AAAAATCAGATCTCCACGGAAGAGTAGTGGA
*
30695 ACGAATTTCTCAACAA
64 ACGAATTTTTCAACAA
30711 GCATGAAAGC
Statistics
Matches: 229, Mismatches: 21, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
172 4 0.02
173 62 0.27
174 161 0.70
175 2 0.01
ACGTcount: A:0.41, C:0.15, G:0.21, T:0.22
Consensus pattern (172 bp):
CTTCACGGAAGAGTAGTGAAGCAAAACAAGATAAAAATCAGATCTCCACGGAAGAGTAGTGGAAC
GAATTTTTCAACAAAGTATGAAGCCTTCATGAAAAAGTAATGAAGTAATGAAAATTCAACCTTCA
CAGAAGAGTAGTGAAGCAAGTCATTTGCAAATCATATTCAGC
Found at i:30846 original size:12 final size:12
Alignment explanation
Indices: 30829--30867 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
30819 GTATCGTTAA
30829 TATTATATATAT
1 TATTATATATAT
*
30841 TATTATATATAA
1 TATTATATATAT
*
30853 TATTAGATATTAT
1 TATTATATA-TAT
30866 TA
1 TA
30868 ATATTATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 19 0.83
13 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (12 bp):
TATTATATATAT
Found at i:30863 original size:19 final size:18
Alignment explanation
Indices: 30841--30892 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
30831 TTATATATAT
30841 TATTATATATAATATTAGA
1 TATTATATATAATATTA-A
*
30860 TATTAT-TAATATTATTAA
1 TATTATAT-ATAATATTAA
30878 TATTA-A-ATAATATTA
1 TATTATATATAATATTA
30893 CAAATAGAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
16 8 0.28
18 7 0.24
19 14 0.48
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
TATTATATATAATATTAA
Found at i:31957 original size:26 final size:25
Alignment explanation
Indices: 31928--31979 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
31918 TTTTCGTACC
**
31928 TTTTAATTTTTTTCATATTTTATTTA
1 TTTTAATTTTAGTCAT-TTTTATTTA
*
31954 TTTTTATTTTAGTCATTTTTATTTA
1 TTTTAATTTTAGTCATTTTTATTTA
31979 T
1 T
31980 ATATATATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.73
Consensus pattern (25 bp):
TTTTAATTTTAGTCATTTTTATTTA
Found at i:31963 original size:15 final size:15
Alignment explanation
Indices: 31943--31977 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
31933 ATTTTTTTCA
* *
31943 TATTTTATTTATTTT
1 TATTTTAGTCATTTT
31958 TATTTTAGTCATTTT
1 TATTTTAGTCATTTT
31973 TATTT
1 TATTT
31978 ATATATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.74
Consensus pattern (15 bp):
TATTTTAGTCATTTT
Found at i:34319 original size:20 final size:19
Alignment explanation
Indices: 34291--34338 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
34281 TTTTTTCTAC
* *
34291 AAAATATTCAAAATTAAAA
1 AAAAAATTCAAAAGTAAAA
*
34310 TAAAAAATTCCAAAGTAAAA
1 -AAAAAATTCAAAAGTAAAA
34330 AAGAAAATT
1 AA-AAAATT
34339 ACATATTGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.67, C:0.06, G:0.04, T:0.23
Consensus pattern (19 bp):
AAAAAATTCAAAAGTAAAA
Found at i:37433 original size:17 final size:17
Alignment explanation
Indices: 37411--37444 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
37401 GAAAAGTTAA
37411 ATAT-AAAATCAGAATAT
1 ATATAAAAAT-AGAATAT
37428 ATATAAAAATAGAATAT
1 ATATAAAAATAGAATAT
37445 GACAGAATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.29
Consensus pattern (17 bp):
ATATAAAAATAGAATAT
Found at i:38108 original size:22 final size:24
Alignment explanation
Indices: 38083--38131 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
38073 ATGTTTATTC
*
38083 AAAATTAAAAAGAC-TAA-ATAAA
1 AAAAATAAAAAGACATAATATAAA
*
38105 AAAAATATAAAGACATAATATAAA
1 AAAAATAAAAAGACATAATATAAA
38129 AAA
1 AAA
38132 TAAAATAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 12 0.52
23 3 0.13
24 8 0.35
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.18
Consensus pattern (24 bp):
AAAAATAAAAAGACATAATATAAA
Found at i:41501 original size:20 final size:20
Alignment explanation
Indices: 41476--41520 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
41466 TTATCCGGAA
* *
41476 AAAAATCCGGTCTGGGGTTT
1 AAAAATCCGGTCTGAGATTT
41496 AAAAATCCGGTCTGAGATTT
1 AAAAATCCGGTCTGAGATTT
41516 AAAAA
1 AAAAA
41521 ATTGGATGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.27
Consensus pattern (20 bp):
AAAAATCCGGTCTGAGATTT
Found at i:42761 original size:59 final size:59
Alignment explanation
Indices: 42618--42763 Score: 170
Period size: 59 Copynumber: 2.4 Consensus size: 59
42608 AAAATAGAGT
** * * *
42618 AAAG-TACATAAATGGTCTCCTGACTATAGGGTATTGCTTTATTAAGTCCCTTGACTATTG
1 AAAGTTACA-AAATGGTCTCC-GACTATAGAATATTGCCTTATTAAGTCCCTCGACTATTA
* * *
42678 AAAGTTACAAAATGATCCTTCGACTATAGAATGTTGCCTTATTAAGT-CCTCGACTATTA
1 AAAGTTACAAAATGGT-CTCCGACTATAGAATATTGCCTTATTAAGTCCCTCGACTATTA
42737 AAAGTTACAAAATGGTCATCCGACTAT
1 AAAGTTACAAAATGGTC-TCCGACTAT
42764 TCATTATGTT
Statistics
Matches: 73, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
58 1 0.01
59 33 0.45
60 32 0.44
61 7 0.10
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Consensus pattern (59 bp):
AAAGTTACAAAATGGTCTCCGACTATAGAATATTGCCTTATTAAGTCCCTCGACTATTA
Found at i:45197 original size:10 final size:10
Alignment explanation
Indices: 45182--45216 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
45172 AACGCTGGAA
45182 ACCGGTTTTG
1 ACCGGTTTTG
*
45192 ACCGGTTCTG
1 ACCGGTTTTG
45202 ACCGG-TTTG
1 ACCGGTTTTG
45211 ACCGGT
1 ACCGGT
45217 CACGACCCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.11, C:0.26, G:0.31, T:0.31
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:45333 original size:29 final size:29
Alignment explanation
Indices: 45271--45346 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
45261 CCCATTGACC
*** *
45271 GGTGCTATTCTGGGAATTAATTCGGTTTT
1 GGTGCTATTCTGGGAATTAATTCGAAATG
*
45300 TGTGCTATTCTGGGAATTAATTCGAAATG
1 GGTGCTATTCTGGGAATTAATTCGAAATG
* *
45329 GGTGCTATTTTGGTAATT
1 GGTGCTATTCTGGGAATT
45347 TTTTTAAAAG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.21, C:0.09, G:0.26, T:0.43
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTCGAAATG
Found at i:52446 original size:19 final size:19
Alignment explanation
Indices: 52422--52459 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
52412 GAACGCTGGA
52422 AACCGGTTTTGACCGGTTT
1 AACCGGTTTTGACCGGTTT
52441 AACCGGTTTTGACCGGTTT
1 AACCGGTTTTGACCGGTTT
52460 GACCAGTCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.16, C:0.21, G:0.26, T:0.37
Consensus pattern (19 bp):
AACCGGTTTTGACCGGTTT
Found at i:52447 original size:9 final size:10
Alignment explanation
Indices: 52422--52459 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
52412 GAACGCTGGA
52422 AACCGGTTTT
1 AACCGGTTTT
*
52432 GACCGG-TTT
1 AACCGGTTTT
52441 AACCGGTTTT
1 AACCGGTTTT
*
52451 GACCGGTTT
1 AACCGGTTT
52460 GACCAGTCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.16, C:0.21, G:0.26, T:0.37
Consensus pattern (10 bp):
AACCGGTTTT
Found at i:52460 original size:9 final size:10
Alignment explanation
Indices: 52423--52463 Score: 59
Period size: 9 Copynumber: 4.3 Consensus size: 10
52413 AACGCTGGAA
52423 ACCGGTTTTG
1 ACCGGTTTTG
*
52433 ACCGG-TTTA
1 ACCGGTTTTG
52442 ACCGGTTTTG
1 ACCGGTTTTG
52452 ACCGG-TTTG
1 ACCGGTTTTG
52461 ACC
1 ACC
52464 AGTCACGACC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
9 15 0.54
10 13 0.46
ACGTcount: A:0.15, C:0.24, G:0.27, T:0.34
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:52594 original size:29 final size:29
Alignment explanation
Indices: 52528--52603 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
52518 ACCGTTGACC
*** *
52528 GGTGCTATTCTGGGAATTAATTCGGTTTT
1 GGTGCTATTCTGGGAATTAATTCGAAATG
* *
52557 TGTGTTATTCTGGGAATTAATTCGAAATG
1 GGTGCTATTCTGGGAATTAATTCGAAATG
* *
52586 GGTGCTATTTTGGTAATT
1 GGTGCTATTCTGGGAATT
52604 TTTTTAAAAA
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.21, C:0.08, G:0.26, T:0.45
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTCGAAATG
Found at i:54384 original size:141 final size:138
Alignment explanation
Indices: 54083--54431 Score: 448
Period size: 141 Copynumber: 2.5 Consensus size: 138
54073 TTACATTTTT
* ** * * * *
54083 ATTGAATCAAATAATTAAATTGAAACCTCGAACAAAAAATAGAAGCCCAAATAAAAAATTCACCC
1 ATTGAATCAAATAATTAAATTGAAACCTCG-AGAAAAAGCA-AGGACCAAATTAAAAATTCACCT
* * * * *
54148 AGATTAAAGGACTAAGGTAATATTAACCTAGAGTGAAGGCTCTAATATTAGAACGTAACAAATTT
64 AAATTAAAGGACTAAGGTAATATAAACCTAAAGTGAAGGCTCTAATATTAAAACCTAACAAATTT
*
54213 TAGAAATTTT
129 TAGAAATTTC
*
54223 ATTGAATCAAATAATTAAATTGTAACCTCGAGTAAAAAGGCAAGGACCAAATTAAAAATTCACCT
1 ATTGAATCAAATAATTAAATTGAAACCTCGAG-AAAAA-GCAAGGACCAAATTAAAAATTCACCT
*
54288 AAATTAAAGGGCTAAGGTGAAGT-TAAACCTAAAGTGAAGGCTCTAATATTAAAACCTAACAAAT
64 AAATTAAAGGACTAAGGT-AA-TATAAACCTAAAGTGAAGGCTCTAATATTAAAACCTAACAAAT
54352 TTTAGAAATTTC
127 TTTAGAAATTTC
* * * * **
54364 ATTGAATCGAATAATTAAATTGGAACCCCAAGAAAAAGCGGGGACCAAATTAAAAATTCACCTAA
1 ATTGAATCAAATAATTAAATTGAAACCTCGAGAAAAAGCAAGGACCAAATTAAAAATTCACCTAA
54429 ATT
66 ATT
54432 TAGCTAAGTT
Statistics
Matches: 184, Mismatches: 21, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
139 30 0.16
140 74 0.40
141 79 0.43
142 1 0.01
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.25
Consensus pattern (138 bp):
ATTGAATCAAATAATTAAATTGAAACCTCGAGAAAAAGCAAGGACCAAATTAAAAATTCACCTAA
ATTAAAGGACTAAGGTAATATAAACCTAAAGTGAAGGCTCTAATATTAAAACCTAACAAATTTTA
GAAATTTC
Found at i:56783 original size:18 final size:18
Alignment explanation
Indices: 56760--56796 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
56750 TGATCATGGC
56760 GGTCTCCCTTCAATTTTG
1 GGTCTCCCTTCAATTTTG
56778 GGTCTCCCTTCAATTTTG
1 GGTCTCCCTTCAATTTTG
56796 G
1 G
56797 CTTTAAAGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.11, C:0.27, G:0.19, T:0.43
Consensus pattern (18 bp):
GGTCTCCCTTCAATTTTG
Found at i:56883 original size:21 final size:21
Alignment explanation
Indices: 56859--56899 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
56849 ATGAGTTATG
56859 TCTATATC-TATCTATAATTTA
1 TCTAT-TCATATCTATAATTTA
*
56880 TCTATTCATATTTATAATTT
1 TCTATTCATATCTATAATTT
56900 GTAATCTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.32, C:0.12, G:0.00, T:0.56
Consensus pattern (21 bp):
TCTATTCATATCTATAATTTA
Found at i:60531 original size:14 final size:14
Alignment explanation
Indices: 60512--60542 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
60502 TTTTATTTTT
60512 AATAAAAATTAATA
1 AATAAAAATTAATA
*
60526 AATAAAAATTATTA
1 AATAAAAATTAATA
60540 AAT
1 AAT
60543 TTAATATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
AATAAAAATTAATA
Found at i:61599 original size:45 final size:45
Alignment explanation
Indices: 61534--61861 Score: 530
Period size: 45 Copynumber: 7.3 Consensus size: 45
61524 ATTATTCATT
* *
61534 ATTTCCATTTATGGCATCCTTTCATGCTTTTATTGCACCGTTATGC
1 ATTT-CATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
*
61580 ATTTCATTTATGGCATCCTTTCATACCTTTAATGCACCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* *
61625 ATTTCATTTATGGTATCCTTTCATGACTTTAATGCACCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
*
61670 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACTGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* * *
61715 ATTTCATTTATGGCATCATTTCATGCCTTTAATGCGCCGTTATAC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
*
61760 ATTTCATTTATGACATCCTTTCATGCCTTTAATGCACCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* **
61805 ATTTCATTTATGGCATCCTTTCTTGCCTTTAATGCACTATTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
61850 ATTTCATTTATG
1 ATTTCATTTATG
61862 TAATAAAAAC
Statistics
Matches: 261, Mismatches: 21, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
45 257 0.98
46 4 0.02
ACGTcount: A:0.21, C:0.22, G:0.12, T:0.45
Consensus pattern (45 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
Found at i:68504 original size:45 final size:45
Alignment explanation
Indices: 68453--68644 Score: 323
Period size: 45 Copynumber: 4.3 Consensus size: 45
68443 ATTATTCATT
*
68453 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGTACCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
*
68498 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCATTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
**
68543 ATTTCATTTATGGTGTCCTTTCATGCCTTTAATGCACCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
*
68588 ATTTCATTTATGGCAT-CTTTCCATGCCTTTAATGCACCGTTATTC
1 ATTTCATTTATGGCATCCTTT-CATGCCTTTAATGCACCGTTATGC
68633 ATTTCATTTATG
1 ATTTCATTTATG
68645 TAACAAAAAC
Statistics
Matches: 138, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
44 4 0.03
45 134 0.97
ACGTcount: A:0.20, C:0.22, G:0.12, T:0.45
Consensus pattern (45 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
Found at i:72366 original size:31 final size:31
Alignment explanation
Indices: 72330--72388 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
72320 AAATTCAAGA
*
72330 GTTAAATTAATATTTTATCTAAAGTTTATAG
1 GTTAAATTAATATTTTATCTAAAATTTATAG
*
72361 GTTAAATTAATCTTTTATCTAAAATTTA
1 GTTAAATTAATATTTTATCTAAAATTTA
72389 GCACCAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.49
Consensus pattern (31 bp):
GTTAAATTAATATTTTATCTAAAATTTATAG
Found at i:72677 original size:18 final size:19
Alignment explanation
Indices: 72622--72685 Score: 82
Period size: 17 Copynumber: 3.5 Consensus size: 19
72612 CGAAACCGGT
72622 TTTTTCGGTTCGGTTCGGG
1 TTTTTCGGTTCGGTTCGGG
*
72641 TTTTT---TAACGGTTCGGG
1 TTTTTCGGT-TCGGTTCGGG
72658 TTTTTCGGTTCGGTTC-GG
1 TTTTTCGGTTCGGTTCGGG
72676 TTTTTCGGTT
1 TTTTTCGGTT
72686 TTTCAATGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
16 1 0.03
17 14 0.36
18 12 0.31
19 11 0.28
20 1 0.03
ACGTcount: A:0.03, C:0.14, G:0.31, T:0.52
Consensus pattern (19 bp):
TTTTTCGGTTCGGTTCGGG
Found at i:76787 original size:23 final size:23
Alignment explanation
Indices: 76745--76788 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
76735 TTGTAAAATA
*
76745 TCGGGGATCCCTATGATTATTTT
1 TCGGGGATCCCTACGATTATTTT
*
76768 TCGGGGATCCCTACGGTTATT
1 TCGGGGATCCCTACGATTATT
76789 CACACGTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.16, C:0.20, G:0.25, T:0.39
Consensus pattern (23 bp):
TCGGGGATCCCTACGATTATTTT
Found at i:78751 original size:24 final size:22
Alignment explanation
Indices: 78727--78767 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
78717 AATTAAGTTT
78727 TTTTTATTATT-AAAAATAATA
1 TTTTTATTATTAAAAAATAATA
78748 TTTTTATTATTAAAAAATAA
1 TTTTTATTATTAAAAAATAA
78768 AAAAATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTTTATTATTAAAAAATAATA
Done.