Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005379.1 Hibiscus syriacus cultivar Beakdansim tig00012280_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: 90577
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:9425 original size:12 final size:14
Alignment explanation
Indices: 9408--9440 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
9398 TCTGACAGAA
9408 AAATAAATAA-TG-
1 AAATAAATAATTGC
9420 AAATAAATAATTGC
1 AAATAAATAATTGC
9434 AAATAAA
1 AAATAAA
9441 ATAAACATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.53
13 2 0.11
14 7 0.37
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.24
Consensus pattern (14 bp):
AAATAAATAATTGC
Found at i:9483 original size:29 final size:26
Alignment explanation
Indices: 9434--9491 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 26
9424 AAATAATTGC
*
9434 AAATAAAATAAACATATAAATATTATGA
1 AAATAAAATAAACATA-AAA-ATTTTGA
* *
9462 AAATATAAGTAAATATAAAAATTTTGA
1 AAATA-AAATAAACATAAAAATTTTGA
9489 AAA
1 AAA
9492 GAGAAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 9 0.35
28 8 0.31
29 9 0.35
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (26 bp):
AAATAAAATAAACATAAAAATTTTGA
Found at i:10156 original size:13 final size:13
Alignment explanation
Indices: 10121--10158 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
10111 GATATTGAAG
10121 AATAAATA-TTAA
1 AATAAATATTTAA
*
10133 AATAATTTATTTAA
1 AATAA-ATATTTAA
10147 AATAAATATTTA
1 AATAAATATTTA
10159 TTTATTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 5 0.23
13 8 0.36
14 9 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
AATAAATATTTAA
Found at i:11565 original size:3 final size:3
Alignment explanation
Indices: 11557--11622 Score: 96
Period size: 3 Copynumber: 22.0 Consensus size: 3
11547 TTAATATATT
* * * *
11557 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TTA TTA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
11605 TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
11623 ATTAATATGG
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:15835 original size:19 final size:19
Alignment explanation
Indices: 15811--15887 Score: 70
Period size: 19 Copynumber: 4.1 Consensus size: 19
15801 AATATACTTG
*
15811 TATATATACTAATATTATA
1 TATATATACTAATAATATA
*
15830 TATATATACTCATAAGTATA
1 TATATATACTAATAA-TATA
* *
15850 -ATGTATACTTATAATATA
1 TATATATACTAATAATATA
*
15868 TAT-TATAAGT-ATAATATA
1 TATATAT-ACTAATAATATA
15886 TA
1 TA
15888 CTTACATACA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
18 17 0.34
19 29 0.58
20 4 0.08
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (19 bp):
TATATATACTAATAATATA
Found at i:15879 original size:31 final size:33
Alignment explanation
Indices: 15825--15891 Score: 102
Period size: 31 Copynumber: 2.1 Consensus size: 33
15815 TATACTAATA
*
15825 TTATATATATATACTCATAAGTATAATGTATAC
1 TTATATATATATACTCATAAGTATAATATATAC
*
15858 TTATA-ATATATA-TTATAAGTATAATATATAC
1 TTATATATATATACTCATAAGTATAATATATAC
15889 TTA
1 TTA
15892 CATACATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 20 0.62
32 7 0.22
33 5 0.16
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (33 bp):
TTATATATATATACTCATAAGTATAATATATAC
Found at i:15995 original size:2 final size:2
Alignment explanation
Indices: 15983--16258 Score: 80
Period size: 2 Copynumber: 140.0 Consensus size: 2
15973 AAGTATATTG
* *
15983 TA TA T- TA TA TA TA TA TA TA TA TA TA AA CTA TA TA GT- TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA
* * * * *
16025 CA TA GTA TA TA AA TA TA AA TA TA AA TA TA TA -A T- TT TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * *
16066 TA GTT TA TA TG TA TT TT TA CA TA -A TA TA TA AA TA TA AA CTA TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * * * *
16109 TA -A AA AA T- TA TA TA GTT TA TA TA CTA TA T- TG TT TA TA TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA
* * * * *
16150 -A TT TA TA -A CA TA TA TA GTT TA TA TA CCA TA GTA TA TA AA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA -TA TA TA TA TA
* * *
16191 TA AA CTA TA TA GTT TA TA CA TA T- TA TA TA -A T- TA TA TA -A TA
1 TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
16231 TG TA TA TA TA TA TA TA TA -A TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16259 ATTTTTTCAA
Statistics
Matches: 200, Mismatches: 46, Indels: 56
0.66 0.15 0.19
Matches are distributed among these distances:
1 16 0.08
2 169 0.85
3 15 0.08
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:16147 original size:27 final size:27
Alignment explanation
Indices: 16117--16174 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
16107 TATAAAAAAT
* *
16117 TATATAGTTTATATAC-TATATTGTTTA
1 TATATAATTTATA-ACATATATAGTTTA
16144 TATATAATTTATAACATATATAGTTTA
1 TATATAATTTATAACATATATAGTTTA
16171 TATA
1 TATA
16175 CCATAGTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 2 0.07
27 26 0.93
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (27 bp):
TATATAATTTATAACATATATAGTTTA
Found at i:18214 original size:158 final size:156
Alignment explanation
Indices: 17991--18355 Score: 491
Period size: 158 Copynumber: 2.3 Consensus size: 156
17981 AGCATGTGGT
* *
17991 TCAAATTTGATAAAAACAACTTAAAATAAATCACA-AATTGAAGGAATAAGTAGATTATGAAAAA
1 TCAAATTTGATAAAAACAACTTAAAATAAATGA-AGAATTGAAGGAATAAGGAGATTATGAAAAA
* *
18055 TTGAAGGACTAAATTGAAAAATAAAAAATTTGTTATCAAAAAGAGAAATTAAAAGTACACATGTA
65 TTGAAAGACTAAATTGAAAAATAAAAAATTTATTATCAAAAAGAGAAATTAAAAGTACACATGTA
18120 TTATACTATGATTTA-AGAGCATGTAAC
130 TTATACTATGATTTAGA-AGCATGTAAC
* * * *
18147 TCAAATTTGGTAAAAAGGAGACTTAAAATAAATGATGAATTGAAGGAATAAGGAGATTATGATAA
1 TCAAATTTGATAAAAA-CA-ACTTAAAATAAATGAAGAATTGAAGGAATAAGGAGATTATGAAAA
* *
18212 ATTGAAAGACTAAATTGAAAAATAAAAAATTTATTATCAAAAAGAGGAATTGAAAGTACACATGT
64 ATTGAAAGACTAAATTGAAAAATAAAAAATTTATTATCAAAAAGAGAAATTAAAAGTACACATGT
* * ***
18277 ATTCTACTATGGTTTAGAAGCATGTGGT
129 ATTATACTATGATTTAGAAGCATGTAAC
* * * *
18305 TCAAATTTGATAAAAAATAAACTTAAAATGAAGGAAGAATTGAAGAAATAA
1 TCAAATTTGAT-AAAAA-CAACTTAAAATAAATGAAGAATTGAAGGAATAA
18356 TGAAATCAGG
Statistics
Matches: 182, Mismatches: 22, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
156 15 0.08
157 1 0.01
158 159 0.87
159 7 0.04
ACGTcount: A:0.51, C:0.06, G:0.16, T:0.27
Consensus pattern (156 bp):
TCAAATTTGATAAAAACAACTTAAAATAAATGAAGAATTGAAGGAATAAGGAGATTATGAAAAAT
TGAAAGACTAAATTGAAAAATAAAAAATTTATTATCAAAAAGAGAAATTAAAAGTACACATGTAT
TATACTATGATTTAGAAGCATGTAAC
Found at i:19650 original size:181 final size:178
Alignment explanation
Indices: 19175--19716 Score: 527
Period size: 181 Copynumber: 3.0 Consensus size: 178
19165 TTATGTGATT
* * * *
19175 AAGTATCAGATATTGTAATCAGGTTTCGGTCAGTTTAGTTTCTTTTTTAGAA-ACAAATTGCAAT
1 AAGTATCACATGTTGTAATCAGG-TTCTGTCAGTTTAGTTTC-TGTTTAGAAGA-AAATTGCAAT
* * ** * * *
19239 TAATGAAGAAGCTGTGAATTTCAGCTAATTTTAAGTTTAATTGAGTGTTAAATCTAAAAGTCTGG
63 TAATCAAGAAGTTGTGAATTGGAGCTAATATTAAGCTTAA-TGA--GTT--GT-TAAAAGTCTGG
* * * * *
19304 TTAAATTGATGAAAAGAGTC-TATT-T-TATATA-TTGTCTTAGAAAAGGAGAAAATTG
122 TTAAATTGATGAAAA-AGTCAT-TTATGTATGTATTTGTCTCACAAAAGGAGAAAACTA
*
19359 AAGTATCACATGTTGTAATCAGG--CT-TCAGTTTAGTTTCTGTTTAAGAAG-AAATTTCAATTA
1 AAGTATCACATGTTGTAATCAGGTTCTGTCAGTTTAGTTTCTGTTT-AGAAGAAAATTGCAATTA
* *
19420 ATCAGGAA-TGTGTGAATTGGAGCTAATATTAAGCTTAATGGAG-TGTTAAAAGTCTAGTTAAAT
65 ATCAAGAAGT-TGTGAATTGGAGCTAATATTAAGCTTAAT-GAGTTGTTAAAAGTCTGGTTAAAT
* *
19483 TGATGAAAATAGTGCATTTATGTATGTATTTGTC-CCCAAAGGGAGAAAACTA
128 TGATGAAAA-AGT-CATTTATGTATGTATTTGTCTCACAAAAGGAGAAAACTA
* *
19535 AAGTATCACATGTTGTGATCAGGCTTCTGTCAATTTAGTTTCTGTTTACGAAGAAAATTGCAATT
1 AAGTATCACATGTTGTAATCAGG-TTCTGTCAGTTTAGTTTCTGTTTA-GAAGAAAATTGCAATT
* *
19600 TATCAAGAAGTTGTGAATTGGAGCTAATATTAAACTTAATGAGTTGTTAAAAGT-TGGGTTAAAT
64 AATCAAGAAGTTGTGAATTGGAGCTAATATTAAGCTTAATGAGTTGTTAAAAGTCT-GGTTAAAT
** * * *
19664 TGAT-AAAACGACCCATTTATGTATGTATTTGTCTCAGAAAAGAAGGAAACTA
128 TGATGAAAA--AGTCATTTATGTATGTATTTGTCTCACAAAAGGAGAAAACTA
19716 A
1 A
19717 TGGAATTTAT
Statistics
Matches: 301, Mismatches: 37, Indels: 43
0.79 0.10 0.11
Matches are distributed among these distances:
173 28 0.09
174 4 0.01
175 2 0.01
176 40 0.13
177 6 0.02
178 1 0.00
179 50 0.17
180 66 0.22
181 82 0.27
182 1 0.00
184 21 0.07
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (178 bp):
AAGTATCACATGTTGTAATCAGGTTCTGTCAGTTTAGTTTCTGTTTAGAAGAAAATTGCAATTAA
TCAAGAAGTTGTGAATTGGAGCTAATATTAAGCTTAATGAGTTGTTAAAAGTCTGGTTAAATTGA
TGAAAAAGTCATTTATGTATGTATTTGTCTCACAAAAGGAGAAAACTA
Found at i:21870 original size:18 final size:17
Alignment explanation
Indices: 21847--21881 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
21837 ATTTTTATTG
21847 AATAAAAATAATTATTTT
1 AATAAAAAT-ATTATTTT
*
21865 AATAAATATATTATTTT
1 AATAAAAATATTATTTT
21882 GGGTTAAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AATAAAAATATTATTTT
Found at i:22246 original size:17 final size:18
Alignment explanation
Indices: 22199--22246 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
22189 ATATATTAAT
22199 TATAATTTTATGAGGTAAAA
1 TATAA-TTTATGA-GTAAAA
*
22219 AATAATATTATGA-TAAAA
1 TATAAT-TTATGAGTAAAA
22237 TATAATTTAT
1 TATAATTTAT
22247 TAAAATAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 4 0.16
18 10 0.40
19 1 0.04
20 10 0.40
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (18 bp):
TATAATTTATGAGTAAAA
Found at i:22888 original size:21 final size:21
Alignment explanation
Indices: 22837--22889 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
22827 ATTATTACTA
22837 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
22858 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
22879 TCGCAATGCGA
1 TCGCAATGCGA
22890 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:22909 original size:41 final size:42
Alignment explanation
Indices: 22864--22972 Score: 121
Period size: 42 Copynumber: 2.6 Consensus size: 42
22854 AATTTCGCGT
* * *
22864 TGCGATTTTCCCAATTCGCAATGCGAA-TAAGTAAATCGCAA
1 TGCGAATTTCCCAAATCGCAATGCGAATTAAGAAAATCGCAA
*** *
22905 TGCGAATTTGGGAAATCGCAATGCGAATTTAGAAAATCGCAA
1 TGCGAATTTCCCAAATCGCAATGCGAATTAAGAAAATCGCAA
***
22947 TGCGAATTTGGAAAATCGCAATGCGA
1 TGCGAATTTCCCAAATCGCAATGCGA
22973 TACTGACTAT
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
41 22 0.37
42 37 0.63
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.25
Consensus pattern (42 bp):
TGCGAATTTCCCAAATCGCAATGCGAATTAAGAAAATCGCAA
Found at i:22922 original size:21 final size:21
Alignment explanation
Indices: 22879--22972 Score: 136
Period size: 21 Copynumber: 4.5 Consensus size: 21
22869 TTTTCCCAAT
* *
22879 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTTAGAAAA
* *
22899 TCGCAATGCGAATTTGGGAAA
1 TCGCAATGCGAATTTAGAAAA
22920 TCGCAATGCGAATTTAGAAAA
1 TCGCAATGCGAATTTAGAAAA
*
22941 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTAGAAAA
22962 TCGCAATGCGA
1 TCGCAATGCGA
22973 TACTGACTAT
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
20 12 0.18
21 55 0.82
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAATTTAGAAAA
Found at i:22950 original size:42 final size:41
Alignment explanation
Indices: 22879--22972 Score: 152
Period size: 42 Copynumber: 2.3 Consensus size: 41
22869 TTTTCCCAAT
* *
22879 TCGCAATGCGAATAAGTAAATCGCAATGCGAATTTGGGAAA
1 TCGCAATGCGAATAAGAAAATCGCAATGCGAATTTGGAAAA
*
22920 TCGCAATGCGAATTTAGAAAATCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TAAGAAAATCGCAATGCGAATTTGGAAAA
22962 TCGCAATGCGA
1 TCGCAATGCGA
22973 TACTGACTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
41 12 0.24
42 37 0.76
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.22
Consensus pattern (41 bp):
TCGCAATGCGAATAAGAAAATCGCAATGCGAATTTGGAAAA
Found at i:22985 original size:41 final size:41
Alignment explanation
Indices: 22898--23033 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
22888 GAATAAGTAA
* * * **
22898 ATCGCAATGCGAATTTGGGAAATCGCAATGCGA-ATTTAGAAA
1 ATCGCAACGCGAATTTGGAAAATCGCAATGCGATA-CT-GACT
*
22940 ATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTTGGAAAATCGCAATGCGATACTGACT
* ** * *
22981 ATCGCAACGCG-ATAATACAAAATCGCAACGCGATACTTACT
1 ATCGCAACGCGAAT-TTGGAAAATCGCAATGCGATACTGACT
*
23022 TTCGCAACGCGA
1 ATCGCAACGCGA
23034 TACTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 2 0.03
41 44 0.55
42 33 0.41
43 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (41 bp):
ATCGCAACGCGAATTTGGAAAATCGCAATGCGATACTGACT
Found at i:22986 original size:20 final size:19
Alignment explanation
Indices: 22961--23075 Score: 95
Period size: 20 Copynumber: 5.7 Consensus size: 19
22951 AATTTGGAAA
*
22961 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACT-ACT
* *
22981 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATACTAC--T
23002 ATCGCAACGCGATACTTACT
1 ATCGCAACGCGATAC-TACT
*
23022 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACT-ACT
* * *
23042 TTCGCAACGAGATAATACAT
1 ATCGCAACGCGATACTAC-T
*
23062 AATCGCAATGCGAT
1 -ATCGCAACGCGAT
23076 TTTCAAAGCG
Statistics
Matches: 78, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
19 5 0.06
20 46 0.59
21 24 0.31
22 3 0.04
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (19 bp):
ATCGCAACGCGATACTACT
Found at i:23034 original size:41 final size:41
Alignment explanation
Indices: 22958--23035 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
22948 GCGAATTTGG
*
22958 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* *
22999 AAAATCGCAACGCGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATA
23036 CTGACTTTCG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.21
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:23564 original size:20 final size:20
Alignment explanation
Indices: 23515--23573 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
23505 TTTATTCTCT
* **
23515 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
23535 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
23555 TGTTGCGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
23574 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:23764 original size:25 final size:24
Alignment explanation
Indices: 23710--23764 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
23700 TGTTTATTAT
* *
23710 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
23734 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
23760 TGTTT
1 TGTTT
23765 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:24913 original size:18 final size:18
Alignment explanation
Indices: 24892--24939 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
24882 TCCACTTCGG
24892 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
24910 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
24928 GAGCCATCACCT
1 GAGCCATCACCT
24940 GATCGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:25513 original size:20 final size:19
Alignment explanation
Indices: 25474--25594 Score: 74
Period size: 19 Copynumber: 6.6 Consensus size: 19
25464 TAGTTTACTT
* *
25474 TCGCAACACAAAATGACTA
1 TCGCAACGCGAAATGACTA
*
25493 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGACTA
* **
25513 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGACTA
25532 TCGCAA--CGACAA--A--A
1 TCGCAACGCGA-AATGACTA
* **
25546 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGACTA
**
25565 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGACTA
*
25584 TCGCAATGCGA
1 TCGCAACGCGA
25595 TTTGTGTTTC
Statistics
Matches: 85, Mismatches: 9, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
14 7 0.08
15 2 0.02
16 4 0.05
17 4 0.05
18 2 0.02
19 50 0.59
20 16 0.19
ACGTcount: A:0.43, C:0.22, G:0.21, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGACTA
Found at i:25566 original size:19 final size:19
Alignment explanation
Indices: 25512--25594 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
25502 GGAAATGGCT
25512 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
25531 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
25545 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
25564 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
25583 ATCGCAATGCGA
1 ATCGCAATGCGA
25595 TTTGTGTTTC
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 39 0.71
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:25639 original size:33 final size:33
Alignment explanation
Indices: 25602--25680 Score: 122
Period size: 33 Copynumber: 2.4 Consensus size: 33
25592 CGATTTGTGT
* *
25602 TTCACGTTGCGATTTTGTCGTTGCGATTTTCAC
1 TTCACATTGCGATTTTATCGTTGCGATTTTCAC
*
25635 TTCACATTGCGATTTTATCGTTGCGATTTTCAT
1 TTCACATTGCGATTTTATCGTTGCGATTTTCAC
*
25668 TTCGCATTGCGAT
1 TTCACATTGCGAT
25681 AGCCATTTCC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.15, C:0.20, G:0.19, T:0.46
Consensus pattern (33 bp):
TTCACATTGCGATTTTATCGTTGCGATTTTCAC
Found at i:25660 original size:14 final size:14
Alignment explanation
Indices: 25606--25664 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
25596 TTGTGTTTCA
*
25606 CGTTGCGATTTTGT
1 CGTTGCGATTTTAT
25620 CGTTGCGATTTTCACTT
1 CGTTGCGATTTT-A--T
*
25637 CACATTGCGATTTTAT
1 --CGTTGCGATTTTAT
25653 CGTTGCGATTTT
1 CGTTGCGATTTT
25665 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 23 0.62
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.30
ACGTcount: A:0.14, C:0.19, G:0.20, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTAT
Found at i:25679 original size:19 final size:18
Alignment explanation
Indices: 25622--25680 Score: 63
Period size: 19 Copynumber: 3.4 Consensus size: 18
25612 GATTTTGTCG
*
25622 TTGCGATTTTCACTTCACA
1 TTGCGATTTTCA-TTCGCA
25641 TTGCGATTTT-A-TCG--
1 TTGCGATTTTCATTCGCA
25655 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCA-TTCGCA
25674 TTGCGAT
1 TTGCGAT
25681 AGCCATTTCC
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 10 0.29
15 1 0.03
16 2 0.06
17 3 0.09
18 1 0.03
19 17 0.50
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (18 bp):
TTGCGATTTTCATTCGCA
Found at i:25699 original size:20 final size:20
Alignment explanation
Indices: 25665--25719 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
25655 TTGCGATTTT
*
25665 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
25684 CATTTCCGCGTTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
*
25704 CATTTCCGTGTTGCGA
1 CATTTCCGCGTTGCGA
25720 AAGTAAGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 5 0.15
20 28 0.85
ACGTcount: A:0.16, C:0.27, G:0.24, T:0.33
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGC
Found at i:26158 original size:42 final size:42
Alignment explanation
Indices: 26087--26175 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 42
26077 GACTCACCTG
* * * *
26087 TCATCCCTCAAGAGTCCTCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCCCCCAACCGTTCAAGAGGCCACTA
** *
26129 TCATCCCTCAAGAGTCCCCCCCCCCCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCCCCAACCGTTCAAGAGGCCACTA
26171 TCATC
1 TCATC
26176 GTTGAAGAGG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.21, C:0.43, G:0.15, T:0.21
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCCCCCCAACCGTTCAAGAGGCCACTA
Found at i:27618 original size:14 final size:14
Alignment explanation
Indices: 27584--27622 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
27574 TTGATTGTTT
27584 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
27598 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
27612 TGTTGATTTGT
1 AATTGATTTGT
27623 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:27852 original size:19 final size:19
Alignment explanation
Indices: 27762--27845 Score: 159
Period size: 19 Copynumber: 4.4 Consensus size: 19
27752 GCAATGAGAG
27762 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
27781 AATTGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
27800 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
27819 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
27838 AATCGCAA
1 AATCGCAA
27846 CGAGAAAATC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 63 1.00
ACGTcount: A:0.48, C:0.15, G:0.20, T:0.17
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:27858 original size:33 final size:36
Alignment explanation
Indices: 27762--27864 Score: 131
Period size: 38 Copynumber: 2.8 Consensus size: 36
27752 GCAATGAGAG
*
27762 AATCGCAATGCGAAATGAAAATTGCAATGCGAAATGAA
1 AATCGCAA-GCG-AATGAAAATCGCAATGCGAAATGAA
27800 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA-GCG-AATGAAAATCGCAATGCGAAATGAA
*
27838 AATCGCAA-CG-A-GAAAATCGCAAAGCGA
1 AATCGCAAGCGAATGAAAATCGCAATGCGA
27865 TTTTCATTTC
Statistics
Matches: 63, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
33 15 0.24
34 1 0.02
36 2 0.03
38 45 0.71
ACGTcount: A:0.48, C:0.17, G:0.21, T:0.15
Consensus pattern (36 bp):
AATCGCAAGCGAATGAAAATCGCAATGCGAAATGAA
Found at i:27908 original size:20 final size:20
Alignment explanation
Indices: 27883--27978 Score: 156
Period size: 20 Copynumber: 4.8 Consensus size: 20
27873 TCGCATTGCG
*
27883 ATTTTCTCGTTGCGATAGCC
1 ATTTTCACGTTGCGATAGCC
27903 ATTTTCACGTTGCGATAGCC
1 ATTTTCACGTTGCGATAGCC
27923 ATTTTCACGTTGCGATAGCC
1 ATTTTCACGTTGCGATAGCC
* *
27943 ATTTTCGCGTTGCGATAGTC
1 ATTTTCACGTTGCGATAGCC
*
27963 ATTTTCGCGTTGCGAT
1 ATTTTCACGTTGCGAT
27979 TTCCCCGTTG
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 73 1.00
ACGTcount: A:0.17, C:0.23, G:0.22, T:0.39
Consensus pattern (20 bp):
ATTTTCACGTTGCGATAGCC
Found at i:28554 original size:20 final size:20
Alignment explanation
Indices: 28524--28635 Score: 118
Period size: 20 Copynumber: 5.5 Consensus size: 20
28514 GATTCTGTAT
* *
28524 TATCCCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* *
28544 AATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
28564 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
** *
28584 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
28605 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
28625 TATCGCATTGC
1 TATCGCGTTGC
28636 AATTTTCCAA
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
19 3 0.04
20 59 0.76
21 14 0.18
22 2 0.03
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:28625 original size:41 final size:41
Alignment explanation
Indices: 28504--28641 Score: 154
Period size: 41 Copynumber: 3.4 Consensus size: 41
28494 AACTTTAAAA
* * *
28504 ATCGCATTGCGATTCTGTATTATCCCGTTGCGATAGTCAGA
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
* * ** * *
28545 ATCTCGTTGCGA--AAGTCAGTATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGT-ATTATCGCGTTGCGATAGTCAGT
*
28585 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
*
28626 ATCGCATTGCAATTTT
1 ATCGCATTGCGATTTT
28642 CCAAATTCGC
Statistics
Matches: 79, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
39 2 0.03
40 30 0.38
41 45 0.57
42 2 0.03
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.35
Consensus pattern (41 bp):
ATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
Found at i:28657 original size:41 final size:41
Alignment explanation
Indices: 28564--28659 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 41
28554 CGAAAGTCAG
* * * ** *
28564 TATCGCGTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTAT
1 TATCGCGTTGCGATAGTCAGTATCGCATTGCAATTTTCAAA
28605 TATCGCGTTGCGATAGTCAGTATCGCATTGCAATTTTCCAAA
1 TATCGCGTTGCGATAGTCAGTATCGCATTGCAATTTT-CAAA
*
28647 T-TCGCATTGCGAT
1 TATCGCGTTGCGAT
28660 TTACTTATTC
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 45 0.96
42 2 0.04
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTCAGTATCGCATTGCAATTTTCAAA
Found at i:28720 original size:21 final size:22
Alignment explanation
Indices: 28668--28720 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
28658 ATTTACTTAT
28668 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
28689 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
28710 TCGCATTGCGA
1 TCGCATTGCGA
28721 TAGTAATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:30806 original size:43 final size:43
Alignment explanation
Indices: 30740--30887 Score: 179
Period size: 43 Copynumber: 3.4 Consensus size: 43
30730 TTTTTTAACA
* * * **
30740 AAAAACACTGCAATAGGTATTGATATTTAGCGGCGTTTGTGTG
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTAAG
* * *
30783 ACAAACGCCGCAATAGGTGTTGATATTTAGTGGCGTTTGTCAG
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTAAG
* * * *
30826 AAAAATGCCACAATAGGTGTTGATATTTAGCGGCATTTTTAAG
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTAAG
*
30869 ATAAACGCCGCAATAGGTG
1 AAAAACGCCGCAATAGGTG
30888 ATGTTTAACG
Statistics
Matches: 88, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 88 1.00
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (43 bp):
AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTAAG
Found at i:33146 original size:31 final size:31
Alignment explanation
Indices: 33069--33146 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
33059 GTTTTAAAAG
* * **
33069 TAACAAATTAGACACTAATATTATTGATTTA
1 TAACAAAATAGTCACTAATATTATCAATTTA
*
33100 TATCAAAAT-GCTCACTAATATTATCAATTTA
1 TAACAAAATAG-TCACTAATATTATCAATTTA
33131 TAACAAAATAGTCACT
1 TAACAAAATAGTCACT
33147 CCACTGTCAT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
30 1 0.03
31 37 0.95
32 1 0.03
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (31 bp):
TAACAAAATAGTCACTAATATTATCAATTTA
Found at i:33470 original size:24 final size:22
Alignment explanation
Indices: 33422--33472 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
33412 ATTTTTAGGT
*
33422 ATTTTAATTCTTAATTTTTACA
1 ATTTTAATTCTTAATTTTTAAA
* *
33444 ATTTTAATATTTTTATTTTTAAA
1 ATTTTAAT-TCTTAATTTTTAAA
*
33467 AATTTA
1 ATTTTA
33473 TTCAAGTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (22 bp):
ATTTTAATTCTTAATTTTTAAA
Found at i:41110 original size:29 final size:29
Alignment explanation
Indices: 41067--41149 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
41057 CTCTCCTAAC
41067 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
41097 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
41126 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
41150 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:45877 original size:29 final size:29
Alignment explanation
Indices: 45834--45916 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
45824 CTCACCTAAC
45834 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
45864 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
45893 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
45917 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:54009 original size:20 final size:20
Alignment explanation
Indices: 53957--54015 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
53947 AATAGTTTCT
** *
53957 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
53977 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
** *
53997 GAATTTGATTATCGCAACG
1 GAAAATGACTATCGCAACG
54016 AGAGAATCGC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.42, C:0.20, G:0.19, T:0.19
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:54305 original size:22 final size:22
Alignment explanation
Indices: 54278--54321 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
54268 GATGGAGATA
54278 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
54300 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
54322 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:54557 original size:20 final size:20
Alignment explanation
Indices: 54510--54561 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
54500 ATTATGTATT
*
54510 ATCGCGCTGCGAAAGTCAGA
1 ATCGCGTTGCGAAAGTCAGA
*
54530 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTCAGA
*
54550 ATCTCGTTGCGA
1 ATCGCGTTGCGA
54562 TTTTGTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.25, C:0.23, G:0.29, T:0.23
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAGA
Found at i:54595 original size:20 final size:20
Alignment explanation
Indices: 54570--54623 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
54560 GATTTTGTAT
54570 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
54590 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
54610 TATCGCATTGCGAT
1 TATCGCATTGCGAT
54624 TTTCTCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:54595 original size:61 final size:61
Alignment explanation
Indices: 54489--54626 Score: 186
Period size: 61 Copynumber: 2.3 Consensus size: 61
54479 CGCTTTGAAA
* * * *
54489 ATCGCATTGCGATTATGTATTATCGCGCTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCACTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * * *
54550 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCACTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
54611 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
54627 CTCAATTCGT
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCACTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:54661 original size:20 final size:21
Alignment explanation
Indices: 54612--54663 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
54602 ATAGTCAGTA
*
54612 TCGCATTGCGATTTTCTCAAT
1 TCGCATTGCGATTTACTCAAT
** *
54633 TCGTGTTGCGATTTACT-TAT
1 TCGCATTGCGATTTACTCAAT
54653 TCGCATTGCGA
1 TCGCATTGCGA
54664 ATTGGGAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 11 0.44
21 14 0.56
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.42
Consensus pattern (21 bp):
TCGCATTGCGATTTACTCAAT
Found at i:54734 original size:21 final size:21
Alignment explanation
Indices: 54694--54734 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
54684 ACTGTAGACC
** *
54694 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
54715 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
54735 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:61676 original size:43 final size:43
Alignment explanation
Indices: 61628--61710 Score: 148
Period size: 43 Copynumber: 1.9 Consensus size: 43
61618 AGCTTAAGAA
* *
61628 TTAATCTTATAAATACCCTAAAGTATAATGACTAAATTATGAT
1 TTAATCTTATAAATACCCTAAAATATAAAGACTAAATTATGAT
61671 TTAATCTTATAAATACCCTAAAATATAAAGACTAAATTAT
1 TTAATCTTATAAATACCCTAAAATATAAAGACTAAATTAT
61711 AATTAACTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.36
Consensus pattern (43 bp):
TTAATCTTATAAATACCCTAAAATATAAAGACTAAATTATGAT
Found at i:79126 original size:18 final size:18
Alignment explanation
Indices: 79086--79124 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
79076 TAATCAATAG
79086 AAAATATAAAAAAAATTT
1 AAAATATAAAAAAAATTT
*
79104 AAAATAT-AAAAGAATTT
1 AAAATATAAAAAAAATTT
79121 AAAA
1 AAAA
79125 ATTTTAGGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAATATAAAAAAAATTT
Found at i:83536 original size:2 final size:2
Alignment explanation
Indices: 83524--83601 Score: 138
Period size: 2 Copynumber: 39.0 Consensus size: 2
83514 ATTATTGAAA
*
83524 AT AT TT AT AT 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 AT AT AT AT AT
*
83566 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
83602 TAATATTTTT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:87873 original size:21 final size:21
Alignment explanation
Indices: 87849--87889 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
87839 AATGATGACT
**
87849 TGATATACCAAGTGGAAATGA
1 TGATATACCAAACGGAAATGA
87870 TGATATACCAAACGGAAATG
1 TGATATACCAAACGGAAATG
87890 GTGGAGCATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.22
Consensus pattern (21 bp):
TGATATACCAAACGGAAATGA
Done.