Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004763.1 Hibiscus syriacus cultivar Beakdansim tig00010743_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: 62859
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Found at i:176 original size:42 final size:41
Alignment explanation
Indices: 99--196 Score: 106
Period size: 42 Copynumber: 2.4 Consensus size: 41
89 TTCACAATTT
* * * *
99 ATAAGTCCTTCGGGCCATCAGCAAGTCTTTCGAGCATGATG
1 ATAAATCCTTCGGGCCATCAGCAAGCCTTTAGAGCAAGATG
* * * *
140 CTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG
1 -ATAAATCCTTCGGGCCATCAGCAAGCCTTTAGAGCAAGATG
*
182 ATAAGTCCTTCGGGC
1 ATAAATCCTTCGGGC
197 TATCCATAAA
Statistics
Matches: 45, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
41 12 0.27
42 33 0.73
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.29
Consensus pattern (41 bp):
ATAAATCCTTCGGGCCATCAGCAAGCCTTTAGAGCAAGATG
Found at i:369 original size:214 final size:214
Alignment explanation
Indices: 1--591 Score: 966
Period size: 214 Copynumber: 2.8 Consensus size: 214
*
1 GGTAGGATGTTTTCAAATGAATTTGAAAATGAG-AAATGACTTTTCAAGAAGA-GGAATTTTTGA
1 GGTAGGATGTTTTC-AATGAATTTGAAAATGAGAAAATGACGTTTCAAGAAGATGGAATTTTTGA
* *
64 AAATGAAGAATGTGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGCAAGTCTTT
65 AAACGAAGAATGTGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTT
*
129 CGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCG
130 CGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGATAAGGCCTTCG
*
194 GGCTATCCATAAAACCTTCG
195 GGCCATCCATAAAACCTTCG
214 GGTAGGATGTTTTCAATGAATTTGAAAATGAGAAAATGACGTTTCAAGAAGATGGAATTTTTGAA
1 GGTAGGATGTTTTCAATGAATTTGAAAATGAGAAAATGACGTTTCAAGAAGATGGAATTTTTGAA
* *
279 AACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAATCCTTCGGGCCATCAGTAAGTCTTTC
66 AACGAAGAATGTGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTC
344 GAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGATAAGGCCTTCGG
131 GAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGATAAGGCCTTCGG
409 GCCATCCATAAAACCTTCG
196 GCCATCCATAAAACCTTCG
* * * * *
428 GGTAGGATGTTTTCACAAGTATTT-AAAATGA-AAAATGATGTTTTAAG-A-ATGGAATTTTTAA
1 GGTAGGATGTTTTCA-ATGAATTTGAAAATGAGAAAATGACGTTTCAAGAAGATGGAATTTTTGA
489 AAACGAAGAA-GTGA-TTTCAAAATTTCAC-ATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTT
65 AAACGAAGAATGTGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTT
* * *
551 CGAGCATGATGCTTAAATCCTTCGGGTAATTTTTAAGCCTT
130 CGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTT
592 CAAAAGAGAG
Statistics
Matches: 358, Mismatches: 17, Indels: 11
0.93 0.04 0.03
Matches are distributed among these distances:
208 71 0.20
209 14 0.04
210 3 0.01
211 22 0.06
212 19 0.05
213 46 0.13
214 177 0.49
215 6 0.02
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (214 bp):
GGTAGGATGTTTTCAATGAATTTGAAAATGAGAAAATGACGTTTCAAGAAGATGGAATTTTTGAA
AACGAAGAATGTGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTC
GAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGATAAGGCCTTCGG
GCCATCCATAAAACCTTCG
Found at i:379 original size:42 final size:42
Alignment explanation
Indices: 314--414 Score: 123
Period size: 42 Copynumber: 2.4 Consensus size: 42
304 TCACAATTTA
* * *
314 TAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCT
1 TAAATCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATGCT
* * *
356 TAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG-A
1 TAAATCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATGCT
**
397 TAAGGCCTTCGGGCCATC
1 TAAATCCTTCGGGCCATC
415 CATAAAACCT
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 15 0.30
42 35 0.70
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.29
Consensus pattern (42 bp):
TAAATCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATGCT
Found at i:4336 original size:35 final size:35
Alignment explanation
Indices: 4293--4362 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
4283 TGATTTATTG
*
4293 TTACATACTCATGAAGATGGTCCTCATGAAAATTA
1 TTACATACTCAAGAAGATGGTCCTCATGAAAATTA
* *
4328 TTACATACTTAAGAAGATGGTCCTCGTGAAAATTA
1 TTACATACTCAAGAAGATGGTCCTCATGAAAATTA
4363 CAACATACCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (35 bp):
TTACATACTCAAGAAGATGGTCCTCATGAAAATTA
Found at i:4369 original size:35 final size:35
Alignment explanation
Indices: 4295--4370 Score: 107
Period size: 35 Copynumber: 2.2 Consensus size: 35
4285 ATTTATTGTT
* **
4295 ACATACTCATGAAGATGGTCCTCATGAAAATTATT
1 ACATACTCAAGAAGATGGTCCTCATGAAAATTACA
* *
4330 ACATACTTAAGAAGATGGTCCTCGTGAAAATTACA
1 ACATACTCAAGAAGATGGTCCTCATGAAAATTACA
4365 ACATAC
1 ACATAC
4371 CAATGCAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.28
Consensus pattern (35 bp):
ACATACTCAAGAAGATGGTCCTCATGAAAATTACA
Found at i:8905 original size:27 final size:26
Alignment explanation
Indices: 8864--8933 Score: 85
Period size: 27 Copynumber: 2.8 Consensus size: 26
8854 TTTAAATAAA
8864 AATAAAATATTTTTAAATTAAGTTAAT
1 AATAAAATA-TTTTAAATTAAGTTAAT
8891 AATAAAATATATTT-AA-TAAGTTAAT
1 AATAAAATAT-TTTAAATTAAGTTAAT
*
8916 -A-AAAATATTTTAAGTTAA
1 AATAAAATATTTTAAATTAA
8934 TATATATAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
22 3 0.08
23 8 0.21
24 4 0.10
25 9 0.23
26 3 0.08
27 12 0.31
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (26 bp):
AATAAAATATTTTAAATTAAGTTAAT
Found at i:8906 original size:22 final size:22
Alignment explanation
Indices: 8881--8945 Score: 64
Period size: 22 Copynumber: 2.9 Consensus size: 22
8871 TATTTTTAAA
8881 TTAAGTTAATAAT-AAAATATAT
1 TTAAGTTAATAATAAAAATAT-T
8903 TTAA--TAAGTTAATAAAAATATT
1 TTAAGTTAA--TAATAAAAATATT
8925 TTAAGTTAATATATATAAAAT
1 TTAAGTTAATA-ATA-AAAAT
8946 TATATTATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
20 3 0.08
22 15 0.42
23 10 0.28
24 8 0.22
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.42
Consensus pattern (22 bp):
TTAAGTTAATAATAAAAATATT
Found at i:8931 original size:19 final size:21
Alignment explanation
Indices: 8890--8935 Score: 69
Period size: 19 Copynumber: 2.2 Consensus size: 21
8880 ATTAAGTTAA
8890 TAATAAAATATATTTAATAAGT
1 TAATAAAATATATTT-ATAAGT
8912 TAATAAAA-ATATTT-TAAGT
1 TAATAAAATATATTTATAAGT
8931 TAATA
1 TAATA
8936 TATATAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 10 0.42
21 6 0.25
22 8 0.33
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (21 bp):
TAATAAAATATATTTATAAGT
Found at i:9237 original size:39 final size:39
Alignment explanation
Indices: 9194--9285 Score: 114
Period size: 39 Copynumber: 2.4 Consensus size: 39
9184 TTTTAAAAAT
9194 AATTTAGAATGTTAATGTG-AAATAATTTAAGAAATTAAG
1 AATTTAGAATGTTAATGTGTAAA-AATTTAAGAAATTAAG
** * * *
9233 AATTTAGAACATTATTGTGTCAAAATTTAAGAAATTAGG
1 AATTTAGAATGTTAATGTGTAAAAATTTAAGAAATTAAG
*
9272 ATTTTAGAATGTTA
1 AATTTAGAATGTTA
9286 GAGTAATAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
39 42 0.95
40 2 0.05
ACGTcount: A:0.45, C:0.02, G:0.15, T:0.38
Consensus pattern (39 bp):
AATTTAGAATGTTAATGTGTAAAAATTTAAGAAATTAAG
Found at i:9780 original size:2 final size:2
Alignment explanation
Indices: 9773--9809 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
9763 ATTTGATGCG
9773 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9810 ACACATTTTG
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11028 original size:2 final size:2
Alignment explanation
Indices: 11021--11047 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11011 GCCAAACAAA
11021 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
11048 ATGAAGAACG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15226 original size:17 final size:17
Alignment explanation
Indices: 15185--15229 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
15175 CAATACTTGA
15185 TTAAATATTTAATAAAT
1 TTAAATATTTAATAAAT
** **
15202 TTTTATATTTTTTAAAT
1 TTAAATATTTAATAAAT
15219 TTAAATATTTA
1 TTAAATATTTA
15230 TTTTTACATG
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTAAATATTTAATAAAT
Found at i:25102 original size:4 final size:4
Alignment explanation
Indices: 25090--26761 Score: 1645
Period size: 4 Copynumber: 430.8 Consensus size: 4
25080 GTGTGTGTGT
*
25090 GTGC ATGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
1 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
25138 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
1 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
25186 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
1 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
25234 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
1 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
* * * * * *
25282 GTGC GTGT GTGTC TGTGT GTGT GTGC GT-C -TGT GTGT GTGC GT-C TGTGT
1 GTGC GTGC GTG-C -GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC -GTGC
* * * * * * *
25330 GTGT GTGC GT-C -TGT GTGT GTCC GT-C -TGT GTGT GTGC GT-C -TGT
1 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
* * * * * *
25372 GTGTC -TGC GTGC GTTGT GTGTC -TGC GTGC GT-T GTGT GTGC GTGT GCGT
1 GTG-C GTGC GTGC G-TGC GTG-C GTGC GTGC GTGC GTGC GTGC GTGC GTGC
* * * * * *
25420 GTGT GTGC GT-C -TGT GTGT GTGC GT-C -TGT GTGT GTGC GTGC GTTGT
1 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC G-TGC
* * * * * *
25465 GTGT GTGT GTGC GTGC GTGC GT-C -TGT GTGT GTGC GTGC GT-T GTGT
1 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
* *
25510 GTGC GT-- GTGC GTGC GTGG GTGG GTGC GTGC GTGC GTGC GTGC GTGC
1 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
25556 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
1 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
25604 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
1 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
25652 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
1 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
25700 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
1 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
* * * * * *
25748 GT-- GTGT GTGT GTGC GT-C TGTGT GTGT GTGC GT-C TGTGT GTGT GTGTC
1 GTGC GTGC GTGC GTGC GTGC -GTGC GTGC GTGC GTGC -GTGC GTGC GTG-C
* * *
25795 -TGT GTGT GTGC GT-C TGTGC GT-C -TGC GTGC GTTGT GTGTC -TGC GTGC
1 GTGC GTGC GTGC GTGC -GTGC GTGC GTGC GTGC G-TGC GTG-C GTGC GTGC
* * * * * * * *
25841 GT-T GTGT GTGC GTGT GCGT GTGT GTGC GT-C -TGT GTGT GTGC GTGC
1 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
* * * * * * *
25886 GTTGT GTGT GTGT GTGC GTGC GT-C -TGT GTGT GTGC GTGC GT-T GTGT
1 G-TGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
* * *
25932 GTGC GTGT GTGC GTGC GTGC GTGT GTGC GTGC GTGG GTGGC GTGC GTGC
1 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GT-GC GTGC GTGC
25981 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
1 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
26029 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
1 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
* * * * *
26077 GTGC GTGC GTGC GTGC GTGC GTGC GTGT GTGT GTGT GT-C -TGT GTGT
1 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
* * * * *
26123 GTGC GT-C -TGT GTGT GTGC GTGT GTGTC -TGC GTGC GT-T GTGT GTGTC
1 GTGC GTGC GTGC GTGC GTGC GTGC GTG-C GTGC GTGC GTGC GTGC GTG-C
* * * * * *
26169 -TGC GTGC GT-T GTGT GTGC GT-C -TGT GTGT GTGC GT-C -TGT GTGT
1 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
* * * * * *
26211 GTGC GTGC GT-T GTGT GTGT GTGT GTGC GTGC GT-C -TGT GTGT GTGC
1 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
* * * *
26256 GTGC GT-T GTGT GTGC GTGT GTGC GTGC GTGG GTG- G-GC GTGC GTGC
1 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
* *
26301 GTGC GTGT GTGC GTGC GTGG GTG- G-GC GTGC GTGC GTGC GTGC GTGC
1 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
26347 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
1 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
26395 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GT-C
1 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
* * * * * *
26442 -TGT GTGT GTGC GT-C -TGT GTGT GTGC GT-C TGTGT GTGC GT-C -TGT
1 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC -GTGC GTGC GTGC GTGC
* * * *
26485 GTGTC -TGC GTGC GTTGT GTGTC -TGC GTGC GT-T GTGT GTGC GT-C -TGT
1 GTG-C GTGC GTGC G-TGC GTG-C GTGC GTGC GTGC GTGC GTGC GTGC GTGC
* * * * * *
26531 GTGT GTGC GTGC GTTGT GTGT GTGT GTGC GTGC GTGC GT-C -TGT GTGT
1 GTGC GTGC GTGC G-TGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
* * * *
26578 GTGC GTGC GT-T GTGT GTGC GTGT GTGC GTGC GTGC GTGT GTGC GTGC
1 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
*
26625 GTGG GTG- G-GC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
1 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
26671 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
1 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
26719 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTG
1 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTG
26762 TGTATTAACT
Statistics
Matches: 1454, Mismatches: 119, Indels: 190
0.82 0.07 0.11
Matches are distributed among these distances:
2 27 0.02
3 58 0.04
4 1344 0.92
5 22 0.02
6 3 0.00
ACGTcount: A:0.00, C:0.19, G:0.48, T:0.33
Consensus pattern (4 bp):
GTGC
Found at i:27204 original size:15 final size:15
Alignment explanation
Indices: 27180--27213 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
27170 CAGTACAGGG
*
27180 GGAACCGTCACCGGA
1 GGAACAGTCACCGGA
*
27195 GGAACAGTCACTGGA
1 GGAACAGTCACCGGA
27210 GGAA
1 GGAA
27214 GTGTAACAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.32, C:0.24, G:0.35, T:0.09
Consensus pattern (15 bp):
GGAACAGTCACCGGA
Found at i:27243 original size:45 final size:45
Alignment explanation
Indices: 27192--27331 Score: 176
Period size: 45 Copynumber: 3.1 Consensus size: 45
27182 AACCGTCACC
* **
27192 GGAGGAACAGTCACTGGAGGAAGTGTAACAGGTGGTTTTAGAGCT
1 GGAGGAACAGTCACCGGAGGAAGTGTAATTGGTGGTTTTAGAGCT
* ** * *
27237 GGAGG-A-AGTTCTACCGGAGGGAGTGTAATTGGTGACTTTACAACT
1 GGAGGAACAG-TC-ACCGGAGGAAGTGTAATTGGTGGTTTTAGAGCT
27282 GGAGGAACAGTCACCGGAGGAAGTGTAATTGGTGGTTTTAGAGCT
1 GGAGGAACAGTCACCGGAGGAAGTGTAATTGGTGGTTTTAGAGCT
27327 GGAGG
1 GGAGG
27332 TAGTCCAACT
Statistics
Matches: 78, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
43 2 0.03
44 3 0.04
45 68 0.87
46 3 0.04
47 2 0.03
ACGTcount: A:0.27, C:0.11, G:0.38, T:0.24
Consensus pattern (45 bp):
GGAGGAACAGTCACCGGAGGAAGTGTAATTGGTGGTTTTAGAGCT
Found at i:27363 original size:44 final size:44
Alignment explanation
Indices: 27300--27387 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 44
27290 AGTCACCGGA
* * * * * *
27300 GGAAGTGTAATTGGTGGTTTTAGAGCTGGAGGTAGTCCAACTGG
1 GGAAGCGTAATTGGCGGTTTAACAACTGGAGGGAGTCCAACTGG
*
27344 GGAAGCGTAATTGGCGGTTTAACAACTGGAGGGAGTTCAACTGG
1 GGAAGCGTAATTGGCGGTTTAACAACTGGAGGGAGTCCAACTGG
27388 TGGCTTCACC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.25, C:0.11, G:0.38, T:0.26
Consensus pattern (44 bp):
GGAAGCGTAATTGGCGGTTTAACAACTGGAGGGAGTCCAACTGG
Found at i:27429 original size:72 final size:71
Alignment explanation
Indices: 27339--27476 Score: 222
Period size: 72 Copynumber: 1.9 Consensus size: 71
27329 AGGTAGTCCA
27339 ACTGGGGAAGCGTAATTGGCGGTTTAACAACTGGAGGGAGTTCAACTGGTGGCTTCACCGGAGGA
1 ACTGGGGAAGCGTAATTGGCGGTTTAACAACTGGAGGGAGTTCAACTGGTGGCTTCACCGGAGGA
27404 ATTGTT
66 ATTGTT
* * ** *
27410 ACTGGAGGAAGCGTGATTGGTGGTTTAACAGTTGGAGGGAGTTCAACTGGTGGCTTCACTGGAGG
1 ACTGG-GGAAGCGTAATTGGCGGTTTAACAACTGGAGGGAGTTCAACTGGTGGCTTCACCGGAGG
27475 AA
65 AA
27477 GTGTGATTGG
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
71 5 0.08
72 56 0.92
ACGTcount: A:0.24, C:0.14, G:0.37, T:0.25
Consensus pattern (71 bp):
ACTGGGGAAGCGTAATTGGCGGTTTAACAACTGGAGGGAGTTCAACTGGTGGCTTCACCGGAGGA
ATTGTT
Found at i:27461 original size:30 final size:29
Alignment explanation
Indices: 27410--27684 Score: 141
Period size: 30 Copynumber: 9.4 Consensus size: 29
27400 AGGAATTGTT
* * *
27410 ACTGGAGGAAGCGTGATTGGTGGTTTAAC
1 ACTGGAGGAAGTGTAACTGGTGGTTTAAC
* * *
27439 AGTTGGAGGGAGT-TCAACTGGTGGCTT--C
1 A-CTGGAGGAAGTGT-AACTGGTGGTTTAAC
* * *
27467 ACTGGAGGAAGTGTGATTGGTGGTTTTAC
1 ACTGGAGGAAGTGTAACTGGTGGTTTAAC
*
27496 AACTGGAGGAAGTGTAATTGGTGGTTTAAC
1 -ACTGGAGGAAGTGTAACTGGTGGTTTAAC
* * *
27526 ATTTGGAGGGAGT-TCAACTGGTGGCTT--C
1 A-CTGGAGGAAGTGT-AACTGGTGGTTTAAC
* * *
27554 ACTGGAGGAAGTGTGATTGGTGGTTTTAC
1 ACTGGAGGAAGTGTAACTGGTGGTTTAAC
* *
27583 AACTGGAGGAAGTGTGATTGGTGGCTTT-AC
1 -ACTGGAGGAAGTGTAACTGGTGG-TTTAAC
* * * * * * *
27613 TGCCGGAGGAAGAGTGATTGGTGGCTTGAC
1 -ACTGGAGGAAGTGTAACTGGTGGTTTAAC
* * * *
27643 GACCGGAGGAAGTGTGATTGGTGGTTTTAC
1 -ACTGGAGGAAGTGTAACTGGTGGTTTAAC
*
27673 AACAGGAGGAAG
1 -ACTGGAGGAAG
27685 AGTGACCGGT
Statistics
Matches: 198, Mismatches: 34, Indels: 27
0.76 0.13 0.10
Matches are distributed among these distances:
27 36 0.18
28 6 0.03
29 8 0.04
30 145 0.73
31 3 0.02
ACGTcount: A:0.23, C:0.10, G:0.38, T:0.29
Consensus pattern (29 bp):
ACTGGAGGAAGTGTAACTGGTGGTTTAAC
Found at i:27518 original size:57 final size:59
Alignment explanation
Indices: 27410--27684 Score: 240
Period size: 57 Copynumber: 4.7 Consensus size: 59
27400 AGGAATTGTT
* * ** * *
27410 ACTGGAGGAAGCGTGATTGGTGGTTTAACAGTTGGAGGGAGT-TCAACTGGTGGCTT-C-
1 ACTGGAGGAAGTGTGATTGGTGGTTTTACAACTGGAGGAAGTGT-AATTGGTGGCTTACA
*
27467 ACTGGAGGAAGTGTGATTGGTGGTTTTACAACTGGAGGAAGTGTAATTGGTGGTTTAACA
1 ACTGGAGGAAGTGTGATTGGTGGTTTTACAACTGGAGGAAGTGTAATTGGTGGCTT-ACA
** * * * * * *
27527 TTTGGAGGGAGT-TCAACTGGTGG-CTT-C-ACTGGAGGAAGTGTGATTGGTGGTTTTACA
1 ACTGGAGGAAGTGT-GATTGGTGGTTTTACAACTGGAGGAAGTGTAATTGGTGG-CTTACA
* ** * * * *
27584 ACTGGAGGAAGTGTGATTGGTGGCTTTACTGCCGGAGGAAGAGTGATTGGTGGCTTGACG
1 ACTGGAGGAAGTGTGATTGGTGGTTTTACAACTGGAGGAAGTGTAATTGGTGGCTT-ACA
* *
27644 ACCGGAGGAAGTGTGATTGGTGGTTTTACAACAGGAGGAAG
1 ACTGGAGGAAGTGTGATTGGTGGTTTTACAACTGGAGGAAG
27685 AGTGACCGGT
Statistics
Matches: 177, Mismatches: 30, Indels: 19
0.78 0.13 0.08
Matches are distributed among these distances:
57 88 0.50
58 8 0.05
59 7 0.04
60 74 0.42
ACGTcount: A:0.23, C:0.10, G:0.38, T:0.29
Consensus pattern (59 bp):
ACTGGAGGAAGTGTGATTGGTGGTTTTACAACTGGAGGAAGTGTAATTGGTGGCTTACA
Found at i:27520 original size:87 final size:87
Alignment explanation
Indices: 27410--27689 Score: 386
Period size: 87 Copynumber: 3.2 Consensus size: 87
27400 AGGAATTGTT
*
27410 ACTGGAGGAAGCGTGATTGGTGGTTTAACAGTTGGAGGGAGTTCAACTGGTGGCTTCACTGGAGG
1 ACTGGAGGAAGTGTGATTGGTGGTTTAACAGTTGGAGGGAGTTCAACTGGTGGCTTCACTGGAGG
27475 AAGTGTGATTGGTGGTTTTACA
66 AAGTGTGATTGGTGGTTTTACA
* *
27497 ACTGGAGGAAGTGTAATTGGTGGTTTAACATTTGGAGGGAGTTCAACTGGTGGCTTCACTGGAGG
1 ACTGGAGGAAGTGTGATTGGTGGTTTAACAGTTGGAGGGAGTTCAACTGGTGGCTTCACTGGAGG
27562 AAGTGTGATTGGTGGTTTTACA
66 AAGTGTGATTGGTGGTTTTACA
* ** * *
27584 ACTGGAGGAAGTGTGATTGGTGGCTTT-ACTGCCGGAGGAAGAG-T-GATTGGTGGCTTGACGAC
1 ACTGGAGGAAGTGTGATTGGTGG-TTTAACAGTTGGAGG--GAGTTCAACTGGTGGCTT--C-AC
*
27646 CGGAGGAAGTGTGATTGGTGGTTTTACA
60 TGGAGGAAGTGTGATTGGTGGTTTTACA
* *
27674 ACAGGAGGAAGAGTGA
1 ACTGGAGGAAGTGTGA
27690 CCGGTGGCAA
Statistics
Matches: 174, Mismatches: 13, Indels: 9
0.89 0.07 0.05
Matches are distributed among these distances:
87 123 0.71
88 4 0.02
89 4 0.02
90 43 0.25
ACGTcount: A:0.23, C:0.10, G:0.38, T:0.29
Consensus pattern (87 bp):
ACTGGAGGAAGTGTGATTGGTGGTTTAACAGTTGGAGGGAGTTCAACTGGTGGCTTCACTGGAGG
AAGTGTGATTGGTGGTTTTACA
Found at i:27696 original size:30 final size:30
Alignment explanation
Indices: 27470--27689 Score: 207
Period size: 30 Copynumber: 7.4 Consensus size: 30
27460 TGGCTTCACT
* *
27470 GGAGGAAGTGTGATTGGTGGTTTTACAACT
1 GGAGGAAGTGTGATTGGTGGCTTTACAACC
* ***
27500 GGAGGAAGTGTAATTGGTGG-TTTAACATTT
1 GGAGGAAGTGTGATTGGTGGCTTT-ACAACC
* * * *
27530 GGAGGGAGT-TCAACTGGTGGC-TT-C-ACT
1 GGAGGAAGTGT-GATTGGTGGCTTTACAACC
* *
27557 GGAGGAAGTGTGATTGGTGGTTTTACAACT
1 GGAGGAAGTGTGATTGGTGGCTTTACAACC
**
27587 GGAGGAAGTGTGATTGGTGGCTTTACTGCC
1 GGAGGAAGTGTGATTGGTGGCTTTACAACC
* * *
27617 GGAGGAAGAGTGATTGGTGGCTTGACGACC
1 GGAGGAAGTGTGATTGGTGGCTTTACAACC
* *
27647 GGAGGAAGTGTGATTGGTGGTTTTACAACA
1 GGAGGAAGTGTGATTGGTGGCTTTACAACC
*
27677 GGAGGAAGAGTGA
1 GGAGGAAGTGTGA
27690 CCGGTGGCAA
Statistics
Matches: 158, Mismatches: 25, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
27 16 0.10
28 4 0.03
29 5 0.03
30 133 0.84
ACGTcount: A:0.24, C:0.09, G:0.39, T:0.29
Consensus pattern (30 bp):
GGAGGAAGTGTGATTGGTGGCTTTACAACC
Found at i:29292 original size:16 final size:16
Alignment explanation
Indices: 29251--29303 Score: 63
Period size: 16 Copynumber: 3.1 Consensus size: 16
29241 TCAAATAAAT
29251 TAAGATTATTAGTGAGAA
1 TAAGATTATTA--GAGAA
29269 TGTAAGATTATTAGAGAA
1 --TAAGATTATTAGAGAA
29287 TAAGATTATTAGA-AA
1 TAAGATTATTAGAGAA
29302 TA
1 TA
29304 TTGTATTTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
15 4 0.12
16 13 0.39
18 5 0.15
20 11 0.33
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.34
Consensus pattern (16 bp):
TAAGATTATTAGAGAA
Found at i:29504 original size:37 final size:36
Alignment explanation
Indices: 29439--29512 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 36
29429 GTTGAAAAAT
* *
29439 ATTTATATATATATTTTACGAAATTTAAATTTATAAA
1 ATTTATATATATATTTTACGAAAATTAAA-ATATAAA
* *
29476 ATTTATATACTTTTTTTTAC-AAAATTAAAATATAAA
1 ATTTATATA-TATATTTTACGAAAATTAAAATATAAA
29512 A
1 A
29513 AGGTTTAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
36 7 0.22
37 17 0.53
38 8 0.25
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (36 bp):
ATTTATATATATATTTTACGAAAATTAAAATATAAA
Found at i:31089 original size:3 final size:3
Alignment explanation
Indices: 31081--31119 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
31071 TTATGTATTT
31081 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
31120 TTATTATTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:31124 original size:3 final size:3
Alignment explanation
Indices: 31118--31149 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
31108 ATAATAATAA
31118 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
31150 CAAATAAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:32893 original size:14 final size:14
Alignment explanation
Indices: 32874--32917 Score: 79
Period size: 14 Copynumber: 3.1 Consensus size: 14
32864 ATTTTTTATC
32874 TTTTAAAATTATTT
1 TTTTAAAATTATTT
32888 TTTTAAAATTATTT
1 TTTTAAAATTATTT
*
32902 TTTTTAAATTATTT
1 TTTTAAAATTATTT
32916 TT
1 TT
32918 AAAAGATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTTAAAATTATTT
Found at i:33349 original size:9 final size:11
Alignment explanation
Indices: 33325--33349 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
33315 AAAATTGTTT
33325 TATATAAATAA
1 TATATAAATAA
33336 TATATAAATAA
1 TATATAAATAA
33347 TAT
1 TAT
33350 TTTTTCTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TATATAAATAA
Found at i:33772 original size:3 final size:3
Alignment explanation
Indices: 33764--33789 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
33754 AATATATAAC
33764 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
33790 AAAATTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:33806 original size:2 final size:2
Alignment explanation
Indices: 33799--33830 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
33789 TAAAATTTAA
33799 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
33831 TTGGAATTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36251 original size:2 final size:2
Alignment explanation
Indices: 36244--36276 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
36234 ACAAACTTTC
36244 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 T
36277 CATCTTAGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41077 original size:8 final size:8
Alignment explanation
Indices: 41060--41100 Score: 57
Period size: 9 Copynumber: 5.0 Consensus size: 8
41050 AAAGGTAAGC
41060 TTTTTC-T
1 TTTTTCTT
41067 TTTTTCTT
1 TTTTTCTT
41075 TTTTTCCTT
1 TTTTT-CTT
41084 TTTTTCGTT
1 TTTTTC-TT
41093 TTTTTCTT
1 TTTTTCTT
41101 GTTCGAATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
7 6 0.19
8 9 0.29
9 16 0.52
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (8 bp):
TTTTTCTT
Found at i:42885 original size:12 final size:12
Alignment explanation
Indices: 42868--42898 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
42858 ATTATATACT
42868 TTTTATTTTTTA
1 TTTTATTTTTTA
42880 TTTTATTTTTTA
1 TTTTATTTTTTA
42892 TTTTATT
1 TTTTATT
42899 CATAATCCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTATTTTTTA
Found at i:43013 original size:39 final size:39
Alignment explanation
Indices: 42909--43014 Score: 128
Period size: 39 Copynumber: 2.7 Consensus size: 39
42899 CATAATCCTC
* * *
42909 AAATTATTTTAC-TCTAACATTCTAAAATCTTAATTTCTT
1 AAATTATTTCACAT-TAACGTTCTAAATTCTTAATTTCTT
*
42948 AAATT-TTGACACCA-TAACGTTCTAAATTCTTAATTTCTT
1 AAATTATT-TCA-CATTAACGTTCTAAATTCTTAATTTCTT
42987 AAATTATTTCACATTAACGTTCTAAATT
1 AAATTATTTCACATTAACGTTCTAAATT
43015 ATTTTTTGAA
Statistics
Matches: 57, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
38 4 0.07
39 50 0.88
40 3 0.05
ACGTcount: A:0.36, C:0.16, G:0.03, T:0.45
Consensus pattern (39 bp):
AAATTATTTCACATTAACGTTCTAAATTCTTAATTTCTT
Found at i:50548 original size:21 final size:21
Alignment explanation
Indices: 50522--50562 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
50512 TTAATTATTA
50522 ATATAT-GTGTAATATATTTTT
1 ATATATAGTGTAAT-TATTTTT
50543 ATATATAAGTGTAATTATTT
1 ATATAT-AGTGTAATTATTT
50563 AAGATTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.33
22 5 0.28
23 7 0.39
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.54
Consensus pattern (21 bp):
ATATATAGTGTAATTATTTTT
Found at i:53950 original size:24 final size:22
Alignment explanation
Indices: 53901--53942 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
53891 CCAGAATGTC
53901 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
53922 TAGGAGGGAACCGATTCCCCC
1 AAGGAGGGAACCGATACCCCC
53943 CTAAAGGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.29, C:0.33, G:0.29, T:0.10
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:54602 original size:31 final size:31
Alignment explanation
Indices: 54540--54617 Score: 79
Period size: 31 Copynumber: 2.5 Consensus size: 31
54530 AGAGTCGAGG
*
54540 GTTTACCTATGTCTTTCGAGACATATAGACA
1 GTTTACCTAGGTCTTTCGAGACATATAGACA
* * *
54571 GTTTACCTAGGT-TCTTCGGGACCTATGGACA
1 GTTTACCTAGGTCT-TTCGAGACATATAGACA
*
54602 G-TTACCGAGGATCTTT
1 GTTTACCTAGG-TCTTT
54618 ATGACCTCTG
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
30 9 0.23
31 29 0.74
32 1 0.03
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.35
Consensus pattern (31 bp):
GTTTACCTAGGTCTTTCGAGACATATAGACA
Found at i:54691 original size:29 final size:30
Alignment explanation
Indices: 54590--54688 Score: 155
Period size: 30 Copynumber: 3.3 Consensus size: 30
54580 GGTTCTTCGG
*
54590 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
54620 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
* * *
54650 GACCTCTGGATAGTTACCG-GGGTCTTTGT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
54679 GACCTCTGGA
1 GACCTCTGGA
54689 TAGGTCCTTC
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
29 18 0.28
30 47 0.72
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.30
Consensus pattern (30 bp):
GACCTCTGGACAGTTACCGAGGATCTTTAT
Found at i:54973 original size:2 final size:2
Alignment explanation
Indices: 54961--55022 Score: 106
Period size: 2 Copynumber: 31.0 Consensus size: 2
54951 GTATGCGTGG
* *
54961 AT AT GT AT AT AT AT AT AC 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
55003 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
55023 GAAAGGTGCA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:59398 original size:31 final size:31
Alignment explanation
Indices: 59336--59400 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
59326 AGAGTCGAGG
*
59336 GTTTACCTATGTCTTTCGAGACATATAGACA
1 GTTTACCTAGGTCTTTCGAGACATATAGACA
* * *
59367 GTTTACCTAGGT-TCTTCGGGACCTATGGACA
1 GTTTACCTAGGTCT-TTCGAGACATATAGACA
59398 GTT
1 GTT
59401 ATCGAGGATC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 1 0.03
31 28 0.97
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (31 bp):
GTTTACCTAGGTCTTTCGAGACATATAGACA
Found at i:59487 original size:29 final size:30
Alignment explanation
Indices: 59386--59484 Score: 146
Period size: 30 Copynumber: 3.3 Consensus size: 30
59376 GGTTCTTCGG
* *
59386 GACCTATGGACAGTTATCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
59416 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
* * *
59446 GACCTCTGGATAGTTACCG-GGGTCTTTGT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
59475 GACCTCTGGA
1 GACCTCTGGA
59485 TAGGTCCATC
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
29 18 0.28
30 46 0.72
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.31
Consensus pattern (30 bp):
GACCTCTGGACAGTTACCGAGGATCTTTAT
Found at i:60664 original size:15 final size:15
Alignment explanation
Indices: 60639--60677 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
60629 TAGAACGATA
*
60639 TTGCATCGGGGGACG
1 TTGCGTCGGGGGACG
* *
60654 TTGTGTCGGGGGATG
1 TTGCGTCGGGGGACG
60669 TTGCGTCGG
1 TTGCGTCGG
60678 CAGATGGTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.08, C:0.15, G:0.49, T:0.28
Consensus pattern (15 bp):
TTGCGTCGGGGGACG
Found at i:62140 original size:18 final size:17
Alignment explanation
Indices: 62117--62200 Score: 82
Period size: 18 Copynumber: 4.8 Consensus size: 17
62107 ATATCCCTTC
62117 AAATAAATAAATCAATCA
1 AAATAAATAAAT-AATCA
* *
62135 AAATAAAT-TATTA-CAA
1 AAATAAATAAATAATC-A
*
62151 AAATAAATAAATTATTCA
1 AAATAAATAAA-TAATCA
62169 AAATAAATAAATAATTCA
1 AAATAAATAAATAA-TCA
*
62187 AAGTAAATAAATAA
1 AAATAAATAAATAA
62201 AAATTACCTC
Statistics
Matches: 54, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
15 1 0.02
16 10 0.19
17 5 0.09
18 37 0.69
19 1 0.02
ACGTcount: A:0.65, C:0.06, G:0.01, T:0.27
Consensus pattern (17 bp):
AAATAAATAAATAATCA
Found at i:62625 original size:4 final size:4
Alignment explanation
Indices: 62618--62859 Score: 259
Period size: 4 Copynumber: 60.5 Consensus size: 4
62608 ATCTTTCTTA
* * * *
62618 ATAC ATAC ATAC ATAC GTAC ATAC ATAT ATAC ATAC ATAC ATAG ATAT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * * * *
62666 ATAC ATAC ATAC ATAC ATGC ATGC ATGC ATGC ATGC ATAC ATGC ATGC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * * *
62714 ATAC ATAC ATGC ATGC ATGC ATAC ATGC ATAC ATAC ATAC ATGC ATGC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * *
62762 ATAC ATAC ATGC ATAC ATGC ATAC ATGC ATAC ATGC ATAC ATAC ATGC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * *
62810 ATAC ATGC ATAC ATGC ATAC ATGC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
62858 AT
1 AT
Statistics
Matches: 205, Mismatches: 33, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 205 1.00
ACGTcount: A:0.41, C:0.24, G:0.10, T:0.26
Consensus pattern (4 bp):
ATAC
Done.