Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006592.1 Hibiscus syriacus cultivar Beakdansim tig00016171_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: 276073
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
File 2 of 2
Found at i:203381 original size:20 final size:20
Alignment explanation
Indices: 203319--203382 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
203309 TCATTGGAGA
*
203319 GTTCATAATAAGAAGAAC-T
1 GTTCATAATGAGAAGAACTT
** *
203338 CATC-TAATGAGGAAGAA-TAA
1 GTTCATAATGA-GAAGAACT-T
203358 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
203378 GTTCA
1 GTTCA
203383 ACCTTGGTTC
Statistics
Matches: 33, Mismatches: 7, Indels: 9
0.67 0.14 0.18
Matches are distributed among these distances:
18 5 0.15
19 8 0.24
20 13 0.39
21 7 0.21
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.27
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:203450 original size:117 final size:117
Alignment explanation
Indices: 203094--203851 Score: 895
Period size: 117 Copynumber: 6.7 Consensus size: 117
203084 GGGATTGACA
* * **
203094 TTTCTAATAGAGAGTTCATAATGAGAAGAACTCAT-C-AT-A-AAAG-AGAAAACTCATAATGAG
1 TTTC-AATGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAG-AAGTTCATAATGAG
* * * *
203154 AAGAACTTGTT---CC-T--TTCAAATT-CACCACAAAAGGAGGTGAACCAACAT
64 AAGAACTTGTTCAACCTTAGTTC-GATTCCACCACAGAAGGAGGTGGATCAACAT
* * *
203202 TTTC-A-GAAGAGTTCATAATTAGAAGAACTCGTCCGAA--AGG-AG-A-AAGTTCATAATGAGA
1 TTTCAATGGAGAGTTCATAATGAGAAGAACTCATCC-AATGAGGAAGAAGAAGTTCATAATGAGA
* * * *
203260 AAAACTTGTT---CC-T--TTCAAGTCCATCGC-CA-AAAGAGGTGGATCAACAT
65 AGAACTTGTTCAACCTTAGTTCGATTCCA-C-CACAGAAGGAGGTGGATCAACAT
* * * *
203307 TTTCATTGGAGAGTTCATAATAAGAAGAACTCATCTAATGAGGAAGAATAAGTTCATAATGAGAA
1 TTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAA
* * * *
203372 GAACTTGTTCAACCTTGGTTCGATTCTATCATAGAAGGAGGTGGATCAACAT
66 GAACTTGTTCAACCTTAGTTCGATTCCACCACAGAAGGAGGTGGATCAACAT
*
203424 TTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAAAAGAAGTTCATAATGAGAA
1 TTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAA
* * * * *
203489 GAACTTGTTCAACCTTAGTTCAAGTCCACCGCAGAAGGAGGTGGATAAACAA
66 GAACTTGTTCAACCTTAGTTCGATTCCACCACAGAAGGAGGTGGATCAACAT
*
203541 TTTCAATGGAGAATTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAA
1 TTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAA
* *
203606 GAACTTGTTCAACCTTTGTTTGATTCCACCACAGAAGGAGGTGGATCAACAT
66 GAACTTGTTCAACCTTAGTTCGATTCCACCACAGAAGGAGGTGGATCAACAT
* * *
203658 TTTCAATTGAGAGTTCATAATGAGAAGAATTCATCCAATGAGAAAGAAGAAGTTCATAATGAGAA
1 TTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAA
* * * * *
203723 TAACTTGTTCAACCTTAGTTTGATTCCATCACAAAATGAGGTGGATCAACAT
66 GAACTTGTTCAACCTTAGTTCGATTCCACCACAGAAGGAGGTGGATCAACAT
* *
203775 TTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAA
1 TTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAA
203840 GAACTTGTTCAA
66 GAACTTGTTCAA
203852 TTCAACAACG
Statistics
Matches: 566, Mismatches: 62, Indels: 35
0.85 0.09 0.05
Matches are distributed among these distances:
104 3 0.01
105 72 0.13
106 7 0.01
107 30 0.05
108 8 0.01
109 2 0.00
110 1 0.00
111 24 0.04
114 2 0.00
115 2 0.00
116 1 0.00
117 414 0.73
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (117 bp):
TTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAA
GAACTTGTTCAACCTTAGTTCGATTCCACCACAGAAGGAGGTGGATCAACAT
Found at i:203720 original size:21 final size:21
Alignment explanation
Indices: 203680--203722 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
203670 GTTCATAATG
203680 AGAAGAATTCATCCAATGAGAA
1 AGAAGAATTCAT-CAATGAGAA
203702 AGAAGAAGTTCAT-AATGAGAA
1 AGAAGAA-TTCATCAATGAGAA
203723 TAACTTGTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 8 0.40
22 7 0.35
23 5 0.25
ACGTcount: A:0.51, C:0.09, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAAGAATTCATCAATGAGAA
Found at i:204031 original size:3 final size:3
Alignment explanation
Indices: 204018--204058 Score: 50
Period size: 3 Copynumber: 13.7 Consensus size: 3
204008 ATTATATTTA
204018 TAT TA- TAT TAT TAT TAT TAT TAT TAT TAAT TAGT T-T TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TA-T TAT TAT TA
204059 CATATGATTG
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
2 4 0.12
3 25 0.74
4 5 0.15
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:204604 original size:14 final size:15
Alignment explanation
Indices: 204577--204605 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
204567 TTAAAGTTTA
204577 AAATATTATTATTAT
1 AAATATTATTATTAT
204592 AAATATT-TTATTAT
1 AAATATTATTATTAT
204606 TCAATATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AAATATTATTATTAT
Found at i:204604 original size:17 final size:18
Alignment explanation
Indices: 204582--204624 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
204572 GTTTAAAATA
204582 TTATTATT-ATAAATA-TT
1 TTATTATTCA-AAATATTT
*
204599 TTATTATTCAATATATTT
1 TTATTATTCAAAATATTT
204617 TTATTATT
1 TTATTATT
204625 TTATGTAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 12 0.52
18 11 0.48
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (18 bp):
TTATTATTCAAAATATTT
Found at i:204611 original size:15 final size:15
Alignment explanation
Indices: 204577--204624 Score: 53
Period size: 18 Copynumber: 3.0 Consensus size: 15
204567 TTAAAGTTTA
204577 AAATATTATTATTA-T
1 AAATATT-TTATTATT
204592 AAATATTTTATTATT
1 AAATATTTTATTATT
204607 CAATATATTTTTATTATT
1 -AA-ATA-TTTTATTATT
204625 TTATGTAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
14 6 0.21
15 8 0.28
16 2 0.07
17 3 0.10
18 10 0.34
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (15 bp):
AAATATTTTATTATT
Found at i:204780 original size:19 final size:20
Alignment explanation
Indices: 204745--204787 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 20
204735 GTAATGTCGA
204745 AATT-TCTTTTCATATTAAAT
1 AATTCTCTTTTCATATT-AAT
204765 AATTCTCTTTT-A-ATTAAT
1 AATTCTCTTTTCATATTAAT
204783 AATTC
1 AATTC
204788 AAACAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 8 0.36
19 3 0.14
20 5 0.23
21 6 0.27
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (20 bp):
AATTCTCTTTTCATATTAAT
Found at i:205950 original size:34 final size:34
Alignment explanation
Indices: 205884--205953 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
205874 TAATCAAACT
*
205884 AAATATCTTTTAATATTCAACATTAAACAGATAA
1 AAATATCTTTTAATATTAAACATTAAACAGATAA
*
205918 AAATATCTTTTAAT-TTGAAATATTCAAA-AGATAA
1 AAATATCTTTTAATATT-AAACATT-AAACAGATAA
205952 AA
1 AA
205954 CTCCTTTTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 2 0.06
34 27 0.84
35 3 0.09
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.36
Consensus pattern (34 bp):
AAATATCTTTTAATATTAAACATTAAACAGATAA
Found at i:206252 original size:190 final size:190
Alignment explanation
Indices: 205926--206327 Score: 610
Period size: 190 Copynumber: 2.1 Consensus size: 190
205916 AAAAATATCT
* *
205926 TTTAATTTGAAATATTCAAAAGATAAAACTCCTTTTACCATTCAAACTTAAATAGATATTATTTT
1 TTTAATTTGAAATAGTCAAAAGATAAAACTCCTTTTACCATTCAAACTTAAACAGATATTATTTT
* * *
205991 AATTTGAAATATACAAAAATATATAATTATTTTTAATATTCAAAGTTAAAAAGGTAACAAATACT
66 AATTTGAAATATACAAAAATATATAATTATTTTTAATATTCAAAATTAAAAAGATAACAAATACC
*
206056 TTTTTAAATTGACATATTCAAAGAGTAATTATCCTACTAATATTCAAATTAAATAATATA
131 TTTTTAAATTGACATATTAAAAGAGTAATTATCCTACTAATATTCAAATTAAATAATATA
* * * * * *
206116 TTTAATTTGCAATGGTCAAAAGGT-AAACTCCTTTTACTATTCAAAGTTAAACATATATTATTTT
1 TTTAATTTGAAATAGTCAAAAGATAAAACTCCTTTTACCATTCAAACTTAAACAGATATTATTTT
*
206180 AATTTGAAATATACAAAATTATATAATTATCTTTTAATATTCAAAATTAAAAAGATAACAAATAC
66 AATTTGAAATATACAAAAATATATAATTAT-TTTTAATATTCAAAATTAAAAAGATAACAAATAC
* * *
206245 CTTTTTAAATTGACTTATTAAAAGAGTAATTATCCTACTAATATTCAAATTAAA-ATTATCT
130 CTTTTTAAATTGACATATTAAAAGAGTAATTATCCTACTAATATTCAAATTAAATAATAT-A
*
206306 TTTAATTTACAAATAGTCAAAA
1 TTTAATTT-GAAATAGTCAAAA
206328 TGATTATGAG
Statistics
Matches: 190, Mismatches: 19, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
189 69 0.36
190 111 0.58
191 10 0.05
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.39
Consensus pattern (190 bp):
TTTAATTTGAAATAGTCAAAAGATAAAACTCCTTTTACCATTCAAACTTAAACAGATATTATTTT
AATTTGAAATATACAAAAATATATAATTATTTTTAATATTCAAAATTAAAAAGATAACAAATACC
TTTTTAAATTGACATATTAAAAGAGTAATTATCCTACTAATATTCAAATTAAATAATATA
Found at i:212860 original size:18 final size:19
Alignment explanation
Indices: 212837--212874 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
212827 ATATTTACTT
212837 TATACTAGTT-TAAT-CATA
1 TATACTA-TTATAATACATA
212855 TATACTATTATAATACATA
1 TATACTATTATAATACATA
212874 T
1 T
212875 CATGTTAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 2 0.11
18 11 0.61
19 5 0.28
ACGTcount: A:0.42, C:0.11, G:0.03, T:0.45
Consensus pattern (19 bp):
TATACTATTATAATACATA
Found at i:214507 original size:23 final size:25
Alignment explanation
Indices: 214477--214522 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
214467 AGCAGCAAAG
*
214477 AAATTG-AAGTACTC-AAAAGAATA
1 AAATTGAAAGCACTCGAAAAGAATA
214500 AAATTGAAAGCACTCGAAAAGAA
1 AAATTGAAAGCACTCGAAAAGAA
214523 AAGAAAAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.11, G:0.15, T:0.17
Consensus pattern (25 bp):
AAATTGAAAGCACTCGAAAAGAATA
Found at i:220895 original size:5 final size:5
Alignment explanation
Indices: 220885--220924 Score: 55
Period size: 5 Copynumber: 8.0 Consensus size: 5
220875 ATAAATTAAT
*
220885 AAATA AAATA AAATA AAATA AAA-A AATAGA AAATA AAATA
1 AAATA AAATA AAATA AAATA AAATA AA-ATA AAATA AAATA
220925 CTAATAATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
4 3 0.09
5 26 0.81
6 3 0.09
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (5 bp):
AAATA
Found at i:220898 original size:18 final size:18
Alignment explanation
Indices: 220859--220924 Score: 64
Period size: 18 Copynumber: 3.5 Consensus size: 18
220849 GCCTAGTTGG
220859 AATAAAATAGAAAATAAT-A
1 AATAAAATA-AAAA-AATAA
*
220878 AAT-TAATAAATAAAATAA
1 AATAAAATAAA-AAAATAA
220896 AATAAAATAAAAAAATAGAA
1 AATAAAATAAAAAAAT--AA
220916 AATAAAATA
1 AATAAAATA
220925 CTAATAATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
17 5 0.12
18 15 0.38
19 9 0.22
20 11 0.28
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (18 bp):
AATAAAATAAAAAAATAA
Found at i:220905 original size:30 final size:31
Alignment explanation
Indices: 220859--220924 Score: 82
Period size: 30 Copynumber: 2.1 Consensus size: 31
220849 GCCTAGTTGG
* *
220859 AATAAAATAGAAAATAATAAATTA-ATAAATAA
1 AATAAAATA-AAAATAAAAAAATAGA-AAATAA
220891 AATAAAAT-AAAATAAAAAAATAGAAAATAA
1 AATAAAATAAAAATAAAAAAATAGAAAATAA
220921 AATA
1 AATA
220925 CTAATAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 22 0.71
31 1 0.03
32 8 0.26
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (31 bp):
AATAAAATAAAAATAAAAAAATAGAAAATAA
Found at i:220921 original size:15 final size:15
Alignment explanation
Indices: 220862--220922 Score: 63
Period size: 15 Copynumber: 4.1 Consensus size: 15
220852 TAGTTGGAAT
*
220862 AAAATAGAAAATAAT
1 AAAATAGAAAATAAA
*
220877 AAATTA-ATAAATAAA
1 AAAATAGA-AAATAAA
*
220892 ATAAA-ATAAAATAAA
1 A-AAATAGAAAATAAA
220907 AAAATAGAAAATAAA
1 AAAATAGAAAATAAA
220922 A
1 A
220923 TACTAATAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
14 4 0.11
15 31 0.82
16 3 0.08
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (15 bp):
AAAATAGAAAATAAA
Found at i:221070 original size:37 final size:37
Alignment explanation
Indices: 221042--221248 Score: 192
Period size: 37 Copynumber: 5.5 Consensus size: 37
221032 AACTAGGTTA
221042 TATATGTTTTCAAAAAACCATTTAAAAAAACTATATAT
1 TATATGTTTTC-AAAAACCATTTAAAAAAACTATATAT
* *
221080 TATATGTTTTCAAAAACCATTTAAAAAAAATATTTAT
1 TATATGTTTTCAAAAACCATTTAAAAAAACTATATAT
* **
221117 TACT-TGTTTTCAAAAA-TATGTTTTCAAAAACTATAT-T
1 TA-TATGTTTTCAAAAACCA--TTTAAAAAAACTATATAT
* *
221154 ATATATGTTTTTTTTCCAAAACCATTTTTAAAAAACTATATAT
1 -TATATG----TTTTCAAAAACCA-TTTAAAAAAACTATATAT
*
221197 TATATGTTTTTCAAAAACCA--T-CAAAAACTATATAT
1 TATATG-TTTTCAAAAACCATTTAAAAAAACTATATAT
*
221232 TATACGTTTTCAAAAAC
1 TATATGTTTTCAAAAAC
221249 TATATTATAT
Statistics
Matches: 144, Mismatches: 14, Indels: 26
0.78 0.08 0.14
Matches are distributed among these distances:
34 11 0.08
35 18 0.12
36 2 0.01
37 40 0.28
38 28 0.19
39 13 0.09
42 30 0.21
43 2 0.01
ACGTcount: A:0.44, C:0.12, G:0.03, T:0.41
Consensus pattern (37 bp):
TATATGTTTTCAAAAACCATTTAAAAAAACTATATAT
Found at i:221249 original size:24 final size:26
Alignment explanation
Indices: 221217--221273 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
221207 TCAAAAACCA
221217 TCAAAAACTATA-TAT-TATACGTTT
1 TCAAAAACTATATTATATATACGTTT
*
221241 TCAAAAACTATATTATATATATGTTT
1 TCAAAAACTATATTATATATACGTTT
221267 TCAAAAA
1 TCAAAAA
221274 AATATTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 12 0.40
25 3 0.10
26 15 0.50
ACGTcount: A:0.46, C:0.11, G:0.04, T:0.40
Consensus pattern (26 bp):
TCAAAAACTATATTATATATACGTTT
Found at i:221340 original size:43 final size:42
Alignment explanation
Indices: 221238--221342 Score: 108
Period size: 41 Copynumber: 2.5 Consensus size: 42
221228 ATATTATACG
*
221238 TTTTCAAAAACTATAT-TATA-TATATGTTTTCAAAAAAATA
1 TTTTCAAAGACTATATATATATTATATGTTTTCAAAAAAATA
** ** ** *
221278 TTTTTTAAGAAAAT-TATATATTATATGTTTTCAAAAACGTC
1 TTTTCAAAGACTATATATATATTATATGTTTTCAAAAAAATA
221319 TTTTCAAAGACTATACTATATATT
1 TTTTCAAAGACTATA-TATATATT
221343 TTCAAAAAGT
Statistics
Matches: 49, Mismatches: 12, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
39 1 0.02
40 13 0.27
41 27 0.55
43 8 0.16
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.45
Consensus pattern (42 bp):
TTTTCAAAGACTATATATATATTATATGTTTTCAAAAAAATA
Found at i:221355 original size:22 final size:21
Alignment explanation
Indices: 221319--221360 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
221309 CAAAAACGTC
*
221319 TTTTCAAAGACTATACTATATA
1 TTTTCAAAAACTATA-TATATA
*
221341 TTTTCAAAAAGTATATATAT
1 TTTTCAAAAACTATATATAT
221361 TATATATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.43, C:0.10, G:0.05, T:0.43
Consensus pattern (21 bp):
TTTTCAAAAACTATATATATA
Found at i:221365 original size:103 final size:100
Alignment explanation
Indices: 221137--221370 Score: 246
Period size: 101 Copynumber: 2.3 Consensus size: 100
221127 CAAAAATATG
* * * **
221137 TTTTCAAAAACTATATTATATATGTTTTTTTTC-CAAAACCA-TTTTTAAAAAACTATATATTAT
1 TTTTCAAAAACTATATTATATA--TATATTTTCAAAAAAATATTTTTTAAAAAACTATATATTAT
221200 ATGTTTTTCAAAAACCATCAAAAACTATATATTATAC
64 ATGTTTTTCAAAAACCATCAAAAACTATATATTATAC
* *
221237 GTTTTCAAAAACTATATTATATATATGTTTTCAAAAAAATATTTTTTAAGAAAATTATATATTAT
1 -TTTTCAAAAACTATATTATATATATATTTTCAAAAAAATATTTTTTAA-AAAACTATATATTAT
* *
221302 ATG-TTTTCAAAAACGTCTTTTCAAAGACTATACTA-TATA-
64 ATGTTTTTCAAAAAC--C--ATCAAAAACTATA-TATTATAC
*
221341 TTTTCAAAAAGTATA-TATATTATATATTTT
1 TTTTCAAAAACTATATTATA-TATATATTTT
221371 TGAAATTATT
Statistics
Matches: 114, Mismatches: 10, Indels: 16
0.81 0.07 0.11
Matches are distributed among these distances:
99 7 0.06
100 5 0.04
101 40 0.35
102 21 0.18
103 24 0.21
105 15 0.13
106 2 0.02
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.44
Consensus pattern (100 bp):
TTTTCAAAAACTATATTATATATATATTTTCAAAAAAATATTTTTTAAAAAACTATATATTATAT
GTTTTTCAAAAACCATCAAAAACTATATATTATAC
Found at i:222329 original size:15 final size:15
Alignment explanation
Indices: 222293--222325 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
222283 TTCTTGTCAA
*
222293 TCTTGATTTTCTGAT
1 TCTTGATTTTCGGAT
222308 TCTTGATTTT-GGAT
1 TCTTGATTTTCGGAT
222322 TCTT
1 TCTT
222326 TGATCATCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.12, C:0.12, G:0.15, T:0.61
Consensus pattern (15 bp):
TCTTGATTTTCGGAT
Found at i:224697 original size:18 final size:19
Alignment explanation
Indices: 224657--224697 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
224647 AAATGTTATT
* *
224657 AAAATTATAATAAATATTA
1 AAAATTATAAGAAATATGA
224676 AAAATT-TAAGAAATATGA
1 AAAATTATAAGAAATATGA
224694 AAAA
1 AAAA
224698 CGTTTGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (19 bp):
AAAATTATAAGAAATATGA
Found at i:226521 original size:29 final size:29
Alignment explanation
Indices: 226488--226591 Score: 181
Period size: 29 Copynumber: 3.6 Consensus size: 29
226478 TTTTTCTTTG
* *
226488 ATTGTAATTTATAAATAGTTTTGGTATTT
1 ATTGTAATTTATAAAAAGTTATGGTATTT
226517 ATTGTAATTTATAAAAAGTTATGGTATTT
1 ATTGTAATTTATAAAAAGTTATGGTATTT
*
226546 ATTGTAGTTTATAAAAAGTTATGGTATTT
1 ATTGTAATTTATAAAAAGTTATGGTATTT
226575 ATTGTAATTTATAAAAA
1 ATTGTAATTTATAAAAA
226592 AATTTGACAT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 71 1.00
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (29 bp):
ATTGTAATTTATAAAAAGTTATGGTATTT
Found at i:226603 original size:29 final size:29
Alignment explanation
Indices: 226488--226682 Score: 117
Period size: 29 Copynumber: 6.7 Consensus size: 29
226478 TTTTTCTTTG
* ** **
226488 ATTGTAATTTATAAATAGTTTTGGTATTT
1 ATTGTAATTTATAAAAAAATTTGACATTT
* **
226517 ATTGTAATTTAT-AAAAAGTTATGGTATTT
1 ATTGTAATTTATAAAAAAATT-TGACATTT
* * **
226546 ATTGTAGTTTAT-AAAAAGTTATGGTATTT
1 ATTGTAATTTATAAAAAAATT-TGACATTT
226575 ATTGTAATTTATAAAAAAATTTGACATTT
1 ATTGTAATTTATAAAAAAATTTGACATTT
* * * *
226604 ATTATAA-TTATTTAAAAAATTAGACTTTT
1 ATTGTAATTTA-TAAAAAAATTTGACATTT
* *** * * *
226633 GTAACAATTTATATAAATATTTAGACTTTT
1 ATTGTAATTTATAAAAAAATTT-GACATTT
226663 ATTGTAATTTAATAAAAAAA
1 ATTGTAATTT-ATAAAAAAA
226683 ATTATATTTT
Statistics
Matches: 135, Mismatches: 25, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
28 8 0.06
29 97 0.72
30 23 0.17
31 7 0.05
ACGTcount: A:0.41, C:0.02, G:0.10, T:0.47
Consensus pattern (29 bp):
ATTGTAATTTATAAAAAAATTTGACATTT
Found at i:226604 original size:58 final size:58
Alignment explanation
Indices: 226488--226621 Score: 171
Period size: 58 Copynumber: 2.3 Consensus size: 58
226478 TTTTTCTTTG
* * * **
226488 ATTGTAATTTATAAATAGTTTTGGTATTTATTGTAATTTATAAAAAGTTATGGTATTT
1 ATTGTAATTTATAAAAAGTTATGGTATTTATTGTAATTTATAAAAAATTATGACATTT
*
226546 ATTGTAGTTTATAAAAAGTTATGGTATTTATTGTAATTTATAAAAAAATT-TGACATTT
1 ATTGTAATTTATAAAAAGTTATGGTATTTATTGTAATTTAT-AAAAAATTATGACATTT
* *
226604 ATTATAATTATTTAAAAA
1 ATTGTAATT-TATAAAAA
226622 ATTAGACTTT
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
58 51 0.78
59 14 0.22
ACGTcount: A:0.40, C:0.01, G:0.11, T:0.49
Consensus pattern (58 bp):
ATTGTAATTTATAAAAAGTTATGGTATTTATTGTAATTTATAAAAAATTATGACATTT
Found at i:226672 original size:30 final size:30
Alignment explanation
Indices: 226572--226680 Score: 107
Period size: 30 Copynumber: 3.7 Consensus size: 30
226562 AGTTATGGTA
* * *
226572 TTTATTGTAATTTATAAAAAAATTT-GACA
1 TTTATTATAATTTATATAAAAATTTAGACT
* *
226601 TTTATTATAA-TTATTTAAAAAATTAGACT
1 TTTATTATAATTTATATAAAAATTTAGACT
* * * *
226630 TTTGTAACAATTTATATAAATATTTAGACT
1 TTTATTATAATTTATATAAAAATTTAGACT
*
226660 TTTATTGTAATTTA-ATAAAAA
1 TTTATTATAATTTATATAAAAA
226681 AAATTATATT
Statistics
Matches: 62, Mismatches: 16, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
28 11 0.18
29 25 0.40
30 26 0.42
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.47
Consensus pattern (30 bp):
TTTATTATAATTTATATAAAAATTTAGACT
Found at i:228241 original size:39 final size:40
Alignment explanation
Indices: 228167--228248 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
228157 CAATATGGGA
228167 GGGGAACTGAAAGCAAAACAAATCAATAAATTTTTTGTAG
1 GGGGAACTGAAAGCAAAACAAATCAATAAATTTTTTGTAG
228207 GGGGAACTGAAAGCAAAACAAATCAATAAATTTTTTGTAG
1 GGGGAACTGAAAGCAAAACAAATCAATAAATTTTTTGTAG
228247 GG
1 GG
228249 AACACTTCCC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.44, C:0.10, G:0.22, T:0.24
Consensus pattern (40 bp):
GGGGAACTGAAAGCAAAACAAATCAATAAATTTTTTGTAG
Found at i:228861 original size:21 final size:21
Alignment explanation
Indices: 228837--228879 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
228827 CACTTTTAAC
228837 ATTTGTTCTCTT-AATTTATTT
1 ATTT-TTCTCTTCAATTTATTT
228858 ATTTTTCTCTTCAATTTATTT
1 ATTTTTCTCTTCAATTTATTT
228879 A
1 A
228880 GTATTGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.21, C:0.12, G:0.02, T:0.65
Consensus pattern (21 bp):
ATTTTTCTCTTCAATTTATTT
Found at i:231901 original size:16 final size:16
Alignment explanation
Indices: 231875--231925 Score: 54
Period size: 15 Copynumber: 3.2 Consensus size: 16
231865 AGATCCAATC
231875 AAGAACAAAAAAG-AA
1 AAGAACAAAAAAGCAA
231890 AAGAAGCAAAAAAGCAA
1 AAGAA-CAAAAAAGCAA
*
231907 AA-AA-AAACAAAGAAA
1 AAGAACAAA-AAAGCAA
231922 AAGA
1 AAGA
231926 GAAACAAGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
14 3 0.10
15 13 0.42
16 11 0.35
17 4 0.13
ACGTcount: A:0.78, C:0.08, G:0.14, T:0.00
Consensus pattern (16 bp):
AAGAACAAAAAAGCAA
Found at i:231922 original size:22 final size:21
Alignment explanation
Indices: 231881--231970 Score: 65
Period size: 23 Copynumber: 3.9 Consensus size: 21
231871 AATCAAGAAC
231881 AAAAAAGAAAAGAAGCAAAAAAG
1 AAAAAAGAAAA-AAG-AAAAAAG
231904 CAAAAAA-AAACAAAGAAAAAGAG
1 -AAAAAAGAAA-AAAGAAAAA-AG
*
231927 AAACAAGAACAAAAGGAAAAAAG
1 AAAAAAGAA-AAAA-GAAAAAAG
**
231950 AGCAAAAATCAAAAAGAAAAA
1 A--AAAAAGAAAAAAGAAAAA
231971 GGGACAAAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 15
0.74 0.05 0.20
Matches are distributed among these distances:
22 10 0.18
23 22 0.40
24 18 0.33
25 5 0.09
ACGTcount: A:0.77, C:0.08, G:0.14, T:0.01
Consensus pattern (21 bp):
AAAAAAGAAAAAAGAAAAAAG
Found at i:232628 original size:22 final size:22
Alignment explanation
Indices: 232600--232643 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
232590 AGCTACCCCA
*
232600 TCAAACCTTTGAACATCAAATG
1 TCAAACCATTGAACATCAAATG
*
232622 TCAAACCATTGAGCATCAAATG
1 TCAAACCATTGAACATCAAATG
232644 GACAAAAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.41, C:0.23, G:0.11, T:0.25
Consensus pattern (22 bp):
TCAAACCATTGAACATCAAATG
Found at i:235242 original size:106 final size:106
Alignment explanation
Indices: 234804--236380 Score: 2381
Period size: 106 Copynumber: 14.9 Consensus size: 106
234794 TTTTAGAGTT
* * *
234804 AAGTTCGACTTCACGATGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTTCAGAGCCAA
1 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAA
* * *
234868 TTTCAACTTCTCAACGAAGGATATTGGACTCCAGACAACGA
66 TTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGC
*
234909 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTTCAGAGCCAA
1 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAA
* * *
234973 TTTTAACTTCACAACGAAGGATATTGGACTCCAGACAATGC
66 TTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGC
*
235014 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTTCAGAGCCAA
1 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAA
* *
235078 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGC
66 TTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGC
* *
235119 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCTCAATTTCAGAGCCAA
1 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAA
* *
235184 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGC
66 TTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGC
* *
235225 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCATAGCCAA
1 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAA
* *
235290 TTTCAACTTCACAACGAAGGATATTGGACTCCAGATAACGC
66 TTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGC
* *
235331 AAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAA
1 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAA
235396 TTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGC
66 TTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGC
*
235437 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAA
1 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAA
* *
235502 TTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACGC
66 TTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGC
* * * *
235543 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAAATAACTTCCAAATTTCAGAGCCAA
1 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAA
235608 TTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGC
66 TTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGC
* * *
235649 AAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAA
1 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAA
* * * *
235714 TTTCAACTTCACAGCGAAAGATATTGGACTTCAGACAATGG
66 TTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGC
* * * *
235755 AAGTTCAACTTCATGACGACGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAA
1 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAA
* *
235820 TTTCAACTTCTCAGCGAAGGATATTGGACTCAAGACAACGC
66 TTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGC
* * * * *
235861 AAGTTCAACTTCACGATGAAGGGACCGCTGATTGTCAATAAATAATTTCCCAATTTTAGAGCCAA
1 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAA
235926 TTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGC
66 TTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGC
* * *
235967 AAGTTCAACTTCACGACGAATGGACCACTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAA
1 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAA
* *
236032 TTTCAACTTCACAGCGAAGGATATTGGACGCCAGATAACGC
66 TTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGC
* *
236073 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAA
1 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAA
* * *
236138 TTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACAC
66 TTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGC
* * *
236179 AAGTTCAACTTCACAACGAAGGGA-CGTCTGATTGTCAACAAACAACTTCCCAATTTCAGAGCCA
1 AAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
** * * *
236243 ATTTCAACTTCACAGCGAAGGGCATTGGACTCGAGACAGCAC
65 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGC
* * * * * * * * * * *
236285 AAGCTCAACTTCA-TAGCGAAGGGGCGGCTGGCTGTCAACAAATAATTTCCTAGTTCCAAATCCA
1 AAGTTCAACTTCACGA-CGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* * *
236349 GTTTCAACTTCACAGTGGAGGATATTGGACTC
65 ATTTCAACTTCACAGCGAAGGATATTGGACTC
236381 GGAGCAAGAT
Statistics
Matches: 1368, Mismatches: 100, Indels: 7
0.93 0.07 0.00
Matches are distributed among these distances:
105 248 0.18
106 1119 0.82
107 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAA
TTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGC
Found at i:237619 original size:21 final size:21
Alignment explanation
Indices: 237595--237637 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
237585 CACTTTTAAC
237595 ATTTGTTCTCTT-AATTTATTT
1 ATTT-TTCTCTTCAATTTATTT
237616 ATTTTTCTCTTCAATTTATTT
1 ATTTTTCTCTTCAATTTATTT
237637 A
1 A
237638 GTATTGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.21, C:0.12, G:0.02, T:0.65
Consensus pattern (21 bp):
ATTTTTCTCTTCAATTTATTT
Found at i:248784 original size:24 final size:24
Alignment explanation
Indices: 248711--248776 Score: 105
Period size: 24 Copynumber: 2.8 Consensus size: 24
248701 GTTAGTTACA
* *
248711 GAAGCTTGTGCTTTTGTAGCCGAT
1 GAAGCTTGTGCTTTTGCAGCAGAT
*
248735 GAATCTTGTGCTTTTGCAGCAGAT
1 GAAGCTTGTGCTTTTGCAGCAGAT
248759 GAAGCTTGTGCTTTTGCA
1 GAAGCTTGTGCTTTTGCA
248777 ACGGATGAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.18, C:0.17, G:0.27, T:0.38
Consensus pattern (24 bp):
GAAGCTTGTGCTTTTGCAGCAGAT
Found at i:252554 original size:7 final size:7
Alignment explanation
Indices: 252542--252572 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
252532 GAATAAAAGG
252542 AAATTTA
1 AAATTTA
252549 AAATTTA
1 AAATTTA
252556 AAATTTA
1 AAATTTA
252563 AAATATTA
1 AAAT-TTA
252571 AA
1 AA
252573 TTACAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.78
8 5 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (7 bp):
AAATTTA
Found at i:253881 original size:17 final size:18
Alignment explanation
Indices: 253851--253884 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
253841 GTTGGAATAA
253851 AATAAAAAAGAATAAATT
1 AATAAAAAAGAATAAATT
*
253869 AATAAAATA-AATAAAT
1 AATAAAAAAGAATAAAT
253885 AAACAACTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (18 bp):
AATAAAAAAGAATAAATT
Found at i:253961 original size:42 final size:41
Alignment explanation
Indices: 253913--254010 Score: 103
Period size: 44 Copynumber: 2.3 Consensus size: 41
253903 ATAATAATAA
*
253913 TATATATATATATA-TTATTTCGAAAACA-ATGTTTTCAAAGAAAC
1 TATATATATATATACAT-TTTC-AAAA-AGATGTTTT-AAA-AAAC
253957 TATATATATTATATACATTTTCAAAAAGATGTTTTAAAAAAC
1 TATATATA-TATATACATTTTCAAAAAGATGTTTTAAAAAAC
*
253999 TATGT-TATATAT
1 TATATATATATAT
254011 GTTTTCCAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
40 5 0.10
41 2 0.04
42 8 0.16
43 4 0.08
44 19 0.39
45 10 0.20
46 1 0.02
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.42
Consensus pattern (41 bp):
TATATATATATATACATTTTCAAAAAGATGTTTTAAAAAAC
Found at i:253961 original size:44 final size:43
Alignment explanation
Indices: 253912--254010 Score: 107
Period size: 42 Copynumber: 2.3 Consensus size: 43
253902 AATAATAATA
*
253912 ATATATATATATATA-TTATTTCGAAAACA-ATGTTTTCAAAGAAACT
1 ATATATATATATATACAT-TTTC-AAAA-AGATGTTTT-AAA-AAACT
253958 ATATATAT-TATATACATTTTCAAAAAGATGTTTTAAAAAACT
1 ATATATATATATATACATTTTCAAAAAGATGTTTTAAAAAACT
*
254000 ATGT-TATATAT
1 ATATATATATAT
254011 GTTTTCCAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
41 3 0.06
42 11 0.23
43 4 0.08
44 11 0.23
45 10 0.21
46 9 0.19
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.41
Consensus pattern (43 bp):
ATATATATATATATACATTTTCAAAAAGATGTTTTAAAAAACT
Found at i:254016 original size:38 final size:37
Alignment explanation
Indices: 253965--254127 Score: 107
Period size: 37 Copynumber: 4.2 Consensus size: 37
253955 ACTATATATA
** *
253965 TTATATACATTTTCAAAAA-GATGTTTTAAAAAACTAT
1 TTATATATGTTTTCAAAAACCAT-TTTTAAAAAACTAT
*
254002 GTTATATATGTTTTCCAAAAAACCATTTTAAAAAAAAACTAT
1 -TTATATATGTTTT-C-AAAAACCATTTT--TAAAAAACTAT
* *
254044 ATATTATATGTTTTTAAAAACCA-TTTTAAAAAACTAT
1 TTA-TATATGTTTTCAAAAACCATTTTTAAAAAACTAT
* * * * *
254081 ATATTACATGTTTTTAAAAA-TATGTTTTCAAAAACTAT
1 TTA-TATATGTTTTCAAAAACCAT-TTTTAAAAAACTAT
*
254119 ATTTTATAT
1 -TTATATAT
254128 ATATATATAT
Statistics
Matches: 103, Mismatches: 13, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
36 1 0.01
37 29 0.28
38 28 0.27
39 5 0.05
40 16 0.16
41 4 0.04
42 20 0.19
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.42
Consensus pattern (37 bp):
TTATATATGTTTTCAAAAACCATTTTTAAAAAACTAT
Found at i:254036 original size:40 final size:37
Alignment explanation
Indices: 253988--254127 Score: 131
Period size: 38 Copynumber: 3.6 Consensus size: 37
253978 CAAAAAGATG
*
253988 TTTTAAAAAACTATGT-TATATATGTTTTCCAAAAAACCA
1 TTTTAAAAAACTATATAT-TATATGTTTT--AAAAAACCA
*
254027 TTTTAAAAAAAAACTATATATTATATGTTTTTAAAAACCA
1 TTTT---AAAAAACTATATATTATATGTTTTAAAAAACCA
* **
254067 TTTTAAAAAACTATATATTACATGTTTTTAAAAATA-TG
1 TTTTAAAAAACTATATATTATATG-TTTTAAAAA-ACCA
* *
254105 TTTTCAAAAACTATATTTTATAT
1 TTTTAAAAAACTATATATTATAT
254128 ATATATATAT
Statistics
Matches: 86, Mismatches: 9, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
37 19 0.22
38 28 0.33
39 5 0.06
40 12 0.14
42 21 0.24
43 1 0.01
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.43
Consensus pattern (37 bp):
TTTTAAAAAACTATATATTATATGTTTTAAAAAACCA
Found at i:254075 original size:37 final size:37
Alignment explanation
Indices: 253988--254127 Score: 140
Period size: 37 Copynumber: 3.6 Consensus size: 37
253978 CAAAAAGATG
* *
253988 TTTTAAAAAACTATGT-TATATATGTTTTCCAAAAAACCA
1 TTTTAAAAAACTATATAT-TATATGTTTT--TAAAAACCA
254027 TTTTAAAAAAAAACTATATATTATATGTTTTTAAAAACCA
1 TTTT---AAAAAACTATATATTATATGTTTTTAAAAACCA
* *
254067 TTTTAAAAAACTATATATTACATGTTTTTAAAAA-TA
1 TTTTAAAAAACTATATATTATATGTTTTTAAAAACCA
* *
254103 TGTTTTCAAAAACTATATTTTATAT
1 --TTTTAAAAAACTATATATTATAT
254128 ATATATATAT
Statistics
Matches: 88, Mismatches: 7, Indels: 13
0.81 0.06 0.12
Matches are distributed among these distances:
36 1 0.01
37 29 0.33
38 20 0.23
39 4 0.05
40 12 0.14
42 21 0.24
43 1 0.01
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.43
Consensus pattern (37 bp):
TTTTAAAAAACTATATATTATATGTTTTTAAAAACCA
Found at i:254130 original size:2 final size:2
Alignment explanation
Indices: 254123--254153 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
254113 AACTATATTT
254123 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 T
254154 TCCAAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:254217 original size:37 final size:35
Alignment explanation
Indices: 254174--254313 Score: 127
Period size: 37 Copynumber: 3.8 Consensus size: 35
254164 TATTTTTTTT
*
254174 AAACTATATATTATATGTTTTTCAAAAACCATTAAA
1 AAACTATATATTATATG-TTTTCAAAAACAATTAAA
* * ** *
254210 AACACTATATATTATACGTTTCCAAAAATACGTTTTCAA
1 AA-ACTATATATTATATGTTTTC-AAAA-AC-AATTAAA
* *
254249 AAACTATATTATATATATGTTTTCAAAAAAAATCAAA
1 AAACTATA-TAT-TATATGTTTTCAAAAACAATTAAA
* *
254286 AAATTATATATTACATGTTTTCAAAAAC
1 AAACTATATATTATATGTTTTCAAAAAC
254314 GTGTTTTCAA
Statistics
Matches: 83, Mismatches: 15, Indels: 13
0.75 0.14 0.12
Matches are distributed among these distances:
35 15 0.18
36 9 0.11
37 28 0.34
38 9 0.11
39 13 0.16
40 9 0.11
ACGTcount: A:0.47, C:0.12, G:0.04, T:0.37
Consensus pattern (35 bp):
AAACTATATATTATATGTTTTCAAAAACAATTAAA
Found at i:254337 original size:75 final size:77
Alignment explanation
Indices: 254174--254339 Score: 180
Period size: 75 Copynumber: 2.2 Consensus size: 77
254164 TATTTTTTTT
** * *
254174 AAACTATA-TAT-TATATGTTTTTCAAAAACCATTAAAAACACTATATATTATACGTTTCCAAAA
1 AAACTATACTATATATATGTTTTTCAAAAAAAATCAAAAACACTATATATTACACGTTTCCAAAA
*
254237 ATACGTTTTCAA
66 ACACGTTTTCAA
* * * *
254249 AAACTATATTATATATATG-TTTTCAAAAAAAATCAAAAA-ATTATATATTACATGTTTTCAAAA
1 AAACTATACTATATATATGTTTTTCAAAAAAAATCAAAAACACTATATATTACACGTTTCCAAAA
**
254312 ACGTGTTTTCAA
66 ACACGTTTTCAA
*
254324 AGAA-TATGCTATATAT
1 A-AACTATACTATATAT
254340 TTTCAAAACT
Statistics
Matches: 76, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
75 48 0.63
76 22 0.29
77 6 0.08
ACGTcount: A:0.45, C:0.11, G:0.05, T:0.38
Consensus pattern (77 bp):
AAACTATACTATATATATGTTTTTCAAAAAAAATCAAAAACACTATATATTACACGTTTCCAAAA
ACACGTTTTCAA
Found at i:265990 original size:26 final size:26
Alignment explanation
Indices: 265954--266006 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
265944 TTGAGCGATG
265954 TTTGGTGAAGAGATAGACTTGTTTTC
1 TTTGGTGAAGAGATAGACTTGTTTTC
265980 TTTGGTGAAGAGATAGACTTGTTTTC
1 TTTGGTGAAGAGATAGACTTGTTTTC
266006 T
1 T
266007 CTGGATATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.23, C:0.08, G:0.26, T:0.43
Consensus pattern (26 bp):
TTTGGTGAAGAGATAGACTTGTTTTC
Found at i:266659 original size:18 final size:17
Alignment explanation
Indices: 266633--266675 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
266623 ATTAAATGTT
*
266633 CAAACAAAAAAATGATAA
1 CAAAAAAAAAAATGA-AA
*
266651 CAAAAAAAATAATGAAA
1 CAAAAAAAAAAATGAAA
*
266668 GAAAAAAA
1 CAAAAAAA
266676 TGCAGCGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.77, C:0.07, G:0.07, T:0.09
Consensus pattern (17 bp):
CAAAAAAAAAAATGAAA
Found at i:269642 original size:30 final size:29
Alignment explanation
Indices: 269602--269658 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
269592 ATAACGACTG
*
269602 ATGATTTAATTGAA-TCAATTAAATAATTAA
1 ATGATCTAATT-AATTCAATTAAA-AATTAA
*
269632 ATGATCTAATTAATTTAATTAAAAATT
1 ATGATCTAATTAATTCAATTAAAAATT
269659 CGATAATCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 6 0.25
30 18 0.75
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (29 bp):
ATGATCTAATTAATTCAATTAAAAATTAA
Found at i:270886 original size:19 final size:19
Alignment explanation
Indices: 270858--270918 Score: 77
Period size: 19 Copynumber: 3.1 Consensus size: 19
270848 TATTTATTTA
270858 TTTAAAAATTATATATATT
1 TTTAAAAATTATATATATT
*
270877 TTTCAAAATTATATATAGATT
1 TTTAAAAATTATATAT--ATT
*
270898 TTTAAAAAATATATAATATT
1 TTTAAAAATTATAT-ATATT
270918 T
1 T
270919 ATATTTTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
19 15 0.42
20 4 0.11
21 15 0.42
22 2 0.06
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (19 bp):
TTTAAAAATTATATATATT
Found at i:270972 original size:29 final size:29
Alignment explanation
Indices: 270940--271033 Score: 84
Period size: 29 Copynumber: 3.1 Consensus size: 29
270930 ATATATATAT
*
270940 ATATATATATATATATATATGTATTTAAA
1 ATATATATATATATATATATATATTTAAA
270969 ATATATATTTCAATATATATATATATATATTAAA
1 ATATATA--T--ATATATATATATATAT-TTAAA
* * *
271003 A-ACCATA-ATATATATTTATATAATTAAA
1 ATA-TATATATATATATATATATATTTAAA
271031 ATA
1 ATA
271034 ATAGAAAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
28 6 0.11
29 22 0.41
31 1 0.02
33 16 0.30
34 9 0.17
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (29 bp):
ATATATATATATATATATATATATTTAAA
Found at i:270973 original size:35 final size:35
Alignment explanation
Indices: 270934--271024 Score: 105
Period size: 35 Copynumber: 2.6 Consensus size: 35
270924 TTTAATATAT
* *
270934 ATATATATATATATATATATATATATGTATTTAAA
1 ATATATATATATATATATATATATATATATTAAAA
*
270969 ATATATATTTCA-ATATATATATATATATATTAAAA
1 ATATATATAT-ATATATATATATATATATATTAAAA
* *
271004 ACCATA-ATATATATTTATATA
1 A-TATATATATATATATATATA
271025 ATTAAAATAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
34 1 0.02
35 42 0.89
36 4 0.09
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.46
Consensus pattern (35 bp):
ATATATATATATATATATATATATATATATTAAAA
Found at i:271017 original size:2 final size:2
Alignment explanation
Indices: 270906--270998 Score: 86
Period size: 2 Copynumber: 48.0 Consensus size: 2
270896 TTTTTAAAAA
* * *
270906 AT AT AT A- AT AT TT AT AT TT TT A- 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
* * * *
270946 AT AT AT AT AT AT AT GT AT TT A- AA AT AT AT AT TT CA- 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
270987 AT AT AT AT AT AT
1 AT AT AT AT AT AT
270999 TAAAAACCAT
Statistics
Matches: 75, Mismatches: 11, Indels: 10
0.78 0.11 0.10
Matches are distributed among these distances:
1 4 0.05
2 71 0.95
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (2 bp):
AT
Found at i:272211 original size:55 final size:55
Alignment explanation
Indices: 272123--272228 Score: 160
Period size: 55 Copynumber: 1.9 Consensus size: 55
272113 TTTTATTTTA
* * **
272123 AGAGAAATTGTCTCGGGTGAGACAAAACTTTTCAAAGG-AAATATCTCAAGGTTTG
1 AGAGAAAATGTCTCGAGTGAGACAAAAAGTTTC-AAGGAAAATATCTCAAGGTTTG
272178 AGAGAAAATGTCTCGAGTGAGACAAAAAGTTTCAAGGAAAATATCTCAAGG
1 AGAGAAAATGTCTCGAGTGAGACAAAAAGTTTCAAGGAAAATATCTCAAGG
272229 GAGATGAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
54 4 0.09
55 42 0.91
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.24
Consensus pattern (55 bp):
AGAGAAAATGTCTCGAGTGAGACAAAAAGTTTCAAGGAAAATATCTCAAGGTTTG
Found at i:272320 original size:72 final size:72
Alignment explanation
Indices: 272178--272425 Score: 340
Period size: 72 Copynumber: 3.5 Consensus size: 72
272168 TCAAGGTTTG
* **
272178 AGAGAAAATGTCTCGAGTGAGACAAAAA-GTTTCAAGGAAAATATCTCAAGGGAGATGAAATTTT
1 AGAGAAACTGTCTCGAGTGAGACAAAAACAATTCAAGGAAAATATCTCAAGGGAGATGAAATTTT
*
272242 CGTTTCA
66 CTTTTCA
* *
272249 AGAGAAACTGTCTCGAGTGAGACAAAAA-AATTCAAGGGAAAATATCTCAAAGGAGATTAAATTT
1 AGAGAAACTGTCTCGAGTGAGACAAAAACAATTCAA-GGAAAATATCTCAAGGGAGATGAAATTT
272313 TCTTTTCA
65 TCTTTTCA
* * ***
272321 AGAGGAATTGTCTCGAGTGAGACAAAAAGTTTTCAAGGAAAATATCTCAAGGGAGATGAAATTTT
1 AGAGAAACTGTCTCGAGTGAGACAAAAACAATTCAAGGAAAATATCTCAAGGGAGATGAAATTTT
272386 -TGTTTCA
66 CT-TTTCA
* *
272393 AGAGTAACTGTCTCGGGTGAGACAAAAACAATT
1 AGAGAAACTGTCTCGAGTGAGACAAAAACAATT
272426 TAAGTGAGAA
Statistics
Matches: 156, Mismatches: 18, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
71 33 0.21
72 118 0.76
73 5 0.03
ACGTcount: A:0.40, C:0.12, G:0.22, T:0.26
Consensus pattern (72 bp):
AGAGAAACTGTCTCGAGTGAGACAAAAACAATTCAAGGAAAATATCTCAAGGGAGATGAAATTTT
CTTTTCA
Found at i:274062 original size:36 final size:35
Alignment explanation
Indices: 274020--274193 Score: 134
Period size: 36 Copynumber: 4.8 Consensus size: 35
274010 CAAGTGAGAT
**
274020 AAAAATTGTTTTTGAGGAAAAACTATCTTTAGTAAG
1 AAAAATTGTTTTTGA-GAAAAACTATCTCGAGTAAG
* * * * * *
274056 ATAAATTCTATTTCAAAAGAAACTATCTCGAGTGAGAC
1 AAAAATTGTTTTTGAGAA-AAACTATCTCGAGT-A-AG
* *
274094 AAAAATTGTTTTTGA-AAAAACTATCTCCAGTGAG
1 AAAAATTGTTTTTGAGAAAAACTATCTCGAGTAAG
* * * *
274128 ATAAAATTATGTTTCGAGAGAAACTATCTCGAGTGAG
1 A-AAAATTGT-TTTTGAGAAAAACTATCTCGAGTAAG
* *
274165 ACAAAATTGTTTTTGAGGAAAATTATCTC
1 A-AAAATTGTTTTTGAGAAAAACTATCTC
274194 AAATGAGATA
Statistics
Matches: 107, Mismatches: 25, Indels: 12
0.74 0.17 0.08
Matches are distributed among these distances:
34 2 0.02
35 9 0.08
36 56 0.52
37 28 0.26
38 12 0.11
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33
Consensus pattern (35 bp):
AAAAATTGTTTTTGAGAAAAACTATCTCGAGTAAG
Found at i:274077 original size:74 final size:74
Alignment explanation
Indices: 273999--274186 Score: 247
Period size: 74 Copynumber: 2.6 Consensus size: 74
273989 TTGTTTTAAG
* * **
273999 AGAAACTATTTCAAGTGAGATAAAAATTGTTTTTGAGGAAAAACTATCTTTAGTAAGAT-AAATT
1 AGAAACTATCTCGAGTGAGA-AAAAATTGTTTTTGAGGAAAAACTATCTCCAGTAAGATAAAATT
*
274063 CTATTTCAAA
65 ATATTTCAAA
*
274073 AGAAACTATCTCGAGTGAGACAAAAATTGTTTTTGA--AAAAACTATCTCCAGTGAGATAAAATT
1 AGAAACTATCTCGAGTGAGA-AAAAATTGTTTTTGAGGAAAAACTATCTCCAGTAAGATAAAATT
* * *
274136 ATGTTTCGAG
65 ATATTTCAAA
*
274146 AGAAACTATCTCGAGTGAGACAAAATTGTTTTTGAGGAAAA
1 AGAAACTATCTCGAGTGAGAAAAAATTGTTTTTGAGGAAAA
274187 TTATCTCAAA
Statistics
Matches: 100, Mismatches: 11, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
72 32 0.32
73 31 0.31
74 37 0.37
ACGTcount: A:0.41, C:0.10, G:0.17, T:0.31
Consensus pattern (74 bp):
AGAAACTATCTCGAGTGAGAAAAAATTGTTTTTGAGGAAAAACTATCTCCAGTAAGATAAAATTA
TATTTCAAA
Found at i:274162 original size:73 final size:74
Alignment explanation
Indices: 273963--274222 Score: 289
Period size: 73 Copynumber: 3.6 Consensus size: 74
273953 TTTTCAAGGG
* * * * * *
273963 AAAA-TATCTCTAGTGAGATGAAATTTTTGTTTTAAGAGAAACTATTTCAAGTGAGATAAAAATT
1 AAAACTATCTCTAGTGAGAT-AAAATTATGTTTCAAGAGAAACTATCTCGAGTGAGACAAAAATT
274027 GTTTTTGAGGA
65 GTTTTTGA-GA
* * * * *
274038 AAAACTATCTTTAGTAAGAT-AAATTCTATTTCAAAAGAAACTATCTCGAGTGAGACAAAAATTG
1 AAAACTATCTCTAGTGAGATAAAATTATGTTTCAAGAGAAACTATCTCGAGTGAGACAAAAATTG
274102 TTTTTGA-A
66 TTTTTGAGA
* *
274110 AAAACTATCTCCAGTGAGATAAAATTATGTTTCGAGAGAAACTATCTCGAGTGAGAC-AAAATTG
1 AAAACTATCTCTAGTGAGATAAAATTATGTTTCAAGAGAAACTATCTCGAGTGAGACAAAAATTG
*
274174 TTTTTGAGG
66 TTTTTGAGA
* * * *
274183 AAAATTATCTCAAATGAGATAAAACTTTTG-TTCAAG-GAAA
1 AAAACTATCTCTAGTGAGATAAAA-TTATGTTTCAAGAGAAA
274223 ACCTCTCATA
Statistics
Matches: 158, Mismatches: 23, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
72 36 0.23
73 58 0.37
74 47 0.30
75 4 0.03
76 13 0.08
ACGTcount: A:0.41, C:0.10, G:0.17, T:0.33
Consensus pattern (74 bp):
AAAACTATCTCTAGTGAGATAAAATTATGTTTCAAGAGAAACTATCTCGAGTGAGACAAAAATTG
TTTTTGAGA
Found at i:274201 original size:36 final size:35
Alignment explanation
Indices: 274075--274193 Score: 148
Period size: 36 Copynumber: 3.3 Consensus size: 35
274065 ATTTCAAAAG
*
274075 AAACTATCTCGAGTGAGACAAAAATTGTTTTTGAAA
1 AAACTATCTCGAGTGAGAC-AAAATTGTTTTTGAGA
* * * *
274111 AAACTATCTCCAGTGAGATAAAATTATGTTTCGAGA
1 AAACTATCTCGAGTGAGACAAAATTGT-TTTTGAGA
274147 GAAACTATCTCGAGTGAGACAAAATTGTTTTTGAGGA
1 -AAACTATCTCGAGTGAGACAAAATTGTTTTTGA-GA
*
274184 AAATTATCTC
1 AAACTATCTC
274194 AAATGAGATA
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
35 7 0.10
36 37 0.53
37 26 0.37
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.31
Consensus pattern (35 bp):
AAACTATCTCGAGTGAGACAAAATTGTTTTTGAGA
Done.