Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002071.1 Hibiscus syriacus cultivar Beakdansim tig00004228_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: 24483
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.33
Found at i:424 original size:21 final size:22
Alignment explanation
Indices: 400--444 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
390 TCATTATTTA
400 TTTATAT-TTTAATT-TTATATG
1 TTTATATATTTAATTATTAT-TG
421 TTTATATATTTAATTATTATTG
1 TTTATATATTTAATTATTATTG
443 TT
1 TT
445 ATTATAGTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.32
22 11 0.50
23 4 0.18
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (22 bp):
TTTATATATTTAATTATTATTG
Found at i:450 original size:22 final size:22
Alignment explanation
Indices: 400--450 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
390 TCATTATTTA
400 TTTATATTTTAATTTTATATG-
1 TTTATATTTTAATTTTATATGT
421 TTTATATATTTAATTATTAT-TGT
1 TTTATAT-TTTAATT-TTATATGT
444 TATTATA
1 T-TTATA
451 GTCATATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
21 7 0.27
22 9 0.35
23 5 0.19
24 5 0.19
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (22 bp):
TTTATATTTTAATTTTATATGT
Found at i:1357 original size:24 final size:24
Alignment explanation
Indices: 1317--1379 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 24
1307 CAAATTTTTA
1317 TATATACTTATTATTTTCA-TAATATT
1 TATATA-TTATT-TTTT-ATTAATATT
*
1343 TATATATTATTTTTTATTAATGTT
1 TATATATTATTTTTTATTAATATT
* *
1367 TTTATTTTATTTT
1 TATATATTATTTT
1380 CAAGTATTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 1 0.03
24 21 0.64
25 5 0.15
26 6 0.18
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.67
Consensus pattern (24 bp):
TATATATTATTTTTTATTAATATT
Found at i:4588 original size:16 final size:16
Alignment explanation
Indices: 4569--4601 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
4559 GATCAATACC
4569 TTTTGCATACATTCAT
1 TTTTGCATACATTCAT
4585 TTTTGCATACATTCAT
1 TTTTGCATACATTCAT
4601 T
1 T
4602 GCATTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.06, T:0.52
Consensus pattern (16 bp):
TTTTGCATACATTCAT
Found at i:11824 original size:9 final size:9
Alignment explanation
Indices: 11810--11848 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
11800 TAAAGAAGAA
11810 GAAAAAAAT
1 GAAAAAAAT
11819 GAAAAAAAT
1 GAAAAAAAT
11828 G---AAAAT
1 GAAAAAAAT
11834 GAAAAAAAT
1 GAAAAAAAT
11843 GAAAAA
1 GAAAAA
11849 TGAAACGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
6 6 0.22
9 21 0.78
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (9 bp):
GAAAAAAAT
Found at i:11839 original size:16 final size:16
Alignment explanation
Indices: 11813--11853 Score: 75
Period size: 15 Copynumber: 2.6 Consensus size: 16
11803 AGAAGAAGAA
11813 AAAAATGAAAAAAATG
1 AAAAATGAAAAAAATG
11829 -AAAATGAAAAAAATG
1 AAAAATGAAAAAAATG
11844 AAAAATGAAA
1 AAAAATGAAA
11854 CGAAAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (16 bp):
AAAAATGAAAAAAATG
Found at i:11847 original size:22 final size:21
Alignment explanation
Indices: 11810--11870 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 21
11800 TAAAGAAGAA
*
11810 GAAAAAAATGAAAAAAATGAAAAT
1 GAAAAAAATG--AAAAATG-AAAC
11834 GAAAAAAATGAAAAATGAAAC
1 GAAAAAAATGAAAAATGAAAC
11855 GAAAAAAATAGAAAAA
1 GAAAAAAAT-GAAAAA
11871 GAGGGTCAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
21 12 0.34
22 13 0.37
24 10 0.29
ACGTcount: A:0.75, C:0.02, G:0.13, T:0.10
Consensus pattern (21 bp):
GAAAAAAATGAAAAATGAAAC
Found at i:12530 original size:19 final size:20
Alignment explanation
Indices: 12506--12549 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
12496 ATGTTTTACA
*
12506 AACCAGTAA-TATGGTGCTG
1 AACCAGTAATTATGGCGCTG
*
12525 AACCAGTAATTATGGCGTTG
1 AACCAGTAATTATGGCGCTG
12545 AACCA
1 AACCA
12550 ATGTTGTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (20 bp):
AACCAGTAATTATGGCGCTG
Found at i:12907 original size:22 final size:22
Alignment explanation
Indices: 12882--12965 Score: 109
Period size: 22 Copynumber: 3.9 Consensus size: 22
12872 TACATTCTTT
12882 AAAGATGATAGATTCTATTTTC
1 AAAGATGATAGATTCTATTTTC
12904 AAAGATGATAGATTCT-TTCTTC
1 AAAGATGATAGATTCTATT-TTC
* *
12926 AAAGATGATACATTCTCTTTTC
1 AAAGATGATAGATTCTATTTTC
* *
12948 AAAGAAGAAAGATT-TATT
1 AAAGATGATAGATTCTATT
12966 GGATTTCTAC
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.09
22 48 0.87
23 2 0.04
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (22 bp):
AAAGATGATAGATTCTATTTTC
Found at i:12934 original size:44 final size:44
Alignment explanation
Indices: 12876--12961 Score: 127
Period size: 44 Copynumber: 2.0 Consensus size: 44
12866 AACATCTACA
* * * *
12876 TTCTTTAAAGATGATAGATTCTATTTTCAAAGATGATAGATTCT
1 TTCTTCAAAGATGATACATTCTATTTTCAAAGAAGAAAGATTCT
*
12920 TTCTTCAAAGATGATACATTCTCTTTTCAAAGAAGAAAGATT
1 TTCTTCAAAGATGATACATTCTATTTTCAAAGAAGAAAGATT
12962 TATTGGATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.40
Consensus pattern (44 bp):
TTCTTCAAAGATGATACATTCTATTTTCAAAGAAGAAAGATTCT
Found at i:13390 original size:17 final size:17
Alignment explanation
Indices: 13331--13391 Score: 50
Period size: 17 Copynumber: 3.2 Consensus size: 17
13321 ACATTTCCCG
13331 AGAAGTTCATAATGAGA
1 AGAAGTTCATAATGAGA
* *
13348 AGAACTTATCTGAAGAATGAAGA
1 AGAA-GT-TC---ATAATG-AGA
13371 AGAAGTTCATAATGAGA
1 AGAAGTTCATAATGAGA
13388 AGAA
1 AGAA
13392 ATTGTTCAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
17 11 0.32
18 6 0.18
19 2 0.06
21 2 0.06
22 6 0.18
23 7 0.21
ACGTcount: A:0.49, C:0.07, G:0.23, T:0.21
Consensus pattern (17 bp):
AGAAGTTCATAATGAGA
Found at i:13614 original size:38 final size:39
Alignment explanation
Indices: 13563--13666 Score: 176
Period size: 39 Copynumber: 2.7 Consensus size: 39
13553 CAACATTTCC
13563 AGAGAAAGTTCATAATGAGAAGAACTTAT-TGAAGAGGA
1 AGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGA
*
13601 AGAGAAAGTTCATAATGAGAATAACTTATCTGAAGAGGA
1 AGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGA
13640 AGA-AGAAGTTCATAATGAGAAGAACTT
1 AGAGA-AAGTTCATAATGAGAAGAACTT
13667 TTCAACCTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
38 29 0.47
39 33 0.53
ACGTcount: A:0.47, C:0.07, G:0.24, T:0.22
Consensus pattern (39 bp):
AGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGA
Found at i:13755 original size:159 final size:160
Alignment explanation
Indices: 13447--13786 Score: 494
Period size: 159 Copynumber: 2.1 Consensus size: 160
13437 TGCCAGGTAG
*
13447 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGGAAAAGTTCATAATGAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGGAAAAGTTCATAATGAGAAGAACTTGTTCA
*
13512 ACCTTTTCATGACTCTATCACAGAAAGAGATAGATCAACATCAACATTTCCAGAGAAAGTTCATA
66 ACCTTTGCATGACTCTATCACAGAAAGAGATAGATCAACATCAACATTTCCAGAGAAAGTTCATA
* *
13577 ATGAGAAGAACTTATTGAAGAGGAAGAG-A-A
131 ATGAGAAAAACTCATTGAAGA--AAGAGAAGA
*
13607 AGTTCATAATGAGAATAACTTATCTGAAGAGGAA-GAAGAAGTTCATAATGAGAAGAACTT-TTC
1 AGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGGAA-AAGTTCATAATGAGAAGAACTTGTTC
* * * *
13670 AACCTTTGCATGACTCTATCACATAAGGAGATAGATCAACATCAACATTTCTA-A-AAGTGTTCA
65 AACCTTTGCATGACTCTATCACAGAAAGAGATAGATCAACATCAACATTTCCAGAGAA-AGTTCA
*
13733 TAATGAGAAAAACTCATCTGAAGAATGAGAAGA
129 TAATGAGAAAAACTCAT-TGAAGAAAGAGAAGA
*
13766 AGTTCATATTGAGAAGAACTT
1 AGTTCATAATGAGAAGAACTT
13787 GTTCAACATT
Statistics
Matches: 163, Mismatches: 12, Indels: 11
0.88 0.06 0.06
Matches are distributed among these distances:
157 6 0.04
158 22 0.13
159 81 0.50
160 54 0.33
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.25
Consensus pattern (160 bp):
AGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGGAAAAGTTCATAATGAGAAGAACTTGTTCA
ACCTTTGCATGACTCTATCACAGAAAGAGATAGATCAACATCAACATTTCCAGAGAAAGTTCATA
ATGAGAAAAACTCATTGAAGAAAGAGAAGA
Found at i:14165 original size:3 final size:3
Alignment explanation
Indices: 14157--14208 Score: 79
Period size: 3 Copynumber: 17.7 Consensus size: 3
14147 TCTATTTGGT
* *
14157 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA ATA -AA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
14204 TTA TT
1 TTA TT
14209 TACATTACAG
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
2 1 0.02
3 44 0.98
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:15592 original size:21 final size:23
Alignment explanation
Indices: 15567--15616 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 23
15557 TATTTTAGTC
15567 ATTATTTATTTATAT-TTTAATT
1 ATTATTTATTTATATATTTAATT
* *
15589 -TTATATGTTTATATATTTAATT
1 ATTATTTATTTATATATTTAATT
15611 ATTATT
1 ATTATT
15617 GTTATTATAG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 12 0.52
22 7 0.30
23 4 0.17
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (23 bp):
ATTATTTATTTATATATTTAATT
Found at i:15621 original size:21 final size:21
Alignment explanation
Indices: 15575--15619 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
15565 TCATTATTTA
15575 TTTATATTTTAATTTTATATG
1 TTTATATTTTAATTTTATATG
15596 TTTATATATTTAATTATTAT-TG
1 TTTATAT-TTTAATT-TTATATG
15618 TT
1 TT
15620 ATTATAGTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.32
22 11 0.50
23 4 0.18
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (21 bp):
TTTATATTTTAATTTTATATG
Found at i:15625 original size:22 final size:22
Alignment explanation
Indices: 15575--15625 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
15565 TCATTATTTA
15575 TTTATATTTTAATTTTATATG-
1 TTTATATTTTAATTTTATATGT
15596 TTTATATATTTAATTATTAT-TGT
1 TTTATAT-TTTAATT-TTATATGT
15619 TATTATA
1 T-TTATA
15626 GTCATATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
21 7 0.27
22 9 0.35
23 5 0.19
24 5 0.19
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (22 bp):
TTTATATTTTAATTTTATATGT
Found at i:19319 original size:21 final size:21
Alignment explanation
Indices: 19281--19320 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
19271 AAATAAAAAA
*
19281 TTGGATCGGATATTCGAATTT
1 TTGGATCGGATATACGAATTT
19302 TTGGATCGGATGA-ACGAAT
1 TTGGATCGGAT-ATACGAAT
19321 CAAATCTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.28, C:0.10, G:0.28, T:0.35
Consensus pattern (21 bp):
TTGGATCGGATATACGAATTT
Found at i:20937 original size:211 final size:210
Alignment explanation
Indices: 20482--21074 Score: 866
Period size: 211 Copynumber: 2.8 Consensus size: 210
20472 AAATTTAAGA
* *
20482 ATTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATG
1 ATTAAATTGAACAAATATGAAATTAAAAATAAAAATTTAAATATATTAAACAACACA-A---A--
*
20547 AGGGATCAAATCGAAATAATTTTAAA-TTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTA
60 AGGGATCAAATCGAAATAATTTTAAATTTG-GAGGTTGAAATTAATATAAAAAAGTACTAAATTA
* * *
20611 TACCCATTTCAAAGGTTATGGGTCAATTTAAAAAT----A-AA--AATAAGTATGAGTCAATTTC
124 TACCCATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGAGTCAATTTC
*
20669 AGATGCAAATAAAATTTGGAGG
189 AGATGCAAATAAAAGTTGGAGG
* * *
20691 ACTAAATTGAACAAATATGAAATTATAATTAAAAATTTAAATATATTAAACAACACAAAAGGGAT
1 ATTAAATTGAACAAATATGAAATTAAAAATAAAAATTTAAATATATTAAACAACACAAAAGGGAT
*
20756 CAAATCGAAATACTTTTAAATTTGGAGGTTGAAATTAATATAAAAAAGTACTAAATTATACCCAT
66 CAAATCGAAATAATTTTAAATTTGGAGGTTGAAATTAATATAAAAAAGTACTAAATTATACCCAT
* * *
20821 TTAAAAAATTTATAGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGAGTCAATTTCAGGTGC
131 TT-AAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGAGTCAATTTCAGATGC
20886 AAATAAAAGTTGGAGG
195 AAATAAAAGTTGGAGG
*
20902 ATTAAATTGAACAAATATGAAATTAAAAATAAAAATTTAAATATATTAAACATCACAAAAGGGAT
1 ATTAAATTGAACAAATATGAAATTAAAAATAAAAATTTAAATATATTAAACAACACAAAAGGGAT
* * *
20967 CAAATCAAAATAATTTTAAATTTTGAGGTTGAAATTAATATAAAAAATGTACTAAATTATACTCA
66 CAAATCGAAATAATTTTAAATTTGGAGGTTGAAATTAATATAAAAAA-GTACTAAATTATACCCA
21032 TTTAAAAAGTTATGGGCCAATTT--AAA-AGAAATAAGTAATAAGT
130 TTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGT
21075 GAGAAAAAAA
Statistics
Matches: 351, Mismatches: 23, Indels: 21
0.89 0.06 0.05
Matches are distributed among these distances:
203 67 0.19
204 24 0.07
205 1 0.00
208 19 0.05
209 58 0.17
211 163 0.46
212 19 0.05
ACGTcount: A:0.50, C:0.08, G:0.12, T:0.30
Consensus pattern (210 bp):
ATTAAATTGAACAAATATGAAATTAAAAATAAAAATTTAAATATATTAAACAACACAAAAGGGAT
CAAATCGAAATAATTTTAAATTTGGAGGTTGAAATTAATATAAAAAAGTACTAAATTATACCCAT
TTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGAGTCAATTTCAGATGCA
AATAAAAGTTGGAGG
Found at i:21126 original size:34 final size:34
Alignment explanation
Indices: 21083--21153 Score: 117
Period size: 34 Copynumber: 2.1 Consensus size: 34
21073 GTGAGAAAAA
21083 AATTAAAACAACTAATATATAATATATATA-ATAT
1 AATTAAAACAACT-ATATATAATATATATATATAT
*
21117 AATTGAAACAACTATATATAATATATATATATAT
1 AATTAAAACAACTATATATAATATATATATATAT
21151 AAT
1 AAT
21154 ATATATATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 16 0.46
34 19 0.54
ACGTcount: A:0.56, C:0.06, G:0.01, T:0.37
Consensus pattern (34 bp):
AATTAAAACAACTATATATAATATATATATATAT
Found at i:21151 original size:19 final size:20
Alignment explanation
Indices: 21126--21286 Score: 88
Period size: 19 Copynumber: 8.1 Consensus size: 20
21116 TAATTGAAAC
21126 AACTATATATAATATATATAT
1 AACTATATAT-ATATATATAT
*
21147 ATA-TAATATATATATATAAAT
1 A-ACT-ATATATATATATATAT
*
21168 AACTATATATAT-TATGTAT
1 AACTATATATATATATATAT
*
21187 AACTATATAGTTTAT-TAATAT
1 AACTATATA-TATATAT-ATAT
* *
21208 AAACTATATAGTGTATAAATA-
1 -AACTATATA-TATATATATAT
* *
21229 AACTATA-ATCTATAAACTAT
1 AACTATATATATATATA-TAT
* *
21249 ATAGT-TATATTTATAT-TAT
1 A-ACTATATATATATATATAT
*
21268 TACTATATATA-AT-TATAT
1 AACTATATATATATATATAT
21286 A
1 A
21287 GTTGATTAAT
Statistics
Matches: 111, Mismatches: 15, Indels: 31
0.71 0.10 0.20
Matches are distributed among these distances:
17 1 0.01
18 14 0.13
19 25 0.23
20 22 0.20
21 25 0.23
22 24 0.22
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (20 bp):
AACTATATATATATATATAT
Found at i:21195 original size:2 final size:2
Alignment explanation
Indices: 21129--21179 Score: 63
Period size: 2 Copynumber: 26.5 Consensus size: 2
21119 TTGAAACAAC
*
21129 TA TA TA TA -A TA TA TA TA TA TA TA -A TA TA TA TA 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 TA
21169 -A CTA TA TA TA T
1 TA -TA TA TA TA T
21180 TATGTATAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
1 3 0.07
2 39 0.91
3 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:21212 original size:22 final size:20
Alignment explanation
Indices: 21187--21235 Score: 71
Period size: 22 Copynumber: 2.4 Consensus size: 20
21177 TATTATGTAT
*
21187 AACTATATAGTTTATTAATATA
1 AACTATATAGTGTA-TAA-ATA
21209 AACTATATAGTGTATAAATA
1 AACTATATAGTGTATAAATA
21229 AACTATA
1 AACTATA
21236 ATCTATAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 10 0.38
21 3 0.12
22 13 0.50
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.39
Consensus pattern (20 bp):
AACTATATAGTGTATAAATA
Found at i:21294 original size:25 final size:22
Alignment explanation
Indices: 21272--21327 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
21262 TATTATTACT
21272 ATATATAATTATATAGTTGATTA
1 ATATA-AATTATATAGTTGATTA
*
21295 ATATAAATTATATAGTT-AAT-
1 ATATAAATTATATAGTTGATTA
21315 ATA-AAATTATATA
1 ATATAAATTATATA
21328 TGAATTATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 10 0.31
20 3 0.09
21 2 0.06
22 12 0.38
23 5 0.16
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (22 bp):
ATATAAATTATATAGTTGATTA
Found at i:21306 original size:22 final size:20
Alignment explanation
Indices: 21234--21327 Score: 74
Period size: 19 Copynumber: 4.9 Consensus size: 20
21224 AAATAAACTA
* *
21234 TAATCTATAAACTATATAGT
1 TAATATATAAATTATATAGT
* * *
21254 T-ATATTTATATTAT-TA-C
1 TAATATATAAATTATATAGT
21271 T-ATATAT-AATTATATAGT
1 TAATATATAAATTATATAGT
*
21289 TGATTAATATAAATTATATAGT
1 T-AAT-ATATAAATTATATAGT
21311 TAATATA-AAATTATATA
1 TAATATATAAATTATATA
21328 TGAATTATTT
Statistics
Matches: 58, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
16 5 0.09
17 8 0.14
18 3 0.05
19 19 0.33
20 5 0.09
21 6 0.10
22 12 0.21
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (20 bp):
TAATATATAAATTATATAGT
Found at i:21740 original size:35 final size:36
Alignment explanation
Indices: 21670--21743 Score: 96
Period size: 37 Copynumber: 2.1 Consensus size: 36
21660 ACAATAATTA
* *
21670 ATATATGTAACCTATAGTATATGTATACATGTAAACT
1 ATATATGTAACCTATAGTACATGTATA-ATATAAACT
* *
21707 ATATATGTAACTTATAGTACATGTAT-GTATAAACT
1 ATATATGTAACCTATAGTACATGTATAATATAAACT
21742 AT
1 AT
21744 GTATAGTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 9 0.27
37 24 0.73
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (36 bp):
ATATATGTAACCTATAGTACATGTATAATATAAACT
Found at i:21752 original size:20 final size:20
Alignment explanation
Indices: 21729--21772 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
21719 TATAGTACAT
* *
21729 GTATGTATAAACTATGTATA
1 GTATATATAAACTATATATA
21749 GTATATATAAACTATATATA
1 GTATATATAAACTATATATA
21769 -TATA
1 GTATA
21773 AACCATATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (20 bp):
GTATATATAAACTATATATA
Found at i:21770 original size:15 final size:15
Alignment explanation
Indices: 21745--21781 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
21735 ATAAACTATG
21745 TATAGTATATATAAAC
1 TATA-TATATATAAAC
21761 TATATATATATAAAC
1 TATATATATATAAAC
*
21776 CATATA
1 TATATA
21782 AAGGAAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (15 bp):
TATATATATATAAAC
Found at i:22020 original size:40 final size:39
Alignment explanation
Indices: 21966--22041 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 39
21956 TACATGTATG
*
21966 TATAAACTATGTATAT-TATATATAAATTATATATATATA
1 TATAAACTATGTATATGT-TATATAAACTATATATATATA
*
22005 TATAACCTATAGTATATGTTATATAAACTATATATAT
1 TATAAACTAT-GTATATGTTATATAAACTATATATAT
22042 GTAACATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
39 9 0.27
40 23 0.70
41 1 0.03
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (39 bp):
TATAAACTATGTATATGTTATATAAACTATATATATATA
Found at i:22199 original size:15 final size:15
Alignment explanation
Indices: 22148--22205 Score: 64
Period size: 15 Copynumber: 3.8 Consensus size: 15
22138 TTAATGTACT
*
22148 ATATAGTTTATATTA
1 ATATAATTTATATTA
*
22163 ATATTAA-TTATCTTA
1 ATA-TAATTTATATTA
22178 ACTATAATTTATATTA
1 A-TATAATTTATATTA
*
22194 ATATAATATATA
1 ATATAATTTATA
22206 ATTTATAAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
15 24 0.67
16 12 0.33
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (15 bp):
ATATAATTTATATTA
Found at i:22219 original size:14 final size:14
Alignment explanation
Indices: 22202--22262 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
22192 TAATATAATA
22202 TATAATTTATAAAC
1 TATAATTTATAAAC
* *
22216 TATAATGTATTAA-
1 TATAATTTATAAAC
*
22229 TATTAATTATATTAAC
1 TA-TAATT-TATAAAC
*
22245 TATAGTTTATAAAC
1 TATAATTTATAAAC
22259 TATA
1 TATA
22263 CTATATAGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
13 2 0.05
14 25 0.64
15 10 0.26
16 2 0.05
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (14 bp):
TATAATTTATAAAC
Found at i:22229 original size:22 final size:21
Alignment explanation
Indices: 22180--22293 Score: 67
Period size: 22 Copynumber: 5.3 Consensus size: 21
22170 TTATCTTAAC
22180 TATAATTTATATTAATATAATA
1 TATAATTTATA-TAATATAATA
*
22202 TATAATTTATA-AACTATAATG
1 TATAATTTATATAA-TATAATA
* *
22223 TATTAATATTA-ATTATATTAA-C
1 TA-TAAT-TTATATAATA-TAATA
* *
22245 TATAGTTTATA-AACTATACTA
1 TATAATTTATATAA-TATAATA
*
22266 TATAGTTTATACTAATATTAAT-
1 TATAATTTATA-TAATA-TAATA
22288 TATAAT
1 TATAAT
22294 AAGTAATTAT
Statistics
Matches: 72, Mismatches: 9, Indels: 22
0.70 0.09 0.21
Matches are distributed among these distances:
20 8 0.11
21 25 0.35
22 27 0.38
23 12 0.17
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (21 bp):
TATAATTTATATAATATAATA
Found at i:22243 original size:15 final size:15
Alignment explanation
Indices: 22155--22243 Score: 58
Period size: 15 Copynumber: 5.6 Consensus size: 15
22145 ACTATATAGT
22155 TTATATTAATATTAA
1 TTATATTAATATTAA
*
22170 TTATCTTAACTA-TAA
1 TTATATTAA-TATTAA
22185 TTTATATTAATA-TAA
1 -TTATATTAATATTAA
*
22200 TATATAATTTATAAACTATAA
1 T-TAT-A-TTA-ATA-T-TAA
*
22221 -TGTATTAATATTAA
1 TTATATTAATATTAA
22235 TTATATTAA
1 TTATATTAA
22244 CTATAGTTTA
Statistics
Matches: 58, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 4 0.07
15 27 0.47
16 13 0.22
17 6 0.10
18 3 0.05
19 2 0.03
21 3 0.05
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.49
Consensus pattern (15 bp):
TTATATTAATATTAA
Done.