Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002643.1 Hibiscus syriacus cultivar Beakdansim tig00005393_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: 61031
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:2954 original size:18 final size:18
Alignment explanation
Indices: 2913--2955 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
2903 AATTCCAACA
*
2913 TTCTTCTTTTTCTCCGTC
1 TTCTTCTTTGTCTCCGTC
*
2931 TCCTTCTTTGTCT-CGTCC
1 TTCTTCTTTGTCTCCGT-C
2949 TTCTTCT
1 TTCTTCT
2956 CGAGGTCTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.00, C:0.35, G:0.07, T:0.58
Consensus pattern (18 bp):
TTCTTCTTTGTCTCCGTC
Found at i:9298 original size:16 final size:16
Alignment explanation
Indices: 9273--9312 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
9263 GAAAACTTGT
*
9273 TGCTCGTTAAGCTCGA
1 TGCTCATTAAGCTCGA
9289 TGCTCATTAAGCTCGA
1 TGCTCATTAAGCTCGA
9305 TGCTCATT
1 TGCTCATT
9313 GCTCGCCTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.35
Consensus pattern (16 bp):
TGCTCATTAAGCTCGA
Found at i:11789 original size:31 final size:30
Alignment explanation
Indices: 11729--11786 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
11719 AAAATTGAAT
*
11729 ATTTTAAATACTTATTTTGACAAAAAAATA
1 ATTTTAAATACTTATTTTAACAAAAAAATA
* *
11759 ATTTTAATTACTTCTTTTAACAAAAAAA
1 ATTTTAAATACTTATTTTAACAAAAAAA
11787 ATACTTGAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (30 bp):
ATTTTAAATACTTATTTTAACAAAAAAATA
Found at i:16296 original size:21 final size:20
Alignment explanation
Indices: 16270--16367 Score: 74
Period size: 21 Copynumber: 4.8 Consensus size: 20
16260 ATCAGTTTCC
16270 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
* **
16291 AAAATCGCAATGCGATAGT-
1 AAAATCGCAACGCGATTTTG
**
16310 ACAAATTCGCATTGCGATTTT-
1 A-AAA-TCGCAACGCGATTTTG
* *
16331 ACAGAATCGCAACGCGAATATG
1 A-A-AATCGCAACGCGATTTTG
16353 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
16368 ACACATAAAT
Statistics
Matches: 63, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
19 1 0.02
20 17 0.27
21 42 0.67
22 3 0.05
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.21
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:16360 original size:20 final size:20
Alignment explanation
Indices: 16335--16523 Score: 209
Period size: 20 Copynumber: 9.4 Consensus size: 20
16325 GATTTTACAG
** *
16335 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATCCGTA
*
16355 AATCGCAACGCGAA-CACATA
1 AATCGCAACGCGAATC-CGTA
*
16375 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
*
16395 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
* *
16415 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
**
16435 AATCGCAACGATAATCCGTA
1 AATCGCAACGCGAATCCGTA
* *
16455 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGAATCCGTA
**
16475 AATCGCAACGATAATCCGTA
1 AATCGCAACGCGAATCCGTA
* *
16495 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGAATCCGTA
*
16515 AATCACAAC
1 AATCGCAAC
16524 ACTGAAATTT
Statistics
Matches: 149, Mismatches: 18, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 148 0.99
21 1 0.01
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATCCGTA
Found at i:16946 original size:20 final size:20
Alignment explanation
Indices: 16915--16978 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
16905 TTTTGGTTGA
16915 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
16935 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
16955 AAATGAAAATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
16976 AAT
1 AAT
16979 CGCAACGCGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 20 0.54
21 17 0.46
ACGTcount: A:0.47, C:0.16, G:0.25, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:16967 original size:21 final size:21
Alignment explanation
Indices: 16913--16977 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
16903 TCTTTTGGTT
16913 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
16934 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
16954 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
16975 GAA
1 GAA
16978 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:17036 original size:19 final size:19
Alignment explanation
Indices: 17003--17110 Score: 82
Period size: 19 Copynumber: 5.7 Consensus size: 19
16993 AAAATCGCAA
**
17003 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
17022 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
17041 TGCGA--TTC---TCTCGT
1 TGCGATTTTCATTTCGCGT
*
17055 TGCGATTTTCATTTTTCTCGT
1 TGCGATTTTCA--TTTCGCGT
** *
17076 TGCAGATAGTCATTTTCACGT
1 TGC-GATTTTCA-TTTCGCGT
17097 TGCGATTTTCATTT
1 TGCGATTTTCATTT
17111 ATCTCGTTGC
Statistics
Matches: 73, Mismatches: 8, Indels: 16
0.75 0.08 0.16
Matches are distributed among these distances:
14 10 0.14
16 3 0.04
17 3 0.04
19 25 0.34
20 6 0.08
21 20 0.27
22 6 0.08
ACGTcount: A:0.12, C:0.19, G:0.20, T:0.48
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:17074 original size:21 final size:21
Alignment explanation
Indices: 17049--17122 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
17039 GTTGCGATTC
17049 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
17070 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
17091 TCACGTTGCGATTTTCATTTA
1 TCTCGTTGCGATTTTCATTTT
17112 TCTCGTTGCGA
1 TCTCGTTGCGA
17123 CTCTTCTGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 6 0.14
21 32 0.73
22 6 0.14
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:17244 original size:33 final size:33
Alignment explanation
Indices: 17202--17272 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
17192 AATACTAACT
*
17202 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACAAGAGAATAGCAACGCGAAA
* *
17235 TGAAAATCGCAACAAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACAAGAGAATAGCAACGCGAAA
17268 TGAAA
1 TGAAA
17273 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.49, C:0.17, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACAAGAGAATAGCAACGCGAAA
Found at i:17676 original size:20 final size:20
Alignment explanation
Indices: 17651--17843 Score: 237
Period size: 20 Copynumber: 9.6 Consensus size: 20
17641 CTTTAAAAAT
17651 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
17671 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
17691 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
17712 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* *
17732 TGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
17752 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
17772 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
17792 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
17812 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
17832 CGCGTTGCGATT
1 CGCGTTGCGATT
17844 CTGTAAAATC
Statistics
Matches: 150, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
20 132 0.88
21 18 0.12
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:17861 original size:21 final size:20
Alignment explanation
Indices: 17837--17886 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
17827 ATATTCGCGT
17837 TGCGATTCTGTAAAATCGCAA
1 TGCGATT-TGTAAAATCGCAA
** *
17858 TGCGAATTTGTACTATCGCAT
1 TGCG-ATTTGTAAAATCGCAA
17879 TGCGATTT
1 TGCGATTT
17887 TCAAGAATCG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 4 0.16
21 18 0.72
22 3 0.12
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (20 bp):
TGCGATTTGTAAAATCGCAA
Found at i:18234 original size:29 final size:29
Alignment explanation
Indices: 18202--18274 Score: 71
Period size: 29 Copynumber: 2.5 Consensus size: 29
18192 AAGAAAATAT
* *
18202 TAAAAATAATTAAAAGTGTTTTAA-AATTC
1 TAAAAATAATTAAAA-TATTTTAATAATTA
*
18231 T-AAAATATTCTAAAATATTTTAATAATTA
1 TAAAAATAAT-TAAAATATTTTAATAATTA
18260 TAAAAA-ATATTAAAA
1 TAAAAATA-ATTAAAA
18275 AATCTACAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
28 14 0.39
29 17 0.47
30 5 0.14
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (29 bp):
TAAAAATAATTAAAATATTTTAATAATTA
Found at i:19194 original size:23 final size:24
Alignment explanation
Indices: 19148--19200 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
19138 TATGTGAGAC
*
19148 CAGATACTAGTAGAGTGTCGCATT
1 CAGATACTAGTAGAGTGTCACATT
*
19172 CAGATACTAGTCG-GTGTCACATT
1 CAGATACTAGTAGAGTGTCACATT
19195 CAGATA
1 CAGATA
19201 ATACATAGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 15 0.56
24 12 0.44
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (24 bp):
CAGATACTAGTAGAGTGTCACATT
Found at i:20188 original size:20 final size:20
Alignment explanation
Indices: 20163--20214 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
20153 ATTGTGTAGT
20163 AGTATCGATACTATTACATC
1 AGTATCGATACTATTACATC
20183 AGTATCGATACTATTACATC
1 AGTATCGATACTATTACATC
20203 AGTATCGATACT
1 AGTATCGATACT
20215 TACTTAACCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.35
Consensus pattern (20 bp):
AGTATCGATACTATTACATC
Found at i:21651 original size:5 final size:5
Alignment explanation
Indices: 21641--21673 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
21631 GAAACAATCT
21641 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATA
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATA
21674 TGCATGAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.61, C:0.18, G:0.00, T:0.21
Consensus pattern (5 bp):
ATAAC
Found at i:23427 original size:16 final size:17
Alignment explanation
Indices: 23395--23427 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
23385 AATTTGAATA
*
23395 AATATTTTTATATTAAT
1 AATATTTATATATTAAT
23412 AATATTTATA-ATTAAT
1 AATATTTATATATTAAT
23428 TATGACAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
AATATTTATATATTAAT
Found at i:23901 original size:21 final size:21
Alignment explanation
Indices: 23844--23909 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
23834 TGTTTTTAAC
23844 AAAAAATTA--AAA-ATTCTTT
1 AAAAAATTAGTAAATATT-TTT
23863 AAGAAAATTAGTAAATATTTTT
1 AA-AAAATTAGTAAATATTTTT
*
23885 AAAAAATTTG-AATATATTTTT
1 AAAAAATTAGTAA-ATATTTTT
23906 AAAA
1 AAAA
23910 TTTAAAATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
19 2 0.05
20 9 0.22
21 19 0.46
22 8 0.20
23 3 0.07
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (21 bp):
AAAAAATTAGTAAATATTTTT
Found at i:24908 original size:18 final size:18
Alignment explanation
Indices: 24881--24921 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
24871 ACATTCTCAT
* *
24881 TAATCTTATTTCCACCGG
1 TAATCCTATTCCCACCGG
*
24899 TAATCCTATTCCCACTGG
1 TAATCCTATTCCCACCGG
24917 TAATC
1 TAATC
24922 TTACATTCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.29, G:0.10, T:0.37
Consensus pattern (18 bp):
TAATCCTATTCCCACCGG
Found at i:31358 original size:23 final size:24
Alignment explanation
Indices: 31332--31380 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
31322 CATTCTAGTC
*
31332 ATATAC-TTTGTTATTTA-TTTCGA
1 ATATACATTTGAT-TTTATTTTCGA
*
31355 ATATGCATTTGATTTTATTTTCGA
1 ATATACATTTGATTTTATTTTCGA
31379 AT
1 AT
31381 TTAGTCACTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (24 bp):
ATATACATTTGATTTTATTTTCGA
Found at i:37409 original size:21 final size:20
Alignment explanation
Indices: 37371--37409 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
37361 GATCATGACA
*
37371 TTTCAATATACATGTATATT
1 TTTCAATATACATATATATT
*
37391 TTTCACTATAACATATATA
1 TTTCAATAT-ACATATATA
37410 ACTATATCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.38, C:0.13, G:0.03, T:0.46
Consensus pattern (20 bp):
TTTCAATATACATATATATT
Found at i:38206 original size:20 final size:20
Alignment explanation
Indices: 38183--38242 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
38173 TCCCTAACTG
*
38183 AGGTATAGATACCCTGTTTA
1 AGGTATAGATACCCTGTATA
* *
38203 AGGTATAGATACCCTATATG
1 AGGTATAGATACCCTGTATA
*
38223 GGGTATAGATACCCTG-ATA
1 AGGTATAGATACCCTGTATA
38242 A
1 A
38243 CATTATGGAA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (20 bp):
AGGTATAGATACCCTGTATA
Found at i:42103 original size:17 final size:17
Alignment explanation
Indices: 42083--42121 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
42073 GTCTACAGTC
42083 GATATTAGCGTAATAAT
1 GATATTAGCGTAATAAT
42100 GATATTAGCGTAATAAT
1 GATATTAGCGTAATAAT
42117 GATAT
1 GATAT
42122 AACCAATCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.41, C:0.05, G:0.18, T:0.36
Consensus pattern (17 bp):
GATATTAGCGTAATAAT
Found at i:44400 original size:22 final size:21
Alignment explanation
Indices: 44379--44478 Score: 81
Period size: 18 Copynumber: 5.0 Consensus size: 21
44369 CACTGAATAT
*
44379 TTGTCCCGAAGGACGACTATA
1 TTGTCCCGAAGGACCACTATA
*
44400 ---TCCCGAAGGATCACTGAT-
1 TTGTCCCGAAGGACCACT-ATA
*
44418 TTGTCCCGAAGTACCAC--TA
1 TTGTCCCGAAGGACCACTATA
44437 -TGTCCCGAAGGACCACTGGATA
1 TTGTCCCGAAGGACCACT--ATA
*
44459 -TGTCCCGAAGGACTACTATA
1 TTGTCCCGAAGGACCACTATA
44479 ACCCTCGACT
Statistics
Matches: 64, Mismatches: 6, Indels: 19
0.72 0.07 0.21
Matches are distributed among these distances:
18 29 0.45
19 2 0.03
20 3 0.05
21 12 0.19
22 18 0.28
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (21 bp):
TTGTCCCGAAGGACCACTATA
Found at i:44426 original size:39 final size:40
Alignment explanation
Indices: 44377--44478 Score: 143
Period size: 39 Copynumber: 2.6 Consensus size: 40
44367 GGCACTGAAT
* *
44377 ATTTGTCCCGAAGGACGACTATATCCCGAAGGATCACT-G
1 ATTTGTCCCGAAGGACCACTATATCCCGAAGGACCACTGG
* *
44416 ATTTGTCCCGAAGTACCACTATGTCCCGAAGGACCACTGG
1 ATTTGTCCCGAAGGACCACTATATCCCGAAGGACCACTGG
* *
44456 ATATGTCCCGAAGGACTACTATA
1 ATTTGTCCCGAAGGACCACTATA
44479 ACCCTCGACT
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
39 34 0.63
40 20 0.37
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (40 bp):
ATTTGTCCCGAAGGACCACTATATCCCGAAGGACCACTGG
Found at i:45133 original size:45 final size:46
Alignment explanation
Indices: 45064--45168 Score: 115
Period size: 45 Copynumber: 2.3 Consensus size: 46
45054 TACCCTATCT
* **
45064 GGGGTATAGATACCATGATAACATTATGGAAATTTTCA-TCTTCAG
1 GGGGTATCGATACCATGATAACATTATGGAAATTTTCATTCAACAG
* * * * *
45109 GGGGTATCGATACCAT-ACTGACATTCTGTAATTTTTCATTCAAGAG
1 GGGGTATCGATACCATGA-TAACATTATGGAAATTTTCATTCAACAG
45155 GGGGTATCGATACC
1 GGGGTATCGATACC
45169 CCTTCATAGG
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
44 1 0.02
45 31 0.62
46 18 0.36
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (46 bp):
GGGGTATCGATACCATGATAACATTATGGAAATTTTCATTCAACAG
Found at i:46273 original size:32 final size:32
Alignment explanation
Indices: 46224--46377 Score: 175
Period size: 32 Copynumber: 4.8 Consensus size: 32
46214 TTGAAGTTCA
* *
46224 TGTGAATTATCTGAATGCAACACTAACTCTAT
1 TGTGCATTATCTGAATGCAACACTGACTCTAT
* * * *
46256 TGTGCATAATCTAAATGCAACACCGACTCTGT
1 TGTGCATTATCTGAATGCAACACTGACTCTAT
* *
46288 TGTACATTATCTGAATGCAACACTGACTCTGT
1 TGTGCATTATCTGAATGCAACACTGACTCTAT
* * *
46320 TATGCATTATCTGAATGCAATATTGACTCTGA-
1 TGTGCATTATCTGAATGCAACACTGACTCT-AT
* *
46352 TGTGCATTATCTAAATGAAACACTGA
1 TGTGCATTATCTGAATGCAACACTGA
46378 TACTACTATG
Statistics
Matches: 101, Mismatches: 20, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
32 101 1.00
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.33
Consensus pattern (32 bp):
TGTGCATTATCTGAATGCAACACTGACTCTAT
Found at i:46389 original size:64 final size:64
Alignment explanation
Indices: 46194--46377 Score: 217
Period size: 64 Copynumber: 2.9 Consensus size: 64
46184 GTATCTGATG
* * * * *
46194 TGCATTATCTAAATGCAATATTGAAGT-TCATGTGAATTATCTGAATGCAACACTAACTCTATTG
1 TGCATTATCTAAATGCAATATTG-ACTCTGATGTGCATTATCTGAATGCAACACTGACTCTATTA
* * ** * * *
46258 TGCATAATCTAAATGCAACACCGACTCTGTTGTACATTATCTGAATGCAACACTGACTCTGTTA
1 TGCATTATCTAAATGCAATATTGACTCTGATGTGCATTATCTGAATGCAACACTGACTCTATTA
* * *
46322 TGCATTATCTGAATGCAATATTGACTCTGATGTGCATTATCTAAATGAAACACTGA
1 TGCATTATCTAAATGCAATATTGACTCTGATGTGCATTATCTGAATGCAACACTGA
46378 TACTACTATG
Statistics
Matches: 98, Mismatches: 21, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
63 2 0.02
64 96 0.98
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (64 bp):
TGCATTATCTAAATGCAATATTGACTCTGATGTGCATTATCTGAATGCAACACTGACTCTATTA
Found at i:48915 original size:17 final size:17
Alignment explanation
Indices: 48893--48926 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
48883 AATATAATTT
48893 TTATTAA-TTAATATAAA
1 TTATTAACTTAA-ATAAA
48910 TTATTAACTTAAATAAA
1 TTATTAACTTAAATAAA
48927 AAATTATATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TTATTAACTTAAATAAA
Found at i:51037 original size:26 final size:27
Alignment explanation
Indices: 50989--51049 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 27
50979 ACCCTGTATC
* *
50989 TGTAAAATGACCAAAATACCCCTAAAG
1 TGTAAAATAACAAAAATACCCCTAAAG
*
51016 TGTAAAATAACAAAAAT-GCCCTAAAG
1 TGTAAAATAACAAAAATACCCCTAAAG
51042 TGTAAAAT
1 TGTAAAAT
51050 GGCCTACAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
26 16 0.52
27 15 0.48
ACGTcount: A:0.51, C:0.16, G:0.11, T:0.21
Consensus pattern (27 bp):
TGTAAAATAACAAAAATACCCCTAAAG
Found at i:52501 original size:43 final size:43
Alignment explanation
Indices: 52405--52690 Score: 297
Period size: 43 Copynumber: 6.7 Consensus size: 43
52395 GAGGAAGTTT
* * * * * *
52405 CAGGCTCCTCTGCTATGTGCAAGGGTAAGTCCTTACCGTTACCG
1 CAGGTTCCTTTGCTGTGTGCAAGGGTAAG-CCTTACAGTTTCCC
* * * *
52449 CATGCTCCTTTACTGTATGCAAGGGTAAGCCTTACAGTTTCCC
1 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
** * *
52492 CAGGTTCCTTTAATGTTTGCAAGGGTAAGCCTTATAGTTTCCC
1 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
* * *
52535 CTAGGTTCTTTTGCTGTGGGGAAGGGTAAGCCTT--AGTTTCCC
1 C-AGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
* *
52577 CAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTAGAGTTTCCC
1 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
* * *
52620 CAGGATCCTTTGTTATGTGCAAGGGTAAGCCTTACAGTTTCCC
1 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
* * * * *
52663 CAGGCTCTTTTGTTATGTGAAAGGGTAA
1 CAGGTTCCTTTGCTGTGTGCAAGGGTAA
52691 TACCTTACCA
Statistics
Matches: 210, Mismatches: 29, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
41 28 0.13
42 9 0.04
43 123 0.59
44 50 0.24
ACGTcount: A:0.19, C:0.22, G:0.25, T:0.34
Consensus pattern (43 bp):
CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
Found at i:52600 original size:85 final size:85
Alignment explanation
Indices: 52467--52690 Score: 288
Period size: 85 Copynumber: 2.6 Consensus size: 85
52457 TTTACTGTAT
** * *
52467 GCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTAATGTTTGCAAGGGTAAGCCTTATAGTTT
1 GCAAGGGTAAGCCTTA-AGTTTCCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTAGAGTTT
* * *
52532 CCCCTAGGTTCTTTTGCTGTGG
65 CCCC-AGGATCCTTTGCTATGG
*
52554 GGAAGGGTAAGCCTT-AGTTTCCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTAGAGTTTC
1 GCAAGGGTAAGCCTTAAGTTTCCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTAGAGTTTC
* *
52618 CCCAGGATCCTTTGTTATGT
66 CCCAGGATCCTTTGCTATGG
* * * *
52638 GCAAGGGTAAGCCTTACAGTTTCCCCAGGCTCTTTTGTTATGTGAAAGGGTAA
1 GCAAGGGTAAGCCTTA-AGTTTCCCCAGGTTCCTTTGTTGTGTGCAAGGGTAA
52691 TACCTTACCA
Statistics
Matches: 120, Mismatches: 15, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
84 26 0.22
85 48 0.40
86 32 0.27
87 14 0.12
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.34
Consensus pattern (85 bp):
GCAAGGGTAAGCCTTAAGTTTCCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTAGAGTTTC
CCCAGGATCCTTTGCTATGG
Found at i:52697 original size:128 final size:128
Alignment explanation
Indices: 52466--52697 Score: 331
Period size: 128 Copynumber: 1.8 Consensus size: 128
52456 CTTTACTGTA
* * * *
52466 TGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTAATGTTTGCAAGGGTAAGCCTTATAGTT
1 TGCAAGGGTAAGCCTTACAGTTTCCCCAGGATCCTTTAATATGTGCAAGGGTAAGCCTTACAGTT
* * * *
52531 TCCCCTAGGTTCTTTTGCTGTGGGGAAGGGTAAGCCTTAGTTTCCCCAGGTTCCTTTGTTGTG
66 TCCCCTAGGCTCTTTTGCTATGGGAAAGGGTAAACCTTAGTTTCCCCAGGTTCCTTTGTTGTG
* **
52594 TGCAAGGGTAAGCCTTAGAGTTTCCCCAGGATCCTTTGTTATGTGCAAGGGTAAGCCTTACAGTT
1 TGCAAGGGTAAGCCTTACAGTTTCCCCAGGATCCTTTAATATGTGCAAGGGTAAGCCTTACAGTT
* *
52659 TCCCC-AGGCTCTTTTGTTATGTGAAAGGGTAATACCTTA
66 TCCCCTAGGCTCTTTTGCTATGGGAAAGGGTAA-ACCTTA
52698 CCATTTTTGC
Statistics
Matches: 90, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
127 22 0.24
128 68 0.76
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.34
Consensus pattern (128 bp):
TGCAAGGGTAAGCCTTACAGTTTCCCCAGGATCCTTTAATATGTGCAAGGGTAAGCCTTACAGTT
TCCCCTAGGCTCTTTTGCTATGGGAAAGGGTAAACCTTAGTTTCCCCAGGTTCCTTTGTTGTG
Found at i:56743 original size:74 final size:73
Alignment explanation
Indices: 56621--56848 Score: 244
Period size: 74 Copynumber: 3.1 Consensus size: 73
56611 CTTAACTGGT
* * * * *
56621 TAAAATAAAATAAG-TACTACCTATTATGTTAAACTACCTACCAGTTTGTTTGAAGGTTACTAAT
1 TAAAATAAAAT-AGCCACTA-CTATTA-CTTAAAATACCTACCGGTTTGTTTAAAGGTTACTAAT
*
56685 AAAGTAAACGG
63 AATGTAAACGG
* *
56696 TAAAATAAAATAGCCACTA-TATTACGTTTAAAATACCTATCGGTTTGTTTAAATGTTACTAATA
1 TAAAATAAAATAGCCACTACTATTAC--TTAAAATACCTACCGGTTTGTTTAAAGGTTACTAATA
56760 ATGTAAACGG
64 ATGTAAACGG
*** * * * *
56770 TAAAATAAAATAGGTGCTACCTATTACCTAAATTAGCTACCGGTTTGTTTAAAGGTTAATAATAA
1 TAAAATAAAATAGCCACTA-CTATTACTTAAAATACCTACCGGTTTGTTTAAAGGTTACTAATAA
*
56835 TGTAAATGG
65 TGTAAACGG
56844 TAAAA
1 TAAAA
56849 ATATACAACT
Statistics
Matches: 130, Mismatches: 18, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
73 5 0.04
74 104 0.80
75 15 0.12
76 6 0.05
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (73 bp):
TAAAATAAAATAGCCACTACTATTACTTAAAATACCTACCGGTTTGTTTAAAGGTTACTAATAAT
GTAAACGG
Found at i:57608 original size:106 final size:107
Alignment explanation
Indices: 57498--57721 Score: 287
Period size: 106 Copynumber: 2.1 Consensus size: 107
57488 GATTTGAGGG
*
57498 CCCATCAGCTTAAAATTTGGTAACATTTTAGG-AGCTACCTAAATATGTTGAT-ATATTAATAAG
1 CCCATCAGCTTAAAATTTGGTAACATTTTAGGCA-CTAACT--ATATGTTGATAATATTAATAA-
* *
57561 AAA-A-TAAATAATTAACCTATTTTGTATCCTCAGATTTCTAA-GT
62 AAATATTAAATAATTAACCAATTTTGTATCCTCAGATTTCTAAGGC
* * * * *
57604 CCCATCAACTTAAACTTTGGTAATATTTTAGGCACTAACTATATGTTTATAATATTGATAAAAAT
1 CCCATCAGCTTAAAATTTGGTAACATTTTAGGCACTAACTATATGTTGATAATATTAATAAAAAT
* *
57669 ATTAAGTAATTAACCAATTTTGTATCGTCAGATTTCTAAGGC
66 ATTAAATAATTAACCAATTTTGTATCCTCAGATTTCTAAGGC
57711 CCCATCAGCTT
1 CCCATCAGCTT
57722 TAACAGACGC
Statistics
Matches: 102, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
104 12 0.12
105 10 0.10
106 68 0.67
107 12 0.12
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (107 bp):
CCCATCAGCTTAAAATTTGGTAACATTTTAGGCACTAACTATATGTTGATAATATTAATAAAAAT
ATTAAATAATTAACCAATTTTGTATCCTCAGATTTCTAAGGC
Found at i:59778 original size:29 final size:29
Alignment explanation
Indices: 59746--59810 Score: 116
Period size: 28 Copynumber: 2.3 Consensus size: 29
59736 GAGACCAGGT
59746 CAATGCTTGAGTTTGTACGGGAACTGTAC
1 CAATGCTTGAGTTTGTACGGGAACTGTAC
59775 CAATGC-TGAGTTTGTACGGGAACTGTAC
1 CAATGCTTGAGTTTGTACGGGAACTGTAC
59803 C-ATGCTTG
1 CAATGCTTG
59811 TGACACTGGG
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
27 4 0.11
28 25 0.71
29 6 0.17
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (29 bp):
CAATGCTTGAGTTTGTACGGGAACTGTAC
Found at i:60001 original size:31 final size:30
Alignment explanation
Indices: 59952--60013 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 30
59942 TATGAGACCA
59952 AATAGTCAGATTTACATTCAAATAATGCAC
1 AATAGTCAGATTTACATTCAAATAATGCAC
* * *
59982 AATATGTCAGGTTTGCATTCAGATAATGCAC
1 AATA-GTCAGATTTACATTCAAATAATGCAC
60013 A
1 A
60014 TAAGTCAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 4 0.14
31 24 0.86
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.31
Consensus pattern (30 bp):
AATAGTCAGATTTACATTCAAATAATGCAC
Done.