Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000169.1 Hibiscus syriacus cultivar Beakdansim tig00000298_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: 63675
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:5500 original size:17 final size:17
Alignment explanation
Indices: 5478--5512 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
5468 TGTATCTATT
*
5478 TTGACATCTCGTTGTCA
1 TTGACATATCGTTGTCA
5495 TTGACATATCGTTGTCA
1 TTGACATATCGTTGTCA
5512 T
1 T
5513 CAATGAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.20, C:0.20, G:0.17, T:0.43
Consensus pattern (17 bp):
TTGACATATCGTTGTCA
Found at i:6841 original size:17 final size:17
Alignment explanation
Indices: 6806--6842 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
6796 GATAGCATGA
*
6806 CCGGTTCGCTAATCAGT
1 CCGGTTCGCTAACCAGT
*
6823 CCGGTTCGCTAACCGGT
1 CCGGTTCGCTAACCAGT
6840 CCG
1 CCG
6843 ATTCTGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.14, C:0.35, G:0.27, T:0.24
Consensus pattern (17 bp):
CCGGTTCGCTAACCAGT
Found at i:10101 original size:20 final size:20
Alignment explanation
Indices: 10060--10103 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
10050 TTTAAAATTA
**
10060 TTATATATTTTATATTTTAT
1 TTATATATTTTATATTAAAT
10080 TTATATATTTT-TATTGAAAT
1 TTATATATTTTATATT-AAAT
10100 TTAT
1 TTAT
10104 TTTTATTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (20 bp):
TTATATATTTTATATTAAAT
Found at i:10174 original size:30 final size:26
Alignment explanation
Indices: 10117--10176 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
10107 TATTCTTTAG
* *
10117 AATTTTATAAGTTCGCCTCTTCTTAA
1 AATTTTATAACTTCGCCTCTTCATAA
10143 AATTTTATAACTTCGTCCTCGTTAACATAA
1 AATTTTATAACTTCG-CCTC-TT--CATAA
10173 AATT
1 AATT
10177 CTGCATCCGC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 14 0.50
27 4 0.14
28 2 0.07
30 8 0.29
ACGTcount: A:0.32, C:0.18, G:0.07, T:0.43
Consensus pattern (26 bp):
AATTTTATAACTTCGCCTCTTCATAA
Found at i:10390 original size:15 final size:15
Alignment explanation
Indices: 10370--10405 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
10360 TTGTAGCAGT
10370 TCAATGTTATGA-GTA
1 TCAATGTTAT-ATGTA
10385 TCAATGTTATATGTA
1 TCAATGTTATATGTA
10400 TCAATG
1 TCAATG
10406 GTGAACAGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 1 0.05
15 19 0.95
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.42
Consensus pattern (15 bp):
TCAATGTTATATGTA
Found at i:13336 original size:6 final size:6
Alignment explanation
Indices: 13325--13357 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
13315 AGGCATAAAT
13325 GGGAGA GGGAGA GGGAGA GGGAGA GGGAGA GGG
1 GGGAGA GGGAGA GGGAGA GGGAGA GGGAGA GGG
13358 GGAGAGAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.30, C:0.00, G:0.70, T:0.00
Consensus pattern (6 bp):
GGGAGA
Found at i:13536 original size:16 final size:18
Alignment explanation
Indices: 13505--13539 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
13495 TGATGTCTTG
13505 ATTATTTATATATTTTAA
1 ATTATTTATATATTTTAA
13523 ATTATTT-T-TATTTTAA
1 ATTATTTATATATTTTAA
13539 A
1 A
13540 AAAATTAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 1 0.06
18 7 0.41
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTATTTATATATTTTAA
Found at i:14575 original size:17 final size:17
Alignment explanation
Indices: 14553--14589 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
14543 TCGATTCAAG
*
14553 CTCGATTCAAGCTTGAA
1 CTCGATTCAAGCTCGAA
*
14570 CTCGATTTAAGCTCGAA
1 CTCGATTCAAGCTCGAA
14587 CTC
1 CTC
14590 AAACTCGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (17 bp):
CTCGATTCAAGCTCGAA
Found at i:14879 original size:2 final size:2
Alignment explanation
Indices: 14872--14896 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
14862 AAAATAACGG
14872 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
14897 AAAGATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18917 original size:101 final size:101
Alignment explanation
Indices: 18735--18917 Score: 242
Period size: 101 Copynumber: 1.8 Consensus size: 101
18725 ATGTTTCTGA
* * * *
18735 TATATGACACCAATATGGATCACTCGTGGTCTGACTCGGCGTACCTTAATGGTGCACGAGGTGGA
1 TATATGACACCAAAATGGATCACTCGTAGTCTGAATCGGCGTACCTTAATGGTACACGAGGTGGA
*
18800 GTGATTCGATGCATCTGGTTAGCTTTATATGTGCAT
66 GTGACTCGATGCATCTGGTTAGCTTTATATGTGCAT
* * * * *
18836 TATATGGCACCAAAATGGGTCACTCGTAGTCTGAATTGG-GTGCCTTAGTGGTACACGAGGTGGA
1 TATATGACACCAAAATGGATCACTCGTAGTCTGAATCGGCGTACCTTAATGGTACACGAGGTGGA
* *
18900 GTTACTCGGTGCAATCTG
66 GTGACTCGATGC-ATCTG
18918 TTCTGACAAT
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
100 31 0.45
101 38 0.55
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (101 bp):
TATATGACACCAAAATGGATCACTCGTAGTCTGAATCGGCGTACCTTAATGGTACACGAGGTGGA
GTGACTCGATGCATCTGGTTAGCTTTATATGTGCAT
Found at i:25284 original size:19 final size:19
Alignment explanation
Indices: 25260--25302 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
25250 AGCTTGGGAG
25260 CATAGTCTATAATGGCGAT
1 CATAGTCTATAATGGCGAT
*
25279 CATAGTCTCTAATGGCGAT
1 CATAGTCTATAATGGCGAT
25298 CATAG
1 CATAG
25303 CCTTTTTAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (19 bp):
CATAGTCTATAATGGCGAT
Found at i:28491 original size:20 final size:21
Alignment explanation
Indices: 28466--28517 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
28456 TTTTCCCAAT
*
28466 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
28486 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
28507 TCGCAATGCGA
1 TCGCAATGCGA
28518 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:28530 original size:41 final size:41
Alignment explanation
Indices: 28503--28634 Score: 124
Period size: 41 Copynumber: 3.2 Consensus size: 41
28493 GCGAATTGGG
* * *
28503 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAC
* * *
28544 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATACTGAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAAT-AC
** * * * *
28586 --TTTTGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAC
*
28625 ATAATCGCAA
1 AAAATCGCAA
28635 TTCGATTTTC
Statistics
Matches: 72, Mismatches: 16, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
39 2 0.03
40 30 0.42
41 38 0.53
42 2 0.03
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAC
Found at i:28531 original size:20 final size:20
Alignment explanation
Indices: 28506--28620 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
28496 AATTGGGAAA
*
28506 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
28526 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
28547 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
28567 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
28587 TTTGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
28607 TTCGCAACGCGATA
1 ATCGCAACGCGATA
28621 ATACATAATC
Statistics
Matches: 79, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.03
20 62 0.78
21 13 0.16
22 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:29168 original size:20 final size:20
Alignment explanation
Indices: 29114--29172 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
29104 GCGATTCTCT
**
29114 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
29134 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
29154 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
29173 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:30513 original size:18 final size:18
Alignment explanation
Indices: 30492--30536 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
30482 TCCACTTCGG
*
30492 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
30510 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
30528 GAGCCATCA
1 GAGCCATCA
30537 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:31049 original size:20 final size:20
Alignment explanation
Indices: 31021--31084 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
31011 TTTACTTTCA
*
31021 CAACACGAAAATGACTATCG
1 CAACGCGAAAATGACTATCG
*
31041 CAACGCGAAAATGGCTATCG
1 CAACGCGAAAATGACTATCG
* **
31061 CAATGCG-AAATGAAAATCG
1 CAACGCGAAAATGACTATCG
31080 CAACG
1 CAACG
31085 ACAAAATCGC
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 13 0.35
20 24 0.65
ACGTcount: A:0.42, C:0.23, G:0.20, T:0.14
Consensus pattern (20 bp):
CAACGCGAAAATGACTATCG
Found at i:31092 original size:14 final size:14
Alignment explanation
Indices: 31073--31130 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
31063 ATGCGAAATG
31073 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
31087 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
31103 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
31119 AAAATCGCAACG
1 AAAATCGCAACG
31131 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:31115 original size:32 final size:33
Alignment explanation
Indices: 31057--31147 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
31047 GAAAATGGCT
31057 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
31090 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
31122 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
31148 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:31185 original size:14 final size:14
Alignment explanation
Indices: 31166--31213 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 14
31156 GTGTTTCGCA
31166 TTGCGATTTTGTCG
1 TTGCGATTTTGTCG
*
31180 TTGCGATTTCATTTCGCG
1 TTGCGATTT--TGT--CG
31198 TTGCGATTTTGTCG
1 TTGCGATTTTGTCG
31212 TT
1 TT
31214 ACAATTTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 13 0.46
16 4 0.14
18 11 0.39
ACGTcount: A:0.08, C:0.17, G:0.25, T:0.50
Consensus pattern (14 bp):
TTGCGATTTTGTCG
Found at i:31202 original size:32 final size:33
Alignment explanation
Indices: 31159--31237 Score: 124
Period size: 32 Copynumber: 2.4 Consensus size: 33
31149 GCGATTTGTG
* *
31159 TTTCGCATTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTACAATTTTCA
*
31191 TTTCGCGTTGCGATTTTGTCGTTACAATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTACAATTTTCA
31224 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
31238 AGACATTTCC
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 24 0.57
33 18 0.43
ACGTcount: A:0.14, C:0.19, G:0.20, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTACAATTTTCA
Found at i:31256 original size:20 final size:19
Alignment explanation
Indices: 31222--31277 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
31212 TTACAATTTT
*
31222 CATTTCGCATTGCGATAGA
1 CATTTCGCGTTGCGATAGA
*
31241 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGA
31261 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
31278 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGA
Found at i:33169 original size:14 final size:14
Alignment explanation
Indices: 33150--33185 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
33140 ATTGTTTAAT
33150 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
33164 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
33178 TGATTTGT
1 TGATTTGT
33186 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:33324 original size:19 final size:19
Alignment explanation
Indices: 33302--33369 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
33292 ATCGCAACGA
33302 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
33321 GAAAATCGTAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
33340 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
33354 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
33370 TTTTCATTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
14 11 0.25
15 1 0.02
16 2 0.05
17 2 0.05
19 28 0.64
ACGTcount: A:0.47, C:0.16, G:0.22, T:0.15
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:33413 original size:20 final size:20
Alignment explanation
Indices: 33388--33445 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
33378 TCGCATTGCG
*
33388 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
33408 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
33428 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
33446 TCAAATGAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:34529 original size:24 final size:24
Alignment explanation
Indices: 34502--34555 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
34492 GTATTCGAAA
* *
34502 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
34526 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
34550 TTTGAT
1 TTTGAT
34556 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:34747 original size:12 final size:12
Alignment explanation
Indices: 34730--34754 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34720 ATATAATCCT
34730 GAAGAAGAAAAA
1 GAAGAAGAAAAA
34742 GAAGAAGAAAAA
1 GAAGAAGAAAAA
34754 G
1 G
34755 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:37061 original size:19 final size:19
Alignment explanation
Indices: 37039--37169 Score: 76
Period size: 19 Copynumber: 7.7 Consensus size: 19
37029 GGAAATTACT
37039 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
37058 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
37072 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATGAAA
* *
37091 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
* *
37105 TTCGCAATGCAAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
37124 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
37138 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
37157 ATCGCAACGCGAA
1 ATCGCAATGCGAA
37170 TTTAATTTCG
Statistics
Matches: 81, Mismatches: 16, Indels: 30
0.64 0.13 0.24
Matches are distributed among these distances:
14 27 0.33
15 3 0.04
16 5 0.06
17 5 0.06
18 3 0.04
19 38 0.47
ACGTcount: A:0.44, C:0.20, G:0.21, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:37081 original size:33 final size:33
Alignment explanation
Indices: 37039--37165 Score: 184
Period size: 33 Copynumber: 3.8 Consensus size: 33
37029 GGAAATTACT
37039 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* **
37072 ATCGCAATGCGAAATAAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
37104 TTTCGCAATGCAAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
37138 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
37166 CGAATTTAAT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
32 1 0.01
33 79 0.98
34 1 0.01
ACGTcount: A:0.44, C:0.20, G:0.21, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:37146 original size:66 final size:66
Alignment explanation
Indices: 37040--37172 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
37030 GAAATTACTA
* *
37040 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATAAAAATCGCAACGCTAAT
1 TCGCAATGCAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATAAAAATCGCAACGCGAAT
37105 T
66 T
* *
37106 TCGCAATGCAAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATAAAAATCGCAACGCGAAT
37171 T
66 T
37172 T
1 T
37173 AATTTCGCGT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.17
Consensus pattern (66 bp):
TCGCAATGCAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATAAAAATCGCAACGCGAAT
T
Found at i:37197 original size:14 final size:14
Alignment explanation
Indices: 37180--37236 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
37170 TTTAATTTCG
37180 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
37194 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
37213 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
37227 CGTTGCGATT
1 CGTTGCGATT
37237 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:37216 original size:33 final size:33
Alignment explanation
Indices: 37165--37254 Score: 153
Period size: 33 Copynumber: 2.7 Consensus size: 33
37155 AAATCGCAAC
* *
37165 GCGAATTTAATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
37198 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
*
37231 GCGATTTTCATTTCGCATTGCGAT
1 GCGATTTTCATTTCGCGTTGCGAT
37255 AGTACTTTTG
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.43
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
Found at i:37218 original size:19 final size:19
Alignment explanation
Indices: 37194--37254 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
37184 GCGATTCTCT
37194 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
37213 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
37227 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
37246 CATTGCGAT
1 CGTTGCGAT
37255 AGTACTTTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
14 10 0.29
16 3 0.09
17 3 0.09
19 18 0.53
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:37379 original size:14 final size:14
Alignment explanation
Indices: 37360--37396 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
37350 CATCAATTAA
37360 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
37374 ACAAATCACCTTTT
1 ACAAATCAACTTTT
37388 ACAAATCAA
1 ACAAATCAA
37397 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:38805 original size:42 final size:42
Alignment explanation
Indices: 38746--38949 Score: 139
Period size: 42 Copynumber: 4.9 Consensus size: 42
38736 GTGAATCGGG
* *
38746 CTCTTGAATGGTGGGAG-GGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGAGGA-CTCTTCAAGGATGACAGTGGC
* * * * *
38788 CTCTTAAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGAGGACTCTTCAAGG-ATGACAGTGGC
* * * * * * *
38830 CTC-TCAATGATAGGAGTGGACTCTTGAGGGATGACAGTGGC
1 CTCTTGAACGGTGGGAGAGGACTCTTCAAGGATGACAGTGGC
* * *
38871 CTCTTGAACGGTGGGAGAGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGAGGACTCTTCAAGG-ATGACAGTGGC
* * * * * *
38913 CTCTT-CACGATAGGAGTGGACTCTTGAGGGATGACAG
1 CTCTTGAACGGTGGGAGAGGACTCTTCAAGGATGACAG
38950 GCGAGTCGGG
Statistics
Matches: 122, Mismatches: 34, Indels: 13
0.72 0.20 0.08
Matches are distributed among these distances:
41 54 0.44
42 65 0.53
43 3 0.02
ACGTcount: A:0.24, C:0.18, G:0.36, T:0.22
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGAGGACTCTTCAAGGATGACAGTGGC
Found at i:38853 original size:41 final size:42
Alignment explanation
Indices: 38785--38946 Score: 175
Period size: 41 Copynumber: 3.9 Consensus size: 42
38775 CGATGACAGT
* * * *
38785 GGCCTCTTAAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGTGGACTCTCGAGGAATGATAGG
* * * * *
38827 GGCCTC-TCAATGATAGGAGTGGACTCTTGAGGGATGACAGT
1 GGCCTCTTCAACGATAGGAGTGGACTCTCGAGGAATGATAGG
* * * *
38868 GGCCTCTTGAACGGTGGGAGAGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGTGGACTCTCGAGGAATGATAGG
* *
38910 GGCCTCTTC-ACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGTGGACTCTCGAGGAATGA
38947 CAGGCGAGTC
Statistics
Matches: 95, Mismatches: 24, Indels: 3
0.78 0.20 0.02
Matches are distributed among these distances:
41 55 0.58
42 40 0.42
ACGTcount: A:0.23, C:0.17, G:0.38, T:0.22
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGTGGACTCTCGAGGAATGATAGG
Found at i:38906 original size:83 final size:83
Alignment explanation
Indices: 38776--38949 Score: 305
Period size: 83 Copynumber: 2.1 Consensus size: 83
38766 CCTCTTCAAC
* *
38776 GATGACAGTGGCCTCTTAAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTC-TCAATGA
1 GATGACAGTGGCCTCTTAAACGGTGGGAGAGGACTCTCGAGGAATGATAGGGGCCTCTTC-ACGA
38840 TAGGAGTGGACTCTTGAGG
65 TAGGAGTGGACTCTTGAGG
*
38859 GATGACAGTGGCCTCTTGAACGGTGGGAGAGGACTCTCGAGGAATGATAGGGGCCTCTTCACGAT
1 GATGACAGTGGCCTCTTAAACGGTGGGAGAGGACTCTCGAGGAATGATAGGGGCCTCTTCACGAT
38924 AGGAGTGGACTCTTGAGG
66 AGGAGTGGACTCTTGAGG
38942 GATGACAG
1 GATGACAG
38950 GCGAGTCGGG
Statistics
Matches: 87, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
83 85 0.98
84 2 0.02
ACGTcount: A:0.24, C:0.17, G:0.37, T:0.21
Consensus pattern (83 bp):
GATGACAGTGGCCTCTTAAACGGTGGGAGAGGACTCTCGAGGAATGATAGGGGCCTCTTCACGAT
AGGAGTGGACTCTTGAGG
Found at i:39275 original size:92 final size:91
Alignment explanation
Indices: 39165--39350 Score: 288
Period size: 91 Copynumber: 2.0 Consensus size: 91
39155 TATATTTCAA
*
39165 ACTTCAACCAAAAGAC-AAA-C-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
1 ACTTCAACCAAAAGACAAAACCAAAAGACAAATACTAACTTCACAGTGTT----AATAAACAGTT
39227 TAGCAGAATTGGCAGCAACCGAATAAATTT
62 TAGCAGAATTGGCAGCAACCGAATAAATTT
*
39257 ACTTCAACCAAAAGACAAAACCAAAAGACAAATATTAACTTCACAGTGTTAATAAACAGTTTAGC
1 ACTTCAACCAAAAGACAAAACCAAAAGACAAATACTAACTTCACAGTGTTAATAAACAGTTTAGC
*
39322 AGTATTGGCAGCAACCGAATAAATTT
66 AGAATTGGCAGCAACCGAATAAATTT
39348 ACT
1 ACT
39351 AAGCAATCTA
Statistics
Matches: 88, Mismatches: 3, Indels: 7
0.90 0.03 0.07
Matches are distributed among these distances:
91 42 0.48
92 16 0.18
93 3 0.03
94 1 0.01
95 26 0.30
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.22
Consensus pattern (91 bp):
ACTTCAACCAAAAGACAAAACCAAAAGACAAATACTAACTTCACAGTGTTAATAAACAGTTTAGC
AGAATTGGCAGCAACCGAATAAATTT
Found at i:39280 original size:13 final size:13
Alignment explanation
Indices: 39262--39288 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
39252 AATTTACTTC
39262 AACCAAAAGACAA
1 AACCAAAAGACAA
39275 AACCAAAAGACAA
1 AACCAAAAGACAA
39288 A
1 A
39289 TATTAACTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.22, G:0.07, T:0.00
Consensus pattern (13 bp):
AACCAAAAGACAA
Found at i:41081 original size:40 final size:37
Alignment explanation
Indices: 41037--41142 Score: 112
Period size: 33 Copynumber: 2.9 Consensus size: 37
41027 TCTTTTGGTT
*
41037 GAAATGAAAATCGCAATGAGATAATGAGAATCGCAACGC
1 GAAATGAAAATCGCAA-GCGA-AATGAGAATCGCAACGC
**
41076 GGAAATGACTATCGCAA-CG--A-GAGAATCGCAACGC
1 -GAAATGAAAATCGCAAGCGAAATGAGAATCGCAACGC
*
41110 GAAATGAAAATCGCAACGCGAAATGAAAATCGC
1 GAAATGAAAATCGCAA-GCGAAATGAGAATCGC
41143 GTTGCGATTT
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
33 14 0.25
34 14 0.25
35 3 0.05
37 1 0.02
38 9 0.16
40 14 0.25
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (37 bp):
GAAATGAAAATCGCAAGCGAAATGAGAATCGCAACGC
Found at i:41149 original size:19 final size:19
Alignment explanation
Indices: 41037--41142 Score: 105
Period size: 19 Copynumber: 5.7 Consensus size: 19
41027 TCTTTTGGTT
* *
41037 GAAATGAAAATCGCAATGA
1 GAAATGAAAATCGCAACGC
*
41056 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
41076 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
41094 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
41110 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
41129 GAAATGAAAATCGC
1 GAAATGAAAATCGC
41143 GTTGCGATTT
Statistics
Matches: 72, Mismatches: 8, Indels: 14
0.77 0.09 0.15
Matches are distributed among these distances:
14 9 0.12
15 1 0.01
16 2 0.03
17 1 0.01
18 2 0.03
19 29 0.40
20 26 0.36
21 2 0.03
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:41161 original size:19 final size:19
Alignment explanation
Indices: 41139--41192 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
41129 GAAATGAAAA
41139 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTTATT
**
41158 TCGCGTTGCGATAGTTATT
1 TCGCGTTGCGATTTTTATT
41177 TCCGCGTTGCGATTTT
1 T-CGCGTTGCGATTTT
41193 CATTCTCGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTTATT
Found at i:41728 original size:20 final size:20
Alignment explanation
Indices: 41703--41755 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
41693 GCGCTATGTA
41703 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
41723 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
41743 TATCTCGTTGCGA
1 AATCGCGTTGCGA
41756 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:41789 original size:20 final size:20
Alignment explanation
Indices: 41764--41817 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
41754 GATTTTGTAT
*
41764 TATCGCATTGTGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
41784 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
41804 TATCGCATTGCGAT
1 TATCGCATTGCGAT
41818 TTTCCCAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Done.