Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002054.1 Hibiscus syriacus cultivar Beakdansim tig00004182_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: 55615
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:28124 original size:20 final size:21
Alignment explanation
Indices: 28099--28191 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
28089 TTTTCCCAAT
*
28099 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
28119 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
28140 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
28160 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
28181 TCGCAATGCGA
1 TCGCAATGCGA
28192 TACTTACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:28144 original size:41 final size:41
Alignment explanation
Indices: 28099--28191 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
28089 TTTTCCCAAT
28099 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
28140 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
28181 TCGCAATGCGA
1 TCGCAATGCGA
28192 TACTTACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:28204 original size:41 final size:41
Alignment explanation
Indices: 28118--28252 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
28108 GAATAAGTAA
** *
28118 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTTACT
28159 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
* * ** * *
28200 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTTACT
*
28241 TTCGCAACGCGA
1 ATCGCAACGCGA
28253 TACTGACTTT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
40 5 0.06
41 74 0.91
42 2 0.02
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
Found at i:28205 original size:20 final size:20
Alignment explanation
Indices: 28180--28273 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
28170 AATTGGGAAA
*
28180 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * *
28200 ATCGCAATGCGATA-ATACAAA
1 ATCGCAACGCGATACTTAC--T
*
28221 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTTACT
* *
28241 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
*
28261 TTCGCAACGCGAT
1 ATCGCAACGCGAT
28274 TTACATAGCG
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 44 0.71
21 12 0.19
22 3 0.05
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:28830 original size:19 final size:19
Alignment explanation
Indices: 28792--28858 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
28782 TTCGAGAATG
28792 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
28812 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
28831 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
28850 AAAATCGCA
1 AAAATCGCA
28859 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 30 0.73
20 11 0.27
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:28900 original size:20 final size:19
Alignment explanation
Indices: 28854--28985 Score: 130
Period size: 19 Copynumber: 7.1 Consensus size: 19
28844 GAAACCAAAA
*
28854 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
28873 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
28892 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
28912 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* * **
28928 T--AGTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
28945 TCGCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
28964 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
28984 TC
1 TC
28986 AACCAAAAGA
Statistics
Matches: 93, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
14 10 0.11
16 1 0.01
17 1 0.01
19 46 0.49
20 35 0.38
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:28935 original size:39 final size:39
Alignment explanation
Indices: 28859--28935 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
28849 CAAAATCGCA
* *
28859 TTGCGATTTTCATTTCGCGTTGCGATTTTTATTTCGCGG
1 TTGCGATTTTCATTTCGCGTTGCGATTTCTATGTCGCGG
28898 TTGCGATTTTCATTTCGCGTTGCGATTGTCTA-GTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATT-TCTATGTCGCG
28936 ATAGTCATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 32 0.91
40 3 0.09
ACGTcount: A:0.10, C:0.19, G:0.25, T:0.45
Consensus pattern (39 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTCTATGTCGCGG
Found at i:29901 original size:15 final size:15
Alignment explanation
Indices: 29881--29917 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
29871 CAATTACTAA
29881 TGTTTGTTATTATAT
1 TGTTTGTTATTATAT
29896 TGTTTGTTATTATAT
1 TGTTTGTTATTATAT
29911 TGTTTGT
1 TGTTTGT
29918 AGATTTGGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (15 bp):
TGTTTGTTATTATAT
Found at i:31082 original size:21 final size:21
Alignment explanation
Indices: 31058--31124 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
31048 TCATTCCTCG
31058 AGAGTCCCCTCTCACCGTTCA
1 AGAGTCCCCTCTCACCGTTCA
* * * * *
31079 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCTCACCGTTCA
* *
31100 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCTCACCGTTCA
31121 AGAG
1 AGAG
31125 CCCGATTCAC
Statistics
Matches: 33, Mismatches: 12, Indels: 3
0.69 0.25 0.06
Matches are distributed among these distances:
20 1 0.03
21 31 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.34, G:0.21, T:0.21
Consensus pattern (21 bp):
AGAGTCCCCTCTCACCGTTCA
Found at i:31082 original size:42 final size:42
Alignment explanation
Indices: 31002--31094 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
30992 GCCCGACTCG
* *
31002 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCTACCGTTCAAGAGGCC
* * *
31044 CCTATCATTCCTCGAGAGTCCCCT-CTCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCT-ACCGTTCAAGAGGCC
* *
31086 ACTGTCATC
1 CCTATCATC
31095 GTTGAAGAGG
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
41 2 0.05
42 40 0.95
ACGTcount: A:0.22, C:0.38, G:0.16, T:0.25
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCTACCGTTCAAGAGGCC
Found at i:32490 original size:14 final size:14
Alignment explanation
Indices: 32471--32506 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
32461 ATTGTTTAAT
32471 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
32485 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
32499 TGATTTGT
1 TGATTTGT
32507 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:32708 original size:19 final size:19
Alignment explanation
Indices: 32686--32802 Score: 119
Period size: 19 Copynumber: 6.7 Consensus size: 19
32676 CGAAATTAAA
*
32686 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
* *
32705 TTCGCATTGTGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
32721 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
32738 TTCGCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
32757 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
32773 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
32790 TTCGCATTGCGAT
1 TTCGCATTGCGAT
32803 AGTAATTTCC
Statistics
Matches: 79, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
14 11 0.14
16 13 0.16
17 13 0.16
19 42 0.53
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:32764 original size:52 final size:52
Alignment explanation
Indices: 32686--32802 Score: 207
Period size: 52 Copynumber: 2.2 Consensus size: 52
32676 CGAAATTAAA
* *
32686 TTCGCGTTGCGATTTTCATTTCGCATTGTGATTCCCTCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCAT
*
32738 TTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCAT
32790 TTCGCATTGCGAT
1 TTCGCATTGCGAT
32803 AGTAATTTCC
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 62 1.00
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (52 bp):
TTCGCATTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCAT
Found at i:32811 original size:52 final size:52
Alignment explanation
Indices: 32703--32822 Score: 177
Period size: 52 Copynumber: 2.3 Consensus size: 52
32693 TGCGATTTTC
* ** *
32703 ATTTCGCATTGTGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGATAGTA
*
32755 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATAGTA
1 ATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGATAGTA
*
32807 ATTTCCGCGTTGCGAT
1 ATTT-CGCATTGCGAT
32823 GGACATTAAG
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
52 51 0.84
53 10 0.16
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.43
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGATAGTA
Found at i:35009 original size:12 final size:12
Alignment explanation
Indices: 34992--35016 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34982 TCTTCGGGGA
34992 CTTTTTCTTCTT
1 CTTTTTCTTCTT
35004 CTTTTTCTTCTT
1 CTTTTTCTTCTT
35016 C
1 C
35017 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:35225 original size:24 final size:24
Alignment explanation
Indices: 35191--35244 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
35181 CTGAAACATC
* *
35191 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
35215 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
35239 ATCAAA
1 ATCAAA
35245 TTTCGAATAC
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:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:36303 original size:20 final size:20
Alignment explanation
Indices: 36278--36335 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
36268 ATTCATTTGA
36278 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
36298 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
36318 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
36336 CGCAACGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:36364 original size:19 final size:19
Alignment explanation
Indices: 36342--36403 Score: 106
Period size: 19 Copynumber: 3.3 Consensus size: 19
36332 AAATCGCAAC
36342 GCGATTTTCATTTCGCATT
1 GCGATTTTCATTTCGCATT
36361 GCGATTTTCATTTCGCATT
1 GCGATTTTCATTTCGCATT
* *
36380 GCGATTTCCATTTCGCGTT
1 GCGATTTTCATTTCGCATT
36399 GCGAT
1 GCGAT
36404 AGTCTGTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 41 1.00
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.44
Consensus pattern (19 bp):
GCGATTTTCATTTCGCATT
Found at i:38345 original size:19 final size:19
Alignment explanation
Indices: 38321--38387 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
38311 GAAACTTAAA
38321 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
* *
38340 ATCGCAACGTGGAAATGGCT
1 ATCGCAACG-CGAAATGACT
* **
38360 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
38379 ATCGCAACG
1 ATCGCAACG
38388 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 23 0.59
20 16 0.41
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.16
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:38395 original size:14 final size:14
Alignment explanation
Indices: 38376--38433 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
38366 ATGCGAAATG
38376 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
38390 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
38406 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
38422 AAAATTGCAACG
1 AAAATCGCAACG
38434 CGAAACACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
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:38418 original size:32 final size:33
Alignment explanation
Indices: 38360--38438 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
38350 GGAAATGGCT
*
38360 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
38393 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
38425 ATTGCAACGCGAAA
1 ATCGCAACGCGAAA
38439 CACAAATCGC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 29 0.66
33 15 0.34
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:38467 original size:19 final size:17
Alignment explanation
Indices: 38445--38539 Score: 69
Period size: 19 Copynumber: 5.6 Consensus size: 17
38435 GAAACACAAA
38445 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGA-TTTCATT
*
38464 TCGCGTTGCGA-TT--TG
1 TCGC-TTGCGATTTCATT
38479 TCG-TTGCGATTTCATT
1 TCGCTTGCGATTTCATT
*
38495 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
38511 TCG-TTGCGATTTTCATT
1 TCGCTTGCGA-TTTCATT
38528 TCGCATTGCGAT
1 TCGC-TTGCGAT
38540 AGCCATTTCC
Statistics
Matches: 61, Mismatches: 5, Indels: 21
0.70 0.06 0.24
Matches are distributed among these distances:
13 6 0.10
14 8 0.13
15 7 0.11
16 8 0.13
17 6 0.10
18 10 0.16
19 16 0.26
ACGTcount: A:0.12, C:0.20, G:0.23, T:0.45
Consensus pattern (17 bp):
TCGCTTGCGATTTCATT
Found at i:38483 original size:13 final size:14
Alignment explanation
Indices: 38467--38523 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
38457 TTTCATTTCG
38467 CGTTGCGA-TTTGT
1 CGTTGCGATTTTGT
*
38480 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
38496 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
38512 CGTTGCGATTTT
1 CGTTGCGATTTT
38524 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
13 8 0.22
14 14 0.38
16 4 0.11
18 11 0.30
ACGTcount: A:0.09, C:0.18, G:0.26, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:38511 original size:32 final size:33
Alignment explanation
Indices: 38450--38539 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
38440 ACAAATCGCA
38450 TTGCGATTTTCATTTCGCGTTGCGA-TTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
38482 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
38514 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
38540 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
31 18 0.33
32 19 0.35
33 18 0.33
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:38558 original size:20 final size:19
Alignment explanation
Indices: 38524--38577 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
38514 TTGCGATTTT
*
38524 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
38543 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
38563 CATTTCGTGTTGCGA
1 CATTTCGCGTTGCGA
38578 AAGTAAATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:38576 original size:19 final size:19
Alignment explanation
Indices: 38512--38577 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
38502 GCGATTTTGT
**
38512 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
38531 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
38551 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
38570 TGTTGCGA
1 CGTTGCGA
38578 AAGTAAATAT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
19 22 0.56
20 17 0.44
ACGTcount: A:0.15, C:0.23, G:0.24, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:39073 original size:18 final size:18
Alignment explanation
Indices: 39047--39091 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
39037 GTCGATCAGA
* * *
39047 TGATGGCTCTGGGTGGGG
1 TGATAGCTCTGGGCGAGG
39065 TGATAGCTCTGGGCGAGG
1 TGATAGCTCTGGGCGAGG
39083 TGATAGCTC
1 TGATAGCTC
39092 CCGAAGTGGA
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:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATAGCTCTGGGCGAGG
Found at i:40643 original size:22 final size:22
Alignment explanation
Indices: 40618--40661 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
40608 GATTTAGATA
40618 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
40640 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
40662 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:40942 original size:20 final size:20
Alignment explanation
Indices: 40829--40942 Score: 81
Period size: 20 Copynumber: 5.7 Consensus size: 20
40819 CGCTTTGAAA
40829 ATCGCATTGCGATTATGTAA--
1 ATCGCATTGCGA-TA-GTAAGT
* * *
40849 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTAAGT
* * *
40869 ATCGCGTTGCAAAAGTAAGT
1 ATCGCATTGCGATAGTAAGT
* * * *
40889 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTAAGT
40910 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTAAGT
40930 ATCGCATTGCGAT
1 ATCGCATTGCGAT
40943 TTTCCCAATT
Statistics
Matches: 75, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
18 3 0.04
19 4 0.05
20 54 0.72
21 12 0.16
22 2 0.03
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTAAGT
Found at i:40960 original size:21 final size:21
Alignment explanation
Indices: 40931--41023 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
40921 ATAGTAAGTA
40931 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
40952 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
40972 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
40993 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
41013 TCGCATTGCGA
1 TCGCATTGCGA
41024 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:40961 original size:41 final size:41
Alignment explanation
Indices: 40870--41004 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
40860 AAAGTCAGTA
* * * * ** *
40870 TCGCGTTGCAAAAGTAAGTATCTCGTTGCGATTTT-GTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
*
40910 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
40952 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
40993 TCGCGTTGCGAT
1 TCGCGTTGCGAT
41005 TTACTTATTC
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:41005 original size:41 final size:41
Alignment explanation
Indices: 40931--41023 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
40921 ATAGTAAGTA
40931 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
40972 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
41013 TCGCATTGCGA
1 TCGCATTGCGA
41024 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:45757 original size:33 final size:34
Alignment explanation
Indices: 45692--45892 Score: 118
Period size: 34 Copynumber: 6.0 Consensus size: 34
45682 ATGTTTGTTA
* * *
45692 TCTATTTAATTTTGAATATTGAAATATAATTATAT
1 TCTATTTAAATTTGAATATTAAAAGAT-ATTATAT
*
45727 TCT-TTTAAATATTTAA-ATTAAAAGATATTAT-T
1 TCTATTTAAAT-TTGAATATTAAAAGATATTATAT
* * * *
45759 ATCTCTTCAAGTTTGAATATT-AAAGGTATCTATA-
1 -TCTATTTAAATTTGAATATTAAAAGATAT-TATAT
* * ** *
45793 TCT-TTTGAATATCT-CAGGTTAAAAGATACTATTAT
1 TCTATTT-AA-ATTTGAATATTAAAAGATATTA-TAT
*
45828 T-TATTTAAATTTGAATATTAAAAGATA-TCTA-
1 TCTATTTAAATTTGAATATTAAAAGATATTATAT
* *
45859 TCTATTTAAATTTTAATATTAAAATATA-TATAT
1 TCTATTTAAATTTGAATATTAAAAGATATTATAT
45892 T
1 T
45893 TGAGAAATCA
Statistics
Matches: 127, Mismatches: 24, Indels: 32
0.69 0.13 0.17
Matches are distributed among these distances:
31 1 0.01
32 32 0.25
33 34 0.27
34 49 0.39
35 11 0.09
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.47
Consensus pattern (34 bp):
TCTATTTAAATTTGAATATTAAAAGATATTATAT
Found at i:45854 original size:34 final size:32
Alignment explanation
Indices: 45811--45887 Score: 100
Period size: 32 Copynumber: 2.3 Consensus size: 32
45801 ATATCTCAGG
* *
45811 TTAAAAGATACTATTATTTATTTAAATTTGAATA
1 TTAAAAGATA-T-CTATCTATTTAAATTTGAATA
*
45845 TTAAAAGATATCTATCTATTTAAATTTTAATA
1 TTAAAAGATATCTATCTATTTAAATTTGAATA
*
45877 TTAAAATATAT
1 TTAAAAGATAT
45888 ATATTTGAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 28 0.72
33 1 0.03
34 10 0.26
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (32 bp):
TTAAAAGATATCTATCTATTTAAATTTGAATA
Found at i:50917 original size:18 final size:19
Alignment explanation
Indices: 50881--50917 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
50871 CGGGGAAGGG
*
50881 CGGCGGGGGAAGAATCGGA
1 CGGCGGGAGAAGAATCGGA
50900 CGGCGGGAGAAG-ATCGGA
1 CGGCGGGAGAAGAATCGGA
50918 GGAGATGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.27, C:0.16, G:0.51, T:0.05
Consensus pattern (19 bp):
CGGCGGGAGAAGAATCGGA
Found at i:52279 original size:28 final size:28
Alignment explanation
Indices: 52239--52373 Score: 220
Period size: 28 Copynumber: 4.9 Consensus size: 28
52229 AGAGTCGATG
*
52239 GTTCTACGCGGTCCTTCGGGACATATGT
1 GTTCTACGTGGTCCTTCGGGACATATGT
52267 GTTCTACGTGGTCCTTCGGGACATA--T
1 GTTCTACGTGGTCCTTCGGGACATATGT
*
52293 GTTCTACGAGGTCCTTCGGGACATATGT
1 GTTCTACGTGGTCCTTCGGGACATATGT
*
52321 GTTCTATGTGGTCCTTCGGGACATATGT
1 GTTCTACGTGGTCCTTCGGGACATATGT
*
52349 GTTCTATGTGGTCCTTCGGGACATA
1 GTTCTACGTGGTCCTTCGGGACATA
52374 GTGGTCCTTT
Statistics
Matches: 101, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
26 25 0.25
28 76 0.75
ACGTcount: A:0.16, C:0.21, G:0.28, T:0.35
Consensus pattern (28 bp):
GTTCTACGTGGTCCTTCGGGACATATGT
Found at i:52321 original size:54 final size:55
Alignment explanation
Indices: 52239--52373 Score: 218
Period size: 54 Copynumber: 2.5 Consensus size: 55
52229 AGAGTCGATG
*
52239 GTTCTACGCGGTCCTTCGGGACATATGTGTTCTACGTGGTCCTTCGGGACATA-T
1 GTTCTACGAGGTCCTTCGGGACATATGTGTTCTACGTGGTCCTTCGGGACATAGT
*
52293 GTTCTACGAGGTCCTTCGGGACATATGTGTTCTATGTGGTCCTTCGGGACATATGT
1 GTTCTACGAGGTCCTTCGGGACATATGTGTTCTACGTGGTCCTTCGGGACATA-GT
* *
52349 GTTCTATGTGGTCCTTCGGGACATA
1 GTTCTACGAGGTCCTTCGGGACATA
52374 GTGGTCCTTT
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
54 51 0.68
56 24 0.32
ACGTcount: A:0.16, C:0.21, G:0.28, T:0.35
Consensus pattern (55 bp):
GTTCTACGAGGTCCTTCGGGACATATGTGTTCTACGTGGTCCTTCGGGACATAGT
Found at i:53905 original size:60 final size:62
Alignment explanation
Indices: 53805--53929 Score: 209
Period size: 60 Copynumber: 2.0 Consensus size: 62
53795 TATATGTGCC
53805 TTTGCTTACACTTTGCTTTGCTTTTATGAAGGCTCTAGAAAAACTGAACCACCAGTTAGCAGAAG
1 TTTGCTTACACTTTGCTTTGCTTTTAT--A-GCTCTAGAAAAACTGAACCACCAGTTAGCAGAAG
53870 TTTGCTTACACTTTGC-TTGCTTTTAT-GCTCTAGAAAAACTGAACCACCAGTTAGCAGAAG
1 TTTGCTTACACTTTGCTTTGCTTTTATAGCTCTAGAAAAACTGAACCACCAGTTAGCAGAAG
53930 CGATGTTGCT
Statistics
Matches: 60, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
60 34 0.57
64 10 0.17
65 16 0.27
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.33
Consensus pattern (62 bp):
TTTGCTTACACTTTGCTTTGCTTTTATAGCTCTAGAAAAACTGAACCACCAGTTAGCAGAAG
Done.