Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007496.1 Hibiscus syriacus cultivar Beakdansim tig00020741_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: 65440
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:740 original size:18 final size:18
Alignment explanation
Indices: 717--784 Score: 73
Period size: 18 Copynumber: 3.7 Consensus size: 18
707 TTCAGTATTC
*
717 GTCCCGTAGGACCACTAT
1 GTCCCGAAGGACCACTAT
*
735 GTCCCGAAGGACTACTGTAT
1 GTCCCGAAGGACCAC--TAT
* * *
755 ATTCCGTAGGACCACTAT
1 GTCCCGAAGGACCACTAT
773 GTCCCGAAGGAC
1 GTCCCGAAGGAC
785 TACTCCTTAA
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
18 25 0.64
20 14 0.36
ACGTcount: A:0.25, C:0.29, G:0.24, T:0.22
Consensus pattern (18 bp):
GTCCCGAAGGACCACTAT
Found at i:5870 original size:18 final size:18
Alignment explanation
Indices: 5847--5916 Score: 77
Period size: 18 Copynumber: 3.7 Consensus size: 18
5837 TTCAGTATTC
*
5847 GTCCCGTAGGACCACTAT
1 GTCCCGAAGGACCACTAT
5865 GTCCCGAAGGACCACTGTATAT
1 GTCCCGAAGGACCAC----TAT
*
5887 GTCCCGTAGGACCACTAT
1 GTCCCGAAGGACCACTAT
*
5905 CTCCCGAAGGAC
1 GTCCCGAAGGAC
5917 TACTCCTTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
18 27 0.61
22 17 0.39
ACGTcount: A:0.24, C:0.33, G:0.23, T:0.20
Consensus pattern (18 bp):
GTCCCGAAGGACCACTAT
Found at i:9692 original size:17 final size:18
Alignment explanation
Indices: 9670--9703 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
9660 TCACCCGGTC
9670 CGGTTC-GAACGGTTCAG
1 CGGTTCTGAACGGTTCAG
*
9687 CGGTTCTGACCGGTTCA
1 CGGTTCTGAACGGTTCA
9704 CTAATAGCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.15, C:0.26, G:0.32, T:0.26
Consensus pattern (18 bp):
CGGTTCTGAACGGTTCAG
Found at i:12670 original size:12 final size:14
Alignment explanation
Indices: 12653--12683 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
12643 TTTTAAAACT
12653 ATTTTTCT-TCTCC
1 ATTTTTCTGTCTCC
12666 ATTTTTCTGTCTCC
1 ATTTTTCTGTCTCC
12680 ATTT
1 ATTT
12684 CCCCTACAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.10, C:0.26, G:0.03, T:0.61
Consensus pattern (14 bp):
ATTTTTCTGTCTCC
Found at i:18768 original size:42 final size:42
Alignment explanation
Indices: 18636--18786 Score: 125
Period size: 42 Copynumber: 3.6 Consensus size: 42
18626 AAGGTTATAT
*
18636 AAAAAATAATAAT-AATAAATAAATTTAAATAAATAAAAAACAT-
1 AAAAAAT-ATAATAAATAAATAAA-TTAAATAAAGAAAAAA-ATA
* ** *
18679 AAAAAATACT-A-AAAT-AATAAATTTAAGGAAGAAAAAAAACA
1 AAAAAATA-TAATAAATAAATAAATTAAATAAAG-AAAAAAATA
18720 ACAAAAATATAATAAATAAATAAA-TAAATAAAGAATAAAAATA
1 A-AAAAATATAATAAATAAATAAATTAAATAAAGAA-AAAAATA
** *
18763 AAAAAATATTTTAAAAAAATAAAT
1 AAAAAATATAATAAATAAATAAAT
18787 AATCAAAGGG
Statistics
Matches: 86, Mismatches: 12, Indels: 20
0.73 0.10 0.17
Matches are distributed among these distances:
40 7 0.08
41 14 0.16
42 34 0.40
43 25 0.29
44 6 0.07
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (42 bp):
AAAAAATATAATAAATAAATAAATTAAATAAAGAAAAAAATA
Found at i:18787 original size:42 final size:43
Alignment explanation
Indices: 18640--18788 Score: 113
Period size: 44 Copynumber: 3.4 Consensus size: 43
18630 TTATATAAAA
* * * *
18640 AATAATAATAATAAATAAATTTAAATAAATAAAA-AACATAAAAAAT
1 AATAA-AAAAATAAATAAA--TAAAGAAAAAAAACAACA-AAAATAT
* * * **
18686 ACTAAAATAATAAATTTAAGGAAGAAAAAAAACAACAAAAATAT
1 AATAAAAAAATAAA-TAAATAAAGAAAAAAAACAACAAAAATAT
* * *
18730 AATAAATAAATAAATAAATAAAGAATAAAAATAA-AAAAATAT
1 AATAAAAAAATAAATAAATAAAGAAAAAAAACAACAAAAATAT
**
18772 TTTAAAAAAATAAATAA
1 AATAAAAAAATAAATAA
18789 TCAAAGGGAA
Statistics
Matches: 83, Mismatches: 18, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
42 22 0.27
43 15 0.18
44 26 0.31
45 13 0.16
46 7 0.08
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (43 bp):
AATAAAAAAATAAATAAATAAAGAAAAAAAACAACAAAAATAT
Found at i:33663 original size:3 final size:3
Alignment explanation
Indices: 33650--33723 Score: 139
Period size: 3 Copynumber: 24.3 Consensus size: 3
33640 ATATTATAAA
33650 TAT TAAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
33696 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
33724 TATTTTCATT
Statistics
Matches: 70, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 67 0.96
4 3 0.04
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:40151 original size:21 final size:21
Alignment explanation
Indices: 40100--40152 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
40090 ATTCTGACTA
40100 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * * *
40121 TTGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
40142 TCGCAATGCGA
1 TCGCATTGCGA
40153 ATACGTAAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:40173 original size:41 final size:40
Alignment explanation
Indices: 40142--40276 Score: 180
Period size: 41 Copynumber: 3.3 Consensus size: 40
40132 TTTTCCTAAT
*
40142 TCGCAATGCGAATACGTAAATCACAACGCGATTACGTAAA
1 TCGCAATGCGAATACGAAAATCACAACGCGATTACGTAAA
* * *
40182 TCGCAATGCGAATTAGGAAAATCGCAACACGATTACGTAAA
1 TCGCAATGCGAA-TACGAAAATCACAACGCGATTACGTAAA
* * * *
40223 TCGCAATGCGAATTAGGAAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAA-TACGAAAATCACAACGCGATTACGTAAA
40264 TCGCAATGCGAAT
1 TCGCAATGCGAAT
40277 CTGACTATCG
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
40 13 0.15
41 74 0.85
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (40 bp):
TCGCAATGCGAATACGAAAATCACAACGCGATTACGTAAA
Found at i:40275 original size:20 final size:20
Alignment explanation
Indices: 40142--40276 Score: 162
Period size: 20 Copynumber: 6.7 Consensus size: 20
40132 TTTTCCTAAT
40142 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
40162 TCACAACGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
40182 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
** *
40203 TCGCAACACGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
40223 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
40244 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
40264 TCGCAATGCGAAT
1 TCGCAATGCGAAT
40277 CTGACTATCG
Statistics
Matches: 93, Mismatches: 20, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
20 60 0.65
21 33 0.35
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:40856 original size:20 final size:20
Alignment explanation
Indices: 40831--40921 Score: 103
Period size: 20 Copynumber: 4.5 Consensus size: 20
40821 TTCTAAACTT
* *
40831 AAAATCACAACATGAAAATG
1 AAAATCGCAACACGAAAATG
40851 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** *
40871 ACTATCGCAACAAGAGAAATG
1 AAAATCGCAACACGA-AAATG
*
40892 AAAATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
*
40911 AAAATCACAAC
1 AAAATCGCAAC
40922 GATATAATCG
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
19 15 0.25
20 30 0.50
21 15 0.25
ACGTcount: A:0.54, C:0.20, G:0.14, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:40995 original size:33 final size:33
Alignment explanation
Indices: 40953--41074 Score: 154
Period size: 33 Copynumber: 3.5 Consensus size: 33
40943 CAAAATCGCA
40953 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
40986 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* **
41019 TTACGATAGTCATTTCCGCGTTGCGATTTTCATTCTCTCG
1 TTGCGATTTTCATTT-CGCGTTGCG------ATTCTCTCG
41059 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
41075 AACCAAATGA
Statistics
Matches: 76, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
33 45 0.59
34 9 0.12
39 1 0.01
40 21 0.28
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:41051 original size:20 final size:19
Alignment explanation
Indices: 40948--41074 Score: 103
Period size: 20 Copynumber: 7.1 Consensus size: 19
40938 GAAACCAAAA
*
40948 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
40967 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
40981 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
41000 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
41014 TCTCGTTACGATAGTCATT
1 TCGCGTTGCGATTTTCATT
41033 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
*
41053 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
41073 TC
1 TC
41075 AACCAAATGA
Statistics
Matches: 85, Mismatches: 11, Indels: 24
0.71 0.09 0.20
Matches are distributed among these distances:
14 19 0.22
16 5 0.06
17 6 0.07
19 23 0.27
20 31 0.36
21 1 0.01
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:42944 original size:14 final size:14
Alignment explanation
Indices: 42925--42979 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
42915 TTAGTATTTA
42925 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
42939 TTGCGATTTTCATTTCGCG
1 TTGCGA--TTC---TCTCG
42958 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
42972 TTGCGATT
1 TTGCGATT
42980 TTCGTTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.24, G:0.22, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:42961 original size:19 final size:19
Alignment explanation
Indices: 42937--43060 Score: 132
Period size: 19 Copynumber: 6.6 Consensus size: 19
42927 GCGATTCTCT
42937 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
42956 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
*
42970 CGTTGCGATTTTCGTTTCG
1 CGTTGCGATTTTCATTTCG
*
42989 CGTTGCGATTTTCATTCTCT
1 CGTTGCGATTTTCATT-TCG
43009 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
** *
43028 CGTTGCGATAGTCATTTTTCA
1 CGTTGCGATTTTCA--TTTCG
43049 CGTTGCGATTTT
1 CGTTGCGATTTT
43061 AAGTTCCAGA
Statistics
Matches: 87, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
14 10 0.11
16 3 0.03
17 3 0.03
19 39 0.45
20 18 0.21
21 14 0.16
ACGTcount: A:0.10, C:0.22, G:0.21, T:0.47
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:42962 original size:33 final size:33
Alignment explanation
Indices: 42925--43036 Score: 161
Period size: 33 Copynumber: 3.2 Consensus size: 33
42915 TTAGTATTTA
42925 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCG
1 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCG
*
42958 TTGCGATTCTCTCGTTGCGATTTTCGTTTCGCG
1 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCG
42991 TTGCGATTTTCATTCTCTCGTTGCGATTTTCATTTCGCG
1 TTGCG------ATTCTCTCGTTGCGATTTTCATTTCGCG
43030 TTGCGAT
1 TTGCGAT
43037 AGTCATTTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 12
0.84 0.02 0.14
Matches are distributed among these distances:
33 39 0.55
39 32 0.45
ACGTcount: A:0.09, C:0.23, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTCTCTCGTTGCGATTTTCATTTCGCG
Found at i:43017 original size:39 final size:37
Alignment explanation
Indices: 42930--43060 Score: 162
Period size: 39 Copynumber: 3.5 Consensus size: 37
42920 ATTTATTGCG
42930 ATTCTCTCGTTGCGATTTTCATTTCGCGTTGCG----
1 ATTCTCTCGTTGCGATTTTCATTTCGCGTTGCGATTC
*
42963 ATTCTCTCGTTGCGATTTTCGTTTCGCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTCATTTCGCGTTGCGA--TTC
43002 ATTCTCTCGTTGCGATTTTCATTTCGCGTTGCGATAGTC
1 ATTCTCTCGTTGCGATTTTCATTTCGCGTTGCGAT--TC
* *
43041 ATTTTTCACGTTGCGATTTT
1 A-TTCTCTCGTTGCGATTTT
43061 AAGTTCCAGA
Statistics
Matches: 85, Mismatches: 4, Indels: 11
0.85 0.04 0.11
Matches are distributed among these distances:
33 32 0.38
37 1 0.01
39 36 0.42
40 16 0.19
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.47
Consensus pattern (37 bp):
ATTCTCTCGTTGCGATTTTCATTTCGCGTTGCGATTC
Found at i:43546 original size:42 final size:42
Alignment explanation
Indices: 43461--43549 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
43451 GACTCGCCTG
* * * * *
43461 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGATGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCACTA
* * *
43503 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCACTA
43545 TCATC
1 TCATC
43550 GTTGAAGAGG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.22, C:0.38, G:0.15, T:0.25
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCACTA
Found at i:43578 original size:21 final size:20
Alignment explanation
Indices: 43519--43579 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
43509 CTCGAGAGTC
*
43519 CCCTCCCACCGTTCAAGAGG
1 CCCTCTCACCGTTCAAGAGG
* * *
43539 CCACTATCATCGTTGAAGAGG
1 CC-CTCTCACCGTTCAAGAGG
*
43560 TCCCTCTCACCATTCAAGAG
1 -CCCTCTCACCGTTCAAGAG
43580 CCCGATTCAC
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.25, C:0.36, G:0.18, T:0.21
Consensus pattern (20 bp):
CCCTCTCACCGTTCAAGAGG
Found at i:44949 original size:14 final size:14
Alignment explanation
Indices: 44930--44965 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
44920 ATTGTTTAAT
44930 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
44944 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
44958 TGATTTGT
1 TGATTTGT
44966 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:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:45088 original size:19 final size:19
Alignment explanation
Indices: 45072--45137 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
45062 AAAAATGACT
*
45072 ATCGAAATGCGAAATGAAA
1 ATCGAAACGCGAAATGAAA
*
45091 ATCGCAACGCGAAATGAAA
1 ATCGAAACGCGAAATGAAA
45110 ATC-ACAACGCGAAATGAAA
1 ATCGA-AACGCGAAATGAAA
*
45129 ATCGCAACG
1 ATCGAAACG
45138 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
19 41 1.00
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.12
Consensus pattern (19 bp):
ATCGAAACGCGAAATGAAA
Found at i:45145 original size:14 final size:13
Alignment explanation
Indices: 45126--45156 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
45116 ACGCGAAATG
45126 AAAATCGCAACGAC
1 AAAATCGCAACG-C
45140 AAAATCGCAACGC
1 AAAATCGCAACGC
45153 AAAA
1 AAAA
45157 CGAAATTCGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.55, C:0.26, G:0.13, T:0.06
Consensus pattern (13 bp):
AAAATCGCAACGC
Found at i:45151 original size:33 final size:36
Alignment explanation
Indices: 45080--45166 Score: 90
Period size: 33 Copynumber: 2.4 Consensus size: 36
45070 CTATCGAAAT
*
45080 GCGAAATGAAAATCGCAACGCGAAATGAAAATCACAAC
1 GCGAAATGAAAATCGCAAC-CG-AATCAAAATCACAAC
*
45118 GCGAAATGAAAATCGCAA-CG-A-CAAAATCGCAAC
1 GCGAAATGAAAATCGCAACCGAATCAAAATCACAAC
* * *
45151 GCAAAACGAAATTCGC
1 GCGAAATGAAAATCGC
45167 GTTGCGATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
33 23 0.52
34 1 0.02
36 2 0.05
38 18 0.41
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.10
Consensus pattern (36 bp):
GCGAAATGAAAATCGCAACCGAATCAAAATCACAAC
Found at i:45208 original size:33 final size:33
Alignment explanation
Indices: 45166--45259 Score: 152
Period size: 33 Copynumber: 2.8 Consensus size: 33
45156 ACGAAATTCG
* *
45166 CGTTGCGATTTTCATATCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
* *
45199 CGTTGCGATTTTCATTTCGCATTACGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
45232 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
45260 AGTCATTTCC
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:45258 original size:19 final size:19
Alignment explanation
Indices: 45201--45279 Score: 69
Period size: 19 Copynumber: 4.4 Consensus size: 19
45191 GATTCCCTCG
45201 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
45220 TTACGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
45234 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
** *
45253 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCA
45273 TTGCGAT
1 TTGCGAT
45280 AGACATTAAG
Statistics
Matches: 47, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
14 5 0.11
16 7 0.15
17 7 0.15
19 18 0.38
20 10 0.21
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.43
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:45278 original size:20 final size:20
Alignment explanation
Indices: 45232--45325 Score: 68
Period size: 20 Copynumber: 4.7 Consensus size: 20
45222 ACGATTCTCT
**
45232 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
*
45251 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* **
45271 CGTTGCGATAGACA-TTAAG
1 CGTTGCGATAGTCATTTCCG
*
45290 ATGATTGCGA-ACGTCATTTCCG
1 -CG-TTGCGATA-GTCATTTCCG
*
45312 TGTTGCGATAGTCA
1 CGTTGCGATAGTCA
45326 AATGAATGCC
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
19 17 0.29
20 26 0.45
21 12 0.21
22 3 0.05
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:47847 original size:24 final size:24
Alignment explanation
Indices: 47780--47839 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
47770 CTGAAAAATC
47780 ATCAAAATTCGAGTATTGACCAAG
1 ATCAAAATTCGAGTATTGACCAAG
* * *
47804 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATTCGAGTATTGACCAAG
*
47828 ATCAAATTTCGA
1 ATCAAAATTCGA
47840 ATACTGACTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.25
Consensus pattern (24 bp):
ATCAAAATTCGAGTATTGACCAAG
Found at i:48710 original size:20 final size:21
Alignment explanation
Indices: 48687--48955 Score: 245
Period size: 20 Copynumber: 13.3 Consensus size: 21
48677 AGAATCTCGT
48687 TGCGATTTAC-TAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
* *
48707 TGCGA-ATACGTAAATTGCAA
1 TGCGATTTACGTAAATCGCAA
* * *
48727 TGCGAATTAGGAAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
*
48748 TGCGA-ATACGTAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
*
48768 TGCGA-ATACGTAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
48788 TGCGA-TTACGTAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
* *
48808 TGCGA-ATACGT-AATCGCAT
1 TGCGATTTACGTAAATCGCAA
* *
48827 TACGATTTACGT-AATCGCAT
1 TGCGATTTACGTAAATCGCAA
* * * *
48847 TGCGATTTTCCTAATTCGCAT
1 TGCGATTTACGTAAATCGCAA
*
48868 TGCGATTTACGT-AATCGCAT
1 TGCGATTTACGTAAATCGCAA
* *
48888 TGCGATTTACGT-ATTCGCAT
1 TGCGATTTACGTAAATCGCAA
* *
48908 TGCGATTTAGGAAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
* * *
48929 CGCGAATTT-GGGAAATCGCAA
1 TGCG-ATTTACGTAAATCGCAA
48950 TGCGAT
1 TGCGAT
48956 AGTCAGAATC
Statistics
Matches: 214, Mismatches: 29, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
19 14 0.07
20 140 0.65
21 56 0.26
22 4 0.02
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (21 bp):
TGCGATTTACGTAAATCGCAA
Found at i:48752 original size:61 final size:60
Alignment explanation
Indices: 48697--48954 Score: 227
Period size: 61 Copynumber: 4.2 Consensus size: 60
48687 TGCGATTTAC
* *
48697 TAAATCGCAATGCGAATACGTAAATTGCAATGCGAATTAGGAAAATCGCAATGCGAATACG
1 TAAATCGCAATGCGAATACGTAAATCGCAATGCG-ATTACGAAAATCGCAATGCGAATACG
*
48758 TAAATCGCAATGCGAATACGTAAATCGCAATGCGATTACGTAAATCGCAATGCGAATACG
1 TAAATCGCAATGCGAATACGTAAATCGCAATGCGATTACGAAAATCGCAATGCGAATACG
* * * * * ** * * *
48818 T-AATCGCATTACGATTTACGT-AATCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACG
1 TAAATCGCAATGCGA-ATACGTAAATCGCAATGCGA-TTACGAAAATCGCAATGCGA-ATACG
* * * * * * **
48879 T-AATCGCATTGCGATTTACGT-ATTCGCATTGCGATTTAGGAAAATCGCAACGCGAATTTGG
1 TAAATCGCAATGCGA-ATACGTAAATCGCAATGCGA-TTACGAAAATCGCAATGCGAA-TACG
*
48940 GAAATCGCAATGCGA
1 TAAATCGCAATGCGA
48955 TAGTCAGAAT
Statistics
Matches: 166, Mismatches: 26, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
59 23 0.14
60 46 0.28
61 85 0.51
62 12 0.07
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (60 bp):
TAAATCGCAATGCGAATACGTAAATCGCAATGCGATTACGAAAATCGCAATGCGAATACG
Found at i:48915 original size:40 final size:41
Alignment explanation
Indices: 48697--48935 Score: 222
Period size: 41 Copynumber: 5.9 Consensus size: 41
48687 TGCGATTTAC
* * * *
48697 TAAATCGCAATGCGA-ATACGTAAATTGCAATGCGAATTAGG
1 TAAATCGCATTGCGATTTACGTAAATCGCAATGCGAA-TACG
* * *
48738 AAAATCGCAATGCGA-ATACGTAAATCGCAATGCGAATACG
1 TAAATCGCATTGCGATTTACGTAAATCGCAATGCGAATACG
*
48778 TAAATCGCAATGCGA-TTACGTAAATCGCAATGCGAATACG
1 TAAATCGCATTGCGATTTACGTAAATCGCAATGCGAATACG
* * * * *
48818 T-AATCGCATTACGATTTACGT-AATCGCATTGCGATTTTCC
1 TAAATCGCATTGCGATTTACGTAAATCGCAATGCGA-ATACG
* * *
48858 TAATTCGCATTGCGATTTACGT-AATCGCATTGCGATTTACG
1 TAAATCGCATTGCGATTTACGTAAATCGCAATGCGA-ATACG
* * * *
48899 T-ATTCGCATTGCGATTTAGGAAAATCGCAACGCGAAT
1 TAAATCGCATTGCGATTTACGTAAATCGCAATGCGAAT
48936 TTGGGAAATC
Statistics
Matches: 174, Mismatches: 20, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
39 23 0.13
40 70 0.40
41 81 0.47
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (41 bp):
TAAATCGCATTGCGATTTACGTAAATCGCAATGCGAATACG
Found at i:48942 original size:22 final size:21
Alignment explanation
Indices: 48912--48954 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
48902 TCGCATTGCG
48912 ATTTAGGAAAATCGCAACGCGA
1 ATTTAGG-AAATCGCAACGCGA
* *
48934 ATTTGGGAAATCGCAATGCGA
1 ATTTAGGAAATCGCAACGCGA
48955 TAGTCAGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.21
Consensus pattern (21 bp):
ATTTAGGAAATCGCAACGCGA
Found at i:49609 original size:18 final size:18
Alignment explanation
Indices: 49583--49639 Score: 96
Period size: 18 Copynumber: 3.2 Consensus size: 18
49573 ACCAGTTACA
* *
49583 ACCCGACCCGACCCATTG
1 ACCCAACCCGACCCGTTG
49601 ACCCAACCCGACCCGTTG
1 ACCCAACCCGACCCGTTG
49619 ACCCAACCCGACCCGTTG
1 ACCCAACCCGACCCGTTG
49637 ACC
1 ACC
49640 GTTGACCACC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.23, C:0.51, G:0.16, T:0.11
Consensus pattern (18 bp):
ACCCAACCCGACCCGTTG
Found at i:52545 original size:32 final size:31
Alignment explanation
Indices: 52472--52593 Score: 95
Period size: 31 Copynumber: 3.9 Consensus size: 31
52462 CTAATGTGAA
* *
52472 TCTTAGGTAGGCTCTGCGGCCCTGAGATCAT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGATCAT
** * **
52503 TCTCGGGTAGGCCCTGTGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGAT-CAT
* * *
52535 TCTTAGGTAGGCCCTACGGCCCCAAAATC-T
1 TCTTAGGTAGGCCCTGCGGCCCTAAGATCAT
* *
52565 ATCTTGGGTAGGCTCT-CAGGCCCTAAGAT
1 -TCTTAGGTAGGCCCTGC-GGCCCTAAGAT
52594 GTTCCCTTAG
Statistics
Matches: 70, Mismatches: 18, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
30 2 0.03
31 45 0.64
32 23 0.33
ACGTcount: A:0.18, C:0.27, G:0.28, T:0.27
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCGGCCCTAAGATCAT
Found at i:52574 original size:63 final size:63
Alignment explanation
Indices: 52472--52595 Score: 151
Period size: 63 Copynumber: 2.0 Consensus size: 63
52462 CTAATGTGAA
* * ** * **
52472 TCTTAGGTAGGCTCTGCGGCCCTGAGATCATTCTCGGGTAGGCCCTGTGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTACGGCCCCAAAATCATTCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
* *
52535 TCTTAGGTAGGCCCTACGGCCCCAAAATC-TATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCTACGGCCCCAAAATCAT-TCTCGGGTAGGCCCTCAGGCCCTAAGATGT
52596 TCCCTTAGGT
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
62 1 0.02
63 50 0.98
ACGTcount: A:0.18, C:0.27, G:0.28, T:0.27
Consensus pattern (63 bp):
TCTTAGGTAGGCCCTACGGCCCCAAAATCATTCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:58753 original size:54 final size:54
Alignment explanation
Indices: 58694--58848 Score: 202
Period size: 57 Copynumber: 2.8 Consensus size: 54
58684 AGCTAAAACT
58694 TTGATTCATTATAGACAAATAAATTGGTACAATAAATACTTGATAATATTAACC
1 TTGATTCATTATAGACAAATAAATTGGTACAATAAATACTTGATAATATTAACC
* * ** * * *
58748 TTGATTCATTATAGATAAATAGATTCACATAATAATTAATACTTGATAATATTAATC
1 TTGATTCATTATAGACAAATAAATT--GGT-ACAATAAATACTTGATAATATTAACC
* *
58805 TTGATTTATTGTAGACAAATAAATTGGTACAATAAATACTTGAT
1 TTGATTCATTATAGACAAATAAATTGGTACAATAAATACTTGAT
58849 TATAATAATT
Statistics
Matches: 83, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
54 37 0.45
55 1 0.01
56 1 0.01
57 44 0.53
ACGTcount: A:0.43, C:0.09, G:0.10, T:0.38
Consensus pattern (54 bp):
TTGATTCATTATAGACAAATAAATTGGTACAATAAATACTTGATAATATTAACC
Found at i:58839 original size:57 final size:54
Alignment explanation
Indices: 58694--58857 Score: 202
Period size: 54 Copynumber: 3.0 Consensus size: 54
58684 AGCTAAAACT
*
58694 TTGATTCATTATAGACAAATAAATTGGTACAATAAATACTTGATAATATTAACC
1 TTGATTCATTATAGACAAATAAATTGGTACAATAAATACTTGATAATATTAATC
* * ** * *
58748 TTGATTCATTATAGATAAATAGATTCACATAATAATTAATACTTGATAATATTAATC
1 TTGATTCATTATAGACAAATAAATT--GGT-ACAATAAATACTTGATAATATTAATC
* * * *
58805 TTGATTTATTGTAGACAAATAAATTGGTACAATAAATACTTGATTATAATAAT
1 TTGATTCATTATAGACAAATAAATTGGTACAATAAATACTTGATAATATTAAT
58858 TTTATTTATT
Statistics
Matches: 90, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
54 44 0.49
55 1 0.01
56 1 0.01
57 44 0.49
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (54 bp):
TTGATTCATTATAGACAAATAAATTGGTACAATAAATACTTGATAATATTAATC
Found at i:63753 original size:27 final size:28
Alignment explanation
Indices: 63709--63761 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
63699 ATTTTGACTA
63709 GTGACTAAAATATAA-TTTAAAAGTTTG
1 GTGACTAAAATATAATTTTAAAAGTTTG
* * *
63736 GTGACTAAAGTGTGATTTTAAAAGTT
1 GTGACTAAAATATAATTTTAAAAGTT
63762 ATATATTTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 12 0.55
28 10 0.45
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.38
Consensus pattern (28 bp):
GTGACTAAAATATAATTTTAAAAGTTTG
Found at i:65155 original size:19 final size:19
Alignment explanation
Indices: 65131--65171 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
65121 AATACATTTA
65131 ATGCATCGATGCACAATCC
1 ATGCATCGATGCACAATCC
65150 ATGCATCGATGCACAATCC
1 ATGCATCGATGCACAATCC
65169 ATG
1 ATG
65172 ATGCATCATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (19 bp):
ATGCATCGATGCACAATCC
Done.