Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006457.1 Hibiscus syriacus cultivar Beakdansim tig00015651_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: 91360
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:7583 original size:15 final size:15
Alignment explanation
Indices: 7563--7591 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
7553 AAAGTTCTTT
7563 CTTTTTCTTTATTTA
1 CTTTTTCTTTATTTA
7578 CTTTTTCTTTATTT
1 CTTTTTCTTTATTT
7592 TTTTCTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (15 bp):
CTTTTTCTTTATTTA
Found at i:7596 original size:12 final size:12
Alignment explanation
Indices: 7564--7617 Score: 54
Period size: 12 Copynumber: 4.2 Consensus size: 12
7554 AAGTTCTTTC
7564 TTTTTCTTTATTT
1 TTTTTCTTTA-TT
7577 ACTTTTTCTTTATT
1 --TTTTTCTTTATT
**
7591 TTTTTCTTTAAA
1 TTTTTCTTTATT
*
7603 GTTTTCTTTATT
1 TTTTTCTTTATT
7615 TTT
1 TTT
7618 AAAATGCTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
12 21 0.64
14 2 0.06
15 10 0.30
ACGTcount: A:0.13, C:0.09, G:0.02, T:0.76
Consensus pattern (12 bp):
TTTTTCTTTATT
Found at i:14297 original size:15 final size:14
Alignment explanation
Indices: 14253--14300 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 14
14243 ATGGAAATAA
14253 GAAATGAAAGAAAT
1 GAAATGAAAGAAAT
14267 GGAAATTGATAAGAAAT
1 -GAAA-TGA-AAGAAAT
14284 GAAATAGAAAGAAAT
1 GAAAT-GAAAGAAAT
14299 GA
1 GA
14301 TATCAAAGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 14 0.47
16 9 0.30
17 7 0.23
ACGTcount: A:0.60, C:0.00, G:0.23, T:0.17
Consensus pattern (14 bp):
GAAATGAAAGAAAT
Found at i:14297 original size:26 final size:24
Alignment explanation
Indices: 14249--14302 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 24
14239 TTAAATGGAA
14249 ATAAGAAATGAAAGAAATGGAAATTG
1 ATAAGAAATGAAAGAAA-GGAAA-TG
14275 ATAAGAAATGAAATAGAAA-GAAATG
1 ATAAGAAATG-AA-AGAAAGGAAATG
14300 ATA
1 ATA
14303 TCAAAGTAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
25 5 0.19
26 14 0.54
27 2 0.08
28 5 0.19
ACGTcount: A:0.61, C:0.00, G:0.20, T:0.19
Consensus pattern (24 bp):
ATAAGAAATGAAAGAAAGGAAATG
Found at i:14843 original size:19 final size:20
Alignment explanation
Indices: 14805--14847 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
14795 TGGATGAATT
14805 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTTAA
14825 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
14844 TGAA
1 TGAA
14848 GATATATGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.47, C:0.05, G:0.12, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:17124 original size:21 final size:21
Alignment explanation
Indices: 17074--17124 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
17064 AATGTTCTCA
*
17074 TTCAGTTTCATTGTCTTTAAG
1 TTCATTTTCATTGTCTTTAAG
*
17095 TTGCTTTTTCATT-TCTTTAATG
1 TT-CATTTTCATTGTCTTTAA-G
17117 TTCATTTT
1 TTCATTTT
17125 GAAATGTGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.16, C:0.14, G:0.10, T:0.61
Consensus pattern (21 bp):
TTCATTTTCATTGTCTTTAAG
Found at i:18982 original size:19 final size:20
Alignment explanation
Indices: 18943--18994 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
18933 GAAACCCCTT
18943 TGAAAATACATGATTTTTTAA
1 TGAAAATACATGA-TTTTTAA
18964 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
18983 TGAAGATACATG
1 TGAAAATACATG
18995 CTCTTGGTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 17 0.57
21 13 0.43
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:33012 original size:17 final size:17
Alignment explanation
Indices: 32990--33028 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
32980 TAAATCAAAT
32990 TAATTAGATACTATTTA
1 TAATTAGATACTATTTA
*
33007 TAATTAGATATTATTTA
1 TAATTAGATACTATTTA
33024 -AATTA
1 TAATTA
33029 ATTGTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (17 bp):
TAATTAGATACTATTTA
Found at i:37319 original size:133 final size:124
Alignment explanation
Indices: 37073--37327 Score: 348
Period size: 133 Copynumber: 2.0 Consensus size: 124
37063 TGAAATGATA
37073 TTGTTTCCTTGTTTTGTAAGTGGGTTGTTTCCTTCCATCCTTTGCTTTGCCTTTTCCCCTTTTCT
1 TTGTTTCCTTGTTTTGTAAGTGGGTTGTTTCCTTCCATCCTTTGCTTTGCCTTTTCCCCTTTTCT
* * *
37138 TTCCTTTTGTGTGGTATTGCTATTTAAGGGATTCACGTGGCACGCAAGGTAAAAGGGTT
66 TTCCTTTTGTGTGGTAATGATATTTAAGGGATTCACATGGCACGCAAGGTAAAAGGGTT
* ** *
37197 TTGTTTTCTTGTTTTGGGTAAGTGGGTTGTTTGTTTCCATCCTTTGCTTTGCTTTTTTCCCCTCT
1 TTGTTTCCTTGTTTT--GTAAGTGGGTTGTTTCCTTCCATCCTTTGCTTTGC-CTTTT-CCC-CT
* *
37262 TTATCTTTCTTTCTTTTGTGTGGTAATGATATTTAGGGGATTCACATGGGACGCAAGGTAAAAGG
61 TT-TCTTTC---CTTTTGTGTGGTAATGATATTTAAGGGATTCACATGGCACGCAAGGTAAAAGG
37327 G
122 G
37328 GAATCTGATT
Statistics
Matches: 113, Mismatches: 9, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
124 14 0.12
126 33 0.29
127 4 0.04
128 3 0.03
129 4 0.04
130 6 0.05
133 49 0.43
ACGTcount: A:0.14, C:0.17, G:0.23, T:0.47
Consensus pattern (124 bp):
TTGTTTCCTTGTTTTGTAAGTGGGTTGTTTCCTTCCATCCTTTGCTTTGCCTTTTCCCCTTTTCT
TTCCTTTTGTGTGGTAATGATATTTAAGGGATTCACATGGCACGCAAGGTAAAAGGGTT
Found at i:39979 original size:29 final size:29
Alignment explanation
Indices: 39894--39968 Score: 150
Period size: 29 Copynumber: 2.6 Consensus size: 29
39884 CCGAGCCCTA
39894 AGGTTTCAATCTCCCTTTGATGAGCTGAG
1 AGGTTTCAATCTCCCTTTGATGAGCTGAG
39923 AGGTTTCAATCTCCCTTTGATGAGCTGAG
1 AGGTTTCAATCTCCCTTTGATGAGCTGAG
39952 AGGTTTCAATCTCCCTT
1 AGGTTTCAATCTCCCTT
39969 CAACGAGCTG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (29 bp):
AGGTTTCAATCTCCCTTTGATGAGCTGAG
Found at i:41356 original size:4 final size:4
Alignment explanation
Indices: 41347--41383 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
41337 AAATTATACA
41347 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
41384 GAAAACAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:41769 original size:12 final size:13
Alignment explanation
Indices: 41737--41769 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
41727 TAATATATCA
*
41737 TTTAAAATTATAT
1 TTTAAAAATATAT
41750 TTTAAAAAT-TAT
1 TTTAAAAATATAT
41762 TTTAAAAA
1 TTTAAAAA
41770 ATAAAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTAAAAATATAT
Found at i:45021 original size:40 final size:41
Alignment explanation
Indices: 44943--45031 Score: 96
Period size: 40 Copynumber: 2.2 Consensus size: 41
44933 TGCGATCGAT
*
44943 AATTCGCAACGCGATCTCTGGTATCGCAAATCAGTTT-CCA
1 AATTCGCAACGCGATCTCTGCTATCGCAAATCAGTTTCCCA
* *
44983 GATTCGCAACGCGAT-TCTGACTATCGC-ATTGC-GATTTCCCA
1 AATTCGCAACGCGATCTCTG-CTATCGCAAAT-CAG-TTTCCCA
45024 AATTCGCA
1 AATTCGCA
45032 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
39 7 0.17
40 24 0.59
41 10 0.24
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (41 bp):
AATTCGCAACGCGATCTCTGCTATCGCAAATCAGTTTCCCA
Found at i:45032 original size:21 final size:21
Alignment explanation
Indices: 45006--45061 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
44996 ATTCTGACTA
45006 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* *
45027 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
45048 TCGCATTGCGATTT
1 TCGCATTGCGATTT
45062 ACGTATTCGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.20, C:0.25, G:0.16, T:0.39
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:45071 original size:20 final size:20
Alignment explanation
Indices: 45006--45086 Score: 90
Period size: 21 Copynumber: 4.0 Consensus size: 20
44996 ATTCTGACTA
* *
45006 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTT-ACATAT
* *
45027 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACAT-AT
*
45048 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACATAT
*
45068 TCGCGTTGCGATTTACATA
1 TCGCATTGCGATTTACATA
45087 GCGCCATTCG
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
20 20 0.38
21 32 0.62
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:45657 original size:21 final size:21
Alignment explanation
Indices: 45596--45674 Score: 94
Period size: 20 Copynumber: 3.9 Consensus size: 21
45586 TTCTAAACTT
45596 AAAATCGCAAC-ATGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
45616 AAAATCGCAAC-ACGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
**
45636 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGAGAAATG
45657 AAAATCGCAACGAGAGAA
1 AAAATCGCAACGAGAGAA
45675 TCGCAACGCG
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
20 30 0.58
21 22 0.42
ACGTcount: A:0.52, C:0.18, G:0.19, T:0.11
Consensus pattern (21 bp):
AAAATCGCAACGAGAGAAATG
Found at i:45694 original size:33 final size:33
Alignment explanation
Indices: 45651--45731 Score: 126
Period size: 33 Copynumber: 2.5 Consensus size: 33
45641 CGCAACGAGA
*
45651 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATCAAAATCGCAACGAGAGAATCGCAACGC
* *
45684 GAAATTAAAATCGCAACGAGATAATCGCAACGC
1 GAAATCAAAATCGCAACGAGAGAATCGCAACGC
*
45717 GAAACCAAAATCGCA
1 GAAATCAAAATCGCA
45732 TTGCGATTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
GAAATCAAAATCGCAACGAGAGAATCGCAACGC
Found at i:45711 original size:14 final size:14
Alignment explanation
Indices: 45659--45715 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
45649 GAGAAATGAA
*
45659 AATCGCAACGAGAG
1 AATCGCAACGAGAT
*
45673 AATCGCAACGCGAAATT
1 AATCGCAA--CGAGA-T
45690 AAAATCGCAACGAGAT
1 --AATCGCAACGAGAT
45706 AATCGCAACG
1 AATCGCAACG
45716 CGAAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 18 0.51
16 5 0.14
17 4 0.11
19 8 0.23
ACGTcount: A:0.44, C:0.23, G:0.21, T:0.12
Consensus pattern (14 bp):
AATCGCAACGAGAT
Found at i:45749 original size:19 final size:19
Alignment explanation
Indices: 45727--45839 Score: 119
Period size: 20 Copynumber: 6.1 Consensus size: 19
45717 GAAACCAAAA
*
45727 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
45746 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
45760 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
45779 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
45798 TCCGCGTTGCGCTTTTCATT
1 T-CGCGTTGCGATTTTCATT
*
45818 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
45838 TC
1 TC
45840 AACCAAAAGA
Statistics
Matches: 77, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
14 10 0.13
16 3 0.04
17 3 0.04
19 29 0.38
20 31 0.40
21 1 0.01
ACGTcount: A:0.11, C:0.25, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:45805 original size:20 final size:19
Alignment explanation
Indices: 45727--45808 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 19
45717 GAAACCAAAA
* **
45727 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATAGTCATT
45746 TCGCGTTGCGAT--TC---
1 TCGCGTTGCGATAGTCATT
* **
45760 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATAGTCATT
45779 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATAGTCATT
45798 TCCGCGTTGCG
1 T-CGCGTTGCG
45809 CTTTTCATTC
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
14 11 0.21
16 2 0.04
17 2 0.04
19 28 0.54
20 9 0.17
ACGTcount: A:0.11, C:0.24, G:0.23, T:0.41
Consensus pattern (19 bp):
TCGCGTTGCGATAGTCATT
Found at i:45837 original size:40 final size:39
Alignment explanation
Indices: 45732--45839 Score: 120
Period size: 33 Copynumber: 2.9 Consensus size: 39
45722 CAAAATCGCA
*
45732 TTGCGATTTTCATTTCGCGTTGCGAT--TC---T-CTCG
1 TTGCGATTTTCATTTCGCGTTGCGATAGTCATTTCCGCG
45765 TTGCGATTTTCATTTCGCGTTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATAGTCATTTCCGCG
* * **
45804 TTGCGCTTTTCATTCTCTCGTTGCGATTTTCATTTC
1 TTGCGATTTTCATT-TCGCGTTGCGATAGTCATTTC
45840 AACCAAAAGA
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
33 26 0.41
35 2 0.03
38 1 0.02
39 16 0.25
40 18 0.29
ACGTcount: A:0.10, C:0.24, G:0.19, T:0.46
Consensus pattern (39 bp):
TTGCGATTTTCATTTCGCGTTGCGATAGTCATTTCCGCG
Found at i:47719 original size:94 final size:93
Alignment explanation
Indices: 47528--47903 Score: 625
Period size: 94 Copynumber: 4.1 Consensus size: 93
47518 TAGATTGCTT
* *
47528 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
47589 ATTTGTCTTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGA
47618 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
47683 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
*
47712 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
47777 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * * *
47806 AGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
47871 ATTTGTCTTTGTTTTTTCTTTTGGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
47899 AGTAA
1 AGTAA
47904 TGCAATCCAT
Statistics
Matches: 274, Mismatches: 7, Indels: 7
0.95 0.02 0.02
Matches are distributed among these distances:
90 35 0.13
92 3 0.01
93 28 0.10
94 208 0.76
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.47
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:48021 original size:20 final size:20
Alignment explanation
Indices: 47996--48057 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
47986 TTTTAGTTGA
47996 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
* * *
48016 AATGAAAATTGCAATGCGA-
1 AATGAAAATCGCAACGAGAG
*
48035 AACGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
48055 AAT
1 AAT
48058 CGCAACGACA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
19 15 0.45
20 18 0.55
ACGTcount: A:0.50, C:0.15, G:0.23, T:0.13
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:48060 original size:14 final size:14
Alignment explanation
Indices: 48039--48078 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
48029 ATGCGAAACG
*
48039 AAAATCGCAACGAG
1 AAAATCGCAACGAC
*
48053 AGAATCGCAACGAC
1 AAAATCGCAACGAC
48067 AAAATCGCAACG
1 AAAATCGCAACG
48079 CGAAACCAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.47, C:0.25, G:0.20, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:48092 original size:20 final size:20
Alignment explanation
Indices: 48067--48124 Score: 116
Period size: 20 Copynumber: 2.9 Consensus size: 20
48057 TCGCAACGAC
48067 AAAATCGCAACGCGAAACCA
1 AAAATCGCAACGCGAAACCA
48087 AAAATCGCAACGCGAAACCA
1 AAAATCGCAACGCGAAACCA
48107 AAAATCGCAACGCGAAAC
1 AAAATCGCAACGCGAAAC
48125 TATAATCGCG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.50, C:0.29, G:0.16, T:0.05
Consensus pattern (20 bp):
AAAATCGCAACGCGAAACCA
Found at i:48152 original size:19 final size:19
Alignment explanation
Indices: 48130--48288 Score: 158
Period size: 19 Copynumber: 8.8 Consensus size: 19
48120 GAAACTATAA
48130 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
48149 TCGCATTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
48163 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
48182 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
48196 TCTCGTTGCGATTTTCGTT
1 TCGCGTTGCGATTTTCATT
*
48215 TCGCGTTGCGATTTTCGTT
1 TCGCGTTGCGATTTTCATT
48234 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
48253 TCGCGTTGCGATAGTCATTTT
1 TCGCGTTGCGATTTTCA--TT
*
48274 TCACGTTGCGATTTT
1 TCGCGTTGCGATTTT
48289 AAGTTCCAGA
Statistics
Matches: 116, Mismatches: 12, Indels: 22
0.77 0.08 0.15
Matches are distributed among these distances:
14 19 0.16
16 6 0.05
17 6 0.05
19 71 0.61
21 14 0.12
ACGTcount: A:0.10, C:0.22, G:0.22, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:48173 original size:14 final size:14
Alignment explanation
Indices: 48154--48208 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
48144 TCATTTCGCA
48154 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
48168 TTGCGATTTTCATTTCGCG
1 TTGCGA--TTC---TCTCG
48187 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
48201 TTGCGATT
1 TTGCGATT
48209 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:48175 original size:33 final size:33
Alignment explanation
Indices: 48133--48264 Score: 192
Period size: 33 Copynumber: 3.8 Consensus size: 33
48123 ACTATAATCG
*
48133 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
48166 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
* *
48199 CGTTGCGATTTTCGTTTCGCGTTGCGATTTTCGTTTCG
1 CGTTGCGATTTTCATTTCGCGTTGCGA--TTC---TCT
48237 CGTTGCGATTTTCATTTCGCGTTGCGAT
1 CGTTGCGATTTTCATTTCGCGTTGCGAT
48265 AGTCATTTTT
Statistics
Matches: 90, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
33 58 0.64
35 3 0.03
36 1 0.01
38 28 0.31
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:48765 original size:42 final size:42
Alignment explanation
Indices: 48719--48807 Score: 101
Period size: 42 Copynumber: 2.1 Consensus size: 42
48709 CCTATCGTTG
* *
48719 AAGAGGCCCCTATCATTCCTCG-AGA-GTCCCCTCCCACCATTT
1 AAGAGGCCACTATCA-TCCTCGAAGAGGT-CCCTCCCACCATTC
* * *
48761 AAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCACCATTC
1 AAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCACCATTC
48803 AAGAG
1 AAGAG
48808 CCCGATTCAC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
41 4 0.10
42 34 0.85
43 2 0.05
ACGTcount: A:0.25, C:0.35, G:0.19, T:0.21
Consensus pattern (42 bp):
AAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCACCATTC
Found at i:48806 original size:21 final size:20
Alignment explanation
Indices: 48747--48807 Score: 50
Period size: 21 Copynumber: 3.0 Consensus size: 20
48737 CTCGAGAGTC
*
48747 CCCTCCCACCATTTAAGAGG
1 CCCTCCCACCATTCAAGAGG
** * * *
48767 CCACTGTCATCGTTGAAGAGG
1 CC-CTCCCACCATTCAAGAGG
48788 TCCCTCCCACCATTCAAGAG
1 -CCCTCCCACCATTCAAGAG
48808 CCCGATTCAC
Statistics
Matches: 29, Mismatches: 10, Indels: 3
0.69 0.24 0.07
Matches are distributed among these distances:
20 2 0.07
21 25 0.86
22 2 0.07
ACGTcount: A:0.25, C:0.36, G:0.18, T:0.21
Consensus pattern (20 bp):
CCCTCCCACCATTCAAGAGG
Found at i:50169 original size:14 final size:14
Alignment explanation
Indices: 50150--50185 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
50140 ATTGTTTAAT
50150 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
50164 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
50178 TGATTTGT
1 TGATTTGT
50186 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:50342 original size:33 final size:33
Alignment explanation
Indices: 50300--50371 Score: 117
Period size: 33 Copynumber: 2.2 Consensus size: 33
50290 CTATCGCAAT
* * *
50300 GCGAAATGAAAATCGTAACGAGAGAATCACAAC
1 GCGAAATGAAAATCGCAACGAAAAAATCACAAC
50333 GCGAAATGAAAATCGCAACGAAAAAATCACAAC
1 GCGAAATGAAAATCGCAACGAAAAAATCACAAC
50366 GCGAAA
1 GCGAAA
50372 CTAAATTCGC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.51, C:0.19, G:0.19, T:0.10
Consensus pattern (33 bp):
GCGAAATGAAAATCGCAACGAAAAAATCACAAC
Found at i:50425 original size:33 final size:33
Alignment explanation
Indices: 50381--50507 Score: 200
Period size: 33 Copynumber: 3.8 Consensus size: 33
50371 ACTAAATTCG
* * *
50381 CGTTGCAATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
50414 CGTTGCGATTTTCATTTCGCATTGTGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
50447 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
**
50480 CGTTATGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
50508 AGTCATTTCC
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 87 1.00
ACGTcount: A:0.13, C:0.23, G:0.17, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:50473 original size:19 final size:19
Alignment explanation
Indices: 50416--50527 Score: 73
Period size: 19 Copynumber: 6.4 Consensus size: 19
50406 GATTCCCTCG
50416 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
50435 TTGTGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
50449 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
50468 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
**
50482 TTATGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
** *
50501 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCA
50521 TTGCGAT
1 TTGCGAT
50528 AGATATTAAG
Statistics
Matches: 69, Mismatches: 13, Indels: 21
0.67 0.13 0.20
Matches are distributed among these distances:
14 9 0.13
16 14 0.20
17 14 0.20
19 22 0.32
20 10 0.14
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:50526 original size:20 final size:20
Alignment explanation
Indices: 50491--50573 Score: 64
Period size: 20 Copynumber: 4.2 Consensus size: 20
50481 GTTATGATTT
*
50491 TCATTT-CGCATTGCGATAG
1 TCATTTCCGCGTTGCGATAG
50510 TCATTTCCGCGTTGCGATAG
1 TCATTTCCGCGTTGCGATAG
** * *
50530 --ATATTAAGATGATTGCGAAAG
1 TCAT-TTCCG-CG-TTGCGATAG
*
50551 TCATTTCCGTGTTGCGATAG
1 TCATTTCCGCGTTGCGATAG
50571 TCA
1 TCA
50574 AATAAATGCC
Statistics
Matches: 50, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
18 2 0.04
19 9 0.18
20 24 0.48
21 10 0.20
22 3 0.06
23 2 0.04
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (20 bp):
TCATTTCCGCGTTGCGATAG
Found at i:53076 original size:24 final size:24
Alignment explanation
Indices: 53042--53095 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
53032 CTGAAAAATC
53042 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
53066 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
53090 ATCAAA
1 ATCAAA
53096 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:53109 original size:24 final size:24
Alignment explanation
Indices: 53042--53109 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
53032 CTGAAAAATC
* * *
53042 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
53066 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
53090 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
53110 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:53995 original size:21 final size:21
Alignment explanation
Indices: 53971--54047 Score: 136
Period size: 21 Copynumber: 3.7 Consensus size: 21
53961 GTGATTACAT
*
53971 AAATCGCAATGCGAATTAGGA
1 AAATCGCAATGCGAATTAGGG
53992 AAATCGCAATGCGAATTAGGG
1 AAATCGCAATGCGAATTAGGG
*
54013 AAATCGCAATGCGAATTTGGG
1 AAATCGCAATGCGAATTAGGG
54034 AAATCGCAATGCGA
1 AAATCGCAATGCGA
54048 TAGTCAGAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 54 1.00
ACGTcount: A:0.39, C:0.16, G:0.26, T:0.19
Consensus pattern (21 bp):
AAATCGCAATGCGAATTAGGG
Found at i:76950 original size:25 final size:25
Alignment explanation
Indices: 76921--76975 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
76911 CATTCAGTCA
76921 TAATTATTTACTTATTTTATCAATT
1 TAATTATTTACTTATTTTATCAATT
76946 TAATTATTTACTTATTTTATCAATT
1 TAATTATTTACTTATTTTATCAATT
76971 TAATT
1 TAATT
76976 TTAATATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (25 bp):
TAATTATTTACTTATTTTATCAATT
Found at i:76987 original size:25 final size:25
Alignment explanation
Indices: 76921--77005 Score: 93
Period size: 25 Copynumber: 3.4 Consensus size: 25
76911 CATTCAGTCA
*
76921 TAATTATTTACTTATTTTATCAATT
1 TAATTATTTACTAATTTTATCAATT
*
76946 TAATTATTTACTTATTTTATCAATT
1 TAATTATTTACTAATTTTATCAATT
* *
76971 TAATT-TTAATA-TAATTTAATAAATT
1 TAATTATT--TACTAATTTTATCAATT
76996 TAATTGATTT
1 TAATT-ATTT
77006 GAGGAAAATT
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
24 2 0.04
25 47 0.89
26 2 0.04
27 2 0.04
ACGTcount: A:0.36, C:0.05, G:0.01, T:0.58
Consensus pattern (25 bp):
TAATTATTTACTAATTTTATCAATT
Found at i:90705 original size:20 final size:20
Alignment explanation
Indices: 90682--90722 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
90672 CAGTTGATGG
90682 AGCTCGATTCACCAAATAAC
1 AGCTCGATTCACCAAATAAC
90702 AGCTCGATTCACCAAATAAC
1 AGCTCGATTCACCAAATAAC
90722 A
1 A
90723 AGCGGTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.29, G:0.10, T:0.20
Consensus pattern (20 bp):
AGCTCGATTCACCAAATAAC
Done.