Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004355.1 Hibiscus syriacus cultivar Beakdansim tig00009543_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: 77783
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:73 original size:21 final size:21
Alignment explanation
Indices: 47--88 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
37 GGGTTCAACG
*
47 TGGTCCTTTGGGACATATCTA
1 TGGTCCTTCGGGACATATCTA
*
68 TGGTCCTTCGGGACATTTCTA
1 TGGTCCTTCGGGACATATCTA
89 CGTGGCACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.38
Consensus pattern (21 bp):
TGGTCCTTCGGGACATATCTA
Found at i:2614 original size:20 final size:20
Alignment explanation
Indices: 2585--2631 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
2575 ATTCCATCAC
*
2585 ATGCAACTATATGCTTCTAA
1 ATGCAACTATATGCTCCTAA
* *
2605 ATGCATCTATATGGTCCTAA
1 ATGCAACTATATGCTCCTAA
2625 ATG-AACT
1 ATGCAACT
2632 TTTAGACAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (20 bp):
ATGCAACTATATGCTCCTAA
Found at i:12710 original size:28 final size:28
Alignment explanation
Indices: 12666--12768 Score: 154
Period size: 28 Copynumber: 3.6 Consensus size: 28
12656 TCCACATTCG
*
12666 AAAATTTCCA-AATTGTCATTTTTTCACA
1 AAAATTCCCAGAA-TGTCATTTTTTCACA
* *
12694 AAAATTCCCAGAATGTCACCTTTTCCACA
1 AAAATTCCCAGAATGTCA-TTTTTTCACA
12723 AAAATTCCCAGAATGTCATTTTTTCACA
1 AAAATTCCCAGAATGTCATTTTTTCACA
12751 AAAATTCCCAGAATGTCA
1 AAAATTCCCAGAATGTCA
12769 CTGGGTCGGG
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
28 40 0.59
29 28 0.41
ACGTcount: A:0.37, C:0.23, G:0.07, T:0.33
Consensus pattern (28 bp):
AAAATTCCCAGAATGTCATTTTTTCACA
Found at i:12799 original size:17 final size:18
Alignment explanation
Indices: 12771--12808 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
12761 GAATGTCACT
*
12771 GGGTCGGGTCAACGGGTC
1 GGGTCGGGTCAACGAGTC
12789 GGGTC-GGTCAACGAGTC
1 GGGTCGGGTCAACGAGTC
12806 GGG
1 GGG
12809 CCGAGTCGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.13, C:0.21, G:0.50, T:0.16
Consensus pattern (18 bp):
GGGTCGGGTCAACGAGTC
Found at i:12838 original size:19 final size:19
Alignment explanation
Indices: 12814--12853 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
12804 TCGGGCCGAG
12814 TCGGACCGGTCAAACCGGT
1 TCGGACCGGTCAAACCGGT
* *
12833 TCGGACCGGTTAAATCGGT
1 TCGGACCGGTCAAACCGGT
12852 TC
1 TC
12854 AGACTGGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.20, C:0.28, G:0.30, T:0.23
Consensus pattern (19 bp):
TCGGACCGGTCAAACCGGT
Found at i:14519 original size:21 final size:21
Alignment explanation
Indices: 14495--14543 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
14485 ATTGTCTTCG
14495 TTGTTGCAATAAACTCTTGCA
1 TTGTTGCAATAAACTCTTGCA
14516 TTGTTGCAATAAACTCTTGCA
1 TTGTTGCAATAAACTCTTGCA
14537 TTGTTGC
1 TTGTTGC
14544 CTCCAAAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.41
Consensus pattern (21 bp):
TTGTTGCAATAAACTCTTGCA
Found at i:20535 original size:15 final size:15
Alignment explanation
Indices: 20494--20535 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
20484 AAAGTACAAT
*
20494 AATTAAAATTAAACA
1 AATTAAAATTATACA
*
20509 AATTAAAA-TATATA
1 AATTAAAATTATACA
*
20523 GATTAAAATTATA
1 AATTAAAATTATA
20536 ACCTACACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (15 bp):
AATTAAAATTATACA
Found at i:24108 original size:21 final size:21
Alignment explanation
Indices: 24065--24109 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
24055 TATCGCATTA
**
24065 CGATTTCCCAAATTCGCGTTG
1 CGATTTCCCAAATTCGCAATG
* *
24086 CGATTTTCCTAATTCGCAATG
1 CGATTTCCCAAATTCGCAATG
24107 CGA
1 CGA
24110 ATACGTAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.18, T:0.33
Consensus pattern (21 bp):
CGATTTCCCAAATTCGCAATG
Found at i:24124 original size:20 final size:20
Alignment explanation
Indices: 24099--24192 Score: 125
Period size: 20 Copynumber: 4.7 Consensus size: 20
24089 TTTTCCTAAT
24099 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * ** *
24119 TCGCAACGTGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
24140 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
24160 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
24180 TCGCAATGCGAAT
1 TCGCAATGCGAAT
24193 CTGACTATCG
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:24144 original size:41 final size:40
Alignment explanation
Indices: 24099--24192 Score: 125
Period size: 41 Copynumber: 2.3 Consensus size: 40
24089 TTTTCCTAAT
* **
24099 TCGCAATGCGAATACGTAAATCGCAACGTGAATTTGGAAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAA-TACGAAAA
* * *
24140 TCGCAATGCGATTACGTAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAATACGAAAA
24180 TCGCAATGCGAAT
1 TCGCAATGCGAAT
24193 CTGACTATCG
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 17 0.37
41 29 0.63
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.22
Consensus pattern (40 bp):
TCGCAATGCGAATACGTAAATCGCAACGCGAATACGAAAA
Found at i:24172 original size:61 final size:60
Alignment explanation
Indices: 24099--24212 Score: 174
Period size: 61 Copynumber: 1.9 Consensus size: 60
24089 TTTTCCTAAT
* *
24099 TCGCAATGCGAATACGTAAATCGCAACGTGAATTTGGAAAATCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAATCT-GAAAATCGCAATGCGATTACGTAAA
* **
24160 TCGCAATGCGAATACGTAAATCGCAATGCGAATCTGACTATCGCAATGCGATT
1 TCGCAATGCGAATACGTAAATCGCAACGCGAATCTGAAAATCGCAATGCGATT
24213 TACATAGCGC
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
60 16 0.33
61 32 0.67
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (60 bp):
TCGCAATGCGAATACGTAAATCGCAACGCGAATCTGAAAATCGCAATGCGATTACGTAAA
Found at i:24813 original size:20 final size:20
Alignment explanation
Indices: 24759--24814 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
24749 TGAAACCGAG
*
24759 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAATGCGAA
24779 AATGACTATCGCAATGCGAA
1 AATGACTATCGCAATGCGAA
**
24799 TTTGACTATCGCAATG
1 AATGACTATCGCAATG
24815 AGAGAATCGC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (20 bp):
AATGACTATCGCAATGCGAA
Found at i:24882 original size:20 final size:20
Alignment explanation
Indices: 24838--24902 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
24828 GCGATTTTCA
* * *
24838 TTTCACGTTGCGATAGTTAA
1 TTTCGCGTTGCGATAGTCAT
*
24858 ATTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* * **
24878 TTTCGTGTTGTGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
24898 TTTCG
1 TTTCG
24903 TGTTACGATT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.15, G:0.22, T:0.46
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:24912 original size:20 final size:20
Alignment explanation
Indices: 24874--24913 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
24864 GTTGCGATAG
**
24874 TCATTTTCGTGTTGTGATTT
1 TCATTTTCGTGTTACGATTT
24894 TCATTTTCGTGTTACGATTT
1 TCATTTTCGTGTTACGATTT
24914 AAAGTTTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.17, T:0.57
Consensus pattern (20 bp):
TCATTTTCGTGTTACGATTT
Found at i:26810 original size:20 final size:20
Alignment explanation
Indices: 26785--26874 Score: 135
Period size: 20 Copynumber: 4.5 Consensus size: 20
26775 AGAATAGTTT
*
26785 ACTATCGCAATACGAAAATG
1 ACTATCGCAATGCGAAAATG
*
26805 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
26825 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
** *
26845 ACTATCGCAATGCGAATTTA
1 ACTATCGCAATGCGAAAATG
26865 ACTATCGCAA
1 ACTATCGCAA
26875 CGAAAGAATC
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.21
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:26946 original size:20 final size:20
Alignment explanation
Indices: 26921--27029 Score: 122
Period size: 20 Copynumber: 5.8 Consensus size: 20
26911 GATTCTCTCG
*
26921 TTGCGATAGTCATTTTCGTA
1 TTGCGATAGTCATTTTCGCA
*
26941 TTGCGATAGTCATTTTTGCA
1 TTGCGATAGTCATTTTCGCA
*
26961 TTGTGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
26981 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
**
26995 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
27015 TTGCGATAGTCATTT
1 TTGCGATAGTCATTT
27030 GCATATTCTA
Statistics
Matches: 73, Mismatches: 10, Indels: 12
0.77 0.11 0.13
Matches are distributed among these distances:
14 7 0.10
16 6 0.08
18 5 0.07
20 55 0.75
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.42
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:27013 original size:34 final size:34
Alignment explanation
Indices: 26902--27021 Score: 123
Period size: 34 Copynumber: 3.4 Consensus size: 34
26892 GAAATGAAAA
*
26902 TCGCATTGTGATTCTCTCGTTGCGATAGTCATTT
1 TCGCATTGCGATTCTCTCGTTGCGATAGTCATTT
* * * *
26936 TCGTATTGCGATAGTCATTTTTGCATTGTGATAGTCATTT
1 TCGCATTGCGAT--TC---TCT-CGTTGCGATAGTCATTT
**
26976 TCGCATTGCGATTCTCTCGTTGCGATAGTCAAAT
1 TCGCATTGCGATTCTCTCGTTGCGATAGTCATTT
27010 TCGCATTGCGAT
1 TCGCATTGCGAT
27022 AGTCATTTGC
Statistics
Matches: 69, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
34 35 0.51
35 2 0.03
36 2 0.03
38 2 0.03
39 2 0.03
40 26 0.38
ACGTcount: A:0.18, C:0.19, G:0.21, T:0.42
Consensus pattern (34 bp):
TCGCATTGCGATTCTCTCGTTGCGATAGTCATTT
Found at i:27598 original size:21 final size:21
Alignment explanation
Indices: 27503--27610 Score: 85
Period size: 21 Copynumber: 5.1 Consensus size: 21
27493 GTCCGACTCA
*
27503 CCTGTCATCGTTCAGGAGGCC
1 CCTGTCATCGTTCAAGAGGCC
**
27524 TCCCCT-ATCGTTCAAGAGGCC
1 -CCTGTCATCGTTCAAGAGGCC
* ** *
27545 CCTATCATCCCTCAAGAGTCC
1 CCTGTCATCGTTCAAGAGGCC
*
27566 CCT-TCCACCGTTCAAGAGGCC
1 CCTGT-CATCGTTCAAGAGGCC
* * *
27587 ACTGTCATCGTTGAAGAGGTC
1 CCTGTCATCGTTCAAGAGGCC
27608 CCT
1 CCT
27611 CCCAACATTC
Statistics
Matches: 66, Mismatches: 17, Indels: 7
0.73 0.19 0.08
Matches are distributed among these distances:
20 4 0.06
21 58 0.88
22 4 0.06
ACGTcount: A:0.19, C:0.36, G:0.20, T:0.24
Consensus pattern (21 bp):
CCTGTCATCGTTCAAGAGGCC
Found at i:28992 original size:14 final size:14
Alignment explanation
Indices: 28973--29008 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
28963 ATTGTTTAAT
28973 TGATTTGTAAACGA
1 TGATTTGTAAACGA
* *
28987 TGATTTGTAAATGT
1 TGATTTGTAAACGA
29001 TGATTTGT
1 TGATTTGT
29009 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:0.28, C:0.03, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAACGA
Found at i:29160 original size:33 final size:33
Alignment explanation
Indices: 29121--29188 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
29111 TCGCAACACG
**
29121 GAAATGACTATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAATGC
*
29154 GAAATGAAAATCGCAACGAGTGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAATGC
29187 GA
1 GA
29189 TTCTCTCGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.41, C:0.19, G:0.25, T:0.15
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAATGC
Found at i:29261 original size:20 final size:19
Alignment explanation
Indices: 29195--29286 Score: 105
Period size: 19 Copynumber: 4.7 Consensus size: 19
29185 GCGATTCTCT
*
29195 CGTTGTGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
29214 CGTTGCGATAGTCAATTC-
1 CGTTGCGATAGTCATTTCG
*
29232 CGCATGCGATAGTCATTTCCG
1 CG-TTGCGATAGTCATTT-CG
* *
29253 TGTTGCGATAGTCATATTTG
1 CGTTGCGATAGTCAT-TTCG
29273 CGTTGCGATAGTCA
1 CGTTGCGATAGTCA
29287 AATGATTGTC
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
18 2 0.03
19 29 0.48
20 27 0.44
21 3 0.05
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:32235 original size:12 final size:12
Alignment explanation
Indices: 32220--32246 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
32210 AGGAACGGAT
32220 GTGCCGGAGAGA
1 GTGCCGGAGAGA
32232 GTGCCGGAGAGA
1 GTGCCGGAGAGA
32244 GTG
1 GTG
32247 GAGATGGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.15, G:0.52, T:0.11
Consensus pattern (12 bp):
GTGCCGGAGAGA
Found at i:32428 original size:20 final size:20
Alignment explanation
Indices: 32405--32494 Score: 101
Period size: 20 Copynumber: 4.5 Consensus size: 20
32395 CAGAATCTCG
32405 TTGCGATTTACAAATTCGCA
1 TTGCGATTTACAAATTCGCA
* *
32425 TTGCGATTAACGTAA-TCGCA
1 TTGCGATTTAC-AAATTCGCA
* *
32445 TTGCGATTTTCCAAATTCGCG
1 TTGCGA-TTTACAAATTCGCA
* *
32466 TTGCAATTTACATATTCGCA
1 TTGCGATTTACAAATTCGCA
32486 TTGCGATTT
1 TTGCGATTT
32495 TCCATTTCGC
Statistics
Matches: 56, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
20 42 0.75
21 14 0.25
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.38
Consensus pattern (20 bp):
TTGCGATTTACAAATTCGCA
Found at i:32460 original size:41 final size:41
Alignment explanation
Indices: 32405--32498 Score: 127
Period size: 41 Copynumber: 2.3 Consensus size: 41
32395 CAGAATCTCG
* * *
32405 TTGCGA-TTTACAAATTCGCATTGCGATTAACGTAATCGCA
1 TTGCGATTTTCCAAATTCGCATTGCAATTAACATAATCGCA
* * *
32445 TTGCGATTTTCCAAATTCGCGTTGCAATTTACATATTCGCA
1 TTGCGATTTTCCAAATTCGCATTGCAATTAACATAATCGCA
32486 TTGCGATTTTCCA
1 TTGCGATTTTCCA
32499 TTTCGCAACG
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 6 0.13
41 41 0.87
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (41 bp):
TTGCGATTTTCCAAATTCGCATTGCAATTAACATAATCGCA
Found at i:32503 original size:20 final size:20
Alignment explanation
Indices: 32440--32505 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 20
32430 ATTAACGTAA
*
32440 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCC-ATT
* * *
32461 TCGCGTTGC-AATTTACATAT
1 TCGCATTGCGATTTTCCAT-T
32481 TCGCATTGCGATTTTCCATT
1 TCGCATTGCGATTTTCCATT
32501 TCGCA
1 TCGCA
32506 ACGCGAATTT
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
19 1 0.03
20 20 0.56
21 15 0.42
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTTCCATT
Found at i:32945 original size:32 final size:31
Alignment explanation
Indices: 32894--32954 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
32884 TTTTTAAATA
** *
32894 ATTATAAAATGTTTATTAAAATTTATCAAACT
1 ATTATAAAATAATTATT-AAACTTATCAAACT
*
32926 ATTATAAAATAATTCTTAAACTTATCAAA
1 ATTATAAAATAATTATTAAACTTATCAAA
32955 ATTTATGGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 11 0.44
32 14 0.56
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.41
Consensus pattern (31 bp):
ATTATAAAATAATTATTAAACTTATCAAACT
Found at i:34247 original size:31 final size:31
Alignment explanation
Indices: 34206--34288 Score: 94
Period size: 32 Copynumber: 2.6 Consensus size: 31
34196 TAATTGTCAA
*
34206 AATTTTATAAATTTAATGATCATTTTATAAC
1 AATTTCATAAATTTAATGATCATTTTATAAC
* * * *
34237 AATTTGATAAATTTATATAATCGTTTTATAAT
1 AATTTCATAAATTTA-ATGATCATTTTATAAC
* *
34269 AACTCCATAAATTTAATGAT
1 AATTTCATAAATTTAATGAT
34289 TTATAGGATA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
31 18 0.42
32 25 0.58
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (31 bp):
AATTTCATAAATTTAATGATCATTTTATAAC
Found at i:34467 original size:31 final size:31
Alignment explanation
Indices: 34426--34508 Score: 94
Period size: 32 Copynumber: 2.6 Consensus size: 31
34416 TAATTGTCAA
*
34426 AATTTTATAAATTTAATGATCATTTTATAAC
1 AATTTCATAAATTTAATGATCATTTTATAAC
* * * *
34457 AATTTGATAAATTTATATAATCGTTTTATAAT
1 AATTTCATAAATTTA-ATGATCATTTTATAAC
* *
34489 AACTCCATAAATTTAATGAT
1 AATTTCATAAATTTAATGAT
34509 TTTTAAAAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
31 18 0.42
32 25 0.58
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (31 bp):
AATTTCATAAATTTAATGATCATTTTATAAC
Found at i:46147 original size:15 final size:16
Alignment explanation
Indices: 46117--46151 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
46107 CTGTCAAACT
46117 AAACATTAACAATAAA
1 AAACATTAACAATAAA
*
46133 AAACA-TAATAATAAA
1 AAACATTAACAATAAA
46148 AAAC
1 AAAC
46152 GAGGGTCAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.71, C:0.11, G:0.00, T:0.17
Consensus pattern (16 bp):
AAACATTAACAATAAA
Found at i:50656 original size:2 final size:2
Alignment explanation
Indices: 50649--50684 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
50639 ACCCAAAGAA
50649 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
50685 TGGATGTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53940 original size:21 final size:21
Alignment explanation
Indices: 53914--53957 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
53904 CGATATTTGG
53914 TGCATCAATGCACTGTAGCAA
1 TGCATCAATGCACTGTAGCAA
* * *
53935 TGCATCGATGCATTGTATCAA
1 TGCATCAATGCACTGTAGCAA
53956 TG
1 TG
53958 TTTATTACTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (21 bp):
TGCATCAATGCACTGTAGCAA
Found at i:57088 original size:4 final size:4
Alignment explanation
Indices: 57081--57123 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
57071 ATAAAGGAAT
* * * *
57081 CATA CATA CATG CATA CATG CATA CATG CATT CATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CAT
57124 GTTTGTAATT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.40, C:0.26, G:0.07, T:0.28
Consensus pattern (4 bp):
CATA
Found at i:57098 original size:8 final size:8
Alignment explanation
Indices: 57085--57124 Score: 62
Period size: 8 Copynumber: 5.0 Consensus size: 8
57075 AGGAATCATA
57085 CATACATG
1 CATACATG
57093 CATACATG
1 CATACATG
57101 CATACATG
1 CATACATG
* *
57109 CATTCATA
1 CATACATG
57117 CATACATG
1 CATACATG
57125 TTTGTAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.38, C:0.25, G:0.10, T:0.28
Consensus pattern (8 bp):
CATACATG
Found at i:57106 original size:16 final size:16
Alignment explanation
Indices: 57081--57124 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
57071 ATAAAGGAAT
57081 CATACATACATGCATA
1 CATACATACATGCATA
* *
57097 CATGCATACATGCATT
1 CATACATACATGCATA
57113 CATACATACATG
1 CATACATACATG
57125 TTTGTAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.39, C:0.25, G:0.09, T:0.27
Consensus pattern (16 bp):
CATACATACATGCATA
Found at i:58301 original size:2 final size:2
Alignment explanation
Indices: 58294--58325 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
58284 TTAGAGGATA
58294 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
58326 GCATGTTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:66784 original size:18 final size:18
Alignment explanation
Indices: 66761--66796 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
66751 GCCAGATAAT
66761 CAAACTACCTGATAGCTG
1 CAAACTACCTGATAGCTG
66779 CAAACTACCTGATAGCTG
1 CAAACTACCTGATAGCTG
66797 TTCGGGCCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (18 bp):
CAAACTACCTGATAGCTG
Found at i:67217 original size:16 final size:16
Alignment explanation
Indices: 67196--67226 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
67186 GTTATGACCC
*
67196 AAGAGAATCGGAGAAG
1 AAGAGAATCGAAGAAG
67212 AAGAGAATCGAAGAA
1 AAGAGAATCGAAGAA
67227 ATAGAAATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.06, G:0.32, T:0.06
Consensus pattern (16 bp):
AAGAGAATCGAAGAAG
Found at i:74822 original size:8 final size:8
Alignment explanation
Indices: 74811--74842 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
74801 AACGTCATCT
*
74811 CTTCTCCT
1 CTTCTCCC
74819 CTTCTCCC
1 CTTCTCCC
74827 CTTCTCCC
1 CTTCTCCC
74835 CTTCTCCC
1 CTTCTCCC
74843 TTCCGTCTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (8 bp):
CTTCTCCC
Done.