Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008618.1 Hibiscus syriacus cultivar Beakdansim tig00111576_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: 85714
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2023 original size:34 final size:35
Alignment explanation
Indices: 1961--2069 Score: 150
Period size: 35 Copynumber: 3.1 Consensus size: 35
1951 CAACTTTGAA
1961 AAAATGGTTTTCAAAGTTTGGTAGATGTTTCTTTG
1 AAAATGGTTTTCAAAGTTTGGTAGATGTTTCTTTG
*
1996 AAAATGGTTTTCAAA-TTTGGTAAATGTTTCTTTG
1 AAAATGGTTTTCAAAGTTTGGTAGATGTTTCTTTG
** *
2030 AAAAATAATTTTTCAAAGTTTGGTAGATGTTT-GTTG
1 -AAAAT-GGTTTTCAAAGTTTGGTAGATGTTTCTTTG
2066 AAAA
1 AAAA
2070 ATGATAATGG
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
34 18 0.27
35 24 0.36
36 11 0.17
37 13 0.20
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (35 bp):
AAAATGGTTTTCAAAGTTTGGTAGATGTTTCTTTG
Found at i:5111 original size:21 final size:20
Alignment explanation
Indices: 5054--5111 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
5044 ATTTACCGTG
* *
5054 ATTGCGGCCGTCGTCGGTGTT
1 ATTGCGGCCGTCG-CGGCGCT
* * *
5075 ATTGTGGTCGTTGCGGACGCT
1 ATTGCGGCCGTCGCGG-CGCT
5096 ATTGCGGCCGTCGCGG
1 ATTGCGGCCGTCGCGG
5112 GTAACTCGGA
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
20 3 0.11
21 25 0.89
ACGTcount: A:0.07, C:0.24, G:0.40, T:0.29
Consensus pattern (20 bp):
ATTGCGGCCGTCGCGGCGCT
Found at i:16353 original size:27 final size:26
Alignment explanation
Indices: 16306--16358 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
16296 CCCTCGAGCC
16306 TCCATCCCCAAATCCTCCCCTCTCTCG
1 TCCATCCCCAAATCCTCCCCTC-CTCG
* *
16333 TCCATTCCC-AATCTCTTCCCTCCTCG
1 TCCATCCCCAAATC-CTCCCCTCCTCG
16359 CCGTTCTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 8 0.35
27 15 0.65
ACGTcount: A:0.13, C:0.53, G:0.04, T:0.30
Consensus pattern (26 bp):
TCCATCCCCAAATCCTCCCCTCCTCG
Found at i:20792 original size:24 final size:24
Alignment explanation
Indices: 20760--20809 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
20750 ATTCTTTCGT
20760 TTCAATTGAGCTCAAATTTTAGGC
1 TTCAATTGAGCTCAAATTTTAGGC
20784 TTCAATTGAGCTCAAATTTTAGGC
1 TTCAATTGAGCTCAAATTTTAGGC
20808 TT
1 TT
20810 TAATCAAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (24 bp):
TTCAATTGAGCTCAAATTTTAGGC
Found at i:21069 original size:30 final size:30
Alignment explanation
Indices: 21035--21095 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
21025 AGTGAACCAG
*
21035 CGGTTCAAACCGATTTTACCGGTTTTCAGC
1 CGGTTCAAACCGATTTTACCAGTTTTCAGC
** * *
21065 CGGTTCACCCCGGTTTTCCCAGTTTTCAGC
1 CGGTTCAAACCGATTTTACCAGTTTTCAGC
21095 C
1 C
21096 AGTTTTTCCT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.15, C:0.33, G:0.20, T:0.33
Consensus pattern (30 bp):
CGGTTCAAACCGATTTTACCAGTTTTCAGC
Found at i:26132 original size:14 final size:14
Alignment explanation
Indices: 26081--26191 Score: 57
Period size: 14 Copynumber: 7.9 Consensus size: 14
26071 GTGCATAACT
*
26081 TAAACCCTAAACCC
1 TAAACTCTAAACCC
* **
26095 TAAACTCTTAACATA
1 TAAACTCTAAAC-CC
26110 TAAACTCTAAACCC
1 TAAACTCTAAACCC
* **
26124 TAAATTCTAAACTT
1 TAAACTCTAAACCC
* **
26138 TAAA-TCCT-ATCATA
1 TAAACT-CTAAAC-CC
*
26152 TAAACCCTAAACCC
1 TAAACTCTAAACCC
*
26166 TAATA-TATAAACCC
1 TAA-ACTCTAAACCC
26180 TAAACTCTAAAC
1 TAAACTCTAAAC
26192 ATTAAATCAT
Statistics
Matches: 71, Mismatches: 19, Indels: 14
0.68 0.18 0.13
Matches are distributed among these distances:
13 4 0.06
14 53 0.75
15 14 0.20
ACGTcount: A:0.45, C:0.28, G:0.00, T:0.27
Consensus pattern (14 bp):
TAAACTCTAAACCC
Found at i:26136 original size:21 final size:21
Alignment explanation
Indices: 26088--26190 Score: 77
Period size: 21 Copynumber: 4.9 Consensus size: 21
26078 ACTTAAACCC
*
26088 TAAACCCTAAACTCTTAACA-TA
1 TAAACCCTAAAC-CCTAA-ATTA
* *
26110 TAAACTCTAAACCCTAAATTC
1 TAAACCCTAAACCCTAAATTA
** * *
26131 TAAACTTTAAATCCTATCA-TA
1 TAAACCCTAAACCCTA-AATTA
26152 TAAACCCTAAACCCT-AATATA
1 TAAACCCTAAACCCTAAAT-TA
*
26173 TAAACCCTAAACTCTAAA
1 TAAACCCTAAACCCTAAA
26191 CATTAAATCA
Statistics
Matches: 64, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
19 1 0.02
20 1 0.02
21 48 0.75
22 14 0.22
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (21 bp):
TAAACCCTAAACCCTAAATTA
Found at i:26177 original size:56 final size:56
Alignment explanation
Indices: 26117--26224 Score: 180
Period size: 56 Copynumber: 1.9 Consensus size: 56
26107 ATATAAACTC
* * *
26117 TAAACCCTAAATTCTAAACTTTAAATCCTATCATATAAACCCTAAACCCTAATATA
1 TAAACCCTAAACTCTAAACATTAAATCATATCATATAAACCCTAAACCCTAATATA
*
26173 TAAACCCTAAACTCTAAACATTAAATCATTTCATATAAACCCTAAACCCTAA
1 TAAACCCTAAACTCTAAACATTAAATCATATCATATAAACCCTAAACCCTAA
26225 CCCTAAATCT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 48 1.00
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.29
Consensus pattern (56 bp):
TAAACCCTAAACTCTAAACATTAAATCATATCATATAAACCCTAAACCCTAATATA
Found at i:26191 original size:35 final size:35
Alignment explanation
Indices: 26152--26231 Score: 83
Period size: 35 Copynumber: 2.3 Consensus size: 35
26142 TCCTATCATA
* *
26152 TAAACCCTAAACCCTAAT-ATATAAACCCTAAACTC
1 TAAACCCTAAACCAT-ATCATATAAACCCTAAACCC
** * *
26187 TAAACATTAAATCATTTCATATAAACCCTAAACCC
1 TAAACCCTAAACCATATCATATAAACCCTAAACCC
26222 T-AACCCTAAA
1 TAAACCCTAAA
26232 TCTTAAATCA
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
34 8 0.22
35 28 0.78
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.25
Consensus pattern (35 bp):
TAAACCCTAAACCATATCATATAAACCCTAAACCC
Found at i:26238 original size:41 final size:41
Alignment explanation
Indices: 26172--26265 Score: 111
Period size: 41 Copynumber: 2.3 Consensus size: 41
26162 ACCCTAATAT
* *
26172 ATAAACCCTAAACTCTAAACATTAAATCAT-TTCATATAAACC
1 ATAAACCCT-AACCCTAAACATTAAATCATATT-ACATAAACC
* *
26214 CTAAACCCTAACCCTAAATC-TTAAATCATATTACATAAACT
1 ATAAACCCTAACCCTAAA-CATTAAATCATATTACATAAACC
26255 ATAAACCCTAA
1 ATAAACCCTAA
26266 ATTCTAAACC
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
41 34 0.76
42 11 0.24
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.28
Consensus pattern (41 bp):
ATAAACCCTAACCCTAAACATTAAATCATATTACATAAACC
Found at i:26699 original size:15 final size:14
Alignment explanation
Indices: 26673--26702 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
26663 TTTATTCATC
26673 AATAATGTATTTTT
1 AATAATGTATTTTT
*
26687 AATAATGTAATTTT
1 AATAATGTATTTTT
26701 AA
1 AA
26703 AAAATCTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
AATAATGTATTTTT
Found at i:26805 original size:5 final size:5
Alignment explanation
Indices: 26795--26845 Score: 66
Period size: 5 Copynumber: 9.4 Consensus size: 5
26785 CGTTAAGAAC
26795 TCGAG TCGAG TTCGAG CTCGAG TCGAG TCGAG TTCGAG CTCGAG TCGAG
1 TCGAG TCGAG -TCGAG -TCGAG TCGAG TCGAG -TCGAG -TCGAG TCGAG
26844 TC
1 TC
26846 TATTTGATCC
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
5 22 0.52
6 20 0.48
ACGTcount: A:0.18, C:0.24, G:0.35, T:0.24
Consensus pattern (5 bp):
TCGAG
Found at i:26823 original size:22 final size:22
Alignment explanation
Indices: 26795--26845 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
26785 CGTTAAGAAC
26795 TCGAGTCGAGTTCGAGCTCGAG
1 TCGAGTCGAGTTCGAGCTCGAG
26817 TCGAGTCGAGTTCGAGCTCGAG
1 TCGAGTCGAGTTCGAGCTCGAG
26839 TCGAGTC
1 TCGAGTC
26846 TATTTGATCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.18, C:0.24, G:0.35, T:0.24
Consensus pattern (22 bp):
TCGAGTCGAGTTCGAGCTCGAG
Found at i:26844 original size:17 final size:16
Alignment explanation
Indices: 26794--26843 Score: 73
Period size: 17 Copynumber: 3.0 Consensus size: 16
26784 TCGTTAAGAA
26794 CTCGAGTCGAGTTCGAG
1 CTCGAGTCGAG-TCGAG
26811 CTCGAGTCGAGTCGAG
1 CTCGAGTCGAGTCGAG
*
26827 TTCGAGCTCGAGTCGAG
1 CTCGAG-TCGAGTCGAG
26844 TCTATTTGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
16 10 0.32
17 21 0.68
ACGTcount: A:0.18, C:0.24, G:0.36, T:0.22
Consensus pattern (16 bp):
CTCGAGTCGAGTCGAG
Found at i:28061 original size:18 final size:18
Alignment explanation
Indices: 28038--28081 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
28028 AAGAGACGGG
28038 GAATGATGATGTTGTTTT
1 GAATGATGATGTTGTTTT
28056 GAATGATGATGTTGTTTT
1 GAATGATGATGTTGTTTT
*
28074 GCATGATG
1 GAATGATG
28082 GCATGGCGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.23, C:0.02, G:0.30, T:0.45
Consensus pattern (18 bp):
GAATGATGATGTTGTTTT
Found at i:37034 original size:20 final size:20
Alignment explanation
Indices: 37009--37048 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
36999 CTATCAAGTG
37009 ATTTTAATGAATAAAAAATA
1 ATTTTAATGAATAAAAAATA
37029 ATTTTAATGAATAAAAAATA
1 ATTTTAATGAATAAAAAATA
37049 TTATTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (20 bp):
ATTTTAATGAATAAAAAATA
Found at i:39554 original size:18 final size:18
Alignment explanation
Indices: 39531--39565 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39521 TTCCATCCGG
*
39531 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
39549 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
39566 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:40685 original size:8 final size:8
Alignment explanation
Indices: 40666--40730 Score: 66
Period size: 8 Copynumber: 8.4 Consensus size: 8
40656 GTCAACAGTA
40666 GTCAAC-G
1 GTCAACGG
40673 GTCAACGG
1 GTCAACGG
40681 GTCAACGG
1 GTCAACGG
40689 GTCAACGG
1 GTCAACGG
40697 GT---CGG
1 GTCAACGG
*
40702 GTCAACGA
1 GTCAACGG
*
40710 GTCGAGTCGG
1 GTC-A-ACGG
40720 GTCAACGG
1 GTCAACGG
40728 GTC
1 GTC
40731 GGGTAAACGG
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
5 5 0.10
7 6 0.12
8 30 0.62
9 2 0.04
10 5 0.10
ACGTcount: A:0.22, C:0.25, G:0.38, T:0.15
Consensus pattern (8 bp):
GTCAACGG
Found at i:40704 original size:13 final size:13
Alignment explanation
Indices: 40672--40748 Score: 73
Period size: 13 Copynumber: 5.3 Consensus size: 13
40662 AGTAGTCAAC
40672 GGTCAACGGGTCAACG
1 GGTCAACGGGT---CG
40688 GGTCAACGGGTCG
1 GGTCAACGGGTCG
40701 GGTCAACGAGTCGAGTCG
1 GGTCAAC--G--G-GTCG
40719 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
40732 GGTAAACGGGTCG
1 GGTCAACGGGTCG
40745 GGTC
1 GGTC
40749 GGGTTGTGAC
Statistics
Matches: 54, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
13 28 0.52
14 1 0.02
15 1 0.02
16 12 0.22
17 1 0.02
18 11 0.20
ACGTcount: A:0.19, C:0.22, G:0.43, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:40720 original size:18 final size:18
Alignment explanation
Indices: 40697--40731 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
40687 GGGTCAACGG
40697 GTCGGGTCAACGAGTCGA
1 GTCGGGTCAACGAGTCGA
*
40715 GTCGGGTCAACGGGTCG
1 GTCGGGTCAACGAGTCG
40732 GGTAAACGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.23, G:0.43, T:0.17
Consensus pattern (18 bp):
GTCGGGTCAACGAGTCGA
Found at i:40724 original size:31 final size:31
Alignment explanation
Indices: 40686--40752 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
40676 AACGGGTCAA
*
40686 CGGGTCAACGGGTCGGGTCAACGAGTCGAGT
1 CGGGTCAACGGGTCGGGTAAACGAGTCGAGT
* *
40717 CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTAAACGAGTCGAGT
40748 CGGGT
1 CGGGT
40753 TGTGACCGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.16, C:0.21, G:0.46, T:0.16
Consensus pattern (31 bp):
CGGGTCAACGGGTCGGGTAAACGAGTCGAGT
Found at i:44532 original size:18 final size:18
Alignment explanation
Indices: 44509--44543 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
44499 TTCCATCCGG
*
44509 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
44527 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
44544 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:45657 original size:7 final size:7
Alignment explanation
Indices: 45645--45684 Score: 62
Period size: 7 Copynumber: 5.4 Consensus size: 7
45635 GTCAACAGTA
45645 GTCAACG
1 GTCAACG
45652 GTCAACG
1 GTCAACG
45659 GTCAACGG
1 GTCAAC-G
45667 GTCAACGG
1 GTCAAC-G
45675 GTCAACG
1 GTCAACG
45682 GTC
1 GTC
45685 GGGTCAACGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 17 0.53
8 15 0.47
ACGTcount: A:0.25, C:0.28, G:0.33, T:0.15
Consensus pattern (7 bp):
GTCAACG
Found at i:45671 original size:8 final size:8
Alignment explanation
Indices: 45645--45715 Score: 64
Period size: 8 Copynumber: 9.4 Consensus size: 8
45635 GTCAACAGTA
45645 GTCAAC-G
1 GTCAACGG
45652 GTCAAC-G
1 GTCAACGG
45659 GTCAACGG
1 GTCAACGG
45667 GTCAACGG
1 GTCAACGG
45675 GTCAAC-G
1 GTCAACGG
45682 GT---CGG
1 GTCAACGG
*
45687 GTCAACGA
1 GTCAACGG
*
45695 GTCGAGTCGG
1 GTC-A-ACGG
45705 GTCAACGG
1 GTCAACGG
45713 GTC
1 GTC
45716 GGGTAAACGG
Statistics
Matches: 53, Mismatches: 4, Indels: 13
0.76 0.06 0.19
Matches are distributed among these distances:
4 1 0.02
5 3 0.06
7 16 0.30
8 26 0.49
9 2 0.04
10 5 0.09
ACGTcount: A:0.23, C:0.25, G:0.37, T:0.15
Consensus pattern (8 bp):
GTCAACGG
Found at i:45671 original size:15 final size:14
Alignment explanation
Indices: 45645--45684 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 14
45635 GTCAACAGTA
45645 GTCAACGGTCAACG
1 GTCAACGGTCAACG
45659 GTCAACGGGTCAACGG
1 GTCAAC-GGTCAAC-G
45675 GTCAACGGTC
1 GTCAACGGTC
45685 GGGTCAACGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.25
15 11 0.46
16 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.33, T:0.15
Consensus pattern (14 bp):
GTCAACGGTCAACG
Found at i:45705 original size:18 final size:18
Alignment explanation
Indices: 45682--45716 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
45672 CGGGTCAACG
45682 GTCGGGTCAACGAGTCGA
1 GTCGGGTCAACGAGTCGA
*
45700 GTCGGGTCAACGGGTCG
1 GTCGGGTCAACGAGTCG
45717 GGTAAACGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.23, G:0.43, T:0.17
Consensus pattern (18 bp):
GTCGGGTCAACGAGTCGA
Found at i:45716 original size:13 final size:13
Alignment explanation
Indices: 45658--45733 Score: 64
Period size: 13 Copynumber: 5.3 Consensus size: 13
45648 AACGGTCAAC
45658 GGTCAACGGGTCAACG
1 GGTCAACGGGT---CG
45674 GGTCAAC-GGTCG
1 GGTCAACGGGTCG
45686 GGTCAACGAGTCGAGTCG
1 GGTCAAC--G--G-GTCG
45704 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
45717 GGTAAACGGGTCG
1 GGTCAACGGGTCG
45730 GGTC
1 GGTC
45734 GGGTTGTGAC
Statistics
Matches: 52, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
12 9 0.17
13 19 0.37
14 1 0.02
15 3 0.06
16 8 0.15
17 1 0.02
18 11 0.21
ACGTcount: A:0.20, C:0.22, G:0.42, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:49519 original size:18 final size:18
Alignment explanation
Indices: 49496--49530 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
49486 TTCCATCCGG
*
49496 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
49514 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
49531 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:50650 original size:8 final size:8
Alignment explanation
Indices: 50631--50703 Score: 82
Period size: 8 Copynumber: 9.4 Consensus size: 8
50621 GTCAACAGTA
50631 GTCAAC-G
1 GTCAACGG
50638 GTCAACGG
1 GTCAACGG
50646 GTCAACGG
1 GTCAACGG
50654 GTCAACGG
1 GTCAACGG
50662 GTCAACGG
1 GTCAACGG
50670 GT---CGG
1 GTCAACGG
*
50675 GTCAACGA
1 GTCAACGG
*
50683 GTCGAGTCGG
1 GTC-A-ACGG
50693 GTCAACGG
1 GTCAACGG
50701 GTC
1 GTC
50704 GGGTAAACGG
Statistics
Matches: 56, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
5 5 0.09
7 6 0.11
8 38 0.68
9 2 0.04
10 5 0.09
ACGTcount: A:0.22, C:0.25, G:0.38, T:0.15
Consensus pattern (8 bp):
GTCAACGG
Found at i:50677 original size:13 final size:13
Alignment explanation
Indices: 50643--50721 Score: 77
Period size: 13 Copynumber: 5.5 Consensus size: 13
50633 CAACGGTCAA
50643 CGGGTCAACGGGT
1 CGGGTCAACGGGT
50656 CAACGGGTCAACGGGT
1 ---CGGGTCAACGGGT
50672 CGGGTCAACGAGTCGAGT
1 CGGGTCAAC--G--G-GT
50690 CGGGTCAACGGGT
1 CGGGTCAACGGGT
*
50703 CGGGTAAACGGGT
1 CGGGTCAACGGGT
50716 CGGGTC
1 CGGGTC
50722 GGGTTGTGAC
Statistics
Matches: 56, Mismatches: 2, Indels: 13
0.79 0.03 0.18
Matches are distributed among these distances:
13 28 0.50
14 1 0.02
15 1 0.02
16 14 0.25
17 1 0.02
18 11 0.20
ACGTcount: A:0.19, C:0.23, G:0.43, T:0.15
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:50693 original size:18 final size:18
Alignment explanation
Indices: 50670--50704 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
50660 GGGTCAACGG
50670 GTCGGGTCAACGAGTCGA
1 GTCGGGTCAACGAGTCGA
*
50688 GTCGGGTCAACGGGTCG
1 GTCGGGTCAACGAGTCG
50705 GGTAAACGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.23, G:0.43, T:0.17
Consensus pattern (18 bp):
GTCGGGTCAACGAGTCGA
Found at i:50694 original size:31 final size:31
Alignment explanation
Indices: 50643--50725 Score: 116
Period size: 31 Copynumber: 2.7 Consensus size: 31
50633 CAACGGTCAA
*
50643 CGGGTCAACGGGTC-A-ACGGGTCAACGGGT
1 CGGGTCAACGGGTCGAGTCGGGTCAACGGGT
*
50672 CGGGTCAACGAGTCGAGTCGGGTCAACGGGT
1 CGGGTCAACGGGTCGAGTCGGGTCAACGGGT
* *
50703 CGGGTAAACGGGTCGGGTCGGGT
1 CGGGTCAACGGGTCGAGTCGGGT
50726 TGTGACCGGT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 13 0.28
30 1 0.02
31 33 0.70
ACGTcount: A:0.18, C:0.22, G:0.45, T:0.16
Consensus pattern (31 bp):
CGGGTCAACGGGTCGAGTCGGGTCAACGGGT
Found at i:54502 original size:18 final size:18
Alignment explanation
Indices: 54479--54513 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
54469 TTCCATCCGG
*
54479 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
54497 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
54514 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:55632 original size:8 final size:8
Alignment explanation
Indices: 55613--55685 Score: 82
Period size: 8 Copynumber: 9.4 Consensus size: 8
55603 GTCAACAGTA
55613 GTCAAC-G
1 GTCAACGG
55620 GTCAACGG
1 GTCAACGG
55628 GTCAACGG
1 GTCAACGG
55636 GTCAACGG
1 GTCAACGG
55644 GTCAACGG
1 GTCAACGG
55652 GT---CGG
1 GTCAACGG
*
55657 GTCAACGA
1 GTCAACGG
*
55665 GTCGAGTCGG
1 GTC-A-ACGG
55675 GTCAACGG
1 GTCAACGG
55683 GTC
1 GTC
55686 GGGTAAACGG
Statistics
Matches: 56, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
5 5 0.09
7 6 0.11
8 38 0.68
9 2 0.04
10 5 0.09
ACGTcount: A:0.22, C:0.25, G:0.38, T:0.15
Consensus pattern (8 bp):
GTCAACGG
Found at i:55659 original size:13 final size:13
Alignment explanation
Indices: 55625--55703 Score: 77
Period size: 13 Copynumber: 5.5 Consensus size: 13
55615 CAACGGTCAA
55625 CGGGTCAACGGGT
1 CGGGTCAACGGGT
55638 CAACGGGTCAACGGGT
1 ---CGGGTCAACGGGT
55654 CGGGTCAACGAGTCGAGT
1 CGGGTCAAC--G--G-GT
55672 CGGGTCAACGGGT
1 CGGGTCAACGGGT
*
55685 CGGGTAAACGGGT
1 CGGGTCAACGGGT
55698 CGGGTC
1 CGGGTC
55704 GGGTTGTGAC
Statistics
Matches: 56, Mismatches: 2, Indels: 13
0.79 0.03 0.18
Matches are distributed among these distances:
13 28 0.50
14 1 0.02
15 1 0.02
16 14 0.25
17 1 0.02
18 11 0.20
ACGTcount: A:0.19, C:0.23, G:0.43, T:0.15
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:55675 original size:18 final size:18
Alignment explanation
Indices: 55652--55686 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
55642 GGGTCAACGG
55652 GTCGGGTCAACGAGTCGA
1 GTCGGGTCAACGAGTCGA
*
55670 GTCGGGTCAACGGGTCG
1 GTCGGGTCAACGAGTCG
55687 GGTAAACGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.23, G:0.43, T:0.17
Consensus pattern (18 bp):
GTCGGGTCAACGAGTCGA
Found at i:55676 original size:31 final size:31
Alignment explanation
Indices: 55625--55707 Score: 116
Period size: 31 Copynumber: 2.7 Consensus size: 31
55615 CAACGGTCAA
*
55625 CGGGTCAACGGGTC-A-ACGGGTCAACGGGT
1 CGGGTCAACGGGTCGAGTCGGGTCAACGGGT
*
55654 CGGGTCAACGAGTCGAGTCGGGTCAACGGGT
1 CGGGTCAACGGGTCGAGTCGGGTCAACGGGT
* *
55685 CGGGTAAACGGGTCGGGTCGGGT
1 CGGGTCAACGGGTCGAGTCGGGT
55708 TGTGACCGGT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 13 0.28
30 1 0.02
31 33 0.70
ACGTcount: A:0.18, C:0.22, G:0.45, T:0.16
Consensus pattern (31 bp):
CGGGTCAACGGGTCGAGTCGGGTCAACGGGT
Found at i:59432 original size:18 final size:18
Alignment explanation
Indices: 59409--59443 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
59399 TTCCATCCGG
*
59409 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
59427 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
59444 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:60576 original size:13 final size:13
Alignment explanation
Indices: 60545--60619 Score: 87
Period size: 13 Copynumber: 5.3 Consensus size: 13
60535 AACGGTCAAC
60545 GGTCAACGGGTCAG
1 GGTCAACGGGTC-G
60559 GGTCAACGGGTCG
1 GGTCAACGGGTCG
60572 GGTCAACGAGTCGAGTCG
1 GGTCAAC--G--G-GTCG
60590 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
60603 GGTAAACGGGTCG
1 GGTCAACGGGTCG
60616 GGTC
1 GGTC
60620 GGGTTGTGAC
Statistics
Matches: 54, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
13 27 0.50
14 13 0.24
15 1 0.02
16 1 0.02
17 1 0.02
18 11 0.20
ACGTcount: A:0.19, C:0.21, G:0.44, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:60591 original size:18 final size:18
Alignment explanation
Indices: 60568--60602 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
60558 GGGTCAACGG
60568 GTCGGGTCAACGAGTCGA
1 GTCGGGTCAACGAGTCGA
*
60586 GTCGGGTCAACGGGTCG
1 GTCGGGTCAACGAGTCG
60603 GGTAAACGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.23, G:0.43, T:0.17
Consensus pattern (18 bp):
GTCGGGTCAACGAGTCGA
Found at i:60596 original size:31 final size:31
Alignment explanation
Indices: 60558--60623 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
60548 CAACGGGTCA
*
60558 GGGTCAACGGGTCGGGTCAACGAGTCGAGTC
1 GGGTCAACGGGTCGGGTAAACGAGTCGAGTC
* *
60589 GGGTCAACGGGTCGGGTAAACGGGTCGGGTC
1 GGGTCAACGGGTCGGGTAAACGAGTCGAGTC
60620 GGGT
1 GGGT
60624 TGTGACCGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.17, C:0.20, G:0.47, T:0.17
Consensus pattern (31 bp):
GGGTCAACGGGTCGGGTAAACGAGTCGAGTC
Found at i:72929 original size:22 final size:23
Alignment explanation
Indices: 72873--72931 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
72863 TTCAAGTTCA
* * *
72873 AACTCGAGTTCGAGCTTGAATTG
1 AACTCAAGTTTGAGCTTCAATTG
*
72896 AGCTCAAGTTTGAGCTTCAATTG
1 AACTCAAGTTTGAGCTTCAATTG
72919 AACT-AAGTTTGAG
1 AACTCAAGTTTGAG
72932 AAGAGTTCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
22 9 0.29
23 22 0.71
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (23 bp):
AACTCAAGTTTGAGCTTCAATTG
Found at i:72965 original size:55 final size:55
Alignment explanation
Indices: 72896--73020 Score: 144
Period size: 55 Copynumber: 2.2 Consensus size: 55
72886 GCTTGAATTG
* * *
72896 AGCTCAAGTTTGAGCTTCAATTGAACTAAGTTTGAGAA-GAGTTCAAGTTTTTTCA
1 AGCTCGAGTCTGAGCTTCAATCGAACTAAG-TTGAGAATGAGTTCAAGTTTTTTCA
* *
72951 AGCTCGAGTCTGAGCTTCAATCGAGCTAAGTTGAGAACGTTTCGAGTTCAAGTTTTTTCG
1 AGCTCGAGTCTGAGCTTCAATCGAACTAAGTTGAGAA----T-GAGTTCAAGTTTTTTCA
73011 AGCTCGAGTC
1 AGCTCGAGTC
73021 GAGTTTGAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
54 7 0.12
55 26 0.44
60 26 0.44
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (55 bp):
AGCTCGAGTCTGAGCTTCAATCGAACTAAGTTGAGAATGAGTTCAAGTTTTTTCA
Done.