Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003107.1 Hibiscus syriacus cultivar Beakdansim tig00006491_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: 65166
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:146 original size:22 final size:22
Alignment explanation
Indices: 77--136 Score: 104
Period size: 22 Copynumber: 2.8 Consensus size: 22
67 TCCCCTGTGG
77 GGGGAATC-GTTCCCCTTCAAA
1 GGGGAATCGGTTCCCCTTCAAA
98 GGGGAATCGGTTCCCCTTCAAA
1 GGGGAATCGGTTCCCCTTCAAA
*
120 GGGGAATCGGTTTCCCT
1 GGGGAATCGGTTCCCCT
137 CATGGGGGGA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
21 8 0.22
22 29 0.78
ACGTcount: A:0.20, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
GGGGAATCGGTTCCCCTTCAAA
Found at i:7173 original size:4 final size:4
Alignment explanation
Indices: 7164--7190 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
7154 TAATGTTAAG
7164 TAAC TAAC TAAC TAAC TAAC TAAC TAA
1 TAAC TAAC TAAC TAAC TAAC TAAC TAA
7191 TTTACAACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAC
Found at i:7358 original size:41 final size:37
Alignment explanation
Indices: 7311--7418 Score: 90
Period size: 41 Copynumber: 2.7 Consensus size: 37
7301 TATTTAACTA
7311 AAACAAACTAATTACATATTTTTTTATATATAACTAAC
1 AAACAAACTAATTA-ATATTTTTTTATATATAACTAAC
* * * *
7349 GACTAACAAATTAACTAATTATTTTTATTAATATGTAACTATC
1 -A--AACAAACTAATTAA-TATTTTT-TT-ATATATAACTAAC
* *
7392 AAACATACTAATTAAATAATTTTTTAT
1 AAACAAACTAATT-AATATTTTTTTAT
7419 TTCTATATGA
Statistics
Matches: 55, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
38 2 0.04
39 3 0.05
40 16 0.29
41 20 0.36
42 3 0.05
43 11 0.20
ACGTcount: A:0.45, C:0.11, G:0.02, T:0.42
Consensus pattern (37 bp):
AAACAAACTAATTAATATTTTTTTATATATAACTAAC
Found at i:7452 original size:21 final size:21
Alignment explanation
Indices: 7428--7467 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
7418 TTTCTATATG
7428 ATATAACTTAAACTAACAATT
1 ATATAACTTAAACTAACAATT
7449 ATATAACTTAAACTAACAA
1 ATATAACTTAAACTAACAA
7468 ACTAATTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (21 bp):
ATATAACTTAAACTAACAATT
Found at i:7516 original size:18 final size:18
Alignment explanation
Indices: 7495--7555 Score: 57
Period size: 18 Copynumber: 3.8 Consensus size: 18
7485 TTATTTTACC
7495 CTAATTTATAATAATAAA
1 CTAATTTATAATAATAAA
*
7513 CTAA--T-T-A-ACT-AA
1 CTAATTTATAATAATAAA
7525 -TAATTTATAATAATAAA
1 CTAATTTATAATAATAAA
7542 CTAATTTA-AATAAT
1 CTAATTTATAATAAT
7556 TATTCTTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
11 3 0.09
12 2 0.06
13 3 0.09
14 2 0.06
15 2 0.06
16 3 0.09
17 8 0.24
18 11 0.32
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (18 bp):
CTAATTTATAATAATAAA
Found at i:7524 original size:26 final size:27
Alignment explanation
Indices: 7495--7556 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 27
7485 TTATTTTACC
7495 CTAATTTATAATAATAAACTAA-TTAA
1 CTAATTTATAATAATAAACTAATTTAA
7521 CTAATAATTTATAATAATAAACTAATTTAA
1 C---TAATTTATAATAATAAACTAATTTAA
*
7551 ATAATT
1 CTAATT
7557 ATTCTTTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
26 1 0.03
27 5 0.16
29 21 0.68
30 4 0.13
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.40
Consensus pattern (27 bp):
CTAATTTATAATAATAAACTAATTTAA
Found at i:7846 original size:21 final size:21
Alignment explanation
Indices: 7793--7832 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
7783 TTTATGTATC
7793 ATATAACTTAAACTAACAATA
1 ATATAACTTAAACTAACAATA
7814 ATATAACTTAAACTAACAA
1 ATATAACTTAAACTAACAA
7833 ACTAATTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (21 bp):
ATATAACTTAAACTAACAATA
Found at i:7864 original size:39 final size:39
Alignment explanation
Indices: 7820--7904 Score: 161
Period size: 39 Copynumber: 2.2 Consensus size: 39
7810 AATAATATAA
7820 CTTAAACTAACAAACTAATTAACTAAAATTTTGTTTTAC
1 CTTAAACTAACAAACTAATTAACTAAAATTTTGTTTTAC
*
7859 CTTAAACTAACTAACTAATTAACTAAAATTTTGTTTTAC
1 CTTAAACTAACAAACTAATTAACTAAAATTTTGTTTTAC
7898 CTTAAAC
1 CTTAAAC
7905 CATAAACTAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.42, C:0.16, G:0.02, T:0.39
Consensus pattern (39 bp):
CTTAAACTAACAAACTAATTAACTAAAATTTTGTTTTAC
Found at i:7928 original size:39 final size:37
Alignment explanation
Indices: 7831--7928 Score: 133
Period size: 39 Copynumber: 2.5 Consensus size: 37
7821 TTAAACTAAC
*
7831 AAACTAATTAACTAAAATTTTGTTTTACCTTAAACTA
1 AAACTAATTAACTAAAATTTTGTTTTACCTTAAACCA
7868 ACTAACTAATTAACTAAAATTTTGTTTTACCTTAAACCA
1 A--AACTAATTAACTAAAATTTTGTTTTACCTTAAACCA
**
7907 TAAACTAACAAACTAATAATTT
1 -AAACTAATTAACTAA-AATTT
7929 AAAATAATAA
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
37 1 0.02
38 12 0.22
39 40 0.74
40 1 0.02
ACGTcount: A:0.45, C:0.15, G:0.02, T:0.38
Consensus pattern (37 bp):
AAACTAATTAACTAAAATTTTGTTTTACCTTAAACCA
Found at i:8153 original size:11 final size:11
Alignment explanation
Indices: 8136--8218 Score: 67
Period size: 11 Copynumber: 7.2 Consensus size: 11
8126 CTGAACGACT
8136 GCAATAATGCA
1 GCAATAATGCA
* * *
8147 ACAATAAGGACT
1 GCAATAATG-CA
8159 GCAATAATGCA
1 GCAATAATGCA
* *
8170 GCAATAAGGGCT
1 GCAATAA-TGCA
8182 GCAATAATGCA
1 GCAATAATGCA
* *
8193 ACAATAAAGTGCT
1 GCAAT-AA-TGCA
8206 GCAATAATGCA
1 GCAATAATGCA
8217 GC
1 GC
8219 TGAATTCACG
Statistics
Matches: 54, Mismatches: 14, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
11 26 0.48
12 21 0.39
13 7 0.13
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.18
Consensus pattern (11 bp):
GCAATAATGCA
Found at i:8162 original size:23 final size:23
Alignment explanation
Indices: 8132--8216 Score: 127
Period size: 23 Copynumber: 3.7 Consensus size: 23
8122 TGAGCTGAAC
8132 GACTGCAATAATGCAACAATAAG
1 GACTGCAATAATGCAACAATAAG
*
8155 GACTGCAATAATGCAGCAATAAG
1 GACTGCAATAATGCAACAATAAG
*
8178 GGCTGCAATAATGCAACAATAAAG
1 GACTGCAATAATGCAACAAT-AAG
8202 TG-CTGCAATAATGCA
1 -GACTGCAATAATGCA
8217 GCTGAATTCA
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
23 40 0.70
24 16 0.28
25 1 0.02
ACGTcount: A:0.44, C:0.18, G:0.20, T:0.19
Consensus pattern (23 bp):
GACTGCAATAATGCAACAATAAG
Found at i:8379 original size:29 final size:29
Alignment explanation
Indices: 8337--8452 Score: 162
Period size: 29 Copynumber: 4.0 Consensus size: 29
8327 GCAAAGCATG
*
8337 CATGTCGCTCGGATGCCTTGGCGACCTAC
1 CATGTCGCTCGGATGCCATGGCGACCTAC
* *
8366 CATGTCGCTGGGATGCCATGGCGTCCTAC
1 CATGTCGCTCGGATGCCATGGCGACCTAC
* *
8395 AATGTCGCTCGGATGCCATGGCGATCT-C
1 CATGTCGCTCGGATGCCATGGCGACCTAC
*
8423 CAAGCTCGCTCGGATGCCATGGCGACCTAC
1 CATG-TCGCTCGGATGCCATGGCGACCTAC
8453 GGCTGCACTG
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
28 3 0.04
29 71 0.95
30 1 0.01
ACGTcount: A:0.16, C:0.33, G:0.28, T:0.22
Consensus pattern (29 bp):
CATGTCGCTCGGATGCCATGGCGACCTAC
Found at i:14701 original size:20 final size:20
Alignment explanation
Indices: 14676--14829 Score: 90
Period size: 20 Copynumber: 7.8 Consensus size: 20
14666 ATGCGAAACA
14676 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
* * **
14696 AAAATCGCAATGTTGA-AAAG
1 AAAATCGCAACG-CGATTTAG
**
14716 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
**
14736 AAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
* *
14757 AAGAATCGCAATGCGATTGAG
1 AA-AATCGCAACGCGATTTAG
*
14778 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTTAG
* *
14798 -GAATCGCAA--TGA-TT-G
1 AAAATCGCAACGCGATTTAG
14813 AAAATCGCAACGCGATT
1 AAAATCGCAACGCGATT
14830 CCAAGAATCG
Statistics
Matches: 102, Mismatches: 21, Indels: 23
0.70 0.14 0.16
Matches are distributed among these distances:
15 1 0.01
16 9 0.09
17 2 0.02
18 3 0.03
19 9 0.09
20 56 0.55
21 8 0.08
22 14 0.14
ACGTcount: A:0.41, C:0.20, G:0.21, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:14780 original size:42 final size:37
Alignment explanation
Indices: 14734--14842 Score: 150
Period size: 35 Copynumber: 2.9 Consensus size: 37
14724 AACGGTCAAA
14734 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAATGCGATT
1 AGAAAATCGCAACGCGA--TTCCAAGAATCGCAAT--GATT
*
14775 GAGAAAATCGCAACGCGATT-CAGGAATCGCAATGATT
1 -AGAAAATCGCAACGCGATTCCAAGAATCGCAATGATT
14812 -GAAAATCGCAACGCGATTCCAAGAATCGCAA
1 AGAAAATCGCAACGCGATTCCAAGAATCGCAA
14843 AACGGCAAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
35 18 0.28
36 11 0.17
37 4 0.06
39 12 0.19
40 2 0.03
42 17 0.27
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.17
Consensus pattern (37 bp):
AGAAAATCGCAACGCGATTCCAAGAATCGCAATGATT
Found at i:14840 original size:20 final size:19
Alignment explanation
Indices: 14738--14842 Score: 90
Period size: 20 Copynumber: 5.4 Consensus size: 19
14728 GTCAAAAGAA
14738 AATCGCAACGCGATCTTCCAAG
1 AATCGCAACGCGA--TT-CAAG
* * *
14760 AATCGCAATGCGATTGAGAA
1 AATCGCAACGCGATTCA-AG
*
14780 AATCGCAACGCGATTCAGG
1 AATCGCAACGCGATTCAAG
* *
14799 AATCGCAA--TGATTGAA-
1 AATCGCAACGCGATTCAAG
14815 AATCGCAACGCGATTCCAAG
1 AATCGCAACGCGATT-CAAG
14835 AATCGCAA
1 AATCGCAA
14843 AACGGCAAAA
Statistics
Matches: 66, Mismatches: 12, Indels: 12
0.73 0.13 0.13
Matches are distributed among these distances:
16 8 0.12
17 5 0.08
18 4 0.06
19 11 0.17
20 26 0.39
22 12 0.18
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.18
Consensus pattern (19 bp):
AATCGCAACGCGATTCAAG
Found at i:14962 original size:6 final size:6
Alignment explanation
Indices: 14951--15007 Score: 114
Period size: 6 Copynumber: 9.5 Consensus size: 6
14941 GACACGTATT
14951 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
14999 ACCACG ACC
1 ACCACG ACC
15008 CGAGACGAGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:15776 original size:6 final size:6
Alignment explanation
Indices: 15760--15857 Score: 169
Period size: 6 Copynumber: 15.8 Consensus size: 6
15750 CCGTCTCGTC
15760 TCGTCGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGT-GG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
15809 TCGTGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTG
1 TC--GTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTG
15858 TAATACGTGT
Statistics
Matches: 89, Mismatches: 0, Indels: 5
0.95 0.00 0.05
Matches are distributed among these distances:
6 79 0.89
7 4 0.04
8 6 0.07
ACGTcount: A:0.00, C:0.17, G:0.49, T:0.34
Consensus pattern (6 bp):
TCGTGG
Found at i:15993 original size:20 final size:20
Alignment explanation
Indices: 15968--16099 Score: 115
Period size: 20 Copynumber: 6.4 Consensus size: 20
15958 TTTTGCCGTT
*
15968 TTGCGATTCTTGGAATCGCG
1 TTGCGATTCTTGGAATCGCA
** *
15988 TTGCGATT-TTCTCAATCGCG
1 TTGCGATTCTT-GGAATCGCA
*
16008 TTGCGATTCTTCGAAGATCGCA
1 TTGCGATTCTT-GGA-ATCGCA
16030 TTGCGATTCTTGGAATCGCA
1 TTGCGATTCTTGGAATCGCA
** *
16050 ACGCGATTCTTTGG-CTCGCA
1 TTGCGATTC-TTGGAATCGCA
*
16070 TTGCGATTCTTGGAAGATCGCG
1 TTGCGATTCTTGG-A-ATCGCA
16092 TTGCGATT
1 TTGCGATT
16100 TTCTTTTGAC
Statistics
Matches: 92, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
19 6 0.07
20 48 0.52
21 10 0.11
22 28 0.30
ACGTcount: A:0.17, C:0.22, G:0.26, T:0.35
Consensus pattern (20 bp):
TTGCGATTCTTGGAATCGCA
Found at i:16074 original size:62 final size:62
Alignment explanation
Indices: 15968--16099 Score: 167
Period size: 62 Copynumber: 2.1 Consensus size: 62
15958 TTTTGCCGTT
*** *
15968 TTGCGATTCTTGGAATCGCGTTGCGATTTTCTCAATCGCGTTGCGATTCTTCGAAGATCGCA
1 TTGCGATTCTTGGAATCGCAACGCGATTTTCTCAATCGCATTGCGATTCTTCGAAGATCGCA
*** * *
16030 TTGCGATTCTTGGAATCGCAACGCGATTCTT-TGGCTCGCATTGCGATTCTTGGAAGATCGCG
1 TTGCGATTCTTGGAATCGCAACGCGATT-TTCTCAATCGCATTGCGATTCTTCGAAGATCGCA
16092 TTGCGATT
1 TTGCGATT
16100 TTCTTTTGAC
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
62 58 0.97
63 2 0.03
ACGTcount: A:0.17, C:0.22, G:0.26, T:0.35
Consensus pattern (62 bp):
TTGCGATTCTTGGAATCGCAACGCGATTTTCTCAATCGCATTGCGATTCTTCGAAGATCGCA
Found at i:16115 original size:20 final size:20
Alignment explanation
Indices: 16090--16161 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
16080 TGGAAGATCG
* *
16090 CGTTGCGATTTTCTTTTGAC
1 CGTTGCGATTTTCTTTTCAA
16110 CGTTGCGATTTTCTTTTCAA
1 CGTTGCGATTTTCTTTTCAA
**
16130 CGTTGCGATTTTCTAAATC-A
1 CGTTGCGATTTTCT-TTTCAA
16150 CGTTGCGATTTT
1 CGTTGCGATTTT
16162 GATATCGCGT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
20 45 0.96
21 2 0.04
ACGTcount: A:0.15, C:0.19, G:0.18, T:0.47
Consensus pattern (20 bp):
CGTTGCGATTTTCTTTTCAA
Found at i:16174 original size:19 final size:19
Alignment explanation
Indices: 16129--16181 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
16119 TTTCTTTTCA
*
16129 ACGTTGCGATTTTCTAAATC
1 ACGTTGCGATTTT-GAAATC
*
16149 ACGTTGCGATTTTGATATC
1 ACGTTGCGATTTTGAAATC
*
16168 GCGTTGCGATTTTG
1 ACGTTGCGATTTTG
16182 TTGGTCATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.19, C:0.17, G:0.23, T:0.42
Consensus pattern (19 bp):
ACGTTGCGATTTTGAAATC
Found at i:16985 original size:14 final size:14
Alignment explanation
Indices: 16966--16992 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
16956 AATTAGATTG
16966 TTGGGTTATCTTTT
1 TTGGGTTATCTTTT
16980 TTGGGTTATCTTT
1 TTGGGTTATCTTT
16993 GTTTCAGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.07, G:0.22, T:0.63
Consensus pattern (14 bp):
TTGGGTTATCTTTT
Found at i:27445 original size:60 final size:60
Alignment explanation
Indices: 27285--27450 Score: 170
Period size: 60 Copynumber: 2.7 Consensus size: 60
27275 ATCTTCATTT
* ** * *
27285 AAATTGGTCTTTAAACTTTTGAATATTATACAATTTCATCCCTAAAATACGTTTTTCATTCT
1 AAATTGGTCTTTAAACTTTTGAATATT-T-CAATTTCATCCCCAAAATACGACTCTCATTCC
* * * * * * * *
27347 AAATTAGTCTTTAAAATTTTAAATATTTAAATTCCATCCCCATATTATGACTCTCATTCC
1 AAATTGGTCTTTAAACTTTTGAATATTTCAATTTCATCCCCAAAATACGACTCTCATTCC
** *
27407 AAATTGGTCCCTAAACTTTTGAATCTTTCAATTTCATCCCCAAA
1 AAATTGGTCTTTAAACTTTTGAATATTTCAATTTCATCCCCAAA
27451 GTCATCTTAA
Statistics
Matches: 82, Mismatches: 22, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
60 57 0.70
61 1 0.01
62 24 0.29
ACGTcount: A:0.33, C:0.20, G:0.05, T:0.42
Consensus pattern (60 bp):
AAATTGGTCTTTAAACTTTTGAATATTTCAATTTCATCCCCAAAATACGACTCTCATTCC
Found at i:36403 original size:20 final size:20
Alignment explanation
Indices: 36374--36411 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
36364 AACACGCTGG
36374 GCATCCGAGGCCATCCGAGA
1 GCATCCGAGGCCATCCGAGA
*
36394 GCATCTGAGGCCATCCGA
1 GCATCCGAGGCCATCCGA
36412 ACGAGCTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.34, G:0.29, T:0.13
Consensus pattern (20 bp):
GCATCCGAGGCCATCCGAGA
Found at i:39621 original size:42 final size:42
Alignment explanation
Indices: 39574--39664 Score: 137
Period size: 42 Copynumber: 2.2 Consensus size: 42
39564 AATTAAATGA
* * * * *
39574 GGACGGGGAAAAATCGTTTATGTTAAATGGGGACGGAGACGG
1 GGACGGGGAAAAACCGTGTATGTTAAACGGAGACGGAGACAG
39616 GGACGGGGAAAAACCGTGTATGTTAAACGGAGACGGAGACAG
1 GGACGGGGAAAAACCGTGTATGTTAAACGGAGACGGAGACAG
39658 GGACGGG
1 GGACGGG
39665 TTTGGTAATC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.32, C:0.12, G:0.42, T:0.14
Consensus pattern (42 bp):
GGACGGGGAAAAACCGTGTATGTTAAACGGAGACGGAGACAG
Found at i:39774 original size:2 final size:2
Alignment explanation
Indices: 39767--39832 Score: 82
Period size: 2 Copynumber: 34.0 Consensus size: 2
39757 TTTAAATTAA
*
39767 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
39808 AT AT AT TT A- AT TT AA AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
39833 CCGGCCCGAT
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
1 2 0.04
2 52 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:42029 original size:8 final size:8
Alignment explanation
Indices: 41998--42031 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
41988 TAAACAATAA
*
41998 TAAAATAT
1 TAAATTAT
42006 TAAATTAT
1 TAAATTAT
42014 TAAATTAT
1 TAAATTAT
*
42022 TAATTTAT
1 TAAATTAT
42030 TA
1 TA
42032 GATTTTACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
TAAATTAT
Found at i:48509 original size:40 final size:40
Alignment explanation
Indices: 48454--48529 Score: 152
Period size: 40 Copynumber: 1.9 Consensus size: 40
48444 ACTATTGCTT
48454 ACTTTCTAGAATAACATTCATATGAGAAATGTCTATCTTA
1 ACTTTCTAGAATAACATTCATATGAGAAATGTCTATCTTA
48494 ACTTTCTAGAATAACATTCATATGAGAAATGTCTAT
1 ACTTTCTAGAATAACATTCATATGAGAAATGTCTAT
48530 AATATTTATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (40 bp):
ACTTTCTAGAATAACATTCATATGAGAAATGTCTATCTTA
Found at i:52760 original size:34 final size:34
Alignment explanation
Indices: 52717--52784 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
52707 GAGGTAATCC
*
52717 CTTTGAATGCCGGAAATGTACTGAGAGCCGAGGA
1 CTTTGAATGCCGGAAATATACTGAGAGCCGAGGA
*
52751 CTTTGAATGCCGGAAATATACTGGGAGCCGAGGA
1 CTTTGAATGCCGGAAATATACTGAGAGCCGAGGA
52785 TAACAGGCCG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.29, C:0.18, G:0.32, T:0.21
Consensus pattern (34 bp):
CTTTGAATGCCGGAAATATACTGAGAGCCGAGGA
Found at i:53091 original size:32 final size:33
Alignment explanation
Indices: 53024--53092 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
53014 ATAGTGTGGC
* *
53024 CTGAAGATGAAAATCAACAAGTTCGTTTTTTCT
1 CTGAAGATGAAAACCAACAAGTTCGATTTTTCT
53057 CTGAAGATGAAAACCAACAAGTTC-ATTTTTCT
1 CTGAAGATGAAAACCAACAAGTTCGATTTTTCT
53089 CTGA
1 CTGA
53093 GATATCTGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 11 0.32
33 23 0.68
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.33
Consensus pattern (33 bp):
CTGAAGATGAAAACCAACAAGTTCGATTTTTCT
Found at i:56248 original size:39 final size:39
Alignment explanation
Indices: 56194--56271 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
56184 AACCATGAAA
56194 CCAAAACCAAAAGTTTCTTTTTTTCTTCTTCTTGTGTGT
1 CCAAAACCAAAAGTTTCTTTTTTTCTTCTTCTTGTGTGT
56233 CCAAAACCAAAAGTTTCTTTTTTTCTTCTTCTTGTGTGT
1 CCAAAACCAAAAGTTTCTTTTTTTCTTCTTCTTGTGTGT
56272 GTGTGTGTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.21, C:0.21, G:0.10, T:0.49
Consensus pattern (39 bp):
CCAAAACCAAAAGTTTCTTTTTTTCTTCTTCTTGTGTGT
Found at i:63858 original size:22 final size:23
Alignment explanation
Indices: 63813--63858 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
63803 TCATCTTTTT
*
63813 AAATTTTATAAATTCATTTTCTA
1 AAATTTTATAAATTCATTTCCTA
*
63836 AAATTTTATAAGTTCA-TTCCTA
1 AAATTTTATAAATTCATTTCCTA
63858 A
1 A
63859 TATAAAATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (23 bp):
AAATTTTATAAATTCATTTCCTA
Found at i:64899 original size:33 final size:33
Alignment explanation
Indices: 64813--64910 Score: 151
Period size: 33 Copynumber: 3.0 Consensus size: 33
64803 AACACGCTAG
** *
64813 GCATCCGAGGCCATCCGGTCAAGATATACGAGA
1 GCATCCGAGGCCATCCGACCGAGATATACGAGA
64846 GCATCCGAGGCCATCCGACCGAGATATACGAGA
1 GCATCCGAGGCCATCCGACCGAGATATACGAGA
* *
64879 GCATCCGAGGCCATCCGACCGAGCTATGCGAG
1 GCATCCGAGGCCATCCGACCGAGATATACGAG
64911 GGGCAGCCGA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.28, C:0.31, G:0.29, T:0.13
Consensus pattern (33 bp):
GCATCCGAGGCCATCCGACCGAGATATACGAGA
Found at i:64920 original size:24 final size:23
Alignment explanation
Indices: 64884--64949 Score: 87
Period size: 24 Copynumber: 2.8 Consensus size: 23
64874 CGAGAGCATC
* * *
64884 CGAGGCCATCCGACCGAGCTATG
1 CGAGGGCAGCCGAGCGAGCTATG
*
64907 CGAGGGGCAGCCGAGCGAACTATG
1 CGA-GGGCAGCCGAGCGAGCTATG
64931 CGAGGGCAGCCGAGCGAGC
1 CGAGGGCAGCCGAGCGAGC
64950 GAGCAAGAGT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 18 0.49
24 19 0.51
ACGTcount: A:0.23, C:0.30, G:0.39, T:0.08
Consensus pattern (23 bp):
CGAGGGCAGCCGAGCGAGCTATG
Found at i:64990 original size:27 final size:27
Alignment explanation
Indices: 64960--65012 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 27
64950 GAGCAAGAGT
64960 AGGTCGCCCG-GAGCATGGCGACCTACA
1 AGGTCG-CCGAGAGCATGGCGACCTACA
64987 AGGTCGCCGAAGAGCATGGCGACCTA
1 AGGTCGCCG-AGAGCATGGCGACCTA
65013 TGTATTGGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 3 0.12
27 6 0.25
28 15 0.62
ACGTcount: A:0.25, C:0.30, G:0.34, T:0.11
Consensus pattern (27 bp):
AGGTCGCCGAGAGCATGGCGACCTACA
Done.