Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008684.1 Hibiscus syriacus cultivar Beakdansim tig00111706_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: 84147
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:6044 original size:64 final size:63
Alignment explanation
Indices: 5975--6198 Score: 197
Period size: 64 Copynumber: 3.5 Consensus size: 63
5965 TTATATGAAT
* *
5975 GTGCATCGATGCATTGGTAGTGCATCGATGCA-CTATTTTAA-AATAAAGACATCGAATGCAATT
1 GTGCATCGATGCATAGGTAGTGCATCGATGCACCCA--TTAATAATAAA-ACATCGAATGCAA-T
6038 C-
62 CG
* * *
6039 GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAGTGAAACATCGAATGCAATCG
1 GTGCATCGATGCATAGGTAGTGCATCGATGCA-CCCATTAATAATAAAACATCGAATGCAATCG
** ** * * ** *
6103 GTGCATCGATGCATAAGG-AGTGCATCGATGCATCCCAACAATAATACTATATCGAATACCTTTG
1 GTGCATCGATGCAT-AGGTAGTGCATCGATGCA-CCCATTAATAATAAAACATCGAATGCAATCG
* *
6167 ATGCACCGATGCATCA-GTAGTGCATCGATGCA
1 GTGCATCGATGCAT-AGGTAGTGCATCGATGCA
6199 TACCTTCATT
Statistics
Matches: 134, Mismatches: 20, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
63 3 0.02
64 123 0.92
65 6 0.04
66 2 0.01
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (63 bp):
GTGCATCGATGCATAGGTAGTGCATCGATGCACCCATTAATAATAAAACATCGAATGCAATCG
Found at i:6525 original size:12 final size:12
Alignment explanation
Indices: 6508--6554 Score: 76
Period size: 12 Copynumber: 3.9 Consensus size: 12
6498 ATATATGTTC
6508 ATGTGATATGAT
1 ATGTGATATGAT
6520 ATGTGATATGAT
1 ATGTGATATGAT
*
6532 ATGTGATATGAC
1 ATGTGATATGAT
*
6544 ATGTAATATGA
1 ATGTGATATGA
6555 GAACATGATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.36, C:0.02, G:0.23, T:0.38
Consensus pattern (12 bp):
ATGTGATATGAT
Found at i:6717 original size:15 final size:15
Alignment explanation
Indices: 6699--6745 Score: 94
Period size: 15 Copynumber: 3.1 Consensus size: 15
6689 GAGGGTATAA
6699 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
6714 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
6729 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
6744 TA
1 TA
6746 ATGGTCCTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.15, C:0.19, G:0.32, T:0.34
Consensus pattern (15 bp):
TAGTCCTTCGGGATG
Found at i:8083 original size:20 final size:18
Alignment explanation
Indices: 8052--8124 Score: 56
Period size: 20 Copynumber: 3.8 Consensus size: 18
8042 AAACATACTG
*
8052 AAAGTATTGATACTAGTCC
1 AAAGTATCGATACTA-TCC
* *
8071 AAGAGTATCGATACTCCTGCA
1 AA-AGTATCGATACT-AT-CC
*
8092 AAAGTTTCGATACTATCC
1 AAAGTATCGATACTATCC
*
8110 TAAAGTTTCGATACT
1 -AAAGTATCGATACT
8125 TTATATAAGT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
18 1 0.02
19 17 0.39
20 23 0.52
21 3 0.07
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (18 bp):
AAAGTATCGATACTATCC
Found at i:13379 original size:21 final size:22
Alignment explanation
Indices: 13342--13382 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
13332 TAATACAATT
*
13342 ATTTTAAGAATTTAAATATTAC
1 ATTTTAAGAATTAAAATATTAC
13364 ATTTTAA-AATTAAAATATT
1 ATTTTAAGAATTAAAATATT
13383 CGAGATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (22 bp):
ATTTTAAGAATTAAAATATTAC
Found at i:22917 original size:28 final size:28
Alignment explanation
Indices: 22877--22934 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
22867 ACTAGTTTTA
22877 CTATGTTAGATTCTTATTTTGCACTAGG
1 CTATGTTAGATTCTTATTTTGCACTAGG
22905 CTATGTTAGATTCTTATTTTGCACTAGG
1 CTATGTTAGATTCTTATTTTGCACTAGG
22933 CT
1 CT
22935 TTATCAACTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.21, C:0.16, G:0.17, T:0.47
Consensus pattern (28 bp):
CTATGTTAGATTCTTATTTTGCACTAGG
Found at i:27152 original size:30 final size:30
Alignment explanation
Indices: 27107--27182 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
27097 CTTTTAAAAC
**
27107 TTACAATACAGTCCCCTAACA-TTAGTCTAT
1 TTACAATATGGTCCCC-AACATTTAGTCTAT
* * *
27137 TTGCAATATGTTCCCCGACATTTAGTCTAT
1 TTACAATATGGTCCCCAACATTTAGTCTAT
27167 TTACAATATGGTCCCC
1 TTACAATATGGTCCCC
27183 GCCGTTTGAC
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 3 0.08
30 35 0.92
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.36
Consensus pattern (30 bp):
TTACAATATGGTCCCCAACATTTAGTCTAT
Found at i:28635 original size:601 final size:601
Alignment explanation
Indices: 27487--28675 Score: 2182
Period size: 601 Copynumber: 2.0 Consensus size: 601
27477 AGACCATCAA
* * **
27487 CGATTCAAGGTGTAATGCTAGATACAGGTCATCTCAGGTGAAGCATAGATGTTCGATGAAATTCT
1 CGATTCAAGGTGTAATGCTAGATACAGGTCATCTCAAGTGAAACATAGATGTTCGATGAAAGGCT
27552 TGTGAGAAAAAATGGGGTTAGAAATGCAGAGTTGACAAATACTACTAAGATGAACTAAGTATCAT
66 TGTGAGAAAAAATGGGGTTAGAAATGCAGAGTTGACAAATACTACTAAGATGAACTAAGTATCAT
*
27617 TGTTGAAAGTCACAAACAAAGCTGAAATTATTTTGTATAAATGGCATATAATAATTTCTTCGTTT
131 TGTTGAAAGTCACAAACAAAGCTGAAATTATTTTGTATAAATGACATATAATAATTTCTTCGTTT
* *
27682 AATCCTTGTGCTTAAAGATTTTCCAACAGATGATCAAATATAATGAAATCCCAACAGCACATTCA
196 AATCCTTGTGCTTAAAGATTTTCCAACAGATGATCAAATATAATAAAATCCCAACAACACATTCA
*
27747 CCTATCGTTTGGTTTTTGTTCTTCAATTTTCCGCCATGTAAATTTGTAAACCCAAGCAGTGCTCT
261 CCTATCGTTTGGTTTTTGTTCTTCAATTTTCCGCCATGTAAATTTGAAAACCCAAGCAGTGCTCT
27812 GTCTTTCAGCTTTTTATTTACAAAGAAAAATGGAGGAAGAATTGCTGGAACACAACACCGATTGC
326 GTCTTTCAGCTTTTTATTTACAAAGAAAAATGGAGGAAGAATTGCTGGAACACAACACCGATTGC
* *
27877 GTTTATTTCTTAGTCCCTCCTCTCACTTGCAAAAAGATATTTATTTTTTCTTTTGGGCTATCCGG
391 GTTTATTTCTTAGTCCCTCCCCTCACTTGCAAAAAGATATATATTTTTTCTTTTGGGCTATCCGG
*
27942 AAGTAAGTTTTTACTCTTTCGCACTTTCCCATTTTCAGCTCGCATTGTGTGTGTTTTGTTGAAAT
456 AAGTAAGTTTTTACTCTTTCACACTTTCCCATTTTCAGCTCGCATTGTGTGTGTTTTGTTGAAAT
*
28007 TTTTATGTTTCTGGAACTGCATGTCAATGATCTGGATATTCAGTGTTAGTTTTGAACCAAAACCA
521 TTTTATGTTTATGGAACTGCATGTCAATGATCTGGATATTCAGTGTTAGTTTTGAACCAAAACCA
28072 TCTCAGGTCATCTCAG
586 TCTCAGGTCATCTCAG
* *
28088 CGATTCAAGGTGTAATGTTAGATACATGTCATCTCAAGTGAAACATAGATGTTCGATGAAAGGCT
1 CGATTCAAGGTGTAATGCTAGATACAGGTCATCTCAAGTGAAACATAGATGTTCGATGAAAGGCT
28153 TGTGAGAAAAAATGGGGTTAGAAATGCAGAGTTGACAAATACTACTAAGAT-AGACTAAGTATCA
66 TGTGAGAAAAAATGGGGTTAGAAATGCAGAGTTGACAAATACTACTAAGATGA-ACTAAGTATCA
*
28217 TTGTTGAAAGTCACAAACAAAGCTGGAATTATTTTGTATAAATGACATATAATAATTTCTTCGTT
130 TTGTTGAAAGTCACAAACAAAGCTGAAATTATTTTGTATAAATGACATATAATAATTTCTTCGTT
28282 TAATCCTTGTGCTTAAAGATTTTCCAACAGATGATCAAATATAATAAAATCCCAACAACACATTC
195 TAATCCTTGTGCTTAAAGATTTTCCAACAGATGATCAAATATAATAAAATCCCAACAACACATTC
28347 ACCTATCGTTTGGTTTTTGTTCTTCAATTTTCCGCCATGTAAATTTGAAAACCCAAGCAGTGCTC
260 ACCTATCGTTTGGTTTTTGTTCTTCAATTTTCCGCCATGTAAATTTGAAAACCCAAGCAGTGCTC
*
28412 TGTCTTTCAGCTTTTTATTTACAAAGAAAAATGGAGGAAGAATTGCTGGAACACAACATCGATTG
325 TGTCTTTCAGCTTTTTATTTACAAAGAAAAATGGAGGAAGAATTGCTGGAACACAACACCGATTG
* *
28477 CGTTTATTTCTTTGTCCCTCCCCTCACTTGCAAAAAGATATATATTTTTTCTTTTGGGCTATCTG
390 CGTTTATTTCTTAGTCCCTCCCCTCACTTGCAAAAAGATATATATTTTTTCTTTTGGGCTATCCG
28542 GAAGTAAGTTTTTACTCTTTCACACTTTCCCATTTTCAGCTCGCATTGTGTGTGTTTTGTTGAAA
455 GAAGTAAGTTTTTACTCTTTCACACTTTCCCATTTTCAGCTCGCATTGTGTGTGTTTTGTTGAAA
* *
28607 TTTTTATGTTTATGGAACTGCTTGTCAATGATCTGGATATTTAGTGTTAGTTTTGAACCAAAACC
520 TTTTTATGTTTATGGAACTGCATGTCAATGATCTGGATATTCAGTGTTAGTTTTGAACCAAAACC
28672 ATCT
585 ATCT
28676 AATTTTCTTT
Statistics
Matches: 567, Mismatches: 20, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
600 1 0.00
601 566 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (601 bp):
CGATTCAAGGTGTAATGCTAGATACAGGTCATCTCAAGTGAAACATAGATGTTCGATGAAAGGCT
TGTGAGAAAAAATGGGGTTAGAAATGCAGAGTTGACAAATACTACTAAGATGAACTAAGTATCAT
TGTTGAAAGTCACAAACAAAGCTGAAATTATTTTGTATAAATGACATATAATAATTTCTTCGTTT
AATCCTTGTGCTTAAAGATTTTCCAACAGATGATCAAATATAATAAAATCCCAACAACACATTCA
CCTATCGTTTGGTTTTTGTTCTTCAATTTTCCGCCATGTAAATTTGAAAACCCAAGCAGTGCTCT
GTCTTTCAGCTTTTTATTTACAAAGAAAAATGGAGGAAGAATTGCTGGAACACAACACCGATTGC
GTTTATTTCTTAGTCCCTCCCCTCACTTGCAAAAAGATATATATTTTTTCTTTTGGGCTATCCGG
AAGTAAGTTTTTACTCTTTCACACTTTCCCATTTTCAGCTCGCATTGTGTGTGTTTTGTTGAAAT
TTTTATGTTTATGGAACTGCATGTCAATGATCTGGATATTCAGTGTTAGTTTTGAACCAAAACCA
TCTCAGGTCATCTCAG
Found at i:29750 original size:31 final size:31
Alignment explanation
Indices: 29688--29760 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 31
29678 CGATCGGGGT
*
29688 CCATATTGCAAACAGACTAAATACTGGAAGA
1 CCATATTGCAAACAGACTAAATACTGAAAGA
* * **
29719 CCATATTGCAAACGGATTAAATGTTGAAAGA
1 CCATATTGCAAACAGACTAAATACTGAAAGA
**
29750 CTGTATTGCAA
1 CCATATTGCAA
29761 GTTTTAAAAG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (31 bp):
CCATATTGCAAACAGACTAAATACTGAAAGA
Found at i:36868 original size:6 final size:6
Alignment explanation
Indices: 36857--37078 Score: 444
Period size: 6 Copynumber: 37.0 Consensus size: 6
36847 AAACTCATGA
36857 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
36905 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
36953 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
37001 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
37049 TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG
37079 GATGTTAACA
Statistics
Matches: 216, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 216 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
TATATG
Found at i:37859 original size:16 final size:16
Alignment explanation
Indices: 37838--37880 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
37828 ACAGAGTCTC
37838 TGAATCATTCAGCATT
1 TGAATCATTCAGCATT
37854 TGAATCATTCAGCATT
1 TGAATCATTCAGCATT
37870 TGAATCATTCA
1 TGAATCATTCA
37881 TCGCTTAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (16 bp):
TGAATCATTCAGCATT
Found at i:46080 original size:21 final size:21
Alignment explanation
Indices: 46054--46101 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
46044 GTTTCCAGAT
* *
46054 TCGCAACGCGAACTTCGACTA
1 TCGCAACACGAACTTCGACAA
*
46075 TCGCAACACGAACTTGGACAA
1 TCGCAACACGAACTTCGACAA
46096 TCGCAA
1 TCGCAA
46102 TGTGAATATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (21 bp):
TCGCAACACGAACTTCGACAA
Found at i:46291 original size:6 final size:6
Alignment explanation
Indices: 46270--46306 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
46260 TCCCGTCTCG
46270 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
46307 AATACGTGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.00, C:0.16, G:0.54, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:46404 original size:21 final size:21
Alignment explanation
Indices: 46380--46451 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
46370 ATGCAATACT
*
46380 ATCGCAACGAAATTGGAATAA
1 ATCGCAACGAATTTGGAATAA
*
46401 ATCGCAACGAATTTGAAATAA
1 ATCGCAACGAATTTGGAATAA
*
46422 ATCGCAACGAATTTAGAATAA
1 ATCGCAACGAATTTGGAATAA
46443 ATCGCAACG
1 ATCGCAACG
46452 CGAACTTAGA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.46, C:0.17, G:0.17, T:0.21
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATAA
Found at i:53067 original size:3 final size:3
Alignment explanation
Indices: 53059--53126 Score: 109
Period size: 3 Copynumber: 22.3 Consensus size: 3
53049 TATTTTTAAA
*
53059 ATT ATT ATT ATT ATT ATA ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
53107 ATT AAAT ATT ATT ATT ATT A
1 ATT -ATT ATT ATT ATT ATT A
53127 CAAGCCCAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
3 58 0.97
4 2 0.03
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:55332 original size:130 final size:130
Alignment explanation
Indices: 55107--55350 Score: 330
Period size: 130 Copynumber: 1.9 Consensus size: 130
55097 GATCGTTGAT
* * *
55107 ATTTATTTATTTCTAAATATTAAGAAAGGATTGTCTTAAATTAACTAGATGTCATATTCTAATAT
1 ATTTATTTATTTCTAAATATTAAGAAAGGACTGTCTTAAAGTAACTAGATGTCATATTATAATAT
*
55172 TTTTTTAATAAATAAATACCTTACTTATAAAAAC-AAATATATATATAATTTTAATTTTATTCAA
66 TTTTTAAATAAATAAATACCTTACTTATAAAAACTAAATATATATATAATTTTAATTTTATTCAA
* * * * * * *
55236 ATTTATTTATTTTTCAATTTTAAAGAAATGGGCTGTCTTAAAGTAACTAGATGTCCTTTTATGAT
1 ATTTATTTATTTCTAAATATT-AAGAAA-GGACTGTCTTAAAGTAACTAGATGTCATATTATAAT
* *
55301 A-TTTTTAAATAAATAAATACCTTATTTATAAAACCTTAAATATATATATA
64 ATTTTTTAAATAAATAAATACCTTACTTATAAAAAC-TAAATATATATATA
55351 TATATATATT
Statistics
Matches: 98, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
129 18 0.18
130 37 0.38
131 30 0.31
132 13 0.13
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (130 bp):
ATTTATTTATTTCTAAATATTAAGAAAGGACTGTCTTAAAGTAACTAGATGTCATATTATAATAT
TTTTTAAATAAATAAATACCTTACTTATAAAAACTAAATATATATATAATTTTAATTTTATTCAA
Found at i:55895 original size:22 final size:22
Alignment explanation
Indices: 55870--55915 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
55860 AAAATCGAGC
* *
55870 AAGTTTTCATAAAAAA-TAGAAA
1 AAGTGTTCACAAAAAACT-GAAA
55892 AAGTGTTCACAAAAAACTGAAA
1 AAGTGTTCACAAAAAACTGAAA
55914 AA
1 AA
55916 TTAGTCTACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.59, C:0.09, G:0.11, T:0.22
Consensus pattern (22 bp):
AAGTGTTCACAAAAAACTGAAA
Found at i:56276 original size:37 final size:37
Alignment explanation
Indices: 56204--56322 Score: 156
Period size: 37 Copynumber: 3.2 Consensus size: 37
56194 GGGTTTGTAT
*
56204 TATATAATTAATAT-AAAAAT---ATAAAATATTATA
1 TATATAATTAATATAAAAAATAAAAAAAAATATTATA
56237 TATATAATTAATATAAAAAATAAAAAAAAATATTATA
1 TATATAATTAATATAAAAAATAAAAAAAAATATTATA
**
56274 TATATAATTAATATAAAAAATATAAAACATTATATATATA
1 TATATAATTAATATAAAAAATA-AAAA-AAAATAT-TATA
56314 TATATAATT
1 TATATAATT
56323 GGGGCCAGGT
Statistics
Matches: 76, Mismatches: 3, Indels: 7
0.88 0.03 0.08
Matches are distributed among these distances:
33 14 0.18
34 6 0.08
37 34 0.45
38 4 0.05
39 5 0.07
40 13 0.17
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (37 bp):
TATATAATTAATATAAAAAATAAAAAAAAATATTATA
Found at i:56989 original size:30 final size:30
Alignment explanation
Indices: 56953--57114 Score: 279
Period size: 30 Copynumber: 5.4 Consensus size: 30
56943 TCCGAAGGAC
*
56953 CTATCCAGAGGTCATAAAGATCTTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
56983 CTATCCAAAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
57013 CTATCCAGAGGTCATAAAGATCTTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
57043 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
57073 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
57103 CTGTCCATAGGT
1 CTATCCAGAGGT
57115 ACCGAAGAAC
Statistics
Matches: 125, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 125 1.00
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:57132 original size:90 final size:91
Alignment explanation
Indices: 56953--57140 Score: 272
Period size: 90 Copynumber: 2.1 Consensus size: 91
56943 TCCGAAGGAC
*
56953 CTATCCAGAGGTCATAAAGATCTTCGGTAACTATCCAAAGGTCATAAAGATCCTCGGTAACTATC
1 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAAAGGTCATAAAGATCCTCGGTAACTATC
* * * *
57018 CAGAGGTCATAAAGATCTTCGGT-AA
66 CAGAGGTCACAAAGAACCTAGGTAAA
* *
57043 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTGTC
1 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAAAGGTCATAAAGATCCTCGGTAACTATC
* *
57108 CATAGGT-ACCGAAGAACCTAGGTAAA
66 CAGAGGTCA-CAAAGAACCTAGGTAAA
57134 CTATCCA
1 CTATCCA
57141 TATGTTCCTT
Statistics
Matches: 87, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
89 1 0.01
90 77 0.89
91 9 0.10
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (91 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAAAGGTCATAAAGATCCTCGGTAACTATC
CAGAGGTCACAAAGAACCTAGGTAAA
Found at i:57189 original size:31 final size:31
Alignment explanation
Indices: 57101--57193 Score: 89
Period size: 31 Copynumber: 3.0 Consensus size: 31
57091 GATCCTCGGT
* * * * *
57101 AACTGTCCATAGGTACCGAAGAACCTAGGTA
1 AACTATCCATATGTTCCAAAGAACATAGGTA
**
57132 AACTATCCATATGTTCCTTAGAACATAGGTA
1 AACTATCCATATGTTCCAAAGAACATAGGTA
* *
57163 TACTATCCATATGTCTCGAAAG-ACATAGGTA
1 AACTATCCATATGT-TCCAAAGAACATAGGTA
57194 GTTCTTTGAC
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
31 47 0.92
32 4 0.08
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.27
Consensus pattern (31 bp):
AACTATCCATATGTTCCAAAGAACATAGGTA
Found at i:57380 original size:4 final size:4
Alignment explanation
Indices: 57371--57954 Score: 1126
Period size: 4 Copynumber: 147.5 Consensus size: 4
57361 TAACCCTTAT
57371 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
57419 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
57467 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
57515 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
57563 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
57611 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
57659 ATAC ATAC ATAC ATAC ATAC ATAC ATAC --AC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
57705 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
57753 ATAC --AC ATAC ATAC ATAC ATAC --AC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
57797 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
57845 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
57893 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
57941 ATAC ATAC ATAC AT
1 ATAC ATAC ATAC AT
57955 GTCATCATTT
Statistics
Matches: 574, Mismatches: 0, Indels: 12
0.98 0.00 0.02
Matches are distributed among these distances:
2 6 0.01
4 568 0.99
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:58846 original size:19 final size:20
Alignment explanation
Indices: 58809--58846 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
58799 TTTTTCATTA
*
58809 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
58829 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
58847 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:58898 original size:21 final size:21
Alignment explanation
Indices: 58874--58916 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
58864 TCATATTCGT
* *
58874 TTGAGGGGGGATCGATTCCCC
1 TTGAAGGGGGACCGATTCCCC
* *
58895 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGGACCGATTCCCC
58916 T
1 T
58917 AGCCCAGAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.16, C:0.26, G:0.30, T:0.28
Consensus pattern (21 bp):
TTGAAGGGGGACCGATTCCCC
Found at i:60635 original size:29 final size:29
Alignment explanation
Indices: 60592--60674 Score: 148
Period size: 29 Copynumber: 2.8 Consensus size: 29
60582 CTCACCTAAC
60592 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTACT
*
60622 TAAATGATGTAAGCAATGACATCTTTACT
1 TAAATGATGTAAGCAATGACATCATTACT
60651 TAAATGATGTAAGCAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
60675 ATTTAGTTTG
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 47 0.92
30 4 0.08
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.31
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTACT
Found at i:65398 original size:29 final size:29
Alignment explanation
Indices: 65351--65433 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
65341 CACACCTAAC
65351 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTACT
* *
65381 TAAATGATGTAAGAAATGACATCTTTACT
1 TAAATGATGTAAGCAATGACATCATTACT
65410 TAAATGATGTAAGCAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
65434 ATTTAGTTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 45 0.92
30 4 0.08
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.31
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTACT
Found at i:73249 original size:2 final size:2
Alignment explanation
Indices: 73242--73267 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
73232 CTTCCTAGAA
73242 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
73268 GAAGTGGACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:74362 original size:19 final size:19
Alignment explanation
Indices: 74323--74363 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
74313 ATTTATTTTT
*
74323 TTATTATTAATTATTATTA
1 TTATTATTAATTATTAATA
74342 TTATTATTAATT-TTACATA
1 TTATTATTAATTATTA-ATA
74361 TTA
1 TTA
74364 CACTTTTGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
TTATTATTAATTATTAATA
Found at i:74937 original size:21 final size:21
Alignment explanation
Indices: 74898--74942 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
74888 GAGAATAGAG
* *
74898 AAAAAAGAGAGATACGAAACA
1 AAAAAAGAGAGAGAAGAAACA
*
74919 AAAAAAGAGAGAGAAGAAAGA
1 AAAAAAGAGAGAGAAGAAACA
74940 AAA
1 AAA
74943 GTTTTACCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.71, C:0.04, G:0.22, T:0.02
Consensus pattern (21 bp):
AAAAAAGAGAGAGAAGAAACA
Found at i:76185 original size:29 final size:29
Alignment explanation
Indices: 76146--76202 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
76136 GACTCTTGAG
76146 TTTCTATTTTTACTATTTTAATCCCTTTAA
1 TTTCTATTTTTACTATTTTAAT-CCTTTAA
*
76176 TTTCTA-TTTTATTATTTTAATCCTTTA
1 TTTCTATTTTTACTATTTTAATCCTTTA
76203 TGTTTAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 6 0.23
29 14 0.54
30 6 0.23
ACGTcount: A:0.23, C:0.14, G:0.00, T:0.63
Consensus pattern (29 bp):
TTTCTATTTTTACTATTTTAATCCTTTAA
Found at i:76213 original size:29 final size:29
Alignment explanation
Indices: 76153--76222 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
76143 GAGTTTCTAT
**
76153 TTTTACTATTTTAATCCCTTTAATTTCTA
1 TTTTACTATTTTAATCCCTTTAATTTAAA
* *
76182 TTTTATTATTTTAAT-CCTTTATGTTTAAA
1 TTTTACTATTTTAATCCCTTTA-ATTTAAA
*
76211 TTTTGCTATTTT
1 TTTTACTATTTT
76223 TGTCCTTCAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 6 0.18
29 28 0.82
ACGTcount: A:0.23, C:0.11, G:0.03, T:0.63
Consensus pattern (29 bp):
TTTTACTATTTTAATCCCTTTAATTTAAA
Done.