Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002035.1 Hibiscus syriacus cultivar Beakdansim tig00004150_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: 79333
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:8517 original size:3 final size:3
Alignment explanation
Indices: 8509--8567 Score: 104
Period size: 3 Copynumber: 20.3 Consensus size: 3
8499 GAGCAGGGAA
8509 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
8556 ATT -TT ATT ATT A
1 ATT ATT ATT ATT A
8568 ATAATAATGT
Statistics
Matches: 54, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 4 0.07
3 50 0.93
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:13077 original size:55 final size:55
Alignment explanation
Indices: 13011--13123 Score: 156
Period size: 55 Copynumber: 2.1 Consensus size: 55
13001 GCATTTATAT
*
13011 GATTCATGAAGAAGAACATTCGACGAATGAAGAAATTTG-AACTTGAATGAAGAAC
1 GATTCATGAAGAAGAACATCCGACGAATGAAGAAATTTGAAAC-TGAATGAAGAAC
* * * * *
13066 GATTCATGAAGAAGGACATCCGATGAATGAATAAATTTGAAACTGATTGAAGACC
1 GATTCATGAAGAAGAACATCCGACGAATGAAGAAATTTGAAACTGAATGAAGAAC
13121 GAT
1 GAT
13124 CCACAAAGAA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
55 48 0.94
56 3 0.06
ACGTcount: A:0.43, C:0.12, G:0.22, T:0.23
Consensus pattern (55 bp):
GATTCATGAAGAAGAACATCCGACGAATGAAGAAATTTGAAACTGAATGAAGAAC
Found at i:13133 original size:55 final size:55
Alignment explanation
Indices: 13019--13141 Score: 133
Period size: 55 Copynumber: 2.2 Consensus size: 55
13009 ATGATTCATG
* * **
13019 AAGAAGAACATTCGACGAATGAAGAAATTTGAACTTGAATGAAGAACGATTCATG
1 AAGAAGAACATCCGACGAATGAAGAAATTTGAACTTGAATGAAGAACGATCCACA
* * * * *
13074 AAGAAGGACATCCGATGAATGAATAAATTTGAAAC-TGATTGAAGACCGATCCACA
1 AAGAAGAACATCCGACGAATGAAGAAATTTG-AACTTGAATGAAGAACGATCCACA
13129 AAGAA-ATACATCC
1 AAGAAGA-ACATCC
13142 TGAAGATGTT
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
55 53 0.95
56 3 0.05
ACGTcount: A:0.46, C:0.15, G:0.20, T:0.20
Consensus pattern (55 bp):
AAGAAGAACATCCGACGAATGAAGAAATTTGAACTTGAATGAAGAACGATCCACA
Found at i:13920 original size:72 final size:72
Alignment explanation
Indices: 13803--13953 Score: 230
Period size: 72 Copynumber: 2.1 Consensus size: 72
13793 CCCTATTACA
* * * * *
13803 CAAGAAAATATGAAGACTTTGGGTGAGAATCTGAATGTTAGTGGTGCAGCCAATGTAATGATAGC
1 CAAGAACAGATGAAGACTTCGAGTGAGAATCTGAATGTTAGTGGTGCAGCCAATATAATGATAGC
13868 AAATGAT
66 AAATGAT
* *
13875 CAAGAACAGATGAAGACTTCGAGTGAGAATCTTAATGTTAGTGGTGCAGCCAATATGATGATAGC
1 CAAGAACAGATGAAGACTTCGAGTGAGAATCTGAATGTTAGTGGTGCAGCCAATATAATGATAGC
*
13940 AACTGAT
66 AAATGAT
13947 CAAGAAC
1 CAAGAAC
13954 CTGTTAGGGG
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.25
Consensus pattern (72 bp):
CAAGAACAGATGAAGACTTCGAGTGAGAATCTGAATGTTAGTGGTGCAGCCAATATAATGATAGC
AAATGAT
Found at i:18557 original size:37 final size:37
Alignment explanation
Indices: 18507--18620 Score: 158
Period size: 37 Copynumber: 3.1 Consensus size: 37
18497 AAAGCCAAGT
*
18507 CTTCACCAAAGAGTAATGAAGCAAATCCATTTTGAGC
1 CTTCACCAAAGAGTAATGAAGCAAATCCATTTTAAGC
* *
18544 CTTCACCAAAGAGTAGTGAAGCAAA-CCATCTTAAGC
1 CTTCACCAAAGAGTAATGAAGCAAATCCATTTTAAGC
* * * *
18580 CTTCACCGAAGAGTAATGAAGCATATCCTTTTTAGGC
1 CTTCACCAAAGAGTAATGAAGCAAATCCATTTTAAGC
18617 CTTC
1 CTTC
18621 TCGGAAGAGT
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
36 31 0.46
37 36 0.54
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (37 bp):
CTTCACCAAAGAGTAATGAAGCAAATCCATTTTAAGC
Found at i:18592 original size:36 final size:36
Alignment explanation
Indices: 18507--18602 Score: 147
Period size: 36 Copynumber: 2.6 Consensus size: 36
18497 AAAGCCAAGT
* *
18507 CTTCACCAAAGAGTAATGAAGCAAATCCATTTTGAGC
1 CTTCACCAAAGAGTAATGAAGCAAA-CCATCTTAAGC
*
18544 CTTCACCAAAGAGTAGTGAAGCAAACCATCTTAAGC
1 CTTCACCAAAGAGTAATGAAGCAAACCATCTTAAGC
*
18580 CTTCACCGAAGAGTAATGAAGCA
1 CTTCACCAAAGAGTAATGAAGCA
18603 TATCCTTTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
36 30 0.56
37 24 0.44
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.21
Consensus pattern (36 bp):
CTTCACCAAAGAGTAATGAAGCAAACCATCTTAAGC
Found at i:18594 original size:73 final size:73
Alignment explanation
Indices: 18507--18646 Score: 185
Period size: 73 Copynumber: 1.9 Consensus size: 73
18497 AAAGCCAAGT
18507 CTTCACCAAAGAGTAATGAAGCAAATCCATTTTGA-GCCTTCACCAAAGAGTAG-TGAAGCAAAC
1 CTTCACCAAAGAGTAATGAAGCAAATCC-TTTTGAGGCCTTCACCAAAGAGT-GTTGAAGCAAAC
18570 CATCTTAAGC
64 CATCTTAAGC
* * * * ** *
18580 CTTCACCGAAGAGTAATGAAGCATATCCTTTTTAGGCCTTCTCGGAAGAGTGTTGGAGCAAACCA
1 CTTCACCAAAGAGTAATGAAGCAAATCCTTTTGAGGCCTTCACCAAAGAGTGTTGAAGCAAACCA
18645 TC
66 TC
18647 AGACTATCAG
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
72 6 0.10
73 52 0.90
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (73 bp):
CTTCACCAAAGAGTAATGAAGCAAATCCTTTTGAGGCCTTCACCAAAGAGTGTTGAAGCAAACCA
TCTTAAGC
Found at i:19069 original size:54 final size:54
Alignment explanation
Indices: 19007--19347 Score: 558
Period size: 54 Copynumber: 6.3 Consensus size: 54
18997 GTAGTAAAGC
*
19007 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGTGAACCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
*
19061 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGAGAGCGAACCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
* * *
19115 AGAAGAAGATATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCTGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
* * *
19169 AGAAGAATATGTTTGAGTTACATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
* *
19223 AGAAGAAGATGCTCGAGTTTCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
* *
19277 AGAAGAATATGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
*
19331 AG-AGAATATGTTCGAGT
1 AGAAGAAGATGTTCGAGT
19348 CTTATACTCT
Statistics
Matches: 267, Mismatches: 20, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
53 15 0.06
54 252 0.94
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.19
Consensus pattern (54 bp):
AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
Found at i:19398 original size:108 final size:107
Alignment explanation
Indices: 19007--19596 Score: 487
Period size: 108 Copynumber: 5.5 Consensus size: 107
18997 GTAGTAAAGC
* * * *
19007 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGT-GAACCCGTAAGAAGAAGA-
1 AGAAGAAGATGTTCGAGTT-TATACTCCCTA-AGAAAGAGGGAGTCGAACACGT-TGTAGAAGAT
* *
19070 TGTTCGAGTTCCATACTCCCTAGAGAAAGAGAGAGCGAACCCGTA
63 TGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTA
*
19115 AGAAGAAGATATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAG-CGAAC-C--TGTAAGAAGAA
1 AGAAGAAGATGTTCGAGTT-TATACTCCCTA-AGAAAGAGGGAGTCGAACACGTTGT-AGAAG-A
* * *
19176 TATGTTTGAGTTACATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
62 T-TGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTA
* * *
19223 AGAAGAAGATGCTCGAGTTTCATACTCCCTAGAGAAAGAGGGAG-CGAACCCG-T-AAGAAGAAT
1 AGAAGAAGATGTTCGAGTTT-ATACTCCCTA-AGAAAGAGGGAGTCGAACACGTTGTAGAAG-AT
19285 ATGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTA
63 -TGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTA
* * * * * *
19331 AG-AGAATATGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGTAG-ACACGATTGTTGAAGAT
1 AGAAGAAGATGTTCGAGT-TTATACTCCCT-AAGAAAGAGGGAGTCGAACACG-TTGTAGAAGAT
* * * ** *
19394 TGTTCGAG-TCTCATACTCTCTAAAGGAATAGGGAGC-AGACACATTT
63 TGTTCGAGTTC-CATACTCCCTAAAGAAAGAGGGAGCGA-AC-CCGTA
** * * * * *
19440 TCAA-AATATTTTCAAGTTTTATACTCCCTAAAGAAAGAGGGAGT-GAACCCGTTTGCAGAAGAT
1 AGAAGAAGATGTTCGAG-TTTATACTCCCT-AAGAAAGAGGGAGTCGAACACG-TTGTAGAAGAT
* * *
19503 T-TTCAAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTA
63 TGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTA
* * * *
19547 GGCAA-AAGATTGTTCGAGTTTCTACTCCCTGAAGGAATAGGGAGT-GAACA
1 AG-AAGAAGA-TGTTCGAGTTTATACTCCCT-AAGAAAGAGGGAGTCGAACA
19597 TGTTTTTCGA
Statistics
Matches: 399, Mismatches: 59, Indels: 48
0.79 0.12 0.09
Matches are distributed among these distances:
104 1 0.00
105 5 0.01
106 1 0.00
107 42 0.11
108 282 0.71
109 61 0.15
110 7 0.02
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (107 bp):
AGAAGAAGATGTTCGAGTTTATACTCCCTAAGAAAGAGGGAGTCGAACACGTTGTAGAAGATTGT
TCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTA
Found at i:19410 original size:162 final size:161
Alignment explanation
Indices: 19007--19576 Score: 541
Period size: 162 Copynumber: 3.5 Consensus size: 161
18997 GTAGTAAAGC
* * * *
19007 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGTGAACCCGTAAGAAGAAGATG
1 AGAAGAATATGTTCGAGTTACATACTCCCTAGAGAAAGAGGGAGAGAACACGTAAGAAGAAGATG
* *
19072 TTCGAGTTCCATACTCCCTAGAGAAAGAGAGAGCGAACCCGTAAGAAGAAGATATTCGAGTTCTA
66 TTCGAGTT-CATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAAGAAGAATATATTCGAGTTCTA
* *
19137 TACTCCCTAGAGAAAGAGGGAGCGAACCTGTA
130 TACTCCCTAAAGAAAGAGGGAGCGAACCCGTA
* * *
19169 AGAAGAATATGTTTGAGTTACATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATG
1 AGAAGAATATGTTCGAGTTACATACTCCCTAGAGAAAGAGGGAGAGAACACGTAAGAAGAAGATG
* * *
19234 CTCGAGTTTCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAAGAAGAATATGTTCGAGTTCCA
66 TTCGAG-TTCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAAGAAGAATATATTCGAGTTCTA
19299 TACTCCCTAAAGAAAGAGGGAGCGAACCCGTA
130 TACTCCCTAAAGAAAGAGGGAGCGAACCCGTA
* * * * * **
19331 AG-AGAATATGTTCGAGTCT-TATACTCTCT-GAAGGAATAGGGAGTAG-ACACG-ATTGTTGAA
1 AGAAGAATATGTTCGAGT-TACATACTCCCTAG-AGAAAGAGGGAG-AGAACACGTA-AGAAGAA
* * * * ** *** * *
19391 GATTGTTCGAGTCTCATACTCTCTAAAGGAATAGGGAGC-AGACACATTTTCAA-AATATTTTCA
62 GA-TGTTCGAGT-TCATACTCCCTAGAGAAAGAGGGAGCGA-AC-CCGTAAGAAGAATATATTCG
* * *
19454 AGTTTTATACTCCCTAAAGAAAGAGGGAGTGAACCCGTT
123 AGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTA
* * * * * * * *
19493 TGCAGAAGATTTTCAAGTT-CTATACTCCCT-GAAGAAAGAGGGAGCGAACCCGTAGGCAA-AAG
1 AGAAGAATATGTTCGAGTTAC-ATACTCCCTAG-AGAAAGAGGGAGAGAACACGTAAG-AAGAAG
19555 ATTGTTCGAGTTTC-TACTCCCT
63 A-TGTTCGAG-TTCATACTCCCT
19577 GAAGGAATAG
Statistics
Matches: 342, Mismatches: 51, Indels: 30
0.81 0.12 0.07
Matches are distributed among these distances:
160 2 0.01
161 44 0.13
162 236 0.69
163 58 0.17
164 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.23
Consensus pattern (161 bp):
AGAAGAATATGTTCGAGTTACATACTCCCTAGAGAAAGAGGGAGAGAACACGTAAGAAGAAGATG
TTCGAGTTCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAAGAAGAATATATTCGAGTTCTAT
ACTCCCTAAAGAAAGAGGGAGCGAACCCGTA
Found at i:19505 original size:54 final size:54
Alignment explanation
Indices: 19460--19595 Score: 114
Period size: 54 Copynumber: 2.5 Consensus size: 54
19450 TTCAAGTTTT
* ** * * * *
19460 ATACTCCCTAAAGAAAGAGGGAGTGAACCCGTTTGCAGAAGATTTTCAAGTTCT
1 ATACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATGTTCGAGTTCC
* * *
19514 ATACTCCCTGAAGAAAGAGGGAGCGAACCCGTAGGCAA-AAGATTGTTCGAGTTTC
1 ATACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAG-AAGAAGA-TGTTCGAGTTCC
* * * *
19569 -TACTCCCTGAAGGAATAGGGAGTGAAC
1 ATACTCCCTAAAGAAAGAGGGAGCGAAC
19596 ATGTTTTTCG
Statistics
Matches: 68, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
54 59 0.87
55 9 0.13
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.22
Consensus pattern (54 bp):
ATACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATGTTCGAGTTCC
Found at i:19786 original size:3 final size:3
Alignment explanation
Indices: 19778--19821 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
19768 TGTCTGGGAA
19778 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT -TT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
19822 ATAATAATGT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.10
3 35 0.90
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:34933 original size:3 final size:3
Alignment explanation
Indices: 34925--35030 Score: 169
Period size: 3 Copynumber: 35.7 Consensus size: 3
34915 ATTTAATATT
* * * *
34925 TAA TAA TAA AAA TAA TAA TAA TAA TAT TAA TAA TAA TAT TAA TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
34973 TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
35020 TAA TAA TAA TA
1 TAA TAA TAA TA
35031 TGGATAAAAA
Statistics
Matches: 94, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
2 2 0.02
3 92 0.98
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:35607 original size:113 final size:113
Alignment explanation
Indices: 35325--35997 Score: 1028
Period size: 113 Copynumber: 5.9 Consensus size: 113
35315 GATATCAAAC
*
35325 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* ** * * * *
35390 CATGAACTTTCTTTGGCCATGTTGATCCATCAAATGATGAATTTAAACAA
66 -ATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGC-A
*
35440 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
35505 ATGAACTTTCTCTGGAAAAT-ATGATCCACCAAATGATGGATTCAGGTA
66 ATGAACTTTCTCTGG-AAATGATGATCCATCAAATGATGGATTCAAGCA
*
35553 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
35618 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
66 ATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGCA
35666 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
35731 ATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTCAAGCA
66 ATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGCA
35779 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * **
35844 ATGAACTTTCTCTGGAAATGCTGATCCATCGAATGATGGATTTGAGCA
66 ATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGCA
* *
35892 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
** * **
35957 ATGAACTCGAC-CTGG-AATGTTGATCCATTGAATGATGGATT
66 ATGAACT-TTCTCTGGAAATGATGATCCATCAAATGATGGATT
35998 TAAACTTTGC
Statistics
Matches: 520, Mismatches: 35, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
112 27 0.05
113 393 0.76
114 35 0.07
115 65 0.12
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.38
Consensus pattern (113 bp):
AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGCA
Found at i:36423 original size:22 final size:22
Alignment explanation
Indices: 36398--36452 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
36388 CATAAAGTTT
*
36398 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
*
36420 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
36442 TCATCTTTGAA
1 TCATCTTTGAA
36453 GAGTGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:38648 original size:83 final size:83
Alignment explanation
Indices: 38508--38689 Score: 303
Period size: 83 Copynumber: 2.2 Consensus size: 83
38498 CTTATTTCTA
*
38508 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATTAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
38573 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* * *
38591 CTATGAACAAATTCATCTTCTAAATTCAATGATTGGTTTTG-CCAAACCAGATCAGATAACTCAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCC-AACCAGATCAGATAACTCAA
38655 AGAACACTTCCAGAAGATG
65 AGAACACTTCCAGAAGATG
*
38674 CTATGAGCACATTCAT
1 CTATGAGCAAATTCAT
38690 TTGTTCCATT
Statistics
Matches: 92, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
82 2 0.02
83 90 0.98
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (83 bp):
CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:47873 original size:3 final size:3
Alignment explanation
Indices: 47865--47974 Score: 184
Period size: 3 Copynumber: 36.7 Consensus size: 3
47855 TTAATATATT
* * * *
47865 TAA TAA TAA AAA TAA TAA TAA TAA TAT TAA TAA TAA TAT TAA TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
47913 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
47961 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
47975 TGGATAAAAA
Statistics
Matches: 99, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 99 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:48125 original size:23 final size:23
Alignment explanation
Indices: 48098--48151 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
48088 GTCCAAACGA
48098 AAACATGCCTGTCCAGTTTGGAT
1 AAACATGCCTGTCCAGTTTGGAT
48121 AAACATGCCTGTCCAGTTTGGAT
1 AAACATGCCTGTCCAGTTTGGAT
48144 AAACATGC
1 AAACATGC
48152 AAGCCTTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (23 bp):
AAACATGCCTGTCCAGTTTGGAT
Found at i:51589 original size:14 final size:16
Alignment explanation
Indices: 51570--51601 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
51560 GAACTCAAAT
51570 ATTAAT-ATTTA-ATA
1 ATTAATAATTTATATA
51584 ATTAATAATTTATATA
1 ATTAATAATTTATATA
51600 AT
1 AT
51602 AAAATAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 5 0.31
16 5 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTAATAATTTATATA
Found at i:51630 original size:23 final size:27
Alignment explanation
Indices: 51579--51628 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 27
51569 TATTAATATT
*
51579 TAATAATTAATAATTTATATAATAAAA
1 TAATAATTAATAATTAATATAATAAAA
51606 TAATAA-TAATAA-TAATA-AATAAA
1 TAATAATTAATAATTAATATAATAAA
51629 TACGACTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 6 0.27
25 4 0.18
26 6 0.27
27 6 0.27
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (27 bp):
TAATAATTAATAATTAATATAATAAAA
Found at i:59521 original size:25 final size:25
Alignment explanation
Indices: 59474--59522 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
59464 AAAGAATAAA
59474 AAATTATTTAAATGTATATTTTATC
1 AAATTATTTAAATGTATATTTTATC
*
59499 AAATTATTTTAAT-TATATATTTAT
1 AAATTATTTAAATGTATAT-TTTAT
59523 TTTTTTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (25 bp):
AAATTATTTAAATGTATATTTTATC
Found at i:60385 original size:20 final size:20
Alignment explanation
Indices: 60360--60413 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
60350 AACTCTAACT
* *
60360 TTAAAATCAAATAATTGAAA
1 TTAAAAGCAAATAATCGAAA
*
60380 TTAAAAGCAAATAATCGAAG
1 TTAAAAGCAAATAATCGAAA
*
60400 TTAAAAGTAAATAA
1 TTAAAAGCAAATAA
60414 GTAAAAGCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.59, C:0.06, G:0.09, T:0.26
Consensus pattern (20 bp):
TTAAAAGCAAATAATCGAAA
Found at i:60420 original size:14 final size:14
Alignment explanation
Indices: 60398--60440 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
60388 AAATAATCGA
60398 AGTTAAAAGTAAAT
1 AGTTAAAAGTAAAT
*
60412 AAG-TAAAAGCAAAT
1 -AGTTAAAAGTAAAT
60426 AGTTTAAAAGTAAAT
1 AG-TTAAAAGTAAAT
60441 GATTGAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 2 0.08
14 10 0.42
15 12 0.50
ACGTcount: A:0.58, C:0.02, G:0.14, T:0.26
Consensus pattern (14 bp):
AGTTAAAAGTAAAT
Found at i:61434 original size:39 final size:39
Alignment explanation
Indices: 61389--61502 Score: 142
Period size: 39 Copynumber: 2.9 Consensus size: 39
61379 AGTTAAAAGA
*
61389 AATAATTTAGATTGTTAGGGTGAAATAGC-TTAAGAAATT
1 AATAATTTAGAATGTTAGGGTGAAATA-CTTTAAGAAATT
61428 AATAATTTAGAATGTT-GTGGTGAAATACTTTAAGAAATT
1 AATAATTTAGAATGTTAG-GGTGAAATACTTTAAGAAATT
* * * * *
61467 AAGAATTTAGAATGTTATGTTGAAATAATTTTAGAA
1 AATAATTTAGAATGTTAGGGTGAAATACTTTAAGAA
61503 TTAGGAATAA
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
38 2 0.03
39 64 0.97
ACGTcount: A:0.42, C:0.02, G:0.18, T:0.38
Consensus pattern (39 bp):
AATAATTTAGAATGTTAGGGTGAAATACTTTAAGAAATT
Found at i:64632 original size:14 final size:14
Alignment explanation
Indices: 64613--64640 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
64603 TCTAATATAC
64613 AAAAGTACTATAAT
1 AAAAGTACTATAAT
64627 AAAAGTACTATAAT
1 AAAAGTACTATAAT
64641 TAATAAATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (14 bp):
AAAAGTACTATAAT
Found at i:67369 original size:56 final size:56
Alignment explanation
Indices: 67281--67440 Score: 241
Period size: 56 Copynumber: 2.9 Consensus size: 56
67271 ACATCACAAG
* * *
67281 AAAGGATTTATCATAATTCATTTCATGTCTCCACATCTAATCATATCTCTTTTATA
1 AAAGGATTTATCCTAATTCCTTTCATGTCTCCACATCTAATCATATCTCTTTCATA
*
67337 AGAGGATTTATCCTAATTCCTTTCATGTCTCCACATCTAATCATATCTCTTTCATA
1 AAAGGATTTATCCTAATTCCTTTCATGTCTCCACATCTAATCATATCTCTTTCATA
* * *
67393 AAAAGATTTATCCTAATTCCTTT-ATTGTCTCCATATCTAATCAAATCT
1 AAAGGATTTATCCTAATTCCTTTCA-TGTCTCCACATCTAATCATATCT
67441 TGAACAAGGT
Statistics
Matches: 95, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
55 1 0.01
56 94 0.99
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.42
Consensus pattern (56 bp):
AAAGGATTTATCCTAATTCCTTTCATGTCTCCACATCTAATCATATCTCTTTCATA
Found at i:75061 original size:3 final size:3
Alignment explanation
Indices: 75053--75109 Score: 69
Period size: 3 Copynumber: 18.3 Consensus size: 3
75043 GAGCTTTGTA
* * *
75053 AAT AAT AAT ACT AAT AAT ATT ATAT AAT ATT ATAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT A-AT AAT AAT AAT AAT
75100 AAT AAT AAT A
1 AAT AAT AAT A
75110 CGTCACTTGG
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
3 42 0.91
4 4 0.09
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (3 bp):
AAT
Found at i:76305 original size:2 final size:2
Alignment explanation
Indices: 76240--76288 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
76230 TAGTCACTGT
*
76240 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
76282 TA TA TA T
1 TA TA TA T
76289 TTAGGTTAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:77596 original size:45 final size:46
Alignment explanation
Indices: 77522--77612 Score: 123
Period size: 45 Copynumber: 2.0 Consensus size: 46
77512 GTTTTTTATT
* * * *
77522 TTATTTTTTAAATAAATGCATGCGAACTAGAAATCATGCGGTTAGG
1 TTATTTTTCAAACAAATGCATGCGAACTAGAAAGCATGAGGTTAGG
77568 TTATTTTTCCAAACAAA-GCATG-GAACTAGAAAGCATGAGGTTAGG
1 TTATTTTT-CAAACAAATGCATGCGAACTAGAAAGCATGAGGTTAGG
77613 ATATGATATT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
45 21 0.52
46 13 0.32
47 6 0.15
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (46 bp):
TTATTTTTCAAACAAATGCATGCGAACTAGAAAGCATGAGGTTAGG
Done.