Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005179.1 Hibiscus syriacus cultivar Beakdansim tig00011690_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: 67004
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:17702 original size:24 final size:24
Alignment explanation
Indices: 17682--17808 Score: 137
Period size: 24 Copynumber: 5.2 Consensus size: 24
17672 AAAATCAAAA
* *
17682 CATAATTCAGGTCAAGTATCATAT
1 CATAATCCATGTCAAGTATCATAT
*
17706 CATAATCCATGTCAATTATCATAT
1 CATAATCCATGTCAAGTATCATAT
*
17730 CAGAATCCATGTCAAGTATCATAT
1 CATAATCCATGTCAAGTATCATAT
* * * *
17754 CAGAATCTATGTCAAAGTATTAAAT
1 CATAATCCATGTC-AAGTATCATAT
* * * *
17779 CAGAATCTAAGTCAAGTATCATAA
1 CATAATCCATGTCAAGTATCATAT
17803 CATAAT
1 CATAAT
17809 TTAAATAAGA
Statistics
Matches: 89, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
24 68 0.76
25 21 0.24
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.31
Consensus pattern (24 bp):
CATAATCCATGTCAAGTATCATAT
Found at i:17766 original size:48 final size:49
Alignment explanation
Indices: 17692--17801 Score: 150
Period size: 49 Copynumber: 2.3 Consensus size: 49
17682 CATAATTCAG
* * * *
17692 GTCAAGTATCATATCATAATCCATGTC-AATTATCATATCAGAATCCAT
1 GTCAAGTATCATATCAGAATCCATGTCAAAGTATCAAATCAGAATCCAA
* * *
17740 GTCAAGTATCATATCAGAATCTATGTCAAAGTATTAAATCAGAATCTAA
1 GTCAAGTATCATATCAGAATCCATGTCAAAGTATCAAATCAGAATCCAA
17789 GTCAAGTATCATA
1 GTCAAGTATCATA
17802 ACATAATTTA
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
48 25 0.46
49 29 0.54
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (49 bp):
GTCAAGTATCATATCAGAATCCATGTCAAAGTATCAAATCAGAATCCAA
Found at i:22032 original size:24 final size:24
Alignment explanation
Indices: 22005--22053 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
21995 AGTGCCCAAA
22005 TTGCCAGATAATGATTGAACAATT
1 TTGCCAGATAATGATTGAACAATT
22029 TTGCCAGATAATGATTGAACAATT
1 TTGCCAGATAATGATTGAACAATT
22053 T
1 T
22054 GAACTTGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (24 bp):
TTGCCAGATAATGATTGAACAATT
Found at i:29878 original size:13 final size:13
Alignment explanation
Indices: 29862--29905 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
29852 CCACTTAGCA
29862 GAGCCACCGAGCC
1 GAGCCACCGAGCC
*
29875 GAGCCACCGAACC
1 GAGCCACCGAGCC
* * *
29888 TAGCCACTGAGTC
1 GAGCCACCGAGCC
29901 GAGCC
1 GAGCC
29906 GAGTCACTGA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.25, C:0.41, G:0.27, T:0.07
Consensus pattern (13 bp):
GAGCCACCGAGCC
Found at i:40654 original size:27 final size:27
Alignment explanation
Indices: 40624--40679 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
40614 CCCTAATTTG
*
40624 CTTATCACAAGGATTATCAACAGTAGC
1 CTTATCACAAGGATCATCAACAGTAGC
40651 CTTATCACAAGGATCATCAACAGTAGC
1 CTTATCACAAGGATCATCAACAGTAGC
40678 CT
1 CT
40680 CCAAGGCTGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (27 bp):
CTTATCACAAGGATCATCAACAGTAGC
Found at i:42576 original size:22 final size:21
Alignment explanation
Indices: 42551--42592 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
42541 AGATTCTATC
42551 TAAAAATCAC-AAAATATATATA
1 TAAAAAT-ACTAAAATA-ATATA
42573 TAAAAATACTAAAATAATAT
1 TAAAAATACTAAAATAATAT
42593 CATTTGATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (21 bp):
TAAAAATACTAAAATAATATA
Found at i:43060 original size:16 final size:16
Alignment explanation
Indices: 43039--43073 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
43029 TTTTATAACA
43039 CAAGTCATATTCAAAG
1 CAAGTCATATTCAAAG
43055 CAAGTCATATTCAAAG
1 CAAGTCATATTCAAAG
43071 CAA
1 CAA
43074 ATAATAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.20, G:0.11, T:0.23
Consensus pattern (16 bp):
CAAGTCATATTCAAAG
Found at i:47100 original size:48 final size:48
Alignment explanation
Indices: 47023--47796 Score: 337
Period size: 48 Copynumber: 16.0 Consensus size: 48
47013 AAATCACAAT
* * * * * *
47023 AACTTTGATGATTTGCCCCACCATCTCTTCACGGAGATCAAATCTGAA
1 AACTTTGACGATTCGCTCCATCATATCTTCATGGAGATCAAATCTGAA
* * * * *
47071 AATTTTGATGATTCGTTCCATCATATCTTCATGGAAATCAAATCTAAAA
1 AACTTTGACGATTCGCTCCATCATATCTTCATGGAGATCAAATCT-GAA
* * ** *
47120 AACTTTGATGATTCGCACCA-C-TATCACTTTGTGGAGATCAAATCTGGA
1 AACTTTGACGATTCGCTCCATCATAT--CTTCATGGAGATCAAATCTGAA
* ** * * * *
47168 AACTTTGGCGATT-TTTCC-TACTATCTCTTCATGGAGATAAAAACTAAA
1 AACTTTGACGATTCGCTCCAT-C-ATATCTTCATGGAGATCAAATCTGAA
* * * * * *
47216 AACTTTGATGATTTGCCCCA-CTATCTCTTCGTGGAGATCAAATATGAA
1 AACTTTGACGATTCGCTCCATC-ATATCTTCATGGAGATCAAATCTGAA
* * * *
47264 AACTTTGATGATTCGTTCCATCATCTCTTCATGGAAATCAAATCTGAA
1 AACTTTGACGATTCGCTCCATCATATCTTCATGGAGATCAAATCTGAA
* * * *
47312 ATACTTTGACGATTCGCTCCACCATCA-CTTCGTGGAGATCCAATTTGAA
1 A-ACTTTGACGATTCGCTCCATCAT-ATCTTCATGGAGATCAAATCTGAA
* *
47361 AACTTTGACGATT-TCTCC--CACTATCTCTTAGTGGAGATCAAATCTGAA
1 AACTTTGACGATTCGCTCCATCA-TATCT-TCA-TGGAGATCAAATCTGAA
* * * *** *
47409 AACTTTGACGATTTGCCCCATCATCTCTTCGCAGAGATCAAATATGAA
1 AACTTTGACGATTCGCTCCATCATATCTTCATGGAGATCAAATCTGAA
* * * *
47457 AACTTTAACGATTTATC-CTACCATC-T-TTTTCGTAGAGATCAAATCTGAA
1 AACTTTGACGA--T-TCGCT-CCATCATATCTTCATGGAGATCAAATCTGAA
** * * * * *
47506 AACTTTGATAATTTGCCCCACCATCTCTT--TGCGAAGATCAAATCTAAA
1 AACTTTGACGATTCGCTCCATCATATCTTCATG-G-AGATCAAATCTGAA
* * * * * * * *
47554 AACTTTAATGATTCGTTCTATCGA-CTCGTCATGGAAATCAAATCTAAAA
1 AACTTTGACGATTCGCTCCATC-ATATCTTCATGGAGATCAAATCT-GAA
* * ** * * * *
47603 AACCTTGATGATTTTCTCTACCATCAT-TTCGTGGAGATCCAATCT-AGA
1 AACTTTGACGATTCGCTCCATCAT-ATCTTCATGGAGATCAAATCTGA-A
** * * * *
47651 AACTTT-AGCGATT-TATCCCACCATCTCTTCATGGACATCAAATTTGAA
1 AACTTTGA-CGATTCGCT-CCATCATATCTTCATGGAGATCAAATCTGAA
* * * * * *** * *
47699 AACTTTAACTATTCG-TCCCACCATCTTTTTGCGGAGATCATATCTTAA
1 AACTTTGACGATTCGCT-CCATCATATCTTCATGGAGATCAAATCTGAA
* * * * * *
47747 AACTTTGATGAGTCGTTCCATCATCTCTTCATGGAAATCAAATATGAA
1 AACTTTGACGATTCGCTCCATCATATCTTCATGGAGATCAAATCTGAA
47795 AA
1 AA
47797 ACCTTGATGA
Statistics
Matches: 551, Mismatches: 133, Indels: 84
0.72 0.17 0.11
Matches are distributed among these distances:
45 3 0.01
46 9 0.02
47 19 0.03
48 353 0.64
49 147 0.27
50 12 0.02
51 8 0.01
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.33
Consensus pattern (48 bp):
AACTTTGACGATTCGCTCCATCATATCTTCATGGAGATCAAATCTGAA
Found at i:47318 original size:145 final size:145
Alignment explanation
Indices: 47023--47704 Score: 567
Period size: 145 Copynumber: 4.7 Consensus size: 145
47013 AAATCACAAT
* ** * ** * * **
47023 AACTTTGATGATTTGCCCCACCATCTCTTCACGGAGATCAAATCTGAAAATTTTGATGATTCGTT
1 AACTTTGACGATTTTTCCTACCATCTCTTCGTGGAGATCAAATCTGAAAACTTTGATGATTTGCC
* * * * * * * **
47088 CCA-TCATATCTTCATGGAAATCAAATCTAAAAAACTTTGATGATTCGCACCA-CTATCACTTTG
66 CCACT-ATCTCTTCGTGGAGATCAAATCT-GAAAACTTTGATGATTCGCTCCATCGATCTCTTCA
* *
47151 TGGAGATCAAATCTGGA
129 TGGAAATCAAATCTGAA
* * * * * *
47168 AACTTTGGCGATTTTTCCTACTATCTCTTCATGGAGATAAAAACTAAAAACTTTGATGATTTGCC
1 AACTTTGACGATTTTTCCTACCATCTCTTCGTGGAGATCAAATCTGAAAACTTTGATGATTTGCC
* *
47233 CCACTATCTCTTCGTGGAGATCAAATATGAAAACTTTGATGATTCGTTCCATC-ATCTCTTCATG
66 CCACTATCTCTTCGTGGAGATCAAATCTGAAAACTTTGATGATTCGCTCCATCGATCTCTTCATG
47297 GAAATCAAATCTGAA
131 GAAATCAAATCTGAA
** * * * *
47312 ATACTTTGACGATTCGCTCC-ACCATCACTTCGTGGAGATCCAATTTGAAAACTTTGACGATTT-
1 A-ACTTTGACGATT-TTTCCTACCATCTCTTCGTGGAGATCAAATCTGAAAACTTTGATGATTTG
* * * *
47375 CTCCCACTATCTCTTAGTGGAGATCAAATCTGAAAACTTTGACGATTTGCCCCATC-ATCTCTTC
64 C-CCCACTATCTCTTCGTGGAGATCAAATCTGAAAACTTTGATGATTCGCTCCATCGATCTCTTC
*** * *
47439 GCAGAGATCAAATATGAA
128 ATGGAAATCAAATCTGAA
* * * * *
47457 AACTTTAACGATTTATCCTACCATCTTTTTCGTAGAGATCAAATCTGAAAACTTTGATAATTTGC
1 AACTTTGACGATTTTTCCTACCATC-TCTTCGTGGAGATCAAATCTGAAAACTTTGATGATTTGC
* * * * * * * * *
47522 CCCACCATCTCTTTGCGAAGATCAAATCTAAAAACTTTAATGATTCGTTCTATCGA-CTCGTCAT
65 CCCACTATCTCTTCGTGGAGATCAAATCTGAAAACTTTGATGATTCGCTCCATCGATCTCTTCAT
*
47586 GGAAATCAAATCTAAAA
130 GGAAATCAAATCT-GAA
* * * *
47603 AACCTTGATGA-TTTTCTCTACCATCAT-TTCGTGGAGATCCAATCT-AGAAACTTT-AGCGATT
1 AACTTTGACGATTTTTC-CTACCATC-TCTTCGTGGAGATCAAATCTGA-AAACTTTGA-TGATT
** * * * *
47664 TATCCCACCATCTCTTCATGGACATCAAATTTGAAAACTTT
62 TGCCCCACTATCTCTTCGTGGAGATCAAATCTGAAAACTTT
47705 AACTATTCGT
Statistics
Matches: 429, Mismatches: 95, Indels: 26
0.78 0.17 0.05
Matches are distributed among these distances:
143 3 0.01
144 62 0.14
145 339 0.79
146 25 0.06
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.33
Consensus pattern (145 bp):
AACTTTGACGATTTTTCCTACCATCTCTTCGTGGAGATCAAATCTGAAAACTTTGATGATTTGCC
CCACTATCTCTTCGTGGAGATCAAATCTGAAAACTTTGATGATTCGCTCCATCGATCTCTTCATG
GAAATCAAATCTGAA
Found at i:47596 original size:193 final size:188
Alignment explanation
Indices: 47023--47841 Score: 659
Period size: 193 Copynumber: 4.2 Consensus size: 188
47013 AAATCACAAT
** * * * *
47023 AACTTTGATGATTTGCCCCACCATCTCTTCACGGAGATCAAATCTGAAAATTTTGATGATTCGT-
1 AACTTTGATGATTTGCCCCA-CATCTCTTCGTGGAGATCAAATATGAAAACTTTAACGATT--TA
* * * * * * *
47087 TCCATCATATCTTCATGGAAATCAAATCTAAAAAACTTTGATGATTCGCACCACTATCACTTTGT
63 TCCACCATCTCTTCATGGAAATCAAATCT-GAAAACTTTGAT-ATTCGCCCCACCATCTCTTTGC
** ** * * * *
47152 GGAGATCAAATCTGGAAACTTTGGCGATT-TTTCC-TACTATCTCTTCATGGAGATAAAAACTAA
126 GGAGATCAAATCTAAAAACTTTGATGATTCGTTCCAT-C-ATCTC-TCATGGAAATCAAATCTAA
47215 A
188 A
* *
47216 AACTTTGATGATTTGCCCCACTATCTCTTCGTGGAGATCAAATATGAAAACTTTGATGATTCGT-
1 AACTTTGATGATTTGCCCCAC-ATCTCTTCGTGGAGATCAAATATGAAAACTTTAACGATT--TA
* * * * * *
47280 TCCATCATCTCTTCATGGAAATCAAATCTGAAATACTTTGACGATTCGCTCCACCATCACTTCGT
63 TCCACCATCTCTTCATGGAAATCAAATCTGAAA-ACTTTGA-TATTCGCCCCACCATCTCTTTGC
* * * * * * * *
47345 GGAGATCCAATTTGAAAACTTTGACGATTTC-TCCCA-CTATCTCTTAGTGGAGATCAAATCTGA
126 GGAGATCAAATCTAAAAACTTTGATGA-TTCGTTCCATC-ATCTCTCA-TGGAAATCAAATCTAA
47408 A
188 A
* **
47409 AACTTTGACGATTTGCCCCATCATCTCTTCGCAGAGATCAAATATGAAAACTTTAACGATTTATC
1 AACTTTGATGATTTGCCCCA-CATCTCTTCGTGGAGATCAAATATGAAAACTTTAACGATTTATC
* * * * *
47474 CTACCATCTTTTTCGTAGAGATCAAATCTGAAAACTTTGATAATTTGCCCCACCATCTCTTTGCG
65 C-ACCATC-TCTTCATGGAAATCAAATCTGAAAACTTTGAT-ATTCGCCCCACCATCTCTTTGCG
* * *
47539 AAGATCAAATCTAAAAACTTTAATGATTCGTTCTATCGA-CTCGTCATGGAAATCAAATCTAAAA
127 GAGATCAAATCTAAAAACTTTGATGATTCGTTCCATC-ATCTC-TCATGGAAATCAAATCT-AAA
* * * * * * *
47603 AACCTTGATGATTTTCTCTACCATCAT-TTCGTGGAGATCCAATCT-AGAAACTTTAGCGATTTA
1 AACTTTGATGATTTGCCCCA-CATC-TCTTCGTGGAGATCAAATATGA-AAACTTTAACGATTTA
* * * * *
47666 TCCCACCATCTCTTCATGGACATCAAATTTGAAAACTTTAACTATTCGTCCCACCATCTTTTTGC
63 T-CCACCATCTCTTCATGGAAATCAAATCTGAAAACTTTGA-TATTCGCCCCACCATCTCTTTGC
* * * *
47731 GGAGATCATATCTTAAAACTTTGATGAGTCGTTCCATCATCTCTTCATGGAAATCAAATATGAAA
126 GGAGATCAAATCTAAAAACTTTGATGATTCGTTCCATCATCTC-TCATGGAAATCAAATCT-AAA
* * * * *
47796 AACCTTGATGATTTACTCCGACATCACTTCGTGTG-GATCCAATATG
1 AACTTTGATGATTTGC-CCCACATCTCTTCGTG-GAGATCAAATATG
47842 GAAATTTTGG
Statistics
Matches: 520, Mismatches: 81, Indels: 49
0.80 0.12 0.08
Matches are distributed among these distances:
191 1 0.00
192 13 0.03
193 412 0.79
194 91 0.17
195 3 0.01
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (188 bp):
AACTTTGATGATTTGCCCCACATCTCTTCGTGGAGATCAAATATGAAAACTTTAACGATTTATCC
ACCATCTCTTCATGGAAATCAAATCTGAAAACTTTGATATTCGCCCCACCATCTCTTTGCGGAGA
TCAAATCTAAAAACTTTGATGATTCGTTCCATCATCTCTCATGGAAATCAAATCTAAA
Found at i:47886 original size:193 final size:193
Alignment explanation
Indices: 47442--47893 Score: 484
Period size: 193 Copynumber: 2.3 Consensus size: 193
47432 TCTCTTCGCA
* * * * * ** *
47442 GAGATCAAATAT-GAAAACTTTAACGATTTATCCTACCATCTTTTTCGTAGAGATCAAATCTGAA
1 GAGATCCAATATAG-AAACTTTAGCGATTTATCCCACCAT-ATCTTAATGGAGATCAAATCTGAA
* * *
47506 AACTTTGATAATTTGCCCCACCATCTCTTTGCGAAGATCAAATCTAAAAACTTTAATGATTCGTT
64 AACTTTAATAATTCGCCCCACCATCTCTTTGCGAAGATCAAATCTAAAAACTTTAATGAGTCGTT
* * * * *
47571 CTATCGACTCGTCATGGAAATCAAATCTAAAAAACCTTGATGATTTTCTCTACCATCATTTCGTG
129 CCATCGACTCGTCATGGAAATCAAATATAAAAAACCTTGATGATTTACTCGACCATCACTTCGTG
* * * * *
47636 GAGATCCAATCTAGAAACTTTAGCGATTTATCCCACCATCTCTTCATGGACATCAAATTTGAAAA
1 GAGATCCAATATAGAAACTTTAGCGATTTATCCCACCATATCTTAATGGAGATCAAATCTGAAAA
* * * * * *
47701 CTTTAACT-ATTCGTCCCACCATCTTTTTGCGGAGATCATATCTTAAAACTTTGATGAGTCGTTC
66 CTTTAA-TAATTCGCCCCACCATCTCTTTGCGAAGATCAAATCTAAAAACTTTAATGAGTCGTTC
* *
47765 CATC-ATCTCTTCATGGAAATCAAATATGAAAAACCTTGATGATTTACTCCGA-CATCACTTCGT
130 CATCGA-CTCGTCATGGAAATCAAATATAAAAAACCTTGATGATTTACT-CGACCATCACTTCGT
47828 G
193 G
* * * * * *
47829 TG-GATCCAATATGGAAATTTTGGTGATTTGTCCCACCATATCTTTAAT-TAGATCAAATCTGAA
1 -GAGATCCAATATAGAAACTTTAGCGATTTATCCCACCATATC-TTAATGGAGATCAAATCTGAA
47892 AA
64 AA
47894 AAATTGACGA
Statistics
Matches: 215, Mismatches: 37, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
192 1 0.00
193 172 0.80
194 41 0.19
195 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (193 bp):
GAGATCCAATATAGAAACTTTAGCGATTTATCCCACCATATCTTAATGGAGATCAAATCTGAAAA
CTTTAATAATTCGCCCCACCATCTCTTTGCGAAGATCAAATCTAAAAACTTTAATGAGTCGTTCC
ATCGACTCGTCATGGAAATCAAATATAAAAAACCTTGATGATTTACTCGACCATCACTTCGTG
Found at i:54651 original size:18 final size:20
Alignment explanation
Indices: 54613--54652 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
54603 ATCGATTTTT
*
54613 AAAAAATAAGAACAATGGAA
1 AAAAAATAAGAACAATAGAA
54633 AAAAAATAAGAA-AA-AGAA
1 AAAAAATAAGAACAATAGAA
54651 AA
1 AA
54653 TATAAGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 2 0.11
20 12 0.63
ACGTcount: A:0.78, C:0.03, G:0.12, T:0.07
Consensus pattern (20 bp):
AAAAAATAAGAACAATAGAA
Found at i:55185 original size:17 final size:17
Alignment explanation
Indices: 55163--55197 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
55153 TGTCCCAGAC
55163 TTCAAAAGCAACTTCAA
1 TTCAAAAGCAACTTCAA
* *
55180 TTCAAAATCAGCTTCAA
1 TTCAAAAGCAACTTCAA
55197 T
1 T
55198 AAAACGTCTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.23, G:0.06, T:0.29
Consensus pattern (17 bp):
TTCAAAAGCAACTTCAA
Found at i:55835 original size:294 final size:296
Alignment explanation
Indices: 55275--55833 Score: 743
Period size: 294 Copynumber: 1.9 Consensus size: 296
55265 CTTGTTCAGA
* * *
55275 AGTAGGGAGGCAAGTCCATGTTCATGTGTTGAAGTGTGATGCGAATATTATACTTAGTAGTGCAC
1 AGTAGGGAAGCAAGTCCATGTTCATGTGTTGAAGTGTGATGCGAATATTATACTCAGTACTGCAC
*
55340 TTTTGGATATGTATTGTAAGAGCGGTAGTTTGGAGGATGCCAAGTCGATTTTCGAGCGGATGGTT
66 TTTTGGATATGTACTGTAAGAGCGGTAGTTTGGAGGATGCCAAGTCGATTTTCGAGCGGATGGTT
* * * * *
55405 CATAAGAATGTGATTTCTTGGAATACAATGATTGGAGGGTTCGCATTGAATAGTGATGGCG-TCG
131 CATAAGAATGTGATTTCATGGAATACAATGATCGGAGGGTT-GCGTTGAATGGTCATGGCGATCG
* * ** * *
55469 AAGATTTGAATCAGTTTAAGAGTATGAAAAGAGCTGGCTTTACAGCTTCTCAAACTACACTAGCA
195 AAGCTTTGAATCAGTTTAAGAGTATGAAAAGAGCTAGCTTTACAGCTGATCAAACCACACTAACA
* * * *
55534 AGTGTTTTAAGAGCCAGTATTGATTTAGCTCTTTTAG
260 AGTGTTCTAAGAGCCTGCACTGATTTAGCTCTTTTAG
* * *
55571 -G-AGGGAAGCAAGTCCATGTTCATGTGTTGAAG-GTTGAAGTGAATATTATACTCAATACTGCA
1 AGTAGGGAAGCAAGTCCATGTTCATGTGTTGAAGTG-TGATGCGAATATTATACTCAGTACTGCA
* ** * * *
55633 CTTTTGGATATGTACTGTAAGAGCGGTTGTCCGGAGGATGCTAAGTTGGTTTTCGAGCGGATGGT
65 CTTTTGGATATGTACTGTAAGAGCGGTAGTTTGGAGGATGCCAAGTCGATTTTCGAGCGGATGGT
* * * *
55698 TCATAAGAATGTGATTTCATGGAATACAATGATTGAAGGGCTTGTGTTGAATGGTCATGACGAT-
130 TCATAAGAATGTGATTTCATGGAATACAATGATCGGAGGG-TTGCGTTGAATGGTCATGGCGATC
*
55762 GAAGCTTTGAATCAGTTAAAGAGTATGAAAAGAGCTAGCTTTAC-GTCTGATCAAACCACACTAA
194 GAAGCTTTGAATCAGTTTAAGAGTATGAAAAGAGCTAGCTTTACAG-CTGATCAAACCACACTAA
55826 CAAGTGTT
258 CAAGTGTT
55834 TTTAGAAGTA
Statistics
Matches: 232, Mismatches: 27, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
293 2 0.01
294 226 0.97
295 4 0.02
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.32
Consensus pattern (296 bp):
AGTAGGGAAGCAAGTCCATGTTCATGTGTTGAAGTGTGATGCGAATATTATACTCAGTACTGCAC
TTTTGGATATGTACTGTAAGAGCGGTAGTTTGGAGGATGCCAAGTCGATTTTCGAGCGGATGGTT
CATAAGAATGTGATTTCATGGAATACAATGATCGGAGGGTTGCGTTGAATGGTCATGGCGATCGA
AGCTTTGAATCAGTTTAAGAGTATGAAAAGAGCTAGCTTTACAGCTGATCAAACCACACTAACAA
GTGTTCTAAGAGCCTGCACTGATTTAGCTCTTTTAG
Found at i:56201 original size:274 final size:280
Alignment explanation
Indices: 55833--56545 Score: 735
Period size: 274 Copynumber: 2.5 Consensus size: 280
55823 TAACAAGTGT
* * * * *
55833 TTTTAGAAGTAGGAAAGCAAGTCCATGTTCATGTGTTGAAGT-TCGACGCGAATTGTATACTAAA
1 TTTTAGAAGTAGGGAAGCAAGTCCATGTTCATGTGTTGAAGTGT-GATGCGAATTCTATACTCAG
* * **
55897 TAATACACTTTTGGATATGTACTGTAAGAGCGGTAGTTTGGAGGATGCCAAGTTTATTTTCGAGC
65 TAATGCACTTTTGGATATGTA-TGTAAGAGCGGTAGTTTGGAGGATGCAAAGTCGATTTTCGAGC
* * * * ** * *
55962 GGATGGTTGATAATAATGCGATCTCATGGAGTATGATGATCGGA-GGTTTTGCCCTGAATAGTGA
129 GGATGGTTCATAAGAAGGCGATCTCATGGAATACAATGATCGGAGGGTTCT-CCCTGAATAGCGA
* * ** * *
56026 TGGCGTCG-A-TGAA-AAGAGC-TG-GC-C-TTACAGCTTCCCAAGCTACACTAGCAAGTGTTCT
193 TGGCATCGAACTAAATAAGAGCATGAGCGCTTTACAGCTGACCAAGCCACACTAACAAGTGTTCT
56084 AAGAGCCTGCACTGGTTTAGCTC
258 AAGAGCCTGCACTGGTTTAGCTC
***
56107 TTTTAGAAGTAGGGAAGCAAGTCCATGTTCATGAACTGAAGTGTGATGCGAATAT-TATACTCAG
1 TTTTAGAAGTAGGGAAGCAAGTCCATGTTCATGTGTTGAAGTGTGATGCGAAT-TCTATACTCAG
* * * * *
56171 TAGTGCACTCTTGGATATGTATTGTAAGAGCGGTAGTTTGGAGGATGCAAAATCGGTTTTCGACC
65 TAATGCACTTTTGGATATGTA-TGTAAGAGCGGTAGTTTGGAGGATGCAAAGTCGATTTTCGAGC
* * * * ** *
56236 GGATAGTTCATAAGAAGGTGATTTCCTGGAATACAATGATCGGAGGGTTCTCGTTGAATGGCGAT
129 GGATGGTTCATAAGAAGGCGATCTCATGGAATACAATGATCGGAGGGTTCTCCCTGAATAGCGAT
*
56301 GGCATCGAAGCCTTAAATCTGTTTAAGAGCATGAAATGAGCAGGCTTTACAGCTGATCAAGCCAC
194 GGCATCGAA--C-TAAA------TAAGAGC-----ATGAGC--GCTTTACAGCTGACCAAGCCAC
*
56366 ACTAACAAGTGTTCTGAGAGCCTGCACTGGTTTAGCTC
243 ACTAACAAGTGTTCTAAGAGCCTGCACTGGTTTAGCTC
* * *
56404 TTTTAGAAGTAGGGAGGCAAGTCCATGTTCATGTGTTGAAGTGTGATGCGGATTCTATACTCGGT
1 TTTTAGAAGTAGGGAAGCAAGTCCATGTTCATGTGTTGAAGTGTGATGCGAATTCTATACTCAGT
* * * * *
56469 ACTGCACTTTTGGACATGTATGTAAGCGTGGTAGTTTGGAGGATGCGAAGTCGATTTTCGAGCGG
66 AATGCACTTTTGGATATGTATGTAAGAGCGGTAGTTTGGAGGATGCAAAGTCGATTTTCGAGCGG
56534 ATGGTTCATAAG
131 ATGGTTCATAAG
56546 GATGTGATTT
Statistics
Matches: 356, Mismatches: 56, Indels: 32
0.80 0.13 0.07
Matches are distributed among these distances:
274 158 0.44
275 8 0.02
279 3 0.01
286 6 0.02
292 2 0.01
293 2 0.01
296 52 0.15
297 125 0.35
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.30
Consensus pattern (280 bp):
TTTTAGAAGTAGGGAAGCAAGTCCATGTTCATGTGTTGAAGTGTGATGCGAATTCTATACTCAGT
AATGCACTTTTGGATATGTATGTAAGAGCGGTAGTTTGGAGGATGCAAAGTCGATTTTCGAGCGG
ATGGTTCATAAGAAGGCGATCTCATGGAATACAATGATCGGAGGGTTCTCCCTGAATAGCGATGG
CATCGAACTAAATAAGAGCATGAGCGCTTTACAGCTGACCAAGCCACACTAACAAGTGTTCTAAG
AGCCTGCACTGGTTTAGCTC
Found at i:57961 original size:28 final size:28
Alignment explanation
Indices: 57919--57976 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
57909 ACGTGTTTAA
* *
57919 TATCTAAACTGTCAGTTTTAGTTCGTTT
1 TATCTAAACTATCAGTTTTAGTCCGTTT
57947 TATCTAAACTATCAGTTTTAGTCCGTTT
1 TATCTAAACTATCAGTTTTAGTCCGTTT
57975 TA
1 TA
57977 GTATGTAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (28 bp):
TATCTAAACTATCAGTTTTAGTCCGTTT
Done.