Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002862.1 Hibiscus syriacus cultivar Beakdansim tig00005901_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: 45322
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:7774 original size:23 final size:24
Alignment explanation
Indices: 7737--7782 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
7727 AAATAACAAA
*
7737 TTTATTTTTTCTTTTATCTTTATC
1 TTTATTTTTTATTTTATCTTTATC
*
7761 TTTA-TTTTTATTTTATTTTTAT
1 TTTATTTTTTATTTTATCTTTAT
7783 TCGTGGATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (24 bp):
TTTATTTTTTATTTTATCTTTATC
Found at i:7775 original size:17 final size:18
Alignment explanation
Indices: 7748--7783 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
7738 TTATTTTTTC
7748 TTTTATCTTTATCTTTAT
1 TTTTATCTTTATCTTTAT
*
7766 TTTTAT-TTTATTTTTAT
1 TTTTATCTTTATCTTTAT
7783 T
1 T
7784 CGTGGATAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTATCTTTATCTTTAT
Found at i:7777 original size:11 final size:11
Alignment explanation
Indices: 7737--7783 Score: 58
Period size: 11 Copynumber: 4.1 Consensus size: 11
7727 AAATAACAAA
*
7737 TTTATTTTTTCT
1 TTTA-TTTTTAT
*
7749 TTTATCTTTAT
1 TTTATTTTTAT
7760 CTTTATTTTTAT
1 -TTTATTTTTAT
7772 TTTATTTTTAT
1 TTTATTTTTAT
7783 T
1 T
7784 CGTGGATAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
11 17 0.55
12 14 0.45
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTATTTTTAT
Found at i:7783 original size:6 final size:6
Alignment explanation
Indices: 7737--7783 Score: 53
Period size: 6 Copynumber: 8.0 Consensus size: 6
7727 AAATAACAAA
* *
7737 TTTATT TTT-TCT TTTATC TTTATC TTTATT TTTA-T TTTATT TTTATT
1 TTTATT TTTAT-T TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
7784 CGTGGATAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
5 6 0.17
6 29 0.81
7 1 0.03
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTATT
Found at i:11689 original size:13 final size:13
Alignment explanation
Indices: 11671--11704 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
11661 AATTTATAGG
11671 GTATTAATGTCAT
1 GTATTAATGTCAT
*
11684 GTATTAATGTTAT
1 GTATTAATGTCAT
*
11697 GCATTAAT
1 GTATTAAT
11705 ATACAACTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.32, C:0.06, G:0.15, T:0.47
Consensus pattern (13 bp):
GTATTAATGTCAT
Found at i:12751 original size:18 final size:18
Alignment explanation
Indices: 12724--12765 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
12714 CTTTAGATTA
*
12724 TTTA-TTAATTATTTTCT
1 TTTATTTAATTATTATCT
*
12741 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
12759 TTTATTT
1 TTTATTT
12766 TAAAAACAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:13008 original size:57 final size:60
Alignment explanation
Indices: 12940--13053 Score: 148
Period size: 57 Copynumber: 1.9 Consensus size: 60
12930 TTTTTTTCTG
12940 AAATTTAATATTTTC-TTCATTT-ATTT-TATTTTTAA-T-ATTTTTATATAATATTTTTGA
1 AAATTTAATA-TTTCATTC-TTTGATTTATATTTTTAATTAATTTTTATATAATATTTTTGA
* *
12997 AAATTTAATATTTCATTCTTTGATTTATTTTTTTAATTCAATTTTTATTTAATATTT
1 AAATTTAATATTTCATTCTTTGATTTATATTTTTAATT-AATTTTTATATAATATTT
13054 CTTTTGTTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
56 7 0.14
57 17 0.35
58 8 0.16
59 1 0.02
61 16 0.33
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (60 bp):
AAATTTAATATTTCATTCTTTGATTTATATTTTTAATTAATTTTTATATAATATTTTTGA
Found at i:20867 original size:270 final size:268
Alignment explanation
Indices: 20387--20996 Score: 888
Period size: 270 Copynumber: 2.3 Consensus size: 268
20377 GAATATCCAA
* * * *
20387 TTCAAAGCTCAACTTCACAACGAATGAGCCACATATGATTTCGACTTCACAATGAAGGATATTGT
1 TTCAAAGCTCAACTTCACAACGAAGGAGCCACCTACGATTTCGACTTCACAA-GAAGGATATCGT
** *
20452 ACCCAAAGATTGACCCAACTTCATGACGAAGGAGTCATATGTAACACAACAATAAAATGCCAGTT
65 ACCCAAAGATTGACCCAACTTCACAACGAAGGAGTCATATGTAACACAACAATAAAATACCAGTT
*
20517 TCATACAAGAGTCTTCAGGTCAAATTTCAGCTTCACGATGAAGTATATTAGGCTAGAAGACGATA
130 TCATACAAGAGTCTTCAGGTCAAATTTCAGCTTCACGACGAAGTATATTAGGCTAGAAGACGATA
* * * * *
20582 CAAGAGTGACTTTCCAATGCTTTGAGCTCGGTTTCAACTTCATGATGAAGGATAT-TGTGCTCAG
195 CAAGAGCGACTTTCCAATGCTTTGAGCCCAGTTTCAACTTCACGAGGAAGGATATCT-TGCTCAG
*
20646 GATTTTTTAG
259 GATTTTTCAG
*
20656 TTCAAAGCTCAACTTCACAACGAAGGAGTCACCTACGATTTCGACTTCACAACGAAGGATATCGT
1 TTCAAAGCTCAACTTCACAACGAAGGAGCCACCTACGATTTCGACTTCACAA-GAAGGATATCGT
* *
20721 ACCCAAATGATTGACCTAACTTCACAACGAAGGAGTCATATGTAACACAACAATGAAAA-ACTAG
65 ACCCAAA-GATTGACCCAACTTCACAACGAAGGAGTCATATGTAACACAACAAT-AAAATACCAG
*
20785 TTTCATACCAA-ATTCTTCAGGTCAAATTTCAGCTTCACGACGAAGTATATT-GGCCTAGAAGAC
128 TTTCATA-CAAGAGTCTTCAGGTCAAATTTCAGCTTCACGACGAAGTATATTAGG-CTAGAAGAC
* *
20848 GATACATGAGCGACTTTCCAATGCTTTGAGCCCAGTTTCAGCTTCACGAGGAAGGATATCTTGCT
191 GATACAAGAGCGACTTTCCAATGCTTTGAGCCCAGTTTCAACTTCACGAGGAAGGATATCTTGCT
20913 CAGGATTTTTCAG
256 CAGGATTTTTCAG
* **
20926 TTCAAAGCTCAACTTCACAATGAAGGAGCCA-CTCACGATTTTAACTTCACGAAGAAGGATATCG
1 TTCAAAGCTCAACTTCACAACGAAGGAGCCACCT-ACGATTTCGACTTCAC-AAGAAGGATATCG
*
20990 TGCCCAA
64 TACCCAA
20997 TGGATCGACT
Statistics
Matches: 308, Mismatches: 26, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
269 70 0.23
270 228 0.74
271 10 0.03
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.27
Consensus pattern (268 bp):
TTCAAAGCTCAACTTCACAACGAAGGAGCCACCTACGATTTCGACTTCACAAGAAGGATATCGTA
CCCAAAGATTGACCCAACTTCACAACGAAGGAGTCATATGTAACACAACAATAAAATACCAGTTT
CATACAAGAGTCTTCAGGTCAAATTTCAGCTTCACGACGAAGTATATTAGGCTAGAAGACGATAC
AAGAGCGACTTTCCAATGCTTTGAGCCCAGTTTCAACTTCACGAGGAAGGATATCTTGCTCAGGA
TTTTTCAG
Found at i:21833 original size:18 final size:18
Alignment explanation
Indices: 21810--21852 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
21800 TCTTTAATTA
*
21810 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATCT
21828 TTTATTTAATTATTATCT
1 TTTATTTAATTATTATCT
21846 TTTATTT
1 TTTATTT
21853 TAAAAACAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:21924 original size:7 final size:7
Alignment explanation
Indices: 21894--22023 Score: 50
Period size: 7 Copynumber: 17.1 Consensus size: 7
21884 TTTTCTACTA
*
21894 TTATTAT
1 TTATTTT
21901 TTATTTT
1 TTATTTT
*
21908 ATTATATT
1 -TTATTTT
*
21916 TTCTTTT
1 TTATTTT
21923 TTATTTT
1 TTATTTT
21930 ATT-TTGTT
1 -TTATT-TT
*
21938 TTA-TCT
1 TTATTTT
21944 TTATTTT
1 TTATTTT
21951 CCCACTTATTTTT
1 -----TTA-TTTT
*
21964 TTATTCTA
1 TTATT-TT
*
21972 TT-TTGT
1 TTATTTT
*
21978 TTAATTT
1 TTATTTT
21985 TTATTTT
1 TTATTTT
21992 TTATTTT
1 TTATTTT
*
21999 AATATTTT
1 -TTATTTT
22007 TTATATTT
1 TTAT-TTT
22015 ATTATTTT
1 -TTATTTT
22023 T
1 T
22024 CTTTTTTGAA
Statistics
Matches: 92, Mismatches: 15, Indels: 32
0.66 0.11 0.23
Matches are distributed among these distances:
6 6 0.07
7 47 0.51
8 28 0.30
9 4 0.04
12 3 0.03
13 4 0.04
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.74
Consensus pattern (7 bp):
TTATTTT
Found at i:21924 original size:17 final size:17
Alignment explanation
Indices: 21904--21939 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
21894 TTATTATTTA
21904 TTTTATTATATTTTCTT
1 TTTTATTATATTTTCTT
* *
21921 TTTTATTTTATTTTGTT
1 TTTTATTATATTTTCTT
21938 TT
1 TT
21940 ATCTTTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.14, C:0.03, G:0.03, T:0.81
Consensus pattern (17 bp):
TTTTATTATATTTTCTT
Found at i:21939 original size:16 final size:16
Alignment explanation
Indices: 21904--21951 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
21894 TTATTATTTA
* *
21904 TTTTATTATATTTTCTT
1 TTTTATTTTATTTTC-G
21921 TTTTATTTTATTTT-G
1 TTTTATTTTATTTTCG
21936 TTTTATCTTTATTTTC
1 TTTTAT-TTTATTTTC
21952 CCACTTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 6 0.22
16 8 0.30
17 13 0.48
ACGTcount: A:0.15, C:0.06, G:0.02, T:0.77
Consensus pattern (16 bp):
TTTTATTTTATTTTCG
Found at i:21988 original size:29 final size:32
Alignment explanation
Indices: 21956--22023 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 32
21946 ATTTTCCCAC
21956 TTATTTTTTTATTCT-AT-TTTGTTTA-ATTT-
1 TTATTTTTTTATTCTAATATTT-TTTATATTTA
*
21985 TTA-TTTTTTATTTTAATATTTTTTATATTTA
1 TTATTTTTTTATTCTAATATTTTTTATATTTA
22016 TTATTTTT
1 TTATTTTT
22024 CTTTTTTGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
28 10 0.30
29 9 0.27
30 7 0.21
31 3 0.09
32 4 0.12
ACGTcount: A:0.21, C:0.01, G:0.01, T:0.76
Consensus pattern (32 bp):
TTATTTTTTTATTCTAATATTTTTTATATTTA
Found at i:22007 original size:16 final size:16
Alignment explanation
Indices: 21986--22023 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
21976 GTTTAATTTT
21986 TATTTTTTAT-TTTAA
1 TATTTTTTATATTTAA
*
22001 TATTTTTTATATTTAT
1 TATTTTTTATATTTAA
22017 TATTTTT
1 TATTTTT
22024 CTTTTTTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TATTTTTTATATTTAA
Found at i:22022 original size:15 final size:15
Alignment explanation
Indices: 21956--22023 Score: 54
Period size: 16 Copynumber: 4.5 Consensus size: 15
21946 ATTTTCCCAC
*
21956 TTATTTTTTTATTCTA
1 TTATTTTTATATT-TA
21972 TT-TTGTTTA-ATTT-
1 TTATT-TTTATATTTA
21985 TTATTTTT-TATTTTA
1 TTATTTTTATA-TTTA
*
22000 ATATTTTTTATATTTA
1 TTA-TTTTTATATTTA
22016 TTATTTTT
1 TTATTTTT
22024 CTTTTTTGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 15
0.70 0.05 0.25
Matches are distributed among these distances:
13 6 0.14
14 6 0.14
15 12 0.29
16 16 0.38
17 2 0.05
ACGTcount: A:0.21, C:0.01, G:0.01, T:0.76
Consensus pattern (15 bp):
TTATTTTTATATTTA
Found at i:22028 original size:22 final size:21
Alignment explanation
Indices: 21900--22066 Score: 67
Period size: 22 Copynumber: 7.7 Consensus size: 21
21890 ACTATTATTA
21900 TTTATTTTATTATATTTTCTTT
1 TTTATTTTATTAT-TTTTCTTT
*
21922 TTTATTTTATT-TTGTTT-TATC
1 TTTATTTTATTATT-TTTCT-TT
*** * *
21943 TTTATTTTCCCACTTAT-TTT
1 TTTATTTTATTATTTTTCTTT
* **
21963 TTTATTCTATT-TTGTTTAATT
1 TTTATTTTATTATT-TTTCTTT
* *
21984 TTTATTTT-TTATTTTAATATTT
1 TTTATTTTATTA-TTT-TTCTTT
22006 TTTATATTTATTATTTTTCTTT
1 TTTAT-TTTATTATTTTTCTTT
* * *
22028 TTTGAAATTTAATA-TTTTCTTCA
1 TTT--ATTTTATTATTTTTCTT-T
22051 TTTATTTTATTTATTT
1 TTTATTTTA-TTATTT
22067 AATATTTATT
Statistics
Matches: 106, Mismatches: 24, Indels: 29
0.67 0.15 0.18
Matches are distributed among these distances:
19 1 0.01
20 14 0.13
21 31 0.29
22 39 0.37
23 17 0.16
24 4 0.04
ACGTcount: A:0.20, C:0.06, G:0.02, T:0.72
Consensus pattern (21 bp):
TTTATTTTATTATTTTTCTTT
Found at i:22076 original size:15 final size:14
Alignment explanation
Indices: 22034--22091 Score: 50
Period size: 15 Copynumber: 4.1 Consensus size: 14
22024 CTTTTTTGAA
22034 ATTTAATATTTTCTT
1 ATTTAATATTTT-TT
22049 CATTT-AT-TTTATTT
1 -ATTTAATATTT-TTT
22063 ATTTAATATTTATTT
1 ATTTAATATTT-TTT
*
22078 ATATAA-ATTTTTT
1 ATTTAATATTTTTT
22091 A
1 A
22092 AATTAAATAT
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
13 8 0.21
14 11 0.29
15 15 0.39
16 4 0.11
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (14 bp):
ATTTAATATTTTTT
Found at i:22089 original size:59 final size:61
Alignment explanation
Indices: 22026--22140 Score: 146
Period size: 59 Copynumber: 1.9 Consensus size: 61
22016 TTATTTTTCT
* *
22026 TTTTTGAAATTTAATATTTTCTTCATTT-ATTT-TATTT-ATTTAATATTTATTTATATAAA
1 TTTTTGAAATTAAATATTTCCTTC-TTTGATTTATATTTAATTTAATATTTATTTATATAAA
* * *
22085 TTTTTTAAATTAAATATTTCCTTCTTTGATTTATTTTTAAATTTAATTTTTATTTA
1 TTTTTGAAATTAAATATTTCCTTCTTTGATTTATATTT-AATTTAATATTTATTTA
22141 ATATTTCTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
58 3 0.06
59 25 0.53
60 4 0.09
62 15 0.32
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.63
Consensus pattern (61 bp):
TTTTTGAAATTAAATATTTCCTTCTTTGATTTATATTTAATTTAATATTTATTTATATAAA
Found at i:28933 original size:42 final size:41
Alignment explanation
Indices: 28865--28966 Score: 120
Period size: 42 Copynumber: 2.5 Consensus size: 41
28855 CTTAGACTTC
* *
28865 GTGTCATTTGTTTACAAACGCCGCTATAG-ACTCGTACTTTA
1 GTGTCATTTGTTTAAAAACGCAGCTATAGAACTC-TACTTTA
* *
28906 GTGTCATTTGGTTTAAAAATGCAGCTATAGAATTCTACTTTA
1 GTGTCATTT-GTTTAAAAACGCAGCTATAGAACTCTACTTTA
*
28948 GTGGC-TTT-TTTAAAAACGC
1 GTGTCATTTGTTTAAAAACGC
28967 TACAATAGTC
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
39 10 0.19
41 12 0.23
42 28 0.53
43 3 0.06
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (41 bp):
GTGTCATTTGTTTAAAAACGCAGCTATAGAACTCTACTTTA
Found at i:28984 original size:39 final size:40
Alignment explanation
Indices: 28941--29066 Score: 139
Period size: 42 Copynumber: 3.1 Consensus size: 40
28931 TATAGAATTC
* *
28941 TACTTTAGTGGC-TTTTTTAA-AAACGCTACAATAGTCTTG
1 TACTTTAGTGGCATTTTTTAATAAACGC-GCAATAGTCATG
* * *
28980 TACTTTAGTGGCGTTTGTATAATAAACGACGCAATAATCATG
1 TACTTTAGTGGCATTT-TTTAATAAACG-CGCAATAGTCATG
*
29022 TAATTTAGTGGCATTTTTTTAATAAACGCCGCAATAGTCATG
1 TACTTTAGTGGCA-TTTTTTAATAAACG-CGCAATAGTCATG
29064 TAC
1 TAC
29067 ATAAGTGGTG
Statistics
Matches: 72, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
39 12 0.17
40 3 0.04
41 4 0.06
42 49 0.68
43 4 0.06
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (40 bp):
TACTTTAGTGGCATTTTTTAATAAACGCGCAATAGTCATG
Found at i:29081 original size:42 final size:42
Alignment explanation
Indices: 28945--29089 Score: 138
Period size: 42 Copynumber: 3.5 Consensus size: 42
28935 GAATTCTACT
** * *
28945 TTAGTGGC--TTTTTTAA-AAACGCTACAATAGTCTTGTACT
1 TTAGTGGCGTTTTTTTAATAAACGCCGCAATAGTCATGTACA
* * * *
28984 TTAGTGGCGTTTGTATAATAAACGACGCAATAATCATGTA-A
1 TTAGTGGCGTTTTTTTAATAAACGCCGCAATAGTCATGTACA
*
29025 TTTAGTGGCATTTTTTTAATAAACGCCGCAATAGTCATGTACA
1 -TTAGTGGCGTTTTTTTAATAAACGCCGCAATAGTCATGTACA
* *
29068 TAAGTGGTGTTTTTATT-ATAAA
1 TTAGTGGCGTTTTT-TTAATAAA
29090 AGTCGCGATA
Statistics
Matches: 84, Mismatches: 16, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
39 8 0.10
41 6 0.07
42 67 0.80
43 3 0.04
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (42 bp):
TTAGTGGCGTTTTTTTAATAAACGCCGCAATAGTCATGTACA
Found at i:29364 original size:20 final size:20
Alignment explanation
Indices: 29339--29382 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
29329 AAATTACTTT
*
29339 GGGTATTCTTTCCCAATCAA
1 GGGTATTATTTCCCAATCAA
*
29359 GGGTATTATTTCCTAATCAA
1 GGGTATTATTTCCCAATCAA
29379 GGGT
1 GGGT
29383 TTACTTTAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.36
Consensus pattern (20 bp):
GGGTATTATTTCCCAATCAA
Found at i:29548 original size:41 final size:41
Alignment explanation
Indices: 29500--29577 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
29490 TTTGTACATA
* *
29500 AAACGCCATTAGAGAGTTGTA-TTGTAGTGGCGTTTTTATAC
1 AAACGCCACTAGAGACTTGTACTT-TAGTGGCGTTTTTATAC
*
29541 AAACGCCACTATAGACTTGTACTTTAGTGGCGTTTTT
1 AAACGCCACTAGAGACTTGTACTTTAGTGGCGTTTTT
29578 GTTCAAATGC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
41 31 0.94
42 2 0.06
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (41 bp):
AAACGCCACTAGAGACTTGTACTTTAGTGGCGTTTTTATAC
Found at i:36176 original size:44 final size:43
Alignment explanation
Indices: 36051--36266 Score: 204
Period size: 44 Copynumber: 4.9 Consensus size: 43
36041 TAAAAGTGGC
* * *
36051 TATCACTTGTCTTTTAGTTATATTTGGATCGATTTAGAAGGG-A
1 TATCACTTGTCGTTTAGTTATATTTGGAT-GACTTAGATGGGAA
* ** *
36094 TATCACTTGTCGTTTAG-TATATTTGGATCGGCCAAGAT-GCAGA
1 TATCACTTGTCGTTTAGTTATATTTGGAT-GACTTAGATGGGA-A
* * **
36137 TATCACTTGTCATTTAGTTATATTTGGATTACCTTAGATGGGCT
1 TATCACTTGTCGTTTAGTTATATTTGGATGA-CTTAGATGGGAA
* *
36181 TTTCACTTGTCGTTTAGTTATATTTGGACCGACTTAGATGGGAA
1 TATCACTTGTCGTTTAGTTATATTTGGA-TGACTTAGATGGGAA
* * *
36225 TATCACTCGTTGTTTAGTTAATATTTGGATTAACTTAGATGG
1 TATCACTTGTCGTTTAGTT-ATATTTGGA-TGACTTAGATGG
36267 ATATATAATT
Statistics
Matches: 139, Mismatches: 27, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
41 1 0.01
42 16 0.12
43 33 0.24
44 68 0.49
45 21 0.15
ACGTcount: A:0.25, C:0.12, G:0.21, T:0.42
Consensus pattern (43 bp):
TATCACTTGTCGTTTAGTTATATTTGGATGACTTAGATGGGAA
Found at i:36241 original size:88 final size:88
Alignment explanation
Indices: 36051--36266 Score: 233
Period size: 86 Copynumber: 2.5 Consensus size: 88
36041 TAAAAGTGGC
* * ** * * * *
36051 TATCACTTGTCTTTTAGTT-ATATTTGGATCGATTTAGAAGGG-ATATCACTTGTCGTTTAGTAT
1 TATCACTCGTCATTTAGTTAATATTTGGATTAACTTAGATGGGCTTTTCACTTGTCGTTTAGTAT
* *
36114 ATTTGGATCGGCCAAGATGCAGA
66 ATTTGGACCGACCAAGATGCAGA
* *
36137 TATCACTTGTCATTTAGTT-ATATTTGGATTACCTTAGATGGGCTTTTCACTTGTCGTTTAGTTA
1 TATCACTCGTCATTTAGTTAATATTTGGATTAACTTAGATGGGCTTTTCACTTGTCGTTTAG-TA
** *
36201 TATTTGGACCGACTTAGATG-GGAA
65 TATTTGGACCGACCAAGATGCAG-A
**
36225 TATCACTCGTTGTTTAGTTAATATTTGGATTAACTTAGATGG
1 TATCACTCGTCATTTAGTTAATATTTGGATTAACTTAGATGG
36267 ATATATAATT
Statistics
Matches: 109, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
86 36 0.33
87 17 0.16
88 35 0.32
89 21 0.19
ACGTcount: A:0.25, C:0.12, G:0.21, T:0.42
Consensus pattern (88 bp):
TATCACTCGTCATTTAGTTAATATTTGGATTAACTTAGATGGGCTTTTCACTTGTCGTTTAGTAT
ATTTGGACCGACCAAGATGCAGA
Found at i:37983 original size:16 final size:16
Alignment explanation
Indices: 37936--37984 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
37926 ACATGTTGGA
*
37936 AGTGGTTGTTTAATGA
1 AGTGGTTGTTTAATGG
37952 AGTGGTTGTTTAATGG
1 AGTGGTTGTTTAATGG
37968 AGTGGTTGTTTAATGG
1 AGTGGTTGTTTAATGG
37984 A
1 A
37985 AAGAAGTTCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.22, C:0.00, G:0.35, T:0.43
Consensus pattern (16 bp):
AGTGGTTGTTTAATGG
Found at i:39834 original size:22 final size:21
Alignment explanation
Indices: 39787--39841 Score: 60
Period size: 19 Copynumber: 2.7 Consensus size: 21
39777 AAAATGGTAT
* *
39787 CGATACCATAGTAGAGTATCA
1 CGATACCATAGTATAGTATAA
39808 -G-TACCATAGTATAGTAGTAA
1 CGATACCATAGTATAGTA-TAA
*
39828 CGATACCATGGTAT
1 CGATACCATAGTAT
39842 GGGTATCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 14 0.50
20 3 0.11
21 1 0.04
22 10 0.36
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.27
Consensus pattern (21 bp):
CGATACCATAGTATAGTATAA
Found at i:40376 original size:77 final size:77
Alignment explanation
Indices: 40266--40409 Score: 236
Period size: 77 Copynumber: 1.9 Consensus size: 77
40256 AAAAGAATAG
* *
40266 TGCATATGGGTGCATTATCGACATAAAAGAATAATGCATATGCGTGCATTATTGGCATGAAATGA
1 TGCATATGGGTGCATTATCGACATAAAAGAATAATGCATATG-GTGCATTATAGGCATGAAAGGA
40331 TGCCATAGTTGAA
65 TGCCATAGTTGAA
* *
40344 TGCATAT-GGTGCATTATCGGCATAAAATAATAATGCATATGGTGCATTATAGGCATGAAAGGAT
1 TGCATATGGGTGCATTATCGACATAAAAGAATAATGCATATGGTGCATTATAGGCATGAAAGGAT
40408 GC
66 GC
40410 ATAAATAAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
76 23 0.37
77 32 0.52
78 7 0.11
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (77 bp):
TGCATATGGGTGCATTATCGACATAAAAGAATAATGCATATGGTGCATTATAGGCATGAAAGGAT
GCCATAGTTGAA
Found at i:40518 original size:24 final size:25
Alignment explanation
Indices: 40435--40516 Score: 114
Period size: 24 Copynumber: 3.3 Consensus size: 25
40425 GACATTAAGG
*
40435 AAGGATGCCAT-AATAAATGTGTGA
1 AAGGATGCCATAAATAAATGTATGA
*
40459 AAGGATGCCATAAATGAAATGTATAA
1 AAGGATGCCATAAAT-AAATGTATGA
*
40485 AAGGATG-CATAAATAAATGCATGA
1 AAGGATGCCATAAATAAATGTATGA
40509 AAGGATGC
1 AAGGATGC
40517 ATGAAGGCAT
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
24 26 0.51
25 10 0.20
26 15 0.29
ACGTcount: A:0.46, C:0.09, G:0.23, T:0.22
Consensus pattern (25 bp):
AAGGATGCCATAAATAAATGTATGA
Done.