Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003754.1 Hibiscus syriacus cultivar Beakdansim tig00008038_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: 63295
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4804 original size:33 final size:34
Alignment explanation
Indices: 4767--4832 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 34
4757 ATTTGGCAAG
*
4767 TTGGAAAATTCATCTTT-GTTGGTGGCCAACTTA
1 TTGGAAAATTCATCTTTGGTAGGTGGCCAACTTA
*
4800 TTGGAAAATTCATTTTTGGTAGGTGGCCAACTT
1 TTGGAAAATTCATCTTTGGTAGGTGGCCAACTT
4833 TGTACATGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 16 0.53
34 14 0.47
ACGTcount: A:0.24, C:0.14, G:0.23, T:0.39
Consensus pattern (34 bp):
TTGGAAAATTCATCTTTGGTAGGTGGCCAACTTA
Found at i:8097 original size:64 final size:63
Alignment explanation
Indices: 8028--8201 Score: 194
Period size: 64 Copynumber: 2.7 Consensus size: 63
8018 TGAAACACTT
* * * *
8028 AGTGCATCGGTGCACTAAGGGTGCATCGATGCATAAAATACATTTGATG-TTTCA-AACAAGCCT
1 AGTGCATCGATGCA-T-AGGGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAA-AAACCT
8091 G
63 G
8092 AGTGCATCGATGCAT-GGTCTGTGCATCGATGCAT-AAATGCATTCGATGTTTTCATAAAAACCT
1 AGTGCATCGATGCATAGG---GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAAACCT
8155 G
63 G
* **
8156 AGTTCATCGATGCATGACAGTGCATCGATGCATAAAATGCATTCGA
1 AGTGCATCGATGCAT-AGGGTGCATCGATGCATAAAATGCATTCGA
8202 AATGGTGTGT
Statistics
Matches: 95, Mismatches: 7, Indels: 16
0.81 0.06 0.14
Matches are distributed among these distances:
61 2 0.02
63 27 0.28
64 64 0.67
65 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.28
Consensus pattern (63 bp):
AGTGCATCGATGCATAGGGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAAACCTG
Found at i:8188 original size:63 final size:64
Alignment explanation
Indices: 8048--8201 Score: 215
Period size: 64 Copynumber: 2.4 Consensus size: 64
8038 TGCACTAAGG
* * * * *
8048 GTGCATCGATGCATAAAATACATTTGATGTTTCAAACAAGCCTGAGTGCATCGATGCATGGTCT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAACAAACCTGAGTGCATCGATGCATGGACA
*
8112 GTGCATCGATGCAT-AAATGCATTCGATGTTTTCATAA-AAACCTGAGTTCATCGATGCAT-GAC
1 GTGCATCGATGCATAAAATGCATTCGATG-TTTCA-AACAAACCTGAGTGCATCGATGCATGGAC
8174 A
64 A
8175 GTGCATCGATGCATAAAATGCATTCGA
1 GTGCATCGATGCATAAAATGCATTCGA
8202 AATGGTGTGT
Statistics
Matches: 81, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
63 28 0.35
64 51 0.63
65 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCAAACAAACCTGAGTGCATCGATGCATGGACA
Found at i:8201 original size:18 final size:18
Alignment explanation
Indices: 8160--8197 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
8150 AACCTGAGTT
* *
8160 CATCGATGCATGACAGTG
1 CATCGATGCATGAAAATG
8178 CATCGATGCAT-AAAATG
1 CATCGATGCATGAAAATG
8195 CAT
1 CAT
8198 TCGAAATGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (18 bp):
CATCGATGCATGAAAATG
Found at i:10662 original size:21 final size:22
Alignment explanation
Indices: 10604--10701 Score: 80
Period size: 21 Copynumber: 4.4 Consensus size: 22
10594 GGCATTGTGC
10604 ATCGATGCACATTCAAGGA-GT
1 ATCGATGCACATTCAAGGATGT
* *
10625 ACATCGGTGCATC-TTC-ATGATGT
1 --ATCGATGCA-CATTCAAGGATGT
*
10648 ATCGATGCACATTCAAAGGGATGC
1 ATCGATGCACATTC-AA-GGATGT
10672 ATCGATGCACATTCATA-G-TGT
1 ATCGATGCACATTCA-AGGATGT
10693 ATCGATGCA
1 ATCGATGCA
10702 TTATGCACAA
Statistics
Matches: 62, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
20 1 0.02
21 22 0.35
22 4 0.06
23 15 0.24
24 20 0.32
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (22 bp):
ATCGATGCACATTCAAGGATGT
Found at i:10694 original size:45 final size:44
Alignment explanation
Indices: 10604--10701 Score: 121
Period size: 45 Copynumber: 2.2 Consensus size: 44
10594 GGCATTGTGC
*
10604 ATCGATGCACATTCAAGGAGTACATCGGTGCATCTTCATGATGT
1 ATCGATGCACATTCAAGGAGTACATCGATGCATCTTCATGATGT
*
10648 ATCGATGCACATTCAAAGG-GATGCATCGATGCA-CATTCAT-AGTGT
1 ATCGATGCACATTC-AAGGAG-TACATCGATGCATC-TTCATGA-TGT
10693 ATCGATGCA
1 ATCGATGCA
10702 TTATGCACAA
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
44 17 0.35
45 31 0.65
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (44 bp):
ATCGATGCACATTCAAGGAGTACATCGATGCATCTTCATGATGT
Found at i:16600 original size:18 final size:18
Alignment explanation
Indices: 16577--16645 Score: 129
Period size: 18 Copynumber: 3.8 Consensus size: 18
16567 TAAAAACCTG
16577 AGTGCATCGATGCATGGA
1 AGTGCATCGATGCATGGA
16595 AGTGCATCGATGCATGGA
1 AGTGCATCGATGCATGGA
*
16613 AGTGCATCGATTCATGGA
1 AGTGCATCGATGCATGGA
16631 AGTGCATCGATGCAT
1 AGTGCATCGATGCAT
16646 AAAATGCATT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 49 1.00
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.25
Consensus pattern (18 bp):
AGTGCATCGATGCATGGA
Found at i:16623 original size:64 final size:64
Alignment explanation
Indices: 16472--16609 Score: 190
Period size: 64 Copynumber: 2.2 Consensus size: 64
16462 CTAAGGGTGT
* * * * **
16472 ATCGATGTATAAAATACATTCGATGTTTCAAACAAGCCTGAGTGCATCGATGTATGGTTTGTGC
1 ATCGATGCATAAAATGCATTCGATGTTTCAAACAAACCTGAGTGCATCGATGCATGGTAAGTGC
16536 ATCGATGCATAAAATGCATTCGATGTTTTCATAA-AAACCTGAGTGCATCGATGCATGG-AAGTG
1 ATCGATGCATAAAATGCATTCGATG-TTTCA-AACAAACCTGAGTGCATCGATGCATGGTAAGTG
16599 C
64 C
16600 ATCGATGCAT
1 ATCGATGCAT
16610 GGAAGTGCAT
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
64 37 0.56
65 27 0.41
66 2 0.03
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (64 bp):
ATCGATGCATAAAATGCATTCGATGTTTCAAACAAACCTGAGTGCATCGATGCATGGTAAGTGC
Found at i:17185 original size:14 final size:14
Alignment explanation
Indices: 17168--17255 Score: 110
Period size: 14 Copynumber: 6.2 Consensus size: 14
17158 TTTAATATTT
*
17168 TAATAATAATTTGA
1 TAATAATGATTTGA
17182 TAATAATGATTTGA
1 TAATAATGATTTGA
17196 TAATATTTAATGATTTGA
1 T-A-A--TAATGATTTGA
17214 TAATAATGATTTGA
1 TAATAATGATTTGA
17228 TAATAATGA-TT--
1 TAATAATGATTTGA
17239 TAATAATGATTTGA
1 TAATAATGATTTGA
17253 TAA
1 TAA
17256 CATTTTTTAT
Statistics
Matches: 66, Mismatches: 1, Indels: 14
0.81 0.01 0.17
Matches are distributed among these distances:
11 9 0.14
12 2 0.03
13 2 0.03
14 37 0.56
15 1 0.02
16 2 0.03
17 1 0.02
18 12 0.18
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (14 bp):
TAATAATGATTTGA
Found at i:17215 original size:32 final size:32
Alignment explanation
Indices: 17171--17232 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
17161 AATATTTTAA
17171 TAATAATTTGATAATAATGATTTGATAATATT
1 TAATAATTTGATAATAATGATTTGATAATATT
*
17203 TAATGATTTGATAATAATGATTTGATAATA
1 TAATAATTTGATAATAATGATTTGATAATA
17233 ATGATTTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.45
Consensus pattern (32 bp):
TAATAATTTGATAATAATGATTTGATAATATT
Found at i:17229 original size:46 final size:44
Alignment explanation
Indices: 17157--17250 Score: 136
Period size: 46 Copynumber: 2.1 Consensus size: 44
17147 AAAATCTTTA
*
17157 ATTTAATATTTTAATAATAATTTGATAATAATGATTTGATAAT-
1 ATTTAATATTTTAATAATAATTTGATAATAATGATTTAATAATG
*
17200 ATTTAATGATTTGATAATAATGATTTGATAATAATGATTTAATAATG
1 ATTTAAT-ATTT--TAATAATAATTTGATAATAATGATTTAATAATG
17247 ATTT
1 ATTT
17251 GATAACATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
43 7 0.16
44 4 0.09
46 30 0.67
47 4 0.09
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.48
Consensus pattern (44 bp):
ATTTAATATTTTAATAATAATTTGATAATAATGATTTAATAATG
Found at i:17242 original size:11 final size:11
Alignment explanation
Indices: 17182--17255 Score: 55
Period size: 11 Copynumber: 6.5 Consensus size: 11
17172 AATAATTTGA
17182 TAATAATGATT
1 TAATAATGATT
*
17193 TGATAAT-ATT
1 TAATAATGATT
*
17203 TAATGAT--TT
1 TAATAATGATT
17212 GATAATAATGATTT
1 --TAATAATGA-TT
17226 GATAATAATGATT
1 --TAATAATGATT
17239 TAATAATGATT
1 TAATAATGATT
*
17250 TGATAA
1 TAATAA
17256 CATTTTTTAT
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
9 2 0.04
10 8 0.15
11 28 0.53
13 2 0.04
14 13 0.25
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (11 bp):
TAATAATGATT
Found at i:17523 original size:13 final size:12
Alignment explanation
Indices: 17483--17541 Score: 50
Period size: 11 Copynumber: 4.8 Consensus size: 12
17473 TAAAAATATT
*
17483 TAATGATTTGATAC
1 TAATGA-TT-ATAA
*
17497 TAATAATT-TAA
1 TAATGATTATAA
17508 TAATGATTACTAA
1 TAATGATTA-TAA
17521 TAATGATT-TAA
1 TAATGATTATAA
*
17532 TAATTATTAT
1 TAATGATTAT
17542 TAATTTAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
11 19 0.50
12 1 0.03
13 13 0.34
14 5 0.13
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (12 bp):
TAATGATTATAA
Found at i:17529 original size:24 final size:24
Alignment explanation
Indices: 17497--17545 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
17487 GATTTGATAC
17497 TAATAATTTAATAATGATTACTAA
1 TAATAATTTAATAATGATTACTAA
* * *
17521 TAATGATTTAATAATTATTATTAA
1 TAATAATTTAATAATGATTACTAA
17545 T
1 T
17546 TTAAAAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (24 bp):
TAATAATTTAATAATGATTACTAA
Found at i:17544 original size:13 final size:13
Alignment explanation
Indices: 17504--17545 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
17494 TACTAATAAT
17504 TTAATAATGATTA
1 TTAATAATGATTA
*
17517 CTAATAATGA-T-
1 TTAATAATGATTA
*
17528 TTAATAATTATTA
1 TTAATAATGATTA
17541 TTAAT
1 TTAAT
17546 TTAAAAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
11 8 0.33
12 2 0.08
13 14 0.58
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (13 bp):
TTAATAATGATTA
Found at i:19086 original size:24 final size:24
Alignment explanation
Indices: 19054--19149 Score: 70
Period size: 24 Copynumber: 3.9 Consensus size: 24
19044 GACCACAATG
19054 AAATCATTATTAGTAATCATTACT
1 AAATCATTATTAGTAATCATTACT
* *
19078 AAATCATTAGTA-TCAAATCATTTCT
1 AAATCATTATTAGT--AATCATTACT
* ** * * *
19103 -TATTTTTAAATTAATAATAATTATT
1 AAATCATT--ATTAGTAATCATTACT
19128 AAATCATTATTAGTAATCATTA
1 AAATCATTATTAGTAATCATTA
19150 GTATGAAATC
Statistics
Matches: 52, Mismatches: 14, Indels: 12
0.67 0.18 0.15
Matches are distributed among these distances:
23 1 0.02
24 27 0.52
25 16 0.31
26 7 0.13
27 1 0.02
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (24 bp):
AAATCATTATTAGTAATCATTACT
Found at i:19425 original size:14 final size:14
Alignment explanation
Indices: 19406--19450 Score: 81
Period size: 14 Copynumber: 3.2 Consensus size: 14
19396 ATCAAAAATG
19406 TTATCAAATCATTA
1 TTATCAAATCATTA
19420 TTATCAAATCATTA
1 TTATCAAATCATTA
*
19434 TTATCAAATTATTA
1 TTATCAAATCATTA
19448 TTA
1 TTA
19451 AATATTAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (14 bp):
TTATCAAATCATTA
Found at i:19466 original size:24 final size:24
Alignment explanation
Indices: 19439--19489 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
19429 CATTATTATC
*
19439 AAATTATTA-TTAAATATTAAATTA
1 AAATT-TTATTTAAATATTAAAATA
19463 AAATTTTATTTAAATATTAAAATA
1 AAATTTTATTTAAATATTAAAATA
19487 AAA
1 AAA
19490 ACATTGTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 3 0.12
24 22 0.88
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
AAATTTTATTTAAATATTAAAATA
Found at i:21694 original size:31 final size:31
Alignment explanation
Indices: 21659--21725 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
21649 TTAAAACTTT
* *
21659 CAATATAATCCCCCAACATTTAGTCCGTTTG
1 CAATATAATCCCCCAAAATTTAGTCCGTTTA
** * *
21690 CAATATGGTCTCTCAAAATTTAGTCCGTTTA
1 CAATATAATCCCCCAAAATTTAGTCCGTTTA
21721 CAATA
1 CAATA
21726 GGTCTGTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.34
Consensus pattern (31 bp):
CAATATAATCCCCCAAAATTTAGTCCGTTTA
Found at i:21911 original size:10 final size:10
Alignment explanation
Indices: 21886--21960 Score: 60
Period size: 10 Copynumber: 6.7 Consensus size: 10
21876 GTTCGTGAAC
*
21886 GTTCGGTTAT
1 GTTCGTTTAT
21896 GTTCGTTTAT
1 GTTCGTTTAT
21906 GTTCGTTCAGTTAT
1 GTTCG-T---TTAT
*
21920 ATTCGTTTAT
1 GTTCGTTTAT
21930 GTTCGTTCAATTAT
1 GTTCG-T---TTAT
21944 GTTCGTTTAT
1 GTTCGTTTAT
21954 GTTCGTT
1 GTTCGTT
21961 CATTTATGTT
Statistics
Matches: 54, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
10 33 0.61
11 2 0.04
13 2 0.04
14 17 0.31
ACGTcount: A:0.13, C:0.12, G:0.20, T:0.55
Consensus pattern (10 bp):
GTTCGTTTAT
Found at i:21912 original size:24 final size:24
Alignment explanation
Indices: 21885--21970 Score: 136
Period size: 24 Copynumber: 3.6 Consensus size: 24
21875 CGTTCGTGAA
*
21885 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCAGTTATGTTCGTTTATGTT
*
21909 CGTTCAGTTATATTCGTTTATGTT
1 CGTTCAGTTATGTTCGTTTATGTT
*
21933 CGTTCAATTATGTTCGTTTATGTT
1 CGTTCAGTTATGTTCGTTTATGTT
*
21957 CGTTCATTTATGTT
1 CGTTCAGTTATGTT
21971 TAACCCAATC
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 57 1.00
ACGTcount: A:0.14, C:0.13, G:0.19, T:0.55
Consensus pattern (24 bp):
CGTTCAGTTATGTTCGTTTATGTT
Found at i:23050 original size:16 final size:16
Alignment explanation
Indices: 23027--23087 Score: 113
Period size: 16 Copynumber: 3.8 Consensus size: 16
23017 GGGTCTCCAA
23027 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
*
23043 CATTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
23059 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
23075 CGTTTATGTTCGT
1 CGTTTATGTTCGT
23088 TATTTATTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.08, C:0.13, G:0.23, T:0.56
Consensus pattern (16 bp):
CGTTTATGTTCGTGTT
Found at i:23907 original size:40 final size:41
Alignment explanation
Indices: 23843--23930 Score: 108
Period size: 40 Copynumber: 2.2 Consensus size: 41
23833 TGTGTACGCC
* *
23843 TATTTAATGATTTCAATAATAAAAAGA-AAACTTTAGATTTT
1 TATTTAATAATTTCAAAAATAAAAAGATAAACTTT-GATTTT
* **
23884 TATTTAATAATTT-AAAAATAAAAATATAAACTTTTCTTTT
1 TATTTAATAATTTCAAAAATAAAAAGATAAACTTTGATTTT
23924 TATTTAA
1 TATTTAA
23931 AAAACTTAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
40 22 0.54
41 19 0.46
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (41 bp):
TATTTAATAATTTCAAAAATAAAAAGATAAACTTTGATTTT
Found at i:27085 original size:35 final size:35
Alignment explanation
Indices: 27046--27115 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
27036 AAAAATATTT
27046 TTAGGTATTTCACCTAACCTAACTCAAGATAGATG
1 TTAGGTATTTCACCTAACCTAACTCAAGATAGATG
27081 TTAGGTATTTCACCTAACCTAACTCAAGATAGATG
1 TTAGGTATTTCACCTAACCTAACTCAAGATAGATG
27116 GTAACTCTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.31
Consensus pattern (35 bp):
TTAGGTATTTCACCTAACCTAACTCAAGATAGATG
Found at i:32102 original size:37 final size:38
Alignment explanation
Indices: 32047--32130 Score: 120
Period size: 37 Copynumber: 2.3 Consensus size: 38
32037 TGGTAACCAA
32047 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
* *
32084 CTTTGAAAAATA-GTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
*
32121 -GTTGAAAAAT
1 CTTTGAAAAAT
32131 GATAATAGGA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
36 9 0.21
37 33 0.77
38 1 0.02
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (38 bp):
CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:36670 original size:21 final size:21
Alignment explanation
Indices: 36646--36706 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
36636 AACTTTGAAA
36646 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
36667 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
36681 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
36702 AAATG
1 AAATG
36707 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:36737 original size:37 final size:37
Alignment explanation
Indices: 36638--36756 Score: 174
Period size: 35 Copynumber: 3.3 Consensus size: 37
36628 TGGTAACCAA
36638 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATA-GGTTTTCAAAGTTTGGTAAATGTTT
36675 CTTTG-AAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
* *
36710 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
*
36747 -GTTGAAAAAT
1 CTTTGAAAAAT
36757 GATAATGGGA
Statistics
Matches: 76, Mismatches: 3, Indels: 7
0.88 0.03 0.08
Matches are distributed among these distances:
35 30 0.39
36 18 0.24
37 28 0.37
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (37 bp):
CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:38477 original size:25 final size:25
Alignment explanation
Indices: 38456--38515 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
38446 TTGAAATAAG
38456 AATAAAATATACATTTTTAAATTAA
1 AATAAAATATACATTTTTAAATTAA
* *
38481 AATAAAATATATATTTTTAAGTTAA
1 AATAAAATATACATTTTTAAATTAA
*
38506 TATAATAATA
1 AATAA-AATA
38516 AATAATATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
25 27 0.87
26 4 0.13
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (25 bp):
AATAAAATATACATTTTTAAATTAA
Found at i:38516 original size:31 final size:29
Alignment explanation
Indices: 38424--38525 Score: 76
Period size: 30 Copynumber: 3.6 Consensus size: 29
38414 GTTAAGATAA
* *
38424 AAAATAAAATATAT-TTCATAAATTGAA-AT
1 AAAATAAAATATATATT-TTTAATT-AATAT
*
38453 AAGAATAAAATATACATTTTT-A--AAT-T
1 AA-AATAAAATATATATTTTTAATTAATAT
38479 AAAATAAAATATATATTTTTAAGTTAATAT
1 AAAATAAAATATATATTTTTAA-TTAATAT
38509 AATAAT-AAATA-ATATTT
1 AA-AATAAAATATATATTT
38526 AATAATTTAA
Statistics
Matches: 60, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
25 17 0.28
26 6 0.10
29 12 0.20
30 20 0.33
31 5 0.08
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (29 bp):
AAAATAAAATATATATTTTTAATTAATAT
Found at i:38577 original size:15 final size:17
Alignment explanation
Indices: 38546--38580 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
38536 GGTAAAAATA
38546 TAATATATTTAATAAGT
1 TAATATATTTAATAAGT
38563 TAATA-ATTT-ATAAGT
1 TAATATATTTAATAAGT
38578 TAA
1 TAA
38581 GATAAGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
16 4 0.22
17 5 0.28
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (17 bp):
TAATATATTTAATAAGT
Found at i:38598 original size:27 final size:27
Alignment explanation
Indices: 38568--38670 Score: 107
Period size: 27 Copynumber: 3.6 Consensus size: 27
38558 TAAGTTAATA
38568 ATTTATAAGTTAAGATAAGAAAAAAAT
1 ATTTATAAGTTAAGATAAGAAAAAAAT
* *
38595 ATTTTTTAGTTAAGATAAGAAAAAAAT
1 ATTTATAAGTTAAGATAAGAAAAAAAT
* *
38622 ATATTCAATAAGTTAAGAAAAAAATAAAATAT
1 AT-TT--ATAAGTTAAGATAAGAA-AAAA-AT
*
38654 ATTTTTAATGTTAAGAT
1 ATTTATAA-GTTAAGAT
38671 GTGATTTTAA
Statistics
Matches: 62, Mismatches: 8, Indels: 9
0.78 0.10 0.11
Matches are distributed among these distances:
27 27 0.44
28 2 0.03
29 3 0.05
30 20 0.32
31 6 0.10
32 4 0.06
ACGTcount: A:0.54, C:0.01, G:0.10, T:0.35
Consensus pattern (27 bp):
ATTTATAAGTTAAGATAAGAAAAAAAT
Found at i:38667 original size:30 final size:29
Alignment explanation
Indices: 38564--38670 Score: 123
Period size: 30 Copynumber: 3.7 Consensus size: 29
38554 TTAATAAGTT
38564 AATA-ATTTATAAGTTAAGATAAGAAAAA
1 AATATATTTATAAGTTAAGATAAGAAAAA
*
38592 AATAT-TTT-TTAGTTAAGATAAGAAAAA
1 AATATATTTATAAGTTAAGATAAGAAAAA
* *
38619 AATATATTCAATAAGTTAAGA-AAAAAATAA
1 AATATATT-TATAAGTTAAGATAAGAAA-AA
*
38649 AATATATTTTTAATGTTAAGAT
1 AATATATTTATAA-GTTAAGAT
38671 GTGATTTTAA
Statistics
Matches: 66, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
27 23 0.35
28 9 0.14
29 8 0.12
30 26 0.39
ACGTcount: A:0.55, C:0.01, G:0.09, T:0.35
Consensus pattern (29 bp):
AATATATTTATAAGTTAAGATAAGAAAAA
Found at i:40570 original size:20 final size:21
Alignment explanation
Indices: 40540--40600 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
40530 TTAATTCAGA
40540 AATATAAAAAATAATAAATTT
1 AATATAAAAAATAATAAATTT
* * *
40561 AATATGAAAAATATTGAATTT
1 AATATAAAAAATAATAAATTT
*
40582 AATTTAAAAATATAA-AAAT
1 AATATAAAAA-ATAATAAAT
40601 AATAAATTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
21 29 0.91
22 3 0.09
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (21 bp):
AATATAAAAAATAATAAATTT
Found at i:40608 original size:28 final size:29
Alignment explanation
Indices: 40561--40618 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
40551 TAATAAATTT
* *
40561 AATATGAAAAATATTGAATTTAATTTAAA
1 AATATGAAAAATAATAAATTTAATTTAAA
*
40590 AATAT-AAAAATAATAAATTTATTTTAAA
1 AATATGAAAAATAATAAATTTAATTTAAA
40618 A
1 A
40619 TTTAAACAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 21 0.81
29 5 0.19
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (29 bp):
AATATGAAAAATAATAAATTTAATTTAAA
Found at i:43826 original size:23 final size:23
Alignment explanation
Indices: 43774--43826 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
43764 CTCATATAAA
*
43774 TGCATCGAAGTACCACGTAGAAT
1 TGCACCGAAGTACCACGTAGAAT
** *
43797 TATACCGAAGTACCGCGTAGAAT
1 TGCACCGAAGTACCACGTAGAAT
43820 TGCACCG
1 TGCACCG
43827 TAATGCCATA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.25, G:0.23, T:0.21
Consensus pattern (23 bp):
TGCACCGAAGTACCACGTAGAAT
Found at i:44597 original size:2 final size:2
Alignment explanation
Indices: 44592--44650 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
44582 TCTCTCTATC
44592 TA TA TA 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
44634 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
44651 CATAACTCCA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:47342 original size:20 final size:22
Alignment explanation
Indices: 47317--47360 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
47307 AACTTTCACT
*
47317 AATATGA-AGGAAGAA-AATAA
1 AATATGAGAGAAAGAAGAATAA
47337 AATATGAGAGAAAGAAGAATAA
1 AATATGAGAGAAAGAAGAATAA
47359 AA
1 AA
47361 CTCGATCTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.33
21 7 0.33
22 7 0.33
ACGTcount: A:0.66, C:0.00, G:0.20, T:0.14
Consensus pattern (22 bp):
AATATGAGAGAAAGAAGAATAA
Found at i:53761 original size:134 final size:134
Alignment explanation
Indices: 53545--53789 Score: 375
Period size: 134 Copynumber: 1.8 Consensus size: 134
53535 CAACTAAATA
* * * *
53545 AGAAAACTTTTTAATGGTGCATTAACACTTCATATCAGAAAAAATGTGTATTTCACATAGGCTAA
1 AGAAAACTTTTCAATGGTGCATTAACACTTCATATCAGAAAAAACGTATATTTCACATAGGCCAA
* *
53610 ATAATACACCATCTCACCAACTTTTTGCAGTTGTCATTTAGTCATCTTTAGTGATATATCAACTC
66 ATAATACACCATCTCACCAAC-TTTTGCAGTGGTCATTTAATCATCTTTAGTGATATATCAACTC
53675 ATTTT
130 ATTTT
* *
53680 AGAAAACTTTTCAGTGGTGCATTATCACTTCATATCAG-AAAAACGTATATTTCACATAGGCCAA
1 AGAAAACTTTTCAATGGTGCATTAACACTTCATATCAGAAAAAACGTATATTTCACATAGGCCAA
* * *
53744 ATAATGCAGCATTTCACCAACTTTTGCAGTGGTCATTTAATCATCT
66 ATAATACACCATCTCACCAACTTTTGCAGTGGTCATTTAATCATCT
53790 GCAACAACTT
Statistics
Matches: 99, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
133 23 0.23
134 41 0.41
135 35 0.35
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.35
Consensus pattern (134 bp):
AGAAAACTTTTCAATGGTGCATTAACACTTCATATCAGAAAAAACGTATATTTCACATAGGCCAA
ATAATACACCATCTCACCAACTTTTGCAGTGGTCATTTAATCATCTTTAGTGATATATCAACTCA
TTTT
Found at i:62607 original size:36 final size:36
Alignment explanation
Indices: 62556--62831 Score: 416
Period size: 36 Copynumber: 7.8 Consensus size: 36
62546 GTGCACTACA
* *
62556 TCCTTCCGTTAGACTTGAATCGGAAGTGTCGATGCT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGTCGATGCC
* * *
62592 TCCTTTCGTTCGACTTGAATCGGAAGTG-CCAGTGCT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGTCGA-TGCC
62628 TCCTTCCGTTCGACTTGAATCGGAAGTGTCGATGCC
1 TCCTTCCGTTCGACTTGAATCGGAAGTGTCGATGCC
* * **
62664 TCATTCTGTTCG-CTTGAATCGGAAGTACCGATGCC
1 TCCTTCCGTTCGACTTGAATCGGAAGTGTCGATGCC
62699 TCCTTCCGTTCGACTTGAATCGGAAGTGTCGATGCC
1 TCCTTCCGTTCGACTTGAATCGGAAGTGTCGATGCC
62735 TCC-TCCGTTCGACTTGAATCGGAAGTGTCGATGCC
1 TCCTTCCGTTCGACTTGAATCGGAAGTGTCGATGCC
*
62770 TCCTT-CGTTCGACTTGAATCGGAAGTGCCGATGCC
1 TCCTTCCGTTCGACTTGAATCGGAAGTGTCGATGCC
*
62805 TCCATCCGTTCGACTTGAATCGGAAGT
1 TCCTTCCGTTCGACTTGAATCGGAAGT
62832 ATAGATGAAA
Statistics
Matches: 219, Mismatches: 16, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
35 101 0.46
36 116 0.53
37 2 0.01
ACGTcount: A:0.18, C:0.26, G:0.25, T:0.31
Consensus pattern (36 bp):
TCCTTCCGTTCGACTTGAATCGGAAGTGTCGATGCC
Found at i:62713 original size:71 final size:72
Alignment explanation
Indices: 62556--62832 Score: 402
Period size: 71 Copynumber: 3.9 Consensus size: 72
62546 GTGCACTACA
* * * * *
62556 TCCTTCCGTTAGACTTGAATCGGAAGTGTCGATGCTTCCTTTCGTTCGACTTGAATCGGAAGTGC
1 TCCTTCCGTTCGACTTGAATCGGAAGTGTCGATGCCTCATTCCGTTCGACTTGAATCGGAAGTAC
*
62621 C-AGTGCT
66 CGA-TGCC
*
62628 TCCTTCCGTTCGACTTGAATCGGAAGTGTCGATGCCTCATTCTGTTCG-CTTGAATCGGAAGTAC
1 TCCTTCCGTTCGACTTGAATCGGAAGTGTCGATGCCTCATTCCGTTCGACTTGAATCGGAAGTAC
62692 CGATGCC
66 CGATGCC
* **
62699 TCCTTCCGTTCGACTTGAATCGGAAGTGTCGATGCCTC-CTCCGTTCGACTTGAATCGGAAGTGT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGTCGATGCCTCATTCCGTTCGACTTGAATCGGAAGTAC
62763 CGATGCC
66 CGATGCC
*
62770 TCCTT-CGTTCGACTTGAATCGGAAGTGCCGATGCCTCCA-TCCGTTCGACTTGAATCGGAAGTA
1 TCCTTCCGTTCGACTTGAATCGGAAGTGTCGATGCCT-CATTCCGTTCGACTTGAATCGGAAGTA
62833 TAGATGAAAT
Statistics
Matches: 188, Mismatches: 13, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
70 37 0.20
71 107 0.57
72 44 0.23
ACGTcount: A:0.18, C:0.26, G:0.25, T:0.31
Consensus pattern (72 bp):
TCCTTCCGTTCGACTTGAATCGGAAGTGTCGATGCCTCATTCCGTTCGACTTGAATCGGAAGTAC
CGATGCC
Done.