Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005722.1 Hibiscus syriacus cultivar Beakdansim tig00013377_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: 54592
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:4861 original size:4 final size:4
Alignment explanation
Indices: 4852--4878 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
4842 AAAGTGCTGA
4852 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
4879 ACAGAAGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:5066 original size:32 final size:31
Alignment explanation
Indices: 5030--5108 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 31
5020 TTAGTTTGTG
5030 CAATAAAATAAATGTTAGTAAGTTAATA-AGAA
1 CAATAAAATAAA-GTTAGTAAGTTAATATA-AA
* * *
5062 CAATAAAA-AAA-TCAGTATGTTAGTATAAA
1 CAATAAAATAAAGTTAGTAAGTTAATATAAA
5091 CAATAAAATAAAAGTTAG
1 CAATAAAAT-AAAGTTAG
5109 AATATTAGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
29 21 0.54
30 1 0.03
31 6 0.15
32 11 0.28
ACGTcount: A:0.57, C:0.05, G:0.11, T:0.27
Consensus pattern (31 bp):
CAATAAAATAAAGTTAGTAAGTTAATATAAA
Found at i:5783 original size:9 final size:9
Alignment explanation
Indices: 5770--5805 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
5760 CGAATAATGT
*
5770 ATAAAATAT
1 ATAAAATAA
5779 ATAAAA-AA
1 ATAAAATAA
5787 ATAAAATAA
1 ATAAAATAA
5796 ATAAAATAA
1 ATAAAATAA
5805 A
1 A
5806 ACGTTAGTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 7 0.28
9 18 0.72
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (9 bp):
ATAAAATAA
Found at i:5961 original size:115 final size:119
Alignment explanation
Indices: 5690--5992 Score: 465
Period size: 120 Copynumber: 2.6 Consensus size: 119
5680 AGTTAGCGGT
*
5690 TAGTGGTTAACAGAGTC-GAGACCATAATAATGTGGATCTTACCCCGGATCGGGTCACCACAAGG
1 TAGTGGTTAGCAGAGTCTGA-ACCATAATAATGTGGATCTTACCCCGGATCGGGTCACCACAAGG
* *
5754 TCGAATCGAATAATGTATAAAATATATAAAAAAATAAAATAAATAAAATAAAACGT
65 TCGAATCGAATAATGCATAAAATATATAAAAAAATAAAAT-AATAAAATAAAACGA
* *
5810 TAGTGGTTAGCAGAGTCTGAACCATAATAATGTGGATCTTACCCCGGATCGGGACACAACAAGGT
1 TAGTGGTTAGCAGAGTCTGAACCATAATAATGTGGATCTTACCCCGGATCGGGTCACCACAAGGT
* *
5875 CGAATCGAATAATGCA-AACAA-ATAT-ATAAAATAAAAT-A-AAAATAAAAGGA
66 CGAATCGAATAATGCATAA-AATATATAAAAAAATAAAATAATAAAATAAAACGA
*
5925 TAGTGGTTAGCAGAGTCTGAACCATAATAATGTGGATCTTACCCCGAATCGGGTCACCACAAGGT
1 TAGTGGTTAGCAGAGTCTGAACCATAATAATGTGGATCTTACCCCGGATCGGGTCACCACAAGGT
5990 CGA
66 CGA
5993 GTAATAAGAG
Statistics
Matches: 171, Mismatches: 10, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
115 75 0.44
116 1 0.01
118 11 0.06
119 6 0.04
120 76 0.44
121 2 0.01
ACGTcount: A:0.42, C:0.16, G:0.20, T:0.22
Consensus pattern (119 bp):
TAGTGGTTAGCAGAGTCTGAACCATAATAATGTGGATCTTACCCCGGATCGGGTCACCACAAGGT
CGAATCGAATAATGCATAAAATATATAAAAAAATAAAATAATAAAATAAAACGA
Found at i:6022 original size:115 final size:115
Alignment explanation
Indices: 5690--6028 Score: 447
Period size: 115 Copynumber: 2.9 Consensus size: 115
5680 AGTTAGCGGT
*
5690 TAGTGGTTAACAGAGTC-GAGACCATAATAATGTGGATCTTACCCCGGATCGGGTCACCACAAGG
1 TAGTGGTTAGCAGAGTCTGA-ACCATAATAATGTGGATCTTACCCCGGATCGGGTCACCACAAGG
* *
5754 TCGAATCGAATAATGTATAA-AATATATAAAAAAATAAAATAAATAAAATAAAACGT
65 TCGAATC-AATAATG-AAAACAATATAT-AAAAAATAAAAT--A-AAAATAAAACGA
* *
5810 TAGTGGTTAGCAGAGTCTGAACCATAATAATGTGGATCTTACCCCGGATCGGGACACAACAAGGT
1 TAGTGGTTAGCAGAGTCTGAACCATAATAATGTGGATCTTACCCCGGATCGGGTCACCACAAGGT
* * *
5875 CGAATCGAATAATGCAAACAA-ATATATAAAATAAAATAAAAATAAAAGGA
66 CGAATC-AATAATGAAAACAATATATAAAAAATAAAATAAAAATAAAACGA
*
5925 TAGTGGTTAGCAGAGTCTGAACCATAATAATGTGGATCTTACCCCGAATCGGGTCACCACAAGGT
1 TAGTGGTTAGCAGAGTCTGAACCATAATAATGTGGATCTTACCCCGGATCGGGTCACCACAAGGT
* *
5990 CGAGT-AATAA-GAGAAACAATAAATAAATAAAT-AAATAAA
66 CGAATCAATAATGA-AAACAATATATAAA-AAATAAAATAAA
6029 CAATGGTTAG
Statistics
Matches: 199, Mismatches: 15, Indels: 16
0.87 0.07 0.07
Matches are distributed among these distances:
112 1 0.01
113 11 0.06
114 12 0.06
115 80 0.40
116 1 0.01
118 11 0.06
119 6 0.03
120 75 0.38
121 2 0.01
ACGTcount: A:0.45, C:0.15, G:0.19, T:0.22
Consensus pattern (115 bp):
TAGTGGTTAGCAGAGTCTGAACCATAATAATGTGGATCTTACCCCGGATCGGGTCACCACAAGGT
CGAATCAATAATGAAAACAATATATAAAAAATAAAATAAAAATAAAACGA
Found at i:6097 original size:29 final size:28
Alignment explanation
Indices: 6041--6109 Score: 68
Period size: 29 Copynumber: 2.5 Consensus size: 28
6031 ATGGTTAGAA
* * * *
6041 TGCAAGAAAATAAAAGTCAGTGGTTAAT
1 TGCAAAAAAATAAAAGTCAATAGATAAT
*
6069 GTGCAAAAAAATAAAAGTTAATAGATAAT
1 -TGCAAAAAAATAAAAGTCAATAGATAAT
*
6098 T-CAAAATAATAA
1 TGCAAAAAAATAA
6110 GAATGCATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 10 0.29
28 1 0.03
29 23 0.68
ACGTcount: A:0.55, C:0.06, G:0.14, T:0.25
Consensus pattern (28 bp):
TGCAAAAAAATAAAAGTCAATAGATAAT
Found at i:7559 original size:219 final size:218
Alignment explanation
Indices: 7179--7814 Score: 809
Period size: 216 Copynumber: 2.9 Consensus size: 218
7169 TAGGACTTCA
* * * * **
7179 GGTCAATTTGGATATAACTTGATGTTGAAGACGACACTGCTCATCCATGTTGAAGAGATCTGGTC
1 GGTCAATATGGAGATAATTTGGTGTTGAAGACGACTTTGCTCATCCATGTTGAAGAGATCTGGTC
* * * * * * *
7244 GCTTACAGATAAATTTTTGTTGAAGATGACATTTTTCCTTCTTGTTGAGAAAGTCGGGTCAATTT
66 ACTTTCAGATAAATTTTTGTTGAAGATGATA-TTTTCCTTCTCGTTGAGGAAGTCGAGTCAATCT
7309 GGAGATAATTTGGAGACAACACGGTTCCTTCGCGTTGAGGAAGGT-TGATTGTCTGAGGATGACA
130 GGAGATAATTTGGAGACAACACGGTTCCTTCGCGTTGAGGAA-GTCTGATTGTCTGAGGATGACA
* * * *
7373 CTTCTCCTTCGCGTTTACGAGATCG
194 CTACTCCTTCACATTAACGAGATCG
*
7398 GGTCAATCTGGAGATAATTTGGTGTTGAAGACGACTTTGCTCATCCATGTTGAAGAGATCTGGTC
1 GGTCAATATGGAGATAATTTGGTGTTGAAGACGACTTTGCTCATCCATGTTGAAGAGATCTGGTC
* * * *
7463 ACTTTCAGATAAATTGTTTATTGAAGATGATGATATTCCTTCTCGTTAAGGAAGTTGAGTCAATC
66 ACTTTCAGATAAATT-TTTGTTGAAGATGAT-ATTTTCCTTCTCGTTGAGGAAGTCGAGTCAATC
* * * * * *
7528 TAGAGATAATTTGGAGACAACAC-GATCCTTCGCATTGAAGAAGTCTTATTGTCTAAGGATGA-A
129 TGGAGATAATTTGGAGACAACACGGTTCCTTCGCGTTGAGGAAGTCTGATTGTCTGAGGATGACA
7591 --ACTCCTTCACATTAACGAGATCG
194 CTACTCCTTCACATTAACGAGATCG
* * * ** *
7614 GTTTAATATGTAGATAATTTGGTGTTGATCAAGACTTTGCTCATCCATGTTGAAGAGATCTGGTC
1 GGTCAATATGGAGATAATTTGGTGTTGAAGACGACTTTGCTCATCCATGTTGAAGAGATCTGGTC
* *
7679 ACTTTCAAATAAATTCTTTGTTGAAGATGACT-TTTTCCTTCTCATTGAGGAAGTCGAGTCAATC
66 ACTTTCAGATAAATT-TTTGTTGAAGATGA-TATTTTCCTTCTCGTTGAGGAAGTCGAGTCAATC
* * *
7743 TGGAGATAA-TTGTAGAGAACACGGTTCCTTCGCGTTGAGGAAGTCTGATTGTCTGAGGATGACG
129 TGGAGATAATTTGGAGACAACACGGTTCCTTCGCGTTGAGGAAGTCTGATTGTCTGAGGATGACA
*
7807 CTGCTCCT
194 CTACTCCT
7815 ATACATTGAG
Statistics
Matches: 358, Mismatches: 51, Indels: 17
0.84 0.12 0.04
Matches are distributed among these distances:
214 11 0.03
215 70 0.20
216 104 0.29
217 1 0.00
218 8 0.02
219 103 0.29
220 60 0.17
221 1 0.00
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (218 bp):
GGTCAATATGGAGATAATTTGGTGTTGAAGACGACTTTGCTCATCCATGTTGAAGAGATCTGGTC
ACTTTCAGATAAATTTTTGTTGAAGATGATATTTTCCTTCTCGTTGAGGAAGTCGAGTCAATCTG
GAGATAATTTGGAGACAACACGGTTCCTTCGCGTTGAGGAAGTCTGATTGTCTGAGGATGACACT
ACTCCTTCACATTAACGAGATCG
Found at i:8014 original size:139 final size:139
Alignment explanation
Indices: 7778--8311 Score: 566
Period size: 139 Copynumber: 3.8 Consensus size: 139
7768 TCCTTCGCGT
* * * * * *
7778 TGAGGAAGTCTGATTGTCTGAGGATGACGCTGCTCCTATAC--ATTGAGGAGATATGGTTGGTGG
1 TGAGGAAGTCTGATTGCCTAAGGATGACGCTGCTCCT-TACGTGTTGAGGAGATCTAGTCGGTGG
* *
7841 ACGACATTATTCCTTCGTGATGAGGACGTTTAGCCATCTTTAGGGATAATTTGGAGACAACACGA
65 ACGACATTATTCCTACGTGATGAGGACGTCTAGCCATCTTTAGGGATAATTTGGAGACAACACGA
7906 TTCCTACGTAA
130 TTCCTACGT-A
* * * * **
7917 TGAAGAAGTCTGGTTGTCTAAGGATGATGCTGCTCCTT-CGTGTTGAGGAGATCTAGTCAATGGA
1 TGAGGAAGTCTGATTGCCTAAGGATGACGCTGCTCCTTACGTGTTGAGGAGATCTAGTCGGTGGA
* * * *
7981 CGACATTATTTCTACGTGATTAGGACGTCTAGCCATCTTTAGGGATAATTTCGAGACAACACGGT
66 CGACATTATTCCTACGTGATGAGGACGTCTAGCCATCTTTAGGGATAATTTGGAGACAACACGAT
*
8046 TCCTATGTGA
131 TCCTACGT-A
* * *
8056 TGAGGAATTCTGATTGCCTAAGGATGACGTTGCTCCTTTAC-T-TTGAGGAGATCTGGTCGGTGG
1 TGAGGAAGTCTGATTGCCTAAGGATGACGCTGCTCC-TTACGTGTTGAGGAGATCTAGTCGGTGG
* * * ** * * * * *
8119 ATGACATTGTTCTTATATGATGAGGACGTCTATCCGTCTCTAGGGATAATTAGGAGACAATAC-A
65 ACGACATTATTCCTACGTGATGAGGACGTCTAGCCATCTTTAGGGATAATTTGGAGACAACACGA
8183 GTTCGTTCT-CGT-
130 -TTC---CTACGTA
* * *
8195 TGAGGAAGTCTGATTGCCTGAGGATGACGCTGCT-CTTACGCGTTGAAGAGATCTAGTCGGTGGA
1 TGAGGAAGTCTGATTGCCTAAGGATGACGCTGCTCCTTACGTGTTGAGGAGATCTAGTCGGTGGA
* * * *
8259 CG-CTATTGTTCCTTCGTGATGAGGACGTCTAGTCGTCTTTAGGGATAATTTGG
66 CGAC-ATTATTCCTACGTGATGAGGACGTCTAGCCATCTTTAGGGATAATTTGG
8312 CTTTGGAAAT
Statistics
Matches: 327, Mismatches: 57, Indels: 22
0.81 0.14 0.05
Matches are distributed among these distances:
137 5 0.02
138 3 0.01
139 311 0.95
140 3 0.01
141 3 0.01
142 2 0.01
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.32
Consensus pattern (139 bp):
TGAGGAAGTCTGATTGCCTAAGGATGACGCTGCTCCTTACGTGTTGAGGAGATCTAGTCGGTGGA
CGACATTATTCCTACGTGATGAGGACGTCTAGCCATCTTTAGGGATAATTTGGAGACAACACGAT
TCCTACGTA
Found at i:8286 original size:278 final size:277
Alignment explanation
Indices: 7760--8309 Score: 655
Period size: 278 Copynumber: 2.0 Consensus size: 277
7750 AATTGTAGAG
* * *
7760 AACACGGTTCCTTCGCGTTGAGGAAGTCTGATTGTCTGAGGATGACGCTGCTCCTATACATTGAG
1 AACACGGTTCCTTCGCGATGAGGAAGTCTGATTGCCTAAGGATGACGCTGCTCCTATACATTGAG
* * * *
7825 GAGATATGGTTGGTGGACGACATTATTCCTTCGTGATGAGGACGTTTAGCCATCTTTAGGGATAA
66 GAGATATGGTCGGTGGACGACATTATTCCTTCATGATGAGGACGTCTAGCCATCTCTAGGGATAA
* * * *
7890 TTTGGAGACAACACGATTCCTACGTAATGAAGAAGTCTGGTTGTCTAAGGATGATGCTGCTCCTT
131 TTAGGAGACAACACGATTCCTACGT-ATGAAGAAGTCTGATTGCCTAAGGATGACGCTGCTCCTT
* * * *
7955 CGTGTTGAGGAGATCTAGTCAATGGACGACATTATTTCTACGTGATTAGGACGTCTAGCCATCTT
195 CGCGTTGAAGAGATCTAGTCAATGGACGACATTATTCCTACGTGATGAGGACGTCTAGCCATCTT
8020 TAGGGATAATTTCGAGAC
260 TAGGGATAATTTCGAGAC
* * * * *
8038 AACACGGTTCCTAT-GTGATGAGGAATTCTGATTGCCTAAGGATGACGTTGCTCCTTTACTTTGA
1 AACACGGTTCCT-TCGCGATGAGGAAGTCTGATTGCCTAAGGATGACGCTGCTCCTATACATTGA
* * * * * *
8102 GGAGATCTGGTCGGTGGATGACATTGTT-CTTATATGATGAGGACGTCTATCCGTCTCTAGGGAT
65 GGAGATATGGTCGGTGGACGACATTATTCCTT-CATGATGAGGACGTCTAGCCATCTCTAGGGAT
* * *
8166 AATTAGGAGACAATAC-AGTTCGTTCT-CGT-TGAGGAAGTCTGATTGCCTGAGGATGACGCTGC
129 AATTAGGAGACAACACGA-TTC---CTACGTATGAAGAAGTCTGATTGCCTAAGGATGACGCTGC
** * *
8228 T-CTTACGCGTTGAAGAGATCTAGTCGGTGGACG-CTATTGTTCCTTCGTGATGAGGACGTCTAG
190 TCCTT-CGCGTTGAAGAGATCTAGTCAATGGACGAC-ATTATTCCTACGTGATGAGGACGTCTAG
* *
8291 TCGTCTTTAGGGATAATTT
253 CCATCTTTAGGGATAATTT
8310 GGCTTTGGAA
Statistics
Matches: 229, Mismatches: 35, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
277 8 0.03
278 215 0.94
279 1 0.00
280 3 0.01
281 2 0.01
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.32
Consensus pattern (277 bp):
AACACGGTTCCTTCGCGATGAGGAAGTCTGATTGCCTAAGGATGACGCTGCTCCTATACATTGAG
GAGATATGGTCGGTGGACGACATTATTCCTTCATGATGAGGACGTCTAGCCATCTCTAGGGATAA
TTAGGAGACAACACGATTCCTACGTATGAAGAAGTCTGATTGCCTAAGGATGACGCTGCTCCTTC
GCGTTGAAGAGATCTAGTCAATGGACGACATTATTCCTACGTGATGAGGACGTCTAGCCATCTTT
AGGGATAATTTCGAGAC
Found at i:8699 original size:66 final size:66
Alignment explanation
Indices: 8629--8772 Score: 175
Period size: 66 Copynumber: 2.2 Consensus size: 66
8619 TGATTCAAGT
* * * **
8629 GAAACAATTTCAA-AATTTGTGTTTTAAGGGAAAACTGTCTCAAGCGAGATGAAATTTG-TTTCG
1 GAAACAATCTCAAGAATTTGTGTTTCAAGAG-AAACTGTCTCAAGCGAGAAAAAATTTGTTTTC-
8692 AGA
64 AGA
* * *
8695 GAAACAATCTCAAGGATTTGTGTTTCGAGAGAAATTGTCTCAAGCGAGAAAAAATTTGTTTTCAG
1 GAAACAATCTCAAGAATTTGTGTTTCAAGAGAAACTGTCTCAAGCGAGAAAAAATTTGTTTTCAG
8760 A
66 A
8761 GAAAACAATCTC
1 G-AAACAATCTC
8773 TAGTGAGATC
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
66 40 0.60
67 27 0.40
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (66 bp):
GAAACAATCTCAAGAATTTGTGTTTCAAGAGAAACTGTCTCAAGCGAGAAAAAATTTGTTTTCAG
A
Found at i:16058 original size:32 final size:31
Alignment explanation
Indices: 16022--16100 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 31
16012 TTAGTTTGTG
16022 CAATAAAATAAATGTTAGTAAGTTAATAAGAA
1 CAATAAAATAAA-GTTAGTAAGTTAATAAGAA
* * * *
16054 CAATAAAA-AAA-TCAGTATGTTAGTATGAA
1 CAATAAAATAAAGTTAGTAAGTTAATAAGAA
16083 CAATAAAATAAAAGTTAG
1 CAATAAAAT-AAAGTTAG
16101 AATATTAGTA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
29 22 0.56
31 6 0.15
32 11 0.28
ACGTcount: A:0.56, C:0.05, G:0.13, T:0.27
Consensus pattern (31 bp):
CAATAAAATAAAGTTAGTAAGTTAATAAGAA
Found at i:16269 original size:29 final size:29
Alignment explanation
Indices: 16237--16294 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
16227 AAATAAACAA
16237 TGGTTAGA-ATACAAGAAAATAAAAGTCAG
1 TGGTTA-ATATACAAGAAAATAAAAGTCAG
* * *
16266 TGGTTAATGTGCAATAAAATAAAAGTCAG
1 TGGTTAATATACAAGAAAATAAAAGTCAG
16295 CAGTTAATTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 1 0.04
29 24 0.96
ACGTcount: A:0.48, C:0.07, G:0.21, T:0.24
Consensus pattern (29 bp):
TGGTTAATATACAAGAAAATAAAAGTCAG
Found at i:19130 original size:28 final size:28
Alignment explanation
Indices: 19090--19145 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
19080 CAATGATTCT
19090 ACATAATATTCCTAAATT-AGTAAGCTAA
1 ACATAATATTCCTAAATTAAG-AAGCTAA
19118 ACATAATATTCCTAAATTAAGAAGCTAA
1 ACATAATATTCCTAAATTAAGAAGCTAA
19146 TCTCTGACAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 25 0.93
29 2 0.07
ACGTcount: A:0.48, C:0.14, G:0.07, T:0.30
Consensus pattern (28 bp):
ACATAATATTCCTAAATTAAGAAGCTAA
Found at i:20507 original size:21 final size:19
Alignment explanation
Indices: 20483--20527 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
20473 AGGTAGTATT
*
20483 TTATATACATTATAGCATATA
1 TTATATA-ATTATA-CAAATA
*
20504 TTATGTAATTATACAAATA
1 TTATATAATTATACAAATA
20523 TTATA
1 TTATA
20528 CAGTTATATC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 9 0.43
20 6 0.29
21 6 0.29
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (19 bp):
TTATATAATTATACAAATA
Found at i:29458 original size:17 final size:19
Alignment explanation
Indices: 29436--29470 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
29426 GCTTTTGTTC
29436 AGTTTG-AGAGGG-AATCT
1 AGTTTGAAGAGGGCAATCT
29453 AGTTTGAAGAGGGCAATC
1 AGTTTGAAGAGGGCAATC
29471 GAGATGTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 6 0.38
19 4 0.25
ACGTcount: A:0.31, C:0.09, G:0.34, T:0.26
Consensus pattern (19 bp):
AGTTTGAAGAGGGCAATCT
Found at i:41175 original size:18 final size:19
Alignment explanation
Indices: 41140--41181 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
41130 TTATCAATAA
* * *
41140 AAAATATACAGAATATTT-
1 AAAATATAAAAAAAATTTG
41158 AAAATATAAAAAAAATTTG
1 AAAATATAAAAAAAATTTG
41177 AAAAT
1 AAAAT
41182 TTTAAGGGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (19 bp):
AAAATATAAAAAAAATTTG
Found at i:44841 original size:15 final size:15
Alignment explanation
Indices: 44796--44856 Score: 65
Period size: 15 Copynumber: 4.2 Consensus size: 15
44786 AATATTATAT
*
44796 TTATTATTATATTTTA
1 TTATTATTA-ATTTAA
44812 TTATTATT-A-TT-A
1 TTATTATTAATTTAA
44824 TTATTATTAATTTAA
1 TTATTATTAATTTAA
* *
44839 TTATTAATAATTAAA
1 TTATTATTAATTTAA
44854 TTA
1 TTA
44857 CATATTACAT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
12 9 0.22
13 3 0.08
14 3 0.08
15 17 0.43
16 8 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTATTATTAATTTAA
Found at i:44844 original size:3 final size:3
Alignment explanation
Indices: 44796--44832 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
44786 AATATTATAT
44796 TTA TTA TTA -TA TT- TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
44833 ATTTAATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.12
3 28 0.88
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:44846 original size:12 final size:13
Alignment explanation
Indices: 44788--44844 Score: 73
Period size: 12 Copynumber: 4.4 Consensus size: 13
44778 TCTACAAAAA
44788 TATTATA-TTTAT
1 TATTATATTTTAT
44800 TATTATATTTTAT
1 TATTATATTTTAT
44813 TATTATTATTATTAT
1 TATTA-TATT-TTAT
*
44828 TATTA-ATTTAAT
1 TATTATATTTTAT
44840 TATTA
1 TATTA
44845 ATAATTAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
12 15 0.37
13 13 0.32
14 4 0.10
15 9 0.22
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
TATTATATTTTAT
Found at i:46368 original size:30 final size:30
Alignment explanation
Indices: 46333--46455 Score: 140
Period size: 30 Copynumber: 4.1 Consensus size: 30
46323 TATTTGTTTA
*
46333 TTTAGACCCTTAAGTTTATATTTTTACTAT
1 TTTAGACCCTTAAGTTTCTATTTTTACTAT
* * *
46363 TTTAGACCTTTAAGTTTCTATTTTTGCCAT
1 TTTAGACCCTTAAGTTTCTATTTTTACTAT
* *
46393 TTTAG-TCCTTAAGTTTCTATTTTTATTAT
1 TTTAGACCCTTAAGTTTCTATTTTTACTAT
* * * *
46422 TTCAGTCCCTTAAGTTTCTTTTGTTTGCTAT
1 TTTAGACCCTTAAGTTTCTATT-TTTACTAT
46453 TTT
1 TTT
46456 GGTCCTTTTA
Statistics
Matches: 76, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
29 23 0.30
30 45 0.59
31 8 0.11
ACGTcount: A:0.20, C:0.15, G:0.09, T:0.57
Consensus pattern (30 bp):
TTTAGACCCTTAAGTTTCTATTTTTACTAT
Found at i:46404 original size:59 final size:60
Alignment explanation
Indices: 46340--46462 Score: 167
Period size: 59 Copynumber: 2.1 Consensus size: 60
46330 TTATTTAGAC
* *
46340 CCTTAAGTTTATATTTTTACTATTTTAGACCTTTAAGTTTCTATT-TTTGCCATTTTAGT
1 CCTTAAGTTTATATTTTTACTATTTCAGACCCTTAAGTTTCTATTGTTTGCCATTTTAGT
* * * * * *
46399 CCTTAAGTTTCTATTTTTATTATTTCAGTCCCTTAAGTTTCTTTTGTTTGCTATTTTGGT
1 CCTTAAGTTTATATTTTTACTATTTCAGACCCTTAAGTTTCTATTGTTTGCCATTTTAGT
46459 CCTT
1 CCTT
46463 TTAAATAGAA
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
59 39 0.71
60 16 0.29
ACGTcount: A:0.18, C:0.15, G:0.10, T:0.57
Consensus pattern (60 bp):
CCTTAAGTTTATATTTTTACTATTTCAGACCCTTAAGTTTCTATTGTTTGCCATTTTAGT
Found at i:47998 original size:4 final size:4
Alignment explanation
Indices: 47989--48022 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
47979 TATGTTTGAT
47989 TTTA TTTA TTTA TTTA TTTA TTTA -TTA -TTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
48023 GTATTGCATG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 6 0.21
4 23 0.79
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:51863 original size:36 final size:37
Alignment explanation
Indices: 51796--51902 Score: 146
Period size: 38 Copynumber: 2.9 Consensus size: 37
51786 GAGATTATCT
*
51796 TCTTAAAAACAAAGTATCGTCTCG-TTAGAGACAA-TTC
1 TCTTAAAAACAAA-TTTCGTCTCGCTT-GAGACAACTTC
**
51833 TCTTAAAAACAAATTTTATCTCGCTTGAGACAACTTTC
1 TCTTAAAAACAAATTTCGTCTCGCTTGAGACAAC-TTC
51871 TCTTAAAAACAAATTTCGTCTCGCTTGAGACA
1 TCTTAAAAACAAATTTCGTCTCGCTTGAGACA
51903 TTTTTCCATA
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
36 14 0.23
37 15 0.24
38 33 0.53
ACGTcount: A:0.36, C:0.21, G:0.11, T:0.33
Consensus pattern (37 bp):
TCTTAAAAACAAATTTCGTCTCGCTTGAGACAACTTC
Found at i:52035 original size:26 final size:27
Alignment explanation
Indices: 51990--52041 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
51980 CCTTGAGACT
*
51990 TTTTTTTCTCTGAGATACAAATTTAAA
1 TTTTTTTCTCTGAGATACAAAGTTAAA
52017 TTTTTTTCATCTGA-A-ACAAAGTTAA
1 TTTTTTTC-TCTGAGATACAAAGTTAA
52042 TATCACTGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 9 0.39
27 9 0.39
28 5 0.22
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.46
Consensus pattern (27 bp):
TTTTTTTCTCTGAGATACAAAGTTAAA
Found at i:53483 original size:53 final size:53
Alignment explanation
Indices: 53419--53591 Score: 310
Period size: 53 Copynumber: 3.3 Consensus size: 53
53409 ACCATGGTGA
*
53419 GGGTATCGATACCAAGCCACATCGAAGCTAATTTTGGTATCGATACCGAAAGG
1 GGGTATCGATACCAAGCCATATCGAAGCTAATTTTGGTATCGATACCGAAAGG
*
53472 GGGTATCGATACCAAGCCATATCGAAGATAATTTTGGTATCGATACCGAAAGG
1 GGGTATCGATACCAAGCCATATCGAAGCTAATTTTGGTATCGATACCGAAAGG
*
53525 GGGTATCGATACCAAGCCATATCGAAGCTAATTTTGGTATCGATACCGGAAGG
1 GGGTATCGATACCAAGCCATATCGAAGCTAATTTTGGTATCGATACCGAAAGG
*
53578 GGGTATCGGTACCA
1 GGGTATCGATACCA
53592 TAGTAGAGTA
Statistics
Matches: 115, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 115 1.00
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (53 bp):
GGGTATCGATACCAAGCCATATCGAAGCTAATTTTGGTATCGATACCGAAAGG
Found at i:53605 original size:22 final size:22
Alignment explanation
Indices: 53580--53621 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
53570 CCGGAAGGGG
*
53580 GTATCGGTACCATAGTAGAGTA
1 GTATCGATACCATAGTAGAGTA
* *
53602 GTATCGATATCATGGTAGAG
1 GTATCGATACCATAGTAGAG
53622 GCATCGATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.31, C:0.12, G:0.29, T:0.29
Consensus pattern (22 bp):
GTATCGATACCATAGTAGAGTA
Found at i:54140 original size:107 final size:105
Alignment explanation
Indices: 53954--54230 Score: 306
Period size: 107 Copynumber: 2.6 Consensus size: 105
53944 TTACCCAATA
* * * * *
53954 GGCACTAAATGTGCATTTCACGAAATTCATCATATGTGGATGAATAACTGTTTCGGCACTATATG
1 GGCACTAAGTGTGCATTTCACG-AATTCATCCTATGTGGATGAATAACCGTTTCAGCACTATATA
* * *
54019 TGCATTTCACGGAATTCATCCTAGGTGGATGAATAATCGTTT-
65 TGCATTTCACGGAATTCAGCCTAGGTGGATG-A-AACCATTTC
* * *
54061 GGCACTTAGTGTGCATTTCACAGAATTCATCCTAGGTTGATGAATAACCGTTTCAGCACTA-AGT
1 GGCACTAAGTGTGCATTTCAC-GAATTCATCCTATGTGGATGAATAACCGTTTCAGCACTATA-T
* *
54125 ATGCATTTCACGGAATTTAGCCTATGTGGATGAAACCATTTC
64 ATGCATTTCACGGAATTCAGCCTAGGTGGATGAAACCATTTC
** * * * * *
54167 GATACTAAGTGTGCATTTCATGGAATTCATCCTATGAGGATGAATAACCATTTCGGAACTATAT
1 GGCACTAAGTGTGCATTTCA-CGAATTCATCCTATGTGGATGAATAACCGTTTCAGCACTATAT
54231 GTGCCAAGCA
Statistics
Matches: 142, Mismatches: 23, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
105 6 0.04
106 53 0.37
107 82 0.58
108 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.33
Consensus pattern (105 bp):
GGCACTAAGTGTGCATTTCACGAATTCATCCTATGTGGATGAATAACCGTTTCAGCACTATATAT
GCATTTCACGGAATTCAGCCTAGGTGGATGAAACCATTTC
Found at i:54250 original size:54 final size:55
Alignment explanation
Indices: 53954--54234 Score: 319
Period size: 54 Copynumber: 5.3 Consensus size: 55
53944 TTACCCAATA
* * * *
53954 GGCACTA-AATGTGCATTTCACGAAATTCATCATATGTGGATGAATAACTGTTTC
1 GGCACTATAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* *
54008 GGCACTATA-TGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAATCGTTT-
1 GGCACTATAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
54061 GGCACT-TAGTGTGCATTTCACAGAATTCATCCTAGGTTGATGAATAACCGTTTC
1 GGCACTATAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * * *
54115 AGCACTA-AGTATGCATTTCACGGAATTTAGCCTATGTGGATG-A-AACCATTTC
1 GGCACTATAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
** * * *
54167 GATACTA-AGTGTGCATTTCATGGAATTCATCCTATGAGGATGAATAACCATTTC
1 GGCACTATAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
*
54221 GGAACTATA-TGTGC
1 GGCACTATAGTGTGC
54235 CAAGCACGGA
Statistics
Matches: 194, Mismatches: 26, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
52 44 0.23
53 49 0.25
54 99 0.51
55 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (55 bp):
GGCACTATAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
Done.