Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007131.1 Hibiscus syriacus cultivar Beakdansim tig00018635_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: 132003
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
File 2 of 2
Found at i:105164 original size:31 final size:31
Alignment explanation
Indices: 105129--105187 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
105119 AGTTGTATGG
* *
105129 ATTATTTAAATTTCAATATTGTAAAACTAAA
1 ATTATTTAAATCTCAATATTGCAAAACTAAA
*
105160 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAATATTGCAAAACT
105188 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAATATTGCAAAACTAAA
Found at i:106829 original size:17 final size:17
Alignment explanation
Indices: 106804--106837 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
106794 TAATGAGAAA
*
106804 AAATTAAATAAACAAAT
1 AAATAAAATAAACAAAT
*
106821 AAATAAAATAAATAAAT
1 AAATAAAATAAACAAAT
106838 TAGGATAAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAAAATAAACAAAT
Found at i:107530 original size:32 final size:32
Alignment explanation
Indices: 107493--107613 Score: 84
Period size: 32 Copynumber: 3.4 Consensus size: 32
107483 GAAACAAAGA
107493 TAAAATATAAAAATAATATCCTAAAACTTAAT
1 TAAAATATAAAAATAATATCCTAAAACTTAAT
*
107525 TAAAATATCAAAACCTGTTTAAACTAAAATACCTAAAAC--AAT
1 TAAAATAT---AA-------AAA-TAATAT-CCTAAAACTTAAT
107567 GATAAAATATAAAAATAATATCCTAAAACTTAAT
1 --TAAAATATAAAAATAATATCCTAAAACTTAAT
107601 TAAAATACTAAAA
1 TAAAATA-TAAAA
107614 CCTATTTAAA
Statistics
Matches: 70, Mismatches: 2, Indels: 33
0.67 0.02 0.31
Matches are distributed among these distances:
32 23 0.33
33 10 0.14
34 6 0.09
35 2 0.03
41 2 0.03
42 6 0.09
43 5 0.07
44 16 0.23
ACGTcount: A:0.59, C:0.12, G:0.02, T:0.28
Consensus pattern (32 bp):
TAAAATATAAAAATAATATCCTAAAACTTAAT
Found at i:107546 original size:76 final size:76
Alignment explanation
Indices: 107445--107654 Score: 352
Period size: 76 Copynumber: 2.8 Consensus size: 76
107435 TCTTAAATCC
* *
107445 TAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCTGAAACAAAGATAAAATATAAAAATAA
1 TAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAA
107509 TATCCTAAAACT
65 TATCCTAAAACT
* *
107521 TAATTAAAATA-TCAAAACCTGTTTAAACTAAAATACCTAAAACAATGATAAAATATAAAAATAA
1 TAATTAAAATACT-AAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAA
107585 TATCCTAAAACT
65 TATCCTAAAACT
107597 TAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1 TAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
107655 TAGTTAAAAT
Statistics
Matches: 125, Mismatches: 6, Indels: 6
0.91 0.04 0.04
Matches are distributed among these distances:
74 1 0.01
75 4 0.03
76 119 0.95
77 1 0.01
ACGTcount: A:0.58, C:0.13, G:0.02, T:0.27
Consensus pattern (76 bp):
TAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAAT
ATCCTAAAACT
Found at i:107561 original size:44 final size:43
Alignment explanation
Indices: 107507--107639 Score: 105
Period size: 44 Copynumber: 3.3 Consensus size: 43
107497 ATATAAAAAT
107507 AATATCCTAAAACTTAATTAAAATATCAAAACCTGTTTAAACTAA
1 AATA-CCTAAAACTTAATTAAAATATCAAAACCT-TTTAAACTAA
107552 AATACCTAAAAC--AATGATAAAATAT---AA------AAA-TAA
1 AATACCTAAAACTTAAT--TAAAATATCAAAACCTTTTAAACTAA
*
107585 TAT-CCTAAAACTTAATTAAAATA-CTAAAACCTATTTAAACTAA
1 AATACCTAAAACTTAATTAAAATATC-AAAACCT-TTTAAACTAA
107628 AATACCTAAAAC
1 AATACCTAAAAC
107640 AAAGATAAAA
Statistics
Matches: 69, Mismatches: 2, Indels: 35
0.65 0.02 0.33
Matches are distributed among these distances:
32 15 0.22
33 5 0.07
34 6 0.09
35 2 0.03
41 2 0.03
42 6 0.09
43 5 0.07
44 24 0.35
45 4 0.06
ACGTcount: A:0.56, C:0.15, G:0.02, T:0.28
Consensus pattern (43 bp):
AATACCTAAAACTTAATTAAAATATCAAAACCTTTTAAACTAA
Found at i:109522 original size:11 final size:11
Alignment explanation
Indices: 109506--109547 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
109496 AAGTTTGCTA
109506 AAAAATAAAAT
1 AAAAATAAAAT
*
109517 AAAAATAAAAC
1 AAAAATAAAAT
109528 AAAAATAAAAT
1 AAAAATAAAAT
*
109539 -GAAATAAAA
1 AAAAATAAAA
109548 AATAGAACGA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
10 8 0.29
11 20 0.71
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.14
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:109548 original size:22 final size:22
Alignment explanation
Indices: 109506--109547 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
109496 AAGTTTGCTA
109506 AAAAATAAAATAAAAATAAAAC
1 AAAAATAAAATAAAAATAAAAC
*
109528 AAAAATAAAAT-GAAATAAAA
1 AAAAATAAAATAAAAATAAAA
109548 AATAGAACGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.14
Consensus pattern (22 bp):
AAAAATAAAATAAAAATAAAAC
Found at i:115258 original size:17 final size:17
Alignment explanation
Indices: 115233--115266 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
115223 AATGAGAAAA
*
115233 AAATTAAATAAACAAAT
1 AAATAAAATAAACAAAT
*
115250 AAATAAAATAAATAAAT
1 AAATAAAATAAACAAAT
115267 TGGGATAAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAAAATAAACAAAT
Found at i:115966 original size:19 final size:19
Alignment explanation
Indices: 115942--115979 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
115932 AAATAATATC
*
115942 CTAAAACTTAATTAAAATA
1 CTAAAACCTAATTAAAATA
*
115961 CTAAAACCTATTTAAAATA
1 CTAAAACCTAATTAAAATA
115980 AAATACCGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (19 bp):
CTAAAACCTAATTAAAATA
Found at i:115972 original size:76 final size:76
Alignment explanation
Indices: 115863--116083 Score: 363
Period size: 76 Copynumber: 2.9 Consensus size: 76
115853 AAGCTAAAAC
* * * *
115863 ATCCTAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATAACTAAAACAAAGATAAAA
1 ATCCTAAAACTTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAA
115927 TATAAAAATAAT
65 TATAAAAATAAT
* *
115939 ATCCTAAAACTTAATTAAAATACTAAAACCTATTTAAAATAAAATACCGAAAACAAAGATAAAAT
1 ATCCTAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAAT
116004 ATAAAAATAAT
66 ATAAAAATAAT
*
116015 ATCATAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAAT
1 ATCCTAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAAT
116080 ATAA
66 ATAA
116084 TATTTAAAAT
Statistics
Matches: 135, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
75 5 0.04
76 130 0.96
ACGTcount: A:0.60, C:0.13, G:0.02, T:0.26
Consensus pattern (76 bp):
ATCCTAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAAT
ATAAAAATAAT
Found at i:118498 original size:17 final size:17
Alignment explanation
Indices: 118471--118512 Score: 75
Period size: 17 Copynumber: 2.4 Consensus size: 17
118461 GTTATAGTTA
118471 AAATAAAAAATAATAATT
1 AAAT-AAAAATAATAATT
118489 AAATAAAAATAATAATT
1 AAATAAAAATAATAATT
118506 AAATAAA
1 AAATAAA
118513 CAAATTAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 20 0.83
18 4 0.17
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
AAATAAAAATAATAATT
Found at i:119242 original size:75 final size:75
Alignment explanation
Indices: 119153--119326 Score: 226
Period size: 76 Copynumber: 2.3 Consensus size: 75
119143 AATACCTACA
* * * * *
119153 AAAATATAATATAATATTCTAAATCCTAATTAAAATACT-AAAACCTATTTAAATTAAAATACAA
1 AAAATATAAAATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATAAAA
119217 AGATAAAGAT
66 AGATAAAGAT
*
119227 AAAATATAAAAATAATATCCTAAAACGTAATTAAAATACTAAAAACCTATTTAAACTAAAATAAA
1 AAAATAT-AAAATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATAAA
119292 AAGATAAA-AT
65 AAGATAAAGAT
* * *
119302 ATAATGTTTAAAATATTATCCTAAA
1 A-AA-ATATAAAATAATATCCTAAA
119327 TTTAAGTTTA
Statistics
Matches: 87, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
74 7 0.08
75 31 0.36
76 47 0.54
77 2 0.02
ACGTcount: A:0.58, C:0.09, G:0.03, T:0.30
Consensus pattern (75 bp):
AAAATATAAAATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATAAAA
AGATAAAGAT
Found at i:120953 original size:16 final size:16
Alignment explanation
Indices: 120929--120962 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
120919 CGAACCAAAT
120929 CTGTTTTTTTT-TGCA
1 CTGTTTTTTTTATGCA
120944 CTGTTTTTTTTATGCA
1 CTGTTTTTTTTATGCA
120960 CTG
1 CTG
120963 CATTGTTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.09, C:0.15, G:0.15, T:0.62
Consensus pattern (16 bp):
CTGTTTTTTTTATGCA
Found at i:121184 original size:11 final size:11
Alignment explanation
Indices: 121168--121213 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
121158 AGTTCGCTAA
121168 AAAATAAAACG
1 AAAATAAAACG
121179 AAAATAAAA--
1 AAAATAAAACG
*
121188 AAAATAAAAACA
1 AAAAT-AAAACG
*
121200 AAAATATAACG
1 AAAATAAAACG
121211 AAA
1 AAA
121214 TGGGTTGCCT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
9 5 0.17
10 4 0.13
11 16 0.53
12 5 0.17
ACGTcount: A:0.78, C:0.07, G:0.04, T:0.11
Consensus pattern (11 bp):
AAAATAAAACG
Found at i:121197 original size:21 final size:20
Alignment explanation
Indices: 121166--121205 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
121156 AAAGTTCGCT
*
121166 AAAAAATAAAACGAAAATAA
1 AAAAAATAAAACAAAAATAA
121186 AAAAAATAAAAACAAAAATA
1 AAAAAAT-AAAACAAAAATA
121206 TAACGAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.82, C:0.05, G:0.03, T:0.10
Consensus pattern (20 bp):
AAAAAATAAAACAAAAATAA
Found at i:124489 original size:15 final size:15
Alignment explanation
Indices: 124469--124502 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
124459 TTCCTCTTGT
124469 TCTTCCTGACGTGCG
1 TCTTCCTGACGTGCG
*
124484 TCTTCCTGATGTGCG
1 TCTTCCTGACGTGCG
124499 TCTT
1 TCTT
124503 TTTCTGCTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.06, C:0.29, G:0.24, T:0.41
Consensus pattern (15 bp):
TCTTCCTGACGTGCG
Found at i:126168 original size:5 final size:5
Alignment explanation
Indices: 126162--126212 Score: 84
Period size: 5 Copynumber: 10.2 Consensus size: 5
126152 ATATATTAAA
* *
126162 ATAAA ATAAT GTAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
126212 A
1 A
126213 ATATATTAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 43 1.00
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (5 bp):
ATAAT
Found at i:126297 original size:15 final size:16
Alignment explanation
Indices: 126279--126309 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
126269 AAAAAATAAG
126279 AATTAAATAAA-AAAT
1 AATTAAATAAACAAAT
126294 AATTAAATAAACAAAT
1 AATTAAATAAACAAAT
126310 TAAAGAGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (16 bp):
AATTAAATAAACAAAT
Found at i:126973 original size:67 final size:73
Alignment explanation
Indices: 126896--127083 Score: 219
Period size: 67 Copynumber: 2.6 Consensus size: 73
126886 TAAAACATCT
* * * *
126896 TAAATTCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATAC-CT-AA-A-AAAATAT-AATA
1 TAAATCCTAATTAAAATACTTAAAACCTATTTAAACTAAAATACAATAAAGATAAAATATAAAAA
*
126955 TAATATTC
66 TAATATCC
*
126963 TAAATCCTAATTAAAATTC-TAAAACCTATTTAAACTAAAATACAAATATAAAGATAAAATATAA
1 TAAATCCTAATTAAAATACTTAAAACCTATTTAAACTAAAATAC--A-ATAAAGATAAAATATAA
127027 AAATAATATCC
63 AAATAATATCC
* * *
127038 TAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAA
1 TAAATCCTAATTAAAATACTTAAAACCTATTTAAACTAAAATACAA
127084 ATATAAAATA
Statistics
Matches: 101, Mismatches: 10, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
66 5 0.05
67 34 0.34
71 1 0.01
72 2 0.02
73 2 0.02
74 8 0.08
75 26 0.26
76 23 0.23
ACGTcount: A:0.57, C:0.12, G:0.01, T:0.30
Consensus pattern (73 bp):
TAAATCCTAATTAAAATACTTAAAACCTATTTAAACTAAAATACAATAAAGATAAAATATAAAAA
TAATATCC
Found at i:126981 original size:19 final size:19
Alignment explanation
Indices: 126959--126996 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
126949 ATAATATAAT
*
126959 ATTCTAAATCCTAATTAAA
1 ATTCTAAAACCTAATTAAA
*
126978 ATTCTAAAACCTATTTAAA
1 ATTCTAAAACCTAATTAAA
126997 CTAAAATACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (19 bp):
ATTCTAAAACCTAATTAAA
Found at i:127022 original size:13 final size:13
Alignment explanation
Indices: 126999--127032 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
126989 TATTTAAACT
126999 AAAATACAAATATA
1 AAAATA-AAATATA
*
127013 AAGATAAAATATA
1 AAAATAAAATATA
127026 AAAATAA
1 AAAATAA
127033 TATCCTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (13 bp):
AAAATAAAATATA
Found at i:127041 original size:75 final size:74
Alignment explanation
Indices: 126896--127118 Score: 246
Period size: 76 Copynumber: 3.1 Consensus size: 74
126886 TAAAACATCT
* * * * *
126896 TAAATTCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATAC----CT-AAA-AAAATATAAT
1 TAAATCCTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAATATAAAATAAAATATAAA
*
126954 ATAATATTC
66 ATAATATCC
*
126963 TAAATCCTAATTAAAATTCT-AAAACCTATTTAAACTAAAATACAAATATAAAGATAAAATATAA
1 TAAATCCTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAATATAAA-ATAAAATAT-A
127027 AAATAATATCC
64 AAATAATATCC
* * * *
127038 TAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAATATAAAATATAATGTTTA
1 TAAATCCTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAATATAAAATA-AA-ATATA
*
127103 AAATATTATCC
64 AAATAATATCC
127114 TAAAT
1 TAAAT
127119 TTGAGTTTAA
Statistics
Matches: 131, Mismatches: 13, Indels: 15
0.82 0.08 0.09
Matches are distributed among these distances:
66 4 0.03
67 35 0.27
71 1 0.01
72 2 0.02
73 1 0.01
74 7 0.05
75 30 0.23
76 49 0.37
77 2 0.02
ACGTcount: A:0.56, C:0.11, G:0.01, T:0.32
Consensus pattern (74 bp):
TAAATCCTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAATATAAAATAAAATATAAA
ATAATATCC
Found at i:129213 original size:158 final size:155
Alignment explanation
Indices: 128886--129421 Score: 594
Period size: 158 Copynumber: 3.4 Consensus size: 155
128876 CTTGATTTCA
* * *
128886 TTATTTCTTCAATTCCA-CCATCATTTAAAGTCCATTTTTTTACCAAA-TTGAATCACATGCTTC
1 TTATTTCTTCAATT-CATCCTTTATTT-AAGTCCA-TTTTTTACCAAATTTGAA-CACATGCTCC
* * * * * * * * * * * *
128949 TAAGCTATCGTATAATATATGTATACTTTCAATTTCTCTTGTTGATAATAAATTTTCTATTTTTC
62 TAAACCAGCATAGAATACATGTACACTTTTAATTCCCCTTTTTGATAATAAATTTT-AATTTTTC
*
129014 AATTTAGT-CATCAACTTTTCATATCTTCC
126 AATTTAGTCCCTCAACTTTTCATATCTTCC
* * * *
129043 TTATTTTTTTCAATTCATCATTTATTTTAAGTCCAATTTTTACTAAATTTGAACAACATGCTCCT
1 TTA-TTTCTTCAATTCATCCTTTA-TTTAAGTCCATTTTTTACCAAATTTGAAC-ACATGCTCCT
* * * *
129108 AAACCATCATAGAATACATTTGCACTTTTGATTCCCCTTTTTGATAATAAAGTTTTAATTTTTCA
63 AAACCAGCATAGAATACATGTACACTTTTAATTCCCCTTTTTGATAATAAA-TTTTAATTTTTCA
129173 ATTTAGTCCCTCAACTTTTCATATCTTCC
127 ATTTAGTCCCTCAACTTTTCATATCTTCC
* * *
129202 TTATTTCTTCAATTCATCCTTTACTTTAAG-CCTGTTTTTTACCAAATTTAAACCATATGCTCCT
1 TTATTTCTTCAATTCATCCTTTA-TTTAAGTCC-ATTTTTTACCAAATTTGAA-CACATGCTCCT
* * * *
129266 AAACTAGCATAGAATACATGTATACTTTTAATTTCTCTTTTTGATAATAAATTTTATATTTTTCA
63 AAACCAGCATAGAATACATGTACACTTTTAATTCCCCTTTTTGATAATAAATTTTA-ATTTTTCA
* *
129331 ATTTAGTCCCACAACTTTTCATTTCTTCC
127 ATTTAGTCCCTCAACTTTTCATATCTTCC
* *
129360 TTATTTCTTCAATTCATCCTGTAATTAAGTCCATTTTTTTACCAAATTTGAATCACATGCTC
1 TTATTTCTTCAATTCATCCTTTATTTAAGTCCA-TTTTTTACCAAATTTGAA-CACATGCTC
129422 ATATATCATA
Statistics
Matches: 321, Mismatches: 46, Indels: 23
0.82 0.12 0.06
Matches are distributed among these distances:
157 28 0.09
158 262 0.82
159 31 0.10
ACGTcount: A:0.29, C:0.20, G:0.06, T:0.46
Consensus pattern (155 bp):
TTATTTCTTCAATTCATCCTTTATTTAAGTCCATTTTTTACCAAATTTGAACACATGCTCCTAAA
CCAGCATAGAATACATGTACACTTTTAATTCCCCTTTTTGATAATAAATTTTAATTTTTCAATTT
AGTCCCTCAACTTTTCATATCTTCC
Found at i:129828 original size:14 final size:14
Alignment explanation
Indices: 129806--129842 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
129796 TTAGTATTAA
129806 AACTCGAATAACTC
1 AACTCGAATAACTC
*
129820 AACTTGAATAACTC
1 AACTCGAATAACTC
*
129834 GACTCGAAT
1 AACTCGAAT
129843 TTCTTAAACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.41, C:0.24, G:0.11, T:0.24
Consensus pattern (14 bp):
AACTCGAATAACTC
Found at i:130495 original size:60 final size:60
Alignment explanation
Indices: 130402--130515 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 60
130392 AATTGGATTA
* *
130402 ATTTGGGGATGAAATTGAAAGATTTTAAAGTTTAGGGACCAATTTGGAATGAGATCCATG
1 ATTTGGGGATGAAATTGAAAGATTTTAAAGTTTAAGGACCAATTTAGAATGAGATCCATG
* *
130462 ATTTGGGGATGAAATT-TAA-ATTTTCAAAAGTTTAAGGACTAATTTAGAATGAGA
1 ATTTGGGGATGAAATTGAAAGATTTT--AAAGTTTAAGGACCAATTTAGAATGAGA
130516 GTCATAGTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
58 5 0.10
59 2 0.04
60 41 0.85
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.33
Consensus pattern (60 bp):
ATTTGGGGATGAAATTGAAAGATTTTAAAGTTTAAGGACCAATTTAGAATGAGATCCATG
Found at i:130555 original size:61 final size:60
Alignment explanation
Indices: 130428--130588 Score: 147
Period size: 60 Copynumber: 2.7 Consensus size: 60
130418 GAAAGATTTT
* * *
130428 AAAGTTTAGGGACCAATTTGGAATGAGA-TCCAT-GATTT-GGGGATGAAATTTAAATTTTCA
1 AAAGTTTAAGGACCAATTT-GAATGAGAGT-CATAG-TTTAAGGGATGAAATTTAAATCTTCA
*
130488 AAAGTTTAAGGACTAATTTAGAATGAGAGTCATAGTTTAAGGGATGAAA-TTAGAATACTT-A
1 AAAGTTTAAGGACCAATTT-GAATGAGAGTCATAGTTTAAGGGATGAAATTTA-AAT-CTTCA
* * *
130549 AAAGTTTAAGG--GAATTTGAAATGATAGTCATATTTTAAGG
1 AAAGTTTAAGGACCAATTTG-AATGAGAGTCATAGTTTAAGG
130589 ACATACGATG
Statistics
Matches: 87, Mismatches: 8, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
58 1 0.01
59 24 0.28
60 34 0.39
61 26 0.30
62 2 0.02
ACGTcount: A:0.39, C:0.06, G:0.22, T:0.33
Consensus pattern (60 bp):
AAAGTTTAAGGACCAATTTGAATGAGAGTCATAGTTTAAGGGATGAAATTTAAATCTTCA
Done.