Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000739.1 Hibiscus syriacus cultivar Beakdansim tig00001429_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: 225954
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 2 of 2
Found at i:151913 original size:14 final size:14
Alignment explanation
Indices: 151894--151930 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
151884 AATCAATTAA
151894 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
151908 ACAAATCATCTTTT
1 ACAAATCAACATTT
151922 ACAAATCAA
1 ACAAATCAA
151931 TTAAACAATA
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:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:151950 original size:3 final size:3
Alignment explanation
Indices: 151937--151965 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
151927 TCAATTAAAC
151937 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
151966 TATTTCCTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:153195 original size:65 final size:65
Alignment explanation
Indices: 153070--153222 Score: 211
Period size: 65 Copynumber: 2.4 Consensus size: 65
153060 TGGAACACTT
* **
153070 GATGCATGAAATGCATTCGATG-TTTGAAAAATAGCCTGGTGCATCGATGCATGGCTTGTGCATC
1 GATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGGTGCATCGATGCATGGAGTGTGCATC
* * **
153134 GATGCATCAAATGCAGTCGATGTTTTG-AAAATATTCAGAGTGCATCGATGCATGGAGTGTGCAT
1 GATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAG-GTGCATCGATGCATGGAGTGTGCAT
153198 C
65 C
*
153199 GGTGCATGAAATGCATTCGATGTT
1 GATGCATGAAATGCATTCGATGTT
153223 CAATTAATTC
Statistics
Matches: 77, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
64 28 0.36
65 49 0.64
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (65 bp):
GATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGGTGCATCGATGCATGGAGTGTGCATC
Found at i:153262 original size:65 final size:64
Alignment explanation
Indices: 153072--153271 Score: 203
Period size: 65 Copynumber: 3.1 Consensus size: 64
153062 GAACACTTGA
* * ** *
153072 TGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG-CTTGTGCATCG
1 TGCATGAAATGCAGTCGATGTTT-CAAAATATTCAGAGTGCATCGATGCATGGAC-TGTGCATCG
*
153135 A
64 G
* * *
153136 TGCATCAAATGCAGTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGAGTGTGCATCGG
1 TGCATGAAATGCAGTCGATG-TTTCAAAATATTCAGAGTGCATCGATGCATGGACTGTGCATCGG
* *
153201 TGCATGAAATGCATTCGATG-TTC-AATTAATTCATCGA-TGCATCGATGCATGGACTGATGCAT
1 TGCATGAAATGCAGTCGATGTTTCAAAAT-ATTCA--GAGTGCATCGATGCATGGACTG-TGCAT
153263 CGG
62 CGG
153266 TGCATG
1 TGCATG
153272 CCTTTGAATA
Statistics
Matches: 116, Mismatches: 13, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
62 3 0.03
63 7 0.06
64 44 0.38
65 62 0.53
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (64 bp):
TGCATGAAATGCAGTCGATGTTTCAAAATATTCAGAGTGCATCGATGCATGGACTGTGCATCGG
Found at i:153889 original size:8 final size:8
Alignment explanation
Indices: 153866--153903 Score: 58
Period size: 8 Copynumber: 4.8 Consensus size: 8
153856 AAATTAAGTT
*
153866 CAAACATT
1 CAAACATC
*
153874 CAAGCATC
1 CAAACATC
153882 CAAACATC
1 CAAACATC
153890 CAAACATC
1 CAAACATC
153898 CAAACA
1 CAAACA
153904 AACATAAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.50, C:0.34, G:0.03, T:0.13
Consensus pattern (8 bp):
CAAACATC
Found at i:161313 original size:65 final size:65
Alignment explanation
Indices: 161187--161339 Score: 211
Period size: 65 Copynumber: 2.4 Consensus size: 65
161177 TGGAACACTT
* **
161187 GATGCATGAAATGCATTCGATG-TTTGAAAAATAGCCTGGTGCATCGATGCATGGCTTGTGCATC
1 GATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGGTGCATCGATGCATGGAGTGTGCATC
* **
161251 GATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGCATCGATGCATGGAGTGTGCAT
1 GATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAG-GTGCATCGATGCATGGAGTGTGCAT
161315 C
65 C
* *
161316 GGTGCATGGAATGCATTCGATGTT
1 GATGCATGAAATGCATTCGATGTT
161340 CAATTAATTC
Statistics
Matches: 78, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
64 29 0.37
65 49 0.63
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.31
Consensus pattern (65 bp):
GATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGGTGCATCGATGCATGGAGTGTGCATC
Found at i:162690 original size:42 final size:42
Alignment explanation
Indices: 162590--162694 Score: 122
Period size: 42 Copynumber: 2.5 Consensus size: 42
162580 TGTTGGGTGA
* * *
162590 GACCTCTTCAACGATGACAGTGGCCTCTTGAACGGTAGGAGG
1 GACCTCTTGAACGATGACAGGGGCCTCTTGAACGATAGGAGG
* ** *
162632 GAACTCTTGAGGGATGATAGGGGCCTCTTGAACGATAGG-GG
1 GACCTCTTGAACGATGACAGGGGCCTCTTGAACGATAGGAGG
*
162673 AGGCCTCTTGAACGATGACAGG
1 -GACCTCTTGAACGATGACAGG
162695 TGAGTCGGGC
Statistics
Matches: 50, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
41 2 0.04
42 48 0.96
ACGTcount: A:0.25, C:0.20, G:0.34, T:0.21
Consensus pattern (42 bp):
GACCTCTTGAACGATGACAGGGGCCTCTTGAACGATAGGAGG
Found at i:163066 original size:34 final size:33
Alignment explanation
Indices: 163017--163113 Score: 113
Period size: 33 Copynumber: 2.9 Consensus size: 33
163007 TCTGAAACTT
* *
163017 AAAATCGCAACGCGAAAATGACTATCGCAACGAG
1 AAAATCGCAACGCG-AAATGACTATCGCAACAAC
* * ** *
163051 AGAATCGCAATGCGAAATGAAAATCACAACAAC
1 AAAATCGCAACGCGAAATGACTATCGCAACAAC
163084 AAAATCGCAACGCGTAAATGACTATCGCAA
1 AAAATCGCAACGCG-AAATGACTATCGCAA
163114 TGCGAAAATG
Statistics
Matches: 50, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
33 26 0.52
34 24 0.48
ACGTcount: A:0.46, C:0.23, G:0.18, T:0.13
Consensus pattern (33 bp):
AAAATCGCAACGCGAAATGACTATCGCAACAAC
Found at i:163112 original size:20 final size:20
Alignment explanation
Indices: 163087--163173 Score: 113
Period size: 20 Copynumber: 4.3 Consensus size: 20
163077 CAACAACAAA
*
163087 ATCGCAACGCGTAA-ATGACT
1 ATCGCAATGCG-AATATGACT
*
163107 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAATATGACT
* *
163127 ATCGCAATGTGAATTTGACT
1 ATCGCAATGCGAATATGACT
*
163147 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAATATGACT
163167 ATCGCAA
1 ATCGCAA
163174 CGAGAGAATC
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
19 2 0.03
20 59 0.97
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGAATATGACT
Found at i:163210 original size:19 final size:19
Alignment explanation
Indices: 163182--163319 Score: 84
Period size: 19 Copynumber: 7.7 Consensus size: 19
163172 AACGAGAGAA
*
163182 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
163201 TCGCATTGCGA--TTC-TT
1 TCGCATTGCGATTTTCATT
**
163217 TCG--TTGCGATAGTCAAATT
1 TCGCATTGCGATTTTC--ATT
**
163236 T-GCATTGCGATAGTCATTT
1 TCGCATTGCGATTTTCA-TT
*
163255 TCGCATTGCGA-TGTCATTT
1 TCGCATTGCGATTTTCA-TT
* *
163274 TCGTATTGCGATTTT--GT
1 TCGCATTGCGATTTTCATT
163291 T-G--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
163307 TCGCATTGCGATT
1 TCGCATTGCGATT
163320 CTCTCGTTGC
Statistics
Matches: 97, Mismatches: 7, Indels: 30
0.72 0.05 0.22
Matches are distributed among these distances:
14 16 0.16
16 10 0.10
17 6 0.06
18 2 0.02
19 41 0.42
20 22 0.23
ACGTcount: A:0.17, C:0.18, G:0.20, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:163225 original size:33 final size:33
Alignment explanation
Indices: 163188--163352 Score: 138
Period size: 33 Copynumber: 4.8 Consensus size: 33
163178 AGAATCGCAA
*
163188 TGCGATTTTCATTTCGCATTGCGATTCTTTCGT
1 TGCGATTGTCATTTCGCATTGCGATTCTTTCGT
*
163221 TGCGATAGTCAAATTT-GCATTGCGATAGTCATTTTCGCAT
1 TGCGATTGTC--ATTTCGCATTGCGAT--TC--TTTCG--T
* *
163261 TGCGA-TGTCATTTTCGTATTGCGATT-TTGTTGT
1 TGCGATTGTCA-TTTCGCATTGCGATTCTT-TCGT
* *
163294 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTGTCATTTCGCATTGCGATTCTTTCGT
* *
163327 TGCGATAGTAATTTTCGCATTGCGAT
1 TGCGATTGTCA-TTTCGCATTGCGAT
163353 AGTAAACTAT
Statistics
Matches: 106, Mismatches: 12, Indels: 27
0.73 0.08 0.19
Matches are distributed among these distances:
33 39 0.37
34 31 0.29
35 6 0.06
36 2 0.02
37 2 0.02
38 8 0.08
39 12 0.11
40 6 0.06
ACGTcount: A:0.17, C:0.18, G:0.21, T:0.44
Consensus pattern (33 bp):
TGCGATTGTCATTTCGCATTGCGATTCTTTCGT
Found at i:163917 original size:18 final size:18
Alignment explanation
Indices: 163877--163917 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
163867 CGGGTCGATC
* *
163877 AGGTGATGGCTCTGGATG
1 AGGTGATGGCTCTCGAAG
163895 AGGTGATGGCTCTCGAAG
1 AGGTGATGGCTCTCGAAG
*
163913 TGGTG
1 AGGTG
163918 GCTGCTCATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.17, C:0.12, G:0.44, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTCGAAG
Found at i:165252 original size:20 final size:20
Alignment explanation
Indices: 165229--165278 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
165219 CTGAAACTTT
165229 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
165249 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
**
165269 CTATCGCAAC
1 AAATCGCAAC
165279 GCAAGAATCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.50, C:0.24, G:0.14, T:0.12
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:165710 original size:22 final size:22
Alignment explanation
Indices: 165648--165713 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
165638 TGATCGTGAA
* *
165648 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
* *
165670 TGATATCGTCGGCGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
165692 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
165714 GAATGTCGCC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.20, C:0.17, G:0.39, T:0.24
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:165939 original size:20 final size:20
Alignment explanation
Indices: 165916--166043 Score: 184
Period size: 20 Copynumber: 6.3 Consensus size: 20
165906 TCAGATTTGT
*
165916 ATTGCGATTTACATATTCGC
1 ATTGCGATTTACGTATTCGC
165936 ATTGCGATTTACGTATTCGC
1 ATTGCGATTTACGTATTCGC
165956 ATTGCGATTTACGTATTCGC
1 ATTGCGATTTACGTATTCGC
* *
165976 ATTGTGATTTACGTAATCGC
1 ATTGCGATTTACGTATTCGC
* **
165996 ATTGCGATTTTCCAAATTCGC
1 ATTGCGA-TTTACGTATTCGC
*
166017 GTTGCGATTTACGTATTCGC
1 ATTGCGATTTACGTATTCGC
166037 ATTGCGA
1 ATTGCGA
166044 ATTAGGAAAA
Statistics
Matches: 94, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
20 79 0.84
21 15 0.16
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.39
Consensus pattern (20 bp):
ATTGCGATTTACGTATTCGC
Found at i:166064 original size:21 final size:21
Alignment explanation
Indices: 166040--166106 Score: 107
Period size: 21 Copynumber: 3.2 Consensus size: 21
166030 TATTCGCATT
* *
166040 GCGAATTAGGAAAATCGCAAC
1 GCGAATTTGGGAAATCGCAAC
166061 GCGAATTTGGGAAATCGCAAC
1 GCGAATTTGGGAAATCGCAAC
*
166082 GCGAATTTGGGAAATCGCAAT
1 GCGAATTTGGGAAATCGCAAC
166103 GCGA
1 GCGA
166107 TAGTCAGAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.36, C:0.18, G:0.28, T:0.18
Consensus pattern (21 bp):
GCGAATTTGGGAAATCGCAAC
Found at i:166178 original size:19 final size:19
Alignment explanation
Indices: 166154--166196 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
166144 CGATACCGGA
* *
166154 GATCGTGTTGCGAATTATC
1 GATCGTATTGCGAATTAGC
*
166173 GATCGTATTGCGATTTAGC
1 GATCGTATTGCGAATTAGC
166192 GATCG
1 GATCG
166197 CATTACGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.21, C:0.16, G:0.28, T:0.35
Consensus pattern (19 bp):
GATCGTATTGCGAATTAGC
Found at i:166205 original size:19 final size:19
Alignment explanation
Indices: 166172--166209 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
166162 TGCGAATTAT
* *
166172 CGATCGTATTGCGATTTAG
1 CGATCGCATTACGATTTAG
166191 CGATCGCATTACGATTTAG
1 CGATCGCATTACGATTTAG
166210 TTGGTCATTT
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:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (19 bp):
CGATCGCATTACGATTTAG
Found at i:166718 original size:2 final size:2
Alignment explanation
Indices: 166711--166741 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
166701 ATGATTTGAG
166711 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
166742 TCGATAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:167471 original size:2 final size:2
Alignment explanation
Indices: 167464--167488 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
167454 TATCACATTG
167464 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
167489 ATTATAAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:169124 original size:2 final size:2
Alignment explanation
Indices: 169117--169142 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
169107 TGAATTGTTC
169117 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
169143 GAAAGAATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:176375 original size:16 final size:16
Alignment explanation
Indices: 176356--176394 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
176346 ATAAATATAA
176356 TAAAATACTAAAAAAT
1 TAAAATACTAAAAAAT
*
176372 TAAATTACTAAAAAAT
1 TAAAATACTAAAAAAT
*
176388 AAAAATA
1 TAAAATA
176395 TATGTTATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (16 bp):
TAAAATACTAAAAAAT
Found at i:176383 original size:24 final size:23
Alignment explanation
Indices: 176340--176392 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
176330 TAAAATTATT
*
176340 TAAAAAATAAATATAATAAAATAC
1 TAAAAAATAAATATAATAAAA-AA
*
176364 TAAAAAATTAAAT-TACTAAAAAA
1 TAAAAAA-TAAATATAATAAAAAA
176387 TAAAAA
1 TAAAAA
176393 TATATGTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 7 0.27
24 14 0.54
25 5 0.19
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.25
Consensus pattern (23 bp):
TAAAAAATAAATATAATAAAAAA
Found at i:185690 original size:16 final size:17
Alignment explanation
Indices: 185671--185708 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
185661 AAGTTCTTTT
185671 AAAAACA-ATTTTAAGA
1 AAAAACATATTTTAAGA
*
185687 AAAAACATTTTTTAAGA
1 AAAAACATATTTTAAGA
*
185704 CAAAA
1 AAAAA
185709 GTTGGTATGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.61, C:0.08, G:0.05, T:0.26
Consensus pattern (17 bp):
AAAAACATATTTTAAGA
Found at i:186048 original size:22 final size:21
Alignment explanation
Indices: 186023--186064 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
186013 AACTTTAAGT
*
186023 ATTAAAATAGCAAAAATAGAAA
1 ATTAAAAGA-CAAAAATAGAAA
*
186045 ATTAAAAGACTAAAATAGAA
1 ATTAAAAGACAAAAATAGAA
186065 CAAACAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.67, C:0.05, G:0.10, T:0.19
Consensus pattern (21 bp):
ATTAAAAGACAAAAATAGAAA
Found at i:186059 original size:30 final size:29
Alignment explanation
Indices: 186025--186165 Score: 87
Period size: 30 Copynumber: 4.8 Consensus size: 29
186015 CTTTAAGTAT
186025 TAAAATAGCAAAAATAGAAAATTAAAAGAC
1 TAAAATAG-AAAAATAGAAAATTAAAAGAC
*
186055 TAAAATAGAACAAACA-AAAATTTAAAA-AGC
1 TAAAATAGAA-AAATAGAAAA-TTAAAAGA-C
* **
186085 TAGAATATTA-AAAAATAGAAATTTTGAAGAC
1 TA-AA-A-TAGAAAAATAGAAAATTAAAAGAC
* * *
186116 CAAATATCA-CAAAAT-GAAATTTAAAAGAC
1 TAAA-AT-AGAAAAATAGAAAATTAAAAGAC
*
186145 TAAAATAGAAAAA-ACAAAATT
1 TAAAATAGAAAAATAGAAAATT
186166 TTTTAAGTTT
Statistics
Matches: 87, Mismatches: 13, Indels: 24
0.70 0.10 0.19
Matches are distributed among these distances:
27 1 0.01
28 11 0.13
29 23 0.26
30 31 0.36
31 12 0.14
32 7 0.08
33 2 0.02
ACGTcount: A:0.63, C:0.08, G:0.09, T:0.21
Consensus pattern (29 bp):
TAAAATAGAAAAATAGAAAATTAAAAGAC
Found at i:187263 original size:21 final size:21
Alignment explanation
Indices: 187223--187263 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
187213 CATGCATTTA
* *
187223 TAGTGAATATTGATTGATGTG
1 TAGTGAATATTCATTAATGTG
*
187244 TAGTGAATTTTCATTAATGT
1 TAGTGAATATTCATTAATGT
187264 TCGAATAGTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.02, G:0.22, T:0.46
Consensus pattern (21 bp):
TAGTGAATATTCATTAATGTG
Found at i:188383 original size:211 final size:208
Alignment explanation
Indices: 188110--188560 Score: 473
Period size: 211 Copynumber: 2.2 Consensus size: 208
188100 TCTTTAGGAA
* * *
188110 GGGTGATAACTCGGTTCCTACGTGATGAGGACTACTGGTTATCTAGGTTGACATAACTCCTACAT
1 GGGTGATGACACGGTTCCTACGTGATGAGGACTACTGGCTATCTAGGTTGACATAACTCCTACAT
* * * *
188175 AATGAGGAA-ATCTAGTCGGGTGATGACAC-GACTCATACGTAATGAAGA-GTCATGGCCATCTA
66 AATGA-GAATATATAGCCAGGTGATGACACAG-CTCATACGTAATGAAGACGACAT-GCCATCT-
*
188237 AAAG-TAATAACACGACTCATACGTGATGAAGAGTTCTGATTATCAAT-GATTGACACAACTCCT
127 AAAGTTAATAACACGACTCATACGTGATGAAGAGGT-TGATTATC--TGGATTGACACAACTCCT
*
188300 ACATAATGAAGAGATCAGAT
189 ACATAATGAAGAAATCAGAT
* * * **
188320 CGGGTGATGACACGGTTCCTACGTGATGATGA-TAGTTGGCTATCTGGGTTGACATGGCTCCTAC
1 -GGGTGATGACACGGTTCCTACGTGATGAGGACTA-CTGGCTATCTAGGTTGACATAACTCCTAC
* * * * * *
188384 ATAATGAGAATATATGGCCAGTTGATGACACAGTTCATATGTGATGAGGACGACATGCCATCTAA
64 ATAATGAGAATATATAGCCAGGTGATGACACAGCTCATACGTAATGAAGACGACATGCCATCTAA
* ** * * * * *
188449 GGTTAATAACACGGTTCCTATGTGATGAGGAGGTTGGTTATCTGGGTTGACACAACTCCTACATA
129 AGTTAATAACACGACTCATACGTGATGAAGAGGTTGATTATCTGGATTGACACAACTCCTACATA
* * *
188514 ATGAGGAAATCTGGT
194 ATGAAGAAATCAGAT
* * *
188529 GGGTGATGACATGTTTCCTACGTGATAAGGAC
1 GGGTGATGACACGGTTCCTACGTGATGAGGAC
188561 GACAGACCAT
Statistics
Matches: 198, Mismatches: 35, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
208 28 0.14
209 31 0.16
210 15 0.08
211 119 0.60
212 5 0.03
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.27
Consensus pattern (208 bp):
GGGTGATGACACGGTTCCTACGTGATGAGGACTACTGGCTATCTAGGTTGACATAACTCCTACAT
AATGAGAATATATAGCCAGGTGATGACACAGCTCATACGTAATGAAGACGACATGCCATCTAAAG
TTAATAACACGACTCATACGTGATGAAGAGGTTGATTATCTGGATTGACACAACTCCTACATAAT
GAAGAAATCAGAT
Found at i:188587 original size:126 final size:128
Alignment explanation
Indices: 188326--188629 Score: 384
Period size: 126 Copynumber: 2.4 Consensus size: 128
188316 AGATCGGGTG
* * * ***
188326 ATGACACGGTTCCTACGTGATGATGATAGTTGGCTATCTGGGTTGACATGGCTCCTACATAATGA
1 ATGACACGGTTCCTACGTGATGAGGATGGTTGGTTATCTGGGTTGACACAACTCCTACATAATGA
* * * *
188391 GAATATATGGCCAGTTGATGACACAGTTCATATGTGATGAGGACGACATGCCATCTAAGGTTA
66 GAATATATGGCCAGGTGATGACACAGTTCATACGTGATAAGGACGACATGCCATCTAAGGATA
* *
188454 ATAACACGGTTCCTATGTGATGAGGA-GGTTGGTTATCTGGGTTGACACAACTCCTACATAATGA
1 ATGACACGGTTCCTACGTGATGAGGATGGTTGGTTATCTGGGTTGACACAACTCCTACATAATGA
* ** * *
188518 GGAA-ATCTGG-TGGGTGATGACA-TGTTTCCTACGTGATAAGGACGACA-GACCATCTAAGGAT
66 -GAATATATGGCCAGGTGATGACACAG-TTCATACGTGATAAGGACGACATG-CCATCTAAGGAT
188579 A
128 A
188580 ATGACACGGTTCCTACGTGATGAGGATGGTTGGTTATCTGGGGTTGACAC
1 ATGACACGGTTCCTACGTGATGAGGATGGTTGGTTATCT-GGGTTGACAC
188630 GGATCCTACG
Statistics
Matches: 152, Mismatches: 19, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
125 2 0.01
126 64 0.42
127 50 0.33
128 36 0.24
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (128 bp):
ATGACACGGTTCCTACGTGATGAGGATGGTTGGTTATCTGGGTTGACACAACTCCTACATAATGA
GAATATATGGCCAGGTGATGACACAGTTCATACGTGATAAGGACGACATGCCATCTAAGGATA
Found at i:188663 original size:21 final size:21
Alignment explanation
Indices: 188639--188687 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
188629 CGGATCCTAC
188639 GTGATGAGGAGATCAGGTCGA
1 GTGATGAGGAGATCAGGTCGA
*
188660 GTGATGAGGAGATCAGGTCGG
1 GTGATGAGGAGATCAGGTCGA
188681 GTGATGA
1 GTGATGA
188688 CACGGTTCCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.27, C:0.08, G:0.45, T:0.20
Consensus pattern (21 bp):
GTGATGAGGAGATCAGGTCGA
Found at i:189155 original size:32 final size:32
Alignment explanation
Indices: 189111--189176 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 32
189101 TATCAGGATA
* *
189111 TTGAATCCCCAAAGATGCCTCAATATTCGATG
1 TTGAATCCCCAAAGATGCCCCAACATTCGATG
* *
189143 TTGAATCTCCAAAGATGCCCCAACATTTGATG
1 TTGAATCCCCAAAGATGCCCCAACATTCGATG
189175 TT
1 TT
189177 AAATATTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.30
Consensus pattern (32 bp):
TTGAATCCCCAAAGATGCCCCAACATTCGATG
Found at i:190268 original size:14 final size:15
Alignment explanation
Indices: 190223--190268 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 15
190213 CTTCTTGTCC
190223 CTTTT-TCTTTG-TT
1 CTTTTCTCTTTGCTT
190236 CATTTTCTCTTTGCTT
1 C-TTTTCTCTTTGCTT
*
190252 CTTTTCT-TTTTCTT
1 CTTTTCTCTTTGCTT
190266 CTT
1 CTT
190269 CTTCAAGTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 1 0.03
14 13 0.45
15 12 0.41
16 3 0.10
ACGTcount: A:0.02, C:0.22, G:0.04, T:0.72
Consensus pattern (15 bp):
CTTTTCTCTTTGCTT
Found at i:191321 original size:32 final size:34
Alignment explanation
Indices: 191285--191354 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
191275 ACCTTACAAC
* * *
191285 TCCCTAG-TTTTTC-CGGGCTAAACTAGAACCTT
1 TCCCTAGCTTTTACACGGGATAAACTAGAACATT
*
191317 TCCCTAGCTTTTACACGGGATAAGCTAGAACATT
1 TCCCTAGCTTTTACACGGGATAAACTAGAACATT
191351 TCCC
1 TCCC
191355 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 5 0.16
34 20 0.62
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.31
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGGGATAAACTAGAACATT
Found at i:191594 original size:20 final size:22
Alignment explanation
Indices: 191569--191608 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
191559 TGTTGTATAT
191569 AGCCA-TTGGGGATG-TTTTGG
1 AGCCATTTGGGGATGATTTTGG
191589 AGCCATTTGGGGATGATTTT
1 AGCCATTTGGGGATGATTTT
191609 TCTACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.17, C:0.10, G:0.35, T:0.38
Consensus pattern (22 bp):
AGCCATTTGGGGATGATTTTGG
Found at i:191750 original size:20 final size:20
Alignment explanation
Indices: 191721--191794 Score: 96
Period size: 20 Copynumber: 3.6 Consensus size: 20
191711 GCAGCCTTCG
*
191721 TGCATGGATGCACAGTAGGA
1 TGCATCGATGCACAGTAGGA
*
191741 TGCATCGATGCACAGCCT-TGA
1 TGCATCGATGCACAG--TAGGA
*
191762 TGCATCGATGCACAGAAGGA
1 TGCATCGATGCACAGTAGGA
191782 TGCATCGATGCAC
1 TGCATCGATGCAC
191795 TAATTGCATT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
20 29 0.62
21 17 0.36
22 1 0.02
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.20
Consensus pattern (20 bp):
TGCATCGATGCACAGTAGGA
Found at i:191757 original size:41 final size:41
Alignment explanation
Indices: 191712--191794 Score: 132
Period size: 41 Copynumber: 2.0 Consensus size: 41
191702 CTAGCCGTTG
* *
191712 CAGCCTTCG-TGCATGGATGCACAGTAGGATGCATCGATGCA
1 CAGCCTT-GATGCATCGATGCACAGAAGGATGCATCGATGCA
191753 CAGCCTTGATGCATCGATGCACAGAAGGATGCATCGATGCA
1 CAGCCTTGATGCATCGATGCACAGAAGGATGCATCGATGCA
191794 C
1 C
191795 TAATTGCATT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
40 1 0.03
41 38 0.97
ACGTcount: A:0.27, C:0.25, G:0.28, T:0.20
Consensus pattern (41 bp):
CAGCCTTGATGCATCGATGCACAGAAGGATGCATCGATGCA
Found at i:191858 original size:21 final size:21
Alignment explanation
Indices: 191816--191858 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
191806 GGTGTTTGAG
* * *
191816 TGCATGGATGCATGTATGCAC
1 TGCAGGGATGCATGGATACAC
191837 TGCAGGGATGCATGGATACAC
1 TGCAGGGATGCATGGATACAC
191858 T
1 T
191859 TTGACACCCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.26
Consensus pattern (21 bp):
TGCAGGGATGCATGGATACAC
Found at i:191959 original size:29 final size:29
Alignment explanation
Indices: 191938--191995 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
191928 AAACTTTGAA
191938 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
191967 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
191996 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:191985 original size:30 final size:30
Alignment explanation
Indices: 191938--191997 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
191928 AAACTTTGAA
191938 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
191967 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
191998 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:198192 original size:23 final size:23
Alignment explanation
Indices: 198128--198184 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
198118 TTTATATGGA
198128 ACTTCGGTGCAATTCTACGCGGC
1 ACTTCGGTGCAATTCTACGCGGC
* *
198151 ACTTCGATGCAATTCTACGTGGC
1 ACTTCGGTGCAATTCTACGCGGC
*
198174 ACTTAGGTGCA
1 ACTTCGGTGCA
198185 TTTATACGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.21, C:0.26, G:0.25, T:0.28
Consensus pattern (23 bp):
ACTTCGGTGCAATTCTACGCGGC
Found at i:201809 original size:22 final size:22
Alignment explanation
Indices: 201782--201838 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
201772 TTTTCCAAAT
201782 TCGTTGCGATAGTCTACAGTTG
1 TCGTTGCGATAGTCTACAGTTG
*
201804 TCGTTGCGAAAGTCTACAGTTG
1 TCGTTGCGATAGTCTACAGTTG
*
201826 TCGTTGCGGTAGT
1 TCGTTGCGATAGT
201839 TAAAAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.18, C:0.18, G:0.30, T:0.35
Consensus pattern (22 bp):
TCGTTGCGATAGTCTACAGTTG
Found at i:201927 original size:10 final size:10
Alignment explanation
Indices: 201912--201955 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
201902 TACCACGACC
201912 ACGACCCGAG
1 ACGACCCGAG
*
201922 ACGACCCGAC
1 ACGACCCGAG
*
201932 CCGACCCGAG
1 ACGACCCGAG
**
201942 ACGAGACGAG
1 ACGACCCGAG
201952 ACGA
1 ACGA
201956 GACGAGACGG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.32, C:0.39, G:0.30, T:0.00
Consensus pattern (10 bp):
ACGACCCGAG
Found at i:201933 original size:15 final size:16
Alignment explanation
Indices: 201906--201935 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
201896 ACGTATTACC
201906 ACGACCACGACCCGAG
1 ACGACCACGACCCGAG
201922 ACGACC-CGACCCGA
1 ACGACCACGACCCGA
201936 CCCGAGACGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.30, C:0.47, G:0.23, T:0.00
Consensus pattern (16 bp):
ACGACCACGACCCGAG
Found at i:201938 original size:20 final size:21
Alignment explanation
Indices: 201907--201945 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
201897 CGTATTACCA
201907 CGACCACGACCCGAGACGACC
1 CGACCACGACCCGAGACGACC
201928 CGACC-CGACCCGAGACGA
1 CGACCACGACCCGAGACGA
201946 GACGAGACGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.28, C:0.46, G:0.26, T:0.00
Consensus pattern (21 bp):
CGACCACGACCCGAGACGACC
Found at i:201946 original size:5 final size:5
Alignment explanation
Indices: 201938--201968 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
201928 CGACCCGACC
201938 CGAGA CGAGA CGAGA CGAGA CGAGA CG-GA CG
1 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CG
201969 GCGGCGGCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.35, C:0.23, G:0.42, T:0.00
Consensus pattern (5 bp):
CGAGA
Found at i:202474 original size:12 final size:11
Alignment explanation
Indices: 202442--202477 Score: 56
Period size: 10 Copynumber: 3.3 Consensus size: 11
202432 GTCCGTCTCG
202442 GGTCGGGTCG-
1 GGTCGGGTCGT
202452 GGTCGGGTCGT
1 GGTCGGGTCGT
202463 GGTCGTGGTCGT
1 GGTCG-GGTCGT
202475 GGT
1 GGT
202478 TATTTTCGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.42
11 5 0.21
12 9 0.38
ACGTcount: A:0.00, C:0.17, G:0.56, T:0.28
Consensus pattern (11 bp):
GGTCGGGTCGT
Found at i:202477 original size:6 final size:5
Alignment explanation
Indices: 202439--202473 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
202429 GCCGTCCGTC
202439 TCGGG TCGGG TCGGG TCGGG TCGTGG TCGTGG TCG
1 TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TCG
202474 TGGTTATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.62
6 11 0.38
ACGTcount: A:0.00, C:0.20, G:0.54, T:0.26
Consensus pattern (5 bp):
TCGGG
Found at i:203038 original size:108 final size:109
Alignment explanation
Indices: 202848--203065 Score: 429
Period size: 108 Copynumber: 2.0 Consensus size: 109
202838 GTTTTGACTT
202848 ATAAATCTAGTATCATAAAAAATCTAATAGAAAAAAAAATTAGTGATCAAAGTAAAAGAAAACAA
1 ATAAATCTAGTATCATAAAAAATCTAATAGAAAAAAAAATTAGTGATCAAAGTAAAAGAAAACAA
202913 AACAGAGGTGCCTTTTGCACAACATACACTTTAAAGAGAGAGAG
66 AACAGAGGTGCCTTTTGCACAACATACACTTTAAAGAGAGAGAG
202957 ATAAATCTAGTATCATAAAAAATCTAATA-AAAAAAAAATTAGTGATCAAAGTAAAAGAAAACAA
1 ATAAATCTAGTATCATAAAAAATCTAATAGAAAAAAAAATTAGTGATCAAAGTAAAAGAAAACAA
203021 AACAGAGGTGCCTTTTGCACAACATACACTTTAAAGAGAGAGAG
66 AACAGAGGTGCCTTTTGCACAACATACACTTTAAAGAGAGAGAG
203065 A
1 A
203066 GAGAGATTGG
Statistics
Matches: 109, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
108 80 0.73
109 29 0.27
ACGTcount: A:0.53, C:0.12, G:0.14, T:0.21
Consensus pattern (109 bp):
ATAAATCTAGTATCATAAAAAATCTAATAGAAAAAAAAATTAGTGATCAAAGTAAAAGAAAACAA
AACAGAGGTGCCTTTTGCACAACATACACTTTAAAGAGAGAGAG
Found at i:209035 original size:15 final size:15
Alignment explanation
Indices: 209015--209044 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
209005 GAAGAGAACA
209015 GCTAAAGTACAATGT
1 GCTAAAGTACAATGT
209030 GCTAAAGTACAATGT
1 GCTAAAGTACAATGT
209045 TAGTGGATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (15 bp):
GCTAAAGTACAATGT
Found at i:209269 original size:23 final size:23
Alignment explanation
Indices: 209243--209287 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
209233 ATCAAGTACA
*
209243 ATAACATATTAGGGAACGCTTAT
1 ATAACATAATAGGGAACGCTTAT
** *
209266 ATAATGTAATAGGTAACGCTTA
1 ATAACATAATAGGGAACGCTTA
209288 AATTAACCTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.31
Consensus pattern (23 bp):
ATAACATAATAGGGAACGCTTAT
Found at i:209717 original size:197 final size:195
Alignment explanation
Indices: 209296--209805 Score: 605
Period size: 198 Copynumber: 2.6 Consensus size: 195
209286 TAAATTAACC
*
209296 TATTTTCTAATTAAACTAGTATATTTATACCGGTAACATTGTAAATTTA-TCTATTACATTATAA
1 TATTTTCTAATT-AACTAGTATATTTAT--CGGTAACATTGTAAATTTACT-TATTATA-TATAA
* *
209360 TTATCGGTTTCGACGTTTTTT-TGATCGATACTTTTAATAAATGTATCGACACTTAATGTGTGCA
61 TTATCGGTTTCGA--TTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTAAGGTGTGCA
* * * * * *
209424 CTTCGTTTGGCATTCATTCTGGACAAAATGTATCGACATAAATTTAAAAAGTGTCGATACATTAT
124 CATCGTTTGGCATTCATTATGGACAAAATATATCGACACAAATTCAAAAAGTATCGATACATTAT
209489 GTTGACA
189 GTTGACA
* * * *
209496 TATTCTCTCATAAAACTAGTATATTTATCGGTTACATTGTAAATTTACTTATTATATATAATTAT
1 TATTTTCTAAT-TAACTAGTATATTTATCGGTAACATTGTAAATTTACTTATTATATATAATTAT
* *
209561 CGGTTTCGATATTTTTGGGATAGATACTTTTAATAAATGTATCGACACTTTAGGTGTGCACATCG
65 CGGTTTCGAT-TTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTAAGGTGTGCACATCG
* * *
209626 TTTGGGCATTCATTATGGACAATAA-ATATCGACACAAATTCCACAAGTATTGATACATTATGTT
129 TTT-GGCATTCATTATGGACAA-AATATATCGACACAAATTCAAAAAGTATCGATACATTATGTT
209690 GACA
192 GACA
* * * * * * *
209694 TGTTTTTTAATTAACTGGTATATTTATATCGGTGACATTGTTAATTTACATA-TATATTTAATTA
1 TATTTTCTAATTAACTAGTATA-TT-TATCGGTAACATTGTAAATTTACTTATTATATATAATTA
* * * * *
209758 TTGGTTTCGATGTTTTGGGGTCGATACTTTTAAAAAATGTATTGACAC
64 TCGGTTTCGATTTTTTGGGATCGATACTTTTAATAAATGTATCGACAC
209806 ATATGTTTAC
Statistics
Matches: 268, Mismatches: 34, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
195 1 0.00
196 5 0.02
197 105 0.39
198 107 0.40
199 26 0.10
200 24 0.09
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (195 bp):
TATTTTCTAATTAACTAGTATATTTATCGGTAACATTGTAAATTTACTTATTATATATAATTATC
GGTTTCGATTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTAAGGTGTGCACATCGTT
TGGCATTCATTATGGACAAAATATATCGACACAAATTCAAAAAGTATCGATACATTATGTTGACA
Found at i:212743 original size:15 final size:15
Alignment explanation
Indices: 212723--212756 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
212713 CATCCACCTC
212723 CTTCTCCATTTTCTT
1 CTTCTCCATTTTCTT
212738 CTTCTCCATTTTCTT
1 CTTCTCCATTTTCTT
212753 CTTC
1 CTTC
212757 ATATTTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.06, C:0.35, G:0.00, T:0.59
Consensus pattern (15 bp):
CTTCTCCATTTTCTT
Found at i:212995 original size:66 final size:65
Alignment explanation
Indices: 212856--212983 Score: 143
Period size: 66 Copynumber: 2.0 Consensus size: 65
212846 CTCTCTTCAC
* * *
212856 CCCCGTAAGTTCACCCCTCAAATCCACAACTTTCTTCACCACTCCATCAATTTTTCCACCCATCA
1 CCCCTTAACTTCACCCCTCAAATCCACAACTTTCTTCACCACTCCATCAATTTTTCCACCAATCA
* * * * *
212921 CCATCTTAACTTCACCCTTCAACTCCA-AA-TCTTCTTTCACCACTTCATCTATTTTTCCACCAA
1 CC-CCTTAACTTCACCCCTCAAATCCACAACT-TTC-TTCACCACTCCATCAATTTTTCCACCAA
212984 CTTTCCCCTT
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
64 1 0.02
65 7 0.13
66 44 0.85
ACGTcount: A:0.26, C:0.41, G:0.02, T:0.32
Consensus pattern (65 bp):
CCCCTTAACTTCACCCCTCAAATCCACAACTTTCTTCACCACTCCATCAATTTTTCCACCAATCA
Found at i:213871 original size:20 final size:21
Alignment explanation
Indices: 213846--213885 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
213836 TGTTTGGCTC
213846 TGAATG-GAACCATTCAGCGT
1 TGAATGTGAACCATTCAGCGT
*
213866 TGAATGTTGAACCGTTCAGC
1 TGAATG-TGAACCATTCAGC
213886 ATTCAGACTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
22 11 0.65
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.28
Consensus pattern (21 bp):
TGAATGTGAACCATTCAGCGT
Found at i:216093 original size:180 final size:182
Alignment explanation
Indices: 215710--216482 Score: 975
Period size: 180 Copynumber: 4.3 Consensus size: 182
215700 GTAGCGCTTA
215710 ACCGG-TTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGA
1 ACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGA
* * * **
215774 CACTTTATAGGTGGTATTAA-TGCTTCTCTTTTTAATTCCAAAGGTGTCGATACTTATATTAAAG
66 CACTTTATAGGCGCTA-TAACTGCTTCTCTTTTAAATTCCAAAACTGTCGATACTTATATTAAAG
** * * *
215838 TATCGACACTTTCAACATAT-TCGGTAGCGTTTTACCCGCTTTGTCATTTCGAG
130 TATCGACACTTTCAACATATCT-GGTAGCACTTTACCGGTTTTGTCATTTCAAG
* *
215891 ATCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAATATCGA
1 ACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGA
* * *
215956 CACTTTATATGCGCTATAATTGC-T-TCTTTTAAATTCCAAAACTGTCCATACTTATATTAAAGT
66 CACTTTATAGGCGCTATAACTGCTTCTCTTTTAAATTCCAAAACTGTCGATACTTATATTAAAGT
*
216019 ATCGACA-TGTTCAACATATCTGGTAGCTCTTTACCGGTTTTGTCATTTCAAG
131 ATCGACACT-TTCAACATATCTGGTAGCACTTTACCGGTTTTGTCATTTCAAG
* * *
216071 ACCGGTTTTGTCATATTTTTACCTATTATATTATTATGGATCGATACATTTTTATAAACTATCGA
1 ACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGA
** * * *
216136 CACTTTATAAACGCTATTACTG-AT-TCTTTTAAATTCC-AAACGTGTCGATACTTATATTAAAA
66 CACTTTATAGGCGCTATAACTGCTTCTCTTTTAAATTCCAAAAC-TGTCGATACTTATATTAAAG
* * * * *
216198 TATCGACACTTTC-A-ATATCCGATAGCACTTTACCAGTTTTGTCATTTCGAT
130 TATCGACACTTTCAACATATCTGGTAGCACTTTACCGGTTTTGTCATTTCAAG
* *
216249 ACCGATTTTGTCATATTTTTGCCTGTTATATTGTTATGGATCGATACATTTTT-TAAAGTATCGA
1 ACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGA
* * * **
216313 CACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTTGATACTTAT-TTCAATC
66 CACTTTATAGGCGCTATAACTGCTTCTCTTTTAAATTCCAAAACTGTCGATACTTATATT-AAAG
* * * *
216377 TAATCGATACTTTCAACATATCTGGTACCACTTTACCGGTTCTT-TCATAATGAA-
130 T-ATCGACACTTTCAACATATCTGGTAGCACTTTACCGGTT-TTGTCAT-TTCAAG
* * *
216431 ACCGGTTTTATCATA-TTTAACCTGTTATATTGCTATGGATCGATACATTTTT
1 ACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
216483 TATTTGTATC
Statistics
Matches: 521, Mismatches: 55, Indels: 32
0.86 0.09 0.05
Matches are distributed among these distances:
177 30 0.06
178 83 0.16
179 34 0.07
180 214 0.41
181 45 0.09
182 111 0.21
183 4 0.01
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.42
Consensus pattern (182 bp):
ACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGA
CACTTTATAGGCGCTATAACTGCTTCTCTTTTAAATTCCAAAACTGTCGATACTTATATTAAAGT
ATCGACACTTTCAACATATCTGGTAGCACTTTACCGGTTTTGTCATTTCAAG
Found at i:216783 original size:3 final size:3
Alignment explanation
Indices: 216775--216830 Score: 82
Period size: 3 Copynumber: 19.3 Consensus size: 3
216765 ACCCCATCTG
216775 TTA TTA TTA TTA TATA TT- TTA TTA TTA TTA -TA TTA TTA TTA TTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
216819 TTA TTA -TA TTA T
1 TTA TTA TTA TTA T
216831 ATTGTTGTCT
Statistics
Matches: 49, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
2 6 0.12
3 40 0.82
4 3 0.06
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:221557 original size:20 final size:20
Alignment explanation
Indices: 221521--221670 Score: 85
Period size: 19 Copynumber: 7.6 Consensus size: 20
221511 AAACATTTGT
*
221521 GTTGCGAAATT-AAATTCGC
1 GTTGCGAATTTGAAATTCGC
*
221540 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGAAATTCGC
* **
221559 GTTGTGAATTTGACTTTCGC
1 GTTGCGAATTTGAAATTCGC
* *
221579 GTTGCGAATTTGGAAAATCGT
1 GTTGCGAATTT-GAAATTCGC
*** * * *
221600 AACGCGAAATTGGAAACT-GA
1 GTTGCG-AATTTGAAATTCGC
* * *
221620 GTTGCGAAATTGGAATTCGT
1 GTTGCGAATTTGAAATTCGC
*
221640 GTTGCGAATTTGAGATAT--C
1 GTTGCGAATTTGAAAT-TCGC
221659 GTTGCGAATTTG
1 GTTGCGAATTTG
221671 TTGGTCATTT
Statistics
Matches: 96, Mismatches: 29, Indels: 12
0.70 0.21 0.09
Matches are distributed among these distances:
19 44 0.46
20 34 0.35
21 14 0.15
22 4 0.04
ACGTcount: A:0.28, C:0.12, G:0.26, T:0.34
Consensus pattern (20 bp):
GTTGCGAATTTGAAATTCGC
Found at i:224681 original size:26 final size:23
Alignment explanation
Indices: 224645--224693 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 23
224635 TGTATACATC
224645 ACCAATCTTCATTGTGCTTGTTTTT
1 ACCAATCTTCATTGT--TTGTTTTT
224670 ACCAACTCTTCATTGTTTGTTTTT
1 ACCAA-TCTTCATTGTTTGTTTTT
224694 GTCACGTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 8 0.35
25 5 0.22
26 10 0.43
ACGTcount: A:0.16, C:0.20, G:0.10, T:0.53
Consensus pattern (23 bp):
ACCAATCTTCATTGTTTGTTTTT
Found at i:225656 original size:19 final size:18
Alignment explanation
Indices: 225622--225663 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
225612 TTAGCATTGT
225622 GAAAAGAAAATAATGAAA
1 GAAAAGAAAATAATGAAA
225640 GAAAAGTAAAA-AGATGAAA
1 GAAAAG-AAAATA-ATGAAA
225659 GAAAA
1 GAAAA
225664 AATAAAACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.71, C:0.00, G:0.19, T:0.10
Consensus pattern (18 bp):
GAAAAGAAAATAATGAAA
Done.