Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008082.1 Hibiscus syriacus cultivar Beakdansim tig00110584_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: 6025995
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 28
Found at i:1289138 original size:40 final size:40
Alignment explanation
Indices: 1288974--1289142 Score: 116
Period size: 40 Copynumber: 4.2 Consensus size: 40
1288964 GACCAATAAA
* * *
1288974 TTCGCAACGCGAAAGTCAAATTCGTAACGCGAACTCCAAT
1 TTCGCAACGCGATAGTCAAATTCGCAACGCGAACTCTAAT
* * * * * *
1289014 TTCGCAACCCTG-T-TTCCAATTTCGTAACGTGAATCTGTAA-
1 TTCGCAACGC-GATAGT-CAAATTCGCAACGCGAA-CTCTAAT
* * * * *
1289054 ATCGCAACGCGAATTTGT-AAA-TCGCAACACAGAAGTC-AAA
1 TTCGCAACGCG-A-TAGTCAAATTCGCAACGC-GAACTCTAAT
1289094 TTCGCAACGCGATAGTCAAATTCGCAACGCGAACTCTAAT
1 TTCGCAACGCGATAGTCAAATTCGCAACGCGAACTCTAAT
1289134 TTCGCAACG
1 TTCGCAACG
1289143 TGAATAATAA
Statistics
Matches: 96, Mismatches: 21, Indels: 24
0.68 0.15 0.17
Matches are distributed among these distances:
38 3 0.03
39 13 0.14
40 68 0.71
41 10 0.10
42 1 0.01
43 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (40 bp):
TTCGCAACGCGATAGTCAAATTCGCAACGCGAACTCTAAT
Found at i:1289139 original size:60 final size:60
Alignment explanation
Indices: 1288971--1289141 Score: 152
Period size: 60 Copynumber: 2.9 Consensus size: 60
1288961 AATGACCAAT
* * * * * **
1288971 AAATTCGCAACGCGAAAGTCAAATTCGTAACGCGAACTCCAATTTCGCAACCCTGTTTCC
1 AAATTCGCAACGCGATAGTCAAATTCGCAACGCGAACTCTAATTTCGCAACACAGAGTCC
* * * * * * *
1289031 AATTTCGTAACGTGAATCTGT-AAA-TCGCAACGCGAATTTGTAA-ATCGCAACACAGAAGT-C
1 AAATTCGCAACGCG-AT-AGTCAAATTCGCAACGCGAA-CTCTAATTTCGCAACACAG-AGTCC
1289091 AAATTCGCAACGCGATAGTCAAATTCGCAACGCGAACTCTAATTTCGCAAC
1 AAATTCGCAACGCGATAGTCAAATTCGCAACGCGAACTCTAATTTCGCAAC
1289142 GTGAATAATA
Statistics
Matches: 83, Mismatches: 21, Indels: 14
0.70 0.18 0.12
Matches are distributed among these distances:
58 2 0.02
59 9 0.11
60 62 0.75
61 8 0.10
62 2 0.02
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (60 bp):
AAATTCGCAACGCGATAGTCAAATTCGCAACGCGAACTCTAATTTCGCAACACAGAGTCC
Found at i:1289159 original size:20 final size:20
Alignment explanation
Indices: 1289135--1289240 Score: 176
Period size: 20 Copynumber: 5.3 Consensus size: 20
1289125 AACTCTAATT
* *
1289135 TCGCAACGTGAATAATAAAA
1 TCGCAATGTGAATAGTAAAA
*
1289155 CCGCAATGTGAATAGTAAAA
1 TCGCAATGTGAATAGTAAAA
1289175 TCGCAATGTGAATAGTAAAA
1 TCGCAATGTGAATAGTAAAA
1289195 TCGCAATGTGAATAGTAAAA
1 TCGCAATGTGAATAGTAAAA
*
1289215 TCGTAATGTGAATAGTAAAA
1 TCGCAATGTGAATAGTAAAA
1289235 TCGCAA
1 TCGCAA
1289241 CGAATCTATA
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 80 1.00
ACGTcount: A:0.45, C:0.12, G:0.19, T:0.24
Consensus pattern (20 bp):
TCGCAATGTGAATAGTAAAA
Found at i:1289179 original size:60 final size:60
Alignment explanation
Indices: 1289105--1289242 Score: 161
Period size: 60 Copynumber: 2.3 Consensus size: 60
1289095 TCGCAACGCG
* **
1289105 ATAGTCAAATTCGCAACGCGAACT-CTAATTTCGCAACGTGAATAATAAAACCGCAATGTGA
1 ATAGT-AAAATCGCAACGCGAA-TACTAAAATCGCAACGTGAATAATAAAACCGCAATGTGA
* * * * * * *
1289166 ATAGTAAAATCGCAATGTGAATAGTAAAATCGCAATGTGAATAGTAAAATCGTAATGTGA
1 ATAGTAAAATCGCAACGCGAATACTAAAATCGCAACGTGAATAATAAAACCGCAATGTGA
1289226 ATAGTAAAATCGCAACG
1 ATAGTAAAATCGCAACG
1289243 AATCTATATG
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
59 1 0.02
60 59 0.91
61 5 0.08
ACGTcount: A:0.43, C:0.15, G:0.18, T:0.24
Consensus pattern (60 bp):
ATAGTAAAATCGCAACGCGAATACTAAAATCGCAACGTGAATAATAAAACCGCAATGTGA
Found at i:1289196 original size:120 final size:120
Alignment explanation
Indices: 1288971--1289200 Score: 259
Period size: 120 Copynumber: 1.9 Consensus size: 120
1288961 AATGACCAAT
* * ** ***
1288971 AAATTCGCAACGCGAAAGTCAAATTCGTAACGCGAACTCCAATTTCGCAACCCTGTTTCCAATTT
1 AAATTCGCAACGCGAAAGTCAAATTCGCAACGCGAACTCCAATTTCGCAACCCTGATAACAAAAC
* * *
1289036 CGTAACGTGAATCTGTAAATCGCAACGCGAATTTGTAAATCGCAACACAGAAGTC
66 CGCAACGTGAATCAGTAAATCGCAACGCGAATTAGTAAATCGCAACACAGAAGTC
* * * *
1289091 AAATTCGCAACGCGATAGTCAAATTCGCAACGCGAACTCTAATTTCGCAA-CGTGAATAATAAAA
1 AAATTCGCAACGCGAAAGTCAAATTCGCAACGCGAACTCCAATTTCGCAACCCTG-ATAACAAAA
* * *
1289155 CCGCAATGTGAAT-AGTAAAATCGCAATGTGAA-TAGTAAAATCGCAA
65 CCGCAACGTGAATCAGT-AAATCGCAACGCGAATTAGT-AAATCGCAA
1289201 TGTGAATAGT
Statistics
Matches: 90, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
119 8 0.09
120 82 0.91
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (120 bp):
AAATTCGCAACGCGAAAGTCAAATTCGCAACGCGAACTCCAATTTCGCAACCCTGATAACAAAAC
CGCAACGTGAATCAGTAAATCGCAACGCGAATTAGTAAATCGCAACACAGAAGTC
Found at i:1289631 original size:20 final size:21
Alignment explanation
Indices: 1289596--1289643 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
1289586 CGCGATTTTA
1289596 CGATTTTCTAAATTCGCATTG
1 CGATTTTCTAAATTCGCATTG
* **
1289617 CGATTTTC-CAATTCGTGTTG
1 CGATTTTCTAAATTCGCATTG
1289637 CGATTTT
1 CGATTTT
1289644 ACTATTCATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.19, C:0.19, G:0.17, T:0.46
Consensus pattern (21 bp):
CGATTTTCTAAATTCGCATTG
Found at i:1289650 original size:20 final size:20
Alignment explanation
Indices: 1289614--1289659 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1289604 TAAATTCGCA
* *
1289614 TTGCGATTTTCCAATTCGTG
1 TTGCGATTTTACAATTCATG
*
1289634 TTGCGATTTTACTATTCATG
1 TTGCGATTTTACAATTCATG
1289654 TTGCGA
1 TTGCGA
1289660 AATTGGAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.20, T:0.46
Consensus pattern (20 bp):
TTGCGATTTTACAATTCATG
Found at i:1298008 original size:226 final size:226
Alignment explanation
Indices: 1297710--1298157 Score: 650
Period size: 226 Copynumber: 2.0 Consensus size: 226
1297700 TAATTACTGT
* * * *
1297710 AAACATTATCAACCATAATAACATAACAGGTAGTGTTTATGTAACATAATAGGTAGCGTCTTTTT
1 AAACATTATCAACCATAATAACATAACAAGTAGCGCTTATGTAACATAATAGGTAGAGTCTTTTT
* * * * *
1297775 AAAGCTGATGAGG-CCTTAGAAATTCGATGATAACAAAATAGGTTAATTACTTGATTTGTTATCA
66 AAAGCTGATG-GGACCTTAGAAATCCGACGATAACAAAACAAGTTAATTACTTCATTTGTTATCA
* * *
1297839 ATATTATCAACATATTAGGTAGCGCCTAAAATGTTACCAAAGTTTAAGCCGATGGAGCCTTAGAA
130 ATATTATCAACATATTAGGTAACACCTAAAATATTACCAAAGTTTAAGCCGATGGAGCCTTAGAA
1297904 ATCC-AGCGAAAACAAAATAGGTTAATTATTAG
195 ATCCGA-CGAAAACAAAATAGGTTAATTATTAG
* *
1297936 AAACATTATCAACCATAATAACATAACAAGTAGCGCTTATTTAATATAATAGGTAGAG-CATTTT
1 AAACATTATCAACCATAATAACATAACAAGTAGCGCTTATGTAACATAATAGGTAGAGTC-TTTT
* *
1298000 TAAAGCTGATGGGATCTTAGAAATCCGACGATAACAAAACAAGTTAATTACTTCCTTTGTTATCA
65 TAAAGCTGATGGGACCTTAGAAATCCGACGATAACAAAACAAGTTAATTACTTCATTTGTTATCA
* * *
1298065 ATATTATCAACATATTAGGTAACACCTAAAATATTATCAAAGTTTAAGCTGATGGGGCCTTAGAA
130 ATATTATCAACATATTAGGTAACACCTAAAATATTACCAAAGTTTAAGCCGATGGAGCCTTAGAA
* * *
1298130 ATCCGACGATAACAAAGTATGTTAATTA
195 ATCCGACGAAAACAAAATAGGTTAATTA
1298158 CTTATTTTGT
Statistics
Matches: 197, Mismatches: 22, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
225 3 0.02
226 193 0.98
227 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (226 bp):
AAACATTATCAACCATAATAACATAACAAGTAGCGCTTATGTAACATAATAGGTAGAGTCTTTTT
AAAGCTGATGGGACCTTAGAAATCCGACGATAACAAAACAAGTTAATTACTTCATTTGTTATCAA
TATTATCAACATATTAGGTAACACCTAAAATATTACCAAAGTTTAAGCCGATGGAGCCTTAGAAA
TCCGACGAAAACAAAATAGGTTAATTATTAG
Found at i:1298191 original size:108 final size:107
Alignment explanation
Indices: 1298002--1298301 Score: 348
Period size: 108 Copynumber: 2.8 Consensus size: 107
1297992 AGCATTTTTA
* * ** *
1298002 AAGCTGATGGGATCTTAGAAATCCGACGATAACAAAACAAGTTAATTACTTCCTTTGTTATCAAT
1 AAGCTGATGGGGTCTTAGAAATCCGACGATAACAAAA-TAGTTAATTACTTATTTTGTTATAAAT
* *
1298067 ATTATCAACATATTAGGTAACACCTAAAATATTATCAAAGTTT
65 ATTATCAACATATTAGGTAACACCTAAAATATTACCAAAGCTT
* * *
1298110 AAGCTGATGGGGCCTTAGAAATCCGACGATAACAAAGTATGTTAATTACTTATTTTGTTATTAAT
1 AAGCTGATGGGGTCTTAGAAATCCGACGATAACAAAATA-GTTAATTACTTATTTTGTTATAAAT
*** *
1298175 ATTATCAACATATTAGGTAGTGCCTAAAATGTTACCAAAGCTT
65 ATTATCAACATATTAGGTAACACCTAAAATATTACCAAAGCTT
* * * * ** *
1298218 AAGTTGACGGGGTCTTCGAAATCCCACGGCAACAAAATAGATTAATTTCTTATTTTGTTATAAAT
1 AAGCTGATGGGGTCTTAGAAATCCGACGATAACAAAATAG-TTAATTACTTATTTTGTTATAAAT
* * *
1298283 AAATATTAACATACTAGGT
65 -ATTATCAACATATTAGGT
1298302 TGCGTCCAAT
Statistics
Matches: 163, Mismatches: 26, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
107 2 0.01
108 146 0.90
109 15 0.09
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (107 bp):
AAGCTGATGGGGTCTTAGAAATCCGACGATAACAAAATAGTTAATTACTTATTTTGTTATAAATA
TTATCAACATATTAGGTAACACCTAAAATATTACCAAAGCTT
Found at i:1298513 original size:17 final size:17
Alignment explanation
Indices: 1298491--1298526 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1298481 TTAGAGTAAG
1298491 TATGAATACATTATTAT
1 TATGAATACATTATTAT
1298508 TATGAATACATTATTAT
1 TATGAATACATTATTAT
1298525 TA
1 TA
1298527 ACCTTTAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.47
Consensus pattern (17 bp):
TATGAATACATTATTAT
Found at i:1298999 original size:74 final size:75
Alignment explanation
Indices: 1298845--1299042 Score: 274
Period size: 74 Copynumber: 2.7 Consensus size: 75
1298835 TTACATTTAC
* * * * * *
1298845 ATTAATAACATTTAAACAAA-CATGTAGGTATTTTAACATAATAGATAGTGACTATTTTATTTTA
1 ATTATTAACATTTAAACAAATC-CGTAAGTATTTTAACGTAATAGGTAGTCACTATTTTATTTTA
1298909 CCGTTTACATT
65 CCGTTTACATT
*
1298920 ATTATTAACATTTAAACAAATCCGTATGTATTTTAACGTAATAGGTAG-CACTATTTTATTTTAC
1 ATTATTAACATTTAAACAAATCCGTAAGTATTTTAACGTAATAGGTAGTCACTATTTTATTTTAC
1298984 CGTTTACATT
66 CGTTTACATT
* * * *
1298994 ATTATTAACCTTTAAACAAATCGGTAACTAGTTTAACGTAATAGGTAGT
1 ATTATTAACATTTAAACAAATCCGTAAGTATTTTAACGTAATAGGTAGT
1299043 GGTTATTTAA
Statistics
Matches: 110, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
74 68 0.62
75 41 0.37
76 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (75 bp):
ATTATTAACATTTAAACAAATCCGTAAGTATTTTAACGTAATAGGTAGTCACTATTTTATTTTAC
CGTTTACATT
Found at i:1299072 original size:23 final size:23
Alignment explanation
Indices: 1299025--1299096 Score: 81
Period size: 23 Copynumber: 3.1 Consensus size: 23
1299015 CGGTAACTAG
* **
1299025 TTTAACGTAATAGGTAGTGGTTA
1 TTTAACGTAATAGGTAGCGCCTA
1299048 TTTAACGTAATAGGTAGCGCCTA
1 TTTAACGTAATAGGTAGCGCCTA
* * * *
1299071 TTCAACATAATATGTAGCACCTA
1 TTTAACGTAATAGGTAGCGCCTA
1299094 TTT
1 TTT
1299097 TATTTTACTG
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (23 bp):
TTTAACGTAATAGGTAGCGCCTA
Found at i:1300230 original size:23 final size:23
Alignment explanation
Indices: 1300198--1300255 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
1300188 CGGTAGCTAG
* *
1300198 TTTAATGTAATAGGTAGCGCTTA
1 TTTAACGTAATAGGTAGCGCCTA
1300221 TTTAACGTAATAGGTAGCGCCTA
1 TTTAACGTAATAGGTAGCGCCTA
*
1300244 TTTAACATAATA
1 TTTAACGTAATA
1300256 AGTTGCGTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.36
Consensus pattern (23 bp):
TTTAACGTAATAGGTAGCGCCTA
Found at i:1300346 original size:75 final size:75
Alignment explanation
Indices: 1300244--1300405 Score: 225
Period size: 75 Copynumber: 2.2 Consensus size: 75
1300234 GTAGCGCCTA
* * * * * *
1300244 TTTAACATAATAAGTTGCGTATGTTTTATTTTACCGTTTACATTATTAATAACCTTTAAACAAAC
1 TTTAACGTAATATGTAGCGTCTATTTTATTTTACCGTTTACATTATTAATAAACTTTAAACAAAC
* * *
1300309 CGGTAGGTAT
66 CGATAGCTAG
* *
1300319 TTTAATGTAATATGTAGCGTCTATTTTATTTTACCGTTTACATTATTATTAAACTTTAAACAAAC
1 TTTAACGTAATATGTAGCGTCTATTTTATTTTACCGTTTACATTATTAATAAACTTTAAACAAAC
1300384 CGATAGCTAG
66 CGATAGCTAG
1300394 TTTAACGTAATA
1 TTTAACGTAATA
1300406 GATATCACTT
Statistics
Matches: 75, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
75 75 1.00
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (75 bp):
TTTAACGTAATATGTAGCGTCTATTTTATTTTACCGTTTACATTATTAATAAACTTTAAACAAAC
CGATAGCTAG
Found at i:1300453 original size:23 final size:23
Alignment explanation
Indices: 1300394--1300455 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
1300384 CGATAGCTAG
* *
1300394 TTTAACGTAATAGATATCACTTA
1 TTTAACGTAATAGGTAACACTTA
1300417 TTTAACGTAATAGGTAACACTTA
1 TTTAACGTAATAGGTAACACTTA
*
1300440 TTTAACCTAATAGGTA
1 TTTAACGTAATAGGTA
1300456 GCGCCTATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (23 bp):
TTTAACGTAATAGGTAACACTTA
Found at i:1300464 original size:23 final size:23
Alignment explanation
Indices: 1300394--1300465 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 23
1300384 CGATAGCTAG
* * * *
1300394 TTTAACGTAATAGATATCACTTA
1 TTTAACCTAATAGGTAACACCTA
* *
1300417 TTTAACGTAATAGGTAACACTTA
1 TTTAACCTAATAGGTAACACCTA
* *
1300440 TTTAACCTAATAGGTAGCGCCTA
1 TTTAACCTAATAGGTAACACCTA
1300463 TTT
1 TTT
1300466 TATTTTACCT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (23 bp):
TTTAACCTAATAGGTAACACCTA
Found at i:1300483 original size:196 final size:196
Alignment explanation
Indices: 1300149--1300595 Score: 642
Period size: 196 Copynumber: 2.3 Consensus size: 196
1300139 AAATTATATA
* * *
1300149 TATTTTACCGTTTACATTAGTATTAACCTTTAAACAAACCGGTAGCTAGTTTAATGTAATAGGTA
1 TATTTTACCGTTTACATTATTATTAACCTTTAAACAAACCGGTAGCTAGTTTAACGTAATAGATA
* * * * * *
1300214 GCGCTTATTTAACGTAATAGGTAGCGCCTATTTAACATAATAAGTTGCGTATGTTTTATTTTACC
66 GCACTTATTTAACGTAATAGGTAACACCTATTTAACATAATAAGTAGCGCATATTTTATTTTACC
* ** * **
1300279 GTTTACATTATTAATAACCTTTAAACAAACCGGTAGGTATTTTAATGTAATATGTAGCGTCTATT
131 GTTTACATTATTAATAACCTTTAAACAAACCGGTAGATATTTTAACATAATAGGTAGCACCTATT
1300344 T
196 T
* *
1300345 TATTTTACCGTTTACATTATTATTAAACTTTAAACAAACCGATAGCTAGTTTAACGTAATAGATA
1 TATTTTACCGTTTACATTATTATTAACCTTTAAACAAACCGGTAGCTAGTTTAACGTAATAGATA
* * * * *
1300410 TCACTTATTTAACGTAATAGGTAACACTTATTTAACCTAATAGGTAGCGCCTATTTTATTTTACC
66 GCACTTATTTAACGTAATAGGTAACACCTATTTAACATAATAAGTAGCGCATATTTTATTTTACC
* *
1300475 TTTTACATTATTAATAATCTTTAAACAAACCGGTAGATATTTTAACATAATAGGTAGCACCTATT
131 GTTTACATTATTAATAACCTTTAAACAAACCGGTAGATATTTTAACATAATAGGTAGCACCTATT
1300540 T
196 T
* * * *
1300541 TATTTTATCGTTTACATTATTAGTAACCTTCAAACAAACCGGTAGGTAGTTTAAC
1 TATTTTACCGTTTACATTATTATTAACCTTTAAACAAACCGGTAGCTAGTTTAAC
1300596 ATATTAGGTA
Statistics
Matches: 221, Mismatches: 30, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
196 221 1.00
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (196 bp):
TATTTTACCGTTTACATTATTATTAACCTTTAAACAAACCGGTAGCTAGTTTAACGTAATAGATA
GCACTTATTTAACGTAATAGGTAACACCTATTTAACATAATAAGTAGCGCATATTTTATTTTACC
GTTTACATTATTAATAACCTTTAAACAAACCGGTAGATATTTTAACATAATAGGTAGCACCTATT
T
Found at i:1300576 original size:75 final size:75
Alignment explanation
Indices: 1300440--1300622 Score: 276
Period size: 75 Copynumber: 2.4 Consensus size: 75
1300430 GTAACACTTA
* * * *
1300440 TTTAACCTAATAGGTAGCGCCTATTTTATTTTACCTTTTACATTATTAATAATCTTTAAACAAAC
1 TTTAACATAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAATAACCTTCAAACAAAC
*
1300505 CGGTAGATAT
66 CGGTAGATAG
* * *
1300515 TTTAACATAATAGGTAGCACCTATTTTATTTTATCGTTTACATTATTAGTAACCTTCAAACAAAC
1 TTTAACATAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAATAACCTTCAAACAAAC
*
1300580 CGGTAGGTAG
66 CGGTAGATAG
*
1300590 TTTAACATATTAGGTAGCGCCTATTTTATTTTA
1 TTTAACATAATAGGTAGCGCCTATTTTATTTTA
1300623 ACCGATTAAG
Statistics
Matches: 97, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
75 97 1.00
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.41
Consensus pattern (75 bp):
TTTAACATAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAATAACCTTCAAACAAAC
CGGTAGATAG
Found at i:1303599 original size:23 final size:23
Alignment explanation
Indices: 1303558--1303616 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 23
1303548 CAACGAACAA
* * *
1303558 AACGGGTTGACTCGATTGACTCT
1 AACGAGTTAACTCGATTGACTCG
** *
1303581 AGTGAGTTAACTCGGTTGACTCG
1 AACGAGTTAACTCGATTGACTCG
1303604 AACGAGTTAACTC
1 AACGAGTTAACTC
1303617 AGTCAACTAG
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.29
Consensus pattern (23 bp):
AACGAGTTAACTCGATTGACTCG
Found at i:1308920 original size:16 final size:16
Alignment explanation
Indices: 1308899--1308931 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1308889 AATGCTGTGG
1308899 AAAAAATATTCATGGA
1 AAAAAATATTCATGGA
1308915 AAAAAATATTCATGGA
1 AAAAAATATTCATGGA
1308931 A
1 A
1308932 TAATGCAGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.06, G:0.12, T:0.24
Consensus pattern (16 bp):
AAAAAATATTCATGGA
Found at i:1311904 original size:29 final size:27
Alignment explanation
Indices: 1311844--1311904 Score: 70
Period size: 26 Copynumber: 2.2 Consensus size: 27
1311834 TGACAAGTAA
** *
1311844 GAATAATAGAAGTGTTTTTTTTTAATT
1 GAATAATAGAAGTGTTGGTTGTTAATT
1311871 -AATAATAGAAGTGCTTGGTTGTTACATT
1 GAATAATAGAAGTG-TTGGTTGTTA-ATT
1311899 GAATAA
1 GAATAA
1311905 CATTTTCGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
26 13 0.46
27 7 0.25
28 3 0.11
29 5 0.18
ACGTcount: A:0.36, C:0.03, G:0.18, T:0.43
Consensus pattern (27 bp):
GAATAATAGAAGTGTTGGTTGTTAATT
Found at i:1313898 original size:23 final size:23
Alignment explanation
Indices: 1313867--1313911 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1313857 TGAAAATTTC
* * *
1313867 AAATTTTCATATAATTTAAGTAG
1 AAATCTTCATACAAGTTAAGTAG
1313890 AAATCTTCATACAAGTTAAGTA
1 AAATCTTCATACAAGTTAAGTA
1313912 TTTTCTTTGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (23 bp):
AAATCTTCATACAAGTTAAGTAG
Found at i:1321634 original size:161 final size:156
Alignment explanation
Indices: 1321315--1321634 Score: 586
Period size: 156 Copynumber: 2.0 Consensus size: 156
1321305 GAACGATCGA
*
1321315 AAAAGGACAACTGGATATCCATTTCATATCGGTTCTACAACATTTTCATGGTCATCAAAGAAGCA
1 AAAAGCACAACTGGATATCCATTTCATATCGGTTCTACAACATTTTCATGGTCATCAAAGAAGCA
1321380 ACAAACGTAGCTCTTTCAACATGTGAAGATACATAGCCGCAACAGCGTGCAGTTGCCAAACAATG
66 ACAAACGTAGCTCTTTCAACATGTGAAGATACATAGCCGCAACAGCGTGCAGTTGCCAAACAATG
1321445 TGGTTAAAAAATATTTTGAACGAGCT
131 TGGTTAAAAAATATTTTGAACGAGCT
1321471 AAAAGCACAACTGGATATCCATTTCATATCGGTTCTACAACATTTTCATGGTCATCAAAGAAGCA
1 AAAAGCACAACTGGATATCCATTTCATATCGGTTCTACAACATTTTCATGGTCATCAAAGAAGCA
1321536 ACAAACGGTAGCTCTTTCAACATGTGAAGCAGAATACATAGCCGCAACAGCGTGCAGTTGCCAAA
66 ACAAAC-GTAGCTCTTTCAACATGTG-A--AG-ATACATAGCCGCAACAGCGTGCAGTTGCCAAA
1321601 CAATGTGGTTAAAAAATATTTTGAACGAGCT
126 CAATGTGGTTAAAAAATATTTTGAACGAGCT
1321632 AAA
1 AAA
1321635 TTTGGCACAA
Statistics
Matches: 158, Mismatches: 1, Indels: 5
0.96 0.01 0.03
Matches are distributed among these distances:
156 70 0.44
157 19 0.12
158 1 0.01
160 2 0.01
161 66 0.42
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (156 bp):
AAAAGCACAACTGGATATCCATTTCATATCGGTTCTACAACATTTTCATGGTCATCAAAGAAGCA
ACAAACGTAGCTCTTTCAACATGTGAAGATACATAGCCGCAACAGCGTGCAGTTGCCAAACAATG
TGGTTAAAAAATATTTTGAACGAGCT
Found at i:1322535 original size:20 final size:20
Alignment explanation
Indices: 1322512--1322550 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1322502 TATCCAGCTT
*
1322512 GATAATATCATTTTAAAAAG
1 GATAATATAATTTTAAAAAG
1322532 GATAATATAATTTTAAAAA
1 GATAATATAATTTTAAAAA
1322551 AATGATAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.36
Consensus pattern (20 bp):
GATAATATAATTTTAAAAAG
Found at i:1322557 original size:22 final size:20
Alignment explanation
Indices: 1322511--1322565 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 20
1322501 ATATCCAGCT
*
1322511 TGATAATATCATTTTAAAAA
1 TGATAATATAATTTTAAAAA
*
1322531 GGATAATATAATTTTAAAAAAA
1 TGATAATATAATTTT--AAAAA
*
1322553 TGATAACATAATT
1 TGATAATATAATT
1322566 AATTATTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 13 0.45
22 16 0.55
ACGTcount: A:0.53, C:0.04, G:0.07, T:0.36
Consensus pattern (20 bp):
TGATAATATAATTTTAAAAA
Found at i:1327136 original size:106 final size:104
Alignment explanation
Indices: 1326916--1327151 Score: 327
Period size: 106 Copynumber: 2.3 Consensus size: 104
1326906 TAAGTGAAAA
1326916 TTTTGAAATTGTTTCACTTGAAAC-AAGAAATTTTATCTCACTCGAGATTGTTATTTCGAAACAA
1 TTTTGAAATTGTTTCACTTGAAACAAAGAAATTTTATCTCACTCGAGATTGTTATTTCGAAACAA
* *
1326980 ATTTCATCTCGCTTGAGATGGTTTCCTTTGAAATACAAG
66 ATTTCATCTCGCTTGAGATAGTTTCCTTTGAAACACAAG
* * * *
1327019 TTTTAAAATTGTTTCACTTGAAACAAAG-AATTTTGTCTCACTTGAGATTGTTTTTTTCTTATGA
1 TTTTGAAATTGTTTCACTTGAAACAAAGAAATTTTATCTCACTCGAGATTG-TTATTTC----GA
*
1327083 AA-AACTTT-ATCTCGCTTGAGATAGTTTCCTTTGAAACACAAG
61 AACAAATTTCATCTCGCTTGAGATAGTTTCCTTTGAAACACAAG
*
1327125 TTTTGAAATTGTTTCACTCGAAACAAA
1 TTTTGAAATTGTTTCACTTGAAACAAA
1327152 ATTCCATCTC
Statistics
Matches: 118, Mismatches: 9, Indels: 9
0.87 0.07 0.07
Matches are distributed among these distances:
103 43 0.36
104 9 0.08
106 57 0.48
107 5 0.04
108 4 0.03
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (104 bp):
TTTTGAAATTGTTTCACTTGAAACAAAGAAATTTTATCTCACTCGAGATTGTTATTTCGAAACAA
ATTTCATCTCGCTTGAGATAGTTTCCTTTGAAACACAAG
Found at i:1327181 original size:106 final size:106
Alignment explanation
Indices: 1326985--1327179 Score: 295
Period size: 106 Copynumber: 1.9 Consensus size: 106
1326975 AACAAATTTC
* * *
1326985 ATCTCGCTTGAGATGGTTTCCTTTGAAATACAAGTTTTAAAATTGTTTCACTTGAAACAAAGAAT
1 ATCTCGCTTGAGATAGTTTCCTTTGAAACACAAGTTTTAAAATTGTTTCACTCGAAACAAAGAAT
*** *
1327050 TTTGTCTCACTTGAGATTGTTTTTTTCTTATGAAAAACTTT
66 TCCATCTCACCTGAGATTGTTTTTTTCTTATGAAAAACTTT
*
1327091 ATCTCGCTTGAGATAGTTTCCTTTGAAACACAAGTTTTGAAATTGTTTCACTCGAAAC-AA-AAT
1 ATCTCGCTTGAGATAGTTTCCTTTGAAACACAAGTTTTAAAATTGTTTCACTCGAAACAAAGAAT
*
1327154 TCCATCTCACCTGAGATAGTTTTTTT
66 TCCATCTCACCTGAGATTGTTTTTTT
1327180 TTTGAACAAA
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
104 24 0.30
105 2 0.03
106 54 0.68
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (106 bp):
ATCTCGCTTGAGATAGTTTCCTTTGAAACACAAGTTTTAAAATTGTTTCACTCGAAACAAAGAAT
TCCATCTCACCTGAGATTGTTTTTTTCTTATGAAAAACTTT
Found at i:1327599 original size:44 final size:45
Alignment explanation
Indices: 1327545--1327653 Score: 141
Period size: 45 Copynumber: 2.4 Consensus size: 45
1327535 ATTCGATTTT
* *
1327545 ATCACAGAAGGAGGTAGATCAACACCTAT-ATT-TTGTTCGATTCC
1 ATCACAGAAGGAGGTGGATCAACA-CTATCATTCTTGCTCGATTCC
* * * *
1327589 ATTACAGAAGGAGGTGGATCAATATTGTCATTCTTGCTCGATTCC
1 ATCACAGAAGGAGGTGGATCAACACTATCATTCTTGCTCGATTCC
1327634 ATCACAGAAGGAGGTGGATC
1 ATCACAGAAGGAGGTGGATC
1327654 GTCATTTCCA
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
43 2 0.04
44 24 0.43
45 30 0.54
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.28
Consensus pattern (45 bp):
ATCACAGAAGGAGGTGGATCAACACTATCATTCTTGCTCGATTCC
Found at i:1327734 original size:20 final size:20
Alignment explanation
Indices: 1327672--1327735 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
1327662 CAATAGAAGA
1327672 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
** ***
1327692 G-TCCGAA-GAGAGAGAAGAA
1 GTTCATAATGAGA-AGAACTT
1327711 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
1327731 GTTCA
1 GTTCA
1327736 ACCTTTTGCT
Statistics
Matches: 31, Mismatches: 10, Indels: 6
0.66 0.21 0.13
Matches are distributed among these distances:
18 4 0.13
19 9 0.29
20 14 0.45
21 4 0.13
ACGTcount: A:0.41, C:0.11, G:0.25, T:0.23
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:1327826 original size:208 final size:206
Alignment explanation
Indices: 1327428--1327860 Score: 591
Period size: 208 Copynumber: 2.1 Consensus size: 206
1327418 ATTCAAATCT
* * * * * *
1327428 ATCACAAAAGGACGTGGATCAACATTTCCAATGGAGGGGGTTCATAATGAGAATAACTCATCCGA
1 ATCACAGAAGGAGGTGGATCAACATTTCCAATAGAGAGAGTTCATAATGAGAAGAACTCATCCGA
* * * * *
1327493 AGAGGAAGAAGTTCATAATGAGAAGAACTTGTTCACCCTTTTATTCGATTTTATCACAGAAGGAG
66 AGAGGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACTCGACTCTATCACAGAAGAAG
* * * * * *
1327558 GTAGATCAACACCTATATTTTGTTCGATTCCATTACAGAAGGAGGTGGATCAATATTGTCATTCT
131 ATAGATAAACAACAATATTTTGTTCGATTCCATTACAAAAGGAGGTGGATCAACATTGTCATTCT
*
1327623 TGCTCGA-TTCC
196 TGCTAGACTT-C
** **
1327634 ATCACAGAAGGAGGTGGATCGTCATTTCCAATAGA-AGAGTTCATAATGAGAAGAACTTGTCCGA
1 ATCACAGAAGGAGGTGGATCAACATTTCCAATAGAGAGAGTTCATAATGAGAAGAACTCATCCG-
*
1327698 AGAGAGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAG
65 A-AGAG-GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACTCGACTCTATCACAGAAG
* *
1327763 AAGATATATAAACAACAATATTTTGTTTGATTCCATTACAAAAGGAGGTGGATCAACATTGTCAT
128 AAGATAGATAAACAACAATATTTTGTTCGATTCCATTACAAAAGGAGGTGGATCAACATTGTCAT
1327828 TCTTGCTAGACTTC
193 TCTTGCTAGACTTC
1327842 ATCACAGAAGGAGGTGGAT
1 ATCACAGAAGGAGGTGGAT
1327861 TAGCATAATC
Statistics
Matches: 198, Mismatches: 25, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
205 23 0.12
206 31 0.16
207 4 0.02
208 138 0.70
209 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.28
Consensus pattern (206 bp):
ATCACAGAAGGAGGTGGATCAACATTTCCAATAGAGAGAGTTCATAATGAGAAGAACTCATCCGA
AGAGGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACTCGACTCTATCACAGAAGAAG
ATAGATAAACAACAATATTTTGTTCGATTCCATTACAAAAGGAGGTGGATCAACATTGTCATTCT
TGCTAGACTTC
Found at i:1330109 original size:16 final size:16
Alignment explanation
Indices: 1330084--1330125 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
1330074 TGAAATATTA
1330084 GCAAAGTTGAAAGTTG
1 GCAAAGTTGAAAGTTG
*
1330100 GCAAAATTGAAAGTTG
1 GCAAAGTTGAAAGTTG
1330116 GCAAAGTTGA
1 GCAAAGTTGA
1330126 CATCTTTGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.40, C:0.07, G:0.29, T:0.24
Consensus pattern (16 bp):
GCAAAGTTGAAAGTTG
Found at i:1334596 original size:15 final size:15
Alignment explanation
Indices: 1334576--1334614 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1334566 TGAAGAAGGA
*
1334576 AAAATTCTACTTCAG
1 AAAATTCTACATCAG
*
1334591 AAAATTGCGACATCAG
1 AAAATT-CTACATCAG
1334607 AAAATTCT
1 AAAATTCT
1334615 GCAGATATGA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.44, C:0.18, G:0.10, T:0.28
Consensus pattern (15 bp):
AAAATTCTACATCAG
Found at i:1334869 original size:16 final size:16
Alignment explanation
Indices: 1334844--1334901 Score: 98
Period size: 16 Copynumber: 3.6 Consensus size: 16
1334834 TGAAATATTA
1334844 GCAAAGTTGAAAGTTG
1 GCAAAGTTGAAAGTTG
*
1334860 GCAAAATTGAAAGTTG
1 GCAAAGTTGAAAGTTG
*
1334876 ACAAAGTTGAAAGTTG
1 GCAAAGTTGAAAGTTG
1334892 GCAAAGTTGA
1 GCAAAGTTGA
1334902 CATCTTTGGT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.41, C:0.07, G:0.28, T:0.24
Consensus pattern (16 bp):
GCAAAGTTGAAAGTTG
Found at i:1334883 original size:9 final size:8
Alignment explanation
Indices: 1334844--1334900 Score: 57
Period size: 7 Copynumber: 7.1 Consensus size: 8
1334834 TGAAATATTA
1334844 GCAAAGTT
1 GCAAAGTT
1334852 G-AAAGTT
1 GCAAAGTT
*
1334859 GGCAAAATT
1 -GCAAAGTT
1334868 G-AAAGTT
1 GCAAAGTT
1334875 GACAAAGTT
1 G-CAAAGTT
1334884 G-AAAGTT
1 GCAAAGTT
1334891 GGCAAAGTT
1 -GCAAAGTT
1334900 G
1 G
1334901 ACATCTTTGG
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
7 18 0.44
8 5 0.12
9 18 0.44
ACGTcount: A:0.40, C:0.07, G:0.28, T:0.25
Consensus pattern (8 bp):
GCAAAGTT
Found at i:1340448 original size:2 final size:2
Alignment explanation
Indices: 1340441--1340474 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1340431 TATGAAATTA
1340441 AT AT AT AT 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 AT AT AT AT
1340475 TTTCCTCATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1342427 original size:22 final size:22
Alignment explanation
Indices: 1342402--1342455 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 22
1342392 ACCCGAACCA
*
1342402 TTGACTGGTCAGACCGTTAACT
1 TTGACTGGTCAGAACGTTAACT
* * * * *
1342424 TTGACCGATCGGAATGTTGACT
1 TTGACTGGTCAGAACGTTAACT
1342446 TTGACTGGTC
1 TTGACTGGTC
1342456 TAACTGTTGA
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.33
Consensus pattern (22 bp):
TTGACTGGTCAGAACGTTAACT
Found at i:1345938 original size:20 final size:20
Alignment explanation
Indices: 1345915--1346103 Score: 195
Period size: 20 Copynumber: 9.4 Consensus size: 20
1345905 GATTCCTACT
1345915 ATCGCAACGAGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
* ** *
1345935 ATCGCAATGACAATACGTAAA
1 ATCGCAACGAGTATCCGT-AA
*
1345956 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
** *
1345976 ATCGCAACGACAATACGTAAA
1 ATCGCAACGAGTATCCGT-AA
* *
1345997 ATCGCAACGCGTATCTGTAA
1 ATCGCAACGAGTATCCGTAA
1346017 ATCGCAACGA-TAATCCGTAA
1 ATCGCAACGAGT-ATCCGTAA
* *
1346037 ATCGCAACGAGAATCTGTAA
1 ATCGCAACGAGTATCCGTAA
1346057 ATCGCAACGA-TAATCCGT-A
1 ATCGCAACGAGT-ATCCGTAA
* *
1346076 ATCGCAACGAGAATCTGTAA
1 ATCGCAACGAGTATCCGTAA
1346096 ATCGCAAC
1 ATCGCAAC
1346104 ACTGAAATTT
Statistics
Matches: 136, Mismatches: 26, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
19 17 0.12
20 89 0.65
21 30 0.22
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (20 bp):
ATCGCAACGAGTATCCGTAA
Found at i:1345970 original size:41 final size:40
Alignment explanation
Indices: 1345915--1346103 Score: 254
Period size: 41 Copynumber: 4.7 Consensus size: 40
1345905 GATTCCTACT
* *
1345915 ATCGCAACGAGTATCCGTAAATCGCAATGACAATACGTAAA
1 ATCGCAACGAGTATCTGTAAATCGCAACGACAATACGT-AA
* *
1345956 ATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAAA
1 ATCGCAACGAGTATCTGTAAATCGCAACGACAATACGT-AA
* * *
1345997 ATCGCAACGCGTATCTGTAAATCGCAACGATAATCCGTAA
1 ATCGCAACGAGTATCTGTAAATCGCAACGACAATACGTAA
* * *
1346037 ATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT-A
1 ATCGCAACGAGTATCTGTAAATCGCAACGACAATACGTAA
*
1346076 ATCGCAACGAGAATCTGTAAATCGCAAC
1 ATCGCAACGAGTATCTGTAAATCGCAAC
1346104 ACTGAAATTT
Statistics
Matches: 141, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
39 29 0.21
40 38 0.27
41 74 0.52
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (40 bp):
ATCGCAACGAGTATCTGTAAATCGCAACGACAATACGTAA
Found at i:1345980 original size:61 final size:60
Alignment explanation
Indices: 1345892--1346103 Score: 202
Period size: 61 Copynumber: 3.5 Consensus size: 60
1345882 CGCGAACATA
* * *
1345892 TAAATCGCAACGCG-ATTCC-TACTATCGCAACGAGTATCCGTAAATCGCAATGACAATACG
1 TAAATCGCAACGCGTA-TCCGTA-AATCGCAACGAGAATCCGTAAATCGCAACGACAATACG
* * *
1345952 TAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAAAATCGCAACG-C-GTATCTG
1 T-AAATCGCAACGCGTATCCGTAAATCGCAACGAGAATCCGT-AAATCGCAACGACAATA-C-G
* * * *
1346014 TAAATCGCAACG-ATAATCCGTAAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCG
1 TAAATCGCAACGCGT-ATCCGTAAATCGCAACGAGAATCCGTAAATCGCAACGACAATACG
* * *
1346074 T-AATCGCAACGAGAATCTGTAAATCGCAAC
1 TAAATCGCAACGCGTATCCGTAAATCGCAAC
1346104 ACTGAAATTT
Statistics
Matches: 126, Mismatches: 16, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
59 25 0.20
60 17 0.13
61 68 0.54
62 16 0.13
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (60 bp):
TAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATCCGTAAATCGCAACGACAATACG
Found at i:1346990 original size:12 final size:12
Alignment explanation
Indices: 1346973--1346997 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1346963 CTATAATCCT
1346973 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1346985 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1346997 G
1 G
1346998 TCCCCGAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1349058 original size:14 final size:14
Alignment explanation
Indices: 1349039--1349126 Score: 50
Period size: 14 Copynumber: 5.6 Consensus size: 14
1349029 TGGAAATTAC
1349039 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1349053 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
1349072 AATTGCAACGAGAG
1 AATCGCAACGAGAG
*
1349086 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
1349105 AATCGCGACGAGAG
1 AATCGCAACGAGAG
1349119 AATCGCAA
1 AATCGCAA
1349127 TGCGAAACTA
Statistics
Matches: 56, Mismatches: 8, Indels: 20
0.67 0.10 0.24
Matches are distributed among these distances:
14 26 0.46
15 2 0.04
16 4 0.07
17 4 0.07
18 2 0.04
19 18 0.32
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.12
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1349068 original size:33 final size:33
Alignment explanation
Indices: 1349039--1349133 Score: 172
Period size: 33 Copynumber: 2.9 Consensus size: 33
1349029 TGGAAATTAC
1349039 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
*
1349072 AATTGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
*
1349105 AATCGCGACGAGAGAATCGCAATGCGAAA
1 AATCGCAACGAGAGAATCGCAATGCGAAA
1349134 CTAATTCACA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.13
Consensus pattern (33 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:1349110 original size:19 final size:19
Alignment explanation
Indices: 1349053--1349110 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
1349043 GCAACGAGAG
1349053 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
1349072 AATTGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1349086 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1349105 AATCGC
1 AATCGC
1349111 GACGAGAGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
14 9 0.30
15 1 0.03
16 2 0.07
17 2 0.07
18 1 0.03
19 15 0.50
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1349186 original size:33 final size:33
Alignment explanation
Indices: 1349142--1349235 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
1349132 AACTAATTCA
1349142 CATTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CATTGCGATTTTCATTTCGCATTGCGATTCTCT
*
1349175 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CATTGCGATTTTCATTTCGCATTGCGATTCTCT
*
1349208 CATTGTGATTTTCATTTCGCATTGCGAT
1 CATTGCGATTTTCATTTCGCATTGCGAT
1349236 AGTCATTTTT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (33 bp):
CATTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:1349243 original size:19 final size:19
Alignment explanation
Indices: 1349142--1349235 Score: 91
Period size: 19 Copynumber: 5.5 Consensus size: 19
1349132 AACTAATTCA
1349142 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
*
1349161 CATTGCGA--TTC-TCTCG
1 CATTGCGATTTTCATTTCG
1349177 --TTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
*
1349194 CATTGCGA--TTC---TCT
1 CATTGCGATTTTCATTTCG
*
1349208 CATTGTGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
1349227 CATTGCGAT
1 CATTGCGAT
1349236 AGTCATTTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 15 0.25
16 10 0.17
17 10 0.17
19 24 0.41
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Found at i:1349361 original size:14 final size:14
Alignment explanation
Indices: 1349342--1349378 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1349332 CATCAATTAA
1349342 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1349356 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1349370 ACAAATCAA
1 ACAAATCAA
1349379 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1350005 original size:21 final size:21
Alignment explanation
Indices: 1349979--1350056 Score: 113
Period size: 21 Copynumber: 3.8 Consensus size: 21
1349969 TTTGCAGAAG
1349979 AATCGCAACGAGAGAAATGAA
1 AATCGCAACGAGAGAAATGAA
* *
1350000 AATCGCAACGCGA-AAATGAC
1 AATCGCAACGAGAGAAATGAA
*
1350020 TATCGCAACGAGAGAAATGAA
1 AATCGCAACGAGAGAAATGAA
*
1350041 AATCGCAACGATAGAA
1 AATCGCAACGAGAGAA
1350057 TCGCAACGCG
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
20 17 0.35
21 32 0.65
ACGTcount: A:0.49, C:0.18, G:0.22, T:0.12
Consensus pattern (21 bp):
AATCGCAACGAGAGAAATGAA
Found at i:1350037 original size:41 final size:38
Alignment explanation
Indices: 1349976--1350088 Score: 146
Period size: 41 Copynumber: 3.0 Consensus size: 38
1349966 CAATTTGCAG
1349976 AAGAATCGCAACGAGAGAAATGAAAATCGCAACGCGAA
1 AAGAATCGCAACGAGAGAAATGAAAATCGCAACGCGAA
1350014 AATGACTATCGCAACGAGAGAAATGAAAATCGCAA--CG-A
1 AA-GA--ATCGCAACGAGAGAAATGAAAATCGCAACGCGAA
* *
1350052 TAGAATCGCAAC--GCGAAATGAAAATCGCAACGCGAA
1 AAGAATCGCAACGAGAGAAATGAAAATCGCAACGCGAA
1350088 A
1 A
1350089 CCAAAATCGC
Statistics
Matches: 66, Mismatches: 3, Indels: 14
0.80 0.04 0.17
Matches are distributed among these distances:
33 17 0.26
35 10 0.15
36 1 0.02
37 2 0.03
38 4 0.06
39 4 0.06
41 28 0.42
ACGTcount: A:0.48, C:0.19, G:0.22, T:0.11
Consensus pattern (38 bp):
AAGAATCGCAACGAGAGAAATGAAAATCGCAACGCGAA
Found at i:1350079 original size:19 final size:19
Alignment explanation
Indices: 1349992--1350099 Score: 100
Period size: 19 Copynumber: 5.8 Consensus size: 19
1349982 CGCAACGAGA
1349992 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
1350011 GAAAATGACTATCGCAACGAGA
1 G-AAATGAAAATCGCAAC--GC
1350033 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
1350050 G--AT-AGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1350066 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
**
1350085 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
1350100 TTGCGATTTT
Statistics
Matches: 71, Mismatches: 10, Indels: 16
0.73 0.10 0.16
Matches are distributed among these distances:
14 9 0.13
15 2 0.03
16 2 0.03
17 1 0.01
18 2 0.03
19 26 0.37
20 14 0.20
21 13 0.18
22 2 0.03
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.11
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1350136 original size:14 final size:14
Alignment explanation
Indices: 1350117--1350173 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1350107 TTTCATTTCG
1350117 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1350131 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
1350148 CGTGTTGCGATTCTCT
1 C--GTTGCGATTCTCT
1350164 CGTTGCGATT
1 CGTTGCGATT
1350174 TTCATTTCCG
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 17 0.47
16 6 0.17
17 6 0.17
19 7 0.19
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1350142 original size:33 final size:33
Alignment explanation
Indices: 1350100--1350221 Score: 172
Period size: 33 Copynumber: 3.5 Consensus size: 33
1350090 CAAAATCGCA
1350100 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
1350133 TTGCGATTTTCATTTCGTGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1350166 TTGCGATTTTCATTTCCGCGTTGCGATAGTCATTCTCTCG
1 TTGCGATTTTCATTT-CGCGTTGC----G--ATTCTCTCG
1350206 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1350222 AACCAAAAGA
Statistics
Matches: 80, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
33 47 0.59
34 7 0.09
38 1 0.01
39 1 0.01
40 24 0.30
ACGTcount: A:0.11, C:0.23, G:0.20, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1352110 original size:93 final size:93
Alignment explanation
Indices: 1351900--1352184 Score: 437
Period size: 94 Copynumber: 3.1 Consensus size: 93
1351890 TAGATTGCTT
* *
1351900 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTATGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTATGAAGTTAGT
1351965 ATTTGTCTTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGA
* * * *
1351994 AGTAAATTTATTCGGTTGATGCCAATTCTGCTAAATTGTGTATTCTTTAACACTGTGAA-ATAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTATGAAGTTAGT
*
1352058 TTTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * **
1352087 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACCCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTATGAAGTTAGT
*
1352152 ATTTGTCTTTGTTTTGTCTATTGGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
1352180 AGTAA
1 AGTAA
1352185 TGCAATCCAT
Statistics
Matches: 173, Mismatches: 16, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
92 20 0.12
93 70 0.40
94 83 0.48
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.47
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTATGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:1352272 original size:19 final size:19
Alignment explanation
Indices: 1352232--1352368 Score: 87
Period size: 19 Copynumber: 7.7 Consensus size: 19
1352222 TAGTTTACTT
* *
1352232 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
1352252 TCTCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1352271 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
*
1352285 TCGCAACGAGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
**
1352304 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
* *
1352323 TCACAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
* **
1352337 TCGCAATGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1352356 TCGCAACGCGAAA
1 TCGCAACGCGAAA
1352369 CTATAATCGC
Statistics
Matches: 94, Mismatches: 13, Indels: 21
0.73 0.10 0.16
Matches are distributed among these distances:
14 20 0.21
15 2 0.02
16 3 0.03
17 4 0.04
18 2 0.02
19 52 0.55
20 11 0.12
ACGTcount: A:0.48, C:0.25, G:0.17, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1352288 original size:14 final size:14
Alignment explanation
Indices: 1352269--1352295 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1352259 GCGAAATGAA
1352269 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1352283 AATCGCAACGAGA
1 AATCGCAACGAGA
1352296 AATGAAAATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.22, G:0.26, T:0.07
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1352311 original size:52 final size:52
Alignment explanation
Indices: 1352248--1352369 Score: 154
Period size: 52 Copynumber: 2.3 Consensus size: 52
1352238 CACGAAACTT
* ** * * * **
1352248 AAAATCTCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGAGAAATG
1 AAAATCGCAACGCGAAACCAAAATCACAACGACAAAATCGCAACGAGAAACC
* *
1352300 AAAATCGCAACGCGAAACCAAAATCACAACGACAAAATCGCAATGCGAAACC
1 AAAATCGCAACGCGAAACCAAAATCACAACGACAAAATCGCAACGAGAAACC
1352352 AAAATCGCAACGCGAAAC
1 AAAATCGCAACGCGAAAC
1352370 TATAATCGCG
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 60 1.00
ACGTcount: A:0.49, C:0.25, G:0.17, T:0.09
Consensus pattern (52 bp):
AAAATCGCAACGCGAAACCAAAATCACAACGACAAAATCGCAACGAGAAACC
Found at i:1352337 original size:33 final size:33
Alignment explanation
Indices: 1352300--1352363 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
1352290 ACGAGAAATG
1352300 AAAATCGCAACGCGAAACCAAAATCACAACGAC
1 AAAATCGCAACGCGAAACCAAAATCACAACGAC
* *
1352333 AAAATCGCAATGCGAAACCAAAATCGCAACG
1 AAAATCGCAACGCGAAACCAAAATCACAACG
1352364 CGAAACTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.50, C:0.28, G:0.14, T:0.08
Consensus pattern (33 bp):
AAAATCGCAACGCGAAACCAAAATCACAACGAC
Found at i:1352378 original size:19 final size:19
Alignment explanation
Indices: 1352283--1352369 Score: 94
Period size: 19 Copynumber: 4.8 Consensus size: 19
1352273 GCAACGAGAG
* **
1352283 AATCGCAACGAGAAATGAA
1 AATCGCAACGCGAAACCAA
1352302 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
*
1352321 AATCACAA--CG--A-CAA
1 AATCGCAACGCGAAACCAA
*
1352335 AATCGCAATGCGAAACCAA
1 AATCGCAACGCGAAACCAA
1352354 AATCGCAACGCGAAAC
1 AATCGCAACGCGAAAC
1352370 TATAATCGCG
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 41 0.72
ACGTcount: A:0.49, C:0.26, G:0.16, T:0.08
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:1352397 original size:19 final size:19
Alignment explanation
Indices: 1352375--1352446 Score: 117
Period size: 19 Copynumber: 3.8 Consensus size: 19
1352365 GAAACTATAA
1352375 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTGGTT
1352394 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTGGTT
**
1352413 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTGGTT
*
1352432 TCTCGTTGCGATTTT
1 TCGCGTTGCGATTTT
1352447 CATTTTGTGT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 50 1.00
ACGTcount: A:0.07, C:0.18, G:0.26, T:0.49
Consensus pattern (19 bp):
TCGCGTTGCGATTTTGGTT
Found at i:1352447 original size:19 final size:19
Alignment explanation
Indices: 1352375--1352461 Score: 111
Period size: 19 Copynumber: 4.6 Consensus size: 19
1352365 GAAACTATAA
**
1352375 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
1352394 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
1352413 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1352432 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1352451 TTGTGTTGCGA
1 TCGCGTTGCGA
1352462 AAGTAAACTA
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 62 1.00
ACGTcount: A:0.08, C:0.17, G:0.26, T:0.48
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1352934 original size:21 final size:21
Alignment explanation
Indices: 1352910--1352976 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1352900 TCATTCCTCG
*
1352910 AGAGTCCCCTCCCACCATTCA
1 AGAGTCCACTCCCACCATTCA
* ** * *
1352931 AGAGGCCACTGTCATCATTGA
1 AGAGTCCACTCCCACCATTCA
*
1352952 AGAGGT-CTCTCCCACCATTCA
1 AGA-GTCCACTCCCACCATTCA
1352973 AGAG
1 AGAG
1352977 CCCGATTCAC
Statistics
Matches: 33, Mismatches: 12, Indels: 3
0.69 0.25 0.06
Matches are distributed among these distances:
20 1 0.03
21 31 0.94
22 1 0.03
ACGTcount: A:0.27, C:0.34, G:0.18, T:0.21
Consensus pattern (21 bp):
AGAGTCCACTCCCACCATTCA
Found at i:1352934 original size:42 final size:42
Alignment explanation
Indices: 1352888--1352976 Score: 101
Period size: 42 Copynumber: 2.1 Consensus size: 42
1352878 CCTATCGTTG
* *
1352888 AAGAGGCCCCTATCATTCCTCG-AGA-GTCCCCTCCCACCATTC
1 AAGAGGCCACTATCA-TCATCGAAGAGGT-CCCTCCCACCATTC
* * *
1352930 AAGAGGCCACTGTCATCATTGAAGAGGTCTCTCCCACCATTC
1 AAGAGGCCACTATCATCATCGAAGAGGTCCCTCCCACCATTC
1352972 AAGAG
1 AAGAG
1352977 CCCGATTCAC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
41 4 0.10
42 34 0.85
43 2 0.05
ACGTcount: A:0.26, C:0.35, G:0.18, T:0.21
Consensus pattern (42 bp):
AAGAGGCCACTATCATCATCGAAGAGGTCCCTCCCACCATTC
Found at i:1354358 original size:14 final size:14
Alignment explanation
Indices: 1354326--1354359 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1354316 GATTGTTTAA
1354326 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
* *
1354340 ATGATTTGTAAACG
1 TTGATTTGTAAAAG
1354354 TTGATT
1 TTGATT
1354360 CAATAGTAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.32, C:0.03, G:0.21, T:0.44
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:1354410 original size:84 final size:85
Alignment explanation
Indices: 1354265--1354444 Score: 335
Period size: 84 Copynumber: 2.1 Consensus size: 85
1354255 GTATGGCTGC
1354265 AAAAGTTGATTCAATAGTAGATGAGGAAATAAGAATTATTGCTTATTTTTTGATTGTTTAATTGA
1 AAAAGTTGATTCAATAGTAGATGAGGAAATAAGAATTATTGCTTATTTTTTGATTGTTTAATTGA
1354330 -TTTGTAAAAGATGATTTGT
66 TTTTGTAAAAGATGATTTGT
* *
1354349 AAACGTTGATTCAATAGTAGATGAGGAAATAAGAATTATTGCTTATTTTTTTATTGTTTAATTGA
1 AAAAGTTGATTCAATAGTAGATGAGGAAATAAGAATTATTGCTTATTTTTTGATTGTTTAATTGA
1354414 TTTTGTAAAAGATGATTTGT
66 TTTTGTAAAAGATGATTTGT
1354434 AAAAGTTGATT
1 AAAAGTTGATT
1354445 TGTTTAATTG
Statistics
Matches: 92, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
84 63 0.68
85 29 0.32
ACGTcount: A:0.36, C:0.03, G:0.18, T:0.43
Consensus pattern (85 bp):
AAAAGTTGATTCAATAGTAGATGAGGAAATAAGAATTATTGCTTATTTTTTGATTGTTTAATTGA
TTTTGTAAAAGATGATTTGT
Found at i:1354431 original size:15 final size:15
Alignment explanation
Indices: 1354411--1354445 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
1354401 ATTGTTTAAT
1354411 TGATTTTGTAAAAGA
1 TGATTTTGTAAAAGA
*
1354426 TGA-TTTGTAAAAGT
1 TGATTTTGTAAAAGA
1354440 TGATTT
1 TGATTT
1354446 GTTTAATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (15 bp):
TGATTTTGTAAAAGA
Found at i:1354432 original size:14 final size:14
Alignment explanation
Indices: 1354415--1354447 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1354405 TTTAATTGAT
1354415 TTTGTAAAAGATGA
1 TTTGTAAAAGATGA
*
1354429 TTTGTAAAAGTTGA
1 TTTGTAAAAGATGA
1354443 TTTGT
1 TTTGT
1354448 TTAATTGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.45
Consensus pattern (14 bp):
TTTGTAAAAGATGA
Found at i:1354570 original size:19 final size:19
Alignment explanation
Indices: 1354554--1354670 Score: 119
Period size: 19 Copynumber: 6.7 Consensus size: 19
1354544 AAAAATGACT
1354554 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
1354573 ATCACAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1354587 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1354606 ATCGCAATGCAAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1354625 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
1354639 ATTGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1354658 ATCGCAATGCGAA
1 ATCGCAATGCGAA
1354671 TTAGTTTCGC
Statistics
Matches: 78, Mismatches: 10, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
14 18 0.23
15 2 0.03
16 4 0.05
17 3 0.04
18 2 0.03
19 49 0.63
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1354624 original size:52 final size:52
Alignment explanation
Indices: 1354554--1354667 Score: 201
Period size: 52 Copynumber: 2.2 Consensus size: 52
1354544 AAAAATGACT
*
1354554 ATCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAATGCAAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAA
* *
1354606 ATCGCAATGCAAAATGAAAATCGCAACGAGAGAATTGCAATGCGAAATGAAA
1 ATCGCAATGCAAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAA
1354658 ATCGCAATGC
1 ATCGCAATGC
1354668 GAATTAGTTT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 59 1.00
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (52 bp):
ATCGCAATGCAAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAA
Found at i:1354712 original size:33 final size:33
Alignment explanation
Indices: 1354675--1354788 Score: 174
Period size: 33 Copynumber: 3.4 Consensus size: 33
1354665 TGCGAATTAG
*
1354675 TTTCGCATTGCGATTCTCTCTTTGCGATTTTCA
1 TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
*
1354708 TTTCGCATTGCGATTCTCTCGTTGAGATTTTCA
1 TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
* *
1354741 TTTCGCATTGCGATTCTCTCGTTGCGATTGTAA
1 TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
*
1354774 TTTCCGCGTTGCGAT
1 TTT-CGCATTGCGAT
1354789 AGTCATTAAG
Statistics
Matches: 74, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
33 64 0.86
34 10 0.14
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (33 bp):
TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
Found at i:1354720 original size:19 final size:19
Alignment explanation
Indices: 1354696--1354755 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
1354686 GATTCTCTCT
1354696 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1354715 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
1354729 TTGAGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1354748 TTGCGATT
1 TTGCGATT
1354756 CTCTCGTTGC
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
14 5 0.16
16 7 0.22
17 7 0.22
19 13 0.41
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1354767 original size:14 final size:14
Alignment explanation
Indices: 1354682--1354769 Score: 50
Period size: 14 Copynumber: 5.6 Consensus size: 14
1354672 TAGTTTCGCA
*
1354682 TTGCGATTCTCTCT
1 TTGCGATTCTCTCG
*
1354696 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
1354713 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
* *
1354729 TTGAGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
1354746 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
1354762 TTGCGATT
1 TTGCGATT
1354770 GTAATTTCCG
Statistics
Matches: 57, Mismatches: 7, Indels: 20
0.68 0.08 0.24
Matches are distributed among these distances:
14 19 0.33
16 14 0.25
17 13 0.23
19 11 0.19
ACGTcount: A:0.12, C:0.23, G:0.18, T:0.47
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:1355966 original size:20 final size:20
Alignment explanation
Indices: 1355939--1356069 Score: 131
Period size: 20 Copynumber: 6.5 Consensus size: 20
1355929 TTAAAAATCG
*
1355939 CGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACT
* * **
1355959 CATTGCGATTTTACGTATTGT
1 CGTTGCGA-TTTACGGATACT
*
1355980 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACT
* **
1356000 CGTTGCGATTTTACGTATTGT
1 CGTTGCGA-TTTACGGATACT
1356021 CGTTGCGATTTACGGATA--
1 CGTTGCGATTTACGGATACT
1356039 CGTTGCGATTTTTACGGATACT
1 CGTTGCGA--TTTACGGATACT
1356061 CGTTGCGAT
1 CGTTGCGAT
1356070 AGTAAGAATC
Statistics
Matches: 89, Mismatches: 16, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
18 8 0.09
20 42 0.47
21 31 0.35
22 8 0.09
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
CGTTGCGATTTACGGATACT
Found at i:1355996 original size:41 final size:41
Alignment explanation
Indices: 1355939--1356069 Score: 194
Period size: 41 Copynumber: 3.2 Consensus size: 41
1355929 TTAAAAATCG
*
1355939 CGTTGCGATTTACGGATACACATTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACACGTTGCGATTTTACGTATTGT
*
1355980 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACACGTTGCGATTTTACGTATTGT
* **
1356021 CGTTGCGATTTACGGAT--ACGTTGCGATTTTTACGGATACT
1 CGTTGCGATTTACGGATACACGTTGCGA-TTTTACGTATTGT
1356061 CGTTGCGAT
1 CGTTGCGAT
1356070 AGTAAGAATC
Statistics
Matches: 83, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
39 8 0.10
40 19 0.23
41 56 0.67
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACACGTTGCGATTTTACGTATTGT
Found at i:1356101 original size:20 final size:20
Alignment explanation
Indices: 1356078--1356130 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
1356068 ATAGTAAGAA
*
1356078 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
*
1356098 TCGCATTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
1356118 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1356131 CTTGAAAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.15, C:0.19, G:0.23, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:1367322 original size:30 final size:30
Alignment explanation
Indices: 1367282--1367346 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
1367272 AATCGGTAAA
* *
1367282 GAACCGGCTGAGAACCGACAAAACCGGGGT
1 GAACCAGCTGAAAACCGACAAAACCGGGGT
** *
1367312 GAACCAGCTGAAAACCGGTAAAACCGGTGT
1 GAACCAGCTGAAAACCGACAAAACCGGGGT
1367342 GAACC
1 GAACC
1367347 GCCGGTTCTC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.35, C:0.26, G:0.29, T:0.09
Consensus pattern (30 bp):
GAACCAGCTGAAAACCGACAAAACCGGGGT
Found at i:1367602 original size:24 final size:25
Alignment explanation
Indices: 1367566--1367612 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
1367556 AAACTCAAAA
*
1367566 AAAATTAGAAGCTCGATTGAAGCCT
1 AAAATTAGAAGCTCAATTGAAGCCT
*
1367591 AAAATTCG-AGCTCAATTGAAGC
1 AAAATTAGAAGCTCAATTGAAGC
1367613 GAAAGAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.23
Consensus pattern (25 bp):
AAAATTAGAAGCTCAATTGAAGCCT
Found at i:1370784 original size:24 final size:24
Alignment explanation
Indices: 1370756--1370809 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1370746 CGTTCGATAA
* *
1370756 TATGTTCGTTTATTTATGTTCATT
1 TATGTTCGTTTATGTACGTTCATT
*
1370780 TATGTTCGTTTATGTCCGTTCATT
1 TATGTTCGTTTATGTACGTTCATT
1370804 TATGTT
1 TATGTT
1370810 TAGCCCAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.15, C:0.11, G:0.15, T:0.59
Consensus pattern (24 bp):
TATGTTCGTTTATGTACGTTCATT
Found at i:1371026 original size:23 final size:23
Alignment explanation
Indices: 1370995--1371083 Score: 72
Period size: 23 Copynumber: 3.8 Consensus size: 23
1370985 GTTTGTTTAC
* *
1370995 GTTCGTTTATGTTCATTTATTGT
1 GTTCATTTACGTTCATTTATTGT
*
1371018 GTTCATTTACGTTCGTTCGT-TTGT
1 GTTCATTTACGTTCATT--TATTGT
** *
1371042 GTTGGTTTACGTTCATTTATTTT
1 GTTCATTTACGTTCATTTATTGT
* * *
1371065 GTTCACTTATGTTCGTTTA
1 GTTCATTTACGTTCATTTA
1371084 CATCCATTCG
Statistics
Matches: 51, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
22 1 0.02
23 31 0.61
24 18 0.35
25 1 0.02
ACGTcount: A:0.12, C:0.12, G:0.18, T:0.57
Consensus pattern (23 bp):
GTTCATTTACGTTCATTTATTGT
Found at i:1379785 original size:32 final size:33
Alignment explanation
Indices: 1379718--1379811 Score: 163
Period size: 32 Copynumber: 2.9 Consensus size: 33
1379708 TGTTCAAAGT
1379718 TTGGCCACCAACCAAGATGAAATTTCCAATAAG
1 TTGGCCACCAACCAAGATGAAATTTCCAATAAG
*
1379751 TTGGCCACCAACCAAGATGAAA-TTCCAATGAG
1 TTGGCCACCAACCAAGATGAAATTTCCAATAAG
*
1379783 TTGGCCACTAACCAAGATGAAATTTCCAA
1 TTGGCCACCAACCAAGATGAAATTTCCAA
1379812 CTTGTCAACT
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
32 30 0.52
33 28 0.48
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.21
Consensus pattern (33 bp):
TTGGCCACCAACCAAGATGAAATTTCCAATAAG
Found at i:1385991 original size:10 final size:10
Alignment explanation
Indices: 1385976--1386006 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
1385966 TATGTTTTGG
1385976 TCAGAAATCA
1 TCAGAAATCA
1385986 TCAGAAATCA
1 TCAGAAATCA
1385996 TCAGAAATCA
1 TCAGAAATCA
1386006 T
1 T
1386007 TATTTCAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.48, C:0.19, G:0.10, T:0.23
Consensus pattern (10 bp):
TCAGAAATCA
Found at i:1397489 original size:23 final size:24
Alignment explanation
Indices: 1397463--1397520 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
1397453 TTATTATTTA
*
1397463 ATTAATTAGGATTTT-AGTTTGCT
1 ATTAATTAGGATTTTAAGATTGCT
*
1397486 ATTACTTAGGATTTTAAGATTGCT
1 ATTAATTAGGATTTTAAGATTGCT
1397510 ATTAATTAGGA
1 ATTAATTAGGA
1397521 CTTAAGTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
23 14 0.45
24 17 0.55
ACGTcount: A:0.31, C:0.05, G:0.17, T:0.47
Consensus pattern (24 bp):
ATTAATTAGGATTTTAAGATTGCT
Found at i:1397572 original size:18 final size:18
Alignment explanation
Indices: 1397549--1397610 Score: 54
Period size: 18 Copynumber: 3.5 Consensus size: 18
1397539 CTTAGGATCA
1397549 TCTTTAAGTATTTTATTT
1 TCTTTAAGTATTTTATTT
* * * *
1397567 TCTTTAGGT-TTTAAATC
1 TCTTTAAGTATTTTATTT
* *
1397584 CCTTTAGGTATTTTATTT
1 TCTTTAAGTATTTTATTT
*
1397602 TCTGTAAGT
1 TCTTTAAGT
1397611 CTTCTCAAGC
Statistics
Matches: 32, Mismatches: 11, Indels: 2
0.71 0.24 0.04
Matches are distributed among these distances:
17 13 0.41
18 19 0.59
ACGTcount: A:0.21, C:0.10, G:0.11, T:0.58
Consensus pattern (18 bp):
TCTTTAAGTATTTTATTT
Found at i:1402266 original size:46 final size:46
Alignment explanation
Indices: 1402213--1402306 Score: 143
Period size: 46 Copynumber: 2.0 Consensus size: 46
1402203 TTTGTTGATA
* * *
1402213 TTGTGTTGTATTTGGTGGTGTTAATATTTTATATCTTATAATTATG
1 TTGTGTTGTATTAGCTGATGTTAATATTTTATATCTTATAATTATG
* *
1402259 TTGTGTTGTATTAGCTGATGTTAGTATTTTATATCTTATAATTGTG
1 TTGTGTTGTATTAGCTGATGTTAATATTTTATATCTTATAATTATG
1402305 TT
1 TT
1402307 ATGACAAGGG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.21, C:0.03, G:0.19, T:0.56
Consensus pattern (46 bp):
TTGTGTTGTATTAGCTGATGTTAATATTTTATATCTTATAATTATG
Found at i:1408970 original size:24 final size:26
Alignment explanation
Indices: 1408930--1408996 Score: 77
Period size: 24 Copynumber: 2.7 Consensus size: 26
1408920 AAGATAGTGT
* *
1408930 TAAG-AAAAATATATATAATCAAAAG
1 TAAGTAAATATATATATAAACAAAAG
* *
1408955 T-A-TATATATATATATAAACAAATG
1 TAAGTAAATATATATATAAACAAAAG
1408979 TAAGTAAATATATATATA
1 TAAGTAAATATATATATA
1408997 TATATGTGTG
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
24 19 0.56
25 2 0.06
26 13 0.38
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (26 bp):
TAAGTAAATATATATATAAACAAAAG
Found at i:1414531 original size:15 final size:15
Alignment explanation
Indices: 1414499--1414542 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
1414489 ATCGTTTTTC
*
1414499 TTCTTTTATTTA--T
1 TTCTTTTCTTTATCT
1414512 TTCTTTTCTTTATCT
1 TTCTTTTCTTTATCT
*
1414527 TTCTTTTCTTGATCT
1 TTCTTTTCTTTATCT
1414542 T
1 T
1414543 ATTTTTCACC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
13 11 0.41
15 16 0.59
ACGTcount: A:0.09, C:0.16, G:0.02, T:0.73
Consensus pattern (15 bp):
TTCTTTTCTTTATCT
Found at i:1418540 original size:91 final size:91
Alignment explanation
Indices: 1418431--1418617 Score: 277
Period size: 91 Copynumber: 2.1 Consensus size: 91
1418421 AGAAGAAACC
* * *
1418431 AATTTTATGTTTCAATGGAGGAAAATTGGAGGAAATGAGCGGGTAATTAAAAAAACTCTAAATTT
1 AATTTTATGTTTCAATGGAGGAAAATTGGAGGAAATGAGCCGGCAATTAAAAAAACACTAAATTT
* *
1418496 TGTGA-GAAACAAGTGGACCCGTCTCA
66 TATGACGAAACAAGT-GACCCGTCACA
* *
1418522 AATTTTATGTTTCAATGGAGGGAAATTGGAGGTAATGAGCCGGCAATTAAAAAAACACTAAATTT
1 AATTTTATGTTTCAATGGAGGAAAATTGGAGGAAATGAGCCGGCAATTAAAAAAACACTAAATTT
* *
1418587 TATGACGGAACATGTGACCCGTCACA
66 TATGACGAAACAAGTGACCCGTCACA
1418613 AATTT
1 AATTT
1418618 GTGATGGTAC
Statistics
Matches: 86, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
91 79 0.92
92 7 0.08
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (91 bp):
AATTTTATGTTTCAATGGAGGAAAATTGGAGGAAATGAGCCGGCAATTAAAAAAACACTAAATTT
TATGACGAAACAAGTGACCCGTCACA
Found at i:1419574 original size:14 final size:12
Alignment explanation
Indices: 1419536--1419570 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
1419526 AGATTAGTGA
1419536 AATTTTAAATATT
1 AATTTTAAAT-TT
1419549 AATTTTAAATTT
1 AATTTTAAATTT
1419561 ATATTTTAAA
1 A-ATTTTAAA
1419571 ATTTTTCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 3 0.14
13 18 0.86
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
AATTTTAAATTT
Found at i:1419714 original size:19 final size:20
Alignment explanation
Indices: 1419686--1419727 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1419676 TGCATGCAAA
* *
1419686 AATATTTTTTTTA-CTTTTT
1 AATATATTTTGTAGCTTTTT
1419705 AATATATTTTGTAGCTTTTT
1 AATATATTTTGTAGCTTTTT
1419725 AAT
1 AAT
1419728 TAATAGTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.64
Consensus pattern (20 bp):
AATATATTTTGTAGCTTTTT
Found at i:1420262 original size:30 final size:28
Alignment explanation
Indices: 1420206--1420272 Score: 77
Period size: 30 Copynumber: 2.4 Consensus size: 28
1420196 TAAAATTACA
1420206 ATATA-AAATAAAATAAAAAAGATAAAT
1 ATATATAAATAAAATAAAAAAGATAAAT
1420233 -TCATATAAATAAAA-AAAGTAAAGGATAAAT
1 AT-ATATAAATAAAATAAA--AAA-GATAAAT
1420263 ATATATAAAT
1 ATATATAAAT
1420273 CATTATATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
26 1 0.03
27 6 0.18
28 8 0.24
29 3 0.09
30 15 0.44
31 1 0.03
ACGTcount: A:0.67, C:0.01, G:0.06, T:0.25
Consensus pattern (28 bp):
ATATATAAATAAAATAAAAAAGATAAAT
Found at i:1422710 original size:30 final size:31
Alignment explanation
Indices: 1422646--1422711 Score: 75
Period size: 32 Copynumber: 2.1 Consensus size: 31
1422636 ATAAAATATT
*
1422646 ATATTATATTTTTAAAAATATTAATGATTTAA
1 ATATTATATTTTTAAAAATATTAA-GATTAAA
1422678 ATATTATCA-TTTTAAATAA-ATTAA-ATTAAA
1 ATATTAT-ATTTTTAAA-AATATTAAGATTAAA
1422708 ATAT
1 ATAT
1422712 ATTTTAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
30 9 0.29
32 19 0.61
33 3 0.10
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (31 bp):
ATATTATATTTTTAAAAATATTAAGATTAAA
Found at i:1422869 original size:21 final size:22
Alignment explanation
Indices: 1422819--1422870 Score: 86
Period size: 22 Copynumber: 2.3 Consensus size: 22
1422809 GACATTATTT
*
1422819 TTTTTATTAAAGTAGATGTGACA
1 TTTTT-TTAAAGTAGATGTAACA
1422842 TTTTTTTAAAGTAGATGTAACA
1 TTTTTTTAAAGTAGATGTAACA
1422864 TTTTTTT
1 TTTTTTT
1422871 TTGTCAAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 23 0.82
23 5 0.18
ACGTcount: A:0.31, C:0.04, G:0.13, T:0.52
Consensus pattern (22 bp):
TTTTTTTAAAGTAGATGTAACA
Found at i:1422992 original size:19 final size:21
Alignment explanation
Indices: 1422968--1423006 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
1422958 TACCATCAAT
*
1422968 ATTTATTA-ATTTTT-CTTTA
1 ATTTATCATATTTTTACTTTA
1422987 ATTTATCATATTTTTACTTT
1 ATTTATCATATTTTTACTTT
1423007 TTTCTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 6 0.35
21 4 0.24
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.67
Consensus pattern (21 bp):
ATTTATCATATTTTTACTTTA
Found at i:1430111 original size:13 final size:13
Alignment explanation
Indices: 1430093--1430125 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
1430083 ATCGGTTCGA
1430093 GTTGACCCGACCC
1 GTTGACCCGACCC
1430106 GTTGACCCGACCC
1 GTTGACCCGACCC
1430119 GTTGACC
1 GTTGACC
1430126 GTTGATTTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.15, C:0.42, G:0.24, T:0.18
Consensus pattern (13 bp):
GTTGACCCGACCC
Found at i:1430859 original size:15 final size:15
Alignment explanation
Indices: 1430839--1430871 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1430829 TGATACGTGA
1430839 TTCCTGAATAT-TGAT
1 TTCCTG-ATATCTGAT
1430854 TTCCTGATATCTGAT
1 TTCCTGATATCTGAT
1430869 TTC
1 TTC
1430872 TGTATTTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.21, C:0.18, G:0.12, T:0.48
Consensus pattern (15 bp):
TTCCTGATATCTGAT
Found at i:1435647 original size:5 final size:5
Alignment explanation
Indices: 1435637--1435667 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
1435627 CAGTGAAGAA
1435637 AAAAG AAAAG AAAAG AAAAG AAAAG AGAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG A-AAAG
1435668 GGAGAAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 21 0.84
6 4 0.16
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:1436422 original size:30 final size:31
Alignment explanation
Indices: 1436372--1436446 Score: 107
Period size: 32 Copynumber: 2.4 Consensus size: 31
1436362 TTATTTATGG
1436372 TTTAGTCCTTTAAATTTCTA-TTTTTACTAT
1 TTTAGTCCTTTAAATTTCTATTTTTTACTAT
* * *
1436402 TTTATTCCCTTAAGTTTCTATTTTTTTACTAT
1 TTTAGTCCTTTAAATTTCTA-TTTTTTACTAT
1436434 TTTAGTCCTTTAA
1 TTTAGTCCTTTAA
1436447 TTTTGTTTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
30 17 0.45
32 21 0.55
ACGTcount: A:0.21, C:0.15, G:0.04, T:0.60
Consensus pattern (31 bp):
TTTAGTCCTTTAAATTTCTATTTTTTACTAT
Found at i:1436457 original size:19 final size:21
Alignment explanation
Indices: 1436433--1436476 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 21
1436423 TTTTTTACTA
*
1436433 TTTTAGTCCTTT-AATTT-TG
1 TTTTAGTCATTTAAATTTATG
1436452 TTTTAGTCATTTAAATTTATG
1 TTTTAGTCATTTAAATTTATG
1436473 TTTT
1 TTTT
1436477 TACTATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.50
20 5 0.23
21 6 0.27
ACGTcount: A:0.20, C:0.07, G:0.09, T:0.64
Consensus pattern (21 bp):
TTTTAGTCATTTAAATTTATG
Found at i:1437516 original size:24 final size:25
Alignment explanation
Indices: 1437459--1437516 Score: 77
Period size: 24 Copynumber: 2.4 Consensus size: 25
1437449 CAAATCACCA
1437459 TTTTTCAAAATAAAAGTCATAATTG
1 TTTTTCAAAATAAAAGTCATAATTG
*
1437484 TTTTT-AAAATAACA-TC-TAATTG
1 TTTTTCAAAATAAAAGTCATAATTG
1437506 TTTTATCAAAA
1 TTTT-TCAAAA
1437517 AATGGTTATG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 10 0.33
23 3 0.10
24 12 0.40
25 5 0.17
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.43
Consensus pattern (25 bp):
TTTTTCAAAATAAAAGTCATAATTG
Found at i:1439172 original size:30 final size:30
Alignment explanation
Indices: 1439131--1439198 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
1439121 TTTTTCCATA
* *
1439131 GGTCACCATGTC-TTCTGAATAACCTACGTT
1 GGTCGCCATGTCTTTC-GAATAACCTACATT
* *
1439161 GGTTGCCATGTCTTTCGAATGACCTACATT
1 GGTCGCCATGTCTTTCGAATAACCTACATT
1439191 GGTCGCCA
1 GGTCGCCA
1439199 AGTGGTTGCA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 29 0.91
31 3 0.09
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (30 bp):
GGTCGCCATGTCTTTCGAATAACCTACATT
Found at i:1439280 original size:29 final size:30
Alignment explanation
Indices: 1439248--1439319 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
1439238 CATGCACACT
* * *
1439248 AGGTCGTCGTGTGCTCAATGCGACC-ATGG
1 AGGTCGCCATGTGCTCAATGCGACCTATGA
**
1439277 AGGTCGCCATGTGCTCCTTGCGACCTATGA
1 AGGTCGCCATGTGCTCAATGCGACCTATGA
1439307 AGGTCGCCATGTG
1 AGGTCGCCATGTG
1439320 ATCCCGGCGA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 21 0.57
30 16 0.43
ACGTcount: A:0.17, C:0.26, G:0.32, T:0.25
Consensus pattern (30 bp):
AGGTCGCCATGTGCTCAATGCGACCTATGA
Found at i:1439330 original size:30 final size:29
Alignment explanation
Indices: 1439267--1439332 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 29
1439257 TGTGCTCAAT
* * **
1439267 GCGACCATGGAGGTCGCCATGTGCTCCTT
1 GCGACCATGAAGGTCGCCATGTGATCCCG
1439296 GCGACCTATGAAGGTCGCCATGTGATCCCG
1 GCGACC-ATGAAGGTCGCCATGTGATCCCG
1439326 GCGACCA
1 GCGACCA
1439333 AGCTTGTTCC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 7 0.22
30 25 0.78
ACGTcount: A:0.18, C:0.32, G:0.30, T:0.20
Consensus pattern (29 bp):
GCGACCATGAAGGTCGCCATGTGATCCCG
Found at i:1439542 original size:20 final size:20
Alignment explanation
Indices: 1439517--1439565 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
1439507 AACGGTTGTA
1439517 AGAAGAAAGAAAGGAAAGGG
1 AGAAGAAAGAAAGGAAAGGG
1439537 AGAAGAAAGAAAGGAAAGGG
1 AGAAGAAAGAAAGGAAAGGG
*
1439557 AGACGAAAG
1 AGAAGAAAG
1439566 TGAGATAGGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.59, C:0.02, G:0.39, T:0.00
Consensus pattern (20 bp):
AGAAGAAAGAAAGGAAAGGG
Found at i:1442345 original size:22 final size:20
Alignment explanation
Indices: 1442291--1442353 Score: 83
Period size: 20 Copynumber: 3.0 Consensus size: 20
1442281 ATGTAAAAAG
1442291 AATA-AATTCGACTATTATA
1 AATATAATTCGACTATTATA
1442310 AATATAATTCGACTATTATA
1 AATATAATTCGACTATTATA
*
1442330 AATAATTAATTTGACTATTTATA
1 AAT-A-TAATTCGACTA-TTATA
1442353 A
1 A
1442354 TTCGATTTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
19 4 0.10
20 18 0.46
21 1 0.03
22 10 0.26
23 6 0.15
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (20 bp):
AATATAATTCGACTATTATA
Found at i:1442568 original size:64 final size:65
Alignment explanation
Indices: 1442500--1442625 Score: 204
Period size: 65 Copynumber: 2.0 Consensus size: 65
1442490 ATATTATTTT
1442500 AAAAATAGGTTATTA-CA-AAATCAAATTTATAAATAC-TAGAAATACATAAATTTTATAAATTT
1 AAAAATAGGTTATTATCACAAATCAAA--TATAAATACATAGAAATACATAAATTTTATAAATTT
1442562 AA
64 AA
*
1442564 AAAAATAGGTTATTATTACAAATCAAATATAAATACATAGAAATACATAAATTTTATAAATT
1 AAAAATAGGTTATTATCACAAATCAAATATAAATACATAGAAATACATAAATTTTATAAATT
1442626 CGATTTAAAT
Statistics
Matches: 58, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
64 24 0.41
65 26 0.45
66 8 0.14
ACGTcount: A:0.55, C:0.06, G:0.05, T:0.34
Consensus pattern (65 bp):
AAAAATAGGTTATTATCACAAATCAAATATAAATACATAGAAATACATAAATTTTATAAATTTAA
Found at i:1442850 original size:10 final size:10
Alignment explanation
Indices: 1442835--1442859 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1442825 AAAATCAAAT
1442835 ATATAAATAC
1 ATATAAATAC
1442845 ATATAAATAC
1 ATATAAATAC
1442855 ATATA
1 ATATA
1442860 TGATTACTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (10 bp):
ATATAAATAC
Found at i:1445414 original size:30 final size:29
Alignment explanation
Indices: 1445295--1445414 Score: 140
Period size: 30 Copynumber: 4.0 Consensus size: 29
1445285 ACTAATTTTT
*
1445295 TATATATATAACTTAAACTAAACAAATATAA
1 TATA-ATATAACTTAAACT-AACAACTATAA
1445326 TATAATATAACTTAAACTAGAAACAACTAT-A
1 TATAATATAACTTAAACT---AACAACTATAA
1445357 -ATAATAT-ACTTAAACT-ACAACCTATAA
1 TATAATATAACTTAAACTAACAA-CTATAA
1445384 TATAATATAACTTAAACTAACAACTAATAA
1 TATAATATAACTTAAACTAACAACT-ATAA
1445414 T
1 T
1445415 TACCAATTAC
Statistics
Matches: 80, Mismatches: 1, Indels: 17
0.82 0.01 0.17
Matches are distributed among these distances:
25 4 0.05
26 4 0.05
27 1 0.01
28 7 0.09
29 20 0.25
30 30 0.38
31 5 0.06
32 9 0.11
ACGTcount: A:0.55, C:0.13, G:0.01, T:0.31
Consensus pattern (29 bp):
TATAATATAACTTAAACTAACAACTATAA
Found at i:1445476 original size:19 final size:20
Alignment explanation
Indices: 1445429--1445481 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
1445419 AATTACCCGA
* *
1445429 TCCTTTC-TTCTTATTCCTT
1 TCCTTTCTTTCTTCTCCCTT
1445448 TCCTTTCTTTCTTCTCCCTT
1 TCCTTTCTTTCTTCTCCCTT
1445468 T-CTTTCTTTCTTCT
1 TCCTTTCTTTCTTCT
1445482 AATTTTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 20 0.65
20 11 0.35
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.64
Consensus pattern (20 bp):
TCCTTTCTTTCTTCTCCCTT
Found at i:1445492 original size:19 final size:19
Alignment explanation
Indices: 1445445--1445494 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
1445435 CTTCTTATTC
**
1445445 CTTTCCTTTCTTTCTTCTCC
1 CTTT-CTTTCTTTCTTCTAA
1445465 CTTTCTTTCTTTCTTCTAA
1 CTTTCTTTCTTTCTTCTAA
* *
1445484 TTTTTTTTCTT
1 CTTTCTTTCTT
1445495 CATTCCCGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 22 0.85
20 4 0.15
ACGTcount: A:0.04, C:0.28, G:0.00, T:0.68
Consensus pattern (19 bp):
CTTTCTTTCTTTCTTCTAA
Found at i:1450132 original size:29 final size:28
Alignment explanation
Indices: 1450099--1450312 Score: 185
Period size: 29 Copynumber: 7.6 Consensus size: 28
1450089 GATTAACATT
*
1450099 TTACACAATTATCACTCTTTTAAAAATAA
1 TTACA-AAATATCACTCTTTTAAAAATAA
1450128 TTACAAAACTATCAC-CTTCTTAAAAATAA
1 TTACAAAA-TATCACTCTT-TTAAAAATAA
* * *
1450157 TTATGAAAATATCACATATTTTCAAAATAA
1 TTA-CAAAATATCAC-TCTTTTAAAAATAA
*
1450187 TTACTAAAATATCACT-TTTTTAAAA-AA
1 TTAC-AAAATATCACTCTTTTAAAAATAA
*
1450214 TTACGAAATTATCAC-CTTTT--AAA-AA
1 TTAC-AAAATATCACTCTTTTAAAAATAA
* * *
1450239 TTACGAAAATAGC-CCCATTTTCAAAATAA
1 TTAC-AAAATATCACTC-TTTTAAAAATAA
1450268 TTACCAAAATATCAC-CATTTTAAAAATAA
1 TTA-CAAAATATCACTC-TTTTAAAAATAA
1450297 TTACAAAATATCACTC
1 TTACAAAATATCACTC
1450313 GGTCAACGGT
Statistics
Matches: 158, Mismatches: 12, Indels: 30
0.79 0.06 0.15
Matches are distributed among these distances:
24 1 0.01
25 17 0.11
26 4 0.03
27 19 0.12
28 27 0.17
29 60 0.38
30 28 0.18
31 2 0.01
ACGTcount: A:0.47, C:0.17, G:0.02, T:0.34
Consensus pattern (28 bp):
TTACAAAATATCACTCTTTTAAAAATAA
Found at i:1457415 original size:29 final size:29
Alignment explanation
Indices: 1457383--1457580 Score: 224
Period size: 29 Copynumber: 6.9 Consensus size: 29
1457373 ATTATAACCC
* * *
1457383 TTTTAAAAATAATTACGAAACTAACATCTT
1 TTTTAAAAATAATTACGAAAATATCA-CCT
1457413 TTTTAAAAATAATTACGAAAATATCACCT
1 TTTTAAAAATAATTACGAAAATATCACCT
* * *
1457442 TTTTCAAAATAATTACTAAAATAT-AACT
1 TTTTAAAAATAATTACGAAAATATCACCT
* *
1457470 TTTTTAAAA-AATTACGAAATTATCA-CT
1 TTTTAAAAATAATTACGAAAATATCACCT
* * *
1457497 TTTTAAAAA-AATTACAAAAATAGCACCA
1 TTTTAAAAATAATTACGAAAATATCACCT
* * *
1457525 TTTTCAAAATAATTACCAAAATATCACCA
1 TTTTAAAAATAATTACGAAAATATCACCT
*
1457554 TTTTAAAAATAATTACAAAAATATCAC
1 TTTTAAAAATAATTACGAAAATATCAC
1457581 TCGATCAACG
Statistics
Matches: 146, Mismatches: 19, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
27 35 0.24
28 21 0.14
29 66 0.45
30 24 0.16
ACGTcount: A:0.50, C:0.14, G:0.02, T:0.34
Consensus pattern (29 bp):
TTTTAAAAATAATTACGAAAATATCACCT
Found at i:1457533 original size:83 final size:86
Alignment explanation
Indices: 1457383--1457581 Score: 260
Period size: 83 Copynumber: 2.3 Consensus size: 86
1457373 ATTATAACCC
* * * * *
1457383 TTTTAAAAATAATTACGAAACTAACATCTTTTTTAAAAATAATTACGAAAATATCACCTTTTTCA
1 TTTTAAAAATAATTACGAAAATATCA-C-TTTTTAAAAATAATTACAAAAATAGCACCATTTTCA
* *
1457448 AAATAATTACTAAAATAT-AACT
64 AAATAATTACCAAAATATCAACA
* *
1457470 TTTTTAAAA-AATTACGAAATTATCACTTTTTAAAAA-AATTACAAAAATAGCACCATTTTCAAA
1 TTTTAAAAATAATTACGAAAATATCACTTTTTAAAAATAATTACAAAAATAGCACCATTTTCAAA
*
1457533 ATAATTACCAAAATATCACCA
66 ATAATTACCAAAATATCAACA
*
1457554 TTTTAAAAATAATTACAAAAATATCACT
1 TTTTAAAAATAATTACGAAAATATCACT
1457582 CGATCAACGG
Statistics
Matches: 98, Mismatches: 12, Indels: 6
0.84 0.10 0.05
Matches are distributed among these distances:
83 39 0.40
84 20 0.20
85 17 0.17
86 14 0.14
87 8 0.08
ACGTcount: A:0.50, C:0.14, G:0.02, T:0.35
Consensus pattern (86 bp):
TTTTAAAAATAATTACGAAAATATCACTTTTTAAAAATAATTACAAAAATAGCACCATTTTCAAA
ATAATTACCAAAATATCAACA
Found at i:1457539 original size:56 final size:56
Alignment explanation
Indices: 1457413--1457576 Score: 197
Period size: 56 Copynumber: 2.9 Consensus size: 56
1457403 CTAACATCTT
* * * *
1457413 TTTTAAAAATAATTACGAAAATATCACCTTTTTCAAAATAATTACTAAAATATAACT
1 TTTTAAAAATAATTACGAAAATATCACCTTTTT-AAAAAAATTACAAAAATACAACA
* * *
1457470 TTTTTAAAA-AATTACGAAATTATCA-CTTTTTAAAAAAATTACAAAAATAGCACCA
1 TTTTAAAAATAATTACGAAAATATCACCTTTTTAAAAAAATTACAAAAATA-CAACA
* * *
1457525 TTTTCAAAATAATTACCAAAATATCACCATTTTAAAAATAATTACAAAAATA
1 TTTTAAAAATAATTACGAAAATATCACCTTTTTAAAAA-AATTACAAAAATA
1457577 TCACTCGATC
Statistics
Matches: 92, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
54 16 0.17
55 16 0.17
56 29 0.32
57 18 0.20
58 13 0.14
ACGTcount: A:0.51, C:0.13, G:0.02, T:0.34
Consensus pattern (56 bp):
TTTTAAAAATAATTACGAAAATATCACCTTTTTAAAAAAATTACAAAAATACAACA
Found at i:1460836 original size:22 final size:22
Alignment explanation
Indices: 1460794--1460837 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1460784 TTAATTTCTG
*
1460794 TTTGGGTGCTATTTGTGTAAAT
1 TTTGGGTGCTATTTGTATAAAT
*
1460816 TTTGGGTGTTAGTTT-TATAAAT
1 TTTGGGTGCTA-TTTGTATAAAT
1460838 ATTTACAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.20, C:0.02, G:0.25, T:0.52
Consensus pattern (22 bp):
TTTGGGTGCTATTTGTATAAAT
Found at i:1462218 original size:17 final size:18
Alignment explanation
Indices: 1462196--1462229 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1462186 TTGAAAGGTC
*
1462196 TGGAA-TAAATGATAAGT
1 TGGAATTAAATAATAAGT
1462213 TGGAATTAAATAATAAG
1 TGGAATTAAATAATAAG
1462230 ACAGAATGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (18 bp):
TGGAATTAAATAATAAGT
Found at i:1463560 original size:2 final size:2
Alignment explanation
Indices: 1463555--1463580 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1463545 TATATATATA
1463555 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
1463581 CTTTAAAAAA
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1464352 original size:20 final size:20
Alignment explanation
Indices: 1464327--1464370 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
1464317 CTGGCGACCA
1464327 ACCCTTAAACTGTAACAAAC
1 ACCCTTAAACTGTAACAAAC
*
1464347 ACCCTTGAACTGTAACAAAC
1 ACCCTTAAACTGTAACAAAC
1464367 ACCC
1 ACCC
1464371 CAAATGAGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.41, C:0.34, G:0.07, T:0.18
Consensus pattern (20 bp):
ACCCTTAAACTGTAACAAAC
Found at i:1466912 original size:26 final size:26
Alignment explanation
Indices: 1466882--1466934 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
1466872 CAACAACCAA
1466882 AGAAAGGATTTAATCCTTTGCAAACC
1 AGAAAGGATTTAATCCTTTGCAAACC
*
1466908 AGAAAGGTTTTAATCCTTTGCAAACC
1 AGAAAGGATTTAATCCTTTGCAAACC
1466934 A
1 A
1466935 CGATATTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (26 bp):
AGAAAGGATTTAATCCTTTGCAAACC
Found at i:1467262 original size:22 final size:22
Alignment explanation
Indices: 1467217--1467261 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
1467207 TTTTATTATA
* *
1467217 TATATTTTAAATTTAATATTTT
1 TATATTTTAAACTAAATATTTT
1467239 TATATTTTAAAACTAAATATTTT
1 TATATTTT-AAACTAAATATTTT
1467262 AATTATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
TATATTTTAAACTAAATATTTT
Found at i:1467321 original size:21 final size:22
Alignment explanation
Indices: 1467296--1467341 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
1467286 ATTTAAGATT
1467296 TTTAAAATAT-AAAATCTTAAA
1 TTTAAAATATAAAAATCTTAAA
*
1467317 TTTAAAATATAAAAATCTTATA
1 TTTAAAATATAAAAATCTTAAA
1467339 TTT
1 TTT
1467342 TTAATTATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTAAAATATAAAAATCTTAAA
Found at i:1469075 original size:15 final size:14
Alignment explanation
Indices: 1469038--1469078 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
1469028 AAGGTAAAAC
1469038 TATTT-TTTA-TTA
1 TATTTATTTATTTA
1469050 TATTATATTTATTTCA
1 TATT-TATTTATTT-A
1469066 TATTTATTTATTT
1 TATTTATTTATTT
1469079 GACCAAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 4 0.16
13 1 0.04
14 4 0.16
15 11 0.44
16 5 0.20
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (14 bp):
TATTTATTTATTTA
Found at i:1470393 original size:18 final size:18
Alignment explanation
Indices: 1470366--1470400 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1470356 GTATACAAAT
* *
1470366 TAAAATATAAATTAATAC
1 TAAAAAATAAATAAATAC
1470384 TAAAAAATAAATAAATA
1 TAAAAAATAAATAAATA
1470401 AAATATTCAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAAAAATAAATAAATAC
Done.