Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009639.1 Hibiscus syriacus cultivar Beakdansim tig00117048_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: 15077257
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 59 of 62
Found at i:14310561 original size:20 final size:19
Alignment explanation
Indices: 14310497--14310581 Score: 59
Period size: 20 Copynumber: 4.4 Consensus size: 19
14310487 TATATATTTA
* *
14310497 TTATTTTATATATTTCAT-T
1 TTATTTT-TATTTTTTATCT
14310516 TTATCTTTTATTTTTTATCT
1 TTAT-TTTTATTTTTTATCT
14310536 TCTATTTTTATTTTTGTAT-T
1 T-TATTTTTATTTTT-TATCT
* * *
14310556 GTTATTGTTATTATCT-TCT
1 -TTATTTTTATTTTTTATCT
14310575 TTATTTT
1 TTATTTT
14310582 CTGTATTTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
18 7 0.13
19 14 0.26
20 26 0.48
21 7 0.13
ACGTcount: A:0.18, C:0.07, G:0.04, T:0.72
Consensus pattern (19 bp):
TTATTTTTATTTTTTATCT
Found at i:14311794 original size:236 final size:237
Alignment explanation
Indices: 14311281--14311797 Score: 738
Period size: 237 Copynumber: 2.2 Consensus size: 237
14311271 CATTAAGTTA
* * * * * *
14311281 TTTTGAAAAATGAGAAAGCGATTTCCAAAGTTTTTTACTTAGTAAGTCCTTCGGGCCATCAGTAA
1 TTTTGAAAAGTAAGAAAACTATTTCCAAAGTTTCTTACTTAGTAAGTCCTTCAGGCCATCAGTAA
* * * *
14311346 GTCTTTCGAGTATGTTGATTAAATTCTTCGTGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGT
66 ATCTTTCGAGTATGATGATTAAATCCTTCGTGTCATCTATAAGTCTTTCGAGCAAGATGATAAGT
** * * *
14311411 CTTTCGGGCTATCCGTAAGACCTTCAGGTAGGATGTTTTCACATGAATTTGAAAAATGGGAAAGC
131 CTTTAAGACTATCCGTAAGACCTTCAAGTAGGATGTTTTCACATGAATTTGAAAAATGGGAAAAC
* * **
14311476 GATTTTCAAAGTTTCCCATTTAATCTTTTCTGAAAATGAAAT
196 GATTTCCAAAGTTTCCCATTTAATATTTTCAAAAAATGAAAT
14311518 TTTTGAAAAGTAAGAAAACTATTTCCAAAGTTTCTTACTTAGTAAGTCCTTCAGGCCATCAGTAA
1 TTTTGAAAAGTAAGAAAACTATTTCCAAAGTTTCTTACTTAGTAAGTCCTTCAGGCCATCAGTAA
*
14311583 ATCTTTCGAGTATGATGATTAAATCCTTCG-GTTCATCTATAAGTCTTTCGAGCGAGATGATAAG
66 ATCTTTCGAGTATGATGATTAAATCCTTCGTG-TCATCTATAAGTCTTTCGAGCAAGATGATAAG
*
14311647 TCCTTTAAGAC-ATCTC-TAAGACCTT-AAGTATGATGTTTTCACATGAATTTGAAAAATGGGAA
130 T-CTTTAAGACTATC-CGTAAGACCTTCAAGTAGGATGTTTTCACATGAATTTGAAAAATGGGAA
** *
14311709 AACGATTTCCAAAGTTTGTCATTTAGTATTTTCAAAAAATGAAAT
193 AACGATTTCCAAAGTTTCCCATTTAATATTTTCAAAAAATGAAAT
*
14311754 TTTTGAAACGTAAGAAAA-TATTTTCCAAAGTTTCTTACTTAGTA
1 TTTTGAAAAGTAAGAAAACTA-TTTCCAAAGTTTCTTACTTAGTA
14311798 GGCTATTTCC
Statistics
Matches: 251, Mismatches: 25, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
235 2 0.01
236 113 0.45
237 129 0.51
238 7 0.03
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (237 bp):
TTTTGAAAAGTAAGAAAACTATTTCCAAAGTTTCTTACTTAGTAAGTCCTTCAGGCCATCAGTAA
ATCTTTCGAGTATGATGATTAAATCCTTCGTGTCATCTATAAGTCTTTCGAGCAAGATGATAAGT
CTTTAAGACTATCCGTAAGACCTTCAAGTAGGATGTTTTCACATGAATTTGAAAAATGGGAAAAC
GATTTCCAAAGTTTCCCATTTAATATTTTCAAAAAATGAAAT
Found at i:14311907 original size:41 final size:42
Alignment explanation
Indices: 14311816--14311936 Score: 120
Period size: 42 Copynumber: 2.9 Consensus size: 42
14311806 CCAAAATTGG
* * *
14311816 TAAGTCCTTCGGGCCATCAGTAAGCCTTTTGAGCAAGATGAT
1 TAAGTCCTTCGGGCCATCTGTAAGCCTTTCGAGCAAGACGAT
* * * * * *
14311858 TAAATCCTTTGGGTCATCTGTCAGTCTTTCGAGTAAGACGA-
1 TAAGTCCTTCGGGCCATCTGTAAGCCTTTCGAGCAAGACGAT
* *
14311899 TAAGTCCTTCGGGCCATCTATAAGACC-TTCTAGCAAGA
1 TAAGTCCTTCGGGCCATCTGTAAG-CCTTTCGAGCAAGA
14311937 TTTTTTCACA
Statistics
Matches: 61, Mismatches: 17, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
41 28 0.46
42 33 0.54
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.30
Consensus pattern (42 bp):
TAAGTCCTTCGGGCCATCTGTAAGCCTTTCGAGCAAGACGAT
Found at i:14312046 original size:261 final size:257
Alignment explanation
Indices: 14311559--14312255 Score: 865
Period size: 261 Copynumber: 2.7 Consensus size: 257
14311549 TTCTTACTTA
* ** * * * *
14311559 GTAAGTCCTTCAGGCCATCAGTAAATCTTTCGAGTATGATGATTAAATCCTTCGGTTCATCTATA
1 GTAAGTCCTTCGGGCCATCAGTAAGCCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTC
* ** * * * * *
14311624 AGTCTTTCGAGCGAGATGATAAGTCCTTTAAGACATCTCTAAGACCTTAAGTATGATGTTTTCAC
66 AGTCTTTCGAGCAAGATGATAAGTCCTTCGAGCCATCTATAAGACCTTCAGCAAGATGTTTTCAC
* * * * * *
14311689 ATGAATTT-GAAAAATGGGAAAACGATTTCCAAAGTTTGTCATTTAGTATTTTCAAAAAATGAAA
131 ATGATTTTAAAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAGTATTTTCAAAAAATGAAA
* * * ** * *
14311753 TTTTTGAAACGTAAGAAAATATTTTCCAAAGTTTCTTACTTAGTAGGCTATTTCCAAAATTG
196 TTTTTGAAAAGTAAGAAAACAATTTCCAAAGTTTCTTACACAATAGACTATTTCCAAAATTG
* * *
14311815 GTAAGTCCTTCGGGCCATCAGTAAGCCTTTTGAGCAAGATGATTAAATCCTTTGGGTCATCTGTC
1 GTAAGTCCTTCGGGCCATCAGTAAGCCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTC
* * * *
14311880 AGTCTTTCGAGTAAGACGATAAGTCCTTCGGGCCATCTATAAGACCTTCTAGCAAGATTTTTTCA
66 AGTCTTTCGAGCAAGATGATAAGTCCTTCGAGCCATCTATAAGACCTTC-AGCAAGATGTTTTCA
* *
14311945 CATGATTTTCAAAAAAAAATGAGAAAGTGATTTTCAAAGTTTCTCATTTAGTATTTTCAGAAAAT
130 CATGATTTT---AAAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAGTATTTTCAAAAAAT
14312010 GAAATTTTTGAAAAGTAAGAAAACAATTTCCAAAGTTTCTTACACAATAGACTATTTCCAAAATT
192 GAAATTTTTGAAAAGTAAGAAAACAATTTCCAAAGTTTCTTACACAATAGACTATTTCCAAAATT
14312075 G
257 G
* * *
14312076 GTAAGTCCTTCGGGCTATCAGTAAGCCTTTCGAGCATTATGATTAAATCCTTCGGGACATCTGTC
1 GTAAGTCCTTCGGGCCATCAGTAAGCCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTC
* * * * * *
14312141 AGTCTTTCAAACAAGATGATAAGTCATTCGATCCATCTATAAGACTTTCATGCAAGATGCTTTCA
66 AGTCTTTCGAGCAAGATGATAAGTCCTTCGAGCCATCTATAAGACCTTCA-GCAAGATGTTTTCA
* ** *
14312206 TATGGTATTTGTATGAAAATGAGAAAGCGATTTTTAAAGTTTCTCATTTA
130 CAT-G-ATTT-TAAAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTA
14312256 AAATAGTTTA
Statistics
Matches: 374, Mismatches: 58, Indels: 13
0.84 0.13 0.03
Matches are distributed among these distances:
256 95 0.25
257 20 0.05
260 1 0.00
261 252 0.67
262 1 0.00
263 4 0.01
264 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (257 bp):
GTAAGTCCTTCGGGCCATCAGTAAGCCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTC
AGTCTTTCGAGCAAGATGATAAGTCCTTCGAGCCATCTATAAGACCTTCAGCAAGATGTTTTCAC
ATGATTTTAAAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAGTATTTTCAAAAAATGAAA
TTTTTGAAAAGTAAGAAAACAATTTCCAAAGTTTCTTACACAATAGACTATTTCCAAAATTG
Found at i:14312320 original size:30 final size:29
Alignment explanation
Indices: 14312272--14312332 Score: 81
Period size: 27 Copynumber: 2.1 Consensus size: 29
14312262 TTTAAAAAGA
14312272 AAAATAAAAAAAATAGAAAGA-AAA-AAT
1 AAAATAAAAAAAATAGAAAGAGAAAGAAT
14312299 AAAATAATAATAAAATGAGAAAGAGAAAGAAT
1 AAAATAA-AA-AAAAT-AGAAAGAGAAAGAAT
14312331 AA
1 AA
14312333 CAAAAAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
27 7 0.24
28 2 0.07
29 5 0.17
30 7 0.24
31 3 0.10
32 5 0.17
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.13
Consensus pattern (29 bp):
AAAATAAAAAAAATAGAAAGAGAAAGAAT
Found at i:14312652 original size:44 final size:45
Alignment explanation
Indices: 14312481--14313444 Score: 915
Period size: 45 Copynumber: 21.7 Consensus size: 45
14312471 ACAAATTGAT
* * * *
14312481 AGAGGAGTCGATCTTTTAGTGTTGTCCTACTTGACTTTCTCATGA
1 AGAGGAGTCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCGTGA
* * ** * * *
14312526 AGAGAAGTCAACCTTTTAGT-TGTGTTGTTTTTTACTTTCTCGTGG
1 AGAGGAGTCAATCTTTTAGTGT-TGTCATTCTTGACTTTCTCGTGA
* * * *
14312571 AGAGAAGTCAACCTTTTAGTGATGTCATTCTTGACTTTCTCATGA
1 AGAGGAGTCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCGTGA
* *
14312616 AGAGGAGTCAATC-TTAAGTGTTTTCATTCTTGACTTTCTCGTGA
1 AGAGGAGTCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCGTGA
* * * *
14312660 AGAGGATTCAATC-TTTAGTGATGTCTTTCTTGACTTTCTTGTGA
1 AGAGGAGTCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCGTGA
* * * **
14312704 AGAGGAGTCAACCATTTAGTGGTGTTGTTCTTGACTTTCTCGTTG-
1 AGAGGAGTCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCG-TGA
* * * * *
14312749 AGAGAAGTCAACCTTTTAGTGATGTCATTCTTGACTTTATCATGA
1 AGAGGAGTCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCGTGA
* *
14312794 AGAGGAGTCAATC-TTTAGTGTTTTTATTCTTGACTTTCTCGTGA
1 AGAGGAGTCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCGTGA
* * * *
14312838 AGAGAAGTCAATC-TTTAGTGATGTCTTTCTTGACTTTCTCATGA
1 AGAGGAGTCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCGTGA
* * * *
14312882 AGAGGAGTCAACCTTTTAGTGGTGAT-GTTCTTGACTTTCTCGTGG
1 AGAGGAGTCAATCTTTTAGTGTTG-TCATTCTTGACTTTCTCGTGA
* * * * **
14312927 ATAGAAGTCAACCTTTTAGTGATGTCATTCTTGACTTTCTTATGA
1 AGAGGAGTCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCGTGA
* *
14312972 AGGGGAGTCAATC-TTTAGTGTTGTCATTCTTGACTTTCTCATGA
1 AGAGGAGTCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCGTGA
* * **
14313016 AGAGAAGTCAATC-TTTAGTGTTGTCATTCTTGACTTTTTTATGA
1 AGAGGAGTCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCGTGA
** * *
14313060 AGATTAGTCAATC-TTTAGTGTTG---TTCTTGAC-TTCTTGTGG
1 AGAGGAGTCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCGTGA
* * * * *
14313100 AGAGAAATCAACCTTTTAGTGATGTCATTCTTGACTTTCTCGTCA
1 AGAGGAGTCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCGTGA
* * * *
14313145 AGATGAGTCAATC-TTTAGTGTTGTTATTCTTAACCTTTTTCGTGA
1 AGAGGAGTCAATCTTTTAGTGTTGTCATTCTTGA-CTTTCTCGTGA
* * * *
14313190 AAAGAAGTCAATCTTTCAGTAG-TGTCA-ACTTGACTTTCTCGTGA
1 AGAGGAGTCAATCTTTTAGT-GTTGTCATTCTTGACTTTCTCGTGA
* *
14313234 AGAGGAGTCAATCTTTTAGTGTTATC-TTCCTTGACTTTCTCGCGA
1 AGAGGAGTCAATCTTTTAGTGTTGTCATT-CTTGACTTTCTCGTGA
* * *
14313279 AGATGAGTCAATCTTTCAGTGTTGTC-TTCCTTGACTTTCTCGTAA
1 AGAGGAGTCAATCTTTTAGTGTTGTCATT-CTTGACTTTCTCGTGA
* * * * *
14313324 AGAGGAGTCAATCTTTCAATATTTTTATTCTTGACTTTCTCGTGA
1 AGAGGAGTCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCGTGA
* * * * * * *
14313369 AGAGAAGTCAATCTTTCAGTGTTGTGATGCTTGACTTTTTCATAA
1 AGAGGAGTCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCGTGA
* *
14313414 ATAGGAGTCAAGT-TTTTAGTGATGTCATTCT
1 AGAGGAGTCAA-TCTTTTAGTGTTGTCATTCT
14313445 CAACTTGACT
Statistics
Matches: 758, Mismatches: 140, Indels: 42
0.81 0.15 0.04
Matches are distributed among these distances:
40 15 0.02
41 17 0.02
43 1 0.00
44 300 0.40
45 409 0.54
46 15 0.02
47 1 0.00
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.42
Consensus pattern (45 bp):
AGAGGAGTCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCGTGA
Found at i:14312794 original size:178 final size:177
Alignment explanation
Indices: 14312481--14313434 Score: 1154
Period size: 178 Copynumber: 5.4 Consensus size: 177
14312471 ACAAATTGAT
* * * * * *
14312481 AGAGGAGTCGATCTTTTAGTGTTGTCCTACTTGACTTTCTCATGAAGAGAAGTCAACCTTTTAGT
1 AGAGAAGTCAATC-TTTAGTGATGTCTTTCTTGACTTTCTCATGAAGAGGAGTCAACCTTTTAG-
* *
14312546 TGTGTTGTTTTTTACTTTCTCGTGGAGAGAAGTCAACCTTTTAGTGATGTCATTCTTGACTTTCT
64 TGTGTTGTTCTTGACTTTCTCGTGGAGAGAAGTCAACCTTTTAGTGATGTCATTCTTGACTTTCT
*
14312611 CATGAAGAGGAGTCAATCTTAAGTGTTTTCATTCTTGACTTTCTCGTGA
129 CATGAAGAGGAGTCAATCTTTAGTGTTTTCATTCTTGACTTTCTCGTGA
* * ** *
14312660 AGAGGATTCAATCTTTAGTGATGTCTTTCTTGACTTTCTTGTGAAGAGGAGTCAACCATTTAGTG
1 AGAGAAGTCAATCTTTAGTGATGTCTTTCTTGACTTTCTCATGAAGAGGAGTCAACCTTTTAGT-
* *
14312725 GTGTTGTTCTTGACTTTCTCGTTGAGAGAAGTCAACCTTTTAGTGATGTCATTCTTGACTTTATC
65 GTGTTGTTCTTGACTTTCTCGTGGAGAGAAGTCAACCTTTTAGTGATGTCATTCTTGACTTTCTC
*
14312790 ATGAAGAGGAGTCAATCTTTAGTGTTTTTATTCTTGACTTTCTCGTGA
130 ATGAAGAGGAGTCAATCTTTAGTGTTTTCATTCTTGACTTTCTCGTGA
14312838 AGAGAAGTCAATCTTTAGTGATGTCTTTCTTGACTTTCTCATGAAGAGGAGTCAACCTTTTAGTG
1 AGAGAAGTCAATCTTTAGTGATGTCTTTCTTGACTTTCTCATGAAGAGGAGTCAACCTTTTAGT-
* * *
14312903 GTGATGTTCTTGACTTTCTCGTGGATAGAAGTCAACCTTTTAGTGATGTCATTCTTGACTTTCTT
65 GTGTTGTTCTTGACTTTCTCGTGGAGAGAAGTCAACCTTTTAGTGATGTCATTCTTGACTTTCTC
* * *
14312968 ATGAAGGGGAGTCAATCTTTAGTGTTGTCATTCTTGACTTTCTCATGA
130 ATGAAGAGGAGTCAATCTTTAGTGTTTTCATTCTTGACTTTCTCGTGA
* * * * ** *
14313016 AGAGAAGTCAATCTTTAGTGTTGTCATTCTTGACTTTTTTATGAAGATTAGTCAATC-TTTA--G
1 AGAGAAGTCAATCTTTAGTGATGTCTTTCTTGACTTTCTCATGAAGAGGAGTCAACCTTTTAGTG
* * *
14313078 TGTTGTTCTTGAC-TTCTTGTGGAGAGAAATCAACCTTTTAGTGATGTCATTCTTGACTTTCTCG
66 TGTTGTTCTTGACTTTCTCGTGGAGAGAAGTCAACCTTTTAGTGATGTCATTCTTGACTTTCTCA
* * * *
14313142 TCAAGATGAGTCAATCTTTAGTGTTGTT-ATTCTTAACCTTTTTCGTGA
131 TGAAGAGGAGTCAATCTTTAGTGTT-TTCATTCTTGA-CTTTCTCGTGA
* ** * *
14313190 AAAGAAGTCAATCTTTCAGT-AGTGTC-AACTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAG
1 AGAGAAGTCAATCTTT-AGTGA-TGTCTTTCTTGACTTTCTCATGAAGAGGAGTCAACCTTTTAG
* * * * * *
14313253 TGT-TATCTTCCTTGACTTTCTCGCGAAGATG-AGTCAATCTTTCAGTGTTGTC-TTCCTTGACT
64 TGTGT-TGTT-CTTGACTTTCTCGTGGAGA-GAAGTCAACCTTTTAGTGATGTCATT-CTTGACT
* * * * *
14313315 TTCTCGTAAAGAGGAGTCAATCTTTCAATATTTTTATTCTTGACTTTCTCGTGA
125 TTCTCATGAAGAGGAGTCAATCTTT-AGTGTTTTCATTCTTGACTTTCTCGTGA
* ** * * * * **
14313369 AGAGAAGTCAATCTTTCAGTGTTGTGATGCTTGACTTTTTCATAAATAGGAGTCAAGTTTTTAGT
1 AGAGAAGTCAATCTTT-AGTGATGTCTTTCTTGACTTTCTCATGAAGAGGAGTCAACCTTTTAGT
14313434 G
65 G
14313435 ATGTCATTCT
Statistics
Matches: 675, Mismatches: 83, Indels: 33
0.85 0.10 0.04
Matches are distributed among these distances:
173 75 0.11
174 62 0.09
175 11 0.02
176 1 0.00
177 10 0.01
178 372 0.55
179 101 0.15
180 43 0.06
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.42
Consensus pattern (177 bp):
AGAGAAGTCAATCTTTAGTGATGTCTTTCTTGACTTTCTCATGAAGAGGAGTCAACCTTTTAGTG
TGTTGTTCTTGACTTTCTCGTGGAGAGAAGTCAACCTTTTAGTGATGTCATTCTTGACTTTCTCA
TGAAGAGGAGTCAATCTTTAGTGTTTTCATTCTTGACTTTCTCGTGA
Found at i:14313506 original size:51 final size:51
Alignment explanation
Indices: 14313441--14313562 Score: 172
Period size: 51 Copynumber: 2.4 Consensus size: 51
14313431 AGTGATGTCA
* *
14313441 TTCTCAACTTGACTTTCTCGCGGAGAAGAGTCAACTTTTCAGTAGTATCAT
1 TTCTCAACTTGACTTTCTCGCAGAGAAGAGTCAACTTTTCAATAGTATCAT
* *
14313492 TTCTCAACTTGACTTTCTCGCAGAGATGAGTTAACTTTTCAATAGTATCAT
1 TTCTCAACTTGACTTTCTCGCAGAGAAGAGTCAACTTTTCAATAGTATCAT
* * * *
14313543 TCCTGAAATTGACGTTCTCG
1 TTCTCAACTTGACTTTCTCG
14313563 TGTAGAGAAG
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 63 1.00
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.37
Consensus pattern (51 bp):
TTCTCAACTTGACTTTCTCGCAGAGAAGAGTCAACTTTTCAATAGTATCAT
Found at i:14314616 original size:134 final size:134
Alignment explanation
Indices: 14314202--14314773 Score: 579
Period size: 134 Copynumber: 4.3 Consensus size: 134
14314192 AGATAAGAGG
* * * * * * **
14314202 AGCAAATCACGTTTGATTCAATCTTCCCTGAAGAACAACGAAGTTGG-TCAACATTTTCTCAAGT
1 AGCAAATCAAGTTTGATTCAATCTTTCCTGAAGAGCAGCGAAG-TGGATCAAAATTTACTTGAGT
* * * * * *
14314266 CTGATCTCCCTTAAAGAGTAGTGGAGCATATTCTTCTTCTTTCAGATTTGGTCTTCCTAAAGAGC
65 CTGATCTCCCCTAAAGAGTAATGGAGAAGATTCTTCTTCTTTCAGATTTGGACTTCCTGAAGAGC
*
14314331 AGCGA
130 AGCAA
* *
14314336 AGCAAATCAAGTTTGATTCAATCTTCCCTGAAGAGCAGTGAAGTGGATCAAAATTTACTTTAAGA
1 AGCAAATCAAGTTTGATTCAATCTTTCCTGAAGAGCAGCGAAGTGGATCAAAATTTAC-TT--GA
* * * *
14314401 GATCTGGTTTTCCCC-AAAGAGTAATGGA-ACAGATCCTAT-TTCTTTCATATTTGGACTTCCTG
63 G-TCT-GATCTCCCCTAAAGAGTAATGGAGA-AGATTCT-TCTTCTTTCAGATTTGGACTTCCTG
* *
14314463 AAGAGTAGCGA
124 AAGAGCAGCAA
* * * * * *
14314474 AGCAAATCAAGTTTTATTCAGTCTTTCCTGAGGAGCAGTGAAGTAGATCAAAATTTTCTTGAGTC
1 AGCAAATCAAGTTTGATTCAATCTTTCCTGAAGAGCAGCGAAGTGGATCAAAATTTACTTGAGTC
* * *
14314539 TCATCTCCCCTAAAGAGTAATGGAGAAGATTCTAT-TTCTTTTAGATTTGGACTTCCTGAAGAGG
66 TGATCTCCCCTAAAGAGTAATGGAGAAGATTCT-TCTTCTTTCAGATTTGGACTTCCTGAAGAGC
*
14314603 AACAA
130 AGCAA
* * * *
14314608 AGCAAATCACGTTCGATTCAATC-TTCTCTAAAGAGCAGCGAAATGGATCAAAATTTAC--GAGT
1 AGCAAATCAAGTTTGATTCAATCTTTC-CTGAAGAGCAGCGAAGTGGATCAAAATTTACTTGAGT
* * * *
14314670 ATGATCT-CCCTAAAGAGTAGTGGAGTAGATTCTTCTTCTTTTAGATTTGGACTTCCTGAAGAGC
65 CTGATCTCCCCTAAAGAGTAATGGAGAAGATTCTTCTTCTTTCAGATTTGGACTTCCTGAAGAGC
* *
14314734 ATCAG
130 AGCAA
*
14314739 AGCAAATCACA-TTTGATTCAATCTTTCCTTAAGAG
1 AGCAAATCA-AGTTTGATTCAATCTTTCCTGAAGAG
14314774 TAGTGTAATA
Statistics
Matches: 370, Mismatches: 54, Indels: 31
0.81 0.12 0.07
Matches are distributed among these distances:
130 1 0.00
131 82 0.22
132 12 0.03
133 12 0.03
134 145 0.39
135 5 0.01
137 4 0.01
138 102 0.28
139 7 0.02
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Consensus pattern (134 bp):
AGCAAATCAAGTTTGATTCAATCTTTCCTGAAGAGCAGCGAAGTGGATCAAAATTTACTTGAGTC
TGATCTCCCCTAAAGAGTAATGGAGAAGATTCTTCTTCTTTCAGATTTGGACTTCCTGAAGAGCA
GCAA
Found at i:14315631 original size:20 final size:20
Alignment explanation
Indices: 14315602--14315654 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
14315592 TGAAGTAGGG
*
14315602 TATCGGTACCA-AGAGGAAAT
1 TATCGATACCATAGA-GAAAT
*
14315622 TATCGATACCATTATAGAAAT
1 TATCGATACCA-TAGAGAAAT
14315643 TATCGATACCAT
1 TATCGATACCAT
14315655 TATAGAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 11 0.38
21 16 0.55
22 2 0.07
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (20 bp):
TATCGATACCATAGAGAAAT
Found at i:14315643 original size:21 final size:21
Alignment explanation
Indices: 14315617--14315662 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
14315607 GTACCAAGAG
14315617 GAAATTATCGATACCATTATA
1 GAAATTATCGATACCATTATA
14315638 GAAATTATCGATACCATTATA
1 GAAATTATCGATACCATTATA
14315659 GAAA
1 GAAA
14315663 AATGGATTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.30
Consensus pattern (21 bp):
GAAATTATCGATACCATTATA
Found at i:14315729 original size:22 final size:22
Alignment explanation
Indices: 14315704--14315746 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
14315694 TACTAAAAGG
*
14315704 AGTATCGGTACCATAGAAGGGA
1 AGTATCGATACCATAGAAGGGA
*
14315726 AGTATCGATACCATAGGAGGG
1 AGTATCGATACCATAGAAGGG
14315747 GTACCTATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.35, C:0.14, G:0.33, T:0.19
Consensus pattern (22 bp):
AGTATCGATACCATAGAAGGGA
Found at i:14316151 original size:54 final size:54
Alignment explanation
Indices: 14316069--14316571 Score: 611
Period size: 54 Copynumber: 9.4 Consensus size: 54
14316059 ATGTACTATT
* * *
14316069 GGCACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTAAGAACGACCATATC
1 GGCACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCGTATC
* *
14316123 GGCACTAAGTGTGCTACCCACGGAATTCATAATAAGTTTATGAATGACCGTATC
1 GGCACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCGTATC
* * ** **
14316177 GGCACTAAGTGTGCAACCAACAGAATTCATAATAAGTTTATGATTGACTATATC
1 GGCACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCGTATC
**
14316231 GGCACTAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAACGACCGTATC
1 GGCACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCGTATC
* *
14316285 GACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATAAACGACCGTATC
1 GGCACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCGTATC
*
14316339 GGCACTAAGTGTGCAACCCACGGAATTTATAATATTAGTTTATGAACGACCGTATC
1 GGCACTAAGTGTGCAACCCACGGAATTCATAATA--AGTTTATGAACGACCGTATC
* *
14316395 AGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGA-C---T-
1 GGCACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCGTATC
* * * * * * * *
14316444 GGTACTATGTGTGCAACCTACGTAATTCATAATGAGCTTATGAATGACTGTATC
1 GGCACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCGTATC
* * * * * * * * *
14316498 GGTACTATGTATGCAGCCCACGTAATTCATAATGAGCTTATGAATGACTGTATC
1 GGCACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCGTATC
* * *
14316552 GGTACTATGTGTGCACCCCA
1 GGCACTAAGTGTGCAACCCA
14316572 AAGAACTTAT
Statistics
Matches: 400, Mismatches: 42, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
49 38 0.09
50 1 0.00
53 2 0.00
54 309 0.77
56 50 0.12
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.27
Consensus pattern (54 bp):
GGCACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCGTATC
Found at i:14317149 original size:201 final size:200
Alignment explanation
Indices: 14316795--14317173 Score: 677
Period size: 201 Copynumber: 1.9 Consensus size: 200
14316785 CGCCCATCTT
* *
14316795 ATTTTATGTATTGATATGAATTATACGATTTTCATTTGTATTTTGATAATTTGGATTATGCTTAT
1 ATTTTATGGATTGATATGAATTATACGATTTTCATTTGTATTTTGATAATTTGGAATATGCTTAT
*
14316860 ATTTAAGCATAATTCATTTTGTATTACTATGTATCACTTAGTAAATACTTAACGTGTGTTGATTT
66 ATTTAAGCATAACTCATTTTGTATTACTATGTATCACTTAGTAAATACTTAACGTGTGTTGATTT
* *
14316925 CACGCGTAGGTAAAAGTCGAGATTAGAAGTAAAGAGTACCGAGCAACTTCAAACAACTCATGTAC
131 CACGCGTAGGTAAAAGTCGAGATTAGAAGTAAAGAGCACCAAGCAACTTCAAACAACTCATGTAC
14316990 CATAC
196 CATAC
* *
14316995 ATTTTGATGGATTGATATGACTTATATGATTTTCATTTGTATTTTGATAATTTGGAATATGCTTA
1 ATTTT-ATGGATTGATATGAATTATACGATTTTCATTTGTATTTTGATAATTTGGAATATGCTTA
*
14317060 TATTTAAGCATAACTCATTTTGTATTACTATGTCTCACTTAGTAAATACTTAACGTGTGTTGATT
65 TATTTAAGCATAACTCATTTTGTATTACTATGTATCACTTAGTAAATACTTAACGTGTGTTGATT
14317125 TCACGCGTAGGTAAAAGTCGAGATTAGAAGTAAAGAGCACCAAGCAACT
130 TCACGCGTAGGTAAAAGTCGAGATTAGAAGTAAAGAGCACCAAGCAACT
14317174 CCGAGCATCA
Statistics
Matches: 170, Mismatches: 8, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
200 5 0.03
201 165 0.97
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.39
Consensus pattern (200 bp):
ATTTTATGGATTGATATGAATTATACGATTTTCATTTGTATTTTGATAATTTGGAATATGCTTAT
ATTTAAGCATAACTCATTTTGTATTACTATGTATCACTTAGTAAATACTTAACGTGTGTTGATTT
CACGCGTAGGTAAAAGTCGAGATTAGAAGTAAAGAGCACCAAGCAACTTCAAACAACTCATGTAC
CATAC
Found at i:14322880 original size:54 final size:54
Alignment explanation
Indices: 14322195--14322866 Score: 966
Period size: 54 Copynumber: 12.4 Consensus size: 54
14322185 CTATATGTAC
*
14322195 TATCGACACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCG
1 TATCGACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCG
* *
14322249 TATCGACACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAAGGACCG
1 TATCGACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCG
* * * *
14322303 TATCGACACTATGTGTGCAACCCACGTAATTCATAATAAGTTTATGAATGACCA
1 TATCGACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCG
* * * *
14322357 TATTGGCACTAAGTGTGCAACCCAAGGAATTCATAATAAGTTTATGAACGACCA
1 TATCGACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCG
* * **
14322411 TATCAACACTAAGTGTGCATCCCACGGAATTCATAATAAGTTTATGAACGACTA
1 TATCGACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCG
* *
14322465 TATCGGCACTAAGTGTGCAACCCACGGAATTCATAATTAGTTTATGAACGACCG
1 TATCGACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCG
* * * *
14322519 TATCGACACTATGTGTGCAACCCACGAAATTTATAATAAGTTTATGAATGACCG
1 TATCGACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCG
* * *
14322573 TATCGACACTATGTGTGCAACCCACGGAATTCATAATATGTTTTTGAACGACCG
1 TATCGACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCG
* * ** *
14322627 TATTGGCACTAAGTGTGCAACCCAAAGAATTCATAATAAGTTTATGAACGACCA
1 TATCGACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCG
* **
14322681 TATCGACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAATGATTG
1 TATCGACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCG
* *
14322735 TATCGGCACTAAGTGTGCAACCCACGTAATTCATAATAAGTTTATGAACGACCG
1 TATCGACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCG
* * * * * *
14322789 TATCGGCACTATGTGTGCAACCCACGTAATTCATAATGAGCTTATGAATGACCG
1 TATCGACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCG
* *
14322843 TATCGACACTACGTGTGCACCCCA
1 TATCGACACTAAGTGTGCAACCCA
14322867 AATAACTTAT
Statistics
Matches: 556, Mismatches: 62, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 556 1.00
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (54 bp):
TATCGACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCG
Found at i:14327649 original size:11 final size:11
Alignment explanation
Indices: 14327633--14327691 Score: 57
Period size: 11 Copynumber: 5.2 Consensus size: 11
14327623 GAGACTCGAA
14327633 CTCGATTGAAG
1 CTCGATTGAAG
14327644 CTCGATTTTG-AG
1 CTCGA--TTGAAG
*
14327656 CTCGATTCAAG
1 CTCGATTGAAG
*
14327667 CTCGATTGTGAG
1 CTCGATTG-AAG
*
14327679 CTCGATTCAAG
1 CTCGATTGAAG
14327690 CT
1 CT
14327692 TGACTTAAGC
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
10 2 0.05
11 18 0.46
12 16 0.41
13 3 0.08
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (11 bp):
CTCGATTGAAG
Found at i:14327659 original size:12 final size:12
Alignment explanation
Indices: 14327642--14327685 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
14327632 ACTCGATTGA
14327642 AGCTCGATTTTG
1 AGCTCGATTTTG
**
14327654 AGCTCGA-TTCA
1 AGCTCGATTTTG
*
14327665 AGCTCGATTGTG
1 AGCTCGATTTTG
14327677 AGCTCGATT
1 AGCTCGATT
14327686 CAAGCTTGAC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 9 0.35
12 17 0.65
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.34
Consensus pattern (12 bp):
AGCTCGATTTTG
Found at i:14327667 original size:23 final size:23
Alignment explanation
Indices: 14327633--14327691 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
14327623 GAGACTCGAA
* *
14327633 CTCGATTGAAGCTCGATTTTGAG
1 CTCGATTCAAGCTCGATTGTGAG
14327656 CTCGATTCAAGCTCGATTGTGAG
1 CTCGATTCAAGCTCGATTGTGAG
14327679 CTCGATTCAAGCT
1 CTCGATTCAAGCT
14327692 TGACTTAAGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (23 bp):
CTCGATTCAAGCTCGATTGTGAG
Found at i:14334560 original size:13 final size:13
Alignment explanation
Indices: 14334538--14334574 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
14334528 CGCACTCTGC
*
14334538 ACTGGTCTGCTAG
1 ACTGGCCTGCTAG
14334551 ACTGGCCTGCTAG
1 ACTGGCCTGCTAG
14334564 ACTGGCCTGCT
1 ACTGGCCTGCT
14334575 GGGTTTCCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.14, C:0.30, G:0.30, T:0.27
Consensus pattern (13 bp):
ACTGGCCTGCTAG
Found at i:14338088 original size:30 final size:30
Alignment explanation
Indices: 14337989--14338088 Score: 78
Period size: 30 Copynumber: 3.3 Consensus size: 30
14337979 AAAGTTATAG
* * *
14337989 AATTG-TTAGTAAATTTATCAAACTGTTAT
1 AATTGATTATTAAATTTATAAAACTTTTAT
* * * * * *
14338018 AAAATAATTATTAAATGTATCAAAACATTAAA
1 -AATTGATTATTAAATTTAT-AAAACTTTTAT
*
14338050 AATT-ATTATTAAATTTATTAAACTTTTAT
1 AATTGATTATTAAATTTATAAAACTTTTAT
14338079 AATTGATTAT
1 AATTGATTAT
14338089 AACATTTCAA
Statistics
Matches: 52, Mismatches: 15, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
29 11 0.21
30 21 0.40
31 14 0.27
32 6 0.12
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (30 bp):
AATTGATTATTAAATTTATAAAACTTTTAT
Found at i:14338971 original size:21 final size:20
Alignment explanation
Indices: 14338945--14338992 Score: 78
Period size: 21 Copynumber: 2.4 Consensus size: 20
14338935 GTTTCCAATT
14338945 TCGCAACATGAATAGTAAAAA
1 TCGCAACATGAATAGT-AAAA
*
14338966 TCGCAACGTGAATAGTAAAA
1 TCGCAACATGAATAGTAAAA
14338986 TCGCAAC
1 TCGCAAC
14338993 GCGAATTGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.46, C:0.19, G:0.17, T:0.19
Consensus pattern (20 bp):
TCGCAACATGAATAGTAAAA
Found at i:14338987 original size:20 final size:20
Alignment explanation
Indices: 14338945--14339010 Score: 87
Period size: 20 Copynumber: 3.2 Consensus size: 20
14338935 GTTTCCAATT
*
14338945 TCGCAACATGAATAGTAAAAA
1 TCGCAACGTGAATAGT-AAAA
14338966 TCGCAACGTGAATAGTAAAA
1 TCGCAACGTGAATAGTAAAA
* * *
14338986 TCGCAACGCGAATTGGAAAA
1 TCGCAACGTGAATAGTAAAA
14339006 TCGCA
1 TCGCA
14339011 CCGCGAATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 26 0.63
21 15 0.37
ACGTcount: A:0.44, C:0.18, G:0.20, T:0.18
Consensus pattern (20 bp):
TCGCAACGTGAATAGTAAAA
Found at i:14339027 original size:21 final size:20
Alignment explanation
Indices: 14338962--14339028 Score: 82
Period size: 20 Copynumber: 3.3 Consensus size: 20
14338952 ATGAATAGTA
*
14338962 AAAATCGCAACGTGAA-TAG
1 AAAATCGCAACGCGAATTAG
*
14338981 TAAAATCGCAACGCGAATTGG
1 -AAAATCGCAACGCGAATTAG
*
14339002 AAAATCGCACCGCGAATTTAG
1 AAAATCGCAACGCGAA-TTAG
14339023 AAAATC
1 AAAATC
14339029 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
20 30 0.73
21 11 0.27
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGAATTAG
Found at i:14339436 original size:21 final size:20
Alignment explanation
Indices: 14339384--14339450 Score: 107
Period size: 20 Copynumber: 3.3 Consensus size: 20
14339374 TATAGATTCA
*
14339384 TTGCGATTTTACTATTCATG
1 TTGCGATTTTACTATTCACG
14339404 TTGCGATTTTACTATTCACG
1 TTGCGATTTTACTATTCACG
*
14339424 TTGCGATTTTTACTATTCACA
1 TTGCGA-TTTTACTATTCACG
14339445 TTGCGA
1 TTGCGA
14339451 ATTTGACTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
20 25 0.57
21 19 0.43
ACGTcount: A:0.21, C:0.18, G:0.15, T:0.46
Consensus pattern (20 bp):
TTGCGATTTTACTATTCACG
Found at i:14339470 original size:41 final size:40
Alignment explanation
Indices: 14339425--14339513 Score: 97
Period size: 40 Copynumber: 2.2 Consensus size: 40
14339415 CTATTCACGT
* *
14339425 TGCGATTTTTACTATTCACATTGCGAATTTGACTTTTGGGC
1 TGCGATTTTGACTA-TCACATTGCGAATTTGACTTCTGGGC
* * * * * *
14339466 TGCGAATTTGACTATCGCGTTGGGAATTTGACTTCTGTGT
1 TGCGATTTTGACTATCACATTGCGAATTTGACTTCTGGGC
14339506 TGCGATTT
1 TGCGATTT
14339514 ACAGGAATCA
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
40 27 0.69
41 12 0.31
ACGTcount: A:0.18, C:0.16, G:0.24, T:0.43
Consensus pattern (40 bp):
TGCGATTTTGACTATCACATTGCGAATTTGACTTCTGGGC
Found at i:14339507 original size:20 final size:20
Alignment explanation
Indices: 14339445--14339510 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
14339435 ACTATTCACA
* *
14339445 TTGCGAATTTGACTTTTGGG
1 TTGCGAATTTGACTTCTGCG
*
14339465 CTGCGAATTTGACTATC-GCG
1 TTGCGAATTTGACT-TCTGCG
* *
14339485 TTGGGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTCTGCG
14339505 TTGCGA
1 TTGCGA
14339511 TTTACAGGAA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 2 0.05
20 34 0.92
21 1 0.03
ACGTcount: A:0.17, C:0.15, G:0.29, T:0.39
Consensus pattern (20 bp):
TTGCGAATTTGACTTCTGCG
Found at i:14339918 original size:61 final size:61
Alignment explanation
Indices: 14339787--14339932 Score: 161
Period size: 61 Copynumber: 2.4 Consensus size: 61
14339777 ATTCGTTGTG
* * * * *
14339787 ATTTTACTATTCACATTGCGATTTTACTATTCACGTTGCGATTTTACTATTCATGTTACGA
1 ATTTTACTATTCACATTGCAATTTTACTATCCACATTGCGATTTGACTATTCACGTTACGA
* * * * *
14339848 TTTTTACTATTCACGTTGCAATTTTACTATCCACATTGTGAATTTGACT-TTCGCGTTGCGA
1 ATTTTACTATTCACATTGCAATTTTACTATCCACATTGCG-ATTTGACTATTCACGTTACGA
*
14339909 ATTTGACTA-TCACATTGCGAATTT
1 ATTTTACTATTCACATTGC-AATTT
14339933 GACTTATGTG
Statistics
Matches: 70, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
60 8 0.11
61 55 0.79
62 7 0.10
ACGTcount: A:0.24, C:0.18, G:0.13, T:0.45
Consensus pattern (61 bp):
ATTTTACTATTCACATTGCAATTTTACTATCCACATTGCGATTTGACTATTCACGTTACGA
Found at i:14339936 original size:20 final size:21
Alignment explanation
Indices: 14339787--14339932 Score: 158
Period size: 20 Copynumber: 7.2 Consensus size: 21
14339777 ATTCGTTGTG
*
14339787 ATTTTACTATTCACATTGCG-
1 ATTTTACTATTCACGTTGCGA
14339807 ATTTTACTATTCACGTTGCG-
1 ATTTTACTATTCACGTTGCGA
* *
14339827 ATTTTACTATTCATGTTACGA
1 ATTTTACTATTCACGTTGCGA
*
14339848 TTTTTACTATTCACGTTGC-A
1 ATTTTACTATTCACGTTGCGA
* * *
14339868 ATTTTACTATCCACATTGTGA
1 ATTTTACTATTCACGTTGCGA
* *
14339889 ATTTGACT-TTCGCGTTGCGA
1 ATTTTACTATTCACGTTGCGA
* *
14339909 ATTTGACTA-TCACATTGCGA
1 ATTTTACTATTCACGTTGCGA
14339929 ATTT
1 ATTT
14339933 GACTTATGTG
Statistics
Matches: 106, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
20 82 0.77
21 24 0.23
ACGTcount: A:0.24, C:0.18, G:0.13, T:0.45
Consensus pattern (21 bp):
ATTTTACTATTCACGTTGCGA
Found at i:14339937 original size:40 final size:42
Alignment explanation
Indices: 14339787--14339936 Score: 175
Period size: 41 Copynumber: 3.7 Consensus size: 42
14339777 ATTCGTTGTG
*
14339787 ATTTTACTATTCACATTGCG-ATTTTACTATTCACGTTGCG-
1 ATTTTACTATTCACATTGCGAATTTGACTATTCACGTTGCGA
** * * *
14339827 ATTTTACTATTCATGTTACGATTTTTACTATTCACGTTGC-A
1 ATTTTACTATTCACATTGCGAATTTGACTATTCACGTTGCGA
* * *
14339868 ATTTTACTATCCACATTGTGAATTTGACT-TTCGCGTTGCGA
1 ATTTTACTATTCACATTGCGAATTTGACTATTCACGTTGCGA
*
14339909 ATTTGACTA-TCACATTGCGAATTTGACT
1 ATTTTACTATTCACATTGCGAATTTGACT
14339937 TATGTGTTGC
Statistics
Matches: 92, Mismatches: 15, Indels: 6
0.81 0.13 0.05
Matches are distributed among these distances:
40 43 0.47
41 49 0.53
ACGTcount: A:0.24, C:0.19, G:0.13, T:0.44
Consensus pattern (42 bp):
ATTTTACTATTCACATTGCGAATTTGACTATTCACGTTGCGA
Found at i:14339946 original size:20 final size:21
Alignment explanation
Indices: 14339887--14339973 Score: 76
Period size: 20 Copynumber: 4.3 Consensus size: 21
14339877 TCCACATTGT
14339887 GAATTTGACTT-TCGCGTTGC
1 GAATTTGACTTATCGCGTTGC
* *
14339907 GAATTTGAC-TATCACATTGC
1 GAATTTGACTTATCGCGTTGC
*
14339927 GAATTTGACTTAT-GTGTTGC
1 GAATTTGACTTATCGCGTTGC
** *
14339947 G-ATTT-ACAGATTCGTGTTGC
1 GAATTTGACTTA-TCGCGTTGC
14339967 GAATTTG
1 GAATTTG
14339974 GAAAATCGCA
Statistics
Matches: 54, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
18 3 0.06
19 6 0.11
20 38 0.70
21 7 0.13
ACGTcount: A:0.22, C:0.15, G:0.23, T:0.40
Consensus pattern (21 bp):
GAATTTGACTTATCGCGTTGC
Found at i:14340066 original size:20 final size:21
Alignment explanation
Indices: 14340017--14340070 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
14340007 CGATTTACAT
14340017 ATTCGCGTTGCGAAATTGGAA
1 ATTCGCGTTGCGAAATTGGAA
* *
14340038 ACTAG-GTTGCGAAATTGG-A
1 ATTCGCGTTGCGAAATTGGAA
*
14340057 GTTCGCGTTGCGAA
1 ATTCGCGTTGCGAA
14340071 TTTGTTGGTC
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
19 3 0.11
20 21 0.78
21 3 0.11
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (21 bp):
ATTCGCGTTGCGAAATTGGAA
Found at i:14340931 original size:23 final size:23
Alignment explanation
Indices: 14340905--14340965 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
14340895 GCAGCAACCG
14340905 ACAAGCATCACTGTATCAATTCA
1 ACAAGCATCACTGTATCAATTCA
* *
14340928 ACAAGCATCATTGCATCAATTCA
1 ACAAGCATCACTGTATCAATTCA
*
14340951 GCAAGCATC-CTGTAT
1 ACAAGCATCACTGTAT
14340966 TTAAAAAGCA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
22 4 0.12
23 29 0.88
ACGTcount: A:0.36, C:0.26, G:0.11, T:0.26
Consensus pattern (23 bp):
ACAAGCATCACTGTATCAATTCA
Found at i:14341114 original size:20 final size:21
Alignment explanation
Indices: 14341072--14341123 Score: 79
Period size: 20 Copynumber: 2.5 Consensus size: 21
14341062 ATAATCAAGC
* *
14341072 AATATCAAACAGAAACAAAAA
1 AATATAAAACAAAAACAAAAA
14341093 AATATAAAACAAAAAC-AAAA
1 AATATAAAACAAAAACAAAAA
14341113 AATATAAAACA
1 AATATAAAACA
14341124 TAATCAAGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.75, C:0.12, G:0.02, T:0.12
Consensus pattern (21 bp):
AATATAAAACAAAAACAAAAA
Found at i:14343786 original size:24 final size:24
Alignment explanation
Indices: 14343736--14343835 Score: 94
Period size: 24 Copynumber: 4.2 Consensus size: 24
14343726 TTGGATTCAA
* * *
14343736 GTTTGGATTCAGATTC-AGATTTAG
1 GTTTGGATTCGGGTTCGAG-TTTGG
14343760 GTTTGGATTCGGGTTCGAGTTTGG
1 GTTTGGATTCGGGTTCGAGTTTGG
* * *
14343784 GTTTGGGTTCGGGTTTGAGTTCGG
1 GTTTGGATTCGGGTTCGAGTTTGG
* * * *
14343808 GTTTGGGTTTGGGTTTGGGTTTGG
1 GTTTGGATTCGGGTTCGAGTTTGG
14343832 GTTT
1 GTTT
14343836 AAGGTTTGGG
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
24 64 0.97
25 2 0.03
ACGTcount: A:0.09, C:0.06, G:0.40, T:0.45
Consensus pattern (24 bp):
GTTTGGATTCGGGTTCGAGTTTGG
Found at i:14343787 original size:6 final size:6
Alignment explanation
Indices: 14343759--14343881 Score: 122
Period size: 6 Copynumber: 20.3 Consensus size: 6
14343749 TTCAGATTTA
* * * * * * *
14343759 GGTTTG GATTCG GGTTCG AGTTTG GGTTTG GGTTCG GGTTTG AGTTCG
1 GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG
*
14343807 GGTTTG GGTTTG GGTTTG GGTTTG GGTTTAA GGTTTG GGTTTG GGTTTAG
1 GGTTTG GGTTTG GGTTTG GGTTTG GGTTT-G GGTTTG GGTTTG GGTTT-G
* * *
14343857 GG-TTG GGTTCG AGTTTG GTTTTG GG
1 GGTTTG GGTTTG GGTTTG GGTTTG GG
14343882 GCGAGTTTGG
Statistics
Matches: 94, Mismatches: 20, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
5 3 0.03
6 83 0.88
7 8 0.09
ACGTcount: A:0.06, C:0.04, G:0.46, T:0.45
Consensus pattern (6 bp):
GGTTTG
Found at i:14344616 original size:61 final size:61
Alignment explanation
Indices: 14344547--14344683 Score: 229
Period size: 61 Copynumber: 2.2 Consensus size: 61
14344537 TCCTAGTTTT
*
14344547 AAATTTGTTCAATTTAGTCCAAATTTAATGATGCAATGTATTAATTTAAGTTTCATATTTA
1 AAATTTGTTCAATTTAGTCCAAATTTAATGATGCAATGTATTAATTTAAGCTTCATATTTA
* * *
14344608 AAATTTGTTCAATTTAGTCCAAATTTAATGTTGTAATTTATTAATTTAAGCTTCATATTTA
1 AAATTTGTTCAATTTAGTCCAAATTTAATGATGCAATGTATTAATTTAAGCTTCATATTTA
*
14344669 AAATTTATTCAATTT
1 AAATTTGTTCAATTT
14344684 GATCCTTATA
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 71 1.00
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (61 bp):
AAATTTGTTCAATTTAGTCCAAATTTAATGATGCAATGTATTAATTTAAGCTTCATATTTA
Found at i:14344779 original size:33 final size:33
Alignment explanation
Indices: 14344742--14344828 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 33
14344732 ATTAATAAAT
14344742 TAATATATAGGTTATATATACTAATGAACTATA
1 TAATATATAGGTTATATATACTAATGAACTATA
*
14344775 TAATATATAGTTTATATATACTAATGAACTATA
1 TAATATATAGGTTATATATACTAATGAACTATA
**
14344808 TGGTATATA-GTTCATATATAC
1 TAATATATAGGTT-ATATATAC
14344829 CATATACTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 2 0.04
33 47 0.96
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.41
Consensus pattern (33 bp):
TAATATATAGGTTATATATACTAATGAACTATA
Found at i:14345004 original size:15 final size:16
Alignment explanation
Indices: 14344981--14345014 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
14344971 ACTTTGAATT
14344981 TATATAGTATAAATAA
1 TATATAGTATAAATAA
*
14344997 TATA-AGTATAAATTA
1 TATATAGTATAAATAA
14345012 TAT
1 TAT
14345015 TATATATAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (16 bp):
TATATAGTATAAATAA
Found at i:14345085 original size:9 final size:9
Alignment explanation
Indices: 14345071--14345112 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
14345061 TCAACTATAG
14345071 TATATAGTT
1 TATATAGTT
*
14345080 TATATA-TA
1 TATATAGTT
*
14345088 AACTATAGTT
1 TA-TATAGTT
14345098 TATATAGTT
1 TATATAGTT
14345107 TATATA
1 TATATA
14345113 TATAGTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
8 2 0.07
9 23 0.85
10 2 0.07
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.50
Consensus pattern (9 bp):
TATATAGTT
Found at i:14345101 original size:27 final size:25
Alignment explanation
Indices: 14345017--14345261 Score: 153
Period size: 27 Copynumber: 9.6 Consensus size: 25
14345007 AATTATATTA
* * *
14345017 TATATAGTATATAAATATCAACTAAAG
1 TATATAGT-T-TATATATAAACTATAG
* *
14345044 TATATAGTATATAAATATCAACTATAG
1 TATATAGT-T-TATATATAAACTATAG
14345071 TATATAGTTTATATATAAACTATAG
1 TATATAGTTTATATATAAACTATAG
** *
14345096 TTTATATAGTTTATATATATAGTTTTTA-
1 --TATATAGTTTATATATA-A-ACTATAG
* * * *
14345124 TTTATAGTTCATATGTAAACTATAC
1 TATATAGTTTATATATAAACTATAG
14345149 TATATAGTTTATATATAAA--ATA-
1 TATATAGTTTATATATAAACTATAG
* * *
14345171 TATAGTA-TATAAATATCAACTATAG
1 TATA-TAGTTTATATATAAACTATAG
*
14345196 TATATAGTATATAAATATAAACTATAG
1 TATATAGT-T-TATATATAAACTATAG
* * *
14345223 TTTATA-TATATAGTATATACTATA-
1 TATATAGTTTATA-TATAAACTATAG
*
14345247 TAAATAGTTTATATA
1 TATATAGTTTATATA
14345262 GTTCATTAAT
Statistics
Matches: 177, Mismatches: 27, Indels: 31
0.75 0.11 0.13
Matches are distributed among these distances:
22 13 0.07
23 5 0.03
24 17 0.10
25 51 0.29
26 16 0.09
27 71 0.40
28 1 0.01
29 3 0.02
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (25 bp):
TATATAGTTTATATATAAACTATAG
Found at i:14345163 original size:2 final size:2
Alignment explanation
Indices: 14345144--14345381 Score: 91
Period size: 2 Copynumber: 113.0 Consensus size: 2
14345134 ATATGTAAAC
* * *
14345144 TA TA CTA TA TA GTT TA TA TA TA -A AA TA TA TA GTA TA TA AA TA
1 TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* * *
14345186 TCA -A CTA TA GTA TA TA GTA TA TA AA TA TA AA CTA TA GTT TA TA
1 T-A TA -TA TA -TA TA TA -TA TA TA TA TA TA TA -TA TA -TA TA TA
* *
14345229 TA TA TA GTA TA TA CTA TA TA AA TA GTT TA TA TA GT- TCA T- TA -A
1 TA TA TA -TA TA TA -TA TA TA TA TA -TA TA TA TA -TA T-A TA TA TA
* * * *
14345271 TA AA CTA TA TA TA TA GT- TCA TA TG TA -A TA -A TG TA AA CTA TA
1 TA TA -TA TA TA TA TA -TA T-A TA TA TA TA TA TA TA TA TA -TA TA
*
14345312 TA TA T- TA TA TA GTA TA TA AA TA TCA -A CTA TA GTA TA TA TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA T-A TA -TA TA -TA TA TA TA TA
14345354 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14345382 GTTCATACGT
Statistics
Matches: 179, Mismatches: 25, Indels: 64
0.67 0.09 0.24
Matches are distributed among these distances:
1 10 0.06
2 139 0.78
3 30 0.17
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.43
Consensus pattern (2 bp):
TA
Found at i:14345203 original size:7 final size:7
Alignment explanation
Indices: 14345191--14345248 Score: 50
Period size: 7 Copynumber: 8.6 Consensus size: 7
14345181 AAATATCAAC
14345191 TATAGTA
1 TATAGTA
14345198 TATAGTA
1 TATAGTA
*
14345205 TATA-AA
1 TATAGTA
*
14345211 TATA-AA
1 TATAGTA
*
14345217 CTATAGTT
1 -TATAGTA
14345225 TATA-TA
1 TATAGTA
14345231 TATAGTA
1 TATAGTA
*
14345238 TATACTA
1 TATAGTA
14345245 TATA
1 TATA
14345249 AATAGTTTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
6 12 0.28
7 31 0.72
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (7 bp):
TATAGTA
Found at i:14345572 original size:20 final size:20
Alignment explanation
Indices: 14345547--14345588 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
14345537 CTATATATAT
14345547 TATATAGTTTACATAGTTTA
1 TATATAGTTTACATAGTTTA
*
14345567 TATATAGTTTATATAGTTTA
1 TATATAGTTTACATAGTTTA
14345587 TA
1 TA
14345589 CATATAGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.02, G:0.10, T:0.52
Consensus pattern (20 bp):
TATATAGTTTACATAGTTTA
Found at i:14345582 original size:9 final size:9
Alignment explanation
Indices: 14345546--14345588 Score: 59
Period size: 9 Copynumber: 4.6 Consensus size: 9
14345536 ACTATATATA
14345546 TTATATAGT
1 TTATATAGT
*
14345555 TTACATAGTT
1 TTATATAG-T
14345565 TATATATAGT
1 T-TATATAGT
14345575 TTATATAGT
1 TTATATAGT
14345584 TTATA
1 TTATA
14345589 CATATAGTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 20 0.67
10 4 0.13
11 6 0.20
ACGTcount: A:0.35, C:0.02, G:0.09, T:0.53
Consensus pattern (9 bp):
TTATATAGT
Found at i:14345626 original size:29 final size:29
Alignment explanation
Indices: 14345590--14345651 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 29
14345580 TAGTTTATAC
* *
14345590 ATATAGTT-AGTATGTAAACTATATAGTGT
1 ATATAGTTCA-TATGTAAAATATATAGTAT
14345619 ATATAGTTCATATGTAAAATATATAGTAT
1 ATATAGTTCATATGTAAAATATATAGTAT
14345648 ATAT
1 ATAT
14345652 GGTTTACATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 29 0.97
30 1 0.03
ACGTcount: A:0.42, C:0.03, G:0.13, T:0.42
Consensus pattern (29 bp):
ATATAGTTCATATGTAAAATATATAGTAT
Found at i:14345791 original size:9 final size:11
Alignment explanation
Indices: 14345779--14346045 Score: 93
Period size: 11 Copynumber: 25.5 Consensus size: 11
14345769 ATATTTAAAC
14345779 TATATAGTTTA
1 TATATAGTTTA
14345790 TATATAGTTTA
1 TATATAGTTTA
* **
14345801 TAT-TAATAAA
1 TATATAGTTTA
*
14345811 CTATATAATTTA
1 -TATATAGTTTA
* *
14345823 TACATAGTATA
1 TATATAGTTTA
14345834 TATATA--TTA
1 TATATAGTTTA
* *
14345843 TTTATA-ATTA
1 TATATAGTTTA
* *
14345853 TACATCA-TATA
1 TATAT-AGTTTA
*
14345864 AATATAAG--T-
1 TATAT-AGTTTA
*
14345873 TGTATAGTTTA
1 TATATAGTTTA
* *
14345884 TATATAATTCA
1 TATATAGTTTA
**
14345895 TATATAAATTA
1 TATATAGTTTA
14345906 TATA-A-TTTA
1 TATATAGTTTA
* **
14345915 TAT-TAATAAA
1 TATATAGTTTA
*
14345925 TTATGTAGTTTA
1 -TATATAGTTTA
*
14345937 TATATAGTTCA
1 TATATAGTTTA
*
14345948 -A-ATAGTTCA
1 TATATAGTTTA
*
14345957 TATATA---AA
1 TATATAGTTTA
14345965 CTATATAGTTTA
1 -TATATAGTTTA
* *
14345977 TACAT-G-GTA
1 TATATAGTTTA
14345986 TATATAGTTTA
1 TATATAGTTTA
* * *
14345997 TACATAATATA
1 TATATAGTTTA
14346008 TATATAGTTTA
1 TATATAGTTTA
* *
14346019 TATATAATATA
1 TATATAGTTTA
14346030 TATATAGTTTA
1 TATATAGTTTA
14346041 TATAT
1 TATAT
14346046 TTTATAAAAT
Statistics
Matches: 187, Mismatches: 49, Indels: 40
0.68 0.18 0.14
Matches are distributed among these distances:
8 3 0.02
9 37 0.20
10 19 0.10
11 118 0.63
12 10 0.05
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (11 bp):
TATATAGTTTA
Found at i:14345803 original size:33 final size:34
Alignment explanation
Indices: 14345757--14345839 Score: 98
Period size: 33 Copynumber: 2.4 Consensus size: 34
14345747 AACCCTAAAC
* *
14345757 CATA-TATACTATATATTTAAACTATATAGTTTATA
1 CATAGTATA-TATATA-ATAAACTATATAATTTATA
* *
14345792 TATAGTTTATAT-TAATAAACTATATAATTTATA
1 CATAGTATATATATAATAAACTATATAATTTATA
14345825 CATAGTATATATATA
1 CATAGTATATATATA
14345840 TTATTTATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
33 27 0.68
34 4 0.10
35 6 0.15
36 3 0.08
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.46
Consensus pattern (34 bp):
CATAGTATATATATAATAAACTATATAATTTATA
Found at i:14345898 original size:20 final size:19
Alignment explanation
Indices: 14345779--14346185 Score: 140
Period size: 20 Copynumber: 20.7 Consensus size: 19
14345769 ATATTTAAAC
*
14345779 TATATAGTTTATATATAGT
1 TATATAGTTTATATATAAT
*
14345798 T-TATA--TTA-ATA-AAC
1 TATATAGTTTATATATAAT
* * *
14345812 TATATAATTTATACATAGT
1 TATATAGTTTATATATAAT
*
14345831 ATATATA-TATTATTTATAAT
1 -TATATAGT-TTATATATAAT
* *
14345851 TATACATCA-TATAAATATAAGT
1 TAT--AT-AGTTTATATATAA-T
*
14345873 TGTATAGTTTATATATAAT
1 TATATAGTTTATATATAAT
**
14345892 TCATATA-TAAATTATATAAT
1 T-ATATAGTTTA-TATATAAT
14345912 T-TATA--TTA-ATA-AAT
1 TATATAGTTTATATATAAT
* *
14345926 TATGTAGTTTATATATAGT
1 TATATAGTTTATATATAAT
* * *
14345945 TCAAATAGTTCATATATAAAC
1 T-ATATAGTTTATATAT-AAT
* **
14345966 TATATAGTTTATACATGGT
1 TATATAGTTTATATATAAT
*
14345985 ATATATAGTTTATACATAATAT
1 -TATATAGTTTATATAT-A-AT
14346007 ATATATAGTTTATATATAATAT
1 -TATATAGTTTATATAT-A-AT
*
14346029 ATATATAGTTTATATAT-TT
1 -TATATAGTTTATATATAAT
* * * *
14346048 TATAAAATAATATAAATATAAAC
1 TAT---ATAGTTTATATAT-AAT
*
14346071 TATATAGTTTATATATATAA
1 TATATAGTTTATATATA-AT
* * ** * *
14346091 TATAAACTAGATATAGAAAC
1 TATATAGTTTATATA-TAAT
*
14346111 TATATAGTTTATACATAAT
1 TATATAGTTTATATATAAT
14346130 ATATATAGTTTATATATAAT
1 -TATATAGTTTATATATAAT
* * * *
14346150 ATATAATAATATAAATATAAAC
1 -TAT-ATAGTTTATATAT-AAT
14346172 TATATAGTTTATAT
1 TATATAGTTTATAT
14346186 TATATATATA
Statistics
Matches: 288, Mismatches: 66, Indels: 67
0.68 0.16 0.16
Matches are distributed among these distances:
14 6 0.02
15 13 0.05
16 3 0.01
17 7 0.02
18 16 0.06
19 18 0.06
20 141 0.49
21 35 0.12
22 46 0.16
23 3 0.01
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (19 bp):
TATATAGTTTATATATAAT
Found at i:14345989 original size:2 final size:2
Alignment explanation
Indices: 14345984--14346196 Score: 79
Period size: 2 Copynumber: 106.5 Consensus size: 2
14345974 TTATACATGG
* * *
14345984 TA TA TA TA GTT TA TA CA TA -A TA TA TA TA TA GTT TA TA TA TA -A
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* * * *
14346026 TA TA TA TA TA GTT TA TA TA T- TT TA TA -A AA TA -A TA TA AA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
14346066 TA AA CTA TA TA GTT TA TA TA TA TA -A TA TA AA CTA GA TA TA GA
1 TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* * * *
14346108 AA CTA TA TA GTT TA TA CA TA -A TA TA TA TA GTT TA TA TA TA -A
1 TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* * *
14346149 TA TA TA -A TA -A TA TA AA TA TA AA CTA TA TA GTT TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA
14346190 TA TA TA T
1 TA TA TA T
14346197 GTAGTTGTTT
Statistics
Matches: 154, Mismatches: 35, Indels: 44
0.66 0.15 0.19
Matches are distributed among these distances:
1 11 0.07
2 132 0.86
3 11 0.07
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.45
Consensus pattern (2 bp):
TA
Found at i:14346093 original size:9 final size:9
Alignment explanation
Indices: 14346017--14346195 Score: 64
Period size: 9 Copynumber: 18.9 Consensus size: 9
14346007 ATATATAGTT
14346017 TATATATAA
1 TATATATAA
14346026 TATATATATA
1 TATATATA-A
* *
14346036 GTTTATATAT
1 -TATATATAA
* *
14346046 TTTATAAAA
1 TATATATAA
14346055 TA-ATATAA
1 TATATATAA
14346063 -ATATA-AA
1 TATATATAA
*
14346070 CTATATAGTTTA
1 -TATATA--TAA
14346082 TATATATAA
1 TATATATAA
*
14346091 TATAAACTAGA
1 TATATA-TA-A
*
14346102 TATAGA-AA
1 TATATATAA
*
14346110 CTATATAGT-T
1 -TATATA-TAA
*
14346120 TATACATAA
1 TATATATAA
*
14346129 TATATATAGTT
1 TATATATA--A
14346140 TATATATAA
1 TATATATAA
14346149 TATATAATAA
1 TATAT-ATAA
14346159 TATAAATATAA
1 TAT--ATATAA
*
14346170 -ACTATATAG
1 TA-TATATAA
* *
14346179 TTTATATTA
1 TATATATAA
14346188 TATATATA
1 TATATATA
14346196 TGTAGTTGTT
Statistics
Matches: 126, Mismatches: 23, Indels: 42
0.66 0.12 0.22
Matches are distributed among these distances:
7 3 0.02
8 10 0.08
9 67 0.53
10 11 0.09
11 32 0.25
12 3 0.02
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.44
Consensus pattern (9 bp):
TATATATAA
Found at i:14346094 original size:11 final size:11
Alignment explanation
Indices: 14345984--14346169 Score: 89
Period size: 11 Copynumber: 16.8 Consensus size: 11
14345974 TTATACATGG
* *
14345984 TATATATAGTT
1 TATATATAATA
*
14345995 TATACATAATA
1 TATATATAATA
* *
14346006 TATATATAGTT
1 TATATATAATA
14346017 TATATATAATA
1 TATATATAATA
* *
14346028 TATATATAGTT
1 TATATATAATA
**
14346039 TATATATTTTA
1 TATATATAATA
*
14346050 TA-AAATAATA
1 TATATATAATA
*
14346060 TAAATATAA-A
1 TATATATAATA
*
14346070 CTATATAGT-TTA
1 -TATATA-TAATA
14346082 TATATATAATA
1 TATATATAATA
14346093 TA-A-ACTAGATA
1 TATATA-TA-ATA
* *
14346104 TAGAAACT-ATA
1 TATATA-TAATA
*
14346115 TAGTTTATACATAA
1 TA-TATATA-AT-A
* *
14346129 TATATATAGTT
1 TATATATAATA
14346140 TATATATAATA
1 TATATATAATA
14346151 TATA-ATAATA
1 TATATATAATA
*
14346161 TAAATATAA
1 TATATATAA
14346170 ACTATATAGT
Statistics
Matches: 132, Mismatches: 29, Indels: 28
0.70 0.15 0.15
Matches are distributed among these distances:
9 1 0.01
10 21 0.16
11 92 0.70
12 5 0.04
13 10 0.08
14 3 0.02
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (11 bp):
TATATATAATA
Found at i:14346175 original size:101 final size:105
Alignment explanation
Indices: 14346008--14346196 Score: 314
Period size: 101 Copynumber: 1.8 Consensus size: 105
14345998 ACATAATATA
* **
14346008 TATATAGTTTATATATAATATATATATAGTTTATATATTTTATAAAATAATATAAATATAAACTA
1 TATATAGTTTATACATAATATATATATAGTTTATATATAATATAAAATAATATAAATATAAACTA
14346073 TATAGTTTATA-TATATA-ATATAAACTAGATATAGAAAC
66 TATAGTTTATATTATATATATATAAACTAGATATAGAAAC
*
14346111 TATATAGTTTATACAT-A-ATATATATAGTTTATATATAATATATAATAATATAAATATAAACTA
1 TATATAGTTTATACATAATATATATATAGTTTATATATAATATAAAATAATATAAATATAAACTA
14346174 TATAGTTTATATTATATATATAT
66 TATAGTTTATATTATATATATAT
14346197 GTAGTTGTTT
Statistics
Matches: 80, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
101 54 0.68
102 7 0.09
103 19 0.24
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (105 bp):
TATATAGTTTATACATAATATATATATAGTTTATATATAATATAAAATAATATAAATATAAACTA
TATAGTTTATATTATATATATATAAACTAGATATAGAAAC
Found at i:14348253 original size:21 final size:21
Alignment explanation
Indices: 14348228--14348292 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
14348218 AAATTACTTG
*
14348228 ATTTAGGAAATAAAAATAGTC
1 ATTTAGGAAATAAAAATAATC
* *
14348249 ATTT----AATAAAACTACTTC
1 ATTTAGGAAATAAAAATA-ATC
*
14348267 GTTTAGGAAATAAAAATAATC
1 ATTTAGGAAATAAAAATAATC
14348288 ATTTA
1 ATTTA
14348293 ATAAAACTAC
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
17 9 0.27
18 5 0.15
21 10 0.30
22 9 0.27
ACGTcount: A:0.49, C:0.08, G:0.09, T:0.34
Consensus pattern (21 bp):
ATTTAGGAAATAAAAATAATC
Found at i:14348272 original size:39 final size:39
Alignment explanation
Indices: 14348216--14348310 Score: 147
Period size: 39 Copynumber: 2.4 Consensus size: 39
14348206 GAAGAGTCAT
* *
14348216 TAAAATTACTT-GATTTAGGAAATAAAAATAGTCATTTAA
1 TAAAACTACTTCG-TTTAGGAAATAAAAATAATCATTTAA
14348255 TAAAACTACTTCGTTTAGGAAATAAAAATAATCATTTAA
1 TAAAACTACTTCGTTTAGGAAATAAAAATAATCATTTAA
*
14348294 TAAAACTACATCGTTTA
1 TAAAACTACTTCGTTTA
14348311 ATGAAACCGT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
39 51 0.98
40 1 0.02
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.35
Consensus pattern (39 bp):
TAAAACTACTTCGTTTAGGAAATAAAAATAATCATTTAA
Found at i:14348297 original size:17 final size:18
Alignment explanation
Indices: 14348275--14348312 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
14348265 TCGTTTAGGA
14348275 AATAAAAATA-ATCATTT
1 AATAAAAATACATCATTT
* *
14348292 AATAAAACTACATCGTTT
1 AATAAAAATACATCATTT
14348310 AAT
1 AAT
14348313 GAAACCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.34
Consensus pattern (18 bp):
AATAAAAATACATCATTT
Found at i:14348312 original size:18 final size:18
Alignment explanation
Indices: 14348250--14348317 Score: 57
Period size: 18 Copynumber: 3.6 Consensus size: 18
14348240 AAAATAGTCA
*
14348250 TTTAATAAAACTACTTCG
1 TTTAATAAAACTACATCG
* *
14348268 TTTAGGAAATAAAAATA-ATCA
1 TTT----AATAAAACTACATCG
14348289 TTTAATAAAACTACATCG
1 TTTAATAAAACTACATCG
*
14348307 TTTAATGAAAC
1 TTTAATAAAAC
14348318 CGTCTAAGTC
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
17 9 0.23
18 16 0.41
21 5 0.13
22 9 0.23
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.34
Consensus pattern (18 bp):
TTTAATAAAACTACATCG
Found at i:14348442 original size:72 final size:72
Alignment explanation
Indices: 14348325--14348469 Score: 245
Period size: 72 Copynumber: 2.0 Consensus size: 72
14348315 AACCGTCTAA
* *
14348325 GTCATTACTGTCGCGGCAAGGAGATACCATGTCATTGTCTCGTTAATGAATTGACGGCGAGATGG
1 GTCATTACCGTCGCGGCAAGGAGATACCATGTCATTGTCTCGTTAATGAATTGACGGCGAGATGA
14348390 TATAATT
66 TATAATT
* * *
14348397 GTCATTACCGTTGCGGCAAGGAGATGCCATGTCATTGTCTCGTTAATGGATTGACGGCGAGATGA
1 GTCATTACCGTCGCGGCAAGGAGATACCATGTCATTGTCTCGTTAATGAATTGACGGCGAGATGA
14348462 TATAATT
66 TATAATT
14348469 G
1 G
14348470 CAATTAAATA
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 68 1.00
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (72 bp):
GTCATTACCGTCGCGGCAAGGAGATACCATGTCATTGTCTCGTTAATGAATTGACGGCGAGATGA
TATAATT
Found at i:14349354 original size:28 final size:28
Alignment explanation
Indices: 14349321--14349377 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
14349311 TCTTAGTTGT
*
14349321 TTTCAAGCACTAGCTCGACGACATAATG
1 TTTCAAGCACTAGCTCGACAACATAATG
* *
14349349 TTTCAAGCATTGGCTCGACAACATAATG
1 TTTCAAGCACTAGCTCGACAACATAATG
14349377 T
1 T
14349378 AAACGAAGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.28
Consensus pattern (28 bp):
TTTCAAGCACTAGCTCGACAACATAATG
Found at i:14352779 original size:20 final size:20
Alignment explanation
Indices: 14352736--14352783 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
14352726 CTTGTCGGTG
*
14352736 CCGATGTCAAGCCAACGTCG
1 CCGATGTCAAGCCAACGTCA
14352756 CCGATGTCAAGCCAAC-TCCA
1 CCGATGTCAAGCCAACGT-CA
14352776 CCGATGTC
1 CCGATGTC
14352784 GAGATAAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.25, C:0.38, G:0.21, T:0.17
Consensus pattern (20 bp):
CCGATGTCAAGCCAACGTCA
Found at i:14358636 original size:22 final size:22
Alignment explanation
Indices: 14358611--14358653 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
14358601 AAAAATTTTA
* *
14358611 ACCTGGTTTCTAAACTCCCTGT
1 ACCTGGTTTCGAAACCCCCTGT
14358633 ACCTGGTTTCGAAACCCCCTG
1 ACCTGGTTTCGAAACCCCCTG
14358654 ACCAGTTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.19, C:0.35, G:0.16, T:0.30
Consensus pattern (22 bp):
ACCTGGTTTCGAAACCCCCTGT
Found at i:14359569 original size:19 final size:19
Alignment explanation
Indices: 14359544--14359593 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
14359534 TGCCTCACAA
**
14359544 TATCGATACTGACCCTTGGG
1 TATCGATACCCACCC-TGGG
14359564 -ATCGATACCCACCCTGGG
1 TATCGATACCCACCCTGGG
14359582 TATCGATACCCA
1 TATCGATACCCA
14359594 AAATAGCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 4 0.15
19 23 0.85
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (19 bp):
TATCGATACCCACCCTGGG
Found at i:14359670 original size:73 final size:73
Alignment explanation
Indices: 14359581--14359723 Score: 223
Period size: 73 Copynumber: 2.0 Consensus size: 73
14359571 CCCACCCTGG
* ** * *
14359581 GTATCGATACCCAAAATAGCTTTGATGTTTTGGGAAAACACTCGATATCGATACTCTTATTTTGA
1 GTATCGATACCAAAAATAGCTTCAATGTTTTAGGAAAACACTCGATATCGATACTCTTATTTGGA
14359646 GTATCTTT
66 GTATCTTT
* *
14359654 GTATCGATACCAAAAATAGCTTCAATTTTTTAGGAAAACACTTGATATCGATACTCTTATTTGGA
1 GTATCGATACCAAAAATAGCTTCAATGTTTTAGGAAAACACTCGATATCGATACTCTTATTTGGA
14359719 GTATC
66 GTATC
14359724 GATACTCTTA
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
73 63 1.00
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.37
Consensus pattern (73 bp):
GTATCGATACCAAAAATAGCTTCAATGTTTTAGGAAAACACTCGATATCGATACTCTTATTTGGA
GTATCTTT
Found at i:14359751 original size:22 final size:21
Alignment explanation
Indices: 14359702--14359751 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
14359692 CACTTGATAT
* *
14359702 CGATACTCTTATTTGGAGTAT
1 CGATACTCTTATTGGGAGTAC
14359723 CGATACTCTTA-TGGGAGGGTAC
1 CGATACTCTTATTGGGA--GTAC
14359745 CGATACT
1 CGATACT
14359752 ACCCTGAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 4 0.16
21 11 0.44
22 10 0.40
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (21 bp):
CGATACTCTTATTGGGAGTAC
Found at i:14360150 original size:70 final size:70
Alignment explanation
Indices: 14360050--14360263 Score: 265
Period size: 70 Copynumber: 3.0 Consensus size: 70
14360040 ATTTTAAACA
* * *
14360050 TTATATTTTATCTTT-GTATTTTAGTTTAAATAGGTTTGAGTATTTTAATTAAGTTTTAGGATAT
1 TTATATTTTATCTTTGGTATTTTAGTTTAAATAGGTTTAAGTATTTTAATTAAGATTTAGAATAT
14360114 TATTT
66 TATTT
* *
14360119 TTATATTTTATCTTTGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATAT
1 TTATATTTTATCTTTGGTATTTTAGTTTAAATAGGTTTAAGTATTTTAATTAAGATTTAGAATAT
14360184 TATTT
66 TATTT
* * * * *
14360189 TAAATATTATT-T-TTTAGATATTTTAGTTTAAATAGTTTTAAGTGTTTTAATTAGGATTTAAGA
1 T-TATATT-TTATCTTT-GGTATTTTAGTTTAAATAGGTTTAAGTATTTTAATTAAGATTT-AGA
14360252 A-ACTTATTT
62 ATA-TTATTT
14360261 TTA
1 TTA
14360264 GGAATTTGAA
Statistics
Matches: 129, Mismatches: 10, Indels: 10
0.87 0.07 0.07
Matches are distributed among these distances:
69 15 0.12
70 54 0.42
71 47 0.36
72 13 0.10
ACGTcount: A:0.30, C:0.01, G:0.12, T:0.56
Consensus pattern (70 bp):
TTATATTTTATCTTTGGTATTTTAGTTTAAATAGGTTTAAGTATTTTAATTAAGATTTAGAATAT
TATTT
Found at i:14360209 original size:14 final size:15
Alignment explanation
Indices: 14360181--14360222 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
14360171 GGATTTAGAA
14360181 TATTATTTTAAATAT
1 TATTATTTTAAATAT
*
14360196 TATT-TTTTAGATAT
1 TATTATTTTAAATAT
*
14360210 T-TTAGTTTAAATA
1 TATTATTTTAAATA
14360223 GTTTTAAGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 2 0.09
14 17 0.74
15 4 0.17
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (15 bp):
TATTATTTTAAATAT
Found at i:14366528 original size:5 final size:5
Alignment explanation
Indices: 14366518--14366625 Score: 74
Period size: 5 Copynumber: 20.8 Consensus size: 5
14366508 TTGTTCTATT
* *
14366518 TTTTA TTTTA TTTTA ATTTA TTTTA TTTTA TTTTTCT TTTTA TTTTA TTTGTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTTT-A TTTTA TTTTA -TT-TTA
**** * * * *
14366572 GCAAA TTTTA TTTTCA TTCTA -TTTA TTTTA TTTTA GTTAA TTTTA TATTA
1 TTTTA TTTTA TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
14366622 TTTT
1 TTTT
14366626 TCTCTGAACA
Statistics
Matches: 77, Mismatches: 20, Indels: 12
0.71 0.18 0.11
Matches are distributed among these distances:
4 3 0.04
5 57 0.74
6 14 0.18
7 3 0.04
ACGTcount: A:0.22, C:0.04, G:0.03, T:0.71
Consensus pattern (5 bp):
TTTTA
Found at i:14368673 original size:69 final size:70
Alignment explanation
Indices: 14368490--14368684 Score: 265
Period size: 70 Copynumber: 2.8 Consensus size: 70
14368480 TTTAAACATC
* * *
14368490 ATATTTTATCCTT--GTATTTTAGTTTAAATAGGTTTTAGTGTTTTAATTAAGTTTTAGGATATT
1 ATATTTTAT-CTTAGGTATTTTAGTTTAAATAGGTTTTAGTGTTTTAATTAGGATTTAGAATATT
*
14368553 ATTTTT
65 ATTTTA
* * *
14368559 ATATTTTATCTTTGGTATTTTAGTTTAAATATGTTTTAGTATTTTAATTAGGATTTAGAATATTA
1 ATATTTTATCTTAGGTATTTTAGTTTAAATAGGTTTTAGTGTTTTAATTAGGATTTAGAATATTA
14368624 TTTTA
66 TTTTA
14368629 ATATTATT-T-TTAGGTATTTTAGTTTAAATA-GTTTTAAGTGTTTTAATTAGGATTTA
1 ATATT-TTATCTTAGGTATTTTAGTTTAAATAGGTTTT-AGTGTTTTAATTAGGATTTA
14368685 AGATGTTTTA
Statistics
Matches: 114, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
68 8 0.07
69 48 0.42
70 56 0.49
71 2 0.02
ACGTcount: A:0.29, C:0.02, G:0.13, T:0.57
Consensus pattern (70 bp):
ATATTTTATCTTAGGTATTTTAGTTTAAATAGGTTTTAGTGTTTTAATTAGGATTTAGAATATTA
TTTTA
Found at i:14369289 original size:12 final size:12
Alignment explanation
Indices: 14369272--14369301 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
14369262 ATTCAGTTAT
14369272 TTTATTTATTTG
1 TTTATTTATTTG
*
14369284 TTTATTTATTTT
1 TTTATTTATTTG
14369296 TTTATT
1 TTTATT
14369302 CTTCTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (12 bp):
TTTATTTATTTG
Found at i:14369839 original size:19 final size:19
Alignment explanation
Indices: 14369814--14369861 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
14369804 TGCCTCACAA
**
14369814 TATCGATACTGACCCTTGGG
1 TATCGATACCCACCC-TGGG
14369834 -ATCGATACCCACCCTGGG
1 TATCGATACCCACCCTGGG
14369852 TATCGATACC
1 TATCGATACC
14369862 AAAAATAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.25
Consensus pattern (19 bp):
TATCGATACCCACCCTGGG
Found at i:14369971 original size:73 final size:73
Alignment explanation
Indices: 14369851--14369992 Score: 205
Period size: 73 Copynumber: 1.9 Consensus size: 73
14369841 CCCACCCTGG
** * *
14369851 GTATCGATACCAAAAATAACTTTGATGTTTTGGGAAAACACTCGATAT-AGATACTCTTATTTTG
1 GTATCGATACCAAAAATAACTTCAATGTTTTAGGAAAACACTCGATATCA-ATACTCTTATTTGG
14369915 AGTATCTGC
65 AGTATCTGC
* * *
14369924 GTATCGATACCAAAAATAGCTTCAATTTTTTAGGAAAACACTTGATATCAATACTCTTATTTGGA
1 GTATCGATACCAAAAATAACTTCAATGTTTTAGGAAAACACTCGATATCAATACTCTTATTTGGA
14369989 GTAT
66 GTAT
14369993 TTGATACTCC
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
73 60 0.98
74 1 0.02
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (73 bp):
GTATCGATACCAAAAATAACTTCAATGTTTTAGGAAAACACTCGATATCAATACTCTTATTTGGA
GTATCTGC
Found at i:14370020 original size:22 final size:22
Alignment explanation
Indices: 14369994--14370044 Score: 86
Period size: 22 Copynumber: 2.3 Consensus size: 22
14369984 TTGGAGTATT
14369994 TGATACTCCTATGGGAGGGTA-
1 TGATACTCCTATGGGAGGGTAC
14370015 TCGATACTCCTATGGGAGGGTAC
1 T-GATACTCCTATGGGAGGGTAC
14370038 TGATACT
1 TGATACT
14370045 ACCCTGAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 1 0.04
22 26 0.93
23 1 0.04
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (22 bp):
TGATACTCCTATGGGAGGGTAC
Found at i:14379466 original size:11 final size:11
Alignment explanation
Indices: 14379450--14379480 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
14379440 ATTAGGATAG
*
14379450 TATTTTGTTAT
1 TATTTTATTAT
14379461 TATTTTATTAT
1 TATTTTATTAT
14379472 TATTTTATT
1 TATTTTATT
14379481 CCTTAATCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (11 bp):
TATTTTATTAT
Found at i:14380768 original size:9 final size:9
Alignment explanation
Indices: 14380754--14380784 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
14380744 ATTTTTCATT
14380754 TTACTTAAA
1 TTACTTAAA
14380763 TTACTTAAA
1 TTACTTAAA
14380772 TTA-TTAAA
1 TTACTTAAA
14380780 TTACT
1 TTACT
14380785 ATTATTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (9 bp):
TTACTTAAA
Found at i:14380790 original size:3 final size:3
Alignment explanation
Indices: 14380779--14380854 Score: 91
Period size: 3 Copynumber: 25.3 Consensus size: 3
14380769 AAATTATTAA
* * * *
14380779 ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT -TA AAT ATT AGT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
14380826 ATT ATT ATA ATT ATTT ATT ATT ATT ATT A
1 ATT ATT ATT ATT A-TT ATT ATT ATT ATT A
14380855 AATAAATACA
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
2 1 0.02
3 57 0.93
4 3 0.05
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:14381909 original size:15 final size:15
Alignment explanation
Indices: 14381880--14381920 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
14381870 TAATTATTTC
*
14381880 AATTTAG-TCTTTAT
1 AATTTAGTTATTTAT
*
14381894 ATTTTAGTTATTTAT
1 AATTTAGTTATTTAT
14381909 AATTTAGTTATT
1 AATTTAGTTATT
14381921 ACTTGTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
14 6 0.26
15 17 0.74
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.61
Consensus pattern (15 bp):
AATTTAGTTATTTAT
Found at i:14382125 original size:27 final size:29
Alignment explanation
Indices: 14382095--14382159 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 29
14382085 TAATCACTAA
14382095 TTATTTTTAC-CATA-AGTTTT-TTTTATT
1 TTATTTTTACACATATAGTTTTATTTTA-T
*
14382122 TTATTATTTACACCTATAGTTTTAATTTTAT
1 TTATT-TTTACACATATAGTTTT-ATTTTAT
14382153 TTATTTT
1 TTATTTT
14382160 AGTAATTGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
27 5 0.16
28 5 0.16
29 3 0.09
30 8 0.25
31 6 0.19
32 5 0.16
ACGTcount: A:0.25, C:0.08, G:0.03, T:0.65
Consensus pattern (29 bp):
TTATTTTTACACATATAGTTTTATTTTAT
Found at i:14382633 original size:145 final size:144
Alignment explanation
Indices: 14382346--14382649 Score: 346
Period size: 145 Copynumber: 2.1 Consensus size: 144
14382336 TAATCATATT
*
14382346 TTAATATTTATTTATTTTTTAATATTAAGAAATGGACAGTCTTAAAGAACCTAGAAGTCCTTTTC
1 TTAATATTTATTTATTTTTTAATATTAAGAAATGGACAGTCTTAAAGAACCTAGAAGTCATTTTC
* * * * * * * * * *
14382411 TGATATTCTTAAATAAATAAATATCTTATTTTTATAAATTATATATTAATTTATTTTAATTTTTT
66 TGATATTCTTAAATAAATAAATATCTTATTTATAAAAATAATAAATAAATATATTATAATATATA
14382476 TTAGAAAAATATTTTA
131 TT--AAAAATATTTTA
** *
14382492 TTAATATTTATTTA-TTTTTAATATTAAGAAATGTG-TTGTCTTAAAGCACCTAGAAGTCATTTT
1 TTAATATTTATTTATTTTTTAATATTAAGAAATG-GACAGTCTTAAAGAACCTAGAAGTCATTTT
*
14382555 CTGATATT-TCTAAGTAAATAAATATCTTATTTATAAAAATAAATAAATAAATATATATATATAT
65 CTGATATTCT-TAAATAAATAAATATCTTATTTATAAAAAT-AATAAATAAATATAT-TATA-AT
* *
14382619 ATATATT-AATATATTTTC
126 ATATATTAAAAATATTTTA
*
14382637 TTAAAATTATATT
1 TTAATATT-TATT
14382650 AATAAATTTG
Statistics
Matches: 134, Mismatches: 18, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
144 1 0.01
145 94 0.70
146 30 0.22
147 3 0.02
148 6 0.04
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (144 bp):
TTAATATTTATTTATTTTTTAATATTAAGAAATGGACAGTCTTAAAGAACCTAGAAGTCATTTTC
TGATATTCTTAAATAAATAAATATCTTATTTATAAAAATAATAAATAAATATATTATAATATATA
TTAAAAATATTTTA
Found at i:14384701 original size:21 final size:21
Alignment explanation
Indices: 14384676--14384719 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
14384666 GAGTAACACC
14384676 TTTTCATAC-ATGCATTTTCAT
1 TTTTCAT-CTATGCATTTTCAT
*
14384697 TTTTCATCTTTGCATTTTCAT
1 TTTTCATCTATGCATTTTCAT
14384718 TT
1 TT
14384720 ATACTTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.18, C:0.18, G:0.05, T:0.59
Consensus pattern (21 bp):
TTTTCATCTATGCATTTTCAT
Found at i:14387263 original size:72 final size:72
Alignment explanation
Indices: 14387146--14387280 Score: 182
Period size: 72 Copynumber: 1.9 Consensus size: 72
14387136 ATACAATAAA
* *
14387146 GCTTGAGTTATCCCCCTAAAGCAATTGGTTAATAGCCCCAACTTTATGGATAATATTCAGCTAGT
1 GCTTGAGTTATCCCCCTAAAGCAAATGGTTAATAGCCCCAACTTTATGAATAATATTCAGCTAGT
14387211 CTGTTAT
66 CTGTTAT
* * * * **
14387218 GCTTGAGTTGTCCCTCTAGAA-CAAATGGTTGATGGCCCCGGCTTTATGAATAATATTCAGCTA
1 GCTTGAGTTATCCCCCTA-AAGCAAATGGTTAATAGCCCCAACTTTATGAATAATATTCAGCTA
14387281 ACCTATTATA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
72 52 0.96
73 2 0.04
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (72 bp):
GCTTGAGTTATCCCCCTAAAGCAAATGGTTAATAGCCCCAACTTTATGAATAATATTCAGCTAGT
CTGTTAT
Found at i:14389047 original size:36 final size:37
Alignment explanation
Indices: 14389007--14389080 Score: 141
Period size: 36 Copynumber: 2.0 Consensus size: 37
14388997 TGAAAGTAAG
14389007 CCTTACAGTTTAGAAGGTT-GGGGCATTTTGAAGGCC
1 CCTTACAGTTTAGAAGGTTGGGGGCATTTTGAAGGCC
14389043 CCTTACAGTTTAGAAGGTTGGGGGCATTTTGAAGGCC
1 CCTTACAGTTTAGAAGGTTGGGGGCATTTTGAAGGCC
14389080 C
1 C
14389081 AATTCAGACA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 19 0.51
37 18 0.49
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.30
Consensus pattern (37 bp):
CCTTACAGTTTAGAAGGTTGGGGGCATTTTGAAGGCC
Found at i:14390896 original size:22 final size:22
Alignment explanation
Indices: 14390843--14390896 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
14390833 TCTACACTCT
*
14390843 TCAAAGATGATAGATTCTCTTT
1 TCAAAGATGATAGATTCTCTTC
*
14390865 TTAAAGATGATAGATTCTCTTC
1 TCAAAGATGATAGATTCTCTTC
*
14390887 TCAAATATGA
1 TCAAAGATGA
14390897 AAGCTTTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (22 bp):
TCAAAGATGATAGATTCTCTTC
Found at i:14392273 original size:22 final size:22
Alignment explanation
Indices: 14392220--14392273 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
14392210 TCTACACTCT
*
14392220 TCAAAGATGATAGATTCTCTTT
1 TCAAAGATGATAGATTCTCTTC
*
14392242 TTAAAGATGATAGATTCTCTTC
1 TCAAAGATGATAGATTCTCTTC
*
14392264 TCAAATATGA
1 TCAAAGATGA
14392274 AAGCTTTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (22 bp):
TCAAAGATGATAGATTCTCTTC
Found at i:14392997 original size:45 final size:45
Alignment explanation
Indices: 14392933--14393964 Score: 1553
Period size: 45 Copynumber: 22.9 Consensus size: 45
14392923 TTCCCACATG
* * * *
14392933 TGTAAGCCCTTCAATGCATGATTTTTTCAAAATCTTTGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
* * * *
14392978 TGTAAGTCCTTTAGTGCATGATGTTTTCAAAACCTTCAGGTTATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
* *
14393023 TGTAATCCCTTCAGTGAATGATGTTTTCAAAACCTTCGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
* *
14393068 TGTAATCCCTTAAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
* *
14393113 TGTAAGCCCTTCAGTGCATGATATTTTCAAAACCTTCAGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
* * * *
14393158 TGTAACCCCTTCAGTGTATAATGTTTTCAAAACCTTCAGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
* * *
14393203 TGTAAGACCTTCAATGCACGATGTTTTCAAAACCTTCGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
14393248 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
14393293 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
* * *
14393338 TGTAAACCTTTCAGTGCATTATGTTTTCAAAACCTTCGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
** *
14393383 TGTAAGCTATTCAGTGCATGATGTTTTCAAAACCTTCGGGTAATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
* * *
14393428 TGTAAGACCTTCAATACATGATGTTTTCAAAACCTTCGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
*
14393473 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAATCTTCGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
*
14393518 TGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
* * *
14393563 TGTAAGCCCTTCAGTACATAATGTTTTCAAAACCTTCGGGTAATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
* * * * *
14393608 TGTAAGACCTTCAATACATGATGTTTTTAAAACCTTTGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
14393653 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
*
14393698 TGTAAACCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
*
14393743 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTAATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
** * *
14393788 TGTAAGATCTTCAATACATGATGTTTTCAAAACCTTCGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
* *
14393833 TGTAAGCCCTTCAGTGCATAATTTTTTCAAAACCTTCGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
* *
14393878 TGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGTGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
** *
14393923 CATAAGACCTGT-AGTGCATGATGTTTTCAAAAAGCCTTCGGG
1 TGTAAGCCCT-TCAGTGCATGATGTTTTC-AAAA-CCTTCGGG
14393965 AGCTTTTTGA
Statistics
Matches: 894, Mismatches: 90, Indels: 4
0.90 0.09 0.00
Matches are distributed among these distances:
45 882 0.99
46 5 0.01
47 7 0.01
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (45 bp):
TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
Found at i:14394194 original size:3 final size:3
Alignment explanation
Indices: 14394186--14394268 Score: 60
Period size: 3 Copynumber: 27.3 Consensus size: 3
14394176 AATTACTTAA
* ** * * * *
14394186 ATT ATT ATT TTT AAA ATT ACT ATT ATT ATT ATT ATT -TA AAT ATT AGT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
14394233 ATT ATT GTT ATA ATT ATT ATTT ATTT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT A-TT A-TT ATT ATT ATT A
14394269 AATAAATACA
Statistics
Matches: 60, Mismatches: 18, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
2 1 0.02
3 52 0.87
4 7 0.12
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:14394816 original size:14 final size:15
Alignment explanation
Indices: 14394783--14394824 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
14394773 ATCAACAGGC
14394783 ACAACCACAACAAACA
1 ACAACCACAA-AAACA
*
14394799 ACAACCA-AAAACCA
1 ACAACCACAAAAACA
*
14394813 ACAACCAGAAAA
1 ACAACCACAAAA
14394825 GAAAAAGAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 11 0.46
15 6 0.25
16 7 0.29
ACGTcount: A:0.64, C:0.33, G:0.02, T:0.00
Consensus pattern (15 bp):
ACAACCACAAAAACA
Found at i:14395346 original size:15 final size:15
Alignment explanation
Indices: 14395317--14395357 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
14395307 TAATTATTTC
*
14395317 AATTTAG-TCTTTAT
1 AATTTAGTTATTTAT
*
14395331 ATTTTAGTTATTTAT
1 AATTTAGTTATTTAT
14395346 AATTTAGTTATT
1 AATTTAGTTATT
14395358 ACTTGTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
14 6 0.26
15 17 0.74
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.61
Consensus pattern (15 bp):
AATTTAGTTATTTAT
Found at i:14399825 original size:26 final size:26
Alignment explanation
Indices: 14399795--14399903 Score: 166
Period size: 26 Copynumber: 4.2 Consensus size: 26
14399785 ATATAGTAAC
* * *
14399795 ATTTATCACTTGCACTCGAAAGTTCC
1 ATTTATCACTCGCACTCGAAAGTGCT
*
14399821 ATTTATCACTCGCACTCG-AAGTTCT
1 ATTTATCACTCGCACTCGAAAGTGCT
*
14399846 ATTTATCACTCGCACTCAAAAGTGCT
1 ATTTATCACTCGCACTCGAAAGTGCT
14399872 ATTTATCACTCGCACTCGAAAGTGCT
1 ATTTATCACTCGCACTCGAAAGTGCT
14399898 ATTTAT
1 ATTTAT
14399904 ACTGAGACTC
Statistics
Matches: 77, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
25 23 0.30
26 54 0.70
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.35
Consensus pattern (26 bp):
ATTTATCACTCGCACTCGAAAGTGCT
Found at i:14399876 original size:51 final size:52
Alignment explanation
Indices: 14399795--14399903 Score: 166
Period size: 51 Copynumber: 2.1 Consensus size: 52
14399785 ATATAGTAAC
* * * *
14399795 ATTTATCACTTGCACTCGAAAGTTCCATTTATCACTCGCACTCG-AAGTTCT
1 ATTTATCACTCGCACTCAAAAGTGCCATTTATCACTCGCACTCGAAAGTGCT
*
14399846 ATTTATCACTCGCACTCAAAAGTGCTATTTATCACTCGCACTCGAAAGTGCT
1 ATTTATCACTCGCACTCAAAAGTGCCATTTATCACTCGCACTCGAAAGTGCT
14399898 ATTTAT
1 ATTTAT
14399904 ACTGAGACTC
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
51 40 0.77
52 12 0.23
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.35
Consensus pattern (52 bp):
ATTTATCACTCGCACTCAAAAGTGCCATTTATCACTCGCACTCGAAAGTGCT
Found at i:14406213 original size:26 final size:26
Alignment explanation
Indices: 14406179--14406253 Score: 93
Period size: 26 Copynumber: 3.0 Consensus size: 26
14406169 TTGCACATAT
*
14406179 AGTGTCATTTATCACTTGCACTCGAA
1 AGTGCCATTTATCACTTGCACTCGAA
14406205 AGTGCCATTTATCAC-T-CACTCG-A
1 AGTGCCATTTATCACTTGCACTCGAA
* * *
14406228 AGTTCTATTTATCACTCGCACTCGAA
1 AGTGCCATTTATCACTTGCACTCGAA
14406254 GTGTTATTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
23 14 0.33
24 6 0.14
25 7 0.17
26 15 0.36
ACGTcount: A:0.27, C:0.27, G:0.13, T:0.33
Consensus pattern (26 bp):
AGTGCCATTTATCACTTGCACTCGAA
Found at i:14406255 original size:25 final size:25
Alignment explanation
Indices: 14406185--14406269 Score: 95
Period size: 25 Copynumber: 3.4 Consensus size: 25
14406175 ATATAGTGTC
* * *
14406185 ATTTATCACTTGCACTCGAAAGTGCC
1 ATTTATCACTCGCACTCG-AAGTTCT
14406211 ATTTATCACT--CACTCGAAGTTCT
1 ATTTATCACTCGCACTCGAAGTTCT
14406234 ATTTATCACTCGCACTCGAAGTGT-T
1 ATTTATCACTCGCACTCGAAGT-TCT
*
14406259 ATTTGTCACTC
1 ATTTATCACTC
14406270 ACAGACGAAC
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
23 15 0.28
24 6 0.11
25 21 0.40
26 11 0.21
ACGTcount: A:0.25, C:0.26, G:0.13, T:0.36
Consensus pattern (25 bp):
ATTTATCACTCGCACTCGAAGTTCT
Found at i:14408953 original size:16 final size:16
Alignment explanation
Indices: 14408932--14408982 Score: 75
Period size: 16 Copynumber: 3.2 Consensus size: 16
14408922 TAAATAAACG
*
14408932 AACATAAATGAACACA
1 AACATAAACGAACACA
*
14408948 AACATAAACGAACACG
1 AACATAAACGAACACA
*
14408964 AACATAAACGAACATA
1 AACATAAACGAACACA
14408980 AAC
1 AAC
14408983 GTTGGAGATC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.61, C:0.22, G:0.08, T:0.10
Consensus pattern (16 bp):
AACATAAACGAACACA
Found at i:14409949 original size:24 final size:24
Alignment explanation
Indices: 14409888--14409943 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
14409878 AGATTGGGTT
* **
14409888 AAACATAAATGAATGAACATAAAC
1 AAACATAACTGAACAAACATAAAC
14409912 AAACATAACTGAACAAACATAAAC
1 AAACATAACTGAACAAACATAAAC
*
14409936 GAACATAA
1 AAACATAA
14409944 TCGAACGTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.62, C:0.16, G:0.07, T:0.14
Consensus pattern (24 bp):
AAACATAACTGAACAAACATAAAC
Found at i:14410433 original size:23 final size:23
Alignment explanation
Indices: 14410407--14410454 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
14410397 ATAAAGTACA
*
14410407 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
14410430 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
14410453 AT
1 AT
14410455 TGACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:14410965 original size:23 final size:23
Alignment explanation
Indices: 14410930--14411002 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
14410920 ATACTTTACA
* *
14410930 ATATAAGCACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
*
14410953 ATATAAACGCTACCTATTATATT
1 ATATAAACGCTACCTATTACATT
* *
14410976 ATATTAACGCTACCTATTACATC
1 ATATAAACGCTACCTATTACATT
14410999 ATAT
1 ATAT
14411003 TTTTACCTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.38, C:0.21, G:0.04, T:0.37
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:14411003 original size:23 final size:23
Alignment explanation
Indices: 14410939--14411003 Score: 103
Period size: 23 Copynumber: 2.8 Consensus size: 23
14410929 AATATAAGCA
*
14410939 CTACCTATTACATTATATAAACG
1 CTACCTATTACATTATATTAACG
*
14410962 CTACCTATTATATTATATTAACG
1 CTACCTATTACATTATATTAACG
*
14410985 CTACCTATTACATCATATT
1 CTACCTATTACATTATATT
14411004 TTTACCTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.35, C:0.22, G:0.03, T:0.40
Consensus pattern (23 bp):
CTACCTATTACATTATATTAACG
Found at i:14411444 original size:23 final size:23
Alignment explanation
Indices: 14411418--14411490 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
14411408 ATATTTTACA
*
14411418 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
14411441 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
14411464 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
14411487 ATAT
1 ATAT
14411491 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:14411928 original size:23 final size:23
Alignment explanation
Indices: 14411902--14411974 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
14411892 ATATTTTACA
*
14411902 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
14411925 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
14411948 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
14411971 ATAT
1 ATAT
14411975 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:14411974 original size:484 final size:490
Alignment explanation
Indices: 14410524--14412708 Score: 4115
Period size: 488 Copynumber: 4.5 Consensus size: 490
14410514 TACATTATAA
*
14410524 TATATTGAAAGTGTCTATACTTTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTT
1 TATATTGAAAGTGTCTATAC-TTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTT
14410589 ATGTTTCAA--TTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCAT
65 ATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCAT
14410652 TTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAAC
130 TTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAAC
14410717 AATATTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAA
195 AATATTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAA
*
14410782 TATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAAC
260 TATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATATTAAAAC
* * *
14410847 TCACTAAAAAAATAACCTTAAATTAATATTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAA
325 TCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAA
*
14410912 AAGGATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTATATTA
390 AAGGATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTA
14410977 TATTAA-CGCTACCTATTACATCATATTTTTACCTAT
455 TA-TAAGCGCTACCTATTACATCATATTTTTACCTAT
14411013 TATATTGAAAGTGTCTATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTA
1 TATATTGAAAGTGTCTATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTA
14411078 TGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATT
66 TGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATT
14411143 TGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACA
131 TGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACA
14411208 ATATTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAAT-A-
196 ATATTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAAT
*
14411271 ATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATATTAAGACT
261 ATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATATTAAAACT
14411336 CACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAA
326 CACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAA
*
14411401 AGGATAGATATTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTAT
391 AGGATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTAT
14411466 ATAAGCGCTACCTATTACATCATATTTTTACCTAT
456 ATAAGCGCTACCTATTACATCATATTTTTACCTAT
14411501 TATATTGAAAGTGTCTATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTA
1 TATATTGAAAGTGTCTATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTA
14411566 TGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATT
66 TGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATT
14411631 TGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACA
131 TGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACA
14411696 ATATTAACCAAAGATAATAAT-AA-ATGT-A-ATATATGTTTATTGTTTTTAATTTAATAAT-A-
196 ATATTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAAT
*
14411755 ATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATATTAAGACT
261 ATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATATTAAAACT
*
14411820 CACTCAAAAGATAACCTTAAATTAATGTTTTCCATAGTGAAAAAAGTATGGACACTTTTATAAAA
326 CACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAA
*
14411885 AGGATAGATATTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTAT
391 AGGATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTAT
14411950 ATAAGCGCTACCTATTACATCATATTTTTACCTAT
456 ATAAGCGCTACCTATTACATCATATTTTTACCTAT
14411985 TATATTGAAAGTGTCTATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTA
1 TATATTGAAAGTGTCTATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTA
14412050 TGTTTCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATT
66 TGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATT
*
14412114 TGCACAAAAATTTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACA
131 TGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACA
14412179 ATATTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAAT
196 ATATTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAAT
*
14412244 ATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACT
261 ATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATATTAAAACT
14412309 CACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAA
326 CACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAA
14412374 AGGATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTAT
391 AGGATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTAT
14412439 ATAAGCGCTACCTATTACATCATATTTTTACCTAT
456 ATAAGCGCTACCTATTACATCATATTTTTACCTAT
14412474 TATATTGAAAGTGTCTATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTA
1 TATATTGAAAGTGTCTATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTA
14412539 TGTTTCAATTTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCAT
66 TGTTTCAA-TTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCAT
* * *
14412604 TTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGTACTTAAATTTAAC
130 TTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAAC
14412669 AATATTAACCAAAGATAATAATAAATATGTAATATATATG
195 AATATTAACCAAAGATAATAATAAATATGTAATATATATG
14412709 GTTCGACACT
Statistics
Matches: 1667, Mismatches: 18, Indels: 20
0.98 0.01 0.01
Matches are distributed among these distances:
483 141 0.08
484 335 0.20
485 5 0.00
486 5 0.00
487 35 0.02
488 488 0.29
489 320 0.19
490 182 0.11
491 156 0.09
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.41
Consensus pattern (490 bp):
TATATTGAAAGTGTCTATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTA
TGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATT
TGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACA
ATATTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAAT
ATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATATTAAAACT
CACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAA
AGGATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTAT
ATAAGCGCTACCTATTACATCATATTTTTACCTAT
Found at i:14412426 original size:23 final size:23
Alignment explanation
Indices: 14412391--14412463 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
14412381 ATACTTTACA
*
14412391 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
14412414 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
14412437 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
14412460 ATAT
1 ATAT
14412464 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:14412883 original size:19 final size:19
Alignment explanation
Indices: 14412859--14412903 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
14412849 ATTCACATAT
14412859 AAAATTATAAATCGTATAC
1 AAAATTATAAATCGTATAC
*
14412878 AAAATTATAAATCTTATAC
1 AAAATTATAAATCGTATAC
14412897 AAAATTA
1 AAAATTA
14412904 ACCCTACATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.56, C:0.09, G:0.02, T:0.33
Consensus pattern (19 bp):
AAAATTATAAATCGTATAC
Found at i:14414735 original size:33 final size:33
Alignment explanation
Indices: 14414698--14414763 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
14414688 CATCTTAATA
*
14414698 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
14414731 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
14414764 CTATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:14414822 original size:21 final size:21
Alignment explanation
Indices: 14414797--14414861 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
14414787 CCCCTTATGC
* *
14414797 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
14414818 CTCTCAAGTTTCTCTTCAACT
1 CTCTCAAGTTTCTCTTCGACT
*
14414839 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
14414860 CT
1 CT
14414862 TGATTGTCTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.18, C:0.31, G:0.09, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:14417077 original size:17 final size:18
Alignment explanation
Indices: 14417055--14417097 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
14417045 ATATATTCGG
14417055 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
14417072 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
14417092 TATCAT
1 TATCAT
14417098 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:14417115 original size:20 final size:19
Alignment explanation
Indices: 14417060--14417106 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
14417050 TTCGGTATCA
14417060 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
14417079 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
14417100 TTTTACC
1 TTTTACC
14417107 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:14417272 original size:20 final size:20
Alignment explanation
Indices: 14417241--14417287 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
14417231 TCCGGTAACA
14417241 TTTTACCAGTTTTATCAT-T
1 TTTTACCAGTTTTATCATAT
*
14417260 TTGTTACCGGTTTTATCATAT
1 TT-TTACCAGTTTTATCATAT
14417281 TTTTACC
1 TTTTACC
14417288 TGGTATATCG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 2 0.08
20 20 0.80
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.09, T:0.55
Consensus pattern (20 bp):
TTTTACCAGTTTTATCATAT
Found at i:14417476 original size:176 final size:177
Alignment explanation
Indices: 14417027--14417493 Score: 659
Period size: 181 Copynumber: 2.6 Consensus size: 177
14417017 CGTACTTACG
* *
14417027 AAAGTATCGACACTTTCAATATATTCGGTATCATTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACATTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
14417092 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
*
14417157 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
131 AGGAGCTAAAACTG----TCTTTTAAATTCACAAAGTGTCGATCCTTATAT
* *
14417208 AAAGTATCGACACTTTCAATATATCCGGTAACATTTTACCAGTTTTATCATTTTGTTACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACATTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
14417273 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
** *
14417338 AGGATTTAAAACTG-C-TTTAAATTCACGAAGTGTCGATCCTTATATT
131 AGGAGCTAAAACTGTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
* * * * ** * *
14417384 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCATTTTAATACTGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACATTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
14417449 TGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
14417494 AATTTGGATC
Statistics
Matches: 258, Mismatches: 27, Indels: 7
0.88 0.09 0.02
Matches are distributed among these distances:
175 28 0.11
176 98 0.38
181 132 0.51
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.42
Consensus pattern (177 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACATTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
AGGAGCTAAAACTGTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
Found at i:14420308 original size:20 final size:19
Alignment explanation
Indices: 14420277--14420321 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
14420267 AAAATGGCCC
14420277 AATTTCACACTCTAACATT
1 AATTTCACACTCTAACATT
* *
14420296 ATTTTCAACACTCTGACATT
1 AATTTC-ACACTCTAACATT
14420316 AATTTC
1 AATTTC
14420322 CATCATTTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.33, C:0.24, G:0.02, T:0.40
Consensus pattern (19 bp):
AATTTCACACTCTAACATT
Found at i:14421897 original size:45 final size:44
Alignment explanation
Indices: 14421844--14421945 Score: 118
Period size: 45 Copynumber: 2.3 Consensus size: 44
14421834 ACCAATCCAC
14421844 GCATCGATGCAC-CA-TTGAATAAATTGAACATCGAATGCATTTTAT
1 GCATCGATGCACTCAGTTGAATAAA---AACATCGAATGCATTTTAT
** * *
14421889 GCATCGATGCACTCAGGTTTTATGAAAACATCGAATGTATTTTAT
1 GCATCGATGCACTCA-GTTGAATAAAAACATCGAATGCATTTTAT
14421934 GCATCGATGCAC
1 GCATCGATGCAC
14421946 AGACCATGTA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
45 42 0.84
46 2 0.04
48 6 0.12
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (44 bp):
GCATCGATGCACTCAGTTGAATAAAAACATCGAATGCATTTTAT
Found at i:14427602 original size:15 final size:15
Alignment explanation
Indices: 14427578--14427622 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
14427568 TTCTATATTG
*
14427578 ATTATTAATAAATT-A
1 ATTATCAAT-AATTAA
14427593 ATTATCAATAATTAA
1 ATTATCAATAATTAA
14427608 ATTAT-AA-AATTAA
1 ATTATCAATAATTAA
14427621 AT
1 AT
14427623 ATATTTAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 8 0.29
14 6 0.21
15 14 0.50
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (15 bp):
ATTATCAATAATTAA
Found at i:14429308 original size:29 final size:27
Alignment explanation
Indices: 14429259--14429321 Score: 65
Period size: 29 Copynumber: 2.3 Consensus size: 27
14429249 CGAATTATTC
* *
14429259 CCTAAATTAGAGGACTAAAGTGTGAGAAA
1 CCTAAATTAGAGGAATAAAGTCT-A-AAA
*
14429288 CCTAAATCTAGA-GAATTAAGTCTAAAA
1 CCTAAAT-TAGAGGAATAAAGTCTAAAA
14429315 CCTAAAT
1 CCTAAAT
14429322 GTAACTAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 10 0.33
28 1 0.03
29 15 0.50
30 4 0.13
ACGTcount: A:0.46, C:0.14, G:0.16, T:0.24
Consensus pattern (27 bp):
CCTAAATTAGAGGAATAAAGTCTAAAA
Found at i:14431534 original size:5 final size:5
Alignment explanation
Indices: 14431519--14431560 Score: 50
Period size: 5 Copynumber: 8.2 Consensus size: 5
14431509 AATTGATAGC
*
14431519 AAAACT AAAAT AAAAT AAAAT AAGAT -AAAT AGAAAT AAAAT A
1 AAAA-T AAAAT AAAAT AAAAT AAAAT AAAAT A-AAAT AAAAT A
14431561 TCACTAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
4 3 0.09
5 20 0.62
6 9 0.28
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:14431710 original size:18 final size:18
Alignment explanation
Indices: 14431684--14431718 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
14431674 TTCAAAATCC
*
14431684 TTTTTCAAAACTATTTTA
1 TTTTCCAAAACTATTTTA
*
14431702 TTTTCCAAAATTATTTT
1 TTTTCCAAAACTATTTT
14431719 TCTAAAACTG
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:0.31, C:0.11, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTCCAAAACTATTTTA
Found at i:14431903 original size:2 final size:2
Alignment explanation
Indices: 14431829--14431886 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
14431819 ACTATATGTA
*
14431829 AT AT AC AT 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 AT AT AT AT
14431871 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
14431887 TAAAATACTA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14432723 original size:43 final size:45
Alignment explanation
Indices: 14432650--14432892 Score: 144
Period size: 44 Copynumber: 5.5 Consensus size: 45
14432640 AGAAAAGCTT
* * *
14432650 ATCCGACTCCTTA-GGCGATGGACGAGCCAAGAAA-ATGATATTG
1 ATCCAACTCCTTATGTCGATGGACAAGCCAAGAAATATGATATTG
* * *
14432693 ATCCAACTTCTTAT-TCGATGGACAATCCAAGAAATATGATGTTG
1 ATCCAACTCCTTATGTCGATGGACAAGCCAAGAAATATGATATTG
*
14432737 ATCCAACTCCTTATGT-GATGGAATCAAGCAAAGAAA-AGTGA-AGTTG
1 ATCCAACTCCTTATGTCGATGG-A-CAAGCCAAGAAATA-TGATA-TTG
* * * * ** * * ** *
14432783 ATTCGACTCCTTATG-AGACGGATGAGCCAACAAAAATGATGCTA
1 ATCCAACTCCTTATGTCGATGGACAAGCCAAGAAATATGATATTG
* * * * * * ** *
14432827 ATCCAACTCCTTATG-CTATGAAGAAGACAATAAATGTGATGCTA
1 ATCCAACTCCTTATGTCGATGGACAAGCCAAGAAATATGATATTG
14432871 ATCCAACTCCTTATGT-GATGGA
1 ATCCAACTCCTTATGTCGATGGA
14432893 ATTGAGCCAG
Statistics
Matches: 155, Mismatches: 34, Indels: 21
0.74 0.16 0.10
Matches are distributed among these distances:
43 28 0.18
44 89 0.57
45 5 0.03
46 33 0.21
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (45 bp):
ATCCAACTCCTTATGTCGATGGACAAGCCAAGAAATATGATATTG
Found at i:14432822 original size:90 final size:90
Alignment explanation
Indices: 14432557--14432841 Score: 267
Period size: 90 Copynumber: 3.2 Consensus size: 90
14432547 CTGAGTGTCA
* * * * *
14432557 TTGATCCAACTCCTTATGTGATAGAATCGAGCGAAGAAAAGTGACGCTGATCCGACTCCCTATGC
1 TTGATCCAACTCCTTATGTGATGGAATCGAGCAAAGAAAAGTGAAGTTGATCCGACTCCTTATGC
* * *
14432622 GACGGATGGGCCAAGAAAAGA-AAAG
66 GACGGATGAGCCAAGAAAA-ATGATG
* * * * * *
14432647 CTT-ATCCGACTCCTTAGGCGATGG-A-CGAGCCAAGAAAA-TGATA-TTGATCCAACTTCTTAT
1 -TTGATCCAACTCCTTATGTGATGGAATCGAGCAAAGAAAAGTGA-AGTTGATCCGACTCCTTAT
* * ** * *
14432707 TCGATGGACAATCCAAGAAATATGATG
64 GCGACGGATGAGCCAAGAAAAATGATG
* * *
14432734 TTGATCCAACTCCTTATGTGATGGAATCAAGCAAAGAAAAGTGAAGTTGATTCGACTCCTTATGA
1 TTGATCCAACTCCTTATGTGATGGAATCGAGCAAAGAAAAGTGAAGTTGATCCGACTCCTTATGC
*
14432799 GACGGATGAGCCAACAAAAATGATG
66 GACGGATGAGCCAAGAAAAATGATG
* *
14432824 CTAATCCAACTCCTTATG
1 TTGATCCAACTCCTTATG
14432842 CTATGAAGAA
Statistics
Matches: 150, Mismatches: 37, Indels: 15
0.74 0.18 0.07
Matches are distributed among these distances:
86 3 0.02
87 50 0.33
88 13 0.09
89 13 0.09
90 69 0.46
91 2 0.01
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.24
Consensus pattern (90 bp):
TTGATCCAACTCCTTATGTGATGGAATCGAGCAAAGAAAAGTGAAGTTGATCCGACTCCTTATGC
GACGGATGAGCCAAGAAAAATGATG
Found at i:14434112 original size:19 final size:18
Alignment explanation
Indices: 14434090--14434139 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 18
14434080 TTTTTTCAAT
14434090 TTTCCTTTTTCTTTTTTTC
1 TTTCC-TTTTCTTTTTTTC
14434109 TTT-C-TTT-TTTTTTTC
1 TTTCCTTTTCTTTTTTTC
14434124 -TTCCTTTTCTTTTTTT
1 TTTCCTTTTCTTTTTTT
14434140 TTTAGCGTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
14 2 0.07
15 9 0.32
16 6 0.21
17 7 0.25
18 1 0.04
19 3 0.11
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTCCTTTTCTTTTTTTC
Found at i:14434118 original size:20 final size:20
Alignment explanation
Indices: 14434089--14434142 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
14434079 CTTTTTTCAA
14434089 TTTTCCTTTTTCTTTTT-TT-C
1 TTTT-CTTTTT-TTTTTCTTCC
14434109 -TTTCTTTTTTTTTTCTTCC
1 TTTTCTTTTTTTTTTCTTCC
14434128 TTTTCTTTTTTTTTT
1 TTTTCTTTTTTTTTT
14434143 AGCGTAATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
17 5 0.16
18 8 0.26
19 4 0.13
20 14 0.45
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (20 bp):
TTTTCTTTTTTTTTTCTTCC
Found at i:14436161 original size:2 final size:2
Alignment explanation
Indices: 14436144--14436186 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
14436134 TGAATAAAAC
14436144 AT AT A- AT AT A- 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 AT AT AT AT
14436184 AT A
1 AT A
14436187 CGCGTGTAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:14447772 original size:54 final size:54
Alignment explanation
Indices: 14447714--14447871 Score: 210
Period size: 54 Copynumber: 2.9 Consensus size: 54
14447704 GTCGTACAGT
* * *
14447714 AATTCACAAACTCATTATGAATTACGTGGGTTTCACACATAGTGCCAATACGGA
1 AATTCATAAACTCATTATGAATTACGTAGGTTGCACACATAGTGCCAATACGGA
* * * *
14447768 AATTCATAAACTCATTATGAATTTCTTAGGTTGCACACATAGTGACAATACGAA
1 AATTCATAAACTCATTATGAATTACGTAGGTTGCACACATAGTGCCAATACGGA
* * *
14447822 AATTCATAAAATCATTATGAATTTA-TTAGGATGCACACATAGTGCCAATA
1 AATTCATAAACTCATTATGAA-TTACGTAGGTTGCACACATAGTGCCAATA
14447872 TGAAAAATGC
Statistics
Matches: 92, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
54 90 0.98
55 2 0.02
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (54 bp):
AATTCATAAACTCATTATGAATTACGTAGGTTGCACACATAGTGCCAATACGGA
Found at i:14457090 original size:2 final size:2
Alignment explanation
Indices: 14457080--14457410 Score: 112
Period size: 2 Copynumber: 169.0 Consensus size: 2
14457070 ATTGAAAAAA
*
14457080 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
14457121 ACT AT AT TT AT AT -T AT AA ACT AT AT A- AT -T AT -T AT A- AG CT
1 A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
* * * * *
14457160 AT AT AT AA AT -T AT GT TT AT GT GA- ACT AT AT AT AT AT AA ACT
1 AT AT AT AT AT AT AT AT AT AT AT -AT A-T AT AT AT AT AT AT A-T
* * * * * *
14457201 AT GT AT AT AA ACT AT AT AT GT AT A- AA AT AT AA AA AGT AT AT AGT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T
* * *
14457245 TT AT A- AA AT AT -T AT TT AT AT -T A- AT AT AGT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
* * * * * * *
14457284 GT AT GT AT AT AA ACT CT AT AT GT AT AA ACT AT AT A- AA AT AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
* *
14457327 AGT TT AT AT AT -T AT A- AT TT AT AT -T A- AT AT AGT AT AT AT AT
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
*
14457367 AT GT AT A- ACT A- AT AT A- ACT A- AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
14457407 AT AT
1 AT AT
14457411 TAAAGAAATA
Statistics
Matches: 241, Mismatches: 51, Indels: 74
0.66 0.14 0.20
Matches are distributed among these distances:
1 22 0.09
2 204 0.85
3 15 0.06
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Done.