Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001095.1 Hibiscus syriacus cultivar Beakdansim tig00002169_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: 842675
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
File 2 of 4
Found at i:234591 original size:85 final size:84
Alignment explanation
Indices: 234394--234591 Score: 263
Period size: 85 Copynumber: 2.3 Consensus size: 84
234384 TTATGACGGT
* *
234394 CATTGCGTGTCATTAAAGCTCCCGTCATAAATTAAAATGACACATATTTGTGTGTCATAAATTTA
1 CATTGCGTGTCATTGAAGC-CCCGTCATAAATTAAAATGACACACATTTGTGTGTCATAAATTTA
*
234459 TGGCACGCATGTATGACTTA
65 TGACACGCATGTATGACTTA
* * *** *
234479 CATTGAGCGTCATTGAAGCCCCTGTCATAAATCT-GCTTGACATACATTTGTGTGTCATAAATTT
1 CATTGCGTGTCATTGAAGCCCC-GTCATAAAT-TAAAATGACACACATTTGTGTGTCATAAATTT
234543 ATGACACGCATGTATGACTTA
64 ATGACACGCATGTATGACTTA
*
234564 CATTGCGTGTCATTGAAGCACACGTCAT
1 CATTGCGTGTCATTGAAGC-CCCGTCAT
234592 TAAAAAAACG
Statistics
Matches: 98, Mismatches: 12, Indels: 6
0.84 0.10 0.05
Matches are distributed among these distances:
84 3 0.03
85 92 0.94
86 3 0.03
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (84 bp):
CATTGCGTGTCATTGAAGCCCCGTCATAAATTAAAATGACACACATTTGTGTGTCATAAATTTAT
GACACGCATGTATGACTTA
Found at i:234647 original size:4 final size:4
Alignment explanation
Indices: 234638--234684 Score: 58
Period size: 4 Copynumber: 11.8 Consensus size: 4
234628 TTTCGTAAAT
* * * *
234638 TATA TATA TATA TATA TATA TTTA TTTA TTTA TATA TATT TATA TAT
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TAT
234685 TGACAAATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (4 bp):
TATA
Found at i:234653 original size:10 final size:10
Alignment explanation
Indices: 234638--234684 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
234628 TTTCGTAAAT
234638 TATATATATA
1 TATATATATA
234648 TATATATATA
1 TATATATATA
* * *
234658 TTTATTTATT
1 TATATATATA
*
234668 TATATATATT
1 TATATATATA
234678 TATATAT
1 TATATAT
234685 TGACAAATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 32 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TATATATATA
Found at i:234673 original size:18 final size:18
Alignment explanation
Indices: 234642--234685 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
234632 GTAAATTATA
*
234642 TATATATATATATATATT
1 TATATATTTATATATATT
*
234660 TATTTATTTATATATATT
1 TATATATTTATATATATT
234678 TATATATT
1 TATATATT
234686 GACAAATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TATATATTTATATATATT
Found at i:236053 original size:15 final size:15
Alignment explanation
Indices: 236033--236074 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
236023 ATGCTTTCTT
236033 TTTTCTTCTT-TGACG
1 TTTTCTTCTTAT-ACG
236048 TTTTCTTCTTATACG
1 TTTTCTTCTTATACG
*
236063 TTATCTTCTTAT
1 TTTTCTTCTTAT
236075 CCCATGAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 24 0.96
16 1 0.04
ACGTcount: A:0.12, C:0.19, G:0.07, T:0.62
Consensus pattern (15 bp):
TTTTCTTCTTATACG
Found at i:238593 original size:20 final size:21
Alignment explanation
Indices: 238563--238607 Score: 83
Period size: 20 Copynumber: 2.2 Consensus size: 21
238553 CCCTTATAAA
238563 ATTTCCTTAACTTATTATTAT
1 ATTTCCTTAACTTATTATTAT
238584 ATTT-CTTAACTTATTATTAT
1 ATTTCCTTAACTTATTATTAT
238604 ATTT
1 ATTT
238608 TTATCAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.29, C:0.11, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTCCTTAACTTATTATTAT
Found at i:252489 original size:2 final size:2
Alignment explanation
Indices: 252482--252513 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
252472 CAAATCTTTC
252482 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
252514 TAATATCACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:253898 original size:3 final size:3
Alignment explanation
Indices: 253890--253954 Score: 62
Period size: 3 Copynumber: 21.0 Consensus size: 3
253880 AATATAAATT
* *
253890 TAA TAA TAA TAA TAA TATA TAA TAT TAA TAA T-A TACA TTA TATA TATA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TA-A TAA TA-A TA-A
253938 TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA
253955 ATTGGCAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
2 4 0.08
3 37 0.70
4 12 0.23
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:254178 original size:39 final size:39
Alignment explanation
Indices: 254135--254480 Score: 458
Period size: 39 Copynumber: 8.9 Consensus size: 39
254125 AGGTTGAATA
* *
254135 AGTTCTCCAGACTATGAACTTCTTCTTCCTCTTCAAATG
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAAATG
* *
254174 AGTTCTTCAGATTATGAACTCCTTCTTCCTCTTCATATG
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAAATG
* * * *
254213 AGTTCTTCAGACTATGAACTTCTTATTCCTCTTCAGACG
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAAATG
* *
254252 AGTTCTTCAGACTATGAACTCCCTCTTCCTCTTCATATG
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAAATG
* * *
254291 AGTTCTTCAGACTATGAACTCATTCTTCCTCTTCAGACG
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAAATG
* * * *
254330 AGTTCTTCAGACTATAAACTACTTCTTCCTCTTCAGACG
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAAATG
* *
254369 AGTCCTTCAGACTATGAACTCCTTCTTCCTCTTCAGATG
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAAATG
* * *
254408 AGTTCTTCAGATTATGAACTCATTCTTCCTCTTCAGATG
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAAATG
* * * *
254447 AGTTCTTCAAATTATAAACTCATTCTTCCTCTTC
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTC
254481 TTCCTCTTCA
Statistics
Matches: 277, Mismatches: 30, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 277 1.00
ACGTcount: A:0.23, C:0.27, G:0.11, T:0.39
Consensus pattern (39 bp):
AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAAATG
Found at i:254268 original size:78 final size:78
Alignment explanation
Indices: 254135--254832 Score: 597
Period size: 78 Copynumber: 8.8 Consensus size: 78
254125 AGGTTGAATA
* * * *
254135 AGTTCTCCAGACTATGAACTTCTTCTTCCTCTTCAAATGAGTTCTTCAGATTATGAACTCCTTCT
1 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCAGACTATGAACTCCTTCT
*
254200 TCCTCTTCATATG
66 TCCTCTTCAGATG
* *
254213 AGTTCTTCAGACTATGAACTTCTTATTCCTCTTCAGACGAGTTCTTCAGACTATGAACTCCCTCT
1 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCAGACTATGAACTCCTTCT
*
254278 TCCTCTTCATATG
66 TCCTCTTCAGATG
* *
254291 AGTTCTTCAGACTATGAAC-TCATTCTTCCTCTTCAGACGAGTTCTTCAGACTATAAACTACTTC
1 AGTTCTTCAGACTATGAACTTC-TTCTTCCTCTTCAGACGAGTTCTTCAGACTATGAACTCCTTC
*
254355 TTCCTCTTCAGACG
65 TTCCTCTTCAGATG
* * * * *
254369 AGTCCTTCAGACTATGAACTCCTTCTTCCTCTTCAGATGAGTTCTTCAGATTATGAACTCATTCT
1 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCAGACTATGAACTCCTTCT
254434 TCCTCTTCAGATG
66 TCCTCTTCAGATG
* * * ** * * ** * * *
254447 AGTTCTTCAAATTATAAAC-TCATTCTTCCTCTTC-TTC---CTCTTCAGACGA-GTTCTTCATA
1 AGTTCTTCAGACTATGAACTTC-TTCTTCCTCTTCAGACGAGTTCTTCAGACTATGAACTCCTTC
* *** ** *
254506 TT-ATGAACTCATT
65 TTCCTCTTCAGATG
** * * * * * *
254519 CTTCCTCTTCAGACGAGTTCTTCAGACTATGAACTCCTTCTTCCTCTTAATATGAGTTCTTCAGA
1 AGT--TCTTCAGAC----T-ATGA-ACT-T---CTTCTT---CCTCTTCAGACGAGTTCTTCAGA
* *
254584 CTATGAACTCCTTCTTTCTCTTCAGACG
51 CTATGAACTCCTTCTTCCTCTTCAGATG
* * * * *
254612 AGTTCTTTAGACTCTGAACTCCTTCTTCCTCTTCAGATGAGTTCTTCAGATTATGAACTCCTTCT
1 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCAGACTATGAACTCCTTCT
*
254677 TCCTCTTCAGA-C
66 TCCTCTTCAGATG
* * * * *
254689 ATTTTCTTCAGATTATGAACTCCTTCTTCCTCTTCAAAC-ATGTTCTTTAGACTATGAACTCCTT
1 A-GTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACGA-GTTCTTCAGACTATGAACTCCTT
* *
254753 CTTCCTCTTCACAAG
64 CTTCCTCTTCAGATG
* * * *
254768 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCACAAGAGTTCTTTAGACTATGAACTCATTCT
1 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCAGACTATGAACTCCTTCT
254833 GAAAATGTTT
Statistics
Matches: 494, Mismatches: 97, Indels: 58
0.76 0.15 0.09
Matches are distributed among these distances:
72 5 0.01
73 6 0.01
74 16 0.03
77 5 0.01
78 402 0.81
79 5 0.01
80 2 0.00
81 5 0.01
82 1 0.00
84 4 0.01
85 4 0.01
86 2 0.00
87 7 0.01
88 1 0.00
91 18 0.04
92 7 0.01
93 4 0.01
ACGTcount: A:0.22, C:0.27, G:0.11, T:0.40
Consensus pattern (78 bp):
AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCAGACTATGAACTCCTTCT
TCCTCTTCAGATG
Found at i:254341 original size:117 final size:117
Alignment explanation
Indices: 254135--254832 Score: 914
Period size: 117 Copynumber: 5.9 Consensus size: 117
254125 AGGTTGAATA
* * * *
254135 AGTTCTCCAGACTATGAACTTCTTCTTCCTCTTCAAATGAGTTCTTCAGATTATGAACTCCTTCT
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGATGAGTTCTTCAGACTATGAACTCCTTCT
* * *
254200 TCCTCTTCATATGAGTTCTTCAGACTATGAACTTCTTATTCCTCTTCAGACG
66 TCCTCTTCAGATGAGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACG
* * *
254252 AGTTCTTCAGACTATGAACTCCCTCTTCCTCTTCATATGAGTTCTTCAGACTATGAACTCATTCT
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGATGAGTTCTTCAGACTATGAACTCCTTCT
* * *
254317 TCCTCTTCAGACGAGTTCTTCAGACTATAAACTACTTCTTCCTCTTCAGACG
66 TCCTCTTCAGATGAGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACG
* * *
254369 AGTCCTTCAGACTATGAACTCCTTCTTCCTCTTCAGATGAGTTCTTCAGATTATGAACTCATTCT
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGATGAGTTCTTCAGACTATGAACTCCTTCT
* * *
254434 TCCTCTTCAGATGAGTTCTTCAAATTATAAACTCATTCTTCCTCTTCTTCCTCTTCAGACG
66 TCCTCTTCAGATGAGTTCTTCAGACTAT-GA---A--C-T-C-CTTCTTCCTCTTCAGACG
* * * *
254495 AGTTCTTCATATTATGAACTCATTCTTCCTCTTCAGACGAGTTCTTCAGACTATGAACTCCTTCT
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGATGAGTTCTTCAGACTATGAACTCCTTCT
* * *
254560 TCCTCTTAATATGAGTTCTTCAGACTATGAACTCCTTCTTTCTCTTCAGACG
66 TCCTCTTCAGATGAGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACG
* * *
254612 AGTTCTTTAGACTCTGAACTCCTTCTTCCTCTTCAGATGAGTTCTTCAGATTATGAACTCCTTCT
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGATGAGTTCTTCAGACTATGAACTCCTTCT
* * * *
254677 TCCTCTTCAGA-CATTTTCTTCAGATTATGAACTCCTTCTTCCTCTTCAAAC-
66 TCCTCTTCAGATGA-GTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACG
* * * *
254728 ATGTTCTTTAGACTATGAACTCCTTCTTCCTCTTCACAAGAGTTCTTCAGACTATGAACTTCTTC
1 A-GTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGATGAGTTCTTCAGACTATGAACTCCTTC
* * * *
254793 TTCCTCTTCACAAGAGTTCTTTAGACTATGAACTCATTCT
65 TTCCTCTTCAGATGAGTTCTTCAGACTATGAACTCCTTCT
254833 GAAAATGTTT
Statistics
Matches: 512, Mismatches: 57, Indels: 24
0.86 0.10 0.04
Matches are distributed among these distances:
116 2 0.00
117 399 0.78
118 4 0.01
119 1 0.00
120 1 0.00
121 1 0.00
122 1 0.00
123 1 0.00
124 1 0.00
125 1 0.00
126 100 0.20
ACGTcount: A:0.22, C:0.27, G:0.11, T:0.40
Consensus pattern (117 bp):
AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGATGAGTTCTTCAGACTATGAACTCCTTCT
TCCTCTTCAGATGAGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACG
Found at i:254486 original size:48 final size:48
Alignment explanation
Indices: 254430--254528 Score: 171
Period size: 48 Copynumber: 2.1 Consensus size: 48
254420 TATGAACTCA
*
254430 TTCTTCCTCTTCAGATGAGTTCTTCAAATTATAAACTCATTCTTCCTC
1 TTCTTCCTCTTCAGACGAGTTCTTCAAATTATAAACTCATTCTTCCTC
* *
254478 TTCTTCCTCTTCAGACGAGTTCTTCATATTATGAACTCATTCTTCCTC
1 TTCTTCCTCTTCAGACGAGTTCTTCAAATTATAAACTCATTCTTCCTC
254526 TTC
1 TTC
254529 AGACGAGTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.20, C:0.28, G:0.07, T:0.44
Consensus pattern (48 bp):
TTCTTCCTCTTCAGACGAGTTCTTCAAATTATAAACTCATTCTTCCTC
Found at i:254490 original size:87 final size:87
Alignment explanation
Indices: 254390--254566 Score: 291
Period size: 87 Copynumber: 2.0 Consensus size: 87
254380 CTATGAACTC
* *
254390 CTTCTTCCTCTTCAGATGAGTTCTTCAGATTATGAACTCATTCTTCCTCTTCAGATGAGTTCTTC
1 CTTCTTCCTCTTCAGACGAGTTCTTCAGATTATGAACTCATTCTTCCTCTTCAGACGAGTTCTTC
*
254455 AAATTATAAACTCATTCTTCCT
66 AAACTATAAACTCATTCTTCCT
*
254477 CTTCTTCCTCTTCAGACGAGTTCTTCATATTATGAACTCATTCTTCCTCTTCAGACGAGTTCTTC
1 CTTCTTCCTCTTCAGACGAGTTCTTCAGATTATGAACTCATTCTTCCTCTTCAGACGAGTTCTTC
* * *
254542 AGACTATGAACTCCTTCTTCCT
66 AAACTATAAACTCATTCTTCCT
254564 CTT
1 CTT
254567 AATATGAGTT
Statistics
Matches: 83, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 83 1.00
ACGTcount: A:0.21, C:0.28, G:0.10, T:0.42
Consensus pattern (87 bp):
CTTCTTCCTCTTCAGACGAGTTCTTCAGATTATGAACTCATTCTTCCTCTTCAGACGAGTTCTTC
AAACTATAAACTCATTCTTCCT
Found at i:254522 original size:39 final size:39
Alignment explanation
Indices: 254477--254832 Score: 482
Period size: 39 Copynumber: 9.1 Consensus size: 39
254467 CATTCTTCCT
* *
254477 CTTCTTCCTCTTCAGACGAGTTCTTCATATTATGAACTC
1 CTTCTTCCTCTTCAGACGAGTTCTTCAGACTATGAACTC
*
254516 ATTCTTCCTCTTCAGACGAGTTCTTCAGACTATGAACTC
1 CTTCTTCCTCTTCAGACGAGTTCTTCAGACTATGAACTC
* * *
254555 CTTCTTCCTCTTAATATGAGTTCTTCAGACTATGAACTC
1 CTTCTTCCTCTTCAGACGAGTTCTTCAGACTATGAACTC
* * *
254594 CTTCTTTCTCTTCAGACGAGTTCTTTAGACTCTGAACTC
1 CTTCTTCCTCTTCAGACGAGTTCTTCAGACTATGAACTC
* *
254633 CTTCTTCCTCTTCAGATGAGTTCTTCAGATTATGAACTC
1 CTTCTTCCTCTTCAGACGAGTTCTTCAGACTATGAACTC
* *
254672 CTTCTTCCTCTTCAGAC-ATTTTCTTCAGATTATGAACTC
1 CTTCTTCCTCTTCAGACGA-GTTCTTCAGACTATGAACTC
* *
254711 CTTCTTCCTCTTCAAAC-ATGTTCTTTAGACTATGAACTC
1 CTTCTTCCTCTTCAGACGA-GTTCTTCAGACTATGAACTC
* * *
254750 CTTCTTCCTCTTCACAAGAGTTCTTCAGACTATGAACTT
1 CTTCTTCCTCTTCAGACGAGTTCTTCAGACTATGAACTC
* * *
254789 CTTCTTCCTCTTCACAAGAGTTCTTTAGACTATGAACTC
1 CTTCTTCCTCTTCAGACGAGTTCTTCAGACTATGAACTC
*
254828 ATTCT
1 CTTCT
254833 GAAAATGTTT
Statistics
Matches: 284, Mismatches: 31, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
38 1 0.00
39 282 0.99
40 1 0.00
ACGTcount: A:0.22, C:0.28, G:0.10, T:0.40
Consensus pattern (39 bp):
CTTCTTCCTCTTCAGACGAGTTCTTCAGACTATGAACTC
Found at i:254678 original size:20 final size:20
Alignment explanation
Indices: 254653--254717 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
254643 TTCAGATGAG
254653 TTCTTCAGATTATGAACTCC
1 TTCTTCAGATTATGAACTCC
*** *
254673 TTCTTCCTCTTCA-G-ACAT-T
1 TTCTTCAGATT-ATGAAC-TCC
254692 TTCTTCAGATTATGAACTCC
1 TTCTTCAGATTATGAACTCC
254712 TTCTTC
1 TTCTTC
254718 CTCTTCAAAC
Statistics
Matches: 32, Mismatches: 8, Indels: 10
0.64 0.16 0.20
Matches are distributed among these distances:
18 1 0.03
19 12 0.38
20 18 0.56
21 1 0.03
ACGTcount: A:0.20, C:0.28, G:0.08, T:0.45
Consensus pattern (20 bp):
TTCTTCAGATTATGAACTCC
Found at i:254958 original size:72 final size:73
Alignment explanation
Indices: 254838--255024 Score: 297
Period size: 72 Copynumber: 2.6 Consensus size: 73
254828 ATTCTGAAAA
* * *
254838 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATGTCGAGTGAAATTTTCTCCAA-CGA
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCT-CAAGCGA
*
254902 GAAATAGTT
65 GAAACAGTT
254911 TGTTTTAAG-AAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCAAGCGAG
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCAAGCGAG
*
254975 AAACATTT
66 AAACAGTT
*
254983 TGTTTTAAGAAAAATAATCTCAAGTGAGATAAATTGCTATTT
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTT
255025 GAAAACATCC
Statistics
Matches: 106, Mismatches: 6, Indels: 4
0.91 0.05 0.03
Matches are distributed among these distances:
71 3 0.03
72 63 0.59
73 40 0.38
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (73 bp):
TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCAAGCGAG
AAACAGTT
Found at i:256242 original size:54 final size:54
Alignment explanation
Indices: 256160--256270 Score: 159
Period size: 54 Copynumber: 2.1 Consensus size: 54
256150 CACTGATTCA
* * * * **
256160 TAAAACATTTGACAGCACATTCATCATTTCTTGTGGCTTCTACTTAGATGTTCG
1 TAAAACATTTGACAACAAATTCATCATTTCCTGTGGCATCTACCCAGATGTTCG
*
256214 TAAAACATTTGACAACAAATTCATCATTTCCTGTGGCATCTGCCCAGATGTTCG
1 TAAAACATTTGACAACAAATTCATCATTTCCTGTGGCATCTACCCAGATGTTCG
256268 TAA
1 TAA
256271 CTCATTCATC
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (54 bp):
TAAAACATTTGACAACAAATTCATCATTTCCTGTGGCATCTACCCAGATGTTCG
Found at i:256843 original size:35 final size:36
Alignment explanation
Indices: 256797--256878 Score: 112
Period size: 38 Copynumber: 2.2 Consensus size: 36
256787 CTTCTTGCTA
*
256797 AAAATGCCCAAA-TATTCATACTGATGTGGGCCTTC
1 AAAATGCCCAAACTATTCATACTAATGTGGGCCTTC
* *
256832 AAAATGCCCAAAGCTTTTTTATACTAATGTGGGCCTTC
1 AAAATGCCCAAA-C-TATTCATACTAATGTGGGCCTTC
256870 AAAATGCCC
1 AAAATGCCC
256879 CACATGGATC
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
35 12 0.29
38 29 0.71
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (36 bp):
AAAATGCCCAAACTATTCATACTAATGTGGGCCTTC
Found at i:257808 original size:34 final size:32
Alignment explanation
Indices: 257755--257824 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 32
257745 ACCTTACAAC
*
257755 TCCCTAGTTTTTCCGGGCTAAACT-GTAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAG-AACCTT
*
257787 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
257821 TCCC
1 TCCC
257825 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 20 0.61
35 1 0.03
ACGTcount: A:0.20, C:0.31, G:0.16, T:0.33
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:258204 original size:20 final size:21
Alignment explanation
Indices: 258179--258233 Score: 85
Period size: 20 Copynumber: 2.7 Consensus size: 21
258169 TTGCAGCCTT
*
258179 GATGCATGGATGCATCGC-AG
1 GATGCATCGATGCATCGCAAG
*
258199 GATGCATCGATGCATGGCAAG
1 GATGCATCGATGCATCGCAAG
258220 GATGCATCGATGCA
1 GATGCATCGATGCA
258234 CTAATTGCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 16 0.50
21 16 0.50
ACGTcount: A:0.27, C:0.20, G:0.33, T:0.20
Consensus pattern (21 bp):
GATGCATCGATGCATCGCAAG
Found at i:258322 original size:21 final size:21
Alignment explanation
Indices: 258296--258353 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
258286 TATTAGTGCA
*
258296 GATGCATGGATGCACTGTAGG
1 GATGCATGGATGCACTGCAGG
258317 GATGCATGGATGCACTGCAGG
1 GATGCATGGATGCACTGCAGG
258338 GATGCATGGATGCACT
1 GATGCATGGATGCACT
258354 TTGACACCCT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.24, C:0.17, G:0.36, T:0.22
Consensus pattern (21 bp):
GATGCATGGATGCACTGCAGG
Found at i:258492 original size:30 final size:30
Alignment explanation
Indices: 258435--258494 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
258425 AACTTTGAAT
*
258435 AAATTCAATTCAAATCCAAAAACATTTTGC
1 AAATTCAATTCAAATACAAAAACATTTTGC
*
258465 AAATTCAATTCAAGTACAAAAACATTTTGC
1 AAATTCAATTCAAATACAAAAACATTTTGC
258495 CTTAAATTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.47, C:0.18, G:0.05, T:0.30
Consensus pattern (30 bp):
AAATTCAATTCAAATACAAAAACATTTTGC
Found at i:259584 original size:9 final size:8
Alignment explanation
Indices: 259566--259626 Score: 50
Period size: 9 Copynumber: 6.9 Consensus size: 8
259556 TTGATTCAAA
259566 TTTTTTTC
1 TTTTTTTC
259574 TTTTTTATC
1 TTTTTT-TC
*
259583 TTTTCTTC
1 TTTTTTTC
*
259591 TTTTTCTTTT
1 -TTTT-TTTC
259601 TTTTCTCTTC
1 TTTT-T-TTC
259611 TTTTTTTC
1 TTTTTTTC
259619 ATTTTTTT
1 -TTTTTTT
259627 ATGATGAACG
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
8 11 0.25
9 25 0.57
10 8 0.18
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTTTC
Found at i:259617 original size:17 final size:19
Alignment explanation
Indices: 259571--259623 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 19
259561 TCAAATTTTT
259571 TTCTTTTTTATCTTTTCTTC
1 TTCTTTTTT-TCTTTTCTTC
259591 TT-TTTCTTTT-TTTTC-TC
1 TTCTTT-TTTTCTTTTCTTC
259608 TTCTTTTTTTCATTTT
1 TTCTTTTTTTC-TTTT
259624 TTTATGATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
17 8 0.28
18 8 0.28
19 8 0.28
20 5 0.17
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (19 bp):
TTCTTTTTTTCTTTTCTTC
Found at i:259623 original size:20 final size:18
Alignment explanation
Indices: 259566--259625 Score: 61
Period size: 20 Copynumber: 3.3 Consensus size: 18
259556 TTGATTCAAA
259566 TTTTT-TTC-TTTTTTAT
1 TTTTTCTTCTTTTTTTAT
* *
259582 CTTTTCTTCTTTTTCTTTT
1 TTTTTCTTCTTTTT-TTAT
259601 TTTTCTCTTCTTTTTTTCAT
1 TTTT-TCTTCTTTTTTT-AT
259621 TTTTT
1 TTTTT
259626 TATGATGAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
16 4 0.11
17 3 0.09
18 4 0.11
19 9 0.26
20 15 0.43
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTTCTTCTTTTTTTAT
Found at i:259626 original size:23 final size:22
Alignment explanation
Indices: 259566--259626 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 22
259556 TTGATTCAAA
* *
259566 TTTTTTTCTTTTTTATCTTTTC
1 TTTTTTTCTTTTTTTTCTCTTC
259588 TTCTTTTTCTTTTTTTTCTCTTC
1 TT-TTTTTCTTTTTTTTCTCTTC
*
259611 TTTTTTTCATTTTTTT
1 TTTTTTTCTTTTTTTT
259627 ATGATGAACG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
22 15 0.43
23 20 0.57
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (22 bp):
TTTTTTTCTTTTTTTTCTCTTC
Found at i:265164 original size:3 final size:3
Alignment explanation
Indices: 265156--265231 Score: 62
Period size: 3 Copynumber: 24.0 Consensus size: 3
265146 AATATAAATT
* *
265156 TAA TAA TAA TAA TAA TAA TATA TAA TAT TAA TAAA TAA TAA TTTA TATA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA T-AA TAA TAA -TAA TA-A
* * * *
265205 TAA TAA TTA TAA AAA AAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
265232 ATGGGCAAAA
Statistics
Matches: 59, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
3 48 0.81
4 11 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:265214 original size:13 final size:13
Alignment explanation
Indices: 265164--265215 Score: 61
Period size: 13 Copynumber: 3.9 Consensus size: 13
265154 TTTAATAATA
*
265164 ATAATAATAATAT
1 ATAATAATTATAT
*
265177 ATAAT-ATTAATAA
1 ATAATAATT-ATAT
265190 ATAATAATTTATAT
1 ATAATAA-TTATAT
265204 ATAATAATTATA
1 ATAATAATTATA
265216 AAAAAAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
12 2 0.06
13 18 0.55
14 11 0.33
15 2 0.06
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATAATAATTATAT
Found at i:265216 original size:27 final size:26
Alignment explanation
Indices: 265145--265225 Score: 80
Period size: 26 Copynumber: 3.1 Consensus size: 26
265135 TTTGGGCATG
265145 TAATATA-AAT-TTAATAATAATAATAA
1 TAATATATAATATTAAT-A-AATAATAA
265171 TAATATATAATATTAATAAATAATAA
1 TAATATATAATATTAATAAATAATAA
* *
265197 TTTATATATAATAATT-ATAAA-AAAAA
1 -TAATATATAAT-ATTAATAAATAATAA
265223 TAA
1 TAA
265226 AAATAAATGG
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
25 2 0.04
26 19 0.40
27 19 0.40
28 8 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (26 bp):
TAATATATAATATTAATAAATAATAA
Found at i:269804 original size:30 final size:27
Alignment explanation
Indices: 269770--269826 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 27
269760 AGGAAAAGAA
*
269770 GAAATGAAAAGATAGAAGAAATGATTTAAG
1 GAAATGAAAAGA-AG--GAAAAGATTTAAG
269800 GAAATGAAAAGAAGGAAAAGATTTAAG
1 GAAATGAAAAGAAGGAAAAGATTTAAG
269827 AACAAGGGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 12 0.46
29 2 0.08
30 12 0.46
ACGTcount: A:0.58, C:0.00, G:0.25, T:0.18
Consensus pattern (27 bp):
GAAATGAAAAGAAGGAAAAGATTTAAG
Found at i:278694 original size:2 final size:2
Alignment explanation
Indices: 278687--278728 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
278677 ATCTGTTTAA
278687 AT AT AT 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
278729 TCTATTAACA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:283876 original size:23 final size:23
Alignment explanation
Indices: 283834--283882 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
283824 GGGCCTGAGA
**
283834 GCCTACCCAAGAAAGTTCTCCGG
1 GCCTACCCAAGAAAAATCTCCGG
* *
283857 GCCTACCCAGGAAAAATCTCTGG
1 GCCTACCCAAGAAAAATCTCCGG
283880 GCC
1 GCC
283883 GCAGAGCCTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.27, C:0.35, G:0.22, T:0.16
Consensus pattern (23 bp):
GCCTACCCAAGAAAAATCTCCGG
Found at i:288227 original size:66 final size:66
Alignment explanation
Indices: 288105--288234 Score: 163
Period size: 66 Copynumber: 2.0 Consensus size: 66
288095 TAGGCCCATA
* * * * * *
288105 AGGAATTACTACTTGGTGTTGAACCTATACAAGGAATTGCCAGCAGTGACTGAACCTGCTAGAGA
1 AGGAATTACCACTTGGTGCTAAACCTATACAAGGAATTACCAGCAGTGACTAAACCTGCCAGAGA
288170 T
66 T
* * *
288171 AGGAATTACCAGTTGGTGCTAAACCTATACAAGGAATTACCAGTA-TCGGCTAAACCTGCCAGAG
1 AGGAATTACCACTTGGTGCTAAACCTATACAAGGAATTACCAGCAGT-GACTAAACCTGCCAGAG
288235 TCTTCATACC
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
65 1 0.02
66 53 0.98
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (66 bp):
AGGAATTACCACTTGGTGCTAAACCTATACAAGGAATTACCAGCAGTGACTAAACCTGCCAGAGA
T
Found at i:292550 original size:18 final size:19
Alignment explanation
Indices: 292529--292564 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
292519 AAAATAAATC
292529 ATAAAAAT-AAAATTGAAA
1 ATAAAAATAAAAATTGAAA
292547 ATAAAAATAAAAATTGAA
1 ATAAAAATAAAAATTGAA
292565 CAAACGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (19 bp):
ATAAAAATAAAAATTGAAA
Found at i:297096 original size:24 final size:24
Alignment explanation
Indices: 297064--297111 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
297054 GGTTGCCCTG
297064 TTCTGCCCCCACGTCAGGGATATT
1 TTCTGCCCCCACGTCAGGGATATT
297088 TTCTGCCCCCACGTCAGGGATATT
1 TTCTGCCCCCACGTCAGGGATATT
297112 CCTCCATGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.17, C:0.33, G:0.21, T:0.29
Consensus pattern (24 bp):
TTCTGCCCCCACGTCAGGGATATT
Found at i:299474 original size:3 final size:3
Alignment explanation
Indices: 299468--299523 Score: 78
Period size: 3 Copynumber: 18.7 Consensus size: 3
299458 TTCATTTAAA
* *
299468 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT TAT AAT AAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
299513 TAT TAT TAT TA
1 TAT TAT TAT TA
299524 AAAAAATAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
2 1 0.02
3 47 0.96
4 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:299531 original size:27 final size:27
Alignment explanation
Indices: 299478--299535 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
299468 TATTATTTAT
** *
299478 ATTATTATTATTATTATTATTATAATA
1 ATTATTATTATTATTATTAAAAAAATA
299505 ATTATTATTATTATTATTAAAAAAATA
1 ATTATTATTATTATTATTAAAAAAATA
299532 ATTA
1 ATTA
299536 CAGGCCCAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
ATTATTATTATTATTATTAAAAAAATA
Found at i:299535 original size:24 final size:24
Alignment explanation
Indices: 299484--299535 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
299474 TTATATTATT
* * *
299484 ATTATTATTATTATTATAATAATT
1 ATTATTATTATTATTAAAAAAATA
299508 ATTATTATTATTATTAAAAAAATA
1 ATTATTATTATTATTAAAAAAATA
299532 ATTA
1 ATTA
299536 CAGGCCCAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
ATTATTATTATTATTAAAAAAATA
Found at i:312397 original size:6 final size:6
Alignment explanation
Indices: 312386--312447 Score: 67
Period size: 6 Copynumber: 10.3 Consensus size: 6
312376 ATTATGCTTG
*
312386 AAGAAA AAGAAAA AAGAAA AA-AAA AGAAAAGA AAGAAA AA-AAA AAG-AA
1 AAGAAA AAG-AAA AAGAAA AAGAAA A-AGAA-A AAGAAA AAGAAA AAGAAA
312434 AAGAAA AAGAAA AA
1 AAGAAA AAGAAA AA
312448 AGGGGGTCAA
Statistics
Matches: 49, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
5 14 0.29
6 22 0.45
7 11 0.22
8 2 0.04
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:312405 original size:5 final size:5
Alignment explanation
Indices: 312397--312446 Score: 57
Period size: 5 Copynumber: 9.8 Consensus size: 5
312387 AGAAAAAGAA
* *
312397 AAAAG AAAAA AAAAG AAAAG -AAAG AAAAAA AAAAG AAAAG AAAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG -AAAAG AAAAG AAAAG -AAAAG AAAA
312447 AAGGGGGTCA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
4 4 0.11
5 26 0.68
6 8 0.21
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:312407 original size:15 final size:14
Alignment explanation
Indices: 312389--312446 Score: 71
Period size: 15 Copynumber: 3.9 Consensus size: 14
312379 ATGCTTGAAG
*
312389 AAAAAGAAAAAAGA
1 AAAAAAAAAAAAGA
312403 AAAAAAAAGAAAAGA
1 AAAAAAAA-AAAAGA
312418 AAGAAAAAAAAAAGA
1 AA-AAAAAAAAAAGA
312433 AAAGAAAAAGAAAA
1 AAA-AAAAA-AAAA
312447 AAGGGGGTCA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
14 8 0.21
15 21 0.54
16 10 0.26
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAGA
Found at i:312427 original size:20 final size:20
Alignment explanation
Indices: 312389--312448 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
312379 ATGCTTGAAG
312389 AAAAAG-AAA-AAAG-AAAA
1 AAAAAGAAAAGAAAGAAAAA
312406 AAAAAGAAAAGAAAGAAAAA
1 AAAAAGAAAAGAAAGAAAAA
312426 AAAAAGAAAAGAAA-AAGAAA
1 AAAAAGAAAAGAAAGAA-AAA
312446 AAA
1 AAA
312449 GGGGGTCAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.15
18 3 0.08
19 6 0.15
20 24 0.62
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (20 bp):
AAAAAGAAAAGAAAGAAAAA
Found at i:312435 original size:26 final size:26
Alignment explanation
Indices: 312391--312445 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 26
312381 GCTTGAAGAA
312391 AAAGAAAAAAGAAAAAAAA-AGAAAAG
1 AAAGAAAAAAGAAAAAAAAGA-AAAAG
312417 AAAGAAAAAA-AAAAGAAAAGAAAAAG
1 AAAGAAAAAAGAAAA-AAAAGAAAAAG
312443 AAA
1 AAA
312446 AAAGGGGGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
25 4 0.15
26 22 0.81
27 1 0.04
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (26 bp):
AAAGAAAAAAGAAAAAAAAGAAAAAG
Found at i:313593 original size:93 final size:91
Alignment explanation
Indices: 313400--313767 Score: 467
Period size: 93 Copynumber: 4.1 Consensus size: 91
313390 GGAACAAGTG
* *
313400 TGTGCTCATAGCATCTTCTGGAAGTGTTC-TTGAGTTATCTAATCTGGTTTGGTATGAACCCCAA
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAA-CCC-G
313464 AAAACCAATCATTGAATTTGAAAATGAA
64 AAAACCAATCATTGAATTTGAAAATGAA
*
313492 TGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCGAA
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCG-A
313557 AAACCAATCATTGAATTTGAAAGATGAA
65 AAACCAATCATTGAATTTGAAA-ATGAA
* * *
313585 TGTGCTCATAGCATCTTCTGGAAGCGTTCTTT--GTTAT-TGATCTGG-TTGATATGAACCTGAA
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCGAA
* *
313646 AACCAATCATTGGATTTGAATAAAG-A
66 AACCAATCATTGAATTTGAA-AATGAA
* *
313672 -G-AC-CAATA--A--TTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACAC-A
1 TGTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCGA
* *
313729 GAACCAATCATTGGATTTGAAAGATGAA
65 AAACCAATCATTGAATTTGAAA-ATGAA
313757 TGTGCTCATAG
1 TGTGCTCATAG
313768 TACAATAAAG
Statistics
Matches: 244, Mismatches: 17, Indels: 34
0.83 0.06 0.12
Matches are distributed among these distances:
81 16 0.07
83 7 0.03
84 32 0.13
85 15 0.06
86 2 0.01
87 5 0.02
88 24 0.10
89 13 0.05
90 8 0.03
91 5 0.02
92 54 0.22
93 63 0.26
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (91 bp):
TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCGAA
AACCAATCATTGAATTTGAAAATGAA
Found at i:315101 original size:16 final size:16
Alignment explanation
Indices: 315047--315104 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 16
315037 AGTTCATAAT
315047 AAGAAGAACTCATCTG
1 AAGAAGAACTCATCTG
* * *
315063 AAAGAAAAAGTTCATAATG
1 -AAGAAGAA-CTCAT-CTG
315082 -AGAAGAACTCATCTG
1 AAGAAGAACTCATCTG
315097 AAGAAGAA
1 AAGAAGAA
315105 GAAATTCACA
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
15 2 0.06
16 11 0.34
17 13 0.41
18 4 0.12
19 2 0.06
ACGTcount: A:0.52, C:0.12, G:0.19, T:0.17
Consensus pattern (16 bp):
AAGAAGAACTCATCTG
Found at i:315118 original size:36 final size:34
Alignment explanation
Indices: 315037--315123 Score: 122
Period size: 34 Copynumber: 2.5 Consensus size: 34
315027 TACCAGTTCG
*
315037 AGTTCATAATAAGAAGAACTCATCTGAAAGAAAA
1 AGTTCATAATGAGAAGAACTCATCTGAAAGAAAA
315071 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAA
1 AGTTCATAATGAGAAGAACTCATCTG-A-AAGAA-AA
*
315108 A-TTCACAATGAGAAGA
1 AGTTCATAATGAGAAGA
315124 GCTTGTTCAA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
34 25 0.52
35 1 0.02
36 19 0.40
37 3 0.06
ACGTcount: A:0.51, C:0.11, G:0.18, T:0.20
Consensus pattern (34 bp):
AGTTCATAATGAGAAGAACTCATCTGAAAGAAAA
Found at i:315292 original size:117 final size:115
Alignment explanation
Indices: 315069--315340 Score: 307
Period size: 117 Copynumber: 2.3 Consensus size: 115
315059 TCTGAAAGAA
*
315069 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAATTCACAATGAGAAGAGCTTGTTCAA
1 AAAGTTCATAATGAGAAGAACTCATCTGAAGAA-AAG-AATTCACAATGAGAAGAGCTTATTCAA
* * * * * * * *
315134 CCTTTTACATAATTTTACACAAAAGGAGATATATTAGCATCAACCTTTCTAG-AG
64 CCTTTGACATAACTCTACACAAAAGGAAATAGATCAACATCAACC---CCAGCAG
* *
315188 AAAGTTCATAATGAGAAGAACT-ATCTGAAGAATAAGAGTTCATAATGAGAAGAGCTTATTCAAC
1 AAAGTTCATAATGAGAAGAACTCATCTGAAGAA-AAGAATTCACAATGAGAAGAGCTTATTCAAC
* * * * *
315252 CTTTGA-ATGACTCTATCACAGAAGGAAATAGGTCAACATCATCCCCAGCGG
65 CTTTGACATAACTCTA-CACAAAAGGAAATAGATCAACATCAACCCCAGCAG
*
315303 AAAGTTCATAATGAGAAAAACTCATCTGAAGAAAAGAA
1 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAGAA
315341 GAATTTATTC
Statistics
Matches: 131, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
114 3 0.02
115 26 0.20
116 16 0.12
117 51 0.39
118 13 0.10
119 22 0.17
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.24
Consensus pattern (115 bp):
AAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAGAATTCACAATGAGAAGAGCTTATTCAACC
TTTGACATAACTCTACACAAAAGGAAATAGATCAACATCAACCCCAGCAG
Found at i:315511 original size:3 final size:3
Alignment explanation
Indices: 315505--315530 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
315495 TATTATTATT
315505 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
315531 TATTATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:329642 original size:23 final size:23
Alignment explanation
Indices: 329616--329674 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
329606 TTTGGCTAGA
*
329616 GTTGACCGCTAACCGGTCAGATC
1 GTTGACCGTTAACCGGTCAGATC
329639 GTTGACCGTTAACCGGTCAGATC
1 GTTGACCGTTAACCGGTCAGATC
*
329662 GTTGGCCGTTAAC
1 GTTGACCGTTAAC
329675 TTTGACCGAA
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:0.20, C:0.27, G:0.27, T:0.25
Consensus pattern (23 bp):
GTTGACCGTTAACCGGTCAGATC
Found at i:329958 original size:24 final size:24
Alignment explanation
Indices: 329912--329961 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
329902 ATCGTTTGAT
**
329912 TGTTCGACTCGGTTCCTTTCGATC
1 TGTTCGACTCGGTTCCTCCCGATC
*
329936 TGTTCGACTCGGTTTCTCCCGATC
1 TGTTCGACTCGGTTCCTCCCGATC
329960 TG
1 TG
329962 CTCGTCTACG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.08, C:0.30, G:0.22, T:0.40
Consensus pattern (24 bp):
TGTTCGACTCGGTTCCTCCCGATC
Found at i:340147 original size:14 final size:14
Alignment explanation
Indices: 340128--340161 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
340118 ACCCAAAATC
340128 AAACCCAAATCCCT
1 AAACCCAAATCCCT
340142 AAACCCAAATCCCT
1 AAACCCAAATCCCT
340156 AAACCC
1 AAACCC
340162 CTAATTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.44, C:0.44, G:0.00, T:0.12
Consensus pattern (14 bp):
AAACCCAAATCCCT
Found at i:341389 original size:21 final size:22
Alignment explanation
Indices: 341363--341409 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
341353 CTACTGTATA
* *
341363 ATTTAC-CAGATTTAAAGCCTG
1 ATTTACTCAAATTTAAAGCATG
*
341384 ATTTACTGAAATTTAAAGCATG
1 ATTTACTCAAATTTAAAGCATG
341406 ATTT
1 ATTT
341410 CTTGATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (22 bp):
ATTTACTCAAATTTAAAGCATG
Found at i:359171 original size:22 final size:22
Alignment explanation
Indices: 359124--359179 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
359114 AAGATTATAG
*
359124 ATTACTTAGGATTTTAATTATTT
1 ATTA-TTAGGATTTTAATTATCT
*
359147 ATTATTAGGATTTTAGTT-TACT
1 ATTATTAGGATTTTAATTAT-CT
359169 ATTAATTAGGA
1 ATT-ATTAGGA
359180 ATTAAGTGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 1 0.03
22 17 0.59
23 11 0.38
ACGTcount: A:0.32, C:0.04, G:0.12, T:0.52
Consensus pattern (22 bp):
ATTATTAGGATTTTAATTATCT
Found at i:359960 original size:15 final size:15
Alignment explanation
Indices: 359940--359968 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
359930 TATCTCTCAT
359940 TACAATTAATTTTTA
1 TACAATTAATTTTTA
359955 TACAATTAATTTTT
1 TACAATTAATTTTT
359969 CTTGCTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (15 bp):
TACAATTAATTTTTA
Found at i:363216 original size:3 final size:3
Alignment explanation
Indices: 363208--363246 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
363198 CATTTTTAAA
363208 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
363247 TATTTATTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:370112 original size:28 final size:27
Alignment explanation
Indices: 370071--370144 Score: 71
Period size: 28 Copynumber: 2.7 Consensus size: 27
370061 AATAAAATAA
370071 AAATATTAAT-AAAAAATAATA-TACATAT
1 AAATATT-ATGAAAAAA-AA-AGTACATAT
*
370099 AAATATTATGAAAATAAAAAGTATATAT
1 AAATATTATGAAAA-AAAAAGTACATAT
* *
370127 AAAAATTTTGAAAAAAAA
1 AAATATTATGAAAAAAAA
370145 GAACTATAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
27 7 0.17
28 31 0.77
29 2 0.05
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (27 bp):
AAATATTATGAAAAAAAAAGTACATAT
Found at i:371062 original size:22 final size:23
Alignment explanation
Indices: 371037--371089 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
371027 TAATAATAAT
*
371037 AACAATCATAATTAAAT-ATA-TA
1 AACAAT-AAAATTAAATGATACTA
371059 AACATATAAAATTAAATGATAGCTA
1 AACA-ATAAAATTAAATGATA-CTA
371084 AACAAT
1 AACAAT
371090 GACTAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 13 0.50
23 5 0.19
24 2 0.08
25 6 0.23
ACGTcount: A:0.58, C:0.09, G:0.04, T:0.28
Consensus pattern (23 bp):
AACAATAAAATTAAATGATACTA
Found at i:372325 original size:3 final size:3
Alignment explanation
Indices: 372317--372372 Score: 76
Period size: 3 Copynumber: 17.7 Consensus size: 3
372307 TTATTTATTA
*
372317 AAT AAT AAT AAAT ATAT AAT ATAT AAT ATT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT -AAT A-AT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
372365 AAT AAT AA
1 AAT AAT AA
372373 AACAAAATAA
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
3 39 0.81
4 9 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:373526 original size:23 final size:20
Alignment explanation
Indices: 373475--373528 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 20
373465 TTTCCCTTCA
* *
373475 AGTGCATTGGTACATTCTAC
1 AGTGCATCGATACATTCTAC
373495 AGTGCATCGATACATTCTTAAC
1 AGTGCATCGATACATTC-T-AC
373517 ATGTGCATCGAT
1 A-GTGCATCGAT
373529 GCACTATCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 15 0.52
21 1 0.03
22 3 0.10
23 10 0.34
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (20 bp):
AGTGCATCGATACATTCTAC
Found at i:375633 original size:10 final size:10
Alignment explanation
Indices: 375618--375646 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
375608 ATATGAAGTA
375618 AGAGAAACAG
1 AGAGAAACAG
375628 AGAGAAACAG
1 AGAGAAACAG
375638 AGAGAAACA
1 AGAGAAACA
375647 TCATATTAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.62, C:0.10, G:0.28, T:0.00
Consensus pattern (10 bp):
AGAGAAACAG
Found at i:375842 original size:27 final size:27
Alignment explanation
Indices: 375777--375843 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
375767 CTTATACTTT
375777 TTAAACTATA-TACATTTCACTTAATG
1 TTAAACTATATTACATTTCACTTAATG
* *
375803 TTGAACAATATTACA-TTCGACTTAATG
1 TTAAACTATATTACATTTC-ACTTAATG
*
375830 TTAAACTACATTAC
1 TTAAACTATATTAC
375844 TTGAATGGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 11 0.32
27 23 0.68
ACGTcount: A:0.39, C:0.16, G:0.06, T:0.39
Consensus pattern (27 bp):
TTAAACTATATTACATTTCACTTAATG
Found at i:378378 original size:19 final size:19
Alignment explanation
Indices: 378354--378399 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
378344 CGTAAGCTTA
*
378354 GTGCAGGTTTAGCACTACG
1 GTGCAGGTTTAACACTACG
378373 GTGCAGGTTTAACACTACG
1 GTGCAGGTTTAACACTACG
378392 GTGCAGGT
1 GTGCAGGT
378400 ATTTTACTCG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.22, C:0.20, G:0.33, T:0.26
Consensus pattern (19 bp):
GTGCAGGTTTAACACTACG
Found at i:378553 original size:24 final size:24
Alignment explanation
Indices: 378525--378601 Score: 63
Period size: 24 Copynumber: 3.3 Consensus size: 24
378515 CGAGCTTATG
378525 AAAATAAATGGTAAGTATATTGAT
1 AAAATAAATGGTAAGTATATTGAT
* * **
378549 AAAAT-AA-GCTTACG-AGCTT-AT
1 AAAATAAATG-GTAAGTATATTGAT
*
378570 GGAAATAAATGGTAAGTATATTGAT
1 -AAAATAAATGGTAAGTATATTGAT
378595 AAAATAA
1 AAAATAA
378602 GCTTACGAGC
Statistics
Matches: 37, Mismatches: 10, Indels: 12
0.63 0.17 0.20
Matches are distributed among these distances:
21 2 0.05
22 8 0.22
23 10 0.27
24 15 0.41
25 2 0.05
ACGTcount: A:0.49, C:0.04, G:0.17, T:0.30
Consensus pattern (24 bp):
AAAATAAATGGTAAGTATATTGAT
Found at i:378645 original size:47 final size:46
Alignment explanation
Indices: 378476--378677 Score: 266
Period size: 46 Copynumber: 4.4 Consensus size: 46
378466 TGGTATATGG
* * * *
378476 TTATGG-AAT-AATGGCAAGTATAATGGTAAAATAAGTTTACGAGC
1 TTATGGAAATAAATGGTAAGTATATTGATAAAATAAGCTTACGAGC
*
378520 TTATGAAAATAAATGGTAAGTATATTGATAAAATAAGCTTACGAGC
1 TTATGGAAATAAATGGTAAGTATATTGATAAAATAAGCTTACGAGC
378566 TTATGGAAATAAATGGTAAGTATATTGATAAAATAAGCTTACGAGC
1 TTATGGAAATAAATGGTAAGTATATTGATAAAATAAGCTTACGAGC
* * * * * *
378612 TTATGGAATTTAAATGTTAAGTATTTTGGTAAAATAAGCTTATGATC
1 TTATGGAA-ATAAATGGTAAGTATATTGATAAAATAAGCTTACGAGC
*
378659 TTATGG-TATAAATGGTAAG
1 TTATGGAAATAAATGGTAAG
378678 AGATTTTATA
Statistics
Matches: 140, Mismatches: 15, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
44 5 0.04
45 13 0.09
46 84 0.60
47 38 0.27
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.34
Consensus pattern (46 bp):
TTATGGAAATAAATGGTAAGTATATTGATAAAATAAGCTTACGAGC
Found at i:379003 original size:20 final size:20
Alignment explanation
Indices: 378978--379024 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
378968 ATGTTTTATT
378978 TGTTCATGGGTATTGTTCAC
1 TGTTCATGGGTATTGTTCAC
* *
378998 TGTTCACGGGTATTGTTCAT
1 TGTTCATGGGTATTGTTCAC
379018 TGTTCAT
1 TGTTCAT
379025 AAAAATATCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.15, C:0.15, G:0.23, T:0.47
Consensus pattern (20 bp):
TGTTCATGGGTATTGTTCAC
Found at i:379534 original size:38 final size:37
Alignment explanation
Indices: 379492--379649 Score: 133
Period size: 38 Copynumber: 4.2 Consensus size: 37
379482 TTATTTAAGG
* *
379492 ATTTATATTCAATTAGATTTCAAATATATTATTTATAA
1 ATTTATATTCAATTAAATAT-AAATATATTATTTATAA
** * * *
379530 ATTTATATTTGATTGAAATGTGAATATATTACTTATAA
1 ATTTATATTCAATT-AAATATAAATATATTATTTATAA
* *
379568 ATATATATT-AGATT-AATATAAATATATTATTTATGA
1 ATTTATATTCA-ATTAAATATAAATATATTATTTATAA
* * * **
379604 ATTTATGTTCAATTAAAAAACAAATATATTA-TTACGA
1 ATTTATATTCAATT-AAATATAAATATATTATTTATAA
379641 ATTTATATT
1 ATTTATATT
379650 TAAGTAAAAT
Statistics
Matches: 97, Mismatches: 18, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
36 28 0.29
37 14 0.14
38 51 0.53
39 4 0.04
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.47
Consensus pattern (37 bp):
ATTTATATTCAATTAAATATAAATATATTATTTATAA
Found at i:379658 original size:37 final size:38
Alignment explanation
Indices: 379587--379658 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 38
379577 AGATTAATAT
* * *
379587 AAATATATTATTTATGAATTTATGTTCAATTAAAAAAC
1 AAATATATTATTTACGAATTTATATTCAAGTAAAAAAC
*
379625 AAATATATTA-TTACGAATTTATATTTAAGTAAAA
1 AAATATATTATTTACGAATTTATATTCAAGTAAAA
379659 TATGATATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 20 0.67
38 10 0.33
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.42
Consensus pattern (38 bp):
AAATATATTATTTACGAATTTATATTCAAGTAAAAAAC
Found at i:380107 original size:13 final size:13
Alignment explanation
Indices: 380089--380120 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
380079 CCTAAACTAA
380089 GGCTACACTACTC
1 GGCTACACTACTC
380102 GGCTACACTACTC
1 GGCTACACTACTC
*
380115 TGCTAC
1 GGCTAC
380121 CCTAGTTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.22, C:0.38, G:0.16, T:0.25
Consensus pattern (13 bp):
GGCTACACTACTC
Found at i:381680 original size:60 final size:59
Alignment explanation
Indices: 381571--381741 Score: 141
Period size: 60 Copynumber: 2.9 Consensus size: 59
381561 TATATGTCGC
* * * * * *
381571 CAAACTATAACCCTT-ATTTTAAATTAGTCC-TCAAACTTTTAAATATTCTAATTCCATCCT
1 CAAACTATGA-CCTTCA-TTTAAATTAATCCAT-AAACTTCTGAACATTCTAATTCCATACT
* * * * * *
381631 TAAACTATGA-CTCTCAATTTAAATTGATCCATAAACTTCTGAACCTTCTAAATGCGTACT
1 CAAACTATGACCT-TC-ATTTAAATTAATCCATAAACTTCTGAACATTCTAATTCCATACT
* * *
381691 CAAACTATGACCTTCATTTTAATTAATCCTTAAACTTTTGAACATTCTAAT
1 CAAACTATGACCTTCATTTAAATTAATCCATAAACTTCTGAACATTCTAAT
381742 AATAAATCAC
Statistics
Matches: 87, Mismatches: 19, Indels: 11
0.74 0.16 0.09
Matches are distributed among these distances:
58 2 0.02
59 31 0.36
60 50 0.57
61 4 0.05
ACGTcount: A:0.35, C:0.22, G:0.05, T:0.39
Consensus pattern (59 bp):
CAAACTATGACCTTCATTTAAATTAATCCATAAACTTCTGAACATTCTAATTCCATACT
Found at i:385926 original size:22 final size:23
Alignment explanation
Indices: 385892--385948 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 23
385882 AGGATGTCAA
*
385892 AGTGTATCCATGCACC-TGCACT
1 AGTGCATCCATGCACCATGCACT
*
385914 AGTGCATCGATGCACCATG--C-
1 AGTGCATCCATGCACCATGCACT
385934 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
385949 TCCATTTCGA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 14 0.45
21 1 0.03
22 14 0.45
23 2 0.06
ACGTcount: A:0.25, C:0.32, G:0.21, T:0.23
Consensus pattern (23 bp):
AGTGCATCCATGCACCATGCACT
Found at i:385994 original size:20 final size:20
Alignment explanation
Indices: 385969--386020 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
385959 ATGCACTTAG
385969 TGCATCGATGCATCTTGATA
1 TGCATCGATGCATCTTGATA
* *
385989 TGCATCGATGCATCTTGTTG
1 TGCATCGATGCATCTTGATA
*
386009 TGCATCCATGCA
1 TGCATCGATGCA
386021 CGAAGGCTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (20 bp):
TGCATCGATGCATCTTGATA
Found at i:389449 original size:22 final size:20
Alignment explanation
Indices: 389386--389480 Score: 90
Period size: 17 Copynumber: 4.8 Consensus size: 20
389376 AGGGTGTCAA
* *
389386 AGTGCATCTATGCACCCCTGC
1 AGTGCATCCATGCA-CCATGC
*
389407 AGTGCATCCATG--TC-TGC
1 AGTGCATCCATGCACCATGC
389424 AGTGCATCCATGCACC-TGCAC
1 AGTGCATCCATGCACCATG--C
*
389445 TAGTGCATCGATGCACCATGC
1 -AGTGCATCCATGCACCATGC
389466 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
389481 TCCATTTCAA
Statistics
Matches: 63, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
17 15 0.24
18 1 0.02
19 3 0.05
20 14 0.22
21 13 0.21
22 15 0.24
23 2 0.03
ACGTcount: A:0.22, C:0.34, G:0.21, T:0.23
Consensus pattern (20 bp):
AGTGCATCCATGCACCATGC
Found at i:389525 original size:20 final size:20
Alignment explanation
Indices: 389500--389552 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
389490 AATGCACTTA
389500 GTGCATCGATGCATCCTGAT
1 GTGCATCGATGCATCCTGAT
*
389520 GTGCATCGATGCATCCTGTT
1 GTGCATCGATGCATCCTGAT
*
389540 GTGCATCCATGCA
1 GTGCATCGATGCA
389553 CGAAGGCTGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.19, C:0.26, G:0.25, T:0.30
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGAT
Found at i:390522 original size:27 final size:27
Alignment explanation
Indices: 390480--390554 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
390470 TGAGGACTTC
*
390480 AGGGTATTTCATTCATTTTAAAGCTCG
1 AGGGTATTTCATTCATTTTAAAGCTCA
* *
390507 AGGTTATTTCATTCATTTGAAAGCTCA
1 AGGGTATTTCATTCATTTTAAAGCTCA
390534 AGGGTATTTCGA-TCATTTTAA
1 AGGGTATTTC-ATTCATTTTAA
390555 TCAATTTAGT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
27 41 0.98
28 1 0.02
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.41
Consensus pattern (27 bp):
AGGGTATTTCATTCATTTTAAAGCTCA
Found at i:393727 original size:20 final size:20
Alignment explanation
Indices: 393690--393727 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
393680 TTAACCACTT
*
393690 AATTATTATTTTAGTTATCA
1 AATTATTATTTTAATTATCA
393710 AATTATT-TTTTAAATTAT
1 AATTATTATTTT-AATTAT
393728 TATTAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (20 bp):
AATTATTATTTTAATTATCA
Found at i:393930 original size:135 final size:135
Alignment explanation
Indices: 393688--393934 Score: 476
Period size: 135 Copynumber: 1.8 Consensus size: 135
393678 ATTTAACCAC
393688 TTAATTATTATTTTAGTTATCAAATTATTTTTTAAATTATTATTAATTTTACGTTTTGATCGATA
1 TTAATTATTATTTTAGTTATCAAATTATTTTTTAAATTATTATTAATTTTACGTTTTGATCGATA
393753 GTTGTTAGAATGAAACAAAACAGTTGAAGTGGTAATTTTTAATTATATATTTAACCACTTAATTA
66 GTTGTTAGAATGAAACAAAACAGTTGAAGTGGTAATTTTTAATTATATATTTAACCACTTAATTA
393818 TTATT
131 TTATT
* *
393823 TTAATTTTTATTTTAGTTGTCAAATTATTTTTTAAATTATTATTAATTTTACGTTTTGATCGATA
1 TTAATTATTATTTTAGTTATCAAATTATTTTTTAAATTATTATTAATTTTACGTTTTGATCGATA
393888 GTTGTTAGAATGAAACAAAACAGTTGAAGTGGTAATTTTTAATTATA
66 GTTGTTAGAATGAAACAAAACAGTTGAAGTGGTAATTTTTAATTATA
393935 ATATGATAAT
Statistics
Matches: 110, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
135 110 1.00
ACGTcount: A:0.35, C:0.05, G:0.11, T:0.49
Consensus pattern (135 bp):
TTAATTATTATTTTAGTTATCAAATTATTTTTTAAATTATTATTAATTTTACGTTTTGATCGATA
GTTGTTAGAATGAAACAAAACAGTTGAAGTGGTAATTTTTAATTATATATTTAACCACTTAATTA
TTATT
Found at i:393946 original size:21 final size:21
Alignment explanation
Indices: 393920--393967 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
393910 GTTGAAGTGG
393920 TAATTTTTAATTATAATATGA
1 TAATTTTTAATTATAATATGA
393941 TAATTTTTAATTATAATATGA
1 TAATTTTTAATTATAATATGA
393962 T-ATTTT
1 TAATTTT
393968 ATTATTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 5 0.19
21 22 0.81
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (21 bp):
TAATTTTTAATTATAATATGA
Found at i:394454 original size:21 final size:21
Alignment explanation
Indices: 394422--394481 Score: 111
Period size: 21 Copynumber: 2.8 Consensus size: 21
394412 CCTTAATTTT
394422 CTTTCTTCTTCAAAATTTACTG
1 CTTTC-TCTTCAAAATTTACTG
394444 CTTTCTCTTCAAAATTTACTG
1 CTTTCTCTTCAAAATTTACTG
394465 CTTTCTCTTCAAAATTT
1 CTTTCTCTTCAAAATTT
394482 TGCTACCTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 33 0.87
22 5 0.13
ACGTcount: A:0.23, C:0.23, G:0.03, T:0.50
Consensus pattern (21 bp):
CTTTCTCTTCAAAATTTACTG
Found at i:403516 original size:13 final size:14
Alignment explanation
Indices: 403498--403528 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
403488 GGTCAAAGGA
403498 GGTCAACGGTC-AC
1 GGTCAACGGTCAAC
403511 GGTCAACGGTCAAC
1 GGTCAACGGTCAAC
403525 GGTC
1 GGTC
403529 GGTCGGGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.23, C:0.29, G:0.32, T:0.16
Consensus pattern (14 bp):
GGTCAACGGTCAAC
Found at i:403539 original size:16 final size:17
Alignment explanation
Indices: 403518--403554 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
403508 CACGGTCAAC
403518 GGTCAACGGTC-GGTCG
1 GGTCAACGGTCGGGTCG
403534 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
403551 GGTC
1 GGTC
403555 GGGTCAAACC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.11, C:0.24, G:0.46, T:0.19
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:403544 original size:7 final size:7
Alignment explanation
Indices: 403498--403528 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
403488 GGTCAAAGGA
403498 GGTCAAC
1 GGTCAAC
403505 GGTC-AC
1 GGTCAAC
403511 GGTCAAC
1 GGTCAAC
403518 GGTCAAC
1 GGTCAAC
403525 GGTC
1 GGTC
403529 GGTCGGGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.23, C:0.29, G:0.32, T:0.16
Consensus pattern (7 bp):
GGTCAAC
Found at i:405810 original size:21 final size:21
Alignment explanation
Indices: 405784--405825 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
405774 CCAGAATGGG
*
405784 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
405805 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
405826 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:405972 original size:19 final size:19
Alignment explanation
Indices: 405931--405978 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
405921 GAGCCTCGGG
* *
405931 TTACTGTTCAAACAGTGAT
1 TTACTGTTCAAACAGTAAA
*
405950 TTACTGTTCAAATAGTAAA
1 TTACTGTTCAAACAGTAAA
*
405969 TTACTATTCA
1 TTACTGTTCA
405979 TAAAAACATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (19 bp):
TTACTGTTCAAACAGTAAA
Found at i:406101 original size:31 final size:31
Alignment explanation
Indices: 406043--406133 Score: 150
Period size: 31 Copynumber: 3.0 Consensus size: 31
406033 AAATTTTGAA
*
406043 TAAATTCAATT-AAGTCCAAAAA-TATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
406072 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
*
406103 TAAATTCAATTCAAGTCTAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
406134 CCTTAAATTG
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
29 11 0.19
30 11 0.19
31 36 0.62
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:406784 original size:26 final size:25
Alignment explanation
Indices: 406749--406797 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
406739 TTTTAAGGGT
406749 CGAATGTATAAAATTTTATAAAGAAA
1 CGAATGTATAAAATTTTA-AAAGAAA
*
406775 CGAATTTATAAAATTTTAAAAGA
1 CGAATGTATAAAATTTTAAAAGA
406798 TAAAAATAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.53, C:0.04, G:0.10, T:0.33
Consensus pattern (25 bp):
CGAATGTATAAAATTTTAAAAGAAA
Found at i:406838 original size:17 final size:17
Alignment explanation
Indices: 406818--406851 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
406808 TTATTAATAA
406818 AAAATATATAAAAATTT
1 AAAATATATAAAAATTT
406835 AAAATATATAAAAATTT
1 AAAATATATAAAAATTT
406852 TAAGAGATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AAAATATATAAAAATTT
Found at i:408278 original size:18 final size:18
Alignment explanation
Indices: 408255--408290 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
408245 ACCAATAGTT
408255 CTATTAATTTTTTAACAG
1 CTATTAATTTTTTAACAG
408273 CTATTAATTTTTTAACAG
1 CTATTAATTTTTTAACAG
408291 TAGGTGACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.06, T:0.50
Consensus pattern (18 bp):
CTATTAATTTTTTAACAG
Found at i:408844 original size:22 final size:22
Alignment explanation
Indices: 408822--408879 Score: 100
Period size: 22 Copynumber: 2.7 Consensus size: 22
408812 TCTAAATATA
408822 AAAT-TTTAATTATTTAATAAT
1 AAATATTTAATTATTTAATAAT
408843 AAATATTTAATTATTTAATAAT
1 AAATATTTAATTATTTAATAAT
*
408865 AAATGTTTAATTATT
1 AAATATTTAATTATT
408880 CATCATCTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
21 4 0.11
22 31 0.89
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
AAATATTTAATTATTTAATAAT
Found at i:410768 original size:22 final size:22
Alignment explanation
Indices: 410742--410810 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 22
410732 TAAAACCAAA
410742 TATATAAAAGTCCAAACAATAT
1 TATATAAAAGTCCAAACAATAT
* * *
410764 TATATGTATA-T-TAAACCAA-A-
1 TATAT-AAAAGTCCAAA-CAATAT
410784 TATATAAAAGTCCAAACAATAT
1 TATATAAAAGTCCAAACAATAT
410806 TATAT
1 TATAT
410811 GTATATTAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 12
0.66 0.11 0.23
Matches are distributed among these distances:
19 2 0.06
20 9 0.26
21 8 0.23
22 14 0.40
23 2 0.06
ACGTcount: A:0.52, C:0.12, G:0.04, T:0.32
Consensus pattern (22 bp):
TATATAAAAGTCCAAACAATAT
Found at i:410781 original size:42 final size:42
Alignment explanation
Indices: 410734--410825 Score: 184
Period size: 42 Copynumber: 2.2 Consensus size: 42
410724 ATATTAAATA
410734 AAACCAAATATATAAAAGTCCAAACAATATTATATGTATATT
1 AAACCAAATATATAAAAGTCCAAACAATATTATATGTATATT
410776 AAACCAAATATATAAAAGTCCAAACAATATTATATGTATATT
1 AAACCAAATATATAAAAGTCCAAACAATATTATATGTATATT
410818 AAACCAAA
1 AAACCAAA
410826 CCAAAGTCCA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.54, C:0.13, G:0.04, T:0.28
Consensus pattern (42 bp):
AAACCAAATATATAAAAGTCCAAACAATATTATATGTATATT
Found at i:410827 original size:47 final size:45
Alignment explanation
Indices: 410724--410830 Score: 157
Period size: 42 Copynumber: 2.4 Consensus size: 45
410714 ATATTAGTCC
410724 ATATTAAATAAAACCAAATATATAAAAGTCCAAACAATATTATATGT
1 ATATT-AA-AAAACCAAATATATAAAAGTCCAAACAATATTATATGT
410771 ATATT---AAACCAAATATATAAAAGTCCAAACAATATTATATGT
1 ATATTAAAAAACCAAATATATAAAAGTCCAAACAATATTATATGT
410813 ATATTAAACCAAACCAAA
1 ATATTAAA--AAACCAAA
410831 GTCCATTACC
Statistics
Matches: 55, Mismatches: 0, Indels: 10
0.85 0.00 0.15
Matches are distributed among these distances:
42 42 0.76
47 13 0.24
ACGTcount: A:0.55, C:0.13, G:0.04, T:0.28
Consensus pattern (45 bp):
ATATTAAAAAACCAAATATATAAAAGTCCAAACAATATTATATGT
Found at i:413024 original size:24 final size:24
Alignment explanation
Indices: 412996--413041 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
412986 TGCATGACAT
412996 TGTACATAGATGTTTTATACATTA
1 TGTACATAGATGTTTTATACATTA
413020 TGTACATAGATGTTTTATACAT
1 TGTACATAGATGTTTTATACAT
413042 CATCAAGAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.46
Consensus pattern (24 bp):
TGTACATAGATGTTTTATACATTA
Found at i:413398 original size:26 final size:25
Alignment explanation
Indices: 413362--413417 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 25
413352 ATGGCACTAA
413362 GTGTATATGGTGGGCATGACCTTAT
1 GTGTATATGGTGGGCATGACCTTAT
*
413387 GTGTATTATGGTGGGCATGATCTTAT
1 GTGTA-TATGGTGGGCATGACCTTAT
413413 GTGTA
1 GTGTA
413418 AGCATTACAG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 5 0.17
26 24 0.83
ACGTcount: A:0.20, C:0.09, G:0.32, T:0.39
Consensus pattern (25 bp):
GTGTATATGGTGGGCATGACCTTAT
Found at i:420090 original size:26 final size:25
Alignment explanation
Indices: 420054--420109 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 25
420044 AGGGAACTGA
420054 GTGTATATGGTGGGCACGACCTTAT
1 GTGTATATGGTGGGCACGACCTTAT
**
420079 GTGTATTATGGTGGGTGCGACCTTAT
1 GTGTA-TATGGTGGGCACGACCTTAT
420105 GTGTA
1 GTGTA
420110 AGCACTACGG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
25 5 0.18
26 23 0.82
ACGTcount: A:0.18, C:0.12, G:0.34, T:0.36
Consensus pattern (25 bp):
GTGTATATGGTGGGCACGACCTTAT
Found at i:420624 original size:2 final size:2
Alignment explanation
Indices: 420617--420643 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
420607 ATACATACAT
420617 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
420644 TACATACCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:421593 original size:16 final size:16
Alignment explanation
Indices: 421566--421615 Score: 91
Period size: 16 Copynumber: 3.1 Consensus size: 16
421556 ACATTATAGG
421566 TTATACATAATCAGTTA
1 TTATA-ATAATCAGTTA
421583 TTATAATAATCAGTTA
1 TTATAATAATCAGTTA
421599 TTATAATAATCAGTTA
1 TTATAATAATCAGTTA
421615 T
1 T
421616 GGCTATAATC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 28 0.85
17 5 0.15
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (16 bp):
TTATAATAATCAGTTA
Found at i:443179 original size:19 final size:19
Alignment explanation
Indices: 443155--443235 Score: 72
Period size: 22 Copynumber: 3.9 Consensus size: 19
443145 ATGCAGAAAT
*
443155 AGTATCGATATCATAATAG
1 AGTATCGATACCATAATAG
*
443174 AGTATCGGTACCATAATATAG
1 AGTATCGATACCAT-A-ATAG
*
443195 AAGTATCGGTACCATAATATAG
1 -AGTATCGATACCAT-A-ATAG
*
443217 AAGTATCGGTACCATAATA
1 -AGTATCGATACCATAATA
443236 TAGAAGTATC
Statistics
Matches: 57, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
19 12 0.21
20 4 0.07
21 5 0.09
22 36 0.63
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (19 bp):
AGTATCGATACCATAATAG
Found at i:443202 original size:22 final size:22
Alignment explanation
Indices: 443170--443250 Score: 155
Period size: 22 Copynumber: 3.7 Consensus size: 22
443160 CGATATCATA
443170 ATAG-AGTATCGGTACCATAAT
1 ATAGAAGTATCGGTACCATAAT
443191 ATAGAAGTATCGGTACCATAAT
1 ATAGAAGTATCGGTACCATAAT
443213 ATAGAAGTATCGGTACCATAAT
1 ATAGAAGTATCGGTACCATAAT
443235 ATAGAAGTATCGGTAC
1 ATAGAAGTATCGGTAC
443251 TGAGAGGAAG
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
21 4 0.07
22 55 0.93
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.27
Consensus pattern (22 bp):
ATAGAAGTATCGGTACCATAAT
Found at i:443762 original size:45 final size:45
Alignment explanation
Indices: 443698--444234 Score: 734
Period size: 45 Copynumber: 11.9 Consensus size: 45
443688 ATTTAATATA
* * *
443698 ATAACGGTGTATTTAAGGCATGAAAGGATACCATAAATAAAATGC
1 ATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGC
* * * *
443743 ATAACGGTACATTAAAGGCATGAAAGGATACCCTAAATAAAATGT
1 ATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGC
* * * *
443788 ATAATGATACATTAAAGGCATGAAAGGATTCCATAAATAAAATG-
1 ATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGC
* * *
443832 ATAACGATGCATTAAATGCATGAAAGGATGCCATAAATAAAATAC
1 ATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGC
443877 ATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGC
1 ATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGC
* * *
443922 ATAACGATGGATTAAAGGCATGAAAGGATGCAATAAATAAAATGC
1 ATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGC
* * *
443967 ATAACAGTGCATTAAAGGGACGAAAGGATGCCATAAATAAAATGC
1 ATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGC
* ** *
444012 ATAACGGTTCATTAAAGGCAAAAAAGGATGCTATAAATAAAATGC
1 ATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGC
* *
444057 ATAACAGTGCATTAAAGGCATTAAAGGATGCCATAAATAAAATGC
1 ATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGC
* * * *
444102 ATAACGGTGCATTAAATGTATTAAAGGATGCCATAAATAAAATAC
1 ATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGC
* * *
444147 ATAACGGTGCATTAAAGGCAAGAAATGATTCCATAAATAAAATGC
1 ATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGC
* * *
444192 ATACCAGTGCATTAAAGGCATGAAATGATGCCATAAATGAAAA
1 ATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAAT-AAAA
444235 AAATGAATAA
Statistics
Matches: 438, Mismatches: 52, Indels: 3
0.89 0.11 0.01
Matches are distributed among these distances:
44 39 0.09
45 395 0.90
46 4 0.01
ACGTcount: A:0.47, C:0.12, G:0.19, T:0.22
Consensus pattern (45 bp):
ATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGC
Found at i:443832 original size:22 final size:22
Alignment explanation
Indices: 443807--443874 Score: 59
Period size: 22 Copynumber: 3.1 Consensus size: 22
443797 CATTAAAGGC
443807 ATGAAAGGATTCCATAAATAAA
1 ATGAAAGGATTCCATAAATAAA
* * **
443829 ATGATAACGA-TGCATTAAAT-GC
1 ATGA-AAGGATTCCA-TAAATAAA
*
443851 ATGAAAGGATGCCATAAATAAA
1 ATGAAAGGATTCCATAAATAAA
443873 AT
1 AT
443875 ACATAACGGT
Statistics
Matches: 33, Mismatches: 9, Indels: 8
0.66 0.18 0.16
Matches are distributed among these distances:
21 9 0.27
22 15 0.45
23 9 0.27
ACGTcount: A:0.50, C:0.10, G:0.16, T:0.24
Consensus pattern (22 bp):
ATGAAAGGATTCCATAAATAAA
Found at i:450034 original size:45 final size:45
Alignment explanation
Indices: 449966--450639 Score: 934
Period size: 45 Copynumber: 15.0 Consensus size: 45
449956 ATTTAATATA
* * *
449966 ATAACGATGCATTAAAGGTATGAAAGGATGTCATAAATAAAATGC
1 ATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGC
* *
450011 ATAACAGTGCATTAAAGGCATGAAATGATGCCATAAATAAAATGC
1 ATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGC
*
450056 ATAACGGTGCACTAAAGGCATGAAAGGATGCCATAAATAAAATGC
1 ATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGC
*
450101 ATAACAGTGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGC
1 ATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGC
* ** *
450146 ATAACGGTGCATTAAATGCATGAAAGGATAACATAAATAAAATGT
1 ATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGC
** * * **
450191 ATAACTATGCATTAAAAGCATAAAAGGATAACATAAATAAAATGC
1 ATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGC
* * *
450236 ATAACGCTGTATTAAAGGTATGAAAGGATGCCATAAATAAAATGC
1 ATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGC
* * **
450281 ATAATGCTGCATTAAAGGCATGAAAAAATGCCATAAATAAAATGC
1 ATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGC
* ** * *
450326 ATAACGGTGTATTAAAGGCATGAATTGATTCCATAAATAAAATAC
1 ATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGC
* * * * *
450371 TTAACAGTGCATTAAAGGTAAGAAAGGATGCCATAAATTAAATGC
1 ATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGC
* * * *
450416 TTAACGGTGCATTAAAGACATGAAAGGATGCAATTAATAAAATGC
1 ATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGC
*
450461 ATAACGATGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGC
1 ATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGC
* * *
450506 ATAACGGTGCATTAAAGGCATGAAAGGATACCTTAAATAAAATTC
1 ATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGC
450551 ATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGC
1 ATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGC
* * *
450596 ATAACAGTGTATTAAACGCATGAAAGGATGCCATAAATGAAAAT
1 ATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAAT-AAAAT
450640 AATGAATAAT
Statistics
Matches: 555, Mismatches: 73, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
45 550 0.99
46 5 0.01
ACGTcount: A:0.47, C:0.12, G:0.19, T:0.23
Consensus pattern (45 bp):
ATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGC
Found at i:454343 original size:199 final size:201
Alignment explanation
Indices: 454002--454403 Score: 774
Period size: 199 Copynumber: 2.0 Consensus size: 201
453992 TATTGCTTCT
454002 CCACTCCTCATACTCTTGTGACATCCTTAAATCAAAGGTAAAGAGATTTACTCTACAAGTGTGGT
1 CCACTCCTCATACTCTTGTGACATCCTTAAATCAAAGGTAAAGAGATTTACTCTACAAGTGTGGT
454067 TCCATGTAATGACAACTCCTTTAACTTTATTATTGTACTAATCTCCTTTGAATGCAAACTCAAAC
66 TCCATGTAATGACAACTCCTTTAACTTTATTATTGTACTAATCTCCTTTGAATGCAAACTCAAAC
454132 CCTGATAAATCCTAAGTTACCAGAACAAACTGTCTTGACCAATACATG-CTGAAAACCA-TAATG
131 CCTGATAAATCCTAAGTTACCAGAACAAACTGTCTTGACCAATAC-TGCCTGAAAACCAGTAATG
454195 AAGTACA
195 AAGTACA
454202 CCACTCCTCATACTCTTGTGACATCCTT-AATCAAAGGTAAAGAGATTTACTCTACAAGTGTGGT
1 CCACTCCTCATACTCTTGTGACATCCTTAAATCAAAGGTAAAGAGATTTACTCTACAAGTGTGGT
454266 TCCATGTAATGACAACTCCTTTAACTTTATTATTGTACTAATCTCCTTTGAATGCAAACTCAAAC
66 TCCATGTAATGACAACTCCTTTAACTTTATTATTGTACTAATCTCCTTTGAATGCAAACTCAAAC
454331 CCTGATAAATCCTAAGTTACCAGAACAAACTGTCTTGACCAATACTGCCTGAAAACCAGTAATGA
131 CCTGATAAATCCTAAGTTACCAGAACAAACTGTCTTGACCAATACTGCCTGAAAACCAGTAATGA
454396 AGTACA
196 AGTACA
454402 CC
1 CC
454404 CTATAGAACC
Statistics
Matches: 200, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
198 2 0.01
199 156 0.78
200 42 0.21
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.30
Consensus pattern (201 bp):
CCACTCCTCATACTCTTGTGACATCCTTAAATCAAAGGTAAAGAGATTTACTCTACAAGTGTGGT
TCCATGTAATGACAACTCCTTTAACTTTATTATTGTACTAATCTCCTTTGAATGCAAACTCAAAC
CCTGATAAATCCTAAGTTACCAGAACAAACTGTCTTGACCAATACTGCCTGAAAACCAGTAATGA
AGTACA
Found at i:457097 original size:131 final size:131
Alignment explanation
Indices: 456938--457288 Score: 431
Period size: 131 Copynumber: 2.7 Consensus size: 131
456928 GAGAAAAATG
* * * * * *
456938 ATATCTAATTATTTACAATTGAGAATAAATGACCTTTCATACCATAAAACAATCATTTATTATTC
1 ATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAACAGTCATTTATTACTC
* ** * * *
457003 CAAATCGAAATGAAGAGATATTACTTTTTGTC-TTAAAATTCAATATCAATTTGAGTGAAAATGA
66 CAAATCGAAATGAAGATATATTACTTTCCGTCTTTAAAA-TCAATATCAATTCGAGAGAAAACGA
457067 TA
130 TA
** *
457069 ATATCTAATGGTTTCCAATCGAAAATAAATGACCTCTCATACCTTAAAGA-AGTCATTTATTACT
1 ATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAA-ACAGTCATTTATTACT
* * *
457133 CC-AATCGAAATGAAGATATATCACAATTCCGTCTTTAAAATCAATATTAATTCGAGAGAAAACG
65 CCAAATCGAAATGAAGATATATTAC-TTTCCGTCTTTAAAATCAATATCAATTCGAGAGAAAACG
457197 ATA
129 ATA
* * * * *
457200 ATATCGAATTATTTCAAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAGTCATTTTTTACTC
1 ATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAACAGTCATTTATTACTC
*
457265 CAAAT-GAAATGAAAATATATTACT
66 CAAATCGAAATGAAGATATATTACT
457289 ACTCTCAATA
Statistics
Matches: 186, Mismatches: 29, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
130 20 0.11
131 156 0.84
132 10 0.05
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.34
Consensus pattern (131 bp):
ATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAACAGTCATTTATTACTC
CAAATCGAAATGAAGATATATTACTTTCCGTCTTTAAAATCAATATCAATTCGAGAGAAAACGAT
A
Found at i:457767 original size:5 final size:5
Alignment explanation
Indices: 457757--457788 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
457747 CAACATGCAA
457757 AAAAT AAAAT AAAAT AAAAT AAAAT GAAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT A
457789 TGACTAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:459426 original size:3 final size:3
Alignment explanation
Indices: 459418--459542 Score: 173
Period size: 3 Copynumber: 42.0 Consensus size: 3
459408 ATTAAAAAGT
* * * *
459418 ATA ATA ATA ATA ATA ATA ATA GTA GTA GTA GTA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
459466 ATA ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
459513 ATA ATA ATAA ATC A-A ATA ATA ATA TTA ATA
1 ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA
459543 TTATCGGGAT
Statistics
Matches: 113, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
2 3 0.03
3 107 0.95
4 3 0.03
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:460506 original size:30 final size:30
Alignment explanation
Indices: 460470--460537 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 30
460460 TCCAAACCGT
460470 AATACTTTCTTCCAAGGTGATACCTTGAGA
1 AATACTTTCTTCCAAGGTGATACCTTGAGA
*
460500 AATACTTTCTTCCAATGTGATACCTTGAGA
1 AATACTTTCTTCCAAGGTGATACCTTGAGA
460530 AATACTTT
1 AATACTTT
460538 ATCACCTACT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (30 bp):
AATACTTTCTTCCAAGGTGATACCTTGAGA
Found at i:463667 original size:31 final size:28
Alignment explanation
Indices: 463632--463688 Score: 87
Period size: 28 Copynumber: 1.9 Consensus size: 28
463622 TTTAAAAACC
463632 TATTTTGACCAAAAAGATAACTTTAAGTATT
1 TATTTTGACC-AAAA-AT-ACTTTAAGTATT
463663 TATTTTGACCAAAAATACTTTAAGTA
1 TATTTTGACCAAAAATACTTTAAGTA
463689 CTTAAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 10 0.38
29 2 0.08
30 4 0.15
31 10 0.38
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.39
Consensus pattern (28 bp):
TATTTTGACCAAAAATACTTTAAGTATT
Found at i:465225 original size:96 final size:96
Alignment explanation
Indices: 465109--465304 Score: 259
Period size: 96 Copynumber: 2.0 Consensus size: 96
465099 AGTACTAACT
* * *
465109 AGTAGATTCCATATTGCATAAATCAGGAACAATCATATTTTATAGTGAAAATAGGAAACCAGATA
1 AGTAGATTCCATATTCCATAAATCAGGAACAATCATATTTTATAGTGAAAACAGGAAACCAGAGA
**
465174 ACATATTTCAGGTAACCATAGTTCAAAAACC
66 ACATATAACAGGTAACCATAGTTCAAAAACC
* * * *
465205 AGTAGATTCCATGA-TCCATAAATCAGGAACTATTATATTTTCTAGTGAAAACAGGTAACCAGAG
1 AGTAGATTCCAT-ATTCCATAAATCAGGAACAATCATATTTTATAGTGAAAACAGGAAACCAGAG
* * * *
465269 AACATATAACATGTAGCTATAGTTCATAAACC
65 AACATATAACAGGTAACCATAGTTCAAAAACC
465301 AGTA
1 AGTA
465305 AATTTGTAAC
Statistics
Matches: 86, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
96 85 0.99
97 1 0.01
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (96 bp):
AGTAGATTCCATATTCCATAAATCAGGAACAATCATATTTTATAGTGAAAACAGGAAACCAGAGA
ACATATAACAGGTAACCATAGTTCAAAAACC
Found at i:468294 original size:192 final size:194
Alignment explanation
Indices: 467967--468346 Score: 746
Period size: 192 Copynumber: 2.0 Consensus size: 194
467957 TTTTATTTTT
467967 CACATATTAGATTAATTGGAAAATTCAAGGCTAAGTCCCTAAACTGAGCATAATTTGAAATCAAC
1 CACATATTAGATTAATTGGAAAATTCAAGGCTAAGTCCCTAAACTGAGCATAATTTGAAATCAAC
468032 CTAAATACTTTCAAAATTCTTCATTTTGGTCCATAAATTTAATTAAATAAATTATATTTTATTTT
66 CTAAATACTTTCAAAATTCTTCATTTTGGTCCATAAATTTAATTAAATAAATTATATTTTATTTT
468097 TATTCT-AAACTGGGTTGTGACCATTCTCT-CCCCTTAAAATAATTTCATCCTCTAAACAACAA
131 TATTCTAAAACTGGGTTGTGACCATTCTCTCCCCCTTAAAATAATTTCATCCTCTAAACAACAA
468159 CACATATTAGATTAATTGGAAAATTCAAGGCTAAGTCCCTAAACTGAGCATAATTTGAAATCAAC
1 CACATATTAGATTAATTGGAAAATTCAAGGCTAAGTCCCTAAACTGAGCATAATTTGAAATCAAC
468224 CTAAATACTTTCAAAATTCTTCATTTTGGTCCATAAATTTAATTAAATAAATTATATTTTATTTT
66 CTAAATACTTTCAAAATTCTTCATTTTGGTCCATAAATTTAATTAAATAAATTATATTTTATTTT
468289 TATTCTAAAACTGGGTTGTGACCATTCTCTCCCCCTTAAAATAATTTCATCCTCTAAA
131 TATTCTAAAACTGGGTTGTGACCATTCTCTCCCCCTTAAAATAATTTCATCCTCTAAA
468347 TTCACCAAAG
Statistics
Matches: 186, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
192 136 0.73
193 23 0.12
194 27 0.15
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (194 bp):
CACATATTAGATTAATTGGAAAATTCAAGGCTAAGTCCCTAAACTGAGCATAATTTGAAATCAAC
CTAAATACTTTCAAAATTCTTCATTTTGGTCCATAAATTTAATTAAATAAATTATATTTTATTTT
TATTCTAAAACTGGGTTGTGACCATTCTCTCCCCCTTAAAATAATTTCATCCTCTAAACAACAA
Found at i:471312 original size:18 final size:17
Alignment explanation
Indices: 471285--471318 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
471275 TCATAAAGGT
471285 ATTTAGGTTATCTTAGA
1 ATTTAGGTTATCTTAGA
*
471302 ATTTGAGGTTATTTTAG
1 ATTT-AGGTTATCTTAG
471319 TAATATAGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.26, C:0.03, G:0.21, T:0.50
Consensus pattern (17 bp):
ATTTAGGTTATCTTAGA
Found at i:473921 original size:17 final size:17
Alignment explanation
Indices: 473895--473928 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
473885 CGTCAAAAAA
473895 CAAAAATTTGAC-TTTT
1 CAAAAATTTGACATTTT
473911 CAAAAATTTTGACATTTT
1 CAAAAA-TTTGACATTTT
473929 TGTAAAAGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 6 0.38
18 4 0.25
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (17 bp):
CAAAAATTTGACATTTT
Found at i:482776 original size:121 final size:121
Alignment explanation
Indices: 482562--482804 Score: 486
Period size: 121 Copynumber: 2.0 Consensus size: 121
482552 GACCTGTGAC
482562 TTCTTCAGGGAATATTTTAGGTGTCATTTTATGGAAGATCATTATCTCGCACAGAGGAGACAGTA
1 TTCTTCAGGGAATATTTTAGGTGTCATTTTATGGAAGATCATTATCTCGCACAGAGGAGACAGTA
482627 GTTTTAGGACTTGGTTTAGGGAGAGATGACTATTTTTGAACATGAGATAGAGTTTT
66 GTTTTAGGACTTGGTTTAGGGAGAGATGACTATTTTTGAACATGAGATAGAGTTTT
482683 TTCTTCAGGGAATATTTTAGGTGTCATTTTATGGAAGATCATTATCTCGCACAGAGGAGACAGTA
1 TTCTTCAGGGAATATTTTAGGTGTCATTTTATGGAAGATCATTATCTCGCACAGAGGAGACAGTA
482748 GTTTTAGGACTTGGTTTAGGGAGAGATGACTATTTTTGAACATGAGATAGAGTTTT
66 GTTTTAGGACTTGGTTTAGGGAGAGATGACTATTTTTGAACATGAGATAGAGTTTT
482804 T
1 T
482805 GAAGTTACAG
Statistics
Matches: 122, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
121 122 1.00
ACGTcount: A:0.28, C:0.10, G:0.26, T:0.37
Consensus pattern (121 bp):
TTCTTCAGGGAATATTTTAGGTGTCATTTTATGGAAGATCATTATCTCGCACAGAGGAGACAGTA
GTTTTAGGACTTGGTTTAGGGAGAGATGACTATTTTTGAACATGAGATAGAGTTTT
Found at i:485421 original size:20 final size:20
Alignment explanation
Indices: 485371--485425 Score: 74
Period size: 22 Copynumber: 2.6 Consensus size: 20
485361 ATATTGGTAG
*
485371 GGGGTATTGATACCATAGTA
1 GGGGTATCGATACCATAGTA
*
485391 GGATAGTATCGATACCATAGTA
1 GG--GGTATCGATACCATAGTA
485413 GGGGTATCGATAC
1 GGGGTATCGATAC
485426 TAAAGGACCA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 12 0.40
22 18 0.60
ACGTcount: A:0.31, C:0.13, G:0.29, T:0.27
Consensus pattern (20 bp):
GGGGTATCGATACCATAGTA
Found at i:485901 original size:45 final size:45
Alignment explanation
Indices: 485837--485985 Score: 201
Period size: 45 Copynumber: 3.3 Consensus size: 45
485827 GTAAAAGAAT
* *
485837 AATGCATATGGGTGTATTATTGTCATGAAAGGATGCCAGAGTTAA
1 AATGCATATGGGTGTATTATTGACATGAAAGGATGCCAGAGTTGA
* *
485882 AATGCATATGAGTGTATTATTGGCATGAAAGGATGCCAGAGTTGA
1 AATGCATATGGGTGTATTATTGACATGAAAGGATGCCAGAGTTGA
* ** * *
485927 AATGCATATGGGTGAATTATCAACA-GAAAAGTATGCTAGAGTTGA
1 AATGCATATGGGTGTATTATTGACATG-AAAGGATGCCAGAGTTGA
485972 AATGCATATGGGTG
1 AATGCATATGGGTG
485986 CGTTATCAAC
Statistics
Matches: 93, Mismatches: 10, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
44 1 0.01
45 92 0.99
ACGTcount: A:0.35, C:0.09, G:0.28, T:0.29
Consensus pattern (45 bp):
AATGCATATGGGTGTATTATTGACATGAAAGGATGCCAGAGTTGA
Found at i:485992 original size:45 final size:45
Alignment explanation
Indices: 485919--486137 Score: 231
Period size: 45 Copynumber: 4.9 Consensus size: 45
485909 AAAGGATGCC
* *
485919 AGAGTTGAAATGCATATGGGTGAATTATCAACAGAAAAGTATGCT
1 AGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACT
* *
485964 AGAGTTGAAATGCATATGGGTGCGTTATCAACAGGAAAGTATACT
1 AGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACT
* * * * * *
486009 AGTGTTGATATGTATATGGGTACATTATCAACATAAAATTATACT
1 AGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACT
** * * ** * *
486054 ATTGTTGTAATGTATATGGGTATATTATCAACATAAAAGTATAAT
1 AGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACT
* * * * *
486099 ATAATTGAAATGCATAGGGGTGCATTGTCAATAGAAAAG
1 AGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAG
486138 ATGTTATAGA
Statistics
Matches: 146, Mismatches: 28, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 146 1.00
ACGTcount: A:0.39, C:0.08, G:0.21, T:0.32
Consensus pattern (45 bp):
AGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACT
Found at i:486002 original size:90 final size:90
Alignment explanation
Indices: 485837--486159 Score: 211
Period size: 90 Copynumber: 3.6 Consensus size: 90
485827 GTAAAAGAAT
* *** * * * * *
485837 AATGCATATGGGTGTATTATTGTCATG-AAAGGATGCCAGAGTTAAAATGCATATGAGTGTATTA
1 AATGCATATGGGTGAATTATCAACA-GAAAAGTATGCTAGAGTTGAAATGCATATGGGTGCATTA
*** * *
485901 TTGGCATGAAAGGATGCCAGAGTTGA
65 TCAACAGGAAAGGATACCAGAGTTGA
*
485927 AATGCATATGGGTGAATTATCAACAGAAAAGTATGCTAGAGTTGAAATGCATATGGGTGCGTTAT
1 AATGCATATGGGTGAATTATCAACAGAAAAGTATGCTAGAGTTGAAATGCATATGGGTGCATTAT
* * *
485992 CAACAGGAAAGTATACTAGTGTTGA
66 CAACAGGAAAGGATACCAGAGTTGA
* * * * * ** * * **
486017 TATGTATATGGGT-ACATTATCAACATAAAATTATACTATTGTTGTAATGTATATGGGTATATTA
1 AATGCATATGGGTGA-ATTATCAACAGAAAAGTATGCTAGAGTTGAAATGCATATGGGTGCATTA
** * ** * *
486081 TCAACATAAAAGTATAATATAATTGA
65 TCAACAGGAAAGGATACCAGAGTTGA
* * * * * * *
486107 AATGCATAGGGGTGCATTGTCAATAGAAAAG-ATGTTATAGATTAAAATGCATA
1 AATGCATATGGGTGAATTATCAACAGAAAAGTATGCTAGAG-TTGAAATGCATA
486160 ATGATGTATT
Statistics
Matches: 179, Mismatches: 50, Indels: 8
0.76 0.21 0.03
Matches are distributed among these distances:
89 8 0.04
90 171 0.96
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.32
Consensus pattern (90 bp):
AATGCATATGGGTGAATTATCAACAGAAAAGTATGCTAGAGTTGAAATGCATATGGGTGCATTAT
CAACAGGAAAGGATACCAGAGTTGA
Found at i:492165 original size:96 final size:95
Alignment explanation
Indices: 491990--492216 Score: 242
Period size: 96 Copynumber: 2.4 Consensus size: 95
491980 TGCCTAATGA
* * * *
491990 AGTGGTATCGATACAATGGTAAGGGTATCTATACCT-GGTAACATCGAACCTAATTTTGGTATCA
1 AGTGGTATCGATACCATAGTAAGGGTATCGATA-CTGGGCAACATCGAACCTAATTTTGGTATCA
* * *
492054 ATATCGTATAAGGGTATCGGTAGCATAGTAT
65 ATATCGTATAAGGGTATCGATACCATAGTAG
* * * **
492085 AGTGGTATCGATACCTATAGTAACGGTATCGATACTGGGCCACATCGAATCTAATTTTGGTATTG
1 AGTGGTATCGATACC-ATAGTAAGGGTATCGATACTGGGCAACATCGAACCTAATTTTGGTATCA
* **
492150 ATACTGGTA-GGGGGTATCGATACCATAGTAG
65 ATA-TCGTATAAGGGTATCGATACCATAGTAG
* * * *
492181 GGTAGTATTGATACCATAGTAGGGGTATCGATACTG
1 AGTGGTATCGATACCATAGTAAGGGTATCGATACTG
492217 AAGGGCCAAA
Statistics
Matches: 109, Mismatches: 20, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
95 35 0.32
96 70 0.64
97 4 0.04
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.31
Consensus pattern (95 bp):
AGTGGTATCGATACCATAGTAAGGGTATCGATACTGGGCAACATCGAACCTAATTTTGGTATCAA
TATCGTATAAGGGTATCGATACCATAGTAG
Found at i:492213 original size:20 final size:20
Alignment explanation
Indices: 492160--492214 Score: 83
Period size: 22 Copynumber: 2.6 Consensus size: 20
492150 ATACTGGTAG
492160 GGGGTATCGATACCATAGTA
1 GGGGTATCGATACCATAGTA
*
492180 GGGTAGTATTGATACCATAGTA
1 GGG--GTATCGATACCATAGTA
492202 GGGGTATCGATAC
1 GGGGTATCGATAC
492215 TGAAGGGCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.39
22 19 0.61
ACGTcount: A:0.29, C:0.13, G:0.31, T:0.27
Consensus pattern (20 bp):
GGGGTATCGATACCATAGTA
Found at i:492753 original size:45 final size:45
Alignment explanation
Indices: 492704--492826 Score: 122
Period size: 45 Copynumber: 2.7 Consensus size: 45
492694 ATAAATGAAT
***
492704 AATGCATATGGGTGCATTATTGGCATG-AAAGGATGCCAGAGTTAA
1 AATGCATATGGGTGCATTATCAACA-GAAAAGGATGCCAGAGTTAA
** * * * *
492749 AATGCATATATGTTCATTATCAACAGAAAAGTATGCTAGAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGGATGCCAGAGTTAA
*
492794 AATGCATATGGGGTTGCATTATCAACAAAAAAG
1 AATGCATAT-GGG-TGCATTATCAACAGAAAAG
492827 TATACTGTTT
Statistics
Matches: 62, Mismatches: 13, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
44 1 0.02
45 43 0.69
46 1 0.02
47 17 0.27
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.28
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATCAACAGAAAAGGATGCCAGAGTTAA
Found at i:492772 original size:79 final size:79
Alignment explanation
Indices: 492616--492779 Score: 224
Period size: 79 Copynumber: 2.1 Consensus size: 79
492606 AAAACGAATG
* * *
492616 TAAAAGAATAATGCATACGGGTGCATTATTGGCATGAAAGGATGCCATATCTGAAATGTATATTG
1 TAAAAGAATAATGCATACGGGTGCATTATTGGCATGAAAGGATGCCAGATCTAAAATGCATATTG
*
492681 GTACATTGTCAACA
66 GTACATTATCAACA
* *
492695 TAAATGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAGAGT-TAAAATGCATATA
1 TAAAAGAATAATGCATACGGGTGCATTATTGGCATGAAAGGATGCCAGA-TCTAAAATGCATAT-
*
492759 T-GTTCATTATCAACA
64 TGGTACATTATCAACA
*
492774 GAAAAG
1 TAAAAG
492780 TATGCTAGAG
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
79 72 0.97
80 2 0.03
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (79 bp):
TAAAAGAATAATGCATACGGGTGCATTATTGGCATGAAAGGATGCCAGATCTAAAATGCATATTG
GTACATTATCAACA
Done.