Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000851.1 Hibiscus syriacus cultivar Beakdansim tig00001644_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: 7304151
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 31
Found at i:4117457 original size:25 final size:25
Alignment explanation
Indices: 4117429--4117482 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
4117419 TTGTCAGTCA
*
4117429 TAATTTAATTTTATGTGATACGGCC
1 TAATTTAATTTTATGTGATAAGGCC
4117454 TAATTTAATTTTATGTGATAAGGCC
1 TAATTTAATTTTATGTGATAAGGCC
4117479 -AATT
1 TAATT
4117483 GTTAGATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 4 0.14
25 24 0.86
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.44
Consensus pattern (25 bp):
TAATTTAATTTTATGTGATAAGGCC
Found at i:4122027 original size:2 final size:2
Alignment explanation
Indices: 4122022--4122104 Score: 159
Period size: 2 Copynumber: 42.0 Consensus size: 2
4122012 CACACACAGG
4122022 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
4122064 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4122105 GTTTAACCAA
Statistics
Matches: 80, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 79 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:4124150 original size:16 final size:17
Alignment explanation
Indices: 4124120--4124152 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
4124110 AGTTTTTAAC
4124120 TGAGAAATTTAAAGATT
1 TGAGAAATTTAAAGATT
*
4124137 TGAG-AATTTGAAGATT
1 TGAGAAATTTAAAGATT
4124153 GTTTCTTATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.36
Consensus pattern (17 bp):
TGAGAAATTTAAAGATT
Found at i:4125723 original size:25 final size:25
Alignment explanation
Indices: 4125695--4125744 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
4125685 TTGTCAGTCA
4125695 TAATTTAATTTTATGTGATAAGGCC
1 TAATTTAATTTTATGTGATAAGGCC
4125720 TAATTTAATTTTATGTGATAAGGCC
1 TAATTTAATTTTATGTGATAAGGCC
4125745 AAATGTTAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (25 bp):
TAATTTAATTTTATGTGATAAGGCC
Found at i:4130604 original size:77 final size:77
Alignment explanation
Indices: 4130514--4130669 Score: 303
Period size: 77 Copynumber: 2.0 Consensus size: 77
4130504 TGACTTGTTC
*
4130514 TAGCCTAGAAGAGAGACTTAAGCACCTTAAGTTTAGGATTCCAACAATTTTCACTTCAACGAGAC
1 TAGCCTAGAAGAGAGACTTAAGCACCTAAAGTTTAGGATTCCAACAATTTTCACTTCAACGAGAC
4130579 CCACAAAACAGG
66 CCACAAAACAGG
4130591 TAGCCTAGAAGAGAGACTTAAGCACCTAAAGTTTAGGATTCCAACAATTTTCACTTCAACGAGAC
1 TAGCCTAGAAGAGAGACTTAAGCACCTAAAGTTTAGGATTCCAACAATTTTCACTTCAACGAGAC
4130656 CCACAAAACAGG
66 CCACAAAACAGG
4130668 TA
1 TA
4130670 AAATTTTATT
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 78 1.00
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.22
Consensus pattern (77 bp):
TAGCCTAGAAGAGAGACTTAAGCACCTAAAGTTTAGGATTCCAACAATTTTCACTTCAACGAGAC
CCACAAAACAGG
Found at i:4132408 original size:32 final size:32
Alignment explanation
Indices: 4132372--4132439 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 32
4132362 ATTCCATAGT
4132372 TTTTCAATGGAT-AACAAGAACCAATCCCTAGC
1 TTTTCAAT-GATAAACAAGAACCAATCCCTAGC
* * *
4132404 TTTTCAATGCTAAACTAGAACCAATCTCTAGC
1 TTTTCAATGATAAACAAGAACCAATCCCTAGC
4132436 TTTT
1 TTTT
4132440 AACAGGCTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
31 2 0.06
32 30 0.94
ACGTcount: A:0.34, C:0.24, G:0.10, T:0.32
Consensus pattern (32 bp):
TTTTCAATGATAAACAAGAACCAATCCCTAGC
Found at i:4132460 original size:33 final size:32
Alignment explanation
Indices: 4132388--4132460 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 32
4132378 ATGGATAACA
* *
4132388 AGAACCAATCCCTAGCTTTTCAATGCTAAACT
1 AGAACCAATCCCTAGCTTTTAAAGGCTAAACT
* * *
4132420 AGAACCAATCTCTAGCTTTTAACAGGCTCAGCT
1 AGAACCAATCCCTAGCTTTTAA-AGGCTAAACT
4132453 AGAACCAA
1 AGAACCAA
4132461 AACCCCTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
32 20 0.57
33 15 0.43
ACGTcount: A:0.36, C:0.27, G:0.12, T:0.25
Consensus pattern (32 bp):
AGAACCAATCCCTAGCTTTTAAAGGCTAAACT
Found at i:4136139 original size:19 final size:20
Alignment explanation
Indices: 4136095--4136144 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
4136085 TACTGTTCAT
* * *
4136095 TACTGTTCACACAATATCAG
1 TACTATTCATACAATATCAA
4136115 TACTATTCATACAATA-CAA
1 TACTATTCATACAATATCAA
4136134 TACTATTCATA
1 TACTATTCATA
4136145 AAAACATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.40, C:0.22, G:0.04, T:0.34
Consensus pattern (20 bp):
TACTATTCATACAATATCAA
Found at i:4137406 original size:14 final size:14
Alignment explanation
Indices: 4137383--4137412 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4137373 TAAATATCCG
*
4137383 AAAAAGAAAAAGGA
1 AAAAACAAAAAGGA
4137397 AAAAACAAAAAGGA
1 AAAAACAAAAAGGA
4137411 AA
1 AA
4137413 GTAAAAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAAACAAAAAGGA
Found at i:4151920 original size:75 final size:74
Alignment explanation
Indices: 4151774--4152413 Score: 729
Period size: 74 Copynumber: 8.8 Consensus size: 74
4151764 TTAATACGAG
* *
4151774 GATTTATCTCACTTGAGA-T-TTTTT-TTAAAACAAGATTCATCTCGTTTGAGATAGTTTCACTC
1 GATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGATTTATCTCGCTTGAGATAGTTTCACTC
4151836 GAAACAGAA
66 GAAACAGAA
* *
4151845 GATTTATCTCACTTGAGATTGTTTTTATTAAAACAAGATTTTATCTAGCTTGAGATAGTTTCACT
1 GATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGA-TTTATCTCGCTTGAGATAGTTTCACT
*
4151910 TGAAACAGAA
65 CGAAACAGAA
* * *
4151920 GATTTATCTCACTTAAGATTGTTTTTTCGTAAAACAA-ATTTTATCTCGCTTGAGATAGTTTCGC
1 GATTTATCTCACTTGAGATTG-TTTTTCTTAAAACAAGA-TTTATCTCGCTTGAGATAGTTTCAC
*
4151984 TCGAAACAAAA
64 TCGAAACAGAA
* *
4151995 TATTTATCTCACTTGAGATTAG-TTTTCTTAAAACAA-ATTTTATCTCGCTTGAGATAGTGTCAC
1 GATTTATCTCACTTGAGATT-GTTTTTCTTAAAACAAGA-TTTATCTCGCTTGAGATAGTTTCAC
4152058 TCGAAAC-GAAA
64 TCGAAACAG-AA
* * *
4152069 GATTTATCTCACTTGATATTGTTTTTCTTAAAACAAGA-TTATCTAGCTTGAGATAGTTTAACTC
1 GATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGATTTATCTCGCTTGAGATAGTTTCACTC
* *
4152133 AAAAACATAA
66 -GAAACAGAA
*
4152143 -ATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGATTTATCTCGCTTGAGACAGTTTTCAC
1 GA-TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGATTTATCTCGCTTGAGATAG-TTTCAC
*
4152207 TCGAAACA-TA
64 TCGAAACAGAA
*
4152217 -ATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGATTCATCTCGCTTGAGATAGTTTTCACT
1 GATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGATTTATCTCGCTTGAGATAG-TTTCACT
*
4152281 C-AAATAGAA
65 CGAAACAGAA
* * * *
4152290 -ATTT-TCTCACTTGA-TTTGTTTTTC-T-AAACAA-A-CT-TCTCGCTTGAGACAGTTTTTACT
1 GATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGATTTATCTCGCTTGAGATAG-TTTCACT
4152347 CGAAACA-AA
65 CGAAACAGAA
* * * *
4152356 -ATTTTATTTCAC-TAAGATTATTTTTCTT--AACAA-ATTTCATCTCGCTTGAGAAAGTTTC
1 GA-TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGATTT-ATCTCGCTTGAGATAGTTTC
4152414 CCTTGAAATA
Statistics
Matches: 499, Mismatches: 47, Indels: 47
0.84 0.08 0.08
Matches are distributed among these distances:
66 25 0.05
67 9 0.02
68 20 0.04
69 8 0.02
70 4 0.01
71 41 0.08
72 15 0.03
73 97 0.19
74 133 0.27
75 126 0.25
76 21 0.04
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (74 bp):
GATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGATTTATCTCGCTTGAGATAGTTTCACTC
GAAACAGAA
Found at i:4151974 original size:112 final size:108
Alignment explanation
Indices: 4151846--4152314 Score: 332
Period size: 112 Copynumber: 4.2 Consensus size: 108
4151836 GAAACAGAAG
*
4151846 ATTTATCTCACTTGAGATTGTTTTTATTAAAACAAGATTTTATCTAGCTTGAGATAGTTTCACTT
1 ATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGATTTTATCTAGCTTGAGATAGTTT-ACTT
* *
4151911 GAAACAGAAGATTTATCTCACTTAAGATTGTTTTTTCGTAAAACAA
65 AAAACA-AA-ATTTATCTCACTTGAGATTGTTTTTTCGTAAAACAA
* * ** ** * *
4151957 ATTTTATCTCGCTTGAGATAGTTTCGCTCGAAACAAAATATTTATCTCA-CTTGAGATTAGTTTT
1 A-TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGAT-TTTATCT-AGCTTGAGA-TAGTTTA
* * * ***
4152021 CTTAAAACAAATTTTATCTCGCTTGAGATAGTGTCACTCG--AAACGAAA
62 CTTAAAACAAAATTTATCTCACTTGAGATTGT-TTTTTCGTAAAAC--AA
*
4152069 GATTTATCTCACTTGATATTGTTTTTCTTAAAACAAGA--TTATCTAGCTTGAGATAGTTTAACT
1 -ATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGATTTTATCTAGCTTGAGATAGTTT-ACT
* *
4152132 CAAAAACATAAATTTTATCTCACTTGAGATTG-TTTTTCTTAAAACAA
64 -TAAAACA-AAA-TTTATCTCACTTGAGATTGTTTTTTCGTAAAACAA
* ** * ** *
4152179 GATTTATCTCGCTTGAGACAGTTTTCACTCGAAACATA-A-TTTATCTCA-CTTGAGATTGTTTT
1 -ATTTATCTCACTTGAGATTGTTTT-TCTTAAAACA-AGATTTTATCT-AGCTTGAGATAG-TTT
* * * * * ** *
4152241 TCTTAAAACAAGATTCATCTCGCTTGAGATAGTTTTCAC-TCAAATAGAA
61 ACTTAAAACAAAATTTATCTCACTTGAGATTGTTTTTTCGT-AAA-ACAA
*
4152290 ATTT-TCTCACTTGA-TTTGTTTTTCT
1 ATTTATCTCACTTGAGATTGTTTTTCT
4152315 AAACAAACTT
Statistics
Matches: 279, Mismatches: 56, Indels: 50
0.72 0.15 0.13
Matches are distributed among these distances:
107 2 0.01
108 12 0.04
109 41 0.15
110 49 0.18
111 37 0.13
112 104 0.37
113 27 0.10
114 7 0.03
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (108 bp):
ATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGATTTTATCTAGCTTGAGATAGTTTACTTA
AAACAAAATTTATCTCACTTGAGATTGTTTTTTCGTAAAACAA
Found at i:4152878 original size:91 final size:91
Alignment explanation
Indices: 4152716--4152952 Score: 262
Period size: 91 Copynumber: 2.6 Consensus size: 91
4152706 CTTCGCTCTT
* ** * * *
4152716 TTCACGACATTTAGAATTAGTGTCGCCTCACAT-GAGGGACTAAAATTTCCAATAGAGAATTCAT
1 TTCACG-CATTTTGAATTAGTAACGCCTCAC-TCGAGGGACCAAAATTTCTAGTAGAGAATTCAT
*
4152780 CAGAAGAACTTGTTCAACCATAGCTCAA
64 CAGAAGAACTTATTCAACCATAGCTCAA
* *
4152808 TTCACGCATTTTGAATTAGCAACGCCTCACTCGAGGGACCAAAATTTCTAGTAGAGAATTCATGA
1 TTCACGCATTTTGAATTAGTAACGCCTCACTCGAGGGACCAAAATTTCTAGTAGAGAATTCATCA
* * *
4152873 GAAGAACTTATTCAACCTTGGCTCGA
66 GAAGAACTTATTCAACCATAGCTCAA
* * * * * *
4152899 TTCATG-ATATTTCAAATCAGTAATGCCTCATTCGAGGGACCAATATTTCTAGTA
1 TTCACGCAT-TTT-GAATTAGTAACGCCTCACTCGAGGGACCAAAATTTCTAGTA
4152953 AAAAGATCAT
Statistics
Matches: 123, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
90 3 0.02
91 79 0.64
92 41 0.33
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (91 bp):
TTCACGCATTTTGAATTAGTAACGCCTCACTCGAGGGACCAAAATTTCTAGTAGAGAATTCATCA
GAAGAACTTATTCAACCATAGCTCAA
Found at i:4154319 original size:20 final size:21
Alignment explanation
Indices: 4154294--4154348 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
4154284 TAATTATTTT
4154294 TTTATTTT-ATTTAG-TCACTG
1 TTTATTTTAATTTAGCT-ACTG
*
4154314 TTTATTTCTGATTTAGCTACTG
1 TTTATTT-TAATTTAGCTACTG
4154336 -TTATTTTAATTTA
1 TTTATTTTAATTTA
4154349 TGCAATTTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
20 13 0.42
21 7 0.23
22 10 0.32
23 1 0.03
ACGTcount: A:0.22, C:0.09, G:0.09, T:0.60
Consensus pattern (21 bp):
TTTATTTTAATTTAGCTACTG
Found at i:4172044 original size:38 final size:38
Alignment explanation
Indices: 4172002--4172709 Score: 521
Period size: 38 Copynumber: 19.0 Consensus size: 38
4171992 CAATCCGATC
* ** *
4172002 TTATTCTCGACTCCCTCACGAAGAGGAGTCACTCTTTG
1 TTATTCTCGACTTCCTCGTGAAGAGGAGTCAATCTTTG
* * * * *
4172040 TTATTATTGACTTCCTCATGAAGAGAAATCAATCTTTG
1 TTATTCTCGACTTCCTCGTGAAGAGGAGTCAATCTTTG
* * *
4172078 TTATTC-CTGACTTCCTCGCGAAGATGATTCAATCTTTG
1 TTATTCTC-GACTTCCTCGTGAAGAGGAGTCAATCTTTG
* * * *
4172116 TTATTCTTGACTTCCTCGTGAACAGAAGTCAATCTTTA
1 TTATTCTCGACTTCCTCGTGAAGAGGAGTCAATCTTTG
* * * *
4172154 TTATTC-CTTACTCCCTCGAGAAGAGGAGTCAATCTTTT
1 TTATTCTC-GACTTCCTCGTGAAGAGGAGTCAATCTTTG
* * * * * *
4172192 TTATTCTTGACTTCTTCGTAAAGAGAAGTCAATTTTTA
1 TTATTCTCGACTTCCTCGTGAAGAGGAGTCAATCTTTG
* * *
4172230 TTATTAC-CTACTCCCTCGTGAAGAGGAGTCAGTCTTTG
1 TTATT-CTCGACTTCCTCGTGAAGAGGAGTCAATCTTTG
* * * *
4172268 TTATCCTTGACTTCCTCGTG-AGAGAATTCAATCTTTG
1 TTATTCTCGACTTCCTCGTGAAGAGGAGTCAATCTTTG
**
4172305 TTATTC-CTGAC-TCCTCACGAAGAGGAGTCAATCTTAT-
1 TTATTCTC-GACTTCCTCGTGAAGAGGAGTCAATCTT-TG
* * * * * *
4172342 TTATTGTTGACTTCATCATGAAGAGAAGTAAATC-TTG
1 TTATTCTCGACTTCCTCGTGAAGAGGAGTCAATCTTTG
* * *
4172379 TTATTC-CTGACTCCCTCGCG-AGTTA-GAGTC-ATTTTTG
1 TTATTCTC-GACTTCCTCGTGAAG--AGGAGTCAATCTTTG
* * * *
4172416 TTATCCTTGACTTCCTTGTGAAGAGAAGTCAATCTTTG
1 TTATTCTCGACTTCCTCGTGAAGAGGAGTCAATCTTTG
* * **
4172454 TTATTC-CTGACTCCCTTGCAAAGAGGAGTCAATCTTTG
1 TTATTCTC-GACTTCCTCGTGAAGAGGAGTCAATCTTTG
* *
4172492 TTATTCTCGAC-TCCTCGTGAAGAGAAATCAATC--T-
1 TTATTCTCGACTTCCTCGTGAAGAGGAGTCAATCTTTG
* * *
4172526 TTATTAT-GAC-TCCTCGCGAAGAGGAGTCAATCTTTA
1 TTATTCTCGACTTCCTCGTGAAGAGGAGTCAATCTTTG
* * *
4172562 TTATT-T--ACTTCCTCGTGAAGAGAATTCAATCTCTG
1 TTATTCTCGACTTCCTCGTGAAGAGGAGTCAATCTTTG
* * * *
4172597 TTATTCTTGACTCCCTCGCT-AAGATGTGTCAATCTTTG
1 TTATTCTCGACTTCCTCG-TGAAGAGGAGTCAATCTTTG
* *
4172635 TTATTCTTGACTTCCACGTGAAGAGGAGTCAATCTTTG
1 TTATTCTCGACTTCCTCGTGAAGAGGAGTCAATCTTTG
* *
4172673 TTATTTTTGACTTCCTCGTGCGAAGA--AGTCAATCTTT
1 TTATTCTCGACTTCCTCGT--GAAGAGGAGTCAATCTTT
4172710 TAGTTTTGTC
Statistics
Matches: 523, Mismatches: 114, Indels: 66
0.74 0.16 0.09
Matches are distributed among these distances:
33 22 0.04
34 8 0.02
35 29 0.06
36 18 0.03
37 99 0.19
38 339 0.65
39 3 0.01
40 5 0.01
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (38 bp):
TTATTCTCGACTTCCTCGTGAAGAGGAGTCAATCTTTG
Found at i:4172100 original size:76 final size:76
Alignment explanation
Indices: 4172002--4172709 Score: 799
Period size: 76 Copynumber: 9.5 Consensus size: 76
4171992 CAATCCGATC
* * * *
4172002 TTATT-CTCGACTCCCTCACGAAGAGGAGTCACTCTTTGTTATTATTGACTTCCTCATGAAGAGA
1 TTATTCCT-GACTCCCTCGCGAAGAGGAGTCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGA
*
4172066 AATCAATCTTTG
65 AGTCAATCTTTG
* * * *
4172078 TTATTCCTGACTTCCTCGCGAAGATGATTCAATCTTTGTTATTCTTGACTTCCTCGTGAACAGAA
1 TTATTCCTGACTCCCTCGCGAAGAGGAGTCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAA
*
4172143 GTCAATCTTTA
66 GTCAATCTTTG
* * * * *
4172154 TTATTCCTTACTCCCTCGAGAAGAGGAGTCAATCTTTTTTATTCTTGACTTCTTCGTAAAGAGAA
1 TTATTCCTGACTCCCTCGCGAAGAGGAGTCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAA
* *
4172219 GTCAATTTTTA
66 GTCAATCTTTG
* * *
4172230 TTATTACCT-ACTCCCTCGTGAAGAGGAGTCAGTCTTTGTTATCCTTGACTTCCTCGTG-AGAGA
1 TTATT-CCTGACTCCCTCGCGAAGAGGAGTCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGA
*
4172293 ATTCAATCTTTG
65 AGTCAATCTTTG
* * * *
4172305 TTATTCCTGACT-CCTCACGAAGAGGAGTCAATCTTAT-TTATTGTTGACTTCATCATGAAGAGA
1 TTATTCCTGACTCCCTCGCGAAGAGGAGTCAATCTT-TGTTATTCTTGACTTCCTCGTGAAGAGA
*
4172368 AGTAAATC-TTG
65 AGTCAATCTTTG
* * *
4172379 TTATTCCTGACTCCCTCGCG-AGTTA-GAGTC-ATTTTTGTTATCCTTGACTTCCTTGTGAAGAG
1 TTATTCCTGACTCCCTCGCGAAG--AGGAGTCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAG
4172441 AAGTCAATCTTTG
64 AAGTCAATCTTTG
* * *
4172454 TTATTCCTGACTCCCTTGCAAAGAGGAGTCAATCTTTGTTATTCTCGAC-TCCTCGTGAAGAGAA
1 TTATTCCTGACTCCCTCGCGAAGAGGAGTCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAA
*
4172518 ATCAATC--T-
66 GTCAATCTTTG
* *
4172526 TTATT-ATGACT-CCTCGCGAAGAGGAGTCAATCTTTATTA-T-TT-ACTTCCTCGTGAAGAGAA
1 TTATTCCTGACTCCCTCGCGAAGAGGAGTCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAA
* *
4172586 TTCAATCTCTG
66 GTCAATCTTTG
* * * * * *
4172597 TTATTCTTGACTCCCTCGCTAAGATGTGTCAATCTTTGTTATTCTTGACTTCCACGTGAAGAGGA
1 TTATTCCTGACTCCCTCGCGAAGAGGAGTCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAA
4172662 GTCAATCTTTG
66 GTCAATCTTTG
** *
4172673 TTATTTTTGACTTCCTCGTGCGAAGA--AGTCAATCTTT
1 TTATTCCTGACTCCCTC--GCGAAGAGGAGTCAATCTTT
4172710 TAGTTTTGTC
Statistics
Matches: 536, Mismatches: 72, Indels: 48
0.82 0.11 0.07
Matches are distributed among these distances:
67 2 0.00
68 22 0.04
69 1 0.00
70 26 0.05
71 10 0.02
72 10 0.02
73 26 0.05
74 90 0.17
75 93 0.17
76 245 0.46
77 5 0.01
78 6 0.01
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (76 bp):
TTATTCCTGACTCCCTCGCGAAGAGGAGTCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAA
GTCAATCTTTG
Found at i:4172806 original size:45 final size:44
Alignment explanation
Indices: 4172757--4172899 Score: 164
Period size: 45 Copynumber: 3.2 Consensus size: 44
4172747 AAATCGTTCG
*
4172757 GTGTTTTCTTCCTAGACTTTCTCATGAAGAGGAGTCAATATTTTA
1 GTGTTTTCTTCCTTGACTTTCTC-TGAAGAGGAGTCAATATTTTA
* *
4172802 GTGTTGTCTTCCTTGACTTTCTCGTGAAGAAGAGTCAATATTTTA
1 GTGTTTTCTTCCTTGACTTTCTC-TGAAGAGGAGTCAATATTTTA
* * * *
4172847 GTGTTGTCCTT-CTTGATTTTCTCTCAAAGAGGAGTCAATCTTTT-
1 GTGTT-TTCTTCCTTGACTTTCTCT-GAAGAGGAGTCAATATTTTA
4172891 GTTGTTTTC
1 G-TGTTTTC
4172900 CTTTTCGACT
Statistics
Matches: 84, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
44 4 0.05
45 77 0.92
46 3 0.04
ACGTcount: A:0.20, C:0.16, G:0.19, T:0.45
Consensus pattern (44 bp):
GTGTTTTCTTCCTTGACTTTCTCTGAAGAGGAGTCAATATTTTA
Found at i:4173839 original size:45 final size:44
Alignment explanation
Indices: 4173784--4174213 Score: 508
Period size: 45 Copynumber: 9.7 Consensus size: 44
4173774 TTCATTAAAA
* ** * *
4173784 CATCCATTCATGCTTATAATGCACCTTATGCATTTTCAATTATAG
1 CATCCTTTCATGCCAATAATGCACCATATGCA-TTTCAATTATGG
* * * *
4173829 CATCCTTTCATGCTAATAATCCACCCATATGTATTTCAATTGTGG
1 CATCCTTTCATGCCAATAATGCA-CCATATGCATTTCAATTATGG
* * * * * * * *
4173874 CATCATTTCTTGTCACTAATGCACCCACATACATTTTAATTATTG
1 CATCCTTTCATGCCAATAATGCA-CCATATGCATTTCAATTATGG
*
4173919 CATCCTTTCATGCCAATAATGCACCTATATGCATTTCAACTATGG
1 CATCCTTTCATGCCAATAATGCACC-ATATGCATTTCAATTATGG
* * * * *
4173964 CAT-CATT--TGTCAATAATGAACCCTATGCATTTCAATTATAG
1 CATCCTTTCATGCCAATAATGCACCATATGCATTTCAATTATGG
* * *
4174005 CATCCTTTCATGCCAATAATTCACCCATATTCATTTTAATTATGG
1 CATCCTTTCATGCCAATAATGCA-CCATATGCATTTCAATTATGG
*
4174050 CATCATTTCATG-CAATAATGCACCATATGCATTTCAATTATGG
1 CATCCTTTCATGCCAATAATGCACCATATGCATTTCAATTATGG
4174093 CATCCTTTCATGCCAATAATGCACCTATATGCATTTCAATTATGG
1 CATCCTTTCATGCCAATAATGCACC-ATATGCATTTCAATTATGG
*
4174138 CATCTTTTCATGCCAATAATGCACCCATATGCATTTCAATTATGG
1 CATCCTTTCATGCCAATAATGCA-CCATATGCATTTCAATTATGG
4174183 CATCCTTTCATGCCAATAATGCACCCATATG
1 CATCCTTTCATGCCAATAATGCA-CCATATG
4174214 TATATTTAAT
Statistics
Matches: 327, Mismatches: 49, Indels: 18
0.83 0.12 0.05
Matches are distributed among these distances:
41 19 0.06
42 16 0.05
43 30 0.09
44 36 0.11
45 217 0.66
46 9 0.03
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.37
Consensus pattern (44 bp):
CATCCTTTCATGCCAATAATGCACCATATGCATTTCAATTATGG
Found at i:4174060 original size:22 final size:22
Alignment explanation
Indices: 4174034--4174193 Score: 85
Period size: 22 Copynumber: 7.2 Consensus size: 22
4174024 TTCACCCATA
*
4174034 TTCATTTTAATTATGGCATCAT
1 TTCATTTCAATTATGGCATCAT
* * *
4174056 TTCA-TGCAATAAT-GCACCAT
1 TTCATTTCAATTATGGCATCAT
* *
4174076 ATGCATTTCAATTATGGCATCCT
1 -TTCATTTCAATTATGGCATCAT
** * *
4174099 TTCATGCCAATAAT-GCACCTAT
1 TTCATTTCAATTATGGCATC-AT
* *
4174121 ATGCATTTCAATTATGGCATCTT
1 -TTCATTTCAATTATGGCATCAT
** * *
4174144 TTCATGCCAATAAT-GCACCCAT
1 TTCATTTCAATTATGGCA-TCAT
* *
4174166 ATGCATTTCAATTATGGCATCCT
1 -TTCATTTCAATTATGGCATCAT
4174189 TTCAT
1 TTCAT
4174194 GCCAATAATG
Statistics
Matches: 95, Mismatches: 34, Indels: 18
0.65 0.23 0.12
Matches are distributed among these distances:
20 6 0.06
21 16 0.17
22 38 0.40
23 28 0.29
24 7 0.07
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.38
Consensus pattern (22 bp):
TTCATTTCAATTATGGCATCAT
Found at i:4178736 original size:22 final size:23
Alignment explanation
Indices: 4178686--4178739 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
4178676 TTTGGTAAAA
4178686 ATATTTAAA-TAATAATAAAAGC
1 ATATTTAAAGTAATAATAAAAGC
4178708 A-ATTTAAAGTAA-AATAAAGAG-
1 ATATTTAAAGTAATAATAAA-AGC
4178729 ATATTTAAAGT
1 ATATTTAAAGT
4178740 TGAAAAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
21 14 0.48
22 15 0.52
ACGTcount: A:0.57, C:0.02, G:0.09, T:0.31
Consensus pattern (23 bp):
ATATTTAAAGTAATAATAAAAGC
Found at i:4184774 original size:21 final size:21
Alignment explanation
Indices: 4184745--4184789 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
4184735 GATTTTGGTA
*
4184745 AAAATATATTTAAA-TAATAAT
1 AAAAGATATTTAAAGTAA-AAT
4184766 AAAAGATATTTAAAGTAAAAT
1 AAAAGATATTTAAAGTAAAAT
4184787 AAA
1 AAA
4184790 GAAAAGATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.31
Consensus pattern (21 bp):
AAAAGATATTTAAAGTAAAAT
Found at i:4186977 original size:20 final size:19
Alignment explanation
Indices: 4186944--4186985 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
4186934 AAGTTCTCTC
4186944 TTTTCTTTTCATTTCAAGT
1 TTTTCTTTTCATTTCAAGT
* *
4186963 TTTTCGTTTTTATTTTAAGT
1 TTTTC-TTTTCATTTCAAGT
4186983 TTT
1 TTT
4186986 ATTTTTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.14, C:0.10, G:0.07, T:0.69
Consensus pattern (19 bp):
TTTTCTTTTCATTTCAAGT
Found at i:4200880 original size:18 final size:18
Alignment explanation
Indices: 4200857--4200892 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
4200847 ACTATTGCTA
4200857 AAAGTTCTTTTTCAGTGG
1 AAAGTTCTTTTTCAGTGG
4200875 AAAGTTCTTTTTCAGTGG
1 AAAGTTCTTTTTCAGTGG
4200893 TAGTATAGTT
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:0.22, C:0.11, G:0.22, T:0.44
Consensus pattern (18 bp):
AAAGTTCTTTTTCAGTGG
Found at i:4208755 original size:18 final size:19
Alignment explanation
Indices: 4208706--4208756 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
4208696 TCAACTTTAC
* *
4208706 ATTATTTATTCTCTTTATT
1 ATTATTTAATCACTTTATT
*
4208725 TTTACTTTAAATCACTTT-TT
1 ATTA-TTT-AATCACTTTATT
4208745 ATTATTTAATCA
1 ATTATTTAATCA
4208757 TATTTTACCA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
18 5 0.19
19 6 0.23
20 8 0.31
21 7 0.27
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTATTTAATCACTTTATT
Found at i:4209592 original size:15 final size:15
Alignment explanation
Indices: 4209560--4209615 Score: 51
Period size: 15 Copynumber: 3.8 Consensus size: 15
4209550 CGGTAAACAT
4209560 CTCCAATAACAGCAA
1 CTCCAATAACAGCAA
* * *
4209575 CTCCATTAATAGCGA
1 CTCCAATAACAGCAA
* *
4209590 CTCCAA-AACAACGA
1 CTCCAATAACAGCAA
*
4209604 CTCTAATAACAG
1 CTCCAATAACAG
4209616 GGGCTCCAAT
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
14 11 0.34
15 21 0.66
ACGTcount: A:0.43, C:0.30, G:0.09, T:0.18
Consensus pattern (15 bp):
CTCCAATAACAGCAA
Found at i:4209725 original size:52 final size:51
Alignment explanation
Indices: 4209619--4209728 Score: 132
Period size: 52 Copynumber: 2.1 Consensus size: 51
4209609 ATAACAGGGG
* * *
4209619 CTCCAATAATAAAATACAATCCCCTAAACTCGGATATTCCAATAACATCAA
1 CTCCAATAATAAAATACAATCCCCTAAACCCAGATACTCCAATAACATCAA
* * * *
4209670 CTCCAATAATAAAAATATAATCCCTTAATCCCCAGATACTCCATTAACATC-A
1 CTCCAATAAT-AAAATACAATCCCCTAA-ACCCAGATACTCCAATAACATCAA
4209722 CTCCAAT
1 CTCCAAT
4209729 CCCCAAACCC
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
51 10 0.20
52 23 0.46
53 17 0.34
ACGTcount: A:0.43, C:0.29, G:0.03, T:0.25
Consensus pattern (51 bp):
CTCCAATAATAAAATACAATCCCCTAAACCCAGATACTCCAATAACATCAA
Found at i:4210458 original size:2 final size:2
Alignment explanation
Indices: 4210410--4210447 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
4210400 TTGATTTTCT
4210410 TA TA TA TA TA 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 TA TA TA TA TA
4210448 AACAAATATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4215584 original size:19 final size:18
Alignment explanation
Indices: 4215556--4215595 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
4215546 GTCTGAAATG
*
4215556 TTTAAAAGTATCGATACT
1 TTTAAAAGTATCGAAACT
4215574 TTTAGAAAGTATCGAAACT
1 TTTA-AAAGTATCGAAACT
4215593 TTT
1 TTT
4215596 GTAGGAGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (18 bp):
TTTAAAAGTATCGAAACT
Found at i:4218231 original size:50 final size:50
Alignment explanation
Indices: 4218156--4218255 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
4218146 GTTTATTTGA
4218156 GCAATTATTCAGATTCTGAAAGATAAGTTGAAATGTCATATTATAAGGTT
1 GCAATTATTCAGATTCTGAAAGATAAGTTGAAATGTCATATTATAAGGTT
4218206 GCAATTATTCAGATTCTGAAAGATAAGTTGAAATGTCATATTATAAGGTT
1 GCAATTATTCAGATTCTGAAAGATAAGTTGAAATGTCATATTATAAGGTT
4218256 CCGATATGAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.36
Consensus pattern (50 bp):
GCAATTATTCAGATTCTGAAAGATAAGTTGAAATGTCATATTATAAGGTT
Found at i:4219328 original size:90 final size:90
Alignment explanation
Indices: 4219175--4219352 Score: 313
Period size: 90 Copynumber: 2.0 Consensus size: 90
4219165 CCTAACACAC
*
4219175 CCTTTTATAGTCAAGTTACCCTAATCATATTAGGGTTTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGTCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
*
4219240 ATTTAATTAATTGAAATTTAATAAT
66 ATTTAATTAATTGAAATTAAATAAT
*
4219265 CCTTTTATA-TCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTATTTAAATCTA
1 CCTTTTATAGT-CAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTA
4219329 TATTTAATTAATTGAAATTAAATA
65 TATTTAATTAATTGAAATTAAATA
4219353 CTCATAATTA
Statistics
Matches: 84, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
89 1 0.01
90 83 0.99
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (90 bp):
CCTTTTATAGTCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGAAATTAAATAAT
Found at i:4223786 original size:533 final size:533
Alignment explanation
Indices: 4222780--4223848 Score: 1976
Period size: 533 Copynumber: 2.0 Consensus size: 533
4222770 ATTCATTGGT
*
4222780 CCACATAGATCATTATGTATTAACCCCAATAAATCACTTGCTCGCTCACCTTTACTATTAAAAGG
1 CCACATACATCATTATGTATTAACCCCAATAAATCACTTGCTCGCTCACCTTTACTATTAAAAGG
* *
4222845 AGCTTTAGTCATTTTTCCCAACAAGCAAGATTCAGATACATCATATTGTTCGAAAACAAATGAAT
66 AGCTTTAGTCATTTTTCCCAACAAGAAAGATTCACATACATCATATTGTTCGAAAACAAATGAAT
*
4222910 CTAAGAATCCATCTTTATGGAGTTTTTATATACGTCTCACTTATATGGCCTAAACGACAATGCCA
131 CTAAGAATCCATCTTTATGGAGTTTTGATATACGTCTCACTTATATGGCCTAAACGACAATGCCA
4222975 AAGATAAGTTTGATTCGAGTCATTTGTTTTTTATCTCTTAGTATTTATGTTATAAATGGTGTTTT
196 AAGATAAGTTTGATTCGAGTCATTTGTTTTTTATCTCTTAGTATTTATGTTATAAATGGTGTTTT
* *
4223040 CTTGATCCAAAATCTAAAGACCATTAACCAATTATGTCGAACCATAAAAAACACTATCGAGATAA
261 CTTGATCCAAAATATAAAGACCATTAACCAATTATGCCGAACCATAAAAAACACTATCGAGATAA
* *
4223105 AAAGAACAATAATTATTCTTAATAATAATCTCAAAACCAATCTTGTCCAAACAAGAAATAGAAAT
326 AAAGAACAACAATTATTCTTAATAATAATCTCAAAACAAATCTTGTCCAAACAAGAAATAGAAAT
4223170 AATGTTCTTAGTCAAACTAGGCACATAATAACAATCCTCTAAATTTAAATCAAGTCCACTAGGAA
391 AATGTTCTTAGTCAAACTAGGCACATAATAACAATCCTCTAAATTTAAATCAAGTCCACTAGGAA
*
4223235 AAGATAAAACATATGTCCCTATAGCTAATGCATCAACTCTTGCTCGATTTCCCACTCGTAGGTCC
456 AAGATAAAACATATGTCCCTATAACTAATGCATCAACTCTTGCTCGATTTCCCACTCGTAGGTCC
4223300 ACGCCTCCTTTAG
521 ACGCCTCCTTTAG
4223313 CCACATACATCATTATGTATTAACCCCAATAAATCACTTGCTCGCTCACCTTTACTATTAAAAGG
1 CCACATACATCATTATGTATTAACCCCAATAAATCACTTGCTCGCTCACCTTTACTATTAAAAGG
4223378 AGCTTTAGTCATTTTTCCCAACAAGAAAGATTCACATACATCATATTGTTCGAAAACAAATGAAT
66 AGCTTTAGTCATTTTTCCCAACAAGAAAGATTCACATACATCATATTGTTCGAAAACAAATGAAT
*
4223443 CTAAGAATCCATCTTTATGGAGTTTTGATATGCGTCTCACTTATATGGCCTAAACGACAATGCCA
131 CTAAGAATCCATCTTTATGGAGTTTTGATATACGTCTCACTTATATGGCCTAAACGACAATGCCA
* *
4223508 AAGATAAGTTTGATTTGAGTCATTTGTTTTTTATCTCTTGGTATTTATGTTATAAATGGTGTTTT
196 AAGATAAGTTTGATTCGAGTCATTTGTTTTTTATCTCTTAGTATTTATGTTATAAATGGTGTTTT
* *
4223573 CTTGATCCAAAATATAGAGACCATTAACCAATTGTGCCGAACCATAAAAAACACTATCGAGATAA
261 CTTGATCCAAAATATAAAGACCATTAACCAATTATGCCGAACCATAAAAAACACTATCGAGATAA
* *
4223638 AAAGAACAACAATTATTCTTAATAATAATCTCAAAACAAATCTTTTCCAAATAAGAAATAGAAAT
326 AAAGAACAACAATTATTCTTAATAATAATCTCAAAACAAATCTTGTCCAAACAAGAAATAGAAAT
*
4223703 AATGTTCTTAGTCAAACTAGGCACATAATAACAATCCTCTAAATTTAAATCAAGTCTACTAGGAA
391 AATGTTCTTAGTCAAACTAGGCACATAATAACAATCCTCTAAATTTAAATCAAGTCCACTAGGAA
4223768 AAGATAAAACATATGTCCCTATAACTAATGCATCAACTCTTGCTCGATTTCCCACTCGTAGGTCC
456 AAGATAAAACATATGTCCCTATAACTAATGCATCAACTCTTGCTCGATTTCCCACTCGTAGGTCC
*
4223833 ACGTCTCCTTTAG
521 ACGCCTCCTTTAG
4223846 CCA
1 CCA
4223849 TATTCCTTAT
Statistics
Matches: 518, Mismatches: 18, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
533 518 1.00
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.32
Consensus pattern (533 bp):
CCACATACATCATTATGTATTAACCCCAATAAATCACTTGCTCGCTCACCTTTACTATTAAAAGG
AGCTTTAGTCATTTTTCCCAACAAGAAAGATTCACATACATCATATTGTTCGAAAACAAATGAAT
CTAAGAATCCATCTTTATGGAGTTTTGATATACGTCTCACTTATATGGCCTAAACGACAATGCCA
AAGATAAGTTTGATTCGAGTCATTTGTTTTTTATCTCTTAGTATTTATGTTATAAATGGTGTTTT
CTTGATCCAAAATATAAAGACCATTAACCAATTATGCCGAACCATAAAAAACACTATCGAGATAA
AAAGAACAACAATTATTCTTAATAATAATCTCAAAACAAATCTTGTCCAAACAAGAAATAGAAAT
AATGTTCTTAGTCAAACTAGGCACATAATAACAATCCTCTAAATTTAAATCAAGTCCACTAGGAA
AAGATAAAACATATGTCCCTATAACTAATGCATCAACTCTTGCTCGATTTCCCACTCGTAGGTCC
ACGCCTCCTTTAG
Found at i:4224793 original size:18 final size:18
Alignment explanation
Indices: 4224770--4224833 Score: 119
Period size: 18 Copynumber: 3.6 Consensus size: 18
4224760 CCGAATTAAA
4224770 ATTTATAAATAGGACTTT
1 ATTTATAAATAGGACTTT
4224788 ATTTATAAATAGGACTTT
1 ATTTATAAATAGGACTTT
4224806 ATTTATAAATAGGACTTT
1 ATTTATAAATAGGACTTT
*
4224824 ATTTACAAAT
1 ATTTATAAAT
4224834 TACTCCCACT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (18 bp):
ATTTATAAATAGGACTTT
Found at i:4229955 original size:2 final size:2
Alignment explanation
Indices: 4229912--4229944 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4229902 TGTGGATTTG
4229912 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4229945 AATGGATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4230494 original size:13 final size:13
Alignment explanation
Indices: 4230476--4230513 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
4230466 ACCCAACCCA
4230476 TTGACCATTGACT
1 TTGACCATTGACT
*
4230489 TTGACCGTTGACT
1 TTGACCATTGACT
4230502 TTGACCATTGAC
1 TTGACCATTGAC
4230514 CGTAGACTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.37
Consensus pattern (13 bp):
TTGACCATTGACT
Found at i:4230512 original size:20 final size:20
Alignment explanation
Indices: 4230489--4230526 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
4230479 ACCATTGACT
*
4230489 TTGACCGTTGACTTTGACCA
1 TTGACCGTAGACTTTGACCA
4230509 TTGACCGTAGACTTTGAC
1 TTGACCGTAGACTTTGAC
4230527 TCGTTGATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (20 bp):
TTGACCGTAGACTTTGACCA
Found at i:4231144 original size:28 final size:28
Alignment explanation
Indices: 4231103--4231196 Score: 109
Period size: 28 Copynumber: 3.4 Consensus size: 28
4231093 CTGATACATC
*
4231103 CCTGATTCTGCATGGACTTAATTCCCGT
1 CCTGATTCTGCATGGGCTTAATTCCCGT
* * * *
4231131 CCTGATTCTACATGGGCTTATTTCGCAT
1 CCTGATTCTGCATGGGCTTAATTCCCGT
*
4231159 CCT-ATTTCTGCATGGGCTTAGTTCCCGT
1 CCTGA-TTCTGCATGGGCTTAATTCCCGT
*
4231187 CCTGTTTCTG
1 CCTGATTCTG
4231197 TTTGGGATCC
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
27 1 0.02
28 53 0.98
ACGTcount: A:0.14, C:0.28, G:0.19, T:0.39
Consensus pattern (28 bp):
CCTGATTCTGCATGGGCTTAATTCCCGT
Found at i:4236142 original size:20 final size:20
Alignment explanation
Indices: 4236117--4236155 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4236107 TTTTCAAGGG
4236117 CATGCACCGATGCACCAATC
1 CATGCACCGATGCACCAATC
* *
4236137 CATGCATCGATGCATCAAT
1 CATGCACCGATGCACCAAT
4236156 TAATTTCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.33, G:0.15, T:0.21
Consensus pattern (20 bp):
CATGCACCGATGCACCAATC
Found at i:4236226 original size:45 final size:46
Alignment explanation
Indices: 4236177--4236265 Score: 144
Period size: 46 Copynumber: 2.0 Consensus size: 46
4236167 ACATCGAATA
* *
4236177 CATTTTATGCATCGATGCAC-ATACCATGCATCGATGCACTCAGTG
1 CATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAGTG
*
4236222 CATTTGATGCATCGATGCACAAGACTATGCATCGATGCACTCAG
1 CATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
4236266 GCTTTTTCAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 19 0.47
46 21 0.52
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (46 bp):
CATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAGTG
Found at i:4243929 original size:20 final size:20
Alignment explanation
Indices: 4243904--4243942 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4243894 TTTTCAAGGG
4243904 CATGCACCGATGCACCAATC
1 CATGCACCGATGCACCAATC
* *
4243924 CATGCATCGATGCATCAAT
1 CATGCACCGATGCACCAAT
4243943 TAATTTCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.33, G:0.15, T:0.21
Consensus pattern (20 bp):
CATGCACCGATGCACCAATC
Found at i:4243997 original size:19 final size:19
Alignment explanation
Indices: 4243973--4244021 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
4243963 GCATTTTATA
4243973 CATCGATGCACATACCATG
1 CATCGATGCACATACCATG
*
4243992 CATCGACGCACATACCATG
1 CATCGATGCACATACCATG
4244011 CATCGATGCAC
1 CATCGATGCAC
4244022 TCAGTGCATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.35, G:0.16, T:0.18
Consensus pattern (19 bp):
CATCGATGCACATACCATG
Found at i:4244127 original size:19 final size:18
Alignment explanation
Indices: 4244095--4244132 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
4244085 ATCGAATACA
*
4244095 TTTTATGCATCGATGCAC
1 TTTTATGCACCGATGCAC
4244113 TTTTAGTGCACCGATGCAC
1 TTTTA-TGCACCGATGCAC
4244132 T
1 T
4244133 AAGGGTCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.37
Consensus pattern (18 bp):
TTTTATGCACCGATGCAC
Found at i:4245421 original size:22 final size:22
Alignment explanation
Indices: 4245393--4245451 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
4245383 CTACATCTAT
4245393 ATTCTTCAAAGATGATAGATTC
1 ATTCTTCAAAGATGATAGATTC
4245415 ATTCTTCAAAGATGATAGATTC
1 ATTCTTCAAAGATGATAGATTC
*
4245437 -TCTTTTCAAAGATGA
1 AT-TCTTCAAAGATGA
4245452 AAGCTTTATT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
21 1 0.03
22 34 0.97
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.37
Consensus pattern (22 bp):
ATTCTTCAAAGATGATAGATTC
Found at i:4246189 original size:36 final size:36
Alignment explanation
Indices: 4246135--4246258 Score: 117
Period size: 36 Copynumber: 3.4 Consensus size: 36
4246125 TAACAATTTA
**
4246135 TCTCACTTGAGATTGTTTTTCTTAAAACAAATTGCG
1 TCTCACTTGAGACAGTTTTTCTTAAAACAAATTGCG
* * * **
4246171 TCTCGCTTGAGACAGTTTTACTCGAAATA-ACAATT-TA
1 TCTCACTTGAGACAGTTTTTCT-TAAA-ACA-AATTGCG
*
4246208 TCTCACTTGAGATAGTTTTTCTTAAAACAAATTGCG
1 TCTCACTTGAGACAGTTTTTCTTAAAACAAATTGCG
* *
4246244 TTTCGCTTGAGACAG
1 TCTCACTTGAGACAG
4246259 ATTCACTCGA
Statistics
Matches: 67, Mismatches: 16, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
35 5 0.07
36 34 0.51
37 23 0.34
38 5 0.07
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (36 bp):
TCTCACTTGAGACAGTTTTTCTTAAAACAAATTGCG
Found at i:4246218 original size:37 final size:34
Alignment explanation
Indices: 4246117--4246287 Score: 92
Period size: 36 Copynumber: 4.7 Consensus size: 34
4246107 GTGCAGGATG
**
4246117 TTTTC-AAATAACAATTTATCTCACTTGAGATTGT
1 TTTTCGAAA-AACAATTTATCTCACTTGAGACAGT
** ** *
4246151 TTTTCTTAAAACAAATTGCGTCTCGCTTGAGACAGT
1 TTTTCGAAAAAC-AATT-TATCTCACTTGAGACAGT
*
4246187 TTTACTCGAAATAACAATTTATCTCACTTGAGATAGT
1 TTT--TCGAAA-AACAATTTATCTCACTTGAGACAGT
** ** * *
4246224 TTTTCTTAAAACAAATTGCGTTTCGCTTGAGACAGAT
1 TTTTCGAAAAAC-AATT-TATCTCACTTGAGACAG-T
**
4246261 TCACTCGAAACAACAATTTATCTCACT
1 T-TTTCGAAA-AACAATTTATCTCACT
4246288 CTAGATTGTT
Statistics
Matches: 99, Mismatches: 27, Indels: 19
0.68 0.19 0.13
Matches are distributed among these distances:
34 11 0.11
35 14 0.14
36 28 0.28
37 24 0.24
38 16 0.16
39 6 0.06
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (34 bp):
TTTTCGAAAAACAATTTATCTCACTTGAGACAGT
Found at i:4246241 original size:73 final size:73
Alignment explanation
Indices: 4246122--4246336 Score: 326
Period size: 73 Copynumber: 2.9 Consensus size: 73
4246112 GGATGTTTTC
4246122 AAATAACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTGCGTCTCGCTTGAGACAGT
1 AAATAACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTGCGTCTCGCTTGAGACAGT
*
4246187 TTTACTCG
66 TTCACTCG
* * *
4246195 AAATAACAATTTATCTCACTTGAGATAGTTTTTCTTAAAACAAATTGCGTTTCGCTTGAGACAGA
1 AAATAACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTGCGTCTCGCTTGAGACAGT
4246260 TTCACTCG
66 TTCACTCG
* * * *
4246268 AAACAACAATTTATCTCACTCT-AGATTGTTTTTCTTAAAACAAGATT-CTTCTCGCTTAAGATA
1 AAATAACAATTTATCTCACT-TGAGATTGTTTTTCTTAAAACAA-ATTGCGTCTCGCTTGAGACA
4246331 GTTTCA
64 GTTTCA
4246337 ATAGAAACAA
Statistics
Matches: 129, Mismatches: 11, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
73 125 0.97
74 4 0.03
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (73 bp):
AAATAACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTGCGTCTCGCTTGAGACAGT
TTCACTCG
Found at i:4246695 original size:20 final size:20
Alignment explanation
Indices: 4246633--4246696 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 20
4246623 TCCAGAGAAA
4246633 GTTCATAATGAGAAGAATTT
1 GTTCATAATGAGAAGAATTT
* *
4246653 ATCTGA-AGATGAAGAAGAA---
1 GT-TCATA-ATG-AGAAGAATTT
4246672 GTTCATAATGAGAAGAATTT
1 GTTCATAATGAGAAGAATTT
4246692 GTTCA
1 GTTCA
4246697 ACCTTTTTGC
Statistics
Matches: 33, Mismatches: 4, Indels: 14
0.65 0.08 0.27
Matches are distributed among these distances:
17 7 0.21
18 5 0.15
19 2 0.06
20 7 0.21
21 5 0.15
22 7 0.21
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.30
Consensus pattern (20 bp):
GTTCATAATGAGAAGAATTT
Found at i:4246897 original size:123 final size:123
Alignment explanation
Indices: 4246371--4247640 Score: 1077
Period size: 137 Copynumber: 10.0 Consensus size: 123
4246361 CACTCGATGG
* * * *
4246371 ATCAACATTTCCAGA-AGAGTTCATAATGAGAAGAACTCATCTGAAGAATG-AGAAGAAGTTCAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCAT
4246434 AATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGC
65 AATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGC
4246493 ATCAACTTTTCCAGAGAAAGTTCATAAT--G-AGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
* * * *
4246555 ATGAGAAAAATTTGTTCAACCTTTTTGCATGACTCTATCACAGAAGGAGATAGATTATC
66 ATGAGAAGAACTTGTTCAACC-TTTTGCATGACTCTATCACAGAAGGAGATAGATCAGC
* *
4246614 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAATTTATCTGAAGATGAAGAAGAAGTTCATA
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
*
4246679 ATGAGAAGAATTTGTTCAACCTTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGC
66 ATGAGAAGAACTTGTTCAACC-TTTTGCATGACTCTATCACAGAAGGAGATAGATCAGC
4246738 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
*
4246803 ATGAGAAGAATTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGC
66 ATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGC
* *
4246861 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
* * * * * * * * *
4246926 ATGAGAATAATTTGTTCAACCTTGCCTT-AATTCATCATATATAACGTTGAATCAACGACACCTC
66 ATGAGAAGAACTTGTTCAACCTT---TTGCA-TGA-C-TCTATCAC-----A-GAAGGAGA--T-
* * * *
4246990 TGTTGAGG
116 AGATCAGC
* * * *
4246998 ATCAGCATTTTCAGAGAAAGTTCATAATGAGAAGAA-TTCATCTGAAGAAGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTT-ATCTGAAGAGGAAGAAGAAGTTCAT
* * * *
4247062 AATGAGAAGAACTTGTTCAACCTTGT-CTTAATTC-ATCACATATGAAGTTGA-ATCAACGA-CA
65 AATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCAC--A-GAAG--GAGAT--A-GATCA
*
4247123 CCTC
122 --GC
* * *
4247127 TTTCGATGATCAGTATTTTCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGA
1 -ATC-A--A-C--T-TTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGA
* * * *
4247192 AGTTCATAATGAGAAGAACTTGTTCAATCTTTT-C-TTAATTTATCACATATGAAGTTGA-ATCA
58 AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCAC--A-GAAG--GAGAT--
*
4247254 ACGACACCTCTTTTAAGG
116 A-G--A--TC-----AGC
* * *
4247272 ATCAACATTTCCAGA-AGAAGTTCATAATGAGAAGAACTTATCTGAAGATGAAGAAGAAATTCAT
1 ATCAACTTTTCCAGAGA-AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCAT
* * * * * * * * *
4247336 AATGAGAAGAACTTGTTCAACTTTTTG-ATAGATTAC-ACCATATAAAGAAAGAGAT-TG-
65 AATGAGAAGAACTTGTTCAACCTTTTGCAT-GACT-CTATCACAGAAGGAGATAGATCAGC
* *
4247393 -TC-A---TTCCAGTAGAAGAGTTCATAATGAGAATAA-TTCATCTGAAGAGGAAGACA-ATGTT
1 ATCAACTTTTCCAG-AGAA-AGTTCATAATGAGAAGAACTT-ATCTGAAGAGGAAGA-AGAAGTT
** * * *
4247451 CATAATCTGAAGAACTTATTCAACCTTTTGC-TCGACTCTATCGCAGAAGGAGATAGAACAGC
62 CATAATGAGAAGAACTTGTTCAACCTTTTGCAT-GACTCTATCACAGAAGGAGATAGATCAGC
* * * * * *
4247513 ATCAACATTTCTAGA-AGGAGTTCGTAATAAGAAGAACTTATCTGAAGGGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAGA-AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCAT
** * * * * * *
4247577 AATCTGAAGAACTTATTCAACCTTTTGCTTAACTC-ATCACAGAGGGAAATAGATCAAC
65 AATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGC
4247635 ATCAAC
1 ATCAAC
4247641 ATTGTTCAAC
Statistics
Matches: 961, Mismatches: 115, Indels: 144
0.79 0.09 0.12
Matches are distributed among these distances:
116 6 0.01
117 5 0.01
118 76 0.08
119 5 0.01
120 49 0.05
121 66 0.07
122 41 0.04
123 203 0.21
124 175 0.18
125 6 0.01
126 5 0.01
127 6 0.01
128 9 0.01
129 2 0.00
130 7 0.01
131 2 0.00
132 1 0.00
133 4 0.00
134 9 0.01
135 1 0.00
136 8 0.01
137 260 0.27
138 2 0.00
139 6 0.01
140 1 0.00
141 1 0.00
142 1 0.00
143 1 0.00
144 2 0.00
147 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (123 bp):
ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGC
Found at i:4247069 original size:23 final size:22
Alignment explanation
Indices: 4247027--4247072 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
4247017 GTTCATAATG
*
4247027 AGAAGAATTCATCTGAAGAAGA
1 AGAAGAATTCATATGAAGAAGA
4247049 AGAAGAAGTTCATAATG-AGAAGA
1 AGAAGAA-TTCAT-ATGAAGAAGA
4247072 A
1 A
4247073 CTTGTTCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 7 0.33
23 12 0.57
24 2 0.10
ACGTcount: A:0.52, C:0.07, G:0.24, T:0.17
Consensus pattern (22 bp):
AGAAGAATTCATATGAAGAAGA
Found at i:4249299 original size:143 final size:147
Alignment explanation
Indices: 4248932--4249308 Score: 539
Period size: 148 Copynumber: 2.6 Consensus size: 147
4248922 TAAATAATAG
** * * *
4248932 TATTTATTTATTTTTAAATATTAAGAAAGGGGTTGTCTTAAAGCAACTAGATGTCCTTTTCTGAT
1 TATTTATTTATTTTT-AATATTAAGAAAATGATTGTCTTAAAGCAACTAGAAGTCATTTTCTGAT
4248997 ATTTTTAAATAAATAAATATCCTACTTTTATAAATTATATATATTAATTTAATTTATTTATTTTT
65 ATTTTTAAATAAATAAATATCCTACTTTTATAAATTATATATATTAATTTAATTTATTTATTTTT
4249062 AGAGAAATGTTTTATTAA
130 AGAGAAATGTTTTATTAA
* *
4249080 TATTTATTTATTTTTTAATATTAAGAAAATGATTGTCTTAAAACAACTAGAATTCATTTTCTGAT
1 TATTTATTTA-TTTTTAATATTAAGAAAATGATTGTCTTAAAGCAACTAGAAGTCATTTTCTGAT
* * *
4249145 ATTTTTGAATAACTAAATATCCTACTTTTATAAA-T-TATATATTAATTTTATTTATTTA-TTTT
65 ATTTTTAAATAAATAAATATCCTACTTTTATAAATTATATATATTAATTTAATTTATTTATTTTT
* *
4249207 AGAGAAATGTTTTTTTTAC
130 AGAGAAATG-TTTTATTAA
* * * *
4249226 TA-TTA-TTATTTTTAATATTAAGAAAATGACTATCTTCAAGTAACTAGAAGTCATTTTCTGATA
1 TATTTATTTATTTTTAATATTAAGAAAATGATTGTCTTAAAGCAACTAGAAGTCATTTTCTGATA
*
4249289 TTTCTAAATAAATAAATATC
66 TTTTTAAATAAATAAATATC
4249309 TTATTTATAA
Statistics
Matches: 206, Mismatches: 21, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
143 66 0.32
144 3 0.01
145 16 0.08
146 31 0.15
147 1 0.00
148 84 0.41
149 5 0.02
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.48
Consensus pattern (147 bp):
TATTTATTTATTTTTAATATTAAGAAAATGATTGTCTTAAAGCAACTAGAAGTCATTTTCTGATA
TTTTTAAATAAATAAATATCCTACTTTTATAAATTATATATATTAATTTAATTTATTTATTTTTA
GAGAAATGTTTTATTAA
Found at i:4249330 original size:25 final size:25
Alignment explanation
Indices: 4249294--4249355 Score: 76
Period size: 25 Copynumber: 2.5 Consensus size: 25
4249284 TGATATTTCT
*
4249294 AAATA-AATAAATATCTTATTTATAA
1 AAATATAATAAATAT-ATATTTATAA
4249319 AAATATAA-AAATTATATATTTATAA
1 AAATATAATAAA-TATATATTTATAA
4249344 AAAT-TAATAAAT
1 AAATATAATAAAT
4249356 TTTCTTGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
24 4 0.12
25 24 0.73
26 5 0.15
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (25 bp):
AAATATAATAAATATATATTTATAA
Found at i:4249357 original size:18 final size:17
Alignment explanation
Indices: 4249322--4249357 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
4249312 TTTATAAAAA
*
4249322 TATAAAAATTATATATT
1 TATAAAAATTATAAATT
4249339 TATAAAAATTAATAAATT
1 TATAAAAATT-ATAAATT
4249357 T
1 T
4249358 TCTTGGAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TATAAAAATTATAAATT
Found at i:4252563 original size:35 final size:35
Alignment explanation
Indices: 4252517--4252622 Score: 176
Period size: 35 Copynumber: 3.0 Consensus size: 35
4252507 AAAAAATAAG
* * *
4252517 TTTATGAGCCCTGTTTTTAATTTAATTTATTAATA
1 TTTATGGGCCCTGCTTTTAATTTAGTTTATTAATA
4252552 TTTATGGGCCCTGCTTTTAATTTAGTTTATTAATA
1 TTTATGGGCCCTGCTTTTAATTTAGTTTATTAATA
*
4252587 TTTATGGGCCCTGCTTTTAATTTAGTATATTAATA
1 TTTATGGGCCCTGCTTTTAATTTAGTTTATTAATA
4252622 T
1 T
4252623 AATTTTTAAC
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 67 1.00
ACGTcount: A:0.25, C:0.10, G:0.12, T:0.52
Consensus pattern (35 bp):
TTTATGGGCCCTGCTTTTAATTTAGTTTATTAATA
Found at i:4253379 original size:41 final size:39
Alignment explanation
Indices: 4253315--4253393 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
4253305 TCGGTTTGCA
* *
4253315 AAAAAACCGGATTTTTTTGGATAAAAATCCAGTTTTTTT
1 AAAAAACCGGATTTTTTTAGATAAAAAACCAGTTTTTTT
*
4253354 AAAAAACCGGATTTTTTTCCAGATAAAAAACCGGTTTTTT
1 AAAAAACCGGATTTTTTT--AGATAAAAAACCAGTTTTTT
4253394 ATCCGGTTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
39 18 0.51
41 17 0.49
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.38
Consensus pattern (39 bp):
AAAAAACCGGATTTTTTTAGATAAAAAACCAGTTTTTTT
Found at i:4253433 original size:26 final size:27
Alignment explanation
Indices: 4253378--4253434 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
4253368 TTTTCCAGAT
* **
4253378 AAAAAACCGGTTTTTTATCCGGTTTGA
1 AAAAAACCGGTTTTTAATCCGGTTAAA
4253405 AAAAAACCGGTTTTTAATCCGG-TAAA
1 AAAAAACCGGTTTTTAATCCGGTTAAA
4253431 AAAA
1 AAAA
4253435 CTGGTCGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 6 0.22
27 21 0.78
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (27 bp):
AAAAAACCGGTTTTTAATCCGGTTAAA
Found at i:4256710 original size:8 final size:8
Alignment explanation
Indices: 4256697--4256723 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
4256687 TACTTTTAAT
4256697 TTTTCTAA
1 TTTTCTAA
4256705 TTTTCTAA
1 TTTTCTAA
4256713 TTTTCTAA
1 TTTTCTAA
4256721 TTT
1 TTT
4256724 AACTTTCGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (8 bp):
TTTTCTAA
Found at i:4263677 original size:27 final size:24
Alignment explanation
Indices: 4263622--4263710 Score: 72
Period size: 23 Copynumber: 3.5 Consensus size: 24
4263612 GAAAATAAAA
* *
4263622 AATAAAGTATTTATAAATTAAGTTAAT
1 AATAAAATATTTATAAGTTAA--T-AT
4263649 AATAAAGCATATTTAATAAGTTAATAT
1 AATAAA--ATATTT-ATAAGTTAATAT
* *
4263676 AA-AAAATATTTTTAAATTAATAT
1 AATAAAATATTTATAAGTTAATAT
4263699 ATATAAAATATT
1 A-ATAAAATATT
4263711 ATGAATTTAT
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
23 11 0.21
24 7 0.13
25 8 0.15
26 3 0.06
27 10 0.19
28 1 0.02
29 5 0.09
30 8 0.15
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.40
Consensus pattern (24 bp):
AATAAAATATTTATAAGTTAATAT
Found at i:4264904 original size:4 final size:4
Alignment explanation
Indices: 4264895--4264929 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
4264885 ACATAAAAGA
4264895 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
4264930 ATATATTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:4266973 original size:4 final size:4
Alignment explanation
Indices: 4266964--4266989 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
4266954 TGTGTCAAAT
4266964 ATTG ATTG ATTG ATTG ATTG ATTG AT
1 ATTG ATTG ATTG ATTG ATTG ATTG AT
4266990 GAATTTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
ATTG
Found at i:4268398 original size:20 final size:19
Alignment explanation
Indices: 4268359--4268399 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
4268349 ACCTACAAAC
*
4268359 TGAAAATAAACAAAGTTAA
1 TGAAAATAAACAAAGCTAA
*
4268378 TGAAAATAAAACAACGCTAA
1 TGAAAAT-AAACAAAGCTAA
4268398 TG
1 TG
4268400 CAATACCATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.59, C:0.10, G:0.12, T:0.20
Consensus pattern (19 bp):
TGAAAATAAACAAAGCTAA
Found at i:4274458 original size:2 final size:2
Alignment explanation
Indices: 4274451--4274478 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4274441 TTTGTTACCA
4274451 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
4274479 TCATCTTGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4279939 original size:41 final size:40
Alignment explanation
Indices: 4279837--4280106 Score: 423
Period size: 41 Copynumber: 6.7 Consensus size: 40
4279827 TAAAATTTAA
* *
4279837 GGGTACTAAAATAAAACAAAAACTAAAGTTTTTAACGGTA
1 GGGTACTAAAATGAAACAAAAACTAAAGTTTTTAACGGTG
* *
4279877 GGGTACTAAAATAAAACAAAAACTAAAGTTTTTAACGGCG
1 GGGTACTAAAATGAAACAAAAACTAAAGTTTTTAACGGTG
* *
4279917 GAGGTACTAAAATGAAATAAAAACTAAAGTTTTTAACTGTG
1 G-GGTACTAAAATGAAACAAAAACTAAAGTTTTTAACGGTG
4279958 GGGTTACTAAAATGAAACAAAAACTAAAGTTTTTAACGGTG
1 GGG-TACTAAAATGAAACAAAAACTAAAGTTTTTAACGGTG
* * *
4279999 GGGTACTAGAATGAAATAAAAACTAAAGTTTTTAACTGTGG
1 GGGTACTAAAATGAAACAAAAACTAAAGTTTTTAACGGT-G
4280040 GGGTACTAAAATGAAACAAAAACTAAAGTTTTTAACGGTG
1 GGGTACTAAAATGAAACAAAAACTAAAGTTTTTAACGGTG
*
4280080 GGGCACTAAAATGAAACAAAAACTAAA
1 GGGTACTAAAATGAAACAAAAACTAAA
4280107 CTTCTTGTAT
Statistics
Matches: 212, Mismatches: 15, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
40 101 0.48
41 111 0.52
ACGTcount: A:0.47, C:0.10, G:0.18, T:0.25
Consensus pattern (40 bp):
GGGTACTAAAATGAAACAAAAACTAAAGTTTTTAACGGTG
Found at i:4279939 original size:81 final size:80
Alignment explanation
Indices: 4279837--4280106 Score: 432
Period size: 81 Copynumber: 3.3 Consensus size: 80
4279827 TAAAATTTAA
* * * *
4279837 GGGTACTAAAATAAAACAAAAACTAAAGTTTTTAACGGTAGGGTACTAAAATAAAACAAAAACTA
1 GGGTACTAAAATGAAACAAAAACTAAAGTTTTTAACTGTGGGGTACTAAAATGAAACAAAAACTA
*
4279902 AAGTTTTTAACGGCG
66 AAGTTTTTAACGGTG
*
4279917 GAGGTACTAAAATGAAATAAAAACTAAAGTTTTTAACTGTGGGGTTACTAAAATGAAACAAAAAC
1 G-GGTACTAAAATGAAACAAAAACTAAAGTTTTTAACTGTGGGG-TACTAAAATGAAACAAAAAC
4279982 TAAAGTTTTTAACGGTG
64 TAAAGTTTTTAACGGTG
* *
4279999 GGGTACTAGAATGAAATAAAAACTAAAGTTTTTAACTGTGGGGGTACTAAAATGAAACAAAAACT
1 GGGTACTAAAATGAAACAAAAACTAAAGTTTTTAACTGT-GGGGTACTAAAATGAAACAAAAACT
4280064 AAAGTTTTTAACGGTG
65 AAAGTTTTTAACGGTG
*
4280080 GGGCACTAAAATGAAACAAAAACTAAA
1 GGGTACTAAAATGAAACAAAAACTAAA
4280107 CTTCTTGTAT
Statistics
Matches: 177, Mismatches: 10, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
80 1 0.01
81 136 0.77
82 40 0.23
ACGTcount: A:0.47, C:0.10, G:0.18, T:0.25
Consensus pattern (80 bp):
GGGTACTAAAATGAAACAAAAACTAAAGTTTTTAACTGTGGGGTACTAAAATGAAACAAAAACTA
AAGTTTTTAACGGTG
Found at i:4285897 original size:32 final size:32
Alignment explanation
Indices: 4285855--4285964 Score: 105
Period size: 32 Copynumber: 3.5 Consensus size: 32
4285845 GCTCATGTGT
* *
4285855 ATTATATGAATACAACACTAACTCTGTTATAC
1 ATTATTTGAATACAACACTAACTCTGTTATGC
* * * *
4285887 ATTATTTGAATGC-ATACTAACTTTGTTGTGC
1 ATTATTTGAATACAACACTAACTCTGTTATGC
* * ** *
4285918 ATTATTTAAATGCAACACTAACTCCATTATGT
1 ATTATTTGAATACAACACTAACTCTGTTATGC
*
4285950 ATTATCTGAATACAA
1 ATTATTTGAATACAA
4285965 TATTGACTCT
Statistics
Matches: 61, Mismatches: 16, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
31 26 0.43
32 35 0.57
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.38
Consensus pattern (32 bp):
ATTATTTGAATACAACACTAACTCTGTTATGC
Found at i:4285921 original size:31 final size:32
Alignment explanation
Indices: 4285867--4285941 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 32
4285857 TATATGAATA
*
4285867 CAACACTAACTCTGTTATACATTATTTGAATG
1 CAACACTAACTCTGTTATACATTATTTAAATG
* * * *
4285899 C-ATACTAACTTTGTTGTGCATTATTTAAATG
1 CAACACTAACTCTGTTATACATTATTTAAATG
4285930 CAACACTAACTC
1 CAACACTAACTC
4285942 CATTATGTAT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
31 26 0.74
32 9 0.26
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.37
Consensus pattern (32 bp):
CAACACTAACTCTGTTATACATTATTTAAATG
Found at i:4286004 original size:32 final size:32
Alignment explanation
Indices: 4285895--4286000 Score: 81
Period size: 32 Copynumber: 3.3 Consensus size: 32
4285885 ACATTATTTG
* * *
4285895 AATGC-ATACTAACTTTGTTGTGCATT-ATTT
1 AATGCAATACTAACTCTATTGTGCATTAACTT
* * * * * *
4285925 AAATGCAACACTAACTCCATTATGTATTATCTG
1 -AATGCAATACTAACTCTATTGTGCATTAACTT
* * *
4285958 AATACAATATTGACTCTATTGTGCATTAACTT
1 AATGCAATACTAACTCTATTGTGCATTAACTT
4285990 AATGCAATACT
1 AATGCAATACT
4286001 GACTTTTCTA
Statistics
Matches: 53, Mismatches: 20, Indels: 3
0.70 0.26 0.04
Matches are distributed among these distances:
31 5 0.09
32 47 0.89
33 1 0.02
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (32 bp):
AATGCAATACTAACTCTATTGTGCATTAACTT
Found at i:4286065 original size:32 final size:32
Alignment explanation
Indices: 4285915--4286065 Score: 131
Period size: 32 Copynumber: 4.7 Consensus size: 32
4285905 AACTTTGTTG
* * * * * *
4285915 TGCATTATTTAAATGCAACACTAACTCCATTA
1 TGCATTATCTAAATACAATATTAACTCTACTA
* * * * *
4285947 TGTATTATCTGAATACAATATTGACTCTATTG
1 TGCATTATCTAAATACAATATTAACTCTACTA
* * * * * * *
4285979 TGCATTAACTTAATGCAATACTGACTTTTCTA
1 TGCATTATCTAAATACAATATTAACTCTACTA
*
4286011 TGAATTATCTAAATACAATATTAACTCTACTA
1 TGCATTATCTAAATACAATATTAACTCTACTA
4286043 TGCATTATCTAAATACAATATTA
1 TGCATTATCTAAATACAATATTA
4286066 TAACTATTAT
Statistics
Matches: 92, Mismatches: 27, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
32 92 1.00
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.39
Consensus pattern (32 bp):
TGCATTATCTAAATACAATATTAACTCTACTA
Found at i:4288854 original size:19 final size:20
Alignment explanation
Indices: 4288809--4288858 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
4288799 TTATGTTTGT
*
4288809 AGTATCGATACTGACCCTTG
1 AGTATCGATACTCACCCTTG
*
4288829 GGTATCGATACTCACCC-TG
1 AGTATCGATACTCACCCTTG
4288848 AGTATCGATAC
1 AGTATCGATAC
4288859 CAAAAATAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (20 bp):
AGTATCGATACTCACCCTTG
Found at i:4295400 original size:22 final size:21
Alignment explanation
Indices: 4295371--4295412 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
4295361 TGATCAAATG
4295371 ATATTATTTTAGT-ATTTTTAT
1 ATATTATTTT-GTGATTTTTAT
4295392 ATATATATTTTGTGATTTTTA
1 ATAT-TATTTTGTGATTTTTA
4295413 GGTAGAATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (21 bp):
ATATTATTTTGTGATTTTTAT
Found at i:4297759 original size:30 final size:30
Alignment explanation
Indices: 4297720--4297807 Score: 85
Period size: 30 Copynumber: 3.0 Consensus size: 30
4297710 TGAAATATAT
*
4297720 AACTTTTAAAAACTATATTTTGGTTC-CTA
1 AACTTTTAAAAACTATATTTTGGTCCACTA
** *
4297749 AACTTTTTAAAATTTATAATTTGG-CCACTA
1 AAC-TTTTAAAAACTATATTTTGGTCCACTA
*
4297779 AAC-TTTCAAAACTTATATTTTGGT-CACTA
1 AACTTTTAAAAAC-TATATTTTGGTCCACTA
4297808 CCTAAAATTT
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
28 6 0.13
29 18 0.38
30 23 0.49
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.43
Consensus pattern (30 bp):
AACTTTTAAAAACTATATTTTGGTCCACTA
Found at i:4297800 original size:29 final size:30
Alignment explanation
Indices: 4297720--4297807 Score: 101
Period size: 29 Copynumber: 3.0 Consensus size: 30
4297710 TGAAATATAT
*
4297720 AACTTTTAAAAAC-TATATTTTGGTTC-CTA
1 AACTTTTCAAAACTTATATTTTGG-TCACTA
* * * *
4297749 AACTTTTTAAAATTTATAATTTGGCCACTA
1 AACTTTTCAAAACTTATATTTTGGTCACTA
4297779 AAC-TTTCAAAACTTATATTTTGGTCACTA
1 AACTTTTCAAAACTTATATTTTGGTCACTA
4297808 CCTAAAATTT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
29 34 0.69
30 15 0.31
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.43
Consensus pattern (30 bp):
AACTTTTCAAAACTTATATTTTGGTCACTA
Found at i:4299480 original size:21 final size:20
Alignment explanation
Indices: 4299430--4299482 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
4299420 CCACCCTTGG
* *
4299430 GTATCGATACCTAATGAATA
1 GTATCGATACCCAATGAACA
* *
4299450 ATATCAATACCCAATGAACA
1 GTATCGATACCCAATGAACA
4299470 TGTATCGATACCC
1 -GTATCGATACCC
4299483 CAACCAAAAC
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.26
Consensus pattern (20 bp):
GTATCGATACCCAATGAACA
Found at i:4300147 original size:17 final size:17
Alignment explanation
Indices: 4300105--4300147 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
4300095 GTAATCCATT
*
4300105 CAAGGCTTATAACAATA
1 CAAGGCTTGTAACAATA
4300122 CAAGGCTTGTAACAATA
1 CAAGGCTTGTAACAATA
4300139 CAAGGCTTG
1 CAAGGCTTG
4300148 CACCTTTGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.23
Consensus pattern (17 bp):
CAAGGCTTGTAACAATA
Found at i:4303048 original size:40 final size:40
Alignment explanation
Indices: 4302997--4303073 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
4302987 TATTACTTAA
* * *
4302997 GTTAAACAATTTAAATTGATGATTATATGTAAAAATTACT
1 GTTAAAAAATTTAAATTAAAGATTATATGTAAAAATTACT
* *
4303037 GTTAAAAAATTTAATTTAAAGATTATATGTATAAATT
1 GTTAAAAAATTTAAATTAAAGATTATATGTAAAAATT
4303074 TATATATATG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.09, T:0.42
Consensus pattern (40 bp):
GTTAAAAAATTTAAATTAAAGATTATATGTAAAAATTACT
Found at i:4303876 original size:245 final size:245
Alignment explanation
Indices: 4303446--4303908 Score: 680
Period size: 245 Copynumber: 1.9 Consensus size: 245
4303436 TATTTCATTC
* * * *
4303446 ATGTTGTGTCACGTGTTACAATCTGATTAAATGATTAAATTTATTAAATTAAATTAAAATTAAGA
1 ATGTTGTGACACGTGTCACAATCTGATTAAAAGATTAAATTTATTAAATTAAATTAAAACTAAGA
* * *
4303511 TCAAATTAGTAGAATGTATAAGTATTGAGGATTAAATGTAGAATTATACTAATTTCATTAACTGC
66 TCAAATTAGTAGAATGTATAACTATTGAGAACTAAATGTAGAATTATACTAATTTCATTAACTGC
* * * * *
4303576 CATGTCAGTATTTTCGTCAGTTGTTATTGGTAAGTGACTTAATTGACAATAATTAAATAGTTAAG
131 AACGTCAGTATTCTCGTCAGTTGTTACTGGCAAGTGACTTAATTGACAATAATTAAATAGTTAAG
* *
4303641 TGGTTTGATTAACAAAATTAAAAGATCAGTTGTAAAAGTAAAAGGGCTAA
196 TGATCTGATTAACAAAATTAAAAGATCAGTTGTAAAAGTAAAAGGGCTAA
4303691 ATGTTGTGACACGTGTCACAATCTGATTAAAAGATTAAATTTATTAAATTAAATTAAAACTAAGA
1 ATGTTGTGACACGTGTCACAATCTGATTAAAAGATTAAATTTATTAAATTAAATTAAAACTAAGA
* *
4303756 TCAAATTAGTAGAATGTATAACTATTGAGAACTAAATGTAGAATTAT-GTCAATTTCATTAATTG
66 TCAAATTAGTAGAATGTATAACTATTGAGAACTAAATGTAGAATTATACT-AATTTCATTAACTG
* * * * *
4303820 TAACGTCAGTATTC-CTGTCAGTTTTTAACT-GCAAGTGATTTGATTGACGATAATTAAATAGTT
130 CAACGTCAGTATTCTC-GTCAGTTGTT-ACTGGCAAGTGACTTAATTGACAATAATTAAATAGTT
*
4303883 AAGTGATCTGATTGACAAAATTAAAA
193 AAGTGATCTGATTAACAAAATTAAAA
4303909 AATTGATGGT
Statistics
Matches: 193, Mismatches: 22, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
244 2 0.01
245 189 0.98
246 2 0.01
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (245 bp):
ATGTTGTGACACGTGTCACAATCTGATTAAAAGATTAAATTTATTAAATTAAATTAAAACTAAGA
TCAAATTAGTAGAATGTATAACTATTGAGAACTAAATGTAGAATTATACTAATTTCATTAACTGC
AACGTCAGTATTCTCGTCAGTTGTTACTGGCAAGTGACTTAATTGACAATAATTAAATAGTTAAG
TGATCTGATTAACAAAATTAAAAGATCAGTTGTAAAAGTAAAAGGGCTAA
Found at i:4304822 original size:18 final size:19
Alignment explanation
Indices: 4304787--4304823 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
4304777 CACGGAATGT
4304787 AAGATTACCAGTGAGAATAA
1 AAGATTACCAG-GAGAATAA
4304807 AAGATTACCA-GAGAATA
1 AAGATTACCAGGAGAATA
4304824 GGATTACTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.51, C:0.11, G:0.19, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGAGAATAA
Found at i:4311030 original size:13 final size:12
Alignment explanation
Indices: 4311012--4311143 Score: 81
Period size: 13 Copynumber: 10.5 Consensus size: 12
4311002 AATAGTAAGT
4311012 AAAATAAATATAA
1 AAAATAAATA-AA
*
4311025 AAAATAAAGAAA
1 AAAATAAATAAA
*
4311037 AAGAAGGAAA-AAA
1 AA-AA-TAAATAAA
* *
4311050 TATATAAATAAA
1 AAAATAAATAAA
4311062 ACAAATAAATAAA
1 A-AAATAAATAAA
*
4311075 ATAAT-AATAAA
1 AAAATAAATAAA
* *
4311086 GAAGTAAA-AATA
1 AAAATAAATAA-A
* *
4311098 ATATATATATAAA
1 A-AAATAAATAAA
4311111 ATAAATAAATAAA
1 A-AAATAAATAAA
4311124 TAAAATAAAATAAA
1 -AAAAT-AAATAAA
4311138 AAAATA
1 AAAATA
4311144 GTAAATATAT
Statistics
Matches: 92, Mismatches: 17, Indels: 21
0.71 0.13 0.16
Matches are distributed among these distances:
11 13 0.14
12 15 0.16
13 51 0.55
14 13 0.14
ACGTcount: A:0.74, C:0.01, G:0.05, T:0.20
Consensus pattern (12 bp):
AAAATAAATAAA
Found at i:4311071 original size:4 final size:4
Alignment explanation
Indices: 4311047--4311172 Score: 60
Period size: 4 Copynumber: 30.8 Consensus size: 4
4311037 AAGAAGGAAA
* * * * *
4311047 AAAT ATAT AAAT AAAAC AAAT AAAT AAA- ATAAT -AAT AAAG AAGT AAAA
1 AAAT AAAT AAAT -AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT
* * *
4311095 ATAAT ATAT ATAT AAAAT AAAT AAAT AAAT AAAAT AAAAT AAAA AAAT
1 A-AAT AAAT AAAT -AAAT AAAT AAAT AAAT -AAAT -AAAT AAAT AAAT
* * * * *
4311143 -AGT AAAT ATAT ATAT ATAT AAAT TAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
4311173 ACTGATAATA
Statistics
Matches: 94, Mismatches: 20, Indels: 16
0.72 0.15 0.12
Matches are distributed among these distances:
3 6 0.06
4 70 0.74
5 18 0.19
ACGTcount: A:0.70, C:0.01, G:0.02, T:0.27
Consensus pattern (4 bp):
AAAT
Found at i:4311073 original size:17 final size:16
Alignment explanation
Indices: 4311044--4311143 Score: 76
Period size: 17 Copynumber: 6.0 Consensus size: 16
4311034 AAAAAGAAGG
*
4311044 AAAAAATATATAAATA
1 AAAAAATAAATAAATA
4311060 AAACAAATAAATAAA-A
1 AAA-AAATAAATAAATA
* * * *
4311076 TAATAATAAAGAAGTA
1 AAAAAATAAATAAATA
* *
4311092 AAAATAATATATATATA
1 AAAA-AATAAATAAATA
4311109 AAATAAATAAATAAATAA
1 AAA-AAATAAATAAAT-A
*
4311127 AATAAAATAAAAAAATA
1 AA-AAAATAAATAAATA
4311144 GTAAATATAT
Statistics
Matches: 64, Mismatches: 14, Indels: 11
0.72 0.16 0.12
Matches are distributed among these distances:
15 8 0.12
16 9 0.14
17 31 0.48
18 15 0.23
19 1 0.02
ACGTcount: A:0.74, C:0.01, G:0.02, T:0.23
Consensus pattern (16 bp):
AAAAAATAAATAAATA
Found at i:4311108 original size:53 final size:55
Alignment explanation
Indices: 4311049--4311165 Score: 161
Period size: 53 Copynumber: 2.2 Consensus size: 55
4311039 GAAGGAAAAA
* *
4311049 ATATATAAATA-AAACAAATAAATAAAATAATAATAAAGAAGTA-AAAATA-ATAT
1 ATATATAAATATAAACAAATAAATAAAATAA-AATAAAAAAATAGAAAATATATAT
* *
4311102 ATATATAAA-ATAAATAAATAAATAAAATAAAATAAAAAAATAGTAAATATATAT
1 ATATATAAATATAAACAAATAAATAAAATAAAATAAAAAAATAGAAAATATATAT
4311156 ATATATAAAT
1 ATATATAAAT
4311166 TAATAAAACT
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
52 11 0.20
53 32 0.57
54 13 0.23
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.27
Consensus pattern (55 bp):
ATATATAAATATAAACAAATAAATAAAATAAAATAAAAAAATAGAAAATATATAT
Found at i:4311164 original size:49 final size:51
Alignment explanation
Indices: 4311013--4311172 Score: 149
Period size: 49 Copynumber: 3.2 Consensus size: 51
4311003 ATAGTAAGTA
* *
4311013 AAATAAATATAA-AAAATAA-AGAAAAAGAAGGAAAA-AATATATA-A-ATA-
1 AAATAAATA-AATAAAATAATA-ATAAAGAAGAAAAATAATATATATATATAT
* *
4311060 AAACAAATAAATAAAATAATAATAAAGAAGTAAAAATAATATATATATAAAAT
1 AAATAAATAAATAAAATAATAATAAAGAAG-AAAAATAATATATATAT-ATAT
* *
4311113 AAATAAATAAATAAAATAA-AATAAA-AA-AATAGTAAATATATATATATAT
1 AAATAAATAAATAAAATAATAATAAAGAAGAAAAAT-AATATATATATATAT
*
4311162 AAATTAATAAA
1 AAATAAATAAA
4311173 ACTGATAATA
Statistics
Matches: 95, Mismatches: 9, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
46 2 0.02
47 23 0.24
48 5 0.05
49 25 0.26
50 12 0.13
51 2 0.02
52 8 0.08
53 18 0.19
ACGTcount: A:0.71, C:0.01, G:0.04, T:0.24
Consensus pattern (51 bp):
AAATAAATAAATAAAATAATAATAAAGAAGAAAAATAATATATATATATAT
Found at i:4311171 original size:53 final size:52
Alignment explanation
Indices: 4311049--4311200 Score: 160
Period size: 53 Copynumber: 3.0 Consensus size: 52
4311039 GAAGGAAAAA
* * *
4311049 ATATATAAATAAAACAAATAAATAAAATAATAATAAAGAAGTAAAAATAATAT
1 ATATATAAAT-AAATAAATAAATAAAATAATAATAAAAAAATAAAAATAATAT
*
4311102 ATATATAAAATAAATAAATAAATAAAATAA-AATAAAAAAATAGTAAAT-ATAT
1 ATATAT-AAATAAATAAATAAATAAAATAATAATAAAAAAATA-AAAATAATAT
*
4311154 ATATAT--ATAAAT---T-AATAAAACTGATAATAAAAAAATAAAAAT-ATAT
1 ATATATAAATAAATAAATAAATAAAA-TAATAATAAAAAAATAAAAATAATAT
4311200 A
1 A
4311201 CTAAAGTAAA
Statistics
Matches: 89, Mismatches: 6, Indels: 15
0.81 0.05 0.14
Matches are distributed among these distances:
45 7 0.08
46 12 0.13
47 12 0.13
49 6 0.07
52 20 0.22
53 28 0.31
54 4 0.04
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.27
Consensus pattern (52 bp):
ATATATAAATAAATAAATAAATAAAATAATAATAAAAAAATAAAAATAATAT
Found at i:4311194 original size:54 final size:52
Alignment explanation
Indices: 4311013--4311194 Score: 146
Period size: 49 Copynumber: 3.5 Consensus size: 52
4311003 ATAGTAAGTA
* * * *
4311013 AAATAAATATAA-AAAATAAAGAAAAAGAAG-GAAAA-AATATATAAATAAAAC
1 AAATAAATA-AATAAAA-AAATAAAAAGAAGTAAAAATAATATATATATAAAAT
* *
4311064 AAATAAATAAA-ATAATAAT--AAAGAAGTAAAAATAATATATATATAAAAT
1 AAATAAATAAATAAAAAAATAAAAAGAAGTAAAAATAATATATATATAAAAT
* *
4311113 AAATAAATAAATAAAATAAAATAAAAAAATAGTAAATAT-ATATATATAT-AAAT
1 AAATAAATAAAT-AAA-AAAATAAAAAGA-AGTAAAAATAATATATATATAAAAT
*
4311166 TAATAAAACTGATAATAAAAAAATAAAAA
1 AAAT-AAA-T-A-AATAAAAAAATAAAAA
4311195 TATATACTAA
Statistics
Matches: 108, Mismatches: 11, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
47 7 0.06
48 4 0.04
49 27 0.25
50 5 0.05
51 11 0.10
52 4 0.04
53 7 0.06
54 17 0.16
55 19 0.18
56 4 0.04
57 3 0.03
ACGTcount: A:0.71, C:0.01, G:0.04, T:0.23
Consensus pattern (52 bp):
AAATAAATAAATAAAAAAATAAAAAGAAGTAAAAATAATATATATATAAAAT
Found at i:4312362 original size:39 final size:35
Alignment explanation
Indices: 4312319--4312407 Score: 106
Period size: 39 Copynumber: 2.4 Consensus size: 35
4312309 CGAGGGTTTG
* *
4312319 GTGTTTCAAGAGAAATATTTTCAAAGGTTTTTTGTGTAT
1 GTGTTTCAAGAGAAATAATTTC-AAGGGTTTTT-T-T-T
* *
4312358 GTGTTTCAAAAGAAATAATTTCGAGGGTTTTTTTT
1 GTGTTTCAAGAGAAATAATTTCAAGGGTTTTTTTT
4312393 GTGTTTCAAGAGAAA
1 GTGTTTCAAGAGAAA
4312408 CTGTCTCAAG
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
35 15 0.33
36 1 0.02
37 1 0.02
38 8 0.18
39 20 0.44
ACGTcount: A:0.30, C:0.06, G:0.21, T:0.43
Consensus pattern (35 bp):
GTGTTTCAAGAGAAATAATTTCAAGGGTTTTTTTT
Found at i:4312436 original size:36 final size:36
Alignment explanation
Indices: 4312394--4312627 Score: 229
Period size: 36 Copynumber: 6.6 Consensus size: 36
4312384 GTTTTTTTTG
*
4312394 TGTTTCAAGAGAAACTGTCTCAAGAGGGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
4312430 TGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * *
4312467 AG-TTCTAAAAGAAACTGTCT-AATAGGAGACAAAATT
1 TGTTTC-AAGAGAAACTGTCTCAAGA-GAGACAAAATT
* * *
4312503 TGTTTCAAG-GAAA-AGATATTC-A-A-AG----ATTT
1 TGTTTCAAGAGAAACTG-T-CTCAAGAGAGACAAAATT
*
4312532 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
4312568 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAGATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAA-AATT
*
4312605 TGTTTCAAGGGAAACTGTCTCAA
1 TGTTTCAAGAGAAACTGTCTCAA
4312628 AACTCGTTTT
Statistics
Matches: 168, Mismatches: 13, Indels: 33
0.79 0.06 0.15
Matches are distributed among these distances:
29 14 0.08
30 6 0.04
31 2 0.01
32 2 0.01
33 2 0.01
34 1 0.01
35 6 0.04
36 80 0.48
37 55 0.33
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:4312628 original size:102 final size:102
Alignment explanation
Indices: 4312428--4312614 Score: 263
Period size: 102 Copynumber: 1.8 Consensus size: 102
4312418 AGGGACAAAA
*
4312428 TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCTAAAAGAAACTGTCTAATAGG
1 TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCTAAAAGAAACTGTCTAAGAGG
4312493 AGACAAAATTTGTTTCAAGGAAAAGATATTCAAAGAT
66 AGACAAAATTTGTTTCAAGGAAAAGATATTCAAAGAT
** * **
4312530 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGTT-TCAAGGGAAACTGTCTCAAGA
1 TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCT-AAAAGAAACTGTCT-AAGA
*
4312593 -GAGACAAGATTTTGTTTCAAGG
64 GGAGACAA-AATTTGTTTCAAGG
4312615 GAAACTGTCT
Statistics
Matches: 75, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
100 1 0.01
101 24 0.32
102 50 0.67
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (102 bp):
TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCTAAAAGAAACTGTCTAAGAGG
AGACAAAATTTGTTTCAAGGAAAAGATATTCAAAGAT
Found at i:4312723 original size:37 final size:37
Alignment explanation
Indices: 4312663--4312851 Score: 107
Period size: 37 Copynumber: 5.4 Consensus size: 37
4312653 AAATATTTTG
*
4312663 TGTTTCAAGGGAAACGT-TTTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAAC-TATCTCAAGGGAGACAAAATTT
* * *
4312700 TGTTTCAAGGGAAACTATCTCAAGAGATACAAAA-CT
1 TGTTTCAAGGGAAACTATCTCAAGGGAGACAAAATTT
** * * * *
4312736 AATTTCAAAGGAAA-TGTTTTCAA---TG------TTT
1 TGTTTCAAGGGAAACT-ATCTCAAGGGAGACAAAATTT
* *
4312764 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGGGAAACTATCTCAAGGGAGACAAAATTT
* * * *
4312802 TGTTTCAAGGGAAACTACCCCAAGCGAGATAAAA-TT
1 TGTTTCAAGGGAAACTATCTCAAGGGAGACAAAATTT
*
4312838 TATTTCAAGGGAAA
1 TGTTTCAAGGGAAA
4312852 TGTTTTCAAT
Statistics
Matches: 112, Mismatches: 26, Indels: 29
0.67 0.16 0.17
Matches are distributed among these distances:
28 1 0.01
29 15 0.13
30 1 0.01
32 1 0.01
35 1 0.01
36 33 0.29
37 57 0.51
38 3 0.03
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.29
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTATCTCAAGGGAGACAAAATTT
Found at i:4312795 original size:102 final size:102
Alignment explanation
Indices: 4312663--4312875 Score: 320
Period size: 102 Copynumber: 2.1 Consensus size: 102
4312653 AAATATTTTG
* * * * *
4312663 TGTTTCAAGGGAAACGTTTTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAT
1 TGTTTCAAGAGAAACGTTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTACCCCAAGAGAG
4312728 ACAAAACTAATTTCAAAGGAAATGTTTTCAATGTTTA
66 ACAAAACTAATTTCAAAGGAAATGTTTTCAATGTTTA
*
4312765 TGTTTCAAGAGAAAC-TGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTACCCCAAGCGA
1 TGTTTCAAGAGAAACGT-TCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTACCCCAAGAGA
* * * *
4312829 GATAAAATTTATTTCAAGGGAAATGTTTTCAATGTTTA
65 GACAAAACTAATTTCAAAGGAAATGTTTTCAATGTTTA
4312867 TGTTTCAAG
1 TGTTTCAAG
4312876 GGAGACAAAA
Statistics
Matches: 100, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
101 1 0.01
102 99 0.99
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (102 bp):
TGTTTCAAGAGAAACGTTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTACCCCAAGAGAG
ACAAAACTAATTTCAAAGGAAATGTTTTCAATGTTTA
Found at i:4312875 original size:87 final size:87
Alignment explanation
Indices: 4312784--4312962 Score: 304
Period size: 87 Copynumber: 2.1 Consensus size: 87
4312774 AGAAACTGTC
* *
4312784 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTTATTTCAAGGG
1 TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTTATTTCAAGAG
4312849 AAATGTTTTCAATGTTTATGTT
66 AAATGTTTTCAATGTTTATGTT
* * *
4312871 TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTATCTCAATCGAGATAAAATTTATTTCAAGAG
1 TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTTATTTCAAGAG
*
4312936 AAATTTTTTCAATGTTTATGTT
66 AAATGTTTTCAATGTTTATGTT
4312958 TCAAG
1 TCAAG
4312963 AGAAACTATC
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 86 1.00
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (87 bp):
TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTTATTTCAAGAG
AAATGTTTTCAATGTTTATGTT
Found at i:4313062 original size:189 final size:188
Alignment explanation
Indices: 4312680--4313067 Score: 489
Period size: 189 Copynumber: 2.1 Consensus size: 188
4312670 AGGGAAACGT
*
4312680 TTTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGATACAAAACTAATTTCAAA
1 TTTCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTATCTCAAGAGATA-AAAACTAATTTCAAA
* * *
4312745 GGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAA
65 GGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTAGTTCCAA
** * * * * * *
4312810 GGGAAACTACCCCAAGCGAGATAAAATTTATTTCAAGGGAAATGTTTTCAATGTTTATG
130 AAGAAAATACCCCAAGCGAGACAAAATTTATTTCAAGGAAAAAGTATTCAATATTTATG
* *
4312869 TTTCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTATCTCAATCGAGAT-AAAATTTATTTC-A
1 TTTCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTATCTCAA--GAGATAAAAACTAATTTCAA
*
4312932 AGAGAAATTTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTAGTTCC
64 AG-GAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTAGTTCC
** * * * *
4312997 AAAAGAAAATGTCTCAAGGGAGACGAAA-TTAGTTTCAATGAAAACAG-ATTCAAATATTT-TG
128 AAAAGAAAATACCCCAAGCGAGACAAAATTTA-TTTCAAGGAAAA-AGTATTC-AATATTTATG
4313058 TTTCAAGGGA
1 TTTCAAGGGA
4313068 AACTTGGAAA
Statistics
Matches: 172, Mismatches: 21, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
188 6 0.03
189 154 0.90
190 7 0.04
191 5 0.03
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (188 bp):
TTTCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTATCTCAAGAGATAAAAACTAATTTCAAAG
GAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTAGTTCCAAA
AGAAAATACCCCAAGCGAGACAAAATTTATTTCAAGGAAAAAGTATTCAATATTTATG
Found at i:4313404 original size:106 final size:106
Alignment explanation
Indices: 4313219--4313541 Score: 432
Period size: 106 Copynumber: 3.0 Consensus size: 106
4313209 TGTATTGTTC
* * * * * * ** *
4313219 CGAGTCCAATATCCTCCGCCGTGAAGTTAAAATTGGCTCTGGAACTAAGAAATTATTTGTTGACA
1 CGAGTCCAATATTCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* * * * * *
4313284 GCCAGCCGCCCCTTCGCTGTGAAGTTGATCTTGTGCTGTCT
66 ACTAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
*
4313325 CGAGTCCAATATTCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATTCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* *
4313390 ACTAGCTGTCCCTTCGTTATGAAGTTGAACTTGTGTTGTCT
66 ACTAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
4313431 CAAGTCCAATA-TCATTCGCTGTGAAGTTGAAATTAGCTCTGAAATTGGGAAATTGTTTGTTGAC
1 CGAGTCCAATATTC-TTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGAC
* *
4313495 AACTAGCCGTCTCTTCGTTGTGGAGTTGAACTTGTGTTGTCT
65 AACTAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
4313537 CGAGT
1 CGAGT
4313542 GGCACGATAT
Statistics
Matches: 190, Mismatches: 26, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
105 2 0.01
106 188 0.99
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (106 bp):
CGAGTCCAATATTCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
ACTAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:4314160 original size:32 final size:32
Alignment explanation
Indices: 4314119--4314206 Score: 106
Period size: 32 Copynumber: 2.8 Consensus size: 32
4314109 TTTGCATCAG
* *
4314119 GATGTTGAAT-TCCCAAAGATGCCCCAATATTC
1 GATGTTGAATCT-ACAAAGATGCCCCAACATTC
* * *
4314151 GATGTTGAATCTAAAAAAATGCCCCAACATTT
1 GATGTTGAATCTACAAAGATGCCCCAACATTC
*
4314183 GATGTTGAATCTTCAAAGATGCCC
1 GATGTTGAATCTACAAAGATGCCC
4314207 TAATTGTTCC
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
32 46 0.98
33 1 0.02
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (32 bp):
GATGTTGAATCTACAAAGATGCCCCAACATTC
Found at i:4315246 original size:69 final size:69
Alignment explanation
Indices: 4315131--4315268 Score: 204
Period size: 69 Copynumber: 2.0 Consensus size: 69
4315121 TGTCTCTCTC
* ** *
4315131 TTGATGCTCTATGATCTTCAAGTGGAGTGATTCAGTGATTTAGAAATGATTATGCTTGATCAATC
1 TTGATGCTCTATGATCTTCAAGTGAAGTGATTCAAAGATTCAGAAATGATTATGCTTGATCAATC
4315196 TCAT
66 TCAT
* * * *
4315200 TTGATGCTCTATGATCTTCGAGTGAAGTGGTTCAAAGATTCGGAAATGATTGTGCTTGATCAATC
1 TTGATGCTCTATGATCTTCAAGTGAAGTGATTCAAAGATTCAGAAATGATTATGCTTGATCAATC
4315265 TCAT
66 TCAT
4315269 AGTTTGAATC
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
69 61 1.00
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.38
Consensus pattern (69 bp):
TTGATGCTCTATGATCTTCAAGTGAAGTGATTCAAAGATTCAGAAATGATTATGCTTGATCAATC
TCAT
Found at i:4318342 original size:27 final size:27
Alignment explanation
Indices: 4318311--4318385 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 27
4318301 ATAAAAAGTT
* * *
4318311 AATAAATAAATAAATAAATTAAATTAA
1 AATAAATAAAAAAACAAATTAAATAAA
*
4318338 AATAAAGAAAAAAACAAATTAAATAAA
1 AATAAATAAAAAAACAAATTAAATAAA
*
4318365 AGATAAGATAAAGAAAGCAAA
1 A-ATAA-ATAAA-AAAACAAA
4318386 GCTAAAATAG
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
27 24 0.62
28 4 0.10
29 4 0.10
30 7 0.18
ACGTcount: A:0.72, C:0.03, G:0.07, T:0.19
Consensus pattern (27 bp):
AATAAATAAAAAAACAAATTAAATAAA
Found at i:4318429 original size:9 final size:9
Alignment explanation
Indices: 4318410--4318449 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
4318400 TAAAATAAAT
4318410 ATAAA-AAA
1 ATAAAGAAA
4318418 ATAAAGAAA
1 ATAAAGAAA
4318427 ATAAAGAAA
1 ATAAAGAAA
4318436 A-AGAAGAAA
1 ATA-AAGAAA
4318445 A-AAAG
1 ATAAAG
4318450 TATATAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
8 9 0.30
9 21 0.70
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.07
Consensus pattern (9 bp):
ATAAAGAAA
Found at i:4318478 original size:48 final size:50
Alignment explanation
Indices: 4318404--4318510 Score: 132
Period size: 48 Copynumber: 2.2 Consensus size: 50
4318394 AGTAAGTAAA
4318404 ATAAATATAAAAAAATAAAGAAAATAA-AGAAAAAGAAG-AAAAA-AAGTAT
1 ATAAATATAAAAAAATAAAGAAAATAATA-AAAAAGAAGTAAAAATAA-TAT
* * *
4318453 ATAAATA-AAACAAATAAATAAAATAATAATAAAGAAGTAAAAATAATAT
1 ATAAATATAAAAAAATAAAGAAAATAATAAAAAAGAAGTAAAAATAATAT
*
4318502 ATATATATA
1 ATAAATATA
4318511 TATATATATA
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
48 25 0.50
49 22 0.44
50 3 0.06
ACGTcount: A:0.72, C:0.01, G:0.07, T:0.21
Consensus pattern (50 bp):
ATAAATATAAAAAAATAAAGAAAATAATAAAAAAGAAGTAAAAATAATAT
Found at i:4318587 original size:2 final size:2
Alignment explanation
Indices: 4318580--4318609 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4318570 ATAATAAGAT
4318580 TA 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 TA
4318610 AAAAAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4320178 original size:3 final size:3
Alignment explanation
Indices: 4320165--4320237 Score: 98
Period size: 3 Copynumber: 24.3 Consensus size: 3
4320155 CTATAAAAAG
4320165 ATT ATTT ATT ATT ATT ATT ATT A-T ATT A-T ATT ATT ATT ATAT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT
4320210 ATT ATT A-T ATT ATT ATT ATT ATGT ATT A
1 ATT ATT ATT ATT ATT ATT ATT AT-T ATT A
4320238 ATTTACTTCG
Statistics
Matches: 64, Mismatches: 0, Indels: 12
0.84 0.00 0.16
Matches are distributed among these distances:
2 6 0.09
3 49 0.77
4 9 0.14
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:4320183 original size:13 final size:13
Alignment explanation
Indices: 4320165--4320237 Score: 91
Period size: 13 Copynumber: 5.8 Consensus size: 13
4320155 CTATAAAAAG
4320165 ATTATTTATTATT
1 ATTATTTATTATT
4320178 ATTA-TTATTA-T
1 ATTATTTATTATT
4320189 ATTA--TATTATT
1 ATTATTTATTATT
*
4320200 ATTATATATTATT
1 ATTATTTATTATT
4320213 ATTATATTATTATT
1 ATTAT-TTATTATT
*
4320227 ATTATGTATTA
1 ATTATTTATTA
4320238 ATTTACTTCG
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
10 5 0.09
11 10 0.19
12 6 0.11
13 21 0.39
14 12 0.22
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (13 bp):
ATTATTTATTATT
Found at i:4320186 original size:16 final size:16
Alignment explanation
Indices: 4320165--4320236 Score: 94
Period size: 16 Copynumber: 4.4 Consensus size: 16
4320155 CTATAAAAAG
4320165 ATTATTTATTATTATT
1 ATTATTTATTATTATT
4320181 ATTATTATATTA-TATT
1 ATTATT-TATTATTATT
4320197 ATTA-TTATATATTATT
1 ATTATTTAT-TATTATT
4320213 ATTATATTATTATTATT
1 ATTAT-TTATTATTATT
4320230 ATGTATT
1 AT-TATT
4320237 AATTTACTTC
Statistics
Matches: 50, Mismatches: 0, Indels: 11
0.82 0.00 0.18
Matches are distributed among these distances:
14 3 0.06
15 3 0.06
16 22 0.44
17 15 0.30
18 7 0.14
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (16 bp):
ATTATTTATTATTATT
Found at i:4321066 original size:14 final size:14
Alignment explanation
Indices: 4321037--4321116 Score: 53
Period size: 14 Copynumber: 5.9 Consensus size: 14
4321027 ATGTTAGATA
4321037 AAAAATAAAAGC-AT
1 AAAAATAAAA-CAAT
4321051 AAAAATAAAACAAT
1 AAAAATAAAACAAT
*
4321065 -AAGA-AAAA-AAT
1 AAAAATAAAACAAT
* * *
4321076 AACAAGAGAAATAA-
1 AAAAATA-AAACAAT
* *
4321090 ATAAATAAAAAAAT
1 AAAAATAAAACAAT
4321104 AAAAATAAAACAA
1 AAAAATAAAACAA
4321117 ATATCAAATA
Statistics
Matches: 51, Mismatches: 9, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
11 3 0.06
12 6 0.12
13 10 0.20
14 30 0.59
15 2 0.04
ACGTcount: A:0.78, C:0.05, G:0.05, T:0.12
Consensus pattern (14 bp):
AAAAATAAAACAAT
Found at i:4321071 original size:16 final size:15
Alignment explanation
Indices: 4321052--4321108 Score: 53
Period size: 16 Copynumber: 3.7 Consensus size: 15
4321042 TAAAAGCATA
4321052 AAAATAAAACAATAAG
1 AAAATAAAA-AATAAG
* *
4321068 AAAA-AAATAACAAG
1 AAAATAAAAAATAAG
*
4321082 AGAAATAAATAAATAAA
1 A-AAATAAA-AAATAAG
4321099 AAAATAAAAA
1 AAAATAAAAA
4321109 TAAAACAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
14 6 0.18
15 8 0.24
16 14 0.42
17 5 0.15
ACGTcount: A:0.79, C:0.04, G:0.05, T:0.12
Consensus pattern (15 bp):
AAAATAAAAAATAAG
Found at i:4321125 original size:16 final size:15
Alignment explanation
Indices: 4321092--4321133 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
4321082 AGAAATAAAT
4321092 AAATAAAA-AAATAA
1 AAATAAAACAAATAA
*
4321106 AAATAAAACAAATATC
1 AAATAAAACAAATA-A
*
4321122 AAATAAATCAAA
1 AAATAAAACAAA
4321134 AGAAAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 8 0.33
15 5 0.21
16 11 0.46
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.17
Consensus pattern (15 bp):
AAATAAAACAAATAA
Found at i:4322503 original size:28 final size:28
Alignment explanation
Indices: 4322472--4322563 Score: 75
Period size: 28 Copynumber: 3.4 Consensus size: 28
4322462 TCAAAAAATG
*
4322472 TTTTTAAAAACTATATAATATATATATA
1 TTTTTAAAAACTATATAATATATATAAA
* * *
4322500 -TTTTAAAAA-TGTAT-ATATTTTAAAAA
1 TTTTTAAAAACTATATAATA-TATATAAA
* *
4322526 TGTTTT-AAAACTATATATTATATATAAG
1 T-TTTTAAAAACTATATAATATATATAAA
*
4322554 TTTTCAAAAA
1 TTTTTAAAAA
4322564 TGTTTTTTAA
Statistics
Matches: 48, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
25 3 0.06
26 9 0.19
27 16 0.33
28 18 0.38
29 2 0.04
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (28 bp):
TTTTTAAAAACTATATAATATATATAAA
Found at i:4322508 original size:39 final size:39
Alignment explanation
Indices: 4322429--4322809 Score: 226
Period size: 39 Copynumber: 9.1 Consensus size: 39
4322419 AAAAAAATAA
* **
4322429 AAAAATG-TTTCAAAAACTATATAATATATA-AT-TTCA
1 AAAAATGTTTTTAAAAACTATATAATATATATATATTTT
4322465 AAAAATGTTTTTAAAAACTATATAATATATATATATTTT
1 AAAAATGTTTTTAAAAACTATATAATATATATATATTTT
* *
4322504 AAAAATGTATATATTTTAAAAATGTTTTAAAACTATATATTATATATAAGTTTT
1 AAAAATG----T-TTTTAAAAA----CT-ATA-TA-ATA-TATATAT-A-TTTT
*
4322558 CAAAAATGTTTTTTAAAAACTATAT-A-ATATATATA-TTC
1 -AAAAATGTTTTT-AAAAACTATATAATATATATATATTTT
*
4322596 AAAAATG-TTTTAAAAACTATATATTATATATA-AGTTTT
1 AAAAATGTTTTTAAAAACTATATAATATATATATA-TTTT
* *
4322634 CAAAAATG-TTTTAAAAACTAAATATTATATATA-AGTTTT
1 -AAAAATGTTTTTAAAAACTATATAATATATATATA-TTTT
4322673 CAAAAATG-TTTTAAAAACTATATATTCGATATATATATATATATAT
1 -AAAAATGTTTTTAAAAACTATATA----ATATATATATAT-T-T-T
*
4322719 ATTCAAAATGTTTTAAAAAAACTATATAATATATATATATTTT
1 A---AAAATGTTTT-TAAAAACTATATAATATATATATATTTT
* * * *
4322762 CAAAATGTTTTTTTCTGAAAACTATATAATATAAAAATATTTT
1 AAAAATG---TTTT-TAAAAACTATATAATATATATATATTTT
*
4322805 CAAAA
1 AAAAA
4322810 CTATATATTA
Statistics
Matches: 284, Mismatches: 20, Indels: 75
0.75 0.05 0.20
Matches are distributed among these distances:
35 11 0.04
36 12 0.04
37 36 0.13
38 6 0.02
39 69 0.24
40 7 0.02
41 7 0.02
42 1 0.00
43 45 0.16
44 12 0.04
45 4 0.01
46 15 0.05
47 1 0.00
48 7 0.02
49 5 0.02
50 18 0.06
51 9 0.03
52 7 0.02
53 1 0.00
54 4 0.01
55 7 0.02
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.43
Consensus pattern (39 bp):
AAAAATGTTTTTAAAAACTATATAATATATATATATTTT
Found at i:4322516 original size:17 final size:17
Alignment explanation
Indices: 4322494--4322528 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
4322484 ATATAATATA
4322494 TATATATTTTAAAAATG
1 TATATATTTTAAAAATG
4322511 TATATATTTTAAAAATG
1 TATATATTTTAAAAATG
4322528 T
1 T
4322529 TTTAAAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (17 bp):
TATATATTTTAAAAATG
Found at i:4322614 original size:76 final size:74
Alignment explanation
Indices: 4322511--4322707 Score: 281
Period size: 76 Copynumber: 2.6 Consensus size: 74
4322501 TTTAAAAATG
*
4322511 TATATATTTTAAAAATGTTTT-AAAACTATATATTATATATAAGTTTTCAAAAATGTTTTTTAAA
1 TATATATTTCAAAAATGTTTTAAAAACTATATATTATATATAAGTTTTCAAAAATG--TTTTAAA
4322575 AACT-ATATAA
64 AACTAATATAA
4322585 TATATATATTCAAAAATGTTTTAAAAACTATATATTATATATAAGTTTTCAAAAATGTTTTAAAA
1 TATATAT-TTCAAAAATGTTTTAAAAACTATATATTATATATAAGTTTTCAAAAATGTTTTAAAA
*
4322650 ACTAAATATTA
65 ACT-AATATAA
4322661 TATATAAGTTTTCAAAAATGTTTTAAAAACTATATATTCGATATATA
1 TATAT-A--TTTCAAAAATGTTTTAAAAACTATATATT--ATATATA
4322708 TATATATATA
Statistics
Matches: 112, Mismatches: 2, Indels: 12
0.89 0.02 0.10
Matches are distributed among these distances:
74 18 0.16
75 13 0.12
76 44 0.39
77 1 0.01
78 28 0.25
79 1 0.01
80 7 0.06
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.44
Consensus pattern (74 bp):
TATATATTTCAAAAATGTTTTAAAAACTATATATTATATATAAGTTTTCAAAAATGTTTTAAAAA
CTAATATAA
Found at i:4322879 original size:81 final size:84
Alignment explanation
Indices: 4322794--4322954 Score: 188
Period size: 81 Copynumber: 1.9 Consensus size: 84
4322784 TATATAATAT
* ** *
4322794 AAAAATATTTTC-AAAACTATATATTATATATATTTTAGAAATGTTTTCATAAACTATA-TA-A-
1 AAAAACATTTTCGAAAACTATATATTATAT-TATTTTA-AAACATTTTCAAAAACTATACTATAT
4322855 TA-TATATATATATATTTTCG
64 TACTATATATATATATTTTCG
* * * *
4322875 AAAAACGTTTTCTGAAAATTATATATTATATTTTTTTAAAACATTTTCAAAAATTATACTATATT
1 AAAAACATTTTC-GAAAACTATATATTATATTATTTTAAAACATTTTCAAAAACTATACTATATT
4322940 ACTATATATATATAT
65 ACTATATATATATAT
4322955 ATATAACAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
81 26 0.39
82 8 0.12
83 17 0.26
84 2 0.03
85 13 0.20
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (84 bp):
AAAAACATTTTCGAAAACTATATATTATATTATTTTAAAACATTTTCAAAAACTATACTATATTA
CTATATATATATATTTTCG
Found at i:4322928 original size:35 final size:37
Alignment explanation
Indices: 4322857--4322938 Score: 96
Period size: 36 Copynumber: 2.2 Consensus size: 37
4322847 CTATATAATA
* *
4322857 TATATATATATATTTTCGAAAAACGTTTTCTGAAAAT
1 TATATATATATATTTTCGAAAAACATTTTCTAAAAAT
***
4322894 TATATAT-TATATTTTTTTAAAACATTTTC-AAAAAT
1 TATATATATATATTTTCGAAAAACATTTTCTAAAAAT
4322929 TATACTATAT
1 TATA-TATAT
4322939 TACTATATAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
35 9 0.24
36 21 0.55
37 8 0.21
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (37 bp):
TATATATATATATTTTCGAAAAACATTTTCTAAAAAT
Found at i:4326249 original size:15 final size:14
Alignment explanation
Indices: 4326216--4326252 Score: 51
Period size: 12 Copynumber: 2.7 Consensus size: 14
4326206 AGATCAATAT
4326216 TTTTGCATC-TGCA
1 TTTTGCATCTTGCA
4326229 -TTTGCATCTTTGCA
1 TTTTGCATC-TTGCA
4326243 TTTTGCATCT
1 TTTTGCATCT
4326253 GTATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 8 0.38
14 5 0.24
15 8 0.38
ACGTcount: A:0.14, C:0.22, G:0.14, T:0.51
Consensus pattern (14 bp):
TTTTGCATCTTGCA
Found at i:4328811 original size:38 final size:37
Alignment explanation
Indices: 4328764--4328836 Score: 94
Period size: 37 Copynumber: 1.9 Consensus size: 37
4328754 TTTGATGTTG
* *
4328764 TTTCTCTCAAAACAAAATATT-ATCTCTCTTGAGACAAA
1 TTTCCCTCAAAA-AAAAT-TTCATCTCACTTGAGACAAA
*
4328802 TTTCCCTCAAAATAAATTTCATCTCACTTGAGACA
1 TTTCCCTCAAAAAAAATTTCATCTCACTTGAGACA
4328837 TAACCCATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 2 0.06
37 18 0.58
38 11 0.35
ACGTcount: A:0.37, C:0.23, G:0.05, T:0.34
Consensus pattern (37 bp):
TTTCCCTCAAAAAAAATTTCATCTCACTTGAGACAAA
Found at i:4328956 original size:31 final size:31
Alignment explanation
Indices: 4328882--4328992 Score: 97
Period size: 31 Copynumber: 3.7 Consensus size: 31
4328872 ATTTTATCCC
* * *
4328882 TTAAGA-CAGTTTCTTTTG-AAGAAAAATCT
1 TTAAGATCTGTTTCTCTTGAAAAAAAAATCT
* * *
4328911 TTGAG-TATGTTTCTCTTGAAAAAAAAAGTTT
1 TTAAGATCTGTTTCTCTTGAAAAAAAAA-TCT
* *
4328942 TTAAG-TCTGTTTCTCTTGAAACAAACATCT
1 TTAAGATCTGTTTCTCTTGAAAAAAAAATCT
*
4328972 TTAAGATC-GTTTCCCTTGAAA
1 TTAAGATCTGTTTCTCTTGAAA
4328993 CAAATTTTGT
Statistics
Matches: 66, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
29 13 0.20
30 26 0.39
31 27 0.41
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.40
Consensus pattern (31 bp):
TTAAGATCTGTTTCTCTTGAAAAAAAAATCT
Found at i:4328984 original size:30 final size:30
Alignment explanation
Indices: 4328882--4328996 Score: 89
Period size: 30 Copynumber: 3.9 Consensus size: 30
4328872 ATTTTATCCC
*
4328882 TTAAGA-CAGTTTCTTTTGAAGA-AAAATCT
1 TTAAGATCAGTTTCTCTTGAA-ACAAAATCT
* * *
4328911 TTGAG-T-ATGTTTCTCTTGAAAAAAAAAGTTT
1 TTAAGATCA-GTTTCTCTTG-AAACAAAA-TCT
*
4328942 TTAAG-TCTGTTTCTCTTGAAACAAACATCT
1 TTAAGATCAGTTTCTCTTGAAACAAA-ATCT
*
4328972 TTAAGATC-GTTTCCCTTGAAACAAA
1 TTAAGATCAGTTTCTCTTGAAACAAA
4328997 TTTTGTTTCC
Statistics
Matches: 70, Mismatches: 8, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
28 1 0.01
29 14 0.20
30 35 0.50
31 20 0.29
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (30 bp):
TTAAGATCAGTTTCTCTTGAAACAAAATCT
Found at i:4329390 original size:134 final size:130
Alignment explanation
Indices: 4329082--4329442 Score: 370
Period size: 134 Copynumber: 2.7 Consensus size: 130
4329072 GATAGCCTAC
* * * * *
4329082 CATCCTCATCACGTAGGAACGTGTCATCTCCCAACTAGACCTCCTCATCACGTAGGAGCCGTGTC
1 CATCCTCATCACGTAAGATCGTGTCATCTCCCGACCAGACCTCCTCATCACGTAGGAGTCGTGTC
* * ** **** *
4329147 ACCCCT-TATAACCAGTCATCCTCATCACGTAGGAACTGTGTTATCATCCCTAAAGATGGTTTAC
66 ACCCCTAGATAACCAGTCATCATCATCACGTAGGAACCATGTTATCATCCCTAAAGATGACAGAA
* * *
4329211 CATCCTCGTCACATAAGAATTGTGTCATC-CCCTGACCAGACCTCCTCATCACGTAGGAGTCGTG
1 CATCCTCATCACGTAAG-ATCGTGTCATCTCCC-GACCAGACCTCCTCATCACGTAGGAGTCGTG
* * *
4329275 TCACCCCTAGATAACCAGTCGTCATCATCGCGTAGGAACCATGTTATCACCCTTCCTAAAGATAG
64 TCACCCCTAGATAACCAGTCATCATCATCACGTAGGAACCATGTTATCA---TCCCTAAAGAT-G
4329340 ACAGAA
125 ACAGAA
* * * *
4329346 C-TCTTCATCACGTATGAGTCGTGTCATCTACCGACCAGATCTCCTCATCACGTAGGAGTCGTGT
1 CATCCTCATCACGTAAGA-TCGTGTCATCTCCCGACCAGACCTCCTCATCACGTAGGAGTCGTGT
* * * *
4329410 CACCCTTAGA-AGACCAGACCTCTTCATCACGTA
65 CACCCCTAGATA-ACCAGTCATCATCATCACGTA
4329443 TGAGTCGTGT
Statistics
Matches: 190, Mismatches: 32, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
129 17 0.09
130 45 0.24
131 34 0.18
133 2 0.01
134 87 0.46
135 5 0.03
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.25
Consensus pattern (130 bp):
CATCCTCATCACGTAAGATCGTGTCATCTCCCGACCAGACCTCCTCATCACGTAGGAGTCGTGTC
ACCCCTAGATAACCAGTCATCATCATCACGTAGGAACCATGTTATCATCCCTAAAGATGACAGAA
Found at i:4329405 original size:40 final size:40
Alignment explanation
Indices: 4329341--4329494 Score: 200
Period size: 40 Copynumber: 3.8 Consensus size: 40
4329331 TAAAGATAGA
* * *
4329341 CAGAACTCTTCATCACGTATGAGTCGTGTCATCTACCGAC
1 CAGATCTCCTCATCACGTAGGAGTCGTGTCATCTACCGAC
* **
4329381 CAGATCTCCTCATCACGTAGGAGTCGTGTCACCCTTAGAAGAC
1 CAGATCTCCTCATCACGTAGGAGTCGTGTCA-TC-TA-CCGAC
* * *
4329424 CAGACCTCTTCATCACGTATGAGTCGTGTCATCTACCGAC
1 CAGATCTCCTCATCACGTAGGAGTCGTGTCATCTACCGAC
4329464 CAGATCTCCTCATCACGTAGGAGTCGTGTCA
1 CAGATCTCCTCATCACGTAGGAGTCGTGTCA
4329495 CCCTTAGAAG
Statistics
Matches: 96, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
40 59 0.61
41 3 0.03
42 3 0.03
43 31 0.32
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (40 bp):
CAGATCTCCTCATCACGTAGGAGTCGTGTCATCTACCGAC
Found at i:4329485 original size:83 final size:83
Alignment explanation
Indices: 4329341--4329539 Score: 364
Period size: 83 Copynumber: 2.4 Consensus size: 83
4329331 TAAAGATAGA
*
4329341 CAGAACTCTTCATCACGTATGAGTCGTGTCATCTACCGACCAGATCTCCTCATCACGTAGGAGTC
1 CAGACCTCTTCATCACGTATGAGTCGTGTCATCTACCGACCAGATCTCCTCATCACGTAGGAGTC
4329406 GTGTCACCCTTAGAAGAC
66 GTGTCACCCTTAGAAGAC
4329424 CAGACCTCTTCATCACGTATGAGTCGTGTCATCTACCGACCAGATCTCCTCATCACGTAGGAGTC
1 CAGACCTCTTCATCACGTATGAGTCGTGTCATCTACCGACCAGATCTCCTCATCACGTAGGAGTC
4329489 GTGTCACCCTTAGAAGAC
66 GTGTCACCCTTAGAAGAC
*
4329507 CAGACCTCTTCATCACGTATTAG-CAGTGTCATC
1 CAGACCTCTTCATCACGTATGAGTC-GTGTCATC
4329540 CCCACCAACA
Statistics
Matches: 113, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
82 1 0.01
83 112 0.99
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.26
Consensus pattern (83 bp):
CAGACCTCTTCATCACGTATGAGTCGTGTCATCTACCGACCAGATCTCCTCATCACGTAGGAGTC
GTGTCACCCTTAGAAGAC
Found at i:4329537 original size:43 final size:43
Alignment explanation
Indices: 4329244--4329525 Score: 220
Period size: 43 Copynumber: 6.5 Consensus size: 43
4329234 GTCATCCCCT
*
4329244 GACCAGACCTCCTCATCACGTAGGAGTCGTGTCACCCCTAGATA
1 GACCAGACCTCCTCATCACGTAGGAGTCGTGTCACCCTTAGA-A
* * * * ** *
4329288 -ACCAGTCGTCATCATCGCGTAGGAACCATGTTATCACCCTTCCTAAAGATA
1 GACCAGACCTCCTCATCACGTAGGAGTC--G-TGTCACCC-T--T--AGA-A
* * * * **
4329339 GA-CAGAACTCTTCATCACGTATGAGTCGTGTCA-TC-TA-CC
1 GACCAGACCTCCTCATCACGTAGGAGTCGTGTCACCCTTAGAA
*
4329378 GACCAGATCTCCTCATCACGTAGGAGTCGTGTCACCCTTAGAA
1 GACCAGACCTCCTCATCACGTAGGAGTCGTGTCACCCTTAGAA
* * * **
4329421 GACCAGACCTCTTCATCACGTATGAGTCGTGTCA-TC-TA-CC
1 GACCAGACCTCCTCATCACGTAGGAGTCGTGTCACCCTTAGAA
*
4329461 GACCAGATCTCCTCATCACGTAGGAGTCGTGTCACCCTTAGAA
1 GACCAGACCTCCTCATCACGTAGGAGTCGTGTCACCCTTAGAA
*
4329504 GACCAGACCTCTTCATCACGTA
1 GACCAGACCTCCTCATCACGTA
4329526 TTAGCAGTGT
Statistics
Matches: 182, Mismatches: 40, Indels: 33
0.71 0.16 0.13
Matches are distributed among these distances:
39 2 0.01
40 59 0.32
41 5 0.03
42 5 0.03
43 73 0.40
45 1 0.01
46 7 0.04
47 1 0.01
48 4 0.02
49 2 0.01
51 22 0.12
52 1 0.01
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.24
Consensus pattern (43 bp):
GACCAGACCTCCTCATCACGTAGGAGTCGTGTCACCCTTAGAA
Found at i:4329703 original size:3 final size:3
Alignment explanation
Indices: 4329695--4329725 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
4329685 CAAAAAGATT
4329695 TTA TTA TTA TTA TTA TTA TTA TTA TGTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
4329726 ATTTACAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:4332112 original size:17 final size:17
Alignment explanation
Indices: 4332083--4332115 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
4332073 ATACTTATTT
4332083 ATATAAAATATAATATA
1 ATATAAAATATAATATA
4332100 ATATGAAAA-ATAATAT
1 ATAT-AAAATATAATAT
4332116 TATAATCTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
ATATAAAATATAATATA
Found at i:4332206 original size:15 final size:16
Alignment explanation
Indices: 4332181--4332223 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
4332171 CTCAAAATTA
*
4332181 AATATTATTTTA-AAT
1 AATAATATTTTACAAT
*
4332196 AATTATATTTTTACAAT
1 AATAATA-TTTTACAAT
4332213 AATAATATTTT
1 AATAATATTTT
4332224 CACCTTATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 5 0.22
16 9 0.39
17 9 0.39
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (16 bp):
AATAATATTTTACAAT
Found at i:4332213 original size:17 final size:16
Alignment explanation
Indices: 4332188--4332223 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
4332178 TTAAATATTA
*
4332188 TTTTAAATAATTATAT
1 TTTTAAATAATAATAT
4332204 TTTTACAATAATAATAT
1 TTTTA-AATAATAATAT
4332221 TTT
1 TTT
4332224 CACCTTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTTAAATAATAATAT
Found at i:4335304 original size:18 final size:18
Alignment explanation
Indices: 4335278--4335320 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
4335268 TTTGATATCA
*
4335278 ATACTCAGGTGATTATAG
1 ATACCCAGGTGATTATAG
*
4335296 ATACCCAGGTGATTATCG
1 ATACCCAGGTGATTATAG
4335314 ATACCCA
1 ATACCCA
4335321 AGGATCTAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.28
Consensus pattern (18 bp):
ATACCCAGGTGATTATAG
Done.