Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 117 of 135
Found at i:42589735 original size:17 final size:18
Alignment explanation
Indices: 42589709--42589747 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
42589699 TTAAAATTCA
42589709 AAAAATAT-AAAATTATTT
1 AAAAATATAAAAATTA-TT
42589727 AAAAA-ATAAAAATTATT
1 AAAAATATAAAAATTATT
42589744 AAAA
1 AAAA
42589748 TTATTTAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAAATATAAAAATTATT
Found at i:42589738 original size:18 final size:18
Alignment explanation
Indices: 42589708--42589747 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
42589698 TTTAAAATTC
42589708 AAAAAATATAAAATTATTT
1 AAAAAATATAAAATTA-TT
42589727 AAAAAATA-AAAATTATT
1 AAAAAATATAAAATTATT
42589744 AAAA
1 AAAA
42589748 TTATTTAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 6 0.29
18 7 0.33
19 8 0.38
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAAAATATAAAATTATT
Found at i:42589770 original size:27 final size:26
Alignment explanation
Indices: 42589709--42589774 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 26
42589699 TTAAAATTCA
42589709 AAAAATA-TAAAATTATTTAAAAAAT
1 AAAAATATTAAAATTATTTAAAAAAT
**
42589734 AAAAATTATTAAAATTATTTAAAGCAT
1 AAAAA-TATTAAAATTATTTAAAAAAT
42589761 ACAAAATATTAAAA
1 A-AAAATATTAAAA
42589775 AATATATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
25 5 0.14
26 2 0.06
27 25 0.69
28 4 0.11
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.32
Consensus pattern (26 bp):
AAAAATATTAAAATTATTTAAAAAAT
Found at i:42591797 original size:16 final size:18
Alignment explanation
Indices: 42591768--42591802 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
42591758 AAACAAATTT
42591768 TTAAAATATATATTTTTA
1 TTAAAATATATATTTTTA
42591786 TTAAAAT-T-TATTTTTA
1 TTAAAATATATATTTTTA
42591802 T
1 T
42591803 AATATATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 1 0.06
18 7 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTAAAATATATATTTTTA
Found at i:42592738 original size:3 final size:3
Alignment explanation
Indices: 42592730--42592975 Score: 492
Period size: 3 Copynumber: 82.0 Consensus size: 3
42592720 NNNNNNNNNN
42592730 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
42592778 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
42592826 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
42592874 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
42592922 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
42592970 ATA ATA
1 ATA ATA
42592976 GACGGGGTTA
Statistics
Matches: 243, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 243 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:42593408 original size:41 final size:42
Alignment explanation
Indices: 42593355--42593439 Score: 163
Period size: 41 Copynumber: 2.0 Consensus size: 42
42593345 TAAAAAAAAG
42593355 TTTCATCATTTTTGTTTTAAAAAAAACAGAGA-AAAACTCTC
1 TTTCATCATTTTTGTTTTAAAAAAAACAGAGAGAAAACTCTC
42593396 TTTCATCATTTTTGTTTTAAAAAAAACAGAGAGAAAACTCTC
1 TTTCATCATTTTTGTTTTAAAAAAAACAGAGAGAAAACTCTC
42593438 TT
1 TT
42593440 CTTCCCTCTC
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 32 0.74
42 11 0.26
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (42 bp):
TTTCATCATTTTTGTTTTAAAAAAAACAGAGAGAAAACTCTC
Found at i:42594689 original size:40 final size:40
Alignment explanation
Indices: 42594664--42595515 Score: 523
Period size: 42 Copynumber: 20.8 Consensus size: 40
42594654 GATTGGTTGT
*
42594664 GATCTGTTCCACTACCACTTAGGGAGATAAGACTTGATGC
1 GATCTGCTCCACTACCACTTAGGGAGATAAGACTTGATGC
* ** **
42594704 GATCTGCTCCGCTACTGCTTAGGGAGATAAGATCTGTGATTTT
1 GATCTGCTCCACTACCACTTAGGGAGATAAGA-CT-TGA-TGC
* * * *
42594747 G-TCTACTCCGCTACTACTTAGGGAGACAAGACTTGATGC
1 GATCTGCTCCACTACCACTTAGGGAGATAAGACTTGATGC
* ** * *
42594786 GATTTGCTCCACTACTGCTTAGAGAGATAAGA-TCTGTAGTTC
1 GATCTGCTCCACTACCACTTAGGGAGATAAGACT-TG-A-TGC
* **
42594828 TG-TCTACTCCACTACTGCTTAGGGAGATAAGACTTGATGC
1 -GATCTGCTCCACTACCACTTAGGGAGATAAGACTTGATGC
* ** * *
42594868 GATATGCTCCACTACTGCTTAGAGAGATAAGA-TCTGTAGTTC
1 GATCTGCTCCACTACCACTTAGGGAGATAAGACT-TG-A-TGC
* **
42594910 TG-TCTACTCCACTACTGCTTAGGGAGATAAGACTTGATGC
1 -GATCTGCTCCACTACCACTTAGGGAGATAAGACTTGATGC
* ** * *
42594950 GATATGCTCCACTACTGCTTAGAGAGATAAGA-TCTGTAGTTC
1 GATCTGCTCCACTACCACTTAGGGAGATAAGACT-TG-A-TGC
* **
42594992 TG-TCTACTCCACTACTGCTTAGGGAGATAAGACTTGATGC
1 -GATCTGCTCCACTACCACTTAGGGAGATAAGACTTGATGC
* ** * *
42595032 GATATGCTCCACTACTGCTTAGAGAGATAAGA-TCTGTAGTTC
1 GATCTGCTCCACTACCACTTAGGGAGATAAGACT-TG-A-TGC
* **
42595074 TG-TCTACTCCACTACTGCTTAGGGAGATAAGACTTGATGC
1 -GATCTGCTCCACTACCACTTAGGGAGATAAGACTTGATGC
* ** * *
42595114 GATATGCTCCACTACTGCTTAGAGAGATAAGA-TCTGTAGTTC
1 GATCTGCTCCACTACCACTTAGGGAGATAAGACT-TG-A-TGC
* **
42595156 TG-TCTACTCCACTACTGCTTAGGGAGATAAGACTTGATGC
1 -GATCTGCTCCACTACCACTTAGGGAGATAAGACTTGATGC
* ** * *
42595196 GATATGCTCCACTACTGCTTAGAGAGATAAGA-TCTGTAGTTC
1 GATCTGCTCCACTACCACTTAGGGAGATAAGACT-TG-A-TGC
* **
42595238 TG-TCTACTCCACTACTGCTTAGGGAGATAAGACTTGATGC
1 -GATCTGCTCCACTACCACTTAGGGAGATAAGACTTGATGC
* ** * *
42595278 GATATGCTCCACTACTGCTTAGAGAGATAAGA-TCTGTAGTTC
1 GATCTGCTCCACTACCACTTAGGGAGATAAGACT-TG-A-TGC
** * *
42595320 TG-TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTC
1 -GATCTGCTCCACTACCACTTAGGGAGATAAGA-CT-TGATGC
* **
42595362 TG-TCTACTCCACTACTGCTTAGGGAGATAAGACTTGATGC
1 -GATCTGCTCCACTACCACTTAGGGAGATAAGACTTGATGC
* ** * *
42595402 GATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTC
1 GATCTGCTCCACTACCACTTAGGGAGATAAGA-CT-T-GATGC
* ** *
42595445 G-TCTGCTCCGCTACTGCTTAGGGAGATAAGACTTGATGT
1 GATCTGCTCCACTACCACTTAGGGAGATAAGACTTGATGC
* *
42595484 GATCTGCTCCATTACTACTTAGGGAGATAAGA
1 GATCTGCTCCACTACCACTTAGGGAGATAAGA
42595516 TCTGTAATCT
Statistics
Matches: 678, Mismatches: 83, Indels: 102
0.79 0.10 0.12
Matches are distributed among these distances:
39 19 0.03
40 305 0.45
41 23 0.03
42 309 0.46
43 19 0.03
44 3 0.00
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.31
Consensus pattern (40 bp):
GATCTGCTCCACTACCACTTAGGGAGATAAGACTTGATGC
Found at i:42595520 original size:82 final size:82
Alignment explanation
Indices: 42594671--42595515 Score: 1287
Period size: 82 Copynumber: 10.3 Consensus size: 82
42594661 TGTGATCTGT
** * * *
42594671 TCCACTACCACTTAGGGAGATAAGACTTGATGCGATCTGCTCCGCTACTGCTTAGGGAGATAAGA
1 TCCACTACTGCTTAGGGAGATAAGACTTGATGCGATATGCTCCACTACTGCTTAGAGAGATAAGA
*
42594736 TCTGT-GATTTTGTCTAC
66 TCTGTAG-TTCTGTCTAC
* * * *
42594753 TCCGCTACTACTTAGGGAGACAAGACTTGATGCGATTTGCTCCACTACTGCTTAGAGAGATAAGA
1 TCCACTACTGCTTAGGGAGATAAGACTTGATGCGATATGCTCCACTACTGCTTAGAGAGATAAGA
42594818 TCTGTAGTTCTGTCTAC
66 TCTGTAGTTCTGTCTAC
42594835 TCCACTACTGCTTAGGGAGATAAGACTTGATGCGATATGCTCCACTACTGCTTAGAGAGATAAGA
1 TCCACTACTGCTTAGGGAGATAAGACTTGATGCGATATGCTCCACTACTGCTTAGAGAGATAAGA
42594900 TCTGTAGTTCTGTCTAC
66 TCTGTAGTTCTGTCTAC
42594917 TCCACTACTGCTTAGGGAGATAAGACTTGATGCGATATGCTCCACTACTGCTTAGAGAGATAAGA
1 TCCACTACTGCTTAGGGAGATAAGACTTGATGCGATATGCTCCACTACTGCTTAGAGAGATAAGA
42594982 TCTGTAGTTCTGTCTAC
66 TCTGTAGTTCTGTCTAC
42594999 TCCACTACTGCTTAGGGAGATAAGACTTGATGCGATATGCTCCACTACTGCTTAGAGAGATAAGA
1 TCCACTACTGCTTAGGGAGATAAGACTTGATGCGATATGCTCCACTACTGCTTAGAGAGATAAGA
42595064 TCTGTAGTTCTGTCTAC
66 TCTGTAGTTCTGTCTAC
42595081 TCCACTACTGCTTAGGGAGATAAGACTTGATGCGATATGCTCCACTACTGCTTAGAGAGATAAGA
1 TCCACTACTGCTTAGGGAGATAAGACTTGATGCGATATGCTCCACTACTGCTTAGAGAGATAAGA
42595146 TCTGTAGTTCTGTCTAC
66 TCTGTAGTTCTGTCTAC
42595163 TCCACTACTGCTTAGGGAGATAAGACTTGATGCGATATGCTCCACTACTGCTTAGAGAGATAAGA
1 TCCACTACTGCTTAGGGAGATAAGACTTGATGCGATATGCTCCACTACTGCTTAGAGAGATAAGA
42595228 TCTGTAGTTCTGTCTAC
66 TCTGTAGTTCTGTCTAC
42595245 TCCACTACTGCTTAGGGAGATAAGACTTGATGCGATATGCTCCACTACTGCTTAGAGAGATAAGA
1 TCCACTACTGCTTAGGGAGATAAGACTTGATGCGATATGCTCCACTACTGCTTAGAGAGATAAGA
*
42595310 TCTGTAGTTCTGTCTGC
66 TCTGTAGTTCTGTCTAC
* * * * *
42595327 TCCACTACTGCTTAGGGAGATAAGATCTGTGGTTCTG-TCTACTCCACTACTGCTTAGGGAGATA
1 TCCACTACTGCTTAGGGAGATAAGA-CT-TGATGC-GATATGCTCCACTACTGCTTAGAGAGATA
*
42595391 AGA-CT-T-GATGC-GATCTAC
63 AGATCTGTAG-TTCTG-TCTAC
* * * * *
42595409 TCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTCG-TCTGCTCCGCTACTGCTTAGGGAGATA
1 TCCACTACTGCTTAGGGAGATAAGA-CT-T-GATGCGATATGCTCCACTACTGCTTAGAGAGATA
* * *
42595473 AGA-CT-T-GATGTGATCTGC
63 AGATCTGTAGTTCTG-TCTAC
* *
42595491 TCCATTACTACTTAGGGAGATAAGA
1 TCCACTACTGCTTAGGGAGATAAGA
42595516 TCTGTAATCT
Statistics
Matches: 727, Mismatches: 28, Indels: 16
0.94 0.04 0.02
Matches are distributed among these distances:
81 2 0.00
82 684 0.94
83 9 0.01
84 31 0.04
85 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.31
Consensus pattern (82 bp):
TCCACTACTGCTTAGGGAGATAAGACTTGATGCGATATGCTCCACTACTGCTTAGAGAGATAAGA
TCTGTAGTTCTGTCTAC
Found at i:42595684 original size:44 final size:44
Alignment explanation
Indices: 42595504--42595688 Score: 126
Period size: 44 Copynumber: 4.2 Consensus size: 44
42595494 ATTACTACTT
* *
42595504 AGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCC
1 AGGGAGATAAGATCTGTAGTCTTCAATCTACTCCACTGCTGCCC
* * * * * *
42595548 AGGGAGAT-AGAACTACTAG-CTTCAATGTACTCCATTG-TAATCTC
1 AGGGAGATAAGATCT-GTAGTCTTCAATCTACTCCACTGCT--GCCC
* * * * * * * **
42595592 AGGGAGGTAAAATCCGCTA-TCTTCGACCTGCTCCACTACTGCTT
1 AGGGAGATAAGATCTG-TAGTCTTCAATCTACTCCACTGCTGCCC
* * *
42595636 AGGGAGATAAGATCTGTAGTCTTCGATCTATTCCACTGTTGCCC
1 AGGGAGATAAGATCTGTAGTCTTCAATCTACTCCACTGCTGCCC
42595680 AGGGAGATA
1 AGGGAGATA
42595689 GAACTACCAG
Statistics
Matches: 102, Mismatches: 31, Indels: 16
0.68 0.21 0.11
Matches are distributed among these distances:
42 1 0.01
43 22 0.22
44 61 0.60
45 17 0.17
46 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (44 bp):
AGGGAGATAAGATCTGTAGTCTTCAATCTACTCCACTGCTGCCC
Found at i:42595789 original size:130 final size:131
Alignment explanation
Indices: 42595487--42595794 Score: 510
Period size: 132 Copynumber: 2.4 Consensus size: 131
42595477 TTGATGTGAT
* * *
42595487 CTGCTCCATTACTACTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGG
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCGATCTATTCCACTGCTGCCCAGGG
* * * *
42595552 AGATAGAACTACTAGCTTCAATGTACTCCATTGTAATCTCAGGGAGGTAAAATCCGCTATCTTCG
66 AGATAGAACTACCAGCTTCAATGTACTCAACTGTAA-CTCAGGGAGGTAAAATCCGCCATCTTCG
42595617 AC
130 AC
* *
42595619 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAGTCTTCGATCTATTCCACTGTTGCCCAGGG
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCGATCTATTCCACTGCTGCCCAGGG
42595684 AGATAGAACTACCAGCTTCAATGTACTCAACTGTAA-TCAGGGAGGTAAAATCCGCCATCTTCGA
66 AGATAGAACTACCAGCTTCAATGTACTCAACTGTAACTCAGGGAGGTAAAATCCGCCATCTTCGA
42595748 C
131 C
*
42595749 CTGCTCCACTACTGCTTAGGAAGATAAGATCTGTAATCTTCGATCT
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCGATCT
42595795 GCTTCGCTGT
Statistics
Matches: 165, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
130 72 0.44
132 93 0.56
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (131 bp):
CTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCGATCTATTCCACTGCTGCCCAGGG
AGATAGAACTACCAGCTTCAATGTACTCAACTGTAACTCAGGGAGGTAAAATCCGCCATCTTCGA
C
Found at i:42595825 original size:45 final size:44
Alignment explanation
Indices: 42595774--42596273 Score: 277
Period size: 45 Copynumber: 11.3 Consensus size: 44
42595764 TTAGGAAGAT
42595774 AAGATCTGTAATCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGC
1 AAGATCTGT-ATCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGC
* * * *
42595819 AAGATCTGATATCTT-TAGTCTGCTCCGCTGTCAGTGCAGGAAAGC
1 AAGATCTG-TATCTTCGA-TCTGCTTCGCTGTCAGTACAGGAAGGC
* * * *
42595864 AAGA-CTAGTTTCTTCGATCTGCTTCGCCGTCGGTACAGAAAGGC
1 AAGATCT-GTATCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGC
* * * **
42595908 AAGATCTGCTATCTT-TAGTTTGCTCCGCTGTCAGTGTAGGAAGGC
1 AAGATCTG-TATCTTCGA-TCTGCTTCGCTGTCAGTACAGGAAGGC
*
42595953 AAGA-CTAGCT-TCTTCGATCTGCTTCGCCGTC-GATACAGGAAGGC
1 AAGATCT-G-TATCTTCGATCTGCTTCGCTGTCAG-TACAGGAAGGC
* * * * * *
42595997 AAGATCTACTATCTT-TAGTCTGCTCCACTGTCTGTGCAGGAAGGC
1 AAGATCT-GTATCTTCGA-TCTGCTTCGCTGTCAGTACAGGAAGGC
* *
42596042 AAGA-CTGGCT-TCTTCGATCTGCTTCGCCGTTAGTACAGGAAGGC
1 AAGATCT-G-TATCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGC
* * * * * * *
42596086 AAGATTTGCTATCTTCAACCAGC-TCTGCT-ACA-AACAAGAGAGGC
1 AAGATCTG-TATCTTCGATCTGCTTC-GCTGTCAGTACAGGA-AGGC
* * * *
42596130 AAGGT-T-TGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGC
1 AAGATCTGTATCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGC
* * * * *
42596172 AAGATCTGTTGTCTTC-AACTCGC-TCTACT-ACA--ACCAAGAGAGGC
1 AAGATCTG-TATCTTCGATCT-GCTTC-GCTGTCAGTA-CAGGA-AGGC
* * * *
42596216 AAGGT-T-TGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGC
1 AAGATCTGTATCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGC
42596258 AAGATCTGTTATCTTC
1 AAGATCTG-TATCTTC
42596274 AACCAGCTCT
Statistics
Matches: 343, Mismatches: 74, Indels: 76
0.70 0.15 0.15
Matches are distributed among these distances:
41 24 0.07
42 27 0.08
43 22 0.06
44 127 0.37
45 141 0.41
46 2 0.01
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (44 bp):
AAGATCTGTATCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGC
Found at i:42595900 original size:89 final size:89
Alignment explanation
Indices: 42595785--42596100 Score: 474
Period size: 89 Copynumber: 3.6 Consensus size: 89
42595775 AGATCTGTAA
*
42595785 TCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGATATCTTTAGTCTGCTCCGCTGT
1 TCTTCGATCTGCTTCGCCGTCAGTACAGGAAGGCAAGATCTGATATCTTTAGTCTGCTCCGCTGT
* *
42595850 CAGTGCAGGAAAGCAAGACTAGTT
66 CAGTGCAGGAAGGCAAGACTAGCT
* * * *
42595874 TCTTCGATCTGCTTCGCCGTCGGTACAGAAAGGCAAGATCTGCTATCTTTAGTTTGCTCCGCTGT
1 TCTTCGATCTGCTTCGCCGTCAGTACAGGAAGGCAAGATCTGATATCTTTAGTCTGCTCCGCTGT
*
42595939 CAGTGTAGGAAGGCAAGACTAGCT
66 CAGTGCAGGAAGGCAAGACTAGCT
*
42595963 TCTTCGATCTGCTTCGCCGTC-GATACAGGAAGGCAAGATCT-ACTATCTTTAGTCTGCTCCACT
1 TCTTCGATCTGCTTCGCCGTCAG-TACAGGAAGGCAAGATCTGA-TATCTTTAGTCTGCTCCGCT
* *
42596026 GTCTGTGCAGGAAGGCAAGACTGGCT
64 GTCAGTGCAGGAAGGCAAGACTAGCT
* * *
42596052 TCTTCGATCTGCTTCGCCGTTAGTACAGGAAGGCAAGATTTGCTATCTT
1 TCTTCGATCTGCTTCGCCGTCAGTACAGGAAGGCAAGATCTGATATCTT
42596101 CAACCAGCTC
Statistics
Matches: 205, Mismatches: 18, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
88 1 0.00
89 203 0.99
90 1 0.00
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.30
Consensus pattern (89 bp):
TCTTCGATCTGCTTCGCCGTCAGTACAGGAAGGCAAGATCTGATATCTTTAGTCTGCTCCGCTGT
CAGTGCAGGAAGGCAAGACTAGCT
Found at i:42596168 original size:86 final size:86
Alignment explanation
Indices: 42596052--42596523 Score: 730
Period size: 86 Copynumber: 5.5 Consensus size: 86
42596042 AAGACTGGCT
* * * * * * *
42596052 TCTTCGATCTGCTTCGCCGTTAGTACAGGAAGGCAAGATTTGCTATCTTCAACCAGCTCTGCTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTAC
* *
42596117 AAACAAGAGAGGCAAGGTTTG
66 AACCGAGAGAGGCAAGGTTTG
*
42596138 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACTC-GCTCTACTA
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAAC-CAGCTCTGCTA
*
42596202 CAACCAAGAGAGGCAAGGTTTG
65 CAACCGAGAGAGGCAAGGTTTG
*
42596224 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTATCTTCAACCAGCTCTGCTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTAC
*
42596289 AACCGAGAGAGGTAAGGTTTG
66 AACCGAGAGAGGCAAGGTTTG
* ** * *
42596310 TCTTCGATCTGCTTCACTGTCAATGCATAAAGACAAGATCTGTTGTATTCAACCAGCTCTGCTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTAC
*
42596375 AATCGAGAGAGGCAAGGTTTG
66 AACCGAGAGAGGCAAGGTTTG
* *
42596396 TCTTCGATCTGCTTCGTTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTACTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTAC
42596461 AACCGAGAGAGGCAAGGTTTG
66 AACCGAGAGAGGCAAGGTTTG
*
42596482 TCTTCGATCTGTTTCGCTGTCAATGCAGGAAGGCAAGATCTG
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTG
42596524 GTAATTTCTT
Statistics
Matches: 353, Mismatches: 31, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
85 1 0.00
86 351 0.99
87 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.28
Consensus pattern (86 bp):
TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTAC
AACCGAGAGAGGCAAGGTTTG
Found at i:42597749 original size:5 final size:5
Alignment explanation
Indices: 42597728--42597789 Score: 74
Period size: 5 Copynumber: 12.2 Consensus size: 5
42597718 CTCTCCCTTA
*
42597728 TCTTT TCGTTAT TCTTT TCTTT TCTTT TCTTT T-TTT TCATT T-TTT TCTTTT
1 TCTTT TC-TT-T TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TC-TTT
42597779 TCTTT TCTTT T
1 TCTTT TCTTT T
42597790 TTGGAATATT
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
4 7 0.14
5 31 0.62
6 9 0.18
7 3 0.06
ACGTcount: A:0.03, C:0.16, G:0.02, T:0.79
Consensus pattern (5 bp):
TCTTT
Found at i:42597801 original size:29 final size:28
Alignment explanation
Indices: 42597742--42597801 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
42597732 TTCGTTATTC
*** *
42597742 TTTTCTTTTCTTTTCTTTTTTTTCATTT
1 TTTTCTTTTCTTTTCTTTTTTGGAATAT
42597770 TTTTCTTTTTCTTTTCTTTTTTGGAATAT
1 TTTTC-TTTTCTTTTCTTTTTTGGAATAT
42597799 TTT
1 TTT
42597802 ATTGTATCGG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 5 0.19
29 22 0.81
ACGTcount: A:0.07, C:0.12, G:0.03, T:0.78
Consensus pattern (28 bp):
TTTTCTTTTCTTTTCTTTTTTGGAATAT
Found at i:42601683 original size:3 final size:3
Alignment explanation
Indices: 42601675--42601920 Score: 492
Period size: 3 Copynumber: 82.0 Consensus size: 3
42601665 ATATACATAT
42601675 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
42601723 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
42601771 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
42601819 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
42601867 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
42601915 ATA ATA
1 ATA ATA
42601921 GACGGGGTTA
Statistics
Matches: 243, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 243 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:42603198 original size:18 final size:18
Alignment explanation
Indices: 42603170--42603210 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
42603160 AATTATATAA
42603170 AAAATTAAAATATGTATC
1 AAAATTAAAATATGTATC
* *
42603188 GAAATTCAAATATGTATC
1 AAAATTAAAATATGTATC
42603206 AAAAT
1 AAAAT
42603211 AATAAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.54, C:0.07, G:0.07, T:0.32
Consensus pattern (18 bp):
AAAATTAAAATATGTATC
Found at i:42605315 original size:18 final size:18
Alignment explanation
Indices: 42605287--42605327 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
42605277 AATTATATAA
42605287 AAAATTAAAATATGTATC
1 AAAATTAAAATATGTATC
* *
42605305 GAAATTCAAATATGTATC
1 AAAATTAAAATATGTATC
42605323 AAAAT
1 AAAAT
42605328 AATAAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.54, C:0.07, G:0.07, T:0.32
Consensus pattern (18 bp):
AAAATTAAAATATGTATC
Found at i:42607007 original size:92 final size:92
Alignment explanation
Indices: 42606850--42607022 Score: 346
Period size: 92 Copynumber: 1.9 Consensus size: 92
42606840 ATGAATTTAT
42606850 AATTACACAAAAACTAACCTAAGTATGCTCAAAATTAAAATAAATACAAAAGAATTAAGTATGCA
1 AATTACACAAAAACTAACCTAAGTATGCTCAAAATTAAAATAAATACAAAAGAATTAAGTATGCA
42606915 AGTTTTAAAAGTTAATATTAATTAAAA
66 AGTTTTAAAAGTTAATATTAATTAAAA
42606942 AATTACACAAAAACTAACCTAAGTATGCTCAAAATTAAAATAAATACAAAAGAATTAAGTATGCA
1 AATTACACAAAAACTAACCTAAGTATGCTCAAAATTAAAATAAATACAAAAGAATTAAGTATGCA
42607007 AGTTTTAAAAGTTAAT
66 AGTTTTAAAAGTTAAT
42607023 CACAATAGCA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 81 1.00
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (92 bp):
AATTACACAAAAACTAACCTAAGTATGCTCAAAATTAAAATAAATACAAAAGAATTAAGTATGCA
AGTTTTAAAAGTTAATATTAATTAAAA
Found at i:42609028 original size:38 final size:37
Alignment explanation
Indices: 42608941--42609028 Score: 113
Period size: 37 Copynumber: 2.4 Consensus size: 37
42608931 CACTATCATG
* * *
42608941 GTGTGTAGGGTGGACGAGCCTACTATAGCCCATTGCG
1 GTGTGTAGGGTGGACGAGCCTACCATAGCCAATTGCA
* *
42608978 GTGTGCAGGGTGGATGAGCCTACCATAGCCAAATTGCA
1 GTGTGTAGGGTGGACGAGCCTACCATAGCC-AATTGCA
*
42609016 GTGTGTAAGGTGG
1 GTGTGTAGGGTGG
42609029 TCGGAGTAGT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
37 27 0.63
38 16 0.37
ACGTcount: A:0.22, C:0.18, G:0.36, T:0.24
Consensus pattern (37 bp):
GTGTGTAGGGTGGACGAGCCTACCATAGCCAATTGCA
Found at i:42611465 original size:86 final size:87
Alignment explanation
Indices: 42611316--42611491 Score: 291
Period size: 86 Copynumber: 2.0 Consensus size: 87
42611306 GCTAACATTC
42611316 ATGTTTTACGTGATTGTCCTATTGTGATTAATTGGGACGTGGCAGAATATTTACCTTGTCAAGTG
1 ATGTTTTACGTGATTGTCCTATTGTG---AATTGGGACGTGGCAGAATATTTACCTTGTCAAGTG
42611381 GTTCAAGATTTCTTTTCGATACCTT
63 GTTCAAGATTTCTTTTCGATACCTT
* *
42611406 ATGTTTTACGTGATTGTCCTATTGTG-GTTGGGACGTGGCAGAGTATTTACCTTGTCAAGTGGTT
1 ATGTTTTACGTGATTGTCCTATTGTGAATTGGGACGTGGCAGAATATTTACCTTGTCAAGTGGTT
*
42611470 CAAGATTTCTTTTTGATACCTT
66 CAAGATTTCTTTTCGATACCTT
42611492 TGCAAGTCTG
Statistics
Matches: 83, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
86 57 0.69
90 26 0.31
ACGTcount: A:0.20, C:0.14, G:0.23, T:0.43
Consensus pattern (87 bp):
ATGTTTTACGTGATTGTCCTATTGTGAATTGGGACGTGGCAGAATATTTACCTTGTCAAGTGGTT
CAAGATTTCTTTTCGATACCTT
Found at i:42615311 original size:86 final size:86
Alignment explanation
Indices: 42615166--42615337 Score: 317
Period size: 86 Copynumber: 2.0 Consensus size: 86
42615156 GCTAACATTC
*
42615166 ATGTTTTACGTGATTGTCCTATTGTGGTTGGGACGTGGTAGAGTATTTACCTTGTCAAGTGGTTC
1 ATGTTTTACGTGATTGTCCTATTGTGGTTGGGACGTGGCAGAGTATTTACCTTGTCAAGTGGTTC
42615231 AAGACTTCTTTTCGATACCTT
66 AAGACTTCTTTTCGATACCTT
42615252 ATGTTTTACGTGATTGTCCTATTGTGGTTGGGACGTGGCAGAGTATTTACCTTGTCAAGTGGTTC
1 ATGTTTTACGTGATTGTCCTATTGTGGTTGGGACGTGGCAGAGTATTTACCTTGTCAAGTGGTTC
* *
42615317 AAGATTTCTTTTTGATACCTT
66 AAGACTTCTTTTCGATACCTT
42615338 TGCAAGACTG
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
86 83 1.00
ACGTcount: A:0.19, C:0.15, G:0.24, T:0.42
Consensus pattern (86 bp):
ATGTTTTACGTGATTGTCCTATTGTGGTTGGGACGTGGCAGAGTATTTACCTTGTCAAGTGGTTC
AAGACTTCTTTTCGATACCTT
Found at i:42616379 original size:12 final size:12
Alignment explanation
Indices: 42616364--42616388 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42616354 TTTAATAAAA
42616364 TTTTTATAATTT
1 TTTTTATAATTT
42616376 TTTTTATAATTT
1 TTTTTATAATTT
42616388 T
1 T
42616389 ATGAATTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTATAATTT
Found at i:42616386 original size:21 final size:23
Alignment explanation
Indices: 42616348--42616397 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
42616338 ATGGATTTGT
42616348 ATTTTTTTTAATAAAATTTTTAT-A
1 ATTTTTTTTAAT-AAA-TTTTATGA
42616372 ATTTTTTTT-AT-AATTTTATGA
1 ATTTTTTTTAATAAATTTTATGA
42616393 ATTTT
1 ATTTT
42616398 AAATGATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 6 0.24
21 8 0.32
23 2 0.08
24 9 0.36
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (23 bp):
ATTTTTTTTAATAAATTTTATGA
Found at i:42617375 original size:5 final size:5
Alignment explanation
Indices: 42617365--42617413 Score: 61
Period size: 5 Copynumber: 10.4 Consensus size: 5
42617355 TTACCACTTT
42617365 TTATA TTATA TTATA TTATA TTATA TT-TA TT-TA TT-TA TT-TA TTACTA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTA-TA
42617412 TT
1 TT
42617414 GCTAACAATT
Statistics
Matches: 42, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
4 16 0.38
5 22 0.52
6 4 0.10
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (5 bp):
TTATA
Found at i:42618007 original size:2 final size:2
Alignment explanation
Indices: 42618002--42618027 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
42617992 TGGTTGAAAA
42618002 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
42618028 TTGTAATTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42622860 original size:20 final size:21
Alignment explanation
Indices: 42622837--42622895 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 21
42622827 TACAAAATCA
42622837 AAACAC-TAAACTCTAAATTC
1 AAACACATAAACTCTAAATTC
*
42622857 AAAC-CATTAA-TACTAAATTC
1 AAACACATAAACT-CTAAATTC
*
42622877 ATACACATAAACTC-AAATT
1 AAACACATAAACTCTAAATT
42622896 TATTGAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
19 2 0.06
20 23 0.72
21 6 0.19
22 1 0.03
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (21 bp):
AAACACATAAACTCTAAATTC
Found at i:42624713 original size:20 final size:20
Alignment explanation
Indices: 42624677--42624725 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
42624667 AATTCTATCC
*
42624677 TTCTTTTATTTTATATTTACT
1 TTCTTTAATTTTATATTTA-T
42624698 TTCTTTAATTTT-TATTTAT
1 TTCTTTAATTTTATATTTAT
*
42624717 TTTTTTAAT
1 TTCTTTAAT
42624726 CTGACTTAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 9 0.35
20 6 0.23
21 11 0.42
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.73
Consensus pattern (20 bp):
TTCTTTAATTTTATATTTAT
Found at i:42627949 original size:104 final size:105
Alignment explanation
Indices: 42627706--42627953 Score: 286
Period size: 105 Copynumber: 2.4 Consensus size: 105
42627696 TTTATATGCC
* * * *
42627706 ACACGGCCTGGACACACATCCATGTCCTTGCCCATGTGGCTCACACGGCCTAGGCACATGCCCAT
1 ACACGGCCTAGACACACACCCGTGTCCTTGCCCATGTGACTCACACGGCCTAGGCACATGCCCAT
* * * * *
42627771 GTCTTCTGCCTGTGTAGTTCTAAAGCATAAAAAGTGATTT
66 GTCTTCGGCCTGTGTAGGTCTAAAGCACAAAAAGAGAGTT
* * * * * * *
42627811 ACATGGCTTAGACACACGCCCGTGTCCTTACCCATGTGACTCATACGGCCTGGGTACATGCCCAT
1 ACACGGCCTAGACACACACCCGTGTCCTTGCCCATGTGACTCACACGGCCTAGGCACATGCCCAT
* *
42627876 GTCCTT-GGCC-GTGT-GGTCTTAAGTCACAAACAGAGAGTT
66 GT-CTTCGGCCTGTGTAGGTCTAAAG-CACAAAAAGAGAGTT
*
42627915 ACACGGCCTAGACACACACCCGTATCCTTGCCCATGTGA
1 ACACGGCCTAGACACACACCCGTGTCCTTGCCCATGTGA
42627954 ACCTTACACT
Statistics
Matches: 118, Mismatches: 23, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
103 7 0.06
104 49 0.42
105 59 0.50
106 3 0.03
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.24
Consensus pattern (105 bp):
ACACGGCCTAGACACACACCCGTGTCCTTGCCCATGTGACTCACACGGCCTAGGCACATGCCCAT
GTCTTCGGCCTGTGTAGGTCTAAAGCACAAAAAGAGAGTT
Found at i:42629771 original size:18 final size:19
Alignment explanation
Indices: 42629748--42629791 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
42629738 ACTAAATTTA
*
42629748 TATTTAAATTTATTA-TAG
1 TATTTAAATTTATAATTAG
*
42629766 TATTT-AATTTATAATTAT
1 TATTTAAATTTATAATTAG
42629784 TATTTAAA
1 TATTTAAA
42629792 AAAATTGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 8 0.36
18 12 0.55
19 2 0.09
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
TATTTAAATTTATAATTAG
Found at i:42640780 original size:27 final size:27
Alignment explanation
Indices: 42640679--42640782 Score: 95
Period size: 27 Copynumber: 3.9 Consensus size: 27
42640669 TTTATTCCTG
*
42640679 TGTTTGCTGT-CCAGGCAGACTACCCCA
1 TGTTTACTGTCCCA-GCAGACTACCCCA
* * ** * **
42640706 TATTTATTGTCCCAATAGGCTACCCTG
1 TGTTTACTGTCCCAGCAGACTACCCCA
*
42640733 TGTTTACTGTCCC-GACGGACTACCCCA
1 TGTTTACTGTCCCAG-CAGACTACCCCA
42640760 TGTTTACTGTCCCAGCAGACTAC
1 TGTTTACTGTCCCAGCAGACTAC
42640783 ATGGGTTGCC
Statistics
Matches: 57, Mismatches: 17, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
27 53 0.93
28 4 0.07
ACGTcount: A:0.20, C:0.32, G:0.18, T:0.30
Consensus pattern (27 bp):
TGTTTACTGTCCCAGCAGACTACCCCA
Found at i:42644762 original size:366 final size:367
Alignment explanation
Indices: 42644090--42644821 Score: 1331
Period size: 366 Copynumber: 2.0 Consensus size: 367
42644080 CAAAGCACGC
42644090 ATTTTGGCTGACTTGAAGGATCAATAAAACTTTGTTCAATCAAAATGCAATGTGGTTTCATTAAT
1 ATTTTGGCTGACTTGAAGGATCAATAAAACTTTGTTCAATCAAAATGCAATGTGGTTTCATTAAT
*
42644155 TTCAAATCGCAAGAGGTGTACCTACTAAGGAGGAGTGAACAAATCCAATGGAGACGAGGTGGGGC
66 TTCAAATCGCAAGAGGTGTACCTACTAAGGAGGAGCGAACAAATCCAATGGAGACGAGGTGGGGC
*
42644220 CTGTAGCTCAAAGGATTAGAGCATGTGGCTACGAACCATGGTGTCGGGGGTTCAAATCCCTCCTC
131 CTGTAGCTCAAAGGATTAAAGCATGTGGCTACGAACCATGGTGTCGGGGGTTCAAATCCCTCCTC
*
42644285 ACCCACAACCGGCCCAAAAGGGAAGGACCTTTCCCTATGGGGGTAGGAAAATCATGATCGGGATA
196 ACCCACAACCGGCCCAAAAGGGAAGGACCTTTCCCTATAGGGGTAGGAAAATCATGATCGGGATA
*
42644350 GCGGACCCAAAGCTATGGAACTTGGGTGTGGGTCTTTTGCCGAAATGGAGTGGCCTTTTATTTAT
261 GCGGACCCAAAGCTATGGAACTTGGGTGTGGGTCTTTTGCCGAAATGGAGTGACCTTTTATTTAT
*
42644415 TA-TTGTCGTATATTTAATTTTCTATTTTCTATTTATATATT
326 TATTTGTCGTATATTTAAGTTTCTATTTTCTATTTATATATT
*
42644456 ATTTTGGCTGATTTGAAGGATCAATAAAACTTTGTTCAATCAAAATGCAATGTGGTTTCATTAAT
1 ATTTTGGCTGACTTGAAGGATCAATAAAACTTTGTTCAATCAAAATGCAATGTGGTTTCATTAAT
* * *
42644521 TTCAAATCGCAAGAGGTGTACCTACTAAGGGGGAGCGAACATATCCAGTGGAGACGAGGTGGGGC
66 TTCAAATCGCAAGAGGTGTACCTACTAAGGAGGAGCGAACAAATCCAATGGAGACGAGGTGGGGC
* * *
42644586 CTGTAGTTCAAAGGATTAAAGCATGTGGCTATGAACCATGGTGTCGGGGGTTCGAATCCCTCCTC
131 CTGTAGCTCAAAGGATTAAAGCATGTGGCTACGAACCATGGTGTCGGGGGTTCAAATCCCTCCTC
* *
42644651 GCCCACAACCGGCCCAAAAGGGAAGGACCTTTCCCTCTAGGGGTAGGAAAATCATGATCGGGATA
196 ACCCACAACCGGCCCAAAAGGGAAGGACCTTTCCCTATAGGGGTAGGAAAATCATGATCGGGATA
42644716 GCGGACCCAAAGCTATGGAACTTGGGTGTGGGTCTTTTGCCGAAATGGAGTGACCTTTTATTTAT
261 GCGGACCCAAAGCTATGGAACTTGGGTGTGGGTCTTTTGCCGAAATGGAGTGACCTTTTATTTAT
42644781 TATTTGTCGTATATTTAAGTTTCTATTTTCTATTTATATAT
326 TATTTGTCGTATATTTAAGTTTCTATTTTCTATTTATATAT
42644822 AGTATTATCG
Statistics
Matches: 351, Mismatches: 14, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
366 314 0.89
367 37 0.11
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.30
Consensus pattern (367 bp):
ATTTTGGCTGACTTGAAGGATCAATAAAACTTTGTTCAATCAAAATGCAATGTGGTTTCATTAAT
TTCAAATCGCAAGAGGTGTACCTACTAAGGAGGAGCGAACAAATCCAATGGAGACGAGGTGGGGC
CTGTAGCTCAAAGGATTAAAGCATGTGGCTACGAACCATGGTGTCGGGGGTTCAAATCCCTCCTC
ACCCACAACCGGCCCAAAAGGGAAGGACCTTTCCCTATAGGGGTAGGAAAATCATGATCGGGATA
GCGGACCCAAAGCTATGGAACTTGGGTGTGGGTCTTTTGCCGAAATGGAGTGACCTTTTATTTAT
TATTTGTCGTATATTTAAGTTTCTATTTTCTATTTATATATT
Found at i:42654840 original size:9 final size:9
Alignment explanation
Indices: 42654826--42654856 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
42654816 GATCAAGTAA
42654826 AATTAAATT
1 AATTAAATT
42654835 AATTAAATT
1 AATTAAATT
42654844 AATTAAAATT
1 AATT-AAATT
42654854 AAT
1 AAT
42654857 ATGATATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 13 0.62
10 8 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
AATTAAATT
Found at i:42655216 original size:17 final size:17
Alignment explanation
Indices: 42655196--42655253 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
42655186 TTTAATAAGG
42655196 TTTAATATTTAATTTAA
1 TTTAATATTTAATTTAA
* *
42655213 TTTAATATTTATTTTGA
1 TTTAATATTTAATTTAA
*
42655230 -TAAATA-TT-ATATTAA
1 TTTAATATTTAAT-TTAA
42655245 TTTAATATT
1 TTTAATATT
42655254 ACCGTGATTA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
14 1 0.03
15 5 0.16
16 10 0.31
17 16 0.50
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (17 bp):
TTTAATATTTAATTTAA
Found at i:42676161 original size:27 final size:27
Alignment explanation
Indices: 42676131--42676190 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
42676121 TTAAATTAAT
* *
42676131 ATAAATATAATAATTAGCTAAG-AAAAA
1 ATAAA-ATAATAATTAACAAAGTAAAAA
*
42676158 ATAAAATAATTATTAACAAAGTAAAAA
1 ATAAAATAATAATTAACAAAGTAAAAA
42676185 ATAAAA
1 ATAAAA
42676191 AAATTAACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 13 0.45
27 16 0.55
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.25
Consensus pattern (27 bp):
ATAAAATAATAATTAACAAAGTAAAAA
Found at i:42676206 original size:24 final size:26
Alignment explanation
Indices: 42676131--42676214 Score: 72
Period size: 27 Copynumber: 3.3 Consensus size: 26
42676121 TTAAATTAAT
* *
42676131 ATAAATATAATAATTAGCTAAG-AAAAA
1 ATAAA-ATAAT-ATTAACAAAGTAAAAA
42676158 ATAAAATAATTATTAACAAAGTAAAAA
1 ATAAAATAA-TATTAACAAAGTAAAAA
42676185 ATAAAA-AA-ATTAACTAAA-T--AAA
1 ATAAAATAATATTAAC-AAAGTAAAAA
42676207 ATAAAATA
1 ATAAAATA
42676215 TCTAATTTAG
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
22 9 0.18
23 1 0.02
24 7 0.14
25 3 0.06
26 14 0.27
27 17 0.33
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.25
Consensus pattern (26 bp):
ATAAAATAATATTAACAAAGTAAAAA
Found at i:42676276 original size:70 final size:72
Alignment explanation
Indices: 42676176--42676321 Score: 224
Period size: 70 Copynumber: 2.1 Consensus size: 72
42676166 ATTATTAACA
* *
42676176 AAGTAAAAAATAAAAAAATTAACTAAATAAAATAAAATATCTAATTTAGTAATTAAGTCTGCCAT
1 AAGTAAAAAATAAAAAAATTAACTAAATAAAATAAAATAACTAATTTAGTAATTAAGTCTGCAAT
*
42676241 ACAAAAT
66 ACAAAAG
* *
42676248 AAGT-AAAAA-AAAACAATTAACTAAATAAAATAAAATAACTAATTTAGTAATTAAGTTTGCAAT
1 AAGTAAAAAATAAAAAAATTAACTAAATAAAATAAAATAACTAATTTAGTAATTAAGTCTGCAAT
*
42676311 GCAAAAG
66 ACAAAAG
42676318 AAGT
1 AAGT
42676322 CGTAGTGATG
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
70 59 0.87
71 5 0.07
72 4 0.06
ACGTcount: A:0.58, C:0.08, G:0.08, T:0.27
Consensus pattern (72 bp):
AAGTAAAAAATAAAAAAATTAACTAAATAAAATAAAATAACTAATTTAGTAATTAAGTCTGCAAT
ACAAAAG
Found at i:42677261 original size:21 final size:21
Alignment explanation
Indices: 42677237--42677276 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
42677227 AATATCTATT
*
42677237 ACTTAAAATAACTAAAAATTA
1 ACTTAAAACAACTAAAAATTA
*
42677258 ACTTAAAACAAGTAAAAAT
1 ACTTAAAACAACTAAAAAT
42677277 AATATAAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.62, C:0.10, G:0.03, T:0.25
Consensus pattern (21 bp):
ACTTAAAACAACTAAAAATTA
Found at i:42688601 original size:18 final size:18
Alignment explanation
Indices: 42688558--42688604 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
42688548 GAAAAGAATG
* *
42688558 AAAAAGAAAAAGTGATCT
1 AAAAAGAAAAAGTCATCA
42688576 AAAAAGAAAAAGTCA-CA
1 AAAAAGAAAAAGTCATCA
42688593 AAAATAGAAAAA
1 AAAA-AGAAAAA
42688605 CTCAGTCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 5 0.19
18 21 0.81
ACGTcount: A:0.70, C:0.06, G:0.13, T:0.11
Consensus pattern (18 bp):
AAAAAGAAAAAGTCATCA
Found at i:42689994 original size:20 final size:20
Alignment explanation
Indices: 42689971--42690012 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
42689961 GGCACCTTAC
42689971 TGTAAACAGAGACACCAAAG
1 TGTAAACAGAGACACCAAAG
* *
42689991 TGTAAACAGAGGCACCGAAG
1 TGTAAACAGAGACACCAAAG
42690011 TG
1 TG
42690013 CGATCCCGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.43, C:0.19, G:0.26, T:0.12
Consensus pattern (20 bp):
TGTAAACAGAGACACCAAAG
Found at i:42690681 original size:10 final size:11
Alignment explanation
Indices: 42690666--42690695 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
42690656 TCAAACACTG
42690666 ATTATTTTA-T
1 ATTATTTTATT
42690676 ATTATTTTATT
1 ATTATTTTATT
42690687 ATTATTTTA
1 ATTATTTTA
42690696 CATATGAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
ATTATTTTATT
Found at i:42695180 original size:40 final size:40
Alignment explanation
Indices: 42695080--42695220 Score: 174
Period size: 40 Copynumber: 3.5 Consensus size: 40
42695070 TAGTGGCGTT
** * * *
42695080 TATGAGAAAAACGTTGCAAAAGGTCTAGCATTAACGACGTT
1 TATGAGAAAAACGCCGCAAAAGGTCAAGCATTAGCGACG-C
* * *
42695121 TATGAGAAAAATGCCGCAAAAGGTCAAGTATTAGCGGCGC
1 TATGAGAAAAACGCCGCAAAAGGTCAAGCATTAGCGACGC
* *
42695161 TATGAAAAAAACGCTGCAAAAGGTCAAGCATTAGCGACGC
1 TATGAGAAAAACGCCGCAAAAGGTCAAGCATTAGCGACGC
*
42695201 TATGAGAAAAGCGCCGCAAA
1 TATGAGAAAAACGCCGCAAA
42695221 GTATCATTTT
Statistics
Matches: 84, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
40 52 0.62
41 32 0.38
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (40 bp):
TATGAGAAAAACGCCGCAAAAGGTCAAGCATTAGCGACGC
Found at i:42695635 original size:25 final size:25
Alignment explanation
Indices: 42695605--42695652 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
42695595 TATTAGCTCA
*
42695605 ATTTTTATTATTTCATTTAACAATT
1 ATTTTTATAATTTCATTTAACAATT
42695630 ATTTTTATAATTTCATTTAACAA
1 ATTTTTATAATTTCATTTAACAA
42695653 AATGTTGCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.56
Consensus pattern (25 bp):
ATTTTTATAATTTCATTTAACAATT
Found at i:42699311 original size:72 final size:72
Alignment explanation
Indices: 42699225--42699443 Score: 255
Period size: 72 Copynumber: 3.1 Consensus size: 72
42699215 ATTAATTATC
**
42699225 AAGTAAAACCGTTTATTTAATTATGTGTTTTTAAAAAGGTTAATTTAGTTCAATTTATT-AAGTT
1 AAGTAAAACCGTTTATTTAATTATGAATTTTTAAAAAGGTTAATTTAGTTCAATTTATTGAA-TT
42699289 TTGATATT
65 TTGATATT
* * * * * ** *
42699297 AAGTGAAACCGTTTATTTAGTTAT-ACA-TTTTCAGAAGCTTAATTTAGTTTGATTTATTGAAAT
1 AAGTAAAACCGTTTATTTAATTATGA-ATTTTTAAAAAGGTTAATTTAGTTCAATTTATTGAATT
42699360 TTGATATT
65 TTGATATT
* * * * * *
42699368 AAGTAAAAACGTTTGTTCAATTATGAATTTATAAAAATGTTAATTTAGTTCAACTTATTGAATTT
1 AAGTAAAACCGTTTATTTAATTATGAATTTTTAAAAAGGTTAATTTAGTTCAATTTATTGAATTT
42699433 TGATATT
66 TGATATT
42699440 AAGT
1 AAGT
42699444 GGAACCATTT
Statistics
Matches: 119, Mismatches: 24, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
71 55 0.46
72 64 0.54
ACGTcount: A:0.36, C:0.05, G:0.13, T:0.46
Consensus pattern (72 bp):
AAGTAAAACCGTTTATTTAATTATGAATTTTTAAAAAGGTTAATTTAGTTCAATTTATTGAATTT
TGATATT
Found at i:42700274 original size:27 final size:27
Alignment explanation
Indices: 42700242--42700303 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
42700232 ACTTACATAA
42700242 TACATAAATATATATCATATCATAACT
1 TACATAAATATATATCATATCATAACT
42700269 TACATAAATATATATCATATCATAACT
1 TACATAAATATATATCATATCATAACT
*
42700296 TATATAAA
1 TACATAAA
42700304 AATTTGGATC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (27 bp):
TACATAAATATATATCATATCATAACT
Found at i:42706989 original size:34 final size:34
Alignment explanation
Indices: 42706946--42707058 Score: 118
Period size: 34 Copynumber: 3.3 Consensus size: 34
42706936 AATCCTTAAC
* *
42706946 ATGTCATATTACCATAAACATATATTAGATCAAA
1 ATGTCATATTACCAAAAACATATATCAGATCAAA
* *
42706980 ATGTCATATTTCCAAAAACATATATCATATCAAA
1 ATGTCATATTACCAAAAACATATATCAGATCAAA
* * * * * * *
42707014 TTGTCATATTTCCAGAAGCATATGTCAAATTAAA
1 ATGTCATATTACCAAAAACATATATCAGATCAAA
*
42707048 ATATCATATTA
1 ATGTCATATTA
42707059 GATCAGAACA
Statistics
Matches: 66, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 66 1.00
ACGTcount: A:0.44, C:0.15, G:0.06, T:0.35
Consensus pattern (34 bp):
ATGTCATATTACCAAAAACATATATCAGATCAAA
Found at i:42713041 original size:13 final size:13
Alignment explanation
Indices: 42713023--42713066 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
42713013 AAGATTTAAT
42713023 ATTTATTAGTATA
1 ATTTATTAGTATA
**
42713036 ATTTATT--TAGC
1 ATTTATTAGTATA
42713047 ATTTATTAGTATA
1 ATTTATTAGTATA
42713060 ATTTATT
1 ATTTATT
42713067 TGACCTATGA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 9 0.36
13 16 0.64
ACGTcount: A:0.34, C:0.02, G:0.07, T:0.57
Consensus pattern (13 bp):
ATTTATTAGTATA
Found at i:42713043 original size:24 final size:24
Alignment explanation
Indices: 42713016--42713067 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
42713006 TTTATATAAG
*
42713016 ATTTAATATTTATTAGTATAATTT
1 ATTTAACATTTATTAGTATAATTT
*
42713040 ATTTAGCATTTATTAGTATAATTT
1 ATTTAACATTTATTAGTATAATTT
42713064 ATTT
1 ATTT
42713068 GACCTATGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.58
Consensus pattern (24 bp):
ATTTAACATTTATTAGTATAATTT
Found at i:42713873 original size:22 final size:22
Alignment explanation
Indices: 42713848--42713899 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
42713838 TAATTTTTAA
*
42713848 ATTTTTTAAAATTATAAAAACT
1 ATTTTTTAAAATTAAAAAAACT
* *
42713870 ATTTTTAAAAATTAAAAAAATT
1 ATTTTTTAAAATTAAAAAAACT
42713892 ATTATTTT
1 ATT-TTTT
42713900 CAATTTTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 22 0.88
23 3 0.12
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTTTTTAAAATTAAAAAAACT
Found at i:42714688 original size:21 final size:21
Alignment explanation
Indices: 42714662--42714709 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
42714652 TTTTTACCTT
42714662 AAATCCTGAATCAAGAACCCC
1 AAATCCTGAATCAAGAACCCC
* * *
42714683 AAATCCTGAATCCAGAATCCT
1 AAATCCTGAATCAAGAACCCC
42714704 AAATCC
1 AAATCC
42714710 CGAACCTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (21 bp):
AAATCCTGAATCAAGAACCCC
Found at i:42714736 original size:13 final size:14
Alignment explanation
Indices: 42714712--42714740 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
42714702 CTAAATCCCG
42714712 AACCTCAAACTCTA
1 AACCTCAAACTCTA
42714726 AACCT-AAACTCTA
1 AACCTCAAACTCTA
42714739 AA
1 AA
42714741 TCTTGAACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.48, C:0.31, G:0.00, T:0.21
Consensus pattern (14 bp):
AACCTCAAACTCTA
Found at i:42714769 original size:7 final size:7
Alignment explanation
Indices: 42714749--42714836 Score: 61
Period size: 7 Copynumber: 12.7 Consensus size: 7
42714739 AATCTTGAAC
42714749 TTAGGGT
1 TTAGGGT
**
42714756 TCGGGGT
1 TTAGGGT
42714763 TTAGGGT
1 TTAGGGT
*
42714770 TTAAGGT
1 TTAGGGT
*
42714777 TTAGAGT
1 TTAGGGT
*
42714784 TTA-AGT
1 TTAGGGT
**
42714790 TTAGACT
1 TTAGGGT
* *
42714797 TCAAGGT
1 TTAGGGT
*
42714804 TTAAGGT
1 TTAGGGT
42714811 TTAGGGT
1 TTAGGGT
*
42714818 CTAGGGT
1 TTAGGGT
*
42714825 CTAGGGT
1 TTAGGGT
42714832 TTAGG
1 TTAGG
42714837 ACTTGGGATT
Statistics
Matches: 64, Mismatches: 16, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
6 6 0.09
7 58 0.91
ACGTcount: A:0.20, C:0.06, G:0.35, T:0.39
Consensus pattern (7 bp):
TTAGGGT
Found at i:42714994 original size:28 final size:28
Alignment explanation
Indices: 42714919--42715000 Score: 69
Period size: 28 Copynumber: 2.9 Consensus size: 28
42714909 TTGAGGCTCA
42714919 ATATTCAAGGTTCCATGTTCTGAGG-TTC
1 ATATTCAAGGTTCCATGTTC-GAGGTTTC
* * * * * *
42714947 ATGTTCATGATT-TAGGGTTCGAGGTTTG
1 ATATTCAAGGTTCCA-TGTTCGAGGTTTC
*
42714975 ATATTCAAGGTTCCATGTTCGGGGTT
1 ATATTCAAGGTTCCATGTTCGAGGTT
42715001 CGAAGTGTAT
Statistics
Matches: 39, Mismatches: 12, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
27 5 0.13
28 33 0.85
29 1 0.03
ACGTcount: A:0.20, C:0.13, G:0.27, T:0.40
Consensus pattern (28 bp):
ATATTCAAGGTTCCATGTTCGAGGTTTC
Found at i:42716155 original size:15 final size:15
Alignment explanation
Indices: 42716135--42716196 Score: 54
Period size: 15 Copynumber: 4.2 Consensus size: 15
42716125 TGATCAATTG
42716135 AAAAATTAAGTACTA
1 AAAAATTAAGTACTA
** *
42716150 AAAAATTAAGTGTTG
1 AAAAATTAAGTACTA
* * *
42716165 AAAAATTGAGTATTG
1 AAAAATTAAGTACTA
*
42716180 AAATATTAAGTAC-A
1 AAAAATTAAGTACTA
42716194 AAA
1 AAA
42716197 TTTAATTTAT
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
14 3 0.08
15 35 0.92
ACGTcount: A:0.55, C:0.03, G:0.13, T:0.29
Consensus pattern (15 bp):
AAAAATTAAGTACTA
Found at i:42716166 original size:30 final size:30
Alignment explanation
Indices: 42716132--42716190 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
42716122 GTTTGATCAA
42716132 TTGAAAAATTAAGTACTAAAAAATTAAGTG
1 TTGAAAAATTAAGTACTAAAAAATTAAGTG
* * * *
42716162 TTGAAAAATTGAGTATTGAAATATTAAGT
1 TTGAAAAATTAAGTACTAAAAAATTAAGT
42716191 ACAAAATTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.49, C:0.02, G:0.15, T:0.34
Consensus pattern (30 bp):
TTGAAAAATTAAGTACTAAAAAATTAAGTG
Found at i:42717564 original size:28 final size:29
Alignment explanation
Indices: 42717502--42717564 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
42717492 TAGCAAATGT
*
42717502 CTATTTTCATAATTAATATGTTTTTCATA
1 CTATTTTCATAATGAATATGTTTTTCATA
*
42717531 CCATTTTCATAATGAATTAT-TTTTT-ATA
1 CTATTTTCATAATGAA-TATGTTTTTCATA
*
42717559 TTATTT
1 CTATTT
42717565 GGGTAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 7 0.24
29 19 0.66
30 3 0.10
ACGTcount: A:0.30, C:0.10, G:0.03, T:0.57
Consensus pattern (29 bp):
CTATTTTCATAATGAATATGTTTTTCATA
Found at i:42717797 original size:15 final size:15
Alignment explanation
Indices: 42717777--42717824 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
42717767 ACAAAAAAAA
42717777 TTGTTAAATATTAAG
1 TTGTTAAATATTAAG
* *
42717792 TTGTTAGATATTAAT
1 TTGTTAAATATTAAG
**
42717807 TTGGAAAATATTAAG
1 TTGTTAAATATTAAG
42717822 TTG
1 TTG
42717825 ATTTTATTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.46
Consensus pattern (15 bp):
TTGTTAAATATTAAG
Found at i:42719837 original size:3 final size:3
Alignment explanation
Indices: 42719829--42719858 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
42719819 TAAGGTTCAG
42719829 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
42719859 TTGAATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:42720091 original size:6 final size:6
Alignment explanation
Indices: 42720080--42720108 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
42720070 ATCCCAGAAT
42720080 CCATAG CCATAG CCATAG CCATAG CCATA
1 CCATAG CCATAG CCATAG CCATAG CCATA
42720109 ATAGTGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.34, G:0.14, T:0.17
Consensus pattern (6 bp):
CCATAG
Found at i:42721932 original size:31 final size:31
Alignment explanation
Indices: 42721874--42721935 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
42721864 ATTTATCAAC
* *
42721874 TAGTAACTTGAATAATAACTTTTAAATAGTT
1 TAGTAACTTAAATAATAAATTTTAAATAGTT
*
42721905 TAGTGACTTAAATAA-AAATTTTCAAATAGTT
1 TAGTAACTTAAATAATAAATTTT-AAATAGTT
42721936 CAATAATCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 6 0.22
31 21 0.78
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (31 bp):
TAGTAACTTAAATAATAAATTTTAAATAGTT
Found at i:42722836 original size:43 final size:43
Alignment explanation
Indices: 42722696--42722862 Score: 176
Period size: 43 Copynumber: 3.9 Consensus size: 43
42722686 TTATGTGAAA
* *
42722696 AAACGCCGCTATAA-AACATGACCTTTAGCGGCGC-TTTCCAAAC
1 AAACGCCGCTA-AAGAACATGACCTTTAGCGGCGCTTTTCC-CAT
* * * ** *
42722739 AAACGCCACTATAGAACATGACATTTAGTAGCGCTTTTTCCAT
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAT
*
42722782 AAACGCCGCTAAAGAACATGACCTTTAACGGCGCTTTTCCCAT
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAT
** ** *
42722825 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTTT
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTT
42722863 AGTAAAAGTG
Statistics
Matches: 101, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
42 1 0.01
43 96 0.95
44 4 0.04
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.27
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAT
Found at i:42723334 original size:17 final size:19
Alignment explanation
Indices: 42723312--42723373 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 19
42723302 TATGGAAACA
42723312 TAATCTT-CA-AGGATATG
1 TAATCTTACATAGGATATG
* *
42723329 TAATCTTAGATATGATATG
1 TAATCTTACATAGGATATG
** *
42723348 TAATCTTGGATATGATATG
1 TAATCTTACATAGGATATG
*
42723367 CAATCTT
1 TAATCTT
42723374 GGAAGATATG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
17 7 0.18
18 1 0.03
19 31 0.79
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (19 bp):
TAATCTTACATAGGATATG
Found at i:42723347 original size:19 final size:19
Alignment explanation
Indices: 42723323--42723399 Score: 91
Period size: 19 Copynumber: 3.8 Consensus size: 19
42723313 AATCTTCAAG
42723323 GATATGTAATCTTAGATAT
1 GATATGTAATCTTAGATAT
*
42723342 GATATGTAATCTTGGATAT
1 GATATGTAATCTTAGATAT
*
42723361 GATATGCAATCTTGGAAGATAT
1 GATATGTAATCTT---AGATAT
*
42723383 GATTTTGTAATCTTAGA
1 GA-TATGTAATCTTAGA
42723400 GATTTAATTT
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
19 30 0.61
20 3 0.06
22 7 0.14
23 9 0.18
ACGTcount: A:0.34, C:0.06, G:0.19, T:0.40
Consensus pattern (19 bp):
GATATGTAATCTTAGATAT
Found at i:42738004 original size:85 final size:85
Alignment explanation
Indices: 42737852--42738022 Score: 227
Period size: 85 Copynumber: 2.0 Consensus size: 85
42737842 GACTCTCCAC
* *
42737852 ATACTTGTGTTGTTACAGGTAAGTCACAGAATTATCTGAAATTGGATCTTGATCTTATCTTTGAC
1 ATACTTGTGTTATTACAGGTAAGTCACAGAATCATCTGAAATTGGATCTTGATCTTATCTTTGAC
42737917 ATTGTATTACCTAAGGTGAA
66 ATTGTATTACCTAAGGTGAA
** * * * *
42737937 ATACTTGTGTTATTGTAGGTATGTCACA-AGATCATCTGAAATTGGATTTTGATCTTATTTTTTA
1 ATACTTGTGTTATTACAGGTAAGTCACAGA-ATCATCTGAAATTGGATCTTGATCTTATCTTTGA
* * *
42738001 CATTGTCTTATCTATGGTGAA
65 CATTGTATTACCTAAGGTGAA
42738022 A
1 A
42738023 GTGAATCTTA
Statistics
Matches: 74, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
84 1 0.01
85 73 0.99
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.42
Consensus pattern (85 bp):
ATACTTGTGTTATTACAGGTAAGTCACAGAATCATCTGAAATTGGATCTTGATCTTATCTTTGAC
ATTGTATTACCTAAGGTGAA
Found at i:42744956 original size:3 final size:3
Alignment explanation
Indices: 42744948--42745017 Score: 122
Period size: 3 Copynumber: 23.3 Consensus size: 3
42744938 AAGAGCAATT
* *
42744948 ATA ATA ATA ATG GTA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
42744996 ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA A
42745018 AAGATATGAT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:42745097 original size:21 final size:21
Alignment explanation
Indices: 42745073--42745123 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 21
42745063 AAGTTATTAT
*
42745073 TTTAGAAAATTTTTAACTTTA
1 TTTAGAAAATTTTTAAATTTA
* * *
42745094 TTTA-TATATTTTTAAATTTT
1 TTTAGAAAATTTTTAAATTTA
*
42745114 TTTTGAAAAT
1 TTTAGAAAAT
42745124 ATAAACTTTA
Statistics
Matches: 22, Mismatches: 7, Indels: 2
0.71 0.23 0.06
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (21 bp):
TTTAGAAAATTTTTAAATTTA
Found at i:42745995 original size:7 final size:7
Alignment explanation
Indices: 42745983--42746009 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
42745973 TAGAATACTA
42745983 AAATAAT
1 AAATAAT
42745990 AAATAAT
1 AAATAAT
42745997 AAATAAT
1 AAATAAT
42746004 AAATAA
1 AAATAA
42746010 AGGAATGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
AAATAAT
Found at i:42749871 original size:152 final size:151
Alignment explanation
Indices: 42749576--42750007 Score: 667
Period size: 152 Copynumber: 2.9 Consensus size: 151
42749566 AACATGTTCA
* * *
42749576 TATTTCAGCCCTTTGTTCGTATTTTTTTCTCGGATTTTATTACTTTAAAAAATATACTATTTTCT
1 TATTTCAGCCATTTGTTCGTATTTTTTTCCCGAATTTTATTACTTTAAAAAATATACTATTTTCT
* * *
42749641 AATTTTATTATTTTACATTATTTTAGTAAATTATGCTTGAAATGTATTAATTTA-CTGTTTTTTA
66 AATTTTATTATTTTACATTATTTTAGTACATTATGCTTGAAATGTATTCATTTATGTGTTTTTTA
42749705 AATAAATTTAAAAAAAACCCT
131 AATAAATTTAAAAAAAACCCT
42749726 TATTTCAGCCATTTGTTCGTATTTTTTTTCCCGAATTTTATTACTTTTAAAAAATATACTATTTT
1 TATTTCAGCCATTTGTTCGTA-TTTTTTTCCCGAATTTTATTAC-TTTAAAAAATATACTATTTT
*
42749791 CTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTATTGTGTTTT
64 CTAATTTTATTATTTTACATTATTTTAGTACATTATGCTTGAAATGTATTCATTTA-TGTGTTTT
*
42749856 TTAAATAAA-TT-AAAAAAATCCT
128 TTAAATAAATTTAAAAAAAACCCT
** * * *
42749878 TATTTTGGCCTTTTGTTCGTA-TTTTTTCCC-AGATTTTAATACTTTAAAAAATATAATATTTTC
1 TATTTCAGCCATTTGTTCGTATTTTTTTCCCGA-ATTTTATTACTTTAAAAAATATACTATTTTC
42749941 TAATTTTATTATTTTACATTATTTTAGTACATTATGCTTGAAATGTATTCATTTAGTGTGTTTTT
65 TAATTTTATTATTTTACATTATTTTAGTACATTATGCTTGAAATGTATTCATTTA-TGTGTTTTT
42750006 TA
129 TA
42750008 TTGAAAGTAA
Statistics
Matches: 262, Mismatches: 15, Indels: 11
0.91 0.05 0.04
Matches are distributed among these distances:
149 86 0.33
150 38 0.15
151 20 0.08
152 101 0.39
153 2 0.01
154 15 0.06
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (151 bp):
TATTTCAGCCATTTGTTCGTATTTTTTTCCCGAATTTTATTACTTTAAAAAATATACTATTTTCT
AATTTTATTATTTTACATTATTTTAGTACATTATGCTTGAAATGTATTCATTTATGTGTTTTTTA
AATAAATTTAAAAAAAACCCT
Found at i:42750509 original size:151 final size:151
Alignment explanation
Indices: 42750011--42750666 Score: 892
Period size: 156 Copynumber: 4.3 Consensus size: 151
42750001 TTTTTTATTG
* *
42750011 AAAGTAATAAAATCCGGGAAAAAAAATACGAACAAAGGGCCGAAATAAAGATTTTTTTAAATTTA
1 AAAGTAATAAAATTC-GGAAAAAAAATACGAACAAAGGGCCGAAATAAGGATTTTTTTAAATTTA
* *
42750076 TTTAAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAA
65 TTT-AAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAA
*
42750141 AATTAGAAAATATTATATTTTTATT
129 AATTAGAAAATAGTATA-TTTT-TT
* *
42750166 GAAAGTAATAAAATCTAGG-AAAAAAATACGAACAAAGGGTCGAAATAAGGATTTTTTTAAAAAT
1 -AAAGTAATAAAAT-TCGGAAAAAAAATACGAACAAAGGGCCGAAATAAGGATTTTTTT--AAAT
* *
42750230 TTATTTAAAAAACACACTAAATGAATACATTTCAAACGTAATGTACTAAAATAATTTAAAATAAT
62 TTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAAT
42750295 AAAATTAGAAAATAGTATATTTTTTT
127 AAAATTAGAAAATAGTATA-TTTTTT
* * *
42750321 AAAGTAATAAAATTCAGAGAAAAAATACGAACAAAGGGCCAAAATAAGG-TTTTTTT-AATTTAT
1 AAAGTAATAAAATTCGGAAAAAAAATACGAACAAAGGGCCGAAATAAGGATTTTTTTAAATTTAT
* * * * *
42750384 TTAAAAAACACAGTAAATTAATACATTTCAAGCATAATATACTAAAATAATGTAAAATAAAAAAA
66 TTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAAT-AATAAA
*
42750449 ATTATAAAATAGTATATTTTTT
130 ATTAGAAAATAGTATATTTTTT
* * * *
42750471 AAAAGTAATCAAATTCGGAAAAAAAATACGAACGAAGGGCCGAAATAAGGGTTTTTTTTAATTTA
1 -AAAGTAATAAAATTCGGAAAAAAAATACGAACAAAGGGCCGAAATAAGGATTTTTTTAAATTTA
** * *
42750536 AATAAAAAACACACTAAATGAATACATTTCAAAGATAATCTACTAAAATAATGTAAAATAATAAA
65 TTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAA
42750601 ATTAGAAAATAGTAT-TTTTTT
130 ATTAGAAAATAGTATATTTTTT
* * * *
42750622 AAAGTAAGAAAA-TC-AAGAAAAAAATACGAACAAAAGGCTGAAATA
1 AAAGTAATAAAATTCGGA-AAAAAAATACGAACAAAGGGCCGAAATA
42750667 CGAACATGTT
Statistics
Matches: 449, Mismatches: 42, Indels: 25
0.87 0.08 0.05
Matches are distributed among these distances:
148 1 0.00
149 27 0.06
150 75 0.17
151 70 0.16
152 26 0.06
153 67 0.15
154 41 0.09
155 39 0.09
156 93 0.21
157 10 0.02
ACGTcount: A:0.53, C:0.08, G:0.10, T:0.29
Consensus pattern (151 bp):
AAAGTAATAAAATTCGGAAAAAAAATACGAACAAAGGGCCGAAATAAGGATTTTTTTAAATTTAT
TTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAA
TTAGAAAATAGTATATTTTTT
Found at i:42755707 original size:19 final size:19
Alignment explanation
Indices: 42755685--42755738 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
42755675 ATTACAAAAT
*
42755685 AATTCAAAATAATTT-TTAA
1 AATTCAAAAT-ATTTATAAA
*
42755704 AATTAAAAATATTTATAAA
1 AATTCAAAATATTTATAAA
*
42755723 AATTCTAAA-ATTTATA
1 AATTCAAAATATTTATA
42755739 TATATTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 11 0.37
19 19 0.63
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.41
Consensus pattern (19 bp):
AATTCAAAATATTTATAAA
Found at i:42755717 original size:18 final size:19
Alignment explanation
Indices: 42755685--42755723 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
42755675 ATTACAAAAT
* *
42755685 AATTCAAAATAATTTTTAA
1 AATTAAAAATAATTTATAA
42755704 AATTAAAAAT-ATTTATAA
1 AATTAAAAATAATTTATAA
42755722 AA
1 AA
42755724 ATTCTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
AATTAAAAATAATTTATAA
Found at i:42755726 original size:28 final size:28
Alignment explanation
Indices: 42755672--42755754 Score: 71
Period size: 28 Copynumber: 2.9 Consensus size: 28
42755662 TCTCTCAACA
* *
42755672 AAAATTACAAAATAATTCA-AAATAATTTTT
1 AAAATTA-AAAAT-ATTTATAAA-AATTTCT
42755702 AAAATTAAAAATATTTATAAAAA-TTCT
1 AAAATTAAAAATATTTATAAAAATTTCT
* * *
42755729 AAAATTTATATATATTTTTAAAAATT
1 AAAA-TTAAAAATATTTATAAAAATT
42755755 ATAAAAATAT
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
27 7 0.16
28 22 0.49
29 9 0.20
30 7 0.16
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (28 bp):
AAAATTAAAAATATTTATAAAAATTTCT
Found at i:42764154 original size:32 final size:32
Alignment explanation
Indices: 42764080--42764154 Score: 75
Period size: 32 Copynumber: 2.3 Consensus size: 32
42764070 TTTGTTACGT
42764080 GCTCGAGCTTTATCAAGCTCAAATTTTCTCAG
1 GCTCGAGCTTTATCAAGCTCAAATTTTCTCAG
* * *
42764112 GATC-AGGCTTT-TCCTAGCTCGAATTTTCTC-G
1 GCTCGA-GCTTTAT-CAAGCTCAAATTTTCTCAG
42764143 AGCTCGAGCTTT
1 -GCTCGAGCTTT
42764155 CTTGAACTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
31 3 0.09
32 31 0.89
33 1 0.03
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.36
Consensus pattern (32 bp):
GCTCGAGCTTTATCAAGCTCAAATTTTCTCAG
Found at i:42766102 original size:18 final size:18
Alignment explanation
Indices: 42766079--42766121 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
42766069 ACTCAATCCA
**
42766079 AACCCAAGTATTCAACCC
1 AACCCAAGTACCCAACCC
*
42766097 AACCCAATTACCCAACCC
1 AACCCAAGTACCCAACCC
42766115 AACCCAA
1 AACCCAA
42766122 TCATAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.42, C:0.44, G:0.02, T:0.12
Consensus pattern (18 bp):
AACCCAAGTACCCAACCC
Found at i:42766239 original size:9 final size:9
Alignment explanation
Indices: 42766225--42766300 Score: 100
Period size: 9 Copynumber: 8.4 Consensus size: 9
42766215 GTAGTGATTC
42766225 AATTCGGTT
1 AATTCGGTT
*
42766234 AATTCGGGT
1 AATTCGGTT
42766243 AATTCGGTT
1 AATTCGGTT
42766252 AATTCAGG-T
1 AATTC-GGTT
*
42766261 AATCCGGTT
1 AATTCGGTT
42766270 AATTCGGTT
1 AATTCGGTT
* *
42766279 AATTTGGGT
1 AATTCGGTT
42766288 AATTCGGTT
1 AATTCGGTT
42766297 AATT
1 AATT
42766301 TTTAACCAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
8 2 0.04
9 53 0.93
10 2 0.04
ACGTcount: A:0.25, C:0.11, G:0.24, T:0.41
Consensus pattern (9 bp):
AATTCGGTT
Found at i:42773440 original size:14 final size:14
Alignment explanation
Indices: 42773421--42773454 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
42773411 ACTAAGCTAG
42773421 TTTTTTTG-TTTGT
1 TTTTTTTGTTTTGT
42773434 TTTTTTTGTTTTGT
1 TTTTTTTGTTTTGT
42773448 TTTTTTT
1 TTTTTTT
42773455 AACAGAATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (14 bp):
TTTTTTTGTTTTGT
Found at i:42776080 original size:11 final size:11
Alignment explanation
Indices: 42776053--42776091 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
42776043 TAAAATATAC
*
42776053 GAAATAGAGGG
1 GAAATAGAGAG
42776064 GAAAATAGAGAG
1 G-AAATAGAGAG
*
42776076 GAAATACAGAG
1 GAAATAGAGAG
42776087 GAAAT
1 GAAAT
42776092 TTGTTTTTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.54, C:0.03, G:0.33, T:0.10
Consensus pattern (11 bp):
GAAATAGAGAG
Found at i:42780869 original size:18 final size:18
Alignment explanation
Indices: 42780828--42780869 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
42780818 GAGCAAATGC
42780828 TTTTTCATTCTTTACGAT
1 TTTTTCATTCTTTACGAT
* **
42780846 TCTTTCATTCTTTTGGAT
1 TTTTTCATTCTTTACGAT
42780864 TTTTTC
1 TTTTTC
42780870 TGCCAAACTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.12, C:0.17, G:0.07, T:0.64
Consensus pattern (18 bp):
TTTTTCATTCTTTACGAT
Found at i:42783252 original size:89 final size:87
Alignment explanation
Indices: 42783157--42783399 Score: 378
Period size: 89 Copynumber: 2.7 Consensus size: 87
42783147 GTATTGGCGT
* * *
42783157 GAAGTAGATCGAGTACAACAGATCTTATTTTCATGTACTGGCGTGAAGTAGATCAAAGACAACAG
1 GAAGTAGATCGAG-AAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGA-AACAG
42783222 ATCTTGTCTTCCCATACTGGTGGC
64 ATCTTGTCTTCCCATACTGGTGGC
42783246 GAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAACACAG
1 GAAGTAGATCG-AGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAA-ACAG
42783311 ATCTTGTCTTCCCATACTGGTGGC
64 ATCTTGTCTTCCCATACTGGTGGC
* * *
42783335 GAAGTAGATCAAAGAAAATAGATCTTGTCTTCATGTACTGGCGTAAAGTAGATCAAAGATAACAG
1 GAAGTAGATC-GAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGA-AACAG
42783400 CCCTAAGGTT
Statistics
Matches: 144, Mismatches: 6, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
88 1 0.01
89 140 0.97
90 3 0.02
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (87 bp):
GAAGTAGATCGAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAACAGAT
CTTGTCTTCCCATACTGGTGGC
Found at i:42783266 original size:45 final size:45
Alignment explanation
Indices: 42783201--42783366 Score: 244
Period size: 45 Copynumber: 3.7 Consensus size: 45
42783191 GTACTGGCGT
*
42783201 GAAGTAGATCAAAGACAACAGATCTTGTCTTCCCATACTGGTGGC
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCCCATACTGGTGGC
* *** * *
42783246 GAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGG-CGT
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCCCATACTGGTGGC
*
42783290 GAAGTAGATCAAAGAACACAGATCTTGTCTTCCCATACTGGTGGC
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCCCATACTGGTGGC
*
42783335 GAAGTAGATCAAAGAAAATAGATCTTGTCTTC
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTC
42783367 ATGTACTGGC
Statistics
Matches: 104, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
44 37 0.36
45 67 0.64
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (45 bp):
GAAGTAGATCAAAGAAAACAGATCTTGTCTTCCCATACTGGTGGC
Found at i:42783374 original size:45 final size:44
Alignment explanation
Indices: 42783139--42783399 Score: 299
Period size: 44 Copynumber: 5.9 Consensus size: 44
42783129 AGCAGATATG
* * *
42783139 GTCTTCATGTATTGGCGTGAAGTAGATC-GAGTACAACAGATCTT
1 GTCTTCATGTACTGGCGTGAAGTAGATCAAAG-AAAACAGATCTT
* * *
42783183 ATTTTCATGTACTGGCGTGAAGTAGATCAAAGACAACAGATCTT
1 GTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAACAGATCTT
*** * * *
42783227 GTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTT
1 GTCTTCATGTACTGG-CGTGAAGTAGATCAAAGAAAACAGATCTT
*
42783272 GTCTTCATGTACTGGCGTGAAGTAGATCAAAGAACACAGATCTT
1 GTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAACAGATCTT
*** * * *
42783316 GTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAAATAGATCTT
1 GTCTTCATGTACTGG-CGTGAAGTAGATCAAAGAAAACAGATCTT
* *
42783361 GTCTTCATGTACTGGCGTAAAGTAGATCAAAGATAACAG
1 GTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAACAG
42783400 CCCTAAGGTT
Statistics
Matches: 179, Mismatches: 35, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
44 103 0.58
45 76 0.42
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (44 bp):
GTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAACAGATCTT
Found at i:42783503 original size:44 final size:44
Alignment explanation
Indices: 42783455--42783769 Score: 169
Period size: 44 Copynumber: 7.2 Consensus size: 44
42783445 CCTGGGCAAC
* *
42783455 AGTGGAATAGATTGAAGATTATAGATCTTATCTCCCTAAGCAGT
1 AGTGGAGTAGATTGAAGATTATAGATTTTATCTCCCTAAGCAGT
* ** ** * *
42783499 AGTGGAGCAGATCAAAGATGGTGGATTTTACCTCCCTAAG--GTT
1 AGTGGAGTAGATTGAAGATTATAGATTTTATCTCCCTAAGCAG-T
* ** * ** **
42783542 ACAGTGGAGTACATTGAAG-CCAGTA-ATTCTATCTCCCTGGGCAAC
1 --AGTGGAGTAGATTGAAGATTA-TAGATTTTATCTCCCTAAGCAGT
* *
42783587 AGTGGAATAGATTGAAGATTATAGATCTTATCTCCCTAAGCAGT
1 AGTGGAGTAGATTGAAGATTATAGATTTTATCTCCCTAAGCAGT
* ** ** * *
42783631 AGTGGAGCAGATCAAAGATGGTGGATTTTACCTCCCTAAG--GTT
1 AGTGGAGTAGATTGAAGATTATAGATTTTATCTCCCTAAGCAG-T
* ** * * ** **
42783674 ACAGTGGAGTACATTGAAG-CCAGTA-ATTCTATCTCCTTGGGCAAC
1 --AGTGGAGTAGATTGAAGATTA-TAGATTTTATCTCCCTAAGCAGT
* *
42783719 AGTGGAATAGATTGAAGATTACAGATTTTATCTCCCTAAGCAGT
1 AGTGGAGTAGATTGAAGATTATAGATTTTATCTCCCTAAGCAGT
42783763 AGTGGAG
1 AGTGGAG
42783770 CATATCAAAG
Statistics
Matches: 186, Mismatches: 69, Indels: 32
0.65 0.24 0.11
Matches are distributed among these distances:
42 2 0.01
43 35 0.19
44 121 0.65
45 28 0.15
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.29
Consensus pattern (44 bp):
AGTGGAGTAGATTGAAGATTATAGATTTTATCTCCCTAAGCAGT
Found at i:42783637 original size:132 final size:132
Alignment explanation
Indices: 42783400--42783867 Score: 785
Period size: 132 Copynumber: 3.6 Consensus size: 132
42783390 AAGATAACAG
42783400 CCCTAAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGGAATAG
1 CCCTAAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGGAATAG
42783465 ATTGAAGATTATAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTAC
66 ATTGAAGATTATAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTAC
42783530 CT
131 CT
42783532 CCCTAAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGGAATAG
1 CCCTAAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGGAATAG
42783597 ATTGAAGATTATAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTAC
66 ATTGAAGATTATAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTAC
42783662 CT
131 CT
*
42783664 CCCTAAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCTTGGGCAACAGTGGAATAG
1 CCCTAAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGGAATAG
* * * **
42783729 ATTGAAGATTACAGATTTTATCTCCCTAAGCAGTAGTGGAGCATATCAAAGATGGCAGATTTTAC
66 ATTGAAGATTATAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTAC
42783794 CT
131 CT
* * * * * * * * *
42783796 CCTTGAGGTTGCAGTGGAGTATATTGAAGTCAGT-ATTCTAACTCACTGGTCAGCAGTGGAATAG
1 CCCTAAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGGAATAG
*
42783860 ATCGAAGA
66 ATTGAAGA
42783868 AAACAGATCT
Statistics
Matches: 319, Mismatches: 17, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
131 32 0.10
132 287 0.90
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (132 bp):
CCCTAAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGGAATAG
ATTGAAGATTATAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTAC
CT
Found at i:42783920 original size:44 final size:44
Alignment explanation
Indices: 42783857--42784503 Score: 897
Period size: 44 Copynumber: 14.6 Consensus size: 44
42783847 AGCAGTGGAA
* * *
42783857 TAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCATGAAG
1 TAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAG
* *
42783901 TAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAG
1 TAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAG
42783945 TAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAG
1 TAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAG
42783989 TAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAG
1 TAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAG
* * * *
42784033 TAGATCGAAGATAGCAGATCTTGTCTTACCA--TACTGGTGGCGAAG
1 TAGATCGAAGAAAGCAGATCTTGTCTT--CATGTATTGG-CGTGAAG
*
42784078 TAGATCGAAGAAAGTAGATCTTGTCTTCATGTATTGGCGTGAAG
1 TAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAG
* *
42784122 TAGAACGAAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAG
1 TAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAG
* * *
42784166 TAGATCGAAGAAAACAGATCTTGTCTTCATGTATTGACATGAAG
1 TAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAG
* *
42784210 TATATCGAAGAAAGCATATCTTGTCTTCATGTATTGGCGTGAAG
1 TAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAG
* * * * *
42784254 CAGATCGAAGATAA-CAGATCTTGTCTTCTTATATTAGCAATGAAG
1 TAGATCGAAGA-AAGCAGATCTTGTCTTCATGTATTGGC-GTGAAG
* * * *
42784299 TAGATCGAGGAAAACAGATCTTGTCTTCATGTATTGTCATGAAG
1 TAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAG
* * *
42784343 CAGATCGAAGAAAGTAGATCTTGTCTTCATGTATTAGCGTGAAG
1 TAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAG
*
42784387 TAGATCGAGGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAG
1 TAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAG
* *
42784431 TAGATAGAAGAAAGCAGATCTTGTCTTCATGTATTGG-GGGCAAAG
1 TAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTG--AAG
* *
42784476 TAGATCGACGAAAGTAGATCTTGTCTTC
1 TAGATCGAAGAAAGCAGATCTTGTCTTC
42784504 CCATATATTG
Statistics
Matches: 540, Mismatches: 53, Indels: 19
0.88 0.09 0.03
Matches are distributed among these distances:
43 4 0.01
44 435 0.81
45 99 0.18
46 2 0.00
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.30
Consensus pattern (44 bp):
TAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAG
Found at i:42784152 original size:177 final size:175
Alignment explanation
Indices: 42783857--42784503 Score: 877
Period size: 177 Copynumber: 3.7 Consensus size: 175
42783847 AGCAGTGGAA
* * * *
42783857 TAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCATGAAGTAGATCGAAGAAAACAGATCT
1 TAGATCGAAGAAAGCAGATCTTGTCTTCA-GTATTGGCGTGAAGTAGATCGAAGAAAGCAGATCT
* *
42783922 TGTCTTCATGTACTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGA
65 TGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTATTGGCGTGA
42783987 AGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAG
130 AGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAG
* * * * *
42784033 TAGATCGAAGATAGCAGATCTTGTCTTACCA-TACTGGTGGCGAAGTAGATCGAAGAAAGTAGAT
1 TAGATCGAAGAAAGCAGATCTTGTCTT--CAGTATTGG-CGTGAAGTAGATCGAAGAAAGCAGAT
*
42784097 CTTGTCTTCATGTATTGGCGTGAAGTAGAACGAAGAAAACAGATCTTGTCTTCATGTATTGGCGT
63 CTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTATTGGCGT
* * *
42784162 GAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTATTGACATGAAG
128 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAG
* * *
42784210 TATATCGAAGAAAGCATATCTTGTCTTCATGTATTGGCGTGAAGCAGATCGAAGATAA-CAGATC
1 TAGATCGAAGAAAGCAGATCTTGTCTTCA-GTATTGGCGTGAAGTAGATCGAAGA-AAGCAGATC
* * * * * * *
42784274 TTGTCTTCTTATATTAGCAATGAAGTAGATCGAGGAAAACAGATCTTGTCTTCATGTATTGTCAT
64 TTGTCTTCATGTATTGGC-GTGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTATTGGCGT
* * *
42784339 GAAGCAGATCGAAGAAAGTAGATCTTGTCTTCATGTATTAGCGTGAAG
128 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAG
* *
42784387 TAGATCGAGGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATAGAAGAAAGCAGATCT
1 TAGATCGAAGAAAGCAGATCTTGTCTTCA-GTATTGGCGTGAAGTAGATCGAAGAAAGCAGATCT
* * **
42784452 TGTCTTCATGTATTGG-GGGCAAAGTAGATCGACGAAAGTAGATCTTGTCTTC
65 TGTCTTCATGTATTGGCGTG--AAGTAGATCGAAGAAAACAGATCTTGTCTTC
42784504 CCATATATTG
Statistics
Matches: 413, Mismatches: 48, Indels: 19
0.86 0.10 0.04
Matches are distributed among these distances:
175 3 0.01
176 68 0.16
177 340 0.82
178 2 0.00
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.30
Consensus pattern (175 bp):
TAGATCGAAGAAAGCAGATCTTGTCTTCAGTATTGGCGTGAAGTAGATCGAAGAAAGCAGATCTT
GTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAA
GTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAG
Found at i:42784240 original size:221 final size:219
Alignment explanation
Indices: 42783857--42784530 Score: 974
Period size: 221 Copynumber: 3.1 Consensus size: 219
42783847 AGCAGTGGAA
*
42783857 TAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCATGAAGTAGATCGAAGAAAACAGATCT
1 TAGATCGAAGAAAACAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAAGAAAACAGATCT
*
42783922 TGTCTTCATGTACTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGA
66 TGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGA
42783987 AGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGAT
131 AGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGAT
* *
42784052 CTTGTCTTACCATACTGGTGGCGAAG
196 CTTGTCTT-CCATA-TAGTGGAGAAG
** * *
42784078 TAGATCGAAGAAAGTAGATCTTGTCTTCATGTATTGGCGTGAAGTAGAACGAAGAAAACAGATCT
1 TAGATCGAAGAAAACAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAAGAAAACAGATCT
* * *
42784143 TGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTATTGACATGA
66 TGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGA
* * * *
42784208 AGTATATCGAAGAAAGCATATCTTGTCTTCATGTATTGGCGTGAAGCAGATCGAAGATAACAGAT
131 AGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGAT
* **
42784273 CTTGTCTTCTTATATTAG-CAATGAAG
196 CTTGTCTTC-CATA-TAGTGGA-GAAG
* * * **
42784299 TAGATCGAGGAAAACAGATCTTGTCTTCATGTATTGTCATGAAGCAGATCGAAGAAAGTAGATCT
1 TAGATCGAAGAAAACAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAAGAAAACAGATCT
* *
42784364 TGTCTTCATGTATTAGCGTGAAGTAGATCGAGGAAAGCAGATCTTGTCTTCATGTATTGGCGTGA
66 TGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGA
* * * * *
42784429 AGTAGATAGAAGAAAGCAGATCTTGTCTTCATGTATTGG-GGGCAAAGTAGATCGACGAAAGTAG
131 AGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTG--AAGTAGATCGAAGATAGCAG
* *
42784493 ATCTTGTCTTCCCATATATTGGAGAAA
194 ATCTTGTCTT-CCATATAGTGGAGAAG
42784520 TAGATCGAAGA
1 TAGATCGAAGA
42784531 TACAAGTCTT
Statistics
Matches: 399, Mismatches: 48, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
220 3 0.01
221 366 0.92
222 29 0.07
223 1 0.00
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (219 bp):
TAGATCGAAGAAAACAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAAGAAAACAGATCT
TGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGA
AGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGAT
CTTGTCTTCCATATAGTGGAGAAG
Found at i:42785293 original size:11 final size:11
Alignment explanation
Indices: 42785266--42785304 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
42785256 TAAAAGATAC
*
42785266 GAAATAGAGGG
1 GAAATAGAGAG
42785277 GAAAATAGAGAG
1 G-AAATAGAGAG
*
42785289 GAAATACAGAG
1 GAAATAGAGAG
42785300 GAAAT
1 GAAAT
42785305 TTATTTTTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.54, C:0.03, G:0.33, T:0.10
Consensus pattern (11 bp):
GAAATAGAGAG
Found at i:42796457 original size:2 final size:2
Alignment explanation
Indices: 42796452--42796484 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
42796442 AAAAAAAAGC
42796452 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
42796485 TACATAAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42802573 original size:5 final size:5
Alignment explanation
Indices: 42802563--42802589 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
42802553 TATTAAATAT
42802563 TAAAA TAAAA TAAAA TAAAA TAAAA TA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TA
42802590 TTTAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
TAAAA
Found at i:42803394 original size:24 final size:24
Alignment explanation
Indices: 42803344--42803395 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
42803334 TTAGTAAGTC
**
42803344 AAATAAACTATACTAATAAATGTT
1 AAATAAACTATACTAATAAATACT
*
42803368 AAATATACTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
42803392 AAAT
1 AAAT
42803396 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:42805692 original size:87 final size:87
Alignment explanation
Indices: 42805528--42805696 Score: 234
Period size: 87 Copynumber: 1.9 Consensus size: 87
42805518 GTTCCCATTT
* * * * * *
42805528 TTATATAAGCAAAATTATAGCTACCCATTATTATTGGGGTCTACTTTGATAAATAGCCGTTCATG
1 TTATACAAACAAAATTATAGCTACCCATTATTATTGGGGGCTAATTTGACAAATAGCCGTTCATC
42805593 TTTTTCAGAAAAAAAACTGTAC
66 TTTTTCAGAAAAAAAACTGTAC
*
42805615 TTATACAAACAAAATTATAGCTACCCCTTATTATTGGGGGCTAATTTGACAAATAGCCGTT-ATT
1 TTATACAAACAAAATTATAGCTACCCATTATTATTGGGGGCTAATTTGACAAATAGCCGTTCA--
42805679 TCTTTTTCTA-AAAAAAAA
64 TCTTTTTC-AGAAAAAAAA
42805697 TTCTTTGCTT
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
86 1 0.01
87 55 0.76
88 15 0.21
89 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (87 bp):
TTATACAAACAAAATTATAGCTACCCATTATTATTGGGGGCTAATTTGACAAATAGCCGTTCATC
TTTTTCAGAAAAAAAACTGTAC
Found at i:42807446 original size:18 final size:17
Alignment explanation
Indices: 42807423--42807459 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
42807413 AATATGTACG
*
42807423 TAATAATATTTTTACATA
1 TAATAATATTCTT-CATA
42807441 TAATAATATTCTTCATA
1 TAATAATATTCTTCATA
42807458 TA
1 TA
42807460 CATATAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (17 bp):
TAATAATATTCTTCATA
Found at i:42811090 original size:20 final size:20
Alignment explanation
Indices: 42811065--42811102 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
42811055 TGTCAAAATT
42811065 GAAATCTAGTGGCATTGATG
1 GAAATCTAGTGGCATTGATG
42811085 GAAATCTAGTGGCATTGA
1 GAAATCTAGTGGCATTGA
42811103 AGTTGAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.11, G:0.29, T:0.29
Consensus pattern (20 bp):
GAAATCTAGTGGCATTGATG
Found at i:42811308 original size:70 final size:70
Alignment explanation
Indices: 42811234--42811450 Score: 166
Period size: 65 Copynumber: 3.1 Consensus size: 70
42811224 CTCTTATCAG
42811234 TAATTGAATTGATTGAATTTAACTTTTATTTTAAAATAATTTTTATATTTTATAATTGTTTAATG
1 TAATTGAATTGATTGAATTTAACTTTTATTTTAAAATAATTTTTATATTTTATAATTGTTTAATG
42811299 TTATT
66 TTATT
* * * * ** * * ** * *
42811304 TAATT-TATT-ATTTATAATTAA-TATTTAAATTTAATGTCATTTTGA-A-GCTAT-CTGGCTCT
1 TAATTGAATTGATTGA-ATTTAACT-TTT-ATTTTAAAATAATTTTTATATTTTATAATTG-T-T
* *
42811363 T-A--TCA-G
61 TAATGTTATT
42811369 TAATTGAATTGATTGAATTTAACTTTTATTTTAAAATAATTTTTATATTTTATAATTGTTTAATG
1 TAATTGAATTGATTGAATTTAACTTTTATTTTAAAATAATTTTTATATTTTATAATTGTTTAATG
42811434 ATTTATT
66 --TTATT
*
42811441 TAATTCAATT
1 TAATTGAATT
42811451 AGATGAACTG
Statistics
Matches: 101, Mismatches: 29, Indels: 32
0.62 0.18 0.20
Matches are distributed among these distances:
65 18 0.18
66 16 0.16
67 12 0.12
68 12 0.12
69 14 0.14
70 18 0.18
71 2 0.02
72 9 0.09
ACGTcount: A:0.34, C:0.04, G:0.07, T:0.54
Consensus pattern (70 bp):
TAATTGAATTGATTGAATTTAACTTTTATTTTAAAATAATTTTTATATTTTATAATTGTTTAATG
TTATT
Found at i:42811322 original size:135 final size:136
Alignment explanation
Indices: 42811165--42811445 Score: 537
Period size: 135 Copynumber: 2.1 Consensus size: 136
42811155 CGTCATCAAA
42811165 ATTTAATATTATTATTTATAATTAATATTTAAATTTAATGTCATTTTGAAGCTATCTGGCTCTTA
1 ATTTAAT-TTATTATTTATAATTAATATTTAAATTTAATGTCATTTTGAAGCTATCTGGCTCTTA
42811230 TCAGTAATTGAATTGATTGAATTTAACTTTTATTTTAAAATAATTTTTATATTTTATAATTGTTT
65 TCAGTAATTGAATTGATTGAATTTAACTTTTATTTTAAAATAATTTTTATATTTTATAATTGTTT
42811295 AATG-TT
130 AATGATT
42811301 ATTTAATTTATTATTTATAATTAATATTTAAATTTAATGTCATTTTGAAGCTATCTGGCTCTTAT
1 ATTTAATTTATTATTTATAATTAATATTTAAATTTAATGTCATTTTGAAGCTATCTGGCTCTTAT
42811366 CAGTAATTGAATTGATTGAATTTAACTTTTATTTTAAAATAATTTTTATATTTTATAATTGTTTA
66 CAGTAATTGAATTGATTGAATTTAACTTTTATTTTAAAATAATTTTTATATTTTATAATTGTTTA
42811431 ATGATTT
131 ATGA-TT
42811438 ATTTAATT
1 ATTTAATT
42811446 CAATTAGATG
Statistics
Matches: 143, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
135 126 0.88
136 7 0.05
137 10 0.07
ACGTcount: A:0.34, C:0.05, G:0.08, T:0.53
Consensus pattern (136 bp):
ATTTAATTTATTATTTATAATTAATATTTAAATTTAATGTCATTTTGAAGCTATCTGGCTCTTAT
CAGTAATTGAATTGATTGAATTTAACTTTTATTTTAAAATAATTTTTATATTTTATAATTGTTTA
ATGATT
Found at i:42811411 original size:65 final size:65
Alignment explanation
Indices: 42811207--42811411 Score: 161
Period size: 65 Copynumber: 3.1 Consensus size: 65
42811197 ATTTAATGTC
42811207 ATTTTGAAGCTATCTGGCTCTTATCAGTAATTGAATTGATTGAATTTAACTTTTATTTTAAAATA
1 ATTTTGAAGCTATCTGGCTCTTATCAGTAATTGAATTGATTGAATTTAACTTTTATTTTAAAATA
* ** * * * * *
42811272 ATTTTTATATTTTATAATTG-T-TTA--ATGTTATTTAATTTATT-ATTTATAATTAA-TATTTA
1 ATTTTGA-A-GCTAT-CTGGCTCTTATCA-GTAATTGAATTGATTGA---AT--TTAACT-TTT-
* ** *
42811331 AATTTAATGTC
55 ATTTTAAAATA
42811342 ATTTTGAAGCTATCTGGCTCTTATCAGTAATTGAATTGATTGAATTTAACTTTTATTTTAAAATA
1 ATTTTGAAGCTATCTGGCTCTTATCAGTAATTGAATTGATTGAATTTAACTTTTATTTTAAAATA
42811407 ATTTT
1 ATTTT
42811412 TATATTTTAT
Statistics
Matches: 99, Mismatches: 24, Indels: 34
0.63 0.15 0.22
Matches are distributed among these distances:
64 2 0.02
65 30 0.30
66 11 0.11
67 9 0.09
68 9 0.09
69 11 0.11
70 25 0.25
71 2 0.02
ACGTcount: A:0.33, C:0.06, G:0.09, T:0.52
Consensus pattern (65 bp):
ATTTTGAAGCTATCTGGCTCTTATCAGTAATTGAATTGATTGAATTTAACTTTTATTTTAAAATA
Found at i:42815254 original size:30 final size:30
Alignment explanation
Indices: 42815220--42815282 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
42815210 ACTTATTTTA
42815220 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
*
42815250 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
42815280 TTG
1 TTG
42815283 CTTGTTAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.27, C:0.03, G:0.13, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:42815328 original size:16 final size:16
Alignment explanation
Indices: 42815304--42815337 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
42815294 GCATCTATCT
*
42815304 TAGTGTTATTTAACTA
1 TAGTATTATTTAACTA
*
42815320 TAGTATTATTTAAGTA
1 TAGTATTATTTAACTA
42815336 TA
1 TA
42815338 CATATTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.12, T:0.50
Consensus pattern (16 bp):
TAGTATTATTTAACTA
Found at i:42833542 original size:45 final size:45
Alignment explanation
Indices: 42833476--42833562 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
42833466 TGCTTTCAAT
* * *
42833476 AAAGATATCTTGTACTGTTTTCTTTATGTACAATATCTGTACTAC
1 AAAGATATCTTGTACTATTTTCTTTATGAAAAATATCTGTACTAC
42833521 AAAGATATCTTGTACTATTTTCTTTATGAAAAATATCTGTAC
1 AAAGATATCTTGTACTATTTTCTTTATGAAAAATATCTGTAC
42833563 AATAAGTTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (45 bp):
AAAGATATCTTGTACTATTTTCTTTATGAAAAATATCTGTACTAC
Found at i:42835063 original size:138 final size:138
Alignment explanation
Indices: 42834886--42835161 Score: 534
Period size: 138 Copynumber: 2.0 Consensus size: 138
42834876 AATAAAGAAT
*
42834886 ACAAGAATTTAACGAGGTTCAGTAAATTTTACCTACGTCCTCGGGCACTACCAAATATATTTCAC
1 ACAAGAATTTAACGAGGTTCAGCAAATTTTACCTACGTCCTCGGGCACTACCAAATATATTTCAC
42834951 TCCAAAATACAAGTGAGAATTTACAGAGAGAGAGAGAGAGAACAATGCCTTAAGTAGAGAATGTC
66 TCCAAAATACAAGTGAGAATTTACAGAGAGAGAGAGAGAGAACAATGCCTTAAGTAGAGAATGTC
42835016 AAATATGA
131 AAATATGA
*
42835024 ACAAGAATTTAACGAGGTTCAGCAAATTTTGCCTACGTCCTCGGGCACTACCAAATATATTTCAC
1 ACAAGAATTTAACGAGGTTCAGCAAATTTTACCTACGTCCTCGGGCACTACCAAATATATTTCAC
42835089 TCCAAAATACAAGTGAGAATTTACAGAGAGAGAGAGAGAGAACAATGCCTTAAGTAGAGAATGTC
66 TCCAAAATACAAGTGAGAATTTACAGAGAGAGAGAGAGAGAACAATGCCTTAAGTAGAGAATGTC
42835154 AAATATGA
131 AAATATGA
42835162 GATACAGAAT
Statistics
Matches: 136, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
138 136 1.00
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (138 bp):
ACAAGAATTTAACGAGGTTCAGCAAATTTTACCTACGTCCTCGGGCACTACCAAATATATTTCAC
TCCAAAATACAAGTGAGAATTTACAGAGAGAGAGAGAGAGAACAATGCCTTAAGTAGAGAATGTC
AAATATGA
Found at i:42835320 original size:30 final size:31
Alignment explanation
Indices: 42835274--42835337 Score: 103
Period size: 30 Copynumber: 2.1 Consensus size: 31
42835264 ATTTCTTATG
*
42835274 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATATCTCGATACCCATATATTTGACTTT
*
42835305 CCAATAT-TTGATACCCATATATTTGACTTT
1 CCAATATCTCGATACCCATATATTTGACTTT
42835335 CCA
1 CCA
42835338 TAAATATGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 24 0.77
31 7 0.23
ACGTcount: A:0.28, C:0.27, G:0.06, T:0.39
Consensus pattern (31 bp):
CCAATATCTCGATACCCATATATTTGACTTT
Found at i:42835326 original size:15 final size:15
Alignment explanation
Indices: 42835284--42835330 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
42835274 CCAATATCTC
*
42835284 GATACCCATATCTTT
1 GATACCCATATATTT
**
42835299 GACTTTCCA-ATATTT
1 GA-TACCCATATATTT
42835314 GATACCCATATATTT
1 GATACCCATATATTT
42835329 GA
1 GA
42835331 CTTTCCATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
14 4 0.16
15 17 0.68
16 4 0.16
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.40
Consensus pattern (15 bp):
GATACCCATATATTT
Found at i:42835822 original size:19 final size:19
Alignment explanation
Indices: 42835798--42835834 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
42835788 GATAAAATTA
42835798 TTTAAA-ATTTTCATAAAAT
1 TTTAAAGATTTTCA-AAAAT
42835817 TTTAAAGATTTTCAAAAA
1 TTTAAAGATTTTCAAAAA
42835835 AAAAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (19 bp):
TTTAAAGATTTTCAAAAAT
Found at i:42835835 original size:20 final size:19
Alignment explanation
Indices: 42835798--42835835 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
42835788 GATAAAATTA
*
42835798 TTTAAAATTTTCATAAAAT
1 TTTAAAATTTTCAAAAAAT
42835817 TTTAAAGATTTTCAAAAAA
1 TTTAAA-ATTTTCAAAAAA
42835836 AAAAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (19 bp):
TTTAAAATTTTCAAAAAAT
Found at i:42843762 original size:286 final size:287
Alignment explanation
Indices: 42843250--42843827 Score: 1149
Period size: 286 Copynumber: 2.0 Consensus size: 287
42843240 ATGTTAAACT
42843250 ATATATGAAAGTAGAATGAGAGTGATAATAAGTAGTAGGAAATAGGAATAATTAATGAGAATCTA
1 ATATATGAAAGTAGAATGAGAGTGATAATAAGTAGTAGGAAATAGGAATAATTAATGAGAATCTA
42843315 TACATTTATTCATTTTTTTTCTTTTGCAGCATAGAATGCTTTGATATTTTCACCATCTTCAAAGC
66 TACATTTATTCATTTTTTTTCTTTTGCAGCATAGAATGCTTTGATATTTTCACCATCTTCAAAGC
42843380 AGTCAAGAGATATTGAAGGCCTCTCTCATGTATGAATTTTTAATAATTTTATATATAAAAACTTT
131 AGTCAAGAGATATTGAAGGCCTCTCTCATGTATGAATTTTTAATAATTTTATATATAAAAACTTT
42843445 CAAACTTATTAAATATGATGAATATTTAATATTTCATATTTTTTTTACTTTGTTACTAGTTAATA
196 CAAACTTATTAAATATGATGAATATTTAATATTTCATATTTTTTTTACTTTGTTACTAGTTAATA
42843510 TAATATTCTTAGAAAA-TCATAAATAA
261 TAATATTCTTAGAAAATTCATAAATAA
42843536 ATATATGAAAGTAGAATGAGAGTGATAATAAGTAGTAGGAAATAGGAATAATTAATGAGAATCTA
1 ATATATGAAAGTAGAATGAGAGTGATAATAAGTAGTAGGAAATAGGAATAATTAATGAGAATCTA
42843601 TACATTTATTCATTTTTTTTCTTTTGCAGCATAGAATGCTTTGATATTTTCACCATCTTCAAAGC
66 TACATTTATTCATTTTTTTTCTTTTGCAGCATAGAATGCTTTGATATTTTCACCATCTTCAAAGC
42843666 AGTCAAGAGATATTGAAGGCCTCTCTCATGTATGAATTTTTAATAATTTTATATATAAAAACTTT
131 AGTCAAGAGATATTGAAGGCCTCTCTCATGTATGAATTTTTAATAATTTTATATATAAAAACTTT
42843731 CAAACTTATTAAATATGATGAATATTTAATATTTCATATTTTTTTTACTTTGTTACTAGTTAATA
196 CAAACTTATTAAATATGATGAATATTTAATATTTCATATTTTTTTTACTTTGTTACTAGTTAATA
42843796 TAATATTCTTAGAAAATTCATAAATAA
261 TAATATTCTTAGAAAATTCATAAATAA
42843823 ATATA
1 ATATA
42843828 AGAATAATTA
Statistics
Matches: 291, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
286 276 0.95
287 15 0.05
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (287 bp):
ATATATGAAAGTAGAATGAGAGTGATAATAAGTAGTAGGAAATAGGAATAATTAATGAGAATCTA
TACATTTATTCATTTTTTTTCTTTTGCAGCATAGAATGCTTTGATATTTTCACCATCTTCAAAGC
AGTCAAGAGATATTGAAGGCCTCTCTCATGTATGAATTTTTAATAATTTTATATATAAAAACTTT
CAAACTTATTAAATATGATGAATATTTAATATTTCATATTTTTTTTACTTTGTTACTAGTTAATA
TAATATTCTTAGAAAATTCATAAATAA
Found at i:42847215 original size:21 final size:19
Alignment explanation
Indices: 42847172--42847208 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
42847162 CATTATCATA
* *
42847172 TATAAAATAATATATAATT
1 TATAAAAAAATATAAAATT
42847191 TATAAAAAAATATAAAAT
1 TATAAAAAAATATAAAAT
42847209 ATTTATATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TATAAAAAAATATAAAATT
Found at i:42847732 original size:35 final size:35
Alignment explanation
Indices: 42847686--42847755 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
42847676 GAGTTACCAA
42847686 GCATCGTGTATAACTAGACTCAAATACAAATAAGC
1 GCATCGTGTATAACTAGACTCAAATACAAATAAGC
42847721 GCATCGTGTATAACTAGACTCAAATACAAATAAGC
1 GCATCGTGTATAACTAGACTCAAATACAAATAAGC
42847756 AGAGCATACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.23
Consensus pattern (35 bp):
GCATCGTGTATAACTAGACTCAAATACAAATAAGC
Found at i:42847967 original size:15 final size:15
Alignment explanation
Indices: 42847912--42847968 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 15
42847902 TGGTATAGAG
*
42847912 CAGAGCAGAGCAGAA
1 CAGAACAGAGCAGAA
* *
42847927 CTGAACAGAACAGAA
1 CAGAACAGAGCAGAA
**
42847942 CA-AAGTTGAGCAGAA
1 CAGAA-CAGAGCAGAA
42847957 CAGAACAGAGCA
1 CAGAACAGAGCA
42847969 TGTATGTTTA
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
14 2 0.06
15 27 0.87
16 2 0.06
ACGTcount: A:0.49, C:0.19, G:0.26, T:0.05
Consensus pattern (15 bp):
CAGAACAGAGCAGAA
Found at i:42848887 original size:42 final size:42
Alignment explanation
Indices: 42848809--42848889 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
42848799 ATAGTGAGTT
* *
42848809 ACACGGCCTAGACACATGCCCATGTCCTTGCCCGTGTGGCTC
1 ACACGGCCTAGACACACGCCCATGTCCCTGCCCGTGTGGCTC
**
42848851 ACACGGCCT-GAGCACACGCCCATGTCCCTGGTCGTGTGG
1 ACACGGCCTAGA-CACACGCCCATGTCCCTGCCCGTGTGG
42848890 TCCTAAACCA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 2 0.06
42 32 0.94
ACGTcount: A:0.16, C:0.37, G:0.27, T:0.20
Consensus pattern (42 bp):
ACACGGCCTAGACACACGCCCATGTCCCTGCCCGTGTGGCTC
Found at i:42848913 original size:104 final size:105
Alignment explanation
Indices: 42848709--42848950 Score: 326
Period size: 104 Copynumber: 2.3 Consensus size: 105
42848699 ACTCACAAGA
* * * *
42848709 CCTAGACACACACCGATGTCCTTACCCGTATGGCTTACACGGCCTAGGCACATACACCCATGTCC
1 CCTAGACACACACCCATGTCCTTGCCCGTGTGGCTCACACGGCCTAGGCACA-ACACCCATGTCC
* *
42848774 CTGGCCATGTAGTCCTAAATCATAAATAGTGAGTTACACGG
65 CTGGCCATGTAGTCCTAAACCATAAACAGTGAGTTACACGG
** *
42848815 CCTAGACACATGCCCATGTCCTTGCCCGTGTGGCTCACACGGCCT-GAGCAC-ACGCCCATGTCC
1 CCTAGACACACACCCATGTCCTTGCCCGTGTGGCTCACACGGCCTAG-GCACAACACCCATGTCC
* * *
42848878 CTGGTCGTGTGGTCCTAAACCATAAACAGTGAGTTACACGG
65 CTGGCCATGTAGTCCTAAACCATAAACAGTGAGTTACACGG
* *
42848919 CCTGGACACACACCTATGTCCTTGCCCGTGTG
1 CCTAGACACACACCCATGTCCTTGCCCGTGTG
42848951 AACCCTACAC
Statistics
Matches: 119, Mismatches: 16, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
104 75 0.63
105 1 0.01
106 43 0.36
ACGTcount: A:0.23, C:0.33, G:0.21, T:0.22
Consensus pattern (105 bp):
CCTAGACACACACCCATGTCCTTGCCCGTGTGGCTCACACGGCCTAGGCACAACACCCATGTCCC
TGGCCATGTAGTCCTAAACCATAAACAGTGAGTTACACGG
Found at i:42849763 original size:15 final size:16
Alignment explanation
Indices: 42849733--42849765 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
42849723 CCACTCTTGG
42849733 TTTCAAACCTCAATTT
1 TTTCAAACCTCAATTT
*
42849749 TTTCTAACC-CAATTT
1 TTTCAAACCTCAATTT
42849764 TT
1 TT
42849766 GGGATGTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.27, C:0.24, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTCAAACCTCAATTT
Found at i:42850897 original size:45 final size:45
Alignment explanation
Indices: 42850829--42850915 Score: 131
Period size: 45 Copynumber: 1.9 Consensus size: 45
42850819 TACGCCTAAA
* **
42850829 ATGAGTAAGACCATAACTAAAAGATTTTATGACATCATGATAAGG
1 ATGAGTAAGACAATAACTAAAAGATACTATGACATCATGATAAGG
42850874 ATGAGTAAGACAATAA-TAGAAAGATACTATGACATCATGATA
1 ATGAGTAAGACAATAACTA-AAAGATACTATGACATCATGATA
42850916 TAAATGATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 2 0.05
45 36 0.95
ACGTcount: A:0.47, C:0.10, G:0.17, T:0.25
Consensus pattern (45 bp):
ATGAGTAAGACAATAACTAAAAGATACTATGACATCATGATAAGG
Found at i:42855716 original size:20 final size:20
Alignment explanation
Indices: 42855693--42855745 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 20
42855683 TTTTAAAACA
42855693 GTTTTAACTTGATTAAAAAT
1 GTTTTAACTTGATTAAAAAT
** * *
42855713 G-TTTAACTCAATTGAAAGT
1 GTTTTAACTTGATTAAAAAT
*
42855732 TTTTTAACTTGATT
1 GTTTTAACTTGATT
42855746 TTATCATTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.34, C:0.08, G:0.11, T:0.47
Consensus pattern (20 bp):
GTTTTAACTTGATTAAAAAT
Found at i:42856597 original size:42 final size:42
Alignment explanation
Indices: 42856538--42856631 Score: 161
Period size: 42 Copynumber: 2.2 Consensus size: 42
42856528 GTTTACAAAA
*
42856538 AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTTG
1 AAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTTG
**
42856580 AAAAAAACGTTGCTAAAGAACATGTTCTTTAGCGGCGCTTTG
1 AAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTTG
42856622 AAAAAAACGC
1 AAAAAAACGC
42856632 NNNNNNNNNN
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.23
Consensus pattern (42 bp):
AAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTTG
Found at i:42872604 original size:113 final size:112
Alignment explanation
Indices: 42872502--42872873 Score: 380
Period size: 113 Copynumber: 3.3 Consensus size: 112
42872492 TCGCTAATAC
* *
42872502 TATTCTTTTGCGGTG-TTTTATAGAAAACGCCACAATGTCTAATATACAATTGAACCAAACGCTG
1 TATTCTTTTACGGCGTTTTTATAGAAAACGCCACAAT-TCTAATATAC-ATTGAACCAAACGCTG
42872566 CGTTTTGGTTAAGGTATTTTGCGGCGCTTACAATAAACGCCACTAATTA
64 CGTTTTGGTTAAGGTATTTTGCGGCGCTTACAATAAACGCCACTAATTA
* * * * * * ** * *
42872615 TGTTCTTTTACGGCGTTTTTCTA-AAAATGCCACTAATACTAATCTACCTCAAGACGAAACGGTG
1 TATTCTTTTACGGCGTTTTTATAGAAAACGCCAC-AATTCTAATATACATTGA-ACCAAACGCTG
* ** * * * * *
42872679 CATTTTCATTAAGATA-TTTGTGGCGCTTTACCGA-AAACGTCGCTAA-TA
64 CGTTTTGGTTAAGGTATTTTGCGGCGC-TTA-CAATAAACGCCACTAATTA
** * *
42872727 CTATTCTTTCGCGGCGTTTTTTATAAAAAACGCCATGAATTCTAATATACATTGAACC-AACGCT
1 -TATTCTTTTACGGCG-TTTTTATAGAAAACGCCA-CAATTCTAATATACATTGAACCAAACGCT
42872791 GCGTTTTGGTTAAGGTATTTTGCGGCGCTTACAATAAACGCCACTAATTA
63 GCGTTTTGGTTAAGGTATTTTGCGGCGCTTACAATAAACGCCACTAATTA
* *
42872841 TGTTCTTTTACGGCGTTTTTTTAG-AAACGCCAC
1 TATTCTTTTACGGCGTTTTTATAGAAAACGCCAC
42872874 TAGTTCTTCA
Statistics
Matches: 200, Mismatches: 47, Indels: 27
0.73 0.17 0.10
Matches are distributed among these distances:
111 8 0.04
112 22 0.11
113 118 0.59
114 31 0.16
115 21 0.10
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (112 bp):
TATTCTTTTACGGCGTTTTTATAGAAAACGCCACAATTCTAATATACATTGAACCAAACGCTGCG
TTTTGGTTAAGGTATTTTGCGGCGCTTACAATAAACGCCACTAATTA
Found at i:42872796 original size:226 final size:226
Alignment explanation
Indices: 42872402--42872875 Score: 837
Period size: 226 Copynumber: 2.1 Consensus size: 226
42872392 NNNNNNNNNN
42872402 CGTTTTTCTAAAAATGCCACTAATACTAATCTACCTCAAGACGAAACGGTGCATTTTCATTAAGA
1 CGTTTTTCTAAAAATGCCACTAATACTAATCTACCTCAAGACGAAACGGTGCATTTTCATTAAGA
* *
42872467 TATTTGTGGCGCTTTACCGAAAACGTCGCTAATACTATTCTTTTGCGGTGTTTTATAGAAAACGC
66 TATTTGTGGCGCTTTACCGAAAACGTCGCTAATACTATTCTTTCGCGGTGTTTTATAAAAAACGC
42872532 CACAATGTCTAATATACAATTGAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGCGCTTAC
131 CACAATGTCTAATATACAATTGAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGCGCTTAC
42872597 AATAAACGCCACTAATTATGTTCTTTTACGG
196 AATAAACGCCACTAATTATGTTCTTTTACGG
42872628 CGTTTTTCTAAAAATGCCACTAATACTAATCTACCTCAAGACGAAACGGTGCATTTTCATTAAGA
1 CGTTTTTCTAAAAATGCCACTAATACTAATCTACCTCAAGACGAAACGGTGCATTTTCATTAAGA
*
42872693 TATTTGTGGCGCTTTACCGAAAACGTCGCTAATACTATTCTTTCGCGGCGTTTTTTATAAAAAAC
66 TATTTGTGGCGCTTTACCGAAAACGTCGCTAATACTATTCTTTCGC-G-GTGTTTTATAAAAAAC
*
42872758 GCCATGAAT-TCTAATATAC-ATTGAACC-AACGCTGCGTTTTGGTTAAGGTATTTTGCGGCGCT
129 GCCA-CAATGTCTAATATACAATTGAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGCGCT
42872820 TACAATAAACGCCACTAATTATGTTCTTTTACGG
193 TACAATAAACGCCACTAATTATGTTCTTTTACGG
* * *
42872854 CGTTTTTTTAGAAACGCCACTA
1 CGTTTTTCTAAAAATGCCACTA
42872876 GTTCTTCAGG
Statistics
Matches: 238, Mismatches: 7, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
226 198 0.83
227 9 0.04
228 28 0.12
229 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.34
Consensus pattern (226 bp):
CGTTTTTCTAAAAATGCCACTAATACTAATCTACCTCAAGACGAAACGGTGCATTTTCATTAAGA
TATTTGTGGCGCTTTACCGAAAACGTCGCTAATACTATTCTTTCGCGGTGTTTTATAAAAAACGC
CACAATGTCTAATATACAATTGAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGCGCTTAC
AATAAACGCCACTAATTATGTTCTTTTACGG
Found at i:42873142 original size:20 final size:20
Alignment explanation
Indices: 42873119--42873156 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
42873109 CAATCTTTAC
*
42873119 TAAAATGTAACGTAATGAAT
1 TAAAATGTAACCTAATGAAT
42873139 TAAAATGTAACCTAATGA
1 TAAAATGTAACCTAATGA
42873157 TTGGAAAAAA
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:0.50, C:0.08, G:0.13, T:0.29
Consensus pattern (20 bp):
TAAAATGTAACCTAATGAAT
Found at i:42880954 original size:14 final size:14
Alignment explanation
Indices: 42880937--42880978 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
42880927 GGGTTAATAT
42880937 AATATTTATATTAA
1 AATATTTATATTAA
42880951 AATATTGT-TA--AA
1 AATATT-TATATTAA
42880963 AATATTTATATTAA
1 AATATTTATATTAA
42880977 AA
1 AA
42880979 ATTATTGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
11 1 0.04
12 10 0.42
14 12 0.50
15 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (14 bp):
AATATTTATATTAA
Found at i:42880989 original size:26 final size:26
Alignment explanation
Indices: 42880937--42880989 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
42880927 GGGTTAATAT
*
42880937 AATATTTATATTAAAATATTGTTAAA
1 AATATTTATATTAAAATATTATTAAA
*
42880963 AATATTTATATTAAAA-ATTATTGAA
1 AATATTTATATTAAAATATTATTAAA
42880988 AA
1 AA
42880990 GCACACCTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 9 0.36
26 16 0.64
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (26 bp):
AATATTTATATTAAAATATTATTAAA
Found at i:42883097 original size:63 final size:63
Alignment explanation
Indices: 42882922--42883097 Score: 219
Period size: 63 Copynumber: 2.8 Consensus size: 63
42882912 GTGTCATTTT
* * * * *
42882922 CCCGTGTAGTCCTTAATGGAAAACAGTGAGTCACATGGCTTGGACACACACTCGTGTCTATGG
1 CCCGTGTGGTCCTTAATGGAAAACAGTGAGTCACATGGCCTGGACACACGCCCGTGTCCATGG
* * * * *
42882985 CCTGTGTGGTCCTTAATGGAAAACAGTAAGTCACACGGCCTGGATACACGCCCGTGTCCCTGG
1 CCCGTGTGGTCCTTAATGGAAAACAGTGAGTCACATGGCCTGGACACACGCCCGTGTCCATGG
* * *
42883048 CCCGTGTGGTTCC-TAATGGCAAATAGTGAGCCACATGGCCTGGACACACG
1 CCCGTGTGG-TCCTTAATGGAAAACAGTGAGTCACATGGCCTGGACACACG
42883098 GCCTACCACA
Statistics
Matches: 95, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
63 92 0.97
64 3 0.03
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.23
Consensus pattern (63 bp):
CCCGTGTGGTCCTTAATGGAAAACAGTGAGTCACATGGCCTGGACACACGCCCGTGTCCATGG
Done.