Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015314.1 Kokia drynarioides strain JFW-HI SEQ_130359, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 241155
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 617 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:154605 original size:208 final size:208
Alignment explanation
Indices: 154387--156029 Score: 2013
Period size: 208 Copynumber: 7.9 Consensus size: 208
154377 GATTTAGTCT
* * * * * * * * *
154387 ACTTCTCTATATCTTATCAGAAAGATGACCGCCTCATT-ATTTCAATCCACTTCTTTGTATCTCA
1 ACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTGCTTT-GATCCACTTCTCTGTATCTCA
* *
154451 TCAGGAAGATTGGGTTTGAAGTC-CTATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACTTC
65 TCAGAAAGATGGGGTTTGAAGTCTC-ATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACTTC
* * *
154515 TCTGTATCTCATC-AGAAAGATGACCACCTCATTGTTTTAA-CTCACTTCTCTGTATCTCATCAA
129 TCTGTATCTCATCAAG-AAGATGACCGCCTCATTGTTTCAATC-CACTTCTCTGTATCTCATCAG
** * * *
154578 GAAGGTGAATTTGATTT
192 GAAGACGGATTTGGTTC
* * * * * *
154595 ACTTCTCTATATTTCATTAGGAAGATGACCACTGTATTGCTTTGACCCACTTCTTTGTATCTCAT
1 ACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTGCTTTGATCCACTTCTCTGTATCTCAT
*
154660 CAGTAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACTTCTC
66 CAGAAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACTTCTC
* * *
154725 TGTATCTCATCAAGAAGATGATCGCTTCATTGATTCAATCCACTTCTCTGTATCTCATCAGGAAG
131 TGTATCTCATCAAGAAGATGACCGCCTCATTGTTTCAATCCACTTCTCTGTATCTCATCAGGAAG
* *
154790 ACAGATTTGGTCC
196 ACGGATTTGGTTC
*
154803 ACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTGCTTTGATCCACTTCTCTGTATCTTAT
1 ACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTGCTTTGATCCACTTCTCTGTATCTCA-
* * *
154868 TC-GAAAGATGGGGTTTGACGTCTCATTCGTATTAAGCTTCGCTTCATTGATTTGGTTTACTTCT
65 TCAGAAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACTTCT
* * * *
154932 CTGTATCTCATCAAGAAGATGATCGCTTCATTGATTCAATCCACTTCTCTGTATCTCATCAAGAA
130 CTGTATCTCATCAAGAAGATGACCGCCTCATTGTTTCAATCCACTTCTCTGTATCTCATCAGGAA
*
154997 GACGGATTTGGTCC
195 GACGGATTTGGTTC
* *
155011 ACTACTCTGTATCTCATCAGGAAGATGACCACTTTATTGCTTTGATCCACTTCTCTGTATCTTAT
1 ACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTGCTTTGATCCACTTCTCTGTATCTCAT
* *
155076 CCGGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACTTCTC
66 CAGAAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACTTCTC
* * * * *
155141 TGTATTTCATCAGGAAGATGACTGCCTCATTGTTTCAATCCACTTCTCTATATCTCTTCAGGAAG
131 TGTATCTCATCAAGAAGATGACCGCCTCATTGTTTCAATCCACTTCTCTGTATCTCATCAGGAAG
*
155206 ACGAATTTGGTTC
196 ACGGATTTGGTTC
* * * * * * *
155219 ACTTTTCTGTATCTCATCAGGAAGATGATCGCTTTATTTCTTTGACCCATTTCTATGTATCTCAT
1 ACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTGCTTTGATCCACTTCTCTGTATCTCAT
* * * * ** * * * * *
155284 CAAAAAGATGAGGTTTGAAGTTTCACTCACATTAAGCCTT-GTTTCATTGACTTGGTCTTCCTCT
66 CAGAAAGATGGGGTTTGAAGTCTCATTCGTATTGAG-CTTCGCTTCATTGATTTGGTCTACTTCT
** * *
155348 CTGTATCTCATCAAGAAGATGACTACCTCATTGTTTCAATCCACTTCTCTATATCTCATTAGGAA
130 CTGTATCTCATCAAGAAGATGACCGCCTCATTGTTTCAATCCACTTCTCTGTATCTCATCAGGAA
*
155413 GACGGATTTGATTC
195 GACGGATTTGGTTC
* * ** * * *
155427 ACTTCTCTGCACCTTGTGAAGAGGATGACCACTTTATTGCTTTGATCCACTTCTCTGTATCTCAT
1 ACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTGCTTTGATCCACTTCTCTGTATCTCAT
* * *
155492 CAGAAAGATGGGGTTTGAAGTCTCATTCGTATTAAGCTTCACTTCATTGATTTGGTCTACTTCTT
66 CAGAAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACTTCTC
* * * * * *
155557 TGTATTTCATCAGGAAGATGACTGTCTTATTGTTTCAATCCACTTCTCTGTATCTCATCAAGAAG
131 TGTATCTCATCAAGAAGATGACCGCCTCATTGTTTCAATCCACTTCTCTGTATCTCATCAGGAAG
*
155622 ATGGATTTGGTTC
196 ACGGATTTGGTTC
* * *** *
155635 ACTTCTTTGTATCTCATCAGAAAGATGATTGCTTTATTGCTTT-AACCAACTTCTCTGTATCTCA
1 ACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTGCTTTGATCC-ACTTCTCTGTATCTCA
* * * * *
155699 TCAGGAAGATGGGGTTTGAAGTCCCATTCGTATTTAGCTTCACTTTATTGATTTGGTCTACTTCT
65 TCAGAAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACTTCT
* * * *
155764 CTGTATCTTATCAAGAAGATGACCGCGTCATTGTTTCAATACACTTCTCTGTATCTCATTAGGAA
130 CTGTATCTCATCAAGAAGATGACCGCCTCATTGTTTCAATCCACTTCTCTGTATCTCATCAGGAA
* * *
155829 GGCGGAGTTGGTTT
195 GACGGATTTGGTTC
* * * * * *
155843 ACTTCTCTATATCTCATTAGGAAGATGACCACTTTATTGCTTTGACCCATTTATTTGTATCTCAT
1 ACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTGCTTTGATCCACTTCTCTGTATCTCAT
* * *
155908 CAGTAAGATGGGGTTTGAAGTCTCATTTGTATTGA-----G---CATTGATTTGGTCTATTTCTC
66 CAGAAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACTTCTC
* * * * *
155965 TTTATCTCATCAGGAAGAT-ACCGCTTCATTGATTCAATCCAATTCTCTGTATCTCATCAGGAAG
131 TGTATCTCATCAAGAAGATGACCGCCTCATTGTTTCAATCCACTTCTCTGTATCTCATCAGGAAG
156029 A
196 A
156030 TGACCACTTT
Statistics
Matches: 1246, Mismatches: 179, Indels: 29
0.86 0.12 0.02
Matches are distributed among these distances:
199 40 0.03
200 35 0.03
207 8 0.01
208 1148 0.92
209 15 0.01
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.39
Consensus pattern (208 bp):
ACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTGCTTTGATCCACTTCTCTGTATCTCAT
CAGAAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACTTCTC
TGTATCTCATCAAGAAGATGACCGCCTCATTGTTTCAATCCACTTCTCTGTATCTCATCAGGAAG
ACGGATTTGGTTC
Found at i:154682 original size:539 final size:539
Alignment explanation
Indices: 153838--154998 Score: 1508
Period size: 539 Copynumber: 2.2 Consensus size: 539
153828 CAGGAAGGCG
* * * ** * * * ** *
153838 GATTTGGTTTACTTTTCTATATCTCATCAAGAAGATGACTACTTTATTGCTTTGACCCACTTCTT
1 GATTTAGTCTACTTCTCTATATCTCATCAAGAAGATGACCGCCTCATTGATTCAATCCACTTCTT
* * *
153903 TGTATCTCATCAGTAAGATGGGGTTTGAAGTTTCATTCGTATTGAGCTTCACTTTATTGATTTGG
66 TGTATCTCATCAGGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCTTCACTTCATTGATTTGG
* * ** *
153968 TTTACTTCTCTATATCTCATCAGGAAGATGACTGCTTCATTGATTTAATCCACTTCTCCGTATCT
131 TCTACTTCTCTATATCTCATCAGAAAGATGACCACCTCATTGATTTAATCCACTTCTCCGTATCT
* * * * * *
154033 CATCAGGAAGACGGATTTGGTCCACTTCTTTGTATCTCATCAAGAAGATGACCACTTTATTACTT
196 CATCAAGAAGACGAATTTGATCCACTTCTCTATATCTCATCAAGAAGATGACCACTGTATTACTT
** *
154098 TGAGTCACCTTTCTGTATCTCATCAAGAAGATAGGGTTTGAAGTCTCAATCGTATTGAGTTTCGC
261 TGACCCACCTTTCTGTATCTCATCAAGAAGATAGGGTTTGAAGTCTCAATCGTATTGAGCTTCGC
* * * *
154163 TTCATTGATTTGATCTACTTTTCTATATTTCATCAGGAAGATGACCGCCTCATTGTTTCAATCCA
326 TTCATTGATTTGATCTACTTCTCTATATCTCATCAAGAAGATGACCGCCTCATTGATTCAATCCA
* * *
154228 CTTTTCTGTATTTGATCAGAAAGACAGATTTGGTCCACTTCTCTGTATCTCATCAAAAAGATGAC
391 CTTCTCTGTATCTCATCAGAAAGACAGATTTGGTCCACTTCTCTGTATCTCATCAAAAAGATGAC
* * * * *
154293 TACTTTATTGCTTTAA-CTCACTTTTCTGTATCTCATTAGGAAGATGGGGTTTGAAGTTTTATTC
456 CACTTTATTGCTTTAATC-CACTTCTCTGTATCTCATTAGAAAGATGGGGTTTGAAGTCTCATTC
154357 AAATTAAACTTCGCTTCATT
520 AAATTAAACTTCGCTTCATT
*
154377 GATTTAGTCTACTTCTCTATATCTTATC-AGAAAGATGACCGCCTCATT-ATTTCAATCCACTTC
1 GATTTAGTCTACTTCTCTATATCTCATCAAG-AAGATGACCGCCTCATTGA-TTCAATCCACTTC
* *
154440 TTTGTATCTCATCAGGAAGATTGGGTTTGAAGTC-CTATTCGTATTGAGCTTCGCTTCATTGATT
64 TTTGTATCTCATCAGGAAGATGGGGTTTGAAGTCTC-ATTCGTATTGAGCTTCACTTCATTGATT
* * *
154504 TGGTCTACTTCTCTGTATCTCATCAGAAAGATGACCACCTCATTGTTTTAA-CTCACTTCTCTGT
128 TGGTCTACTTCTCTATATCTCATCAGAAAGATGACCACCTCATTGATTTAATC-CACTTCTCCGT
** ** * * *
154568 ATCTCATCAAGAAGGTGAATTTGATTTACTTCTCTATATTTCATTAGGAAGATGACCACTGTATT
192 ATCTCATCAAGAAGACGAATTTGATCCACTTCTCTATATCTCATCAAGAAGATGACCACTGTATT
* * * *
154633 GCTTTGACCCA-CTTCTTTGTATCTCATC-AGTAAGATGGGGTTTGAAGTCTCATTCGTATTGAG
257 ACTTTGACCCACCTT-TCTGTATCTCATCAAG-AAGATAGGGTTTGAAGTCTCAATCGTATTGAG
* * * *
154696 CTTCGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGATCGCTTCATTGATTC
320 CTTCGCTTCATTGATTTGATCTACTTCTCTATATCTCATCAAGAAGATGACCGCCTCATTGATTC
* **
154761 AATCCACTTCTCTGTATCTCATCAGGAAGACAGATTTGGTCCACTTCTCTGTATCTCATCAGGAA
385 AATCCACTTCTCTGTATCTCATCAGAAAGACAGATTTGGTCCACTTCTCTGTATCTCATCAAAAA
* * * *
154826 GATGACCACTTTATTGCTTTGATCCACTTCTCTGTATCTTATTCGAAAGATGGGGTTTGACGTCT
450 GATGACCACTTTATTGCTTTAATCCACTTCTCTGTATCTCATTAGAAAGATGGGGTTTGAAGTCT
** *
154891 CATTCGTATTAAGCTTCGCTTCATT
515 CATTCAAATTAAACTTCGCTTCATT
* * * * * *
154916 GATTTGGTTTACTTCTCTGTATCTCATCAAGAAGATGATCGCTTCATTGATTCAATCCACTTCTC
1 GATTTAGTCTACTTCTCTATATCTCATCAAGAAGATGACCGCCTCATTGATTCAATCCACTTCTT
*
154981 TGTATCTCATCAAGAAGA
66 TGTATCTCATCAGGAAGA
154999 CGGATTTGGT
Statistics
Matches: 534, Mismatches: 79, Indels: 18
0.85 0.13 0.03
Matches are distributed among these distances:
538 9 0.02
539 521 0.98
540 4 0.01
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.39
Consensus pattern (539 bp):
GATTTAGTCTACTTCTCTATATCTCATCAAGAAGATGACCGCCTCATTGATTCAATCCACTTCTT
TGTATCTCATCAGGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCTTCACTTCATTGATTTGG
TCTACTTCTCTATATCTCATCAGAAAGATGACCACCTCATTGATTTAATCCACTTCTCCGTATCT
CATCAAGAAGACGAATTTGATCCACTTCTCTATATCTCATCAAGAAGATGACCACTGTATTACTT
TGACCCACCTTTCTGTATCTCATCAAGAAGATAGGGTTTGAAGTCTCAATCGTATTGAGCTTCGC
TTCATTGATTTGATCTACTTCTCTATATCTCATCAAGAAGATGACCGCCTCATTGATTCAATCCA
CTTCTCTGTATCTCATCAGAAAGACAGATTTGGTCCACTTCTCTGTATCTCATCAAAAAGATGAC
CACTTTATTGCTTTAATCCACTTCTCTGTATCTCATTAGAAAGATGGGGTTTGAAGTCTCATTCA
AATTAAACTTCGCTTCATT
Found at i:154753 original size:48 final size:48
Alignment explanation
Indices: 154698--154790 Score: 141
Period size: 48 Copynumber: 1.9 Consensus size: 48
154688 GTATTGAGCT
*** *
154698 TCGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGA
1 TCGCTTCATTGATTCAATCCACTTCTCTGTATCTCATCAAGAAGATGA
*
154746 TCGCTTCATTGATTCAATCCACTTCTCTGTATCTCATCAGGAAGA
1 TCGCTTCATTGATTCAATCCACTTCTCTGTATCTCATCAAGAAGA
154791 CAGATTTGGT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.38
Consensus pattern (48 bp):
TCGCTTCATTGATTCAATCCACTTCTCTGTATCTCATCAAGAAGATGA
Found at i:154851 original size:85 final size:85
Alignment explanation
Indices: 154708--154864 Score: 242
Period size: 85 Copynumber: 1.8 Consensus size: 85
154698 TCGCTTCATT
* * *
154708 GATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGATCGCTTCATTGATTCAATCCACTTCTC
1 GATTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGACCACTTCATTGATTCAATCCACTTCTC
154773 TGTATCTCATCAGGAAGACA
66 TGTATCTCATCAGGAAGACA
* * * **
154793 GATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTGCTTTGATCCACTTCTC
1 GATTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGACCACTTCATTGATTCAATCCACTTCTC
154858 TGTATCT
66 TGTATCT
154865 TATTCGAAAG
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
85 64 1.00
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.38
Consensus pattern (85 bp):
GATTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGACCACTTCATTGATTCAATCCACTTCTC
TGTATCTCATCAGGAAGACA
Found at i:155083 original size:85 final size:85
Alignment explanation
Indices: 154916--155072 Score: 224
Period size: 85 Copynumber: 1.8 Consensus size: 85
154906 TCGCTTCATT
** * * *
154916 GATTTGGTTTACTTCTCTGTATCTCATCAAGAAGATGATCGCTTCATTGATTCAATCCACTTCTC
1 GATTTGGTCCACTACTCTGTATCTCATCAAGAAGATGACCACTTCATTGATTCAATCCACTTCTC
154981 TGTATCTCATCAAGAAGACG
66 TGTATCTCATCAAGAAGACG
* * * **
155001 GATTTGGTCCACTACTCTGTATCTCATCAGGAAGATGACCACTTTATTGCTTTGATCCACTTCTC
1 GATTTGGTCCACTACTCTGTATCTCATCAAGAAGATGACCACTTCATTGATTCAATCCACTTCTC
155066 TGTATCT
66 TGTATCT
155073 TATCCGGAAG
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
85 62 1.00
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.38
Consensus pattern (85 bp):
GATTTGGTCCACTACTCTGTATCTCATCAAGAAGATGACCACTTCATTGATTCAATCCACTTCTC
TGTATCTCATCAAGAAGACG
Found at i:155084 original size:747 final size:747
Alignment explanation
Indices: 153690--155206 Score: 2233
Period size: 747 Copynumber: 2.0 Consensus size: 747
153680 TTTGACCCAT
* *
153690 TTCTTTCTATCTCATTAGGAAGATAGGGTTTGAAGTCCCATTCGTATTATGCTTCGCTTCATTGA
1 TTCTTTATATCTCATCAGGAAGATAGGGTTTGAAGTCCCATTCGTATTATGCTTCGCTTCATTGA
* *
153755 TTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCATTATTTTAATCCACTTCTCTA
66 TTTGGTCTACTTCTCTGTATCTCATCAGAAAGATGACCACCTCATTATTTTAATCCACTTCTCTA
* * * * * *
153820 TATCTCATCAGGAAGGCGGATTTGGTTTACTTTTCTATATCTCATCAAGAAGATGACTACTTTAT
131 TATCTCATCAAGAAGGCGAATTTGATTTACTTCTCTATATCTCATCAAGAAGATGACCACTGTAT
*
153885 TGCTTTGACCCACTTCTTTGTATCTCATCAGTAAGATGGGGTTTGAAGTTTCATTCGTATTGAGC
196 TGCTTTGACCCACTTCTTTGTATCTCATCAGTAAGATGGGGTTTGAAGTCTCATTCGTATTGAGC
* * * *
153950 TTCACTTTATTGATTTGGTTTACTTCTCTATATCTCATCAGGAAGATGACTGCTTCATTGATTTA
261 TTCACTTCATTGATTTGGTCTACTTCTCTATATCTCATCAAGAAGATGACTGCTTCATTGATTCA
* *
154015 ATCCACTTCTCCGTATCTCATCAGGAAGACGGATTTGGTCCACTTCTTTGTATCTCATCAAGAAG
326 ATCCACTTCTCCGTATCTCATCAGGAAGACAGATTTGGTCCACTTCTCTGTATCTCATCAAGAAG
154080 ATGACCACTTTATTACTTTGAGTCACCTTTCTGTATCTCATCAAGAAGATAGGGTTTGAAGTCTC
391 ATGACCACTTTATTACTTTGAGTCACCTTTCTGTATCTCATCAAGAAGATAGGGTTTGAAGTCTC
* * * * *
154145 AATCGTATTGAGTTTCGCTTCATTGATTTGATCTACTTTTCTATATTTCATCAGGAAGATGACCG
456 AATCGTATTAAGCTTCGCTTCATTGATTTGATCTACTTCTCTATATCTCATCAAGAAGATGACCG
* * * * *
154210 CCTCATTGTTTCAATCCACTTTTCTGTATTTGATCAGAAAGACAGATTTGGTCCACTTCTCTGTA
521 CCTCATTGATTCAATCCACTTCTCTGTATCTCATCAGAAAGACAGATTTGGTCCACTACTCTGTA
* * *
154275 TCTCATCAAAAAGATGACTACTTTATTGCTTTAACTCACTTTTCTGTATCTCATTAGGAAGATGG
586 TCTCATCAAAAAGATGACCACTTTATTGCTTTAACTCACTTCTCTGTATCTCATCAGGAAGATGG
* *
154340 GGTTTGAAGTTTTATTCAAATTAAACTTCGCTTCATTGATTTAGTCTACTTCTCTATATCTT-AT
651 GGTTTGAAGTCTCATTCAAATTAAACTTCGCTTCATTGATTTAGTCTACTTCTCTATAT-TTCAT
154404 CAGAAAGATGACCGCCTCATTATTTCAATCCAC
715 CAGAAAGATGACCGCCTCATTATTTCAATCCAC
* * *
154437 TTCTTTGTATCTCATCAGGAAGATTGGGTTTGAAGTCCTATTCGTATTGA-GCTTCGCTTCATTG
1 TTCTTTATATCTCATCAGGAAGATAGGGTTTGAAGTCCCATTCGTATT-ATGCTTCGCTTCATTG
*
154501 ATTTGGTCTACTTCTCTGTATCTCATCAGAAAGATGACCACCTCATTGTTTTAA-CTCACTTCTC
65 ATTTGGTCTACTTCTCTGTATCTCATCAGAAAGATGACCACCTCATTATTTTAATC-CACTTCTC
* * * * *
154565 TGTATCTCATCAAGAAGGTGAATTTGATTTACTTCTCTATATTTCATTAGGAAGATGACCACTGT
129 TATATCTCATCAAGAAGGCGAATTTGATTTACTTCTCTATATCTCATCAAGAAGATGACCACTGT
154630 ATTGCTTTGACCCACTTCTTTGTATCTCATCAGTAAGATGGGGTTTGAAGTCTCATTCGTATTGA
194 ATTGCTTTGACCCACTTCTTTGTATCTCATCAGTAAGATGGGGTTTGAAGTCTCATTCGTATTGA
* *
154695 GCTTCGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGA-TCGCTTCATTGAT
259 GCTTCACTTCATTGATTTGGTCTACTTCTCTATATCTCATCAAGAAGATGACT-GCTTCATTGAT
* *
154759 TCAATCCACTTCTCTGTATCTCATCAGGAAGACAGATTTGGTCCACTTCTCTGTATCTCATCAGG
323 TCAATCCACTTCTCCGTATCTCATCAGGAAGACAGATTTGGTCCACTTCTCTGTATCTCATCAAG
* * * *
154824 AAGATGACCACTTTATTGCTTTGA-TC-CACTTCTCTGTATCTTATTCGA-AAGATGGGGTTTGA
388 AAGATGACCACTTTATTACTTTGAGTCAC-CTT-TCTGTATCTCA-TCAAGAAGATAGGGTTTGA
* * * * *
154886 CGTCTCATTCGTATTAAGCTTCGCTTCATTGATTTGGTTTACTTCTCTGTATCTCATCAAGAAGA
450 AGTCTCAATCGTATTAAGCTTCGCTTCATTGATTTGATCTACTTCTCTATATCTCATCAAGAAGA
* * *
154951 TGATCGCTTCATTGATTCAATCCACTTCTCTGTATCTCATCA-AGAAGACGGATTTGGTCCACTA
515 TGACCGCCTCATTGATTCAATCCACTTCTCTGTATCTCATCAGA-AAGACAGATTTGGTCCACTA
** * * *
155015 CTCTGTATCTCATCAGGAAGATGACCACTTTATTGCTTTGA-TCCACTTCTCTGTATCTTATCCG
579 CTCTGTATCTCATCAAAAAGATGACCACTTTATTGCTTTAACT-CACTTCTCTGTATCTCATCAG
** * * * *
155079 GAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACTTCTCTGT
643 GAAGATGGGGTTTGAAGTCTCATTCAAATTAAACTTCGCTTCATTGATTTAGTCTACTTCTCTAT
* * *
155144 ATTTCATCAGGAAGATGACTGCCTCATTGTTTCAATCCAC
708 ATTTCATCAGAAAGATGACCGCCTCATTATTTCAATCCAC
* *
155184 TTCTCTATATCTCTTCAGGAAGA
1 TTCTTTATATCTCATCAGGAAGA
155207 CGAATTTGGT
Statistics
Matches: 688, Mismatches: 73, Indels: 18
0.88 0.09 0.02
Matches are distributed among these distances:
745 1 0.00
746 11 0.02
747 672 0.98
748 4 0.01
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (747 bp):
TTCTTTATATCTCATCAGGAAGATAGGGTTTGAAGTCCCATTCGTATTATGCTTCGCTTCATTGA
TTTGGTCTACTTCTCTGTATCTCATCAGAAAGATGACCACCTCATTATTTTAATCCACTTCTCTA
TATCTCATCAAGAAGGCGAATTTGATTTACTTCTCTATATCTCATCAAGAAGATGACCACTGTAT
TGCTTTGACCCACTTCTTTGTATCTCATCAGTAAGATGGGGTTTGAAGTCTCATTCGTATTGAGC
TTCACTTCATTGATTTGGTCTACTTCTCTATATCTCATCAAGAAGATGACTGCTTCATTGATTCA
ATCCACTTCTCCGTATCTCATCAGGAAGACAGATTTGGTCCACTTCTCTGTATCTCATCAAGAAG
ATGACCACTTTATTACTTTGAGTCACCTTTCTGTATCTCATCAAGAAGATAGGGTTTGAAGTCTC
AATCGTATTAAGCTTCGCTTCATTGATTTGATCTACTTCTCTATATCTCATCAAGAAGATGACCG
CCTCATTGATTCAATCCACTTCTCTGTATCTCATCAGAAAGACAGATTTGGTCCACTACTCTGTA
TCTCATCAAAAAGATGACCACTTTATTGCTTTAACTCACTTCTCTGTATCTCATCAGGAAGATGG
GGTTTGAAGTCTCATTCAAATTAAACTTCGCTTCATTGATTTAGTCTACTTCTCTATATTTCATC
AGAAAGATGACCGCCTCATTATTTCAATCCAC
Found at i:155687 original size:85 final size:85
Alignment explanation
Indices: 155540--155710 Score: 242
Period size: 85 Copynumber: 2.0 Consensus size: 85
155530 TCACTTCATT
* *
155540 GATTTGGTCTACTTCTTTGTATTTCATCAGGAAGATGACTGTCTTATTGTTTCAATCCACTTCTC
1 GATTTGGTCTACTTCTTTGTATCTCATCAGAAAGATGACTGTCTTATTGTTTCAATCCACTTCTC
155605 TGTATCTCATCAAGAAGATG
66 TGTATCTCATCAAGAAGATG
*
155625 GATTTGGT-TCACTTCTTTGTATCTCATCAGAAAGATGATTG-CTTTATTGCTTT-AA-CCAACT
1 GATTTGGTCT-ACTTCTTTGTATCTCATCAGAAAGATGACTGTC-TTATTG-TTTCAATCC-ACT
*
155686 TCTCTGTATCTCATCAGGAAGATG
62 TCTCTGTATCTCATCAAGAAGATG
155710 G
1 G
155711 GGTTTGAAGT
Statistics
Matches: 78, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
84 4 0.05
85 71 0.91
86 3 0.04
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (85 bp):
GATTTGGTCTACTTCTTTGTATCTCATCAGAAAGATGACTGTCTTATTGTTTCAATCCACTTCTC
TGTATCTCATCAAGAAGATG
Found at i:156066 original size:48 final size:47
Alignment explanation
Indices: 155960--156079 Score: 150
Period size: 48 Copynumber: 2.5 Consensus size: 47
155950 TTTGGTCTAT
* *
155960 TTCTCTTTATCTCATCAGGAAGATACCGCTTCATTGATTCAATCCAA
1 TTCTCTGTATCTCATCAGGAAGATACCACTTCATTGATTCAATCCAA
* * ** *
156007 TTCTCTGTATCTCATCAGGAAGATGACCACTTTATTGCTTTGATCCAC
1 TTCTCTGTATCTCATCAGGAAGAT-ACCACTTCATTGATTCAATCCAA
* *
156055 TTCTCTGTATCTTATCAAGAAGATA
1 TTCTCTGTATCTCATCAGGAAGATA
156080 GGGTTTGAAG
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
47 24 0.38
48 39 0.62
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (47 bp):
TTCTCTGTATCTCATCAGGAAGATACCACTTCATTGATTCAATCCAA
Found at i:156361 original size:160 final size:159
Alignment explanation
Indices: 156045--156351 Score: 445
Period size: 160 Copynumber: 1.9 Consensus size: 159
156035 ACTTTATTGC
* *
156045 TTTGATCCACTTCTCTGTATCTTATCAAGAAGATAGGGTTTGAAGTCTCATTCGTATTAAGCTTT
1 TTTGATCCACTTCTCTGTATCTCATCAAGAAGATAGGGTTTGAAGTCTCATTCGTATTAAGCTTC
* * ** *
156110 GCTTATTGATTTGGTCTACTTCTCTGTATTTCATCAGGAACATGACTGCCTCATTGTTTCAATCC
66 ACTTATTAATTTACTCTACTTCTCTGTATTTCATCAGGAACATGACTGCCTCATTATTTCAATCC
* *
156175 ACTTCTTTGTATCTCATCAAGAAGATGGA
131 ACTTCTCTATATCTCATCAAGAAGATGGA
* * * *
156204 TTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCTTC
1 TTTGATCCACTTCTCTGTATCTCATCAAGAAGATAGGGTTTGAAGTCTCATTCGTATTAAGCTTC
* * *
156269 ACTTCATTAATTTACTCTACTTCTTTGTATCTT-ATTAGGAAGATGACTGCCTCATTATTTCAAT
66 ACTT-ATTAATTTACTCTACTTCTCTGTAT-TTCATCAGGAACATGACTGCCTCATTATTTCAAT
156333 CCACTTCTCTATATCTCAT
129 CCACTTCTCTATATCTCAT
156352 TTGGAAGATG
Statistics
Matches: 130, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
159 62 0.48
160 66 0.51
161 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.41
Consensus pattern (159 bp):
TTTGATCCACTTCTCTGTATCTCATCAAGAAGATAGGGTTTGAAGTCTCATTCGTATTAAGCTTC
ACTTATTAATTTACTCTACTTCTCTGTATTTCATCAGGAACATGACTGCCTCATTATTTCAATCC
ACTTCTCTATATCTCATCAAGAAGATGGA
Found at i:156595 original size:42 final size:42
Alignment explanation
Indices: 156549--156704 Score: 194
Period size: 42 Copynumber: 3.7 Consensus size: 42
156539 TGCAATTTAC
* *
156549 CCCATGA-CAGGGGTAAGAGATTAGATGATGGCTGTAATTTAA
1 CCCATGATCAGGGGTAAGAGATTGGATGATGGCTGTAATCT-A
* *
156591 CCCATGATCA-GGGTAAGAAATTGGGTGATGGCTGTAATCTA
1 CCCATGATCAGGGGTAAGAGATTGGATGATGGCTGTAATCTA
* *
156632 CCCAATGAT-AGGGGTAAGAGATTGGATGATGGTTGTAATCTG
1 CCC-ATGATCAGGGGTAAGAGATTGGATGATGGCTGTAATCTA
*
156674 CCTCATGATC-TGGGTAAGAGATTGGATGATG
1 CC-CATGATCAGGGGTAAGAGATTGGATGATG
156705 ATGTAACTTC
Statistics
Matches: 100, Mismatches: 9, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
41 5 0.05
42 92 0.92
43 3 0.03
ACGTcount: A:0.29, C:0.12, G:0.31, T:0.28
Consensus pattern (42 bp):
CCCATGATCAGGGGTAAGAGATTGGATGATGGCTGTAATCTA
Found at i:156689 original size:84 final size:84
Alignment explanation
Indices: 156546--156704 Score: 221
Period size: 84 Copynumber: 1.9 Consensus size: 84
156536 GAATGCAATT
* *
156546 TACCCCATGACAGGGGTAAGAGATTAGATGATGGCTGTAATTTAACCCATGATCAGGGTAAGAAA
1 TACCCAATGACAGGGGTAAGAGATTAGATGATGGCTGTAATCTAACCCATGATCAGGGTAAGAAA
*
156611 TTGGGTGATGGCTGTAATC
66 TTGGATGATGGCTGTAATC
* * * * * *
156630 TACCCAATGATAGGGGTAAGAGATTGGATGATGGTTGTAATCT-GCCTCATGATCTGGGTAAGAG
1 TACCCAATGACAGGGGTAAGAGATTAGATGATGGCTGTAATCTAACC-CATGATCAGGGTAAGAA
156694 ATTGGATGATG
65 ATTGGATGATG
156705 ATGTAACTTC
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
83 2 0.03
84 63 0.97
ACGTcount: A:0.30, C:0.13, G:0.30, T:0.28
Consensus pattern (84 bp):
TACCCAATGACAGGGGTAAGAGATTAGATGATGGCTGTAATCTAACCCATGATCAGGGTAAGAAA
TTGGATGATGGCTGTAATC
Found at i:164329 original size:59 final size:59
Alignment explanation
Indices: 164265--164382 Score: 211
Period size: 59 Copynumber: 2.0 Consensus size: 59
164255 TAAATATACC
*
164265 CAAATCGAAATTGGTTCATCCCATTTGATTTTTTTTTTTTCC-TTTTTTAAAAAAAAAA
1 CAAATCGAAATTGGTTCATCCCATTTGATTATTTTTTTTTCCTTTTTTTAAAAAAAAAA
164323 NCAAATCGAAATTGGTTCATCCCATTTGATTATTTTTTTTTCCTTTTTTTAAAAAAAAAA
1 -CAAATCGAAATTGGTTCATCCCATTTGATTATTTTTTTTTCCTTTTTTTAAAAAAAAAA
164383 GCTTGTATTG
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
59 41 0.72
60 16 0.28
ACGTcount: A:0.33, C:0.14, G:0.07, T:0.46
Consensus pattern (59 bp):
CAAATCGAAATTGGTTCATCCCATTTGATTATTTTTTTTTCCTTTTTTTAAAAAAAAAA
Found at i:166359 original size:42 final size:42
Alignment explanation
Indices: 166291--166395 Score: 165
Period size: 42 Copynumber: 2.5 Consensus size: 42
166281 GCGTTTTTGT
** *
166291 TGTGCATCCACAACCCAATGGCAACTATTATCTACAAACATGC
1 TGTGCATCCAC-GGCCAATGGAAACTATTATCTACAAACATGC
*
166334 TGTGCATCCACGGCCAATGGAAACTATTATCTACAAACATGT
1 TGTGCATCCACGGCCAATGGAAACTATTATCTACAAACATGC
166376 TGTGCATCCACGGCCAATGG
1 TGTGCATCCACGGCCAATGG
166396 TAGTTTTTAC
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
42 47 0.81
43 11 0.19
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (42 bp):
TGTGCATCCACGGCCAATGGAAACTATTATCTACAAACATGC
Found at i:170822 original size:26 final size:27
Alignment explanation
Indices: 170770--170836 Score: 82
Period size: 26 Copynumber: 2.4 Consensus size: 27
170760 AAAAATACTC
170770 TATTTTTATAAATAATTTAAATCTTATAT
1 TATTTTTATAAATAATTT--ATCTTATAT
* *
170799 TATTTTTATAATTAATTT-TTTTATAT
1 TATTTTTATAAATAATTTATCTTATAT
*
170825 TATTTTGATAAA
1 TATTTTTATAAA
170837 AATCCTAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
26 17 0.50
29 17 0.50
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (27 bp):
TATTTTTATAAATAATTTATCTTATAT
Found at i:170829 original size:13 final size:13
Alignment explanation
Indices: 170793--170830 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
170783 AATTTAAATC
170793 TTATATTATTTTT
1 TTATATTATTTTT
*
170806 ATA-ATTAATTTTT
1 TTATATT-ATTTTT
170819 TTATATTATTTT
1 TTATATTATTTT
170831 GATAAAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
12 3 0.14
13 15 0.71
14 3 0.14
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTATATTATTTTT
Found at i:180397 original size:21 final size:21
Alignment explanation
Indices: 180371--180416 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
180361 AAAACGAGCG
*
180371 TTTTTT-GCCTTTAAATTTTAA
1 TTTTTTCG-CTTTAAATTTGAA
*
180392 TTTTTTCGGTTTAAATTTGAA
1 TTTTTTCGCTTTAAATTTGAA
180413 TTTT
1 TTTT
180417 GAAACATTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.22, C:0.07, G:0.09, T:0.63
Consensus pattern (21 bp):
TTTTTTCGCTTTAAATTTGAA
Found at i:180926 original size:41 final size:41
Alignment explanation
Indices: 180855--181104 Score: 187
Period size: 41 Copynumber: 6.2 Consensus size: 41
180845 TTTAAATAAA
** * *
180855 TTAGCGGCATTTTTCCCAT-AGCGCCGCTATTCCTCTGACCT
1 TTAGCGGCGCTTTT-CCATAAGCGCCACTATTGCTCTGACCT
* * *
180896 TTAGCGGCGCTTTTCCATAAGCGTCACTATTACTGTGACCT
1 TTAGCGGCGCTTTTCCATAAGCGCCACTATTGCTCTGACCT
* ** * ** *
180937 TTAGCGGCGCTTATTGC-TCTG-ACCTTTAGT-CTCTGACCT
1 TTAGCGGCGCTT-TTCCATAAGCGCCACTATTGCTCTGACCT
* *
180976 TTAGCAGCGCTTTTCCATAAGCGCCACTATTGCTTTGACCT
1 TTAGCGGCGCTTTTCCATAAGCGCCACTATTGCTCTGACCT
*** *
181017 TTAGCGGCGCTTATGGGA-AAGCGCCGCTATTGCTCTGACCT
1 TTAGCGGCGCTT-TTCCATAAGCGCCACTATTGCTCTGACCT
* * *
181058 TTAGCGACG----TCCGA-AAGCGCCGCTATTGCTCTAACCT
1 TTAGCGGCGCTTTTCC-ATAAGCGCCACTATTGCTCTGACCT
181095 TTAGCGGCGC
1 TTAGCGGCGC
181105 CTGTTGCTCT
Statistics
Matches: 165, Mismatches: 36, Indels: 19
0.75 0.16 0.09
Matches are distributed among these distances:
37 31 0.19
38 3 0.02
39 21 0.13
40 13 0.08
41 92 0.56
42 5 0.03
ACGTcount: A:0.17, C:0.30, G:0.22, T:0.32
Consensus pattern (41 bp):
TTAGCGGCGCTTTTCCATAAGCGCCACTATTGCTCTGACCT
Found at i:180972 original size:14 final size:14
Alignment explanation
Indices: 180953--180979 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
180943 GCGCTTATTG
180953 CTCTGACCTTTAGT
1 CTCTGACCTTTAGT
180967 CTCTGACCTTTAG
1 CTCTGACCTTTAG
180980 CAGCGCTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.30, G:0.15, T:0.41
Consensus pattern (14 bp):
CTCTGACCTTTAGT
Found at i:181171 original size:41 final size:41
Alignment explanation
Indices: 181108--181196 Score: 135
Period size: 41 Copynumber: 2.2 Consensus size: 41
181098 GCGGCGCCTG
* *
181108 TTGCTCTGACCTTTAGTAGCGCTT-TCCAATAAGCGTCGCTA
1 TTGCTCTGACCTTTAGCAGCGCTTGACC-ATAAGCGTCGCTA
*
181149 TTGCTCTGACCTTTAGCGGCGCTTGACCATAAGCGTCGCTA
1 TTGCTCTGACCTTTAGCAGCGCTTGACCATAAGCGTCGCTA
181190 TTGCTCT
1 TTGCTCT
181197 ATCTTTTGCG
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
41 42 0.95
42 2 0.05
ACGTcount: A:0.17, C:0.28, G:0.21, T:0.34
Consensus pattern (41 bp):
TTGCTCTGACCTTTAGCAGCGCTTGACCATAAGCGTCGCTA
Found at i:181723 original size:14 final size:14
Alignment explanation
Indices: 181700--181733 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
181690 TGTCGTTTCG
*
181700 TTATTATATTGTTA
1 TTATTTTATTGTTA
181714 TTATTTTATTGTTA
1 TTATTTTATTGTTA
181728 TT-TTTT
1 TTATTTT
181734 GGATATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.74
Consensus pattern (14 bp):
TTATTTTATTGTTA
Found at i:184686 original size:43 final size:43
Alignment explanation
Indices: 184626--184820 Score: 211
Period size: 43 Copynumber: 4.6 Consensus size: 43
184616 GTTTTTAACA
* **
184626 GCGC-TTTCCCACAAACGCTACTAAAGACCATGATCTTTAGCG
1 GCGCTTTTTCCACAAACGCCGCTAAAGACCATGATCTTTAGCG
*
184668 GCGCTTTTTCCACAAACGCCGCTAAAGACCATGTTCTTTAGCG
1 GCGCTTTTTCCACAAACGCCGCTAAAGACCATGATCTTTAGCG
* * *
184711 ACGC-TTTTCTCACAAACGCCGCTAAAAGA-CATGGTCTTTAACG
1 GCGCTTTTTC-CACAAACGCCGCT-AAAGACCATGATCTTTAGCG
* * * * *
184754 GTGCTTTCT-CACAAATGCCGCTAAAAAACATGATCTTTAGCG
1 GCGCTTTTTCCACAAACGCCGCTAAAGACCATGATCTTTAGCG
*
184796 GCG-TTTTTCCCACAAACGCCACTAA
1 GCGCTTTTT-CCACAAACGCCGCTAA
184821 CATTAACAAA
Statistics
Matches: 128, Mismatches: 18, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
41 8 0.06
42 35 0.27
43 77 0.60
44 8 0.06
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.26
Consensus pattern (43 bp):
GCGCTTTTTCCACAAACGCCGCTAAAGACCATGATCTTTAGCG
Found at i:184791 original size:85 final size:87
Alignment explanation
Indices: 184630--184820 Score: 244
Period size: 85 Copynumber: 2.2 Consensus size: 87
184620 TTAACAGCGC
* * *
184630 TTTCCCACAAACGCTACT-AAAGACCATGATCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAA
1 TTTCCCACAAACGCCACTAAAAGACCATGATCTTTAACGGCGCTTTCTCCACAAACGCCGCTAAA
* * *
184694 GACCATGTTCTTTAGCGACGCT
66 AAACATGATCTTTAGCGACGCT
* * * * *
184716 TTTCTCACAAACGCCGCTAAAAGA-CATGGTCTTTAACGGTGCTTTCT-CACAAATGCCGCTAAA
1 TTTCCCACAAACGCCACTAAAAGACCATGATCTTTAACGGCGCTTTCTCCACAAACGCCGCTAAA
* *
184779 AAACATGATCTTTAGCGGCGTT
66 AAACATGATCTTTAGCGACGCT
184801 TTTCCCACAAACGCCACTAA
1 TTTCCCACAAACGCCACTAA
184821 CATTAACAAA
Statistics
Matches: 89, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
85 50 0.56
86 34 0.38
87 5 0.06
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.27
Consensus pattern (87 bp):
TTTCCCACAAACGCCACTAAAAGACCATGATCTTTAACGGCGCTTTCTCCACAAACGCCGCTAAA
AAACATGATCTTTAGCGACGCT
Found at i:185145 original size:20 final size:20
Alignment explanation
Indices: 185120--185157 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
185110 AATTCTTAAC
185120 AAAATTGAAACAAAAAATGT
1 AAAATTGAAACAAAAAATGT
* *
185140 AAAATTTAGACAAAAAAT
1 AAAATTGAAACAAAAAAT
185158 TTCTAAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.66, C:0.05, G:0.08, T:0.21
Consensus pattern (20 bp):
AAAATTGAAACAAAAAATGT
Found at i:186529 original size:33 final size:33
Alignment explanation
Indices: 186468--186534 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
186458 GACGCTAATG
* ** *
186468 CTCTCACCTTTAGCGGCTTTTCCGCACAAGCGC
1 CTCTCACCTTTAGAGGCGCTTCCCCACAAGCGC
*
186501 CTCTGACCTTTAGAGGCGCTTCCCCACAAGCGC
1 CTCTCACCTTTAGAGGCGCTTCCCCACAAGCGC
186534 C
1 C
186535 GCTAATGCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.16, C:0.40, G:0.19, T:0.24
Consensus pattern (33 bp):
CTCTCACCTTTAGAGGCGCTTCCCCACAAGCGC
Found at i:186568 original size:40 final size:40
Alignment explanation
Indices: 186506--186591 Score: 127
Period size: 40 Copynumber: 2.1 Consensus size: 40
186496 AGCGCCTCTG
186506 ACCTTTAGAGGCGCTTCCCCACAAGCGCCGCTAATGCTTT
1 ACCTTTAGAGGCGCTTCCCCACAAGCGCCGCTAATGCTTT
* * ** *
186546 ATCTTTAGCGGCGCTTTTCCACAAGCGTCGCTAATGCTTT
1 ACCTTTAGAGGCGCTTCCCCACAAGCGCCGCTAATGCTTT
186586 ACCTTT
1 ACCTTT
186592 TATGGCGTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.19, C:0.31, G:0.19, T:0.31
Consensus pattern (40 bp):
ACCTTTAGAGGCGCTTCCCCACAAGCGCCGCTAATGCTTT
Found at i:187027 original size:28 final size:30
Alignment explanation
Indices: 186985--187041 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 30
186975 ATTTTAAATA
* *
186985 TAAAATTATTAAAATTATTATATTATTTTT
1 TAAAATTATTAAAATTATTAAATAATTTTT
187015 TAAAA-TA-TAAAATTATTAAATAATTTT
1 TAAAATTATTAAAATTATTAAATAATTTT
187042 ATTTTCAACC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 18 0.72
29 2 0.08
30 5 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (30 bp):
TAAAATTATTAAAATTATTAAATAATTTTT
Found at i:190948 original size:30 final size:30
Alignment explanation
Indices: 190912--190976 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
190902 CAATATAACA
* *
190912 AACAAATGCCTCTAAAATAGTAATAAAATT
1 AACAAATGCCTCTAAAATAATAACAAAATT
*
190942 AACAAATGTCTCTAAAATAATAACAAAATT
1 AACAAATGCCTCTAAAATAATAACAAAATT
190972 AACAA
1 AACAA
190977 TAAAATAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.57, C:0.14, G:0.05, T:0.25
Consensus pattern (30 bp):
AACAAATGCCTCTAAAATAATAACAAAATT
Found at i:195620 original size:30 final size:30
Alignment explanation
Indices: 195545--195683 Score: 133
Period size: 30 Copynumber: 4.6 Consensus size: 30
195535 ACTCGGGATG
* * *
195545 AAAATGAAATTTT-AAAGAAGTTCGAGGGTC
1 AAAATGTAATTTTGGAA-AAGTTCGAGGGTT
195575 AAATATG--ATTTTGGAAAAGTTCGAGGGTT
1 AAA-ATGTAATTTTGGAAAAGTTCGAGGGTT
* * * *
195604 AAAATGTGATTCTGGAAAAGTT-TAGGGGTC
1 AAAATGTAATTTTGGAAAAGTTCGA-GGGTT
* *
195634 AAAATGTAATTTTGGAAAAGTTTGGGGGGTT
1 AAAATGTAATTTTGGAAAAG-TTCGAGGGTT
195665 AAAATGTAATTTTGGAAAA
1 AAAATGTAATTTTGGAAAA
195684 TTTTAAGGAC
Statistics
Matches: 92, Mismatches: 10, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
28 3 0.03
29 21 0.23
30 40 0.43
31 28 0.30
ACGTcount: A:0.38, C:0.04, G:0.27, T:0.32
Consensus pattern (30 bp):
AAAATGTAATTTTGGAAAAGTTCGAGGGTT
Found at i:195669 original size:31 final size:30
Alignment explanation
Indices: 195582--195683 Score: 141
Period size: 30 Copynumber: 3.4 Consensus size: 30
195572 GTCAAATATG
* * *
195582 ATTTTGGAAAAGTTCGAGGGTTAAAATGTG
1 ATTTTGGAAAAGTTTGGGGGTTAAAATGTA
* * *
195612 ATTCTGGAAAAGTTTAGGGGTCAAAATGTA
1 ATTTTGGAAAAGTTTGGGGGTTAAAATGTA
195642 ATTTTGGAAAAGTTTGGGGGGTTAAAATGTA
1 ATTTTGGAAAAGTTT-GGGGGTTAAAATGTA
195673 ATTTTGGAAAA
1 ATTTTGGAAAA
195684 TTTTAAGGAC
Statistics
Matches: 62, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
30 38 0.61
31 24 0.39
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.33
Consensus pattern (30 bp):
ATTTTGGAAAAGTTTGGGGGTTAAAATGTA
Found at i:195681 original size:61 final size:59
Alignment explanation
Indices: 195570--195688 Score: 159
Period size: 61 Copynumber: 2.0 Consensus size: 59
195560 AGAAGTTCGA
*
195570 GGGTCAAATATGATTTTGGAAAAGTTCGAGGGTTAAAATGTGATTCTGGAAAAGTTTAG
1 GGGTCAAATATGATTTTGGAAAAGTTCGAGGGTTAAAATGTAATTCTGGAAAAGTTTAG
* * * *
195629 GGGTCAAA-ATGTAATTTTGGAAAAGTTTGGGGGGTTAAAATGTAATTTTGGAAAATTTTA
1 GGGTCAAATATG--ATTTTGGAAAAG-TTCGAGGGTTAAAATGTAATTCTGGAAAAGTTTA
195689 AGGACCTCTT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
58 3 0.06
59 8 0.15
60 12 0.23
61 29 0.56
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.34
Consensus pattern (59 bp):
GGGTCAAATATGATTTTGGAAAAGTTCGAGGGTTAAAATGTAATTCTGGAAAAGTTTAG
Found at i:196850 original size:24 final size:24
Alignment explanation
Indices: 196818--196866 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
196808 ATCAAAATGC
* *
196818 ATATTTATGTATGTATATATATAT
1 ATATATATGTATGCATATATATAT
*
196842 ATATATATGTATGCGTATATATAT
1 ATATATATGTATGCATATATATAT
196866 A
1 A
196867 AAAAGCAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.39, C:0.02, G:0.10, T:0.49
Consensus pattern (24 bp):
ATATATATGTATGCATATATATAT
Found at i:198199 original size:58 final size:58
Alignment explanation
Indices: 198129--198245 Score: 216
Period size: 58 Copynumber: 2.0 Consensus size: 58
198119 TCTAAGTTAC
*
198129 CGGGTTCGCTGTTGCGATCGTAACCTTTCCCTCCATATCTTCGTGGTACTGGATTCGT
1 CGGGTTCGCTGTTACGATCGTAACCTTTCCCTCCATATCTTCGTGGTACTGGATTCGT
*
198187 CGGGTTCGCTGTTACGGTCGTAACCTTTCCCTCCATATCTTCGTGGTACTGGATTCGT
1 CGGGTTCGCTGTTACGATCGTAACCTTTCCCTCCATATCTTCGTGGTACTGGATTCGT
198245 C
1 C
198246 ATTACGACCT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.12, C:0.28, G:0.24, T:0.36
Consensus pattern (58 bp):
CGGGTTCGCTGTTACGATCGTAACCTTTCCCTCCATATCTTCGTGGTACTGGATTCGT
Found at i:198264 original size:49 final size:49
Alignment explanation
Indices: 198211--198860 Score: 473
Period size: 49 Copynumber: 13.2 Consensus size: 49
198201 CGGTCGTAAC
* * * * *
198211 CTTTCCCTCCATATCTTCGTGGTACTGGATTCGTCATTACGACCTAAAT
1 CTTTCCCTTCATATCTTCGTGGTACTGGATTCGCCGTTGCGACTTAAAT
* * * * * * *
198260 CTTTCCCTTCAT-GCTTTTGAGGTACAAGG-TTCGTCGTTGTGACTTAAAC
1 CTTTCCCTTCATATC-TTCGTGGTAC-TGGATTCGCCGTTGCGACTTAAAT
* * * *
198309 CTTTCCCTTTAAATCTTCGTGGTACTGGATTCGCCATTGC-AGTTTAAAT
1 CTTTCCCTTCATATCTTCGTGGTACTGGATTCGCCGTTGCGA-CTTAAAT
* * * * *
198358 CTTTCCCTTCAT-GCTTTTGAGGTACAAGG-TTCGTCGTTGCGACTTAAAT
1 CTTTCCCTTCATATC-TTCGTGGTAC-TGGATTCGCCGTTGCGACTTAAAT
* * *
198407 CTTTCCCTTTAAATCTTCGTGGTACTGGATTCACCGTTGCGACTTAAAT
1 CTTTCCCTTCATATCTTCGTGGTACTGGATTCGCCGTTGCGACTTAAAT
* * * * *
198456 CTTTCCCTTCAT-GCTTCTGAGGTA-TAAGG-TTCGCCATTGCGACTAAAAAC
1 CTTTCCCTTCATATCTTC-GTGGTACT--GGATTCGCCGTTGCGACT-TAAAT
** * * * * *
198506 CTTTCCCTTTTGTGTCTTCGTGGTATTAGATTCGTCGTTGCGGCTTAAAT
1 CTTTCCC-TTCATATCTTCGTGGTACTGGATTCGCCGTTGCGACTTAAAT
* * * * * * *
198556 CTTTCCCTTCATGTCTTTGAGGTACAAGG-TTCGCTGTTGCAACTTAAAC
1 CTTTCCCTTCATATCTTCGTGGTAC-TGGATTCGCCGTTGCGACTTAAAT
* * ** * *
198605 CTTTCCC-TCTGTGTCTTCACGGTACTAGATTCGCCGTTGCGGCTTAAAT
1 CTTTCCCTTC-ATATCTTCGTGGTACTGGATTCGCCGTTGCGACTTAAAT
* * * * *
198654 TTTTCCCTTCATATCTTCGTAGTATTGGATTCGTCGTTGCGGCTTAAAT
1 CTTTCCCTTCATATCTTCGTGGTACTGGATTCGCCGTTGCGACTTAAAT
*
198703 CTTTCCCTTCATATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAAT
1 CTTTCCCTTCATATCTTCGTGGTACTGGATTCGCCGTTGCGACTTAAAT
* * *
198752 CTTTCCCTTCAT-GCTTC-TAAGGTA-TAAGG-TTCGCCATTGCGACTTAAAC
1 CTTTCCCTTCATATCTTCGT--GGTACT--GGATTCGCCGTTGCGACTTAAAT
* * * * **
198801 CTTTCCCTTCAAATCTTCATGGTACTAGATTCGCCATTGCGGTTTAAAT
1 CTTTCCCTTCATATCTTCGTGGTACTGGATTCGCCGTTGCGACTTAAAT
*
198850 TTTTCCCTTCA
1 CTTTCCCTTCA
198861 AATTTTCATG
Statistics
Matches: 469, Mismatches: 102, Indels: 60
0.74 0.16 0.10
Matches are distributed among these distances:
47 1 0.00
48 21 0.04
49 381 0.81
50 40 0.09
51 21 0.04
52 5 0.01
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.39
Consensus pattern (49 bp):
CTTTCCCTTCATATCTTCGTGGTACTGGATTCGCCGTTGCGACTTAAAT
Found at i:198358 original size:98 final size:98
Alignment explanation
Indices: 198208--198860 Score: 731
Period size: 98 Copynumber: 6.6 Consensus size: 98
198198 TTACGGTCGT
** * * * * *
198208 AACCTTTCCCTCCATATCTTCGTGGTACTGGATTCGTCATTACGACCTAAATCTTTCCCTTCATG
1 AACCTTTCCCTTTATATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG
*
198273 CTTTTGAGGTACAAGGTTCGTCGTTGTGACTTA
66 CTTTTGAGGTACAAGGTTCGTCGTTGCGACTTA
* * * *
198306 AACCTTTCCCTTTAAATCTTCGTGGTACTGGATTCGCCATTGCAGTTTAAATCTTTCCCTTCATG
1 AACCTTTCCCTTTATATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG
198371 CTTTTGAGGTACAAGGTTCGTCGTTGCGACTTA
66 CTTTTGAGGTACAAGGTTCGTCGTTGCGACTTA
* * * *
198404 AATCTTTCCCTTTAAATCTTCGTGGTACTGGATTCACCGTTGCGACTTAAATCTTTCCCTTCATG
1 AACCTTTCCCTTTATATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG
* * * * *
198469 CTTCTGAGGTATAAGGTTCGCCATTGCGACTAAA
66 CTTTTGAGGTACAAGGTTCGTCGTTGCGACT-TA
* * * * *
198503 AACCTTTCCCTTTTGTGTCTTCGTGGTATTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCAT
1 AACCTTTCCC-TTTATATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCAT
*
198568 G-TCTTTGAGGTACAAGGTTCG-CTGTTGCAACTTA
65 GCT-TTTGAGGTACAAGGTTCGTC-GTTGCGACTTA
* * * ** * *
198602 AACCTTTCCCTCTGTGTCTTCACGGTACTAGATTCGCCGTTGCGGCTTAAATTTTTCCCTTCAT-
1 AACCTTTCCCTTTATATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG
* * ** *
198666 ATCTTCGTA-GTA-TTGGATTCGTCGTTGCGGCTTA
66 CT-TTTG-AGGTACAAGG-TTCGTCGTTGCGACTTA
* *
198700 AATCTTTCCCTTCATATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG
1 AACCTTTCCCTTTATATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG
* * * * *
198765 CTTCTAAGGTATAAGGTTCGCCATTGCGACTTA
66 CTTTTGAGGTACAAGGTTCGTCGTTGCGACTTA
* * * * * * *
198798 AACCTTTCCCTTCAAATCTTCATGGTACTAGATTCGCCATTGCGGTTTAAATTTTTCCCTTCA
1 AACCTTTCCCTTTATATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCA
198861 AATTTTCATG
Statistics
Matches: 473, Mismatches: 71, Indels: 22
0.84 0.13 0.04
Matches are distributed among these distances:
97 3 0.01
98 372 0.79
99 28 0.06
100 70 0.15
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.39
Consensus pattern (98 bp):
AACCTTTCCCTTTATATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG
CTTTTGAGGTACAAGGTTCGTCGTTGCGACTTA
Found at i:198758 original size:296 final size:294
Alignment explanation
Indices: 198208--198860 Score: 848
Period size: 296 Copynumber: 2.2 Consensus size: 294
198198 TTACGGTCGT
* * * * * *
198208 AACCTTTCCCTCCATATCTTCGTGGTACTGGATTCGTCATTACGACCTAAATCTTTCCCTTCATG
1 AACCTTTCCCTTCAAATCTTCGTGGTACTAGATTCGTCATTGCGGCTTAAATCTTTCCCTTCATG
** * ** *
198273 CTTTTGAGGTACAAGGTTCGTCGTTGTGACTTAAACCTTTCCCTTTAAATCTTCGTGGTACTGGA
66 CTTTTGAGGTACAAGGTTCGTCGTTGCAACTTAAACCTTTCCCTCTAAATCTTCACGGTACTAGA
* *
198338 TTCGCCATTGCAGTTTAAATCTTTCCCTTCATGCTTTTGAGGTACAAGGTTCGTCGTTGCGACTT
131 TTCGCCATTGCAGCTTAAATCTTTCCCTTCATGCTTGTGAGGTACAAGGTTCGTCGTTGCGACTT
*
198403 AAATCTTTCCCTTTAAATCTTCGTGGTACTGGATTCACCGTTGCGACTTAAATCTTTCCCTTCAT
196 AAATCTTTCCCTTCAAATCTTCGTGGTACTGGATTCACCGTTGCGACTTAAATCTTTCCCTTCAT
*
198468 GCTTCTGAGGTATAAGGTTCGCCATTGCGACTAAA
261 GCTTCTAAGGTATAAGGTTCGCCATTGCGACT-AA
**** * *
198503 AACCTTTCCCTTTTGTGTCTTCGTGGTATTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCAT
1 AACCTTTCCC-TTCAAATCTTCGTGGTACTAGATTCGTCATTGCGGCTTAAATCTTTCCCTTCAT
***
198568 G-TCTTTGAGGTACAAGGTTCG-CTGTTGCAACTTAAACCTTTCCCTCTGTGTCTTCACGGTACT
65 GCT-TTTGAGGTACAAGGTTCGTC-GTTGCAACTTAAACCTTTCCCTCTAAATCTTCACGGTACT
* * * * **
198631 AGATTCGCCGTTGCGGCTTAAATTTTTCCCTTCATATCTTCGT-A-GTA-TTGGATTCGTCGTTG
128 AGATTCGCCATTGCAGCTTAAATCTTTCCCTTCAT-GCTT-GTGAGGTACAAGG-TTCGTCGTTG
* * * *
198693 CGGCTTAAATCTTTCCCTTCATATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCC
190 CGACTTAAATCTTTCCCTTCAAATCTTCGTGGTACTGGATTCACCGTTGCGACTTAAATCTTTCC
*
198758 CTTCATGCTTCTAAGGTATAAGGTTCGCCATTGCGACTTA
255 CTTCATGCTTCTAAGGTATAAGGTTCGCCATTGCGACTAA
* * * *
198798 AACCTTTCCCTTCAAATCTTCATGGTACTAGATTCGCCATTGCGGTTTAAATTTTTCCCTTCA
1 AACCTTTCCCTTCAAATCTTCGTGGTACTAGATTCGTCATTGCGGCTTAAATCTTTCCCTTCA
198861 AATTTTCATG
Statistics
Matches: 308, Mismatches: 44, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
294 43 0.14
295 25 0.08
296 235 0.76
297 4 0.01
298 1 0.00
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.39
Consensus pattern (294 bp):
AACCTTTCCCTTCAAATCTTCGTGGTACTAGATTCGTCATTGCGGCTTAAATCTTTCCCTTCATG
CTTTTGAGGTACAAGGTTCGTCGTTGCAACTTAAACCTTTCCCTCTAAATCTTCACGGTACTAGA
TTCGCCATTGCAGCTTAAATCTTTCCCTTCATGCTTGTGAGGTACAAGGTTCGTCGTTGCGACTT
AAATCTTTCCCTTCAAATCTTCGTGGTACTGGATTCACCGTTGCGACTTAAATCTTTCCCTTCAT
GCTTCTAAGGTATAAGGTTCGCCATTGCGACTAA
Found at i:198792 original size:147 final size:147
Alignment explanation
Indices: 198208--198860 Score: 576
Period size: 147 Copynumber: 4.4 Consensus size: 147
198198 TTACGGTCGT
* * * * * * *
198208 AACCTTTCCCTCCATATCTTCGTGGTACTGGATTCGTCATTACGACCTAAATCTTTCCCTTCAT-
1 AACCTTTCCCTTCATATCTTCGTGGTATTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATA
* * * * * * * *
198272 GCTTTTGAGGTACAAGG-TTCGTCGTTGTGACTTAAACCTTTCCCTTTAAAT-CTTCGT--GGTA
66 TC-TTCGTGGTAC-TGGATTCGCCGTTGCGACTTAAATCTTTCCC-TT-CATGCTTC-TAAGGTA
*
198333 CT--GGATTCGCCATTGC-AGTTTA
126 -TAAGG-TTCGCCATTGCGA-CTTA
* * * * ** * * * *
198355 AATCTTTCCCTTCAT-GCTTTTGAGGTACAAGGTTCGTCGTTGCGACTTAAATCTTTCCCTTTAA
1 AACCTTTCCCTTCATATC-TTCGTGGTATTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCAT
* *
198419 ATCTTCGTGGTACTGGATTCACCGTTGCGACTTAAATCTTTCCCTTCATGCTTCTGAGGTATAAG
65 ATCTTCGTGGTACTGGATTCGCCGTTGCGACTTAAATCTTTCCCTTCATGCTTCTAAGGTATAAG
*
198484 GTTCGCCATTGCGACTAAA
130 GTTCGCCATTGCGACT-TA
** *
198503 AACCTTTCCCTTTTGTGTCTTCGTGGTATTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCAT
1 AACCTTTCCC-TTCATATCTTCGTGGTATTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCAT
* * * * * * * * *
198568 GTCTTTGAGGTACAAGG-TTCGCTGTTGCAACTTAAACCTTTCCC-TCTGTGTCTTC-ACGGTAC
65 ATCTTCGTGGTAC-TGGATTCGCCGTTGCGACTTAAATCTTTCCCTTC-ATG-CTTCTAAGGTA-
* * *
198630 T-AGATTCGCCGTTGCGGCTTA
126 TAAGGTTCGCCATTGCGACTTA
** * *
198651 AATTTTTCCCTTCATATCTTCGTAGTATTGGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATA
1 AACCTTTCCCTTCATATCTTCGTGGTATTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATA
*
198716 TCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTAAGGTATAAGG
66 TCTTCGTGGTACTGGATTCGCCGTTGCGACTTAAATCTTTCCCTTCATGCTTCTAAGGTATAAGG
198781 TTCGCCATTGCGACTTA
131 TTCGCCATTGCGACTTA
* * * * * * *
198798 AACCTTTCCCTTCAAATCTTCATGGTACTAGATTCGCCATTGCGGTTTAAATTTTTCCCTTCA
1 AACCTTTCCCTTCATATCTTCGTGGTATTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCA
198861 AATTTTCATG
Statistics
Matches: 404, Mismatches: 82, Indels: 40
0.77 0.16 0.08
Matches are distributed among these distances:
145 3 0.01
146 17 0.04
147 254 0.63
148 27 0.07
149 95 0.24
150 8 0.02
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.39
Consensus pattern (147 bp):
AACCTTTCCCTTCATATCTTCGTGGTATTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATA
TCTTCGTGGTACTGGATTCGCCGTTGCGACTTAAATCTTTCCCTTCATGCTTCTAAGGTATAAGG
TTCGCCATTGCGACTTA
Found at i:204891 original size:30 final size:29
Alignment explanation
Indices: 204857--204957 Score: 91
Period size: 30 Copynumber: 3.4 Consensus size: 29
204847 TGAAAATGAA
204857 ATTTT-AAAGAAGTTCGAGGGTCAAAATATG
1 ATTTTGAAA-AAGTTCGAGGGT-AAAATATG
* * *
204887 ATTTTGGAAAAGTTCGAGGGTTAAATGTG
1 ATTTTGAAAAAGTTCGAGGGTAAAATATG
*
204916 ATTTTGGAAAAGTAT--AGGAGTTAAAATATG
1 ATTTTGAAAAAGT-TCGAGG-G-TAAAATATG
*
204946 ATTTTGGAAAAG
1 ATTTTGAAAAAG
204958 ATTAGGGTTA
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
28 3 0.05
29 20 0.32
30 37 0.60
31 2 0.03
ACGTcount: A:0.39, C:0.03, G:0.26, T:0.33
Consensus pattern (29 bp):
ATTTTGAAAAAGTTCGAGGGTAAAATATG
Found at i:204942 original size:59 final size:58
Alignment explanation
Indices: 204873--205197 Score: 379
Period size: 59 Copynumber: 5.5 Consensus size: 58
204863 AAGAAGTTCG
* * * * *
204873 AGGGTCAAAATATGATTTTGGAAAAGTTCGAGGGTT-AAATGTGATTTTGGAAAAGTAT
1 AGGGTCAAAATGTAATTTTGGAAAAGTT-TAGGGTTAAAATGTAATTTTGGAAAAGTTT
* * * * * *
204931 AGGAGTTAAAATATGATTTTGGAAAAGATTAGGGTTAAATTGTAATATTGGAAAAGTTT
1 AGG-GTCAAAATGTAATTTTGGAAAAGTTTAGGGTTAAAATGTAATTTTGGAAAAGTTT
* *
204990 AGGGGGTCAAAATGTAATTTTGGAAAAATTTATGGGTTAAAATGTAATTTTGGAATAGTTT
1 A--GGGTCAAAATGTAATTTTGGAAAAGTTTA-GGGTTAAAATGTAATTTTGGAAAAGTTT
* *
205051 -GGCATCAAAATGTAACTTTGGAAAAGTTTAGGGATTAAAATGTAATTTTGGAAAAGTTT
1 AGG-GTCAAAATGTAATTTTGGAAAAGTTTAGGG-TTAAAATGTAATTTTGGAAAAGTTT
* *
205110 GAGGGTTAAAATGTAATTTTGG-AAAGTTTAAGGGTTAAAATGTATTTTTGG-AAAGTTT
1 -AGGGTCAAAATGTAATTTTGGAAAAGTTT-AGGGTTAAAATGTAATTTTGGAAAAGTTT
205168 AAGGGTCAAAATGTAATTTTGGAAAAGTTT
1 -AGGGTCAAAATGTAATTTTGGAAAAGTTT
205198 GGGGGACTTC
Statistics
Matches: 231, Mismatches: 25, Indels: 21
0.83 0.09 0.08
Matches are distributed among these distances:
58 41 0.18
59 120 0.52
60 41 0.18
61 29 0.13
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.36
Consensus pattern (58 bp):
AGGGTCAAAATGTAATTTTGGAAAAGTTTAGGGTTAAAATGTAATTTTGGAAAAGTTT
Found at i:205034 original size:30 final size:29
Alignment explanation
Indices: 204873--205197 Score: 361
Period size: 29 Copynumber: 11.0 Consensus size: 29
204863 AAGAAGTTCG
* * * *
204873 AGGGTCAAAATATGATTTTGGAAAAGTTCG
1 AGGGTTAAAATGTAATTTTGGAAAAGTT-T
* *
204903 AGGGTT-AAATGTGATTTTGGAAAAGTAT
1 AGGGTTAAAATGTAATTTTGGAAAAGTTT
* * *
204931 AGGAGTTAAAATATGATTTTGGAAAAGATT
1 AGG-GTTAAAATGTAATTTTGGAAAAGTTT
* *
204961 AGGGTTAAATTGTAATATTGGAAAAGTTT
1 AGGGTTAAAATGTAATTTTGGAAAAGTTT
* *
204990 AGGGGGTCAAAATGTAATTTTGGAAAAATTT
1 A--GGGTTAAAATGTAATTTTGGAAAAGTTT
*
205021 ATGGGTTAAAATGTAATTTTGGAATAGTTT
1 A-GGGTTAAAATGTAATTTTGGAAAAGTTT
* * *
205051 -GGCATCAAAATGTAACTTTGGAAAAGTTT
1 AGG-GTTAAAATGTAATTTTGGAAAAGTTT
205080 AGGGATTAAAATGTAATTTTGGAAAAGTTT
1 AGGG-TTAAAATGTAATTTTGGAAAAGTTT
205110 GAGGGTTAAAATGTAATTTTGG-AAAGTTT
1 -AGGGTTAAAATGTAATTTTGGAAAAGTTT
*
205139 AAGGGTTAAAATGTATTTTTGG-AAAGTTT
1 -AGGGTTAAAATGTAATTTTGGAAAAGTTT
*
205168 AAGGGTCAAAATGTAATTTTGGAAAAGTTT
1 -AGGGTTAAAATGTAATTTTGGAAAAGTTT
205198 GGGGGACTTC
Statistics
Matches: 255, Mismatches: 31, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
28 5 0.02
29 120 0.47
30 101 0.40
31 29 0.11
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.36
Consensus pattern (29 bp):
AGGGTTAAAATGTAATTTTGGAAAAGTTT
Found at i:205917 original size:104 final size:104
Alignment explanation
Indices: 205737--205944 Score: 371
Period size: 104 Copynumber: 2.0 Consensus size: 104
205727 ACCCTAAAGA
*
205737 CACCATTTTTCTTCTTTTTTTGCCCCAATTCCAAATCTAGAGTAAAAAATCCCCAAATTCGACTC
1 CACCATTTTTCTTCTTTTTTTGCCCCAATTCCAAATCTAGAGTAAAAAATCCCCAAATCCGACTC
*
205802 CAAAGCTTCGAAAAATAAGGTAAAGTCCGAATCTTTGAG
66 AAAAGCTTCGAAAAATAAGGTAAAGTCCGAATCTTTGAG
* *
205841 CACCATTTTTCTTCTTTTTTTGCCCCAATTCCAAATCTAGTGTCAAAAATCCCCAAATCCGACTC
1 CACCATTTTTCTTCTTTTTTTGCCCCAATTCCAAATCTAGAGTAAAAAATCCCCAAATCCGACTC
*
205906 AAAAGCTTCGAAAAATAAGGTAAAGTTCGAATCTTTGAG
66 AAAAGCTTCGAAAAATAAGGTAAAGTCCGAATCTTTGAG
205945 TTTTTTTTCT
Statistics
Matches: 99, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
104 99 1.00
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.31
Consensus pattern (104 bp):
CACCATTTTTCTTCTTTTTTTGCCCCAATTCCAAATCTAGAGTAAAAAATCCCCAAATCCGACTC
AAAAGCTTCGAAAAATAAGGTAAAGTCCGAATCTTTGAG
Found at i:206334 original size:10 final size:10
Alignment explanation
Indices: 206322--206372 Score: 75
Period size: 10 Copynumber: 5.1 Consensus size: 10
206312 AATTAAAATG
* *
206322 TATATTTATG
1 TATATATATA
206332 TATATATATA
1 TATATATATA
206342 TATATATATA
1 TATATATATA
206352 TATATATATA
1 TATATATATA
*
206362 TATATACATA
1 TATATATATA
206372 T
1 T
206373 GCGTATATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 38 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (10 bp):
TATATATATA
Found at i:206343 original size:6 final size:6
Alignment explanation
Indices: 206322--206372 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
206312 AATTAAAATG
* * *
206322 TATATT TATGTA TATATA TATATA TATATA TATATA TATATA TATACA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
206370 TAT
1 TAT
206373 GCGTATATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (6 bp):
TATATA
Found at i:206383 original size:4 final size:4
Alignment explanation
Indices: 206322--206372 Score: 75
Period size: 4 Copynumber: 12.8 Consensus size: 4
206312 AATTAAAATG
* * *
206322 TATA TTTA TGTA TATA TATA TATA TATA TATA TATA TATA TATA TACA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
206370 TAT
1 TAT
206373 GCGTATATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (4 bp):
TATA
Found at i:209519 original size:52 final size:52
Alignment explanation
Indices: 209441--209545 Score: 174
Period size: 52 Copynumber: 2.0 Consensus size: 52
209431 GCTCCCATTT
* *
209441 TGGTAGCATCAAAGAAACGAAACAAAAAGTGTCGCTATGGTAAGAAGTTAGG
1 TGGTAGCATCAAAGAAACGAAACAAAAAGTGTCACTATAGTAAGAAGTTAGG
* *
209493 TGGTAGCATCAAAGAAACGAGACAAAATGTGTCACTATAGTAAGAAGTTAGG
1 TGGTAGCATCAAAGAAACGAAACAAAAAGTGTCACTATAGTAAGAAGTTAGG
209545 T
1 T
209546 CATGTCAAAG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.42, C:0.11, G:0.26, T:0.21
Consensus pattern (52 bp):
TGGTAGCATCAAAGAAACGAAACAAAAAGTGTCACTATAGTAAGAAGTTAGG
Found at i:219093 original size:111 final size:111
Alignment explanation
Indices: 218971--219195 Score: 317
Period size: 111 Copynumber: 2.0 Consensus size: 111
218961 ATCCTTTTAA
* * * * * * *
218971 AGTTTGGTGCCGTCATACTGTTAGGCGGCACCTTGAAGTGT-TTTTCCAGCTGTCAATTAAAACG
1 AGTTTGATGCCGCCATACTGTCAGGCAGCACCTTGAAGCGTATTTT-CAGCTGCCAATTAAAACA
**
219035 AAAAATTTACATATAAGGTCCTTAGAGTTTTTAGATCGTCACATTTT
65 AAAAATTTACATATAAAATCCTTAGAGTTTTTAGATCGTCACATTTT
** *
219082 AGTTTGATGCCGCCATACTGTCAGGCAGTGCCTTGAAGCGTATTTTCAGCTGCCAATTAAATCAA
1 AGTTTGATGCCGCCATACTGTCAGGCAGCACCTTGAAGCGTATTTTCAGCTGCCAATTAAAACAA
*
219147 AAAATTTACATATAAAATCCTTAGCGTTTTTAGATCGTCACATTTT
66 AAAATTTACATATAAAATCCTTAGAGTTTTTAGATCGTCACATTTT
219193 AGT
1 AGT
219196 CTGGTGCCAT
Statistics
Matches: 100, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
111 96 0.96
112 4 0.04
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.35
Consensus pattern (111 bp):
AGTTTGATGCCGCCATACTGTCAGGCAGCACCTTGAAGCGTATTTTCAGCTGCCAATTAAAACAA
AAAATTTACATATAAAATCCTTAGAGTTTTTAGATCGTCACATTTT
Found at i:235219 original size:6 final size:6
Alignment explanation
Indices: 235208--235232 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
235198 GTAAGCAAAG
235208 GTGAAA GTGAAA GTGAAA GTGAAA G
1 GTGAAA GTGAAA GTGAAA GTGAAA G
235233 AGATTTTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.36, T:0.16
Consensus pattern (6 bp):
GTGAAA
Found at i:235874 original size:4 final size:4
Alignment explanation
Indices: 235867--235952 Score: 68
Period size: 4 Copynumber: 21.2 Consensus size: 4
235857 AAATAAACAG
* * * *
235867 GAAA GAAA GAAA GAAAA GAAG GAAA TAAA GGAA GAAG GAGAA GAAA GAAA
1 GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
* * *
235917 G-AA TAAG GAAA GGAAA GAAA G-AA TAAA GAAA GAAA G
1 GAAA GAAA GAAA -GAAA GAAA GAAA GAAA GAAA GAAA G
235953 GTAATGTATT
Statistics
Matches: 63, Mismatches: 14, Indels: 10
0.72 0.16 0.11
Matches are distributed among these distances:
3 4 0.06
4 48 0.76
5 11 0.17
ACGTcount: A:0.67, C:0.00, G:0.29, T:0.03
Consensus pattern (4 bp):
GAAA
Found at i:235903 original size:16 final size:17
Alignment explanation
Indices: 235873--235919 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
235863 ACAGGAAAGA
235873 AAGAAAGAAAAGAAGGA-
1 AAGAAAG-AAAGAAGGAG
* *
235890 AATAAAGGAAGAAGGAG
1 AAGAAAGAAAGAAGGAG
235907 AAGAAAGAAAGAA
1 AAGAAAGAAAGAA
235920 TAAGGAAAGG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 8 0.32
17 17 0.68
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.02
Consensus pattern (17 bp):
AAGAAAGAAAGAAGGAG
Found at i:235932 original size:20 final size:19
Alignment explanation
Indices: 235865--235952 Score: 99
Period size: 20 Copynumber: 4.6 Consensus size: 19
235855 GTAAATAAAC
235865 AGGAAAGAAAGAAAGAA-A
1 AGGAAAGAAAGAAAGAATA
* * *
235883 A-GAAGGAAATAAAGGAAGA
1 AGGAAAGAAAGAAA-GAATA
235902 AGGAGAAGAAAGAAAGAATA
1 AGGA-AAGAAAGAAAGAATA
235922 AGGAAAGGAAAGAAAGAATA
1 AGGAAA-GAAAGAAAGAATA
*
235942 AAGAAAGAAAG
1 AGGAAAGAAAG
235953 GTAATGTATT
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
17 10 0.17
18 4 0.07
19 9 0.15
20 28 0.47
21 8 0.14
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.03
Consensus pattern (19 bp):
AGGAAAGAAAGAAAGAATA
Found at i:239473 original size:45 final size:44
Alignment explanation
Indices: 239343--239479 Score: 175
Period size: 45 Copynumber: 3.0 Consensus size: 44
239333 GGGAGGAATA
* * * **
239343 GAGTATCGCGATGGCTCGTCAAACTCAGCCTGATATCCTTCCCTT
1 GAGTATTGCGGTGGCTCGTCAAACTAAG-CTGATATCCTTGGCTT
* * *
239388 GAGTATTGCGGTGGTTCATCAAATTAAGGCTGATATCCTTGGCTT
1 GAGTATTGCGGTGGCTCGTCAAACTAA-GCTGATATCCTTGGCTT
239433 GAGTATTGCGGTGGCTCGTCAAACTGAAGCTGATATCCTTGGCTT
1 GAGTATTGCGGTGGCTCGTCAAACT-AAGCTGATATCCTTGGCTT
239478 GA
1 GA
239480 TGAGCTATGC
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
45 76 0.96
46 3 0.04
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.31
Consensus pattern (44 bp):
GAGTATTGCGGTGGCTCGTCAAACTAAGCTGATATCCTTGGCTT
Done.