Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold241
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: 818039
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.32
Warning! 31082 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:782708 original size:44 final size:44
Alignment explanation
Indices: 782607--783371 Score: 391
Period size: 44 Copynumber: 17.6 Consensus size: 44
782597 CTTTCTCGAG
* * * * *
782607 TCTGCTCCACTGCAACTTTAGGGAGATAAGA-C--TCGATATGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAA
* * *
782648 TCTCCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAA
* * * * * *
782692 TCCGCTCCACTGCAACTTCAGGGAGACAGGATTTGT-TTATTTAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGT-TTTAA
* * *** * *
782736 TATGCCCCACTGCAACTTCAGGGAGATAAGAT-TCGACATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCT-GTGGT-TTTAA
* * *
782781 TCTGC-CTCATTGCAACTTCA-GGAGGATAAGA-CT-TGATTACTTAG
1 TCTGCTC-CACTGCAACTTCAGGGA-GATAAGATCTGTGGTT--TTAA
* * * * * *
782825 TCTGCTCCATTGCAACTTCAGGGAGACAGGATTTGT-TTATTTAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGT-TTTAA
* * * **
782869 TATGCCCCACTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAA
** * * * *
782913 TCAACTCCACTGCAACTTCAGGAAGATAGGAT-TATCGGCTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGT-GGTTTTAA
* * *** *
782957 CCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGT-TTTAA
* *
783002 TCTGC-CTCACTGCAACTTCA-GGAGGATAAGA-CT-TGCTTGCTTAG
1 TCTGCTC-CACTGCAACTTCAGGGA-GATAAGATCTGTGGTT--TTAA
* * * ***
783046 TCTGCTCCATTGCAACTTCAGGGAGATAAGA-C--TAGATACGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAA
* * *
783087 TCTGCT-CTCTGCAACTTCAGAGAGATAAGATCTGT-GATTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAA
* * *
783129 TCTGCTCCACTGCAACTTCAGAGAGATAGGAT-TGTCGGCTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGT-GGTTTTAA
* * * *** * *
783173 TTTGCTCCACTGCAACCTCAGGGAGATAAGATTTGCCATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGT-TTTAA
* * *
783218 TCTGC-CTCACTGCAACTTCA-GAAGGATAAGA-CT-TGCTTACTTAG
1 TCTGCTC-CACTGCAACTTCAGGGA-GATAAGATCTGTGGTT--TTAA
* * * * **
783262 TCTGCTCCACTGCAACTTTAGGGAGATAAG-GC--TAGATGCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAA
* * ****
783303 TCTGCT-CTCTGCAACTTCAGAGAGATAAGATCCAAAGTTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAA
783346 TCTGCTCCACTGCAACTTCAGGGAGA
1 TCTGCTCCACTGCAACTTCAGGGAGA
783372 CAAGGCTTGG
Statistics
Matches: 553, Mismatches: 126, Indels: 87
0.72 0.16 0.11
Matches are distributed among these distances:
40 41 0.07
41 42 0.08
42 17 0.03
43 47 0.08
44 304 0.55
45 100 0.18
46 2 0.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (44 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAA
Found at i:782833 original size:133 final size:129
Alignment explanation
Indices: 782613--782900 Score: 386
Period size: 133 Copynumber: 2.2 Consensus size: 129
782603 CGAGTCTGCT
* * *
782613 CCACTGCAACTTTAGGGAGATAAGACTCGATATGATCTCCTCTACTGCAACTTCAGAGAGATAAG
1 CCACTGCAACTTCAGGGAGATAAGATTCGATATCATCTCCTCTACTGCAACTTCAGAGAGATAAG
*
782678 ATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGACAGGATTTGTTTATTTAGTATGCC
66 ATCTGTGATTTTAATCCGCTCCACTGCAACTTCAGGGAGACAGGATTTGTTTATTTAGTATGCC
* *
782742 CCACTGCAACTTCAGGGAGATAAGATTCGACATCTTCAGTCTGCCTC-ATTGCAACTTCAG-GAG
1 CCACTGCAACTTCAGGGAGATAAGATTCG--AT-ATCA-TCT-CCTCTACTGCAACTTCAGAGA-
* * *
782805 GATAAGA-CT-TGATTACTTAGTCTGCTCCATTGCAACTTCAGGGAGACAGGATTTGTTTATTTA
60 GATAAGATCTGTGATT--TTAATCCGCTCCACTGCAACTTCAGGGAGACAGGATTTGTTTATTTA
782868 GTATGCC
123 GTATGCC
*
782875 CCACTGCAACTTCAGAGAGATAAGAT
1 CCACTGCAACTTCAGGGAGATAAGAT
782901 CTAAGGTTTT
Statistics
Matches: 141, Mismatches: 10, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
129 27 0.19
131 6 0.04
132 6 0.04
133 98 0.70
134 4 0.03
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.30
Consensus pattern (129 bp):
CCACTGCAACTTCAGGGAGATAAGATTCGATATCATCTCCTCTACTGCAACTTCAGAGAGATAAG
ATCTGTGATTTTAATCCGCTCCACTGCAACTTCAGGGAGACAGGATTTGTTTATTTAGTATGCC
Found at i:782840 original size:89 final size:88
Alignment explanation
Indices: 782605--783371 Score: 445
Period size: 89 Copynumber: 8.8 Consensus size: 88
782595 TGCTTTCTCG
* * * * *
782605 AGTCTGCTCCACTGCAACTTTAGG-GAGATAAGACTCGA-TA--TGATCTCCTCTACTGCAACTT
1 AGTCTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGATTACTTAATCTGCTCCACTGCAACTT
* **
782666 CAGAGAGATAAGA-TCTGTGGTTTT
66 CAGGGAGATAAGATTC-GT-CATTT
* * * * * * * * * *
782690 AATCCGCTCCACTGCAACTTCAGG-GAGACAGGATTTGTTTATTTAGTATGCCCCACTGCAACTT
1 AGTCTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGATTACTTAATCTGCTCCACTGCAACTT
*
782754 CAGGGAGATAAGATTCGACATCTT
66 CAGGGAGATAAGATTCGTCAT-TT
* * *
782778 CAGTCTGC-CTCATTGCAACTTCAGGAG-GATAAGACTTGATTACTTAGTCTGCTCCATTGCAAC
1 -AGTCTGCTC-CACTGCAACTTCAGGAGAGATAAGACTTGATTACTTAATCTGCTCCACTGCAAC
* * * *
782841 TTCAGGGAGACAGGATTTGTTTATTT
64 TTCAGGGAGATAAGATTCG-TCATTT
* * * * **
782867 AGTATGCCCCACTGCAACTTCA-GAGAGATAAGATCTAAGGTT--TTAATCAACTCCACTGCAAC
1 AGTCTGCTCCACTGCAACTTCAGGAGAGATAAGA-CT-TGATTACTTAATCTGCTCCACTGCAAC
* * *
782929 TTCAGGAAGATAGGATTATCGGC-TTT
64 TTCAGGGAGATAAGA-T-TCGTCATTT
** *
782955 AACCTGCTCCACTGCAACTTCAGG-GAGATAAGATTTGCCA-T-CTTCAATCTGC-CTCACTGCA
1 AGTCTGCTCCACTGCAACTTCAGGAGAGATAAGACTTG--ATTACTT-AATCTGCTC-CACTGCA
*
783016 ACTTCA-GGAGGATAAGACTT-G-CTTGCTT
62 ACTTCAGGGA-GATAAGA-TTCGTCAT--TT
* * * *
783044 AGTCTGCTCCATTGCAACTTCAGG-GAGATAAGACTAGA-TAC--GATCTGCT-CTCTGCAACTT
1 AGTCTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGATTACTTAATCTGCTCCACTGCAACTT
* *
783104 CAGAGAGATAAGA-TCTGTGATTT
66 CAGGGAGATAAGATTC-GTCATTT
* * ** *
783127 AATCTGCTCCACTGCAACTTCA-GAGAGATAGGA-TTG-TCGGCTTTAATTTGCTCCACTGCAAC
1 AGTCTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGAT-TAC-TTAATCTGCTCCACTGCAAC
* * *
783189 CTCAGGGAGATAAGATTTGCCATCTT
64 TTCAGGGAGATAAGATTCGTCAT-TT
* * *
783215 CAGTCTGC-CTCACTGCAACTTCAGAAG-GATAAGACTTGCTTACTTAGTCTGCTCCACTGCAAC
1 -AGTCTGCTC-CACTGCAACTTCAGGAGAGATAAGACTTGATTACTTAATCTGCTCCACTGCAAC
* ** * **
783278 TTTAGGGAGATAAGGCTAG--ATGC
64 TTCAGGGAGATAAGATTCGTCATTT
* * ***
783301 AATCTGCT-CTCTGCAACTTCA-GAGAGATAAGATCCAAAGTT--TTAATCTGCTCCACTGCAAC
1 AGTCTGCTCCACTGCAACTTCAGGAGAGATAAGA-CTTGA-TTACTTAATCTGCTCCACTGCAAC
783362 TTCAGGGAGA
64 TTCAGGGAGA
783372 CAAGGCTTGG
Statistics
Matches: 527, Mismatches: 106, Indels: 99
0.72 0.14 0.14
Matches are distributed among these distances:
82 4 0.01
83 33 0.06
84 67 0.13
85 46 0.09
86 12 0.02
87 36 0.07
88 126 0.24
89 188 0.36
90 14 0.03
91 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (88 bp):
AGTCTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGATTACTTAATCTGCTCCACTGCAACTT
CAGGGAGATAAGATTCGTCATTT
Found at i:783067 original size:133 final size:133
Alignment explanation
Indices: 782658--783078 Score: 411
Period size: 133 Copynumber: 3.2 Consensus size: 133
782648 TCTCCTCTAC
**
782658 TGCAACTTCA-GAGAGATAAGA-TCTG-TGGTTTTAATCC-GCTCCACTGCAACTTCAGGGAGAC
1 TGCAACTTCAGGA-AGATAAGACT-TGATGACTTTAA-CCTGCTCCACTGCAACTTCAGGGAGAC
*
782719 AGGATTTGTTTATTTAGTATGCCCCACTGCAACTTCAGG-GAGATAAGA-TTCGACATCTTCAGT
63 AGGATTTGTTTATTTAGTATGCCCCACTGCAACTTCAGGAGAGATAAGACTT-G-CTTCTT-AGT
782782 CTGC-CTCAT
125 CTGCTC-CAT
* * ** *
782791 TGCAACTTCAGGAGGATAAGACTTGATTAC-TTAGTCTGCTCCATTGCAACTTCAGGGAGACAGG
1 TGCAACTTCAGGAAGATAAGACTTGATGACTTTAACCTGCTCCACTGCAACTTCAGGGAGACAGG
* * * **
782855 ATTTGTTTATTTAGTATGCCCCACTGCAACTTCA-GAGAGATAAGATCTAAGGTT-TTAATCAAC
66 ATTTGTTTATTTAGTATGCCCCACTGCAACTTCAGGAGAGATAAGA-CT-TGCTTCTTAGTCTGC
*
782918 TCCAC
129 TCCAT
* * * *
782923 TGCAACTTCAGGAAGATAGGA-TT-ATCGGCTTTAACCTGCTCCACTGCAACTTCAGGGAGATAA
1 TGCAACTTCAGGAAGATAAGACTTGAT-GACTTTAACCTGCTCCACTGCAACTTCAGGGAGACAG
** * * *
782986 GATTTG-CCATCTTCAATCTGCCTCACTGCAACTTCAGGAG-GATAAGACTTGCTTGCTTAGTCT
65 GATTTGTTTAT-TT-AGTATGCCCCACTGCAACTTCAGGAGAGATAAGACTTGCTT-CTTAGTCT
783049 GCTCCAT
127 GCTCCAT
*
783056 TGCAACTTCAGGGAGATAAGACT
1 TGCAACTTCAGGAAGATAAGACT
783079 AGATACGATC
Statistics
Matches: 235, Mismatches: 36, Indels: 33
0.77 0.12 0.11
Matches are distributed among these distances:
130 2 0.01
131 8 0.03
132 65 0.28
133 149 0.63
134 9 0.04
135 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (133 bp):
TGCAACTTCAGGAAGATAAGACTTGATGACTTTAACCTGCTCCACTGCAACTTCAGGGAGACAGG
ATTTGTTTATTTAGTATGCCCCACTGCAACTTCAGGAGAGATAAGACTTGCTTCTTAGTCTGCTC
CAT
Found at i:783179 original size:127 final size:129
Alignment explanation
Indices: 782966--783203 Score: 308
Period size: 127 Copynumber: 1.9 Consensus size: 129
782956 ACCTGCTCCA
* *
782966 CTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAATCTGCCTCACTGCAACTTCAGGAGGATAA
1 CTGCAACTTCAGAGAGATAAGATCTGCCATCTTCAATCTGCCTCACTGCAACTTCAGGAGGATAA
* * * *
783031 GACTTGCTTGCTTAGTCTGCTCCATTGCAACTTCAGGGAGATAAGACTAGATACGATCTGCTCT
66 GACTTGCTGGCTTAATCTGCTCCACTGCAACCTCAGGGAGATAAGACTAGATACGATCTGCTCT
**
783095 CTGCAACTTCAGAGAGATAAGATCTGTGAT-TT-AATCTG-CTCCACTGCAACTTCA-GAGAGAT
1 CTGCAACTTCAGAGAGATAAGATCTGCCATCTTCAATCTGCCT-CACTGCAACTTCAGGAG-GAT
* *
783156 AGGA-TTG-TCGGCTTTAATTTGCTCCACTGCAACCTCAGGGAGATAAGA
64 AAGACTTGCT-GGC-TTAATCTGCTCCACTGCAACCTCAGGGAGATAAGA
783204 TTTGCCATCT
Statistics
Matches: 95, Mismatches: 10, Indels: 10
0.83 0.09 0.09
Matches are distributed among these distances:
125 1 0.01
126 10 0.11
127 56 0.59
128 2 0.02
129 26 0.27
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (129 bp):
CTGCAACTTCAGAGAGATAAGATCTGCCATCTTCAATCTGCCTCACTGCAACTTCAGGAGGATAA
GACTTGCTGGCTTAATCTGCTCCACTGCAACCTCAGGGAGATAAGACTAGATACGATCTGCTCT
Found at i:783210 original size:216 final size:216
Alignment explanation
Indices: 782564--783371 Score: 1017
Period size: 216 Copynumber: 3.7 Consensus size: 216
782554 TTATTTAGTA
* * * ** * * *
782564 TGCCCCACTGCAATTTCAGGGGGATAAGGGTTGCTTTCTCGAGTCTGCTCCACTGCAACTTTAGG
1 TGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACT-TAGTCTGCTCCACTGCAACTTCAGG
* * *
782629 GAGATAAGACTCGATATGATCTCCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATC
65 GAGATAAGACTAGATACGATCTGCTCT-CTGCAACTTCAGAGAGATAAGATCTGT-GTTTTAATC
* * *** * *
782694 CGCTCCACTGCAACTTCAGGGAGACAGGATTTGT-TTATTTAGTATGCCCCACTGCAACTTCAGG
128 TGCTCCACTGCAACTTCAGGGAGATAGGA-TTGTCGGCTTTAATATGCTCCACTGCAACTTCAGG
* *
782758 GAGATAAGATTCGACATCTTCAGTC
192 GAGATAAGATTTGCCATCTTCAGTC
* * *
782783 TGCCTCATTGCAACTTCAGGAGGATAAGACTTGATTACTTAGTCTGCTCCATTGCAACTTCAGGG
1 TGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGG
* * * * * ** * * *
782848 AGACAGGATTTGTTTATTTAGTATGCCCCACTGCAACTTCAGAGAGATAAGATCTAAG-GTTTTA
66 AGATAAGACTAG-ATA-CGA-TCTG-CTCTCTGCAACTTCAGAGAGATAAGATCT--GTGTTTTA
** * * **
782912 ATCAACTCCACTGCAACTTCAGGAAGATAGGATTATCGGCTTTAACCTGCTCCACTGCAACTTCA
125 ATCTGCTCCACTGCAACTTCAGGGAGATAGGATTGTCGGCTTTAATATGCTCCACTGCAACTTCA
*
782977 GGGAGATAAGATTTGCCATCTTCAATC
190 GGGAGATAAGATTTGCCATCTTCAGTC
* *
783004 TGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTGCTTAGTCTGCTCCATTGCAACTTCAGGG
1 TGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGG
*
783069 AGATAAGACTAGATACGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGTGATTTAATCTGC
66 AGATAAGACTAGATACGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGTGTTTTAATCTGC
* * *
783134 TCCACTGCAACTTCAGAGAGATAGGATTGTCGGCTTTAATTTGCTCCACTGCAACCTCAGGGAGA
131 TCCACTGCAACTTCAGGGAGATAGGATTGTCGGCTTTAATATGCTCCACTGCAACTTCAGGGAGA
783199 TAAGATTTGCCATCTTCAGTC
196 TAAGATTTGCCATCTTCAGTC
* *
783220 TGCCTCACTGCAACTTCAGAAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTTAGGG
1 TGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGG
* * * ***
783285 AGATAAGGCTAGATGCAATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAAGTTTTAATCTG
66 AGATAAGACTAGATACGATCTGCTCTCTGCAACTTCAGAGAGATAAGAT-CTGTGTTTTAATCTG
783350 CTCCACTGCAACTTCAGGGAGA
130 CTCCACTGCAACTTCAGGGAGA
783372 CAAGGCTTGG
Statistics
Matches: 509, Mismatches: 71, Indels: 20
0.85 0.12 0.03
Matches are distributed among these distances:
215 1 0.00
216 195 0.38
217 59 0.12
218 34 0.07
219 34 0.07
220 7 0.01
221 176 0.35
222 2 0.00
223 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (216 bp):
TGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGG
AGATAAGACTAGATACGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGTGTTTTAATCTGC
TCCACTGCAACTTCAGGGAGATAGGATTGTCGGCTTTAATATGCTCCACTGCAACTTCAGGGAGA
TAAGATTTGCCATCTTCAGTC
Found at i:783465 original size:132 final size:131
Alignment explanation
Indices: 783363--783748 Score: 592
Period size: 132 Copynumber: 2.9 Consensus size: 131
783353 CACTGCAACT
* *
783363 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATATGATTTACCG
1 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTATCG
* * *
783428 TCTTCGACCTGCTCCACTACTGCTTAGAGAGATAAGATCTACAATCTTCAACCTACTCTGCTGCT
66 TCTTCGATCTACTCCACTACTGCTTAGAGAGATAAGATCTACAATCTTCAACCTACTCCGCTGC-
*
783493 GC
130 AC
*
783495 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCG
1 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTATCG
* * * * *
783560 TCTTCAATCTTCTCCACTACTACTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCT
66 TCTTCGATCTACTCCACTACTGCTTAGAGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCA
783625 C
131 C
* * *
783626 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTACTTCCCACTATCTTGGAAAGATAAGATTTTTTG
1 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTATCG
* * * *
783691 TCCTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTACGATCCTCAACCTACTC
66 TCTTCGATCTACTCCACTACTGCTTAGAGAGATAAGATCTACAATCTTCAACCTACTC
783749 TGCTATTGCT
Statistics
Matches: 235, Mismatches: 19, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
131 115 0.49
132 120 0.51
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (131 bp):
TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTATCG
TCTTCGATCTACTCCACTACTGCTTAGAGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCA
C
Found at i:793812 original size:19 final size:21
Alignment explanation
Indices: 793774--793812 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
793764 CCTTTTTTAA
*
793774 AATCGTAAATAAGTAAAAAAT
1 AATCGTAAATAAGAAAAAAAT
793795 AATCG-AAA-AAGAAAAAAA
1 AATCGTAAATAAGAAAAAAA
793813 AGAAAACAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.69, C:0.05, G:0.10, T:0.15
Consensus pattern (21 bp):
AATCGTAAATAAGAAAAAAAT
Found at i:794045 original size:19 final size:19
Alignment explanation
Indices: 794021--794073 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
794011 AACCATATCT
*
794021 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
794040 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
794059 TCTAAGATTGCATAT
1 TCTAAGATTGCATAT
794074 GCTCGAAGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:804140 original size:13 final size:13
Alignment explanation
Indices: 804122--804159 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
804112 GTAGATTTGT
804122 AAAAAAATTGT-C
1 AAAAAAATTGTAC
*
804134 AAAAAAATCGTAC
1 AAAAAAATTGTAC
804147 AAAAAAAGTTGTA
1 AAAAAAA-TTGTA
804160 TTTATTTTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 10 0.45
13 8 0.36
14 4 0.18
ACGTcount: A:0.61, C:0.08, G:0.11, T:0.21
Consensus pattern (13 bp):
AAAAAAATTGTAC
Found at i:817694 original size:33 final size:34
Alignment explanation
Indices: 817643--817717 Score: 107
Period size: 33 Copynumber: 2.2 Consensus size: 34
817633 AGATTTAAAC
* *
817643 AAATTAATTACTAACACTTTTTTAAGGTGAACTA
1 AAATTAATTACTAACACTTATTTAAGCTGAACTA
*
817677 AAATTAATT-CTAACACTTATTTGAGCTGAACTA
1 AAATTAATTACTAACACTTATTTAAGCTGAACTA
*
817710 AATTTAAT
1 AAATTAAT
817718 AAACTAACTC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 28 0.76
34 9 0.24
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (34 bp):
AAATTAATTACTAACACTTATTTAAGCTGAACTA
Done.