Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold264
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: 1000627
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Warning! 64 characters in sequence are not A, C, G, or T
File 6 of 6
Found at i:934867 original size:24 final size:24
Alignment explanation
Indices: 934818--934887 Score: 112
Period size: 24 Copynumber: 3.1 Consensus size: 24
934808 TAAACCCAGA
934818 ATGTATCGATACAATGAACAATGT
1 ATGTATCGATACAATGAACAATGT
934842 A--T-T-GATACAATGAACAATGT
1 ATGTATCGATACAATGAACAATGT
934862 ATGTATCGATACAATGAACAATGT
1 ATGTATCGATACAATGAACAATGT
934886 AT
1 AT
934888 CGACACAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
20 18 0.43
21 1 0.02
22 2 0.05
23 1 0.02
24 20 0.48
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Consensus pattern (24 bp):
ATGTATCGATACAATGAACAATGT
Found at i:935782 original size:37 final size:37
Alignment explanation
Indices: 935736--935807 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
935726 CCTGTTCTTT
935736 GAGGACAAAGGAAAAAAGGAAAAGGCGTCCTGCTCAA
1 GAGGACAAAGGAAAAAAGGAAAAGGCGTCCTGCTCAA
* * *
935773 GAGGGCAAAGGAGAAAAGGAAAAGGCGTCTTGCTC
1 GAGGACAAAGGAAAAAAGGAAAAGGCGTCCTGCTC
935808 TTTGAGGACT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.42, C:0.15, G:0.33, T:0.10
Consensus pattern (37 bp):
GAGGACAAAGGAAAAAAGGAAAAGGCGTCCTGCTCAA
Found at i:935858 original size:62 final size:61
Alignment explanation
Indices: 935786--937475 Score: 849
Period size: 62 Copynumber: 27.6 Consensus size: 61
935776 GGCAAAGGAG
* * *
935786 AAAAGGAAAAGGCGTCTTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTT
1 AAAAGGAAAAGGTGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT
* *
935847 GAAAAGAAAAAGGTGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACCTGTGTGGGCTTT
1 -AAAAGGAAAAGGTGTCCTGCTCTTTGAGGACTA-AAAAGTGCCACCAACTTGTGTGGGCTTT
* * * *
935910 AAAAGGAAAAGGCGTCCTACTCTTTGAGGACTAAAAGGGTGCCACCAGCTTGTGTGGGCTTT
1 AAAAGGAAAAGGTGTCCTGCTCTTTGAGGACTAAAA-AGTGCCACCAACTTGTGTGGGCTTT
* * *
935972 GAAAAGAAAAAGATGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACCTGTGTGGGCTTT
1 -AAAAGGAAAAGGTGTCCTGCTCTTTGAGGACTA-AAAAGTGCCACCAACTTGTGTGGGCTTT
* * * * *
936035 AAAAGGAAAAGGTTTCCTACTCTTTGAGGACTAAAAGGGTGCCACCAGCTTGTGTAGGCTTT
1 AAAAGGAAAAGGTGTCCTGCTCTTTGAGGACTAAAA-AGTGCCACCAACTTGTGTGGGCTTT
* * *
936097 GAAAAGAAAAAGGTATCCTGCTCTTCGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTT
1 -AAAAGGAAAAGGTGTCCTGCTCTTTGAGGACTA-AAAAGTGCCACCAACTTGTGTGGGCTTT
* *
936160 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACT-AAAAGTGTTCCACCAGCTTGTGTGGGCTTT
1 AAAAGGAAAAGGTGTCCTGCTCTTTGAGGACTAAAAAGTG--CCACCAACTTGTGTGGGCTTT
* **** * * *
936222 GAAAGGAAAAAACATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGACTTT
1 AAAAGGAAAAGGTGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT
* * *
936283 AAAAGGAAAAGGTGTCTTGCTCTTTGAGGACTAGAAAAGTGCCACCAGCTTATGTGGGCTTT
1 AAAAGGAAAAGGTGTCCTGCTCTTTGAGGACTA-AAAAGTGCCACCAACTTGTGTGGGCTTT
* * ** * *
936345 ------AAAAGGCGTCATGCTCTTTGAAAACTAGAAAA-TGCCACTAAC-TGATGAGGGCTTT
1 AAAAGGAAAAGGTGTCCTGCTCTTTGAGGACTA-AAAAGTGCCACCAACTTG-TGTGGGCTTT
* * ** * ** ** *** * ***
936400 -----GAAAA-GCGTCCTGCACTTTGAGGACTAAAGGGCGAAAGGAGAGAGCGTCCTACTCTTT
1 AAAAGGAAAAGGTGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCA-A-CTTGT-GTGGGCTTT
** * * * * * * **
936458 GAAGACTAGG--AA-GTG-CCACCAACTTGTGTGGGCTTTAAGAGGAGAAGGCATCCTGCTCT-T
1 -AA-A--AGGAAAAGGTGTCCTGC-TCTT-TGAGGAC--TAA-A-AAG-TGCCA-CCAACT-TGT
*
936518 -TGAGG-ATT
53 GTG-GGCTTT
* * * * * * * *
936526 ----GG--AAGGTG-CC-ACTAACTTGTGTGGGCTTTAAGAAGAGAAGGCATCCTACTCTTTGAG
1 AAAAGGAAAAGGTGTCCTGCT--CTT-TGAGGAC--TAA-AA-AG-TGCCA-CCAACT-TGTGTG
*
936583 GAC--T
56 GGCTTT
** * * * * * ** *
936587 ---A-G--AAGGTG-CCACCAACTTGTGTGGGCTTTAAAAG-G--A-AAAGGTGT-TCGGCTCTT
1 AAAAGGAAAAGGTGTCCTGC-TCTT-TGAGGAC-TAAAAAGTGCCACCAACTTGTGT-GG-GCTT
936640 T
61 T
* * ** * * * * ** * *
936641 GAGGACTA-GAAAA-ATG-CCACCAACTTGTGTGGGCTTTAAAAG-G-CATCCTGCTCTTTGAGG
1 -A--A-AAGGAAAAGGTGTCCTGC-TCTT-TGAGGAC-TAAAAAGTGCCA-CCAACT-TGTGTGG
*
936701 AC--T
57 GCTTT
* * * **
936704 AAAGGGTGAAAGGAGAGAGTGTCATGCTCTCTGAGGACT-GGAAGTGCCACCAACTTGTGTGGGC
1 AAA-AG-G-AA--A-AG-GTGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGC
936768 TTT
59 TTT
* * * * **
936771 AAAAAGAAAAAAGCGTCCTACTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTT
1 -AAAAGGAAAAGGTGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT
* * * * *
936833 -AAAGGAGATGGCGTCTTGCTCTTTGAGGAC-AAAAAGGTGCCACCAACTTGTGTAGGCTTT
1 AAAAGGAAAAGGTGTCCTGCTCTTTGAGGACTAAAAA-GTGCCACCAACTTGTGTGGGCTTT
* * * * * *
936893 CAAAA--AGAAGGCGTCCTGCTCTTTGATGATTAGAAGGTGCCACCAACTTGTGTGGGCTTT
1 -AAAAGGAAAAGGTGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT
* * * * *
936953 AAAAAGAAAAAAGTGTCCTACTTTTTGAGGACTAAAAGGTGCCACCAACTT-TGTGGGCTTT
1 -AAAAGGAAAAGGTGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT
* * *
937014 AAAAGGAAAAGGTGTCTTGCTCTTTGAGGACT-AAAGGTGCCACCAACTCGTGTGGGCTTT
1 AAAAGGAAAAGGTGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT
* * ** * ** * *
937074 GAGAAGAAAAAGGCATCCTACTCTTTGAGGACTAAAGGGTGCCATCAACTCGTGTGGGCTTT
1 -AAAAGGAAAAGGTGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT
* * * * *
937136 GAAAAGAAAAAGGTGTCCTACTTTTTGAGGACTAAAAGGTGCCACTAACTTGTGTGGGCTTT
1 -AAAAGGAAAAGGTGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT
* *
937198 AAAAGGAAAAGGTGTCCTGCTCTTTGAGAACTAAAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAAGGAAAAGGTGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT
* * *
937259 AAAAGGAAAAGGTGT-CTGTTCTTTGAGGACT-AAAGGTGCCACCAACTCGTGTGGGCTTT
1 AAAAGGAAAAGGTGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT
* ** * * * * *
937318 AAAAAGAAAAAAATGTCATGCTTTTTGAGGACT-AAAAGTGCTACCAACTCGTGTGGGGTTT
1 -AAAAGGAAAAGGTGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT
* * **
937379 GAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTG-CACCAACTTGTGTGGGCTTT
1 -AAAAGGAAAAGGTGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT
* ** *
937440 AAAAAGAAAAAGACGTCTTGCTCTTTGAGGACTAAA
1 -AAAAGGAAAAGGTGTCCTGCTCTTTGAGGACTAAA
937476 GGGCTAAAAG
Statistics
Matches: 1301, Mismatches: 234, Indels: 187
0.76 0.14 0.11
Matches are distributed among these distances:
51 4 0.00
52 2 0.00
54 5 0.00
55 38 0.03
56 34 0.03
57 1 0.00
58 7 0.01
59 48 0.04
60 174 0.13
61 356 0.27
62 414 0.32
63 141 0.11
64 9 0.01
65 21 0.02
66 16 0.01
67 10 0.01
68 13 0.01
69 3 0.00
70 3 0.00
71 2 0.00
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26
Consensus pattern (61 bp):
AAAAGGAAAAGGTGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT
Found at i:936007 original size:125 final size:124
Alignment explanation
Indices: 935786--937473 Score: 915
Period size: 125 Copynumber: 13.8 Consensus size: 124
935776 GGCAAAGGAG
* * *
935786 AAAAGGAAAAGGCGTCTTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAA
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAA
*
935851 AGAAAAAGGTGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACCTGTGTGGGCTTT
66 AGAAAAAGATGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACCTGTGTGGGCTTT
* *
935910 AAAAGGAAAAGGCGTCCTACTCTTTGAGGACTAAAAGGGTGCCACCAGCTTGTGTGGGCTTTGAA
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAA-GGTGCCACCAACTTGTGTGGGCTTTGAA
935975 AAGAAAAAGATGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACCTGTGTGGGCTTT
65 AAGAAAAAGATGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACCTGTGTGGGCTTT
** * * *
936035 AAAAGGAAAAGGTTTCCTACTCTTTGAGGACTAAAAGGGTGCCACCAGCTTGTGTAGGCTTTGAA
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAA-GGTGCCACCAACTTGTGTGGGCTTTGAA
* * * *
936100 AAGAAAAAGGTATCCTGCTCTTCGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTT
65 AAGAAAAAGATGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACCTGTGTGGGCTTT
* *
936160 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAGTGTTCCACCAGCTTGTGTGGGCTTTGAA
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAG-GTGCCACCAACTTGTGTGGGCTTTGAA
* ** * * *
936225 AGGAAAAA-ACATCCTGCTCTTTGAGGACTAG-AAGGTGCCACCAACTTGTGTGGACTTT
65 AAGAAAAAGATGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACCTGTGTGGGCTTT
* * * * *
936283 AAAAGGAAAAGGTGTCTTGCTCTTTGAGGACTAGAAAAGTGCCACCAGCTTATGTGGGCTTT-AA
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTA-AAAGGTGCCACCAACTTGTGTGGGCTTTGAA
* * ** * *
936347 AAG-----G-CGTCATGCTCTTTGAAAACTAGAAAA-TGCCACTAA-CTGATGAGGGCTTT
65 AAGAAAAAGATGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACCTG-TGTGGGCTTT
* * * ** ** *** * ***
936400 -----GAAAA-GCGTCCTGCACTTTGAGGACTAAAGGGCGAAAGGAGAGAGCGTCCTACTCTTTG
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCA-A-CTTGT-GTGGGCTTTG
** * * ** * * * ** * ** * * *
936459 --AAGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAGAG-GAGAAGGCATCCTG-CT---CT
63 AAAAGAAAAAGATGT-CCTGC-TCTT-TGAGGACTAGAAAAGTG-CCA-CCAACCTGTGTGGGCT
936517 TT
123 TT
* * * * * * * * *
936519 --GAGGATTGGAAGGTG-CC-ACTAACTTGTGTGGGCTTTAAGAAGAGAAGGCATCCTACTCT-T
1 AAAAGGA---AAAGGCGTCCTGCT--CTT-TGAGGAC--TAA-AAG-G-TGCCA-CCAACT-TGT
* ** * ** * * * ** * **
936579 -TGAG----GACTAG---AAGGTG-CCACCAACTTGTGTGGGCTTTAAAAG-G--A-AAAGGTGT
53 GTGGGCTTTGAAAAGAAAAAGATGTCCTGC-TCTT-TGAGGACTAGAAAAGTGCCACCAACCTGT
*
936631 -TCGGCTCTTT
116 GT-GG-GCTTT
* * * ** ** * * * ** * * *
936641 GAGGACTAGAAAAATGCCACCAACT-TGTGTGGGCTTTAAAA-G-G-CATCCTGCTCTTTGAGGA
1 -A--A-AAGGAAAAGGCGTCCTGCTCTTTGAGGAC--TAAAAGGTGCCA-CCAACT-TGTGTGGG
* * * * * * * *
936702 CTAAAGGGTGAAAGGAGAGAG-TGTCATGCTCTCTGAGGACT-G-GAAGTGCCACCAACTTGTGT
58 CT-----TTGAAAAGAAAAAGATGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACCTGTGT
936764 GGGCTTT
118 GGGCTTT
* * * *
936771 AAAAAGAAAAAAGCGTCCTACTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTT--A
1 -AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAA
* * * ** * * *
936834 AAGGAGATGGCGTCTTGCTCTTTGAGGAC-A-AAAAGGTGCCACCAACTTGTGTAGGCTTT
65 AAGAAAAAGATGTCCTGCTCTTTGAGGACTAGAAAA-GTGCCACCAACCTGTGTGGGCTTT
* * * * *
936893 CAAAA--AGAAGGCGTCCTGCTCTTTGATGATTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAA
1 -AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAA
* * * *
936956 AAGAAAAA-AGTGTCCTACTTTTTGAGGACTA-AAAGGTGCCACCAA-CTTTGTGGGCTTT
65 AAGAAAAAGA-TGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACCTGTGTGGGCTTT
* * * *
937014 AAAAGGAAAAGGTGTCTTGCTCTTTGAGGACT-AAAGGTGCCACCAACTCGTGTGGGCTTTGAGA
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAA
*** * ** *
937078 AGAAAAAGGCATCCTACTCTTTGAGGACTA-AAGGGTGCCATCAA-CTCGTGTGGGCTTT
66 AGAAAAAGATGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACCT-GTGTGGGCTTT
* * * * *
937136 GAAAAGAAAAAGGTGTCCTACTTTTTGAGGACTAAAAGGTGCCACTAACTTGTGTGGGCTTT-AA
1 -AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAA
* * * * *
937200 AAGGAAAAGGTGTCCTGCTCTTTGAGAACTA-AAAGGTGCCACCAACTTGTGTGGGCTTT
65 AAGAAAAAGATGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACCTGTGTGGGCTTT
* * * *
937259 AAAAGGAAAAGGTGT-CTGTTCTTTGAGGACT-AAAGGTGCCACCAACTCGTGTGGGCTTTAAAA
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAA
* * * * *
937322 AGAAAAAAATGTCATGCTTTTTGAGGACT--AAAAGTGCTACCAA-CTCGTGTGGGGTTT
66 AGAAAAAGATGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACCT-GTGTGGGCTTT
* * *
937379 GAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTG-CACCAACTTGTGTGGGCTTTAAA
1 -AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAA
* *
937443 AAGAAAAAGACGTCTTGCTCTTTGAGGACTA
65 AAGAAAAAGATGTCCTGCTCTTTGAGGACTA
937474 AAGGGCTAAA
Statistics
Matches: 1227, Mismatches: 236, Indels: 203
0.74 0.14 0.12
Matches are distributed among these distances:
110 6 0.00
111 19 0.02
112 9 0.01
113 5 0.00
116 2 0.00
117 49 0.04
118 6 0.00
119 9 0.01
120 108 0.09
121 155 0.13
122 206 0.17
123 179 0.15
124 93 0.08
125 275 0.22
126 11 0.01
127 35 0.03
128 19 0.02
129 12 0.01
130 12 0.01
131 13 0.01
132 4 0.00
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26
Consensus pattern (124 bp):
AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAA
AGAAAAAGATGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACCTGTGTGGGCTTT
Found at i:936372 original size:56 final size:56
Alignment explanation
Indices: 936288--936420 Score: 153
Period size: 55 Copynumber: 2.4 Consensus size: 56
936278 ACTTTAAAAG
* * ** * * *
936288 GAAAAGGTGTCTTGCTCTTTGAGGACTAGAAAAGTGCCACCAGCTTATGTGGGCTTT
1 GAAAAGGCGTCATGCTCTTTGAAAACTAGAAAA-TGCCACCAACTGATGAGGGCTTT
*
936345 -AAAAGGCGTCATGCTCTTTGAAAACTAGAAAATGCCACTAACTGATGAGGGCTTT
1 GAAAAGGCGTCATGCTCTTTGAAAACTAGAAAATGCCACCAACTGATGAGGGCTTT
* *
936400 GAAAA-GCGTCCTGCACTTTGA
1 GAAAAGGCGTCATGCTCTTTGA
936421 GGACTAAAGG
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
55 33 0.51
56 32 0.49
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (56 bp):
GAAAAGGCGTCATGCTCTTTGAAAACTAGAAAATGCCACCAACTGATGAGGGCTTT
Found at i:936535 original size:61 final size:62
Alignment explanation
Indices: 936447--936704 Score: 318
Period size: 61 Copynumber: 4.3 Consensus size: 62
936437 GGAGAGAGCG
* *
936447 TCCTACTCTTTGAAGACTAGGAA-GTGCCACCAACTTGTGTGGGCTTTAAGAGGAGAAGGCA
1 TCCTGCTCTTTGAGGACTAGGAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGAGAAGGCA
* * *
936508 TCCTGCTCTTTGAGGA-TTGGAAGGTGCCACTAACTTGTGTGGGCTTTAAGAAGAGAAGGCA
1 TCCTGCTCTTTGAGGACTAGGAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGAGAAGGCA
* * * **
936569 TCCTACTCTTTGAGGACTA-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTG
1 TCCTGCTCTTTGAGGACTAGGAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGAGAAGGCA
* * * **
936630 TTCGGCTCTTTGAGGACTAGAAAAATGCCACCAACTTGTGTGGGCTTT---A--A-AAGGCA
1 TCCTGCTCTTTGAGGACTAGGAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGAGAAGGCA
936686 TCCTGCTCTTTGAGGACTA
1 TCCTGCTCTTTGAGGACTA
936705 AAGGGTGAAA
Statistics
Matches: 171, Mismatches: 23, Indels: 11
0.83 0.11 0.05
Matches are distributed among these distances:
56 21 0.12
57 1 0.01
59 1 0.01
60 5 0.03
61 117 0.68
62 26 0.15
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.27
Consensus pattern (62 bp):
TCCTGCTCTTTGAGGACTAGGAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGAGAAGGCA
Found at i:937011 original size:61 final size:62
Alignment explanation
Indices: 936722--937475 Score: 899
Period size: 61 Copynumber: 12.4 Consensus size: 62
936712 AAAGGAGAGA
* * ** *
936722 GTGTCATGCTCTCTGAGGACTGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAA
1 GTGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAG
* * * * * *
936783 GCGTCCTACTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTT--AAAGGAGATG
1 GTGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAG
* * * *
936843 GCGTCTTGCTCTTTGAGGACAAAAAGGTGCCACCAACTTGTGTAGGCTTTCAAAAAG---AAG
1 GTGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAAGAAAAAG
* * * * *
936903 GCGTCCTGCTCTTTGATGATTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAA
1 GTGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAG
* * *
936965 GTGTCCTACTTTTTGAGGACTAAAAGGTGCCACCAACTT-TGTGGGCTTT-AAAAGGAAAAG
1 GTGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAG
* * * *
937025 GTGTCTTGCTCTTTGAGGACT-AAAGGTGCCACCAACTCGTGTGGGCTTTGAGAAGAAAAAG
1 GTGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAG
** * * * * *
937086 GCATCCTACTCTTTGAGGACTAAAGGGTGCCATCAACTCGTGTGGGCTTTGAAAAGAAAAAG
1 GTGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAG
* * * *
937148 GTGTCCTACTTTTTGAGGACTAAAAGGTGCCACTAACTTGTGTGGGCTTT-AAAAGGAAAAG
1 GTGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAG
* *
937209 GTGTCCTGCTCTTTGAGAACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAG
1 GTGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAG
* * *
937270 GTGT-CTGTTCTTTGAGGACT-AAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAA
1 GTGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAG
* * * * * * *
937330 ATGTCATGCTTTTTGAGGACTAAAA-GTGCTACCAACTCGTGTGGGGTTTGAAAAGAAAAAG
1 GTGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAG
* *
937391 GCGTCCTGCTCTTTGAGGACTAAAGGGTG-CACCAACTTGTGTGGGCTTTAAAAAGAAAAAG
1 GTGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAG
** *
937452 ACGTCTTGCTCTTTGAGGACTAAA
1 GTGTCCTGCTCTTTGAGGACTAAA
937476 GGGCTAAAAG
Statistics
Matches: 598, Mismatches: 81, Indels: 28
0.85 0.11 0.04
Matches are distributed among these distances:
59 49 0.08
60 160 0.27
61 240 0.40
62 145 0.24
63 4 0.01
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (62 bp):
GTGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAG
Found at i:937353 original size:182 final size:184
Alignment explanation
Indices: 936728--937477 Score: 1018
Period size: 182 Copynumber: 4.1 Consensus size: 184
936718 GAGAGTGTCA
* * * *
936728 TGCTCTCTGAGGACTGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAGCGTCCTAC
1 TGCTCTTTGAGGACT-AAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAAGTGTCCTAC
* * * * *
936792 TCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTT-AAAGGAGATGGCGTCTTGCTCTT
65 TTTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTT
* *
936856 TGAGGACAAAAAGGTGCCACCAACTTGTGTAGGCTTTCAAAAAG---AAGGCGTCC
130 TGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAAGAAAAAGGCGTCC
* * *
936909 TGCTCTTTGATGATTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAGTGTCCTAC
1 TGCTCTTTGAGGACTA-AAGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAAGTGTCCTAC
* *
936974 TTTTTGAGGACTAAAAGGTGCCACCAACTT-TGTGGGCTTTAAAAGGAAAAGGTGTCTTGCTCTT
65 TTTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTT
* * * *
937038 TGAGGACT-AAAGGTGCCACCAACTCGTGTGGGCTTTGAGAAGAAAAAGGCATCC
130 TGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGGCGTCC
* * * *
937092 TACTCTTTGAGGACTAAAGGGTGCCATCAACTCGTGTGGGCTTTGAAAAGAAAAAGGTGTCCTAC
1 TGCTCTTTGAGGACTAAA-GGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAAGTGTCCTAC
* *
937157 TTTTTGAGGACTAAAAGGTGCCACTAACTTGTGTGGGCTTTAAAAGGAAAAGGTGTCCTGCTCTT
65 TTTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTT
* * *
937222 TGAGAACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAGGTGT-C
130 TGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGGCGTCC
* * * *
937275 TGTTCTTTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAAATGTCATGCT
1 TGCTCTTTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAAGTGTCCTACT
* * * *
937340 TTTTGAGGACTAAAA-GTGCTACCAACTCGTGTGGGGTTTGAAAAGAAAAAGGCGTCCTGCTCTT
66 TTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAGGCGTCCTGCTCTT
* * *
937404 TGAGGACTAAAGGGTG-CACCAACTTGTGTGGGCTTTAAAAAGAAAAAGACGTCT
130 TGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGGCGTCC
937458 TGCTCTTTGAGGACTAAAGG
1 TGCTCTTTGAGGACTAAAGG
937478 GCTAAAAGGG
Statistics
Matches: 505, Mismatches: 52, Indels: 22
0.87 0.09 0.04
Matches are distributed among these distances:
180 4 0.01
181 90 0.18
182 205 0.41
183 128 0.25
184 51 0.10
185 27 0.05
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (184 bp):
TGCTCTTTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAAGTGTCCTACT
TTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTT
GAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGGCGTCC
Found at i:940945 original size:49 final size:49
Alignment explanation
Indices: 940787--941255 Score: 476
Period size: 49 Copynumber: 9.5 Consensus size: 49
940777 GAAGAATGAT
* ** * *
940787 AATGTGCTGATTCATGGCCAGCGACATTAGATTTAAAGAAG-A-ATGCC
1 AATGTGCTGATTCAAGGCCAGCGACATCGGACTTAAAGATGAAGATGCC
** * * * *
940834 AATGTGCTGAGACAAGGCCAGCGACATTGGGCTTAGGAATGTTAAAGATGCC
1 AATGTGCTGATTCAAGGCCAGCGACATCGGACTTA--AA-GATGAAGATGCC
* * * *
940886 AATATACTGATTCAAGGCCAACGATATCGGACTTAAAGATGAAGATGCC
1 AATGTGCTGATTCAAGGCCAGCGACATCGGACTTAAAGATGAAGATGCC
* * *
940935 AATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGACAG-TGCT
1 AATGTGCTGATTCAAGGCCAGCGACATCGGACTTAAAGATGA-AGATGCC
* ** * *
940984 AATATGCTGATTCAAGGTTAGCGATATCGGACTTACAGATGAAGATGCC
1 AATGTGCTGATTCAAGGCCAGCGACATCGGACTTAAAGATGAAGATGCC
* * * * *
941033 AATGTACTAATTCAAGGCCAGTGACATTGGACTTAAAGATAGTGAAGGTGCC
1 AATGTGCTGATTCAAGGCCAGCGACATCGGACTTAAAG--A-TGAAGATGCC
* ** * * *
941085 AATGTGCTGATTTAAGGCCAATGACATCAGTCTTAAAGATGAAGGTGCC
1 AATGTGCTGATTCAAGGCCAGCGACATCGGACTTAAAGATGAAGATGCC
* * * *
941134 AATATGCTGATTCAAGGCCAGCGATATCAGACTTACAGATGAAGATGCC
1 AATGTGCTGATTCAAGGCCAGCGACATCGGACTTAAAGATGAAGATGCC
* * *
941183 AATGTGCTGATTCAAGGCCAACGACATCGGTCTTAAAGATGAAGGTGCC
1 AATGTGCTGATTCAAGGCCAGCGACATCGGACTTAAAGATGAAGATGCC
*
941232 AATATGCTGATTCAAGGCCAGCGA
1 AATGTGCTGATTCAAGGCCAGCGA
941256 TATCAGGCTT
Statistics
Matches: 344, Mismatches: 68, Indels: 18
0.80 0.16 0.04
Matches are distributed among these distances:
47 29 0.08
48 2 0.01
49 233 0.68
50 6 0.02
51 2 0.01
52 72 0.21
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (49 bp):
AATGTGCTGATTCAAGGCCAGCGACATCGGACTTAAAGATGAAGATGCC
Found at i:941087 original size:199 final size:199
Alignment explanation
Indices: 940882--941252 Score: 492
Period size: 199 Copynumber: 1.9 Consensus size: 199
940872 ATGTTAAAGA
* * *
940882 TGCCAATATACTGATTCAAGGCCAACGATATCGGACTTAAAGATGAAGATGCCAATGTGCTGATT
1 TGCCAATATACTGATTCAAGGCCAACGACATCAGACTTAAAGATGAAGATGCCAATATGCTGATT
** * * ** * *
940947 CAAGGCCAGCGACATTGGTCTTAAAGATGACAG-TGCTAATATGCTGATTCAAGGTTAGCGATAT
66 CAAGGCCAGCGACATCAGACTTAAAGATGA-AGATGCCAATATGCTGATTCAAGGCCAACGACAT
* *
941011 CGGACTTACAGATGAAGATGCCAATGTACTAATTCAAGGCCAGTGACATTGGACTTAAAGATAGT
130 CGGACTTAAAGATGAAGATGCCAATATACTAATTCAAGGCCAGTGACATTGGACTTAAAGATAGT
941076 GAAGG
195 GAAGG
* * * * * *
941081 TGCCAATGTGCTGATTTAAGGCCAATGACATCAGTCTTAAAGATGAAGGTGCCAATATGCTGATT
1 TGCCAATATACTGATTCAAGGCCAACGACATCAGACTTAAAGATGAAGATGCCAATATGCTGATT
* * *
941146 CAAGGCCAGCGATATCAGACTTACAGATGAAGATGCCAATGTGCTGATTCAAGGCCAACGACATC
66 CAAGGCCAGCGACATCAGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAACGACATC
* * * *
941211 GGTCTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAG
131 GGACTTAAAGATGAAGATGCCAATATACTAATTCAAGGCCAG
941253 CGATATCAGG
Statistics
Matches: 145, Mismatches: 26, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
198 2 0.01
199 143 0.99
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (199 bp):
TGCCAATATACTGATTCAAGGCCAACGACATCAGACTTAAAGATGAAGATGCCAATATGCTGATT
CAAGGCCAGCGACATCAGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAACGACATC
GGACTTAAAGATGAAGATGCCAATATACTAATTCAAGGCCAGTGACATTGGACTTAAAGATAGTG
AAGG
Found at i:964212 original size:79 final size:78
Alignment explanation
Indices: 964041--964244 Score: 252
Period size: 79 Copynumber: 2.6 Consensus size: 78
964031 AATAAAATCA
* * * * *
964041 GGGTTAGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCTCGA-TGTGGAAAATCGATGCTT
1 GGGTTGGAGTATCCCCTC-AAAATAACGGGGTTGGAGTATCCCCAATTGTGGAAAATCAATGATT
*
964105 TAGAAATAAGGCCG
65 TAGAAATAAAGCCG
* *
964119 AGGTTGGAGTATCCCCGCGAAAATAACGGGGTTGGAGTATCCCCAATTGT-GAGAAATCAAT-AT
1 GGGTTGGAGTATCCCCTC-AAAATAACGGGGTTGGAGTATCCCCAATTGTGGA-AAATCAATGAT
964182 TTCAGAAATAAAGCCG
64 TT-AGAAATAAAGCCG
* *
964198 GGGTTGGAGTATCCCCTCAGGAATAATGGGGTTGGAGTATCCCCAAT
1 GGGTTGGAGTATCCCCTCA-AAATAACGGGGTTGGAGTATCCCCAAT
964245 GAAATAACAA
Statistics
Matches: 109, Mismatches: 13, Indels: 7
0.84 0.10 0.05
Matches are distributed among these distances:
78 46 0.42
79 63 0.58
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.24
Consensus pattern (78 bp):
GGGTTGGAGTATCCCCTCAAAATAACGGGGTTGGAGTATCCCCAATTGTGGAAAATCAATGATTT
AGAAATAAAGCCG
Found at i:964241 original size:107 final size:108
Alignment explanation
Indices: 964120--964348 Score: 311
Period size: 109 Copynumber: 2.1 Consensus size: 108
964110 ATAAGGCCGA
* ** *
964120 GGTTGGAGTATCCCC-GCGAAAATAACGGGGTTGGAGTATCCCCAATTGTG-AGAAATCAATATT
1 GGTTGGAGTATCCCCAACG-AAATAACAAGGTTGGAGTATCCCCAATTGTGAAAAAATCAATATT
* * *
964183 TCAGAAATAAAGCCGGGGTTGGAGTATCCCCTC-AGGAATAATGG
65 TCAGAAATAAAGCCGGAGTTGGAGTATCCCCTCGA-AAATAACGG
* *
964227 GGTTGGAGTATCCCCAATGAAATAACAAGGTTGGAGTATCCCCGATTGTGAAAAAAATCAATATT
1 GGTTGGAGTATCCCCAACGAAATAACAAGGTTGGAGTATCCCCAATTGTG-AAAAAATCAATATT
*
964292 TTAGAAATAAAGCCGGAGTTGGAGTATCCCCTCGAAAATAACGG
65 TCAGAAATAAAGCCGGAGTTGGAGTATCCCCTCGAAAATAACGG
*
964336 GGTTGAAGTATCC
1 GGTTGGAGTATCC
964349 TCGTTTAAGA
Statistics
Matches: 107, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
107 43 0.40
108 1 0.01
109 62 0.58
110 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (108 bp):
GGTTGGAGTATCCCCAACGAAATAACAAGGTTGGAGTATCCCCAATTGTGAAAAAATCAATATTT
CAGAAATAAAGCCGGAGTTGGAGTATCCCCTCGAAAATAACGG
Found at i:964250 original size:28 final size:28
Alignment explanation
Indices: 964196--964269 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 28
964186 GAAATAAAGC
* *
964196 CGGGGTTGGAGTATCCCCTCAGGAATAA
1 CGGGGTTGGAGTATCCCCTAAGAAATAA
*
964224 TGGGGTTGGAGTATCCCC-AATGAAATAA
1 CGGGGTTGGAGTATCCCCTAA-GAAATAA
**
964252 CAAGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
964270 GATTGTGAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 1 0.03
28 38 0.97
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCTAAGAAATAA
Found at i:966799 original size:13 final size:13
Alignment explanation
Indices: 966752--966781 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
966742 GTAAACCCAA
966752 AATGTATCGATAC
1 AATGTATCGATAC
966765 AATGTATCGATAC
1 AATGTATCGATAC
966778 AATG
1 AATG
966782 AACAATGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:970197 original size:32 final size:32
Alignment explanation
Indices: 970143--970214 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
970133 ACAAATAGTA
* *
970143 AATGTATCGATACATAAGTGTTGTATCAATAC
1 AATGTATCAATACATAAATGTTGTATCAATAC
* * *
970175 AATGTATTAATACGTAAATGTTGTATCGATAC
1 AATGTATCAATACATAAATGTTGTATCAATAC
970207 AATGTATC
1 AATGTATC
970215 GTTACAAAGC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (32 bp):
AATGTATCAATACATAAATGTTGTATCAATAC
Found at i:970210 original size:16 final size:16
Alignment explanation
Indices: 970145--970211 Score: 50
Period size: 16 Copynumber: 4.0 Consensus size: 16
970135 AAATAGTAAA
970145 TGTATCGATACATAAGTGT
1 TGTATCGATAC--AA-TGT
*
970164 TGTATCAATACAATGT
1 TGTATCGATACAATGT
970180 AT-TAATACG-TA-AATGT
1 -TGT-AT-CGATACAATGT
970196 TGTATCGATACAATGT
1 TGTATCGATACAATGT
970212 ATCGTTACAA
Statistics
Matches: 40, Mismatches: 2, Indels: 15
0.70 0.04 0.26
Matches are distributed among these distances:
14 2 0.05
15 5 0.12
16 15 0.38
17 7 0.17
18 1 0.03
19 10 0.25
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.37
Consensus pattern (16 bp):
TGTATCGATACAATGT
Found at i:970270 original size:20 final size:20
Alignment explanation
Indices: 970245--970292 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
970235 GAAACATATG
970245 GATACATT-ATTCAATGTATC
1 GATACATTGA-TCAATGTATC
**
970265 GATACATTGATCTTTGTATC
1 GATACATTGATCAATGTATC
970285 GATACATT
1 GATACATT
970293 TAGGAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (20 bp):
GATACATTGATCAATGTATC
Found at i:982538 original size:462 final size:462
Alignment explanation
Indices: 981674--982597 Score: 1670
Period size: 462 Copynumber: 2.0 Consensus size: 462
981664 CTACCAAATA
981674 TACTTTCGGAGTCATTTCGGGTAAGCTTTTAGGCTTTATAGTTAGCAAAAAAGGGATTAAAGTTG
1 TACTTTCGGAGTCATTTCGGGTAAGCTTTTAGGCTTTATAGTTAGCAAAAAAGGGATTAAAGTTG
* *
981739 ACCCAGACAAAGTCAAAGCCATTCAAGATATGCCACCACCTCAAACCCAAAAAGAGGTAAGAGAC
66 ACCCAGACAAAATCAAAGCCATTCAAGATATGCCACCACCTCAAACCCAAAAAGAAGTAAGAGAC
*
981804 TTTTTAGGGAGACTGAACTATATTTCCAAGTTCATATCCCAGCTCACTGACAAATGTGACCCCAT
131 TTTTTAGGGAGACTGAACTATATTTCCAAGTTCATATCCCAGCTCACTAACAAATGTGACCCCAT
*
981869 CTTCTGACTTCTTCGCAAACAAAATCTGGGGGAATGGAATGAGGCATGTCAAGAAGCCTTTGACA
196 CTTCCGACTTCTTCGCAAACAAAATCTGGGGGAATGGAATGAGGCATGTCAAGAAGCCTTTGACA
* *
981934 AGGTCAAAAATTATTTGTCAAACCCACCAGTATTGGTACCACCGGCGCTCGGTCAACCTTTAATC
261 AGGTCAAAAATTATTTGTCAAACCCACCAGTATTGGTACCACCGGCACTCGGTCAACCCTTAATC
*
981999 CTTTATTTGGCAGTCTTTGATAAATCCATGGGCTGTGTACTGGACAACATGATGAGTCAGGGAAG
326 CTTTATTTGGCAGTCTTTGATAAATCCATGGCCTGTGTACTGGACAACATGATGAGTCAGGGAAG
*
982064 AAAGAACAAGCCATCTATTACTTAAGCAAAAAGTTCACTGAATGTGAGTGCAATTATCCCACCGT
391 AAAGAACAAGCCATCTATTACTTAAGCAAAAAGTTCACTGAATATGAGTGCAATTATCCCACCGT
982129 CGAGAAG
456 CGAGAAG
*
982136 TACTTTCGGAGTCATTTCGGGTAAGCTTTTAGGCTTTATAGTTAGCAAAAAAGGGATTGAAGTTG
1 TACTTTCGGAGTCATTTCGGGTAAGCTTTTAGGCTTTATAGTTAGCAAAAAAGGGATTAAAGTTG
* * *
982201 ACCCAGACAAAATGAAAGCCATTCAAGATATGCCACCACCTCAAATCCAAAAAGAAGTAAGAGGC
66 ACCCAGACAAAATCAAAGCCATTCAAGATATGCCACCACCTCAAACCCAAAAAGAAGTAAGAGAC
*
982266 TTTTTAGGGAGACTGAACTATATTTCCAGGTTCATATCCCAGCTCACTAACAAATGTGACCCCAT
131 TTTTTAGGGAGACTGAACTATATTTCCAAGTTCATATCCCAGCTCACTAACAAATGTGACCCCAT
*
982331 CTTCCGACTTCTTCGCAAATAAAATCTGGGGGAATGGAATGAGGCATGTCAAGAAGCCTTTGACA
196 CTTCCGACTTCTTCGCAAACAAAATCTGGGGGAATGGAATGAGGCATGTCAAGAAGCCTTTGACA
* * *
982396 GGGTCAAACATTATTTGTCAAACCCACCAGTATTGGTACCACCGGCACTCGGTCGACCCTTAATC
261 AGGTCAAAAATTATTTGTCAAACCCACCAGTATTGGTACCACCGGCACTCGGTCAACCCTTAATC
*
982461 CTTTATTTGGCAGTCTTTGATAAATCCAT-GCCTGTGTACTGGGACAACATGATGAGTCGGGGAA
326 CTTTATTTGGCAGTCTTTGATAAATCCATGGCCTGTGTACT-GGACAACATGATGAGTCAGGGAA
982525 GAAAGAACAAGCCATCTATTACTTAAGCAAAAAGTTCACTGAATATGAGTGCAATTATCCCACCG
390 GAAAGAACAAGCCATCTATTACTTAAGCAAAAAGTTCACTGAATATGAGTGCAATTATCCCACCG
982590 TCGAGAAG
455 TCGAGAAG
982598 CTATGCTGTG
Statistics
Matches: 443, Mismatches: 18, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
461 10 0.02
462 433 0.98
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.26
Consensus pattern (462 bp):
TACTTTCGGAGTCATTTCGGGTAAGCTTTTAGGCTTTATAGTTAGCAAAAAAGGGATTAAAGTTG
ACCCAGACAAAATCAAAGCCATTCAAGATATGCCACCACCTCAAACCCAAAAAGAAGTAAGAGAC
TTTTTAGGGAGACTGAACTATATTTCCAAGTTCATATCCCAGCTCACTAACAAATGTGACCCCAT
CTTCCGACTTCTTCGCAAACAAAATCTGGGGGAATGGAATGAGGCATGTCAAGAAGCCTTTGACA
AGGTCAAAAATTATTTGTCAAACCCACCAGTATTGGTACCACCGGCACTCGGTCAACCCTTAATC
CTTTATTTGGCAGTCTTTGATAAATCCATGGCCTGTGTACTGGACAACATGATGAGTCAGGGAAG
AAAGAACAAGCCATCTATTACTTAAGCAAAAAGTTCACTGAATATGAGTGCAATTATCCCACCGT
CGAGAAG
Found at i:984691 original size:9 final size:9
Alignment explanation
Indices: 984680--984749 Score: 61
Period size: 9 Copynumber: 7.6 Consensus size: 9
984670 AAGAAGGAAG
*
984680 AAAAAAAAGA
1 AAAAAAAA-C
984690 AAAAAAAAC
1 AAAAAAAAC
984699 AAACAAACAA-
1 AAA-AAA-AAC
*
984709 AAAAATAAC
1 AAAAAAAAC
*
984718 AAAATAAAC
1 AAAAAAAAC
984727 AAAAAAAAC
1 AAAAAAAAC
* *
984736 CAAAAAAAT
1 AAAAAAAAC
984745 AAAAA
1 AAAAA
984750 GGGTCCGGAT
Statistics
Matches: 49, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
8 2 0.04
9 31 0.63
10 14 0.29
11 2 0.04
ACGTcount: A:0.84, C:0.10, G:0.01, T:0.04
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:984739 original size:19 final size:18
Alignment explanation
Indices: 984681--984749 Score: 84
Period size: 18 Copynumber: 3.7 Consensus size: 18
984671 AGAAGGAAGA
*
984681 AAAAAAAGAAAAAAAAAC
1 AAAAAAACAAAAAAAAAC
*
984699 AAACAAACAAAAAAATAAC
1 AAAAAAACAAAAAAA-AAC
*
984718 AAAATAAACAAAAAAAACC
1 AAAA-AAACAAAAAAAAAC
*
984737 AAAAAAATAAAAA
1 AAAAAAACAAAAA
984750 GGGTCCGGAT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
18 21 0.48
19 12 0.27
20 11 0.25
ACGTcount: A:0.84, C:0.10, G:0.01, T:0.04
Consensus pattern (18 bp):
AAAAAAACAAAAAAAAAC
Found at i:988623 original size:19 final size:19
Alignment explanation
Indices: 988577--988648 Score: 83
Period size: 19 Copynumber: 3.7 Consensus size: 19
988567 TTTCAACAAT
988577 TTGTATCGATACA-AATAGTAA
1 TTGTATCGATACATAAT--T-A
*
988598 ATGTATCGATACATAATTA
1 TTGTATCGATACATAATTA
* *
988617 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAATTA
988636 TTGTATCGATACA
1 TTGTATCGATACA
988649 ATGTATCGCT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
19 30 0.65
20 1 0.02
21 12 0.26
22 3 0.07
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (19 bp):
TTGTATCGATACATAATTA
Found at i:993152 original size:20 final size:20
Alignment explanation
Indices: 993127--993166 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
993117 TCGAAGATTT
993127 TGGTTGGTTTGATGATTGAG
1 TGGTTGGTTTGATGATTGAG
993147 TGGTTGGTTTGATGATTGAG
1 TGGTTGGTTTGATGATTGAG
993167 CACATTACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.40, T:0.45
Consensus pattern (20 bp):
TGGTTGGTTTGATGATTGAG
Found at i:993780 original size:20 final size:19
Alignment explanation
Indices: 993738--993828 Score: 83
Period size: 20 Copynumber: 4.6 Consensus size: 19
993728 ACCCTTGAAA
* *
993738 GTATCGATACATATCCAGAT
1 GTATCGATACATATGCA-TT
*
993758 GTATCGATACATAATGCTTT
1 GTATCGATACAT-ATGCATT
* *
993778 GTATCGATACATGTTCATT
1 GTATCGATACATATGCATT
***
993797 GTATCGATACATGCACAATT
1 GTATCGATACATATGC-ATT
993817 GTATCGATACAT
1 GTATCGATACAT
993829 GAAACTGGTA
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
19 18 0.30
20 40 0.66
21 3 0.05
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (19 bp):
GTATCGATACATATGCATT
Found at i:993829 original size:20 final size:19
Alignment explanation
Indices: 993776--993829 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
993766 ACATAATGCT
**
993776 TTGTATCGATACATGTTCA
1 TTGTATCGATACATGCACA
993795 TTGTATCGATACATGCACAA
1 TTGTATCGATACATGCAC-A
993815 TTGTATCGATACATG
1 TTGTATCGATACATG
993830 AAACTGGTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACATGCACA
Found at i:993900 original size:20 final size:20
Alignment explanation
Indices: 993858--993909 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
993848 CCACCACTAT
* ** *
993858 TTGTATTGATACATGGCACA
1 TTGTATCGATACATAACAAA
993878 TTGTATCGATACATAACAAA
1 TTGTATCGATACATAACAAA
993898 TTGTATCGATAC
1 TTGTATCGATAC
993910 GTTGTCCCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (20 bp):
TTGTATCGATACATAACAAA
Found at i:995524 original size:15 final size:15
Alignment explanation
Indices: 995504--995538 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
995494 AATCATCAAA
995504 GATGATGAAGATAAT
1 GATGATGAAGATAAT
*
995519 GATGATGATGATAAT
1 GATGATGAAGATAAT
995534 GATGA
1 GATGA
995539 AGTGACTCGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (15 bp):
GATGATGAAGATAAT
Found at i:996418 original size:34 final size:35
Alignment explanation
Indices: 996380--996446 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
996370 CCTTACAACA
996380 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
996414 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
996447 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:996943 original size:13 final size:13
Alignment explanation
Indices: 996925--996950 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
996915 CTATTTATGA
996925 TGTATCGATACAC
1 TGTATCGATACAC
996938 TGTATCGATACAC
1 TGTATCGATACAC
996951 ACAAATATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:997038 original size:10 final size:10
Alignment explanation
Indices: 997011--997049 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
997001 TAATGATACG
997011 TGAACAGTG-
1 TGAACAGTGA
997020 TGAACAGTGA
1 TGAACAGTGA
*
997030 TGAATAGTGA
1 TGAACAGTGA
*
997040 TGAATAGTGA
1 TGAACAGTGA
997050 AAATGAGATT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
9 9 0.32
10 19 0.68
ACGTcount: A:0.38, C:0.05, G:0.31, T:0.26
Consensus pattern (10 bp):
TGAACAGTGA
Found at i:997189 original size:20 final size:20
Alignment explanation
Indices: 997126--997196 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
997116 GCCAATGACC
**
997126 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
997146 TGTATCGATAC-TATGCAATT
1 TGTATCGATACATAT-TAATG
997166 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
997186 TGTATCGATAC
1 TGTATCGATAC
997197 TTTTCAGGAT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:997262 original size:21 final size:21
Alignment explanation
Indices: 997236--997276 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
997226 GTCAACCTTG
997236 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
997257 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
997277 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Done.