Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008798.1 Hibiscus syriacus cultivar Beakdansim tig00111947_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1825372
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 9
Found at i:472094 original size:41 final size:41
Alignment explanation
Indices: 471995--472346 Score: 321
Period size: 41 Copynumber: 8.6 Consensus size: 41
471985 AAACTTGCGC
* * *
471995 CGTTTGTCCTAAAAATGCCA-TAAAAGTAC-AGTCTTTAGCGG
1 CGTTTGT-ATAAAAACGCCACT-AAAGTACTAGTCTATAGCGG
* * *
472036 AGTTGTTGTATACAAACGCCACTAAAGTACTAGTCTATAGCGA
1 CG-T-TTGTATAAAAACGCCACTAAAGTACTAGTCTATAGCGG
* *
472079 CATTTGTATAAAAACGCCAC-AAATGTACTAGTCTATAGAGG
1 CGTTTGTATAAAAACGCCACTAAA-GTACTAGTCTATAGCGG
* *
472120 CGTTTGT-TCAAAAATGCCACTAAAGTA-TAGTACTTTAGCGG
1 CGTTTGTAT-AAAAACGCCACTAAAGTACTAGT-CTATAGCGG
* *
472161 CGTTTGTATAAAAATGCCACAAAAGTACTAGTCTATAGCGG
1 CGTTTGTATAAAAACGCCACTAAAGTACTAGTCTATAGCGG
* * * *
472202 CATTATTTCA-AAAAACGCCACTAAA--A-TATTCTTTAGCGG
1 CGTT-TGT-ATAAAAACGCCACTAAAGTACTAGTCTATAGCGG
* *
472241 CGTTTGTATAAAAACGCCACTAAAATACTAATCTATAGCGG
1 CGTTTGTATAAAAACGCCACTAAAGTACTAGTCTATAGCGG
* * * * *
472282 CGTTTGTTTTGAAAACGCGACTAAAG-ACTA-TACTTTGGCGG
1 CGTTTG-TATAAAAACGCCACTAAAGTACTAGT-CTATAGCGG
472323 CGTTTGTATAAAAACGCCACTAAA
1 CGTTTGTATAAAAACGCCACTAAA
472347 CCACTAAAGT
Statistics
Matches: 257, Mismatches: 36, Indels: 37
0.78 0.11 0.11
Matches are distributed among these distances:
37 1 0.00
38 17 0.07
39 14 0.05
40 26 0.10
41 127 0.49
42 56 0.22
43 16 0.06
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (41 bp):
CGTTTGTATAAAAACGCCACTAAAGTACTAGTCTATAGCGG
Found at i:472286 original size:162 final size:164
Alignment explanation
Indices: 471995--472342 Score: 406
Period size: 162 Copynumber: 2.1 Consensus size: 164
471985 AAACTTGCGC
* * * * *
471995 CGTTTGTCCTAAAAATGCCATAAAAGTACAGTCTTTAGCGGAGTTGTTGTATACAAACGCCACTA
1 CGTTTGT-ATAAAAATGCCACAAAAGTACAGTCTATAGCGGAGTTATTGTATAAAAACGCCACTA
* *
472060 AAGTACTAGTCTATAGCGACATTTGTATAAAAACGCCACAAATGTACTAGTCTATAGAGGCGTTT
65 AAG-ACTAGTCTATAGCGACATTTGTATAAAAACGCCACAAATATACTAATCTATAGAGGCGTTT
*
472125 G-TTCAAAAATGCCACTAAAGTA-TAGTACTTTAGCGG
129 GTTTCAAAAACGCCACTAAAG-ACTA-TACTTTAGCGG
472161 CGTTTGTATAAAAATGCCACAAAAGTACTAGTCTATAGCGGCA-TTATT-TCA-AAAAACGCCAC
1 CGTTTGTATAAAAATGCCACAAAAGTAC-AGTCTATAGCGG-AGTTATTGT-ATAAAAACGCCAC
* * * * *
472223 TAAA-A-TATTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAA-ATACTAATCTATAGCGGCGT
63 TAAAGACTAGTCTATAGCGACATTTGTATAAAAACGCCAC-AAATATACTAATCTATAGAGGCGT
** * *
472285 TTGTTTTGAAAACGCGACTAAAGACTATACTTTGGCGG
127 TTGTTTCAAAAACGCCACTAAAGACTATACTTTAGCGG
*
472323 CGTTTGTATAAAAACGCCAC
1 CGTTTGTATAAAAATGCCAC
472343 TAAACCACTA
Statistics
Matches: 158, Mismatches: 18, Indels: 16
0.82 0.09 0.08
Matches are distributed among these distances:
162 79 0.50
163 21 0.13
165 34 0.22
166 23 0.15
167 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (164 bp):
CGTTTGTATAAAAATGCCACAAAAGTACAGTCTATAGCGGAGTTATTGTATAAAAACGCCACTAA
AGACTAGTCTATAGCGACATTTGTATAAAAACGCCACAAATATACTAATCTATAGAGGCGTTTGT
TTCAAAAACGCCACTAAAGACTATACTTTAGCGG
Found at i:474295 original size:17 final size:17
Alignment explanation
Indices: 474261--474296 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
474251 TTTAATTTTG
* *
474261 ATTTATTATTATTTAAA
1 ATTTATTATTAATAAAA
474278 ATTTATTATTAATAAAA
1 ATTTATTATTAATAAAA
474295 AT
1 AT
474297 ATAAAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTATTATTAATAAAA
Found at i:474389 original size:22 final size:22
Alignment explanation
Indices: 474358--474408 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
474348 ATATATATAA
*
474358 TAAAAAAATTAT-TTAAAATATT
1 TAAAATAATTATATTAAAAT-TT
474380 TAAAATAATTATGATTAAAATTT
1 TAAAATAATTAT-ATTAAAATTT
*
474403 AAAAAT
1 TAAAAT
474409 TTTAACTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 11 0.44
23 7 0.28
24 7 0.28
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (22 bp):
TAAAATAATTATATTAAAATTT
Found at i:481066 original size:15 final size:15
Alignment explanation
Indices: 481046--481076 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
481036 ATCTTGGACG
481046 GGGCAGCACCGGTAA
1 GGGCAGCACCGGTAA
481061 GGGCAGCACCGGTAA
1 GGGCAGCACCGGTAA
481076 G
1 G
481077 TGCATACGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.42, T:0.06
Consensus pattern (15 bp):
GGGCAGCACCGGTAA
Found at i:484316 original size:151 final size:144
Alignment explanation
Indices: 484102--484397 Score: 378
Period size: 155 Copynumber: 2.0 Consensus size: 144
484092 GGTTTTATAG
*
484102 TCACTTTTAATAAATAATGTAAATTCTCTGTACCACCAACCCTACAAGATACATATATGGATAC-
1 TCACTTTTAATAAATAATGTAAATTCTCTGTACCACCAACCCTAAAAGATACATATATGGATACA
** * * *
484166 AAGTCCTAAGGGGAAAAAATTAGGTACCAAATTGAATTTAAAGGACGACTTTAGGGACTTGATTG
66 AAGTCCTAAGGAAAAAAAATCAGGTACCAAACTGAATTTAAAGGACAACTTTAGGGACTTGATTG
*
484231 AATAAAGTAGAGCT
131 AATAAAATAGAGCT
*
484245 TCACTTTTACTAAATAATGTAAATTCTCTGTACCACCAAGGCACCAACCCTAAAAGATACATATA
1 TCACTTTTAATAAATAATGTAAATTCTCTGT---A-C----CACCAACCCTAAAAGATACATATA
* * *
484310 TGGATACAAGTAAGTCCTTAGGAAAAAAAATCAGGTGCCAAACTGAATTTAAAGGACAAGTTTAG
58 TGGATAC-A--AAGTCCTAAGGAAAAAAAATCAGGTACCAAACTGAATTTAAAGGACAACTTTAG
*
484375 GGACTTTATTGAATAAAATAGAG
120 GGACTTGATTGAATAAAATAGAG
484398 TTTAGTATCA
Statistics
Matches: 129, Mismatches: 12, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
143 30 0.23
146 1 0.01
147 1 0.01
151 30 0.23
155 67 0.52
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (144 bp):
TCACTTTTAATAAATAATGTAAATTCTCTGTACCACCAACCCTAAAAGATACATATATGGATACA
AAGTCCTAAGGAAAAAAAATCAGGTACCAAACTGAATTTAAAGGACAACTTTAGGGACTTGATTG
AATAAAATAGAGCT
Found at i:485201 original size:369 final size:369
Alignment explanation
Indices: 484522--485259 Score: 1476
Period size: 369 Copynumber: 2.0 Consensus size: 369
484512 CCAAACGTTG
484522 ATGTTCTCTCAACCACCAATTCAGCAGCTTGAAATTCCACCCTCCACAAATTACATGAAATAAAT
1 ATGTTCTCTCAACCACCAATTCAGCAGCTTGAAATTCCACCCTCCACAAATTACATGAAATAAAT
484587 AGTCCATGGATTTCAACAATCAACCAATTCTTTTTTCTCCTGGAAAGTTTCCACTTTCCCACTCC
66 AGTCCATGGATTTCAACAATCAACCAATTCTTTTTTCTCCTGGAAAGTTTCCACTTTCCCACTCC
484652 CTGTATTGCTTGAAAGTGCAATGGCCACGTTACCTTCACAAAACCTGCAATCAGGGCGGCCTCTG
131 CTGTATTGCTTGAAAGTGCAATGGCCACGTTACCTTCACAAAACCTGCAATCAGGGCGGCCTCTG
484717 TGTTTTCCTTCATTGAATTCTCCTAAAGTTTCTTCATTGAAATTCCCCATTTTCTCTCCTAGAAA
196 TGTTTTCCTTCATTGAATTCTCCTAAAGTTTCTTCATTGAAATTCCCCATTTTCTCTCCTAGAAA
484782 ACTAAAACCACTCGAGCTTTTCACCAGAAGCGATGGCTTCAGCAACTCTCGGCTCGTGGGAAGAG
261 ACTAAAACCACTCGAGCTTTTCACCAGAAGCGATGGCTTCAGCAACTCTCGGCTCGTGGGAAGAG
484847 CCTCTGCCTCTGCCTCTGAATTCAAAGCAGATATGCCTGAGATC
326 CCTCTGCCTCTGCCTCTGAATTCAAAGCAGATATGCCTGAGATC
484891 ATGTTCTCTCAACCACCAATTCAGCAGCTTGAAATTCCACCCTCCACAAATTACATGAAATAAAT
1 ATGTTCTCTCAACCACCAATTCAGCAGCTTGAAATTCCACCCTCCACAAATTACATGAAATAAAT
484956 AGTCCATGGATTTCAACAATCAACCAATTCTTTTTTCTCCTGGAAAGTTTCCACTTTCCCACTCC
66 AGTCCATGGATTTCAACAATCAACCAATTCTTTTTTCTCCTGGAAAGTTTCCACTTTCCCACTCC
485021 CTGTATTGCTTGAAAGTGCAATGGCCACGTTACCTTCACAAAACCTGCAATCAGGGCGGCCTCTG
131 CTGTATTGCTTGAAAGTGCAATGGCCACGTTACCTTCACAAAACCTGCAATCAGGGCGGCCTCTG
485086 TGTTTTCCTTCATTGAATTCTCCTAAAGTTTCTTCATTGAAATTCCCCATTTTCTCTCCTAGAAA
196 TGTTTTCCTTCATTGAATTCTCCTAAAGTTTCTTCATTGAAATTCCCCATTTTCTCTCCTAGAAA
485151 ACTAAAACCACTCGAGCTTTTCACCAGAAGCGATGGCTTCAGCAACTCTCGGCTCGTGGGAAGAG
261 ACTAAAACCACTCGAGCTTTTCACCAGAAGCGATGGCTTCAGCAACTCTCGGCTCGTGGGAAGAG
485216 CCTCTGCCTCTGCCTCTGAATTCAAAGCAGATATGCCTGAGATC
326 CCTCTGCCTCTGCCTCTGAATTCAAAGCAGATATGCCTGAGATC
485260 CTTGGGGATG
Statistics
Matches: 369, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
369 369 1.00
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (369 bp):
ATGTTCTCTCAACCACCAATTCAGCAGCTTGAAATTCCACCCTCCACAAATTACATGAAATAAAT
AGTCCATGGATTTCAACAATCAACCAATTCTTTTTTCTCCTGGAAAGTTTCCACTTTCCCACTCC
CTGTATTGCTTGAAAGTGCAATGGCCACGTTACCTTCACAAAACCTGCAATCAGGGCGGCCTCTG
TGTTTTCCTTCATTGAATTCTCCTAAAGTTTCTTCATTGAAATTCCCCATTTTCTCTCCTAGAAA
ACTAAAACCACTCGAGCTTTTCACCAGAAGCGATGGCTTCAGCAACTCTCGGCTCGTGGGAAGAG
CCTCTGCCTCTGCCTCTGAATTCAAAGCAGATATGCCTGAGATC
Found at i:487710 original size:42 final size:42
Alignment explanation
Indices: 487659--487786 Score: 220
Period size: 42 Copynumber: 3.0 Consensus size: 42
487649 ACCAGCCTTG
*
487659 GTATGATTTCTGTGGAGGAGGATATTATTATCAGCAGCCAAT
1 GTATGATTTCTATGGAGGAGGATATTATTATCAGCAGCCAAT
487701 GTATGATTTCTATGGAGGAGGATATTATTATCAGCAGCCAAT
1 GTATGATTTCTATGGAGGAGGATATTATTATCAGCAGCCAAT
* * *
487743 GTATGATTTCTATAGAGGAGGTTATTTTTATCAGCAGCCAAT
1 GTATGATTTCTATGGAGGAGGATATTATTATCAGCAGCCAAT
487785 GT
1 GT
487787 GTTTTGATCA
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 82 1.00
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (42 bp):
GTATGATTTCTATGGAGGAGGATATTATTATCAGCAGCCAAT
Found at i:495957 original size:21 final size:20
Alignment explanation
Indices: 495918--495957 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
495908 CCTTTATTAA
* *
495918 AAATCCTGCGCCTTTTGAAG
1 AAATCATGCGCCATTTGAAG
495938 AAATCATGCGCCCATTTGAA
1 AAATCATGCG-CCATTTGAA
495958 TTCCTTCATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (20 bp):
AAATCATGCGCCATTTGAAG
Found at i:498068 original size:24 final size:25
Alignment explanation
Indices: 498041--498091 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
498031 GTCGATGGTG
498041 GACA-GTGGTCGACAGAGAGAAAAT
1 GACAGGTGGTCGACAGAGAGAAAAT
* *
498065 GACATGGTGGTCGGCGGAGAGAAAAT
1 GACA-GGTGGTCGACAGAGAGAAAAT
498091 G
1 G
498092 GAGAAGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 4 0.17
26 19 0.83
ACGTcount: A:0.35, C:0.12, G:0.39, T:0.14
Consensus pattern (25 bp):
GACAGGTGGTCGACAGAGAGAAAAT
Found at i:498777 original size:29 final size:29
Alignment explanation
Indices: 498735--498823 Score: 178
Period size: 29 Copynumber: 3.1 Consensus size: 29
498725 CTACAGTGGT
498735 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
498764 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
498793 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
498822 CT
1 CT
498824 GTGTGTACAG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.13, C:0.31, G:0.37, T:0.18
Consensus pattern (29 bp):
CTTGGAGGTCGCCATGGCATCCGGGCGAC
Found at i:498892 original size:44 final size:44
Alignment explanation
Indices: 498842--498933 Score: 175
Period size: 44 Copynumber: 2.1 Consensus size: 44
498832 AGAATAGGGC
*
498842 CATGCAATCAACATGGGACGTGGGAATGCATTGGGGAGGGGATG
1 CATGCAATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATG
498886 CATGCAATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATG
1 CATGCAATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATG
498930 CATG
1 CATG
498934 GGGTGGGAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.27, C:0.14, G:0.41, T:0.17
Consensus pattern (44 bp):
CATGCAATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATG
Found at i:498945 original size:15 final size:15
Alignment explanation
Indices: 498905--499084 Score: 137
Period size: 15 Copynumber: 11.1 Consensus size: 15
498895 AACATGGGAC
498905 GTGGGAATGCATGGGG
1 GTGGGAATGCAT-GGG
* *
498921 GAGGGGATGCATGGG
1 GTGGGAATGCATGGG
498936 GTGGGAATGCATGGG
1 GTGGGAATGCATGGG
* *
498951 G-GAGGGATCAACATGGG
1 GTG-GGAAT--GCATGGG
498968 ATGTGGGAATGCATGGGG
1 --GTGGGAATGCAT-GGG
* *
498986 GAGGGGATGCATGGG
1 GTGGGAATGCATGGG
499001 ACGTGGGAATGCATGGG
1 --GTGGGAATGCATGGG
499018 GTGGGAATGCATGGGG
1 GTGGGAATGCAT-GGG
* * *
499034 GAGGGGATGGTGCATTGGAC
1 G-TGGGA--ATGCA-TGG-G
499054 GTGGGAATGCATGGG
1 GTGGGAATGCATGGG
499069 GTGGGAATGCATGGG
1 GTGGGAATGCATGGG
499084 G
1 G
499085 GAGGGGATGG
Statistics
Matches: 131, Mismatches: 18, Indels: 31
0.73 0.10 0.17
Matches are distributed among these distances:
14 1 0.01
15 52 0.40
16 27 0.21
17 30 0.23
18 3 0.02
19 15 0.11
20 3 0.02
ACGTcount: A:0.21, C:0.08, G:0.53, T:0.18
Consensus pattern (15 bp):
GTGGGAATGCATGGG
Found at i:498966 original size:65 final size:66
Alignment explanation
Indices: 498892--499018 Score: 229
Period size: 65 Copynumber: 1.9 Consensus size: 66
498882 GATGCATGCA
498892 ATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGG-GTGGGAATGCATGGGGGAGG
1 ATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGGAGTGGGAATGCATGGGGGAGG
498956 G
66 G
*
498957 ATCAACATGGGATGTGGGAATGCATGGGGGAGGGGATGCATGGGACGTGGGAATGCATGGGG
1 ATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGGA-GTGGGAATGCATGGGG
499019 TGGGAATGCA
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
65 43 0.73
67 16 0.27
ACGTcount: A:0.24, C:0.09, G:0.50, T:0.17
Consensus pattern (66 bp):
ATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGGAGTGGGAATGCATGGGGGAGG
G
Found at i:499013 original size:82 final size:83
Alignment explanation
Indices: 498907--499083 Score: 234
Period size: 82 Copynumber: 2.2 Consensus size: 83
498897 CATGGGACGT
* * *
498907 GGGAATGCATGGG-GGAGGGGATGCATGGGGTGGGAATGCATGGGGGA-GGGAT-CAACATGGGA
1 GGGAATGCATGGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGGAGGGGATGCAACATGGGA
*
498969 TGTGGGAATGCATGGGGGA
66 CGTGGGAATGCAT-GGGGA
* *** *
498988 GGGGATGCATGGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGGAGGGGATGGTGCATTGGA
1 GGGAATGCATGGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGGAGGGGATGCAACATGGGA
*
499053 CGTGGGAATGCATGGGGT
66 CGTGGGAATGCATGGGGA
499071 GGGAATGCATGGG
1 GGGAATGCATGGG
499084 GGAGGGGATG
Statistics
Matches: 82, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
81 12 0.15
82 31 0.38
83 21 0.26
84 18 0.22
ACGTcount: A:0.21, C:0.08, G:0.53, T:0.18
Consensus pattern (83 bp):
GGGAATGCATGGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGGAGGGGATGCAACATGGGA
CGTGGGAATGCATGGGGA
Found at i:499031 original size:65 final size:64
Alignment explanation
Indices: 498895--499088 Score: 207
Period size: 65 Copynumber: 3.0 Consensus size: 64
498885 GCATGCAATC
*
498895 AACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGGGTGGGAATGCATGGGGGAGGGAT
1 AACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGGGTGGGAATGCATGGGGGAGGAAT
*
498959 CAACATGGGATGTGGGAATGCATGGGGGAGGGGATGCATGGGACGTGGGAATGCATGGGGTG-GG
1 -AACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGG--GTGGGAATGCATGGGG-GAGG
499023 AAT
62 AAT
* * ** * *
499026 -GCATGGGGGA-G-GGGATGGTGCATTGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGGAG
1 AACAT--GGGACGTGGGA--ATGCA-TGGGGGAGGGGATGCATGGGGTGGGAATGCATGGGGGAG
499088 G
61 G
499089 GGATGGTGCA
Statistics
Matches: 112, Mismatches: 8, Indels: 17
0.82 0.06 0.12
Matches are distributed among these distances:
65 48 0.43
66 19 0.17
67 28 0.25
68 17 0.15
ACGTcount: A:0.22, C:0.08, G:0.53, T:0.17
Consensus pattern (64 bp):
AACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGGGTGGGAATGCATGGGGGAGGAAT
Found at i:499069 original size:51 final size:51
Alignment explanation
Indices: 498970--499111 Score: 254
Period size: 51 Copynumber: 2.8 Consensus size: 51
498960 AACATGGGAT
*
498970 GTGGGAATGCATGGGGGAGGGGA---TGCATGGGACGTGGGAATGCATGGG
1 GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAATGCATGGG
499018 GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAATGCATGGG
1 GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAATGCATGGG
499069 GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAA
1 GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAA
499112 CTGTGCATGG
Statistics
Matches: 90, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
48 23 0.26
51 67 0.74
ACGTcount: A:0.20, C:0.08, G:0.54, T:0.18
Consensus pattern (51 bp):
GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAATGCATGGG
Found at i:499225 original size:32 final size:32
Alignment explanation
Indices: 499184--499247 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
499174 AAGGTCCTGC
499184 TGCATGCATGCGTTGCATCATAGCTCATAGCT
1 TGCATGCATGCGTTGCATCATAGCTCATAGCT
499216 TGCATGCATGCGTTGCATCATAGCTCATAGCT
1 TGCATGCATGCGTTGCATCATAGCTCATAGCT
499248 CAGAGATTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (32 bp):
TGCATGCATGCGTTGCATCATAGCTCATAGCT
Found at i:499603 original size:21 final size:21
Alignment explanation
Indices: 499555--499603 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
499545 ACTAAAATCT
*
499555 AGTTAATTAGTTTGTTAGTATA
1 AGTT-ATTAGTTTGTAAGTATA
* *
499577 AATTATTAGTTTGTAAGTTTA
1 AGTTATTAGTTTGTAAGTATA
499598 AGTTAT
1 AGTTAT
499604 ATTATATTAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (21 bp):
AGTTATTAGTTTGTAAGTATA
Found at i:499613 original size:28 final size:28
Alignment explanation
Indices: 499580--499633 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
499570 TAGTATAAAT
*
499580 TATTAGTTTGTAAGTTTAAGTTATATTA
1 TATTAGTTTATAAGTTTAAGTTATATTA
*
499608 TATTAGTTTATTAGTTTAAGTTATAT
1 TATTAGTTTATAAGTTTAAGTTATAT
499634 ATTATATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (28 bp):
TATTAGTTTATAAGTTTAAGTTATATTA
Found at i:500190 original size:20 final size:21
Alignment explanation
Indices: 500146--500190 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
500136 AAATATTGTG
**
500146 TTTAAAAATATTTAGTGTTGT
1 TTTAAAAATATTTAGTGTTAA
*
500167 TTTAAAAATATTTTGT-TTAA
1 TTTAAAAATATTTAGTGTTAA
500187 TTTA
1 TTTA
500191 CATTGTATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (21 bp):
TTTAAAAATATTTAGTGTTAA
Found at i:500475 original size:26 final size:25
Alignment explanation
Indices: 500446--500504 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
500436 AAATCATATT
*
500446 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AGTAAATATCAAATC
*
500472 ATTAGATT-AATAGTAATTATCAAATC
1 ATT--ATTAAATAGTAAATATCAAATC
500498 ATTATTA
1 ATTATTA
500505 GGTTATTAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
24 3 0.11
26 19 0.68
27 3 0.11
28 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
ATTATTAAATAGTAAATATCAAATC
Found at i:503408 original size:26 final size:26
Alignment explanation
Indices: 503379--503876 Score: 384
Period size: 26 Copynumber: 20.2 Consensus size: 26
503369 TTTGATGATT
503379 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
503405 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
* *
503431 TAATAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* *
503453 TA--AAT-ATTTAATGAACAAAT-ATT-
1 TAGTAATGATTTGAT-AA-TAATCATTA
503476 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
*
503502 TAGTAATGATTTGATATTAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
*
503528 TAATAATGATTT-ATTAATAATCATTA
1 TAGTAATGATTTGA-TAATAATCATTA
** *
503554 TAAAAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* * * *
503576 TA--AAT-ATTTAATGATTTGATGATT-
1 TAGTAATGATTTGAT-A-ATAATCATTA
503600 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
503626 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
* *
503652 TAATAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* * * *
503674 TA--AAT-ATTTAATGATTTGATGATT-
1 TAGTAATGATTTGAT-A-ATAATCATTA
503698 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
503724 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
*
503750 TAATAATGATTT-AGTAATAATCATTA
1 TAGTAATGATTTGA-TAATAATCATTA
** *
503776 TAAAAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* * * *
503798 TA--AAT-ATTTAATGATTTGATGATT-
1 TAGTAATGATTTGAT-A-ATAATCATTA
503822 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
* * *
503848 TAATAATGATTTTATAATAATTATT-
1 TAGTAATGATTTGATAATAATCATTA
503873 TAGT
1 TAGT
503877 TATTATTTAG
Statistics
Matches: 396, Mismatches: 37, Indels: 79
0.77 0.07 0.15
Matches are distributed among these distances:
19 4 0.01
20 20 0.05
22 12 0.03
23 50 0.13
24 33 0.08
25 39 0.10
26 220 0.56
27 18 0.05
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.44
Consensus pattern (26 bp):
TAGTAATGATTTGATAATAATCATTA
Found at i:503516 original size:97 final size:98
Alignment explanation
Indices: 503324--503741 Score: 383
Period size: 98 Copynumber: 4.3 Consensus size: 98
503314 ATGTATTTAT
* ****
503324 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAATAATGATTTAATAATGATTTAAATATTTAATGAACAAATGATTTAGTAATGAT
503389 TTGATAATAATCATTATAGTAATGATTTGATAA
66 TTGATAATAATCATTATAGTAATGATTTGATAA
503422 TAATCATTATAATAATGATTTAATAATGATTTAAATATTTAATGAACAAAT-ATTTAGTAATGAT
1 TAATCATTATAATAATGATTTAATAATGATTTAAATATTTAATGAACAAATGATTTAGTAATGAT
*
503486 TTGATAATAATCATTATAGTAATGATTTGATAT
66 TTGATAATAATCATTATAGTAATGATTTGATAA
* * * * * *
503519 TAATCATTATAATAATGATTTATTAATAATCATTATAAA-AATGATTTAA-TAATGATTTA--AA
1 TAATCATTATAATAATGA--T-TTAATAATGATT-TAAATATTTAATGAACAAATGATTTAGTAA
* * * *
503580 T-ATTTAATGATTTGATGATT-TAGTAATGATTTGATAA
62 TGATTTGAT-A-ATAATCATTATAGTAATGATTTGATAA
* * * * * * * *
503617 TAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAA-TAATGATTTA--AAT
1 TAATCATTATAATAATGATTTAATAATGAT--TTA-AATATTTAATGAACAAATGATTTAGTAAT
* * * *
503679 -ATTTAATGATTTGATGATT-TAGTAATGATTTGATAA
63 GATTTGAT-A-ATAATCATTATAGTAATGATTTGATAA
* *
503715 TAATCATTATAGTAATGATTTGATAAT
1 TAATCATTATAATAATGATTTAATAAT
503742 AATCATTATA
Statistics
Matches: 289, Mismatches: 20, Indels: 22
0.87 0.06 0.07
Matches are distributed among these distances:
95 9 0.03
96 3 0.01
97 72 0.25
98 169 0.58
99 10 0.03
100 22 0.08
101 4 0.01
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.44
Consensus pattern (98 bp):
TAATCATTATAATAATGATTTAATAATGATTTAAATATTTAATGAACAAATGATTTAGTAATGAT
TTGATAATAATCATTATAGTAATGATTTGATAA
Found at i:503622 original size:98 final size:98
Alignment explanation
Indices: 503405--503767 Score: 463
Period size: 98 Copynumber: 3.7 Consensus size: 98
503395 ATAATCATTA
* * * * *
503405 TAGTAATGATTTGATAATAATCATTATAATAATGA-TT--TAATAATGATT-TAAATATTTAATG
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTGATAATAATCATTATAAA-AATGATTT
* * * * *
503466 AACAAAT-ATTTAGTAATGATTTGAT-A-ATAATCATT
65 AA-TAATGATTTA--AAT-ATTTAATGATTTGATGATT
*
503501 ATAGTAATGATTTGATATTAATCATTATAATAATGATTT-ATTAATAATCATTATAAAAATGATT
1 -TAGTAATGATTTGATAATAATCATTATAATAATGATTTGA-TAATAATCATTATAAAAATGATT
503565 TAATAATGATTTAAATATTTAATGATTTGATGATT
64 TAATAATGATTTAAATATTTAATGATTTGATGATT
* *
503600 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTGATAATAATCATTATAAAAATGATTTA
503665 ATAATGATTTAAATATTTAATGATTTGATGATT
66 ATAATGATTTAAATATTTAATGATTTGATGATT
* *
503698 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTGATAATAATCATTATAAAAATGATTTA
*
503763 GTAAT
66 ATAAT
503768 AATCATTATA
Statistics
Matches: 243, Mismatches: 15, Indels: 15
0.89 0.05 0.05
Matches are distributed among these distances:
97 40 0.16
98 168 0.69
99 10 0.04
100 21 0.09
101 4 0.02
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.44
Consensus pattern (98 bp):
TAGTAATGATTTGATAATAATCATTATAATAATGATTTGATAATAATCATTATAAAAATGATTTA
ATAATGATTTAAATATTTAATGATTTGATGATT
Found at i:503794 original size:124 final size:124
Alignment explanation
Indices: 503379--503876 Score: 548
Period size: 124 Copynumber: 4.0 Consensus size: 124
503369 TTTGATGATT
* * * *
503379 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATT--ATA-ATAATGAT
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAATGAT--TTAAATATTTAATGA-
* * *
503441 TTAATAATGATTTA--AAT-ATTTAATGAACAAAT-ATT-TAGTAATGATTTGATAATAATCATT
63 TT--TGATGATTTAGTAATGATTTGAT-AA-TAATCATTATAGTAATGATTTGATAATAATCATT
503501 A
124 A
* *
503502 TAGTAATGATTTGATATTAATCATTATAATAATGATTTATTAATAATCATTATAAAAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAATAATGA--T-TTAATAATGATT-T--AAAT-ATTTA
* * * *
503567 AT-A----ATGATTTA--AAT-ATTTAATGATTTGATGATT-TAGTAATGATTTGATAATAATCA
59 ATGATTTGATGATTTAGTAATGATTTGAT-A-ATAATCATTATAGTAATGATTTGATAATAATCA
503623 TTA
122 TTA
503626 TAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAATGATTTAAATATTTAATGATTT
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAATGATTTAAATATTTAATGATTT
503691 GATGATTTAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTA
66 GATGATTTAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTA
* *
503750 TAATAATGATTT-AGTAATAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATT
1 TAGTAATGATTTGA-TAATAATCATTATAATAATGATTTAATAATGATTTAAATATTTAATGATT
* * *
503814 TGATGATTTAGTAATGATTTGATAATAATCATTATAATAATGATTTTATAATAATTATT-
65 TGATGATTTAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTA
503873 TAGT
1 TAGT
503877 TATTATTTAG
Statistics
Matches: 333, Mismatches: 20, Indels: 44
0.84 0.05 0.11
Matches are distributed among these distances:
117 7 0.02
118 5 0.02
120 1 0.00
121 11 0.03
122 9 0.03
123 65 0.20
124 210 0.63
125 8 0.02
126 9 0.03
129 2 0.01
130 2 0.01
131 4 0.01
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.44
Consensus pattern (124 bp):
TAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAATGATTTAAATATTTAATGATTT
GATGATTTAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTA
Found at i:504101 original size:17 final size:17
Alignment explanation
Indices: 504076--504108 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
504066 ACTAAATATC
*
504076 TAATTATTTGATACTAG
1 TAATGATTTGATACTAG
504093 TAATGATTTGATACTA
1 TAATGATTTGATACTA
504109 AAAATCATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (17 bp):
TAATGATTTGATACTAG
Found at i:511138 original size:21 final size:20
Alignment explanation
Indices: 511099--511138 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
511089 CCTTTGTTAA
*
511099 AAATCATGCGCCTTTTGAAG
1 AAATCATGCGCCATTTGAAG
511119 AAATCATGCGCCCATTTGAA
1 AAATCATGCG-CCATTTGAA
511139 TTTCTTCAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.28
Consensus pattern (20 bp):
AAATCATGCGCCATTTGAAG
Found at i:514486 original size:39 final size:39
Alignment explanation
Indices: 514443--514517 Score: 105
Period size: 39 Copynumber: 1.9 Consensus size: 39
514433 AGTTAAATCT
514443 GAAGACTCCACGACTGCATGGCGTCTTCAGACCAATGGA
1 GAAGACTCCACGACTGCATGGCGTCTTCAGACCAATGGA
* * * * *
514482 GAAGATTCCAGGAGTGTATGGCGTCTTCAGGCCAAT
1 GAAGACTCCACGACTGCATGGCGTCTTCAGACCAAT
514518 AGTGGAGGCT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.27, C:0.24, G:0.28, T:0.21
Consensus pattern (39 bp):
GAAGACTCCACGACTGCATGGCGTCTTCAGACCAATGGA
Found at i:514716 original size:25 final size:25
Alignment explanation
Indices: 514683--514739 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
514673 GAAACAAGCA
*
514683 AATAATGGTGCCACTATTGGGCACT
1 AATAATGGTGCCACTATTGGGCACC
* * *
514708 AATAATGGTGTCATTATTGTGCACC
1 AATAATGGTGCCACTATTGGGCACC
514733 AATAATG
1 AATAATG
514740 CATCACACGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.32
Consensus pattern (25 bp):
AATAATGGTGCCACTATTGGGCACC
Found at i:515142 original size:107 final size:105
Alignment explanation
Indices: 514931--515207 Score: 312
Period size: 107 Copynumber: 2.6 Consensus size: 105
514921 AGTGATCTGG
* * *
514931 TAAGTTTAGTGTAAATTTTATTGTTTCATTTTTAATTTTTATTTTAAATATAAATTGATTAGATT
1 TAAGTTTAATGTAAATTTTATTGTTTCATTTTT-ATTTTTATTTTAAATAT-AATTAATTAGACT
* * *
514996 AATTATTTTTATTTTACAGATTAAACTGTATTCGGGTGGTTTGA
64 AATTAATTTAATTTTACAGATTAAACTGTATTCGAGTGG--TGA
515040 TAAGTTTAAT-TAAAATTTTATTGTTT-ATTTATTATTTTTATTTTAAATAATAATT-ATTAGAC
1 TAAGTTTAATGT-AAATTTTATTGTTTCATTT-TTATTTTTATTTTAAAT-ATAATTAATTAGAC
* * *
515102 TATTTAATTTAATTTTACATATTAAA-TCGTA-TCTGAGTGGTGG
63 TAATTAATTTAATTTTACAGATTAAACT-GTATTC-GAGTGGTGA
* * *
515145 TAAGTTTAGTGTAATTTTTATTGTTTCATTTTTTGTTTTTATTTTAAATATAAGTTAATTAGA
1 TAAGTTTAATGTAAATTTTATTGTTTCA-TTTTTATTTTTATTTTAAATATAA-TTAATTAGA
515208 GTTAAATGTG
Statistics
Matches: 147, Mismatches: 11, Indels: 22
0.82 0.06 0.12
Matches are distributed among these distances:
105 28 0.19
106 23 0.16
107 45 0.31
108 24 0.16
109 27 0.18
ACGTcount: A:0.31, C:0.03, G:0.11, T:0.54
Consensus pattern (105 bp):
TAAGTTTAATGTAAATTTTATTGTTTCATTTTTATTTTTATTTTAAATATAATTAATTAGACTAA
TTAATTTAATTTTACAGATTAAACTGTATTCGAGTGGTGA
Found at i:530659 original size:3 final size:3
Alignment explanation
Indices: 530651--530712 Score: 56
Period size: 3 Copynumber: 21.0 Consensus size: 3
530641 GCAAAAATTG
* * **
530651 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA CAA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
530695 AAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
530713 CGGAAAAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
2 3 0.06
3 43 0.88
4 3 0.06
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (3 bp):
TAA
Found at i:530675 original size:18 final size:19
Alignment explanation
Indices: 530651--530712 Score: 74
Period size: 18 Copynumber: 3.3 Consensus size: 19
530641 GCAAAAATTG
530651 TAATAATAAATAATAATAA
1 TAATAATAAATAATAATAA
* **
530670 -AATAATAAGACAACGATAA
1 TAATAATAA-ATAATAATAA
530689 TAATAA-AAATAATAATAA
1 TAATAATAAATAATAATAA
530707 TAATAA
1 TAATAA
530713 CGGAAAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
18 21 0.60
19 9 0.26
20 5 0.14
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (19 bp):
TAATAATAAATAATAATAA
Found at i:531071 original size:90 final size:89
Alignment explanation
Indices: 530956--531125 Score: 279
Period size: 90 Copynumber: 1.9 Consensus size: 89
530946 CTTTAGGAAG
* *
530956 GGTGATAACTCGGTTCCTACATGATGAGGACGGCTGGTTATCCTAAT-GTTGACACGGCTCTTAC
1 GGTGATAACACGGTTCCTACATGATGAGGACGGCTGGTTAT-CT-ATGGTTGACACGGCTCATAC
531020 ATGATGAAGAGATCTGGCCATCTAAA
64 ATGATGAAGAGATCTGGCCATCTAAA
* *
531046 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACGT
1 GGTGATAACACGGTTCCTACATGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACAT
531111 GATGAAGAGATCTGG
66 GATGAAGAGATCTGG
531126 TCTGGGGATG
Statistics
Matches: 75, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
88 2 0.03
89 34 0.45
90 39 0.52
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (89 bp):
GGTGATAACACGGTTCCTACATGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACAT
GATGAAGAGATCTGGCCATCTAAA
Found at i:531089 original size:46 final size:46
Alignment explanation
Indices: 530956--531089 Score: 132
Period size: 46 Copynumber: 3.0 Consensus size: 46
530946 CTTTAGGAAG
*
530956 GGTGATAACTCGGTTCCTACATGATGAGGACGGCTGGTTATCCT-AA
1 GGTGATAACACGGTTCCTACATGATGAGGACGGCTGGTTAT-CTAAA
* * * * * * **
531002 --TGTTGACACGGCTCTTACATGATGAAGA-GATCTGGCCATCTAAA
1 GGTGATAACACGGTTCCTACATGATGAGGACG-GCTGGTTATCTAAA
*
531046 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTA
1 GGTGATAACACGGTTCCTACATGATGAGGACGGCTGGTTATCTA
531090 TGGTTGACAC
Statistics
Matches: 65, Mismatches: 18, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
43 3 0.05
44 30 0.46
46 31 0.48
47 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (46 bp):
GGTGATAACACGGTTCCTACATGATGAGGACGGCTGGTTATCTAAA
Found at i:531110 original size:43 final size:44
Alignment explanation
Indices: 530977--531115 Score: 131
Period size: 46 Copynumber: 3.1 Consensus size: 44
530967 GGTTCCTACA
* *
530977 TGATGAGGACGGCTGGTTATCCTAAT-GTTGACACGGCTCTTACA
1 TGATGAGGACGGCTGGTTAT-CTAATGGTTGACACGGCTCATACG
* * ** * * * *
531021 TGATGAAGA-GATCTGGCCATCTAAAGGTGATAACACGGTTCCTACG
1 TGATGAGGACG-GCTGGTTATCTAATGGT--TGACACGGCTCATACG
531067 TGATGAGGACGGCTGGTTATCT-ATGGTTGACACGGCTCATACG
1 TGATGAGGACGGCTGGTTATCTAATGGTTGACACGGCTCATACG
531110 TGATGA
1 TGATGA
531116 AGAGATCTGG
Statistics
Matches: 73, Mismatches: 17, Indels: 11
0.72 0.17 0.11
Matches are distributed among these distances:
43 24 0.33
44 16 0.22
45 4 0.05
46 28 0.38
47 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (44 bp):
TGATGAGGACGGCTGGTTATCTAATGGTTGACACGGCTCATACG
Found at i:531126 original size:43 final size:44
Alignment explanation
Indices: 530989--531126 Score: 129
Period size: 43 Copynumber: 3.1 Consensus size: 44
530979 ATGAGGACGG
* *
530989 CTGGTTATCCTAAT-GTTGACACGGCTCTTACATGATGAAGAGAT
1 CTGGTTAT-CTAATGGTTGACACGGCTCATACGTGATGAAGAGAT
** * * * * * *
531033 CTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACG-G
1 CTGGTTATCTAATGGT--TGACACGGCTCATACGTGATGAAGA-GAT
531079 CTGGTTATCT-ATGGTTGACACGGCTCATACGTGATGAAGAGAT
1 CTGGTTATCTAATGGTTGACACGGCTCATACGTGATGAAGAGAT
531122 CTGGT
1 CTGGT
531127 CTGGGGATGA
Statistics
Matches: 72, Mismatches: 17, Indels: 11
0.72 0.17 0.11
Matches are distributed among these distances:
42 1 0.01
43 30 0.42
44 8 0.11
45 4 0.06
46 28 0.39
47 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (44 bp):
CTGGTTATCTAATGGTTGACACGGCTCATACGTGATGAAGAGAT
Found at i:545986 original size:3 final size:3
Alignment explanation
Indices: 545978--546039 Score: 56
Period size: 3 Copynumber: 21.0 Consensus size: 3
545968 GCAAAAATTG
* * **
545978 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA CAA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
546022 AAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
546040 CGGAAAAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
2 3 0.06
3 43 0.88
4 3 0.06
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (3 bp):
TAA
Found at i:546002 original size:18 final size:19
Alignment explanation
Indices: 545978--546039 Score: 74
Period size: 18 Copynumber: 3.3 Consensus size: 19
545968 GCAAAAATTG
545978 TAATAATAAATAATAATAA
1 TAATAATAAATAATAATAA
* **
545997 -AATAATAAGACAACGATAA
1 TAATAATAA-ATAATAATAA
546016 TAATAA-AAATAATAATAA
1 TAATAATAAATAATAATAA
546034 TAATAA
1 TAATAA
546040 CGGAAAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
18 21 0.60
19 9 0.26
20 5 0.14
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (19 bp):
TAATAATAAATAATAATAA
Found at i:546322 original size:21 final size:22
Alignment explanation
Indices: 546297--546337 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
546287 AAGTTACCAC
546297 ACACC-TCGCCAAGA-GCGAATA
1 ACACCGTCG-CAAGATGCGAATA
546318 ACACCGTCGCAAGATGCGAA
1 ACACCGTCGCAAGATGCGAA
546338 ACCATCCGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.37, C:0.32, G:0.22, T:0.10
Consensus pattern (22 bp):
ACACCGTCGCAAGATGCGAATA
Found at i:552301 original size:56 final size:56
Alignment explanation
Indices: 552234--552341 Score: 216
Period size: 56 Copynumber: 1.9 Consensus size: 56
552224 ATGCATATAA
552234 AACAAATACATTTATATTTATCATAAATAAAATATACCGATAATCCATTAGTTGTT
1 AACAAATACATTTATATTTATCATAAATAAAATATACCGATAATCCATTAGTTGTT
552290 AACAAATACATTTATATTTATCATAAATAAAATATACCGATAATCCATTAGT
1 AACAAATACATTTATATTTATCATAAATAAAATATACCGATAATCCATTAGT
552342 GACAACCTAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.46, C:0.13, G:0.05, T:0.36
Consensus pattern (56 bp):
AACAAATACATTTATATTTATCATAAATAAAATATACCGATAATCCATTAGTTGTT
Found at i:552713 original size:31 final size:31
Alignment explanation
Indices: 552644--552717 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
552634 CCTAACATTT
* * *
552644 ACTTTTTGTTTCATTTTAGTACTCGAGATTT
1 ACTTTTTGTTTCATTTTAGTACCCCAGATTA
*
552675 ACTTTTTTTTTCATTTTAGTACCCCATTG-TTA
1 ACTTTTTGTTTCATTTTAGTACCCCA--GATTA
552707 ACTTTTTGTTT
1 ACTTTTTGTTT
552718 TGTTTAGTAC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
31 23 0.64
32 12 0.33
33 1 0.03
ACGTcount: A:0.18, C:0.15, G:0.09, T:0.58
Consensus pattern (31 bp):
ACTTTTTGTTTCATTTTAGTACCCCAGATTA
Found at i:555506 original size:20 final size:20
Alignment explanation
Indices: 555481--555519 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
555471 TGAAGGAAAA
*
555481 TGCTTGCCTTTAATAAAGAC
1 TGCTTGCATTTAATAAAGAC
555501 TGCTTGCATTTAATAAAGA
1 TGCTTGCATTTAATAAAGA
555520 ATGCACTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (20 bp):
TGCTTGCATTTAATAAAGAC
Found at i:558538 original size:21 final size:21
Alignment explanation
Indices: 558486--558540 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
558476 GATTTACATA
* * *
558486 TTCGCATTGCAATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
*
558507 TTCGAGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
558528 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
558541 TTATTACAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:559299 original size:20 final size:20
Alignment explanation
Indices: 559274--559381 Score: 153
Period size: 20 Copynumber: 5.4 Consensus size: 20
559264 GACTATCAGT
*
559274 GTTGCGACAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
*
559294 GTTGCGATAGTCAGAATCTC
1 GTTGCGATAGTCAGAATCGC
*
559314 GTTGCGATAGTCAGAATTGC
1 GTTGCGATAGTCAGAATCGC
*
559334 GTTGCGATAGTCAGAATTGC
1 GTTGCGATAGTCAGAATCGC
* *
559354 ATTGCGATAGTCATAATCGC
1 GTTGCGATAGTCAGAATCGC
*
559374 ATTGCGAT
1 GTTGCGAT
559382 TTATATATTC
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 81 1.00
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.29
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:565325 original size:29 final size:30
Alignment explanation
Indices: 565255--565325 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 30
565245 TTTAACTGCC
*
565255 CAGTGGTATAATTGAAATGAAAATCAATGTT
1 CAGTGGTATAATTG-AATGAAAATCAAAGTT
* * *
565286 CGGTGCTATAATTG-AT-AAAATTTAAAGTT
1 CAGTGGTATAATTGAATGAAAA-TCAAAGTT
565315 CAGTGGTATAA
1 CAGTGGTATAA
565326 ACGATATAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
28 4 0.12
29 17 0.52
31 12 0.36
ACGTcount: A:0.39, C:0.07, G:0.20, T:0.34
Consensus pattern (30 bp):
CAGTGGTATAATTGAATGAAAATCAAAGTT
Found at i:578349 original size:15 final size:15
Alignment explanation
Indices: 578331--578373 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
578321 ATCCGCCCTG
*
578331 CATCCGCCCGCCTCA
1 CATCCGCCCGCCCCA
* *
578346 CATCCTCCCTCCCCA
1 CATCCGCCCGCCCCA
578361 CATCCGCCCGCCC
1 CATCCGCCCGCCC
578374 ACTAAATACC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.12, C:0.65, G:0.09, T:0.14
Consensus pattern (15 bp):
CATCCGCCCGCCCCA
Found at i:583237 original size:23 final size:23
Alignment explanation
Indices: 583211--583254 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
583201 TCTACATGTC
* * *
583211 ATAACTATTTTTTTTGAAAACAA
1 ATAAATATTATTTTTAAAAACAA
583234 ATAAATATTATTTTTAAAAAC
1 ATAAATATTATTTTTAAAAAC
583255 GATTATGACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (23 bp):
ATAAATATTATTTTTAAAAACAA
Found at i:583743 original size:3 final size:3
Alignment explanation
Indices: 583735--583769 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
583725 AATATTTGAT
583735 TAA TAA TAA TAA TAAA TAA TAA TAA -AA TAA TAA TA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TA
583770 TTTTTGTAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 25 0.83
4 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:588403 original size:17 final size:17
Alignment explanation
Indices: 588368--588403 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
588358 CTCTAAAGAT
* *
588368 TAATAATAATGTATTCA
1 TAATAATAATGCATCCA
588385 TAATAATAATGCATCCA
1 TAATAATAATGCATCCA
588402 TA
1 TA
588404 CTTACTCTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.11, G:0.06, T:0.36
Consensus pattern (17 bp):
TAATAATAATGCATCCA
Found at i:588821 original size:106 final size:107
Alignment explanation
Indices: 588587--588888 Score: 347
Period size: 106 Copynumber: 2.8 Consensus size: 107
588577 AACATTATTG
* * * * * * * *
588587 GGCGCAACCTAATATGTTAATATTTATTTATAGCAAAATAAGAAATTAACATATTTTGTTGTCAT
1 GGCGCTACCTAATATGTTGATA-ATATTAATAACAAAATAAGTAATTAACATATTTTGTTATCGT
* * ** * *
588652 TAGATTTCAAAGTTTCCATCAACTTAAACTTTGGTGAAATTTTA
65 CAGATTTCTAAG-ACCCATCAACCTAAACTTTGATGAAATTTTA
* * *
588696 AGCGCTATCTAATATGTTGATAATATTAATAACAAAATAAGTAATTAACTTATTTTGTTATCGTC
1 GGCGCTACCTAATATGTTGATAATATTAATAACAAAATAAGTAATTAACATATTTTGTTATCGTC
* *
588761 GGATTTCTAAGACCCATCAGCCT-AACTTTGAT-AATATTTTA
66 AGATTTCTAAGACCCATCAACCTAAACTTTGATGAA-ATTTTA
* * *
588802 GGCGCTACCTAATATGTTGATAATATTGATAACAAATTAAGTAATTAACCTATTTTGTTATCGTC
1 GGCGCTACCTAATATGTTGATAATATTAATAACAAAATAAGTAATTAACATATTTTGTTATCGTC
*
588867 AGATTTCTAAGATCTCATCAAC
66 AGATTTCTAAGA-CCCATCAAC
588889 TTTAAAAAGG
Statistics
Matches: 164, Mismatches: 27, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
105 2 0.01
106 85 0.52
107 15 0.09
108 44 0.27
109 18 0.11
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (107 bp):
GGCGCTACCTAATATGTTGATAATATTAATAACAAAATAAGTAATTAACATATTTTGTTATCGTC
AGATTTCTAAGACCCATCAACCTAAACTTTGATGAAATTTTA
Found at i:589181 original size:226 final size:224
Alignment explanation
Indices: 588735--589195 Score: 611
Period size: 226 Copynumber: 2.0 Consensus size: 224
588725 TAACAAAATA
* *
588735 AGTAATTAACTTATTTTGTTATCGTCGGATTTCTAAGACCCATCAGCCTAACTTTGATAATATTT
1 AGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGACCCATCAGCCTAACTTTGATAACATTT
* * *
588800 TAGGCGCTACCTAATATGTTGATAATATTGATAACAAATTAAGTAATTAACCTATTTTGTTATCG
66 TAGGCACGACCTAATATGTTGATAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTATCG
* * * * *
588865 TCAGATTTCTAAGATCTCATCAACTTTAAAAAGGCGTTACATATTACATTAAATAAGCGTTGCTT
131 TCAGATTTCTAAGACCTCATCAACTTTAAAAAGGCGCTACATATTACATTAAATAAGCGATACCT
*
588930 GTTATGTTATTATGGTTGATAATGTTTCT
196 GATATGTTATTATGGTTGATAATGTTTCT
* * ** * *
588959 AGTAGTTAACCTATTTTGTTGTCGTTTGATTTCTAAGACTCTATCAG-CTAAAATTTTGATAACA
1 AGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGAC-CCATCAGCCT--AACTTTGATAACA
*
589023 TTTTAGGCACGGCCTAATATGTTGATAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTA
63 TTTTAGGCACGACCTAATATGTTGATAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTA
* * * * * * * * * *
589088 TCGTCGGATTTTTATGGCCTCATCAGCTTTTAAAAGGCGCTACCTATTTCCTTACATAAGCGATA
128 TCGTCAGATTTCTAAGACCTCATCAACTTTAAAAAGGCGCTACATATTACATTAAATAAGCGATA
589153 CCTGATATGTTATTATGGTTGATAATGTTT-T
193 CCTGATATGTTATTATGGTTGATAATGTTTCT
*
589184 CAATAATTAACC
1 -AGTAATTAACC
589196 GGTTATGTTA
Statistics
Matches: 203, Mismatches: 30, Indels: 6
0.85 0.13 0.03
Matches are distributed among these distances:
224 36 0.18
225 7 0.03
226 160 0.79
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (224 bp):
AGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGACCCATCAGCCTAACTTTGATAACATTT
TAGGCACGACCTAATATGTTGATAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTATCG
TCAGATTTCTAAGACCTCATCAACTTTAAAAAGGCGCTACATATTACATTAAATAAGCGATACCT
GATATGTTATTATGGTTGATAATGTTTCT
Found at i:592102 original size:20 final size:21
Alignment explanation
Indices: 592072--592115 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 21
592062 CCGAACATAA
592072 AAAAAACGGGGGA-CTGAACAG
1 AAAAAACGGGGGATC-GAACAG
592093 AAAAAA-GGGGGATCGAACAG
1 AAAAAACGGGGGATCGAACAG
592113 AAA
1 AAA
592116 TCAAAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.52, C:0.11, G:0.32, T:0.05
Consensus pattern (21 bp):
AAAAAACGGGGGATCGAACAG
Found at i:592699 original size:16 final size:17
Alignment explanation
Indices: 592666--592703 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
592656 CAACATGAAG
592666 ATAAAAAGGTAAAGAAA
1 ATAAAAAGGTAAAGAAA
592683 ATAAAAAGG-AACA-AAA
1 ATAAAAAGGTAA-AGAAA
592699 ATAAA
1 ATAAA
592704 TAGACGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.74, C:0.03, G:0.13, T:0.11
Consensus pattern (17 bp):
ATAAAAAGGTAAAGAAA
Found at i:592950 original size:31 final size:28
Alignment explanation
Indices: 592909--592970 Score: 79
Period size: 31 Copynumber: 2.1 Consensus size: 28
592899 TTAGAAGTAT
*
592909 ATATTTACATAAAGTATAATAAAGATATAAA
1 ATATGTACATAAA-TAT-ATAAAGAT-TAAA
*
592940 ATATGTACATAAATATATATAGATTAAA
1 ATATGTACATAAATATATAAAGATTAAA
592968 ATA
1 ATA
592971 ATGAAAACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 7 0.24
29 7 0.24
30 3 0.10
31 12 0.41
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.34
Consensus pattern (28 bp):
ATATGTACATAAATATATAAAGATTAAA
Found at i:593011 original size:2 final size:2
Alignment explanation
Indices: 593004--593058 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
592994 TACCAGAATA
593004 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
593046 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
593059 ATGATAATAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:596276 original size:14 final size:13
Alignment explanation
Indices: 596258--596300 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
596248 ACTCTAAACG
596258 TTTTTCTCTTTTT
1 TTTTTCTCTTTTT
596271 TATTTT-TCCTTTTT
1 T-TTTTCT-CTTTTT
596285 CTTTTTCTCTTTTT
1 -TTTTTCTCTTTTT
596299 TT
1 TT
596301 CAACTTAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
13 4 0.15
14 20 0.77
15 2 0.08
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTCTCTTTTT
Found at i:596289 original size:13 final size:14
Alignment explanation
Indices: 596258--596298 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
596248 ACTCTAAACG
596258 TTTTTCTCTTTTTTA
1 TTTTTCTC-TTTTTA
*
596273 TTTTTC-CTTTTTC
1 TTTTTCTCTTTTTA
596286 TTTTTCTCTTTTT
1 TTTTTCTCTTTTT
596299 TTCAACTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 11 0.46
14 7 0.29
15 6 0.25
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTTCTCTTTTTA
Found at i:606355 original size:12 final size:12
Alignment explanation
Indices: 606338--606363 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
606328 TTATTGTTCT
606338 TGCTCCTCGGGC
1 TGCTCCTCGGGC
606350 TGCTCCTCGGGC
1 TGCTCCTCGGGC
606362 TG
1 TG
606364 TTTAGGCTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.38, G:0.35, T:0.27
Consensus pattern (12 bp):
TGCTCCTCGGGC
Found at i:609972 original size:21 final size:21
Alignment explanation
Indices: 609948--609990 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
609938 TTCTAGGTTG
609948 TGTGCATCGATGCA-TCTTCAA
1 TGTGCATCGATGCACTC-TCAA
609969 TGTGCATCGATGCACTCTCAA
1 TGTGCATCGATGCACTCTCAA
609990 T
1 T
609991 TAAACAAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.33
Consensus pattern (21 bp):
TGTGCATCGATGCACTCTCAA
Found at i:611012 original size:23 final size:23
Alignment explanation
Indices: 610944--610996 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
610934 CATTATTATA
610944 TGGCACTACAGTGCAATTCTACG
1 TGGCACTACAGTGCAATTCTACG
*
610967 CGGCACTACAGTGCAATTCTACG
1 TGGCACTACAGTGCAATTCTACG
610990 TGGCACT
1 TGGCACT
610997 TCGGTGCATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (23 bp):
TGGCACTACAGTGCAATTCTACG
Found at i:615602 original size:21 final size:21
Alignment explanation
Indices: 615576--615618 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
615566 TTCTGGGTTG
615576 TGTGCATCGATGCA-TCTTCAA
1 TGTGCATCGATGCACTC-TCAA
615597 TGTGCATCGATGCACTCTCAA
1 TGTGCATCGATGCACTCTCAA
615618 T
1 T
615619 TAAACAAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.33
Consensus pattern (21 bp):
TGTGCATCGATGCACTCTCAA
Found at i:616683 original size:23 final size:23
Alignment explanation
Indices: 616592--616675 Score: 132
Period size: 23 Copynumber: 3.7 Consensus size: 23
616582 CATTATTATA
616592 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
616615 CGGCACTACAGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
*
616638 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
*
616661 TGGCACTTCGGTGCA
1 TGGCACTACGGTGCA
616676 TTTATACGAG
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.20, C:0.27, G:0.26, T:0.26
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:624573 original size:675 final size:678
Alignment explanation
Indices: 623280--624633 Score: 2491
Period size: 675 Copynumber: 2.0 Consensus size: 678
623270 TCAATCTCTT
* * *
623280 GTATTACAACACCTTTGTCCATTGATTCAGATTATTTTGTGTGTAATGATTGCTTTTTAGGGATC
1 GTATTACAACACCTTTGTCCATTGATTCAGATTATTTTGTGTGTAATAAATACTTTTTAGGGATC
* *
623345 AATAACCTCTTTTTATGATGCAAATGCTAAAAAACAAACACAAAGGCAAAAAAGTTAGTGAAATA
66 AATAACCTCTTGTTATGATGCAAATGCTAAAAAACAAACACAAAGGCAAAAAAGTTAGTAAAATA
*
623410 AAAATAAACAAAAATGACAAAAGGAAAAAAAACAAAGACATGGTTAGGGTAAAAAATATCCTAGG
131 AAAATAAACAAAAATGACAAAAGGAAAAAAAACAAAGACATGGTTAGGGTAAAAAATATCATAGG
623475 TTTTGAAATGTGGTTTCGGGGTAGGCTCTAATTCTCCATAGTCTCCCGGCTTAGATTTTAAAAAA
196 TTTTGAAATGTGGTTTCGGGGTAGGCTCTAATTCTCCATAGTCTCCCGGCTTAGATTTTAAAAAA
623540 TGGTACCCGAGTTCTCCTTGTCGGTGCCCCCTTGGGCTTGCCAGACCCTTAGTCCTAAACCCATC
261 TGGTACCCGAGTTCTCCTTGTCGGTGCCCCCTTGGGCTTGCCAGACCCTTAGTCCTAAACCCATC
*
623605 ACAGGCTTGTGTGGACTAAGTTAAACTCGATAGGACCCATTCCCTTATGCCCGTACGGTGAATAA
326 ACAGGCTTGTGTGGACTAAGTTAAACTCGACAGGACCCATTCCCTTATGCCCGTACGGTGAATAA
* *
623670 ATTCACACGAAGATATGAGGTATATGAATCCCGAAGGCTACTTGCTAGGCTCGCACGGTGAATAA
391 ATTCACACGAAGACATGAGGTATATGAATCCCGAAGGCTACTTGCTAGGCTCGAACGGTGAATAA
*
623735 ATTCACACAAAGGCTTCGCTTTCACCCCCACCTAAAATAAAGTTCAGAGCTCGGGTATAGAGCCT
456 ATTCACACAAAGGCTTCGCTTTCACCCCCACCTAAAACAAAGTTCAGAGCTCGGGTATAGAGCCT
623800 TAAGTGAAAAAGAAGCTTTGAAGGCTGAAATCATTAGAAAACGATTAGTACAACTATTTACTCGA
521 TAAGTGAAAAAGAAGCTTTGAAGGCTGAAATCATTAGAAAACGATTAGTACAACTATTTACTCGA
*
623865 AAATATAATCAAAAGTAAGTAATAAGGATCGAAATGTTATCTCAAAATTTAAACTTA-CTCTTTT
586 AAATATAATCAAAAGTAAGTAATAAGGATCGAAATGTTATCTCAAAATTTAAACATATC-CTTTT
623929 CGTTAAAAAGACAACTGGAAATTACCTTA
650 CGTTAAAAAGACAACTGGAAATTACCTTA
* *
623958 GTATTACAACACTTTTGTCCATTGATTCGGATTATTTTGTGTGTAATAAATACTTTTTAGGGATC
1 GTATTACAACACCTTTGTCCATTGATTCAGATTATTTTGTGTGTAATAAATACTTTTTAGGGATC
624023 AATAACCTCTTGTTATGATGCAAATGCTAAAAAACAAACACAAAGGCAAAAAAGTTAGTAAAATA
66 AATAACCTCTTGTTATGATGCAAATGCTAAAAAACAAACACAAAGGCAAAAAAGTTAGTAAAATA
624088 AAAATAAACAAAAATGA-AAAAGG-AAAAAAACAAAGACATGGTTAGGGTAAAAAATATCATAGG
131 AAAATAAACAAAAATGACAAAAGGAAAAAAAACAAAGACATGGTTAGGGTAAAAAATATCATAGG
*
624151 TTTTGAAATGTGGTTTCGGGGTAGGCTCTAATTCTCCATAGTCTCCCGGCTTAGGTTTTAAAAAA
196 TTTTGAAATGTGGTTTCGGGGTAGGCTCTAATTCTCCATAGTCTCCCGGCTTAGATTTTAAAAAA
624216 TGGTACCCGAGTTCTCCTTGTCGGTGCCCCCTTGGGCTTGCCAGACCCTTAGTCCTAAACCCATC
261 TGGTACCCGAGTTCTCCTTGTCGGTGCCCCCTTGGGCTTGCCAGACCCTTAGTCCTAAACCCATC
624281 ACAGGCTTGTGTGGACTAAGTTAAACTCGACAGGACCCATT-CCTTATGCCCGTACGGTGAATAA
326 ACAGGCTTGTGTGGACTAAGTTAAACTCGACAGGACCCATTCCCTTATGCCCGTACGGTGAATAA
624345 ATTCACACGAAGACATGAGGTATATGAATCCCGAAGGCTACTTGCTAGGCTCGAACGGTGAATAA
391 ATTCACACGAAGACATGAGGTATATGAATCCCGAAGGCTACTTGCTAGGCTCGAACGGTGAATAA
* * * *
624410 ATTCACACGAAGGCTTCGCTTTCACCCCCACTTACAACAAGGTTCAGAGCTCGGGTATAGAGCCT
456 ATTCACACAAAGGCTTCGCTTTCACCCCCACCTAAAACAAAGTTCAGAGCTCGGGTATAGAGCCT
*
624475 TAAGTGAAAAAGAAGCTTTGAAGGCTGAAATCATTAGAAAATGATTAGTACAACTATTTACTCGA
521 TAAGTGAAAAAGAAGCTTTGAAGGCTGAAATCATTAGAAAACGATTAGTACAACTATTTACTCGA
*
624540 AAATGTAATCAAAAGTAAGTAATAAGGATCGAAATGTTATCTCAAAATTTAAACATATCCTTTTC
586 AAATATAATCAAAAGTAAGTAATAAGGATCGAAATGTTATCTCAAAATTTAAACATATCCTTTTC
624605 GTTAAAAAGACAACTGGAAATTACCTTA
651 GTTAAAAAGACAACTGGAAATTACCTTA
624633 G
1 G
624634 CCTGACTCAC
Statistics
Matches: 655, Mismatches: 20, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
675 300 0.46
676 209 0.32
677 6 0.01
678 140 0.21
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (678 bp):
GTATTACAACACCTTTGTCCATTGATTCAGATTATTTTGTGTGTAATAAATACTTTTTAGGGATC
AATAACCTCTTGTTATGATGCAAATGCTAAAAAACAAACACAAAGGCAAAAAAGTTAGTAAAATA
AAAATAAACAAAAATGACAAAAGGAAAAAAAACAAAGACATGGTTAGGGTAAAAAATATCATAGG
TTTTGAAATGTGGTTTCGGGGTAGGCTCTAATTCTCCATAGTCTCCCGGCTTAGATTTTAAAAAA
TGGTACCCGAGTTCTCCTTGTCGGTGCCCCCTTGGGCTTGCCAGACCCTTAGTCCTAAACCCATC
ACAGGCTTGTGTGGACTAAGTTAAACTCGACAGGACCCATTCCCTTATGCCCGTACGGTGAATAA
ATTCACACGAAGACATGAGGTATATGAATCCCGAAGGCTACTTGCTAGGCTCGAACGGTGAATAA
ATTCACACAAAGGCTTCGCTTTCACCCCCACCTAAAACAAAGTTCAGAGCTCGGGTATAGAGCCT
TAAGTGAAAAAGAAGCTTTGAAGGCTGAAATCATTAGAAAACGATTAGTACAACTATTTACTCGA
AAATATAATCAAAAGTAAGTAATAAGGATCGAAATGTTATCTCAAAATTTAAACATATCCTTTTC
GTTAAAAAGACAACTGGAAATTACCTTA
Found at i:625105 original size:16 final size:17
Alignment explanation
Indices: 625072--625110 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
625062 CAACATGAAG
625072 ATAAAAAGGTAAAGAAA
1 ATAAAAAGGTAAAGAAA
625089 ATAAAAAGG-AACA-AAA
1 ATAAAAAGGTAA-AGAAA
625105 ATAAAA
1 ATAAAA
625111 TTAAAAATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.74, C:0.03, G:0.13, T:0.10
Consensus pattern (17 bp):
ATAAAAAGGTAAAGAAA
Found at i:625379 original size:31 final size:28
Alignment explanation
Indices: 625338--625399 Score: 79
Period size: 31 Copynumber: 2.1 Consensus size: 28
625328 TTAGAAGTAT
*
625338 ATATTTACATAAAGTATAATAAAGATATAAA
1 ATATGTACATAAA-TAT-ATAAAGAT-TAAA
*
625369 ATATGTACATAAATATATATAGATTAAA
1 ATATGTACATAAATATATAAAGATTAAA
625397 ATA
1 ATA
625400 ATGAAAACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 7 0.24
29 7 0.24
30 3 0.10
31 12 0.41
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.34
Consensus pattern (28 bp):
ATATGTACATAAATATATAAAGATTAAA
Found at i:627432 original size:25 final size:25
Alignment explanation
Indices: 627404--627466 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 25
627394 TCGTTCAATC
*
627404 TTTTTATTTATTATAATCCTAATAT
1 TTTTTATTTATTATAACCCTAATAT
** * **
627429 TTTTGGTTTATTTTAACCCTTTTAT
1 TTTTTATTTATTATAACCCTAATAT
627454 TTTTTAATTTATT
1 TTTTT-ATTTATT
627467 TTATTTACAG
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
25 23 0.79
26 6 0.21
ACGTcount: A:0.24, C:0.08, G:0.03, T:0.65
Consensus pattern (25 bp):
TTTTTATTTATTATAACCCTAATAT
Found at i:630317 original size:40 final size:40
Alignment explanation
Indices: 630273--630354 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
630263 CCTCTATTAC
630273 TTAATTGTCACTCGAGGTGACAAGTGACCACTTAGAGACA
1 TTAATTGTCACTCGAGGTGACAAGTGACCACTTAGAGACA
630313 TTAATTGTCACTCGAGGTGACAAGTGACCACTTAGAGACA
1 TTAATTGTCACTCGAGGTGACAAGTGACCACTTAGAGACA
630353 TT
1 TT
630355 CTTTCTATCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.27
Consensus pattern (40 bp):
TTAATTGTCACTCGAGGTGACAAGTGACCACTTAGAGACA
Found at i:634397 original size:149 final size:150
Alignment explanation
Indices: 634208--634523 Score: 555
Period size: 150 Copynumber: 2.1 Consensus size: 150
634198 GGGTAGAGGG
* *
634208 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTT-GAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
* *
634272 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGTATATGTATATGATCCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
634337 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
*
634357 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
*
634422 TACTTGATCTCTAGTATATGTATATGATCCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGTATATGTATATGATCCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
634487 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
634507 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
634524 TGCATTTATA
Statistics
Matches: 159, Mismatches: 6, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
149 52 0.33
150 107 0.67
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.34
Consensus pattern (150 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
TACTTGATCCCTAGTATATGTATATGATCCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
ATATGGCACTACGGTGCAAT
Found at i:634535 original size:23 final size:23
Alignment explanation
Indices: 634491--634535 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
634481 ATCATTATAT
*
634491 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
634514 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
634536 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:641438 original size:149 final size:150
Alignment explanation
Indices: 641247--641562 Score: 555
Period size: 150 Copynumber: 2.1 Consensus size: 150
641237 GGGTAGAGGG
* *
641247 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTAGAACATGTGTGAAGTCTT-GAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTAGAACATGTGTGAAGTCTTGGAAAGACACA
* *
641311 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGTATATGTATATGATCCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
641376 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
* *
641396 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTAGAACATGTGTGAAGTCTTGGAAAGACACA
641461 TACTTGATCCCTAGTATATGTATATGATCCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGTATATGTATATGATCCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
641526 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
641546 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
641563 TGCATTTATA
Statistics
Matches: 159, Mismatches: 6, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
149 51 0.32
150 108 0.68
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (150 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTAGAACATGTGTGAAGTCTTGGAAAGACACA
TACTTGATCCCTAGTATATGTATATGATCCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
ATATGGCACTACGGTGCAAT
Found at i:641574 original size:23 final size:23
Alignment explanation
Indices: 641530--641574 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
641520 ATCATTATAT
*
641530 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
641553 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
641575 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:644577 original size:3 final size:3
Alignment explanation
Indices: 644549--644607 Score: 61
Period size: 3 Copynumber: 19.7 Consensus size: 3
644539 CAAAATCATT
*
644549 TTA TTA -TA TTA TATA TTTA TTTA TTA TTA TTA TTA TTA TTA -TA TTT
1 TTA TTA TTA TTA T-TA -TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
644595 TTA TT- TTA TTA TT
1 TTA TTA TTA TTA TT
644608 TTTGTAGGCC
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
2 6 0.12
3 34 0.69
4 8 0.16
5 1 0.02
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:644603 original size:19 final size:19
Alignment explanation
Indices: 644548--644608 Score: 72
Period size: 20 Copynumber: 3.2 Consensus size: 19
644538 ACAAAATCAT
644548 TTTATTA-TATTATATATTTA
1 TTTATTATTATTAT-TA-TTA
644568 TTTATTATTATTATTATTA
1 TTTATTATTATTATTATTA
*
644587 TTATATTTTTATT-TTATTA
1 TT-TATTATTATTATTATTA
644606 TTT
1 TTT
644609 TTGTAGGCCC
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
18 1 0.03
19 13 0.34
20 18 0.47
21 6 0.16
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTATTATTATTATTATTA
Found at i:644701 original size:33 final size:33
Alignment explanation
Indices: 644664--644726 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
644654 AATAAACCAG
644664 CGTATTTGAGTCCTATTAAAACACTAAAACTAA
1 CGTATTTGAGTCCTATTAAAACACTAAAACTAA
*
644697 CGTATTTGAGTCCTATTGAAACACTAAAAC
1 CGTATTTGAGTCCTATTAAAACACTAAAAC
644727 CGAAACATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.30
Consensus pattern (33 bp):
CGTATTTGAGTCCTATTAAAACACTAAAACTAA
Found at i:645108 original size:2 final size:2
Alignment explanation
Indices: 645101--645195 Score: 92
Period size: 2 Copynumber: 49.5 Consensus size: 2
645091 TTTACATTGT
*
645101 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA T- TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
645141 TA T- TA TA TA T- TA TA T- TA TA CTT TT TA TA TA TA TA TT TT TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
*
645181 CA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
645196 TATTTTTTAT
Statistics
Matches: 80, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
1 5 0.06
2 74 0.93
3 1 0.01
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:645149 original size:15 final size:15
Alignment explanation
Indices: 645100--645219 Score: 67
Period size: 16 Copynumber: 7.9 Consensus size: 15
645090 TTTTACATTG
645100 TTATATATATATATATA
1 TTATAT-TAT-TATATA
645117 TATATATATATATATATA
1 T-TATAT-TAT-TATATA
*
645135 TTATTTTATTATATA
1 TTATATTATTATATA
645150 TTATATTA-TACT-T-
1 TTATATTATTA-TATA
645163 TT-TA-TA-TATATA
1 TTATATTATTATATA
*
645175 TT-T-TTACATATATA
1 TTATATTA-TTATATA
* *
645189 TATATATTATTTTTTA
1 T-TATATTATTATATA
645205 TTAATATTATTATAT
1 TT-ATATTATTATAT
645220 TAATACTTTT
Statistics
Matches: 85, Mismatches: 7, Indels: 23
0.74 0.06 0.20
Matches are distributed among these distances:
10 1 0.01
11 5 0.06
12 7 0.08
13 2 0.02
14 10 0.12
15 16 0.19
16 19 0.22
17 8 0.09
18 17 0.20
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATATTATTATATA
Found at i:645159 original size:25 final size:26
Alignment explanation
Indices: 645100--645176 Score: 90
Period size: 25 Copynumber: 3.1 Consensus size: 26
645090 TTTTACATTG
* *
645100 TTATATATATA-TATATATATATATA
1 TTATATATATACTTTTTATATATATA
*
645125 -TATATATATATTATTTTAT-TATATA
1 TTATATATATACT-TTTTATATATATA
645150 TTATAT-TATACTTTTTATATATATA
1 TTATATATATACTTTTTATATATATA
645175 TT
1 TT
645177 TTTACATATA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
24 16 0.36
25 20 0.44
26 9 0.20
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (26 bp):
TTATATATATACTTTTTATATATATA
Found at i:645168 original size:64 final size:65
Alignment explanation
Indices: 645100--645232 Score: 200
Period size: 64 Copynumber: 2.1 Consensus size: 65
645090 TTTTACATTG
*
645100 TTATATATATATATATATATATATATATATATATATTATTTTATT-ATA-TATTATATT-ATACT
1 TTATATATATATATATACATATATATATATAT-TATT-TTTTATTAATATTATTATATTAATACT
645162 TT
64 TT
* *
645164 TTATATATATATTTTTACATATATATATATATTATTTTTTATTAATATTATTATATTAATACTTT
1 TTATATATATATATATACATATATATATATATTATTTTTTATTAATATTATTATATTAATACTTT
645229 TTAT
1 TTAT
645233 TATTCTTTTC
Statistics
Matches: 63, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
62 7 0.11
63 7 0.11
64 38 0.60
65 11 0.17
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.59
Consensus pattern (65 bp):
TTATATATATATATATACATATATATATATATTATTTTTTATTAATATTATTATATTAATACTTT
Found at i:645216 original size:9 final size:8
Alignment explanation
Indices: 645107--645221 Score: 55
Period size: 10 Copynumber: 13.9 Consensus size: 8
645097 TTGTTATATA
645107 TATATATAT
1 TATAT-TAT
645116 ATATATATAT
1 -TATAT-TAT
645126 ATATATATAT
1 -TATAT-TAT
*
645136 TATTTTAT
1 TATATTAT
645144 TATA-TAT
1 TATATTAT
645151 TATATTA-
1 TATATTAT
645158 TACT-TT-T
1 TA-TATTAT
645165 TATA-TA-
1 TATATTAT
*
645171 TATATTTT
1 TATATTAT
645179 TACATATATAT
1 T--ATAT-TAT
645190 ATATATTAT
1 -TATATTAT
*
645199 T-TTTTAT
1 TATATTAT
645206 TAATATTAT
1 T-ATATTAT
645215 TATATTA
1 TATATTA
645222 ATACTTTTTA
Statistics
Matches: 86, Mismatches: 6, Indels: 28
0.72 0.05 0.23
Matches are distributed among these distances:
6 6 0.07
7 20 0.23
8 17 0.20
9 13 0.15
10 27 0.31
11 2 0.02
12 1 0.01
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (8 bp):
TATATTAT
Found at i:649140 original size:110 final size:110
Alignment explanation
Indices: 648947--649492 Score: 787
Period size: 110 Copynumber: 5.0 Consensus size: 110
648937 GATGGTGGTT
* * * *
648947 GCTCAACTTCACAGTGAAGGGGCGACTGACGGTCAACAAATAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAATTTCATTCAGAGTC
* *
649012 AATTTCAACTTCACATCGAATGATATTGGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* * * *
649057 GCTCAACTTCACAGCGAATGAGCGACTGACTGTTAACAAACAACTTTTCAATTTCATTTAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAATTTCATTCAGAGTC
* *
649122 AATTTTAACTTCACATCGAAGGATATTGGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* * *
649167 GCTCAACTTCACAGCGAAAGGGCGGCTGACTGTCAACAAATAACTTTTCAGA-TTCATTCAGAGT
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCA-ATTTCATTCAGAGT
*
649231 CAATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAACACAA
65 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* *
649277 GCTCAACTTCACAGCGAAGGGGCGACTGATTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAATTTCATTCAGAGTC
*
649342 AATTTCAACTTCACAGCGAAAGATATTGGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* * * * *
649387 GTTTAACTTCACAGCGAAGGGCCGACTGGCTGTCAACAAACAACTTTTC-AGTT--TT-AGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAATTTCATTCAGAGTC
* * * * *
649448 AATTTCAACTTCACGGAGAAGGTTATTGGCCTCGAAACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
649493 ATATTTGGAT
Statistics
Matches: 395, Mismatches: 39, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
106 45 0.11
107 2 0.01
109 2 0.01
110 345 0.87
111 1 0.00
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (110 bp):
GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAATTTCATTCAGAGTC
AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
Found at i:649836 original size:84 final size:83
Alignment explanation
Indices: 649599--650113 Score: 494
Period size: 84 Copynumber: 6.3 Consensus size: 83
649589 AATCGTGCCC
* * *
649599 ACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTACAACATAGCTTAAGT
1 ACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTACAACATAACTTAAGT
* *
649664 TGAGAAGGGCTATC--TG
66 CGAGAAGGGTTATCTGTG
* * * * * *
649680 -CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAATATAACTCAAG
1 ACCAAAGACCTTCGAGTTCGACTACACTCAGC-TCCAAGGCACATCATTTACAACATAACTTAA-
*
649744 GT-TAGAAGGGTTATCTGTG
64 GTCGAGAAGGGTTATCTGTG
* * * *
649763 ACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAACATAACTTATG
1 ACC-AAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTACAACATAACTTAAG
**
649828 TCGAGAAGGGTTATCTGCCA
65 TCGAGAAGGGTTATCTG-TG
* * ** *
649848 ACCAAAGACCTTCAAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGTAGCATAACTTAAGT
1 ACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTACAACATAACTTAAGT
649913 CGAGAAGGGTTATC--TG
66 CGAGAAGGGTTATCTGTG
* * * ** * * * *
649929 -CCAAAGACCCTCGAGTTCGATTATACTCAATTTCGAGGGCACATCATTTACGACATAACTCAAG
1 ACCAAAGACCTTCGAGTTCGACTACACTC-AGCTCCAAGGCACATCATTTACAACATAACTTAAG
* * *
649993 GCTAGAAGGGTTATCTGTC
65 TCGAGAAGGGTTATCTGTG
* * * * * *
650012 AACAAAGACCTTCGAGTTCTACTTCACTCAGCTCAAAGGCACTATCATTTGCAACAT-AGTTCAA
1 ACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCAC-ATCATTTACAACATAACTT-AA
* * *
650076 GACAAGAATGGTTATC--TG
64 GTCGAGAAGGGTTATCTGTG
650094 -CCAAAGACCTTCGAGTTCGA
1 ACCAAAGACCTTCGAGTTCGA
650114 TTTCATTCAG
Statistics
Matches: 352, Mismatches: 68, Indels: 28
0.79 0.15 0.06
Matches are distributed among these distances:
80 50 0.14
81 94 0.27
82 3 0.01
83 16 0.05
84 160 0.45
85 29 0.08
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.25
Consensus pattern (83 bp):
ACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTACAACATAACTTAAGT
CGAGAAGGGTTATCTGTG
Found at i:649977 original size:165 final size:163
Alignment explanation
Indices: 649600--650126 Score: 535
Period size: 165 Copynumber: 3.2 Consensus size: 163
649590 ATCGTGCCCA
* * * * *
649600 CCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTACAACATAGCTTAAGTT
1 CCAAAGACCTTCGAGTTCGATTACACTCAGCTCCAAGGCACATCATTTACAACATAACTTAAGTC
* * * * *
649665 GAGAAGGGCTATCTG---CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
66 GAGAAGGGTTATCTGCAACCAAAGACCTTCGAGTTCGACTACACTCAGC-TCAAAGGCACATCAT
* * * *
649727 TTACAATATAACTCAAGGT-TAGAAGGGTTATCTGTG
130 TTGCAACATAACTTAA-GTCAAGAAGGGTTATC--TG
* * * * *
649763 ACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAACATAACTTATG
1 -CC-AAAGACCTTCGAGTTCGATTACACTCAGCTCCAAGGCACATCATTTACAACATAACTTAAG
* * *
649828 TCGAGAAGGGTTATCTGCCAACCAAAGACCTTCAAGTTCGACTACGCTCAGCTCCAAGGCACATC
64 TCGAGAAGGGTTATCTG-CAACCAAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCACATC
* * *
649893 ATTTGTAGCATAACTTAAGTCGAGAAGGGTTATCTG
128 ATTTGCAACATAACTTAAGTCAAGAAGGGTTATCTG
* * ** * * * * *
649929 CCAAAGACCCTCGAGTTCGATTATACTCAATTTCGAGGGCACATCATTTACGACATAACTCAAGG
1 CCAAAGACCTTCGAGTTCGATTACACTC-AGCTCCAAGGCACATCATTTACAACATAACTTAAGT
* * *
649994 CTAGAAGGGTTATCTGTCAA-CAAAGACCTTCGAGTTCTACTTCACTCAGCTCAAAGGCACTATC
65 CGAGAAGGGTTATCTG-CAACCAAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCAC-ATC
* * *
650058 ATTTGCAACAT-AGTTCAAGACAAGAATGGTTATCTG
128 ATTTGCAACATAACTT-AAGTCAAGAAGGGTTATCTG
* *
650094 CCAAAGACCTTCGAGTTCGATTTCATTCAGCTC
1 CCAAAGACCTTCGAGTTCGATTACACTCAGCTC
650127 GAGGGCGTAT
Statistics
Matches: 302, Mismatches: 52, Indels: 18
0.81 0.14 0.05
Matches are distributed among these distances:
164 65 0.22
165 170 0.56
166 2 0.01
167 2 0.01
168 36 0.12
169 27 0.09
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.26
Consensus pattern (163 bp):
CCAAAGACCTTCGAGTTCGATTACACTCAGCTCCAAGGCACATCATTTACAACATAACTTAAGTC
GAGAAGGGTTATCTGCAACCAAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCACATCATT
TGCAACATAACTTAAGTCAAGAAGGGTTATCTG
Found at i:650060 original size:249 final size:249
Alignment explanation
Indices: 649594--650069 Score: 747
Period size: 249 Copynumber: 1.9 Consensus size: 249
649584 AAGGGAATCG
* * * *
649594 TGCCCACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTACAACATAGCT
1 TGCCAACCAAAGACCTTCAAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAACATAACT
* *
649659 TAAGTTGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
66 TAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAACTTCGAGGGCACAT
* * * *
649724 CATTTACAATATAACTCAAGGTTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTAC
131 CATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGACTAC
* *
649789 GCTCAGCTCCAAGGCATATCATTTGCAACATAACTTATGTCGAGAAGGGTTATC
196 ACTCAGCTCAAAGGCATATCATTTGCAACATAACTTATGTCGAGAAGGGTTATC
** *
649843 TGCCAACCAAAGACCTTCAAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGTAGCATAACT
1 TGCCAACCAAAGACCTTCAAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAACATAACT
* * *
649908 TAAGTCGAGAAGGGTTATCTGCCAAAGACCCTCGAGTTCGATTATACTCAATTTCGAGGGCACAT
66 TAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAACTTCGAGGGCACAT
* * *
649973 CATTTACGACATAACTCAAGGCTAGAAGGGTTATCTGTCAAC-AAAGACCTTCGAGTTCTACTTC
131 CATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGACTAC
650037 ACTCAGCTCAAAGGCACTATCATTTGCAACATA
196 ACTCAGCTCAAAGGCA-TATCATTTGCAACATA
650070 GTTCAAGACA
Statistics
Matches: 205, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
248 34 0.17
249 171 0.83
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (249 bp):
TGCCAACCAAAGACCTTCAAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAACATAACT
TAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAACTTCGAGGGCACAT
CATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGACTAC
ACTCAGCTCAAAGGCATATCATTTGCAACATAACTTATGTCGAGAAGGGTTATC
Found at i:650468 original size:5 final size:5
Alignment explanation
Indices: 650458--650495 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
650448 AAAAACATTT
650458 TATTA TATTA TATTA TA-TA TA-TA TATATA TATTA TATT
1 TATTA TATTA TATTA TATTA TATTA TAT-TA TATTA TATT
650496 TTTATTTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 8 0.26
5 18 0.58
6 5 0.16
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TATTA
Found at i:650601 original size:33 final size:33
Alignment explanation
Indices: 650559--650629 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
650549 TTCAGAAAAT
650559 AAACCAACGTATTTGAGTCCTATTGAAACACTA
1 AAACCAACGTATTTGAGTCCTATTGAAACACTA
**
650592 AAACCAACGTATTTGAGTTTTATTGAAACACTA
1 AAACCAACGTATTTGAGTCCTATTGAAACACTA
650625 AAACC
1 AAACC
650630 GAAGCATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.28
Consensus pattern (33 bp):
AAACCAACGTATTTGAGTCCTATTGAAACACTA
Found at i:651070 original size:24 final size:24
Alignment explanation
Indices: 651021--651070 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
651011 ATATATATAT
* *
651021 TTATTTATTTATTTTTTATTAATA
1 TTATTTATTAATATTTTATTAATA
*
651045 TTATTATATTAATATTTT-TTATTA
1 TTATT-TATTAATATTTTATTAATA
651069 TT
1 TT
651071 CTTTTCTCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (24 bp):
TTATTTATTAATATTTTATTAATA
Found at i:653361 original size:20 final size:20
Alignment explanation
Indices: 653336--653397 Score: 69
Period size: 18 Copynumber: 3.3 Consensus size: 20
653326 AACAACAATT
653336 TAAAACTACTGAACAACCAG
1 TAAAACTACTGAACAACCAG
* **
653356 TAAAAC-A-TCAACAA--TT
1 TAAAACTACTGAACAACCAG
653372 TAAAACTACTGAACAACCAG
1 TAAAACTACTGAACAACCAG
653392 TAAAAC
1 TAAAAC
653398 ATCAAAGAAC
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
16 6 0.19
17 1 0.03
18 12 0.38
19 1 0.03
20 12 0.38
ACGTcount: A:0.53, C:0.23, G:0.06, T:0.18
Consensus pattern (20 bp):
TAAAACTACTGAACAACCAG
Found at i:653369 original size:36 final size:36
Alignment explanation
Indices: 653328--653402 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
653318 CCTACATAAA
653328 CAACAATTTAAAACTACTGAACAACCAGTAAAACAT
1 CAACAATTTAAAACTACTGAACAACCAGTAAAACAT
653364 CAACAATTTAAAACTACTGAACAACCAGTAAAACAT
1 CAACAATTTAAAACTACTGAACAACCAGTAAAACAT
653400 CAA
1 CAA
653403 AGAACAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.53, C:0.23, G:0.05, T:0.19
Consensus pattern (36 bp):
CAACAATTTAAAACTACTGAACAACCAGTAAAACAT
Found at i:664033 original size:18 final size:18
Alignment explanation
Indices: 664007--664041 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
663997 TAAAATTTTA
* *
664007 TAAATTTATGTATATTAT
1 TAAAATTATATATATTAT
664025 TAAAATTATATATATTA
1 TAAAATTATATATATTA
664042 AAATTCACTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
TAAAATTATATATATTAT
Found at i:664042 original size:15 final size:14
Alignment explanation
Indices: 664017--664046 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
664007 TAAATTTATG
664017 TATATTATTAAAAT
1 TATATTATTAAAAT
664031 TATATATATTAAAAT
1 TATAT-TATTAAAAT
664046 T
1 T
664047 CACTCTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TATATTATTAAAAT
Found at i:671493 original size:18 final size:16
Alignment explanation
Indices: 671483--671534 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
671473 TCTTAATATT
671483 AAAAATTATCTAAATA
1 AAAAATTATCTAAATA
* *
671499 AAAAATTA-ATAACT-
1 AAAAATTATCTAAATA
* *
671513 AAAACTTTTCTAAATA
1 AAAAATTATCTAAATA
671529 AAAAAT
1 AAAAAT
671535 AATCATATAT
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
14 6 0.22
15 8 0.30
16 13 0.48
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (16 bp):
AAAAATTATCTAAATA
Found at i:671500 original size:15 final size:15
Alignment explanation
Indices: 671482--671532 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
671472 ATCTTAATAT
671482 TAAAAATTATCTAAA
1 TAAAAATTATCTAAA
* *
671497 TAAAAAATTA-ATAAC
1 T-AAAAATTATCTAAA
* *
671512 TAAAACTTTTCTAAA
1 TAAAAATTATCTAAA
671527 TAAAAA
1 TAAAAA
671533 ATAATCATAT
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
14 6 0.22
15 13 0.48
16 8 0.30
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (15 bp):
TAAAAATTATCTAAA
Found at i:672246 original size:22 final size:24
Alignment explanation
Indices: 672176--672247 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 24
672166 TAAAAATTAC
672176 AATAATTATAATTTACACATTTAATCT
1 AATAATTATAATTT--A-ATTTAATCT
* *
672203 CAATATTTATATATTTTA-TTAAT-T
1 -AATAATTATA-ATTTAATTTAATCT
672227 -ATAATTATAATTTAATTTAAT
1 AATAATTATAATTTAATTTAAT
672248 AAATTTAATG
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
21 5 0.13
22 13 0.34
24 1 0.03
25 5 0.13
26 1 0.03
28 9 0.24
29 4 0.11
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (24 bp):
AATAATTATAATTTAATTTAATCT
Found at i:672627 original size:41 final size:41
Alignment explanation
Indices: 672548--672628 Score: 101
Period size: 41 Copynumber: 2.0 Consensus size: 41
672538 AAAAAATGCC
* * *
672548 GCTAAAGGTAATGATATTTAGCGGTTTTTTTAATAAACGAT
1 GCTAAAGGTAATAATATTTAGCGGATTTTTTAACAAACGAT
* *
672589 GCTAAAGGTTATAATATTTAGCGGCATTTTTT-CCAAACGA
1 GCTAAAGGTAATAATATTTAGCGG-ATTTTTTAACAAACGA
672629 CACTATTTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 28 0.82
42 6 0.18
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (41 bp):
GCTAAAGGTAATAATATTTAGCGGATTTTTTAACAAACGAT
Found at i:673638 original size:3 final size:3
Alignment explanation
Indices: 673624--673659 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
673614 AGTTAAAAAA
673624 TAT TAT TAAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TA
673660 AGTGTGTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:674837 original size:2 final size:2
Alignment explanation
Indices: 674830--674863 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
674820 TTCTTTGTTC
674830 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
674864 TTAATGTGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:674992 original size:2 final size:2
Alignment explanation
Indices: 674985--675019 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
674975 TTGTTAAACG
674985 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
675020 TTATTTATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:675068 original size:50 final size:49
Alignment explanation
Indices: 675010--675145 Score: 191
Period size: 50 Copynumber: 2.7 Consensus size: 49
675000 ATATATATAT
* * *
675010 ATATATATATTTATTTATTTAATGTGTCTTGGAAACTGATTTTTTTGTTC
1 ATATATATATATATTTGTTTAATGTGTCTTGGAAACTGA-TTCTTTGTTC
**
675060 ATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTCTTTGTTC
1 ATATATATATATATTTGTTTAATGTGTCTTGGAAACTGATTCTTTGTTC
675109 ATATACATATATATATTTGTTTAATGTGTCTTAGGAA
1 ATAT--ATATATATATTTGTTTAATGTGTCTT-GGAA
675146 GAATAGCCAT
Statistics
Matches: 76, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
49 13 0.17
50 35 0.46
51 24 0.32
52 4 0.05
ACGTcount: A:0.29, C:0.07, G:0.12, T:0.51
Consensus pattern (49 bp):
ATATATATATATATTTGTTTAATGTGTCTTGGAAACTGATTCTTTGTTC
Found at i:675258 original size:50 final size:51
Alignment explanation
Indices: 675199--675311 Score: 174
Period size: 50 Copynumber: 2.2 Consensus size: 51
675189 TTTGTTAAAC
*
675199 ATATATATATTTTTATTTAATGTGTCTTGGAAACTGATTTTTTTTCAT-AT
1 ATATATATATTTATATTTAATGTGTCTTGGAAACTGATTTTTTTTCATCAT
* * **
675249 ATATATATATATATATTTAATGTGTCTTGGAAATTGATTTTTTTTGTTCAT
1 ATATATATATTTATATTTAATGTGTCTTGGAAACTGATTTTTTTTCATCAT
675300 ATATATATATTT
1 ATATATATATTT
675312 GTTTAACATG
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
50 43 0.77
51 13 0.23
ACGTcount: A:0.30, C:0.04, G:0.10, T:0.56
Consensus pattern (51 bp):
ATATATATATTTATATTTAATGTGTCTTGGAAACTGATTTTTTTTCATCAT
Found at i:675379 original size:2 final size:2
Alignment explanation
Indices: 675372--675430 Score: 97
Period size: 2 Copynumber: 31.0 Consensus size: 2
675362 GCTTAGCTGG
675372 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
675414 A- AT AT -T AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
675431 TTAATTAGCC
Statistics
Matches: 54, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
1 3 0.06
2 51 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:675390 original size:185 final size:185
Alignment explanation
Indices: 674998--675393 Score: 534
Period size: 185 Copynumber: 2.1 Consensus size: 185
674988 ATATATATAT
674998 ATATATATATATATATATATATTTATTTATTTAATGTGTCTTGGAAACTGATTTTTTTGTTCATA
1 ATATATATATATATATATATA-TTATTTATTTAATGTGTCTTGGAAACTGATTTTTTTGTTCATA
*
675063 TATATATATATTTGTTTAACATGTCTTGGAAACTGATTCTTTGTTCATATACATATATATATTTG
65 TATATATATATTTATTTAACATGTCTTGGAAACTGATTCTTTGTTCA-ATA-ATATATATATTTG
** *
675128 TTTAATGTGTCTTAGGAAGAATAGCCATTATTTATTTGTTTAACATATAGCTTAGTTG
128 TTTAACATGTCTTAGGAAGAATAGCCATTATTTATTTGTTTAACATATAGCTTAGTGG
* * * *
675186 ATATTTGTTAAACATATATATATT-TTTATTTAATGTGTCTTGGAAACTGA-TTTTTT-TTCATA
1 ATATAT-ATATATATATATATATTATTTATTTAATGTGTCTTGGAAACTGATTTTTTTGTTCATA
** * *
675248 TATATATATATATATATTTAATGTGTCTTGGAAATTGATTTTTTTTGTTC-AT-ATATATATATT
65 TATATATATAT-T-TATTTAACATGTCTTGGAAACTGA--TTCTTTGTTCAATAATATATATATT
* *
675311 TGTTTAACATGTCTTAGGAAGAATAGGCA-TATTTTATTTGTTTAACGTATAGCTTAGCTGG
126 TGTTTAACATGTCTTAGGAAGAATAGCCATTA-TTTATTTGTTTAACATATAGCTTAG-TGG
675372 ATATATATATATATATATATAT
1 ATATATATATATATATATATAT
675394 ATATATATAT
Statistics
Matches: 183, Mismatches: 18, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
184 2 0.01
185 91 0.50
186 14 0.08
187 48 0.26
188 7 0.04
189 21 0.11
ACGTcount: A:0.32, C:0.07, G:0.12, T:0.50
Consensus pattern (185 bp):
ATATATATATATATATATATATTATTTATTTAATGTGTCTTGGAAACTGATTTTTTTGTTCATAT
ATATATATATTTATTTAACATGTCTTGGAAACTGATTCTTTGTTCAATAATATATATATTTGTTT
AACATGTCTTAGGAAGAATAGCCATTATTTATTTGTTTAACATATAGCTTAGTGG
Found at i:675537 original size:24 final size:24
Alignment explanation
Indices: 675510--675555 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
675500 ATATTCTTGA
675510 TATCATTTATTTAATAAGTATAGT
1 TATCATTTATTTAATAAGTATAGT
675534 TATCATTTATTTAATAAGTATA
1 TATCATTTATTTAATAAGTATA
675556 ATGTTCCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (24 bp):
TATCATTTATTTAATAAGTATAGT
Found at i:687303 original size:15 final size:14
Alignment explanation
Indices: 687274--687363 Score: 71
Period size: 15 Copynumber: 6.4 Consensus size: 14
687264 CTTGAAGAAA
*
687274 AAAAAAGGAACAAAT
1 AAAAAATGAA-AAAT
687289 AAAAAGATGAAAAAT
1 AAAAA-ATGAAAAAT
687304 GAAAAAATG-AAAA-
1 -AAAAAATGAAAAAT
*
687317 AGAAAA--AAAAAT
1 AAAAAATGAAAAAT
* *
687329 GAAAAATGAAAAAA
1 AAAAAATGAAAAAT
687343 AAAGAAATGAAAAAAT
1 AAA-AAATG-AAAAAT
687359 AAAAA
1 AAAAA
687364 GAGAAAAAGG
Statistics
Matches: 60, Mismatches: 7, Indels: 16
0.72 0.08 0.19
Matches are distributed among these distances:
11 4 0.07
12 9 0.15
14 11 0.18
15 19 0.32
16 17 0.28
ACGTcount: A:0.78, C:0.01, G:0.12, T:0.09
Consensus pattern (14 bp):
AAAAAATGAAAAAT
Found at i:687351 original size:47 final size:47
Alignment explanation
Indices: 687268--687371 Score: 133
Period size: 48 Copynumber: 2.2 Consensus size: 47
687258 ACTATGCTTG
*
687268 AAGAAAAAAAAAGGAACAAATAAAAAGATGAAAAATGAAAAAATGAAA
1 AAGAAAAAAAAAGGAACAAATAAAAAGATAAAAAATGAAAAAAT-AAA
*
687316 AAGAAAAAAAAATGAA-AAATGAAAAA-A-AAAGAAATGAAAAAATAAA
1 AAGAAAAAAAAAGGAACAAAT-AAAAAGATAAA-AAATGAAAAAATAAA
*
687362 AAGAGAAAAA
1 AAGAAAAAAA
687372 GGAGGGTTTG
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
46 14 0.27
47 17 0.33
48 20 0.39
ACGTcount: A:0.78, C:0.01, G:0.13, T:0.08
Consensus pattern (47 bp):
AAGAAAAAAAAAGGAACAAATAAAAAGATAAAAAATGAAAAAATAAA
Found at i:687362 original size:17 final size:17
Alignment explanation
Indices: 687300--687362 Score: 57
Period size: 17 Copynumber: 3.9 Consensus size: 17
687290 AAAAGATGAA
687300 AAATGAAAAAATGAAAAAG
1 AAATGAAAAAAT--AAAAG
*
687319 AAA--AAAAAAT-GAA-
1 AAATGAAAAAATAAAAG
687332 AAATG-AAAAA-AAAAG
1 AAATGAAAAAATAAAAG
687347 AAATGAAAAAATAAAA
1 AAATGAAAAAATAAAA
687363 AGAGAAAAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
13 3 0.08
14 9 0.25
15 5 0.14
16 5 0.14
17 11 0.31
19 3 0.08
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.10
Consensus pattern (17 bp):
AAATGAAAAAATAAAAG
Found at i:687362 original size:28 final size:27
Alignment explanation
Indices: 687313--687371 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 27
687303 TGAAAAAATG
*
687313 AAAAAGAAAAAAAAATGAAAAATGAAAA
1 AAAAAGAAAAAAAAAT-AAAAAAGAAAA
687341 AAAAAGAAATGAAAAAATAAAAAGAGAAAA
1 AAAAAGAAA--AAAAAATAAAAA-AGAAAA
687371 A
1 A
687372 GGAGGGTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 9 0.33
29 5 0.19
30 13 0.48
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.07
Consensus pattern (27 bp):
AAAAAGAAAAAAAAATAAAAAAGAAAA
Found at i:688483 original size:136 final size:136
Alignment explanation
Indices: 688239--688717 Score: 583
Period size: 136 Copynumber: 3.6 Consensus size: 136
688229 GGAGGTGAAC
*
688239 CAACATTTCCAAT-AGAGAGTTCATAATGAGAAGAACTCTTCCGACAGAGGGAGAAGAAGTTCAT
1 CAACATTTCCAATGA-AGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCAT
* * *** *
688303 AATGAGAAGATCTT-TTATGACCTATCACTCGATTCACGGCATTTCGAATCAGTGATGTCTCGCT
65 AATGAGAAGAGCTTGTT-CGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACACCTCACT
688367 TGAGGGAT
129 TGAGGGAT
*
688375 CAACATTTCCAGTGAAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATA
1 CAACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATA
* * *
688440 ATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACAGCATTTCAAATTAGTGACACCTCACTTG
66 ATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACACCTCACTTG
688505 AGGGATT
131 AGGGA-T
* * * * *
688512 GAA-ATTTTCAATTG-AGAGTTCATAAT---AAG-A-TCATCTGACAAAGGAAGAAGAAGTTCAT
1 CAACATTTCCAA-TGAAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCAT
* * *
688570 AATGAGAAGAGCTTGTTTGACCTATCACTCGATTTACGGTATTTCGAATCAGTGACACCTCACTT
65 AATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACACCTCACTT
*
688635 GGGGGAT
130 GAGGGAT
** * * *
688642 TGACATTT-CAATTAAGAGTTCATAATGAGAAGAACTCGTCCTA-A-A-GGAG-A-AAGTTCATA
1 CAACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATA
*
688701 ATGAGAAGAACTTGTTC
66 ATGAGAAGAGCTTGTTC
688718 CTTTCAAGTC
Statistics
Matches: 299, Mismatches: 33, Indels: 28
0.83 0.09 0.08
Matches are distributed among these distances:
129 1 0.00
130 41 0.14
131 94 0.31
132 4 0.01
133 7 0.02
134 2 0.01
135 5 0.02
136 137 0.46
137 8 0.03
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.27
Consensus pattern (136 bp):
CAACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATA
ATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACACCTCACTTG
AGGGAT
Found at i:688971 original size:3 final size:3
Alignment explanation
Indices: 688956--688998 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
688946 AGTTAAAAAA
*
688956 TAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
688999 AGTGTGTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 1 0.03
3 36 0.97
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:690174 original size:2 final size:2
Alignment explanation
Indices: 690167--690194 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
690157 TTCTTTGTTC
690167 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
690195 TTAATGTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:690373 original size:48 final size:47
Alignment explanation
Indices: 690316--690444 Score: 177
Period size: 48 Copynumber: 2.7 Consensus size: 47
690306 TGTTAAACGT
* *
690316 ATATATATATATTTATTTAATGTGTCTTGGAAACTGATTTTTTTGTTC
1 ATATATATATATTTGTTTAATGTGTCTTGGAAACTGA-TTCTTTGTTC
**
690364 ATATATATATATTTGTTTAACATGTCTTGGAAACTGATTCTTTGTTC
1 ATATATATATATTTGTTTAATGTGTCTTGGAAACTGATTCTTTGTTC
* *
690411 ATATACATATATATTGTTTAATGTGCCTTAGGAA
1 ATATATATATAT-TTGTTTAATGTGTCTT-GGAA
690445 GAATAGCCAT
Statistics
Matches: 71, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
47 20 0.28
48 47 0.66
49 4 0.06
ACGTcount: A:0.29, C:0.09, G:0.13, T:0.49
Consensus pattern (47 bp):
ATATATATATATTTGTTTAATGTGTCTTGGAAACTGATTCTTTGTTC
Found at i:690392 original size:185 final size:184
Alignment explanation
Indices: 690179--690563 Score: 680
Period size: 185 Copynumber: 2.1 Consensus size: 184
690169 ATATATATAT
**
690179 ATATATATATATATATTTAATGTGTCTTGGAAACTGATTCTTTGTTCATATACATATATATTGTT
1 ATATATATATATATATTTAACATGTCTTGGAAACTGATTCTTTGTTCATATACATATATATTGTT
* *
690244 TAACGTGTCTTAGGAAGAATAACCATTGTTTATTTGTTTAACATATAGCTTAGTTGGATATTTGT
66 TAACGTGCCTTAGGAAGAATAACCATTATTTATTTGTTTAACATATAGCTTAGTTGGATATTTGT
690309 TAAACGTATATATATATATTTATTTAATGTGTCTTGGAAACTGATTTTTTTGTTC
131 TAAACGTATATATATATATTTATTTAATGTGTCTTGGAAACTGA-TTTTTTGTTC
* *
690364 ATATATATATATTTGTTTAACATGTCTTGGAAACTGATTCTTTGTTCATATACATATATATTGTT
1 ATATATATATATATATTTAACATGTCTTGGAAACTGATTCTTTGTTCATATACATATATATTGTT
* *
690429 TAATGTGCCTTAGGAAGAATAGCCATTATTTATTTGTTTAACATATAGCTTAGTTGGATATTTGT
66 TAACGTGCCTTAGGAAGAATAACCATTATTTATTTGTTTAACATATAGCTTAGTTGGATATTTGT
*
690494 TAAACGTATATATATATTTTTATTTAATGTGTCTTGGAAACTGATTTTTTGTTC
131 TAAACGTATATATATATATTTATTTAATGTGTCTTGGAAACTGATTTTTTGTTC
690548 ATATATATATATATAT
1 ATATATATATATATAT
690564 ATATATTATT
Statistics
Matches: 189, Mismatches: 11, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
184 24 0.13
185 165 0.87
ACGTcount: A:0.31, C:0.08, G:0.14, T:0.48
Consensus pattern (184 bp):
ATATATATATATATATTTAACATGTCTTGGAAACTGATTCTTTGTTCATATACATATATATTGTT
TAACGTGCCTTAGGAAGAATAACCATTATTTATTTGTTTAACATATAGCTTAGTTGGATATTTGT
TAAACGTATATATATATATTTATTTAATGTGTCTTGGAAACTGATTTTTTGTTC
Found at i:690588 original size:60 final size:60
Alignment explanation
Indices: 690500--690627 Score: 231
Period size: 62 Copynumber: 2.1 Consensus size: 60
690490 TTGTTAAACG
690500 TATATATATATTTTTATTTAATGTGTCTTGGAAACTGA-TTTTTTGTTCATATATATATA
1 TATATATATATTTTTATTTAATGTGTCTTGGAAACTGATTTTTTTGTTCATATATATATA
690559 TATATATATATTATTTATTTAATGTGTCTTGGAAACTGATTTTTTTTGTTCATATATATATA
1 TATATATATATT-TTTATTTAATGTGTCTTGGAAACTGA-TTTTTTTGTTCATATATATATA
690621 TATATAT
1 TATATAT
690628 TTGTTTAACA
Statistics
Matches: 66, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
59 12 0.18
60 26 0.39
62 28 0.42
ACGTcount: A:0.31, C:0.05, G:0.09, T:0.55
Consensus pattern (60 bp):
TATATATATATTTTTATTTAATGTGTCTTGGAAACTGATTTTTTTGTTCATATATATATA
Found at i:690697 original size:2 final size:2
Alignment explanation
Indices: 690690--690727 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
690680 GCTTAGCTGG
690690 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
690728 TTAAATTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:690915 original size:28 final size:24
Alignment explanation
Indices: 690829--690898 Score: 140
Period size: 24 Copynumber: 2.9 Consensus size: 24
690819 ATATTCTTTA
690829 TATCATTTATTTAATAAGTATAGT
1 TATCATTTATTTAATAAGTATAGT
690853 TATCATTTATTTAATAAGTATAGT
1 TATCATTTATTTAATAAGTATAGT
690877 TATCATTTATTTAATAAGTATA
1 TATCATTTATTTAATAAGTATA
690899 ATGTTCCATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (24 bp):
TATCATTTATTTAATAAGTATAGT
Found at i:699211 original size:2 final size:2
Alignment explanation
Indices: 699204--699235 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
699194 AGTGTATGTG
699204 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
699236 TATTGCATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:699716 original size:18 final size:18
Alignment explanation
Indices: 699693--699727 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
699683 TATGTGATAT
699693 GTGGTCCTTT-GGGACATA
1 GTGGT-CTTTCGGGACATA
699711 GTGGTCTTTCGGGACAT
1 GTGGTCTTTCGGGACAT
699728 TTCTACGCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.14, C:0.17, G:0.34, T:0.34
Consensus pattern (18 bp):
GTGGTCTTTCGGGACATA
Found at i:701719 original size:55 final size:51
Alignment explanation
Indices: 701653--701780 Score: 163
Period size: 51 Copynumber: 2.5 Consensus size: 51
701643 CTGTGATTAT
*
701653 CAAGAACAGACACATACGCACGAATAACTGCATACTTAGAAAAGAAAAGAAAAAA
1 CAAGAACAGACACATAC-CACGAATAACTACATACTTAGAAAAG--AA-AAAAAA
*
701708 CAAGAACAGACA-A-A-TACGAATAACTACATACTTAGAAAAGAAAAAAAA
1 CAAGAACAGACACATACCACGAATAACTACATACTTAGAAAAGAAAAAAAA
*
701756 CAAGAATAGACACATACACACGAAT
1 CAAGAACAGACACATAC-CACGAAT
701781 TGCGGTGATT
Statistics
Matches: 65, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
48 17 0.26
49 3 0.05
50 1 0.02
51 24 0.37
52 6 0.09
53 1 0.02
54 1 0.02
55 12 0.18
ACGTcount: A:0.58, C:0.18, G:0.12, T:0.12
Consensus pattern (51 bp):
CAAGAACAGACACATACCACGAATAACTACATACTTAGAAAAGAAAAAAAA
Found at i:705781 original size:14 final size:14
Alignment explanation
Indices: 705745--705781 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
705735 AGTTTAAGAA
*
705745 ATTTGAGTCGAATT
1 ATTTGAGTTGAATT
*
705759 ATTTGAGTTGAGTT
1 ATTTGAGTTGAATT
705773 ATTTGAGTT
1 ATTTGAGTT
705782 TCTATGCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.24, C:0.03, G:0.24, T:0.49
Consensus pattern (14 bp):
ATTTGAGTTGAATT
Found at i:707167 original size:26 final size:26
Alignment explanation
Indices: 707103--707168 Score: 64
Period size: 26 Copynumber: 2.6 Consensus size: 26
707093 TGAGACATTC
* *
707103 AAAA-TTATCATTATATATTTTATTT
1 AAAATTTATAATTATATATATTATTT
* * *
707128 TAAATTTATTATTATATATATTGTTT
1 AAAATTTATAATTATATATATTATTT
707154 AAAACTTT-TAATTAT
1 AAAA-TTTATAATTAT
707169 TTTTCTCTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
25 3 0.09
26 27 0.82
27 3 0.09
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (26 bp):
AAAATTTATAATTATATATATTATTT
Done.