Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001174.1 Hibiscus syriacus cultivar Beakdansim tig00002338_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: 2182627
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 11
Found at i:262895 original size:20 final size:20
Alignment explanation
Indices: 262872--262915 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
262862 CGATAGTCAT
262872 TTTCGCGTTGCGATTATAAG
1 TTTCGCGTTGCGATTATAAG
* *
262892 TTTCGTGTTGCGATTTTAAG
1 TTTCGCGTTGCGATTATAAG
262912 TTTC
1 TTTC
262916 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.14, G:0.23, T:0.48
Consensus pattern (20 bp):
TTTCGCGTTGCGATTATAAG
Found at i:263468 original size:21 final size:21
Alignment explanation
Indices: 263444--263513 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
263434 ATATCATCCC
263444 TCAAGAGTCCCCTCCCACCGT
1 TCAAGAGTCCCCTCCCACCGT
* ** *
263465 TCAAGAGGCCCCTGTCATCGT
1 TCAAGAGTCCCCTCCCACCGT
* * *
263486 TGAAGGAGT-CACTCCCACCAT
1 TCAA-GAGTCCCCTCCCACCGT
263507 TCAAGAG
1 TCAAGAG
263514 CCTGATTCAC
Statistics
Matches: 36, Mismatches: 12, Indels: 3
0.71 0.24 0.06
Matches are distributed among these distances:
20 3 0.08
21 30 0.83
22 3 0.08
ACGTcount: A:0.24, C:0.36, G:0.20, T:0.20
Consensus pattern (21 bp):
TCAAGAGTCCCCTCCCACCGT
Found at i:263483 original size:42 final size:42
Alignment explanation
Indices: 263391--263483 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
263381 GCCCGACTCA
** * * *
263391 CCTGTCATCGTTCAAGAGGCCTCTCCTATCGTTCAAGAGGCC
1 CCTGTCATCCCTCAAGAGGCCCCTCCCACCGTTCAAGAGGCC
* * *
263433 CATATCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTGTCATCCCTCAAGAGGCCCCTCCCACCGTTCAAGAGGCC
263475 CCTGTCATC
1 CCTGTCATC
263484 GTTGAAGGAG
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.20, C:0.39, G:0.17, T:0.24
Consensus pattern (42 bp):
CCTGTCATCCCTCAAGAGGCCCCTCCCACCGTTCAAGAGGCC
Found at i:263501 original size:42 final size:42
Alignment explanation
Indices: 263402--263513 Score: 109
Period size: 42 Copynumber: 2.7 Consensus size: 42
263392 CTGTCATCGT
* * * *
263402 TCAAGAGGCCTCTCCTATCGTTCAAGAGGCCCATATCATCCC
1 TCAAGAGTCCACTCCCACCGTTCAAGAGGCCCATATCATCCC
* * * **
263444 TCAAGAGTCCCCTCCCACCGTTCAAGAGGCCCCTGTCATCGT
1 TCAAGAGTCCACTCCCACCGTTCAAGAGGCCCATATCATCCC
* *
263486 TGAAGGAGT-CACTCCCACCATTCAAGAG
1 TCAA-GAGTCCACTCCCACCGTTCAAGAG
263514 CCTGATTCAC
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
42 54 0.93
43 4 0.07
ACGTcount: A:0.24, C:0.36, G:0.19, T:0.21
Consensus pattern (42 bp):
TCAAGAGTCCACTCCCACCGTTCAAGAGGCCCATATCATCCC
Found at i:264917 original size:14 final size:14
Alignment explanation
Indices: 264898--264934 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
264888 GCTTGTTTAA
264898 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
264912 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
264926 TTGATTTGT
1 TTGATTTGT
264935 TTAATTGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:265079 original size:20 final size:20
Alignment explanation
Indices: 265070--265107 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
265060 CGCTAAACTT
*
265070 AAAATCGCAATGCGAAAGCC
1 AAAATCGCAACGCGAAAGCC
265090 AAAATCGCAACGCGAAAG
1 AAAATCGCAACGCGAAAG
265108 TCAATTCGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.24, G:0.21, T:0.08
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAGCC
Found at i:265139 original size:20 final size:20
Alignment explanation
Indices: 265101--265246 Score: 153
Period size: 20 Copynumber: 7.7 Consensus size: 20
265091 AAATCGCAAC
*
265101 GCGAAAGTC-AATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
* *
265120 GCGATAATCAAATTCACGTT
1 GCGATAGTCAAATTCGCGTT
*
265140 GCGATAGTCAAATTCGTGTT
1 GCGATAGTCAAATTCGCGTT
265160 GCGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
*
265180 GCGAT--T----TTTGCGTT
1 GCGATAGTCAAATTCGCGTT
* *
265194 GCGGTAGTCAAATTCGTGTT
1 GCGATAGTCAAATTCGCGTT
*
265214 ACGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
* *
265234 GTGATATTCAAAT
1 GCGATAGTCAAAT
265247 GAATGTGTAA
Statistics
Matches: 103, Mismatches: 17, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
14 11 0.11
16 1 0.01
18 1 0.01
19 7 0.07
20 83 0.81
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (20 bp):
GCGATAGTCAAATTCGCGTT
Found at i:265440 original size:18 final size:18
Alignment explanation
Indices: 265417--265451 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
265407 AAGCCGGTTG
*
265417 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
265435 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
265452 GCCTTTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:268599 original size:20 final size:20
Alignment explanation
Indices: 268574--268740 Score: 122
Period size: 20 Copynumber: 8.2 Consensus size: 20
268564 GAAATTCAGT
268574 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
*
268594 GTTGCGATGGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
* * ** *
268614 GTTGTGATTTTGT-ATTATTGC
1 GTTGCGA--TAGTCAGAATCGC
268635 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
* ** * **
268655 ATTGCGATTTTTTATTATCGC
1 GTTGCGA-TAGTCAGAATCGC
*
268676 GTTACGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
* * **
268696 TTTGCGATTTTGT-ATTATCGC
1 GTTGCGA--TAGTCAGAATCGC
268717 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
268737 GTTG
1 GTTG
268741 TGATTTTCTA
Statistics
Matches: 107, Mismatches: 33, Indels: 14
0.69 0.21 0.09
Matches are distributed among these distances:
19 6 0.06
20 59 0.55
21 36 0.34
22 6 0.06
ACGTcount: A:0.21, C:0.16, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:268721 original size:21 final size:21
Alignment explanation
Indices: 268609--268724 Score: 78
Period size: 21 Copynumber: 5.6 Consensus size: 21
268599 GATGGTCAGA
*
268609 ATCGCGTTGTGATTTTGTATT
1 ATCGCGTTGCGATTTTGTATT
* * **
268630 ATTGCGTTGCGA--TAGTCAGA
1 ATCGCGTTGCGATTTTGT-ATT
* *
268650 ATCGCATTGCGATTTTTTATT
1 ATCGCGTTGCGATTTTGTATT
* * **
268671 ATCGCGTTACGA--TAGTCAGA
1 ATCGCGTTGCGATTTTGT-ATT
*
268691 ATCGCTTTGCGATTTTGTATT
1 ATCGCGTTGCGATTTTGTATT
268712 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
268725 AGTCAGAATC
Statistics
Matches: 66, Mismatches: 23, Indels: 12
0.65 0.23 0.12
Matches are distributed among these distances:
19 5 0.08
20 22 0.33
21 34 0.52
22 5 0.08
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.41
Consensus pattern (21 bp):
ATCGCGTTGCGATTTTGTATT
Found at i:268757 original size:41 final size:41
Alignment explanation
Indices: 268589--268747 Score: 246
Period size: 41 Copynumber: 3.9 Consensus size: 41
268579 GATAGTCAGA
* *
268589 ATCGCGTTGCGATGGTCAGAATCGCGTTGTGATTTTGTATT
1 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTTTGTATT
* * *
268630 ATTGCGTTGCGATAGTCAGAATCGCATTGCGATTTTTTATT
1 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTTTGTATT
* *
268671 ATCGCGTTACGATAGTCAGAATCGCTTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTTTGTATT
*
268712 ATCGCGTTGCGATAGTCAGAATCGCGTTGTGATTTT
1 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTTT
268748 CTAAAATCGC
Statistics
Matches: 106, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 106 1.00
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.39
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTTTGTATT
Found at i:268843 original size:20 final size:19
Alignment explanation
Indices: 268820--268865 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
268810 GGAAACTGAT
* *
268820 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
268840 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
268859 TTGCGAT
1 TTGCGAT
268866 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:268855 original size:19 final size:19
Alignment explanation
Indices: 268831--268867 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
268821 TGCGATACTG
*
268831 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
268850 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
268868 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:276602 original size:229 final size:227
Alignment explanation
Indices: 276197--276645 Score: 799
Period size: 229 Copynumber: 2.0 Consensus size: 227
276187 GTAAATTATC
* * *
276197 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
276262 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
276327 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
276392 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAACTTT-AAAAAAGTATA
*
276425 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
276490 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
* *
276555 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
276620 GAAACATAAATTACATAACTTTAAAA
195 GAAACATAAATTACATAACTTTAAAA
276646 GCAGTTTTAA
Statistics
Matches: 211, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
228 40 0.19
229 171 0.81
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.39
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:276734 original size:20 final size:19
Alignment explanation
Indices: 276711--276756 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
276701 CGATATACCA
276711 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
276731 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
276751 GGTAAA
1 GGTAAA
276757 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:276926 original size:17 final size:19
Alignment explanation
Indices: 276887--276929 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
276877 ATGTAAAAAT
276887 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
276907 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
276924 ATGATA
1 ATGATA
276930 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:279191 original size:21 final size:21
Alignment explanation
Indices: 279144--279208 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
279134 AAGACAATCA
* *
279144 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
279166 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
279186 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
279207 AG
1 AG
279209 GCATAAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:279284 original size:33 final size:33
Alignment explanation
Indices: 279242--279307 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
279232 AAATAGATGG
*
279242 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
279275 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
279308 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:281103 original size:19 final size:19
Alignment explanation
Indices: 281079--281127 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
281069 AATGTAGGGT
281079 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
281098 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
281117 TATTTTTGTAT
1 TAATTTTGTAT
281128 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:281992 original size:196 final size:197
Alignment explanation
Indices: 281242--282888 Score: 2818
Period size: 196 Copynumber: 8.5 Consensus size: 197
281232 GGCCAAAAGG
* *
281242 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTGA-GAGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
*
281306 TGTCGACACTAATATAGTTTGTGTCGATA-TTATTTCCAGAATGAATGGAAAACA-GGTGCACCC
66 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAAAACAGGGTGCA-CC
281369 ATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
130 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
281432 AAT
195 AAT
281435 ATGTAATTTTTCAATCTAACC-GTACAATTATACCGGTTTTTATGTGAGAATATGTCTAAATAAT
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGG-TTTTATGTGAGAATATGTCTAAATAAT
*
281499 GTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTTCAAGAATGAATGGAAAACAGGGTGCA
65 GTGTCGACACTAATATAGTTTGTGTCGATA--TTTTTTTCCAGAATGAATGGAAAACAGGGTGCA
*
281564 CCATAAAGTGTCGATCCATA-AT--AAAGTGTTGATCCCAAAA-CATCGAACCCAAAAGTATAAT
128 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
281625 GTAAT
193 GTAAT
281630 ATGTAATTTTTCAATCTAACC-GTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
281694 T-TCGACACT-ATATA-TTTGTG--GATA-TTTTTTCCAGAATGAATGGAAAACA-GGTGCACCC
66 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAAAACAGGGTGCA-CC
* *
281752 ATAAAGTGTCGATCCA-ATATATAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATATTGT
130 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
281816 AAT
195 AAT
281819 ATGTAA-TTTTCAATCT-ACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
*
281882 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCAAGAATGAATGGAAAACAGGGTGCACC
66 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATGGAAAACAGGGTGCA-C
281947 CATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCC-AAAGTAT-ATG
129 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
282009 TAAT
194 TAAT
*
282013 ATGTAATTTTTCAATCTAACCGGTACAATTATACTGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
282078 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGG-AAACAGGGTGCACC
66 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATGGAAAACAGGGTGCA-C
282142 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
129 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
282207 TAAT
194 TAAT
*
282211 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
*
282276 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCA
66 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCA
282341 TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
131 TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
282406 AT
196 AT
* *
282408 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGG-TTTATGAGAGAATATGTCTAAATAATA
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
*
282472 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCA
66 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCA
282537 TAAAGTGTCGAT-CATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
131 TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
282601 AT
196 AT
* *
282603 ATGTAATTTTTCAATCTAACTGGTACAATTATACCGGTTTTA--TGAG-AGATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
* *
282665 TGTCAACACTAATATAGTTTGTGTCGATA-TTTATTCCAGAATGAATGGAAAACAGGGTGCACCA
66 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCA
282729 TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
131 TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
282794 AT
196 AT
282796 ATGTAATTTTTCAATCTAACCGGTAC-ATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
*
282860 TGTCGACACTAATAGAGTTTGTGTCGATA
66 TGTCGACACTAATATAGTTTGTGTCGATA
282889 CTAATTTAAA
Statistics
Matches: 1392, Mismatches: 28, Indels: 66
0.94 0.02 0.04
Matches are distributed among these distances:
185 7 0.01
186 44 0.03
187 3 0.00
188 71 0.05
189 43 0.03
190 5 0.00
191 12 0.01
192 80 0.06
193 158 0.11
194 98 0.07
195 271 0.19
196 303 0.22
197 177 0.13
198 119 0.09
199 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (197 bp):
ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCA
TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
AT
Found at i:282361 original size:392 final size:393
Alignment explanation
Indices: 281242--282888 Score: 2830
Period size: 388 Copynumber: 4.2 Consensus size: 393
281232 GGCCAAAAGG
* *
281242 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTGA-GAGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
281306 TGTCGACACTAATATAGTTTGTGTCGATATTATTTCCAGAATGAATGGAAAACAGGTGCACCCAT
66 TGTCGACACTAATATAGTTTGTGTCGATATTATTTCCAGAATGAATGGAAAACAGGTGCACCCAT
281371 AAAGTGTCGATCC-ATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAAT
131 AAAGTGTCGATCCAATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAAT
*
281435 ATGTAATTTTTCAATCTAACC-GTACAATTATACCGGTTTTTATGTGAGAATATGTCTAAATAAT
196 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGG-TTTTATGAGAGAATATGTCTAAATAAT
*
281499 GTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTTCAAGAATGAATGGAAAACAGGGTGCA
260 GTGTCGACACTAATATAGTTTGTGTCGATA-TTTTATTTCAAGAATGAATGGAAAACAGGGTGCA
*
281564 CCATAAAGTGTCGATCCATA-AT--AAAGTGTTGATCCCAAAA-CATCGAACCCAAAAGTATAAT
324 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
281625 GTAAT
389 GTAAT
281630 ATGTAATTTTTCAATCTAACC-GTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
*
281694 T-TCGACACT-ATATA-TTTGTG--GATATTTTTTCCAGAATGAATGGAAAACAGGTGCACCCAT
66 TGTCGACACTAATATAGTTTGTGTCGATATTATTTCCAGAATGAATGGAAAACAGGTGCACCCAT
* *
281754 AAAGTGTCGATCCAATATATAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATATTGTAAT
131 AAAGTGTCGATCCAATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAAT
*
281819 ATGTAA-TTTTCAATCT-ACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
196 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATG
*
281882 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCAAGAATGAATGGAAAACAGGGTGCACC
261 TGTCGACACTAATATAGTTTGTGTCGATATTTTATTTCAAGAATGAATGGAAAACAGGGTGCA-C
281947 CATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCC-AAAGTAT-ATG
325 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
282009 TAAT
390 TAAT
*
282013 ATGTAATTTTTCAATCTAACCGGTACAATTATACTGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
*
282078 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGG-AAACAGGGTGCACC
66 TGTCGACACTAATATAGTTTGTGTCGATA--TTATTTCCAGAATGAATGGAAAACA-GGTGCACC
282142 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
128 CATAAAGTGTCGATCCA-ATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
282207 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
192 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
*
282272 AATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTATTTCCAGAATGAATGGAAAACAGGGTG
257 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTATTTCAAGAATGAATGGAAAACAGGGTG
282336 CACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
322 CACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
282401 ATGTAAT
387 ATGTAAT
* *
282408 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGG-TTTATGAGAGAATATGTCTAAATAATA
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
282472 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCA-CC
66 TGTCGACACTAATATAGTTTGTGTCGATA-TTATTTCCAGAATGAATGGAAAACA-GGTGCACCC
282536 ATAAAGTGTCGAT-CATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
129 ATAAAGTGTCGATCCA-ATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
*
282600 AATATGTAATTTTTCAATCTAACTGGTACAATTATACCGGTTTTATGAGAG---ATGTCTAAATA
193 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATA
* *
282662 ATGTGTCAACACTAATATAGTTTGTGTCGATA-TTTA-TTCCAGAATGAATGGAAAACAGGGTGC
258 ATGTGTCGACACTAATATAGTTTGTGTCGATATTTTATTTCAAGAATGAATGGAAAACAGGGTGC
282725 ACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
323 ACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
282790 TGTAAT
388 TGTAAT
282796 ATGTAATTTTTCAATCTAACCGGTAC-ATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
*
282860 TGTCGACACTAATAGAGTTTGTGTCGATA
66 TGTCGACACTAATATAGTTTGTGTCGATA
282889 CTAATTTAAA
Statistics
Matches: 1214, Mismatches: 21, Indels: 48
0.95 0.02 0.04
Matches are distributed among these distances:
381 34 0.03
382 80 0.07
383 107 0.09
384 122 0.10
385 24 0.02
386 10 0.01
387 43 0.04
388 220 0.18
389 50 0.04
390 5 0.00
391 44 0.04
392 179 0.15
393 105 0.09
394 148 0.12
395 43 0.04
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (393 bp):
ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
TGTCGACACTAATATAGTTTGTGTCGATATTATTTCCAGAATGAATGGAAAACAGGTGCACCCAT
AAAGTGTCGATCCAATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAAT
ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATG
TGTCGACACTAATATAGTTTGTGTCGATATTTTATTTCAAGAATGAATGGAAAACAGGGTGCACC
ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
AAT
Found at i:284340 original size:18 final size:18
Alignment explanation
Indices: 284319--284380 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
284309 AGCGGTCGCA
284319 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* * *
284337 GAAGATGACGATGATGAT
1 GAAGATGAAGCTGACGAT
* *
284355 GATGATGAAGCTGGCGAT
1 GAAGATGAAGCTGACGAT
284373 GAAGATGA
1 GAAGATGA
284381 CGATGATGAT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.37, C:0.08, G:0.35, T:0.19
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:284343 original size:6 final size:6
Alignment explanation
Indices: 284319--284392 Score: 58
Period size: 6 Copynumber: 12.3 Consensus size: 6
284309 AGCGGTCGCA
* * * * * *
284319 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GATGAT GAAGCT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
** * *
284367 GGCGAT GAAGAT GACGAT GATGAT GA
1 GAAGAT GAAGAT GAAGAT GAAGAT GA
284393 TGAAGATGAT
Statistics
Matches: 53, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.36, C:0.08, G:0.35, T:0.20
Consensus pattern (6 bp):
GAAGAT
Found at i:284354 original size:3 final size:3
Alignment explanation
Indices: 284334--284405 Score: 63
Period size: 3 Copynumber: 24.0 Consensus size: 3
284324 TGAAGCTGAC
* * * * ** * *
284334 GAT GAA GAT GAC GAT GAT GAT GAT GAT GAA GCT GGC GAT GAA GAT GAC
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
*
284382 GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT
284406 CCAAACAAGT
Statistics
Matches: 52, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.36, C:0.06, G:0.35, T:0.24
Consensus pattern (3 bp):
GAT
Found at i:284366 original size:36 final size:36
Alignment explanation
Indices: 284322--284395 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
284312 GGTCGCAGAA
284322 GATGAAGCTGACGATGAAGATGACGATGATGATGAT
1 GATGAAGCTGACGATGAAGATGACGATGATGATGAT
*
284358 GATGAAGCTGGCGATGAAGATGACGATGATGATGAT
1 GATGAAGCTGACGATGAAGATGACGATGATGATGAT
284394 GA
1 GA
284396 AGATGATGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.35, C:0.08, G:0.35, T:0.22
Consensus pattern (36 bp):
GATGAAGCTGACGATGAAGATGACGATGATGATGAT
Found at i:284405 original size:12 final size:12
Alignment explanation
Indices: 284322--284392 Score: 88
Period size: 12 Copynumber: 5.9 Consensus size: 12
284312 GGTCGCAGAA
*
284322 GATGAAGCTGAC
1 GATGAAGATGAC
284334 GATGAAGATGAC
1 GATGAAGATGAC
* *
284346 GATGATGATGAT
1 GATGAAGATGAC
* *
284358 GATGAAGCTGGC
1 GATGAAGATGAC
284370 GATGAAGATGAC
1 GATGAAGATGAC
*
284382 GATGATGATGA
1 GATGAAGATGA
284393 TGAAGATGAT
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 49 1.00
ACGTcount: A:0.35, C:0.08, G:0.35, T:0.21
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:284585 original size:87 final size:90
Alignment explanation
Indices: 284431--284607 Score: 333
Period size: 87 Copynumber: 2.0 Consensus size: 90
284421 GTGTCTGCAA
284431 CGCCGCCTTCAAGAAAACTTTTAATTTTTGATCTCAATGGTGTCCTTGCCTACATCCCAAGACTG
1 CGCCGCCTTCAAGAAAACTTTTAATTTTTGATCTCAATGGTGTCCTTGCCTACATCCCAAGACTG
284496 CCGGCAGGTTTTAATTCTATTCTTT
66 CCGGCAGGTTTTAATTCTATTCTTT
284521 CGCCG-CTTCAAGAAAAC-TTTAA-TTTTGATCTCAATGGTGTCCTTGCCTACATCCCAAGACTG
1 CGCCGCCTTCAAGAAAACTTTTAATTTTTGATCTCAATGGTGTCCTTGCCTACATCCCAAGACTG
284583 CCGGCAGGTTTTAATTCTATTCTTT
66 CCGGCAGGTTTTAATTCTATTCTTT
284608 TGTATCCATT
Statistics
Matches: 87, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
87 65 0.75
88 5 0.06
89 12 0.14
90 5 0.06
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (90 bp):
CGCCGCCTTCAAGAAAACTTTTAATTTTTGATCTCAATGGTGTCCTTGCCTACATCCCAAGACTG
CCGGCAGGTTTTAATTCTATTCTTT
Found at i:286490 original size:181 final size:182
Alignment explanation
Indices: 285950--286591 Score: 1128
Period size: 179 Copynumber: 3.6 Consensus size: 182
285940 TTATAATAAA
* * *
285950 ATAGGTAAATTTGCAATATAACCGG-ATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACC
1 ATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACC
286014 TATATCGACACTTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGA
66 TATATCGACAC-TTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGA
286079 TACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATAATTATAATGT
130 TACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATAATTATAATGT
286132 AATAGATAATTTTGTAATATAACCGGTATAAATATA-CGGTTTTATGCGCGAATAGGTCTACAAC
1 -ATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAAC
286196 CTATATCGACACTTTTTAATA---TGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGA
65 CTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGA
286258 TACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATAATTATAATGT
130 TACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATAATTATAATGT
*
286311 ATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTGTATGCGCGAATAGGTCTACAACC
1 ATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACC
286376 TATATCGACAC-TTTTAATATTGTGTCGGTACTTTATGTCC-TATTGGAAGAAAAATGTGTCGAT
66 TATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGAT
286439 ACGATTTAAAAAAAGTGTCGACATTTACACATCGGAACCCATAATTATAATG-
131 ACGATTT-AAAAAAGTGTCGACATTTACACATCGGAACCCATAATTATAATGT
*
286491 -TA-ATAA-TTTGTAATATAA-CGGTATAAATATACCGGTTTTATGCGCGAAAAGGTCTACAACC
1 ATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACC
286552 TATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTC
66 TATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTC
286592 TAAAATGTGT
Statistics
Matches: 446, Mismatches: 6, Indels: 20
0.94 0.01 0.04
Matches are distributed among these distances:
176 52 0.12
177 40 0.09
178 47 0.11
179 135 0.30
180 30 0.07
181 62 0.14
182 9 0.02
183 62 0.14
184 9 0.02
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.34
Consensus pattern (182 bp):
ATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACC
TATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGAT
ACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATAATTATAATGT
Found at i:289091 original size:25 final size:25
Alignment explanation
Indices: 289057--289114 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
289047 TTATCATTAA
289057 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
289082 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
289107 ATTTAGGT
1 ATTTAGGT
289115 TATATCATCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.43
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:289492 original size:23 final size:23
Alignment explanation
Indices: 289462--289524 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
289452 ATAGGTAAAC
289462 ATAT-ATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
289484 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
289507 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
289525 TGGTTATATT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
22 4 0.11
23 32 0.89
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:289531 original size:23 final size:23
Alignment explanation
Indices: 289462--289533 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
289452 ATAGGTAAAC
**
289462 ATAT-ATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
289484 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
289507 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
289530 ATAT
1 ATAT
289534 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
22 4 0.09
23 38 0.88
24 1 0.02
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:290683 original size:23 final size:23
Alignment explanation
Indices: 290656--290712 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
290646 AATATCTTTA
* *
290656 TCTTTATGGCACGCTTTCTTCC-G
1 TCTTTATGACACACTTTC-TCCTG
*
290679 TCTTTACGACACACTTTCTCCTG
1 TCTTTATGACACACTTTCTCCTG
290702 TCTTTATGACA
1 TCTTTATGACA
290713 TATTTTCTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 3 0.10
23 26 0.90
ACGTcount: A:0.16, C:0.30, G:0.12, T:0.42
Consensus pattern (23 bp):
TCTTTATGACACACTTTCTCCTG
Found at i:290750 original size:22 final size:23
Alignment explanation
Indices: 290700--290752 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
290690 CACTTTCTCC
*
290700 TGTC-TTTATGACATATTTTCTT
1 TGTCTTTTTTGACATATTTTCTT
*
290722 T-TATTTTTTGACATATTTT-TT
1 TGTCTTTTTTGACATATTTTCTT
290743 TGTCTTTTTT
1 TGTCTTTTTT
290753 ATTAGTCCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 4 0.15
22 22 0.85
ACGTcount: A:0.15, C:0.09, G:0.08, T:0.68
Consensus pattern (23 bp):
TGTCTTTTTTGACATATTTTCTT
Found at i:295407 original size:177 final size:177
Alignment explanation
Indices: 295123--295450 Score: 426
Period size: 177 Copynumber: 1.9 Consensus size: 177
295113 CGAAATGTCG
** * *
295123 TGAATCGAGCAAAGGTAATGCTAATCCCTCAAGTGAGGTGTCATTAATTCAAAATATCATGAATC
1 TGAATCGAGCAAAGCAAATGCTAATCCCTCAAGCGAGGCGTCATTAATTCAAAATATCATGAATC
** * * * *
295188 GAGCAAAGGAAATGTTAATCCCATAAGCGAGGTGTTGCTGATTCGAAATGCCGTGAATCGAGCAA
66 GAGCAAAGGAAATGTTAATCCCATAAGCGAGGCATCGCTGATTCAAAATGCCATGAATCAAGCAA
*
295253 AGGAAATATTAATCCCTCAAGCGAGACGTTACTGATTCGAAAGACCA
131 AGAAAATATTAATCCCTCAAGCGAGACGTTACTGATTCGAAAGACCA
* * * * *
295300 TGAATCGAGCAAAGCAAATGTTAATCCTTCAAGCGAGGCGTTGA-TGATTCAAAATATCGTGAAT
1 TGAATCGAGCAAAGCAAATGCTAATCCCTCAAGCGAGGCG-TCATTAATTCAAAATATCATGAAT
* * * * *
295364 CGATCAAAGGAAATGTTAATCCC-TCAAGTGAGGCATCGCTGATTCAAAATGGCATGAATTAAGT
65 CGAGCAAAGGAAATGTTAATCCCAT-AAGCGAGGCATCGCTGATTCAAAATGCCATGAATCAAGC
*
295428 AAAGAAAATGTTAATCCCTCAAG
129 AAAGAAAATATTAATCCCTCAAG
295451 TGAGGCATTG
Statistics
Matches: 127, Mismatches: 22, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
176 1 0.01
177 124 0.98
178 2 0.02
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.24
Consensus pattern (177 bp):
TGAATCGAGCAAAGCAAATGCTAATCCCTCAAGCGAGGCGTCATTAATTCAAAATATCATGAATC
GAGCAAAGGAAATGTTAATCCCATAAGCGAGGCATCGCTGATTCAAAATGCCATGAATCAAGCAA
AGAAAATATTAATCCCTCAAGCGAGACGTTACTGATTCGAAAGACCA
Found at i:295457 original size:59 final size:59
Alignment explanation
Indices: 295088--295474 Score: 384
Period size: 59 Copynumber: 6.6 Consensus size: 59
295078 GAAATTTTGG
* * * * *
295088 TCCCTCGAGTGAGGCGTCT-CTGATTCGAAATGTCGTGAATCGAGCAAAGGTAATGCTAA
1 TCCCTCAAGTGAGGCGT-TGCTGATTCAAAATGTCATGAATCGAGCAAAGGAAATGTTAA
* *** * *
295147 TCCCTCAAGTGAGGTGTCATTAATTCAAAATATCATGAATCGAGCAAAGGAAATGTTAA
1 TCCCTCAAGTGAGGCGTTGCTGATTCAAAATGTCATGAATCGAGCAAAGGAAATGTTAA
* * * * * *
295206 TCCCAT-AAGCGAGGTGTTGCTGATTCGAAATGCCGTGAATCGAGCAAAGGAAATATTAA
1 TCCC-TCAAGTGAGGCGTTGCTGATTCAAAATGTCATGAATCGAGCAAAGGAAATGTTAA
* * * * * *
295265 TCCCTCAAGCGAGACGTTACTGATTCGAAA-GACCATGAATCGAGCAAAGCAAATGTTAA
1 TCCCTCAAGTGAGGCGTTGCTGATTCAAAATG-TCATGAATCGAGCAAAGGAAATGTTAA
* * * * * *
295324 TCCTTCAAGCGAGGCGTTGATGATTCAAAATATCGTGAATCGATCAAAGGAAATGTTAA
1 TCCCTCAAGTGAGGCGTTGCTGATTCAAAATGTCATGAATCGAGCAAAGGAAATGTTAA
* * * ** * *
295383 TCCCTCAAGTGAGGCATCGCTGATTCAAAATGGCATGAATTAAGTAAAGAAAATGTTAA
1 TCCCTCAAGTGAGGCGTTGCTGATTCAAAATGTCATGAATCGAGCAAAGGAAATGTTAA
* *
295442 TCCCTCAAGTGAGGCATTGTTGATTCAAAATGT
1 TCCCTCAAGTGAGGCGTTGCTGATTCAAAATGT
295475 AGTGAAGAAG
Statistics
Matches: 271, Mismatches: 52, Indels: 10
0.81 0.16 0.03
Matches are distributed among these distances:
58 2 0.01
59 268 0.99
60 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.26
Consensus pattern (59 bp):
TCCCTCAAGTGAGGCGTTGCTGATTCAAAATGTCATGAATCGAGCAAAGGAAATGTTAA
Found at i:295559 original size:59 final size:60
Alignment explanation
Indices: 295482--295758 Score: 323
Period size: 59 Copynumber: 4.7 Consensus size: 60
295472 TGTAGTGAAG
* * * * * * *
295482 AAGCGAGGCGTTACTGATTCGAAA-GACCATGAATCGAGCGAAGGAAATGCTAATCCTTC
1 AAGCGAGGCGTTGCTGATTCAAAATGATCATGAATCGAGCAAAGAAAATGTTAATCCCTC
* * * *
295541 AAGCGAGGCATTGCTGATTCAAAAT-ATCGTGAATCGATCAAAGGAAATGTTAATCCCTC
1 AAGCGAGGCGTTGCTGATTCAAAATGATCATGAATCGAGCAAAGAAAATGTTAATCCCTC
* * * * *
295600 AAGTGAGGCATCGCTGATTCAAAATG-GCATGAATTGAGCAAAGAAAATGTTAATCCCTC
1 AAGCGAGGCGTTGCTGATTCAAAATGATCATGAATCGAGCAAAGAAAATGTTAATCCCTC
* * *
295659 AAGTGAGGCGTTGTTGATTCAAAATG-T-AGTGAATCGAGCAAAGAAAATGTTAATCCCTT
1 AAGCGAGGCGTTGCTGATTCAAAATGATCA-TGAATCGAGCAAAGAAAATGTTAATCCCTC
*
295718 AAGCGAGGCGTTGTTGATTCAAAATG-TCATGAATCGAGCAA
1 AAGCGAGGCGTTGCTGATTCAAAATGATCATGAATCGAGCAA
295759 TATGTTGAAC
Statistics
Matches: 191, Mismatches: 23, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
58 1 0.01
59 189 0.99
60 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (60 bp):
AAGCGAGGCGTTGCTGATTCAAAATGATCATGAATCGAGCAAAGAAAATGTTAATCCCTC
Found at i:295606 original size:152 final size:152
Alignment explanation
Indices: 295330--295625 Score: 398
Period size: 152 Copynumber: 1.9 Consensus size: 152
295320 TTAATCCTTC
* * * * * *
295330 AAGCGAGGCGTTGATGATTCAAAATATCGTGAATCGATCAAAGGAAATGTTAATCCCTCAAGTGA
1 AAGCGAGGCGTTGATGATTCAAAAGACCATGAATCGAGCAAAGGAAATGCTAATCCCTCAAGCGA
* * *
295395 GGCATCGCTGATTCAAAATGGCATGAATTAAGTAAAGAAAATGTTAATCCCTCAAGTGAGGCATT
66 GGCATCGCTGATTCAAAATAGCATGAATCAAGTAAAGAAAATGTTAATCCCTCAAGTGAGGCATC
*
295460 GTTGATTCAAAATGTAGTGAAG
131 GCTGATTCAAAATGTAGTGAAG
* * *
295482 AAGCGAGGCGTT-ACTGATTCGAAAGACCATGAATCGAGCGAAGGAAATGCTAATCCTTCAAGCG
1 AAGCGAGGCGTTGA-TGATTCAAAAGACCATGAATCGAGCAAAGGAAATGCTAATCCCTCAAGCG
* * * * *
295546 AGGCATTGCTGATTCAAAATATCGTGAATCGA-TCAAAGGAAATGTTAATCCCTCAAGTGAGGCA
65 AGGCATCGCTGATTCAAAATAGCATGAATCAAGT-AAAGAAAATGTTAATCCCTCAAGTGAGGCA
295610 TCGCTGATTCAAAATG
129 TCGCTGATTCAAAATG
295626 GCATGAATTG
Statistics
Matches: 124, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
151 2 0.02
152 122 0.98
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (152 bp):
AAGCGAGGCGTTGATGATTCAAAAGACCATGAATCGAGCAAAGGAAATGCTAATCCCTCAAGCGA
GGCATCGCTGATTCAAAATAGCATGAATCAAGTAAAGAAAATGTTAATCCCTCAAGTGAGGCATC
GCTGATTCAAAATGTAGTGAAG
Found at i:295645 original size:211 final size:211
Alignment explanation
Indices: 295271--295691 Score: 761
Period size: 211 Copynumber: 2.0 Consensus size: 211
295261 TTAATCCCTC
*
295271 AAGCGAGACGTTACTGATTCGAAAGACCATGAATCGAGCAAAGCAAATGTTAATCCTTCAAGCGA
1 AAGCGAGACGTTACTGATTCGAAAGACCATGAATCGAGCAAAGCAAATGCTAATCCTTCAAGCGA
*
295336 GGCGTTGATGATTCAAAATATCGTGAATCGATCAAAGGAAATGTTAATCCCTCAAGTGAGGCATC
66 GGCATTGATGATTCAAAATATCGTGAATCGATCAAAGGAAATGTTAATCCCTCAAGTGAGGCATC
*
295401 GCTGATTCAAAATGGCATGAATTAAGTAAAGAAAATGTTAATCCCTCAAGTGAGGCATTGTTGAT
131 GCTGATTCAAAATGGCATGAATTAAGCAAAGAAAATGTTAATCCCTCAAGTGAGGCATTGTTGAT
295466 TCAAAATGTAGTGAAG
196 TCAAAATGTAGTGAAG
* * *
295482 AAGCGAGGCGTTACTGATTCGAAAGACCATGAATCGAGCGAAGGAAATGCTAATCCTTCAAGCGA
1 AAGCGAGACGTTACTGATTCGAAAGACCATGAATCGAGCAAAGCAAATGCTAATCCTTCAAGCGA
*
295547 GGCATTGCTGATTCAAAATATCGTGAATCGATCAAAGGAAATGTTAATCCCTCAAGTGAGGCATC
66 GGCATTGATGATTCAAAATATCGTGAATCGATCAAAGGAAATGTTAATCCCTCAAGTGAGGCATC
* *
295612 GCTGATTCAAAATGGCATGAATTGAGCAAAGAAAATGTTAATCCCTCAAGTGAGGCGTTGTTGAT
131 GCTGATTCAAAATGGCATGAATTAAGCAAAGAAAATGTTAATCCCTCAAGTGAGGCATTGTTGAT
295677 TCAAAATGTAGTGAA
196 TCAAAATGTAGTGAA
295692 TCGAGCAAAG
Statistics
Matches: 201, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
211 201 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (211 bp):
AAGCGAGACGTTACTGATTCGAAAGACCATGAATCGAGCAAAGCAAATGCTAATCCTTCAAGCGA
GGCATTGATGATTCAAAATATCGTGAATCGATCAAAGGAAATGTTAATCCCTCAAGTGAGGCATC
GCTGATTCAAAATGGCATGAATTAAGCAAAGAAAATGTTAATCCCTCAAGTGAGGCATTGTTGAT
TCAAAATGTAGTGAAG
Found at i:295947 original size:136 final size:136
Alignment explanation
Indices: 295703--295984 Score: 406
Period size: 136 Copynumber: 2.1 Consensus size: 136
295693 CGAGCAAAGA
* ** * * *
295703 AAATGTTAATCCCTTAAGCGAGGCGTTGTTGATTCAAAATGTCATGAATCGAGCAATATGTTGAA
1 AAATGTTGATCCCTTAAGCGAGGCGTTACTGATTCAAAATGACATGAATCGAGCAATAGGTCGAA
* *
295768 CAAGTTCTTCTTACTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTC
66 CAAGTTCTTCTTACTATAAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACTCTC
295833 CATTGG
131 CATTGG
* ** *
295839 AAATGTTGATCCCTTAAGCGAGGTGTTACTGATTTGAAAT-ACAGTGAATTGAGCAATAGGTCGA
1 AAATGTTGATCCCTTAAGCGAGGCGTTACTGATTCAAAATGACA-TGAATCGAGCAATAGGTCGA
* *
295903 ACAAGTTCTT-TTCATTATAAACTTCTTCTCCTTCTATCGGATGAGTTCTTCTCATTATGAACTC
65 ACAAGTTCTTCTT-ACTATAAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACTC
295967 TCCATTGG
129 TCCATTGG
295975 AAATGTTGAT
1 AAATGTTGAT
295985 TGGTTTATCT
Statistics
Matches: 130, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
135 4 0.03
136 126 0.97
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.37
Consensus pattern (136 bp):
AAATGTTGATCCCTTAAGCGAGGCGTTACTGATTCAAAATGACATGAATCGAGCAATAGGTCGAA
CAAGTTCTTCTTACTATAAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACTCTC
CATTGG
Found at i:299396 original size:10 final size:10
Alignment explanation
Indices: 299381--299483 Score: 57
Period size: 10 Copynumber: 9.8 Consensus size: 10
299371 AAGTGTTTGA
299381 TCTTTTTTTT
1 TCTTTTTTTT
299391 TCTTTTTTTT
1 TCTTTTTTTT
299401 TCTCTCTTTTTT
1 TCT-T-TTTTTT
299413 T-TGCTTTTTTT
1 TCT--TTTTTTT
* * *
299424 ACTTATTCTT
1 TCTTTTTTTT
* *
299434 TCTTTTTCTA
1 TCTTTTTTTT
* *
299444 TC-TCTTCTT
1 TCTTTTTTTT
299453 TCTTTATTTCATT
1 TCTTT-TTT--TT
*
299466 TCTTTTTATT
1 TCTTTTTTTT
299476 TCTTTTTT
1 TCTTTTTT
299484 ATGTTTTTTG
Statistics
Matches: 73, Mismatches: 12, Indels: 16
0.72 0.12 0.16
Matches are distributed among these distances:
9 7 0.10
10 37 0.51
11 10 0.14
12 12 0.16
13 7 0.10
ACGTcount: A:0.06, C:0.17, G:0.01, T:0.77
Consensus pattern (10 bp):
TCTTTTTTTT
Found at i:305022 original size:58 final size:58
Alignment explanation
Indices: 304927--305061 Score: 245
Period size: 58 Copynumber: 2.3 Consensus size: 58
304917 GACGCGTAGG
304927 GCCCCAAAAAATAGGGGCCCCGAAATCGAGTATATCTATCAGTTATTGCCATTAAGAA
1 GCCCCAAAAAATAGGGGCCCCGAAATCGAGTATATCTATCAGTTATTGCCATTAAGAA
* *
304985 GCCCTAAAAAATAGGGGCCCCGAAATCGAGTATATCTATCAGTTGTTGCCATTAAGAA
1 GCCCCAAAAAATAGGGGCCCCGAAATCGAGTATATCTATCAGTTATTGCCATTAAGAA
305043 -CCCCAAAAAATAGGGGCCC
1 GCCCCAAAAAATAGGGGCCC
305062 AAAAATAAGG
Statistics
Matches: 74, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
57 18 0.24
58 56 0.76
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.21
Consensus pattern (58 bp):
GCCCCAAAAAATAGGGGCCCCGAAATCGAGTATATCTATCAGTTATTGCCATTAAGAA
Found at i:306445 original size:22 final size:22
Alignment explanation
Indices: 306402--306446 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
306392 AGTTTCAAAG
306402 GCTTAATCACTTACATTTAAAT
1 GCTTAATCACTTACATTTAAAT
306424 GCTTAATCACTTACATTTAAAT
1 GCTTAATCACTTACATTTAAAT
306446 G
1 G
306447 AATATTTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.18, G:0.07, T:0.40
Consensus pattern (22 bp):
GCTTAATCACTTACATTTAAAT
Found at i:307440 original size:26 final size:24
Alignment explanation
Indices: 307398--307449 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 24
307388 AAATTTTATA
* *
307398 TAAAGGGACAAATTTATTAAATTT
1 TAAAGGGACAAACTTATAAAATTT
307422 TAAAGGGAAACAAACTTATAAAATTT
1 TAAAGGG--ACAAACTTATAAAATTT
307448 TA
1 TA
307450 GATGAAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 7 0.29
26 17 0.71
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.33
Consensus pattern (24 bp):
TAAAGGGACAAACTTATAAAATTT
Found at i:310282 original size:16 final size:16
Alignment explanation
Indices: 310258--310297 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
310248 AGTCATATTT
*
310258 CATTTTTTTTTGTATA
1 CATTGTTTTTTGTATA
*
310274 CATTGTTTTTTTTATA
1 CATTGTTTTTTGTATA
*
310290 TATTGTTT
1 CATTGTTT
310298 CGTTTGTTCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.17, C:0.05, G:0.07, T:0.70
Consensus pattern (16 bp):
CATTGTTTTTTGTATA
Found at i:321986 original size:106 final size:105
Alignment explanation
Indices: 321500--322063 Score: 968
Period size: 105 Copynumber: 5.4 Consensus size: 105
321490 CAGGTTTTAC
*
321500 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
* *
321565 GACGAAGGGACCGCTGGTTGTCAACAAATATTTCTCAATG
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
321605 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
*
321670 GACGAAGGGACCGCTGCTTGTCAACAAACATTTCTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
*
321710 TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
* *
321775 GATGAAGGGACCGCTGCTTGTCAACAAACATTTCTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
*
321815 TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
* * *
321880 GAAGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATT
* *
321921 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAATGCAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
321986 GACGAAGGGACCGCTGGTTGTCAACAAACAATTTC-CAAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTC-AATT
*
322027 TCGGAGCCAATTTCAACTTCACAACGAAGGATATTGG
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
322064 CCTCGGAACA
Statistics
Matches: 441, Mismatches: 16, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
105 297 0.67
106 144 0.33
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.23
Consensus pattern (105 bp):
TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
Found at i:324321 original size:19 final size:19
Alignment explanation
Indices: 324276--324326 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
324266 TTTTCATTGC
*
324276 TTTATATTTTATTTTATTA
1 TTTATATTTTATTTTATCA
* *
324295 TGTGTATTTT-TTTTATCCA
1 TTTATATTTTATTTTAT-CA
324314 TTTATATTTTATT
1 TTTATATTTTATT
324327 ATATTTTCTT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 6 0.24
19 17 0.68
20 2 0.08
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.71
Consensus pattern (19 bp):
TTTATATTTTATTTTATCA
Found at i:324348 original size:38 final size:38
Alignment explanation
Indices: 324276--324348 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
324266 TTTTCATTGC
* *
324276 TTTATATTTTATTTTATTATGTGTATTTTTTTTATCCA
1 TTTATATTTTATTATATTATCTGTATTTTTTTTATCCA
* *
324314 TTTATATTTTATTATATTTTCT-TCTTTTTCTTTAT
1 TTTATATTTTATTATATTATCTGTATTTTT-TTTAT
324349 TTGTATTTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 6 0.20
38 24 0.80
ACGTcount: A:0.19, C:0.07, G:0.03, T:0.71
Consensus pattern (38 bp):
TTTATATTTTATTATATTATCTGTATTTTTTTTATCCA
Found at i:324428 original size:16 final size:16
Alignment explanation
Indices: 324404--324443 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
324394 AGTCATATTT
*
324404 CATTTTTTTTTGTATA
1 CATTGTTTTTTGTATA
*
324420 CATTGTTTTTTTTATA
1 CATTGTTTTTTGTATA
*
324436 TATTGTTT
1 CATTGTTT
324444 CGTTTGTTCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.17, C:0.05, G:0.07, T:0.70
Consensus pattern (16 bp):
CATTGTTTTTTGTATA
Found at i:327034 original size:12 final size:12
Alignment explanation
Indices: 327017--327042 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
327007 ATTTGTATAA
327017 TTTTTTATATTT
1 TTTTTTATATTT
327029 TTTTTTATATTT
1 TTTTTTATATTT
327041 TT
1 TT
327043 ATCTCTTAAA
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:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTTATATTT
Found at i:329223 original size:29 final size:29
Alignment explanation
Indices: 329190--329277 Score: 90
Period size: 29 Copynumber: 3.0 Consensus size: 29
329180 TAAATTGGTT
*
329190 CTTAAACTTTTGGATATGCTAATTTTATC
1 CTTAAACTTTTGGATATTCTAATTTTATC
* * * *
329219 CTTAAAC-TCT-GACTCATTTTAAATTAATC
1 CTTAAACTTTTGGA-T-ATTCTAATTTTATC
*
329248 CTTAAACTTTTGAATATTCTAATTTTATC
1 CTTAAACTTTTGGATATTCTAATTTTATC
329277 C
1 C
329278 CTAGACTATG
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
27 2 0.04
28 3 0.07
29 36 0.80
30 3 0.07
31 1 0.02
ACGTcount: A:0.31, C:0.17, G:0.06, T:0.47
Consensus pattern (29 bp):
CTTAAACTTTTGGATATTCTAATTTTATC
Found at i:329317 original size:60 final size:58
Alignment explanation
Indices: 329193--329338 Score: 150
Period size: 60 Copynumber: 2.5 Consensus size: 58
329183 ATTGGTTCTT
* * * * **
329193 AAACTTTTGGATATGCTAATTTTATCCTTAAACTCTGACTCATTTTAAATTAATCCTT
1 AAACTTTTGAATATTCTAATTTTATCCCTAAACTATGACTCATTTTAAATTAATCCCC
* **
329251 AAACTTTTGAATATTCTAATTTTATCCCTAGACTATGACCCTC-TTTCTAAATTGGTCCCC
1 AAACTTTTGAATATTCTAATTTTATCCCTAAACTATGA--CTCATTT-TAAATTAATCCCC
* * *
329311 AAACTTTTGAATGTTCCAATTTCATCCC
1 AAACTTTTGAATATTCTAATTTTATCCC
329339 CAAATTCATC
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
58 33 0.45
59 3 0.04
60 37 0.51
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.42
Consensus pattern (58 bp):
AAACTTTTGAATATTCTAATTTTATCCCTAAACTATGACTCATTTTAAATTAATCCCC
Found at i:329541 original size:60 final size:60
Alignment explanation
Indices: 329448--329574 Score: 168
Period size: 60 Copynumber: 2.1 Consensus size: 60
329438 GTATATACAT
* * *
329448 ATAGTTTGGGATGAAATTGGAATGTTTAAGAAGTCTGGGGACTAATTTAGAATGA-ATATC
1 ATAGTTTGGGATGAAATTGAAATATTTAAGAAGTCTGAGGACTAATTTAGAATGATA-ATC
* * *
329508 ATAGTTTGGGGATGAAATTGAAATATTT-AGAAGTTTGAGGACTACTTTAGAATGGTAATC
1 ATAGTTT-GGGATGAAATTGAAATATTTAAGAAGTCTGAGGACTAATTTAGAATGATAATC
329568 ATAGTTT
1 ATAGTTT
329575 ATGGGTGAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
60 40 0.68
61 19 0.32
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (60 bp):
ATAGTTTGGGATGAAATTGAAATATTTAAGAAGTCTGAGGACTAATTTAGAATGATAATC
Found at i:329584 original size:60 final size:60
Alignment explanation
Indices: 329448--329603 Score: 167
Period size: 60 Copynumber: 2.6 Consensus size: 60
329438 GTATATACAT
* * * *
329448 ATAG-TTTGGGATGAAATTGGAATGTTTAAGAAGTCTGGGGACTAATTTAGAATGAATATC
1 ATAGTTTTGGGATGAAATTGAAATATTT-AGAAGTTTGAGGACTAATTTAGAATGAATATC
* * *
329508 ATAGTTTGGGGATGAAATTGAAATATTTAGAAGTTTGAGGACTACTTTAGAATG-GTAATC
1 ATAGTTTTGGGATGAAATTGAAATATTTAGAAGTTTGAGGACTAATTTAGAATGAAT-ATC
* *
329568 ATAGTTTATGGG-TGAAA-TAAGAATATTTAAAAGTTT
1 ATAGTTT-TGGGATGAAATTGA-AATATTTAGAAGTTT
329604 AGGGATCAAT
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
59 3 0.04
60 56 0.68
61 23 0.28
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.35
Consensus pattern (60 bp):
ATAGTTTTGGGATGAAATTGAAATATTTAGAAGTTTGAGGACTAATTTAGAATGAATATC
Found at i:332417 original size:31 final size:32
Alignment explanation
Indices: 332375--332437 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
332365 TTTAAAACTG
*
332375 TAAAATGATTTATAGA-TAAAATATA-AATTCA
1 TAAAATCATTTATAGATTAAAA-ATAGAATTCA
*
332406 TAAAATCATTTATATATTAAAAATAGAATTCA
1 TAAAATCATTTATAGATTAAAAATAGAATTCA
332438 ACAATATCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 17 0.61
32 11 0.39
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.37
Consensus pattern (32 bp):
TAAAATCATTTATAGATTAAAAATAGAATTCA
Found at i:336287 original size:23 final size:23
Alignment explanation
Indices: 336261--336334 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 23
336251 AAGTGCCACA
*
336261 TAGATTTGTCCCGAAGGACTGCG
1 TAGAATTGTCCCGAAGGACTGCG
* * * *
336284 TAGAATTATCCTGAAGGAAC-ACA
1 TAGAATTGTCCCGAAGG-ACTGCG
336307 TAGAATTGTCCCGAAGGA-TCGCG
1 TAGAATTGTCCCGAAGGACT-GCG
336330 TAGAA
1 TAGAA
336335 ACCCTCGACT
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
22 1 0.03
23 36 0.92
24 2 0.05
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (23 bp):
TAGAATTGTCCCGAAGGACTGCG
Found at i:340579 original size:16 final size:16
Alignment explanation
Indices: 340553--340599 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
340543 TTAGTTGAAT
*
340553 CGAAAGTAACCCGAAC
1 CGAAAGCAACCCGAAC
* * *
340569 TGAAATCAACCAGAAC
1 CGAAAGCAACCCGAAC
340585 CGAAAGCAACCCGAA
1 CGAAAGCAACCCGAA
340600 TTTAATTTAC
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.47, C:0.30, G:0.17, T:0.06
Consensus pattern (16 bp):
CGAAAGCAACCCGAAC
Found at i:340687 original size:3 final size:3
Alignment explanation
Indices: 340679--340717 Score: 69
Period size: 3 Copynumber: 12.7 Consensus size: 3
340669 AATGAATAAT
340679 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TT
340718 GTTAATATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:342445 original size:14 final size:16
Alignment explanation
Indices: 342428--342459 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
342418 TTACTACTTA
342428 TTATT-TGA-ACTGAT
1 TTATTGTGATACTGAT
342442 TTATTGTGATACTGAT
1 TTATTGTGATACTGAT
342458 TT
1 TT
342460 GGGTAGGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 3 0.19
16 8 0.50
ACGTcount: A:0.25, C:0.06, G:0.16, T:0.53
Consensus pattern (16 bp):
TTATTGTGATACTGAT
Found at i:350200 original size:15 final size:15
Alignment explanation
Indices: 350180--350214 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
350170 AAGCTTTGTT
350180 TTTTATCCTTATCTA
1 TTTTATCCTTATCTA
**
350195 TTTTATTTTTATCTA
1 TTTTATCCTTATCTA
350210 TTTTA
1 TTTTA
350215 ATTATAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTATCCTTATCTA
Found at i:362284 original size:28 final size:28
Alignment explanation
Indices: 362225--362286 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
362215 TTCGTGATGG
* ***
362225 CTCTTTTCAAACCAGGCCACTAAAATGG
1 CTCTTTTCAAACCAGGCCACCAAAACAA
*
362253 CTCTTTTCAAACCAGGCCACCAAACCAA
1 CTCTTTTCAAACCAGGCCACCAAAACAA
362281 CTCTTT
1 CTCTTT
362287 AATTCTTGGC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.31, C:0.34, G:0.10, T:0.26
Consensus pattern (28 bp):
CTCTTTTCAAACCAGGCCACCAAAACAA
Found at i:373866 original size:21 final size:21
Alignment explanation
Indices: 373837--373877 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
373827 ATTGAGTAGG
*
373837 TTCACATTTTTCTAAATTAGC
1 TTCAAATTTTTCTAAATTAGC
*
373858 TTCAAATTTTTCTAAGTTAG
1 TTCAAATTTTTCTAAATTAG
373878 TTAAGTATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.15, G:0.07, T:0.49
Consensus pattern (21 bp):
TTCAAATTTTTCTAAATTAGC
Found at i:382315 original size:43 final size:44
Alignment explanation
Indices: 382267--382352 Score: 156
Period size: 44 Copynumber: 2.0 Consensus size: 44
382257 AGTCAAAGGT
382267 CTATGTGGTCCT-TGGGACAATTATGTGGCACTTCGGTGCAAAC
1 CTATGTGGTCCTCTGGGACAATTATGTGGCACTTCGGTGCAAAC
*
382310 CTATGTGGTCCTCTGGGACAATTATGTGGCACTTTGGTGCAAA
1 CTATGTGGTCCTCTGGGACAATTATGTGGCACTTCGGTGCAAA
382353 TTATGAGCTG
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
43 12 0.29
44 29 0.71
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.31
Consensus pattern (44 bp):
CTATGTGGTCCTCTGGGACAATTATGTGGCACTTCGGTGCAAAC
Found at i:386515 original size:18 final size:18
Alignment explanation
Indices: 386487--386523 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
386477 ACTATAGATT
386487 AATGAAAAAATGAGAAAAA
1 AATGAAAAAATGA-AAAAA
386506 AATG-AAAAATGAAAAAA
1 AATGAAAAAATGAAAAAA
386523 A
1 A
386524 GAATAATGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
18 8 0.44
19 4 0.22
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.11
Consensus pattern (18 bp):
AATGAAAAAATGAAAAAA
Found at i:386698 original size:56 final size:56
Alignment explanation
Indices: 386613--386727 Score: 230
Period size: 56 Copynumber: 2.1 Consensus size: 56
386603 TTTCGTAGGC
386613 TCATCATTTGAGATATTAGGCCAAGACTAAACGAGAAGATTTTCGAATACATGGGA
1 TCATCATTTGAGATATTAGGCCAAGACTAAACGAGAAGATTTTCGAATACATGGGA
386669 TCATCATTTGAGATATTAGGCCAAGACTAAACGAGAAGATTTTCGAATACATGGGA
1 TCATCATTTGAGATATTAGGCCAAGACTAAACGAGAAGATTTTCGAATACATGGGA
386725 TCA
1 TCA
386728 GATCATTGAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 59 1.00
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (56 bp):
TCATCATTTGAGATATTAGGCCAAGACTAAACGAGAAGATTTTCGAATACATGGGA
Found at i:388809 original size:15 final size:14
Alignment explanation
Indices: 388768--388820 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
388758 AATTTTAGCC
*
388768 TTTAAATTTCAGTG
1 TTTAAATTTCAGTA
*
388782 TTTATATTTCAGTCA
1 TTTAAATTTCAGT-A
* *
388797 TTTAAATTCCAGTT
1 TTTAAATTTCAGTA
*
388811 TTTAATTTTC
1 TTTAAATTTC
388821 TGCACCGTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
14 20 0.65
15 11 0.35
ACGTcount: A:0.26, C:0.11, G:0.08, T:0.55
Consensus pattern (14 bp):
TTTAAATTTCAGTA
Found at i:388820 original size:29 final size:28
Alignment explanation
Indices: 388753--388820 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 28
388743 ATTTTCTGTA
* *
388753 TTTTTAATTTT-AGCCTTTAAATTTCAG
1 TTTTTAATTTTCAGCATTTAAATTCCAG
*
388780 TGTTT-ATATTTCAGTCATTTAAATTCCAG
1 TTTTTAAT-TTTCAG-CATTTAAATTCCAG
388809 TTTTTAATTTTC
1 TTTTTAATTTTC
388821 TGCACCGTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
26 2 0.06
27 7 0.21
28 2 0.06
29 20 0.61
30 2 0.06
ACGTcount: A:0.25, C:0.12, G:0.07, T:0.56
Consensus pattern (28 bp):
TTTTTAATTTTCAGCATTTAAATTCCAG
Found at i:389308 original size:138 final size:136
Alignment explanation
Indices: 389059--389426 Score: 413
Period size: 137 Copynumber: 2.7 Consensus size: 136
389049 AATTGAGGAT
* * * * * ***
389059 TTTTTATTTGGTCATCACTTTTGCTCGATGTTTCATTTTAATTATTCGATTCAATAAATGGGTTA
1 TTTTAATTTGGTCCTCACTTTTGCTCGAGGTTCCATTTTAATTATTCGAATCAAT-AATTAATTA
* *
389124 AAATTGATTAGG-TTAATAATTAGAGTCTCCACTTTAGGCTTAATTTCACACTTAGTCTTTTAAT
65 AAATTGATTAGGATTAAT-ATTAGAGCCTCCACTTTAGGCTTAATTTCA-ACTTAATCTTTTAAT
*
389188 TTATTAGAAA
128 TTA-GAGAAA
*
389198 TTTTAATTTGGTCCTCACTTTTGCTCGAGGTTCCACTTT-ATTCATTCGAATCAATAATTAATTA
1 TTTTAATTTGGTCCTCACTTTTGCTCGAGGTTCCATTTTAATT-ATTCGAATCAATAATTAATTA
* **
389262 AAATTGATTAGGATTAATATTAGAGCCTTCACTTTAGG-TCTAATTTCATTTTAATCTTTTAATT
65 AAATTGATTAGGATTAATATTAGAGCCTCCACTTTAGGCT-TAATTTCAACTTAATCTTTTAATT
* *
389326 TAGGGGAA
129 TAGAGAAA
* * * * *
389334 TTCTTAATTTGGTCCACGCTTATGCTCGAGGTTCCATTTTGATTATTC-AACTCAATAATTTATT
1 TT-TTAATTTGGTCCTCACTTTTGCTCGAGGTTCCATTTTAATTATTCGAA-TCAATAATTAATT
*
389398 AAAAATT-ATTTGGATTAATATTAGAGCCT
64 -AAAATTGATTAGGATTAATATTAGAGCCT
389427 ACATTTTTAG
Statistics
Matches: 199, Mismatches: 23, Indels: 16
0.84 0.10 0.07
Matches are distributed among these distances:
136 7 0.04
137 86 0.43
138 56 0.28
139 50 0.25
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.45
Consensus pattern (136 bp):
TTTTAATTTGGTCCTCACTTTTGCTCGAGGTTCCATTTTAATTATTCGAATCAATAATTAATTAA
AATTGATTAGGATTAATATTAGAGCCTCCACTTTAGGCTTAATTTCAACTTAATCTTTTAATTTA
GAGAAA
Found at i:391066 original size:20 final size:19
Alignment explanation
Indices: 391043--391089 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
391033 CGATATACCA
*
391043 GGTAAAAATATGATAAAACC
1 GGTAAAAA-AAGATAAAACC
391063 GGTAACAAAAAGATAAAACC
1 GGTAA-AAAAAGATAAAACC
391083 GGTAAAA
1 GGTAAAA
391090 CGTTACCGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 2 0.08
20 20 0.80
21 3 0.12
ACGTcount: A:0.57, C:0.11, G:0.17, T:0.15
Consensus pattern (19 bp):
GGTAAAAAAAGATAAAACC
Found at i:391177 original size:181 final size:182
Alignment explanation
Indices: 390831--391303 Score: 705
Period size: 181 Copynumber: 2.6 Consensus size: 182
390821 GATCCAAATT
* * * * **
390831 AAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACCAGTATTGAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * * * *
390896 AAACCGGTAAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATTGACACTTC
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
* * *
390961 GTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTTTA
131 GTGAATTTAAAAGAGAAGCAATTTTAAAGCCTATAAAGTGTCGATACTTTAA
* * *
391013 AAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGGTAACAAAAAGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* *
391078 AAACCGGTAAAACGTTACCGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
** *
391142 GTGAATTTAAAAGAGAAGCAATTTTAGCGCCTATAATGTGTCGATACTTTAA
131 GTGAATTTAAAAGAGAAGCAATTTTAAAGCCTATAAAGTGTCGATACTTTAA
* *
391194 AAAAATATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
*
391259 AAACCGGTAAAATGATACCGGATATATTGAAAGTGTCGATACTTT
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
391304 CGTAAGTACG
Statistics
Matches: 262, Mismatches: 29, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
181 166 0.63
182 96 0.37
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (182 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAGCAATTTTAAAGCCTATAAAGTGTCGATACTTTAA
Found at i:391247 original size:20 final size:19
Alignment explanation
Indices: 391224--391270 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
391214 CGATATAACA
391224 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
391244 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
391264 GGTAAAA
1 GGTAAAA
391271 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:391272 original size:17 final size:19
Alignment explanation
Indices: 391233--391275 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
391223 AGGTAAAAAT
391233 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
391253 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
391270 ATGATA
1 ATGATA
391276 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:393526 original size:21 final size:21
Alignment explanation
Indices: 393500--393564 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
393490 AAGACAATCA
*
393500 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
393521 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
393542 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
393563 AG
1 AG
393565 GCATAAGGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.42, C:0.11, G:0.31, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:393640 original size:33 final size:32
Alignment explanation
Indices: 393598--393662 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 32
393588 AAATAGATGG
393598 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTT-AGGGGTGA
* *
393631 AGTGGTGAAAGAAGTTGGGGTGTTAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAGGGGTGA
393663 TATTAAGATG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 8 0.27
33 22 0.73
ACGTcount: A:0.28, C:0.00, G:0.49, T:0.23
Consensus pattern (32 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAGGGGTGA
Found at i:395475 original size:19 final size:19
Alignment explanation
Indices: 395451--395499 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
395441 AATGTAGGGT
395451 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
395470 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
395489 TAATTTTGTAT
1 TAATTTTGTAT
395500 GTGAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:396289 original size:200 final size:200
Alignment explanation
Indices: 395620--396552 Score: 1699
Period size: 200 Copynumber: 4.7 Consensus size: 200
395610 CAATATGGCC
*
395620 AACAGGGTGCAACCATAAAGTGTCGAACCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
395685 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
*
395750 GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
131 GAATATGTCTAAACAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
395815 TGGAA
196 TGGAA
395820 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
395885 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTAT--GA
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
*
395948 GAATATGTCTAAACAATGTATCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
131 GAATATGTCTAAACAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
396013 TGGAA
196 TGGAA
396018 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
396083 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
*
396148 GAATATGTCTAAACAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAAAATGAA
131 GAATATGTCTAAACAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
396213 TGGAA
196 TGGAA
* *
396218 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAACTGTCGATCCCAAAAACATCAAAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
* *
396283 CCAAAAGTATAATGCAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
* * *
396348 TAATAGGTCTAAATAATGTGTCGACACTTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGA
131 GAATATGTCTAAACAATGTGTCGACAC-TTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGA
*
396413 ATGGCA
195 ATGGAA
* * *
396419 AACAAGCTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
*
396484 CCAAAAGTACAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
396549 GAAT
131 GAAT
396553 TAGTATATAA
Statistics
Matches: 707, Mismatches: 23, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
198 196 0.28
200 345 0.49
201 166 0.23
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (200 bp):
AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
GAATATGTCTAAACAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
TGGAA
Found at i:398891 original size:183 final size:183
Alignment explanation
Indices: 398578--399514 Score: 1671
Period size: 183 Copynumber: 5.1 Consensus size: 183
398568 TAAAGTTTTC
* * * *
398578 ACACTTTTTAATATTGTGTCTGTACTTTATGTCCAAATTGGAAGAAAAATGTGTCAATATCATT-
1 ACACTTTTTAATATTGTGTCGGAACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATA-CATTG
* *
398642 TAAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTATAATA
65 TCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATA
398707 TAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
130 TAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
398761 ACACTTTTTAATATTGTGTCGGAACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATTGT
1 ACACTTTTTAATATTGTGTCGGAACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATTGT
*
398826 CAAAAAGTGTCGACATTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
*
398891 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATTG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
398944 ACACTTTTTAATATTGTGTCGGAACTTTATGTCCAGATTGGAAGAAAAATATGTCGATACATTGT
1 ACACTTTTTAATATTGTGTCGGAACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATTGT
* *
399009 CAAAAAGTGTCGACATTTACACATCGGAACCCATAATTATAATTTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
*
399074 AACCGGTATAAATATACCGGTTTTATGAACGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
* *
399127 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATT-
1 ACACTTTTTAATATTGTGTCGGAACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATA-CATTG
*
399191 TAAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATA
65 TCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATA
* * *
399256 TAACCAGTATAAATATACCGGTTTTATGAGTGAATAGGTCTACAACCTGTATCG
130 TAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
399310 ACACTTTTTAATATTGTGTCGGAACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATTGT
1 ACACTTTTTAATATTGTGTCGGAACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATTGT
399375 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
*
399440 AACCGGTATAAATATACCAGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
399493 ACACTTTTTAATATTGTGTCGG
1 ACACTTTTTAATATTGTGTCGG
399515 TAATTTTAAG
Statistics
Matches: 722, Mismatches: 29, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
182 8 0.01
183 710 0.98
184 4 0.01
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (183 bp):
ACACTTTTTAATATTGTGTCGGAACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATTGT
CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
Found at i:400630 original size:48 final size:48
Alignment explanation
Indices: 400559--400652 Score: 170
Period size: 48 Copynumber: 2.0 Consensus size: 48
400549 TACTCATTTT
* *
400559 TACGAAGGGTTCATTGAATTCTTTGGTGGGAGTCCAATGTGTGCTATA
1 TACGAAGGGTTCATTGAATTCTTTGGAGGGAGTCCAATGTGCGCTATA
400607 TACGAAGGGTTCATTGAATTCTTTGGAGGGAGTCCAATGTGCGCTA
1 TACGAAGGGTTCATTGAATTCTTTGGAGGGAGTCCAATGTGCGCTA
400653 GAGACATTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.23, C:0.14, G:0.30, T:0.33
Consensus pattern (48 bp):
TACGAAGGGTTCATTGAATTCTTTGGAGGGAGTCCAATGTGCGCTATA
Found at i:401667 original size:15 final size:15
Alignment explanation
Indices: 401649--401679 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
401639 ATTTTCTTTC
*
401649 AAGTTTTTTTTTTAA
1 AAGTTTTGTTTTTAA
401664 AAGTTTTGTTTTTAA
1 AAGTTTTGTTTTTAA
401679 A
1 A
401680 TATGCTATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (15 bp):
AAGTTTTGTTTTTAA
Found at i:412300 original size:2 final size:2
Alignment explanation
Indices: 412293--412331 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
412283 TTATGAAAAC
412293 TA TA 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 TA TA T
412332 TGTTTCTCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:419761 original size:18 final size:19
Alignment explanation
Indices: 419722--419761 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
419712 AAATTCTCTC
*
419722 TTTTATTTT-CTTTCAAGT
1 TTTTATTTTACTTTAAAGT
*
419740 TTTTATTTTATTTTAAAGT
1 TTTTATTTTACTTTAAAGT
419759 TTT
1 TTT
419762 GTTTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.70
Consensus pattern (19 bp):
TTTTATTTTACTTTAAAGT
Found at i:424216 original size:1 final size:1
Alignment explanation
Indices: 424210--424257 Score: 51
Period size: 1 Copynumber: 48.0 Consensus size: 1
424200 AAAACACTGC
* * * * *
424210 AAAAAAAAAAAAAAAAACAAAACAAAACAAAAAACAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
424258 GAATCAGACG
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:424231 original size:17 final size:17
Alignment explanation
Indices: 424211--424257 Score: 67
Period size: 17 Copynumber: 2.7 Consensus size: 17
424201 AAACACTGCA
424211 AAAAAAAAAAAAAAAAC
1 AAAAAAAAAAAAAAAAC
* *
424228 AAAACAAAACAAAAAAC
1 AAAAAAAAAAAAAAAAC
424245 AAAACAAAAAAAA
1 AAAA-AAAAAAAA
424258 GAATCAGACG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 19 0.76
18 6 0.24
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAAAAAAC
Found at i:426939 original size:29 final size:27
Alignment explanation
Indices: 426906--426961 Score: 94
Period size: 29 Copynumber: 2.0 Consensus size: 27
426896 TTTTATTATT
426906 AAATTTAAACTTAAAGTTATATAAAAAAA
1 AAATTTAAACTTAAAGTT-T-TAAAAAAA
426935 AAATTTAAACTTAAAGTTTTAAAAAAA
1 AAATTTAAACTTAAAGTTTTAAAAAAA
426962 TCCCTAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 8 0.30
28 1 0.04
29 18 0.67
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.32
Consensus pattern (27 bp):
AAATTTAAACTTAAAGTTTTAAAAAAA
Found at i:430355 original size:2 final size:2
Alignment explanation
Indices: 430348--430391 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
430338 TATAAAATAG
430348 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
430390 AT
1 AT
430392 TAATATTCAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:431998 original size:47 final size:46
Alignment explanation
Indices: 431944--432042 Score: 130
Period size: 45 Copynumber: 2.1 Consensus size: 46
431934 GTTTATTTTC
431944 ATTTTTCGAATAAATGCATAG-GAACTAGATATCATGCGGTTAGG-TTT
1 ATTTTTCGAA-AAA-GCAT-GCGAACTAGATATCATGCGGTTAGGATTT
* *
431991 ATTTTTCGAACAAGCATGCGAATTAGATATCATGCGGTTAGGATTT
1 ATTTTTCGAAAAAGCATGCGAACTAGATATCATGCGGTTAGGATTT
*
432037 CTTTTT
1 ATTTTT
432043 ATGAATAACA
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
44 1 0.02
45 26 0.55
46 10 0.21
47 10 0.21
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.38
Consensus pattern (46 bp):
ATTTTTCGAAAAAGCATGCGAACTAGATATCATGCGGTTAGGATTT
Found at i:441704 original size:10 final size:10
Alignment explanation
Indices: 441684--441723 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
441674 TCGCTTGAAG
441684 AAAA-AATGA
1 AAAATAATGA
*
441693 AAAATGATGA
1 AAAATAATGA
441703 AAAA-AAT-A
1 AAAATAATGA
441711 AAAATAATGA
1 AAAATAATGA
441721 AAA
1 AAA
441724 GAAGAAAGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
8 5 0.19
9 9 0.35
10 12 0.46
ACGTcount: A:0.75, C:0.00, G:0.10, T:0.15
Consensus pattern (10 bp):
AAAATAATGA
Found at i:441706 original size:18 final size:17
Alignment explanation
Indices: 441683--441723 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
441673 TTCGCTTGAA
*
441683 GAAAAAATGAAAAATGAT
1 GAAAAAAT-AAAAATAAT
441701 GAAAAAAATAAAAATAAT
1 G-AAAAAATAAAAATAAT
441719 GAAAA
1 GAAAA
441724 GAAGAAAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 4 0.19
18 10 0.48
19 7 0.33
ACGTcount: A:0.73, C:0.00, G:0.12, T:0.15
Consensus pattern (17 bp):
GAAAAAATAAAAATAAT
Found at i:441708 original size:21 final size:21
Alignment explanation
Indices: 441679--441741 Score: 51
Period size: 18 Copynumber: 3.0 Consensus size: 21
441669 ATATTTCGCT
*
441679 TGAAGAAAAAATGAAAAATGA
1 TGAAAAAAAAATGAAAAATGA
*
441700 TG--AAAAAAAT-AAAAATAA
1 TGAAAAAAAAATGAAAAATGA
*
441718 TGAAAAGAAGAAAGAGAAAAATGA
1 TGAAAA-AA-AAA-TGAAAAATGA
441742 AAAATGAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 9
0.71 0.09 0.20
Matches are distributed among these distances:
18 9 0.28
19 7 0.22
20 2 0.06
21 4 0.12
22 3 0.09
24 7 0.22
ACGTcount: A:0.70, C:0.00, G:0.17, T:0.13
Consensus pattern (21 bp):
TGAAAAAAAAATGAAAAATGA
Found at i:443131 original size:37 final size:38
Alignment explanation
Indices: 443090--443161 Score: 128
Period size: 37 Copynumber: 1.9 Consensus size: 38
443080 AATTCAATCT
443090 TAAGCCTTCACGGAAGAGTAGTGAAG-AAAATCATCAA
1 TAAGCCTTCACGGAAGAGTAGTGAAGCAAAATCATCAA
*
443127 TAAGCCTTCACGGAAGAGTAGTGAAGCAAACTCAT
1 TAAGCCTTCACGGAAGAGTAGTGAAGCAAAATCAT
443162 TTTATGAAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
37 26 0.79
38 7 0.21
ACGTcount: A:0.40, C:0.18, G:0.22, T:0.19
Consensus pattern (38 bp):
TAAGCCTTCACGGAAGAGTAGTGAAGCAAAATCATCAA
Found at i:443332 original size:102 final size:102
Alignment explanation
Indices: 443166--443404 Score: 302
Period size: 102 Copynumber: 2.3 Consensus size: 102
443156 ACTCATTTTA
* * ** *
443166 TGAAGATCGAGTCCTATACTCTCTGAAGGAATAGGGAGTAGACACGTTTGTTGAAGATCGAGTCT
1 TGAAGATTGAGTCTTATACTCTCTGAAGGAATAGGGACCAGACACGTTTGTTGAAGATCAAGTCT
* *
443231 TATACTCTCTGAATGAATACGGAGCAAACATGTTTGT
66 TATACTCTCTGAAGGAATACGGAGCAAACACGTTTGT
*
443268 TGAAGATTGAGTCTTATACTCTCTGAAGGAATAGGGACCAGACATGCTTT-TTGAAGATCAAGTC
1 TGAAGATTGAGTCTTATACTCTCTGAAGGAATAGGGACCAGACACG-TTTGTTGAAGATCAAGTC
* ** *
443332 TTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTGT
65 TTATACTCTCTGAAGGAATACGGAGCAAACACGTTTGT
443370 TGAAGATTATTCGAGT-TCTATACTCTCTGAAGGAA
1 TGAAG---ATT-GAGTCT-TATACTCTCTGAAGGAA
443405 AGGAGAGCGG
Statistics
Matches: 119, Mismatches: 12, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
102 91 0.76
103 3 0.03
105 4 0.03
106 21 0.18
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (102 bp):
TGAAGATTGAGTCTTATACTCTCTGAAGGAATAGGGACCAGACACGTTTGTTGAAGATCAAGTCT
TATACTCTCTGAAGGAATACGGAGCAAACACGTTTGT
Found at i:443413 original size:55 final size:55
Alignment explanation
Indices: 443172--443695 Score: 465
Period size: 55 Copynumber: 9.7 Consensus size: 55
443162 TTTATGAAGA
* ** *
443172 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGTAGACACGTTTGTTGAAGA----
1 TCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTGTTGAAGATTGT
* * ** **
443223 TCGAGTCTTATACTCTCTGAATGAATACGGAGCAAACATGTTTGTTGAAGA---T
1 TCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTGTTGAAGATTGT
* * **
443275 T-GAGTCTTATACTCTCTGAAGGAATAGGGACCAGACATGCTTT-TTGAAGA----
1 TCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACCCG-TTTGTTGAAGATTGT
* *
443325 TCAAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTGTTGAAGATTAT
1 TCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTGTTGAAGATTGT
**
443380 TCGAGT-TCTATACTCTCTGAAGGAA-AGGAGAGCGGACCCGTTTCATGAAGATTGT
1 TCGAGTCT-TATACTCTCTGAAGGAATAGG-GAGCGGACCCGTTTGTTGAAGATTGT
* *
443435 TCGAGT-TCTATACTCTCTGAAGGAATAGAGAGCGGAACCGTTT-TATGAAGATTGT
1 TCGAGTCT-TATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTGT-TGAAGATTGT
* * * * * *
443490 TCAAGT-TCTATGCTCCCTAAACGAATAGGGAGCGGACCCGTTTATTGAAGATTGT
1 TCGAGTCT-TATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTGTTGAAGATTGT
* ** * * * *
443545 TCGAGTCTTATACT-TCCTGAACGAATAGGGAGCATACACGTTTGCTGAAAAGTGT
1 TCGAGTCTTATACTCT-CTGAAGGAATAGGGAGCGGACCCGTTTGTTGAAGATTGT
* * * * * * *
443600 TCGAGTCTTATACTCCCTTAACGAATAGGGAGCAGACACATTTGCTGAAGATTGT
1 TCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTGTTGAAGATTGT
* * *
443655 TCGAGTCTTATAGTCCCTGAAGGAATAGGGAGCAGACCCGT
1 TCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACCCGT
443696 CATTCGAAGA
Statistics
Matches: 406, Mismatches: 51, Indels: 28
0.84 0.11 0.06
Matches are distributed among these distances:
50 4 0.01
51 126 0.31
52 4 0.01
54 4 0.01
55 264 0.65
56 4 0.01
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.29
Consensus pattern (55 bp):
TCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTGTTGAAGATTGT
Found at i:446993 original size:58 final size:59
Alignment explanation
Indices: 446901--447020 Score: 172
Period size: 58 Copynumber: 2.1 Consensus size: 59
446891 GGAGGGTTGG
* *
446901 TTAGAGCCATATGATCGAGTTTGCCTTTTTATTGCGACTA-AAGGGTTTGATAGGACAC
1 TTAGAGCCATATGATCGAGTTTGCCTTTTTATTGCGAATAGAAGGGTTCGATAGGACAC
* * *
446959 TTAGAGCCATATTATTGAGTTTG-CTTTTTCATTGCGAATAGGAGGGTTCGATAGGACAC
1 TTAGAGCCATATGATCGAGTTTGCCTTTTT-ATTGCGAATAGAAGGGTTCGATAGGACAC
447018 TTA
1 TTA
447021 TCCATCTATT
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
57 6 0.11
58 30 0.55
59 19 0.35
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (59 bp):
TTAGAGCCATATGATCGAGTTTGCCTTTTTATTGCGAATAGAAGGGTTCGATAGGACAC
Found at i:449033 original size:45 final size:45
Alignment explanation
Indices: 448978--449381 Score: 492
Period size: 45 Copynumber: 9.0 Consensus size: 45
448968 AATGAATGAG
*
448978 CAAAATAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGC
1 CAAAATAATAATGCATATGGGTGCATTATCGACATGAAAGGATGC
* * * * *
449023 CAAAATAATAATCCATGTGGGTGCATTATTGGCATGAAAGGATAC
1 CAAAATAATAATGCATATGGGTGCATTATCGACATGAAAGGATGC
* **
449068 CAAAATAGTAATGCATATGGGTGCATTA-CGACATGAAATAATGC
1 CAAAATAATAATGCATATGGGTGCATTATCGACATGAAAGGATGC
**
449112 CAAAATAATAATGCATATGGGTGCATTATCGGTATGAAAGGATGC
1 CAAAATAATAATGCATATGGGTGCATTATCGACATGAAAGGATGC
*
449157 CAAAATAATATTGCATATGGGTGCATTATCGACATGAAAGGATGC
1 CAAAATAATAATGCATATGGGTGCATTATCGACATGAAAGGATGC
* ** *
449202 GAAAATAATAATGCATATAAGTGCATTATTGACATGAAAGGATGC
1 CAAAATAATAATGCATATGGGTGCATTATCGACATGAAAGGATGC
*
449247 CAAAATAATAATGCATATGGGTGCATTATCGACAGGAAAGGATGC
1 CAAAATAATAATGCATATGGGTGCATTATCGACATGAAAGGATGC
** * * * * * *
449292 CATAGTTGA-AATGCATATGGGTGAATTATCAACATAAAAGTATGT
1 CA-AAATAATAATGCATATGGGTGCATTATCGACATGAAAGGATGC
** *
449337 CATAAATGAA-AATGCATAAT-GGTGCATTATAAACATGAATGGATG
1 CA-AAAT-AATAATGCAT-ATGGGTGCATTATCGACATGAAAGGATG
449382 GTATTAATGA
Statistics
Matches: 308, Mismatches: 47, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
44 38 0.12
45 237 0.77
46 31 0.10
47 2 0.01
ACGTcount: A:0.40, C:0.12, G:0.22, T:0.26
Consensus pattern (45 bp):
CAAAATAATAATGCATATGGGTGCATTATCGACATGAAAGGATGC
Found at i:458117 original size:11 final size:11
Alignment explanation
Indices: 458101--458125 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
458091 TTCCATCACA
458101 TTTTTTTTATT
1 TTTTTTTTATT
458112 TTTTTTTTATT
1 TTTTTTTTATT
458123 TTT
1 TTT
458126 CATTTCTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTTATT
Found at i:459091 original size:21 final size:21
Alignment explanation
Indices: 459067--459114 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
459057 AACTGTTCGG
459067 AAAAAAAAG-GAAAAAAAGAAA
1 AAAAAAAAGTG-AAAAAAGAAA
* *
459088 AAAAATACGTGAAAAAAGAAA
1 AAAAAAAAGTGAAAAAAGAAA
*
459109 ACAAAA
1 AAAAAA
459115 CAACAACAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.79, C:0.04, G:0.12, T:0.04
Consensus pattern (21 bp):
AAAAAAAAGTGAAAAAAGAAA
Found at i:463005 original size:45 final size:45
Alignment explanation
Indices: 462950--463267 Score: 408
Period size: 45 Copynumber: 7.0 Consensus size: 45
462940 AATGAATGAA
* * *
462950 CAAAATAATAATGCATATGAGTGTATTATCGGCATGAAATGATGC
1 CAAAATAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGC
* * *
462995 CAAAATAATAAT-CTATATGGGTGTATTATCAGCATGAAAGGATAC
1 CAAAATAATAATGC-ATATGGGTGCATTATCGGCATGAAAGGATGC
* *
463040 CAAAATAATAATGCATATGGATGCATTATCGGCATGAAATGATGC
1 CAAAATAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGC
* * * *
463085 CAAAAATAATAATGCATATAGGTGCATTATTGGTATGAAAAGATGC
1 C-AAAATAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGC
* * * *
463131 CAAAATAATAATGCGTAAT-GGTGCATTATCGACATGAATGAATGC
1 CAAAATAATAATGCAT-ATGGGTGCATTATCGGCATGAAAGGATGC
* *
463176 TAAAATAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGC
1 CAAAATAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGC
*
463221 CAAAACAATAATGCATATGGGTGCATTATCGGCA-GAAAAGGATGC
1 CAAAATAATAATGCATATGGGTGCATTATCGGCATG-AAAGGATGC
463266 CA
1 CA
463268 TAGTTGAAAT
Statistics
Matches: 237, Mismatches: 30, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
44 4 0.02
45 190 0.80
46 43 0.18
ACGTcount: A:0.41, C:0.12, G:0.21, T:0.27
Consensus pattern (45 bp):
CAAAATAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGC
Found at i:463279 original size:45 final size:45
Alignment explanation
Indices: 462959--463321 Score: 167
Period size: 45 Copynumber: 8.0 Consensus size: 45
462949 ACAAAATAAT
* * * * *
462959 AATGCATATGAGTGTATTATCGGCATG-AAATGATGCCA-AAATAA
1 AATGCATATGGGTGCATTATCGGCA-GAAAAGGATGCCATAATTGA
* * * * *
463003 TAAT-CTATATGGGTGTATTATCAGCATG-AAAGGATACCA-AAATAA
1 -AATGC-ATATGGGTGCATTATCGGCA-GAAAAGGATGCCATAATTGA
* * * * *
463048 TAATGCATATGGATGCATTATCGGCATG-AAATGATGCCAAAAATAA
1 -AATGCATATGGGTGCATTATCGGCA-GAAAAGGATGCCATAATTGA
* * * * *
463094 TAATGCATATAGGTGCATTATTGGTATGAAAA-GATGCCA-AAATAA
1 -AATGCATATGGGTGCATTATCGGCA-GAAAAGGATGCCATAATTGA
* * * * * * *
463139 TAATGCGTAAT-GGTGCATTATCGACATG-AATGAATGCTA-AAATAA
1 -AATGCAT-ATGGGTGCATTATCGGCA-GAAAAGGATGCCATAATTGA
* ***
463184 TAATGCATATGGGTGCATTATTGGCATG-AAAGGATGCCA-AAACAA
1 -AATGCATATGGGTGCATTATCGGCA-GAAAAGGATGCCATAATTGA
*
463229 TAATGCATATGGGTGCATTATCGGCAGAAAAGGATGCCATAGTTGA
1 -AATGCATATGGGTGCATTATCGGCAGAAAAGGATGCCATAATTGA
* * * * * *
463275 AATGCATATGAGTGCACTATCAGCATAAAAGTATGTCATAATTGA
1 AATGCATATGGGTGCATTATCGGCAGAAAAGGATGCCATAATTGA
463320 AA
1 AA
463322 ACACATAATG
Statistics
Matches: 270, Mismatches: 39, Indels: 18
0.83 0.12 0.06
Matches are distributed among these distances:
44 6 0.02
45 219 0.81
46 42 0.16
47 3 0.01
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATCGGCAGAAAAGGATGCCATAATTGA
Found at i:463339 original size:181 final size:181
Alignment explanation
Indices: 462950--463355 Score: 432
Period size: 181 Copynumber: 2.2 Consensus size: 181
462940 AATGAATGAA
** * *
462950 CAAAATAATAATGCAT-ATGAGTGTATTATCGGCATGAAATG-ATGCCAAAATAATAATCTATAT
1 CAAAATAATAACACATAATG-GTGCATTATCGACATG-AATGAATGCCAAAATAATAATCTATAT
* *
463013 GGGTGTATTATCAGCATGAAAGGATACCAAAATAATAATGCATATGGATGCATTATCGGCATGAA
64 GGGTGCATTATCAGCATGAAAGGATACCAAAACAATAATGCATATGGATGCATTATCGGCATGAA
* * ** *
463078 ATGATGCCAAAAATAATAATGCATATAGGTGCATTATTGGTATGAAAAGATGC
129 AGGATGCCAAAAATAATAATGCATATAGGTGCACTATCAGCATGAAAAGATGC
** * *
463131 CAAAATAATAATGCGTAATGGTGCATTATCGACATGAATGAATGCTAAAATAATAATGC-ATATG
1 CAAAATAATAACACATAATGGTGCATTATCGACATGAATGAATGCCAAAATAATAAT-CTATATG
** * *
463195 GGTGCATTATTGGCATGAAAGGATGCCAAAACAATAATGCATATGGGTGCATTATCGGCA-GAAA
65 GGTGCATTATCAGCATGAAAGGATACCAAAACAATAATGCATATGGATGCATTATCGGCATG-AA
* ** * *
463259 AGGATGCCATAGTTGA-AATGCATAT-GAGTGCACTATCAGCAT-AAAAGTATGT
129 AGGATGCCAAAAATAATAATGCATATAG-GTGCACTATCAGCATGAAAAG-ATGC
* * **
463311 CATAATTGAA-AACACATAATGTTGCATTATAAACATGAATGAATG
1 CA-AAAT-AATAACACATAATGGTGCATTATCGACATGAATGAATG
463356 TTATTAATGA
Statistics
Matches: 190, Mismatches: 27, Indels: 16
0.82 0.12 0.07
Matches are distributed among these distances:
179 6 0.03
180 30 0.16
181 148 0.78
182 6 0.03
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (181 bp):
CAAAATAATAACACATAATGGTGCATTATCGACATGAATGAATGCCAAAATAATAATCTATATGG
GTGCATTATCAGCATGAAAGGATACCAAAACAATAATGCATATGGATGCATTATCGGCATGAAAG
GATGCCAAAAATAATAATGCATATAGGTGCACTATCAGCATGAAAAGATGC
Found at i:467305 original size:36 final size:36
Alignment explanation
Indices: 467258--467332 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
467248 ATATGATAGA
467258 TTACATGAACAAATCATAAG-ACTATTTGAAATTTTT
1 TTACATGAACAAATCATAAGAAC-ATTTGAAATTTTT
* *
467294 TTACATGAACAATTCATAAGAACATTTGAATTTTTT
1 TTACATGAACAAATCATAAGAACATTTGAAATTTTT
467330 TTA
1 TTA
467333 GAAATGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 34 0.94
37 2 0.06
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.41
Consensus pattern (36 bp):
TTACATGAACAAATCATAAGAACATTTGAAATTTTT
Found at i:480354 original size:21 final size:21
Alignment explanation
Indices: 480330--480398 Score: 84
Period size: 21 Copynumber: 3.2 Consensus size: 21
480320 GAATCGATAC
480330 CCCCTTGAAGGGGAACCGATT
1 CCCCTTGAAGGGGAACCGATT
480351 CCCCCTTTGAAGGGGAACCGATT
1 -CCCC-TTGAAGGGGAACCGATT
* * * *
480374 CCCCCTGTAGGGGAATCGATA
1 CCCCTTGAAGGGGAACCGATT
480395 CCCC
1 CCCC
480399 CCCTGGGGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
21 17 0.40
22 8 0.19
23 17 0.40
ACGTcount: A:0.22, C:0.33, G:0.26, T:0.19
Consensus pattern (21 bp):
CCCCTTGAAGGGGAACCGATT
Found at i:480399 original size:21 final size:22
Alignment explanation
Indices: 480318--480399 Score: 103
Period size: 23 Copynumber: 3.7 Consensus size: 22
480308 ATAGGGCAGA
*
480318 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATACCCCCTTGAAG
*
480340 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCC-TTGAAG
* *
480363 GGGAACCGATTCCCCC-TGTAG
1 GGGAACCGATACCCCCTTGAAG
*
480384 GGGAATCGATACCCCC
1 GGGAACCGATACCCCC
480400 CCTGGGGTTC
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
21 18 0.33
22 14 0.26
23 22 0.41
ACGTcount: A:0.23, C:0.32, G:0.27, T:0.18
Consensus pattern (22 bp):
GGGAACCGATACCCCCTTGAAG
Found at i:480401 original size:23 final size:22
Alignment explanation
Indices: 480318--480400 Score: 87
Period size: 22 Copynumber: 3.8 Consensus size: 22
480308 ATAGGGCAGA
* *
480318 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATACCCCCCTGAAG
* *
480340 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCC-CTGAAG
* *
480363 GGGAACCGAT-TCCCCCTGTAG
1 GGGAACCGATACCCCCCTGAAG
*
480384 GGGAATCGATACCCCCC
1 GGGAACCGATACCCCCC
480401 CTGGGGTTCT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
21 13 0.25
22 23 0.44
23 16 0.31
ACGTcount: A:0.23, C:0.33, G:0.27, T:0.18
Consensus pattern (22 bp):
GGGAACCGATACCCCCCTGAAG
Found at i:482108 original size:21 final size:21
Alignment explanation
Indices: 482073--482113 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
482063 TTCCGATATG
* * *
482073 CTTCCATGGATTCTCGCTTCA
1 CTTCCATAGAATCTCACTTCA
482094 CTTCCATAGAATCTCACTTC
1 CTTCCATAGAATCTCACTTC
482114 TCGAGGGAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.34, G:0.10, T:0.37
Consensus pattern (21 bp):
CTTCCATAGAATCTCACTTCA
Found at i:490965 original size:15 final size:15
Alignment explanation
Indices: 490945--490974 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
490935 ACAAAAACCC
490945 TTTTTTTTTT-CTTT
1 TTTTTTTTTTCCTTT
490959 TTTTTTTTTTCCTTT
1 TTTTTTTTTTCCTTT
490974 T
1 T
490975 ATTTGCTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTTTTTTTCCTTT
Found at i:491225 original size:60 final size:60
Alignment explanation
Indices: 491123--491297 Score: 235
Period size: 60 Copynumber: 2.9 Consensus size: 60
491113 ATTTAGTCCT
* * *
491123 CCAATTATTGGGCACCACTTTATTGAGTCTCCTACTAATAAAAGTTATAAAATGAATCCC
1 CCAACTATAGGGCACCACTTTATTGAGTCTCCTACTATTAAAAGTTATAAAATGAATCCC
491183 CCAACTATAGGGCACCACTTTATTGAGTCTCCTACTATTAAAAGTTATAAAATGAATCCC
1 CCAACTATAGGGCACCACTTTATTGAGTCTCCTACTATTAAAAGTTATAAAATGAATCCC
* ** * * * *
491243 CTAACTATAGGGCATTATTTTTTTGAATGT-TTCGACTATTAAAAGTTATAAAATG
1 CCAACTATAGGGCACCACTTTATTG-A-GTCTCCTACTATTAAAAGTTATAAAATG
491298 GTTATCGGAC
Statistics
Matches: 103, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
60 77 0.75
61 24 0.23
62 2 0.02
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (60 bp):
CCAACTATAGGGCACCACTTTATTGAGTCTCCTACTATTAAAAGTTATAAAATGAATCCC
Found at i:494040 original size:15 final size:15
Alignment explanation
Indices: 494022--494052 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
494012 AAATTCTAAA
494022 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
494037 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
494052 T
1 T
494053 CTATTTGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:494964 original size:14 final size:14
Alignment explanation
Indices: 494942--494982 Score: 57
Period size: 13 Copynumber: 3.0 Consensus size: 14
494932 TACTTCAAAG
494942 AAGAAGATTCCAAC
1 AAGAAGATTCCAAC
* *
494956 AAGACGATTCGAA-
1 AAGAAGATTCCAAC
494969 AAGAAGATTCCAAC
1 AAGAAGATTCCAAC
494983 TAAGTAATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.49, C:0.20, G:0.17, T:0.15
Consensus pattern (14 bp):
AAGAAGATTCCAAC
Found at i:494966 original size:69 final size:69
Alignment explanation
Indices: 494851--494988 Score: 267
Period size: 69 Copynumber: 2.0 Consensus size: 69
494841 AATAGCACAT
494851 TTCCATTTCCCCTACTTCAAAGAAGAAGATTCCAACAAGACAATTCGAAAAGAAGATTCCAACTA
1 TTCCATTTCCCCTACTTCAAAGAAGAAGATTCCAACAAGACAATTCGAAAAGAAGATTCCAACTA
494916 AGTA
66 AGTA
*
494920 TTCCATTTCCCCTACTTCAAAGAAGAAGATTCCAACAAGACGATTCGAAAAGAAGATTCCAACTA
1 TTCCATTTCCCCTACTTCAAAGAAGAAGATTCCAACAAGACAATTCGAAAAGAAGATTCCAACTA
494985 AGTA
66 AGTA
494989 ATTAACATAT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.41, C:0.23, G:0.12, T:0.23
Consensus pattern (69 bp):
TTCCATTTCCCCTACTTCAAAGAAGAAGATTCCAACAAGACAATTCGAAAAGAAGATTCCAACTA
AGTA
Found at i:497976 original size:22 final size:21
Alignment explanation
Indices: 497934--497973 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
497924 GTGTTTATTT
*
497934 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
497955 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
497974 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:504732 original size:2 final size:2
Alignment explanation
Indices: 504727--504756 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
504717 TGTGTGTGTG
504727 TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
504757 GTTTGTTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:509583 original size:2 final size:2
Alignment explanation
Indices: 509576--509600 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
509566 GAGAAAGACC
509576 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
509601 TGTAAATAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:511255 original size:29 final size:29
Alignment explanation
Indices: 511213--511298 Score: 147
Period size: 29 Copynumber: 3.0 Consensus size: 29
511203 AGTGTTGGTC
511213 GTAGGTCGCCATGC-CTTCCGGGCGACCTT
1 GTAGGTCGCCATGCAC-TCCGGGCGACCTT
511242 GTAGGTCGCCATGCACTCCGGGCGACCTT
1 GTAGGTCGCCATGCACTCCGGGCGACCTT
*
511271 GTAGGTCGCCATGCACTCTGGGCGACCT
1 GTAGGTCGCCATGCACTCCGGGCGACCT
511299 ACCCTTGCTC
Statistics
Matches: 55, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
29 54 0.98
30 1 0.02
ACGTcount: A:0.13, C:0.34, G:0.31, T:0.22
Consensus pattern (29 bp):
GTAGGTCGCCATGCACTCCGGGCGACCTT
Found at i:511394 original size:29 final size:29
Alignment explanation
Indices: 511357--511441 Score: 152
Period size: 29 Copynumber: 2.9 Consensus size: 29
511347 TCCCAACACA
*
511357 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
*
511386 TAGGCCGCCATGCACTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
511415 TAGGTCGCCATGCACTCCGGGCGACCT
1 TAGGTCGCCATGCACTCCGGGCGACCT
511442 ACCCTCGCTC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.13, C:0.38, G:0.31, T:0.19
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCGGGCGACCTTG
Found at i:511486 original size:33 final size:33
Alignment explanation
Indices: 511445--511528 Score: 114
Period size: 33 Copynumber: 2.5 Consensus size: 33
511435 GCGACCTACC
* *
511445 CTCGCTCGGCTGCCCTCGGATTCCCTCACATAG
1 CTCGCTCGGATGCCCTCGGATGCCCTCACATAG
* *
511478 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
1 CTCGCTCGGATGCCCTCGGATGCCCTCACATAG
* *
511511 CTCGTTCGGATGCTCTCG
1 CTCGCTCGGATGCCCTCG
511529 AATAGCCTCG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.10, C:0.39, G:0.25, T:0.26
Consensus pattern (33 bp):
CTCGCTCGGATGCCCTCGGATGCCCTCACATAG
Found at i:511520 original size:23 final size:24
Alignment explanation
Indices: 511493--511552 Score: 77
Period size: 23 Copynumber: 2.5 Consensus size: 24
511483 TCGGTTGCCC
* *
511493 TCGGATGCCCTCGCATAG-CTCGT
1 TCGGATGCCCTCGAATAGCCTCGG
*
511516 TCGGATGCTCTCGAATAGCCTCGG
1 TCGGATGCCCTCGAATAGCCTCGG
*
511540 TCGGATGGCCTCG
1 TCGGATGCCCTCG
511553 GATGCCCAGC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
23 16 0.52
24 15 0.48
ACGTcount: A:0.13, C:0.32, G:0.30, T:0.25
Consensus pattern (24 bp):
TCGGATGCCCTCGAATAGCCTCGG
Found at i:522328 original size:21 final size:21
Alignment explanation
Indices: 522303--522354 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
522293 TTTAACCTAT
*
522303 TTATAAGATTGTATGAAATGA
1 TTATAAGATAGTATGAAATGA
*
522324 TTATAAGATAGTCTGAAATGA
1 TTATAAGATAGTATGAAATGA
522345 TTATAAGATA
1 TTATAAGATA
522355 ATATTTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.44, C:0.02, G:0.17, T:0.37
Consensus pattern (21 bp):
TTATAAGATAGTATGAAATGA
Found at i:522950 original size:16 final size:16
Alignment explanation
Indices: 522925--522972 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
522915 ATTGCTCAAA
*
522925 TCGTTGCTCATTAAGT
1 TCGTTTCTCATTAAGT
*
522941 TCGTTTCTCATTAAGC
1 TCGTTTCTCATTAAGT
* *
522957 TCGTTTATCGTTAAGT
1 TCGTTTCTCATTAAGT
522973 CCATCGAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.19, C:0.19, G:0.17, T:0.46
Consensus pattern (16 bp):
TCGTTTCTCATTAAGT
Found at i:523121 original size:28 final size:28
Alignment explanation
Indices: 523089--523152 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
523079 AAGAGTGTAT
523089 GAAACAATTTCAAAATCTAAACTCCAAA
1 GAAACAATTTCAAAATCTAAACTCCAAA
*
523117 GAAACAATTTCAAAATCTAAACTTCAAA
1 GAAACAATTTCAAAATCTAAACTCCAAA
*
523145 GTAACAAT
1 GAAACAAT
523153 CAACAAATAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.53, C:0.19, G:0.05, T:0.23
Consensus pattern (28 bp):
GAAACAATTTCAAAATCTAAACTCCAAA
Found at i:527400 original size:205 final size:207
Alignment explanation
Indices: 527016--527427 Score: 810
Period size: 205 Copynumber: 2.0 Consensus size: 207
527006 AAAAGATTTC
527016 GAGCACCAAAAGAGTGGCTTAAAATCTATCTTAAGGAAACTATGTAGAGACAAGCCTCAACTGTT
1 GAGCACCAAAAGAGTGGCTTAAAATCTATCTTAAGGAAACTATGTAGAGACAAGCCTCAACTGTT
527081 TCCAATCGATGGATCAATAAAAAAGAATATCAATAAAGAAGAGTATTTTTTCTGTCTATATTATT
66 TCCAATCGATGGATCAATAAAAAAGAATATCAATAAAGAAGAGTATTTTTTCTGTCTATATTATT
527146 TTATTTATTATTTAATAAATTTGATTTCTTTTTTTTTATTTTCTCTCAAATTGTTATTTTGGATA
131 TTATTTATTATTTAATAAATTTGATTTCTTTTTTTTTATTTTCTCTCAAATTGTTATTTTGGATA
527211 ATAATC-TAAGA
196 ATAATCTTAAGA
527222 GAGCACCAAAAGAGTGGCTTAAAATCTATCTTAAGGAAACTATGTAGAGACAAGCCTCAACTGTT
1 GAGCACCAAAAGAGTGGCTTAAAATCTATCTTAAGGAAACTATGTAGAGACAAGCCTCAACTGTT
527287 TCCAATCGATGGATCAAT-AAAAAGAATATCAATAAAGAAGAGTATTTTTTCTGTCTATATTATT
66 TCCAATCGATGGATCAATAAAAAAGAATATCAATAAAGAAGAGTATTTTTTCTGTCTATATTATT
527351 TTATTTATTATTTAATAAATTTGATTTCTTTTTTTTTATTTTCTCTCAAATTGTTATTTTGGATA
131 TTATTTATTATTTAATAAATTTGATTTCTTTTTTTTTATTTTCTCTCAAATTGTTATTTTGGATA
527416 ATAATCTTAAGA
196 ATAATCTTAAGA
527428 CATATTTAAA
Statistics
Matches: 205, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
205 117 0.57
206 88 0.43
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.40
Consensus pattern (207 bp):
GAGCACCAAAAGAGTGGCTTAAAATCTATCTTAAGGAAACTATGTAGAGACAAGCCTCAACTGTT
TCCAATCGATGGATCAATAAAAAAGAATATCAATAAAGAAGAGTATTTTTTCTGTCTATATTATT
TTATTTATTATTTAATAAATTTGATTTCTTTTTTTTTATTTTCTCTCAAATTGTTATTTTGGATA
ATAATCTTAAGA
Found at i:530791 original size:3 final size:3
Alignment explanation
Indices: 530785--530819 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
530775 TATTATTATT
530785 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
530820 GGTAAATATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Done.