Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003142.1 Hibiscus syriacus cultivar Beakdansim tig00006613_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: 553945
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 2 of 3
Found at i:293062 original size:21 final size:21
Alignment explanation
Indices: 293023--293062 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
293013 CTACCTCTAA
*
293023 CTTAAACCATAAATTATAAAT
1 CTTAAACCATAAATCATAAAT
* *
293044 CTTAAACCCTATATCATAA
1 CTTAAACCATAAATCATAA
293063 CTATATATCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (21 bp):
CTTAAACCATAAATCATAAAT
Found at i:297728 original size:2 final size:2
Alignment explanation
Indices: 297721--297762 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
297711 TTGTACTCTT
297721 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
297763 CCAAATCGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:297986 original size:21 final size:21
Alignment explanation
Indices: 297960--298051 Score: 118
Period size: 21 Copynumber: 4.4 Consensus size: 21
297950 TTGAAAATCG
297960 CGTTGCGATAGTCTACAGTGT
1 CGTTGCGATAGTCTACAGTGT
297981 CGTTGCGATAGTCTACAGTGT
1 CGTTGCGATAGTCTACAGTGT
* * *
298002 CGTTGCGAT--TTTCCA-TTT
1 CGTTGCGATAGTCTACAGTGT
298020 CGCGTTGCGATAGTCTACAGTGT
1 --CGTTGCGATAGTCTACAGTGT
298043 CGTTGCGAT
1 CGTTGCGAT
298052 TTTCCATTTC
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
18 2 0.03
19 4 0.07
20 9 0.15
21 39 0.65
22 4 0.07
23 2 0.03
ACGTcount: A:0.16, C:0.21, G:0.27, T:0.36
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAGTGT
Found at i:298027 original size:20 final size:20
Alignment explanation
Indices: 298002--298071 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
297992 TCTACAGTGT
298002 CGTTGCGATTTTCCATTTCG
1 CGTTGCGATTTTCCATTTCG
* * *
298022 CGTTGCGATAGTCTACA-GT-G
1 CGTTGCGAT--TTTCCATTTCG
298042 TCGTTGCGATTTTCCATTTCG
1 -CGTTGCGATTTTCCATTTCG
298063 CGTTGCGAT
1 CGTTGCGAT
298072 AGTTGAAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
19 4 0.10
20 20 0.51
21 11 0.28
22 4 0.10
ACGTcount: A:0.13, C:0.23, G:0.24, T:0.40
Consensus pattern (20 bp):
CGTTGCGATTTTCCATTTCG
Found at i:298030 original size:41 final size:41
Alignment explanation
Indices: 297981--298074 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
297971 TCTACAGTGT
297981 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
1 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
298022 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
1 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
298063 CGTTGCGATAGT
1 CGTTGCGATAGT
298075 TGAAAATCGC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.15, C:0.21, G:0.26, T:0.38
Consensus pattern (41 bp):
CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
Found at i:298037 original size:62 final size:59
Alignment explanation
Indices: 297957--298213 Score: 194
Period size: 62 Copynumber: 4.4 Consensus size: 59
297947 GCGTTGAAAA
297957 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGAT-GT-TACA-TGTCGTTGCGATTTTCCATT
* * * * ** **
298019 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATGTTACATGT--CGTTGCGAT-TTTCCATT
* *
298081 TCGCGTTGCGATAGTGTACAGTGTCATTGC---G----A--TCGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATGTTACATGTCGTTGCGATTTTCCATT
* * * *
298131 TCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATAGTGTACAGTGTCATTGCGATTTTCCATC
1 TCGCGTTGCGATAGTCT-ACAGT-GTCGTTGCGAT-GT-TACA-TGTCGTTGCGATTTTCCATT
* *
298193 TCGCATTGCGATAGTGTACAG
1 TCGCGTTGCGATAGTCTACAG
298214 ATAGTCTACA
Statistics
Matches: 153, Mismatches: 24, Indels: 36
0.72 0.11 0.17
Matches are distributed among these distances:
49 1 0.01
50 26 0.17
51 10 0.07
53 1 0.01
54 1 0.01
55 1 0.01
59 3 0.02
60 3 0.02
61 10 0.07
62 96 0.63
63 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (59 bp):
TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATGTTACATGTCGTTGCGATTTTCCATT
Found at i:298088 original size:41 final size:41
Alignment explanation
Indices: 297981--298092 Score: 156
Period size: 41 Copynumber: 2.7 Consensus size: 41
297971 TCTACAGTGT
* *
297981 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
1 CGTTGCGATAGTCTAAAATGTCGTTGCGATTTTCCATTTCG
* *
298022 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
1 CGTTGCGATAGTCTAAAATGTCGTTGCGATTTTCCATTTCG
298063 CGTTGCGATAGT-TGAAAATCG-CGTTGCGAT
1 CGTTGCGATAGTCT-AAAAT-GTCGTTGCGAT
298093 AGTGTACAGT
Statistics
Matches: 67, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
40 1 0.01
41 65 0.97
42 1 0.01
ACGTcount: A:0.17, C:0.21, G:0.26, T:0.37
Consensus pattern (41 bp):
CGTTGCGATAGTCTAAAATGTCGTTGCGATTTTCCATTTCG
Found at i:298158 original size:71 final size:71
Alignment explanation
Indices: 298042--298184 Score: 286
Period size: 71 Copynumber: 2.0 Consensus size: 71
298032 GTCTACAGTG
298042 TCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTGTACAGTGTCA
1 TCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTGTACAGTGTCA
298107 TTGCGA
66 TTGCGA
298113 TCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTGTACAGTGTCA
1 TCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTGTACAGTGTCA
298178 TTGCGA
66 TTGCGA
298184 T
1 T
298185 TTTCCATCTC
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 72 1.00
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.36
Consensus pattern (71 bp):
TCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTGTACAGTGTCA
TTGCGA
Found at i:298843 original size:5 final size:5
Alignment explanation
Indices: 298835--298860 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
298825 CGCCGTCTCG
298835 TCGTC TCGTC TCGTC TCGTC TCGTC T
1 TCGTC TCGTC TCGTC TCGTC TCGTC T
298861 AGTCGTGGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.38, G:0.19, T:0.42
Consensus pattern (5 bp):
TCGTC
Found at i:298873 original size:6 final size:6
Alignment explanation
Indices: 298862--298887 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
298852 GTCTCGTCTA
298862 GTCGTG GTCGTG GTCGTG GTCGTG GT
1 GTCGTG GTCGTG GTCGTG GTCGTG GT
298888 AATACGTGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.50, T:0.35
Consensus pattern (6 bp):
GTCGTG
Found at i:298964 original size:21 final size:21
Alignment explanation
Indices: 298938--299009 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 21
298928 TAGAGAAAAT
298938 TATCGCAACGACACTGTAGAC
1 TATCGCAACGACACTGTAGAC
* *
298959 TATCGCAACG-CGAAATG--GAA
1 TATCGCAACGAC--ACTGTAGAC
*
298979 AATCGCAACGACACTGTAGAC
1 TATCGCAACGACACTGTAGAC
299000 TATCGCAACG
1 TATCGCAACG
299010 CGAAAAGGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
19 3 0.08
20 12 0.30
21 22 0.55
22 3 0.08
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.17
Consensus pattern (21 bp):
TATCGCAACGACACTGTAGAC
Found at i:298985 original size:41 final size:40
Alignment explanation
Indices: 298957--299259 Score: 450
Period size: 41 Copynumber: 7.4 Consensus size: 40
298947 GACACTGTAG
* *
298957 ACTATCGCAACGCGAAATGGAAAATCGCAACGAC-ACTGT-A
1 ACTATCGCAACGCGAAATAGAAAATCGCAACG-CGA-TTTCA
298997 GACTATCGCAACGCGAAA-AGGAAAATCGCAACGCGATTTCCA
1 -ACTATCGCAACGCGAAATA-GAAAATCGCAACGCGATTT-CA
*
299039 ACTATCGCAACGCGAAATAGAAAATCGCAATGCGATTTTCA
1 ACTATCGCAACGCGAAATAGAAAATCGCAACGCGA-TTTCA
299080 ACTATCGCAACGCGAAATAGAAAATCGCAACGCGATTTCCA
1 ACTATCGCAACGCGAAATAGAAAATCGCAACGCGATTT-CA
299121 ACTATCGCAACGCGAAATAGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATAGAAAATCGCAACGCGA-TTTCA
299162 ACTATCGCAACGCGAAATAGAAAATCGCAACGCGATTTCCA
1 ACTATCGCAACGCGAAATAGAAAATCGCAACGCGATTT-CA
* *
299203 ACTATCGCAACGCGAAATAGAAAATCACAATGCGATTTTCA
1 ACTATCGCAACGCGAAATAGAAAATCGCAACGCGA-TTTCA
299244 ACTATCGCAACGCGAA
1 ACTATCGCAACGCGAA
299260 TTTGCGATTT
Statistics
Matches: 246, Mismatches: 6, Indels: 20
0.90 0.02 0.07
Matches are distributed among these distances:
40 9 0.04
41 226 0.92
42 11 0.04
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (40 bp):
ACTATCGCAACGCGAAATAGAAAATCGCAACGCGATTTCA
Found at i:299047 original size:82 final size:82
Alignment explanation
Indices: 298957--299259 Score: 504
Period size: 82 Copynumber: 3.7 Consensus size: 82
298947 GACACTGTAG
* * *
298957 ACTATCGCAACGCGAAATGGAAAATCGCAACGAC-ACTGT-AGACTATCGCAACGCGAAA-AGGA
1 ACTATCGCAACGCGAAATAGAAAATCGCAACG-CGATTTTCA-ACTATCGCAACGCGAAATA-GA
299019 AAATCGCAACGCGATTTCCA
63 AAATCGCAACGCGATTTCCA
*
299039 ACTATCGCAACGCGAAATAGAAAATCGCAATGCGATTTTCAACTATCGCAACGCGAAATAGAAAA
1 ACTATCGCAACGCGAAATAGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATAGAAAA
299104 TCGCAACGCGATTTCCA
66 TCGCAACGCGATTTCCA
299121 ACTATCGCAACGCGAAATAGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATAGAAAA
1 ACTATCGCAACGCGAAATAGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATAGAAAA
299186 TCGCAACGCGATTTCCA
66 TCGCAACGCGATTTCCA
* *
299203 ACTATCGCAACGCGAAATAGAAAATCACAATGCGATTTTCAACTATCGCAACGCGAA
1 ACTATCGCAACGCGAAATAGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAA
299260 TTTGCGATTT
Statistics
Matches: 211, Mismatches: 7, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
81 1 0.00
82 208 0.99
83 2 0.01
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (82 bp):
ACTATCGCAACGCGAAATAGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATAGAAAA
TCGCAACGCGATTTCCA
Found at i:302908 original size:60 final size:59
Alignment explanation
Indices: 302722--302910 Score: 175
Period size: 60 Copynumber: 3.2 Consensus size: 59
302712 ATATACGTAT
* * * *
302722 AATTTAGGATAAAATTGAAATATTCAAAAAGTTTGA-GACCAATTTAGAATGAAGATCACA
1 AATTAAGGATAAAATTGAAATATT-AAAAAGTTTGAGGACTAATTTAAAATGAA-ATCATA
* ** * * * *
302782 ATTTGGGGATGAAAA-TGAAATGTTAAAAATTTTGAGGACTAATTTATAATGATAATAATA
1 AATTAAGGAT-AAAATTGAAATATTAAAAAGTTTGAGGACTAATTTAAAATGA-AATCATA
** * **
302842 GGTTAAGGATAAAATTGAAATATTTAAAAGTTCAAGGACTAATTTAAAATGAGAATCATA
1 AATTAAGGATAAAATTGAAATATTAAAAAGTTTGAGGACTAATTTAAAATGA-AATCATA
302902 AATTAAGGA
1 AATTAAGGA
302911 CGTAATATAA
Statistics
Matches: 102, Mismatches: 23, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
59 14 0.14
60 83 0.81
61 5 0.05
ACGTcount: A:0.48, C:0.05, G:0.17, T:0.31
Consensus pattern (59 bp):
AATTAAGGATAAAATTGAAATATTAAAAAGTTTGAGGACTAATTTAAAATGAAATCATA
Found at i:302946 original size:14 final size:14
Alignment explanation
Indices: 302929--302956 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
302919 AATTATTCAA
302929 GTAAAATTTTAAAG
1 GTAAAATTTTAAAG
302943 GTAAAATTTTAAAG
1 GTAAAATTTTAAAG
302957 TGCTTAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (14 bp):
GTAAAATTTTAAAG
Found at i:304532 original size:41 final size:41
Alignment explanation
Indices: 304469--304550 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
304459 CTACACTCCC
*
304469 TCCTTTACTATACTATCTGTTTTCAATGACATCTGCTTTAT
1 TCCTTTACTATACTATCCGTTTTCAATGACATCTGCTTTAT
* *
304510 TCCTTTACTATATTATCCGTTTTCGATGACATCTGCTTTAT
1 TCCTTTACTATACTATCCGTTTTCAATGACATCTGCTTTAT
304551 ATGCTTGACT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.21, C:0.22, G:0.09, T:0.49
Consensus pattern (41 bp):
TCCTTTACTATACTATCCGTTTTCAATGACATCTGCTTTAT
Found at i:310548 original size:21 final size:21
Alignment explanation
Indices: 310524--310563 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
310514 TTTATTTTAT
310524 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
310545 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
310564 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:310612 original size:33 final size:32
Alignment explanation
Indices: 310558--310656 Score: 153
Period size: 33 Copynumber: 3.0 Consensus size: 32
310548 TTTGTTTCAA
310558 TTATCGAACTTGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGAAGTTTTTAAGTATTTGAAT
310590 TTATCGAACTTGAAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTG-AAGTTTTTAAGTATTTGAAT
* * *
310623 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
310656 T
1 T
310657 ATGTTGAGTT
Statistics
Matches: 62, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
32 12 0.19
33 49 0.79
34 1 0.02
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.45
Consensus pattern (32 bp):
TTATCGAACTTGAAGTTTTTAAGTATTTGAAT
Found at i:310685 original size:13 final size:13
Alignment explanation
Indices: 310642--310696 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
310632 TTGGAAGTAT
310642 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
310655 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
310669 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
310682 TTAAGTATTTGAA
1 TTAAGTATTTCAA
310695 TT
1 TT
310697 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:310918 original size:21 final size:21
Alignment explanation
Indices: 310892--310948 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
310882 TGGAGCGTGG
*
310892 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
310913 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
310934 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
310949 AAGTGTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:311167 original size:15 final size:15
Alignment explanation
Indices: 311115--311169 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
311105 ATCTGGAATA
*
311115 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
* *
311130 TTATAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
311145 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
311162 TTAAAACC
1 TTAAAACC
311170 AAAACCGATT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
15 21 0.64
17 12 0.36
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.45
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:312209 original size:32 final size:32
Alignment explanation
Indices: 312148--312255 Score: 139
Period size: 32 Copynumber: 3.4 Consensus size: 32
312138 TTTTATTCAA
* * *
312148 TAAATTTT-T-AAAAAAATATAAAATCATCAT
1 TAAATTTTATCAAAATATTATAAAATAATCAT
*
312178 TAAATTTTATCAAAATATTATAATATAATCAT
1 TAAATTTTATCAAAATATTATAAAATAATCAT
* * *
312210 TAAATTTTATCAAATTATTACAAAATGATCAT
1 TAAATTTTATCAAAATATTATAAAATAATCAT
312242 TAAATTTTATCAAA
1 TAAATTTTATCAAA
312256 CTTCTATAAT
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
30 8 0.12
31 1 0.01
32 59 0.87
ACGTcount: A:0.51, C:0.07, G:0.01, T:0.41
Consensus pattern (32 bp):
TAAATTTTATCAAAATATTATAAAATAATCAT
Found at i:317631 original size:2 final size:2
Alignment explanation
Indices: 317624--317651 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
317614 AAAGTTAATA
317624 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
317652 TATTTTGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:322269 original size:30 final size:30
Alignment explanation
Indices: 322235--322338 Score: 147
Period size: 30 Copynumber: 3.4 Consensus size: 30
322225 TTACAGTTCG
*
322235 AATGAAAGTCGTCGGGTGGTTTGGGCGACC
1 AATGAAGGTCGTCGGGTGGTTTGGGCGACC
*
322265 AATGAAGGTCGTCGGGTGGTCTGGGCGACCAAC
1 AATGAAGGTCGTCGGGTGGTTTGGGCGA-C--C
322298 AATGAAGGTCGTCGGGT-GTTCTGGGCGACC
1 AATGAAGGTCGTCGGGTGGTT-TGGGCGACC
322328 AATGAAGGTCG
1 AATGAAGGTCG
322339 ACAGGTGATC
Statistics
Matches: 67, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
30 38 0.57
31 1 0.01
32 3 0.04
33 25 0.37
ACGTcount: A:0.21, C:0.18, G:0.39, T:0.21
Consensus pattern (30 bp):
AATGAAGGTCGTCGGGTGGTTTGGGCGACC
Found at i:322306 original size:33 final size:33
Alignment explanation
Indices: 322235--322329 Score: 142
Period size: 33 Copynumber: 3.0 Consensus size: 33
322225 TTACAGTTCG
* *
322235 AATGAAAGTCGTCGGGTGGTTTGGGCGA-C--C
1 AATGAAGGTCGTCGGGTGGTCTGGGCGACCAAC
322265 AATGAAGGTCGTCGGGTGGTCTGGGCGACCAAC
1 AATGAAGGTCGTCGGGTGGTCTGGGCGACCAAC
*
322298 AATGAAGGTCGTCGGGTGTTCTGGGCGACCAA
1 AATGAAGGTCGTCGGGTGGTCTGGGCGACCAA
322330 TGAAGGTCGA
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
30 26 0.44
31 1 0.02
33 32 0.54
ACGTcount: A:0.21, C:0.19, G:0.39, T:0.21
Consensus pattern (33 bp):
AATGAAGGTCGTCGGGTGGTCTGGGCGACCAAC
Found at i:322362 original size:63 final size:62
Alignment explanation
Indices: 322235--322363 Score: 154
Period size: 63 Copynumber: 2.0 Consensus size: 62
322225 TTACAGTTCG
* * * **
322235 AATGAAAGTCGTCGGGTGGTTTGGGCGACCAATGAAGGTCGTCGGGTGGTCTGGGCGACCAAC
1 AATGAAAGTCGTCGGGTGGTTTGGGCGACCAATGAAGGTCGACAGGTGATCTGGAAGA-CAAC
*
322298 AATGAAGGTCGTCGGGT-GTTCTGGGCGACCAATGAAGGTCGACAGGTGATCCATGGAAGA-AAC
1 AATGAAAGTCGTCGGGTGGTT-TGGGCGACCAATGAAGGTCGACAGGTGAT-C-TGGAAGACAAC
322361 AAT
1 AAT
322364 CAAACAATAA
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
62 3 0.05
63 48 0.84
64 1 0.02
65 5 0.09
ACGTcount: A:0.26, C:0.18, G:0.36, T:0.20
Consensus pattern (62 bp):
AATGAAAGTCGTCGGGTGGTTTGGGCGACCAATGAAGGTCGACAGGTGATCTGGAAGACAAC
Found at i:322542 original size:50 final size:50
Alignment explanation
Indices: 322485--322587 Score: 206
Period size: 50 Copynumber: 2.1 Consensus size: 50
322475 GTTTATCCTA
322485 ATTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGT
1 ATTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGT
322535 ATTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGT
1 ATTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGT
322585 ATT
1 ATT
322588 CAATAATTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.26, C:0.02, G:0.16, T:0.56
Consensus pattern (50 bp):
ATTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGT
Found at i:324367 original size:28 final size:29
Alignment explanation
Indices: 324336--324393 Score: 68
Period size: 28 Copynumber: 2.0 Consensus size: 29
324326 CTTGTGAGAA
324336 AAAAATA-AATAGAAG-AGAAAACTT-TAAT
1 AAAAATAGAA-AGAAGAAGAAAA-TTGTAAT
*
324364 AAAACTAGAAAGAAGAAGAAAATTGTAAT
1 AAAAATAGAAAGAAGAAGAAAATTGTAAT
324393 A
1 A
324394 TGAGTTGTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
28 13 0.50
29 13 0.50
ACGTcount: A:0.64, C:0.03, G:0.14, T:0.19
Consensus pattern (29 bp):
AAAAATAGAAAGAAGAAGAAAATTGTAAT
Found at i:325827 original size:16 final size:16
Alignment explanation
Indices: 325806--325838 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
325796 CACTATTCAT
*
325806 GTGAATAGTGAATTTC
1 GTGAATAGTGAAATTC
325822 GTGAATAGTGAAATTC
1 GTGAATAGTGAAATTC
325838 G
1 G
325839 GTCGGCGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.33
Consensus pattern (16 bp):
GTGAATAGTGAAATTC
Found at i:332286 original size:43 final size:43
Alignment explanation
Indices: 332216--332440 Score: 324
Period size: 43 Copynumber: 5.2 Consensus size: 43
332206 GCAAAAAATA
* *
332216 TTGATATTTTAGCGGCGTTTGTCATAAAAACGCCGCAATAGGTG
1 TTGATA-TTTAGTGGCGTTTGTTATAAAAACGCCGCAATAGGTG
* *
332260 TTGATATTTAGTGGCGTTTGTTATAAAAACACCGCAATAAGTG
1 TTGATATTTAGTGGCGTTTGTTATAAAAACGCCGCAATAGGTG
*
332303 TTGATATTTAGTGGCGTTTGTTATAAAAACACCGCAATAGGTG
1 TTGATATTTAGTGGCGTTTGTTATAAAAACGCCGCAATAGGTG
* *
332346 TTGATATTTAGTGGCGTTTGTTATATAAACGCCGTAATAGGTG
1 TTGATATTTAGTGGCGTTTGTTATAAAAACGCCGCAATAGGTG
* * * * * *
332389 TTGATATTTAGCGGTGTTTGTCATGAAAACGCCACAGTAGGTG
1 TTGATATTTAGTGGCGTTTGTTATAAAAACGCCGCAATAGGTG
332432 TTGATATTT
1 TTGATATTT
332441 TACGGCGTTT
Statistics
Matches: 165, Mismatches: 16, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
43 159 0.96
44 6 0.04
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.36
Consensus pattern (43 bp):
TTGATATTTAGTGGCGTTTGTTATAAAAACGCCGCAATAGGTG
Found at i:332491 original size:129 final size:129
Alignment explanation
Indices: 332214--332508 Score: 315
Period size: 129 Copynumber: 2.3 Consensus size: 129
332204 CCGCAAAAAA
* * *
332214 TATTGATATTTTAGCGGCGTTTGTCATAAAAACGCCGCAATAGGTGTTGATATTTAGTGGCGTTT
1 TATTAATATTTT-GCGGCGTTTGTTATAAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTT
* * *
332279 GTTATAAAAACACCGCAATAAGTGTTGATATTTAGTGGCGTTTGTTATAAAAACACCGCAATAGG
65 GTCATAAAAACACCACAATAAGTGTTGATATTTAGCGGCGTTTGTTATAAAAACACCGCAATAGG
* * * * * * *
332344 TGTTGATATTTAGTGGCGTTTGTTATATAAACGCCGTAATAGGTGTTGATATTTAGCGGTGTTTG
1 TATTAATATTTTGCGGCGTTTGTTATAAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTG
* * * * * * ** * *
332409 TCATGAAAACGCCACAGTAGGTGTTGATATTTTA-CGGCGTTT-TTTTCACAAACGTCGCAGTAT
66 TCATAAAAACACCACAATAAGTGTTGATA-TTTAGCGGCGTTTGTTAT-AAAAACACCGCAATAG
332472 G
129 G
* * *
332473 TATTAATGTTTTGCGGCGTTTCTTCTAAAAACGCCG
1 TATTAATATTTTGCGGCGTTTGTTATAAAAACGCCG
332509 GTATAAGTCT
Statistics
Matches: 134, Mismatches: 29, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
128 3 0.02
129 117 0.87
130 14 0.10
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (129 bp):
TATTAATATTTTGCGGCGTTTGTTATAAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTG
TCATAAAAACACCACAATAAGTGTTGATATTTAGCGGCGTTTGTTATAAAAACACCGCAATAGG
Found at i:332574 original size:44 final size:41
Alignment explanation
Indices: 332498--332599 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 41
332488 GCGTTTCTTC
* * *
332498 TAAAAACGCCGGTATAA-GTCTGTATATAGCGGCGTTTGTATGA
1 TAAAAACGCCGCTA-AATGTATGTATATAGCGGCGGTTGT-T-A
* *
332541 TAAAAACGCCGCTAAATGTATGGTATATTGCGGCGGTTGTTT
1 TAAAAACGCCGCTAAATGTAT-GTATATAGCGGCGGTTGTTA
*
332583 TACAAACGCCGCTAAAT
1 TAAAAACGCCGCTAAAT
332600 AACACAGAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
42 18 0.35
43 17 0.33
44 16 0.31
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (41 bp):
TAAAAACGCCGCTAAATGTATGTATATAGCGGCGGTTGTTA
Found at i:333329 original size:22 final size:22
Alignment explanation
Indices: 333304--333347 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
333294 ATTAATTAAT
333304 TAAA-ATAAA-AAATGTCATGGTA
1 TAAATATAAATAAA-GTCA-GGTA
333326 TAAATATAAATAAAGTCAGGTA
1 TAAATATAAATAAAGTCAGGTA
333348 AATTTAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 8 0.40
23 9 0.45
24 3 0.15
ACGTcount: A:0.55, C:0.05, G:0.14, T:0.27
Consensus pattern (22 bp):
TAAATATAAATAAAGTCAGGTA
Found at i:335411 original size:36 final size:36
Alignment explanation
Indices: 335366--335436 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
335356 AAAATATTGA
335366 CATTGGTGTAGCTAATTATTCTAGGTAAACTATATT
1 CATTGGTGTAGCTAATTATTCTAGGTAAACTATATT
*
335402 CATTGGTGTAGTTAATTATTCTAGGTAAACTATAT
1 CATTGGTGTAGCTAATTATTCTAGGTAAACTATAT
335437 ATAATAATCC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (36 bp):
CATTGGTGTAGCTAATTATTCTAGGTAAACTATATT
Found at i:337502 original size:41 final size:40
Alignment explanation
Indices: 337254--337511 Score: 189
Period size: 41 Copynumber: 6.2 Consensus size: 40
337244 ATAAATATTT
** * *
337254 GCGGCGTTTGT-TGAAAAAACGCTGCTAAAGTATGAGTCTTTA
1 GCGGCGTTTGTAT--AAAAACGCCACTAAAGTACGA-TCTATA
* * *
337296 GCGGCGTTT-TCATTCAAAACGTCACTAAAGTACGAGTTTATA
1 GCGGCGTTTGT-A-TAAAAACGCCACTAAAGTACGA-TCTATA
* * * *
337338 GCGGCGTTTAG-ATTGAAAACACCACTAAAGTATGAATATATA
1 GCGGCGTTT-GTA-TAAAAACGCCACTAAAGTACG-ATCTATA
* * * * * *
337380 GCGACATTTGTATAGAAACACCACTAAAGTACTAGTATATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGA-TCTATA
* * * *
337421 GCAGTGTTTGTATAAAAGCGCCACTAACGTACGATTCTATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGA-TCTATA
*
337462 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGTACCTATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACG-ATCTATA
337503 GCGGCGTTT
1 GCGGCGTTT
337512 ATTGGAAAAA
Statistics
Matches: 173, Mismatches: 34, Indels: 19
0.77 0.15 0.08
Matches are distributed among these distances:
40 1 0.01
41 98 0.57
42 72 0.42
43 1 0.01
44 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (40 bp):
GCGGCGTTTGTATAAAAACGCCACTAAAGTACGATCTATA
Found at i:338940 original size:41 final size:41
Alignment explanation
Indices: 338894--339056 Score: 193
Period size: 41 Copynumber: 4.0 Consensus size: 41
338884 TAACATTTTG
*
338894 CGGCGTTTATAAAAAAAACGCCACTATTGATT-ACACTATTA
1 CGGCGTTTAT-CAAAAAACGCCACTATTGATTAACACTATTA
* * * * * *
338935 TGGCGTTTGTTAAAAAATGTCACTATTGATTAAAACTATTA
1 CGGCGTTTATCAAAAAACGCCACTATTGATTAACACTATTA
* * *
338976 CGGCGTTTTTCTAAAAACGCCACTATTGATTAACACTGTTA
1 CGGCGTTTATCAAAAAACGCCACTATTGATTAACACTATTA
* * *
339017 CGGCGTTTATCTAAAAACGCCACTATTTATTATCACTATT
1 CGGCGTTTATCAAAAAACGCCACTATTGATTAACACTATT
339057 GCAGCATTTT
Statistics
Matches: 103, Mismatches: 18, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
40 18 0.17
41 85 0.83
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (41 bp):
CGGCGTTTATCAAAAAACGCCACTATTGATTAACACTATTA
Found at i:338961 original size:40 final size:40
Alignment explanation
Indices: 338906--339084 Score: 182
Period size: 41 Copynumber: 4.4 Consensus size: 40
338896 GCGTTTATAA
*
338906 AAAAAACGCCACTATTGATT-ACACTATTATGGCGTTTGTT
1 AAAAAACGCCACTATTGATTAACACTATTACGGCGTTT-TT
* * *
338946 AAAAAATGTCACTATTGATTAAAACTATTACGGCGTTTTT
1 AAAAAACGCCACTATTGATTAACACTATTACGGCGTTTTT
* *
338986 CTAAAAACGCCACTATTGATTAACACTGTTACGGCGTTTATCT
1 -AAAAAACGCCACTATTGATTAACACTATTACGGCGTTT-T-T
* * * * * *
339029 -AAAAACGCCACTATTTATTATCACTATTGCAGCATTTTA
1 AAAAAACGCCACTATTGATTAACACTATTACGGCGTTTTT
339068 AGAATAAACGCCACTAT
1 A-AA-AAACGCCACTAT
339085 ATGTGTAATA
Statistics
Matches: 116, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
40 21 0.18
41 81 0.70
42 13 0.11
43 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34
Consensus pattern (40 bp):
AAAAAACGCCACTATTGATTAACACTATTACGGCGTTTTT
Found at i:340518 original size:31 final size:31
Alignment explanation
Indices: 340468--340554 Score: 131
Period size: 31 Copynumber: 2.8 Consensus size: 31
340458 TGAGCCCATT
340468 TTAATTAAA-AAAAACGAAAGTGATCATATC
1 TTAATTAAATAAAAACGAAAGTGATCATATC
* *
340498 TTAATTAAATAAAAATGAAAGTGGTCATATC
1 TTAATTAAATAAAAACGAAAGTGATCATATC
* *
340529 TTAACTAAATAAAAACAAAAGTGATC
1 TTAATTAAATAAAAACGAAAGTGATC
340555 GTATATTATG
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
30 9 0.18
31 41 0.82
ACGTcount: A:0.53, C:0.09, G:0.10, T:0.28
Consensus pattern (31 bp):
TTAATTAAATAAAAACGAAAGTGATCATATC
Found at i:355147 original size:32 final size:31
Alignment explanation
Indices: 355111--355175 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
355101 CATTTCAACG
*
355111 TTATAATAAATTG-TAAAATTGTAATGATTATT
1 TTATAAT-AATTGATAAAATT-TAATGATCATT
**
355143 TTATAATGTTTGATAAAATTTAATGATCATT
1 TTATAATAATTGATAAAATTTAATGATCATT
355174 TT
1 TT
355176 GTAACCACTC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
31 15 0.52
32 14 0.48
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (31 bp):
TTATAATAATTGATAAAATTTAATGATCATT
Found at i:356833 original size:12 final size:12
Alignment explanation
Indices: 356818--356845 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
356808 CTGCTGCTGC
356818 TGCTGCTGGGTT
1 TGCTGCTGGGTT
356830 TGCTGCTGGGTT
1 TGCTGCTGGGTT
356842 TGCT
1 TGCT
356846 ACTGCCAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.18, G:0.39, T:0.43
Consensus pattern (12 bp):
TGCTGCTGGGTT
Found at i:359859 original size:60 final size:60
Alignment explanation
Indices: 359741--359864 Score: 144
Period size: 60 Copynumber: 2.1 Consensus size: 60
359731 TTTGGATGAA
* * * * *
359741 TTTGGGGATGAAATTAGGAGATCTAAAAGTTTAGGGACTAATTTAGAATGAGATTCATAG
1 TTTGAGGATGAAATTAGAAGATCTAAAAGTTTAAGGAATAATTTAGAATGAGAGTCATAG
* * *
359801 TTTGAGGATGAAATTAGAATGTTC-AAAAGTTTAAGGAATAATTT-GAAATGAGGGTCATAT
1 TTTGAGGATGAAATTAGAA-GATCTAAAAGTTTAAGGAATAATTTAG-AATGAGAGTCATAG
359861 TTTG
1 TTTG
359865 GGGACAAGTA
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
59 1 0.02
60 50 0.93
61 3 0.06
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.34
Consensus pattern (60 bp):
TTTGAGGATGAAATTAGAAGATCTAAAAGTTTAAGGAATAATTTAGAATGAGAGTCATAG
Found at i:367345 original size:36 final size:36
Alignment explanation
Indices: 367291--367369 Score: 117
Period size: 37 Copynumber: 2.2 Consensus size: 36
367281 CCCATTCCTA
367291 TTTTC-AACAAACTTTACCAAACTTTG-AAAAACAT
1 TTTTCAAACAAACTTTACCAAACTTTGAAAAAACAT
* *
367325 TTTTCAAAGAAACATTTACCAAACTTTGAAAAAATAT
1 TTTTCAAACAAAC-TTTACCAAACTTTGAAAAAACAT
367362 TTTTCAAA
1 TTTTCAAA
367370 ATTGATTGTC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
34 5 0.12
35 6 0.15
36 14 0.35
37 15 0.38
ACGTcount: A:0.46, C:0.16, G:0.04, T:0.34
Consensus pattern (36 bp):
TTTTCAAACAAACTTTACCAAACTTTGAAAAAACAT
Found at i:371835 original size:20 final size:20
Alignment explanation
Indices: 371810--371856 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
371800 TGTTGTTCGG
371810 TAAACTACTCA-TTTAATACT
1 TAAACTA-TCAGTTTAATACT
*
371830 TAAACTATCAGTTTTAGTACT
1 TAAACTATCAG-TTTAATACT
371851 TAAACT
1 TAAACT
371857 TTAATTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 3 0.12
20 7 0.29
21 14 0.58
ACGTcount: A:0.38, C:0.17, G:0.04, T:0.40
Consensus pattern (20 bp):
TAAACTATCAGTTTAATACT
Found at i:371865 original size:21 final size:21
Alignment explanation
Indices: 371821--371865 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
371811 AAACTACTCA
*
371821 TTTAATACTTAAACTATCAGT
1 TTTAATACTTAAACTATAAGT
* * *
371842 TTTAGTACTTAAACTTTAATT
1 TTTAATACTTAAACTATAAGT
371863 TTT
1 TTT
371866 TTTCAAAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.11, G:0.04, T:0.51
Consensus pattern (21 bp):
TTTAATACTTAAACTATAAGT
Found at i:372721 original size:16 final size:16
Alignment explanation
Indices: 372680--372722 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
372670 AATCTGAAGC
*
372680 AAAATTAACTCGAACTG
1 AAAA-TAACTCGAACCG
**
372697 AAAGCAACTCGAACCG
1 AAAATAACTCGAACCG
372713 AAAATAACTC
1 AAAATAACTC
372723 AAATATAAAC
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 18 0.86
17 3 0.14
ACGTcount: A:0.49, C:0.23, G:0.12, T:0.16
Consensus pattern (16 bp):
AAAATAACTCGAACCG
Found at i:373009 original size:32 final size:32
Alignment explanation
Indices: 372973--373073 Score: 109
Period size: 32 Copynumber: 3.2 Consensus size: 32
372963 TGACTCAAAT
*
372973 CGAAAATCAATCGATCTAATATTGACTCGACC
1 CGAAAATCAATCGATCTGATATTGACTCGACC
* * * *
373005 CG-AAATCTAATTGGTCTGGTATTAACTCGACC
1 CGAAAATC-AATCGATCTGATATTGACTCGACC
*
373037 C-AAAATCAATCGATCTGATATTGA-TCCGAAC
1 CGAAAATCAATCGATCTGATATTGACT-CGACC
373068 CGAAAA
1 CGAAAA
373074 ACAACTGTTT
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
30 1 0.02
31 23 0.42
32 31 0.56
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.26
Consensus pattern (32 bp):
CGAAAATCAATCGATCTGATATTGACTCGACC
Found at i:376911 original size:28 final size:28
Alignment explanation
Indices: 376864--376920 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
376854 TTACCACGAC
* *
376864 TCTTTTATTACAGATGTCACTTGATTCA
1 TCTTTTATGACAGATATCACTTGATTCA
*
376892 TCTTTTATGACCGATATCACTTGATTCA
1 TCTTTTATGACAGATATCACTTGATTCA
376920 T
1 T
376921 ATCTTCTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.25, C:0.19, G:0.11, T:0.46
Consensus pattern (28 bp):
TCTTTTATGACAGATATCACTTGATTCA
Found at i:377632 original size:42 final size:42
Alignment explanation
Indices: 377580--377668 Score: 144
Period size: 42 Copynumber: 2.1 Consensus size: 42
377570 CTCCAAACCA
377580 GACCCGAATAAAATTAAA-CTGAATATAATCTAGACATGAAAT
1 GACCCGAATAAAATTAAATC-GAATATAATCTAGACATGAAAT
* *
377622 GACCTGAATAAAATTAAATCGAATATAATCTAGACCTGAAAT
1 GACCCGAATAAAATTAAATCGAATATAATCTAGACATGAAAT
377664 GACCC
1 GACCC
377669 AAACCAAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
42 42 0.98
43 1 0.02
ACGTcount: A:0.47, C:0.17, G:0.12, T:0.24
Consensus pattern (42 bp):
GACCCGAATAAAATTAAATCGAATATAATCTAGACATGAAAT
Found at i:377678 original size:42 final size:42
Alignment explanation
Indices: 377580--377678 Score: 119
Period size: 42 Copynumber: 2.4 Consensus size: 42
377570 CTCCAAACCA
* *
377580 GACCCGAATAAAATTAAACTGAATATAATCTAGACATGAAAT
1 GACCCAAACAAAATTAAACTGAATATAATCTAGACATGAAAT
** * *
377622 GACCTGAATAAAATTAAA-TCGAATATAATCTAGACCTGAAAT
1 GACCCAAACAAAATTAAACT-GAATATAATCTAGACATGAAAT
*
377664 GACCCAAACCAAATT
1 GACCCAAACAAAATT
377679 GACCCGACCC
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
41 1 0.02
42 49 0.98
ACGTcount: A:0.48, C:0.17, G:0.11, T:0.23
Consensus pattern (42 bp):
GACCCAAACAAAATTAAACTGAATATAATCTAGACATGAAAT
Found at i:377963 original size:18 final size:17
Alignment explanation
Indices: 377936--377969 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
377926 AAGATGAAAA
377936 CATTTATTCTTCTTCTTT
1 CATTTATTCTT-TTCTTT
*
377954 CATTTCTTCTTTTCTT
1 CATTTATTCTTTTCTT
377970 CTTCCTTCCG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.09, C:0.24, G:0.00, T:0.68
Consensus pattern (17 bp):
CATTTATTCTTTTCTTT
Found at i:380221 original size:23 final size:22
Alignment explanation
Indices: 380172--380215 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
380162 AGAGGTACTG
* *
380172 TAGCAGGGGAATCGGTTCCCTA
1 TAGCAGGGGAATCGATCCCCTA
380194 TAGCAGGGGAATCGATACCCCT
1 TAGCAGGGGAATCGAT-CCCCT
380216 TAAGCAATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.25, C:0.25, G:0.30, T:0.20
Consensus pattern (22 bp):
TAGCAGGGGAATCGATCCCCTA
Found at i:386417 original size:21 final size:21
Alignment explanation
Indices: 386361--386418 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 21
386351 TGACAGATGG
* *
386361 ACTACCACATCAGCACCGTGG
1 ACTACCACATCAACACCGTGA
* * * * *
386382 ACTGCTACGTTAACATCGTGA
1 ACTACCACATCAACACCGTGA
386403 ACTACCACATCAACAC
1 ACTACCACATCAACAC
386419 TATAATGGTC
Statistics
Matches: 25, Mismatches: 12, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.33, C:0.34, G:0.14, T:0.19
Consensus pattern (21 bp):
ACTACCACATCAACACCGTGA
Found at i:388270 original size:2 final size:2
Alignment explanation
Indices: 388265--388296 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
388255 TCTCTGTGTG
388265 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
388297 CCGAAGGAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:392924 original size:19 final size:18
Alignment explanation
Indices: 392897--392933 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
392887 CCGACAAAAG
392897 CACTAATTACAAACTACAT
1 CACTAATTACAAA-TACAT
*
392916 CACTCATTACAAATACAT
1 CACTAATTACAAATACAT
392934 AACCATATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.46, C:0.27, G:0.00, T:0.27
Consensus pattern (18 bp):
CACTAATTACAAATACAT
Found at i:398539 original size:23 final size:23
Alignment explanation
Indices: 398509--398553 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
398499 TCTCTCCGCT
398509 GGGCACCACGTCATTTTCATTCC
1 GGGCACCACGTCATTTTCATTCC
398532 GGGCACCACGTCATTTTCATTC
1 GGGCACCACGTCATTTTCATTC
398554 TAGCCACCGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.18, C:0.33, G:0.18, T:0.31
Consensus pattern (23 bp):
GGGCACCACGTCATTTTCATTCC
Found at i:398561 original size:23 final size:23
Alignment explanation
Indices: 398512--398561 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
398502 CTCCGCTGGG
* *
398512 CACCACGTCATTTTCATTCCGGG
1 CACCACGTCATTTTCATTCCAGC
*
398535 CACCACGTCATTTTCATTCTAGC
1 CACCACGTCATTTTCATTCCAGC
398558 CACC
1 CACC
398562 GTCGACCGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.20, C:0.38, G:0.12, T:0.30
Consensus pattern (23 bp):
CACCACGTCATTTTCATTCCAGC
Found at i:402153 original size:2 final size:2
Alignment explanation
Indices: 402146--402174 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
402136 TATCCGCAAC
402146 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 T
402175 GTGTGCGCGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:402254 original size:36 final size:38
Alignment explanation
Indices: 402202--402274 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 38
402192 TTAATATTGT
*
402202 GTACTACAATATAAT-AAGTCAGTATTCATTTTAAAAG
1 GTACTACAATATAATAAAGTCAATATTCATTTTAAAAG
*
402239 GTAC-ACAATATAATAAAGTCAATATTTATTTTAAAA
1 GTACTACAATATAATAAAGTCAATATTCATTTTAAAA
402275 TAAAAATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
36 10 0.30
37 23 0.70
ACGTcount: A:0.47, C:0.10, G:0.08, T:0.36
Consensus pattern (38 bp):
GTACTACAATATAATAAAGTCAATATTCATTTTAAAAG
Found at i:402434 original size:8 final size:8
Alignment explanation
Indices: 402421--402451 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
402411 TCGTATATTT
402421 AATAAATG
1 AATAAATG
402429 AATAAATG
1 AATAAATG
402437 AATAAATG
1 AATAAATG
402445 AATAAAT
1 AATAAAT
402452 ATTTAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.26
Consensus pattern (8 bp):
AATAAATG
Found at i:405402 original size:39 final size:39
Alignment explanation
Indices: 405308--405408 Score: 157
Period size: 39 Copynumber: 2.6 Consensus size: 39
405298 ACCTAAAGTT
* * *
405308 TAGTTTTTATTTCATTATAATACCCGTTGTTAAAAATTA
1 TAGTTTTTGTTTCATTCTAGTACCCGTTGTTAAAAATTA
**
405347 TAGTTTTTGTTTCATTCTAGTACCCGTTGTTAAGCATTA
1 TAGTTTTTGTTTCATTCTAGTACCCGTTGTTAAAAATTA
405386 TAGTTTTTGTTTCATTCTAGTAC
1 TAGTTTTTGTTTCATTCTAGTAC
405409 ACCCGTTCAA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 57 1.00
ACGTcount: A:0.25, C:0.13, G:0.12, T:0.50
Consensus pattern (39 bp):
TAGTTTTTGTTTCATTCTAGTACCCGTTGTTAAAAATTA
Found at i:410859 original size:6 final size:6
Alignment explanation
Indices: 410848--410883 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
410838 ACAATGATGG
410848 CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC
1 CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC
410884 TATAACTCTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (6 bp):
CTCTTC
Found at i:423169 original size:13 final size:13
Alignment explanation
Indices: 423151--423187 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
423141 GTTTGGTAAT
423151 CCCGCCCCGATTA
1 CCCGCCCCGATTA
423164 CCCGCCCCGATTA
1 CCCGCCCCGATTA
* *
423177 CTCGGCCCGAT
1 CCCGCCCCGAT
423188 ACCGACCCGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.14, C:0.51, G:0.19, T:0.16
Consensus pattern (13 bp):
CCCGCCCCGATTA
Found at i:432666 original size:7 final size:7
Alignment explanation
Indices: 432654--432684 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
432644 GTCAAAGAAA
432654 GTCAACG
1 GTCAACG
432661 GTCAACG
1 GTCAACG
432668 GTCAACG
1 GTCAACG
432675 GTCAACG
1 GTCAACG
432682 GTC
1 GTC
432685 GGGTCGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:432702 original size:22 final size:22
Alignment explanation
Indices: 432674--432716 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
432664 AACGGTCAAC
432674 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
432696 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
432717 AGACCGGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:432731 original size:9 final size:9
Alignment explanation
Indices: 432713--432811 Score: 72
Period size: 9 Copynumber: 10.3 Consensus size: 9
432703 GGTCGGGTCG
*
432713 GGTCAGACC
1 GGTCAAACC
432722 GGTCAAACC
1 GGTCAAACC
* *
432731 GATTCAGACC
1 G-GTCAAACC
*
432741 GGACAAACC
1 GGTCAAACC
*
432750 GGTTCGAACC
1 GG-TCAAACC
*
432760 GGTTGAAACC
1 GG-TCAAACC
432770 GGTCAAACC
1 GGTCAAACC
432779 GGTCAGAACC
1 GGTCA-AACC
*
432789 GGTTGAAAACC
1 GG-T-CAAACC
*
432800 GGTTAAACC
1 GGTCAAACC
432809 GGT
1 GGT
432812 TTCCAGCAGC
Statistics
Matches: 72, Mismatches: 13, Indels: 10
0.76 0.14 0.11
Matches are distributed among these distances:
9 35 0.49
10 29 0.40
11 7 0.10
12 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:432770 original size:29 final size:31
Alignment explanation
Indices: 432738--432812 Score: 111
Period size: 29 Copynumber: 2.5 Consensus size: 31
432728 ACCGATTCAG
*
432738 ACCGGACAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
432767 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
432797 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
432813 TCCAGCAGCC
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 2 0.05
29 23 0.56
30 15 0.37
31 1 0.02
ACGTcount: A:0.31, C:0.27, G:0.27, T:0.16
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:432790 original size:19 final size:19
Alignment explanation
Indices: 432713--432811 Score: 71
Period size: 19 Copynumber: 5.2 Consensus size: 19
432703 GGTCGGGTCG
432713 GGTCAG-ACCGGTCAAACC
1 GGTCAGAACCGGTCAAACC
* *
432731 GATTCAG-ACCGGACAAACC
1 G-GTCAGAACCGGTCAAACC
*
432750 GGTTC-GAACCGGTTGAAACC
1 GG-TCAGAACCGG-TCAAACC
432770 GGTCA-AACCGGTCAGAACC
1 GGTCAGAACCGGTCA-AACC
* * *
432789 GGTTGAAAACCGGTTAAACC
1 GG-TCAGAACCGGTCAAACC
432809 GGT
1 GGT
432812 TTCCAGCAGC
Statistics
Matches: 65, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
18 4 0.06
19 38 0.58
20 15 0.23
21 8 0.12
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.15
Consensus pattern (19 bp):
GGTCAGAACCGGTCAAACC
Found at i:440000 original size:17 final size:17
Alignment explanation
Indices: 439980--440035 Score: 112
Period size: 17 Copynumber: 3.3 Consensus size: 17
439970 GAAAGTCAAC
439980 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
439997 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
440014 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
440031 GGTCA
1 GGTCA
440036 GACCGGTCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.12, C:0.23, G:0.46, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:440055 original size:19 final size:19
Alignment explanation
Indices: 440033--440088 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
440023 TCGGGTCGGG
440033 TCAGACCGGTCAAACCGAT
1 TCAGACCGGTCAAACCGAT
* *
440052 TCAGACCGGACAAACCGGT
1 TCAGACCGGTCAAACCGAT
440071 TC-GAACCGGTCAGAACCG
1 TCAG-ACCGGTCA-AACCG
440089 GTTGAAAACC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 1 0.03
19 26 0.81
20 5 0.16
ACGTcount: A:0.30, C:0.32, G:0.25, T:0.12
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGAT
Found at i:440077 original size:10 final size:11
Alignment explanation
Indices: 440033--440111 Score: 52
Period size: 9 Copynumber: 8.1 Consensus size: 11
440023 TCGGGTCGGG
440033 TCAG-ACCGG-
1 TCAGAACCGGT
*
440042 TCA-AACCGAT
1 TCAGAACCGGT
440052 TCAG-ACCGG-
1 TCAGAACCGGT
*
440061 ACA-AACCGGT
1 TCAGAACCGGT
440071 TC-GAACCGG-
1 TCAGAACCGGT
440080 TCAGAACCGGT
1 TCAGAACCGGT
* *
440091 TGAAAACCGGT
1 TCAGAACCGGT
440102 T-A-AACCGGT
1 TCAGAACCGGT
440111 T
1 T
440112 TCCAGCAGCC
Statistics
Matches: 56, Mismatches: 6, Indels: 16
0.72 0.08 0.21
Matches are distributed among these distances:
9 24 0.43
10 22 0.39
11 10 0.18
ACGTcount: A:0.30, C:0.28, G:0.25, T:0.16
Consensus pattern (11 bp):
TCAGAACCGGT
Found at i:448749 original size:28 final size:27
Alignment explanation
Indices: 448693--448750 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
448683 TCTTAAACAT
*
448693 GATCTTAAAATTATAAATTTTAATTTC
1 GATCTTAAAATTATAAATTTTAATCTC
* *
448720 GATCTTTAAAATTGTATAGTTTT-ATCTC
1 GATC-TTAAAATTATA-AATTTTAATCTC
448748 GAT
1 GAT
448751 TCTAATACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 4 0.15
28 17 0.65
29 5 0.19
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.48
Consensus pattern (27 bp):
GATCTTAAAATTATAAATTTTAATCTC
Found at i:451253 original size:13 final size:13
Alignment explanation
Indices: 451235--451259 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
451225 GAAAATAAAT
451235 TATTAATAAAAAA
1 TATTAATAAAAAA
451248 TATTAATAAAAA
1 TATTAATAAAAA
451260 TTTAAAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TATTAATAAAAAA
Found at i:451274 original size:20 final size:20
Alignment explanation
Indices: 451244--451318 Score: 66
Period size: 20 Copynumber: 3.7 Consensus size: 20
451234 TTATTAATAA
451244 AAAATAT-TAATAAAAATTT
1 AAAATATATAATAAAAATTT
*
451263 AAAATATATAAT--AATTTAAT
1 AAAATATATAATAAAAATT--T
* *
451283 AAAAGATATAAAGAAAAAATTT
1 AAAATATAT-AA-TAAAAATTT
451305 AAAATATATAATAA
1 AAAATATATAATAA
451319 TTTAAAATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 13
0.69 0.10 0.21
Matches are distributed among these distances:
18 4 0.09
19 7 0.16
20 15 0.35
21 4 0.09
22 9 0.21
24 4 0.09
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (20 bp):
AAAATATATAATAAAAATTT
Found at i:451300 original size:41 final size:42
Alignment explanation
Indices: 451237--451323 Score: 140
Period size: 42 Copynumber: 2.1 Consensus size: 42
451227 AAATAAATTA
* *
451237 TTAATAAAAAATATTAA-TAAAAATTTAAAATATATAATAAT
1 TTAATAAAAAATATAAAGAAAAAATTTAAAATATATAATAAT
*
451278 TTAATAAAAGATATAAAGAAAAAATTTAAAATATATAATAAT
1 TTAATAAAAAATATAAAGAAAAAATTTAAAATATATAATAAT
451320 TTAA
1 TTAA
451324 AATTTTCAGA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 15 0.36
42 27 0.64
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (42 bp):
TTAATAAAAAATATAAAGAAAAAATTTAAAATATATAATAAT
Found at i:454130 original size:21 final size:21
Alignment explanation
Indices: 454106--454166 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
454096 CCAACTTTGA
454106 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
454127 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
454141 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
454162 AAATG
1 AAATG
454167 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:454187 original size:36 final size:35
Alignment explanation
Indices: 454100--454214 Score: 187
Period size: 35 Copynumber: 3.3 Consensus size: 35
454090 TGGCAACCAA
454100 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
454135 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
454170 CTTTGAAAAATGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
454206 -GTTGAAAAT
1 CTTTGAAAAT
454215 AGGAATGGGT
Statistics
Matches: 76, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
34 5 0.07
35 43 0.57
36 28 0.37
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (35 bp):
CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:458750 original size:21 final size:21
Alignment explanation
Indices: 458726--458786 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
458716 CCAACTTTGA
458726 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
458747 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
458761 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
458782 AAATG
1 AAATG
458787 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:458807 original size:36 final size:35
Alignment explanation
Indices: 458720--458834 Score: 187
Period size: 35 Copynumber: 3.3 Consensus size: 35
458710 TGGCAACCAA
458720 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
458755 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
458790 CTTTGAAAAATGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
458826 -GTTGAAAAT
1 CTTTGAAAAT
458835 AGGAATGGGT
Statistics
Matches: 76, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
34 5 0.07
35 43 0.57
36 28 0.37
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (35 bp):
CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:460500 original size:199 final size:199
Alignment explanation
Indices: 460160--460557 Score: 769
Period size: 199 Copynumber: 2.0 Consensus size: 199
460150 GCCTGGCTAC
*
460160 TTCTTTCTGCAGATGCTTGATAATTTACTTATTCGAAACAACCTAACAAAGTTTCCAAACAAAAA
1 TTCTTTCTGCAGATGCTTGACAATTTACTTATTCGAAACAACCTAACAAAGTTTCCAAACAAAAA
460225 ATTATTGTCAGTTCATTTGGAAATCCTTGTCAATCTCGTAGAGCGGGAATGAAAGATAAGTACCA
66 ATTATTGTCAGTTCATTTGGAAATCCTTGTCAATCTCGTAGAGCGGGAATGAAAGATAAGTACCA
460290 TGTTGACTTGTGCATTATTTGTCACTTCCTTTCCCCGGGTAGCGAAGAAGAGAGTATTACGAGAT
131 TGTTGACTTGTGCATTATTTGTCACTTCCTTTCCCCGGGTAGCGAAGAAGAGAGTATTACGAGAT
460355 TGTT
196 TGTT
*
460359 TTCTTTCTGCAGATGCTTGACAATTTGCTTATTCGAAACAACCTAACAAAGTTTCCAAACAAAAA
1 TTCTTTCTGCAGATGCTTGACAATTTACTTATTCGAAACAACCTAACAAAGTTTCCAAACAAAAA
460424 ATTATTGTCAGTTCATTTGGAAATCCTTGTCAATCTCGTAGAGCGGGAATGAAAGATAAGTACCA
66 ATTATTGTCAGTTCATTTGGAAATCCTTGTCAATCTCGTAGAGCGGGAATGAAAGATAAGTACCA
*
460489 TGTTGACTTGTGCATTATTTGTCACTTCCTTTGCCCGGGTAGCGAAGAAGAGAGTATTACGAGAT
131 TGTTGACTTGTGCATTATTTGTCACTTCCTTTCCCCGGGTAGCGAAGAAGAGAGTATTACGAGAT
460554 TGTT
196 TGTT
460558 CAAATTGACC
Statistics
Matches: 196, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
199 196 1.00
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (199 bp):
TTCTTTCTGCAGATGCTTGACAATTTACTTATTCGAAACAACCTAACAAAGTTTCCAAACAAAAA
ATTATTGTCAGTTCATTTGGAAATCCTTGTCAATCTCGTAGAGCGGGAATGAAAGATAAGTACCA
TGTTGACTTGTGCATTATTTGTCACTTCCTTTCCCCGGGTAGCGAAGAAGAGAGTATTACGAGAT
TGTT
Found at i:462365 original size:50 final size:51
Alignment explanation
Indices: 462244--462370 Score: 193
Period size: 51 Copynumber: 2.5 Consensus size: 51
462234 TTAGCAATAA
** *
462244 AGCGCGCCCCCTGCACCGCGCTATACGATGATTTGGTGCCACGTGAGGTAT
1 AGCGCGCCCCCTGCACCGCGCTATACGATGAGCTGGCGCCACGTGAGGTAT
*
462295 AGCGCGCCCCCTGCACCGCGCTATACGGTGAGCTGGCGCCACGTG-GGTAT
1 AGCGCGCCCCCTGCACCGCGCTATACGATGAGCTGGCGCCACGTGAGGTAT
* *
462345 AGCGCGGCCCCTGCAGCGCGCTATAC
1 AGCGCGCCCCCTGCACCGCGCTATAC
462371 TTGTATATCT
Statistics
Matches: 70, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
50 29 0.41
51 41 0.59
ACGTcount: A:0.16, C:0.35, G:0.31, T:0.17
Consensus pattern (51 bp):
AGCGCGCCCCCTGCACCGCGCTATACGATGAGCTGGCGCCACGTGAGGTAT
Found at i:462487 original size:19 final size:20
Alignment explanation
Indices: 462463--462503 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
462453 TTTTATCACA
*
462463 CTAAATTT-TCTCAAATTCT
1 CTAAATTTCTCTCAAATACT
462482 CTAAATTTCTCTCAAATACT
1 CTAAATTTCTCTCAAATACT
462502 CT
1 CT
462504 CTTTTTAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.44
Consensus pattern (20 bp):
CTAAATTTCTCTCAAATACT
Found at i:464353 original size:50 final size:51
Alignment explanation
Indices: 464278--464402 Score: 171
Period size: 51 Copynumber: 2.5 Consensus size: 51
464268 CCCTACGTGG
* ** **
464278 CGTATAGCGCGCTGCAGGGACCGCGCTATAC-CCACGTGGCGCCAGCTCAC
1 CGTATAGCGCGGTGCAGGGGGCGCGCTATACTCCACGTGGCGCCAAATCAC
* *
464328 CGTATAGTGCGGTGCAGGGGGCGCGCTATACTCCACGTGGCGCCAAATCAT
1 CGTATAGCGCGGTGCAGGGGGCGCGCTATACTCCACGTGGCGCCAAATCAC
*
464379 CGTATAGCGCGGTGCAGAGGGCGC
1 CGTATAGCGCGGTGCAGGGGGCGC
464403 TTTACTGCTA
Statistics
Matches: 65, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 27 0.42
51 38 0.58
ACGTcount: A:0.18, C:0.31, G:0.34, T:0.16
Consensus pattern (51 bp):
CGTATAGCGCGGTGCAGGGGGCGCGCTATACTCCACGTGGCGCCAAATCAC
Found at i:464626 original size:11 final size:11
Alignment explanation
Indices: 464593--464642 Score: 58
Period size: 11 Copynumber: 5.1 Consensus size: 11
464583 GTAAAATATT
464593 TAATTATTAAA
1 TAATTATTAAA
464604 T-A-T-TTAAA
1 TAATTATTAAA
464612 -AATTATTAAA
1 TAATTATTAAA
464622 TAATTATTAAA
1 TAATTATTAAA
464633 T--TTATTAAA
1 TAATTATTAAA
464642 T
1 T
464643 TATCATAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
8 6 0.17
9 11 0.31
10 6 0.17
11 12 0.34
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TAATTATTAAA
Found at i:473243 original size:23 final size:23
Alignment explanation
Indices: 473208--473253 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
473198 ATCAAGTACA
*
473208 ATAATATATTAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
*
473231 ATAATGTAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
473254 TTTGACATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.09, G:0.20, T:0.37
Consensus pattern (23 bp):
ATAATATAATAGGTAGCGCTTAT
Found at i:473501 original size:20 final size:20
Alignment explanation
Indices: 473484--473522 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
473474 CCAGTATATT
473484 TTTACCGGTTACATTATAAA
1 TTTACCGGTTACATTATAAA
* *
473504 TTTACCTGTTACATAATAA
1 TTTACCGGTTACATTATAA
473523 TTATTATTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (20 bp):
TTTACCGGTTACATTATAAA
Found at i:473784 original size:22 final size:22
Alignment explanation
Indices: 473759--473805 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
473749 GTGAGTTTCT
473759 CAATGTTATTCTTTTGTTACTG
1 CAATGTTATTCTTTTGTTACTG
473781 CAATGTTATTCTTTTGTTACTG
1 CAATGTTATTCTTTTGTTACTG
473803 CAA
1 CAA
473806 AGTTTTTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.21, C:0.15, G:0.13, T:0.51
Consensus pattern (22 bp):
CAATGTTATTCTTTTGTTACTG
Found at i:474485 original size:112 final size:112
Alignment explanation
Indices: 474091--474591 Score: 814
Period size: 112 Copynumber: 4.5 Consensus size: 112
474081 TCTTTATCGG
474091 TTTGTCATTTTTTTACCTG--ATATTGTTATGGATCAATACA-TTTTATAAAGTATCGACACTTT
1 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATACATTTTTATAAAGTATCGACACTTT
* * *
474153 CAATATATCTGGTAGCGCTTTACTTGTTTTGTCATTTTATAGACCGGT
66 CAATATATCCGGTAGCGCTTTACCTGTTTTGTCA-TTTATAGACCGAT
*
474201 TTTGTCATTTTTTTAACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTT
1 TTTGTCATTTTTTT-ACCTGTTATATTGTTATGGATCAATACATTTTTATAAAGTATCGACACTT
* *
474266 TCAATATATCCGGTAGCGCTTTACCTATTTTGTCATTTGTAGACC-A-
65 TCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
* * *
474312 GTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATGGACACTTT
1 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATACATTTTTATAAAGTATCGACACTTT
*
474377 CAATATATCCGGTAACGCTTTACCTGTTTTGTCATTTATAGACCGAT
66 CAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
* *
474424 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATTAATATATTTTTATAAAGTATCGACACTTT
1 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATACATTTTTATAAAGTATCGACACTTT
*
474489 CAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACTGAT
66 CAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
* *
474536 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATTAATATATTTTTATAAAGTAT
1 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATACATTTTTATAAAGTAT
474592 AGATACAAAC
Statistics
Matches: 367, Mismatches: 18, Indels: 10
0.93 0.05 0.03
Matches are distributed among these distances:
110 105 0.29
111 19 0.05
112 161 0.44
113 29 0.08
114 53 0.14
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.47
Consensus pattern (112 bp):
TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATACATTTTTATAAAGTATCGACACTTT
CAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
Found at i:476209 original size:2 final size:2
Alignment explanation
Indices: 476202--476277 Score: 122
Period size: 2 Copynumber: 39.5 Consensus size: 2
476192 TCCAAATCCC
*
476202 AT AT AT AT AT AT AT AT AT AT AT AT -T AG 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
476243 AT AT AT AT AT AT AT AT AT AT -T AT AT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
476278 CGAAAAATTA
Statistics
Matches: 69, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
1 3 0.04
2 66 0.96
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:485377 original size:13 final size:13
Alignment explanation
Indices: 485352--485385 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
485342 CTTCCCATTA
485352 TAGACTCGCATATG
1 TAGACT-GCATATG
485366 TAGACTGCATATG
1 TAGACTGCATATG
*
485379 AAGACTG
1 TAGACTG
485386 TTCAACTATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (13 bp):
TAGACTGCATATG
Found at i:485405 original size:4 final size:4
Alignment explanation
Indices: 485396--485457 Score: 63
Period size: 4 Copynumber: 15.5 Consensus size: 4
485386 TTCAACTATG
* * * *
485396 TATT TATT TATT TATT TATT TATT TATT TATA TATG CATT GTATT T-TA
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT -TATT TATT
*
485444 TATT TATT TTTT TA
1 TATT TATT TATT TA
485458 ATTTTCTGAC
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
3 2 0.04
4 42 0.89
5 3 0.06
ACGTcount: A:0.26, C:0.02, G:0.03, T:0.69
Consensus pattern (4 bp):
TATT
Found at i:489345 original size:54 final size:54
Alignment explanation
Indices: 489278--489386 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
489268 AATCAAGTGG
489278 TTTCTACGGTAAAAGAATTGTTATTATTCTTTGAAGATCCGAATTTGAGCATCA
1 TTTCTACGGTAAAAGAATTGTTATTATTCTTTGAAGATCCGAATTTGAGCATCA
489332 TTTCTACGGTAAAAGAATTGTTATTATTCTTTGAAGATCCGAATTTGAGCATCA
1 TTTCTACGGTAAAAGAATTGTTATTATTCTTTGAAGATCCGAATTTGAGCATCA
489386 T
1 T
489387 AAATGTCAGG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39
Consensus pattern (54 bp):
TTTCTACGGTAAAAGAATTGTTATTATTCTTTGAAGATCCGAATTTGAGCATCA
Found at i:491396 original size:16 final size:16
Alignment explanation
Indices: 491360--491398 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
491350 AATGCATGTC
*
491360 AGATGGAATGATAAGA
1 AGATTGAATGATAAGA
491376 AGATTGAATGATAAGA
1 AGATTGAATGATAAGA
491392 AGATTGA
1 AGATTGA
491399 GTAATAAGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.49, C:0.00, G:0.28, T:0.23
Consensus pattern (16 bp):
AGATTGAATGATAAGA
Found at i:491405 original size:16 final size:16
Alignment explanation
Indices: 491360--491407 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
491350 AATGCATGTC
* *
491360 AGATGGAATGATAAGA
1 AGATTGAATAATAAGA
*
491376 AGATTGAATGATAAGA
1 AGATTGAATAATAAGA
*
491392 AGATTGAGTAATAAGA
1 AGATTGAATAATAAGA
491408 GACTAAAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.50, C:0.00, G:0.27, T:0.23
Consensus pattern (16 bp):
AGATTGAATAATAAGA
Found at i:501856 original size:22 final size:22
Alignment explanation
Indices: 501828--501872 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
501818 TACCCATTTG
*
501828 CTTATTATATATATACTAATCC
1 CTTATTATATATATACGAATCC
501850 CTTATTATATATATACGAATCC
1 CTTATTATATATATACGAATCC
501872 C
1 C
501873 ACCTACCATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.20, G:0.02, T:0.42
Consensus pattern (22 bp):
CTTATTATATATATACGAATCC
Found at i:502561 original size:2 final size:2
Alignment explanation
Indices: 502554--502581 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
502544 TTTAATTAAC
502554 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
502582 ACTATGTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:502831 original size:15 final size:15
Alignment explanation
Indices: 502811--502905 Score: 65
Period size: 15 Copynumber: 6.7 Consensus size: 15
502801 TGTATTTAAT
502811 ATAATTTATTACTTA
1 ATAATTTATTACTTA
*
502826 ATAATTTAATA-TTA
1 ATAATTTATTACTTA
* * ***
502840 A-CA-TCATTAAAAA
1 ATAATTTATTACTTA
*
502853 ATAATTTATTATTTA
1 ATAATTTATTACTTA
* * *
502868 GTAATGTATT-TTTA
1 ATAATTTATTACTTA
502882 ATAA-TTATTACTTA
1 ATAATTTATTACTTA
502896 ATAATTTATT
1 ATAATTTATT
502906 TTATATTTTT
Statistics
Matches: 59, Mismatches: 16, Indels: 10
0.69 0.19 0.12
Matches are distributed among these distances:
12 4 0.07
13 7 0.12
14 19 0.32
15 29 0.49
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (15 bp):
ATAATTTATTACTTA
Found at i:502900 original size:28 final size:29
Alignment explanation
Indices: 502852--502907 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
502842 ATCATTAAAA
* *
502852 AATAATTTATTATTTAGTAATGTATTTTT
1 AATAATTTATTACTTAATAATGTATTTTT
*
502881 AATAA-TTATTACTTAATAATTTATTTT
1 AATAATTTATTACTTAATAATGTATTTT
502908 ATATTTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 19 0.79
29 5 0.21
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.57
Consensus pattern (29 bp):
AATAATTTATTACTTAATAATGTATTTTT
Found at i:502913 original size:11 final size:13
Alignment explanation
Indices: 502853--502926 Score: 57
Period size: 15 Copynumber: 5.6 Consensus size: 13
502843 TCATTAAAAA
502853 ATAATTTATTATTT
1 ATAATTTATTA-TT
* *
502867 AGTAATGTATTTTT
1 A-TAATTTATTATT
502881 AATAA-TTATTACTT
1 -ATAATTTATTA-TT
502895 AATAATTTATT-TT
1 -ATAATTTATTATT
502908 AT-ATTT-TTATT
1 ATAATTTATTATT
502919 ATAATTTA
1 ATAATTTA
502927 ATTGATATAT
Statistics
Matches: 49, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
10 2 0.04
11 8 0.16
12 6 0.12
13 6 0.12
14 13 0.27
15 14 0.29
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.59
Consensus pattern (13 bp):
ATAATTTATTATT
Found at i:502925 original size:23 final size:24
Alignment explanation
Indices: 502896--502941 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
502886 TTATTACTTA
* *
502896 ATAATTTATTTTATAT-TTTTATT
1 ATAATTTAATTGATATATTTTATT
502919 ATAATTTAATTGATATATTTTAT
1 ATAATTTAATTGATATATTTTAT
502942 GTAACACAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (24 bp):
ATAATTTAATTGATATATTTTATT
Found at i:503729 original size:228 final size:223
Alignment explanation
Indices: 503312--503751 Score: 765
Period size: 228 Copynumber: 1.9 Consensus size: 223
503302 TATCTATCCT
*
503312 TTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGTTAATAT
1 TTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTA-CTTTAGTTAATAT
503377 TGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTGTGTAAA
65 TGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTGTGTAAA
503442 TTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAA
130 TTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAA
503507 ATTACATAACTTTCAAAAAAGTATATATCA
195 ATTACATAACTTT-AAAAAAGTATATATCA
*
503537 TTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTAAATTA-TTTGGTTAAT
1 TTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATT--ATTACTTTAGTTAAT
*
503601 ATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTTTGTG
63 ATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAAT--AATTTTGTG
* *
503666 TAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACGTGAAACACTATTAAATAAATTGAAAC
126 TAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAAC
503731 ATAAATTACATAACTTTAAAA
191 ATAAATTACATAACTTTAAAA
503752 GCAGTTTTAA
Statistics
Matches: 205, Mismatches: 5, Indels: 8
0.94 0.02 0.04
Matches are distributed among these distances:
225 31 0.15
226 77 0.38
227 4 0.02
228 93 0.45
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.39
Consensus pattern (223 bp):
TTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTACTTTAGTTAATATT
GTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTGTGTAAAT
TAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAA
TTACATAACTTTAAAAAAGTATATATCA
Found at i:504004 original size:20 final size:19
Alignment explanation
Indices: 503981--504027 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
503971 CGATATAACA
503981 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
504001 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
504021 GGTAAAA
1 GGTAAAA
504028 TGATACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:504029 original size:17 final size:18
Alignment explanation
Indices: 503985--504032 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
503975 ATAACAGGTA
503985 AAAATATGATAAAACCGGT
1 AAAA-ATGATAAAACCGGT
504004 AACAAAATGATAAAACCGGT
1 -A-AAAATGATAAAACCGGT
504024 -AAAATGATA
1 AAAAATGATA
504033 CCGGATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 9 0.33
20 15 0.56
21 3 0.11
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.19
Consensus pattern (18 bp):
AAAAATGATAAAACCGGT
Found at i:506319 original size:32 final size:32
Alignment explanation
Indices: 506278--506341 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
506268 AAAAATATGG
*
506278 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGTGA
* *
506310 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGTGA
506342 TATTAAGATG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.30, C:0.00, G:0.47, T:0.23
Consensus pattern (32 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGTGA
Found at i:508148 original size:19 final size:19
Alignment explanation
Indices: 508124--508172 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
508114 AATGTCGAGT
508124 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
508143 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
508162 TATTTTTGTAT
1 TAATTTTGTAT
508173 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:508637 original size:199 final size:199
Alignment explanation
Indices: 508291--509859 Score: 2883
Period size: 199 Copynumber: 7.9 Consensus size: 199
508281 CAATATGGCC
* *
508291 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAATCATCGAAC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAAC
* * *
508356 CCAAAAGTATAATGTAATAAGTAAGTTTACAATCTAACCGGTACAATTATATCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
*
508421 CAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA
508486 TTAAA
195 TTAAA
508491 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
508556 CAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACCGATTTTATGAGAG
66 CAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
508621 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
508686 TAAA
196 TAAA
508690 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
508755 CAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACTGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
508820 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTTCCAGAATGAA
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTTCCAGAATGAA
508885 TTAAA
195 TTAAA
508890 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
508954 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
509019 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
509084 TAAA
196 TAAA
509088 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
509153 CAAAAGTATAATGTAATATA-TAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
66 CAAAAGTATAATGTAATA-AGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
*
509217 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA
**
509282 TGGAA
195 TTAAA
509287 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
509352 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
509417 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
**
509482 GGAA
196 TAAA
509486 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
* *
509551 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATGCCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
509616 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
**
509681 GGAA
196 TAAA
509685 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
509749 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
509814 AATATGTCTAAATAATGTGTCAACACTAATATAGTTTGTGTCGATA
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
509860 CTAATTTAAA
Statistics
Matches: 1346, Mismatches: 19, Indels: 10
0.98 0.01 0.01
Matches are distributed among these distances:
198 196 0.15
199 1058 0.79
200 92 0.07
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.31
Consensus pattern (199 bp):
AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
TAAA
Found at i:511331 original size:6 final size:6
Alignment explanation
Indices: 511307--511395 Score: 54
Period size: 6 Copynumber: 14.3 Consensus size: 6
511297 AGCGGTCGCA
* * * * *
511307 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GATA-AT GACGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GA-AGAT GAAGAT
* ** *
511355 GAAGCT GGCGAT GAAGAT GATGACGAT GATGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GA--A-GAT GAAGAT GAAGAT GA
511396 TGATCCAAAC
Statistics
Matches: 61, Mismatches: 17, Indels: 10
0.69 0.19 0.11
Matches are distributed among these distances:
6 55 0.90
8 1 0.02
9 5 0.08
ACGTcount: A:0.38, C:0.08, G:0.34, T:0.20
Consensus pattern (6 bp):
GAAGAT
Found at i:511342 original size:3 final size:3
Alignment explanation
Indices: 511322--511399 Score: 57
Period size: 3 Copynumber: 26.0 Consensus size: 3
511312 TGAAGCTGAC
* * * * * * ** *
511322 GAT GAA GAT GAC GAT GAT GAT GAT AAT GAC GAT GAA GCT GGC GAT GAA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
511370 GAT GAT GAC GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
511400 CCAAACAAGT
Statistics
Matches: 54, Mismatches: 21, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.37, C:0.06, G:0.33, T:0.23
Consensus pattern (3 bp):
GAT
Found at i:511343 original size:18 final size:18
Alignment explanation
Indices: 511307--511399 Score: 62
Period size: 18 Copynumber: 5.0 Consensus size: 18
511297 AGCGGTCGCA
* *
511307 GAAGATGAAGCTGACGAT
1 GAAGATGAAGATGATGAT
*
511325 GAAGATGACGATGATGAT
1 GAAGATGAAGATGATGAT
* * *
511343 GATA-ATGACGATGAAGCT
1 GA-AGATGAAGATGATGAT
**
511361 GGCGATGAAGATGATGACGAT
1 GAAGATGAAGATGAT---GAT
*
511382 GATGATGAAGATGATGAT
1 GAAGATGAAGATGATGAT
511400 CCAAACAAGT
Statistics
Matches: 58, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
18 42 0.72
19 1 0.02
21 15 0.26
ACGTcount: A:0.38, C:0.08, G:0.33, T:0.22
Consensus pattern (18 bp):
GAAGATGAAGATGATGAT
Found at i:515138 original size:25 final size:25
Alignment explanation
Indices: 515104--515168 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 25
515094 TTATCATTAA
515104 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
515129 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
* *
515154 ATTTAGATATATACA
1 ATTTAGGTATGTACA
515169 TCTTTTGAGT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.42
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:515483 original size:21 final size:23
Alignment explanation
Indices: 515452--515513 Score: 74
Period size: 21 Copynumber: 2.8 Consensus size: 23
515442 ATAGGTAAAC
*
515452 ATATGATGTAATAGGTAGC-CCT
1 ATATAATGTAATAGGTAGCGCCT
* **
515474 -TATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCCT
515496 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
515514 TGGTTATATT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
21 16 0.48
22 1 0.03
23 16 0.48
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.37
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCCT
Found at i:515520 original size:23 final size:23
Alignment explanation
Indices: 515474--515522 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
515464 AGGTAGCCCT
*
515474 TATAATGTAATAGGTATCGTTTA
1 TATAATGTAATAGGTATCGGTTA
515497 TATAATGTAATAGGTAGT-GGTTA
1 TATAATGTAATAGGTA-TCGGTTA
515520 TAT
1 TAT
515523 TGTAAAGTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 23 0.96
24 1 0.04
ACGTcount: A:0.35, C:0.02, G:0.20, T:0.43
Consensus pattern (23 bp):
TATAATGTAATAGGTATCGGTTA
Found at i:515526 original size:21 final size:21
Alignment explanation
Indices: 515458--515527 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
515448 AAACATATGA
** *
515458 TGTAATAGGTAGCCCTTATAA
1 TGTAATAGGTAGTGCTTATAT
*
515479 TGTAATAGGTA-TCGTTTATAT
1 TGTAATAGGTAGT-GCTTATAT
*
515500 AATGTAATAGGTAGTGGTTATAT
1 --TGTAATAGGTAGTGCTTATAT
515523 TGTAA
1 TGTAA
515528 AGTGTCTATC
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
21 21 0.52
23 18 0.45
24 1 0.03
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.40
Consensus pattern (21 bp):
TGTAATAGGTAGTGCTTATAT
Found at i:515822 original size:25 final size:25
Alignment explanation
Indices: 515788--515838 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
515778 ACAACAAATC
*
515788 AATTAAACATTGTTGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
515813 AATTGAACATTGTTATGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
515838 A
1 A
515839 TTTGGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
AATTAAACATTGTTATGGGTACATT
Found at i:516152 original size:18 final size:18
Alignment explanation
Indices: 516131--516167 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
516121 GTAATTGGAG
516131 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
516149 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
516167 T
1 T
516168 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:516175 original size:24 final size:24
Alignment explanation
Indices: 516123--516169 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
516113 ATTCATATGT
* *
516123 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
516147 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
516170 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:516468 original size:39 final size:38
Alignment explanation
Indices: 516425--516510 Score: 145
Period size: 39 Copynumber: 2.2 Consensus size: 38
516415 TCCGATGCTC
*
516425 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGG-A
*
516464 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGA
516502 ATCAAAATC
1 ATCAAAATC
516511 TACAACTTGA
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 10 0.22
39 35 0.78
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.17
Consensus pattern (38 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGA
Found at i:516944 original size:23 final size:23
Alignment explanation
Indices: 516913--516976 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
516903 ATAGGTAAAC
*
516913 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
516936 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
516959 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
516977 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:516983 original size:23 final size:23
Alignment explanation
Indices: 516913--516985 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
516903 ATAGGTAAAC
* **
516913 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
516936 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
516959 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
516982 ATAT
1 ATAT
516986 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:519844 original size:32 final size:32
Alignment explanation
Indices: 519795--519872 Score: 111
Period size: 32 Copynumber: 2.4 Consensus size: 32
519785 TTCCAACTTA
519795 AGGGGGACAAAATATAATTAATCATAAAAAATG
1 AGGGGG-CAAAATATAATTAATCATAAAAAATG
* *
519828 AGGGGGCAAAGTATAATTAATCATAGAAAATG
1 AGGGGGCAAAATATAATTAATCATAAAAAATG
*
519860 AGAGGGACAAAAT
1 AG-GGGGCAAAAT
519873 CAAAATAACT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 26 0.65
33 14 0.35
ACGTcount: A:0.51, C:0.06, G:0.23, T:0.19
Consensus pattern (32 bp):
AGGGGGCAAAATATAATTAATCATAAAAAATG
Found at i:520064 original size:27 final size:27
Alignment explanation
Indices: 520025--520079 Score: 94
Period size: 27 Copynumber: 2.0 Consensus size: 27
520015 GTCGAGAATA
520025 TTTAAACACATACTATTTTATATTCAT
1 TTTAAACACATACTATTTTATATTCAT
520052 TTTAAAC-CTATACTATTTTATATTCAT
1 TTTAAACAC-ATACTATTTTATATTCAT
520079 T
1 T
520080 CTTATTTATC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 1 0.04
27 26 0.96
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.51
Consensus pattern (27 bp):
TTTAAACACATACTATTTTATATTCAT
Done.