Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000482.1 Hibiscus syriacus cultivar Beakdansim tig00000916_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: 2886609
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 16
Found at i:2173440 original size:21 final size:21
Alignment explanation
Indices: 2173414--2173529 Score: 112
Period size: 21 Copynumber: 5.5 Consensus size: 21
2173404 TTCACCTGTC
2173414 ATCGTTCAAGAGGCCCCTCCT
1 ATCGTTCAAGAGGCCCCTCCT
* *
2173435 ATCGTTCAAGAGACCTCT-CT
1 ATCGTTCAAGAGGCCCCTCCT
2173455 CATCGTTCAAGAGGCCCCTCAC-
1 -ATCGTTCAAGAGGCCCCTC-CT
* *
2173477 ACCGTTCAAGAGGTCCCT-CT
1 ATCGTTCAAGAGGCCCCTCCT
* * *
2173497 CATCGTTCAAGAGGTCTCTCCC
1 -ATCGTTCAAGAGGCCCCTCCT
*
2173519 ACCGTTCAAGA
1 ATCGTTCAAGA
2173530 ACCCGATTCA
Statistics
Matches: 79, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
19 1 0.01
20 2 0.03
21 74 0.94
22 1 0.01
23 1 0.01
ACGTcount: A:0.22, C:0.35, G:0.18, T:0.24
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCCCTCCT
Found at i:2173459 original size:42 final size:41
Alignment explanation
Indices: 2173412--2173529 Score: 157
Period size: 42 Copynumber: 2.8 Consensus size: 41
2173402 GATTCACCTG
*
2173412 TCATCGTTCAAGAGGCCCCTCCTATCGTTCAAGA-GACCTCTC
1 TCATCGTTCAAGAGGCCCCTCC-ACCGTTCAAGAGGACC-CTC
*
2173454 TCATCGTTCAAGAGGCCCCTCACACCGTTCAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC-CACCGTTCAAGAGGACCCTC
* *
2173496 TCATCGTTCAAGAGGTCTCTCCCACCGTTCAAGA
1 TCATCGTTCAAGAGGCCCCT-CCACCGTTCAAGA
2173530 ACCCGATTCA
Statistics
Matches: 69, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
42 64 0.93
43 5 0.07
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.25
Consensus pattern (41 bp):
TCATCGTTCAAGAGGCCCCTCCACCGTTCAAGAGGACCCTC
Found at i:2175021 original size:20 final size:20
Alignment explanation
Indices: 2174996--2175037 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2174986 AAGGTACACT
2174996 TTCGCAACGCGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
** *
2175016 TTCGCATTGCGATAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
2175036 TT
1 TT
2175038 TGTGTTGCCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.26
Consensus pattern (20 bp):
TTCGCAACGCGAAAGTCAAA
Found at i:2175064 original size:20 final size:20
Alignment explanation
Indices: 2175041--2175100 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
2175031 TCAAATTTGT
* *
2175041 GTTGCCATTTTGATTTTCGC
1 GTTGCCAATTTGACTTTCGC
*
2175061 GTTGCGAATTTGACTTTCGC
1 GTTGCCAATTTGACTTTCGC
* * *
2175081 ATTGCGAATTTGTCTTTCGC
1 GTTGCCAATTTGACTTTCGC
2175101 AACAATCGCA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.13, C:0.20, G:0.22, T:0.45
Consensus pattern (20 bp):
GTTGCCAATTTGACTTTCGC
Found at i:2175101 original size:20 final size:20
Alignment explanation
Indices: 2175049--2175101 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
2175039 GTGTTGCCAT
* *
2175049 TTTGATTTTCGCGTTGCGAA
1 TTTGACTTTCGCATTGCGAA
2175069 TTTGACTTTCGCATTGCGAA
1 TTTGACTTTCGCATTGCGAA
*
2175089 TTTGTCTTTCGCA
1 TTTGACTTTCGCA
2175102 ACAATCGCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.15, C:0.19, G:0.21, T:0.45
Consensus pattern (20 bp):
TTTGACTTTCGCATTGCGAA
Found at i:2175119 original size:29 final size:29
Alignment explanation
Indices: 2175084--2175146 Score: 108
Period size: 29 Copynumber: 2.2 Consensus size: 29
2175074 CTTTCGCATT
* *
2175084 GCGAATTTGTCTTTCGCAACAATCGCAAC
1 GCGAATTTGACTTTCGCAACAACCGCAAC
2175113 GCGAATTTGACTTTCGCAACAACCGCAAC
1 GCGAATTTGACTTTCGCAACAACCGCAAC
2175142 GCGAA
1 GCGAA
2175147 AATCGCAACG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (29 bp):
GCGAATTTGACTTTCGCAACAACCGCAAC
Found at i:2175504 original size:18 final size:18
Alignment explanation
Indices: 2175478--2175518 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
2175468 AGGTGAAGCC
* *
2175478 GATTATGATTGGGATTTT
1 GATTTTGATTGCGATTTT
2175496 GATTTTGATTGCGATTTT
1 GATTTTGATTGCGATTTT
2175514 GATTT
1 GATTT
2175519 CCTTTTGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.20, C:0.02, G:0.24, T:0.54
Consensus pattern (18 bp):
GATTTTGATTGCGATTTT
Found at i:2177815 original size:24 final size:24
Alignment explanation
Indices: 2177781--2177834 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2177771 CTGAAACATC
2177781 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
2177805 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
2177829 ATCAAA
1 ATCAAA
2177835 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:2177848 original size:24 final size:24
Alignment explanation
Indices: 2177781--2177848 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
2177771 CTGAAACATC
* * *
2177781 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
2177805 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
2177829 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
2177849 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:2177981 original size:12 final size:12
Alignment explanation
Indices: 2177960--2177993 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2177950 GGTTGTGGGT
*
2177960 TTTGAGATTGTG
1 TTTGATATTGTG
2177972 TTTGATATTGTG
1 TTTGATATTGTG
*
2177984 TTTGGTATTG
1 TTTGATATTG
2177994 GAAATATGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:2178624 original size:15 final size:16
Alignment explanation
Indices: 2178588--2178625 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
2178578 AATCATTGAC
*
2178588 AAAATTATATAGAAAT
1 AAAATTATATAGAAAA
*
2178604 AAAATTATGTA-AAAA
1 AAAATTATATAGAAAA
2178619 AAAATTA
1 AAAATTA
2178626 GAGATGGTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (16 bp):
AAAATTATATAGAAAA
Found at i:2178761 original size:20 final size:20
Alignment explanation
Indices: 2178736--2178908 Score: 90
Period size: 20 Copynumber: 8.7 Consensus size: 20
2178726 CAAAACATTT
2178736 GTGTTGCGAAATTAAAATTC
1 GTGTTGCGAAATTAAAATTC
2178756 GTGTTGCG-AATTCGAAAA-TC
1 GTGTTGCGAAATT--AAAATTC
* **
2178776 GAGTTGCGAAAACAAAATTC
1 GTGTTGCGAAATTAAAATTC
* * *
2178796 GTATTGCG-ATTTAGAAAATC
1 GTGTTGCGAAATTA-AAATTC
* ** *
2178816 TTGTTGCGAAAAGGAAACTT-
1 GTGTTGCG-AAATTAAAATTC
*
2178836 GTGTTGCGAAA-AAGAAATTC
1 GTGTTGCGAAATTA-AAATTC
* *
2178856 GCGTTGCG-AATTGAAATTCC
1 GTGTTGCGAAATTAAAATT-C
* * *
2178876 GTGTTGCGAATTTGGAAACT-
1 GTGTTGCGAAATT-AAAATTC
2178896 GTGTTGCGAAATT
1 GTGTTGCGAAATT
2178909 GGAGTTCGCG
Statistics
Matches: 114, Mismatches: 26, Indels: 26
0.69 0.16 0.16
Matches are distributed among these distances:
18 1 0.01
19 24 0.21
20 70 0.61
21 12 0.11
22 7 0.06
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (20 bp):
GTGTTGCGAAATTAAAATTC
Found at i:2178793 original size:40 final size:40
Alignment explanation
Indices: 2178738--2178887 Score: 124
Period size: 40 Copynumber: 3.8 Consensus size: 40
2178728 AAACATTTGT
** *
2178738 GTTGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATCGA
1 GTTGCGAAAACAAAATTCGTGTTGCGAATTAGAAAATCGA
* * **
2178778 GTTGCGAAAACAAAATTCGTATTGCGATTTAGAAAATCTT
1 GTTGCGAAAACAAAATTCGTGTTGCGAATTAGAAAATCGA
* * ** * *
2178818 GTTGCGAAAAGGAAACTT-GTGTTGCGAAAAAGAAATTCGC
1 GTTGCGAAAA-CAAAATTCGTGTTGCGAATTAGAAAATCGA
***
2178858 GTTGCG-AATTGAAATTCCGTGTTGCGAATT
1 GTTGCGAAAACAAAATT-CGTGTTGCGAATT
2178888 TGGAAACTGT
Statistics
Matches: 85, Mismatches: 22, Indels: 6
0.75 0.19 0.05
Matches are distributed among these distances:
38 4 0.05
39 2 0.02
40 74 0.87
41 5 0.06
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (40 bp):
GTTGCGAAAACAAAATTCGTGTTGCGAATTAGAAAATCGA
Found at i:2178842 original size:60 final size:60
Alignment explanation
Indices: 2178739--2178906 Score: 148
Period size: 60 Copynumber: 2.8 Consensus size: 60
2178729 AACATTTGTG
* ** * * *
2178739 TTGCGAAATT-AAAATTCGTGTTGCGAAT-TCGAAAATCGAGTTGCGAAAACA-AAATTCGTA
1 TTGCG-AATTGAAAATCCGTGTTGCGAATAAGGAAACT-GTGTTGCGAAAA-AGAAATTCGCA
* * *
2178799 TTGCGATTTAGAAAAT-CTTGTTGCGAA-AAGGAAACTTGTGTTGCGAAAAAGAAATTCGCG
1 TTGCGAATT-GAAAATCCGTGTTGCGAATAAGGAAAC-TGTGTTGCGAAAAAGAAATTCGCA
* **
2178859 TTGCGAATTGAAATTCCGTGTTGCGAATTTGGAAACTGTGTTGCGAAA
1 TTGCGAATTGAAAATCCGTGTTGCGAATAAGGAAACTGTGTTGCGAAA
2178907 TTGGAGTTCG
Statistics
Matches: 88, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
59 9 0.10
60 67 0.76
61 12 0.14
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.30
Consensus pattern (60 bp):
TTGCGAATTGAAAATCCGTGTTGCGAATAAGGAAACTGTGTTGCGAAAAAGAAATTCGCA
Found at i:2179978 original size:15 final size:16
Alignment explanation
Indices: 2179958--2180000 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
2179948 TAAGGAGGAG
2179958 AAGAAAAAAGAGAA-A
1 AAGAAAAAAGAGAAGA
*
2179973 AAGAAAGAAGAGAAGA
1 AAGAAAAAAGAGAAGA
*
2179989 AGGAAGAAAAGA
1 AAGAA-AAAAGA
2180001 AATAGTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 13 0.57
16 5 0.22
17 5 0.22
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (16 bp):
AAGAAAAAAGAGAAGA
Found at i:2180621 original size:30 final size:30
Alignment explanation
Indices: 2180587--2180643 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
2180577 ATCATTAGTT
* *
2180587 ACCATTTTGTAACAGTTGATAAATTAAATC
1 ACCATTTTATAACAGTTGAAAAATTAAATC
**
2180617 ACCATTTTATAACTTTTGAAAAATTAA
1 ACCATTTTATAACAGTTGAAAAATTAA
2180644 TGATCAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.39
Consensus pattern (30 bp):
ACCATTTTATAACAGTTGAAAAATTAAATC
Found at i:2180754 original size:3 final size:3
Alignment explanation
Indices: 2180746--2180803 Score: 89
Period size: 3 Copynumber: 19.0 Consensus size: 3
2180736 GTCGAAAAAA
* *
2180746 TAT TAT TAT TAT TAT TAT GAT TAT TAC TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2180794 TAT TAAT TAT
1 TAT T-AT TAT
2180804 AGTTTTACAG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
3 47 0.94
4 3 0.06
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:2182361 original size:30 final size:30
Alignment explanation
Indices: 2182267--2182427 Score: 128
Period size: 30 Copynumber: 5.4 Consensus size: 30
2182257 TTAATTTATG
* * * * *
2182267 TTTTAATCCCTTAAGTTTCTATTTTTACCA
1 TTTTAGTCCTTTAAATTTCTGTTTTTACTA
* * * * *
2182297 ATTTAGTCCCTTAACTTTTTGTTTTTAATA
1 TTTTAGTCCTTTAAATTTCTGTTTTTACTA
* *
2182327 TTTTAGTCCTTTAACTTTCTGTTTTTACTG
1 TTTTAGTCCTTTAAATTTCTGTTTTTACTA
* * * **
2182357 TTTTAATCCTTTAAATATATGTTTTTGTTA
1 TTTTAGTCCTTTAAATTTCTGTTTTTACTA
* * *
2182387 TTTTAGTCCTGTAAATTT-TTTTTTTGCTA
1 TTTTAGTCCTTTAAATTTCTGTTTTTACTA
2182416 -TTTAGTCCTTTA
1 TTTTAGTCCTTTA
2182428 TTTTAATAAG
Statistics
Matches: 106, Mismatches: 25, Indels: 2
0.80 0.19 0.02
Matches are distributed among these distances:
28 11 0.10
29 9 0.08
30 86 0.81
ACGTcount: A:0.20, C:0.14, G:0.07, T:0.58
Consensus pattern (30 bp):
TTTTAGTCCTTTAAATTTCTGTTTTTACTA
Found at i:2186823 original size:14 final size:14
Alignment explanation
Indices: 2186806--2186836 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
2186796 ACCGATATTT
2186806 CTACACTACCTTAA
1 CTACACTACCTTAA
2186820 CTACACTACCTTAA
1 CTACACTACCTTAA
2186834 CTA
1 CTA
2186837 GAAGAGTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.29
Consensus pattern (14 bp):
CTACACTACCTTAA
Found at i:2188065 original size:67 final size:66
Alignment explanation
Indices: 2187975--2188176 Score: 237
Period size: 67 Copynumber: 3.0 Consensus size: 66
2187965 CTTTTATAGC
* * *
2187975 AAATTTTATCTCTTCTGAGACAGTTTCTTTTGAAGAAAAATCTATGAGCATGTTTCTTTGAAAAC
1 AAATTTTGTCTCTTTTGAGACAGTTTCTTTTGAAGAAAAATCTTTGAGCATGTTTCTTTGAAAA-
2188040 CA
65 CA
* * * * *
2188042 AAATTTTGTCTATTTTGAAACAGTTTCTGTTGAAGAAAAATCTTTGAGTATGTTTCTTTGGAAAC
1 AAATTTTGTCTCTTTTGAGACAGTTTCTTTTGAAGAAAAATCTTTGAGCATGTTTCTTTGAAAAC
*
2188107 G
66 A
* *** *
2188108 AAATTTTGTCTCTCTTGAGACAAAATCTTTTGAAGGAAAATCTTTGAGTC-TGTTTCTCTTG-AA
1 AAATTTTGTCTCTTTTGAGACAGTTTCTTTTGAAGAAAAATCTTTGAG-CATGTTTCT-TTGAAA
2188171 ACA
64 ACA
2188174 AAA
1 AAA
2188177 CCATCTTTGA
Statistics
Matches: 114, Mismatches: 19, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
66 55 0.48
67 59 0.52
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (66 bp):
AAATTTTGTCTCTTTTGAGACAGTTTCTTTTGAAGAAAAATCTTTGAGCATGTTTCTTTGAAAAC
A
Found at i:2188148 original size:66 final size:66
Alignment explanation
Indices: 2188000--2188176 Score: 212
Period size: 66 Copynumber: 2.7 Consensus size: 66
2187990 TGAGACAGTT
* * * * *
2188000 TCTTTTGAAGAAAAATCTATGAGCATGTTTCTTTGAAAACCAAAATTTTGTCTATTTTGAAACAG
1 TCTTTTGAAGAAAAATCTTTGAGTATGTTTCTTTGGAAA-CAAAATTTTGTCTATCTTGAAACAA
**
2188065 TT
65 AA
* * * *
2188067 TCTGTTGAAGAAAAATCTTTGAGTATGTTTCTTTGGAAACGAAATTTTGTCTCTCTTGAGACAAA
1 TCTTTTGAAGAAAAATCTTTGAGTATGTTTCTTTGGAAACAAAATTTTGTCTATCTTGAAACAAA
2188132 A
66 A
* *
2188133 TCTTTTGAAGGAAAATCTTTGAGTCTGTTTCTCTT-GAAACAAAA
1 TCTTTTGAAGAAAAATCTTTGAGTATGTTTCT-TTGGAAACAAAA
2188177 CCATCTTTGA
Statistics
Matches: 94, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
66 57 0.61
67 37 0.39
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (66 bp):
TCTTTTGAAGAAAAATCTTTGAGTATGTTTCTTTGGAAACAAAATTTTGTCTATCTTGAAACAAA
A
Found at i:2190178 original size:29 final size:30
Alignment explanation
Indices: 2190152--2190307 Score: 113
Period size: 30 Copynumber: 5.3 Consensus size: 30
2190142 TTTATTTATG
* * *
2190152 TTTTAGTCCCTTAAGTTTCTATTTTTACCA
1 TTTTAGTCCCTTAACTTTCTGTTTTTACTA
* *
2190182 ATTGAGTCCCTTAACTTT-TGTTTTTGA-TA
1 TTTTAGTCCCTTAACTTTCTGTTTTT-ACTA
* *
2190211 TTTTAGTCCTTTAACTTTCTGTTTTTACTG
1 TTTTAGTCCCTTAACTTTCTGTTTTTACTA
* ** * **
2190241 TTTTAATCATTTAAATATT-TGTTTTTGTTA
1 TTTTAGTCCCTTAACT-TTCTGTTTTTACTA
* * * *
2190271 TTTTAGTCCTTTAAATTTCTATTTTTGCTA
1 TTTTAGTCCCTTAACTTTCTGTTTTTACTA
2190301 -TTTAGTC
1 TTTTAGTC
2190308 TTTTATTTTA
Statistics
Matches: 102, Mismatches: 19, Indels: 11
0.77 0.14 0.08
Matches are distributed among these distances:
29 32 0.31
30 68 0.67
31 2 0.02
ACGTcount: A:0.20, C:0.13, G:0.09, T:0.58
Consensus pattern (30 bp):
TTTTAGTCCCTTAACTTTCTGTTTTTACTA
Found at i:2190230 original size:59 final size:60
Alignment explanation
Indices: 2190152--2190296 Score: 166
Period size: 60 Copynumber: 2.4 Consensus size: 60
2190142 TTTATTTATG
* * * * *
2190152 TTTTAGTCCCTTAAGTTTCTATTTTTACCAATTGAGTCCCTTAACT-TTTGTTTTTGATA
1 TTTTAGTCCTTTAAATTTCTATTTTTACCAATTGAATCACTTAAATATTTGTTTTTGATA
* * *** * * *
2190211 TTTTAGTCCTTTAACTTTCTGTTTTTACTGTTTTAATCATTTAAATATTTGTTTTTGTTA
1 TTTTAGTCCTTTAAATTTCTATTTTTACCAATTGAATCACTTAAATATTTGTTTTTGATA
2190271 TTTTAGTCCTTTAAATTTCTATTTTT
1 TTTTAGTCCTTTAAATTTCTATTTTT
2190297 GCTATTTAGT
Statistics
Matches: 71, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
59 35 0.49
60 36 0.51
ACGTcount: A:0.20, C:0.13, G:0.08, T:0.59
Consensus pattern (60 bp):
TTTTAGTCCTTTAAATTTCTATTTTTACCAATTGAATCACTTAAATATTTGTTTTTGATA
Found at i:2190236 original size:30 final size:29
Alignment explanation
Indices: 2190186--2190312 Score: 114
Period size: 30 Copynumber: 4.3 Consensus size: 29
2190176 TTACCAATTG
* *
2190186 AGTCCCTTAACTTTTGTTTTTGATATTTT
1 AGTCCTTTAAATTTTGTTTTTGATATTTT
* *
2190215 AGTCCTTTAACTTTCTGTTTTT-ACTGTTTT
1 AGTCCTTTAAATTT-TGTTTTTGA-TATTTT
* * *
2190245 AATCATTTAAATATTTGTTTTTGTTATTTT
1 AGTCCTTTAAAT-TTTGTTTTTGATATTTT
* *
2190275 AGTCCTTTAAATTTCTATTTTTGCTA-TTT
1 AGTCCTTTAAATTT-TGTTTTTGATATTTT
*
2190304 AGTCTTTTA
1 AGTCCTTTA
2190313 TTTTATTAAT
Statistics
Matches: 81, Mismatches: 12, Indels: 10
0.79 0.12 0.10
Matches are distributed among these distances:
29 27 0.33
30 52 0.64
31 2 0.02
ACGTcount: A:0.20, C:0.12, G:0.09, T:0.60
Consensus pattern (29 bp):
AGTCCTTTAAATTTTGTTTTTGATATTTT
Found at i:2191449 original size:18 final size:18
Alignment explanation
Indices: 2191426--2191460 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2191416 ACTAAATATT
2191426 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
2191444 TGTCCCGAATGACCACT
1 TGTCCCGAAGGACCACT
2191461 GATAATCCCT
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:0.26, C:0.34, G:0.20, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:2200941 original size:21 final size:21
Alignment explanation
Indices: 2200915--2200993 Score: 104
Period size: 21 Copynumber: 3.8 Consensus size: 21
2200905 ATTTACCGTG
* * **
2200915 ATTGCGGCCGTCACGGGCGCT
1 ATTGAGGCCGTCGCGGATGCT
* *
2200936 ATTGCGGCCATCGCGGATGCT
1 ATTGAGGCCGTCGCGGATGCT
2200957 ATTGAGGCCGTCGCGGATGCT
1 ATTGAGGCCGTCGCGGATGCT
2200978 ATTGAGGCCGTCGCGG
1 ATTGAGGCCGTCGCGG
2200994 GTAACTCGGA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.13, C:0.28, G:0.38, T:0.22
Consensus pattern (21 bp):
ATTGAGGCCGTCGCGGATGCT
Found at i:2209937 original size:29 final size:29
Alignment explanation
Indices: 2209901--2210016 Score: 146
Period size: 29 Copynumber: 4.0 Consensus size: 29
2209891 CCAAAATTTG
*
2209901 TTTGAAAATTATTAACCGAATCGAATTAA
1 TTTGAAAATTATTAACCGAAACGAATTAA
* * **
2209930 TTTGAAAATTATTAACCGAACCAAATTTT
1 TTTGAAAATTATTAACCGAAACGAATTAA
2209959 TTTGAAAATTATTAACC-AAACTGAATTAA
1 TTTGAAAATTATTAACCGAAAC-GAATTAA
*
2209988 TTTGAAAATTATTAA-CTAAACTGAATTAA
1 TTTGAAAATTATTAACCGAAAC-GAATTAA
2210017 CTAATTTTTT
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
28 4 0.05
29 73 0.95
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.36
Consensus pattern (29 bp):
TTTGAAAATTATTAACCGAAACGAATTAA
Found at i:2209963 original size:58 final size:59
Alignment explanation
Indices: 2209882--2210003 Score: 194
Period size: 58 Copynumber: 2.1 Consensus size: 59
2209872 TTCGGTTCGG
* *
2209882 TTAATCGAACCAAAATTTGTTTGAAAATTATTAACCGAA-TCGAATTAATTTGAAAATTA
1 TTAACCGAACCAAAATTTGTTTGAAAATTATTAACCAAACT-GAATTAATTTGAAAATTA
*
2209941 TTAACCGAACC-AAATTTTTTTGAAAATTATTAACCAAACTGAATTAATTTGAAAATTA
1 TTAACCGAACCAAAATTTGTTTGAAAATTATTAACCAAACTGAATTAATTTGAAAATTA
2209999 TTAAC
1 TTAAC
2210004 TAAACTGAAT
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
58 48 0.81
59 11 0.19
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.36
Consensus pattern (59 bp):
TTAACCGAACCAAAATTTGTTTGAAAATTATTAACCAAACTGAATTAATTTGAAAATTA
Found at i:2210134 original size:29 final size:29
Alignment explanation
Indices: 2210098--2210155 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
2210088 TCAAAATTTG
2210098 TTTGAAAATTATT-ATCCGAACCGAATTAA
1 TTTGAAAATTATTAAT-CGAACCGAATTAA
*
2210127 TTTGAAAATTATTAATCGAATCGAATTAA
1 TTTGAAAATTATTAATCGAACCGAATTAA
2210156 CCGAATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 25 0.93
30 2 0.07
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.36
Consensus pattern (29 bp):
TTTGAAAATTATTAATCGAACCGAATTAA
Found at i:2211736 original size:20 final size:20
Alignment explanation
Indices: 2211711--2211748 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2211701 CACATGTTAA
2211711 AGAATGCATCGATGCACTAT
1 AGAATGCATCGATGCACTAT
*
2211731 AGAATGTATCGATGCACT
1 AGAATGCATCGATGCACT
2211749 TCAAGGGGAA
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:0.34, C:0.18, G:0.21, T:0.26
Consensus pattern (20 bp):
AGAATGCATCGATGCACTAT
Found at i:2212634 original size:24 final size:21
Alignment explanation
Indices: 2212586--2212634 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
2212576 TTATATGTGG
* *
2212586 TCCTTCGGGACATCTACGTGG
1 TCCTTCGGGACATCTACGCGC
2212607 TCCTTCGGGACAAATTCTACGCGC
1 TCCTTCGGGAC--A-TCTACGCGC
2212631 TCCT
1 TCCT
2212635 AGTGTGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 11 0.48
23 1 0.04
24 11 0.48
ACGTcount: A:0.16, C:0.33, G:0.22, T:0.29
Consensus pattern (21 bp):
TCCTTCGGGACATCTACGCGC
Found at i:2216410 original size:19 final size:20
Alignment explanation
Indices: 2216373--2216410 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
2216363 GTTACTTTGT
*
2216373 GTATCTAATTTATTATTTTC
1 GTATCTAATTTAGTATTTTC
*
2216393 GTAT-TAATTTAGTCTTTT
1 GTATCTAATTTAGTATTTT
2216411 AATATTTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.24, C:0.08, G:0.08, T:0.61
Consensus pattern (20 bp):
GTATCTAATTTAGTATTTTC
Found at i:2216516 original size:14 final size:14
Alignment explanation
Indices: 2216497--2216530 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2216487 ATCTCATAAC
2216497 TTTTAAACTCTAAA
1 TTTTAAACTCTAAA
* *
2216511 TTTTAAACTTTAAT
1 TTTTAAACTCTAAA
2216525 TTTTAA
1 TTTTAA
2216531 TTTAAAACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (14 bp):
TTTTAAACTCTAAA
Found at i:2216538 original size:20 final size:21
Alignment explanation
Indices: 2216509--2216547 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2216499 TTAAACTCTA
*
2216509 AATTTTAAAC-TTTAATTTTT
1 AATTTAAAACTTTTAATTTTT
2216529 AATTTAAAACTTTTAATTT
1 AATTTAAAACTTTTAATTT
2216548 AAGATTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (21 bp):
AATTTAAAACTTTTAATTTTT
Found at i:2216871 original size:2 final size:2
Alignment explanation
Indices: 2216866--2216953 Score: 167
Period size: 2 Copynumber: 43.5 Consensus size: 2
2216856 TATTTTATTA
2216866 AT AT AT AT AT AT AT AT AT AT AT ACT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
2216909 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
2216951 AT A
1 AT A
2216954 CACCAGATGG
Statistics
Matches: 85, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 83 0.98
3 2 0.02
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2224022 original size:21 final size:21
Alignment explanation
Indices: 2223993--2224038 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
2223983 ATTTACCGTG
* *
2223993 ATTGTGGCCGTCGCGGGCGCT
1 ATTGCGGCCGTCGCGGACGCT
*
2224014 ATTGCGGCCGTCGCGGACGTT
1 ATTGCGGCCGTCGCGGACGCT
2224035 ATTG
1 ATTG
2224039 TGAGCGTCGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.09, C:0.26, G:0.39, T:0.26
Consensus pattern (21 bp):
ATTGCGGCCGTCGCGGACGCT
Found at i:2227029 original size:27 final size:27
Alignment explanation
Indices: 2226997--2227048 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
2226987 AAACAACCAT
2226997 AAAAAATCAT-AATAATAAATAAAAAGG
1 AAAAAATCATAAATAA-AAATAAAAAGG
**
2227024 AAAAAATGTTAAATAAAAATAAAAA
1 AAAAAATCATAAATAAAAATAAAAA
2227049 AAATTAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 17 0.77
28 5 0.23
ACGTcount: A:0.73, C:0.02, G:0.06, T:0.19
Consensus pattern (27 bp):
AAAAAATCATAAATAAAAATAAAAAGG
Found at i:2227047 original size:20 final size:20
Alignment explanation
Indices: 2227007--2227080 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
2226997 AAAAAATCAT
* *
2227007 AATAATAAATAAAAAGGAAAA
1 AATATTAAATAAAAA-TAAAA
*
2227028 AATGTTAAATAAAAATAAAA
1 AATATTAAATAAAAATAAAA
*
2227048 AAAATTAAAT-AAAATAAAGA
1 AATATTAAATAAAAATAAA-A
*
2227068 TATATTAAATAAA
1 AATATTAAATAAA
2227081 TCAAAGTAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
19 8 0.18
20 21 0.48
21 15 0.34
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (20 bp):
AATATTAAATAAAAATAAAA
Found at i:2227118 original size:14 final size:14
Alignment explanation
Indices: 2227038--2227194 Score: 54
Period size: 16 Copynumber: 10.6 Consensus size: 14
2227028 AATGTTAAAT
2227038 AAAAATAAAAA-AA
1 AAAAATAAAAATAA
*
2227051 ATTAAAT-AAAATAA
1 A-AAAATAAAAATAA
* * *
2227065 AGATATATTAAATAA
1 AAAAATA-AAAATAA
*
2227080 ATCAAAGTAAAAATGTAA
1 A--AAAATAAAAA--TAA
2227098 AAAAATAAAAATAA
1 AAAAATAAAAATAA
*
2227112 AATAATAAAAGAATAA
1 AAAAAT-AAA-AATAA
* *
2227128 TAAAATAACGAATCAA
1 AAAAATAA-AAAT-AA
*
2227144 AGAAATAAAAGA-AA
1 AAAAATAAAA-ATAA
* *
2227158 GAAAAT-AAGATAA
1 AAAAATAAAAATAA
2227171 AAATAGAT-AAAATAA
1 AAA-A-ATAAAAATAA
*
2227186 AAGAATAAA
1 AAAAATAAA
2227195 TAAAAGAATC
Statistics
Matches: 105, Mismatches: 22, Indels: 33
0.66 0.14 0.21
Matches are distributed among these distances:
12 1 0.01
13 16 0.15
14 25 0.24
15 26 0.25
16 30 0.29
17 3 0.03
18 4 0.04
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.18
Consensus pattern (14 bp):
AAAAATAAAAATAA
Found at i:2229281 original size:80 final size:81
Alignment explanation
Indices: 2228710--2229920 Score: 1358
Period size: 80 Copynumber: 14.6 Consensus size: 81
2228700 ACCTGAATAG
* * * * * *
2228710 AATCAAACTCGAAGGTCTTTATTGACAGATAACACTTCTCT-CCTTGAGCTATGCTGTAAATTTG
1 AATCGAACTCGAAGGTC--TGTTGGCAGATAGCCCTTCT-TGCCTTGAGCTATGCTGCAAA--TG
2228774 ATGTGCCTTTGAGCTGAGTGT
61 ATGTGCCTTTGAGCTGAGTGT
* * * * * * *
2228795 AATCGAACTCGAAGGTATTTTGTTGGTAGATAGCTCTT-TTCTCCTTGAACTATGTTGTAAATTT
1 AATCGAACTCGAAGG---TCTGTTGGCAGATAGCCCTTCTT-GCCTTGAGCTATGCTGCAAA--T
* * *
2228859 GATATGCCTTTGAGATGAATGT
60 GATGTGCCTTTGAGCTGAGTGT
* * * * * *
2228881 AATCGAACTTGAAGGTATTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCGAATTTG
1 AATCGAACTCGAAGG---TCTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGC-AA-ATG
2228946 ATGTGCCTTTGAGCTGAGTGT
61 ATGTGCCTTTGAGCTGAGTGT
* * * ** * *
2228967 AGTTGAACTCGAAGGTCTTTTGTTGGCAGATAACTTTTCTCGCCTTGAGCTATGCTGTAAATGAT
1 AATCGAACTCGAAGGTC---TGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGAT
*
2229032 GTGCCTTTGAGTTGAGTGT
63 GTGCCTTTGAGCTGAGTGT
* * * * * *
2229051 AATCAAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTAAGCTGTGCTGCAAATGTT
1 AATCGAACTCGAAGGTC---TGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGAT
* *
2229116 ATGCCTTTGAGTTGAGTGT
63 GTGCCTTTGAGCTGAGTGT
* *
2229135 AATCGAACTCGAAGGTCTTTTGGTGGCAGATAGCCATTCTTGCCTTGAGCTATGCTGCAAATGAT
1 AATCGAACTCGAAGGTC---TGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGAT
2229200 GTGCCTTTGAGCTGAGTGT
63 GTGCCTTTGAGCTGAGTGT
* *
2229219 AATCGAACTCGAAGGTCT-TTGACAGATAGCCCTTCTTGCCTTGAGCTATGGTGCAAATGATGTG
1 AATCGAACTCGAAGGTCTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTG
* *
2229283 CCTTTAAGATGAGTGT
66 CCTTTGAGCTGAGTGT
* * *
2229299 AATCGAACTCGAAGTTCTTTTGTTGGCAGATAGCCCTTCTCGCCTTGAGCTATGCTACAAATGAT
1 AATCGAACTCGAAGGTC---TGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGAT
*
2229364 GTGCCTTTGAGCTGAATGT
63 GTGCCTTTGAGCTGAGTGT
* * *
2229383 AATCGAACTCGAAGGTCT-TTGGCAGATAGCCCTTCTCGCCTTGAGCTATACTGTAAATGATGTG
1 AATCGAACTCGAAGGTCTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTG
*
2229447 CCTTTGAGTTGAGTGT
66 CCTTTGAGCTGAGTGT
* *
2229463 AATCGAACTCGAAGGTCT-TTGGTAGATAGTCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTG
1 AATCGAACTCGAAGGTCTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTG
*
2229527 CCTTTGAGCTTAGTGT
66 CCTTTGAGCTGAGTGT
* * *
2229543 AATCGATCTCGAAGGTCT-TTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAATTGATGTG
1 AATCGAACTCGAAGGTCTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTG
*
2229607 CATTTGAGCTGAGTGT
66 CCTTTGAGCTGAGTGT
* * * *
2229623 AATCGAACTCGAAGGTCTTTTATTGGCAGATAACCCTTCTCGCCTTGAGTTATGCTGCAAATGAT
1 AATCGAACTCGAAGGTC---TGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGAT
2229688 GTGCCTTTGAGCTGAGTGT
63 GTGCCTTTGAGCTGAGTGT
* * * *
2229707 ATTCGAACTCGAAGGTCT-TTGGCAGATAGCCCTTCTTGCCTTAAGTTATACTGCAAATGATGTG
1 AATCGAACTCGAAGGTCTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTG
2229771 CCTTTGAGCTGAGTGT
66 CCTTTGAGCTGAGTGT
* * *
2229787 AATCGAACTCGAAGGTCT-TTGGCAGGTAGCCCTTCTTGCCTTAAACTATGCTGCAAATGATGTG
1 AATCGAACTCGAAGGTCTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTG
* *
2229851 CATTTGAGCTAAGTGT
66 CCTTTGAGCTGAGTGT
* * * * * *
2229867 AATCGAACTCAAAAGGTCATGGTTGACAAATAACCCTTCTCGCCTTGAGTTATG
1 AATCGAACTC-GAAGGTC-T-GTTGGCAGATAGCCCTTCTTGCCTTGAGCTATG
2229921 ATGTAAATTG
Statistics
Matches: 986, Mismatches: 117, Indels: 47
0.86 0.10 0.04
Matches are distributed among these distances:
80 432 0.44
81 9 0.01
82 1 0.00
83 3 0.00
84 357 0.36
85 17 0.02
86 163 0.17
87 3 0.00
88 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (81 bp):
AATCGAACTCGAAGGTCTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTG
CCTTTGAGCTGAGTGT
Found at i:2229346 original size:164 final size:165
Alignment explanation
Indices: 2228710--2229920 Score: 1476
Period size: 164 Copynumber: 7.3 Consensus size: 165
2228700 ACCTGAATAG
* * * * *
2228710 AATCAAACTCGAAGGTCTTTATTGACAGATAACACTTCTCT-CCTTGAGCTATGCTGTAAATTTG
1 AATCGAACTCGAAGGTC--TGTTGGCAGATAACCCTTCT-TGCCTTGAGCTATGCTGCAAA--TG
* * * * *
2228774 ATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTATTTTGTTGGTAGATAGCTCTTTTCTCC
61 ATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTCGCC
* * * * * *
2228839 TTGAACTATGTTGTAAATTTGATATGCCTTTGAGATGAATGT
126 TTGAGCTATGCTGCAAA--TGATGTGCCTTTGAGCTGAGTGT
* * * * *
2228881 AATCGAACTTGAAGGTATTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCGAATTTG
1 AATCGAACTCGAAGG---TCTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGC-AA-ATG
* * * **
2228946 ATGTGCCTTTGAGCTGAGTGTAGTTGAACTCGAAGGTCTTTTGTTGGCAGATAACTTTTCTCGCC
61 ATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTCGCC
* *
2229011 TTGAGCTATGCTGTAAATGATGTGCCTTTGAGTTGAGTGT
126 TTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGT
* * * * *
2229051 AATCAAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTAAGCTGTGCTGCAAATGTT
1 AATCGAACTCGAAGGTC---TGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGAT
* * * * *
2229116 ATGCCTTTGAGTTGAGTGTAATCGAACTCGAAGGTCTTTTGGTGGCAGATAGCCATTCTTGCCTT
63 GTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTCGCCTT
2229181 GAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGT
128 GAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGT
* * *
2229219 AATCGAACTCGAAGGTCT-TTGACAGATAGCCCTTCTTGCCTTGAGCTATGGTGCAAATGATGTG
1 AATCGAACTCGAAGGTCTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTG
* * *
2229283 CCTTTAAGATGAGTGTAATCGAACTCGAAGTTCTTTTGTTGGCAGATAGCCCTTCTCGCCTTGAG
66 CCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTCGCCTTGAG
* *
2229348 CTATGCTACAAATGATGTGCCTTTGAGCTGAATGT
131 CTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGT
* * * *
2229383 AATCGAACTCGAAGGTCT-TTGGCAGATAGCCCTTCTCGCCTTGAGCTATACTGTAAATGATGTG
1 AATCGAACTCGAAGGTCTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTG
* * * *
2229447 CCTTTGAGTTGAGTGTAATCGAACTCGAAGGTC---T-TTGGTAGATAGTCCTTCTTGCCTTGAG
66 CCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTCGCCTTGAG
*
2229508 CTATGCTGCAAATGATGTGCCTTTGAGCTTAGTGT
131 CTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGT
* *
2229543 AATCGATCTCGAAGGTCT-TTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAATTGATGTG
1 AATCGAACTCGAAGGTCTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTG
* * *
2229607 CATTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTATTGGCAGATAACCCTTCTCGCCTTGAG
66 CCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTCGCCTTGAG
*
2229672 TTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGT
131 CTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGT
* * * * *
2229707 ATTCGAACTCGAAGGTCT-TTGGCAGATAGCCCTTCTTGCCTTAAGTTATACTGCAAATGATGTG
1 AATCGAACTCGAAGGTCTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTG
* * * *
2229771 CCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC---T-TTGGCAGGTAGCCCTTCTTGCCTTAAA
66 CCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTCGCCTTGAG
* *
2229832 CTATGCTGCAAATGATGTGCATTTGAGCTAAGTGT
131 CTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGT
* * * * *
2229867 AATCGAACTCAAAAGGTCATGGTTGACAAATAACCCTTCTCGCCTTGAGTTATG
1 AATCGAACTC-GAAGGTC-T-GTTGGCAGATAACCCTTCTTGCCTTGAGCTATG
2229921 ATGTAAATTG
Statistics
Matches: 911, Mismatches: 112, Indels: 41
0.86 0.11 0.04
Matches are distributed among these distances:
160 208 0.23
161 8 0.01
162 1 0.00
163 1 0.00
164 390 0.43
165 1 0.00
167 1 0.00
168 111 0.12
169 2 0.00
170 67 0.07
171 13 0.01
172 105 0.12
173 2 0.00
174 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (165 bp):
AATCGAACTCGAAGGTCTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTG
CCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTCGCCTTGAG
CTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGT
Found at i:2229521 original size:244 final size:246
Alignment explanation
Indices: 2228710--2229920 Score: 1465
Period size: 244 Copynumber: 4.9 Consensus size: 246
2228700 ACCTGAATAG
* * * * *
2228710 AATCAAACTCGAAGGTCTTTATTGACAGATAACACTTCTCT-CCTTGAGCTATGCTGTAAATTTG
1 AATCGAACTCGAAGGTC--T-TTGGCAGATAGCCCTTCT-TGCCTTGAGCTATGCTGCAAA--TG
* * * * *
2228774 ATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTATTTTGTTGGTAGATAGCTCTTTTCTCC
60 ATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTCGCC
* * * * * * *
2228839 TTGAACTATGTTGTAAATTTGATATGCCTTTGAGATGAATGTAATCGAACTTGAAGGTATTTTGT
125 TTGAGCTATGCTGCAAA--TGATGTGCCTTTGAGCTGAATGTAATCGAACTCGAAGG--TCTTGT
* *
2228904 TGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCGAATTTGATGTGCCTTTGAGCTGAGTGT
186 TGGCAGATAACCCTTCTCGCCTTGAGTTATGCTGC-AA-ATGATGTGCCTTTGAGCTGAGTGT
* * * ** * *
2228967 AGTTGAACTCGAAGGTCTTTTGTTGGCAGATAACTTTTCTCGCCTTGAGCTATGCTGTAAATGAT
1 AATCGAACTCGAAGGTC---T-TTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGAT
* * *
2229032 GTGCCTTTGAGTTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTT
62 GTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTCGCCTT
* * * * * * *
2229097 AAGCTGTGCTGCAAATGTTATGCCTTTGAGTTGAGTGTAATCGAACTCGAAGGTCTTTTGGTGGC
127 GAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTC--TTGTTGGC
* * * *
2229162 AGATAGCCATTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGT
190 AGATAACCCTTCTCGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGT
* *
2229219 AATCGAACTCGAAGGTCTTTGACAGATAGCCCTTCTTGCCTTGAGCTATGGTGCAAATGATGTGC
1 AATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGC
* * *
2229284 CTTTAAGATGAGTGTAATCGAACTCGAAGTTCTTTTGTTGGCAGATAGCCCTTCTCGCCTTGAGC
66 CTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTCGCCTTGAGC
* *
2229349 TATGCTACAAATGATGTGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTC-T-TTGGCAGATAG
131 TATGCTGCAAATGATGTGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTGTTGGCAGATAA
* * * *
2229412 CCCTTCTCGCCTTGAGCTATACTGTAAATGATGTGCCTTTGAGTTGAGTGT
196 CCCTTCTCGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGT
* *
2229463 AATCGAACTCGAAGGTCTTTGGTAGATAGTCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGC
1 AATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGC
* * * *
2229528 CTTTGAGCTTAGTGTAATCGATCTCGAAGGTC---T-TTGGCAGATAACCCTTCTTGCCTTGAGC
66 CTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTCGCCTTGAGC
* * * *
2229589 TATGCTGCAATTGATGTGCATTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTATTGGCAGAT
131 TATGCTGCAAATGATGTGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTC--TTGTTGGCAGAT
2229654 AACCCTTCTCGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGT
194 AACCCTTCTCGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGT
* * * *
2229707 ATTCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTTGCCTTAAGTTATACTGCAAATGATGTGC
1 AATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGC
* * * *
2229772 CTTTGAGCTGAGTGTAATCGAACTCGAAGGTC---T-TTGGCAGGTAGCCCTTCTTGCCTTAAAC
66 CTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTCGCCTTGAGC
* * * * *
2229833 TATGCTGCAAATGATGTGCATTTGAGCT-AAGTGTAATCGAACTCAAAAGGTCATGGTTGACAAA
131 TATGCTGCAAATGATGTGCCTTTGAGCTGAA-TGTAATCGAACTC-GAAGGTC-TTGTTGGCAGA
2229897 TAACCCTTCTCGCCTTGAGTTATG
193 TAACCCTTCTCGCCTTGAGTTATG
2229921 ATGTAAATTG
Statistics
Matches: 845, Mismatches: 99, Indels: 33
0.86 0.10 0.03
Matches are distributed among these distances:
240 73 0.09
241 1 0.00
243 2 0.00
244 386 0.46
245 7 0.01
248 144 0.17
249 1 0.00
252 39 0.05
253 2 0.00
254 68 0.08
256 71 0.08
257 14 0.02
258 37 0.04
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (246 bp):
AATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGC
CTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTCGCCTTGAGC
TATGCTGCAAATGATGTGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTGTTGGCAGATAA
CCCTTCTCGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGT
Found at i:2231142 original size:100 final size:99
Alignment explanation
Indices: 2230970--2231177 Score: 328
Period size: 100 Copynumber: 2.1 Consensus size: 99
2230960 GGACAATTCA
* * *
2230970 ATATTATAATCACCTTTATTAGGTTAGCTGAATATTATTCATAAAGCCGGGGCGTTTAACCAATT
1 ATATTATAATCACCTTTATCAGGTTAGCTGAATATTATCCATAAAGCCGGGGCATTTAACCAATT
*
2231035 GCTCTAGAGTGACAACTCAAGCTTTATTGTATAT
66 GCTCTAGAGGGACAACTCAAGCTTTATTGTATAT
* *
2231069 ATATTATAATCACCTTTATCAGGCTTAGCTGAATCTTATCCATAAAGCTGGGGCATTTAACCAAT
1 ATATTATAATCACCTTTATCAGG-TTAGCTGAATATTATCCATAAAGCCGGGGCATTTAACCAAT
* *
2231134 TGCTCTAGAGGGATAGCTCAAGCTTTATTGTATAT
65 TGCTCTAGAGGGACAACTCAAGCTTTATTGTATAT
2231169 ATA-TATAAT
1 ATATTATAAT
2231178 TATAATTTGA
Statistics
Matches: 100, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
99 28 0.28
100 72 0.72
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (99 bp):
ATATTATAATCACCTTTATCAGGTTAGCTGAATATTATCCATAAAGCCGGGGCATTTAACCAATT
GCTCTAGAGGGACAACTCAAGCTTTATTGTATAT
Found at i:2233800 original size:10 final size:11
Alignment explanation
Indices: 2233783--2233811 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
2233773 GAAAACAACC
2233783 ATAAAAAATAA
1 ATAAAAAATAA
2233794 A-AAAAAATAA
1 ATAAAAAATAA
2233804 ATAAAAAA
1 ATAAAAAA
2233812 ATCACAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (11 bp):
ATAAAAAATAA
Found at i:2233807 original size:21 final size:21
Alignment explanation
Indices: 2233783--2233889 Score: 78
Period size: 21 Copynumber: 5.0 Consensus size: 21
2233773 GAAAACAACC
*
2233783 ATAAAAAATAAAAAAAAATAA
1 ATAAAAAATAAAAAATAATAA
* *
2233804 ATAAAAAA-ATCACAATAATAA
1 ATAAAAAATA-AAAAATAATAA
* *
2233825 ATAAAAAAGGGAAAACAATATTAA
1 ATAAAAAA--TAAAA-AATAATAA
* *
2233849 ATAAAAAAT-AATAATCAT-A
1 ATAAAAAATAAAAAATAATAA
2233868 ATAAAAAATAAAATAA-AATAA
1 ATAAAAAATAAAA-AATAATAA
2233889 A
1 A
2233890 GATATATTAA
Statistics
Matches: 66, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
19 10 0.15
20 9 0.14
21 30 0.45
23 1 0.02
24 16 0.24
ACGTcount: A:0.75, C:0.04, G:0.03, T:0.19
Consensus pattern (21 bp):
ATAAAAAATAAAAAATAATAA
Found at i:2233870 original size:26 final size:26
Alignment explanation
Indices: 2233841--2233904 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
2233831 AAGGGAAAAC
*
2233841 AATATTAAATAAAA-AATAATAATCAT
1 AATATTAAATAAAATAA-AATAAACAT
** *
2233867 AATAAAAAATAAAATAAAATAAAGAT
1 AATATTAAATAAAATAAAATAAACAT
2233893 -ATATTAAATAAA
1 AATATTAAATAAA
2233905 TCAAAGTAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
25 10 0.32
26 19 0.61
27 2 0.06
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.27
Consensus pattern (26 bp):
AATATTAAATAAAATAAAATAAACAT
Found at i:2233915 original size:42 final size:41
Alignment explanation
Indices: 2233856--2233945 Score: 98
Period size: 41 Copynumber: 2.2 Consensus size: 41
2233846 TAAATAAAAA
*
2233856 ATAAT-AATCATAATAAAAA-ATAAAATAAAATAAAGATATATT
1 ATAATAAATCATAATAAAAACAT-AAA-AAAATAAAAATA-ATT
*
2233898 A-AATAAATCA-AAGTAAAAACGTAAAAAAATAAAAATAATT
1 ATAATAAATCATAA-TAAAAACATAAAAAAATAAAAATAATT
2233938 ATAATAAA
1 ATAATAAA
2233946 AAATCAACGA
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
40 4 0.10
41 22 0.52
42 15 0.36
43 1 0.02
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.24
Consensus pattern (41 bp):
ATAATAAATCATAATAAAAACATAAAAAAATAAAAATAATT
Found at i:2243535 original size:18 final size:17
Alignment explanation
Indices: 2243512--2243561 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
2243502 TGATGCTTTC
2243512 TTTCTTGTTTCTCT-ATG
1 TTTCTTGTTTCT-TGATG
*
2243529 ATTTCTTGTTACTTGATG
1 -TTTCTTGTTTCTTGATG
2243547 TTTCTTGTTT-TTGAT
1 TTTCTTGTTTCTTGAT
2243562 CAATAGCTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 5 0.17
17 10 0.34
18 14 0.48
ACGTcount: A:0.10, C:0.12, G:0.14, T:0.64
Consensus pattern (17 bp):
TTTCTTGTTTCTTGATG
Found at i:2251199 original size:18 final size:17
Alignment explanation
Indices: 2251176--2251223 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
2251166 ATGCTTTTTC
2251176 TCTTGTTTCTCT-ATGATT
1 TCTTGTTTCT-TGATG-TT
*
2251194 TCTTGTTGCTTGATGTT
1 TCTTGTTTCTTGATGTT
2251211 TCTTGTTT-TTGAT
1 TCTTGTTTCTTGAT
2251224 CAATGGCTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 5 0.19
17 10 0.37
18 12 0.44
ACGTcount: A:0.08, C:0.12, G:0.17, T:0.62
Consensus pattern (17 bp):
TCTTGTTTCTTGATGTT
Found at i:2254568 original size:29 final size:28
Alignment explanation
Indices: 2254525--2254583 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 28
2254515 TTTAAAGGTG
* * *
2254525 TTTATATTATGTTTGTGTTCGTTTAATTT
1 TTTATATTATATTTGTATTCATTT-ATTT
*
2254554 TTTATATTGTATTTGTATTCATTTATTT
1 TTTATATTATATTTGTATTCATTTATTT
2254582 TT
1 TT
2254584 GATGGTGTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 6 0.23
29 20 0.77
ACGTcount: A:0.19, C:0.03, G:0.10, T:0.68
Consensus pattern (28 bp):
TTTATATTATATTTGTATTCATTTATTT
Found at i:2256798 original size:3 final size:3
Alignment explanation
Indices: 2256790--2256852 Score: 72
Period size: 3 Copynumber: 20.0 Consensus size: 3
2256780 TTTACCCATT
* * *
2256790 TTA TTA TTA TTA TAA TTA TTA TCA TAA TTA TTA TTA TTA TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
2256836 TATA TATA TTA TTA TTA
1 T-TA T-TA TTA TTA TTA
2256853 AAAAAAATAT
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
3 43 0.80
4 11 0.20
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:2256824 original size:24 final size:27
Alignment explanation
Indices: 2256791--2256852 Score: 85
Period size: 24 Copynumber: 2.4 Consensus size: 27
2256781 TTACCCATTT
2256791 TATTATTATTATAATTAT-TAT-CATA
1 TATTATTATTATAATTATATATACATA
* *
2256816 -ATTATTATTATTATTATATATATATA
1 TATTATTATTATAATTATATATACATA
2256842 TATTATTATTA
1 TATTATTATTA
2256853 AAAAAAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 16 0.50
25 3 0.09
26 3 0.09
27 10 0.31
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (27 bp):
TATTATTATTATAATTATATATACATA
Found at i:2257323 original size:17 final size:17
Alignment explanation
Indices: 2257297--2257335 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
2257287 AGAGACCAGC
* *
2257297 AAAAATAGAGAAGAAAA
1 AAAAACAGAGAACAAAA
2257314 AAAAACAGAGAACAAAA
1 AAAAACAGAGAACAAAA
2257331 AAAAA
1 AAAAA
2257336 GAAAACCTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.79, C:0.05, G:0.13, T:0.03
Consensus pattern (17 bp):
AAAAACAGAGAACAAAA
Found at i:2262315 original size:15 final size:15
Alignment explanation
Indices: 2262295--2262326 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2262285 ATCAATACCT
2262295 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
2262310 TTTTGCATACATTCA
1 TTTTGCATACATGCA
2262325 TT
1 TT
2262327 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:2269674 original size:7 final size:6
Alignment explanation
Indices: 2269656--2269758 Score: 86
Period size: 7 Copynumber: 16.5 Consensus size: 6
2269646 ATTATGCTTG
* * *
2269656 AAGAAA ACAGAAGA AAGAAA AGGAAAA AAGAAAA AAGAAA GAGAAA AA-AAG
1 AAGAAA A-AGAA-A AAGAAA AAG-AAA AAG-AAA AAGAAA AAGAAA AAGAAA
*
2269707 AA-AAA AAGAAA GA-AAA AAGAGAA AAGAGAA AAGAAAA AAGAAA AAGAAA
1 AAGAAA AAGAAA AAGAAA AAGA-AA AAGA-AA AAG-AAA AAGAAA AAGAAA
2269756 AAG
1 AAG
2269759 GGGGGTCAAG
Statistics
Matches: 82, Mismatches: 8, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
5 12 0.15
6 30 0.37
7 37 0.45
8 3 0.04
ACGTcount: A:0.79, C:0.01, G:0.20, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:2269675 original size:14 final size:13
Alignment explanation
Indices: 2269656--2269758 Score: 78
Period size: 12 Copynumber: 8.2 Consensus size: 13
2269646 ATTATGCTTG
2269656 AAGAAAACAGAAGA
1 AAGAAAA-AGAAGA
* *
2269670 AAGAAAAGGAAAA
1 AAGAAAAAGAAGA
2269683 AAG-AAAA-AAGA
1 AAGAAAAAGAAGA
*
2269694 AAG-AGAA-AA-A
1 AAGAAAAAGAAGA
2269704 AAGAAAAA-AAGA
1 AAGAAAAAGAAGA
2269716 AAGAAAAA-AGAGAA
1 AAGAAAAAGA-AG-A
*
2269730 AAGAGAAAAGAAAA
1 AAGA-AAAAGAAGA
2269744 AAGAAAAAGAA-A
1 AAGAAAAAGAAGA
2269756 AAG
1 AAG
2269759 GGGGGTCAAG
Statistics
Matches: 76, Mismatches: 7, Indels: 14
0.78 0.07 0.14
Matches are distributed among these distances:
10 4 0.05
11 16 0.21
12 17 0.22
13 16 0.21
14 17 0.22
15 5 0.07
16 1 0.01
ACGTcount: A:0.79, C:0.01, G:0.20, T:0.00
Consensus pattern (13 bp):
AAGAAAAAGAAGA
Found at i:2269687 original size:20 final size:19
Alignment explanation
Indices: 2269656--2269758 Score: 118
Period size: 20 Copynumber: 5.2 Consensus size: 19
2269646 ATTATGCTTG
*
2269656 AAGAAAACAGAAGAAAGAAA
1 AAGAAAAAAGAA-AAAGAAA
*
2269676 AGGAAAAAAGAAAAAAGAAA
1 AAGAAAAAAG-AAAAAGAAA
*
2269696 GAGAAAAAAAGAAAAA-AAGA
1 AAG-AAAAAAGAAAAAGAA-A
2269716 AAGAAAAAAGAGAAAAGAGAA
1 AAGAAAAAAGA-AAAAGA-AA
2269737 AAGAAAAAAGAAAAAGAAA
1 AAGAAAAAAGAAAAAGAAA
2269756 AAG
1 AAG
2269759 GGGGGTCAAG
Statistics
Matches: 72, Mismatches: 5, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
19 15 0.21
20 34 0.47
21 22 0.31
22 1 0.01
ACGTcount: A:0.79, C:0.01, G:0.20, T:0.00
Consensus pattern (19 bp):
AAGAAAAAAGAAAAAGAAA
Found at i:2271479 original size:83 final size:83
Alignment explanation
Indices: 2271091--2271479 Score: 733
Period size: 83 Copynumber: 4.7 Consensus size: 83
2271081 AACAAACGCC
*
2271091 AATAATGTGCTCATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGGTAAAAC
1 AATAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT-GGTAAAAC
2271156 CAATCATTGAATTTGGAAG
65 CAATCATTGAATTTGGAAG
*
2271175 AATAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGGTAAAACC
1 AATAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
2271240 AATCATTGAATTTGGAAG
66 AATCATTGAATTTGGAAG
2271258 AATAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
1 AATAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
2271323 AATCATTGAATTTGGAAG
66 AATCATTGAATTTGGAAG
*
2271341 AATAATGTGCTCATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
1 AATAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
2271406 AATCATTGAATTTGGAAG
66 AATCATTGAATTTGGAAG
*
2271424 AATAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGGTTT
1 AATAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
2271480 AGTAGGAACC
Statistics
Matches: 299, Mismatches: 6, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
83 245 0.82
84 54 0.18
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (83 bp):
AATAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
AATCATTGAATTTGGAAG
Found at i:2272413 original size:113 final size:113
Alignment explanation
Indices: 2272215--2272967 Score: 1381
Period size: 113 Copynumber: 6.7 Consensus size: 113
2272205 ATCCATAACA
* *
2272215 ATGGATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
1 ATGGATCAGCTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
*
2272280 TCATAATGAGAAGAGCTTGTTCGACCTTTTGCTCAAATCCATCACTTG
66 TCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTG
2272328 ATGGATCAGCTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
1 ATGGATCAGCTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
*
2272393 TCATAATGAGAAGAGCTTGTTCGACCTTTTGCTCAAATCCATCACTTG
66 TCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTG
2272441 ATGGATCAGCTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
1 ATGGATCAGCTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
2272506 TCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTG
66 TCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTG
2272554 ATGGATCAGCTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
1 ATGGATCAGCTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
* *
2272619 TCATAATGAGAAGAGCTTGTTCGACCTTTTGCTCAAATTCATCACTTG
66 TCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTG
2272667 ATGGATCAGCTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
1 ATGGATCAGCTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
2272732 TCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTG
66 TCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTG
*
2272780 ATGGATCAACTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
1 ATGGATCAGCTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
*
2272845 TCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTCG
66 TCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTG
*
2272893 ATGGATCAGCTTTTCCAG-AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA-G-AG-A-AAG
1 ATGGATCAGCTTTTCCAGAAG-AAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
2272953 TTCATAATGAGAAGA
65 TTCATAATGAGAAGA
2272968 ACTCATCTGA
Statistics
Matches: 628, Mismatches: 11, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
109 18 0.03
110 1 0.00
111 2 0.00
112 3 0.00
113 604 0.96
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (113 bp):
ATGGATCAGCTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
TCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTG
Found at i:2272956 original size:36 final size:36
Alignment explanation
Indices: 2272909--2273100 Score: 285
Period size: 36 Copynumber: 5.1 Consensus size: 36
2272899 CAGCTTTTCC
2272909 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
2272945 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
2272981 AGGAATAAGAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 A-G-A-GA-AAGTTCATAATGAGAAGAACTCATCTGAAGA
*
2273021 AGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGA
1 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
2273057 AGGAAGAAGAAGTTCATAATGAAAAGAACTCATCTGAAGA
1 A-G-AG-A-AAGTTCATAATGAGAAGAACTCATCTGAAGA
2273097 AGAG
1 AGAG
2273101 CTTATTCAAC
Statistics
Matches: 143, Mismatches: 5, Indels: 14
0.88 0.03 0.09
Matches are distributed among these distances:
36 68 0.48
37 3 0.02
38 6 0.04
39 4 0.03
40 62 0.43
ACGTcount: A:0.48, C:0.10, G:0.22, T:0.19
Consensus pattern (36 bp):
AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
Found at i:2272965 original size:20 final size:20
Alignment explanation
Indices: 2272909--2272967 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
2272899 CAGCTTTTCC
2272909 AGAGAAAGTTCATAATGAG-
1 AGAGAAAGTTCATAATGAGA
* *
2272928 A-AG-AA-CTCAT-CTGAAGA
1 AGAGAAAGTTCATAATG-AGA
2272945 AGAGAAAGTTCATAATGAGA
1 AGAGAAAGTTCATAATGAGA
2272965 AGA
1 AGA
2272968 ACTCATCTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 11
0.67 0.09 0.24
Matches are distributed among these distances:
15 2 0.07
16 6 0.20
17 3 0.10
18 4 0.13
19 3 0.10
20 10 0.33
21 2 0.07
ACGTcount: A:0.49, C:0.08, G:0.24, T:0.19
Consensus pattern (20 bp):
AGAGAAAGTTCATAATGAGA
Found at i:2272968 original size:18 final size:18
Alignment explanation
Indices: 2272911--2272968 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
2272901 GCTTTTCCAG
2272911 AGAAAGTTCATAATGAGA
1 AGAAAGTTCATAATGAGA
* *
2272929 AG-AA-CTCAT-CTGAAGAA
1 AGAAAGTTCATAATG-AG-A
2272946 GAGAAAGTTCATAATGAGA
1 -AGAAAGTTCATAATGAGA
2272965 AGAA
1 AGAA
2272969 CTCATCTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 12
0.65 0.09 0.26
Matches are distributed among these distances:
15 2 0.07
16 6 0.20
17 3 0.10
18 8 0.27
19 3 0.10
20 6 0.20
21 2 0.07
ACGTcount: A:0.50, C:0.09, G:0.22, T:0.19
Consensus pattern (18 bp):
AGAAAGTTCATAATGAGA
Found at i:2273042 original size:76 final size:76
Alignment explanation
Indices: 2272914--2273100 Score: 347
Period size: 76 Copynumber: 2.5 Consensus size: 76
2272904 TTTCCAGAGA
*
2272914 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAGAAAGTTCATAATAAGAAGAACTCATCTGAA
*
2272979 GAAGGAATAAG
66 GAAGGAAGAAG
2272990 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAGAAAGTTCATAATAAGAAGAACTCATCTGAA
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAGAAAGTTCATAATAAGAAGAACTCATCTGAA
2273055 GAAGGAAGAAG
66 GAAGGAAGAAG
*
2273066 AAGTTCATAATGAAAAGAACTCATCTGAAGAAGAG
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAG
2273101 CTTATTCAAC
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 108 1.00
ACGTcount: A:0.48, C:0.11, G:0.22, T:0.19
Consensus pattern (76 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAGAAAGTTCATAATAAGAAGAACTCATCTGAA
GAAGGAAGAAG
Found at i:2273062 original size:20 final size:20
Alignment explanation
Indices: 2273003--2273064 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
2272993 TTCATAATGA
2273003 GAAGAACTCATCTGAAGAAG
1 GAAGAACTCATCTGAAGAAG
** *
2273023 AGAA-AGTTCA--T-AATAA-
1 -GAAGAACTCATCTGAAGAAG
2273039 GAAGAACTCATCTGAAGAAG
1 GAAGAACTCATCTGAAGAAG
2273059 GAAGAA
1 GAAGAA
2273065 GAAGTTCATA
Statistics
Matches: 30, Mismatches: 6, Indels: 11
0.64 0.13 0.23
Matches are distributed among these distances:
15 3 0.10
16 4 0.13
17 4 0.13
18 2 0.07
19 4 0.13
20 10 0.33
21 3 0.10
ACGTcount: A:0.50, C:0.11, G:0.23, T:0.16
Consensus pattern (20 bp):
GAAGAACTCATCTGAAGAAG
Found at i:2273063 original size:43 final size:40
Alignment explanation
Indices: 2272914--2273098 Score: 262
Period size: 40 Copynumber: 4.8 Consensus size: 40
2272904 TTTCCAGAGA
*
2272914 AAGTTCATAATGAGAAGAACTCATCTGAAGAA-G-AG-A-
1 AAGTTCATAATGAAAAGAACTCATCTGAAGAAGGAAGAAG
* *
2272950 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAATAAG
1 AAGTTCATAATGAAAAGAACTCATCTGAAGAAGGAAGAAG
*
2272990 AAGTTCATAATGAGAAGAACTCATCTGAAGAA-G-AG-A-
1 AAGTTCATAATGAAAAGAACTCATCTGAAGAAGGAAGAAG
2273026 AAGTTCATAAT-AAGAAGAACTCATCTGAAGAAGGAAGAAG
1 AAGTTCATAATGAA-AAGAACTCATCTGAAGAAGGAAGAAG
2273066 AAGTTCATAATGAAAAGAACTCATCTGAAGAAG
1 AAGTTCATAATGAAAAGAACTCATCTGAAGAAG
2273099 AGCTTATTCA
Statistics
Matches: 136, Mismatches: 3, Indels: 16
0.88 0.02 0.10
Matches are distributed among these distances:
35 1 0.01
36 61 0.45
37 3 0.02
38 4 0.03
39 3 0.02
40 62 0.46
41 2 0.01
ACGTcount: A:0.48, C:0.11, G:0.22, T:0.19
Consensus pattern (40 bp):
AAGTTCATAATGAAAAGAACTCATCTGAAGAAGGAAGAAG
Found at i:2273348 original size:3 final size:3
Alignment explanation
Indices: 2273340--2273406 Score: 73
Period size: 3 Copynumber: 22.0 Consensus size: 3
2273330 TTTACCCATT
* * * *
2273340 TTA TTA TTA TTA TAA TTA TTA TCA TAA TTA TTA TTA TTA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2273388 -TA TATA TATA TTA TTA TTA
1 TTA T-TA T-TA TTA TTA TTA
2273407 AAAAAATATA
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
2 2 0.04
3 46 0.84
4 7 0.13
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:2273846 original size:10 final size:10
Alignment explanation
Indices: 2273817--2273846 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
2273807 GAAAGAAAAA
*
2273817 GAGAGAGACA
1 GAGAGAGACC
2273827 GAGAGAGACC
1 GAGAGAGACC
2273837 GAGAGAGACC
1 GAGAGAGACC
2273847 AGCAAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.43, C:0.17, G:0.40, T:0.00
Consensus pattern (10 bp):
GAGAGAGACC
Found at i:2273876 original size:17 final size:17
Alignment explanation
Indices: 2273850--2273888 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
2273840 AGAGACCAGC
* *
2273850 AAAAATAGAGAAGAAAA
1 AAAAACAGAGAACAAAA
2273867 AAAAACAGAGAACAAAA
1 AAAAACAGAGAACAAAA
2273884 AAAAA
1 AAAAA
2273889 AGAAAACCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.79, C:0.05, G:0.13, T:0.03
Consensus pattern (17 bp):
AAAAACAGAGAACAAAA
Found at i:2276315 original size:19 final size:20
Alignment explanation
Indices: 2276283--2276320 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
2276273 ATTTACATAA
2276283 TTAATATTAAAATT-AAAAT
1 TTAATATTAAAATTGAAAAT
* *
2276302 TTAATGTTATAATTGAAAA
1 TTAATATTAAAATTGAAAA
2276321 AATTAAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (20 bp):
TTAATATTAAAATTGAAAAT
Found at i:2285675 original size:2 final size:2
Alignment explanation
Indices: 2285668--2285718 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
2285658 ATGTAAGATG
2285668 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
2285710 TA TA TA TA T
1 TA TA TA TA T
2285719 GAACGAATAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2291921 original size:12 final size:12
Alignment explanation
Indices: 2291904--2291938 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2291894 TTGTTCATTT
2291904 CTACAGTAACTG
1 CTACAGTAACTG
*
2291916 CTACAGTAATTG
1 CTACAGTAACTG
*
2291928 TTACAGTAACT
1 CTACAGTAACT
2291939 TCCGAAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.31
Consensus pattern (12 bp):
CTACAGTAACTG
Found at i:2292570 original size:61 final size:60
Alignment explanation
Indices: 2292463--2292577 Score: 144
Period size: 61 Copynumber: 1.9 Consensus size: 60
2292453 GTAGTGCTAA
* *
2292463 ACCTGCACTAAGCTTAAGTCATAGTGCTAATCCGGAATATACACATAAGGTCGTGCCCACC
1 ACCTACACTAAGCTTAAGTCATAGTGCTAATCCAGAATATA-ACATAAGGTCGTGCCCACC
* *
2292524 ACCTACACTAAGCTTACG-CTATAGTGTTAATCCAGACATGAT-ACATAAGGTCGT
1 ACCTACACTAAGCTTAAGTC-ATAGTGCTAATCCAGA-AT-ATAACATAAGGTCGT
2292578 ATCAACCTTC
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
60 1 0.02
61 42 0.89
62 2 0.04
63 2 0.04
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.25
Consensus pattern (60 bp):
ACCTACACTAAGCTTAAGTCATAGTGCTAATCCAGAATATAACATAAGGTCGTGCCCACC
Found at i:2299282 original size:19 final size:19
Alignment explanation
Indices: 2299260--2299318 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
2299250 GAAAATTACT
2299260 ATCGCAATACGAAATGAAA
1 ATCGCAATACGAAATGAAA
*
2299279 ATCGC-A-ACG--A-GAGA
1 ATCGCAATACGAAATGAAA
*
2299293 ATCGCAATGCGAAATGAAA
1 ATCGCAATACGAAATGAAA
2299312 ATCGCAA
1 ATCGCAA
2299319 CGCTAATTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 8 0.25
15 2 0.06
16 2 0.06
17 3 0.09
18 2 0.06
19 15 0.47
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.14
Consensus pattern (19 bp):
ATCGCAATACGAAATGAAA
Found at i:2299306 original size:33 final size:33
Alignment explanation
Indices: 2299260--2299386 Score: 175
Period size: 33 Copynumber: 3.8 Consensus size: 33
2299250 GAAAATTACT
* *
2299260 ATCGCAATACGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAAAGA
* *
2299293 ATCGCAATGCGAAATGAAAATCGCAACGCTAA-T
1 ATCGCAATGCGAAATGAAAATCGCAACG-AAAGA
* *
2299326 TTCGCAATGCGAAATGAAAATTGCAACGAAAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAAAGA
*
2299359 ATCGCAATGCAAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
2299387 CGAATTTAAT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
32 2 0.02
33 78 0.96
34 1 0.01
ACGTcount: A:0.46, C:0.19, G:0.20, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAAAGA
Found at i:2299367 original size:66 final size:66
Alignment explanation
Indices: 2299261--2299393 Score: 221
Period size: 66 Copynumber: 2.0 Consensus size: 66
2299251 AAAATTACTA
* * *
2299261 TCGCAATACGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATACGAAATGAAAATCGCAACGAAAGAATCGCAATGCAAAATGAAAATCGCAACGCGAAT
2299326 T
66 T
* *
2299327 TCGCAATGCGAAATGAAAATTGCAACGAAAGAATCGCAATGCAAAATGAAAATCGCAACGCGAAT
1 TCGCAATACGAAATGAAAATCGCAACGAAAGAATCGCAATGCAAAATGAAAATCGCAACGCGAAT
2299392 T
66 T
2299393 T
1 T
2299394 AATTTCGCGT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.44, C:0.19, G:0.20, T:0.17
Consensus pattern (66 bp):
TCGCAATACGAAATGAAAATCGCAACGAAAGAATCGCAATGCAAAATGAAAATCGCAACGCGAAT
T
Found at i:2299437 original size:33 final size:33
Alignment explanation
Indices: 2299386--2299475 Score: 144
Period size: 33 Copynumber: 2.7 Consensus size: 33
2299376 AAATCGCAAC
* * *
2299386 GCGAATTTAATTTCGCGTTGCGTTTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
2299419 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
*
2299452 GCGATTTTCATTTCGCATTGCGAT
1 GCGATTTTCATTTCGCGTTGCGAT
2299476 AGTACTTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.44
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
Found at i:2299439 original size:19 final size:19
Alignment explanation
Indices: 2299415--2299475 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
2299405 GCGTTTCTCT
2299415 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
2299434 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
2299448 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
2299467 CATTGCGAT
1 CGTTGCGAT
2299476 AGTACTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
14 10 0.29
16 3 0.09
17 3 0.09
19 18 0.53
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:2299455 original size:14 final size:14
Alignment explanation
Indices: 2299401--2299457 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
2299391 TTTAATTTCG
*
2299401 CGTTGCGTTTCTCT
1 CGTTGCGATTCTCT
*
2299415 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2299434 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2299448 CGTTGCGATT
1 CGTTGCGATT
2299458 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.07, C:0.25, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2299601 original size:14 final size:14
Alignment explanation
Indices: 2299582--2299618 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2299572 CATCAATTAA
2299582 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2299596 ACAAATCACCTTTT
1 ACAAATCAACTTTT
2299610 ACAAATCAA
1 ACAAATCAA
2299619 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2301386 original size:93 final size:89
Alignment explanation
Indices: 2301274--2301458 Score: 257
Period size: 89 Copynumber: 2.0 Consensus size: 89
2301264 ATATTTCAAA
* *
2301274 ACTTCAACCAAAAGACAAAA-C-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
1 ACTTAAACCAAAAGACAAAACCAAAAGAC--ATACTAACTTCACAGTGTT----AATAAACAGTT
* *
2301337 TAGCAGAATTTGCAGCAACCGAATAAATTT
60 TAGCAGAATTGGAAGCAACCGAATAAATTT
2301367 ACTTAAACCAAAAGACAAAACCAAAAGACATACTAACTTCACAGTGTTAATAAACAGTTTAGCAG
1 ACTTAAACCAAAAGACAAAACCAAAAGACATACTAACTTCACAGTGTTAATAAACAGTTTAGCAG
*
2301432 TATTGGAAGCAACCGAATAAATTT
66 AATTGGAAGCAACCGAATAAATTT
2301456 ACT
1 ACT
2301459 AAGCAATCTA
Statistics
Matches: 85, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
89 40 0.47
93 38 0.45
94 1 0.01
95 6 0.07
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (89 bp):
ACTTAAACCAAAAGACAAAACCAAAAGACATACTAACTTCACAGTGTTAATAAACAGTTTAGCAG
AATTGGAAGCAACCGAATAAATTT
Found at i:2301389 original size:13 final size:13
Alignment explanation
Indices: 2301371--2301396 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2301361 AAATTTACTT
2301371 AAACCAAAAGACA
1 AAACCAAAAGACA
2301384 AAACCAAAAGACA
1 AAACCAAAAGACA
2301397 TACTAACTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.23, G:0.08, T:0.00
Consensus pattern (13 bp):
AAACCAAAAGACA
Found at i:2301722 original size:63 final size:63
Alignment explanation
Indices: 2301620--2301750 Score: 235
Period size: 63 Copynumber: 2.1 Consensus size: 63
2301610 CCACGTAAAC
* *
2301620 ACCTCCACACGCCATGAACCATCGTTATCGTGTATAGTACCGATCTCCTCACGCAAGGCATTG
1 ACCTCCACACGCCATGAACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
*
2301683 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
1 ACCTCCACACGCCATGAACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
2301746 ACCTC
1 ACCTC
2301751 ATCACGTAAC
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
63 65 1.00
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.22
Consensus pattern (63 bp):
ACCTCCACACGCCATGAACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
Found at i:2302326 original size:21 final size:22
Alignment explanation
Indices: 2302284--2302326 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
2302274 AATAACAAAC
*
2302284 ATTAGTAATTGTTAAATAATTA
1 ATTAGTAATTGTTAAAAAATTA
2302306 ATTA-TAATT-TTAAAAACATTA
1 ATTAGTAATTGTTAAAAA-ATTA
2302327 TATAGAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 9 0.47
22 4 0.21
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (22 bp):
ATTAGTAATTGTTAAAAAATTA
Found at i:2303255 original size:52 final size:53
Alignment explanation
Indices: 2303179--2303279 Score: 132
Period size: 52 Copynumber: 1.9 Consensus size: 53
2303169 TTGAAATGAA
* * **
2303179 AATCGCAATGAGATAATGAGAATCGCAACGAGAAATGACTATCGCAACGAGAG
1 AATCGCAACGAGATAATGAAAATCGCAACGAGAAATGAAAATCGCAACGAGAG
* * *
2303232 AATCGCAACGCGA-AATGAAAATCGCAATGCGAAATGAAAATCGCAACG
1 AATCGCAACGAGATAATGAAAATCGCAACGAGAAATGAAAATCGCAACG
2303280 CGAAATGAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
52 30 0.73
53 11 0.27
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.14
Consensus pattern (53 bp):
AATCGCAACGAGATAATGAAAATCGCAACGAGAAATGAAAATCGCAACGAGAG
Found at i:2303283 original size:38 final size:38
Alignment explanation
Indices: 2303171--2303301 Score: 173
Period size: 38 Copynumber: 3.6 Consensus size: 38
2303161 TCTTTTGGTT
* *
2303171 GAAATGAAAATCGCAATGAGATAATGAGAATCGCAACGA
1 GAAATGAAAATCGCAATGCGA-AATGAGAATCGCAACGC
**
2303210 GAAATGACTATCGCAA--CG--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAATGCGAAATGAGAATCGCAACGC
*
2303243 GAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAATGCGAAATGAGAATCGCAACGC
2303281 GAAATGAAAATCGCAATGCGA
1 GAAATGAAAATCGCAATGCGA
2303302 TTTTTTGGTT
Statistics
Matches: 80, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
33 27 0.34
34 1 0.01
35 2 0.03
37 2 0.03
38 34 0.43
39 14 0.17
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.14
Consensus pattern (38 bp):
GAAATGAAAATCGCAATGCGAAATGAGAATCGCAACGC
Found at i:2303301 original size:19 final size:19
Alignment explanation
Indices: 2303171--2303301 Score: 137
Period size: 19 Copynumber: 7.1 Consensus size: 19
2303161 TCTTTTGGTT
* *
2303171 GAAATGAAAATCGCAATGA
1 GAAATGAAAATCGCAACGC
* *
2303190 GATAATGAGAATCGCAACGA
1 GA-AATGAAAATCGCAACGC
**
2303210 GAAATGACTATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
2303227 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
2303243 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
2303262 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
2303281 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
2303300 GA
1 GA
2303302 TTTTTTGGTT
Statistics
Matches: 95, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
14 9 0.09
15 1 0.01
16 2 0.02
17 1 0.01
18 1 0.01
19 64 0.67
20 17 0.18
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:2303965 original size:20 final size:20
Alignment explanation
Indices: 2303937--2303990 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
2303927 GATTTTGTAT
*
2303937 TATCACATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
2303957 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
2303977 TATCGCATTGCGAT
1 TATCGCATTGCGAT
2303991 TTTTCCAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:2304101 original size:21 final size:21
Alignment explanation
Indices: 2304061--2304101 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2304051 ACTGTAGACC
**
2304061 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
2304082 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
2304102 GCGAATTTGC
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:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:2305895 original size:196 final size:199
Alignment explanation
Indices: 2305556--2306085 Score: 689
Period size: 196 Copynumber: 2.7 Consensus size: 199
2305546 ATAGTTGTGC
* *
2305556 AGTGTCGATACATTATGAATATATATTTTCTCATAAAACCGGTATATTTCTACCGGGTACATTGT
1 AGTGTCGATACATTATGAATACATATTTTCTCATAAAACCGGTATATTTCTAACGGGTACATTGT
* *
2305621 AAATTTACCTATTACATTGTAATTATCGGTTTCGATATTTTTGGGATCGATACTTTTAATAAATG
66 AAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATG
*
2305686 TATCGACACTTTATGCGTGCACCTCGTTGGGCATTCA-T-T-GA-AAAAAATATCGACACAAACT
131 TATCGAAACTTTATGCGTGCACCTC-TTGGGCATTCATTCTGGACAAAAAATATCGACACAAA-T
2305747 T-AAAA
194 TCAAAA
* ** * * *
2305752 AGTGTCGATACATTATGAATACATATTCTCTCATAAAATTGGTGTATTTCTATCGGGTATATTGT
1 AGTGTCGATACATTATGAATACATATTTTCTCATAAAACCGGTATATTTCTAACGGGTACATTGT
* *
2305817 AAATTTACCTATTACATTATAATTATCAGTTTCGATGTTTTTGAGATCGATACTTTTAATAAATG
66 AAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATG
* * * *
2305882 TATCGAAACTTTATGTGTGCACCTCTTTGGCATTCATTCTGGACAATAAGTATCGACACAAATTC
131 TATCGAAACTTTATGCGTGCACCTCTTGGGCATTCATTCTGGACAAAAAATATCGACACAAATTC
* *
2305947 CACA
196 AAAA
* * * * * * * *
2305951 AGTGTCGATACATTATG-TTGACATGTTTTCTAAT-TAACCGATATATTTATAACAGTTACATTG
1 AGTGTCGATACATTATGAAT-ACATATTTTCTCATAAAACCGGTATATTTCTAACGGGTACATTG
* * * *
2306014 TTAATTTACCTATTACATTATAATTATTGGTTTCGATGTTTTTGGGGTCAATACTTTT-ATAAAA
65 TAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAAT-AAA
2306078 TGTATCGA
129 TGTATCGA
2306086 CACATATGTT
Statistics
Matches: 289, Mismatches: 38, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
195 10 0.03
196 143 0.49
197 3 0.01
198 87 0.30
199 46 0.16
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.40
Consensus pattern (199 bp):
AGTGTCGATACATTATGAATACATATTTTCTCATAAAACCGGTATATTTCTAACGGGTACATTGT
AAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATG
TATCGAAACTTTATGCGTGCACCTCTTGGGCATTCATTCTGGACAAAAAATATCGACACAAATTC
AAAA
Found at i:2309968 original size:15 final size:15
Alignment explanation
Indices: 2309950--2309978 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2309940 GGAGGTTATC
2309950 GTTGAGAAGAGCTTG
1 GTTGAGAAGAGCTTG
2309965 GTTGAGAAGAGCTT
1 GTTGAGAAGAGCTT
2309979 TGAGAAAGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.07, G:0.38, T:0.28
Consensus pattern (15 bp):
GTTGAGAAGAGCTTG
Found at i:2310725 original size:201 final size:201
Alignment explanation
Indices: 2310281--2311448 Score: 1662
Period size: 201 Copynumber: 5.8 Consensus size: 201
2310271 ACAAAAATTT
* * *
2310281 AAAAACGTATCGACACAAATTTAAAAAGTGTTGATACATTATGTTAACCGCTTTTCTCATTAAAC
1 AAAAA-GTATCGACACAAATTTAAAAAGTGTCGATACATTATGTTGACCGCTTTTCTAATTAAAC
* * * *
2310346 CGATATATTTATACCGGTTACATTGTAAATTTTCCTATTACATTATAAATATCGGTTTCGATGTT
65 CGGTATATTTATACCGGTTATATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTT
* ** * * *
2310411 TTTGGGATCCATACAATTT-TAAATGTATCGACATTTTATGCGTACACCTCATTTGGGCATTGAT
130 TTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTGAT
2310475 TCTGGAC
195 TCTGGAC
* **
2310482 AACAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTTGACTTCTTTTCTAATTAAACC
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTTGACCGCTTTTCTAATTAAACC
* * * *
2310547 GGTATATTTATACCGGTTAAATTATAAATTTACCAATTACATTATAATTAT-GAGTTTCGATATT
66 GGTATATTTATACCGGTTATATTGTAAATTTACCTATTACATTATAATTATCG-GTTTCGATGTT
* * *
2310611 TTTGGGATTGATATTTTTTATAAATGTATCGACACTTTATGCATGCACCTCGTTTGGGCATTGAT
130 TTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTGAT
2310676 TCTGGAC
195 TCTGGAC
*
2310683 AAAAAGTATCGACACAAATTTAAAAAGTGTCAATACATTATGTTGACCGCTTTTCTAATTAAACC
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTTGACCGCTTTTCTAATTAAACC
*
2310748 AGTATATTTATACCGGTTATATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
66 GGTATATTTATACCGGTTATATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
* *
2310813 TTGGGATCGATACTTTTTATAAATGTATCGACATTTTATGCGTGCAACTCGTTTGGGCATTGATT
131 TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTGATT
2310878 CTGGAC
196 CTGGAC
* *
2310884 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTTGACCGCTTTTATAATTAAACA
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTTGACCGCTTTTCTAATTAAACC
* * * *
2310949 GATATATTTATACCGATTATATTGTAAATTTACCTATAACATTATAATTATTGGTTTCGATGTTT
66 GGTATATTTATACCGGTTATATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
* * * * *
2311014 TTAGGATTGGTACTTTTTATAAATGTATCGACATTTTATGCGTGCACCTCGTTTGGGCATTCATT
131 TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTGATT
2311079 CTGGAC
196 CTGGAC
* ** * * *
2311085 AAAAAGTATTGACACAAATTCCATATGTGTCGATACATTATGTTGACCGCTTTTCTAATTAAACT
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTTGACCGCTTTTCTAATTAAACC
* * * *
2311150 GGTATATTTATACTGGTTATATTGTAAATGTATCTATTACATTATAATTATCGATTTCGATGTTT
66 GGTATATTTATACCGGTTATATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
* ** * *
2311215 TTGGGATCAATAAGTTTTATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGTATTCATT
131 TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTGATT
2311280 CTGGAC
196 CTGGAC
** * * *
2311286 AAAAAGTATCGACACAAATTCCACAAGTGTCGAAACATTATGTTGACTTG-TTTTCTAATT-AAC
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTTGAC-CGCTTTTCTAATTAAAC
* * * * *
2311349 CGGTATATTTATACTGGTTACATTGTTAATTTACCTATTACATTATAATTATTGGTTTTGATGTT
65 CGGTATATTTATACCGGTTATATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTT
* * * *
2311414 TTAGGGTTTGATAC-TTTTAGAAAATGTATCGACAC
130 TTTGGGATCGATACTTTTTA-TAAATGTATCGACAC
2311449 ATCTGTTTAC
Statistics
Matches: 871, Mismatches: 91, Indels: 11
0.90 0.09 0.01
Matches are distributed among these distances:
199 6 0.01
200 207 0.24
201 656 0.75
202 2 0.00
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.40
Consensus pattern (201 bp):
AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTTGACCGCTTTTCTAATTAAACC
GGTATATTTATACCGGTTATATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTGATT
CTGGAC
Found at i:2316420 original size:182 final size:182
Alignment explanation
Indices: 2316110--2316711 Score: 859
Period size: 182 Copynumber: 3.3 Consensus size: 182
2316100 TACGCGTACT
* * * *
2316110 TATTAAAGTATCGACACTTTCAATATATTCGGTAGCGCTTTACCAGTTTTGTCATTTTGAGACCG
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTCGAGACCG
*
2316175 GTTTTGTCATATTTTTACCTGTTATATTATTATGGATCAATACATTTTTATAAAGTATCGACACT
66 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCAATACATTTTTATAAAGTATCGACACT
* * *
2316240 TTATAGGCGTTATTATTGCTTCTCTTTTAAATTCTAAAAGTATCGATATTTA
131 TTATAGGCGTTATTATTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* * **
2316292 TACTAAAGTATCGACACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCATTTCGAGACTA
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTCGAGACCG
* **
2316357 GTTTTGTCATATTTTTGCCTGTTATATTGTTATAAATCAATACATTTTTATAAAGTATCGACACT
66 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCAATACATTTTTATAAAGTATCGACACT
* * *
2316422 TTATAAGC-TCTACTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
131 TTATAGGCGT-TATTATTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* **
2316474 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACTGACTTTGTCATTTCGAGACCG
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTCGAGACCG
* * * * *
2316539 GTTTTGTCATATTTTTACATATTATATTGTTATGGATCGATACATTTCTATAAATTATCGACACT
66 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCAATACATTTTTATAAAGTATCGACACT
*
2316604 TTATAGGCGCTATTACTT-CTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
131 TTATAGGCGTTATTA-TTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
** * * *
2316656 T-TTCAATCTAATCGATATTTTCAACATATCTGGTAGCGCTTTACCGGTTTTGTCAT
1 TATT-AAAGT-ATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCAT
2316712 ATTTTTACTT
Statistics
Matches: 370, Mismatches: 45, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
181 3 0.01
182 326 0.88
183 41 0.11
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.42
Consensus pattern (182 bp):
TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTCGAGACCG
GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCAATACATTTTTATAAAGTATCGACACT
TTATAGGCGTTATTATTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
Found at i:2320400 original size:23 final size:23
Alignment explanation
Indices: 2320374--2320428 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
2320364 CAGGGACGGA
2320374 GTCAAATCTAGATCTCAACAGAG
1 GTCAAATCTAGATCTCAACAGAG
2320397 GTCAAATCTAGATCTCAACAGAG
1 GTCAAATCTAGATCTCAACAGAG
2320420 GTCAAATCT
1 GTCAAATCT
2320429 TTTTTACAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (23 bp):
GTCAAATCTAGATCTCAACAGAG
Found at i:2322871 original size:23 final size:23
Alignment explanation
Indices: 2322824--2322947 Score: 185
Period size: 23 Copynumber: 5.3 Consensus size: 23
2322814 ACCGAAGTGT
* *
2322824 CACATAGAATTTTTCCTGAAGGAC
1 CACATAG-ATTTGTCCCGAAGGAC
* *
2322848 CACATAGATTTGTTCCGAACGAC
1 CACATAGATTTGTCCCGAAGGAC
*
2322871 CACATAGATTTGTCCCGAATGAC
1 CACATAGATTTGTCCCGAAGGAC
*
2322894 CACATAGATTTGTCCCGAAGAAC
1 CACATAGATTTGTCCCGAAGGAC
2322917 CACATAGATTTGTCCCGAAGGAC
1 CACATAGATTTGTCCCGAAGGAC
2322940 CACATAGA
1 CACATAGA
2322948 ACCCTCGACT
Statistics
Matches: 91, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
23 84 0.92
24 7 0.08
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (23 bp):
CACATAGATTTGTCCCGAAGGAC
Found at i:2326031 original size:3 final size:3
Alignment explanation
Indices: 2326025--2326081 Score: 91
Period size: 3 Copynumber: 19.7 Consensus size: 3
2326015 TATTTGCTTA
*
2326025 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TGT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2326071 TAT TAT TAT TA
1 TAT TAT TAT TA
2326082 AATAATTAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
2 3 0.06
3 47 0.94
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:2327720 original size:20 final size:19
Alignment explanation
Indices: 2327695--2327736 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
2327685 TTATTTTATA
2327695 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
2327715 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
2327734 AAT
1 AAT
2327737 ATCGAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:2327727 original size:119 final size:117
Alignment explanation
Indices: 2327591--2327827 Score: 325
Period size: 120 Copynumber: 2.0 Consensus size: 117
2327581 ATTTTAATCC
* * * *
2327591 TGTTTTAATATTTATTTATTTTTTAATAT-TAAG-AAAGGGCAGTCTTAAAACAACTGGATGTCT
1 TGTTTTAATATTTATTTATTTTTTAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTC-
* *
2327654 ATTTTCTGATATTTTTAAATAAATAAATATCTTATTTTATAAATTATATATTAAT
65 ATTTTCTGATATTTCTAAATAAATAAATATCTTA-TTTATAAA-TATATATAAAT
* ** *
2327709 TGTTTTAATTATTTATTTATTTTTTAATATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTC
1 TGTTTTAA-TATTTATTTATTTTTTAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTC
*
2327774 ATTTTCTGATATTTCTAAATAAATAAATATTTTATTTATAAATATATATAAAT
65 ATTTTCTGATATTTCTAAATAAATAAATATCTTATTTATAAATATATATAAAT
2327827 T
1 T
2327828 AATATATTTT
Statistics
Matches: 105, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
118 19 0.18
119 29 0.28
120 35 0.33
121 22 0.21
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.47
Consensus pattern (117 bp):
TGTTTTAATATTTATTTATTTTTTAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCA
TTTTCTGATATTTCTAAATAAATAAATATCTTATTTATAAATATATATAAAT
Found at i:2327825 original size:29 final size:31
Alignment explanation
Indices: 2327792--2327850 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
2327782 ATATTTCTAA
2327792 ATAAA-TAA-ATATTTTATTT-ATAAATATAT
1 ATAAATTAATATATTTT-TTTCATAAATATAT
*
2327821 ATAAATTAATATATTTTTTTCATAATTATA
1 ATAAATTAATATATTTTTTTCATAAATATA
2327851 ATTTTGAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 5 0.19
30 6 0.23
31 15 0.58
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (31 bp):
ATAAATTAATATATTTTTTTCATAAATATAT
Found at i:2332889 original size:7 final size:7
Alignment explanation
Indices: 2332877--2333005 Score: 73
Period size: 8 Copynumber: 16.4 Consensus size: 7
2332867 TCCAGCAAAG
2332877 AAAGAAA
1 AAAGAAA
2332884 AAAGAAA
1 AAAGAAA
2332891 AATCCAGCAAA
1 AA---AG-AAA
2332902 GAAAGAAA
1 -AAAGAAA
2332910 AAAGAAAA
1 AAAG-AAA
2332918 AAGATGAAA
1 AA-A-GAAA
2332927 AAAGAAA
1 AAAGAAA
2332934 AATGAGAAA
1 AA--AGAAA
2332943 AAAGAAAA
1 AAAG-AAA
2332951 AAAGAAAA
1 AAAG-AAA
2332959 AAAGATGAA
1 AAAGA--AA
2332968 AAAGGAAA
1 AAA-GAAA
* *
2332976 AATG-AG
1 AAAGAAA
2332982 AAA-AAA
1 AAAGAAA
*
2332988 AGAGAAA
1 AAAGAAA
2332995 AAAGGAAA
1 AAA-GAAA
2333003 AAA
1 AAA
2333006 ATTGAACCAA
Statistics
Matches: 99, Mismatches: 6, Indels: 33
0.72 0.04 0.24
Matches are distributed among these distances:
6 6 0.06
7 28 0.28
8 35 0.35
9 20 0.20
10 5 0.05
11 3 0.03
12 2 0.02
ACGTcount: A:0.76, C:0.02, G:0.18, T:0.04
Consensus pattern (7 bp):
AAAGAAA
Found at i:2332896 original size:26 final size:26
Alignment explanation
Indices: 2332866--2332918 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
2332856 TCTTATACTC
2332866 ATCCAGCAAAGAAAGAAAAAAGAAAA
1 ATCCAGCAAAGAAAGAAAAAAGAAAA
2332892 ATCCAGCAAAGAAAGAAAAAAGAAAA
1 ATCCAGCAAAGAAAGAAAAAAGAAAA
2332918 A
1 A
2332919 AGATGAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.70, C:0.11, G:0.15, T:0.04
Consensus pattern (26 bp):
ATCCAGCAAAGAAAGAAAAAAGAAAA
Found at i:2332927 original size:9 final size:8
Alignment explanation
Indices: 2332903--2332996 Score: 79
Period size: 7 Copynumber: 11.4 Consensus size: 8
2332893 TCCAGCAAAG
2332903 AAAGA-AA
1 AAAGAGAA
2332910 AAAGA-AA
1 AAAGAGAA
2332917 AAAGATGAA
1 AAAGA-GAA
2332926 AAA-AGAA
1 AAAGAGAA
2332933 AAATGAGAAA
1 AAA-GAG-AA
*
2332943 AAAGAAAA
1 AAAGAGAA
*
2332951 AAAGAAAA
1 AAAGAGAA
2332959 AAAGATGAA
1 AAAGA-GAA
2332968 AAAG-GAA
1 AAAGAGAA
2332975 AAATGAGAAAA
1 AAA-GAG--AA
2332986 AAAGAGAA
1 AAAGAGAA
2332994 AAA
1 AAA
2332997 AGGAAAAAAA
Statistics
Matches: 75, Mismatches: 2, Indels: 19
0.78 0.02 0.20
Matches are distributed among these distances:
7 24 0.32
8 22 0.29
9 16 0.21
10 8 0.11
11 5 0.07
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (8 bp):
AAAGAGAA
Found at i:2332928 original size:17 final size:16
Alignment explanation
Indices: 2332905--2333005 Score: 107
Period size: 17 Copynumber: 5.9 Consensus size: 16
2332895 CAGCAAAGAA
2332905 AGAAAAAAGAAAAAAG
1 AGAAAAAAGAAAAAAG
*
2332921 ATGAAAAAAGAAAAATG
1 A-GAAAAAAGAAAAAAG
2332938 AGAAAAAAGAAAAAA-
1 AGAAAAAAGAAAAAAG
2332953 AGAAAAAAAGATGAAAAAG
1 AG-AAAAAAGA--AAAAAG
2332972 -GAAAAATGAGAAAAAAAG
1 AGAAAAA--AG-AAAAAAG
2332990 AGAAAAAAGGAAAAAA
1 AGAAAAAA-GAAAAAA
2333006 ATTGAACCAA
Statistics
Matches: 73, Mismatches: 2, Indels: 19
0.78 0.02 0.20
Matches are distributed among these distances:
15 2 0.03
16 22 0.30
17 27 0.37
18 13 0.18
19 8 0.11
20 1 0.01
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (16 bp):
AGAAAAAAGAAAAAAG
Found at i:2332944 original size:27 final size:25
Alignment explanation
Indices: 2332899--2333006 Score: 110
Period size: 26 Copynumber: 4.1 Consensus size: 25
2332889 AAAATCCAGC
* *
2332899 AAAGAAAGAAAAAAGAAAAAAGATGAA
1 AAAGAAA-AAAAGAGAAAAAAGA-AAA
*
2332926 AAA-AGAAAAATGAGAAAAAAGAAAA
1 AAAGA-AAAAAAGAGAAAAAAGAAAA
*
2332951 AAAGAAAAAAAGATGAAAAAGGAAAA
1 AAAGAAAAAAAGA-GAAAAAAGAAAA
*
2332977 ATGAGAAAAAAAGAGAAAAAAGGAAAA
1 A-AAGAAAAAAAGAGAAAAAA-GAAAA
2333004 AAA
1 AAA
2333007 TTGAACCAAG
Statistics
Matches: 68, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
25 12 0.18
26 34 0.50
27 22 0.32
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.04
Consensus pattern (25 bp):
AAAGAAAAAAAGAGAAAAAAGAAAA
Found at i:2332960 original size:42 final size:43
Alignment explanation
Indices: 2332880--2333006 Score: 170
Period size: 42 Copynumber: 2.9 Consensus size: 43
2332870 AGCAAAGAAA
* *
2332880 GAAAAAAGAAAAATCCAGCAAAGAAAG-AAAAAAG-AAAAAAGAT
1 GAAAAAAGAAAAAT-GAG-AAAAAAAGAAAAAAAGAAAAAAAGAT
2332923 GAAAAAAGAAAAATGAG-AAAAAAGAAAAAAAGAAAAAAAGAT
1 GAAAAAAGAAAAATGAGAAAAAAAGAAAAAAAGAAAAAAAGAT
*
2332965 GAAAAAGGAAAAATGAGAAAAAAAGAGAAAAAAGGAAAAAAA
1 GAAAAAAGAAAAATGAGAAAAAAAGA-AAAAAA-GAAAAAAA
2333007 TTGAACCAAG
Statistics
Matches: 76, Mismatches: 3, Indels: 8
0.87 0.03 0.09
Matches are distributed among these distances:
40 6 0.08
41 7 0.09
42 27 0.36
43 22 0.29
44 6 0.08
45 8 0.11
ACGTcount: A:0.76, C:0.02, G:0.18, T:0.04
Consensus pattern (43 bp):
GAAAAAAGAAAAATGAGAAAAAAAGAAAAAAAGAAAAAAAGAT
Found at i:2333005 original size:10 final size:9
Alignment explanation
Indices: 2332899--2333006 Score: 57
Period size: 10 Copynumber: 12.2 Consensus size: 9
2332889 AAAATCCAGC
2332899 AAAGAAAGAA
1 AAAGAAA-AA
*
2332909 AAA-AGAAA
1 AAAGAAAAA
*
2332917 AAAGATGAAA
1 AAAGA-AAAA
2332927 AAAG--AAA
1 AAAGAAAAA
* *
2332934 AATGAGAAA
1 AAAGAAAAA
2332943 AAAG-AAAA
1 AAAGAAAAA
2332951 AAAG-AAAA
1 AAAGAAAAA
**
2332959 AAAGATGAA
1 AAAGAAAAA
*
2332968 AAAG-GAAA
1 AAAGAAAAA
*
2332976 AATGAGAAAA
1 AAAGA-AAAA
2332986 AAAGAGAAAA
1 AAAGA-AAAA
*
2332996 AAGGAAAAA
1 AAAGAAAAA
2333005 AA
1 AA
2333007 TTGAACCAAG
Statistics
Matches: 79, Mismatches: 12, Indels: 15
0.75 0.11 0.14
Matches are distributed among these distances:
7 6 0.08
8 25 0.32
9 21 0.27
10 27 0.34
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.04
Consensus pattern (9 bp):
AAAGAAAAA
Found at i:2333006 original size:9 final size:8
Alignment explanation
Indices: 2332903--2333006 Score: 88
Period size: 9 Copynumber: 12.4 Consensus size: 8
2332893 TCCAGCAAAG
2332903 AAAG-AAA
1 AAAGAAAA
2332910 AAAG-AAA
1 AAAGAAAA
2332917 AAAGATGAAA
1 AAAGA--AAA
2332927 AAAG-AAA
1 AAAGAAAA
*
2332934 AATGAGAAA
1 AAAGA-AAA
2332943 AAAGAAAA
1 AAAGAAAA
2332951 AAAGAAAA
1 AAAGAAAA
2332959 AAAGATGAAA
1 AAAGA--AAA
*
2332969 AAGGAAAA
1 AAAGAAAA
*
2332977 ATGAGAAAA
1 A-AAGAAAA
2332986 AAAGAGAAA
1 AAAGA-AAA
2332995 AAAGGAAAA
1 AAA-GAAAA
2333004 AAA
1 AAA
2333007 TTGAACCAAG
Statistics
Matches: 81, Mismatches: 6, Indels: 18
0.77 0.06 0.17
Matches are distributed among these distances:
7 17 0.21
8 23 0.28
9 25 0.31
10 16 0.20
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (8 bp):
AAAGAAAA
Found at i:2337697 original size:22 final size:22
Alignment explanation
Indices: 2337671--2337769 Score: 162
Period size: 22 Copynumber: 4.5 Consensus size: 22
2337661 ATCTACACTC
2337671 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
2337693 TTCAAAGATAATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
2337715 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
* *
2337737 TTTAAAGATGATATATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
2337759 TTCAAAAATGA
1 TTCAAAGATGA
2337770 AAGCTTTATT
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 71 1.00
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.41
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:2338713 original size:76 final size:76
Alignment explanation
Indices: 2338614--2338912 Score: 562
Period size: 76 Copynumber: 3.9 Consensus size: 76
2338604 CTATTTCCTA
*
2338614 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2338679 AGCCTTAGGGT
66 AGCCTTAGGGT
2338690 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
2338755 AGCCTTAGGGC
66 AGCCTTAGGGT
2338766 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2338831 AGCCTTAGGGT
66 AGCCTTAGGGT
*
2338842 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
2338907 AACCTT
66 AGCCTT
2338913 CGATGGATCA
Statistics
Matches: 218, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
76 218 1.00
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.34
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:2339059 original size:113 final size:113
Alignment explanation
Indices: 2338912--2339349 Score: 603
Period size: 113 Copynumber: 3.9 Consensus size: 113
2338902 TTCAAAACCT
* * * *
2338912 TCGATGGATCAGCATTACCAGGTAGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TCGATGGATCAACATTTCCAGGTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* * *
2338977 AGTTCATAATGATAAGAGCTTGTTCAACCTTTTGCTCAAATTCATCAC
66 AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCAC
* *
2339025 TCGATGGATCAGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1 TCGATGGATCAACATTTCCAG-GTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
* * *
2339089 AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCAT
65 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCAC
* * * * *
2339138 TTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCCGAAGAAGGAAGAAGA
1 TCGATGGATCAACATTTCCAGGTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* * * * *
2339203 AATTCATAATGAGAAGAATTTGTTCAACTTTTTGTTTGAATTCATCAC
66 AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCAC
* * *
2339251 TCGATAGATCAACTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTTATCTGAAGAA-GAAGAAG
1 TCGATGGATCAACATTTCCAG-GTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
*
2339314 AAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
65 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
2339350 ATAACTCTAT
Statistics
Matches: 288, Mismatches: 34, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
112 39 0.14
113 247 0.86
114 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.28
Consensus pattern (113 bp):
TCGATGGATCAACATTTCCAGGTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCAC
Found at i:2339672 original size:3 final size:3
Alignment explanation
Indices: 2339664--2339702 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
2339654 TATTTGCTTA
*
2339664 TAT TAT TAT TAT TAT TAT TAT TA- TGT TA- TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2339703 AATAATTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 3 0.09
3 29 0.91
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:2339714 original size:28 final size:28
Alignment explanation
Indices: 2339653--2339710 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
2339643 GTATTTTTTC
* *
2339653 TTATT-TGCTTATATTATTATTATTATTA
1 TTATTATG-TTATATTATTATTATAATAA
2339681 TTATTATGTTATATTATTATTA-AATAA
1 TTATTATGTTATATTATTATTATAATAA
2339708 TTA
1 TTA
2339711 ATTAATACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 6 0.22
28 19 0.70
29 2 0.07
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.60
Consensus pattern (28 bp):
TTATTATGTTATATTATTATTATAATAA
Found at i:2341334 original size:119 final size:116
Alignment explanation
Indices: 2341199--2341434 Score: 298
Period size: 119 Copynumber: 2.0 Consensus size: 116
2341189 ATTTTAATCA
* * * *
2341199 TGTTTTAATATTTATTTATTTTTCAATAT-TAAGAAAGGA-CAGTCTTAAAACAACTGGATGTCC
1 TGTTTTAATATTTATTTATTTTT-AATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGT-C
*
2341262 ATTTTCTGATA-TTCTTAAATAAATAAATATCCTATTTTATAAATTATATATTAAT
64 ATTTTCTGATATTTC-TAAATAAATAAATATCCTA-TTTATAAA-TATATATAAAT
* ** *
2341317 TGTTTTAATTATTTATTTATTTTTAATATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCA
1 TGTTTTAA-TATTTATTTATTTTTAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCA
**
2341382 TTTTCTGATATTTCTAAATAAATAAATATTTTATTTATAAATATATATAAAT
65 TTTTCTGATATTTCTAAATAAATAAATATCCTATTTATAAATATATATAAAT
2341434 T
1 T
2341435 AATATATTTT
Statistics
Matches: 103, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
117 11 0.11
118 21 0.20
119 52 0.50
120 19 0.18
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.45
Consensus pattern (116 bp):
TGTTTTAATATTTATTTATTTTTAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCAT
TTTCTGATATTTCTAAATAAATAAATATCCTATTTATAAATATATATAAAT
Found at i:2341450 original size:29 final size:29
Alignment explanation
Indices: 2341399--2341455 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
2341389 ATATTTCTAA
*
2341399 ATAAATAAATATTTTATTTATAAATATAT
1 ATAAATAAATATTTTATTCATAAATATAT
* *
2341428 ATAAATTAATATATTT-TTCATAATTATA
1 ATAAATAAATAT-TTTATTCATAAATATA
2341456 ATTTTGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 21 0.88
30 3 0.12
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (29 bp):
ATAAATAAATATTTTATTCATAAATATAT
Found at i:2346551 original size:21 final size:21
Alignment explanation
Indices: 2346527--2346627 Score: 89
Period size: 21 Copynumber: 4.7 Consensus size: 21
2346517 GGTTCTACGA
2346527 GGTCCTTCGAGACATATATGT
1 GGTCCTTCGAGACATATATGT
* *
2346548 GGTCCTTCGGGATATATATGT
1 GGTCCTTCGAGACATATATGT
* *
2346569 GGTCCTTC-AGGACAATTCTATGA
1 GGTCCTTCGA-GAC-A-TATATGT
*
2346592 GGTCCTT-TACGACATATATGT
1 GGTCCTTCGA-GACATATATGT
* *
2346613 GGTCTTTCGGGACAT
1 GGTCCTTCGAGACAT
2346628 TCTATATGGC
Statistics
Matches: 63, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
21 45 0.71
22 2 0.03
23 16 0.25
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.35
Consensus pattern (21 bp):
GGTCCTTCGAGACATATATGT
Found at i:2348093 original size:3 final size:3
Alignment explanation
Indices: 2348087--2348117 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2348077 TTGGTTTGTA
2348087 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2348118 TAGGGGTAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2351523 original size:15 final size:15
Alignment explanation
Indices: 2351484--2351525 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
2351474 AATACTAAAC
2351484 AAATTA-AATAAATA
1 AAATTACAATAAATA
*
2351498 AATATTAACAATAATTA
1 AA-ATT-ACAATAAATA
2351515 AAATTACAATA
1 AAATTACAATA
2351526 TAATTTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 2 0.08
15 9 0.38
16 4 0.17
17 9 0.38
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (15 bp):
AAATTACAATAAATA
Found at i:2352154 original size:3 final size:3
Alignment explanation
Indices: 2352146--2352174 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2352136 AAGGAGAATA
2352146 TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
2352175 TTGTTCTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.34, T:0.34
Consensus pattern (3 bp):
TGC
Found at i:2356589 original size:2 final size:2
Alignment explanation
Indices: 2356575--2356628 Score: 60
Period size: 2 Copynumber: 28.5 Consensus size: 2
2356565 AATATGTGAT
* * *
2356575 TA TA TA -A TG TA TA TA TA T- TA TA -A TG TG 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
2356614 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
2356629 GTTATTTACA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
1 3 0.07
2 42 0.93
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2356598 original size:16 final size:17
Alignment explanation
Indices: 2356575--2356628 Score: 76
Period size: 16 Copynumber: 3.3 Consensus size: 17
2356565 AATATGTGAT
2356575 TATATAATGTATATATA
1 TATATAATGTATATATA
*
2356592 T-TATAATGTGTATATA
1 TATATAATGTATATATA
*
2356608 TATAT-ATATATATATA
1 TATATAATGTATATATA
2356624 TATAT
1 TATAT
2356629 GTTATTTACA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
16 29 0.88
17 4 0.12
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (17 bp):
TATATAATGTATATATA
Found at i:2362977 original size:106 final size:106
Alignment explanation
Indices: 2361339--2362967 Score: 2825
Period size: 106 Copynumber: 15.4 Consensus size: 106
2361329 TACAGCCTTT
2361339 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
2361404 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
*
2361445 AGAGCCAATTTTAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
2361510 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
*
2361551 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
2361616 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
*
2361657 AGAGCCAATTTCAACTTCACAACGAAGGATATTAGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
2361722 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
*
2361763 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCATACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
2361828 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
*
2361869 AGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
2361934 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
* *
2361975 AGAGCCAATTTCAACTTCACAACGATGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAAGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
2362040 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
*
2362081 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCTCGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
2362146 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
* *
2362187 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCATACAACGCAAGTTCAACTTTACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
2362252 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
2362293 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
2362358 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
*
2362399 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
2362464 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
* * *
2362505 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCATGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * *
2362570 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTT
66 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
*
2362611 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
2362676 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
* * *
2362717 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGAGAACGCATGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
2362782 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
* * * * *
2362823 AGAGCCAATTTCAACTTCACAGCGAAGGATATGGGACTCCAGACAATGCATGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * * ** *
2362888 CGAAGGGA-CGACTGATTGTCAACAAACAA-TT-TACGGGTTCC
66 CGAAGGGACCG-CTGGTTGTCAATAACCAACTTCT-C-AATTTC
* *
2362929 AGAGCTAATTTCAACTTCACGAC-AGAGGATATTGGACTC
1 AGAGCCAATTTCAACTTCACAACGA-AGGATATTGGACTC
2362968 GGAACAATGC
Statistics
Matches: 1462, Mismatches: 57, Indels: 8
0.96 0.04 0.01
Matches are distributed among these distances:
104 1 0.00
105 6 0.00
106 1455 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
Done.