Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008826.1 Hibiscus syriacus cultivar Beakdansim tig00112000_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: 3884024
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 18
Found at i:1771097 original size:24 final size:24
Alignment explanation
Indices: 1771049--1771097 Score: 57
Period size: 24 Copynumber: 2.0 Consensus size: 24
1771039 TCTCCCTTGC
*
1771049 TTTTTTTATTTATTTTTTTTATAT
1 TTTTTTTATTTATTTATTTTATAT
1771073 TTTTTTTACTTT-TGTTATTTT-TAT
1 TTTTTTTA-TTTAT-TTATTTTATAT
1771097 T
1 T
1771098 GTTATGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.14, C:0.02, G:0.02, T:0.82
Consensus pattern (24 bp):
TTTTTTTATTTATTTATTTTATAT
Found at i:1771148 original size:57 final size:57
Alignment explanation
Indices: 1771060--1771167 Score: 132
Period size: 57 Copynumber: 1.9 Consensus size: 57
1771050 TTTTTTATTT
* * *
1771060 ATTTTTTTTATATTTTTTTTACTTTTGTTA-TTTTTATTGTTATGT-TTTTTTCTCTTA
1 ATTTATTTAATATTTTTATTACTTTTGTTATTTTTTATT-TTAT-TCTTTTTTCTCTTA
*
1771117 ATTTATTTAATATTTTTATTA-TTTTATTTATTTTTTATTTTATTCTTTTTT
1 ATTTATTTAATATTTTTATTACTTTT-GTTATTTTTTATTTTATTCTTTTTT
1771168 GATTTACTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
56 5 0.11
57 31 0.70
58 8 0.18
ACGTcount: A:0.18, C:0.04, G:0.03, T:0.76
Consensus pattern (57 bp):
ATTTATTTAATATTTTTATTACTTTTGTTATTTTTTATTTTATTCTTTTTTCTCTTA
Found at i:1771154 original size:32 final size:31
Alignment explanation
Indices: 1771050--1771166 Score: 87
Period size: 33 Copynumber: 3.6 Consensus size: 31
1771040 CTCCCTTGCT
*
1771050 TTTTTTATTTATTTTTTTTA-TATTTTTTTTA
1 TTTTTTATTTATTATTTTTATTA-TTTTTTTA
* *
1771081 CTTTTGTTATTT-TTATTGTTATGT-TTTTTTCTC
1 -TTTT-TTATTTATTATTTTTAT-TATTTTTT-TA
* *
1771114 TTAATTTATTTAATATTTTTATTATTTTATTTA
1 TT-TTTTATTTATTATTTTTATTATTTT-TTTA
*
1771147 TTTTTTATTTTATTCTTTTT
1 TTTTTTA-TTTATTATTTTT
1771167 TGATTTACTT
Statistics
Matches: 66, Mismatches: 10, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
32 30 0.45
33 33 0.50
34 3 0.05
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.77
Consensus pattern (31 bp):
TTTTTTATTTATTATTTTTATTATTTTTTTA
Found at i:1771155 original size:25 final size:24
Alignment explanation
Indices: 1771117--1771173 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
1771107 TTTTCTCTTA
1771117 ATTTATTTAATATTTTTATTATTTT
1 ATTTATTTAATA-TTTTATTATTTT
** *
1771142 ATTTATTTTTTATTTTATTCTTTT
1 ATTTATTTAATATTTTATTATTTT
*
1771166 -TTGATTTA
1 ATTTATTTA
1771174 CTTTTTTTGT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 6 0.22
24 11 0.41
25 10 0.37
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.74
Consensus pattern (24 bp):
ATTTATTTAATATTTTATTATTTT
Found at i:1771216 original size:4 final size:4
Alignment explanation
Indices: 1771207--1771231 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1771197 TTTTATTTGA
1771207 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
1771232 TTCCAATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:1775268 original size:95 final size:94
Alignment explanation
Indices: 1775096--1775353 Score: 329
Period size: 95 Copynumber: 2.7 Consensus size: 94
1775086 TATATATATA
* * * * *
1775096 TATATATAT-AATAAAGCTTGAGTTGTCCCTCTAAAGTAATTGGTTAAACGCCCCTACTTTATGG
1 TATA-ATATCAATAAAGATTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGAATTTATGG
1775160 ATAAGATTCAGCTAGCCTGATAAAGGTGAT
65 ATAAGATTCAGCTAGCCTGATAAAGGTGAT
* * * *
1775190 TATAATGTACAATAAAGATTGAGTTTTCCATCTAGAGCAATTGGTTAAATGCCCCGAATTTATGG
1 TATAATAT-CAATAAAGATTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGAATTTATGG
*
1775255 ATAATATTCAGCTAGCCTGATAAAGGTGAT
65 ATAAGATTCAGCTAGCCTGATAAAGGTGAT
* * * *
1775285 TATAATATCTATACAATGATATTAGGTTGTCCCTCTAGAGCAATTGGTTAAACGCTCCGATTTTA
1 TATAATATCAATA-AA-GAT-TGA-GTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGAATTTA
1775350 TGGA
62 TGGA
1775354 ATCAGCTAGC
Statistics
Matches: 140, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
93 3 0.02
94 8 0.06
95 85 0.61
96 3 0.02
97 2 0.01
98 39 0.28
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (94 bp):
TATAATATCAATAAAGATTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGAATTTATGGA
TAAGATTCAGCTAGCCTGATAAAGGTGAT
Found at i:1776796 original size:15 final size:15
Alignment explanation
Indices: 1776772--1776810 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
1776762 ATTTGTCTCT
*
1776772 CTTGAGACAGTTCCC
1 CTTGAAACAGTTCCC
1776787 CTTGAAACAGTTCCC
1 CTTGAAACAGTTCCC
1776802 CTTGAAACA
1 CTTGAAACA
1776811 AAGTTTTGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.26
Consensus pattern (15 bp):
CTTGAAACAGTTCCC
Found at i:1776947 original size:33 final size:33
Alignment explanation
Indices: 1776900--1776984 Score: 127
Period size: 33 Copynumber: 2.6 Consensus size: 33
1776890 CCTGGAGACA
* *
1776900 GTTTATCTTGAAACACAAAAAACCTTTG-AAAT
1 GTTTCTCTTGAAACACAAAAAAACTTTGAAAAT
*
1776932 CGTTTCTCTTGAAACAAAAAAAAACTTTGAAAAT
1 -GTTTCTCTTGAAACACAAAAAAACTTTGAAAAT
1776966 GTTTCTCTTGAAACACAAA
1 GTTTCTCTTGAAACACAAA
1776985 GACCTTCGAG
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
33 43 0.91
34 4 0.09
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (33 bp):
GTTTCTCTTGAAACACAAAAAAACTTTGAAAAT
Found at i:1779186 original size:18 final size:19
Alignment explanation
Indices: 1779163--1779198 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1779153 TTTTACTCCT
1779163 TTTATTTG-ATATTTTTTA
1 TTTATTTGTATATTTTTTA
*
1779181 TTTATTTGTTTATTTTTT
1 TTTATTTGTATATTTTTT
1779199 CAATTTAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.78
Consensus pattern (19 bp):
TTTATTTGTATATTTTTTA
Found at i:1784904 original size:72 final size:70
Alignment explanation
Indices: 1784632--1785159 Score: 380
Period size: 75 Copynumber: 7.4 Consensus size: 70
1784622 AGTCATTTCA
* * * * * * * *
1784632 AGAAAATGTCTCGAGTGTGACGGAATTTTTCAAGAGAAAATATATCAAGTGAGATAAAATTTTGG
1 AGAAACTGTCTCGAGTGAGAC-AAAATTTTCAAGGGAAAATATCTCAAGGGAGATGAAATTTT-G
***
1784697 TTTCCCC
64 TTTCGAG
* * * * * * * *
1784704 CGAAACTGTTTCAAGTAAGAC-AAATCTTCAATGG-AAATATCTTAAGGGAGATGTAATTTTGTT
1 AGAAACTGTCTCGAGTGAGACAAAATTTTCAAGGGAAAATATCTCAAGGGAGATGAAATTTTGTT
1784767 TCGAG
66 TCGAG
* * * *
1784772 AGAAACTGTCTCGTGTGAGAAAAAATTTCCAAGGGAAAATATCTCTAGGGAGATGAAATTTTGTT
1 AGAAACTGTCTCGAGTGAGACAAAATTTTCAAGGGAAAATATCTCAAGGGAGATGAAATTTTGTT
* *
1784837 TCAAA
66 TCGAG
* * * *
1784842 AGAAACTTTCTCAAGTGAGACGAACAATTTTCAAGGGAAAATATCTCAAGGGATATGGAATTTTG
1 AGAAACTGTCTCGAGTGAGAC-AA-AATTTTCAAGGGAAAATATCTCAAGGGAGATGAAATTTTG
1784907 TTTCGAG
64 TTTCGAG
* * * *
1784914 AGAATCTGTCTCGAGTGAGACAAATATTTTCAAGGGAAAATATCTCAAAGGAGATGAAAATTTAT
1 AGAAACTGTCTCGAGTGAGACAAA-ATTTTCAAGGGAAAATATCTCAAGGGAGATGAAATTTTGT
**
1784979 TTTAAG
65 TTCGAG
* ** * * *
1784985 TGAAACTGTCTCGAGTGAGACAAAAATTATTTTTGAGGAAAAATTATCT-ACAGTGAGATAAAAT
1 AGAAACTGTCTCGAGTGAGAC--AAA--ATTTTCAAGGGAAAA-TATCTCA-AGGGAGATGAAAT
* * *
1785049 TCTATTTCAAG
60 TTTGTTTCGAG
* * * ** ** *
1785060 AGAAACTCTCTCAAGTGAGGCAAAAACTGTTT-TTGAGGAAAACCTATCTCAAGCAAGATAAAAT
1 AGAAACTGTCTCGAGTGAGAC-AAAA-T-TTTCAAG-GGAAAA--TATCTCAAGGGAGATGAAAT
*
1785124 TTTGTTTAGAG
60 TTTGTTTCGAG
* *
1785135 AGAAATTGTTTCGAGTGAGACAAAA
1 AGAAACTGTCTCGAGTGAGACAAAA
1785160 AAATTTTTTG
Statistics
Matches: 359, Mismatches: 82, Indels: 28
0.77 0.17 0.06
Matches are distributed among these distances:
68 20 0.06
69 31 0.09
70 56 0.16
71 62 0.17
72 75 0.21
73 5 0.01
74 30 0.08
75 79 0.22
76 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (70 bp):
AGAAACTGTCTCGAGTGAGACAAAATTTTCAAGGGAAAATATCTCAAGGGAGATGAAATTTTGTT
TCGAG
Found at i:1784994 original size:71 final size:71
Alignment explanation
Indices: 1784626--1785083 Score: 310
Period size: 72 Copynumber: 6.5 Consensus size: 71
1784616 GAGTTGAGTC
* * * *
1784626 ATTTCAAGA-AAA-TGTCTCGAGTGTGACGGAAT-TTTTCAAGAGAAAATATATC-AAGTGAGAT
1 ATTTCAAGAGAAACTGTCTCGAGTGAGAC-AAATATTTTCAAGGGAAAATATCTCAAAG-GAGAT
1784687 -AAAATTTT
64 GAAAA-TTT
* **** * * * * * * *
1784695 GGTTTCCCCCGAAACTGTTTCAAGTAAGAC-AA-ATCTTCAATGG-AAATATCTTAAGGGAGATG
1 -ATTTCAAGAGAAACTGTCTCGAGTGAGACAAATATTTTCAAGGGAAAATATCTCAAAGGAGATG
* *
1784757 TAATTTT
65 AAAATTT
* * * * * * *
1784764 GTTTCGAGAGAAACTGTCTCGTGTGAGA-AAAAATTTCCAAGGGAAAATATCTCTAGGGAGATGA
1 ATTTCAAGAGAAACTGTCTCGAGTGAGACAAATATTTTCAAGGGAAAATATCTCAAAGGAGATGA
*
1784828 AATTTT
66 AAATTT
* * * * * *
1784834 GTTTCAAAAGAAACTTTCTCAAGTGAGACGAACA-ATTTTCAAGGGAAAATATCTCAAGGGATAT
1 ATTTCAAGAGAAACTGTCTCGAGTGAGAC-AA-ATATTTTCAAGGGAAAATATCTCAAAGGAGAT
* *
1784898 GGAATTTT
64 GAAAATTT
* * *
1784906 GTTTCGAGAGAATCTGTCTCGAGTGAGACAAATATTTTCAAGGGAAAATATCTCAAAGGAGATGA
1 ATTTCAAGAGAAACTGTCTCGAGTGAGACAAATATTTTCAAGGGAAAATATCTCAAAGGAGATGA
1784971 AAATTT
66 AAATTT
* * ** * *
1784977 ATTTTAAGTGAAACTGTCTCGAGTGAGACAAAAATTATTTTTGAGGAAAAATTATCT-ACAGTGA
1 ATTTCAAGAGAAACTGTCTCGAGTGAGAC--AAA-TATTTTCAAGGGAAAA-TATCTCAAAG-GA
1785041 GAT-AAAATTCT
61 GATGAAAATT-T
* * *
1785052 ATTTCAAGAGAAACTCTCTCAAGTGAGGCAAA
1 ATTTCAAGAGAAACTGTCTCGAGTGAGACAAA
1785084 AACTGTTTTT
Statistics
Matches: 307, Mismatches: 63, Indels: 33
0.76 0.16 0.08
Matches are distributed among these distances:
68 22 0.07
69 23 0.07
70 64 0.21
71 63 0.21
72 71 0.23
73 7 0.02
74 22 0.07
75 35 0.11
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (71 bp):
ATTTCAAGAGAAACTGTCTCGAGTGAGACAAATATTTTCAAGGGAAAATATCTCAAAGGAGATGA
AAATTT
Found at i:1785016 original size:36 final size:37
Alignment explanation
Indices: 1784919--1785017 Score: 91
Period size: 37 Copynumber: 2.8 Consensus size: 37
1784909 TCGAGAGAAT
1784919 CTGTCTCGAGTGAGAC--AAA-TATTTTCAAGGGAAA
1 CTGTCTCGAGTGAGACAAAAATTATTTTCAAGGGAAA
* * * * * *
1784953 ATATCTCAAAG-GAGATGAAAATTTATTTT-AAGTGAAA
1 CTGTCTC-GAGTGAGA-CAAAAATTATTTTCAAGGGAAA
1784990 CTGTCTCGAGTGAGACAAAAATTATTTT
1 CTGTCTCGAGTGAGACAAAAATTATTTT
1785018 TGAGGAAAAA
Statistics
Matches: 48, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
34 9 0.19
35 2 0.04
36 13 0.27
37 18 0.38
38 6 0.12
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.31
Consensus pattern (37 bp):
CTGTCTCGAGTGAGACAAAAATTATTTTCAAGGGAAA
Found at i:1785065 original size:75 final size:74
Alignment explanation
Indices: 1784907--1785235 Score: 276
Period size: 75 Copynumber: 4.4 Consensus size: 74
1784897 TGGAATTTTG
* * ** * *
1784907 TTTCGAGAGAATCTGTCTCGAGTGAGAC--AAATATTTTCAAGGGAAAA-TATCTCAAAG-GAGA
1 TTTCAAGAGAAACTGTCTCGAGTGAGACAAAAATATTTTTGAGGAAAAACTATCT-ACAGTGAGA
1784968 TGAAAATT-TA
65 T-AAAATTCTA
* * *
1784978 TTTTAAGTGAAACTGTCTCGAGTGAGACAAAAATTATTTTTGAGGAAAAATTATCTACAGTGAGA
1 TTTCAAGAGAAACTGTCTCGAGTGAGACAAAAA-TATTTTTGAGGAAAAACTATCTACAGTGAGA
1785043 TAAAATTCTA
65 TAAAATTCTA
* * * * * **
1785053 TTTCAAGAGAAACTCTCTCAAGTGAGGCAAAAACTGTTTTTGAGGAAAACCTATCT-CAAGCAAG
1 TTTCAAGAGAAACTGTCTCGAGTGAGACAAAAA-TATTTTTGAGGAAAAACTATCTAC-AGTGAG
* *
1785117 ATAAAATTTTG
64 ATAAAATTCTA
* * * * * *
1785128 TTT-AGAGAGAAATTGTTTCGAGTGAGACAAAAAAATTTTTTGAGAAAAAAACTATCTCCAATGA
1 TTTCA-AGAGAAACTGTCTCGAGTGAGACAAAAATA-TTTTTGAG-GAAAAACTATCTACAGTGA
*
1785192 GATAAAATTCTG
63 GATAAAATTCTA
* * * *
1785204 TTTCGAGAAAAACTATCTCGAGTGAGCCAAAA
1 TTTCAAGAGAAACTGTCTCGAGTGAGACAAAA
1785236 TTTGGAGTGA
Statistics
Matches: 206, Mismatches: 40, Indels: 19
0.78 0.15 0.07
Matches are distributed among these distances:
71 24 0.12
73 3 0.01
74 24 0.12
75 106 0.51
76 48 0.23
77 1 0.00
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.29
Consensus pattern (74 bp):
TTTCAAGAGAAACTGTCTCGAGTGAGACAAAAATATTTTTGAGGAAAAACTATCTACAGTGAGAT
AAAATTCTA
Found at i:1832287 original size:20 final size:20
Alignment explanation
Indices: 1832264--1832314 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
1832254 CACGGAATGT
1832264 AAGATTATCAGTGGGAATAA
1 AAGATTATCAGTGGGAATAA
*
1832284 AAGATTACCAGTGGGAATAA
1 AAGATTATCAGTGGGAATAA
1832304 AAGATTATCAG
1 AAGATTATCAG
1832315 GGAATAGGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.45, C:0.08, G:0.24, T:0.24
Consensus pattern (20 bp):
AAGATTATCAGTGGGAATAA
Found at i:1834893 original size:20 final size:20
Alignment explanation
Indices: 1834868--1834907 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1834858 CCGGTTTCTG
*
1834868 TTCTGTTGATTGCTAACCAA
1 TTCTGTTGATTACTAACCAA
1834888 TTCTGTTGATTACTAACCAA
1 TTCTGTTGATTACTAACCAA
1834908 ATAGAGTGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (20 bp):
TTCTGTTGATTACTAACCAA
Found at i:1835999 original size:66 final size:64
Alignment explanation
Indices: 1835851--1836111 Score: 335
Period size: 66 Copynumber: 4.0 Consensus size: 64
1835841 TAAAAACCAA
* *
1835851 GTGAATTGGAACTGATGATGTTGCCATTTGCATGCCCATCTCTTGATAAGCTCTCCATTACATCT
1 GTGAATTGGAACTGATGATGTTGCCATTTGCAT--CCATCTCTTGATAAGCACTCCATTTCATCT
1835916 G
64 G
* * * * *
1835917 GTGAGTTGGAACTGATGATGTTGCCATGTGCAT-CATCTCTTGATGAGCGCTCCTTTTCATCTG
1 GTGAATTGGAACTGATGATGTTGCCATTTGCATCCATCTCTTGATAAGCACTCCATTTCATCTG
* *
1835980 GTGAATTGGAACTGATGATGTTGCTATTTGCATGCCCATCTCTTGATAAACACTCCATTTCATCT
1 GTGAATTGGAACTGATGATGTTGCCATTTGCAT--CCATCTCTTGATAAGCACTCCATTTCATCT
1836045 G
64 G
* ** * *
1836046 GTGAATTGGAACTGATAATGTCACCAATTGTATGCCCATCTCTTGATAAGCACTCCATTTCATCT
1 GTGAATTGGAACTGATGATGTTGCCATTTGCAT--CCATCTCTTGATAAGCACTCCATTTCATCT
1836111 G
64 G
1836112 ATTTTTGCAC
Statistics
Matches: 172, Mismatches: 20, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
63 56 0.33
66 116 0.67
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (64 bp):
GTGAATTGGAACTGATGATGTTGCCATTTGCATCCATCTCTTGATAAGCACTCCATTTCATCTG
Found at i:1848808 original size:16 final size:15
Alignment explanation
Indices: 1848784--1848849 Score: 69
Period size: 16 Copynumber: 4.2 Consensus size: 15
1848774 TGCTTTTGAT
*
1848784 TTTGATTACTTTCGG
1 TTTGATTACTTTCAG
*
1848799 TTTGACTTACTTTCGG
1 TTTGA-TTACTTTCAG
* *
1848815 TTCGAGTTATTTTCAG
1 TTTGA-TTACTTTCAG
1848831 TTTGGATTACTTTCAG
1 TTT-GATTACTTTCAG
1848847 TTT
1 TTT
1848850 AAATTATTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
15 5 0.12
16 36 0.84
17 2 0.05
ACGTcount: A:0.15, C:0.14, G:0.18, T:0.53
Consensus pattern (15 bp):
TTTGATTACTTTCAG
Found at i:1850172 original size:33 final size:33
Alignment explanation
Indices: 1850132--1850199 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
1850122 ATGCTTCGAC
* *
1850132 TTTAGTGTTTTAATATGACTCAAATACGTTGGT
1 TTTAGTGTTTCAATAGGACTCAAATACGTTGGT
1850165 TTTAGTGTTTCAATAGGACTCAAATACGTTGGT
1 TTTAGTGTTTCAATAGGACTCAAATACGTTGGT
1850198 TT
1 TT
1850200 ATTTTCTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.26, C:0.10, G:0.19, T:0.44
Consensus pattern (33 bp):
TTTAGTGTTTCAATAGGACTCAAATACGTTGGT
Found at i:1850303 original size:12 final size:13
Alignment explanation
Indices: 1850248--1850312 Score: 50
Period size: 12 Copynumber: 5.2 Consensus size: 13
1850238 GGGCCTATAA
1850248 AAATAATA-AAAT
1 AAATAATATAAAT
*
1850260 AAA-AATATATTAT
1 AAATAATATA-AAT
*
1850273 TAATAATGAT-AAT
1 AAATAAT-ATAAAT
1850286 AAATAA-ATAAAT
1 AAATAATATAAAT
*
1850298 ATATAATAT-AAT
1 AAATAATATAAAT
1850310 AAA
1 AAA
1850313 ATGTTTTTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
11 6 0.15
12 17 0.41
13 13 0.32
14 3 0.07
15 2 0.05
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (13 bp):
AAATAATATAAAT
Found at i:1850773 original size:84 final size:80
Alignment explanation
Indices: 1850642--1851586 Score: 726
Period size: 84 Copynumber: 11.4 Consensus size: 80
1850632 TGATACGCCC
* * * * * ** *
1850642 TCGAGCTGAATGGAATCGAATTCGAAGGTCTTTGGCAGATAACCCTTCTTGTTTTGAGCTATGCT
1 TCGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGACTTGAGTTATGCT
*
1850707 GCAAATTATGGTGCCT
66 GCAAATGAT-GTGCCT
* * * * * *
1850723 TTGAGTTGAGTGGAGTTGAAATCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTAT
1 TCGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTG--G-CAGATAACCCTTCTAGACTTGAGTTAT
* * *
1850788 GCCGTAAATGATGTGCCC
63 GCTGCAAATGATGTGCCT
* * * * * *
1850806 TCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGA
1 TCG-AGCTGAGTGTAGTCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGACTTGAGTTATGC
1850871 TGCAAATGATGTGCCT
65 TGCAAATGATGTGCCT
* * * * *
1850887 TGGAG-TAGAGTGTAGTCGAACTCGAAGGTCTTTGTTAACAAATAACCTTTCTAGCCTTGAGTTA
1 TCGAGCT-GAGTGTAGTCGAACTCGAAGGTCTTTG---GCAGATAACCCTTCTAGACTTGAGTTA
* * *
1850951 TGCCGTAAATGATGTTTCC-
62 TGCTGCAAATGATG-TGCCT
* * * * * *
1850970 TCGAAGCTGAGTGTAATCAAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATGC
1 TCG-AGCTGAGTGTAGTCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGACTTGAGTTATGC
1851035 TGCAAATGATGTGCCT
65 TGCAAATGATGTGCCT
* * * *
1851051 TGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGGTTGGTAGATAACCCTTCTCGACTTAAGTTA
1 TCGAGCTGAGTGTAGTCGAACTCGAAGGTC--T--TTGGCAGATAACCCTTCTAGACTTGAGTTA
*
1851116 TGCTGCAAATGATATGCCT
62 TGCTGCAAATGATGTGCCT
* * * * * *
1851135 TGGAGCTGAGCGTAGTCAAACTTGAAGGTCTTTTGGTCATATATAACCCTTCTAGCCTTGAGTTA
1 TCGAGCTGAGTGTAGTCGAACTCGAAGGTC-TTTGG-C--AGATAACCCTTCTAGACTTGAGTTA
* *
1851200 TGCTG-TAATGATGTGCCC
62 TGCTGCAAATGATGTGCCT
* * * * * * * * * * *
1851218 TCAAAGCTGGGTATAATCGAACTCGAGGGTCTTTAGCAGATAACTCTTCTCGACTTAAGCTATGT
1 TC-GAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGACTTGAGTTATGC
*
1851283 TACAAATGATGTGCCT
65 TGCAAATGATGTGCCT
* ** * * *
1851299 TGGAGCTGAGCATAGTCAAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTA
1 TCGAGCTGAGTGTAGTCGAACTCGAAGGTC--T--TTGGCAGATAACCCTTCTAGACTTGAGTTA
* * *
1851364 TGTTGTAAATGATATGCCT
62 TGCTGCAAATGATGTGCCT
* * ** *
1851383 TGGAGCTGAGCGTAGTTAAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTA
1 TCGAGCTGAGTGTAGTCGAACTCGAAGGTC-TTTGG---CAGATAACCCTTCTAGACTTGAGTTA
* * *
1851448 TGTTGTAAATGATGTGCCC
62 TGCTGCAAATGATGTGCCT
* * * * * *
1851467 TCGAAGCTGAGTGTAATCGAACTTGAGGGTCTTCGGTTGACAGATAACCCTTCTTGACTTAAGTT
1 TCG-AGCTGAGTGTAGTCGAACTCGAAGGTC-T---TTGGCAGATAACCCTTCTAGACTTGAGTT
* *
1851532 ATGCTGTAAATGATGTGTCT
61 ATGCTGCAAATGATGTGCCT
* * * * * *
1851552 TGGAGTTGAGCGTAGGCCAACTCGAAGGCCTTTGG
1 TCGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGG
1851587 TGGGCACGAT
Statistics
Matches: 693, Mismatches: 139, Indels: 65
0.77 0.15 0.07
Matches are distributed among these distances:
79 1 0.00
80 101 0.15
81 121 0.17
82 4 0.01
83 61 0.09
84 337 0.49
85 65 0.09
88 3 0.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (80 bp):
TCGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGACTTGAGTTATGCT
GCAAATGATGTGCCT
Found at i:1850948 original size:164 final size:165
Alignment explanation
Indices: 1850638--1851585 Score: 901
Period size: 164 Copynumber: 5.7 Consensus size: 165
1850628 CGGTTGATAC
* * * * * ** * *
1850638 GCCCTCG-AGCTGAATGGAATCGAATTCGAAGGTC-TTTGGCAGATAACCCTTCTTGTTTTGAGC
1 GCCCTCGAAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGGCAGATAACCCTTCTCGACTTAAGT
* * * * * * *
1850701 TATGCTGCAAATTATGGTGCCTTTGAGTTGAGTGGAGTTGAAATCGAAGGTCTTTGTTGACAGAT
66 TATGCTGCAAATGAT-GTGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGTTAACAGAT
*
1850766 AACCCTTCTAGCCTTGAGTTATGCCGTAAATGATGT
130 AACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
* * *
1850802 GCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTC-TTTGGCAGATAACCCTTCTCGACTTAAGC
1 GCCCTCGAAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGGCAGATAACCCTTCTCGACTTAAGT
* *
1850866 TATGATGCAAATGATGTGCCTTGGAG-TAGAGTGTAGTCGAACTCGAAGGTCTTTGTTAACAAAT
66 TATGCTGCAAATGATGTGCCTTGGAGCT-GAGTGTAGTCGAACTCGAAGGTCTTTGTTAACAGAT
* *
1850930 AACCTTTCTAGCCTTGAGTTATGCCGTAAATGATGT
130 AACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
** * *
1850966 TTCCTCGAAGCTGAGTGTAATCAAACTCGAGGGTC-TTTGGCAGATAGCCCTTCTCGACTTAAGT
1 GCCCTCGAAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGGCAGATAACCCTTCTCGACTTAAGT
***
1851030 TATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGGTTGGTAGAT
66 TATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTT-GTTAACAGAT
* * * * *
1851095 AACCCTTCTCGACTTAAGTTATGCTGCAAATGATAT
130 AACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
* * * * * * * * *
1851131 G-CCTTGGAGCTGAGCGTAGTCAAACTTGAAGGTCTTTTGGTCATATATAACCCTTCTAGCCTTG
1 GCCCTCGAAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGG-C--AGATAACCCTTCTCGACTTA
* *** * * * * *
1851195 AGTTATGCTG-TAATGATGTGCCCTCAAAGCTGGGTATAATCGAACTCGAGGGTC--T-TTAGCA
63 AGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGTTAACA
* * * * * * **
1851256 GATAACTCTTCTCGACTTAAGCTATGTTACAAATGATGT
127 GATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
* * ** *
1851295 G-CCTTGGAGCTGAGCATAGTCAAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
1 GCCCTCGAAGCTGAGTGTAATCAAACTCGAAGGTC-TT--TTGGCAGATAACCCTTCTCGACTTA
* * * * ** * *
1851359 AGTTATGTTGTAAATGATATGCCTTGGAGCTGAGCGTAGTTAAACTCGAAGGTCTTTTGGTCACA
63 AGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTC-TTTGTTAACA
*
1851424 GATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGT
127 GATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
* * * * *
1851463 GCCCTCGAAGCTGAGTGTAATCGAACTTGAGGGTCTTCGGTTGACAGATAACCCTTCTTGACTTA
1 GCCCTCGAAGCTGAGTGTAATCAAACTCGAAGGTCTT---TTGGCAGATAACCCTTCTCGACTTA
* * * * * * *
1851528 AGTTATGCTGTAAATGATGTGTCTTGGAGTTGAGCGTAGGCCAACTCGAAGGCCTTTG
63 AGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTG
1851586 GTGGGCACGA
Statistics
Matches: 657, Mismatches: 108, Indels: 34
0.82 0.14 0.04
Matches are distributed among these distances:
163 1 0.00
164 338 0.51
165 112 0.17
166 3 0.00
167 14 0.02
168 93 0.14
169 96 0.15
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (165 bp):
GCCCTCGAAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGGCAGATAACCCTTCTCGACTTAAGT
TATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGTTAACAGATA
ACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
Found at i:1851128 original size:248 final size:249
Alignment explanation
Indices: 1850761--1851592 Score: 1084
Period size: 248 Copynumber: 3.3 Consensus size: 249
1850751 TCTTTGTTGA
* * * * * * * * *
1850761 CAGATAACCCTTCTAGCCTTGAGTTATGCCGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGA
* * *
1850826 ACTCGAGGGTC--T--TTGGCAGATAACCCTTCTCGACTTAAGCTATGATGCAAATGATGTGCCT
65 ACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGATGCAAATGATATGCCT
* * * * *
1850887 TGGAG-TAGAGTGTAGTCGAACTCGAAGGTC-TTTGTTAACAAATAACCTTTCTAGCCTTGAGTT
130 TGGAGCT-GAGCGTAGTCAAACTCGAAGGTCTTTTGGTCACAAATAACCCTTCTAGCCTTGAGTT
* ** *
1850950 ATGCCGTAAATGATGTTTCCTCGAAGCTGAGTGTAATCAAACTCGAGGGTCTTTGG
194 ATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGG
* *
1851006 CAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCGAA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* *
1851071 CTCGAAGGTCTTTGGTTGGTAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTT
66 CTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGATGCAAATGATATGCCTT
* * *
1851136 GGAGCTGAGCGTAGTCAAACTTGAAGGTCTTTTGGTCATATATAACCCTTCTAGCCTTGAGTTAT
131 GGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGGTCACAAATAACCCTTCTAGCCTTGAGTTAT
* * * *
1851201 GCTGT-AATGATGTGCCCTCAAAGCTGGGTATAATCGAACTCGAGGGTCTTTAG
196 GCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGG
* * * * * *
1851254 CAGATAACTCTTCTCGACTTAAGCTATGTTACAAATGATGTGCCTTGGAGCTGAGCATAGTCAAA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* *
1851319 CTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGTTGTAAATGATATGCCTT
66 CTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGATGCAAATGATATGCCTT
* *
1851384 GGAGCTGAGCGTAGTTAAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTAT
131 GGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGGTCACAAATAACCCTTCTAGCCTTGAGTTAT
* * *
1851449 GTTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGAGGGTCTTCGGTTGA
196 GCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTC-T---TTGG
* * * * * *
1851507 CAGATAACCCTTCTTGACTTAAGTTATGCTGTAAATGATGTGTCTTGGAGTTGAGCGTAGGCCAA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* *
1851572 CTCGAAGGCCTTTGGTGGGCA
66 CTCGAAGGTCTTTGGTTGGCA
1851593 CGATTCCCTT
Statistics
Matches: 511, Mismatches: 65, Indels: 14
0.87 0.11 0.02
Matches are distributed among these distances:
244 29 0.06
245 36 0.07
246 1 0.00
248 295 0.58
249 74 0.14
250 1 0.00
253 75 0.15
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (249 bp):
CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
CTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGATGCAAATGATATGCCTT
GGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGGTCACAAATAACCCTTCTAGCCTTGAGTTAT
GCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGG
Found at i:1851914 original size:110 final size:110
Alignment explanation
Indices: 1851694--1852129 Score: 675
Period size: 110 Copynumber: 4.0 Consensus size: 110
1851684 ATCCAAATAT
* * * *
1851694 TTGTGTTGTTTCGAGGCCAATATCCTTCACTGTGAAGTTGAAATTGACTC----TGAAACTAAAA
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAA
* * * *
1851755 AGTTATTTGTTGACAGCCAGCCGCCCCTTCGCTGTGAAGTTGAGC
66 AGTTGTTTGTTGACAGTCAGTCACCCCTTCGCTGTGAAGTTGAGC
1851800 TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAA
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAA
1851865 AGTTGTTTGTTGACAGTCAGTCACCCCTTCGCTGTGAAGTTGAGC
66 AGTTGTTTGTTGACAGTCAGTCACCCCTTCGCTGTGAAGTTGAGC
* * *
1851910 TTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTAAAATTGAAATTGACTCTGAATGAAACTGAAA
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAA
* *
1851975 AGTTGTTTATTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGC
66 AGTTGTTTGTTGACAGTCAGTCACCCCTTCGCTGTGAAGTTGAGC
* * *
1852020 TTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTGAATGAAACTCAAA
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAA
*
1852085 AGTTGTTTGTTGACCGTCAGTCGA-CCCTTCGCTGTGAAGTTGAGC
66 AGTTGTTTGTTGACAGTCAGTC-ACCCCTTCGCTGTGAAGTTGAGC
1852130 AACCACCGTC
Statistics
Matches: 305, Mismatches: 20, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
106 47 0.15
110 258 0.85
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (110 bp):
TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAA
AGTTGTTTGTTGACAGTCAGTCACCCCTTCGCTGTGAAGTTGAGC
Found at i:1853128 original size:95 final size:94
Alignment explanation
Indices: 1852960--1853145 Score: 248
Period size: 95 Copynumber: 2.0 Consensus size: 94
1852950 ATATGTAAAC
* * ** *
1852960 ACCTTTATCAGGTTAACTGAATCTTATCAATAAAGTCGGGGCGTCTAACCAATTGCCTTAGAGGG
1 ACCTTTATCAGGCTAACTGAATATTATCAATAAAACCGAGGCGTCTAACCAATTGCCTTAGAGGG
*
1853025 ACATCTCAAGCTTTATTGTATAGTATAATT
66 ACAACTCAAGCTTTATTGTATA-TATAATT
* * * *
1853055 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAACCGAGGTGTTTAACCAATTG-CTCTAGAGG
1 ACCTTTATCAGGCTAACTGAATATTATCAATAAAACCGAGGCGTCTAACCAATTGCCT-TAGAGG
*
1853119 GACAACTCAAGGTTTATTGTATATATA
65 GACAACTCAAGCTTTATTGTATATATA
1853146 TAATATTATA
Statistics
Matches: 79, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
94 6 0.08
95 73 0.92
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Consensus pattern (94 bp):
ACCTTTATCAGGCTAACTGAATATTATCAATAAAACCGAGGCGTCTAACCAATTGCCTTAGAGGG
ACAACTCAAGCTTTATTGTATATATAATT
Found at i:1855176 original size:29 final size:30
Alignment explanation
Indices: 1855126--1855184 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
1855116 AACTCGAGAG
1855126 GATACATTCCCTTATGCCCATACAGAGAAT
1 GATACATTCCCTTATGCCCATACAGAGAAT
* *
1855156 GATACATTCCCTTTTG-CCATACGGAGAAT
1 GATACATTCCCTTATGCCCATACAGAGAAT
1855185 AAATTCACAC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 12 0.44
30 15 0.56
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (30 bp):
GATACATTCCCTTATGCCCATACAGAGAAT
Found at i:1856466 original size:3 final size:3
Alignment explanation
Indices: 1856443--1856499 Score: 66
Period size: 3 Copynumber: 19.3 Consensus size: 3
1856433 GGTCTACAAA
*
1856443 AAT AAT AA- AAT AAA AAT -AT AAT AAT AAT AAT AAT AAT AAT ATAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
1856487 ATAT AAT -AT AAT A
1 A-AT AAT AAT AAT A
1856500 TATTATAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
2 6 0.12
3 35 0.73
4 7 0.15
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1856500 original size:12 final size:11
Alignment explanation
Indices: 1856443--1856511 Score: 72
Period size: 11 Copynumber: 6.4 Consensus size: 11
1856433 GGTCTACAAA
*
1856443 AATAATAAAAT
1 AATAATATAAT
*
1856454 AAAAATATAAT
1 AATAATATAAT
1856465 AATAATAATAAT
1 AATAAT-ATAAT
1856477 AATAATAT-AT
1 AATAATATAAT
1856487 ATATAATATAAT
1 A-ATAATATAAT
*
1856499 -ATATTATAA-
1 AATAATATAAT
1856508 AATA
1 AATA
1856512 TTTTTGTAGA
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
10 14 0.28
11 23 0.46
12 13 0.26
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AATAATATAAT
Found at i:1856512 original size:12 final size:12
Alignment explanation
Indices: 1856444--1856512 Score: 56
Period size: 12 Copynumber: 6.0 Consensus size: 12
1856434 GTCTACAAAA
1856444 ATAATAAAATA-
1 ATAATAAAATAT
* *
1856455 AAAATATAATA-
1 ATAATAAAATAT
1856466 ATAATAATAATA-
1 ATAATAA-AATAT
*
1856478 ATAAT-ATATAT
1 ATAATAAAATAT
*
1856489 ATAATATAATAT
1 ATAATAAAATAT
*
1856501 ATTATAAAATAT
1 ATAATAAAATAT
1856513 TTTTGTAGAC
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
10 3 0.07
11 20 0.43
12 23 0.50
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
ATAATAAAATAT
Found at i:1857095 original size:27 final size:26
Alignment explanation
Indices: 1857008--1857094 Score: 99
Period size: 25 Copynumber: 3.4 Consensus size: 26
1856998 TTAAATGCAT
* *
1857008 AATATTTTATA-TATATTAACTTAAA
1 AATATTTTATATTAAATTAATTTAAA
*
1857033 AATATTTGTATATTAACTT-A-TTAAA
1 AATATTT-TATATTAAATTAATTTAAA
*
1857058 TATATTTTATTATTAAATTAATTTAAA
1 AATATTTTA-TATTAAATTAATTTAAA
1857085 AATATTTTAT
1 AATATTTTAT
1857095 TTTTATTTTC
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
24 2 0.04
25 26 0.50
26 7 0.13
27 17 0.33
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (26 bp):
AATATTTTATATTAAATTAATTTAAA
Found at i:1857108 original size:27 final size:27
Alignment explanation
Indices: 1857008--1857116 Score: 102
Period size: 27 Copynumber: 4.2 Consensus size: 27
1856998 TTAAATGCAT
* *
1857008 AATATTTTA-TA-TATATTAACTTAAA
1 AATATTTTATTATTAAATTAATTTAAA
*
1857033 AATATTTGTA-TATTAACTT-A-TTAAA
1 AATATTT-TATTATTAAATTAATTTAAA
*
1857058 TATATTTTATTATTAAATTAATTTAAA
1 AATATTTTATTATTAAATTAATTTAAA
* ** *
1857085 AATATTTTATTTTTATTTTCATTTAAA
1 AATATTTTATTATTAAATTAATTTAAA
1857112 AATAT
1 AATAT
1857117 ATATTTTATG
Statistics
Matches: 70, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
24 2 0.03
25 26 0.37
26 6 0.09
27 36 0.51
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (27 bp):
AATATTTTATTATTAAATTAATTTAAA
Found at i:1857220 original size:20 final size:22
Alignment explanation
Indices: 1857195--1857247 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
1857185 ATGTGTGATT
1857195 AAAATATATTT-ATA-ATTTCA
1 AAAATATATTTGATATATTTCA
* *
1857215 AAAATAAATTTTGATATATTTTA
1 AAAATATA-TTTGATATATTTCA
1857238 AAAA-ATATTT
1 AAAATATATTT
1857248 TTCTAATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
20 7 0.26
21 6 0.22
22 5 0.19
23 9 0.33
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (22 bp):
AAAATATATTTGATATATTTCA
Found at i:1859822 original size:18 final size:17
Alignment explanation
Indices: 1859791--1859824 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1859781 AAAAAGCCTC
*
1859791 CCCTTTCCTTCTCCCCA
1 CCCTTTCCTCCTCCCCA
1859808 CCCTTGTCCTCCTCCCC
1 CCCTT-TCCTCCTCCCC
1859825 TGCAAACAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.03, C:0.62, G:0.03, T:0.32
Consensus pattern (17 bp):
CCCTTTCCTCCTCCCCA
Found at i:1864781 original size:2 final size:2
Alignment explanation
Indices: 1864774--1864815 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1864764 TTGTAAGAGG
1864774 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
1864816 GGTTCCACGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1869873 original size:19 final size:18
Alignment explanation
Indices: 1869861--1869919 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 18
1869851 AGGGGGTACA
1869861 GATTCCCCCAGGGGTATC
1 GATTCCCCCAGGGGTATC
*
1869879 GATT-CCCC--GGG-AAC
1 GATTCCCCCAGGGGTATC
*
1869893 AGATTCCCCCCAGAGGTATC
1 -GATT-CCCCCAGGGGTATC
1869913 GATTCCC
1 GATTCCC
1869920 GGGTACAGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 12
0.68 0.06 0.26
Matches are distributed among these distances:
14 2 0.06
15 7 0.22
17 8 0.25
18 7 0.22
19 6 0.19
20 2 0.06
ACGTcount: A:0.20, C:0.36, G:0.24, T:0.20
Consensus pattern (18 bp):
GATTCCCCCAGGGGTATC
Found at i:1869911 original size:34 final size:33
Alignment explanation
Indices: 1869858--1869935 Score: 122
Period size: 33 Copynumber: 2.4 Consensus size: 33
1869848 TCCAGGGGGT
*
1869858 ACAGATT-CCCCCAGGGGTATCGATTCCCCGGGA
1 ACAGATTCCCCCCAGAGGTATCGATT-CCCGGGA
*
1869891 ACAGATTCCCCCCAGAGGTATCGATTCCCGGGT
1 ACAGATTCCCCCCAGAGGTATCGATTCCCGGGA
1869924 ACAGATTCCCCC
1 ACAGATTCCCCC
1869936 TGCATGGTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
33 25 0.60
34 17 0.40
ACGTcount: A:0.22, C:0.36, G:0.23, T:0.19
Consensus pattern (33 bp):
ACAGATTCCCCCCAGAGGTATCGATTCCCGGGA
Found at i:1870072 original size:21 final size:21
Alignment explanation
Indices: 1870048--1870089 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1870038 ATTTGAATAT
**
1870048 TATGAAGGGGTATTGATTCCC
1 TATGAAGGGGTACCGATTCCC
1870069 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1870090 CCCATTCTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.29
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:1870151 original size:21 final size:21
Alignment explanation
Indices: 1870118--1870157 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
1870108 TTTTTGCAGA
*
1870118 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
1870140 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
1870158 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:1870411 original size:34 final size:32
Alignment explanation
Indices: 1870372--1870441 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
1870362 TTTTGTAAAG
* *
1870372 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAAGTTCTAGCTTAGCCCG-G-AAAAACTA
*
1870406 GGGAAAAGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAAGTTCTAGCTTAGCCCGGAAAAACTA
1870438 GGGA
1 GGGA
1870442 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.33, C:0.16, G:0.30, T:0.21
Consensus pattern (32 bp):
GGGAAAAGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:1871452 original size:3 final size:3
Alignment explanation
Indices: 1871431--1871468 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
1871421 TGAAGAAAGG
* *
1871431 GAA G-A GAA GAA AAA CAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1871469 TGAGGACGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.68, C:0.03, G:0.29, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1873437 original size:20 final size:20
Alignment explanation
Indices: 1873412--1873505 Score: 69
Period size: 20 Copynumber: 5.0 Consensus size: 20
1873402 ATCAGATTGT
1873412 CCAGGGGGTACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
* * * *
1873432 CCAGGGAGAATAAATTCCCC
1 CCAGGGGGTACAGATTCCCC
1873452 CCAGGGGGTATC-GATT--CC
1 CCAGGGGGTA-CAGATTCCCC
*
1873470 CC---GGGAACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
1873487 CCA-GGGGTATC-GATTCCCC
1 CCAGGGGGTA-CAGATTCCCC
1873506 GGGTACAGAT
Statistics
Matches: 57, Mismatches: 10, Indels: 15
0.70 0.12 0.18
Matches are distributed among these distances:
14 1 0.02
15 8 0.14
17 4 0.07
18 4 0.07
19 12 0.21
20 28 0.49
ACGTcount: A:0.22, C:0.34, G:0.27, T:0.17
Consensus pattern (20 bp):
CCAGGGGGTACAGATTCCCC
Found at i:1873494 original size:34 final size:35
Alignment explanation
Indices: 1873445--1873522 Score: 140
Period size: 34 Copynumber: 2.3 Consensus size: 35
1873435 GGGAGAATAA
1873445 ATTCCCCCCAGGGGGTATCGATTCCCCGGGAACAG
1 ATTCCCCCCAGGGGGTATCGATTCCCCGGGAACAG
*
1873480 ATTCCCCCCA-GGGGTATCGATTCCCCGGGTACAG
1 ATTCCCCCCAGGGGGTATCGATTCCCCGGGAACAG
1873514 ATTCCCCCC
1 ATTCCCCCC
1873523 TGCATGGTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
34 32 0.76
35 10 0.24
ACGTcount: A:0.18, C:0.38, G:0.24, T:0.19
Consensus pattern (35 bp):
ATTCCCCCCAGGGGGTATCGATTCCCCGGGAACAG
Found at i:1873516 original size:15 final size:15
Alignment explanation
Indices: 1873464--1873520 Score: 53
Period size: 15 Copynumber: 3.5 Consensus size: 15
1873454 AGGGGGTATC
*
1873464 GATTCCCCGGGAACA
1 GATTCCCCGGGTACA
1873479 GATTCCCCCCAGGGGTATC-
1 GATT--CCCC--GGGTA-CA
1873498 GATTCCCCGGGTACA
1 GATTCCCCGGGTACA
1873513 GATTCCCC
1 GATTCCCC
1873521 CCTGCATGGT
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
14 1 0.03
15 17 0.49
17 8 0.23
19 8 0.23
20 1 0.03
ACGTcount: A:0.19, C:0.37, G:0.25, T:0.19
Consensus pattern (15 bp):
GATTCCCCGGGTACA
Found at i:1873650 original size:21 final size:21
Alignment explanation
Indices: 1873624--1873665 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1873614 ATTTGAATAT
*
1873624 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1873645 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1873666 CTCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:1876547 original size:15 final size:15
Alignment explanation
Indices: 1876527--1876563 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1876517 CTTTTTTTAA
*
1876527 AACATTTTGAGTTTC
1 AACATTTTGAATTTC
*
1876542 AACATTTTGAATTTT
1 AACATTTTGAATTTC
1876557 AACATTT
1 AACATTT
1876564 CATTTTAGGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.49
Consensus pattern (15 bp):
AACATTTTGAATTTC
Found at i:1877847 original size:40 final size:40
Alignment explanation
Indices: 1877739--1877850 Score: 154
Period size: 40 Copynumber: 2.8 Consensus size: 40
1877729 ACATATAAGA
* * *
1877739 ATTTTAGTGGCGTTTTTAAACAAACGCCACCAAAGAATCT
1 ATTTTAGTGGCATTTTTAAACAAACGCCGCAAAAGAATCT
* *
1877779 ACTTTAGTGGCATTTCTAAACAAACGCCGCAAAAGAATCGT
1 ATTTTAGTGGCATTTTTAAACAAACGCCGCAAAAGAATC-T
*
1877820 -TTTTAGTAGCATTTTTAAACAAACGCCGCAA
1 ATTTTAGTGGCATTTTTAAACAAACGCCGCAA
1877851 TTGGGTACAT
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
40 62 0.98
41 1 0.02
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.29
Consensus pattern (40 bp):
ATTTTAGTGGCATTTTTAAACAAACGCCGCAAAAGAATCT
Found at i:1879354 original size:23 final size:23
Alignment explanation
Indices: 1879324--1879375 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
1879314 TTGAAGCAAT
* *
1879324 AATTTTACTTTCATGTAGTTCAA
1 AATTTTACTCTCATGCAGTTCAA
*
1879347 AATTTTACTCTGATGCAGTTCAA
1 AATTTTACTCTCATGCAGTTCAA
1879370 AATTTT
1 AATTTT
1879376 GCATGGTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.46
Consensus pattern (23 bp):
AATTTTACTCTCATGCAGTTCAA
Found at i:1880142 original size:46 final size:46
Alignment explanation
Indices: 1880092--1880182 Score: 182
Period size: 46 Copynumber: 2.0 Consensus size: 46
1880082 TATTTTTACT
1880092 TAATTCGAGTCGTAATTAAATTTTAAGGTGTTGTTATTGGATATTA
1 TAATTCGAGTCGTAATTAAATTTTAAGGTGTTGTTATTGGATATTA
1880138 TAATTCGAGTCGTAATTAAATTTTAAGGTGTTGTTATTGGATATT
1 TAATTCGAGTCGTAATTAAATTTTAAGGTGTTGTTATTGGATATT
1880183 GTTACATGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.30, C:0.04, G:0.20, T:0.46
Consensus pattern (46 bp):
TAATTCGAGTCGTAATTAAATTTTAAGGTGTTGTTATTGGATATTA
Found at i:1881629 original size:213 final size:217
Alignment explanation
Indices: 1881085--1881691 Score: 945
Period size: 213 Copynumber: 2.8 Consensus size: 217
1881075 TTAGAGTGTG
* * * *
1881085 GTTGAAGGAAAGCAAACCAATCAAAATTGGGGACAAGAGAATTCAATTCAAGGGGTTTAAGAAAT
1 GTTGAAGGAAAACAAATCAATCAAAATTGGGGACAAGAGGATTCAATTCAAGGGGCTTAAGAAAT
*
1881150 CAAGCATAAACCTAACCACCGAACCAAGACCACTCATTGTTTTAAAGTAGACAACAATATGTATA
66 CAAGCATAAACCTAACCACCGAACCAAGACCACTTATTGTTTTAAAGTAGACAACAATATGTATA
*
1881215 TATTTTGTATCTTACTGTAAAATAGTTAATTTAAATTTATTTTCATTTAATATATTTATTTTCTA
131 TATTTTGTATCTTAATGT-AAATAGTTAATTTAAATTTATTTTC--------TATTTATTTTCTA
**
1881280 CTGATTAGAGTGTGACATGTGTCATCCTCTA
187 CCAATTAGAGTGTGACATGTGTCATCCTCTA
1881311 GTTGAAGGAAAACAAATCAATCAAAATTGGGGACAAGAGGATTCAATTCAAGGGGCTTAAGAAAT
1 GTTGAAGGAAAACAAATCAATCAAAATTGGGGACAAGAGGATTCAATTCAAGGGGCTTAAGAAAT
*
1881376 CAAGCATAAACCTAACCACCGAACCAAGACCACATATTGTTTTACAA-TAGACAACAATATGTAT
66 CAAGCATAAACCTAACCACCGAACCAAGACCACTTATTGTTTTA-AAGTAGACAACAATATGTAT
1881440 ATATTTTGTATCTTAATGT-AA-AGTTAATTTAAATTTATTTTC-A-TTATTTTCTACCAATTAG
130 ATATTTTGTATCTTAATGTAAATAGTTAATTTAAATTTATTTTCTATTTATTTTCTACCAATTAG
*
1881501 ATTGTGACATGTGTCATCCTCTA
195 AGTGTGACATGTGTCATCCTCTA
1881524 GTTGAAGGAAAACAAATCAATCAAAATTGGGGACAAGAGGATTCAATTCAAGGGGCTTAAGAAAT
1 GTTGAAGGAAAACAAATCAATCAAAATTGGGGACAAGAGGATTCAATTCAAGGGGCTTAAGAAAT
* * *
1881589 CAAGCATAAACCTAACCACTGAATCAATACCACTTATTGTTTTTAAAGTAGACAACAATATGTAT
66 CAAGCATAAACCTAACCACCGAACCAAGACCACTTATTG-TTTTAAAGTAGACAACAATATGTAT
*
1881654 ATATTTTGTATCTTAGTGTAAAATAGTTAATTTAAATT
130 ATATTTTGTATCTTAATGT-AAATAGTTAATTTAAATT
1881692 AATATTTTTT
Statistics
Matches: 360, Mismatches: 15, Indels: 21
0.91 0.04 0.05
Matches are distributed among these distances:
213 140 0.39
214 41 0.11
216 2 0.01
217 14 0.04
223 21 0.06
224 2 0.01
226 138 0.38
227 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (217 bp):
GTTGAAGGAAAACAAATCAATCAAAATTGGGGACAAGAGGATTCAATTCAAGGGGCTTAAGAAAT
CAAGCATAAACCTAACCACCGAACCAAGACCACTTATTGTTTTAAAGTAGACAACAATATGTATA
TATTTTGTATCTTAATGTAAATAGTTAATTTAAATTTATTTTCTATTTATTTTCTACCAATTAGA
GTGTGACATGTGTCATCCTCTA
Found at i:1881761 original size:30 final size:29
Alignment explanation
Indices: 1881721--1882011 Score: 116
Period size: 31 Copynumber: 10.0 Consensus size: 29
1881711 TTAAAATATA
* *
1881721 TATT-TTATCTTAACTTATTAAATATATTT
1 TATTATTATCTTAATTTA-AAAATATATTT
* *
1881750 TATTATTATCTTAATTTAAAAAAATACTT
1 TATTATTATCTTAATTTAAAAATATATTT
* *
1881779 CATTATTATTTTAATTTAAAAATATATATAT
1 TATTATTATCTTAATTTAAAAATATAT-T-T
* * *
1881810 TATTTTTATTTTAAATT-AAAATATA-TT
1 TATTATTATCTTAATTTAAAAATATATTT
** ** * * *
1881837 TA--A-TAAGTTAAAATACAAAATAAAATA
1 TATTATTATCTTAATTTA-AAAATATATTT
* ***
1881864 TATGT-TTAAACTTAAAAAATAAAATATATTT
1 TAT-TATT-ATCTTAATTTA-AAAATATATTT
* * *
1881895 TATCATTAACTTAATTT-AAGA-ATATTT
1 TATTATTATCTTAATTTAAAAATATATTT
*
1881922 TATTACTA-CTATAATTTAAAAATATATATTT
1 TATTATTATCT-TAATTT-AAAA-ATATATTT
* * * **
1881953 TTTTCTTATCTTATTTTAAATATATATAAAT
1 TATTATTATCTTAATTTAAA-A-ATATATTT
* * *
1881984 TATTTTTATTTTAACTTAAAAATATATT
1 TATTATTATCTTAATTTAAAAATATATT
1882012 CAATAAGTTA
Statistics
Matches: 199, Mismatches: 44, Indels: 38
0.71 0.16 0.14
Matches are distributed among these distances:
24 8 0.04
26 9 0.05
27 24 0.12
28 4 0.02
29 42 0.21
30 34 0.17
31 76 0.38
32 2 0.01
ACGTcount: A:0.44, C:0.05, G:0.01, T:0.50
Consensus pattern (29 bp):
TATTATTATCTTAATTTAAAAATATATTT
Found at i:1881816 original size:26 final size:27
Alignment explanation
Indices: 1881740--1881824 Score: 75
Period size: 29 Copynumber: 3.0 Consensus size: 27
1881730 TTAACTTATT
* *
1881740 AAATATATTTTATTATTATCTTAATTTAA
1 AAATATACTATATTATT-T-TTAATTTAA
*
1881769 AAAAATACT-TCATTATTATTTTAATTTAA
1 AAATATACTAT-ATTA-T-TTTTAATTTAA
*
1881798 AAATATA-TATATTATTTTTATTTTAA
1 AAATATACTATATTATTTTTAATTTAA
1881824 A
1 A
1881825 TTAAAATATA
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
26 11 0.23
27 1 0.02
28 6 0.12
29 27 0.56
30 2 0.04
31 1 0.02
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.53
Consensus pattern (27 bp):
AAATATACTATATTATTTTTAATTTAA
Found at i:1881833 original size:26 final size:25
Alignment explanation
Indices: 1881782--1881836 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
1881772 AATACTTCAT
*
1881782 TATTATTTTAATTTAAAAATATATA
1 TATTATTTTAATTTAAAAATAAATA
* * *
1881807 TATTATTTTTATTTTAAATTAAAATA
1 TATTATTTTAATTTAAAAAT-AAATA
1881833 TATT
1 TATT
1881837 TAATAAGTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 17 0.68
26 8 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TATTATTTTAATTTAAAAATAAATA
Found at i:1881921 original size:27 final size:27
Alignment explanation
Indices: 1881883--1881946 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
1881873 ACTTAAAAAA
*
1881883 TAAAATATATTTTATCATTAACT-TAATT
1 TAAAA-ATATTTTATCACT-ACTATAATT
* *
1881911 TAAGAATATTTTATTACTACTATAATT
1 TAAAAATATTTTATCACTACTATAATT
1881938 TAAAAATAT
1 TAAAAATAT
1881947 ATATTTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
26 3 0.10
27 24 0.77
28 4 0.13
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (27 bp):
TAAAAATATTTTATCACTACTATAATT
Found at i:1882035 original size:175 final size:169
Alignment explanation
Indices: 1881718--1882041 Score: 454
Period size: 174 Copynumber: 1.9 Consensus size: 169
1881708 CATTTAAAAT
*
1881718 ATATATTTTATCTTAACTTATTAAATATATTTTATTATTATCTTAATTTAAAAAAATACTTCATT
1 ATATATTTTATCTTAACTTATTAAATATATTTTATTACTATCTTAATTTAAAAAAATACTTCATT
* * *
1881783 ATTATTTTAATTTAAAAATATATATATTATTTTTATTTTAAATTAAAATATATTTAATAAGTTAA
66 ATTATCTTAATTTAAAAATATATAAATTATTTTTATTTTAAATTAAAATATATTCAATAAGTTAA
1881848 AATACAAAATAAAATATATGTTTAAACTTAAAAAATAAA
131 AATACAAAATAAAATATATGTTTAAACTTAAAAAATAAA
1881887 ATATATTTTATCATTAACTTAATTTAAGA-ATATTTTATTACTA-CTATAATTTAAAAATATATA
1 ATATATTTTATC-TTAACTT-A-TTAA-ATATATTTTATTACTATCT-TAATTTAAAAA-A-ATA
* ** * * * *
1881950 TTTTTTTCTTATCTTATTTTAAATATATATAAATTATTTTTATTTTAACTTAAAAATATATTCAA
59 CTTCATTATTATCTTAATTTAAAAATATATAAATTATTTTTATTTTAAATT-AAAATATATTCAA
*
1882015 TAAGTTAAAATACAAAATAAACTATAT
123 TAAGTTAAAATACAAAATAAAATATAT
1882042 TTTTTTCTAT
Statistics
Matches: 135, Mismatches: 12, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
169 12 0.09
170 7 0.05
171 3 0.02
172 28 0.21
173 2 0.01
174 45 0.33
175 38 0.28
ACGTcount: A:0.46, C:0.05, G:0.01, T:0.48
Consensus pattern (169 bp):
ATATATTTTATCTTAACTTATTAAATATATTTTATTACTATCTTAATTTAAAAAAATACTTCATT
ATTATCTTAATTTAAAAATATATAAATTATTTTTATTTTAAATTAAAATATATTCAATAAGTTAA
AATACAAAATAAAATATATGTTTAAACTTAAAAAATAAA
Found at i:1882906 original size:36 final size:36
Alignment explanation
Indices: 1882866--1882938 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
1882856 AGATATTTTC
*
1882866 ATGTTGACTTGTCATTATAAACAAGAAAAGATACAA
1 ATGTTGACCTGTCATTATAAACAAGAAAAGATACAA
*
1882902 ATGTTGACCTGTCATTATAAACAAGAAAAGATGCAA
1 ATGTTGACCTGTCATTATAAACAAGAAAAGATACAA
1882938 A
1 A
1882939 ATTTTATATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.47, C:0.12, G:0.15, T:0.26
Consensus pattern (36 bp):
ATGTTGACCTGTCATTATAAACAAGAAAAGATACAA
Found at i:1885464 original size:47 final size:48
Alignment explanation
Indices: 1885411--1885510 Score: 166
Period size: 48 Copynumber: 2.1 Consensus size: 48
1885401 AAAGTAAAAT
* * *
1885411 ATTCATAAAAAAAGCTTA-GGGTTGTTTGTTTGTCTCTTAATGTAACC
1 ATTCATAAAAAAAACTTAGGGGTTGTTTGTTTGACTCTTAATGGAACC
1885458 ATTCATAAAAAAAACTTAGGGGTTGTTTGTTTGACTCTTAATGGAACC
1 ATTCATAAAAAAAACTTAGGGGTTGTTTGTTTGACTCTTAATGGAACC
1885506 ATTCA
1 ATTCA
1885511 GCATTCAGCG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
47 17 0.35
48 32 0.65
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (48 bp):
ATTCATAAAAAAAACTTAGGGGTTGTTTGTTTGACTCTTAATGGAACC
Found at i:1886864 original size:17 final size:18
Alignment explanation
Indices: 1886831--1886864 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1886821 TTGTTATTAG
1886831 TGAATCGGTCAGAACCGT
1 TGAATCGGTCAGAACCGT
*
1886849 TGAATCGTTC-GAACCG
1 TGAATCGGTCAGAACCG
1886865 GACCGACTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (18 bp):
TGAATCGGTCAGAACCGT
Found at i:1888794 original size:14 final size:14
Alignment explanation
Indices: 1888745--1888796 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
1888735 GTTTATATTC
1888745 TTTTTTATTGAATTT
1 TTTTTTATTG-ATTT
1888760 TAATTTTTATT-ATTGT
1 T--TTTTTATTGATT-T
*
1888776 ATTTTTATTGATTT
1 TTTTTTATTGATTT
1888790 TTTTTTA
1 TTTTTTA
1888797 AAAATGAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
14 15 0.48
15 7 0.23
16 1 0.03
17 8 0.26
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.73
Consensus pattern (14 bp):
TTTTTTATTGATTT
Found at i:1889640 original size:87 final size:87
Alignment explanation
Indices: 1889494--1889656 Score: 292
Period size: 87 Copynumber: 1.9 Consensus size: 87
1889484 TATGTTATAT
1889494 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
1 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
1889559 AGCGCTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGG
* *
1889581 TATTTAA-CGAGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGG
1 TATTTAACCG-GAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGA
1889645 TAGCGCTTATAT
65 TAGCGCTTATAT
1889657 TGACCTATTT
Statistics
Matches: 73, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
86 2 0.03
87 71 0.97
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (87 bp):
TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
AGCGCTTATATAATAAAATAGG
Found at i:1896058 original size:20 final size:19
Alignment explanation
Indices: 1896031--1896091 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 19
1896021 CATTTTGGTG
1896031 CAGAGGGAATCGATCCCCC
1 CAGAGGGAATCGATCCCCC
*
1896050 CATGAGGGAACCGATTCCCCC
1 CA-GAGGGAATCGA-TCCCCC
*
1896071 CACAGGGGAATCGATACCCCC
1 CAGA-GGGAATCGAT-CCCCC
1896092 TGGGGTTCTG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
19 2 0.06
20 12 0.34
21 21 0.60
ACGTcount: A:0.26, C:0.38, G:0.25, T:0.11
Consensus pattern (19 bp):
CAGAGGGAATCGATCCCCC
Found at i:1896070 original size:21 final size:20
Alignment explanation
Indices: 1896033--1896072 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1896023 TTTTGGTGCA
*
1896033 GAGGGAATCGATCCCCCCAT
1 GAGGGAACCGATCCCCCCAT
1896053 GAGGGAACCGATTCCCCCCA
1 GAGGGAACCGA-TCCCCCCA
1896073 CAGGGGAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.25, C:0.38, G:0.25, T:0.12
Consensus pattern (20 bp):
GAGGGAACCGATCCCCCCAT
Found at i:1902725 original size:183 final size:183
Alignment explanation
Indices: 1902417--1902986 Score: 984
Period size: 183 Copynumber: 3.1 Consensus size: 183
1902407 TTAAAATTAG
*
1902417 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAATCGGTATATTT
1 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
1902482 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
* *
1902547 TACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTATGGACATAAAGTAC
131 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTAC
1902600 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
1 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
*
1902665 ATACCGGTTATATTATAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
*
1902730 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTCGACATAAAGTAC
131 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTAC
*
1902783 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACTTATTCGCTCATAAAACCGGTATATTT
1 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
* * * *
1902848 ATACCGATTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTTTTTTCAA--T
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATG---TGTAAATGT
* *
1902911 CGACACTTTTTGAAAAGGTATCAACACATTTTT-TTCCATTCTGGACATAAAGTAC
128 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTAC
1902966 CGACACAATATTAAAAAGTGT
1 CGACACAATATTAAAAAGTGT
1902987 GAAAACTTTG
Statistics
Matches: 370, Mismatches: 14, Indels: 6
0.95 0.04 0.02
Matches are distributed among these distances:
183 334 0.90
184 32 0.09
186 4 0.01
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (183 bp):
CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTAC
Found at i:1904207 original size:6 final size:6
Alignment explanation
Indices: 1904196--1904257 Score: 70
Period size: 6 Copynumber: 10.3 Consensus size: 6
1904186 ACTTGTTTGG
* * * *
1904196 ATCATC ATCATC ATCATC ATCATC ATCGTC ATCTTC ATCTTC ATCGTC
1 ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC
* *
1904244 ATCTTC ATCTTC AT
1 ATCATC ATCATC AT
1904258 TGACCGCTTG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 52 1.00
ACGTcount: A:0.24, C:0.32, G:0.03, T:0.40
Consensus pattern (6 bp):
ATCATC
Found at i:1904219 original size:18 final size:18
Alignment explanation
Indices: 1904196--1904257 Score: 88
Period size: 18 Copynumber: 3.4 Consensus size: 18
1904186 ACTTGTTTGG
* *
1904196 ATCATCATCATCATCATC
1 ATCATCATCGTCATCTTC
1904214 ATCATCATCGTCATCTTC
1 ATCATCATCGTCATCTTC
*
1904232 ATCTTCATCGTCATCTTC
1 ATCATCATCGTCATCTTC
*
1904250 ATCTTCAT
1 ATCATCAT
1904258 TGACCGCTTG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.24, C:0.32, G:0.03, T:0.40
Consensus pattern (18 bp):
ATCATCATCGTCATCTTC
Found at i:1906404 original size:200 final size:200
Alignment explanation
Indices: 1905750--1906706 Score: 1667
Period size: 198 Copynumber: 4.8 Consensus size: 200
1905740 AACATTAAAC
* * * *
1905750 AGTGTCGATACA-TA--TATACCAATTCTCCCATAAAACCGGTATACTTATACCGGTTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
* *
1905812 AAAATTACCTAATACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
* * *
1905877 GATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACTAAAAATATCGACACAAACT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
1905942 ACAAA
196 ACAAA
*
1905947 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1906012 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACAC-TTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
1906076 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACC-AAAATATCGACACAAACT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
1906140 ACAAA
196 ACAAA
* *
1906145 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACAGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
*
1906210 AAATTTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
*
1906275 GATCGACACTTTATTGTTGCACCCTGTTTGCGATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
1906340 ACAAA
196 ACAAA
1906345 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
*
1906410 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTAT-CGATCGACAC-TTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
*
1906473 GATTGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
1906538 ACAAA
196 ACAAA
* *
1906543 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACAGGTATACTTGTACCGATTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
* * *
1906608 AAAATTACCTATTACATTATATTTTTGGGTTTCGATGTTTATGGGATCGACATTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
*
1906673 GATCGACACTTTATGGTTGCACCCTGTTTGCCAT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCAT
1906707 ATTGTAAATT
Statistics
Matches: 726, Mismatches: 27, Indels: 11
0.95 0.04 0.01
Matches are distributed among these distances:
197 11 0.02
198 323 0.44
199 127 0.17
200 265 0.37
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (200 bp):
AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
ACAAA
Found at i:1906526 original size:398 final size:398
Alignment explanation
Indices: 1905771--1906706 Score: 1703
Period size: 398 Copynumber: 2.4 Consensus size: 398
1905761 ATATATACCA
* * * *
1905771 ATTCTCCCATAAAACCGGTATACTTATACCGGTTAGATTGAAAAATTACCTAATACATTATACTT
1 ATTCTCTCATAAAACAGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTT
1905836 TTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
66 TTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
* *
1905901 TGTTTTCCATTCATTCTGGACTAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTA
131 TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTA
1905966 GACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTA
196 GACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTA
*
1906031 TACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTATATATGGATCGACACTTTATTGTTGC
261 TACTTATGGGTTTCGATGTTTATGCGATCGACACTTTTATATATGGATCGACACTTTATTGTTGC
1906096 ACCCTGTTTGCCATTCATTCTGGACCAAAATATCGACACAAACTACAAAAGTGTCGACACATTAT
326 ACCCTGTTTGCCATTCATTCTGGACCAAAATATCGACACAAACTACAAAAGTGTCGACACATTAT
1906161 TTAGACCT
391 TTAGACCT
*
1906169 ATTCTCTCATAAAACAGGTATACTTGTACCGGTTAGATTGAAAATTTACCTATTACATTATACTT
1 ATTCTCTCATAAAACAGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTT
* *
1906234 ATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCC
66 TTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
* *
1906299 TGTTTGCGATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGATACATTATTTA
131 TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTA
1906364 GACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTA
196 GACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTA
*
1906429 TACTTATGGGTTTCGATGTTTAT-CGATCGACACTTTTATATATGGATTGACACTTTATTGTTGC
261 TACTTATGGGTTTCGATGTTTATGCGATCGACACTTTTATATATGGATCGACACTTTATTGTTGC
*
1906493 ACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGATACATTA
326 ACCCTGTTTGCCATTCATTCTGGACC-AAAATATCGACACAAACTACAAAAGTGTCGACACATTA
1906558 TTTAGACCT
390 TTTAGACCT
* *
1906567 ATTCTCTCATAAAACAGGTATACTTGTACCGATTAGATTGAAAAATTACCTATTACATTATATTT
1 ATTCTCTCATAAAACAGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTT
*
1906632 TTGGGTTTCGATGTTTATGGGATCGACATTTTTTATATATGGATCGACACTTTATGGTTGCACCC
66 TTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
1906697 TGTTTGCCAT
131 TGTTTGCCAT
1906707 ATTGTAAATT
Statistics
Matches: 516, Mismatches: 21, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
397 65 0.13
398 451 0.87
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (398 bp):
ATTCTCTCATAAAACAGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTT
TTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTA
GACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTA
TACTTATGGGTTTCGATGTTTATGCGATCGACACTTTTATATATGGATCGACACTTTATTGTTGC
ACCCTGTTTGCCATTCATTCTGGACCAAAATATCGACACAAACTACAAAAGTGTCGACACATTAT
TTAGACCT
Found at i:1906951 original size:18 final size:18
Alignment explanation
Indices: 1906928--1906988 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
1906918 TCTCATTCAT
*
1906928 AATTATATTCACATACAA
1 AATTATAATCACATACAA
**
1906946 AATTATAAATCGTATACAA
1 AATTAT-AATCACATACAA
**
1906965 AATTATAAATCTTATACAA
1 AATTAT-AATCACATACAA
1906984 AATTA
1 AATTA
1906989 ACCCTACATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
18 6 0.16
19 32 0.84
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (18 bp):
AATTATAATCACATACAA
Found at i:1906964 original size:19 final size:19
Alignment explanation
Indices: 1906940--1906988 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1906930 TTATATTCAC
1906940 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
1906959 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
1906978 ATACAAAATTA
1 ATACAAAATTA
1906989 ACCCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:1908808 original size:33 final size:33
Alignment explanation
Indices: 1908771--1908836 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1908761 CATCTTAATA
*
1908771 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
1908804 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
1908837 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:1908895 original size:21 final size:21
Alignment explanation
Indices: 1908870--1908913 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1908860 CCCCTTATGC
1908870 CTCTCAAGTGTATCTTCAACT
1 CTCTCAAGTGTATCTTCAACT
* * *
1908891 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTATCTTCAACT
1908912 CT
1 CT
1908914 TGATTGTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.18, C:0.32, G:0.09, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTGTATCTTCAACT
Found at i:1909018 original size:15 final size:15
Alignment explanation
Indices: 1908998--1909026 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1908988 TATGTTTTCC
1908998 CTCACCGTCATCCCA
1 CTCACCGTCATCCCA
1909013 CTCACCGTCATCCC
1 CTCACCGTCATCCC
1909027 CCAATACAAC
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:0.17, C:0.55, G:0.07, T:0.21
Consensus pattern (15 bp):
CTCACCGTCATCCCA
Found at i:1911138 original size:19 final size:18
Alignment explanation
Indices: 1911085--1911141 Score: 69
Period size: 20 Copynumber: 3.0 Consensus size: 18
1911075 TCCGGTATCG
1911085 TTTACCGGTTTTATCATT
1 TTTACCGGTTTTATCATT
1911103 TTGATACCGGTTTTATCATAT
1 TT--TACCGGTTTTATCAT-T
* *
1911124 TTTACCTGTTATATCATT
1 TTTACCGGTTTTATCATT
1911142 GTGGATCGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 3 0.09
19 13 0.38
20 15 0.44
21 3 0.09
ACGTcount: A:0.21, C:0.16, G:0.11, T:0.53
Consensus pattern (18 bp):
TTTACCGGTTTTATCATT
Found at i:1911306 original size:20 final size:19
Alignment explanation
Indices: 1911260--1911306 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1911250 TCTGGTAACG
1911260 TTTTACCAGTTTTATCATT
1 TTTTACCAGTTTTATCATT
* *
1911279 TTGATACCGGTTTTATCATAT
1 TT-TTACCAGTTTTATCAT-T
1911300 TTTTACC
1 TTTTACC
1911307 TGGTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.21, C:0.17, G:0.09, T:0.53
Consensus pattern (19 bp):
TTTTACCAGTTTTATCATT
Found at i:1911498 original size:182 final size:176
Alignment explanation
Indices: 1911053--1911520 Score: 620
Period size: 182 Copynumber: 2.6 Consensus size: 176
1911043 CGTACTTACG
* *
1911053 AAAGTATCGACCACTTT-CA-ATATCCGGTATCGTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGA-CACTTTAAATATATCCGGTAACGTTTACCGGTTTTATCATTTTGATACCGGTTT
* * * ** *
1911116 TATCATATTTTACCTGTTATATCATTGTGGATCGATA-TTTTTTTTAAGTATCGACACATTATAG
65 TATCATATTTTACCTGTTATATCGTTTTGGATCGATACATTTTTAAAAGTATCGACACATTATAA
*
1911180 GCGCTAAAATGCTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
130 GAGCTAAAATGCTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
* * *
1911227 AAAGTATCGACACTTTCAATATATCTGGTAACGTTTTACCAGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACG-TTTACCGGTTTTATCATTTTGATACCGGTTT
* *
1911292 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTCTTAAAAGTATCGACACTTTAT
65 TATCATA-TTTTACCTGTTATATCGTTTTGGATCGATACATTT-TTAAAAGTATCGACACATTAT
** *
1911357 AAGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
128 AAGAGCTAAAA-TGC-TCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
* * *
1911409 AAAGT-TCCGACACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCATTTTAATACCGGTT
1 AAAGTAT-CGACACTTTAAATATATCCGGTAACG-TTTACCGGTTTTATCATTTTGATACCGGTT
* *
1911473 TTGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTTAA
64 TTATCATA-TTTTACCTGTTATATCGTTTTGGATCGATACATTTTTAA
1911521 TTTGGATCGA
Statistics
Matches: 257, Mismatches: 27, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
173 6 0.02
174 11 0.04
175 11 0.04
176 37 0.14
177 27 0.11
178 3 0.01
179 25 0.10
180 3 0.01
181 38 0.15
182 96 0.37
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (176 bp):
AAAGTATCGACACTTTAAATATATCCGGTAACGTTTACCGGTTTTATCATTTTGATACCGGTTTT
ATCATATTTTACCTGTTATATCGTTTTGGATCGATACATTTTTAAAAGTATCGACACATTATAAG
AGCTAAAATGCTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
Found at i:1911688 original size:11 final size:11
Alignment explanation
Indices: 1911672--1911696 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1911662 ATCCGGTAAC
1911672 ACCGTATATTA
1 ACCGTATATTA
1911683 ACCGTATATTA
1 ACCGTATATTA
1911694 ACC
1 ACC
1911697 CGTCTTTCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.24, G:0.08, T:0.32
Consensus pattern (11 bp):
ACCGTATATTA
Found at i:1913229 original size:6 final size:6
Alignment explanation
Indices: 1913218--1913245 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1913208 AGGTGATTTT
1913218 TTATAA TTATAA TTATAA TTATAA TTAT
1 TTATAA TTATAA TTATAA TTATAA TTAT
1913246 TATATTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTATAA
Found at i:1914401 original size:38 final size:38
Alignment explanation
Indices: 1914350--1914428 Score: 122
Period size: 38 Copynumber: 2.1 Consensus size: 38
1914340 TAAGTTATAT
* * *
1914350 AACACTGTCCACATTAAATGGTTGTATTTTCAACAGCA
1 AACACGGTCCACATTAAATGATTGTATTTTCAACAACA
*
1914388 AACACGGTCCACATTAAATGATTGTATTTTCAGCAACA
1 AACACGGTCCACATTAAATGATTGTATTTTCAACAACA
1914426 AAC
1 AAC
1914429 GTAATAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.29
Consensus pattern (38 bp):
AACACGGTCCACATTAAATGATTGTATTTTCAACAACA
Found at i:1914697 original size:38 final size:38
Alignment explanation
Indices: 1914655--1914774 Score: 150
Period size: 38 Copynumber: 3.1 Consensus size: 38
1914645 ATAAGTAAAT
*
1914655 AAATAACACCATAACACTATTAAGTCTCAATAAATCTAAAA
1 AAATAACACCATAACACTATTAAGTCTCAATAAGTCT---A
* *
1914696 TAAATAACACCATAACACCATTAAGTCTCAATAAGTTTA
1 -AAATAACACCATAACACTATTAAGTCTCAATAAGTCTA
* * *
1914735 AAATAACATCATAACACTAATAAGTCTTAATAAGTCTA
1 AAATAACACCATAACACTATTAAGTCTCAATAAGTCTA
1914773 AA
1 AA
1914775 TAAAATCAAC
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
38 35 0.50
39 1 0.01
42 34 0.49
ACGTcount: A:0.51, C:0.18, G:0.04, T:0.27
Consensus pattern (38 bp):
AAATAACACCATAACACTATTAAGTCTCAATAAGTCTA
Found at i:1914702 original size:42 final size:41
Alignment explanation
Indices: 1914650--1914778 Score: 174
Period size: 42 Copynumber: 3.2 Consensus size: 41
1914640 GATAAATAAG
*
1914650 TAAATAAATAACACCATAACACTATTAAGTCTCAATAAATC
1 TAAATAAATAACACCATAACACTATTAAGTCTCAATAAGTC
*
1914691 TAAAATAAATAACACCATAACACCATTAAGTCTCAATAAGT-
1 T-AAATAAATAACACCATAACACTATTAAGTCTCAATAAGTC
* * * *
1914732 T-TA-AAATAACATCATAACACTAATAAGTCTTAATAAGTC
1 TAAATAAATAACACCATAACACTATTAAGTCTCAATAAGTC
1914771 TAAATAAA
1 TAAATAAA
1914779 ATCAACATCA
Statistics
Matches: 76, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
38 31 0.41
39 2 0.03
40 1 0.01
41 5 0.07
42 37 0.49
ACGTcount: A:0.52, C:0.17, G:0.04, T:0.27
Consensus pattern (41 bp):
TAAATAAATAACACCATAACACTATTAAGTCTCAATAAGTC
Found at i:1919490 original size:16 final size:16
Alignment explanation
Indices: 1919448--1919492 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 16
1919438 ATTACAATAA
* *
1919448 TAATATTAAAAGGGTT
1 TAATAGTAAAAGAGTT
1919464 TAATTTAGTAAAAGAGTT
1 TAA--TAGTAAAAGAGTT
1919482 TAATAGTAAAA
1 TAATAGTAAAA
1919493 TATTATTACC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 11 0.44
18 14 0.56
ACGTcount: A:0.49, C:0.00, G:0.16, T:0.36
Consensus pattern (16 bp):
TAATAGTAAAAGAGTT
Found at i:1920498 original size:6 final size:6
Alignment explanation
Indices: 1920487--1920520 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
1920477 TGGCTTGTAC
1920487 TTTTAT TTTTA- TTTTAT TTTTA- TTTTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
1920521 GATTTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 10 0.38
6 16 0.62
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTAT
Found at i:1920503 original size:11 final size:11
Alignment explanation
Indices: 1920487--1920520 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
1920477 TGGCTTGTAC
1920487 TTTTATTTTTA
1 TTTTATTTTTA
1920498 TTTTATTTTTA
1 TTTTATTTTTA
1920509 TTTTATTTTTA
1 TTTTATTTTTA
1920520 T
1 T
1920521 GATTTTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:1933719 original size:15 final size:15
Alignment explanation
Indices: 1933699--1933729 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1933689 ACAGATGAGA
1933699 CCTCTTCATGAATAC
1 CCTCTTCATGAATAC
1933714 CCTCTTCATGAATAC
1 CCTCTTCATGAATAC
1933729 C
1 C
1933730 AGGCTCTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.35, G:0.06, T:0.32
Consensus pattern (15 bp):
CCTCTTCATGAATAC
Found at i:1942930 original size:9 final size:9
Alignment explanation
Indices: 1942916--1942940 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1942906 AGCATAACAA
1942916 CTTCATCAT
1 CTTCATCAT
1942925 CTTCATCAT
1 CTTCATCAT
1942934 CTTCATC
1 CTTCATC
1942941 TACAAGGTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.36, G:0.00, T:0.44
Consensus pattern (9 bp):
CTTCATCAT
Found at i:1944070 original size:15 final size:15
Alignment explanation
Indices: 1944050--1944083 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
1944040 CTCTTTTGAG
1944050 TATTTACTCTTCCTC
1 TATTTACTCTTCCTC
1944065 TATTTACTCTTCCTC
1 TATTTACTCTTCCTC
1944080 TATT
1 TATT
1944084 CATCAGAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.15, C:0.29, G:0.00, T:0.56
Consensus pattern (15 bp):
TATTTACTCTTCCTC
Found at i:1945640 original size:61 final size:54
Alignment explanation
Indices: 1945523--1945653 Score: 154
Period size: 61 Copynumber: 2.3 Consensus size: 54
1945513 CTGTGATTAT
* * *
1945523 CAAGAACAGACTCATACGCAAACGAATACTGCATACTTAAAAAAGGAAAAAAAA
1 CAAGAACAGACACATACGAAAACGAATACTGCATACTTAAAAAAAGAAAAAAAA
*
1945577 CAAGAACAGACACATACGAAATTACGAATAACTGTATACTTAGAAAAGAAAAGAAAAAAAA
1 CAAGAACAGACACATACGAAA--ACGAAT-ACTGCATACTT---AAA-AAAAGAAAAAAAA
*
1945638 CAAGAACAAACACATA
1 CAAGAACAGACACATA
1945654 AGCACGAATT
Statistics
Matches: 65, Mismatches: 5, Indels: 7
0.84 0.06 0.09
Matches are distributed among these distances:
54 19 0.29
56 6 0.09
57 10 0.15
60 3 0.05
61 27 0.42
ACGTcount: A:0.58, C:0.17, G:0.12, T:0.13
Consensus pattern (54 bp):
CAAGAACAGACACATACGAAAACGAATACTGCATACTTAAAAAAAGAAAAAAAA
Found at i:1949769 original size:30 final size:32
Alignment explanation
Indices: 1949678--1949789 Score: 174
Period size: 32 Copynumber: 3.6 Consensus size: 32
1949668 CTTCAACTCT
*
1949678 TTCTTTGGAACATATGGACAGGATTACCTATG
1 TTCTTCGGAACATATGGACAGGATTACCTATG
*
1949710 TTCTTCGGAACATATGGACATGATTACCTATG
1 TTCTTCGGAACATATGGACAGGATTACCTATG
*
1949742 TTCTCCGGAACATATGGACA-G-TTACCTATG
1 TTCTTCGGAACATATGGACAGGATTACCTATG
*
1949772 TTATTCGGAACATATGGA
1 TTCTTCGGAACATATGGA
1949790 TAGGTCCTTC
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
30 25 0.33
31 1 0.01
32 49 0.65
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.33
Consensus pattern (32 bp):
TTCTTCGGAACATATGGACAGGATTACCTATG
Found at i:1960243 original size:64 final size:64
Alignment explanation
Indices: 1960110--1960266 Score: 162
Period size: 64 Copynumber: 2.5 Consensus size: 64
1960100 TAATGAAGGT
* * ** *
1960110 ATGCATCGATGCAC-CACTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATTACTGGG
1 ATGCATCGATGCACTC-CTAATGCATCGATGCATAAAATGCATTCGATGTTGTATTATTAAAGAG
* * *
1960174 ATGCATCGATGCACTCCTTATGCATCGATGCATTAATTGCATTCGATGTT-T-TTATCTTAAA-A
1 ATGCATCGATGCACTCCTAATGCATCGATGCATAAAATGCATTCGATGTTGTATTA--TTAAAGA
1960236 G
64 G
1960237 AGTGCATCGATGCACTACC-AATGCATCGAT
1 A-TGCATCGATGCACT-CCTAATGCATCGAT
1960267 ACACCTTCAA
Statistics
Matches: 80, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
62 3 0.04
63 3 0.04
64 71 0.89
65 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.32
Consensus pattern (64 bp):
ATGCATCGATGCACTCCTAATGCATCGATGCATAAAATGCATTCGATGTTGTATTATTAAAGAG
Found at i:1981373 original size:14 final size:15
Alignment explanation
Indices: 1981354--1981384 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1981344 TGTTTCGGCT
1981354 GATGAAATTT-TTTG
1 GATGAAATTTATTTG
1981368 GATGAAATTTATTTG
1 GATGAAATTTATTTG
1981383 GA
1 GA
1981385 GGGGGTTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.32, C:0.00, G:0.23, T:0.45
Consensus pattern (15 bp):
GATGAAATTTATTTG
Found at i:1983132 original size:23 final size:22
Alignment explanation
Indices: 1983082--1983132 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
1983072 TGATTACAAA
* * *
1983082 AATATTGATATTAAAATAATAC
1 AATATAGACATTAAAAGAATAC
1983104 ATATATAGACATTAAAAGATATAC
1 A-ATATAGACATTAAAAGA-ATAC
1983128 AATAT
1 AATAT
1983133 GGTTATCACT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 1 0.04
23 18 0.75
24 5 0.21
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.33
Consensus pattern (22 bp):
AATATAGACATTAAAAGAATAC
Found at i:1987033 original size:193 final size:193
Alignment explanation
Indices: 1986704--1987088 Score: 734
Period size: 193 Copynumber: 2.0 Consensus size: 193
1986694 TTAATATAAC
1986704 ACTAATTCTTAGAAAGTTAGATAGATAAGGATAATTACTAAGTAGTTTAGTTTAAATTAAATACT
1 ACTAATTCTTAGAAAGTTAGATAGATAAGGATAATTACTAAGTAGTTTAGTTTAAATTAAATACT
1986769 TGTTCTCACCTACTGTATATATTTATTAAACTTGAAACCTATTTTTAATGAATATACGACAGTGA
66 TGTTCTCACCTACTGTATATATTTATTAAACTTGAAACCTATTTTTAATGAATATACGACAGTGA
*
1986834 AGTTTTTCATTTTTCCTTACCTTTTTCATTTGATTTATTTCGTCACTTAATTCCTTTTACTTA
131 AGTTTTTCATTTTTCCTTACCTTTGTCATTTGATTTATTTCGTCACTTAATTCCTTTTACTTA
*
1986897 ACTAATTCTTAGAAAGTTTGATAGATAAGGATAATTACTAAGTAGTTTAGTTTAAATTAAATACT
1 ACTAATTCTTAGAAAGTTAGATAGATAAGGATAATTACTAAGTAGTTTAGTTTAAATTAAATACT
* *
1986962 TGTTCTCACCTACTGTATATATTTATTAAACTTGTAACCTGTTTTTAATGAATATACGACAGTGA
66 TGTTCTCACCTACTGTATATATTTATTAAACTTGAAACCTATTTTTAATGAATATACGACAGTGA
1987027 AGTTTTTCATTTTTCCTTACCTTTGTCATTTGATTTATTTCGTCACTTAATTCCTTTTACTT
131 AGTTTTTCATTTTTCCTTACCTTTGTCATTTGATTTATTTCGTCACTTAATTCCTTTTACTT
1987089 CACTTTACAT
Statistics
Matches: 188, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
193 188 1.00
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.45
Consensus pattern (193 bp):
ACTAATTCTTAGAAAGTTAGATAGATAAGGATAATTACTAAGTAGTTTAGTTTAAATTAAATACT
TGTTCTCACCTACTGTATATATTTATTAAACTTGAAACCTATTTTTAATGAATATACGACAGTGA
AGTTTTTCATTTTTCCTTACCTTTGTCATTTGATTTATTTCGTCACTTAATTCCTTTTACTTA
Found at i:2009504 original size:255 final size:250
Alignment explanation
Indices: 2009060--2009570 Score: 909
Period size: 255 Copynumber: 2.0 Consensus size: 250
2009050 TCTTTCAAAG
2009060 GTTTACAAACTGCCTGCCAATTACCCAGTGCATTCGATTTTGTTTGAGCTTTCCCCCCTAATAAA
1 GTTTACAAACTGCCTGCCAATTACCCAGTGCATTCGATTTTGTTTGAGCTTTCCCCCCTAATAAA
2009125 GTTAGCATCAATGTATTAACTTTATCCTTACTTTGATCGGGATTTTAAAAAGGATAAGAAAAATC
66 GTTAGCATCAATGTATTAACTTTATCCTTACTTTGATCGGGATTTTAAAAAGGATAAGAAAAATC
2009190 GGTAATGATGATAATACCGATTTTATAAGCATTAGTCTGCCCGCCATTGACAGTGAAGCAGCCTT
131 GGTAATGATGATAATACCGATTTTATAAGCATTAGTCTGCCCGCCATTGACAGTGAAGCAGCCTT
2009255 -CAACCAGCTAACTTATTGTTAAAA-TGTAGAACCAACTCCCAAAGTACTTCAGA
196 CCAACCAGCTAACTTATTGTTAAAATTGTAGAACCAACTCCCAAAGTACTTCAGA
2009308 GTTTACAAACTGCCTGCCAATTAACCCAGTGCATTCGATTTTTGTTTGAGCTTTCCCCCCTAATA
1 GTTTACAAACTGCCTGCCAATT-ACCCAGTGCATTCGA-TTTTGTTTGAGCTTTCCCCCCTAATA
* *
2009373 AAGTTAGCCATCAATGTATTAACTTTCTTCCTTACTTTGATCGGGATTTTGAAAATGGATAAGAA
64 AAGTTAG-CATCAATGTATTAACTTT-ATCCTTACTTTGATCGGGATTTT-AAAAAGGATAAG--
2009438 AAAAATCGGTAATGATGATAATACCGATTTTATAAGCATTAGTCTGCCCGCCATTGACAGTGAAG
124 AAAAATCGGTAATGATGATAATACCGATTTTATAAGCATTAGTCTGCCCGCCATTGACAGTGAAG
2009503 CAGCCTTCCAACCAGCTAACTTATTGTTAAAATTCTGTAGAACCAACTCCCAAAGTACTTCAGA
189 CAGCCTTCCAACCAGCTAACTTATTGTTAAAA-T-TGTAGAACCAACTCCCAAAGTACTTCAGA
2009567 GTTT
1 GTTT
2009571 TTCTTTGCAC
Statistics
Matches: 250, Mismatches: 2, Indels: 11
0.95 0.01 0.04
Matches are distributed among these distances:
248 22 0.09
249 15 0.06
250 33 0.13
251 18 0.07
252 22 0.09
253 11 0.04
255 72 0.29
256 24 0.10
259 33 0.13
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.32
Consensus pattern (250 bp):
GTTTACAAACTGCCTGCCAATTACCCAGTGCATTCGATTTTGTTTGAGCTTTCCCCCCTAATAAA
GTTAGCATCAATGTATTAACTTTATCCTTACTTTGATCGGGATTTTAAAAAGGATAAGAAAAATC
GGTAATGATGATAATACCGATTTTATAAGCATTAGTCTGCCCGCCATTGACAGTGAAGCAGCCTT
CCAACCAGCTAACTTATTGTTAAAATTGTAGAACCAACTCCCAAAGTACTTCAGA
Found at i:2017016 original size:397 final size:394
Alignment explanation
Indices: 2016286--2017076 Score: 1546
Period size: 397 Copynumber: 2.0 Consensus size: 394
2016276 TAGTCAACAA
2016286 ACGACATCCATTCCTCACCGGAAGACAAAGAAACATTCAAATTTTCTCTCTCACTCTCACTTCTA
1 ACGACATCCATTCCTCACCGGAAGACAAAGAAACATTCAAATTTTCTCTCTCACTCTCACTTCTA
2016351 TTCTTTCTCCTAGACATTCTCTCTCCATACTGTGCTCAACTTGTTATATAGATCAATCCGGAACC
66 TTCTTTCTCCTAGACATTCTCTCTCCATACTGTGCTCAACTTGTTATATAGATCAATCCGGAACC
2016416 GTTAAGAGCTTTTGTTAAAATATCTCCTAGATGTAATCTAGTTTTCACCTAGCCGGTAGTAACCA
131 GTTAAGAGCTTTTGTTAAAATATCTCCTAGATGTAATCTAGTTTTCACCTAGCCGGTAGTAACCA
*
2016481 AACCTTACTGAATCTTTTCGAGAATGAAATGACAAGCAACCTCAATCTATTTTGTTTGTTCAAGA
196 AACCTTACTGAATCTTTTCGAGAATGAAATGACAAGCAACCTCAATATATTTTGTTTGTTCAAGA
2016546 AAAACTAGATTAGAAGCAATGTGAAGCACAACTTGATTATCACACCATAGCTTTGCAGGTATTGA
261 AAAACTAGATTAGAAGCAATGTGAAGCACAACTTGATTATCACACCATAGCTTTGCAGGTATTGA
2016611 AACCTTAATTCCTACTTCATTGAGAAGTTGATATACCCATATGATTTCACACACAGACTTGGTCA
326 AACCTTAATTCCTACTTCATTGAGAAGTTGATATACCCATATGATTTCACACACAGACTTGGTCA
2016676 TAGC
391 TAGC
2016680 ACGACATCCATTCCTCACCGGAAGACAAAGAAACATTCAAATTTTCTCTCTCACTCTCACTTCTA
1 ACGACATCCATTCCTCACCGGAAGACAAAGAAACATTCAAATTTTCTCTCTCACTCTCACTTCTA
2016745 TTCTTTCTCCTAGACATTCTCTCTCCATACTGTGCTCAACTTGTTATATAGATAATCAATCCGGA
66 TTCTTTCTCCTAGACATTCTCTCTCCATACTGTGCTCAACTTGTTATATAG---ATCAATCCGGA
2016810 ACCGTTAAGAGCTTTTGTTAAAATATCTCCTAGATGTAATCTAGTTTTCACCTAGCCGGTAGTAA
128 ACCGTTAAGAGCTTTTGTTAAAATATCTCCTAGATGTAATCTAGTTTTCACCTAGCCGGTAGTAA
2016875 CCAAACCTTACTGAATCTTTTCGAGAATGAAATGACAAGCAACCTCAATATATTTTGTTTGTTCA
193 CCAAACCTTACTGAATCTTTTCGAGAATGAAATGACAAGCAACCTCAATATATTTTGTTTGTTCA
2016940 AGAAAAACTAGATTAGAAGCAATGTGAAGCACAACTTGATTATCACACCATAGCTTTGCAGGTAT
258 AGAAAAACTAGATTAGAAGCAATGTGAAGCACAACTTGATTATCACACCATAGCTTTGCAGGTAT
2017005 TGAAACCTTAATTCCTACTTCATTGAGAAGTTGATATACCCATATGATTTCACACACAGACTTGG
323 TGAAACCTTAATTCCTACTTCATTGAGAAGTTGATATACCCATATGATTTCACACACAGACTTGG
2017070 TCATAGC
388 TCATAGC
2017077 TCAATATTCA
Statistics
Matches: 393, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
394 116 0.30
397 277 0.70
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (394 bp):
ACGACATCCATTCCTCACCGGAAGACAAAGAAACATTCAAATTTTCTCTCTCACTCTCACTTCTA
TTCTTTCTCCTAGACATTCTCTCTCCATACTGTGCTCAACTTGTTATATAGATCAATCCGGAACC
GTTAAGAGCTTTTGTTAAAATATCTCCTAGATGTAATCTAGTTTTCACCTAGCCGGTAGTAACCA
AACCTTACTGAATCTTTTCGAGAATGAAATGACAAGCAACCTCAATATATTTTGTTTGTTCAAGA
AAAACTAGATTAGAAGCAATGTGAAGCACAACTTGATTATCACACCATAGCTTTGCAGGTATTGA
AACCTTAATTCCTACTTCATTGAGAAGTTGATATACCCATATGATTTCACACACAGACTTGGTCA
TAGC
Found at i:2023528 original size:23 final size:23
Alignment explanation
Indices: 2023498--2023543 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
2023488 ATATGATTAA
2023498 GATTGATAAAGCTATCAAAACTG
1 GATTGATAAAGCTATCAAAACTG
2023521 GATTGATAAAGCTATCAAAACTG
1 GATTGATAAAGCTATCAAAACTG
2023544 TTCAAGGCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.26
Consensus pattern (23 bp):
GATTGATAAAGCTATCAAAACTG
Found at i:2023655 original size:21 final size:21
Alignment explanation
Indices: 2023631--2023680 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
2023621 TGTCCTCCAA
* *
2023631 CCGCCGTCTGTCGTTCGACAT
1 CCGCCGTCTGCCGTCCGACAT
2023652 CCGCCGTCTGCCGTCCGACAT
1 CCGCCGTCTGCCGTCCGACAT
2023673 CCGCCGTC
1 CCGCCGTC
2023681 CACCGCCACT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.08, C:0.46, G:0.24, T:0.22
Consensus pattern (21 bp):
CCGCCGTCTGCCGTCCGACAT
Found at i:2027168 original size:38 final size:38
Alignment explanation
Indices: 2027082--2027230 Score: 244
Period size: 38 Copynumber: 3.9 Consensus size: 38
2027072 AGCAGTAAAT
** *
2027082 TATTTGATTTAGTAGACTAGATTAACTAGAACTCTATCC
1 TATTTGATTTAGTAGTTTAGATTAACTATAACTC-ATCC
2027121 TATTTGATTTAGTAGTTTAGATTAACTATAACTCATCC
1 TATTTGATTTAGTAGTTTAGATTAACTATAACTCATCC
**
2027159 TATTTGATTTAGCGGTTTAGATTAACTATAACTCATCC
1 TATTTGATTTAGTAGTTTAGATTAACTATAACTCATCC
2027197 TATTTGATTTAGTAGTTTAGATTAACTATAACTC
1 TATTTGATTTAGTAGTTTAGATTAACTATAACTC
2027231 TTATCTTTTA
Statistics
Matches: 103, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
38 72 0.70
39 31 0.30
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (38 bp):
TATTTGATTTAGTAGTTTAGATTAACTATAACTCATCC
Found at i:2039550 original size:25 final size:25
Alignment explanation
Indices: 2039500--2039550 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
2039490 GAATGAAAAT
* * *
2039500 TTAATGAAAATACATTAAAATTATA
1 TTAATAAAAATACATAAAAATCATA
2039525 TTAATAAAAATA-ATAAAAATCCATA
1 TTAATAAAAATACATAAAAAT-CATA
2039550 T
1 T
2039551 GGCAATTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (25 bp):
TTAATAAAAATACATAAAAATCATA
Found at i:2041423 original size:3 final size:3
Alignment explanation
Indices: 2041417--2041459 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
2041407 TATGTTTTTT
2041417 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2041460 ATATGATGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2052065 original size:44 final size:44
Alignment explanation
Indices: 2052017--2052105 Score: 133
Period size: 44 Copynumber: 2.0 Consensus size: 44
2052007 TATTTCTCAC
* *
2052017 ACTATGTTGGAGCTATTACCAATATCACCCAACTTATTCCCTAA
1 ACTATGTTGGAACTATTACCAACATCACCCAACTTATTCCCTAA
* * *
2052061 ACTATGTTGGAACTATTACCAGCATTACCCAACTTATTTCCTAA
1 ACTATGTTGGAACTATTACCAACATCACCCAACTTATTCCCTAA
2052105 A
1 A
2052106 GCTCTCTTCT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.33, C:0.26, G:0.09, T:0.33
Consensus pattern (44 bp):
ACTATGTTGGAACTATTACCAACATCACCCAACTTATTCCCTAA
Found at i:2056615 original size:17 final size:17
Alignment explanation
Indices: 2056593--2056634 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
2056583 CCAAATCCAT
*
2056593 AATAGATTCAAGCATCA
1 AATAGATACAAGCATCA
*
2056610 AATAGATAGAAGCATCA
1 AATAGATACAAGCATCA
2056627 AATAGATA
1 AATAGATA
2056635 GTTCTATACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.52, C:0.12, G:0.14, T:0.21
Consensus pattern (17 bp):
AATAGATACAAGCATCA
Found at i:2056635 original size:17 final size:17
Alignment explanation
Indices: 2056602--2056635 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2056592 TAATAGATTC
2056602 AAGCATCAAATAGATAG
1 AAGCATCAAATAGATAG
2056619 AAGCATCAAATAGATAG
1 AAGCATCAAATAGATAG
2056636 TTCTATACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.12, G:0.18, T:0.18
Consensus pattern (17 bp):
AAGCATCAAATAGATAG
Found at i:2058406 original size:20 final size:19
Alignment explanation
Indices: 2058361--2058406 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
2058351 AAAATAGTCA
*
2058361 AATTTCACATTCTAACACT
1 AATTTCACACTCTAACACT
* *
2058380 AAATTCATCACTCTAACATT
1 AATTTCA-CACTCTAACACT
2058400 AATTTCA
1 AATTTCA
2058407 GAATAGTACT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (19 bp):
AATTTCACACTCTAACACT
Found at i:2059606 original size:31 final size:30
Alignment explanation
Indices: 2059561--2059618 Score: 89
Period size: 31 Copynumber: 1.9 Consensus size: 30
2059551 CAAAACACCT
*
2059561 AACTTTTTAAAATTACACTTTTGGTCCATG
1 AACTTTTGAAAATTACACTTTTGGTCCATG
*
2059591 AACTTTTAGAAAATTACCCTTTTGGTCC
1 AACTTTT-GAAAATTACACTTTTGGTCC
2059619 TTAATTTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 7 0.28
31 18 0.72
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.41
Consensus pattern (30 bp):
AACTTTTGAAAATTACACTTTTGGTCCATG
Found at i:2062965 original size:17 final size:17
Alignment explanation
Indices: 2062914--2062965 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 17
2062904 AGGGATTATC
2062914 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTT-GGGACAT
* *
2062932 AGTGCTCCATCGGGACAT
1 AGTGGTCC-TTGGGACAT
2062950 AGTGGTCCTTGGGACA
1 AGTGGTCCTTGGGACA
2062966 AATTTTCAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 7 0.24
18 21 0.72
19 1 0.03
ACGTcount: A:0.19, C:0.23, G:0.33, T:0.25
Consensus pattern (17 bp):
AGTGGTCCTTGGGACAT
Found at i:2065641 original size:19 final size:17
Alignment explanation
Indices: 2065613--2065651 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
2065603 AGAGTGAAGG
2065613 AAGTTAAAGATTGATAGAA
1 AAGTTAAAGA-TGATA-AA
*
2065632 AAGTTTAAGATGATAAA
1 AAGTTAAAGATGATAAA
2065649 AAG
1 AAG
2065652 GGATATGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 5 0.26
19 9 0.47
ACGTcount: A:0.54, C:0.00, G:0.21, T:0.26
Consensus pattern (17 bp):
AAGTTAAAGATGATAAA
Found at i:2065695 original size:18 final size:18
Alignment explanation
Indices: 2065672--2065706 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2065662 ATTATGATTT
2065672 GAATAAGGATTT-TGCAAA
1 GAATAAGG-TTTATGCAAA
2065690 GAATAAGGTTTATGCAA
1 GAATAAGGTTTATGCAA
2065707 GTAATGCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.43, C:0.06, G:0.23, T:0.29
Consensus pattern (18 bp):
GAATAAGGTTTATGCAAA
Found at i:2067481 original size:21 final size:17
Alignment explanation
Indices: 2067436--2067477 Score: 75
Period size: 17 Copynumber: 2.4 Consensus size: 17
2067426 TTCCGGAGCA
2067436 ATCGAAGAAGTAAAAATG
1 ATCG-AGAAGTAAAAATG
2067454 ATCGAGAAGTAAAAATG
1 ATCGAGAAGTAAAAATG
2067471 ATCGAGA
1 ATCGAGA
2067478 GAGAGAGAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 20 0.83
18 4 0.17
ACGTcount: A:0.52, C:0.07, G:0.24, T:0.17
Consensus pattern (17 bp):
ATCGAGAAGTAAAAATG
Found at i:2078697 original size:25 final size:25
Alignment explanation
Indices: 2078666--2078737 Score: 94
Period size: 25 Copynumber: 2.9 Consensus size: 25
2078656 GAGAAGATGT
2078666 GGATGTTG-AGGCATTCTGGAGAAA-
1 GGATGTTGTA-GCATTCTGGAGAAAC
*
2078690 GAGATGTTGTAGCATGCTGGAGAAAC
1 G-GATGTTGTAGCATTCTGGAGAAAC
*
2078716 GGATGTTGTAGCATTATGGAGA
1 GGATGTTGTAGCATTCTGGAGA
2078738 TGAAAAGCTA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
24 1 0.02
25 39 0.93
26 2 0.05
ACGTcount: A:0.29, C:0.08, G:0.36, T:0.26
Consensus pattern (25 bp):
GGATGTTGTAGCATTCTGGAGAAAC
Found at i:2090965 original size:52 final size:51
Alignment explanation
Indices: 2090845--2091022 Score: 284
Period size: 51 Copynumber: 3.5 Consensus size: 51
2090835 TGATAAGTCT
* * *
2090845 GCTCCCTATTTCTTCAGAGAGTATAAGACTTGATCTTCAACAAACGTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGATCTTCAATAAACGTGTCC
* * *
2090896 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTTCAATAAAATGTGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGATCTTCAAT-AAACGTGTCC
2090948 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGATCTTCAATAAACGTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGATCTTCAATAAACGTGTCC
*
2090999 GCTCCCTATTGCTTCAGAGAGTAT
1 GCTCCCTATTCCTTCAGAGAGTAT
2091023 GGATCCCGAG
Statistics
Matches: 116, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
51 68 0.59
52 48 0.41
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.31
Consensus pattern (51 bp):
GCTCCCTATTCCTTCAGAGAGTATAAGACTCGATCTTCAATAAACGTGTCC
Found at i:2091059 original size:54 final size:54
Alignment explanation
Indices: 2091017--2091259 Score: 360
Period size: 54 Copynumber: 4.5 Consensus size: 54
2091007 TTGCTTCAGA
* * *
2091017 GAGTATGGATCCCGAGCATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
1 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
* * *
2091071 GAGTATGGAACTCAAACATATTCTTCTTACAGGTTCGCTCCCTCTTTCTCTAGG
1 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
* *
2091125 GAGTATGGAACTCGAATATCTTCTTCTTACGGGTTTGCTCCCTCTTTCTCTAGG
1 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
* * * * * *
2091179 GAGTATGAAACTTGAATATCTTCTTCTTACGGGTTCACTCCCTCTTTATCTAAG
1 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
2091233 GAGTATGGAACTCGAACATCTTCTTCT
1 GAGTATGGAACTCGAACATCTTCTTCT
2091260 GCTTTACTAC
Statistics
Matches: 169, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 169 1.00
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.37
Consensus pattern (54 bp):
GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
Found at i:2091332 original size:37 final size:37
Alignment explanation
Indices: 2091259--2091338 Score: 99
Period size: 37 Copynumber: 2.2 Consensus size: 37
2091249 CATCTTCTTC
* * * *
2091259 TGCTTTACTACTTTCTTGTGAAGACTTCTAGATGATT
1 TGCTTCACTACTCTCTCGTGAAGACTTCAAGATGATT
*
2091296 TGCTTCACTACTCTCTCGTGAAGACTT-AAGTTTGATT
1 TGCTTCACTACTCTCTCGTGAAGACTTCAAG-ATGATT
2091333 TGCTTC
1 TGCTTC
2091339 GAAAGTCGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 2 0.05
37 35 0.95
ACGTcount: A:0.20, C:0.20, G:0.16, T:0.44
Consensus pattern (37 bp):
TGCTTCACTACTCTCTCGTGAAGACTTCAAGATGATT
Found at i:2091706 original size:36 final size:37
Alignment explanation
Indices: 2091654--2091759 Score: 128
Period size: 36 Copynumber: 2.9 Consensus size: 37
2091644 GAGAATGTTT
* * *
2091654 AAAAAGGATATGCTTCACTACTCTTCGA-TGAAGGCTT
1 AAAATGGATTTGCTTCACTACTCTT-GAGTGAAGGCTC
* *
2091691 AAGATGG-TTTGCTTCACTACTCTTTAGTGAAGGCTC
1 AAAATGGATTTGCTTCACTACTCTTGAGTGAAGGCTC
2091727 AAAATGGATTTGCTTCACTACTCTTTG-GTGAAG
1 AAAATGGATTTGCTTCACTACTC-TTGAGTGAAG
2091760 ACTTGGCTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
35 1 0.02
36 30 0.51
37 26 0.44
38 2 0.03
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (37 bp):
AAAATGGATTTGCTTCACTACTCTTGAGTGAAGGCTC
Found at i:2091748 original size:37 final size:37
Alignment explanation
Indices: 2091654--2091759 Score: 135
Period size: 37 Copynumber: 2.9 Consensus size: 37
2091644 GAGAATGTTT
* * * *
2091654 AAAAAGGATATGCTTCACTACTC-TTCGATGAAGGCTT
1 AAAATGGATTTGCTTCACTACTCTTTAG-TGAAGGCTC
*
2091691 AAGATGG-TTTGCTTCACTACTCTTTAGTGAAGGCTC
1 AAAATGGATTTGCTTCACTACTCTTTAGTGAAGGCTC
*
2091727 AAAATGGATTTGCTTCACTACTCTTTGGTGAAG
1 AAAATGGATTTGCTTCACTACTCTTTAGTGAAG
2091760 ACTTGGCTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
36 28 0.47
37 32 0.53
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (37 bp):
AAAATGGATTTGCTTCACTACTCTTTAGTGAAGGCTC
Found at i:2096525 original size:72 final size:72
Alignment explanation
Indices: 2096406--2096556 Score: 248
Period size: 72 Copynumber: 2.1 Consensus size: 72
2096396 CCCCTAACAG
* * *
2096406 GTTCTTGATCAGTTGCTATCATCATATTGGCTGCACCACTAATATTCAGATTCTCACTCGAAGTC
1 GTTCTTGATCAGTTGCTATCATCATATTGACTGCACCACTAACATTCAGATTCTCACCCGAAGTC
*
2096471 TTCATCT
66 TTCATAT
*
2096478 GTTCTTGATCATTTGCTATCATCATATTGACTGCACCACTAACATTCAGATTCTCACCCGAAGTC
1 GTTCTTGATCAGTTGCTATCATCATATTGACTGCACCACTAACATTCAGATTCTCACCCGAAGTC
2096543 TTCATAT
66 TTCATAT
*
2096550 TTTCTTG
1 GTTCTTG
2096557 TGTAATAGGG
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.24, C:0.25, G:0.13, T:0.38
Consensus pattern (72 bp):
GTTCTTGATCAGTTGCTATCATCATATTGACTGCACCACTAACATTCAGATTCTCACCCGAAGTC
TTCATAT
Found at i:2107321 original size:3 final size:3
Alignment explanation
Indices: 2107313--2107341 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
2107303 CTGTAACGGT
2107313 ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2107342 CAACAGTGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2108204 original size:5 final size:5
Alignment explanation
Indices: 2108178--2108220 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
2108168 CATGCCTCTC
* *
2108178 TTTCTT TTTCT TATCC TTTCT TTTCT TTT-T TTTCT TTTCT TTT
1 TTTC-T TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
2108221 TTGTGCGTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
4 4 0.12
5 24 0.75
6 4 0.12
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTCT
Found at i:2108213 original size:14 final size:14
Alignment explanation
Indices: 2108194--2108222 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2108184 TTTCTTATCC
2108194 TTTCTTTTCTTTTT
1 TTTCTTTTCTTTTT
2108208 TTTCTTTTCTTTTT
1 TTTCTTTTCTTTTT
2108222 T
1 T
2108223 GTGCGTATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTCTTTTCTTTTT
Found at i:2108928 original size:69 final size:69
Alignment explanation
Indices: 2108817--2109076 Score: 292
Period size: 69 Copynumber: 3.8 Consensus size: 69
2108807 GCCTTGAATA
* *
2108817 GGTGGAGCAGGT-CCTCTGTGAGAGGAATTAGTAGTAGAGGTTGCCATTGGAGGTGGTGGCGGTG
1 GGTGGAGCAGGTCCCT-TGTGAGAGGAACTAGCAGTAGAGGTTGCCATTGGAGGTGGTGGCGGTG
* *
2108881 GCGGT
65 GAGGC
* * *
2108886 GGTGGAGTAGGTCCCTTGTGAGAGGAACTAGCAATAGAGGTTGCCATTGGAGGTGGTGGTGGTGG
1 GGTGGAGCAGGTCCCTTGTGAGAGGAACTAGCAGTAGAGGTTGCCATTGGAGGTGGTGGCGGTGG
2108951 AGGC
66 AGGC
* * * * *
2108955 GGTGGAGCAGGCCCCCTT-TGAGAGGAACTACCAGTAGAGGTTGCCATTGGAGGCGGAGGCGGCG
1 GGTGGAGCAGG-TCCCTTGTGAGAGGAACTAGCAGTAGAGGTTGCCATTGGAGGTGGTGGCGGTG
*
2109019 GTGGC
65 GAGGC
* * * * * * *
2109024 GGCGGAGTAGGTAACC-TATGAGAGGAACTAGTAGTAGAGATTGCCCTTGGAGG
1 GGTGGAGCAGGT-CCCTTGTGAGAGGAACTAGCAGTAGAGGTTGCCATTGGAGG
2109077 AGCAGGAGGT
Statistics
Matches: 163, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
68 1 0.01
69 154 0.94
70 8 0.05
ACGTcount: A:0.21, C:0.15, G:0.43, T:0.21
Consensus pattern (69 bp):
GGTGGAGCAGGTCCCTTGTGAGAGGAACTAGCAGTAGAGGTTGCCATTGGAGGTGGTGGCGGTGG
AGGC
Found at i:2108999 original size:138 final size:138
Alignment explanation
Indices: 2108817--2109076 Score: 342
Period size: 138 Copynumber: 1.9 Consensus size: 138
2108807 GCCTTGAATA
* * * ** * * *
2108817 GGTGGAGCAGGTCCTCTGTGAGAGGAATTAGTAGTAGAGGTTGCCATTGGAGGTGGTGGCGGTGG
1 GGTGGAGCAGGCCCCCTGTGAGAGGAACTACCAGTAGAGGTTGCCATTGGAGGCGGAGGCGGCGG
* * * * *
2108882 CGGTGGTGGAGTAGGT-CCCTTGTGAGAGGAACTAGCAATAGAGGTTGCCATTGGAGGTGGTGGT
66 CGGCGGCGGAGTAGGTAACC-TATGAGAGGAACTAGCAATAGAGATTGCCATTGGAGGTGGTGGT
2108946 GGTGGAGGC
130 GGTGGAGGC
*
2108955 GGTGGAGCAGGCCCCCTTTGAGAGGAACTACCAGTAGAGGTTGCCATTGGAGGCGGAGGCGGCGG
1 GGTGGAGCAGGCCCCCTGTGAGAGGAACTACCAGTAGAGGTTGCCATTGGAGGCGGAGGCGGCGG
* * * *
2109020 TGGCGGCGGAGTAGGTAACCTATGAGAGGAACTAGTAGTAGAGATTGCCCTTGGAGG
66 CGGCGGCGGAGTAGGTAACCTATGAGAGGAACTAGCAATAGAGATTGCCATTGGAGG
2109077 AGCAGGAGGT
Statistics
Matches: 103, Mismatches: 18, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
138 101 0.98
139 2 0.02
ACGTcount: A:0.21, C:0.15, G:0.43, T:0.21
Consensus pattern (138 bp):
GGTGGAGCAGGCCCCCTGTGAGAGGAACTACCAGTAGAGGTTGCCATTGGAGGCGGAGGCGGCGG
CGGCGGCGGAGTAGGTAACCTATGAGAGGAACTAGCAATAGAGATTGCCATTGGAGGTGGTGGTG
GTGGAGGC
Found at i:2112386 original size:16 final size:16
Alignment explanation
Indices: 2112365--2112398 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
2112355 TTTTTACATG
2112365 AACCAAAA-TACTATTA
1 AACCAAAATTA-TATTA
2112381 AACCAAAATTATATTA
1 AACCAAAATTATATTA
2112397 AA
1 AA
2112399 TATATAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.88
17 2 0.12
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.26
Consensus pattern (16 bp):
AACCAAAATTATATTA
Found at i:2116363 original size:51 final size:51
Alignment explanation
Indices: 2116308--2116501 Score: 232
Period size: 51 Copynumber: 3.8 Consensus size: 51
2116298 TGGTGTTATA
2116308 CTTTCAATTTATGCATTTTAGTCACTGTTTATTTATGATTTATCTATTGTT
1 CTTTCAATTTATGCATTTTAGTCACTGTTTATTTATGATTTATCTATTGTT
*
2116359 CTTTCAATTTATGCATTTTA-TGCATTGTTTATTTATGATTTATCTATTGTT
1 CTTTCAATTTATGCATTTTAGT-CACTGTTTATTTATGATTTATCTATTGTT
* * * * * * *
2116410 CTTTTATTTTATGCATTCTAGTCACTGTTTATTTCTGATTTAGCTAGTGAT
1 CTTTCAATTTATGCATTTTAGTCACTGTTTATTTATGATTTATCTATTGTT
* * * *
2116461 CTTT-TATTTCATGTATTTTATTCACT-TCTTATTTATAATTT
1 CTTTCAATTT-ATGCATTTTAGTCACTGT-TTATTTATGATTT
2116502 GTTTGCTATT
Statistics
Matches: 123, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
50 5 0.04
51 117 0.95
52 1 0.01
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.58
Consensus pattern (51 bp):
CTTTCAATTTATGCATTTTAGTCACTGTTTATTTATGATTTATCTATTGTT
Done.